                                  ehmmpfam



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Function

   Search one or more sequences against an HMM database

Description

   EMBASSY HMMER is a suite of application wrappers to the original hmmer
   v2.3.2 applications written by Sean Eddy. hmmer v2.3.2 must be
   installed on the same system as EMBOSS and the location of the hmmer
   executables must be defined in your path for EMBASSY HMMER to work.

   Usage:
   ehmmpfam [options] hmmfile seqfile outfile

   The outfile parameter is new to EMBASSY HMMER.

   hmmpfam reads a sequence file and compares each sequence in it, one at
   a time, against all the HMMs in a file looking for signifcantly similar
   sequence matches. hmmfile will be looked for first in the current
   working directory, then in a directory named by the environment
   variable HMMERDB. This lets administrators install HMM library(s) such
   as Pfam in a common location. There is a separate output report
   (written to file for each sequence in seqfile. This report consists of
   three sections: a ranked list of the best scoring HMMs, a list of the
   best scoring domains in order of their occurrence in the sequence, and
   alignments for all the best scoring domains. A sequence score may be
   higher than a domain score for the same sequence if there is more than
   one domain in the sequence; the sequence score takes into account all
   the domains. All sequences scoring above the -E and -T cutoffs are
   shown in the first list, then every domain found in this list is shown
   in the second list of domain hits. If desired, E-value and bit score
   thresholds may also be applied to the domain list using the -domE and
   -domT options.

Algorithm

   Please read the Userguide.pdf distributed with the original HMMER and
   included in the EMBASSY HMMER distribution under the DOCS directory.

Usage

   Here is a sample session with ehmmpfam


% ehmmpfam ../ehmmcalibrate-ex2-keep/myhmmso 7LES_DROME myhmmso.ehmmpfam -A 10 -
E 10
Search one or more sequences against an HMM database.


/shared/software/bin/hmmpfam -A 10 -E 10.000000 -T -1000000.000000 -Z 59021 --do
mE 1000000.000000 --domT -1000000.000000  --informat FASTA ../ehmmcalibrate-ex2-
keep/myhmmso ./ehmmpfam-1234567890.1234 > myhmmso.ehmmpfam



   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   Where possible, the same command-line qualifier names and parameter
   order is used as in the original hmmer. There are however several
   unavoidable differences and these are clearly documented in the "Notes"
   section below.

   More or less all options documented as "expert" in the original hmmer
   user guide are given in ACD as "advanced" options (-options must be
   specified on the command-line in order to be prompted for a value for
   them).

Search one or more sequences against an HMM database.
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers:
  [-hmmfile]           infile     File of HMMs.
  [-seqfile]           seqall     File of sequences.
   -a                  integer    [100] Limits the alignment output to the
                                  best scoring domains. -A0 shuts off the
                                  alignment output and can be used to reduce
                                  the size of output files. (Any integer
                                  value)
   -e                  float      [10.] Set the E-value cutoff for the
                                  per-sequence ranked hit list to , where
                                   is a positive real number. The default
                                  is 10.0. Hits with E-values better than
                                  (less than) this threshold will be shown.
                                  (Any numeric value)
  [-outfile]           outfile    [*.ehmmpfam] There is a separate output
                                  report for each sequence in seqfile. This
                                  report consists of three sections: a ranked
                                  list of the best scoring HMMs, a list of the
                                  best scoring domains in order of their
                                  occurrence in the sequence, and alignments
                                  for all the best scoring domains.

   Additional (Optional) qualifiers:
   -nuc                boolean    [N] Specify that models and sequence are
                                  nucleic acid, not protein. Other HMMER
                                  programs autodetect this; but because of the
                                  order in which hmmpfam accesses data, it
                                  can't reliably determine the correct
                                  'alphabet' by itself.
   -t                  float      [-1000000.] Set the bit score cutoff for the
                                  per-sequence ranked hit list to , where
                                   is a real number. The default is
                                  negative infinity; by default, the threshold
                                  is controlled by E-value and not by bit
                                  score. Hits with bit scores better than
                                  (greater than) this threshold will be shown.
                                  (Any numeric value)
   -z                  integer    [59021] Calculate the E-value scores as if
                                  we had seen a sequence database of
                                  sequences. The default is arbitrarily set to
                                  59021, the size of Swissprot 34. (Any
                                  integer value)

   Advanced (Unprompted) qualifiers:
   -acc                boolean    [N] Report HMM accessions instead of names
                                  in the output reports. Useful for
                                  high-throughput annotation, where the data
                                  are being parsed for storage in a relational
                                  database.
   -compat             boolean    [N] Use the output format of HMMER 2.1.1,
                                  the 1998-2001 public release; provided so
                                  2.1.1 parsers don't have to be rewritten.
   -cpu                integer    [0] Sets the maximum number of CPUs that the
                                  program will run on. The default is to use
                                  all CPUs in the machine. Overrides the HMMER
                                  NCPU environment variable. Only affects
                                  threaded versions of HMMER (the default on
                                  most systems). (Any integer value)
   -cutga              boolean    [N] Use Pfam GA (gathering threshold) score
                                  cutoffs. Equivalent to -globT  -domT
                                  , but the GA1 and GA2 cutoffs are read
                                  from each HMM in the input HMM database
                                  individually. hmmbuild puts these cutoffs
                                  there if the alignment file was annotated in
                                  a Pfam-friendly alignment format (extended
                                  SELEX or Stockholm format) and the optional
                                  GA annotation line was present. If these
                                  cutoffs are not set in the HMM file, -cut ga
                                  doesn't work.
   -cuttc              boolean    [N] Use Pfam TC (trusted cutoff) score
                                  cutoffs. Equivalent to -globT  -domT
                                  , but the TC1 and TC2 cutoffs are read
                                  from each HMM in hmmfile individually.
                                  hmmbuild puts these cutoffs there if the
                                  alignment file was annotated in a
                                  Pfam-friendly alignment format (extended
                                  SELEX or Stockholm format) and the optional
                                  TC annotation line was present. If these
                                  cutoffs are not set in the HMM file, -cut tc
                                  doesn't work.
   -cutnc              boolean    [N] Use Pfam NC (noise cutoff) score
                                  cutoffs. Equivalent to -globT  -domT
                                  , but the NC1 and NC2 cutoffs are read
                                  from each HMM in hmmfile individually.
                                  hmmbuild puts these cutoffs there if the
                                  alignment file was annotated in a
                                  Pfam-friendly alignment format (extended
                                  SELEX or Stockholm format) and the optional
                                  NC annotation line was present. If these
                                  cutoffs are not set in the HMM file, -cut nc
                                  doesn't work.
   -dome               float      [1000000.] Set the E-value cutoff for the
                                  per-domain ranked hit list to , where
                                  is a positive real number. The default is
                                  infinity; by default, all domains in the
                                  sequences that passed the frst threshold
                                  will be reported in the second list, so that
                                  the number of domains reported in the
                                  per-sequence list is consistent with the
                                  number that appear in the per-domain list.
                                  (Any numeric value)
   -domt               float      [-1000000.] Set the bit score cutoff for the
                                  per-domain ranked hit list to , where
                                   is a real number. The default is
                                  negative infinity; by default, all domains
                                  in the sequences that passed the frst
                                  threshold will be reported in the second
                                  list, so that the number of domains reported
                                  in the per-sequence list is consistent with
                                  the number that appear in the per-domain
                                  list. Important note: only one domain in a
                                  sequence is absolutely controlled by this
                                  parameter, or by --domT. The second and
                                  subsequent domains in a sequence have a de
                                  facto bit score threshold of 0 because of
                                  the details of how HMMER works. HMMER
                                  requires at least one pass through the main
                                  model per sequence; to do more than one pass
                                  (more than one domain) the multidomain
                                  alignment must have a better score than the
                                  single domain alignment, and hence the extra
                                  domains must contribute positive score. See
                                  the Users' Guide for more detail. (Any
                                  numeric value)
   -forward            boolean    [N] Use the Forward algorithm instead of the
                                  Viterbi algorithm to determine the
                                  per-sequence scores. Per-domain scores are
                                  still determined by the Viterbi algorithm.
                                  Some have argued that Forward is a more
                                  sensitive algorithm for detecting remote
                                  sequence homologues; my experiments with
                                  HMMER have not confrmed this, however.
   -nulltwo            boolean    [N] Turn off the post hoc second null model.
                                  By default, each alignment is rescored by a
                                  postprocessing step that takes into account
                                  possible biased composition in either the
                                  HMM or the target sequence. This is almost
                                  essential in database searches, especially
                                  with local alignment models. There is a very
                                  small chance that this postprocessing might
                                  remove real matches, and in these cases
                                  --null2 may improve sensitivity at the
                                  expense of reducing specifcity by letting
                                  biased composition hits through.
   -pvm                boolean    [N] Run on a Parallel Virtual Machine (PVM).
                                  The PVM must already be running. The client
                                  program hmmpfam-pvm must be installed on
                                  all the PVM nodes. The HMM database hmmfile
                                  and an associated GSI index file hmmfile.gsi
                                  must also be installed on all the PVM
                                  nodes. (The GSI index is produced by the
                                  program hmmindex.) Because the PVM
                                  implementation is I/O bound, it is highly
                                  recommended that each node have a local copy
                                  of hmmfile rather than NFS mounting a
                                  shared copy. Optional PVM support must have
                                  been compiled into HMMER for -pvm to
                                  function.
   -xnu                boolean    [N] Turn on XNU filtering of target protein
                                  sequences. Has no effect on nucleic acid
                                  sequences. In trial experiments, -xnu
                                  appears to perform less well than the
                                  default post hoc null2 model.

   Associated qualifiers:

   "-seqfile" associated qualifiers
   -sbegin2            integer    Start of each sequence to be used
   -send2              integer    End of each sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-outfile" associated qualifiers
   -odirectory3        string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

  Alignment and sequence formats

   Input and output of alignments and sequences is limited to the formats
   that the original hmmer supports. These include stockholm, SELEX, MSF,
   Clustal, Phylip and A2M /aligned FASTA (alignments) and FASTA, GENBANK,
   EMBL, GCG, PIR (sequences). It would be fairly straightforward to adapt
   the code to support all EMBOSS-supported formats.

  Compressed input files

   Automatic processing of gzipped files is not supported.

   ehmmpfam reads any normal sequence USAs.

  Input files for usage example

  File: ../ehmmcalibrate-ex2-keep/myhmmso

HMMER2.0  [2.3.2]
NAME  rrm
LENG  77
ALPH  Amino
RF    no
CS    no
MAP   yes
COM   /shared/software/bin/hmmbuild -n rrm --pbswitch 1000 --archpri 0.850000 --
idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../
data/hmmnew/rrm.sto
COM   /shared/software/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.00
0000 --seed 1 ../ehmmbuild-ex4-keep/myhmms
NSEQ  90
DATE  Thu Jan  7 16:51:40 2010
CKSUM 8325
XT      -8455     -4  -1000  -1000  -8455     -4  -8455     -4
NULT      -4  -8455
NULE     595  -1558     85    338   -294    453  -1158    197    249    902  -10
85   -142    -21   -313     45    531    201    384  -1998   -644
EVD   -45.860321   0.213107
HMM        A      C      D      E      F      G      H      I      K      L
 M      N      P      Q      R      S      T      V      W      Y
         m->m   m->i   m->d   i->m   i->i   d->m   d->d   b->m   m->e
          -16      *  -6492
     1  -1084    390  -8597  -8255  -5793  -8424  -8268   2395  -8202   2081  -1
197  -8080  -8115  -8020  -8297  -7789  -5911   1827  -7525  -7140     1
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378    -16      *
     2  -2140  -3785  -6293  -2251   3226  -2495   -727   -638  -2421   -545   -
675  -5146  -5554  -4879  -1183  -2536  -1928    267     76   3171     2
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     3  -2542    458  -8584  -8273  -6055  -8452  -8531   2304  -8255   -324
101  -8104  -8170  -8221  -8440  -7840  -5878   3145  -7857  -7333     3
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     4  -1505  -5144  -1922   -558  -1842   2472  -3303  -2213   1099  -5160  -4
233    372  -4738   -530   1147    168    498  -4766  -5327  -1476     4
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     5  -3724  -5184    300  -3013  -1655   1803  -3353  -5245  -1569  -2686  -4
276   3495  -1963  -1331  -1054  -1472  -3664  -4803  -5369     -2     5
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     6  -1569  -6106  -8967  -8363    555  -8531  -7279    654  -8092   2953
-94  -8220  -7908  -1643  -7682  -7771  -6460    -59  -6191  -6284     6
     -   -151   -504    230     45   -380    399    101   -621    211   -470   -
713    278    399     48     91    360    113   -364   -299   -254
     -   -178  -3113 -12684  -1600   -578   -701  -1378      *      *
     7   -409  -5130   -215  -2987  -1709   -956    690  -5188   -395  -5144  -4
224    729   3054  -2862  -3409    354   1293  -1381  -5321  -4644    13
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     8  -3674  -5118  -1004    639    420  -4652    176  -2050    404  -1039   -
935     16   1755    168    147   -275    198  -1472   1889   1977    14
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
     9   -408  -5134   2415   1299   -950    -66   -767  -1296  -2889  -1843  -4
224   1084   -968  -1439  -1854    540   -314  -2304  -5320    -60    15
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
    10    586   1804  -6294   -631  -1627  -1671  -4374   1029  -2223   -162   1
172  -5147  -5554  -1870  -5058  -2327   1741   1687  -4242    687    16
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11642 -12684   -894  -1115   -701  -1378      *      *
    11  -2134  -5144    845  -1187  -1652  -1667  -3303  -5216   -513   -801  -4
233   1026  -1873   -543   -619    575   2956  -4766  -5327  -4644    17


  [Part of this file has been deleted for brevity]

     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   279  -7207  -7306  -8076  -6588  -8459  -7223  -5448  -7982  -1500  -7531  -6
953  -6369  -7277  -5081   4236  -7139  -6862  -7777  -7053  -7277   454
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   280   -694   -163  -5922  -5286  -1204  -2048   -610   1082  -1800   1434  -2
618  -4776   2951  -4509  -4688  -1216  -1648  -2829    202     21   455
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -  -3168 -11253   -171   -894  -1115   -701  -1378      *      *
   281  -1412  -2132  -2007  -2293  -4366   3113  -2847  -4225  -3107  -4377  -3
503   1660  -2881  -2661  -3396    961  -1821  -3134  -4516  -4119   456
     -   -150   -489    232     42   -382    400    104   -627    211   -465   -
722    274    393     51     95    359    116   -370   -296   -245
     -  -2121   -637  -2975   -831  -1191  -6099    -21      *      *
   282   -968  -1818  -1787  -1351  -3112    953  -1494  -2818  -1122  -2911  -2
044  -1365  -2340  -1133   1510   1816   2121  -2205  -3137  -2649   459
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -   -228  -7899  -2816   -894  -1115  -4964    -47      *      *
   283    840  -1663   -994    969   1159    503   -604  -1413   -325  -1594   -
814   -688  -1996   -267   1103   -851   -755  -1179   2900  -1437   460
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -9  -7938  -8980   -894  -1115    -89  -4060      *      *
   284  -3257  -4642   -697  -2590  -1218   -252  -2907  -4655  -1306  -2353   -
529    482  -1607  -2459  -1398   2112   2745  -4246  -4848  -4187   461
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11183 -12226   -894  -1115   -186  -3045      *      *
   285   2163    763  -1619  -5296   2250  -2060  -4007   1241  -4891   -489
484  -4781   -226  -4515  -4692   -678  -1688   -813    264  -3530   462
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   286   -268   -329   -158    917   -541  -1990    350  -4851   1273  -1075
388  -1130    233    840    993   -602    801   -595  -4964   -857   463
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   287    109   -243    672   2304  -5103  -4283    488  -4854  -1317  -2269   -
656   -492  -1519   2679   -655   -618  -3248  -4404  -4965  -1114   464
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   288   1312   1294  -6215  -5593   -206  -1244  -4339   2188  -5201   1409
395  -5091  -5478  -4828  -5009  -4538  -3794   1162  -4187  -3846   465
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -    -23 -11253  -6022   -894  -1115   -701  -1378      *      *
   289  -3562    799  -5767  -2054  -1235  -2075    318    138    237   2164   1
713  -1454  -5145  -1272   -730  -4172  -1640   1071  -3865    -34   466
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11231 -12273   -894  -1115  -1470   -646      *      *
   290     73   1351   -674   1236  -1549  -2008   1350  -4834   1049  -2498  -3
851   1801  -4356   1813   -115   -223  -1582  -1052  -4945  -4262   467
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11231 -12273   -894  -1115   -369  -2147      *      *
   291  -1739   -320    777  -2654  -1419  -2051   4360  -4707  -1358  -2412   -
689  -1300  -4399   -224    537    531   -289  -2010  -4905  -1057   468
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -11253 -12295   -894  -1115   -701  -1378      *      *
   292  -3345  -4494   -233   -332   -563  -1986  -3051    333     99   1063  -3
616  -3072   2953  -1026  -1490   -943  -1528  -1070  -4753  -4151   469
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -10815 -11857   -894  -1115   -701  -1378      *      *
   293  -6409  -5751  -7614  -7636   2593  -7311  -4003  -5084  -7219   -150   -
151  -6210  -7172   -849  -6723  -6510  -6299  -1387   4881   2807   470
     -   -149   -500    233     43   -381    399    106   -626    210   -466   -
720    275    394     45     96    359    117   -369   -294   -249
     -     -1 -10749 -11791   -894  -1115   -701  -1378      *      *
   294  -4057  -3817  -6415  -5791   3203  -1638  -4541   1679  -5412    765   1
434  -5333  -5617  -4930  -5182  -4791  -3987   1226    750  -3959   471
     -      *      *      *      *      *      *      *      *      *      *
  *      *      *      *      *      *      *      *      *      *
     -      *      *      *      *      *      *      *      *      0
//

  File: 7LES_DROME

ID   7LES_DROME     STANDARD;      PRT;  2554 AA.
AC   P13368;
DT   01-JAN-1990 (Rel. 13, Created)
DT   01-JAN-1990 (Rel. 13, Last sequence update)
DT   01-NOV-1997 (Rel. 35, Last annotation update)
DE   SEVENLESS PROTEIN (EC 2.7.1.112).
GN   SEV.
OS   Drosophila melanogaster (Fruit fly).
OC   Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta;
OC   Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
OC   Ephydroidea; Drosophilidae; Drosophila.
RN   [1]
RP   SEQUENCE FROM N.A.
RC   STRAIN=CANTON-S;
RX   MEDLINE; 88282538.
RA   BASLER K., HAFEN E.;
RT   "Control of photoreceptor cell fate by the sevenless protein requires
RT   a functional tyrosine kinase domain.";
RL   Cell 54:299-311(1988).
RN   [2]
RP   SEQUENCE FROM N.A.
RC   STRAIN=OREGON-R;
RX   MEDLINE; 88329706.
RA   BOWTELL D.L.L., SIMON M.A., RUBIN G.M.;
RT   "Nucleotide sequence and structure of the sevenless gene of
RT   Drosophila melanogaster.";
RL   Genes Dev. 2:620-634(1988).
RN   [3]
RP   IDENTIFICATION OF FN-III REPEATS.
RX   MEDLINE; 90199889.
RA   NORTON P.A., HYNES R.O., RESS D.J.G.;
RT   "Sevenless: seven found?";
RL   Cell 61:15-16(1990).
CC   -!- FUNCTION: RECEPTOR FOR AN EXTRACELLULAR SIGNAL REQUIRED TO
CC       INSTRUCT A CELL TO DIFFERENTIATE INTO A R7 PHOTORECEPTOR. THE
CC       LIGAND FOR SEV IS THE BOSS (BRIDE OF SEVENLESS) PROTEIN ON THE
CC       SURFACE OF THE NEIGHBORING R8 CELL.
CC   -!- CATALYTIC ACTIVITY: ATP + A PROTEIN TYROSINE = ADP +
CC       PROTEIN TYROSINE PHOSPHATE.
CC   -!- SUBUNIT: MAY FORM A COMPLEX WITH DRK AND SOS.
CC   -!- SIMILARITY: BELONGS TO THE INSULIN RECEPTOR FAMILY OF TYROSINE-
CC       PROTEIN KINASES. SEVENLESS SUBFAMILY.
CC   -!- SIMILARITY: CONTAINS 7 FIBRONECTIN TYPE III-LIKE DOMAINS.
CC   -!- CAUTION: UNCLEAR WHETHER THE POTENTIAL MEMBRANE SPANNING REGION
CC       NEAR THE N-TERMINUS IS PRESENT AS A TRANSMEMBRANE DOMAIN IN THE
CC       NATIVE PROTEIN OR SERVES AS A CLEAVED SIGNAL SEQUENCE.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its


  [Part of this file has been deleted for brevity]

FT   VARIANT    1703   1703       N -> H.
FT   VARIANT    1730   1730       R -> K.
FT   VARIANT    1731   1731       G -> E.
FT   VARIANT    1741   1741       V -> M.
FT   VARIANT    2271   2271       R -> C.
FT   CONFLICT   1823   1823       E -> Q (IN REF. 2).
SQ   SEQUENCE   2554 AA;  287107 MW;  1143D891 CRC32;
     MTMFWQQNVD HQSDEQDKQA KGAAPTKRLN ISFNVKIAVN VNTKMTTTHI NQQAPGTSSS
     SSNSQNASPS KIVVRQQSSS FDLRQQLARL GRQLASGQDG HGGISTILII NLLLLILLSI
     CCDVCRSHNY TVHQSPEPVS KDQMRLLRPK LDSDVVEKVA IWHKHAAAAP PSIVEGIAIS
     SRPQSTMAHH PDDRDRDRDP SEEQHGVDER MVLERVTRDC VQRCIVEEDL FLDEFGIQCE
     KADNGEKCYK TRCTKGCAQW YRALKELESC QEACLSLQFY PYDMPCIGAC EMAQRDYWHL
     QRLAISHLVE RTQPQLERAP RADGQSTPLT IRWAMHFPEH YLASRPFNIQ YQFVDHHGEE
     LDLEQEDQDA SGETGSSAWF NLADYDCDEY YMCEILEALI PYTQYRFRFE LPFGENRDEV
     LYSPATPAYQ TPPEGAPISA PVIEHLMGLD DSHLAVHWHP GRFTNGPIEG YRLRLSSSEG
     NATSEQLVPA GRGSYIFSQL QAGTNYTLAL SMINKQGEGP VAKGFVQTHS ARNEKPAKDL
     TESVLLVGRR AVMWQSLEPA GENSMIYQSQ EELADIAWSK REQQLWLLNV HGELRSLKFE
     SGQMVSPAQQ LKLDLGNISS GRWVPRRLSF DWLHHRLYFA MESPERNQSS FQIISTDLLG
     ESAQKVGESF DLPVEQLEVD ALNGWIFWRN EESLWRQDLH GRMIHRLLRI RQPGWFLVQP
     QHFIIHLMLP QEGKFLEISY DGGFKHPLPL PPPSNGAGNG PASSHWQSFA LLGRSLLLPD
     SGQLILVEQQ GQAASPSASW PLKNLPDCWA VILLVPESQP LTSAGGKPHS LKALLGAQAA
     KISWKEPERN PYQSADAARS WSYELEVLDV ASQSAFSIRN IRGPIFGLQR LQPDNLYQLR
     VRAINVDGEP GEWTEPLAAR TWPLGPHRLR WASRQGSVIH TNELGEGLEV QQEQLERLPG
     PMTMVNESVG YYVTGDGLLH CINLVHSQWG CPISEPLQHV GSVTYDWRGG RVYWTDLARN
     CVVRMDPWSG SRELLPVFEA NFLALDPRQG HLYYATSSQL SRHGSTPDEA VTYYRVNGLE
     GSIASFVLDT QQDQLFWLVK GSGALRLYRA PLTAGGDSLQ MIQQIKGVFQ AVPDSLQLLR
     PLGALLWLER SGRRARLVRL AAPLDVMELP TPDQASPASA LQLLDPQPLP PRDEGVIPMT
     VLPDSVRLDD GHWDDFHVRW QPSTSGGNHS VSYRLLLEFG QRLQTLDLST PFARLTQLPQ
     AQLQLKISIT PRTAWRSGDT TRVQLTTPPV APSQPRRLRV FVERLATALQ EANVSAVLRW
     DAPEQGQEAP MQALEYHISC WVGSELHEEL RLNQSALEAR VEHLQPDQTY HFQVEARVAA
     TGAAAGAASH ALHVAPEVQA VPRVLYANAE FIGELDLDTR NRRRLVHTAS PVEHLVGIEG
     EQRLLWVNEH VELLTHVPGS APAKLARMRA EVLALAVDWI QRIVYWAELD ATAPQAAIIY
     RLDLCNFEGK ILQGERVWST PRGRLLKDLV ALPQAQSLIW LEYEQGSPRN GSLRGRNLTD
     GSELEWATVQ PLIRLHAGSL EPGSETLNLV DNQGKLCVYD VARQLCTASA LRAQLNLLGE
     DSIAGQLAQD SGYLYAVKNW SIRAYGRRRQ QLEYTVELEP EEVRLLQAHN YQAYPPKNCL
     LLPSSGGSLL KATDCEEQRC LLNLPMITAS EDCPLPIPGV RYQLNLTLAR GPGSEEHDHG
     VEPLGQWLLG AGESLNLTDL LPFTRYRVSG ILSSFYQKKL ALPTLVLAPL ELLTASATPS
     PPRNFSVRVL SPRELEVSWL PPEQLRSESV YYTLHWQQEL DGENVQDRRE WEAHERRLET
     AGTHRLTGIK PGSGYSLWVQ AHATPTKSNS SERLHVRSFA ELPELQLLEL GPYSLSLTWA
     GTPDPLGSLQ LECRSSAEQL RRNVAGNHTK MVVEPLQPRT RYQCRLLLGY AATPGAPLYH
     GTAEVYETLG DAPSQPGKPQ LEHIAEEVFR VTWTAARGNG APIALYNLEA LQARSDIRRR
     RRRRRRNSGG SLEQLPWAEE PVVVEDQWLD FCNTTELSCI VKSLHSSRLL LFRVRARSLE
     HGWGPYSEES ERVAEPFVSP EKRGSLVLAI IAPAAIVSSC VLALVLVRKV QKRRLRAKKL
     LQQSRPSIWS NLSTLQTQQQ LMAVRNRAFS TTLSDADIAL LPQINWSQLK LLRFLGSGAF
     GEVYEGQLKT EDSEEPQRVA IKSLRKGASE FAELLQEAQL MSNFKHENIV RLVGICFDTE
     SISLIMEHME AGDLLSYLRA ARATSTQEPQ PTAGLSLSEL LAMCIDVANG CSYLEDMHFV
     HRDLACRNCL VTESTGSTDR RRTVKIGDFG LARDIYKSDY YRKEGEGLLP VRWMSPESLV
     DGLFTTQSDV WAFGVLCWEI LTLGQQPYAA RNNFEVLAHV KEGGRLQQPP MCTEKLYSLL
     LLCWRTDPWE RPSFRRCYNT LHAISTDLRR TQMASATADT VVSCSRPEFK VRFDGQPLEE
     HREHNERPED ENLTLREVPL KDKQLYANEG VSRL
//

Output file format

   ehmmpfam outputs a graph to the specified graphics device. outputs a
   report format file. The default format is ...

  Output files for usage example

  File: myhmmso.ehmmpfam

hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file:                 ../ehmmcalibrate-ex2-keep/myhmmso
Sequence file:            ./ehmmpfam-1234567890.1234
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query sequence: 7LES_DROME
Accession:      [none]
Description:    P13368 SEVENLESS PROTEIN (EC 2.7.1.112).

Scores for sequence family classification (score includes all domains):
Model    Description                                    Score    E-value  N
-------- -----------                                    -----    ------- ---
pkinase  Protein kinase domain                          314.6    1.2e-90   1
fn3      Fibronectin type III domain                    176.6      4e-49   6

Parsed for domains:
Model    Domain  seq-f seq-t    hmm-f hmm-t      score  E-value
-------- ------- ----- -----    ----- -----      -----  -------
fn3        1/6     437   522 ..     1    84 []    48.3  1.7e-10
fn3        2/6     825   914 ..     1    84 []    13.4     0.09
fn3        3/6    1292  1389 ..     1    84 []    15.9     0.05
fn3        4/6    1799  1891 ..     1    84 []    63.5  4.5e-15
fn3        5/6    1899  1978 ..     1    84 []    15.2     0.06
fn3        6/6    1993  2107 ..     1    84 []    20.3    0.018
pkinase    1/1    2209  2483 ..     1   294 []   314.6  1.2e-90

Alignments of top-scoring domains:
fn3: domain 1 of 6, from 437 to 522: score 48.3, E = 1.7e-10
                CS    C CCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC
                   *->P.saPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge
                      P saP   + +++ ++ l ++W p +  ngpi+gY++++ +++ g+
  7LES_DROME   437    PiSAPVIEHLMGLDDSHLAVHWHPGRfTNGPIEGYRLRL-SSSEGNA 482

                CS CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC
                   wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
                   + e+ vp    sy+++ L++gt+Y++ +  +n +G+Gp
  7LES_DROME   483 TSEQLVPAGRGSYIFSQLQAGTNYTLALSMINKQGeGPVA    522

fn3: domain 2 of 6, from 825 to 914: score 13.4, E = 0.09
                CS    CCCCCEEEEEECCTTCCEEEEECCC       CCCCCCCEEEEE.EC
                   *->PsaPtnltvtdvtstsltlsWsppt.......gngpitgYevtyRqp
                       ++P  l++   ++  + +sW+ p++++ ++ + +   +Ye+++  +
  7LES_DROME   825    GGKPHSLKALL-GAQAAKISWKEPErnpyqsaDAARSWSYELEV-LD 869

                CS CCCCCCCCCE EECCCCCECECCEEEEECCCCEEEEEECCC  CCCC
                   knggewnelt.vpgtttsytltgLkPgteYevrVqAvnggG..GpeS<-*


  [Part of this file has been deleted for brevity]

                CS CCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC
                   eltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
                   +++v g+ t ++++ L+P t+Y+ r+    ++++G++
  7LES_DROME  1941 RRNVAGNHTKMVVEPLQPRTRYQCRLLLGYAATpGAPL    1978

fn3: domain 6 of 6, from 1993 to 2107: score 20.3, E = 0.018
                CS    CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC
                   *->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge.
                      Ps+P+ ++ + + +  ++++W++++++++pi  Y+++   ++++  +
  7LES_DROME  1993    PSQPGKPQLEHIAEEVFRVTWTAARgNGAPIALYNLEA-LQARSDIr 2038

                CS                            CCCCEEECCCC CECECCEEEEE
                   ...........................wneltvpgttt.sytltgLkPgt
                   +++++++++++++ ++ +  +++   ++++l+  +tt  s++++ L   +
  7LES_DROME  2039 rrrrrrrrnsggsleqlpwaeepvvveDQWLDFCNTTElSCIVKSLHSSR 2088

                CS CCCCEEEEEE CCC CCCC
                   eYevrVqAvn.ggG.GpeS<-*
                      +rV+A++ ++G Gp+S
  7LES_DROME  2089 LLLFRVRARSlEHGwGPYS    2107

pkinase: domain 1 of 1, from 2209 to 2483: score 314.6, E = 1.2e-90
                   *->yelleklGeGsfGkVykakhkd...ktgkiVAvKilkkekesikekr
                      ++ll+ lG+G+fG+Vy++++k+++++  ++VA+K l+k+++++ e
  7LES_DROME  2209    LKLLRFLGSGAFGEVYEGQLKTedsEEPQRVAIKSLRKGASEFAE-- 2253

                   flrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrrng
                   +l E+q++ +++H+NIvrl g++  + +++ l+mE+me GdL++ylr+ +
  7LES_DROME  2254 LLQEAQLMSNFKHENIVRLVGICF-DTESISLIMEHMEAGDLLSYLRAAR 2302

                   ..........gplsekeakkialQilrGleYLHsngivHRDLKpeNILld
                    +++++++++  ls  e++ ++ ++++G +YL+++++vHRDL+ +N+L++
  7LES_DROME  2303 atstqepqptAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVT 2352

                   en......dgtvKiaDFGLArlle..sssklttfvGTpwYmmAPEvileg
                   e +++++++ tvKi+DFGLAr++++++++++ + +  p+++m+PE  l +
  7LES_DROME  2353 EStgstdrRRTVKIGDFGLARDIYksDYYRKEGEGLLPVRWMSPES-LVD 2401

                   rgysskvDvWSlGviLyElltggplfpgadlpaftggdevdqliifvlkl
                     +++++DvW++Gv+++E+lt g                         ++
  7LES_DROME  2402 GLFTTQSDVWAFGVLCWEILTLG-------------------------QQ 2426

                   PfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcLnkDP
                   P+         ++ +e+++++k+ g+rl +p+ c e l++Ll  c++ DP
  7LES_DROME  2427 PYAA-------RNNFEVLAHVKE-GGRLQQPPMCTEKLYSLLLLCWRTDP 2468

                   skRpGsatakeilnhpwf<-*
                   ++Rp   +++ + n +
  7LES_DROME  2469 WERP---SFRRCYNTLHA    2483

//

Data files

   None.

Notes

  1. Command-line arguments

   The following original HMMER options are not supported:
-h         : Use -help to get help information instead.
-informat  : All common sequence file formats are supported automatically.
-n         : Use -nuc instead (-n causes problems for GUI developers)

   The following additional options are provided:
-outfile   : Output file with HMM.

  2. Installing EMBASSY HMMER

   The EMBASSY HMMER package contains "wrapper" applications providing an
   EMBOSS-style interface to the applications in the original HMMER
   package version 2.3.2 developed by Sean Eddy. Please read the file
   INSTALL in the EMBASSY HMMER package distribution for installation
   instructions.

  3. Installing original HMMER

   To use EMBASSY HMMER, you will first need to download and install the
   original HMMER package. Please read the file 00README in the the
   original HMMER package distribution for installation instructions:
WWW home:       http://hmmer.wustl.edu/
Distribution:   ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/

  4. Setting up HMMER

   For the EMBASSY HMMER package to work, the directory containing the
   original HMMER executables *must* be in your path. For example if you
   executables were installed to "/usr/local/hmmer/bin", then type:
set path=(/usr/local/hmmer/bin/ $path)
rehash

  5. Getting help

   Please read the Userguide.pdf distributed with the original HMMER and
   included in the EMBASSY HMMER distribution under the DOCS directory.
   The first 3 chapters (Introduction, Installation and Tutorial) are
   particularly useful.

   Please read the 'Notes' section below for a description of the
   differences between the original and EMBASSY HMMER, particularly which
   application command line options are supported.

References

   None.

Warnings

  Types of input data

   hmmer v3.2.1 and therefore EMBASSY HMMER is only recommended for use
   with protein sequences. If you provide a non-protein sequence you will
   be reprompted for a protein sequence. To accept nucleic acid sequences
   you must replace instances of < type: "protein" > in the application
   ACD files with .

  Environment variables

   The original hmmer uses BLAST environment variables (below), if
   defined, to locate files. The EMBASSY HMMER does not.
BLASTDB   location of sequence databases to be searched
BLASMAT   location of substitution matrices
HMMERDB   location of HMMs

  Disk space requirements

   ehmmpfam makes a temporary local copy of its input sequence data. You
   must ensure there is sufficient disk space for this in the directory
   that ehmmpfam is run.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

                    Program name                   Description
                    ehmmalign     Align sequences to an HMM profile
                    ehmmbuild     Build a profile HMM from an alignment
   ehmmcalibrate    Calibrate HMM search statistics
                    ehmmconvert   Convert between profile HMM file formats
                    ehmmemit      Generate sequences from a profile HMM
                    ehmmfetch     Retrieve an HMM from an HMM database
                    ehmmindex     Create a binary SSI index for an HMM database
                    ehmmsearch    Search a sequence database with a profile HMM
                    oalistat      Statistics for multiple alignment files
                    ohmmalign     Align sequences with an HMM
                    ohmmbuild     Build HMM
   ohmmcalibrate    Calibrate a hidden Markov model
                    ohmmconvert   Convert between HMM formats
                    ohmmemit      Extract HMM sequences
                    ohmmfetch     Extract HMM from a database
                    ohmmindex     Index an HMM database
                    ohmmpfam      Align single sequence with an HMM
                    ohmmsearch    Search sequence database with an HMM

Author(s)

                    This program is an EMBOSS conversion of a program written by Sean Eddy
                    as part of his HMMER package.

                    Although we take every care to ensure that the results of the EMBOSS
                    version are identical to those from the original package, we recommend
                    that you check your inputs give the same results in both versions
                    before publication.

                    Please report all bugs in the EMBOSS version to the EMBOSS bug team,
                    not to the original author. Jon Ison (jison (c) ebi.ac.uk)
   European         Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton,         Cambridge CB10 1SD, UK

                    This program is an EMBASSY wrapper to a program written by Sean Eddy as
                    part of his hmmer package.

                    Please report any bugs to the EMBOSS bug team in the first instance,
                    not to Sean Eddy.

History

Target users

                    This program is intended to be used by everyone and everything, from
                    naive users to embedded scripts.
