Example of FASTA search output

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fasta - SEARCH DATABASE Swissprot WITH FILE: yee_C.seq
Run on: Mon Oct  3 16:32:30 MET 1994 on mendel.sis.pasteur.
.
 
 yee_C.seq :  287 aa
 >YEEC_ECOLI  Length: 347, 287 bases, 52DE1AA3 che: 287 aa
 vs Swiss-Prot Release 29 library
 searching Swiss-Prot library


 Distribution of initial scores with ktup=2.
   |
 v initn   init1
<  2     2     2:=
   4     0     0:
   6     4     4:==
   8    18    18:=========
  10    73    73:=====================================
  12   326   326:==================================================
  14   370   370:==================================================
  16  1248  1248:==================================================
  18  1354  1354:==================================================
  20  2746  2746:==================================================
  22  3151  3151:==================================================
  24  6401  6401:==================================================
  26  5110  5110:==================================================
  28  5724  5763:==================================================
  30  3887  4303:==================================================
  32  2238  2682:==================================================
  34  1401  1735:==================================================
  36   863  1144:==================================================
  38   533   690:==================================================
  40   346   411:==================================================
  42   481   250:==================================================
  44   419   166:==================================================
  46   346   110:==================================================
  48   295    84:------------------------------------------++++++++
  50   203    47:------------------------++++++++++++++++++++++++++
  52   184    46:-----------------------+++++++++++++++++++++++++++
  54   110    39:--------------------++++++++++++++++++++++++++++++
  56    82     9:-----++++++++++++++++++++++++++++++++++++
  58    69     8:----+++++++++++++++++++++++++++++++
  60    71     3:--++++++++++++++++++++++++++++++++++
  62    75     1:-+++++++++++++++++++++++++++++++++++++
  64    36     1:-+++++++++++++++++
  66    31     0:++++++++++++++++
  68    17     2:-++++++++
  70    12     0:++++++
  72    12     0:++++++
  74     6     0:+++
  76    10     1:-++++
  78    28     0:++++++++++++++
  80     2     0:+
> 80    19     5:---+++++++
13464008 residues in 38303 sequences
 statistics exclude scores greater than 73
 mean initn score:  26.8 (7.79)
 mean init1 score:  26.0 (6.05)
 5349 scores better than 33 saved, ktup: 2, variable pamfact
 joining threshold: 28  scan time:  0:00:30

 The best scores are:                                  initn init1   opt
sp|P33013|YEEC_ECOLI HYPOTHETICAL 38.9 KD PROTEIN IN S 1422  1422  1422
sp|P04287|DACA_ECOLI PENICILLIN-BINDING PROTEIN 5 PREC  789   789   797
sp|P08506|DACC_ECOLI PENICILLIN-BINDING PROTEIN 6 PREC  738   738   766
sp|Q05523|DACA_BACST D-ALANYL-D-ALANINE CARBOXYPEPTIDA  176   116   129
......................................................................

ALignments

sp|P33013|YEEC_ECOLI HYPOTHETICAL 38.9 KD PROTEIN IN S 1422  1422  1422
 100.0% identity in 287 aa overlap

                                             10        20        30
YEEC_E                               FVGSSLMFLKEGDRVSVRDLSRGLIVDSGN
                                     X:::::::::::::::::::::::::::::
sp|P33 VVDRAIDSHRITPDDIVTVGRDAWAKDNPVFVGSSLMFLKEGDRVSVRDLSRGLIVDSGN
               40        50        60        70        80        90

               40        50        60        70        80        90
YEEC_E DACVALADYIAGGQRQFVEMMNNYAEKLHLKDTHFETVHGLDAPGQHSSAYDLAVLSRAI
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
sp|P33 DACVALADYIAGGQRQFVEMMNNYAEKLHLKDTHFETVHGLDAPGQHSSAYDLAVLSRAI
              100       110       120       130       140       150

              100       110       120       130       140       150
YEEC_E IHGEPEFYHMYSEKSLTWNGITQQNRNGLLWDKTMNVDGLKTGHTSGAGFNLIASAVDGQ
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
sp|P33 IHGEPEFYHMYSEKSLTWNGITQQNRNGLLWDKTMNVDGLKTGHTSGAGFNLIASAVDGQ
              160       170       180       190       200       210

              160       170       180       190       200       210
YEEC_E RRLIAVVMGADSAKGREEEARKLLRWGQQNFTTVQILHRGKKVGTERIWYGDKENIDLGT
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
sp|P33 RRLIAVVMGADSAKGREEEARKLLRWGQQNFTTVQILHRGKKVGTERIWYGDKENIDLGT
              220       230       240       250       260       270

              220       230       240       250       260       270
YEEC_E EQEFWMVLPKAEIPHIKAKYTLDGKELTAPISAHQRVGEIELYDRDKQVAHWPLVTLESV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
sp|P33 EQEFWMVLPKAEIPHIKAKYTLDGKELTAPISAHQRVGEIELYDRDKQVAHWPLVTLESV
              280       290       300       310       320       330

              280       
YEEC_E GEGSMFSRLSDYFHHKA
       ::::::::::::::::X
sp|P33 GEGSMFSRLSDYFHHKA
              340       

 sp|P04287|DACA_ECOLI PENICILLIN-BINDING PROTEIN 5 PREC  789   789   797
  50.2% identity in 283 aa overlap

                                             10        20        30
YEEC_E                               FVGSSLMFLKEGDRVSVRDLSRGLIVDSGN
                                     : X::::::: : .:.:..: ::. ..:::
sp|P04 VIGQAMKAGKFKETDLVTIGNDAWATGNPVFKGSSLMFLKPGMQVPVSQLIRGINLQSGN
              90       100       110       120       130       140 

               40        50        60        70        80        90
YEEC_E DACVALADYIAGGQRQFVEMMNNYAEKLHLKDTHFETVHGLDAPGQHSSAYDLAVLSRAI
       :::::.::. ::.: .::..::.:.. : ::.:::.::::::: ::.::: :.:....:.
sp|P04 DACVAMADFAAGSQDAFVGLMNSYVNALGLKNTHFQTVHGLDADGQYSSARDMALIGQAL
             150       160       170       180       190       200 

              100       110       120       130       140       150
YEEC_E IHGEPEFYHMYSEKSLTWNGITQQNRNGLLWDKTMNVDGLKTGHTSGAGFNLIASAVDGQ
       :.. :. : .:.::..:.::: : ::::::::...::::.:::::. ::.::.:::..::
sp|P04 IRDVPNEYSIYKEKEFTFNGIRQLNRNGLLWDNSLNVDGIKTGHTDKAGYNLVASATEGQ
             210       220       230       240       250       260 

              160       170       180       190       200       210
YEEC_E RRLIAVVMGADSAKGREEEARKLLRWGQQNFTTVQILHRGKKVGTERIWYGDKENIDLGT
       .:::..:::. . ::::.:..::: :: . :.::. :. ::. ..:..:.::... .::.
sp|P04 MRLISAVMGGRTFKGREAESKKLLTWGFRFFETVNPLKVGKEFASEPVWFGDSDRASLGV
             270       280       290       300       310       320 

              220       230       240       250       260       270
YEEC_E EQEFWMVLPKAEIPHIKAKYTLDGKELTAPISAHQRVGEIELYDRDKQVAHWPLVTLESV
       ... ....:.. . ..::.:.:...:: ::.  .: ::.:..   .: ....:::.:...
sp|P04 DKDVYLTIPRGRMKDLKASYVLNSSELHAPLQKNQVVGTINFQLDGKTIEQRPLVVLQEI
             330       340       350       360       370       380 

              280            
YEEC_E GEGSMFSRLSDYFHHKA     
        ::..:... :X..        
sp|P04 PEGNFFGKIIDYIKLMFHHWFG
             390       400   

sp|P08506|DACC_ECOLI PENICILLIN-BINDING PROTEIN 6 PREC  738   738   766
  49.3% identity in 280 aa overlap

                                           10        20        30  
YEEC_E                             FVGSSLMFLKEGDRVSVRDLSRGLIVDSGNDA
                                     X::.:::: ::.::: ::..:.:..:::::
sp|P08 GQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDA
         80        90       100       110       120       130      

             40        50        60        70        80        90  
YEEC_E CVALADYIAGGQRQFVEMMNNYAEKLHLKDTHFETVHGLDAPGQHSSAYDLAVLSRAIIH
       :.:::::.::.:  :...::.::.:: :..: :.:::::::::: :.: :.:.:..:.::
sp|P08 CIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIH
        140       150       160       170       180       190      

            100       110       120       130       140       150  
YEEC_E GEPEFYHMYSEKSLTWNGITQQNRNGLLWDKTMNVDGLKTGHTSGAGFNLIASAVDGQRR
       . :: : ...::..:.: : :.::: :::....: ::.::: :.:::.::.:::..:..:
sp|P08 DVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNEDGMKTGTTAGAGYNLVASATQGDMR
        200       210       220       230       240       250      

            160       170       180       190       200       210  
YEEC_E LIAVVMGADSAKGREEEARKLLRWGQQNFTTVQILHRGKKVGTERIWYGDKENIDLGTEQ
       ::.::.::.... : .:. ::: :: . :.::  .... .  :.:.:.:::....::...
sp|P08 LISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGE
        260       270       280       290       300       310      

            220       230       240       250       260       270  
YEEC_E EFWMVLPKAEIPHIKAKYTLDGKELTAPISAHQRVGEIELYDRDKQVAHWPLVTLESVGE
       .  ...:.... ..::.:::.. .::::..  : ::.:..  ..: ....::...:.:.:
sp|P08 AGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEE
        320       330       340       350       360       370      

            280                
YEEC_E GSMFSRLSDYFHHKA         
       X..:.:. :.              
sp|P08 GGFFGRVWDFVMMKFHQWFGSWFS
        380       390       400

sp|Q05523|DACA_BACST D-ALANYL-D-ALANINE CARBOXYPEPTIDA  176   116   129
  41.3% identity in 63 aa overlap

                                     10        20        30        
YEEC_E                       FVGSSLMFLKEGDRVSVRDLSRGLIVDSGNDACVALAD
                                     :..... .X:.:  .. . :.:.: ::.:.
sp|Q05 KAKRVKWDQMYTPSDYVYRLSQDRALSNVPLRKDGKYTVRELYEAMAIYSANGATVAIAE
               90       100       110       120       130       140

       40        50        60        70        80        90        
YEEC_E YIAGGQRQFVEMMNNYAEKLHLKDTHFETVHGLDAPGQHSSAYDLAVLSRAIIHGEPEFY
        :::....::.:::. :..: ::: .: .. :X.                          
sp|Q05 IIAGSEKNFVKMMNDKAKELGLKDYKFVNATGLSNKDLKGFHPEGTSTNEENVMSARAMA
              150       160       170       180       190       200

      100       110       120       130       140       150        
YEEC_E HMYSEKSLTWNGITQQNRNGLLWDKTMNVDGLKTGHTSGAGFNLIASAVDGQRRLIAVVM
                                                                   
sp|Q05 MLAYRLLKDHPEVLKTASIPHKVFREGTKDEIKMDNWNWMLPGLVYGYEGVDGLKTGYTE
              210       220       230       240       250       260
..................................................................



Library scan:  0:00:30  total CPU time:  0:00:31

up intervall
 < 2 : represents scores in the interval < 2.
   4 : represents scores in the interval ]2-4]
   6 : represents scores in the interval  ]4-6]
 etc.......

up initn
This column represents the number of library sequences that obtained 
an initial similarity score in their corresponding histogram interval

up init1
This column represents the number of sequences with a best single initial 
region similarity score in their corresponding histogram interval

up =
When the number of sequences reported in columns initn and init1
are equal, they are represented by "=" signs in the histogram.

up +-
When the number of sequences reported in columns initn and init1
are not equal, initn values are graphed with a "+" and the init1 
values with a "-".

up mean and standard deviation
mean score and it's corresponding standard deviation ().

up initn and init1
While the initn score, which is used to rank the library sequences, 
provides a very sensitive measure of protein sequence similarity, the 
relationship between the init1 score and the optimized score provides a
more selective perspective.

up : and .
The initial score for this comparison is 789 (initn), the score of the 
best single initial region is 789 (init1), and the score of the aligned 
amino acids in the optimized region denoted by ":" and "." is 797 (opt).
Aligned amino acid identities are denoted by ":"; substitutions 
with PAM250
scores of zero or greater are denoted by ".".

up X
The amino-acid-terminal boundary of the init1 initial region is 
denoted by an "X".



Comments and suggestions are welcome. Fredj Tekaia tekaia@pasteur.fr.