Result of FASTA (omim) for pF1KSDB1384
FASTA searches a protein or DNA sequence data bank 36.3.4 Apr, 2011
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: pF1KSDB1384, 674 aa
  1>>>pF1KSDB1384 674 - 674 aa - 674 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 7.3197+/-0.000445; mu= 9.5459+/- 0.028
 mean_var=120.0210+/-24.041, 0's: 0 Z-trim(113.6): 7  B-trim: 567 in 2/56
 Lambda= 0.117070
 statistics sampled from 23066 (23070) to 23066 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.634), E-opt: 0.2 (0.27), width:  16
 Scan time:  9.790

The best scores are:                                      opt bits E(85289)
NP_060557 (OMIM: 610115) nucleoporin NDC1 isoform  ( 674) 4503 772.4       0
XP_011540068 (OMIM: 610115) PREDICTED: nucleoporin ( 673) 4369 749.8 7.7e-216
NP_001162023 (OMIM: 610115) nucleoporin NDC1 isofo ( 634) 3625 624.1 4.9e-178


>>NP_060557 (OMIM: 610115) nucleoporin NDC1 isoform 1 [H  (674 aa)
 initn: 4503 init1: 4503 opt: 4503  Z-score: 4118.3  bits: 772.4 E(85289):    0
Smith-Waterman score: 4503; 100.0% identity (100.0% similar) in 674 aa overlap (1-674:1-674)

               10        20        30        40        50        60
pF1KSD MATAVSRPCAGRSRDILWRVLGWRIVASIVWSVLFLPICTTVFIIFSRIDLFHPIQWLSD
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 MATAVSRPCAGRSRDILWRVLGWRIVASIVWSVLFLPICTTVFIIFSRIDLFHPIQWLSD
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KSD SFSDLYSSYVIFYFLLLSVVIIIISIFNVEFYAVVPSIPCSRLALIGKIIHPQQLMHSFI
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 SFSDLYSSYVIFYFLLLSVVIIIISIFNVEFYAVVPSIPCSRLALIGKIIHPQQLMHSFI
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KSD HAAMGMVMAWCAAVITQGQYSFLVVPCTGTNSFGSPAAQTCLNEYHLFFLLTGAFMGYSY
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 HAAMGMVMAWCAAVITQGQYSFLVVPCTGTNSFGSPAAQTCLNEYHLFFLLTGAFMGYSY
              130       140       150       160       170       180

              190       200       210       220       230       240
pF1KSD SLLYFVNNMNYLPFPIIQQYKFLRFRRSLLLLVKHSCVESLFLVRNFCILYYFLGYIPKA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 SLLYFVNNMNYLPFPIIQQYKFLRFRRSLLLLVKHSCVESLFLVRNFCILYYFLGYIPKA
              190       200       210       220       230       240

              250       260       270       280       290       300
pF1KSD WISTAMNLHIDEQVHRPLDTVSGLLNLSLLYHVWLCGVFLLTTWYVSWILFKIYATEAHV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 WISTAMNLHIDEQVHRPLDTVSGLLNLSLLYHVWLCGVFLLTTWYVSWILFKIYATEAHV
              250       260       270       280       290       300

              310       320       330       340       350       360
pF1KSD FPVQPPFAEGSDECLPKVLNSNPPPIIKYLALQDLMLLSQYSPSRRQEVFSLSQPGGHPH
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 FPVQPPFAEGSDECLPKVLNSNPPPIIKYLALQDLMLLSQYSPSRRQEVFSLSQPGGHPH
              310       320       330       340       350       360

              370       380       390       400       410       420
pF1KSD NWTAISRECLNLLNGMTQKLILYQEAAATNGRVSSSYPVEPKKLNSPEETAFQTPKSSQM
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 NWTAISRECLNLLNGMTQKLILYQEAAATNGRVSSSYPVEPKKLNSPEETAFQTPKSSQM
              370       380       390       400       410       420

              430       440       450       460       470       480
pF1KSD PRPSVPPLVKTSLFSSKLSTPDVVSPFGTPFGSSVMNRMAGIFDVNTCYGSPQSPQLIRR
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 PRPSVPPLVKTSLFSSKLSTPDVVSPFGTPFGSSVMNRMAGIFDVNTCYGSPQSPQLIRR
              430       440       450       460       470       480

              490       500       510       520       530       540
pF1KSD GPRLWTSASDQQMTEFSNPSPSTSISAEGKTMRQPSVIYSWIQNKREQIKNFLSKRVLIM
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 GPRLWTSASDQQMTEFSNPSPSTSISAEGKTMRQPSVIYSWIQNKREQIKNFLSKRVLIM
              490       500       510       520       530       540

              550       560       570       580       590       600
pF1KSD YFFSKHPEASIQAVFSDAQMHIWALEGLSHLVAASFTEDRFGVVQTTLPAILNTLLTLQE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 YFFSKHPEASIQAVFSDAQMHIWALEGLSHLVAASFTEDRFGVVQTTLPAILNTLLTLQE
              550       560       570       580       590       600

              610       620       630       640       650       660
pF1KSD AVDKYFKLPHASSKPPRISGSLVDTSYKTLRFAFRASLKTAIYRITTTFGEHLNAVQASA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 AVDKYFKLPHASSKPPRISGSLVDTSYKTLRFAFRASLKTAIYRITTTFGEHLNAVQASA
              610       620       630       640       650       660

              670    
pF1KSD EHQKRLQQFLEFKE
       ::::::::::::::
NP_060 EHQKRLQQFLEFKE
              670    

>>XP_011540068 (OMIM: 610115) PREDICTED: nucleoporin NDC  (673 aa)
 initn: 4369 init1: 4369 opt: 4369  Z-score: 3996.0  bits: 749.8 E(85289): 7.7e-216
Smith-Waterman score: 4369; 100.0% identity (100.0% similar) in 655 aa overlap (20-674:19-673)

               10        20        30        40        50        60
pF1KSD MATAVSRPCAGRSRDILWRVLGWRIVASIVWSVLFLPICTTVFIIFSRIDLFHPIQWLSD
                          :::::::::::::::::::::::::::::::::::::::::
XP_011  MEIGIGSEAEFYARVPYPVLGWRIVASIVWSVLFLPICTTVFIIFSRIDLFHPIQWLSD
                10        20        30        40        50         

               70        80        90       100       110       120
pF1KSD SFSDLYSSYVIFYFLLLSVVIIIISIFNVEFYAVVPSIPCSRLALIGKIIHPQQLMHSFI
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 SFSDLYSSYVIFYFLLLSVVIIIISIFNVEFYAVVPSIPCSRLALIGKIIHPQQLMHSFI
      60        70        80        90       100       110         

              130       140       150       160       170       180
pF1KSD HAAMGMVMAWCAAVITQGQYSFLVVPCTGTNSFGSPAAQTCLNEYHLFFLLTGAFMGYSY
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 HAAMGMVMAWCAAVITQGQYSFLVVPCTGTNSFGSPAAQTCLNEYHLFFLLTGAFMGYSY
     120       130       140       150       160       170         

              190       200       210       220       230       240
pF1KSD SLLYFVNNMNYLPFPIIQQYKFLRFRRSLLLLVKHSCVESLFLVRNFCILYYFLGYIPKA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 SLLYFVNNMNYLPFPIIQQYKFLRFRRSLLLLVKHSCVESLFLVRNFCILYYFLGYIPKA
     180       190       200       210       220       230         

              250       260       270       280       290       300
pF1KSD WISTAMNLHIDEQVHRPLDTVSGLLNLSLLYHVWLCGVFLLTTWYVSWILFKIYATEAHV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 WISTAMNLHIDEQVHRPLDTVSGLLNLSLLYHVWLCGVFLLTTWYVSWILFKIYATEAHV
     240       250       260       270       280       290         

              310       320       330       340       350       360
pF1KSD FPVQPPFAEGSDECLPKVLNSNPPPIIKYLALQDLMLLSQYSPSRRQEVFSLSQPGGHPH
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 FPVQPPFAEGSDECLPKVLNSNPPPIIKYLALQDLMLLSQYSPSRRQEVFSLSQPGGHPH
     300       310       320       330       340       350         

              370       380       390       400       410       420
pF1KSD NWTAISRECLNLLNGMTQKLILYQEAAATNGRVSSSYPVEPKKLNSPEETAFQTPKSSQM
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 NWTAISRECLNLLNGMTQKLILYQEAAATNGRVSSSYPVEPKKLNSPEETAFQTPKSSQM
     360       370       380       390       400       410         

              430       440       450       460       470       480
pF1KSD PRPSVPPLVKTSLFSSKLSTPDVVSPFGTPFGSSVMNRMAGIFDVNTCYGSPQSPQLIRR
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 PRPSVPPLVKTSLFSSKLSTPDVVSPFGTPFGSSVMNRMAGIFDVNTCYGSPQSPQLIRR
     420       430       440       450       460       470         

              490       500       510       520       530       540
pF1KSD GPRLWTSASDQQMTEFSNPSPSTSISAEGKTMRQPSVIYSWIQNKREQIKNFLSKRVLIM
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 GPRLWTSASDQQMTEFSNPSPSTSISAEGKTMRQPSVIYSWIQNKREQIKNFLSKRVLIM
     480       490       500       510       520       530         

              550       560       570       580       590       600
pF1KSD YFFSKHPEASIQAVFSDAQMHIWALEGLSHLVAASFTEDRFGVVQTTLPAILNTLLTLQE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 YFFSKHPEASIQAVFSDAQMHIWALEGLSHLVAASFTEDRFGVVQTTLPAILNTLLTLQE
     540       550       560       570       580       590         

              610       620       630       640       650       660
pF1KSD AVDKYFKLPHASSKPPRISGSLVDTSYKTLRFAFRASLKTAIYRITTTFGEHLNAVQASA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 AVDKYFKLPHASSKPPRISGSLVDTSYKTLRFAFRASLKTAIYRITTTFGEHLNAVQASA
     600       610       620       630       640       650         

              670    
pF1KSD EHQKRLQQFLEFKE
       ::::::::::::::
XP_011 EHQKRLQQFLEFKE
     660       670   

>>NP_001162023 (OMIM: 610115) nucleoporin NDC1 isoform 2  (634 aa)
 initn: 3611 init1: 3611 opt: 3625  Z-score: 3317.2  bits: 624.1 E(85289): 4.9e-178
Smith-Waterman score: 4133; 94.1% identity (94.1% similar) in 674 aa overlap (1-674:1-634)

               10        20        30        40        50        60
pF1KSD MATAVSRPCAGRSRDILWRVLGWRIVASIVWSVLFLPICTTVFIIFSRIDLFHPIQWLSD
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 MATAVSRPCAGRSRDILWRVLGWRIVASIVWSVLFLPICTTVFIIFSRIDLFHPIQWLSD
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KSD SFSDLYSSYVIFYFLLLSVVIIIISIFNVEFYAVVPSIPCSRLALIGKIIHPQQLMHSFI
       ::::::::::::::::::::::::::::::::::                          
NP_001 SFSDLYSSYVIFYFLLLSVVIIIISIFNVEFYAV--------------------------
               70        80        90                              

              130       140       150       160       170       180
pF1KSD HAAMGMVMAWCAAVITQGQYSFLVVPCTGTNSFGSPAAQTCLNEYHLFFLLTGAFMGYSY
                     ::::::::::::::::::::::::::::::::::::::::::::::
NP_001 --------------ITQGQYSFLVVPCTGTNSFGSPAAQTCLNEYHLFFLLTGAFMGYSY
                        100       110       120       130       140

              190       200       210       220       230       240
pF1KSD SLLYFVNNMNYLPFPIIQQYKFLRFRRSLLLLVKHSCVESLFLVRNFCILYYFLGYIPKA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 SLLYFVNNMNYLPFPIIQQYKFLRFRRSLLLLVKHSCVESLFLVRNFCILYYFLGYIPKA
              150       160       170       180       190       200

              250       260       270       280       290       300
pF1KSD WISTAMNLHIDEQVHRPLDTVSGLLNLSLLYHVWLCGVFLLTTWYVSWILFKIYATEAHV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 WISTAMNLHIDEQVHRPLDTVSGLLNLSLLYHVWLCGVFLLTTWYVSWILFKIYATEAHV
              210       220       230       240       250       260

              310       320       330       340       350       360
pF1KSD FPVQPPFAEGSDECLPKVLNSNPPPIIKYLALQDLMLLSQYSPSRRQEVFSLSQPGGHPH
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 FPVQPPFAEGSDECLPKVLNSNPPPIIKYLALQDLMLLSQYSPSRRQEVFSLSQPGGHPH
              270       280       290       300       310       320

              370       380       390       400       410       420
pF1KSD NWTAISRECLNLLNGMTQKLILYQEAAATNGRVSSSYPVEPKKLNSPEETAFQTPKSSQM
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 NWTAISRECLNLLNGMTQKLILYQEAAATNGRVSSSYPVEPKKLNSPEETAFQTPKSSQM
              330       340       350       360       370       380

              430       440       450       460       470       480
pF1KSD PRPSVPPLVKTSLFSSKLSTPDVVSPFGTPFGSSVMNRMAGIFDVNTCYGSPQSPQLIRR
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 PRPSVPPLVKTSLFSSKLSTPDVVSPFGTPFGSSVMNRMAGIFDVNTCYGSPQSPQLIRR
              390       400       410       420       430       440

              490       500       510       520       530       540
pF1KSD GPRLWTSASDQQMTEFSNPSPSTSISAEGKTMRQPSVIYSWIQNKREQIKNFLSKRVLIM
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 GPRLWTSASDQQMTEFSNPSPSTSISAEGKTMRQPSVIYSWIQNKREQIKNFLSKRVLIM
              450       460       470       480       490       500

              550       560       570       580       590       600
pF1KSD YFFSKHPEASIQAVFSDAQMHIWALEGLSHLVAASFTEDRFGVVQTTLPAILNTLLTLQE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 YFFSKHPEASIQAVFSDAQMHIWALEGLSHLVAASFTEDRFGVVQTTLPAILNTLLTLQE
              510       520       530       540       550       560

              610       620       630       640       650       660
pF1KSD AVDKYFKLPHASSKPPRISGSLVDTSYKTLRFAFRASLKTAIYRITTTFGEHLNAVQASA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 AVDKYFKLPHASSKPPRISGSLVDTSYKTLRFAFRASLKTAIYRITTTFGEHLNAVQASA
              570       580       590       600       610       620

              670    
pF1KSD EHQKRLQQFLEFKE
       ::::::::::::::
NP_001 EHQKRLQQFLEFKE
              630    




674 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Thu Nov  3 08:35:16 2016 done: Thu Nov  3 08:35:18 2016
 Total Scan time:  9.790 Total Display time:  0.010

Function used was FASTA [36.3.4 Apr, 2011]
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