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: pF1KB6918, 225 aa
  1>>>pF1KB6918 225 - 225 aa - 225 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 5.8933+/-0.00036; mu= 13.7038+/- 0.023
 mean_var=127.0954+/-27.209, 0's: 0 Z-trim(116.8): 149  B-trim: 1746 in 1/56
 Lambda= 0.113765
 statistics sampled from 28051 (28208) to 28051 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.691), E-opt: 0.2 (0.331), width:  16
 Scan time:  6.370

The best scores are:                                      opt bits E(85289)
NP_937863 (OMIM: 603520) U2 small nuclear ribonucl ( 225) 1470 251.8 6.7e-67
NP_003083 (OMIM: 603520) U2 small nuclear ribonucl ( 225) 1470 251.8 6.7e-67
NP_004587 (OMIM: 182285) U1 small nuclear ribonucl ( 282)  616 111.8 1.2e-24


>>NP_937863 (OMIM: 603520) U2 small nuclear ribonucleopr  (225 aa)
 initn: 1470 init1: 1470 opt: 1470  Z-score: 1322.1  bits: 251.8 E(85289): 6.7e-67
Smith-Waterman score: 1470; 99.6% identity (99.6% similar) in 225 aa overlap (1-225:1-225)

               10        20        30        40        50        60
pF1KB6 MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_937 MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB6 SSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTATTT
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_937 SSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTATTT
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KB6 NKKSGQGTPNSANTQGNSTPNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEV
       ::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_937 NKKPGQGTPNSANTQGNSTPNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEV
              130       140       150       160       170       180

              190       200       210       220     
pF1KB6 RLVPGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK
       :::::::::::::::::::::::::::::::::::::::::::::
NP_937 RLVPGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK
              190       200       210       220     

>>NP_003083 (OMIM: 603520) U2 small nuclear ribonucleopr  (225 aa)
 initn: 1470 init1: 1470 opt: 1470  Z-score: 1322.1  bits: 251.8 E(85289): 6.7e-67
Smith-Waterman score: 1470; 99.6% identity (99.6% similar) in 225 aa overlap (1-225:1-225)

               10        20        30        40        50        60
pF1KB6 MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_003 MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELG
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB6 SSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTATTT
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_003 SSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTATTT
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KB6 NKKSGQGTPNSANTQGNSTPNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEV
       ::: ::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_003 NKKPGQGTPNSANTQGNSTPNPQVPDYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEV
              130       140       150       160       170       180

              190       200       210       220     
pF1KB6 RLVPGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK
       :::::::::::::::::::::::::::::::::::::::::::::
NP_003 RLVPGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK
              190       200       210       220     

>>NP_004587 (OMIM: 182285) U1 small nuclear ribonucleopr  (282 aa)
 initn: 636 init1: 599 opt: 616  Z-score: 563.4  bits: 111.8 E(85289): 1.2e-24
Smith-Waterman score: 840; 54.7% identity (71.1% similar) in 256 aa overlap (2-203:5-260)

                  10        20        30        40        50       
pF1KB6    MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFK
           . ::::::::::.:.::::.:::.::::.:::::...::.. ...:::::::::::
NP_004 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK
               10        20        30        40        50        60

        60        70        80        90       100       110       
pF1KB6 ELGSSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTA
       :..:.:::::..:::::: :::::::::::::::.::.:::.....:.::.: :. :  :
NP_004 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA
               70        80        90       100       110       120

       120       130                                   140         
pF1KB6 TTTNKKSGQGTPNSANTQG----------------------------NSTPNP-----QV
       :    ..: .::  . .::                            .  : :     :.
NP_004 TKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI
              130       140       150       160       170       180

                               150       160       170       180   
pF1KB6 P---------------------DYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLV
       :                     . :::.::::.::::::::.::::::::::::::::::
NP_004 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV
              190       200       210       220       230       240

           190       200       210       220     
pF1KB6 PGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK
       :::::::::::.:. :::::                      
NP_004 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
              250       260       270       280  




225 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Sat Nov  5 08:19:45 2016 done: Sat Nov  5 08:19:46 2016
 Total Scan time:  6.370 Total Display time: -0.020

Function used was FASTA [36.3.4 Apr, 2011]