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: pF1KB6320, 282 aa
  1>>>pF1KB6320 282 - 282 aa - 282 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 11.7692+/-0.000457; mu= -10.7773+/- 0.029
 mean_var=502.2075+/-104.271, 0's: 0 Z-trim(123.6): 3  B-trim: 813 in 1/56
 Lambda= 0.057231
 statistics sampled from 43654 (43667) to 43654 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.793), E-opt: 0.2 (0.512), width:  16
 Scan time:  7.150

The best scores are:                                      opt bits E(85289)
NP_004587 (OMIM: 182285) U1 small nuclear ribonucl ( 282) 1917 171.8 1.3e-42
NP_003083 (OMIM: 603520) U2 small nuclear ribonucl ( 225)  614 64.1 2.8e-10
NP_937863 (OMIM: 603520) U2 small nuclear ribonucl ( 225)  614 64.1 2.8e-10


>>NP_004587 (OMIM: 182285) U1 small nuclear ribonucleopr  (282 aa)
 initn: 1917 init1: 1917 opt: 1917  Z-score: 885.8  bits: 171.8 E(85289): 1.3e-42
Smith-Waterman score: 1917; 100.0% identity (100.0% similar) in 282 aa overlap (1-282:1-282)

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

               70        80        90       100       110       120
pF1KB6 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_004 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KB6 TKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_004 TKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI
              130       140       150       160       170       180

              190       200       210       220       230       240
pF1KB6 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_004 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV
              190       200       210       220       230       240

              250       260       270       280  
pF1KB6 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
       ::::::::::::::::::::::::::::::::::::::::::
NP_004 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
              250       260       270       280  

>>NP_003083 (OMIM: 603520) U2 small nuclear ribonucleopr  (225 aa)
 initn: 634 init1: 597 opt: 614  Z-score: 305.6  bits: 64.1 E(85289): 2.8e-10
Smith-Waterman score: 949; 56.5% identity (72.7% similar) in 278 aa overlap (5-282:2-225)

               10        20        30        40        50        60
pF1KB6 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK
           . ::::::::::.:.::::.:::.::::.:::::...::.. ...:::::::::::
NP_003    MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFK
                  10        20        30        40        50       

               70        80        90       100       110       120
pF1KB6 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA
       :..:.:::::..:::::: :::::::::::::::.::.:::.....:.::.: :. :  :
NP_003 ELGSSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTA
        60        70        80        90       100       110       

              130       140       150       160       170       180
pF1KB6 TKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI
       :    . : .::  . .::                            .  : :     :.
NP_003 TTTNKKPGQGTPNSANTQG----------------------------NSTPNP-----QV
       120       130                                   140         

              190       200       210       220       230       240
pF1KB6 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV
       :                     . :::.::::.::::::::.::::::::::::::::::
NP_003 P---------------------DYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLV
                               150       160       170       180   

              250       260       270       280  
pF1KB6 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
       :::::::::::.:. ::::::::::::::: ..::::..:::
NP_003 PGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK
           190       200       210       220     

>>NP_937863 (OMIM: 603520) U2 small nuclear ribonucleopr  (225 aa)
 initn: 634 init1: 597 opt: 614  Z-score: 305.6  bits: 64.1 E(85289): 2.8e-10
Smith-Waterman score: 949; 56.5% identity (72.7% similar) in 278 aa overlap (5-282:2-225)

               10        20        30        40        50        60
pF1KB6 MAVPETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFK
           . ::::::::::.:.::::.:::.::::.:::::...::.. ...:::::::::::
NP_937    MDIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFK
                  10        20        30        40        50       

               70        80        90       100       110       120
pF1KB6 EVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTFVERDRKREKRKPKSQETPA
       :..:.:::::..:::::: :::::::::::::::.::.:::.....:.::.: :. :  :
NP_937 ELGSSTNALRQLQGFPFYGKPMRIQYAKTDSDIISKMRGTFADKEKKKEKKKAKTVEQTA
        60        70        80        90       100       110       

              130       140       150       160       170       180
pF1KB6 TKKAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQI
       :    . : .::  . .::                            .  : :     :.
NP_937 TTTNKKPGQGTPNSANTQG----------------------------NSTPNP-----QV
       120       130                                   140         

              190       200       210       220       230       240
pF1KB6 PPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLV
       :                     . :::.::::.::::::::.::::::::::::::::::
NP_937 P---------------------DYPPNYILFLNNLPEETNEMMLSMLFNQFPGFKEVRLV
                               150       160       170       180   

              250       260       270       280  
pF1KB6 PGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK
       :::::::::::.:. ::::::::::::::: ..::::..:::
NP_937 PGRHDIAFVEFENDGQAGAARDALQGFKITPSHAMKITYAKK
           190       200       210       220     




282 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Fri Nov  4 20:30:16 2016 done: Fri Nov  4 20:30:17 2016
 Total Scan time:  7.150 Total Display time: -0.030

Function used was FASTA [36.3.4 Apr, 2011]