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: pF1KE3556, 244 aa
  1>>>pF1KE3556 244 - 244 aa - 244 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 5.3518+/-0.000329; mu= 14.2222+/- 0.021
 mean_var=65.5987+/-13.148, 0's: 0 Z-trim(115.1): 10  B-trim: 0 in 0/51
 Lambda= 0.158353
 statistics sampled from 25349 (25355) to 25349 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.679), E-opt: 0.2 (0.297), width:  16
 Scan time:  6.270

The best scores are:                                      opt bits E(85289)
NP_006322 (OMIM: 211180,611531) ribosomal RNA smal ( 244) 1617 377.9 8.9e-105
NP_001306978 (OMIM: 211180,611531) ribosomal RNA s ( 194) 1056 249.7 2.8e-66


>>NP_006322 (OMIM: 211180,611531) ribosomal RNA small su  (244 aa)
 initn: 1617 init1: 1617 opt: 1617  Z-score: 2002.0  bits: 377.9 E(85289): 8.9e-105
Smith-Waterman score: 1617; 100.0% identity (100.0% similar) in 244 aa overlap (1-244:1-244)

               10        20        30        40        50        60
pF1KE3 MAAPSDGFKPRERSGGEQAQDWDALPPKRPRLGAGNKIGGRRLIVVLEGASLETVKVGKT
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_006 MAAPSDGFKPRERSGGEQAQDWDALPPKRPRLGAGNKIGGRRLIVVLEGASLETVKVGKT
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KE3 YELLNCDKHKSILLKNGRDPGEARPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNVLIEV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_006 YELLNCDKHKSILLKNGRDPGEARPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNVLIEV
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KE3 NPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPQKLLKVIKNPVSDHFPVGCMKVGTSFSI
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_006 NPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPQKLLKVIKNPVSDHFPVGCMKVGTSFSI
              130       140       150       160       170       180

              190       200       210       220       230       240
pF1KE3 PVVSDVRELVPSSDPIVFVVGAFAHGKVSVEYTEKMVSISNYPLSAALTCAKLTTAFEEV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_006 PVVSDVRELVPSSDPIVFVVGAFAHGKVSVEYTEKMVSISNYPLSAALTCAKLTTAFEEV
              190       200       210       220       230       240

           
pF1KE3 WGVI
       ::::
NP_006 WGVI
           

>>NP_001306978 (OMIM: 211180,611531) ribosomal RNA small  (194 aa)
 initn: 1056 init1: 1056 opt: 1056  Z-score: 1310.9  bits: 249.7 E(85289): 2.8e-66
Smith-Waterman score: 1171; 79.5% identity (79.5% similar) in 244 aa overlap (1-244:1-194)

               10        20        30        40        50        60
pF1KE3 MAAPSDGFKPRERSGGEQAQDWDALPPKRPRLGAGNKIGGRRLIVVLEGASLETVKVGKT
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 MAAPSDGFKPRERSGGEQAQDWDALPPKRPRLGAGNKIGGRRLIVVLEGASLETVKVGKT
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KE3 YELLNCDKHKSILLKNGRDPGEARPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNVLIEV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 YELLNCDKHKSILLKNGRDPGEARPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNVLIEV
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KE3 NPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPQKLLKVIKNPVSDHFPVGCMKVGTSFSI
       ::::::::::::::::::::::::::::::::::::::                      
NP_001 NPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPQKLLKV----------------------
              130       140       150                              

              190       200       210       220       230       240
pF1KE3 PVVSDVRELVPSSDPIVFVVGAFAHGKVSVEYTEKMVSISNYPLSAALTCAKLTTAFEEV
                                   ::::::::::::::::::::::::::::::::
NP_001 ----------------------------SVEYTEKMVSISNYPLSAALTCAKLTTAFEEV
                                  160       170       180       190

           
pF1KE3 WGVI
       ::::
NP_001 WGVI
           




244 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Mon Nov  7 14:41:49 2016 done: Mon Nov  7 14:41:50 2016
 Total Scan time:  6.270 Total Display time: -0.030

Function used was FASTA [36.3.4 Apr, 2011]