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: pF1KB6878, 200 aa
  1>>>pF1KB6878 200 - 200 aa - 200 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 6.1002+/-0.000286; mu= 11.2920+/- 0.018
 mean_var=90.6690+/-18.061, 0's: 0 Z-trim(119.5): 21  B-trim: 0 in 0/58
 Lambda= 0.134693
 statistics sampled from 33544 (33565) to 33544 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.754), E-opt: 0.2 (0.394), width:  16
 Scan time:  5.060

The best scores are:                                      opt bits E(85289)
NP_598395 (OMIM: 185641) mediator of RNA polymeras ( 200) 1291 259.9   2e-69
NP_852468 (OMIM: 185641) mediator of RNA polymeras ( 140)  859 175.8 2.8e-44


>>NP_598395 (OMIM: 185641) mediator of RNA polymerase II  (200 aa)
 initn: 1291 init1: 1291 opt: 1291  Z-score: 1367.3  bits: 259.9 E(85289): 2e-69
Smith-Waterman score: 1291; 100.0% identity (100.0% similar) in 200 aa overlap (1-200:1-200)

               10        20        30        40        50        60
pF1KB6 MAQQRALPQSKETLLQSYNKRLKDDIKSIMDNFTEIIKTAKIEDETQVSRATQGEQDNYE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_598 MAQQRALPQSKETLLQSYNKRLKDDIKSIMDNFTEIIKTAKIEDETQVSRATQGEQDNYE
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB6 MHVRAANIVRAGESLMKLVSDLKQFLILNDFPSVNEAIDQRNQQLRTLQEECDRKLITLR
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_598 MHVRAANIVRAGESLMKLVSDLKQFLILNDFPSVNEAIDQRNQQLRTLQEECDRKLITLR
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KB6 DEISIDLYELEEEYYSSSSSLCEANDLPLCEAYGRLDLDTDSADGLSAPLLASPEPSAGP
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_598 DEISIDLYELEEEYYSSSSSLCEANDLPLCEAYGRLDLDTDSADGLSAPLLASPEPSAGP
              130       140       150       160       170       180

              190       200
pF1KB6 LQVAAPAHSHAGGPGPTEHA
       ::::::::::::::::::::
NP_598 LQVAAPAHSHAGGPGPTEHA
              190       200

>>NP_852468 (OMIM: 185641) mediator of RNA polymerase II  (140 aa)
 initn: 859 init1: 859 opt: 859  Z-score: 915.9  bits: 175.8 E(85289): 2.8e-44
Smith-Waterman score: 859; 100.0% identity (100.0% similar) in 137 aa overlap (1-137:1-137)

               10        20        30        40        50        60
pF1KB6 MAQQRALPQSKETLLQSYNKRLKDDIKSIMDNFTEIIKTAKIEDETQVSRATQGEQDNYE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_852 MAQQRALPQSKETLLQSYNKRLKDDIKSIMDNFTEIIKTAKIEDETQVSRATQGEQDNYE
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB6 MHVRAANIVRAGESLMKLVSDLKQFLILNDFPSVNEAIDQRNQQLRTLQEECDRKLITLR
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_852 MHVRAANIVRAGESLMKLVSDLKQFLILNDFPSVNEAIDQRNQQLRTLQEECDRKLITLR
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KB6 DEISIDLYELEEEYYSSSSSLCEANDLPLCEAYGRLDLDTDSADGLSAPLLASPEPSAGP
       :::::::::::::::::                                           
NP_852 DEISIDLYELEEEYYSSRYK                                        
              130       140                                        




200 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Sat Nov  5 00:18:51 2016 done: Sat Nov  5 00:18:52 2016
 Total Scan time:  5.060 Total Display time: -0.020

Function used was FASTA [36.3.4 Apr, 2011]