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: pF1KB6991, 221 aa
  1>>>pF1KB6991 221 - 221 aa - 221 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 6.9863+/-0.000266; mu= 10.0859+/- 0.017
 mean_var=159.5038+/-31.650, 0's: 0 Z-trim(124.6): 2  B-trim: 156 in 1/58
 Lambda= 0.101552
 statistics sampled from 46559 (46561) to 46559 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.833), E-opt: 0.2 (0.546), width:  16
 Scan time:  6.720

The best scores are:                                      opt bits E(85289)
NP_060062 (OMIM: 612914) mediator of RNA polymeras ( 221) 1487 228.1 8.8e-60
NP_001304699 (OMIM: 612914) mediator of RNA polyme ( 217)  939 147.8 1.3e-35


>>NP_060062 (OMIM: 612914) mediator of RNA polymerase II  (221 aa)
 initn: 1487 init1: 1487 opt: 1487  Z-score: 1194.3  bits: 228.1 E(85289): 8.8e-60
Smith-Waterman score: 1487; 100.0% identity (100.0% similar) in 221 aa overlap (1-221:1-221)

               10        20        30        40        50        60
pF1KB6 MLKSNGERRSRNALPAVYARKMAASQQQASAASSAAGVSGPSSAGGPGPQQQPQPPAQLV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 MLKSNGERRSRNALPAVYARKMAASQQQASAASSAAGVSGPSSAGGPGPQQQPQPPAQLV
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB6 GPAQSGLLQQQQQDFDPVQRYKMLIPQLKESLQTLMKVAAQNLIQNTNIDNGQKSSDGPI
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 GPAQSGLLQQQQQDFDPVQRYKMLIPQLKESLQTLMKVAAQNLIQNTNIDNGQKSSDGPI
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KB6 QRFDKCLEEFYALCDQLELCLRLAHECLSQSCDSAKHSPTLVPTATKPDAVQPDSLPYPQ
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_060 QRFDKCLEEFYALCDQLELCLRLAHECLSQSCDSAKHSPTLVPTATKPDAVQPDSLPYPQ
              130       140       150       160       170       180

              190       200       210       220 
pF1KB6 YLAVIKAQISCAKDIHTALLDCANKVTGKTPAPPAGPGGTL
       :::::::::::::::::::::::::::::::::::::::::
NP_060 YLAVIKAQISCAKDIHTALLDCANKVTGKTPAPPAGPGGTL
              190       200       210       220 

>>NP_001304699 (OMIM: 612914) mediator of RNA polymerase  (217 aa)
 initn: 938 init1: 938 opt: 939  Z-score: 760.5  bits: 147.8 E(85289): 1.3e-35
Smith-Waterman score: 939; 83.3% identity (86.7% similar) in 180 aa overlap (1-179:1-175)

               10        20        30        40        50        60
pF1KB6 MLKSNGERRSRNALPAVYARKMAASQQQASAASSAAGVSGPSSAGGPGPQQQPQPPAQLV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 MLKSNGERRSRNALPAVYARKMAASQQQASAASSAAGVSGPSSAGGPGPQQQPQPPAQLV
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB6 GPAQSGLLQQQQQDFDPVQRYKMLIPQLKESLQTLMKVAAQNLIQNTNIDNGQKSSDGPI
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 GPAQSGLLQQQQQDFDPVQRYKMLIPQLKESLQTLMKVAAQNLIQNTNIDNGQKSSDGPI
               70        80        90       100       110       120

              130       140       150       160        170         
pF1KB6 QRFDKCLEEFYALCDQLELCLRLAHECLSQSCDSAKHSPTLVP-TATKPDAVQPDSLPYP
       :::::::::::::::::::::  .      .: :   :::     ..::    : ..  :
NP_001 QRFDKCLEEFYALCDQLELCLPPS----PTQC-SLTASPTHSTWRSSKPRFPVPRTFTPP
              130       140            150       160       170     

     180       190       200       210       220 
pF1KB6 QYLAVIKAQISCAKDIHTALLDCANKVTGKTPAPPAGPGGTL
                                                 
NP_001 CWTVPTRSRARHPHHLLALGALCEVGDREWGRQWLVGGVQRE
         180       190       200       210       




221 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Fri Nov  4 10:12:08 2016 done: Fri Nov  4 10:12:09 2016
 Total Scan time:  6.720 Total Display time: -0.010

Function used was FASTA [36.3.4 Apr, 2011]