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: pF1KB7541, 178 aa
  1>>>pF1KB7541 178 - 178 aa - 178 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 5.1750+/-0.000263; mu= 15.2903+/- 0.017
 mean_var=75.4663+/-14.892, 0's: 0 Z-trim(120.9): 4  B-trim: 0 in 0/54
 Lambda= 0.147638
 statistics sampled from 36651 (36655) to 36651 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.785), E-opt: 0.2 (0.43), width:  16
 Scan time:  6.200

The best scores are:                                      opt bits E(85289)
NP_542382 (OMIM: 610237) mediator of RNA polymeras ( 178) 1191 261.7 4.4e-70
XP_011515662 (OMIM: 610237) PREDICTED: mediator of ( 157)  992 219.3 2.3e-57
NP_001269915 (OMIM: 610237) mediator of RNA polyme ( 143)  762 170.3 1.2e-42


>>NP_542382 (OMIM: 610237) mediator of RNA polymerase II  (178 aa)
 initn: 1191 init1: 1191 opt: 1191  Z-score: 1379.1  bits: 261.7 E(85289): 4.4e-70
Smith-Waterman score: 1191; 100.0% identity (100.0% similar) in 178 aa overlap (1-178:1-178)

               10        20        30        40        50        60
pF1KB7 MSTPPLAASGMAPGPFAGPQAQQAAREVNTASLCRIGQETVQDIVYRTMEIFQLLRNMQL
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_542 MSTPPLAASGMAPGPFAGPQAQQAAREVNTASLCRIGQETVQDIVYRTMEIFQLLRNMQL
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB7 PNGVTYHTGTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVEE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_542 PNGVTYHTGTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVEE
               70        80        90       100       110       120

              130       140       150       160       170        
pF1KB7 DGSKNDDRAGPPRFASEERREIAEVNKKLKQKNQQLKQIMDQLRNLIWDINAMLAMRN
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_542 DGSKNDDRAGPPRFASEERREIAEVNKKLKQKNQQLKQIMDQLRNLIWDINAMLAMRN
              130       140       150       160       170        

>>XP_011515662 (OMIM: 610237) PREDICTED: mediator of RNA  (157 aa)
 initn: 1006 init1: 992 opt: 992  Z-score: 1150.8  bits: 219.3 E(85289): 2.3e-57
Smith-Waterman score: 992; 99.3% identity (99.3% similar) in 149 aa overlap (1-149:1-149)

               10        20        30        40        50        60
pF1KB7 MSTPPLAASGMAPGPFAGPQAQQAAREVNTASLCRIGQETVQDIVYRTMEIFQLLRNMQL
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 MSTPPLAASGMAPGPFAGPQAQQAAREVNTASLCRIGQETVQDIVYRTMEIFQLLRNMQL
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB7 PNGVTYHTGTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVEE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_011 PNGVTYHTGTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVEE
               70        80        90       100       110       120

              130       140       150       160       170        
pF1KB7 DGSKNDDRAGPPRFASEERREIAEVNKKLKQKNQQLKQIMDQLRNLIWDINAMLAMRN
       ::::::::::::::::::::::::::: :                             
XP_011 DGSKNDDRAGPPRFASEERREIAEVNKALSSVPEFLP                     
              130       140       150                            

>>NP_001269915 (OMIM: 610237) mediator of RNA polymerase  (143 aa)
 initn: 794 init1: 762 opt: 762  Z-score: 886.6  bits: 170.3 E(85289): 1.2e-42
Smith-Waterman score: 878; 80.3% identity (80.3% similar) in 178 aa overlap (1-178:1-143)

               10        20        30        40        50        60
pF1KB7 MSTPPLAASGMAPGPFAGPQAQQAAREVNTASLCRIGQETVQDIVYRTMEIFQLLRNMQL
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 MSTPPLAASGMAPGPFAGPQAQQAAREVNTASLCRIGQETVQDIVYRTMEIFQLLRNMQL
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB7 PNGVTYHTGTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVEQLIPYVEE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::        
NP_001 PNGVTYHTGTYQDRLTKLQDNLRQLSVLFRKLRLVYDKCNENCGGMDPIPVE--------
               70        80        90       100       110          

              130       140       150       160       170        
pF1KB7 DGSKNDDRAGPPRFASEERREIAEVNKKLKQKNQQLKQIMDQLRNLIWDINAMLAMRN
                                  :::::::::::::::::::::::::::::::
NP_001 ---------------------------KLKQKNQQLKQIMDQLRNLIWDINAMLAMRN
                                       120       130       140   




178 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Fri Nov  4 08:33:46 2016 done: Fri Nov  4 08:33:47 2016
 Total Scan time:  6.200 Total Display time: -0.040

Function used was FASTA [36.3.4 Apr, 2011]