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: pF1KB8202, 194 aa
  1>>>pF1KB8202 194 - 194 aa - 194 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 10.5626+/-0.000339; mu= -7.7452+/- 0.021
 mean_var=377.9548+/-78.670, 0's: 0 Z-trim(126.9): 2  B-trim: 1714 in 1/61
 Lambda= 0.065971
 statistics sampled from 53987 (53992) to 53987 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.867), E-opt: 0.2 (0.633), width:  16
 Scan time:  5.130

The best scores are:                                      opt bits E(85289)
NP_703151 (OMIM: 612385) mediator of RNA polymeras ( 211) 1388 144.3 1.3e-34
NP_001304007 (OMIM: 612385) mediator of RNA polyme ( 261) 1370 142.7 4.9e-34


>>NP_703151 (OMIM: 612385) mediator of RNA polymerase II  (211 aa)
 initn: 1388 init1: 1388 opt: 1388  Z-score: 742.4  bits: 144.3 E(85289): 1.3e-34
Smith-Waterman score: 1388; 100.0% identity (100.0% similar) in 194 aa overlap (1-194:18-211)

                                10        20        30        40   
pF1KB8                  MENFTALFGAQADPPPPPTALGFGPGKPPPPPPPPAGGGPGTA
                        :::::::::::::::::::::::::::::::::::::::::::
NP_703 MKITNGRHGDSAGAEGTMENFTALFGAQADPPPPPTALGFGPGKPPPPPPPPAGGGPGTA
               10        20        30        40        50        60

            50        60        70        80        90       100   
pF1KB8 PPPTAATAPPGADKSGAGCGPFYLMRELPGSTELTGSTNLITHYNLEQAYNKFCGKKVKE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_703 PPPTAATAPPGADKSGAGCGPFYLMRELPGSTELTGSTNLITHYNLEQAYNKFCGKKVKE
               70        80        90       100       110       120

           110       120       130       140       150       160   
pF1KB8 KLSNFLPDLPGMIDLPGSHDNSSLRSLIEKPPILSSSFNPITGTMLAGFRLHTGPLPEQC
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_703 KLSNFLPDLPGMIDLPGSHDNSSLRSLIEKPPILSSSFNPITGTMLAGFRLHTGPLPEQC
              130       140       150       160       170       180

           170       180       190    
pF1KB8 RLMHIQPPKKKNKHKHKQSRTQDPVPPGKPS
       :::::::::::::::::::::::::::::::
NP_703 RLMHIQPPKKKNKHKHKQSRTQDPVPPGKPS
              190       200       210 

>>NP_001304007 (OMIM: 612385) mediator of RNA polymerase  (261 aa)
 initn: 1370 init1: 1370 opt: 1370  Z-score: 732.0  bits: 142.7 E(85289): 4.9e-34
Smith-Waterman score: 1370; 99.0% identity (99.0% similar) in 194 aa overlap (1-194:18-211)

                                10        20        30        40   
pF1KB8                  MENFTALFGAQADPPPPPTALGFGPGKPPPPPPPPAGGGPGTA
                        :::::::::::::::::::::::::::::::::::::::::::
NP_001 MKITNGRHGDSAGAEGTMENFTALFGAQADPPPPPTALGFGPGKPPPPPPPPAGGGPGTA
               10        20        30        40        50        60

            50        60        70        80        90       100   
pF1KB8 PPPTAATAPPGADKSGAGCGPFYLMRELPGSTELTGSTNLITHYNLEQAYNKFCGKKVKE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 PPPTAATAPPGADKSGAGCGPFYLMRELPGSTELTGSTNLITHYNLEQAYNKFCGKKVKE
               70        80        90       100       110       120

           110       120       130       140       150       160   
pF1KB8 KLSNFLPDLPGMIDLPGSHDNSSLRSLIEKPPILSSSFNPITGTMLAGFRLHTGPLPEQC
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 KLSNFLPDLPGMIDLPGSHDNSSLRSLIEKPPILSSSFNPITGTMLAGFRLHTGPLPEQC
              130       140       150       160       170       180

           170       180       190                                 
pF1KB8 RLMHIQPPKKKNKHKHKQSRTQDPVPPGKPS                             
       :::::::::::::::::::::::::::  ::                             
NP_001 RLMHIQPPKKKNKHKHKQSRTQDPVPPETPSDSDHKKKKKKKEEDPERKRKKKEKKKKKN
              190       200       210       220       230       240

NP_001 RHSPDHPGMGSSQASSSSSLR
              250       260 




194 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Fri Nov  4 10:31:09 2016 done: Fri Nov  4 10:31:09 2016
 Total Scan time:  5.130 Total Display time: -0.030

Function used was FASTA [36.3.4 Apr, 2011]