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: pF1KB8192, 224 aa
  1>>>pF1KB8192 224 - 224 aa - 224 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 6.7603+/-0.000314; mu= 9.2128+/- 0.020
 mean_var=129.6299+/-25.711, 0's: 0 Z-trim(120.6): 4  B-trim: 714 in 2/53
 Lambda= 0.112648
 statistics sampled from 36031 (36035) to 36031 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.774), E-opt: 0.2 (0.423), width:  16
 Scan time:  5.840

The best scores are:                                      opt bits E(85289)
NP_001257558 (OMIM: 605718) mediator of RNA polyme ( 224) 1473 249.6   3e-66
XP_016876038 (OMIM: 605718) PREDICTED: mediator of ( 248) 1473 249.7 3.3e-66
NP_054885 (OMIM: 605718) mediator of RNA polymeras ( 270) 1473 249.7 3.5e-66


>>NP_001257558 (OMIM: 605718) mediator of RNA polymerase  (224 aa)
 initn: 1473 init1: 1473 opt: 1473  Z-score: 1310.2  bits: 249.6 E(85289): 3e-66
Smith-Waterman score: 1473; 100.0% identity (100.0% similar) in 224 aa overlap (1-224:1-224)

               10        20        30        40        50        60
pF1KB8 MLAISRNQKLLQAGEENQVLELLIHRDGEFQELMKLALNQGKIHHEMQVLEKEVEKRDSD
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 MLAISRNQKLLQAGEENQVLELLIHRDGEFQELMKLALNQGKIHHEMQVLEKEVEKRDSD
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB8 IQQLQKQLKEAEQILATAVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCAPLT
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 IQQLQKQLKEAEQILATAVYQAKEKLKSIEKARKGAISSEEIIKYAHRISASNAVCAPLT
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KB8 WVPGDPRRPYPTDLEMRSGLLGQMNNPSTNGVNGHLPGDALAAGRLPDVLAPQYPWQSND
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 WVPGDPRRPYPTDLEMRSGLLGQMNNPSTNGVNGHLPGDALAAGRLPDVLAPQYPWQSND
              130       140       150       160       170       180

              190       200       210       220    
pF1KB8 MSMNMLPPNHSSDFLLEPPGHNKENEDDVEIMSTDSSSSSSESD
       ::::::::::::::::::::::::::::::::::::::::::::
NP_001 MSMNMLPPNHSSDFLLEPPGHNKENEDDVEIMSTDSSSSSSESD
              190       200       210       220    

>>XP_016876038 (OMIM: 605718) PREDICTED: mediator of RNA  (248 aa)
 initn: 1473 init1: 1473 opt: 1473  Z-score: 1309.6  bits: 249.7 E(85289): 3.3e-66
Smith-Waterman score: 1473; 100.0% identity (100.0% similar) in 224 aa overlap (1-224:25-248)

                                       10        20        30      
pF1KB8                         MLAISRNQKLLQAGEENQVLELLIHRDGEFQELMKL
                               ::::::::::::::::::::::::::::::::::::
XP_016 MKLLWWCDWLPERSHVFTQRELIEMLAISRNQKLLQAGEENQVLELLIHRDGEFQELMKL
               10        20        30        40        50        60

         40        50        60        70        80        90      
pF1KB8 ALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARKGA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_016 ALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIEKARKGA
               70        80        90       100       110       120

        100       110       120       130       140       150      
pF1KB8 ISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDLEMRSGLLGQMNNPSTNGVNGHL
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_016 ISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDLEMRSGLLGQMNNPSTNGVNGHL
              130       140       150       160       170       180

        160       170       180       190       200       210      
pF1KB8 PGDALAAGRLPDVLAPQYPWQSNDMSMNMLPPNHSSDFLLEPPGHNKENEDDVEIMSTDS
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
XP_016 PGDALAAGRLPDVLAPQYPWQSNDMSMNMLPPNHSSDFLLEPPGHNKENEDDVEIMSTDS
              190       200       210       220       230       240

        220    
pF1KB8 SSSSSESD
       ::::::::
XP_016 SSSSSESD
               

>>NP_054885 (OMIM: 605718) mediator of RNA polymerase II  (270 aa)
 initn: 1473 init1: 1473 opt: 1473  Z-score: 1309.1  bits: 249.7 E(85289): 3.5e-66
Smith-Waterman score: 1473; 100.0% identity (100.0% similar) in 224 aa overlap (1-224:47-270)

                                             10        20        30
pF1KB8                               MLAISRNQKLLQAGEENQVLELLIHRDGEF
                                     ::::::::::::::::::::::::::::::
NP_054 GLGVAGGNSTRERLLSALEDLEVLSRELIEMLAISRNQKLLQAGEENQVLELLIHRDGEF
         20        30        40        50        60        70      

               40        50        60        70        80        90
pF1KB8 QELMKLALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_054 QELMKLALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLKSIE
         80        90       100       110       120       130      

              100       110       120       130       140       150
pF1KB8 KARKGAISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDLEMRSGLLGQMNNPSTN
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_054 KARKGAISSEEIIKYAHRISASNAVCAPLTWVPGDPRRPYPTDLEMRSGLLGQMNNPSTN
        140       150       160       170       180       190      

              160       170       180       190       200       210
pF1KB8 GVNGHLPGDALAAGRLPDVLAPQYPWQSNDMSMNMLPPNHSSDFLLEPPGHNKENEDDVE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_054 GVNGHLPGDALAAGRLPDVLAPQYPWQSNDMSMNMLPPNHSSDFLLEPPGHNKENEDDVE
        200       210       220       230       240       250      

              220    
pF1KB8 IMSTDSSSSSSESD
       ::::::::::::::
NP_054 IMSTDSSSSSSESD
        260       270




224 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Fri Nov  4 10:23:23 2016 done: Fri Nov  4 10:23:24 2016
 Total Scan time:  5.840 Total Display time: -0.030

Function used was FASTA [36.3.4 Apr, 2011]