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: pF1KE0906, 212 aa
  1>>>pF1KE0906 212 - 212 aa - 212 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 6.6424+/-0.000308; mu= 10.2297+/- 0.019
 mean_var=141.5900+/-28.668, 0's: 0 Z-trim(121.4): 3  B-trim: 1044 in 1/57
 Lambda= 0.107785
 statistics sampled from 38064 (38067) to 38064 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.782), E-opt: 0.2 (0.446), width:  16
 Scan time:  6.910

The best scores are:                                      opt bits E(85289)
NP_443109 (OMIM: 607956) mediator of RNA polymeras ( 301) 1412 230.0 3.1e-60
NP_001001653 (OMIM: 607956) mediator of RNA polyme ( 179) 1186 194.7   8e-50
NP_963836 (OMIM: 607956) mediator of RNA polymeras ( 268) 1186 194.8 1.1e-49


>>NP_443109 (OMIM: 607956) mediator of RNA polymerase II  (301 aa)
 initn: 1412 init1: 1412 opt: 1412  Z-score: 1202.5  bits: 230.0 E(85289): 3.1e-60
Smith-Waterman score: 1412; 100.0% identity (100.0% similar) in 212 aa overlap (1-212:90-301)

                                             10        20        30
pF1KE0                               MRQTEGRVPVFSHEVVPDHLRTKPDPEVEE
                                     ::::::::::::::::::::::::::::::
NP_443 NKVLKHEKTPLFRNQVIIPLVLSPDRDEDLMRQTEGRVPVFSHEVVPDHLRTKPDPEVEE
      60        70        80        90       100       110         

               40        50        60        70        80        90
pF1KE0 QEKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKISKEERESESGGLRPNKQTFNPTDTN
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_443 QEKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKISKEERESESGGLRPNKQTFNPTDTN
     120       130       140       150       160       170         

              100       110       120       130       140       150
pF1KE0 ALVAAVAFGKGLSNWRPSGSSGPGQAGQPGAGTILAGTSGLQQVQMAGAPSQQQPMLSGV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_443 ALVAAVAFGKGLSNWRPSGSSGPGQAGQPGAGTILAGTSGLQQVQMAGAPSQQQPMLSGV
     180       190       200       210       220       230         

              160       170       180       190       200       210
pF1KE0 QMAQAGQPGKMPSGIKTNIKSASMHPYQRPSCLGFILAIPLRRKVKKLLGQEGKKNAHLQ
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_443 QMAQAGQPGKMPSGIKTNIKSASMHPYQRPSCLGFILAIPLRRKVKKLLGQEGKKNAHLQ
     240       250       260       270       280       290         

         
pF1KE0 LW
       ::
NP_443 LW
     300 

>>NP_001001653 (OMIM: 607956) mediator of RNA polymerase  (179 aa)
 initn: 1186 init1: 1186 opt: 1186  Z-score: 1015.4  bits: 194.7 E(85289): 8e-50
Smith-Waterman score: 1186; 100.0% identity (100.0% similar) in 179 aa overlap (1-179:1-179)

               10        20        30        40        50        60
pF1KE0 MRQTEGRVPVFSHEVVPDHLRTKPDPEVEEQEKQLTTDAARIGADAAQKQIQSLNKMCSN
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 MRQTEGRVPVFSHEVVPDHLRTKPDPEVEEQEKQLTTDAARIGADAAQKQIQSLNKMCSN
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KE0 LLEKISKEERESESGGLRPNKQTFNPTDTNALVAAVAFGKGLSNWRPSGSSGPGQAGQPG
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 LLEKISKEERESESGGLRPNKQTFNPTDTNALVAAVAFGKGLSNWRPSGSSGPGQAGQPG
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KE0 AGTILAGTSGLQQVQMAGAPSQQQPMLSGVQMAQAGQPGKMPSGIKTNIKSASMHPYQRP
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 
NP_001 AGTILAGTSGLQQVQMAGAPSQQQPMLSGVQMAQAGQPGKMPSGIKTNIKSASMHPYQR 
              130       140       150       160       170          

              190       200       210  
pF1KE0 SCLGFILAIPLRRKVKKLLGQEGKKNAHLQLW

>>NP_963836 (OMIM: 607956) mediator of RNA polymerase II  (268 aa)
 initn: 1186 init1: 1186 opt: 1186  Z-score: 1013.2  bits: 194.8 E(85289): 1.1e-49
Smith-Waterman score: 1186; 100.0% identity (100.0% similar) in 179 aa overlap (1-179:90-268)

                                             10        20        30
pF1KE0                               MRQTEGRVPVFSHEVVPDHLRTKPDPEVEE
                                     ::::::::::::::::::::::::::::::
NP_963 NKVLKHEKTPLFRNQVIIPLVLSPDRDEDLMRQTEGRVPVFSHEVVPDHLRTKPDPEVEE
      60        70        80        90       100       110         

               40        50        60        70        80        90
pF1KE0 QEKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKISKEERESESGGLRPNKQTFNPTDTN
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_963 QEKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKISKEERESESGGLRPNKQTFNPTDTN
     120       130       140       150       160       170         

              100       110       120       130       140       150
pF1KE0 ALVAAVAFGKGLSNWRPSGSSGPGQAGQPGAGTILAGTSGLQQVQMAGAPSQQQPMLSGV
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_963 ALVAAVAFGKGLSNWRPSGSSGPGQAGQPGAGTILAGTSGLQQVQMAGAPSQQQPMLSGV
     180       190       200       210       220       230         

              160       170       180       190       200       210
pF1KE0 QMAQAGQPGKMPSGIKTNIKSASMHPYQRPSCLGFILAIPLRRKVKKLLGQEGKKNAHLQ
       :::::::::::::::::::::::::::::                               
NP_963 QMAQAGQPGKMPSGIKTNIKSASMHPYQR                               
     240       250       260                                       




212 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Sat Nov  5 04:25:41 2016 done: Sat Nov  5 04:25:41 2016
 Total Scan time:  6.910 Total Display time: -0.020

Function used was FASTA [36.3.4 Apr, 2011]