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: pF1KE3585, 531 aa
  1>>>pF1KE3585 531 - 531 aa - 531 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 11.2828+/-0.000486; mu= -9.7229+/- 0.031
 mean_var=326.6729+/-64.486, 0's: 0 Z-trim(119.4): 39  B-trim: 214 in 2/52
 Lambda= 0.070961
 statistics sampled from 33430 (33470) to 33430 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.709), E-opt: 0.2 (0.392), width:  16
 Scan time: 11.710

The best scores are:                                      opt bits E(85289)
NP_061961 (OMIM: 610506) RNA polymerase II-associa ( 531) 3523 374.7 3.8e-103
NP_001243755 (OMIM: 610506) RNA polymerase II-asso ( 485) 2457 265.5 2.5e-70


>>NP_061961 (OMIM: 610506) RNA polymerase II-associated   (531 aa)
 initn: 3523 init1: 3523 opt: 3523  Z-score: 1972.7  bits: 374.7 E(85289): 3.8e-103
Smith-Waterman score: 3523; 100.0% identity (100.0% similar) in 531 aa overlap (1-531:1-531)

               10        20        30        40        50        60
pF1KE3 MAPTIQTQAQREDGHRPNSHRTLPERSGVVCRVKYCNSLPDIPFDPKFITYPFDQNRFVQ
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_061 MAPTIQTQAQREDGHRPNSHRTLPERSGVVCRVKYCNSLPDIPFDPKFITYPFDQNRFVQ
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KE3 YKATSLEKQHKHDLLTEPDLGVTIDLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKR
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_061 YKATSLEKQHKHDLLTEPDLGVTIDLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKR
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KE3 SQQHAKVVPWMRKTEYISTEFNRYGISNEKPEVKIGVSVKQQFTEEEIYKDRDSQITAIE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_061 SQQHAKVVPWMRKTEYISTEFNRYGISNEKPEVKIGVSVKQQFTEEEIYKDRDSQITAIE
              130       140       150       160       170       180

              190       200       210       220       230       240
pF1KE3 KTFEDAQKSISQHYSKPRVTPVEVMPVFPDFKMWINPCAQVIFDSDPAPKDTSGAAALEM
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_061 KTFEDAQKSISQHYSKPRVTPVEVMPVFPDFKMWINPCAQVIFDSDPAPKDTSGAAALEM
              190       200       210       220       230       240

              250       260       270       280       290       300
pF1KE3 MSQAMIRGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVK
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_061 MSQAMIRGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVK
              250       260       270       280       290       300

              310       320       330       340       350       360
pF1KE3 NKASKGYEENYFFIFREGDGVYYNELETRVRLSKRRAKAGVQSGTNALLVVKHRDMNEKE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_061 NKASKGYEENYFFIFREGDGVYYNELETRVRLSKRRAKAGVQSGTNALLVVKHRDMNEKE
              310       320       330       340       350       360

              370       380       390       400       410       420
pF1KE3 LEAQEARKAQLENHEPEEEEEEEMETEEKEAGGSDEEQEKGSSSEKEGSEDEHSGSESER
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_061 LEAQEARKAQLENHEPEEEEEEEMETEEKEAGGSDEEQEKGSSSEKEGSEDEHSGSESER
              370       380       390       400       410       420

              430       440       450       460       470       480
pF1KE3 EEGDRDEASDKSGSGEDESSEDEARAARDKEEIFGSDADSEDDADSDDEDRGQAQGGSDN
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_061 EEGDRDEASDKSGSGEDESSEDEARAARDKEEIFGSDADSEDDADSDDEDRGQAQGGSDN
              430       440       450       460       470       480

              490       500       510       520       530 
pF1KE3 DSDSGSNGGGQRSRSHSRSASPFPSGSEHSAQEDGSEAAASDSSEADSDSD
       :::::::::::::::::::::::::::::::::::::::::::::::::::
NP_061 DSDSGSNGGGQRSRSHSRSASPFPSGSEHSAQEDGSEAAASDSSEADSDSD
              490       500       510       520       530 

>>NP_001243755 (OMIM: 610506) RNA polymerase II-associat  (485 aa)
 initn: 2455 init1: 2455 opt: 2457  Z-score: 1383.5  bits: 265.5 E(85289): 2.5e-70
Smith-Waterman score: 2527; 97.5% identity (97.5% similar) in 394 aa overlap (1-394:1-384)

               10        20        30        40        50        60
pF1KE3 MAPTIQTQAQREDGHRPNSHRTLPERSGVVCRVKYCNSLPDIPFDPKFITYPFDQNRFVQ
       ::::::::::::::::          ::::::::::::::::::::::::::::::::::
NP_001 MAPTIQTQAQREDGHR----------SGVVCRVKYCNSLPDIPFDPKFITYPFDQNRFVQ
               10                  20        30        40        50

               70        80        90       100       110       120
pF1KE3 YKATSLEKQHKHDLLTEPDLGVTIDLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKR
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 YKATSLEKQHKHDLLTEPDLGVTIDLINPDTYRIDPNVLLDPADEKLLEEEIQAPTSSKR
               60        70        80        90       100       110

              130       140       150       160       170       180
pF1KE3 SQQHAKVVPWMRKTEYISTEFNRYGISNEKPEVKIGVSVKQQFTEEEIYKDRDSQITAIE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 SQQHAKVVPWMRKTEYISTEFNRYGISNEKPEVKIGVSVKQQFTEEEIYKDRDSQITAIE
              120       130       140       150       160       170

              190       200       210       220       230       240
pF1KE3 KTFEDAQKSISQHYSKPRVTPVEVMPVFPDFKMWINPCAQVIFDSDPAPKDTSGAAALEM
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 KTFEDAQKSISQHYSKPRVTPVEVMPVFPDFKMWINPCAQVIFDSDPAPKDTSGAAALEM
              180       190       200       210       220       230

              250       260       270       280       290       300
pF1KE3 MSQAMIRGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVK
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 MSQAMIRGMMDEEGNQFVAYFLPVEETLKKRKRDQEEEMDYAPDDVYDYKIAREYNWNVK
              240       250       260       270       280       290

              310       320       330       340       350       360
pF1KE3 NKASKGYEENYFFIFREGDGVYYNELETRVRLSKRRAKAGVQSGTNALLVVKHRDMNEKE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 NKASKGYEENYFFIFREGDGVYYNELETRVRLSKRRAKAGVQSGTNALLVVKHRDMNEKE
              300       310       320       330       340       350

              370       380       390       400       410       420
pF1KE3 LEAQEARKAQLENHEPEEEEEEEMETEEKEAGGSDEEQEKGSSSEKEGSEDEHSGSESER
       ::::::::::::::::::::::::::::::::::                          
NP_001 LEAQEARKAQLENHEPEEEEEEEMETEEKEAGGSVMLILRTMPTLMMRTEDRPKVAVTMI
              360       370       380       390       400       410

              430       440       450       460       470       480
pF1KE3 EEGDRDEASDKSGSGEDESSEDEARAARDKEEIFGSDADSEDDADSDDEDRGQAQGGSDN
                                                                   
NP_001 QTAAAMGVASGAGATAAAPVPSPVAASTRPRRMAVKLQLLIPVKLIVTVTESQGIQGWFR
              420       430       440       450       460       470




531 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Sun Nov  6 06:07:30 2016 done: Sun Nov  6 06:07:31 2016
 Total Scan time: 11.710 Total Display time: -0.010

Function used was FASTA [36.3.4 Apr, 2011]