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: pF1KB9588, 233 aa
  1>>>pF1KB9588 233 - 233 aa - 233 aa
Library: /omim/omim.rfq.tfa
  60827320 residues in 85289 sequences

Statistics:  Expectation_n fit: rho(ln(x))= 5.7264+/-0.000262; mu= 14.3757+/- 0.017
 mean_var=95.5277+/-19.340, 0's: 0 Z-trim(121.6): 3  B-trim: 0 in 0/57
 Lambda= 0.131223
 statistics sampled from 38367 (38372) to 38367 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.781), E-opt: 0.2 (0.45), width:  16
 Scan time:  5.980

The best scores are:                                      opt bits E(85289)
NP_004261 (OMIM: 605045) mediator of RNA polymeras ( 233) 1583 308.8 5.2e-84
NP_001094286 (OMIM: 605045) mediator of RNA polyme ( 233) 1583 308.8 5.2e-84


>>NP_004261 (OMIM: 605045) mediator of RNA polymerase II  (233 aa)
 initn: 1583 init1: 1583 opt: 1583  Z-score: 1629.2  bits: 308.8 E(85289): 5.2e-84
Smith-Waterman score: 1583; 99.6% identity (100.0% similar) in 233 aa overlap (1-233:1-233)

               10        20        30        40        50        60
pF1KB9 MGEPQQVSALPPPPMQYIKEYTDENIQEGLAPKPPPPIKDSYMMFGNQFQCDDLIIRPLE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_004 MGEPQQVSALPPPPMQYIKEYTDENIQEGLAPKPPPPIKDSYMMFGNQFQCDDLIIRPLE
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB9 SQGIERLHPMQFDHEKELRKLNMSILINFLDLLDILIRSPGSIKREEKLEDLKLLFVHVH
       ::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::
NP_004 SQGIERLHPMQFDHKKELRKLNMSILINFLDLLDILIRSPGSIKREEKLEDLKLLFVHVH
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KB9 HLINEYRPHQARETLRVMMEVQKRQRLETAERFQKHLERVIEMIQNCLASLPDDLPHSEA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_004 HLINEYRPHQARETLRVMMEVQKRQRLETAERFQKHLERVIEMIQNCLASLPDDLPHSEA
              130       140       150       160       170       180

              190       200       210       220       230   
pF1KB9 GMRVKTEPMDADDSNNCTGQNEHQRENSGHRRDQIIEKDAALCVLIDEMNERP
       :::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_004 GMRVKTEPMDADDSNNCTGQNEHQRENSGHRRDQIIEKDAALCVLIDEMNERP
              190       200       210       220       230   

>>NP_001094286 (OMIM: 605045) mediator of RNA polymerase  (233 aa)
 initn: 1583 init1: 1583 opt: 1583  Z-score: 1629.2  bits: 308.8 E(85289): 5.2e-84
Smith-Waterman score: 1583; 99.6% identity (100.0% similar) in 233 aa overlap (1-233:1-233)

               10        20        30        40        50        60
pF1KB9 MGEPQQVSALPPPPMQYIKEYTDENIQEGLAPKPPPPIKDSYMMFGNQFQCDDLIIRPLE
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 MGEPQQVSALPPPPMQYIKEYTDENIQEGLAPKPPPPIKDSYMMFGNQFQCDDLIIRPLE
               10        20        30        40        50        60

               70        80        90       100       110       120
pF1KB9 SQGIERLHPMQFDHEKELRKLNMSILINFLDLLDILIRSPGSIKREEKLEDLKLLFVHVH
       ::::::::::::::.:::::::::::::::::::::::::::::::::::::::::::::
NP_001 SQGIERLHPMQFDHKKELRKLNMSILINFLDLLDILIRSPGSIKREEKLEDLKLLFVHVH
               70        80        90       100       110       120

              130       140       150       160       170       180
pF1KB9 HLINEYRPHQARETLRVMMEVQKRQRLETAERFQKHLERVIEMIQNCLASLPDDLPHSEA
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 HLINEYRPHQARETLRVMMEVQKRQRLETAERFQKHLERVIEMIQNCLASLPDDLPHSEA
              130       140       150       160       170       180

              190       200       210       220       230   
pF1KB9 GMRVKTEPMDADDSNNCTGQNEHQRENSGHRRDQIIEKDAALCVLIDEMNERP
       :::::::::::::::::::::::::::::::::::::::::::::::::::::
NP_001 GMRVKTEPMDADDSNNCTGQNEHQRENSGHRRDQIIEKDAALCVLIDEMNERP
              190       200       210       220       230   




233 residues in 1 query   sequences
60827320 residues in 85289 library sequences
 Tcomplib [36.3.4 Apr, 2011] (8 proc)
 start: Fri Nov  4 17:32:27 2016 done: Fri Nov  4 17:32:28 2016
 Total Scan time:  5.980 Total Display time: -0.020

Function used was FASTA [36.3.4 Apr, 2011]