BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 042488
         (78 letters)

Database: swissprot 
           539,616 sequences; 191,569,459 total letters

Searching..................................................done



>sp|Q9D7M8|RPB4_MOUSE DNA-directed RNA polymerase II subunit RPB4 OS=Mus musculus
           GN=Polr2d PE=2 SV=2
          Length = 142

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 3/65 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           I  V  +L + +L +FEL  L NLCPET EE+ A++PS++ R    +DE ++++L+D+  
Sbjct: 80  IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FEDEELQQILDDIQT 136

Query: 74  IKKFE 78
            + F+
Sbjct: 137 KRSFQ 141


>sp|O15514|RPB4_HUMAN DNA-directed RNA polymerase II subunit RPB4 OS=Homo sapiens
           GN=POLR2D PE=1 SV=1
          Length = 142

 Score = 52.0 bits (123), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 3/65 (4%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           I  V  +L + +L +FEL  L NLCPET EE+ A++PS++ R    +DE ++++L+D+  
Sbjct: 80  IASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGR---FEDEELQQILDDIQT 136

Query: 74  IKKFE 78
            + F+
Sbjct: 137 KRSFQ 141


>sp|Q54S04|RPB4_DICDI DNA-directed RNA polymerase II subunit rpb4 OS=Dictyostelium
           discoideum GN=polr2d PE=3 SV=1
          Length = 155

 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 42/64 (65%), Gaps = 4/64 (6%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLSL 73
           I  V   LS+  L EFE+  L NLCPE  +EA +++PS+K   +  DDE ++ +L++LS 
Sbjct: 95  IKQVRTALSKQNLEEFEIASLANLCPEISDEAKSLIPSLK---KMEDDE-LQAILDELSN 150

Query: 74  IKKF 77
           ++KF
Sbjct: 151 LRKF 154


>sp|Q9VEA5|RPB4_DROME DNA-directed RNA polymerase II 16 kDa polypeptide OS=Drosophila
           melanogaster GN=Rpb4 PE=2 SV=5
          Length = 139

 Score = 47.8 bits (112), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 37/52 (71%), Gaps = 3/52 (5%)

Query: 20  ILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDL 71
           +L + +L +FEL  LGNLCPE  EEA A++PS++ R    +DE + ++L+D+
Sbjct: 83  LLMQKKLHKFELAALGNLCPEAPEEAKALIPSLEGR---FEDEELRQILDDI 131


>sp|O74825|RPB4_SCHPO DNA-directed RNA polymerase II subunit rpb4 OS=Schizosaccharomyces
           pombe (strain 972 / ATCC 24843) GN=rpb4 PE=1 SV=1
          Length = 135

 Score = 40.0 bits (92), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 27/94 (28%), Positives = 46/94 (48%), Gaps = 25/94 (26%)

Query: 7   ENAAELKIGDV-------FRILSRYQLAE---------------FELCVLGNLCPETVEE 44
           E   E+ + DV       F + +R++ AE               FE   LG LC E  EE
Sbjct: 44  ETNGEIPMTDVMKKTVAYFNVFARFKTAEATYACERILGNRFHKFERAQLGTLCCEDAEE 103

Query: 45  AIAMVPSIKTRGRAHDDEAIEKMLNDLSLIKKFE 78
           A  ++PS+  +    DD+ ++ +L++LS ++KF+
Sbjct: 104 ARTLIPSLANK---IDDQNLQGILDELSTLRKFQ 134


>sp|P20433|RPB4_YEAST DNA-directed RNA polymerase II subunit RPB4 OS=Saccharomyces
           cerevisiae (strain ATCC 204508 / S288c) GN=RPB4 PE=1
           SV=1
          Length = 221

 Score = 37.4 bits (85), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 3/59 (5%)

Query: 14  IGDVFRILSRYQLAEFELCVLGNLCPETVEEAIAMVPSIKTRGRAHDDEAIEKMLNDLS 72
           +G V ++L    L  FE+  LG+L  +T +EA  ++PS+    +  DDE +E++L +LS
Sbjct: 160 VGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLN--NKISDDE-LERILKELS 215


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.316    0.135    0.367 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 26,809,971
Number of Sequences: 539616
Number of extensions: 843999
Number of successful extensions: 2222
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 2213
Number of HSP's gapped (non-prelim): 9
length of query: 78
length of database: 191,569,459
effective HSP length: 49
effective length of query: 29
effective length of database: 165,128,275
effective search space: 4788719975
effective search space used: 4788719975
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)