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= 020974
(319 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd
Finger Protein 3
Length = 120
Score = 64.3 bits (155), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 36/109 (33%), Positives = 59/109 (54%), Gaps = 13/109 (11%)
Query: 136 SFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKFK 195
S ++I+ ++L D+ KV +E A KV A +E ++ + ++ YK K
Sbjct: 19 SLKDILMKRLTDSNLKVPEEKAAKV-------------ATKIEKELFSFFRDTDAKYKNK 65
Query: 196 YRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHH 244
YR L+FN+ DP+N +KVL G V P+ +I MS +E+AS ++ W
Sbjct: 66 YRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAWRRR 114
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
Length = 173
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 47/174 (27%), Positives = 76/174 (43%), Gaps = 18/174 (10%)
Query: 137 FREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYE-KWCRSN-GMYKF 194
R+ V + LYD L+K S+ + + A +ES M + C +N YK
Sbjct: 12 LRDQVLKALYDVLAKESEHPPQSI----------LHTAKAIESEMNKVNNCDTNEAAYKA 61
Query: 195 KYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTG 254
+YR + N+ N D + K+ G + PE + AK++A ++ + K L
Sbjct: 62 RYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQN-LYNA 120
Query: 255 HIFPVGLSRKIIVSDIYECGRCGHNKIS-YQHSSILDDYNLTRHVTCLNCNQYW 307
G + + V+D + CG+C K+S YQ + D+ LT TC C W
Sbjct: 121 Q----GATIERSVTDRFTCGKCKEKKVSYYQLQTRSADHPLTTFCTCEACGNRW 170
>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|S Chain S, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
Length = 179
Score = 57.8 bits (138), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 47/174 (27%), Positives = 75/174 (43%), Gaps = 18/174 (10%)
Query: 137 FREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYE-KWCRSN-GMYKF 194
R+ V + LYD L+K S+ + + A +ES M + C +N YK
Sbjct: 18 LRDQVLKALYDVLAKESEHPPQSI----------LHTAKAIESEMNKVNNCDTNEAAYKA 67
Query: 195 KYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTG 254
+YR + N+ N D + K+ G + PE + AK++A ++ + K L
Sbjct: 68 RYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQN-LYNA 126
Query: 255 HIFPVGLSRKIIVSDIYECGRCGHNKIS-YQHSSILDDYNLTRHVTCLNCNQYW 307
G + + V+D + CG+C K+S YQ + D LT TC C W
Sbjct: 127 Q----GATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRW 176
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
Length = 309
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 47/174 (27%), Positives = 75/174 (43%), Gaps = 18/174 (10%)
Query: 137 FREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYE-KWCRSN-GMYKF 194
R+ V + LYD L+K S+ + + A +ES M + C +N YK
Sbjct: 148 LRDQVLKALYDVLAKESEHPPQSI----------LHTAKAIESEMNKVNNCDTNEAAYKA 197
Query: 195 KYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTG 254
+YR + N+ N D + K+ G + PE + AK++A ++ + K L
Sbjct: 198 RYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQN-LYNA 256
Query: 255 HIFPVGLSRKIIVSDIYECGRCGHNKIS-YQHSSILDDYNLTRHVTCLNCNQYW 307
G + + V+D + CG+C K+S YQ + D LT TC C W
Sbjct: 257 Q----GATIERSVTDRFTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRW 306
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
Length = 178
Score = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 46/174 (26%), Positives = 74/174 (42%), Gaps = 18/174 (10%)
Query: 137 FREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYE-KWCRSN-GMYKF 194
R+ V + LYD L+K S+ + + A +ES M + C +N YK
Sbjct: 17 LRDQVLKALYDVLAKESEHPPQSI----------LHTAKAIESEMNKVNNCDTNEAAYKA 66
Query: 195 KYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTG 254
+YR + N+ N D + K+ G + PE + AK++A ++ + K L
Sbjct: 67 RYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQN-LYNA 125
Query: 255 HIFPVGLSRKIIVSDIYECGRCGHNKIS-YQHSSILDDYNLTRHVTCLNCNQYW 307
G + + V+D + CG+C K+S YQ + LT TC C W
Sbjct: 126 Q----GATIERSVTDRFTCGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRW 175
>pdb|2LW4|A Chain A, Solution Nmr Structure Of Human Transcription Elongation
Factor A Protein 2, Central Domain, Northeast Structural
Genomics Consortium (Nesg) Target Hr8682b
Length = 113
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 52/105 (49%), Gaps = 8/105 (7%)
Query: 135 DSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCRSNGMYKF 194
D+ R RE L AL D A D +++ +E ++ ++ YK
Sbjct: 10 DAVRNKCREMLTAALQTDHDHVA--------IGADCERLSAQIEECIFRDVGNTDMKYKN 61
Query: 195 KYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDKIQ 239
+ R + N+ D +N D RR VL G + P+ I M+++EMASD+++
Sbjct: 62 RVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDELK 106
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii
Length = 108
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 35/116 (30%), Positives = 58/116 (50%), Gaps = 16/116 (13%)
Query: 122 VPKKSISCMIKCNDSFREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAM 181
P S S +KC RE L AL + D D + I D ++ +E A+
Sbjct: 9 APSTSDSVRLKC--------REMLAAAL-RTGD---DYIAI----GADEEELGSQIEEAI 52
Query: 182 YEKWCRSNGMYKFKYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMASDK 237
Y++ ++ YK + R + N+ D +N + R+ VL G++ P+ M+A+EMASD+
Sbjct: 53 YQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDE 108
>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii
Length = 114
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 46/100 (46%), Gaps = 12/100 (12%)
Query: 137 FREIVREKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYE-KWCRSN-GMYKF 194
R+ V + LYD L+K S+ + + A +ES M + C +N YK
Sbjct: 22 LRDQVLKALYDVLAKESEHPPQSI----------LHTAKAIESEMNKVNNCDTNEAAYKA 71
Query: 195 KYRCLLFNISDPENQDFRRKVLLGHVKPETIINMSAKEMA 234
+YR + N+ N D + K+ G + PE + AK++A
Sbjct: 72 RYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111
>pdb|2WZN|A Chain A, 3d Structure Of Tet3 From Pyrococcus Horikoshii
Length = 354
Score = 28.9 bits (63), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 216 LLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVG 260
++ H K + M A M DKI + +H+DKDG L HI P+G
Sbjct: 55 VIAHFKGSSPRIMVAAHM--DKIGVMVNHIDKDGYL---HIVPIG 94
>pdb|2PE3|A Chain A, Crystal Structure Of Frv Operon Protein Frvx (Ph1821)from
Pyrococcus Horikoshii Ot3
pdb|2PE3|B Chain B, Crystal Structure Of Frv Operon Protein Frvx (Ph1821)from
Pyrococcus Horikoshii Ot3
pdb|2PE3|C Chain C, Crystal Structure Of Frv Operon Protein Frvx (Ph1821)from
Pyrococcus Horikoshii Ot3
pdb|2PE3|D Chain D, Crystal Structure Of Frv Operon Protein Frvx (Ph1821)from
Pyrococcus Horikoshii Ot3
Length = 354
Score = 28.9 bits (63), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 25/45 (55%), Gaps = 5/45 (11%)
Query: 216 LLGHVKPETIINMSAKEMASDKIQLWNHHLDKDGALVTGHIFPVG 260
++ H K + M A M DKI + +H+DKDG L HI P+G
Sbjct: 55 VIAHFKGSSPRIMVAAHM--DKIGVMVNHIDKDGYL---HIVPIG 94
>pdb|1GE8|A Chain A, Proliferating Cell Nuclear Antigen (Pcna) Homolog From
Pyrococcus Furiosus
pdb|1ISQ|A Chain A, Pyrococcus Furiosus Pcna Complexed With Rfcl Pip-Box
Peptide
Length = 249
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 5/47 (10%)
Query: 144 KLYDALSKVSDEAADKVTIDLV--KACDPIQVAIL---VESAMYEKW 185
+L D SK+ DEAA KVT D + +A DP +V ++ + S+++ K+
Sbjct: 15 QLIDTASKLIDEAAFKVTEDGISMRAMDPSRVVLIDLNLPSSIFSKY 61
>pdb|1IZ4|A Chain A, Pyrococcus Furiosus Pcna Mutant (Met73leuASP143ALA):
Tetragonal Form
Length = 249
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 5/47 (10%)
Query: 144 KLYDALSKVSDEAADKVTIDLV--KACDPIQVAIL---VESAMYEKW 185
+L D SK+ DEAA KVT D + +A DP +V ++ + S+++ K+
Sbjct: 15 QLIDTASKLIDEAAFKVTEDGISMRAMDPSRVVLIDLNLPSSIFSKY 61
>pdb|1IZ5|A Chain A, Pyrococcus Furiosus Pcna Mutant (Met73leu, Asp143ala,
Asp147ala): Orthorhombic Form
pdb|1IZ5|B Chain B, Pyrococcus Furiosus Pcna Mutant (Met73leu, Asp143ala,
Asp147ala): Orthorhombic Form
Length = 249
Score = 28.5 bits (62), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 5/47 (10%)
Query: 144 KLYDALSKVSDEAADKVTIDLV--KACDPIQVAIL---VESAMYEKW 185
+L D SK+ DEAA KVT D + +A DP +V ++ + S+++ K+
Sbjct: 15 QLIDTASKLIDEAAFKVTEDGISMRAMDPSRVVLIDLNLPSSIFSKY 61
>pdb|3A2F|B Chain B, Crystal Structure Of Pyrococcus Furiosus Dna
PolymerasePCNA Monomer Mutant Complex
Length = 248
Score = 28.1 bits (61), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 30/47 (63%), Gaps = 5/47 (10%)
Query: 144 KLYDALSKVSDEAADKVTIDLV--KACDPIQVAIL---VESAMYEKW 185
+L D SK+ DEAA KVT D + +A DP +V ++ + S+++ K+
Sbjct: 14 QLIDTASKLIDEAAFKVTEDGISXRAXDPSRVVLIDLNLPSSIFSKY 60
>pdb|1MG7|A Chain A, Crystal Structure Of Xol-1
pdb|1MG7|B Chain B, Crystal Structure Of Xol-1
Length = 417
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 27/105 (25%), Positives = 43/105 (40%), Gaps = 13/105 (12%)
Query: 83 CWDVEDVEYVAVTKKAKLVENVKVEEVTNGEERRHDSGNVPKKSISCMIKCNDSFREIVR 142
C +VE VA+ K E V+ EV G I +K + F + +
Sbjct: 272 CLEVEFDSQVALEKLMNEHEQVEGFEVQQG-------------GILVALKKDSFFDDELI 318
Query: 143 EKLYDALSKVSDEAADKVTIDLVKACDPIQVAILVESAMYEKWCR 187
EK+ A++ S ++ V+ DL+K + L S +E CR
Sbjct: 319 EKIAIAIATESRQSVSSVSFDLLKLGPGASLVTLANSRRFEPECR 363
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.320 0.135 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,106,801
Number of Sequences: 62578
Number of extensions: 347716
Number of successful extensions: 858
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 844
Number of HSP's gapped (non-prelim): 22
length of query: 319
length of database: 14,973,337
effective HSP length: 99
effective length of query: 220
effective length of database: 8,778,115
effective search space: 1931185300
effective search space used: 1931185300
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)