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= 036389
(198 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 = 62.8 bits (151), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 39/112 (34%), Positives = 60/112 (53%), Gaps = 6/112 (5%)
Query: 21 DCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYK 80
D IR+ VR +L L K D N+ +V +VA +E ++ + + YK
Sbjct: 10 DQIRQSVRHSLKDILMK----RLTDSNL--KVPEEKAAKVATKIEKELFSFFRDTDAKYK 63
Query: 81 FKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENS 132
KYR L+FN DPKN+ KKVL G+V P+ ++ M+ +E+AS ++ W S
Sbjct: 64 NKYRSLMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKELAAWRRRS 115
>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 = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 53/106 (50%), Gaps = 9/106 (8%)
Query: 21 DCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYK 80
D +R R+ L AL + HD I + +++ +E ++ G + YK
Sbjct: 10 DAVRNKCREMLTAAL-----QTDHDHVAI----GADCERLSAQIEECIFRDVGNTDMKYK 60
Query: 81 FKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQ 126
+ R + N D KN + R+ VL G + P+ I MT++EMASD+++
Sbjct: 61 NRVRSRISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDELK 106
>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii
Length = 108
Score = 50.4 bits (119), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 38/66 (57%)
Query: 59 QVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAK 118
++ +E A+Y++ + YK + R + N D KN RK VL G++ P+ MTA+
Sbjct: 43 ELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKNPNLRKNVLCGNIPPDLFARMTAE 102
Query: 119 EMASDK 124
EMASD+
Sbjct: 103 EMASDE 108
>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
Length = 178
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 42/176 (23%), Positives = 70/176 (39%), Gaps = 29/176 (16%)
Query: 23 IREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYE--KWGRSSETYK 80
+R+ V K LY L+K E+ H I + A ++ES M + + YK
Sbjct: 17 LRDQVLKALYDVLAK---ESEHPPQSI--------LHTAKAIESEMNKVNNCDTNEAAYK 65
Query: 81 FKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKM-QLWYENSRKGRAET 139
+YR + N N + + K+ GD+ PE + AK++A + Q E +++
Sbjct: 66 ARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNA 125
Query: 140 NGRIFSGLVSPKNIVYGICKCSRCGHKRMSF---------IPLRRHITCLNCYQYW 186
G V+ + C +C K++S+ PL TC C W
Sbjct: 126 QGATIERSVTDRFT------CGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRW 175
>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 = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 42/176 (23%), Positives = 70/176 (39%), Gaps = 29/176 (16%)
Query: 23 IREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYE--KWGRSSETYK 80
+R+ V K LY L+K E+ H I + A ++ES M + + YK
Sbjct: 18 LRDQVLKALYDVLAK---ESEHPPQSI--------LHTAKAIESEMNKVNNCDTNEAAYK 66
Query: 81 FKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKM-QLWYENSRKGRAET 139
+YR + N N + + K+ GD+ PE + AK++A + Q E +++
Sbjct: 67 ARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNA 126
Query: 140 NGRIFSGLVSPKNIVYGICKCSRCGHKRMSFI---------PLRRHITCLNCYQYW 186
G V+ + C +C K++S+ PL TC C W
Sbjct: 127 QGATIERSVTDRFT------CGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRW 176
>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
Length = 173
Score = 40.4 bits (93), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 42/176 (23%), Positives = 70/176 (39%), Gaps = 29/176 (16%)
Query: 23 IREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYE--KWGRSSETYK 80
+R+ V K LY L+K E+ H I + A ++ES M + + YK
Sbjct: 12 LRDQVLKALYDVLAK---ESEHPPQSI--------LHTAKAIESEMNKVNNCDTNEAAYK 60
Query: 81 FKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKM-QLWYENSRKGRAET 139
+YR + N N + + K+ GD+ PE + AK++A + Q E +++
Sbjct: 61 ARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNA 120
Query: 140 NGRIFSGLVSPKNIVYGICKCSRCGHKRMSFI---------PLRRHITCLNCYQYW 186
G V+ + C +C K++S+ PL TC C W
Sbjct: 121 QGATIERSVTDRFT------CGKCKEKKVSYYQLQTRSADHPLTTFCTCEACGNRW 170
>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
Length = 309
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 42/176 (23%), Positives = 70/176 (39%), Gaps = 29/176 (16%)
Query: 23 IREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYE--KWGRSSETYK 80
+R+ V K LY L+K E+ H I + A ++ES M + + YK
Sbjct: 148 LRDQVLKALYDVLAK---ESEHPPQSI--------LHTAKAIESEMNKVNNCDTNEAAYK 196
Query: 81 FKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKM-QLWYENSRKGRAET 139
+YR + N N + + K+ GD+ PE + AK++A + Q E +++
Sbjct: 197 ARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNA 256
Query: 140 NGRIFSGLVSPKNIVYGICKCSRCGHKRMSFI---------PLRRHITCLNCYQYW 186
G V+ + C +C K++S+ PL TC C W
Sbjct: 257 QGATIERSVTDR------FTCGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRW 306
>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii
Length = 114
Score = 35.0 bits (79), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 28/101 (27%), Positives = 46/101 (45%), Gaps = 13/101 (12%)
Query: 23 IREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYE--KWGRSSETYK 80
+R+ V K LY L+K E+ H I + A ++ES M + + YK
Sbjct: 22 LRDQVLKALYDVLAK---ESEHPPQSI--------LHTAKAIESEMNKVNNCDTNEAAYK 70
Query: 81 FKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMA 121
+YR + N N + + K+ GD+ PE + AK++A
Sbjct: 71 ARYRIIYSNVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111
>pdb|3GF0|A Chain A, Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant
E145q From Methanocaldococcus Jannaschii In Complex With
Pyrophosphate And Magnesium
Length = 204
Score = 30.8 bits (68), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 6/63 (9%)
Query: 115 MTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFIPLR 174
+T + +A DK + Y+N R G+ IFS L+SP ++ Y K S+ +++ S +P
Sbjct: 142 ITLQIVAFDKPVILYKNQRIGQL-----IFSKLLSPADVGYSERKTSKYAYQK-SVMPSL 195
Query: 175 RHI 177
H+
Sbjct: 196 IHL 198
>pdb|1OGH|A Chain A, Structure Of The Bifunctional Dctp Deaminase-Dutpase From
Methanocaldococcus Jannaschii
pdb|1OGH|B Chain B, Structure Of The Bifunctional Dctp Deaminase-Dutpase From
Methanocaldococcus Jannaschii
pdb|1PKH|A Chain A, Structural Basis For Recognition And Catalysis By The
Bifunctional Dctp Deaminase And Dutpase From
Methanococcus Jannaschii
pdb|1PKH|B Chain B, Structural Basis For Recognition And Catalysis By The
Bifunctional Dctp Deaminase And Dutpase From
Methanococcus Jannaschii
pdb|1PKJ|A Chain A, Structural Basis For Recognition And Catalysis By The
Bifunctional Dctp Deaminase And Dutpase From
Methanococcus Jannaschii
pdb|1PKJ|B Chain B, Structural Basis For Recognition And Catalysis By The
Bifunctional Dctp Deaminase And Dutpase From
Methanococcus Jannaschii
pdb|1PKK|A Chain A, Structural Basis For Recognition And Catalysis By The
Bifunctional Dctp Deaminase And Dutpase From
Methanococcus Jannaschii
pdb|1PKK|B Chain B, Structural Basis For Recognition And Catalysis By The
Bifunctional Dctp Deaminase And Dutpase From
Methanococcus Jannaschii
pdb|2HXB|A Chain A, Dctp Deaminase-Dutpase From Methanocaldococcus Jannaschii
Length = 204
Score = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 6/63 (9%)
Query: 115 MTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFIPLR 174
+T + +A DK + Y+N R G+ IFS L+SP ++ Y K S+ +++ S +P
Sbjct: 142 ITLEIVAFDKPVILYKNQRIGQL-----IFSKLLSPADVGYSERKTSKYAYQK-SVMPSL 195
Query: 175 RHI 177
H+
Sbjct: 196 IHL 198
>pdb|2HXD|A Chain A, Bifunctional Dctp Deaminase-Dutpase Mutant Enzyme Variant
E145a From Methanocaldococcus Jannaschii In Complex With
Alpha,Beta-Imido Dutp And Magnesium
Length = 204
Score = 30.0 bits (66), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 115 MTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFIPLR 174
+T +A DK + Y+N R G+ IFS L+SP ++ Y K S+ +++ S +P
Sbjct: 142 ITLAIVAFDKPVILYKNQRIGQL-----IFSKLLSPADVGYSERKTSKYAYQK-SVMPSL 195
Query: 175 RHI 177
H+
Sbjct: 196 IHL 198
>pdb|2ODO|A Chain A, Crystal Structure Of Pseudomonas Fluorescens Alanine
Racemase
pdb|2ODO|B Chain B, Crystal Structure Of Pseudomonas Fluorescens Alanine
Racemase
pdb|2ODO|C Chain C, Crystal Structure Of Pseudomonas Fluorescens Alanine
Racemase
pdb|2ODO|D Chain D, Crystal Structure Of Pseudomonas Fluorescens Alanine
Racemase
Length = 357
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 1/45 (2%)
Query: 47 NVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFN 91
+ I+Q + PI V + ++S M+ + G YK Y+RL + N
Sbjct: 106 DAIEQARLAKPIHVWLXLDSGMH-RVGLHPNDYKAAYQRLQASAN 149
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
0.322 0.135 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,604,814
Number of Sequences: 62578
Number of extensions: 207605
Number of successful extensions: 489
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 478
Number of HSP's gapped (non-prelim): 17
length of query: 198
length of database: 14,973,337
effective HSP length: 94
effective length of query: 104
effective length of database: 9,091,005
effective search space: 945464520
effective search space used: 945464520
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)