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= 037764
(155 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2BGH|A Chain A, Crystal Structure Of Vinorine Synthase
pdb|2BGH|B Chain B, Crystal Structure Of Vinorine Synthase
Length = 421
Score = 90.1 bits (222), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 51/119 (42%), Positives = 72/119 (60%), Gaps = 2/119 (1%)
Query: 36 VQIISTEAIKPSSPTPKHLRTYKLSLPDQLCSKLYAPLVFFYSTNCKQQ-DLRKKSDLLK 94
++ +S E I PSSPTP+ L+ YK+S DQL + P + FY D + S LK
Sbjct: 5 MEKVSEELILPSSPTPQSLKCYKISHLDQLLLTCHIPFILFYPNPLDSNLDPAQTSQHLK 64
Query: 95 QSLAKSLTHYYPFAGRLIDSFSVDCNDHGAAFIDANVGCDISKFLQP-PDMELLQQLIP 152
QSL+K LTH+YP AGR+ + SVDCND G F++A V +S+ +Q ++E L Q +P
Sbjct: 65 QSLSKVLTHFYPLAGRINVNSSVDCNDSGVPFVEARVQAQLSQAIQNVVELEKLDQYLP 123
>pdb|4G22|A Chain A, Structure Of A Lys-Hct Mutant From Coffea Canephora
(Crystal Form 1)
pdb|4G22|B Chain B, Structure Of A Lys-Hct Mutant From Coffea Canephora
(Crystal Form 1)
Length = 439
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/122 (27%), Positives = 57/122 (46%), Gaps = 10/122 (8%)
Query: 36 VQIISTEAIKPSSPTPKHLRTYKLSLPDQLCSKLYAPLVFFYSTNCKQQDLRKKSDLLKQ 95
+++ + ++P+ TP R S D + + P V+FY K +LK
Sbjct: 8 IEVKESTMVRPAQETPG--RNLWNSNVDLVVPNFHTPSVYFYRPTGSSNFFDAK--VLKD 63
Query: 96 SLAKSLTHYYPFAGRLI----DSFSVDCNDHGAAFIDANVGCDISKFLQ-PPDMELLQQL 150
+L+++L +YP AGRL ++CN G F++A + F P +E L++L
Sbjct: 64 ALSRALVPFYPMAGRLKRDEDGRIEIECNGEGVLFVEAESDGVVDDFGDFAPTLE-LRRL 122
Query: 151 IP 152
IP
Sbjct: 123 IP 124
>pdb|4G2M|A Chain A, Structure Of A Lys-Hct Mutant From Coffea Canephora
(Crystal Form 2)
Length = 439
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/122 (27%), Positives = 57/122 (46%), Gaps = 10/122 (8%)
Query: 36 VQIISTEAIKPSSPTPKHLRTYKLSLPDQLCSKLYAPLVFFYSTNCKQQDLRKKSDLLKQ 95
+++ + ++P+ TP R S D + + P V+FY K +LK
Sbjct: 8 IEVKESTMVRPAQETPG--RNLWNSNVDLVVPNFHTPSVYFYRPTGSSNFFDAK--VLKD 63
Query: 96 SLAKSLTHYYPFAGRLI----DSFSVDCNDHGAAFIDANVGCDISKFLQ-PPDMELLQQL 150
+L+++L +YP AGRL ++CN G F++A + F P +E L++L
Sbjct: 64 ALSRALVPFYPMAGRLKRDEDGRIEIECNGEGVLFVEAESDGVVDDFGDFAPTLE-LRRL 122
Query: 151 IP 152
IP
Sbjct: 123 IP 124
>pdb|4G0B|A Chain A, Structure Of Native Hct From Coffea Canephora
pdb|4G0B|B Chain B, Structure Of Native Hct From Coffea Canephora
Length = 436
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/122 (27%), Positives = 57/122 (46%), Gaps = 10/122 (8%)
Query: 36 VQIISTEAIKPSSPTPKHLRTYKLSLPDQLCSKLYAPLVFFYSTNCKQQDLRKKSDLLKQ 95
+++ + ++P+ TP R S D + + P V+FY K +LK
Sbjct: 5 IEVKESTMVRPAQETPG--RNLWNSNVDLVVPNFHTPSVYFYRPTGSSNFFDAK--VLKD 60
Query: 96 SLAKSLTHYYPFAGRLI----DSFSVDCNDHGAAFIDANVGCDISKFLQ-PPDMELLQQL 150
+L+++L +YP AGRL ++CN G F++A + F P +E L++L
Sbjct: 61 ALSRALVPFYPMAGRLKRDEDGRIEIECNGEGVLFVEAESDGVVDDFGDFAPTLE-LRRL 119
Query: 151 IP 152
IP
Sbjct: 120 IP 121
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii
Length = 215
Score = 30.8 bits (68), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 23/51 (45%)
Query: 104 YYPFAGRLIDSFSVDCNDHGAAFIDANVGCDISKFLQPPDMELLQQLIPPS 154
+ PF G ++D V C+ HG + ++K L P D+ PPS
Sbjct: 79 FKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPS 129
>pdb|1NT9|G Chain G, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|G Chain G, Rna Polymerase Ii-Tfiis Complex
pdb|1WCM|G Chain G, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|G Chain G, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|G Chain G, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|G Chain G, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|G Chain G, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|1Y14|B Chain B, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|1Y14|D Chain D, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|2B63|G Chain G, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2JA5|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|S Chain S, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2R7Z|G Chain G, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|G Chain G, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|G Chain G, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|G Chain G, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3FKI|G Chain G, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3H3V|H Chain H, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|G Chain G, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|S Chain S, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|G Chain G, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|G Chain G, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|G Chain G, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|G Chain G, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3PO2|G Chain G, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|G Chain G, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|G Chain G, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3J0K|G Chain G, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|G Chain G, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|G Chain G, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|G Chain G, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|G Chain G, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 171
Score = 30.4 bits (67), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 23/51 (45%)
Query: 104 YYPFAGRLIDSFSVDCNDHGAAFIDANVGCDISKFLQPPDMELLQQLIPPS 154
+ PF G ++D V C+ HG + ++K L P D+ PPS
Sbjct: 79 FKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPS 129
>pdb|2E1T|A Chain A, Crystal Structure Of Dendranthema Morifolium Dmat
Complexed With Malonyl-coa
pdb|2E1T|B Chain B, Crystal Structure Of Dendranthema Morifolium Dmat
Complexed With Malonyl-coa
pdb|2E1U|A Chain A, Crystal Structure Of Dendranthema Morifolium Dmat
pdb|2E1U|B Chain B, Crystal Structure Of Dendranthema Morifolium Dmat
Length = 454
Score = 29.6 bits (65), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 93 LKQSLAKSLTHYYPFAGRLI 112
+K SL+ +L H+YPF G+L+
Sbjct: 65 IKHSLSITLKHFYPFVGKLV 84
>pdb|2E1V|A Chain A, Crystal Structure Of Dendranthema Morifolium Dmat, Seleno-
Methionine Derivative
pdb|2E1V|B Chain B, Crystal Structure Of Dendranthema Morifolium Dmat, Seleno-
Methionine Derivative
Length = 454
Score = 29.6 bits (65), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 10/20 (50%), Positives = 16/20 (80%)
Query: 93 LKQSLAKSLTHYYPFAGRLI 112
+K SL+ +L H+YPF G+L+
Sbjct: 65 IKHSLSITLKHFYPFVGKLV 84
>pdb|1SD4|A Chain A, Crystal Structure Of A Semet Derivative Of Blai At 2.0 A
pdb|1SD4|B Chain B, Crystal Structure Of A Semet Derivative Of Blai At 2.0 A
Length = 126
Score = 26.2 bits (56), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 39 ISTEAIKPSSPTPKHLRTYKLSLPDQLCSKLY-APLVFFYSTNCKQQDLRKKS 90
I E K + K +RT L + K Y + ++FYS+N K+ D++ K+
Sbjct: 30 IVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSENIYFYSSNIKEDDIKXKT 82
>pdb|1XSD|A Chain A, Crystal Structure Of The Blai Repressor In Complex With
Dna
Length = 126
Score = 26.2 bits (56), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 39 ISTEAIKPSSPTPKHLRTYKLSLPDQLCSKLY-APLVFFYSTNCKQQDLRKKS 90
I E K + K +RT L + K Y + ++FYS+N K+ D++ K+
Sbjct: 30 IVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSENIYFYSSNIKEDDIKMKT 82
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
0.321 0.134 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,093,918
Number of Sequences: 62578
Number of extensions: 143407
Number of successful extensions: 438
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 430
Number of HSP's gapped (non-prelim): 11
length of query: 155
length of database: 14,973,337
effective HSP length: 91
effective length of query: 64
effective length of database: 9,278,739
effective search space: 593839296
effective search space used: 593839296
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: 47 (22.7 bits)