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= 030846
(170 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3H0G|E Chain E, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|Q Chain Q, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 210
Score = 122 bits (305), Expect = 1e-28, Method: Compositional matrix adjust.
Identities = 64/170 (37%), Positives = 101/170 (59%), Gaps = 4/170 (2%)
Query: 1 MTLSDEEIKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIA---KFGENMKREDLVIN 57
M+ ++ I R+FR +T Q++ DRGY V E++++ +QF A G N+ R L
Sbjct: 1 MSAEEKNIVRVFRAWKTAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFY 60
Query: 58 KALRNDSS-DQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQE 116
NDS+ IY+ F E VG+K M+T+ + + N IL+ ++TP A I
Sbjct: 61 AKPSNDSNKGTIYIEFAKEPSVGIKEMRTFVHTLGDHNHKTGILIYANSMTPSAAKIIAT 120
Query: 117 ISAKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQV 166
++ +F +E FQE++L+VNI H LVP+H +L+ +EKK LL RY ++ETQ+
Sbjct: 121 VTGQFTIETFQESDLIVNITHHELVPKHILLSPDEKKELLDRYKLRETQL 170
>pdb|1DZF|A Chain A, Rpb5 From S.Cerevisiae
pdb|1I3Q|E Chain E, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|E Chain E, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|E Chain E, Rna Polymerase Ii Elongation Complex
pdb|1K83|E Chain E, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|E Chain E, Wild Type Rna Polymerase Ii
pdb|1NT9|E Chain E, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|E Chain E, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|E Chain E, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|E Chain E, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|E Chain E, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|E Chain E, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|E Chain E, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|E Chain E, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|E Chain E, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|E Chain E, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|E Chain E, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|E Chain E, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|E Chain E, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|E Chain E, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|E Chain E, 12-Subunit Rna Polymerase Ii
pdb|2E2H|E Chain E, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|E Chain E, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|E Chain E, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|Q Chain Q, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|E Chain E, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|E Chain E, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|E Chain E, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|E Chain E, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|E Chain E, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|E Chain E, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|E Chain E, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|E Chain E, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|E Chain E, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|E Chain E, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|E Chain E, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|E Chain E, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|E Chain E, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|E Chain E, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|F Chain F, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|E Chain E, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|Q Chain Q, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|E Chain E, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|E Chain E, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|E Chain E, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|E Chain E, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|E Chain E, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|E Chain E, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|E Chain E, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|E Chain E, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|E Chain E, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|E Chain E, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|E Chain E, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|E Chain E, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|E Chain E, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|E Chain E, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|E Chain E, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|E Chain E, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|E Chain E, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|E Chain E, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|E Chain E, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|E Chain E, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|E Chain E, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|E Chain E, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|E Chain E, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|E Chain E, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|E Chain E, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 215
Score = 115 bits (288), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 67/169 (39%), Positives = 97/169 (57%), Gaps = 10/169 (5%)
Query: 8 IKRLFRIRRTVMQMLRDRGYFVGDFEINMSKEQFIAKFGENMKREDLVINKALRNDSSDQ 67
I RL+R RTV +M++DRGYF+ E+ + E F AK+ ++M R + N + +
Sbjct: 9 ISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEES 68
Query: 68 I---------YVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEIS 118
I +V F DE VGVKTMKT+ ++ +N I V Q N+TP A + I
Sbjct: 69 ISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIP 128
Query: 119 AKFHLEVFQEAELLVNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
+E F EA L+VNI H LVP+H L+++EK+ LLKRY +KE+Q+
Sbjct: 129 PA-TIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLP 176
>pdb|1HMJ|A Chain A, Solution Structure Of Rna Polymerase Subunit H
Length = 78
Score = 35.0 bits (79), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 24/33 (72%)
Query: 135 IKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
+ +H+LVP+H+++ EE + +LKRY +K Q+
Sbjct: 3 VTDHILVPKHEIVPKEEVEEILKRYNIKIQQLP 35
>pdb|3C67|A Chain A, Escherichia Coli K12 Ygjk In A Complexed With Glucose
pdb|3C67|B Chain B, Escherichia Coli K12 Ygjk In A Complexed With Glucose
pdb|3C68|A Chain A, Escherichia Coli K12 Ygjk In A Complexed With Mannose
pdb|3C68|B Chain B, Escherichia Coli K12 Ygjk In A Complexed With Mannose
pdb|3C69|A Chain A, Escherichia Coli K12 Ygjk In A Complexed With Galactose
pdb|3C69|B Chain B, Escherichia Coli K12 Ygjk In A Complexed With Galactose
Length = 761
Score = 32.3 bits (72), Expect = 0.14, Method: Composition-based stats.
Identities = 21/97 (21%), Positives = 43/97 (44%), Gaps = 5/97 (5%)
Query: 38 KEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFR 97
+ + KF EN ++ ++ +L +S DQ + D + M T + + +R
Sbjct: 525 RSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLA--EMATILGKPEEAKRYR 582
Query: 98 AILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVN 134
+ Q L + TC+ + + +F+ +V E + L N
Sbjct: 583 QL---AQQLADYINTCMFDPTTQFYYDVRIEDKPLAN 616
>pdb|2HHF|B Chain B, X-ray Crystal Structure Of Oxidized Human Mitochondrial
Branched Chain Aminotransferase (hbcatm)
Length = 365
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 10/79 (12%)
Query: 44 KFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAIL--- 100
K G N LV +AL+ ++++ PD Q V TM + + V +
Sbjct: 202 KLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPL 261
Query: 101 -------VVQQNLTPFART 112
VV+Q+L A+T
Sbjct: 262 NGVILPGVVRQSLLDMAQT 280
>pdb|2HHF|A Chain A, X-ray Crystal Structure Of Oxidized Human Mitochondrial
Branched Chain Aminotransferase (hbcatm)
Length = 365
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 10/79 (12%)
Query: 44 KFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAIL--- 100
K G N LV +AL+ ++++ PD Q V TM + + V +
Sbjct: 202 KLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPL 261
Query: 101 -------VVQQNLTPFART 112
VV+Q+L A+T
Sbjct: 262 NGVILPGVVRQSLLDMAQT 280
>pdb|1EKF|A Chain A, Crystallographic Structure Of Human Branched Chain Amino
Acid Aminotransferase (Mitochondrial) Complexed With
Pyridoxal-5'- Phosphate At 1.95 Angstroms (Orthorhombic
Form)
pdb|1EKF|B Chain B, Crystallographic Structure Of Human Branched Chain Amino
Acid Aminotransferase (Mitochondrial) Complexed With
Pyridoxal-5'- Phosphate At 1.95 Angstroms (Orthorhombic
Form)
pdb|1EKP|A Chain A, Crystal Structure Of Human Branched Chain Amino Acid
Aminotransferase (Mitochondrial) Complexed With
Pyridoxal-5'-Phosphate At 2.5 Angstroms (Monoclinic
Form).
pdb|1EKP|B Chain B, Crystal Structure Of Human Branched Chain Amino Acid
Aminotransferase (Mitochondrial) Complexed With
Pyridoxal-5'-Phosphate At 2.5 Angstroms (Monoclinic
Form).
pdb|1EKV|A Chain A, Human Branched Chain Amino Acid Aminotransferase
(Mitochondrial): Three Dimensional Structure Of Enzyme
Inactivated By Tris Bound To The Pyridoxal-5'-Phosphate
On One End And Active Site Lys202 Nz On The Other.
pdb|1EKV|B Chain B, Human Branched Chain Amino Acid Aminotransferase
(Mitochondrial): Three Dimensional Structure Of Enzyme
Inactivated By Tris Bound To The Pyridoxal-5'-Phosphate
On One End And Active Site Lys202 Nz On The Other.
pdb|1KT8|A Chain A, Human Branched Chain Amino Acid Aminotransferase
(Mitochondrial): Three Dimensional Structure Of Enzyme
In Its Ketimine Form With The Substrate L-Isoleucine
pdb|1KT8|B Chain B, Human Branched Chain Amino Acid Aminotransferase
(Mitochondrial): Three Dimensional Structure Of Enzyme
In Its Ketimine Form With The Substrate L-Isoleucine
pdb|1KTA|A Chain A, Human Branched Chain Amino Acid Aminotransferase : Three
Dimensional Structure Of The Enzyme In Its Pyridoxamine
Phosphate Form.
pdb|1KTA|B Chain B, Human Branched Chain Amino Acid Aminotransferase : Three
Dimensional Structure Of The Enzyme In Its Pyridoxamine
Phosphate Form.
pdb|2A1H|A Chain A, X-Ray Crystal Structure Of Human Mitochondrial Branched
Chain Aminotransferase (Bcatm) Complexed With Gabapentin
pdb|2A1H|B Chain B, X-Ray Crystal Structure Of Human Mitochondrial Branched
Chain Aminotransferase (Bcatm) Complexed With Gabapentin
Length = 365
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 10/79 (12%)
Query: 44 KFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAIL--- 100
K G N LV +AL+ ++++ PD Q V TM + + V +
Sbjct: 202 KLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPL 261
Query: 101 -------VVQQNLTPFART 112
VV+Q+L A+T
Sbjct: 262 NGVILPGVVRQSLLDMAQT 280
>pdb|2HG8|A Chain A, Crystal Structure Of Cys315ala Mutant Of Human
Mitochondrial Branched Chain Aminotransferase Complexed
With Its Substrate Mimic, N-Methyl Leucine.
pdb|2HG8|B Chain B, Crystal Structure Of Cys315ala Mutant Of Human
Mitochondrial Branched Chain Aminotransferase Complexed
With Its Substrate Mimic, N-Methyl Leucine.
pdb|2HGX|A Chain A, Crystal Structure Of Cys315ala Mutant Of Human
Mitochondrial Branched Chain Aminotransferase
pdb|2HGX|B Chain B, Crystal Structure Of Cys315ala Mutant Of Human
Mitochondrial Branched Chain Aminotransferase
Length = 365
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 10/79 (12%)
Query: 44 KFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAIL--- 100
K G N LV +AL+ ++++ PD Q V TM + + V +
Sbjct: 202 KLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPL 261
Query: 101 -------VVQQNLTPFART 112
VV+Q+L A+T
Sbjct: 262 NGVILPGVVRQSLLDMAQT 280
>pdb|2HGW|A Chain A, Crystal Structure Of Cys318ala Mutant Of Human
Mitochondrial Branched Chain Aminotransferase
pdb|2HGW|B Chain B, Crystal Structure Of Cys318ala Mutant Of Human
Mitochondrial Branched Chain Aminotransferase
Length = 365
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 10/79 (12%)
Query: 44 KFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAIL--- 100
K G N LV +AL+ ++++ PD Q V TM + + V +
Sbjct: 202 KLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPL 261
Query: 101 -------VVQQNLTPFART 112
VV+Q+L A+T
Sbjct: 262 NGVILPGVVRQSLLDMAQT 280
>pdb|2HDK|A Chain A, Crystal Structure Of Cys315ala-Cys318ala Mutant Of Human
Mitochondrial Branched Chain Aminotransferase
pdb|2HDK|B Chain B, Crystal Structure Of Cys315ala-Cys318ala Mutant Of Human
Mitochondrial Branched Chain Aminotransferase
Length = 365
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 32/79 (40%), Gaps = 10/79 (12%)
Query: 44 KFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAIL--- 100
K G N LV +AL+ ++++ PD Q V TM + + V +
Sbjct: 202 KLGGNYGPTVLVQQEALKRGCEQVLWLYGPDHQLTEVGTMNIFVYWTHEDGVLELVTPPL 261
Query: 101 -------VVQQNLTPFART 112
VV+Q+L A+T
Sbjct: 262 NGVILPGVVRQSLLDMAQT 280
>pdb|3D3I|A Chain A, Crystal Structural Of Escherichia Coli K12 Ygjk, A
Glucosidase Belonging To Glycoside Hydrolase Family 63
pdb|3D3I|B Chain B, Crystal Structural Of Escherichia Coli K12 Ygjk, A
Glucosidase Belonging To Glycoside Hydrolase Family 63
Length = 761
Score = 28.1 bits (61), Expect = 2.7, Method: Composition-based stats.
Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 5/97 (5%)
Query: 38 KEQFIAKFGENMKREDLVINKALRNDSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFR 97
+ + KF EN ++ ++ +L +S DQ + D + + T K E R
Sbjct: 525 RSDWTVKFAENRSQDGTLLGYSLLQESVDQASYXYSDNHYLA----EXATILGKPEEAKR 580
Query: 98 AILVVQQNLTPFARTCIQEISAKFHLEVFQEAELLVN 134
+ QQ L + TC + + +F+ +V E + L N
Sbjct: 581 YRQLAQQ-LADYINTCXFDPTTQFYYDVRIEDKPLAN 616
>pdb|2WAQ|H Chain H, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|H Chain H, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|Z Chain Z, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|H Chain H, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|Z Chain Z, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|H Chain H, Rnap At 3.2ang
pdb|4B1O|H Chain H, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|Z Chain Z, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 84
Score = 27.7 bits (60), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 22/35 (62%)
Query: 133 VNIKEHVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
++ + H LVP+H+VL+ +E +LK ++ Q+
Sbjct: 9 IDPRIHYLVPKHEVLSIDEAYKILKELGIRPEQLP 43
>pdb|2PMZ|H Chain H, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|V Chain V, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|H Chain H, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|T Chain T, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 84
Score = 26.9 bits (58), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 138 HVLVPEHQVLTNEEKKTLLKRYTVKETQVS 167
H LVP+H+VL +E +LK ++ Q+
Sbjct: 14 HYLVPKHEVLNIDEAYKILKELGIRPEQLP 43
>pdb|2YA0|A Chain A, Catalytic Module Of The Multi-Modular Glycogen-Degrading
Pneumococcal Virulence Factor Spua
Length = 714
Score = 26.9 bits (58), Expect = 5.6, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 63 DSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFH 122
DSSD + F + G K Y +KS + + ++ ++Q+ F +Q+I + H
Sbjct: 556 DSSDAVNKFDWTKATDG----KAYPENVKSRDYMKGLIALRQSTDAFRLKSLQDIKDRVH 611
Query: 123 L 123
L
Sbjct: 612 L 612
>pdb|2YA2|A Chain A, Catalytic Module Of The Multi-Modular Glycogen-Degrading
Pneumococcal Virulence Factor Spua In Complex With An
Inhibitor
Length = 708
Score = 26.9 bits (58), Expect = 5.9, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 63 DSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFH 122
DSSD + F + G K Y +KS + + ++ ++Q+ F +Q+I + H
Sbjct: 557 DSSDAVNKFDWTKATDG----KAYPENVKSRDYMKGLIALRQSTDAFRLKSLQDIKDRVH 612
Query: 123 L 123
L
Sbjct: 613 L 613
>pdb|2YA1|A Chain A, Product Complex Of A Multi-Modular Glycogen-Degrading
Pneumococcal Virulence Factor Spua
Length = 1014
Score = 26.9 bits (58), Expect = 6.3, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 63 DSSDQIYVFFPDEQKVGVKTMKTYTNRMKSENVFRAILVVQQNLTPFARTCIQEISAKFH 122
DSSD + F + G K Y +KS + + ++ ++Q+ F +Q+I + H
Sbjct: 863 DSSDAVNKFDWTKATDG----KAYPENVKSRDYMKGLIALRQSTDAFRLKSLQDIKDRVH 918
Query: 123 L 123
L
Sbjct: 919 L 919
>pdb|3ZYY|X Chain X, Reductive Activator For Corrinoid,Iron-Sulfur Protein
pdb|3ZYY|Y Chain Y, Reductive Activator For Corrinoid,Iron-Sulfur Protein
Length = 631
Score = 26.6 bits (57), Expect = 7.1, Method: Composition-based stats.
Identities = 12/54 (22%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 103 QQNLTPFARTCIQEISAKFHL--EVFQEAELLVNIKEHVLVPEHQVLTNEEKKT 154
Q+ + + + +EI+ + L + + E++L++ I + +HQ++T++EK +
Sbjct: 55 QKRVESYGKLKQEEIAQGYVLACQTYPESDLIIEIPFDSRLTQHQIVTDDEKAS 108
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 0.135 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,263,464
Number of Sequences: 62578
Number of extensions: 152461
Number of successful extensions: 421
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 406
Number of HSP's gapped (non-prelim): 25
length of query: 170
length of database: 14,973,337
effective HSP length: 92
effective length of query: 78
effective length of database: 9,216,161
effective search space: 718860558
effective search space used: 718860558
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: 48 (23.1 bits)