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= 026620
(236 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 119 bits (298), Expect = 1e-27, Method: Compositional matrix adjust.
Identities = 73/197 (37%), Positives = 109/197 (55%), Gaps = 13/197 (6%)
Query: 48 TVLEMLKDRGYAVALSEINLSVQDFRAIYGQDPDVDRLRISISHQSDPSKR--------- 98
TV EM+KDRGY + E+ L ++DF+A Y D R +S Q++P++
Sbjct: 18 TVKEMVKDRGYFITQEEVELPLEDFKAKYC-DSMGRPQRKMMSFQANPTEESISKFPDMG 76
Query: 99 -ILVVFCGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAV-GLFQFKVEMF 156
+ V FC V V +++ + I ++ TG I + QN IT A K V + +E F
Sbjct: 77 SLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTG-IFVYQNNITPSAMKLVPSIPPATIETF 135
Query: 157 QITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQV 216
L+VNIT H L PKH L+ EK +LLK+Y ++E QLPR+ + D +A Y GL+RG+V
Sbjct: 136 NEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEV 195
Query: 217 VKVTYSGEITESHVTYR 233
VK+ E + + +YR
Sbjct: 196 VKIIRKSETSGRYASYR 212
>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 = 119 bits (297), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 69/192 (35%), Positives = 115/192 (59%), Gaps = 7/192 (3%)
Query: 48 TVLEMLKDRGYAVALSEINLSVQDFRAIY-GQDPDVDRLRISI-SHQSDPSKR--ILVVF 103
T +++ DRGY V+ +E++L++ F+A++ G ++DR +S + S+ S + I + F
Sbjct: 17 TAHQLVHDRGYGVSQAELDLTLDQFKAMHCGMGRNLDRTTLSFYAKPSNDSNKGTIYIEF 76
Query: 104 CGPGIVKVNVIRSIISQIVNRDTLTGLILILQNQITSQATKAVGLF--QFKVEMFQITDL 161
V + +R+ + + + + TG ILI N +T A K + QF +E FQ +DL
Sbjct: 77 AKEPSVGIKEMRTFVHTLGDHNHKTG-ILIYANSMTPSAAKIIATVTGQFTIETFQESDL 135
Query: 162 LVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTY 221
+VNIT H L PKH +L+ EK++LL +Y + E QLPR+ D +A+Y GL+RG+VVK+
Sbjct: 136 IVNITHHELVPKHILLSPDEKKELLDRYKLRETQLPRIQLADPVARYLGLKRGEVVKIVR 195
Query: 222 SGEITESHVTYR 233
E + + +YR
Sbjct: 196 RSETSGRYNSYR 207
>pdb|1HMJ|A Chain A, Solution Structure Of Rna Polymerase Subunit H
Length = 78
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 45/73 (61%)
Query: 163 VNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYS 222
+ +T H+L PKH+++ +E E++LK+Y+I+ +QLP++ + D + Q G + G VV+V
Sbjct: 1 MKVTDHILVPKHEIVPKEEVEEILKRYNIKIQQLPKIYEDDPVIQEIGAKEGDVVRVIRK 60
Query: 223 GEITESHVTYRCV 235
+ YR V
Sbjct: 61 SPTAGVSIAYRLV 73
>pdb|1EIK|A Chain A, Solution Structure Of Rna Polymerase Subunit Rpb5 From
Methanobacterium Thermoautotrophicum
Length = 77
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 41/72 (56%)
Query: 164 NITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSG 223
I KH L P+H +L + E +++LK+ +QLP++ D +A+ G +RG +VK+
Sbjct: 4 EILKHQLVPEHVILNESEAKRVLKELDAHPEQLPKIKTTDPVAKAIGAKRGDIVKIIRKS 63
Query: 224 EITESHVTYRCV 235
E VTYR V
Sbjct: 64 PTAEEFVTYRLV 75
>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 = 44.3 bits (103), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 38/68 (55%)
Query: 168 HVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITE 227
H L PKH+VL+ E K+LK+ I +QLP + D +A+ + G ++++ ++
Sbjct: 14 HYLVPKHEVLSIDEAYKILKELGIRPEQLPWIRASDPVARSINAKPGDIIRIIRKSQLYG 73
Query: 228 SHVTYRCV 235
V+YR V
Sbjct: 74 EVVSYRYV 81
>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 = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 37/68 (54%)
Query: 168 HVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVTYSGEITE 227
H L PKH+VL E K+LK+ I +QLP + D +A+ + G ++++ ++
Sbjct: 14 HYLVPKHEVLNIDEAYKILKELGIRPEQLPWIRASDPVARSINAKPGDIIRIIRKSQLYG 73
Query: 228 SHVTYRCV 235
V+YR V
Sbjct: 74 EVVSYRYV 81
>pdb|3V4X|A Chain A, The Biochemical And Structural Basis For Inhibition Of
Enterococcus Faecalis Hmg-Coa Synthase, Mvas, By
Hymeglusin
pdb|3V4X|B Chain B, The Biochemical And Structural Basis For Inhibition Of
Enterococcus Faecalis Hmg-Coa Synthase, Mvas, By
Hymeglusin
pdb|3V4X|C Chain C, The Biochemical And Structural Basis For Inhibition Of
Enterococcus Faecalis Hmg-Coa Synthase, Mvas, By
Hymeglusin
pdb|3V4X|D Chain D, The Biochemical And Structural Basis For Inhibition Of
Enterococcus Faecalis Hmg-Coa Synthase, Mvas, By
Hymeglusin
Length = 388
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 129 GLILILQNQITSQATKAVGLFQF---KVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKL 185
GLI +L+N T A +GLF + V F +L+ H+ K H L D E
Sbjct: 289 GLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELS 348
Query: 186 LKKY 189
+ +Y
Sbjct: 349 IAEY 352
>pdb|3V4N|A Chain A, The Biochemical And Structural Basis For Inhibition Of
Enterococcus Faecalis Hmg-coa Synthatse, Mvas, By
Hymeglusin
pdb|3V4N|B Chain B, The Biochemical And Structural Basis For Inhibition Of
Enterococcus Faecalis Hmg-coa Synthatse, Mvas, By
Hymeglusin
pdb|3V4N|C Chain C, The Biochemical And Structural Basis For Inhibition Of
Enterococcus Faecalis Hmg-coa Synthatse, Mvas, By
Hymeglusin
pdb|3V4N|D Chain D, The Biochemical And Structural Basis For Inhibition Of
Enterococcus Faecalis Hmg-coa Synthatse, Mvas, By
Hymeglusin
Length = 388
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 129 GLILILQNQITSQATKAVGLFQF---KVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKL 185
GLI +L+N T A +GLF + V F +L+ H+ K H L D E
Sbjct: 289 GLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELS 348
Query: 186 LKKY 189
+ +Y
Sbjct: 349 IAEY 352
>pdb|2HDB|A Chain A, Hmg-coa Synthase From Enterococcus Faecalis. Mutation
Alanine 110 To Glycine
pdb|2HDB|B Chain B, Hmg-coa Synthase From Enterococcus Faecalis. Mutation
Alanine 110 To Glycine
Length = 383
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 129 GLILILQNQITSQATKAVGLFQF---KVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKL 185
GLI +L+N T A +GLF + V F +L+ H+ K H L D E
Sbjct: 284 GLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELS 343
Query: 186 LKKY 189
+ +Y
Sbjct: 344 IAEY 347
>pdb|1YSL|A Chain A, Crystal Structure Of Hmg-Coa Synthase From Enterococcus
Faecalis With Acetoacetyl-Coa Ligand
Length = 402
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 129 GLILILQNQITSQATKAVGLFQF---KVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKL 185
GLI +L+N T A +GLF + V F +L+ H+ K H L D E
Sbjct: 303 GLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELS 362
Query: 186 LKKY 189
+ +Y
Sbjct: 363 IAEY 366
>pdb|1X9E|A Chain A, Crystal Structure Of Hmg-Coa Synthase From Enterococcus
Faecalis
pdb|1X9E|B Chain B, Crystal Structure Of Hmg-Coa Synthase From Enterococcus
Faecalis
Length = 383
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 129 GLILILQNQITSQATKAVGLFQF---KVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKL 185
GLI +L+N T A +GLF + V F +L+ H+ K H L D E
Sbjct: 284 GLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELS 343
Query: 186 LKKY 189
+ +Y
Sbjct: 344 IAEY 347
>pdb|1YSL|B Chain B, Crystal Structure Of Hmg-Coa Synthase From Enterococcus
Faecalis With Acetoacetyl-Coa Ligand
Length = 384
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 129 GLILILQNQITSQATKAVGLFQF---KVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKL 185
GLI +L+N T A +GLF + V F +L+ H+ K H L D E
Sbjct: 285 GLISLLENATTLTAGNQIGLFSYGSGAVAEFFTGELVAGYQNHLQKETHLALLDNRTELS 344
Query: 186 LKKY 189
+ +Y
Sbjct: 345 IAEY 348
>pdb|2PTH|A Chain A, Peptidyl-Trna Hydrolase From Escherichia Coli
Length = 193
Score = 30.4 bits (67), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 26/52 (50%)
Query: 69 VQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQ 120
++D + G +P+ RLRI I H D +K + V P + + +I I +
Sbjct: 116 LKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDE 167
>pdb|3VJR|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Escherichia Coli In Complex With The
Cca-Acceptor-T[psi]c Domain Of Trna
pdb|3VJR|C Chain C, Crystal Structure Of Peptidyl-Trna Hydrolase From
Escherichia Coli In Complex With The
Cca-Acceptor-T[psi]c Domain Of Trna
Length = 197
Score = 30.4 bits (67), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 26/52 (50%)
Query: 69 VQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQ 120
++D + G +P+ RLRI I H D +K + V P + + +I I +
Sbjct: 120 LKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDE 171
>pdb|3OFV|A Chain A, Crystal Structure Of Peptidyl-Trna Hydrolase From
Escherichia Coli, I222 Crystal Form
pdb|3OFV|B Chain B, Crystal Structure Of Peptidyl-Trna Hydrolase From
Escherichia Coli, I222 Crystal Form
pdb|3OFV|C Chain C, Crystal Structure Of Peptidyl-Trna Hydrolase From
Escherichia Coli, I222 Crystal Form
Length = 211
Score = 30.4 bits (67), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 26/52 (50%)
Query: 69 VQDFRAIYGQDPDVDRLRISISHQSDPSKRILVVFCGPGIVKVNVIRSIISQ 120
++D + G +P+ RLRI I H D +K + V P + + +I I +
Sbjct: 137 LKDIISKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDE 188
>pdb|3FFZ|A Chain A, Domain Organization In Clostridium Butulinum Neurotoxin
Type E Is Unique: Its Implication In Faster
Translocation
pdb|3FFZ|B Chain B, Domain Organization In Clostridium Butulinum Neurotoxin
Type E Is Unique: Its Implication In Faster
Translocation
Length = 1252
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 34/132 (25%), Positives = 58/132 (43%), Gaps = 17/132 (12%)
Query: 103 FCGPGIVKVNVIRSIISQIVNRDTLTGLI--LILQNQITSQATKAVGLFQFKVEMFQITD 160
F G K VI++I + + RD + I+ N +T T+ + K +M+Q
Sbjct: 653 FLGSSDNKNKVIKAINNALKERDEKWKEVYSFIVSNWMTKINTQ---FNKRKEQMYQALQ 709
Query: 161 LLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAIAQYYGLERGQVVKVT 220
VN K +++ K+ T +EK +L KY I KQ+ L + ++R
Sbjct: 710 NQVNAIKTIIESKYNSYTLEEKNELTNKYDI--KQIENELNQKVSIAMNNIDRF------ 761
Query: 221 YSGEITESHVTY 232
+TES ++Y
Sbjct: 762 ----LTESSISY 769
>pdb|2XGT|A Chain A, Asparaginyl-Trna Synthetase From Brugia Malayi Complexed
With The Sulphamoyl Analogue Of Asparaginyl-Adenylate
pdb|2XGT|B Chain B, Asparaginyl-Trna Synthetase From Brugia Malayi Complexed
With The Sulphamoyl Analogue Of Asparaginyl-Adenylate
Length = 435
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 158 ITDLLVNITKHVLKPKHQVLTDQEKEKLLK----KYSIEEKQLPRMLKKDAIA--QYYGL 211
+ DL+ I + V ++L D+E +KLL+ K+ E+ RM KDAI Q + +
Sbjct: 233 LDDLMEKIEELVCDTVDRLLADEEAKKLLEHINPKFQPPERPFLRMEYKDAIKWLQEHNV 292
Query: 212 ERGQVVKVTYSGEITES 228
E TY +I E+
Sbjct: 293 ENEFGNTFTYGEDIAEA 309
>pdb|2XTI|A Chain A, Asparaginyl-Trna Synthetase From Brugia Malayi Complexed
With Atp:mg And L-Asp-Beta-Noh Adenylate:ppi:mg
pdb|2XTI|B Chain B, Asparaginyl-Trna Synthetase From Brugia Malayi Complexed
With Atp:mg And L-Asp-Beta-Noh Adenylate:ppi:mg
Length = 437
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 6/77 (7%)
Query: 158 ITDLLVNITKHVLKPKHQVLTDQEKEKLLK----KYSIEEKQLPRMLKKDAIA--QYYGL 211
+ DL+ I + V ++L D+E +KLL+ K+ E+ RM KDAI Q + +
Sbjct: 235 LDDLMEKIEELVCDTVDRLLADEEAKKLLEHINPKFQPPERPFLRMEYKDAIKWLQEHNV 294
Query: 212 ERGQVVKVTYSGEITES 228
E TY +I E+
Sbjct: 295 ENEFGNTFTYGEDIAEA 311
>pdb|3S0M|A Chain A, A Structural Element That Modulates Proton-Coupled
Electron Transfer In Oxalate Decarboxylase
Length = 377
Score = 28.1 bits (61), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 25/51 (49%)
Query: 155 MFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAI 205
+FQ+TD L + K V+ V ++ K+ I E QLP LK D +
Sbjct: 160 VFQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIV 210
>pdb|1J58|A Chain A, Crystal Structure Of Oxalate Decarboxylase
Length = 385
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 156 FQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAI 205
FQ+TD L + K V+ V ++ K+ I E QLP LK D +
Sbjct: 166 FQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIV 215
>pdb|2UY8|A Chain A, R92a Mutant Of Bacillus Subtilis Oxalate Decarboxylase
Oxdc
Length = 385
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 156 FQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAI 205
FQ+TD L + K V+ V ++ K+ I E QLP LK D +
Sbjct: 166 FQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIV 215
>pdb|2V09|A Chain A, Sens161-164dssn Mutant Of Bacillus Subtilis Oxalate
Decarboxylase Oxdc
Length = 385
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 156 FQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAI 205
FQ+TD L + K V+ V ++ K+ I E QLP LK D +
Sbjct: 166 FQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIV 215
>pdb|2UYA|A Chain A, Del162-163 Mutant Of Bacillus Subtilis Oxalate
Decarboxylase Oxdc
Length = 383
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 156 FQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAI 205
FQ+TD L + K V+ V ++ K+ I E QLP LK D +
Sbjct: 164 FQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIV 213
>pdb|2UY9|A Chain A, E162a Mutant Of Bacillus Subtilis Oxalate Decarboxylase
Oxdc
Length = 385
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 156 FQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAI 205
FQ+TD L + K V+ V ++ K+ I E QLP LK D +
Sbjct: 166 FQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIV 215
>pdb|1L3J|A Chain A, Crystal Structure Of Oxalate Decarboxylase Formate Complex
pdb|1UW8|A Chain A, Crystal Structure Of Oxalate Decarboxylase
Length = 385
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 156 FQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAI 205
FQ+TD L + K V+ V ++ K+ I E QLP LK D +
Sbjct: 166 FQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIV 215
>pdb|2UYB|A Chain A, S161a Mutant Of Bacillus Subtilis Oxalate Decarboxylase
Oxdc
Length = 385
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 156 FQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDAI 205
FQ+TD L + K V+ V ++ K+ I E QLP LK D +
Sbjct: 166 FQLTDWLAHTPKEVIAANFGVTKEEISNLPGKEKYIFENQLPGSLKDDIV 215
>pdb|4F9I|A Chain A, Crystal Structure Of Proline Utilization A (Puta) From
Geobacter Sulfurreducens Pca
pdb|4F9I|B Chain B, Crystal Structure Of Proline Utilization A (Puta) From
Geobacter Sulfurreducens Pca
Length = 1026
Score = 27.3 bits (59), Expect = 6.5, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 12/79 (15%)
Query: 150 QFKVEMFQITDLLVNITKHVLKPKHQVLTDQEKEKLLKKYSIEEKQLPRMLKKDA-IAQY 208
QFK++MF+ D+ ++T L +H +++Y E+ +P + A +A
Sbjct: 69 QFKIQMFRFVDVFPSLTTSKLLTEH-----------IREYFGNEQDMPAFMSTGAKVAGM 117
Query: 209 YGLERGQVVKVTYSGEITE 227
G G V+ + I E
Sbjct: 118 LGSFGGAVLNKVLTSNIEE 136
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
0.319 0.136 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,800,365
Number of Sequences: 62578
Number of extensions: 195682
Number of successful extensions: 703
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 668
Number of HSP's gapped (non-prelim): 42
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)