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= psy12829
(181 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1I3Q|C Chain C, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|C Chain C, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|C Chain C, Rna Polymerase Ii Elongation Complex
pdb|1K83|C Chain C, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|C Chain C, Wild Type Rna Polymerase Ii
pdb|1NT9|C Chain C, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|C Chain C, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|C Chain C, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|C Chain C, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|C Chain C, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|C Chain C, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|C Chain C, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|C Chain C, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|C Chain C, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|C Chain C, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|C Chain C, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|C Chain C, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|C Chain C, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|C Chain C, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|C Chain C, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|C Chain C, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|C Chain C, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|C Chain C, 12-Subunit Rna Polymerase Ii
pdb|2E2H|C Chain C, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|C Chain C, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|C Chain C, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|C Chain C, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|C Chain C, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|C Chain C, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|C Chain C, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|C Chain C, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|O Chain O, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|C Chain C, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|C Chain C, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|C Chain C, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|C Chain C, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|C Chain C, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|C Chain C, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|C Chain C, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|C Chain C, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|C Chain C, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|C Chain C, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|C Chain C, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|C Chain C, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|C Chain C, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|C Chain C, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|C Chain C, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|C Chain C, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|D Chain D, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|C Chain C, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|O Chain O, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|C Chain C, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3K1F|C Chain C, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|C Chain C, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|C Chain C, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|C Chain C, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|C Chain C, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|C Chain C, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|C Chain C, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|C Chain C, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|C Chain C, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|C Chain C, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|C Chain C, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|C Chain C, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|C Chain C, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|C Chain C, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4A3C|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|C Chain C, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|C Chain C, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|C Chain C, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|C Chain C, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|C Chain C, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 318
Score = 155 bits (393), Expect = 8e-39, Method: Compositional matrix adjust.
Identities = 84/174 (48%), Positives = 113/174 (64%), Gaps = 5/174 (2%)
Query: 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA
Sbjct: 6 PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 65
Query: 67 RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
R+GLIPL S + ++++ YSRDC C D C +CSV TL + T +V + DL
Sbjct: 66 RLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDL----VI 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
V + RN + + E + +LI KLRKGQEL+L AKKG KEHAKW P A
Sbjct: 121 VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAA 174
>pdb|3I4M|C Chain C, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|C Chain C, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
Length = 324
Score = 155 bits (393), Expect = 8e-39, Method: Compositional matrix adjust.
Identities = 84/174 (48%), Positives = 113/174 (64%), Gaps = 5/174 (2%)
Query: 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA
Sbjct: 12 PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 71
Query: 67 RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
R+GLIPL S + ++++ YSRDC C D C +CSV TL + T +V + DL
Sbjct: 72 RLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDL----VI 126
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
V + RN + + E + +LI KLRKGQEL+L AKKG KEHAKW P A
Sbjct: 127 VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAA 180
>pdb|3J0K|C Chain C, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 268
Score = 155 bits (393), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 84/175 (48%), Positives = 113/175 (64%), Gaps = 5/175 (2%)
Query: 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA
Sbjct: 6 PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 65
Query: 67 RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
R+GLIPL S + ++++ YSRDC C D C +CSV TL + T +V + DL
Sbjct: 66 RLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDL----VI 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
V + RN + + E + +LI KLRKGQEL+L AKKG KEHAKW P A
Sbjct: 121 VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAA 175
>pdb|3HOW|C Chain C, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|C Chain C, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|C Chain C, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|C Chain C, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
Length = 347
Score = 155 bits (393), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 84/174 (48%), Positives = 113/174 (64%), Gaps = 5/174 (2%)
Query: 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
P V I + + +NV F + + +L++ANSLRRV IAE PT+AID V++E N+TVL+DEFIA
Sbjct: 35 PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAH 94
Query: 67 RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
R+GLIPL S + ++++ YSRDC C D C +CSV TL + T +V + DL
Sbjct: 95 RLGLIPLQSMD-IEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDL----VI 149
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
V + RN + + E + +LI KLRKGQEL+L AKKG KEHAKW P A
Sbjct: 150 VSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAA 203
>pdb|3H0G|C Chain C, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|O Chain O, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 297
Score = 137 bits (344), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 77/180 (42%), Positives = 109/180 (60%), Gaps = 17/180 (9%)
Query: 10 HIT--DLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
HIT +++ +V F + +T L+VANSLRRV +AE PT+AID V++ N++V+ DEF+A R
Sbjct: 6 HITIRNISKNSVDFVLTNTSLAVANSLRRVVLAEIPTVAIDLVEINVNTSVMPDEFLAHR 65
Query: 68 IGLIPLTSDEVVDR----ILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADL--K 121
+G+IPL S + + + Y+R+C C +C +CSVE L+ KC + T + DL
Sbjct: 66 LGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVELFLNAKCTGEGTMEIYARDLVVS 125
Query: 122 STDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
S + P+ AD G LI KLRK QE+ LR AKKG KEHAKW+PT+
Sbjct: 126 SNSSLGHPIL-----ADPKSRGP----LICKLRKEQEISLRCIAKKGIAKEHAKWSPTSA 176
>pdb|2WAQ|D Chain D, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|D Chain D, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|S Chain S, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|D Chain D, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|S Chain S, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|D Chain D, Rnap At 3.2ang
pdb|4B1O|D Chain D, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|S Chain S, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 265
Score = 90.5 bits (223), Expect = 5e-19, Method: Compositional matrix adjust.
Identities = 51/174 (29%), Positives = 90/174 (51%), Gaps = 16/174 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
S+++ D+ + E L N++RR + P M+ID V N++ L DE +A R
Sbjct: 2 SINLLHKDDKRIDLVFEGYPLEFVNAIRRAAMLYVPVMSIDDVYFIENNSPLYDEILAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+ LIP TS+E +D + +C C + C +C + ++ + + ++ + + + D+KS D
Sbjct: 62 LALIPFTSEEALDTYRWPEECIDCTENCEKCYTKIYIEAEAL-NEPKMLYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
+VP++ DI IV L Q++ L A + G+GKEHAK+ P +
Sbjct: 121 IVPISG--------------DIPIVLLGANQKISLEARLRLGYGKEHAKFIPVS 160
>pdb|2PA8|D Chain D, X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE
SULFOLOBUS Solfataricus Rna Polymerase
pdb|2PMZ|D Chain D, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|S Chain S, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|D Chain D, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|O Chain O, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 265
Score = 89.7 bits (221), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 52/174 (29%), Positives = 87/174 (50%), Gaps = 16/174 (9%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
S+++ D + E L N++RR + P MA+D V N++ L DE +A R
Sbjct: 2 SINLLHKDDTRIDLVFEGYPLEFVNAIRRASMLYVPIMAVDDVYFIENNSPLYDEILAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+ LIP S+E +D + +C C + C +C + ++ + ++ R + + D+KS D
Sbjct: 62 LALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYIEAE-APNEPRMIYSKDIKSEDPS 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTA 180
VVP++ DI IV L Q++ L A + G+GKEHAK+ P +
Sbjct: 121 VVPISG--------------DIPIVLLGTNQKISLEARLRLGYGKEHAKFIPVS 160
>pdb|1ZJC|A Chain A, Aminopeptidase S From S. Aureus
Length = 418
Score = 30.0 bits (66), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 30/125 (24%), Positives = 55/125 (44%), Gaps = 12/125 (9%)
Query: 12 TDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLI 71
TDLT K + + S N + FIA PT + A D ++ ++ +
Sbjct: 222 TDLTVGLAKNHIWEDATSYVNGKEQAFIANIPTEEV----FTAPDRNRVDGYVTNK---L 274
Query: 72 PLTSD-EVVDRI-LYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVP 129
PL+ + ++D+ L +D +DF +E D+ D+ +R + L D+ P
Sbjct: 275 PLSYNGTIIDQFKLMFKDGEIIDFSAEKGEAVLKDLINTDEGSRRLGEVALVPDDS---P 331
Query: 130 VTSRN 134
+++RN
Sbjct: 332 ISNRN 336
>pdb|2HDH|A Chain A, Biochemical Characterization And Structure Determination
Of Human Heart Short Chain L-3-Hydroxyacyl Coa
Dehydrogenase Provide Insight Into Catalytic Mechanism
pdb|2HDH|B Chain B, Biochemical Characterization And Structure Determination
Of Human Heart Short Chain L-3-Hydroxyacyl Coa
Dehydrogenase Provide Insight Into Catalytic Mechanism
Length = 293
Score = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 35 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 66
>pdb|3RQS|A Chain A, Crystal Structure Of Human L-3- Hydroxyacyl-Coa
Dehydrogenase (Ec1.1.1.35) From Mitochondria At The
Resolution 2.0 A, Northeast Structural Genomics
Consortium Target Hr487, Mitochondrial Protein
Partnership
pdb|3RQS|B Chain B, Crystal Structure Of Human L-3- Hydroxyacyl-Coa
Dehydrogenase (Ec1.1.1.35) From Mitochondria At The
Resolution 2.0 A, Northeast Structural Genomics
Consortium Target Hr487, Mitochondrial Protein
Partnership
Length = 324
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 68 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 99
>pdb|1M75|A Chain A, Crystal Structure Of The N208s Mutant Of L-3-Hydroxyacyl-
Coa Dehydrogenase In Complex With Nad And
Acetoacetyl-Coa
pdb|1M75|B Chain B, Crystal Structure Of The N208s Mutant Of L-3-Hydroxyacyl-
Coa Dehydrogenase In Complex With Nad And
Acetoacetyl-Coa
Length = 302
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 46 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 77
>pdb|1F0Y|A Chain A, L-3-Hydroxyacyl-Coa Dehydrogenase Complexed With
Acetoacetyl-Coa And Nad+
pdb|1F0Y|B Chain B, L-3-Hydroxyacyl-Coa Dehydrogenase Complexed With
Acetoacetyl-Coa And Nad+
Length = 302
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 46 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 77
>pdb|1LSO|A Chain A, Crystal Structure Of The S137a Mutant Of L-3-Hydroxyacyl-
Coa Dehydrogenase In Complex With Nad
pdb|1LSO|B Chain B, Crystal Structure Of The S137a Mutant Of L-3-Hydroxyacyl-
Coa Dehydrogenase In Complex With Nad
Length = 302
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 46 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 77
>pdb|1LSJ|A Chain A, Crystal Structure Of The E110q Mutant Of L-3-hydroxyacyl-
Coa Dehydrogenase In Complex With Nad
pdb|1LSJ|B Chain B, Crystal Structure Of The E110q Mutant Of L-3-hydroxyacyl-
Coa Dehydrogenase In Complex With Nad
Length = 302
Score = 27.3 bits (59), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 46 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 77
>pdb|1IL0|A Chain A, X-Ray Crystal Structure Of The E170q Mutant Of Human L-3-
Hydroxyacyl-Coa Dehydrogenase
pdb|1IL0|B Chain B, X-Ray Crystal Structure Of The E170q Mutant Of Human L-3-
Hydroxyacyl-Coa Dehydrogenase
Length = 302
Score = 27.3 bits (59), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 46 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 77
>pdb|1M76|A Chain A, Crystal Structure Of The S137c Mutant Of L-3-Hydroxyacyl-
Coa Dehydrogenase In Complex With Nad And
Acetoacetyl-Coa
pdb|1M76|B Chain B, Crystal Structure Of The S137c Mutant Of L-3-Hydroxyacyl-
Coa Dehydrogenase In Complex With Nad And
Acetoacetyl-Coa
Length = 302
Score = 27.3 bits (59), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 46 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 77
>pdb|3HDH|A Chain A, Pig Heart Short Chain L-3-Hydroxyacyl Coa Dehydrogenase
Revisited: Sequence Analysis And Crystal Structure
Determination
pdb|3HDH|B Chain B, Pig Heart Short Chain L-3-Hydroxyacyl Coa Dehydrogenase
Revisited: Sequence Analysis And Crystal Structure
Determination
pdb|3HDH|C Chain C, Pig Heart Short Chain L-3-Hydroxyacyl Coa Dehydrogenase
Revisited: Sequence Analysis And Crystal Structure
Determination
Length = 302
Score = 26.9 bits (58), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 46 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 77
>pdb|1F12|A Chain A, L-3-Hydroxyacyl-Coa Dehydrogenase Complexed With 3-
Hydroxybutyryl-Coa
pdb|1F12|B Chain B, L-3-Hydroxyacyl-Coa Dehydrogenase Complexed With 3-
Hydroxybutyryl-Coa
pdb|1F14|A Chain A, L-3-Hydroxyacyl-Coa Dehydrogenase (Apo)
pdb|1F14|B Chain B, L-3-Hydroxyacyl-Coa Dehydrogenase (Apo)
pdb|1F17|A Chain A, L-3-Hydroxyacyl-Coa Dehydrogenase Complexed With Nadh
pdb|1F17|B Chain B, L-3-Hydroxyacyl-Coa Dehydrogenase Complexed With Nadh
Length = 310
Score = 26.9 bits (58), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 46 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 77
>pdb|3HAD|A Chain A, Biochemical Characterization And Structure Determination
Of Human Heart Short Chain L-3-Hydroxyacyl Coa
Dehydrogenase Provide Insight Into Catalytic Mechanism
pdb|3HAD|B Chain B, Biochemical Characterization And Structure Determination
Of Human Heart Short Chain L-3-Hydroxyacyl Coa
Dehydrogenase Provide Insight Into Catalytic Mechanism
Length = 308
Score = 26.9 bits (58), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 6/38 (15%)
Query: 144 ETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
+T+DIL K +KG E LR AKK F + NP AG
Sbjct: 46 QTEDIL-AKSKKGIEESLRKVAKKKFAE-----NPKAG 77
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
0.318 0.132 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,104,695
Number of Sequences: 62578
Number of extensions: 186657
Number of successful extensions: 416
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 396
Number of HSP's gapped (non-prelim): 21
length of query: 181
length of database: 14,973,337
effective HSP length: 93
effective length of query: 88
effective length of database: 9,153,583
effective search space: 805515304
effective search space used: 805515304
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)