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= psy5332
(287 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 = 174 bits (441), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 94/234 (40%), Positives = 147/234 (62%), Gaps = 13/234 (5%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
+AID V++E N+TVL+DEFIA R+GLIPL S ++ +++ YSRDC C D C +CSV TL
Sbjct: 44 LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEYSRDCFCEDHCDKCSVVLTLQ 102
Query: 61 VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
+ T +V + DL V + RN + + E + +LI KLRKGQEL+L
Sbjct: 103 AFGESESTTNVYSKDL----VIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCV 158
Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLF----PKPDEWPKSEYSELDETQHEA-P 175
AKKG KEHAKW P A + FEYDP N ++HT + EWP+S+ E ++ +E P
Sbjct: 159 AKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDP 218
Query: 176 YNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL---QTQLAHDRVFY 226
++++A+ + ++ NVES G++ + +V+ G+ L++K++++ TQ+ D+V +
Sbjct: 219 FDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNF 272
>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 = 174 bits (441), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 94/234 (40%), Positives = 147/234 (62%), Gaps = 13/234 (5%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
+AID V++E N+TVL+DEFIA R+GLIPL S ++ +++ YSRDC C D C +CSV TL
Sbjct: 50 LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEYSRDCFCEDHCDKCSVVLTLQ 108
Query: 61 VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
+ T +V + DL V + RN + + E + +LI KLRKGQEL+L
Sbjct: 109 AFGESESTTNVYSKDL----VIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCV 164
Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLF----PKPDEWPKSEYSELDETQHEA-P 175
AKKG KEHAKW P A + FEYDP N ++HT + EWP+S+ E ++ +E P
Sbjct: 165 AKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDP 224
Query: 176 YNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL---QTQLAHDRVFY 226
++++A+ + ++ NVES G++ + +V+ G+ L++K++++ TQ+ D+V +
Sbjct: 225 FDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNF 278
>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 = 174 bits (441), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 94/235 (40%), Positives = 147/235 (62%), Gaps = 13/235 (5%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
+AID V++E N+TVL+DEFIA R+GLIPL S ++ +++ YSRDC C D C +CSV TL
Sbjct: 73 LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEYSRDCFCEDHCDKCSVVLTLQ 131
Query: 61 VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
+ T +V + DL V + RN + + E + +LI KLRKGQEL+L
Sbjct: 132 AFGESESTTNVYSKDL----VIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCV 187
Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLF----PKPDEWPKSEYSELDETQHEA-P 175
AKKG KEHAKW P A + FEYDP N ++HT + EWP+S+ E ++ +E P
Sbjct: 188 AKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDP 247
Query: 176 YNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL---QTQLAHDRVFYV 227
++++A+ + ++ NVES G++ + +V+ G+ L++K++++ TQ+ D+V +
Sbjct: 248 FDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNFA 302
>pdb|3J0K|C Chain C, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 268
Score = 171 bits (433), Expect = 4e-43, Method: Compositional matrix adjust.
Identities = 91/226 (40%), Positives = 141/226 (62%), Gaps = 10/226 (4%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
+AID V++E N+TVL+DEFIA R+GLIPL S ++ +++ YSRDC C D C +CSV TL
Sbjct: 44 LAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDI-EQLEYSRDCFCEDHCDKCSVVLTLQ 102
Query: 61 VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
+ T +V + DL V + RN + + E + +LI KLRKGQEL+L
Sbjct: 103 AFGESESTTNVYSKDL----VIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCV 158
Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLF----PKPDEWPKSEYSELDETQHEA-P 175
AKKG KEHAKW P A + FEYDP N ++HT + EWP+S+ E ++ +E P
Sbjct: 159 AKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDP 218
Query: 176 YNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221
++++A+ + ++ NVES G++ + +V+ G+ L++K++++ L
Sbjct: 219 FDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQ 264
>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 = 163 bits (413), Expect = 9e-41, Method: Compositional matrix adjust.
Identities = 89/234 (38%), Positives = 139/234 (59%), Gaps = 20/234 (8%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVD----RILYSRDCTCVDFCSECSVE 56
+AID V++ N++V+ DEF+A R+G+IPL S + + + Y+R+C C +C +CSVE
Sbjct: 43 VAIDLVEINVNTSVMPDEFLAHRLGMIPLDSSNIDEPPPVGLEYTRNCDCDQYCPKCSVE 102
Query: 57 FTLDVKCVDDQTRHVTTADL--KSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQE 114
L+ KC + T + DL S + P+ AD G LI KLRK QE
Sbjct: 103 LFLNAKCTGEGTMEIYARDLVVSSNSSLGHPIL-----ADPKSRGP----LICKLRKEQE 153
Query: 115 LRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLF----PKPDEWPKSEYSELDET 170
+ LR AKKG KEHAKW+PT+ V FEYDP N ++HT + EWPKS+ ++ +E
Sbjct: 154 ISLRCIAKKGIAKEHAKWSPTSAVAFEYDPWNKLQHTDYWFENDADAEWPKSKNADWEEP 213
Query: 171 QHEA-PYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAHDR 223
E P+N++ +P +++ +VES G++ P I++ G+ +L++KL+ L L ++
Sbjct: 214 PREGEPFNFQEEPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLVRDLDEEQ 267
>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 = 86.3 bits (212), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 64/239 (26%), Positives = 108/239 (45%), Gaps = 33/239 (13%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTL 59
MA+D V N++ L DE +A R+ LIP S+E +D + +C C + C +C + +
Sbjct: 39 MAVDDVYFIENNSPLYDEILAHRLALIPFMSEEALDTYRWPEECIECTENCEKCYTKIYI 98
Query: 60 DVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRA 119
+ + ++ R + + D+KS D VVP++ DI IV L Q++ L A
Sbjct: 99 EAE-APNEPRMIYSKDIKSEDPSVVPISG--------------DIPIVLLGTNQKISLEA 143
Query: 120 YAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEY----------SELDE 169
+ G+GKEHAK+ P + Y P + + P+ + +EL
Sbjct: 144 RLRLGYGKEHAKFIPVSLSVVRYYPKVEILANCEKAVNVCPEGVFELKDGKLSVKNELSC 203
Query: 170 TQHEAPYNW-------EAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221
T E + +KY +ES G+LKPE I++ + +K+ L+ +L
Sbjct: 204 TLCEECLRYCNGSIRISFVEDKYILEIESVGSLKPERILLEAGKSIIRKIEELEKKLVE 262
>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 = 85.9 bits (211), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 63/239 (26%), Positives = 110/239 (46%), Gaps = 33/239 (13%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCT-CVDFCSECSVEFTL 59
M+ID V N++ L DE +A R+ LIP TS+E +D + +C C + C +C + +
Sbjct: 39 MSIDDVYFIENNSPLYDEILAHRLALIPFTSEEALDTYRWPEECIDCTENCEKCYTKIYI 98
Query: 60 DVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRA 119
+ + + ++ + + + D+KS D +VP++ DI IV L Q++ L A
Sbjct: 99 EAEAL-NEPKMLYSKDIKSEDPSIVPISG--------------DIPIVLLGANQKISLEA 143
Query: 120 YAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEY----------SELDE 169
+ G+GKEHAK+ P + Y P + P+ + +EL
Sbjct: 144 RLRLGYGKEHAKFIPVSLAIVRYYPKVEILGNCEKGATVCPEGVFELKDGKLSVKNELAC 203
Query: 170 TQHEAPYNW-------EAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221
T E + + +KY +ES G+LKPE I++ + +K+ L+ +L
Sbjct: 204 TLCEECLRYCNGLIRISSVEDKYILELESVGSLKPERILLEAGKSIIRKIEELEKKLVE 262
>pdb|1HN0|A Chain A, Crystal Structure Of Chondroitin Abc Lyase I From Proteus
Vulgaris At 1.9 Angstroms Resolution
Length = 1021
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 10/64 (15%)
Query: 216 QTQLAHDRVFYVINEAPYNWE--------AKPNKYFFNVESAGALKPENIVIMGVTVLKQ 267
Q ++ DR+ + +++A Y W ++P F NV+ + PEN+ + +++Q
Sbjct: 205 QGEIYIDRIMFSVDDARYQWSDYQVKTRLSEPEIQFHNVKPQLPVTPENLA--AIDLIRQ 262
Query: 268 KLSN 271
+L N
Sbjct: 263 RLIN 266
>pdb|2E8Y|A Chain A, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168
pdb|2E8Y|B Chain B, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168
pdb|2E8Z|A Chain A, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168 Complexed With Alpha-Cyclodextrin
pdb|2E8Z|B Chain B, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168 Complexed With Alpha-Cyclodextrin
pdb|2E9B|A Chain A, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168 Complexed With Maltose
pdb|2E9B|B Chain B, Crystal Structure Of Pullulanase Type I From Bacillus
Subtilis Str. 168 Complexed With Maltose
Length = 718
Score = 27.3 bits (59), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 30/113 (26%), Positives = 50/113 (44%), Gaps = 8/113 (7%)
Query: 160 PKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQT-- 217
P ++++ +DE + YNW P +FF E + A P + T LKQ ++ L
Sbjct: 272 PVNDFAGVDEEKPLDAYNWGYNP-LHFFAPEGSYASNPHDPQTRK-TELKQMINTLHQHG 329
Query: 218 -QLAHDRVF-YVINEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQK 268
++ D VF +V +E YFF + G KP N +G + ++
Sbjct: 330 LRVILDVVFNHVYKRENSPFEKTVPGYFFRHDECG--KPSNGTGVGNDIASER 380
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
0.317 0.132 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,567,155
Number of Sequences: 62578
Number of extensions: 348978
Number of successful extensions: 867
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 830
Number of HSP's gapped (non-prelim): 26
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
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: 51 (24.3 bits)