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= psy6534
(309 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1C9B|A Chain A, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|E Chain E, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|I Chain I, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|M Chain M, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
pdb|1C9B|Q Chain Q, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
Core Domain Complex Bound To An Extended, Modified
Adenoviral Major Late Promoter (Admlp)
Length = 207
Score = 328 bits (841), Expect = 2e-90, Method: Compositional matrix adjust.
Identities = 157/207 (75%), Positives = 175/207 (84%)
Query: 103 SDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACR 162
SDRA++NA +EI +MADRINL + IVDR NNLFKQV++ K+LKGR+NDAIASACLYIACR
Sbjct: 1 SDRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACR 60
Query: 163 QEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQ 222
QEGVPRTFKEICAVS+ISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNL LP VQ
Sbjct: 61 QEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQ 120
Query: 223 KAATHIARKAVELDIVPGRSPIXXXXXXXXXXXXXXXDKRSQKEIGDIAGVAEVTIRQSY 282
AATHIARKAVELD+VPGRSPI +KR+QKEIGDIAGVA+VTIRQSY
Sbjct: 121 MAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSY 180
Query: 283 KLMYPHASKLFPQDFVFHTPIHELPQL 309
+L+YP A LFP DF F TP+ +LPQL
Sbjct: 181 RLIYPRAPDLFPTDFKFDTPVDKLPQL 207
>pdb|1TFB|A Chain A, Nmr Studies Of Human General Transcription Factor Tfiib:
Dynamics And Interaction With Vp16 Activation Domain, 20
Structures
Length = 208
Score = 325 bits (833), Expect = 2e-89, Method: Compositional matrix adjust.
Identities = 155/207 (74%), Positives = 174/207 (84%)
Query: 103 SDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACR 162
+ RA++NA +EI +MADRINL + IVDR NNLFKQV++ K+LKGR+NDAIASACLYIACR
Sbjct: 2 ASRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACR 61
Query: 163 QEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQ 222
QEGVPRTFKEICAVS+ISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNL LP VQ
Sbjct: 62 QEGVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQ 121
Query: 223 KAATHIARKAVELDIVPGRSPIXXXXXXXXXXXXXXXDKRSQKEIGDIAGVAEVTIRQSY 282
AATHIARKAVELD+VPGRSPI +KR+QKEIGDIAGVA+VTIRQSY
Sbjct: 122 MAATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSY 181
Query: 283 KLMYPHASKLFPQDFVFHTPIHELPQL 309
+L+YP A LFP DF F TP+ +LPQL
Sbjct: 182 RLIYPRAPDLFPTDFKFDTPVDKLPQL 208
>pdb|2PHG|A Chain A, Model For Vp16 Binding To Tfiib
Length = 206
Score = 325 bits (832), Expect = 3e-89, Method: Compositional matrix adjust.
Identities = 155/205 (75%), Positives = 173/205 (84%)
Query: 105 RALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQE 164
RA++NA +EI +MADRINL + IVDR NNLFKQV++ K+LKGR+NDAIASACLYIACRQE
Sbjct: 2 RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 61
Query: 165 GVPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKA 224
GVPRTFKEICAVS+ISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNL LP VQ A
Sbjct: 62 GVPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMA 121
Query: 225 ATHIARKAVELDIVPGRSPIXXXXXXXXXXXXXXXDKRSQKEIGDIAGVAEVTIRQSYKL 284
ATHIARKAVELD+VPGRSPI +KR+QKEIGDIAGVA+VTIRQSY+L
Sbjct: 122 ATHIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRL 181
Query: 285 MYPHASKLFPQDFVFHTPIHELPQL 309
+YP A LFP DF F TP+ +LPQL
Sbjct: 182 IYPRAPDLFPTDFKFDTPVDKLPQL 206
>pdb|1VOL|A Chain A, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT
Ternary Complex
Length = 204
Score = 317 bits (811), Expect = 6e-87, Method: Compositional matrix adjust.
Identities = 151/204 (74%), Positives = 170/204 (83%)
Query: 106 ALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEG 165
A++NA +EI +MADRINL + VDR NNLF+Q ++ K+LKGR+NDAIASACLYIACRQEG
Sbjct: 1 AMMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEG 60
Query: 166 VPRTFKEICAVSKISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLSLPNMVQKAA 225
VPRTFKEICAVS+ISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNL LP VQ AA
Sbjct: 61 VPRTFKEICAVSRISKKEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAA 120
Query: 226 THIARKAVELDIVPGRSPIXXXXXXXXXXXXXXXDKRSQKEIGDIAGVAEVTIRQSYKLM 285
THIARKAVELD+VPGRSPI +KR+QKEIGDIAGVA+VTIRQSY+L+
Sbjct: 121 THIARKAVELDLVPGRSPISVAAAAIYMASQASAEKRTQKEIGDIAGVADVTIRQSYRLI 180
Query: 286 YPHASKLFPQDFVFHTPIHELPQL 309
YP A LFP DF F TP+ +LPQL
Sbjct: 181 YPRAPDLFPTDFKFDTPVDKLPQL 204
>pdb|3K7A|M Chain M, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|4BBR|M Chain M, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|M Chain M, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 345
Score = 174 bits (441), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 108/311 (34%), Positives = 163/311 (52%), Gaps = 17/311 (5%)
Query: 1 MNINKVC--CYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNE-KSGVDP 57
+NI C C +P ++E + GD +C+ CGLV+ D+++D SEWRTFSN+ +G DP
Sbjct: 18 LNIVLTCPECKVYP-PKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDP 76
Query: 58 SRVGGPENPLLNGSDLSTMIGPGRGDASFDGFGMSKYQNRRTMNSSDRALLNAIREINSM 117
SRVG NPLL+G++LST IG G ++K Q + M+ D + A +I +
Sbjct: 77 SRVGEASNPLLDGNNLSTRIGKGETTDMRFTKELNKAQGKNVMDKKDNEVQAAFAKITML 136
Query: 118 ADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEICAVS 177
D L K + D A +K HD K LKG+S ++I +A + I CR+ V RTFKEI ++
Sbjct: 137 CDAAELPKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFKEIQSLI 196
Query: 178 KISKKEIGRCFKL---ILKA------LETSVDLITTGD---FMSRFCSNLSLPNMVQKAA 225
+ KE G+ + IL+ L+ D ++ ++ RFCS+L LP V +A
Sbjct: 197 HVKTKEFGKTLNIMKNILRGKSEDGFLKIDTDNMSGAQNLTYIPRFCSHLGLPMQVTTSA 256
Query: 226 THIARKAVELDIVPGRSPIXXXXXXXXXXXXXXXDKRSQKEIGDIAGVAEVTIRQSYKLM 285
+ A+K E+ + G+SPI + ++G V E TI+ YK++
Sbjct: 257 EYTAKKCKEIKEIAGKSPITIAVVSIYLNILLFQIPITAAKVGQTLQVTEGTIKSGYKIL 316
Query: 286 YPHASKLF-PQ 295
Y H KL PQ
Sbjct: 317 YEHRDKLVDPQ 327
>pdb|1AIS|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box
Complex From Pyrococcus Woesei
Length = 200
Score = 103 bits (256), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 53/185 (28%), Positives = 102/185 (55%), Gaps = 2/185 (1%)
Query: 101 NSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIA 160
++++R L A+ E++ + ++ L + + + A L+++ ++GRS +++ +AC+Y A
Sbjct: 3 DAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAA 62
Query: 161 CRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVD--LITTGDFMSRFCSNLSLP 218
CR VPRT EI ++++ KKEIGR ++ I + L + + D++++F L L
Sbjct: 63 CRLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLS 122
Query: 219 NMVQKAATHIARKAVELDIVPGRSPIXXXXXXXXXXXXXXXDKRSQKEIGDIAGVAEVTI 278
V++ A I +A + + G+SP +KR+Q+E+ ++A V EVT+
Sbjct: 123 EKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTV 182
Query: 279 RQSYK 283
R YK
Sbjct: 183 RNRYK 187
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 46/86 (53%)
Query: 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEI 173
+N AD + L++ + RA + + + G+S + +A LYIA EG RT +E+
Sbjct: 112 VNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREV 171
Query: 174 CAVSKISKKEIGRCFKLILKALETSV 199
V+++++ + +K +++ L+ V
Sbjct: 172 AEVARVTEVTVRNRYKELVEKLKIKV 197
Score = 35.0 bits (79), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 6/97 (6%)
Query: 208 MSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPIXXXXXXXXXXXXXXXDKRSQKEI 267
+ R + L LP V++ A + R+AV ++ GRS R+ EI
Sbjct: 16 LDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEI 75
Query: 268 GDIAGVAEVTIRQSYKLMYPHAS----KLF--PQDFV 298
DIA V + I +SY+ + + + KLF P D+V
Sbjct: 76 ADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYV 112
>pdb|1D3U|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA-
Box Complex From Pyrococcus Woesei
Length = 201
Score = 102 bits (255), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 53/185 (28%), Positives = 102/185 (55%), Gaps = 2/185 (1%)
Query: 101 NSSDRALLNAIREINSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIA 160
++++R L A+ E++ + ++ L + + + A L+++ ++GRS +++ +AC+Y A
Sbjct: 4 DAAERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAA 63
Query: 161 CRQEGVPRTFKEICAVSKISKKEIGRCFKLILKALETSVD--LITTGDFMSRFCSNLSLP 218
CR VPRT EI ++++ KKEIGR ++ I + L + + D++++F L L
Sbjct: 64 CRLLKVPRTLDEIADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYVNKFADELGLS 123
Query: 219 NMVQKAATHIARKAVELDIVPGRSPIXXXXXXXXXXXXXXXDKRSQKEIGDIAGVAEVTI 278
V++ A I +A + + G+SP +KR+Q+E+ ++A V EVT+
Sbjct: 124 EKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTV 183
Query: 279 RQSYK 283
R YK
Sbjct: 184 RNRYK 188
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 46/86 (53%)
Query: 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQEGVPRTFKEI 173
+N AD + L++ + RA + + + G+S + +A LYIA EG RT +E+
Sbjct: 113 VNKFADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREV 172
Query: 174 CAVSKISKKEIGRCFKLILKALETSV 199
V+++++ + +K +++ L+ V
Sbjct: 173 AEVARVTEVTVRNRYKELVEKLKIKV 198
Score = 35.0 bits (79), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 6/97 (6%)
Query: 208 MSRFCSNLSLPNMVQKAATHIARKAVELDIVPGRSPIXXXXXXXXXXXXXXXDKRSQKEI 267
+ R + L LP V++ A + R+AV ++ GRS R+ EI
Sbjct: 17 LDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEI 76
Query: 268 GDIAGVAEVTIRQSYKLMYPHAS----KLF--PQDFV 298
DIA V + I +SY+ + + + KLF P D+V
Sbjct: 77 ADIARVDKKEIGRSYRFIARNLNLTPKKLFVKPTDYV 113
>pdb|1RLY|A Chain A, Rdc-Derived Models Of The Zinc Ribbon Domain Of Human
General Transcription Tfiib (Zinc Bound Structures)
pdb|1RO4|A Chain A, Rdc-Derived Models Of The Zinc Ribbon Domain Of Human
General Transcription Factor Tfiib (Zinc Free
Structures)
Length = 60
Score = 88.6 bits (218), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 39/51 (76%), Positives = 44/51 (86%)
Query: 3 INKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKS 53
+ +V C HPDA L+EDYRAGD IC ECGLVVGDRVIDVGSEWRTFSN+K+
Sbjct: 10 LPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKA 60
>pdb|1DL6|A Chain A, Solution Structure Of Human Tfiib N-Terminal Domain
Length = 58
Score = 87.8 bits (216), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 39/50 (78%), Positives = 43/50 (86%)
Query: 3 INKVCCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEK 52
+ +V C HPDA L+EDYRAGD IC ECGLVVGDRVIDVGSEWRTFSN+K
Sbjct: 9 LPRVTCPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDK 58
>pdb|3K1F|M Chain M, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
Length = 197
Score = 50.1 bits (118), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 34/52 (65%), Gaps = 3/52 (5%)
Query: 1 MNINKVC--CYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSN 50
+NI C C +P ++E + GD +C+ CGLV+ D+++D SEWRTFSN
Sbjct: 18 LNIVLTCPECKVYPPK-IVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSN 68
>pdb|1PFT|A Chain A, N-Terminal Domain Of Tfiib, Nmr
Length = 50
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/50 (42%), Positives = 30/50 (60%), Gaps = 5/50 (10%)
Query: 1 MNINKVC--CYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTF 48
+N KVC C A LI D G+ +C++CG V+ + +ID+G EWR F
Sbjct: 2 VNKQKVCPAC---ESAELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAF 48
>pdb|1ZP2|A Chain A, Structure Of The Mediator Subunit Cyclin C
Length = 235
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 114 INSMADRINLTKTIVDRANNLFKQVHDGKNL-KGRSNDAIASACLYIACRQEGVPRTFKE 172
+ + DR+ L + ++ A L ++ KN KG S +A+ + C+Y++C+ E P +
Sbjct: 35 VQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKGFSLEALVATCIYLSCKVEECPVHIRT 94
Query: 173 IC 174
IC
Sbjct: 95 IC 96
>pdb|3RGF|B Chain B, Crystal Structure Of Human Cdk8CYCC
Length = 285
Score = 29.6 bits (65), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 35/77 (45%), Gaps = 2/77 (2%)
Query: 114 INSMADRINLTKTIVDRANNLFKQVHDGKNLKGRSNDAIASACLYIACRQE--GVPRTFK 171
I ++ + + L + ++ A FK+ + +LK +A C+++A + E GV +
Sbjct: 50 IQALGEHLKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTR 109
Query: 172 EICAVSKISKKEIGRCF 188
I A + + K F
Sbjct: 110 LIAAATSVLKTRFSYAF 126
>pdb|3A0F|A Chain A, The Crystal Structure Of Geotrichum Sp. M128 Xyloglucanase
Length = 763
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 7 CCYEHPDAPLIEDYRAGDQICSECGLVVGDRVIDVGSEWRTFSNEKSGVDPS--RVGGPE 64
CC+ + P+ + RAG+ S G+ + D G+ + + S ++P+ +G P+
Sbjct: 630 CCWTYTGTPVTSNLRAGELWVSVKGVGI-YHSTDFGNTFTALAGSGSSLNPAVFSIGAPQ 688
Query: 65 NP 66
P
Sbjct: 689 TP 690
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 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,587,948
Number of Sequences: 62578
Number of extensions: 331654
Number of successful extensions: 626
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 595
Number of HSP's gapped (non-prelim): 25
length of query: 309
length of database: 14,973,337
effective HSP length: 99
effective length of query: 210
effective length of database: 8,778,115
effective search space: 1843404150
effective search space used: 1843404150
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)