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= 030755
(172 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 103 bits (256), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 63/168 (37%), Positives = 91/168 (54%), Gaps = 5/168 (2%)
Query: 6 CSDCKKHT-EVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGD-NDPVRVGGPT 63
C +CK + ++V S GD VC+ CGLVL +D SEWRTF+N+ + +DP RVG +
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEAS 83
Query: 64 NPLLADGGLSTVIAKPNGASGEFLSSSLGRWQ--NRGSNPDRGLILAFKTIATMSDRLGL 121
NPLL LST I K F + L + Q N D + AF I + D L
Sbjct: 84 NPLLDGNNLSTRIGKGETTDMRF-TKELNKAQGKNVMDKKDNEVQAAFAKITMLCDAAEL 142
Query: 122 VATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK 169
+KD A E YK D+K+ +G++ ++++AA + I CR+ + RT K
Sbjct: 143 PKIVKDCAKEAYKLCHDEKTLKGKSMESIMAASILIGCRRAEVARTFK 190
>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 = 82.0 bits (201), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 38/68 (55%), Positives = 49/68 (72%)
Query: 102 DRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQ 161
DR ++ AFK I TM+DR+ L I DR N ++K+V +QKS +GR DA+ +ACLYIACRQ
Sbjct: 2 DRAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQ 61
Query: 162 EDKPRTVK 169
E PRT K
Sbjct: 62 EGVPRTFK 69
>pdb|2PHG|A Chain A, Model For Vp16 Binding To Tfiib
Length = 206
Score = 79.7 bits (195), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 37/67 (55%), Positives = 48/67 (71%)
Query: 103 RGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQE 162
R ++ AFK I TM+DR+ L I DR N ++K+V +QKS +GR DA+ +ACLYIACRQE
Sbjct: 2 RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 61
Query: 163 DKPRTVK 169
PRT K
Sbjct: 62 GVPRTFK 68
>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 = 79.7 bits (195), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 37/67 (55%), Positives = 48/67 (71%)
Query: 103 RGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQE 162
R ++ AFK I TM+DR+ L I DR N ++K+V +QKS +GR DA+ +ACLYIACRQE
Sbjct: 4 RAMMNAFKEITTMADRINLPRNIVDRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQE 63
Query: 163 DKPRTVK 169
PRT K
Sbjct: 64 GVPRTFK 70
>pdb|1VOL|A Chain A, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT
Ternary Complex
Length = 204
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 33/66 (50%), Positives = 45/66 (68%)
Query: 104 GLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQED 163
++ AFK I TM+DR+ L DR N ++++ +QKS +GR DA+ +ACLYIACRQE
Sbjct: 1 AMMNAFKEITTMADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEG 60
Query: 164 KPRTVK 169
PRT K
Sbjct: 61 VPRTFK 66
>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 = 49.7 bits (117), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 28/44 (63%), Gaps = 2/44 (4%)
Query: 9 CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANE 50
C H + + D+ AGD +C ECGLV+ ID SEWRTF+N+
Sbjct: 15 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 58
>pdb|1DL6|A Chain A, Solution Structure Of Human Tfiib N-Terminal Domain
Length = 58
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 28/44 (63%), Gaps = 2/44 (4%)
Query: 9 CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANE 50
C H + + D+ AGD +C ECGLV+ ID SEWRTF+N+
Sbjct: 14 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57
>pdb|3K1F|M Chain M, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
Length = 197
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/45 (48%), Positives = 29/45 (64%), Gaps = 1/45 (2%)
Query: 6 CSDCKKHT-EVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFAN 49
C +CK + ++V S GD VC+ CGLVL +D SEWRTF+N
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSN 68
>pdb|1PFT|A Chain A, N-Terminal Domain Of Tfiib, Nmr
Length = 50
Score = 42.0 bits (97), Expect = 2e-04, Method: Composition-based stats.
Identities = 17/42 (40%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 6 CSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTF 47
C C+ E+++D G+ VC++CG V+E + ID EWR F
Sbjct: 8 CPACES-AELIYDPERGEIVCAKCGYVIEENIIDMGPEWRAF 48
>pdb|1AIS|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BTATA-Box
Complex From Pyrococcus Woesei
Length = 200
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 39/67 (58%)
Query: 102 DRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQ 161
+R L A + ++ +L L +++ A +Y++ + RGR+ ++++AAC+Y ACR
Sbjct: 6 ERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRL 65
Query: 162 EDKPRTV 168
PRT+
Sbjct: 66 LKVPRTL 72
Score = 33.1 bits (74), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 27/101 (26%), Positives = 46/101 (45%), Gaps = 6/101 (5%)
Query: 72 LSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANE 131
++ V K G S F++ +N P + + + +D LGL ++ RA E
Sbjct: 78 IARVDKKEIGRSYRFIA------RNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIE 131
Query: 132 IYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA 172
I + + + G++ L+AA LYIA E + RT + A
Sbjct: 132 ILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVA 172
>pdb|1D3U|B Chain B, Tata-Binding ProteinTRANSCRIPTION FACTOR (II)BBRE+TATA-
Box Complex From Pyrococcus Woesei
Length = 201
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 39/67 (58%)
Query: 102 DRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQ 161
+R L A + ++ +L L +++ A +Y++ + RGR+ ++++AAC+Y ACR
Sbjct: 7 ERNLAFALSELDRITAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRL 66
Query: 162 EDKPRTV 168
PRT+
Sbjct: 67 LKVPRTL 73
Score = 33.1 bits (74), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 27/101 (26%), Positives = 46/101 (45%), Gaps = 6/101 (5%)
Query: 72 LSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANE 131
++ V K G S F++ +N P + + + +D LGL ++ RA E
Sbjct: 79 IARVDKKEIGRSYRFIA------RNLNLTPKKLFVKPTDYVNKFADELGLSEKVRRRAIE 132
Query: 132 IYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKGTA 172
I + + + G++ L+AA LYIA E + RT + A
Sbjct: 133 ILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVA 173
>pdb|1ZP2|A Chain A, Structure Of The Mediator Subunit Cyclin C
Length = 235
Score = 35.4 bits (80), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 3/85 (3%)
Query: 86 FLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSS-RG 144
FLS+ L + + D I +K + T DRL L + A + ++ +K+ +G
Sbjct: 11 FLSTDLESLEPTCLSKDT--IYQWKVVQTFGDRLRLRQRVLATAIVLLRRYMLKKNEEKG 68
Query: 145 RNQDALLAACLYIACRQEDKPRTVK 169
+ +AL+A C+Y++C+ E+ P ++
Sbjct: 69 FSLEALVATCIYLSCKVEECPVHIR 93
>pdb|3DFV|D Chain D, Adjacent Gata Dna Binding
pdb|3DFV|C Chain C, Adjacent Gata Dna Binding
pdb|3DFX|A Chain A, Opposite Gata Dna Binding
pdb|3DFX|B Chain B, Opposite Gata Dna Binding
Length = 63
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 6 CSDCKKHTEVVFDHSA-GDTVCSECGLVLESHSIDE 40
C++C+ T ++ +A GD VC+ CGL + H+I+
Sbjct: 10 CANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINR 45
>pdb|3GAT|A Chain A, Solution Nmr Structure Of The C-Terminal Domain Of
Chicken Gata-1 Bound To Dna, 34 Structures
pdb|2GAT|A Chain A, Solution Structure Of The C-Terminal Domain Of Chicken
Gata- 1 Bound To Dna, Nmr, Regularized Mean Structure
Length = 66
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGLVLESHSIDE 40
CS+C+ T ++ S GD VC+ CGL + H ++
Sbjct: 5 TVCSNCQTSTTTLWRRSPMGDPVCNACGLYYKLHQVNR 42
>pdb|1GAT|A Chain A, Solution Structure Of The Specific Dna Complex Of The
Zinc Containing Dna Binding Domain Of The Erythroid
Transcription Factor Gata-1 By Multidimensional Nmr
pdb|1GAU|A Chain A, Solution Structure Of The Specific Dna Complex Of The
Zinc Containing Dna Binding Domain Of The Erythroid
Transcription Factor Gata-1 By Multidimensional Nmr
Length = 60
Score = 32.0 bits (71), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGLVLESHSIDE 40
CS+C+ T ++ S GD VC+ CGL + H ++
Sbjct: 5 TVCSNCQTSTTTLWRRSPMGDPVCNACGLYYKLHQVNR 42
>pdb|4HC7|A Chain A, Crystal Structure Of The Full Dna Binding Domain Of
Gata3-Complex 2
pdb|4HC7|B Chain B, Crystal Structure Of The Full Dna Binding Domain Of
Gata3-Complex 2
pdb|4HC9|A Chain A, Dna Binding By Gata Transcription Factor-Complex 3
pdb|4HCA|A Chain A, Dna Binding By Gata Transcription Factor-Complex 1
Length = 115
Score = 32.0 bits (71), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 6 CSDCKKHTEVVFDHSA-GDTVCSECGLVLESHSIDE 40
C++C+ T ++ +A GD VC+ CGL + H+I+
Sbjct: 62 CANCQTTTTTLWRRNANGDPVCNACGLYYKLHNINR 97
>pdb|13PK|A Chain A, Ternary Complex Of Phosphoglycerate Kinase From
Trypanosoma Brucei
pdb|13PK|B Chain B, Ternary Complex Of Phosphoglycerate Kinase From
Trypanosoma Brucei
pdb|13PK|C Chain C, Ternary Complex Of Phosphoglycerate Kinase From
Trypanosoma Brucei
pdb|13PK|D Chain D, Ternary Complex Of Phosphoglycerate Kinase From
Trypanosoma Brucei
pdb|16PK|A Chain A, Phosphoglycerate Kinase From Trypanosoma Brucei
Bisubstrate Analog
Length = 415
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 30/130 (23%), Positives = 47/130 (36%), Gaps = 3/130 (2%)
Query: 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTN 64
F DC +VV S GD V E + + + A V +
Sbjct: 105 FAPDCLNAADVVSKMSPGDVVLLENVRFYKEEGSKKAKDREAMAKILASYGDVYISDAFG 164
Query: 65 PLLADGGLSTVIAKP--NGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLV 122
D T I K NGA+G + + + NP R L+ A A +SD++ L+
Sbjct: 165 TAHRDSATMTGIPKILGNGAAGYLMEKEISYFAKVLGNPPRPLV-AIVGGAKVSDKIQLL 223
Query: 123 ATIKDRANEI 132
+ R + +
Sbjct: 224 DNMLQRIDYL 233
>pdb|7GAT|A Chain A, Solution Nmr Structure Of The L22v Mutant Dna Binding
Domain Of Area Complexed To A 13 Bp Dna Containing A
Tgata Site, 34 Structures
pdb|6GAT|A Chain A, Solution Nmr Structure Of The L22v Mutant Dna Binding
Domain Of Area Complexed To A 13 Bp Dna Containing A
Tgata Site, Regularized Mean Structure
Length = 66
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 6 CSDCKKHTEVVFDHSA-GDTVCSECGLVLESHSI 38
C++C T V+ + G +C+ CGL L+ H +
Sbjct: 12 CTNCFTQTTPVWRRNPEGQPLCNACGLFLKLHGV 45
>pdb|3VD6|C Chain C, Both Zn Fingers Of Gata1 Bound To Palindromic Dna
Recognition Site, P21 Crystal Form
pdb|3VEK|C Chain C, Both Zn Fingers Of Gata1 Bound To Palindromic Dna
Recognition Site, P1 Crystal Form
pdb|3VEK|F Chain F, Both Zn Fingers Of Gata1 Bound To Palindromic Dna
Recognition Site, P1 Crystal Form
Length = 119
Score = 26.9 bits (58), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 8/22 (36%), Positives = 15/22 (68%)
Query: 19 HSAGDTVCSECGLVLESHSIDE 40
+++GD VC+ CGL + H ++
Sbjct: 73 NASGDPVCNACGLYFKLHQVNR 94
>pdb|4AQ7|A Chain A, Ternary Complex Of E. Coli Leucyl-Trna Synthetase,
Trna(Leu) And Leucyl-Adenylate Analogue In The
Aminoacylation Conformation
pdb|4AQ7|D Chain D, Ternary Complex Of E. Coli Leucyl-Trna Synthetase,
Trna(Leu) And Leucyl-Adenylate Analogue In The
Aminoacylation Conformation
pdb|4ARC|A Chain A, Ternary Complex Of E. Coli Leucyl-Trna Synthetase,
Trna(Leu) And Leucine In The Editing Conformation
pdb|4ARI|A Chain A, Ternary Complex Of E. Coli Leucyl-Trna Synthetase,
Trna(Leu) And The Benzoxaborole An2679 In The Editing
Conformation
pdb|4AS1|A Chain A, Ternary Complex Of E. Coli Leucyl-Trna Synthetase,
Trna(Leu) And The Benzoxaborole An2679 In The Editing
Conformation
pdb|3ZGZ|A Chain A, Ternary Complex Of E. Coli Leucyl-trna Synthetase,
Trna(leu) And Toxic Moiety From Agrocin 84 (tm84) In
Aminoacylation- Like Conformation
pdb|3ZGZ|D Chain D, Ternary Complex Of E. Coli Leucyl-trna Synthetase,
Trna(leu) And Toxic Moiety From Agrocin 84 (tm84) In
Aminoacylation- Like Conformation
Length = 880
Score = 26.9 bits (58), Expect = 5.4, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 7/50 (14%)
Query: 110 KTIATMSDRLG-------LVATIKDRANEIYKKVEDQKSSRGRNQDALLA 152
KTIA ++D +G +A I + N++ K D + R Q+ALLA
Sbjct: 727 KTIAKVTDDIGRRQTFNTAIAAIMELMNKLAKAPTDGEQDRALMQEALLA 776
>pdb|1WFK|A Chain A, Fyve Domain Of Fyve Domain Containing 19 Protein From
Mus Musculus
Length = 88
Score = 26.9 bits (58), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 5/44 (11%)
Query: 4 AFCSDCKKHTEVVFDHSAGDT---VCSECGLVLESHSIDETSEW 44
AFC+ C + +V AG+T VC +C +L S D S+W
Sbjct: 34 AFCNGCLSFSALV--PRAGNTQQKVCKQCHTILTRGSSDNASKW 75
>pdb|1QXF|A Chain A, Solution Structure Of 30s Ribosomal Protein S27e From
Archaeoglobus Fulgidus: Gr2, A Nesg Target Protein
Length = 66
Score = 26.6 bits (57), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 6 CSDCKKHTEVVFDHSAGDTVCSECG 30
C DC+ H +V+FDH + C CG
Sbjct: 10 CPDCE-HEQVIFDHPSTIVKCIICG 33
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
0.315 0.131 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,382,722
Number of Sequences: 62578
Number of extensions: 213962
Number of successful extensions: 340
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 319
Number of HSP's gapped (non-prelim): 30
length of query: 172
length of database: 14,973,337
effective HSP length: 92
effective length of query: 80
effective length of database: 9,216,161
effective search space: 737292880
effective search space used: 737292880
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)