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= 030241
(181 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 = 70.9 bits (172), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 44/116 (37%), Positives = 60/116 (51%), Gaps = 5/116 (4%)
Query: 6 CSDCKKHT-EVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGD-NDPVRVGGPT 63
C +CK + ++V S GD VC+ CGLVL +D SEWRTF+N+ + +DP RVG +
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGDDPSRVGEAS 83
Query: 64 NPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSD 117
NPLL LST I K F + L + Q + D + AF I + D
Sbjct: 84 NPLLDGNNLSTRIGKGETTDMRF-TKELNKAQGKNVMDKKDNEVQAAFAKITMLCD 138
>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 = 1e-06, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 9 CKKHTEVVF--DHSAGDTVCSECGLVLESHSIDETSEWRTFANESG 52
C H + + D+ AGD +C ECGLV+ ID SEWRTF+N+
Sbjct: 15 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSNDKA 60
>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 = 47.4 bits (111), Expect = 4e-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 = 42.7 bits (99), Expect = 1e-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|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 = 32.0 bits (71), Expect = 0.21, 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 = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 5 FCSDCKKHTEVVFDHSA-GDTVCSECGLVLESHSIDE 40
CS+C+ T ++ S GD VC+ CGL + H ++
Sbjct: 6 VCSNCQTSTTTLWRRSPMGDPVCNACGLYYKLHQVNR 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 = 31.6 bits (70), Expect = 0.28, 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|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 = 30.0 bits (66), Expect = 0.65, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 6 CSDCKKHTEVVFDHSA-GDTVCSECGLVLESHSID 39
CS+C+ T ++ S GD VC+ CGL + H ++
Sbjct: 7 CSNCQTSTTTLWRRSPMGDPVCNACGLYYKLHQVN 41
>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 = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 102 DRGLILAFKTIATMSDRIGQMRYI 125
DR ++ AFK I TM+DRI R I
Sbjct: 2 DRAMMNAFKEITTMADRINLPRNI 25
>pdb|2PUK|A Chain A, Crystal Srtucture Of The Binary Complex Between
Ferredoxin: Thioredoxin Reductase And Thioredoxin M
pdb|2PUK|E Chain E, Crystal Srtucture Of The Binary Complex Between
Ferredoxin: Thioredoxin Reductase And Thioredoxin M
pdb|2PUO|A Chain A, Crystal Srtucture Of The Nem Modified
Ferredoxin:thioredoxin Reductase
Length = 109
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 135 EAEIKTHYWLLACTLLVDKKTSHALLRVQP 164
EAE+K +W C + ++K H +L + P
Sbjct: 58 EAEVKNTFWNCPCVPMRERKECHCMLFLTP 87
>pdb|1DJ7|A Chain A, Crystal Structure Of Ferredoxin Thioredoxin Reductase
Length = 117
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 135 EAEIKTHYWLLACTLLVDKKTSHALLRVQP 164
EAE+K +W C + ++K H +L + P
Sbjct: 64 EAEVKNTFWNCPCVPMRERKECHCMLFLTP 93
>pdb|2PVD|A Chain A, Crystal Srtucture Of The Reduced Ferredoxin:thioredoxin
Reductase
Length = 107
Score = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 135 EAEIKTHYWLLACTLLVDKKTSHALLRVQP 164
EAE+K +W C + ++K H +L + P
Sbjct: 54 EAEVKNTFWNCPCVPMRERKECHCMLFLTP 83
>pdb|2PU9|A Chain A, Crystal Srtucture Of The Binary Complex Between
Ferredoxin: Thioredoxin Reductase And Thioredoxin F
pdb|2PVO|A Chain A, Crystal Srtucture Of The Ternary Complex Between
Thioredoxin F, Ferredoxin, And Ferredoxin: Thioredoxin
Reductase
Length = 110
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 135 EAEIKTHYWLLACTLLVDKKTSHALLRVQP 164
EAE+K +W C + ++K H +L + P
Sbjct: 57 EAEVKNTFWNCPCVPMRERKECHCMLFLTP 86
>pdb|2PVG|A Chain A, Crystal Srtucture Of The Binary Complex Between Ferredoxin
And Ferredoxin:thioredoxin Reductase
Length = 108
Score = 28.1 bits (61), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 135 EAEIKTHYWLLACTLLVDKKTSHALLRVQP 164
EAE+K +W C + ++K H +L + P
Sbjct: 57 EAEVKNTFWNCPCVPMRERKECHCMLFLTP 86
>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 = 6.1, 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|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 = 26.9 bits (58), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 29/117 (24%), Positives = 41/117 (35%), Gaps = 3/117 (2%)
Query: 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTN 64
F DC +VV S GD V E + + + A V +
Sbjct: 105 FAPDCLNAADVVSKMSPGDVVLLENVRFYKEEGSKKAKDREAMAKILASYGDVYISDAFG 164
Query: 65 PLLADGGLSTVIAK--PNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRI 119
D T I K NGA+G + + + NP R L+ A A +SD+I
Sbjct: 165 TAHRDSATMTGIPKILGNGAAGYLMEKEISYFAKVLGNPPRPLV-AIVGGAKVSDKI 220
>pdb|1WFK|A Chain A, Fyve Domain Of Fyve Domain Containing 19 Protein From
Mus Musculus
Length = 88
Score = 26.6 bits (57), Expect = 7.7, 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
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
0.320 0.135 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,654,446
Number of Sequences: 62578
Number of extensions: 221751
Number of successful extensions: 395
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 383
Number of HSP's gapped (non-prelim): 19
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 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)