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= 030129
(182 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 = 70.5 bits (171), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 46/117 (39%), Positives = 61/117 (52%), Gaps = 7/117 (5%)
Query: 6 CSDCKKHT-EVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANE--SGDNDPVRVGGP 62
C +CK + ++V S GD VC+ CGLVL +D SEWRTF+N+ +GD DP RVG
Sbjct: 24 CPECKVYPPKIVERFSEGDVVCALCGLVLSDKLVDTRSEWRTFSNDDHNGD-DPSRVGEA 82
Query: 63 TNPLLADGGLSTVIAKPNGASGEFLSSSLGRWQNRG--SNPDRGLILAFKTIATMSD 117
+NPLL LST I K F + L + Q + D + AF I + D
Sbjct: 83 SNPLLDGNNLSTRIGKGETTDMRF-TKELNKAQGKNVMDKKDNEVQAAFAKITMLCD 138
>pdb|1DL6|A Chain A, Solution Structure Of Human Tfiib N-Terminal Domain
Length = 58
Score = 50.1 bits (118), Expect = 7e-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: 14 CPNHPDAILVEDYRAGDMICPECGLVVGDRVIDVGSEWRTFSND 57
>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 = 49.3 bits (116), Expect = 1e-06, Method: Composition-based stats.
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|3K1F|M Chain M, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
Length = 197
Score = 48.1 bits (113), Expect = 3e-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 = 43.1 bits (100), Expect = 8e-05, 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 = 32.3 bits (72), Expect = 0.15, 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 = 32.0 bits (71), Expect = 0.18, 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 = 32.0 bits (71), Expect = 0.22, 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 = 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|1YIS|A Chain A, Structural Genomics Of Caenorhabditis Elegans:
Adenylosuccinate Lyase
Length = 478
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 34/119 (28%), Positives = 51/119 (42%), Gaps = 22/119 (18%)
Query: 59 VGGPTNPL--LADGGLSTVIAKPNGASGEFLSSSLGRWQNRGSNPDRGLILAFKTIATMS 116
+ P L LAD GL L S GR R PD ++L + + T
Sbjct: 308 INAPQEALTILADQGLERT-----------LDDSAGR---RXLIPD--VLLTAEALLTTL 351
Query: 117 DRIGQMRYIRRWKIKSLVEAEIKTHYWLLACTLL----VDKKTSHALLRKSALSPMELQ 171
I + ++ +K +VE EI A L VD++ +HA++RK+AL +LQ
Sbjct: 352 QNIFEGLSVQTDNVKKIVEDEIAFLGLEKAXXXLTEEGVDRQQAHAVIRKTALEAKQLQ 410
>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 = 28.5 bits (62), Expect = 2.4, 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|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 = 27.3 bits (59), Expect = 5.0, 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 = 5.9, 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 = 26.9 bits (58), Expect = 7.0, 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 = 8.7, 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
0.317 0.131 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,546,458
Number of Sequences: 62578
Number of extensions: 217530
Number of successful extensions: 405
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 397
Number of HSP's gapped (non-prelim): 18
length of query: 182
length of database: 14,973,337
effective HSP length: 93
effective length of query: 89
effective length of database: 9,153,583
effective search space: 814668887
effective search space used: 814668887
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)