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= 033001
(129 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GAT|A Chain A, Solution Nmr Structure Of The Wild Type Dna Binding
Domain Of Area Complexed To A 13bp Dna Containing A
Cgata Site, Regularized Mean Structure
pdb|5GAT|A Chain A, Solution Nmr Structure Of The Wild Type Dna Binding
Domain Of Area Complexed To A 13bp Dna Containing A
Cgata Site, 35 Structures
Length = 66
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 56
+C +C T TPLWR P G + LCNACG+
Sbjct: 11 TCTNCFTQTTPLWRRNPEG-QPLCNACGL 38
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 56
+C +C T TP+WR P G + LCNACG+
Sbjct: 11 TCTNCFTQTTPVWRRNPEG-QPLCNACGL 38
>pdb|2VUS|I Chain I, Crystal Structure Of Unliganded Nmra-Area Zinc Finger
Complex
pdb|2VUS|J Chain J, Crystal Structure Of Unliganded Nmra-Area Zinc Finger
Complex
pdb|2VUS|K Chain K, Crystal Structure Of Unliganded Nmra-Area Zinc Finger
Complex
pdb|2VUS|L Chain L, Crystal Structure Of Unliganded Nmra-Area Zinc Finger
Complex
pdb|2VUS|M Chain M, Crystal Structure Of Unliganded Nmra-Area Zinc Finger
Complex
pdb|2VUS|N Chain N, Crystal Structure Of Unliganded Nmra-Area Zinc Finger
Complex
pdb|2VUS|O Chain O, Crystal Structure Of Unliganded Nmra-Area Zinc Finger
Complex
pdb|2VUS|P Chain P, Crystal Structure Of Unliganded Nmra-Area Zinc Finger
Complex
pdb|2VUT|I Chain I, Crystal Structure Of Nad-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUT|J Chain J, Crystal Structure Of Nad-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUT|K Chain K, Crystal Structure Of Nad-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUT|L Chain L, Crystal Structure Of Nad-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUT|M Chain M, Crystal Structure Of Nad-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUT|N Chain N, Crystal Structure Of Nad-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUT|O Chain O, Crystal Structure Of Nad-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUT|P Chain P, Crystal Structure Of Nad-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUU|I Chain I, Crystal Structure Of Nadp-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUU|J Chain J, Crystal Structure Of Nadp-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUU|K Chain K, Crystal Structure Of Nadp-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUU|L Chain L, Crystal Structure Of Nadp-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUU|M Chain M, Crystal Structure Of Nadp-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUU|N Chain N, Crystal Structure Of Nadp-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUU|O Chain O, Crystal Structure Of Nadp-Bound Nmra-Area Zinc Finger
Complex
pdb|2VUU|P Chain P, Crystal Structure Of Nadp-Bound Nmra-Area Zinc Finger
Complex
Length = 43
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/29 (55%), Positives = 20/29 (68%), Gaps = 1/29 (3%)
Query: 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGI 56
+C +C T TPLWR P G + LCNACG+
Sbjct: 3 TCTNCFTQTTPLWRRNPEG-QPLCNACGL 30
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 24 EMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 59
M + C++C T TPLWR G LCNACG+ ++
Sbjct: 3 HMGRECVNCGATSTPLWRRDGTG-HYLCNACGLYHK 37
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 59
SC +C TT T LWR G +CNACG+ Y+
Sbjct: 61 SCANCQTTTTTLWRRNANGD-PVCNACGLYYK 91
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 28 SCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 59
SC +C TT T LWR G +CNACG+ Y+
Sbjct: 9 SCANCQTTTTTLWRRNANGD-PVCNACGLYYK 39
>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 = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 29 CIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 59
C +C T+ T LWR P G +CNACG+ Y+
Sbjct: 7 CSNCQTSTTTLWRRSPMGD-PVCNACGLYYK 36
>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 = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 20/31 (64%), Gaps = 1/31 (3%)
Query: 29 CIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 59
C +C T+ T LWR P G +CNACG+ Y+
Sbjct: 7 CSNCQTSTTTLWRRSPMGD-PVCNACGLYYK 36
>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 = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYRKTKKLALLGRDKGR 73
+ C++C T TPLWR G LCNACG+ ++ + L R K R
Sbjct: 3 RECVNCGATATPLWRRDRTG-HYLCNACGLYHKMNGQNRPLIRPKKR 48
>pdb|2L6Y|A Chain A, Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid
pdb|2L6Z|A Chain A, Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid With Fog
Length = 39
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 59
+ C++C T TPLWR G LCNACG+ ++
Sbjct: 3 RECVNCGATATPLWRRDRTG-HYLCNACGLYHK 34
>pdb|1GNF|A Chain A, Solution Structure Of The N-Terminal Zinc Finger Of
Murine Gata-1, Nmr, 25 Structures
Length = 46
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 59
+ C++C T TPLWR G LCNACG+ ++
Sbjct: 5 RECVNCGATATPLWRRDRTG-HYLCNACGLYHK 36
>pdb|1Y0J|A Chain A, Zinc Fingers As Protein Recognition Motifs: Structural
Basis For The Gata-1FRIEND OF GATA INTERACTION
Length = 46
Score = 34.3 bits (77), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 1/33 (3%)
Query: 27 KSCIDCHTTRTPLWRGGPAGPRSLCNACGIRYR 59
+ C++C T TPLWR G LCNACG+ ++
Sbjct: 5 RECVNCGATATPLWRRDRTG-HYLCNACGLYHK 36
>pdb|2KAE|A Chain A, Data-Driven Model Of Med1:dna Complex
Length = 71
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 6/56 (10%)
Query: 24 EMNK---SCIDCHTTRTPLWRGGPAGPRSLCNACGI---RYRKTKKLALLGRDKGR 73
MNK C +C T T WR + CNAC I +Y KT+ + + + + R
Sbjct: 3 HMNKKSFQCSNCSVTETIRWRNIRSKEGIQCNACFIYQRKYNKTRPVTAVNKYQKR 58
>pdb|1FGJ|A Chain A, X-Ray Structure Of Hydroxylamine Oxidoreductase
pdb|1FGJ|B Chain B, X-Ray Structure Of Hydroxylamine Oxidoreductase
Length = 546
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 27 KSCIDCHTTRTPLW 40
K C++CH+ TP+W
Sbjct: 77 KDCVECHSDETPVW 90
>pdb|2YHB|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid-Piwi
Domains
Length = 437
Score = 26.9 bits (58), Expect = 2.8, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 13 MMKSPPAGTFNEMNKSCIDCHTTRTPLWRGGPAGPRSL 50
M+ + P G M + D TR LWR PA RSL
Sbjct: 199 MVWNNPHGQ-ESMTEQFTDKFKTRLELWRSNPANNRSL 235
>pdb|2YHA|A Chain A, Crystal Structure Of The N. Crassa Qde-2 Ago Mid-Piwi
Domains
Length = 388
Score = 26.9 bits (58), Expect = 3.2, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 18/38 (47%), Gaps = 1/38 (2%)
Query: 13 MMKSPPAGTFNEMNKSCIDCHTTRTPLWRGGPAGPRSL 50
M+ + P G M + D TR LWR PA RSL
Sbjct: 199 MVWNNPHGQ-ESMTEQFTDKFKTRLELWRSNPANNRSL 235
>pdb|2CO8|A Chain A, Solution Structures Of The Lim Domain Of Human Nedd9
Interacting Protein With Calponin Homology And Lim
Domains
Length = 82
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 25 MNKSCIDCHTTRTPLWRGG 43
++SC CHT LW GG
Sbjct: 38 FHRSCFRCHTCEATLWPGG 56
>pdb|2FTC|D Chain D, Structural Model For The Large Subunit Of The Mammalian
Mitochondrial Ribosome
pdb|3IY9|D Chain D, Leishmania Tarentolae Mitochondrial Large Ribosomal
Subunit Model
Length = 175
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 21/44 (47%), Gaps = 12/44 (27%)
Query: 34 TTRTPLWRG-----GPAGPRSL-------CNACGIRYRKTKKLA 65
+ R+PLWRG GP GP S A G++ T KLA
Sbjct: 44 SIRSPLWRGGGVAHGPRGPTSYYYMLPMKVRALGLKVALTVKLA 87
>pdb|1AQE|A Chain A, Crystal Structure Of The Y73e Mutant Of Cytochrome C Of
Class Iii (Ambler) 26 Kd
Length = 111
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 21 TFNEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 57
T + KSC+ CH L R GP+ CN+C ++
Sbjct: 78 TTKDSEKSCVGCHRE---LKRQGPSDAPLACNSCHVQ 111
>pdb|1CZJ|A Chain A, Cytochrome C Of Class Iii (Ambler) 26 Kd
Length = 111
Score = 26.2 bits (56), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 21 TFNEMNKSCIDCHTTRTPLWRGGPAGPRSLCNACGIR 57
T + KSC+ CH L R GP+ CN+C ++
Sbjct: 78 TTKDSEKSCVGCHRE---LKRQGPSDAPLACNSCHVQ 111
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
0.318 0.133 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,103,516
Number of Sequences: 62578
Number of extensions: 94830
Number of successful extensions: 202
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 171
Number of HSP's gapped (non-prelim): 24
length of query: 129
length of database: 14,973,337
effective HSP length: 88
effective length of query: 41
effective length of database: 9,466,473
effective search space: 388125393
effective search space used: 388125393
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: 45 (21.9 bits)