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= psy15437
(143 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 32.7 bits (73), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 84 KSHDGRRG--PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQS 138
+ H RG PK+PR + T QRR A F+ + +P ++++ +++ GL + V +
Sbjct: 87 QEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSN 143
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 32.7 bits (73), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 2/57 (3%)
Query: 84 KSHDGRRG--PKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQS 138
+ H RG PK+PR + T QRR A F+ + +P ++++ +++ GL + V +
Sbjct: 85 QEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSN 141
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 31.2 bits (69), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
KR RT +T +Q + + P RK+ + +A + GL R+VQ
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQ 62
>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class Of
Transcription Factors, The Lim-Homeodomain Proteins, In
Neural Cell Type Specification
pdb|3MMK|B Chain B, The Structural Basis For Partial Redundancy In A Class Of
Transcription Factors, The Lim-Homeodomain Proteins, In
Neural Cell Type Specification
Length = 169
Score = 30.4 bits (67), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 6 KCLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSRLQRGEQF-VIKQGQLFCRPDYE 62
KC C + + P ++V K D +L G++F +++ G+L C+ DYE
Sbjct: 67 KCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDYE 124
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat
Insulin Gene Enhancer Protein Isl-1, 50 Structures
Length = 66
Score = 30.4 bits (67), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 94 RPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
R RT+L +Q + + +P+P ++E L TGLS R+++
Sbjct: 5 RVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR 48
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.0 bits (66), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 93 KRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLSVRIVQ 137
KRPRT +T Q R + F+I+ P + + +A +GL ++++
Sbjct: 8 KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52
>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
pdb|2DFY|C Chain C, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
Length = 195
Score = 29.3 bits (64), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 22/54 (40%)
Query: 7 CLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSRLQRGEQFVIKQGQLFCRPD 60
C C + + ELVM+ N +RL G++F G LFC D
Sbjct: 70 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHD 123
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 29.3 bits (64), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 22/54 (40%)
Query: 7 CLGCSEKLGPDELVMKTLDNXXXXXXXXXXXXGSRLQRGEQFVIKQGQLFCRPD 60
C C + + ELVM+ N +RL G++F G LFC D
Sbjct: 72 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHD 125
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 26.6 bits (57), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLS 132
+R RT T+QQ + +A+F+ + P RE +A T L+
Sbjct: 2 SQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLT 43
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 26.2 bits (56), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 33/80 (41%), Gaps = 5/80 (6%)
Query: 57 CRPDYEKEVEMLQGYAQGIPFDLITSSKSHDGRRGPKRPRTILTTQQRRAFKASFEISPK 116
RP EK VE +L SKS + KR RT + + R + + F SPK
Sbjct: 66 LRPLLEKWVEEADNNE-----NLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPK 120
Query: 117 PCRKVREGLARDTGLSVRIV 136
P + +A GL +V
Sbjct: 121 PSLQQITHIANQLGLEKDVV 140
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex With
A Taatcc Dna Binding Site
Length = 68
Score = 25.8 bits (55), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 23/42 (54%)
Query: 91 GPKRPRTILTTQQRRAFKASFEISPKPCRKVREGLARDTGLS 132
+R RT T+QQ + +A+F+ + P RE +A T L+
Sbjct: 2 SQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLT 43
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
0.321 0.139 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,589,663
Number of Sequences: 62578
Number of extensions: 114707
Number of successful extensions: 202
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 191
Number of HSP's gapped (non-prelim): 11
length of query: 143
length of database: 14,973,337
effective HSP length: 89
effective length of query: 54
effective length of database: 9,403,895
effective search space: 507810330
effective search space used: 507810330
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: 46 (22.3 bits)