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= 023113
(287 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%)
Query: 130 RKKLRLSKEQSLLLEETFKEHSTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTKLKQTE 189
++++ +K Q+ LE F++ P QV++WFQN R +TK Q E
Sbjct: 14 KRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQNE 73
Query: 190 VDCE 193
E
Sbjct: 74 KGYE 77
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 33.1 bits (74), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 29/64 (45%)
Query: 130 RKKLRLSKEQSLLLEETFKEHSTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTKLKQTE 189
++++ +K Q+ LE F++ P QV++WFQN R +TK Q E
Sbjct: 11 KRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE 70
Query: 190 VDCE 193
E
Sbjct: 71 KGYE 74
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox
Protein Nkx-3.1 From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6470a
Length = 69
Score = 31.2 bits (69), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 12/17 (70%), Positives = 15/17 (88%)
Query: 171 QVEVWFQNRRARTKLKQ 187
QV++WFQNRR +TK KQ
Sbjct: 47 QVKIWFQNRRYKTKRKQ 63
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 25/51 (49%)
Query: 132 KLRLSKEQSLLLEETFKEHSTXXXXXXXXXXXXXXXRPRQVEVWFQNRRAR 182
++R S +Q++ LE+ F+ RQV+ WFQNRRA+
Sbjct: 11 QVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
Length = 81
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 172 VEVWFQNRRARTKLKQTEV 190
++VWFQNRRAR + + T V
Sbjct: 62 IQVWFQNRRARLRKQHTSV 80
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 171 QVEVWFQNRRARTK 184
QV++WFQNRRA+ K
Sbjct: 43 QVKIWFQNRRAKAK 56
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi
Tarazu Homeodomain From Drosophila And Comparison With
The Antennapedia Homeodomain
Length = 70
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 170 RQVEVWFQNRRARTKLKQT 188
RQ+++WFQNRR ++K +T
Sbjct: 45 RQIKIWFQNRRMKSKKDRT 63
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 28.9 bits (63), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%)
Query: 136 SKEQSLLLEETFKEHSTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 184
+K Q+L LE+ F + RQV++WFQNRR + K
Sbjct: 21 TKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 23/49 (46%)
Query: 136 SKEQSLLLEETFKEHSTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 184
+K Q+L LE+ F + RQV++WFQNRR + K
Sbjct: 9 TKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 21/50 (42%)
Query: 135 LSKEQSLLLEETFKEHSTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 184
+S + LEE F+ + P QV VWF N+R R+K
Sbjct: 12 ISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 171 QVEVWFQNRRARTK 184
QV++WFQNRRA+ K
Sbjct: 50 QVKIWFQNRRAKWK 63
>pdb|2Z23|A Chain A, Crystal Structure Of Y.Pestis Oligo Peptide Binding
Protein Oppa With Tri-Lysine Ligand
Length = 517
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 16 CAARNEPSLRLNHMPLSSSQSMQNHHKRSPWTELFHSS 53
CA NEPS LN M LS+S + H+K S + +L +
Sbjct: 417 CADYNEPSSFLNMM-LSNSSNNTTHYKSSVFDKLIEDT 453
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 28.1 bits (61), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 170 RQVEVWFQNRRARTK 184
RQV +WFQNRR + K
Sbjct: 49 RQVTIWFQNRRVKEK 63
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 27.7 bits (60), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 21/50 (42%)
Query: 135 LSKEQSLLLEETFKEHSTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 184
+S + LE+ F+ + P QV VWF N+R R+K
Sbjct: 372 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 170 RQVEVWFQNRRARTK 184
RQ+++WFQNRR + K
Sbjct: 62 RQIKIWFQNRRMKLK 76
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 27.7 bits (60), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 21/48 (43%)
Query: 135 LSKEQSLLLEETFKEHSTXXXXXXXXXXXXXXXRPRQVEVWFQNRRAR 182
+ EQ LE F+E R +VEVWF+NRRA+
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 61
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 27.3 bits (59), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 171 QVEVWFQNRRARTK 184
Q+++WFQN+RA+ K
Sbjct: 46 QIKIWFQNKRAKIK 59
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
0.314 0.128 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,283,252
Number of Sequences: 62578
Number of extensions: 178512
Number of successful extensions: 409
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 23
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 386
Number of HSP's gapped (non-prelim): 43
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 51 (24.3 bits)