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= 019530
(339 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 = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 30/68 (44%)
Query: 163 NGLTRKKLRLSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTKL 222
N ++++ +K Q+ LE F++ P QV++WFQN R +TK
Sbjct: 10 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69
Query: 223 KQTEVDCE 230
Q E E
Sbjct: 70 AQNEKGYE 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 = 0.22, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 30/68 (44%)
Query: 163 NGLTRKKLRLSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTKL 222
N ++++ +K Q+ LE F++ P QV++WFQN R +TK
Sbjct: 7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
Query: 223 KQTEVDCE 230
Q E E
Sbjct: 67 AQNEKGYE 74
>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 = 32.7 bits (73), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 23/50 (46%)
Query: 172 LSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
+S + AFLE+ F+ + P QV VWF N+R R+K
Sbjct: 372 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 32.3 bits (72), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 23/50 (46%)
Query: 172 LSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
+S + AFLEE F+ + P QV VWF N+R R+K
Sbjct: 12 ISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 31.6 bits (70), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 12/17 (70%), Positives = 15/17 (88%)
Query: 208 QVEVWFQNRRARTKLKQ 224
QV++WFQNRR +TK KQ
Sbjct: 47 QVKIWFQNRRYKTKRKQ 63
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 31.6 bits (70), Expect = 0.71, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 163 NGLTRK-KLRLSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
NGL R+ + ++ Q+ LE+ F ++ RQ+++WFQNRR + K
Sbjct: 17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLK 76
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 31.2 bits (69), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 23/50 (46%)
Query: 172 LSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
+S + AFLE+ F+ + P QV VWF N+R R+K
Sbjct: 4 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1YRN|A Chain A, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1F43|A Chain A, Solution Structure Of The Mata1 Homeodomain
Length = 61
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 23/50 (46%)
Query: 172 LSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
+S + AFLE+ F+ + P QV VWF N+R R+K
Sbjct: 12 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 16/20 (80%)
Query: 208 QVEVWFQNRRARTKLKQTEV 227
+++VWFQNRRAR + + T V
Sbjct: 61 RIQVWFQNRRARLRKQHTSV 80
>pdb|1HJB|A Chain A, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
pdb|1HJB|B Chain B, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
pdb|1HJB|D Chain D, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
pdb|1HJB|E Chain E, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
Length = 87
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 4/63 (6%)
Query: 216 RRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQEL-RALKTSQPFYMQLPATTLTMC 274
R++R K K ++ ++ + E LT EN RLQK++++L R L T + + QLP L
Sbjct: 28 RKSRDKAKMRNLETQH--KVLE-LTAENERLQKKVEQLSRELSTLRNLFKQLPEPLLASS 84
Query: 275 PSC 277
C
Sbjct: 85 GHC 87
>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 = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 207 RQVEVWFQNRRARTKLKQT 225
RQ+++WFQNRR ++K +T
Sbjct: 45 RQIKIWFQNRRMKSKKDRT 63
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 208 QVEVWFQNRRARTK 221
QV++WFQNRRA+ K
Sbjct: 43 QVKIWFQNRRAKAK 56
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 29.3 bits (64), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 25/53 (47%)
Query: 169 KLRLSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
++R S +Q+ LE+ F+ RQV+ WFQNRRA+ +
Sbjct: 11 QVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 28.9 bits (63), Expect = 4.5, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 23/55 (41%)
Query: 167 RKKLRLSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
+K++ SK Q LE + + RQ+ +WFQNRR + K
Sbjct: 9 KKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 28.5 bits (62), Expect = 5.1, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 25/55 (45%)
Query: 167 RKKLRLSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
+K+ +K Q+ LE+ F + RQV++WFQNRR + K
Sbjct: 15 KKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 13/14 (92%)
Query: 208 QVEVWFQNRRARTK 221
QV++WFQNRRA+ K
Sbjct: 50 QVKIWFQNRRAKWK 63
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 88
Score = 28.5 bits (62), Expect = 5.2, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 163 NGLT-RKKLRLSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
NG T R++ ++ Q+ LE+ F + RQ+++WFQNRR + K
Sbjct: 25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 28.5 bits (62), Expect = 5.7, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 23/55 (41%)
Query: 167 RKKLRLSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
+K++ +K Q LE + + RQV +WFQNRR + K
Sbjct: 9 KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 28.5 bits (62), Expect = 5.8, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 23/55 (41%)
Query: 167 RKKLRLSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
+K++ +K Q LE + + RQV +WFQNRR + K
Sbjct: 3 KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 28.5 bits (62), Expect = 5.8, Method: Composition-based stats.
Identities = 16/55 (29%), Positives = 25/55 (45%)
Query: 167 RKKLRLSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
+K+ +K Q+ LE+ F + RQV++WFQNRR + K
Sbjct: 3 KKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|2E43|A Chain A, Crystal Structure Of CEBPBETA BZIP HOMODIMER K269A MUTANT
Bound To A High Affinity Dna Fragment
pdb|2E43|B Chain B, Crystal Structure Of CEBPBETA BZIP HOMODIMER K269A MUTANT
Bound To A High Affinity Dna Fragment
Length = 78
Score = 28.5 bits (62), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 33/53 (62%), Gaps = 4/53 (7%)
Query: 216 RRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQEL-RALKTSQPFYMQLP 267
R++R K K ++ ++ + E LT EN RLQK++++L R L T + + QLP
Sbjct: 28 RKSRDKAKMRNLETQH--KVLE-LTAENERLQKKVEQLSRELSTLRNLFKQLP 77
>pdb|1IO4|A Chain A, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN-
Cbfbeta Core Domain Heterodimer And CEBPBETA BZIP
Homodimer Bound To A Dna Fragment From The Csf-1r
Promoter
pdb|1IO4|B Chain B, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN-
Cbfbeta Core Domain Heterodimer And CEBPBETA BZIP
Homodimer Bound To A Dna Fragment From The Csf-1r
Promoter
pdb|1H88|A Chain A, Crystal Structure Of Ternary Protein-Dna Complex1
pdb|1H88|B Chain B, Crystal Structure Of Ternary Protein-Dna Complex1
pdb|1H8A|A Chain A, Crystal Structure Of Ternary Protein-Dna Complex3
pdb|1H8A|B Chain B, Crystal Structure Of Ternary Protein-Dna Complex3
pdb|1GU4|A Chain A, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
High Affinity Dna Fragment
pdb|1GU4|B Chain B, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
High Affinity Dna Fragment
pdb|1GU5|A Chain A, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
Dna Fragment From The Mim-1 Promoter
pdb|1GU5|B Chain B, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
Dna Fragment From The Mim-1 Promoter
pdb|1GTW|A Chain A, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
Dna Fragment From The Tom-1a Promoter
pdb|1GTW|B Chain B, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
Dna Fragment From The Tom-1a Promoter
Length = 78
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 33/53 (62%), Gaps = 4/53 (7%)
Query: 216 RRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQEL-RALKTSQPFYMQLP 267
R++R K K ++ ++ + E LT EN RLQK++++L R L T + + QLP
Sbjct: 28 RKSRDKAKMRNLETQH--KVLE-LTAENERLQKKVEQLSRELSTLRNLFKQLP 77
>pdb|2E42|A Chain A, Crystal Structure Of CEBPBETA BZIP HOMODIMER V285A MUTANT
Bound To A High Affinity Dna Fragment
pdb|2E42|B Chain B, Crystal Structure Of CEBPBETA BZIP HOMODIMER V285A MUTANT
Bound To A High Affinity Dna Fragment
Length = 78
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 33/53 (62%), Gaps = 4/53 (7%)
Query: 216 RRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQEL-RALKTSQPFYMQLP 267
R++R K K ++ ++ + E LT EN RLQK++++L R L T + + QLP
Sbjct: 28 RKSRDKAKMRNLETQH--KVLE-LTAENERLQKKVEQLSRELSTLRNLFKQLP 77
>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 = 27.7 bits (60), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 22/50 (44%)
Query: 172 LSKEQSAFLEESFKEHNTXXXXXXXXXXXXXXXRPRQVEVWFQNRRARTK 221
S EQ A L+ F E+ Q+++WFQN+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 27.7 bits (60), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 208 QVEVWFQNRRARTKLKQTE 226
QV++WFQNRR + K ++ E
Sbjct: 77 QVKIWFQNRRMKQKKRERE 95
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 27.7 bits (60), Expect = 9.7, Method: Composition-based stats.
Identities = 11/25 (44%), Positives = 20/25 (80%), Gaps = 2/25 (8%)
Query: 208 QVEVWFQNRRARTKLKQTEVDCEYL 232
++++WFQNRRA KLK++ + ++L
Sbjct: 44 RIQIWFQNRRA--KLKRSHRESQFL 66
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
0.315 0.128 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,977,056
Number of Sequences: 62578
Number of extensions: 255546
Number of successful extensions: 617
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 30
Number of HSP's that attempted gapping in prelim test: 603
Number of HSP's gapped (non-prelim): 44
length of query: 339
length of database: 14,973,337
effective HSP length: 99
effective length of query: 240
effective length of database: 8,778,115
effective search space: 2106747600
effective search space used: 2106747600
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)