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= 031304
(162 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DA6|A Chain A, Solution Structure Of The Homeobox Domain Of Hepatocyte
Nuclear Factor 1-Beta (Hnf-1beta)
Length = 102
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 35/80 (43%), Gaps = 18/80 (22%)
Query: 15 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAK-------------H 61
GS + R R+ PA QIL YD K P K++ + + E + H
Sbjct: 1 GSSGSSGRNRFKWGPASQQILYQAYDRQK-NPSKEEREALVEECNRAECLQRGVSPSKAH 59
Query: 62 GQ----ISETNVYNWFQNRR 77
G ++E VYNWF NRR
Sbjct: 60 GLGSNLVTEVRVYNWFANRR 79
>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 = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/29 (58%), Positives = 22/29 (75%)
Query: 56 AELAKHGQISETNVYNWFQNRRARLKRKQ 84
A LAK+ +++ET V WFQNRR + KRKQ
Sbjct: 35 AHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>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 = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 37/68 (54%), Gaps = 9/68 (13%)
Query: 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA--ELAKHGQISETNVYNWFQNRRAR 79
R R T + +QL LE ++ + + D+ ELA+ ++E + WFQNRRAR
Sbjct: 20 RSRTTFSASQLDELERAFE-------RTQYPDIYTREELAQRTNLTEARIQVWFQNRRAR 72
Query: 80 LKRKQSGV 87
L+++ + V
Sbjct: 73 LRKQHTSV 80
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 40/80 (50%), Gaps = 6/80 (7%)
Query: 4 GNPYFDPFVA-SGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHG 62
N F P++A +G+ L R R T T Q LE + R+++I E+A
Sbjct: 3 SNHTFYPWMAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRI-----EMAHAL 57
Query: 63 QISETNVYNWFQNRRARLKR 82
++E + WFQNRR +LK+
Sbjct: 58 SLTERQIKIWFQNRRMKLKK 77
>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 = 34.7 bits (78), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 12/78 (15%)
Query: 15 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA--ELAKHGQISETNVYNW 72
GSQ+ RQR T QLQ LE T ++ + DM+ E+A ++E V W
Sbjct: 1 GSQR---RQRTHFTSQQLQELE-------ATFQRNRYPDMSTREEIAVWTNLTEARVRVW 50
Query: 73 FQNRRARLKRKQSGVVPN 90
F+NRRA+ ++++ +V +
Sbjct: 51 FKNRRAKWRKREEFIVTD 68
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 33.9 bits (76), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%), Gaps = 9/62 (14%)
Query: 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQD--MTAELAKHGQISETNVYNWFQNRRAR 79
R+R T T AQL +LE ++ K + D M E+A + E+ V WF+NRRA+
Sbjct: 9 RERTTFTRAQLDVLEALFA-------KTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
Query: 80 LK 81
+
Sbjct: 62 CR 63
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 33.5 bits (75), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 18/25 (72%)
Query: 58 LAKHGQISETNVYNWFQNRRARLKR 82
LAK Q+SE V WFQNRRA+ +R
Sbjct: 40 LAKMLQLSERQVKTWFQNRRAKWRR 64
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 33.5 bits (75), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 12/78 (15%)
Query: 15 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA--ELAKHGQISETNVYNW 72
GSQ+ RQR T QLQ LE T ++ DM+ E+A ++E V W
Sbjct: 1 GSQR---RQRTHFTSQQLQELE-------ATFQRNHYPDMSTREEIAVWTNLTEARVRVW 50
Query: 73 FQNRRARLKRKQSGVVPN 90
F+NRRA+ ++++ +V +
Sbjct: 51 FKNRRAKWRKREEFIVTD 68
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 33.5 bits (75), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 9/70 (12%)
Query: 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMT--AELAKHGQISETNVYNWFQNRRAR 79
R+R T QL LE + CK K +T +++A ++SE V WFQNRRA+
Sbjct: 9 RRRTAFTSEQLLELEKEFH-CK------KYLSLTERSQIAHALKLSEVQVKIWFQNRRAK 61
Query: 80 LKRKQSGVVP 89
KR ++G V
Sbjct: 62 WKRIKAGNVS 71
>pdb|2H8R|A Chain A, Hepatocyte Nuclear Factor 1b Bound To Dna: Mody5 Gene
Product
pdb|2H8R|B Chain B, Hepatocyte Nuclear Factor 1b Bound To Dna: Mody5 Gene
Product
Length = 221
Score = 33.1 bits (74), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 36/86 (41%), Gaps = 18/86 (20%)
Query: 9 DPFVASGSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAK-------- 60
D + + K R R+ PA QIL YD K P K++ + + E +
Sbjct: 131 DDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKN-PSKEEREALVEECNRAECLQRGV 189
Query: 61 -----HGQ----ISETNVYNWFQNRR 77
HG ++E VYNWF NRR
Sbjct: 190 SPSKAHGLGSNLVTEVRVYNWFANRR 215
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 5/55 (9%)
Query: 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82
T AQL LE + + + ++ AE + ++ET V WFQNRRA+ KR
Sbjct: 8 TTAQLLALERKFRQKQYLSIAER-----AEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 32.0 bits (71), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 34/65 (52%), Gaps = 13/65 (20%)
Query: 22 RQRWTPTPAQLQILEHVYDECK----GTPRKQKIQDMTAELAKHGQISETNVYNWFQNRR 77
R R T QL+ LE+++ E K GT R+Q LA+ + E V WF+NRR
Sbjct: 9 RHRTIFTDEQLEALENLFQETKYPDVGT-REQ--------LARKVHLREEKVEVWFKNRR 59
Query: 78 ARLKR 82
A+ +R
Sbjct: 60 AKWRR 64
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 22 RQRWTPTPAQLQILEHVYD-ECK-GTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79
R R T Q+++LE+V+ C G D+ +LA+ + + WFQNRRA+
Sbjct: 3 RPRTAFTQNQIEVLENVFRVNCYPGI-------DILEDLAQKLNLELDRIQIWFQNRRAK 55
Query: 80 LKR 82
LKR
Sbjct: 56 LKR 58
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 31.6 bits (70), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 9/50 (18%)
Query: 36 EHVYDECKGTPRK--QKIQDMTAELAKHGQISETNVYNWFQNRRARLKRK 83
E + + C +K +K+ D+ +++ VYNWF NRR +KR+
Sbjct: 38 EEIANACNAVIQKPGKKLSDLE-------RVTSLKVYNWFANRRKEIKRR 80
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 31.2 bits (69), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 9/65 (13%)
Query: 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA--ELAKHGQISETNVYNWFQNRRAR 79
R R T T QL+ LE V+ K D+ A +LA ++E V WFQNRRA+
Sbjct: 11 RNRTTFTSYQLEELEKVFQ-------KTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK 63
Query: 80 LKRKQ 84
++++
Sbjct: 64 WRKRE 68
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 30.8 bits (68), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 25/40 (62%), Gaps = 4/40 (10%)
Query: 47 RKQKIQDMT----AELAKHGQISETNVYNWFQNRRARLKR 82
R QK Q + AELA +++T V WFQN+R+++K+
Sbjct: 25 RFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 30.8 bits (68), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 10/66 (15%)
Query: 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTA--ELAKHGQISETNVYNWFQNRRAR 79
R R T T QL+ LE ++ + D+ ELA+ +++E V WF NRRAR
Sbjct: 4 RSRTTFTAEQLEELERAFE-------RTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 56
Query: 80 LKRKQS 85
RKQ+
Sbjct: 57 W-RKQA 61
>pdb|1KVD|B Chain B, Killer Toxin From Halotolerant Yeast
pdb|1KVD|D Chain D, Killer Toxin From Halotolerant Yeast
pdb|1KVE|B Chain B, Killer Toxin From Halotolerant Yeast
pdb|1KVE|D Chain D, Killer Toxin From Halotolerant Yeast
Length = 77
Score = 30.8 bits (68), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 17/20 (85%)
Query: 43 KGTPRKQKIQDMTAELAKHG 62
KGTP K +Q+M+A+LAK+G
Sbjct: 17 KGTPSKNDLQNMSADLAKNG 36
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 30.8 bits (68), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 5/57 (8%)
Query: 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKRKQ 84
T QL LE + K R +++ E+A +++ET V WFQNRR + K+++
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRV-----EIAATLELNETQVKIWFQNRRMKQKKRE 93
>pdb|2LFB|A Chain A, Homeodomain From Rat Liver Lfb1HNF1 TRANSCRIPTION
FACTOR, Nmr, 20 Structures
Length = 100
Score = 29.6 bits (65), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 18/73 (24%)
Query: 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMT-----AELAKHG------------QI 64
R R+ PA QIL Y+ K P K++ + + AE + G +
Sbjct: 12 RNRFKWGPASQQILFQAYERQK-NPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLV 70
Query: 65 SETNVYNWFQNRR 77
+E VYNWF NRR
Sbjct: 71 TEVRVYNWFANRR 83
>pdb|1LFB|A Chain A, The X-Ray Structure Of An Atypical Homeodomain Present
In The Rat Liver Transcription Factor Lfb1(Slash)hnf1
And Implications For Dna Binding
Length = 99
Score = 29.6 bits (65), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 18/73 (24%)
Query: 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMT-----AELAKHG------------QI 64
R R+ PA QIL Y+ K P K++ + + AE + G +
Sbjct: 11 RNRFKWGPASQQILFQAYERQK-NPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLV 69
Query: 65 SETNVYNWFQNRR 77
+E VYNWF NRR
Sbjct: 70 TEVRVYNWFANRR 82
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 29.6 bits (65), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79
R R T TP QL+IL Y RK M +A + + V WFQN RAR
Sbjct: 19 RLRTTITPEQLEILYQKYLLDSNPTRK-----MLDHIAHEVGLKKRVVQVWFQNTRAR 71
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 29.6 bits (65), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 52 QDMTAELAKHGQISETNVYNWFQNRRARLKR 82
++ ELAK I+ + V NWF N+R R K+
Sbjct: 33 EEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex
With Dna
pdb|2H1K|B Chain B, Crystal Structure Of The Pdx1 Homeodomain In Complex
With Dna
Length = 63
Score = 29.6 bits (65), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 12/72 (16%)
Query: 15 GSQKLTARQRWTPTPAQLQILE--HVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNW 72
GS K R R T AQL LE ++++ PR+ ELA ++E ++ W
Sbjct: 1 GSNK---RTRTAYTRAQLLELEKEFLFNKYISRPRR-------VELAVMLNLTERHIKIW 50
Query: 73 FQNRRARLKRKQ 84
FQNRR + K+++
Sbjct: 51 FQNRRMKWKKEE 62
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 29.6 bits (65), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 36/73 (49%), Gaps = 8/73 (10%)
Query: 15 GSQKLTARQRWTP-TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWF 73
GS + R++ P + QL+ LE Y K +D +++ +SE + WF
Sbjct: 1 GSSGSSGRKKRIPYSKGQLRELEREYAANKFI-----TKDKRRKISAATSLSERQITIWF 55
Query: 74 QNRRARLKRKQSG 86
QNRR +K K+SG
Sbjct: 56 QNRR--VKEKKSG 66
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 29.6 bits (65), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 52 QDMTAELAKHGQISETNVYNWFQNRRARLKR 82
++ ELAK I+ + V NWF N+R R K+
Sbjct: 32 EEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|1IC8|A Chain A, Hepatocyte Nuclear Factor 1a Bound To Dna : Mody3 Gene
Product
pdb|1IC8|B Chain B, Hepatocyte Nuclear Factor 1a Bound To Dna : Mody3 Gene
Product
Length = 194
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 18/73 (24%)
Query: 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMT-----AELAKHG------------QI 64
R R+ PA QIL Y+ K P K++ + + AE + G +
Sbjct: 117 RNRFKWGPASQQILFQAYERQK-NPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLV 175
Query: 65 SETNVYNWFQNRR 77
+E VYNWF NRR
Sbjct: 176 TEVRVYNWFANRR 188
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 52 QDMTAELAKHGQISETNVYNWFQNRRARLKR 82
++ ELAK I+ + V NWF N+R R K+
Sbjct: 31 EEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 56 AELAKHGQISETNVYNWFQNRRARLKRK 83
A LAK ++++ V WFQNRR + +R+
Sbjct: 28 AALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 52 QDMTAELAKHGQISETNVYNWFQNRRARLKR 82
++ ELAK I+ + V NWF N+R R K+
Sbjct: 31 EEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 16/23 (69%)
Query: 57 ELAKHGQISETNVYNWFQNRRAR 79
ELA+ ++ T V NWF+NRR R
Sbjct: 526 ELAEATGLTTTQVSNWFKNRRQR 548
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 6/68 (8%)
Query: 16 SQKLTARQRWTP-TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 74
S L R++ P T QL+ LE Y K +D ++ +SE V WFQ
Sbjct: 2 SHMLEGRKKRVPYTKVQLKELEREYATNKFIT-----KDKRRRISATTNLSERQVTIWFQ 56
Query: 75 NRRARLKR 82
NRR + K+
Sbjct: 57 NRRVKEKK 64
>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 = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 20 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79
T RQR + T Q LE + + R+++I E+A ++E + WFQNRR +
Sbjct: 28 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRI-----EIAHALSLTERQIKIWFQNRRMK 82
Query: 80 LKR 82
K+
Sbjct: 83 WKK 85
>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 = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82
+ QL L+ ++E + +++ Q +++EL ++E + WFQN+RA++K+
Sbjct: 11 SSEQLARLKREFNENRYLTERRR-QQLSSELG----LNEAQIKIWFQNKRAKIKK 60
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 28.1 bits (61), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 19/31 (61%)
Query: 52 QDMTAELAKHGQISETNVYNWFQNRRARLKR 82
++ ELA+ I+ + V NWF N+R R K+
Sbjct: 31 EEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 28.1 bits (61), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 52 QDMTAELAKHGQISETNVYNWFQNRRARLKR 82
+D E+A+ ++E V WFQNRR ++K+
Sbjct: 28 RDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82
+ QL L+ ++E + +++ Q +++EL ++E + WFQN+RA++K+
Sbjct: 9 SSEQLARLKREFNENRYLTERRR-QQLSSELG----LNEAQIKIWFQNKRAKIKK 58
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 57 ELAKHGQISETNVYNWFQNRRARLKRKQSGV 87
ELA ++E + WFQNRRA+ RKQ V
Sbjct: 31 ELAMKIGLTEARIQVWFQNRRAKW-RKQEKV 60
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
Length = 67
Score = 27.7 bits (60), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 57 ELAKHGQISETNVYNWFQNRRARLKRKQSGV 87
ELA ++E + WFQNRRA+ RKQ V
Sbjct: 38 ELAMKIGLTEARIQVWFQNRRAKW-RKQEKV 67
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 27.7 bits (60), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 20/31 (64%)
Query: 52 QDMTAELAKHGQISETNVYNWFQNRRARLKR 82
+D E+A+ ++E V WFQNRR ++K+
Sbjct: 40 RDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
pdb|3A01|E Chain E, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
Length = 93
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 56 AELAKHGQISETNVYNWFQNRRARLKR 82
A LA+ ++++ V WFQNRR + +R
Sbjct: 48 AALARGLKMTDAQVKTWFQNRRTKWRR 74
>pdb|4A17|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|M Chain M, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 301
Score = 27.3 bits (59), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 98 TVTHAESRKQNPESIQSLEDSAPPPRD-EDIYP 129
T HAE RK NPE ++S + + P RD + YP
Sbjct: 248 TKVHAEIRK-NPERVKSTKKNDKPKRDHKKFYP 279
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 27.3 bits (59), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 5/55 (9%)
Query: 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82
T QL+ LE Y K +D ++ +SE V WFQNRR + K+
Sbjct: 9 TKVQLKELEREYATNKFIT-----KDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 27.3 bits (59), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 19/28 (67%)
Query: 57 ELAKHGQISETNVYNWFQNRRARLKRKQ 84
ELA ++E + WFQNRRA+ ++++
Sbjct: 31 ELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOS|B Chain B, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOT|A Chain A, Phage Selected Homeodomain Bound To Modified Dna
pdb|2HOT|B Chain B, Phage Selected Homeodomain Bound To Modified Dna
Length = 63
Score = 26.9 bits (58), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 32/55 (58%), Gaps = 5/55 (9%)
Query: 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82
+ QL L+ ++E + +++ Q +++EL ++E V WF+N RA++K+
Sbjct: 12 SSEQLARLKREFNENRYLTERRR-QQLSSELG----LNEAQVKGWFKNMRAKIKK 61
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 26.9 bits (58), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 22 RQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLK 81
R R T QL LE +++ K +I +LA+ +S+ V W+QNRR + K
Sbjct: 19 RSRTVFTELQLMGLEKRFEKQKYLSTPDRI-----DLAESLGLSQLQVKTWYQNRRMKWK 73
Query: 82 R 82
+
Sbjct: 74 K 74
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 26.9 bits (58), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 32/55 (58%), Gaps = 5/55 (9%)
Query: 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82
+ QL L+ ++E + +++ Q +++EL ++E + WFQN RA++K+
Sbjct: 9 SSEQLARLKREFNENRYLTERRR-QQLSSELG----LNEAQIKIWFQNERAKIKK 58
>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 = 26.6 bits (57), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 20 TARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRAR 79
+ R R T T Q LE + + R+++I ++A +SE + WFQNRR +
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRI-----DIANALSLSERQIKIWFQNRRMK 57
Query: 80 LKRKQS 85
K+ ++
Sbjct: 58 SKKDRT 63
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 26.6 bits (57), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 11/31 (35%), Positives = 21/31 (67%), Gaps = 4/31 (12%)
Query: 52 QDMTAELAKHGQISETNVYNWFQNRRARLKR 82
Q +++EL ++E + WFQN+RA+++R
Sbjct: 34 QQLSSELG----LNEAQIKIWFQNKRAKIRR 60
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 26.6 bits (57), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 18/29 (62%)
Query: 56 AELAKHGQISETNVYNWFQNRRARLKRKQ 84
ELA + E+ + WFQNRR + KR++
Sbjct: 32 CELAAQLNLPESTIKVWFQNRRMKDKRQR 60
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 26.6 bits (57), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 15 GSQKLTARQRWTPTPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQ 74
G+ + ++R T + A LE + E P Q+I M EL ++ V WF
Sbjct: 82 GANERKRKRRTTISIAAKDALERHFGE-HSKPSSQEIMRMAEELNLEKEV----VRVWFC 136
Query: 75 NRRARLKR 82
NRR R KR
Sbjct: 137 NRRQREKR 144
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 26.6 bits (57), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 33/55 (60%), Gaps = 5/55 (9%)
Query: 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82
+ QL L+ ++E + +++ Q +++EL ++E + WF+N+RA++K+
Sbjct: 11 SSEQLARLKREFNENRYLTERRR-QQLSSELG----LNEAQIKIWFKNKRAKIKK 60
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52a
Length = 59
Score = 26.6 bits (57), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 32/55 (58%), Gaps = 5/55 (9%)
Query: 28 TPAQLQILEHVYDECKGTPRKQKIQDMTAELAKHGQISETNVYNWFQNRRARLKR 82
+ QL L+ ++E + +++ Q +++EL ++E + WFQN RA++K+
Sbjct: 9 SSEQLARLKREFNENRYLTERRR-QQLSSELG----LNEAQIKIWFQNARAKIKK 58
>pdb|4DUP|A Chain A, Crystal Structure Of A Quinone Oxidoreductase From
Rhizobium Etli Cfn 42
pdb|4DUP|B Chain B, Crystal Structure Of A Quinone Oxidoreductase From
Rhizobium Etli Cfn 42
Length = 353
Score = 25.8 bits (55), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 5/49 (10%)
Query: 89 PNNAESEAETVTHAESRKQNPESIQSLEDSAPPPRDEDIYPQSPDLGID 137
P E E + AE+ N I + S PPP+D SP LG++
Sbjct: 49 PLPVAGEGEVLVRAEAIGVNRPDIAQRQGSYPPPKD-----ASPILGLE 92
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 0.130 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,094,444
Number of Sequences: 62578
Number of extensions: 189947
Number of successful extensions: 378
Number of sequences better than 100.0: 67
Number of HSP's better than 100.0 without gapping: 41
Number of HSP's successfully gapped in prelim test: 26
Number of HSP's that attempted gapping in prelim test: 335
Number of HSP's gapped (non-prelim): 67
length of query: 162
length of database: 14,973,337
effective HSP length: 91
effective length of query: 71
effective length of database: 9,278,739
effective search space: 658790469
effective search space used: 658790469
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 47 (22.7 bits)