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= psy2123
(143 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 83.6 bits (205), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 37/54 (68%), Positives = 43/54 (79%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
F S QL LEK F RTHYPD F REELA K+ L+EAR+QVWFQNRRAK+R+ E+
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>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 = 82.4 bits (202), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 37/54 (68%), Positives = 43/54 (79%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
F S QL LEK F RTHYPD F REELA K+ L+EAR+QVWFQNRRAK+R+ E+
Sbjct: 13 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 82.4 bits (202), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 37/53 (69%), Positives = 42/53 (79%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
F S QL LEK F RTHYPD F REELA K+ L+EAR+QVWFQNRRAK+R+ E
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 81.6 bits (200), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 36/54 (66%), Positives = 45/54 (83%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
F S+QL LEKVF++THYPD + RE+LA + L+EARVQVWFQNRRAK+R+ ER
Sbjct: 16 FTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRER 69
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 81.3 bits (199), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 39/67 (58%), Positives = 46/67 (68%), Gaps = 1/67 (1%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
F Q+ ALEK FERTHYPD F RE LA K+ L EAR+QVWF NRRAK+RR E+ + R
Sbjct: 14 FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK-LRNQR 72
Query: 94 NLDAPTS 100
P+S
Sbjct: 73 RQSGPSS 79
>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 = 75.1 bits (183), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 31/52 (59%), Positives = 42/52 (80%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F++ QL+ LE+ FERT YPD + REELA++ L+EAR+QVWFQNRRA+ R+
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 75.1 bits (183), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 32/52 (61%), Positives = 41/52 (78%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F + QL LE+ FERTHYPD + REELA++ L+EARVQVWF NRRA++R+
Sbjct: 9 FTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 30/52 (57%), Positives = 39/52 (75%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F QL ALE +F+ T YPD RE+LA+KV L E +V+VWF+NRRAK+RR+
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 66.6 bits (161), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 31/53 (58%), Positives = 38/53 (71%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
F S QL LE F+R HYPD REE+A L+EARV+VWF+NRRAK+R+ E
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 66.2 bits (160), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 30/50 (60%), Positives = 38/50 (76%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
F QL+ LE +F +T YPD F+REE+A K+ L E+RVQVWF+NRRAK R
Sbjct: 14 FTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>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 = 63.5 bits (153), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 30/53 (56%), Positives = 37/53 (69%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
F S QL LE F+R YPD REE+A L+EARV+VWF+NRRAK+R+ E
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/52 (50%), Positives = 34/52 (65%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F HQL ++ F H PDA ++LA+K L++ +QVWFQN RAKFRRN
Sbjct: 14 FKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN 65
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 35/54 (64%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
F +Q+ LE VF YP + E+LA+K+ L R+Q+WFQNRRAK +R+ R
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 49.7 bits (117), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 37/52 (71%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
++S QL AL++ F++T Y R ELA + L++ +V++WFQN+R+K +++
Sbjct: 14 YSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS 65
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/52 (50%), Positives = 34/52 (65%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F++ Q LEK FE Y R+ LAK + LSE +V+ WFQNRRAK+RR+
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS 65
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 32/51 (62%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
F + QL ALE+ F + Y R E + + L+E +V++WFQNRRAK +R
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 35/58 (60%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFIS 91
F S QL LEK F Y R ++A + LSE +V++WFQNRRAK++R + +S
Sbjct: 14 FTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIKAGNVS 71
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 33/52 (63%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F QL LEK FE+ Y R +LA+ + LS+ +V+ W+QNRR K++++
Sbjct: 24 FTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKS 75
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 35/52 (67%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F+S QL ++ F Y R++L+ ++ L+EA++++WFQN+RAK RR+
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRRS 61
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 36/52 (69%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F+S QL L++ F Y R++L+ ++ L+EA++++WFQN+RAK +++
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 59
>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 = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 36/52 (69%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F+S QL L++ F Y R++L+ ++ L+EA++++WFQN+RAK +++
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 32/54 (59%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
F + QL LEK F Y R E+A + L+E +V++WFQNRR K ++ ER
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 33/52 (63%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F+ Q+ LE+ F R Y + R LAK + +++A+V+ WFQNRR K+RR
Sbjct: 4 FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 43.9 bits (102), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 33/49 (67%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82
F+S QL L++ F Y R++L+ ++ L+EA++++WFQN+RAK
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>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 = 43.5 bits (101), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 35/52 (67%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F+S QL L++ F Y R++L+ ++ L+EA++++WFQN RAK +++
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 59
>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 = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 32/52 (61%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F Q+ LEK F + Y + R LA+ + +++A+V+ WFQNRR K+RR
Sbjct: 24 FTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
>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 = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 36/52 (69%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F+S QL L++ F Y R++L+ ++ L+EA++++WF+N+RAK +++
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61
>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 = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 35/52 (67%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F+S QL L++ F Y R++L+ ++ L+EA++++WFQN RAK +++
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 35/52 (67%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F+S QL L++ F Y R++L+ ++ L+EA++++WF N+RAK +++
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ +Q LEK F HY R E+A + L+E ++++WFQNRR K ++
Sbjct: 27 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 30/49 (61%)
Query: 38 QLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
Q+ LE+ F Y A R LAK + L+E +V++WFQNRR K +R +
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 34/52 (65%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F+S QL L++ F Y R++L+ ++ L+EA+V+ WF+N RAK +++
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKS 62
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 31/51 (60%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
F QL LEK F + +Y R ELA ++ L E+ ++VWFQNRR K +R
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The
Antennapedia Homeodomain From Drosophila In Solution By
1h Nuclear Magnetic Resonance Spectroscopy
Length = 68
Score = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 31/51 (60%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ +Q LEK F Y R E+A +CL+E ++++WFQNRR K+++
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59
>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 = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR--NERNFIS 91
F Q LE+ F + Y A RE LA + L+ +V++WFQN R K +R NE+ +
Sbjct: 16 FTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEG 75
Query: 92 H 92
H
Sbjct: 76 H 76
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 33/55 (60%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88
F+ Q+ LE+ F++ Y A RE LA + L+ +V++WFQN R K +R ++
Sbjct: 9 FSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD 63
>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 = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 27/48 (56%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
N QL+ L + PDA ++E+L + LS ++VWFQN+R K
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK 57
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
pdb|3RKQ|B Chain B, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
Length = 58
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 31/48 (64%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
F+ Q+ LE+ F++ Y A R++LA + L+ +V++WFQNRR K
Sbjct: 9 FSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR--NERNFIS 91
F Q LE+ F + Y A RE L + L+ +V++WFQN R K +R NE+ +
Sbjct: 19 FTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEG 78
Query: 92 H 92
H
Sbjct: 79 H 79
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%)
Query: 51 YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHRNLDAPTS 100
YP +EELAKK ++ ++V WF N+R ++++N F N+ A +
Sbjct: 29 YPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKT 78
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 30/51 (58%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ HQ LEK F Y R E+A+ + L+E +V++WFQNRR K ++
Sbjct: 20 YTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%)
Query: 51 YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHRNLDAPTS 100
YP +EELAKK ++ ++V WF N+R ++++N F N+ A +
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKT 77
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 30/53 (56%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
+ QL LEK F Y R ELA + L+E +++WFQNRR K+++ E
Sbjct: 10 YTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>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 = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ +Q LEK F Y R E+A + L+E ++++WFQNRR K+++
Sbjct: 35 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85
>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The
Nmr Solution Structure And The Dna Binding Affinity
With The Intact Antennapedia Homeodomain
Length = 62
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ +Q LEK F Y R E+A + L+E ++++WFQNRR K+++
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 53
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 24/35 (68%)
Query: 51 YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
YP +EELAKK ++ ++V WF N+R ++++N
Sbjct: 30 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 64
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88
F+S QL L F+R Y +EL+ + LS +V+ WFQN+R K +R ++N
Sbjct: 29 FSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN 83
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
F S Q+ LE+ F + Y A +L+ K+ L A+V++WF+NRR + +
Sbjct: 9 FTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An
Antennapedia Homeodomain-Dna Complex
pdb|2HOA|A Chain A, Structure Determination Of The Antp(C39->s) Homeodomain
From Nuclear Magnetic Resonance Data In Solution Using
A Novel Strategy For The Structure Calculation With The
Programs Diana, Caliba, Habas And Glomsa
Length = 68
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ +Q LEK F Y R E+A + L+E ++++WFQNRR K+++
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59
>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 = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
+ +Q LEK F Y R ++A + LSE ++++WFQNRR K +++
Sbjct: 10 YTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ +Q LEK F Y R E+A + L+E ++++WFQNRR K+++
Sbjct: 10 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 27/45 (60%)
Query: 51 YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHRNL 95
YP +EELAKK ++ ++V WF N+R ++++N F N+
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANI 72
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ +Q LEK F Y R E+A+ + L+E +V++WFQNRR K ++
Sbjct: 8 YTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 35.8 bits (81), Expect = 0.008, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 30/43 (69%)
Query: 43 EKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
++ F Y R++L+ ++ L+EA++++WFQN+RAK +++
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 44
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 35.4 bits (80), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 29/52 (55%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
++ QL LE+ + + R +++ LSE ++ +WFQNRR K +++
Sbjct: 14 YSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS 65
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 35.0 bits (79), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 27/52 (51%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F +QL L+ F+ YP E+L+ + L + VWFQN R K R++
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65
>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 = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 26/38 (68%)
Query: 42 LEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79
LE+VF R ++ +EE+AKK ++ +V+VWF N+R
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR 417
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
F+ QL AL+ F++ Y +EL+ + LS +V+ WFQN+R K +R
Sbjct: 10 FSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 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 = 34.3 bits (77), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 51 YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
YP +EELA+K ++ ++V WF N+R ++++N
Sbjct: 28 YPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKN 62
>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 = 33.9 bits (76), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 26/38 (68%)
Query: 42 LEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79
LE+VF R ++ +EE+AKK ++ +V+VWF N+R
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR 57
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 33.9 bits (76), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 27/40 (67%)
Query: 42 LEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
LE+VF R ++ +EE+AKK ++ +V+VWF N+R +
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 33.9 bits (76), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 26/38 (68%)
Query: 42 LEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79
LE+VF R ++ +EE+AKK ++ +V+VWF N+R
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKR 57
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 33.1 bits (74), Expect = 0.056, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 24/53 (45%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
F L + + YP + ELA+ L+ +V WF+NRR + R E
Sbjct: 501 FKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 553
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 32.3 bits (72), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
+ QL LE+ + + R ++ LSE +V +WFQNRR K
Sbjct: 14 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 61
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 32.3 bits (72), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
+ QL LE+ + + R ++ LSE +V +WFQNRR K
Sbjct: 8 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 55
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%)
Query: 38 QLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79
QL+AL+ F R +P E L K LS V+ WF +RR
Sbjct: 19 QLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 31.6 bits (70), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 26/41 (63%), Gaps = 1/41 (2%)
Query: 40 NALEKVF-ERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79
+ LEKVF T YPD + L+K++ S ++Q WF++RR
Sbjct: 21 DTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 61
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
Length = 96
Score = 30.8 bits (68), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%)
Query: 38 QLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
QL+ L+ F RT +P ++LAK+ L+ + WF + R ++
Sbjct: 36 QLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNG 83
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 30.8 bits (68), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 38 QLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
QL L + + P + + +A +V L + VQVWFQN RA+ R++
Sbjct: 28 QLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS 75
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 30.8 bits (68), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 38 QLNALEKVFERTH-YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
Q+ LE F + + +PD +A + L+E + Q WF+ R A++RR+E
Sbjct: 13 QVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 30.4 bits (67), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 29/50 (58%), Gaps = 1/50 (2%)
Query: 38 QLNALEKVFERTH-YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
Q+ LE F + + +PD +A + L+E + Q WF+ R A++RR+E
Sbjct: 12 QVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 29.3 bits (64), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 41 ALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
ALEK F P + +A+++ + + ++VWF NRR K +R
Sbjct: 115 ALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 29.3 bits (64), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 15/61 (24%)
Query: 39 LNALEKVFERTHYPDAFVREELA-----------KKVC----LSEARVQVWFQNRRAKFR 83
L +E F YPD REE+A KK+ ++ +V WF NRR + +
Sbjct: 19 LAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIK 78
Query: 84 R 84
R
Sbjct: 79 R 79
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 29.3 bits (64), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 41 ALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
ALEK F P + +A ++ + + ++VWF NRR K +R
Sbjct: 114 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKR 157
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 29.3 bits (64), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 22/50 (44%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
F + AL FE+ P E AK++ V+VWF NRR +
Sbjct: 100 FTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRRQTLK 149
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%)
Query: 41 ALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
+LE +F ++ P +A ++ L + V+VWF NRR K +R+
Sbjct: 110 SLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS 154
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 28.5 bits (62), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 23/45 (51%)
Query: 40 NALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
ALE F + P A LA + L + V+VWF NRR K +R
Sbjct: 112 GALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR 156
>pdb|1X2M|A Chain A, Solution Structure Of The Homeobox Domain Of Mouse Lag1
Longevity Assurance Homolog 6
Length = 64
Score = 28.1 bits (61), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 35 NSHQLNA-LEKVFER-THYPDAFVREELAKKVCLSEARVQVWFQNRR 79
+ Q NA LEKVF T +PD E L+K++ +Q WF+ RR
Sbjct: 7 GTAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRR 53
>pdb|1OHF|A Chain A, The Refined Structure Of Nudaurelia Capensis Omega Virus
pdb|1OHF|B Chain B, The Refined Structure Of Nudaurelia Capensis Omega Virus
pdb|1OHF|C Chain C, The Refined Structure Of Nudaurelia Capensis Omega Virus
pdb|1OHF|D Chain D, The Refined Structure Of Nudaurelia Capensis Omega Virus
Length = 644
Score = 27.7 bits (60), Expect = 2.1, Method: Composition-based stats.
Identities = 15/27 (55%), Positives = 16/27 (59%), Gaps = 6/27 (22%)
Query: 88 NFISHRNLDAPT------SEQPLPPCT 108
N I+ RNLDA T SE PLPP T
Sbjct: 404 NVINFRNLDAETTAASNRSEVPLPPLT 430
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 41 ALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
ALEK F P + +A ++ + + ++VWF NRR K +R
Sbjct: 118 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 161
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 27.3 bits (59), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 41 ALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
ALEK F P + +A ++ + + ++VWF NRR K +R
Sbjct: 117 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 160
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 41 ALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
ALEK F P + +A ++ + + ++VWF NRR K +R
Sbjct: 110 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 153
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 25.8 bits (55), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 41 ALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
ALEK F P + +A ++ + + ++VWF NRR K +R
Sbjct: 21 ALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
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
0.324 0.133 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,211,055
Number of Sequences: 62578
Number of extensions: 84803
Number of successful extensions: 253
Number of sequences better than 100.0: 91
Number of HSP's better than 100.0 without gapping: 88
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 164
Number of HSP's gapped (non-prelim): 91
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: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 46 (22.3 bits)