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= psy15100
(165 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 70.9 bits (172), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 32/57 (56%), Positives = 41/57 (71%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
+AFT EQL+ LE +F +YLS+ ER +A +L L+E QVKIWFQNRR KWK+ G
Sbjct: 12 TAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIKAG 68
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 70.1 bits (170), Expect = 5e-13, Method: Compositional matrix adjust.
Identities = 34/55 (61%), Positives = 41/55 (74%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
P + FT QL+ALE KF+ +YLS+ ER + SLSLTETQVKIWFQNRR K K+
Sbjct: 3 PRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 67.8 bits (164), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 31/58 (53%), Positives = 43/58 (74%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
P + ++ QL AL+ +F+ T+YL++ ER LA SL LT+TQVKIWFQN+R+K KK P
Sbjct: 10 PRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP 67
>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 = 66.6 bits (161), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 30/64 (46%), Positives = 42/64 (65%)
Query: 34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
+TP + P ++FT Q+ LE +F +YL+ ER LA L +T+ QVK WFQNRRTK
Sbjct: 12 RTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTK 71
Query: 94 WKKQ 97
W++Q
Sbjct: 72 WRRQ 75
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 65.5 bits (158), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 29/56 (51%), Positives = 40/56 (71%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
+ FT QL+ LE +F+ +YLS +R++LA SL L++ QVK W+QNRR KWKK P
Sbjct: 22 TVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP 77
>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 = 63.9 bits (154), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 29/56 (51%), Positives = 38/56 (67%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
+T Q + LE +F RYL+ R+ +A +LSLTE Q+KIWFQNRR KWKK+N
Sbjct: 7 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
>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 = 63.5 bits (153), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 29/54 (53%), Positives = 38/54 (70%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
+T Q + LE +F RYL+ R+ +A +LSLTE Q+KIWFQNRR KWKK+N
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 63.2 bits (152), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 29/55 (52%), Positives = 38/55 (69%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
+T Q + LE +F RYL+ R+ +A +LSLTE Q+KIWFQNRR KWKK+N
Sbjct: 8 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 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 = 62.8 bits (151), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 28/56 (50%), Positives = 40/56 (71%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
+++T Q + LE +F RYL+ R+ +A +LSLTE Q+KIWFQNRR KWKK++
Sbjct: 33 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88
>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 = 61.6 bits (148), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 28/56 (50%), Positives = 37/56 (66%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
+T Q + LE +F RYL+ R+ +A +L LTE Q+KIWFQNRR KWKK+N
Sbjct: 7 QTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/55 (52%), Positives = 37/55 (67%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
F+ +Q + LE KF+T +YLS ER LA L L+E QVK WFQNRR KW++ P
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS 68
>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 = 60.8 bits (146), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 28/54 (51%), Positives = 39/54 (72%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
+A+T QL+ LE +F +Y+S R+ LA+ L+LTE +KIWFQNRR KWKK+
Sbjct: 8 TAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 60.8 bits (146), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 39/54 (72%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
++F+ Q++ LE +F +YL+ ER LA +L +T+ QVK WFQNRRTKW++Q
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 60.8 bits (146), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 29/52 (55%), Positives = 35/52 (67%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
FT QL LE +F +YLS R+ +A +L L ETQVKIWFQNRR K KK+
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR 92
>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 = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/54 (53%), Positives = 38/54 (70%)
Query: 50 QLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
Q++ LE KF +YLS ER +LA +L LTETQVKIWFQNRR K K++ ++
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSEL 68
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/54 (50%), Positives = 36/54 (66%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
FT EQL ALEN F+ T+Y V R LA + L E +V++WF+NRR KW++ P
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP 67
>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 = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/52 (57%), Positives = 33/52 (63%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
P F+ Q+ LE +FK RYLS ER LA L LT TQVKIWFQNRR K
Sbjct: 5 PRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 57.0 bits (136), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 27/52 (51%), Positives = 36/52 (69%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
+T Q + LE +F T YL+ R+ +A +LSLTE Q+KIWFQNRR K KK+
Sbjct: 27 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>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 = 56.2 bits (134), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/55 (49%), Positives = 35/55 (63%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
P +AF+ EQL L+ +F RYL+ R L+ L L E Q+KIWFQN+R K KK
Sbjct: 6 PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/55 (49%), Positives = 35/55 (63%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
P +AF+ EQL L+ +F RYL+ R L+ L L E Q+KIWFQN+R K KK
Sbjct: 4 PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 40/68 (58%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDV 103
++FT EQ+ ALE +F+ T Y V R LA + L E ++++WF NRR KW+++ +
Sbjct: 12 TSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRNQ 71
Query: 104 NSPTVPTC 111
+ P+
Sbjct: 72 RRQSGPSS 79
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 33/54 (61%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
FT QL LE F T Y V R LA+ + LTE ++++WFQNRR KW+KQ
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 = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 34/56 (60%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
+ FT QL LE F T Y V R LA+ + LTE ++++WFQNRR KW+KQ
Sbjct: 11 TTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
>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 = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/55 (49%), Positives = 34/55 (61%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
P +AF+ EQL L+ +F RYL+ R L+ L L E Q+KIWFQN R K KK
Sbjct: 4 PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/52 (53%), Positives = 35/52 (67%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
F+ Q+ LE +FK +YLS ER +LA + LT TQVKIWFQN R K K+Q
Sbjct: 9 FSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 34/55 (61%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
+ FT QL LE F T Y V R LA+ + LTE ++++WFQNRR KW+KQ
Sbjct: 4 TTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>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 = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/55 (49%), Positives = 34/55 (61%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
P +AF+ EQL L+ +F RYL+ R L+ L L E Q+KIWFQN R K KK
Sbjct: 4 PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>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 = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 35/55 (63%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
P +AF+ EQL L+ +F RYL+ R L+ L L E Q+KIWF+N+R K KK
Sbjct: 6 PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>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 = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 36/51 (70%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
+T Q + LE +F RY++ R+++A +LSL+E Q+KIWFQNRR K KK
Sbjct: 10 YTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 34/54 (62%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
+ FT QL LE F+ T Y V R LA+ LTE +V++WFQNRR KW+K+
Sbjct: 14 TTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 53.5 bits (127), Expect = 5e-08, Method: Composition-based stats.
Identities = 25/52 (48%), Positives = 33/52 (63%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
P +AF+ EQL L+ +F RYL+ R L+ L L E Q+KIWFQN+R K
Sbjct: 2 PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>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 = 53.5 bits (127), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 34/55 (61%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
P +AF+ EQL L+ +F RYL+ R L+ L L E Q+KIWF N+R K KK
Sbjct: 2 PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>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 = 53.5 bits (127), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 28/51 (54%), Positives = 33/51 (64%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
FT Q LE +F+ RYLS ER +LA + LT TQVKIWFQN R K K+
Sbjct: 16 FTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 53.1 bits (126), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 33/54 (61%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
+ FT EQL LE F+ T Y + R LA LTE +V++WF NRR +W+KQ
Sbjct: 7 TTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 34/55 (61%)
Query: 42 PESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
P +AF+ EQL + +F RYL+ R L+ L L E Q+KIWFQN+R K ++
Sbjct: 6 PRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/60 (45%), Positives = 36/60 (60%)
Query: 37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
S++ P +AF+ EQL L+ +F RYL+ R L+ L L E QVK WF+N R K KK
Sbjct: 2 SDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/51 (52%), Positives = 32/51 (62%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
FT Q LE +F+ RYLS ER +L + LT TQVKIWFQN R K K+
Sbjct: 19 FTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69
>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 = 50.8 bits (120), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 36/56 (64%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM 101
FT +QL LE F+ RY + R +A+ +LTE +V++WF+NRR KW+K+ +
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI 65
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 50.1 bits (118), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/55 (49%), Positives = 33/55 (60%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
+T Q + LE +F YL+ R +A L+LTE QVKIWFQNRR K KK N
Sbjct: 20 YTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD 74
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 49.3 bits (116), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 27/53 (50%), Positives = 33/53 (62%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
+T Q + LE +F YL+ R +A L+LTE QVKIWFQNRR K KK N
Sbjct: 8 YTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 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 = 49.3 bits (116), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 35/54 (64%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97
+AFT +QL LE +F Y+S R LA L+L E+ +K+WFQNRR K K+Q
Sbjct: 6 TAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>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 = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 36/58 (62%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM 101
+ F+ QL LE F+ T+Y + R LA +LTE ++++WFQNRR + +KQ+ +
Sbjct: 23 TTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTSV 80
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 35/56 (62%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM 101
FT +QL LE F+ Y + R +A+ +LTE +V++WF+NRR KW+K+ +
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFI 65
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 34/54 (62%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
++ QL LE ++ ++++ +R ++ + SL+E Q+ IWFQNRR K KK P
Sbjct: 14 YSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP 67
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
+ FT QL LE F TRY + R +AL ++L E++V++WF+NRR K
Sbjct: 12 TTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 43/78 (55%), Gaps = 9/78 (11%)
Query: 30 SPNTQTPSEDLVP------ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQV 83
+ N+ ED VP + F+ QL L ++F+ +YLS+ + L+ L+L+ QV
Sbjct: 7 AENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV 66
Query: 84 KIWFQNRRTK---WKKQN 98
K WFQN+R K W+K N
Sbjct: 67 KTWFQNQRMKSKRWQKNN 84
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 35/57 (61%), Gaps = 4/57 (7%)
Query: 42 PESAFTYEQLVALENKFKTTRY--LSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
P +AFT Q+ LEN F+ Y + + E +LA L+L +++IWFQNRR K K+
Sbjct: 4 PRTAFTQNQIEVLENVFRVNCYPGIDILE--DLAQKLNLELDRIQIWFQNRRAKLKR 58
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 32/55 (58%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
+ FT Q+ LE F RYL+ +L+ L+L QVKIWF+NRR + K Q+
Sbjct: 7 TTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61
>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 = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 36/53 (67%)
Query: 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
+ F+ QL AL+++F+ +YLS+ + L+ L+L+ QVK WFQN+R K K+
Sbjct: 8 TVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 44.3 bits (103), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 34/51 (66%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
+T QL LE ++ T ++++ +R ++ + +L+E QV IWFQNRR K KK
Sbjct: 14 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 43.9 bits (102), Expect = 4e-05, Method: Composition-based stats.
Identities = 20/42 (47%), Positives = 26/42 (61%)
Query: 55 ENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
+ +F RYL+ R L+ L L E Q+KIWFQN+R K KK
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 34/51 (66%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
+T QL LE ++ T ++++ +R ++ + +L+E QV IWFQNRR K KK
Sbjct: 8 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|2NZZ|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
pdb|2O00|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
Length = 37
Score = 37.7 bits (86), Expect = 0.003, Method: Composition-based stats.
Identities = 13/16 (81%), Positives = 15/16 (93%)
Query: 82 QVKIWFQNRRTKWKKQ 97
Q+KIWFQNRR KWKK+
Sbjct: 2 QIKIWFQNRRMKWKKR 17
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 37.0 bits (84), Expect = 0.005, Method: Composition-based stats.
Identities = 13/15 (86%), Positives = 14/15 (93%)
Query: 82 QVKIWFQNRRTKWKK 96
Q+KIWFQNRR KWKK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 36.6 bits (83), Expect = 0.007, Method: Composition-based stats.
Identities = 13/15 (86%), Positives = 14/15 (93%)
Query: 82 QVKIWFQNRRTKWKK 96
Q+KIWFQNRR KWKK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 32.7 bits (73), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 25/48 (52%)
Query: 53 ALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
ALE+ F S E LA SL L + V++WF NRR K K+ P
Sbjct: 113 ALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA 160
>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 = 31.2 bits (69), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 52 VALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
VALE F + + E +A L++ + +++WF NRR K K+ NP
Sbjct: 117 VALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 164
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 30.8 bits (68), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 28/54 (51%)
Query: 43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
++F + QL +++ F + LA LT+ +++WFQN R K+++
Sbjct: 11 RTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64
>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 = 30.4 bits (67), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 52 VALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
VALE F + + E +A L++ + +++WF NRR K K+ NP
Sbjct: 116 VALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 163
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 30.4 bits (67), Expect = 0.52, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 19/31 (61%)
Query: 63 YLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
Y S E+ LA + LT TQV WF+NRR +
Sbjct: 518 YPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.0 bits (66), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 26/55 (47%)
Query: 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100
FT QL L++ F Y E L+ L+L + +WFQN R K +K P
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS 68
>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 = 30.0 bits (66), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 54 LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
LE F+ + L+ E+ +A +T QV++WF N+R +
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>pdb|2AM1|A Chain A, Sp Protein Ligand 1
pdb|2AM2|A Chain A, Sp Protein Ligand 2
Length = 454
Score = 30.0 bits (66), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 5/46 (10%)
Query: 72 LALSLSLTETQVKIWFQN-----RRTKWKKQNPGMDVNSPTVPTCP 112
+AL ++E Q+++ FQ+ RT+WKK G D+ S P
Sbjct: 284 VALQEGVSEEQIRLAFQHLELTRNRTEWKKAANGADILSDVYNANP 329
>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 = 30.0 bits (66), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%)
Query: 52 VALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
VALE F + + E +A L++ + +++WF NRR K K+ NP
Sbjct: 109 VALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRINP 156
>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 = 29.6 bits (65), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 24/50 (48%)
Query: 49 EQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
EQL L++ F T++ S E LA L T + WF + R WK N
Sbjct: 35 EQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN 84
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 29.6 bits (65), Expect = 0.84, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 29/53 (54%)
Query: 43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
+S+ + + LE F+ + L+ E+ +A +T QV++WF N+R + K
Sbjct: 1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 29.3 bits (64), Expect = 0.98, Method: Composition-based stats.
Identities = 11/15 (73%), Positives = 14/15 (93%)
Query: 82 QVKIWFQNRRTKWKK 96
Q+KI+FQNRR K+KK
Sbjct: 2 QIKIFFQNRRMKFKK 16
>pdb|1HDP|A Chain A, Solution Structure Of A Pou-Specific Homeodomain: 3d-Nmr
Studies Of Human B-Cell Transcription Factor Oct-2
Length = 63
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 26/47 (55%)
Query: 53 ALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99
ALE F + + E L +A L + + +++WF NRR K K+ NP
Sbjct: 15 ALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKRINP 61
>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 = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 52 VALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
VALE F + + E +A L++ + +++WF NRR K K+ N
Sbjct: 113 VALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKRIN 159
>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 = 28.5 bits (62), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 54 LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
LE F+ + L+ E+ +A +T QV++WF N+R + K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 28.5 bits (62), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 54 LENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
LE F+ + L+ E+ +A +T QV++WF N+R + K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 26/47 (55%)
Query: 52 VALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98
VALE F + + + +A L++ + +++WF NRR K K+ N
Sbjct: 114 VALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRIN 160
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 47 TYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR 91
++EQL AL+ F ++ E +L L+ +V+ WF +RR
Sbjct: 16 SHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
>pdb|1MNM|C Chain C, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
pdb|1MNM|D Chain D, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
Length = 87
Score = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 32/69 (46%), Gaps = 10/69 (14%)
Query: 37 SEDLVPESA-------FTYEQLVALENKFKTTR---YLSVCERLNLALSLSLTETQVKIW 86
++D++ +S FT E + LE+ F YL NL + SL+ Q+K W
Sbjct: 18 TQDMINKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNW 77
Query: 87 FQNRRTKWK 95
NRR K K
Sbjct: 78 VSNRRRKEK 86
>pdb|1APL|C Chain C, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1APL|D Chain D, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1YRN|B Chain B, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1AKH|B Chain B, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 83
Score = 27.3 bits (59), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 25/53 (47%), Gaps = 3/53 (5%)
Query: 46 FTYEQLVALENKFKTTR---YLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95
FT E + LE+ F YL NL + SL+ Q+K W NRR K K
Sbjct: 9 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 61
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 26.9 bits (58), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 10/72 (13%)
Query: 34 QTPSEDLVPESAFTYEQLVALENKFK-----TTRYLSVCERLNLALSLSLTETQVKIWFQ 88
+ P D + T EQL L K+ T + L ++A + L + V++WFQ
Sbjct: 12 EEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLD-----HIAHEVGLKKRVVQVWFQ 66
Query: 89 NRRTKWKKQNPG 100
N R + +K P
Sbjct: 67 NTRARERKSGPS 78
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 26.9 bits (58), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 72 LALSLSLTETQVKIWFQNRRTKWKK 96
LA +T +QV WF N+R ++KK
Sbjct: 39 LAKKCGITVSQVSNWFGNKRIRYKK 63
>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 = 6.2, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%)
Query: 53 ALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96
ALE F S E + +A L+L + V++WF NRR + K+
Sbjct: 101 ALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144
>pdb|1LGA|A Chain A, Crystallographic Refinement Of Lignin Peroxidase At 2
Angstroms
pdb|1LGA|B Chain B, Crystallographic Refinement Of Lignin Peroxidase At 2
Angstroms
pdb|1LLP|A Chain A, Lignin Peroxidase (isozyme H2) Pi 4.15
Length = 343
Score = 26.6 bits (57), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 28 GRSPNTQTPSEDLVPESAFTYEQLVALENK 57
GR P TQ + LVPE T +Q++A N
Sbjct: 131 GRKPATQPAPDGLVPEPFHTVDQIIARVND 160
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 26.6 bits (57), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 72 LALSLSLTETQVKIWFQNRRTKWKK 96
LA +T +QV WF N+R ++KK
Sbjct: 37 LAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 26.2 bits (56), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 72 LALSLSLTETQVKIWFQNRRTKWKK 96
+A LTE Q + WF+ R +W++
Sbjct: 35 IAAEAGLTEEQTQKWFKQRLAEWRR 59
>pdb|1K61|A Chain A, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|B Chain B, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|C Chain C, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|D Chain D, Matalpha2 Homeodomain Bound To Dna
Length = 60
Score = 26.2 bits (56), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 46 FTYEQLVALENKFKTTR---YLSVCERLNLALSLSLTETQVKIWFQNRRTK 93
FT E + LE+ F YL NL + SL+ Q+K W NRR K
Sbjct: 5 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK 55
>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 = 26.2 bits (56), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 83 VKIWFQNRRTKWKKQNPGM 101
+++WFQN+R K KK++ M
Sbjct: 47 IRVWFQNKRCKDKKRSIMM 65
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 26.2 bits (56), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 72 LALSLSLTETQVKIWFQNRRTKWKK 96
LA +T +QV WF N+R ++KK
Sbjct: 37 LAKKCGITVSQVSNWFGNKRIRYKK 61
>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 = 26.2 bits (56), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 72 LALSLSLTETQVKIWFQNRRTKWKK 96
LA +T +QV WF N+R ++KK
Sbjct: 37 LARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 26.2 bits (56), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 72 LALSLSLTETQVKIWFQNRRTKWKK 96
+A LTE Q + WF+ R +W++
Sbjct: 36 IAAEAGLTEEQTQKWFKQRLAEWRR 60
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 0.131 0.411
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,112,658
Number of Sequences: 62578
Number of extensions: 153229
Number of successful extensions: 367
Number of sequences better than 100.0: 97
Number of HSP's better than 100.0 without gapping: 95
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 267
Number of HSP's gapped (non-prelim): 102
length of query: 165
length of database: 14,973,337
effective HSP length: 91
effective length of query: 74
effective length of database: 9,278,739
effective search space: 686626686
effective search space used: 686626686
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 47 (22.7 bits)