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= psy4877
(120 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 21/43 (48%), Positives = 33/43 (76%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
+ KYL+ ++R L++ L +T+ Q+KTWFQNRRTKW++Q A +
Sbjct: 37 HKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE 79
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 28/42 (66%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLL 44
L++ L +T+ Q+KTWFQNRRTKW+ ++R ++L+
Sbjct: 50 LARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAERQAANRLM 91
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 21/36 (58%), Positives = 30/36 (83%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
KYL+ ++R L+K L +T+ Q+KTWFQNRRTKW++Q
Sbjct: 20 KYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 16/24 (66%), Positives = 21/24 (87%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWK 26
L+K L +T+ Q+KTWFQNRRTKW+
Sbjct: 30 LAKALRMTDAQVKTWFQNRRTKWR 53
>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 = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/37 (62%), Positives = 30/37 (81%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
+KY+S +R+EL+ +LNLTE IK WFQNRR KWKK+
Sbjct: 25 NKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/26 (69%), Positives = 21/26 (80%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWK 26
+EL+ +LNLTE IK WFQNRR KWK
Sbjct: 34 VELAVMLNLTERHIKIWFQNRRMKWK 59
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 20/38 (52%), Positives = 30/38 (78%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
+ KYLS+++R +++ L L+EVQ+K WFQNRR KWK+
Sbjct: 27 HCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 15/27 (55%), Positives = 21/27 (77%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWKYV 28
+++ L L+EVQ+K WFQNRR KWK +
Sbjct: 39 QIAHALKLSEVQVKIWFQNRRAKWKRI 65
>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 = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/43 (51%), Positives = 33/43 (76%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
+ ++YL+ +R+E++ L+LTE QIK WFQNRR KWKK+ +K
Sbjct: 22 HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 64
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/30 (60%), Positives = 23/30 (76%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
+E++ L+LTE QIK WFQNRR KWK +K
Sbjct: 33 IEIAHALSLTERQIKIWFQNRRMKWKKENK 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 = 50.4 bits (119), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/43 (51%), Positives = 33/43 (76%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
+ ++YL+ +R+E++ L+LTE QIK WFQNRR KWKK+ +K
Sbjct: 16 HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 58
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/30 (60%), Positives = 23/30 (76%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
+E++ L+LTE QIK WFQNRR KWK +K
Sbjct: 27 IEIAHALSLTERQIKIWFQNRRMKWKKENK 56
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 21/39 (53%), Positives = 31/39 (79%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
+ ++YL+ +R+E++ L+LTE QIK WFQNRR KWKK+
Sbjct: 48 HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 86
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/26 (65%), Positives = 21/26 (80%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWK 26
+E++ L+LTE QIK WFQNRR KWK
Sbjct: 59 IEIAHALSLTERQIKIWFQNRRMKWK 84
>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 = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/43 (51%), Positives = 32/43 (74%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
+ ++YL+ +R+E++ L LTE QIK WFQNRR KWKK+ +K
Sbjct: 22 HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKTK 64
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/30 (60%), Positives = 22/30 (73%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
+E++ L LTE QIK WFQNRR KWK +K
Sbjct: 33 IEIAHALCLTERQIKIWFQNRRMKWKKENK 62
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 21/39 (53%), Positives = 31/39 (79%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
+ ++YL+ +R+E++ L+LTE QIK WFQNRR KWKK+
Sbjct: 23 HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
Score = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/26 (65%), Positives = 21/26 (80%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWK 26
+E++ L+LTE QIK WFQNRR KWK
Sbjct: 34 IEIAHALSLTERQIKIWFQNRRMKWK 59
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 48.5 bits (114), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 21/37 (56%), Positives = 28/37 (75%)
Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
KYLS +R L+K+L L+E Q+KTWFQNRR KW++
Sbjct: 28 TQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 16/24 (66%), Positives = 21/24 (87%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWK 26
L+K+L L+E Q+KTWFQNRR KW+
Sbjct: 40 LAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 20/35 (57%), Positives = 29/35 (82%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
KYLS R++L++ L L+++Q+KTW+QNRR KWKK
Sbjct: 40 KYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 23/26 (88%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWK 26
++L++ L L+++Q+KTW+QNRR KWK
Sbjct: 48 IDLAESLGLSQLQVKTWYQNRRMKWK 73
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/34 (61%), Positives = 27/34 (79%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
YL+ +R E+++LLNLTE Q+K WFQNRR K KK
Sbjct: 37 YLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 18/29 (62%), Positives = 24/29 (82%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
E+++LLNLTE Q+K WFQNRR K K ++K
Sbjct: 45 EVARLLNLTERQVKIWFQNRRMKMKKINK 73
>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 = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/43 (60%), Positives = 31/43 (72%), Gaps = 1/43 (2%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK-KQLASKL 70
KYLS +R L+K L LTE Q+K WFQNRR K K KQL+S+L
Sbjct: 26 QKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSEL 68
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/24 (66%), Positives = 18/24 (75%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWK 26
L+K L LTE Q+K WFQNRR K K
Sbjct: 37 LAKNLKLTETQVKIWFQNRRYKTK 60
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 31/42 (73%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS 68
+ + YL+ +R+E++ L+LTE QIK WFQNRR K KK++ +
Sbjct: 40 HTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQA 81
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/26 (61%), Positives = 20/26 (76%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWK 26
+E++ L+LTE QIK WFQNRR K K
Sbjct: 51 IEMAHALSLTERQIKIWFQNRRMKLK 76
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 46.6 bits (109), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 20/39 (51%), Positives = 29/39 (74%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
+ +KYLS ++R+E++ L L E Q+K WFQNRR K KK+
Sbjct: 54 HFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR 92
Score = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
+E++ L L E Q+K WFQNRR K K ++
Sbjct: 65 VEIAATLELNETQVKIWFQNRRMKQKKRER 94
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 20/35 (57%), Positives = 27/35 (77%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
+YLS+++R E S L+LTE Q+K WFQNRR K K+
Sbjct: 23 QYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/25 (64%), Positives = 18/25 (72%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
E S L+LTE Q+K WFQNRR K K
Sbjct: 32 EFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 45.8 bits (107), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 20/34 (58%), Positives = 27/34 (79%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
YL+ +R E++++LNLTE Q+K WFQNRR K KK
Sbjct: 25 YLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/25 (64%), Positives = 21/25 (84%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
E++++LNLTE Q+K WFQNRR K K
Sbjct: 33 EVARVLNLTERQVKIWFQNRRMKMK 57
>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 = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/36 (55%), Positives = 27/36 (75%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
KYLS+ + ELS +LNL+ Q+KTWFQN+R K K+
Sbjct: 25 QKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 16/25 (64%), Positives = 20/25 (80%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
ELS +LNL+ Q+KTWFQN+R K K
Sbjct: 35 ELSSILNLSYKQVKTWFQNQRMKCK 59
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 27/35 (77%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
+YL++ +R EL+ L LT+ Q+K WFQN+R+K KK
Sbjct: 30 QYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
Score = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 19/25 (76%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL+ L LT+ Q+K WFQN+R+K K
Sbjct: 39 ELAASLGLTQTQVKIWFQNKRSKIK 63
>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 = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/39 (53%), Positives = 26/39 (66%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
Y + Y+S +R EL+ LNL E IK WFQNRR K K+Q
Sbjct: 21 YKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
Score = 32.0 bits (71), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 16/26 (61%), Positives = 17/26 (65%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWK 26
EL+ LNL E IK WFQNRR K K
Sbjct: 32 CELAAQLNLPESTIKVWFQNRRMKDK 57
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 19/35 (54%), Positives = 24/35 (68%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
Y V R EL+ + LTE +I+ WFQNRR KW+KQ
Sbjct: 23 YPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 21/29 (72%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
EL+ + LTE +I+ WFQNRR KW+ +K
Sbjct: 31 ELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 42.0 bits (97), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/35 (57%), Positives = 27/35 (77%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
KYLS+ + ELS +LNL+ Q+KTWFQN+R K K+
Sbjct: 45 KYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 16/25 (64%), Positives = 20/25 (80%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
ELS +LNL+ Q+KTWFQN+R K K
Sbjct: 54 ELSNILNLSYKQVKTWFQNQRMKSK 78
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/35 (54%), Positives = 24/35 (68%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
Y V R EL+ + LTE +I+ WFQNRR KW+KQ
Sbjct: 23 YPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 19/25 (76%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL+ + LTE +I+ WFQNRR KW+
Sbjct: 31 ELAMKIGLTEARIQVWFQNRRAKWR 55
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/35 (54%), Positives = 24/35 (68%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
Y V R EL+ + LTE +I+ WFQNRR KW+KQ
Sbjct: 30 YPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/29 (51%), Positives = 21/29 (72%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
EL+ + LTE +I+ WFQNRR KW+ +K
Sbjct: 38 ELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
++YL+ +R +LS L L E QIK WFQN+R K KK
Sbjct: 23 NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
Score = 32.0 bits (71), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 17/25 (68%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+LS L L E QIK WFQN+R K K
Sbjct: 33 QLSSELGLNEAQIKIWFQNKRAKIK 57
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
++YL+ +R +LS L L E QIK WFQN+R K KK
Sbjct: 25 NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
Score = 32.3 bits (72), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 17/25 (68%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+LS L L E QIK WFQN+R K K
Sbjct: 35 QLSSELGLNEAQIKIWFQNKRAKIK 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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 17/38 (44%), Positives = 29/38 (76%)
Query: 27 YVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
+ ++Y++ +R++++ L+L+E QIK WFQNRR K KK
Sbjct: 23 HFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
Score = 32.7 bits (73), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 20/26 (76%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWK 26
++++ L+L+E QIK WFQNRR K K
Sbjct: 34 IDIANALSLSERQIKIWFQNRRMKSK 59
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 25/36 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
++YL+ +R +LS L L E QIK WFQN+R K KK
Sbjct: 8 NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
Score = 32.0 bits (71), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 17/25 (68%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+LS L L E QIK WFQN+R K K
Sbjct: 18 QLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/41 (46%), Positives = 26/41 (63%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69
KYLS +R L+ +++LT Q+K WFQN R K K+Q K
Sbjct: 24 QKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK 64
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 17/24 (70%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWK 26
L+ +++LT Q+K WFQN R K K
Sbjct: 35 LASMIHLTPTQVKIWFQNHRYKMK 58
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 24/36 (66%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
++YL+ +R +LS L L E QIK WFQN R K KK
Sbjct: 23 NRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
Score = 31.2 bits (69), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 16/25 (64%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+LS L L E QIK WFQN R K K
Sbjct: 33 QLSSELGLNEAQIKIWFQNERAKIK 57
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 27/37 (72%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
++Y +S R E++ NLTE +++ WF+NRR KW+K+
Sbjct: 25 NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 23/31 (74%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYL 32
E++ NLTE +++ WF+NRR KW+ ++++
Sbjct: 35 EIAVWTNLTEARVRVWFKNRRAKWRKREEFI 65
>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 = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/39 (46%), Positives = 26/39 (66%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS 68
+Y + R EL++ NLTE +I+ WFQNRR + +KQ S
Sbjct: 41 QYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHTS 79
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 24/34 (70%), Gaps = 2/34 (5%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVS 35
EL++ NLTE +I+ WFQNRR + + ++ SVS
Sbjct: 50 ELAQRTNLTEARIQVWFQNRRARLR--KQHTSVS 81
>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 = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 24/36 (66%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
++YL+ +R +LS L L E QIK WFQN R K KK
Sbjct: 23 NRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 16/25 (64%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+LS L L E QIK WFQN R K K
Sbjct: 33 QLSSELGLNEAQIKIWFQNARAKIK 57
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
++YL+ +R +LS L L E QIK WFQN+R K ++
Sbjct: 25 NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 14/24 (58%), Positives = 16/24 (66%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTK 24
+LS L L E QIK WFQN+R K
Sbjct: 34 QQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 26/37 (70%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
+ Y +S R E++ NLTE +++ WF+NRR KW+K+
Sbjct: 25 NHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 23/31 (74%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYL 32
E++ NLTE +++ WF+NRR KW+ ++++
Sbjct: 35 EIAVWTNLTEARVRVWFKNRRAKWRKREEFI 65
>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 = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 25/36 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
++YL+ +R +LS L L E QIK WF+N+R K KK
Sbjct: 25 NRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
Score = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 17/25 (68%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+LS L L E QIK WF+N+R K K
Sbjct: 35 QLSSELGLNEAQIKIWFKNKRAKIK 59
>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 = 6e-04, Method: Compositional matrix adjust.
Identities = 18/35 (51%), Positives = 24/35 (68%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
+YLS +R +L+ +L LT Q+K WFQNRR K K
Sbjct: 24 QRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
Score = 32.3 bits (72), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 18/25 (72%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+L+ +L LT Q+K WFQNRR K K
Sbjct: 34 QLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 23/33 (69%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK 61
++YL+ +R +LS L L E QIK WFQN+R K
Sbjct: 21 NRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/23 (60%), Positives = 16/23 (69%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTK 24
+LS L L E QIK WFQN+R K
Sbjct: 31 QLSSELGLNEAQIKIWFQNKRAK 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 = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 18/36 (50%), Positives = 24/36 (66%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
++YL+ +R +LS L L E QIK WF N+R K KK
Sbjct: 21 NRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 14/25 (56%), Positives = 16/25 (64%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+LS L L E QIK WF N+R K K
Sbjct: 31 QLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
+K+++ KR +S NL+E Q+ WFQNRR K KK + +KLK +
Sbjct: 23 NKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK-VINKLKTTS 67
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWKYV 28
+S NL+E Q+ WFQNRR K K V
Sbjct: 34 ISATTNLSERQVTIWFQNRRVKEKKV 59
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVA 74
+K+++ KR +S NL+E Q+ WFQNRR K KK + +KLK +
Sbjct: 29 NKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK-VINKLKTTS 73
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 17/26 (65%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWKYV 28
+S NL+E Q+ WFQNRR K K V
Sbjct: 40 ISATTNLSERQVTIWFQNRRVKEKKV 65
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/37 (45%), Positives = 25/37 (67%)
Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
+K+++ KR ++S +L+E QI WFQNRR K KK
Sbjct: 28 ANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 17/25 (68%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
++S +L+E QI WFQNRR K K
Sbjct: 39 KISAATSLSERQITIWFQNRRVKEK 63
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
Y + R EL++ LTE +++ WF NRR +W+KQ
Sbjct: 26 YPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
Score = 32.3 bits (72), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 18/25 (72%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL++ LTE +++ WF NRR +W+
Sbjct: 34 ELAQRAKLTEARVQVWFSNRRARWR 58
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 23/36 (63%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
+YLS +R L+ L+ LT Q+K WFQN R K K+
Sbjct: 34 QRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWK 26
L+ L+ LT Q+K WFQN R K K
Sbjct: 45 LTSLIRLTPTQVKIWFQNHRYKTK 68
>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 = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 23/36 (63%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
+YLS +R L+ L+ LT Q+K WFQN R K K+
Sbjct: 31 QRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 16/24 (66%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWK 26
L+ L+ LT Q+K WFQN R K K
Sbjct: 42 LASLIRLTPTQVKIWFQNHRYKTK 65
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 37.7 bits (86), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 24/35 (68%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
Y V R +L+ +LTE +++ WFQNRR KW+K+
Sbjct: 33 YPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 22/30 (73%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKY 31
+L+ +LTE +++ WFQNRR KW+ +++
Sbjct: 41 QLAMRTDLTEARVQVWFQNRRAKWRKRERF 70
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
++YL+ +R +LS L L E Q+K WF+N R K KK
Sbjct: 26 NRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 16/25 (64%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+LS L L E Q+K WF+N R K K
Sbjct: 36 QLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 25/35 (71%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
KY V R +L++ ++L E +++ WF+NRR KW++
Sbjct: 30 KYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 20/25 (80%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+L++ ++L E +++ WF+NRR KW+
Sbjct: 39 QLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
Y V R L+ ++L E +I+ WF NRR KW+++
Sbjct: 31 YPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65
Score = 32.7 bits (73), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 19/28 (67%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDK 30
L+ ++L E +I+ WF NRR KW+ +K
Sbjct: 40 LAAKIDLPEARIQVWFSNRRAKWRREEK 67
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 32.3 bits (72), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
+YL+ + +LS L L Q+K WF+NRR + K Q
Sbjct: 25 RYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+LS L L Q+K WF+NRR + K
Sbjct: 34 DLSAKLALGTAQVKIWFKNRRRRHK 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 = 32.0 bits (71), Expect = 0.079, Method: Composition-based stats.
Identities = 13/17 (76%), Positives = 15/17 (88%)
Query: 50 QIKTWFQNRRTKWKKQL 66
QIK WFQNRR KWKK++
Sbjct: 2 QIKIWFQNRRMKWKKRV 18
Score = 30.0 bits (66), Expect = 0.38, Method: Composition-based stats.
Identities = 12/14 (85%), Positives = 12/14 (85%)
Query: 13 QIKTWFQNRRTKWK 26
QIK WFQNRR KWK
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 25/41 (60%), Gaps = 4/41 (9%)
Query: 23 TKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
K +Y D ++ R E++ +NL E +++ WF+NRR K +
Sbjct: 27 AKTRYPDIFM----REEVALKINLPESRVQVWFKNRRAKCR 63
Score = 28.5 bits (62), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 18/25 (72%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
E++ +NL E +++ WF+NRR K +
Sbjct: 39 EVALKINLPESRVQVWFKNRRAKCR 63
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 24 KWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK 61
+W + Y S ++ EL++ LT Q+ WF+NRR +
Sbjct: 511 EWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTK 24
EL++ LT Q+ WF+NRR +
Sbjct: 526 ELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66
Y S + EL+K +T Q+ WF N+R ++KK +
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI 63
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL+K +T Q+ WF N+R ++K
Sbjct: 36 ELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 23/37 (62%)
Query: 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
V+ Y + +L++ LNL +I+ WFQNRR K K+
Sbjct: 22 VNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58
Score = 28.9 bits (63), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 18/25 (72%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+L++ LNL +I+ WFQNRR K K
Sbjct: 33 DLAQKLNLELDRIQIWFQNRRAKLK 57
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA 67
Y S + EL+K +T Q+ WF N+R ++KK +
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIG 64
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL+K +T Q+ WF N+R ++K
Sbjct: 36 ELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 13/15 (86%), Positives = 13/15 (86%)
Query: 50 QIKTWFQNRRTKWKK 64
QIK WFQNRR KWKK
Sbjct: 2 QIKIWFQNRRMKWKK 16
Score = 29.3 bits (64), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 12/14 (85%), Positives = 12/14 (85%)
Query: 13 QIKTWFQNRRTKWK 26
QIK WFQNRR KWK
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 13/15 (86%), Positives = 13/15 (86%)
Query: 50 QIKTWFQNRRTKWKK 64
QIK WFQNRR KWKK
Sbjct: 2 QIKIWFQNRRMKWKK 16
Score = 28.9 bits (63), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 12/14 (85%), Positives = 12/14 (85%)
Query: 13 QIKTWFQNRRTKWK 26
QIK WFQNRR KWK
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64
Y S + EL+K +T Q+ WF N+R ++KK
Sbjct: 30 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL+K +T Q+ WF N+R ++K
Sbjct: 38 ELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 29.6 bits (65), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66
Y S + EL+K +T Q+ WF N+R ++KK +
Sbjct: 29 YPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKKNI 64
Score = 25.8 bits (55), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL+K +T Q+ WF N+R ++K
Sbjct: 37 ELAKKSGITVSQVSNWFGNKRIRYK 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 = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66
Y S + EL++ +T Q+ WF N+R ++KK +
Sbjct: 28 YPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKNI 63
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 16/25 (64%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
EL++ +T Q+ WF N+R ++K
Sbjct: 36 ELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 14/26 (53%), Positives = 16/26 (61%)
Query: 39 ELSKLLNLTEVQIKTWFQNRRTKWKK 64
+LS LLNL I WFQN R K +K
Sbjct: 39 QLSNLLNLPTRVIVVWFQNARQKARK 64
Score = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/25 (52%), Positives = 15/25 (60%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
+LS LLNL I WFQN R K +
Sbjct: 39 QLSNLLNLPTRVIVVWFQNARQKAR 63
>pdb|3NGB|G Chain G, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|A Chain A, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|D Chain D, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3NGB|I Chain I, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc01 In Complex With Hiv-1 Gp120
pdb|3SE8|G Chain G, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc03 In Complex With Hiv-1 Gp120
pdb|3SE9|G Chain G, Crystal Structure Of Broadly And Potently Neutralizing
Antibody Vrc- Pg04 In Complex With Hiv-1 Gp120
pdb|3TGT|A Chain A, Crystal Structure Of Unliganded Hiv-1 Clade AE STRAIN
93TH057 GP120 Core
Length = 353
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 28/111 (25%), Positives = 45/111 (40%), Gaps = 9/111 (8%)
Query: 6 LLN--LTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI----KTWFQNRR 59
LLN L E +I +N K + +L+ S + ++ N K + +
Sbjct: 144 LLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEING 203
Query: 60 TKWKK---QLASKLKMVAHNRPTGFYFPGGGPLIFGAQHGSPTAPYFFSAS 107
TKW K Q+ KLK +N+ F P GG L H + +F+ +
Sbjct: 204 TKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNT 254
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 32 LSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
L+ ++ E++K +T +Q++ WF N+R + K
Sbjct: 390 LNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26
E++K +T +Q++ WF N+R + K
Sbjct: 397 EVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWKYVD 29
++ LN+ + I+ WF NRR K K +D
Sbjct: 40 IADQLNMEKEVIRVWFCNRRQKEKRID 66
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 1 MELSKLLNLTEVQIKTWFQNRRTKWKYV 28
M +++ LNL + ++ WF NRR + K V
Sbjct: 118 MRMAEELNLEKEVVRVWFCNRRQREKRV 145
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 38 MELSKLLNLTEVQIKTWFQNRRTKWKK 64
M +++ LNL + ++ WF NRR + K+
Sbjct: 118 MRMAEELNLEKEVVRVWFCNRRQREKR 144
>pdb|3U7Y|G Chain G, Structure Of Nih45-46 Fab In Complex With Gp120 Of 93th057
Hiv
Length = 361
Score = 26.9 bits (58), Expect = 2.6, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 3/56 (5%)
Query: 52 KTWFQNRRTKWKK---QLASKLKMVAHNRPTGFYFPGGGPLIFGAQHGSPTAPYFF 104
K + + TKW K Q+ KLK +N+ F P GG L H + +F+
Sbjct: 196 KAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFY 251
>pdb|3D00|A Chain A, Crystal Structure Of A Tungsten Formylmethanofuran
Dehydrogenase Subunit E (Fmde)-Like Protein (Syn_00638)
From Syntrophus Aciditrophicus At 1.90 A Resolution
Length = 191
Score = 26.6 bits (57), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 34/86 (39%), Gaps = 8/86 (9%)
Query: 13 QIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKM 72
+I+ WF +TK + + L R +L L V++K F ++ K K L + +
Sbjct: 112 EIRNWFLKLKTKKEQDSERLFKEIREAGPDILELRNVKLKPGFLEKKHKGKIVLCPQCRE 171
Query: 73 VAHNRPTGFYFPGGGPLIFGAQHGSP 98
Y G L Q GSP
Sbjct: 172 A--------YPAQDGELCLSCQGGSP 189
>pdb|2DA6|A Chain A, Solution Structure Of The Homeobox Domain Of Hepatocyte
Nuclear Factor 1-Beta (Hnf-1beta)
Length = 102
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 21/35 (60%), Gaps = 2/35 (5%)
Query: 46 LTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTG 80
+TEV++ WF NRR ++ KL M A++ +G
Sbjct: 66 VTEVRVYNWFANRRK--EEAFRQKLAMDAYSSNSG 98
>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 = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
YL L K +L+ +QIK W NRR K K
Sbjct: 29 YLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 61
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWKYV 28
L K +L+ +QIK W NRR K K +
Sbjct: 38 LMKNTSLSRIQIKNWVSNRRRKEKTI 63
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 26.6 bits (57), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 18/27 (66%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWKYVD 29
+++ LN+ + I+ WF NRR K K ++
Sbjct: 134 IAEQLNMEKEVIRVWFSNRRQKEKRIN 160
Score = 25.4 bits (54), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 40 LSKLLNLTEVQIKTWFQNRRTKWKK 64
+++ LN+ + I+ WF NRR K K+
Sbjct: 134 IAEQLNMEKEVIRVWFSNRRQKEKR 158
>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 = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
YL L K +L+ +QIK W NRR K K
Sbjct: 54 YLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 86
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 10/28 (35%), Positives = 19/28 (67%)
Query: 39 ELSKLLNLTEVQIKTWFQNRRTKWKKQL 66
+L++ LT+ ++ WFQN R K+++ L
Sbjct: 39 QLAQKTGLTKRVLQVWFQNARAKFRRNL 66
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 50 QIKTWFQNRRTKWKK 64
QIK +FQNRR K+KK
Sbjct: 2 QIKIFFQNRRMKFKK 16
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 32 LSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
L+ ++ E++K +T +Q++ WF N+R + K
Sbjct: 30 LNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 7 LNLTEVQIKTWFQNRRTKWKYVD 29
LN+ + I+ WF NRR K K ++
Sbjct: 137 LNMEKEVIRVWFSNRRQKEKRIN 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 = 25.8 bits (55), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 32 LSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
L+ ++ E++K +T +Q++ WF N+R + K
Sbjct: 30 LNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 25.8 bits (55), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
YL L K +L+ +QIK W NRR K K
Sbjct: 25 YLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 57
Score = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 3 LSKLLNLTEVQIKTWFQNRRTKWKYV 28
L K +L+ +QIK W NRR K K +
Sbjct: 34 LMKNTSLSRIQIKNWVSNRRRKEKTI 59
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 25.4 bits (54), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 21/32 (65%)
Query: 32 LSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63
L+ ++ E++K +T +Q++ WF N+R + K
Sbjct: 22 LNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|3EJN|A Chain A, Crystal Structure Of A Susd Homolog (Bf3025) From
Bacteroides Fragilis Nctc 9343 At 1.50 A Resolution
Length = 474
Score = 25.4 bits (54), Expect = 8.2, Method: Composition-based stats.
Identities = 15/56 (26%), Positives = 25/56 (44%)
Query: 42 KLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTGFYFPGGGPLIFGAQHGS 97
KL+N +++ N T +AS+ K +A N P G L++ Q G+
Sbjct: 170 KLINSFRLKVLXTLSNHTTVGNINIASEFKNIATNSPLXNSLADNGQLVYLDQQGN 225
>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 = 25.0 bits (53), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 39 ELSKLLNLTEVQIKTWFQNRRTKWKKQ 65
+L ++ L+ I+ WFQN+R K KK+
Sbjct: 35 QLVEMTGLSPRVIRVWFQNKRCKDKKR 61
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
0.319 0.133 0.410
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,625,532
Number of Sequences: 62578
Number of extensions: 133859
Number of successful extensions: 515
Number of sequences better than 100.0: 88
Number of HSP's better than 100.0 without gapping: 82
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 352
Number of HSP's gapped (non-prelim): 169
length of query: 120
length of database: 14,973,337
effective HSP length: 82
effective length of query: 38
effective length of database: 9,841,941
effective search space: 373993758
effective search space used: 373993758
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)