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= psy3429
(192 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 109 bits (273), Expect = 9e-25, Method: Compositional matrix adjust.
Identities = 53/58 (91%), Positives = 56/58 (96%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99
RKPRTPFTT QLL+LE+KFR+KQYLSIAERAEFSSSL LTETQVKIWFQNRRAKAKRL
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 77.8 bits (190), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 35/64 (54%), Positives = 50/64 (78%)
Query: 41 NRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100
+R+ RT FT++QLL LEK+F K+YLS+ ER++ + +L L+E QVKIWFQNRRAK KR++
Sbjct: 7 SRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIK 66
Query: 101 EAEI 104
+
Sbjct: 67 AGNV 70
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 73.9 bits (180), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 32/58 (55%), Positives = 49/58 (84%)
Query: 41 NRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
RKPRT +++ QL +L+++F++ QYL++ ERAE ++SL LT+TQVKIWFQN+R+K K+
Sbjct: 7 GRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 67.0 bits (162), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 33/54 (61%), Positives = 40/54 (74%)
Query: 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
RT FTT+QL LEK+F +YLS A R E +++L L ETQVKIWFQNRR K K+
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
>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 = 66.6 bits (161), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 31/56 (55%), Positives = 42/56 (75%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97
RKPR F+ Q+ LE++F++++YLS ER + +S L LT TQVKIWFQNRR K+K
Sbjct: 3 RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 65.5 bits (158), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 33/70 (47%), Positives = 46/70 (65%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101
+KPRT FT Q+ LEK+F +++YL+ AERA + L +T+ QVK WFQNRR K +R
Sbjct: 18 KKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTA 77
Query: 102 AEIEKIKMSA 111
E E + +A
Sbjct: 78 EEREAERQAA 87
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 64.7 bits (156), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 30/62 (48%), Positives = 43/62 (69%)
Query: 37 KHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKA 96
K K R+ RT FT QL+ LEK+F +++YLS +R + + SL L++ QVK W+QNRR K
Sbjct: 13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKW 72
Query: 97 KR 98
K+
Sbjct: 73 KK 74
>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 = 62.8 bits (151), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 42/57 (73%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++PRT F+++QL L+++F E +YL+ R + SS L L E Q+KIWFQN+RAK K+
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 62.8 bits (151), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 32/59 (54%), Positives = 39/59 (66%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100
RK R FT Q LE++FR+++YLS ER +S + LT TQVKIWFQN R K KR Q
Sbjct: 13 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQ 71
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 42/57 (73%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++PRT F+++QL L+++F E +YL+ R + SS L L E Q+KIWFQN+RAK K+
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 62.4 bits (150), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/58 (51%), Positives = 40/58 (68%)
Query: 41 NRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
RK R F+ Q+ LE++F++++YLS ER +S +HLT TQVKIWFQN R K KR
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKR 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 = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 32/59 (54%), Positives = 39/59 (66%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100
RK R FT Q LE++FR+++YLS ER +S + LT TQVKIWFQN R K KR Q
Sbjct: 10 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/63 (49%), Positives = 40/63 (63%)
Query: 39 KPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
+ RK R P+T Q L LEK+F YL+ R E + L+LTE QVKIWFQNRR K K+
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
Query: 99 LQE 101
+ +
Sbjct: 71 INK 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 = 61.6 bits (148), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/49 (61%), Positives = 37/49 (75%)
Query: 52 QLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100
Q++ LE+KF ++YLS ERA + +L LTETQVKIWFQNRR K KR Q
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>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 = 61.6 bits (148), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 41/57 (71%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++PRT F+++QL L+++F E +YL+ R + SS L L E Q+KIWFQN RAK K+
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 61.2 bits (147), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 41/57 (71%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++PRT F+++QL +++F E +YL+ R + SS L L E Q+KIWFQN+RAK +R
Sbjct: 4 KRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>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 = 60.8 bits (146), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 42/57 (73%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++PRT F+++QL L+++F E +YL+ R + SS L L E Q+KIWF+N+RAK K+
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52a
Length = 59
Score = 60.8 bits (146), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 41/57 (71%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++PRT F+++QL L+++F E +YL+ R + SS L L E Q+KIWFQN RAK K+
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 60.8 bits (146), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 27/53 (50%), Positives = 39/53 (73%)
Query: 43 KPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAK 95
+PRT F+++QL L+++F E +YL+ R + SS L L E Q+KIWFQN+RAK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 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 = 59.7 bits (143), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 40/56 (71%)
Query: 43 KPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
+PRT F+++QL L+++F E +YL+ R + SS L L E Q+KIWF N+RAK K+
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 59.7 bits (143), Expect = 1e-09, Method: Composition-based stats.
Identities = 31/58 (53%), Positives = 38/58 (65%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99
RK R P+T Q L LEK+F YL+ R E + L+LTE QVKIWFQNRR K K++
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKM 59
>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 = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 39/59 (66%)
Query: 40 PNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
N++ RT +T QLL LEK+F +Y+S R E + L+LTE +KIWFQNRR K K+
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 59.3 bits (142), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 26/53 (49%), Positives = 38/53 (71%)
Query: 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
T F+ Q+L LE++F ++YL+ AERA + +L +T+ QVK WFQNRR K +R
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 57.8 bits (138), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 27/60 (45%), Positives = 42/60 (70%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101
+K RT F++ QL L +F+ ++YLS+ + E S+ L+L+ QVK WFQN+R K+KR Q+
Sbjct: 23 QKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK 82
>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 = 57.4 bits (137), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 40/57 (70%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++PRT F+++QL L+++F E +YL+ R + SS L L E QVK WF+N RAK K+
Sbjct: 5 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>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 = 57.0 bits (136), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 38/57 (66%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++ RT +T Q L LEK+F +YL+ R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 57.0 bits (136), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 36/57 (63%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
R+ R +T Q L LEK+F YL+ R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
>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 = 56.6 bits (135), Expect = 9e-09, Method: Composition-based stats.
Identities = 28/59 (47%), Positives = 42/59 (71%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100
+K RT F+ QL +L+ +F++++YLS+ + E SS L+L+ QVK WFQN+R K KR Q
Sbjct: 4 QKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 25/59 (42%), Positives = 39/59 (66%)
Query: 40 PNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
R+ RT FT +QL +LE F+E +Y + R + + +HL E +V++WF+NRRAK +R
Sbjct: 6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
>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 = 55.8 bits (133), Expect = 1e-08, Method: Composition-based stats.
Identities = 28/57 (49%), Positives = 39/57 (68%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
R+ RT FT QL LEK+F ++ Y+S R E ++ L+L E+ +K+WFQNRR K KR
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/51 (52%), Positives = 34/51 (66%)
Query: 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
F+ Q + LEKKF ++YLS ER + L L+E QVK WFQNRRAK +R
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>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 = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 41/60 (68%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101
R+ RT FT+QQL LE F+ +Y ++ R E + +LTE +V++WF+NRRAK ++ +E
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
Length = 81
Score = 54.3 bits (129), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 37/60 (61%)
Query: 39 KPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
+ R+ RT F+ QL LE+ F QY I R E + +LTE ++++WFQNRRA+ ++
Sbjct: 16 RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 54.3 bits (129), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 40/60 (66%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101
R+ RT FT+QQL LE F+ Y ++ R E + +LTE +V++WF+NRRAK ++ +E
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>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 = 53.9 bits (128), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 37/57 (64%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++ R +T Q L LEK+F +YL+ R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 45/70 (64%), Gaps = 4/70 (5%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101
RK R P+T QL LE+++ ++++ +R S++ +L+E QV IWFQNRR K K++
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV-- 65
Query: 102 AEIEKIKMSA 111
I K+K ++
Sbjct: 66 --INKLKTTS 73
>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 = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 37/57 (64%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++ R +T Q L LEK+F +YL+ R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 45/70 (64%), Gaps = 4/70 (5%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101
RK R P+T QL LE+++ ++++ +R S++ +L+E QV IWFQNRR K K++
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV-- 59
Query: 102 AEIEKIKMSA 111
I K+K ++
Sbjct: 60 --INKLKTTS 67
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 53.5 bits (127), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 37/57 (64%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++ R +T Q L LEK+F +YL+ R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 4 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 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 = 53.5 bits (127), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 40/59 (67%)
Query: 40 PNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
+++ R +T Q L LEK+F +Y++ R + +++L L+E Q+KIWFQNRR K+K+
Sbjct: 2 DSKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
>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 = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/52 (50%), Positives = 34/52 (65%)
Query: 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
+T Q L LEK+F +YL+ R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 53
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 37/57 (64%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
R+ RT FT+ QL LEK F++ Y + R + + LTE +V++WFQNRRAK ++
Sbjct: 10 RRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 34/57 (59%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
R+PRT FT Q+ LE FR Y I + + L+L +++IWFQNRRAK KR
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58
>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 = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 37/60 (61%)
Query: 39 KPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
+ R+ RT FT+ QL LEK F Y + R E + + LTE ++++WFQNRRAK ++
Sbjct: 4 RKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 63
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 36/56 (64%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97
R+ RT FT+ Q+ LE+ F + +YL+ A+ S+ L L QVKIWF+NRR + K
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 38/59 (64%)
Query: 40 PNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
RK R P++ QL LE+++ ++++ +R + S++ L+E Q+ IWFQNRR K K+
Sbjct: 6 SGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 50.1 bits (118), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 34/57 (59%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
R+ RT FT +QL LE+ F Y I R E + LTE +V++WF NRRA+ ++
Sbjct: 3 RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 59
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 49.7 bits (117), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 35/56 (62%)
Query: 43 KPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
+ RT FT+ QL LEK F Y + R E + + LTE ++++WFQNRRAK ++
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 41 NRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97
R+ RT FT QL LE F + +Y I R E + ++L E++V++WF+NRRAK +
Sbjct: 7 GRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 35/56 (62%)
Query: 43 KPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
+ RT FT +Q+ +LEK+F Y + R ++ + L E ++++WF NRRAK +R
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 64
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 46.6 bits (109), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 21/41 (51%), Positives = 29/41 (70%)
Query: 58 KKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++F E +YL+ R + SS L L E Q+KIWFQN+RAK K+
Sbjct: 3 REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 46.6 bits (109), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 32/52 (61%)
Query: 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
FT+ QL LEK F Y + R E + + LTE ++++WFQNRRAK ++
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>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 = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99
RK RT T ++LEK F E Q + E + L++ + +++WF NRR K KR+
Sbjct: 105 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRI 162
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 33/62 (53%)
Query: 38 HKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97
H RK RT T ++LEK F E Q + E + L++ + +++WF NRR K K
Sbjct: 4 HMRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
Query: 98 RL 99
R+
Sbjct: 64 RI 65
>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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99
RK RT T ++LEK F E Q + E + L++ + +++WF NRR K KR+
Sbjct: 101 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKRI 158
>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 = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99
RK RT T ++LEK F E Q + E + L++ + +++WF NRR K KR+
Sbjct: 104 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRI 161
>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 = 40.4 bits (93), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99
RK RT T ++LEK F E Q + E + L++ + +++WF NRR K KR+
Sbjct: 97 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRI 154
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99
RK RT T ++LEK F E Q + + + L++ + +++WF NRR K KR+
Sbjct: 102 RKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 159
>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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 56 LEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97
LE+ FR KQ L+ E+ E + +T QV++WF N+R ++K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 30/58 (51%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99
RK RT T +LEK F Q + E + LH+ + +++WF NRR K KR+
Sbjct: 2 RKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKRI 59
>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 = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 56 LEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97
LE+ FR KQ L+ E+ E + +T QV++WF N+R ++K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 32/55 (58%)
Query: 43 KPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97
K ++ + Q LE+ FR KQ L+ E+ E + +T QV++WF N+R ++K
Sbjct: 7 KGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 56 LEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97
LE+ FR KQ L+ E+ E + +T QV++WF N+R ++K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 34.3 bits (77), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 29 PKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIW 88
K+ N RK RK RT + +LE+ F E S E + L+L + V++W
Sbjct: 79 EKVGANERK----RKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVW 134
Query: 89 FQNRRAKAKRLQ 100
F NRR + KR++
Sbjct: 135 FCNRRQREKRVK 146
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 33.9 bits (76), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 1/74 (1%)
Query: 26 GDPPKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQV 85
G P L+ + RK RT +LE F + S E + SL L + V
Sbjct: 85 GSPTNLD-KIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVV 143
Query: 86 KIWFQNRRAKAKRL 99
++WF NRR K KR+
Sbjct: 144 RVWFCNRRQKEKRM 157
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 33.1 bits (74), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 27/53 (50%)
Query: 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
T FT QL L+ F Y E + S+ L+L + +WFQN R KA++
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>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 = 30.8 bits (68), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 26/52 (50%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRR 93
RK RT FT Q + +L F + + E E + L+ V++WF NRR
Sbjct: 94 RKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRR 145
>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 = 0.64, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 21/36 (58%)
Query: 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIE 105
E+ E + + LT TQV WF+NRR + + + E E
Sbjct: 523 EKRELAEATGLTTTQVSNWFKNRRQRDRAAEAKERE 558
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++ RT + SLE F + S+ + ++ L L + V++WF NRR K KR
Sbjct: 97 KRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 30.0 bits (66), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 29/59 (49%)
Query: 40 PNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++ RT F QL +++ F + + + LT+ +++WFQN RAK +R
Sbjct: 6 SGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 29/57 (50%)
Query: 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98
++ RT + SLE F + S+ + ++ L L + V++WF NRR K KR
Sbjct: 9 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65
>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 = 29.3 bits (64), Expect = 1.6, Method: Composition-based stats.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 84 QVKIWFQNRRAKAKR 98
Q+KIWFQNRR K K+
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 28.5 bits (62), Expect = 2.1, Method: Composition-based stats.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 84 QVKIWFQNRRAKAKR 98
Q+KIWFQNRR K K+
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 28.1 bits (61), Expect = 3.0, Method: Composition-based stats.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 84 QVKIWFQNRRAKAKR 98
Q+KIWFQNRR K K+
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|3CGL|A Chain A, Crystal Structure And Raman Studies Of Dsfp483, A Cyan
Fluorescent Protein From Discosoma Striata
pdb|3CGL|B Chain B, Crystal Structure And Raman Studies Of Dsfp483, A Cyan
Fluorescent Protein From Discosoma Striata
pdb|3CGL|C Chain C, Crystal Structure And Raman Studies Of Dsfp483, A Cyan
Fluorescent Protein From Discosoma Striata
pdb|3CGL|D Chain D, Crystal Structure And Raman Studies Of Dsfp483, A Cyan
Fluorescent Protein From Discosoma Striata
pdb|3CGL|E Chain E, Crystal Structure And Raman Studies Of Dsfp483, A Cyan
Fluorescent Protein From Discosoma Striata
pdb|3CGL|F Chain F, Crystal Structure And Raman Studies Of Dsfp483, A Cyan
Fluorescent Protein From Discosoma Striata
Length = 241
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 21/47 (44%), Gaps = 10/47 (21%)
Query: 77 SLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKMSAIAAARPHPLYGP 123
H +T++ IW ++ E K++ IA AR HP Y P
Sbjct: 201 GYHYVDTKLVIWNNDK----------EFMKVEEHEIAVARHHPFYEP 237
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 26.9 bits (58), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 15/63 (23%)
Query: 51 QQLLSLEKKFREKQYLSIAERAEFSSSLH---------------LTETQVKIWFQNRRAK 95
+ L +E F E QY A+R E +++ + +T +V WF NRR +
Sbjct: 17 ECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKE 76
Query: 96 AKR 98
KR
Sbjct: 77 IKR 79
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
0.316 0.131 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,954,300
Number of Sequences: 62578
Number of extensions: 159763
Number of successful extensions: 448
Number of sequences better than 100.0: 92
Number of HSP's better than 100.0 without gapping: 79
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 368
Number of HSP's gapped (non-prelim): 92
length of query: 192
length of database: 14,973,337
effective HSP length: 93
effective length of query: 99
effective length of database: 9,153,583
effective search space: 906204717
effective search space used: 906204717
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 49 (23.5 bits)