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= 010311
(513 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 43/72 (59%), Gaps = 9/72 (12%)
Query: 1 MHSEENKVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWF 60
M + + S+E NI+ +ALEK + E++ PT E + +A+Q+ + ++ + WF
Sbjct: 5 MRRRKKRTSIETNIR---------VALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWF 55
Query: 61 CHRRLKEKRLSV 72
C+RR KEKR+ +
Sbjct: 56 CNRRQKEKRIDI 67
>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 = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 41/65 (63%), Gaps = 9/65 (13%)
Query: 7 KVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLK 66
+ S+E NI+ +ALEK + E++ PT E + +A+Q+ + ++ + WFC+RR K
Sbjct: 108 RTSIETNIR---------VALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 158
Query: 67 EKRLS 71
EKR++
Sbjct: 159 EKRIN 163
>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 = 47.0 bits (110), Expect = 3e-05, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 42/67 (62%), Gaps = 9/67 (13%)
Query: 5 ENKVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
+ + S+E NI+ +ALEK + E++ PT E + +A+Q+ + ++ + WFC+RR
Sbjct: 98 KKRTSIETNIR---------VALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 148
Query: 65 LKEKRLS 71
KEKR++
Sbjct: 149 QKEKRIN 155
>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 = 46.2 bits (108), Expect = 4e-05, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 42/67 (62%), Gaps = 9/67 (13%)
Query: 5 ENKVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
+ + S+E NI+ +ALEK + E++ PT E + +A+Q+ + ++ + WFC+RR
Sbjct: 105 KKRTSIETNIR---------VALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 155
Query: 65 LKEKRLS 71
KEKR++
Sbjct: 156 QKEKRIN 162
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 42/70 (60%)
Query: 1 MHSEENKVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWF 60
+++E+ + K +R + A ALE+ + EH P+ + ++AE++ L ++ V WF
Sbjct: 76 LYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWF 135
Query: 61 CHRRLKEKRL 70
C+RR +EKR+
Sbjct: 136 CNRRQREKRV 145
>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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 32/47 (68%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
Q+ L++ +NE++Y TE + Q++ ++GL E QV GWF + R K K+
Sbjct: 15 QLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 42.7 bits (99), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 39/61 (63%)
Query: 10 LEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
LE KR T Q+ LE+ Y +K+ T++ + +++ L+E+QV+ WF +RR+KEK+
Sbjct: 5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
Query: 70 L 70
+
Sbjct: 65 V 65
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 42.7 bits (99), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/67 (34%), Positives = 41/67 (61%), Gaps = 9/67 (13%)
Query: 5 ENKVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
+ + S+E NI+ +ALEK + E++ PT E + +AEQ+ + ++ + WF +RR
Sbjct: 103 KKRTSIETNIR---------VALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRR 153
Query: 65 LKEKRLS 71
KEKR++
Sbjct: 154 QKEKRIN 160
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 42.4 bits (98), Expect = 6e-04, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 37/61 (60%)
Query: 15 KRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDE 74
KR T Q + LEK + + Y T + + +VA + LTE+QV WF +RR+K K+++ D
Sbjct: 16 KRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR 75
Query: 75 A 75
A
Sbjct: 76 A 76
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 42.0 bits (97), Expect = 7e-04, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 37/58 (63%), Gaps = 3/58 (5%)
Query: 16 RRYKTP---AQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRL 70
R+ +TP AQ++ALE+ + + +Y + +++ + + LTE QV WF +RR K KRL
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>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 = 42.0 bits (97), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 39/67 (58%), Gaps = 9/67 (13%)
Query: 5 ENKVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
+ + S+E N++ ALEK + ++ PT E +AEQ+ + ++ + WFC+RR
Sbjct: 3 KKRTSIETNVR---------FALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRR 53
Query: 65 LKEKRLS 71
KEKR++
Sbjct: 54 QKEKRIN 60
>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 = 42.0 bits (97), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 41/67 (61%), Gaps = 9/67 (13%)
Query: 5 ENKVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
+ + S+E NI+ +ALEK + E++ PT E + +A+Q+ + ++ + WF +RR
Sbjct: 102 KKRTSIETNIR---------VALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRR 152
Query: 65 LKEKRLS 71
KEKR++
Sbjct: 153 QKEKRIN 159
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 37/60 (61%)
Query: 10 LEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
+E+ R+ T Q + LEK ++ ++Y T + ++A + LTE+Q+ WF +RR+K K+
Sbjct: 1 MERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 30/50 (60%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
T Q+ ALE + E KYP + Q+A ++ L E++V WF +RR K +R
Sbjct: 15 TDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 32/50 (64%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
T Q+M LEK + + KY + + +AE +GL++ QV W+ +RR+K K+
Sbjct: 25 TELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 34/50 (68%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
+ Q+ LE+ Y +K+ T++ + +++ L+E+Q++ WF +RR+KEK+
Sbjct: 15 SKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 37/56 (66%)
Query: 15 KRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRL 70
KR T Q+ LE+ Y +K+ T++ + +++ L+E+QV+ WF +RR+KEK++
Sbjct: 4 KRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 59
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 35/57 (61%)
Query: 15 KRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71
KR T Q + LEK + + Y T + + +VA + LTE+QV WF +RR+K K+++
Sbjct: 4 KRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 31/50 (62%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
T Q + LEK ++ ++Y T + +A + L+E+Q+ WF +RR+K K+
Sbjct: 11 TRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 40.0 bits (92), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 36/57 (63%), Gaps = 2/57 (3%)
Query: 15 KRRYKTPAQVMALEKFYNE--HKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
+R + A + E FY+ + YP+EE K ++A++ G+T QVS WF ++R++ K+
Sbjct: 5 RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 22/56 (39%), Positives = 34/56 (60%)
Query: 15 KRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRL 70
+R T Q++ LEK ++ KY + +SQ+A + L+E QV WF +RR K KR+
Sbjct: 10 RRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRI 65
>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 = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 39/73 (53%)
Query: 2 HSEENKVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFC 61
H +N+ ++ R T QV LEK +++ KY ++ +A + +T+ QV WF
Sbjct: 7 HPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQ 66
Query: 62 HRRLKEKRLSVDE 74
+RR K +R + +E
Sbjct: 67 NRRTKWRRQTAEE 79
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 16 RRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
R+ T Q + LEK ++ + Y T + ++A + LTE+Q+ WF +RR+K K+
Sbjct: 24 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 40.0 bits (92), Expect = 0.003, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 36/57 (63%), Gaps = 2/57 (3%)
Query: 15 KRRYKTPAQVMALEKFYNE--HKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
+R + A + E FY+ + YP+EE K ++A++ G+T QVS WF ++R++ K+
Sbjct: 5 RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 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 = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 15 KRRYKTPAQVMALEKFYNE--HKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
+R + A + E FY+ + YP+EE K ++A + G+T QVS WF ++R++ K+
Sbjct: 5 RRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 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 = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 35/59 (59%)
Query: 11 EKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
E +R T Q + LEK ++ ++Y T + ++A + LTE+Q+ WF +RR+K K+
Sbjct: 27 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85
>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 = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 34/54 (62%)
Query: 16 RRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
R+ T Q + LEK ++ ++Y T + ++A + LTE+Q+ WF +RR+K K+
Sbjct: 6 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59
>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 = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 34/54 (62%)
Query: 16 RRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
R+ T Q + LEK ++ ++Y T + ++A + LTE+Q+ WF +RR+K K+
Sbjct: 6 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 32/47 (68%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
Q+ L++ +NE++Y TE + Q++ ++GL E Q+ WF ++R K K+
Sbjct: 10 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>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 = 39.7 bits (91), Expect = 0.004, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 12 KNIKRRYKT---PAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68
K +RRY+T Q+ LEK ++ YP + ++A +IGLTE ++ WF +RR K +
Sbjct: 3 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
Query: 69 R 69
+
Sbjct: 63 K 63
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 36/57 (63%), Gaps = 2/57 (3%)
Query: 15 KRRYKTPAQVMALEKFYNE--HKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
+R + A + E FY+ + YP+EE K ++A++ G+T QVS WF ++R++ K+
Sbjct: 6 RRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 39.3 bits (90), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 26/34 (76%)
Query: 36 YPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
YP+EE K ++A++ G+T QVS WF ++R++ K+
Sbjct: 30 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>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 = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 30/47 (63%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
QV+ LE+ ++ KY + ++ +A+ + LTE QV WF +RR K KR
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
Length = 67
Score = 39.3 bits (90), Expect = 0.005, Method: Composition-based stats.
Identities = 17/42 (40%), Positives = 27/42 (64%)
Query: 34 HKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEA 75
H YP+EE K Q+A+ GLT QV+ WF + R + + +D++
Sbjct: 23 HPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPXIDQS 64
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLK 66
T AQ+ LE + + +YP M+ +VA +I L E +V WF +RR K
Sbjct: 15 TRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
>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 = 38.9 bits (89), Expect = 0.006, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 32/50 (64%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
T Q + LEK ++ ++Y T + ++A + LTE+Q+ WF +RR+K K+
Sbjct: 4 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 53
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 26 ALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDE 74
L ++Y + YP+ K ++AE GLT QVS WF +RR +++ E
Sbjct: 508 VLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEAKE 556
>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 = 38.5 bits (88), Expect = 0.010, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 32/47 (68%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
Q+ L++ +NE++Y TE + Q++ ++GL E Q+ WF ++R K K+
Sbjct: 14 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>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 = 38.1 bits (87), Expect = 0.011, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 32/47 (68%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
Q+ L++ +NE++Y TE + Q++ ++GL E Q+ WF ++R K K+
Sbjct: 14 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 38.1 bits (87), Expect = 0.012, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 32/47 (68%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
Q+ L++ +NE++Y TE + Q++ ++GL E Q+ WF ++R K K+
Sbjct: 12 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 38.1 bits (87), Expect = 0.013, Method: Composition-based stats.
Identities = 22/61 (36%), Positives = 33/61 (54%)
Query: 15 KRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDE 74
+R + AQV LE+ + + KY + + +A I LT QV WF + R K KR + D+
Sbjct: 5 RRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK 64
Query: 75 A 75
A
Sbjct: 65 A 65
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 37.7 bits (86), Expect = 0.015, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 30/44 (68%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLK 66
Q+ L++ +NE++Y TE + Q++ ++GL E Q+ WF ++R K
Sbjct: 10 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 37.7 bits (86), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
T Q+ LEK ++ +KY + + ++A + L E QV WF +RR+K+K+
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 37.7 bits (86), Expect = 0.016, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
T Q+ LEK ++ YP + ++A +IGLTE ++ WF +RR K ++
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 37.4 bits (85), Expect = 0.018, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 17 RYKT---PAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
RY+T Q+ LEK ++ YP + ++A +IGLTE ++ WF +RR K ++
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex
With Dna
pdb|2H1K|B Chain B, Crystal Structure Of The Pdx1 Homeodomain In Complex
With Dna
Length = 63
Score = 37.4 bits (85), Expect = 0.021, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 33/54 (61%)
Query: 16 RRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
R T AQ++ LEK + +KY + + ++A + LTE+ + WF +RR+K K+
Sbjct: 7 RTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>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 = 37.4 bits (85), Expect = 0.022, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 31/47 (65%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
Q+ L++ +NE++Y TE + Q++ ++GL E Q+ WF + R K K+
Sbjct: 12 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 37.4 bits (85), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 16/31 (51%), Positives = 20/31 (64%)
Query: 34 HKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
H YPTE+ K Q+A Q LT QV+ WF + R
Sbjct: 32 HPYPTEDEKKQIAAQTNLTLLQVNNWFINAR 62
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 37.0 bits (84), Expect = 0.025, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 16 RRYKTP---AQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
RRY+T Q+ LEK + + Y + + ++A Q+ L E + WF +RR+K+KR
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 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 = 37.0 bits (84), Expect = 0.026, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 31/47 (65%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
Q+ L++ +NE++Y TE + Q++ ++GL E Q+ WF + R K K+
Sbjct: 12 QLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 36.6 bits (83), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
T Q+ ALEK + YP + ++A +I L E ++ WF +RR K +R
Sbjct: 15 TQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 64
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 36.6 bits (83), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 29/47 (61%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
Q + LEK + KY + + ++A+ + L+E+QV WF +RR K +R
Sbjct: 18 QTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>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 = 36.6 bits (83), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 27/47 (57%)
Query: 22 AQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68
AQV LE+ + + +Y + + Q+A + LT QV WF +RR K K
Sbjct: 12 AQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 36.2 bits (82), Expect = 0.043, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 31/47 (65%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
Q+ ++ +NE++Y TE + Q++ ++GL E Q+ WF ++R K +R
Sbjct: 14 QLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 35.8 bits (81), Expect = 0.055, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 27/39 (69%)
Query: 31 YNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
+NE++Y TE + Q++ ++GL E Q+ WF ++R K K+
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 35.4 bits (80), Expect = 0.068, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 27/46 (58%)
Query: 26 ALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71
+LE + + P+ + + +A Q+GL + V WFC+RR K KR S
Sbjct: 22 SLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRSS 67
>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 = 35.4 bits (80), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 30/59 (50%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEAFVG 78
T AQ LE+ + + +Y + + +A I LT QV WF + R K KR ++ + G
Sbjct: 17 TKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEKGYEG 75
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 35.4 bits (80), Expect = 0.075, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 29/48 (60%)
Query: 22 AQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
+QV+ LE+ + KY ++ +A+ + +T+ QV WF +RR K +R
Sbjct: 7 SQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 35.4 bits (80), Expect = 0.079, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 15 KRRYKTPAQVM---ALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71
KR+ +T +V ALE + + P+ + +A+ + L ++ V WFC+RR KEKR++
Sbjct: 99 KRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMT 158
>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 = 35.4 bits (80), Expect = 0.082, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 30/55 (54%)
Query: 15 KRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
+R + T Q+ LE + ++YP + ++A LTE +V WF +RR K ++
Sbjct: 6 QRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 35.4 bits (80), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 36/66 (54%)
Query: 4 EENKVSLEKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHR 63
+E+KV ++K R + Q+ L + KY + + +++ + L+ KQV WF ++
Sbjct: 14 KEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQ 73
Query: 64 RLKEKR 69
R+K KR
Sbjct: 74 RMKSKR 79
>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 = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 33/58 (56%)
Query: 12 KNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
K R + AQ+ AL+ + + KY + + +++ + L+ KQV WF ++R+K KR
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>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 = 34.7 bits (78), Expect = 0.14, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 27/50 (54%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSV 72
Q+ L Y + P MK Q+ E GL+ + + WF ++R K+K+ S+
Sbjct: 14 QLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>pdb|2DMN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Tgif2lx
Length = 83
Score = 34.3 bits (77), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 15 KRRYKTPAQ-VMALEKFYNEHK---YPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
KR+ PA+ V L + +H+ YP+EE K ++E+ L+ Q+S WF + R
Sbjct: 9 KRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINAR 62
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 34.3 bits (77), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 28/53 (52%)
Query: 14 IKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLK 66
K + + P Q+ ALE + ++ P +E ++ + +T +++ WF RR K
Sbjct: 9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 34.3 bits (77), Expect = 0.17, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 29/55 (52%)
Query: 15 KRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
+R + T Q+ LE + + YP + ++A LTE +V WF +RR K ++
Sbjct: 6 QRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 34.3 bits (77), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 33/68 (48%)
Query: 11 EKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRL 70
+K +R T AQ LE+ + + +Y + + + I LT QV WF + R K KR
Sbjct: 11 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRA 70
Query: 71 SVDEAFVG 78
++ + G
Sbjct: 71 QNEKGYEG 78
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 33.9 bits (76), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
TP Q+ L + Y PT +M +A ++GL ++ V WF + R +E++
Sbjct: 25 TPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 33.9 bits (76), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 26/47 (55%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLK 66
T Q+ LEK + + YP + Q+A + LTE +V WF +RR K
Sbjct: 17 TSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK 63
>pdb|2ECB|A Chain A, The Solution Structure Of The Third Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein
Length = 89
Score = 33.1 bits (74), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 4/65 (6%)
Query: 15 KRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR----LKEKRL 70
K + KT Q+ L+ + T+E +++ Q LT +++ WF ++ LKE+++
Sbjct: 14 KFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKM 73
Query: 71 SVDEA 75
+DE+
Sbjct: 74 EIDES 78
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 33.1 bits (74), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 30/50 (60%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
T Q+ L ++++ + P+EE ++A++ GL +K + WF + KE++
Sbjct: 15 TDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQ 64
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 32.7 bits (73), Expect = 0.52, Method: Composition-based stats.
Identities = 16/46 (34%), Positives = 26/46 (56%)
Query: 26 ALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71
+LE + + P+ + + +A Q+GL + V WF +RR K KR S
Sbjct: 110 SLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRSS 155
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 32.0 bits (71), Expect = 0.75, Method: Composition-based stats.
Identities = 15/47 (31%), Positives = 30/47 (63%)
Query: 23 QVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
Q+ AL++ + + +Y ++++A +GLT+ QV WF ++R K K+
Sbjct: 18 QLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 32.0 bits (71), Expect = 0.80, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 28/50 (56%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
T Q+ LE+ + YP + ++A++ LTE +V WF +RR + ++
Sbjct: 10 TAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 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 = 32.0 bits (71), Expect = 0.84, Method: Composition-based stats.
Identities = 17/67 (25%), Positives = 38/67 (56%), Gaps = 2/67 (2%)
Query: 5 ENKVSLEKNIKRRYKT--PAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCH 62
E ++L++ +R T +Q+ LE+ + +YP + ++A++ LTE ++ WF +
Sbjct: 9 EPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQN 68
Query: 63 RRLKEKR 69
RR + ++
Sbjct: 69 RRARLRK 75
>pdb|2LK2|A Chain A, Solution Nmr Structure Of Homeobox Domain (171-248) Of
Human Homeobox Protein Tgif1, Northeast Structural
Genomics Consortium Target Hr4411b
Length = 89
Score = 31.6 bits (70), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 7/75 (9%)
Query: 24 VMALEKFYNEHKY---PTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEAFVGGR 80
V L + EH+Y P+E+ K+ +++Q L+ QV WF + R +RL D G+
Sbjct: 17 VQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINAR---RRLLPDMLRKDGK 73
Query: 81 QDRSSGVIQDRGSGL 95
D + I RG+ +
Sbjct: 74 -DPNQFTISRRGAKI 87
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 31.6 bits (70), Expect = 1.1, Method: Composition-based stats.
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLSVDEAFV 77
T Q+ LE + + YP ++ +A+++ L ++ WF +RR K KR + F+
Sbjct: 9 TQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQFL 66
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 15 KRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
K + KT QV LE + + +PT+ ++ + L+ +++ WF RR
Sbjct: 16 KFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR 65
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 25/42 (59%)
Query: 27 LEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68
LE+ + + + K +VA++ G+T QV WF ++R++ K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 31.2 bits (69), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 26 ALEK-FYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68
LEK F + KYP E+ +++Q+ + +++ WF HRR ++K
Sbjct: 22 TLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 30.8 bits (68), Expect = 2.0, Method: Composition-based stats.
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
T Q L + E+K P++E++ +++Q+GL VS +F + R
Sbjct: 103 TDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 147
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 30.8 bits (68), Expect = 2.0, Method: Composition-based stats.
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
T Q L + E+K P++E++ +++Q+GL VS +F + R
Sbjct: 105 TDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 149
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 30.4 bits (67), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 20 TPAQVMALEKFYNE-HKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71
T QV LE +N+ +K+P +A + GLTE+Q WF +RL E R S
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWF-KQRLAEWRRS 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 30.4 bits (67), Expect = 2.6, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68
+P LE+ + + + K +VA++ G+T QV WF ++R++ K
Sbjct: 5 SPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 30.0 bits (66), Expect = 3.1, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 20 TPAQVMALEKFYNE-HKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKRLS 71
T QV LE +N+ +K+P +A + GLTE+Q WF +RL E R S
Sbjct: 9 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWF-KQRLAEWRRS 60
>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 = 29.6 bits (65), Expect = 4.0, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 11 EKNIKRRYKTPAQVMA-LEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68
EK+ K + Q A LE+ + + + K +VA++ G+T QV WF ++R++ K
Sbjct: 3 EKSPKGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 29.6 bits (65), Expect = 4.2, Method: Composition-based stats.
Identities = 14/54 (25%), Positives = 29/54 (53%)
Query: 11 EKNIKRRYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRR 64
+K +R TP + AL ++ ++ PT + ++ A+++ + V WF +RR
Sbjct: 92 KKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRR 145
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 29.6 bits (65), Expect = 4.6, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 11 EKNIKRRYKTPAQVMA-LEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68
EK+ K + Q A LE+ + + + K +VA++ G+T QV WF ++R++ K
Sbjct: 3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And
Homeoboxes Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And
Homeoboxes Protein 2, Homeodomain 2)
Length = 66
Score = 29.3 bits (64), Expect = 5.3, Method: Composition-based stats.
Identities = 13/53 (24%), Positives = 26/53 (49%)
Query: 17 RYKTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEKR 69
R KT Q+ L+ + + ++P + ++ E GL ++ WF R + +R
Sbjct: 9 RKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
Length = 96
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 25/50 (50%)
Query: 19 KTPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68
KTP Q+ L+ + ++P+ E ++A++ GL + WF R K
Sbjct: 32 KTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWK 81
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 28.9 bits (63), Expect = 7.2, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 20 TPAQVMALEKFYNEHKYPTEEMKSQVAEQIGLTEKQVSGWFCHRRLKEK 68
T +Q+ LE+ + + +Y T + ++ ++ L QV WF +RR + K
Sbjct: 10 TSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|1W30|A Chain A, Pyrr Of Mycobacterium Tuberculosis As A Potential Drug
Target
pdb|1W30|B Chain B, Pyrr Of Mycobacterium Tuberculosis As A Potential Drug
Target
Length = 201
Score = 28.5 bits (62), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 5/87 (5%)
Query: 223 YRED---GPPLGVDFDPLPPGAFESPSGDPVNEPFYVGNSRWSNSPEVPEIDKPRALGTR 279
YR+D PP + +P G + V++ Y G S S + ++ +PRA+
Sbjct: 88 YRDDLMIKPPRPLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLA 147
Query: 280 YEVDSS--KMDLQDSYIDENLNSKRSD 304
VD ++ L+ Y+ +N+ + RS+
Sbjct: 148 VLVDRGHRELPLRADYVGKNVPTSRSE 174
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
0.310 0.128 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,414,799
Number of Sequences: 62578
Number of extensions: 657954
Number of successful extensions: 1538
Number of sequences better than 100.0: 102
Number of HSP's better than 100.0 without gapping: 90
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1446
Number of HSP's gapped (non-prelim): 103
length of query: 513
length of database: 14,973,337
effective HSP length: 103
effective length of query: 410
effective length of database: 8,527,803
effective search space: 3496399230
effective search space used: 3496399230
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (25.4 bits)