RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy8301
(157 letters)
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 86.6 bits (215), Expect = 2e-23
Identities = 34/58 (58%), Positives = 41/58 (70%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
K R Q+QV+ELER+F+ +YLS ERE L I+L+PTQVKIWFQN RYK KR
Sbjct: 4 KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 86.2 bits (214), Expect = 2e-23
Identities = 28/58 (48%), Positives = 37/58 (63%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
KMRT Q+Q+ L+ +FQ +YLS + + L +NLS QVK WFQN+R K KR Q
Sbjct: 5 KMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62
>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic
development, complex (homeodomain/DNA); HET: DNA; NMR
{Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P*
1vnd_A 1qry_A
Length = 77
Score = 86.4 bits (214), Expect = 3e-23
Identities = 34/64 (53%), Positives = 42/64 (65%)
Query: 3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
++ K R ++Q +ELER+F+ RYLS ERE L I L+PTQVKIWFQN RYK
Sbjct: 5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKT 64
Query: 63 KRLQ 66
KR Q
Sbjct: 65 KRAQ 68
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 85.8 bits (213), Expect = 3e-23
Identities = 30/57 (52%), Positives = 37/57 (64%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
K RT +Q+ LERKF+ +YLS ER ++L+ TQVKIWFQNRR K KRL
Sbjct: 2 KPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 85.4 bits (212), Expect = 3e-23
Identities = 32/55 (58%), Positives = 39/55 (70%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
K R Q+QV+ELER+F+ RYLS ER+ L + L+ TQVKIWFQNRRYK K
Sbjct: 4 KPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 85.1 bits (211), Expect = 5e-23
Identities = 33/62 (53%), Positives = 41/62 (66%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
++ +QV ELERKF H +YLS ER L K + L+ TQVKIWFQNRRYK KR Q
Sbjct: 6 HHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS 65
Query: 69 NQ 70
++
Sbjct: 66 SE 67
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 83.7 bits (207), Expect = 3e-22
Identities = 27/61 (44%), Positives = 35/61 (57%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
K RT +Q+ L +FQ +YLS + + L +NLS QVK WFQN+R K KR Q
Sbjct: 24 KTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN 83
Query: 69 N 69
N
Sbjct: 84 N 84
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 82.7 bits (205), Expect = 4e-22
Identities = 25/49 (51%), Positives = 33/49 (67%)
Query: 16 QSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
+SQV ELER+F +YL+ ER L K + ++ QVK WFQNRR K +R
Sbjct: 6 RSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 80.1 bits (198), Expect = 5e-21
Identities = 26/64 (40%), Positives = 35/64 (54%)
Query: 3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
K RT Q+ L+R+FQ +YL+ ER L + L+ TQVKIWFQN+R K
Sbjct: 3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKI 62
Query: 63 KRLQ 66
K+
Sbjct: 63 KKSG 66
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 79.9 bits (197), Expect = 1e-20
Identities = 26/64 (40%), Positives = 39/64 (60%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
K RT+ + QV ELE++F +YL+ ER L + + ++ QVK WFQNRR K +R A
Sbjct: 19 KPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAE 78
Query: 69 NQNS 72
+ +
Sbjct: 79 EREA 82
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 70
Score = 73.6 bits (181), Expect = 2e-18
Identities = 27/56 (48%), Positives = 34/56 (60%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
+ Q ELE+KF+ +YLSP ER+ L K + LS QVK WFQNRR K +R
Sbjct: 9 GGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding
proteins/DNA), complex, DNA- binding protein, DNA; HET:
DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1
PDB: 1f43_A 1yrn_A*
Length = 61
Score = 71.5 bits (176), Expect = 1e-17
Identities = 16/61 (26%), Positives = 34/61 (55%)
Query: 3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
+ ++ K +++ LE F+ + L+ E+E + K+ ++P QV++WF N+R +
Sbjct: 1 KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS 60
Query: 63 K 63
K
Sbjct: 61 K 61
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with
the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 71.4 bits (175), Expect = 2e-17
Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
+ RT + Q+ LE++F+ +YLS +R L + + LS QVK W+QNRR K K+
Sbjct: 19 RSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSG 76
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 69.0 bits (169), Expect = 2e-16
Identities = 18/71 (25%), Positives = 30/71 (42%)
Query: 4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
S A + Q+ L+ F ++ +E E L K LS +V+ WF +RRY +
Sbjct: 5 SSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCR 64
Query: 64 RLQAMNQNSNG 74
L+ +
Sbjct: 65 NLKGSRSGPSS 75
>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double
helix, helix-turn-helix; NMR {Drosophila melanogaster}
SCOP: a.4.1.1
Length = 68
Score = 67.1 bits (164), Expect = 6e-16
Identities = 23/65 (35%), Positives = 35/65 (53%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
+ RT SQ+ ELE+ F RYL+ L ++ L QVKIWF+NRR + K
Sbjct: 4 RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQ 63
Query: 69 NQNSN 73
+++ +
Sbjct: 64 HKDQS 68
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 67.3 bits (164), Expect = 4e-15
Identities = 20/67 (29%), Positives = 27/67 (40%)
Query: 1 MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
+ R K RT+ LE F S E L + L V++WF NRR
Sbjct: 93 IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQ 152
Query: 61 KQKRLQA 67
K+KR+
Sbjct: 153 KEKRMTP 159
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU
domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP:
a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A
1oct_C* 1pou_A 1pog_A 1hdp_A
Length = 160
Score = 66.5 bits (162), Expect = 1e-14
Identities = 16/65 (24%), Positives = 34/65 (52%)
Query: 1 MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
+ R K RT+ + LE+ F + + + ++ +++N+ +++WF NRR
Sbjct: 95 IEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQ 154
Query: 61 KQKRL 65
K+KR+
Sbjct: 155 KEKRI 159
>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary,
CPHD, POU domain, transcription factor,
transcription/DNA complex; HET: DNA; 2.30A {Rattus
norvegicus} SCOP: a.4.1.1 a.35.1.1
Length = 146
Score = 65.8 bits (160), Expect = 1e-14
Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
K RT + LER F S E + +E+NL V++WF NRR ++KR++
Sbjct: 89 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 146
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA
binding protein/DNA), transcription/DNA complex; HET:
DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB:
1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A
1du0_A* 1ztr_A 1enh_A 2p81_A
Length = 61
Score = 62.7 bits (153), Expect = 3e-14
Identities = 22/54 (40%), Positives = 33/54 (61%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
RT Q+ L+R+F RYL+ R+ L E+ L+ Q+KIWF+N+R K K+
Sbjct: 7 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA
complex, transcription/DNA complex; 2.00A {Drosophila
melanogaster} SCOP: a.4.1.1
Length = 60
Score = 61.6 bits (150), Expect = 6e-14
Identities = 22/58 (37%), Positives = 34/58 (58%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
+ RT + Q+ LE++F Y+S R L ++NL + +K+WFQNRR K KR +
Sbjct: 3 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60
>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex,
DNA-binding protein, protein/DNA complex; HET: DNA;
2.35A {Homo sapiens} SCOP: a.4.1.1
Length = 97
Score = 60.3 bits (146), Expect = 6e-13
Identities = 27/56 (48%), Positives = 36/56 (64%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
+RTN Q+ ELE++F +YLS R + + L+ TQVKIWFQNRR KQK+
Sbjct: 36 GLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain,
three helices with the DNA binding helix- turn-helix
motif, structural genomics; NMR {Homo sapiens}
Length = 70
Score = 59.3 bits (144), Expect = 7e-13
Identities = 17/56 (30%), Positives = 24/56 (42%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
RT Q+ L+ F Y E E L +NL + +WFQN R K ++
Sbjct: 9 SSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 59.0 bits (143), Expect = 9e-13
Identities = 14/68 (20%), Positives = 30/68 (44%), Gaps = 1/68 (1%)
Query: 7 AGKMRTNGIQSQVFELERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
+ + + + QV LE F + ++ PT ++ E L+ Q + WF+ R + +R
Sbjct: 2 SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61
Query: 66 QAMNQNSN 73
+ +
Sbjct: 62 EGLPSECR 69
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex,
helix-turn-helix (HTH), DNA-binding, homeobox, nucleus,
transcription regulation; 2.51A {Homo sapiens}
Length = 151
Score = 60.8 bits (147), Expect = 1e-12
Identities = 16/62 (25%), Positives = 26/62 (41%)
Query: 3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
+ + K RT+ + L F+ + E + KE+N V++WF NRR
Sbjct: 89 EPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTL 148
Query: 63 KR 64
K
Sbjct: 149 KN 150
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 58.2 bits (141), Expect = 2e-12
Identities = 23/56 (41%), Positives = 35/56 (62%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
+ RT ++Q+ ELE++F +Y+S R L +NL+ +KIWFQNRR K K+
Sbjct: 5 RTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 89
Score = 58.5 bits (141), Expect = 2e-12
Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 3/68 (4%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
K +T Q QV LE F + + E + L E LS ++ WF RR + ++
Sbjct: 18 KEKT---QGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQA 74
Query: 69 NQNSNGKN 76
+S G
Sbjct: 75 VLDSMGSG 82
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor,
homeodomain, domain swapping, structural oxford protein
production facility, OPPF; 2.70A {Homo sapiens}
Length = 66
Score = 57.5 bits (139), Expect = 3e-12
Identities = 15/64 (23%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 1 MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
M H + +T + Q+ L+ F ++ E L + L+ +++K WF + RY
Sbjct: 1 MAHHHHHHRKKT---KEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRY 57
Query: 61 KQKR 64
+ +R
Sbjct: 58 RCQR 61
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 57.6 bits (139), Expect = 4e-12
Identities = 23/73 (31%), Positives = 39/73 (53%)
Query: 1 MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
M K R + Q+ ELER++ ++++ +R + NLS QV IWFQNRR
Sbjct: 1 MSHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 60
Query: 61 KQKRLQAMNQNSN 73
K+K++ + ++
Sbjct: 61 KEKKVINKLKTTS 73
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA
binding, homeodomain, homeotic proteins, development,
specificity; HET: DNA; 2.40A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 9ant_A*
Length = 81
Score = 57.1 bits (138), Expect = 5e-12
Identities = 21/56 (37%), Positives = 32/56 (57%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
+ R + Q ELE++F YL+ R + ++L+ Q+KIWFQNRR K K+
Sbjct: 22 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain,
three helices with the DNA binding helix- turn-helix
motif, structural genomics; NMR {Homo sapiens}
Length = 80
Score = 57.1 bits (138), Expect = 7e-12
Identities = 14/64 (21%), Positives = 30/64 (46%)
Query: 3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
+ R ++RT Q+ L +K+ + + + E+ L V++WFQN R ++
Sbjct: 13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARE 72
Query: 63 KRLQ 66
++
Sbjct: 73 RKSG 76
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA;
NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A
1hom_A 1ftz_A
Length = 68
Score = 56.3 bits (136), Expect = 9e-12
Identities = 22/58 (37%), Positives = 33/58 (56%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
+ R + Q ELE++F RYL+ R + ++L+ Q+KIWFQNRR K K+
Sbjct: 4 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 75
Score = 56.4 bits (136), Expect = 1e-11
Identities = 14/66 (21%), Positives = 22/66 (33%), Gaps = 3/66 (4%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
K R Q+ LE F E + L E ++ ++ WF RR K +
Sbjct: 12 KERA---PEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETK 68
Query: 69 NQNSNG 74
+
Sbjct: 69 KSGPSS 74
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation,
helix-turn-helix, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: a.4.1.1
Length = 70
Score = 56.0 bits (135), Expect = 1e-11
Identities = 20/64 (31%), Positives = 34/64 (53%)
Query: 3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
K R + Q+ ELER++ ++++ +R + +LS Q+ IWFQNRR K+
Sbjct: 3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKE 62
Query: 63 KRLQ 66
K+
Sbjct: 63 KKSG 66
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 56.4 bits (136), Expect = 1e-11
Identities = 23/56 (41%), Positives = 35/56 (62%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
+ RT+ + Q ELE++F RYL+ R + ++L+ Q+KIWFQNRR K K+
Sbjct: 30 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85
>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA
complex, HOX hexapeptide, TALE homeodomain, homeodomain
interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB:
1san_A
Length = 77
Score = 54.9 bits (132), Expect = 4e-11
Identities = 24/58 (41%), Positives = 34/58 (58%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
K R + Q ELE++F YL+ R + + +NL+ QVKIWFQNRR K K++
Sbjct: 15 KKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription
factor DNA complex, pore, stem cells; HET: DNA; 2.80A
{Mus musculus} PDB: 1ocp_A
Length = 155
Score = 57.0 bits (137), Expect = 4e-11
Identities = 16/56 (28%), Positives = 25/56 (44%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
+ RT+ + LE F S + + ++ L V++WF NRR K KR
Sbjct: 98 RKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain,
three helices with the DNA binding helix- turn-helix
motif, structural genomics; NMR {Homo sapiens}
Length = 70
Score = 53.5 bits (129), Expect = 1e-10
Identities = 12/64 (18%), Positives = 25/64 (39%)
Query: 3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
+ RT Q+ L + F S + + + + L +K WF+N +K+
Sbjct: 3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKE 62
Query: 63 KRLQ 66
++
Sbjct: 63 RQSG 66
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with
the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 53.2 bits (128), Expect = 2e-10
Identities = 15/74 (20%), Positives = 30/74 (40%)
Query: 3 QSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQ 62
+MRT+ Q+ ++ F + + L ++ L+ +++WFQN R K
Sbjct: 3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKF 62
Query: 63 KRLQAMNQNSNGKN 76
+R +N
Sbjct: 63 RRNLLRQENGGVSG 76
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain,
transcription factor, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: a.4.1.1
Length = 89
Score = 52.7 bits (126), Expect = 4e-10
Identities = 11/67 (16%), Positives = 25/67 (37%), Gaps = 3/67 (4%)
Query: 9 KMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
K +T Q+ L+ F + L+ E L + L+ ++ WF ++ + +
Sbjct: 16 KEKT---AEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEK 72
Query: 69 NQNSNGK 75
+
Sbjct: 73 MEIDESN 79
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein,
DNA-binding, N gene regulation; 1.00A {Drosophila
melanogaster} PDB: 3lnq_A 3cmy_A
Length = 60
Score = 51.9 bits (125), Expect = 4e-10
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAM 68
Q+ ELE+ F Y RE L +I L+ ++++WFQNRR K ++ + +
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 54.5 bits (130), Expect = 4e-10
Identities = 11/73 (15%), Positives = 26/73 (35%)
Query: 1 MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRY 60
+ + K R Q L F+ + S + + +++ L + V +F N R
Sbjct: 91 KDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARR 150
Query: 61 KQKRLQAMNQNSN 73
+ + + +
Sbjct: 151 RSLDKWLEHHHHH 163
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding
protein, homeodomain, LIM domain; NMR {Rattus
norvegicus} SCOP: a.4.1.1
Length = 66
Score = 52.0 bits (125), Expect = 4e-10
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 10 MRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69
+RT + Q+ L + +E L + LSP +++WFQN+R K K+ M
Sbjct: 6 VRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSIMM 65
Query: 70 Q 70
+
Sbjct: 66 K 66
>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain
variant, DNA binding protein, developmental protein,
disease mutation, DNA-binding; NMR {Homo sapiens}
Length = 67
Score = 51.9 bits (125), Expect = 4e-10
Identities = 23/60 (38%), Positives = 33/60 (55%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ 70
RT Q+Q+ LE F+ Y E L +++NL +++IWFQNRR K KR +Q
Sbjct: 5 RTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQ 64
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac
development, riken structural genomics/proteomics
initiative, RSGI, transcription; NMR {Mus musculus}
SCOP: a.4.1.1
Length = 72
Score = 51.6 bits (124), Expect = 7e-10
Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 11 RTNGIQSQVFELERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69
+ QV LE F + ++ PT ++ E L+ Q + WF+ R + +R + +
Sbjct: 5 AATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGLP 64
Query: 70 QNS 72
Sbjct: 65 SEC 67
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the
DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Mus musculus}
Length = 80
Score = 51.3 bits (123), Expect = 9e-10
Identities = 23/64 (35%), Positives = 35/64 (54%)
Query: 10 MRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69
RT ++Q+ LE F RY RE + +INL ++V++WF+NRR K ++ Q
Sbjct: 10 ERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQ 69
Query: 70 QNSN 73
QN
Sbjct: 70 QNGG 73
>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA
complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P
2lkx_A* 2l7m_P
Length = 68
Score = 50.4 bits (121), Expect = 1e-09
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ 70
RT+ Q+ +LE FQ RY + RE + NL+ +V++WF+NRR K ++ +
Sbjct: 7 RTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEFIV 66
Query: 71 N 71
Sbjct: 67 T 67
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 50.9 bits (122), Expect = 2e-09
Identities = 20/66 (30%), Positives = 34/66 (51%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQ 70
RT+ Q Q+ LE++F+ Y RE L +I+L ++++WF NRR K +R + +
Sbjct: 11 RTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLRN 70
Query: 71 NSNGKN 76
Sbjct: 71 QRRQSG 76
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 71
Score = 49.8 bits (119), Expect = 3e-09
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 1/57 (1%)
Query: 9 KMRTNGIQSQVFELERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKR 64
+ RT + L+ + Y L +++L + +FQN+RY K
Sbjct: 9 RSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with
the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 70
Score = 49.6 bits (119), Expect = 4e-09
Identities = 20/59 (33%), Positives = 32/59 (54%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMN 69
RT Q+ LE FQ +Y RE L ++++L +V++WF+NRR K +R +
Sbjct: 11 RTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGPSS 69
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription
factor, structural genomics, loop insertion, NPPSFA;
NMR {Homo sapiens} SCOP: a.4.1.1
Length = 95
Score = 49.3 bits (117), Expect = 9e-09
Identities = 15/77 (19%), Positives = 26/77 (33%), Gaps = 15/77 (19%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------LSPTQVKIWF 55
R + + +E F +Y +RE + N ++ +V WF
Sbjct: 11 RFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWF 70
Query: 56 QNRRYKQKRLQAMNQNS 72
NRR + KR +
Sbjct: 71 ANRRKEIKRRANIAAIL 87
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription
regulation; HET: DNA; 2.00A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 3a01_B
Length = 81
Score = 48.9 bits (117), Expect = 9e-09
Identities = 21/56 (37%), Positives = 33/56 (58%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
RT SQ+ ELER F+ +Y RE L + NL+ ++++WFQNRR + ++
Sbjct: 22 RTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQH 77
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding
domain, transcription, structural genomics, NPPSFA; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 72
Score = 47.9 bits (114), Expect = 2e-08
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 17 SQVFELERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
LE+ F + +Y + L K+++ S +++ WF++RR + K
Sbjct: 18 EPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor,
homeodomain, structural genomics, oxford production
facility, OPPF, transcription; 2.60A {Homo sapiens}
Length = 96
Score = 46.7 bits (110), Expect = 9e-08
Identities = 16/63 (25%), Positives = 25/63 (39%)
Query: 4 SHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
+ Q+ L+ F ++ SP E + L KE L+ T + WF + RY K
Sbjct: 22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWK 81
Query: 64 RLQ 66
Sbjct: 82 NGN 84
>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain,
transcription factor, leucine zipper- containing
factor, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: a.4.1.1
Length = 76
Score = 42.7 bits (100), Expect = 2e-06
Identities = 12/59 (20%), Positives = 23/59 (38%)
Query: 8 GKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
G + Q+ L+ F ++ + + L + L ++ WF + RY K Q
Sbjct: 4 GSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ 62
>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Mus musculus}
SCOP: a.4.1.1
Length = 64
Score = 42.1 bits (99), Expect = 2e-06
Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 22 LERKFQHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
LE+ F I ++ E L K+++ ++ WF+ RR ++K
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain,
hoogsteen base PAIR, transcription/DNA complex; HET:
5IU; 2.10A {Synthetic} SCOP: a.4.1.1
Length = 60
Score = 40.7 bits (96), Expect = 6e-06
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 2/42 (4%)
Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRL 65
++I YL E L K +LS Q+K W NRR K+K +
Sbjct: 18 AKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration
calorimetry, protein-DNA complex, transcription/DNA
complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1
PDB: 1akh_B* 1apl_C* 1yrn_B*
Length = 83
Score = 39.4 bits (92), Expect = 3e-05
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSNGKN 76
++I YL E L K +LS Q+K W RR K+K + + ++ +
Sbjct: 22 AKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIAPELADLLS 74
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription
regulation, transcriptional repression, DNA- binding
protein; HET: DNA; 2.25A {Saccharomyces cerevisiae}
SCOP: a.4.1.1
Length = 87
Score = 39.5 bits (92), Expect = 3e-05
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
++I YL E L K +LS Q+K W NRR K+K
Sbjct: 47 AKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 86
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 38.2 bits (89), Expect = 9e-05
Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQN--RRYKQKRLQAMNQNSN 73
++H Y S E+ +L ++ +LS QV WF N RR L+ ++ N
Sbjct: 25 YEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRKDGKDPN 76
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 37.7 bits (88), Expect = 9e-05
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQN--RRYKQKRLQAMNQ 70
FQH+ Y S +++ L ++ L+ QV WF N RR Q + N+
Sbjct: 18 FQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNR 66
>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein,
X-linked TGF(beta) induced transcription factor 2-like
protein, TGIF-like on the X; NMR {Homo sapiens}
Length = 83
Score = 37.4 bits (87), Expect = 2e-04
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQN--RRYKQKRLQAMNQNSNG 74
++H Y S E++ML ++ NLS Q+ WF N RR LQ + +G
Sbjct: 27 YKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQRRNDPSG 79
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 38.5 bits (88), Expect = 3e-04
Identities = 15/75 (20%), Positives = 25/75 (33%), Gaps = 21/75 (28%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------------LSPT 49
R + L + + + S ERE L +E N ++
Sbjct: 146 RFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEV 205
Query: 50 QVKIWFQNRRYKQKR 64
+V WF NRR ++
Sbjct: 206 RVYNWFANRRKEEAF 220
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation,
DNA-binding, POU domain, diabetes, disease mutation,
MODY3, transcription/DNA comple; 2.60A {Homo sapiens}
SCOP: a.4.1.1 a.35.1.1
Length = 194
Score = 38.3 bits (88), Expect = 4e-04
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 21/75 (28%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------------LSPT 49
R + L + ++ + S ERE L +E N ++
Sbjct: 119 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 178
Query: 50 QVKIWFQNRRYKQKR 64
+V WF NRR ++
Sbjct: 179 RVYNWFANRRKEEAF 193
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 36.7 bits (84), Expect = 5e-04
Identities = 15/83 (18%), Positives = 29/83 (34%), Gaps = 21/83 (25%)
Query: 11 RTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN---------------------LSPT 49
R + L + ++ + S ERE L +E N ++
Sbjct: 13 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEV 72
Query: 50 QVKIWFQNRRYKQKRLQAMNQNS 72
+V WF NRR ++ + ++
Sbjct: 73 RVYNWFANRRKEEAFRHKLAMDT 95
>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein,
protein/DNA complex; HET: DNA; 2.35A {Homo sapiens}
SCOP: a.4.1.1 PDB: 1lfu_P
Length = 87
Score = 35.2 bits (81), Expect = 0.001
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQN--RRYKQKRLQAMNQ 70
+ H+ Y S +E L K+ ++ +QV WF N RYK+ + +
Sbjct: 21 YSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEE 69
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 64
Score = 34.2 bits (79), Expect = 0.002
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 4/41 (9%)
Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQN--RRYKQ 62
+ H+ Y S +E L K+ ++ +QV WF N RYK+
Sbjct: 23 YSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian,
protein-DNA complex, HOX hexapeptide, TALE homeodomain,
homeodomain interaction; 1.90A {Homo sapiens} SCOP:
a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*
Length = 73
Score = 33.9 bits (78), Expect = 0.002
Identities = 14/49 (28%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQN--RRYKQKRLQAMNQ 70
+ H+ Y S +E L K+ ++ +QV WF N RYK+ + +
Sbjct: 21 YSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEE 69
>2ys9_A Homeobox and leucine zipper protein homez; homeodomain,
structural genomics, NPPSFA, national project on
protein structural and functional analyses; NMR {Homo
sapiens}
Length = 70
Score = 34.0 bits (77), Expect = 0.003
Identities = 13/51 (25%), Positives = 21/51 (41%)
Query: 17 SQVFELERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67
+ LER + + L T+ L + LS QV WF +R + +
Sbjct: 16 PDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQPAEVSG 66
>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 73
Score = 33.1 bits (76), Expect = 0.005
Identities = 16/46 (34%), Positives = 23/46 (50%), Gaps = 4/46 (8%)
Query: 26 FQHIR--YLSPTEREMLGKEINLSPTQVKIWFQN--RRYKQKRLQA 67
FQHI Y + E++ + + NL+ QV WF N RR Q +
Sbjct: 27 FQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPSS 72
>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 33.4 bits (75), Expect = 0.006
Identities = 14/66 (21%), Positives = 28/66 (42%), Gaps = 4/66 (6%)
Query: 4 SHRAGKMRTNGIQSQVFELERKFQ----HIRYLSPTEREMLGKEINLSPTQVKIWFQNRR 59
S A + RT + L++ + + + + E + E+N+ V+ W NRR
Sbjct: 5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRR 64
Query: 60 YKQKRL 65
K + +
Sbjct: 65 RKYRLM 70
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 32.7 bits (74), Expect = 0.006
Identities = 10/35 (28%), Positives = 16/35 (45%)
Query: 33 SPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQA 67
S E + +NL VK WF+ + Q +Q+
Sbjct: 29 SAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQS 63
>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding
cooperativity, maltose binding protein, MBP, sugar
binding, DNA binding protein; 2.10A {Escherichia coli}
SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A
Length = 421
Score = 33.6 bits (77), Expect = 0.016
Identities = 14/41 (34%), Positives = 27/41 (65%)
Query: 23 ERKFQHIRYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQK 63
E+ F+ + L+ E+E + K+ ++P QV++WF N+R + K
Sbjct: 381 EQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices
with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 71
Score = 27.1 bits (59), Expect = 0.89
Identities = 8/34 (23%), Positives = 13/34 (38%)
Query: 33 SPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQ 66
+ E + + L VK WF+ R+ Q
Sbjct: 31 NSDELLKISIAVGLPQEFVKEWFEQRKVYQYSNS 64
>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational
analysis, G protein, GAS subunit, A2A adenosine
receptor, cell-penetrating peptides; NMR {Synthetic}
PDB: 2o00_A
Length = 37
Score = 26.2 bits (57), Expect = 0.93
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 50 QVKIWFQNRRYKQKR 64
Q+KIWFQNRR K K+
Sbjct: 2 QIKIWFQNRRMKWKK 16
>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca
cleavage, DNA damage, DNA repair, DNA replication,
DNA-BIND hydrolase; 1.37A {Thermotoga maritima}
Length = 196
Score = 27.5 bits (62), Expect = 1.8
Identities = 7/34 (20%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 16 QSQVFELERKFQHIRYLSPTEREMLGKEINLSPT 49
Q +V +F P+ RE+ + ++P
Sbjct: 7 QRKVLLFIEEFIEKNGYPPSVREI-ARRFRITPR 39
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 27.7 bits (61), Expect = 2.2
Identities = 24/164 (14%), Positives = 50/164 (30%), Gaps = 52/164 (31%)
Query: 16 QSQVFELERKF-QHI-RYLSPTEREMLGKEINLSPTQVKIWFQNRRYKQKRLQAMNQNSN 73
+ EL KF ++ + P++ + +NL T+ F+ Y L+
Sbjct: 54 PTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTE----FE-NCY----LE------- 97
Query: 74 GKNVFKIKHIFTRKTKPTSAQATIGCP--------EAKKIGRKPETDFP---------AE 116
G ++ H K T+ A+ + ++P
Sbjct: 98 GNDI----HALAAKL-LQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG 152
Query: 117 EHNIFVPNF----DQSDFLDNKWEDIDILDELHDQYVPNCTDIM 156
+ F + D+ + E L +L+ Y D++
Sbjct: 153 NAQLVA-IFGGQGNTDDYFE---E----LRDLYQTYHVLVGDLI 188
>2jks_A BSR4, bradyzoite surface antigen BSR4; immune system; 1.90A
{Toxoplasma gondii}
Length = 315
Score = 27.0 bits (59), Expect = 2.6
Identities = 12/38 (31%), Positives = 14/38 (36%), Gaps = 11/38 (28%)
Query: 85 TRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEHNIFV 122
T K TSA TI P+TD P + V
Sbjct: 247 TETQKRTSATLTI-----------PQTDLPEADQQFLV 273
>3ttj_A Mitogen-activated protein kinase 10; JNK3, protein kinase in
transferase-transferase inhibitor complex; HET: JBI;
2.10A {Homo sapiens} PDB: 3tti_A* 1jnk_A*
Length = 464
Score = 26.7 bits (59), Expect = 3.9
Identities = 14/97 (14%), Positives = 42/97 (43%), Gaps = 16/97 (16%)
Query: 1 MFQSHRAGKMRTNGIQSQVFELERKFQHIRYLSPTEREMLGKEIN-LSPTQV---KIW-- 54
M +S + + + F + +++Q+++ + + ++ + + V K+
Sbjct: 39 MSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRP 98
Query: 55 FQNRRYKQ------KRLQAMNQNSNGKNVFKIKHIFT 85
FQN+ + + ++ +N KN+ + ++FT
Sbjct: 99 FQNQTHAKRAYRELVLMKCVNH----KNIISLLNVFT 131
>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices
with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 102
Score = 25.6 bits (55), Expect = 4.1
Identities = 15/72 (20%), Positives = 27/72 (37%), Gaps = 21/72 (29%)
Query: 22 LERKFQHIRYLSPTEREMLGKEIN---------------------LSPTQVKIWFQNRRY 60
L + + + S ERE L +E N ++ +V WF NRR
Sbjct: 21 LYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK 80
Query: 61 KQKRLQAMNQNS 72
++ Q + ++
Sbjct: 81 EEAFRQKLAMDA 92
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 26.4 bits (57), Expect = 5.4
Identities = 22/150 (14%), Positives = 44/150 (29%), Gaps = 43/150 (28%)
Query: 16 QSQVFELERKFQH-IRYLSPTE-REM---LG---KEINLSPTQV--KIWFQNRRY----- 60
+L + + L P E R+M L ++ PT + IWF +
Sbjct: 349 HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI-PTILLSLIWFDVIKSDVMVV 407
Query: 61 --KQKRLQAMNQNSNGKNVFKIKHIFTRKTKPTSAQATIGCPEAKKIGRKPETDFPAEEH 118
K + + + ++ I I+ + + H
Sbjct: 408 VNKLHKYSLVEKQPK-ESTISIPSIYLELKVKLENEYAL--------------------H 446
Query: 119 NIFVPNFDQSDFLDNKWEDIDILDELHDQY 148
V +++ D+ D++ DQY
Sbjct: 447 RSIVDHYNIPKTFDSD----DLIPPYLDQY 472
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.134 0.402
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,376,156
Number of extensions: 128328
Number of successful extensions: 393
Number of sequences better than 10.0: 1
Number of HSP's gapped: 382
Number of HSP's successfully gapped: 84
Length of query: 157
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 71
Effective length of database: 4,300,587
Effective search space: 305341677
Effective search space used: 305341677
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (24.4 bits)