RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy2123
(143 letters)
>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 = 124 bits (312), Expect = 2e-38
Identities = 38/77 (49%), Positives = 53/77 (68%)
Query: 12 DGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARV 71
+ + K K RR+RTTF++ QL+ LE+ FERT YPD + REELA++ L+EAR+
Sbjct: 3 ISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARI 62
Query: 72 QVWFQNRRAKFRRNERN 88
QVWFQNRRA+ R+ +
Sbjct: 63 QVWFQNRRARLRKQHTS 79
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 121 bits (305), Expect = 3e-37
Identities = 40/64 (62%), Positives = 47/64 (73%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
+RNRT+F Q+ ALEK FERTHYPD F RE LA K+ L EAR+QVWF NRRAK+R
Sbjct: 4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
Query: 84 RNER 87
R E+
Sbjct: 64 REEK 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 = 120 bits (304), Expect = 4e-37
Identities = 35/65 (53%), Positives = 46/65 (70%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
RR RTTF QL+ LE +F +T YPD F+REE+A K+ L E+RVQVWF+NRRAK R
Sbjct: 4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
Query: 84 RNERN 88
+ ++
Sbjct: 64 QQQQQ 68
>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 = 119 bits (301), Expect = 9e-37
Identities = 34/65 (52%), Positives = 45/65 (69%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
RR+RT F QL ALE +F+ T YPD RE+LA+KV L E +V+VWF+NRRAK+R
Sbjct: 4 GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
Query: 84 RNERN 88
R+ +
Sbjct: 64 RSGPS 68
>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 = 119 bits (300), Expect = 1e-36
Identities = 34/66 (51%), Positives = 43/66 (65%)
Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
RR RT F S QL LE F+R YPD REE+A L+EARV+VWF+NRRAK+R+
Sbjct: 2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 61
Query: 86 ERNFIS 91
E ++
Sbjct: 62 EEFIVT 67
>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 = 118 bits (297), Expect = 4e-36
Identities = 29/65 (44%), Positives = 39/65 (60%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
+R RT+F HQL ++ F H PDA ++LA+K L++ +QVWFQN RAKFR
Sbjct: 4 GSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFR 63
Query: 84 RNERN 88
RN
Sbjct: 64 RNLLR 68
>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 = 117 bits (295), Expect = 6e-36
Identities = 29/61 (47%), Positives = 39/61 (63%)
Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
RR RT F +Q+ LE VF YP + E+LA+K+ L R+Q+WFQNRRAK +R+ R
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 88 N 88
Sbjct: 62 E 62
>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 = 115 bits (290), Expect = 4e-35
Identities = 38/58 (65%), Positives = 45/58 (77%)
Query: 30 NRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
+ TF S QL LEK F RTHYPD F REELA K+ L+EAR+QVWFQNRRAK+R+ E+
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>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 = 115 bits (290), Expect = 4e-35
Identities = 21/65 (32%), Positives = 32/65 (49%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
R +RT F +QL L+ F+ YP E+L+ + L + VWFQN R K R
Sbjct: 4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
Query: 84 RNERN 88
++ +
Sbjct: 64 KSGPS 68
>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 = 113 bits (284), Expect = 3e-34
Identities = 22/62 (35%), Positives = 33/62 (53%)
Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
K R RT N QL+ L + PDA ++E+L + LS ++VWFQN+R K ++
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
Query: 86 ER 87
Sbjct: 62 SI 63
>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 = 109 bits (275), Expect = 1e-32
Identities = 21/74 (28%), Positives = 34/74 (45%)
Query: 15 DDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVW 74
+ +R RTT QL L + + P + + +A +V L + VQVW
Sbjct: 5 SSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVW 64
Query: 75 FQNRRAKFRRNERN 88
FQN RA+ R++ +
Sbjct: 65 FQNTRARERKSGPS 78
>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 = 102 bits (257), Expect = 4e-30
Identities = 17/65 (26%), Positives = 30/65 (46%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
+R RT QL L + F+ + P +E+A K L + ++ WF+N K R
Sbjct: 4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKER 63
Query: 84 RNERN 88
++ +
Sbjct: 64 QSGPS 68
>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 = 102 bits (255), Expect = 8e-30
Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 1/70 (1%)
Query: 28 RRNRTTFNSHQLNALEKVFERTH-YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
T Q+ LE F + + +PD +A + L+E + Q WF+ R A++RR+E
Sbjct: 2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 61
Query: 87 RNFISHRNLD 96
R++
Sbjct: 62 GLPSECRSVT 71
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 96.4 bits (240), Expect = 2e-27
Identities = 18/69 (26%), Positives = 34/69 (49%), Gaps = 1/69 (1%)
Query: 28 RRNRTTFNSHQLNALEKVFERTH-YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
+ + Q+ LE F + + +PD +A + L+E + Q WF+ R A++RR+E
Sbjct: 3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62
Query: 87 RNFISHRNL 95
R++
Sbjct: 63 GLPSECRSV 71
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 92.5 bits (230), Expect = 6e-26
Identities = 18/68 (26%), Positives = 27/68 (39%)
Query: 21 ERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRA 80
+ + QL+AL+ F R +P E L K LS V+ WF +RR
Sbjct: 2 SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY 61
Query: 81 KFRRNERN 88
R + +
Sbjct: 62 HCRNLKGS 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 = 89.7 bits (222), Expect = 1e-24
Identities = 20/79 (25%), Positives = 29/79 (36%), Gaps = 15/79 (18%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC---------------LSE 68
R +R T+ L +E F YPD REE+A ++
Sbjct: 4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTS 63
Query: 69 ARVQVWFQNRRAKFRRNER 87
+V WF NRR + +R
Sbjct: 64 LKVYNWFANRRKEIKRRAN 82
>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 = 89.4 bits (221), Expect = 7e-24
Identities = 19/75 (25%), Positives = 35/75 (46%)
Query: 11 CDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEAR 70
+ + E +R RT+ + +LE +F ++ P +A ++ L +
Sbjct: 80 NENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDV 139
Query: 71 VQVWFQNRRAKFRRN 85
V+VWF NRR K +R+
Sbjct: 140 VRVWFSNRRQKGKRS 154
>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 = 89.3 bits (221), Expect = 7e-24
Identities = 19/73 (26%), Positives = 34/73 (46%)
Query: 12 DGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARV 71
+ + R+ RTT + +ALE+ F P + +A+++ L + V
Sbjct: 72 QVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVV 131
Query: 72 QVWFQNRRAKFRR 84
+VWF NRR + +R
Sbjct: 132 RVWFCNRRQREKR 144
>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 = 89.3 bits (221), Expect = 9e-24
Identities = 20/75 (26%), Positives = 32/75 (42%)
Query: 10 RCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEA 69
+ ++ K R+ RT+F + AL FE+ P E+AK++
Sbjct: 76 QEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDRE 135
Query: 70 RVQVWFQNRRAKFRR 84
V+VWF NRR +
Sbjct: 136 VVRVWFSNRRQTLKN 150
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 87.0 bits (215), Expect = 1e-22
Identities = 21/64 (32%), Positives = 30/64 (46%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
+ + R+ RT+ ALE F + P A LA + L + V+VWF NRR K +
Sbjct: 96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEK 155
Query: 84 RNER 87
R
Sbjct: 156 RMTP 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 = 83.1 bits (205), Expect = 2e-21
Identities = 18/84 (21%), Positives = 35/84 (41%)
Query: 1 MEYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREEL 60
+ + + R+ RT+ ++ ALEK F P + +
Sbjct: 75 EANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLI 134
Query: 61 AKKVCLSEARVQVWFQNRRAKFRR 84
A+++ + + ++VWF NRR K +R
Sbjct: 135 AEQLNMEKEVIRVWFSNRRQKEKR 158
>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 = 79.5 bits (197), Expect = 5e-21
Identities = 18/59 (30%), Positives = 35/59 (59%)
Query: 23 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
+K K + +++ + LE+VF R ++ +EE+AKK ++ +V+VWF N+R +
Sbjct: 1 KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>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 = 79.1 bits (195), Expect = 8e-21
Identities = 11/63 (17%), Positives = 26/63 (41%)
Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
+ Q+ L+ F ++ +PD L + L+ + ++ WF + R + +R
Sbjct: 3 HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG 62
Query: 86 ERN 88
+
Sbjct: 63 IVH 65
>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 = 77.2 bits (190), Expect = 4e-20
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 1/61 (1%)
Query: 26 KPRRNRTTFNSHQLNALEKVFERT-HYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
R+RT + L L+ YPD L+ ++ L + + +FQN+R +
Sbjct: 6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH 65
Query: 85 N 85
+
Sbjct: 66 S 66
>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 = 75.6 bits (186), Expect = 3e-19
Identities = 26/75 (34%), Positives = 41/75 (54%)
Query: 13 GEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQ 72
+ + K RR+RT F QL LEK FE+ Y R +LA+ + LS+ +V+
Sbjct: 3 SGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVK 62
Query: 73 VWFQNRRAKFRRNER 87
W+QNRR K++++
Sbjct: 63 TWYQNRRMKWKKSGP 77
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 72.8 bits (179), Expect = 2e-18
Identities = 23/64 (35%), Positives = 42/64 (65%)
Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
R+ RT ++S QL AL++ F++T Y R ELA + L++ +V++WFQN+R+K ++
Sbjct: 5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
Query: 85 NERN 88
+ +
Sbjct: 65 SGPS 68
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 73.7 bits (181), Expect = 2e-18
Identities = 26/63 (41%), Positives = 40/63 (63%)
Query: 22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
R PK ++ RT+F Q+ LEK F + Y + R LA+ + +++A+V+ WFQNRR K
Sbjct: 12 RTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTK 71
Query: 82 FRR 84
+RR
Sbjct: 72 WRR 74
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 72.4 bits (178), Expect = 3e-18
Identities = 21/63 (33%), Positives = 34/63 (53%)
Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
+ + + Q+ LE+ F Y A R LAK + L+E +V++WFQNRR K +R
Sbjct: 3 HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 62
Query: 86 ERN 88
+ +
Sbjct: 63 QLS 65
>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 = 72.1 bits (177), Expect = 5e-18
Identities = 26/64 (40%), Positives = 37/64 (57%)
Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ + F++ Q LEK FE Y R+ LAK + LSE +V+ WFQNRRAK+RR
Sbjct: 5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
Query: 85 NERN 88
+ +
Sbjct: 65 SGPS 68
>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 = 75.3 bits (184), Expect = 5e-18
Identities = 21/95 (22%), Positives = 31/95 (32%), Gaps = 21/95 (22%)
Query: 11 CDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC----- 65
++ E K RRNR + L + +ER P RE L ++
Sbjct: 99 GGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECI 158
Query: 66 ----------------LSEARVQVWFQNRRAKFRR 84
++E RV WF NRR +
Sbjct: 159 QRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAF 193
>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 = 72.1 bits (177), Expect = 6e-18
Identities = 23/66 (34%), Positives = 33/66 (50%)
Query: 22 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
K R+ R F Q LE+ F + Y A RE LA + L+ +V++WFQN R K
Sbjct: 4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK 63
Query: 82 FRRNER 87
+R +
Sbjct: 64 TKRAQN 69
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 71.1 bits (175), Expect = 9e-18
Identities = 25/57 (43%), Positives = 36/57 (63%)
Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
R+ RT F + QL ALE+ F + Y R E + + L+E +V++WFQNRRAK +R
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 71.4 bits (175), Expect = 1e-17
Identities = 24/75 (32%), Positives = 39/75 (52%)
Query: 14 EDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQV 73
++ K ++ RT F+S QL L F+R Y +EL+ + LS +V+
Sbjct: 9 NSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKT 68
Query: 74 WFQNRRAKFRRNERN 88
WFQN+R K +R ++N
Sbjct: 69 WFQNQRMKSKRWQKN 83
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 75.1 bits (183), Expect = 1e-17
Identities = 25/95 (26%), Positives = 34/95 (35%), Gaps = 23/95 (24%)
Query: 12 DGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC------ 65
G+ DD E K RRNR + L + ++R P RE L ++
Sbjct: 127 PGQSDDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQ 186
Query: 66 ---------------LSEARVQVWFQNRR--AKFR 83
++E RV WF NRR FR
Sbjct: 187 RGVSPSKAHGLGSNLVTEVRVYNWFANRRKEEAFR 221
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 70.4 bits (173), Expect = 2e-17
Identities = 21/61 (34%), Positives = 35/61 (57%)
Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
++ RT F+ QL AL+ F++ Y +EL+ + LS +V+ WFQN+R K +R
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61
Query: 86 E 86
+
Sbjct: 62 Q 62
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 70.5 bits (173), Expect = 2e-17
Identities = 22/61 (36%), Positives = 36/61 (59%)
Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
R+ R F+ Q+ LE+ F++ Y A RE LA + L+ +V++WFQN R K +R +
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
Query: 88 N 88
+
Sbjct: 63 D 63
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 68.8 bits (169), Expect = 6e-17
Identities = 21/56 (37%), Positives = 35/56 (62%)
Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
R+ R F+ Q+ LE+ F++ Y A R++LA + L+ +V++WFQNRR K +
Sbjct: 3 RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 69.9 bits (170), Expect = 9e-17
Identities = 20/85 (23%), Positives = 29/85 (34%), Gaps = 21/85 (24%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC------------------ 65
K RRNR + L + +ER P RE L ++
Sbjct: 6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLG 65
Query: 66 ---LSEARVQVWFQNRRAKFRRNER 87
++E RV WF NRR + +
Sbjct: 66 SNLVTEVRVYNWFANRRKEEAFRHK 90
>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 = 68.1 bits (166), Expect = 3e-16
Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 3/68 (4%)
Query: 20 YERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79
Y P+ + +T Q+ LE F ++ +P + L + LS + WF RR
Sbjct: 9 YPDFAPQKFKEKT---QGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR 65
Query: 80 AKFRRNER 87
E+
Sbjct: 66 KLRDSMEQ 73
>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 = 4e-16
Identities = 24/62 (38%), Positives = 36/62 (58%)
Query: 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
PRR RTTF S Q+ LE+ F + Y A +L+ K+ L A+V++WF+NRR + +
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQS 61
Query: 87 RN 88
Sbjct: 62 DQ 63
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 66.6 bits (163), Expect = 5e-16
Identities = 23/53 (43%), Positives = 35/53 (66%)
Query: 32 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
T+F+ Q+ LE+ F R Y + R LAK + +++A+V+ WFQNRR K+RR
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>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 = 67.2 bits (164), Expect = 7e-16
Identities = 31/87 (35%), Positives = 42/87 (48%), Gaps = 1/87 (1%)
Query: 1 MEYDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREEL 60
+DWM R + E P RT F + QL LEK F Y R E+
Sbjct: 9 RTFDWMKVKRNPPKTAKVS-EPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEI 67
Query: 61 AKKVCLSEARVQVWFQNRRAKFRRNER 87
A + L+E +V++WFQNRR K ++ ER
Sbjct: 68 AATLELNETQVKIWFQNRRMKQKKRER 94
>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 = 64.7 bits (158), Expect = 3e-15
Identities = 21/58 (36%), Positives = 40/58 (68%)
Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
+R RT F+S QL L++ F Y R++L+ ++ L+EA++++WF+N+RAK +++
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61
>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 = 63.9 bits (156), Expect = 6e-15
Identities = 27/57 (47%), Positives = 35/57 (61%)
Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
RR RT F QL LEK F + +Y R ELA ++ L E+ ++VWFQNRR K +R
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 66.1 bits (160), Expect = 1e-14
Identities = 14/85 (16%), Positives = 31/85 (36%)
Query: 10 RCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEA 69
+ + R P++ R F Q L +F+ P ++ +++++ L +
Sbjct: 80 AACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELS 139
Query: 70 RVQVWFQNRRAKFRRNERNFISHRN 94
V +F N R + H +
Sbjct: 140 TVSNFFMNARRRSLDKWLEHHHHHH 164
>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 = 63.8 bits (155), Expect = 1e-14
Identities = 16/64 (25%), Positives = 23/64 (35%), Gaps = 3/64 (4%)
Query: 23 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82
P + R QL ALE F + P + L + ++ + WF RR K
Sbjct: 6 SGPTKYKERA---PEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62
Query: 83 RRNE 86
E
Sbjct: 63 NAEE 66
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 64.1 bits (156), Expect = 1e-14
Identities = 24/85 (28%), Positives = 43/85 (50%), Gaps = 5/85 (5%)
Query: 3 YDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAK 62
Y WM + + + + +R RT++ +Q LEK F Y R E+A
Sbjct: 9 YPWMKRVHLGTSTVNAN-----GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAH 63
Query: 63 KVCLSEARVQVWFQNRRAKFRRNER 87
+ L+E ++++WFQNRR K+++ +
Sbjct: 64 ALSLTERQIKIWFQNRRMKWKKEHK 88
>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 = 63.9 bits (155), Expect = 1e-14
Identities = 12/80 (15%), Positives = 25/80 (31%), Gaps = 3/80 (3%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
P+ + +T + QL L+ F + L + L+ + WF ++
Sbjct: 11 TPQKFKEKT---AEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKA 67
Query: 84 RNERNFISHRNLDAPTSEQP 103
E + +S
Sbjct: 68 LKEEKMEIDESNAGSSSGPS 87
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 61.6 bits (150), Expect = 5e-14
Identities = 24/61 (39%), Positives = 34/61 (55%)
Query: 26 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
+R RT + QL LEK F Y R ELA + L+E +++WFQNRR K+++
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
Query: 86 E 86
E
Sbjct: 62 E 62
>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 = 61.4 bits (149), Expect = 1e-13
Identities = 27/85 (31%), Positives = 40/85 (47%), Gaps = 12/85 (14%)
Query: 3 YDWMLTLRCDGEDDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAK 62
Y WM +G RR R T+ +Q LEK F HY R E+A
Sbjct: 8 YPWMAIAGTNGL------------RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAH 55
Query: 63 KVCLSEARVQVWFQNRRAKFRRNER 87
+ L+E ++++WFQNRR K ++ +
Sbjct: 56 ALSLTERQIKIWFQNRRMKLKKEIQ 80
>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 = 60.1 bits (146), Expect = 2e-13
Identities = 21/62 (33%), Positives = 35/62 (56%)
Query: 27 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNE 86
+R R T+ +Q LEK F Y R E+A + L+E ++++WFQNRR K+++
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
Query: 87 RN 88
+
Sbjct: 62 KT 63
>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 = 59.5 bits (144), Expect = 4e-13
Identities = 17/64 (26%), Positives = 33/64 (51%)
Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
R+ R ++ QL LE+ + + R +++ LSE ++ +WFQNRR K ++
Sbjct: 5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
Query: 85 NERN 88
+ +
Sbjct: 65 SGPS 68
>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 = 58.7 bits (141), Expect = 2e-12
Identities = 15/69 (21%), Positives = 27/69 (39%)
Query: 18 YDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQN 77
+ K QL+ L+ F RT +P ++LAK+ L+ + WF +
Sbjct: 16 FQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGD 75
Query: 78 RRAKFRRNE 86
R ++
Sbjct: 76 TRYAWKNGN 84
>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 = 57.9 bits (140), Expect = 2e-12
Identities = 22/66 (33%), Positives = 35/66 (53%)
Query: 23 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKF 82
R+ R + HQ LEK F Y R E+A+ + L+E +V++WFQNRR K
Sbjct: 9 HARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKM 68
Query: 83 RRNERN 88
++ ++
Sbjct: 69 KKINKD 74
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 56.8 bits (137), Expect = 5e-12
Identities = 18/63 (28%), Positives = 30/63 (47%)
Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ R+ R + QL LE+ + + R ++ LSE +V +WFQNRR K ++
Sbjct: 5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
Query: 85 NER 87
Sbjct: 65 VIN 67
>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 = 51.2 bits (122), Expect = 7e-10
Identities = 10/62 (16%), Positives = 22/62 (35%), Gaps = 3/62 (4%)
Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRR 84
+ +T QL L+ F + + ++L + L + WF + R +
Sbjct: 4 GSSGKRKT---KEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60
Query: 85 NE 86
+
Sbjct: 61 GQ 62
>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 = 50.6 bits (121), Expect = 1e-09
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 29 RNRTTFNSHQLNALEKVFER-THYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
++ + LEKVF T YPD + L+K++ S ++Q WF++RR + + +
Sbjct: 10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS 67
>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 = 44.4 bits (105), Expect = 2e-07
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 5/59 (8%)
Query: 26 KPRRNRTTFNSHQLNALEKVF-ERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFR 83
N+ LEKVF T +PD E L+K++ +Q WF+ RR + +
Sbjct: 3 SGSSGTAQPNA----ILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 43.9 bits (103), Expect = 4e-07
Identities = 11/51 (21%), Positives = 21/51 (41%)
Query: 37 HQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
+ L+ L+ + P A ++A V L V+ WF+ +A +
Sbjct: 13 NLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQS 63
>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 = 42.6 bits (99), Expect = 2e-06
Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 4/65 (6%)
Query: 24 KPKPRRNRTTFNSHQLNALEKVFER----THYPDAFVREELAKKVCLSEARVQVWFQNRR 79
++RT F+ L L+K ++ E +A ++ + V+ W NRR
Sbjct: 5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRR 64
Query: 80 AKFRR 84
K+R
Sbjct: 65 RKYRL 69
>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 = 38.2 bits (88), Expect = 7e-05
Identities = 10/52 (19%), Positives = 24/52 (46%)
Query: 37 HQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERN 88
++ L+ + P++ +++ V L + V+ WF+ R+ N R+
Sbjct: 15 DHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYSNSRS 66
>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 = 37.2 bits (85), Expect = 3e-04
Identities = 18/100 (18%), Positives = 31/100 (31%), Gaps = 23/100 (23%)
Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVC------------------- 65
RNR + L + ++R P RE L ++
Sbjct: 4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGS 63
Query: 66 --LSEARVQVWFQNRRAKFRRNERNFISHRNLDAPTSEQP 103
++E RV WF NRR + R ++ + +
Sbjct: 64 NLVTEVRVYNWFANRRKEEAF--RQKLAMDAYSSNSGPSS 101
>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; NMR {Arabidopsis thaliana} SCOP:
a.4.1.1
Length = 80
Score = 35.0 bits (80), Expect = 0.001
Identities = 11/65 (16%), Positives = 23/65 (35%), Gaps = 4/65 (6%)
Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHY----PDAFVREELAKKVCLSEARVQVWFQNRRA 80
+R RT F + Q + ER + D E+ + + +++W N +
Sbjct: 15 GTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKN 74
Query: 81 KFRRN 85
+
Sbjct: 75 SGPSS 79
>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 = 33.1 bits (75), Expect = 0.029
Identities = 23/146 (15%), Positives = 43/146 (29%), Gaps = 51/146 (34%)
Query: 33 TFNSHQLNALEKVFE---RTH--YPDAFVREELAKK--------------VC-LSEARVQ 72
+F A+ +F R + YP+ + + + + L++ +VQ
Sbjct: 291 SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ 350
Query: 73 VWFQNRRAKFRRNERNFISHRN-----------------------LDAPTS-EQPLPPCT 108
+ + ++ IS N AP+ +Q
Sbjct: 351 DYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQ------ 404
Query: 109 NATPLSSAPPSSSHSFDFCAMP-HSQ 133
+ P S S+ F A P HS
Sbjct: 405 SRIPFSERKLKFSNRFLPVASPFHSH 430
>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 = 30.6 bits (69), Expect = 0.055
Identities = 17/83 (20%), Positives = 25/83 (30%), Gaps = 21/83 (25%)
Query: 12 DGEDDDYDYERRKPKPRRN---------RTTFNSHQLNALEKVFERTHYPDAFVREELAK 62
+ D + KP + F + N Y D E L K
Sbjct: 15 NVVTQDMINKSTKPYRGHRFTKENVRILESWFAKNIENP---------YLDTKGLENLMK 65
Query: 63 KVCLSEARVQVWFQNRRAKFRRN 85
LS +++ W NRR R+
Sbjct: 66 NTSLSRIQIKNWVSNRR---RKE 85
>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger
homeobox family protein, riken structural
genomics/proteomics initiative; NMR {Arabidopsis
thaliana} SCOP: a.4.1.1
Length = 80
Score = 30.4 bits (68), Expect = 0.055
Identities = 12/65 (18%), Positives = 26/65 (40%), Gaps = 4/65 (6%)
Query: 25 PKPRRNRTTFNSHQLNALEKVFERTHY----PDAFVREELAKKVCLSEARVQVWFQNRRA 80
+R+RT F + Q + + ER + D V + ++ + ++VW N +
Sbjct: 15 GIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKH 74
Query: 81 KFRRN 85
+
Sbjct: 75 SGPSS 79
>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 = 30.2 bits (68), Expect = 0.076
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 4/56 (7%)
Query: 51 YPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHRNLDAPTSEQPLPP 106
Y D E L K LS +++ W RR + + I+ L S +PL
Sbjct: 29 YLDTKGLENLMKNTSLSRIQIKNWVAARR---AKEKTITIA-PELADLLSGEPLAK 80
>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 = 28.0 bits (63), Expect = 0.24
Identities = 14/52 (26%), Positives = 19/52 (36%), Gaps = 12/52 (23%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F + N Y D E L K LS +++ W NRR R+
Sbjct: 17 FAKNIENP---------YLDTKGLENLMKNTSLSRIQIKNWVSNRR---RKE 56
>2fgc_A Acetolactate synthase, small subunit; regulatory subunit,
structural genomi protein structure initiative; 2.30A
{Thermotoga maritima} SCOP: d.58.18.6 d.58.18.6
Length = 193
Score = 28.8 bits (65), Expect = 0.50
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 4/40 (10%)
Query: 38 QLNALE---KVFERTHYPDAFVREELA-KKVCLSEARVQV 73
Q L KV P+ V E+A KV E + ++
Sbjct: 90 QAYKLVEVVKVTPIDPLPENRVEREMALIKVRFDEDKQEI 129
>2i71_A Hypothetical protein; structural genomics, APC6294, PSI-2, protein
structure initia midwest center for structural genomics,
MCSG; 1.70A {Sulfolobus solfataricus} SCOP: e.72.1.1
Length = 400
Score = 29.0 bits (64), Expect = 0.56
Identities = 8/57 (14%), Positives = 18/57 (31%), Gaps = 3/57 (5%)
Query: 38 QLNALEKVFERTHYPDAFVREELAK--KVCLSEARVQVWFQNRRAKFRRNERNFISH 92
L + + A + E+ K K + R + + ++R +H
Sbjct: 311 TLRHYAETYADKVT-RAIIENEVDKIEKYQMGSERKLLGEYMKVEGKGFDKRILYAH 366
>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 = 27.1 bits (60), Expect = 2.5
Identities = 15/39 (38%), Positives = 26/39 (66%)
Query: 43 EKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAK 81
E+VF R ++ +EE+AKK ++ +V+VWF N+R +
Sbjct: 381 EQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>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 = 25.0 bits (54), Expect = 2.5
Identities = 7/15 (46%), Positives = 14/15 (93%)
Query: 70 RVQVWFQNRRAKFRR 84
++++WFQNRR K+++
Sbjct: 2 QIKIWFQNRRMKWKK 16
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.7 bits (58), Expect = 2.6
Identities = 8/48 (16%), Positives = 19/48 (39%), Gaps = 10/48 (20%)
Query: 57 REELAKKVCLSEARVQVWFQNRRAKFRRNERN-------FISHRNLDA 97
+E +K ++ ++ W Q + + +N+ N F + D
Sbjct: 109 EQEWREK---AKKDLEEWNQRQSEQVEKNKINNRIADKAFYQQPDADI 153
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 64
Score = 25.4 bits (56), Expect = 2.6
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 9/52 (17%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRN 85
F SH N YP +EELAKK ++ ++V WF N+R ++++N
Sbjct: 22 FYSHLSNP---------YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 64
>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 = 25.5 bits (56), Expect = 3.0
Identities = 24/96 (25%), Positives = 37/96 (38%), Gaps = 21/96 (21%)
Query: 26 KPRRN---------RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQ 76
+ RRN F SH N YP +EELAKK ++ ++V WF
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNP---------YPSEEAKEELAKKCGITVSQVSNWFG 53
Query: 77 NRRAKFRRNERNFISHRNLDAPTSEQPLPPCTNATP 112
N+R R ++N + + + TN +
Sbjct: 54 NKR---IRYKKNIGKFQEEANIYAAKTAVTATNVSA 86
>3rfw_A Cell-binding factor 2; SURA-like, chaperone; 2.20A {Campylobacter
jejuni}
Length = 252
Score = 26.3 bits (58), Expect = 3.7
Identities = 6/35 (17%), Positives = 17/35 (48%)
Query: 58 EELAKKVCLSEARVQVWFQNRRAKFRRNERNFISH 92
E++ + + A+V+ ++ + K+ + R H
Sbjct: 83 EKILNTIKIDAAKVKAFYDQNKDKYVKPARVQAKH 117
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 25.5 bits (56), Expect = 3.7
Identities = 14/68 (20%), Positives = 20/68 (29%), Gaps = 18/68 (26%)
Query: 21 ERRKPKPRRN---------RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARV 71
R H+ NA YP + L+++ LS +V
Sbjct: 2 GHHHHHHSHMLPKESVQILRDWLYEHRYNA---------YPSEQEKALLSQQTHLSTLQV 52
Query: 72 QVWFQNRR 79
WF N R
Sbjct: 53 CNWFINAR 60
>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural
genomics, protein structure initiativ midwest center
for structural genomics; 2.15A {Escherichia coli}
Length = 120
Score = 25.7 bits (57), Expect = 4.5
Identities = 6/37 (16%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 35 NSHQLNALEKVFE--RTHYPDAFVREELAKKVCLSEA 69
N+ Q N +V + + +A ++ +S +
Sbjct: 2 NALQPNMRTRVCTVINNNIAHEWTLARIASELLMSPS 38
>1t6e_X Xylanase inhibitor; two beta-barrel domain structure, hydrolase
inhibitor; 1.70A {Triticum aestivum} SCOP: b.50.1.2 PDB:
1t6g_A 2b42_A 3hd8_A
Length = 381
Score = 25.9 bits (56), Expect = 5.2
Identities = 6/36 (16%), Positives = 10/36 (27%), Gaps = 2/36 (5%)
Query: 106 PCTN--ATPLSSAPPSSSHSFDFCAMPHSQCNSTCT 139
P SS ++++ P C S
Sbjct: 41 GGQPPAEIPCSSPTCLLANAYPAPGCPAPSCGSDKH 76
>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix,
ARAC family, activator, DNA-binding transcription,
transcription regulation; HET: PAM; 1.90A {Vibrio
cholerae}
Length = 276
Score = 25.7 bits (56), Expect = 6.8
Identities = 5/44 (11%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 28 RRNRTTFNSHQLNALEKVFE--RTHYPDAFVREELAKKVCLSEA 69
++ + F + L+A+EK+ ++ + ++ ++ +
Sbjct: 157 KKYNSIFITDDLDAMEKISCLVKSDITRNWRWADICGELRTNRM 200
>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 = 24.2 bits (53), Expect = 7.8
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 12/61 (19%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNERNFISHR 93
F SH N YP +EELAKK ++ ++V WF N+R R ++N +
Sbjct: 20 FYSHLSNP---------YPSEEAKEELAKKCGITVSQVSNWFGNKR---IRYKKNIGKFQ 67
Query: 94 N 94
Sbjct: 68 E 68
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 25.3 bits (55), Expect = 7.9
Identities = 10/70 (14%), Positives = 23/70 (32%)
Query: 28 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRRAKFRRNER 87
++ T L+ ++E+ +E +A K+ + ++ V F A N
Sbjct: 4 KKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAA 63
Query: 88 NFISHRNLDA 97
+
Sbjct: 64 LLAKILKVSV 73
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 23.8 bits (52), Expect = 9.5
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 9/46 (19%)
Query: 34 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVWFQNRR 79
H + YP +++LA+ L+ +V WF N R
Sbjct: 17 LFQHLTHP---------YPSEEQKKQLAQDTGLTILQVNNWFINAR 53
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 0.131 0.419
Gapped
Lambda K H
0.267 0.0571 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,199,879
Number of extensions: 114484
Number of successful extensions: 409
Number of sequences better than 10.0: 1
Number of HSP's gapped: 388
Number of HSP's successfully gapped: 102
Length of query: 143
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 59
Effective length of database: 4,356,429
Effective search space: 257029311
Effective search space used: 257029311
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: 52 (24.2 bits)