RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4078
(269 letters)
>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 = 106 bits (267), Expect = 5e-30
Identities = 59/65 (90%), Positives = 61/65 (93%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
K TRVRTVLNEKQLHTLRTCY ANPRPDALMKEQLVEMT LSPRVIRVWFQNKRCKDKKR
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
Query: 141 ALAMK 145
++ MK
Sbjct: 62 SIMMK 66
Score = 65.8 bits (161), Expect = 1e-14
Identities = 39/47 (82%), Positives = 40/47 (85%)
Query: 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
K TRVRTVLNEKQLHTLRTCY ANPRPDALMKEQLVEMT L +R
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR 48
>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 = 94.5 bits (235), Expect = 3e-25
Identities = 19/66 (28%), Positives = 31/66 (46%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
+ R+RT + +QL L Y + P M + + L RV++VWFQN R
Sbjct: 11 GEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRA 70
Query: 136 KDKKRA 141
+++K
Sbjct: 71 RERKSG 76
Score = 62.5 bits (152), Expect = 4e-13
Identities = 15/61 (24%), Positives = 23/61 (37%)
Query: 13 SRTSSSGKVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRV 72
S SS G + R+RT + +QL L Y + P M + + L V
Sbjct: 2 SSGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVV 61
Query: 73 R 73
+
Sbjct: 62 Q 62
>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 = 92.4 bits (230), Expect = 1e-24
Identities = 16/63 (25%), Positives = 31/63 (49%)
Query: 78 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKD 137
R RT + + QL LR ++ N P +++ + + L +VI+ WF+N K+
Sbjct: 3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKE 62
Query: 138 KKR 140
++
Sbjct: 63 RQS 65
>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 = 73.9 bits (181), Expect = 1e-16
Identities = 16/64 (25%), Positives = 32/64 (50%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
G + + + RT ++ L + + +P + ++ E NL V+RVWF N+R
Sbjct: 81 VGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQ 140
Query: 136 KDKK 139
++K+
Sbjct: 141 REKR 144
>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 = 70.2 bits (172), Expect = 5e-16
Identities = 24/70 (34%), Positives = 37/70 (52%)
Query: 78 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKD 137
R+RT QL T+++ + N PDA +QL + T L+ RV++VWFQN R K
Sbjct: 3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKF 62
Query: 138 KKRALAMKQQ 147
++ L +
Sbjct: 63 RRNLLRQENG 72
Score = 41.3 bits (97), Expect = 2e-05
Identities = 14/50 (28%), Positives = 23/50 (46%)
Query: 24 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
R+RT QL T+++ + N PDA +QL + T L ++
Sbjct: 3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 52
>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 = 68.9 bits (169), Expect = 1e-15
Identities = 24/60 (40%), Positives = 30/60 (50%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
RT + QL L+ ++AN P EQL + NL RVI VWFQN R K +K
Sbjct: 6 SGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65
Score = 38.5 bits (90), Expect = 1e-04
Identities = 13/41 (31%), Positives = 18/41 (43%)
Query: 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNL 67
RT + QL L+ ++AN P EQL + NL
Sbjct: 6 SGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNL 46
>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 = 1e-15
Identities = 17/65 (26%), Positives = 29/65 (44%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
S G + + + +QL L+ + N P E L ++T LS R +R WF ++R
Sbjct: 2 SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRY 61
Query: 136 KDKKR 140
+
Sbjct: 62 HCRNL 66
Score = 38.9 bits (91), Expect = 1e-04
Identities = 14/53 (26%), Positives = 22/53 (41%)
Query: 22 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRK 74
S G + + + +QL L+ + N P E L ++T L VRK
Sbjct: 2 SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRK 54
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 70.4 bits (172), Expect = 4e-15
Identities = 18/64 (28%), Positives = 29/64 (45%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
G+ + RT + L + + P+P A L + L V+RVWF N+R
Sbjct: 93 IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQ 152
Query: 136 KDKK 139
K+K+
Sbjct: 153 KEKR 156
Score = 38.5 bits (89), Expect = 6e-04
Identities = 11/52 (21%), Positives = 18/52 (34%)
Query: 22 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
G+ + RT + L + + P+P A L + L VR
Sbjct: 93 IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVR 144
>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 = 69.2 bits (169), Expect = 9e-15
Identities = 17/61 (27%), Positives = 28/61 (45%)
Query: 79 DGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138
+ + RT + L + N +P + + E N+ VIRVWF N+R K+K
Sbjct: 98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
Query: 139 K 139
+
Sbjct: 158 R 158
Score = 39.2 bits (91), Expect = 3e-04
Identities = 11/73 (15%), Positives = 27/73 (36%)
Query: 1 SSESGSTKGGIVSRTSSSGKVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQ 60
+ + S+ + S ++ + G + + RT + L + N +P +
Sbjct: 74 AEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITL 133
Query: 61 LVEMTNLFLGRVR 73
+ E N+ +R
Sbjct: 134 IAEQLNMEKEVIR 146
>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 = 66.0 bits (161), Expect = 1e-14
Identities = 12/60 (20%), Positives = 27/60 (45%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
++Q+ L+ + + PD +L+E+T L+ I+ WF + R + ++
Sbjct: 2 AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61
Score = 39.4 bits (92), Expect = 6e-05
Identities = 9/49 (18%), Positives = 20/49 (40%)
Query: 26 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRK 74
++Q+ L+ + + PD +L+E+T L ++K
Sbjct: 2 AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKK 50
>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 = 66.0 bits (161), Expect = 2e-14
Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 1/66 (1%)
Query: 77 GGDGKPTRVRTVLNEKQLHTLRTCY-NANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
R RT ++ + L L++ + PD L +L I +FQN+R
Sbjct: 2 SSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY 61
Query: 136 KDKKRA 141
K
Sbjct: 62 HVKHSG 67
>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 = 65.1 bits (158), Expect = 2e-13
Identities = 23/103 (22%), Positives = 38/103 (36%)
Query: 37 EKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRVRTVLNEKQLHT 96
EK T ++ P + + E + + V G K + RT + +
Sbjct: 48 EKLDITPKSAQKLKPVLEKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEA 107
Query: 97 LRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
L + NP P ++ + N V+RVWF N+R K
Sbjct: 108 LNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150
>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 = 60.0 bits (146), Expect = 2e-12
Identities = 23/61 (37%), Positives = 33/61 (54%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
G R RT +QL L + N PD +E++ TNL+ +RVWF+N+R K +K
Sbjct: 1 GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 140 R 140
R
Sbjct: 61 R 61
Score = 39.6 bits (93), Expect = 5e-05
Identities = 17/48 (35%), Positives = 22/48 (45%)
Query: 26 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
G R RT +QL L + N PD +E++ TNL RVR
Sbjct: 1 GSQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVR 48
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 62.2 bits (150), Expect = 3e-12
Identities = 14/91 (15%), Positives = 28/91 (30%)
Query: 57 MKEQLVEMTNLFLGRVRKVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLV 116
+ + + P + R V + Q TL + N RP ++ +
Sbjct: 72 QRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITIS 131
Query: 117 EMTNLSPRVIRVWFQNKRCKDKKRALAMKQQ 147
+ L + +F N R + + L
Sbjct: 132 QQLGLELSTVSNFFMNARRRSLDKWLEHHHH 162
Score = 31.4 bits (70), Expect = 0.15
Identities = 12/47 (25%), Positives = 19/47 (40%)
Query: 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
P + R V + Q TL + N RP ++ + + L L V
Sbjct: 96 TPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVS 142
>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 = 62.1 bits (150), Expect = 3e-12
Identities = 17/56 (30%), Positives = 27/56 (48%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT + + +L T + +P+P + L V+RVWF N+R K K+
Sbjct: 98 RKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
Score = 33.9 bits (77), Expect = 0.023
Identities = 11/60 (18%), Positives = 18/60 (30%)
Query: 14 RTSSSGKVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
K R RT + + +L T + +P+P + L VR
Sbjct: 82 NLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVR 141
>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 = 59.5 bits (144), Expect = 4e-12
Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 1/64 (1%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
S G PT+ + +QL L + + NP P ++L T ++ R I WF +R
Sbjct: 2 SSGSSGPTKYKE-RAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRK 60
Query: 136 KDKK 139
K
Sbjct: 61 KVNA 64
Score = 33.3 bits (76), Expect = 0.009
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 22 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNL 67
S G PT+ + +QL L + + NP P ++L T +
Sbjct: 2 SSGSSGPTKYKE-RAPEQLRALESSFAQNPLPLDEELDRLRSETKM 46
>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 = 59.7 bits (145), Expect = 4e-12
Identities = 19/70 (27%), Positives = 31/70 (44%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
R RT QL L + PD M+E++ NL ++VWF+N+R K +++
Sbjct: 6 SGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQ 65
Query: 141 ALAMKQQLQQ 150
+ Q
Sbjct: 66 QQQQQNGGQS 75
Score = 36.2 bits (84), Expect = 0.001
Identities = 14/47 (29%), Positives = 19/47 (40%)
Query: 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
R RT QL L + PD M+E++ NL RV+
Sbjct: 6 SGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 52
>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 = 57.6 bits (140), Expect = 1e-11
Identities = 13/60 (21%), Positives = 29/60 (48%)
Query: 79 DGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138
K + ++ ++ + L + ++ KE++ + ++P +RVWF NKR + K
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 1e-11
Identities = 16/68 (23%), Positives = 25/68 (36%)
Query: 91 EKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQLQQ 150
+ Q+ L + + P ++L T LS R I WF +R A+ +
Sbjct: 22 QGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLDSMGS 81
Query: 151 EKDGRKMG 158
K G G
Sbjct: 82 GKSGPSSG 89
Score = 31.1 bits (70), Expect = 0.086
Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 1/52 (1%)
Query: 16 SSSGKVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNL 67
SS + D P + + Q+ L + + P ++L T L
Sbjct: 2 SSGSSGAYPDFAPQKFKEKTQG-QVKILEDSFLKSSFPTQAELDRLRVETKL 52
>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 = 57.7 bits (140), Expect = 2e-11
Identities = 19/65 (29%), Positives = 30/65 (46%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143
R RT + Q+ L + N P + E L + NL I++WFQN+R K K+
Sbjct: 3 RPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE 62
Query: 144 MKQQL 148
+ +
Sbjct: 63 SQFLM 67
>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 = 56.2 bits (135), Expect = 8e-11
Identities = 12/64 (18%), Positives = 21/64 (32%)
Query: 92 KQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQLQQE 151
+QL L+ + + +L T L+ R I WF K+ + M+
Sbjct: 21 EQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDESNA 80
Query: 152 KDGR 155
Sbjct: 81 GSSS 84
Score = 30.7 bits (69), Expect = 0.095
Identities = 6/30 (20%), Positives = 11/30 (36%)
Query: 38 KQLHTLRTCYNANPRPDALMKEQLVEMTNL 67
+QL L+ + + +L T L
Sbjct: 21 EQLRVLQASFLNSSVLTDEELNRLRAQTKL 50
>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 = 55.4 bits (133), Expect = 1e-10
Identities = 13/71 (18%), Positives = 24/71 (33%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
G ++QL L++ + ++L ++T L I WF + R K
Sbjct: 1 GSSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60
Query: 140 RALAMKQQLQQ 150
L +
Sbjct: 61 GQLKWFRDNAS 71
Score = 34.6 bits (79), Expect = 0.004
Identities = 7/42 (16%), Positives = 16/42 (38%)
Query: 26 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNL 67
G ++QL L++ + ++L ++T L
Sbjct: 1 GSSGSSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGL 42
>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 = 55.0 bits (133), Expect = 1e-10
Identities = 18/60 (30%), Positives = 29/60 (48%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
R RT+ ++QL L + PD +EQL +L + VWF+N+R K ++
Sbjct: 6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65
Score = 35.0 bits (81), Expect = 0.002
Identities = 13/47 (27%), Positives = 20/47 (42%)
Query: 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
R RT+ ++QL L + PD +EQL +L +V
Sbjct: 6 SGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE 52
>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 = 54.7 bits (132), Expect = 3e-10
Identities = 22/60 (36%), Positives = 33/60 (55%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
K R RT + QL L + PD +E+L + TNL+ I+VWFQN+R + +K+
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76
Score = 34.7 bits (80), Expect = 0.003
Identities = 15/47 (31%), Positives = 22/47 (46%)
Query: 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
K R RT + QL L + PD +E+L + TNL R++
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 63
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 54.0 bits (130), Expect = 4e-10
Identities = 10/59 (16%), Positives = 22/59 (37%), Gaps = 1/59 (1%)
Query: 83 TRVRTVLNEKQLHTLRTCYN-ANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
+ + E Q+ L +N N PD + L+ + WF+ + + ++
Sbjct: 3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61
Score = 30.1 bits (68), Expect = 0.14
Identities = 9/47 (19%), Positives = 16/47 (34%), Gaps = 1/47 (2%)
Query: 29 TRVRTVLNEKQLHTLRTCYN-ANPRPDALMKEQLVEMTNLFLGRVRK 74
+ + E Q+ L +N N PD + L + +K
Sbjct: 3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQK 49
>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 = 54.4 bits (130), Expect = 5e-10
Identities = 15/70 (21%), Positives = 25/70 (35%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
T +QLH L++ + P ++L + + L+ I WF + R K
Sbjct: 24 GSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNG 83
Query: 141 ALAMKQQLQQ 150
L Q
Sbjct: 84 NLKWYYYYQS 93
Score = 34.8 bits (79), Expect = 0.005
Identities = 9/55 (16%), Positives = 18/55 (32%)
Query: 13 SRTSSSGKVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNL 67
S + T +QLH L++ + P ++L + + L
Sbjct: 10 SGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGL 64
>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 = 52.6 bits (127), Expect = 9e-10
Identities = 17/55 (30%), Positives = 26/55 (47%)
Query: 86 RTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
QL L ++ PD +E+L L+ I+VWFQN+R K +K+
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
Score = 32.2 bits (74), Expect = 0.018
Identities = 9/42 (21%), Positives = 15/42 (35%)
Query: 32 RTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
QL L ++ PD +E+L L R++
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 53.2 bits (128), Expect = 9e-10
Identities = 19/71 (26%), Positives = 31/71 (43%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
R RT ++Q+ L + PD +E+L +L I+VWF N+R K ++
Sbjct: 6 SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65
Query: 141 ALAMKQQLQQE 151
Q+ Q
Sbjct: 66 EKLRNQRRQSG 76
Score = 33.1 bits (76), Expect = 0.011
Identities = 11/47 (23%), Positives = 20/47 (42%)
Query: 27 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
R RT ++Q+ L + PD +E+L +L R++
Sbjct: 6 SGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 52
>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 = 50.8 bits (121), Expect = 9e-09
Identities = 14/79 (17%), Positives = 28/79 (35%), Gaps = 15/79 (18%)
Query: 77 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTN---------------L 121
R ++ L + + +N N PD +E++ N +
Sbjct: 2 SSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERV 61
Query: 122 SPRVIRVWFQNKRCKDKKR 140
+ + WF N+R + K+R
Sbjct: 62 TSLKVYNWFANRRKEIKRR 80
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 49.3 bits (117), Expect = 2e-08
Identities = 11/49 (22%), Positives = 21/49 (42%)
Query: 91 EKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+ L L+ Y N +P A ++ + NL V++ WF+ +
Sbjct: 12 KNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQIS 60
>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 = 47.4 bits (113), Expect = 1e-07
Identities = 9/59 (15%), Positives = 22/59 (37%), Gaps = 1/59 (1%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPR-PDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
+ + E Q+ L +N + PD + L+ + WF+ + + ++
Sbjct: 2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60
Score = 28.9 bits (65), Expect = 0.33
Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 1/47 (2%)
Query: 29 TRVRTVLNEKQLHTLRTCYNANPR-PDALMKEQLVEMTNLFLGRVRK 74
+ + E Q+ L +N + PD + L + +K
Sbjct: 2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQK 48
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein, transcription
regulation, NUC homeobox; 2.6A {Mus musculus}
Length = 62
Score = 43.8 bits (104), Expect = 1e-06
Identities = 18/61 (29%), Positives = 32/61 (52%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
G ++RTV ++ QL L+ + ++L + NLS + ++ WFQN+R K K+
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
Query: 140 R 140
Sbjct: 61 W 61
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A
{Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 44.8 bits (105), Expect = 1e-06
Identities = 16/82 (19%), Positives = 23/82 (28%), Gaps = 21/82 (25%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTN-------------------- 120
K R R L Y P +E LVE N
Sbjct: 8 KGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSN 67
Query: 121 -LSPRVIRVWFQNKRCKDKKRA 141
++ + WF N+R ++ R
Sbjct: 68 LVTEVRVYNWFANRRKEEAFRH 89
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 43.9 bits (104), Expect = 2e-06
Identities = 20/69 (28%), Positives = 30/69 (43%), Gaps = 10/69 (14%)
Query: 77 GGDGKPTRVRTVLNEKQLHTL-----RTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQ 131
+ RT+ + QL L +T Y A P + +L L+ +++WFQ
Sbjct: 2 SSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPE-----RAELAASLGLTQTQVKIWFQ 56
Query: 132 NKRCKDKKR 140
NKR K KK
Sbjct: 57 NKRSKIKKS 65
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative; NMR {Homo sapiens}
Length = 69
Score = 43.5 bits (103), Expect = 2e-06
Identities = 14/64 (21%), Positives = 30/64 (46%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
G + ++ Q+ L ++ A + L + L+ +++WFQN+R K K+
Sbjct: 2 GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
Query: 140 RALA 143
+ L+
Sbjct: 62 KQLS 65
>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 = 46.0 bits (108), Expect = 2e-06
Identities = 16/81 (19%), Positives = 23/81 (28%), Gaps = 21/81 (25%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTN-------------------- 120
K R R L Y P +E LVE N
Sbjct: 114 KGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSN 173
Query: 121 -LSPRVIRVWFQNKRCKDKKR 140
++ + WF N+R ++ R
Sbjct: 174 LVTEVRVYNWFANRRKEEAFR 194
>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 = 43.2 bits (101), Expect = 3e-06
Identities = 9/64 (14%), Positives = 21/64 (32%), Gaps = 1/64 (1%)
Query: 77 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCK 136
G G + + L+ Y N P++ ++ L ++ WF+ ++
Sbjct: 1 GSSGSSGSPINPYKD-HMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY 59
Query: 137 DKKR 140
Sbjct: 60 QYSN 63
Score = 26.3 bits (57), Expect = 3.2
Identities = 8/52 (15%), Positives = 17/52 (32%), Gaps = 1/52 (1%)
Query: 23 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRK 74
G G + + L+ Y N P++ ++ L V++
Sbjct: 1 GSSGSSGSPINPYKD-HMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKE 51
>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 = 41.6 bits (98), Expect = 9e-06
Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 7/58 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
TR + EK+ + Y + PR + +L NL I+VWFQN+R KDK++
Sbjct: 9 TRDQLGRLEKEFYKEN--YVSRPR-----RCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>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 = 41.3 bits (97), Expect = 1e-05
Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 6/69 (8%)
Query: 82 PTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMT---NLSPRVIRVWFQNKRCKDK 138
P R RT Q+ L + L +L +++ L +++WF+N+R + K
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRY---LTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
Query: 139 KRALAMKQQ 147
++ K Q
Sbjct: 59 IQSDQHKDQ 67
>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 = 41.3 bits (97), Expect = 1e-05
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 6/79 (7%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
G K + R + + Q + L + A +E L + L+P +++WFQN R
Sbjct: 3 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRY 62
Query: 136 KDKKRALAMKQQLQQEKDG 154
K K + Q ++ +G
Sbjct: 63 KTK------RAQNEKGYEG 75
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 44.2 bits (103), Expect = 1e-05
Identities = 16/88 (18%), Positives = 25/88 (28%), Gaps = 21/88 (23%)
Query: 74 KVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTN------------- 120
+ K R R L Y+ P +E LVE N
Sbjct: 134 CSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSK 193
Query: 121 --------LSPRVIRVWFQNKRCKDKKR 140
++ + WF N+R ++ R
Sbjct: 194 AHGLGSNLVTEVRVYNWFANRRKEEAFR 221
>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 = 41.3 bits (97), Expect = 2e-05
Identities = 22/69 (31%), Positives = 29/69 (42%), Gaps = 10/69 (14%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTL-----RTCYNANPRPDALMKEQLVEMTNLSPRVIRVWF 130
K R RTV E QL L + Y + P + L E LS ++ W+
Sbjct: 11 GTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPD-----RIDLAESLGLSQLQVKTWY 65
Query: 131 QNKRCKDKK 139
QN+R K KK
Sbjct: 66 QNRRMKWKK 74
>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 = 40.9 bits (96), Expect = 2e-05
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 92 KQLHTLRTCY-NANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+ TL + + PD + L + + S R I+ WF+++R +DK
Sbjct: 18 EPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKP 66
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 40.4 bits (95), Expect = 2e-05
Identities = 18/64 (28%), Positives = 33/64 (51%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALA 143
+ R + ++ Q++ L + A +E L M +L+P +++WFQN R K K++A
Sbjct: 4 KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKD 63
Query: 144 MKQQ 147
Q
Sbjct: 64 KAAQ 67
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 39.9 bits (94), Expect = 3e-05
Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 84 RVRTVLNEKQLHTL-----RTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138
+ RT QL L + Y + + + +L+ +++WFQN+R K K
Sbjct: 2 KPRTPFTTAQLLALERKFRQKQYLSIAE-----RAEFSSSLSLTETQVKIWFQNRRAKAK 56
Query: 139 K 139
+
Sbjct: 57 R 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 = 40.6 bits (95), Expect = 3e-05
Identities = 19/67 (28%), Positives = 31/67 (46%)
Query: 73 RKVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQN 132
+K K + RTV + QL L + ++L + NLS + ++ WFQN
Sbjct: 13 KKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQN 72
Query: 133 KRCKDKK 139
+R K K+
Sbjct: 73 QRMKSKR 79
>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 = 40.0 bits (94), Expect = 3e-05
Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 10/61 (16%)
Query: 84 RVRTVLNEKQLHTLRTCYNAN-----PRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138
R RT + +QL L+ +N N R ++QL L+ I++WF+NKR K K
Sbjct: 5 RPRTAFSSEQLARLKREFNENRYLTERR-----RQQLSSELGLNEAQIKIWFKNKRAKIK 59
Query: 139 K 139
K
Sbjct: 60 K 60
>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 = 39.8 bits (93), Expect = 4e-05
Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 7/57 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
++ + E++ + + + + ++ T+LS R I +WFQN+R K+KK
Sbjct: 15 SKGQLRELEREYAANK--FITKDK-----RRKISAATSLSERQITIWFQNRRVKEKK 64
>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 = 43.7 bits (102), Expect = 4e-05
Identities = 38/230 (16%), Positives = 72/230 (31%), Gaps = 60/230 (26%)
Query: 23 GGDGKPTRVRTVLNEKQLH----------TLRTCYNANPRPDALMKEQLVEMTNLFLGRV 72
G GK V ++ L+ C P+ ++ EM L ++
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCN----SPETVL-----EMLQKLLYQI 209
Query: 73 RK--VSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNL-SPRVIRVW 129
S D + ++ ++ Q LR + P + L LV + N+ + +
Sbjct: 210 DPNWTSRSDH-SSNIKLRIHSIQAE-LRRLLKSKPYENCL----LV-LLNVQNAKAWNA- 261
Query: 130 FQNKRCK------DKKRALAMKQQLQQEKDGRKMGYG----------------SMQGIP- 166
F N CK K+ + Q +P
Sbjct: 262 F-NLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR 320
Query: 167 -MVASSPVRHDSPIGMNALEVTSYQPPWKALSDFALHT----DLDRLDPS 211
++ ++P R S I + + + WK ++ L T L+ L+P+
Sbjct: 321 EVLTTNP-RRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPA 369
Score = 37.1 bits (85), Expect = 0.005
Identities = 18/90 (20%), Positives = 26/90 (28%), Gaps = 14/90 (15%)
Query: 73 RKVSGGDGKPTRVRTVLNEKQLHTLRTC-YNANPRPDAL---M----KEQLVEMTNLSPR 124
R D + V + LR P + L + K + LS +
Sbjct: 116 RDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYK 175
Query: 125 VIRV------WFQNKRCKDKKRALAMKQQL 148
V W K C + L M Q+L
Sbjct: 176 VQCKMDFKIFWLNLKNCNSPETVLEMLQKL 205
Score = 37.1 bits (85), Expect = 0.005
Identities = 20/149 (13%), Positives = 40/149 (26%), Gaps = 46/149 (30%)
Query: 24 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFL-GRVRKVSGGDGKP 82
D + V + LR AL+ +L N+ + G G GK
Sbjct: 121 NDNQVFAKYNVSRLQPYLKLRQ---------ALL--ELRPAKNVLIDGV-----LGSGKT 164
Query: 83 TRVRTVLNEKQLH----------TLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQN 132
V ++ L+ C P+ +++ + L ++ W
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCN----SPETVLE----MLQKLLYQIDPNWTSR 216
Query: 133 KR-----------CKDKKRALAMKQQLQQ 150
+ + R L + +
Sbjct: 217 SDHSSNIKLRIHSIQAELRRLLKSKPYEN 245
>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 = 39.3 bits (92), Expect = 6e-05
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 7/58 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
+ +T+ EK+ T + Y + P +++L +M LS R ++ WFQN+R K ++
Sbjct: 15 SNDQTIELEKKFETQK--YLSPPE-----RKRLAKMLQLSERQVKTWFQNRRAKWRRS 65
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA
complex, transcription/DNA complex; 2.42A {Mesocricetus
auratus}
Length = 63
Score = 39.3 bits (92), Expect = 6e-05
Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
TR + + EK+ + Y + PR + +L M NL+ R I++WFQN+R K KK
Sbjct: 11 TRAQLLELEKEFLFNK--YISRPR-----RVELAVMLNLTERHIKIWFQNRRMKWKK 60
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB:
2ld5_A*
Length = 73
Score = 38.7 bits (90), Expect = 1e-04
Identities = 17/57 (29%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
T+V+ E++ T + + + + ++ TNLS R + +WFQN+R K+KK
Sbjct: 15 TKVQLKELEREYATNK--FITKDK-----RRRISATTNLSERQVTIWFQNRRVKEKK 64
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 39.5 bits (92), Expect = 1e-04
Identities = 13/75 (17%), Positives = 31/75 (41%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
+ K + RT Q+ L ++ + + L ++ ++ WFQN+R
Sbjct: 11 NRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRT 70
Query: 136 KDKKRALAMKQQLQQ 150
K +++ ++ +Q
Sbjct: 71 KWRRQTAEEREAERQ 85
>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 = 38.6 bits (90), Expect = 1e-04
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
TR +T+ EK+ H R Y R + ++ +L+ R I++WFQN+R K KK
Sbjct: 10 TRYQTLELEKEFHFNR--YLTRRR-----RIEIAHALSLTERQIKIWFQNRRMKWKK 59
>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 = 38.6 bits (90), Expect = 1e-04
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 6/69 (8%)
Query: 74 KVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMT---NLSPRVIRVWF 130
++G +G R R Q L ++ N L + + +EM +L+ R I++WF
Sbjct: 12 AIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHY---LTRRRRIEMAHALSLTERQIKIWF 68
Query: 131 QNKRCKDKK 139
QN+R K KK
Sbjct: 69 QNRRMKLKK 77
>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 = 38.4 bits (88), Expect = 2e-04
Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 4/68 (5%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCY----NANPRPDALMKEQLVEMTNLSPRVIRVWFQ 131
S G + RT +++ L TL+ + + E + N+ ++R W
Sbjct: 2 SSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIG 61
Query: 132 NKRCKDKK 139
N+R K +
Sbjct: 62 NRRRKYRL 69
>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 = 41.6 bits (97), Expect = 2e-04
Identities = 43/244 (17%), Positives = 75/244 (30%), Gaps = 90/244 (36%)
Query: 21 VSGGDGKPT---RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVRKVSG 77
+ +G P+ + L ++Q+ + V TN L
Sbjct: 328 LENNEGVPSPMLSISN-LTQEQV------------------QDYVNKTNSHL-------- 360
Query: 78 GDGKPTRVRTVLNEKQLH-TLRTCYNANPRPDALMKEQLVEMTNLS--PRVIRVWFQNKR 134
P KQ+ +L N + LV +S P+ + R
Sbjct: 361 ----PA-------GKQVEISL---VNG-AK-------NLV----VSGPPQSLYGLNLTLR 394
Query: 135 CKDKKRALAMKQQLQQEKDGRKMGYGSMQGIPMVASSPVRHDSPIGMNALE-----VTSY 189
K +A + Q + RK+ S + +P+ +SP H S + + A + +
Sbjct: 395 ---KAKAPSGLDQSRIPFSERKL-KFSNRFLPV--ASPF-H-SHLLVPASDLINKDLVKN 446
Query: 190 QPPWKALSDFAL---HT----DLDRLDPSAAPFQHLVSQM-----HGYELGHGPPPPH-- 235
+ A D + T DL L S + +V + +E H
Sbjct: 447 NVSFNA-KDIQIPVYDTFDGSDLRVLSGSISER--IVDCIIRLPVK-WETTTQFKATHIL 502
Query: 236 DMGP 239
D GP
Sbjct: 503 DFGP 506
Score = 33.1 bits (75), Expect = 0.092
Identities = 30/201 (14%), Positives = 51/201 (25%), Gaps = 74/201 (36%)
Query: 32 RTVLNEKQLHTL-------------------RTCYNA---------NPRPDALMKEQLVE 63
L +H L + A AL +
Sbjct: 93 NCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG 152
Query: 64 MTNLFLGRVRKVSGGDGKPTRVRTVLNEKQLHTLRTCYNA-NPRPDALMK---EQLVEMT 119
L + GG G E LR Y + L+K E L E+
Sbjct: 153 NAQLVA-----IFGGQGNT---DDYFEE-----LRDLYQTYHVLVGDLIKFSAETLSELI 199
Query: 120 NLSPRVIRVWFQNKRCKDKKRALAMKQQLQQEKDGRKMGYGSMQGIPMVASSPVRHDS-P 178
+ +V+ + L + + L+ + Y + S P+ S P
Sbjct: 200 RTTLDAEKVF---------TQGLNILEWLENPSNTPDKDY--------LLSIPI---SCP 239
Query: 179 -IG-------MNALEVTSYQP 191
IG + ++ + P
Sbjct: 240 LIGVIQLAHYVVTAKLLGFTP 260
Score = 33.1 bits (75), Expect = 0.095
Identities = 31/202 (15%), Positives = 59/202 (29%), Gaps = 63/202 (31%)
Query: 31 VRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLG----RVRK-------VSGGD 79
+ V N H + Y + ++ V +T F G R+R+ + D
Sbjct: 1642 AQDVWNRADNH-FKDTYGFSIL--DIVINNPVNLTIHFGGEKGKRIRENYSAMIFETIVD 1698
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKE----Q----LVEMTNLSPRVIRVWFQ 131
GK + + E H+ + + L+ Q L+E ++
Sbjct: 1699 GK-LKTEKIFKEINEHSTSYTFRS---EKGLLSATQFTQPALTLMEKAAF--EDLKSKGL 1752
Query: 132 NKRCK-----------------------D-----KKRALAMKQQLQQEKDGRKMGYGSMQ 163
R + M+ + +++ GR YG
Sbjct: 1753 IPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSN-YG--- 1808
Query: 164 GIPMVASSPVRHDSPIGMNALE 185
M+A +P R + AL+
Sbjct: 1809 ---MIAINPGRVAASFSQEALQ 1827
>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 = 37.9 bits (88), Expect = 2e-04
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 7/57 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
T+ +T+ EK+ Y R + ++ + NL+ R +++WFQN+R K KK
Sbjct: 21 TKHQTLELEKEFLFNM--YLTRDR-----RYEVARLLNLTERQVKIWFQNRRMKMKK 70
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 37.9 bits (88), Expect = 3e-04
Identities = 20/58 (34%), Positives = 31/58 (53%), Gaps = 7/58 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
TR +T+ EK+ H R Y R + ++ +L+ R I++WFQN+R K KK
Sbjct: 36 TRYQTLELEKEFHFNR--YLTRRR-----RIEIAHALSLTERQIKIWFQNRRMKWKKE 86
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 37.2 bits (87), Expect = 3e-04
Identities = 14/55 (25%), Positives = 29/55 (52%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138
+ R + ++ Q++ L + A ++QL + L+ +++WFQN+R K K
Sbjct: 4 KPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 37.9 bits (88), Expect = 4e-04
Identities = 22/68 (32%), Positives = 35/68 (51%), Gaps = 6/68 (8%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMT---NLSPRVIRVWFQN 132
G G P+ +RT +QL L ++ N L + + VE+ L+ +++WFQN
Sbjct: 28 EPGLGSPSGLRTNFTTRQLTELEKEFHFNKY---LSRARRVEIAATLELNETQVKIWFQN 84
Query: 133 KRCKDKKR 140
+R K KKR
Sbjct: 85 RRMKQKKR 92
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 36.5 bits (85), Expect = 5e-04
Identities = 10/54 (18%), Positives = 24/54 (44%)
Query: 87 TVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
T + Q+ L + + + L + ++ ++ WFQN+R K +++
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 36.3 bits (84), Expect = 0.001
Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 3/65 (4%)
Query: 82 PTRVRTVLNEKQLHTLRTCYNA---NPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138
++ + L + + NP D E L++ T+LS I+ W +R K+K
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEK 61
Query: 139 KRALA 143
+A
Sbjct: 62 TITIA 66
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 37.8 bits (87), Expect = 0.001
Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 16/55 (29%)
Query: 106 RPDALMKEQLVEMTNLSPRVIRVWF--QNKRC--KD---KKRALAMKQQLQQEKD 153
+ D L +E P IR W Q KR D K +++ +++ +
Sbjct: 76 QADRLTQE---------PESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLE 121
>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 = 36.0 bits (83), Expect = 0.002
Identities = 15/64 (23%), Positives = 26/64 (40%), Gaps = 3/64 (4%)
Query: 78 GDGKPTRVRTVLNEKQLHTLRTCYNA---NPRPDALMKEQLVEMTNLSPRVIRVWFQNKR 134
++ + L + + NP D E L++ T+LS I+ W N+R
Sbjct: 23 NKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRR 82
Query: 135 CKDK 138
K+K
Sbjct: 83 RKEK 86
>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 = 35.2 bits (81), Expect = 0.002
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 102 NANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
PD E L + + R I+ WF+ +R ++K
Sbjct: 21 AITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP 58
>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 = 34.6 bits (80), Expect = 0.002
Identities = 14/37 (37%), Positives = 20/37 (54%)
Query: 104 NPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
NP D E L++ T+LS I+ W N+R K+K
Sbjct: 23 NPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59
>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 = 33.2 bits (76), Expect = 0.015
Identities = 23/85 (27%), Positives = 31/85 (36%), Gaps = 8/85 (9%)
Query: 78 GDGKPTRVRTVLNEKQLHTLRTCYNA---NPRPDALMKEQLVEMTNLSPRVIRVWFQNKR 134
+ + L + + LR P K+ L E TNLS I WF N R
Sbjct: 3 SGSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINAR 62
Query: 135 CKDKKRAL-AMKQQLQQEKDGRKMG 158
+R L M QQ + + G G
Sbjct: 63 ----RRILPDMLQQRRNDPSGPSSG 83
>2fi2_A Zinc finger protein 42; SCAN domain, ZNF-42, MZF-1, homodimer,
transcription factor, structural genomics, PSI, protein
structure initiative; NMR {Homo sapiens} SCOP: a.28.3.2
Length = 94
Score = 32.9 bits (75), Expect = 0.019
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 106 RPDALMKEQLVEMTNLS------PRVIRVWFQNKRCKDKKRALAMKQQLQQEKDG 154
RP+ KEQ++E+ L P I+ Q +R + A A+ L++E G
Sbjct: 40 RPEVRSKEQMLELLVLEQFLGALPPEIQARVQGQRPGSPEEAAALVDGLRREPGG 94
>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein
ISL-1; protein-protein complex, LIM domain, Zn finger,
activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A
Length = 169
Score = 33.7 bits (77), Expect = 0.034
Identities = 19/30 (63%), Positives = 22/30 (73%)
Query: 164 GIPMVASSPVRHDSPIGMNALEVTSYQPPW 193
G PMVA+SP RHD + N +EV SYQPPW
Sbjct: 140 GTPMVAASPERHDGGLQANPVEVQSYQPPW 169
>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 = 31.6 bits (72), Expect = 0.044
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 84 RVRTVLNEKQLHTLRTCYNA---NPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
R R N++ L + + NP P KE+L + ++ + WF NKR + KK
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 62
Query: 141 ALAMKQQ 147
+++
Sbjct: 63 IGKFQEE 69
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 30.4 bits (69), Expect = 0.099
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 104 NPRPDALMKEQLVEMTNLSPRVIRVWFQNKR 134
+P P K+QL + T L+ + WF N R
Sbjct: 23 HPYPSEEQKKQLAQDTGLTILQVNNWFINAR 53
>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding
protein 1; B-tandem zipper, protein binding; 1.30A {Mus
musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB:
2dfy_X 2xjz_I 2xjy_B
Length = 188
Score = 32.3 bits (73), Expect = 0.10
Identities = 15/77 (19%), Positives = 27/77 (35%), Gaps = 11/77 (14%)
Query: 30 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQL----------VEMTNLFLGRVRKVSGGD 79
R R V ++ + + + + RP AL+ L + +G + G
Sbjct: 104 RNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSGGSGGSGGSGGDVMVVGEPTLMGGEF 163
Query: 80 G-KPTRVRTVLNEKQLH 95
G + R+ T L Q
Sbjct: 164 GDEDERLITRLENTQFD 180
Score = 30.4 bits (68), Expect = 0.42
Identities = 10/42 (23%), Positives = 13/42 (30%), Gaps = 1/42 (2%)
Query: 1 SSESGSTKGGIVSRTSSSGKVSGGDG-KPTRVRTVLNEKQLH 41
S GG V + G G + R+ T L Q
Sbjct: 139 GSGGSGGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFD 180
>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 = 30.5 bits (69), Expect = 0.12
Identities = 17/73 (23%), Positives = 30/73 (41%), Gaps = 3/73 (4%)
Query: 84 RVRTVLNEKQLHTLRTCYNA---NPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
R R N++ L + + NP P KE+L + ++ + WF NKR + KK
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 62
Query: 141 ALAMKQQLQQEKD 153
+++
Sbjct: 63 IGKFQEEANIYAA 75
>3iz5_C 60S ribosomal protein L3 (L3P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_C
Length = 389
Score = 31.4 bits (71), Expect = 0.12
Identities = 8/108 (7%), Positives = 16/108 (14%), Gaps = 25/108 (23%)
Query: 57 MKEQLVEMTN-LFLGRVRKVSGGDGKPT----------RVRTVLNEKQLHTLRTCYNANP 105
K + + +LH TC
Sbjct: 19 RKRCSRHRGKVKSFPKDDQQKPCHLTAFLGYKAGMTHIVREVEKPGSKLHKKETCE---- 74
Query: 106 RPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQLQQEKD 153
++E L + + Q +
Sbjct: 75 ------AVTIIETPPLVIVGLV----AYVKTPRGLRTLNSVWAQHLSE 112
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus
musculus} SCOP: a.4.1.1
Length = 64
Score = 30.0 bits (68), Expect = 0.13
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 104 NPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
NP P KE+L + ++ + WF NKR + KK
Sbjct: 28 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>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 = 29.7 bits (67), Expect = 0.20
Identities = 15/60 (25%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 78 GDGKPTRVRTVLNEKQLHTLRTCYNA---NPRPDALMKEQLVEMTNLSPRVIRVWFQNKR 134
R VL + + +R+ +P P K+Q+ TNL+ + WF N R
Sbjct: 3 SGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINAR 62
>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 = 28.8 bits (64), Expect = 0.20
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 124 RVIRVWFQNKRCKDKKRAL 142
R I++WFQN+R K KKR
Sbjct: 1 RQIKIWFQNRRMKWKKRVF 19
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 29.8 bits (67), Expect = 0.22
Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 6/64 (9%)
Query: 104 NPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQLQQEKDGRKMGYGSMQ 163
N P K L + T+LS + WF N R +R L L+++ S +
Sbjct: 30 NAYPSEQEKALLSQQTHLSTLQVCNWFINAR----RRLL--PDMLRKDGKDPNQFTISRR 83
Query: 164 GIPM 167
G +
Sbjct: 84 GAKI 87
>3jyw_X 60S ribosomal protein L35; eukaryotic ribosome, RACK1 protein,
flexible fitting; 8.90A {Thermomyces lanuginosus}
Length = 86
Score = 29.9 bits (67), Expect = 0.23
Identities = 10/55 (18%), Positives = 21/55 (38%), Gaps = 15/55 (27%)
Query: 57 MKEQLVEMTNLFLGRVRKVSGGDGKPTRVR----------TVLNEKQLHTLRTCY 101
+ + E+ L +V+K+S +++ TV+NE+Q
Sbjct: 20 LVDLKKELAEL---KVQKLSRP--SLPKIKTVRKSIACVLTVINEQQAAAAAAAA 69
>3lhr_A Zinc finger protein 24; SCAN domain, protein structure initiative,
center for eukary structural genomics, PSI-2, CESG,
nucleus, phosphoprotein; 1.90A {Homo sapiens}
Length = 93
Score = 29.4 bits (66), Expect = 0.38
Identities = 13/54 (24%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 106 RPDALMKEQLVEMTNLS------PRVIRVWFQNKRCKDKKRALAMKQQLQQEKD 153
RP+ KEQ++E+ L P+ ++ W ++ ++ + A+ + + L+ E D
Sbjct: 39 RPETHTKEQILELVVLEQFVAILPKELQTWVRDHHPENGEEAVTVLEDLESELD 92
>4a17_U RPL35, 60S ribosomal protein L21; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_U 4a1c_U 4a1e_U
Length = 124
Score = 29.1 bits (65), Expect = 0.75
Identities = 20/109 (18%), Positives = 42/109 (38%), Gaps = 26/109 (23%)
Query: 57 MKEQLVEM-TNLFLGRVRKVSGG-DGKPTRVR----------TVLNEKQLHTLRTCYNAN 104
+ +L ++ T L R+ K++GG K R+ T++NEK+ ++ +
Sbjct: 18 LVGELGKLQTELSQLRIAKIAGGTANKLGRIGIVRKAIAKYLTIINEKRRQAVKDQF--- 74
Query: 105 PRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQLQQEKD 153
K + ++ ++ + R R K K+ Q+K
Sbjct: 75 -------KGKSLKPLDIRVKKTR----AIRRKLTKKQREAVLVKTQKKL 112
>3u5e_H L8, RP24, YL11, 60S ribosomal protein L9-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3izc_F
1s1i_H 3izs_F* 3j16_F 3o5h_I 3o58_I 3u5i_H 3jyw_H
Length = 191
Score = 28.4 bits (63), Expect = 1.2
Identities = 5/106 (4%), Positives = 17/106 (16%), Gaps = 23/106 (21%)
Query: 57 MKEQLVEMTN-LFLGRVRKVSGGDGKP--------TRVRTVLNEKQLHTLRTCYNANPRP 107
+ + + V N + H
Sbjct: 17 TVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNGGRKHVAALRT------ 70
Query: 108 DALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQLQQEKD 153
+ LV+ + + + + ++
Sbjct: 71 ----VKSLVDNMITGVTKGY----KYKMRYVYAHFPINVNIVEKDG 108
>2b9s_A Topoisomerase I-like protein; vanadate complex, isomerase/DNA
complex; HET: DNA; 2.27A {Leishmania donovani}
Length = 432
Score = 29.6 bits (66), Expect = 1.3
Identities = 9/55 (16%), Positives = 21/55 (38%), Gaps = 3/55 (5%)
Query: 109 ALMKEQLVEMTNLSP---RVIRVWFQNKRCKDKKRALAMKQQLQQEKDGRKMGYG 160
++ ++ + L I W +R K R K+ +++++D Y
Sbjct: 87 EILDKRQHPIRRLELCDFEPIYQWHLVQREKKLSRTKEEKKAIKEKQDAEAEPYR 141
>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 = 29.4 bits (66), Expect = 1.5
Identities = 13/56 (23%), Positives = 26/56 (46%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138
T ++ + L + ++ KE++ + ++P +RVWF NKR + K
Sbjct: 366 TAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>2zkr_v 60S ribosomal protein L35; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 123
Score = 28.0 bits (62), Expect = 1.6
Identities = 28/109 (25%), Positives = 43/109 (39%), Gaps = 26/109 (23%)
Query: 57 MKEQLVEM-TNLFLGRVRKVSGGDGKPT-----------RVRTVLNEKQLHTLRTCYNAN 104
+ +QL ++ L RV KV+GG RV TV+N+ Q LR Y
Sbjct: 17 LLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVINQTQKENLRKFY--- 73
Query: 105 PRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRALAMKQQLQQEKD 153
K + + +L P+ R R + K +K + QQ K+
Sbjct: 74 -------KGKKYKPLDLRPKKTR----AMRRRLNKHEENLKTKKQQRKE 111
>2l3k_A Rhombotin-2, linker, LIM domain-binding protein 1;
LMO2(LIM2)-LDB1(LID), chimera, fusion protein,
oncoprotein; NMR {Mus musculus} PDB: 2l6y_B 2l6z_C
Length = 123
Score = 28.1 bits (62), Expect = 1.6
Identities = 8/41 (19%), Positives = 14/41 (34%)
Query: 1 SSESGSTKGGIVSRTSSSGKVSGGDGKPTRVRTVLNEKQLH 41
S SG + G ++ + + R+ T L Q
Sbjct: 75 SGGSGGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFD 115
Score = 26.2 bits (57), Expect = 6.0
Identities = 7/27 (25%), Positives = 10/27 (37%), Gaps = 1/27 (3%)
Query: 70 GRVRKVSGGDG-KPTRVRTVLNEKQLH 95
G + G G + R+ T L Q
Sbjct: 89 GEPTLMGGEFGDEDERLITRLENTQFD 115
>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 = 26.9 bits (59), Expect = 1.9
Identities = 7/29 (24%), Positives = 16/29 (55%)
Query: 106 RPDALMKEQLVEMTNLSPRVIRVWFQNKR 134
R D + ++ + T + +V++VW N +
Sbjct: 45 RQDDEVIQRFCQETGVPRQVLKVWLHNNK 73
>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 = 27.5 bits (60), Expect = 2.1
Identities = 17/86 (19%), Positives = 25/86 (29%), Gaps = 21/86 (24%)
Query: 77 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTN---------------- 120
G G R R L Y+ P +E LVE N
Sbjct: 1 GSSGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHG 60
Query: 121 -----LSPRVIRVWFQNKRCKDKKRA 141
++ + WF N+R ++ R
Sbjct: 61 LGSNLVTEVRVYNWFANRRKEEAFRQ 86
>2hz7_A Glutaminyl-tRNA synthetase; rossmann fold, GLNRS core, class I
aminoacyl-tRNA synthetase, ligase; 2.30A {Deinococcus
radiodurans}
Length = 851
Score = 27.5 bits (61), Expect = 6.3
Identities = 9/44 (20%), Positives = 16/44 (36%)
Query: 49 ANPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRVRTVLNEK 92
ANP + + F G+V + + G P + L +
Sbjct: 806 ANPDKAEAYRGGKTALLGFFTGQVMRATAGKADPQALAAALKDA 849
>1ois_A DNA topoisomerase I; DNA-binding protein; HET: DNA; 1.90A
{Saccharomyces cerevisiae} SCOP: e.15.1.1
Length = 223
Score = 26.8 bits (59), Expect = 7.7
Identities = 7/35 (20%), Positives = 19/35 (54%)
Query: 126 IRVWFQNKRCKDKKRALAMKQQLQQEKDGRKMGYG 160
+ +FQ ++ + K+ K+Q++ E++ + Y
Sbjct: 97 MFDYFQLQKEQKKQLTSQEKKQIRLEREKFEEDYK 131
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
0.313 0.131 0.390
Gapped
Lambda K H
0.267 0.0583 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,117,815
Number of extensions: 242223
Number of successful extensions: 580
Number of sequences better than 10.0: 1
Number of HSP's gapped: 565
Number of HSP's successfully gapped: 142
Length of query: 269
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 177
Effective length of database: 4,133,061
Effective search space: 731551797
Effective search space used: 731551797
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (25.7 bits)