RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14049
(93 letters)
>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 = 87.0 bits (215), Expect = 1e-23
Identities = 49/73 (67%), Positives = 61/73 (83%)
Query: 12 QNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIR 71
Q +L EF+G EPSKKRKRRTSFTPQA+E LNA+FE+N P+G EIT +A +L Y+REV+R
Sbjct: 79 QQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVR 138
Query: 72 IWFCNKRQALKNT 84
+WF N+RQ LKNT
Sbjct: 139 VWFSNRRQTLKNT 151
>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 = 81.6 bits (201), Expect = 1e-21
Identities = 28/75 (37%), Positives = 40/75 (53%)
Query: 8 YKSGQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYER 67
L +KRKRRT+ + A + L HF ++ PS EI +A +L E+
Sbjct: 69 EAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEK 128
Query: 68 EVIRIWFCNKRQALK 82
EV+R+WFCN+RQ K
Sbjct: 129 EVVRVWFCNRRQREK 143
>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 = 79.6 bits (196), Expect = 9e-21
Identities = 28/81 (34%), Positives = 39/81 (48%)
Query: 2 STVCFRYKSGQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAH 61
+ S + L S++RK+RTS L F N P+ +IT +A
Sbjct: 77 NLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAE 136
Query: 62 QLGYEREVIRIWFCNKRQALK 82
QL E+EVIR+WF N+RQ K
Sbjct: 137 QLNMEKEVIRVWFSNRRQKEK 157
>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 = 77.8 bits (191), Expect = 5e-20
Identities = 22/62 (35%), Positives = 38/62 (61%)
Query: 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
++++RTS + L F ++ PS +IT +A+QLG E++V+R+WF N+RQ K
Sbjct: 93 VQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
Query: 83 NT 84
+
Sbjct: 153 RS 154
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 77.0 bits (189), Expect = 1e-19
Identities = 30/82 (36%), Positives = 39/82 (47%)
Query: 10 SGQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREV 69
S + +KRK+RTS L +HF + PS EIT LA L E+EV
Sbjct: 83 SSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEV 142
Query: 70 IRIWFCNKRQALKNTVRMMSKG 91
+R+WFCN+RQ K G
Sbjct: 143 VRVWFCNRRQKEKRMTPAAGAG 164
>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 = 66.8 bits (163), Expect = 1e-16
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHF-ERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
G S + RT + +AL +L + + +P I TL+ QL + I +F N+R
Sbjct: 1 GSSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQR 60
Query: 79 QALK 82
+K
Sbjct: 61 YHVK 64
>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 = 60.8 bits (148), Expect = 2e-14
Identities = 19/59 (32%), Positives = 30/59 (50%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
G S ++ RT T L +L +F+ N PS +I +A + G ++VI+ WF N
Sbjct: 1 GSSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTL 59
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 59.0 bits (143), Expect = 1e-13
Identities = 16/66 (24%), Positives = 25/66 (37%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
S + + + L L F RN P +E+ L G +R WF ++R +N
Sbjct: 6 SGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRN 65
Query: 84 TVRMMS 89
S
Sbjct: 66 LKGSRS 71
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor,
homeodomain, domain swapping, structural oxford protein
production facility, OPPF; 2.70A {Homo sapiens}
Length = 66
Score = 57.9 bits (140), Expect = 3e-13
Identities = 13/60 (21%), Positives = 22/60 (36%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
+ T + + L A F ++ P E+ L G R I+ WF + R +
Sbjct: 2 AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 75
Score = 57.2 bits (138), Expect = 9e-13
Identities = 15/64 (23%), Positives = 24/64 (37%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G S + P+ L L + F +N P E+ L + R I WF +R+
Sbjct: 1 GSSGSSGPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRK 60
Query: 80 ALKN 83
+
Sbjct: 61 KVNA 64
>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 = 56.3 bits (135), Expect = 3e-12
Identities = 21/61 (34%), Positives = 27/61 (44%)
Query: 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
S + TP+ L +L + F R PS E LA + G R I WF + R A K
Sbjct: 22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWK 81
Query: 83 N 83
N
Sbjct: 82 N 82
>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 = 53.8 bits (129), Expect = 2e-11
Identities = 13/73 (17%), Positives = 29/73 (39%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G P ++ T +++L F +++ P+ E+ L + R I WF +R+
Sbjct: 7 GAYPDFAPQKFKEKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRK 66
Query: 80 ALKNTVRMMSKGS 92
+ + +
Sbjct: 67 LRDSMEQAVLDSM 79
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain,
transcription factor, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: a.4.1.1
Length = 89
Score = 52.3 bits (125), Expect = 1e-10
Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 3/61 (4%)
Query: 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+K K +T + L +L A F ++ + E+ L Q R I WF K+++
Sbjct: 11 TPQKFKEKT---AEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKA 67
Query: 83 N 83
Sbjct: 68 L 68
>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 = 51.7 bits (124), Expect = 1e-10
Identities = 19/59 (32%), Positives = 39/59 (66%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
G EP + ++ RT+ TP+ LE+L + +++P+ + +AH++G ++ V+++WF N R
Sbjct: 11 GEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTR 69
>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 = 51.2 bits (123), Expect = 2e-10
Identities = 22/60 (36%), Positives = 28/60 (46%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G S R RT FT L +L F+ N +P E L++ L VI +WF N RQ
Sbjct: 1 GSSGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQ 60
>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 = 50.4 bits (120), Expect = 4e-10
Identities = 14/56 (25%), Positives = 21/56 (37%)
Query: 28 KRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
T + L +L + F + + L G R I WF + R ALK+
Sbjct: 5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH 60
>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 = 47.8 bits (114), Expect = 4e-09
Identities = 19/74 (25%), Positives = 35/74 (47%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G S ++ RTSF L + ++F N +P ++ LA + G + V+++WF N R
Sbjct: 1 GSSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARA 60
Query: 80 ALKNTVRMMSKGSL 93
+ + G +
Sbjct: 61 KFRRNLLRQENGGV 74
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 46.2 bits (109), Expect = 1e-08
Identities = 12/42 (28%), Positives = 22/42 (52%)
Query: 38 LELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
L LL A++ N PS E++ +A + +V++ WF +
Sbjct: 15 LSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQA 56
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 48.3 bits (114), Expect = 1e-08
Identities = 20/79 (25%), Positives = 32/79 (40%)
Query: 5 CFRYKSGQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLG 64
R + + E + +K R FT L+A F+ N PS T++ QLG
Sbjct: 76 ALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLG 135
Query: 65 YEREVIRIWFCNKRQALKN 83
E + +F N R+ +
Sbjct: 136 LELSTVSNFFMNARRRSLD 154
>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 = 45.0 bits (107), Expect = 4e-08
Identities = 20/64 (31%), Positives = 24/64 (37%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84
K + RT + L L + N P L G VIR+WF NKR K
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
Query: 85 VRMM 88
MM
Sbjct: 62 SIMM 65
>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 = 44.1 bits (105), Expect = 7e-08
Identities = 19/58 (32%), Positives = 28/58 (48%), Gaps = 2/58 (3%)
Query: 22 EPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLG-YEREVIRIWFCNKR 78
+ K K ++S +PQA L F R + E +A + G +V R+WF NKR
Sbjct: 1 KKEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQV-RVWFINKR 57
>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 = 45.0 bits (106), Expect = 8e-08
Identities = 14/85 (16%), Positives = 32/85 (37%), Gaps = 15/85 (17%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREV---------- 69
G S R R ++ + L ++ ++F N +P + +A+ +
Sbjct: 1 GSSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLER 60
Query: 70 -----IRIWFCNKRQALKNTVRMMS 89
+ WF N+R+ +K + +
Sbjct: 61 VTSLKVYNWFANRRKEIKRRANIAA 85
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 43.6 bits (103), Expect = 2e-07
Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 10 SGQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREV 69
S +N + + P KK+K RT F+ L +LN F+R + S ++ L++ L +
Sbjct: 6 SAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQ 65
Query: 70 IRIWFCNKRQALK 82
++ WF N+R K
Sbjct: 66 VKTWFQNQRMKSK 78
>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 = 43.6 bits (103), Expect = 2e-07
Identities = 18/73 (24%), Positives = 33/73 (45%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G S R+ RT+FT L++L A F + +P +A ++ +++WF N+R
Sbjct: 1 GSSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRA 60
Query: 80 ALKNTVRMMSKGS 92
+ + G
Sbjct: 61 KCRQQQQQQQNGG 73
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 43.2 bits (102), Expect = 2e-07
Identities = 21/63 (33%), Positives = 31/63 (49%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G S RK RT ++ L L F++ + + E LA LG + ++IWF NKR
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 80 ALK 82
+K
Sbjct: 61 KIK 63
>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 = 44.5 bits (104), Expect = 4e-07
Identities = 20/101 (19%), Positives = 34/101 (33%), Gaps = 23/101 (22%)
Query: 5 CFRYKSGQNHLTEFIGMEPSKKRKR--RTSFTPQALELLNAHFERNTHPSGTEITTLAHQ 62
F + + E G E K+ R R + P + ++L +ER +PS E TL +
Sbjct: 92 QFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEE 151
Query: 63 LGYEREV---------------------IRIWFCNKRQALK 82
+ + WF N+R+
Sbjct: 152 CNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEA 192
>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 = 42.4 bits (100), Expect = 5e-07
Identities = 21/60 (35%), Positives = 27/60 (45%)
Query: 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
P+KKRKRR FT L F + + S E LA + ++IWF N R K
Sbjct: 6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTK 65
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 42.0 bits (99), Expect = 7e-07
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 27 RKRRTSFTPQALELLNAHFER-NTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+ + T +E+L +F + N HP T + +A + G E + WF +
Sbjct: 3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRL 55
>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 = 41.3 bits (97), Expect = 1e-06
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 28 KRRTSFTPQALELLNAHFERNT-HPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
K + + L F T +P + L+ QL + I+ WF ++R
Sbjct: 10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRN 62
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 40.7 bits (96), Expect = 1e-06
Identities = 17/57 (29%), Positives = 26/57 (45%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+RK R F+ + L F++ + S E LA L ++IWF N+R K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 40.3 bits (95), Expect = 2e-06
Identities = 16/58 (27%), Positives = 28/58 (48%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
K+K RT F+ L L F++ + S ++ L+ L + ++ WF N+R K
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>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 = 40.5 bits (95), Expect = 2e-06
Identities = 19/59 (32%), Positives = 29/59 (49%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
G + K R+ RT FT L L FE+ + S + LA LG + ++ W+ N+R
Sbjct: 11 GTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRR 69
>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 = 40.4 bits (95), Expect = 3e-06
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
G S R+ RT FT + LE L F+ +P LA ++ E + +WF N+R
Sbjct: 1 GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRR 59
>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 = 42.0 bits (98), Expect = 6e-06
Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 13/86 (15%)
Query: 15 LTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYE-------- 66
+ +F+G S + Q L L FE + G +I LA +L E
Sbjct: 61 VGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFEN-CYLEGNDIHALAAKLLQENDTTLVKT 119
Query: 67 REVIRIWFCNKRQALKNTVRMMSKGS 92
+E+I+ + A R K S
Sbjct: 120 KELIKNYI----TARIMAKRPFDKKS 141
Score = 29.6 bits (66), Expect = 0.11
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 35 PQALELLNAHFERNTHPSGTE 55
PQ+L LN + PSG +
Sbjct: 383 PQSLYGLNLTLRKAKAPSGLD 403
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 41.5 bits (96), Expect = 6e-06
Identities = 14/83 (16%), Positives = 27/83 (32%), Gaps = 21/83 (25%)
Query: 21 MEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREV----------- 69
K R+ R + P + ++L ++R +PS E L + +
Sbjct: 137 PTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHG 196
Query: 70 ----------IRIWFCNKRQALK 82
+ WF N+R+
Sbjct: 197 LGSNLVTEVRVYNWFANRRKEEA 219
>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 = 39.4 bits (91), Expect = 6e-06
Identities = 10/55 (18%), Positives = 25/55 (45%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
S + + +L A++ N P+ E+ ++ +G +E ++ WF ++
Sbjct: 3 SGSSGSPINPYKDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRK 57
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 39.8 bits (93), Expect = 6e-06
Identities = 18/60 (30%), Positives = 28/60 (46%)
Query: 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
P K++K RTSFT + L F + + + E LA L ++ WF N+R +
Sbjct: 14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWR 73
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 38.8 bits (91), Expect = 9e-06
Identities = 17/52 (32%), Positives = 23/52 (44%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
RK RT FT L L F + + S E + L ++IWF N+R
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRR 52
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 38.9 bits (91), Expect = 1e-05
Identities = 20/59 (33%), Positives = 30/59 (50%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
G S ++ RTSFT + +E L FER +P LA ++ I++WF N+R
Sbjct: 1 GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRR 59
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 38.5 bits (90), Expect = 1e-05
Identities = 17/57 (29%), Positives = 27/57 (47%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+RKRR F+ + L F++ + S E LA + ++IWF N R +K
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 38.1 bits (89), Expect = 2e-05
Identities = 12/55 (21%), Positives = 19/55 (34%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+ + + L F + S E LA L ++IWF N+R
Sbjct: 2 GHHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRR 56
>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 = 37.4 bits (87), Expect = 3e-05
Identities = 15/63 (23%), Positives = 23/63 (36%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G S + + F+ L FE + S E LA L ++ WF N+R
Sbjct: 1 GSSGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRA 60
Query: 80 ALK 82
+
Sbjct: 61 KWR 63
>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 = 37.3 bits (87), Expect = 4e-05
Identities = 19/54 (35%), Positives = 30/54 (55%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+R++RT FT Q L+ L A F+RN +P + +A +R+WF N+R
Sbjct: 2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRR 55
>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 = 37.0 bits (86), Expect = 6e-05
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 22 EPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
K+R+ RT+F+ L+ L FER +P LA + I++WF N+R
Sbjct: 14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRR 70
>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 = 37.1 bits (86), Expect = 6e-05
Identities = 15/65 (23%), Positives = 25/65 (38%), Gaps = 3/65 (4%)
Query: 21 MEPSKKRKRRTSFTPQALELLNAHFERNTH---PSGTEITTLAHQLGYEREVIRIWFCNK 77
+ S K R FT + + +L + F +N + L R I+ W N+
Sbjct: 22 INKSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNR 81
Query: 78 RQALK 82
R+ K
Sbjct: 82 RRKEK 86
>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 = 35.8 bits (83), Expect = 2e-04
Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 27 RKRRTSFTPQALELLNAHFER-NTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+ + T +E+L +F + N HP T + +A + G E + WF +
Sbjct: 2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRL 54
>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 = 35.8 bits (83), Expect = 2e-04
Identities = 23/64 (35%), Positives = 34/64 (53%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86
R+ RT+FT +E+L F N +P + LA +L E + I+IWF N+R LK + R
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 87 MMSK 90
Sbjct: 62 ESQF 65
>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 = 35.3 bits (80), Expect = 3e-04
Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 4/63 (6%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGT----EITTLAHQLGYEREVIRIWFCNKRQ 79
S + RT F+ + L L +++ G+ +I +A +L + E++R W N+R+
Sbjct: 6 SGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRR 65
Query: 80 ALK 82
+
Sbjct: 66 KYR 68
>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 = 34.4 bits (79), Expect = 4e-04
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 4/54 (7%)
Query: 26 KRKRRTSFTPQALELLNAHFERNT-HPSGTEITTLAHQLGYEREVIRIWFCNKR 78
T Q +L F T HP + L+ QL ++ I+ WF +R
Sbjct: 3 SGSSGT---AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRR 53
>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 = 34.4 bits (79), Expect = 7e-04
Identities = 13/62 (20%), Positives = 21/62 (33%), Gaps = 3/62 (4%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTH---PSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
K R FT + + +L + F +N + L R I+ W +R K
Sbjct: 2 KPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEK 61
Query: 83 NT 84
Sbjct: 62 TI 63
>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 = 34.3 bits (79), Expect = 7e-04
Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 6/76 (7%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNA----HFERNTHPSGTEITTLAHQLGYEREVIRIWFC 75
G S +KR+ + +++++L H +PS E L+ + I WF
Sbjct: 1 GSSGSSGKKRKGNLPAESVKILRDWMYKHR-FKAYPSEEEKQMLSEKTNLSLLQISNWFI 59
Query: 76 NKRQ-ALKNTVRMMSK 90
N R+ L + ++
Sbjct: 60 NARRRILPDMLQQRRN 75
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 34.0 bits (77), Expect = 0.001
Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 21 MEPSKKRKR-RTSFTPQALELLNAHFERNTHPSGTEITTLAHQ 62
++P+KK +R R + P + ++L +ER +PS E TL +
Sbjct: 3 IDPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEE 45
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 64
Score = 33.1 bits (76), Expect = 0.001
Identities = 18/62 (29%), Positives = 23/62 (37%), Gaps = 3/62 (4%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTH---PSGTEITTLAHQLGYEREVIRIWFCNKRQA 80
S QA E+LN +F + PS LA + G + WF NKR
Sbjct: 1 SSGHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIR 60
Query: 81 LK 82
K
Sbjct: 61 YK 62
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 32.7 bits (75), Expect = 0.002
Identities = 14/52 (26%), Positives = 22/52 (42%)
Query: 31 TSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
TSF+ + L F R + + E LA L ++ WF N+R +
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>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 = 32.6 bits (74), Expect = 0.003
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 6/65 (9%)
Query: 23 PSKKRKRRTSFTPQALELLNAHFER-----NTHPSGTEITTLAHQLGYEREVIRIWFCNK 77
++ RT FT + E + A ER H + + G R+V++IW N
Sbjct: 14 GGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDV-AVEQFCAETGVRRQVLKIWMHNN 72
Query: 78 RQALK 82
+ +
Sbjct: 73 KNSGP 77
>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 = 32.3 bits (74), Expect = 0.003
Identities = 18/57 (31%), Positives = 30/57 (52%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+++ RT+F+ + L L F N + + L+ +LG I+IWF NKR +K
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>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 = 31.6 bits (72), Expect = 0.006
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 5/63 (7%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNA----HFERNTHPSGTEITTLAHQLGYEREVIRIWFC 75
G S + +R A ++ + H + +P+ E +A Q + WF
Sbjct: 1 GSSGSSGKNKRGVLPKHATNVMRSWLFQHI-GHPYPTEDEKKQIAAQTNLTLLQVNNWFI 59
Query: 76 NKR 78
N R
Sbjct: 60 NAR 62
>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 = 31.9 bits (72), Expect = 0.007
Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 6/67 (8%)
Query: 23 PSKKRKRRTSFTPQALELLNAHFER-----NTHPSGTEITTLAHQLGYEREVIRIWFCNK 77
+++ RT FT + E + A ER I + G R+V+++W N
Sbjct: 14 GGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDE-VIQRFCQETGVPRQVLKVWLHNN 72
Query: 78 RQALKNT 84
+ + ++
Sbjct: 73 KHSGPSS 79
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein,
DNA-binding, N gene regulation; 1.00A {Drosophila
melanogaster} PDB: 3lnq_A 3cmy_A
Length = 60
Score = 31.1 bits (71), Expect = 0.007
Identities = 16/49 (32%), Positives = 23/49 (46%)
Query: 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
+FT LE L F R +P LA ++G I++WF N+R
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRR 51
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 31.7 bits (72), Expect = 0.008
Identities = 10/58 (17%), Positives = 19/58 (32%), Gaps = 3/58 (5%)
Query: 24 SKKRKRRTSFTPQALELLNAHFERNTH---PSGTEITTLAHQLGYEREVIRIWFCNKR 78
+++++L + + PS E L+ Q + WF N R
Sbjct: 3 HHHHHHSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINAR 60
>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 = 30.9 bits (70), Expect = 0.011
Identities = 17/66 (25%), Positives = 30/66 (45%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86
R+ RT+FT + L HF + + + + L+ +L ++IWF N+R+ K
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62
Query: 87 MMSKGS 92
S
Sbjct: 63 QHKDQS 68
>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 = 30.0 bits (68), Expect = 0.020
Identities = 19/56 (33%), Positives = 26/56 (46%)
Query: 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
R+ RT+FT L L F + + S LA QL I++WF N+R K
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 57
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain,
hoogsteen base PAIR, transcription/DNA complex; HET:
5IU; 2.10A {Synthetic} SCOP: a.4.1.1
Length = 60
Score = 30.0 bits (68), Expect = 0.021
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 29 RRTSFTPQALELLNAHFERNTH---PSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83
R FT + + +L + F +N + L R I+ W N+R+ K
Sbjct: 1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58
>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 = 0.021
Identities = 21/68 (30%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 27 RKRRTSFTPQALELLNA----HFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
R++R +F QA E+LN H N +PS LA + G + WF NKR K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHL-SNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 83 NTVRMMSK 90
+ +
Sbjct: 61 KNIGKFQE 68
>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 = 30.0 bits (68), Expect = 0.026
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 27 RKRRTSFTPQALELLNAHFERNTH---PSGTEITTLAHQLGYEREVIRIWFCNKRQ-ALK 82
R++R +F QA E+LN +F + PS LA + G + WF NKR K
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
Query: 83 NTVRMMSKGSL 93
N + + ++
Sbjct: 62 NIGKFQEEANI 72
>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 = 29.8 bits (67), Expect = 0.030
Identities = 15/63 (23%), Positives = 24/63 (38%)
Query: 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
G S RK+R ++ L L + N + + ++ I IWF N+R
Sbjct: 1 GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRV 60
Query: 80 ALK 82
K
Sbjct: 61 KEK 63
>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 = 29.4 bits (66), Expect = 0.045
Identities = 16/70 (22%), Positives = 28/70 (40%)
Query: 21 MEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQA 80
+ RK+R +T L F N + + +A L ++IWF N+R
Sbjct: 8 LHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67
Query: 81 LKNTVRMMSK 90
+K + +K
Sbjct: 68 MKKINKDRAK 77
>2ylm_A Ubiquitin carboxyl-terminal hydrolase 7; UBL; 2.70A {Homo
sapiens}
Length = 530
Score = 29.2 bits (65), Expect = 0.13
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 56 ITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86
+ +L+ +G+ ++ IR+W R T R
Sbjct: 52 VQSLSQTMGFPQDQIRLWPMQARS--NGTKR 80
>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 = 27.9 bits (62), Expect = 0.22
Identities = 18/76 (23%), Positives = 27/76 (35%)
Query: 7 RYKSGQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYE 66
+ K + RT+FT + L L F N + S +A L
Sbjct: 15 KVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELN 74
Query: 67 REVIRIWFCNKRQALK 82
++IWF N+R K
Sbjct: 75 ETQVKIWFQNRRMKQK 90
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 27.3 bits (61), Expect = 0.26
Identities = 18/58 (31%), Positives = 25/58 (43%)
Query: 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
++ RT++T L L F N + S LA L I+IWF N+R K
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWK 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 = 27.5 bits (61), Expect = 0.29
Identities = 22/66 (33%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 19 IGMEPSKKRKRRTSFTPQALELLNA-HFERN-THPSGTEITTLAHQLGYEREVIRIWFCN 76
G ++R R+T Q LEL H T E+ AH L I+IWF N
Sbjct: 14 AGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEM---AHALSLTERQIKIWFQN 70
Query: 77 KRQALK 82
+R LK
Sbjct: 71 RRMKLK 76
>2kvr_A Ubiquitin carboxyl-terminal hydrolase 7; USP7, ubiquitin-like
domain, UBL, ubiquitin specific protease, HOST-virus
interaction, nucleus, protease; NMR {Homo sapiens}
Length = 130
Score = 27.9 bits (62), Expect = 0.29
Identities = 8/31 (25%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 56 ITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86
+ +L+ +G+ ++ IR+W R T R
Sbjct: 72 VQSLSQTMGFPQDQIRLWPMQARS--NGTKR 100
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 27.1 bits (60), Expect = 0.31
Identities = 13/71 (18%), Positives = 24/71 (33%), Gaps = 1/71 (1%)
Query: 22 EPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQAL 81
++KR Q EL + N + + ++ + IWF N+R
Sbjct: 4 MLEGRKKRVPYTKVQLKELER-EYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKE 62
Query: 82 KNTVRMMSKGS 92
K + + S
Sbjct: 63 KKVINKLKTTS 73
>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 = 28.2 bits (63), Expect = 0.33
Identities = 13/44 (29%), Positives = 18/44 (40%)
Query: 39 ELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
L F R + E +A + G +R+WF NKR K
Sbjct: 378 AFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 27.0 bits (60), Expect = 0.39
Identities = 15/57 (26%), Positives = 25/57 (43%)
Query: 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82
+++ R ++T L F N + + +AH L I+IWF N+R K
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 27.1 bits (60), Expect = 0.39
Identities = 23/63 (36%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 22 EPSKKRKRRTSFTPQALELLNA-HFERN-THPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79
KR+R + Q LEL HF R T EI AH L I+IWF N+R
Sbjct: 25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEI---AHALSLTERQIKIWFQNRRM 81
Query: 80 ALK 82
K
Sbjct: 82 KWK 84
>4e1o_A HDC, histidine decarboxylase; lyase; HET: PLP PVH; 1.80A {Homo
sapiens}
Length = 481
Score = 27.8 bits (62), Expect = 0.42
Identities = 9/19 (47%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 1 MSTVCFRYKSGQNHLTEFI 19
+ V FR K G N LTE +
Sbjct: 410 LGLVVFRLK-GPNSLTENV 427
>1js3_A DDC;, DOPA decarboxylase; carbidopa, parkinson'S disease, vitamin;
HET: PLP 142; 2.25A {Sus scrofa} SCOP: c.67.1.6 PDB:
1js6_A* 3rch_A* 3rbl_A 3rbf_A*
Length = 486
Score = 27.4 bits (61), Expect = 0.59
Identities = 8/17 (47%), Positives = 10/17 (58%), Gaps = 1/17 (5%)
Query: 1 MSTVCFRYKSGQNHLTE 17
+ VCFR K G + L E
Sbjct: 406 LGLVCFRLK-GSDGLNE 421
>3k40_A Aromatic-L-amino-acid decarboxylase; PLP dependent protein, alpha
beta protein, alternative splicing, catecholamine
biosynthesis, lyase; HET: LLP; 1.75A {Drosophila
melanogaster}
Length = 475
Score = 27.4 bits (61), Expect = 0.69
Identities = 9/17 (52%), Positives = 9/17 (52%), Gaps = 1/17 (5%)
Query: 1 MSTVCFRYKSGQNHLTE 17
M VCFR K G N E
Sbjct: 403 MGLVCFRLK-GSNERNE 418
>3a24_A Alpha-galactosidase; glycoside hydrolase family 97, retaining
glycosidase; HET: MES; 2.30A {Bacteroides
thetaiotaomicron}
Length = 641
Score = 26.5 bits (58), Expect = 1.6
Identities = 5/31 (16%), Positives = 9/31 (29%)
Query: 33 FTPQALELLNAHFERNTHPSGTEITTLAHQL 63
+T A+ + + T QL
Sbjct: 479 YTQGAMRNASKGNYYPCYSEPMSQGTRCRQL 509
>2qma_A Diaminobutyrate-pyruvate transaminase and L-2,4- diaminobutyrate
decarboxylase; structural genomics, APC91511.1,
glutamate decarboxylase; HET: MSE; 1.81A {Vibrio
parahaemolyticus}
Length = 497
Score = 26.1 bits (58), Expect = 1.6
Identities = 6/22 (27%), Positives = 11/22 (50%), Gaps = 3/22 (13%)
Query: 1 MSTVCFRYK---SGQNHLTEFI 19
+STV FR + + L + +
Sbjct: 424 LSTVLFRATHETADLDELNKAL 445
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 25.0 bits (55), Expect = 2.2
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 1/38 (2%)
Query: 41 LNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78
L H + +PS + LA G + WF N R
Sbjct: 17 LFQHL-THPYPSEEQKKQLAQDTGLTILQVNNWFINAR 53
>3nem_A Aspartyl-tRNA synthetase; rossmann fold, OB fold, ligase; HET: AMO
ATP; 1.89A {Thermococcus kodakarensis} PDB: 3nel_A*
3nen_A 1b8a_A*
Length = 438
Score = 25.2 bits (56), Expect = 3.6
Identities = 3/10 (30%), Positives = 5/10 (50%)
Query: 14 HLTEFIGMEP 23
HL E ++
Sbjct: 223 HLNEAWSIDS 232
>3i7f_A Aspartyl-tRNA synthetase; tRNA ligase, APO, ATP-binding,
aminoacyl-tRNA synthetase, LI nucleotide-binding,
protein biosynthesis; 2.80A {Entamoeba histolytica}
Length = 548
Score = 25.2 bits (55), Expect = 4.2
Identities = 6/10 (60%), Positives = 8/10 (80%)
Query: 14 HLTEFIGMEP 23
HLTEF G++
Sbjct: 330 HLTEFEGLDI 339
>1eov_A ASPRS, aspartyl-tRNA synthetase; aminoacyl tRNA synthetase, tRNA
ligase, APO-enzyme, OB-fold,; 2.30A {Saccharomyces
cerevisiae} SCOP: b.40.4.1 d.104.1.1 PDB: 1asy_A*
1asz_A*
Length = 487
Score = 25.0 bits (55), Expect = 4.3
Identities = 5/10 (50%), Positives = 8/10 (80%)
Query: 14 HLTEFIGMEP 23
H+TEF G++
Sbjct: 264 HMTEFTGLDM 273
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 24.8 bits (54), Expect = 4.7
Identities = 9/63 (14%), Positives = 18/63 (28%), Gaps = 3/63 (4%)
Query: 10 SGQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGY-ERE 68
+ N ++ + + + + LE L E PS + L + E
Sbjct: 1240 ASPNLNMKYRKRQLVTREAQIKDWVENELEALKLEAE-EI-PSEDQNEFLLERTREIHNE 1297
Query: 69 VIR 71
Sbjct: 1298 AES 1300
>1n9w_A Aspartyl-tRNA synthetase 2; biosynthetic protein; 2.30A {Thermus
thermophilus} SCOP: b.40.4.1 d.104.1.1 PDB: 3kfu_A*
Length = 422
Score = 24.8 bits (55), Expect = 5.4
Identities = 3/10 (30%), Positives = 7/10 (70%)
Query: 14 HLTEFIGMEP 23
HL E++ ++
Sbjct: 210 HLNEYLSLDV 219
>1wyd_A Hypothetical aspartyl-tRNA synthetase; archaea, LIGA; HET: EPE;
2.30A {Sulfolobus tokodaii}
Length = 429
Score = 24.8 bits (55), Expect = 5.5
Identities = 6/10 (60%), Positives = 7/10 (70%)
Query: 14 HLTEFIGMEP 23
HL EFI M+
Sbjct: 219 HLAEFISMDV 228
>2d73_A Alpha-glucosidase SUSB; glycoside hydrolase family 97, TIM barrel;
1.60A {Bacteroides thetaiotaomicron vpi-5482} PDB:
2zq0_A* 2jke_A* 2jka_A* 2jkp_A*
Length = 738
Score = 24.7 bits (53), Expect = 6.4
Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 2/32 (6%)
Query: 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLG 64
+TP E + N + +T+A QL
Sbjct: 559 YTPGIFE--THCNKMNPANNSQVRSTIARQLA 588
>2okj_A Glutamate decarboxylase 1; PLP-dependent decarboxylase, lyase; HET:
LLP PLZ; 2.30A {Homo sapiens} PDB: 2okk_A*
Length = 504
Score = 24.2 bits (53), Expect = 7.0
Identities = 12/76 (15%), Positives = 21/76 (27%), Gaps = 13/76 (17%)
Query: 1 MSTVCFRYKSGQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLA 60
+ VCF Y S + + + L + + SGT +
Sbjct: 418 HTNVCFWYIP------------QSLRGVPDSPQRREKLHKVAPKIKALMMESGTTMVGYQ 465
Query: 61 HQLGYEREVIRIWFCN 76
Q + R+ N
Sbjct: 466 PQGD-KANFFRMVISN 480
>2ib1_A Death domain containing membrane protein nradd; apoptosis, NOGO,
FADD; NMR {Mus musculus}
Length = 91
Score = 23.7 bits (51), Expect = 7.0
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 57 TTLAHQLGYEREVIRIWFCNKRQA 80
LA LGY+ E + C++ A
Sbjct: 22 QELAGHLGYQAEAVETMACDQMPA 45
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
0.321 0.131 0.391
Gapped
Lambda K H
0.267 0.0679 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,341,320
Number of extensions: 62976
Number of successful extensions: 273
Number of sequences better than 10.0: 1
Number of HSP's gapped: 244
Number of HSP's successfully gapped: 97
Length of query: 93
Length of database: 6,701,793
Length adjustment: 60
Effective length of query: 33
Effective length of database: 5,026,533
Effective search space: 165875589
Effective search space used: 165875589
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 (21.9 bits)
S2: 51 (23.5 bits)