RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9565
(288 letters)
>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 = 98.2 bits (245), Expect = 1e-26
Identities = 25/51 (49%), Positives = 33/51 (64%)
Query: 87 KSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
S + RR RT FT EQL LE LF ET YPD RE+L++++ L E +V+
Sbjct: 2 SSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE 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 = 97.8 bits (244), Expect = 3e-26
Identities = 30/54 (55%), Positives = 37/54 (68%)
Query: 84 SSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
KQRRSRT F+ QL+ELER F+ T YPD + REEL+QR L+EAR+Q
Sbjct: 10 PGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 63
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 97.1 bits (242), Expect = 5e-26
Identities = 25/50 (50%), Positives = 36/50 (72%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
S + +R+RT+FT EQ+ LE+ F+ THYPD F RE L+ ++ L EAR+Q
Sbjct: 3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 52
>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 = 96.6 bits (241), Expect = 5e-26
Identities = 23/47 (48%), Positives = 30/47 (63%)
Query: 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
QRR RT+FT +QL +LE F YPD REE++ L+EARV+
Sbjct: 2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVR 48
>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 = 95.9 bits (239), Expect = 1e-25
Identities = 27/50 (54%), Positives = 35/50 (70%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
S + RR RT FT QL+ LE LF +T YPD FMREE++ ++ L E+RVQ
Sbjct: 3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 52
>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 = 92.9 bits (231), Expect = 2e-24
Identities = 17/50 (34%), Positives = 29/50 (58%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
S + +R RT+F QL ++ F H PDA ++L+Q+ GL++ +Q
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 = 92.4 bits (230), Expect = 3e-24
Identities = 19/50 (38%), Positives = 23/50 (46%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
S + R SRT FT QL L+ FD YP E+LS L L +
Sbjct: 3 SGSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIV 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 = 91.2 bits (227), Expect = 6e-24
Identities = 19/45 (42%), Positives = 26/45 (57%)
Query: 93 RRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
RR RT FT Q+ LE +F YP + E+L+Q+L L R+Q
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQ 46
>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 = 88.2 bits (219), Expect = 8e-23
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
K R RT +QL+ L + PDA M+E+L + GLS ++
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR 48
>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 = 87.7 bits (218), Expect = 1e-22
Identities = 25/43 (58%), Positives = 31/43 (72%)
Query: 95 SRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
S FT QL ELE+ F THYPD F REEL+ ++GL+EAR+Q
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44
>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 = 85.2 bits (211), Expect = 2e-21
Identities = 15/57 (26%), Positives = 26/57 (45%)
Query: 81 SPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
S + + + +R RT T EQL L + + P M + ++ +GL + VQ
Sbjct: 6 SGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQ 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 = 77.8 bits (192), Expect = 6e-19
Identities = 14/50 (28%), Positives = 26/50 (52%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
S + +R RT T +QL L + FD + P +E++ + GL + ++
Sbjct: 3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52
>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 = 72.8 bits (179), Expect = 5e-17
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 93 RRSRTNFTLEQLNELERLFDETH-YPDAFMREELSQRLGLSEARVQ 137
T +Q+ LE F++ + +PD ++ GL+E + Q
Sbjct: 2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ 47
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 71.3 bits (175), Expect = 2e-16
Identities = 11/46 (23%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 93 RRSRTNFTLEQLNELERLFDETH-YPDAFMREELSQRLGLSEARVQ 137
++ + T +Q+ LE F++ + +PD ++ GL+E + Q
Sbjct: 3 AQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ 48
>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 = 70.1 bits (171), Expect = 1e-15
Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 15/66 (22%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREEL---------------SQRLGLS 132
S + R SR + E L +E F+E YPD REE+ S ++
Sbjct: 3 SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVT 62
Query: 133 EARVQN 138
+V N
Sbjct: 63 SLKVYN 68
>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 = 13/50 (26%), Positives = 22/50 (44%)
Query: 89 SNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQN 138
S+ + + EQL+ L+ F +P E L++ GLS V+
Sbjct: 5 SSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRK 54
>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 = 68.5 bits (167), Expect = 2e-14
Identities = 16/115 (13%), Positives = 42/115 (36%), Gaps = 2/115 (1%)
Query: 25 ECDDSNRLPSSESSRHLYFTDSNSD-LKVNNENECDDSNRLPSSESSRHHISRHLSLSPI 83
+ + ++E + S + L + ++ L + ++ + +
Sbjct: 24 QTQVGQAMTATEGPAYSQSAISRFEKLDITPKSAQKLKPVLEKWLNEAELRNQEGQQNLM 83
Query: 84 S-SCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137
+K+R+ RT+FT + + L F++ P E+++ L V+
Sbjct: 84 EFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVR 138
>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 = 64.4 bits (157), Expect = 7e-14
Identities = 12/51 (23%), Positives = 22/51 (43%), Gaps = 1/51 (1%)
Query: 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQN-FS 140
T EQ+ L+ F ++ +PD L + GL+ + ++ FS
Sbjct: 3 HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFS 53
>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 = 64.1 bits (156), Expect = 9e-14
Identities = 18/56 (32%), Positives = 25/56 (44%), Gaps = 1/56 (1%)
Query: 87 KSSNKQRRSRTNFTLEQLNELERLFDET-HYPDAFMREELSQRLGLSEARVQNFSQ 141
S + RSRT +LE L L+ + YPD LS +L L + + F Q
Sbjct: 2 SSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQ 57
>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary,
CPHD, POU domain, transcription factor,
transcription/DNA complex; HET: DNA; 2.30A {Rattus
norvegicus} SCOP: a.4.1.1 a.35.1.1
Length = 146
Score = 65.4 bits (159), Expect = 2e-13
Identities = 14/75 (18%), Positives = 32/75 (42%)
Query: 63 RLPSSESSRHHISRHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMR 122
+L + S + + ++ ++R+ RT ++ + LER F E P +
Sbjct: 58 KLKAILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEI 117
Query: 123 EELSQRLGLSEARVQ 137
+++ L L + V+
Sbjct: 118 MRMAEELNLEKEVVR 132
>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 = 62.6 bits (151), Expect = 5e-12
Identities = 24/131 (18%), Positives = 41/131 (31%)
Query: 23 ENECDDSNRLPSSESSRHLYFTDSNSDLKVNNENECDDSNRLPSSESSRHHISRHLSLSP 82
+ E D+ L S S+HL K + ++ H L P
Sbjct: 46 QREVVDTTGLNQSHLSQHLNKGTPMKTQKRAALYTWYVRKQREVAQQFTHAGQGGLIEEP 105
Query: 83 ISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQV 142
+ K RR+R + L + ++ P RE L + +E + S
Sbjct: 106 TGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPS 165
Query: 143 LNLLIDVSTVT 153
+ + VT
Sbjct: 166 QAQGLGSNLVT 176
>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 = 9/53 (16%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 90 NKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
K + +++ + + LE +F ++ +EE++++ G++ +V N
Sbjct: 3 EKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFIN 55
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 60.4 bits (146), Expect = 2e-11
Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 6/74 (8%)
Query: 64 LPSSESSRHHISRHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMRE 123
L ++SS + ++ ++R+ RT+ + LE F + P A
Sbjct: 77 LEETDSSSGSPTNLDKIAA------QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEIT 130
Query: 124 ELSQRLGLSEARVQ 137
L+ L L + V+
Sbjct: 131 GLADSLQLEKEVVR 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 = 58.8 bits (142), Expect = 6e-11
Identities = 11/71 (15%), Positives = 28/71 (39%)
Query: 67 SESSRHHISRHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELS 126
+ S S + +++R+ RT+ LE+ F E P + ++
Sbjct: 76 ANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIA 135
Query: 127 QRLGLSEARVQ 137
++L + + ++
Sbjct: 136 EQLNMEKEVIR 146
>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 = 58.6 bits (141), Expect = 6e-11
Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 1/83 (1%)
Query: 56 NECDDSNRLPSSESSRHHISRHLSLSPISSCKSSN-KQRRSRTNFTLEQLNELERLFDET 114
+ + S P E + +L IS ++ ++R RT+ LE +F ++
Sbjct: 59 SLKNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKS 118
Query: 115 HYPDAFMREELSQRLGLSEARVQ 137
P ++ +LGL + V+
Sbjct: 119 PKPSLQQITHIANQLGLEKDVVR 141
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 60.0 bits (144), Expect = 7e-11
Identities = 17/110 (15%), Positives = 31/110 (28%)
Query: 44 TDSNSDLKVNNENECDDSNRLPSSESSRHHISRHLSLSPISSCKSSNKQRRSRTNFTLEQ 103
+ N ++ L S ++ K RR+R +
Sbjct: 94 FNQTVQSSGNMTDKSSQDQLLFLFPEFSQQSHGPGQSDDACSEPTNKKMRRNRFKWGPAS 153
Query: 104 LNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVSTVT 153
L + +D P RE L + +E + S + + VT
Sbjct: 154 QQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVT 203
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 54.5 bits (132), Expect = 2e-10
Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 92 QRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
+R+ R F+ Q+ ELER F + Y A R++L+ L L+ +V QN
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQN 52
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 57.2 bits (137), Expect = 3e-10
Identities = 18/80 (22%), Positives = 28/80 (35%)
Query: 62 NRLPSSESSRHHISRHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFM 121
S ++ N ++ R FT Q L +F E P +
Sbjct: 67 QEPEFQRMSALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKEL 126
Query: 122 REELSQRLGLSEARVQNFSQ 141
+ +SQ+LGL + V NF
Sbjct: 127 QITISQQLGLELSTVSNFFM 146
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein, transcription
regulation, NUC homeobox; 2.6A {Mus musculus}
Length = 62
Score = 53.8 bits (130), Expect = 4e-10
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
+++ RT F+ QL L+ F + Y +ELS L LS +V QN
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQN 53
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 53.8 bits (130), Expect = 4e-10
Identities = 21/50 (42%), Positives = 25/50 (50%), Gaps = 4/50 (8%)
Query: 93 RRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
R+ RT FT QL LER F + Y R E S L L+E +V QN
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQN 50
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A
{Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 54.8 bits (131), Expect = 4e-10
Identities = 13/65 (20%), Positives = 24/65 (36%)
Query: 89 SNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLID 148
+ K RR+R + L + ++ P RE L + +E + S +
Sbjct: 6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLG 65
Query: 149 VSTVT 153
+ VT
Sbjct: 66 SNLVT 70
>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 = 54.0 bits (130), Expect = 4e-10
Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 84 SSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
+S NK+R+ R FT Q ELER F + Y A RE L+ + L+ +V QN
Sbjct: 1 ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQN 59
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 53.6 bits (129), Expect = 6e-10
Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
S + R+ RT ++ QL L+R F +T Y R EL+ LGL++ +V QN
Sbjct: 3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQN 57
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 52.7 bits (127), Expect = 1e-09
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 92 QRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
+R+ R F+ Q+ ELER F + Y A RE L+ + L+ +V QN
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQN 52
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative; NMR {Homo sapiens}
Length = 69
Score = 52.4 bits (126), Expect = 2e-09
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
++ + Q+ ELER F Y A R L++ L L+E +V QN
Sbjct: 3 HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQN 54
>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 = 52.5 bits (126), Expect = 2e-09
Identities = 24/62 (38%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 81 SPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV---- 136
S + K RRSRT FT QL LE+ F++ Y R +L++ LGLS+ +V
Sbjct: 6 SGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWY 65
Query: 137 QN 138
QN
Sbjct: 66 QN 67
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for eukaryotic
structural genomics; NMR {Homo sapiens}
Length = 84
Score = 51.7 bits (124), Expect = 4e-09
Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 4/62 (6%)
Query: 81 SPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV---- 136
K K++++RT F+ QL L F Y +ELS L LS +V
Sbjct: 11 VAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWF 70
Query: 137 QN 138
QN
Sbjct: 71 QN 72
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 49.9 bits (119), Expect = 2e-08
Identities = 18/56 (32%), Positives = 34/56 (60%), Gaps = 4/56 (7%)
Query: 87 KSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
++ K+++ RT+FT Q+ ELE+ F + Y + R L++ L +++A+V QN
Sbjct: 12 RTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQN 67
>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 = 48.5 bits (116), Expect = 3e-08
Identities = 21/51 (41%), Positives = 32/51 (62%), Gaps = 4/51 (7%)
Query: 92 QRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
++R RT F+ EQL L+R F+E Y R++LS LGL+EA++ +N
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKN 53
>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 = 48.6 bits (116), Expect = 3e-08
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
S + + + F+ +Q ELE+ F+ Y R+ L++ L LSE +V QN
Sbjct: 3 SGSSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQN 57
>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 = 48.4 bits (115), Expect = 5e-08
Identities = 9/51 (17%), Positives = 16/51 (31%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQN 138
S + EQL LE F + P + L ++ + +
Sbjct: 3 SGSSGPTKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDS 53
>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 = 46.9 bits (111), Expect = 2e-07
Identities = 9/39 (23%), Positives = 16/39 (41%)
Query: 100 TLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQN 138
T Q+ LE F ++ +P + L LS + +
Sbjct: 21 TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDS 59
>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 = 46.5 bits (110), Expect = 3e-07
Identities = 9/48 (18%), Positives = 15/48 (31%), Gaps = 2/48 (4%)
Query: 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQN 138
Q+ T EQL L+ F + L + L+ +
Sbjct: 12 PQKFKEK--TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDA 57
>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 = 46.4 bits (110), Expect = 5e-07
Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 4/70 (5%)
Query: 73 HISRHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLS 132
+ R+ + S RTNFT QL ELE+ F Y R E++ L L+
Sbjct: 15 KVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELN 74
Query: 133 EARV----QN 138
E +V QN
Sbjct: 75 ETQVKIWFQN 84
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 45.0 bits (107), Expect = 5e-07
Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 97 TNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
T+F+ Q+ ELER F Y + R L++ L +++A+V QN
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQN 47
>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 = 45.0 bits (107), Expect = 5e-07
Identities = 20/50 (40%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 93 RRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
RR RT FT +QL LE+ F + +Y R EL+ +L L E+ + QN
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQN 51
>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 = 45.6 bits (107), Expect = 7e-07
Identities = 13/70 (18%), Positives = 25/70 (35%)
Query: 69 SSRHHISRHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQR 128
+ HH + T EQL+ L+ F T +P ++L++
Sbjct: 2 AHHHHHHSSGLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKE 61
Query: 129 LGLSEARVQN 138
GL+ + +
Sbjct: 62 SGLARTDIVS 71
>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 = 44.7 bits (106), Expect = 7e-07
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 92 QRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
RR+RT FT Q+ ELE+ F + Y A +LS +L L A+V +N
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKN 52
>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 = 48.1 bits (114), Expect = 2e-06
Identities = 49/284 (17%), Positives = 86/284 (30%), Gaps = 90/284 (31%)
Query: 27 DDSNRLPSSES---SRHLYFTDSNSD----------LKVN-NENECD--DSN-------R 63
DD P++ + + L + S + L + E E + N +
Sbjct: 51 DDE---PTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAK 107
Query: 64 LPSSESS----RHHI------SRHLSLSPISSCKSSNKQRRSRTN-------F-----TL 101
L + + +R ++ P +S R F T
Sbjct: 108 LLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTD 167
Query: 102 EQLNELERLFDETHYPD------AFMREELSQRLGLSEARVQNFSQVLNL---LIDVSTV 152
+ EL L+ Y F E LS+ + + + F+Q LN+ L + S
Sbjct: 168 DYFEELRDLYQ--TYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNT 225
Query: 153 TINNTLNPAGIILSNHQPVSTPL-EPCRVAPYVNVPRLPTLPFSASTAAAFSAFDPTLLS 211
P L P+S PL ++A YV +L F P L
Sbjct: 226 -------PDKDYLL-SIPISCPLIGVIQLAHYVVTAKL-------------LGFTPGELR 264
Query: 212 AAHQYAA--AAATVAALGNAPNGSIFSAASQYPSFSLATLAALH 253
+ + A + V A+ + + SF ++ A+
Sbjct: 265 SYLKGATGHSQGLVTAV-------AIAETDSWESFFVSVRKAIT 301
Score = 35.4 bits (81), Expect = 0.025
Identities = 36/211 (17%), Positives = 57/211 (27%), Gaps = 86/211 (40%)
Query: 73 HISRHLSLS--------PISSCKSSNKQRRSRTNFTLEQLNE--LERLFDETHYPDAFMR 122
+ +R L+LS + + + F QL E + L + T + F
Sbjct: 4 YSTRPLTLSHGSLEHVLLVPT----------ASFFIASQLQEQFNKILPEPT---EGFAA 50
Query: 123 E-------ELSQR-LGLSEARVQN-----FSQVLNLLIDVSTVTINNTLNPAGIILSN-- 167
+ EL + LG + V+ F QVLNL + N L
Sbjct: 51 DDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLT----EFENC------YLEGND 100
Query: 168 -HQPVSTPLEPCRVAPYVNVPRLPTLPFSASTAAAFSAFDPTLLSAAHQ-----YAAAAA 221
H + AA + T L + A
Sbjct: 101 IH----------------------------ALAAKLLQENDTTLVKTKELIKNYITARIM 132
Query: 222 TVAALGNAPNGSIFSAASQYPSFSLATLAAL 252
N ++F A + A L A+
Sbjct: 133 AKRPFDKKSNSALFRAVGE----GNAQLVAI 159
Score = 29.2 bits (65), Expect = 2.0
Identities = 25/107 (23%), Positives = 40/107 (37%), Gaps = 26/107 (24%)
Query: 3 HQSQIIKSSTDS-NSDLKVNNENECDDSNRLPSSESSRHLYFTDSNSDLKVNNENE---- 57
H S ++ ++D N DL NN + ++P +Y T SDL+V + +
Sbjct: 428 H-SHLLVPASDLINKDLVKNNVSFNAKDIQIP-------VYDTFDGSDLRVLSGSISERI 479
Query: 58 CDDSNRLP-----SSESSRHHISRHLSLSP-----ISSCKSSNKQRR 94
D RLP +++ HI L P + NK
Sbjct: 480 VDCIIRLPVKWETTTQFKATHI---LDFGPGGASGLGVLTHRNKDGT 523
>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 = 47.2 bits (111), Expect = 4e-06
Identities = 49/278 (17%), Positives = 83/278 (29%), Gaps = 75/278 (26%)
Query: 50 LKVNNENECDDSNRLPSSESSRHHISRHLSLSPISSCKSSNKQRRSRTNFTLEQL-NELE 108
L + N N + L + + I + + S S + + EL
Sbjct: 187 LNLKNCNSPET--VLEMLQKLLYQIDPNWT---------SRSDHSSNIKLRIHSIQAELR 235
Query: 109 RLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLN-------LLI---DVSTVTINNTL 158
RL Y + L L L VQN ++ N +L+ +
Sbjct: 236 RLLKSKPYENC-----L---LVLLN--VQN-AKAWNAFNLSCKILLTTRFKQVTDFLSAA 284
Query: 159 NPAGIILSNHQPVSTPLEPCRV-APYVNVP--RLP-----TLPFSASTAAAF-----SAF 205
I L +H TP E + Y++ LP T P S A + +
Sbjct: 285 TTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATW 344
Query: 206 DPTLLSAAHQYAAA-AATVAALGNAPNG--------SIFSAASQYPSFSLATL------- 249
D + +++ L P S+F ++ P+ L+ +
Sbjct: 345 DNWKHVNCDKLTTIIESSLNVL--EPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS 402
Query: 250 ------AALHQDRLLSKNS-----SIADLRLKAKKHAE 276
LH+ L+ K SI + L+ K E
Sbjct: 403 DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLE 440
Score = 34.8 bits (79), Expect = 0.034
Identities = 23/147 (15%), Positives = 39/147 (26%), Gaps = 56/147 (38%)
Query: 22 NENECDDSNRLPSSESSRHLYFTDSNSDLKVNNENE---------------CDDSNRLPS 66
+ + + +P +Y +LKV ENE DS+ L
Sbjct: 418 EKQPKESTISIP------SIYL-----ELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP 466
Query: 67 SESSR---HHISRHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLF-DETHYPDAFMR 122
+ HI HL E++ +F D F+
Sbjct: 467 PYLDQYFYSHIGHHLK-----------NIEHP------ERMTLFRMVFLD-----FRFLE 504
Query: 123 EELSQRLGLSEARVQNFSQVLNLLIDV 149
Q++ +LN L +
Sbjct: 505 ----QKIRHDSTAWNASGSILNTLQQL 527
>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 = 41.1 bits (96), Expect = 2e-05
Identities = 11/45 (24%), Positives = 17/45 (37%)
Query: 94 RSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQN 138
S T EQL L+ F + + ++L Q GL +
Sbjct: 5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQ 49
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA
complex, transcription/DNA complex; 2.42A {Mesocricetus
auratus}
Length = 63
Score = 40.1 bits (94), Expect = 3e-05
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
+R+RT +T QL ELE+ F Y R EL+ L L+E + QN
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQN 53
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 40.2 bits (94), Expect = 5e-05
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 81 SPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV---- 136
S+ ++ + +R RT++T Q ELE+ F Y R E++ L L+E ++
Sbjct: 17 LGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWF 76
Query: 137 QN 138
QN
Sbjct: 77 QN 78
>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 = 39.8 bits (93), Expect = 6e-05
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 84 SSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
+ ++ +RR R +T Q ELE+ F HY R E++ L L+E ++ QN
Sbjct: 12 AIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQN 70
>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 = 38.7 bits (90), Expect = 1e-04
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
S + R+ R ++ QL ELER + + R ++S LSE ++ QN
Sbjct: 3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQN 57
>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 = 16/51 (31%), Positives = 25/51 (49%), Gaps = 4/51 (7%)
Query: 92 QRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
++R R +T Q ELE+ F Y R E++ L L+E ++ QN
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQN 52
>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 = 38.3 bits (89), Expect = 2e-04
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 81 SPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV---- 136
+P ++ + R+ R +T Q ELE+ F Y R E+++ L L+E +V
Sbjct: 2 NPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWF 61
Query: 137 QN 138
QN
Sbjct: 62 QN 63
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB:
2ld5_A*
Length = 73
Score = 38.3 bits (89), Expect = 2e-04
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARV----QN 138
+ R+ R +T QL ELER + + R +S LSE +V QN
Sbjct: 3 HMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQN 57
>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 = 35.9 bits (83), Expect = 0.001
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 94 RSRTNFTLEQLNELERLF-DETHYPDAFMREELSQRLGLSEARVQ 137
+ +E + LE++F T YPD + LS++L S ++Q
Sbjct: 10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQ 54
>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 = 30.2 bits (68), Expect = 0.12
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 107 LERLF-DETHYPDAFMREELSQRLGLSEARVQ 137
LE++F T +PD E LS++L +Q
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQ 46
>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 = 31.0 bits (69), Expect = 0.13
Identities = 10/40 (25%), Positives = 15/40 (37%)
Query: 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQ 127
SS R+R + L + +D P RE L +
Sbjct: 2 SSGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVE 41
>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 = 29.6 bits (66), Expect = 0.26
Identities = 8/33 (24%), Positives = 14/33 (42%)
Query: 84 SSCKSSNKQRRSRTNFTLEQLNELERLFDETHY 116
+ S +R RT FT EQ ++ + +
Sbjct: 9 NPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGW 41
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna;
HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 30.7 bits (68), Expect = 0.29
Identities = 8/30 (26%), Positives = 12/30 (40%)
Query: 28 DSNRLPSSESSRHLYFTDSNSDLKVNNENE 57
+ L ++S LY DS L + E
Sbjct: 18 EKQALKKLQASLKLYADDSAPALAIKATME 47
>1ut9_A Cellulose 1,4-beta-cellobiosidase; hydrolase, glycoside hydrolase,
family 9, cellobiohydrolase; 2.1A {Clostridium
thermocellum} SCOP: a.102.1.2 b.1.18.2 PDB: 1rq5_A*
Length = 609
Score = 30.0 bits (67), Expect = 0.95
Identities = 17/84 (20%), Positives = 24/84 (28%), Gaps = 8/84 (9%)
Query: 168 HQPVSTPLEPCRVAPYVNVPRLPTLPFSASTAAA---FSAFDP----TLLSAAHQ-YAAA 219
P E + V TL F+A+ A + + +DP L A + AA
Sbjct: 267 TALGMLPHEDPQPRYLRPVSTAATLNFAATLAQSARLWKDYDPTFAADCLEKAEIAWQAA 326
Query: 220 AATVAALGNAPNGSIFSAASQYPS 243
GS Y
Sbjct: 327 LKHPDIYAEYTPGSGGPGGGPYND 350
>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 = 28.0 bits (62), Expect = 0.99
Identities = 18/81 (22%), Positives = 30/81 (37%), Gaps = 20/81 (24%)
Query: 81 SPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLS-----EAR 135
S S+ ++R RT FT EQ + L++R+G +
Sbjct: 6 SGSSAEAGGGIRKRHRTKFTAEQKERM---------------LALAERIGWRIQRQDDEV 50
Query: 136 VQNFSQVLNLLIDVSTVTINN 156
+Q F Q + V V ++N
Sbjct: 51 IQRFCQETGVPRQVLKVWLHN 71
>3htr_A Uncharacterized PRC-barrel domain protein; beta-barrel,
photo-reaction-center domain, structural genomics,
PSI-2; HET: MSE; 2.06A {Rhodopseudomonas palustris}
Length = 120
Score = 28.0 bits (62), Expect = 1.7
Identities = 8/59 (13%), Positives = 20/59 (33%), Gaps = 1/59 (1%)
Query: 74 ISRHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLS 132
I P + K + + + T++QL + + D ++ G++
Sbjct: 61 IGDDHYPLPWPALKYNVELGGYQVMVTVDQLERAPK-YGPGSEWDWRGARKVDDYYGVA 118
>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix,
transcription factor, CAMP-B proteins, CAMP receptor
protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP:
a.4.5.4 b.82.3.2
Length = 207
Score = 28.0 bits (63), Expect = 3.4
Identities = 7/68 (10%), Positives = 13/68 (19%), Gaps = 1/68 (1%)
Query: 203 SAFDPTLLSAAHQYAAAAATVAALGNAPNGSIFSAASQYPSFSLATLAALHQDRLLSKNS 262
F+ A + + Q + + RL
Sbjct: 69 GLFEKEGSEQERSAWVRAKVECEVAEISYAKFRELSQQDSEILYTLGSQMAD-RLRKTTR 127
Query: 263 SIADLRLK 270
+ DL
Sbjct: 128 KVGDLAFL 135
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 28.0 bits (62), Expect = 3.5
Identities = 9/47 (19%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 95 SRTNFTLEQLNELERL---FDETHYPDAFMREELSQRLGLSEARVQN 138
+ T EQL + RL +++ +E ++ ++G+ ++ V
Sbjct: 3 KKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGA 49
>2vn2_A DNAD, chromosome replication initiation protein; DNA replication,
primosome; 2.3A {Geobacillus kaustophilus HTA426}
Length = 128
Score = 27.2 bits (60), Expect = 3.9
Identities = 9/42 (21%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 123 EELSQRLGLSEARVQNFSQVLNLLIDVSTVTINNTLNPAGII 164
EL++R+ +S A ++ L+ + I + GI
Sbjct: 55 AELAERMTVSAAECME---MVRRLLQKGMIAIEEHTDEQGIR 93
>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 = 26.4 bits (58), Expect = 4.1
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 3/53 (5%)
Query: 89 SNKQRRSRTNFTLEQLNELERLFDETH---YPDAFMREELSQRLGLSEARVQN 138
+ + FT E + LE F + Y D E L + LS +++N
Sbjct: 24 KSTKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKN 76
>3pm0_A Cypib1, cytochrome P450 1B1; CYP1B1, monooxygenase,
alpha-naphthoflavone, 17BETA-estradiol, oxidoreductase;
HET: HEM BHF; 2.70A {Homo sapiens}
Length = 507
Score = 27.9 bits (63), Expect = 4.5
Identities = 15/92 (16%), Positives = 30/92 (32%), Gaps = 9/92 (9%)
Query: 76 RHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYP----DAFMREELSQRLGL 131
++ + + + R+ +NF L++ P DAF+ + G
Sbjct: 208 QYFPNPVRTVFREFEQLNRNFSNFILDKFLRHCESLRPGAAPRDMMDAFILSAEKKAAGD 267
Query: 132 SEARVQNFS--QVLNLLIDV---STVTINNTL 158
S V + D+ S T++ L
Sbjct: 268 SHGGGARLDLENVPATITDIFGASQDTLSTAL 299
>1clc_A Endoglucanase CELD; EC: 3.2.1.4; cellulase, glycosyl hydrolase;
1.90A {Clostridium thermocellum} SCOP: a.102.1.2
b.1.18.2
Length = 639
Score = 27.9 bits (62), Expect = 4.5
Identities = 18/88 (20%), Positives = 25/88 (28%), Gaps = 11/88 (12%)
Query: 166 SNHQPVSTPLEPCRVAPYVNVPRLPTLPFSASTAAA---FSAFDP----TLLSAAHQ-YA 217
N P +V T F A TA A F +DP ++AA Y
Sbjct: 264 RNFGGFIMPENEHDERFFVPWSSAATADFVAMTAMAARIFRPYDPQYAEKCINAAKVSYE 323
Query: 218 AAAATVAALGNAPNGSIFSAASQYPSFS 245
N + +Y + S
Sbjct: 324 FLKNN---PANVFANQSGFSTGEYATVS 348
>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding,
transcription, transcription regulator, transcription
regulation; 3.20A {Klebsiella pneumoniae}
Length = 315
Score = 27.5 bits (61), Expect = 5.0
Identities = 3/24 (12%), Positives = 11/24 (45%)
Query: 115 HYPDAFMREELSQRLGLSEARVQN 138
+Y + ++++ LG+ +
Sbjct: 17 YYEQDMTQAQIARELGIYRTTISR 40
>2g38_B PPE family protein; protein-protein complex, structural genomics,
PSI, protein S initiative, TB structural genomics
consortium, TBSGC; 2.20A {Mycobacterium tuberculosis}
SCOP: a.25.4.2
Length = 198
Score = 27.4 bits (60), Expect = 5.2
Identities = 12/73 (16%), Positives = 22/73 (30%), Gaps = 3/73 (4%)
Query: 182 PYVNVPRLPTLPFSAS---TAAAFSAFDPTLLSAAHQYAAAAATVAALGNAPNGSIFSAA 238
P VN + P S A A+ + D + + + ++ P A
Sbjct: 8 PEVNSANIYAGPGPDSMLAAARAWRSLDVEMTAVQRSFNRTLLSLMDAWAGPVVMQLMEA 67
Query: 239 SQYPSFSLATLAA 251
++ L L
Sbjct: 68 AKPFVRWLTDLCV 80
>2cu2_A Putative mannose-1-phosphate guanylyl transferase;
mannose-1-phosphate geranyltransferase, thermus
thermophilus structural genomics; 2.20A {Thermus
thermophilus} SCOP: b.81.4.1 c.68.1.20
Length = 337
Score = 27.5 bits (62), Expect = 5.3
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 194 FSAST-AAAFSAFDPTLLSAAHQYAAAAATVAALGNAPNGSI 234
F+ +T A F P+ A + A A+ P SI
Sbjct: 192 FAPATMAELFRRHLPSHHEALERLLAGASLEEVYAGLPKISI 233
>1s1e_A KV channel interacting protein 1; kchip, calcium-binding protein,
EF-finger, transport protein; 2.30A {Homo sapiens} SCOP:
a.39.1.5
Length = 224
Score = 27.3 bits (60), Expect = 5.7
Identities = 11/41 (26%), Positives = 15/41 (36%)
Query: 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGL 131
+Q ++TNFT +L L R F E Q
Sbjct: 40 EQLEAQTNFTKRELQVLYRGFKNECPSGVVNEETFKQIYAQ 80
>2jul_A Calsenilin; EF-hand, calcium, LXXLL, DNA binding protein, dimer,
alternative splicing, apoptosis, cytoplasm, endoplasmic
reticulum, golgi apparatus; NMR {Mus musculus}
Length = 256
Score = 26.9 bits (59), Expect = 6.5
Identities = 19/112 (16%), Positives = 34/112 (30%), Gaps = 5/112 (4%)
Query: 16 SDLKVNNENECDDSNRLPSSESSRHLYFTDSNSDLKVNNENECDDSNRLPSSESSRHHIS 75
+K ++ N D R+P S+ C + SS + + S
Sbjct: 6 EAVKASDGNLLGDPGRIPLSKRES---IKWQRPRFTRQALMRCCLIKWILSSAAPQGSDS 62
Query: 76 RHLSLSPISSCKSSN--KQRRSRTNFTLEQLNELERLFDETHYPDAFMREEL 125
L + Q +++T FT ++L L R F +
Sbjct: 63 SDSELELSTVRHQPEGLDQLQAQTKFTKKELQSLYRGFKNECPTGLVDEDTF 114
>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET:
DNA; 2.00A {Bacillus subtilis}
Length = 135
Score = 26.4 bits (58), Expect = 7.2
Identities = 8/42 (19%), Positives = 15/42 (35%), Gaps = 3/42 (7%)
Query: 123 EELSQRLGLSEARVQNFSQVLNLLIDVSTVTINNTLNPAGII 164
+L + + +S N L + I + I + GI
Sbjct: 55 NQLQEGMSISVEECTN---RLRMFIQKGFLFIEECEDQNGIK 93
>1o3u_A Conserved hypothetical protein TM0613; structural genomics, joint
center for structural genomics, J protein structure
initiative, PSI; 1.75A {Thermotoga maritima} SCOP:
a.24.16.3
Length = 135
Score = 26.2 bits (57), Expect = 7.5
Identities = 12/64 (18%), Positives = 18/64 (28%), Gaps = 9/64 (14%)
Query: 72 HHISRHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGL 131
+ + L R ++ EL++ T YPDA R
Sbjct: 61 YSVPDFLGELS---------SRFEIPEELMDHALELDKACIPTRYPDALPSGSPRNRYSR 111
Query: 132 SEAR 135
EA
Sbjct: 112 IEAE 115
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus
musculus} SCOP: a.4.1.1
Length = 64
Score = 25.0 bits (55), Expect = 8.3
Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 5/53 (9%)
Query: 90 NKQRRSRTNFTLEQLNELERLFDETH----YPDAFMREELSQRLGLSEARVQN 138
+ + + L F H YP +EEL+++ G++ ++V N
Sbjct: 1 SSGHIEGRHMNKQATEILNEYFYS-HLSNPYPSEEAKEELAKKCGITVSQVSN 52
>2hpk_A Photoprotein berovin; structural genomics, PSI, protein structure
initiative, southeast collaboratory for structural
genomics, secsg; 2.00A {Beroe abyssicola}
Length = 208
Score = 26.7 bits (59), Expect = 8.5
Identities = 5/24 (20%), Positives = 12/24 (50%)
Query: 89 SNKQRRSRTNFTLEQLNELERLFD 112
N+ + + + + L+ L + FD
Sbjct: 20 GNQWQFNVEDLHPKMLSRLYKRFD 43
>3qrx_A Centrin; calcium-binding, EF-hand, cell division, calcium binding,
ME binding protein-toxin complex; 2.20A {Chlamydomonas
reinhardtii} PDB: 2ggm_A 2ami_A 1zmz_A
Length = 169
Score = 26.4 bits (59), Expect = 8.5
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 78 LSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFD 112
+S + + Q++ R T EQ E+ FD
Sbjct: 1 MSYKAKTVVSARRDQKKGRVGLTEEQKQEIREAFD 35
>1u8b_A ADA polyprotein; protein-DNA complex, methylation, zinc,
helix-turn-helix, metal binding protein/DNA complex;
2.10A {Escherichia coli} PDB: 1zgw_A* 1wpk_A* 1adn_A
1eyf_A
Length = 133
Score = 25.8 bits (56), Expect = 9.4
Identities = 8/75 (10%), Positives = 27/75 (36%), Gaps = 2/75 (2%)
Query: 63 RLPSSESSRHHISRHLSLSPISSCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMR 122
R E+ + + +L+ + + + + + N +L+++
Sbjct: 39 RHALRENVSFYANASEALA--AGFRPCKRCQPDKANPRQHRLDKITHACRLLEQETPVTL 96
Query: 123 EELSQRLGLSEARVQ 137
E L+ ++ +S +
Sbjct: 97 EALADQVAMSPFHLH 111
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
0.311 0.123 0.336
Gapped
Lambda K H
0.267 0.0477 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,964,176
Number of extensions: 225373
Number of successful extensions: 729
Number of sequences better than 10.0: 1
Number of HSP's gapped: 722
Number of HSP's successfully gapped: 97
Length of query: 288
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 195
Effective length of database: 4,105,140
Effective search space: 800502300
Effective search space used: 800502300
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: 57 (26.3 bits)