RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy5909
(130 letters)
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 103 bits (259), Expect = 1e-30
Identities = 26/50 (52%), Positives = 37/50 (74%)
Query: 49 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+RNRT+FT Q+ LE+ FE++HYPDV++RE LA K++LPE R+Q
Sbjct: 3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 52
>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 = 103 bits (259), Expect = 1e-30
Identities = 24/50 (48%), Positives = 33/50 (66%)
Query: 49 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR+RT FT QL LE F+++ YPDV +RE+LA KV+L E +V+
Sbjct: 3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE 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 = 103 bits (259), Expect = 1e-30
Identities = 31/50 (62%), Positives = 40/50 (80%)
Query: 49 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
K+K RR+RTTF+ QL ELERAFE++ YPD+Y+REELA + NL E R+Q
Sbjct: 14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 63
>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 = 101 bits (254), Expect = 9e-30
Identities = 28/49 (57%), Positives = 34/49 (69%)
Query: 50 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR RTTFT QL LE F K+ YPD++ REE+A+K+NLPE RVQ
Sbjct: 4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 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 = 100 bits (251), Expect = 2e-29
Identities = 23/47 (48%), Positives = 33/47 (70%)
Query: 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR RT FT+ QL +LE F+++ YPD+ +REE+A+ NL E RV+
Sbjct: 2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVR 48
>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 = 98.2 bits (245), Expect = 2e-28
Identities = 20/45 (44%), Positives = 26/45 (57%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
RR RT FT Q+ LE F + YP + E+LA K+NL R+Q
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQ 46
>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 = 97.5 bits (243), Expect = 4e-28
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 49 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+R RT+F +QL ++ F +H PD ++LA K L + +Q
Sbjct: 3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 52
>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 = 95.0 bits (237), Expect = 2e-27
Identities = 26/43 (60%), Positives = 36/43 (83%)
Query: 56 NRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+ TFT++QL ELE+AF ++HYPDV++REELAMK+ L E R+Q
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44
>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 = 93.6 bits (233), Expect = 1e-26
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 50 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
R +RT FT YQL L+ F+ + YP E+L+ +NLP +
Sbjct: 4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIV 52
>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 = 89.7 bits (223), Expect = 3e-25
Identities = 13/47 (27%), Positives = 19/47 (40%)
Query: 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
K R RT QLH L + + PD +E+L L ++
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 = 86.4 bits (214), Expect = 1e-23
Identities = 15/57 (26%), Positives = 25/57 (43%)
Query: 42 SPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
S + ++ +R RTT T QL L + + P + +A +V L + VQ
Sbjct: 6 SGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQ 62
>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 = 79.3 bits (196), Expect = 4e-21
Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 54 RRNRTTFTTYQLHELERAFEKSH-YPDVYSREELAMKVNLPEVRVQ 98
T T Q+ LE F K + +PD + +A + L E + Q
Sbjct: 2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQ 47
>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 = 78.9 bits (195), Expect = 6e-21
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 49 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+R RT T QL L + F+ ++ P +E+A K LP+ ++
Sbjct: 3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 74.4 bits (183), Expect = 4e-19
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 1/46 (2%)
Query: 54 RRNRTTFTTYQLHELERAFEKSH-YPDVYSREELAMKVNLPEVRVQ 98
+ + T Q+ LE F K + +PD + +A + L 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 = 73.5 bits (180), Expect = 2e-18
Identities = 15/65 (23%), Positives = 24/65 (36%), Gaps = 15/65 (23%)
Query: 49 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVN---------------LP 93
R +R T+ L +E F ++ YPD REE+A N +
Sbjct: 3 SGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVT 62
Query: 94 EVRVQ 98
++V
Sbjct: 63 SLKVY 67
>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 = 69.1 bits (168), Expect = 8e-16
Identities = 20/97 (20%), Positives = 31/97 (31%)
Query: 4 GNSSSDEQAVSDLRRKPSDTVDSDLEIDDDKCSRGGSLSPSLSPVDKKKHRRNRTTFTTY 63
+ Q + L + G P+ + KK RRNR +
Sbjct: 66 KGTPMKTQKRAALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPA 125
Query: 64 QLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAV 100
L +A+E+ P RE L + N E + V
Sbjct: 126 SQQILFQAYERQKNPSKEERETLVEECNRAECIQRGV 162
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A
{Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 66.4 bits (161), Expect = 1e-15
Identities = 16/55 (29%), Positives = 22/55 (40%)
Query: 49 DKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQAVGML 103
KK RRNR + L +A+E+ P RE L + N E + V
Sbjct: 5 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPS 59
>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 = 67.7 bits (165), Expect = 1e-15
Identities = 17/71 (23%), Positives = 28/71 (39%)
Query: 28 LEIDDDKCSRGGSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELA 87
L + + G + K R+ RT+FT + L FEK+ P E+A
Sbjct: 68 LNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMA 127
Query: 88 MKVNLPEVRVQ 98
++N V+
Sbjct: 128 KELNYDREVVR 138
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 65.1 bits (159), Expect = 2e-15
Identities = 9/52 (17%), Positives = 17/52 (32%)
Query: 47 PVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+ + QL L+ +F ++ +P E L L V+
Sbjct: 2 SSGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVR 53
>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 = 65.9 bits (160), Expect = 8e-15
Identities = 14/67 (20%), Positives = 26/67 (38%)
Query: 32 DDKCSRGGSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVN 91
++ + S S + +R RT+ LE F KS P + +A ++
Sbjct: 75 EEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLG 134
Query: 92 LPEVRVQ 98
L + V+
Sbjct: 135 LEKDVVR 141
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 66.6 bits (161), Expect = 1e-14
Identities = 18/95 (18%), Positives = 34/95 (35%)
Query: 6 SSSDEQAVSDLRRKPSDTVDSDLEIDDDKCSRGGSLSPSLSPVDKKKHRRNRTTFTTYQL 65
+ + + + + + D + + G + S KK RRNR +
Sbjct: 95 NQTVQSSGNMTDKSSQDQLLFLFPEFSQQSHGPGQSDDACSEPTNKKMRRNRFKWGPASQ 154
Query: 66 HELERAFEKSHYPDVYSREELAMKVNLPEVRVQAV 100
L +A+++ P RE L + N E + V
Sbjct: 155 QILYQAYDRQKNPSKEEREALVEECNRAECLQRGV 189
>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 = 61.7 bits (150), Expect = 3e-14
Identities = 10/48 (20%), Positives = 18/48 (37%)
Query: 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
H + T Q+ L+ +F +S +PD L L ++
Sbjct: 2 AHHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIK 49
>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 = 63.1 bits (153), Expect = 6e-14
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 1/84 (1%)
Query: 15 DLRRKPSDTVDSDLEIDDDKCSRGGSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEK 74
L K + + + L ++ + G+L +++K R+ RTT + LER F +
Sbjct: 50 QLSFKNACKLKAILSKWLEEAEQVGALYNEKVGANERK-RKRRTTISIAAKDALERHFGE 108
Query: 75 SHYPDVYSREELAMKVNLPEVRVQ 98
P +A ++NL + V+
Sbjct: 109 HSKPSSQEIMRMAEELNLEKEVVR 132
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 61.6 bits (149), Expect = 4e-13
Identities = 12/57 (21%), Positives = 21/57 (36%)
Query: 42 SPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+ + + R+ RT+ LE F K P + LA + L + V+
Sbjct: 88 TNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVR 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 = 59.6 bits (144), Expect = 2e-12
Identities = 14/74 (18%), Positives = 31/74 (41%)
Query: 25 DSDLEIDDDKCSRGGSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSRE 84
D++ + D S S + R+ RT+ T LE++F ++ P
Sbjct: 73 DAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDIT 132
Query: 85 ELAMKVNLPEVRVQ 98
+A ++N+ + ++
Sbjct: 133 LIAEQLNMEKEVIR 146
>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 = 55.3 bits (134), Expect = 1e-11
Identities = 10/49 (20%), Positives = 24/49 (48%)
Query: 50 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
K+K + +++ + LE F + + +EE+A K + ++V+
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVR 50
>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 = 54.4 bits (131), Expect = 3e-11
Identities = 22/59 (37%), Positives = 29/59 (49%)
Query: 39 GSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
S KK RR+RT FT QL LE+ FEK Y R +LA + L +++V
Sbjct: 3 SGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQV 61
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 52.4 bits (126), Expect = 2e-10
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
R+ RT ++++QL L+R F+K+ Y + R ELA + L + +V
Sbjct: 5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQV 51
>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-10
Identities = 14/46 (30%), Positives = 20/46 (43%)
Query: 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
H + + + Q+ ELER F Y R LA + L E +V
Sbjct: 3 HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQV 48
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 51.9 bits (125), Expect = 2e-10
Identities = 18/44 (40%), Positives = 25/44 (56%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
R+ RT FTT QL LER F + Y + R E + ++L E +V
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQV 44
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 51.5 bits (124), Expect = 3e-10
Identities = 15/44 (34%), Positives = 25/44 (56%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
R+ R F+ Q++ELER F++ Y R++LA + L +V
Sbjct: 3 RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQV 46
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 51.1 bits (123), Expect = 4e-10
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
++ RT F+ QL L+ F+K Y + +EL+ +NL +V
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQV 47
>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 = 51.3 bits (123), Expect = 5e-10
Identities = 19/52 (36%), Positives = 24/52 (46%)
Query: 46 SPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
S K R+ R FT Q +ELER F + Y RE LA + L +V
Sbjct: 2 SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQV 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 = 51.0 bits (122), Expect = 6e-10
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 52 KHRRNRTTFTTYQLHELERAF-EKSHYPDVYSREELAMKVNLPEVRVQ 98
R+RT + L L+ + YPD + L+ +++LP+ +
Sbjct: 6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTII 53
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 51.0 bits (122), Expect = 1e-09
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
K ++ RT+FT Q+ ELE+ F K Y R LA + + + +V
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQV 61
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 49.7 bits (119), Expect = 2e-09
Identities = 16/45 (35%), Positives = 25/45 (55%)
Query: 53 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
R+ R F+ Q++ELER F++ Y RE LA ++L +V
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQV 46
>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 = 49.3 bits (118), Expect = 2e-09
Identities = 14/47 (29%), Positives = 21/47 (44%)
Query: 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
+ + F+ Q ELE+ FE Y R+ LA + L E +V
Sbjct: 5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQV 51
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 49.4 bits (118), Expect = 4e-09
Identities = 14/65 (21%), Positives = 28/65 (43%)
Query: 33 DKCSRGGSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNL 92
+ + + K ++ RT F++ QL L F++ Y + +EL+ +NL
Sbjct: 2 KQPTSAENSVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNL 61
Query: 93 PEVRV 97
+V
Sbjct: 62 SYKQV 66
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 48.7 bits (115), Expect = 3e-08
Identities = 9/52 (17%), Positives = 19/52 (36%)
Query: 47 PVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
++ R FT Q L F+++ P + ++ ++ L V
Sbjct: 91 KDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVS 142
>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 = 46.2 bits (110), Expect = 3e-08
Identities = 21/44 (47%), Positives = 26/44 (59%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
RR RT FT QL LE+ F K +Y R ELA ++NLPE +
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTI 45
>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 = 46.3 bits (110), Expect = 4e-08
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 53 HRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
RR RTTFT+ Q+ ELE+ F + Y +L+ K+ L +V
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQV 46
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 45.4 bits (108), Expect = 6e-08
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 58 TTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRV 97
T+F+ Q+ ELER F + Y R LA + + + +V
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQV 41
>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 = 44.6 bits (106), Expect = 1e-07
Identities = 14/41 (34%), Positives = 25/41 (60%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE 94
+R RT F++ QL L+R F ++ Y R++L+ ++ L E
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNE 44
>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 = 45.4 bits (107), Expect = 1e-07
Identities = 14/63 (22%), Positives = 24/63 (38%), Gaps = 7/63 (11%)
Query: 36 SRGGSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEV 95
S P +P +K + T Q+ LE +F KS +P + L ++ L
Sbjct: 3 SGSSGAYPDFAP--QKFKEK-----TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRR 55
Query: 96 RVQ 98
+
Sbjct: 56 EID 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 = 44.5 bits (105), Expect = 4e-07
Identities = 21/64 (32%), Positives = 28/64 (43%)
Query: 34 KCSRGGSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLP 93
K R + +S RT FTT QL ELE+ F + Y R E+A + L
Sbjct: 15 KVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELN 74
Query: 94 EVRV 97
E +V
Sbjct: 75 ETQV 78
>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 = 43.8 bits (103), Expect = 4e-07
Identities = 13/62 (20%), Positives = 20/62 (32%), Gaps = 7/62 (11%)
Query: 37 RGGSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVR 96
GS P +P +K + T QL L+ +F S L + L
Sbjct: 2 SSGSSGPDFTP--QKFKEK-----TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRRE 54
Query: 97 VQ 98
+
Sbjct: 55 ID 56
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 42.4 bits (100), Expect = 8e-07
Identities = 18/43 (41%), Positives = 25/43 (58%)
Query: 52 KHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE 94
++R RT +T QL ELE+ F + Y R ELA+ +NL E
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTE 44
>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 = 42.5 bits (99), Expect = 2e-06
Identities = 14/60 (23%), Positives = 22/60 (36%)
Query: 39 GSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
G P K T QLH L+ AF ++ +P ++LA + L +
Sbjct: 11 GLEVLFQGPAPKSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIV 70
>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 = 41.4 bits (97), Expect = 3e-06
Identities = 9/49 (18%), Positives = 16/49 (32%), Gaps = 5/49 (10%)
Query: 50 KKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
K R QL LE +F ++ P + L + + +
Sbjct: 9 TKYKER-----APEQLRALESSFAQNPLPLDEELDRLRSETKMTRREID 52
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 41.8 bits (98), Expect = 3e-06
Identities = 16/53 (30%), Positives = 27/53 (50%)
Query: 42 SPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE 94
+ + + +R RT++T YQ ELE+ F + Y R E+A ++L E
Sbjct: 17 LGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTE 69
>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 = 40.6 bits (95), Expect = 7e-06
Identities = 18/44 (40%), Positives = 24/44 (54%)
Query: 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE 94
RR R T+T YQ ELE+ F +HY R E+A ++L E
Sbjct: 18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTE 61
>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 = 40.1 bits (94), Expect = 7e-06
Identities = 16/41 (39%), Positives = 23/41 (56%)
Query: 54 RRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE 94
+R R T+T YQ ELE+ F + Y R E+A ++L E
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTE 43
>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 = 40.2 bits (94), Expect = 1e-05
Identities = 16/53 (30%), Positives = 28/53 (52%)
Query: 42 SPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE 94
+P+ + + + R+ R +T +Q ELE+ F + Y R E+A +NL E
Sbjct: 2 NPAANWLHARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTE 54
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 39.8 bits (93), Expect = 1e-05
Identities = 13/44 (29%), Positives = 21/44 (47%)
Query: 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE 94
+ R+ R +T QL ELER + + + R ++ NL E
Sbjct: 5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSE 48
>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 = 39.4 bits (92), Expect = 2e-05
Identities = 11/44 (25%), Positives = 21/44 (47%)
Query: 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPE 94
R+ R ++ QL ELER + + + R +++ +L E
Sbjct: 5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSE 48
>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 = 36.8 bits (84), Expect = 3e-04
Identities = 11/45 (24%), Positives = 17/45 (37%)
Query: 51 KKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEV 95
RNR + L +A+++ P RE L + N E
Sbjct: 4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAEC 48
>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 = 34.6 bits (79), Expect = 0.001
Identities = 8/44 (18%), Positives = 15/44 (34%)
Query: 55 RNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQ 98
+ T QL L+ F + + ++L LP +
Sbjct: 5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEII 48
>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 = 30.2 bits (68), Expect = 0.051
Identities = 8/53 (15%), Positives = 19/53 (35%), Gaps = 1/53 (1%)
Query: 47 PVDKKKHRRNRTTFTTYQLHELERAFEK-SHYPDVYSREELAMKVNLPEVRVQ 98
++ LE+ F + YPD + L+ +++ ++Q
Sbjct: 2 SSGSSGGIKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQ 54
>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 = 28.0 bits (62), Expect = 0.32
Identities = 9/36 (25%), Positives = 14/36 (38%)
Query: 42 SPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHY 77
S S +R RT FT Q ++ E+ +
Sbjct: 6 SGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGW 41
>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 = 27.6 bits (60), Expect = 0.48
Identities = 8/47 (17%), Positives = 19/47 (40%), Gaps = 4/47 (8%)
Query: 50 KKKHRRNRTTFTTYQLHELERAFEKS----HYPDVYSREELAMKVNL 92
++RT F+ L L++ ++ E +A ++N+
Sbjct: 5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNV 51
>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 = 25.7 bits (56), Expect = 5.0
Identities = 5/38 (13%), Positives = 7/38 (18%), Gaps = 1/38 (2%)
Query: 30 IDDDKCSRGGSLSPSLSP-VDKKKHRRNRTTFTTYQLH 66
P+L + R T Q
Sbjct: 143 SGGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFD 180
>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 = 24.0 bits (52), Expect = 7.2
Identities = 8/32 (25%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 68 LERAFEKSH-YPDVYSREELAMKVNLPEVRVQ 98
LE+ F +PD E L+ +++ +Q
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQ 46
>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 = 25.4 bits (55), Expect = 7.3
Identities = 11/67 (16%), Positives = 19/67 (28%)
Query: 20 PSDTVDSDLEIDDDKCSRGGSLSPSLSPVDKKKHRRNRTTFTTYQLHELERAFEKSHYPD 79
+ S D LS + + +T FT +L L R F+
Sbjct: 48 IKWILSSAAPQGSDSSDSELELSTVRHQPEGLDQLQAQTKFTKKELQSLYRGFKNECPTG 107
Query: 80 VYSREEL 86
+ +
Sbjct: 108 LVDEDTF 114
>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 = 25.0 bits (54), Expect = 9.3
Identities = 9/44 (20%), Positives = 14/44 (31%), Gaps = 10/44 (22%)
Query: 97 VQAVGMLYYSVELQDIEFNIRVPEPSHPIG----------LPAP 130
+ A ++ +E + VP S I LP P
Sbjct: 1 MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEP 44
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 0.130 0.366
Gapped
Lambda K H
0.267 0.0770 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,980,639
Number of extensions: 106728
Number of successful extensions: 158
Number of sequences better than 10.0: 1
Number of HSP's gapped: 155
Number of HSP's successfully gapped: 68
Length of query: 130
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 47
Effective length of database: 4,384,350
Effective search space: 206064450
Effective search space used: 206064450
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 (21.8 bits)
S2: 52 (23.7 bits)