RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14727
(67 letters)
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription
regulation; HET: DNA; 2.00A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 3a01_B
Length = 81
Score = 94.0 bits (234), Expect = 9e-28
Identities = 32/49 (65%), Positives = 42/49 (85%)
Query: 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+RKQRR+RTTF+ QL+ELE AF +T YPD++TRE+LA + NLTEAR+Q
Sbjct: 15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 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 = 93.6 bits (233), Expect = 1e-27
Identities = 29/49 (59%), Positives = 36/49 (73%)
Query: 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+RNRT+FT +Q+E LE F +THYPDVF RE LA KI+L EAR+Q
Sbjct: 4 GSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 52
>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 = 92.9 bits (231), Expect = 3e-27
Identities = 29/49 (59%), Positives = 36/49 (73%)
Query: 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
RR RTTFT QL+ LE FA+T YPD+F RE++A+KINL E+RVQ
Sbjct: 4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 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 = 92.0 bits (229), Expect = 4e-27
Identities = 26/49 (53%), Positives = 33/49 (67%)
Query: 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
RR+RT FT +QLE LE F +T YPDV TRE LA K++L E +V+
Sbjct: 4 GSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE 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 = 88.9 bits (221), Expect = 6e-26
Identities = 27/47 (57%), Positives = 35/47 (74%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
QRR RT FT QQL++LE F + YPD+ TRE++A+ NLTEARV+
Sbjct: 2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVR 48
>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 = 88.3 bits (219), Expect = 2e-25
Identities = 17/48 (35%), Positives = 25/48 (52%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+R RT+F QL +++ FA H PD + LA K LT+ +Q
Sbjct: 5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQ 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 = 85.1 bits (211), Expect = 2e-24
Identities = 15/48 (31%), Positives = 20/48 (41%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
R +RT FT QL L+ F YP E L+ +NL +
Sbjct: 5 SSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIV 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 = 84.7 bits (210), Expect = 3e-24
Identities = 22/45 (48%), Positives = 26/45 (57%)
Query: 23 RRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
RR RT FT Q+E LE F YP + EDLA K+NL R+Q
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQ 46
>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 = 82.7 bits (205), Expect = 1e-23
Identities = 32/43 (74%), Positives = 37/43 (86%)
Query: 25 NRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+ TFT QLEELE AF++THYPDVFTRE+LAMKI LTEAR+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 = 79.8 bits (197), Expect = 3e-22
Identities = 14/54 (25%), Positives = 24/54 (44%)
Query: 14 DDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
++ +R RTT T +QLE L + P + +A ++ L + VQ
Sbjct: 9 TGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQ 62
>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 = 79.3 bits (196), Expect = 4e-22
Identities = 14/47 (29%), Positives = 20/47 (42%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
K R RT +QL L T +A PD +E L L+ ++
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIR 48
>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 = 73.6 bits (181), Expect = 9e-20
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 1/46 (2%)
Query: 23 RRNRTTFTLQQLEELETAFAQTH-YPDVFTREDLAMKINLTEARVQ 67
T T Q+E LE F + + +PD T +A + LTE + 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 = 70.5 bits (173), Expect = 1e-18
Identities = 12/48 (25%), Positives = 20/48 (41%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+R RT T QL L F + P +++A K L + ++
Sbjct: 5 SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIK 52
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 69.0 bits (169), Expect = 6e-18
Identities = 14/46 (30%), Positives = 23/46 (50%), Gaps = 1/46 (2%)
Query: 23 RRNRTTFTLQQLEELETAFAQTH-YPDVFTREDLAMKINLTEARVQ 67
+ + T Q+E LE F + + +PD T +A + LTE + 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 = 69.3 bits (169), Expect = 7e-18
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 15/63 (23%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKIN---------------LTEA 64
R +R T+ + L +E+ F + YPD RE++A N +T
Sbjct: 5 SSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSL 64
Query: 65 RVQ 67
+V
Sbjct: 65 KVY 67
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 63.2 bits (154), Expect = 1e-15
Identities = 9/45 (20%), Positives = 18/45 (40%)
Query: 23 RRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+ + +QL L+ +F + +P E L L+ V+
Sbjct: 9 SIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVR 53
>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 = 64.7 bits (157), Expect = 2e-15
Identities = 14/55 (25%), Positives = 24/55 (43%)
Query: 13 HDDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
K+R+ RT+FT Q +E L F + P ++A ++N V+
Sbjct: 84 EFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVR 138
>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 = 63.7 bits (154), Expect = 1e-14
Identities = 14/55 (25%), Positives = 21/55 (38%)
Query: 13 HDDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
D +K RRNR + + L A+ + P RE L + N E +
Sbjct: 106 TGDELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQR 160
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 62.7 bits (151), Expect = 3e-14
Identities = 13/63 (20%), Positives = 20/63 (31%)
Query: 3 HTSYSYHPAIHDDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLT 62
+ +K RRNR + + L A+ + P RE L + N
Sbjct: 123 QSHGPGQSDDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRA 182
Query: 63 EAR 65
E
Sbjct: 183 ECL 185
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 58.3 bits (140), Expect = 2e-13
Identities = 13/45 (28%), Positives = 19/45 (42%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEA 64
+K RRNR + + L A+ + P RE L + N E
Sbjct: 7 KKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAEC 51
>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 = 59.6 bits (144), Expect = 2e-13
Identities = 13/66 (19%), Positives = 28/66 (42%)
Query: 2 LHTSYSYHPAIHDDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINL 61
L + ++ ++R+ RTT ++ + LE F + P +A ++NL
Sbjct: 67 LEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNL 126
Query: 62 TEARVQ 67
+ V+
Sbjct: 127 EKEVVR 132
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 57.7 bits (139), Expect = 1e-12
Identities = 15/63 (23%), Positives = 26/63 (41%)
Query: 5 SYSYHPAIHDDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEA 64
S S P D + ++R+ RT+ + LE+ F + P LA + L +
Sbjct: 82 SSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKE 141
Query: 65 RVQ 67
V+
Sbjct: 142 VVR 144
>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 = 57.4 bits (138), Expect = 2e-12
Identities = 11/55 (20%), Positives = 25/55 (45%)
Query: 13 HDDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+ + ++R RT+ + LET F ++ P + +A ++ L + V+
Sbjct: 87 SKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVR 141
>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 = 53.3 bits (128), Expect = 9e-12
Identities = 9/47 (19%), Positives = 19/47 (40%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+ T +Q+ L+ +F Q+ +PD L L + ++
Sbjct: 3 HHHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIK 49
>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 = 53.4 bits (128), Expect = 6e-11
Identities = 9/54 (16%), Positives = 22/54 (40%)
Query: 14 DDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
++R+ RT+ LE +F + P +A ++N+ + ++
Sbjct: 93 PGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIR 146
>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 = 49.4 bits (118), Expect = 3e-10
Identities = 11/48 (22%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQT-HYPDVFTREDLAMKINLTEARVQ 67
R+RT +L+ L L++ YPD L+ +++L + +
Sbjct: 6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTII 53
>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 = 47.2 bits (113), Expect = 2e-09
Identities = 10/49 (20%), Positives = 24/49 (48%)
Query: 19 RRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+ K + +++ + Q LE F + + +E++A K +T +V+
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVR 50
>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 = 46.7 bits (111), Expect = 5e-09
Identities = 20/47 (42%), Positives = 23/47 (48%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
K+R+ R FT Q ELE F Q Y RE LA I LT +V
Sbjct: 7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQV 53
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 45.7 bits (109), Expect = 6e-09
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 22 QRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
+R+ R F+ Q+ ELE F Q Y R+ LA + LT +V
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQV 46
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 44.7 bits (106), Expect = 2e-08
Identities = 15/47 (31%), Positives = 25/47 (53%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
R+ RT ++ QL L+ F +T Y + R +LA + LT+ +V
Sbjct: 5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQV 51
>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 = 45.2 bits (107), Expect = 2e-08
Identities = 19/47 (40%), Positives = 26/47 (55%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
+K RR+RT FT QL LE F + Y R DLA + L++ +V
Sbjct: 15 KKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQV 61
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 44.7 bits (106), Expect = 3e-08
Identities = 13/46 (28%), Positives = 20/46 (43%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
+ + + Q+ ELE F+ Y R LA + LTE +V
Sbjct: 3 HHHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQV 48
>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 = 45.0 bits (106), Expect = 3e-08
Identities = 10/54 (18%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 14 DDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
D + + K++ T Q++ LE +F ++ +P + L ++ L+ +
Sbjct: 11 DFAPQKFKEK------TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREID 58
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 43.8 bits (104), Expect = 3e-08
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 23 RRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
R+ RT FT QL LE F Q Y + R + + ++LTE +V
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQV 44
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 44.3 bits (105), Expect = 3e-08
Identities = 18/45 (40%), Positives = 24/45 (53%)
Query: 22 QRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
+R+ R F+ Q+ ELE F Q Y RE LA I+LT +V
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQV 46
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 44.4 bits (105), Expect = 3e-08
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
K+++ RT F+ QL L F + Y + ++L+ +NL+ +V
Sbjct: 20 VKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV 66
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 43.8 bits (104), Expect = 4e-08
Identities = 12/46 (26%), Positives = 25/46 (54%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
+++ RT F+ QL L+ F + Y + ++L+ +NL+ +V
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQV 47
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 43.7 bits (103), Expect = 8e-08
Identities = 17/47 (36%), Positives = 27/47 (57%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
K+++ RT+FT Q+ ELE F + Y R LA + +T+A+V
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQV 61
>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 = 42.7 bits (100), Expect = 2e-07
Identities = 10/54 (18%), Positives = 20/54 (37%), Gaps = 6/54 (11%)
Query: 14 DDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
D + + K++ T +QL L+ +F + L + LT +
Sbjct: 9 DFTPQKFKEK------TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREID 56
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 43.3 bits (101), Expect = 3e-07
Identities = 10/67 (14%), Positives = 20/67 (29%)
Query: 1 MLHTSYSYHPAIHDDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKIN 60
L + ++ R FT Q L F + P + ++ ++
Sbjct: 76 ALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLG 135
Query: 61 LTEARVQ 67
L + V
Sbjct: 136 LELSTVS 142
>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 = 41.8 bits (98), Expect = 4e-07
Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 4/54 (7%)
Query: 14 DDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
S K + +QL LE++FAQ P + L + +T +
Sbjct: 3 SGSSGPTKYKE----RAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREID 52
>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 = 40.5 bits (95), Expect = 8e-07
Identities = 13/47 (27%), Positives = 20/47 (42%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
+ + F+ Q ELE F Y R+ LA + L+E +V
Sbjct: 5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQV 51
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 39.2 bits (92), Expect = 3e-06
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 27 TTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
T+F+ Q+ ELE F + Y R LA + +T+A+V
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQV 41
>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 = 38.6 bits (89), Expect = 1e-05
Identities = 11/48 (22%), Positives = 19/48 (39%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
T +QL L++AF +T +P + LA + L +
Sbjct: 23 SGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIV 70
>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 = 36.9 bits (86), Expect = 2e-05
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 22 QRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
++R RT F+ +QL L+ F + Y R+ L+ ++ L EA++
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQI 47
>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 = 36.2 bits (84), Expect = 4e-05
Identities = 20/45 (44%), Positives = 24/45 (53%)
Query: 22 QRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
RR RTTFT Q+ ELE F Q Y DL+ K+ L A+V
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQV 46
>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 = 35.8 bits (82), Expect = 9e-05
Identities = 8/44 (18%), Positives = 15/44 (34%)
Query: 24 RNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
+ T +QL L++ F Q + + L L +
Sbjct: 5 SSGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEII 48
>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 = 34.6 bits (80), Expect = 1e-04
Identities = 18/44 (40%), Positives = 25/44 (56%)
Query: 23 RRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
RR RT FT QL LE F + +Y R +LA ++NL E+ +
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTI 45
>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 = 34.5 bits (79), Expect = 3e-04
Identities = 16/46 (34%), Positives = 21/46 (45%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
RT FT +QL ELE F Y R ++A + L E +V
Sbjct: 33 SPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQV 78
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 33.5 bits (77), Expect = 5e-04
Identities = 18/46 (39%), Positives = 24/46 (52%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
+R RT +T QL ELE F Y R +LA+ +NLTE +
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHI 47
>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 = 33.2 bits (76), Expect = 6e-04
Identities = 9/45 (20%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 24 RNRTTFTLQQLEELETAFA-QTHYPDVFTREDLAMKINLTEARVQ 67
++ ++ + LE F T YPD + L+ +++ + ++Q
Sbjct: 10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQ 54
>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 = 33.8 bits (76), Expect = 0.001
Identities = 8/36 (22%), Positives = 18/36 (50%), Gaps = 8/36 (22%)
Query: 32 QQLEELETAFAQTHYPDVFTREDLAMKINLTEARVQ 67
Q L++L+ + + + D + LA+K A ++
Sbjct: 20 QALKKLQASL-KLYADD--SAPALAIK-----ATME 47
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 32.5 bits (74), Expect = 0.001
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
+ R+ R +T QL+ELE +A + R ++ NL+E +V
Sbjct: 5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQV 51
>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 = 32.9 bits (75), Expect = 0.001
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
+RR R T+T Q ELE F HY R ++A ++LTE ++
Sbjct: 18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQI 64
>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 = 32.4 bits (74), Expect = 0.001
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 22 QRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
++R R T+T Q ELE F Y R ++A ++LTE ++
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQI 46
>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 = 32.1 bits (73), Expect = 0.002
Identities = 11/47 (23%), Positives = 22/47 (46%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
R+ R ++ QL ELE +A + R ++ +L+E ++
Sbjct: 5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQI 51
>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 = 32.9 bits (74), Expect = 0.002
Identities = 11/45 (24%), Positives = 16/45 (35%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEA 64
RNR + + L A+ + P RE L + N E
Sbjct: 4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAEC 48
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 31.7 bits (72), Expect = 0.003
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
+ +R RT++T Q ELE F Y R ++A ++LTE ++
Sbjct: 27 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQI 72
>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 = 31.4 bits (71), Expect = 0.004
Identities = 17/47 (36%), Positives = 23/47 (48%)
Query: 20 RKQRRNRTTFTLQQLEELETAFAQTHYPDVFTREDLAMKINLTEARV 66
R R+ R +T Q ELE F Y R ++A +NLTE +V
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQV 57
>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 = 27.5 bits (61), Expect = 0.11
Identities = 10/37 (27%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 32 QQLEELETAFA-QTHYPDVFTREDLAMKINLTEARVQ 67
Q LE F T +PD E L+ +++ +Q
Sbjct: 10 QPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQ 46
>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 = 26.1 bits (56), Expect = 0.44
Identities = 10/56 (17%), Positives = 21/56 (37%), Gaps = 4/56 (7%)
Query: 16 SFVRRKQRRNRTTFTLQQLEELETAFAQ----THYPDVFTREDLAMKINLTEARVQ 67
S ++RT F+ + L L+ + E +A ++N+ V+
Sbjct: 2 SSGSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVR 57
>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 = 25.2 bits (54), Expect = 1.6
Identities = 16/77 (20%), Positives = 21/77 (27%), Gaps = 36/77 (46%)
Query: 5 SYSY-HPAIH------------------DDSFVRRKQRRNRTTF--------TLQQLEEL 37
Y Y H H D F+ +K R + T + TLQQL+
Sbjct: 471 QYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKF- 529
Query: 38 ETAFAQTHYPDVFTRED 54
Y D
Sbjct: 530 --------YKPYICDND 538
>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 = 24.2 bits (52), Expect = 2.6
Identities = 9/23 (39%), Positives = 15/23 (65%), Gaps = 1/23 (4%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQ 43
++R+RT FT +Q E + A A+
Sbjct: 16 IRKRHRTKFTAEQKERML-ALAE 37
>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 = 23.4 bits (50), Expect = 4.3
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 21 KQRRNRTTFTLQQLEELETAFAQT 44
+R RT FT +Q E++ AFA+
Sbjct: 16 TTKRFRTKFTAEQKEKML-AFAER 38
>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 = 23.7 bits (52), Expect = 5.1
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 19 RRKQRRNRTTFTLQQLEELETAF 41
RR Q++ R T +Q +E+ AF
Sbjct: 12 RRDQKKGRVGLTEEQKQEIREAF 34
>1oy3_C Transcription factor P65; protein-protein complex, transcription
factors, nuclear localization, DNA binding protein;
2.05A {Mus musculus} SCOP: b.1.18.1 PDB: 1k3z_A
Length = 136
Score = 23.4 bits (50), Expect = 6.5
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 6 YSYHPAIHDDSFVRRKQRRNRTTF 29
+ Y P D + K++R TF
Sbjct: 96 FQYLPDTDDRHRIEEKRKRTYETF 119
>2v5c_A O-GLCNACASE NAGJ; glycosidase, GH84, GH84C, hydrolase, coiled coil,
family 84 glycoside hydrolase, carbohydrate binding
module; 2.10A {Clostridium perfringens} PDB: 2cbj_A*
2cbi_A 2vur_A* 2x0y_A* 2j62_A* 2wb5_A* 2xpk_A* 2yds_A*
2ydr_A* 2ydq_A*
Length = 594
Score = 23.6 bits (50), Expect = 7.0
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 2/49 (4%)
Query: 4 TSYSYHPAIHDDSFVRRKQRRNRTTFTLQQLEELETAFAQTHYPDVFTR 52
+Y Y P DD + R K R +Q+++EL A A+ VF
Sbjct: 181 NTYIYAP--KDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGI 227
>1nfk_A Protein (nuclear factor kappa-B (NF-KB)); NF-KB P50, complex
(transcription factor/DNA), transcription/DNA complex;
HET: DNA; 2.30A {Mus musculus} SCOP: b.1.18.1 b.2.5.3
PDB: 2v2t_B 1ooa_A 1lei_B* 1le9_B 1le5_B* 2i9t_B 1vkx_B*
3gut_B 2o61_B
Length = 325
Score = 23.2 bits (49), Expect = 8.0
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 8 YHPAIHDDSFVRRKQRR 24
Y+P I D V+RK+++
Sbjct: 309 YYPEIKDKEEVQRKRQK 325
>1svc_P Protein (nuclear factor kappa-B (NF-KB)); DNA-binding,
transcription regulation, activator, nuclear protein,
phosphorylation, repeat, DNA; HET: DNA; 2.60A {Homo
sapiens} SCOP: b.1.18.1 b.2.5.3
Length = 365
Score = 23.3 bits (49), Expect = 8.2
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 8 YHPAIHDDSFVRRKQRR 24
Y+P I D V+RK+++
Sbjct: 349 YYPEIKDKEEVQRKRQK 365
>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase,
hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli}
SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*
Length = 608
Score = 23.1 bits (50), Expect = 9.4
Identities = 6/17 (35%), Positives = 9/17 (52%)
Query: 28 TFTLQQLEELETAFAQT 44
+ +L E ET +A T
Sbjct: 521 SVQPSRLPEHETTWAMT 537
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
0.322 0.131 0.372
Gapped
Lambda K H
0.267 0.0569 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,004,801
Number of extensions: 43379
Number of successful extensions: 258
Number of sequences better than 10.0: 1
Number of HSP's gapped: 254
Number of HSP's successfully gapped: 75
Length of query: 67
Length of database: 6,701,793
Length adjustment: 38
Effective length of query: 29
Effective length of database: 5,640,795
Effective search space: 163583055
Effective search space used: 163583055
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 (22.0 bits)
S2: 51 (23.8 bits)