RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy16514
(155 letters)
>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 = 88.3 bits (219), Expect = 4e-24
Identities = 30/71 (42%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 8 RGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRM 67
G P + RR +F+ Q LE+RF+ Q+Y+S P+R+ LA + L +QVKIWFQN R
Sbjct: 3 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRY 62
Query: 68 KW-RNSKEREL 77
K R E+
Sbjct: 63 KTKRAQNEKGY 73
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 87.7 bits (218), Expect = 5e-24
Identities = 28/54 (51%), Positives = 37/54 (68%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
R +FS Q LE+RF+ Q+Y+S P+R +LA L L +QVKIWFQNRR K +
Sbjct: 5 PRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 87.4 bits (217), Expect = 5e-24
Identities = 27/51 (52%), Positives = 34/51 (66%)
Query: 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
FS Q LE+RF QKY++ +R LA+ L + D+QVK WFQNRR KWR
Sbjct: 3 SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 87.8 bits (218), Expect = 5e-24
Identities = 30/70 (42%), Positives = 38/70 (54%), Gaps = 4/70 (5%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G + S Q LE++F QKY+S P+R LA+ L L ++QVKIWFQNRR K
Sbjct: 2 GHHHH---HHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYK 58
Query: 69 W-RNSKEREL 77
R EL
Sbjct: 59 TKRKQLSSEL 68
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 87.0 bits (216), Expect = 9e-24
Identities = 27/62 (43%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G ++ R VFS Q L+ RFQ QKY+S ++L+ L L QVK WFQN+RMK
Sbjct: 1 GTKQK---MRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMK 57
Query: 69 WR 70
+
Sbjct: 58 CK 59
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 86.2 bits (214), Expect = 2e-23
Identities = 30/62 (48%), Positives = 41/62 (66%), Gaps = 1/62 (1%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKW-RNSKER 75
RR +FS Q LE+RF+ QKY+S P+R+ LA + L +QVKIWFQN R K R +K++
Sbjct: 5 RRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK 64
Query: 76 EL 77
Sbjct: 65 AA 66
>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 = 86.4 bits (214), Expect = 3e-23
Identities = 38/62 (61%), Positives = 44/62 (70%), Gaps = 3/62 (4%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
K RR R VF++LQ GLEKRF+ QKY+S PDR LAE LGL QVK W+QNRRMK
Sbjct: 15 KKGRR---SRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMK 71
Query: 69 WR 70
W+
Sbjct: 72 WK 73
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 85.4 bits (212), Expect = 3e-23
Identities = 22/54 (40%), Positives = 35/54 (64%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
R F+ Q LE++F+ ++Y+S +R + + L L ++QVKIWFQNRR K +
Sbjct: 3 PRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 84.9 bits (210), Expect = 1e-22
Identities = 31/84 (36%), Positives = 43/84 (51%)
Query: 6 FDRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNR 65
+ P + R F+ +Q LEKRF QKY++ +R LA L + D+QVK WFQNR
Sbjct: 9 YQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNR 68
Query: 66 RMKWRNSKERELLANGGSREQTLP 89
R KWR E A + + +
Sbjct: 69 RTKWRRQTAEEREAERQAANRLML 92
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 82.4 bits (204), Expect = 5e-22
Identities = 27/66 (40%), Positives = 40/66 (60%), Gaps = 3/66 (4%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R+ R ++S Q L++RFQ +Y++ P+R +LA LGL +QVKIWFQN+R K
Sbjct: 5 SSGRK---PRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSK 61
Query: 69 WRNSKE 74
+ S
Sbjct: 62 IKKSGP 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 = 81.8 bits (202), Expect = 2e-21
Identities = 28/73 (38%), Positives = 38/73 (52%)
Query: 2 STTIFDRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIW 61
S + P + R VFS Q L RFQ QKY+S ++L+ L L QVK W
Sbjct: 10 SVAKKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTW 69
Query: 62 FQNRRMKWRNSKE 74
FQN+RMK + ++
Sbjct: 70 FQNQRMKSKRWQK 82
>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 = 80.2 bits (198), Expect = 4e-21
Identities = 31/62 (50%), Positives = 41/62 (66%), Gaps = 3/62 (4%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
+ G + FS+ Q LEK+F+ QKY+S P+RK+LA+ L L + QVK WFQNRR K
Sbjct: 5 SSGKGG---QVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61
Query: 69 WR 70
WR
Sbjct: 62 WR 63
>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 = 72.2 bits (178), Expect = 5e-18
Identities = 15/54 (27%), Positives = 35/54 (64%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
++ S R LE+ F+ ++ ++ +++++A+K G+ QV++WF N+RM+ +
Sbjct: 8 GKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 70.5 bits (173), Expect = 3e-17
Identities = 24/66 (36%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 11 PRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
PRR R F+ Q LE+ F +Y++ P L+ KL L +QVKIWF+NRR + +
Sbjct: 2 PRRT---RTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
Query: 71 NSKERE 76
++
Sbjct: 59 IQSDQH 64
>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 = 67.7 bits (166), Expect = 3e-16
Identities = 21/55 (38%), Positives = 37/55 (67%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R FS Q L++ F +Y+++ R++L+ +LGL ++Q+KIWF+N+R K + S
Sbjct: 7 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 67.8 bits (166), Expect = 4e-16
Identities = 16/66 (24%), Positives = 28/66 (42%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76
+ S Q L+ F ++ + + + L + GL +V+ WF +RR RN K
Sbjct: 11 YKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSR 70
Query: 77 LLANGG 82
+ G
Sbjct: 71 SGPSSG 76
>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 = 66.6 bits (163), Expect = 6e-16
Identities = 25/56 (44%), Positives = 36/56 (64%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73
R F+ Q LEK F + Y+S+P R +LA +L L +S +K+WFQNRRMK + +
Sbjct: 5 RTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60
>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 = 67.6 bits (165), Expect = 7e-16
Identities = 28/62 (45%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G P R F+ Q LEK F KY+S+ R ++A L L ++QVKIWFQNRRMK
Sbjct: 32 GSPSGL---RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMK 88
Query: 69 WR 70
+
Sbjct: 89 QK 90
>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 = 68.5 bits (167), Expect = 2e-15
Identities = 17/60 (28%), Positives = 28/60 (46%)
Query: 11 PRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
R +R R LEK F + + D +AE+L ++ +++WF NRR K +
Sbjct: 98 LSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
>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 = 66.4 bits (162), Expect = 2e-15
Identities = 16/67 (23%), Positives = 33/67 (49%), Gaps = 3/67 (4%)
Query: 7 DRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRR 66
+ + +R R + Q + L +++ + ++ +A ++GLK V++WFQN R
Sbjct: 13 EPQRDKR---LRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTR 69
Query: 67 MKWRNSK 73
+ R S
Sbjct: 70 ARERKSG 76
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 65.9 bits (161), Expect = 2e-15
Identities = 29/66 (43%), Positives = 39/66 (59%), Gaps = 3/66 (4%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G +R R ++ Q LEK F KYIS+P R +LA L L + +KIWFQNRRMK
Sbjct: 1 GSNKRT---RTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMK 57
Query: 69 WRNSKE 74
W+ ++
Sbjct: 58 WKKEED 63
>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 = 65.5 bits (160), Expect = 2e-15
Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 3/63 (4%)
Query: 10 KPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKW 69
R R F+D Q + L+ F Y + ++L+ L L + +WFQN R K
Sbjct: 6 SGRS---SRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKA 62
Query: 70 RNS 72
R S
Sbjct: 63 RKS 65
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 65.6 bits (160), Expect = 4e-15
Identities = 26/69 (37%), Positives = 42/69 (60%), Gaps = 3/69 (4%)
Query: 2 STTIFDRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIW 61
++T+ G+ +R R ++ Q LEK F +Y+++ R ++A L L + Q+KIW
Sbjct: 19 TSTVNANGETKRQ---RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIW 75
Query: 62 FQNRRMKWR 70
FQNRRMKW+
Sbjct: 76 FQNRRMKWK 84
>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 = 65.2 bits (159), Expect = 4e-15
Identities = 26/62 (41%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G RRG R ++ Q LEK F Y+++ R ++A L L + Q+KIWFQNRRMK
Sbjct: 18 GLRRRG---RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMK 74
Query: 69 WR 70
+
Sbjct: 75 LK 76
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 64.1 bits (156), Expect = 9e-15
Identities = 21/65 (32%), Positives = 37/65 (56%)
Query: 12 RRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71
G +R ++ +Q K LE+ + K+I+K R++++ L + QV IWFQNRR+K +
Sbjct: 5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
Query: 72 SKERE 76
+
Sbjct: 65 VINKL 69
>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 = 66.2 bits (161), Expect = 9e-15
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 3/73 (4%)
Query: 1 MSTTIFDRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKI 60
+ + + R+ RR S + LE+ F S + ++AE+L L+ V++
Sbjct: 77 YNEKVGANERKRK---RRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRV 133
Query: 61 WFQNRRMKWRNSK 73
WF NRR + + K
Sbjct: 134 WFCNRRQREKRVK 146
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 65.8 bits (160), Expect = 2e-14
Identities = 19/73 (26%), Positives = 30/73 (41%), Gaps = 3/73 (4%)
Query: 1 MSTTIFDRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKI 60
I +G+ R+ +R + LE F S + LA+ L L+ V++
Sbjct: 89 NLDKIAAQGRKRK---KRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRV 145
Query: 61 WFQNRRMKWRNSK 73
WF NRR K +
Sbjct: 146 WFCNRRQKEKRMT 158
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex,
helix-turn-helix (HTH), DNA-binding, homeobox, nucleus,
transcription regulation; 2.51A {Homo sapiens}
Length = 151
Score = 65.1 bits (158), Expect = 2e-14
Identities = 17/72 (23%), Positives = 33/72 (45%)
Query: 1 MSTTIFDRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKI 60
+ F G+P + RR F+ + L F+ + + ++A++L V++
Sbjct: 80 QNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRV 139
Query: 61 WFQNRRMKWRNS 72
WF NRR +N+
Sbjct: 140 WFSNRRQTLKNT 151
>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 = 62.4 bits (152), Expect = 4e-14
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 7 DRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRR 66
+R R +D Q + L + F I S+ K++A+K GL +K WF+N
Sbjct: 3 SGSSGKR---PRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTL 59
Query: 67 MKWRNSK 73
K R S
Sbjct: 60 FKERQSG 66
>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 = 61.8 bits (150), Expect = 7e-14
Identities = 22/67 (32%), Positives = 36/67 (53%)
Query: 10 KPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKW 69
G +R +S Q + LE+ + K+I+K R+K++ L + Q+ IWFQNRR+K
Sbjct: 3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKE 62
Query: 70 RNSKERE 76
+ S
Sbjct: 63 KKSGPSS 69
>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 = 61.7 bits (150), Expect = 8e-14
Identities = 23/59 (38%), Positives = 36/59 (61%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76
R ++ Q LEK F +Y+++ R ++A L L + Q+KIWFQNRRMKW+ + +
Sbjct: 6 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 64
>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 = 60.6 bits (147), Expect = 3e-13
Identities = 23/60 (38%), Positives = 34/60 (56%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76
+R ++ Q LEK F Y+++ R ++A L L + QVKIWFQNRRMK + +
Sbjct: 16 KRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR 75
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 62.2 bits (150), Expect = 4e-13
Identities = 19/60 (31%), Positives = 32/60 (53%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76
R VF+D+QR+ L F+ K SK + ++++LGL+ S V +F N R + +
Sbjct: 100 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWLEH 159
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 59.8 bits (145), Expect = 4e-13
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 17 RRAVFSDLQRKGLEKRFQ-IQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73
+ ++ Q + LE F + K+ +A + GL + Q + WF+ R +WR S+
Sbjct: 5 TVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE 62
>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 = 59.2 bits (144), Expect = 5e-13
Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 10/75 (13%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPD---RKKLAEKLGLKDSQVKIWFQNR 65
G RR +R F+ Q + LE FQ +Y PD R+++A L +++V++WF+NR
Sbjct: 1 GSQRR---QRTHFTSQQLQQLEATFQRNRY---PDMSTREEIAVWTNLTEARVRVWFKNR 54
Query: 66 RMKWRNSKERELLAN 80
R KWR +E ++ +
Sbjct: 55 RAKWRK-REEFIVTD 68
>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 = 56.9 bits (138), Expect = 5e-12
Identities = 24/56 (42%), Positives = 35/56 (62%), Gaps = 6/56 (10%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPD---RKKLAEKLGLKDSQVKIWFQNRRMKWR 70
F+ Q + LEK F Y PD R++LA K+GL ++++++WFQNRR KWR
Sbjct: 3 HMTFTSFQLEELEKAFSRTHY---PDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>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 = 57.1 bits (138), Expect = 6e-12
Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 7 DRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRR 66
+R R F Q + ++ F I D K+LA+K GL +++WFQN R
Sbjct: 3 SGSSGKR---MRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNAR 59
Query: 67 MKWRNSKERELLANGGS 83
K+R + R+
Sbjct: 60 AKFRRNLLRQENGGVSG 76
>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 = 56.7 bits (137), Expect = 7e-12
Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 9/64 (14%)
Query: 10 KPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPD---RKKLAEKLGLKDSQVKIWFQNRR 66
RR R F+ Q LE F +Y PD R+++A K+ L +S+V++WF+NRR
Sbjct: 6 SGRR---ERTTFTRAQLDVLEALFAKTRY---PDIFMREEVALKINLPESRVQVWFKNRR 59
Query: 67 MKWR 70
K R
Sbjct: 60 AKCR 63
>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 = 56.4 bits (136), Expect = 8e-12
Identities = 13/65 (20%), Positives = 23/65 (35%), Gaps = 4/65 (6%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQ-IQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRM 67
R R S L+ + Y + L+ +L L + +FQN+R
Sbjct: 5 SSGPR---SRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRY 61
Query: 68 KWRNS 72
++S
Sbjct: 62 HVKHS 66
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 56.6 bits (137), Expect = 9e-12
Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 9/67 (13%)
Query: 7 DRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPD---RKKLAEKLGLKDSQVKIWFQ 63
+R R F+ Q + LEK F+ Y PD R++LA K+ L ++++++WF
Sbjct: 3 SGSSGQR---NRTSFTQEQIEALEKEFERTHY---PDVFARERLAAKIDLPEARIQVWFS 56
Query: 64 NRRMKWR 70
NRR KWR
Sbjct: 57 NRRAKWR 63
>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 = 9e-12
Identities = 18/56 (32%), Positives = 26/56 (46%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
+R + R LE F S +A +LGL+ V++WF NRR K + S
Sbjct: 99 KRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS 154
>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 = 55.4 bits (134), Expect = 2e-11
Identities = 22/59 (37%), Positives = 33/59 (55%), Gaps = 6/59 (10%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPD---RKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73
R F+ Q + LE F++ Y P + LA+KL L+ +++IWFQNRR K + S
Sbjct: 5 RTAFTQNQIEVLENVFRVNCY---PGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH 60
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with
the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 70
Score = 55.4 bits (134), Expect = 2e-11
Identities = 28/64 (43%), Positives = 40/64 (62%), Gaps = 9/64 (14%)
Query: 10 KPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPD---RKKLAEKLGLKDSQVKIWFQNRR 66
RR R +F+D Q + LE FQ KY PD R++LA K+ L++ +V++WF+NRR
Sbjct: 6 SGRR---HRTIFTDEQLEALENLFQETKY---PDVGTREQLARKVHLREEKVEVWFKNRR 59
Query: 67 MKWR 70
KWR
Sbjct: 60 AKWR 63
>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 = 55.4 bits (134), Expect = 2e-11
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 10 KPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKW 69
K R R V ++ Q L + +++L E GL +++WFQN+R K
Sbjct: 2 KTTR---VRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKD 58
Query: 70 R 70
+
Sbjct: 59 K 59
>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 = 55.8 bits (134), Expect = 2e-11
Identities = 13/66 (19%), Positives = 27/66 (40%)
Query: 22 SDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELLANG 81
+ Q K LE F + ++ + +L + L ++ WF RR + ++ L + G
Sbjct: 21 TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAVLDSMG 80
Query: 82 GSREQT 87
+
Sbjct: 81 SGKSGP 86
>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 = 54.4 bits (131), Expect = 5e-11
Identities = 12/57 (21%), Positives = 23/57 (40%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73
+ Q L+ F ++ + +L E GL S++K WF + R + +
Sbjct: 7 HHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRGI 63
>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 = 54.3 bits (131), Expect = 5e-11
Identities = 16/64 (25%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 21 FSDLQRKGLEKRFQ-IQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELLA 79
++ Q + LE F + K+ +A + GL + Q + WF+ R +WR + L +
Sbjct: 8 MTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR--RSEGLPS 65
Query: 80 NGGS 83
S
Sbjct: 66 ECRS 69
>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 = 52.8 bits (127), Expect = 3e-10
Identities = 24/67 (35%), Positives = 39/67 (58%), Gaps = 9/67 (13%)
Query: 7 DRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPD---RKKLAEKLGLKDSQVKIWFQ 63
+ K RR R FS Q LE+ F+ +Y PD R++LA++ L ++++++WFQ
Sbjct: 14 LKRKQRR---SRTTFSASQLDELERAFERTQY---PDIYTREELAQRTNLTEARIQVWFQ 67
Query: 64 NRRMKWR 70
NRR + R
Sbjct: 68 NRRARLR 74
>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 = 51.4 bits (123), Expect = 7e-10
Identities = 11/66 (16%), Positives = 24/66 (36%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76
+ + Q + LE F + +L + + ++ WF RR K + ++
Sbjct: 10 KYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKK 69
Query: 77 LLANGG 82
+ G
Sbjct: 70 SGPSSG 75
>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 = 51.2 bits (122), Expect = 2e-09
Identities = 9/65 (13%), Positives = 25/65 (38%)
Query: 25 QRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELLANGGSR 84
Q + L+ F ++ + +L + L ++ WF ++ +E+ + +
Sbjct: 22 QLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKMEIDESNAG 81
Query: 85 EQTLP 89
+ P
Sbjct: 82 SSSGP 86
>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 = 48.1 bits (114), Expect = 2e-08
Identities = 13/81 (16%), Positives = 24/81 (29%), Gaps = 16/81 (19%)
Query: 9 GKPRRGMMR-RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLG--------------- 52
G R + +E F +Y + R+++A
Sbjct: 1 GSSGSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLER 60
Query: 53 LKDSQVKIWFQNRRMKWRNSK 73
+ +V WF NRR + +
Sbjct: 61 VTSLKVYNWFANRRKEIKRRA 81
>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 = 46.7 bits (111), Expect = 4e-08
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 29 LEKRFQIQ-KYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
LEK F KY + K L+++L +++ WF++RR + + S
Sbjct: 23 LEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPS 67
>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 = 45.9 bits (108), Expect = 1e-07
Identities = 14/61 (22%), Positives = 27/61 (44%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76
+ + Q L+ F ++ S + KLA++ GL + + WF + R W+N +
Sbjct: 28 KICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKW 87
Query: 77 L 77
Sbjct: 88 Y 88
>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 = 41.7 bits (98), Expect = 3e-06
Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 1/45 (2%)
Query: 29 LEKRFQIQ-KYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
LEK F K+ + + L+++L ++ WF+ RR + + S
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS 59
>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 = 39.9 bits (92), Expect = 2e-05
Identities = 16/75 (21%), Positives = 28/75 (37%), Gaps = 4/75 (5%)
Query: 12 RRGMMRRAVFSDLQRKGLEKRFQ----IQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRM 67
+ R FSD L+K + + + + +A +L + V+ W NRR
Sbjct: 6 SGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRR 65
Query: 68 KWRNSKERELLANGG 82
K+R + G
Sbjct: 66 KYRLMGIEVSGPSSG 80
>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 = 39.2 bits (91), Expect = 3e-05
Identities = 11/51 (21%), Positives = 24/51 (47%)
Query: 25 QRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKER 75
Q L+ F ++ + D +KL + GL ++ WF + R ++ + +
Sbjct: 14 QLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK 64
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 37.3 bits (86), Expect = 1e-04
Identities = 9/49 (18%), Positives = 20/49 (40%)
Query: 25 QRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73
L+ + + S + K+A+ + L VK WF+ + + +
Sbjct: 14 LLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQ 62
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain,
hoogsteen base PAIR, transcription/DNA complex; HET:
5IU; 2.10A {Synthetic} SCOP: a.4.1.1
Length = 60
Score = 34.6 bits (80), Expect = 0.001
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
Y+ + L + L Q+K W NRR K +
Sbjct: 25 YLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 33.5 bits (77), Expect = 0.003
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQN-RRMKWRNSKERE 76
Y S+ +K+LA+ GL QV WF N RR + ++
Sbjct: 25 YPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQS 64
>2ys9_A Homeobox and leucine zipper protein homez; homeodomain,
structural genomics, NPPSFA, national project on
protein structural and functional analyses; NMR {Homo
sapiens}
Length = 70
Score = 33.7 bits (76), Expect = 0.004
Identities = 10/44 (22%), Positives = 21/44 (47%)
Query: 25 QRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
+ LE+ + + + + D +L++ L QV WF +R +
Sbjct: 17 DIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQ 60
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 34.0 bits (77), Expect = 0.004
Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 21/81 (25%)
Query: 11 PRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKL------------------- 51
++G R + ++ L + ++ QK SK +R+ L E+
Sbjct: 6 TKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLG 65
Query: 52 --GLKDSQVKIWFQNRRMKWR 70
+ + +V WF NRR +
Sbjct: 66 SNLVTEVRVYNWFANRRKEEA 86
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration
calorimetry, protein-DNA complex, transcription/DNA
complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1
PDB: 1akh_B* 1apl_C* 1yrn_B*
Length = 83
Score = 33.2 bits (76), Expect = 0.005
Identities = 9/38 (23%), Positives = 14/38 (36%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKER 75
Y+ + L + L Q+K W RR K +
Sbjct: 29 YLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTITIA 66
>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding
cooperativity, maltose binding protein, MBP, sugar
binding, DNA binding protein; 2.10A {Escherichia coli}
SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A
Length = 421
Score = 34.4 bits (79), Expect = 0.010
Identities = 16/51 (31%), Positives = 33/51 (64%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
A S R LE+ F+ ++ ++ +++++A+K G+ QV++WF N+RM+
Sbjct: 369 AAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein,
protein/DNA complex; HET: DNA; 2.35A {Homo sapiens}
SCOP: a.4.1.1 PDB: 1lfu_P
Length = 87
Score = 31.7 bits (72), Expect = 0.020
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQN-RRMKWRNSKERELLANGGSREQTLPNKNNPNP 96
Y S+ +++LA+K G+ SQV WF N R +N + + AN + + N +
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEANIYAAKTA-VTATNVSA 86
>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 = 31.8 bits (72), Expect = 0.024
Identities = 10/33 (30%), Positives = 15/33 (45%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
Y+ + L + L Q+K W NRR K +
Sbjct: 54 YLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEK 86
>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 73
Score = 31.2 bits (71), Expect = 0.030
Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQN-RRMKWRNS 72
Y ++ ++K++A + L QV WF N RR ++
Sbjct: 34 YPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSG 69
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 31.3 bits (71), Expect = 0.032
Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQN-RRMKWRNSKERELLANGGSREQTLPNKNNPNP 96
Y S+ ++ L+++ L QV WF N RR + + + T+ +
Sbjct: 32 YPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK---DGKDPNQFTISRRGAKIS 88
Query: 97 D 97
+
Sbjct: 89 E 89
>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein,
X-linked TGF(beta) induced transcription factor 2-like
protein, TGIF-like on the X; NMR {Homo sapiens}
Length = 83
Score = 30.9 bits (70), Expect = 0.037
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQN-RRMKWRNSKERE 76
Y S+ +++ L+EK L Q+ WF N RR + ++
Sbjct: 34 YPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQR 73
>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian,
protein-DNA complex, HOX hexapeptide, TALE homeodomain,
homeodomain interaction; 1.90A {Homo sapiens} SCOP:
a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*
Length = 73
Score = 30.8 bits (70), Expect = 0.041
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQN-RRMKWRNSKERELLAN 80
Y S+ +++LA+K G+ SQV WF N R +N + + AN
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEEAN 71
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 64
Score = 30.4 bits (69), Expect = 0.043
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQN-RRMKWRN 71
Y S+ +++LA+K G+ SQV WF N R +N
Sbjct: 30 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 64
>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices
with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 71
Score = 30.5 bits (68), Expect = 0.046
Identities = 9/51 (17%), Positives = 22/51 (43%)
Query: 23 DLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73
L+ + + + + K++ +GL VK WF+ R++ ++
Sbjct: 14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQYSNS 64
>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational
analysis, G protein, GAS subunit, A2A adenosine
receptor, cell-penetrating peptides; NMR {Synthetic}
PDB: 2o00_A
Length = 37
Score = 29.2 bits (65), Expect = 0.059
Identities = 12/14 (85%), Positives = 14/14 (100%)
Query: 57 QVKIWFQNRRMKWR 70
Q+KIWFQNRRMKW+
Sbjct: 2 QIKIWFQNRRMKWK 15
>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 = 30.6 bits (68), Expect = 0.14
Identities = 17/83 (20%), Positives = 32/83 (38%), Gaps = 21/83 (25%)
Query: 7 DRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKL--------------- 51
D ++G R + ++ L + ++ QK SK +R+ L E+
Sbjct: 108 DELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQA 167
Query: 52 ------GLKDSQVKIWFQNRRMK 68
+ + +V WF NRR +
Sbjct: 168 QGLGSNLVTEVRVYNWFANRRKE 190
>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage,
structural evolution, transcription; 1.40A {Xylella
fastidiosa}
Length = 79
Score = 29.1 bits (65), Expect = 0.19
Identities = 11/46 (23%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 45 KKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELLANGG-SREQTLP 89
LA LG++ S + W R+ + E + NG + P
Sbjct: 15 SALAASLGVRQSAISNWRARGRVPAERCIDIERVTNGAVICRELRP 60
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 30.0 bits (66), Expect = 0.22
Identities = 15/81 (18%), Positives = 28/81 (34%), Gaps = 21/81 (25%)
Query: 7 DRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKL--------------- 51
++ R + ++ L + + QK SK +R+ L E+
Sbjct: 135 SEPTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKA 194
Query: 52 ------GLKDSQVKIWFQNRR 66
+ + +V WF NRR
Sbjct: 195 HGLGSNLVTEVRVYNWFANRR 215
>1jmt_A Splicing factor U2AF 35 kDa subunit; RRM, RNA splicing, proline,
PPII helix, peptide recognition, RNA binding protein;
2.20A {Homo sapiens} SCOP: d.58.7.3
Length = 104
Score = 27.1 bits (60), Expect = 1.4
Identities = 17/63 (26%), Positives = 23/63 (36%), Gaps = 2/63 (3%)
Query: 92 NNPNPDLSDADCDRPKIDLSNVNIDYDEEEEDDLMRPKTKFTDNEAESSEVEDDGDDDEE 151
NP AD R + + YDE E+ + K+ E E V D+ D
Sbjct: 11 RNPQNSSQSADGLRSAVSDVEMQEHYDEFFEEVFTEMEEKY--GEVEEMNVCDNLGDHLV 68
Query: 152 INV 154
NV
Sbjct: 69 GNV 71
>1sez_A Protoporphyrinogen oxidase, mitochondrial; FAD-binding,
para-hydroxy-benzoate-hydroxylase fold (PHBH- fold),
monotopic membrane-binding domain; HET: FAD OMN TON;
2.90A {Nicotiana tabacum} SCOP: c.3.1.2 d.16.1.5
Length = 504
Score = 27.4 bits (60), Expect = 2.2
Identities = 14/44 (31%), Positives = 20/44 (45%)
Query: 40 SKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERELLANGGS 83
S+ D L + LGL++ Q QN+R RN L +N
Sbjct: 72 SEGDVTFLIDSLGLREKQQFPLSQNKRYIARNGTPVLLPSNPID 115
>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A
{Enterobacteria phage lambda}
Length = 236
Score = 26.9 bits (59), Expect = 3.1
Identities = 12/68 (17%), Positives = 27/68 (39%), Gaps = 5/68 (7%)
Query: 16 MRRAVFSDLQRKGLEK---RFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
++ + Q + + ++ +K ++ +A+K+G+ S V F N+
Sbjct: 2 TKKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINA--LNA 59
Query: 73 KERELLAN 80
LLA
Sbjct: 60 YNAALLAK 67
>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 = 26.6 bits (58), Expect = 5.3
Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 16/59 (27%)
Query: 100 DADCDRPKIDLSNVNIDYD---------------EEEEDDLMRPKTKFTDNEAESSEVE 143
DA RP + LS+ ++++ E+ L P F ++ ++ E
Sbjct: 2 DAYSTRP-LTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAE 59
>2der_A TRNA-specific 2-thiouridylase MNMA; protein-RNA complex,
transferase/RNA complex; 3.10A {Escherichia coli} PDB:
2det_A 2deu_A*
Length = 380
Score = 26.0 bits (58), Expect = 5.8
Identities = 11/24 (45%), Positives = 14/24 (58%), Gaps = 5/24 (20%)
Query: 39 ISKPDRKKLAEKLGL-----KDSQ 57
+ KP +K+AE LGL KDS
Sbjct: 185 LEKPQVRKIAEDLGLVTAKKKDST 208
>2hma_A Probable tRNA (5-methylaminomethyl-2-thiouridylat
methyltransferase; alpha-beta, beta barrel, structural
genomics, PSI-2; HET: MSE SAM; 2.41A {Streptococcus
pneumoniae}
Length = 376
Score = 25.6 bits (57), Expect = 7.4
Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 5/24 (20%)
Query: 39 ISKPDRKKLAEKLGL-----KDSQ 57
+ KP+ ++LAE+ GL KDS
Sbjct: 177 LEKPEVRRLAEEAGLSTAKKKDST 200
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 0.131 0.373
Gapped
Lambda K H
0.267 0.0686 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,447,545
Number of extensions: 139286
Number of successful extensions: 515
Number of sequences better than 10.0: 1
Number of HSP's gapped: 495
Number of HSP's successfully gapped: 109
Length of query: 155
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 69
Effective length of database: 4,300,587
Effective search space: 296740503
Effective search space used: 296740503
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: 53 (24.3 bits)