RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15889
(92 letters)
>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 = 52.3 bits (126), Expect = 6e-11
Identities = 20/36 (55%), Positives = 23/36 (63%), Gaps = 5/36 (13%)
Query: 1 MGELMALWL-----RVRVWFKNRRAKWRKRERNAMN 31
E +A+W RVRVWFKNRRAKWRKRE +
Sbjct: 32 TREEIAVWTNLTEARVRVWFKNRRAKWRKREEFIVT 67
>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 = 50.8 bits (122), Expect = 3e-10
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 5/33 (15%)
Query: 1 MGELMALWL-----RVRVWFKNRRAKWRKRERN 28
E +A R++VWF+NRRA+ RK+ +
Sbjct: 47 TREELAQRTNLTEARIQVWFQNRRARLRKQHTS 79
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein,
DNA-binding, N gene regulation; 1.00A {Drosophila
melanogaster} PDB: 3lnq_A 3cmy_A
Length = 60
Score = 49.2 bits (118), Expect = 6e-10
Identities = 15/30 (50%), Positives = 23/30 (76%), Gaps = 5/30 (16%)
Query: 3 ELMALWL-----RVRVWFKNRRAKWRKRER 27
E +A+ + R++VWF+NRRAKWRK+E+
Sbjct: 30 EELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>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 = 49.7 bits (119), Expect = 6e-10
Identities = 17/41 (41%), Positives = 25/41 (60%), Gaps = 5/41 (12%)
Query: 1 MGELMALWL-----RVRVWFKNRRAKWRKRERNAMNAAAAA 36
M E +AL + RV+VWFKNRRAK R++++ N +
Sbjct: 36 MREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGGQSG 76
>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 = 48.5 bits (116), Expect = 2e-09
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 5/34 (14%)
Query: 1 MGELMALWL-----RVRVWFKNRRAKWRKRERNA 29
E +A + +V VWFKNRRAKWR+ ++
Sbjct: 36 TREQLARKVHLREEKVEVWFKNRRAKWRRSGPSS 69
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 48.5 bits (116), Expect = 2e-09
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 10 RVRVWFKNRRAKWRKRERNAMNAAAAAA 37
R++VWF NRRAKWR+ E+ +
Sbjct: 50 RIQVWFSNRRAKWRREEKLRNQRRQSGP 77
>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 = 48.1 bits (115), Expect = 3e-09
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 10 RVRVWFKNRRAKWRKRERNA 29
R+++WF+NRRAK ++ R +
Sbjct: 44 RIQIWFQNRRAKLKRSHRES 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 = 47.4 bits (113), Expect = 5e-09
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 5/30 (16%)
Query: 3 ELMALWL-----RVRVWFKNRRAKWRKRER 27
L+A + + WFK R A+WR+ E
Sbjct: 33 CLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 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 = 46.2 bits (110), Expect = 1e-08
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 10 RVRVWFKNRRAKWRKRER 27
+RVWF+N+R K +KR
Sbjct: 46 VIRVWFQNKRCKDKKRSI 63
>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 = 45.9 bits (109), Expect = 2e-08
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 10 RVRVWFKNRRAKWRKRERNAMNAAAAA 36
++VWF+N RAK+R+ N +
Sbjct: 50 VLQVWFQNARAKFRRNLLRQENGGVSG 76
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 45.5 bits (108), Expect = 3e-08
Identities = 10/30 (33%), Positives = 15/30 (50%), Gaps = 5/30 (16%)
Query: 3 ELMALWL-----RVRVWFKNRRAKWRKRER 27
L+A + + WFK R A+WR+ E
Sbjct: 34 CLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 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 = 44.3 bits (105), Expect = 8e-08
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 10 RVRVWFKNRRAKWRKRERNA 29
+ VWF+N R K RK ++
Sbjct: 50 VIVVWFQNARQKARKSGPSS 69
>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 = 44.0 bits (104), Expect = 1e-07
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 10 RVRVWFKNRRAKWRKRERNA 29
V+VWF+N RA+ RK ++
Sbjct: 60 VVQVWFQNTRARERKSGPSS 79
>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 = 43.1 bits (102), Expect = 2e-07
Identities = 5/20 (25%), Positives = 11/20 (55%)
Query: 10 RVRVWFKNRRAKWRKRERNA 29
++ WF+N K R+ ++
Sbjct: 50 VIKHWFRNTLFKERQSGPSS 69
>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 = 43.5 bits (102), Expect = 3e-07
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 10 RVRVWFKNRRAKWRKRERNAMNAAA 34
+V WF NRR + ++R A +
Sbjct: 65 KVYNWFANRRKEIKRRANIAAILES 89
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 41.3 bits (97), Expect = 1e-06
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 10 RVRVWFKNRRAKWRKRERNAMNAAAA 35
VR WF +RR R + + ++
Sbjct: 51 EVRKWFSDRRYHCRNLKGSRSGPSSG 76
>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 = 40.8 bits (95), Expect = 7e-06
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 10 RVRVWFKNRRAKWRK 24
VRVWF NRR +
Sbjct: 136 VVRVWFSNRRQTLKN 150
>1lfb_A Liver transcription factor (LFB1); transcription regulation;
2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 39.0 bits (90), Expect = 1e-05
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 9 LRVRVWFKNRRAKWRKRERNAMNA 32
+RV WF NRR + R + AM+
Sbjct: 72 VRVYNWFANRRKEEAFRHKLAMDT 95
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 39.6 bits (92), Expect = 2e-05
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 10 RVRVWFKNRRAKWRKRERNA 29
VRVWF NRR K ++ A
Sbjct: 142 VVRVWFCNRRQKEKRMTPAA 161
>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 = 38.4 bits (89), Expect = 4e-05
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 10 RVRVWFKNRRAKWRK 24
VRVWF NRR + ++
Sbjct: 130 VVRVWFCNRRQREKR 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 = 37.8 bits (87), Expect = 9e-05
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 10 RVRVWFKNRRAKWRK 24
VRVWF NRR K ++
Sbjct: 139 VVRVWFSNRRQKGKR 153
>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 = 37.3 bits (86), Expect = 1e-04
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 10 RVRVWFKNRRAKWRK 24
+RVWF NRR K ++
Sbjct: 144 VIRVWFSNRRQKEKR 158
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 36.0 bits (83), Expect = 2e-04
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 11 VRVWFKNRRAKWRKRERNAMNAAAAAA 37
V+ WF+NRR KWR++ A AA
Sbjct: 61 VKTWFQNRRTKWRRQTAEEREAERQAA 87
>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 = 34.0 bits (78), Expect = 7e-04
Identities = 3/19 (15%), Positives = 10/19 (52%)
Query: 10 RVRVWFKNRRAKWRKRERN 28
++ WF + R + ++ +
Sbjct: 47 EIKKWFSDHRYRCQRGIVH 65
>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 = 34.2 bits (78), Expect = 0.001
Identities = 5/26 (19%), Positives = 11/26 (42%)
Query: 10 RVRVWFKNRRAKWRKRERNAMNAAAA 35
+ WF RR E+ +++ +
Sbjct: 56 EIDSWFSERRKLRDSMEQAVLDSMGS 81
>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 = 33.3 bits (77), Expect = 0.001
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 11 VRVWFKNRRAKWR 23
VRVWF N+R + +
Sbjct: 49 VRVWFINKRMRSK 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 = 33.5 bits (77), Expect = 0.001
Identities = 7/21 (33%), Positives = 13/21 (61%)
Query: 11 VRVWFKNRRAKWRKRERNAMN 31
V++WFKNRR + + + +
Sbjct: 46 VKIWFKNRRRRHKIQSDQHKD 66
>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 = 32.9 bits (75), Expect = 0.002
Identities = 3/16 (18%), Positives = 8/16 (50%)
Query: 10 RVRVWFKNRRAKWRKR 25
+ +F+N+R +
Sbjct: 51 TIIKFFQNQRYHVKHS 66
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 32.3 bits (74), Expect = 0.002
Identities = 9/15 (60%), Positives = 13/15 (86%)
Query: 11 VRVWFKNRRAKWRKR 25
V+ WF+NRR KWR++
Sbjct: 41 VKTWFQNRRTKWRRQ 55
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for
eukaryotic structural genomics; NMR {Homo sapiens}
Length = 84
Score = 32.9 bits (75), Expect = 0.002
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 11 VRVWFKNRRAKWRKRERN 28
V+ WF+N+R K ++ ++N
Sbjct: 66 VKTWFQNQRMKSKRWQKN 83
>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 = 32.4 bits (74), Expect = 0.003
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 11 VRVWFKNRRAKWRKRERNA 29
V+ WF+NRRAKWR+ ++
Sbjct: 51 VKTWFQNRRAKWRRSGPSS 69
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast
structural genomics consortiu PSI-biology, protein
structure initiative; NMR {Homo sapiens}
Length = 69
Score = 32.3 bits (74), Expect = 0.003
Identities = 7/19 (36%), Positives = 16/19 (84%)
Query: 11 VRVWFKNRRAKWRKRERNA 29
V++WF+NRR K ++++ ++
Sbjct: 48 VKIWFQNRRYKTKRKQLSS 66
>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 = 32.9 bits (75), Expect = 0.003
Identities = 11/17 (64%), Positives = 15/17 (88%)
Query: 11 VRVWFKNRRAKWRKRER 27
V++WF+NRR K +KRER
Sbjct: 78 VKIWFQNRRMKQKKRER 94
>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 = 32.1 bits (73), Expect = 0.004
Identities = 8/19 (42%), Positives = 14/19 (73%)
Query: 11 VRVWFKNRRAKWRKRERNA 29
V+ W++NRR KW+K ++
Sbjct: 61 VKTWYQNRRMKWKKSGPSS 79
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein,
transcription regulation, NUC homeobox; 2.6A {Mus
musculus}
Length = 62
Score = 31.9 bits (73), Expect = 0.004
Identities = 6/16 (37%), Positives = 12/16 (75%)
Query: 11 VRVWFKNRRAKWRKRE 26
V+ WF+N+R K ++ +
Sbjct: 47 VKTWFQNQRMKCKRWQ 62
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 31.4 bits (72), Expect = 0.005
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 11 VRVWFKNRRAKWRK 24
V++WF+NRRAK ++
Sbjct: 44 VKIWFQNRRAKAKR 57
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 32.1 bits (73), Expect = 0.005
Identities = 8/17 (47%), Positives = 14/17 (82%)
Query: 11 VRVWFKNRRAKWRKRER 27
+++WF+NRR KW+K +
Sbjct: 72 IKIWFQNRRMKWKKEHK 88
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 31.9 bits (73), Expect = 0.005
Identities = 6/18 (33%), Positives = 14/18 (77%)
Query: 11 VRVWFKNRRAKWRKRERN 28
V++WF+N R K +++ ++
Sbjct: 46 VKIWFQNHRYKMKRQAKD 63
>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 = 32.0 bits (73), Expect = 0.005
Identities = 6/17 (35%), Positives = 12/17 (70%)
Query: 11 VRVWFKNRRAKWRKRER 27
V++WF+N R K ++ +
Sbjct: 53 VKIWFQNHRYKTKRAQN 69
>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 = 31.5 bits (72), Expect = 0.005
Identities = 8/14 (57%), Positives = 13/14 (92%)
Query: 11 VRVWFKNRRAKWRK 24
+++WFKN+RAK +K
Sbjct: 47 IKIWFKNKRAKIKK 60
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 31.6 bits (72), Expect = 0.006
Identities = 7/18 (38%), Positives = 14/18 (77%)
Query: 11 VRVWFKNRRAKWRKRERN 28
V++WF+N+R+K +K +
Sbjct: 51 VKIWFQNKRSKIKKSGPS 68
>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 = 31.8 bits (72), Expect = 0.006
Identities = 6/25 (24%), Positives = 9/25 (36%)
Query: 10 RVRVWFKNRRAKWRKRERNAMNAAA 34
+ WF RR K E ++
Sbjct: 50 EIDSWFSERRKKVNAEETKKSGPSS 74
>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 = 31.6 bits (72), Expect = 0.007
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 11 VRVWFKNRRAKWRKRERN 28
+++WF+NRR KW+K +
Sbjct: 46 IKIWFQNRRMKWKKENKT 63
>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 = 31.3 bits (71), Expect = 0.008
Identities = 7/17 (41%), Positives = 13/17 (76%)
Query: 11 VRVWFKNRRAKWRKRER 27
+++WF+NRR K +K +
Sbjct: 64 IKIWFQNRRMKLKKEIQ 80
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA
complex, transcription/DNA complex; 2.00A {Drosophila
melanogaster} SCOP: a.4.1.1
Length = 60
Score = 30.8 bits (70), Expect = 0.010
Identities = 7/16 (43%), Positives = 13/16 (81%)
Query: 11 VRVWFKNRRAKWRKRE 26
++VWF+NRR K +++
Sbjct: 45 IKVWFQNRRMKDKRQR 60
>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 = 30.6 bits (69), Expect = 0.013
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 11 VRVWFKNRRAKWRKRERN 28
+ +WF+NRR K +K +
Sbjct: 51 ITIWFQNRRVKEKKSGPS 68
>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 = 30.6 bits (69), Expect = 0.016
Identities = 8/18 (44%), Positives = 14/18 (77%)
Query: 11 VRVWFKNRRAKWRKRERN 28
V++WF+NRR K +K ++
Sbjct: 57 VKIWFQNRRMKMKKINKD 74
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain;
protein-DNA complex, transcription/DNA complex; 2.42A
{Mesocricetus auratus}
Length = 63
Score = 30.0 bits (68), Expect = 0.019
Identities = 9/16 (56%), Positives = 14/16 (87%)
Query: 11 VRVWFKNRRAKWRKRE 26
+++WF+NRR KW+K E
Sbjct: 47 IKIWFQNRRMKWKKEE 62
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 31.4 bits (70), Expect = 0.020
Identities = 4/18 (22%), Positives = 7/18 (38%)
Query: 10 RVRVWFKNRRAKWRKRER 27
V +F N R + +
Sbjct: 140 TVSNFFMNARRRSLDKWL 157
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens}
PDB: 2ld5_A*
Length = 73
Score = 30.2 bits (68), Expect = 0.025
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 11 VRVWFKNRRAKWRKRER 27
V +WF+NRR K +K
Sbjct: 51 VTIWFQNRRVKEKKVIN 67
>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 = 0.026
Identities = 10/19 (52%), Positives = 16/19 (84%)
Query: 10 RVRVWFKNRRAKWRKRERN 28
++++WF+NRR KW+KR N
Sbjct: 2 QIKIWFQNRRMKWKKRVFN 20
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 29.5 bits (67), Expect = 0.033
Identities = 7/13 (53%), Positives = 11/13 (84%)
Query: 11 VRVWFKNRRAKWR 23
V++WF+NRR K +
Sbjct: 46 VKIWFQNRRYKSK 58
>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 = 29.6 bits (66), Expect = 0.046
Identities = 3/22 (13%), Positives = 7/22 (31%)
Query: 10 RVRVWFKNRRAKWRKRERNAMN 31
+ WF ++ +E
Sbjct: 54 EIDAWFTEKKKSKALKEEKMEI 75
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 30.4 bits (67), Expect = 0.050
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 10 RVRVWFKNRRAKWRKR 25
RV WF NRR + R
Sbjct: 206 RVYNWFANRRKEEAFR 221
>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 = 30.2 bits (67), Expect = 0.060
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 10 RVRVWFKNRRAKWRKR 25
RV WF NRR + R
Sbjct: 179 RVYNWFANRRKEEAFR 194
>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 = 27.5 bits (61), Expect = 0.26
Identities = 4/15 (26%), Positives = 11/15 (73%)
Query: 10 RVRVWFKNRRAKWRK 24
+++ WF++RR + +
Sbjct: 52 KIQCWFRHRRNQDKP 66
>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 = 28.5 bits (63), Expect = 0.30
Identities = 11/64 (17%), Positives = 21/64 (32%), Gaps = 8/64 (12%)
Query: 11 VRVWFKNRRAKWRKRERNAMNAAAAAAVDFKNGFSTQFNGLMQ-----TFPDTDSLYTSA 65
++ + R R ++ + +A A + F G Q F + LY +
Sbjct: 123 IKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG--QGNTDDYFEELRDLYQT- 179
Query: 66 YSSY 69
Y
Sbjct: 180 YHVL 183
Score = 25.4 bits (55), Expect = 3.4
Identities = 14/62 (22%), Positives = 21/62 (33%), Gaps = 19/62 (30%)
Query: 34 AAAAVDFKNGFSTQFNGLMQ------TFPDTDSLYTSAYSSYNNWASKVPSPLGTIGVND 87
+D + F+ N +++ PD D L + S PL IGV
Sbjct: 199 IRTTLDAEKVFTQGLN-ILEWLENPSNTPDKDYLLSIPIS----C------PL--IGVIQ 245
Query: 88 LG 89
L
Sbjct: 246 LA 247
>2x7l_M HIV REV; nuclear export, immune system, post-transcriptional
regulation; 3.17A {Human immunodeficiency virus type 3}
Length = 115
Score = 26.8 bits (60), Expect = 0.72
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 16 KNRRAKWRKRER 27
+NRR +WR+R+R
Sbjct: 38 RNRRRRWRERQR 49
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 25.8 bits (56), Expect = 1.1
Identities = 4/17 (23%), Positives = 8/17 (47%)
Query: 11 VRVWFKNRRAKWRKRER 27
V+ WF+ +A +
Sbjct: 47 VKKWFEKMQAGQISVQS 63
>3lph_A Protein REV; helix-loop-helix, RNA-binding arginine rich motif,
protein oligomerization, AIDS, HOST cytoplasm, HOST
nucleus; 2.50A {Human immunodeficiency virus type 1}
Length = 72
Score = 24.9 bits (55), Expect = 1.9
Identities = 7/12 (58%), Positives = 11/12 (91%)
Query: 16 KNRRAKWRKRER 27
+NRR +WR+R+R
Sbjct: 41 RNRRRRWRERQR 52
>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 = 25.3 bits (54), Expect = 2.1
Identities = 8/19 (42%), Positives = 9/19 (47%)
Query: 11 VRVWFKNRRAKWRKRERNA 29
VR W NRR K+R
Sbjct: 56 VRTWIGNRRRKYRLMGIEV 74
>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 = 24.8 bits (54), Expect = 2.4
Identities = 4/15 (26%), Positives = 9/15 (60%)
Query: 10 RVRVWFKNRRAKWRK 24
++ WF+ RR + +
Sbjct: 44 SIQRWFRQRRNQEKP 58
>2am1_A SP protein, UDP-N-acetylmuramoylalanine-D-glutamyl-lysine-D-A
alanine ligase, MURF protein; HET: 1LG; 2.50A
{Streptococcus pneumoniae} PDB: 2am2_A*
Length = 454
Score = 25.6 bits (57), Expect = 2.5
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 28 NAMNAAAAAAV 38
NA NA A+ V
Sbjct: 274 NATNAMIASYV 284
>1gg4_A UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-
diaminopimelate-D-alanyl-D-alanyl ligase...; alpha/beta
sheet; 2.30A {Escherichia coli} SCOP: c.98.1.1 c.59.1.1
c.72.2.1
Length = 452
Score = 25.6 bits (57), Expect = 2.7
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 28 NAMNAAAAAAV 38
N NA AAAA+
Sbjct: 282 NIANALAAAAL 292
>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 = 25.1 bits (54), Expect = 2.9
Identities = 4/14 (28%), Positives = 7/14 (50%)
Query: 11 VRVWFKNRRAKWRK 24
+ WF + R W+
Sbjct: 69 IVSWFGDTRYAWKN 82
>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 = 24.8 bits (53), Expect = 3.2
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 9 LRVRVWFKNRRAKWRKRERNAMNAA 33
+RV WF NRR + R++ AM+A
Sbjct: 69 VRVYNWFANRRKEEAFRQKLAMDAY 93
>3ckk_A TRNA (guanine-N(7)-)-methyltransferase; mettl1,
S-adenosyl-L-methionine, tRNA Pro structural genomics,
structural genomics consortium, SGC; HET: SAM; 1.55A
{Homo sapiens}
Length = 235
Score = 25.0 bits (55), Expect = 3.5
Identities = 5/10 (50%), Positives = 6/10 (60%)
Query: 14 WFKNRRAKWR 23
FK + KWR
Sbjct: 135 HFKRTKHKWR 144
>2vdv_E TRNA (guanine-N(7)-)-methyltransferase; S-adenosyl-L-methionine,
phosphorylation, M7G, spout MT, tRNA processing; HET:
SAM; 2.30A {Saccharomyces cerevisiae} PDB: 2vdu_E
Length = 246
Score = 24.7 bits (54), Expect = 4.7
Identities = 5/10 (50%), Positives = 6/10 (60%)
Query: 14 WFKNRRAKWR 23
FK R+ K R
Sbjct: 140 HFKQRKHKAR 149
>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain
cytoplasmic; motor protein, AAA+ protein, ASCE protein,
P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma
japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A
Length = 2695
Score = 24.8 bits (54), Expect = 5.1
Identities = 8/43 (18%), Positives = 12/43 (27%), Gaps = 1/43 (2%)
Query: 44 FSTQFNGLMQTFPDTDSLYTSAYSSYNNWASKVPSPLGTIGVN 86
F+ L +P SL Y Y K+ +
Sbjct: 1406 FTRHAAILYLGYPSGKSLSQ-IYEIYYKAIFKLVPEFRSYTEP 1447
>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 = 24.0 bits (51), Expect = 5.2
Identities = 5/18 (27%), Positives = 9/18 (50%)
Query: 11 VRVWFKNRRAKWRKRERN 28
V+ WF+ R+ R+
Sbjct: 49 VKEWFEQRKVYQYSNSRS 66
>3ltl_A Brefeldin A-inhibited guanine nucleotide-exchange 1; all alpha,
guanine-nucleotide releasing factor, signaling PR; 2.20A
{Homo sapiens} PDB: 3l8n_A 3swv_A
Length = 211
Score = 24.3 bits (53), Expect = 5.9
Identities = 8/27 (29%), Positives = 12/27 (44%), Gaps = 3/27 (11%)
Query: 44 FSTQF---NGLMQTFPDTDSLYTSAYS 67
F+ ++ N F D+ Y AYS
Sbjct: 124 FAARYLECNQGQTLFASADTAYVLAYS 150
>3hn7_A UDP-N-acetylmuramate-L-alanine ligase; ATP-binding,
nucleotide-binding, structural genomics, joint for
structural genomics, JCSG; HET: MSE; 1.65A
{Psychrobacter arcticus 273-4}
Length = 524
Score = 24.6 bits (54), Expect = 6.3
Identities = 5/11 (45%), Positives = 5/11 (45%)
Query: 28 NAMNAAAAAAV 38
N NA A A
Sbjct: 343 NVNNALVAIAA 353
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 24.0 bits (51), Expect = 7.9
Identities = 5/22 (22%), Positives = 9/22 (40%)
Query: 14 WFKNRRAKWRKRERNAMNAAAA 35
W + + + K + N A A
Sbjct: 123 WNQRQSEQVEKNKINNRIADKA 144
>1j6u_A UDP-N-acetylmuramate-alanine ligase MURC; structural genomics,
TM0231, JCSG, PSI, protein structure initiative; 2.30A
{Thermotoga maritima} SCOP: c.5.1.1 c.59.1.1 c.72.2.1
Length = 469
Score = 24.0 bits (53), Expect = 7.9
Identities = 5/11 (45%), Positives = 7/11 (63%)
Query: 28 NAMNAAAAAAV 38
N +NA A A+
Sbjct: 278 NVLNALAVIAL 288
>3mfd_A D-alanyl-D-alanine carboxypeptidase DACB; penicillin-binding
protein 5*, beta-lactamase, structural GE PSI-2, protein
structure initiative; HET: CIT; 1.75A {Bacillus
subtilis}
Length = 334
Score = 24.1 bits (53), Expect = 8.2
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 11/40 (27%)
Query: 30 MNAAAAAAVDFKNGFSTQF---NGLMQTFPDTDSLYTSAY 66
MN A + KN T+F +GL D ++ Y++AY
Sbjct: 114 MNQKAEQ-LGMKN---TRFQNPHGL----DDHENHYSTAY 145
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
0.319 0.129 0.408
Gapped
Lambda K H
0.267 0.0625 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,465,891
Number of extensions: 70761
Number of successful extensions: 233
Number of sequences better than 10.0: 1
Number of HSP's gapped: 233
Number of HSP's successfully gapped: 86
Length of query: 92
Length of database: 6,701,793
Length adjustment: 59
Effective length of query: 33
Effective length of database: 5,054,454
Effective search space: 166796982
Effective search space used: 166796982
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (23.6 bits)