RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14571
(123 letters)
>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 = 71.1 bits (174), Expect = 2e-17
Identities = 36/57 (63%), Positives = 45/57 (78%)
Query: 63 PPSAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
P +A +S+ + RTNFT +QLTELEKEFHFNKYL+RARR+EIA+ L+LNETQ
Sbjct: 21 PKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQ 77
>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 = 66.2 bits (162), Expect = 4e-16
Identities = 20/41 (48%), Positives = 26/41 (63%)
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT FT QL LEKEF+ Y++R RR E+A+ L L E+
Sbjct: 4 YRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPEST 44
>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 = 65.8 bits (161), Expect = 6e-16
Identities = 20/41 (48%), Positives = 30/41 (73%)
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F+++QL L++EF+ N+YLT RR +++S L LNE Q
Sbjct: 6 PRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 46
>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 = 64.0 bits (156), Expect = 3e-15
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT FT+ Q+ ELE+ F +YLT R ++++ L L Q
Sbjct: 5 TRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQ 45
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 64.1 bits (156), Expect = 6e-15
Identities = 27/41 (65%), Positives = 30/41 (73%)
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT++T Q ELEKEFHFN+YLTR RRIEIA L L E Q
Sbjct: 31 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQ 71
>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 = 63.7 bits (155), Expect = 7e-15
Identities = 26/51 (50%), Positives = 29/51 (56%)
Query: 69 SQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
+ L GR +T Q ELEKEFH N YLTR RRIE+A L L E Q
Sbjct: 13 IAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQ 63
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA
complex, transcription/DNA complex; 2.42A {Mesocricetus
auratus}
Length = 63
Score = 62.4 bits (152), Expect = 1e-14
Identities = 23/41 (56%), Positives = 29/41 (70%)
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT +T QL ELEKEF FNKY++R RR+E+A +L L E
Sbjct: 6 TRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERH 46
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 70
Score = 61.7 bits (150), Expect = 3e-14
Identities = 19/41 (46%), Positives = 26/41 (63%)
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
G+ F+N Q ELEK+F KYL+ R +A +LQL+E Q
Sbjct: 10 GQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQ 50
>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 = 60.9 bits (148), Expect = 5e-14
Identities = 27/45 (60%), Positives = 30/45 (66%)
Query: 75 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
+ GR +T Q ELEKEFHFN+YLTR RRIEIA L L E Q
Sbjct: 1 MRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQ 45
>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 = 60.2 bits (146), Expect = 1e-13
Identities = 19/40 (47%), Positives = 24/40 (60%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT FT QL LEK F KYL+ RI++A L L++ Q
Sbjct: 21 RTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQ 60
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 58.0 bits (141), Expect = 6e-13
Identities = 20/40 (50%), Positives = 25/40 (62%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT FT QL LE++F +YL+ A R E +S L L ETQ
Sbjct: 4 RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQ 43
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 56.3 bits (136), Expect = 4e-12
Identities = 15/40 (37%), Positives = 24/40 (60%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT +++ QL L++ F +YL R E+A+ L L +TQ
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQ 50
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative; NMR {Homo sapiens}
Length = 69
Score = 55.8 bits (135), Expect = 5e-12
Identities = 15/40 (37%), Positives = 25/40 (62%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
++ ++ Q+ ELE++F KYL+ R +A L+L ETQ
Sbjct: 8 HSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQ 47
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 56.0 bits (135), Expect = 7e-12
Identities = 19/41 (46%), Positives = 25/41 (60%)
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT+FT Q+ ELEK FH KYL A R +A L++ + Q
Sbjct: 20 PRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQ 60
>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 = 54.9 bits (132), Expect = 2e-11
Identities = 23/41 (56%), Positives = 26/41 (63%)
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
R +T Q ELEKEF FN YLTR RR E+A +L L E Q
Sbjct: 16 KRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQ 56
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein, transcription
regulation, NUC homeobox; 2.6A {Mus musculus}
Length = 62
Score = 54.6 bits (132), Expect = 2e-11
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F+ QL L+ F KYL+ + E++S+L L+ Q
Sbjct: 7 RTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQ 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 = 54.5 bits (131), Expect = 2e-11
Identities = 15/41 (36%), Positives = 27/41 (65%)
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
R ++ QL ELE+E+ NK++T+ +R +I++ L+E Q
Sbjct: 10 KRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQ 50
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 53.5 bits (129), Expect = 4e-11
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 81 TNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
T+F+ Q+ ELE+ F KYL A R +A L++ + Q
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQ 40
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 53.0 bits (128), Expect = 6e-11
Identities = 17/40 (42%), Positives = 25/40 (62%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
R F+ Q+ ELE+ F +YL+ R ++ASVL+L TQ
Sbjct: 6 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQ 45
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for eukaryotic
structural genomics; NMR {Homo sapiens}
Length = 84
Score = 51.7 bits (124), Expect = 3e-10
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F++ QL L F KYL+ + E++++L L+ Q
Sbjct: 26 RTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQ 65
>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 = 50.9 bits (122), Expect = 5e-10
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
R FT Q ELE+ F +YL+ R +AS+++L TQ
Sbjct: 13 RVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQ 52
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB:
2ld5_A*
Length = 73
Score = 50.2 bits (120), Expect = 1e-09
Identities = 16/41 (39%), Positives = 26/41 (63%)
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
R +T QL ELE+E+ NK++T+ +R I++ L+E Q
Sbjct: 10 KRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQ 50
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 50.0 bits (120), Expect = 1e-09
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
R F+ Q+ ELE+ F KYL+ R +AS++ L TQ
Sbjct: 6 RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQ 45
>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 = 48.0 bits (115), Expect = 4e-09
Identities = 7/40 (17%), Positives = 17/40 (42%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
+++ + + LE+ F + L + E+A + Q
Sbjct: 9 KSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQ 48
>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 = 44.2 bits (104), Expect = 1e-06
Identities = 11/40 (27%), Positives = 15/40 (37%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT+ LEK F N+ T IA L + +
Sbjct: 105 RTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEV 144
>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 = 38.8 bits (91), Expect = 2e-05
Identities = 15/38 (39%), Positives = 18/38 (47%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
FT+ QL ELEK F Y R E+A + L E
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTE 40
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 40.8 bits (95), Expect = 2e-05
Identities = 10/58 (17%), Positives = 15/58 (25%)
Query: 62 YPPSAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
P+ RT+ LE F + +A LQL +
Sbjct: 85 GSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEV 142
>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 = 38.5 bits (90), Expect = 3e-05
Identities = 12/40 (30%), Positives = 19/40 (47%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT FT+ QL L+ F N Y +++++L L
Sbjct: 11 RTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRV 50
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 38.6 bits (90), Expect = 4e-05
Identities = 7/42 (16%), Positives = 20/42 (47%)
Query: 78 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
+ +++QL+ L+ F N++ ++ + V L+ +
Sbjct: 10 IYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTRE 51
>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 = 38.1 bits (89), Expect = 4e-05
Identities = 13/38 (34%), Positives = 16/38 (42%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT FT Q+ LE F N Y ++A L L
Sbjct: 5 RTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLEL 42
>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 = 39.2 bits (91), Expect = 6e-05
Identities = 8/40 (20%), Positives = 15/40 (37%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT + LE+ F + + + +A L L +
Sbjct: 91 RTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEV 130
>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 = 36.9 bits (86), Expect = 1e-04
Identities = 17/38 (44%), Positives = 23/38 (60%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT+FT++QL +LE F N+Y + R EIA L E
Sbjct: 7 RTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTE 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 = 37.1 bits (86), Expect = 1e-04
Identities = 11/38 (28%), Positives = 18/38 (47%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT T +QL L +++ + TR IA + L +
Sbjct: 21 RTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKK 58
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 36.6 bits (85), Expect = 1e-04
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 1/42 (2%)
Query: 80 RTNFTNKQLTELEKEFH-FNKYLTRARRIEIASVLQLNETQT 120
+ T Q+ LE F+ NK+ IA+ L E QT
Sbjct: 6 VSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQT 47
>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 = 38.1 bits (88), Expect = 3e-04
Identities = 20/78 (25%), Positives = 33/78 (42%), Gaps = 21/78 (26%)
Query: 40 LGVHPHPTSPSTDYTTPLTALKYPPSAALSQHQSLLNNSGR-------TNFTNKQLTELE 92
+GV + P T+L PPS SL NN G +N T +Q+ +
Sbjct: 306 IGVRCY-------EAYPNTSL--PPSI---LEDSLENNEGVPSPMLSISNLTQEQVQDYV 353
Query: 93 KEFHFNKYLTRARRIEIA 110
+ N +L +++EI+
Sbjct: 354 NKT--NSHLPAGKQVEIS 369
>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 = 35.8 bits (83), Expect = 3e-04
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT F+ QL ELE+ F +Y R E+A L E
Sbjct: 22 RTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTE 59
>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 = 35.4 bits (82), Expect = 4e-04
Identities = 15/38 (39%), Positives = 20/38 (52%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT FT++QL LE F KY R ++A + L E
Sbjct: 11 RTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLRE 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 = 35.9 bits (83), Expect = 4e-04
Identities = 9/38 (23%), Positives = 16/38 (42%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT+F + QL ++ F N ++A L +
Sbjct: 11 RTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTK 48
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA
binding helix- turn-helix motif, structural genomics,
NPPSFA; NMR {Mus musculus}
Length = 80
Score = 35.1 bits (81), Expect = 6e-04
Identities = 15/38 (39%), Positives = 18/38 (47%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT FT QL LE F +Y R E+A + L E
Sbjct: 11 RTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPE 48
>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 = 34.6 bits (80), Expect = 8e-04
Identities = 11/38 (28%), Positives = 17/38 (44%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT T+ QL L + F N + + E+A L +
Sbjct: 11 RTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQ 48
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 34.7 bits (80), Expect = 8e-04
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT+FT +Q+ LEKEF Y R +A+ + L E
Sbjct: 11 RTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPE 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 = 35.0 bits (80), Expect = 9e-04
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIA 110
R + + L +E F+ N+Y A+R EIA
Sbjct: 11 RFTWRKECLAVMESYFNENQYPDEAKREEIA 41
>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 = 35.9 bits (82), Expect = 0.001
Identities = 10/38 (26%), Positives = 17/38 (44%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT+ N+ LE F + + + IA+ L L +
Sbjct: 100 RTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEK 137
>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 = 33.5 bits (77), Expect = 0.002
Identities = 8/38 (21%), Positives = 14/38 (36%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
RT KQL L + N + ++ + L+
Sbjct: 7 RTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSP 44
>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 = 33.8 bits (77), Expect = 0.006
Identities = 11/40 (27%), Positives = 16/40 (40%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT+FT + + L F N T E+A L +
Sbjct: 97 RTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREV 136
>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 = 32.4 bits (74), Expect = 0.007
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 1/42 (2%)
Query: 80 RTNFTNKQLTELEKEFH-FNKYLTRARRIEIASVLQLNETQT 120
T Q+ LE F+ NK+ IA+ L E QT
Sbjct: 5 AATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQT 46
>2iub_A CORA, divalent cation transport-related protein; membrane
protein, ION transporter; 2.9A {Thermotoga maritima}
SCOP: d.328.1.1 f.17.3.1 PDB: 2hn2_A 2bbj_A
Length = 363
Score = 33.1 bits (76), Expect = 0.016
Identities = 12/105 (11%), Positives = 27/105 (25%), Gaps = 17/105 (16%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPSELSPLGVHPHPTSPST-DYTTPLTA 59
M K ++K+ KK P L G + +Y+
Sbjct: 1 MGSDKIHHHHHHMEEKRLSAKKG--------LPPGTLVYTGKYREDFEIEVMNYSI--EE 50
Query: 60 LKYPPSAALSQHQSLLNNSGRT-----NFTNK-QLTELEKEFHFN 98
+ + + ++S T + + + F +
Sbjct: 51 FREFKTTDVESVLPFRDSSTPTWINITGIHRTDVVQRVGEFFGIH 95
>1b6a_A Methionine aminopeptidase; angiogenesis inhibitor; HET: TN4; 1.60A
{Homo sapiens} SCOP: a.4.5.25 d.127.1.1 PDB: 1qzy_A*
1boa_A* 1kq0_A 1kq9_A 1bn5_A* 1b59_A* 1yw9_A* 1r5g_A*
1r5h_A* 1r58_A* 1yw8_A* 1yw7_A* 2adu_A* 2ea2_A* 2ea4_A*
2ga2_A* 2oaz_A*
Length = 478
Score = 32.6 bits (74), Expect = 0.022
Identities = 19/47 (40%), Positives = 23/47 (48%), Gaps = 6/47 (12%)
Query: 5 KKEKKKKKKKKKKKKKKKKKKKRITKVQ-----IP-SELSPLGVHPH 45
++ KKKKKKKKKR KVQ +P +L P GV P
Sbjct: 85 DEDGDGDGDGATGKKKKKKKKKRGPKVQTDPPSVPICDLYPNGVFPK 131
Score = 29.1 bits (65), Expect = 0.38
Identities = 10/23 (43%), Positives = 12/23 (52%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKK 25
+ KKKKKKKKK+ K
Sbjct: 89 DGDGDGATGKKKKKKKKKRGPKV 111
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 31.9 bits (71), Expect = 0.036
Identities = 8/92 (8%), Positives = 25/92 (27%)
Query: 19 KKKKKKKKRITKVQIPSELSPLGVHPHPTSPSTDYTTPLTALKYPPSAALSQHQSLLNNS 78
+K+++ ++ + S + + A S+ +
Sbjct: 85 RKQREILRQFNQTVQSSGNMTDKSSQDQLLFLFPEFSQQSHGPGQSDDACSEPTNKKMRR 144
Query: 79 GRTNFTNKQLTELEKEFHFNKYLTRARRIEIA 110
R + L + + K ++ R +
Sbjct: 145 NRFKWGPASQQILYQAYDRQKNPSKEEREALV 176
>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 = 29.4 bits (66), Expect = 0.066
Identities = 7/42 (16%), Positives = 16/42 (38%)
Query: 78 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
T +Q+ L+ F +++ A + V L ++
Sbjct: 6 HHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSE 47
>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane,
nucleotide-binding, translation; 2.80A {Escherichia
coli} PDB: 3deg_C*
Length = 599
Score = 31.3 bits (72), Expect = 0.068
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 11 KKKKKKKKKKKKKKKKRITKVQIPSE 36
KKK +K+K+ KK+ K+I V++P E
Sbjct: 561 KKKLLQKQKEGKKRMKQIGNVELPQE 586
>2ywe_A GTP-binding protein LEPA; G domain, beta-barrel, ferredoxin-like
domain, structural GE NPPSFA; 2.05A {Aquifex aeolicus}
PDB: 2ywf_A* 2ywg_A* 2ywh_A*
Length = 600
Score = 31.3 bits (72), Expect = 0.069
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 11 KKKKKKKKKKKKKKKKRITKVQIPSE 36
KKK + +K+ KK+ K+ KVQ+P E
Sbjct: 566 KKKLLENQKEGKKRMKQFGKVQLPQE 591
>2hz7_A Glutaminyl-tRNA synthetase; rossmann fold, GLNRS core, class I
aminoacyl-tRNA synthetase, ligase; 2.30A {Deinococcus
radiodurans}
Length = 851
Score = 31.0 bits (70), Expect = 0.092
Identities = 11/48 (22%), Positives = 19/48 (39%)
Query: 5 KKEKKKKKKKKKKKKKKKKKKKRITKVQIPSELSPLGVHPHPTSPSTD 52
K+ ++K + KK+ K + +V+ SP H P T
Sbjct: 632 GKQGGGTQQKAEGKKRPSTKGRGPDEVRGEGSSSPAKAHAPKAQPLTP 679
Score = 27.5 bits (61), Expect = 1.4
Identities = 5/31 (16%), Positives = 11/31 (35%)
Query: 6 KEKKKKKKKKKKKKKKKKKKKRITKVQIPSE 36
K+ K+ ++K + KK+
Sbjct: 628 KDTWGKQGGGTQQKAEGKKRPSTKGRGPDEV 658
>3pe5_A Uncharacterized protein; structural genomics, PSI-biology,
protein structure initiati northeast structural
genomics consortium, NESG; 2.38A {Clostridium leptum}
Length = 403
Score = 30.3 bits (68), Expect = 0.14
Identities = 3/26 (11%), Positives = 9/26 (34%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKRI 28
+ + + K K+ +K +
Sbjct: 11 QNRDISSRSNGKNPFKRSTGRKVSNV 36
Score = 29.9 bits (67), Expect = 0.20
Identities = 5/30 (16%), Positives = 10/30 (33%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITKV 31
+ R + K K+ +K I +
Sbjct: 11 QNRDISSRSNGKNPFKRSTGRKVSNVIIII 40
Score = 28.4 bits (63), Expect = 0.62
Identities = 3/30 (10%), Positives = 12/30 (40%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITKV 31
+ + + + K K+ ++++ V
Sbjct: 7 YQEPQNRDISSRSNGKNPFKRSTGRKVSNV 36
Score = 26.8 bits (59), Expect = 1.9
Identities = 4/22 (18%), Positives = 7/22 (31%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKK 22
+ R K K+ +K
Sbjct: 15 ISSRSNGKNPFKRSTGRKVSNV 36
Score = 26.8 bits (59), Expect = 2.0
Identities = 4/33 (12%), Positives = 11/33 (33%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKRITKVQI 33
++ + + K K+ +K + I
Sbjct: 7 YQEPQNRDISSRSNGKNPFKRSTGRKVSNVIII 39
Score = 25.7 bits (56), Expect = 5.3
Identities = 4/29 (13%), Positives = 10/29 (34%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITK 30
R ++ + + + K K+ R
Sbjct: 6 RYQEPQNRDISSRSNGKNPFKRSTGRKVS 34
Score = 25.3 bits (55), Expect = 7.2
Identities = 3/26 (11%), Positives = 10/26 (38%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
R+ ++ + + + K K+
Sbjct: 5 RRYQEPQNRDISSRSNGKNPFKRSTG 30
>3bbn_K Ribosomal protein S11; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea} SCOP:
i.1.1.1
Length = 140
Score = 29.2 bits (66), Expect = 0.20
Identities = 4/26 (15%), Positives = 10/26 (38%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKK 26
M K + ++ + +K +K
Sbjct: 1 MAKPIPKIGSRRNGRISSRKSASARK 26
Score = 26.5 bits (59), Expect = 1.9
Identities = 4/29 (13%), Positives = 9/29 (31%)
Query: 5 KKEKKKKKKKKKKKKKKKKKKKRITKVQI 33
K K ++ + +K R +
Sbjct: 3 KPIPKIGSRRNGRISSRKSASARKIPKGV 31
Score = 26.5 bits (59), Expect = 1.9
Identities = 3/34 (8%), Positives = 12/34 (35%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPS 35
+ K ++ + +K +K + + +
Sbjct: 3 KPIPKIGSRRNGRISSRKSASARKIPKGVIHVQA 36
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 29.4 bits (65), Expect = 0.22
Identities = 6/27 (22%), Positives = 17/27 (62%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKR 27
+RK ++E++K+ ++ K +++ R
Sbjct: 87 IRKWREEQRKRLQELDAASKVMEQEWR 113
Score = 27.4 bits (60), Expect = 1.1
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKK 25
RKR +E K +++ ++K KK
Sbjct: 95 RKRLQELDAASKVMEQEWREKAKK 118
Score = 25.1 bits (54), Expect = 5.8
Identities = 5/38 (13%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 1 MRKRKKEKKKKKKKKKKKKKK------KKKKKRITKVQ 32
+++ K +++ ++K KK +++ +++ K +
Sbjct: 98 LQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEKNK 135
Score = 24.7 bits (53), Expect = 9.0
Identities = 5/25 (20%), Positives = 12/25 (48%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKR 27
+R+ E+ +K K + K ++
Sbjct: 125 QRQSEQVEKNKINNRIADKAFYQQP 149
>1v9d_A Diaphanous protein homolog 1; helix bundle, protein binding; 2.60A
{Mus musculus} SCOP: a.207.1.1
Length = 340
Score = 29.3 bits (66), Expect = 0.26
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
R+ +EK ++ K K+K +K++ +K+
Sbjct: 315 RRETEEKMRRAKLAKEKAEKERLEKQ 340
Score = 28.6 bits (64), Expect = 0.52
Identities = 7/26 (26%), Positives = 19/26 (73%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
++R+ E+K ++ K K+K +K++ ++
Sbjct: 314 KRRETEEKMRRAKLAKEKAEKERLEK 339
Score = 27.4 bits (61), Expect = 1.1
Identities = 8/27 (29%), Positives = 19/27 (70%)
Query: 4 RKKEKKKKKKKKKKKKKKKKKKKRITK 30
+K+ + ++K ++ K K+K +K+R+ K
Sbjct: 313 QKRRETEEKMRRAKLAKEKAEKERLEK 339
Score = 27.4 bits (61), Expect = 1.4
Identities = 7/27 (25%), Positives = 18/27 (66%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKR 27
+KR++ ++K ++ K K+K +K++
Sbjct: 312 NQKRRETEEKMRRAKLAKEKAEKERLE 338
>1ul1_X Flap endonuclease-1; protein complex, DNA-binding protein, flap
DNA, flap endonuclease, sliding clamp, DNA clamp; 2.90A
{Homo sapiens} SCOP: a.60.7.1 c.120.1.2
Length = 379
Score = 29.5 bits (66), Expect = 0.27
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
RK + K KKK K K K+ +
Sbjct: 354 RKEPEPKGSTKKKAKTGAAGKFKRGK 379
Score = 28.7 bits (64), Expect = 0.46
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKR 27
KRK+ + K KKK K K KR
Sbjct: 353 KRKEPEPKGSTKKKAKTGAAGKFKR 377
>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 = 29.1 bits (64), Expect = 0.27
Identities = 4/31 (12%), Positives = 10/31 (32%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIA 110
R + L + + K ++ R +
Sbjct: 119 RFKWGPASQQILFQAYERQKNPSKEERETLV 149
>2xzm_K RPS14E; ribosome, translation; 3.93A {Tetrahymena thermophila}
PDB: 2xzn_K 3j0o_K 3j0l_K 2zkq_k 3iz6_K 3jyv_K*
Length = 151
Score = 28.6 bits (64), Expect = 0.35
Identities = 4/35 (11%), Positives = 9/35 (25%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPS 35
M +K +K+ + I +
Sbjct: 1 MAPKKTAPVQKEVISYGPPNVGANENVFGVCHIMA 35
>2ew5_A Peptide deformylase; inhibitor, hydrolase; HET: Y12; 2.20A
{Helicobacter pylori} PDB: 2ew6_A* 2ew7_A
Length = 181
Score = 28.6 bits (65), Expect = 0.38
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKR 27
KRKK +K+ K+ +KK+K K +
Sbjct: 155 KRKKFEKELKELQKKQKHKLEHHHH 179
Score = 25.6 bits (57), Expect = 5.0
Identities = 7/26 (26%), Positives = 15/26 (57%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
RK+ +++ K+ +KK+K K +
Sbjct: 156 RKKFEKELKELQKKQKHKLEHHHHHH 181
>1v3y_A Peptide deformylase; protein synthesis, riken structural
genomics/proteomics initiative, RSGI, structural
genomics, hydrolase; 1.81A {Thermus thermophilus} SCOP:
d.167.1.1
Length = 192
Score = 28.7 bits (65), Expect = 0.42
Identities = 3/28 (10%), Positives = 12/28 (42%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKRITK 30
KR+ + + + + +K+ + +
Sbjct: 163 KREAFLEANRAELVRFQKEARALLKELS 190
Score = 26.4 bits (59), Expect = 2.2
Identities = 3/28 (10%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 2 RKR--KKEKKKKKKKKKKKKKKKKKKKR 27
R+ + + + + +K+ + K+ +
Sbjct: 164 REAFLEANRAELVRFQKEARALLKELSQ 191
>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase,
ribosylating toxin, GTP-binding, lipoprotein,
prenylation; HET: GDP; 2.66A {Homo sapiens}
Length = 206
Score = 28.4 bits (64), Expect = 0.43
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKR 27
+R RK E K+K KKK+K K+ +
Sbjct: 175 IRARKMEDSKEKNGKKKRKSLAKRIRE 201
>3owq_A LIN1025 protein; structural genomics, PSI-biology, protein
structure initiati northeast structural genomics
consortium, NESG, unknown FUN; 2.61A {Listeria innocua}
PDB: 3nro_A
Length = 321
Score = 28.5 bits (64), Expect = 0.43
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKK 22
M + + E K+KK K K
Sbjct: 1 MTETRTETKQKKPSTFTKVMKI 22
Score = 25.5 bits (56), Expect = 5.0
Identities = 5/23 (21%), Positives = 10/23 (43%)
Query: 7 EKKKKKKKKKKKKKKKKKKKRIT 29
+ + + K+KK K K +
Sbjct: 2 TETRTETKQKKPSTFTKVMKIAS 24
Score = 25.1 bits (55), Expect = 7.5
Identities = 4/24 (16%), Positives = 10/24 (41%)
Query: 10 KKKKKKKKKKKKKKKKKRITKVQI 33
+ + + K+KK K + +
Sbjct: 2 TETRTETKQKKPSTFTKVMKIASV 25
Score = 25.1 bits (55), Expect = 7.9
Identities = 6/26 (23%), Positives = 12/26 (46%)
Query: 8 KKKKKKKKKKKKKKKKKKKRITKVQI 33
+ + + K+KK K +I V +
Sbjct: 2 TETRTETKQKKPSTFTKVMKIASVTL 27
Score = 25.1 bits (55), Expect = 8.0
Identities = 6/23 (26%), Positives = 9/23 (39%)
Query: 6 KEKKKKKKKKKKKKKKKKKKKRI 28
E + + K+KK K K
Sbjct: 2 TETRTETKQKKPSTFTKVMKIAS 24
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A
{Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 27.9 bits (61), Expect = 0.46
Identities = 4/32 (12%), Positives = 10/32 (31%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIAS 111
R + L + + K ++ R +
Sbjct: 13 RFKWGPASQQILFQAYERQKNPSKEERETLVE 44
>3vbb_A Seryl-tRNA synthetase, cytoplasmic; coiled-coil, ligase; 2.89A
{Homo sapiens}
Length = 522
Score = 28.5 bits (64), Expect = 0.47
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPSELSPLGV 42
K +++ KK+KK+ + KKK V + + L + V
Sbjct: 472 KPAPIEQEPSKKQKKQHEGSKKKAAARDVTLENRLQNMEV 511
>1kxf_A Sindbis virus capsid protein; chymotrypsin-like serine proteinase,
wild type, viral protein; 2.38A {Sindbis virus} SCOP:
b.47.1.3 PDB: 1ld4_A 3j0f_A
Length = 264
Score = 28.2 bits (62), Expect = 0.55
Identities = 11/55 (20%), Positives = 21/55 (38%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPSELSPLGVHPHPTSPSTDYTTP 56
+ + ++KK+ K+ K KK K + K + P++ P D
Sbjct: 63 PRPRPPPRQKKQAPKQPPKPKKPKPQEKKKKQPAKTKPGKRQRMALKLEADRLFD 117
Score = 26.3 bits (57), Expect = 2.7
Identities = 11/49 (22%), Positives = 21/49 (42%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPSELSPLGVHPHPTSP 49
R+K++ K+ K KK K ++KKK+ P + + +
Sbjct: 67 PPPRQKKQAPKQPPKPKKPKPQEKKKKQPAKTKPGKRQRMALKLEADRL 115
Score = 24.8 bits (53), Expect = 8.7
Identities = 9/38 (23%), Positives = 19/38 (50%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPSELSPL 40
+K + ++KKKK+ K K K+++ K++
Sbjct: 82 PKKPKPQEKKKKQPAKTKPGKRQRMALKLEADRLFDVK 119
>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 = 27.3 bits (60), Expect = 0.57
Identities = 8/39 (20%), Positives = 16/39 (41%)
Query: 84 TNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122
T Q+ LE F + + T+A + +L+ +
Sbjct: 21 TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDS 59
>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 = 26.7 bits (59), Expect = 0.70
Identities = 8/42 (19%), Positives = 16/42 (38%), Gaps = 1/42 (2%)
Query: 80 RTNFTNKQLTELEKEFH-FNKYLTRARRIEIASVLQLNETQT 120
RT + + L L+ H Y + +++ L L +
Sbjct: 11 RTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTI 52
>3o2u_A NEDD8-conjugating enzyme UBC12; E2 conjugase, ligase; 2.00A
{Saccharomyces cerevisiae} PDB: 3tdi_C
Length = 190
Score = 27.8 bits (62), Expect = 0.71
Identities = 7/34 (20%), Positives = 17/34 (50%), Gaps = 4/34 (11%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKK----KKRITK 30
M K ++ +KKK+K+ + + + R+ +
Sbjct: 3 MLKLRQLQKKKQKENENSSSIQPNLSAARIRLKR 36
>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase,
conformational change, cysteine-modified, G-protein
hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B*
2ht6_A*
Length = 192
Score = 28.0 bits (63), Expect = 0.71
Identities = 6/22 (27%), Positives = 15/22 (68%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKK 22
+R R+ K+K +++ +K+K+
Sbjct: 170 VRLRRDSKEKNERRLAYQKRKE 191
Score = 26.1 bits (58), Expect = 2.6
Identities = 5/21 (23%), Positives = 13/21 (61%)
Query: 4 RKKEKKKKKKKKKKKKKKKKK 24
R + K+K +++ +K+K+
Sbjct: 171 RLRRDSKEKNERRLAYQKRKE 191
>3vmt_A Monofunctional glycosyltransferase; transmembrane, bacterial cell
WALL SYNT membrane; HET: LHI; 2.30A {Staphylococcus
aureus} PDB: 3vmr_A* 3vms_A 3vmq_A*
Length = 263
Score = 27.3 bits (61), Expect = 1.2
Identities = 8/27 (29%), Positives = 10/27 (37%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRI 28
+ + K KKKK KRI
Sbjct: 10 HSSGLVPRGSHMQPVGKPPKKKKSKRI 36
>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis,
structural genomics, structural genomics consortium,
SGC, transport protein; HET: GDP; 1.90A {Homo sapiens}
SCOP: c.37.1.8
Length = 199
Score = 27.2 bits (61), Expect = 1.3
Identities = 5/27 (18%), Positives = 11/27 (40%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKR 27
+R K+ K+K+ + K +
Sbjct: 169 ETRRNMSLNIDGKRSGKQKRTDRVKGK 195
>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 = 26.0 bits (57), Expect = 1.3
Identities = 7/43 (16%), Positives = 12/43 (27%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122
+QL LE F N + S ++ +
Sbjct: 11 YKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDS 53
>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 = 26.5 bits (58), Expect = 1.3
Identities = 8/36 (22%), Positives = 15/36 (41%)
Query: 84 TNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
T +QL L+ F + LT + + +L +
Sbjct: 19 TAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRRE 54
>3st8_A Bifunctional protein GLMU; acetyltransferase, pyrophosphorylase,
rossmann fold, LEFT-handed-beta-helix, cell shape; HET:
COA GP1 UD1; 1.98A {Mycobacterium tuberculosis} PDB:
3spt_A* 3foq_A 3dk5_A 3d8v_A 3d98_A* 3dj4_A 2qkx_A*
Length = 501
Score = 27.1 bits (61), Expect = 1.3
Identities = 7/43 (16%), Positives = 15/43 (34%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPSELSPLGVHP 44
+R E ++K+ + K+ Q P++ P
Sbjct: 459 PQRNIENWVQRKRPGSPAAQASKRASEMACQQPTQPPDADQTP 501
>2yew_A Capsid protein, coat protein; alphavirus, molecular dynamics;
5.00A {Barmah forest virus}
Length = 253
Score = 27.3 bits (60), Expect = 1.5
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
K KK +K KK +KKK K KR
Sbjct: 69 TPPPKPKKTQKPKKPTQKKKSKPGKR 94
>2j1d_G DAAM1, disheveled-associated activator of morphogenesis; actin
assembly, protein binding; 2.55A {Homo sapiens} PDB:
2z6e_A
Length = 483
Score = 27.2 bits (60), Expect = 1.5
Identities = 5/29 (17%), Positives = 22/29 (75%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITK 30
++KKE+++++ + + + K++++++R +
Sbjct: 398 MRKKKEEEERRARMEAQLKEQRERERKMR 426
Score = 25.6 bits (56), Expect = 5.9
Identities = 6/31 (19%), Positives = 21/31 (67%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITKVQ 32
+K ++E++ + + + K+++++++K R K
Sbjct: 401 KKEEEERRARMEAQLKEQRERERKMRKAKEN 431
Score = 25.2 bits (55), Expect = 7.7
Identities = 5/41 (12%), Positives = 21/41 (51%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPSELSPLGV 42
RKK+++++++ + + + K+++++ + G
Sbjct: 397 NMRKKKEEEERRARMEAQLKEQRERERKMRKAKENSEESGE 437
>3u5e_D 60S ribosomal protein L5; translation, ribosome, ribosomal R
ribosomal protein, STM1, eukaryotic ribosome; 3.00A
{Saccharomyces cerevisiae} PDB: 3u5i_D 3izc_Q 3izs_Q
3o58_E 3o5h_E 3jyw_E 1s1i_E
Length = 297
Score = 27.0 bits (59), Expect = 1.9
Identities = 7/29 (24%), Positives = 17/29 (58%)
Query: 4 RKKEKKKKKKKKKKKKKKKKKKKRITKVQ 32
K +KK K++ + KK ++ +++K +
Sbjct: 253 FKPTEKKFTKEQYAAESKKYRQTKLSKEE 281
>3psf_A Transcription elongation factor SPT6; nucleus; 2.59A {Saccharomyces
cerevisiae}
Length = 1030
Score = 27.2 bits (60), Expect = 2.0
Identities = 5/29 (17%), Positives = 15/29 (51%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITK 30
K++ E ++++K + + K+ R+
Sbjct: 998 LKQELEDAEEERKLMMAEARAKRTHRVIN 1026
>3iz5_Q 60S ribosomal protein L5 (L18P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel ribosomal
proteins, ribosome; 5.50A {Triticum aestivum} PDB:
3izr_Q
Length = 304
Score = 26.9 bits (59), Expect = 2.0
Identities = 8/29 (27%), Positives = 12/29 (41%)
Query: 4 RKKEKKKKKKKKKKKKKKKKKKKRITKVQ 32
R K KK+ K+ K++T Q
Sbjct: 248 RADPTMAKSTKKEPATHKRYNLKKLTYEQ 276
Score = 25.0 bits (54), Expect = 8.2
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITK 30
+ KKE K+ KK +++K + +
Sbjct: 255 KSTKKEPATHKRYNLKKLTYEQRKASLVE 283
>2jul_A Calsenilin; EF-hand, calcium, LXXLL, DNA binding protein, dimer,
alternative splicing, apoptosis, cytoplasm, endoplasmic
reticulum, golgi apparatus; NMR {Mus musculus}
Length = 256
Score = 26.5 bits (58), Expect = 2.3
Identities = 15/85 (17%), Positives = 30/85 (35%), Gaps = 4/85 (4%)
Query: 12 KKKKKKKKKKKKKKKRITKVQIPSELSPLGVHPHPTSPSTDYTTPLTALKYPPSAALSQH 71
+ K++ K ++ R T+ + + +D + + S Q
Sbjct: 21 RIPLSKRESIKWQRPRFTRQALMRCCLIKWILSSAAPQGSDSSDS----ELELSTVRHQP 76
Query: 72 QSLLNNSGRTNFTNKQLTELEKEFH 96
+ L +T FT K+L L + F
Sbjct: 77 EGLDQLQAQTKFTKKELQSLYRGFK 101
>2jmi_A Protein YNG1, ING1 homolog 1; PHD, histone, recognition, yeast,
protein binding; NMR {Saccharomyces cerevisiae} PDB:
2jmj_A*
Length = 90
Score = 25.5 bits (55), Expect = 2.6
Identities = 5/17 (29%), Positives = 12/17 (70%)
Query: 8 KKKKKKKKKKKKKKKKK 24
K+ ++ K K++K++K
Sbjct: 74 KEIANQRSKSKRQKRRK 90
Score = 25.5 bits (55), Expect = 2.6
Identities = 5/17 (29%), Positives = 12/17 (70%)
Query: 9 KKKKKKKKKKKKKKKKK 25
K+ ++ K K++K++K
Sbjct: 74 KEIANQRSKSKRQKRRK 90
Score = 25.5 bits (55), Expect = 2.6
Identities = 5/17 (29%), Positives = 12/17 (70%)
Query: 10 KKKKKKKKKKKKKKKKK 26
K+ ++ K K++K++K
Sbjct: 74 KEIANQRSKSKRQKRRK 90
Score = 25.1 bits (54), Expect = 3.6
Identities = 4/17 (23%), Positives = 12/17 (70%)
Query: 4 RKKEKKKKKKKKKKKKK 20
++ ++ K K++K++K
Sbjct: 74 KEIANQRSKSKRQKRRK 90
Score = 25.1 bits (54), Expect = 4.2
Identities = 6/17 (35%), Positives = 12/17 (70%)
Query: 6 KEKKKKKKKKKKKKKKK 22
KE ++ K K++K++K
Sbjct: 74 KEIANQRSKSKRQKRRK 90
Score = 24.7 bits (53), Expect = 4.8
Identities = 5/18 (27%), Positives = 12/18 (66%)
Query: 4 RKKEKKKKKKKKKKKKKK 21
K+ ++ K K++K++K
Sbjct: 73 CKEIANQRSKSKRQKRRK 90
Score = 24.7 bits (53), Expect = 5.4
Identities = 4/17 (23%), Positives = 12/17 (70%)
Query: 11 KKKKKKKKKKKKKKKKR 27
K+ ++ K K++K+++
Sbjct: 74 KEIANQRSKSKRQKRRK 90
Score = 24.7 bits (53), Expect = 5.8
Identities = 4/17 (23%), Positives = 12/17 (70%)
Query: 7 EKKKKKKKKKKKKKKKK 23
++ ++ K K++K++K
Sbjct: 74 KEIANQRSKSKRQKRRK 90
Score = 24.3 bits (52), Expect = 6.6
Identities = 4/17 (23%), Positives = 12/17 (70%)
Query: 2 RKRKKEKKKKKKKKKKK 18
++ ++ K K++K++K
Sbjct: 74 KEIANQRSKSKRQKRRK 90
Score = 24.3 bits (52), Expect = 8.6
Identities = 5/18 (27%), Positives = 11/18 (61%)
Query: 2 RKRKKEKKKKKKKKKKKK 19
K ++ K K++K++K
Sbjct: 73 CKEIANQRSKSKRQKRRK 90
>4a17_V RPL7, 60S ribosomal protein L7; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_V 4a1c_V 4a1e_V
Length = 239
Score = 26.3 bits (57), Expect = 2.8
Identities = 5/26 (19%), Positives = 15/26 (57%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
R ++ +K K +++K + K+++
Sbjct: 13 LARDEKLRKAKAEQRKASSAQMKQRK 38
Score = 25.5 bits (55), Expect = 5.8
Identities = 7/32 (21%), Positives = 17/32 (53%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITKVQI 33
+K +++K +K K +++K + K+ I
Sbjct: 11 KKLARDEKLRKAKAEQRKASSAQMKQRKAEWI 42
>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein,
ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP;
1.78A {Arabidopsis thaliana}
Length = 212
Score = 26.2 bits (58), Expect = 2.9
Identities = 2/19 (10%), Positives = 11/19 (57%)
Query: 8 KKKKKKKKKKKKKKKKKKK 26
+ ++K+ +++K ++
Sbjct: 180 QPPRRKEVPRRRKNHRRSG 198
Score = 25.8 bits (57), Expect = 3.6
Identities = 2/19 (10%), Positives = 11/19 (57%)
Query: 7 EKKKKKKKKKKKKKKKKKK 25
+ ++K+ +++K ++
Sbjct: 180 QPPRRKEVPRRRKNHRRSG 198
Score = 25.8 bits (57), Expect = 4.5
Identities = 2/20 (10%), Positives = 11/20 (55%)
Query: 4 RKKEKKKKKKKKKKKKKKKK 23
+ ++K+ +++K ++
Sbjct: 179 LQPPRRKEVPRRRKNHRRSG 198
Score = 25.4 bits (56), Expect = 4.6
Identities = 2/19 (10%), Positives = 11/19 (57%)
Query: 6 KEKKKKKKKKKKKKKKKKK 24
+ ++K+ +++K ++
Sbjct: 180 QPPRRKEVPRRRKNHRRSG 198
Score = 25.4 bits (56), Expect = 5.4
Identities = 1/20 (5%), Positives = 12/20 (60%)
Query: 1 MRKRKKEKKKKKKKKKKKKK 20
++ ++++ +++K ++
Sbjct: 179 LQPPRRKEVPRRRKNHRRSG 198
Score = 25.4 bits (56), Expect = 5.7
Identities = 2/19 (10%), Positives = 11/19 (57%)
Query: 9 KKKKKKKKKKKKKKKKKKR 27
+ ++K+ +++K ++
Sbjct: 180 QPPRRKEVPRRRKNHRRSG 198
Score = 25.0 bits (55), Expect = 8.1
Identities = 2/20 (10%), Positives = 10/20 (50%)
Query: 2 RKRKKEKKKKKKKKKKKKKK 21
+ + K+ +++K ++
Sbjct: 179 LQPPRRKEVPRRRKNHRRSG 198
>1rl4_A Formylmethionine deformylase; crystal engineering, drug design,
malaria, PDF, peptide DEFO plasmodium, hydrolase; HET:
BRR BL5; 2.18A {Plasmodium falciparum} SCOP: d.167.1.1
PDB: 1rqc_A 1jym_A
Length = 188
Score = 26.0 bits (58), Expect = 3.1
Identities = 3/26 (11%), Positives = 9/26 (34%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
+K+ + K + + K +
Sbjct: 161 KKKVRPKLNELIRDYKATHSLEHHHH 186
Score = 25.2 bits (56), Expect = 5.5
Identities = 2/24 (8%), Positives = 6/24 (25%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKK 24
+ K + + K +
Sbjct: 163 KVRPKLNELIRDYKATHSLEHHHH 186
Score = 24.8 bits (55), Expect = 6.9
Identities = 4/25 (16%), Positives = 9/25 (36%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKR 27
+KK + K + + K +
Sbjct: 160 DKKKVRPKLNELIRDYKATHSLEHH 184
>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase;
HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A*
4dso_A*
Length = 189
Score = 26.0 bits (58), Expect = 3.2
Identities = 12/22 (54%), Positives = 15/22 (68%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKK 22
+RK K++ K KKKKKK K K
Sbjct: 164 IRKHKEKMSKDGKKKKKKSKTK 185
>3qne_A Seryl-tRNA synthetase, cytoplasmic; amino acid biosynthesis,
CTG-clade, codon ambiguity, pathoge II aminoacyl-tRNA
synthetase family; 2.00A {Candida albicans} PDB: 3qo7_A*
3qo8_A* 3qo5_A
Length = 485
Score = 26.0 bits (58), Expect = 3.3
Identities = 7/29 (24%), Positives = 10/29 (34%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITK 30
++ K KK K K K K+
Sbjct: 446 KELPKNTTSVKKAKGKNPKNTTSVKKAKG 474
Score = 25.3 bits (56), Expect = 6.8
Identities = 8/21 (38%), Positives = 8/21 (38%)
Query: 5 KKEKKKKKKKKKKKKKKKKKK 25
KE K KK K K K
Sbjct: 445 IKELPKNTTSVKKAKGKNPKN 465
Score = 24.9 bits (55), Expect = 8.9
Identities = 11/38 (28%), Positives = 14/38 (36%)
Query: 8 KKKKKKKKKKKKKKKKKKKRITKVQIPSELSPLGVHPH 45
K+ K KK K K K T V+ + H H
Sbjct: 446 KELPKNTTSVKKAKGKNPKNTTSVKKAKGKNGSRHHHH 483
>3izc_e 60S ribosomal protein RPL7 (L30P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins; NMR {Saccharomyces cerevisiae} PDB:
3izs_e 3o58_G 3o5h_G 3u5e_F 3u5i_F
Length = 244
Score = 25.9 bits (56), Expect = 3.3
Identities = 5/26 (19%), Positives = 14/26 (53%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
K +++ ++ ++ +K K+KR
Sbjct: 16 SKAQQKTAEQVAAERAARKAANKEKR 41
Score = 25.2 bits (54), Expect = 7.8
Identities = 4/29 (13%), Positives = 11/29 (37%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITK 30
+ ++ +K K+K+ +R
Sbjct: 22 TAEQVAAERAARKAANKEKRAIILERNAA 50
>1ois_A DNA topoisomerase I; DNA-binding protein; HET: DNA; 1.90A
{Saccharomyces cerevisiae} SCOP: e.15.1.1
Length = 223
Score = 26.0 bits (57), Expect = 3.4
Identities = 7/28 (25%), Positives = 18/28 (64%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKRITK 30
+ +KE+KK+ ++KK+ + +++K
Sbjct: 102 QLQKEQKKQLTSQEKKQIRLEREKFEED 129
>2q8k_A Proliferation-associated protein 2G4; EBP1, PA2G4, methionine
aminopeptidase, PITA-bread, transcri; 1.60A {Homo
sapiens} PDB: 2v6c_A
Length = 401
Score = 25.9 bits (57), Expect = 3.8
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 10 KKKKKKKKKKKKKKKKKRITKVQIPSE 36
+K +KKKKKK K + T + E
Sbjct: 370 SRKTQKKKKKKASKTAENATSGETLEE 396
Score = 25.5 bits (56), Expect = 6.5
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 6 KEKKKKKKKKKKKKKKKKKKKRITKVQ 32
K +KKKKKK K + T +
Sbjct: 370 SRKTQKKKKKKASKTAENATSGETLEE 396
Score = 25.1 bits (55), Expect = 8.2
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 5 KKEKKKKKKKKKKKKKKKKKKKR 27
+ +K +KKKKKK K +
Sbjct: 366 QSSASRKTQKKKKKKASKTAENA 388
>3t18_A Aminotransferase class I and II; PSI-biology, MCSG, midwest center
for structural genomics, P 5'-phosphate binding; HET:
PLP; 2.86A {Anaerococcus prevotii}
Length = 413
Score = 25.7 bits (57), Expect = 4.4
Identities = 8/31 (25%), Positives = 13/31 (41%)
Query: 82 NFTNKQLTELEKEFHFNKYLTRARRIEIASV 112
+ + +LEKE F + R+ I V
Sbjct: 364 DKAFDIVKDLEKENIFTIPSAKGIRVAICGV 394
>1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene,
replication block, mutagenesis, transferase/electron
transport/DNA complex; HET: DNA 2DT 8FG; 2.10A
{Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB:
1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A*
1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A*
1zyq_A* 2ajq_A*
Length = 698
Score = 26.0 bits (57), Expect = 4.5
Identities = 2/35 (5%), Positives = 8/35 (22%)
Query: 12 KKKKKKKKKKKKKKKRITKVQIPSELSPLGVHPHP 46
++ K K + ++ +
Sbjct: 341 QEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQA 375
>3iz5_e 60S ribosomal protein L7 (L30P); eukaryotic ribosome,homology
modeling,de novo modeling,ribos proteins,novel
ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
PDB: 3izr_e
Length = 244
Score = 25.6 bits (55), Expect = 4.6
Identities = 7/26 (26%), Positives = 14/26 (53%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
R+R++ +KK+K +K K +
Sbjct: 18 RRREEVWAAEKKQKVAAEKIKAAENT 43
Score = 25.2 bits (54), Expect = 7.9
Identities = 11/32 (34%), Positives = 17/32 (53%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITKVQI 33
KR++E+ +KK+K +K K TKV
Sbjct: 16 LKRRREEVWAAEKKQKVAAEKIKAAENTKVIY 47
>2wxf_A Phosphatidylinositol-4,5-bisphosphate 3-kinase Ca subunit delta
isoform; transferase, phosphoprotein, isoform-specific
inhibitors; HET: 039; 1.90A {Mus musculus} PDB: 2wxg_A*
2wxh_A* 2wxi_A* 2wxj_A* 2wxk_A* 2wxl_A* 2wxm_A* 2wxn_A*
2wxo_A* 2wxp_A* 2wxq_A* 2wxr_A 2x38_A*
Length = 940
Score = 26.0 bits (56), Expect = 4.9
Identities = 10/50 (20%), Positives = 18/50 (36%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPSELSPLGVHPHPTSPS 50
+ K K K +K K + K+ ++ + + L P PS
Sbjct: 585 LSKLKALNDFVKVSSQKTTKPQTKEMMHMCMRQETYMEALSHLQSPLDPS 634
>2zkr_n 60S ribosomal protein L5; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 297
Score = 25.8 bits (56), Expect = 5.0
Identities = 8/28 (28%), Positives = 17/28 (60%)
Query: 5 KKEKKKKKKKKKKKKKKKKKKKRITKVQ 32
++ +KK KK+ KKK+ + +++ Q
Sbjct: 248 RENPVYEKKPKKEVKKKRWNRPKMSLAQ 275
>1914_A Signal recognition particle 9/14 fusion protein; ALU domain, RNA
binding, signal recognition particle (SRP), translation
regulation; 2.53A {Mus musculus} SCOP: d.49.1.1 d.49.1.1
PDB: 1e8o_A* 1e8s_A 1ry1_C*
Length = 232
Score = 25.3 bits (55), Expect = 5.1
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 7 EKKKKKKKKKKKKKKKKKKKRITKVQIPSELSP 39
+K+ KK K KK K + ++++ + S SP
Sbjct: 114 KKRDKKNKSKKSKPAQGGEQKLISEEDDSAGSP 146
>3kio_B Ribonuclease H2 subunit B; aicardi-goutieres syndrome, RNAse H2,
protein complex, autoimmune disease, endonuclease,
hydrolase, metal-binding; 2.90A {Mus musculus} PDB:
3p5j_B 3puf_B 3p56_B
Length = 332
Score = 25.6 bits (55), Expect = 5.1
Identities = 7/30 (23%), Positives = 10/30 (33%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKRITK 30
+ K+ K KK K +K K
Sbjct: 284 TKFNTKDLKTGKKNSKMTAAQKALAKVDKS 313
Score = 25.2 bits (54), Expect = 6.7
Identities = 9/29 (31%), Positives = 11/29 (37%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKRITKV 31
K K K KK K +K + KV
Sbjct: 282 DYTKFNTKDLKTGKKNSKMTAAQKALAKV 310
Score = 25.2 bits (54), Expect = 6.9
Identities = 9/29 (31%), Positives = 10/29 (34%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKRITK 30
K K KK K +K K K K
Sbjct: 288 TKDLKTGKKNSKMTAAQKALAKVDKSGMK 316
>2b9s_A Topoisomerase I-like protein; vanadate complex, isomerase/DNA
complex; HET: DNA; 2.27A {Leishmania donovani}
Length = 432
Score = 25.8 bits (56), Expect = 5.2
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKRITK 30
++EKK + K++KK K+K+
Sbjct: 112 LVQREKKLSRTKEEKKAIKEKQDAEAEP 139
>3bn0_A 30S ribosomal protein S16; ribonucleoprotein, ribosome; 2.00A
{Aquifex aeolicus} SCOP: d.27.1.1
Length = 112
Score = 25.0 bits (55), Expect = 5.5
Identities = 5/22 (22%), Positives = 9/22 (40%)
Query: 5 KKEKKKKKKKKKKKKKKKKKKK 26
K +K++ KK K +
Sbjct: 89 MKRVGDYYVFEKRESKKSKGGE 110
Score = 25.0 bits (55), Expect = 5.8
Identities = 6/24 (25%), Positives = 10/24 (41%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKK 26
E K+ +K++ KK K
Sbjct: 84 PEGYEMKRVGDYYVFEKRESKKSK 107
Score = 24.6 bits (54), Expect = 6.5
Identities = 5/24 (20%), Positives = 11/24 (45%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKK 26
+ K+ +K++ KK K +
Sbjct: 88 EMKRVGDYYVFEKRESKKSKGGEA 111
Score = 24.6 bits (54), Expect = 6.9
Identities = 4/27 (14%), Positives = 13/27 (48%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKR 27
+++ E + K+ +K++ K+
Sbjct: 79 LKEVVPEGYEMKRVGDYYVFEKRESKK 105
Score = 24.2 bits (53), Expect = 8.8
Identities = 4/27 (14%), Positives = 11/27 (40%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKR 27
+ + K+ +K++ KK +
Sbjct: 81 EVVPEGYEMKRVGDYYVFEKRESKKSK 107
>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase,
hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP:
b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19
d.315.1.1
Length = 1151
Score = 25.4 bits (56), Expect = 5.8
Identities = 5/34 (14%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 12 KKKKKKKKKKKKKKKRITKVQIPSELSP--LGVH 43
++ ++++ ++ T ++ +EL VH
Sbjct: 455 ERVARRRQDSRRTINPDTLIRNLAELHIGQPVVH 488
>3qx3_A DNA topoisomerase 2-beta; toprim domain, winged-helix domain,
coiled-coil domain, DNA and cleavage, nucleus; HET: DNA
EVP; 2.16A {Homo sapiens}
Length = 803
Score = 25.5 bits (55), Expect = 5.9
Identities = 7/28 (25%), Positives = 8/28 (28%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKRITK 30
K + K K K K I K
Sbjct: 11 KGADDDDKVPDPTSVDSVKYSKIKGIPK 38
>3qye_A TBC1 domain family member 1; rabgap, RAB, myocytes, hydrolase
activator; 2.20A {Homo sapiens} PDB: 3qyb_A
Length = 331
Score = 25.5 bits (56), Expect = 6.2
Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 57 LTALK-YPPSAALSQHQSLLNNSGRTNFTNKQLTELEKEFH 96
+ +K P+ L Q + +N + KQL E E+H
Sbjct: 282 VDFIKSTLPNLGLVQMEKTINQVFEMDIA-KQLQAYEVEYH 321
>3pn3_A Peptide deformylase 1B, chloroplastic; PDF, N-terminal excision
pathway, N induced-FIT, hydrolase-hydrolase inhibitor
complex; HET: PN3; 1.30A {Arabidopsis thaliana} PDB:
3m6p_A* 3o3j_A* 3pn2_A 3m6o_A* 3pn4_A* 3pn5_A 3m6q_A
3pn6_A 3m6r_A 3cpm_A
Length = 193
Score = 25.2 bits (56), Expect = 6.5
Identities = 4/33 (12%), Positives = 15/33 (45%)
Query: 1 MRKRKKEKKKKKKKKKKKKKKKKKKKRITKVQI 33
+ + +KK ++K ++ + ++ K +
Sbjct: 156 REELEALEKKYEEKTGLPSPERVEARQKRKAGV 188
>3u5e_P L20A, YL17, 60S ribosomal protein L17-A; translation, ribosome,
ribosomal R ribosomal protein, STM1, eukaryotic
ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 2wwa_I
2ww9_I 2wwb_I 3o5h_Q 3o58_Q 3u5i_P 1s1i_N 3izc_V 3izs_V
3jyw_N
Length = 184
Score = 24.9 bits (54), Expect = 6.7
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 5 KKEKKKKKKKKKKKKKKKKKKKRIT 29
K +KK + +++ + +KRI
Sbjct: 159 KAAEKKVVRLTSRQRGRIAAQKRIA 183
>4a17_M RPL5, 60S ribosomal protein L5; eukaryotic ribosome, ribosome,
eukaryotic initiation factor 60S, translation, large
ribosomal subunit; 3.52A {Tetrahymena thermophila} PDB:
4a1a_M 4a1c_M 4a1e_M
Length = 301
Score = 25.0 bits (54), Expect = 6.9
Identities = 9/27 (33%), Positives = 13/27 (48%)
Query: 6 KEKKKKKKKKKKKKKKKKKKKRITKVQ 32
+ K KK K K+ KK ++T Q
Sbjct: 260 RVKSTKKNDKPKRDHKKFYPTKLTAAQ 286
>3h6l_A Histone-lysine N-methyltransferase SETD2; SET domain-containing
protein 2, S-adenos methionine, structural genomics,
structural genomics consor SGC; HET: SAM; 1.99A {Homo
sapiens}
Length = 278
Score = 25.1 bits (55), Expect = 7.5
Identities = 4/20 (20%), Positives = 10/20 (50%)
Query: 3 KRKKEKKKKKKKKKKKKKKK 22
+ + + K KK++ +K
Sbjct: 259 ENRVSIRAAGGKMKKERSRK 278
>2w3t_A Peptide deformylase; protein biosynthesis, iron, nickel, hydrolase,
metal-binding; 1.69A {Escherichia coli} PDB: 2w3u_A
Length = 188
Score = 24.8 bits (55), Expect = 7.7
Identities = 7/43 (16%), Positives = 17/43 (39%), Gaps = 7/43 (16%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKRITKVQIPSELSPLGVHPH 45
K+++ ++K +K + K + +L+ H H
Sbjct: 150 KQQRIRQKVEKLDRLKARAPNSSSV-------DKLAAALEHHH 185
>2lgz_A Dolichyl-diphosphooligosaccharide--protein glycosyltransferase
subunit STT3; catalytic domain, oligosaccharyl
transferase; NMR {Saccharomyces cerevisiae}
Length = 273
Score = 25.2 bits (54), Expect = 7.8
Identities = 3/29 (10%), Positives = 13/29 (44%)
Query: 3 KRKKEKKKKKKKKKKKKKKKKKKKRITKV 31
+ ++ + + K ++ K+ + +V
Sbjct: 245 RTLRDVGELTRSSTKTRRSIKRPELGLRV 273
>4a17_A RPL8; eukaryotic ribosome, ribosome, eukaryotic initiation factor
60S, translation, large ribosomal subunit; 3.52A
{Tetrahymena thermophila} PDB: 4a1a_A 4a1c_A 4a1e_A
Length = 264
Score = 24.5 bits (54), Expect = 9.9
Identities = 4/26 (15%), Positives = 10/26 (38%)
Query: 2 RKRKKEKKKKKKKKKKKKKKKKKKKR 27
+K ++ + +K+K K
Sbjct: 234 QKVGLRAARRTGLVRGGQKEKMAMKA 259
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
0.308 0.123 0.331
Gapped
Lambda K H
0.267 0.0713 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,721,042
Number of extensions: 93355
Number of successful extensions: 3576
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2340
Number of HSP's successfully gapped: 780
Length of query: 123
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,412,271
Effective search space: 180903111
Effective search space used: 180903111
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 51 (23.5 bits)