RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6707
(257 letters)
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA recognition,
chromatin, DNA binding protein, DNA sequence specific,
testis determining.; NMR {Mus musculus} SCOP: a.21.1.1
Length = 81
Score = 69.5 bits (171), Expect = 7e-16
Identities = 33/42 (78%), Positives = 40/42 (95%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRT 184
G+RWKAM+N EKQPYYEEQ+RLSK H+EK+PDY+Y+PRPKRT
Sbjct: 40 GSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYKYKPRPKRT 81
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain,
activator, DNA-binding, NUC transcription; HET: DNA;
2.77A {Homo sapiens}
Length = 106
Score = 67.0 bits (164), Expect = 1e-14
Identities = 17/42 (40%), Positives = 29/42 (69%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRT 184
G W+ ++ +EK+P+ EE RL H + HPDY+Y+PR +++
Sbjct: 65 GKLWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQPRRRKS 106
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation,
transcription-DNA CO; HET: DNA; 2.40A {Mus musculus}
Length = 79
Score = 65.7 bits (161), Expect = 2e-14
Identities = 19/41 (46%), Positives = 27/41 (65%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKR 183
G RWK + +++K P+ +E RL HM +PDY+YRPR K
Sbjct: 38 GKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYRPRKKV 78
>1j46_A SRY, sex-determining region Y protein; MALE sex determining factor,
SRY, sex-reversal mutation; NMR {Homo sapiens} SCOP:
a.21.1.1 PDB: 1j47_A
Length = 85
Score = 65.3 bits (160), Expect = 3e-14
Identities = 19/44 (43%), Positives = 31/44 (70%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCI 186
G +WK ++ AEK P+++E +L +H EK+P+Y+YRPR K +
Sbjct: 40 GYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKML 83
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain,
endodermal, activator, DNA- nucleus, transcription
regulation, transcrip complex; HET: DNA; 2.75A {Mus
musculus} PDB: 2yul_A
Length = 83
Score = 64.5 bits (158), Expect = 6e-14
Identities = 21/41 (51%), Positives = 30/41 (73%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKR 183
G WKA++ AEK+P+ EE RL HM+ HP+Y+YRPR ++
Sbjct: 42 GKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYKYRPRRRK 82
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX
domain, structural genomics, NPPSFA, riken structural
genomics/proteomics initiative; NMR {Mus musculus}
Length = 82
Score = 63.8 bits (156), Expect = 1e-13
Identities = 10/38 (26%), Positives = 14/38 (36%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPR 180
W + EKQ Y + M+ +P YR P
Sbjct: 43 ADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRSGPS 80
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG,
TCR-A, transcription factor; HET: DNA; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 86
Score = 63.4 bits (155), Expect = 1e-13
Identities = 14/41 (34%), Positives = 22/41 (53%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKR 183
G RW A+S E+ YYE + +LHM+ +P + R +
Sbjct: 38 GRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGK 78
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus
musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B
Length = 80
Score = 62.6 bits (153), Expect = 3e-13
Identities = 23/41 (56%), Positives = 30/41 (73%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKR 183
GA WK +S EK+P+ +E RL LHM++HPDY+YRPR K
Sbjct: 38 GAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKT 78
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA
complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1
PDB: 1hrz_A*
Length = 76
Score = 61.8 bits (151), Expect = 4e-13
Identities = 17/37 (45%), Positives = 28/37 (75%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRP 179
G +WK ++ AEK P+++E +L +H EK+P+Y+YRP
Sbjct: 40 GYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRP 76
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens}
Length = 71
Score = 54.5 bits (132), Expect = 2e-10
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 9/52 (17%)
Query: 134 KMPEETPDK---------GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYR 176
++ ++ PD G WKA++ AEK+P+ EE RL HM+ HP+Y+
Sbjct: 20 RLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNYK 71
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG BOX,
amphoterin, DNA/structural protein complex; NMR {Homo
sapiens} SCOP: a.21.1.1 a.21.1.1
Length = 159
Score = 54.1 bits (130), Expect = 2e-09
Identities = 21/135 (15%), Positives = 41/135 (30%), Gaps = 15/135 (11%)
Query: 53 NYSSLSSSAGKMSMSSPGKEKTPEYNMHGMYSPHHDKNMYSPHDKNMYSPHDKNMYSPHH 112
S +S G EK P + H + Y +
Sbjct: 31 RNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKY----PNYKYRKGETKKKFKDP 86
Query: 113 DKSEEQDLLMSVWGAGGESPYKMPEETPDK---------GARWKAMSNAEKQPYYEEQSR 163
+ + ++ + E K+ E P G W + +KQPY ++ ++
Sbjct: 87 NAPKRPPSAFFLFCS--EYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAK 144
Query: 164 LSKLHMEKHPDYRYR 178
L + + + YR +
Sbjct: 145 LKEKYEKDIAAYRAK 159
Score = 47.5 bits (113), Expect = 5e-07
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIV--DGKKMRISEYKTL 200
G +WK ++ AEK P+++E +L +H EK+P+Y+YR + + K S +
Sbjct: 40 GYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLF 99
Query: 201 MRQRRNEMRQ 210
+ R +++
Sbjct: 100 CSEYRPKIKG 109
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box transcription
factor 1, high mobility group box transcription factor
1, structural genomics; NMR {Homo sapiens}
Length = 87
Score = 50.9 bits (122), Expect = 6e-09
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 9/50 (18%)
Query: 134 KMPEETPDK---------GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPD 174
+ + P K G RWK M N E++ Y E L++ +PD
Sbjct: 35 EYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRLNPD 84
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus musculus}
SCOP: a.21.1.1
Length = 90
Score = 44.3 bits (105), Expect = 2e-06
Identities = 6/34 (17%), Positives = 10/34 (29%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYR 176
W +S +K Y ++ L K
Sbjct: 56 ARMWNDLSEKKKAKYKAREAALKAQSERKSGPSS 89
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of
chromatin subfamily...; structural DNA-binding protein
BRAF35, DNA-bending; NMR {Mus musculus}
Length = 92
Score = 42.4 bits (100), Expect = 8e-06
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPK 182
GA W + AEKQ Y +E + + ++++ Y+ K
Sbjct: 43 GAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQSEAYK 82
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A
1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A
Length = 77
Score = 41.9 bits (99), Expect = 9e-06
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYR 178
G W + +KQPY ++ ++L + + + YR +
Sbjct: 42 GEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 77
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 40.5 bits (95), Expect = 5e-05
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYR 178
GA W A+S+ EK+PY + + +Y R
Sbjct: 60 GAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQR 95
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 37.8 bits (88), Expect = 4e-04
Identities = 8/41 (19%), Positives = 17/41 (41%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKR 183
+ W + +KQ Y ++ K ++++ YR K
Sbjct: 53 ASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLVSKS 93
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 36.3 bits (84), Expect = 0.001
Identities = 7/42 (16%), Positives = 15/42 (35%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRT 184
WK +S EK Y E+ ++ + + + +
Sbjct: 43 EELWKTLSEEEKLKYEEKATKDLERYNSQMKRAIEQESQMSL 84
>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA
recognition, chromatin, DNA binding protein; NMR
{Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A
1lwm_A
Length = 93
Score = 34.2 bits (79), Expect = 0.007
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYR 176
G +WKA++ EKQPY + K + + Y
Sbjct: 56 GEKWKALTPEEKQPYEAKAQADKKRYESEKELYN 89
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 33.0 bits (76), Expect = 0.010
Identities = 5/34 (14%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYR 176
G WK + +K + + ++ + + ++ +Y+
Sbjct: 39 GEMWKELK--DKSKWEDAAAKDKQRYHDEMRNYK 70
>3nm9_A HMG-D, high mobility group protein D; DNA bending,
non-sequence-specific, HMG chromosomal protein; HET:
DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A* 1hma_A
1qrv_A*
Length = 73
Score = 32.6 bits (75), Expect = 0.015
Identities = 5/34 (14%), Positives = 14/34 (41%), Gaps = 2/34 (5%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYR 176
G W+AM +K + + ++ + ++
Sbjct: 39 GELWRAMK--DKSEWEAKAAKAKDDYDRAVKEFE 70
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding
protein; NMR {Homo sapiens} SCOP: a.21.1.1
Length = 99
Score = 31.2 bits (71), Expect = 0.074
Identities = 7/45 (15%), Positives = 15/45 (33%), Gaps = 7/45 (15%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHME-------KHPDYRYRPR 180
++K + +K Y ++ R + HPD +
Sbjct: 46 SKKYKELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAK 90
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding,
helix-turn-helix motif, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 173
Score = 32.3 bits (73), Expect = 0.080
Identities = 9/36 (25%), Positives = 19/36 (52%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYR 178
G W + +KQPY ++ ++L + + + YR +
Sbjct: 137 GEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 172
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT
DNA, protein-drug-DNA compl regulation-DNA complex; HET:
DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1 PDB:
1j3x_A
Length = 71
Score = 30.0 bits (68), Expect = 0.15
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDY 175
RWK MS EK + + + + Y
Sbjct: 39 SERWKTMSAKEKGKFEDMAKADKARYEREMKTY 71
>1v63_A Nucleolar transcription factor 1; DNA binding, structural genomics,
riken structural genomics/proteomics initiative, RSGI,
DNA binding protein; NMR {Mus musculus} SCOP: a.21.1.1
Length = 101
Score = 30.7 bits (69), Expect = 0.15
Identities = 7/41 (17%), Positives = 18/41 (43%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKR 183
G+RW+ +S ++K+ Y + + + + P+
Sbjct: 42 GSRWQRISQSQKEHYKKLAEEQQRQYKVHLDLWVKSLSPQD 82
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 30.0 bits (68), Expect = 0.16
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 143 GARWKAMSNAEKQPYYEE 160
RWK MS EK + +
Sbjct: 45 SERWKTMSAKEKGKFEDM 62
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial
transcription, activator, DNA- binding, mitochondrion,
phosphoprotein; 1.35A {Homo sapiens}
Length = 67
Score = 29.6 bits (67), Expect = 0.17
Identities = 6/18 (33%), Positives = 11/18 (61%)
Query: 143 GARWKAMSNAEKQPYYEE 160
WK +S++EK+ Y +
Sbjct: 34 KENWKNLSDSEKELYIQH 51
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group
protein 2A, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 86
Score = 29.6 bits (67), Expect = 0.20
Identities = 8/18 (44%), Positives = 9/18 (50%)
Query: 143 GARWKAMSNAEKQPYYEE 160
RWK MS EK + E
Sbjct: 53 SERWKTMSGKEKSKFDEM 70
>1lwu_C Fibrinogen gamma chain; heterotrimer, protein-peptide complex,
blood clotting; HET: NDG MAN NAG BMA GAL; 2.80A
{Petromyzon marinus} SCOP: d.171.1.1 h.1.8.1 PDB:
1n73_C*
Length = 323
Score = 29.4 bits (66), Expect = 1.1
Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 15 ESQQKQQMEIHRFHQEQFKRQQEHLLQQQHKIQELQ 50
+S QK +I E+ + ++ + +IQEL
Sbjct: 1 DSGQKTVQKI----LEEVRILEQIGVSHDAQIQELS 32
>1v64_A Nucleolar transcription factor 1; DNA binding, structural genomics,
riken structural genomics/proteomics initiative, RSGI;
NMR {Mus musculus} SCOP: a.21.1.1
Length = 108
Score = 27.6 bits (61), Expect = 1.7
Identities = 7/41 (17%), Positives = 17/41 (41%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKR 183
+WK +S EK Y+++ + K + + + +
Sbjct: 49 SQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFLESLPEEE 89
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.0 bits (61), Expect = 1.9
Identities = 8/22 (36%), Positives = 11/22 (50%), Gaps = 4/22 (18%)
Query: 153 EKQPYYEEQSRLSKLHMEKHPD 174
EKQ + Q+ L KL+ D
Sbjct: 18 EKQALKKLQASL-KLYA---DD 35
>1a31_A Protein (topoisomerase I); topoisomerase I/DNA, DNA, isomerase/DNA
complex; HET: DNA 5IU PTR; 2.10A {Homo sapiens} SCOP:
d.163.1.2 e.15.1.1 PDB: 1k4t_A* 1k4s_A* 1sc7_A* 1t8i_A*
1tl8_A* 1seu_A* 1a35_A* 1a36_A* 1r49_A* 1rrj_A* 1nh3_A*
1lpq_A* 1rr8_C* 1ej9_A*
Length = 591
Score = 28.6 bits (63), Expect = 2.6
Identities = 25/109 (22%), Positives = 34/109 (31%), Gaps = 21/109 (19%)
Query: 141 DKGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTL 200
+ K MS EK EE +L K + CI+D K RI+ +K
Sbjct: 137 AQTEARKQMSKEEKLKIKEENEKLLKEYG--------------FCIMDNHKERIANFKI- 181
Query: 201 MRQRRNEMRQLWCRGEAGPSGSGGPAFPFPGDGSLSPSDMMPFSPGSPG 249
+ R RG G P D ++ S PG
Sbjct: 182 --EPPGLFRG---RGNHPKMGMLKRRI-MPEDIIINCSKDAKVPSPPPG 224
>2x7x_A Sensor protein; transferase, sensor histidine kinase; HET: FRU;
2.64A {Bacteroides thetaiotaomicron}
Length = 325
Score = 28.1 bits (63), Expect = 3.0
Identities = 5/21 (23%), Positives = 9/21 (42%)
Query: 30 EQFKRQQEHLLQQQHKIQELQ 50
+ Q H+ + KI+ L
Sbjct: 282 HVMQLQTTHISELDKKIETLN 302
>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 = 3.1
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 6/36 (16%)
Query: 39 LLQQQHKIQELQVF------NYSSLSSSAGKMSMSS 68
L+ + I F Y++L+S A MS+ S
Sbjct: 1746 DLKSKGLIPADATFAGHSLGEYAALASLADVMSIES 1781
>4f78_A D,D-dipeptidase/D,D-carboxypeptidase; center for structural
genomics of infectious diseases; HET: MSE; 1.95A
{Enterococcus faecalis}
Length = 255
Score = 27.7 bits (61), Expect = 3.4
Identities = 18/105 (17%), Positives = 35/105 (33%), Gaps = 8/105 (7%)
Query: 108 YSPHHDKSEEQDLLMSVWGAGGESPYKMPEETPDKGARWKAMSNAEK----QPYYEEQSR 163
Y + SE Q L G + + + P G + A Q Y ++
Sbjct: 99 YVALPNHSEHQTGLAIDLGLNKKDIDFIRPDFPYDGICDEFRRAAPDYGFTQRYARDKEE 158
Query: 164 LSKLHMEK-HPDYRYRPRPKRTCIVDGKKMRISEYKTLMRQRRNE 207
++ + E H +RY P + + + EY ++ +
Sbjct: 159 ITGISHEPWH--FRYVGYPHSKIMQE-NGFSLEEYTQFIKAYLED 200
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group,
transcription, LSP1, mitochon transcription-DNA complex;
HET: DNA; 2.50A {Homo sapiens}
Length = 238
Score = 27.5 bits (60), Expect = 3.6
Identities = 8/67 (11%), Positives = 30/67 (44%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMR 202
RW+ + +++K+ Y + +++ E+ ++ + P + ++ + M + M
Sbjct: 77 AQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMT 136
Query: 203 QRRNEMR 209
+++
Sbjct: 137 KKKELTL 143
Score = 27.1 bits (59), Expect = 6.2
Identities = 6/34 (17%), Positives = 14/34 (41%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYR 176
WK +S++EK+ Y + + + +
Sbjct: 178 KENWKNLSDSEKELYIQHAKEDETRYHNEMKSWE 211
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 27.7 bits (61), Expect = 4.3
Identities = 15/95 (15%), Positives = 26/95 (27%), Gaps = 5/95 (5%)
Query: 39 LLQQQHKIQELQVFNYSSLSSSAGKMSMSSPGKEKTPEYNMHGMYSPHHDKNMYSPHDKN 98
+ Q + + + +G + P TP SP D D
Sbjct: 1449 IYLDQDMLMNYSLGTAVPTLAGSGMGTSQLPEGAGTP-----YERSPMVDSGFVGSPDAA 1503
Query: 99 MYSPHDKNMYSPHHDKSEEQDLLMSVWGAGGESPY 133
+SP + + L + G +SP
Sbjct: 1504 AFSPLVQGGSEGREGFGDYGLLGAASPYKGVQSPG 1538
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription
regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo
sapiens}
Length = 214
Score = 27.4 bits (60), Expect = 4.4
Identities = 8/67 (11%), Positives = 30/67 (44%)
Query: 143 GARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMR 202
RW+ + +++K+ Y + +++ E+ ++ + P + ++ + M + M
Sbjct: 45 AQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMT 104
Query: 203 QRRNEMR 209
+++
Sbjct: 105 KKKELTL 111
>1nkp_A C-MYC, MYC proto-oncogene protein; transcription, DNA, BHLHZ,
heterodimer, transcription/DNA complex; 1.80A {Homo
sapiens} SCOP: a.38.1.1
Length = 88
Score = 26.1 bits (58), Expect = 4.4
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 1 MDKSVILSSLKLASESQQKQQMEIHRFHQE--QFKRQQEHLLQQQHKIQELQ 50
K VIL A+ Q E + E ++++E L +HK+++L
Sbjct: 41 APKVVILKK---ATAYILSVQAEEQKLISEEDLLRKRREQL---KHKLEQLG 86
>1bf5_A Signal transducer and activator of transcription 1-alpha/beta;
complex (SH2 domain/DNA), SH2 domain, transcription
factor; HET: DNA PTR; 2.90A {Homo sapiens} SCOP:
a.47.1.1 b.2.5.5 d.93.1.1
Length = 575
Score = 27.5 bits (60), Expect = 5.4
Identities = 10/66 (15%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 20 QQMEIHRFHQEQFKRQQ--EHLLQQQHKIQELQVFNYSSLSSSAGKMSMSSPGKEKTPEY 77
+Q E+ + + EH ++ +Q+ F +L + + + + +K +
Sbjct: 3 KQKELDSKVRNVKDKVMCIEHEIKSLEDLQDEYDFKCKTLQNREHETNGVAKSDQKQEQL 62
Query: 78 NMHGMY 83
+ MY
Sbjct: 63 LLKKMY 68
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 26.7 bits (58), Expect = 6.4
Identities = 12/93 (12%), Positives = 29/93 (31%), Gaps = 31/93 (33%)
Query: 116 EEQDLLMSVWGAGGESPYKMPEETPDKGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDY 175
EEQ + ++ + W+ + + + + + QS +EK+
Sbjct: 92 EEQRKRLQ----------ELDAASKVMEQEWREKAKKDLEEWNQRQSE----QVEKNK-- 135
Query: 176 RYRPRPKRTCIVDGKKMRISEYKTLMRQRRNEM 208
RI++ K +Q ++
Sbjct: 136 --------------INNRIAD-KAFYQQPDADI 153
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
0.312 0.128 0.384
Gapped
Lambda K H
0.267 0.0559 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,859,267
Number of extensions: 218009
Number of successful extensions: 470
Number of sequences better than 10.0: 1
Number of HSP's gapped: 461
Number of HSP's successfully gapped: 72
Length of query: 257
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 165
Effective length of database: 4,133,061
Effective search space: 681955065
Effective search space used: 681955065
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: 56 (25.7 bits)