RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12430
(146 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 = 125 bits (316), Expect = 7e-39
Identities = 62/73 (84%), Positives = 70/73 (95%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVWAKDERRKIL+A PDMHNSNISKILG+RWKAM+N EKQPYYEEQ+RLSK H+EK
Sbjct: 9 MNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK 68
Query: 61 HPDYRYRPRPKRT 73
+PDY+Y+PRPKRT
Sbjct: 69 YPDYKYKPRPKRT 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 = 121 bits (306), Expect = 5e-37
Identities = 34/73 (46%), Positives = 51/73 (69%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVWA+ RRK+ P +HN+ +SK LG W+ ++ +EK+P+ EE RL H +
Sbjct: 34 MNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKD 93
Query: 61 HPDYRYRPRPKRT 73
HPDY+Y+PR +++
Sbjct: 94 HPDYKYQPRRRKS 106
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional
regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus
musculus}
Length = 79
Score = 118 bits (298), Expect = 3e-36
Identities = 40/72 (55%), Positives = 53/72 (73%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVW++ ERRKI++ PDMHN+ ISK LG RWK + +++K P+ +E RL HM
Sbjct: 7 MNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMAD 66
Query: 61 HPDYRYRPRPKR 72
+PDY+YRPR K
Sbjct: 67 YPDYKYRPRKKV 78
>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 = 118 bits (297), Expect = 6e-36
Identities = 21/69 (30%), Positives = 32/69 (46%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAF+++ K R + + P + N +KIL W + EKQ Y + M+
Sbjct: 12 MNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKA 71
Query: 61 HPDYRYRPR 69
+P YR P
Sbjct: 72 NPGYRSGPS 80
>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 = 117 bits (296), Expect = 9e-36
Identities = 37/75 (49%), Positives = 54/75 (72%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAF+VW++D+RRK+ P M NS ISK LG +WK ++ AEK P+++E +L +H EK
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 61 HPDYRYRPRPKRTCI 75
+P+Y+YRPR K +
Sbjct: 69 YPNYKYRPRRKAKML 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 = 117 bits (296), Expect = 1e-35
Identities = 40/72 (55%), Positives = 57/72 (79%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVWAKDER+++ + PD+HN+ +SK+LG WKA++ AEK+P+ EE RL HM+
Sbjct: 11 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQD 70
Query: 61 HPDYRYRPRPKR 72
HP+Y+YRPR ++
Sbjct: 71 HPNYKYRPRRRK 82
>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 = 117 bits (295), Expect = 1e-35
Identities = 35/68 (51%), Positives = 51/68 (75%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAF+VW++D+RRK+ P M NS ISK LG +WK ++ AEK P+++E +L +H EK
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 61 HPDYRYRP 68
+P+Y+YRP
Sbjct: 69 YPNYKYRP 76
>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 = 117 bits (295), Expect = 1e-35
Identities = 23/72 (31%), Positives = 41/72 (56%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+NAFM++ K+ R ++ ++ I++ILG RW A+S E+ YYE + +LHM+
Sbjct: 7 LNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQL 66
Query: 61 HPDYRYRPRPKR 72
+P + R +
Sbjct: 67 YPGWSARDNYGK 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 = 115 bits (290), Expect = 7e-35
Identities = 42/72 (58%), Positives = 54/72 (75%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVW++ +RRK+ + P MHNS ISK LGA WK +S EK+P+ +E RL LHM++
Sbjct: 7 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 66
Query: 61 HPDYRYRPRPKR 72
HPDY+YRPR K
Sbjct: 67 HPDYKYRPRRKT 78
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens}
Length = 71
Score = 109 bits (275), Expect = 8e-33
Identities = 36/65 (55%), Positives = 51/65 (78%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFMVWAKDER+++ + PD+HN+ +SK+LG WKA++ AEK+P+ EE RL HM+
Sbjct: 7 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQD 66
Query: 61 HPDYR 65
HP+Y+
Sbjct: 67 HPNYK 71
>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 = 105 bits (264), Expect = 6e-31
Identities = 26/63 (41%), Positives = 35/63 (55%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAFM++AK R + + P N IS ILG RWK M N E++ Y E L++
Sbjct: 22 MNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRL 81
Query: 61 HPD 63
+PD
Sbjct: 82 NPD 84
>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 = 95.3 bits (237), Expect = 5e-26
Identities = 17/67 (25%), Positives = 35/67 (52%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+AF ++ + R KI P + +++K LG W + +KQPY ++ ++L + + +
Sbjct: 93 PSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD 152
Query: 61 HPDYRYR 67
YR +
Sbjct: 153 IAAYRAK 159
Score = 94.5 bits (235), Expect = 9e-26
Identities = 37/101 (36%), Positives = 60/101 (59%), Gaps = 2/101 (1%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MNAF+VW++D+RRK+ P M NS ISK LG +WK ++ AEK P+++E +L +H EK
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 61 HPDYRYRPRPKRTCIV--DGKKMRISEYKTLMRQRRNEMRQ 99
+P+Y+YR + + K S + + R +++
Sbjct: 69 YPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKG 109
>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 = 92.1 bits (229), Expect = 1e-25
Identities = 12/65 (18%), Positives = 33/65 (50%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
++A ++++++RR++ + P++ S ++++L W +S +K Y ++ L K
Sbjct: 25 VSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERK 84
Query: 61 HPDYR 65
Sbjct: 85 SGPSS 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 = 79.7 bits (197), Expect = 9e-21
Identities = 18/71 (25%), Positives = 36/71 (50%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+ ++ + + R +I PD+ I+K+LGA W + AEKQ Y +E + + ++++
Sbjct: 12 VTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKE 71
Query: 61 HPDYRYRPRPK 71
Y+ K
Sbjct: 72 LWAYQQSEAYK 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 = 78.1 bits (193), Expect = 3e-20
Identities = 17/67 (25%), Positives = 35/67 (52%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+AF ++ + R KI P + +++K LG W + +KQPY ++ ++L + + +
Sbjct: 11 PSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD 70
Query: 61 HPDYRYR 67
YR +
Sbjct: 71 IAAYRAK 77
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 73.6 bits (181), Expect = 2e-18
Identities = 13/73 (17%), Positives = 29/73 (39%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
M+A ++ +D R + L P + + + WK +S EK Y E+ ++ + + +
Sbjct: 12 MSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQ 71
Query: 61 HPDYRYRPRPKRT 73
+
Sbjct: 72 MKRAIEQESQMSL 84
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 69.6 bits (171), Expect = 5e-17
Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 2/65 (3%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
AFM+W D R I + P + + I+K G WK + +K + + ++ + + ++
Sbjct: 8 TTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDE 65
Query: 61 HPDYR 65
+Y+
Sbjct: 66 MRNYK 70
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 69.0 bits (169), Expect = 1e-16
Identities = 19/69 (27%), Positives = 39/69 (56%), Gaps = 2/69 (2%)
Query: 1 MNAFMVWAKDERRKILKACPDMHN--SNISKILGARWKAMSNAEKQPYYEEQSRLSKLHM 58
++++M +AK++R +I+ P++ + I K++GA W A+S+ EK+PY +
Sbjct: 27 LSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYE 86
Query: 59 EKHPDYRYR 67
+ +Y R
Sbjct: 87 REKAEYAQR 95
>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 = 67.7 bits (166), Expect = 3e-16
Identities = 11/65 (16%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
++A+ +W R I + P + + ++K G W+AM +K + + ++ +
Sbjct: 8 LSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRA 65
Query: 61 HPDYR 65
++
Sbjct: 66 VKEFE 70
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 68.6 bits (168), Expect = 3e-16
Identities = 15/72 (20%), Positives = 34/72 (47%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
++A+ ++ +D + I P+ +SKI+ + W + +KQ Y ++ K ++++
Sbjct: 22 VSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQ 81
Query: 61 HPDYRYRPRPKR 72
YR K
Sbjct: 82 LAAYRASLVSKS 93
>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 = 64.3 bits (157), Expect = 9e-15
Identities = 19/65 (29%), Positives = 33/65 (50%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
++A+M +A + R + PD+ + K LG +WKA++ EKQPY + K + +
Sbjct: 25 LSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE 84
Query: 61 HPDYR 65
Y
Sbjct: 85 KELYN 89
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding
protein; NMR {Homo sapiens} SCOP: a.21.1.1
Length = 99
Score = 64.4 bits (157), Expect = 1e-14
Identities = 16/76 (21%), Positives = 33/76 (43%), Gaps = 7/76 (9%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHME- 59
+ + + ++R K K P+M N +++KIL ++K + +K Y ++ R +
Sbjct: 15 LTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERN 74
Query: 60 ------KHPDYRYRPR 69
HPD +
Sbjct: 75 LARFREDHPDLIQNAK 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 = 59.2 bits (143), Expect = 6e-12
Identities = 17/67 (25%), Positives = 35/67 (52%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+AF ++ + R KI P + +++K LG W + +KQPY ++ ++L + + +
Sbjct: 106 PSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD 165
Query: 61 HPDYRYR 67
YR +
Sbjct: 166 IAAYRAK 172
Score = 42.7 bits (100), Expect = 7e-06
Identities = 17/82 (20%), Positives = 30/82 (36%), Gaps = 2/82 (2%)
Query: 1 MNAFMVWAKDERRKILKACPD--MHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHM 58
M+++ + + R + K PD ++ S SK RWK MS EK + + +
Sbjct: 20 MSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE 79
Query: 59 EKHPDYRYRPRPKRTCIVDGKK 80
+ Y + D
Sbjct: 80 REMKTYIPPKGETKKKFKDPNA 101
>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 = 55.5 bits (134), Expect = 2e-11
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 2/66 (3%)
Query: 1 MNAFMVWAKDERRKILKACPDMHN--SNISKILGARWKAMSNAEKQPYYEEQSRLSKLHM 58
M+++ + + R + K PD S SK RWK MS EK + + +
Sbjct: 6 MSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE 65
Query: 59 EKHPDY 64
+ Y
Sbjct: 66 REMKTY 71
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 53.8 bits (130), Expect = 7e-11
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 1 MNAFMVWAKDERRKILKACPD--MHNSNISKILGARWKAMSNAEKQPYYEE 49
M+++ + + R + K PD ++ S SK RWK MS EK + +
Sbjct: 12 MSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDM 62
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group
protein 2A, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 86
Score = 53.1 bits (128), Expect = 2e-10
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSN--ISKILGARWKAMSNAEKQPYYEE 49
M+A+ + + R + K P++ + SK RWK MS EK + E
Sbjct: 20 MSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEM 70
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription
regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo
sapiens}
Length = 214
Score = 52.4 bits (125), Expect = 2e-09
Identities = 11/98 (11%), Positives = 46/98 (46%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+++++ ++K++ PD + + + + RW+ + +++K+ Y + +++ E+
Sbjct: 14 VSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEE 73
Query: 61 HPDYRYRPRPKRTCIVDGKKMRISEYKTLMRQRRNEMR 98
++ + P + ++ + M + M +++
Sbjct: 74 ISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTL 111
Score = 42.8 bits (100), Expect = 8e-06
Identities = 9/65 (13%), Positives = 24/65 (36%), Gaps = 4/65 (6%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+A+ V+ + ++ K + WK +S++EK+ Y + + +
Sbjct: 119 RSAYNVYVAERFQEA----KGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNE 174
Query: 61 HPDYR 65
+
Sbjct: 175 MKSWE 179
>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 = 52.1 bits (124), Expect = 4e-09
Identities = 11/98 (11%), Positives = 46/98 (46%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+++++ ++K++ PD + + + + RW+ + +++K+ Y + +++ E+
Sbjct: 46 VSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEE 105
Query: 61 HPDYRYRPRPKRTCIVDGKKMRISEYKTLMRQRRNEMR 98
++ + P + ++ + M + M +++
Sbjct: 106 ISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTL 143
Score = 42.1 bits (98), Expect = 2e-05
Identities = 9/65 (13%), Positives = 24/65 (36%), Gaps = 4/65 (6%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
+A+ V+ + ++ K + WK +S++EK+ Y + + +
Sbjct: 151 RSAYNVYVAERFQEA----KGDSPQEKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNE 206
Query: 61 HPDYR 65
+
Sbjct: 207 MKSWE 211
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial
transcription, activator, DNA- binding, mitochondrion,
phosphoprotein; 1.35A {Homo sapiens}
Length = 67
Score = 46.9 bits (112), Expect = 3e-08
Identities = 10/49 (20%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEE 49
+A+ V+ + ++ P K + WK +S++EK+ Y +
Sbjct: 7 RSAYNVYVAERFQEAKGDSPQE----KLKTVKENWKNLSDSEKELYIQH 51
>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group
box domain, helix-turn-helix, structural genomics,
NPPSFA; NMR {Homo sapiens}
Length = 81
Score = 44.8 bits (105), Expect = 2e-07
Identities = 12/50 (24%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 1 MNAFMVWAKDERRKILKACPDMHN-SNISKILGARWKAMSNAEKQPYYEE 49
F +W ++ R IL PD + ++I K R++ +S E++ + +
Sbjct: 10 KTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANK 59
>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 = 41.8 bits (98), Expect = 4e-06
Identities = 9/72 (12%), Positives = 27/72 (37%), Gaps = 2/72 (2%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
MN + ++++ + +G+RW+ +S ++K+ Y + + +
Sbjct: 13 MNGYQKFSQELLSN--GELNHLPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQYKVH 70
Query: 61 HPDYRYRPRPKR 72
+ P+
Sbjct: 71 LDLWVKSLSPQD 82
>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 = 39.2 bits (91), Expect = 5e-05
Identities = 9/72 (12%), Positives = 29/72 (40%), Gaps = 4/72 (5%)
Query: 1 MNAFMVWAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEK 60
N++ ++ + + D+ ++ + +WK +S EK Y+++ + K + +
Sbjct: 22 PNSYSLYCAELMANM----KDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDYEVE 77
Query: 61 HPDYRYRPRPKR 72
+ +
Sbjct: 78 LLRFLESLPEEE 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 = 28.4 bits (62), Expect = 0.62
Identities = 8/22 (36%), Positives = 11/22 (50%), Gaps = 4/22 (18%)
Query: 42 EKQPYYEEQSRLSKLHMEKHPD 63
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 = 0.81
Identities = 25/106 (23%), Positives = 33/106 (31%), Gaps = 21/106 (19%)
Query: 33 ARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKTLMRQ 92
K MS EK EE +L K + CI+D K RI+ +K +
Sbjct: 140 EARKQMSKEEKLKIKEENEKLLKEYG--------------FCIMDNHKERIANFKI---E 182
Query: 93 RRNEMRQLWCRGEAGPSGSGGPAFPFPGDGSLSPSDMMPFSPGSPG 138
R RG G P D ++ S PG
Sbjct: 183 PPGLFRG---RGNHPKMGMLKRRI-MPEDIIINCSKDAKVPSPPPG 224
>2b9s_A Topoisomerase I-like protein; vanadate complex, isomerase/DNA
complex; HET: DNA; 2.27A {Leishmania donovani}
Length = 432
Score = 27.3 bits (60), Expect = 2.1
Identities = 13/92 (14%), Positives = 35/92 (38%), Gaps = 19/92 (20%)
Query: 2 NAFMVWAK--DERRKILKACPDMHNSNISKILGA---RWKAMSNAEKQPYYEEQSRLSKL 56
N F W + D+R+ ++ I + + + + EK+ E+Q ++
Sbjct: 80 NFFESWREILDKRQHPIRRLELCDFEPIYQWHLVQREKKLSRTKEEKKAIKEKQDAEAEP 139
Query: 57 HMEKHPDYRYRPRPKRTCIVDGKKMRISEYKT 88
+ C+ DG++ +++ ++
Sbjct: 140 YR--------------YCVWDGRREQVANFRV 157
>2wux_A Polyhedrin; microcrystals, polyhedra, viral protein, viral
occlusion BODY, viral capsid; 1.84A {Autographa
californica nuclearpolyhedrosis virus} PDB: 3jw6_A*
2wuy_A 3jvb_A
Length = 245
Score = 26.5 bits (58), Expect = 3.5
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 62 PDYRYRPRPKRTCIVDGKKMR 82
PDY YRP RT + D K +
Sbjct: 2 PDYSYRPTIGRTYVYDNKYYK 22
>1m1j_C Fibrinogen gamma chain; coiled coils, disulfide rings, fibrinogen,
blood clotting; HET: NDG NAG; 2.70A {Gallus gallus}
SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_C
Length = 409
Score = 26.0 bits (57), Expect = 5.1
Identities = 11/30 (36%), Positives = 14/30 (46%)
Query: 104 GEAGPSGSGGPAFPFPGDGSLSPSDMMPFS 133
GEAG + G P D S + + M FS
Sbjct: 284 GEAGDAFDGFNFGDDPSDKSYTYHNGMRFS 313
>2o8s_A AGR_C_984P; all alpha-helical protein, structural genomics, PSI-2,
prote structure initiative; 2.40A {Agrobacterium
tumefaciens} SCOP: a.295.1.1
Length = 323
Score = 25.9 bits (56), Expect = 5.3
Identities = 10/45 (22%), Positives = 20/45 (44%), Gaps = 4/45 (8%)
Query: 1 MNAF----MVWAKDERRKILKACPDMHNSNISKILGARWKAMSNA 41
+ A M +AK RK+L N+ +K+ R+ ++ +
Sbjct: 112 LKAHGLEDMAYAKAFIRKVLTEGASDKNAFANKLSDNRYAELAKS 156
>3tqy_A Single-stranded DNA-binding protein; DNA replication, transferase;
2.60A {Coxiella burnetii}
Length = 158
Score = 25.5 bits (56), Expect = 5.6
Identities = 12/52 (23%), Positives = 19/52 (36%)
Query: 95 NEMRQLWCRGEAGPSGSGGPAFPFPGDGSLSPSDMMPFSPGSPGSMDSHDED 146
NEM L RG G + + +P+ + G S+ D+D
Sbjct: 107 NEMHMLDNRGGGNSGNYGNHSEGGASNKQSAPTSSQTPTAGDDSSVADFDDD 158
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 26.2 bits (57), Expect = 6.3
Identities = 8/39 (20%), Positives = 11/39 (28%)
Query: 104 GEAGPSGSGGPAFPFPGDGSLSPSDMMPFSPGSPGSMDS 142
+G + SP +P SPG S
Sbjct: 1500 SNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVS 1538
>2hg4_A DEBS, 6-deoxyerythronolide B synthase; ketosynthase,
acyltransferase, module 5, transferase; 2.73A
{Saccharopolyspora erythraea}
Length = 917
Score = 25.7 bits (57), Expect = 6.6
Identities = 8/21 (38%), Positives = 10/21 (47%), Gaps = 2/21 (9%)
Query: 103 RGEAGPSGSGGPAFPFPGDGS 123
G+A G A FPG G+
Sbjct: 544 TGQARTRR--GVAMVFPGQGA 562
>3q1n_A Galactose mutarotase related enzyme; structural genomics, joint
center for structural genomics, J protein structure
initiative, PSI-biology; HET: MSE; 1.61A {Lactobacillus
casei}
Length = 294
Score = 25.6 bits (56), Expect = 6.9
Identities = 4/30 (13%), Positives = 9/30 (30%)
Query: 91 RQRRNEMRQLWCRGEAGPSGSGGPAFPFPG 120
+ + +W + + FP G
Sbjct: 25 VNKADNYEYVWTGDKTFWNRHAPILFPSIG 54
>2fji_1 Exocyst complex component SEC6; exocytosis, tandem helical bundles,
endocytosis/exocytosis complex; 2.40A {Saccharomyces
cerevisiae}
Length = 399
Score = 25.6 bits (55), Expect = 7.9
Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 1/62 (1%)
Query: 9 KDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRP 68
D +K L+ D + IL R K +S++E++ ++ + + +
Sbjct: 326 LDIWQKYLEVYWDSRIDLLVGILKCR-KDVSSSERKKIVQQATEMLHEYRRNMEANGVDR 384
Query: 69 RP 70
P
Sbjct: 385 EP 386
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 25.1 bits (54), Expect = 8.3
Identities = 16/91 (17%), Positives = 35/91 (38%), Gaps = 27/91 (29%)
Query: 7 WAKDERRKILKACPDMHNSNISKILGARWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRY 66
W ++E+RK L+ SK++ W+ + + + + + QS +EK+
Sbjct: 90 W-REEQRKRLQE-----LDAASKVMEQEWREKAKKDLEEWNQRQSE----QVEKNK---- 135
Query: 67 RPRPKRTCIVDGKKMRISEYKTLMRQRRNEM 97
RI++ K +Q ++
Sbjct: 136 ------------INNRIAD-KAFYQQPDADI 153
>1ois_A DNA topoisomerase I; DNA-binding protein; HET: DNA; 1.90A
{Saccharomyces cerevisiae} SCOP: e.15.1.1
Length = 223
Score = 25.3 bits (55), Expect = 8.6
Identities = 8/55 (14%), Positives = 23/55 (41%), Gaps = 14/55 (25%)
Query: 34 RWKAMSNAEKQPYYEEQSRLSKLHMEKHPDYRYRPRPKRTCIVDGKKMRISEYKT 88
+ K +++ EK+ E+ + + + C +DG++ ++ +K
Sbjct: 107 QKKQLTSQEKKQIRLEREKFEEDYK--------------FCELDGRREQVGNFKV 147
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
0.317 0.133 0.419
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,336,415
Number of extensions: 128228
Number of successful extensions: 411
Number of sequences better than 10.0: 1
Number of HSP's gapped: 396
Number of HSP's successfully gapped: 58
Length of query: 146
Length of database: 6,701,793
Length adjustment: 85
Effective length of query: 61
Effective length of database: 4,328,508
Effective search space: 264038988
Effective search space used: 264038988
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.3 bits)