RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy15634
(113 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 = 64.5 bits (158), Expect = 2e-15
Identities = 23/35 (65%), Positives = 26/35 (74%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
G HIKRPMNAFMVW++ +RRKI P MHNS I
Sbjct: 1 GSPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNI 35
>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 = 64.3 bits (157), Expect = 3e-15
Identities = 12/46 (26%), Positives = 18/46 (39%)
Query: 15 PPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+ KRPMNAFM++++ R + P N I
Sbjct: 3 SGSSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAI 48
>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 = 64.2 bits (157), Expect = 3e-15
Identities = 10/35 (28%), Positives = 20/35 (57%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
G +RPMNAF+++ + R + ++P++ N
Sbjct: 4 GSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGA 38
>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 = 63.3 bits (155), Expect = 5e-15
Identities = 23/34 (67%), Positives = 29/34 (85%)
Query: 27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+ +KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens}
Length = 71
Score = 62.2 bits (152), Expect = 1e-14
Identities = 16/32 (50%), Positives = 26/32 (81%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
I+RPMNAFMVW++ +R+++A NP +HN+ +
Sbjct: 2 SIRRPMNAFMVWAKDERKRLAQQNPDLHNAEL 33
>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 = 62.2 bits (152), Expect = 2e-14
Identities = 16/35 (45%), Positives = 26/35 (74%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
I+RPMNAFMVW++ +R+++A NP +HN+ +
Sbjct: 3 FTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAEL 37
>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 = 61.8 bits (151), Expect = 2e-14
Identities = 23/34 (67%), Positives = 29/34 (85%)
Query: 27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+ +KRPMNAF+VWSR QRRK+AL+NP+M NS I
Sbjct: 2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEI 35
>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 = 62.4 bits (152), Expect = 3e-14
Identities = 21/60 (35%), Positives = 31/60 (51%)
Query: 1 MSLSSHHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
M+ HH + + H+KRPMNAFMVW++ RRK+A P +HN+ +
Sbjct: 1 MAHHHHHHVDDDDKMSENLYFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAEL 60
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional
regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus
musculus}
Length = 79
Score = 61.4 bits (150), Expect = 4e-14
Identities = 23/32 (71%), Positives = 27/32 (84%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
HIKRPMNAFMVWS+I+RRKI +P MHN+ I
Sbjct: 2 HIKRPMNAFMVWSQIERRKIMEQSPDMHNAEI 33
>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 = 61.5 bits (150), Expect = 4e-14
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
HIK+P+NAFM++ + R + ++ ++ I
Sbjct: 2 HIKKPLNAFMLYMKEMRANVVAESTLKESAAI 33
>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 = 60.3 bits (147), Expect = 8e-14
Identities = 25/32 (78%), Positives = 28/32 (87%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
+KRPMNAFMVWSR QRRK+A +NPKMHNS I
Sbjct: 2 RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEI 33
>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 = 60.1 bits (146), Expect = 2e-13
Identities = 10/35 (28%), Positives = 22/35 (62%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNSII 60
G + KRP++A ++S +RR++ + P++ S +
Sbjct: 17 GSEKPKRPVSAMFIFSEEKRRQLQEERPELSESEL 51
>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 = 57.5 bits (139), Expect = 7e-12
Identities = 22/32 (68%), Positives = 28/32 (87%)
Query: 27 EQHIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
+ +KRPMNAF+VWSR QRRK+AL+NP+M NS
Sbjct: 2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNS 33
Score = 42.1 bits (99), Expect = 4e-06
Identities = 11/53 (20%), Positives = 19/53 (35%)
Query: 6 HHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
H + +T KRP +AF ++ R KI ++P +
Sbjct: 65 HREKYPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIG 117
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 49.4 bits (118), Expect = 2e-09
Identities = 10/33 (30%), Positives = 18/33 (54%)
Query: 26 GEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
G IK+PM+A ++ + R + ++NPK
Sbjct: 4 GSSGIKKPMSASALFVQDHRPQFLIENPKTSLE 36
>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 = 48.1 bits (115), Expect = 7e-09
Identities = 5/30 (16%), Positives = 13/30 (43%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
K P+ ++ + +R +I +P +
Sbjct: 7 GPKAPVTGYVRFLNERREQIRTRHPDLPFP 36
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 44.6 bits (106), Expect = 1e-07
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
KR AFM+W R I +NP + +
Sbjct: 5 KRATTAFMLWLNDTRESIKRENPGIKVT 32
>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 = 43.8 bits (104), Expect = 2e-07
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
KRP +AF ++ R KI ++P +
Sbjct: 6 APKRPPSAFFLFCSEYRPKIKGEHPGLSIG 35
>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 = 43.0 bits (102), Expect = 4e-07
Identities = 9/28 (32%), Positives = 16/28 (57%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
KRP++A+ +W R I +NP + +
Sbjct: 5 KRPLSAYALWLNSARESIKRENPGIKVT 32
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 43.1 bits (102), Expect = 6e-07
Identities = 7/31 (22%), Positives = 20/31 (64%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHNSI 59
KR ++++M +++ +R +I +NP++ +
Sbjct: 22 APKRALSSYMFFAKEKRVEIIAENPEIAKDV 52
>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 = 40.6 bits (94), Expect = 6e-06
Identities = 9/29 (31%), Positives = 11/29 (37%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNPKMHN 57
RP F +W R I DNP +
Sbjct: 5 SSGRPKTGFQMWLEENRSNILSDNPDFSD 33
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 38.9 bits (91), Expect = 3e-05
Identities = 6/28 (21%), Positives = 14/28 (50%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
++P++A+ ++ R + I NP
Sbjct: 19 QKPVSAYALFFRDTQAAIKGQNPNATFG 46
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding
protein; NMR {Homo sapiens} SCOP: a.21.1.1
Length = 99
Score = 38.5 bits (90), Expect = 3e-05
Identities = 8/28 (28%), Positives = 15/28 (53%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
K+P+ + + +R K A +P+M N
Sbjct: 12 KKPLTPYFRFFMEKRAKYAKLHPEMSNL 39
>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 = 37.7 bits (88), Expect = 7e-05
Identities = 7/28 (25%), Positives = 15/28 (53%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
KR ++A+M ++ R + +NP +
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFG 49
>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 = 35.4 bits (82), Expect = 3e-04
Identities = 3/29 (10%), Positives = 12/29 (41%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNSI 59
+ M+++ + + R + +P +
Sbjct: 3 RGKMSSYAFFVQTCREEHKKKHPDASVNF 31
>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 = 35.7 bits (82), Expect = 9e-04
Identities = 12/53 (22%), Positives = 22/53 (41%)
Query: 6 HHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPKMHNS 58
+ + +PP +T KRP +AF ++ R KI ++P +
Sbjct: 78 YEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIG 130
Score = 32.3 bits (73), Expect = 0.015
Identities = 3/25 (12%), Positives = 11/25 (44%)
Query: 29 HIKRPMNAFMVWSRIQRRKIALDNP 53
+ M+++ + + R + +P
Sbjct: 15 KPRGKMSSYAFFVQTCREEHKKKHP 39
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group
protein 2A, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 86
Score = 34.6 bits (80), Expect = 0.001
Identities = 6/29 (20%), Positives = 14/29 (48%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNSI 59
K M+A+ + + R + NP++ +
Sbjct: 17 KGKMSAYAFFVQTCREEHKKKNPEVPVNF 45
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 33.0 bits (76), Expect = 0.004
Identities = 3/25 (12%), Positives = 11/25 (44%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKM 55
+ M+++ + + R + +P
Sbjct: 9 RGKMSSYAFFVQTSREEHKKKHPDA 33
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial
transcription, activator, DNA- binding, mitochondrion,
phosphoprotein; 1.35A {Homo sapiens}
Length = 67
Score = 31.5 bits (72), Expect = 0.009
Identities = 7/24 (29%), Positives = 15/24 (62%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPK 54
KRP +A+ V+ + ++ D+P+
Sbjct: 4 KRPRSAYNVYVAERFQEAKGDSPQ 27
>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 = 32.5 bits (73), Expect = 0.018
Identities = 14/70 (20%), Positives = 25/70 (35%), Gaps = 12/70 (17%)
Query: 1 MSLSSHHQHSYFSMPPGLDTSHLNLGEQHI------------KRPMNAFMVWSRIQRRKI 48
M S HH H + P G Q + K+P+++++ +S+ Q
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSSSVLASCPKKPVSSYLRFSKEQLPIF 60
Query: 49 ALDNPKMHNS 58
NP +
Sbjct: 61 KAQNPDAKTT 70
Score = 30.2 bits (67), Expect = 0.10
Identities = 7/54 (12%), Positives = 17/54 (31%)
Query: 1 MSLSSHHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPK 54
+ + KRP +A+ V+ + ++ D+P+
Sbjct: 118 IMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ 171
>3tq6_A Transcription factor A, mitochondrial; transcription,
transcription regulation, mitochondrion; HET: DNA BRU
1PE; 2.45A {Homo sapiens}
Length = 214
Score = 30.9 bits (69), Expect = 0.062
Identities = 6/28 (21%), Positives = 15/28 (53%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKMHNS 58
K+P+++++ +S+ Q NP +
Sbjct: 11 KKPVSSYLRFSKEQLPIFKAQNPDAKTT 38
Score = 27.0 bits (59), Expect = 1.4
Identities = 7/54 (12%), Positives = 17/54 (31%)
Query: 1 MSLSSHHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIALDNPK 54
+ + KRP +A+ V+ + ++ D+P+
Sbjct: 86 IMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ 139
>3eby_A Beta subunit of A putative aromatic-ring-hydroxyl dioxygenase;
YP_001165631.1; 1.75A {Novosphingobium aromaticivorans
dsm 12ORGANISM_TAXID} SCOP: d.17.4.4
Length = 163
Score = 28.4 bits (63), Expect = 0.35
Identities = 3/20 (15%), Positives = 8/20 (40%)
Query: 42 RIQRRKIALDNPKMHNSIIF 61
R++ R D ++ +
Sbjct: 142 RLKSRTCIYDTLRIATLLAT 161
>3th5_A RAS-related C3 botulinum toxin substrate 1; rossmann fold,
GTPase, GTP binding, protein binding, signali protein;
HET: GNP; 2.30A {Homo sapiens}
Length = 204
Score = 27.8 bits (62), Expect = 0.67
Identities = 11/30 (36%), Positives = 13/30 (43%)
Query: 2 SLSSHHQHSYFSMPPGLDTSHLNLGEQHIK 31
S HH HS +P G +L Q IK
Sbjct: 3 SSHHHHHHSSGLVPRGSHMENLYFQGQAIK 32
>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 = 27.7 bits (61), Expect = 0.80
Identities = 17/98 (17%), Positives = 28/98 (28%), Gaps = 37/98 (37%)
Query: 36 AFMVWSRIQR----------RKIALDNPKMHNSIIFNCHIMHFLCP--QKIE---LKSKR 80
A VW+R I ++NP ++ HF ++I
Sbjct: 1642 AQDVWNRADNHFKDTYGFSILDIVINNPV---NLTI-----HFGGEKGKRIRENYSAMIF 1693
Query: 81 DIHVEACRKSN-------------LFDRDKG-LDITNN 104
+ V+ K+ F +KG L T
Sbjct: 1694 ETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQF 1731
Score = 26.6 bits (58), Expect = 2.6
Identities = 20/137 (14%), Positives = 42/137 (30%), Gaps = 57/137 (41%)
Query: 3 LSSHHQHSYFSMPP---------------------GLDTSHLNLGEQHIKRPMNAFM-VW 40
+ + + S+PP L + + ++ + N+ +
Sbjct: 308 VRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQV---QDYVNK-TNSHLPAG 363
Query: 41 SRIQRRKIALDN-PKMHNSII---------FNCHIMHFLCP----Q-KIELKSKRDIHVE 85
+++ I+L N K N ++ N + P Q +I S+R +
Sbjct: 364 KQVE---ISLVNGAK--NLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPF-SERKLKF- 416
Query: 86 ACRKSNLFDRDKGLDIT 102
SN F L +
Sbjct: 417 ----SNRF-----LPVA 424
>1jx6_A LUXP protein; protein-ligand complex, signaling protein; HET: AI2;
1.50A {Vibrio harveyi} SCOP: c.93.1.1 PDB: 1zhh_A*
2hj9_A*
Length = 342
Score = 27.5 bits (61), Expect = 0.99
Identities = 2/31 (6%), Positives = 10/31 (32%), Gaps = 1/31 (3%)
Query: 75 ELKSKRDIHVEACRKSNLFDRDKGLDITNNI 105
++ + +++ + + G D
Sbjct: 199 QVNRDNNFELQSAYYTK-ATKQSGYDAAKAS 228
>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 = 26.0 bits (57), Expect = 1.6
Identities = 6/25 (24%), Positives = 12/25 (48%)
Query: 31 KRPMNAFMVWSRIQRRKIALDNPKM 55
K PMN + +S+ L++ +
Sbjct: 10 KPPMNGYQKFSQELLSNGELNHLPL 34
>1gud_A ALBP, D-allose-binding periplasmic protein; periplasmic binding
protein, X-RAY crystallography, hinge bending,
conformational change; 1.7A {Escherichia coli} SCOP:
c.93.1.1 PDB: 1gub_A 1rpj_A*
Length = 288
Score = 26.6 bits (59), Expect = 1.7
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 75 ELKSKRDIHVEACRKSNLFDRDKGLDITNNI 105
K I + A + ++ +DR K LD+ N+
Sbjct: 158 AFKKASQIKLVASQPAD-WDRIKALDVATNV 187
>2ioy_A Periplasmic sugar-binding protein; ribose binding protein,
thermophilic proteins; HET: RIP; 1.90A
{Thermoanaerobacter tengcongensis}
Length = 283
Score = 26.5 bits (59), Expect = 1.9
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 76 LKSKRDIHVEACRKSNLFDRDKGLDITNNI 105
+ DI + A + ++ FDR KGL + NI
Sbjct: 149 IAKYPDIKIVAKQAAD-FDRSKGLSVMENI 177
>2rjo_A Twin-arginine translocation pathway signal protei; PSI-2, NYSGXRC,
twin arginine translocation pathway signal P structural
genomics; HET: GAL; 2.05A {Burkholderia phytofirmans}
Length = 332
Score = 26.6 bits (59), Expect = 2.0
Identities = 5/30 (16%), Positives = 11/30 (36%), Gaps = 1/30 (3%)
Query: 76 LKSKRDIHVEACRKSNLFDRDKGLDITNNI 105
LK I + + ++ ++ K I
Sbjct: 162 LKKFPGIQLLDFQVAD-WNSQKAFPIMQAW 190
>8abp_A L-arabinose-binding protein; binding proteins; HET: GLA GAL; 1.49A
{Escherichia coli} SCOP: c.93.1.1 PDB: 7abp_A* 6abp_A*
1abe_A* 1abf_A* 5abp_A* 1bap_A* 1apb_A* 9abp_A* 2wrz_A
Length = 306
Score = 26.3 bits (58), Expect = 2.3
Identities = 3/13 (23%), Positives = 5/13 (38%)
Query: 93 FDRDKGLDITNNI 105
D D N++
Sbjct: 177 NDIPGAFDAANSM 189
>3l6u_A ABC-type sugar transport system periplasmic component; structural
genomics, nysgrc, target 11006S, PSI-2, protein
structure initiative; 1.90A {Exiguobacterium sibiricum}
Length = 293
Score = 26.2 bits (58), Expect = 2.3
Identities = 2/30 (6%), Positives = 11/30 (36%), Gaps = 1/30 (3%)
Query: 76 LKSKRDIHVEACRKSNLFDRDKGLDITNNI 105
++++ + + N +D + +
Sbjct: 161 IENEPTLSIVDSVSGN-YDPVTSERVMRQV 189
>2dri_A D-ribose-binding protein; sugar transport; HET: RIP; 1.60A
{Escherichia coli} SCOP: c.93.1.1 PDB: 1urp_A* 1ba2_A
1dbp_A* 1drj_A* 1drk_A* 2gx6_A*
Length = 271
Score = 25.7 bits (57), Expect = 4.0
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 93 FDRDKGLDITNNI 105
FDR KGL++ N+
Sbjct: 164 FDRIKGLNVMQNL 176
>3h75_A Periplasmic sugar-binding domain protein; protein structure
initiative II (PSI II), sugar binding PROT alpha/beta
fold; 1.60A {Pseudomonas fluorescens pf-5}
Length = 350
Score = 25.5 bits (56), Expect = 4.2
Identities = 3/30 (10%), Positives = 10/30 (33%), Gaps = 1/30 (3%)
Query: 76 LKSKRDIHVEACRKSNLFDRDKGLDITNNI 105
L +H+ ++R++ +
Sbjct: 171 LAEHPQVHLRQLVYGE-WNRERAYRQAQQL 199
>2x7x_A Sensor protein; transferase, sensor histidine kinase; HET: FRU;
2.64A {Bacteroides thetaiotaomicron}
Length = 325
Score = 25.4 bits (56), Expect = 4.7
Identities = 3/30 (10%), Positives = 11/30 (36%), Gaps = 1/30 (3%)
Query: 76 LKSKRDIHVEACRKSNLFDRDKGLDITNNI 105
+ DI + + ++R +++
Sbjct: 154 ISKFPDIKLIDKADAA-WERGPAEIEMDSM 182
>3e99_A Benzoate 1,2-dioxygenase beta subunit; structural genomics, joint
center for structural genomics, J protein structure
initiative; 1.90A {Burkholderia mallei atcc 23344} SCOP:
d.17.4.4
Length = 164
Score = 24.8 bits (54), Expect = 5.8
Identities = 4/20 (20%), Positives = 9/20 (45%)
Query: 42 RIQRRKIALDNPKMHNSIIF 61
+I + + L N ++ I
Sbjct: 142 KIVSKYVVLKNDYINQLIDI 161
>3k3p_A D-alanine--D-alanine ligase; D-alanyl-alanine synthetase,
ATP-binding, cell shape, cell W biogenesis/degradation,
magnesium, manganese; 2.23A {Streptococcus mutans}
Length = 383
Score = 24.5 bits (54), Expect = 8.7
Identities = 11/49 (22%), Positives = 19/49 (38%), Gaps = 9/49 (18%)
Query: 2 SLSSHHQHSYFSMPPGLDTSHLNLGEQHIKRPMNAFMVWSRIQRRKIAL 50
S HH HS +P G + + G+Q + M+ + + L
Sbjct: 3 SSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMS---------KETLVL 42
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
0.325 0.135 0.426
Gapped
Lambda K H
0.267 0.0662 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,708,237
Number of extensions: 84409
Number of successful extensions: 261
Number of sequences better than 10.0: 1
Number of HSP's gapped: 261
Number of HSP's successfully gapped: 60
Length of query: 113
Length of database: 6,701,793
Length adjustment: 77
Effective length of query: 36
Effective length of database: 4,551,876
Effective search space: 163867536
Effective search space used: 163867536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.6 bits)