RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy7578
(280 letters)
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 69.8 bits (171), Expect = 1e-15
Identities = 16/71 (22%), Positives = 37/71 (52%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+A L+ + R + + NP+ + ++ ELW T+ EK ++ +A + +Y +M
Sbjct: 13 SASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLERYNSQM 72
Query: 138 SKAPAQKTKST 148
+A Q+++ +
Sbjct: 73 KRAIEQESQMS 83
>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 = 67.0 bits (164), Expect = 1e-14
Identities = 16/77 (20%), Positives = 40/77 (51%), Gaps = 3/77 (3%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
T Y+ + + R+++ +P++ F +++K LG W + EK + +A++ +Y +++
Sbjct: 13 TGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKEL 72
Query: 138 S---KAPAQKTKSTYTP 151
++ A K + P
Sbjct: 73 WAYQQSEAYKVCTESGP 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 = 65.9 bits (161), Expect = 4e-14
Identities = 13/74 (17%), Positives = 30/74 (40%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
T Y + + R K K +PEM ++K L + + +P +K + + R ++ + +
Sbjct: 16 TPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNL 75
Query: 138 SKAPAQKTKSTYTP 151
++
Sbjct: 76 ARFREDHPDLIQNA 89
>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 = 67.2 bits (164), Expect = 5e-14
Identities = 19/62 (30%), Positives = 37/62 (59%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
A+++W++ R+K+ NP M S++SK+LG W + EK+ + ++A +L A + +K
Sbjct: 10 NAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKY 69
Query: 138 SK 139
Sbjct: 70 PN 71
Score = 64.9 bits (158), Expect = 4e-13
Identities = 18/64 (28%), Positives = 37/64 (57%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKY 133
K +A+ L+ + R K+ +P + V+KKLGE+W+ ++K ++++A +L KY
Sbjct: 90 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY 149
Query: 134 TQKM 137
+ +
Sbjct: 150 EKDI 153
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 65.5 bits (160), Expect = 5e-14
Identities = 17/76 (22%), Positives = 37/76 (48%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+AY L+ + + + NP F +VSK + +W + +K +K++ + +Y +++
Sbjct: 23 SAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQL 82
Query: 138 SKAPAQKTKSTYTPHG 153
+ A +YT G
Sbjct: 83 AAYRASLVSKSYTDSG 98
>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 = 64.2 bits (157), Expect = 8e-14
Identities = 17/60 (28%), Positives = 36/60 (60%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+A+ L+ + R K+ +P + V+KKLGE+W+ ++K ++++A +L KY + +
Sbjct: 12 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI 71
>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 = 64.7 bits (158), Expect = 8e-14
Identities = 13/65 (20%), Positives = 36/65 (55%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+A +++++ R++L + PE+ S++++ L +W+ + +K +K + L A+ +K
Sbjct: 26 SAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSERKS 85
Query: 138 SKAPA 142
+
Sbjct: 86 GPSSG 90
>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 = 64.6 bits (158), Expect = 9e-14
Identities = 12/58 (20%), Positives = 29/58 (50%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+ML+ K++R ++ + + + +++ LG WH + E+ + A + + Q
Sbjct: 9 AFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQLHMQL 66
>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 = 64.1 bits (157), Expect = 1e-13
Identities = 20/58 (34%), Positives = 37/58 (63%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+M+W++ R+K+ + NP+M S++SK+LG W + EK + +A RL A + ++
Sbjct: 9 AFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 66
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation,
transcription-DNA CO; HET: DNA; 2.40A {Mus musculus}
Length = 79
Score = 64.1 bits (157), Expect = 1e-13
Identities = 17/58 (29%), Positives = 40/58 (68%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+M+W++ R+K+++ +P+M +++SK+LG+ W + ++K + ++A+RL K+
Sbjct: 9 AFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMAD 66
>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 = 63.9 bits (156), Expect = 2e-13
Identities = 20/62 (32%), Positives = 32/62 (51%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+AYM +A + R + NP++ F QV KKLGE W + EK ++ +A +Y +
Sbjct: 26 SAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEK 85
Query: 138 SK 139
Sbjct: 86 EL 87
>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 = 2e-13
Identities = 19/58 (32%), Positives = 37/58 (63%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+++W++ R+K+ NP M S++SK+LG W + EK+ + ++A +L A + +K
Sbjct: 11 AFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
>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 = 63.0 bits (154), Expect = 3e-13
Identities = 20/58 (34%), Positives = 37/58 (63%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+M+WAK R++L + NP++ +++SK LG+ W + EK + +A+RL ++ Q
Sbjct: 13 AFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQD 70
>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 = 63.0 bits (154), Expect = 3e-13
Identities = 19/58 (32%), Positives = 37/58 (63%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+++W++ R+K+ NP M S++SK+LG W + EK+ + ++A +L A + +K
Sbjct: 11 AFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
>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 = 62.7 bits (153), Expect = 3e-13
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+AY LW R+ + + NP + ++V+K+ GELW + +K W+ +A + Y + +
Sbjct: 9 SAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAKDDYDRAV 66
>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 = 62.8 bits (153), Expect = 4e-13
Identities = 16/58 (27%), Positives = 29/58 (50%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+ML+AK+ R + + P D +S LG+ W + E+ + +A LA + +
Sbjct: 24 AFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKALAEEQKRL 81
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription
regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo
sapiens}
Length = 214
Score = 65.9 bits (160), Expect = 5e-13
Identities = 15/109 (13%), Positives = 41/109 (37%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKY 133
K ++Y+ ++K+ NP+ +++ +++ + W +P ++K ++ Y
Sbjct: 11 KKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVY 70
Query: 134 TQKMSKAPAQKTKSTYTPHGRVGRPPLNKQTVEAVIETKPSPPAAPRVP 182
+++S+ Q T S + K+ + R
Sbjct: 71 KEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPR 119
Score = 46.3 bits (109), Expect = 3e-06
Identities = 17/98 (17%), Positives = 34/98 (34%), Gaps = 4/98 (4%)
Query: 73 EKARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAK 132
K +AY ++ + Q+ +P + K + E W + +EK + + A +
Sbjct: 115 PKRPRSAYNVYVAERFQEAKGDSP----QEKLKTVKENWKNLSDSEKELYIQHAKEDETR 170
Query: 133 YTQKMSKAPAQKTKSTYTPHGRVGRPPLNKQTVEAVIE 170
Y +M Q + R K E ++
Sbjct: 171 YHNEMKSWEEQMIEVGRKDLLRRTIKKQRKYGAEECLQ 208
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens}
Length = 71
Score = 61.8 bits (151), Expect = 6e-13
Identities = 20/58 (34%), Positives = 37/58 (63%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+M+WAK R++L + NP++ +++SK LG+ W + EK + +A+RL ++ Q
Sbjct: 9 AFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQD 66
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 61.5 bits (150), Expect = 7e-13
Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
TA+MLW R+ + + NP + ++++KK GE+W + +K W+ A + +Y +M
Sbjct: 9 TAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQRYHDEM 66
>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 = 61.8 bits (151), Expect = 7e-13
Identities = 12/58 (20%), Positives = 26/58 (44%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A++L+ K+ R + + +P +D +K L + W + EK + A + +
Sbjct: 14 AFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKA 71
>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 = 61.8 bits (151), Expect = 7e-13
Identities = 20/58 (34%), Positives = 36/58 (62%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+M+WAK R+K++++ P+M S +SK LG W + EK + + RL+ ++ +K
Sbjct: 11 AFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEK 68
>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 = 62.8 bits (153), Expect = 7e-13
Identities = 19/58 (32%), Positives = 36/58 (62%)
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
A+M+WA+ R+KL P + +++SK LG+LW + +EK + +A+RL ++ +
Sbjct: 36 AFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKD 93
>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 = 59.3 bits (144), Expect = 5e-12
Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEM--DFSQVSKKLGELWHTVPFNEKYGWKRQADRLAA 131
+ + ++Y + + R++ K +P+ +FS+ SKK E W T+ EK ++ A A
Sbjct: 3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 62
Query: 132 KYTQKM 137
+Y ++M
Sbjct: 63 RYEREM 68
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 59.7 bits (145), Expect = 7e-12
Identities = 18/62 (29%), Positives = 36/62 (58%), Gaps = 2/62 (3%)
Query: 78 TAYMLWAKQIRQKLIKSNPEM--DFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
++YM +AK+ R ++I NPE+ D + + K +G W+ + EK ++R +D +Y +
Sbjct: 28 SSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYER 87
Query: 136 KM 137
+
Sbjct: 88 EK 89
>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 = 61.8 bits (149), Expect = 1e-11
Identities = 15/107 (14%), Positives = 41/107 (38%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKY 133
K ++Y+ ++K+ NP+ +++ +++ + W +P ++K ++ Y
Sbjct: 43 KKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVY 102
Query: 134 TQKMSKAPAQKTKSTYTPHGRVGRPPLNKQTVEAVIETKPSPPAAPR 180
+++S+ Q T S + K+ + R
Sbjct: 103 KEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKR 149
Score = 45.2 bits (106), Expect = 7e-06
Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 73 EKARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAK 132
K +AY ++ + Q+ +P+ + K + E W + +EK + + A +
Sbjct: 147 PKRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAKEDETR 202
Query: 133 YTQKMSK 139
Y +M
Sbjct: 203 YHNEMKS 209
>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 = 60.0 bits (145), Expect = 2e-11
Identities = 17/60 (28%), Positives = 36/60 (60%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+A+ L+ + R K+ +P + V+KKLGE+W+ ++K ++++A +L KY + +
Sbjct: 107 SAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDI 166
Score = 53.8 bits (129), Expect = 5e-09
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 4/86 (4%)
Query: 78 TAYMLWAKQIRQKLIKSNPE--MDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQ 135
++Y + + R++ K +P+ ++FS+ SKK E W T+ EK ++ A A+Y +
Sbjct: 21 SSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYER 80
Query: 136 KMSKAPAQKTKSTYTPHGRVG--RPP 159
+M K ++ RPP
Sbjct: 81 EMKTYIPPKGETKKKFKDPNAPKRPP 106
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 57.3 bits (139), Expect = 3e-11
Identities = 18/66 (27%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPE--MDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAA 131
+ + ++Y + + R++ K +P+ ++FS+ SKK E W T+ EK ++ A A
Sbjct: 9 RGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 68
Query: 132 KYTQKM 137
+Y ++M
Sbjct: 69 RYEREM 74
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group
protein 2A, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 86
Score = 57.4 bits (139), Expect = 4e-11
Identities = 20/66 (30%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 74 KARFTAYMLWAKQIRQKLIKSNPEM--DFSQVSKKLGELWHTVPFNEKYGWKRQADRLAA 131
K + +AY + + R++ K NPE+ +F++ SKK E W T+ EK + A
Sbjct: 17 KGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKV 76
Query: 132 KYTQKM 137
+Y ++M
Sbjct: 77 RYDREM 82
>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 = 51.0 bits (121), Expect = 7e-09
Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 78 TAYMLWAKQIRQKLIKSNPEM-DFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQK 136
T + +W ++ R ++ NP+ D + + K+ + + E+ W +A A +
Sbjct: 11 TGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAKGETASEGTE 70
Query: 137 MSK 139
K
Sbjct: 71 AKK 73
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial
transcription, activator, DNA- binding, mitochondrion,
phosphoprotein; 1.35A {Homo sapiens}
Length = 67
Score = 49.2 bits (118), Expect = 2e-08
Identities = 12/60 (20%), Positives = 27/60 (45%), Gaps = 4/60 (6%)
Query: 78 TAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKM 137
+AY ++ + Q+ +P+ + K + E W + +EK + + A +Y +M
Sbjct: 8 SAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEM 63
>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 = 51.2 bits (122), Expect = 2e-07
Identities = 50/301 (16%), Positives = 90/301 (29%), Gaps = 93/301 (30%)
Query: 13 EVNISDISDSELYNSAQAVGSGADEEFGEADSSLDAESIGSGDLADNLLIDEDDLSQESI 72
E + + + + ++Q E+F + L + + D++ + +
Sbjct: 17 EHVLL-VPTASFFIASQL-----QEQF---NKILPEPT-------EGFAADDEPTTPAEL 60
Query: 73 EKARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQAD--RLA 130
+F Y+ + + + F QV L F Y D LA
Sbjct: 61 -VGKFLGYV--SSLVEP-----SKVGQFDQVLNLC--LTE---FENCY--LEGNDIHALA 105
Query: 131 AKYTQKMSKAPAQKT---KSTYTPHGRVGRPPLNKQTVEAVIETKPSPPAAPRVPLVK-- 185
AK Q+ + K+ T RP K S A L +
Sbjct: 106 AKLLQENDTTLVKTKELIKNYITARIMAKRPF-----------DKKSNSA-----LFRAV 149
Query: 186 PTLPADLFKVTGTQ-----PLDIAAHLR--------LLGDNLTIIGERLKD-----TQGR 227
A L + G Q + LR L+GD + E L +
Sbjct: 150 GEGNAQLVAIFGGQGNTDDYFE---ELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAE 206
Query: 228 MAISGGMSLL--LD--------SFLCAL---GPLLCLTQ-----QIPEENGCSPETLSHV 269
+ G+++L L+ +L ++ PL+ + Q + G +P L
Sbjct: 207 KVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSY 266
Query: 270 L 270
L
Sbjct: 267 L 267
Score = 33.5 bits (76), Expect = 0.091
Identities = 46/303 (15%), Positives = 86/303 (28%), Gaps = 121/303 (39%)
Query: 17 SDISDSELYNSAQAV------GSGADEEFGEADSSL----DAESIGSGDLADNLLIDEDD 66
+D +S + +A+ G E + D+ G + L I +
Sbjct: 286 TDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSIS--N 343
Query: 67 LSQESIEK--ARFTAYMLWAKQIRQKLI-------------------------KSNPEMD 99
L+QE ++ + +++ KQ+ L+ K+ +D
Sbjct: 344 LTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLD 403
Query: 100 -----FSQVSKKLGELWH-----TVPFNEKYGWKRQADRLAAKYTQKMSKAPAQKTKSTY 149
FS+ +KL + + PF+ + A
Sbjct: 404 QSRIPFSE--RKL-KFSNRFLPVASPFHSHL----------------LVPASDL------ 438
Query: 150 TPHGRVGRPPLNKQTVEAVIETKPSPPAAPRVPLVKPTLPADLFKVTGTQPLDIAAHLRL 209
+NK V+ + P V T G + LR+
Sbjct: 439 ----------INKDLVKNNVSFNAKDIQIP----VYDT-------FDG-------SDLRV 470
Query: 210 LGDNLTIIGERLKDTQGRM------AISGGMSLLLDSFLCALGP-----LLCLTQQIPEE 258
L +++ ER+ D R+ + +LD GP L LT + +
Sbjct: 471 LSGSIS---ERIVDCIIRLPVKWETTTQFKATHILD-----FGPGGASGLGVLTHRNKDG 522
Query: 259 NGC 261
G
Sbjct: 523 TGV 525
>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 = 44.5 bits (105), Expect = 2e-06
Identities = 8/67 (11%), Positives = 28/67 (41%), Gaps = 2/67 (2%)
Query: 73 EKARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAK 132
+K Y +++++ ++ + + ++G W + ++K +K+ A+ +
Sbjct: 9 KKPPMNGYQKFSQELLSNGELNH--LPLKERMVEIGSRWQRISQSQKEHYKKLAEEQQRQ 66
Query: 133 YTQKMSK 139
Y +
Sbjct: 67 YKVHLDL 73
>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 = 43.0 bits (101), Expect = 8e-06
Identities = 8/82 (9%), Positives = 28/82 (34%), Gaps = 9/82 (10%)
Query: 73 EKARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAK 132
K +Y L+ ++ + ++ ++ + W + EK + ++ D+
Sbjct: 18 TKPPPNSYSLYCAELMANM----KDVPSTERMVLCSQQWKLLSQKEKDAYHKKCDQKKKD 73
Query: 133 YTQKMSKAPAQKTKSTYTPHGR 154
Y ++ + + +
Sbjct: 74 YEVEL-----LRFLESLPEEEQ 90
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 42.9 bits (100), Expect = 8e-05
Identities = 46/290 (15%), Positives = 79/290 (27%), Gaps = 96/290 (33%)
Query: 36 DEEFGEADSS---------------LDAESIGSGDLADNLLIDE--DDLSQESIEKARFT 78
D E GE D + + D+ ++L E D + + T
Sbjct: 8 DFETGEHQYQYKDILSVFEDAFVDNFDCKDVQ--DMPKSILSKEEIDHIIMSKDAVSG-T 64
Query: 79 AYMLWAKQIRQKLIKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAKYTQKMS 138
+ W + S E V K + E+ Y + L + +
Sbjct: 65 LRLFW-------TLLSKQE---EMVQKFVEEV-----LRINYKF------LMSPI-KTEQ 102
Query: 139 KAPAQKTKSTYTPHGR------------VGRPPLNKQTVEAVIETKPSPPAAPRVPLV-- 184
+ P+ T+ R V R + +A++E +P A V +
Sbjct: 103 RQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRP----AKNVLIDGV 158
Query: 185 ----KPTLPADL-----------FKV------TGTQPLDIAAHLRLLGDNLTIIGERLKD 223
K + D+ FK+ P + L+ L + +
Sbjct: 159 LGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQID------PN 212
Query: 224 TQGRMAISGGMSLLLDSFLCALGPLLCLTQQIPEENGCSPETLSHVLDNI 273
R S + L + S L LL L VL N+
Sbjct: 213 WTSRSDHSSNIKLRIHSIQAELRRLLKSKPY--------ENCLL-VLLNV 253
Score = 30.2 bits (67), Expect = 0.84
Identities = 34/236 (14%), Positives = 69/236 (29%), Gaps = 67/236 (28%)
Query: 52 GSGD--LADNLLIDEDDLSQESIEKARFTAYMLWAKQIRQKLIKSNPEMDFSQVSKKLGE 109
GSG +A ++ + + + + W ++ EM L +
Sbjct: 160 GSGKTWVALDVCLSYK-------VQCKMDFKIFWLNLKNCNSPETVLEM--------LQK 204
Query: 110 LWHTVPFNEKYGWKRQADRLAAKYTQKMSKAPAQKTKSTYTPHGRVGRPPL-------NK 162
L + + N W ++D + + S + P+ L N
Sbjct: 205 LLYQIDPN----WTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENC----LLVLLNVQNA 256
Query: 163 QTVEA-------VIETKP-------SPPAAPRVPLVKPTLP------ADLF-KVTGTQPL 201
+ A ++ T+ S + L ++ L K +P
Sbjct: 257 KAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQ 316
Query: 202 DI-----AAHLRLLGDNLTIIGERLKDTQGR-----MAISGGMSLLLDSFLCALGP 247
D+ + R L II E ++D ++ +++S L L P
Sbjct: 317 DLPREVLTTNPRRLS----IIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEP 368
>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 = 28.8 bits (63), Expect = 1.3
Identities = 7/30 (23%), Positives = 16/30 (53%), Gaps = 5/30 (16%)
Query: 162 KQTVEAVIET--KP-SPPAAPRVPLVKPTL 188
KQ ++ ++ K + +AP + +K T+
Sbjct: 19 KQALKK-LQASLKLYADDSAPALA-IKATM 46
Score = 26.8 bits (58), Expect = 6.3
Identities = 10/31 (32%), Positives = 12/31 (38%), Gaps = 3/31 (9%)
Query: 118 EKYGWKRQADRLAAKYTQKMSKAPAQKTKST 148
EK K+ L Y APA K+T
Sbjct: 18 EKQALKKLQASLK-LYAD--DSAPALAIKAT 45
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR;
fatty acid synthase, acyl-carrier-protein, beta-ketoacyl
RED beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 1688
Score = 29.5 bits (66), Expect = 1.8
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 7/44 (15%)
Query: 134 TQKMSKAPAQKTKSTYTPHGRVGRP----PLN---KQTVEAVIE 170
T + SK +S Y +G G P N KQ VEA+IE
Sbjct: 508 TSRFSKQVTDYYQSIYAKYGAKGSTLIVVPFNQGSKQDVEALIE 551
>3iox_A AGI/II, PA; alpha helix, PPII helix, supersandwich fold, surface
adhesin WALL, peptidoglycan-anchor, cell adhesion; HET:
PMS; 1.80A {Streptococcus mutans} PDB: 3ipk_A* 1jmm_A
Length = 497
Score = 29.1 bits (63), Expect = 2.0
Identities = 14/73 (19%), Positives = 21/73 (28%), Gaps = 1/73 (1%)
Query: 119 KYGWKRQADRLAAKYTQKMSKAPAQKTKSTYTPHGRVGRPPLNKQTVEAVIE-TKPSPPA 177
+K Y+ +G++ + K T E KP+ P
Sbjct: 402 ATSATNVMPVSDMPVVPGKDNTDGKKPNIWYSLNGKIRAVNVPKVTKEKPTPPVKPTAPT 461
Query: 178 APRVPLVKPTLPA 190
P KP PA
Sbjct: 462 KPTYETEKPLKPA 474
Score = 27.2 bits (58), Expect = 7.3
Identities = 12/68 (17%), Positives = 16/68 (23%)
Query: 133 YTQKMSKAPAQKTKSTYTPHGRVGRPPLNKQTVEAVIETKPSPPAAPRVPLVKPTLPADL 192
T + A S K + + K P+V KPT P
Sbjct: 398 VTVGATSATNVMPVSDMPVVPGKDNTDGKKPNIWYSLNGKIRAVNVPKVTKEKPTPPVKP 457
Query: 193 FKVTGTQP 200
T
Sbjct: 458 TAPTKPTY 465
>2cto_A Novel protein; high mobility group box domain, helix-turn-helix,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 93
Score = 26.7 bits (58), Expect = 3.3
Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 3/84 (3%)
Query: 74 KARFTAYMLWAKQIRQKL-IKSNPEMDFSQVSKKLGELWHTVPFNEKYGWKRQADRLAAK 132
KA AY + ++ +L + P + W + EK + A +
Sbjct: 12 KASRNAYYFFVQEKIPELRRRGLPVARVADAIPYCSSDWALLREEEKEKYAEMAREW--R 69
Query: 133 YTQKMSKAPAQKTKSTYTPHGRVG 156
Q P++K K +T G
Sbjct: 70 AAQGKDPGPSEKQKPVFTSGPSSG 93
>4ev0_A Transcription regulator, CRP family; CAMP binding, winged
helix-turn-helix motif, DNA binding, transcription
activator; HET: CMP; 2.40A {Thermus thermophilus}
Length = 216
Score = 27.6 bits (62), Expect = 4.1
Identities = 23/88 (26%), Positives = 33/88 (37%), Gaps = 13/88 (14%)
Query: 190 ADLFKVTGTQPLDIAAHL-RLLGDNLTIIGERL-----KDTQGRMAISGGMSLLLDSFLC 243
D + P +A +L LL L L ++ + R+A LL
Sbjct: 103 EDYLALIRRLP-LVAHNLAALLARRLREADLELDLLSFEEARNRVA-----YALLKLLRQ 156
Query: 244 ALGPLLCLTQQ-IPEENGCSPETLSHVL 270
LGPL + + G S ET+S VL
Sbjct: 157 GLGPLFQIRHHELAALAGTSRETVSRVL 184
>1wfo_A Sidekick 2; FN3, cell adhesion, structural genomics, riken
structural genomics/proteomics initiative, RSGI; NMR
{Homo sapiens} SCOP: b.1.2.1
Length = 130
Score = 26.6 bits (59), Expect = 5.0
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 158 PPLNKQTVEAVIETKPSPPAAPRVPLVKPT 187
PP+ ++T++ V P PP P V+ T
Sbjct: 17 PPILERTLDDV----PGPPMGILFPEVRTT 42
>2z73_A Rhodopsin; visual pigment, GQ-type, G-protein coupled receptor,
chromophore, glycoprotein, lipoprotein, membrane,
palmitate phosphorylation; HET: BOG RET PLM TWT PC1;
2.50A {Todarodes pacificus} PDB: 3aym_A* 3ayn_A* 2ziy_A*
Length = 448
Score = 26.8 bits (59), Expect = 8.2
Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 2/53 (3%)
Query: 227 RMAISGGMSLLLDSFLCALGPLLCLTQQIPEENG--CSPETLSHVLDNIAYIM 277
R A + + L S L A+GP+ E CS + +S + I+
Sbjct: 150 RRAFIMIIFVWLWSVLWAIGPIFGWGAYTLEGVLCNCSFDYISRDSTTRSNIL 202
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
0.314 0.132 0.380
Gapped
Lambda K H
0.267 0.0774 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,187,488
Number of extensions: 245788
Number of successful extensions: 488
Number of sequences better than 10.0: 1
Number of HSP's gapped: 474
Number of HSP's successfully gapped: 56
Length of query: 280
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 188
Effective length of database: 4,133,061
Effective search space: 777015468
Effective search space used: 777015468
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 (21.9 bits)
S2: 57 (25.6 bits)