RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy13343
(396 letters)
>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 = 149 bits (378), Expect = 5e-45
Identities = 55/83 (66%), Positives = 69/83 (83%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRPMNAF+VWSR QRRKMA +NP+M NSEISK+LG +WK+L E K PF EA++L+
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
Query: 141 AVHMKEHPDYKYRPRRKTKTLLK 163
A+H +++P+YKYRPRRK K L K
Sbjct: 63 AMHREKYPNYKYRPRRKAKMLPK 85
>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 = 148 bits (376), Expect = 9e-45
Identities = 75/80 (93%), Positives = 78/80 (97%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRPMNAFMVWSRGQRRKMAQ+NPKMHNSEISKRLGAEWKLL+E KRPFIDEAKRLR
Sbjct: 1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 60
Query: 141 AVHMKEHPDYKYRPRRKTKT 160
A+HMKEHPDYKYRPRRKTKT
Sbjct: 61 ALHMKEHPDYKYRPRRKTKT 80
>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 = 145 bits (369), Expect = 1e-43
Identities = 40/77 (51%), Positives = 55/77 (71%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
+KRPMNAFMVW++ +RRK+ Q P MHNS ISK LG+ WK + K+P+ +E RL
Sbjct: 3 PHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLS 62
Query: 141 AVHMKEHPDYKYRPRRK 157
H++++PDYKY+PR K
Sbjct: 63 KQHLEKYPDYKYKPRPK 79
>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 = 145 bits (369), Expect = 1e-43
Identities = 23/76 (30%), Positives = 42/76 (55%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
+RPMNAF+++ + R + Q++P++ N +K L W +L+ + K+ + D AK +
Sbjct: 6 SGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYK 65
Query: 141 AVHMKEHPDYKYRPRR 156
MK +P Y+ P
Sbjct: 66 DAFMKANPGYRSGPSS 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 = 146 bits (370), Expect = 2e-43
Identities = 49/98 (50%), Positives = 68/98 (69%)
Query: 60 HPSHNTNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGA 119
H + + + + ++ VKRPMNAFMVW++ RRK+A P +HN+E+SK LG
Sbjct: 7 HHVDDDDKMSENLYFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGK 66
Query: 120 EWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYKYRPRRK 157
W+LLNE KRPF++EA+RLR H K+HPDYKY+PRR+
Sbjct: 67 LWRLLNESEKRPFVEEAERLRVQHKKDHPDYKYQPRRR 104
>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 = 145 bits (367), Expect = 2e-43
Identities = 45/79 (56%), Positives = 64/79 (81%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
R++RPMNAFMVW++ +R+++AQ NP +HN+E+SK LG WK L KRPF++EA+RLR
Sbjct: 5 SRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLR 64
Query: 141 AVHMKEHPDYKYRPRRKTK 159
HM++HP+YKYRPRR+ +
Sbjct: 65 VQHMQDHPNYKYRPRRRKQ 83
>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 = 145 bits (367), Expect = 2e-43
Identities = 21/84 (25%), Positives = 47/84 (55%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
+K+P+NAFM++ + R + ++ ++ I++ LG W L+ + + + + A++ R +
Sbjct: 3 IKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQL 62
Query: 143 HMKEHPDYKYRPRRKTKTLLKKDK 166
HM+ +P + R K K++K
Sbjct: 63 HMQLYPGWSARDNYGKKKKRKREK 86
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional regulation,
transcription-DNA CO; HET: DNA; 2.40A {Mus musculus}
Length = 79
Score = 145 bits (367), Expect = 2e-43
Identities = 50/77 (64%), Positives = 62/77 (80%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
+KRPMNAFMVWS+ +RRK+ + +P MHN+EISKRLG WKLL + K PFI EA+RLR
Sbjct: 3 IKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLK 62
Query: 143 HMKEHPDYKYRPRRKTK 159
HM ++PDYKYRPR+K K
Sbjct: 63 HMADYPDYKYRPRKKVK 79
>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 = 140 bits (356), Expect = 7e-42
Identities = 49/74 (66%), Positives = 63/74 (85%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRPMNAF+VWSR QRRKMA +NP+M NSEISK+LG +WK+L E K PF EA++L+
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
Query: 141 AVHMKEHPDYKYRP 154
A+H +++P+YKYRP
Sbjct: 63 AMHREKYPNYKYRP 76
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens}
Length = 71
Score = 133 bits (337), Expect = 4e-39
Identities = 39/69 (56%), Positives = 56/69 (81%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
++RPMNAFMVW++ +R+++AQ NP +HN+E+SK LG WK L KRPF++EA+RLR
Sbjct: 3 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62
Query: 143 HMKEHPDYK 151
HM++HP+YK
Sbjct: 63 HMQDHPNYK 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 = 131 bits (331), Expect = 5e-38
Identities = 26/83 (31%), Positives = 45/83 (54%)
Query: 67 NNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNE 126
++ +S + + + ++ KRPMNAFM++++ R + Q P N IS LG WK +
Sbjct: 2 SSGSSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKN 61
Query: 127 QAKRPFIDEAKRLRAVHMKEHPD 149
+ +R + EAK L + +PD
Sbjct: 62 EERRMYTLEAKALAEEQKRLNPD 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 = 119 bits (299), Expect = 2e-33
Identities = 17/81 (20%), Positives = 41/81 (50%)
Query: 71 STNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKR 130
+ + ++ KRP++A ++S +RR++ ++ P++ SE+++ L W L+E+ K
Sbjct: 9 PSQEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKA 68
Query: 131 PFIDEAKRLRAVHMKEHPDYK 151
+ L+A ++
Sbjct: 69 KYKAREAALKAQSERKSGPSS 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 = 118 bits (297), Expect = 3e-32
Identities = 49/86 (56%), Positives = 64/86 (74%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRPMNAF+VWSR QRRKMA +NP+M NSEISK+LG +WK+L E K PF EA++L+
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
Query: 141 AVHMKEHPDYKYRPRRKTKTLLKKDK 166
A+H +++P+YKYR K +
Sbjct: 63 AMHREKYPNYKYRKGETKKKFKDPNA 88
Score = 116 bits (291), Expect = 2e-31
Identities = 19/91 (20%), Positives = 41/91 (45%)
Query: 63 HNTNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWK 122
+ K + KRP +AF ++ R K+ ++P + +++K+LG W
Sbjct: 69 YPNYKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWN 128
Query: 123 LLNEQAKRPFIDEAKRLRAVHMKEHPDYKYR 153
K+P+ +A +L+ + K+ Y+ +
Sbjct: 129 NTAADDKQPYEKKAAKLKEKYEKDIAAYRAK 159
>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 = 108 bits (271), Expect = 3e-29
Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 3/87 (3%)
Query: 74 SKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFI 133
S + K P+ ++ + +R ++ +P + EI+K LGAEW L K+ ++
Sbjct: 2 SSGSSGP---KAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYL 58
Query: 134 DEAKRLRAVHMKEHPDYKYRPRRKTKT 160
DEA++ + ++KE Y+ K T
Sbjct: 59 DEAEKEKQQYLKELWAYQQSEAYKVCT 85
>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 = 101 bits (254), Expect = 6e-27
Identities = 18/70 (25%), Positives = 38/70 (54%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
KRP +AF ++ R K+ ++P + +++K+LG W K+P+ +A +L+ +
Sbjct: 8 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKY 67
Query: 144 MKEHPDYKYR 153
K+ Y+ +
Sbjct: 68 EKDIAAYRAK 77
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 96.7 bits (241), Expect = 6e-25
Identities = 14/78 (17%), Positives = 37/78 (47%)
Query: 82 RVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
+K+PM+A ++ + R + +NPK + + ++ WK L+E+ K + ++A +
Sbjct: 7 GIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSEEEKLKYEEKATKDLE 66
Query: 142 VHMKEHPDYKYRPRRKTK 159
+ + + + +
Sbjct: 67 RYNSQMKRAIEQESQMSL 84
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 92.7 bits (231), Expect = 1e-23
Identities = 22/68 (32%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
KR AFM+W R + ++NP + +EI+K+ G WK L + K + D A + + +
Sbjct: 5 KRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKD--KSKWEDAAAKDKQRY 62
Query: 144 MKEHPDYK 151
E +YK
Sbjct: 63 HDEMRNYK 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 = 92.5 bits (230), Expect = 2e-23
Identities = 18/75 (24%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHN--SEISKRLGAEWKLLNEQAKRPFIDEAKR 138
+ KR ++++M +++ +R ++ +NP++ + I K +GA W L+++ K+P+ +
Sbjct: 21 NAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDE 80
Query: 139 LRAVHMKEHPDYKYR 153
R + +E +Y R
Sbjct: 81 DRVRYEREKAEYAQR 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 = 90.4 bits (225), Expect = 7e-23
Identities = 16/71 (22%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
D+ KRP++A+ +W R + ++NP + +E++KR G W+ + + K + +A + +
Sbjct: 2 DKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD--KSEWEAKAAKAK 59
Query: 141 AVHMKEHPDYK 151
+ + +++
Sbjct: 60 DDYDRAVKEFE 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 = 89.8 bits (223), Expect = 2e-22
Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 7/86 (8%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
D K+P+ + + +R K A+ +P+M N +++K L ++K L E+ K +I + +R +
Sbjct: 9 DFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREK 68
Query: 141 AVHMKE-------HPDYKYRPRRKTK 159
+ HPD ++
Sbjct: 69 QEFERNLARFREDHPDLIQNAKKLEH 94
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 87.9 bits (218), Expect = 1e-21
Identities = 16/77 (20%), Positives = 39/77 (50%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
++P++A+ ++ R + + NP E+SK + + W L E+ K+ + + + + +
Sbjct: 19 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEY 78
Query: 144 MKEHPDYKYRPRRKTKT 160
+K+ Y+ K+ T
Sbjct: 79 LKQLAAYRASLVSKSYT 95
>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 = 83.1 bits (206), Expect = 5e-20
Identities = 18/68 (26%), Positives = 37/68 (54%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
KR ++A+M ++ R + +NP + ++ K+LG +WK L + K+P+ +A+ + +
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRY 81
Query: 144 MKEHPDYK 151
E Y
Sbjct: 82 ESEKELYN 89
>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 = 75.1 bits (185), Expect = 2e-17
Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNP--KMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
+ M+++ + + R + + +P ++ SE SK+ WK ++ + K F D AK +A
Sbjct: 3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 62
Query: 142 VHMKEHPDY 150
+ +E Y
Sbjct: 63 RYEREMKTY 71
>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 = 77.0 bits (189), Expect = 7e-17
Identities = 21/122 (17%), Positives = 46/122 (37%)
Query: 32 SLSQSPSSVVHHQNIGPHVTHNPMSNPLHPSHNTNNNNNSTNSKNQNAIDRVKRPMNAFM 91
S+ ++ + T K + KRP +AF
Sbjct: 51 KCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFF 110
Query: 92 VWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYK 151
++ R K+ ++P + +++K+LG W K+P+ +A +L+ + K+ Y+
Sbjct: 111 LFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR 170
Query: 152 YR 153
+
Sbjct: 171 AK 172
Score = 55.0 bits (132), Expect = 3e-09
Identities = 18/85 (21%), Positives = 37/85 (43%), Gaps = 2/85 (2%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNP--KMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
+ M+++ + + R + + +P ++ SE SK+ WK ++ + K F D AK +A
Sbjct: 17 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 76
Query: 142 VHMKEHPDYKYRPRRKTKTLLKKDK 166
+ +E Y K +
Sbjct: 77 RYEREMKTYIPPKGETKKKFKDPNA 101
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 73.5 bits (181), Expect = 1e-16
Identities = 17/70 (24%), Positives = 35/70 (50%), Gaps = 2/70 (2%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNP--KMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
+ M+++ + + R + + +P ++ SE SK+ WK ++ + K F D AK +A
Sbjct: 9 RGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 68
Query: 142 VHMKEHPDYK 151
+ +E Y
Sbjct: 69 RYEREMKTYI 78
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group
protein 2A, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 86
Score = 70.5 bits (173), Expect = 1e-15
Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNS--EISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
K M+A+ + + R + + NP++ + E SK+ WK ++ + K F + AK +
Sbjct: 17 KGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKV 76
Query: 142 VHMKEHPDY 150
+ +E DY
Sbjct: 77 RYDREMKDY 85
>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 = 71.0 bits (173), Expect = 3e-14
Identities = 20/115 (17%), Positives = 49/115 (42%), Gaps = 4/115 (3%)
Query: 46 IGPHVTHNPMSNPLHPSHNTNNNNNSTNSKNQNAIDRV----KRPMNAFMVWSRGQRRKM 101
+G H+ S+ L P + + + + + K+P+++++ +S+ Q
Sbjct: 1 MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSSSVLASCPKKPVSSYLRFSKEQLPIF 60
Query: 102 AQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYKYRPRR 156
NP +E+ +R+ W+ L + K+ + D + V+ +E +K +
Sbjct: 61 KAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVYKEEISRFKEQLTP 115
Score = 64.5 bits (156), Expect = 5e-12
Identities = 26/127 (20%), Positives = 46/127 (36%), Gaps = 10/127 (7%)
Query: 48 PHVTHNPMSNPLHPSHNTNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPK 107
MS T K + + KRP +A+ V+ + ++ D+P+
Sbjct: 112 QLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ 171
Query: 108 MHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYK------YRPRRKTKTL 161
E K + WK L++ K +I AK + E ++ R +T+
Sbjct: 172 ----EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQMIEVGRKDLLRRTI 227
Query: 162 LKKDKYP 168
K+ KY
Sbjct: 228 KKQRKYG 234
>3tq6_A Transcription factor A, mitochondrial; transcription, transcription
regulation, mitochondrion; HET: DNA BRU 1PE; 2.45A {Homo
sapiens}
Length = 214
Score = 67.9 bits (165), Expect = 2e-13
Identities = 15/76 (19%), Positives = 36/76 (47%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
K+P+++++ +S+ Q NP +E+ +R+ W+ L + K+ + D + V+
Sbjct: 11 KKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQVY 70
Query: 144 MKEHPDYKYRPRRKTK 159
+E +K +
Sbjct: 71 KEEISRFKEQLTPSQI 86
Score = 56.7 bits (136), Expect = 1e-09
Identities = 21/103 (20%), Positives = 38/103 (36%), Gaps = 4/103 (3%)
Query: 49 HVTHNPMSNPLHPSHNTNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKM 108
MS T K + + KRP +A+ V+ + ++ D+P+
Sbjct: 81 LTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQ- 139
Query: 109 HNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKEHPDYK 151
E K + WK L++ K +I AK + E ++
Sbjct: 140 ---EKLKTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWE 179
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial
transcription, activator, DNA- binding, mitochondrion,
phosphoprotein; 1.35A {Homo sapiens}
Length = 67
Score = 62.7 bits (153), Expect = 6e-13
Identities = 17/67 (25%), Positives = 31/67 (46%), Gaps = 4/67 (5%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
KRP +A+ V+ + ++ D+P+ E K + WK L++ K +I AK +
Sbjct: 4 KRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKENWKNLSDSEKELYIQHAKEDETRY 59
Query: 144 MKEHPDY 150
E +
Sbjct: 60 HNEMKSW 66
>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 = 62.1 bits (150), Expect = 1e-12
Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 6/77 (7%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHN-SEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
RP F +W R + DNP + ++I K +++L+ + ++ + ++AK
Sbjct: 7 GRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLSTEERKVWANKAK----- 61
Query: 143 HMKEHPDYKYRPRRKTK 159
+ + R+
Sbjct: 62 GETASEGTEAKKRKSGP 78
>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 = 49.5 bits (118), Expect = 5e-08
Identities = 11/83 (13%), Positives = 31/83 (37%), Gaps = 2/83 (2%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
K PMN + +S+ ++ + E +G+ W+ +++ K + A+ + +
Sbjct: 10 KPPMNGYQKFSQELLSNGELNHLPL--KERMVEIGSRWQRISQSQKEHYKKLAEEQQRQY 67
Query: 144 MKEHPDYKYRPRRKTKTLLKKDK 166
+ + + K+
Sbjct: 68 KVHLDLWVKSLSPQDRAAYKEYI 90
>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 = 45.4 bits (107), Expect = 2e-06
Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 6/83 (7%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
K P N++ ++ M E +WKLL+++ K + + + + +
Sbjct: 19 KPPPNSYSLYCAELMANMKDVPST----ERMVLCSQQWKLLSQKEKDAYHKKCDQKKKDY 74
Query: 144 MKEHPDYK--YRPRRKTKTLLKK 164
E + + + L ++
Sbjct: 75 EVELLRFLESLPEEEQQRVLGEE 97
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 37.4 bits (86), Expect = 0.009
Identities = 21/123 (17%), Positives = 36/123 (29%), Gaps = 3/123 (2%)
Query: 196 QQNSAARESMYQMPNGYMPNGYMMDPAT-YQQHSAYTTHMSSGYPRYDMTGMHPSSTSLN 254
S +G + T Y++ + + + +
Sbjct: 1457 MNYSLGTAVPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQGGSE-- 1514
Query: 255 SYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSG 314
YG+ A+ G SP ++ SS G + S SPSS G +P
Sbjct: 1515 GREGFGDYGLLGAASPYKGVQSPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPS 1574
Query: 315 PPT 317
P+
Sbjct: 1575 SPS 1577
Score = 36.2 bits (83), Expect = 0.020
Identities = 28/126 (22%), Positives = 41/126 (32%), Gaps = 7/126 (5%)
Query: 194 SAQQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSL 253
Y + P + P S +++ MS GY + S
Sbjct: 1510 QGGSEGREGFGDYGLLGAASPYKGVQSPGYT---SPFSSAMSPGYGLTSPSYSPSSPGYS 1566
Query: 254 NSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPS--GSSVKSEPVSPSSGGGILTPTP 311
S S Y+ + SP +S S+SP+ S S SP+S +PT
Sbjct: 1567 TSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSY--SPTS 1624
Query: 312 GSGPPT 317
S PT
Sbjct: 1625 PSYSPT 1630
Score = 32.4 bits (73), Expect = 0.35
Identities = 37/151 (24%), Positives = 50/151 (33%), Gaps = 7/151 (4%)
Query: 167 YPLGSGNLIQNTSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQ 226
P + S +T S S ++ S + Y P P T
Sbjct: 1536 SPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSP---AYMPSSPSYSPTSPSYSP-TSPS 1591
Query: 227 HSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSH 286
+S + S P Y T S TS SY S T+ + P SP +S S+
Sbjct: 1592 YSPTSPSYSPTSPSYSATSPSYSPTS-PSYSPTSPSYSPTSPSYSP--TSPSYSPTSPSY 1648
Query: 287 SPSGSSVKSEPVSPSSGGGILTPTPGSGPPT 317
SP+ S S S +PT S PT
Sbjct: 1649 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1679
Score = 30.4 bits (68), Expect = 1.2
Identities = 15/91 (16%), Positives = 23/91 (25%), Gaps = 11/91 (12%)
Query: 257 MNGSSYGMYTTATTLPGAGSPYHS--MQPSSH---------SPSGSSVKSEPVSPSSGGG 305
+ + T+ GAG+PY M S SP G
Sbjct: 1465 VPTLAGSGMGTSQLPEGAGTPYERSPMVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGL 1524
Query: 306 ILTPTPGSGPPTGLHLVKREYGSPNGLPPNS 336
+ +P G + + G S
Sbjct: 1525 LGAASPYKGVQSPGYTSPFSSAMSPGYGLTS 1555
Score = 29.3 bits (65), Expect = 3.0
Identities = 28/111 (25%), Positives = 36/111 (32%), Gaps = 6/111 (5%)
Query: 209 PNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTA 268
Y P P T +S + S P Y T S TS + +S T+
Sbjct: 1624 SPSYSPTSPSYSP-TSPSYSPTSPSYSPTSPSYSPTSPSYSPTS--PSYSPTSPSYSPTS 1680
Query: 269 TTLPGAGSPYHSMQPSSHSPS-GSSVKSEPVSPSSGGGILTPTPGSGPPTG 318
+ Y PS S S S SP+S +PT S PT
Sbjct: 1681 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS--YSPTSPSYSPTS 1729
Score = 28.1 bits (62), Expect = 7.1
Identities = 34/139 (24%), Positives = 47/139 (33%), Gaps = 19/139 (13%)
Query: 180 SSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYP 239
+S + S S + ++ S S Y P P T +S + S P
Sbjct: 1616 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP-TSPSYSPTSPSYSPTSP 1674
Query: 240 RYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGA-----GSPYHS------------MQ 282
Y T S TS SY S T+ + P + SP +S
Sbjct: 1675 SYSPTSPSYSPTS-PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1733
Query: 283 PSSHSPSGSSVKSEPVSPS 301
P+S S S +S P SPS
Sbjct: 1734 PTSPSYSPTSPSYSPTSPS 1752
Score = 27.7 bits (61), Expect = 9.2
Identities = 33/140 (23%), Positives = 45/140 (32%), Gaps = 15/140 (10%)
Query: 187 NSSSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGM 246
S S + ++ S S Y P T +S + S P Y T
Sbjct: 1581 TSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSP-TSPSYSPTSPSYSPTSPSYSPTSP 1639
Query: 247 H---------PSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEP 297
P+S S + S + + T P S P+S S S +S P
Sbjct: 1640 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1699
Query: 298 VSPSSGGGILTPTPGSGPPT 317
SPS +PT S PT
Sbjct: 1700 TSPSY-----SPTSPSYSPT 1714
>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 = 36.2 bits (83), Expect = 0.023
Identities = 38/147 (25%), Positives = 47/147 (31%), Gaps = 14/147 (9%)
Query: 178 TSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSG 237
S SND + A A P + P S + S
Sbjct: 1497 DSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPG----FSPTSPTYSPT 1552
Query: 238 YPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSP-----SGSS 292
P Y T S TS SY S T+ + P SP +S S+SP S +S
Sbjct: 1553 SPAYSPTSPSYSPTS-PSYSPTSPSYSPTSPSYSPT--SPSYSPTSPSYSPTSPSYSPTS 1609
Query: 293 VKSEPVSP--SSGGGILTPTPGSGPPT 317
P SP S +PT S PT
Sbjct: 1610 PSYSPTSPSYSPTSPSYSPTSPSYSPT 1636
Score = 34.7 bits (79), Expect = 0.069
Identities = 42/192 (21%), Positives = 60/192 (31%), Gaps = 18/192 (9%)
Query: 168 PLGSGNLIQNTSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQH 227
+S +S + ++ S + Y P P T +
Sbjct: 1519 ATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSP-TSPSY 1577
Query: 228 SAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYG----MYTTATTLPGAGSPYHSMQP 283
S + S P Y T S TS + SY Y+ + SP +S P
Sbjct: 1578 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS--P 1635
Query: 284 SSHSPSGSSVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREYGSPNGLPPNSTDLHLVK 343
+S S S +S P SPS +PT + PT + P S
Sbjct: 1636 TSPSYSPTSPSYSPTSPSY-----SPTSPAYSPT----SPSYSPTSPSYSPTSPSYSPTS 1686
Query: 344 REYS--SPNGAP 353
YS SPN +P
Sbjct: 1687 PSYSPTSPNYSP 1698
Score = 33.9 bits (77), Expect = 0.11
Identities = 11/75 (14%), Positives = 23/75 (30%)
Query: 239 PRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPV 298
P + +G+ + + + S + + G + Y + + P
Sbjct: 1472 PYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPT 1531
Query: 299 SPSSGGGILTPTPGS 313
SP G +P S
Sbjct: 1532 SPGFGVSSPGFSPTS 1546
Score = 32.8 bits (74), Expect = 0.24
Identities = 40/196 (20%), Positives = 63/196 (32%), Gaps = 26/196 (13%)
Query: 168 PLGSG--NLIQNTSSSNDVTRNSSSVTTSAQQNSAA----RESMYQMPNGYMPNGYMMDP 221
P+G+G +++ + S Q+ ES + + + M P
Sbjct: 1435 PIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSP 1494
Query: 222 ATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSM 281
S M+ G+ Y ++ S +G Y A T PG G
Sbjct: 1495 L---VDSGSNDAMAGGFTAYGGADYGEAT---------SPFGAYGEAPTSPGFGVSSPGF 1542
Query: 282 QPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREYGSP--NGLPPNSTDL 339
P+S + S +S P SPS +P P + + SP P S
Sbjct: 1543 SPTSPTYSPTSPAYSPTSPSYSP----TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1598
Query: 340 HLVKREYS--SPNGAP 353
YS SP+ +P
Sbjct: 1599 SPTSPSYSPTSPSYSP 1614
Score = 30.1 bits (67), Expect = 1.8
Identities = 34/158 (21%), Positives = 49/158 (31%), Gaps = 9/158 (5%)
Query: 167 YPLGSGNLIQNTSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQ 226
P S + +S + S S + ++ S S Y P P T
Sbjct: 1574 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP-TSPS 1632
Query: 227 HSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYG----MYTTATTLPGAGSPYHSMQ 282
+S + S P Y T S TS SY Y+ + SP +S
Sbjct: 1633 YSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1692
Query: 283 PSSHSPSGSSVKSEPVSP--SSGGGILTPTPGSGPPTG 318
++SP+ S P SP S G +P
Sbjct: 1693 SPNYSPT--SPSYSPTSPGYSPGSPAYSPKQDEQKHNE 1728
>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 = 34.8 bits (79), Expect = 0.056
Identities = 27/189 (14%), Positives = 51/189 (26%), Gaps = 46/189 (24%)
Query: 81 DRVKRPMNAFMVW-SRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRL 139
+V+ M+ + W + + +M + ++ W ++ + +L
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNS-PETVLEMLQK-LLYQIDPNWTSRSDHSSNI------KL 225
Query: 140 RAVHMKEHPDYKYRPRRKTKTLLKKDKYP--LGSGNLI-QNTSSSNDV------------ 184
R + RR LLK Y L L+ N ++
Sbjct: 226 RIH------SIQAELRR----LLKSKPYENCL----LVLLNVQNAKAWNAFNLSCKILLT 271
Query: 185 TRNSSSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMT 244
TR VT + S+ P Y PR ++
Sbjct: 272 TRFK-QVTDFLSAATTTHISLDHHSMTLTP------DEVKSLLLKYLDCRPQDLPR-EVL 323
Query: 245 GMHPSSTSL 253
+P S+
Sbjct: 324 TTNPRRLSI 332
>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
interaction, metal-binding, nucleus, receptor,
transcription, transcription regulation, zinc-FIN
activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
3dzu_A* 3e00_A*
Length = 467
Score = 32.8 bits (74), Expect = 0.17
Identities = 15/118 (12%), Positives = 33/118 (27%)
Query: 220 DPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYH 279
D + + +G +HPS + T ++ + G G P+
Sbjct: 12 DDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMGPPFS 71
Query: 280 SMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREYGSPNGLPPNST 337
+ S S + + S+G L+ + +P + +
Sbjct: 72 VISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVPAHPS 129
Score = 32.8 bits (74), Expect = 0.20
Identities = 17/117 (14%), Positives = 34/117 (29%)
Query: 276 SPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREYGSPNGLPPN 335
+H + V S SP+ G + P+ G+ + + + L
Sbjct: 3 HHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSP 62
Query: 336 STDLHLVKREYSSPNGAPPNAGDLRHMISMYLPEQQEQARLQAMYQQQAGHPPEGMP 392
+ SSP G + + Q + + + + PP G+
Sbjct: 63 INGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLN 119
Score = 30.8 bits (69), Expect = 0.90
Identities = 26/125 (20%), Positives = 45/125 (36%), Gaps = 7/125 (5%)
Query: 214 PNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPG 273
N + P +A + H S G +H ++L+S +NG ++
Sbjct: 20 VNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSSPINGMG-----PPFSVIS 74
Query: 274 AGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREYGSPNGLP 333
+ HSM + G S S +S + + PP GL+ V + P+G
Sbjct: 75 SPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPV--SSSEDIKPPLGLNGVLKVPAHPSGNM 132
Query: 334 PNSTD 338
+ T
Sbjct: 133 ASFTK 137
Score = 30.1 bits (67), Expect = 1.5
Identities = 25/136 (18%), Positives = 46/136 (33%), Gaps = 5/136 (3%)
Query: 228 SAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHS 287
+ + H + T ++ S TS + ++ ++ + G+ HS + S
Sbjct: 2 AHHHHHHVDDDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLSS 61
Query: 288 P-----SGSSVKSEPVSPSSGGGILTPTPGSGPPTGLHLVKREYGSPNGLPPNSTDLHLV 342
P SV S P+ P S TPT G + S + L+ V
Sbjct: 62 PINGMGPPFSVISSPMGPHSMSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGV 121
Query: 343 KREYSSPNGAPPNAGD 358
+ + P+G +
Sbjct: 122 LKVPAHPSGNMASFTK 137
Score = 28.9 bits (64), Expect = 2.9
Identities = 20/130 (15%), Positives = 37/130 (28%), Gaps = 5/130 (3%)
Query: 189 SSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHP 248
+ Q +++ S + P+ + H + GM P
Sbjct: 11 DDDKMFSTQVNSSLTSPTGRGSMAAPSLHPSLGPGIGSPGQL--HSPISTLSSPINGMGP 68
Query: 249 SSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILT 308
+ ++S M S + TT S S +P SS +P +G +
Sbjct: 69 PFSVISSPMGPHS---MSVPTTPTLGFSTGSPQLSSPMNPVSSSEDIKPPLGLNGVLKVP 125
Query: 309 PTPGSGPPTG 318
P +
Sbjct: 126 AHPSGNMASF 135
>2id4_A Kexin; KEX2, kexin, furin, proprotein, prohormone, convertase, SUBT
like protease, serine protease; HET: NDG; 1.90A
{Saccharomyces cerevisiae} SCOP: b.18.1.20 c.41.1.1 PDB:
1r64_A* 1ot5_A*
Length = 503
Score = 31.2 bits (70), Expect = 0.55
Identities = 18/109 (16%), Positives = 34/109 (31%), Gaps = 1/109 (0%)
Query: 206 YQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMY 265
Y G +G + + A ++ G +S + + + +Y Y
Sbjct: 156 YSCSWGPADDGRHLQGPSDLVKKALVKGVTEGRDSKGAI-YVFASGNGGTRGDNCNYDGY 214
Query: 266 TTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSG 314
T + G+ H +S S+V + S SG I +
Sbjct: 215 TNSIYSITIGAIDHKDLHPPYSEGCSAVMAVTYSSGSGEYIHSSDINGR 263
>1k3v_A Capsid protein VP2; icosahadral, beta sheet, icosahedral virus;
3.50A {Porcine parvovirus} SCOP: b.121.5.2
Length = 579
Score = 30.9 bits (69), Expect = 0.76
Identities = 17/171 (9%), Positives = 44/171 (25%), Gaps = 4/171 (2%)
Query: 174 LIQNTSSSNDVTRNSSSVTTSAQQNSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTH 233
L+ ++ D + + + + Y P + +
Sbjct: 292 LLTEPTTEGDQHPGTLPAANTRKGYHQTINNSYTEATAIRPAQVGYNTPYMNFEYSNGGP 351
Query: 234 MSSGYPRYDMTGMHPSSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSV 293
+ T + + + T ++ ++ +P
Sbjct: 352 FLTPIVPTADTQYNDDEPNGAIRFTMDYQHGHLTTSSQELERYTFNPQSKCGRAPKQQFN 411
Query: 294 KSEPVSPSSG-GGILTPTPGSGPPTGLHL--VKREYGSPNGLPPNSTDLHL 341
+ P++ + G L P+ G + +H YG L N+ +
Sbjct: 412 QQAPLNLENTNNGTLLPSDPIGGKSNMHFMNTLNTYGPLTAL-NNTAPVFP 461
>3l5i_A Interleukin-6 receptor subunit beta; cytokine receptor, fibronectin
type III domain, alternative cell membrane, disulfide
bond; 1.90A {Homo sapiens} PDB: 3l5j_A
Length = 290
Score = 30.5 bits (69), Expect = 0.89
Identities = 11/87 (12%), Positives = 18/87 (20%)
Query: 249 SSTSLNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILT 308
++T L + Y T L G P+ + V P +
Sbjct: 61 NATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPACDFQATHPVMDLKAFPKDNMLWVE 120
Query: 309 PTPGSGPPTGLHLVKREYGSPNGLPPN 335
T L +
Sbjct: 121 WTTPRESVKKYILEWCVLSDKAPCITD 147
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex,
RNA-RNA complex, PROT complex, peptidyl transferase
reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
{Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y*
1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y*
1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y*
1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ...
Length = 241
Score = 29.8 bits (66), Expect = 1.4
Identities = 8/108 (7%), Positives = 25/108 (23%), Gaps = 6/108 (5%)
Query: 62 SHNTNNNNNSTNSKNQNAIDRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEW 121
+ + + ++ QR ++ + + KR+ W
Sbjct: 85 GGEEAPDEDVETELQARGLTEKTPDLSDEDARLLTQRHRVGKPQFNRQDHHKKKRVSTSW 144
Query: 122 KLLNEQAKRPFIDEAKRLRAVHMKEHPDYKYRPRRKTKTLLKKDKYPL 169
+ K +R + + +R + +
Sbjct: 145 R------KPRGQLSKQRRGIKGKGDTVEAGFRSPTAVRGKHPSGFEEV 186
>1rmg_A Rgase A, rhamnogalacturonase A; hydrolase, inverting, parallel
beta-helix, glycosidase; HET: NAG BMA MAN GLC; 2.00A
{Aspergillus aculeatus} SCOP: b.80.1.3
Length = 422
Score = 29.8 bits (67), Expect = 1.9
Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 5/63 (7%)
Query: 255 SYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPGSG 314
GS Y + + + Y + + +PSG S + ++ G+ P
Sbjct: 351 RSAYGSGYCLKD-----SSSHTSYTTTSTVTAAPSGYSATTMAADLATAFGLTASIPIPT 405
Query: 315 PPT 317
PT
Sbjct: 406 IPT 408
>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 = 2.5
Identities = 7/27 (25%), Positives = 11/27 (40%), Gaps = 9/27 (33%)
Query: 369 EQQEQARLQA---MYQQQAGHPPEGMP 392
E+Q +LQA +Y + P
Sbjct: 18 EKQALKKLQASLKLYA------DDSAP 38
>1gvh_A Flavohemoprotein; oxidoreductase, NADP, heme, flavoprotein, FAD,
iron transpor; HET: FAD HEM; 2.19A {Escherichia coli}
SCOP: a.1.1.2 b.43.4.2 c.25.1.5
Length = 396
Score = 28.9 bits (65), Expect = 3.3
Identities = 22/110 (20%), Positives = 35/110 (31%), Gaps = 12/110 (10%)
Query: 253 LNSYMNGSSYGMYTTATTLPGAGSPYHSMQPSSHSPSGSSVKSEPVSPSSGGGILTPTPG 312
L + +Y + G + + +P + + S + P GG + PG
Sbjct: 127 LANVFINREAEIYNENASKAGGWEGTRDFRIVAKTPRSALITSFELEPVDGGAVAEYRPG 186
Query: 313 ------SGPPTGLHLVKREYGSPNGLPPNSTDLHL-VKREYSSPNGAPPN 355
P H R+Y S P+ + VKRE G N
Sbjct: 187 QYLGVWLKPEGFPHQEIRQY-SLTR-KPDGKGYRIAVKRE---EGGQVSN 231
>2c1l_A Restriction endonuclease; BFII, domain fusion, hydrolase; HET: TAR
TLA SRT MES; 1.9A {Bacillus firmus}
Length = 358
Score = 27.9 bits (61), Expect = 6.1
Identities = 11/43 (25%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 108 MHNSEISKRLGAEWKLL-NEQAKRPFIDEAKRLRAVHMKEHPD 149
+HN + W LL +E+ +DE +R+ + H D
Sbjct: 167 IHNMTNATDASPGWNLLYDERTTNLTLDETERVTLIVTLGHAD 209
>3fip_A Outer membrane usher protein PAPC; beta barrel, protein
translocase, cell membrane, cell outer fimbrium,
transmembrane, transport; 3.15A {Escherichia coli} PDB:
2vqi_A*
Length = 493
Score = 28.0 bits (62), Expect = 6.1
Identities = 18/77 (23%), Positives = 27/77 (35%), Gaps = 6/77 (7%)
Query: 168 PLGSGNLIQNTSSSNDVTRNSSSVTTSAQQN------SAARESMYQMPNGYMPNGYMMDP 221
PLG+G + S SND N + T + +A S + + N Y
Sbjct: 403 PLGTGTASYSGSMSNDRYVNMAGYTDTFNDGLDSYSLNAGLNSGGGLTSQRQINAYYSHR 462
Query: 222 ATYQQHSAYTTHMSSGY 238
+ SA + GY
Sbjct: 463 SPLANLSANIASLQKGY 479
>3dax_A Cytochrome P450 7A1; cholesterol, cholesterol 7-alpha hydroxylase,
structural genomics, structural genomics consortium,
SGC, cholesterol metabolism; HET: HEM; 2.15A {Homo
sapiens} PDB: 3sn5_A*
Length = 491
Score = 27.7 bits (62), Expect = 8.4
Identities = 9/39 (23%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 120 EWKLLNEQAKRPFIDEAKRLRAVHMKEHP-DYKYRPRRK 157
E +L+ QAK P +D+++ + + ++KY+ +
Sbjct: 449 ELELIEGQAKCPPLDQSRAGLGILPPLNDIEFKYKFKHH 487
>3qr3_A Endoglucanase EG-II; TIM barrel, hydrolase; 2.05A {Hypocrea
jecorina}
Length = 340
Score = 27.3 bits (60), Expect = 9.9
Identities = 8/55 (14%), Positives = 15/55 (27%), Gaps = 3/55 (5%)
Query: 198 NSAARESMYQMPNGYMPNGYMMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTS 252
N + + +P + + H Y D +G H T+
Sbjct: 184 NDWQSAGAFISDGSAAALSQVTNPDGSTTNLIFDVHK---YLDSDNSGTHAECTT 235
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
0.310 0.124 0.369
Gapped
Lambda K H
0.267 0.0460 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 5,913,399
Number of extensions: 334358
Number of successful extensions: 826
Number of sequences better than 10.0: 1
Number of HSP's gapped: 736
Number of HSP's successfully gapped: 87
Length of query: 396
Length of database: 6,701,793
Length adjustment: 96
Effective length of query: 300
Effective length of database: 4,021,377
Effective search space: 1206413100
Effective search space used: 1206413100
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 (21.8 bits)
S2: 58 (26.8 bits)