RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy6569
(164 letters)
>3cw1_L U1 small nuclear ribonucleoprotein C; PRE-mRNA splicing,
spliceosome, RNA-binding domain, SM fold, finger, RNA
recognition motif, 5' splice site; 5.49A {Homo sapiens}
PDB: 1uw2_A 2vrd_A
Length = 77
Score = 103 bits (259), Expect = 5e-30
Identities = 55/73 (75%), Positives = 60/73 (82%)
Query: 1 MPKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAG 60
MPK+YCDYCDTYLTHDSPSVRKTHC GRKHK+NVK YY KWMEEQAQ+LID TTAA++ G
Sbjct: 1 MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYCKWMEEQAQSLIDKTTAAFQQG 60
Query: 61 KIANNPFGNKGGA 73
KI PF A
Sbjct: 61 KIPPTPFSAPPPA 73
>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP,
translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A
Length = 504
Score = 51.1 bits (123), Expect = 2e-08
Identities = 13/67 (19%), Positives = 22/67 (32%), Gaps = 3/67 (4%)
Query: 95 GMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRP 154
G++ G M + + MM R ++ MGGM + +M M
Sbjct: 436 GIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPR-VLHHMGGMAGLQSM--MRQFQQGAA 492
Query: 155 PMMQDHP 161
M+
Sbjct: 493 GNMKGMM 499
Score = 48.4 bits (116), Expect = 2e-07
Identities = 12/57 (21%), Positives = 16/57 (28%)
Query: 94 PGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMG 150
M + M + MM + M GM + M A G MG
Sbjct: 444 GDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGLQSMMRQFQQGAAGNMKGMMG 500
Score = 46.9 bits (112), Expect = 7e-07
Identities = 14/67 (20%), Positives = 24/67 (35%), Gaps = 2/67 (2%)
Query: 88 RQVGPPPGMQQGP--PPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGP 145
+++G G+ +G + M M M+P ++ M G+ M G
Sbjct: 432 KKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGLQSMMRQFQQGA 491
Query: 146 MGPMGPM 152
G M M
Sbjct: 492 AGNMKGM 498
Score = 46.1 bits (110), Expect = 1e-06
Identities = 13/61 (21%), Positives = 19/61 (31%), Gaps = 3/61 (4%)
Query: 104 MMPGM--MPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHP 161
M+ M + M N M + M M + MG M + MM+
Sbjct: 430 MVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGL-QSMMRQFQ 488
Query: 162 Q 162
Q
Sbjct: 489 Q 489
Score = 46.1 bits (110), Expect = 1e-06
Identities = 16/58 (27%), Positives = 18/58 (31%), Gaps = 3/58 (5%)
Query: 91 GPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMM--GGMGGMGPMMAMGPM 146
Q M MM P + M GM G+ M G G M MM M
Sbjct: 448 KNVSQSQMAKLNQQMAKMMDPRVLHHMGGM-AGLQSMMRQFQQGAAGNMKGMMGFNNM 504
Score = 46.1 bits (110), Expect = 1e-06
Identities = 14/70 (20%), Positives = 23/70 (32%), Gaps = 2/70 (2%)
Query: 70 KGGAAIPPPSNLSSLMPPRQV-GPPPGMQQGPPPGMMPGMM-PPGMNMMMMGMNPGMMGM 127
G + ++S + Q+ M + P ++ M G+ MM G G
Sbjct: 435 GGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGLQSMMRQFQQGAAGN 494
Query: 128 RPMMGGMGGM 137
M G M
Sbjct: 495 MKGMMGFNNM 504
Score = 45.7 bits (109), Expect = 2e-06
Identities = 11/67 (16%), Positives = 20/67 (29%)
Query: 81 LSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPM 140
+ + + G + M M+ ++ GM G++ MM
Sbjct: 434 MGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGMAGLQSMMRQFQQGAAG 493
Query: 141 MAMGPMG 147
G MG
Sbjct: 494 NMKGMMG 500
Score = 39.9 bits (94), Expect = 2e-04
Identities = 7/45 (15%), Positives = 12/45 (26%), Gaps = 1/45 (2%)
Query: 113 MNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMM 157
M+ M G+ G+ + M M P +
Sbjct: 427 FAQMVKKMG-GIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRV 470
Score = 33.0 bits (76), Expect = 0.039
Identities = 13/80 (16%), Positives = 21/80 (26%), Gaps = 4/80 (5%)
Query: 44 EQAQNLIDATTAAYKAGKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPG 103
+ ++ K + ++ +M PR + GM
Sbjct: 425 TKFAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPRVLHHMGGM--AGLQS 482
Query: 104 MMPGMMPPGMNMM--MMGMN 121
MM M MMG N
Sbjct: 483 MMRQFQQGAAGNMKGMMGFN 502
Score = 31.8 bits (73), Expect = 0.093
Identities = 8/35 (22%), Positives = 10/35 (28%)
Query: 124 MMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQ 158
M MGG+ G+ M M Q
Sbjct: 427 FAQMVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQ 461
Score = 30.7 bits (70), Expect = 0.18
Identities = 7/40 (17%), Positives = 12/40 (30%)
Query: 124 MMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQR 163
M+ + G+ G M M + M + R
Sbjct: 430 MVKKMGGIKGLFKGGDMSKNVSQSQMAKLNQQMAKMMDPR 469
>1m2v_B SEC24, protein transport protein SEC24, SEC24P, SEC24 protein,
abnormal nuclear; zinc-finger, beta barrel, VWA domain,
gelsolin domain,; 2.75A {Saccharomyces cerevisiae} SCOP:
a.71.2.1 b.2.8.1 c.62.1.2 d.109.2.1 g.41.10.1
Length = 926
Score = 47.5 bits (112), Expect = 4e-07
Identities = 18/100 (18%), Positives = 29/100 (29%), Gaps = 1/100 (1%)
Query: 63 ANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNP 122
N + +PP ++ M Q+G PP P G + P +
Sbjct: 18 QNATPLQQPAQFMPPQDPAAAGMSYGQMGMPP-QGAVPSMGQQQFLTPAQEQLHQQIDQA 76
Query: 123 GMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQ 162
+ + + P M P P+ P Q P
Sbjct: 77 TTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPM 116
Score = 46.4 bits (109), Expect = 1e-06
Identities = 19/98 (19%), Positives = 30/98 (30%), Gaps = 2/98 (2%)
Query: 65 NPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGM 124
F A S MPP+ P G QQ P + ++ MN
Sbjct: 27 AQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQ--LHQQIDQATTSMNDMH 84
Query: 125 MGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQ 162
+ P++ M P + + P+ + PM
Sbjct: 85 LHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYG 122
Score = 44.4 bits (104), Expect = 6e-06
Identities = 14/96 (14%), Positives = 21/96 (21%)
Query: 68 GNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGM 127
G G PP M +Q P Q M + ++P
Sbjct: 39 GMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQ 98
Query: 128 RPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQR 163
+ MG P M + +
Sbjct: 99 PQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRP 134
Score = 43.3 bits (101), Expect = 1e-05
Identities = 14/86 (16%), Positives = 21/86 (24%)
Query: 73 AAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMG 132
A + N + L P Q PP GM P G M +
Sbjct: 12 AQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQ 71
Query: 133 GMGGMGPMMAMGPMGPMGPMRPPMMQ 158
+ M + + + P
Sbjct: 72 QIDQATTSMNDMHLHNVPLVDPNAYM 97
Score = 43.3 bits (101), Expect = 1e-05
Identities = 14/100 (14%), Positives = 22/100 (22%), Gaps = 1/100 (1%)
Query: 63 ANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNP 122
A +G P + P M P + + ++
Sbjct: 12 AQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQ 71
Query: 123 GMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQ 162
+ M M + P M P P M Q
Sbjct: 72 QIDQATTSMNDMHLHNVPLV-DPNAYMQPQVPVQMGTPLQ 110
Score = 41.0 bits (95), Expect = 8e-05
Identities = 15/111 (13%), Positives = 22/111 (19%), Gaps = 3/111 (2%)
Query: 52 ATTAAYKAGKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPP 111
A G++ P G + +Q+ +P + P
Sbjct: 35 PAAAGMSYGQMGMPPQGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPN 94
Query: 112 GMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQ 162
M P MG P MRP
Sbjct: 95 A---YMQPQVPVQMGTPLQQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPID 142
Score = 39.4 bits (91), Expect = 3e-04
Identities = 12/87 (13%), Positives = 17/87 (19%), Gaps = 2/87 (2%)
Query: 76 PPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMG 135
P P M P GM M M G P M + +
Sbjct: 10 PQAQLQYGQNATPLQQPAQFMPPQDPA--AAGMSYGQMGMPPQGAVPSMGQQQFLTPAQE 67
Query: 136 GMGPMMAMGPMGPMGPMRPPMMQDHPQ 162
+ + + P
Sbjct: 68 QLHQQIDQATTSMNDMHLHNVPLVDPN 94
Score = 38.7 bits (89), Expect = 5e-04
Identities = 9/100 (9%), Positives = 16/100 (16%)
Query: 63 ANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNP 122
+ P + M P + P + MG
Sbjct: 50 QGAVPSMGQQQFLTPAQEQLHQQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPL 109
Query: 123 GMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQ 162
G M ++ + P
Sbjct: 110 QQQQQPMAAPAYGQPSAAMGQNMRPMNQLYPIDLLTELPP 149
Score = 38.7 bits (89), Expect = 5e-04
Identities = 17/84 (20%), Positives = 22/84 (26%), Gaps = 8/84 (9%)
Query: 86 PPRQVGPPPGMQQG-------PPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMG 138
++V P +Q G P MP P M M G P MG +
Sbjct: 4 HKKRVYPQAQLQYGQNATPLQQPAQFMPPQDPAAAGMSYGQMGMPPQGAVPSMGQQQFLT 63
Query: 139 PMMAMGPMGPMGPMRPPMMQDHPQ 162
P + M H
Sbjct: 64 PAQ-EQLHQQIDQATTSMNDMHLH 86
Score = 34.0 bits (77), Expect = 0.015
Identities = 13/89 (14%), Positives = 23/89 (25%), Gaps = 2/89 (2%)
Query: 76 PPPSNLSSLMPPRQV-GPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGM 134
++ M + P +P M + M G P
Sbjct: 71 QQIDQATTSMNDMHLHNVPLVDPNAYMQPQVPVQMGTPLQQQQQPMAAPAYGQ-PSAAMG 129
Query: 135 GGMGPMMAMGPMGPMGPMRPPMMQDHPQR 163
M PM + P+ + + PP+
Sbjct: 130 QNMRPMNQLYPIDLLTELPPPITDLTLPP 158
>3lvg_A Clathrin heavy chain 1; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus} PDB: 3lvh_A
Length = 624
Score = 45.0 bits (106), Expect = 3e-06
Identities = 7/48 (14%), Positives = 11/48 (22%), Gaps = 3/48 (6%)
Query: 105 MPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPM 152
P + M+ G + + P G P G
Sbjct: 579 QPIVYGQPQLMLTAGPSVAVP---PQAPFGYGYTAPAYGQPQPGFGYS 623
Score = 44.6 bits (105), Expect = 4e-06
Identities = 9/48 (18%), Positives = 14/48 (29%), Gaps = 3/48 (6%)
Query: 97 QQGPPPGMMPGMMPP-GMNMMMMGMNPGMMGMRP--MMGGMGGMGPMM 141
+ P P +M G ++ + P G G G M
Sbjct: 577 ETQPIVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGYSM 624
Score = 44.6 bits (105), Expect = 5e-06
Identities = 10/45 (22%), Positives = 11/45 (24%)
Query: 87 PRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMM 131
P G P M P +P P G G M
Sbjct: 580 PIVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGYSM 624
Score = 41.1 bits (96), Expect = 7e-05
Identities = 6/46 (13%), Positives = 8/46 (17%)
Query: 92 PPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGM 137
P + P + G G G G
Sbjct: 578 TQPIVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGYS 623
Score = 38.8 bits (90), Expect = 4e-04
Identities = 8/44 (18%), Positives = 10/44 (22%), Gaps = 2/44 (4%)
Query: 83 SLMPPRQVGPPPGMQQGPPPGMMP--GMMPPGMNMMMMGMNPGM 124
+ Q+ G PP G P G M
Sbjct: 581 IVYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQPGFGYSM 624
Score = 36.1 bits (83), Expect = 0.003
Identities = 8/44 (18%), Positives = 10/44 (22%), Gaps = 1/44 (2%)
Query: 74 AIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMM 117
P + + P V P G PG M
Sbjct: 582 VYGQPQLMLTAGPSVAVPPQAPFGYGYTAPAYGQPQ-PGFGYSM 624
Score = 34.2 bits (78), Expect = 0.016
Identities = 8/45 (17%), Positives = 10/45 (22%), Gaps = 5/45 (11%)
Query: 64 NNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGM 108
G ++ P P G P PG M
Sbjct: 585 QPQLMLTAGPSVAVPP-----QAPFGYGYTAPAYGQPQPGFGYSM 624
Score = 33.8 bits (77), Expect = 0.020
Identities = 10/42 (23%), Positives = 13/42 (30%), Gaps = 1/42 (2%)
Query: 121 NPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQ 162
P + G +M G + P G G P Q P
Sbjct: 579 QPIVYGQPQLMLTAGPSVAVPPQAPFG-YGYTAPAYGQPQPG 619
>1zu1_A DSRBP-ZFA, RNA binding protein ZFA; zinc finger protein,
helix-loop-helix, helix-turn-helix; NMR {Xenopus
laevis} SCOP: g.37.1.4 g.37.1.4
Length = 127
Score = 39.6 bits (91), Expect = 7e-05
Identities = 13/48 (27%), Positives = 17/48 (35%), Gaps = 2/48 (4%)
Query: 1 MPKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQN 48
C C L S S + H Q RKH + V+ Y E +
Sbjct: 30 FSDTQCKVCSAVLI--SESQKLAHYQSRKHANKVRRYMAINQGEDSVP 75
Score = 34.2 bits (77), Expect = 0.005
Identities = 10/38 (26%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 2 PKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQ 39
C C+ + SP V ++H G+ H N++ Q
Sbjct: 92 RSKCCPVCNMTFS--SPVVAESHYIGKTHIKNLRLREQ 127
>3q2s_C Cleavage and polyadenylation specificity factor S; CFIM, CFIM25,
CFIM68, CPSF5, CPSF6, CPSF, 3' END processing,
processing, cleavage factor; 2.90A {Homo sapiens} PDB:
3q2t_C
Length = 229
Score = 36.6 bits (84), Expect = 0.001
Identities = 16/83 (19%), Positives = 18/83 (21%), Gaps = 2/83 (2%)
Query: 78 PSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGM 137
LS + G G PG G P GG
Sbjct: 149 KQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVP--GGDRFP 206
Query: 138 GPMMAMGPMGPMGPMRPPMMQDH 160
GP GP P + H
Sbjct: 207 GPAGPGGPPPPFPAGQTHHHHHH 229
Score = 35.1 bits (80), Expect = 0.005
Identities = 16/78 (20%), Positives = 20/78 (25%), Gaps = 4/78 (5%)
Query: 85 MPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMG 144
+ ++ Q G G P G + G P G P G
Sbjct: 152 LSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFP----G 207
Query: 145 PMGPMGPMRPPMMQDHPQ 162
P GP GP P
Sbjct: 208 PAGPGGPPPPFPAGQTHH 225
Score = 33.2 bits (75), Expect = 0.025
Identities = 9/81 (11%), Positives = 11/81 (13%), Gaps = 3/81 (3%)
Query: 59 AGKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMM 118
K + F + G P G PG
Sbjct: 147 VNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRA---AFPQGGRGRGRFPGAVPGGD 203
Query: 119 GMNPGMMGMRPMMGGMGGMGP 139
P G
Sbjct: 204 RFPGPAGPGGPPPPFPAGQTH 224
Score = 30.5 bits (68), Expect = 0.20
Identities = 7/78 (8%), Positives = 14/78 (17%)
Query: 52 ATTAAYKAGKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPP 111
++ + G + + + P + G P
Sbjct: 147 VNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGGDRFP 206
Query: 112 GMNMMMMGMNPGMMGMRP 129
G P G
Sbjct: 207 GPAGPGGPPPPFPAGQTH 224
Score = 30.1 bits (67), Expect = 0.24
Identities = 16/86 (18%), Positives = 26/86 (30%), Gaps = 4/86 (4%)
Query: 33 NVKFYYQKWMEEQAQNLIDATTAAYKAGKIANNPFGNKGGAAIPPPS----NLSSLMPPR 88
V ++++ + T + +G+ P G AA P +P
Sbjct: 143 VVTPVNKQFLSQFEMQSRKTTQSGQMSGEGKAGPPGGSSRAAFPQGGRGRGRFPGAVPGG 202
Query: 89 QVGPPPGMQQGPPPGMMPGMMPPGMN 114
P P GPPP G +
Sbjct: 203 DRFPGPAGPGGPPPPFPAGQTHHHHH 228
>3od3_A Blue copper oxidase CUEO; multicopper oxidase, Cu(I) oxidase,
oxidoreductase; 1.10A {Escherichia coli} PDB: 1n68_A
2fqd_A* 2fqe_A* 2fqf_A* 2fqg_A* 3nsd_A 1kv7_A 3pau_A
3pav_A 3nsf_A 1pf3_A 3qqx_A 3nsc_A 3nt0_A 3uad_A 3uaa_A
3uac_A 3uab_A 3uae_A 3nsy_A ...
Length = 488
Score = 36.1 bits (83), Expect = 0.003
Identities = 17/97 (17%), Positives = 27/97 (27%), Gaps = 7/97 (7%)
Query: 69 NKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGM-------MPPGMNMMMMGMN 121
++ G AI P +M + + +P + + M ++
Sbjct: 273 SQMGMAIAPFDKPHPVMRIQPIAISASGALPDTLSSLPALPSLEGLTVRKLQLSMDPMLD 332
Query: 122 PGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQ 158
M M G M M MG MG M
Sbjct: 333 MMGMQMLMEKYGDQAMAGMDHSQMMGHMGHGNMNHMN 369
>1kp8_A Groel protein; chaperonin, assisted protein folding, chaperone;
HET: ATP; 2.00A {Escherichia coli} SCOP: a.129.1.1
c.8.5.1 d.56.1.1 PDB: 1gr5_A 2c7e_A* 1grl_A 1oel_A
1xck_A 1gru_A 1mnf_A 1aon_A 2c7c_A 2c7d_A 2cgt_A 2nwc_A
3e76_A* 2eu1_A 1j4z_A 1kpo_O 1sx3_A* 3c9v_A 1ss8_A
3cau_A ...
Length = 547
Score = 35.2 bits (82), Expect = 0.006
Identities = 11/21 (52%), Positives = 13/21 (61%)
Query: 121 NPGMMGMRPMMGGMGGMGPMM 141
+ +G MGGMGGMG MM
Sbjct: 527 DAADLGAAGGMGGMGGMGGMM 547
Score = 30.6 bits (70), Expect = 0.23
Identities = 6/20 (30%), Positives = 7/20 (35%)
Query: 106 PGMMPPGMNMMMMGMNPGMM 125
+ M MG GMM
Sbjct: 528 AADLGAAGGMGGMGGMGGMM 547
Score = 29.4 bits (67), Expect = 0.53
Identities = 10/21 (47%), Positives = 11/21 (52%), Gaps = 4/21 (19%)
Query: 117 MMGMNPGMMGMRPMMGGMGGM 137
+G GM MGGMGGM
Sbjct: 530 DLGAAGGM----GGMGGMGGM 546
Score = 29.1 bits (66), Expect = 0.80
Identities = 9/18 (50%), Positives = 10/18 (55%)
Query: 129 PMMGGMGGMGPMMAMGPM 146
+G GGMG M MG M
Sbjct: 529 ADLGAAGGMGGMGGMGGM 546
Score = 27.9 bits (63), Expect = 1.8
Identities = 9/26 (34%), Positives = 9/26 (34%), Gaps = 2/26 (7%)
Query: 92 PPPGMQQGPPPGMMPGMMPPGMNMMM 117
P G M GM GM MM
Sbjct: 524 PKNDAADLGAAGGMGGMG--GMGGMM 547
Score = 27.5 bits (62), Expect = 2.4
Identities = 6/24 (25%), Positives = 6/24 (25%)
Query: 86 PPRQVGPPPGMQQGPPPGMMPGMM 109
P G M GMM
Sbjct: 524 PKNDAADLGAAGGMGGMGGMGGMM 547
Score = 27.1 bits (61), Expect = 2.7
Identities = 9/32 (28%), Positives = 9/32 (28%), Gaps = 8/32 (25%)
Query: 100 PPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMM 131
P GM GM GM MM
Sbjct: 524 PKNDAADLGAAGGM--------GGMGGMGGMM 547
>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 = 35.2 bits (80), Expect = 0.007
Identities = 13/113 (11%), Positives = 26/113 (23%), Gaps = 41/113 (36%)
Query: 30 HKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIANNPFGNKGGAAIPPPSNLSSLMPPRQ 89
+ N KF EQ Q + + ++ N+ +
Sbjct: 87 LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN----------------QVFAKYN 130
Query: 90 VGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMG----GMGGMG 138
V + + ++ +RP G+ G G
Sbjct: 131 VSRLQPYLK---------------------LRQALLELRPAKNVLIDGVLGSG 162
>4dgw_A PRE-mRNA-splicing factor PRP9; zinc finger; 3.11A {Saccharomyces
cerevisiae}
Length = 402
Score = 33.7 bits (76), Expect = 0.021
Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 3/52 (5%)
Query: 2 PKYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNV-KFYYQKWMEEQAQNLIDA 52
YC +C + + SV ++H G+ HK N K + E + +
Sbjct: 291 KGIYCPFCSRWFK--TSSVFESHLVGKIHKKNESKRRNFVYSEYKLHRYLKY 340
>1zr9_A Zinc finger protein 593; DNA binding, structural genomics, PSI,
protein structure initiative, center for eukaryotic
structural genomics, CESG; NMR {Homo sapiens} SCOP:
g.37.1.4
Length = 124
Score = 32.4 bits (73), Expect = 0.028
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 7/54 (12%)
Query: 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAA 56
+ C C Y + KTH + + HK +K + + + +A AA
Sbjct: 50 LHRCLACARYFIDS--TNLKTHFRSKDHKKRLKQ-----LSVEPYSQEEAERAA 96
>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
vesicle, membrane, Ca structural protein; 7.94A {Bos
taurus}
Length = 190
Score = 32.4 bits (73), Expect = 0.038
Identities = 8/23 (34%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 39 QKWMEEQAQNL--IDATTAAYKA 59
+KW EEQ + L +DA + +
Sbjct: 88 RKWREEQRKRLQELDAASKVMEQ 110
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 32.7 bits (74), Expect = 0.049
Identities = 15/71 (21%), Positives = 21/71 (29%), Gaps = 5/71 (7%)
Query: 91 GPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGM----GGMGPMMAMGPM 146
G G Q P P P M +P P++ G G G +G
Sbjct: 1470 GSGMGTSQLPEGAGTPYERSP-MVDSGFVGSPDAAAFSPLVQGGSEGREGFGDYGLLGAA 1528
Query: 147 GPMGPMRPPMM 157
P ++ P
Sbjct: 1529 SPYKGVQSPGY 1539
>3aw5_A Multicopper oxidase; beta barrel, oxidoreductase; 2.00A
{Pyrobaculum aerophilum}
Length = 448
Score = 32.6 bits (74), Expect = 0.051
Identities = 10/101 (9%), Positives = 23/101 (22%), Gaps = 2/101 (1%)
Query: 49 LIDATTAAYKAGKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGM 108
+++ Y +P + G + S + P +
Sbjct: 246 VVELGEGVYLLKNTPFDPMHLEMGHGMQEALPEGSEYTIATFLVEGKGEAVPVEALSDPP 305
Query: 109 MPPGMNMMMMGMNPGMMGMRPMMGG--MGGMGPMMAMGPMG 147
P + GM+ + G P+ +
Sbjct: 306 PEPPKPTRTRRFALSLSGMQWTINGMFWNASNPLFEHVSVE 346
>3pgw_B SM B; protein-RNA complex, U1 snRNA, SM fold, SM core, RRM, splici
SNRNPS, splicing factors; HET: DNA; 4.40A {Homo sapiens}
PDB: 3cw1_A
Length = 231
Score = 31.5 bits (71), Expect = 0.081
Identities = 17/83 (20%), Positives = 19/83 (22%)
Query: 76 PPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMG 135
P P GP G+ M P G G
Sbjct: 114 IPAGVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRG 173
Query: 136 GMGPMMAMGPMGPMGPMRPPMMQ 158
G P M G P PP M+
Sbjct: 174 GPPPPMGRGAPPPGMMGPPPGMR 196
Score = 29.6 bits (66), Expect = 0.33
Identities = 23/92 (25%), Positives = 26/92 (28%)
Query: 66 PFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMM 125
P GG + + G P PG P M PGMM
Sbjct: 130 PVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMM 189
Query: 126 GMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMM 157
G P M G + G PMG P M
Sbjct: 190 GPPPGMRPPMGPPMGIPPGRGTPMGMPPPGMR 221
Score = 29.2 bits (65), Expect = 0.50
Identities = 24/94 (25%), Positives = 32/94 (34%)
Query: 60 GKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMG 119
G + +G + + ++ P + GPPP M G PPGM G
Sbjct: 135 GGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPPPPMGRGAPPPGMMGPPPG 194
Query: 120 MNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMR 153
M P M + G G M G P MR
Sbjct: 195 MRPPMGPPMGIPPGRGTPMGMPPPGMRPPPPGMR 228
Score = 28.5 bits (63), Expect = 0.90
Identities = 16/99 (16%), Positives = 20/99 (20%)
Query: 59 AGKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMM 118
+ P G G + + P + P
Sbjct: 117 GVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPP 176
Query: 119 GMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMM 157
MMG GM P M P G P M
Sbjct: 177 PPMGRGAPPPGMMGPPPGMRPPMGPPMGIPPGRGTPMGM 215
Score = 27.3 bits (60), Expect = 2.2
Identities = 15/91 (16%), Positives = 21/91 (23%)
Query: 71 GGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPM 130
G P+ L+ + M + ++ P
Sbjct: 117 GVPMPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAAAAAATASIAGAPTQYPPGRGGPP 176
Query: 131 MGGMGGMGPMMAMGPMGPMGPMRPPMMQDHP 161
G P MGP M P P M P
Sbjct: 177 PPMGRGAPPPGMMGPPPGMRPPMGPPMGIPP 207
>3ruv_A Chaperonin, CPN; double-ring, protein folding machinery, group II
chaperonin, binding, chaperone; HET: ANP; 2.24A
{Methanococcus maripaludis} PDB: 3rus_A* 3ruw_A* 3ruq_A*
3los_A 3kfb_A* 3izi_A 3izj_A 3izm_A 3izh_A 3kfe_A*
3iyf_A* 3kfk_A* 3izk_A 3izl_A 3j03_A 3izn_A 3j02_A
Length = 543
Score = 31.4 bits (72), Expect = 0.12
Identities = 10/25 (40%), Positives = 11/25 (44%), Gaps = 1/25 (4%)
Query: 86 PPRQVGPPPGMQQGPP-PGMMPGMM 109
+ P G G P G MPGMM
Sbjct: 519 EKLRGAPDMGDMGGMPGMGGMPGMM 543
Score = 29.1 bits (66), Expect = 0.75
Identities = 12/35 (34%), Positives = 13/35 (37%), Gaps = 13/35 (37%)
Query: 97 QQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMM 131
+ P G M GM PGM GM MM
Sbjct: 522 RGAPDMGDMGGM-------------PGMGGMPGMM 543
Score = 27.5 bits (62), Expect = 2.4
Identities = 10/20 (50%), Positives = 10/20 (50%)
Query: 122 PGMMGMRPMMGGMGGMGPMM 141
MG M GMGGM MM
Sbjct: 524 APDMGDMGGMPGMGGMPGMM 543
Score = 26.0 bits (58), Expect = 6.9
Identities = 10/27 (37%), Positives = 10/27 (37%), Gaps = 2/27 (7%)
Query: 91 GPPPGMQQGPPPGMMPGMMPPGMNMMM 117
G G MPGM GM MM
Sbjct: 519 EKLRGAPDMGDMGGMPGMG--GMPGMM 543
>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone,
hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus
influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*
Length = 310
Score = 29.9 bits (68), Expect = 0.33
Identities = 4/25 (16%), Positives = 10/25 (40%), Gaps = 1/25 (4%)
Query: 113 MNMMMMGMN-PGMMGMRPMMGGMGG 136
N++M+G G + + +
Sbjct: 51 KNILMIGPTGVGKTEIARRLAKLAN 75
>2yvr_A Transcription intermediary factor 1-beta; ZF-B_BOX domain,
structural genomics, NPPSFA; 1.80A {Homo sapiens}
Length = 50
Score = 27.4 bits (61), Expect = 0.39
Identities = 10/30 (33%), Positives = 12/30 (40%), Gaps = 8/30 (26%)
Query: 3 KYYCDYCDTYLTHDSPSVRKTHCQGRKHKD 32
+C+ CDT D CQ HKD
Sbjct: 18 VLFCESCDTLTCRD--------CQLNAHKD 39
>1ybx_A Conserved hypothetical protein; ST genomics, PSI, protein structure
initiative, southeast COLL for structural genomics,
secsg; HET: MSE; 1.80A {Clostridium thermocellum}
Length = 143
Score = 29.0 bits (65), Expect = 0.39
Identities = 7/36 (19%), Positives = 14/36 (38%)
Query: 106 PGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMM 141
G++P G + G+M G G + ++
Sbjct: 12 SGLVPRGSQSTSLYKKAGLMAKGGFPGFGGNINNLV 47
Score = 26.7 bits (59), Expect = 2.6
Identities = 9/43 (20%), Positives = 14/43 (32%), Gaps = 1/43 (2%)
Query: 101 PPGMMPGMMPPGMNMMMMGMNPGMMG-MRPMMGGMGGMGPMMA 142
P G + +M G PG G + ++ M M
Sbjct: 16 PRGSQSTSLYKKAGLMAKGGFPGFGGNINNLVKQAQKMQRDME 58
>3eph_A TRNA isopentenyltransferase; transferase, alternative initiation,
ATP-binding, cytoplasm, mitochondrion,
nucleotide-binding, nucleus; 2.95A {Saccharomyces
cerevisiae} PDB: 3epj_A 3epk_A* 3epl_A*
Length = 409
Score = 29.2 bits (66), Expect = 0.60
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 9/48 (18%)
Query: 3 KYYCDYCDTYLTHDSPSVRKT----HCQGRKHKDNVK-----FYYQKW 41
Y C+ C + ++ + H R+HK N+K ++KW
Sbjct: 360 HYTCNVCRNADGKNVVAIGEKYWKIHLGSRRHKSNLKRNTRQADFEKW 407
>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent
proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus
influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A*
1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E*
1ht1_E* 1ht2_E*
Length = 444
Score = 29.2 bits (66), Expect = 0.63
Identities = 5/33 (15%), Positives = 11/33 (33%)
Query: 104 MMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGG 136
+ G+ M GM ++ + +G
Sbjct: 177 VSAGVSMGVEIMAPPGMEEMTNQLQSLFQNLGS 209
>1iok_A Chaperonin 60; chaperone; 3.20A {Paracoccus denitrificans} SCOP:
a.129.1.1 c.8.5.1 d.56.1.1
Length = 545
Score = 28.7 bits (65), Expect = 0.82
Identities = 10/23 (43%), Positives = 10/23 (43%), Gaps = 3/23 (13%)
Query: 87 PRQVGPPPGMQQGPPPGMMPGMM 109
P P GM P G M GMM
Sbjct: 526 PEPKAPAGGM---PDMGGMGGMM 545
Score = 26.8 bits (60), Expect = 4.1
Identities = 8/13 (61%), Positives = 8/13 (61%)
Query: 129 PMMGGMGGMGPMM 141
M MGGMG MM
Sbjct: 533 GGMPDMGGMGGMM 545
Score = 26.0 bits (58), Expect = 7.6
Identities = 10/17 (58%), Positives = 10/17 (58%), Gaps = 1/17 (5%)
Query: 121 NPGMMGMRPMMGGMGGM 137
GM P MGGMGGM
Sbjct: 529 KAPAGGM-PDMGGMGGM 544
Score = 25.6 bits (57), Expect = 8.7
Identities = 9/18 (50%), Positives = 9/18 (50%), Gaps = 2/18 (11%)
Query: 100 PPPGMMPGMMPPGMNMMM 117
P G MP M GM MM
Sbjct: 530 APAGGMPDM--GGMGGMM 545
>3aq1_B Thermosome subunit; group II chaperonin, protein folding,
chaperone; 2.75A {Methanococcoides burtonii}
Length = 500
Score = 28.7 bits (65), Expect = 0.88
Identities = 7/21 (33%), Positives = 8/21 (38%)
Query: 93 PPGMQQGPPPGMMPGMMPPGM 113
QG PG +P M M
Sbjct: 476 KGSANQGMGPGGLPDMPDLDM 496
>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 = 28.7 bits (64), Expect = 0.95
Identities = 3/18 (16%), Positives = 7/18 (38%)
Query: 102 PGMMPGMMPPGMNMMMMG 119
M +NM+++
Sbjct: 1077 QESFINTMSAWVNMLLIS 1094
>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 = 28.5 bits (63), Expect = 1.3
Identities = 13/98 (13%), Positives = 18/98 (18%), Gaps = 5/98 (5%)
Query: 63 ANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNP 122
+N G A + P G P P + +P
Sbjct: 1499 GSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSP 1558
Query: 123 GMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDH 160
P P P P P +
Sbjct: 1559 TSPSYSPTSPSYSPTSP-----SYSPTSPSYSPTSPSY 1591
>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal
recognition particle, SRP-GTPase, protein targeting,
cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus
furiosus}
Length = 443
Score = 27.5 bits (62), Expect = 2.2
Identities = 3/21 (14%), Positives = 5/21 (23%)
Query: 127 MRPMMGGMGGMGPMMAMGPMG 147
M+ + M G
Sbjct: 422 MKKLFKSMNKRQLSRLARRFG 442
>1q3q_A Thermosome alpha subunit; chaperone, chaperonin; HET: ANP; 2.30A
{Thermococcus SP} SCOP: a.129.1.2 c.8.5.2 d.56.1.2 PDB:
1q2v_A* 1q3s_A* 1q3r_A
Length = 548
Score = 27.5 bits (62), Expect = 2.3
Identities = 7/25 (28%), Positives = 8/25 (32%)
Query: 91 GPPPGMQQGPPPGMMPGMMPPGMNM 115
+ G GM GM M M
Sbjct: 524 AKATKPEGGQGGGMPGGMGGMDMGM 548
Score = 25.6 bits (57), Expect = 9.8
Identities = 10/25 (40%), Positives = 12/25 (48%), Gaps = 1/25 (4%)
Query: 93 PPGMQQGPPPGMMPGMMPPGMNMMM 117
+G G MPG M GM+M M
Sbjct: 525 KATKPEGGQGGGMPGGMG-GMDMGM 548
Score = 25.6 bits (57), Expect = 9.9
Identities = 11/20 (55%), Positives = 11/20 (55%)
Query: 101 PPGMMPGMMPPGMNMMMMGM 120
P G G MP GM M MGM
Sbjct: 529 PEGGQGGGMPGGMGGMDMGM 548
>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 = 27.6 bits (61), Expect = 2.4
Identities = 15/47 (31%), Positives = 15/47 (31%), Gaps = 1/47 (2%)
Query: 66 PFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPG 112
P G PP P Q PP G PP G P PP
Sbjct: 390 PQGYAPPPQGYPPQGYPPQGYPPQGYPPQG-YPPPPQGAPPQGAPPA 435
>1g9l_A Polyadenylate-binding protein 1; all-helical domain, RNA binding
protein; NMR {Homo sapiens} SCOP: a.144.1.1 PDB: 1jgn_A
1jh4_A
Length = 144
Score = 26.7 bits (58), Expect = 2.4
Identities = 7/62 (11%), Positives = 15/62 (24%)
Query: 101 PPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDH 160
P G P + G+ + + + + P+ M+
Sbjct: 2 PLGSAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASA 61
Query: 161 PQ 162
P
Sbjct: 62 PP 63
>3zx1_A Oxidoreductase, putative; laccase, metallo-oxidase, cuprous
oxidase; 1.95A {Campylobacter jejuni subsp}
Length = 481
Score = 26.8 bits (59), Expect = 3.4
Identities = 11/89 (12%), Positives = 22/89 (24%)
Query: 53 TTAAYKAGKIANNPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPG 112
+A Y K+ N A + +P P + ++
Sbjct: 294 ESAYYDRDKMMVKEEPNTLFLANINLKKENVELPKNLKIFKPSEEPKEFKEIIMSEDHMQ 353
Query: 113 MNMMMMGMNPGMMGMRPMMGGMGGMGPMM 141
M+ MM + M + +
Sbjct: 354 MHGMMGKSEGELKIALASMFLINRKSYDL 382
>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting,
protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP:
a.4.5.54 a.4.5.54
Length = 566
Score = 26.9 bits (58), Expect = 3.5
Identities = 8/133 (6%), Positives = 28/133 (21%)
Query: 5 YCDYCDTYLTHDSPSVRKTHCQGRKHKDNVKFYYQKWMEEQAQNLIDATTAAYKAGKIAN 64
C+ C L + S K + + + + ++++
Sbjct: 196 NCEICGHRLPNASKVRSKLNRLNFHDSRVHIELEKNSLARNKSSHSALSSSSSTGSSTEF 255
Query: 65 NPFGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGM 124
+ + + + + M G +
Sbjct: 256 VQLSFRKSDGVLFSQATERALENILTEKNKHIFNQNVVSVNGVDMRKGASSHEYNNEVPF 315
Query: 125 MGMRPMMGGMGGM 137
+ + G+ +
Sbjct: 316 IETKLSRIGISSL 328
>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair,
proteasome-mediated degradation, protein- protein
interaction, replication; NMR {Homo sapiens} SCOP:
a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A
Length = 368
Score = 26.5 bits (57), Expect = 5.6
Identities = 10/84 (11%), Positives = 25/84 (29%), Gaps = 1/84 (1%)
Query: 80 NLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMGGMGGMGP 139
L + +P +Q+ + + P MR ++ + P
Sbjct: 202 YLLTGIPGSPEPEHGSVQESQVSEQPATEAAGENPLEFLRDQPQFQNMRQVIQQNPALLP 261
Query: 140 MMAMGPMGPMGPMRPPMMQDHPQR 163
+ + +G P + H ++
Sbjct: 262 AL-LQQLGQENPQLLQQISRHQEQ 284
Score = 26.1 bits (56), Expect = 5.9
Identities = 11/91 (12%), Positives = 21/91 (23%)
Query: 73 AAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGMRPMMG 132
P S +S P + P + P + +
Sbjct: 108 FPPAPTSGMSHPPPAAREDKSPSEESAPTTSPESVSGSVPSSGSSGREEDAASTLVTGSE 167
Query: 133 GMGGMGPMMAMGPMGPMGPMRPPMMQDHPQR 163
+ +M+MG ++P R
Sbjct: 168 YETMLTEIMSMGYERERVVAALRASYNNPHR 198
>1o91_A Collagen alpha 1(VIII) chain; C1Q_LIKE_domain, extracellular
matrix, adhesion, connective tissue, repeat; HET: CPS;
1.9A {Mus musculus} SCOP: b.22.1.1
Length = 178
Score = 25.8 bits (56), Expect = 6.0
Identities = 7/40 (17%), Positives = 10/40 (25%), Gaps = 3/40 (7%)
Query: 122 PGMMGMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHP 161
+M G P M +G G P +
Sbjct: 6 HAVMPTP---SPQGEYLPDMGLGIDGVKTPHAYAGKKGKH 42
>2uva_G Fatty acid synthase beta subunits; fungal, dehydratase, enoyl
reductase, ketoacyl synthase, ketoacyl reductase; HET:
FMN; 3.10A {Thermomyces lanuginosus} PDB: 2uvc_G*
Length = 2060
Score = 26.2 bits (57), Expect = 6.5
Identities = 15/78 (19%), Positives = 24/78 (30%), Gaps = 10/78 (12%)
Query: 43 EEQAQNLIDATTAAYKAGKIANNP-FGNKGGAAIPPPSNLSSLMPPRQVGPPPGMQQ--- 98
+ +I A ++ P ++ A+ + PR V G
Sbjct: 515 DGTGVRVILAGAIDGTNTEVGYKPELFDRDDNAVQFAVDWVKEHGPRLVKTSVGQTFVDT 574
Query: 99 ------GPPPGMMPGMMP 110
G PP M+ GM P
Sbjct: 575 KMSRLLGVPPVMVAGMTP 592
>3v1v_A 2-MIB synthase, 2-methylisoborneol synthase; class I terpenoid
cyclase fold, DDXXXXD motif, NDXXSXXXE MOT
methylisoborneol biosynthesis; HET: GST; 1.80A
{Streptomyces coelicolor} PDB: 3v1x_A*
Length = 433
Score = 25.9 bits (56), Expect = 7.0
Identities = 17/99 (17%), Positives = 28/99 (28%), Gaps = 7/99 (7%)
Query: 72 GAAIPPPSNLSSLMPPRQVGPPPGMQQGP--PPGMMPGMMPPGMNMMMMGMNP----GMM 125
++ P ++P V PP +P PP G P G
Sbjct: 10 HSSGLVPRGSHMVIPSASVTSAASDFLAALHPPVTVPDPAPPPPPAPAAGNPPDTVTGDS 69
Query: 126 GMRPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHPQRK 164
++ ++ G G G ++ P G P
Sbjct: 70 VLQRILRGPTGPGT-TSLAPAVRYGRQPGPEAPASAPPA 107
>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 = 26.2 bits (57), Expect = 8.2
Identities = 6/23 (26%), Positives = 10/23 (43%)
Query: 104 MMPGMMPPGMNMMMMGMNPGMMG 126
+P N M+ +NPG +
Sbjct: 1796 AVPRDELGRSNYGMIAINPGRVA 1818
>2gfp_A EMRD, multidrug resistance protein D; membrane protein, multidrug
transporter; 3.50A {Escherichia coli}
Length = 375
Score = 25.7 bits (57), Expect = 8.8
Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 8/53 (15%)
Query: 107 GMMPPGMNMMMMGMNP-------GMMGMRPMMGGMGGMGPMMAMGPMGPMGPM 152
GM+ P M P ++G +G G + + AM P G +
Sbjct: 306 GMLFPLATSGAMEPFPFLAGTAGALVGGLQNIGS-GVLASLSAMLPQTGQGSL 357
>1vq8_3 50S ribosomal protein L44E; 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: g.41.8.3 PDB:
1jj2_2 1k73_4* 1k8a_4* 1k9m_4* 1kc8_4* 1kd1_4* 1kqs_2*
1m1k_4* 1m90_4* 1n8r_4* 1nji_4* 1q7y_4* 1q81_4* 1q82_4*
1q86_4* 1qvf_2 1qvg_2 1s72_3* 1vq4_3* 1vq5_3* ...
Length = 92
Score = 24.7 bits (54), Expect = 8.8
Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 7/39 (17%)
Query: 1 MPKY---YCDYCDTYLTHDSPSVRK----THCQGRKHKD 32
MP+ YC +C+ + H+ VR + ++
Sbjct: 3 MPRRFNTYCPHCNEHQEHEVEKVRSGRQTGMKWIDRQRE 41
>2qs7_A Uncharacterized protein; putative oxidoreductase of the
DSRE/DSRF-like family, struct genomics, joint center for
structural genomics; HET: MSE EPE; 2.09A {Sulfolobus
solfataricus P2}
Length = 144
Score = 25.3 bits (55), Expect = 8.9
Identities = 6/23 (26%), Positives = 9/23 (39%)
Query: 103 GMMPGMMPPGMNMMMMGMNPGMM 125
+ PP ++ M P MM
Sbjct: 54 RSLNSQQPPQIDKNYEQMGPIMM 76
>2xu9_A Laccase; oxidoreductase, multicopper oxidases; 1.50A {Thermus
thermophilus} PDB: 2xuw_A 2xvb_A 2yae_A 2yaf_A 2yah_A
2yam_A 2yao_A 2yap_A 2yaq_A 2yar_A 4ai7_A
Length = 439
Score = 25.6 bits (56), Expect = 8.9
Identities = 15/97 (15%), Positives = 27/97 (27%), Gaps = 7/97 (7%)
Query: 70 KGGAAIPPPSNLSSLMPPRQVGPPPGMQQGPPPGMMPGMMPPGMNMMMMGMNPGMMGM-- 127
+G + L + P+ + P + P + MM + G
Sbjct: 284 QGPSRPETLLYLIAPKNPKPLPLPKALSPFPTLPAPVVTRRLVLTEDMMAARFFINGQVF 343
Query: 128 ---RPMMGGMGGMGPMMAMGPMGPMGPMRPPMMQDHP 161
R + G + + G M P + HP
Sbjct: 344 DHRRVDLKGQAQTVEVWEVENQGDMD--HPFHLHVHP 378
>2bji_A Inositol-1(OR 4)-monophosphatase; hydrolase, aspartic proteinase
mechanism, aspartyl protease, succinimide, zymogen;
1.30A {Bos taurus} PDB: 1imb_A* 1ima_A* 1imc_A 1imd_A
1ime_A 1imf_A 2hhm_A 1awb_A
Length = 277
Score = 25.2 bits (56), Expect = 9.8
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 42 MEEQAQNLID-ATTAAYKAGKIANNPFGN 69
M + Q +D A T A +AG++ N
Sbjct: 1 MADPWQECMDYAVTLAGQAGEVVREALKN 29
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
0.319 0.136 0.450
Gapped
Lambda K H
0.267 0.0437 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,803,118
Number of extensions: 172685
Number of successful extensions: 2063
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1284
Number of HSP's successfully gapped: 328
Length of query: 164
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 78
Effective length of database: 4,300,587
Effective search space: 335445786
Effective search space used: 335445786
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.9 bits)