Query 046997
Match_columns 807
No_of_seqs 397 out of 2171
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 06:35:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046997.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046997hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07220 DNA topoisomerase I; 100.0 5E-147 1E-151 1311.1 70.4 663 11-724 3-666 (740)
2 PRK14973 DNA topoisomerase I; 100.0 2E-146 3E-151 1317.6 69.9 664 8-726 1-668 (936)
3 PRK07219 DNA topoisomerase I; 100.0 6E-145 1E-149 1309.2 71.1 673 10-725 2-679 (822)
4 PRK05776 DNA topoisomerase I; 100.0 9E-143 2E-147 1258.9 69.9 639 9-686 2-650 (670)
5 TIGR01057 topA_arch DNA topois 100.0 1E-138 3E-143 1222.8 67.5 617 13-666 1-618 (618)
6 PRK06319 DNA topoisomerase I/S 100.0 1E-137 3E-142 1245.7 66.7 626 7-725 1-678 (860)
7 PRK08173 DNA topoisomerase III 100.0 5E-137 1E-141 1235.1 63.1 605 7-672 1-652 (862)
8 PRK07726 DNA topoisomerase III 100.0 1E-136 3E-141 1210.7 63.3 618 10-691 2-657 (658)
9 TIGR01056 topB DNA topoisomera 100.0 3E-136 7E-141 1203.1 63.5 600 10-669 2-642 (660)
10 KOG1956 DNA topoisomerase III 100.0 5E-137 1E-141 1128.3 51.4 659 8-711 1-661 (758)
11 PRK06599 DNA topoisomerase I; 100.0 1E-134 3E-139 1197.8 68.3 631 7-725 1-670 (675)
12 PRK05582 DNA topoisomerase I; 100.0 3E-134 5E-139 1192.3 63.9 622 7-724 1-644 (650)
13 PRK14724 DNA topoisomerase III 100.0 1E-134 3E-139 1225.8 62.2 613 8-672 1-678 (987)
14 PRK07561 DNA topoisomerase I s 100.0 4E-133 9E-138 1209.2 66.9 625 9-706 2-665 (859)
15 TIGR01051 topA_bact DNA topois 100.0 1E-132 2E-137 1168.2 61.1 580 11-672 1-609 (610)
16 COG0550 TopA Topoisomerase IA 100.0 7E-131 1E-135 1128.3 56.7 545 9-606 1-556 (570)
17 PRK08780 DNA topoisomerase I; 100.0 4E-129 8E-134 1160.0 63.4 585 7-667 1-626 (780)
18 PRK09401 reverse gyrase; Revie 100.0 5E-115 1E-119 1071.4 57.7 532 6-600 599-1172(1176)
19 PTZ00407 DNA topoisomerase IA; 100.0 2E-113 4E-118 1003.1 51.5 549 10-590 11-667 (805)
20 TIGR01054 rgy reverse gyrase. 100.0 6E-112 1E-116 1045.2 57.1 530 7-598 600-1169(1171)
21 PRK14701 reverse gyrase; Provi 100.0 1.4E-96 3E-101 923.7 55.0 540 7-599 579-1636(1638)
22 cd00186 TOP1Ac DNA Topoisomera 100.0 8.1E-94 1.8E-98 799.4 39.1 373 173-599 1-379 (381)
23 PF01131 Topoisom_bac: DNA top 100.0 7.3E-94 1.6E-98 806.4 33.1 395 171-591 2-403 (403)
24 COG1110 Reverse gyrase [DNA re 100.0 1.1E-83 2.3E-88 741.0 41.2 533 7-599 616-1185(1187)
25 KOG1957 DNA topoisomerase III 100.0 4.5E-79 9.8E-84 647.8 17.7 512 7-595 1-530 (555)
26 smart00437 TOP1Ac Bacterial DN 100.0 4.7E-65 1E-69 538.0 23.7 252 294-552 2-259 (259)
27 cd03362 TOPRIM_TopoIA_TopoIII 100.0 7.4E-36 1.6E-40 291.9 14.7 148 10-168 2-151 (151)
28 cd01028 TOPRIM_TopoIA TOPRIM_T 100.0 1.8E-34 4E-39 279.2 15.1 142 9-168 1-142 (142)
29 cd03361 TOPRIM_TopoIA_RevGyr T 100.0 1E-31 2.3E-36 266.8 15.1 149 9-168 1-170 (170)
30 smart00436 TOP1Bc Bacterial DN 100.0 1.7E-31 3.6E-36 235.8 8.2 89 148-247 1-89 (89)
31 cd03363 TOPRIM_TopoIA_TopoI TO 100.0 1.4E-30 3E-35 245.2 13.7 122 10-168 2-123 (123)
32 PF01751 Toprim: Toprim domain 99.9 9.6E-23 2.1E-27 185.6 7.8 100 10-156 1-100 (100)
33 COG0551 TopA Zn-finger domain 99.0 2.7E-10 5.8E-15 110.2 6.3 78 634-726 16-96 (140)
34 PF01396 zf-C4_Topoisom: Topoi 98.9 7.3E-10 1.6E-14 82.6 4.1 37 636-674 2-38 (39)
35 PRK06319 DNA topoisomerase I/S 98.9 1.2E-09 2.5E-14 134.0 8.4 101 611-724 606-728 (860)
36 COG0551 TopA Zn-finger domain 98.6 4.4E-08 9.5E-13 94.8 6.2 82 607-695 26-113 (140)
37 smart00493 TOPRIM topoisomeras 98.4 1.1E-06 2.4E-11 75.5 8.9 73 9-141 1-73 (76)
38 PRK07219 DNA topoisomerase I; 98.4 4.8E-07 1E-11 111.1 7.5 121 225-350 391-519 (822)
39 cd01025 TOPRIM_recR TOPRIM_rec 97.7 0.00026 5.7E-09 65.4 9.7 45 107-153 47-93 (112)
40 cd00188 TOPRIM Topoisomerase-p 97.1 0.0048 1E-07 52.3 10.0 81 10-152 2-82 (83)
41 PRK07561 DNA topoisomerase I s 96.7 0.0022 4.7E-08 79.7 6.3 83 612-706 601-723 (859)
42 PRK06599 DNA topoisomerase I; 96.5 0.0026 5.6E-08 77.1 4.7 60 613-674 601-674 (675)
43 cd01027 TOPRIM_RNase_M5_like T 96.4 0.0075 1.6E-07 52.8 5.8 42 106-152 39-80 (81)
44 PRK00076 recR recombination pr 96.1 0.084 1.8E-06 53.8 12.4 55 113-169 132-194 (196)
45 PRK05582 DNA topoisomerase I; 96.0 0.0048 1E-07 74.5 3.8 58 614-672 587-647 (650)
46 PF00098 zf-CCHC: Zinc knuckle 95.7 0.0068 1.5E-07 37.5 1.7 17 761-777 2-18 (18)
47 PF01396 zf-C4_Topoisom: Topoi 94.2 0.031 6.7E-07 41.8 2.0 32 684-726 2-35 (39)
48 PF09151 DUF1936: Domain of un 93.8 0.071 1.5E-06 37.1 3.0 32 637-669 3-35 (36)
49 smart00437 TOP1Ac Bacterial DN 93.3 0.31 6.7E-06 52.2 8.5 111 226-339 124-244 (259)
50 COG4026 Uncharacterized protei 93.3 0.49 1.1E-05 48.3 9.1 105 5-167 4-114 (290)
51 PF13662 Toprim_4: Toprim doma 92.7 0.19 4.1E-06 43.7 4.9 35 115-151 46-80 (81)
52 KOG2906 RNA polymerase III sub 92.4 0.22 4.8E-06 44.3 4.8 79 637-724 3-102 (105)
53 PF01131 Topoisom_bac: DNA top 92.3 0.41 9E-06 54.6 8.3 115 224-341 226-351 (403)
54 TIGR01057 topA_arch DNA topois 90.3 0.49 1.1E-05 57.1 6.6 114 416-537 195-310 (618)
55 PF13696 zf-CCHC_2: Zinc knuck 90.1 0.15 3.3E-06 36.3 1.2 23 755-777 4-26 (32)
56 PF06839 zf-GRF: GRF zinc fing 89.6 0.43 9.3E-06 36.8 3.5 35 637-673 2-43 (45)
57 PRK07220 DNA topoisomerase I; 89.5 0.78 1.7E-05 56.4 7.5 108 418-536 202-311 (740)
58 COG1594 RPB9 DNA-directed RNA 89.4 0.83 1.8E-05 42.6 5.9 81 636-725 3-110 (113)
59 cd00186 TOP1Ac DNA Topoisomera 89.4 1 2.3E-05 51.0 7.9 111 226-339 197-317 (381)
60 TIGR01051 topA_bact DNA topois 89.0 1.5 3.2E-05 53.0 9.1 110 227-339 370-495 (610)
61 PRK13844 recombination protein 88.7 1.5 3.2E-05 45.0 7.5 53 114-169 138-198 (200)
62 smart00529 HTH_DTXR Helix-turn 88.5 1.6 3.6E-05 38.8 7.1 67 512-590 7-73 (96)
63 COG1754 Uncharacterized C-term 88.4 0.31 6.8E-06 51.7 2.6 36 635-671 23-58 (298)
64 PRK04031 DNA primase; Provisio 88.4 0.51 1.1E-05 52.9 4.4 61 106-171 202-266 (408)
65 TIGR00615 recR recombination p 88.2 1.7 3.7E-05 44.4 7.6 52 114-167 134-193 (195)
66 PRK05776 DNA topoisomerase I; 87.9 1 2.2E-05 54.7 7.0 111 418-536 200-312 (670)
67 TIGR01056 topB DNA topoisomera 87.3 2 4.3E-05 52.3 8.9 117 223-340 392-536 (660)
68 COG0353 RecR Recombinational D 87.3 5 0.00011 40.8 10.2 43 108-152 128-171 (198)
69 PF09664 DUF2399: Protein of u 87.1 4.6 0.0001 39.7 9.8 72 10-140 20-91 (152)
70 COG1658 Small primase-like pro 87.1 1.2 2.5E-05 42.4 5.3 63 106-169 47-120 (127)
71 TIGR00334 5S_RNA_mat_M5 ribonu 86.7 2.1 4.5E-05 42.9 7.1 68 103-171 36-111 (174)
72 PRK14973 DNA topoisomerase I; 86.4 1.6 3.4E-05 54.9 7.5 112 225-338 382-501 (936)
73 PRK07726 DNA topoisomerase III 85.8 2.8 6.1E-05 51.0 9.1 113 226-339 393-532 (658)
74 PRK03573 transcriptional regul 85.5 7.6 0.00017 37.3 10.4 51 502-556 47-103 (144)
75 PRK03564 formate dehydrogenase 85.4 0.79 1.7E-05 50.1 3.7 76 634-728 186-265 (309)
76 PF04606 Ogr_Delta: Ogr/Delta- 84.7 0.74 1.6E-05 35.9 2.3 32 637-670 1-37 (47)
77 COG0550 TopA Topoisomerase IA 83.4 3.1 6.8E-05 49.5 7.8 116 223-340 363-488 (570)
78 COG1107 Archaea-specific RecJ- 83.3 1.4 3E-05 51.2 4.6 17 761-777 97-117 (715)
79 TIGR01562 FdhE formate dehydro 82.2 1 2.3E-05 49.2 3.0 77 635-730 184-267 (305)
80 PRK10870 transcriptional repre 81.9 12 0.00027 37.6 10.4 55 498-556 68-128 (176)
81 PRK08173 DNA topoisomerase III 81.8 4.2 9.1E-05 50.9 8.5 113 225-339 403-540 (862)
82 TIGR01384 TFS_arch transcripti 81.3 2.7 5.8E-05 38.4 5.0 39 682-724 61-99 (104)
83 PRK13777 transcriptional regul 81.2 7.9 0.00017 39.4 8.7 51 502-556 60-116 (185)
84 PRK03902 manganese transport t 79.7 4.5 9.8E-05 39.0 6.3 57 513-579 31-87 (142)
85 PF13917 zf-CCHC_3: Zinc knuck 79.0 0.92 2E-05 34.5 0.9 18 760-777 5-22 (42)
86 PRK04017 hypothetical protein; 78.7 2.9 6.2E-05 40.1 4.3 33 112-144 62-94 (132)
87 PF08259 Periviscerokin: Periv 77.2 1 2.2E-05 24.1 0.5 9 335-343 3-11 (11)
88 PF09151 DUF1936: Domain of un 76.6 1.7 3.7E-05 30.4 1.6 31 685-723 3-34 (36)
89 PF04216 FdhE: Protein involve 76.3 1.9 4.1E-05 47.0 2.8 45 635-691 172-219 (290)
90 PF15288 zf-CCHC_6: Zinc knuck 76.3 1.4 3.1E-05 33.1 1.2 18 760-777 2-21 (40)
91 PF13601 HTH_34: Winged helix 76.0 2 4.4E-05 37.4 2.3 45 511-556 21-72 (80)
92 PRK11512 DNA-binding transcrip 74.7 6.4 0.00014 38.0 5.7 50 502-555 55-110 (144)
93 PRK08780 DNA topoisomerase I; 74.7 15 0.00031 45.8 10.1 113 226-340 381-510 (780)
94 COG1846 MarR Transcriptional r 74.1 3.8 8.3E-05 37.4 3.9 39 518-556 49-93 (126)
95 TIGR00373 conserved hypothetic 73.7 3.1 6.6E-05 41.2 3.2 31 313-343 33-63 (158)
96 PRK14724 DNA topoisomerase III 73.5 7.8 0.00017 49.3 7.5 121 226-350 414-568 (987)
97 PF06677 Auto_anti-p27: Sjogre 73.5 2.4 5.1E-05 32.2 1.8 15 681-696 15-29 (41)
98 PF14947 HTH_45: Winged helix- 73.3 2.7 6E-05 36.2 2.5 45 511-557 26-70 (77)
99 TIGR01889 Staph_reg_Sar staphy 73.0 5.5 0.00012 36.6 4.6 55 498-556 40-100 (109)
100 COG3432 Predicted transcriptio 71.6 3.8 8.3E-05 36.9 3.0 36 523-558 49-87 (95)
101 PHA00626 hypothetical protein 70.4 4 8.7E-05 32.8 2.5 33 685-726 2-34 (59)
102 PRK14559 putative protein seri 70.2 3.2 6.9E-05 50.1 2.9 12 717-729 44-55 (645)
103 PF14787 zf-CCHC_5: GAG-polypr 69.9 3.1 6.7E-05 30.4 1.6 28 759-786 2-29 (36)
104 PF14803 Nudix_N_2: Nudix N-te 69.8 3 6.5E-05 30.3 1.6 30 685-724 2-31 (34)
105 TIGR02337 HpaR homoprotocatech 69.7 8.2 0.00018 35.8 5.0 51 502-556 43-99 (118)
106 PF02150 RNA_POL_M_15KD: RNA p 69.4 5.8 0.00013 29.0 3.0 30 637-672 3-32 (35)
107 PRK14165 winged helix-turn-hel 68.6 7.4 0.00016 40.6 4.9 53 498-554 18-73 (217)
108 PF02002 TFIIE_alpha: TFIIE al 68.4 4.2 9.1E-05 37.1 2.7 32 312-343 31-62 (105)
109 smart00343 ZnF_C2HC zinc finge 68.2 2.6 5.6E-05 28.4 0.9 18 761-778 1-18 (26)
110 PRK00420 hypothetical protein; 67.8 3.1 6.6E-05 38.7 1.6 13 682-695 22-34 (112)
111 PRK06266 transcription initiat 67.2 5.9 0.00013 40.0 3.7 30 313-342 41-70 (178)
112 TIGR02647 DNA conserved hypoth 67.0 3.7 8.1E-05 35.1 1.8 28 322-351 33-60 (77)
113 PRK03564 formate dehydrogenase 66.7 4.6 9.9E-05 44.3 3.0 10 684-693 188-197 (309)
114 smart00347 HTH_MARR helix_turn 65.1 9.8 0.00021 33.4 4.4 51 502-556 25-81 (101)
115 COG1645 Uncharacterized Zn-fin 64.9 2.9 6.4E-05 39.7 1.0 31 680-726 25-55 (131)
116 COG2888 Predicted Zn-ribbon RN 63.8 3.6 7.8E-05 33.5 1.1 9 715-724 51-59 (61)
117 COG1198 PriA Primosomal protei 62.6 7.7 0.00017 47.4 4.1 41 635-692 444-484 (730)
118 COG1675 TFA1 Transcription ini 61.2 8.5 0.00018 38.7 3.5 32 312-343 36-67 (176)
119 PF07848 PaaX: PaaX-like prote 61.1 6.4 0.00014 33.5 2.2 49 500-549 19-70 (70)
120 COG1198 PriA Primosomal protei 60.8 9.6 0.00021 46.7 4.5 21 178-198 74-94 (730)
121 KOG0109 RNA-binding protein LA 60.6 6.5 0.00014 42.1 2.6 27 754-780 155-181 (346)
122 COG1321 TroR Mn-dependent tran 60.6 8.2 0.00018 38.1 3.2 65 518-593 37-101 (154)
123 PRK09678 DNA-binding transcrip 60.5 8.4 0.00018 33.0 2.8 32 637-670 3-39 (72)
124 cd03364 TOPRIM_DnaG_primases T 60.3 27 0.00059 29.9 6.1 29 115-143 43-71 (79)
125 COG5082 AIR1 Arginine methyltr 59.2 4.4 9.5E-05 41.0 1.1 17 760-776 98-114 (190)
126 PTZ00407 DNA topoisomerase IA; 58.1 13 0.00027 46.1 4.9 52 287-339 561-613 (805)
127 PF14392 zf-CCHC_4: Zinc knuck 57.6 3.9 8.4E-05 32.1 0.3 18 759-776 31-48 (49)
128 COG1594 RPB9 DNA-directed RNA 57.1 8.1 0.00018 36.1 2.4 31 684-726 3-33 (113)
129 PRK14714 DNA polymerase II lar 57.0 8.5 0.00019 49.0 3.2 28 490-517 432-459 (1337)
130 PF14205 Cys_rich_KTR: Cystein 56.4 8.9 0.00019 30.8 2.1 7 685-691 6-12 (55)
131 TIGR00595 priA primosomal prot 56.3 11 0.00024 44.4 4.0 41 635-692 222-262 (505)
132 smart00661 RPOL9 RNA polymeras 56.1 10 0.00022 29.8 2.5 31 637-672 2-32 (52)
133 COG0266 Nei Formamidopyrimidin 55.9 8.9 0.00019 41.3 2.8 29 682-722 244-272 (273)
134 TIGR01562 FdhE formate dehydro 55.9 6.3 0.00014 43.2 1.7 9 685-693 186-194 (305)
135 cd01029 TOPRIM_primases TOPRIM 55.7 25 0.00054 29.8 5.1 28 115-142 43-70 (79)
136 PF08063 PADR1: PADR1 (NUC008) 55.4 4.3 9.3E-05 32.9 0.2 34 635-673 14-51 (55)
137 KOG2907 RNA polymerase I trans 55.1 7.5 0.00016 35.8 1.7 33 634-669 73-111 (116)
138 PF03119 DNA_ligase_ZBD: NAD-d 53.8 13 0.00028 25.8 2.4 26 637-666 1-26 (28)
139 PRK04023 DNA polymerase II lar 53.4 8.4 0.00018 47.9 2.3 40 479-518 401-440 (1121)
140 PRK10445 endonuclease VIII; Pr 52.8 10 0.00022 40.8 2.7 28 683-722 235-262 (263)
141 PF13408 Zn_ribbon_recom: Reco 52.3 14 0.00029 29.5 2.7 28 635-663 5-32 (58)
142 PRK09416 lstR lineage-specific 52.1 29 0.00063 33.4 5.3 54 503-556 57-118 (135)
143 PRK14810 formamidopyrimidine-D 51.5 11 0.00025 40.6 2.8 31 502-539 141-171 (272)
144 PF07191 zinc-ribbons_6: zinc- 51.3 17 0.00036 30.9 3.1 41 637-697 3-43 (70)
145 COG1321 TroR Mn-dependent tran 51.0 18 0.0004 35.6 3.9 40 312-351 28-67 (154)
146 smart00440 ZnF_C2C2 C2C2 Zinc 51.0 15 0.00033 27.6 2.6 30 637-669 2-37 (40)
147 PF01047 MarR: MarR family; I 50.9 22 0.00048 28.3 3.8 32 312-343 21-52 (59)
148 PF13412 HTH_24: Winged helix- 50.8 24 0.00052 27.1 3.8 29 311-339 20-48 (48)
149 PLN02189 cellulose synthase 50.6 9.3 0.0002 47.9 2.1 50 634-691 33-84 (1040)
150 PF04216 FdhE: Protein involve 50.4 7.6 0.00016 42.3 1.2 12 684-695 173-184 (290)
151 PF13463 HTH_27: Winged helix 50.4 7.9 0.00017 31.8 1.1 32 518-549 31-68 (68)
152 PF01325 Fe_dep_repress: Iron 49.9 23 0.00049 29.1 3.7 31 312-342 26-56 (60)
153 COG0484 DnaJ DnaJ-class molecu 49.9 25 0.00055 39.5 5.2 65 634-709 158-222 (371)
154 TIGR02277 PaaX_trns_reg phenyl 49.9 23 0.0005 38.5 4.8 54 501-555 17-73 (280)
155 PF13719 zinc_ribbon_5: zinc-r 49.7 9 0.0002 28.3 1.2 8 683-690 25-32 (37)
156 TIGR03655 anti_R_Lar restricti 49.4 17 0.00036 29.0 2.7 33 636-671 2-37 (53)
157 TIGR01054 rgy reverse gyrase. 49.4 17 0.00037 47.2 4.3 53 484-537 867-920 (1171)
158 TIGR00577 fpg formamidopyrimid 48.5 14 0.00029 40.0 2.8 29 682-722 244-272 (272)
159 TIGR02702 SufR_cyano iron-sulf 48.4 73 0.0016 32.6 8.1 48 502-553 16-71 (203)
160 PF14354 Lar_restr_allev: Rest 47.9 18 0.0004 29.4 2.9 30 635-668 3-37 (61)
161 PF01022 HTH_5: Bacterial regu 47.5 28 0.0006 26.8 3.7 28 313-340 20-47 (47)
162 PRK14811 formamidopyrimidine-D 46.9 14 0.00031 39.8 2.6 30 682-723 234-263 (269)
163 PRK01103 formamidopyrimidine/5 46.8 15 0.00032 39.8 2.7 31 502-539 142-172 (274)
164 PF09851 SHOCT: Short C-termin 46.0 13 0.00029 26.3 1.5 17 323-339 2-18 (31)
165 PRK05580 primosome assembly pr 46.0 20 0.00043 44.0 4.0 41 635-692 390-430 (679)
166 PRK13945 formamidopyrimidine-D 45.9 15 0.00033 39.8 2.8 32 502-540 151-182 (282)
167 smart00346 HTH_ICLR helix_turn 45.9 80 0.0017 27.3 6.9 53 500-556 19-72 (91)
168 smart00419 HTH_CRP helix_turn_ 45.4 34 0.00075 25.7 3.9 31 311-341 11-41 (48)
169 cd00223 TOPRIM_TopoIIB_SPO TOP 45.4 2E+02 0.0043 28.2 10.4 48 116-163 52-102 (160)
170 COG3058 FdhE Uncharacterized p 45.0 16 0.00034 39.1 2.5 12 761-772 227-238 (308)
171 PLN02436 cellulose synthase A 44.8 14 0.0003 46.6 2.4 50 634-691 35-86 (1094)
172 PRK09710 lar restriction allev 44.5 23 0.0005 29.5 2.9 32 634-669 5-36 (64)
173 COG3058 FdhE Uncharacterized p 43.8 56 0.0012 35.1 6.3 83 633-734 183-271 (308)
174 cd07377 WHTH_GntR Winged helix 43.0 36 0.00079 27.3 4.0 30 312-341 29-58 (66)
175 PRK11050 manganese transport r 42.9 22 0.00048 34.8 3.1 42 514-556 61-102 (152)
176 PRK14890 putative Zn-ribbon RN 42.7 14 0.00031 30.2 1.4 8 715-723 49-56 (59)
177 PF06969 HemN_C: HemN C-termin 42.5 19 0.00041 29.6 2.2 35 515-550 31-65 (66)
178 PF03833 PolC_DP2: DNA polymer 42.2 8.4 0.00018 47.1 0.0 42 478-519 413-454 (900)
179 TIGR00595 priA primosomal prot 42.1 27 0.00059 41.2 4.2 6 685-690 242-247 (505)
180 PHA00626 hypothetical protein 41.7 27 0.00058 28.3 2.7 11 637-647 2-12 (59)
181 PF13155 Toprim_2: Toprim-like 41.6 58 0.0013 28.7 5.4 28 116-143 48-75 (96)
182 PF09114 MotA_activ: Transcrip 41.4 23 0.00049 31.5 2.5 32 522-554 49-80 (96)
183 TIGR02719 repress_PhaQ poly-be 41.1 1.1E+02 0.0024 29.7 7.4 52 503-554 39-100 (138)
184 PRK14296 chaperone protein Dna 40.6 43 0.00094 37.9 5.4 48 635-691 166-214 (372)
185 smart00418 HTH_ARSR helix_turn 40.3 41 0.00089 26.4 3.9 30 313-342 15-44 (66)
186 PF09821 AAA_assoc_C: C-termin 40.0 86 0.0019 29.6 6.4 74 524-598 16-95 (120)
187 PF10087 DUF2325: Uncharacteri 40.0 65 0.0014 28.8 5.5 57 106-168 40-96 (97)
188 PF13717 zinc_ribbon_4: zinc-r 39.8 17 0.00037 26.7 1.3 27 664-690 6-32 (36)
189 PF09723 Zn-ribbon_8: Zinc rib 39.5 30 0.00065 26.2 2.6 9 683-691 26-34 (42)
190 TIGR03433 padR_acidobact trans 39.4 74 0.0016 28.7 5.8 52 502-554 18-82 (100)
191 COG5082 AIR1 Arginine methyltr 38.3 16 0.00035 37.1 1.3 35 757-791 58-92 (190)
192 PRK05978 hypothetical protein; 37.9 18 0.00038 35.5 1.5 31 683-726 33-63 (148)
193 cd00924 Cyt_c_Oxidase_Vb Cytoc 37.9 50 0.0011 30.0 4.3 34 654-691 54-87 (97)
194 PRK09401 reverse gyrase; Revie 37.6 28 0.00062 45.3 3.7 52 485-537 868-920 (1176)
195 PF11023 DUF2614: Protein of u 37.4 17 0.00038 33.6 1.3 17 756-772 82-98 (114)
196 smart00834 CxxC_CXXC_SSSS Puta 37.2 28 0.00062 25.6 2.2 9 683-691 26-34 (41)
197 PRK00082 hrcA heat-inducible t 36.8 93 0.002 34.8 7.2 77 514-597 37-116 (339)
198 PRK14873 primosome assembly pr 36.8 32 0.00069 42.0 3.8 40 635-692 392-431 (665)
199 PF02044 Bombesin: Bombesin-li 36.6 7.5 0.00016 22.3 -0.7 8 63-70 4-11 (14)
200 PF09788 Tmemb_55A: Transmembr 36.5 61 0.0013 34.4 5.2 25 635-660 85-109 (256)
201 PF06827 zf-FPG_IleRS: Zinc fi 36.5 23 0.0005 24.6 1.5 16 683-699 1-16 (30)
202 PRK06266 transcription initiat 36.4 17 0.00036 36.8 1.1 14 682-696 135-148 (178)
203 PLN02400 cellulose synthase 36.2 26 0.00056 44.4 2.9 50 634-691 35-86 (1085)
204 TIGR02098 MJ0042_CXXC MJ0042 f 36.1 18 0.00038 26.5 0.9 8 684-691 26-33 (38)
205 COG1695 Predicted transcriptio 35.3 2.6E+02 0.0057 26.4 9.2 53 503-555 24-88 (138)
206 PF14569 zf-UDP: Zinc-binding 35.3 8.6 0.00019 33.1 -1.0 50 634-691 8-59 (80)
207 PF10571 UPF0547: Uncharacteri 34.9 22 0.00048 24.2 1.1 6 685-690 16-21 (26)
208 PF09332 Mcm10: Mcm10 replicat 34.9 36 0.00078 38.0 3.5 28 655-691 283-311 (344)
209 PF13240 zinc_ribbon_2: zinc-r 34.9 19 0.00041 23.7 0.8 6 685-690 15-20 (23)
210 PRK14714 DNA polymerase II lar 34.8 24 0.00052 45.2 2.3 8 635-642 667-674 (1337)
211 PF02037 SAP: SAP domain; Int 34.6 42 0.00092 24.3 2.7 31 501-531 3-33 (35)
212 PF01978 TrmB: Sugar-specific 34.6 57 0.0012 27.0 3.9 30 312-341 26-55 (68)
213 PF09862 DUF2089: Protein of u 34.4 33 0.0007 32.1 2.6 22 638-670 1-22 (113)
214 PRK14873 primosome assembly pr 34.2 42 0.00091 41.0 4.2 10 179-188 92-101 (665)
215 KOG1705 Uncharacterized conser 34.1 22 0.00048 31.4 1.3 20 762-781 72-91 (110)
216 PF04182 B-block_TFIIIC: B-blo 33.9 43 0.00093 28.7 3.1 31 309-339 19-49 (75)
217 KOG0119 Splicing factor 1/bran 33.8 51 0.0011 38.0 4.4 21 758-778 284-304 (554)
218 PF09986 DUF2225: Uncharacteri 33.4 41 0.00089 35.0 3.5 9 683-691 48-56 (214)
219 COG1645 Uncharacterized Zn-fin 33.2 28 0.0006 33.3 1.9 28 635-671 28-55 (131)
220 cd00092 HTH_CRP helix_turn_hel 32.9 77 0.0017 25.6 4.4 31 312-342 29-59 (67)
221 TIGR00686 phnA alkylphosphonat 32.7 23 0.0005 32.6 1.3 7 685-691 4-10 (109)
222 PRK14701 reverse gyrase; Provi 32.4 53 0.0012 44.3 5.0 65 483-550 838-903 (1638)
223 COG1656 Uncharacterized conser 32.3 15 0.00033 36.3 0.1 40 682-723 96-138 (165)
224 KOG3116 Predicted C3H1-type Zn 32.2 11 0.00025 36.3 -0.8 22 756-777 24-45 (177)
225 PF10007 DUF2250: Uncharacteri 32.1 61 0.0013 29.2 3.8 30 312-341 25-54 (92)
226 PF08274 PhnA_Zn_Ribbon: PhnA 31.9 17 0.00037 25.7 0.2 7 685-691 4-10 (30)
227 PF01927 Mut7-C: Mut7-C RNAse 31.6 32 0.0007 33.5 2.2 42 683-726 91-135 (147)
228 PF09538 FYDLN_acid: Protein o 31.5 29 0.00062 32.2 1.7 30 682-726 8-37 (108)
229 COG2238 RPS19A Ribosomal prote 31.5 29 0.00063 33.4 1.7 34 522-556 98-131 (147)
230 PF03962 Mnd1: Mnd1 family; I 31.4 43 0.00093 34.2 3.1 40 302-341 9-48 (188)
231 cd00092 HTH_CRP helix_turn_hel 31.1 50 0.0011 26.7 3.0 43 501-547 25-67 (67)
232 COG3809 Uncharacterized protei 30.9 72 0.0016 27.7 3.8 37 685-733 3-45 (88)
233 PF14277 DUF4364: Domain of un 30.8 1.4E+02 0.0031 29.7 6.6 58 500-557 14-75 (163)
234 COG2176 PolC DNA polymerase II 30.7 32 0.00069 43.8 2.3 51 110-160 290-346 (1444)
235 PRK00432 30S ribosomal protein 29.7 35 0.00076 27.0 1.7 29 635-671 20-48 (50)
236 PRK14298 chaperone protein Dna 29.6 1.1E+02 0.0023 34.9 6.2 45 635-691 158-206 (377)
237 TIGR01385 TFSII transcription 29.5 1E+02 0.0022 33.9 5.8 21 564-591 200-220 (299)
238 TIGR03830 CxxCG_CxxCG_HTH puta 29.3 28 0.00061 32.5 1.3 10 682-691 30-39 (127)
239 smart00345 HTH_GNTR helix_turn 29.2 88 0.0019 24.4 4.1 29 312-340 24-52 (60)
240 PF09339 HTH_IclR: IclR helix- 29.1 84 0.0018 24.6 3.8 29 312-340 22-50 (52)
241 PF01726 LexA_DNA_bind: LexA D 29.1 46 0.001 27.8 2.4 34 507-540 28-61 (65)
242 PF03833 PolC_DP2: DNA polymer 29.0 18 0.0004 44.3 0.0 8 635-642 655-662 (900)
243 PRK14300 chaperone protein Dna 28.9 70 0.0015 36.2 4.6 43 635-691 162-206 (372)
244 PF13730 HTH_36: Helix-turn-he 28.8 72 0.0016 25.0 3.4 27 312-338 29-55 (55)
245 PRK00398 rpoP DNA-directed RNA 28.5 55 0.0012 25.1 2.6 9 683-691 21-29 (46)
246 PF01096 TFIIS_C: Transcriptio 28.4 64 0.0014 24.1 2.8 35 685-723 2-36 (39)
247 PRK14279 chaperone protein Dna 28.3 82 0.0018 35.9 5.1 43 635-691 190-234 (392)
248 PRK05580 primosome assembly pr 28.0 56 0.0012 40.1 3.9 12 304-315 142-153 (679)
249 PHA02998 RNA polymerase subuni 27.9 65 0.0014 32.4 3.5 35 634-671 142-182 (195)
250 COG1568 Predicted methyltransf 27.9 55 0.0012 35.4 3.2 35 522-557 51-85 (354)
251 PF10281 Ish1: Putative stress 27.9 77 0.0017 23.3 3.2 30 502-531 4-36 (38)
252 PF09862 DUF2089: Protein of u 27.7 35 0.00076 31.9 1.6 9 682-690 11-19 (113)
253 KOG1956 DNA topoisomerase III 27.7 87 0.0019 37.4 5.1 66 285-351 467-533 (758)
254 KOG4400 E3 ubiquitin ligase in 27.4 42 0.0009 35.9 2.4 37 752-789 137-176 (261)
255 COG1110 Reverse gyrase [DNA re 27.4 77 0.0017 40.1 4.8 72 484-556 880-952 (1187)
256 PF03444 HrcA_DNA-bdg: Winged 27.4 1.1E+02 0.0023 26.8 4.4 39 314-352 29-68 (78)
257 PRK10220 hypothetical protein; 27.0 36 0.00078 31.4 1.5 7 685-691 5-11 (111)
258 COG5179 TAF1 Transcription ini 26.9 26 0.00056 41.3 0.7 24 755-778 933-958 (968)
259 TIGR01884 cas_HTH CRISPR locus 26.9 49 0.0011 34.0 2.7 43 503-549 159-203 (203)
260 PF14952 zf-tcix: Putative tre 26.8 36 0.00078 26.2 1.2 28 635-671 11-38 (44)
261 TIGR02605 CxxC_CxxC_SSSS putat 26.6 67 0.0014 25.2 2.8 11 684-694 27-37 (52)
262 smart00418 HTH_ARSR helix_turn 26.5 95 0.0021 24.2 3.9 44 510-554 16-63 (66)
263 PF01726 LexA_DNA_bind: LexA D 26.5 98 0.0021 25.8 3.9 30 312-341 29-59 (65)
264 PRK14290 chaperone protein Dna 26.4 1E+02 0.0023 34.7 5.4 45 635-691 165-213 (365)
265 TIGR00373 conserved hypothetic 26.3 94 0.002 30.8 4.4 32 502-537 29-60 (158)
266 PRK14289 chaperone protein Dna 26.2 1E+02 0.0022 35.1 5.3 45 635-691 171-219 (386)
267 PRK04023 DNA polymerase II lar 26.2 46 0.00099 41.8 2.6 12 158-169 98-109 (1121)
268 PRK14284 chaperone protein Dna 26.2 86 0.0019 35.8 4.7 43 635-691 175-219 (391)
269 PRK03902 manganese transport t 25.9 81 0.0017 30.3 3.9 40 312-351 26-65 (142)
270 PRK14295 chaperone protein Dna 25.8 91 0.002 35.5 4.8 45 635-691 183-227 (389)
271 PTZ00368 universal minicircle 25.7 42 0.0009 32.6 1.8 18 760-777 130-147 (148)
272 smart00420 HTH_DEOR helix_turn 25.5 1.1E+02 0.0023 23.2 3.8 34 305-342 15-48 (53)
273 TIGR03831 YgiT_finger YgiT-typ 25.4 28 0.00062 26.2 0.5 10 682-691 31-40 (46)
274 PHA02998 RNA polymerase subuni 25.3 73 0.0016 32.0 3.3 41 682-726 142-182 (195)
275 PRK14288 chaperone protein Dna 25.3 95 0.0021 35.1 4.8 43 635-691 156-200 (369)
276 PF02082 Rrf2: Transcriptional 25.3 89 0.0019 27.0 3.6 32 312-343 29-60 (83)
277 PF00376 MerR: MerR family reg 25.2 61 0.0013 24.0 2.2 31 312-347 3-35 (38)
278 PRK14301 chaperone protein Dna 25.1 73 0.0016 36.1 3.9 43 635-691 161-205 (373)
279 PF09788 Tmemb_55A: Transmembr 25.1 1.8E+02 0.0038 31.1 6.3 72 634-726 64-136 (256)
280 PHA02031 putative DnaG-like pr 25.0 1.9E+02 0.0041 31.2 6.6 52 108-161 198-251 (266)
281 smart00550 Zalpha Z-DNA-bindin 25.0 1.1E+02 0.0023 25.6 4.0 32 311-342 25-56 (68)
282 PF13545 HTH_Crp_2: Crp-like h 25.0 1.1E+02 0.0023 25.6 4.1 38 302-343 26-63 (76)
283 PF05502 Dynactin_p62: Dynacti 24.9 71 0.0015 37.5 3.8 12 711-723 83-94 (483)
284 PF08271 TF_Zn_Ribbon: TFIIB z 24.7 81 0.0017 23.9 2.9 29 637-671 2-30 (43)
285 cd00729 rubredoxin_SM Rubredox 24.7 69 0.0015 23.2 2.3 25 657-691 2-26 (34)
286 PF09382 RQC: RQC domain; Int 24.6 1.2E+02 0.0027 27.2 4.7 55 501-555 19-96 (106)
287 COG1439 Predicted nucleic acid 24.6 67 0.0015 32.4 3.0 29 656-697 138-166 (177)
288 PRK07714 hypothetical protein; 24.4 2.8E+02 0.006 25.1 6.8 75 102-187 24-98 (100)
289 PLN03122 Poly [ADP-ribose] pol 24.3 69 0.0015 39.9 3.7 35 635-675 111-149 (815)
290 COG4742 Predicted transcriptio 24.3 73 0.0016 34.2 3.4 39 518-557 39-77 (260)
291 PF12802 MarR_2: MarR family; 24.2 1.1E+02 0.0024 24.4 3.8 30 311-340 24-53 (62)
292 PF09855 DUF2082: Nucleic-acid 24.2 76 0.0017 26.6 2.8 14 682-695 35-48 (64)
293 COG1706 FlgI Flagellar basal-b 24.1 92 0.002 34.6 4.2 34 305-339 326-359 (365)
294 PRK02935 hypothetical protein; 24.0 52 0.0011 30.2 1.9 20 756-775 83-102 (110)
295 PF00325 Crp: Bacterial regula 24.0 1.4E+02 0.003 21.5 3.6 27 312-338 6-32 (32)
296 PRK04172 pheS phenylalanyl-tRN 23.8 82 0.0018 37.1 4.1 37 518-554 33-71 (489)
297 smart00540 LEM in nuclear memb 23.7 84 0.0018 24.3 2.7 32 500-531 4-39 (44)
298 TIGR02300 FYDLN_acid conserved 23.6 47 0.001 31.5 1.6 10 682-691 8-17 (129)
299 PF09297 zf-NADH-PPase: NADH p 23.4 59 0.0013 23.0 1.7 12 683-695 3-14 (32)
300 TIGR01889 Staph_reg_Sar staphy 23.2 1E+02 0.0023 28.1 3.9 34 311-344 46-79 (109)
301 PF05402 PqqD: Coenzyme PQQ sy 23.2 1.5E+02 0.0032 24.3 4.5 36 304-339 29-68 (68)
302 PRK14291 chaperone protein Dna 23.2 1.3E+02 0.0027 34.3 5.3 44 635-691 173-216 (382)
303 smart00659 RPOLCX RNA polymera 23.1 82 0.0018 24.3 2.6 10 682-691 18-27 (44)
304 PF01215 COX5B: Cytochrome c o 23.1 73 0.0016 30.8 2.8 39 653-697 85-124 (136)
305 smart00345 HTH_GNTR helix_turn 23.0 1.2E+02 0.0027 23.5 3.9 38 500-541 18-56 (60)
306 PF09397 Ftsk_gamma: Ftsk gamm 23.0 1.2E+02 0.0027 25.4 3.8 35 306-344 22-56 (65)
307 KOG0978 E3 ubiquitin ligase in 22.8 19 0.0004 43.6 -1.5 14 755-768 674-687 (698)
308 smart00513 SAP Putative DNA-bi 22.7 1.2E+02 0.0027 21.7 3.4 31 501-531 3-33 (35)
309 smart00843 Ftsk_gamma This dom 22.7 94 0.002 26.0 3.0 34 306-343 21-54 (63)
310 PTZ00368 universal minicircle 22.7 48 0.001 32.2 1.6 19 760-778 78-96 (148)
311 TIGR01206 lysW lysine biosynth 22.6 71 0.0015 25.8 2.2 7 685-691 24-30 (54)
312 PRK14285 chaperone protein Dna 22.5 1E+02 0.0022 34.8 4.4 43 635-691 163-207 (365)
313 PLN02638 cellulose synthase A 22.5 48 0.001 42.1 1.9 51 633-691 15-67 (1079)
314 COG1592 Rubrerythrin [Energy p 22.4 61 0.0013 32.4 2.2 23 658-691 135-157 (166)
315 PRK12789 flgI flagellar basal 22.3 1.3E+02 0.0028 33.9 4.9 32 306-338 329-360 (367)
316 PRK00423 tfb transcription ini 22.3 76 0.0016 35.0 3.2 44 683-739 11-54 (310)
317 TIGR03829 YokU_near_AblA uncha 22.2 62 0.0013 28.9 2.0 11 637-647 1-11 (89)
318 COG3478 Predicted nucleic-acid 22.2 61 0.0013 27.0 1.8 8 636-643 5-12 (68)
319 COG0358 DnaG DNA primase (bact 22.0 2.2E+02 0.0047 34.3 7.2 38 106-143 281-318 (568)
320 COG1675 TFA1 Transcription ini 22.0 99 0.0021 31.3 3.6 32 616-648 111-144 (176)
321 PF13730 HTH_36: Helix-turn-he 22.0 44 0.00095 26.3 1.0 24 511-535 32-55 (55)
322 TIGR01391 dnaG DNA primase, ca 22.0 2.8E+02 0.006 31.9 7.9 47 113-161 298-345 (415)
323 PF13463 HTH_27: Winged helix 21.9 1.4E+02 0.003 24.2 4.0 28 312-339 22-49 (68)
324 PF03215 Rad17: Rad17 cell cyc 21.9 1.3E+02 0.0027 35.9 5.1 60 102-168 150-225 (519)
325 PRK06683 hypothetical protein; 21.8 2.9E+02 0.0064 24.1 6.2 54 102-166 17-70 (82)
326 PF03882 KicB: KicB killing fa 21.8 5.8E+02 0.013 29.1 9.7 92 501-594 46-157 (440)
327 KOG1220 Phosphoglucomutase/pho 21.6 2E+02 0.0043 34.2 6.4 12 393-404 526-537 (607)
328 cd00090 HTH_ARSR Arsenical Res 21.6 87 0.0019 25.3 2.8 49 509-559 25-76 (78)
329 PTZ00043 cytochrome c oxidase 21.5 1.4E+02 0.003 31.2 4.5 34 654-691 154-189 (268)
330 COG5204 SPT4 Transcription elo 21.5 68 0.0015 28.8 2.1 21 327-347 91-111 (112)
331 smart00531 TFIIE Transcription 21.4 47 0.001 32.4 1.2 39 653-695 95-134 (147)
332 PF03501 S10_plectin: Plectin/ 21.4 93 0.002 28.2 2.9 40 525-564 43-85 (95)
333 TIGR02698 CopY_TcrY copper tra 21.3 1.6E+02 0.0035 28.0 4.9 38 305-342 19-56 (130)
334 TIGR02698 CopY_TcrY copper tra 21.1 3.2E+02 0.007 25.9 6.9 36 502-538 19-55 (130)
335 PRK14281 chaperone protein Dna 21.0 1.3E+02 0.0027 34.5 4.8 45 635-691 179-227 (397)
336 PF01927 Mut7-C: Mut7-C RNAse 20.9 76 0.0017 30.9 2.6 13 634-647 90-102 (147)
337 PF12840 HTH_20: Helix-turn-he 20.9 1.3E+02 0.0029 24.2 3.6 32 304-339 24-55 (61)
338 cd07377 WHTH_GntR Winged helix 20.8 1E+02 0.0022 24.6 3.0 39 503-545 27-65 (66)
339 PRK13601 putative L7Ae-like ri 20.8 3.3E+02 0.0073 23.9 6.3 54 102-166 14-67 (82)
340 cd04449 DEP_DEPDC5-like DEP (D 20.7 3.1E+02 0.0067 23.9 6.1 61 277-339 4-66 (83)
341 PF10872 DUF2740: Protein of u 20.6 76 0.0016 23.8 1.8 27 408-434 3-30 (48)
342 cd03365 TOPRIM_TopoIIA TOPRIM_ 20.4 95 0.0021 29.4 3.0 25 116-140 78-102 (120)
343 PF09012 FeoC: FeoC like trans 20.2 1.3E+02 0.0028 25.1 3.5 28 312-339 18-45 (69)
344 PF07282 OrfB_Zn_ribbon: Putat 20.1 43 0.00093 27.9 0.6 10 682-691 27-36 (69)
345 PF03965 Penicillinase_R: Peni 20.1 81 0.0018 29.1 2.5 43 305-347 18-60 (115)
346 PLN02195 cellulose synthase A 20.0 57 0.0012 41.1 1.8 49 635-691 6-56 (977)
No 1
>PRK07220 DNA topoisomerase I; Validated
Probab=100.00 E-value=4.6e-147 Score=1311.14 Aligned_cols=663 Identities=28% Similarity=0.481 Sum_probs=565.5
Q ss_pred EEEEcChHHHHHHHHHhCCCC-CcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCCC
Q 046997 11 LNVAEKPSVAKSVAGILSKNQ-GLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADLY 89 (807)
Q Consensus 11 LiIaEKPs~Ak~IA~~Lg~~~-~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L~ 89 (807)
||||||||+|++||++||++. ...+.+|. ++|+|.+ +|. +++|+|+.|||++|++|++|..|..|++.+|+
T Consensus 3 LiIaEKPs~Ak~Ia~~Lg~~~~~~~~~~g~----~~y~~~~--~g~--~~~v~~~~GHl~~l~~P~~y~~w~~~~~~~l~ 74 (740)
T PRK07220 3 LIITEKNIAARRIAQILAPKKPKKTRVSGV----DVYRYED--NGD--DTVVVGLSGHIVNIDFPKEYNNWQKVDARDLI 74 (740)
T ss_pred EEEEeCHHHHHHHHHHhCCCCccccccCCc----ceeEEec--CCC--CEEEEEeCcccccCCCCccccccCCCChhHcC
Confidence 999999999999999998532 12245563 3344432 343 58999999999999999999999999988887
Q ss_pred CCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHcCC
Q 046997 90 HAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQNLV 169 (807)
Q Consensus 90 ~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~nl~ 169 (807)
+.++. ...+++++++.|++++++||+||||||||||||+|||||+++++..+++++++|+|||+||+++|++||+||+
T Consensus 75 ~~~~~--~~~~~~~~~~~lk~l~k~ad~viiAtD~DREGE~I~~~i~~~l~~~~~~~~~~R~~fs~iT~~~I~~A~~n~~ 152 (740)
T PRK07220 75 DAEII--TTPTQKKIVTALKKLGKEADRVTIATDYDREGELIGVEALNIIKKVNPDIKFDRVRYSAITKKEIERAFSNPV 152 (740)
T ss_pred CcceE--ecCCHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHHHhcCCCCceEEEEEccCCHHHHHHHHhCCC
Confidence 65543 2346788999999999999999999999999999999999999876666789999999999999999999999
Q ss_pred CCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccceEEEE
Q 046997 170 DPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEFWTIN 249 (807)
Q Consensus 170 ~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~~i~ 249 (807)
++|.+|++||+|||++||||||||||++|+.+++++ ..++|+||||||||+|||+||+||+||+|++||+|.
T Consensus 153 ~~d~~l~~A~~aR~~~D~lvG~nlSr~~t~~~~~~~--------~~~lS~GRVQtptL~lIv~Re~eI~~F~p~~y~~i~ 224 (740)
T PRK07220 153 EVDFNLADAGHSRQVIDLVWGAALTRYISLAAGRLG--------KMFLSVGRVQSPTLALIVDREKEREAFVPTPYWEIY 224 (740)
T ss_pred CCChhHHHHHHHHHHHHHHhchhcCHHHHHHHHhhC--------CccccccccchhhhHHHHhhHHHHHhCCCCccEEEE
Confidence 999999999999999999999999999999876421 237999999999999999999999999999999999
Q ss_pred EEeecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHHHH
Q 046997 250 CSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVA 329 (807)
Q Consensus 250 ~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~ia 329 (807)
+.+..++..|.+.|..++++|++.|+.+++.+ . ..++|++|+.++++..||+||||++||++||+ +||||++||++|
T Consensus 225 ~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~-~-~~~~V~~v~~~~~~~~pP~pf~ts~Lq~~a~~-~g~s~~~tm~ia 301 (740)
T PRK07220 225 ATLENNGETFVAQHSTRRFWEKEEADRVFEKL-G-KTAEVTEVEKGTKTDKPPTPFNTTEFISAANS-IGFSAANAMRIA 301 (740)
T ss_pred EEEEcCCceEEEEeccCcCCCHHHHHHHHHhh-C-CCeEEEEEeeeeEecCCCCCcCHHHHHHHHHH-cCCCHHHHHHHH
Confidence 99987778899999888999999999999988 3 46999999999999999999999999999996 899999999999
Q ss_pred HHHhhcCceeccCCCCcccCCcccHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCCCCCCCCCCcCCCCCCCCCC
Q 046997 330 EDLYQAGFISYPRTETDSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFSSGESR 409 (807)
Q Consensus 330 Q~LYE~g~ISYPRTds~~l~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~aH~aI~PT~~~~~~~~ 409 (807)
|+|||+||||||||||++||+++++.++++.+... .|+.++..+++.. . ..|..+..++.||||||||... ..+.
T Consensus 302 Q~LYe~g~ITYPRTDs~~l~~~~~~~~~i~~l~~~-~~~~~~~~~l~~~--~-~~~~~~~~~~~~H~aI~PT~~~-~~~~ 376 (740)
T PRK07220 302 ESLYTNGYISYPRTDNTVYPESLDLREQIEIFAEG-PFGEYAQKLLEKG--E-LVPTRGKKETTDHPPIYPASLA-KKSE 376 (740)
T ss_pred HHHHhCCceeecccCCeecCchhhHHHHHHHHHHH-HHHHHHHHhcccC--C-ccCCCCCCCCCCCCCCCcccCC-Cccc
Confidence 99999999999999999999988888888887643 4777776666521 1 1233334456799999999974 3468
Q ss_pred CCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccCCccCCccCCCCeeeeeee
Q 046997 410 WSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWGGLVIPTYVHGQQFIPTTL 489 (807)
Q Consensus 410 Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~~~~~~ 489 (807)
|+++|++||+||+|||||+||+||+|++|+|+++++++.|+++|++++++||++||+++.+++..||.|++||.+.+.++
T Consensus 377 L~~de~~lY~LI~rRfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~vy~~~~~~~~~LP~l~~Ge~~~~~~~ 456 (740)
T PRK07220 377 LKEDEWKVYELVVRRFFATFAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNAPEDRLLPELSEGEELKVKKK 456 (740)
T ss_pred CCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEECCeEEEEeeeEEeeCChHHHcCccccccccCCCCCCCCEeeeeee
Confidence 99999999999999999999999999999999999999999999999999999999876555667999999999999999
Q ss_pred EeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCccccCchhh
Q 046997 490 TLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKPNLR 569 (807)
Q Consensus 490 ~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~T 569 (807)
.+.+++|+||+||||++||++||+.|||||||||+||++|++||||+ + +.|+||++|+.|+++|....+.|++|+||
T Consensus 457 ~~~ek~TkPP~ryTea~Li~~Me~~GIGTpATra~iI~~L~~R~Yi~--~-k~l~pT~~G~~v~~~l~~~~~~i~~~~~T 533 (740)
T PRK07220 457 EMLDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYIH--G-NPIQPTNTAFAVVDALEKYAPTITKPDMT 533 (740)
T ss_pred eecccccCCCCCCCHHHHHHHHHhCCCCCCCcHHHHHHHHHhcCCcc--C-CcccccHHHHHHHHHHHHhchhhcChhHH
Confidence 99999999999999999999999999999999999999999999997 3 35899999999999998776789999999
Q ss_pred HHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccccCCCCCcceEEE
Q 046997 570 SMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKLLEAMGIFFERWSGGEDQQAAGEVVRQCGICQESNMVLK 649 (807)
Q Consensus 570 a~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~~lv~r 649 (807)
|.||..|++|++|+.++++||+++++++.+.+.+...+...+.+.+ ..+. ........||+| |+.|+++
T Consensus 534 a~~E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~------~~~~~~~~CP~C-g~~l~~r 602 (740)
T PRK07220 534 SRLEEDMDKIAEGKIKEDAVLEESREMLEQVFDELDKNREKIRESL----REGL------REDKIIGKCPLC-GSDLMVR 602 (740)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh----hhhh------cccccccccccC-CCeeeEE
Confidence 9999999999999999999999999998887766554433322111 1000 011234689999 5789888
Q ss_pred ecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChh
Q 046997 650 KSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDET 724 (807)
Q Consensus 650 ~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~ 724 (807)
++++|+.||+|++||+|+++.|+|..+ ...+++..||+||.+ ++++.. +++. +++++|| .|++.
T Consensus 603 ~~r~g~~f~gCs~yp~C~~~~~l~~~g-~~~~~~~~Cp~Cg~~-~~k~~~---~g~~-----~~~~~Cp-~C~~~ 666 (740)
T PRK07220 603 RSKRGSRFIGCEGYPECTFSLPLPKSG-QIIVTDKVCEAHGLN-HIRIIN---GGKR-----PWDLGCP-QCNFI 666 (740)
T ss_pred ecCCCceEEEcCCCCCCCceeeCCCCC-ccccCCCCCCCCCCc-eEEEEe---cCCc-----cceeeCC-CCCCc
Confidence 888877789999999999999987642 335678899999953 443332 2211 1247899 99873
No 2
>PRK14973 DNA topoisomerase I; Provisional
Probab=100.00 E-value=1.6e-146 Score=1317.63 Aligned_cols=664 Identities=28% Similarity=0.466 Sum_probs=558.9
Q ss_pred ceEEEEEcChHHHHHHHHHhCCCCCc-ccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCC--
Q 046997 8 INVLNVAEKPSVAKSVAGILSKNQGL-RIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCD-- 84 (807)
Q Consensus 8 ~~~LiIaEKPs~Ak~IA~~Lg~~~~~-~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~-- 84 (807)
|+ ||||||||+|++||++||++... .+++|. .++|+| |+ .+|||++|||++|+|++.|++|+..+
T Consensus 1 m~-LiIAEKPSvAk~IA~~L~~~~~~~~k~~g~---~~~y~~-----~~---~~vt~~~GHLl~l~y~~~yk~W~~~~LP 68 (936)
T PRK14973 1 MH-LIIAEKNIAANRIAQILAGKTKVQVKKDGG---VSTYSF-----DD---TVVVGLRGHVVEVDFEPGYTNWRSEEHT 68 (936)
T ss_pred CE-EEEEcCHHHHHHHHHHhCCCCccccccCCC---cceEEe-----CC---CEEEEEcccceecccCcccCCCccccCC
Confidence 44 99999999999999999865211 244552 223332 32 48999999999999999999998653
Q ss_pred CCCCCCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHH
Q 046997 85 PADLYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQA 164 (807)
Q Consensus 85 p~~L~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A 164 (807)
|.+|++.++ .+..+++++++.|++++++||.||||||||||||+|||||+++++..+++++|+|+|||+||+++|++|
T Consensus 69 P~~l~~~~~--~~~~~~kk~~~~Ik~l~k~ad~IiiAtD~DREGE~I~~~i~e~~~~~~~~~~v~R~~fs~iT~~~I~~A 146 (936)
T PRK14973 69 PRSLIDADT--IKKPTEKKIVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELVRAVNPKVPIDRARFSAITKEEIVTA 146 (936)
T ss_pred hhhccCcce--eecCchHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHhhhccCCCceEEEEEccCCHHHHHHH
Confidence 344544442 233467889999999999999999999999999999999999998777678999999999999999999
Q ss_pred HHcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccc
Q 046997 165 VQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEE 244 (807)
Q Consensus 165 ~~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~ 244 (807)
|+||+++|.+|++||+||+++||||||||||++|+.++.. ...+||+||||||||+|||+||+||+||+|++
T Consensus 147 ~~nl~~~d~~l~~A~~aR~~~D~lvG~nlSr~lt~~~~~g--------~~~~lS~GRVQTPtL~lIveRe~EI~~Fvp~~ 218 (936)
T PRK14973 147 FAEPTDLDFALAAAGEARQIIDLIWGASLTRFISLAAHRG--------GDNILSVGRVQSPTLAMIVDREKEIEAFVPEK 218 (936)
T ss_pred HhCCCCCcHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhcC--------CCcceeeccccchHHHHHHhHHHHHHcCCCCc
Confidence 9999999999999999999999999999999999987641 12479999999999999999999999999999
Q ss_pred eEEEEEEeecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHH
Q 046997 245 FWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEH 324 (807)
Q Consensus 245 y~~i~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~ 324 (807)
||+|.+.+..+++.|.+.|.+++++|++.|+.+++.+. ..++|++|+++++++.||+||||++||++|++ |||||++
T Consensus 219 Yw~I~~~~~~~~~~~~a~~~~~r~~d~~~A~~i~~~~~--~~~~V~~v~~k~~~~~pP~Pf~ts~LQ~~ask-lg~Sa~k 295 (936)
T PRK14973 219 YWMLSLATEKDGEGIEARHTHGRFTDSAAAEAAYDATK--EPLVVTEVKEGHKVDRAPTPFDTTTFIVAASR-LGFSAAN 295 (936)
T ss_pred eEEEEEEEecCCceEEEEEcCCCCCCHHHHHHHHHHcC--CCeEEEEEEeeeEeccCCCCccHHHHHHHHHH-cCCCHHH
Confidence 99999999877788999999999999999999999884 46999999999999999999999999999986 9999999
Q ss_pred HHHHHHHHhhcCceeccCCCCcccCCcccHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCCCCCCCCCCcCCCCC
Q 046997 325 TMKVAEDLYQAGFISYPRTETDSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFS 404 (807)
Q Consensus 325 tl~iaQ~LYE~g~ISYPRTds~~l~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~aH~aI~PT~~~ 404 (807)
||+|||+|||+||||||||||++||+++++.+++..+... .|+.++..+ ....+.| |.++++++.||||||||...
T Consensus 296 Tm~iAQ~LYE~glITYPRTDS~~l~~~~~~~~il~~l~~~-~~~~~~~~l-~~~~~~~--~~~~kk~~~aH~AI~PT~~~ 371 (936)
T PRK14973 296 AMRIAEDLYMNGYISYPRTDNTIYPKSLDLNGVLATLAKG-AFSKDVAWV-KDNRRPV--PTRGKKSSTDHPPIHPTGVA 371 (936)
T ss_pred HHHHHHHHHhCCeeeccCcccccCchhhhHHHHHHHHHHh-hhHHHHHHH-hhcCCcc--CCCCCCCcCCcCCccCcCCc
Confidence 9999999999999999999999999987788888766543 244444333 2222333 33445567899999999865
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccCCccCCccCCCCee
Q 046997 405 SGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWGGLVIPTYVHGQQF 484 (807)
Q Consensus 405 ~~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~ 484 (807)
. ...|+++|++||+||||||||+||+||+|++|+|.++++++.|+++|++++++||+.||+++++++..||.|++||.+
T Consensus 372 ~-~~~Ls~de~klY~LI~rRfLA~~~~~a~~~~t~v~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~LP~l~~Ge~~ 450 (936)
T PRK14973 372 T-REELGDDRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEAKENILPAFALGEKL 450 (936)
T ss_pred C-hhhCCHHHHHHHHHHHHHHHHHhChhheEEEEEEEEEECCEEEEEEEEEEeecCeeEeecccccccccCCCccCCCEE
Confidence 3 357999999999999999999999999999999999999999999999999999999998665556679999999999
Q ss_pred eeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCcccc
Q 046997 485 IPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELW 564 (807)
Q Consensus 485 ~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~ 564 (807)
.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||+ ++ .|+||++|+.|+++|....++|+
T Consensus 451 ~~~~~~~~e~~T~PP~ryTEatLik~ME~~GIGTpATrA~II~~L~~R~Yve--~k-~l~pT~~G~~li~~L~~~~~~l~ 527 (936)
T PRK14973 451 PILAVNLEEKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYIE--GN-PLRPTLVGRAVTESLEEHAGTIT 527 (936)
T ss_pred EeeeeEEeecCCCCCCCCCHHHHHHHhccCCCCCcccHHHHHHHHHHccCee--CC-ceeEcHHHHHHHHHHHHhchhhc
Confidence 9999999999999999999999999999999999999999999999999995 33 58999999999999988777899
Q ss_pred CchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccccCCCCCc
Q 046997 565 KPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKLLEAMGIFFERWSGGEDQQAAGEVVRQCGICQES 644 (807)
Q Consensus 565 ~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~ 644 (807)
+|+|||.||..|++|++|+.++++||+++++++.+.+.+...+...+...+. .. ........+||+| ++
T Consensus 528 ~p~lTA~~E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~----~~------~~~~~~~~~CP~C-G~ 596 (936)
T PRK14973 528 EPDMTQTLEEHMQQIKERKRTRDDVVTESRKMLHRAFDELEANEAVIGRDIM----ER------TAEELTIGPCPVC-GK 596 (936)
T ss_pred CHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhhhhHHhhhhhhc----cc------cccccccccCCcc-cc
Confidence 9999999999999999999999999999999999887766543322211110 00 0011235689999 57
Q ss_pred ceEEEecCCCCceeeccCCCCCCcceecCCCc-cccccccCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCCh
Q 046997 645 NMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSV-SEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDE 723 (807)
Q Consensus 645 ~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~-~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~ 723 (807)
.++++++++|+ ||+|++||+|+|+.+++... .....++..||+||. +++++-+++|+|. +++|| .|.+
T Consensus 597 ~l~ik~~k~gk-FigCS~Yp~Ck~t~~L~~~~~g~~~~~~~~Cp~CG~-p~~~~~r~Gr~g~--------fl~CP-~C~~ 665 (936)
T PRK14973 597 DLRIKHIGSSQ-FIGCSGYPDCTFNIGLPGTTWGWAIRTDEVCPIHHL-NHVRLIRKGARPW--------DIGCP-LCSH 665 (936)
T ss_pred cceeecccCce-eEECCCCCCCCccccCCccccccCCCCCCCCCCCCC-CceEEeecCCCcc--------cccCc-cccc
Confidence 78877777776 69999999999999887432 123335788999995 5555545566653 38999 9987
Q ss_pred hHH
Q 046997 724 TLR 726 (807)
Q Consensus 724 ~~~ 726 (807)
.-.
T Consensus 666 ~~~ 668 (936)
T PRK14973 666 IES 668 (936)
T ss_pred hhh
Confidence 444
No 3
>PRK07219 DNA topoisomerase I; Validated
Probab=100.00 E-value=5.5e-145 Score=1309.24 Aligned_cols=673 Identities=31% Similarity=0.552 Sum_probs=564.5
Q ss_pred EEEEEcChHHHHHHHHHhCCCC-CcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCC
Q 046997 10 VLNVAEKPSVAKSVAGILSKNQ-GLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADL 88 (807)
Q Consensus 10 ~LiIaEKPs~Ak~IA~~Lg~~~-~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L 88 (807)
.||||||||+|++||++|+++. ..++.+|. ++|+|.+ +| .+++|||+.|||++|++|++|++|+..+|..|
T Consensus 2 ~LiIaEKps~Ak~Ia~~L~~g~~~~~~~~g~----~~~~~~~--~g--~~~~v~~~~GHl~~l~~p~~y~~w~~~~l~~l 73 (822)
T PRK07219 2 ELIIAEKNNAARRIADILSGGKAKKKRVNGV----PYYEFER--KG--EKWIVIGLSGHIVTVDFPEEYGDWRDVDPAEL 73 (822)
T ss_pred EEEEEeCHHHHHHHHHHhcCCCcccccCCCc----ceEEecC--CC--CeEEEEEecCcccccCCchhcCCcCcCChhhc
Confidence 6999999999999999995432 12345663 3455533 23 36899999999999999999999987665444
Q ss_pred CCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHcC
Q 046997 89 YHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQNL 168 (807)
Q Consensus 89 ~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~nl 168 (807)
+..++ ....+++++++.|++++++||+||||||||||||+|||||++++... .+++|+|+|||+||+++|++||+||
T Consensus 74 ~~~~~--~~~~~~~~~~~~lk~l~~~ad~iiiAtD~DREGE~I~~ei~~i~~~~-~~~~v~R~~fs~iT~~~I~~A~~n~ 150 (822)
T PRK07219 74 IDADP--VKKITKQNYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREV-CQVPVKRARFSSLTKKEIRKAFENP 150 (822)
T ss_pred cccce--eecCCHHHHHHHHHHHHhcCCEEEEcCCCChhHHHHHHHHHHHHHhc-CCCceeEEEEccCCHHHHHHHHhCc
Confidence 43332 22346788999999999999999999999999999997777666544 3468999999999999999999999
Q ss_pred CCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccceEEE
Q 046997 169 VDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEFWTI 248 (807)
Q Consensus 169 ~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~~i 248 (807)
+++|.+|++||+|||++||||||||||++|+.+++.+ ...++|+||||||||+|||+||+||+||+|++||+|
T Consensus 151 ~~~d~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~g-------~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~yw~i 223 (822)
T PRK07219 151 DEIDFNLADAGEARQIIDLYWGAALTRFLSLSVRQLG-------RWDFLSVGRVQTPTLAFIVDREREIRAFDPEDYWKI 223 (822)
T ss_pred ccCCHHHHHHHHHHHHHHHHhhhhhCHHHHHHHHhcc-------ccCccccccccchhhHHHHHHHHHHHcCCCcccEEE
Confidence 9999999999999999999999999999999886521 124899999999999999999999999999999999
Q ss_pred EEEeecCCceEEEEe----ccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHH
Q 046997 249 NCSHKSEEGTATFSW----MRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEH 324 (807)
Q Consensus 249 ~~~~~~~~~~~~~~~----~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~ 324 (807)
.+.+..+++.+.+.| ..++++|++.|+.+++.+.+...++|++|+++++++.||+||||++||++||++|||||++
T Consensus 224 ~~~~~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~t~~Lq~~a~~~~g~sa~~ 303 (822)
T PRK07219 224 EALLDKEAQYFYRDLIGGHEAEKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKR 303 (822)
T ss_pred EEEEEecCcceeeecccccccCccCCHHHHHHHHHHhcCCCCeEEEEEEEeeEEccCCCCccHHHHHHHHHHHcCCCHHH
Confidence 999876555556655 3568999999999999997645799999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCceeccCCCCcccCCcccHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCCCCCCCCCCcCCCCC
Q 046997 325 TMKVAEDLYQAGFISYPRTETDSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFS 404 (807)
Q Consensus 325 tl~iaQ~LYE~g~ISYPRTds~~l~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~aH~aI~PT~~~ 404 (807)
||+|||+|||+||||||||||++||+++++.++|+.+...+.|+.++..+++.. + ..|.++..+++||||||||...
T Consensus 304 tm~iaQ~LYe~glITYpRTds~~l~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~-~--~~~~~~~~~~~aH~aI~PT~~~ 380 (822)
T PRK07219 304 AMEIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQE-N--IKPTEGKKETTDHPPIHPVDVP 380 (822)
T ss_pred HHHHHHHHHhCCceeccCcccccCCHHHHHHHHHHHhhcccchhhHhhhhcccC-C--cccCCCCCCCCCCCCCCCcCCC
Confidence 999999999999999999999999998777888888876667777776666521 1 2344555668899999999976
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccCCccCCccCCCCee
Q 046997 405 SGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWGGLVIPTYVHGQQF 484 (807)
Q Consensus 405 ~~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~ 484 (807)
+. +.|+++|++||+||+|||||+||+||+|++|+|+++++++.|+++|++++++||++||+++.+++..||.|++||.+
T Consensus 381 ~~-~~L~~~e~~lY~LI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~vy~~~~~~~~~lP~l~~G~~~ 459 (822)
T PRK07219 381 KR-EELSDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEKFDEKELPDLEEGEKL 459 (822)
T ss_pred Cc-ccCCHHHHHHHHHHHHHHHHHhCccceeeEEEEEEEeCCeEEEEEEEEEccCCcHhhcCccccccccCCCCCCCCEe
Confidence 65 68999999999999999999999999999999999999999999999999999999998766666679999999999
Q ss_pred eeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCcccc
Q 046997 485 IPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELW 564 (807)
Q Consensus 485 ~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~ 564 (807)
.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++|||| +++ +.|+||++|+.|+++|+...+.|+
T Consensus 460 ~~~~~~~~~~~T~PP~rytea~Li~~Me~~GIGT~ATra~iI~~L~~R~Yv-~~~-~~l~pT~~G~~l~~~l~~~~~~l~ 537 (822)
T PRK07219 460 KVNKIEIEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYV-IEG-DPPRPTDLGIAVIEALEKYAPEIV 537 (822)
T ss_pred eeeeeEecccccCCCCCCCHHHHHHHHHhCCCCCCccHHHHHHHHHhcCcE-ecC-CEeeecHHHHHHHHHHHHhchhhc
Confidence 999999999999999999999999999999999999999999999999999 655 469999999999999987767899
Q ss_pred CchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccccCCCCCc
Q 046997 565 KPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKLLEAMGIFFERWSGGEDQQAAGEVVRQCGICQES 644 (807)
Q Consensus 565 ~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~ 644 (807)
+|+|||.||..|++|++|+.++++||+++.+++++.+.+...+...+.+.+...+... ........+||+| ++
T Consensus 538 ~~~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~CP~C-g~ 610 (822)
T PRK07219 538 SEEMTAQLEADMQAIEDGKKKKEDVTEESREMLKEILSELKEKRKEIGDHLAGSLKAE------NRSLKTIGKCPEC-GG 610 (822)
T ss_pred ChhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccc------cccccccCcCCCC-CC
Confidence 9999999999999999999999999999999999888776554333222211111000 0011235789999 57
Q ss_pred ceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChh
Q 046997 645 NMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDET 724 (807)
Q Consensus 645 ~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~ 724 (807)
.|+++++++|..||+|+|||+|++++|+|... ...+....||.||. +++++. .++.+.+ ++|| .|...
T Consensus 611 ~l~~r~~~~g~~F~gCs~yp~C~~t~~lp~~~-~~~~~~~~Cp~CG~-~lvk~~-~~r~~~~--------~~CP-~C~~~ 678 (822)
T PRK07219 611 DLIIIRTDKGSRFVGCSGYPDCRNTFPLPSTG-RIKVLDEVCEKCGL-PVIKIL-RGKQTFV--------VGCP-DCEAE 678 (822)
T ss_pred cceeeeccCCceeeecCCCcCCCCeeecCCCC-ccccccCCCCCCCc-ceEEEe-ccCcccc--------ccCC-CCCCC
Confidence 78888877775579999999999999998642 23445788999994 555442 2333322 6788 88754
Q ss_pred H
Q 046997 725 L 725 (807)
Q Consensus 725 ~ 725 (807)
.
T Consensus 679 ~ 679 (822)
T PRK07219 679 K 679 (822)
T ss_pred c
Confidence 3
No 4
>PRK05776 DNA topoisomerase I; Provisional
Probab=100.00 E-value=9e-143 Score=1258.94 Aligned_cols=639 Identities=25% Similarity=0.361 Sum_probs=546.6
Q ss_pred eEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccc-cCcCcCCCCCC
Q 046997 9 NVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDER-YRKWHSCDPAD 87 (807)
Q Consensus 9 ~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~-y~~W~~~~p~~ 87 (807)
++||||||||+|++||++||.+...++.+|. ++|+|.+ +|. +++|+|+.|||++|++|+. |..+.. +
T Consensus 2 ~~LiIaEKPs~Ak~Ia~~Lg~~~~~~~~~g~----~~~e~~~--~g~--~~~V~~~~GHl~~L~~~~~~~~~~~~----~ 69 (670)
T PRK05776 2 YILVIAEKPKAARKIAEALSEKPIRCRIYGV----PYWIVKR--DGK--KIVVAPAAGHLFGLHTKSKGFPVFDY----E 69 (670)
T ss_pred CEEEEEcCHHHHHHHHHHhCCCccccccCCC----ceEEEec--CCC--CEEEEEecccCccCCCcccCCCCCCc----C
Confidence 5799999999999999999853212233442 3466543 343 6899999999999998873 432210 0
Q ss_pred CCCCCcccccC--CChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHH
Q 046997 88 LYHAPVRKHVP--EDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAV 165 (807)
Q Consensus 88 L~~~p~~~~v~--~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~ 165 (807)
..|.+...+ ..++++++.|++++++||+||||||||||||+|||||+++++. .++++|+|||+||+++|++||
T Consensus 70 --~~p~~~~~~~~~~~~~~~~~lk~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~~---~~~v~R~~fs~iT~~~I~~A~ 144 (670)
T PRK05776 70 --WKPLYEIDKGSKYTKKYYELLSSLSKYADEFINACDYDIEGSVIGYLIIKYLGD---PKKAKRMKFSALTKSDIRRAF 144 (670)
T ss_pred --cccceEeccCcccHHHHHHHHHHHHhcCCEEEECCCCChhHHHHHHHHHHHhCC---CCCeeEEEEccCCHHHHHHHH
Confidence 012211111 2345899999999999999999999999999999999999973 347999999999999999999
Q ss_pred HcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccce
Q 046997 166 QNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEF 245 (807)
Q Consensus 166 ~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y 245 (807)
+||+++|.+|++||+|||++||||||||||++|+.+++.. +...+||+||||||||+|||+||+||++|+|++|
T Consensus 145 ~n~~~~d~~l~~A~~aR~~lD~lvG~nlSr~lt~~~~~~~------g~~~~lS~GRVQsptL~lVveRe~eI~~Fvp~~y 218 (670)
T PRK05776 145 RNLETLDYEMINAGIARHELDWLWGINVSRALMSSVRDAS------GKRVILSAGRVQSPTLKYVVEREIERNLFVPLPY 218 (670)
T ss_pred hCccccchhHHHHHHHHHHHHHHHhHHHhHHHHHHhhhhc------CCccceecceecCchhhHhHhhHHHHHcCCCCcc
Confidence 9999999999999999999999999999999999876410 1223799999999999999999999999999999
Q ss_pred EEEEEEeecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHH
Q 046997 246 WTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHT 325 (807)
Q Consensus 246 ~~i~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~t 325 (807)
|.|.+.+..+++.|.+.|..++++|++.|+.+++.+.+.+.++|++|+.++++++||+||||++||++||++|||||++|
T Consensus 219 w~i~~~~~~~~~~f~~~~~~~~~~~~~~a~~i~~~~~~~~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~As~~lg~sa~kt 298 (670)
T PRK05776 219 FSVSIIIEKNGYEFTLKYENKKFETKEEAKEILEEIKKTGYLKVTKVEVKIEILEPPPPFNLGDLQVEAARIYGFSPYKT 298 (670)
T ss_pred eEEEEEEecCCceEEEEEcCCccCCHHHHHHHHHHhcCCCCEEEEEEEeeeEEcCCCCCCCHHHHHHHHHhhcCCCHHHH
Confidence 99999998878889999987889999999999999976357999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcCceeccCCCCcccCCcccHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCCCCCCCCCCcCCCCCC
Q 046997 326 MKVAEDLYQAGFISYPRTETDSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFSS 405 (807)
Q Consensus 326 l~iaQ~LYE~g~ISYPRTds~~l~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~aH~aI~PT~~~~ 405 (807)
|+|||+|||+||||||||||++||++.++.++++.+...+.|+.+++.+++...+.+ .|.++.++++||||||||...+
T Consensus 299 m~iAQ~LYe~glISYPRTDs~~ls~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~-~~~~~~k~~~aH~AI~PT~~~p 377 (670)
T PRK05776 299 QSIAEDLYLDGLISYPRTNSQKLPPTLNIRNILKGLSRSPQYRPLVNLLLKETKGVL-KPVQGPKDDPAHPAIYPTGEPP 377 (670)
T ss_pred HHHHHHHHhcCceecCCCccCCCChhhCHHHHHHHHhcchhHHHHHHHhhcccCCcc-ccCCCCCCCCCCCCCCCCCCCc
Confidence 999999999999999999999999988888999988777778888877765322222 3444455567999999998754
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCe--EEEEEEEEEEecCeeeeecccccCCccCCccCCCCe
Q 046997 406 GESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGE--VFSTSGRVILAKNYLDVYRFESWGGLVIPTYVHGQQ 483 (807)
Q Consensus 406 ~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~--~F~a~g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~ 483 (807)
..|+++|++||+||||||||+||+||+|++|+|++.++++ .|+++|++++++||++||+++++++..||.|++||.
T Consensus 378 --~~L~~de~klY~LI~rRflA~~~~~a~~~~t~v~~~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~LP~l~~G~~ 455 (670)
T PRK05776 378 --KNLSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPGFPLVFSASGQRIEERGWLKYYPFHKFDEEELPLLKKGER 455 (670)
T ss_pred --ccCCHHHHHHHHHHHHHHHHHhChhheEEEEEEEEEECCeEEEEEEEEEEEEECCceeecccCccccccCCCcCCCCE
Confidence 4799999999999999999999999999999999999999 999999999999999999876666667999999999
Q ss_pred eeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCccc
Q 046997 484 FIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYEL 563 (807)
Q Consensus 484 ~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l 563 (807)
+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||+++++ .|+||++|+.|++.|....++|
T Consensus 456 ~~~~~~~~~~~~TkPP~ryTeasLi~~ME~~GIGtpATra~iI~~L~~R~Yv~~~~k-~l~pT~~G~~v~~~L~~~~~~l 534 (670)
T PRK05776 456 VKIVDVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLTSNGK-YIEVTPLGFGVAEVLEKYFPDI 534 (670)
T ss_pred eEeeeeeeeccccCCCCCCCHHHHHHHHhhCCCCCCccHHHHHHHHHhCCCEEeeCC-EEeECHHHHHHHHHHHHhcccc
Confidence 999999999999999999999999999999999999999999999999999997654 6899999999999998776789
Q ss_pred cCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccccCCCCC
Q 046997 564 WKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKLLEAMGIFFERWSGGEDQQAAGEVVRQCGICQE 643 (807)
Q Consensus 564 ~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g 643 (807)
++|+|||.||..|++|++|+.++++||+++++++++.+.++..+..++.+.++..++ ...+.++||+| |
T Consensus 535 ~~~~~Ta~~E~~Ld~I~~G~~~~~~vl~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~----------~~~~~~~Cp~C-g 603 (670)
T PRK05776 535 VSVELTRDFEEKLEMIRTGKATREEVIEEAKETLNKLLEEFKKNKDEIGEELAKALG----------LIKPVGKCKIC-G 603 (670)
T ss_pred CCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc----------CcCCCCcCCCC-C
Confidence 999999999999999999999999999999999999888877666655444443322 11235789999 6
Q ss_pred cce----EEEecCCC-CceeeccCCCCCCcceecCCCccccccccCcc
Q 046997 644 SNM----VLKKSRDG-NLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTC 686 (807)
Q Consensus 644 ~~l----v~r~~k~G-~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~C 686 (807)
++| +.+.+++| ++|++|++||+|+++.++++.+.. ..+...|
T Consensus 604 ~~l~~~~~~~~~~~~~~~f~~c~~~p~c~~~~~~~~~~~~-~~~~~~~ 650 (670)
T PRK05776 604 REAYKDGLCKYHYEAKKRLVKAYEEWKERTGYDHKEYLEK-ISKLKST 650 (670)
T ss_pred CccccCceEEecccCCccceecCCCccccCCCCcchhHHh-hhccccc
Confidence 789 88888887 468999999999999998865432 2234556
No 5
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=100.00 E-value=1.2e-138 Score=1222.77 Aligned_cols=617 Identities=27% Similarity=0.414 Sum_probs=523.1
Q ss_pred EEcChHHHHHHHHHhCCCCC-cccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCCCCC
Q 046997 13 VAEKPSVAKSVAGILSKNQG-LRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADLYHA 91 (807)
Q Consensus 13 IaEKPs~Ak~IA~~Lg~~~~-~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L~~~ 91 (807)
||||||+|++||++||.+.. .++++|. ++|+|. ++|. +++|||+.|||++|++|++ .+|..|+...|+.+
T Consensus 1 iAEKPs~A~~ia~~l~~~~~~~~~~~g~----~y~~~~--~~g~--~~~Vt~~~GHl~~l~~p~~-~~~~~w~~~~lP~~ 71 (618)
T TIGR01057 1 IAEKPKVAAKIAGALSDGRVLKKSEYGV----PYWEVR--RDGK--KIIVASAVGHLFGLHPKSR-GGYPVFDIEWVPIF 71 (618)
T ss_pred CCCChHHHHHHHHHhCCCCcccccCCCc----eEEEEe--cCCC--eEEEEEeccccccCCCccc-cCCCCCCcccCcee
Confidence 79999999999999987520 1345663 225543 2343 6899999999999999886 34444443334444
Q ss_pred CcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHcCCCC
Q 046997 92 PVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQNLVDP 171 (807)
Q Consensus 92 p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~nl~~~ 171 (807)
|.. .....++++++.|++++++||+||||||||||||+|||+|+++++.. ++|+|+|||++|+++|++||+||++.
T Consensus 72 ~~~-~~~~~~~~~~~~ik~l~~~~d~ii~AtD~DREGE~I~~~i~~~~~~~---~~v~Rl~~~~lt~~~I~~a~~nl~~~ 147 (618)
T TIGR01057 72 EFD-KGKGYVSKYIKALSKLAKGADEYINACDYDIEGEVIGFKALKYFCGV---ERAKRMKFSTLTKQDIRRAYANPEEI 147 (618)
T ss_pred eec-CCcccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhccC---CCceEEEEccCCHHHHHHHHhCcccC
Confidence 432 11223468999999999999999999999999999999999999643 37999999999999999999999988
Q ss_pred CcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccceEEEEEE
Q 046997 172 NQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEFWTINCS 251 (807)
Q Consensus 172 ~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~~i~~~ 251 (807)
+.+|++||+|||++||||||||||++|+.++.. .+...++|+||||||||+|||+||+||+||+|++||.|.+.
T Consensus 148 ~~~l~~a~~aR~~~D~liG~n~Sr~~t~~~~~~------~~~~~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~ 221 (618)
T TIGR01057 148 DYGMVDAGMARHILDWYWGINLSRALMEAIRAA------AGRWVILSAGRVQGPTLAFLVEREREINLFVPKPYWVIKAT 221 (618)
T ss_pred CHhHHHHHHHHHHHHHHHhhhhhHHHHHHhhcc------CCCcccccccccchhHHHHHHHhHHHHHcCcCCccEEEEEE
Confidence 899999999999999999999999999987641 01234799999999999999999999999999999999999
Q ss_pred eecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHH
Q 046997 252 HKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAED 331 (807)
Q Consensus 252 ~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~iaQ~ 331 (807)
+..+++.|.+.|.+++++|++.|+.+++.+.+.+.++|++|++++++..||+||||++||++||++|||||++||++||+
T Consensus 222 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~ 301 (618)
T TIGR01057 222 LEKGGGVFDARPEKWKIWSEEEAKSIKEELKKSPWAAVEEVRSERSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIAQE 301 (618)
T ss_pred EecCCceEEEEEccCCcCCHHHHHHHHHHHhCCCCeEEEEEEeeeeeccCCCCccHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence 98888889999988999999999999999986547999999999999999999999999999999999999999999999
Q ss_pred HhhcCceeccCCCCcccCCcccHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCCCCCCCCCCcCCCCCCCCCCCC
Q 046997 332 LYQAGFISYPRTETDSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFSSGESRWS 411 (807)
Q Consensus 332 LYE~g~ISYPRTds~~l~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~aH~aI~PT~~~~~~~~Ls 411 (807)
|||+||||||||||++||+++++.++++.+...+.|+.+++.++.. . ...+.++++.++||||||||...+.. .|+
T Consensus 302 LYe~g~ISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~aH~aI~PT~~~~~~-~L~ 377 (618)
T TIGR01057 302 LYEEALISYPRTSSQKLPPSINYRAILDNLAKGPLYREAAERLLET--G-VLKPVEGKKEDPAHPAIHPTGEIPSQ-ELS 377 (618)
T ss_pred HHhcCceeecCcccCccCHHHhHHHHHHHHhcccchHHHHHHhhcc--c-ccccCCCCCCCCCCCCcCccCCCccc-cCC
Confidence 9999999999999999999877788888887665666666554421 1 11233444445699999999876643 799
Q ss_pred HHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccCCccCCccCCCCeeeeeeeEe
Q 046997 412 QDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWGGLVIPTYVHGQQFIPTTLTL 491 (807)
Q Consensus 412 ~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~~~~~~~i 491 (807)
++|++||+||+|||||+||+||+|++|+|.+.++++.|.++|++++++||++||+++++++..||.+++||.+.+.++.+
T Consensus 378 ~~e~~iY~lI~~r~la~~~~~a~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~v~~~~~~~~~~lp~~~~gd~~~~~~~~~ 457 (618)
T TIGR01057 378 KDEKKVYDLIVRRFLAAFSEEAIREKSKVLLRIGQEKFRLSGLRVVKLGWLEYYHYSKFEEKELPPLDRGDKIKVVRVDV 457 (618)
T ss_pred HHHHHHHHHHHHHHHHHhChhhheeEEEEEEEECCeEEEEEEEEEEeCCcceeccCcccccccCCCCCCCCEeeeeeeee
Confidence 99999999999999999999999999999999999999999999999999999976555556799999999999999999
Q ss_pred ecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCccccCchhhHH
Q 046997 492 DSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKPNLRSM 571 (807)
Q Consensus 492 ~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~ 571 (807)
.+++|+||+||||++||++||+.|||||||||+||++|++||||+.+ + .|+||++|+.|+++|+...+.|++|+|||.
T Consensus 458 ~e~~TkPP~~~Te~tLi~~Me~~GIGTpATra~iIe~L~~r~Yi~~~-~-~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~ 535 (618)
T TIGR01057 458 RVKETQPPARYDKASLIREMESRGLGTKATRARIIETLYKRGYIEGK-K-SIKVTPLGEAVIETLQRYCPEIISEELTRR 535 (618)
T ss_pred cccccCCCCCCCHHHHHHHHHhCCCCCCCcHHHHHHHHHhCCcEeEC-C-EEeeehHHHHHHHHHHHhchhhcChhhHHH
Confidence 99999999999999999999999999999999999999999999864 4 489999999999999876668999999999
Q ss_pred HHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccccCCCCCcceEEEec
Q 046997 572 MESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKLLEAMGIFFERWSGGEDQQAAGEVVRQCGICQESNMVLKKS 651 (807)
Q Consensus 572 ~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~~lv~r~~ 651 (807)
||..|++|++|+.++++||+++.+++++.+.+...+...+...+..-+ .......+||+| ++.|+.++.
T Consensus 536 ~E~~L~~I~~G~~~~~~fl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~CPkC-g~~l~~~~~ 604 (618)
T TIGR01057 536 FESKLEDIMSGRITKDEVIDEAKKRLRKILEEFKKRLDDIGIELGKSL----------GSVEVVGKCPKC-GGKLVSKYA 604 (618)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhc----------ccccccCCCCcC-CCeeeeeec
Confidence 999999999999999999999999999888776654333221111100 001234689999 567776666
Q ss_pred CCCCceeeccCCCCC
Q 046997 652 RDGNLMVGCLAFPQC 666 (807)
Q Consensus 652 k~G~~f~gCs~yP~C 666 (807)
++|. ||||||||+|
T Consensus 605 k~g~-f~gCs~yp~C 618 (618)
T TIGR01057 605 KKGR-FVGCSNYPEC 618 (618)
T ss_pred CCcc-EEECCCCCCC
Confidence 6665 6999999998
No 6
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=100.00 E-value=1.2e-137 Score=1245.67 Aligned_cols=626 Identities=23% Similarity=0.357 Sum_probs=525.5
Q ss_pred CceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCC
Q 046997 7 PINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPA 86 (807)
Q Consensus 7 ~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~ 86 (807)
||+.|||||||++|++|+++||.+ ++|+|+.|||++| |+.+..|.. .
T Consensus 1 m~~~LvIvEsP~kak~I~~~Lg~~----------------------------~~V~as~GHl~dL--p~~~~~~~~---~ 47 (860)
T PRK06319 1 MKKSLIIVESPAKIKTLQKLLGEG----------------------------FIFASSLGHIVDL--PAKEFGIDI---E 47 (860)
T ss_pred CCCeEEEEeCHHHHHHHHHHhCCC----------------------------CEEEecccCcccC--CcccCCcCC---C
Confidence 678999999999999999999852 4799999999999 455555653 2
Q ss_pred CCCCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHH
Q 046997 87 DLYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQ 166 (807)
Q Consensus 87 ~L~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~ 166 (807)
+ ...|. +.+..+++++++.|++++++||.||||||||||||+|+|||+++++. +++|+|+|||+||+++|++||+
T Consensus 48 ~-~f~p~-y~~~~~k~~~~~~ik~~~k~ad~iilAtDpDREGE~I~~~i~~~l~~---~~~v~Rv~f~~iT~~aI~~A~~ 122 (860)
T PRK06319 48 N-DFEPD-YQILPDKEEVINKICKLAKKCDVVYLSPDPDREGEAIAWHIANQLPK---NTKIQRISFNAITKGAVTEALK 122 (860)
T ss_pred C-CCCcc-eEECccHHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHcCC---CCCeeEEEEccCCHHHHHHHHh
Confidence 2 12342 34556789999999999999999999999999999999999999864 3589999999999999999999
Q ss_pred cCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccceE
Q 046997 167 NLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEFW 246 (807)
Q Consensus 167 nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~ 246 (807)
|++++|++|++||+||+++|||||||+||++|+.++. ...+|+||||||||+|||+||+||+||+|++||
T Consensus 123 ~~~~~d~~l~~A~~aR~~lD~lvG~nlSr~l~~~~~~----------~~~lSaGRVQsp~L~lIveRe~eI~~F~p~~yw 192 (860)
T PRK06319 123 HPREIDMALVNAQQARRLLDRIVGYKISPILSRKLQR----------RSGVSAGRVQSVALKLVVDREKAIEAFVPVEYW 192 (860)
T ss_pred CccccCHHHHHHHHHHHHHHHHhhhhcCHHHHHhhcc----------CCCCcCCccchhhhHHHHHHHHHHHcCCCCceE
Confidence 9999999999999999999999999999999987642 126999999999999999999999999999999
Q ss_pred EEEEEeecC--CceEEEEecc-------------------CCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCC
Q 046997 247 TINCSHKSE--EGTATFSWMR-------------------GHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPL 305 (807)
Q Consensus 247 ~i~~~~~~~--~~~~~~~~~~-------------------~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf 305 (807)
+|.+.+..+ +..|.+.|.. .++.|++.|+.+++.+.. ..++|++|++++++++||+||
T Consensus 193 ~i~~~~~~~~~~~~f~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~l~~-~~~~V~~v~~k~~~~~pp~pf 271 (860)
T PRK06319 193 NIRVHLKDPKTQKTFWAHLYSVDGKKWEKEIPEGKTEDEVLLINSKEKADHIVELLES-ATYTVTRVESKEKRRNAYPPF 271 (860)
T ss_pred EEEEEEecCCCCcceEEEeecccCcccccccccccccccccccCCHHHHHHHHHHhcC-CCeEEEEEEeeEeecCCCCCc
Confidence 999998753 3567776631 136789999999999875 479999999999999999999
Q ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHhhc---------CceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhh
Q 046997 306 STIELEKRASRYFRMSSEHTMKVAEDLYQA---------GFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRL 374 (807)
Q Consensus 306 ~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~---------g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~ 374 (807)
+|++||++||++|||||++||++||+|||. ||||||||||++||++. ++..+|..+. ...+
T Consensus 272 ~ts~LQ~~As~~~g~sa~~tm~iAQ~LYE~~~~~~~~~~glITYpRTDs~~ls~~~~~~~~~~i~~~~--------g~~~ 343 (860)
T PRK06319 272 ITSTLQQEASRHFRFSSSRTMNIAQTLYEGVDLDSEGATGLITYMRTDSVRTDPEALKQVRKYIEGTF--------GKEF 343 (860)
T ss_pred cHHHHHHHHHHHcCCCHHHHHHHHHHHHhccccccCCceeEEeecCcCcccCCHHHHHHHHHHHHHhh--------hhhh
Confidence 999999999999999999999999999994 99999999999999865 4555554432 1233
Q ss_pred cccccCCccCCCCCCCCCCCCCCCcCCCCC--CC--CCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECC-eEE
Q 046997 375 LDHAAGLWRNPGSGGHDDKAHPPIHPTKFS--SG--ESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAG-EVF 449 (807)
Q Consensus 375 l~~~~~~~~~~~~~~~~~~aH~aI~PT~~~--~~--~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~-~~F 449 (807)
++..++.|++. +.+++||||||||... ++ ...|+++|++||+|||+||||+||+||+|++|+|++.+++ +.|
T Consensus 344 ~~~~~~~~~~~---k~~q~aH~AI~PT~~~~~p~~~~~~L~~de~klY~LI~~RflAs~m~~a~~~~t~v~~~~~~~~~F 420 (860)
T PRK06319 344 LPSSPNVYTTK---KMAQDAHEAIRPTDITLTPEKLRSKLTEDQYKLYSLIWKRFVASQMIPAIYDTLAIRITTNKGIDL 420 (860)
T ss_pred cccCCcccCCC---CCCCCCcCCCccCCCCcChhHhhccCCHHHHHHHHHHHHHHHHHhCchhheEEEEEEEEeCCeeEE
Confidence 44334555443 3467899999999853 22 1479999999999999999999999999999999999997 699
Q ss_pred EEEEEEEEecCeeeeecccc------cCCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchH
Q 046997 450 STSGRVILAKNYLDVYRFES------WGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMH 523 (807)
Q Consensus 450 ~a~g~~i~~~Gw~~v~~~~~------~~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra 523 (807)
+++|++++++||++||..+. +++..||.|.+||.+.+.++.+.+++|+||+||||++||++||+.|||||||||
T Consensus 421 ~a~G~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~Ge~~~~~~~~~~~~~T~PP~ryTeasLvk~me~~GIGtpsT~A 500 (860)
T PRK06319 421 RATGSLLKFKGFLAVYEEKRDDEGDEEENIHLPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYA 500 (860)
T ss_pred EEEeEEEeeCCHHHHhCccccccccccccccCCCCCCCCEeeeeeeeecccccCCCCCCCHHHHHHHHHhcCCCchhhHH
Confidence 99999999999999996432 123469999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhcccceEEEcCCceeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHH
Q 046997 524 DHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLD 603 (807)
Q Consensus 524 ~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~ 603 (807)
+||++|++|+||.++++ .|+||++|+.|++.|....+.|++|+|||.||..|++|++|+.+|++||+++++.|...+..
T Consensus 501 ~iI~~L~~R~Yv~~~~k-~l~pT~~G~~v~~~L~~~f~~i~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~~f~~~~~~~~~~ 579 (860)
T PRK06319 501 TIMNKIQSREYTLKENQ-RLRPTELGKIISQFLETNFPRIMDIGFTALMEDELELIADNKKPWKLLLQEFWELFLPVVVT 579 (860)
T ss_pred HHHHHHhhCCeEEccCC-EEEECHHHHHHHHHHHHhchhhcChhHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHH
Confidence 99999999999987654 69999999999999987656899999999999999999999999999999999998876655
Q ss_pred HHHHHHHhhhhhhhhhccCCCCCCcccccccccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCc---c---
Q 046997 604 ARLKKVKLLEAMGIFFERWSGGEDQQAAGEVVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSV---S--- 677 (807)
Q Consensus 604 ~~~~~~k~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~---~--- 677 (807)
...+. .. ........||+|+++.|+++.+++|. ||+||+||+|+++.++.... .
T Consensus 580 ~~~~~-~~------------------~~~~~~~~CP~Cg~~~L~~k~gr~G~-Fl~Cs~yP~C~~t~~~~~~~~~~~~~~ 639 (860)
T PRK06319 580 AEKEA-FI------------------PRIVTEIDCPKCHKGKLVKIWAKNRY-FYGCSEYPECDYKTSEEELTFNKEDYA 639 (860)
T ss_pred Hhhhh-cc------------------cccccCcccCCCCCcceeEEecCCCc-eeeccCCccccccCCcccccccccccc
Confidence 33210 00 01123568999977789999999987 69999999999997765310 0
Q ss_pred ccccccCccCCCCCCceEEEEeeccCccCCCCCccCcccc---CCCCChhH
Q 046997 678 EAAVTTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGC---IGGCDETL 725 (807)
Q Consensus 678 ~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C---~~~C~~~~ 725 (807)
....+...||+||+ .++. +++++|++ ++| | .|++..
T Consensus 640 ~~~~~~~~CP~Cg~-~m~l--K~gr~G~F--------l~Cs~yP-~Ck~~~ 678 (860)
T PRK06319 640 EDTPWDSPCPLCGG-EMKV--RHGRFGTF--------LGCENYP-ECRGII 678 (860)
T ss_pred cccccCCcCccCCC-eeEE--ecCCCCce--------eeCCCCc-cccccc
Confidence 01123568999995 4553 36677764 789 5 798653
No 7
>PRK08173 DNA topoisomerase III; Validated
Probab=100.00 E-value=4.9e-137 Score=1235.11 Aligned_cols=605 Identities=24% Similarity=0.341 Sum_probs=509.8
Q ss_pred CceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccC-cCcCCCC
Q 046997 7 PINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYR-KWHSCDP 85 (807)
Q Consensus 7 ~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~-~W~~~~p 85 (807)
||++||||||||+|++||++||.. .+++|| ++|. +++||||+|||++|++|++|. .|..|+.
T Consensus 1 Mm~~LiIAEKPs~Ak~Ia~~Lg~~---~k~~gy------------~e~~--~~~Vtwa~GHL~el~~Pe~Y~~~~~~W~~ 63 (862)
T PRK08173 1 MSKALIIAEKPSVANDIARALGGF---TKHDEY------------FESD--EYVLSSAVGHLLEIAAPEEYEVKRGKWSF 63 (862)
T ss_pred CCCEEEEEeCHHHHHHHHHHhCCC---cCCCCe------------EeCC--cEEEEeeccccccCCCchhcccccccccc
Confidence 889999999999999999999864 356773 2343 589999999999999999884 3444444
Q ss_pred CCCCCCCc--ccccCCChHHHHHHHHHHHh--hcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHH
Q 046997 86 ADLYHAPV--RKHVPEDKKDIKKTLEEEAR--RCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREI 161 (807)
Q Consensus 86 ~~L~~~p~--~~~v~~~k~~~~~~lk~~~~--~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I 161 (807)
.+|+.+|. ...+..++++++++|+++++ ++|+||||||||||||+|+|+|+++++. +++|+||||||||+++|
T Consensus 64 ~~LPi~p~~f~~~~~~~~~~q~~~ik~l~k~~~~d~Ii~AtD~dREGElI~~~I~~~~~~---~kpv~Rlw~sslt~~aI 140 (862)
T PRK08173 64 AHLPVIPPHFDLNPIAKTESRLKVLTKLIKRKDVTRLINACDAGREGELIFRLIAQHAKA---KKPVKRLWLQSMTPQAI 140 (862)
T ss_pred cccCCCCccccccccccHHHHHHHHHHHHhhCCCCEEEECCCCChhHHHHHHHHHHHhCC---CCCeEEEEEccCCHHHH
Confidence 44554443 23345667889999999995 5899999999999999999999999874 35899999999999999
Q ss_pred HHHHHcCCCCC--cchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHc
Q 046997 162 HQAVQNLVDPN--QWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQA 239 (807)
Q Consensus 162 ~~A~~nl~~~~--~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~ 239 (807)
++||+||++++ .+|++||+||+++|||||||+||++|++.++.+ ...++|+||||||||+|||+||+||+|
T Consensus 141 ~~a~~nl~~~~~~~~L~~aa~aR~~aDwlvG~N~TR~~T~~~~~~g-------~~~~lSvGRVQTPtL~lVv~Re~eI~~ 213 (862)
T PRK08173 141 RDGFANLRSDEDMQPLADAARCRSEADWLVGINGTRAMTAFNSKGG-------GFFLTTVGRVQTPTLSIVVEREEKIRR 213 (862)
T ss_pred HHHHhcCCCchhhHHHHHHHHHHHHHHHHhhHHHhHHHHHhHhhcC-------CccccccccchhhHHHHHHHHHHHHHc
Confidence 99999999886 489999999999999999999999998654321 123789999999999999999999999
Q ss_pred ccccceEEEEEEeecCCceEEEEec--------------cCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCC
Q 046997 240 HESEEFWTINCSHKSEEGTATFSWM--------------RGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPL 305 (807)
Q Consensus 240 F~p~~y~~i~~~~~~~~~~~~~~~~--------------~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf 305 (807)
|+|++||+|.+.+...++.+.+.|. .+|++|++.|+.+++.|.+. .++|++ +.+++++.||+||
T Consensus 214 F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~d~~~A~~i~~~~~~~-~~~V~~-~~k~~~~~pP~~f 291 (862)
T PRK08173 214 FVPRDYWEVRAEFVAAAGFYEGRWFDPKFKKDEFDPEKRASRLWSEAAAEAIVAACRGK-PGTVTE-ESKPSTQLSPLLF 291 (862)
T ss_pred CCCCccEEEEEEEecCCccEEEEEeccccccccccccccccccCCHHHHHHHHHHhcCC-CcEEEE-eeeEEecCCCCCC
Confidence 9999999999999888888888883 25899999999999999764 789998 8899999999999
Q ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHhhc-CceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhccc-----
Q 046997 306 STIELEKRASRYFRMSSEHTMKVAEDLYQA-GFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDH----- 377 (807)
Q Consensus 306 ~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~-g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~----- 377 (807)
||++||++||++|||||++||+|||+|||+ |+||||||||+|||+++ ++.++|+.+..++.|..++..+++.
T Consensus 292 ~Lt~LQ~~A~~~~g~sa~~tL~iaQ~LYE~~k~iTYPRTDs~~l~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~ 371 (862)
T PRK08173 292 DLTSLQREANGRFGFSAKNTLGLAQALYEKHKVLTYPRTDSRALPEDYLGTVKQTLEMLKESNNYLPHAKQILDKGWVKP 371 (862)
T ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCEEEecCCCCccCCHHHHHHHHHHHHHHhCCcccHHHHHHhhcccccCC
Confidence 999999999999999999999999999997 89999999999999986 6788888886545566666555431
Q ss_pred ccCCccCCCCCCCCCCCCCCCcCCCCCCCCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEE
Q 046997 378 AAGLWRNPGSGGHDDKAHPPIHPTKFSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVIL 457 (807)
Q Consensus 378 ~~~~~~~~~~~~~~~~aH~aI~PT~~~~~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~ 457 (807)
..+.|++. ++.||||||||...+ ..||++|++||+||+|||||+|||||+|+.|+|++.++++.|+++|++++
T Consensus 372 ~~r~~~~~-----kv~dH~AIiPT~~~~--~~Ls~~E~~iY~lI~rRfla~f~~~a~~~~t~v~~~v~~~~F~a~G~~~~ 444 (862)
T PRK08173 372 NKRIFDNS-----KISDHFAIIPTLQAP--KSLSEPEQKLYDLVVKRFLAVFFPAAEFLVTTRITEVAGHHFKTEGKVLV 444 (862)
T ss_pred CCCcCCCC-----CCCCCCCcCccCCCc--ccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCCcEEEEEEEEEe
Confidence 12333221 245899999998765 36999999999999999999999999999999999999999999999999
Q ss_pred ecCeeeeeccccc-CCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHH----------------hCCCCCcc
Q 046997 458 AKNYLDVYRFESW-GGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMD----------------KAGIGTDA 520 (807)
Q Consensus 458 ~~Gw~~v~~~~~~-~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me----------------~~GIGTpA 520 (807)
++||++||+.+.+ ++..||.|++||.+.+.++.+.+++|+||+||||++||++|| +.||||||
T Consensus 445 ~~Gw~~vy~~~~~~~~~~LP~l~~Ge~~~~~~~~~~e~~TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~~~~GIGTpA 524 (862)
T PRK08173 445 NPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPA 524 (862)
T ss_pred eCChHHHhCcccccccccCCCcCCCCEeeeeeeeecccccCCCCCcCHHHHHHHHHhhhhccccHHHHhhhhcCCCCchh
Confidence 9999999975432 345699999999999999999999999999999999999999 47999999
Q ss_pred chHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCc-cccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHH
Q 046997 521 TMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGY-ELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKA 599 (807)
Q Consensus 521 Tra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~-~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~ 599 (807)
|||+||++|++||||+++++ .|+||++|+.||++|+...+ .|++|+|||.||..|++|++|+.++++||+++.+++.+
T Consensus 525 TRA~IIe~L~~r~Yi~~~~k-~l~pT~~G~~li~~l~~~~~~~l~~p~lTa~wE~~L~~I~~G~~~~~~f~~~i~~~~~~ 603 (862)
T PRK08173 525 TRAAIIEGLLGEKYLVREGR-ELIPTAKAFQLMTLLRGLGVEELTSPELTGEWEYKLSQIERGKLSRDAFMQEIAQMTQQ 603 (862)
T ss_pred hHHHHHHHHHhCCcEEecCC-EechhHHHHHHHHHHhhcCcccccChhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 99999999999999998755 58999999999999976433 69999999999999999999999999999999999887
Q ss_pred HHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccccCCCCCcceEEEecCCCCceeeccCCCCCCcceec
Q 046997 600 CFLDARLKKVKLLEAMGIFFERWSGGEDQQAAGEVVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWL 672 (807)
Q Consensus 600 ~~~~~~~~~~k~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~ 672 (807)
.+.+...... ..+ +... ....++||+| ++.++. .++ +|+|++ |+|.+|.
T Consensus 604 ~v~~~~~~~~------~~~------~~~~---~~~~~~CP~C-g~~~~~----~~~-~~~Cs~---C~f~~~~ 652 (862)
T PRK08173 604 IVKRAKEYDS------DTI------PGDY---ATLQTPCPNC-GGVVKE----NYR-RFACTK---CDFSISK 652 (862)
T ss_pred HHHHHHhhhh------ccc------cccc---ccccccCCcc-cccccc----cCc-eeEcCC---CCcccch
Confidence 6655432100 000 0000 0123689999 455532 122 489998 9999984
No 8
>PRK07726 DNA topoisomerase III; Provisional
Probab=100.00 E-value=1.3e-136 Score=1210.67 Aligned_cols=618 Identities=27% Similarity=0.412 Sum_probs=519.2
Q ss_pred EEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccC-cCcCCCCCCC
Q 046997 10 VLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYR-KWHSCDPADL 88 (807)
Q Consensus 10 ~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~-~W~~~~p~~L 88 (807)
.||||||||+|++||++||.. .+++|+ +.|. +++|||+.|||++|++|++|. +|..|...+|
T Consensus 2 ~LiIaEKPs~Ak~Ia~~L~~~---~~~~g~------------~~g~--~~~Vt~~~GHl~~L~~p~~y~~~~~~W~~~~l 64 (658)
T PRK07726 2 RLFIAEKPSVGRDIADVLKPH---KKGDGY------------IEGN--GYIVTWAIGHLLELAEPEAYDERYKRWRLEDL 64 (658)
T ss_pred eEEEEeCHHHHHHHHHHhCCc---cCCCCe------------EeCC--CEEEEechhhhccCCCchhcccccCccccccC
Confidence 699999999999999999854 356673 2343 589999999999999887663 3333333344
Q ss_pred CCCC--cccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHH
Q 046997 89 YHAP--VRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQ 166 (807)
Q Consensus 89 ~~~p--~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~ 166 (807)
+..| +...+..++++++++|++++++||+||||||||||||+|||+|+++++. +++|+|+|||++|+++|++||+
T Consensus 65 pi~p~~~~~~~~~~~~~~~~~ik~l~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~---~~~v~Rl~~sslt~~~I~~A~~ 141 (658)
T PRK07726 65 PIIPEKWKLVVKKKTAKQFNVVKKLLKQATEIVIATDADREGELIAREILDYCGV---RKPIKRLWISSLTDKAIKRAFA 141 (658)
T ss_pred CCCcccceeeeccchHHHHHHHHHHHhhCCeEEEcCCCCccccHHHHHHHHHhCC---CCCeEEEEEccCCHHHHHHHHH
Confidence 4444 3334456788999999999999999999999999999999999999975 3589999999999999999999
Q ss_pred cCCCCC--cchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccc
Q 046997 167 NLVDPN--QWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEE 244 (807)
Q Consensus 167 nl~~~~--~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~ 244 (807)
||++++ .+|++||+||+++||||||||||++|+.+++.+ ...++|+||||||||+|||+|++||+||+|++
T Consensus 142 nl~~~~~~~~l~~aa~aR~~~D~liG~nlSr~~t~~~~~~g-------~~~~lS~GRVQTPtL~lVv~Re~eI~~F~p~~ 214 (658)
T PRK07726 142 NLKPGKETIPLYYSALARSRADWLVGINMTRAYTLLGRKAG-------YNGVLSVGRVQTPTLALVVRRDEEIENFVPKP 214 (658)
T ss_pred hcCCchhhHHHHHHHHHHHHHHHHhhhhHhHHHHHHHhhcC-------CCcceeecccccchhHHHHHHHHHHHcCCCcc
Confidence 999874 589999999999999999999999999877521 12489999999999999999999999999999
Q ss_pred eEEEEEEeecCCceEEEEec--------cCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHH
Q 046997 245 FWTINCSHKSEEGTATFSWM--------RGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASR 316 (807)
Q Consensus 245 y~~i~~~~~~~~~~~~~~~~--------~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask 316 (807)
||+|.+.+ .+++.+.+.|. ++|++|++.|+.+++.+.+ ..++|++|+++++++.||+||||++||++||+
T Consensus 215 y~~i~~~~-~~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~pP~pf~ls~Lq~~a~~ 292 (658)
T PRK07726 215 YWEVEAHL-TPGERFTAKWQPSEPYQDEEGRLLDRPLAEQVVARIQG-QPAKVTEVETKRKKEYAPLLYDLSELQIDANK 292 (658)
T ss_pred cEEEEEEE-cCCCeEEEEEeccccccccccccCCHHHHHHHHHHhcC-CCeEEEEEEeeEEecCCCCCCCHHHHHHHHHH
Confidence 99999998 56778889996 3689999999999999965 47999999999999999999999999999999
Q ss_pred hcCCCHHHHHHHHHHHhhc-CceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhcccc--cCCccCCCCCCCC
Q 046997 317 YFRMSSEHTMKVAEDLYQA-GFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDHA--AGLWRNPGSGGHD 391 (807)
Q Consensus 317 ~~g~s~~~tl~iaQ~LYE~-g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~~--~~~~~~~~~~~~~ 391 (807)
+|||||++||++||+|||+ ||||||||||++||++. ++.++++.+...+.|..++..+++.. .+.|++ ..
T Consensus 293 ~~g~s~~~tl~iaQ~LYE~~glITYPRTds~~ls~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~-----~~ 367 (658)
T PRK07726 293 RFGLSAKETLDIAQSLYETHKLITYPRTDSRYLPEDMVATLPEVLNAISKVDPYLLLAPPVLDPSIRSRAWND-----KK 367 (658)
T ss_pred hcCCCHHHHHHHHHHHHHhcCEEEecCCCCccCCHHHHHHHHHHHHHHhccCcchhhhhhhhccccccCcCCC-----Cc
Confidence 9999999999999999997 99999999999999986 67888888764455655444444311 122211 13
Q ss_pred CCCCCCCcCCCCCCCCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccC
Q 046997 392 DKAHPPIHPTKFSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWG 471 (807)
Q Consensus 392 ~~aH~aI~PT~~~~~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~ 471 (807)
++||||||||...++..+|+++|++||+||+|||||+||+||+|++|+|++.++++.|.++|++++++||+.+|+.+.++
T Consensus 368 ~~aH~AI~PT~~~~~~~~L~~~e~~iY~lI~~r~la~~~~~~~~~~t~v~~~~~~~~F~~~g~~i~~~Gw~~v~~~~~~~ 447 (658)
T PRK07726 368 VTAHHAIIPTEQPPNLSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEED 447 (658)
T ss_pred CCCCCCcCccCCCCCcccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECCEEEEEEEEEEccCCHHHHccccccc
Confidence 57999999999877667899999999999999999999999999999999999999999999999999999999753322
Q ss_pred ---CccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhC-----------------CCCCccchHHHHHhhcc
Q 046997 472 ---GLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKA-----------------GIGTDATMHDHIKKLLD 531 (807)
Q Consensus 472 ---~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~-----------------GIGTpATra~iI~~L~~ 531 (807)
+..||.|.+||.+.+.++.+.+++|+||+||||++||++||+. |||||||||+||++|++
T Consensus 448 ~~~~~~lp~l~~g~~~~~~~~~~~e~~TkPP~~yTe~tLi~~Me~~~k~v~d~~~~~~l~e~~GIGTpATra~iIe~L~~ 527 (658)
T PRK07726 448 EEKEQPLPVLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFK 527 (658)
T ss_pred ccccccCCCcCCCCEeeecccccccccCCCCCCcCHHHHHHHHHhhhhhccCHHHHHhhcccCCCCccccHHHHHHHHHh
Confidence 2359999999999999999999999999999999999999875 99999999999999999
Q ss_pred cceEEEcCCceeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHh
Q 046997 532 RFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKL 611 (807)
Q Consensus 532 R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~ 611 (807)
||||+.+++ .|+||++|++|++.|+. .|++|+|||.||..|++|++|+.++++||+++++++++.+.+.......
T Consensus 528 R~Yi~~~~k-~l~pT~~G~~li~~l~~---~l~~p~~Ta~~E~~L~~I~~G~~~~~~fl~~~~~~~~~~v~~~~~~~~~- 602 (658)
T PRK07726 528 RGYLEKKGK-YIHATDKGKQLIDALPE---ELTSPDMTAKWEQALDQISEGQLSYQDFMQPLKQWLKQLVEQAKQSSEK- 602 (658)
T ss_pred CCCEEecCC-EEEECHHHHHHHHHHHH---HcCChhhHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhcccc-
Confidence 999998654 69999999999998865 4999999999999999999999999999999999888765543221000
Q ss_pred hhhhhhhhccCCCCCCcccccccccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 612 LEAMGIFFERWSGGEDQQAAGEVVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 612 ~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
. . ........||+| ++.++.+.+++|+ ||+|+||| |.+..|.++ .+...||.|+.
T Consensus 603 ---~-------~------~~~~~~~~CP~C-~~~~~~~~~~~~~-f~~Cs~~~-~~~~~~~~~------~~~~~~~~~~~ 657 (658)
T PRK07726 603 ---Y-------K------FDNLTGPKCPDC-GKPMLKVKGKNGK-MLVCQDRE-CGKRKNVSK------KTNARCPNCKK 657 (658)
T ss_pred ---c-------c------cccCCccccccc-CccceeecccCCe-eEecCCCc-ccccccccc------ccCCCCCccCC
Confidence 0 0 001134689999 5677776666676 69999977 544466542 24567999973
No 9
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=100.00 E-value=3.3e-136 Score=1203.11 Aligned_cols=600 Identities=25% Similarity=0.376 Sum_probs=508.6
Q ss_pred EEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCccccccccccc----CcCcCCCC
Q 046997 10 VLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERY----RKWHSCDP 85 (807)
Q Consensus 10 ~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y----~~W~~~~p 85 (807)
.||||||||+|++||++||... +++|+ |++ |. +++|+|+.|||++|++|++| ++|+..
T Consensus 2 ~LiIaEKPs~Ak~Ia~~L~~~~---~~~gy------~e~-----g~--~~~V~~~~GHl~~L~~p~~~~~~~~~W~~~-- 63 (660)
T TIGR01056 2 TLVLCEKPSQARDLATVLAKKK---KGNGY------LEI-----GV--GGFVTWAVGHLVELAEPEEYDEKYKNWRTY-- 63 (660)
T ss_pred eEEEEeCHHHHHHHHHHhCCCc---CCCCc------EEE-----CC--cEEEEeCchhhhcCCChhhcccccCccccC--
Confidence 4999999999999999998753 56673 221 43 58999999999999977654 566543
Q ss_pred CCCCCCC--cccccCCChHHHHHHHHHHHh--hcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHH
Q 046997 86 ADLYHAP--VRKHVPEDKKDIKKTLEEEAR--RCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREI 161 (807)
Q Consensus 86 ~~L~~~p--~~~~v~~~k~~~~~~lk~~~~--~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I 161 (807)
+|+..| +...+..+++++++.|+++++ +||+||||||||||||+|||||+++++..+ ..+++|+|||++|+++|
T Consensus 64 -~lp~~p~~f~~~~~~~~~~~~~~ik~l~k~~~ad~Ii~AtDpDREGE~I~~~i~~~l~~~~-~~~v~Ri~f~~iT~~~I 141 (660)
T TIGR01056 64 -DLPLEPEDWQLVVSDKTKKQFNVIKRILKENKVDEVVIATDPDREGELIAREILDYLKVTD-KVTIKRLWISSLVDSSI 141 (660)
T ss_pred -CCCcccccceeeeccchHHHHHHHHHHhhhcCCCEEEECCCCCcchHHHHHHHHHHhCCCC-CCceEEEEeccCCHHHH
Confidence 333233 233445678899999999999 999999999999999999999999997422 24899999999999999
Q ss_pred HHHHHcCCCC--CcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHc
Q 046997 162 HQAVQNLVDP--NQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQA 239 (807)
Q Consensus 162 ~~A~~nl~~~--~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~ 239 (807)
++||+||+++ +.+|++||+||+++|||||||+||++|+.+++.+ ...++|+||||||||+|||+||+||+|
T Consensus 142 ~~A~~n~~~~~~~~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~g-------~~~~lS~GRVQtptL~lIveRe~eI~~ 214 (660)
T TIGR01056 142 RKAFKNLRPKSETEGLYKSGVARARADWLVGINLTRAFTKLGREAG-------NDGVLSVGRVQTPTLAMVVKRENEIKN 214 (660)
T ss_pred HHHHHcCCCchhhhhHHHHHHHHHHHHHHHHHhHhHHHHHhhhhcC-------CCCceecccchhhhhHHHHHHHHHHHc
Confidence 9999999976 6789999999999999999999999999876532 124799999999999999999999999
Q ss_pred ccccceEEEEEEeecCCceEEEEecc-----CCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHH
Q 046997 240 HESEEFWTINCSHKSEEGTATFSWMR-----GHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRA 314 (807)
Q Consensus 240 F~p~~y~~i~~~~~~~~~~~~~~~~~-----~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~a 314 (807)
|+|++||+|.+.+..+++.|.+.|.+ .+++|++.|+.+++.+.+. .++|.+|+.+++++.||+||||++||++|
T Consensus 215 F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~~~~~-~~~V~~v~~k~~~~~pP~pf~ts~LQ~~a 293 (660)
T TIGR01056 215 FVGKPFYEVSATINKDEQEFTTEWQPYKDEEERELHEFLAENVVTDLTQK-PALVTDIEKERKKTSAPLFYDLSALQEDA 293 (660)
T ss_pred CCCCccEEEEEEEEcCCceEEEEEeccCCcccCcCCHHHHHHHHHHhhCC-CeEEEEEEeeeeecCCCCCCCHHHHHHHH
Confidence 99999999999998777789899964 4789999999999999764 59999999999999999999999999999
Q ss_pred HHhcCCCHHHHHHHHHHHhhc-CceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhccc--ccCCccCCCCCC
Q 046997 315 SRYFRMSSEHTMKVAEDLYQA-GFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDH--AAGLWRNPGSGG 389 (807)
Q Consensus 315 sk~~g~s~~~tl~iaQ~LYE~-g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~ 389 (807)
|++|||||++||++||+|||+ ||||||||||++||++. ++.++|+.+.... +..+.....+. ..+.|+ .
T Consensus 294 s~~~g~s~~~tm~iAQ~LYE~~glITYpRTDS~~ls~~~~~~~~~~i~~~~~~~-~~~~~~~~~~~~~~~~~~~-----~ 367 (660)
T TIGR01056 294 NKRFGISAKRTLDIAQKLYETHKLITYPRTDSRYLPEDEKEMLLEVLDALKVIT-PALLPIKKRDELTNNRLWN-----D 367 (660)
T ss_pred HHhcCCCHHHHHHHHHHHHHhCCEEEEecCCCccCCHHHHHHHHHHHHHhhccc-hhhhcccccccccccCcCC-----C
Confidence 999999999999999999998 99999999999999986 4666666654321 11111111110 112221 1
Q ss_pred CCCCCCCCCcCCCCCCCCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccc
Q 046997 390 HDDKAHPPIHPTKFSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFES 469 (807)
Q Consensus 390 ~~~~aH~aI~PT~~~~~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~ 469 (807)
.+++||||||||...+....|+++|++||+||++||||+||+||+|++|+|++.++++.|+++|++++++||+.||+.+.
T Consensus 368 ~~~~aH~AI~PT~~~~~~~~L~~de~klY~LI~~Rflas~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~ 447 (660)
T TIGR01056 368 KKIEDHHAIIPTGNDFNLSDLSEEERNVYKLIAQNYLMQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQE 447 (660)
T ss_pred CccCCcCCccccCCccccccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECCEEEEEEEEEEcccCHHHHhcccc
Confidence 24679999999987666678999999999999999999999999999999999999999999999999999999997533
Q ss_pred c----CCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHH-----------------hCCCCCccchHHHHHh
Q 046997 470 W----GGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMD-----------------KAGIGTDATMHDHIKK 528 (807)
Q Consensus 470 ~----~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me-----------------~~GIGTpATra~iI~~ 528 (807)
. ++..||.|++||.+.+.++.+.+++|+||+||||++||++|| +.|||||||||+||++
T Consensus 448 ~~~~~~~~~LP~l~~G~~~~~~~~~~~~~~TkPP~ryTeasLi~~Me~~~k~v~d~~l~~~l~e~~GIGtpATrA~iI~~ 527 (660)
T TIGR01056 448 EDEETEDTTLPAFQKGDELDVETLELLEKQTKPPARYTEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGTEATRADIIEN 527 (660)
T ss_pred cccccccccCCCCCCCCEeeeeecccccCcCCCCCCcCHHHHHHHHHhhhhcccCHHHHHHhhhccCCCCcccHHHHHHH
Confidence 2 223599999999999999999999999999999999999999 7899999999999999
Q ss_pred hcccceEEEcCCceeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHH
Q 046997 529 LLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKK 608 (807)
Q Consensus 529 L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~ 608 (807)
|++||||+.+++ .|+||++|+.|++.|+. .|++|+|||.||..|++|++|+.++++||+++++.+.+.+.+...+.
T Consensus 528 L~~R~Yv~~~~k-~l~pT~~G~~v~~~L~~---~i~~~~~Ta~~E~~Ld~I~~G~~~~~~~~~~~~~~~~~~~~~~~~~~ 603 (660)
T TIGR01056 528 LFKRGFIQKKKN-KIYITKNGKLLCLLLPE---LLTKPDLTAQWEQYLNGISAGEKDDDDFINTINEMIKQTINEEKKNP 603 (660)
T ss_pred HHhCCCEEeeCC-EEEEcHHHHHHHHHhHH---hcCChhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence 999999997654 69999999999998863 69999999999999999999999999999999999888766544322
Q ss_pred HHhhhhhhhhhccCCCCCCcccccccccccCCCCCcceEEEecCCCCceeeccCCCCCCcc
Q 046997 609 VKLLEAMGIFFERWSGGEDQQAAGEVVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNA 669 (807)
Q Consensus 609 ~k~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~ 669 (807)
... .......|| | |+.|+.+++++|. |++|++||+|++.
T Consensus 604 ~~~-------------------~~~~~~~cp-c-g~~l~~~~~~~g~-f~~c~~~p~C~~~ 642 (660)
T TIGR01056 604 ETI-------------------QKVAKEPVS-C-GGIAKCPAKDNGR-LIDCKKFPECTEY 642 (660)
T ss_pred hhh-------------------cCCCCccCC-C-CCceeeeecCCCe-eecCCCCCCccCc
Confidence 111 012456799 9 6889999988886 6999999999864
No 10
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=100.00 E-value=5.1e-137 Score=1128.33 Aligned_cols=659 Identities=53% Similarity=0.872 Sum_probs=607.9
Q ss_pred ceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCC
Q 046997 8 INVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPAD 87 (807)
Q Consensus 8 ~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~ 87 (807)
|++|+||||+|+|+.+|.+|+++. .++++|.+.|+.+|+|+|...|..+++++|++.|||++++||.+|.+|..++|.+
T Consensus 1 ~~vl~vAekn~~ak~va~il~~g~-~~~re~rSk~~kiy~f~~~~~g~~~~~~mtsvsghl~~~~f~~~~s~w~s~~~~~ 79 (758)
T KOG1956|consen 1 MRVLCVAEKNSIAKSVASILSGGT-VRRREGRSKYNKIYDFDFNLFGQNCDVTMTSVSGHLTEADFPSEYSKWQSCPPDE 79 (758)
T ss_pred CCcccccccchhhhhhhhhcCCCC-cCCccchhhhhhhhhhhhhhcCCcceeEEeeccccccccCCcccccceeecCHHH
Confidence 679999999999999999999886 8899999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHc
Q 046997 88 LYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQN 167 (807)
Q Consensus 88 L~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~n 167 (807)
||++|+.+.++.+.+.+.++|++++++||.+|||||||||||+|||||+++|+..++...|.|+.||+||+.+|+.|.+|
T Consensus 80 lf~a~~~~~~~~~~~~i~~~ir~eAr~ad~LviwtDcDREGE~Ig~eI~~v~~~~~~~~~V~RA~Fs~it~~~I~sA~~n 159 (758)
T KOG1956|consen 80 LFDAPVIKSVPENAKDIAKTIREEARRADYLVIWTDCDREGENIGWEIIDVCRAVKRLLQVRRARFSEITRSAIKSAARN 159 (758)
T ss_pred HhhhhhhhcCchhhhHHHHHHHHHHhhcceEEEeccCCccchhhhHHHHHHHHhhCccceeehhhhhcccHHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999999999988999999999999999999999
Q ss_pred CCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhh-cccccccccCCcccccCccchhhHHHHHHHHHHHHcccccceE
Q 046997 168 LVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKN-FHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEFW 246 (807)
Q Consensus 168 l~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~-~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~ 246 (807)
|+++|+.+++|++||+++|++||..|||++|++|++ |.+ . ...++|+|+||+|||+|||||+++|++|+|+.||
T Consensus 160 lreid~~~v~AvdaR~ELDlrIGa~FTRlqT~~L~r~f~~--~---~~~viSyG~cQfpTLgfVvdR~~eIe~FvPEefW 234 (758)
T KOG1956|consen 160 LREIDEKLVHAVDARIELDLRIGAAFTRLQTLLLRRKFPI--L---GEQVISYGPCQFPTLGFVVDRYKEIENFVPEEFW 234 (758)
T ss_pred ccccchHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhhhh--h---hccccccccccCcceeeeeehHHHHhccCCcceE
Confidence 999999999999999999999999999999999987 542 1 2369999999999999999999999999999999
Q ss_pred EEEEEeecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHH
Q 046997 247 TINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTM 326 (807)
Q Consensus 247 ~i~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl 326 (807)
+|.+.+..+++..+|.|.++++||...+..+++.|.+.+.+.|+++.+++++++||+||+|++||+.|+++|.||+++||
T Consensus 235 tl~~~~~~~~~~~~fnw~R~~lfdr~s~~~~~e~c~e~k~a~Vv~~~kkpktKyrP~pl~TvELqK~~s~~lrlSak~TM 314 (758)
T KOG1956|consen 235 TLKFKHTHKGGLTEFNWKRGHLFDRLSVVILYEICVEEKEATVVKVTKKPKTKYRPLPLDTVELQKLASRKLRLSAKHTM 314 (758)
T ss_pred EEEEEEeccCceeEEeecccccccHHHHHHHHHHHhcccceeEEecccCCccCCCCCcchHHHHHhhhhhheeccHHHHH
Confidence 99999999999999999999999999999999999998899999999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCceeccCCCCcccCCcccHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCCCCCCCCCCcCCCCCCC
Q 046997 327 KVAEDLYQAGFISYPRTETDSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFSSG 406 (807)
Q Consensus 327 ~iaQ~LYE~g~ISYPRTds~~l~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~aH~aI~PT~~~~~ 406 (807)
+||++||.+|+||||||+++.||.+++++.+++.+..++.|+.||+++++... ++|++|+++|.||++|+||.....
T Consensus 315 ~iAE~ly~~gfisyprtetd~F~s~~~lk~lv~~qt~~~~wg~yA~~ll~~~~---r~Prng~~~d~Ahppihp~k~~s~ 391 (758)
T KOG1956|consen 315 KIAEKLYQKGFISYPRTETDNFPSDMDLKALVEKQTQDPAWGSYAQRLLQPEN---RNPRNGKHNDKAHPPIHPTKFTSR 391 (758)
T ss_pred HHHHHHHhccceeccccccccCCCcCchHHHHHhhccCchhHHHHHHhhccCC---CCCCCCccccccCCCccceeeccc
Confidence 99999999999999999999999999999999999888999999999998532 479999999999999999987766
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccCCccCCccCCCCeeee
Q 046997 407 ESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWGGLVIPTYVHGQQFIP 486 (807)
Q Consensus 407 ~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~~~ 486 (807)
..+|+.|+++||++|+||||||.+.||+..+|+|+++++.+.|.++|..+++.+|++||++++|++..||.|..|+.+.+
T Consensus 392 ~~~~s~d~~~vye~v~rhflAc~S~dakg~et~vel~~~~E~F~asgl~vl~~NyldVy~yekwe~k~Lp~y~~ge~fq~ 471 (758)
T KOG1956|consen 392 EANLSGDHRKVYELVVRHFLACCSQDAKGAETTVELDIAQERFSASGLRVLERNYLDVYPYEKWEDKQLPVYEDGELFQP 471 (758)
T ss_pred cccCCcchHHHHHHHHHHHHHhhcccccccceEEEEeehhhhccccccchhhccccccccccccccccCccccccccccc
Confidence 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEE-cCCceeeechhHHHHHhhccccCccccC
Q 046997 487 TTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIK-DANTRFAPTNIGEALVMGYDDMGYELWK 565 (807)
Q Consensus 487 ~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~-~~~~~l~pT~~G~~li~~l~~~~~~l~~ 565 (807)
..+++.++.|+||++|||++||+.|+++|||||||+|+||++|+.|+||.+ ++..+|+||.+|.+|+++|+.++.++++
T Consensus 472 ~~lem~~g~T~~P~~ltEaeLI~lMdk~GIGtdAT~aehi~kiq~R~Yv~~~~~~~~~~P~~lg~aLv~gyd~~g~e~sK 551 (758)
T KOG1956|consen 472 GELEMKDGETSPPKYLTEAELISLMDKNGIGTDATIAEHIEKIQERGYVTKKNKVGRFVPTFLGVALVEGYDDMGLEMSK 551 (758)
T ss_pred ceEEeccCccCCCCccCHHHHHHHHHHcCCCCchhHHHHHHHHHhhcceeeeccccccCchHHHHHHHHhHHhhhhhcCC
Confidence 999999999999999999999999999999999999999999999999987 4444588999999999999999999999
Q ss_pred chhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccccCCCCCcc
Q 046997 566 PNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKLLEAMGIFFERWSGGEDQQAAGEVVRQCGICQESN 645 (807)
Q Consensus 566 p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~~ 645 (807)
|.+||.||.+|++|+.|..++.++|.+++..++.+|.....+...+.+.+..|+.-.+.+. .+ |-- .+
T Consensus 552 p~lra~mE~~Lk~Is~G~~~k~~vl~~~v~kyra~f~~~~~~~~~l~~~l~~y~~~~a~~~-------~~---~~~--p~ 619 (758)
T KOG1956|consen 552 PFLRAEMEVDLKNISDGRKDKKEVLRDIVTKYRAYFHETERKIGCLGESLQRYLEFIASTL-------TG---PDD--PE 619 (758)
T ss_pred hHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc-------cC---CCC--CC
Confidence 9999999999999999999999999999999999998877665555555555554333110 00 110 11
Q ss_pred eEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEEEeeccCccCCCCCc
Q 046997 646 MVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPPGFN 711 (807)
Q Consensus 646 lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~ 711 (807)
+|| |..+.....+...||+||+.++++...++++|.+||.++
T Consensus 620 ----------------~~P--------p~~~l~~s~~~~v~p~cgp~p~y~~~~~~~rg~ipp~~~ 661 (758)
T KOG1956|consen 620 ----------------GEP--------PLLGLEGSTSEKVGPKCGPKPVYRQLGKFKRGGIPPAAN 661 (758)
T ss_pred ----------------CCC--------CCCCCCCCCCCccCCCCCCCCcceeccccCCCCCCCCCC
Confidence 344 223334455678899999888998888899999998765
No 11
>PRK06599 DNA topoisomerase I; Validated
Probab=100.00 E-value=1.4e-134 Score=1197.75 Aligned_cols=631 Identities=25% Similarity=0.391 Sum_probs=521.9
Q ss_pred CceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCC
Q 046997 7 PINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPA 86 (807)
Q Consensus 7 ~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~ 86 (807)
||++||||||||+|++||++||.+ ++||||+|||++|..| +..|. |.
T Consensus 1 m~~~LiIaEKPs~ak~Ia~~lg~~----------------------------~~V~~~~GHl~~l~~~--~~~~~---~~ 47 (675)
T PRK06599 1 MAKKLVIVESPAKAKTIKKYLGKD----------------------------YKVLASFGHVRDLPKK--KGGVD---PD 47 (675)
T ss_pred CCCeEEEEeCHHHHHHHHHHcCCC----------------------------CEEEecccchhcCCcc--ccCCC---cc
Confidence 778999999999999999999742 4799999999999543 33454 33
Q ss_pred CCCCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhh-cCCCCeEEEEEecccCHHHHHHHH
Q 046997 87 DLYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRA-VNCHLVLRRARFSALIDREIHQAV 165 (807)
Q Consensus 87 ~L~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~-~~~~~~v~R~~~s~lt~~~I~~A~ 165 (807)
+.+ ++.+.+.++++++++.|++++++||+||||||||||||+|||+|+++++. .+.+++|+|+|||++|+++|++||
T Consensus 48 ~~~--~~~~~~~~~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~~~~~~~v~Rl~~s~lt~~~I~~a~ 125 (675)
T PRK06599 48 NDF--APKYEIIEGKEKVVDALKKAAKKADAVYLATDPDREGEAIAWHIAEVLKEAKLKDKNVKRVVFNEITKKAVQEAI 125 (675)
T ss_pred cCC--CceEEECCcHHHHHHHHHHHHhhCCEEEECCCCCcchHHHHHHHHHHHHhhcCCCCCeeEEEEccCCHHHHHHHH
Confidence 322 33334556788999999999999999999999999999999999999952 123468999999999999999999
Q ss_pred HcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccce
Q 046997 166 QNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEF 245 (807)
Q Consensus 166 ~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y 245 (807)
+||++++.+|++||+||+++||+||||+||++|+.++ ..+|+||||||||+|||+||+||+||+|++|
T Consensus 126 ~n~~~~~~~l~~a~~aR~~~D~liG~n~tr~~t~~~~------------~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y 193 (675)
T PRK06599 126 ENPRDIDMDLVDAQQARRALDYLVGFKLSPLLWKKVR------------RGLSAGRVQSVALRLICEREDEIEAFIPQEY 193 (675)
T ss_pred hCcccCCHHHHHHHHHHHHHHHHhhhhhCHHHHHhcc------------CCCccceeHHHHhHHHHHhHHHHHhcCCCce
Confidence 9999999999999999999999999999999998763 2599999999999999999999999999999
Q ss_pred EEEEEEeec-CCceEEEEecc------C--CcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHH
Q 046997 246 WTINCSHKS-EEGTATFSWMR------G--HLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASR 316 (807)
Q Consensus 246 ~~i~~~~~~-~~~~~~~~~~~------~--r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask 316 (807)
|.|.+.+.. ++..|.+.|.. . |++|++.|+.+++.+... .++|++|+++++++.||+||||++||++|++
T Consensus 194 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~~~~-~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~ 272 (675)
T PRK06599 194 WTIEADLATSNGEPFTAKLVEVNGKKLEKFSITNEEQAKALVKALEGQ-AYTVDKIEKKERKRNPPPPFITSTLQQEASR 272 (675)
T ss_pred EEEEEEEEcCCCCeeEEEEEeccCccccccCCCCHHHHHHHHHHhcCC-CeEEEEEEeeEEecCCCCCCcHHHHHHHHHH
Confidence 999999876 45667766531 1 689999999999999754 6899999999999999999999999999999
Q ss_pred hcCCCHHHHHHHHHHHhhc--------CceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhcccccCCccCCC
Q 046997 317 YFRMSSEHTMKVAEDLYQA--------GFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPG 386 (807)
Q Consensus 317 ~~g~s~~~tl~iaQ~LYE~--------g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~ 386 (807)
+|||||++||++||+|||+ ||||||||||++||++. ++.+++..+.+ ..++....+.|++
T Consensus 273 ~~g~s~~~tl~~aQ~LYe~~~~~~~~~g~iSYPRTds~~l~~~~~~~~~~~l~~~~~--------~~~~~~~~~~~~~-- 342 (675)
T PRK06599 273 KLGFSAKKTMRIAQKLYEGIDLGEGTVGLITYMRTDSVRLSNEALDEARKYITKKYG--------KEYLPAKPRVYKK-- 342 (675)
T ss_pred HcCCCHHHHHHHHHHHHhccccccccceeEEeccCCCccCCHHHHHHHHHHHHHHhc--------hhhccccCcccCC--
Confidence 9999999999999999995 99999999999999874 45555554322 1122112344432
Q ss_pred CCCCCCCCCCCCcCCCCC--CCC--CCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEE--CCeEEEEEEEEEEecC
Q 046997 387 SGGHDDKAHPPIHPTKFS--SGE--SRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINI--AGEVFSTSGRVILAKN 460 (807)
Q Consensus 387 ~~~~~~~aH~aI~PT~~~--~~~--~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~--~~~~F~a~g~~i~~~G 460 (807)
+++.++.|||||+||... ++. +.|+++|++||+||+|||||+||+||+|++|+|++.+ +++.|.++|++++++|
T Consensus 343 ~~~~~~~aH~aI~Pt~~~~~~~~~~~~l~~~e~~iY~lI~~rfla~~~~~~~~~~t~v~~~~~~~~~~F~a~g~~~~~~G 422 (675)
T PRK06599 343 KSKNAQEAHEAIRPTSINRTPESLKPYLTPDQFKLYELIWKRTVASQMAPAILDQTSVDIASENGKYVFRATGSVILFPG 422 (675)
T ss_pred CCCCCCCCCCCCccCCCCCChhHhhccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEEcCCCeEEEEEEEEEEecC
Confidence 223356899999999863 222 5799999999999999999999999999999999999 9999999999999999
Q ss_pred eeeeecccccC-----CccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceE
Q 046997 461 YLDVYRFESWG-----GLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYA 535 (807)
Q Consensus 461 w~~v~~~~~~~-----~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv 535 (807)
|+++|+++.++ +..||.+.+||.+.+.++.+.+++|+||+||||++||++||++|||||||||+||++|++||||
T Consensus 423 w~~~~~~~~~~~~~~~~~~lp~~~~g~~~~~~~~~~~~~~T~PP~r~te~tLi~~Me~~GIGT~ATra~iIe~L~~r~Yi 502 (675)
T PRK06599 423 FLKVYGESKDDEEEDDEKLLPPLKEGEKLKLDELLPEQHFTEPPPRYSEASLVKKLEEYGIGRPSTYASIISTLQDREYV 502 (675)
T ss_pred eeeeeccccccccccccccCCCCCCCCEeeeeeeeecccccCCCCCCCHHHHHHHHhhCCCCccccHHHHHHHHhhCCeE
Confidence 99999764322 3459999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEcCCceeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 046997 536 IKDANTRFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKLLEAM 615 (807)
Q Consensus 536 ~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~~~~~ 615 (807)
+.+++ .|+||++|++|++.|....+.|++|+|||.||..|++|++|+.++++||+++++.+...+.+........
T Consensus 503 ~~~~~-~l~~T~~G~~l~~~l~~~~~~l~~p~lTa~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~---- 577 (675)
T PRK06599 503 ELEKK-RFIPTDLGRIVNDFLVEHFPKYVDYDFTAGLEDELDEIAEGKKDWKPVLREFWEPFISNLEKVEEDVRTE---- 577 (675)
T ss_pred EeeCC-EEeecHHHHHHHHHHHHhchhhCCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhhhhh----
Confidence 87754 6899999999999997655579999999999999999999999999999999998887665543321110
Q ss_pred hhhhccCCCCCCcccccccccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCcccccc-----ccCccCCCC
Q 046997 616 GIFFERWSGGEDQQAAGEVVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAV-----TTNTCNSCT 690 (807)
Q Consensus 616 g~fl~cs~~p~~~~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~-----t~~~CP~Cg 690 (807)
. . ........||.|+++.|+.+++++|. ||+|++||.|+++.|++........ ....||+|+
T Consensus 578 ~--~----------~~~~~~~~CP~C~~~~l~~k~~k~g~-F~~Cs~~p~C~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~ 644 (675)
T PRK06599 578 K--V----------TQEETDETCPKCGGGPLVLKLGKNGK-FLGCSGYPECKYTKNITRDEDEPIEEEEIVEEEKCPKCG 644 (675)
T ss_pred c--c----------cccccCccccccCCCcceEEecCCCc-eeeCCCCCccCCCCCCccccccccccccccccCCCCCCC
Confidence 0 0 00112468999966788888888887 6999999999999887642110011 112899999
Q ss_pred CCceEEEEeeccCccCCCCCccCcccc---CCCCChhH
Q 046997 691 PGPVYLIQFKFRQHEIPPGFNVNHLGC---IGGCDETL 725 (807)
Q Consensus 691 ~~~l~~~~~k~~~g~~~~~~~~~~~~C---~~~C~~~~ 725 (807)
.+ ++. ++++.+.+ ++| | .|+++.
T Consensus 645 ~~-~~~--kkgk~g~f--------~~Cs~yp-~ck~~~ 670 (675)
T PRK06599 645 GP-LVL--KKGRYGKF--------LACSGYP-ECKHIK 670 (675)
T ss_pred Ce-eEE--EeCCCCce--------eeCCCCC-CCCcee
Confidence 63 332 35555543 678 4 687654
No 12
>PRK05582 DNA topoisomerase I; Validated
Probab=100.00 E-value=2.5e-134 Score=1192.28 Aligned_cols=622 Identities=25% Similarity=0.385 Sum_probs=515.7
Q ss_pred CceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCC
Q 046997 7 PINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPA 86 (807)
Q Consensus 7 ~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~ 86 (807)
||++||||||||+|++||++||.+ ++|||+.|||++|..| .+. .+|.
T Consensus 1 mm~~LiIaEkps~a~~ia~~lg~~----------------------------~~V~~~~GHl~~l~~~-~~~----~~~~ 47 (650)
T PRK05582 1 MMKKLVIVESPAKAKTIEKYLGKN----------------------------YKVVASMGHIRDLPKS-QLG----IDIE 47 (650)
T ss_pred CCCeEEEEeCHHHHHHHHHHcCCC----------------------------CEEEeccCchhcCCCc-cCC----CCcc
Confidence 788999999999999999999742 4899999999999864 110 1121
Q ss_pred CCCCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHH
Q 046997 87 DLYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQ 166 (807)
Q Consensus 87 ~L~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~ 166 (807)
+.+ .|. +.+.++++++++.|++++++||+||||||||||||+|||||+++++... ++++|+||||+|+++|++||+
T Consensus 48 ~~~-~~~-~~~~~~~~~~~~~ik~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~~~--~~~~R~~~s~lt~~~I~~a~~ 123 (650)
T PRK05582 48 NNF-EPK-YITIRGKGPVIKELKKAAKKAKKVYLATDPDREGEAIAWHLAHILGLDE--KEKNRIVFNEITKDAIKNAFK 123 (650)
T ss_pred cCC-cee-eEECCcHHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhCCCC--CCceEEEEcccCHHHHHHHHh
Confidence 111 121 1334568899999999999999999999999999999999999997531 468999999999999999999
Q ss_pred cCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccceE
Q 046997 167 NLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEFW 246 (807)
Q Consensus 167 nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~ 246 (807)
||++++.+|++||+||+++||+||||+||++|+.++ ..+|+||||||||+|||+||+||+||+|++||
T Consensus 124 nl~~~~~~l~~a~~aR~~~D~liG~n~tr~~t~~~~------------~~ls~GRVQtPtL~lvv~Re~eI~~F~p~~y~ 191 (650)
T PRK05582 124 NPRKIDMNLVDAQQARRILDRLVGYKLSPLLWKKVK------------KGLSAGRVQSVALKLIIDREKEIRAFVPEEYW 191 (650)
T ss_pred CcccccHHHHHHHHHHHHHHHHhhhhcCHHHHHhhc------------CCCccccchHhHHHHHHhHHHHHHhCCCCccE
Confidence 999999999999999999999999999999998643 25999999999999999999999999999999
Q ss_pred EEEEEeecCCceEEEEec-----cCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCC
Q 046997 247 TINCSHKSEEGTATFSWM-----RGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMS 321 (807)
Q Consensus 247 ~i~~~~~~~~~~~~~~~~-----~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s 321 (807)
+|.+.+..+++.+.+.|. +++++|++.|+.+++.+.+ ..++|++|+++++++.||+||||++||++||++||||
T Consensus 192 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~v~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s 270 (650)
T PRK05582 192 TIDAEFKKGKKKFEASFYGYKGKKIELKNEEDVKEILAELKK-KDFKVSKVKKKERKRNPPPPFTTSTLQQEAARKLNFS 270 (650)
T ss_pred EEEEEEecCCccEEEEEEecCCCccccCCHHHHHHHHHHhcC-CCeEEEEEeeeeeecCCCCCccHHHHHHHHHHHcCCC
Confidence 999999766666777763 4589999999999999976 5799999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhh---------cCceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCC
Q 046997 322 SEHTMKVAEDLYQ---------AGFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGH 390 (807)
Q Consensus 322 ~~~tl~iaQ~LYE---------~g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 390 (807)
|++||++||+||| +||||||||||++||+++ .+.+++..+.+ ..++....+.+.++ ..
T Consensus 271 ~~~tl~~aQ~LYe~~~~~~~~~~gliSYPRTds~~l~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~---~k 339 (650)
T PRK05582 271 TKKTMMIAQQLYEGIDLGKQGTVGLITYMRTDSTRISDTAQEEAREFIEEKYG--------KEYLPKKPKVYKKK---SG 339 (650)
T ss_pred HHHHHHHHHHHhcccccCCCCceEEEEecCCCcccCCHHHHHHHHHHHHHHhH--------HHhhccCCcccCCC---cC
Confidence 9999999999999 699999999999999975 34444443211 12222111222221 23
Q ss_pred CCCCCCCCcCCCCC--CCC--CCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeec
Q 046997 391 DDKAHPPIHPTKFS--SGE--SRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYR 466 (807)
Q Consensus 391 ~~~aH~aI~PT~~~--~~~--~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~ 466 (807)
.++|||||+||... ++. +.|+++|++||+||+|||||+||+||+|++|+|.++++++.|.++|++++++||+.||+
T Consensus 340 ~~~~H~aI~PT~~~~~p~~~~~~L~~~e~~iY~lI~~rfla~~~~~~~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~~~~ 419 (650)
T PRK05582 340 AQDAHEAIRPTSVFLTPESAKKYLTKDQLKLYKLIWNRFVASQMAPAVFDTVSVDLENNGVKFRASGSKVKFDGFMKVYV 419 (650)
T ss_pred CCCCCCCEeecCCCcChhHHhccCCHHHHHHHHHHHHHHHHHhCchhheeEEEEEEEeCCEEEEEEEEEEeeCChHhhcC
Confidence 45699999999863 332 57999999999999999999999999999999999999999999999999999999997
Q ss_pred ccccCCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeec
Q 046997 467 FESWGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPT 546 (807)
Q Consensus 467 ~~~~~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT 546 (807)
.+..++..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||+.+++ .|+||
T Consensus 420 ~~~~~~~~lp~l~~g~~~~~~~~~~~~~~T~PP~~~Te~~Ll~~Me~~GIGT~ATra~iI~~L~~r~Yi~~~~k-~l~pT 498 (650)
T PRK05582 420 GDEEKDKMLPELEEGEKVKLKKIEPEQHFTQPPARYTEASLIKTLEELGIGRPSTYAPTISTIQKRGYVKLEKK-RLVPT 498 (650)
T ss_pred CcccccccCCCCCCCCEeEEEEeeecccccCCCCCCCHHHHHHHHHHcCCCCcccHHHHHHHHHhCCeEEeeCC-EEeec
Confidence 54444557999999999999999999999999999999999999999999999999999999999999987654 69999
Q ss_pred hhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCCC
Q 046997 547 NIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKLLEAMGIFFERWSGGE 626 (807)
Q Consensus 547 ~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~~~~~g~fl~cs~~p~ 626 (807)
++|++|+++|+...++|++|+|||.||..|++|++|+.++++||+++.+++++.+.+....... +. + .
T Consensus 499 ~~G~~l~~~l~~~~~~l~~p~lTa~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~----~~-~------~- 566 (650)
T PRK05582 499 ELGEIVNELLEEFFPDIVDVEFTAEMEEKLDEIEEGKEDWKKVLDDFYKPFEKEIEKAEKEIEK----IK-I------K- 566 (650)
T ss_pred HHHHHHHHHHHHhchhhcCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhhhc----cc-c------c-
Confidence 9999999999876567999999999999999999999999999999999998876654321110 00 0 0
Q ss_pred CcccccccccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEEEeeccCccC
Q 046997 627 DQQAAGEVVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEI 706 (807)
Q Consensus 627 ~~~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~ 706 (807)
.......||+| ++.++.+.+++|. ||+|++||.|++..+.+. .....||+|+. .++.+ ++++++.
T Consensus 567 ----~~~~~~~CP~C-g~~l~~~~~k~gk-f~~Cs~~~~C~~~~~~~~------~~~~~CP~C~~-~l~l~--k~k~gk~ 631 (650)
T PRK05582 567 ----DEPAGEDCPKC-GSPMVIKMGRYGK-FIACSNFPDCRNTKPIVK------EIGVKCPKCGG-QIVER--KSKKGRK 631 (650)
T ss_pred ----ccccCCCCCCC-CCEeEEEecCCCc-eeecCCccccccCCCccc------ccCCCCCCCCC-ceEEE--cCCCCce
Confidence 00123579999 5678877777776 699999999999876532 13467999985 44432 3444543
Q ss_pred CCCCccCccccCC--CCChh
Q 046997 707 PPGFNVNHLGCIG--GCDET 724 (807)
Q Consensus 707 ~~~~~~~~~~C~~--~C~~~ 724 (807)
+ ++|.. .|++.
T Consensus 632 f-------~~Cs~~p~C~~~ 644 (650)
T PRK05582 632 F-------YGCSRYPECDFV 644 (650)
T ss_pred e-------eccCCCCCCCcc
Confidence 3 67831 68754
No 13
>PRK14724 DNA topoisomerase III; Provisional
Probab=100.00 E-value=1.4e-134 Score=1225.82 Aligned_cols=613 Identities=24% Similarity=0.312 Sum_probs=503.8
Q ss_pred ceEEEEEcChHHHHHHHHHhCCCC-CcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccC-cCcCCCC
Q 046997 8 INVLNVAEKPSVAKSVAGILSKNQ-GLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYR-KWHSCDP 85 (807)
Q Consensus 8 ~~~LiIaEKPs~Ak~IA~~Lg~~~-~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~-~W~~~~p 85 (807)
|++||||||||+|++||++|+... +..+++|+ ++|. +++||||+|||++|.+|++|. .|..|+.
T Consensus 1 Mk~LiIAEKPSvAk~IA~aL~~~~g~~~k~~gy------------~eg~--~~~Vtwa~GHL~eL~~Pe~y~~~~~~W~~ 66 (987)
T PRK14724 1 TKTLVIAEKPSVAQDIVRALTPVAGKFEKHDEH------------FESD--SYVVTSAVGHLVEIQAPEEFDVKRGKWSF 66 (987)
T ss_pred CCEEEEEeCHHHHHHHHHHhhhccCCCcCCCce------------ecCC--CEEEEecccccccCCChhhcccccCCccc
Confidence 568999999999999999995221 12355662 2343 589999999999999998874 3444444
Q ss_pred CCCCCCCc--ccccCCChHHHHHHHHHHHh--hcCeEEEeecCChhhhHHHHHHHHHhhhc--CCCCeEEEEEecccCHH
Q 046997 86 ADLYHAPV--RKHVPEDKKDIKKTLEEEAR--RCQWLVLWLDCDREGENIAFEVIEVCRAV--NCHLVLRRARFSALIDR 159 (807)
Q Consensus 86 ~~L~~~p~--~~~v~~~k~~~~~~lk~~~~--~~d~IiiAtD~DREGE~I~~ei~~~~~~~--~~~~~v~R~~~s~lt~~ 159 (807)
.+|+.+|. ...+.+++++++++|+++++ ++|+||||||||||||+|+|+|+++++.. +.+++|+||||||||++
T Consensus 67 ~~LPiiP~~f~~~~~~~~k~q~~~Ik~l~k~~~~~~II~AtD~DREGElI~~~I~~~~~~~~~~~~kpv~Rlw~sslT~~ 146 (987)
T PRK14724 67 ANLPVIPPYFDLKPVDKTKTRLNAVVKLAKRKDVTELVNACDAGREGELIFRLIEQYAGGAKGGLGKPVKRLWLQSMTPQ 146 (987)
T ss_pred cccccCCccceeeeccchHHHHHHHHHHHhhCCCCeEEECCCCCcchhHHHHHHHHHhCcccccCCCceEEEEEccCCHH
Confidence 45555553 23355667889999999995 45799999999999999999999999752 12368999999999999
Q ss_pred HHHHHHHcCCCCC--cchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHH
Q 046997 160 EIHQAVQNLVDPN--QWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEI 237 (807)
Q Consensus 160 ~I~~A~~nl~~~~--~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI 237 (807)
+|++||+||++.+ .+|++||+||+++|||||||+||++|++.+..+ ...++|+||||||||+|||+||+||
T Consensus 147 aI~~af~nlr~~~~~~~L~~Aa~aR~~aDwLvG~N~SR~~T~~~~~~~-------~~~~lSvGRVQTPtL~lVv~Re~eI 219 (987)
T PRK14724 147 AIRDGFDNLRSDAQMQGLASAARSRSEADWLVGINGTRAMTAFNSRDG-------GFFLTTVGRVQTPTLSLVVEREEKI 219 (987)
T ss_pred HHHHHHhCCCCchhhhhHHHHHHHHHHHHHHhHHHHhHHHHHHHHhcC-------CcceeccccchhHHHHHHHHHHHHH
Confidence 9999999999887 489999999999999999999999998544210 1126899999999999999999999
Q ss_pred HcccccceEEEEEEeecCCceEEEEec--------------cCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCC
Q 046997 238 QAHESEEFWTINCSHKSEEGTATFSWM--------------RGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPY 303 (807)
Q Consensus 238 ~~F~p~~y~~i~~~~~~~~~~~~~~~~--------------~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~ 303 (807)
+||+|++||+|.+.+..+++.+.+.|. .++++|++.|+.+++.|.+ ..++|++ +.+++++.||+
T Consensus 220 ~~F~p~~Y~~i~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~A~~i~~~~~~-~~~~V~~-~~k~~~~~pP~ 297 (987)
T PRK14724 220 RKFVSRDYWEIHAGFHAEAGEYLGKWFDPQWKKASDDPEARADRVWSEREARAIADAVRG-KAATVTE-ESKPTTQASPL 297 (987)
T ss_pred HhCCCCccEEEEEEEecCCCceeEEEeecccccccccccccccccCCHHHHHHHHHHhcC-CCeEEEE-eeeeEecCCCC
Confidence 999999999999999887788888773 1578999999999999976 4689998 89999999999
Q ss_pred CCCHHHHHHHHHHhcCCCHHHHHHHHHHHhhc-CceeccCCCCcccCCcc--cHHHHHHHHhcC--CCchhhHHhhcc--
Q 046997 304 PLSTIELEKRASRYFRMSSEHTMKVAEDLYQA-GFISYPRTETDSFSSGT--NLHGIVQEQIGH--PDWGPYAQRLLD-- 376 (807)
Q Consensus 304 pf~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~-g~ISYPRTds~~l~~~~--~~~~il~~~~~~--~~~~~~~~~~l~-- 376 (807)
||||++||++||++|||||++||+|||+|||+ ||||||||||+|||+++ .+..+|+.+... +.|..++...++
T Consensus 298 pf~Lt~LQ~eA~~~~g~Sa~~TL~iAQ~LYE~~klITYPRTDS~~l~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~ 377 (987)
T PRK14724 298 LFDLTSLQREANGKFGFSAKTTLALAQSLYERHKALTYPRTDSRALPEDYLPVAKQTFEMLATSGMRHLAPFAQQALDGN 377 (987)
T ss_pred CCcHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCeEeecCcCCccCCHHHHHHHHHHHHHHhcccchhHHHHHHHHhccc
Confidence 99999999999999999999999999999996 99999999999999986 567777776432 234444443332
Q ss_pred ---cccCCccCCCCCCCCCCCCCCCcCCCCCCCCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEE
Q 046997 377 ---HAAGLWRNPGSGGHDDKAHPPIHPTKFSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSG 453 (807)
Q Consensus 377 ---~~~~~~~~~~~~~~~~~aH~aI~PT~~~~~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g 453 (807)
...+.|++. .+.||||||||...+ ..||++|++||+||+|||||+|||||+|+.|+|++.++++.|.++|
T Consensus 378 ~~~~~~r~~~~~-----Kv~~H~AIiPT~~~p--~~Ls~~E~kiY~lI~rRfla~f~~~a~~~~t~v~~~~~~~~F~a~G 450 (987)
T PRK14724 378 YVRPSKRIFDNS-----KVSDHFAIIPTTQAP--SGLSEAEQKLYDLVVRRFMAVFFPSAEYQVTTRISQVVGHSFKTEG 450 (987)
T ss_pred ccCCCCCcCCCC-----CCCCcCCcCCCCCCc--ccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEecCcEEEEEE
Confidence 112233221 236999999998765 6899999999999999999999999999999999999999999999
Q ss_pred EEEEecCeeeeecccc----------cCCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHH-----------
Q 046997 454 RVILAKNYLDVYRFES----------WGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMD----------- 512 (807)
Q Consensus 454 ~~i~~~Gw~~v~~~~~----------~~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me----------- 512 (807)
++++++||++||+.+. .++..||.|++||.+.+.++.+.+++|+||+||||++||++||
T Consensus 451 ~~i~~~GW~~vy~~~~~~~~~~~~~~~~~~~LP~l~~Ge~v~~~~~~~~e~~TkPP~ryTEatLl~aME~~gk~v~d~el 530 (987)
T PRK14724 451 KVLVKPGWLAIYGKEAANEVEDAKDGDKGQPLVPVKPGEMVRTEFAEAKGLKTKPPARYSEATLLGAMESAGKQIDDDEL 530 (987)
T ss_pred EEECcCChHHHhCccccccccccccccccccCCCcCCCCEeeeeeccccccccCCCCCcCHHHHHHHHHhhhhcccchhh
Confidence 9999999999986432 1123599999999999999999999999999999999999999
Q ss_pred -----hCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccC-ccccCchhhHHHHHHHHHHHcCCCCh
Q 046997 513 -----KAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMG-YELWKPNLRSMMESDMKEVSVGNKSK 586 (807)
Q Consensus 513 -----~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~-~~l~~p~~Ta~~E~~L~~I~~G~~~~ 586 (807)
+.|||||||||+||++|++||||+++++ .|+||++|+.||+.|+... .+|++|+|||.||..|++|++|+.++
T Consensus 531 ~~~~~~~GIGTpATRA~IIe~L~~r~Yi~~~~k-~l~pT~~G~~li~~L~~~~~~~l~~pelTa~wE~~L~~I~~G~~~~ 609 (987)
T PRK14724 531 REAMQEKGLGTPATRAAIIEGLLTEKYMLREGR-ELIPTAKAFQLMTLLRGLGVEELSRAELTGEWEYKLAQMEKGQLSR 609 (987)
T ss_pred hhhhhcCCCCCcccHHHHHHHHHhCCcEEecCC-EEeEcHHHHHHHHHHHhcCchhhcChhHHHHHHHHHHHHHhCCCCH
Confidence 5699999999999999999999998654 6899999999999997643 36999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhccCCCCCCcccccccccccCCCCCcceEEEecCCCCceeeccCC---
Q 046997 587 ADVLANCLQQMKACFLDARLKKVKLLEAMGIFFERWSGGEDQQAAGEVVRQCGICQESNMVLKKSRDGNLMVGCLAF--- 663 (807)
Q Consensus 587 ~~~l~~~~~~~~~~~~~~~~~~~k~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~y--- 663 (807)
++||+++.+++.+.+.+....... .+.. ......++||+| ++.++. .++ +|+|+++
T Consensus 610 ~~fl~~i~~~~~~~v~~~~~~~~~-------~~~~--------~~~~~~~~CP~C-g~~~~~----~~~-~~~Cs~~~~~ 668 (987)
T PRK14724 610 EAFMQQIAAMTEKLVKKAKEYDRD-------TIPG--------DYATLSTPCPNC-GGVVKE----NYR-RYACTGANGA 668 (987)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccc-------cccc--------ccccccccCCcc-cccccc----cCc-eeecCCCcCC
Confidence 999999999988766554321000 0000 000113689999 465521 122 4999995
Q ss_pred -CCCCcceec
Q 046997 664 -PQCRNAVWL 672 (807)
Q Consensus 664 -P~C~~~~~~ 672 (807)
++|+|++|.
T Consensus 669 ~~~C~f~~~k 678 (987)
T PRK14724 669 GEGCGFSFTK 678 (987)
T ss_pred CCCCCcccch
Confidence 379999874
No 14
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=100.00 E-value=4.3e-133 Score=1209.17 Aligned_cols=625 Identities=23% Similarity=0.348 Sum_probs=517.7
Q ss_pred eEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCccccccc-----ccccCcCcCC
Q 046997 9 NVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDF-----DERYRKWHSC 83 (807)
Q Consensus 9 ~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~-----p~~y~~W~~~ 83 (807)
+.|||||||++|++|+++||.+ ++|+|++|||++|.. |++|+.|. |
T Consensus 2 ~~LvIvEkP~kak~I~~~Lg~~----------------------------~~V~~s~GHi~dL~~~~~~~~~~~k~~~-w 52 (859)
T PRK07561 2 KSLVIVESPAKAKTINKYLGSD----------------------------YVVKASVGHIRDLPTSASSVPAKEKGAL-W 52 (859)
T ss_pred CEEEEEeCHHHHHHHHHHcCCC----------------------------CEEEeccCChhhCCCccccChhhhhhch-H
Confidence 3699999999999999999842 479999999999986 44555442 2
Q ss_pred C--CCCCC-CCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHH
Q 046997 84 D--PADLY-HAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDRE 160 (807)
Q Consensus 84 ~--p~~L~-~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~ 160 (807)
+ |.+.. .+.+.+.+..+++++++.|++++++||+||||||||||||+|+|||+++++. .+++|+|+|||+||+++
T Consensus 53 ~~l~i~~~~~f~~~y~~~~~k~~~~~~lk~~~k~ad~iilAtD~DREGE~I~~~i~~~l~~--~~~~v~Ri~f~~iT~~a 130 (859)
T PRK07561 53 ARMGVDPDHDFEALYEVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGG--DDVPVKRVVFNEITKNA 130 (859)
T ss_pred hhcCcCcccCcceeEEECccHHHHHHHHHHHHhcCCEEEECCCCCccchHHHHHHHHHhCC--CCCCeEEEEEccCCHHH
Confidence 2 11111 1122345567789999999999999999999999999999999999999973 34689999999999999
Q ss_pred HHHHHHcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcc
Q 046997 161 IHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAH 240 (807)
Q Consensus 161 I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F 240 (807)
|++||+|++++|++|++||+||+++|||||||+||++|..++ ..||+||||||||+|||+||+||++|
T Consensus 131 I~~A~~n~~~~~~~l~~A~~aRr~lD~lvG~~lS~~l~~~~~------------~~lSaGRVQsp~L~lIv~Re~eI~~F 198 (859)
T PRK07561 131 IQEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIA------------RGLSAGRVQSVAVRLIVEREREIEAF 198 (859)
T ss_pred HHHHHhCcccCCHHHHHHHHHHHHHHHHhhhhcCHHHHHhhc------------cCCCcccchhhhhHHHHHHHHHHHhc
Confidence 999999999999999999999999999999999999887643 26999999999999999999999999
Q ss_pred cccceEEEEEEeec-CCceEEEEec--cC------CcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHH
Q 046997 241 ESEEFWTINCSHKS-EEGTATFSWM--RG------HLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELE 311 (807)
Q Consensus 241 ~p~~y~~i~~~~~~-~~~~~~~~~~--~~------r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq 311 (807)
+|++||.|.+.+.. +++.|.+.|. .+ +++|++.|+.+++.+.+ ..++|++|+.+++++.||+||+|++||
T Consensus 199 ~p~~yw~i~~~~~~~~~~~f~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~pp~pf~ts~LQ 277 (859)
T PRK07561 199 VPEEYWDIHADLTTPRGDAFEARLTHLDGKKFAPVDLLNEAQAEAAVAALEG-ARYSVASVEDKPTTRKPSAPFTTSTLQ 277 (859)
T ss_pred CCCccEEEEEEEEecCCCeEEEEEEeeCCceecccccCCHHHHHHHHHHhcC-CCeEEEEEEeceeEecCCCCccHHHHH
Confidence 99999999999976 5566777653 22 47899999999999975 478999999999999999999999999
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCC
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGG 389 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 389 (807)
++||++|||||++||++||+|||.||||||||||++||++. ++.++|..+ |+ ..+++..++.|.+. ++
T Consensus 278 ~~As~klg~s~~~tm~~aQ~LYE~glITYpRTDs~~ls~~~~~~~~~~i~~~-----~g---~~~~~~~~r~~~~~--~k 347 (859)
T PRK07561 278 QEASRKLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIGDN-----YG---KKYLPEKPRQYSSK--AK 347 (859)
T ss_pred HHHHHhcCCCHHHHHHHHHHHHhCCeEEecCCCCCcCCHHHHHHHHHHHHHH-----hh---hhhcccCCccCCCc--CC
Confidence 99999999999999999999999999999999999999864 345555543 22 23444334555432 23
Q ss_pred CCCCCCCCCcCCCCC--CCC-CCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeec
Q 046997 390 HDDKAHPPIHPTKFS--SGE-SRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYR 466 (807)
Q Consensus 390 ~~~~aH~aI~PT~~~--~~~-~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~ 466 (807)
.+++||||||||... ++. ..|+++|++||+|||+||||+||+||+|++|+|++.++++.|+++|++++++||+.||.
T Consensus 348 ~~q~aHeAI~Pt~~~~~~~~~~~L~~~e~~lY~LI~~R~lAs~m~~a~~~~~~v~~~~~~~~F~a~g~~i~~~G~~~vy~ 427 (859)
T PRK07561 348 NAQEAHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKRFVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYV 427 (859)
T ss_pred CCCCCcCCcccCCCCcChhhhccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCCEEEEEEEEEEeeCCchheec
Confidence 467899999999653 322 47999999999999999999999999999999999999999999999999999999997
Q ss_pred cccc-----CCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCc
Q 046997 467 FESW-----GGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANT 541 (807)
Q Consensus 467 ~~~~-----~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~ 541 (807)
.+.+ ++..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.++++
T Consensus 428 ~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~T~PP~ryTeasLv~~me~~GIGtpsT~a~iI~~L~~R~Yv~~~~~- 506 (859)
T PRK07561 428 EGRDDALDDEDRRLPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRLENR- 506 (859)
T ss_pred cccccccccccccCCCCCCCCEeeeeeeEecccccCCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhhcCeEEeeCC-
Confidence 5432 2346999999999999999999999999999999999999999999999999999999999999998654
Q ss_pred eeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhcc
Q 046997 542 RFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKLLEAMGIFFER 621 (807)
Q Consensus 542 ~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~~~~~g~fl~c 621 (807)
.|+||++|+.|++.|....+.|++|+|||.||..|++|++|+.++++||+++++.|...+.+..... . .+..
T Consensus 507 ~l~pT~~G~~v~~~l~~~f~~l~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~-~----~~~~--- 578 (859)
T PRK07561 507 RFYPEKMGRIVTDRLEEFFPRLVDYDFTARMEEELDDIANGEADWKPVLDDFYKDFSQQLEKAEELR-E----EGGM--- 578 (859)
T ss_pred EEeecHHHHHHHHHHHHhhhhhcCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhhhc-c----cccc---
Confidence 6999999999999998765689999999999999999999999999999999998887665443221 0 0000
Q ss_pred CCCCCCcccccccccccCCCCCcceEEEecCCCCceeeccCC---CCCCcceecCCCcc---------ccccccCccCCC
Q 046997 622 WSGGEDQQAAGEVVRQCGICQESNMVLKKSRDGNLMVGCLAF---PQCRNAVWLPGSVS---------EAAVTTNTCNSC 689 (807)
Q Consensus 622 s~~p~~~~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~y---P~C~~~~~~p~~~~---------~~~~t~~~CP~C 689 (807)
. ..........||.| |+.|++|.+++|. ||+|++| |+|++..+++.... ........||+|
T Consensus 579 -~----~~~~~~~~~~CP~C-g~~l~~r~gr~G~-Fl~Cs~y~~~p~C~~~~~l~~~~~~~~~~~~~~~~~~~lg~~P~c 651 (859)
T PRK07561 579 -R----PNQMVITDRDCPTC-GRGMGIRTGKTGV-FLGCSGYALKERCKTTRNLTPEEETLNVLEGEDAETRALGADPEC 651 (859)
T ss_pred -c----ccccccccccCccc-CCcceEEecCCCC-eeeccCCcCCCCCCCCCCCCccchhhhhhhccccCccccCCCCCC
Confidence 0 00011235789999 5679999999997 5999999 99999988764210 000113458999
Q ss_pred CCCceEEEEeeccCccC
Q 046997 690 TPGPVYLIQFKFRQHEI 706 (807)
Q Consensus 690 g~~~l~~~~~k~~~g~~ 706 (807)
|. +++. +.+|+|.+
T Consensus 652 g~-~i~~--r~Gr~Gpy 665 (859)
T PRK07561 652 GT-AMVL--RSGRFGPY 665 (859)
T ss_pred CC-eeEE--ecCCCCCe
Confidence 95 4543 35666643
No 15
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=100.00 E-value=1.1e-132 Score=1168.24 Aligned_cols=580 Identities=25% Similarity=0.382 Sum_probs=495.7
Q ss_pred EEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCCCC
Q 046997 11 LNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADLYH 90 (807)
Q Consensus 11 LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L~~ 90 (807)
||||||||+|++||++||.+ ++||||.|||++|+.|+.+.+|+. + +
T Consensus 1 LiIaEkps~a~~Ia~~lg~~----------------------------~~Vt~~~GHl~~l~~~~~~~~~~~----~-~- 46 (610)
T TIGR01051 1 LVIVESPAKAKTIKKYLGDE----------------------------YEVEASMGHIRDLPKSRLGVDIEK----D-F- 46 (610)
T ss_pred CEEEeChHHHHHHHHHhCCC----------------------------CEEEeccCeeccCCCcccCCChhh----c-C-
Confidence 79999999999999999742 479999999999988866666753 1 1
Q ss_pred CCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHcCCC
Q 046997 91 APVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQNLVD 170 (807)
Q Consensus 91 ~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~nl~~ 170 (807)
++.+.+.+++++++++|++++++||+||||||||||||+|+|+|+++++..++ .++|+|||+||+++|++||+||++
T Consensus 47 -~~~~~~~~~~~~~~~~i~~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~~~~--~~~Rl~~s~lt~~~I~~a~~~l~~ 123 (610)
T TIGR01051 47 -EPEYVVSKGKKKVVKELKTLAKKADEVYLATDPDREGEAIAWHLAEVLKPKDP--VYKRIVFNEITKKAIRAALKNPRE 123 (610)
T ss_pred -ceeEEEcccHHHHHHHHHHHHhcCCEEEECCCCCcchhHHHHHHHHHhCCCCC--CceEEEEccCCHHHHHHHHhCccc
Confidence 22344556788999999999999999999999999999999999999986443 249999999999999999999999
Q ss_pred CCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccceEEEEE
Q 046997 171 PNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEFWTINC 250 (807)
Q Consensus 171 ~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~~i~~ 250 (807)
+|.+|++||.||+++||||||||||++|+.++ ..+|+||||||||+|||+||+||+||+|++||.|.+
T Consensus 124 ~~~~l~~aa~aR~~~D~liG~n~Tr~~t~~~~------------~~lSvGRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~ 191 (610)
T TIGR01051 124 IDMNLVNAQQARRILDRLVGYTLSPLLWKKVA------------KGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDA 191 (610)
T ss_pred cchhHHHHHHHHHHHHHHHhHhhhHHHHHhhc------------CCCCcceehHHHHHHHHHHHHHHHhcCCCceEEEEE
Confidence 99999999999999999999999999997542 259999999999999999999999999999999999
Q ss_pred EeecCCceEEEEec--------cCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCH
Q 046997 251 SHKSEEGTATFSWM--------RGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSS 322 (807)
Q Consensus 251 ~~~~~~~~~~~~~~--------~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~ 322 (807)
.+..+++.|.+.|. .++++|++.|+.+++.+.+ ..++|++|+.+++++.||+||||++||++||++|||||
T Consensus 192 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~S~ 270 (610)
T TIGR01051 192 TFQKGEETFEALLTEVNGKKLKAGSDLDEAEATALKEQLKG-EELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSA 270 (610)
T ss_pred EEecCCcceEEEEEecCCccccccccCCHHHHHHHHHHhcC-CCeEEEEEeeceeeeCCCCCcCHHHHHHHHHHhcCCCH
Confidence 99877778887773 2478999999999999975 47999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhc--------CceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCCCC
Q 046997 323 EHTMKVAEDLYQA--------GFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDD 392 (807)
Q Consensus 323 ~~tl~iaQ~LYE~--------g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 392 (807)
++||++||+|||+ ||||||||||++||++. .+..++..+.. ..+++...+.+ +.+++..+
T Consensus 271 ~~tl~iaQ~LYe~~~~~~~~~g~iSYPRTds~~l~~~~~~~~~~~l~~~~~--------~~~~~~~~~~~--~~~~k~~~ 340 (610)
T TIGR01051 271 KKTMMIAQRLYEGVSTGDGTIGLITYMRTDSTRLSNQAVNEARNLIDKNYG--------KEYLGPKPKRY--KSKEKNAQ 340 (610)
T ss_pred HHHHHHHHHHHhcccccCCceeEEeecCcCccccCHHHHHHHHHHHHHhhh--------HhhccccCccc--CCCCCCCC
Confidence 9999999999999 99999999999999975 34444443311 12222111122 22223245
Q ss_pred CCCCCCcCCCCC--CCC--CCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEE--CCeEEEEEEEEEEecCeeeeec
Q 046997 393 KAHPPIHPTKFS--SGE--SRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINI--AGEVFSTSGRVILAKNYLDVYR 466 (807)
Q Consensus 393 ~aH~aI~PT~~~--~~~--~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~--~~~~F~a~g~~i~~~Gw~~v~~ 466 (807)
.||||||||... ++. +.|+++|++||+||+|||||+||+||+|++|+|++.+ +++.|.++|++++++||++||+
T Consensus 341 ~~H~aI~Pt~~~~~~~~~~~~Ls~~e~~iY~lI~rr~la~~~~~~~~~~t~v~~~~~~~~~~F~a~g~~i~~~Gw~~v~~ 420 (610)
T TIGR01051 341 EAHEAIRPTSVFRTPEELKDYLKRDEFRLYELIWKRFVASQMADARYDSTSVRLTNEDGEYVFKATGRKLIFDGYYKVYV 420 (610)
T ss_pred CCcCCCCCCCCCcChhhhhccCCHHHHHHHHHHHHHHHHHhCccceEEEEEEEEEEcCCCeEEEEEEEEEEeCCHHHhcc
Confidence 899999999863 332 4799999999999999999999999999999999999 9999999999999999999997
Q ss_pred cccc-----CCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCc
Q 046997 467 FESW-----GGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANT 541 (807)
Q Consensus 467 ~~~~-----~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~ 541 (807)
.+.. ++..||.+.+||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||+++++
T Consensus 421 ~~~~~~~~~~~~~Lp~l~~g~~~~~~~~~~~~~~T~PP~~yTe~tLl~~Me~~GIGTpATra~iIe~L~~r~Yi~~~~~- 499 (610)
T TIGR01051 421 EGSDDPLEEKDRILPPLKEGDAVKLVEVKPNQHFTQPPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKKENK- 499 (610)
T ss_pred cccccccccccccCCCCCCCCEeEeeeeeeccccccCCCCCCHHHHHHHHhcCCCCccccHHHHHHHHhhCCeEEeeCC-
Confidence 5421 2346999999999999999999999999999999999999999999999999999999999999997654
Q ss_pred eeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhcc
Q 046997 542 RFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVKLLEAMGIFFER 621 (807)
Q Consensus 542 ~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k~~~~~g~fl~c 621 (807)
.|+||++|+.|+++|+...++|++|+|||.||..|++|++|+.++++||+++.+++.+.+.+..... .
T Consensus 500 ~l~pT~~G~~li~~l~~~~~~l~~p~lTa~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~v~~~~~~~-------~----- 567 (610)
T TIGR01051 500 RLYPTELGFAVTDLLEKHFGDVVDYDFTAKMEKDLDEIAEGKAEWKPVLKNFYTGFSSKVKKLRNMR-------I----- 567 (610)
T ss_pred EEeECHHHHHHHHHHHHhhhhhcCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhhhcc-------c-----
Confidence 6999999999999998765579999999999999999999999999999999998877654432110 0
Q ss_pred CCCCCCcccccccccccCCCCCcceEEEecCCCCceeeccCCCCCCcceec
Q 046997 622 WSGGEDQQAAGEVVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWL 672 (807)
Q Consensus 622 s~~p~~~~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~ 672 (807)
.. ......+||+| ++.+..+++++|+ ||+|+|||+|+++.++
T Consensus 568 ~~-------~~~~~~~CP~C-g~~~~~~~~~~gk-f~gCs~y~~C~~~~~l 609 (610)
T TIGR01051 568 IV-------DFKTSQDCPLC-GRPMVVKLGKYGP-FLACSNFPECKYTKSI 609 (610)
T ss_pred cc-------ccccCCCCCCC-CCeeEEEecCCCc-eeeCCCCCCCCCCCCC
Confidence 00 00124689999 5778888888887 5999999999987653
No 16
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=100.00 E-value=6.5e-131 Score=1128.30 Aligned_cols=545 Identities=31% Similarity=0.461 Sum_probs=478.2
Q ss_pred eEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCC
Q 046997 9 NVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADL 88 (807)
Q Consensus 9 ~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L 88 (807)
+.|||||||++||+||++||.+ ++|+|++|||++|++|++++.|...+ +
T Consensus 1 ~~LiIvEsPskAk~Ia~~Lg~~----------------------------~~V~as~GHi~dl~~~~~~~~~~~~~---~ 49 (570)
T COG0550 1 KRLIIVESPSKAKTIAKYLGKG----------------------------YVVTASVGHLRDLPFPEEYKGWVDVD---L 49 (570)
T ss_pred CeEEEEeCHHHHHHHHHhcCCC----------------------------cEEEEcccccccCCChhhccCCcCCc---c
Confidence 3699999999999999999963 48999999999999999988887643 2
Q ss_pred CCCCcccccCCC-hHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHc
Q 046997 89 YHAPVRKHVPED-KKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQN 167 (807)
Q Consensus 89 ~~~p~~~~v~~~-k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~n 167 (807)
..++....+.+. ++.+++.|+.++++||.||||||||||||+|||||+++++..++ .+++|+|||+||+++|++||+|
T Consensus 50 ~~~~~~~~~~~~~k~~~v~~lk~~ak~ad~v~lAtD~DREGE~I~~~i~~~l~~~~~-~~~~R~~F~eiT~~aI~~A~~~ 128 (570)
T COG0550 50 PIFEPKYIIKPGKKKKVVKKLKKLAKKADEVYLATDPDREGEAIGWHILEVLKLKNP-SKVKRVVFSEITKKAILSAFKN 128 (570)
T ss_pred cccccceeccchhhHHHHHHHHHHhccCCEEEECCCCCcchHHHHHHHHHHhCccCC-CceeEEEEecCCHHHHHHHHhC
Confidence 222222333344 78888999999999999999999999999999999999987654 4699999999999999999999
Q ss_pred CCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccceEE
Q 046997 168 LVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEFWT 247 (807)
Q Consensus 168 l~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~~ 247 (807)
++++|++|++||+||+++|||||+|+||++|+.+++ + +||+||||||||+|||+||+||++|+|++||+
T Consensus 129 p~~id~~lv~A~~aR~~lD~lvG~~lSr~l~~~~~~----------~-~LSaGRVQSpaL~lVveRE~EI~~F~p~~yw~ 197 (570)
T COG0550 129 PREIDMNLVDAQLARRILDRLVGYNLSRLLWKKLKR----------G-VLSAGRVQSPALRLVVEREREIEAFVPEEYWE 197 (570)
T ss_pred chhhchHHHHHHHHHHHHHHHhhhhhhHHHHHhhcc----------C-CCCCccccchhhhhhHhhHHHHHhCCCCcceE
Confidence 999999999999999999999999999999987642 1 69999999999999999999999999999999
Q ss_pred EEEEeecCCceEEEEecc------CCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCC
Q 046997 248 INCSHKSEEGTATFSWMR------GHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMS 321 (807)
Q Consensus 248 i~~~~~~~~~~~~~~~~~------~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s 321 (807)
|.+.+..+++.|.+.|.. .++.+...|..+++.+.+ ..+.|+++++++++..||+||+|++||++||++||||
T Consensus 198 i~a~~~~~~~~f~a~~~~~~~~~~~~~~~~~~a~~~~~~l~~-~~~~V~~ve~k~~~~~pp~Pf~tstLQq~As~~lgfs 276 (570)
T COG0550 198 IKAIFEKGGGEFSARLTEIEGKKEGRLKDKDEAEEIVNKLKG-KPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFS 276 (570)
T ss_pred EEEEEecCCccEEEEEeccccccccccccHHHHHHHHHHccC-CceEEEEEeeeeeccCCCCCCcHHHHHHHHHHhCCCC
Confidence 999998877668888862 366788899999999984 4799999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhc-CceeccCCCCcccCCcccHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCCCCCCCCCCcC
Q 046997 322 SEHTMKVAEDLYQA-GFISYPRTETDSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHP 400 (807)
Q Consensus 322 ~~~tl~iaQ~LYE~-g~ISYPRTds~~l~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~aH~aI~P 400 (807)
|++||+|||+|||. ||||||||||++||++........ +.... |+..+++..++. .+++++++++|||||||
T Consensus 277 ~kktm~iAQ~LYE~~glITYpRTDs~~ls~~~~~~~~~~-i~~~~----yg~~~l~~~~~~--~~~~~~~~q~AHeAIrP 349 (570)
T COG0550 277 AKKTMDIAQKLYEGHGLITYPRTDSTRLSEEALAEARLY-ILAIA----YGKEYLPLKPRR--YPSKGKKAQEAHEAIRP 349 (570)
T ss_pred HHHHHHHHHHHhcCCCcEEecCCCCCcCCHHHHHHHHHH-HHhhc----cHHhhccccccc--CCCCCCCCcCCCCCcCC
Confidence 99999999999998 999999999999999763222211 11110 556666532222 34455678899999999
Q ss_pred CC-CCCCCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeeccc--ccCCccCCc
Q 046997 401 TK-FSSGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFE--SWGGLVIPT 477 (807)
Q Consensus 401 T~-~~~~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~--~~~~~~lP~ 477 (807)
|. ..+....+ .||++||+|||||||||||+||+|+.++|++.++++.|+++|++++++||++||++. .+.+..||.
T Consensus 350 T~~~~p~~~~~-~de~klY~LI~rrflAs~m~~A~~~~~~v~l~~~~~~F~a~g~~~~~~Gw~~vy~~~~~~~~~~~lP~ 428 (570)
T COG0550 350 TDFETPESLKA-YDELKLYDLIWRRFLASQMPDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEEDKELPE 428 (570)
T ss_pred CCCCCcccccc-hhHHHHHHHHHHHHHHHhCchhhheEEEEEEEecCcEEEEeeeEEecCcHHHhhcccccccccccCCC
Confidence 97 33322233 799999999999999999999999999999999999999999999999999999865 335678999
Q ss_pred cCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhcc
Q 046997 478 YVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYD 557 (807)
Q Consensus 478 l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~ 557 (807)
+++||.+.+.++++.+++|+||+|||||+||++||+.|||||||||+||++|++||||..++ +.|+||++|+.|++.|+
T Consensus 429 l~~gd~l~~~~~~~~~~~T~PP~rytEasLvk~mE~~GIGrpSTyA~iI~~L~~RgYv~~~~-~~~~pT~~G~~v~~~L~ 507 (570)
T COG0550 429 LKEGDELKVEKLEVEEHFTKPPPRYTEASLVKAMEKLGIGTPSTYASIIETLQKRGYVEKKG-KRLVPTELGEAVIELLE 507 (570)
T ss_pred CCCCCeeEEeeeeecccccCCcCCCCHHHHHHHHHhCCCCCcccHHHHHHHHhcCCcEEecC-CeeEEcHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999875 46999999999999999
Q ss_pred ccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHH
Q 046997 558 DMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARL 606 (807)
Q Consensus 558 ~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~ 606 (807)
...+.+++|+|||.||+.||+|++|+.+|++||++++..+.+.+.....
T Consensus 508 ~~f~~l~~~~~Ta~mE~~Ld~I~~gk~~~~~~l~e~~~~~~~~~~~~~~ 556 (570)
T COG0550 508 EYFPELVDPDFTAKMEEKLDEIAEGKLEWKDVLDEFKKKFSKLLEEAKK 556 (570)
T ss_pred HhchhhcCHHHHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHh
Confidence 8878999999999999999999999999999999999988887665443
No 17
>PRK08780 DNA topoisomerase I; Provisional
Probab=100.00 E-value=3.8e-129 Score=1159.96 Aligned_cols=585 Identities=23% Similarity=0.341 Sum_probs=494.8
Q ss_pred CceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCC
Q 046997 7 PINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPA 86 (807)
Q Consensus 7 ~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~ 86 (807)
|++.|||||||++|++|+++||.+ ++|+|+.|||++|..|+.+- |+.
T Consensus 1 m~~~LiIvEsPskAk~I~~~Lg~~----------------------------y~V~as~GHi~dL~~~~~~v-----d~~ 47 (780)
T PRK08780 1 MSKHLVIVESPAKAKTINKYLGKD----------------------------FTVLASYGHVRDLVPKEGAV-----DPE 47 (780)
T ss_pred CCCeEEEEeCHHHHHHHHHHcCCC----------------------------CEEEeccCCcccCCCcccCC-----Chh
Confidence 678899999999999999999852 47999999999998776531 111
Q ss_pred CCCCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcC--CCCeEEEEEecccCHHHHHHH
Q 046997 87 DLYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVN--CHLVLRRARFSALIDREIHQA 164 (807)
Q Consensus 87 ~L~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~--~~~~v~R~~~s~lt~~~I~~A 164 (807)
..| .+.+.+..+++++++.|++++++||.||||||||||||+|||||+++++..+ +.++++|+|||+||+++|++|
T Consensus 48 ~~f--~~~y~~~~~k~~~~~~lk~~~k~ad~vilAtD~DREGE~Ia~~i~~~l~~~~~~~~~~v~Ri~f~eiT~~aI~~A 125 (780)
T PRK08780 48 NGF--AMRYDLIDKNEKHVEAIAKAAKSADDLYLATDPDREGEAISWHLAEILKERGLLKDKPMQRVVFTEITPRAIKEA 125 (780)
T ss_pred hCC--ceEEEEcCchHHHHHHHHHHHHhCCEEEECCCCCcccHHHHHHHHHHhcccccCCCCceEEEEEccCCHHHHHHH
Confidence 111 1123345678889999999999999999999999999999999999997432 246899999999999999999
Q ss_pred HHcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccc
Q 046997 165 VQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEE 244 (807)
Q Consensus 165 ~~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~ 244 (807)
|+|++++|++|++||+||+++|||||||+||++|..++ ..+|+||||||||+|||+||+||++|+|++
T Consensus 126 ~~n~r~~d~~l~~A~~aRr~lD~lvG~~lSr~l~~~~~------------~~lSaGRVQspaL~lIveRE~eI~~F~p~~ 193 (780)
T PRK08780 126 MAKPRDIASDLVDAQQARRALDYLVGFNLSPLLWRKIQ------------RGLSAGRVQSPALRMIVEREEEIEAFIARE 193 (780)
T ss_pred HhCCCcCcHhHHHHHHHHHHHHHhcCeeecHHHHHhhC------------CCCcccccHHHHHHHHHHHHHHHHhCCCcc
Confidence 99999999999999999999999999999999987653 259999999999999999999999999999
Q ss_pred eEEEEEEeecCCceEEEEecc--------CCcCCHHHHHHHHHHhcc--CCCeEEEEEEeeeeeeCCCCCCCHHHHHHHH
Q 046997 245 FWTINCSHKSEEGTATFSWMR--------GHLFDYTSAVIIYEMCVQ--EPTATVTKVRQQEKLKYPPYPLSTIELEKRA 314 (807)
Q Consensus 245 y~~i~~~~~~~~~~~~~~~~~--------~r~~d~~~a~~~~~~~~~--~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~a 314 (807)
||.|.+.+..++..|.+.|.. .+++|++.|+.+++.|.. ...++|++|+++++++.||+||+|++||++|
T Consensus 194 yw~i~~~~~~~~~~f~a~~~~~~~~~~~~~~~~~~~~a~~i~~~~~~~~~~~~~V~~v~~k~~~~~pp~Pf~tstLQq~A 273 (780)
T PRK08780 194 YWSIEADCAHPSQPFNAKLIKLDGQKFEQFTITDGDTAEAARLRIQQAAQGTLHVTDVESKERKRNPAPPFTTSTLQQEA 273 (780)
T ss_pred eEEEEEEEecCCceEEEEEEecCCccccccccCCHHHHHHHHHHHhhccCCCeEEEEEEeeeeecCCCCCccHHHHHHHH
Confidence 999999998767778777642 358899999999999864 2468999999999999999999999999999
Q ss_pred HHhcCCCHHHHHHHHHHHhhc---------CceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhcccccCCcc
Q 046997 315 SRYFRMSSEHTMKVAEDLYQA---------GFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDHAAGLWR 383 (807)
Q Consensus 315 sk~~g~s~~~tl~iaQ~LYE~---------g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~ 383 (807)
|++|||||++||++||+|||. ||||||||||++||++. ++.++|..+ |+. .++....+.|.
T Consensus 274 s~klg~s~~~Tm~iAQ~LYE~~~~~~~~~~glITYpRTDS~~ls~~~~~~~~~~i~~~-----~g~---~~~~~~~~~~~ 345 (780)
T PRK08780 274 SRKLGFTTRRTMQVAQKLYEGVDLGDEGSVGLITYMRTDSVNLSQDALAEIRDVIARD-----YGT---ASLPDQPNTYK 345 (780)
T ss_pred HHHcCCCHHHHHHHHHHHHhhcccccCCceeEEEecccCCccCCHHHHHHHHHHHHHH-----hCh---hhhhhcccccC
Confidence 999999999999999999997 99999999999999864 344444433 221 22221123332
Q ss_pred CCCCCCCCCCCCCCCcCCCCC--CC--CCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECC-eEEEEEEEEEEe
Q 046997 384 NPGSGGHDDKAHPPIHPTKFS--SG--ESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAG-EVFSTSGRVILA 458 (807)
Q Consensus 384 ~~~~~~~~~~aH~aI~PT~~~--~~--~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~-~~F~a~g~~i~~ 458 (807)
.+++++++||||||||... ++ ...|+++|++||+||||||||+||+||+|++|+|.+.+++ +.|+++|+++++
T Consensus 346 --~~~~~~q~aHeAI~PT~~~~~p~~~~~~L~~de~klY~LI~~R~lAs~m~~a~~~~t~v~~~~~~~~~F~a~G~~i~~ 423 (780)
T PRK08780 346 --TKSKNAQEAHEAVRPTSALRTPAQVARFLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAGSEHVFRATGSTVVV 423 (780)
T ss_pred --CCCCCCcCCCCCCCCCCCCcChhhhhccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEeCCeeEEEEEEEEEeE
Confidence 2234568899999999754 22 1479999999999999999999999999999999999987 799999999999
Q ss_pred cCeeeeeccccc------CC--ccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhc
Q 046997 459 KNYLDVYRFESW------GG--LVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLL 530 (807)
Q Consensus 459 ~Gw~~v~~~~~~------~~--~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~ 530 (807)
+||+++|.+..+ ++ ..||.|.+||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|+
T Consensus 424 ~G~~~vy~~~~~~~~~~~~~~~~~LP~l~~G~~~~~~~~~~~~~~T~PP~ryTEasLik~mE~~GIGtpST~A~iI~~L~ 503 (780)
T PRK08780 424 PGFLAVYEEGKDDKSAEDEDEGRKLPPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGRPSTYASIISTLQ 503 (780)
T ss_pred cCeEEeeccccccccccccchhccCCCcCCCCEeeeeeeeeeeeecCCCCCCCHHHHHHHHHhCCCCchhhHHHHHHHHH
Confidence 999999975321 11 4699999999999999999999999999999999999999999999999999999999
Q ss_pred ccceEEEcCCceeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHHHHHHHHHHHH
Q 046997 531 DRFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKACFLDARLKKVK 610 (807)
Q Consensus 531 ~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~~~k 610 (807)
+|+||.++++ .|+||++|+.|++.|....+.|++|+|||.||..|++|++|+.+|++||+++++.|...+.+.......
T Consensus 504 ~R~Yv~~~~k-~l~pT~~G~~v~~~L~~~f~~l~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~~~~~~~~~~~~~~~~~i~~ 582 (780)
T PRK08780 504 FRKYVEMEGR-RFRPTDVGRAVNKFLTGHFTRYVDYDFTARLEDDLDAVSRGEKEWIPLMEKFWGPFKELVEEKKDSVDR 582 (780)
T ss_pred hCCcEeccCC-EEeecHHHHHHHHHHHHhchhcCCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 9999997655 599999999999999776568999999999999999999999999999999999988766553332111
Q ss_pred hhhhhhhhhccCCCCCCcccccccccccCCCCCcceEEEecCCCCceeec-----cCCCCCC
Q 046997 611 LLEAMGIFFERWSGGEDQQAAGEVVRQCGICQESNMVLKKSRDGNLMVGC-----LAFPQCR 667 (807)
Q Consensus 611 ~~~~~g~fl~cs~~p~~~~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gC-----s~yP~C~ 667 (807)
... ......+.||+| |+.|+++.+++|. |+.| ++||.|-
T Consensus 583 ----~~~------------~~~r~lG~cP~C-G~~l~~r~gr~G~-fl~~g~~~~~~~p~~a 626 (780)
T PRK08780 583 ----TEA------------GQVRELGTDPKS-GKPVSVRIGRFGP-MVQIGTKDDEEKPRFA 626 (780)
T ss_pred ----ccc------------cccccCCCCCCC-CCEEEEEeCCCCC-eeeccCcccccccccc
Confidence 000 001235689999 6899999999998 5999 5689884
No 18
>PRK09401 reverse gyrase; Reviewed
Probab=100.00 E-value=5e-115 Score=1071.36 Aligned_cols=532 Identities=26% Similarity=0.348 Sum_probs=448.5
Q ss_pred CCceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCC
Q 046997 6 RPINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDP 85 (807)
Q Consensus 6 ~~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p 85 (807)
.+.++||||||||+|++||++||.+. +++.|+ .++||+.. |+ ..++|||+.|||++|+.|++|..|...+
T Consensus 599 ~~k~~LiIaEkPskAk~IA~~lg~~~--~r~~g~---~~~ye~~~---~~-~~~~Vt~s~GHl~dL~~~~~y~g~~~~~- 668 (1176)
T PRK09401 599 LIKTTLLIVESPTKARTIANFFGRPS--RRRIGG---LVVYETVT---GD-RILTITASKGHVYDLTTEIGYYGVLVKD- 668 (1176)
T ss_pred cCCCEEEEEcCHHHHHHHHHHhCCCc--cccCCC---ceeEEEec---CC-cEEEEEEeccccccCCCccccCcccccC-
Confidence 45789999999999999999999764 344452 23455432 22 2348999999999999999999887533
Q ss_pred CCCCCCCcccc------------------------cCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhh
Q 046997 86 ADLYHAPVRKH------------------------VPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRA 141 (807)
Q Consensus 86 ~~L~~~p~~~~------------------------v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~ 141 (807)
++..|.... ..++++++++.|++++++||+||||||||||||+|||+|+++++.
T Consensus 669 --~p~~P~y~~~k~c~~~g~~f~~~~~~~~~c~~~~~~~k~~~~~~Lr~l~~~~d~IiiAtDpDrEGE~Ia~~i~~~l~~ 746 (1176)
T PRK09401 669 --GGFVPVYDTIKRCRDCGYQFTDESDKCPRCGSTNIEDKEEIIEALRELALEVDEVLIATDPDTEGEKIAWDLYLLLSP 746 (1176)
T ss_pred --CcccceeeeeccccccccccccccccccccccccCCCHHHHHHHHHHHHhcCCEEEEccCcChhHHHHHHHHHHHhcc
Confidence 222342111 115688999999999999999999999999999999999999975
Q ss_pred cCCCCeEEEEEecccCHHHHHHHHHcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCc
Q 046997 142 VNCHLVLRRARFSALIDREIHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGP 221 (807)
Q Consensus 142 ~~~~~~v~R~~~s~lt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GR 221 (807)
.+ ++|+|+|||++|+++|++||+|++++|.+|++||.|||++||+|||||||++|+.+++ ..+|+||
T Consensus 747 ~~--~~i~R~~f~eiT~~aI~~A~~n~r~~~~~l~~A~~aRr~~D~~iG~~lSr~l~~~~~~-----------~~lSaGR 813 (1176)
T PRK09401 747 YN--SNIKRIEFHEVTRKAILEALRNPRDVNENLVKAQIVRRIEDRWIGFELSQKLQKKFGK-----------RNLSAGR 813 (1176)
T ss_pred cC--CCEEEEEeecCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-----------cCccccc
Confidence 33 4799999999999999999999999999999999999999999999999999976532 3699999
Q ss_pred cchhhHHHHHHHHHHHHcccccceEEEEEEeecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCC
Q 046997 222 CQFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYP 301 (807)
Q Consensus 222 VQtPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~p 301 (807)
||||||+|||+|++||++|++ ||.+ ... .++..+.+.| +++|++.|+.+++.+. +|.+++.++++++|
T Consensus 814 VQTPtL~~IVeRe~ei~~f~~--~~~~-~~~-~~~~~~~~~~---~~~~~~~a~~~~~~l~-----~V~~v~~k~~~~~p 881 (1176)
T PRK09401 814 VQTPVLGWIVERYKEYKKSKG--YVLV-IKL-ENGGGLELEG---EFSEKEEAEKFYNNLI-----EVEKVEEKEEELNP 881 (1176)
T ss_pred cccchhhhhhhhHHHhcccCC--EEEE-EEe-cCCceEEEEE---eeCCHHHHHHHHHhCC-----eeeEEEeeEEEecC
Confidence 999999999999999999965 4444 332 3455566654 5789999999888774 78999999999999
Q ss_pred CCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhccccc
Q 046997 302 PYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDHAA 379 (807)
Q Consensus 302 P~pf~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~~~ 379 (807)
|+||||++||++||++|||||++||++||+|||+||||||||||+++|++. .+..+++.+.+. .+
T Consensus 882 P~Pf~t~~Lq~~As~~lg~Sa~~tm~iAQ~LYE~glITYpRTDS~~ls~~~~~~a~~~l~~~~~~--------~~----- 948 (1176)
T PRK09401 882 LPPYTTDTLLSDASRKLRLSAQETMRIAQDLFELGLITYHRTDSTRVSDVGISVAKEYLEKRGGE--------EY----- 948 (1176)
T ss_pred CCCCccHHHHHHHHHHcCCCHHHHHHHHHHHHhCCceeecCCCCCcCCHHHHHHHHHHHHHhhCc--------cc-----
Confidence 999999999999999999999999999999999999999999999999853 233444433211 01
Q ss_pred CCccCCCCCCCCCCCCCCCcCCCCCCC--------------CCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEEC
Q 046997 380 GLWRNPGSGGHDDKAHPPIHPTKFSSG--------------ESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIA 445 (807)
Q Consensus 380 ~~~~~~~~~~~~~~aH~aI~PT~~~~~--------------~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~ 445 (807)
+ .|+.. .+++||||||||...+. ...||++|++||+||+|||||+||+||+|++|++.+.++
T Consensus 949 --~-~~r~~-~~~~aH~AI~PT~~~~~~~l~~~~~~g~~~~~~~Lt~~e~~lY~LI~rRflAs~~~~a~~~~t~v~~~~~ 1024 (1176)
T PRK09401 949 --F-VPRSW-GEGGAHEAIRPTRPLDAEELRQMIEEGILKLSEGLTKNHLRLYDLIFRRFMASQMKPAKVRYQKVLIKAD 1024 (1176)
T ss_pred --c-CCCCC-CCCCCcCCcCccCCCCchhhhhhhccccccccccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEEC
Confidence 1 23322 24789999999985432 147999999999999999999999999999999999999
Q ss_pred CeEEEEE-EEEEEecCeeeeecccccCCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHH
Q 046997 446 GEVFSTS-GRVILAKNYLDVYRFESWGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHD 524 (807)
Q Consensus 446 ~~~F~a~-g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~ 524 (807)
++.|.++ |++++++||+.+|+.. .+|.++.|+.+.. ++.++|+||+|||||+||++||+.|||||||||+
T Consensus 1025 ~~~f~~~~g~~i~~~Gw~~v~~~~-----~~p~~~~g~~~~~----~~~~~~~pp~~yTea~Li~~Me~~GIGtpAT~A~ 1095 (1176)
T PRK09401 1025 GKELELELVVEILEDGFNKVLPLK-----LYPLLEGKVKVKE----KKTYKKSKVPLYTQGDLISEMKERGIGRPSTYAK 1095 (1176)
T ss_pred CEEEEEeeeeEEeeCChheeeccc-----cCCCCCCCCEeee----eccccCCCcCCCCHHHHHHHHHhCCCCCcCcHHH
Confidence 9999999 9999999999999753 3889999998763 5666666799999999999999999999999999
Q ss_pred HHHhhcccceEEEcCC-ceeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHHH
Q 046997 525 HIKKLLDRFYAIKDAN-TRFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKAC 600 (807)
Q Consensus 525 iI~~L~~R~Yv~~~~~-~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~ 600 (807)
||++|++||||..+++ +.|+||++|++|++.|....+.|++|++||.||+.|++|++|+.++++||+++++.+++.
T Consensus 1096 IIe~L~~R~YV~~~~~~k~l~pT~~G~~l~~~L~~~~~~l~s~e~Ta~~E~~ld~Ie~G~~~~~~~l~~~~~~i~~~ 1172 (1176)
T PRK09401 1096 IVETLLRRGYVIESKGKKRLIPTKLGIKVYEYLSEKYKDLVSEERTRKLEEKMDKVEEGKEDYQEVLKELYEEIKEL 1172 (1176)
T ss_pred HHHHHhccCcEEEcCCcceEeECHHHHHHHHHHHHhhhhcCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Confidence 9999999999986443 469999999999999976555799999999999999999999999999999999887653
No 19
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=100.00 E-value=2e-113 Score=1003.13 Aligned_cols=549 Identities=21% Similarity=0.276 Sum_probs=428.4
Q ss_pred EEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeec----cccCCCceEEEEeccCcccccccccccCcCcCC--
Q 046997 10 VLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNY----SIRGQPCHMLMTSVTGHLMELDFDERYRKWHSC-- 83 (807)
Q Consensus 10 ~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~----~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~-- 83 (807)
-|+|+|+|++.-.+...|+.++ . . |-|.|.- .++-+....+...+.||.+.|..- .|.--
T Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~-~--~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~ 76 (805)
T PTZ00407 11 KLVIVESPNKVIKVEGLLSDPK-V--I-------PDWSFKQSHLRRIGTGAEKAVAMATTGHFMALKEI----TWSPQAS 76 (805)
T ss_pred heeEEecCCceEEEeecccCCC-c--C-------CCcccccccceeeccchHHHHHHhhcccceeehhe----ecccCCC
Confidence 4899999999999988888764 1 0 1121111 122223346777889999998631 12200
Q ss_pred CCCC-----CCCCCc---------ccccCCChH--HHHH-HHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcC--C
Q 046997 84 DPAD-----LYHAPV---------RKHVPEDKK--DIKK-TLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVN--C 144 (807)
Q Consensus 84 ~p~~-----L~~~p~---------~~~v~~~k~--~~~~-~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~--~ 144 (807)
.|.. -..+|- .+.+.+++. +++. .|++++++||+||||||||||||+|+|||+++++..+ .
T Consensus 77 ~~~~~~~~~~~~~~~~~~~~~f~~~y~~~~~~~~~~~i~~~i~~~ak~ad~IIlATDpDREGE~Ia~hIle~l~~~~~~~ 156 (805)
T PTZ00407 77 SPASVVGAGDEPFPSNGTLAEYTLEWELLPGRRIQETLERYIEEKADNVTEIILATDPDREGELIAVHALQTIKRLYPKL 156 (805)
T ss_pred CCcccCCCCCCCCCCCCceEEEEEEEEEcCCCchhHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhchhcccc
Confidence 0000 001111 123334443 4444 6999999999999999999999999999999998543 2
Q ss_pred CCeEEEEEecccCHHHHHHHHHcC--CCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCcc
Q 046997 145 HLVLRRARFSALIDREIHQAVQNL--VDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPC 222 (807)
Q Consensus 145 ~~~v~R~~~s~lt~~~I~~A~~nl--~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRV 222 (807)
+++++|+|||+||+++|++||+|+ +++|++|++||+|||++|||||||+||+++... ...+|+|||
T Consensus 157 ~k~v~Rv~FseITk~aI~~A~~nlkp~~~d~~L~~Aa~ARr~lD~LVG~nlS~~l~~~~------------~~~lSaGRV 224 (805)
T PTZ00407 157 KVPFSRAYMHSITEDGIRKAMRERHVEACDYDLANAAETRHAMDRIFGFLGSSVVRAAN------------SQMRSIGRV 224 (805)
T ss_pred CCcceEEEEccCCHHHHHHHHhCCCCCcccHhHHHHHHHHHHHHHHhhhhhhHHHHhhc------------cCceeeccc
Confidence 458999999999999999999994 667889999999999999999999999987532 237999999
Q ss_pred chhhHHHHHHHHHHHHccccc--ceEEEEEEeec---CCceEEEEec------c--CCcCCHHHHHHHHHHhc--cCCCe
Q 046997 223 QFPTLGFVVERYWEIQAHESE--EFWTINCSHKS---EEGTATFSWM------R--GHLFDYTSAVIIYEMCV--QEPTA 287 (807)
Q Consensus 223 QtPtL~lIv~Re~eI~~F~p~--~y~~i~~~~~~---~~~~~~~~~~------~--~r~~d~~~a~~~~~~~~--~~~~~ 287 (807)
|||||+|||+||+||++|+|+ +||.|.+.+.. ++..|.+.|. . .++.|++.|+.+++.+. ....+
T Consensus 225 QTPtL~LIVeRE~EIe~Fkpee~~Yw~I~a~~~~~~~~g~~F~a~~~~~~~~~~~~~~~~~~~eA~~~~~~~~~~~~~~~ 304 (805)
T PTZ00407 225 QTPALILINEREDKIKAFLESNKSTFEVQAMCQFPSPHGTTFSQVVTITPDRKGGASHWATEAEARRCLEQWKLNNCTGF 304 (805)
T ss_pred chHHHHHHHHHHHHHHhcCCccCceEEEEEEEeecCCCCcceeEEeeccccccccccccCCHHHHHHHHHHhhhccCCcE
Confidence 999999999999999999999 59999988752 3456766553 1 24668889998888764 22346
Q ss_pred EEE-EEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccCCCCcccCCcccHHHHHHHHhcCCC
Q 046997 288 TVT-KVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTETDSFSSGTNLHGIVQEQIGHPD 366 (807)
Q Consensus 288 ~V~-~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTds~~l~~~~~~~~il~~~~~~~~ 366 (807)
+|. .+++++++++||+||||++||++||++|||||++||++||+|||.||||||||||++||++. +.++...+.. .
T Consensus 305 ~V~~~v~~k~kk~~PP~PF~tstLQqeAsrkLG~Sa~kTM~iAQ~LYE~GlITYPRTDS~~l~~e~-~~~i~~~I~~--~ 381 (805)
T PTZ00407 305 SVPLEPKPQPSVVPPPQPFTMATAIAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESA-LPDIYAAVKK--E 381 (805)
T ss_pred EEEEEEEEEEEEcCCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCceeccCCCCCcCCHHH-HHHHHHHHHH--h
Confidence 663 46679999999999999999999999999999999999999999999999999999999986 3333332221 1
Q ss_pred chhhHHhhc----------ccccCCccC-----CCCCC-------CCCCCCCCCcCCCCCCCC--CCCCHHHHHHHHHHH
Q 046997 367 WGPYAQRLL----------DHAAGLWRN-----PGSGG-------HDDKAHPPIHPTKFSSGE--SRWSQDHYKLYELVV 422 (807)
Q Consensus 367 ~~~~~~~~l----------~~~~~~~~~-----~~~~~-------~~~~aH~aI~PT~~~~~~--~~Ls~~e~~vY~lI~ 422 (807)
|+ .+++ ....+.+.. ++++. +.++|||||+||...... ..|+++|++||+|||
T Consensus 382 ~g---~~~l~~~~~~~~~~~~~~~~~k~~k~~~~~~k~~~d~~~~kvqeAHeAIrPT~~~~~~~~~~Ls~de~kLYdLI~ 458 (805)
T PTZ00407 382 FG---KEFLYRLEDRTVSAQEGKGSKKTGKKRSTKQKKGADTPVGNVEDAHEAIRPTNIDTTGESLSLSPPTRAVYDLVR 458 (805)
T ss_pred hh---hhhhhhhcccccccccccccccccccccccccccccccccCCCCCcCCCCccCCCCChhhccCCHHHHHHHHHHH
Confidence 21 2222 101111110 01111 234589999999876543 369999999999999
Q ss_pred HHHHHhcCcccEEEEEEEEEEEC-----CeEEEEEEEEEEecCeeeeecccc----------c------C--CccCCccC
Q 046997 423 RHFLACVSQPAVGAETIVEINIA-----GEVFSTSGRVILAKNYLDVYRFES----------W------G--GLVIPTYV 479 (807)
Q Consensus 423 rrfla~~~~~a~~~~t~v~~~~~-----~~~F~a~g~~i~~~Gw~~v~~~~~----------~------~--~~~lP~l~ 479 (807)
|||||+||+||+|++|+|++.+. ++.|+++|++++++||++||++.. . + +..||.|+
T Consensus 459 rRfLAs~m~~a~~e~t~v~i~~~~~~g~~~~F~asGk~v~~~Gw~~vy~~~~~~~~~~~~e~~e~~~~~~e~~~~LP~l~ 538 (805)
T PTZ00407 459 RNTLAVFMIPMKTEKIVATVKFTSGSGEKLEFELQGKRVVEPGWTRAFHKGDKGTTGPAEETDEDITAVEEGAPVVPSLS 538 (805)
T ss_pred HHHHHHhCchhEEEEEEEEEEEeccCCCceEEEEEEEEEeeCCHHHHhcccccccccccccccccccccccccccCCccc
Confidence 99999999999999999999873 458999999999999999997311 0 1 13599999
Q ss_pred CCC------------------eeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCc
Q 046997 480 HGQ------------------QFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANT 541 (807)
Q Consensus 480 ~G~------------------~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~ 541 (807)
+|| .+.+.++++.+++|+||+||||++||++||++|||||||||+||++|++|+||.+++++
T Consensus 539 ~Gd~~~~~~~~~~~g~~~~q~~~~i~~~~l~ek~TkPPpryTEAtLIk~ME~~GIGTPATrAsIIetL~~R~YV~~~~kk 618 (805)
T PTZ00407 539 QEEFKAIMNLRSQLGSGVQKGFFELRSPQVRENRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKG 618 (805)
T ss_pred CCccccccccccccccccccceeecceeeeecccCCCCCCCCHHHHHHHHHhCCCCCcccHHHHHHHHHhcCCEEeccCc
Confidence 998 34566789999999999999999999999999999999999999999999999987344
Q ss_pred eeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHH
Q 046997 542 RFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVL 590 (807)
Q Consensus 542 ~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l 590 (807)
.|+||++|+.|+++|....++|++|+|||.||.+|++|++|+.+++.++
T Consensus 619 rl~PT~lG~~Li~~L~~~fp~lv~p~~TA~~E~~Ld~Ia~G~~~~~~~~ 667 (805)
T PTZ00407 619 RCETTPVGRMLVETAKSTFPSIVDIGFTAAFEKKLDRIAKPGPAKRPAL 667 (805)
T ss_pred eeeecHHHHHHHHHHHHhhhhhcChHHHHHHHHHHHHHHcCCcchhhhc
Confidence 6999999999999998776789999999999999999999999988444
No 20
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=100.00 E-value=6.4e-112 Score=1045.18 Aligned_cols=530 Identities=23% Similarity=0.311 Sum_probs=443.4
Q ss_pred CceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCC
Q 046997 7 PINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPA 86 (807)
Q Consensus 7 ~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~ 86 (807)
++++|||||||++|++||++||.+. .++.+|.. +|||.+ | +..++|||+.|||++|+.|+.|..|...
T Consensus 600 ~k~~LiIvEsP~kAk~Ia~~lg~~~-~r~~~g~~----~yE~~~---g-~~~~~Vtas~GHl~dL~~~~~~~g~~~~--- 667 (1171)
T TIGR01054 600 VKTALLVVESPNKARTIARFFGKPS-VRKIGGSV----VYEVPV---G-DLILMITASGGHVFDLVTDKGFHGVLVE--- 667 (1171)
T ss_pred cCceEEEEcChHHHHHHHHHhCCCc-ccccCCcc----eEEEec---C-CeeEEEEEeCceeeeCCCccccCccccc---
Confidence 5789999999999999999999864 44446643 455543 2 2345999999999999999888777642
Q ss_pred CCCCCCc---cc-c--------------------cCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhc
Q 046997 87 DLYHAPV---RK-H--------------------VPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAV 142 (807)
Q Consensus 87 ~L~~~p~---~~-~--------------------v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~ 142 (807)
+++..|. ++ . ..++++++++.|++++++||+||||||||||||+|||+|+++++..
T Consensus 668 ~~~f~P~y~~~k~~~~~~~~f~~~~~~~p~~~~~~~~~k~~~~~~lr~l~~~~d~ViiATDpDrEGE~Ia~~i~~~l~~~ 747 (1171)
T TIGR01054 668 NGRYVPVYTSIKRCRDCGYQFTEDRESCPKCGSENIEDSKSIIEILRELAHEVDEVFIGTDPDTEGEKIGWDLALLLSPY 747 (1171)
T ss_pred CCcccccccccccCCchhhhccccccccccccccccccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhccc
Confidence 2322332 11 0 1256788999999999999999999999999999999999998754
Q ss_pred CCCCeEEEEEecccCHHHHHHHHHcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCcc
Q 046997 143 NCHLVLRRARFSALIDREIHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPC 222 (807)
Q Consensus 143 ~~~~~v~R~~~s~lt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRV 222 (807)
+ ++|+|+|||++|+++|++||+|++++|.+|++||.||+++||+||||+||++|+.++ +..+|+|||
T Consensus 748 ~--~~i~R~~f~eiT~~aI~~A~~n~r~~~~~L~~A~~aRr~~D~liG~~lSr~lt~~~~-----------~~~lSaGRV 814 (1171)
T TIGR01054 748 N--PNVKRAEFHEVTRRAILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFN-----------KRWLSAGRV 814 (1171)
T ss_pred C--CCeEEEEEccCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhhhhCHHHHHhhc-----------CCCccccee
Confidence 3 479999999999999999999999999999999999999999999999999997542 236999999
Q ss_pred chhhHHHHHHHHHHHHcccccceEEEEEEeecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCC
Q 046997 223 QFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPP 302 (807)
Q Consensus 223 QtPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP 302 (807)
|||||+|||+|++||++|+ +||.+.+.. ++..+.+.| .|+..|+.+++.+. .++|.+|+.++++++||
T Consensus 815 QTPtL~lIVeRe~ei~~~~--~~~~i~~~~--~~~~~~~~~-----~~~~~a~~~~~~~~---~~~V~~v~~k~~~~~pP 882 (1171)
T TIGR01054 815 QTPVLGWIIDRYRESREKR--GYLLIFALE--SDFRLGLEH-----DNRLEAKEFEKDLT---WLDVEDIAEREEERNPL 882 (1171)
T ss_pred cchhhHHHHHHHHHHhCCC--ceEEEEEec--CCeEEEEEe-----CCHHHHHHHHHhCC---CcEEEEEEeeEEeccCC
Confidence 9999999999999999965 599987643 233444444 46788888888773 58999999999999999
Q ss_pred CCCCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhcccccC
Q 046997 303 YPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDHAAG 380 (807)
Q Consensus 303 ~pf~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~~~~ 380 (807)
+||+|++||++||++|||||++||++||+|||+||||||||||++||++. .+++++..... ..++. ++
T Consensus 883 ~Pf~t~~Lq~~As~~lg~sa~~tm~iAQ~LYE~GlITYpRTDS~~ls~~~~~~~~~~l~~~~~--------~~~~~--~r 952 (1171)
T TIGR01054 883 PPYTTDTMLEDANRKLGLSVKETMQIAQELFENGLITYHRTDSTRVSDVGMRVAKEYLASRLG--------GEYFY--PR 952 (1171)
T ss_pred CCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCEEEecCCCCCcCCHHHHHHHHHHHHHHhc--------ccccC--CC
Confidence 99999999999999999999999999999999999999999999999864 23333332211 11111 22
Q ss_pred CccCCCCCCCCCCCCCCCcCCCCCCC-------------CCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECC-
Q 046997 381 LWRNPGSGGHDDKAHPPIHPTKFSSG-------------ESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAG- 446 (807)
Q Consensus 381 ~~~~~~~~~~~~~aH~aI~PT~~~~~-------------~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~- 446 (807)
.| .+++|||||+||..... ...||++|++||+||+|||||+||+||+|+++++.+.+++
T Consensus 953 ~~-------~~~~aHeAI~PT~~~~~~~l~~~~~~g~~~~~~Ls~~e~~lY~LI~rRflAs~~~~a~~~~t~v~~~~~~~ 1025 (1171)
T TIGR01054 953 EW-------GEGGAHECIRPTRPLDVDDLQRLILEGVIELEGLTREHLRLYDLIFRRFMASQMRPAKVDTKEITLKADGK 1025 (1171)
T ss_pred CC-------CCCCCcCCcCCcCCCChhhhhhhhcccccccccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCCe
Confidence 23 24689999999986331 1368999999999999999999999999999999999976
Q ss_pred eEEEEEEEEEEecCeeeeecccccCCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHH
Q 046997 447 EVFSTSGRVILAKNYLDVYRFESWGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHI 526 (807)
Q Consensus 447 ~~F~a~g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI 526 (807)
+.|.++|++++++||+.+|+.+. .+.+.+|+.+.+.++.+.++. ||+||||++||++||+.|||||||||+||
T Consensus 1026 ~~f~~~g~~i~~~Gw~~v~~~~~-----~~~~~~G~~~~~~~~~~~~~~--~~p~yTe~~Li~~Me~~GIGtpsT~A~II 1098 (1171)
T TIGR01054 1026 EAEEEGIVEIVERGFELVYPLWR-----KNELEKGSTFIVKDKELRSVP--KVYPYTQGEIVQEMKERGIGRPSTYATIV 1098 (1171)
T ss_pred eEEEEEEEEEeeCCHHHHcCccc-----cccccCCCEeeeecceeeecC--CCCCCCHHHHHHHHHhCCCCCcccHHHHH
Confidence 89999999999999999997543 445788999888777776655 44599999999999999999999999999
Q ss_pred HhhcccceEEEcCCceeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHH
Q 046997 527 KKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMK 598 (807)
Q Consensus 527 ~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~ 598 (807)
++|++||||..+++ .|+||++|+.|++.|....+.|++|++||.||+.|++|++|+.++++||++++++++
T Consensus 1099 ~~L~~R~YV~~~~k-~l~pT~lG~~v~~~L~~~~~~l~~~~~Ta~~E~~Ld~Ie~G~~~~~~~l~~~~~~i~ 1169 (1171)
T TIGR01054 1099 EKLLRRGYVVESKG-FLIPTKLGIEVYNYLTNRYPKLVSEDRTRELEEAMDKIERGELDYLEVLESVYREIK 1169 (1171)
T ss_pred HHhhccCcEEeeCC-EEeECHHHHHHHHHHHhhhhhcCCHhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHh
Confidence 99999999987554 689999999999999765558999999999999999999999999999999988764
No 21
>PRK14701 reverse gyrase; Provisional
Probab=100.00 E-value=1.4e-96 Score=923.72 Aligned_cols=540 Identities=24% Similarity=0.339 Sum_probs=426.4
Q ss_pred CceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCC
Q 046997 7 PINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPA 86 (807)
Q Consensus 7 ~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~ 86 (807)
++++||||||||+|++||++||.+. .++.+|+ .+|++. .| ++.++|||+.|||++|+.|++|..|...+
T Consensus 579 ~~~~LiIaEkPs~Ak~IA~~lg~~~-~r~~g~~----~~ye~~---~g-~~~~~Vtas~GHl~dL~~~~~~~g~~~~~-- 647 (1638)
T PRK14701 579 VKSALMIVESPNKARTIANFFGQPS-VRKIGDL----VAYEVS---IG-DHMLIITASGGHVFDLVTNEGFHGVLINN-- 647 (1638)
T ss_pred cCCeEEEEeChHHHHHHHHHhCCCc-cccCCCc----ceEEEe---cC-CcEEEEEEecceeccCCCccccCcccccc--
Confidence 5789999999999999999999764 3333343 234432 12 23689999999999999888876665321
Q ss_pred CCCCCCc---ccc-----------------------cCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhh
Q 046997 87 DLYHAPV---RKH-----------------------VPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCR 140 (807)
Q Consensus 87 ~L~~~p~---~~~-----------------------v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~ 140 (807)
++..|. ++. ...+++++++.|++++++||+||||||||||||+|||+|++++.
T Consensus 648 -~~f~P~y~~~k~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~lr~l~~~ad~viiatD~DrEGE~I~~~i~~~~~ 726 (1638)
T PRK14701 648 -NLFIPIYDSIKRCRDCGHQFTDWEDKGVCPRCGSKNVDDAKENIKAMRELAHEVDEILIGTDPDTEGEKIAWDIRNVLA 726 (1638)
T ss_pred -CccCCcccccccCCCchhhccccccccccccccccccccHHHHHHHHHHHHHhCCeEEECCCCChhhHHHHHHHHHHhc
Confidence 111222 000 01346778999999999999999999999999999999999986
Q ss_pred hcCCCCeEEEEEecccCHHHHHHHHHcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccC
Q 046997 141 AVNCHLVLRRARFSALIDREIHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYG 220 (807)
Q Consensus 141 ~~~~~~~v~R~~~s~lt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~G 220 (807)
..+ ++++|+|||++|+++|++||+||+++|+++++||.||+++||+|||||||++|..+++ ..+|+|
T Consensus 727 ~~~--~~i~R~~fs~lT~~aI~~A~~nlr~~d~~l~~A~~aRr~~D~~iG~nlSr~l~~~~~~-----------~~lS~G 793 (1638)
T PRK14701 727 PYG--PNIKRIEFHEVTRRAILKAIKEARDIDENRVKAQIVRRIEDRWIGFELSQKLWEVFED-----------RNLSAG 793 (1638)
T ss_pred cCC--CCeeEEEEccCCHHHHHHHHhCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhccC-----------Cceeec
Confidence 543 4799999999999999999999999999999999999999999999999999976532 369999
Q ss_pred ccchhhHHHHHHHHHHHHcccccceEEEEEEeecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeC
Q 046997 221 PCQFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKY 300 (807)
Q Consensus 221 RVQtPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~ 300 (807)
|||||||+|||+|++||+| +|++||.|.+.. + +.+.|... ++ ...++|.+|+.++++.+
T Consensus 794 RVQTPtL~~Iv~Re~ei~~-~~~~~~~i~~~~---~--~~~~~~~~----~~-----------~~~~~V~~v~~k~~~~~ 852 (1638)
T PRK14701 794 RVQTPVLGWIIQRYKEFTE-SKVPFLGIILEN---D--LTVTIEDS----KD-----------EVEVEVELVEEEEKERN 852 (1638)
T ss_pred ccccchhhhhHhhHHHHhc-CCCceEEEEEcC---c--eEEEeccc----cc-----------CCeEEEEEEEeeEEEcc
Confidence 9999999999999999999 599999986542 2 33443211 10 02478999999999999
Q ss_pred CCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccCCCCc--------------------------c-------
Q 046997 301 PPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTETD--------------------------S------- 347 (807)
Q Consensus 301 pP~pf~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTds~--------------------------~------- 347 (807)
||+||||++||++||++|||||++||++||+|||+|++|||||... .
T Consensus 853 pP~pf~t~~Lq~~As~~~g~s~~~tm~iAQ~LYE~g~~~~p~t~V~l~dG~~~~I~el~e~~~~~vl~~~~~~~~~~~~~ 932 (1638)
T PRK14701 853 PLPPYTTDTMLRDASAFLKLSAKETMKLAQDLFEAGLCVTPDTYVSLHDGRIKEIDEIVEGSERNVLGLNGLKPKEAKAL 932 (1638)
T ss_pred CCCCcCHHHHHHHHHHhcCCCHHHHHHHHHHHHhCceeeCCCceeecCchHHHHHHHHHhhccceeecccCceeccccee
Confidence 9999999999999999999999999999999999999999999750 0
Q ss_pred ------------------------------cC----------------------------Cc---c------------c-
Q 046997 348 ------------------------------FS----------------------------SG---T------------N- 353 (807)
Q Consensus 348 ------------------------------l~----------------------------~~---~------------~- 353 (807)
|. ++ . +
T Consensus 933 ~~~~~~~~~~~~~i~~~~G~~i~~T~dH~~lv~~~g~~~~~~a~~lk~gD~vav~~~~~~~~~~~i~~~~ll~~~~~~~~ 1012 (1638)
T PRK14701 933 KFWEIDYNGPIKVITLKNNYEIKATPDHGLLVMRDGKLGWVSAKNIREGDYVAFAFNTGVEGRKDYSLLKLLKELGITDV 1012 (1638)
T ss_pred EEEEeccCCcEEEEEECCCCEEEeCCCceEEeecCCceeeEEHHHCCcCCEEEecccCCCCccccccHHHHhhhccccce
Confidence 00 00 0 0
Q ss_pred --------------------------------------------------------------------------------
Q 046997 354 -------------------------------------------------------------------------------- 353 (807)
Q Consensus 354 -------------------------------------------------------------------------------- 353 (807)
T Consensus 1013 ~~~~~~~~~~~~~~~~~i~~i~~~~~~~~lr~~~~pl~~l~e~g~~~~~~~~~~~~~~~~~~~~~~i~~~k~de~~~yLl 1092 (1638)
T PRK14701 1013 CVEFDENSKLFEKLAEKIRGIATSTKYKYLRNRVIPLKYLIEWNVNLDEVEREAKAIYRQRAGSKKIPIFKLDERFWYLF 1092 (1638)
T ss_pred eeeeccchhHHHHHHHHHHhhccchhhhhccCCcccHHHHHHhcccccccchhhhhhhhcccCcccccccccChhHHhHh
Confidence
Q ss_pred --------------------------------------------------HHHHHHH-----------------------
Q 046997 354 --------------------------------------------------LHGIVQE----------------------- 360 (807)
Q Consensus 354 --------------------------------------------------~~~il~~----------------------- 360 (807)
+..+++.
T Consensus 1093 G~~lgdG~~~~~~~~i~~~~~~~v~~i~~~~~~~~~~~~~~~~v~i~~~~l~~l~~~lG~~~~~ip~~vf~~p~e~~~~f 1172 (1638)
T PRK14701 1093 GLVLGDGTLRDSKVAIAQTPLKDVKSILEDILPFLRTWESGNQVGFSNSIIAEILRRLGVRNGKLNGLVFSLPEEYINAM 1172 (1638)
T ss_pred heeEecceeccCeEEEecccHHHHHHHHHHHhhhhhccCCCceEEEccHHHHHHHHHhCCccCCCCHHHHcCCHHHHHHH
Confidence 0000000
Q ss_pred Hhc----C-----------C---------------------------------------Cc-----h----hhH------
Q 046997 361 QIG----H-----------P---------------------------------------DW-----G----PYA------ 371 (807)
Q Consensus 361 ~~~----~-----------~---------------------------------------~~-----~----~~~------ 371 (807)
|.+ + . .| + .|.
T Consensus 1173 L~G~fd~DG~v~~~~~~~~~~~~~~i~~~s~s~~ll~~v~~lLlrlGI~s~l~~~~~~~~~~l~I~g~~l~~F~e~Ig~~ 1252 (1638)
T PRK14701 1173 IAGYFDTDGCFSLLFDKKTGKHNLRIVLTSKRRDVLEKLGVYLYSIGILNTLHRDERNGVWTLIISNRSLETFKEKIYKY 1252 (1638)
T ss_pred HhheEeCCCceEecccccCCccceEEEEecCCHHHHHHHHHHHHHCCceeEEEEcccCccEEEEEccHHHHHHHHHhCcc
Confidence 000 0 0 00 0 000
Q ss_pred ------H---------------------------------------------------------------------h---
Q 046997 372 ------Q---------------------------------------------------------------------R--- 373 (807)
Q Consensus 372 ------~---------------------------------------------------------------------~--- 373 (807)
+ +
T Consensus 1253 ~~~k~~~l~~~~~~~~~~~~~~~~D~iP~~~~~~~v~~~~g~~~~~~~~~g~~~~~~~~~~~isR~~l~~~~~~~~~~~~ 1332 (1638)
T PRK14701 1253 LRIKKEQFDRAYSVYKNEHKQFEGDLLPVAKVFKKLKFKRGIKNRILKEFGIDVWNWNKCVEIPREKLRKVLEYAEDSPE 1332 (1638)
T ss_pred cHHHHHHHHHHHHHHhccccCCCcCccchHHHHHHHHHhcCCchHHHHhhccccccccccCCcCHHHHHHHHHHHhhhhH
Confidence 0 0
Q ss_pred ------------------------hc-------------------ccc---------------------------cCCcc
Q 046997 374 ------------------------LL-------------------DHA---------------------------AGLWR 383 (807)
Q Consensus 374 ------------------------~l-------------------~~~---------------------------~~~~~ 383 (807)
+. .++ ...+.
T Consensus 1333 ~~~L~~la~~dv~~~~i~~ie~~~~~g~vyd~~v~~~nf~angiv~HN~TY~RTDS~~lS~~~~~~~~~~i~~~~g~~y~ 1412 (1638)
T PRK14701 1333 KEFLLSLVNANVTWVKVKKVEERYYTGYVYDFTTTTENFISNGMVSHNCTYHRTDSTRVSNTGIRVAREYLTQENGEDYF 1412 (1638)
T ss_pred HHHHHHHhhCCeEEEEEEEEEEeccCCeEEEeEecccceeEccEeecCcccccCCCCccCHHHHHHHHHHHHHhhChhhc
Confidence 00 000 01122
Q ss_pred CCCCCCCCCCCCCCCcCCCCCCCC-------------CCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEE
Q 046997 384 NPGSGGHDDKAHPPIHPTKFSSGE-------------SRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFS 450 (807)
Q Consensus 384 ~~~~~~~~~~aH~aI~PT~~~~~~-------------~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~ 450 (807)
.|+.+ .+++||||||||+....+ ..|+++|++||+|||+||||+||+||+|+.|++.+.++++.|+
T Consensus 1413 ~~r~~-~~q~AHeAIrPT~~~~~~~~~~~~~~~~~~~~~Ls~de~klY~LI~rRflAs~m~~a~~~~t~v~~~~~~~~F~ 1491 (1638)
T PRK14701 1413 KPRDW-FMEGAHECIRPTRPIDTDRLIQLIREGIIQVPGLTRNHLRLYDLIFRRFMASQMKPAKVLYEKALIRYDGKDVE 1491 (1638)
T ss_pred CcccC-CCcCCcCCCCCCCCCcChhhhhcccccccccccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEECCEEEE
Confidence 35443 478999999999754321 2599999999999999999999999999999999999999999
Q ss_pred EEEEE-EEecCeeeeecccccCCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhh
Q 046997 451 TSGRV-ILAKNYLDVYRFESWGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKL 529 (807)
Q Consensus 451 a~g~~-i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L 529 (807)
++|++ ++++||+++|+.+ +..||.|++| .+.+.+ +.+.+|.||+|||||+||++||+.|||||||||+||++|
T Consensus 1492 a~G~~~i~~~Gw~~vy~~~---~~~LP~l~~G-~l~~~~--~~~t~~ppP~ryTEasLI~~Me~~GIGTpATrA~IIe~L 1565 (1638)
T PRK14701 1492 VEGYVEIEGDGWSRLYSLP---LRVLPKLEKG-KLKVLE--AKIRKAPKVPLYTQGDIVALMKERGIGRPSTYAKIVDTL 1565 (1638)
T ss_pred EEeEEEEEEcCchhccccc---cccCCccccC-ceEEec--cceeECCCCCCCCHHHHHHHHhhCCCCCcccHHHHHHHH
Confidence 99995 7999999998642 3469999999 887754 355666667999999999999999999999999999999
Q ss_pred cccceEEEcCCc-eeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHH
Q 046997 530 LDRFYAIKDANT-RFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKA 599 (807)
Q Consensus 530 ~~R~Yv~~~~~~-~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~ 599 (807)
++||||..++++ .|+||++|++|++.|....+.|++|+|||.||.+|++|++|+.++++||+++++++++
T Consensus 1566 ~~R~YV~~~~~k~~l~pT~lG~~li~~L~~~~~~l~~p~~TA~~E~~Ld~Ia~G~~~~~~~l~~~~~~i~~ 1636 (1638)
T PRK14701 1566 LMRGYVIETKGRKKLIPTKKGIKVYNYLISNYGDLVSEERTRELEEIMDAVEEGELDYIKVLQELYEEIRR 1636 (1638)
T ss_pred HhCCCEEEeCCCceEEECHHHHHHHHHHHhhchhhcChhhHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHh
Confidence 999999876543 5999999999999997666689999999999999999999999999999999987764
No 22
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=100.00 E-value=8.1e-94 Score=799.39 Aligned_cols=373 Identities=36% Similarity=0.550 Sum_probs=329.1
Q ss_pred cchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccceEEEEEEe
Q 046997 173 QWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEFWTINCSH 252 (807)
Q Consensus 173 ~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~~i~~~~ 252 (807)
.+|++||+||+++|||||||+||++|+.+++ ..++|+||||||||+|||+||+||+||+|++||.|
T Consensus 1 ~~l~~a~~aR~~~D~liG~n~sr~~t~~~~~----------~~~lS~GRVQtPtL~liv~Re~ei~~F~p~~y~~i---- 66 (381)
T cd00186 1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRR----------KGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI---- 66 (381)
T ss_pred CcHHHHHHHHHHHHHHhhhhhhHHHHHHhCC----------CCCCccccchhhHhHHHHHHHHHHHhCCCcceEEe----
Confidence 3689999999999999999999999987652 13799999999999999999999999999999998
Q ss_pred ecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHH
Q 046997 253 KSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDL 332 (807)
Q Consensus 253 ~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~iaQ~L 332 (807)
..++|++++++++++.||+||||++||++||++|||||++||++||+|
T Consensus 67 --------------------------------~~~~v~~~~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~L 114 (381)
T cd00186 67 --------------------------------KEAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKL 114 (381)
T ss_pred --------------------------------eeEEEEEEEeeeeecCCCCCcCHHHHHHHHHHhcCCCHHHHHHHHHHH
Confidence 247899999999999999999999999999999999999999999999
Q ss_pred hhcCceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCCCCCCCCCCcCCCCCCC---C
Q 046997 333 YQAGFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFSSG---E 407 (807)
Q Consensus 333 YE~g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~aH~aI~PT~~~~~---~ 407 (807)
||+||||||||||++||+++ .+..++..+... +..+....+. .+.+..+..+++||||||||...+. .
T Consensus 115 Ye~glISYPRTds~~ls~~~~~~~~~~~~~~~~~--~~~~~~~~~~-----~~~~~~~~~~~~aH~AI~PT~~~~~~~~~ 187 (381)
T cd00186 115 YEAGLITYPRTDSTRLSEEAILEAREYIQAIYGK--EYLYPAPLLG-----RRNPKRGKKEQGAHEAIRPTKVAPTPELE 187 (381)
T ss_pred HcCCeeeecCCCCccCCHHHHHHHHHHHHHhcCc--cccchhhccc-----cccccCCCCCcCCCCCCCcCCCCcCchhh
Confidence 99999999999999999986 344455544322 1111111111 1122223446789999999998764 4
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccC-CccCCccCCCCeeee
Q 046997 408 SRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWG-GLVIPTYVHGQQFIP 486 (807)
Q Consensus 408 ~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~-~~~lP~l~~G~~~~~ 486 (807)
..|+++|++||+||+|||||+||+||+|++++|.++++++.|.++|++++++||++||+.+.++ +..+|.|.+|+.+.+
T Consensus 188 ~~l~~~e~~iY~LI~rrfla~~~~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~p~l~~g~~~~~ 267 (381)
T cd00186 188 ANLSEDEFKLYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKL 267 (381)
T ss_pred ccCCHHHHHHHHHHHHHHHHHhCchhhEEEEEEEEEECCeEEEEEEEEEeeCCHHHHhCcccccccccCCCCCCCCEEee
Confidence 6899999999999999999999999999999999999999999999999999999999865443 335799999999999
Q ss_pred eeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCccccCc
Q 046997 487 TTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKP 566 (807)
Q Consensus 487 ~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p 566 (807)
.++.+.+++|+||+||||++||++||++|||||||||+||++|++||||..+++ .|+||++|+.|+++|+...+.|++|
T Consensus 268 ~~~~~~~~~T~PP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~k-~l~pT~~G~~li~~l~~~~~~l~~p 346 (381)
T cd00186 268 EEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEKK-KLIPTELGFAVIELLEKHFPELVDP 346 (381)
T ss_pred eeeeeeecccCCCCCCCHHHHHHHHHhCCCCccccHHHHHHHHHhCCcEEeeCC-EEeECHHHHHHHHHHHHhchhccCH
Confidence 999999999999999999999999999999999999999999999999998765 6999999999999998766689999
Q ss_pred hhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHH
Q 046997 567 NLRSMMESDMKEVSVGNKSKADVLANCLQQMKA 599 (807)
Q Consensus 567 ~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~ 599 (807)
+|||.||+.|++|++|+.++++||+++.+++++
T Consensus 347 ~lTa~~E~~L~~I~~G~~~~~~~l~~~~~~~~~ 379 (381)
T cd00186 347 EFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKK 379 (381)
T ss_pred hHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHh
Confidence 999999999999999999999999999987764
No 23
>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....
Probab=100.00 E-value=7.3e-94 Score=806.43 Aligned_cols=395 Identities=33% Similarity=0.481 Sum_probs=316.0
Q ss_pred CCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccceEEEEE
Q 046997 171 PNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEEFWTINC 250 (807)
Q Consensus 171 ~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~~i~~ 250 (807)
.+++|+.||.||+++|||||||+||++| . ..++|+||||||||+|||+||+||+||+|++||.|.+
T Consensus 2 ~~~~l~~a~~aR~~~D~liG~n~Sr~~t---~-----------~~~ls~GRVQtp~L~li~~Re~ei~~f~~~~y~~i~~ 67 (403)
T PF01131_consen 2 EDKNLYNAAEARQEADWLIGMNLSRALT---G-----------NGVLSVGRVQTPTLGLIVEREREIENFKPEPYYEIKA 67 (403)
T ss_dssp -GHHHHHHHHHHHHHHHHHHHHHHHHHH---H-----------STT-TTHTTHHHHHHHHHHHHHHHHCEEEEEEEEEEE
T ss_pred CCHhHHHHHHHHHHHHHhcChhcCHhhc---C-----------CCccccCcccchHHHHHHHHHhhhhccCCCceEEEEE
Confidence 4678999999999999999999999997 1 2489999999999999999999999999999999999
Q ss_pred EeecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHHHHH
Q 046997 251 SHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAE 330 (807)
Q Consensus 251 ~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~iaQ 330 (807)
.+..++.. ...|.+.+++|++.|+.+++.+... +|++++.+++++.||+||||++||++||++|||||++||++||
T Consensus 68 ~~~~~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~---~v~~~~~~~~~~~pP~p~~l~~Lq~~a~k~~g~s~~~tl~iaQ 143 (403)
T PF01131_consen 68 QFKKGGFE-FKNDDKKRFDDKEEAEQILEKLKNS---KVTEVEEKEKKKPPPLPFNLSTLQKEASKKLGFSAKETLDIAQ 143 (403)
T ss_dssp EEETCCS--EETTEES-CTSHHHHHHHHHHHHHC---EEEEEEEEEEEE----SB-HHHHHHHHHHHH---HHHHHHHHH
T ss_pred Eecccccc-cccccccccccHHHHHHHhhcccCc---eEEEEEEEEeeecCCChHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 98765554 3445578899999999999999753 8999999999999999999999999999999999999999999
Q ss_pred HHhhc-CceeccCCCCcccCCcccHHHHHHHHhcC-C-CchhhHHhhcccccCCccCCCC-CCCCCCCCCCCcCCCCCC-
Q 046997 331 DLYQA-GFISYPRTETDSFSSGTNLHGIVQEQIGH-P-DWGPYAQRLLDHAAGLWRNPGS-GGHDDKAHPPIHPTKFSS- 405 (807)
Q Consensus 331 ~LYE~-g~ISYPRTds~~l~~~~~~~~il~~~~~~-~-~~~~~~~~~l~~~~~~~~~~~~-~~~~~~aH~aI~PT~~~~- 405 (807)
+|||+ ||||||||||++||++.++.++++.+..+ + .|..++.... ..++. +...+.|||||+||...+
T Consensus 144 ~LYE~~g~ISYPRTds~~l~~~~~~~~i~~~l~~~~~~~~~~~~~~~~-------~~~~~~~~~kv~aH~AI~PT~~~~~ 216 (403)
T PF01131_consen 144 KLYEKHGLISYPRTDSRYLPEDEDLKEILKYLKKHYGEDYFPEAPNLL-------KSPKSKNDSKVTAHHAIIPTGKIPP 216 (403)
T ss_dssp HHHHTTTSBS-SS-S---B-HHHGHHHHHHHHHHHTTGGGS-SS--TT-------SSSTTC-CCC-SSSS-B-BSSSTTH
T ss_pred HHHhhhheeeeeccchhhhcchhhHHHHHHHHHHhccccccccchhhh-------hcccccCCccccCCCCccccccCcc
Confidence 99997 99999999999999986677887776542 1 1222221111 11111 112248999999998776
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccCCc--cCCccCCCCe
Q 046997 406 GESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWGGL--VIPTYVHGQQ 483 (807)
Q Consensus 406 ~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~--~lP~l~~G~~ 483 (807)
+...|+++|++||+||+|||||+||+||+|+++++++.++++.|.++|++++++||+++++.....+. .||.|++|+.
T Consensus 217 ~~~~Ls~~e~~vY~LI~rr~la~~~~~~~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~~~~~~~~~~~~~~lp~l~~g~~ 296 (403)
T PF01131_consen 217 DLSNLSEDERKVYDLIARRFLAAFMPDAKYEKTTVTFEVGGEEFKASGKVIIDPGWKKVYPYEEEEDEEEDLPSLKEGDE 296 (403)
T ss_dssp CGHHCHHHHHHHHHHHHHHHHHHTS--EEEEEEEEEEEETTEEEEEEEEEEEEHGGGGCS-HCHCCTTSBB-----TTEE
T ss_pred chhhcCHHHHHHHHHHHHHHHHHHHHHHheeeEEEEEEecCcEEEEEEeEEEECceeEEEEcccccccccccccccCCcE
Confidence 55789999999999999999999999999999999999999999999999999999999975544333 6999999999
Q ss_pred eeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCccc
Q 046997 484 FIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYEL 563 (807)
Q Consensus 484 ~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l 563 (807)
+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++|+||+..+++.|+||++|+.|++.|+.. +.|
T Consensus 297 ~~~~~~~~~e~~TkPP~~~Te~~Ll~~Me~~GIGTpATra~iI~~L~~r~Yi~~~k~~~l~~T~~G~~li~~l~~~-~~l 375 (403)
T PF01131_consen 297 IPIEDVEIKEKKTKPPKRYTEASLLKAMEKAGIGTPATRASIIEKLIKRGYIERSKGKKLIPTPKGRALIEALPNF-PEL 375 (403)
T ss_dssp EEEEEEEEEEEEEESS--EBHHHHHHHHHHTTSS-TTTHHHHHHHHHHTTSEEE-ETTEEEEBHHHHHHHHHHHHC-CCC
T ss_pred EeecccchhhhccCCCCCCCHHHHHhhhhhcCCCccccHHHHHHHhhccceeecccCceeeeehHHHHHHHHHHhh-HHh
Confidence 9999999999999999999999999999999999999999999999999999996556799999999999999643 589
Q ss_pred cCchhhHHHHHHHHHHHcCCCChHHHHH
Q 046997 564 WKPNLRSMMESDMKEVSVGNKSKADVLA 591 (807)
Q Consensus 564 ~~p~~Ta~~E~~L~~I~~G~~~~~~~l~ 591 (807)
++|++||.||+.|++|++|+.++++||+
T Consensus 376 ~~p~~Ta~~E~~L~~I~~G~~~~~~fl~ 403 (403)
T PF01131_consen 376 ISPEMTAQWEEKLDKIAEGKASKEEFLK 403 (403)
T ss_dssp CSHHHHHHHHHHHHHHHTTSS-HHHHHH
T ss_pred cCHHHHHHHHHHHHHHHcCCCCHHHHhC
Confidence 9999999999999999999999999985
No 24
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.1e-83 Score=740.96 Aligned_cols=533 Identities=24% Similarity=0.361 Sum_probs=414.4
Q ss_pred CceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCc-------
Q 046997 7 PINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRK------- 79 (807)
Q Consensus 7 ~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~------- 79 (807)
+...|+|+|+|++||+||.++|.++ .++.+|... ||- .-|+. -.+||++.||+++|...+.|..
T Consensus 616 vkt~L~IVESPnKARTIA~FFgrPS-~R~~~~~~v----YEv---~~gD~-vL~ItAS~GHv~DLvt~~g~hGvl~~~~~ 686 (1187)
T COG1110 616 VKTALMIVESPNKARTIASFFGRPS-VRRLGGGVV----YEV---AIGDL-VLTITASGGHVFDLVTEPGVHGVLVKDGK 686 (1187)
T ss_pred hhceEEEEeCChHHHHHHHHhCCcc-eeeeCCeeE----EEE---ecCCe-EEEEEecCCeeEEeecccccceeeccCCc
Confidence 6779999999999999999999886 666677544 331 12322 3679999999999965443311
Q ss_pred C----------cCCCCC---CCCCCCcccc-cCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCC
Q 046997 80 W----------HSCDPA---DLYHAPVRKH-VPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCH 145 (807)
Q Consensus 80 W----------~~~~p~---~L~~~p~~~~-v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~ 145 (807)
| ..|... .-..+|.-.. -..++...++.|+++|..+|+|+||||||.|||-|||+|..++...++
T Consensus 687 ~vPvY~tIKrC~dcg~q~~~~~~~cP~Cgs~~v~d~~~~ve~lRelA~EvDeVlIgTDPDtEGEKIawDv~~~l~Py~~- 765 (1187)
T COG1110 687 YVPVYDTIKRCRDCGEQFVDSEDKCPRCGSRNVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFNYLRPYNP- 765 (1187)
T ss_pred eEehHHHHHHHhhcCceeccccccCCCCCCccccccHHHHHHHHHHHhhcCEEEEcCCCCCccchhHHHHHHhhCcCCC-
Confidence 1 111100 0011232111 124677889999999999999999999999999999999999998876
Q ss_pred CeEEEEEecccCHHHHHHHHHcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchh
Q 046997 146 LVLRRARFSALIDREIHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFP 225 (807)
Q Consensus 146 ~~v~R~~~s~lt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtP 225 (807)
+|+|+.|+++|+.+|.+|++|+++.|.|++.||..|++.|++||+.||+-+... |+ +..||+||||||
T Consensus 766 -nikR~eFHEVTrrAIleAl~n~r~vd~nlVkAQiVRRIeDRWIGF~LS~~Lw~~---F~--------~~nLsAGRVQTP 833 (1187)
T COG1110 766 -NVKRIEFHEVTRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLWDV---FN--------NKNLSAGRVQTP 833 (1187)
T ss_pred -ceeEEEeeeecHHHHHHHHhCccccchhhhHHHhhhhhhhcccceeecHHHHHH---hC--------ccCccccccccc
Confidence 799999999999999999999999999999999999999999999999853322 42 358999999999
Q ss_pred hHHHHHHHHHHHHcccccceEEEEEEeecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCC
Q 046997 226 TLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPL 305 (807)
Q Consensus 226 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf 305 (807)
+|+|||+|++|-+.-+. |..+.. .+.+. +-+...++.+...... ....|.++..++...+||+||
T Consensus 834 VLGWIV~Ry~e~~~~~~--~~~~~~-------~~~~~-----~~~~~~~~~~~~~~~~-~~v~v~~~~e~ee~~~PlPPy 898 (1187)
T COG1110 834 VLGWIVNRYEEYKEKRG--YLVIQL-------DLDLP-----SGNREEVENVKRKLKL-IVVEVVDVVEREEEKNPLPPY 898 (1187)
T ss_pred cceeehhhHHHHhhccc--eeEeec-------cceee-----ccchhhhhhhhhhccc-ceEEEeehhhhhhccCCCCCc
Confidence 99999999999765443 444411 11111 1233444444444432 245666666677778999999
Q ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccCCCCcccCCcccHHHHHHHHhcCCCchhhHHhhcccccCCccCC
Q 046997 306 STIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTETDSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNP 385 (807)
Q Consensus 306 ~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTds~~l~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~ 385 (807)
+|++|+.+||++||+|+++||+|||.|+|.|||||+||||+.+|+.- ..+.+..... .+...++. ++.|.
T Consensus 899 TTDt~L~dAs~~L~lsa~~~M~iaQdLFE~GlITYHRTDSTrVS~~G--i~vAreyl~~----~~~e~~f~--pR~Wg-- 968 (1187)
T COG1110 899 TTDTMLRDASRRLRLSADETMQIAQDLFEGGLITYHRTDSTRVSDVG--IRVAREYLRK----EFGEEYFR--PRSWG-- 968 (1187)
T ss_pred CcchHHHHHHHHhCCChhHHHHHHHHHHhccceEEeecCCcccchhh--HHHHHHHHHH----hhcccccc--CCccc--
Confidence 99999999999999999999999999999999999999999999853 2222221110 11111111 34442
Q ss_pred CCCCCCCCCCCCCcCCCCCC--------------CCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEEE
Q 046997 386 GSGGHDDKAHPPIHPTKFSS--------------GESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFST 451 (807)
Q Consensus 386 ~~~~~~~~aH~aI~PT~~~~--------------~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a 451 (807)
..+||+||+||+... .+..|+..+.+||+||.|||||+||+|++.....+.+.+++..-..
T Consensus 969 -----e~GAHEaIRPtrPid~~eL~~~i~~G~i~~~~~Lt~~HlrvYdLIFrRFmASQm~pa~v~~~~~~i~~~~~~~~~ 1043 (1187)
T COG1110 969 -----EEGAHEAIRPTRPIDVEELITLIEEGVIQLPIRLTKNHLRVYDLIFRRFMASQMRPAKVLKEKAEVKADGKDVEL 1043 (1187)
T ss_pred -----cCCcccccCCCCCCCHHHHHHHHHcCCeeccchhhHHHHHHHHHHHHHHHHhhCCceeEEEEEEEEecCcceeee
Confidence 357999999998654 1235899999999999999999999999999999999998766555
Q ss_pred EE-EEEEecCeeeeecccccCCccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhc
Q 046997 452 SG-RVILAKNYLDVYRFESWGGLVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLL 530 (807)
Q Consensus 452 ~g-~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~ 530 (807)
.+ ..+...||..+|+. ..+|.|.+|+ +.+....+...... .+||++++++.|++.|||+|||||.||++|.
T Consensus 1044 e~~ve~~~~G~~~vy~~-----~~~p~l~~g~-l~v~~~~~~~~~kv--~lytqg~vi~~MKerGIGRPSTYAkive~L~ 1115 (1187)
T COG1110 1044 EALVEILEDGFALVYPT-----RVLPELEKGT-LKVTEVEIRKVSKV--YLYTQGEVVEEMKERGIGRPSTYAKIVETLL 1115 (1187)
T ss_pred eehhhhhccchhhhccc-----cccCccCCCc-eeeeeeEEEEcccc--cccccchHHHHHHhcCCCCCcHHHHHHHHHh
Confidence 54 45778999999872 3578899998 77665555544333 4799999999999999999999999999999
Q ss_pred ccceEEEcCCce-eeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHHHHHH
Q 046997 531 DRFYAIKDANTR-FAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQQMKA 599 (807)
Q Consensus 531 ~R~Yv~~~~~~~-l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~ 599 (807)
+||||...+++. ++||++|+.+++.|......++|.+.|.++|+.||+|++|+.+++++|.++++.++.
T Consensus 1116 ~RgYvie~kg~~~lipTk~Gi~Vy~yL~~~~~~lVSEerTR~LEe~MD~vE~gk~dy~~vL~ely~ei~~ 1185 (1187)
T COG1110 1116 RRGYVIESKGRKKLIPTKLGIEVYEYLSEKYKKLVSEERTRRLEEIMDKVEEGKADYQEVLKELYEEIKS 1185 (1187)
T ss_pred cCCeEEEecCceEeccccccHHHHHHHHHhcccccchhHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHh
Confidence 999997766544 899999999998887666699999999999999999999999999999999876653
No 25
>KOG1957 consensus DNA topoisomerase III beta [Replication, recombination and repair]
Probab=100.00 E-value=4.5e-79 Score=647.84 Aligned_cols=512 Identities=36% Similarity=0.568 Sum_probs=455.7
Q ss_pred CceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCC
Q 046997 7 PINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPA 86 (807)
Q Consensus 7 ~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~ 86 (807)
|.++|+||||||.|.+||.+|++++ ..++.|. ..++||+..+.|....+.||++.||+++||||++|++|...||.
T Consensus 1 ~~tvlmvaekpsla~sia~ils~g~-~s~~kg~---csvhe~~g~f~g~~~~fk~tsvcghvmsldf~~kyn~w~~vdp~ 76 (555)
T KOG1957|consen 1 MKTVLMVAEKPSLADSIANILSNGQ-ASKRKGW---CSVHEYDGQFRGRAARFKVTSVCGHVMSLDFPPKYNNWDKVDPA 76 (555)
T ss_pred CCceeEeecCchHHHHHHHHhhCCc-cccccCc---eeeeeccccccCceeeEEEeeeeceeEeccCchhcCCccccCHH
Confidence 6789999999999999999999987 6777774 78999999999999999999999999999999999999999999
Q ss_pred CCCCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhc--CCCCeEEEEEecccCHHHHHHH
Q 046997 87 DLYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAV--NCHLVLRRARFSALIDREIHQA 164 (807)
Q Consensus 87 ~L~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~--~~~~~v~R~~~s~lt~~~I~~A 164 (807)
+||.+|..+.-.+.|..+.+.|..+++.||.+|+|.|||+|||+|.+||++..+.. ......+|++||++|+++|.+|
T Consensus 77 elf~apt~kkeanpk~~m~kfl~~eargcdy~vlwldcdkegenicfevidav~~~m~~~~~~tyra~fsaitekdi~~a 156 (555)
T KOG1957|consen 77 ELFSAPTEKKEANPKMNMNKFLASEARGCDYLVLWLDCDKEGENICFEVIDAVKCVMNRSDFKTYRAHFSAITEKDIKKA 156 (555)
T ss_pred HHhCCcchhcccCchhhHHHHHhhhccCCcEEEEEeecCCCcCeeehhhhhhhhhhhccCcceEEeeeeccccHHHHHHH
Confidence 99999998776666888889999999999999999999999999999999987653 1223579999999999999999
Q ss_pred HHcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhHHHHHHHHHHHHcccccc
Q 046997 165 VQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTLGFVVERYWEIQAHESEE 244 (807)
Q Consensus 165 ~~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~ 244 (807)
+.||.+||.|.+.|++|||++|+.| + .+..+|+|+||||||+|.|+|...|+.|||+.
T Consensus 157 m~~lg~p~~nea~svdarqeldlri----------l------------ds~~isygpcqtptlgfcv~rhd~i~tfkpe~ 214 (555)
T KOG1957|consen 157 MRNLGEPDQNEALSVDARQELDLRI----------L------------DSSLISYGPCQTPTLGFCVTRHDQIQTFKPEQ 214 (555)
T ss_pred HHhcCCCCcchhcccchhhhhhhhh----------h------------hhcceeecCCCCCcceeeeeehhhhhccCccc
Confidence 9999999999999999999999988 1 13489999999999999999999999999999
Q ss_pred eEEEEEEeecCCceEEEEeccCCcCCHHHHHHHHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHH
Q 046997 245 FWTINCSHKSEEGTATFSWMRGHLFDYTSAVIIYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEH 324 (807)
Q Consensus 245 y~~i~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~ 324 (807)
||.+...+..++ +.+.|+++|+||.+.|..++++++..++|.|.+|.+|+..+..|..+||.+|.+.|
T Consensus 215 ~w~l~~~~~~~~--~~lew~r~rvfd~eia~~f~~~vk~~~~a~v~~vs~ke~~k~rp~alntvel~rv~---------- 282 (555)
T KOG1957|consen 215 YWVLQTNFTTDD--LSLEWQRGRVFDAEIARVFLNRVKECKTALVEDVSKKEARKERPCALNTVELMRVA---------- 282 (555)
T ss_pred eEEEeeecCCCC--ccchhhhcchhhHHHHHHHHHHHHhhhhheehhhhhhHHhhcCCcccchhheeeee----------
Confidence 999999987665 88999999999999999999999988899999999999999999999999999887
Q ss_pred HHHHHHHHhhcCceeccCCCCcccCCcccHHHHHHHHhcCCCchhhHHhhcccccCCccCCCCCCCCCCCCCCCcCCCCC
Q 046997 325 TMKVAEDLYQAGFISYPRTETDSFSSGTNLHGIVQEQIGHPDWGPYAQRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFS 404 (807)
Q Consensus 325 tl~iaQ~LYE~g~ISYPRTds~~l~~~~~~~~il~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~aH~aI~PT~~~ 404 (807)
+|+++.+|.++|-..++- ..+. .++. +.+.++|+||.|.+..
T Consensus 283 -----------------itett~y~~nfd~si~~~------------D~L~--------~~s~-gtdAgdgpPitpmr~~ 324 (555)
T KOG1957|consen 283 -----------------ITETTAYPANFDTSIILG------------DTLF--------EASF-GTDAGDGPPITPMRKC 324 (555)
T ss_pred -----------------EeecccCccccccccccc------------cccc--------cccc-cCcCCCCCCcCccccc
Confidence 499999999876211110 1111 1222 2356789999999752
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeEEE--EEEEEEEecCeeeeecccc---c----CCccC
Q 046997 405 SGESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEVFS--TSGRVILAKNYLDVYRFES---W----GGLVI 475 (807)
Q Consensus 405 ~~~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~F~--a~g~~i~~~Gw~~v~~~~~---~----~~~~l 475 (807)
+....+.+-++||..+.++|++.-+...+|..+++...++++.|. .+|+.+.+.||..+.+... | ++-..
T Consensus 325 -~R~m~~~dtkRLY~~vCqhf~~tp~~~~~k~it~~k~slgdeqf~lw~~Gk~~~~~gft~fm~n~p~m~wgagcdECth 403 (555)
T KOG1957|consen 325 -NRYMKSGDTKRLYCYVCQHFYATPQFKCKKVITTVKCSLGDEQFILWCTGKRLREFGFTPFMPNNPKMPWGAGCDECTH 403 (555)
T ss_pred -ccccccccceeecchhhhhheeccCcCceEEEeeeeeccCCeeEEeccCcceeccCCccccccCCCccccccCCCccCC
Confidence 334567788899999999999999999999999999999999999 9999999999999875211 1 34456
Q ss_pred CccCC-------CCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeechh
Q 046997 476 PTYVH-------GQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNI 548 (807)
Q Consensus 476 P~l~~-------G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~ 548 (807)
|..+. |+.+.+.++.+.+..|.||-++|++.|+..|+++||||+|..+-+|.++-+|+|+..+.|+.+.||++
T Consensus 404 PScq~slSmlgiG~~vEc~~v~Lv~~qTsPkwylTcnkcisvme~hgigtdasI~VhinsiceRnYv~Ve~gr~~~Pt~L 483 (555)
T KOG1957|consen 404 PSCQQSLSMLGIGQCVECESVELVLDQTSPKWYLTCNKCISVMEKHGIGTDASIPVHINSICERNYVTVESGRALVPTPL 483 (555)
T ss_pred chHHhhhhcccceeEEEeccEEEEecCCCCCceeehhhhHHHHHhhcccceeeEEEeecchhhhheEeeecCcccCCCcc
Confidence 66555 99999999999999999999999999999999999999999999999999999999988888999999
Q ss_pred HHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHHHH
Q 046997 549 GEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANCLQ 595 (807)
Q Consensus 549 G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~ 595 (807)
|+.++.++...++++.-|.+++..|+.+-.++.|..+.+.++....+
T Consensus 484 g~~l~~Gy~~~DP~l~lpt~r~~~es~~~lvA~G~A~~q~v~R~r~r 530 (555)
T KOG1957|consen 484 GETLVRGYVKCDPELVLPTMRKEAESQLPLVAGGPADFQDVWRNRGR 530 (555)
T ss_pred chhhhcCceeeCcceechhHHHHHHhhchhhhCCccchhhhhhccee
Confidence 99999999989999999999999999999999999999988876554
No 26
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=100.00 E-value=4.7e-65 Score=537.96 Aligned_cols=252 Identities=36% Similarity=0.585 Sum_probs=216.0
Q ss_pred eeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccCCCCcccCCcc--cHHHHHHHHhcCCCchhhH
Q 046997 294 QQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTETDSFSSGT--NLHGIVQEQIGHPDWGPYA 371 (807)
Q Consensus 294 ~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTds~~l~~~~--~~~~il~~~~~~~~~~~~~ 371 (807)
+++++..||+||||++||++||++|||||++||++||+|||+||||||||||++||+++ ++..++..+.+ +.|..++
T Consensus 2 ~~~~~~~pP~pf~l~~Lq~~a~~~~g~sa~~tl~iaQ~LYe~g~iTYPRTds~~l~~~~~~~~~~~l~~~~~-~~~~~~~ 80 (259)
T smart00437 2 EKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYEKGLITYPRTDSTRLSEEAVLEARNYISKHYG-KEYLPLA 80 (259)
T ss_pred CCcccCCCCCCccHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCeeEecCCCCCcCCHHHHHHHHHHHHHhhc-hhhhhhh
Confidence 45778899999999999999999999999999999999999999999999999999986 34455555433 2233322
Q ss_pred HhhcccccCCccCCCCCCCCCCCCCCCcCCCCCCC---CCCCCHHHHHHHHHHHHHHHHhcCcccEEEEEEEEEEECCeE
Q 046997 372 QRLLDHAAGLWRNPGSGGHDDKAHPPIHPTKFSSG---ESRWSQDHYKLYELVVRHFLACVSQPAVGAETIVEINIAGEV 448 (807)
Q Consensus 372 ~~~l~~~~~~~~~~~~~~~~~~aH~aI~PT~~~~~---~~~Ls~~e~~vY~lI~rrfla~~~~~a~~~~t~v~~~~~~~~ 448 (807)
..+.....+.| +..+++||||||||...+. ..+|+++|++||+||+|||||+||+||+|++++|.+.++++.
T Consensus 81 ~~~~~~~~~~~-----~~~k~~~H~aI~PT~~~~~~~~~~~L~~~e~~iY~lI~rr~la~~~~~~~~~~t~v~~~~~~~~ 155 (259)
T smart00437 81 VSLLKPRKPRW-----GKKEQGAHEAIRPTKPIPTPELEKELSEDEKKLYELIWRRFLASQMPDAKYEETKVIIKIGGEK 155 (259)
T ss_pred hhhccCccccC-----CCCCCCCCCCCCccCCCCCchhhhhCCHHHHHHHHHHHHHHHHHhChhheEEEEEEEEEECCeE
Confidence 22121111222 2334679999999987664 257999999999999999999999999999999999999999
Q ss_pred EEEEEEEEEecCeeeeecccccCC-ccCCccCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCccchHHHHH
Q 046997 449 FSTSGRVILAKNYLDVYRFESWGG-LVIPTYVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTDATMHDHIK 527 (807)
Q Consensus 449 F~a~g~~i~~~Gw~~v~~~~~~~~-~~lP~l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~ 527 (807)
|.++|++++++||++||+++.+++ ..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||+
T Consensus 156 F~a~g~~i~~~Gw~~v~~~~~~~~~~~lp~~~~g~~~~~~~~~~~e~~TkPP~~~Te~tLl~~Me~~GIGTpATra~iIe 235 (259)
T smart00437 156 FKAKGKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKKTKPPARYTEASLIKLMEKRGIGRPSTYAEIIE 235 (259)
T ss_pred EEEEEEEEeECCHHHhhcccccCccccCCCcCCCCEeeeeeeEEEecccCCCCCCCHHHHHHHHHHCCCCchhhHHHHHH
Confidence 999999999999999998655433 5699999999999999999999999999999999999999999999999999999
Q ss_pred hhcccceEEEcCCceeeechhHHHH
Q 046997 528 KLLDRFYAIKDANTRFAPTNIGEAL 552 (807)
Q Consensus 528 ~L~~R~Yv~~~~~~~l~pT~~G~~l 552 (807)
+|++||||.++++ .|+||++|+.|
T Consensus 236 ~L~~r~Yi~~~~k-~l~~T~~G~~l 259 (259)
T smart00437 236 TLLDRGYVTKEKK-KLIPTELGIAV 259 (259)
T ss_pred HHHhCCcEEeeCC-EEeEccceecC
Confidence 9999999998754 68999999863
No 27
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=100.00 E-value=7.4e-36 Score=291.89 Aligned_cols=148 Identities=41% Similarity=0.628 Sum_probs=120.8
Q ss_pred EEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCC--
Q 046997 10 VLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPAD-- 87 (807)
Q Consensus 10 ~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~-- 87 (807)
+||||||||+|++||++||++. ..+|... +++|.+ +| ++++|||+.|||++|++|++|..|...++.+
T Consensus 2 ~LiIAEKPs~Ak~ia~~L~~~~---~~~~~~~---~~~~~~--~~--~~~~vt~~~GHl~~l~~p~~y~~~~~~~~~~~p 71 (151)
T cd03362 2 VLIIAEKPSVAKAIAKILGGGS---KKKGKGR---YYEFYG--EG--GGYVVTWASGHLLELDFPEEYDPWDKVWPLEDP 71 (151)
T ss_pred EEEEecCHHHHHHHHHHhCCCC---ccCCccc---ccceec--CC--CCEEEEEEhhHhhcccChHHhccCCCCCccccC
Confidence 6999999999999999999764 2222111 344433 33 3699999999999999999998876544443
Q ss_pred CCCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHc
Q 046997 88 LYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQN 167 (807)
Q Consensus 88 L~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~n 167 (807)
+++.++...+..+++++++.|++++++||.||||||||||||+|||+|+++++.. .+++++|||||++|+++|++||+|
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~~i~~~~~~~-~~~~v~R~~fsslT~~~I~~A~~n 150 (151)
T cd03362 72 LFPAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCV-KRKPVKRAWFSSLTPKAIRRAFKN 150 (151)
T ss_pred CcCCceEEEECccHHHHHHHHHHHHhCCCeEEEccCCCccccHHHHHHHHHhCCC-CCCcEEEEEEccCCHHHHHHHHhc
Confidence 4444444555667899999999999999999999999999999999999999863 356899999999999999999998
Q ss_pred C
Q 046997 168 L 168 (807)
Q Consensus 168 l 168 (807)
|
T Consensus 151 l 151 (151)
T cd03362 151 L 151 (151)
T ss_pred C
Confidence 6
No 28
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b
Probab=100.00 E-value=1.8e-34 Score=279.22 Aligned_cols=142 Identities=39% Similarity=0.561 Sum_probs=116.2
Q ss_pred eEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCC
Q 046997 9 NVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADL 88 (807)
Q Consensus 9 ~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L 88 (807)
++||||||||+|++||++||... +..+. + .+| .+++|||+.|||++|++|++|..|....+.++
T Consensus 1 ~~LiIaEKPs~a~~ia~~L~~~~---~~~~~----------~-~~~--~~~~v~~~~GHl~~l~~~~~~~~~~~~~~~~~ 64 (142)
T cd01028 1 KVLIIAEKPSKAKTIAKILGKGS---KKKGF----------Y-GEG--GGYVVTASVGHLLELPFPEEYVDWDKDWPLEL 64 (142)
T ss_pred CEEEEEeCHHHHHHHHHHhCCCc---ccCCc----------e-ecC--CCEEEEEEccccccCCCcccccccccCCchhh
Confidence 36999999999999999999754 22221 1 123 25899999999999999999987754333333
Q ss_pred CCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHcC
Q 046997 89 YHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQNL 168 (807)
Q Consensus 89 ~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~nl 168 (807)
+..++...+.+++.++++.|++++++||+||||||||||||+|||+|+++++. .+++++|+|||++|+++|++||+||
T Consensus 65 ~~~~~~~~~~~~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~--~~~~v~R~~fsslT~~~I~~A~~nl 142 (142)
T cd01028 65 FPFEPKYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC--DNKPVKRAWFSEITPKAIREAFKNL 142 (142)
T ss_pred CCCCceEEeCCcHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHhCC--CCCCeEEEEEccCCHHHHHHHHhCc
Confidence 33344445566788999999999999999999999999999999999999986 3468999999999999999999986
No 29
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=99.97 E-value=1e-31 Score=266.81 Aligned_cols=149 Identities=26% Similarity=0.342 Sum_probs=116.0
Q ss_pred eEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCc-------
Q 046997 9 NVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWH------- 81 (807)
Q Consensus 9 ~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~------- 81 (807)
++||||||||+|++||++||... .++.| |.++|+|.+ +++.++|||+.|||++|++|+.|..|.
T Consensus 1 ~~LiIaEKPs~Ak~Ia~~L~~~~--~~~~~---~~~~~e~~~----~~~~~~Vt~~~GHl~~l~~~~~~~~~~~~~~~~~ 71 (170)
T cd03361 1 TALMIVESPNKARTIANFFGRPS--VRRLG---GLVVYEVST----GDGVLMITASGGHVYDLVTKEGGHGVVEDDGRYV 71 (170)
T ss_pred CeEEEEeChHHHHHHHHHhCCCc--ccccC---CceeEEEec----CCeEEEEEeCCCeeecCCCccCccCccccCCcce
Confidence 37999999999999999999653 23333 456677643 234678999999999999888775432
Q ss_pred -------CCCCC------CCCCCCccc-ccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCe
Q 046997 82 -------SCDPA------DLYHAPVRK-HVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLV 147 (807)
Q Consensus 82 -------~~~p~------~L~~~p~~~-~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~ 147 (807)
.+.|. +++..|... .+++++++++++|+++++++|+||||||||||||+|+|+|+++++..+ .+
T Consensus 72 p~~~~~~~c~pc~~lF~~~~~~cp~c~~~~~~~~~~~~~~l~~l~~~~~~iiiatD~drEGe~I~~~i~~~~~~~~--~~ 149 (170)
T cd03361 72 PVYDSIKRCRDCGYQFTEDSDKCPRCGSENIDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPYN--KN 149 (170)
T ss_pred eeeeEeeccCCcccccccccccCCcCCCcCCcchHHHHHHHHHHHhhCCEEEEecCCCccHHHHHHHHHHHhccCC--CC
Confidence 22221 122234322 334678899999999999999999999999999999999999997543 47
Q ss_pred EEEEEecccCHHHHHHHHHcC
Q 046997 148 LRRARFSALIDREIHQAVQNL 168 (807)
Q Consensus 148 v~R~~~s~lt~~~I~~A~~nl 168 (807)
++|+|||+||+++|++||+||
T Consensus 150 v~R~~fs~it~~~I~~a~~n~ 170 (170)
T cd03361 150 IKRAEFHEVTRRAILEALRNP 170 (170)
T ss_pred eEEEEEecCCHHHHHHHHhCc
Confidence 999999999999999999986
No 30
>smart00436 TOP1Bc Bacterial DNA topoisomeraes I ATP-binding domain. Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit
Probab=99.97 E-value=1.7e-31 Score=235.79 Aligned_cols=89 Identities=34% Similarity=0.526 Sum_probs=84.2
Q ss_pred EEEEEecccCHHHHHHHHHcCCCCCcchHHHHHHHHHHhHhhhccchHHHHHhhhhcccccccccCCcccccCccchhhH
Q 046997 148 LRRARFSALIDREIHQAVQNLVDPNQWFADAVDARQEIDLRIGASFTRFQTMLLKNFHIDSVTDDRNLVLSYGPCQFPTL 227 (807)
Q Consensus 148 v~R~~~s~lt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~n~SR~~Tl~~~~~~~~~~~~~~~~~lS~GRVQtPtL 227 (807)
|+|+|||++|+++|++||+|+++.+.++++||+||+++||++|||+||++|+.++. ..+|+||||||||
T Consensus 1 v~R~~fs~lt~~~I~~a~~~l~~~~~~l~~a~~aR~~~D~l~G~n~Sr~~t~~~~~-----------~~ls~GRVQtptL 69 (89)
T smart00436 1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRK-----------GVLSAGRVQTPTL 69 (89)
T ss_pred CEEEEEecCCHHHHHHHHHCcccccHHHHHHHHHHHHHHHHHhHhhhHHHHHHhCC-----------CCcceecchHHHH
Confidence 58999999999999999999999888999999999999999999999999987642 3799999999999
Q ss_pred HHHHHHHHHHHcccccceEE
Q 046997 228 GFVVERYWEIQAHESEEFWT 247 (807)
Q Consensus 228 ~lIv~Re~eI~~F~p~~y~~ 247 (807)
+|||+||+||+||+|++||.
T Consensus 70 ~lIv~R~~ei~~F~~~~y~~ 89 (89)
T smart00436 70 GLIVEREREIKNFVPKPYWE 89 (89)
T ss_pred HHHHHHHHHHHcCCCCCCCC
Confidence 99999999999999999994
No 31
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=99.97 E-value=1.4e-30 Score=245.24 Aligned_cols=122 Identities=27% Similarity=0.339 Sum_probs=104.6
Q ss_pred EEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCCC
Q 046997 10 VLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADLY 89 (807)
Q Consensus 10 ~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L~ 89 (807)
.||||||||+|++||++||.. ++||||.|||++|+.|++|..|.. ++
T Consensus 2 ~LiIaEKp~~a~~ia~~Lg~~----------------------------~~v~~~~GHl~~l~~p~~~~~~~~-----~~ 48 (123)
T cd03363 2 KLVIVESPAKAKTIKKYLGKE----------------------------YEVLASVGHIRDLPKKGLGVDGED-----DG 48 (123)
T ss_pred EEEEEeCHHHHHHHHHHhCCC----------------------------cEEEeccCccccCCCcccCCChhc-----cC
Confidence 599999999999999999751 479999999999999999865531 21
Q ss_pred CCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHcC
Q 046997 90 HAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQNL 168 (807)
Q Consensus 90 ~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~nl 168 (807)
..| ...+.++++++++.|+++++++|+||||||||||||+|+|+|+++++. +.+|+|+|||++|+++|++||+||
T Consensus 49 ~~~-~~~~~~~~~~~~~~ik~l~~~~~eiiiAtD~drEGe~i~~~i~~~~~~---~~~v~Rl~~sslt~~~I~~A~~n~ 123 (123)
T cd03363 49 FEP-KYVVIPGKKKVVKELKKLAKKADEIYLATDPDREGEAIAWHLAEVLKL---KKNVKRVVFNEITKEAIKEALKNP 123 (123)
T ss_pred cCc-eEEECccHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHcCC---CCCeEEEEEccCCHHHHHHHHhCc
Confidence 112 233456788899999999999999999999999999999999999875 458999999999999999999986
No 32
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=99.87 E-value=9.6e-23 Score=185.59 Aligned_cols=100 Identities=37% Similarity=0.538 Sum_probs=87.2
Q ss_pred EEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCCC
Q 046997 10 VLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADLY 89 (807)
Q Consensus 10 ~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L~ 89 (807)
.||||||||+|++|+++|+.. .+.|+|+.||++++..|+.|..
T Consensus 1 ~liIvE~ps~a~~i~~~l~~~---------------------------~~~v~~~~Ghl~~~~~~~~~~~---------- 43 (100)
T PF01751_consen 1 ELIIVEKPSDAKAIAKALGGE---------------------------EYIVIATSGHLLELAKPEDYDP---------- 43 (100)
T ss_dssp EEEEESSHHHHHHHHHHSSTT---------------------------TEEEEEESSSSEESTTSSHHHC----------
T ss_pred CEEEEeCHHHHHHHHHHcCCC---------------------------CEEEEEeCCccccccccccccc----------
Confidence 489999999999999999832 2579999999999999988742
Q ss_pred CCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEeccc
Q 046997 90 HAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSAL 156 (807)
Q Consensus 90 ~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~l 156 (807)
.++.++++.|++++.++|.||+|||||||||+|+|+|+++++..++.. ++|+|||++
T Consensus 44 ---------~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i~~~~~~~~~~~-~~R~~~~~i 100 (100)
T PF01751_consen 44 ---------KDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWEIIELLGKNNPKL-IKRVWFSSI 100 (100)
T ss_dssp ---------HTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHHHHHHHHHSHHH-TTEEEEESS
T ss_pred ---------ccccccchhhHHHhhhccEeeecCCCChHHHHHHHHHHHHHhHhCCCc-CCEEEEecC
Confidence 246788899999999999999999999999999999999999877543 799999986
No 33
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=99.04 E-value=2.7e-10 Score=110.24 Aligned_cols=78 Identities=31% Similarity=0.489 Sum_probs=57.4
Q ss_pred cccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEEEeeccCccCCCCCccC
Q 046997 634 VVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVN 713 (807)
Q Consensus 634 ~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~ 713 (807)
+...||+| ++.|+++.+++| .|+|||+||+|++ ...+ ......+...||+|+.+.+++. +++.++.|
T Consensus 16 ~~~~Cp~C-g~~m~~~~~~~g-~f~gCs~yP~C~~-~~~~--~~~~~~~~~~Cp~C~~~~~~~k--~~~~~~~f------ 82 (140)
T COG0551 16 TGQICPKC-GKNMVKKFGKYG-IFLGCSNYPKCDY-YEPE--KAIAEKTGVKCPKCGKGLLVLK--KGRFGKNF------ 82 (140)
T ss_pred cCccCCcC-CCeeEEEEccCC-eEEEeCCCCCCCC-Cccc--ccccccCceeCCCCCCCceEEE--eccCCceE------
Confidence 57789999 689999999999 7899999999997 2221 1223456889999997555543 55555444
Q ss_pred cccc---CCCCChhHH
Q 046997 714 HLGC---IGGCDETLR 726 (807)
Q Consensus 714 ~~~C---~~~C~~~~~ 726 (807)
++| | .|.++.+
T Consensus 83 -~~~~~~P-kc~~~~~ 96 (140)
T COG0551 83 -LGCSNYP-KCRFTEK 96 (140)
T ss_pred -EeecCCC-cCceeec
Confidence 444 7 8998887
No 34
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=98.95 E-value=7.3e-10 Score=82.64 Aligned_cols=37 Identities=30% Similarity=0.847 Sum_probs=33.3
Q ss_pred cccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCC
Q 046997 636 RQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPG 674 (807)
Q Consensus 636 ~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~ 674 (807)
..||+| ++.|++|.+++| .|||||+||+|+++.|+++
T Consensus 2 ~~CP~C-g~~lv~r~~k~g-~F~~Cs~yP~C~~~~~~~~ 38 (39)
T PF01396_consen 2 EKCPKC-GGPLVLRRGKKG-KFLGCSNYPECKYTEPLPK 38 (39)
T ss_pred cCCCCC-CceeEEEECCCC-CEEECCCCCCcCCeEeCCC
Confidence 479999 589999999999 5799999999999999864
No 35
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=98.95 E-value=1.2e-09 Score=134.02 Aligned_cols=101 Identities=21% Similarity=0.434 Sum_probs=69.4
Q ss_pred hhhhhhhhhccCCCCCCc---ccc------------cccccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCC
Q 046997 611 LLEAMGIFFERWSGGEDQ---QAA------------GEVVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGS 675 (807)
Q Consensus 611 ~~~~~g~fl~cs~~p~~~---~~~------------~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~ 675 (807)
...++|.|++|++||.+. +.. ......||+| ++.|+++.+++|. ||+|++||+|+++.++++.
T Consensus 606 k~gr~G~Fl~Cs~yP~C~~t~~~~~~~~~~~~~~~~~~~~~~CP~C-g~~m~lK~gr~G~-Fl~Cs~yP~Ck~~~~l~k~ 683 (860)
T PRK06319 606 IWAKNRYFYGCSEYPECDYKTSEEELTFNKEDYAEDTPWDSPCPLC-GGEMKVRHGRFGT-FLGCENYPECRGIINIHKK 683 (860)
T ss_pred EecCCCceeeccCCccccccCCcccccccccccccccccCCcCccC-CCeeEEecCCCCc-eeeCCCCccccccccCCcc
Confidence 356789999999999431 111 0124579999 5789999999998 5999999999988766532
Q ss_pred cccc--ccccCccCC--CCCCceEEEEeeccCccCCCCCccCcccc---CCCCChh
Q 046997 676 VSEA--AVTTNTCNS--CTPGPVYLIQFKFRQHEIPPGFNVNHLGC---IGGCDET 724 (807)
Q Consensus 676 ~~~~--~~t~~~CP~--Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C---~~~C~~~ 724 (807)
.... ..++..||+ |+ +.++. +++|+|+.| ++| | .|++.
T Consensus 684 ~~~~~~~~~~~~CP~~~C~-g~l~~--r~gr~G~~f-------~~Cs~yp-~C~~~ 728 (860)
T PRK06319 684 GEEGIEPEETVPCPAIGCT-GHIVK--RRSRFNKMF-------YSCSEYP-ACSVI 728 (860)
T ss_pred cccccCcccCCCCCCcCCC-CcEEE--EecCCCCee-------eccCCCC-CCcee
Confidence 1100 113578996 77 45553 467777644 678 4 78866
No 36
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=98.63 E-value=4.4e-08 Score=94.84 Aligned_cols=82 Identities=26% Similarity=0.436 Sum_probs=61.6
Q ss_pred HHHHhhhhhhhhhccCCCCCCc------ccccccccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccc
Q 046997 607 KKVKLLEAMGIFFERWSGGEDQ------QAAGEVVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAA 680 (807)
Q Consensus 607 ~~~k~~~~~g~fl~cs~~p~~~------~~~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~ 680 (807)
.++....+++.|++|++||... .....+...||.|+.+.+++++++.|+.|++|++||+|+++.|...
T Consensus 26 ~m~~~~~~~g~f~gCs~yP~C~~~~~~~~~~~~~~~~Cp~C~~~~~~~k~~~~~~~f~~~~~~Pkc~~~~~~~~------ 99 (140)
T COG0551 26 NMVKKFGKYGIFLGCSNYPKCDYYEPEKAIAEKTGVKCPKCGKGLLVLKKGRFGKNFLGCSNYPKCRFTEKPKP------ 99 (140)
T ss_pred eeEEEEccCCeEEEeCCCCCCCCCcccccccccCceeCCCCCCCceEEEeccCCceEEeecCCCcCceeecCCc------
Confidence 3334455667999999999433 2223457899999658899999999988899999999999998633
Q ss_pred cccCccCCCCCCceE
Q 046997 681 VTTNTCNSCTPGPVY 695 (807)
Q Consensus 681 ~t~~~CP~Cg~~~l~ 695 (807)
....||+|++..++
T Consensus 100 -~~~~cp~c~~~~~~ 113 (140)
T COG0551 100 -KEKKCPKCGSRKLV 113 (140)
T ss_pred -ccccCCcCCCceeE
Confidence 34569999963333
No 37
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=98.43 E-value=1.1e-06 Score=75.45 Aligned_cols=73 Identities=33% Similarity=0.439 Sum_probs=56.8
Q ss_pred eEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCC
Q 046997 9 NVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADL 88 (807)
Q Consensus 9 ~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L 88 (807)
+.|+|+|.|.-|.++.++++.+ ..+.++.||+.
T Consensus 1 ~~l~ivEg~~da~~~~~~~~~~----------------------------~~~~~~~G~~~------------------- 33 (76)
T smart00493 1 KVLIIVEGPADAIALEKAGGFG----------------------------GNVVALGGHLL------------------- 33 (76)
T ss_pred CEEEEEcCHHHHHHHHHhcCCC----------------------------EEEEEEeeeec-------------------
Confidence 3689999999999999876521 24566679861
Q ss_pred CCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhh
Q 046997 89 YHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRA 141 (807)
Q Consensus 89 ~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~ 141 (807)
...+++.|++...+ ++||||+|+|+||+.++++|.+++..
T Consensus 34 ------------~~~~~~~l~~~~~~-~~Iii~~D~D~~G~~~~~~i~~~l~~ 73 (76)
T smart00493 34 ------------KKEIIKLLKRLAKK-KEVILATDPDREGEAIAWKLAELLKP 73 (76)
T ss_pred ------------HHHHHHHHHHHhcC-CEEEEEcCCChhHHHHHHHHHHHhhh
Confidence 12345667777665 88999999999999999999998764
No 38
>PRK07219 DNA topoisomerase I; Validated
Probab=98.38 E-value=4.8e-07 Score=111.10 Aligned_cols=121 Identities=16% Similarity=0.216 Sum_probs=77.5
Q ss_pred hhHHHHHHHHHHHHcccccceEEEEEEeecCCceEEEEec----cC--CcCCHHHH-HHHHHHhccCCCeEEEEEEeeee
Q 046997 225 PTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWM----RG--HLFDYTSA-VIIYEMCVQEPTATVTKVRQQEK 297 (807)
Q Consensus 225 PtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--r~~d~~~a-~~~~~~~~~~~~~~V~~v~~k~~ 297 (807)
-+-.||++|...... .|-.|=...+.+..++..|.+... .| .++..+.. +..+-.+..+..+.+.+++.+++
T Consensus 391 ~lY~LI~rrfla~~~-~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~vy~~~~~~~~~lP~l~~G~~~~~~~~~~~~~ 469 (822)
T PRK07219 391 KVYELIVRRFLATLA-DPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEKFDEKELPDLEEGEKLKVNKIEIEAK 469 (822)
T ss_pred HHHHHHHHHHHHHhC-ccceeeEEEEEEEeCCeEEEEEEEEEccCCcHhhcCccccccccCCCCCCCCEeeeeeeEeccc
Confidence 445689999887432 344455566666666666665432 11 12211100 11122333345677888888899
Q ss_pred eeCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHhhcCceeccCCCCcccCC
Q 046997 298 LKYPPYPLSTIELEKRASRYFRMSSEHTMK-VAEDLYQAGFISYPRTETDSFSS 350 (807)
Q Consensus 298 ~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~-iaQ~LYE~g~ISYPRTds~~l~~ 350 (807)
.+.||.+|+-++|.++|-+ .|+.-.-|.. |.+.|+++||| +-....+|.
T Consensus 470 ~T~PP~rytea~Li~~Me~-~GIGT~ATra~iI~~L~~R~Yv---~~~~~l~pT 519 (822)
T PRK07219 470 ETQPPKRYTQSSLIKEMEK-RGLGTKATRHDIIEKLYKRGYV---IEGDPPRPT 519 (822)
T ss_pred ccCCCCCCCHHHHHHHHHh-CCCCCCccHHHHHHHHHhcCcE---ecCCEeeec
Confidence 9999999999999999987 6996665655 89999999999 444434444
No 39
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=97.69 E-value=0.00026 Score=65.45 Aligned_cols=45 Identities=18% Similarity=0.211 Sum_probs=35.5
Q ss_pred HHHHHHhh--cCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEe
Q 046997 107 TLEEEARR--CQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARF 153 (807)
Q Consensus 107 ~lk~~~~~--~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~ 153 (807)
.|.+.+++ .++||+|||||+|||.+++.|.+.++..+ .+|.|+-+
T Consensus 47 ~L~~ri~~~~i~EVIlA~~pt~EGe~Ta~yi~~~l~~~~--~kvsRlA~ 93 (112)
T cd01025 47 KLLERIAKGQVKEVILATNPTVEGEATALYIAKLLKDFG--VKVTRLAQ 93 (112)
T ss_pred HHHHHHhcCCCcEEEEecCCCchHHHHHHHHHHHHhHcC--CCeEEEEE
Confidence 34444443 48999999999999999999999998643 46888754
No 40
>cd00188 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=97.10 E-value=0.0048 Score=52.31 Aligned_cols=81 Identities=25% Similarity=0.337 Sum_probs=56.8
Q ss_pred EEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCCC
Q 046997 10 VLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADLY 89 (807)
Q Consensus 10 ~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L~ 89 (807)
.+||+|.++-+..+......+ ..+.++.||...
T Consensus 2 ~viivEg~~d~~~l~~~~~~~----------------------------~~~~~~~G~~~~------------------- 34 (83)
T cd00188 2 KLIIVEGPSDALALAQAGGYG----------------------------GAVVALGGHALN------------------- 34 (83)
T ss_pred EEEEEecHHHHHHHHHHcCCC----------------------------EEEEEEccEEcH-------------------
Confidence 589999999999999875421 245666777532
Q ss_pred CCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEE
Q 046997 90 HAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRAR 152 (807)
Q Consensus 90 ~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~ 152 (807)
.....+..+.+....|++++|+|.+|+.+++.+.+..... ...+.|++
T Consensus 35 -------------~~~~~~~~~~~~~~~v~i~~D~D~~g~~~~~~~~~~~~~~--~~~~~~~~ 82 (83)
T cd00188 35 -------------KTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLKSL--GKKVRRLL 82 (83)
T ss_pred -------------HHHHHHHHHhcCCCEEEEEcCCChhHHHHHHHHHHHHHhc--CCceEEee
Confidence 1112344444446899999999999999999999987653 23466654
No 41
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=96.70 E-value=0.0022 Score=79.69 Aligned_cols=83 Identities=18% Similarity=0.172 Sum_probs=54.8
Q ss_pred hhhhhhhhccCCC---CCCcc----cc--------------cccccccCCCCCcceEEEecCCCCceee-----------
Q 046997 612 LEAMGIFFERWSG---GEDQQ----AA--------------GEVVRQCGICQESNMVLKKSRDGNLMVG----------- 659 (807)
Q Consensus 612 ~~~~g~fl~cs~~---p~~~~----~~--------------~~~~~~CP~C~g~~lv~r~~k~G~~f~g----------- 659 (807)
.+++|.|++|++| |.+.. .+ ....+.||.| |..++++.+++|.| +.
T Consensus 601 ~gr~G~Fl~Cs~y~~~p~C~~~~~l~~~~~~~~~~~~~~~~~~~lg~~P~c-g~~i~~r~Gr~Gpy-v~~~~~~~~~~~s 678 (859)
T PRK07561 601 TGKTGVFLGCSGYALKERCKTTRNLTPEEETLNVLEGEDAETRALGADPEC-GTAMVLRSGRFGPY-VQEGEGDKPRRLS 678 (859)
T ss_pred ecCCCCeeeccCCcCCCCCCCCCCCCccchhhhhhhccccCccccCCCCCC-CCeeEEecCCCCCe-eecccCCCCceec
Confidence 4678899999998 53211 00 0124679999 67899999999975 66
Q ss_pred -c-cCCCCCCcce------ecCCCccccccccCccCCCCCCceEEEEeeccCccC
Q 046997 660 -C-LAFPQCRNAV------WLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEI 706 (807)
Q Consensus 660 -C-s~yP~C~~~~------~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~ 706 (807)
| +.+|+|.... .+|+ ....||+||. +++. +++|+|.+
T Consensus 679 ic~~~~p~c~~~e~a~~ll~~pr-------~lg~cPecg~-~i~~--k~gr~G~y 723 (859)
T PRK07561 679 LPKGNNPECVGLEIALGLLSLPR-------PVGEHPECGS-EIQA--KIGRFGPY 723 (859)
T ss_pred cCCCCCCCcCCHHHHHhhhcccc-------ccCcCCCCCC-eeEE--ecCCCCCe
Confidence 9 6789997431 2222 2346999995 4553 36777765
No 42
>PRK06599 DNA topoisomerase I; Validated
Probab=96.46 E-value=0.0026 Score=77.07 Aligned_cols=60 Identities=25% Similarity=0.459 Sum_probs=43.5
Q ss_pred hhhhhhhccCCCCCCccc---ccc------cc-----cccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCC
Q 046997 613 EAMGIFFERWSGGEDQQA---AGE------VV-----RQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPG 674 (807)
Q Consensus 613 ~~~g~fl~cs~~p~~~~~---~~~------~~-----~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~ 674 (807)
...|.|++|+++|++... +.. .. ..||+|+ ..+++++++.|. |++|++||.|+++.++|+
T Consensus 601 ~k~g~F~~Cs~~p~C~~~~~~~~~~~~~~~~~~~~~~~~Cp~C~-~~~~~kkgk~g~-f~~Cs~yp~ck~~~~~~~ 674 (675)
T PRK06599 601 GKNGKFLGCSGYPECKYTKNITRDEDEPIEEEEIVEEEKCPKCG-GPLVLKKGRYGK-FLACSGYPECKHIKPLEK 674 (675)
T ss_pred cCCCceeeCCCCCccCCCCCCccccccccccccccccCCCCCCC-CeeEEEeCCCCc-eeeCCCCCCCCceeeCCC
Confidence 356789999998743211 000 12 2899995 568888888887 689999999999998865
No 43
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=96.36 E-value=0.0075 Score=52.79 Aligned_cols=42 Identities=21% Similarity=0.269 Sum_probs=32.5
Q ss_pred HHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEE
Q 046997 106 KTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRAR 152 (807)
Q Consensus 106 ~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~ 152 (807)
+.|++. .+.||++||+|+.||.|.+.+.++++. +...++|+.
T Consensus 39 ~~l~~~---~~~VIiltD~D~aG~~i~~~~~~~l~~--~~~~~~~~~ 80 (81)
T cd01027 39 ELIKKA---YRGVIILTDPDRKGEKIRKKLSEYLSG--PVPEIKRAF 80 (81)
T ss_pred HHHHHh---CCEEEEEECCCHHHHHHHHHHHHHhcc--cCCCeeecc
Confidence 444444 689999999999999999999999865 223467654
No 44
>PRK00076 recR recombination protein RecR; Reviewed
Probab=96.08 E-value=0.084 Score=53.80 Aligned_cols=55 Identities=13% Similarity=0.177 Sum_probs=42.4
Q ss_pred hhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEE--------ecccCHHHHHHHHHcCC
Q 046997 113 RRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRAR--------FSALIDREIHQAVQNLV 169 (807)
Q Consensus 113 ~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~--------~s~lt~~~I~~A~~nl~ 169 (807)
.+.++||+||+|+.|||..++.|.+.++..+ .+|.|+= +.=++.-.+.+||++-+
T Consensus 132 ~~v~EVIlA~~pt~EGe~Ta~yi~~~lk~~~--ikvtRiA~GiP~G~~ley~D~~TL~~Al~~R~ 194 (196)
T PRK00076 132 GEVKEVILATNPTVEGEATAHYIARLLKPLG--VKVTRLAHGVPVGGELEYVDEGTLSRALEGRR 194 (196)
T ss_pred CCCCEEEEeCCCCchHHHHHHHHHHHHHHcC--CCeeeeeeCCCCCcceeeCCHHHHHHHHHhCc
Confidence 4578999999999999999999999998654 4688874 23455666777776543
No 45
>PRK05582 DNA topoisomerase I; Validated
Probab=96.02 E-value=0.0048 Score=74.53 Aligned_cols=58 Identities=24% Similarity=0.524 Sum_probs=42.0
Q ss_pred hhhhhhccCCCCCCccc---ccccccccCCCCCcceEEEecCCCCceeeccCCCCCCcceec
Q 046997 614 AMGIFFERWSGGEDQQA---AGEVVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWL 672 (807)
Q Consensus 614 ~~g~fl~cs~~p~~~~~---~~~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~ 672 (807)
..+.|++|++++++... .......||+| +..+++++++.|+.|++|++||.|+++.|.
T Consensus 587 k~gkf~~Cs~~~~C~~~~~~~~~~~~~CP~C-~~~l~l~k~k~gk~f~~Cs~~p~C~~~~~~ 647 (650)
T PRK05582 587 RYGKFIACSNFPDCRNTKPIVKEIGVKCPKC-GGQIVERKSKKGRKFYGCSRYPECDFVSWD 647 (650)
T ss_pred CCCceeecCCccccccCCCcccccCCCCCCC-CCceEEEcCCCCceeeccCCCCCCCcccCC
Confidence 34678999998744211 11234689999 567777777778778999999999987653
No 46
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=95.71 E-value=0.0068 Score=37.46 Aligned_cols=17 Identities=41% Similarity=1.099 Sum_probs=16.0
Q ss_pred ccccccCCCccCCCCCC
Q 046997 761 ACIYCQQMGHSSSDCPS 777 (807)
Q Consensus 761 ~c~~c~~~g~~~~~~~~ 777 (807)
.|..|++.||+..+||+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 59999999999999995
No 47
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=94.21 E-value=0.031 Score=41.83 Aligned_cols=32 Identities=31% Similarity=0.712 Sum_probs=22.5
Q ss_pred CccCCCCCCceEEEEeeccCccCCCCCccCccccCC--CCChhHH
Q 046997 684 NTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIG--GCDETLR 726 (807)
Q Consensus 684 ~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~--~C~~~~~ 726 (807)
..||+|| ++|+. +++++|.+ ++|.+ .|+++.+
T Consensus 2 ~~CP~Cg-~~lv~--r~~k~g~F--------~~Cs~yP~C~~~~~ 35 (39)
T PF01396_consen 2 EKCPKCG-GPLVL--RRGKKGKF--------LGCSNYPECKYTEP 35 (39)
T ss_pred cCCCCCC-ceeEE--EECCCCCE--------EECCCCCCcCCeEe
Confidence 5799999 56664 35666633 89942 8998765
No 48
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=93.84 E-value=0.071 Score=37.05 Aligned_cols=32 Identities=19% Similarity=0.450 Sum_probs=17.0
Q ss_pred ccCCCCCcceEEEecCCCC-ceeeccCCCCCCcc
Q 046997 637 QCGICQESNMVLKKSRDGN-LMVGCLAFPQCRNA 669 (807)
Q Consensus 637 ~CP~C~g~~lv~r~~k~G~-~f~gCs~yP~C~~~ 669 (807)
.||+|+-+.|+--...+|. ..+.||| |.|++-
T Consensus 3 lcpkcgvgvl~pvy~~kgeikvfrcsn-pacdye 35 (36)
T PF09151_consen 3 LCPKCGVGVLEPVYNQKGEIKVFRCSN-PACDYE 35 (36)
T ss_dssp B-TTTSSSBEEEEE-TTS-EEEEEES--TT---E
T ss_pred cCCccCceEEEEeecCCCcEEEEEcCC-CccccC
Confidence 5999965666544444553 3579998 999863
No 49
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=93.32 E-value=0.31 Score=52.25 Aligned_cols=111 Identities=14% Similarity=0.177 Sum_probs=73.2
Q ss_pred hHHHHHHHHHHHHcccccc-eEEEEEEeecCCceEEEEec----cC--CcCCHHHH--HHHHHHhccCCCeEEEEEEeee
Q 046997 226 TLGFVVERYWEIQAHESEE-FWTINCSHKSEEGTATFSWM----RG--HLFDYTSA--VIIYEMCVQEPTATVTKVRQQE 296 (807)
Q Consensus 226 tL~lIv~Re~eI~~F~p~~-y~~i~~~~~~~~~~~~~~~~----~~--r~~d~~~a--~~~~~~~~~~~~~~V~~v~~k~ 296 (807)
+-.||+.|... +|-|.. |-...+.+..++..|.+... .| .++..+.. ...+-.+..+..+.|.+++..+
T Consensus 124 iY~lI~rr~la--~~~~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~lp~~~~g~~~~~~~~~~~e 201 (259)
T smart00437 124 LYELIWRRFLA--SQMPDAKYEETKVIIKIGGEKFKAKGKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEE 201 (259)
T ss_pred HHHHHHHHHHH--HhChhheEEEEEEEEEECCeEEEEEEEEEeECCHHHhhcccccCccccCCCcCCCCEeeeeeeEEEe
Confidence 45688888776 455543 44555666666656665422 11 12221111 1112223344567888899999
Q ss_pred eeeCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHhhcCcee
Q 046997 297 KLKYPPYPLSTIELEKRASRYFRMSSEHTMK-VAEDLYQAGFIS 339 (807)
Q Consensus 297 ~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~-iaQ~LYE~g~IS 339 (807)
++..||.+|+-++|..+|-+ .|+.-.-|.. |.++|.++|||.
T Consensus 202 ~~TkPP~~~Te~tLl~~Me~-~GIGTpATra~iIe~L~~r~Yi~ 244 (259)
T smart00437 202 KKTKPPARYTEASLIKLMEK-RGIGRPSTYAEIIETLLDRGYVT 244 (259)
T ss_pred cccCCCCCCCHHHHHHHHHH-CCCCchhhHHHHHHHHHhCCcEE
Confidence 99999999999999999987 6996655554 899999999996
No 50
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=93.25 E-value=0.49 Score=48.27 Aligned_cols=105 Identities=17% Similarity=0.295 Sum_probs=69.6
Q ss_pred CCCceEEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCC
Q 046997 5 GRPINVLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCD 84 (807)
Q Consensus 5 ~~~~~~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~ 84 (807)
-++..+=||+|=.|-+..|+++|-.-. . | + .++..|+|.
T Consensus 4 k~pVDVRIiVEGAsDvE~iSkalQr~a----L-G---------------~-eYnITisSI-------------------- 42 (290)
T COG4026 4 KTPVDVRIIVEGASDVEVISKALQRLA----L-G---------------S-EYNITISSI-------------------- 42 (290)
T ss_pred CCcceEEEEeeccchHHHHHHHHHHhh----h-c---------------c-cceeEEEee--------------------
Confidence 467778899999999999999985421 0 1 1 012334432
Q ss_pred CCCCCCCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEec------ccCH
Q 046997 85 PADLYHAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFS------ALID 158 (807)
Q Consensus 85 p~~L~~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s------~lt~ 158 (807)
+|..... +-++.+..||.|+||||+||-|--+|....+.++..- ..|.||.+- -++.
T Consensus 43 ------------iPTT~~e---IA~raaeGADlvlIATDaD~~GReLA~kf~eeLrg~V--GhiERmK~PiGHDvEhiD~ 105 (290)
T COG4026 43 ------------IPTTNVE---IAKRAAEGADLVLIATDADRVGRELAEKFFEELRGMV--GHIERMKIPIGHDVEHIDV 105 (290)
T ss_pred ------------ccCchHH---HHHHhhccCCEEEEeecCcchhHHHHHHHHHHHHHhh--hhhheeccCCCCCccccCH
Confidence 1122222 3467888999999999999999999999988876542 257888763 3444
Q ss_pred HHHHHHHHc
Q 046997 159 REIHQAVQN 167 (807)
Q Consensus 159 ~~I~~A~~n 167 (807)
+=|++-++|
T Consensus 106 elvrkEl~n 114 (290)
T COG4026 106 ELVRKELKN 114 (290)
T ss_pred HHHHHHHHH
Confidence 444444443
No 51
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=92.72 E-value=0.19 Score=43.68 Aligned_cols=35 Identities=17% Similarity=0.312 Sum_probs=23.7
Q ss_pred cCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEE
Q 046997 115 CQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRA 151 (807)
Q Consensus 115 ~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~ 151 (807)
..+||+|+|+|.+|+..+.+|.+.+...+ .+|+|+
T Consensus 46 ~~~Vii~~D~D~~G~~~a~~i~~~l~~~g--i~v~~v 80 (81)
T PF13662_consen 46 VKEVIIAFDNDKAGEKAAQKIAKKLLPLG--IRVTRV 80 (81)
T ss_dssp -SEEEEEEESSHHHHHHHHHHHHHHG-----------
T ss_pred CceEEEEeCcCHHHHHHHHHHHHHHHhhc--cccccC
Confidence 57899999999999999999999876443 356654
No 52
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=92.44 E-value=0.22 Score=44.33 Aligned_cols=79 Identities=19% Similarity=0.472 Sum_probs=43.7
Q ss_pred ccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCC---------------------CccccccccCccCCCCCCceE
Q 046997 637 QCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPG---------------------SVSEAAVTTNTCNSCTPGPVY 695 (807)
Q Consensus 637 ~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~---------------------~~~~~~~t~~~CP~Cg~~~l~ 695 (807)
.||.| |..|++..+..-. -+.|+ .|-|..++.. .......|+..||.||....+
T Consensus 3 FCP~C-gn~Live~g~~~~-rf~C~---tCpY~~~I~~ei~~r~~~~~Kevd~vlgg~~a~~nv~~t~~~Cp~Cgh~ray 77 (105)
T KOG2906|consen 3 FCPTC-GNMLIVESGESCN-RFSCR---TCPYVFPISREISSRKYPKLKEVDDVLGGDEAWENVDQTEATCPTCGHERAY 77 (105)
T ss_pred ccCCC-CCEEEEecCCeEe-eEEcC---CCCceeeEeeeeeccccCchhhhhhhcCCcccccchhhccCcCCCCCCCceE
Confidence 59999 5666666543322 26775 4666544321 112233468889999976655
Q ss_pred EEEeeccCccCCCCCccCccccCCCCChh
Q 046997 696 LIQFKFRQHEIPPGFNVNHLGCIGGCDET 724 (807)
Q Consensus 696 ~~~~k~~~g~~~~~~~~~~~~C~~~C~~~ 724 (807)
-.+..-|...-|. ..++.|. +|.+.
T Consensus 78 F~qlQtRSADEPm---T~FYkC~-~C~~~ 102 (105)
T KOG2906|consen 78 FMQLQTRSADEPM---TTFYKCC-KCKHR 102 (105)
T ss_pred EEEeeeccCCCcH---hHhhhhh-ccccc
Confidence 4444444332221 1336688 78654
No 53
>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....
Probab=92.31 E-value=0.41 Score=54.64 Aligned_cols=115 Identities=14% Similarity=0.180 Sum_probs=72.1
Q ss_pred hhhHHHHHHHHHHHHcccccc-eEEEEEEeecCCceEEEEecc----C--CcCCHHHHHH---HHHHhccCCCeEEEEEE
Q 046997 224 FPTLGFVVERYWEIQAHESEE-FWTINCSHKSEEGTATFSWMR----G--HLFDYTSAVI---IYEMCVQEPTATVTKVR 293 (807)
Q Consensus 224 tPtL~lIv~Re~eI~~F~p~~-y~~i~~~~~~~~~~~~~~~~~----~--r~~d~~~a~~---~~~~~~~~~~~~V~~v~ 293 (807)
--+-.||+.|..+. |-|.. |-...+.+..++..|.+.... | .+++...... .+..+..+..+.+.+++
T Consensus 226 ~~vY~LI~rr~la~--~~~~~~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~~~~~~~~~~~~~~lp~l~~g~~~~~~~~~ 303 (403)
T PF01131_consen 226 RKVYDLIARRFLAA--FMPDAKYEKTTVTFEVGGEEFKASGKVIIDPGWKKVYPYEEEEDEEEDLPSLKEGDEIPIEDVE 303 (403)
T ss_dssp HHHHHHHHHHHHHH--TS--EEEEEEEEEEEETTEEEEEEEEEEEEHGGGGCS-HCHCCTTSBB-----TTEEEEEEEEE
T ss_pred HHHHHHHHHHHHHH--HHHHHheeeEEEEEEecCcEEEEEEeEEEECceeEEEEcccccccccccccccCCcEEeecccc
Confidence 34667888888774 55554 445666777766677765421 1 2222111110 12334444457788899
Q ss_pred eeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHhhcCceecc
Q 046997 294 QQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMK-VAEDLYQAGFISYP 341 (807)
Q Consensus 294 ~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~-iaQ~LYE~g~ISYP 341 (807)
.++++..||.+|+-++|...|-+ .|+.-.-|.. |.+.|.++|||.--
T Consensus 304 ~~e~~TkPP~~~Te~~Ll~~Me~-~GIGTpATra~iI~~L~~r~Yi~~~ 351 (403)
T PF01131_consen 304 IKEKKTKPPKRYTEASLLKAMEK-AGIGTPATRASIIEKLIKRGYIERS 351 (403)
T ss_dssp EEEEEEESS--EBHHHHHHHHHH-TTSS-TTTHHHHHHHHHHTTSEEE-
T ss_pred hhhhccCCCCCCCHHHHHhhhhh-cCCCccccHHHHHHHhhccceeecc
Confidence 99999999999999999999965 6997665554 89999999999875
No 54
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=90.34 E-value=0.49 Score=57.07 Aligned_cols=114 Identities=11% Similarity=0.070 Sum_probs=76.5
Q ss_pred HHHHHHHHHHHHh-cCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccCCccCCccCCCCeeeeeeeEeecC
Q 046997 416 KLYELVVRHFLAC-VSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWGGLVIPTYVHGQQFIPTTLTLDSG 494 (807)
Q Consensus 416 ~vY~lI~rrfla~-~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~~~~~~~i~e~ 494 (807)
=+-.||+.|.... -..|..|-...+.+..++..|.+.... + .++..+ ..+..+-.++..+.+.+.++.-+++
T Consensus 195 PtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~----~--~~~~~~-~a~~~~~~~~~~~~~~V~~v~~~~~ 267 (618)
T TIGR01057 195 PTLAFLVEREREINLFVPKPYWVIKATLEKGGGVFDARPEK----W--KIWSEE-EAKSIKEELKKSPWAAVEEVRSERS 267 (618)
T ss_pred hHHHHHHHhHHHHHcCcCCccEEEEEEEecCCceEEEEEcc----C--CcCCHH-HHHHHHHHHhCCCCeEEEEEEeeee
Confidence 3456777777663 234556666677777777677765310 0 111111 0111122333333567778889999
Q ss_pred ccCCCCCCCHHHHHHHHH-hCCCCCccchHHHHHhhcccceEEE
Q 046997 495 VTRPPPLLSEADLLSCMD-KAGIGTDATMHDHIKKLLDRFYAIK 537 (807)
Q Consensus 495 ~T~PP~~~Tea~Li~~Me-~~GIGTpATra~iI~~L~~R~Yv~~ 537 (807)
++.||.+|+-++|...|- +.|++..-|. .|.++|.+.|||.-
T Consensus 268 ~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~iaQ~LYe~g~ISY 310 (618)
T TIGR01057 268 ILKPPPPFDLGTLQREAYRIFGFSPKKTQ-SIAQELYEEALISY 310 (618)
T ss_pred eccCCCCccHHHHHHHHHHhcCCCHHHHH-HHHHHHHhcCceee
Confidence 999999999999999876 5699999988 89999999999963
No 55
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=90.10 E-value=0.15 Score=36.27 Aligned_cols=23 Identities=35% Similarity=0.678 Sum_probs=19.6
Q ss_pred CcccccccccccCCCccCCCCCC
Q 046997 755 SNHRQRACIYCQQMGHSSSDCPS 777 (807)
Q Consensus 755 ~~~~~~~c~~c~~~g~~~~~~~~ 777 (807)
..|..-.|-.|+++|||-.+||.
T Consensus 4 ~pP~~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 4 KPPPGYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCCCCCEeecCCCCCccHhHCCC
Confidence 34555679999999999999998
No 56
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=89.64 E-value=0.43 Score=36.83 Aligned_cols=35 Identities=23% Similarity=0.600 Sum_probs=25.4
Q ss_pred ccCCCCCcceEEEecC-----CCCceeeccCCCC--CCcceecC
Q 046997 637 QCGICQESNMVLKKSR-----DGNLMVGCLAFPQ--CRNAVWLP 673 (807)
Q Consensus 637 ~CP~C~g~~lv~r~~k-----~G~~f~gCs~yP~--C~~~~~~p 673 (807)
.|+ | |...+++..+ .|+.||.|.++.+ |+|..|.+
T Consensus 2 ~C~-C-g~~~~~~~s~k~~~N~GR~Fy~C~~~~~~~C~fF~W~D 43 (45)
T PF06839_consen 2 KCP-C-GEPAVRRTSKKTGPNPGRRFYKCPNYKDKGCNFFQWED 43 (45)
T ss_pred CCC-C-CCEeEEEEEeCCCCCCCCcceECCCCCCCCcCCEEecc
Confidence 588 8 4555554433 4678999999874 99999974
No 57
>PRK07220 DNA topoisomerase I; Validated
Probab=89.51 E-value=0.78 Score=56.43 Aligned_cols=108 Identities=16% Similarity=0.209 Sum_probs=70.3
Q ss_pred HHHHHHHHHH--hcCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccCCccCCccCCCCeeeeeeeEeecCc
Q 046997 418 YELVVRHFLA--CVSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWGGLVIPTYVHGQQFIPTTLTLDSGV 495 (807)
Q Consensus 418 Y~lI~rrfla--~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~~~~~~~i~e~~ 495 (807)
-.||+.|-.. .|- |..|-+..+.+..++..|.+.-.. + .+... ...+..+-.+ +..+.+.++...+++
T Consensus 202 L~lIv~Re~eI~~F~-p~~y~~i~~~~~~~~~~~~~~~~~----~--r~~~~-~~a~~~~~~~--~~~~~V~~v~~~~~~ 271 (740)
T PRK07220 202 LALIVDREKEREAFV-PTPYWEIYATLENNGETFVAQHST----R--RFWEK-EEADRVFEKL--GKTAEVTEVEKGTKT 271 (740)
T ss_pred hHHHHhhHHHHHhCC-CCccEEEEEEEEcCCceEEEEecc----C--cCCCH-HHHHHHHHhh--CCCeEEEEEeeeeEe
Confidence 4566666654 444 445556666666666667665310 0 11111 1111122233 445778888999999
Q ss_pred cCCCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEE
Q 046997 496 TRPPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAI 536 (807)
Q Consensus 496 T~PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~ 536 (807)
..||++|+-++|..++-+.|+ +|..--.|.+.|++.|||.
T Consensus 272 ~~pP~pf~ts~Lq~~a~~~g~-s~~~tm~iaQ~LYe~g~IT 311 (740)
T PRK07220 272 DKPPTPFNTTEFISAANSIGF-SAANAMRIAESLYTNGYIS 311 (740)
T ss_pred cCCCCCcCHHHHHHHHHHcCC-CHHHHHHHHHHHHhCCcee
Confidence 999999999999999988777 4444457999999999996
No 58
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=89.43 E-value=0.83 Score=42.63 Aligned_cols=81 Identities=25% Similarity=0.455 Sum_probs=45.4
Q ss_pred cccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCC--------------C---cc----c-----cccc-cCccCC
Q 046997 636 RQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPG--------------S---VS----E-----AAVT-TNTCNS 688 (807)
Q Consensus 636 ~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~--------------~---~~----~-----~~~t-~~~CP~ 688 (807)
..||+| |+.|+-++...+. .+.|+ .|.+...... . .. + ..++ ...||+
T Consensus 3 ~FCp~C-gsll~p~~~~~~~-~l~C~---kCgye~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cpk 77 (113)
T COG1594 3 RFCPKC-GSLLYPKKDDEGG-KLVCR---KCGYEEEASNKKVYRYSVKEAVEKKKEVVLVVEDETQGAKTLPTAKEKCPK 77 (113)
T ss_pred cccCCc-cCeeEEeEcCCCc-EEECC---CCCcchhccccceeEEEEeeccCCcceeeeeecccccCccccccccccCCC
Confidence 469999 6777766654444 58885 4766544321 0 00 0 0001 356999
Q ss_pred CCCCceEEEEeeccCccCCCCCccCccccCCCCChhH
Q 046997 689 CTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDETL 725 (807)
Q Consensus 689 Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~~ 725 (807)
||....+..+...|.+.-| -..++-|. .|.+..
T Consensus 78 Cg~~ea~y~~~QtRsaDEp---~T~Fy~C~-~Cg~~w 110 (113)
T COG1594 78 CGNKEAYYWQLQTRSADEP---ETRFYKCT-RCGYRW 110 (113)
T ss_pred CCCceeEEEeeehhccCCC---ceEEEEec-ccCCEe
Confidence 9965555555555554332 12446788 887653
No 59
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=89.40 E-value=1 Score=51.01 Aligned_cols=111 Identities=13% Similarity=0.139 Sum_probs=72.7
Q ss_pred hHHHHHHHHHHHHccccc-ceEEEEEEeecCCceEEEEec----cC--CcCCH--HHHHHHHHHhccCCCeEEEEEEeee
Q 046997 226 TLGFVVERYWEIQAHESE-EFWTINCSHKSEEGTATFSWM----RG--HLFDY--TSAVIIYEMCVQEPTATVTKVRQQE 296 (807)
Q Consensus 226 tL~lIv~Re~eI~~F~p~-~y~~i~~~~~~~~~~~~~~~~----~~--r~~d~--~~a~~~~~~~~~~~~~~V~~v~~k~ 296 (807)
+-.||+.|.... |-|. .|=...+.+..++..|.+... .| .+++. .......-.+..+..+.+.+++..+
T Consensus 197 iY~LI~rrfla~--~~~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~p~l~~g~~~~~~~~~~~~ 274 (381)
T cd00186 197 LYELIWRRFLAS--QMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEE 274 (381)
T ss_pred HHHHHHHHHHHH--hCchhhEEEEEEEEEECCeEEEEEEEEEeeCCHHHHhCcccccccccCCCCCCCCEEeeeeeeeee
Confidence 456888888774 4443 444556666665555655321 11 11111 0001111123334457788888899
Q ss_pred eeeCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHhhcCcee
Q 046997 297 KLKYPPYPLSTIELEKRASRYFRMSSEHTMK-VAEDLYQAGFIS 339 (807)
Q Consensus 297 ~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~-iaQ~LYE~g~IS 339 (807)
+...||.+|+-++|.++|-+ .|+.-.-|.. |.+.|.++|||.
T Consensus 275 ~~T~PP~~~Te~~Li~~Me~-~GIGTpATra~iI~~L~~r~Yi~ 317 (381)
T cd00186 275 KETQPPPRYTEASLIKLMEK-RGIGRPSTYASIIETLLDRGYVE 317 (381)
T ss_pred cccCCCCCCCHHHHHHHHHh-CCCCccccHHHHHHHHHhCCcEE
Confidence 99999999999999999876 5997666665 899999999997
No 60
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=89.00 E-value=1.5 Score=52.95 Aligned_cols=110 Identities=10% Similarity=0.186 Sum_probs=70.4
Q ss_pred HHHHHHHHHHHHccccc-ceEEEEEEeec--CCceEEEEec----cC--CcCCH------HHHHHHHHHhccCCCeEEEE
Q 046997 227 LGFVVERYWEIQAHESE-EFWTINCSHKS--EEGTATFSWM----RG--HLFDY------TSAVIIYEMCVQEPTATVTK 291 (807)
Q Consensus 227 L~lIv~Re~eI~~F~p~-~y~~i~~~~~~--~~~~~~~~~~----~~--r~~d~------~~a~~~~~~~~~~~~~~V~~ 291 (807)
-.||+.|... .|-|. -|-+..+.+.. ++..|.++-. .| .++.. +.....+-.+..+..+.+.+
T Consensus 370 Y~lI~rr~la--~~~~~~~~~~t~v~~~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~~~~Lp~l~~g~~~~~~~ 447 (610)
T TIGR01051 370 YELIWKRFVA--SQMADARYDSTSVRLTNEDGEYVFKATGRKLIFDGYYKVYVEGSDDPLEEKDRILPPLKEGDAVKLVE 447 (610)
T ss_pred HHHHHHHHHH--HhCccceEEEEEEEEEEcCCCeEEEEEEEEEEeCCHHHhcccccccccccccccCCCCCCCCEeEeee
Confidence 3588888876 45444 44455566555 4445544321 11 11110 01111122233334567778
Q ss_pred EEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHhhcCcee
Q 046997 292 VRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMK-VAEDLYQAGFIS 339 (807)
Q Consensus 292 v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~-iaQ~LYE~g~IS 339 (807)
++..++.+.||.+|+-++|..+|-+ .|+.-.-|.. |.++|.++|||.
T Consensus 448 ~~~~~~~T~PP~~yTe~tLl~~Me~-~GIGTpATra~iIe~L~~r~Yi~ 495 (610)
T TIGR01051 448 VKPNQHFTQPPARYTEASLVKELEE-LGIGRPSTYASIISTIQDRGYVK 495 (610)
T ss_pred eeeccccccCCCCCCHHHHHHHHhc-CCCCccccHHHHHHHHhhCCeEE
Confidence 8888999999999999999999987 5997666665 899999999998
No 61
>PRK13844 recombination protein RecR; Provisional
Probab=88.67 E-value=1.5 Score=44.98 Aligned_cols=53 Identities=15% Similarity=0.182 Sum_probs=41.6
Q ss_pred hcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEE--------ecccCHHHHHHHHHcCC
Q 046997 114 RCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRAR--------FSALIDREIHQAVQNLV 169 (807)
Q Consensus 114 ~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~--------~s~lt~~~I~~A~~nl~ 169 (807)
+.++||+||.|+-|||.-+..|.+.++. ..+|.|+= +.=++...+.+||++-+
T Consensus 138 ~v~EVIlAt~~t~EGe~Ta~yi~~~lk~---~vkvtRlA~GiP~G~~ley~D~~TL~~Al~~R~ 198 (200)
T PRK13844 138 KIDEVILAISPTVEGETTAHFISQMIAK---DIKISRIGFGVPFGGELEYLDQQTLLHAFNART 198 (200)
T ss_pred CCcEEEEeCCCCccHHHHHHHHHHHhcC---CCcEEeeeecCcCCcceeecCHHHHHHHHHhCc
Confidence 4789999999999999999999999875 35788873 33456667777777644
No 62
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=88.53 E-value=1.6 Score=38.77 Aligned_cols=67 Identities=16% Similarity=0.185 Sum_probs=47.4
Q ss_pred HhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHH
Q 046997 512 DKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVL 590 (807)
Q Consensus 512 e~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l 590 (807)
+..|| +++|...+|..|.+.|||.+..++.+.+|+.|..++..+. .....++..+.... | .+.+++-
T Consensus 7 ~~l~i-s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~---------~~~~~~~~~l~~~~-~-~~~~e~~ 73 (96)
T smart00529 7 ERLNV-SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLL---------RKHRLLERFLVDVL-G-VDEEEVH 73 (96)
T ss_pred HHhCC-ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHH---------HHHHHHHHHHHHHh-C-CCHHHHH
Confidence 44577 7889999999999999999987667899999999875442 23345555555422 3 5555444
No 63
>COG1754 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]
Probab=88.43 E-value=0.31 Score=51.74 Aligned_cols=36 Identities=25% Similarity=0.664 Sum_probs=30.9
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCCCCCCccee
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVW 671 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~ 671 (807)
...||.|+.+.+.++-+++|.| +.|+|||+|.+.-.
T Consensus 23 ~rt~~~~~~~~~slk~GKyGpy-l~~an~Pe~~~~~e 58 (298)
T COG1754 23 PRTCPLCGTGELSLKLGKYGPY-LECANYPECTTPKE 58 (298)
T ss_pred CcccccccccceeEEecccccc-ceeccCccccChhh
Confidence 4579999888888999999985 99999999997643
No 64
>PRK04031 DNA primase; Provisional
Probab=88.42 E-value=0.51 Score=52.92 Aligned_cols=61 Identities=30% Similarity=0.372 Sum_probs=46.0
Q ss_pred HHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEE----EEecccCHHHHHHHHHcCCCC
Q 046997 106 KTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRR----ARFSALIDREIHQAVQNLVDP 171 (807)
Q Consensus 106 ~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R----~~~s~lt~~~I~~A~~nl~~~ 171 (807)
..++++++ .+.|++.+|+|+-||.|.+++++.++.. -|-| .-.-++++++|.+||.+..+.
T Consensus 202 ~~i~~l~k-~~~Vil~~DgD~aGe~I~k~l~~v~~~d----~VaraP~G~dVE~ls~eeI~kAL~~~~p~ 266 (408)
T PRK04031 202 ETIIELSK-KKTVTAFLDGDRGGELILKELLQVADID----YVARAPPGKEVEELTKKEIAKALRNKVPV 266 (408)
T ss_pred HHHHHHhc-CCCEEEEECCCHHHHHHHHHHHhhccee----EEecCCCCCChhhCCHHHHHHHHHhcCCH
Confidence 45677776 7899999999999999999999853210 1112 245678999999999987753
No 65
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.23 E-value=1.7 Score=44.35 Aligned_cols=52 Identities=13% Similarity=0.184 Sum_probs=39.4
Q ss_pred hcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEE--------ecccCHHHHHHHHHc
Q 046997 114 RCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRAR--------FSALIDREIHQAVQN 167 (807)
Q Consensus 114 ~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~--------~s~lt~~~I~~A~~n 167 (807)
+..+||+||+|+-|||.-+..|.+.++..+ .+|.|+= +.=++.-.+.+||++
T Consensus 134 ~v~EVIlAt~~tvEGe~Ta~yi~~~lk~~~--ikvtRlA~GiP~G~~ley~D~~TL~~Al~~ 193 (195)
T TIGR00615 134 SVKEVILATNPTVEGEATALYIARLLQPFG--VKVTRIASGLPVGGDLEYADEVTLARALEG 193 (195)
T ss_pred CCcEEEEeCCCCchHHHHHHHHHHHhhhcC--CcEEeeeecCCCCcceeecCHHHHHHHHHc
Confidence 478999999999999999999999988643 4677873 233455566666654
No 66
>PRK05776 DNA topoisomerase I; Provisional
Probab=87.92 E-value=1 Score=54.71 Aligned_cols=111 Identities=15% Similarity=0.055 Sum_probs=73.6
Q ss_pred HHHHHHHHHHh-cCcccEEEEEEEEEEECCeEEEEEEEEEEecCeeeeecccccCCccCCccCCCCeeeeeeeEeecCcc
Q 046997 418 YELVVRHFLAC-VSQPAVGAETIVEINIAGEVFSTSGRVILAKNYLDVYRFESWGGLVIPTYVHGQQFIPTTLTLDSGVT 496 (807)
Q Consensus 418 Y~lI~rrfla~-~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~lP~l~~G~~~~~~~~~i~e~~T 496 (807)
-.||+.|..+. -+.|..|-...+.+..++..|.+.-. +++ +...+ .....+-.++....+.+.+++.++++.
T Consensus 200 L~lVveRe~eI~~Fvp~~yw~i~~~~~~~~~~f~~~~~-----~~~-~~~~~-~a~~i~~~~~~~~~~~V~~v~~k~~~~ 272 (670)
T PRK05776 200 LKYVVEREIERNLFVPLPYFSVSIIIEKNGYEFTLKYE-----NKK-FETKE-EAKEILEEIKKTGYLKVTKVEVKIEIL 272 (670)
T ss_pred hhHhHhhHHHHHcCCCCcceEEEEEEecCCceEEEEEc-----CCc-cCCHH-HHHHHHHHhcCCCCEEEEEEEeeeEEc
Confidence 34666666653 22355555666777666667776531 121 22111 111112233332457788899999999
Q ss_pred CCCCCCCHHHHHHHHH-hCCCCCccchHHHHHhhcccceEE
Q 046997 497 RPPPLLSEADLLSCMD-KAGIGTDATMHDHIKKLLDRFYAI 536 (807)
Q Consensus 497 ~PP~~~Tea~Li~~Me-~~GIGTpATra~iI~~L~~R~Yv~ 536 (807)
.||++|+-++|...+- +.|++..-|.. |.+.|.+.|||.
T Consensus 273 ~pP~pf~ts~LQ~~As~~lg~sa~ktm~-iAQ~LYe~glIS 312 (670)
T PRK05776 273 EPPPPFNLGDLQVEAARIYGFSPYKTQS-IAEDLYLDGLIS 312 (670)
T ss_pred CCCCCCCHHHHHHHHHhhcCCCHHHHHH-HHHHHHhcCcee
Confidence 9999999999999986 45998888875 999999999996
No 67
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=87.34 E-value=2 Score=52.27 Aligned_cols=117 Identities=16% Similarity=0.137 Sum_probs=74.5
Q ss_pred chhhHHHHHHHHHHHHcccccceEEEEEEeecCCceEEEEec----cC--CcCC-----HHHHHHHHHHhccCCCeEEEE
Q 046997 223 QFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWM----RG--HLFD-----YTSAVIIYEMCVQEPTATVTK 291 (807)
Q Consensus 223 QtPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--r~~d-----~~~a~~~~~~~~~~~~~~V~~ 291 (807)
+--+-.||++|..+..- .|-.|-...+.+..++..|.+.-. .| .++. .+.....+-.+..+..+.|.+
T Consensus 392 e~klY~LI~~Rflas~~-~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~~~LP~l~~G~~~~~~~ 470 (660)
T TIGR01056 392 ERNVYKLIAQNYLMQFM-PKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEETEDTTLPAFQKGDELDVET 470 (660)
T ss_pred HHHHHHHHHHHHHHHhC-chhEEEEEEEEEEECCEEEEEEEEEEcccCHHHHhcccccccccccccCCCCCCCCEeeeee
Confidence 33456799999887543 344455666777666666665421 11 1111 100011112233344567778
Q ss_pred EEeeeeeeCCCCCCCHHHHHHHHHH----------------hcCCCHHHHHH-HHHHHhhcCceec
Q 046997 292 VRQQEKLKYPPYPLSTIELEKRASR----------------YFRMSSEHTMK-VAEDLYQAGFISY 340 (807)
Q Consensus 292 v~~k~~~~~pP~pf~l~~Lq~~ask----------------~~g~s~~~tl~-iaQ~LYE~g~ISY 340 (807)
++..++.+.||..|+-++|.++|-+ ..|+.-.-|.. |.+.|.++|||.-
T Consensus 471 ~~~~~~~TkPP~ryTeasLi~~Me~~~k~v~d~~l~~~l~e~~GIGtpATrA~iI~~L~~R~Yv~~ 536 (660)
T TIGR01056 471 LELLEKQTKPPARYTEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQK 536 (660)
T ss_pred cccccCcCCCCCCcCHHHHHHHHHhhhhcccCHHHHHHhhhccCCCCcccHHHHHHHHHhCCCEEe
Confidence 8888999999999999999999862 46885555544 8999999999973
No 68
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=87.31 E-value=5 Score=40.76 Aligned_cols=43 Identities=21% Similarity=0.258 Sum_probs=33.9
Q ss_pred HHHHHhhc-CeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEE
Q 046997 108 LEEEARRC-QWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRAR 152 (807)
Q Consensus 108 lk~~~~~~-d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~ 152 (807)
++++.... ++||+||+|--|||.-|..|.+.++..+ .+|.|+=
T Consensus 128 ~~Rl~~~~~~EvIlAtnpTvEGeaTA~YI~~~l~~~~--ikvtRlA 171 (198)
T COG0353 128 LQRLAEGSIKEVILATNPTVEGEATALYIARLLKPLG--LKVTRLA 171 (198)
T ss_pred HHHHhcCCCceEEEecCCCccchHHHHHHHHHHhhcC--CeEEEEe
Confidence 34444443 3999999999999999999999998764 4688873
No 69
>PF09664 DUF2399: Protein of unknown function C-terminus (DUF2399); InterPro: IPR024465 This domain is found in archaeal, bacterial and eukaryotic proteins. Its function is unknown.
Probab=87.14 E-value=4.6 Score=39.73 Aligned_cols=72 Identities=24% Similarity=0.230 Sum_probs=51.0
Q ss_pred EEEEEcChHHHHHHHHHhCCCCCcccccCcccccceeeeeccccCCCceEEEEeccCcccccccccccCcCcCCCCCCCC
Q 046997 10 VLNVAEKPSVAKSVAGILSKNQGLRIREGRSRYNKIYEFNYSIRGQPCHMLMTSVTGHLMELDFDERYRKWHSCDPADLY 89 (807)
Q Consensus 10 ~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~G~~~~~~~~ef~~~~~g~~~~~~Vt~~~GHl~~l~~p~~y~~W~~~~p~~L~ 89 (807)
.++|+|.|+|-..++..|+... .-+.++.|+.
T Consensus 20 ~V~VvENp~Vf~~~~~~~~~~~---------------------------~pLVCt~G~p--------------------- 51 (152)
T PF09664_consen 20 RVYVVENPAVFSALADELGASC---------------------------PPLVCTSGQP--------------------- 51 (152)
T ss_pred EEEEEecHHHHHHHHHhcCCCC---------------------------CeEEEcCCcH---------------------
Confidence 3899999999999999987532 1233446763
Q ss_pred CCCcccccCCChHHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhh
Q 046997 90 HAPVRKHVPEDKKDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCR 140 (807)
Q Consensus 90 ~~p~~~~v~~~k~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~ 140 (807)
+......|..++..--.++.++|-|.||=.|+..+++..+
T Consensus 52 -----------~~A~~~LL~~L~~~g~~l~y~GDfDp~Gl~IA~~l~~r~~ 91 (152)
T PF09664_consen 52 -----------SAAARRLLDRLAAAGARLYYSGDFDPEGLRIANRLIQRYG 91 (152)
T ss_pred -----------HHHHHHHHHHHHhCCCEEEEecCCCHHHHHHHHHHHHHhC
Confidence 1112234455544334899999999999999999988754
No 70
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=87.09 E-value=1.2 Score=42.40 Aligned_cols=63 Identities=13% Similarity=0.193 Sum_probs=43.2
Q ss_pred HHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhh-cCC--C----Ce---EEE-EEecccCHHHHHHHHHcCC
Q 046997 106 KTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRA-VNC--H----LV---LRR-ARFSALIDREIHQAVQNLV 169 (807)
Q Consensus 106 ~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~-~~~--~----~~---v~R-~~~s~lt~~~I~~A~~nl~ 169 (807)
+.|+++. +-..|||-||||+.||-|...+.+++.. .+. + .+ ..| +-+-++...+++.|+.+..
T Consensus 47 e~i~~~~-~~k~VIILTD~D~~Ge~Irk~l~~~l~~~~~~~id~~~~~~~~~~~~i~gVE~~~~~~~~~~l~~~~ 120 (127)
T COG1658 47 ELIKKAQ-KYKGVIILTDPDRKGERIRKKLKEYLPGAKGAFIDREIRNKLKINGKIIGVEEASSEALRKALKEVP 120 (127)
T ss_pred HHHHHhh-ccCCEEEEeCCCcchHHHHHHHHHHhcccccccccHHHhhhcccccccccceecChHHHHHHHHhCC
Confidence 3444433 3357999999999999999999999876 221 0 01 111 3445778888888888776
No 71
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=86.73 E-value=2.1 Score=42.85 Aligned_cols=68 Identities=16% Similarity=0.216 Sum_probs=46.5
Q ss_pred HHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcC----C-CCeE---EEEEecccCHHHHHHHHHcCCCC
Q 046997 103 DIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVN----C-HLVL---RRARFSALIDREIHQAVQNLVDP 171 (807)
Q Consensus 103 ~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~----~-~~~v---~R~~~s~lt~~~I~~A~~nl~~~ 171 (807)
+.++.|+++.++ .-||+-||||.-||.|=..|.+++.... + ...+ .-+=+-..++++|++||.++...
T Consensus 36 ~~i~~i~~~~~~-rgVIIfTDpD~~GekIRk~i~~~vp~~khafi~~~~a~~~~~~iGVE~As~e~I~~AL~~~~~~ 111 (174)
T TIGR00334 36 ETINLIKKAQKK-QGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPKHLAKPNKKKIGVEEASVEAIIAALENVHEE 111 (174)
T ss_pred HHHHHHHHHhhc-CCEEEEeCCCCchHHHHHHHHHHCCCCeEEeeeHHhcCcCCCCcccCCCCHHHHHHHHHHhccc
Confidence 344566666544 5699999999999999888888754211 0 0000 11455567899999999998853
No 72
>PRK14973 DNA topoisomerase I; Provisional
Probab=86.41 E-value=1.6 Score=54.92 Aligned_cols=112 Identities=19% Similarity=0.236 Sum_probs=72.3
Q ss_pred hhHHHHHHHHHHHHcccccceEEEEEEeecCCceEEEEec----cC--CcCCH-HHHHHHHHHhccCCCeEEEEEEeeee
Q 046997 225 PTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWM----RG--HLFDY-TSAVIIYEMCVQEPTATVTKVRQQEK 297 (807)
Q Consensus 225 PtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--r~~d~-~~a~~~~~~~~~~~~~~V~~v~~k~~ 297 (807)
-+--||+.|.....- .|-.|=+..+.+..++..|.++.. .| .+++. +..+..+-.+..+..+.+.+++.+++
T Consensus 382 klY~LI~rRfLA~~~-~~a~~~~t~v~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~LP~l~~Ge~~~~~~~~~~e~ 460 (936)
T PRK14973 382 KLYELVVRRFLATLS-PDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEAKENILPAFALGEKLPILAVNLEEK 460 (936)
T ss_pred HHHHHHHHHHHHHhC-hhheEEEEEEEEEECCEEEEEEEEEEeecCeeEeecccccccccCCCccCCCEEEeeeeEEeec
Confidence 345689999887532 333444556666655555554321 11 12221 11111122334445677888899999
Q ss_pred eeCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHhhcCce
Q 046997 298 LKYPPYPLSTIELEKRASRYFRMSSEHTMK-VAEDLYQAGFI 338 (807)
Q Consensus 298 ~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~-iaQ~LYE~g~I 338 (807)
.+.||.+|+-++|.+.|-+ .|+.-.-|.. |.+.|+++|||
T Consensus 461 ~T~PP~ryTEatLik~ME~-~GIGTpATrA~II~~L~~R~Yv 501 (936)
T PRK14973 461 ETQPPARYSQSRLIQRMEE-LGLGTKSTRHEVIGKLVSRKYI 501 (936)
T ss_pred CCCCCCCCCHHHHHHHhcc-CCCCCcccHHHHHHHHHHccCe
Confidence 9999999999999999977 5986555554 89999999999
No 73
>PRK07726 DNA topoisomerase III; Provisional
Probab=85.80 E-value=2.8 Score=51.00 Aligned_cols=113 Identities=16% Similarity=0.168 Sum_probs=72.3
Q ss_pred hHHHHHHHHHHHHcccccceEEEEEEeecCCceEEEEec----cC--CcCC----HHHHHHHHHHhccCCCeEEEEEEee
Q 046997 226 TLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWM----RG--HLFD----YTSAVIIYEMCVQEPTATVTKVRQQ 295 (807)
Q Consensus 226 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--r~~d----~~~a~~~~~~~~~~~~~~V~~v~~k 295 (807)
+-.||++|..... ..|--|-...+.+..++..|.+... .| .++. .+.....+-.+..+..+.+.+++..
T Consensus 393 iY~lI~~r~la~~-~~~~~~~~t~v~~~~~~~~F~~~g~~i~~~Gw~~v~~~~~~~~~~~~~lp~l~~g~~~~~~~~~~~ 471 (658)
T PRK07726 393 VYDLIARRYLAQF-LPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEKEQPLPVLAKGDELKVEKGEVK 471 (658)
T ss_pred HHHHHHHHHHHHh-CchhEEEEEEEEEEECCEEEEEEEEEEccCCHHHHcccccccccccccCCCcCCCCEeeecccccc
Confidence 4568999988743 2444555666666666666655421 11 1221 0000111122333445677788888
Q ss_pred eeeeCCCCCCCHHHHHHHHHHh----------------cCCCHHHHHH-HHHHHhhcCcee
Q 046997 296 EKLKYPPYPLSTIELEKRASRY----------------FRMSSEHTMK-VAEDLYQAGFIS 339 (807)
Q Consensus 296 ~~~~~pP~pf~l~~Lq~~ask~----------------~g~s~~~tl~-iaQ~LYE~g~IS 339 (807)
++.+.||.+|+-++|.+.|-+. .|+.-.-|.. |.++|.++|||.
T Consensus 472 e~~TkPP~~yTe~tLi~~Me~~~k~v~d~~~~~~l~e~~GIGTpATra~iIe~L~~R~Yi~ 532 (658)
T PRK07726 472 EGQTQPPKRFTEGTLLSAMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLE 532 (658)
T ss_pred cccCCCCCCcCHHHHHHHHHhhhhhccCHHHHHhhcccCCCCccccHHHHHHHHHhCCCEE
Confidence 9999999999999999998653 3886555555 899999999997
No 74
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=85.46 E-value=7.6 Score=37.33 Aligned_cols=51 Identities=16% Similarity=0.223 Sum_probs=38.7
Q ss_pred CCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCC------ceeeechhHHHHHhhc
Q 046997 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDAN------TRFAPTNIGEALVMGY 556 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~------~~l~pT~~G~~li~~l 556 (807)
.|.++|...|. + +++|...+|+.|.++|||++... ..+.+|++|+.+++.+
T Consensus 47 ~t~~eLa~~l~---~-~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~ 103 (144)
T PRK03573 47 QSQIQLAKAIG---I-EQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEV 103 (144)
T ss_pred CCHHHHHHHhC---C-ChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHH
Confidence 45667666663 3 56789999999999999987421 3489999999988644
No 75
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=85.41 E-value=0.79 Score=50.11 Aligned_cols=76 Identities=17% Similarity=0.354 Sum_probs=43.9
Q ss_pred cccccCCCCCcc---eEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEEEeeccCccCCCC-
Q 046997 634 VVRQCGICQESN---MVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPPG- 709 (807)
Q Consensus 634 ~~~~CP~C~g~~---lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~~- 709 (807)
....||.||+.+ ++...+..|..++.|+- |.+.....+ ..||.||...-+ . +..+...
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~Csl---C~teW~~~R---------~~C~~Cg~~~~l--~----y~~~~~~~ 247 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNL---CESEWHVVR---------VKCSNCEQSGKL--H----YWSLDSEQ 247 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCC---CCCcccccC---------ccCCCCCCCCce--e----eeeecCCC
Confidence 357899996543 23334457878899975 887665533 469999852111 1 1111100
Q ss_pred CccCccccCCCCChhHHHH
Q 046997 710 FNVNHLGCIGGCDETLRQL 728 (807)
Q Consensus 710 ~~~~~~~C~~~C~~~~~~l 728 (807)
-...-..|- .|+..++-+
T Consensus 248 ~~~r~e~C~-~C~~YlK~~ 265 (309)
T PRK03564 248 AAVKAESCG-DCGTYLKIL 265 (309)
T ss_pred cceEeeecc-cccccceec
Confidence 011236798 998888744
No 76
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=84.67 E-value=0.74 Score=35.89 Aligned_cols=32 Identities=28% Similarity=0.707 Sum_probs=23.2
Q ss_pred ccCCCCCcceEEEecCC-----CCceeeccCCCCCCcce
Q 046997 637 QCGICQESNMVLKKSRD-----GNLMVGCLAFPQCRNAV 670 (807)
Q Consensus 637 ~CP~C~g~~lv~r~~k~-----G~~f~gCs~yP~C~~~~ 670 (807)
.||.| |..+.+++++. ...++.|+| ++|.++.
T Consensus 1 ~CP~C-g~~a~ir~S~~~s~~~~~~Y~qC~N-~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHC-GSKARIRTSRQLSPLTRELYCQCTN-PECGHTF 37 (47)
T ss_pred CcCCC-CCeeEEEEchhhCcceEEEEEEECC-CcCCCEE
Confidence 49999 67787776532 235688998 6898764
No 77
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=83.39 E-value=3.1 Score=49.47 Aligned_cols=116 Identities=13% Similarity=0.175 Sum_probs=76.0
Q ss_pred chhhHHHHHHHHHHHHcccccceEEEEEEeecCCceEEEEec----cC--CcCC---HHHHHHHHHHhccCCCeEEEEEE
Q 046997 223 QFPTLGFVVERYWEIQAHESEEFWTINCSHKSEEGTATFSWM----RG--HLFD---YTSAVIIYEMCVQEPTATVTKVR 293 (807)
Q Consensus 223 QtPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--r~~d---~~~a~~~~~~~~~~~~~~V~~v~ 293 (807)
+--+=-||+.|...-.- .+-.|=...+.+...++.|.+.-. .| +++. .+..+..+-.+..+....+.+++
T Consensus 363 e~klY~LI~rrflAs~m-~~A~~~~~~v~l~~~~~~F~a~g~~~~~~Gw~~vy~~~~~~~~~~~lP~l~~gd~l~~~~~~ 441 (570)
T COG0550 363 ELKLYDLIWRRFLASQM-PDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEEDKELPELKEGDELKVEKLE 441 (570)
T ss_pred HHHHHHHHHHHHHHHhC-chhhheEEEEEEEecCcEEEEeeeEEecCcHHHhhcccccccccccCCCCCCCCeeEEeeee
Confidence 33344589999887432 333444556666655556655311 11 1111 11222222334445578889999
Q ss_pred eeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHhhcCceec
Q 046997 294 QQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMK-VAEDLYQAGFISY 340 (807)
Q Consensus 294 ~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~-iaQ~LYE~g~ISY 340 (807)
..+..+.||..|+=++|.+.+-+ .|+.-.-|.. |.+.|+++|||.=
T Consensus 442 ~~~~~T~PP~rytEasLvk~mE~-~GIGrpSTyA~iI~~L~~RgYv~~ 488 (570)
T COG0550 442 VEEHFTKPPPRYTEASLVKAMEK-LGIGTPSTYASIIETLQKRGYVEK 488 (570)
T ss_pred ecccccCCcCCCCHHHHHHHHHh-CCCCCcccHHHHHHHHhcCCcEEe
Confidence 99999999999999999999955 8997666655 9999999999973
No 78
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=83.29 E-value=1.4 Score=51.23 Aligned_cols=17 Identities=18% Similarity=0.532 Sum_probs=14.6
Q ss_pred ccccccCCCc----cCCCCCC
Q 046997 761 ACIYCQQMGH----SSSDCPS 777 (807)
Q Consensus 761 ~c~~c~~~g~----~~~~~~~ 777 (807)
.|+.|+..+| +++.|.-
T Consensus 97 lc~~c~~~~~~vy~l~~~c~~ 117 (715)
T COG1107 97 LCPECRRKPKIVYVLDNSCTM 117 (715)
T ss_pred cChhHhhCCceeEEeccccch
Confidence 7999999999 7788864
No 79
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=82.22 E-value=1 Score=49.17 Aligned_cols=77 Identities=14% Similarity=0.337 Sum_probs=44.1
Q ss_pred ccccCCCCCcce--EEEe--cCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEEEeeccCccCCC--
Q 046997 635 VRQCGICQESNM--VLKK--SRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPP-- 708 (807)
Q Consensus 635 ~~~CP~C~g~~l--v~r~--~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~-- 708 (807)
-+.||.||+.++ +++. +..|..++.|+- |.+.....+ ..||.||...-+ . +..+-.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~Csl---C~teW~~~R---------~~C~~Cg~~~~l--~----y~~~e~~~ 245 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSL---CATEWHYVR---------VKCSHCEESKHL--A----YLSLEHDA 245 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCC---CCCcccccC---------ccCCCCCCCCce--e----eEeecCCC
Confidence 458999965443 2333 257878899975 887665533 469999953211 1 111100
Q ss_pred CC-ccCccccCCCCChhHHHHHH
Q 046997 709 GF-NVNHLGCIGGCDETLRQLIE 730 (807)
Q Consensus 709 ~~-~~~~~~C~~~C~~~~~~l~~ 730 (807)
+. ...-..|- .|+..++.+.+
T Consensus 246 ~~~~~r~e~C~-~C~~YlK~~~~ 267 (305)
T TIGR01562 246 EKAVLKAETCD-SCQGYLKILYQ 267 (305)
T ss_pred CCcceEEeecc-ccccchhhhcc
Confidence 00 11225698 99988885543
No 80
>PRK10870 transcriptional repressor MprA; Provisional
Probab=81.90 E-value=12 Score=37.57 Aligned_cols=55 Identities=9% Similarity=0.119 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCC------ceeeechhHHHHHhhc
Q 046997 498 PPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDAN------TRFAPTNIGEALVMGY 556 (807)
Q Consensus 498 PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~------~~l~pT~~G~~li~~l 556 (807)
++...|.++|-..|.- +++|-..+|+.|.++|||++... ..+.+|+.|+.+++.+
T Consensus 68 ~~~~it~~eLa~~l~l----~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i 128 (176)
T PRK10870 68 ENHSIQPSELSCALGS----SRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREV 128 (176)
T ss_pred CCCCcCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHH
Confidence 3445667777777753 45888999999999999987421 3489999999998644
No 81
>PRK08173 DNA topoisomerase III; Validated
Probab=81.83 E-value=4.2 Score=50.94 Aligned_cols=113 Identities=11% Similarity=0.060 Sum_probs=72.7
Q ss_pred hhHHHHHHHHHHHHcccccceEE-EEEEeecCCceEEEEec----cC--CcCCHHH--HHHHHHHhccCCCeEEEEEEee
Q 046997 225 PTLGFVVERYWEIQAHESEEFWT-INCSHKSEEGTATFSWM----RG--HLFDYTS--AVIIYEMCVQEPTATVTKVRQQ 295 (807)
Q Consensus 225 PtL~lIv~Re~eI~~F~p~~y~~-i~~~~~~~~~~~~~~~~----~~--r~~d~~~--a~~~~~~~~~~~~~~V~~v~~k 295 (807)
-+-.|||+|..+ .|-|..-|. ..+.+..++..|.++.. .| .++..+. .+..+-.+..+..+.+.+++..
T Consensus 403 ~iY~lI~rRfla--~f~~~a~~~~t~v~~~v~~~~F~a~G~~~~~~Gw~~vy~~~~~~~~~~LP~l~~Ge~~~~~~~~~~ 480 (862)
T PRK08173 403 KLYDLVVKRFLA--VFFPAAEFLVTTRITEVAGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAV 480 (862)
T ss_pred HHHHHHHHHHHH--HhCchheEEEEEEEEEeCCcEEEEEEEEEeeCChHHHhCcccccccccCCCcCCCCEeeeeeeeec
Confidence 345689999887 565655443 44555556656665421 11 1111100 0111122333446778889999
Q ss_pred eeeeCCCCCCCHHHHHHHHHH---------------hcCCCHHHHH-HHHHHHhhcCcee
Q 046997 296 EKLKYPPYPLSTIELEKRASR---------------YFRMSSEHTM-KVAEDLYQAGFIS 339 (807)
Q Consensus 296 ~~~~~pP~pf~l~~Lq~~ask---------------~~g~s~~~tl-~iaQ~LYE~g~IS 339 (807)
++.+.||.+|+=++|+++|-. ..|+.-.-|. .|.+.|+++|||.
T Consensus 481 e~~TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~~~~GIGTpATRA~IIe~L~~r~Yi~ 540 (862)
T PRK08173 481 ALTTKPPARYNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGEKYLV 540 (862)
T ss_pred ccccCCCCCcCHHHHHHHHHhhhhccccHHHHhhhhcCCCCchhhHHHHHHHHHhCCcEE
Confidence 999999999999999999873 4688555554 4899999999997
No 82
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=81.30 E-value=2.7 Score=38.41 Aligned_cols=39 Identities=21% Similarity=0.479 Sum_probs=22.0
Q ss_pred ccCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChh
Q 046997 682 TTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDET 724 (807)
Q Consensus 682 t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~ 724 (807)
++..||+||....+-.+..-|...-+ -..++.|. +|.+.
T Consensus 61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~---~T~fy~C~-~C~~~ 99 (104)
T TIGR01384 61 TRVECPKCGHKEAYYWLLQTRRADEP---ETRFYKCT-KCGYV 99 (104)
T ss_pred ccCCCCCCCCCeeEEEEeccCCCCCC---cEEEEEeC-CCCCe
Confidence 47889999976555444333321111 11346798 88753
No 83
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=81.19 E-value=7.9 Score=39.40 Aligned_cols=51 Identities=25% Similarity=0.210 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcC------CceeeechhHHHHHhhc
Q 046997 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDA------NTRFAPTNIGEALVMGY 556 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~------~~~l~pT~~G~~li~~l 556 (807)
.|..+|-..| ++ +.+|-..+|+.|.++|||.+.. .+.+.+|++|+.+++-+
T Consensus 60 itq~eLa~~l---~l-~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l 116 (185)
T PRK13777 60 ASISEIAKFG---VM-HVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLET 116 (185)
T ss_pred cCHHHHHHHH---CC-CHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHH
Confidence 4566655543 22 5689999999999999998742 13489999999987543
No 84
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=79.73 E-value=4.5 Score=39.02 Aligned_cols=57 Identities=12% Similarity=0.149 Sum_probs=42.3
Q ss_pred hCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCccccCchhhHHHHHHHHHH
Q 046997 513 KAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEV 579 (807)
Q Consensus 513 ~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I 579 (807)
..|+ +++|-..+|..|.++|||.....+.+.+|+.|+.+...+. .-...||..|+.+
T Consensus 31 ~l~v-s~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~~---------~~h~~~e~~l~~l 87 (142)
T PRK03902 31 ALSV-HPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRLV---------YRHELLEQFLRII 87 (142)
T ss_pred HhCC-ChhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHHH---------HHHHHHHHHHHHh
Confidence 3466 6888999999999999998644456899999998754331 3446777777654
No 85
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=79.03 E-value=0.92 Score=34.54 Aligned_cols=18 Identities=39% Similarity=0.894 Sum_probs=16.5
Q ss_pred cccccccCCCccCCCCCC
Q 046997 760 RACIYCQQMGHSSSDCPS 777 (807)
Q Consensus 760 ~~c~~c~~~g~~~~~~~~ 777 (807)
+.|..|++.|||+-.||.
T Consensus 5 ~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 5 VRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CcCcccCCCCcchhhCCC
Confidence 469999999999999994
No 86
>PRK04017 hypothetical protein; Provisional
Probab=78.69 E-value=2.9 Score=40.07 Aligned_cols=33 Identities=27% Similarity=0.382 Sum_probs=28.6
Q ss_pred HhhcCeEEEeecCChhhhHHHHHHHHHhhhcCC
Q 046997 112 ARRCQWLVLWLDCDREGENIAFEVIEVCRAVNC 144 (807)
Q Consensus 112 ~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~ 144 (807)
+.+...|||.||||.-||.|...|.+++...+.
T Consensus 62 a~~~r~VIILTD~D~~GekIr~~l~~~l~~~G~ 94 (132)
T PRK04017 62 ASRGKEVIILTDFDRKGEELAKKLSEYLQGYGI 94 (132)
T ss_pred HhcCCeEEEEECCCcchHHHHHHHHHHHHhCCC
Confidence 456789999999999999999999998877653
No 87
>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects. They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].
Probab=77.23 E-value=1 Score=24.08 Aligned_cols=9 Identities=44% Similarity=1.165 Sum_probs=7.9
Q ss_pred cCceeccCC
Q 046997 335 AGFISYPRT 343 (807)
Q Consensus 335 ~g~ISYPRT 343 (807)
.|+|++|||
T Consensus 3 sGlI~fpR~ 11 (11)
T PF08259_consen 3 SGLIPFPRV 11 (11)
T ss_pred ccccccCCC
Confidence 489999997
No 88
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=76.64 E-value=1.7 Score=30.42 Aligned_cols=31 Identities=26% Similarity=0.545 Sum_probs=13.7
Q ss_pred ccCCCCCCceEEEEeeccCccCCCCCccCccccCC-CCCh
Q 046997 685 TCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIG-GCDE 723 (807)
Q Consensus 685 ~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~-~C~~ 723 (807)
.||+||-|.++-+ ...+|.+ .-+-|.+ .||+
T Consensus 3 lcpkcgvgvl~pv--y~~kgei------kvfrcsnpacdy 34 (36)
T PF09151_consen 3 LCPKCGVGVLEPV--YNQKGEI------KVFRCSNPACDY 34 (36)
T ss_dssp B-TTTSSSBEEEE--E-TTS-E------EEEEES-TT---
T ss_pred cCCccCceEEEEe--ecCCCcE------EEEEcCCCcccc
Confidence 6999998766544 2333322 1145731 7886
No 89
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=76.29 E-value=1.9 Score=47.01 Aligned_cols=45 Identities=16% Similarity=0.457 Sum_probs=20.0
Q ss_pred ccccCCCCCcceE-EEecCC--CCceeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMV-LKKSRD--GNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv-~r~~k~--G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
.+.||.||+.+.. .-.+.. |..|+.||- |.+.....+ ..||.||.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~---C~t~W~~~R---------~~Cp~Cg~ 219 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSL---CGTEWRFVR---------IKCPYCGN 219 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETT---T--EEE--T---------TS-TTT--
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCC---CCCeeeecC---------CCCcCCCC
Confidence 4689999544332 222222 777899975 987766544 36999985
No 90
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=76.26 E-value=1.4 Score=33.05 Aligned_cols=18 Identities=33% Similarity=0.852 Sum_probs=15.4
Q ss_pred cccccccCCCccC--CCCCC
Q 046997 760 RACIYCQQMGHSS--SDCPS 777 (807)
Q Consensus 760 ~~c~~c~~~g~~~--~~~~~ 777 (807)
++|..||+.||.+ ..||-
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred ccccccccccccccCccCCC
Confidence 5799999999998 56886
No 91
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=75.98 E-value=2 Score=37.42 Aligned_cols=45 Identities=27% Similarity=0.442 Sum_probs=33.0
Q ss_pred HHhCCCCCccchHHHHHhhcccceEEEcC----C---ceeeechhHHHHHhhc
Q 046997 511 MDKAGIGTDATMHDHIKKLLDRFYAIKDA----N---TRFAPTNIGEALVMGY 556 (807)
Q Consensus 511 Me~~GIGTpATra~iI~~L~~R~Yv~~~~----~---~~l~pT~~G~~li~~l 556 (807)
.+..|| |+++-..|+++|.+.|||+..+ + ..+..|++|+..++.+
T Consensus 21 ~~~l~l-t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~ 72 (80)
T PF13601_consen 21 KEELGL-TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERY 72 (80)
T ss_dssp HHHTT---HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHH
T ss_pred HHHhCc-CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHH
Confidence 345688 8999999999999999997642 1 2388999999877654
No 92
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=74.74 E-value=6.4 Score=38.00 Aligned_cols=50 Identities=12% Similarity=0.161 Sum_probs=38.6
Q ss_pred CCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCC------ceeeechhHHHHHhh
Q 046997 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDAN------TRFAPTNIGEALVMG 555 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~------~~l~pT~~G~~li~~ 555 (807)
.|.++|-..|-- +++|...+|+.|.++|||++... ..+.+|++|+.+++.
T Consensus 55 ~t~~eLa~~l~i----~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 55 ITPVELKKVLSV----DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred CCHHHHHHHHCC----CHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 566676666532 67899999999999999987421 348999999998753
No 93
>PRK08780 DNA topoisomerase I; Provisional
Probab=74.66 E-value=15 Score=45.80 Aligned_cols=113 Identities=10% Similarity=0.124 Sum_probs=74.4
Q ss_pred hHHHHHHHHHHHHcccccceEEEEEEeecCC-ceEEEEec----cC--CcCC----H---H--HHHHHHHHhccCCCeEE
Q 046997 226 TLGFVVERYWEIQAHESEEFWTINCSHKSEE-GTATFSWM----RG--HLFD----Y---T--SAVIIYEMCVQEPTATV 289 (807)
Q Consensus 226 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~-~~~~~~~~----~~--r~~d----~---~--~a~~~~~~~~~~~~~~V 289 (807)
+-.||++|..+..- .|-.|-+..+.+..++ ..|.+.-. .| .++. . + .....+-.+..+..+.+
T Consensus 381 lY~LI~~R~lAs~m-~~a~~~~t~v~~~~~~~~~F~a~G~~i~~~G~~~vy~~~~~~~~~~~~~~~~~LP~l~~G~~~~~ 459 (780)
T PRK08780 381 LYELIWKRAVACQM-IPATLNTVSVDLAAGSEHVFRATGSTVVVPGFLAVYEEGKDDKSAEDEDEGRKLPPMKEGDNVPL 459 (780)
T ss_pred HHHHHHHHHHHHhC-chhEEEEEEEEEEeCCeeEEEEEEEEEeEcCeEEeeccccccccccccchhccCCCcCCCCEeee
Confidence 35689999887543 4555666777776544 24443211 11 1111 0 0 11122333444556778
Q ss_pred EEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHhhcCceec
Q 046997 290 TKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMK-VAEDLYQAGFISY 340 (807)
Q Consensus 290 ~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~-iaQ~LYE~g~ISY 340 (807)
.+++..++.+.||..|+-++|.+.+-+ .|+.-.-|.. |.+.|.++|||.-
T Consensus 460 ~~~~~~~~~T~PP~ryTEasLik~mE~-~GIGtpST~A~iI~~L~~R~Yv~~ 510 (780)
T PRK08780 460 ERIRAEQHFTEPPPRYTEASLVKALEE-YGIGRPSTYASIISTLQFRKYVEM 510 (780)
T ss_pred eeeeeeeeecCCCCCCCHHHHHHHHHh-CCCCchhhHHHHHHHHHhCCcEec
Confidence 888889999999999999999999987 7997666665 8999999999973
No 94
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=74.09 E-value=3.8 Score=37.43 Aligned_cols=39 Identities=18% Similarity=0.151 Sum_probs=32.2
Q ss_pred CccchHHHHHhhcccceEEEcCC------ceeeechhHHHHHhhc
Q 046997 518 TDATMHDHIKKLLDRFYAIKDAN------TRFAPTNIGEALVMGY 556 (807)
Q Consensus 518 TpATra~iI~~L~~R~Yv~~~~~------~~l~pT~~G~~li~~l 556 (807)
+++|-..+|+.|.++|||.+... ..+.+|++|..++..+
T Consensus 49 ~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~ 93 (126)
T COG1846 49 DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQL 93 (126)
T ss_pred CHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHh
Confidence 68889999999999999987432 2489999999988644
No 95
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=73.65 E-value=3.1 Score=41.24 Aligned_cols=31 Identities=26% Similarity=0.348 Sum_probs=27.3
Q ss_pred HHHHhcCCCHHHHHHHHHHHhhcCceeccCC
Q 046997 313 RASRYFRMSSEHTMKVAEDLYQAGFISYPRT 343 (807)
Q Consensus 313 ~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRT 343 (807)
+.+..+|++...+-+++++|||.|||+|-|+
T Consensus 33 eLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~ 63 (158)
T TIGR00373 33 EISLELGIKLNEVRKALYALYDAGLADYKRR 63 (158)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCceeeee
Confidence 3445579999999999999999999999984
No 96
>PRK14724 DNA topoisomerase III; Provisional
Probab=73.50 E-value=7.8 Score=49.30 Aligned_cols=121 Identities=10% Similarity=0.045 Sum_probs=73.9
Q ss_pred hHHHHHHHHHHHHcccccceE-EEEEEeecCCceEEEEec----cC--CcCCH------H-----HHHHHHHHhccCCCe
Q 046997 226 TLGFVVERYWEIQAHESEEFW-TINCSHKSEEGTATFSWM----RG--HLFDY------T-----SAVIIYEMCVQEPTA 287 (807)
Q Consensus 226 tL~lIv~Re~eI~~F~p~~y~-~i~~~~~~~~~~~~~~~~----~~--r~~d~------~-----~a~~~~~~~~~~~~~ 287 (807)
+--||+.|..+ .|-|..-| ...+.+..++..|.++-. .| .++.. + .....+-.+..+..+
T Consensus 414 iY~lI~rRfla--~f~~~a~~~~t~v~~~~~~~~F~a~G~~i~~~GW~~vy~~~~~~~~~~~~~~~~~~~LP~l~~Ge~v 491 (987)
T PRK14724 414 LYDLVVRRFMA--VFFPSAEYQVTTRISQVVGHSFKTEGKVLVKPGWLAIYGKEAANEVEDAKDGDKGQPLVPVKPGEMV 491 (987)
T ss_pred HHHHHHHHHHH--HhCchhEEEEEEEEEEecCcEEEEEEEEECcCChHHHhCccccccccccccccccccCCCcCCCCEe
Confidence 45689999887 45565544 444555555555654321 11 11110 0 000111223334456
Q ss_pred EEEEEEeeeeeeCCCCCCCHHHHHHHHHH---------------hcCCCHHHH-HHHHHHHhhcCceeccCCCCcccCC
Q 046997 288 TVTKVRQQEKLKYPPYPLSTIELEKRASR---------------YFRMSSEHT-MKVAEDLYQAGFISYPRTETDSFSS 350 (807)
Q Consensus 288 ~V~~v~~k~~~~~pP~pf~l~~Lq~~ask---------------~~g~s~~~t-l~iaQ~LYE~g~ISYPRTds~~l~~ 350 (807)
.+.+++.+++.+.||.+|+=++|+++|-. ..|+.-.-| ..|.+.|.++|||. |-....+|.
T Consensus 492 ~~~~~~~~e~~TkPP~ryTEatLl~aME~~gk~v~d~el~~~~~~~GIGTpATRA~IIe~L~~r~Yi~--~~~k~l~pT 568 (987)
T PRK14724 492 RTEFAEAKGLKTKPPARYSEATLLGAMESAGKQIDDDELREAMQEKGLGTPATRAAIIEGLLTEKYML--REGRELIPT 568 (987)
T ss_pred eeeeccccccccCCCCCcCHHHHHHHHHhhhhcccchhhhhhhhcCCCCCcccHHHHHHHHHhCCcEE--ecCCEEeEc
Confidence 77788889999999999999999998862 357744444 45899999999997 444334444
No 97
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=73.45 E-value=2.4 Score=32.20 Aligned_cols=15 Identities=20% Similarity=0.629 Sum_probs=11.2
Q ss_pred cccCccCCCCCCceEE
Q 046997 681 VTTNTCNSCTPGPVYL 696 (807)
Q Consensus 681 ~t~~~CP~Cg~~~l~~ 696 (807)
..++.||.|+ .|+++
T Consensus 15 ML~~~Cp~C~-~PL~~ 29 (41)
T PF06677_consen 15 MLDEHCPDCG-TPLMR 29 (41)
T ss_pred HhcCccCCCC-CeeEE
Confidence 3578899998 46664
No 98
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=73.27 E-value=2.7 Score=36.23 Aligned_cols=45 Identities=20% Similarity=0.290 Sum_probs=31.6
Q ss_pred HHhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhcc
Q 046997 511 MDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYD 557 (807)
Q Consensus 511 Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~ 557 (807)
|...|+- ..+-..+|+.|.++|+|...+ ..+..|++|..+++.+.
T Consensus 26 ~~~~~L~-~~~~~~yL~~L~~~gLI~~~~-~~Y~lTekG~~~l~~l~ 70 (77)
T PF14947_consen 26 MYKANLN-YSTLKKYLKELEEKGLIKKKD-GKYRLTEKGKEFLEELE 70 (77)
T ss_dssp HTTST---HHHHHHHHHHHHHTTSEEEET-TEEEE-HHHHHHHHHHH
T ss_pred HHHhCcC-HHHHHHHHHHHHHCcCeeCCC-CEEEECccHHHHHHHHH
Confidence 3344443 234567999999999997754 46899999999987765
No 99
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=73.00 E-value=5.5 Score=36.64 Aligned_cols=55 Identities=13% Similarity=0.109 Sum_probs=41.2
Q ss_pred CCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcC----C--ceeeechhHHHHHhhc
Q 046997 498 PPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDA----N--TRFAPTNIGEALVMGY 556 (807)
Q Consensus 498 PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~----~--~~l~pT~~G~~li~~l 556 (807)
++...|..+|-..|.- +++|...+|+.|.++|||.+.. + ..+.+|+.|+.+++.+
T Consensus 40 ~~~~~t~~eL~~~l~~----~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~ 100 (109)
T TIGR01889 40 NEGKLTLKEIIKEILI----KQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESL 100 (109)
T ss_pred cCCcCcHHHHHHHHCC----CHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHH
Confidence 4456677777666643 4789999999999999998632 1 2388999999988644
No 100
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=71.61 E-value=3.8 Score=36.90 Aligned_cols=36 Identities=22% Similarity=0.372 Sum_probs=29.1
Q ss_pred HHHHHhhcccceEEEcCCc---eeeechhHHHHHhhccc
Q 046997 523 HDHIKKLLDRFYAIKDANT---RFAPTNIGEALVMGYDD 558 (807)
Q Consensus 523 a~iI~~L~~R~Yv~~~~~~---~l~pT~~G~~li~~l~~ 558 (807)
..+|+-|.++|.+..+.++ .+..|++|+.+++.|..
T Consensus 49 ~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~~ 87 (95)
T COG3432 49 QKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYSE 87 (95)
T ss_pred HHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHHH
Confidence 4699999999977665443 58999999999987754
No 101
>PHA00626 hypothetical protein
Probab=70.42 E-value=4 Score=32.82 Aligned_cols=33 Identities=18% Similarity=0.403 Sum_probs=19.1
Q ss_pred ccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChhHH
Q 046997 685 TCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDETLR 726 (807)
Q Consensus 685 ~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~~~ 726 (807)
.||+||+..+++-.+ -+. ....+.|+ .|.+.+.
T Consensus 2 ~CP~CGS~~Ivrcg~-cr~-------~snrYkCk-dCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEKT-MRG-------WSDDYVCC-DCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeece-ecc-------cCcceEcC-CCCCeec
Confidence 599999865663211 111 11236799 9987553
No 102
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=70.23 E-value=3.2 Score=50.11 Aligned_cols=12 Identities=17% Similarity=0.542 Sum_probs=7.6
Q ss_pred cCCCCChhHHHHH
Q 046997 717 CIGGCDETLRQLI 729 (807)
Q Consensus 717 C~~~C~~~~~~l~ 729 (807)
|| .|...+...+
T Consensus 44 C~-~CG~~~~~~~ 55 (645)
T PRK14559 44 CP-NCGAETGTIW 55 (645)
T ss_pred cc-ccCCcccchh
Confidence 88 8876555433
No 103
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=69.94 E-value=3.1 Score=30.42 Aligned_cols=28 Identities=25% Similarity=0.327 Sum_probs=17.3
Q ss_pred ccccccccCCCccCCCCCCCCCCCcccc
Q 046997 759 QRACIYCQQMGHSSSDCPSQFSGSRNAR 786 (807)
Q Consensus 759 ~~~c~~c~~~g~~~~~~~~~~~~~~~~~ 786 (807)
.+.|+.|+...||.++|=+...-+++.-
T Consensus 2 ~~~CprC~kg~Hwa~~C~sk~d~~G~pl 29 (36)
T PF14787_consen 2 PGLCPRCGKGFHWASECRSKTDVDGNPL 29 (36)
T ss_dssp --C-TTTSSSCS-TTT---TCCCCCEE-
T ss_pred CccCcccCCCcchhhhhhhhhcccCCCC
Confidence 3579999999999999999887776653
No 104
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=69.81 E-value=3 Score=30.29 Aligned_cols=30 Identities=30% Similarity=0.605 Sum_probs=14.3
Q ss_pred ccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChh
Q 046997 685 TCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDET 724 (807)
Q Consensus 685 ~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~ 724 (807)
.||.||. ++.. .+|.+.......|+ .|.++
T Consensus 2 fC~~CG~-~l~~--------~ip~gd~r~R~vC~-~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGG-PLER--------RIPEGDDRERLVCP-ACGFI 31 (34)
T ss_dssp B-TTT---B-EE--------E--TT-SS-EEEET-TTTEE
T ss_pred ccccccC-hhhh--------hcCCCCCccceECC-CCCCE
Confidence 5999994 4442 13444444567799 89764
No 105
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=69.74 E-value=8.2 Score=35.83 Aligned_cols=51 Identities=16% Similarity=0.083 Sum_probs=36.3
Q ss_pred CCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcC------CceeeechhHHHHHhhc
Q 046997 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDA------NTRFAPTNIGEALVMGY 556 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~------~~~l~pT~~G~~li~~l 556 (807)
.|.++|-.. .||-.+ |-..+|++|.++|||++.. ...+.+|+.|+.+++.+
T Consensus 43 ~t~~ela~~---~~~~~~-tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~ 99 (118)
T TIGR02337 43 MEFTQLANQ---ACILRP-SLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASL 99 (118)
T ss_pred cCHHHHHHH---hCCCch-hHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHh
Confidence 344444433 355444 8899999999999998732 13589999999988644
No 106
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=69.37 E-value=5.8 Score=28.96 Aligned_cols=30 Identities=17% Similarity=0.431 Sum_probs=20.1
Q ss_pred ccCCCCCcceEEEecCCCCceeeccCCCCCCcceec
Q 046997 637 QCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWL 672 (807)
Q Consensus 637 ~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~ 672 (807)
.||+| ++.|..+..+.+.. .|. .|.+....
T Consensus 3 FCp~C-~nlL~p~~~~~~~~--~C~---~C~Y~~~~ 32 (35)
T PF02150_consen 3 FCPEC-GNLLYPKEDKEKRV--ACR---TCGYEEPI 32 (35)
T ss_dssp BETTT-TSBEEEEEETTTTE--EES---SSS-EEE-
T ss_pred eCCCC-CccceEcCCCccCc--CCC---CCCCccCC
Confidence 59999 67777777665553 785 48887654
No 107
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=68.64 E-value=7.4 Score=40.59 Aligned_cols=53 Identities=17% Similarity=0.206 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcC---CceeeechhHHHHHh
Q 046997 498 PPPLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDA---NTRFAPTNIGEALVM 554 (807)
Q Consensus 498 PP~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~---~~~l~pT~~G~~li~ 554 (807)
-|...|.++|-+.| |+ +++|-+.+|+.|.+.|||++.. +..+.+|++|+.+++
T Consensus 18 ~~~~IS~~eLA~~L---~i-S~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~ 73 (217)
T PRK14165 18 NTVKISSSEFANHT---GT-SSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLY 73 (217)
T ss_pred CCCCcCHHHHHHHH---Cc-CHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHH
Confidence 34467788888777 45 8899999999999999998742 456999999998763
No 108
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=68.41 E-value=4.2 Score=37.13 Aligned_cols=32 Identities=22% Similarity=0.490 Sum_probs=26.1
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceeccCC
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYPRT 343 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRT 343 (807)
.+.++.+|++++++-+++++|++.|+|+|-|.
T Consensus 31 e~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~ 62 (105)
T PF02002_consen 31 EDLAKKLGLKPKEVRKILYKLYEDGLVSYRRR 62 (105)
T ss_dssp HHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEE
Confidence 66778899999999999999999999999853
No 109
>smart00343 ZnF_C2HC zinc finger.
Probab=68.21 E-value=2.6 Score=28.35 Aligned_cols=18 Identities=39% Similarity=1.010 Sum_probs=15.9
Q ss_pred ccccccCCCccCCCCCCC
Q 046997 761 ACIYCQQMGHSSSDCPSQ 778 (807)
Q Consensus 761 ~c~~c~~~g~~~~~~~~~ 778 (807)
.|..|+..||+..+||..
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 499999999999999953
No 110
>PRK00420 hypothetical protein; Validated
Probab=67.81 E-value=3.1 Score=38.72 Aligned_cols=13 Identities=23% Similarity=0.789 Sum_probs=8.1
Q ss_pred ccCccCCCCCCceE
Q 046997 682 TTNTCNSCTPGPVY 695 (807)
Q Consensus 682 t~~~CP~Cg~~~l~ 695 (807)
.+..||.|| .|++
T Consensus 22 l~~~CP~Cg-~pLf 34 (112)
T PRK00420 22 LSKHCPVCG-LPLF 34 (112)
T ss_pred ccCCCCCCC-Ccce
Confidence 345677787 3555
No 111
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.20 E-value=5.9 Score=40.03 Aligned_cols=30 Identities=20% Similarity=0.293 Sum_probs=27.0
Q ss_pred HHHHhcCCCHHHHHHHHHHHhhcCceeccC
Q 046997 313 RASRYFRMSSEHTMKVAEDLYQAGFISYPR 342 (807)
Q Consensus 313 ~ask~~g~s~~~tl~iaQ~LYE~g~ISYPR 342 (807)
+++..+|++...+-+++++|||.|||+|-|
T Consensus 41 eLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r 70 (178)
T PRK06266 41 EIAEQTGIKLNTVRKILYKLYDARLADYKR 70 (178)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCeEEee
Confidence 445568999999999999999999999987
No 112
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=67.05 E-value=3.7 Score=35.14 Aligned_cols=28 Identities=21% Similarity=0.247 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhhcCceeccCCCCcccCCc
Q 046997 322 SEHTMKVAEDLYQAGFISYPRTETDSFSSG 351 (807)
Q Consensus 322 ~~~tl~iaQ~LYE~g~ISYPRTds~~l~~~ 351 (807)
+.++..++++|||+||||=|.-- ||++.
T Consensus 33 ~p~~i~a~~RLheKGLI~~pdGg--yLT~~ 60 (77)
T TIGR02647 33 SPAAVAAAARLHEKGLTTQPDGG--YLTSL 60 (77)
T ss_pred CHHHHHHHHHHHHcCCccCCCCC--EecHH
Confidence 45677899999999999998544 98875
No 113
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=66.70 E-value=4.6 Score=44.28 Aligned_cols=10 Identities=30% Similarity=0.766 Sum_probs=6.0
Q ss_pred CccCCCCCCc
Q 046997 684 NTCNSCTPGP 693 (807)
Q Consensus 684 ~~CP~Cg~~~ 693 (807)
..||-||+.|
T Consensus 188 ~~CPvCGs~P 197 (309)
T PRK03564 188 QFCPVCGSMP 197 (309)
T ss_pred CCCCCCCCcc
Confidence 4577776554
No 114
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=65.07 E-value=9.8 Score=33.43 Aligned_cols=51 Identities=18% Similarity=0.232 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCC------ceeeechhHHHHHhhc
Q 046997 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDAN------TRFAPTNIGEALVMGY 556 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~------~~l~pT~~G~~li~~l 556 (807)
.|-.+|...| +| +++|...+|.+|.++|||..... ..+.+|++|..++..+
T Consensus 25 ~~~~~la~~~---~~-s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~ 81 (101)
T smart00347 25 LSVSELAKRL---GV-SPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEEL 81 (101)
T ss_pred cCHHHHHHHH---CC-CchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHH
Confidence 5566666555 45 46778899999999999986532 2488999999987543
No 115
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=64.92 E-value=2.9 Score=39.74 Aligned_cols=31 Identities=19% Similarity=0.529 Sum_probs=20.8
Q ss_pred ccccCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChhHH
Q 046997 680 AVTTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDETLR 726 (807)
Q Consensus 680 ~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~~~ 726 (807)
+-++..||.||. |+++ +.|.++ || .|+....
T Consensus 25 kML~~hCp~Cg~-PLF~-----KdG~v~---------CP-vC~~~~~ 55 (131)
T COG1645 25 KMLAKHCPKCGT-PLFR-----KDGEVF---------CP-VCGYREV 55 (131)
T ss_pred HHHHhhCcccCC-ccee-----eCCeEE---------CC-CCCceEE
Confidence 345778999994 6773 345554 99 8886443
No 116
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=63.78 E-value=3.6 Score=33.53 Aligned_cols=9 Identities=22% Similarity=0.534 Sum_probs=6.2
Q ss_pred cccCCCCChh
Q 046997 715 LGCIGGCDET 724 (807)
Q Consensus 715 ~~C~~~C~~~ 724 (807)
+.|| +|.|.
T Consensus 51 Y~Cp-~CGF~ 59 (61)
T COG2888 51 YRCP-KCGFE 59 (61)
T ss_pred eECC-CcCcc
Confidence 5688 88763
No 117
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=62.61 E-value=7.7 Score=47.44 Aligned_cols=41 Identities=24% Similarity=0.661 Sum_probs=28.1
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPG 692 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~ 692 (807)
...||.| ...|+..+.+ | -+-| .-|++.... ...||+||+.
T Consensus 444 v~~Cp~C-d~~lt~H~~~-~--~L~C---H~Cg~~~~~----------p~~Cp~Cgs~ 484 (730)
T COG1198 444 IAECPNC-DSPLTLHKAT-G--QLRC---HYCGYQEPI----------PQSCPECGSE 484 (730)
T ss_pred cccCCCC-CcceEEecCC-C--eeEe---CCCCCCCCC----------CCCCCCCCCC
Confidence 4579999 6778776654 2 2667 358877543 3579999974
No 118
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=61.23 E-value=8.5 Score=38.74 Aligned_cols=32 Identities=19% Similarity=0.464 Sum_probs=28.5
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceeccCC
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYPRT 343 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRT 343 (807)
.+.+..+|+...++.++...|||.|+|+|.|.
T Consensus 36 eela~~l~i~~~~vrriL~~L~e~~li~~~k~ 67 (176)
T COG1675 36 EELAELLGIKKNEVRRILYALYEDGLISYRKK 67 (176)
T ss_pred HHHHHHhCccHHHHHHHHHHHHhCCceEEEee
Confidence 45677799999999999999999999999853
No 119
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=61.05 E-value=6.4 Score=33.49 Aligned_cols=49 Identities=16% Similarity=0.232 Sum_probs=35.9
Q ss_pred CCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCc---eeeechhH
Q 046997 500 PLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANT---RFAPTNIG 549 (807)
Q Consensus 500 ~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~---~l~pT~~G 549 (807)
....-++|+..|+..||..+|+|.. +..|.++|.++..+-. .+.+|+.|
T Consensus 19 ~~i~~~~Li~ll~~~Gv~e~avR~a-lsRl~~~G~L~~~r~Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 19 GWIWVASLIRLLAAFGVSESAVRTA-LSRLVRRGWLESERRGRRSYYRLTERG 70 (70)
T ss_dssp S-EEHHHHHHHHCCTT--HHHHHHH-HHHHHHTTSEEEECCCTEEEEEE-HHH
T ss_pred CceeHHHHHHHHHHcCCChHHHHHH-HHHHHHcCceeeeecCccceEeeCCCC
Confidence 4456789999999999999999976 5799999999875322 36788876
No 120
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=60.83 E-value=9.6 Score=46.65 Aligned_cols=21 Identities=5% Similarity=0.018 Sum_probs=12.9
Q ss_pred HHHHHHHHhHhhhccchHHHH
Q 046997 178 AVDARQEIDLRIGASFTRFQT 198 (807)
Q Consensus 178 a~~aR~~~D~liG~n~SR~~T 198 (807)
....+..+||+..+-++..-+
T Consensus 74 ~~~~~~L~~w~s~yy~~~~g~ 94 (730)
T COG1198 74 TPELLRLIEWAADYYLSPLGD 94 (730)
T ss_pred CHHHHHHHHHHHHhhcCcHHH
Confidence 345666777777666665444
No 121
>KOG0109 consensus RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification; General function prediction only]
Probab=60.60 E-value=6.5 Score=42.10 Aligned_cols=27 Identities=30% Similarity=0.616 Sum_probs=22.2
Q ss_pred CCcccccccccccCCCccCCCCCCCCC
Q 046997 754 QSNHRQRACIYCQQMGHSSSDCPSQFS 780 (807)
Q Consensus 754 ~~~~~~~~c~~c~~~g~~~~~~~~~~~ 780 (807)
.+-.-|-.|-.||..|||+--||.-..
T Consensus 155 pgmgDq~~cyrcGkeghwskEcP~~~~ 181 (346)
T KOG0109|consen 155 PGMGDQSGCYRCGKEGHWSKECPVDRT 181 (346)
T ss_pred CCCCCHHHheeccccccccccCCccCC
Confidence 345667789999999999999998543
No 122
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=60.56 E-value=8.2 Score=38.06 Aligned_cols=65 Identities=9% Similarity=0.017 Sum_probs=46.5
Q ss_pred CccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhccccCccccCchhhHHHHHHHHHHHcCCCChHHHHHHH
Q 046997 518 TDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDDMGYELWKPNLRSMMESDMKEVSVGNKSKADVLANC 593 (807)
Q Consensus 518 TpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~ 593 (807)
.|+|...++++|.+.|||+..+.+.+..|++|..+...+. ..-..+|.-|..+.. .+++.+-++.
T Consensus 37 sp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~~---------r~hrlle~fL~~~lg--~~~~~~~~ea 101 (154)
T COG1321 37 SPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKELL---------RKHRLLERFLVDVLG--LDWEEAHEEA 101 (154)
T ss_pred CcHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHHHH---------HHHHHHHHHHHHHhC--CCHHHHHHHH
Confidence 5788999999999999999866556899999998654332 344566666666543 5555555443
No 123
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=60.53 E-value=8.4 Score=32.97 Aligned_cols=32 Identities=22% Similarity=0.472 Sum_probs=20.9
Q ss_pred ccCCCCCcceEEEecCC-----CCceeeccCCCCCCcce
Q 046997 637 QCGICQESNMVLKKSRD-----GNLMVGCLAFPQCRNAV 670 (807)
Q Consensus 637 ~CP~C~g~~lv~r~~k~-----G~~f~gCs~yP~C~~~~ 670 (807)
.||.|+ .....++++. -..++.|.| ++|.++.
T Consensus 3 ~CP~Cg-~~a~irtSr~~s~~~~~~Y~qC~N-~eCg~tF 39 (72)
T PRK09678 3 HCPLCQ-HAAHARTSRYITDTTKERYHQCQN-VNCSATF 39 (72)
T ss_pred cCCCCC-CccEEEEChhcChhhheeeeecCC-CCCCCEE
Confidence 699994 5556665432 134678988 6788654
No 124
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=60.27 E-value=27 Score=29.89 Aligned_cols=29 Identities=21% Similarity=0.373 Sum_probs=25.3
Q ss_pred cCeEEEeecCChhhhHHHHHHHHHhhhcC
Q 046997 115 CQWLVLWLDCDREGENIAFEVIEVCRAVN 143 (807)
Q Consensus 115 ~d~IiiAtD~DREGE~I~~ei~~~~~~~~ 143 (807)
...||+|+|.|..|..-+..+.+.+...+
T Consensus 43 ~~~vii~~D~D~aG~~a~~~~~~~l~~~g 71 (79)
T cd03364 43 AKEVILAFDGDEAGQKAALRALELLLKLG 71 (79)
T ss_pred CCeEEEEECCCHHHHHHHHHHHHHHHHCC
Confidence 47899999999999999999988887654
No 125
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=59.20 E-value=4.4 Score=41.01 Aligned_cols=17 Identities=41% Similarity=1.001 Sum_probs=15.6
Q ss_pred cccccccCCCccCCCCC
Q 046997 760 RACIYCQQMGHSSSDCP 776 (807)
Q Consensus 760 ~~c~~c~~~g~~~~~~~ 776 (807)
-+|..||+.||++.+|+
T Consensus 98 ~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 98 KKCYNCGETGHLSRDCN 114 (190)
T ss_pred cccccccccCccccccC
Confidence 46999999999999995
No 126
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=58.14 E-value=13 Score=46.05 Aligned_cols=52 Identities=19% Similarity=0.278 Sum_probs=43.8
Q ss_pred eEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHhhcCcee
Q 046997 287 ATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMK-VAEDLYQAGFIS 339 (807)
Q Consensus 287 ~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~-iaQ~LYE~g~IS 339 (807)
..|.+++..++++.||++|+=++|.++|-+ .|+.-.-|.. |.+.|.++|||.
T Consensus 561 ~~i~~~~l~ek~TkPPpryTEAtLIk~ME~-~GIGTPATrAsIIetL~~R~YV~ 613 (805)
T PTZ00407 561 FELRSPQVRENRPVPPLPHSEGTLIEELKN-NGVGRPSTYPMIVKTLLARGYIA 613 (805)
T ss_pred eecceeeeecccCCCCCCCCHHHHHHHHHh-CCCCCcccHHHHHHHHHhcCCEE
Confidence 346677888899999999999999999877 6996555554 899999999997
No 127
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=57.58 E-value=3.9 Score=32.13 Aligned_cols=18 Identities=44% Similarity=1.187 Sum_probs=16.1
Q ss_pred ccccccccCCCccCCCCC
Q 046997 759 QRACIYCQQMGHSSSDCP 776 (807)
Q Consensus 759 ~~~c~~c~~~g~~~~~~~ 776 (807)
...|..||..||....||
T Consensus 31 p~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECP 48 (49)
T ss_pred ChhhcCCCCcCcCHhHcC
Confidence 345999999999999998
No 128
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=57.12 E-value=8.1 Score=36.07 Aligned_cols=31 Identities=19% Similarity=0.351 Sum_probs=17.2
Q ss_pred CccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChhHH
Q 046997 684 NTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDETLR 726 (807)
Q Consensus 684 ~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~~~ 726 (807)
..||+||+ +|+- +.....+ .+.|+ .|.+...
T Consensus 3 ~FCp~Cgs-ll~p-~~~~~~~---------~l~C~-kCgye~~ 33 (113)
T COG1594 3 RFCPKCGS-LLYP-KKDDEGG---------KLVCR-KCGYEEE 33 (113)
T ss_pred cccCCccC-eeEE-eEcCCCc---------EEECC-CCCcchh
Confidence 46999985 3332 1111111 26798 8887654
No 129
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=56.99 E-value=8.5 Score=49.00 Aligned_cols=28 Identities=18% Similarity=0.147 Sum_probs=21.7
Q ss_pred EeecCccCCCCCCCHHHHHHHHHhCCCC
Q 046997 490 TLDSGVTRPPPLLSEADLLSCMDKAGIG 517 (807)
Q Consensus 490 ~i~e~~T~PP~~~Tea~Li~~Me~~GIG 517 (807)
.++...+-.|+-|++...+..++..|.-
T Consensus 432 FlENNh~L~P~~y~~EWw~~e~~~~~~~ 459 (1337)
T PRK14714 432 FVENNHPLLPASYCEEWWIQELVKAGAD 459 (1337)
T ss_pred hhhcCCcCCCccchHHHHHHHHHhcccc
Confidence 4566677888899999988888876654
No 130
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=56.43 E-value=8.9 Score=30.78 Aligned_cols=7 Identities=29% Similarity=0.809 Sum_probs=5.3
Q ss_pred ccCCCCC
Q 046997 685 TCNSCTP 691 (807)
Q Consensus 685 ~CP~Cg~ 691 (807)
.||.||.
T Consensus 6 ~CP~Cgn 12 (55)
T PF14205_consen 6 LCPICGN 12 (55)
T ss_pred ECCCCCC
Confidence 5888885
No 131
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=56.32 E-value=11 Score=44.37 Aligned_cols=41 Identities=22% Similarity=0.578 Sum_probs=28.3
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPG 692 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~ 692 (807)
...||.| +..|+..+.. . .+.|. -|++....| ..||.||+.
T Consensus 222 ~~~C~~C-~~~l~~h~~~--~-~l~Ch---~Cg~~~~~~----------~~Cp~C~s~ 262 (505)
T TIGR00595 222 ILCCPNC-DVSLTYHKKE--G-KLRCH---YCGYQEPIP----------KTCPQCGSE 262 (505)
T ss_pred ccCCCCC-CCceEEecCC--C-eEEcC---CCcCcCCCC----------CCCCCCCCC
Confidence 4579999 5677765432 2 37885 599886653 469999964
No 132
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=56.13 E-value=10 Score=29.75 Aligned_cols=31 Identities=16% Similarity=0.429 Sum_probs=18.0
Q ss_pred ccCCCCCcceEEEecCCCCceeeccCCCCCCcceec
Q 046997 637 QCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWL 672 (807)
Q Consensus 637 ~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~ 672 (807)
.||.| |..|..+...... .+.| |.|++....
T Consensus 2 FCp~C-g~~l~~~~~~~~~-~~vC---~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKC-GNMLIPKEGKEKR-RFVC---RKCGYEEPI 32 (52)
T ss_pred CCCCC-CCccccccCCCCC-EEEC---CcCCCeEEC
Confidence 49999 4555443322222 4678 458887665
No 133
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=55.93 E-value=8.9 Score=41.28 Aligned_cols=29 Identities=24% Similarity=0.563 Sum_probs=19.4
Q ss_pred ccCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCC
Q 046997 682 TTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCD 722 (807)
Q Consensus 682 t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~ 722 (807)
++++|+.|| +++.++....| +. +.|| .|+
T Consensus 244 ~GepC~~CG-t~I~k~~~~gR-~t---------~~CP-~CQ 272 (273)
T COG0266 244 AGEPCRRCG-TPIEKIKLGGR-ST---------FYCP-VCQ 272 (273)
T ss_pred CCCCCCccC-CEeEEEEEcCC-cC---------EeCC-CCC
Confidence 578999999 56666544333 33 3499 895
No 134
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=55.86 E-value=6.3 Score=43.20 Aligned_cols=9 Identities=33% Similarity=1.006 Sum_probs=5.2
Q ss_pred ccCCCCCCc
Q 046997 685 TCNSCTPGP 693 (807)
Q Consensus 685 ~CP~Cg~~~ 693 (807)
.||-||+.|
T Consensus 186 ~CPvCGs~P 194 (305)
T TIGR01562 186 LCPACGSPP 194 (305)
T ss_pred cCCCCCChh
Confidence 466666544
No 135
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Probab=55.70 E-value=25 Score=29.84 Aligned_cols=28 Identities=25% Similarity=0.369 Sum_probs=23.9
Q ss_pred cCeEEEeecCChhhhHHHHHHHHHhhhc
Q 046997 115 CQWLVLWLDCDREGENIAFEVIEVCRAV 142 (807)
Q Consensus 115 ~d~IiiAtD~DREGE~I~~ei~~~~~~~ 142 (807)
...||+|.|.|..|+..+..+.+.+...
T Consensus 43 ~~~vii~~D~D~~G~~~~~~~~~~~~~~ 70 (79)
T cd01029 43 ARTVILAFDNDEAGKKAAARALELLLAL 70 (79)
T ss_pred CCEEEEEECCCHHHHHHHHHHHHHHHHC
Confidence 4789999999999998888888877653
No 136
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=55.43 E-value=4.3 Score=32.86 Aligned_cols=34 Identities=18% Similarity=0.503 Sum_probs=17.8
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCC----CCCCcceecC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAF----PQCRNAVWLP 673 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~y----P~C~~~~~~p 673 (807)
..+||+|+++.++.... -|.|.+| -.|.|....|
T Consensus 14 l~~Cp~C~~~~l~~~~~-----~Y~C~G~~sewtkC~~~t~~p 51 (55)
T PF08063_consen 14 LEPCPKCKGGQLYFDGS-----GYKCTGYISEWTKCTYSTKDP 51 (55)
T ss_dssp E---SSSSE-EEEEETT-----EEEEESECCTTCEEEEEESS-
T ss_pred CCCCCCCCCCeEEecCC-----ccEeCcccCceeEcccCcCCC
Confidence 45899996555553322 3788765 4577665443
No 137
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=55.07 E-value=7.5 Score=35.83 Aligned_cols=33 Identities=24% Similarity=0.787 Sum_probs=21.1
Q ss_pred cccccCCCCCcce-----EEEecCCCC-ceeeccCCCCCCcc
Q 046997 634 VVRQCGICQESNM-----VLKKSRDGN-LMVGCLAFPQCRNA 669 (807)
Q Consensus 634 ~~~~CP~C~g~~l-----v~r~~k~G~-~f~gCs~yP~C~~~ 669 (807)
+..+||+||...| .+|..-.|. .||.| |+|+|.
T Consensus 73 I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC---~kC~~k 111 (116)
T KOG2907|consen 73 IKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTC---PKCKYK 111 (116)
T ss_pred hhccCcccCCchhhhhhhhcccccCCceEEEEc---Ccccee
Confidence 4568999964444 455555663 46888 458765
No 138
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=53.80 E-value=13 Score=25.76 Aligned_cols=26 Identities=27% Similarity=0.737 Sum_probs=11.8
Q ss_pred ccCCCCCcceEEEecCCCCceeeccCCCCC
Q 046997 637 QCGICQESNMVLKKSRDGNLMVGCLAFPQC 666 (807)
Q Consensus 637 ~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C 666 (807)
.||.| ++.++.. .|...+.|.|.-.|
T Consensus 1 ~CP~C-~s~l~~~---~~ev~~~C~N~l~C 26 (28)
T PF03119_consen 1 TCPVC-GSKLVRE---EGEVDIRCPNPLSC 26 (28)
T ss_dssp B-TTT---BEEE----CCTTCEEE--CGC-
T ss_pred CcCCC-CCEeEcC---CCCEeEECCCCCcC
Confidence 49999 6777733 23345889883255
No 139
>PRK04023 DNA polymerase II large subunit; Validated
Probab=53.40 E-value=8.4 Score=47.88 Aligned_cols=40 Identities=18% Similarity=0.114 Sum_probs=27.4
Q ss_pred CCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCC
Q 046997 479 VHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGT 518 (807)
Q Consensus 479 ~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGT 518 (807)
..||.+..-.=.++...+-.|+.|++...+..++..|.-.
T Consensus 401 dlGeiLi~yGdFlENNhpL~Ps~y~~EWW~qe~~~~~~~~ 440 (1121)
T PRK04023 401 DLGEILINYGDFLENNHPLLPSSYCEEWWIQELEAAGAEY 440 (1121)
T ss_pred hhhhhhcccchhhhcCCcCCCccccHHHHHHHHHhccccc
Confidence 3455443322346667788899999999999998776553
No 140
>PRK10445 endonuclease VIII; Provisional
Probab=52.79 E-value=10 Score=40.77 Aligned_cols=28 Identities=25% Similarity=0.623 Sum_probs=18.6
Q ss_pred cCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCC
Q 046997 683 TNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCD 722 (807)
Q Consensus 683 ~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~ 722 (807)
++.||.|| +++.+++.-+|.. +.|| .|+
T Consensus 235 g~~Cp~Cg-~~I~~~~~~gR~t----------~~CP-~CQ 262 (263)
T PRK10445 235 GEACERCG-GIIEKTTLSSRPF----------YWCP-GCQ 262 (263)
T ss_pred CCCCCCCC-CEeEEEEECCCCc----------EECC-CCc
Confidence 56899999 5676654433332 4499 885
No 141
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=52.30 E-value=14 Score=29.50 Aligned_cols=28 Identities=25% Similarity=0.479 Sum_probs=21.0
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAF 663 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~y 663 (807)
...|+.| |..|..++.+.+..+|.|+++
T Consensus 5 ~l~C~~C-G~~m~~~~~~~~~~yy~C~~~ 32 (58)
T PF13408_consen 5 LLRCGHC-GSKMTRRKRKGKYRYYRCSNR 32 (58)
T ss_pred cEEcccC-CcEeEEEECCCCceEEEcCCC
Confidence 4579999 677877766555567999875
No 142
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=52.08 E-value=29 Score=33.44 Aligned_cols=54 Identities=15% Similarity=0.261 Sum_probs=42.7
Q ss_pred CHHHHHHHHHhCCCCC----ccchHHHHHhhcccceEEEc----CCceeeechhHHHHHhhc
Q 046997 503 SEADLLSCMDKAGIGT----DATMHDHIKKLLDRFYAIKD----ANTRFAPTNIGEALVMGY 556 (807)
Q Consensus 503 Tea~Li~~Me~~GIGT----pATra~iI~~L~~R~Yv~~~----~~~~l~pT~~G~~li~~l 556 (807)
+=-+|++.++..|.|. ++|.=.++..|.+.|||... .++.+.+|+.|+..+..+
T Consensus 57 yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~ 118 (135)
T PRK09416 57 TGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKA 118 (135)
T ss_pred CHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHH
Confidence 4567888888777765 88999999999999999752 235689999999977544
No 143
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=51.48 E-value=11 Score=40.64 Aligned_cols=31 Identities=13% Similarity=0.024 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcC
Q 046997 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDA 539 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~ 539 (807)
+|...|.+.+.+ .+..|-..|.+..+|.--+
T Consensus 141 ~~~~~~~~~~~~-------~~~~ik~~Lldq~viaGiG 171 (272)
T PRK14810 141 ISFEDFAALFRG-------RKTRIKSALLNQTLLRGVG 171 (272)
T ss_pred CCHHHHHHHHhc-------CCccHHHHhhcCceecccc
Confidence 555666666643 2345777777777775444
No 144
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=51.32 E-value=17 Score=30.94 Aligned_cols=41 Identities=22% Similarity=0.618 Sum_probs=20.6
Q ss_pred ccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEE
Q 046997 637 QCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLI 697 (807)
Q Consensus 637 ~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~ 697 (807)
.||.| ..+|.... |. |-|.. |.-.+.. ...||.|+. ++-+.
T Consensus 3 ~CP~C-~~~L~~~~---~~--~~C~~---C~~~~~~----------~a~CPdC~~-~Le~L 43 (70)
T PF07191_consen 3 TCPKC-QQELEWQG---GH--YHCEA---CQKDYKK----------EAFCPDCGQ-PLEVL 43 (70)
T ss_dssp B-SSS--SBEEEET---TE--EEETT---T--EEEE----------EEE-TTT-S-B-EEE
T ss_pred cCCCC-CCccEEeC---CE--EECcc---cccccee----------cccCCCccc-HHHHH
Confidence 69999 56765443 22 67864 7754432 346999995 55544
No 145
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=51.02 E-value=18 Score=35.62 Aligned_cols=40 Identities=13% Similarity=0.245 Sum_probs=33.8
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceeccCCCCcccCCc
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYPRTETDSFSSG 351 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTds~~l~~~ 351 (807)
++.++.++.+|.-+.+.+++|.+.|||.|-+-.--.|++.
T Consensus 28 ~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~ 67 (154)
T COG1321 28 KDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTEK 67 (154)
T ss_pred HHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeEEChh
Confidence 6778889999999999999999999999965555566653
No 146
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=50.96 E-value=15 Score=27.58 Aligned_cols=30 Identities=17% Similarity=0.492 Sum_probs=16.7
Q ss_pred ccCCCCCcceEEEe--cC---CCC-ceeeccCCCCCCcc
Q 046997 637 QCGICQESNMVLKK--SR---DGN-LMVGCLAFPQCRNA 669 (807)
Q Consensus 637 ~CP~C~g~~lv~r~--~k---~G~-~f~gCs~yP~C~~~ 669 (807)
+||+|+..+.+..+ .+ .++ .||-|.+ |++.
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~---C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTK---CGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCC---CCCE
Confidence 69999655554322 22 232 4677754 6654
No 147
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=50.92 E-value=22 Score=28.32 Aligned_cols=32 Identities=16% Similarity=0.283 Sum_probs=26.9
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceeccCC
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYPRT 343 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRT 343 (807)
.+.++.+++++..+-.++.+|+++|||+--+.
T Consensus 21 ~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~ 52 (59)
T PF01047_consen 21 SELAEKLGISRSTVTRIIKRLEKKGLIERERD 52 (59)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHCCChhHHHHHHHHHHHCCCEEeccC
Confidence 46677899999999999999999999986554
No 148
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=50.85 E-value=24 Score=27.06 Aligned_cols=29 Identities=17% Similarity=0.280 Sum_probs=25.2
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHhhcCcee
Q 046997 311 EKRASRYFRMSSEHTMKVAEDLYQAGFIS 339 (807)
Q Consensus 311 q~~ask~~g~s~~~tl~iaQ~LYE~g~IS 339 (807)
+.+.++.+|+|...+-.+.++|-++|+|.
T Consensus 20 ~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 20 QKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 46778889999999999999999999984
No 149
>PLN02189 cellulose synthase
Probab=50.56 E-value=9.3 Score=47.95 Aligned_cols=50 Identities=32% Similarity=0.660 Sum_probs=35.0
Q ss_pred cccccCCCCCcceEEEecCCCCceeecc--CCCCCCcceecCCCccccccccCccCCCCC
Q 046997 634 VVRQCGICQESNMVLKKSRDGNLMVGCL--AFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 634 ~~~~CP~C~g~~lv~r~~k~G~~f~gCs--~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
.+..|..| |.++-+. ..|..|++|. +||-|+..+-.+.. .-...||+|+.
T Consensus 33 ~~~~C~iC-gd~vg~~--~~g~~fvaC~~C~fpvCr~Cyeyer~-----eg~q~CpqCkt 84 (1040)
T PLN02189 33 DGQVCEIC-GDEIGLT--VDGDLFVACNECGFPVCRPCYEYERR-----EGTQNCPQCKT 84 (1040)
T ss_pred cCcccccc-ccccCcC--CCCCEEEeeccCCCccccchhhhhhh-----cCCccCcccCC
Confidence 45589999 5665443 5788899996 56888877655432 23567999985
No 150
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=50.42 E-value=7.6 Score=42.32 Aligned_cols=12 Identities=33% Similarity=0.786 Sum_probs=5.4
Q ss_pred CccCCCCCCceE
Q 046997 684 NTCNSCTPGPVY 695 (807)
Q Consensus 684 ~~CP~Cg~~~l~ 695 (807)
..||-||+.|.+
T Consensus 173 g~CPvCGs~P~~ 184 (290)
T PF04216_consen 173 GYCPVCGSPPVL 184 (290)
T ss_dssp SS-TTT---EEE
T ss_pred CcCCCCCCcCce
Confidence 568888876554
No 151
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=50.40 E-value=7.9 Score=31.82 Aligned_cols=32 Identities=28% Similarity=0.354 Sum_probs=23.6
Q ss_pred CccchHHHHHhhcccceEEEc-----CC-ceeeechhH
Q 046997 518 TDATMHDHIKKLLDRFYAIKD-----AN-TRFAPTNIG 549 (807)
Q Consensus 518 TpATra~iI~~L~~R~Yv~~~-----~~-~~l~pT~~G 549 (807)
+.+|...+|+.|.++|||++. ++ ..+.+|+.|
T Consensus 31 ~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 31 SKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp -HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred CHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 456778999999999999653 11 358999988
No 152
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=49.91 E-value=23 Score=29.11 Aligned_cols=31 Identities=16% Similarity=0.319 Sum_probs=26.6
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceeccC
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYPR 342 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPR 342 (807)
.+.++++|+|+.-+-+..++|=++|||.|-+
T Consensus 26 ~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 26 KDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 4567789999999999999999999999854
No 153
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=49.89 E-value=25 Score=39.49 Aligned_cols=65 Identities=22% Similarity=0.386 Sum_probs=32.1
Q ss_pred cccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEEEeeccCccCCCC
Q 046997 634 VVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPPG 709 (807)
Q Consensus 634 ~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~~ 709 (807)
....||.|+|.-.+....+.|.+ ..=.-.|.|+=+ -.....+|+.|.. .-+..+.+.-..++|++
T Consensus 158 ~~~tC~tC~G~G~v~~~~~~g~~-~~~~~C~~C~G~---------G~~i~~pC~~C~G-~G~v~~~~~i~V~IPaG 222 (371)
T COG0484 158 DPKTCPTCNGSGQVRTVQRTGFF-SFQQTCPTCNGT---------GKIIKDPCGKCKG-KGRVKKKKSISVNIPAG 222 (371)
T ss_pred CCCcCCCCCCcCeEEEEEeeeEE-EEEEECCCCccc---------eeECCCCCCCCCC-CCeEeeeeEEEEECCCC
Confidence 35679999765544433333432 221222668633 1223568999973 32322222223455555
No 154
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=49.85 E-value=23 Score=38.45 Aligned_cols=54 Identities=11% Similarity=0.190 Sum_probs=44.3
Q ss_pred CCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCC---ceeeechhHHHHHhh
Q 046997 501 LLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDAN---TRFAPTNIGEALVMG 555 (807)
Q Consensus 501 ~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~---~~l~pT~~G~~li~~ 555 (807)
...-++||..|+-.||...+.| .++..|.++|+|+.... +.+.+|+.|+...+.
T Consensus 17 ~i~~~~Li~l~~~~gi~~~~vr-~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~ 73 (280)
T TIGR02277 17 AIWLGSLIEFLAGLGINERLVR-TAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAA 73 (280)
T ss_pred ceeHHHHHHHHHhcCCCcchHH-HHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHH
Confidence 4556899999999999988877 57889999999987532 458999999987653
No 155
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=49.73 E-value=9 Score=28.26 Aligned_cols=8 Identities=25% Similarity=0.783 Sum_probs=4.3
Q ss_pred cCccCCCC
Q 046997 683 TNTCNSCT 690 (807)
Q Consensus 683 ~~~CP~Cg 690 (807)
...||+|+
T Consensus 25 ~vrC~~C~ 32 (37)
T PF13719_consen 25 KVRCPKCG 32 (37)
T ss_pred EEECCCCC
Confidence 34566665
No 156
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=49.35 E-value=17 Score=29.04 Aligned_cols=33 Identities=18% Similarity=0.459 Sum_probs=16.6
Q ss_pred cccCCCCCcceEEEec---CCCCceeeccCCCCCCccee
Q 046997 636 RQCGICQESNMVLKKS---RDGNLMVGCLAFPQCRNAVW 671 (807)
Q Consensus 636 ~~CP~C~g~~lv~r~~---k~G~~f~gCs~yP~C~~~~~ 671 (807)
.+||.|++....++.+ +.+..++.|+ .|.....
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~---~Cga~~~ 37 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECS---TCGASGP 37 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECC---CCCCCcc
Confidence 4799996544434421 1223334564 3665543
No 157
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=49.35 E-value=17 Score=47.24 Aligned_cols=53 Identities=15% Similarity=0.198 Sum_probs=45.5
Q ss_pred eeeeeeEeecCccCCCCCCCHHHHHHHHH-hCCCCCccchHHHHHhhcccceEEE
Q 046997 484 FIPTTLTLDSGVTRPPPLLSEADLLSCMD-KAGIGTDATMHDHIKKLLDRFYAIK 537 (807)
Q Consensus 484 ~~~~~~~i~e~~T~PP~~~Tea~Li~~Me-~~GIGTpATra~iI~~L~~R~Yv~~ 537 (807)
+.+.++..++.+..||++||-++|+..+- +.|++..-|. .|.+.|++.|||.-
T Consensus 867 ~~V~~v~~k~~~~~pP~Pf~t~~Lq~~As~~lg~sa~~tm-~iAQ~LYE~GlITY 920 (1171)
T TIGR01054 867 LDVEDIAEREEERNPLPPYTTDTMLEDANRKLGLSVKETM-QIAQELFENGLITY 920 (1171)
T ss_pred cEEEEEEeeEEeccCCCCCCHHHHHHHHHHhcCCCHHHHH-HHHHHHHhCCEEEe
Confidence 55667788889999999999999999986 4699888876 59999999999974
No 158
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=48.45 E-value=14 Score=40.02 Aligned_cols=29 Identities=24% Similarity=0.494 Sum_probs=18.7
Q ss_pred ccCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCC
Q 046997 682 TTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCD 722 (807)
Q Consensus 682 t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~ 722 (807)
.+..||.|| .++.+....+|. . +.|| .|+
T Consensus 244 ~g~pC~~Cg-~~I~~~~~~gR~-t---------~~CP-~CQ 272 (272)
T TIGR00577 244 KGEPCRRCG-TPIEKIKVGGRG-T---------HFCP-QCQ 272 (272)
T ss_pred CCCCCCCCC-CeeEEEEECCCC-C---------EECC-CCC
Confidence 367899999 566655443333 2 4499 885
No 159
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=48.39 E-value=73 Score=32.64 Aligned_cols=48 Identities=15% Similarity=0.213 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEc-----CCc---eeeechhHHHHH
Q 046997 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKD-----ANT---RFAPTNIGEALV 553 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~-----~~~---~l~pT~~G~~li 553 (807)
.|-.+|-..| || +++|-..|++.|.+.|+|+.. .++ .+.+|+.|..++
T Consensus 16 ~t~~eLA~~l---gi-s~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~ 71 (203)
T TIGR02702 16 ATAAALAEAL---AI-SPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQF 71 (203)
T ss_pred CCHHHHHHHH---Cc-CHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhc
Confidence 5666665555 77 678999999999999999764 112 258899998765
No 160
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=47.89 E-value=18 Score=29.36 Aligned_cols=30 Identities=30% Similarity=0.682 Sum_probs=16.7
Q ss_pred ccccCCCCCcceEEEecCCCC-----ceeeccCCCCCCc
Q 046997 635 VRQCGICQESNMVLKKSRDGN-----LMVGCLAFPQCRN 668 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~-----~f~gCs~yP~C~~ 668 (807)
..+||.| |...+......+. +++.|.+ |..
T Consensus 3 LkPCPFC-G~~~~~~~~~~~~~~~~~~~V~C~~---Cga 37 (61)
T PF14354_consen 3 LKPCPFC-GSADVLIRQDEGFDYGMYYYVECTD---CGA 37 (61)
T ss_pred CcCCCCC-CCcceEeecccCCCCCCEEEEEcCC---CCC
Confidence 4689999 5544443332221 5566754 654
No 161
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=47.45 E-value=28 Score=26.79 Aligned_cols=28 Identities=14% Similarity=0.215 Sum_probs=24.0
Q ss_pred HHHHhcCCCHHHHHHHHHHHhhcCceec
Q 046997 313 RASRYFRMSSEHTMKVAEDLYQAGFISY 340 (807)
Q Consensus 313 ~ask~~g~s~~~tl~iaQ~LYE~g~ISY 340 (807)
+.++.+|+|...+-.....|.+.|+|+|
T Consensus 20 el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 20 ELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred hHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 4466689999999999999999999986
No 162
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=46.90 E-value=14 Score=39.81 Aligned_cols=30 Identities=23% Similarity=0.419 Sum_probs=18.8
Q ss_pred ccCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCCh
Q 046997 682 TTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDE 723 (807)
Q Consensus 682 t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~ 723 (807)
.+++||.|| .++.++..-+|.. +.|| .|+-
T Consensus 234 ~g~pC~~Cg-~~I~~~~~~gR~t----------y~Cp-~CQ~ 263 (269)
T PRK14811 234 EGQPCPRCG-TPIEKIVVGGRGT----------HFCP-QCQP 263 (269)
T ss_pred CcCCCCcCC-CeeEEEEECCCCc----------EECC-CCcC
Confidence 367899999 4666554333332 4499 8863
No 163
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=46.82 E-value=15 Score=39.81 Aligned_cols=31 Identities=16% Similarity=0.100 Sum_probs=18.2
Q ss_pred CCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcC
Q 046997 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDA 539 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~ 539 (807)
|+...+.+.|.+ .+..|-..|++...|---+
T Consensus 142 ~~~~~~~~~l~~-------~~~~Ik~~LLDQ~~iaGiG 172 (274)
T PRK01103 142 FDGEYLAAKLRK-------KKTAIKPALLDQTVVVGVG 172 (274)
T ss_pred CCHHHHHHHHhc-------CCccHHHHhhcCCeEeccc
Confidence 444566666643 2346666777777775444
No 164
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=46.03 E-value=13 Score=26.27 Aligned_cols=17 Identities=35% Similarity=0.589 Sum_probs=14.8
Q ss_pred HHHHHHHHHHhhcCcee
Q 046997 323 EHTMKVAEDLYQAGFIS 339 (807)
Q Consensus 323 ~~tl~iaQ~LYE~g~IS 339 (807)
.+.|+.++.||++|.||
T Consensus 2 ~~~L~~L~~l~~~G~Is 18 (31)
T PF09851_consen 2 EDRLEKLKELYDKGEIS 18 (31)
T ss_pred hHHHHHHHHHHHcCCCC
Confidence 46788999999999996
No 165
>PRK05580 primosome assembly protein PriA; Validated
Probab=46.00 E-value=20 Score=43.99 Aligned_cols=41 Identities=22% Similarity=0.664 Sum_probs=27.5
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPG 692 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~ 692 (807)
...||.| +..|+..+.. . .+-|. .|++....| ..||.||+.
T Consensus 390 ~~~C~~C-~~~l~~h~~~--~-~l~Ch---~Cg~~~~~~----------~~Cp~Cg~~ 430 (679)
T PRK05580 390 VAECPHC-DASLTLHRFQ--R-RLRCH---HCGYQEPIP----------KACPECGST 430 (679)
T ss_pred ccCCCCC-CCceeEECCC--C-eEECC---CCcCCCCCC----------CCCCCCcCC
Confidence 4579999 5677655432 2 37784 499876643 469999963
No 166
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=45.95 E-value=15 Score=39.81 Aligned_cols=32 Identities=22% Similarity=0.109 Sum_probs=19.4
Q ss_pred CCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCC
Q 046997 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDAN 540 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~ 540 (807)
||...|.+.+.+ .+..|=.-|++...|.--+|
T Consensus 151 ~~~~~~~~~l~~-------~~~~IK~~LLDQ~~vaGIGN 182 (282)
T PRK13945 151 FSVEYLKKKLKK-------RTRSIKTALLDQSIVAGIGN 182 (282)
T ss_pred CCHHHHHHHHhc-------CCccHHHHhhcCCeEeccch
Confidence 555666666643 24566667777777765543
No 167
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=45.85 E-value=80 Score=27.34 Aligned_cols=53 Identities=25% Similarity=0.279 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcC-CceeeechhHHHHHhhc
Q 046997 500 PLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDA-NTRFAPTNIGEALVMGY 556 (807)
Q Consensus 500 ~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~-~~~l~pT~~G~~li~~l 556 (807)
..+|-.+|-+.| || +.+|-..++..|.+.|||.... ++.+.+++....+...+
T Consensus 19 ~~~t~~~ia~~l---~i-~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~~~~~~~ 72 (91)
T smart00346 19 GGLTLAELAERL---GL-SKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVLELGQSY 72 (91)
T ss_pred CCcCHHHHHHHh---CC-CHHHHHHHHHHHHHCCCeeecCCCCceeecHHHHHHHHHH
Confidence 357777777666 66 5678889999999999998753 33477877766654433
No 168
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=45.43 E-value=34 Score=25.66 Aligned_cols=31 Identities=16% Similarity=0.299 Sum_probs=27.3
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHhhcCceecc
Q 046997 311 EKRASRYFRMSSEHTMKVAEDLYQAGFISYP 341 (807)
Q Consensus 311 q~~ask~~g~s~~~tl~iaQ~LYE~g~ISYP 341 (807)
+.++++.+|+|...+.++.+.|-+.|+|.+-
T Consensus 11 ~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 11 RQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4567778999999999999999999999864
No 169
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=45.42 E-value=2e+02 Score=28.24 Aligned_cols=48 Identities=17% Similarity=0.065 Sum_probs=30.0
Q ss_pred CeEEEeecCChhhhHHHHHHHHHhhh---cCCCCeEEEEEecccCHHHHHH
Q 046997 116 QWLVLWLDCDREGENIAFEVIEVCRA---VNCHLVLRRARFSALIDREIHQ 163 (807)
Q Consensus 116 d~IiiAtD~DREGE~I~~ei~~~~~~---~~~~~~v~R~~~s~lt~~~I~~ 163 (807)
-.++.++|.|..|=.|+..+..-... ......+.++++-.+.++++.+
T Consensus 52 ~~~~~l~D~DP~Gi~I~~~y~~gs~~~~~~~~~~~~~~l~~~G~~~~d~~~ 102 (160)
T cd00223 52 LPVYILVDGDPYGISILLTYKYGSIKLAYESESLATPDLRWLGLRPSDIIR 102 (160)
T ss_pred CCEEEEECCCcchhhhhHHHHhCccccccccccccCCCcEEccCCHHHHhh
Confidence 36999999999999998776542111 0111123366666666666654
No 170
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=44.99 E-value=16 Score=39.12 Aligned_cols=12 Identities=25% Similarity=0.545 Sum_probs=10.4
Q ss_pred ccccccCCCccC
Q 046997 761 ACIYCQQMGHSS 772 (807)
Q Consensus 761 ~c~~c~~~g~~~ 772 (807)
+|..|++++|+.
T Consensus 227 KC~nC~~t~~l~ 238 (308)
T COG3058 227 KCSNCEQSKKLH 238 (308)
T ss_pred HhccccccCCcc
Confidence 499999999876
No 171
>PLN02436 cellulose synthase A
Probab=44.80 E-value=14 Score=46.60 Aligned_cols=50 Identities=30% Similarity=0.637 Sum_probs=34.6
Q ss_pred cccccCCCCCcceEEEecCCCCceeecc--CCCCCCcceecCCCccccccccCccCCCCC
Q 046997 634 VVRQCGICQESNMVLKKSRDGNLMVGCL--AFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 634 ~~~~CP~C~g~~lv~r~~k~G~~f~gCs--~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
.+..|..| |.++-+. ..|..|++|. +||-|+..+-.+. +.-...||+|+.
T Consensus 35 ~~~iCqIC-GD~Vg~t--~dGe~FVACn~C~fpvCr~Cyeyer-----~eg~~~Cpqckt 86 (1094)
T PLN02436 35 SGQTCQIC-GDEIELT--VDGEPFVACNECAFPVCRPCYEYER-----REGNQACPQCKT 86 (1094)
T ss_pred CCcccccc-ccccCcC--CCCCEEEeeccCCCccccchhhhhh-----hcCCccCcccCC
Confidence 45689999 5555433 5788899996 4678887765543 223567999985
No 172
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=44.53 E-value=23 Score=29.49 Aligned_cols=32 Identities=22% Similarity=0.520 Sum_probs=17.7
Q ss_pred cccccCCCCCcceEEEecCCCCceeeccCCCCCCcc
Q 046997 634 VVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNA 669 (807)
Q Consensus 634 ~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~ 669 (807)
...+||-|+...+..+. ..|-+++.|- +|.-.
T Consensus 5 ~lKPCPFCG~~~~~v~~-~~g~~~v~C~---~CgA~ 36 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKA-ISGYYRAKCN---GCESR 36 (64)
T ss_pred cccCCCCCCCceeEEEe-cCceEEEEcC---CCCcC
Confidence 45689999544444443 3444445553 46554
No 173
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=43.80 E-value=56 Score=35.10 Aligned_cols=83 Identities=20% Similarity=0.425 Sum_probs=42.5
Q ss_pred ccccccCCCCCcc---eEEEe-cCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEEEeeccCccCCC
Q 046997 633 EVVRQCGICQESN---MVLKK-SRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPP 708 (807)
Q Consensus 633 ~~~~~CP~C~g~~---lv~r~-~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~ 708 (807)
+...-||.||+.+ |+.-. .-.|-.|+.||- |- +.|. ..-.+|-.|+.. .+-..+.+-.
T Consensus 183 e~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~Csl---C~-teW~--------~VR~KC~nC~~t------~~l~y~sl~s 244 (308)
T COG3058 183 ESRQYCPVCGSMPVASMVQIGETEQGLRYLHCSL---CE-TEWH--------YVRVKCSNCEQS------KKLHYWSLES 244 (308)
T ss_pred cccccCCCcCCCCcceeeeecCccccchhhhhhh---HH-HHHH--------HHHHHhcccccc------CCccceeccc
Confidence 4566899996433 33333 346777889974 43 3342 123468888741 1111222110
Q ss_pred C--CccCccccCCCCChhHHHHHHhhCC
Q 046997 709 G--FNVNHLGCIGGCDETLRQLIEICGT 734 (807)
Q Consensus 709 ~--~~~~~~~C~~~C~~~~~~l~~~~~~ 734 (807)
+ --.....|. .|..-++.+.+-.-.
T Consensus 245 ~E~A~vkAEtC~-~C~sYlKilyqekdp 271 (308)
T COG3058 245 SELAAVKAETCG-DCNSYLKILYQEKDP 271 (308)
T ss_pred hhhhHhhhhcCC-cHHHHHHHHHHhcCC
Confidence 0 001224587 888777766554443
No 174
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=43.01 E-value=36 Score=27.27 Aligned_cols=30 Identities=10% Similarity=0.187 Sum_probs=25.7
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceecc
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYP 341 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYP 341 (807)
.+.++.+|+|...+.++..+|-+.|+|++-
T Consensus 29 ~~la~~~~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 29 RELAEELGVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 345667899999999999999999999853
No 175
>PRK11050 manganese transport regulator MntR; Provisional
Probab=42.86 E-value=22 Score=34.84 Aligned_cols=42 Identities=19% Similarity=0.131 Sum_probs=33.4
Q ss_pred CCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhc
Q 046997 514 AGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGY 556 (807)
Q Consensus 514 ~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l 556 (807)
.||. ++|-..+|..|.+.|||.....+.+.+|+.|..++..+
T Consensus 61 l~is-~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~ 102 (152)
T PRK11050 61 LGVS-QPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQES 102 (152)
T ss_pred HCCC-HHHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHH
Confidence 3554 67788999999999999876545689999999987543
No 176
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=42.67 E-value=14 Score=30.20 Aligned_cols=8 Identities=25% Similarity=0.600 Sum_probs=5.7
Q ss_pred cccCCCCCh
Q 046997 715 LGCIGGCDE 723 (807)
Q Consensus 715 ~~C~~~C~~ 723 (807)
+.|| +|.|
T Consensus 49 Y~CP-~CGF 56 (59)
T PRK14890 49 YTCP-KCGF 56 (59)
T ss_pred eECC-CCCC
Confidence 5588 7776
No 177
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=42.55 E-value=19 Score=29.61 Aligned_cols=35 Identities=20% Similarity=0.271 Sum_probs=24.7
Q ss_pred CCCCccchHHHHHhhcccceEEEcCCceeeechhHH
Q 046997 515 GIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGE 550 (807)
Q Consensus 515 GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~ 550 (807)
|.--.......|+.+++.|+|+.+++ .|.+|++|+
T Consensus 31 g~~~~~~~~~~l~~l~~~Gll~~~~~-~l~lT~~G~ 65 (66)
T PF06969_consen 31 GIDFAEEFQKELEELQEDGLLEIDGG-RLRLTEKGR 65 (66)
T ss_dssp T--THHH-HHHHHHHHHTTSEEE-SS-EEEE-TTTG
T ss_pred CcCHHHHHHHHHHHHHHCCCEEEeCC-EEEECcccC
Confidence 44444555788999999999998865 689999996
No 178
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=42.24 E-value=8.4 Score=47.10 Aligned_cols=42 Identities=19% Similarity=0.157 Sum_probs=0.0
Q ss_pred cCCCCeeeeeeeEeecCccCCCCCCCHHHHHHHHHhCCCCCc
Q 046997 478 YVHGQQFIPTTLTLDSGVTRPPPLLSEADLLSCMDKAGIGTD 519 (807)
Q Consensus 478 l~~G~~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~~GIGTp 519 (807)
|-.||.+..-.=.++...+=.|+.|.+...+..+++.|.+.+
T Consensus 413 LdlGeiLv~yGdFlENNh~L~Ps~y~~EWW~qe~~~~~~~~~ 454 (900)
T PF03833_consen 413 LDLGEILVNYGDFLENNHPLVPSSYCEEWWIQELEKAGPEYD 454 (900)
T ss_dssp ------------------------------------------
T ss_pred eeccceeeecchHhhcCCcCCCccchHHHHHHHHHHhccccC
Confidence 334554443333566677888999999999999998885554
No 179
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=42.13 E-value=27 Score=41.18 Aligned_cols=6 Identities=33% Similarity=1.165 Sum_probs=2.9
Q ss_pred ccCCCC
Q 046997 685 TCNSCT 690 (807)
Q Consensus 685 ~CP~Cg 690 (807)
.|+-||
T Consensus 242 ~Ch~Cg 247 (505)
T TIGR00595 242 RCHYCG 247 (505)
T ss_pred EcCCCc
Confidence 355554
No 180
>PHA00626 hypothetical protein
Probab=41.67 E-value=27 Score=28.30 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=7.1
Q ss_pred ccCCCCCcceE
Q 046997 637 QCGICQESNMV 647 (807)
Q Consensus 637 ~CP~C~g~~lv 647 (807)
.||.|+...++
T Consensus 2 ~CP~CGS~~Iv 12 (59)
T PHA00626 2 SCPKCGSGNIA 12 (59)
T ss_pred CCCCCCCceee
Confidence 59999433454
No 181
>PF13155 Toprim_2: Toprim-like
Probab=41.56 E-value=58 Score=28.66 Aligned_cols=28 Identities=21% Similarity=0.242 Sum_probs=24.6
Q ss_pred CeEEEeecCChhhhHHHHHHHHHhhhcC
Q 046997 116 QWLVLWLDCDREGENIAFEVIEVCRAVN 143 (807)
Q Consensus 116 d~IiiAtD~DREGE~I~~ei~~~~~~~~ 143 (807)
..|++|.|.|.-|..-...+.+.+...+
T Consensus 48 ~~i~l~~DnD~aG~~~~~~~~~~l~~~~ 75 (96)
T PF13155_consen 48 KKIVLAFDNDEAGRKAAEKLQKELKEEG 75 (96)
T ss_pred CcEEEEeCCCHHHHHHHHHHHHHHHhhC
Confidence 5799999999999999999998877643
No 182
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=41.37 E-value=23 Score=31.47 Aligned_cols=32 Identities=16% Similarity=0.264 Sum_probs=25.5
Q ss_pred hHHHHHhhcccceEEEcCCceeeechhHHHHHh
Q 046997 522 MHDHIKKLLDRFYAIKDANTRFAPTNIGEALVM 554 (807)
Q Consensus 522 ra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~ 554 (807)
-.+-|..|++.|||++.+.. ++.|..|..++.
T Consensus 49 V~SNIGvLIKkglIEKSGDG-lv~T~~g~~Ii~ 80 (96)
T PF09114_consen 49 VNSNIGVLIKKGLIEKSGDG-LVITEEGMDIII 80 (96)
T ss_dssp HHHHHHHHHHTTSEEEETTE-EEE-HHHHHHHH
T ss_pred HHHhHHHHHHcCcccccCCc-eEEechHHHHHH
Confidence 33458899999999998775 899999999874
No 183
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=41.15 E-value=1.1e+02 Score=29.70 Aligned_cols=52 Identities=15% Similarity=0.198 Sum_probs=39.4
Q ss_pred CHHHHHHHHHhCCC--CCccchHHHHHhhcccceEEEc----C----CceeeechhHHHHHh
Q 046997 503 SEADLLSCMDKAGI--GTDATMHDHIKKLLDRFYAIKD----A----NTRFAPTNIGEALVM 554 (807)
Q Consensus 503 Tea~Li~~Me~~GI--GTpATra~iI~~L~~R~Yv~~~----~----~~~l~pT~~G~~li~ 554 (807)
.=-.|++.++..|+ =+++|--.++.+|.+.|||... . .+.+.+|+.|+..++
T Consensus 39 hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~ 100 (138)
T TIGR02719 39 HGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLS 100 (138)
T ss_pred CHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHH
Confidence 45678888888764 2577888999999999999752 1 234789999999663
No 184
>PRK14296 chaperone protein DnaJ; Provisional
Probab=40.61 E-value=43 Score=37.89 Aligned_cols=48 Identities=21% Similarity=0.474 Sum_probs=26.0
Q ss_pred ccccCCCCCcceEEEecCCCCceeec-cCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGC-LAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gC-s~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...|+.|+|...+......|.+.+.+ +..+.|.=. -......|+.|..
T Consensus 166 ~~~C~~C~G~G~~~~~~~~g~~~~q~~~~C~~C~G~---------G~~~~~~C~~C~G 214 (372)
T PRK14296 166 IHICNNCHGTGEVLVQKNMGFFQFQQSAKCNVCNGA---------GKIIKNKCKNCKG 214 (372)
T ss_pred CccCCCCCCCceEEEEEeccceEEEEEecCCCcCCc---------ceeecccccCCCC
Confidence 45799998766655544455432221 112456522 1123456999973
No 185
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=40.27 E-value=41 Score=26.42 Aligned_cols=30 Identities=17% Similarity=0.267 Sum_probs=25.7
Q ss_pred HHHHhcCCCHHHHHHHHHHHhhcCceeccC
Q 046997 313 RASRYFRMSSEHTMKVAEDLYQAGFISYPR 342 (807)
Q Consensus 313 ~ask~~g~s~~~tl~iaQ~LYE~g~ISYPR 342 (807)
++++.+|+|...+.++.+.|.+.|+|++-+
T Consensus 15 ~i~~~l~is~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 15 ELAEILGLSQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCeeeee
Confidence 456678999999999999999999998543
No 186
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=40.01 E-value=86 Score=29.60 Aligned_cols=74 Identities=11% Similarity=0.063 Sum_probs=52.2
Q ss_pred HHHHhhcccceEEEcCCceeeechhHHHHHhhccc----c-CccccC-chhhHHHHHHHHHHHcCCCChHHHHHHHHHHH
Q 046997 524 DHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYDD----M-GYELWK-PNLRSMMESDMKEVSVGNKSKADVLANCLQQM 597 (807)
Q Consensus 524 ~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~~----~-~~~l~~-p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~ 597 (807)
.+++.+.--|+++..+| -+..|+.|+.++++=.. + ...+.+ .-+.+.+...|++=..+++..+.|++.+...+
T Consensus 16 p~~eAaelLgf~~~~~G-di~LT~~G~~f~~a~~~~rK~if~~~l~~~~Pl~~~I~~~L~~~~~~~~~~~~~~~~L~~~~ 94 (120)
T PF09821_consen 16 PIVEAAELLGFAEVEEG-DIRLTPLGRRFAEADIDERKEIFREQLLRHVPLAAHIRRVLRERPNHRLPEERFLDELEDHF 94 (120)
T ss_pred HHHHHHHHcCCeeecCC-cEEeccchHHHHHCChHHHHHHHHHHHHhcCCHHHHHHHHHHhCCCCCCCHHHHHHHHHHHC
Confidence 35666777799998765 58999999998864210 0 012333 45666788888887889999999988877665
Q ss_pred H
Q 046997 598 K 598 (807)
Q Consensus 598 ~ 598 (807)
.
T Consensus 95 ~ 95 (120)
T PF09821_consen 95 S 95 (120)
T ss_pred C
Confidence 4
No 187
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=40.00 E-value=65 Score=28.80 Aligned_cols=57 Identities=12% Similarity=0.241 Sum_probs=42.1
Q ss_pred HHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHcC
Q 046997 106 KTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQNL 168 (807)
Q Consensus 106 ~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~nl 168 (807)
..|...+++||.||+-||+= .-...|.+.+.|+..+ +|+....- -...+|.++++++
T Consensus 40 ~~l~~~i~~aD~VIv~t~~v--sH~~~~~vk~~akk~~--ip~~~~~~--~~~~~l~~~l~~~ 96 (97)
T PF10087_consen 40 SRLPSKIKKADLVIVFTDYV--SHNAMWKVKKAAKKYG--IPIIYSRS--RGVSSLERALERL 96 (97)
T ss_pred hHHHHhcCCCCEEEEEeCCc--ChHHHHHHHHHHHHcC--CcEEEECC--CCHHHHHHHHHhh
Confidence 35788899999999999985 4467788999888765 35544433 5555899988764
No 188
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=39.80 E-value=17 Score=26.65 Aligned_cols=27 Identities=15% Similarity=0.379 Sum_probs=11.9
Q ss_pred CCCCcceecCCCccccccccCccCCCC
Q 046997 664 PQCRNAVWLPGSVSEAAVTTNTCNSCT 690 (807)
Q Consensus 664 P~C~~~~~~p~~~~~~~~t~~~CP~Cg 690 (807)
|.|+..+.+++...........|+.|+
T Consensus 6 p~C~~~y~i~d~~ip~~g~~v~C~~C~ 32 (36)
T PF13717_consen 6 PNCQAKYEIDDEKIPPKGRKVRCSKCG 32 (36)
T ss_pred CCCCCEEeCCHHHCCCCCcEEECCCCC
Confidence 345544444432222222344577666
No 189
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=39.46 E-value=30 Score=26.23 Aligned_cols=9 Identities=22% Similarity=0.726 Sum_probs=6.7
Q ss_pred cCccCCCCC
Q 046997 683 TNTCNSCTP 691 (807)
Q Consensus 683 ~~~CP~Cg~ 691 (807)
...||.||+
T Consensus 26 ~~~CP~Cg~ 34 (42)
T PF09723_consen 26 PVPCPECGS 34 (42)
T ss_pred CCcCCCCCC
Confidence 456899985
No 190
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=39.41 E-value=74 Score=28.71 Aligned_cols=52 Identities=10% Similarity=0.184 Sum_probs=39.1
Q ss_pred CCHHHHHHHHHhCC-----CCCccchHHHHHhhcccceEEEc-----C---CceeeechhHHHHHh
Q 046997 502 LSEADLLSCMDKAG-----IGTDATMHDHIKKLLDRFYAIKD-----A---NTRFAPTNIGEALVM 554 (807)
Q Consensus 502 ~Tea~Li~~Me~~G-----IGTpATra~iI~~L~~R~Yv~~~-----~---~~~l~pT~~G~~li~ 554 (807)
.+=-+|.+.|++.. |. +.|.-.++..|.+.|||+.. . .+.+.+|+.|+.+++
T Consensus 18 ~~GYei~~~l~~~~~~~~~i~-~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~ 82 (100)
T TIGR03433 18 LHGYGIAQRIQQISEDVLQVE-EGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLA 82 (100)
T ss_pred CCHHHHHHHHHHHcCCccccC-CCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHH
Confidence 35567888887642 33 47888999999999999862 1 245899999999875
No 191
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=38.34 E-value=16 Score=37.07 Aligned_cols=35 Identities=26% Similarity=0.502 Sum_probs=23.0
Q ss_pred ccccccccccCCCccCCCCCCCCCCCccccCCCCC
Q 046997 757 HRQRACIYCQQMGHSSSDCPSQFSGSRNARANGMN 791 (807)
Q Consensus 757 ~~~~~c~~c~~~g~~~~~~~~~~~~~~~~~~~~~~ 791 (807)
-.+..|..|++.||..-+||-++=-.++---|.+|
T Consensus 58 ~~~~~C~nCg~~GH~~~DCP~~iC~~C~~~~H~s~ 92 (190)
T COG5082 58 EENPVCFNCGQNGHLRRDCPHSICYNCSWDGHRSN 92 (190)
T ss_pred ccccccchhcccCcccccCChhHhhhcCCCCcccc
Confidence 34455999999999999999444333322334443
No 192
>PRK05978 hypothetical protein; Provisional
Probab=37.92 E-value=18 Score=35.47 Aligned_cols=31 Identities=19% Similarity=0.502 Sum_probs=19.6
Q ss_pred cCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChhHH
Q 046997 683 TNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDETLR 726 (807)
Q Consensus 683 ~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~~~ 726 (807)
..+||.||.|.+++ +.-++ ...|+ .|...+.
T Consensus 33 ~grCP~CG~G~LF~-----g~Lkv-------~~~C~-~CG~~~~ 63 (148)
T PRK05978 33 RGRCPACGEGKLFR-----AFLKP-------VDHCA-ACGEDFT 63 (148)
T ss_pred cCcCCCCCCCcccc-----ccccc-------CCCcc-ccCCccc
Confidence 45799999887763 12222 25598 8876554
No 193
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=37.92 E-value=50 Score=30.01 Aligned_cols=34 Identities=21% Similarity=0.643 Sum_probs=22.8
Q ss_pred CCceeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 654 GNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 654 G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
....+||...|+-+.++|+-=. .. ....||+||.
T Consensus 54 ~~RiVGC~g~~~~h~v~W~~l~---~g-~~~rC~eCG~ 87 (97)
T cd00924 54 DKRIVGCICEPDSHDVIWMWLE---KG-KPKRCPECGH 87 (97)
T ss_pred CCeEEeeeCCCCCceEEEEEEe---CC-CceeCCCCCc
Confidence 3456999999986677775210 11 3567999985
No 194
>PRK09401 reverse gyrase; Reviewed
Probab=37.58 E-value=28 Score=45.26 Aligned_cols=52 Identities=15% Similarity=0.120 Sum_probs=45.0
Q ss_pred eeeeeEeecCccCCCCCCCHHHHHHHHHh-CCCCCccchHHHHHhhcccceEEE
Q 046997 485 IPTTLTLDSGVTRPPPLLSEADLLSCMDK-AGIGTDATMHDHIKKLLDRFYAIK 537 (807)
Q Consensus 485 ~~~~~~i~e~~T~PP~~~Tea~Li~~Me~-~GIGTpATra~iI~~L~~R~Yv~~ 537 (807)
.+.++..++++..||++||-.+|+..+-+ .|++..-|+ .|.+.|++.|||.-
T Consensus 868 ~V~~v~~k~~~~~pP~Pf~t~~Lq~~As~~lg~Sa~~tm-~iAQ~LYE~glITY 920 (1176)
T PRK09401 868 EVEKVEEKEEELNPLPPYTTDTLLSDASRKLRLSAQETM-RIAQDLFELGLITY 920 (1176)
T ss_pred eeeEEEeeEEEecCCCCCccHHHHHHHHHHcCCCHHHHH-HHHHHHHhCCceee
Confidence 55677888999999999999999999865 699888887 48999999999974
No 195
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=37.37 E-value=17 Score=33.56 Aligned_cols=17 Identities=24% Similarity=0.368 Sum_probs=12.3
Q ss_pred cccccccccccCCCccC
Q 046997 756 NHRQRACIYCQQMGHSS 772 (807)
Q Consensus 756 ~~~~~~c~~c~~~g~~~ 772 (807)
-+|++.|.+|++|=++-
T Consensus 82 LGr~D~CM~C~~pLTLd 98 (114)
T PF11023_consen 82 LGRVDACMHCKEPLTLD 98 (114)
T ss_pred hchhhccCcCCCcCccC
Confidence 34556799999886654
No 196
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=37.16 E-value=28 Score=25.63 Aligned_cols=9 Identities=33% Similarity=0.759 Sum_probs=6.2
Q ss_pred cCccCCCCC
Q 046997 683 TNTCNSCTP 691 (807)
Q Consensus 683 ~~~CP~Cg~ 691 (807)
...||.||.
T Consensus 26 ~~~CP~Cg~ 34 (41)
T smart00834 26 LATCPECGG 34 (41)
T ss_pred CCCCCCCCC
Confidence 346888884
No 197
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=36.84 E-value=93 Score=34.78 Aligned_cols=77 Identities=18% Similarity=0.144 Sum_probs=46.2
Q ss_pred CCCCCccchHHHHHhhcccceEEEcCC-ceeeechhHHHHH-hhccccCccccCchhhHHHHHHHHHHHc-CCCChHHHH
Q 046997 514 AGIGTDATMHDHIKKLLDRFYAIKDAN-TRFAPTNIGEALV-MGYDDMGYELWKPNLRSMMESDMKEVSV-GNKSKADVL 590 (807)
Q Consensus 514 ~GIGTpATra~iI~~L~~R~Yv~~~~~-~~l~pT~~G~~li-~~l~~~~~~l~~p~~Ta~~E~~L~~I~~-G~~~~~~~l 590 (807)
.|+- +||.-..+..|-+.||+++--+ ..-+||++|..++ +.+.. . ..++......++.+-. ...+.++++
T Consensus 37 l~~S-~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR~YVd~L~~--~----~~~~~~~~~~i~~~~~~~~~~~~~~l 109 (339)
T PRK00082 37 LGVS-SATIRNDMADLEELGLLEKPHTSSGRIPTDKGYRYFVDHLLE--V----KPLSEEERRAIEKFLDERGVSLEDVL 109 (339)
T ss_pred CCCC-hHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHHHHHHHhCC--C----CCCCHHHHHHHHHHHHhccCCHHHHH
Confidence 4443 8999999999999999975311 1148999998864 32211 1 1233333334444333 236777777
Q ss_pred HHHHHHH
Q 046997 591 ANCLQQM 597 (807)
Q Consensus 591 ~~~~~~~ 597 (807)
++..+.+
T Consensus 110 ~~aa~~L 116 (339)
T PRK00082 110 QEAAQLL 116 (339)
T ss_pred HHHHHHH
Confidence 7665543
No 198
>PRK14873 primosome assembly protein PriA; Provisional
Probab=36.79 E-value=32 Score=42.00 Aligned_cols=40 Identities=20% Similarity=0.447 Sum_probs=26.4
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPG 692 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~ 692 (807)
...||.| +..|+..+.. . -+.|. -|.+.. . ...||.||+.
T Consensus 392 ~~~C~~C-~~~L~~h~~~--~-~l~Ch---~CG~~~-~----------p~~Cp~Cgs~ 431 (665)
T PRK14873 392 PARCRHC-TGPLGLPSAG--G-TPRCR---WCGRAA-P----------DWRCPRCGSD 431 (665)
T ss_pred eeECCCC-CCceeEecCC--C-eeECC---CCcCCC-c----------CccCCCCcCC
Confidence 4579999 5778765422 2 36784 488753 1 3479999963
No 199
>PF02044 Bombesin: Bombesin-like peptide; InterPro: IPR000874 Bombesin-like peptides comprise a large family of peptides which were initially isolated from amphibian skin, where they stimulate smooth muscle contraction. They were later found to be widely distributed in mammalian neural and endocrine cells. The amphibian peptides which belong to this family are currently classified into three subfamilies [, ]; the Bombesin group, which includes bombesin and alytesin; the Ranatensin group, which includes ranatensins, litorin, and Rohdei litorin; and the Phyllolitorin group, which includes Leu(8)- and Phe(8)-phyllolitorins. In mammals and birds two categories of bombesin-like peptides are known [, ], gastrin-releasing peptide (GRP), which stimulates the release of gastrin as well as other gastrointestinal hormones, and neuromedin B (NMB), a neuropeptide whose function is not yet clear. Bombesin-like peptides, like many other active peptides, are synthesized as larger protein precursors that are enzymatically converted to their mature forms. The final peptides are eight to fourteen residues long.; GO: 0007218 neuropeptide signaling pathway; PDB: 1C9A_A 1C98_A.
Probab=36.60 E-value=7.5 Score=22.25 Aligned_cols=8 Identities=38% Similarity=0.621 Sum_probs=5.4
Q ss_pred eccCcccc
Q 046997 63 SVTGHLME 70 (807)
Q Consensus 63 ~~~GHl~~ 70 (807)
|++||++.
T Consensus 4 WAvGh~Mg 11 (14)
T PF02044_consen 4 WAVGHFMG 11 (14)
T ss_dssp CHHHCT--
T ss_pred cceeeeec
Confidence 88999874
No 200
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=36.50 E-value=61 Score=34.43 Aligned_cols=25 Identities=28% Similarity=0.763 Sum_probs=12.6
Q ss_pred ccccCCCCCcceEEEecCCCCceeec
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGC 660 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gC 660 (807)
..+|+.|+.. --+|....||.|+.|
T Consensus 85 VVkC~~CnEA-TPIr~aPpGKKYVRC 109 (256)
T PF09788_consen 85 VVKCSVCNEA-TPIRNAPPGKKYVRC 109 (256)
T ss_pred eEECCCCCcc-ccccCCCCCCeeEec
Confidence 4456666422 234444455555666
No 201
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=36.45 E-value=23 Score=24.62 Aligned_cols=16 Identities=19% Similarity=0.308 Sum_probs=8.1
Q ss_pred cCccCCCCCCceEEEEe
Q 046997 683 TNTCNSCTPGPVYLIQF 699 (807)
Q Consensus 683 ~~~CP~Cg~~~l~~~~~ 699 (807)
+++||.|+. .+..+..
T Consensus 1 G~~C~rC~~-~~~~~~~ 16 (30)
T PF06827_consen 1 GEKCPRCWN-YIEDIGI 16 (30)
T ss_dssp TSB-TTT---BBEEEEE
T ss_pred CCcCccCCC-cceEeEe
Confidence 357999984 5555443
No 202
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=36.43 E-value=17 Score=36.81 Aligned_cols=14 Identities=14% Similarity=0.192 Sum_probs=9.9
Q ss_pred ccCccCCCCCCceEE
Q 046997 682 TTNTCNSCTPGPVYL 696 (807)
Q Consensus 682 t~~~CP~Cg~~~l~~ 696 (807)
.+-.||.|| ++++.
T Consensus 135 ~~F~Cp~Cg-~~L~~ 148 (178)
T PRK06266 135 YGFRCPQCG-EMLEE 148 (178)
T ss_pred cCCcCCCCC-CCCee
Confidence 356799999 56653
No 203
>PLN02400 cellulose synthase
Probab=36.19 E-value=26 Score=44.39 Aligned_cols=50 Identities=26% Similarity=0.604 Sum_probs=35.0
Q ss_pred cccccCCCCCcceEEEecCCCCceeeccC--CCCCCcceecCCCccccccccCccCCCCC
Q 046997 634 VVRQCGICQESNMVLKKSRDGNLMVGCLA--FPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 634 ~~~~CP~C~g~~lv~r~~k~G~~f~gCs~--yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
.+..|-.| |.++-+. ..|..|++|.. ||-|+-.+-.++. .-.+.||+|+.
T Consensus 35 ~gqiCqIC-GD~VG~t--~dGe~FVAC~eCaFPVCRpCYEYERk-----eGnq~CPQCkT 86 (1085)
T PLN02400 35 NGQICQIC-GDDVGVT--ETGDVFVACNECAFPVCRPCYEYERK-----DGTQCCPQCKT 86 (1085)
T ss_pred CCceeeec-ccccCcC--CCCCEEEEEccCCCccccchhheecc-----cCCccCcccCC
Confidence 46689999 5555443 47888999965 5788877665442 23568999984
No 204
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=36.07 E-value=18 Score=26.54 Aligned_cols=8 Identities=25% Similarity=0.787 Sum_probs=4.8
Q ss_pred CccCCCCC
Q 046997 684 NTCNSCTP 691 (807)
Q Consensus 684 ~~CP~Cg~ 691 (807)
..||.|+.
T Consensus 26 v~C~~C~~ 33 (38)
T TIGR02098 26 VRCGKCGH 33 (38)
T ss_pred EECCCCCC
Confidence 45676663
No 205
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=35.29 E-value=2.6e+02 Score=26.43 Aligned_cols=53 Identities=11% Similarity=0.137 Sum_probs=41.5
Q ss_pred CHHHHHHHHHhCCCC----CccchHHHHHhhcccceEEEc----C----CceeeechhHHHHHhh
Q 046997 503 SEADLLSCMDKAGIG----TDATMHDHIKKLLDRFYAIKD----A----NTRFAPTNIGEALVMG 555 (807)
Q Consensus 503 Tea~Li~~Me~~GIG----TpATra~iI~~L~~R~Yv~~~----~----~~~l~pT~~G~~li~~ 555 (807)
+--+|.+.++..+-| .+.|.=.++.+|.+.|||... . .+.+.+|+.|+..+..
T Consensus 24 ~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~ 88 (138)
T COG1695 24 HGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAE 88 (138)
T ss_pred hHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHH
Confidence 345788888887766 578899999999999999752 1 3568999999997753
No 206
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=35.26 E-value=8.6 Score=33.15 Aligned_cols=50 Identities=26% Similarity=0.625 Sum_probs=19.5
Q ss_pred cccccCCCCCcceEEEecCCCCceeeccC--CCCCCcceecCCCccccccccCccCCCCC
Q 046997 634 VVRQCGICQESNMVLKKSRDGNLMVGCLA--FPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 634 ~~~~CP~C~g~~lv~r~~k~G~~f~gCs~--yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
.+..|-.| |..+-+. -.|..|++|.. ||-|+-.+-.+. +.-...||+|+.
T Consensus 8 ~~qiCqiC-GD~VGl~--~~Ge~FVAC~eC~fPvCr~CyEYEr-----keg~q~CpqCkt 59 (80)
T PF14569_consen 8 NGQICQIC-GDDVGLT--ENGEVFVACHECAFPVCRPCYEYER-----KEGNQVCPQCKT 59 (80)
T ss_dssp SS-B-SSS---B--B---SSSSB--S-SSS-----HHHHHHHH-----HTS-SB-TTT--
T ss_pred CCcccccc-cCccccC--CCCCEEEEEcccCCccchhHHHHHh-----hcCcccccccCC
Confidence 45679999 5555443 36888999964 455554433322 223567999984
No 207
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=34.90 E-value=22 Score=24.22 Aligned_cols=6 Identities=33% Similarity=1.032 Sum_probs=2.9
Q ss_pred ccCCCC
Q 046997 685 TCNSCT 690 (807)
Q Consensus 685 ~CP~Cg 690 (807)
.||.||
T Consensus 16 ~Cp~CG 21 (26)
T PF10571_consen 16 FCPHCG 21 (26)
T ss_pred cCCCCC
Confidence 355554
No 208
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=34.88 E-value=36 Score=37.97 Aligned_cols=28 Identities=21% Similarity=0.584 Sum_probs=11.4
Q ss_pred CceeeccCCCCCCcce-ecCCCccccccccCccCCCCC
Q 046997 655 NLMVGCLAFPQCRNAV-WLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 655 ~~f~gCs~yP~C~~~~-~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
+.||-|. +|++.. .+.. .....|+.||.
T Consensus 283 KRFFkC~---~C~~Rt~sl~r------~P~~~C~~Cg~ 311 (344)
T PF09332_consen 283 KRFFKCK---DCGNRTISLER------LPKKHCSNCGS 311 (344)
T ss_dssp -EEEE-T----TS-EEEESSS------S--S--TTT-S
T ss_pred eeeEECC---CCCCeeeeccc------CCCCCCCcCCc
Confidence 4589995 588742 2322 12357999995
No 209
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=34.86 E-value=19 Score=23.75 Aligned_cols=6 Identities=33% Similarity=1.093 Sum_probs=3.1
Q ss_pred ccCCCC
Q 046997 685 TCNSCT 690 (807)
Q Consensus 685 ~CP~Cg 690 (807)
.||.||
T Consensus 15 fC~~CG 20 (23)
T PF13240_consen 15 FCPNCG 20 (23)
T ss_pred chhhhC
Confidence 455555
No 210
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=34.79 E-value=24 Score=45.22 Aligned_cols=8 Identities=38% Similarity=0.949 Sum_probs=6.1
Q ss_pred ccccCCCC
Q 046997 635 VRQCGICQ 642 (807)
Q Consensus 635 ~~~CP~C~ 642 (807)
..+||+|+
T Consensus 667 ~rkCPkCG 674 (1337)
T PRK14714 667 RRRCPSCG 674 (1337)
T ss_pred EEECCCCC
Confidence 36899994
No 211
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=34.64 E-value=42 Score=24.33 Aligned_cols=31 Identities=23% Similarity=0.368 Sum_probs=27.0
Q ss_pred CCCHHHHHHHHHhCCCCCccchHHHHHhhcc
Q 046997 501 LLSEADLLSCMDKAGIGTDATMHDHIKKLLD 531 (807)
Q Consensus 501 ~~Tea~Li~~Me~~GIGTpATra~iI~~L~~ 531 (807)
.+|-++|-..+++.||-+.-|.+.+|+.|.+
T Consensus 3 ~l~v~eLk~~l~~~gL~~~G~K~~Li~Rl~~ 33 (35)
T PF02037_consen 3 KLTVAELKEELKERGLSTSGKKAELIERLKE 33 (35)
T ss_dssp TSHHHHHHHHHHHTTS-STSSHHHHHHHHHH
T ss_pred cCcHHHHHHHHHHCCCCCCCCHHHHHHHHHH
Confidence 4678899999999999999999999998864
No 212
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=34.64 E-value=57 Score=26.97 Aligned_cols=30 Identities=10% Similarity=0.227 Sum_probs=26.2
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceecc
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYP 341 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYP 341 (807)
.+.++.+|++...+-++..+|.++|+|.--
T Consensus 26 ~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 26 EEIAEELGISRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHHHHHHTSSHHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 456777999999999999999999999643
No 213
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=34.44 E-value=33 Score=32.08 Aligned_cols=22 Identities=23% Similarity=0.908 Sum_probs=14.8
Q ss_pred cCCCCCcceEEEecCCCCceeeccCCCCCCcce
Q 046997 638 CGICQESNMVLKKSRDGNLMVGCLAFPQCRNAV 670 (807)
Q Consensus 638 CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~ 670 (807)
||.| |+.|+..+ +.|. .|+..+
T Consensus 1 CPvC-g~~l~vt~-------l~C~---~C~t~i 22 (113)
T PF09862_consen 1 CPVC-GGELVVTR-------LKCP---SCGTEI 22 (113)
T ss_pred CCCC-CCceEEEE-------EEcC---CCCCEE
Confidence 9999 57776654 6774 476554
No 214
>PRK14873 primosome assembly protein PriA; Provisional
Probab=34.23 E-value=42 Score=41.03 Aligned_cols=10 Identities=30% Similarity=-0.034 Sum_probs=6.1
Q ss_pred HHHHHHHhHh
Q 046997 179 VDARQEIDLR 188 (807)
Q Consensus 179 ~~aR~~~D~l 188 (807)
..++-.+|+.
T Consensus 92 ~L~~~ia~yY 101 (665)
T PRK14873 92 RLARAVADRY 101 (665)
T ss_pred HHHHHHHHHh
Confidence 3566667763
No 215
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=34.06 E-value=22 Score=31.43 Aligned_cols=20 Identities=20% Similarity=0.556 Sum_probs=12.5
Q ss_pred cccccCCCccCCCCCCCCCC
Q 046997 762 CIYCQQMGHSSSDCPSQFSG 781 (807)
Q Consensus 762 c~~c~~~g~~~~~~~~~~~~ 781 (807)
|..|-..+.-.+.||..+|-
T Consensus 72 c~ectr~ekdrdgCpri~nl 91 (110)
T KOG1705|consen 72 CKECTRQEKDRDGCPKIVNL 91 (110)
T ss_pred HHHHHhhccccccChhhhhc
Confidence 34444445566889988775
No 216
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=33.87 E-value=43 Score=28.66 Aligned_cols=31 Identities=13% Similarity=0.187 Sum_probs=27.5
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHhhcCcee
Q 046997 309 ELEKRASRYFRMSSEHTMKVAEDLYQAGFIS 339 (807)
Q Consensus 309 ~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~IS 339 (807)
.+|.+.++.+|+++...-.+.++|.+.|||+
T Consensus 19 i~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~ 49 (75)
T PF04182_consen 19 ITQSDLSKLLGIDPRSIFYRLKKLEKKGLIV 49 (75)
T ss_pred EehhHHHHHhCCCchHHHHHHHHHHHCCCEE
Confidence 3567778889999999999999999999984
No 217
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=33.80 E-value=51 Score=38.03 Aligned_cols=21 Identities=33% Similarity=0.770 Sum_probs=18.2
Q ss_pred cccccccccCCCccCCCCCCC
Q 046997 758 RQRACIYCQQMGHSSSDCPSQ 778 (807)
Q Consensus 758 ~~~~c~~c~~~g~~~~~~~~~ 778 (807)
...+|+.|+..||++-+|+..
T Consensus 284 ~~n~c~~cg~~gH~~~dc~~~ 304 (554)
T KOG0119|consen 284 TTNVCKICGPLGHISIDCKVN 304 (554)
T ss_pred ccccccccCCcccccccCCCc
Confidence 344899999999999999985
No 218
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=33.41 E-value=41 Score=35.00 Aligned_cols=9 Identities=22% Similarity=0.523 Sum_probs=6.9
Q ss_pred cCccCCCCC
Q 046997 683 TNTCNSCTP 691 (807)
Q Consensus 683 ~~~CP~Cg~ 691 (807)
-..||.||-
T Consensus 48 V~vCP~Cgy 56 (214)
T PF09986_consen 48 VWVCPHCGY 56 (214)
T ss_pred EEECCCCCC
Confidence 456999985
No 219
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=33.25 E-value=28 Score=33.30 Aligned_cols=28 Identities=29% Similarity=0.697 Sum_probs=18.5
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCCCCCCccee
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVW 671 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~ 671 (807)
...||+| |.+|.. +.|. +.| |.|.+..-
T Consensus 28 ~~hCp~C-g~PLF~---KdG~--v~C---PvC~~~~~ 55 (131)
T COG1645 28 AKHCPKC-GTPLFR---KDGE--VFC---PVCGYREV 55 (131)
T ss_pred HhhCccc-CCccee---eCCe--EEC---CCCCceEE
Confidence 4569999 677765 4555 456 67876543
No 220
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=32.85 E-value=77 Score=25.59 Aligned_cols=31 Identities=19% Similarity=0.390 Sum_probs=27.1
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceeccC
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYPR 342 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPR 342 (807)
.+++..+|+|...+.++.+.|=++|+|.+-+
T Consensus 29 ~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 29 QEIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 4556678999999999999999999999865
No 221
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=32.74 E-value=23 Score=32.56 Aligned_cols=7 Identities=29% Similarity=1.103 Sum_probs=4.2
Q ss_pred ccCCCCC
Q 046997 685 TCNSCTP 691 (807)
Q Consensus 685 ~CP~Cg~ 691 (807)
.||+|++
T Consensus 4 ~CP~C~s 10 (109)
T TIGR00686 4 PCPKCNS 10 (109)
T ss_pred cCCcCCC
Confidence 4666665
No 222
>PRK14701 reverse gyrase; Provisional
Probab=32.37 E-value=53 Score=44.25 Aligned_cols=65 Identities=12% Similarity=0.198 Sum_probs=53.5
Q ss_pred eeeeeeeEeecCccCCCCCCCHHHHHHHHHh-CCCCCccchHHHHHhhcccceEEEcCCceeeechhHH
Q 046997 483 QFIPTTLTLDSGVTRPPPLLSEADLLSCMDK-AGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGE 550 (807)
Q Consensus 483 ~~~~~~~~i~e~~T~PP~~~Tea~Li~~Me~-~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~ 550 (807)
.+.+.+++.++++..||++||-.+|.+.+-+ .|++..-|+ .|.+.|.+.||+.- ... .+.|+-|.
T Consensus 838 ~~~V~~v~~k~~~~~pP~pf~t~~Lq~~As~~~g~s~~~tm-~iAQ~LYE~g~~~~-p~t-~V~l~dG~ 903 (1638)
T PRK14701 838 EVEVELVEEEEKERNPLPPYTTDTMLRDASAFLKLSAKETM-KLAQDLFEAGLCVT-PDT-YVSLHDGR 903 (1638)
T ss_pred eEEEEEEEeeEEEccCCCCcCHHHHHHHHHHhcCCCHHHHH-HHHHHHHhCceeeC-CCc-eeecCchH
Confidence 4567778888999999999999999999975 599888776 59999999999974 333 46788896
No 223
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=32.27 E-value=15 Score=36.34 Aligned_cols=40 Identities=15% Similarity=0.384 Sum_probs=23.5
Q ss_pred ccCccCCCCCCceEEEEeeccCccCCCC---CccCccccCCCCCh
Q 046997 682 TTNTCNSCTPGPVYLIQFKFRQHEIPPG---FNVNHLGCIGGCDE 723 (807)
Q Consensus 682 t~~~CP~Cg~~~l~~~~~k~~~g~~~~~---~~~~~~~C~~~C~~ 723 (807)
....||.|+ +++..+...--.+++|+. ....++-|| +|.-
T Consensus 96 e~~RCp~CN-~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~-~Cgk 138 (165)
T COG1656 96 EFSRCPECN-GELEKVSREEVKEKVPEKVYRNYEEFYRCP-KCGK 138 (165)
T ss_pred ccccCcccC-CEeccCcHHHHhhccchhhhhcccceeECC-CCcc
Confidence 356799999 677765433333445532 122446699 9964
No 224
>KOG3116 consensus Predicted C3H1-type Zn-finger protein [General function prediction only]
Probab=32.21 E-value=11 Score=36.28 Aligned_cols=22 Identities=27% Similarity=0.576 Sum_probs=18.2
Q ss_pred cccccccccccCCCccCCCCCC
Q 046997 756 NHRQRACIYCQQMGHSSSDCPS 777 (807)
Q Consensus 756 ~~~~~~c~~c~~~g~~~~~~~~ 777 (807)
.+....|.+|-|+|||+--|..
T Consensus 24 ~~~~~rCQKClq~GHWtYECk~ 45 (177)
T KOG3116|consen 24 VGSSARCQKCLQAGHWTYECKN 45 (177)
T ss_pred cccchhHHHHHhhccceeeecC
Confidence 3445579999999999999975
No 225
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=32.05 E-value=61 Score=29.18 Aligned_cols=30 Identities=20% Similarity=0.318 Sum_probs=26.5
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceecc
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYP 341 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYP 341 (807)
+.+++.++++.+++..+.++|.+.|||.+-
T Consensus 25 k~ia~~l~~~~~~v~~~l~~Le~~GLler~ 54 (92)
T PF10007_consen 25 KSIARRLKIPLEEVREALEKLEEMGLLERV 54 (92)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 456778999999999999999999999863
No 226
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=31.87 E-value=17 Score=25.67 Aligned_cols=7 Identities=29% Similarity=0.923 Sum_probs=2.6
Q ss_pred ccCCCCC
Q 046997 685 TCNSCTP 691 (807)
Q Consensus 685 ~CP~Cg~ 691 (807)
+||+|++
T Consensus 4 ~Cp~C~s 10 (30)
T PF08274_consen 4 KCPLCGS 10 (30)
T ss_dssp --TTT--
T ss_pred CCCCCCC
Confidence 5888886
No 227
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=31.59 E-value=32 Score=33.49 Aligned_cols=42 Identities=21% Similarity=0.525 Sum_probs=25.5
Q ss_pred cCccCCCCCCceEEEEeeccCccCCCCC---ccCccccCCCCChhHH
Q 046997 683 TNTCNSCTPGPVYLIQFKFRQHEIPPGF---NVNHLGCIGGCDETLR 726 (807)
Q Consensus 683 ~~~CP~Cg~~~l~~~~~k~~~g~~~~~~---~~~~~~C~~~C~~~~~ 726 (807)
...|+.|+ +++..+.+..-.+.+|++. ...++-|| .|+-...
T Consensus 91 ~sRC~~CN-~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~-~C~kiyW 135 (147)
T PF01927_consen 91 FSRCPKCN-GPLRPVSKEEVKDRVPPYVYETYDEFWRCP-GCGKIYW 135 (147)
T ss_pred CCccCCCC-cEeeechhhccccccCccccccCCeEEECC-CCCCEec
Confidence 45799998 4666654433334455442 23467798 8876554
No 228
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=31.55 E-value=29 Score=32.19 Aligned_cols=30 Identities=30% Similarity=0.662 Sum_probs=17.8
Q ss_pred ccCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChhHH
Q 046997 682 TTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDETLR 726 (807)
Q Consensus 682 t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~~~ 726 (807)
+...||.||. ..|= -.+ -| ..|| .|...+.
T Consensus 8 tKR~Cp~CG~-kFYD----Lnk--~P-------ivCP-~CG~~~~ 37 (108)
T PF09538_consen 8 TKRTCPSCGA-KFYD----LNK--DP-------IVCP-KCGTEFP 37 (108)
T ss_pred CcccCCCCcc-hhcc----CCC--CC-------ccCC-CCCCccC
Confidence 5677999995 2221 111 12 4599 8877665
No 229
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=31.46 E-value=29 Score=33.42 Aligned_cols=34 Identities=18% Similarity=0.150 Sum_probs=26.4
Q ss_pred hHHHHHhhcccceEEEcCCceeeechhHHHHHhhc
Q 046997 522 MHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGY 556 (807)
Q Consensus 522 ra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l 556 (807)
--.+++.|-+-|||++..+.+ +.|+.|+.|++.+
T Consensus 98 ~RkilqqLE~~G~V~k~~~GR-~ltp~GrsllD~~ 131 (147)
T COG2238 98 IRKVLQQLEKAGLVEKTPKGR-VLTPKGRSLLDRI 131 (147)
T ss_pred HHHHHHHHHHCCceeecCCCc-eeCccchhHHHHH
Confidence 345778888899999876444 6899999998754
No 230
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=31.36 E-value=43 Score=34.16 Aligned_cols=40 Identities=23% Similarity=0.169 Sum_probs=36.1
Q ss_pred CCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceecc
Q 046997 302 PYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYP 341 (807)
Q Consensus 302 P~pf~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYP 341 (807)
.-.|++-+|.+.|.+.-|+++..+-++.|.|-..|+|.==
T Consensus 9 ~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~E 48 (188)
T PF03962_consen 9 KDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVE 48 (188)
T ss_pred CCcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhh
Confidence 4589999999999997799999999999999999998643
No 231
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=31.12 E-value=50 Score=26.75 Aligned_cols=43 Identities=14% Similarity=0.251 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeeech
Q 046997 501 LLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTN 547 (807)
Q Consensus 501 ~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~ 547 (807)
.+|..+|-+. .|+ +++|-..+|..|.+.|||.....+.+.+|+
T Consensus 25 ~~s~~ela~~---~g~-s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 25 PLTRQEIADY---LGL-TRETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred CcCHHHHHHH---HCC-CHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 4566665544 455 678889999999999999986523466653
No 232
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.92 E-value=72 Score=27.66 Aligned_cols=37 Identities=24% Similarity=0.336 Sum_probs=22.9
Q ss_pred ccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCC------hhHHHHHHhhC
Q 046997 685 TCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCD------ETLRQLIEICG 733 (807)
Q Consensus 685 ~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~------~~~~~l~~~~~ 733 (807)
.||.|+- .+++..+ .+ .+.-.|| .|. ..+++|++..+
T Consensus 3 lCP~C~v-~l~~~~r---s~-------vEiD~CP-rCrGVWLDrGELdKli~r~r 45 (88)
T COG3809 3 LCPICGV-ELVMSVR---SG-------VEIDYCP-RCRGVWLDRGELDKLIERSR 45 (88)
T ss_pred ccCcCCc-eeeeeee---cC-------ceeeeCC-ccccEeecchhHHHHHHHhc
Confidence 5999984 4554332 22 1235699 885 46777887766
No 233
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=30.77 E-value=1.4e+02 Score=29.72 Aligned_cols=58 Identities=12% Similarity=0.174 Sum_probs=47.8
Q ss_pred CCCCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEc----CCceeeechhHHHHHhhcc
Q 046997 500 PLLSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKD----ANTRFAPTNIGEALVMGYD 557 (807)
Q Consensus 500 ~~~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~----~~~~l~pT~~G~~li~~l~ 557 (807)
.++|.+.|...+-..|+=+==|..+.|..|.+-|+|... ++..+..|++|+..++.+.
T Consensus 14 ~pltn~qit~~iL~~~~~nYF~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~F~ 75 (163)
T PF14277_consen 14 FPLTNSQITEFILENEYTNYFTLQQALSELVESGLITLETDSDNKTRYSITEKGKETLEFFE 75 (163)
T ss_pred CCCCHHHHHHHHHhcCcccHHHHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHHHH
Confidence 468888888888888888888889999999999999853 2356899999999887664
No 234
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=30.66 E-value=32 Score=43.83 Aligned_cols=51 Identities=12% Similarity=0.102 Sum_probs=33.0
Q ss_pred HHHhhcCeEEEeecC-----ChhhhHHHHHHHHHhhhc-CCCCeEEEEEecccCHHH
Q 046997 110 EEARRCQWLVLWLDC-----DREGENIAFEVIEVCRAV-NCHLVLRRARFSALIDRE 160 (807)
Q Consensus 110 ~~~~~~d~IiiAtD~-----DREGE~I~~ei~~~~~~~-~~~~~v~R~~~s~lt~~~ 160 (807)
+.++..++|-.-++- -|+...|+.+|.+..... ....+-+|+-++.=|+=+
T Consensus 290 ~~ik~g~wvk~~g~v~~d~f~~~l~m~i~~I~ei~~~~r~D~~~eKRVELh~HTkMS 346 (1444)
T COG2176 290 DGIKKGMWVKARGNVQLDTFTRDLTMIINDINEIENAKRKDLAKEKRVELHFHTKMS 346 (1444)
T ss_pred hhcccCcEEEEEEEEEecccccceEEEhhhhhhhhcccccccCccceEEEEeccchh
Confidence 344455555544433 468899999998876433 223568999998877733
No 235
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=29.74 E-value=35 Score=27.04 Aligned_cols=29 Identities=17% Similarity=0.377 Sum_probs=16.5
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCCCCCCccee
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVW 671 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~ 671 (807)
...||.|+ +.+.... .+ .+.|. .|.++.+
T Consensus 20 ~~fCP~Cg-~~~m~~~--~~--r~~C~---~Cgyt~~ 48 (50)
T PRK00432 20 NKFCPRCG-SGFMAEH--LD--RWHCG---KCGYTEF 48 (50)
T ss_pred cCcCcCCC-cchhecc--CC--cEECC---CcCCEEe
Confidence 45799994 5322211 12 26784 4888765
No 236
>PRK14298 chaperone protein DnaJ; Provisional
Probab=29.59 E-value=1.1e+02 Score=34.86 Aligned_cols=45 Identities=18% Similarity=0.524 Sum_probs=23.6
Q ss_pred ccccCCCCCcceEEEecCCC-Cce---eeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDG-NLM---VGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G-~~f---~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...||.|+|..++....+.+ .++ ..| +.|.-. -......|+.|..
T Consensus 158 ~~~C~~C~G~G~~~~~~~~~~g~~~~~~~C---~~C~G~---------G~~~~~~C~~C~G 206 (377)
T PRK14298 158 PKRCPTCGGTGQVTTTRSTPLGQFVTTTTC---STCHGR---------GQVIESPCPVCSG 206 (377)
T ss_pred CCcCCCCCCccEEEEEEecCceeEEEEEeC---CCCCCC---------CcccCCCCCCCCC
Confidence 45799997655544332221 111 235 457532 1123456999974
No 237
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=29.49 E-value=1e+02 Score=33.90 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=14.9
Q ss_pred cCchhhHHHHHHHHHHHcCCCChHHHHH
Q 046997 564 WKPNLRSMMESDMKEVSVGNKSKADVLA 591 (807)
Q Consensus 564 ~~p~~Ta~~E~~L~~I~~G~~~~~~~l~ 591 (807)
.+|+|+.. |..|+++++.|+.
T Consensus 200 kNp~Lr~~-------vl~G~i~p~~lv~ 220 (299)
T TIGR01385 200 NNPDLRHN-------VLTGEITPEKLAT 220 (299)
T ss_pred CCHHHHHH-------HHcCCCCHHHHhc
Confidence 44666643 6789999888875
No 238
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=29.30 E-value=28 Score=32.46 Aligned_cols=10 Identities=20% Similarity=0.504 Sum_probs=7.5
Q ss_pred ccCccCCCCC
Q 046997 682 TTNTCNSCTP 691 (807)
Q Consensus 682 t~~~CP~Cg~ 691 (807)
....||.||.
T Consensus 30 ~~~~C~~CGe 39 (127)
T TIGR03830 30 PGWYCPACGE 39 (127)
T ss_pred eeeECCCCCC
Confidence 3457999985
No 239
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=29.22 E-value=88 Score=24.39 Aligned_cols=29 Identities=10% Similarity=0.167 Sum_probs=25.3
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceec
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISY 340 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISY 340 (807)
.+.+..||+|..-+.++.+.|-+.|+|+.
T Consensus 24 ~~la~~~~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 24 RELAAQLGVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 45677799999999999999999999963
No 240
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=29.13 E-value=84 Score=24.57 Aligned_cols=29 Identities=10% Similarity=0.335 Sum_probs=23.7
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceec
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISY 340 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISY 340 (807)
.+.++.+|++...+..+.+.|-+.||+..
T Consensus 22 ~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 22 SEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 34456689999999999999999999864
No 241
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=29.08 E-value=46 Score=27.80 Aligned_cols=34 Identities=21% Similarity=0.371 Sum_probs=27.8
Q ss_pred HHHHHHhCCCCCccchHHHHHhhcccceEEEcCC
Q 046997 507 LLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDAN 540 (807)
Q Consensus 507 Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~ 540 (807)
+-+.++..|+--++|-..|++.|.++|||....+
T Consensus 28 ~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 28 VREIAEALGLKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred HHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence 3344556688889999999999999999998765
No 242
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=29.04 E-value=18 Score=44.31 Aligned_cols=8 Identities=38% Similarity=0.937 Sum_probs=0.0
Q ss_pred ccccCCCC
Q 046997 635 VRQCGICQ 642 (807)
Q Consensus 635 ~~~CP~C~ 642 (807)
...||.|+
T Consensus 655 ~r~Cp~Cg 662 (900)
T PF03833_consen 655 RRRCPKCG 662 (900)
T ss_dssp --------
T ss_pred cccCcccC
Confidence 45799994
No 243
>PRK14300 chaperone protein DnaJ; Provisional
Probab=28.93 E-value=70 Score=36.18 Aligned_cols=43 Identities=21% Similarity=0.581 Sum_probs=23.8
Q ss_pred ccccCCCCCcceEEEecCCCCc--eeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNL--MVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~--f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
..+||.|+|..++... .|.+ -..| +.|.-.= ......|+.|..
T Consensus 162 ~~~C~~C~G~G~~~~~--~g~~~~~~~C---~~C~G~G---------~~~~~~C~~C~G 206 (372)
T PRK14300 162 VTTCDACSGVGATRMQ--QGFFTIEQAC---HKCQGNG---------QIIKNPCKKCHG 206 (372)
T ss_pred CccCCCccCeEEEEEe--eceEEEEEeC---CCCCccc---------eEeCCCCCCCCC
Confidence 4689999776555443 2422 1245 4565321 123456999984
No 244
>PF13730 HTH_36: Helix-turn-helix domain
Probab=28.81 E-value=72 Score=25.01 Aligned_cols=27 Identities=15% Similarity=0.318 Sum_probs=22.6
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCce
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFI 338 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~I 338 (807)
...++.+|+|...+.++...|-+.|||
T Consensus 29 ~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 29 ETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 444455799999999999999999987
No 245
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=28.47 E-value=55 Score=25.14 Aligned_cols=9 Identities=22% Similarity=0.464 Sum_probs=6.6
Q ss_pred cCccCCCCC
Q 046997 683 TNTCNSCTP 691 (807)
Q Consensus 683 ~~~CP~Cg~ 691 (807)
...||.||.
T Consensus 21 ~~~Cp~CG~ 29 (46)
T PRK00398 21 GVRCPYCGY 29 (46)
T ss_pred ceECCCCCC
Confidence 457888885
No 246
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=28.40 E-value=64 Score=24.07 Aligned_cols=35 Identities=20% Similarity=0.486 Sum_probs=17.6
Q ss_pred ccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCCh
Q 046997 685 TCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDE 723 (807)
Q Consensus 685 ~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~ 723 (807)
.||+||....+..+...|...-+ -..++.|. +|+.
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~---~T~fy~C~-~C~~ 36 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEP---MTLFYVCC-NCGH 36 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSS---SEEEEEES-SSTE
T ss_pred CCcCCCCCeEEEEEeeccCCCCC---CeEEEEeC-CCCC
Confidence 59999976566555555443221 12335687 7753
No 247
>PRK14279 chaperone protein DnaJ; Provisional
Probab=28.31 E-value=82 Score=35.94 Aligned_cols=43 Identities=21% Similarity=0.676 Sum_probs=23.8
Q ss_pred ccccCCCCCcceEEEecCCCCc--eeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNL--MVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~--f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...||.|+|...+.... |.+ -..| +.|.=.= ......|+.|..
T Consensus 190 ~~~C~~C~G~G~~~~~~--g~~~~~~~C---~~C~G~G---------~~i~~~C~~C~G 234 (392)
T PRK14279 190 PKVCPTCNGSGVISRNQ--GAFGFSEPC---TDCRGTG---------SIIEDPCEECKG 234 (392)
T ss_pred CCCCCCCcceEEEEEEe--cceEEEEec---CCCCcee---------EEeCCcCCCCCC
Confidence 46799997655554432 321 1345 4576331 123456999973
No 248
>PRK05580 primosome assembly protein PriA; Validated
Probab=27.98 E-value=56 Score=40.08 Aligned_cols=12 Identities=17% Similarity=0.044 Sum_probs=5.8
Q ss_pred CCCHHHHHHHHH
Q 046997 304 PLSTIELEKRAS 315 (807)
Q Consensus 304 pf~l~~Lq~~as 315 (807)
|+.|+.-|++|-
T Consensus 142 ~~~Lt~~Q~~ai 153 (679)
T PRK05580 142 PPTLNPEQAAAV 153 (679)
T ss_pred CCCCCHHHHHHH
Confidence 444555555443
No 249
>PHA02998 RNA polymerase subunit; Provisional
Probab=27.90 E-value=65 Score=32.36 Aligned_cols=35 Identities=17% Similarity=0.459 Sum_probs=19.9
Q ss_pred cccccCCCCCcceE--EEecC---CCC-ceeeccCCCCCCccee
Q 046997 634 VVRQCGICQESNMV--LKKSR---DGN-LMVGCLAFPQCRNAVW 671 (807)
Q Consensus 634 ~~~~CP~C~g~~lv--~r~~k---~G~-~f~gCs~yP~C~~~~~ 671 (807)
+..+||+|++.... ..+.| .++ .|+.|. +|.+...
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~---~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACR---DCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcC---CCCCccC
Confidence 56789999654432 22222 232 467784 4776643
No 250
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=27.90 E-value=55 Score=35.35 Aligned_cols=35 Identities=17% Similarity=0.097 Sum_probs=29.9
Q ss_pred hHHHHHhhcccceEEEcCCceeeechhHHHHHhhcc
Q 046997 522 MHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYD 557 (807)
Q Consensus 522 ra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~ 557 (807)
-++||+.|.+-|+|....++ +..|++|+.|++.+.
T Consensus 51 v~~i~~~l~~egiv~~~~g~-v~~TekG~E~~e~~g 85 (354)
T COG1568 51 VASILEILEDEGIVKIEEGG-VELTEKGEELAEELG 85 (354)
T ss_pred HHHHHHHHHhcCcEEEecCc-EeehhhhHHHHHHhC
Confidence 47899999999999998765 789999999998653
No 251
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=27.86 E-value=77 Score=23.35 Aligned_cols=30 Identities=27% Similarity=0.298 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHhCCCCCc---cchHHHHHhhcc
Q 046997 502 LSEADLLSCMDKAGIGTD---ATMHDHIKKLLD 531 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTp---ATra~iI~~L~~ 531 (807)
-|+.+|-+.|+++||-.+ .||...|+.+.+
T Consensus 4 Ws~~~L~~wL~~~gi~~~~~~~~rd~Ll~~~k~ 36 (38)
T PF10281_consen 4 WSDSDLKSWLKSHGIPVPKSAKTRDELLKLAKK 36 (38)
T ss_pred CCHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHH
Confidence 478899999999999887 488888877643
No 252
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=27.75 E-value=35 Score=31.89 Aligned_cols=9 Identities=44% Similarity=0.837 Sum_probs=4.4
Q ss_pred ccCccCCCC
Q 046997 682 TTNTCNSCT 690 (807)
Q Consensus 682 t~~~CP~Cg 690 (807)
+.-.||.|+
T Consensus 11 t~l~C~~C~ 19 (113)
T PF09862_consen 11 TRLKCPSCG 19 (113)
T ss_pred EEEEcCCCC
Confidence 344455554
No 253
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=27.74 E-value=87 Score=37.43 Aligned_cols=66 Identities=12% Similarity=0.147 Sum_probs=55.6
Q ss_pred CCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcCCCHHHHHH-HHHHHhhcCceeccCCCCcccCCc
Q 046997 285 PTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFRMSSEHTMK-VAEDLYQAGFISYPRTETDSFSSG 351 (807)
Q Consensus 285 ~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g~s~~~tl~-iaQ~LYE~g~ISYPRTds~~l~~~ 351 (807)
..+.+.+++-+...+.||++++=.+|...|-+ +|+.-+-||. +.++|-++||++=-+-+-..+|..
T Consensus 467 e~fq~~~lem~~g~T~~P~~ltEaeLI~lMdk-~GIGtdAT~aehi~kiq~R~Yv~~~~~~~~~~P~~ 533 (758)
T KOG1956|consen 467 ELFQPGELEMKDGETSPPKYLTEAELISLMDK-NGIGTDATIAEHIEKIQERGYVTKKNKVGRFVPTF 533 (758)
T ss_pred cccccceEEeccCccCCCCccCHHHHHHHHHH-cCCCCchhHHHHHHHHHhhcceeeeccccccCchH
Confidence 45677888889999999999999999999876 8998888876 899999999999866666666653
No 254
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=27.45 E-value=42 Score=35.95 Aligned_cols=37 Identities=24% Similarity=0.446 Sum_probs=0.0
Q ss_pred CCCCcccccccccccCCCccCCCCC---CCCCCCccccCCC
Q 046997 752 GQQSNHRQRACIYCQQMGHSSSDCP---SQFSGSRNARANG 789 (807)
Q Consensus 752 ~~~~~~~~~~c~~c~~~g~~~~~~~---~~~~~~~~~~~~~ 789 (807)
+...... ..|..|+..||++.+|| ..+--......|.
T Consensus 137 ~~~~~~~-~~Cy~Cg~~GH~s~~C~~~~~~~c~~c~~~~h~ 176 (261)
T KOG4400|consen 137 PVDGPKP-AKCYSCGEQGHISDDCPENKGGTCFRCGKVGHG 176 (261)
T ss_pred cccCCCC-CccCCCCcCCcchhhCCCCCCCccccCCCccee
No 255
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=27.41 E-value=77 Score=40.07 Aligned_cols=72 Identities=13% Similarity=0.155 Sum_probs=46.5
Q ss_pred eeeeeeEeecCccCCCCCCCHHHHHHH-HHhCCCCCccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhc
Q 046997 484 FIPTTLTLDSGVTRPPPLLSEADLLSC-MDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGY 556 (807)
Q Consensus 484 ~~~~~~~i~e~~T~PP~~~Tea~Li~~-Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l 556 (807)
+.+.++..++..-.|||+||..|+|.. =.+.|++.+-|+ .|.+.|++-|+|+--.--.-..++.|+.+..-|
T Consensus 880 v~v~~~~e~ee~~~PlPPyTTDt~L~dAs~~L~lsa~~~M-~iaQdLFE~GlITYHRTDSTrVS~~Gi~vArey 952 (1187)
T COG1110 880 VEVVDVVEREEEKNPLPPYTTDTMLRDASRRLRLSADETM-QIAQDLFEGGLITYHRTDSTRVSDVGIRVAREY 952 (1187)
T ss_pred EEEeehhhhhhccCCCCCcCcchHHHHHHHHhCCChhHHH-HHHHHHHhccceEEeecCCcccchhhHHHHHHH
Confidence 444444445555677788888887764 456677666655 688999999999642111135678887655444
No 256
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=27.40 E-value=1.1e+02 Score=26.75 Aligned_cols=39 Identities=13% Similarity=0.195 Sum_probs=33.8
Q ss_pred HHHhcCCCHHHHHHHHHHHhhcCcee-ccCCCCcccCCcc
Q 046997 314 ASRYFRMSSEHTMKVAEDLYQAGFIS-YPRTETDSFSSGT 352 (807)
Q Consensus 314 ask~~g~s~~~tl~iaQ~LYE~g~IS-YPRTds~~l~~~~ 352 (807)
.++.+++|+.-+-..++.|-+-|||. =|=|.+.++|...
T Consensus 29 ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~ 68 (78)
T PF03444_consen 29 IAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIPTDK 68 (78)
T ss_pred HHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHH
Confidence 34458999999999999999999995 7999999999853
No 257
>PRK10220 hypothetical protein; Provisional
Probab=26.96 E-value=36 Score=31.39 Aligned_cols=7 Identities=29% Similarity=1.084 Sum_probs=4.2
Q ss_pred ccCCCCC
Q 046997 685 TCNSCTP 691 (807)
Q Consensus 685 ~CP~Cg~ 691 (807)
.||+|++
T Consensus 5 ~CP~C~s 11 (111)
T PRK10220 5 HCPKCNS 11 (111)
T ss_pred cCCCCCC
Confidence 4666664
No 258
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=26.93 E-value=26 Score=41.26 Aligned_cols=24 Identities=33% Similarity=0.783 Sum_probs=19.8
Q ss_pred CcccccccccccCCCccCC--CCCCC
Q 046997 755 SNHRQRACIYCQQMGHSSS--DCPSQ 778 (807)
Q Consensus 755 ~~~~~~~c~~c~~~g~~~~--~~~~~ 778 (807)
.++-.+.|..|||-||+.+ .||--
T Consensus 933 RK~Ttr~C~nCGQvGHmkTNK~CP~f 958 (968)
T COG5179 933 RKNTTRTCGNCGQVGHMKTNKACPKF 958 (968)
T ss_pred CCCcceecccccccccccccccCccc
Confidence 3677889999999999986 48863
No 259
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=26.86 E-value=49 Score=33.95 Aligned_cols=43 Identities=19% Similarity=0.350 Sum_probs=31.5
Q ss_pred CHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcC--CceeeechhH
Q 046997 503 SEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDA--NTRFAPTNIG 549 (807)
Q Consensus 503 Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~--~~~l~pT~~G 549 (807)
|-.+|-+.+ |+ .++|-..++..|.+.|||...+ .+.+.+|++|
T Consensus 159 s~~eia~~l---~i-s~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G 203 (203)
T TIGR01884 159 SVKNIAKKL---GK-SLSTISRHLRELEKKGLVEQKGRKGKRYSLTKLG 203 (203)
T ss_pred CHHHHHHHH---Cc-CHHHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence 444444443 66 4567779999999999998764 3458899987
No 260
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=26.82 E-value=36 Score=26.18 Aligned_cols=28 Identities=21% Similarity=0.599 Sum_probs=18.3
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCCCCCCccee
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVW 671 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~ 671 (807)
+.+||+|+ .. +|..-+.|.| +.|.....
T Consensus 11 irkCp~CG--t~------NG~R~~~CKN-~~C~~~~~ 38 (44)
T PF14952_consen 11 IRKCPKCG--TY------NGTRGLSCKN-KSCPQVFN 38 (44)
T ss_pred cccCCcCc--Cc------cCcccccccC-Cccchhhh
Confidence 57899994 22 2444477988 77876543
No 261
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=26.60 E-value=67 Score=25.17 Aligned_cols=11 Identities=27% Similarity=0.673 Sum_probs=7.4
Q ss_pred CccCCCCCCce
Q 046997 684 NTCNSCTPGPV 694 (807)
Q Consensus 684 ~~CP~Cg~~~l 694 (807)
..||.||+..+
T Consensus 27 ~~CP~Cg~~~~ 37 (52)
T TIGR02605 27 ATCPECGGEKL 37 (52)
T ss_pred CCCCCCCCCce
Confidence 46999986333
No 262
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=26.52 E-value=95 Score=24.22 Aligned_cols=44 Identities=18% Similarity=0.234 Sum_probs=29.8
Q ss_pred HHHhCCCCCccchHHHHHhhcccceEEEcCC---ceeeech-hHHHHHh
Q 046997 510 CMDKAGIGTDATMHDHIKKLLDRFYAIKDAN---TRFAPTN-IGEALVM 554 (807)
Q Consensus 510 ~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~---~~l~pT~-~G~~li~ 554 (807)
.++..|+ +++|-..+|+.|.++|+|....+ ..+.+|+ .|..++.
T Consensus 16 i~~~l~i-s~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~ 63 (66)
T smart00418 16 LAEILGL-SQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLE 63 (66)
T ss_pred HHHHHCC-CHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHH
Confidence 3444466 45678899999999999985431 2366777 6666553
No 263
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=26.49 E-value=98 Score=25.85 Aligned_cols=30 Identities=10% Similarity=0.243 Sum_probs=25.3
Q ss_pred HHHHHhcCCC-HHHHHHHHHHHhhcCceecc
Q 046997 312 KRASRYFRMS-SEHTMKVAEDLYQAGFISYP 341 (807)
Q Consensus 312 ~~ask~~g~s-~~~tl~iaQ~LYE~g~ISYP 341 (807)
++..+.||++ +.-+...++.|-++|||.-.
T Consensus 29 rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 29 REIAEALGLKSTSTVQRHLKALERKGYIRRD 59 (65)
T ss_dssp HHHHHHHTSSSHHHHHHHHHHHHHTTSEEEG
T ss_pred HHHHHHhCCCChHHHHHHHHHHHHCcCccCC
Confidence 5556678996 99999999999999999854
No 264
>PRK14290 chaperone protein DnaJ; Provisional
Probab=26.37 E-value=1e+02 Score=34.69 Aligned_cols=45 Identities=16% Similarity=0.457 Sum_probs=24.8
Q ss_pred ccccCCCCCcceEEEecCCCCc----eeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNL----MVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~----f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...||.|+|...+......|.+ -..| +.|.-.= ......|+.|..
T Consensus 165 ~~~C~~C~G~G~~~~~~~~g~~~~~~~~~C---~~C~G~G---------~~~~~~C~~C~G 213 (365)
T PRK14290 165 LITCPTCHGTGQQRIVRGQGFFRMVTVTTC---RTCGGRG---------RIPEEKCPRCNG 213 (365)
T ss_pred CccCCCCCCcCEEEEEeccCeEEEEEEEeC---CCCCCce---------eEccCCCCCCCC
Confidence 4579999765555444334432 1356 4575321 112457999974
No 265
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=26.32 E-value=94 Score=30.76 Aligned_cols=32 Identities=16% Similarity=0.160 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHhCCCCCccchHHHHHhhcccceEEE
Q 046997 502 LSEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIK 537 (807)
Q Consensus 502 ~Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~ 537 (807)
+|+.+|-..| || ..++--.++.+|.+.|+|..
T Consensus 29 ~tdEeLa~~L---gi-~~~~VRk~L~~L~e~~Lv~~ 60 (158)
T TIGR00373 29 FTDEEISLEL---GI-KLNEVRKALYALYDAGLADY 60 (158)
T ss_pred CCHHHHHHHH---CC-CHHHHHHHHHHHHHCCCcee
Confidence 6777777766 66 44555678888888888864
No 266
>PRK14289 chaperone protein DnaJ; Provisional
Probab=26.20 E-value=1e+02 Score=35.07 Aligned_cols=45 Identities=22% Similarity=0.629 Sum_probs=23.8
Q ss_pred ccccCCCCCcceEEEecCC--CCc--eeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRD--GNL--MVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~--G~~--f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...||.|+|...+....+. |.+ -..| +.|.-.= ......|+.|+.
T Consensus 171 ~~~C~~C~G~G~~~~~~~~~~G~~~~~~~C---~~C~G~G---------~~~~~~C~~C~G 219 (386)
T PRK14289 171 SETCPTCKGSGSVTRVQNTILGTMQTQSTC---PTCNGEG---------KIIKKKCKKCGG 219 (386)
T ss_pred CCcCCCCcCeEEEEEEEecccceEEEEEec---CCCCccc---------cccCcCCCCCCC
Confidence 4679999765555443222 321 1235 4565321 123457999984
No 267
>PRK04023 DNA polymerase II large subunit; Validated
Probab=26.19 E-value=46 Score=41.81 Aligned_cols=12 Identities=25% Similarity=0.421 Sum_probs=6.7
Q ss_pred HHHHHHHHHcCC
Q 046997 158 DREIHQAVQNLV 169 (807)
Q Consensus 158 ~~~I~~A~~nl~ 169 (807)
+.+|+-|++=|.
T Consensus 98 d~AvRtalAilT 109 (1121)
T PRK04023 98 DQAVRTALAILT 109 (1121)
T ss_pred HHHHHHHHHHHh
Confidence 456666665443
No 268
>PRK14284 chaperone protein DnaJ; Provisional
Probab=26.15 E-value=86 Score=35.75 Aligned_cols=43 Identities=28% Similarity=0.746 Sum_probs=24.2
Q ss_pred ccccCCCCCcceEEEecCCCCce--eeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLM--VGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f--~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...||.|++...+.... |.+- ..| |.|.-. -......|+.|..
T Consensus 175 ~~~C~~C~G~G~v~~~~--G~~~~~~~C---~~C~G~---------G~~~~~~C~~C~G 219 (391)
T PRK14284 175 IKVCDRCKGSGQVVQSR--GFFSMASTC---PECGGE---------GRVITDPCSVCRG 219 (391)
T ss_pred CeecCccCCeeEEEEEe--ceEEEEEEC---CCCCCC---------CcccCCcCCCCCC
Confidence 46799997655554432 4321 235 567633 1123457999973
No 269
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=25.94 E-value=81 Score=30.29 Aligned_cols=40 Identities=8% Similarity=0.179 Sum_probs=33.5
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceeccCCCCcccCCc
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYPRTETDSFSSG 351 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTds~~l~~~ 351 (807)
.++++.+++|+..+-...++|-++|||.|-|...-.|++.
T Consensus 26 ~ela~~l~vs~~svs~~l~~L~~~Gli~~~~~~~i~LT~~ 65 (142)
T PRK03902 26 SDIAEALSVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTPK 65 (142)
T ss_pred HHHHHHhCCChhHHHHHHHHHHHCCCEEEecCceEEECHH
Confidence 6778889999999999999999999999876555556654
No 270
>PRK14295 chaperone protein DnaJ; Provisional
Probab=25.78 E-value=91 Score=35.53 Aligned_cols=45 Identities=22% Similarity=0.527 Sum_probs=25.3
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...||.|+|...+.... |. |.-.+..+.|.-.= ......|+.|..
T Consensus 183 ~~~C~~C~G~G~~~~~~--g~-~~~~~~C~~C~G~G---------~~~~~~C~~C~G 227 (389)
T PRK14295 183 PRVCPTCSGTGQVSRNS--GG-FSLSEPCPDCKGRG---------LIADDPCLVCKG 227 (389)
T ss_pred CcCCCCCCCEeEEEEEe--cc-eEEEEecCCCccee---------EEeccCCCCCCC
Confidence 46799997655554432 43 23333446676331 123457999973
No 271
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=25.65 E-value=42 Score=32.60 Aligned_cols=18 Identities=50% Similarity=1.149 Sum_probs=14.0
Q ss_pred cccccccCCCccCCCCCC
Q 046997 760 RACIYCQQMGHSSSDCPS 777 (807)
Q Consensus 760 ~~c~~c~~~g~~~~~~~~ 777 (807)
..|..|++.||+..+||+
T Consensus 130 ~~C~~Cg~~gH~~~dCp~ 147 (148)
T PTZ00368 130 KTCYNCGQTGHLSRDCPD 147 (148)
T ss_pred CccccCCCcCcccccCCC
Confidence 468888888888888875
No 272
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=25.55 E-value=1.1e+02 Score=23.20 Aligned_cols=34 Identities=18% Similarity=0.229 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccC
Q 046997 305 LSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPR 342 (807)
Q Consensus 305 f~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPR 342 (807)
++..+|.. .+++|...+-...+.|.+.|+|....
T Consensus 15 ~s~~~l~~----~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 15 VSVEELAE----LLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred cCHHHHHH----HHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 56665554 47999999999999999999998643
No 273
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=25.38 E-value=28 Score=26.20 Aligned_cols=10 Identities=20% Similarity=0.614 Sum_probs=7.4
Q ss_pred ccCccCCCCC
Q 046997 682 TTNTCNSCTP 691 (807)
Q Consensus 682 t~~~CP~Cg~ 691 (807)
....|+.||.
T Consensus 31 p~~~C~~CGE 40 (46)
T TIGR03831 31 PALVCPQCGE 40 (46)
T ss_pred CccccccCCC
Confidence 3457999984
No 274
>PHA02998 RNA polymerase subunit; Provisional
Probab=25.30 E-value=73 Score=32.02 Aligned_cols=41 Identities=15% Similarity=0.442 Sum_probs=24.7
Q ss_pred ccCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChhHH
Q 046997 682 TTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDETLR 726 (807)
Q Consensus 682 t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~~~ 726 (807)
+...||+|+.....-.+..-|...-| ...++.|. .|....+
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEP---mT~FYkC~-~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEP---PLVRHACR-DCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCC---ceEEEEcC-CCCCccC
Confidence 56789999976555444444443222 12447798 8876665
No 275
>PRK14288 chaperone protein DnaJ; Provisional
Probab=25.27 E-value=95 Score=35.12 Aligned_cols=43 Identities=19% Similarity=0.593 Sum_probs=23.5
Q ss_pred ccccCCCCCcceEEEecCCCCce--eeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLM--VGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f--~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...|+.|+|..++.... |.+. ..| +.|.-.= ......|+.|..
T Consensus 156 ~~~C~~C~G~G~~~~~~--g~~~~~~~C---~~C~G~G---------~~~~~~C~~C~G 200 (369)
T PRK14288 156 LETCKQCNGQGQVFMRQ--GFMSFAQTC---GACQGKG---------KIIKTPCQACKG 200 (369)
T ss_pred CcCCCCCCCCcEEEEEe--ceEEEEEec---CCCCCCc---------eEccccCccCCC
Confidence 46799997655554432 3321 234 4565321 113456999974
No 276
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=25.27 E-value=89 Score=27.05 Aligned_cols=32 Identities=25% Similarity=0.331 Sum_probs=25.5
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCceeccCC
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFISYPRT 343 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRT 343 (807)
++.++++++++..+-++.|+|-++|+|.=-|-
T Consensus 29 ~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G 60 (83)
T PF02082_consen 29 KEIAERLGISPSYLRKILQKLKKAGLIESSRG 60 (83)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETS
T ss_pred HHHHHHHCcCHHHHHHHHHHHhhCCeeEecCC
Confidence 34455789999999999999999999975543
No 277
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=25.16 E-value=61 Score=24.04 Aligned_cols=31 Identities=19% Similarity=0.344 Sum_probs=21.7
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhc-Cce-eccCCCCcc
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQA-GFI-SYPRTETDS 347 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~-g~I-SYPRTds~~ 347 (807)
.++++.+|+|++.. +-||+ |+| +-.||++.+
T Consensus 3 ~e~A~~~gvs~~tl-----R~ye~~Gll~~~~r~~~g~ 35 (38)
T PF00376_consen 3 GEVAKLLGVSPRTL-----RYYEREGLLPPPERTEGGY 35 (38)
T ss_dssp HHHHHHHTS-HHHH-----HHHHHTTSS-SSEETTTS-
T ss_pred HHHHHHHCCCHHHH-----HHHHHCCCCCCCccCCCCe
Confidence 46788889987633 45765 999 888998764
No 278
>PRK14301 chaperone protein DnaJ; Provisional
Probab=25.15 E-value=73 Score=36.09 Aligned_cols=43 Identities=33% Similarity=0.668 Sum_probs=23.3
Q ss_pred ccccCCCCCcceEEEecCCCCc--eeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNL--MVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~--f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...||.|+|...+... .|.+ -..| +.|.-.= ......|+.|..
T Consensus 161 ~~~C~~C~G~G~v~~~--~G~~~~~~~C---~~C~G~G---------~~~~~~C~~C~G 205 (373)
T PRK14301 161 PETCRHCGGSGQVRQS--QGFFQIAVPC---PVCRGEG---------RVITHPCPKCKG 205 (373)
T ss_pred CcccCCccCeeEEEEE--eeeEEEEEeC---CCCCcee---------eecCCCCCCCCC
Confidence 3579999765555443 2421 1235 4565321 123457999973
No 279
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=25.11 E-value=1.8e+02 Score=31.07 Aligned_cols=72 Identities=19% Similarity=0.435 Sum_probs=39.8
Q ss_pred cccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEEEeeccCccCCCCCccC
Q 046997 634 VVRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLIQFKFRQHEIPPGFNVN 713 (807)
Q Consensus 634 ~~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~ 713 (807)
....|-.| +. ++--.++.-...+.|++ |+-..++-... ....-..|| |.- +.+-+... .
T Consensus 64 p~v~CrVC-q~-~I~i~gk~~QhVVkC~~---CnEATPIr~aP--pGKKYVRCP-CNC---LLICk~sS----------~ 122 (256)
T PF09788_consen 64 PVVTCRVC-QS-LIDIEGKMHQHVVKCSV---CNEATPIRNAP--PGKKYVRCP-CNC---LLICKSSS----------Q 122 (256)
T ss_pred ceEEeecC-Cc-eecccCccceeeEECCC---CCccccccCCC--CCCeeEecC-Cce---EEEeeccc----------c
Confidence 46789999 44 44444444455688965 77665542211 111245698 653 22222111 1
Q ss_pred ccccCC-CCChhHH
Q 046997 714 HLGCIG-GCDETLR 726 (807)
Q Consensus 714 ~~~C~~-~C~~~~~ 726 (807)
..+||. +|+-.|+
T Consensus 123 rIaCPRp~CkRiI~ 136 (256)
T PF09788_consen 123 RIACPRPNCKRIIN 136 (256)
T ss_pred cccCCCCCCcceEE
Confidence 267973 8998887
No 280
>PHA02031 putative DnaG-like primase
Probab=25.01 E-value=1.9e+02 Score=31.17 Aligned_cols=52 Identities=12% Similarity=0.146 Sum_probs=35.1
Q ss_pred HHHHHhh-cCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEe-cccCHHHH
Q 046997 108 LEEEARR-CQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARF-SALIDREI 161 (807)
Q Consensus 108 lk~~~~~-~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~-s~lt~~~I 161 (807)
++.+.+- +++||++-|.|.=|..=++..++.+...+. .++-+.+ ...+|+++
T Consensus 198 ~~~L~r~~~~~Vil~fDgD~AG~~Aa~ra~~~l~~~~~--~v~vv~lP~g~DPDd~ 251 (266)
T PHA02031 198 AAILLQQTCPRVLIFLDGDPAGVDGSAGAMRRLRPLLI--EGQVIITPDGFDPKDL 251 (266)
T ss_pred HHHHHhcCCCCEEEEeCCCHHHHHHHHHHHHHHHHcCC--ceEEEECCCCCChHHH
Confidence 4444454 799999999999999888888888765543 3433232 35555443
No 281
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=24.98 E-value=1.1e+02 Score=25.64 Aligned_cols=32 Identities=9% Similarity=0.133 Sum_probs=26.8
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHhhcCceeccC
Q 046997 311 EKRASRYFRMSSEHTMKVAEDLYQAGFISYPR 342 (807)
Q Consensus 311 q~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPR 342 (807)
+.+.++.+|++...+-.+..+|=+.|+|..-.
T Consensus 25 a~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 25 ALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 35556779999999999999999999998743
No 282
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=24.96 E-value=1.1e+02 Score=25.58 Aligned_cols=38 Identities=24% Similarity=0.445 Sum_probs=30.7
Q ss_pred CCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccCC
Q 046997 302 PYPLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRT 343 (807)
Q Consensus 302 P~pf~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRT 343 (807)
|.|++. .+.+..+|.|...+.++...|=++|+|++-+.
T Consensus 26 ~~~lt~----~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 26 PLPLTQ----EEIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp EEESSH----HHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred EecCCH----HHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 445554 45566789999999999999999999997654
No 283
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=24.89 E-value=71 Score=37.52 Aligned_cols=12 Identities=25% Similarity=0.346 Sum_probs=8.9
Q ss_pred ccCccccCCCCCh
Q 046997 711 NVNHLGCIGGCDE 723 (807)
Q Consensus 711 ~~~~~~C~~~C~~ 723 (807)
.+.++.|+ .|.|
T Consensus 83 ~~~~l~C~-~C~W 94 (483)
T PF05502_consen 83 KPYYLSCS-YCRW 94 (483)
T ss_pred CCEEEECC-Ccee
Confidence 34568899 9977
No 284
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=24.74 E-value=81 Score=23.86 Aligned_cols=29 Identities=17% Similarity=0.480 Sum_probs=13.8
Q ss_pred ccCCCCCcceEEEecCCCCceeeccCCCCCCccee
Q 046997 637 QCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVW 671 (807)
Q Consensus 637 ~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~ 671 (807)
.||.|+. ..+.--...|. +-|+ .|..++.
T Consensus 2 ~Cp~Cg~-~~~~~D~~~g~--~vC~---~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGS-KEIVFDPERGE--LVCP---NCGLVLE 30 (43)
T ss_dssp SBTTTSS-SEEEEETTTTE--EEET---TT-BBEE
T ss_pred CCcCCcC-CceEEcCCCCe--EECC---CCCCEee
Confidence 5899954 33333333343 4563 3655543
No 285
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=24.72 E-value=69 Score=23.19 Aligned_cols=25 Identities=16% Similarity=0.280 Sum_probs=15.4
Q ss_pred eeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 657 MVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 657 f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
+|-|+ .|.+++-... ....||.||.
T Consensus 2 ~~~C~---~CG~i~~g~~-------~p~~CP~Cg~ 26 (34)
T cd00729 2 VWVCP---VCGYIHEGEE-------APEKCPICGA 26 (34)
T ss_pred eEECC---CCCCEeECCc-------CCCcCcCCCC
Confidence 36675 4887754321 2357999985
No 286
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=24.58 E-value=1.2e+02 Score=27.18 Aligned_cols=55 Identities=22% Similarity=0.344 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHH----------------hCCCCCccchH---HHHHhhcccceEEEcCC----ceeeechhHHHHHhh
Q 046997 501 LLSEADLLSCMD----------------KAGIGTDATMH---DHIKKLLDRFYAIKDAN----TRFAPTNIGEALVMG 555 (807)
Q Consensus 501 ~~Tea~Li~~Me----------------~~GIGTpATra---~iI~~L~~R~Yv~~~~~----~~l~pT~~G~~li~~ 555 (807)
+||-..++..+. ..|+|-.=++. .+|..|+..||+....+ ..|.+|++|..++.+
T Consensus 19 ~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~~~~~~~~l~g 96 (106)
T PF09382_consen 19 RFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDNGGFAYPYLKLTPKGKELLNG 96 (106)
T ss_dssp -S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE-GGGHHHHCT
T ss_pred cccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecCCcccccEEEECHHHHHHHCC
Confidence 677777777663 35888876655 47889999999976543 358999999998753
No 287
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=24.56 E-value=67 Score=32.38 Aligned_cols=29 Identities=17% Similarity=0.430 Sum_probs=18.0
Q ss_pred ceeeccCCCCCCcceecCCCccccccccCccCCCCCCceEEE
Q 046997 656 LMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTPGPVYLI 697 (807)
Q Consensus 656 ~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~ 697 (807)
|-+.|.+ |.-.++. ....||.||+ ++.+.
T Consensus 138 w~~rC~G---C~~~f~~---------~~~~Cp~CG~-~~~~~ 166 (177)
T COG1439 138 WRLRCHG---CKRIFPE---------PKDFCPICGS-PLKRK 166 (177)
T ss_pred eeEEEec---CceecCC---------CCCcCCCCCC-ceEEe
Confidence 4467865 7655442 2457999995 55543
No 288
>PRK07714 hypothetical protein; Provisional
Probab=24.38 E-value=2.8e+02 Score=25.09 Aligned_cols=75 Identities=12% Similarity=0.109 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHHcCCCCCcchHHHHHH
Q 046997 102 KDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQNLVDPNQWFADAVDA 181 (807)
Q Consensus 102 ~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~nl~~~~~~l~~a~~a 181 (807)
..+.+.|++ .++..||+|.|++.. +..+|...|...+ .|+. .-.|.+++-.|+-.-...--.+.+.+.|
T Consensus 24 ~~v~~al~~--g~~~lViiA~D~s~~---~~~ki~~~~~~~~--vp~~----~~~sk~eLG~a~Gk~~~~~vai~d~g~a 92 (100)
T PRK07714 24 ELVLKEVRS--GKAKLVLLSEDASVN---TTKKITDKCTYYN--VPMR----KVENRQQLGHAIGKDERVVVAVLDEGFA 92 (100)
T ss_pred HHHHHHHHh--CCceEEEEeCCCCHH---HHHHHHHHHHhcC--CCEE----EeCCHHHHHHHhCCCcceEEEEeCchhH
Confidence 444444543 357899999999876 5667777776544 3553 2258899999997532122345667777
Q ss_pred HHHHhH
Q 046997 182 RQEIDL 187 (807)
Q Consensus 182 R~~~D~ 187 (807)
+.....
T Consensus 93 ~~l~~~ 98 (100)
T PRK07714 93 KKLRSM 98 (100)
T ss_pred HHHHHH
Confidence 766553
No 289
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=24.30 E-value=69 Score=39.93 Aligned_cols=35 Identities=17% Similarity=0.477 Sum_probs=24.0
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCC----CCCCcceecCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAF----PQCRNAVWLPGS 675 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~y----P~C~~~~~~p~~ 675 (807)
..+||.|+ +.|+... . .|.|++| ..|.|+..-|+.
T Consensus 111 l~~Cp~C~-g~l~~~g----~-~Y~C~G~iSeWtKC~y~T~~P~R 149 (815)
T PLN03122 111 LEKCPLCG-GALECDG----H-RYTCTGFISEWSSCTFSTKNPPR 149 (815)
T ss_pred CCCCCCCC-CeEEEcC----C-eeEeccccCCCcccccccCCCCc
Confidence 45799995 6665442 2 3899775 679988766554
No 290
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=24.28 E-value=73 Score=34.20 Aligned_cols=39 Identities=21% Similarity=0.459 Sum_probs=31.5
Q ss_pred CccchHHHHHhhcccceEEEcCCceeeechhHHHHHhhcc
Q 046997 518 TDATMHDHIKKLLDRFYAIKDANTRFAPTNIGEALVMGYD 557 (807)
Q Consensus 518 TpATra~iI~~L~~R~Yv~~~~~~~l~pT~~G~~li~~l~ 557 (807)
++++...+|++|.+.|.|..++ +.+..|++|+.++..++
T Consensus 39 s~~ai~pqiKkL~~~~LV~~~~-~~Y~LS~~G~iiv~km~ 77 (260)
T COG4742 39 SSSAILPQIKKLKDKGLVVQEG-DRYSLSSLGKIIVEKME 77 (260)
T ss_pred CcHHHHHHHHHHhhCCCEEecC-CEEEecchHHHHHHHHH
Confidence 4555778999999999999875 46899999998776543
No 291
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=24.24 E-value=1.1e+02 Score=24.36 Aligned_cols=30 Identities=10% Similarity=0.272 Sum_probs=25.0
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHhhcCceec
Q 046997 311 EKRASRYFRMSSEHTMKVAEDLYQAGFISY 340 (807)
Q Consensus 311 q~~ask~~g~s~~~tl~iaQ~LYE~g~ISY 340 (807)
+.+.++.+++++.-+-.+..+|=++|||.=
T Consensus 24 ~~~la~~l~~~~~~vs~~v~~L~~~Glv~r 53 (62)
T PF12802_consen 24 QSELAERLGISKSTVSRIVKRLEKKGLVER 53 (62)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 456677799999999999999999999963
No 292
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=24.17 E-value=76 Score=26.57 Aligned_cols=14 Identities=36% Similarity=0.733 Sum_probs=8.8
Q ss_pred ccCccCCCCCCceE
Q 046997 682 TTNTCNSCTPGPVY 695 (807)
Q Consensus 682 t~~~CP~Cg~~~l~ 695 (807)
+...|+.||-..++
T Consensus 35 ~~v~C~~CGYTE~Y 48 (64)
T PF09855_consen 35 TTVSCTNCGYTEFY 48 (64)
T ss_pred EEEECCCCCCEEEE
Confidence 34569999853344
No 293
>COG1706 FlgI Flagellar basal-body P-ring protein [Cell motility and secretion]
Probab=24.14 E-value=92 Score=34.62 Aligned_cols=34 Identities=12% Similarity=0.200 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCcee
Q 046997 305 LSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFIS 339 (807)
Q Consensus 305 f~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~IS 339 (807)
-++..|-+..++ +|-+|++.|.|.|.||++|.+.
T Consensus 326 ~~l~~lV~aLn~-iGa~P~diiaILQalk~AGal~ 359 (365)
T COG1706 326 TTLNNLVRALNA-IGATPQDIIAILQALKSAGALQ 359 (365)
T ss_pred CcHHHHHHHHHH-hcCCHHHHHHHHHHHHHcCccc
Confidence 367777777776 8999999999999999998763
No 294
>PRK02935 hypothetical protein; Provisional
Probab=24.05 E-value=52 Score=30.17 Aligned_cols=20 Identities=25% Similarity=0.296 Sum_probs=14.6
Q ss_pred cccccccccccCCCccCCCC
Q 046997 756 NHRQRACIYCQQMGHSSSDC 775 (807)
Q Consensus 756 ~~~~~~c~~c~~~g~~~~~~ 775 (807)
-+|.+.|.+|++|=++..+.
T Consensus 83 LGrvD~CM~C~~PLTLd~~l 102 (110)
T PRK02935 83 LGRVDACMHCNQPLTLDRSL 102 (110)
T ss_pred ccceeecCcCCCcCCcCccc
Confidence 35567799999987776543
No 295
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=23.95 E-value=1.4e+02 Score=21.51 Aligned_cols=27 Identities=19% Similarity=0.464 Sum_probs=23.0
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCce
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFI 338 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~I 338 (807)
++.+..+|++++-+-.+.-+|-++|+|
T Consensus 6 ~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 466778999999999999999999987
No 296
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=23.81 E-value=82 Score=37.05 Aligned_cols=37 Identities=8% Similarity=0.042 Sum_probs=31.1
Q ss_pred CccchHHHHHhhcccceEEEcC--CceeeechhHHHHHh
Q 046997 518 TDATMHDHIKKLLDRFYAIKDA--NTRFAPTNIGEALVM 554 (807)
Q Consensus 518 TpATra~iI~~L~~R~Yv~~~~--~~~l~pT~~G~~li~ 554 (807)
+++|-..+|+.|.++|||+... .+.+.+|+.|+.+++
T Consensus 33 ~~~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~~ 71 (489)
T PRK04172 33 PPEAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAE 71 (489)
T ss_pred CHHHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHHH
Confidence 6788889999999999998754 235899999999875
No 297
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=23.72 E-value=84 Score=24.31 Aligned_cols=32 Identities=34% Similarity=0.288 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHHHhCCC----CCccchHHHHHhhcc
Q 046997 500 PLLSEADLLSCMDKAGI----GTDATMHDHIKKLLD 531 (807)
Q Consensus 500 ~~~Tea~Li~~Me~~GI----GTpATra~iI~~L~~ 531 (807)
..+|+++|...|.+.|+ =|++||.-.+.+|.+
T Consensus 4 ~~LSd~eL~~~L~~~G~~~gPIt~sTR~vy~kkL~~ 39 (44)
T smart00540 4 DRLSDAELRAELKQYGLPPGPITDTTRKLYEKKLRK 39 (44)
T ss_pred hHcCHHHHHHHHHHcCCCCCCcCcchHHHHHHHHHH
Confidence 46899999999999875 389999998888863
No 298
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=23.58 E-value=47 Score=31.55 Aligned_cols=10 Identities=20% Similarity=0.421 Sum_probs=7.3
Q ss_pred ccCccCCCCC
Q 046997 682 TTNTCNSCTP 691 (807)
Q Consensus 682 t~~~CP~Cg~ 691 (807)
+...||.||+
T Consensus 8 tKr~Cp~cg~ 17 (129)
T TIGR02300 8 TKRICPNTGS 17 (129)
T ss_pred ccccCCCcCc
Confidence 4567888885
No 299
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=23.42 E-value=59 Score=22.99 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=5.9
Q ss_pred cCccCCCCCCceE
Q 046997 683 TNTCNSCTPGPVY 695 (807)
Q Consensus 683 ~~~CP~Cg~~~l~ 695 (807)
...|+.||. ++.
T Consensus 3 ~rfC~~CG~-~t~ 14 (32)
T PF09297_consen 3 HRFCGRCGA-PTK 14 (32)
T ss_dssp TSB-TTT---BEE
T ss_pred CcccCcCCc-ccc
Confidence 457999994 444
No 300
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=23.24 E-value=1e+02 Score=28.10 Aligned_cols=34 Identities=21% Similarity=0.333 Sum_probs=28.1
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHhhcCceeccCCC
Q 046997 311 EKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTE 344 (807)
Q Consensus 311 q~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTd 344 (807)
|++.+..+++++..+-.+..+|+++|||+=-|.+
T Consensus 46 ~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~ 79 (109)
T TIGR01889 46 LKEIIKEILIKQSALVKIIKKLSKKGYLSKERSE 79 (109)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCc
Confidence 3566677899999999999999999999854444
No 301
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=23.22 E-value=1.5e+02 Score=24.29 Aligned_cols=36 Identities=19% Similarity=0.338 Sum_probs=24.6
Q ss_pred CCCHHHHHHHHHHhcCCCHH----HHHHHHHHHhhcCcee
Q 046997 304 PLSTIELEKRASRYFRMSSE----HTMKVAEDLYQAGFIS 339 (807)
Q Consensus 304 pf~l~~Lq~~ask~~g~s~~----~tl~iaQ~LYE~g~IS 339 (807)
+.+..++.+....+|+.+++ ++....+.|.++|+|.
T Consensus 29 ~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 29 PRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT---
T ss_pred CCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCcC
Confidence 45678999999999999987 4566788888899874
No 302
>PRK14291 chaperone protein DnaJ; Provisional
Probab=23.21 E-value=1.3e+02 Score=34.29 Aligned_cols=44 Identities=20% Similarity=0.528 Sum_probs=23.8
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...||.|+|...+... +.++---+..+.|.-.= .....|+.|..
T Consensus 173 ~~~C~~C~G~G~~~~~---~g~~~~~~~C~~C~G~G----------~~~~~C~~C~G 216 (382)
T PRK14291 173 EKVCPTCGGSGEIYQR---GGFFRISQTCPTCGGEG----------VLREPCSKCNG 216 (382)
T ss_pred CccCCCCCCceEEEEe---cceEEEEecCCCCCCce----------EEccCCCCCCC
Confidence 4579999765555443 22222222235575331 12457999984
No 303
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=23.13 E-value=82 Score=24.29 Aligned_cols=10 Identities=20% Similarity=0.564 Sum_probs=7.6
Q ss_pred ccCccCCCCC
Q 046997 682 TTNTCNSCTP 691 (807)
Q Consensus 682 t~~~CP~Cg~ 691 (807)
....||.||.
T Consensus 18 ~~irC~~CG~ 27 (44)
T smart00659 18 DVVRCRECGY 27 (44)
T ss_pred CceECCCCCc
Confidence 3567999995
No 304
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits, which is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion [, ]. Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0005740 mitochondrial envelope; PDB: 2EIL_S 2ZXW_S 3ASN_S 1OCO_S 3AG4_S 3ABK_S 1OCZ_S 1OCC_F 3ASO_S 3ABL_S ....
Probab=23.06 E-value=73 Score=30.80 Aligned_cols=39 Identities=21% Similarity=0.528 Sum_probs=22.8
Q ss_pred CCCceeeccCCCCCC-cceecCCCccccccccCccCCCCCCceEEE
Q 046997 653 DGNLMVGCLAFPQCR-NAVWLPGSVSEAAVTTNTCNSCTPGPVYLI 697 (807)
Q Consensus 653 ~G~~f~gCs~yP~C~-~~~~~p~~~~~~~~t~~~CP~Cg~~~l~~~ 697 (807)
....++||..+|+=. .++|+--. .. ....||+||. .++.
T Consensus 85 ~~~RiVGC~g~~~~sH~v~W~~l~---~g-~~~RCpeCG~--~fkL 124 (136)
T PF01215_consen 85 FDERIVGCTGEPDDSHDVIWFWLH---KG-KPQRCPECGQ--VFKL 124 (136)
T ss_dssp SSCEEEEESSSTT-SSS-EEEEEE---TT-SEEEETTTEE--EEEE
T ss_pred CCceEEeeccCCCCcceeEEEEEe---CC-CccCCCCCCe--EEEE
Confidence 445579999998654 46665110 11 2468999985 4544
No 305
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=23.04 E-value=1.2e+02 Score=23.50 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=27.6
Q ss_pred CCC-CHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCc
Q 046997 500 PLL-SEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANT 541 (807)
Q Consensus 500 ~~~-Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~ 541 (807)
.++ |+.+| ++..|+ +.+|-..+++.|.+.|+|....++
T Consensus 18 ~~l~s~~~l---a~~~~v-s~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 18 DKLPSEREL---AAQLGV-SRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CcCcCHHHH---HHHHCC-CHHHHHHHHHHHHHCCCEEEecCC
Confidence 344 55554 555688 568888999999999999765443
No 306
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=22.97 E-value=1.2e+02 Score=25.41 Aligned_cols=35 Identities=20% Similarity=0.368 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccCCC
Q 046997 306 STIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTE 344 (807)
Q Consensus 306 ~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTd 344 (807)
|++.||. +|+++-..+..+...|-+.|+||-+-+.
T Consensus 22 S~S~lQR----~~rIGynrAariid~LE~~GiVs~~~~~ 56 (65)
T PF09397_consen 22 SISLLQR----KFRIGYNRAARIIDQLEEEGIVSPANGS 56 (65)
T ss_dssp CHHHHHH----HHT--HHHHHHHHHHHHHCTSBE---TT
T ss_pred cHHHHHH----HhCCCHHHHHHHHHHHHHCCCCCCCCCC
Confidence 4566775 5788889999999999999999987543
No 307
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=22.85 E-value=19 Score=43.64 Aligned_cols=14 Identities=36% Similarity=0.679 Sum_probs=10.1
Q ss_pred CcccccccccccCC
Q 046997 755 SNHRQRACIYCQQM 768 (807)
Q Consensus 755 ~~~~~~~c~~c~~~ 768 (807)
...||+.||.|+.+
T Consensus 674 ~etRqRKCP~Cn~a 687 (698)
T KOG0978|consen 674 YETRQRKCPKCNAA 687 (698)
T ss_pred HHHhcCCCCCCCCC
Confidence 34567789999854
No 308
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=22.75 E-value=1.2e+02 Score=21.73 Aligned_cols=31 Identities=26% Similarity=0.438 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHhCCCCCccchHHHHHhhcc
Q 046997 501 LLSEADLLSCMDKAGIGTDATMHDHIKKLLD 531 (807)
Q Consensus 501 ~~Tea~Li~~Me~~GIGTpATra~iI~~L~~ 531 (807)
.+|.++|-+.+...||-|.-+++.+|+.|.+
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~ 33 (35)
T smart00513 3 KLKVSELKDELKKRGLSTSGTKAELVDRLLE 33 (35)
T ss_pred cCcHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 5778999999999999999999999998865
No 309
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=22.72 E-value=94 Score=25.97 Aligned_cols=34 Identities=18% Similarity=0.331 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccCC
Q 046997 306 STIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRT 343 (807)
Q Consensus 306 ~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRT 343 (807)
+++-||+ +|++.-..+..++..|-+.|+||=+..
T Consensus 21 S~S~lQR----~~~IGynrAariid~lE~~GiV~p~~g 54 (63)
T smart00843 21 STSLLQR----RLRIGYNRAARLIDQLEEEGIVGPANG 54 (63)
T ss_pred ChHHHHH----HHhcchhHHHHHHHHHHHCcCCCCCCC
Confidence 4677776 577788999999999999999986543
No 310
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=22.72 E-value=48 Score=32.17 Aligned_cols=19 Identities=47% Similarity=1.135 Sum_probs=12.7
Q ss_pred cccccccCCCccCCCCCCC
Q 046997 760 RACIYCQQMGHSSSDCPSQ 778 (807)
Q Consensus 760 ~~c~~c~~~g~~~~~~~~~ 778 (807)
..|..|++.||+..+||..
T Consensus 78 ~~C~~Cg~~GH~~~~C~~~ 96 (148)
T PTZ00368 78 RSCYNCGQTGHISRECPNR 96 (148)
T ss_pred cccCcCCCCCcccccCCCc
Confidence 4577777777777777663
No 311
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=22.64 E-value=71 Score=25.84 Aligned_cols=7 Identities=29% Similarity=1.142 Sum_probs=5.1
Q ss_pred ccCCCCC
Q 046997 685 TCNSCTP 691 (807)
Q Consensus 685 ~CP~Cg~ 691 (807)
.||.||.
T Consensus 24 ~Cp~CGa 30 (54)
T TIGR01206 24 ICDECGA 30 (54)
T ss_pred eCCCCCC
Confidence 5888874
No 312
>PRK14285 chaperone protein DnaJ; Provisional
Probab=22.55 E-value=1e+02 Score=34.78 Aligned_cols=43 Identities=28% Similarity=0.746 Sum_probs=22.8
Q ss_pred ccccCCCCCcceEEEecCCCCc--eeeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNL--MVGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~--f~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...||.|+|..++... .|.+ -..| |.|.-. -......|+.|..
T Consensus 163 ~~~C~~C~G~G~~~~~--~G~~~~~~~C---~~C~G~---------G~~~~~~C~~C~G 207 (365)
T PRK14285 163 PSICNMCNGSGRVMQG--GGFFRVTTTC---PKCYGN---------GKIISNPCKSCKG 207 (365)
T ss_pred CccCCCccCceeEEec--CceeEEeeec---CCCCCc---------ccccCCCCCCCCC
Confidence 4579999765555432 2321 1235 456532 1123457999973
No 313
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=22.47 E-value=48 Score=42.12 Aligned_cols=51 Identities=27% Similarity=0.541 Sum_probs=34.7
Q ss_pred ccccccCCCCCcceEEEecCCCCceeeccC--CCCCCcceecCCCccccccccCccCCCCC
Q 046997 633 EVVRQCGICQESNMVLKKSRDGNLMVGCLA--FPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 633 ~~~~~CP~C~g~~lv~r~~k~G~~f~gCs~--yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
..+..|-.| |.++-+. ..|..|++|.- ||-|+-.+-.++. .-.+.||+|+.
T Consensus 15 ~~~qiCqIC-GD~vg~~--~~Ge~FVAC~eC~FPVCrpCYEYEr~-----eG~q~CPqCkt 67 (1079)
T PLN02638 15 GGGQVCQIC-GDNVGKT--VDGEPFVACDVCAFPVCRPCYEYERK-----DGNQSCPQCKT 67 (1079)
T ss_pred cCCceeeec-ccccCcC--CCCCEEEEeccCCCccccchhhhhhh-----cCCccCCccCC
Confidence 346689999 5665444 47888999954 5777766655442 23567999984
No 314
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=22.43 E-value=61 Score=32.42 Aligned_cols=23 Identities=22% Similarity=0.435 Sum_probs=14.3
Q ss_pred eeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 658 VGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 658 ~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
|-| |.|.|+.-. ..+..||.||.
T Consensus 135 ~vC---~vCGy~~~g--------e~P~~CPiCga 157 (166)
T COG1592 135 WVC---PVCGYTHEG--------EAPEVCPICGA 157 (166)
T ss_pred EEc---CCCCCcccC--------CCCCcCCCCCC
Confidence 566 456665433 13568999994
No 315
>PRK12789 flgI flagellar basal body P-ring protein; Reviewed
Probab=22.31 E-value=1.3e+02 Score=33.90 Aligned_cols=32 Identities=9% Similarity=0.222 Sum_probs=28.2
Q ss_pred CHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCce
Q 046997 306 STIELEKRASRYFRMSSEHTMKVAEDLYQAGFI 338 (807)
Q Consensus 306 ~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~I 338 (807)
++.+|-...|+ +|.+|.+.+.|.|.|.++|.+
T Consensus 329 tl~~lV~aLN~-lG~tp~DlIsILqalk~aGAL 360 (367)
T PRK12789 329 DLQTLVRGLNQ-IGLKPSDIIAILQAIKTAGAL 360 (367)
T ss_pred CHHHHHHHHHH-cCCChHHHHHHHHHHHhcCcc
Confidence 77888777776 999999999999999999865
No 316
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=22.28 E-value=76 Score=34.96 Aligned_cols=44 Identities=18% Similarity=0.363 Sum_probs=27.0
Q ss_pred cCccCCCCCCceEEEEeeccCccCCCCCccCccccCCCCChhHHHHHHhhCCCCCCC
Q 046997 683 TNTCNSCTPGPVYLIQFKFRQHEIPPGFNVNHLGCIGGCDETLRQLIEICGTGSRIP 739 (807)
Q Consensus 683 ~~~CP~Cg~~~l~~~~~k~~~g~~~~~~~~~~~~C~~~C~~~~~~l~~~~~~~~~~~ 739 (807)
...||.||+..++. ....|. ..|. +|..++.+-+=-.+.+|+.-
T Consensus 11 ~~~Cp~Cg~~~iv~---d~~~Ge---------~vC~-~CG~Vl~e~~iD~g~EWR~f 54 (310)
T PRK00423 11 KLVCPECGSDKLIY---DYERGE---------IVCA-DCGLVIEENIIDQGPEWRAF 54 (310)
T ss_pred CCcCcCCCCCCeeE---ECCCCe---------Eeec-ccCCcccccccccCCCccCC
Confidence 45699999644432 234444 4498 99988876444455566543
No 317
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=22.21 E-value=62 Score=28.93 Aligned_cols=11 Identities=27% Similarity=0.921 Sum_probs=7.7
Q ss_pred ccCCCCCcceE
Q 046997 637 QCGICQESNMV 647 (807)
Q Consensus 637 ~CP~C~g~~lv 647 (807)
+|+.|+++..+
T Consensus 1 ~C~~C~~~~~~ 11 (89)
T TIGR03829 1 KCRWCEEEKAI 11 (89)
T ss_pred CCcccCCCcee
Confidence 49999655554
No 318
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.19 E-value=61 Score=27.04 Aligned_cols=8 Identities=25% Similarity=0.729 Sum_probs=5.9
Q ss_pred cccCCCCC
Q 046997 636 RQCGICQE 643 (807)
Q Consensus 636 ~~CP~C~g 643 (807)
.+||+|+.
T Consensus 5 ~kCpKCgn 12 (68)
T COG3478 5 FKCPKCGN 12 (68)
T ss_pred ccCCCcCC
Confidence 35999963
No 319
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=22.04 E-value=2.2e+02 Score=34.27 Aligned_cols=38 Identities=18% Similarity=0.320 Sum_probs=30.7
Q ss_pred HHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcC
Q 046997 106 KTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVN 143 (807)
Q Consensus 106 ~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~ 143 (807)
++|+.+.+..+.||++.|.|+=|+.++|..++.+....
T Consensus 281 ehi~~L~r~~~~vil~fDgD~AG~~Aa~ral~~~~~~~ 318 (568)
T COG0358 281 EHIKLLSRGKKKVILCFDGDRAGRKAAKRALQLVLPLD 318 (568)
T ss_pred HHHHHHHhcCCCEEEEeCChHHHHHHHHHHHHHhhhhc
Confidence 45666666778899999999999999999998655444
No 320
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.02 E-value=99 Score=31.26 Aligned_cols=32 Identities=13% Similarity=0.097 Sum_probs=17.3
Q ss_pred hhhhccCCCC--CCcccccccccccCCCCCcceEE
Q 046997 616 GIFFERWSGG--EDQQAAGEVVRQCGICQESNMVL 648 (807)
Q Consensus 616 g~fl~cs~~p--~~~~~~~~~~~~CP~C~g~~lv~ 648 (807)
..||-|.+.- .+...+......||+| |+.|..
T Consensus 111 ~~~y~C~~~~~r~sfdeA~~~~F~Cp~C-g~~L~~ 144 (176)
T COG1675 111 NNYYVCPNCHVKYSFDEAMELGFTCPKC-GEDLEE 144 (176)
T ss_pred CCceeCCCCCCcccHHHHHHhCCCCCCC-Cchhhh
Confidence 4577774311 0111222356889999 677763
No 321
>PF13730 HTH_36: Helix-turn-helix domain
Probab=22.00 E-value=44 Score=26.29 Aligned_cols=24 Identities=21% Similarity=0.300 Sum_probs=20.6
Q ss_pred HHhCCCCCccchHHHHHhhcccceE
Q 046997 511 MDKAGIGTDATMHDHIKKLLDRFYA 535 (807)
Q Consensus 511 Me~~GIGTpATra~iI~~L~~R~Yv 535 (807)
++..|++ ..|...+|+.|.++|||
T Consensus 32 a~~~g~s-~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 32 AKDLGVS-RRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHCcC-HHHHHHHHHHHHHCcCC
Confidence 4455999 89999999999999986
No 322
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=21.96 E-value=2.8e+02 Score=31.91 Aligned_cols=47 Identities=19% Similarity=0.293 Sum_probs=33.9
Q ss_pred hhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEec-ccCHHHH
Q 046997 113 RRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFS-ALIDREI 161 (807)
Q Consensus 113 ~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s-~lt~~~I 161 (807)
+.+..||+|.|.|..|..-+..+++.+...+. .++.+.+. ..++.++
T Consensus 298 r~~~~vvl~~D~D~aG~~aa~r~~~~l~~~g~--~v~v~~lp~gkDpdd~ 345 (415)
T TIGR01391 298 RYADEIILCFDGDKAGRKAALRAIELLLPLGI--NVKVIKLPGGKDPDEY 345 (415)
T ss_pred hhCCeEEEEeCCCHHHHHHHHHHHHHHHHcCC--eEEEEECCCCCCHHHH
Confidence 34568999999999999999999888776543 45555443 3444444
No 323
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=21.93 E-value=1.4e+02 Score=24.24 Aligned_cols=28 Identities=11% Similarity=0.285 Sum_probs=23.3
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCcee
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFIS 339 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~IS 339 (807)
.+.++.++++...+..+.++|-++|||.
T Consensus 22 ~~l~~~~~~~~~~vs~~i~~L~~~glv~ 49 (68)
T PF13463_consen 22 SDLAERLGISKSTVSRIIKKLEEKGLVE 49 (68)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 5667789999999999999999999994
No 324
>PF03215 Rad17: Rad17 cell cycle checkpoint protein
Probab=21.87 E-value=1.3e+02 Score=35.85 Aligned_cols=60 Identities=12% Similarity=0.290 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHhhc---CeEEEeecCCh-hhh------------HHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHH
Q 046997 102 KDIKKTLEEEARRC---QWLVLWLDCDR-EGE------------NIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAV 165 (807)
Q Consensus 102 ~~~~~~lk~~~~~~---d~IiiAtD~DR-EGE------------~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~ 165 (807)
...-+.|++.+... =.|||.||+|- +|. +++.+|++. ..|.++.||.+++..+++||
T Consensus 150 ~~f~~~L~~~l~~~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~-------~~i~~I~FNpIa~T~mkKaL 222 (519)
T PF03215_consen 150 SRFREALRQYLRSSRCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNH-------PGITRIKFNPIAPTFMKKAL 222 (519)
T ss_pred HHHHHHHHHHHHcCCCCCEEEEEecccccCCCCcccccchhhhhccCHHHHhC-------CCceEEEecCCCHHHHHHHH
Confidence 44446677766543 46889998753 443 344455532 24899999999999999999
Q ss_pred HcC
Q 046997 166 QNL 168 (807)
Q Consensus 166 ~nl 168 (807)
+..
T Consensus 223 ~rI 225 (519)
T PF03215_consen 223 KRI 225 (519)
T ss_pred HHH
Confidence 864
No 325
>PRK06683 hypothetical protein; Provisional
Probab=21.84 E-value=2.9e+02 Score=24.14 Aligned_cols=54 Identities=13% Similarity=0.185 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHH
Q 046997 102 KDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQ 166 (807)
Q Consensus 102 ~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~ 166 (807)
+...+.|++ .++..||+|.|++.. +-..|.+.|...+ .|+. ++. |..++=.|+-
T Consensus 17 ~~v~kaik~--gkaklViiA~Da~~~---~~~~i~~~~~~~~--Vpv~--~~~--t~~eLG~A~G 70 (82)
T PRK06683 17 KRTLEAIKN--GIVKEVVIAEDADMR---LTHVIIRTALQHN--IPIT--KVE--SVRKLGKVAG 70 (82)
T ss_pred HHHHHHHHc--CCeeEEEEECCCCHH---HHHHHHHHHHhcC--CCEE--EEC--CHHHHHHHhC
Confidence 444455544 578899999999876 7788888887654 3552 333 7788777764
No 326
>PF03882 KicB: KicB killing factor; InterPro: IPR005582 This family contains MukF, which are proteins involved in chromosome condensation, segregation and cell cycle progression. MukE (IPR007385 from INTERPRO) along with MukF interact with MukB (IPR007406 from INTERPRO) in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli []. The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC []. ScpA (IPR003768 from INTERPRO) and ScpB (IPR005234 from INTERPRO) have little sequence similarity to MukE or MukF, though they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. ; GO: 0005509 calcium ion binding, 0006260 DNA replication, 0007059 chromosome segregation, 0005737 cytoplasm; PDB: 1T98_B 3RPU_X 3EUH_B 3EUK_J 3EUJ_B.
Probab=21.81 E-value=5.8e+02 Score=29.12 Aligned_cols=92 Identities=14% Similarity=0.160 Sum_probs=55.8
Q ss_pred CCCHHHHHHHHHh------CCCCCccchHH-HHHhhcccceEEE------cCCceeeechhHHHHHhhccccCccccCch
Q 046997 501 LLSEADLLSCMDK------AGIGTDATMHD-HIKKLLDRFYAIK------DANTRFAPTNIGEALVMGYDDMGYELWKPN 567 (807)
Q Consensus 501 ~~Tea~Li~~Me~------~GIGTpATra~-iI~~L~~R~Yv~~------~~~~~l~pT~~G~~li~~l~~~~~~l~~p~ 567 (807)
-|.|++|+.+..- -.=-|++.||. .|+.|++.+++.+ .++..+.+|++|..+.+-|... -++.+-.
T Consensus 46 e~~E~~L~D~Fr~Vs~~f~q~~et~~~RANNAIndlv~QrlLsRf~se~~eg~~iYRLT~L~~gI~dyyirq-refs~lr 124 (440)
T PF03882_consen 46 ELSEGELHDAFRYVSKGFEQSAETSTVRANNAINDLVRQRLLSRFTSEFTEGASIYRLTPLGIGISDYYIRQ-REFSTLR 124 (440)
T ss_dssp SEEHHHHHHHHHHHHHHTT--STTHHHHHHHHHHHHHHTTSEEEEE-SSSTTSEEEEE-HHHHHHHHHHHS------HHH
T ss_pred ccchhHHHHHHHHHHHhhccCcchHHHHHHHHHHHHHHHHHHHHhccccccccceeeechhhhchhHHHHHH-HHHhHHH
Confidence 4789999998862 24458888887 6899999888865 3455689999999998876431 1333332
Q ss_pred -------hhHHHHHHHHHHHcCCCChHHHHHHHH
Q 046997 568 -------LRSMMESDMKEVSVGNKSKADVLANCL 594 (807)
Q Consensus 568 -------~Ta~~E~~L~~I~~G~~~~~~~l~~~~ 594 (807)
+.++++...+..++|. +-.....++.
T Consensus 125 LS~qls~va~El~~aa~aa~e~~-~e~~W~~~V~ 157 (440)
T PF03882_consen 125 LSIQLSIVAQELQRAADAAEEGG-DESHWRRNVF 157 (440)
T ss_dssp HHHHHHHHHHHHHHHHHHHHT---SHHHHHHHTH
T ss_pred HHHHHHHHHHHHHHHHHHHHhcC-ChHHHHHhhh
Confidence 2355666666666663 3333333333
No 327
>KOG1220 consensus Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism]
Probab=21.63 E-value=2e+02 Score=34.25 Aligned_cols=12 Identities=25% Similarity=0.382 Sum_probs=9.2
Q ss_pred CCCCCCcCCCCC
Q 046997 393 KAHPPIHPTKFS 404 (807)
Q Consensus 393 ~aH~aI~PT~~~ 404 (807)
.+|.|+.|+...
T Consensus 526 ~d~ka~lpv~~s 537 (607)
T KOG1220|consen 526 PDHKAVLPVSTS 537 (607)
T ss_pred CCCccccccccc
Confidence 479999998643
No 328
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=21.61 E-value=87 Score=25.26 Aligned_cols=49 Identities=20% Similarity=0.354 Sum_probs=0.0
Q ss_pred HHHHhCCCCCccchHHHHHhhcccceEEEcCCce---eeechhHHHHHhhcccc
Q 046997 509 SCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTR---FAPTNIGEALVMGYDDM 559 (807)
Q Consensus 509 ~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~---l~pT~~G~~li~~l~~~ 559 (807)
..++..|| +.+|-..+++.|.+.|+|....+.. +..|+ |..+++.+..+
T Consensus 25 ei~~~~~i-~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~~~~ 76 (78)
T cd00090 25 ELAERLGL-SQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALLESL 76 (78)
T ss_pred HHHHHHCc-CHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHHHHh
No 329
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=21.48 E-value=1.4e+02 Score=31.20 Aligned_cols=34 Identities=18% Similarity=0.388 Sum_probs=21.0
Q ss_pred CCceeeccCCCCC--CcceecCCCccccccccCccCCCCC
Q 046997 654 GNLMVGCLAFPQC--RNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 654 G~~f~gCs~yP~C--~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...++||++++.- +.++|+--. +-....||+||.
T Consensus 154 deRyVGCTGg~~EDeH~VvWFwLr----EGkpqRCpECGq 189 (268)
T PTZ00043 154 TERVVGCTGGTGEHEHVPLWFRCR----EGFLYRCGECDQ 189 (268)
T ss_pred CceEEeccCCCccCCceeEEEEec----CCCCccCCCCCc
Confidence 3446999997543 456665111 113567999985
No 330
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=21.46 E-value=68 Score=28.80 Aligned_cols=21 Identities=52% Similarity=0.656 Sum_probs=17.5
Q ss_pred HHHHHHhhcCceeccCCCCcc
Q 046997 327 KVAEDLYQAGFISYPRTETDS 347 (807)
Q Consensus 327 ~iaQ~LYE~g~ISYPRTds~~ 347 (807)
++.+.|-+.|.|-||||.|..
T Consensus 91 dvve~L~~~g~~Y~pR~gs~~ 111 (112)
T COG5204 91 DVVEDLEQHGRIYYPRTGSFT 111 (112)
T ss_pred HHHHHHHHhCccccCCCCccc
Confidence 467788889999999999853
No 331
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.41 E-value=47 Score=32.36 Aligned_cols=39 Identities=18% Similarity=0.356 Sum_probs=0.0
Q ss_pred CCCceeeccCCCCCCcceecCCCcccccccc-CccCCCCCCceE
Q 046997 653 DGNLMVGCLAFPQCRNAVWLPGSVSEAAVTT-NTCNSCTPGPVY 695 (807)
Q Consensus 653 ~G~~f~gCs~yP~C~~~~~~p~~~~~~~~t~-~~CP~Cg~~~l~ 695 (807)
.+..||-| |.|+..+...........++ -.||.|| +.+.
T Consensus 95 ~~~~~Y~C---p~C~~~y~~~ea~~~~d~~~~f~Cp~Cg-~~l~ 134 (147)
T smart00531 95 TNNAYYKC---PNCQSKYTFLEANQLLDMDGTFTCPRCG-EELE 134 (147)
T ss_pred cCCcEEEC---cCCCCEeeHHHHHHhcCCCCcEECCCCC-CEEE
No 332
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=21.40 E-value=93 Score=28.17 Aligned_cols=40 Identities=20% Similarity=0.179 Sum_probs=26.5
Q ss_pred HHHhhcccceEEEcC---CceeeechhHHHHHhhccccCcccc
Q 046997 525 HIKKLLDRFYAIKDA---NTRFAPTNIGEALVMGYDDMGYELW 564 (807)
Q Consensus 525 iI~~L~~R~Yv~~~~---~~~l~pT~~G~~li~~l~~~~~~l~ 564 (807)
+.+.|..||||...= --...+|+.|+..+..+..++.+++
T Consensus 43 ~mqSL~SrgyVke~faWrh~Yw~LT~eGIeyLR~yL~LP~eiv 85 (95)
T PF03501_consen 43 AMQSLKSRGYVKEQFAWRHYYWYLTNEGIEYLREYLHLPAEIV 85 (95)
T ss_dssp HHHHHHHCTSEEEEECTTEEEEEE-HHHHHHHHHHC-SSTT--
T ss_pred HHhcccchhhhcCeecceEEEEEEcchhHHHHHHHhCCChhhC
Confidence 345688999997531 1237899999999988877766554
No 333
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=21.28 E-value=1.6e+02 Score=27.98 Aligned_cols=38 Identities=8% Similarity=0.090 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccC
Q 046997 305 LSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPR 342 (807)
Q Consensus 305 f~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPR 342 (807)
-+..++...+....+++..-++.+..+|.++|+|+.-+
T Consensus 19 ~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k 56 (130)
T TIGR02698 19 TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEK 56 (130)
T ss_pred CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeec
Confidence 36688888888888999999999999999999998653
No 334
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=21.11 E-value=3.2e+02 Score=25.93 Aligned_cols=36 Identities=14% Similarity=0.309 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHh-CCCCCccchHHHHHhhcccceEEEc
Q 046997 502 LSEADLLSCMDK-AGIGTDATMHDHIKKLLDRFYAIKD 538 (807)
Q Consensus 502 ~Tea~Li~~Me~-~GIGTpATra~iI~~L~~R~Yv~~~ 538 (807)
.|-.+++..|.. .|+- .+|-.++|..|.++|||...
T Consensus 19 ~t~~eI~~~l~~~~~~~-~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 19 TTSRDIIRILAEKKDWS-DSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred CCHHHHHHHHhhccCCc-HHHHHHHHHHHHHCCceeee
Confidence 477888888854 3444 67899999999999999865
No 335
>PRK14281 chaperone protein DnaJ; Provisional
Probab=20.99 E-value=1.3e+02 Score=34.48 Aligned_cols=45 Identities=27% Similarity=0.649 Sum_probs=23.4
Q ss_pred ccccCCCCCcceEEEecC--CCCce--eeccCCCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSR--DGNLM--VGCLAFPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k--~G~~f--~gCs~yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...|+.|+|...+....+ .|.+. ..| +.|.-.= ......|+.|..
T Consensus 179 ~~~C~~C~G~G~~~~~~~~~~g~~~~~~~C---~~C~G~G---------~~~~~~C~~C~G 227 (397)
T PRK14281 179 TETCPTCHGSGEVRQASKTMFGQFVNITAC---PTCGGEG---------RVVKDRCPACYG 227 (397)
T ss_pred CccCCCCCCCcEEEEEEecccceEEEEEec---CCCccee---------eeeCCCCCCCCC
Confidence 457999976555543322 22211 235 4575321 112456999974
No 336
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=20.89 E-value=76 Score=30.87 Aligned_cols=13 Identities=15% Similarity=0.636 Sum_probs=9.2
Q ss_pred cccccCCCCCcceE
Q 046997 634 VVRQCGICQESNMV 647 (807)
Q Consensus 634 ~~~~CP~C~g~~lv 647 (807)
....||.|+ +.++
T Consensus 90 ~~sRC~~CN-~~L~ 102 (147)
T PF01927_consen 90 IFSRCPKCN-GPLR 102 (147)
T ss_pred CCCccCCCC-cEee
Confidence 357899995 5554
No 337
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=20.87 E-value=1.3e+02 Score=24.24 Aligned_cols=32 Identities=25% Similarity=0.371 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCcee
Q 046997 304 PLSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFIS 339 (807)
Q Consensus 304 pf~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~IS 339 (807)
|.+.++| +..+|++...+....+.|-+.|+|+
T Consensus 24 ~~t~~el----a~~l~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 24 PMTVSEL----AEELGISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp TBEHHHH----HHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHH----HHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 4445554 4457999999999999999999996
No 338
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=20.82 E-value=1e+02 Score=24.58 Aligned_cols=39 Identities=15% Similarity=0.239 Sum_probs=27.2
Q ss_pred CHHHHHHHHHhCCCCCccchHHHHHhhcccceEEEcCCceeee
Q 046997 503 SEADLLSCMDKAGIGTDATMHDHIKKLLDRFYAIKDANTRFAP 545 (807)
Q Consensus 503 Tea~Li~~Me~~GIGTpATra~iI~~L~~R~Yv~~~~~~~l~p 545 (807)
|+.+| ++..|| +..|-..+|..|.+.|||....++.+..
T Consensus 27 ~~~~l---a~~~~i-s~~~v~~~l~~L~~~G~i~~~~~~~~~l 65 (66)
T cd07377 27 SEREL---AEELGV-SRTTVREALRELEAEGLVERRPGRGTFV 65 (66)
T ss_pred CHHHH---HHHHCC-CHHHHHHHHHHHHHCCCEEecCCCeEEe
Confidence 45554 444588 4677889999999999998654433443
No 339
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=20.76 E-value=3.3e+02 Score=23.86 Aligned_cols=54 Identities=13% Similarity=0.177 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHhhcCeEEEeecCChhhhHHHHHHHHHhhhcCCCCeEEEEEecccCHHHHHHHHH
Q 046997 102 KDIKKTLEEEARRCQWLVLWLDCDREGENIAFEVIEVCRAVNCHLVLRRARFSALIDREIHQAVQ 166 (807)
Q Consensus 102 ~~~~~~lk~~~~~~d~IiiAtD~DREGE~I~~ei~~~~~~~~~~~~v~R~~~s~lt~~~I~~A~~ 166 (807)
....+.|++ .++..||+|.|++ +.+-..|.++|...+ .|+. ..-|..++=.|+-
T Consensus 14 ~~vlkaIk~--gkakLViiA~Da~---~~~~k~i~~~c~~~~--Vpv~----~~~t~~eLG~A~G 67 (82)
T PRK13601 14 KQTLKAITN--CNVLQVYIAKDAE---EHVTKKIKELCEEKS--IKIV----YIDTMKELGVMCG 67 (82)
T ss_pred HHHHHHHHc--CCeeEEEEeCCCC---HHHHHHHHHHHHhCC--CCEE----EeCCHHHHHHHHC
Confidence 444455544 5778999999999 588899999987654 3562 2236777777764
No 340
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=20.74 E-value=3.1e+02 Score=23.93 Aligned_cols=61 Identities=15% Similarity=0.139 Sum_probs=43.7
Q ss_pred HHHHhccCCCeEEEEEEeeeeeeCCCCCCCHHHHHHHHHHhcC--CCHHHHHHHHHHHhhcCcee
Q 046997 277 IYEMCVQEPTATVTKVRQQEKLKYPPYPLSTIELEKRASRYFR--MSSEHTMKVAEDLYQAGFIS 339 (807)
Q Consensus 277 ~~~~~~~~~~~~V~~v~~k~~~~~pP~pf~l~~Lq~~ask~~g--~s~~~tl~iaQ~LYE~g~IS 339 (807)
|++.+.......|.+- ....+.+|.=|.-+++-.=+-+.++ -|-.++..++|+|-+.|+|.
T Consensus 4 i~~~m~~~~~~~i~~r--~~~~~~~~~cF~G~e~VdWL~~~~~~~~~r~eAv~lgq~Ll~~g~I~ 66 (83)
T cd04449 4 IAEAMRDPSGIGIFDR--SWHKGLPSNCFIGSEAVSWLINNFEDVDTREEAVELGQELMNEGLIE 66 (83)
T ss_pred HHHHHhCCCCCceeec--hhcCccCCcceEhHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCEE
Confidence 4444443322234432 3457788888999998887777766 57889999999999999985
No 341
>PF10872 DUF2740: Protein of unknown function (DUF2740); InterPro: IPR022626 This entry is represented by Bacteriophage P22, Orf48. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins with unknown function has a highly conserved sequence. They are found in Enterobacteria and Enterobacteria phages.
Probab=20.62 E-value=76 Score=23.84 Aligned_cols=27 Identities=26% Similarity=0.409 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHHHHHH-HHHHhcCcccE
Q 046997 408 SRWSQDHYKLYELVVR-HFLACVSQPAV 434 (807)
Q Consensus 408 ~~Ls~~e~~vY~lI~r-rfla~~~~~a~ 434 (807)
..||+++-+|-.-|.| |||++|-.|..
T Consensus 3 kqlsp~qdk~hk~ilrdrflssfkqpgr 30 (48)
T PF10872_consen 3 KQLSPYQDKIHKHILRDRFLSSFKQPGR 30 (48)
T ss_pred cccCccHHHHHHHHHHHHHHHHhcCcch
Confidence 3688888888887765 89999987754
No 342
>cd03365 TOPRIM_TopoIIA TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofact
Probab=20.40 E-value=95 Score=29.36 Aligned_cols=25 Identities=24% Similarity=0.318 Sum_probs=21.7
Q ss_pred CeEEEeecCChhhhHHHHHHHHHhh
Q 046997 116 QWLVLWLDCDREGENIAFEVIEVCR 140 (807)
Q Consensus 116 d~IiiAtD~DREGE~I~~ei~~~~~ 140 (807)
+.|||.||+|..|-.|.-.++.+.-
T Consensus 78 ~kiiimtDaD~DG~hI~~Llltff~ 102 (120)
T cd03365 78 GRLMIMTDQDHDGSHIKGLLINFIH 102 (120)
T ss_pred CeEEEEeCCCCCccHHHHHHHHHHH
Confidence 5899999999999999888877643
No 343
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=20.19 E-value=1.3e+02 Score=25.08 Aligned_cols=28 Identities=29% Similarity=0.456 Sum_probs=22.5
Q ss_pred HHHHHhcCCCHHHHHHHHHHHhhcCcee
Q 046997 312 KRASRYFRMSSEHTMKVAEDLYQAGFIS 339 (807)
Q Consensus 312 ~~ask~~g~s~~~tl~iaQ~LYE~g~IS 339 (807)
.+.++.|++|++.+....+.|-.+|+|-
T Consensus 18 ~eLa~~~~~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 18 AELAREFGISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHCCTSCE
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 4556779999999999999999999985
No 344
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.11 E-value=43 Score=27.88 Aligned_cols=10 Identities=40% Similarity=0.896 Sum_probs=7.9
Q ss_pred ccCccCCCCC
Q 046997 682 TTNTCNSCTP 691 (807)
Q Consensus 682 t~~~CP~Cg~ 691 (807)
|...||.||.
T Consensus 27 TSq~C~~CG~ 36 (69)
T PF07282_consen 27 TSQTCPRCGH 36 (69)
T ss_pred CccCccCccc
Confidence 5677999984
No 345
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=20.08 E-value=81 Score=29.13 Aligned_cols=43 Identities=9% Similarity=0.125 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHhcCCCHHHHHHHHHHHhhcCceeccCCCCcc
Q 046997 305 LSTIELEKRASRYFRMSSEHTMKVAEDLYQAGFISYPRTETDS 347 (807)
Q Consensus 305 f~l~~Lq~~ask~~g~s~~~tl~iaQ~LYE~g~ISYPRTds~~ 347 (807)
-+..++...+....+++..-++.+..+|.++|+|+.-+..-.+
T Consensus 18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~gr~~ 60 (115)
T PF03965_consen 18 ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIGRAY 60 (115)
T ss_dssp EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEETTCE
T ss_pred CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecCCce
Confidence 4568888888888899999999999999999999997765433
No 346
>PLN02195 cellulose synthase A
Probab=20.05 E-value=57 Score=41.05 Aligned_cols=49 Identities=18% Similarity=0.527 Sum_probs=32.4
Q ss_pred ccccCCCCCcceEEEecCCCCceeeccC--CCCCCcceecCCCccccccccCccCCCCC
Q 046997 635 VRQCGICQESNMVLKKSRDGNLMVGCLA--FPQCRNAVWLPGSVSEAAVTTNTCNSCTP 691 (807)
Q Consensus 635 ~~~CP~C~g~~lv~r~~k~G~~f~gCs~--yP~C~~~~~~p~~~~~~~~t~~~CP~Cg~ 691 (807)
...|-.| |..+-+. ..|..|++|.- ||-|+-.+-.++. .-...||+|+.
T Consensus 6 ~~~c~~c-gd~~~~~--~~g~~fvaC~eC~~pvCrpCyeyer~-----eg~q~CpqCkt 56 (977)
T PLN02195 6 APICATC-GEEVGVD--SNGEAFVACHECSYPLCKACLEYEIK-----EGRKVCLRCGG 56 (977)
T ss_pred Cccceec-ccccCcC--CCCCeEEEeccCCCccccchhhhhhh-----cCCccCCccCC
Confidence 4579999 5555443 46778899953 5777766655432 23567999984
Done!