Query psy8714
Match_columns 562
No_of_seqs 201 out of 1554
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 17:23:27 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8714.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8714hhsearch_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 3E-131 6E-136 1118.9 52.4 532 6-562 1-540 (740)
2 PRK08173 DNA topoisomerase III 100.0 6E-131 1E-135 1126.1 52.9 530 6-562 3-580 (862)
3 PRK05776 DNA topoisomerase I; 100.0 3E-130 6E-135 1097.8 55.7 534 6-562 2-547 (670)
4 PRK14973 DNA topoisomerase I; 100.0 1E-129 2E-134 1117.2 53.3 532 6-562 1-539 (936)
5 TIGR01057 topA_arch DNA topois 100.0 5E-129 1E-133 1085.6 54.0 531 10-562 1-540 (618)
6 PRK07219 DNA topoisomerase I; 100.0 4E-129 8E-134 1114.6 53.1 540 6-562 1-549 (822)
7 PRK14724 DNA topoisomerase III 100.0 2E-128 4E-133 1116.7 51.5 540 6-562 2-599 (987)
8 COG0550 TopA Topoisomerase IA 100.0 4E-128 9E-133 1053.5 48.5 511 6-562 1-526 (570)
9 TIGR01056 topB DNA topoisomera 100.0 2E-127 4E-132 1074.3 50.8 530 6-562 1-571 (660)
10 PRK07726 DNA topoisomerase III 100.0 5E-127 1E-131 1074.3 52.3 528 6-562 1-568 (658)
11 TIGR01051 topA_bact DNA topois 100.0 7E-123 1E-127 1032.8 47.6 501 8-562 1-534 (610)
12 PRK05582 DNA topoisomerase I; 100.0 5E-121 1E-125 1026.5 47.9 499 6-562 3-528 (650)
13 PRK08780 DNA topoisomerase I; 100.0 2E-120 5E-125 1032.3 50.8 507 6-562 3-548 (780)
14 PRK07561 DNA topoisomerase I s 100.0 4E-120 9E-125 1043.0 49.6 506 6-562 2-541 (859)
15 PRK06599 DNA topoisomerase I; 100.0 1E-119 2E-124 1018.5 51.7 507 6-562 3-542 (675)
16 PRK06319 DNA topoisomerase I/S 100.0 2E-119 5E-124 1034.2 49.4 502 6-562 3-552 (860)
17 PTZ00407 DNA topoisomerase IA; 100.0 4E-112 8E-117 947.1 45.4 531 5-562 9-653 (805)
18 PRK09401 reverse gyrase; Revie 100.0 5E-112 1E-116 994.9 48.6 504 6-562 602-1148(1176)
19 KOG1956|consensus 100.0 3E-112 6E-117 894.4 36.7 553 6-562 2-562 (758)
20 TIGR01054 rgy reverse gyrase. 100.0 2E-109 5E-114 973.5 50.5 503 6-562 602-1147(1171)
21 PF01131 Topoisom_bac: DNA top 100.0 2.8E-95 6E-100 777.8 28.1 380 166-562 2-388 (403)
22 cd00186 TOP1Ac DNA Topoisomera 100.0 5.9E-94 1.3E-98 761.4 34.3 348 169-562 2-356 (381)
23 PRK14701 reverse gyrase; Provi 100.0 3.4E-91 7.3E-96 833.8 49.0 289 6-336 581-897 (1638)
24 COG1110 Reverse gyrase [DNA re 100.0 1.1E-77 2.4E-82 662.0 37.2 499 7-562 619-1162(1187)
25 KOG1957|consensus 100.0 4.1E-74 9E-79 584.7 18.9 485 8-562 5-511 (555)
26 smart00437 TOP1Ac Bacterial DN 100.0 4.4E-68 9.6E-73 534.1 24.4 250 285-538 2-259 (259)
27 cd03362 TOPRIM_TopoIA_TopoIII 100.0 1.8E-33 3.9E-38 261.7 11.4 147 6-163 1-151 (151)
28 cd01028 TOPRIM_TopoIA TOPRIM_T 100.0 7.3E-33 1.6E-37 255.1 12.3 142 6-163 1-142 (142)
29 smart00436 TOP1Bc Bacterial DN 100.0 1.6E-32 3.4E-37 231.0 6.7 89 143-238 1-89 (89)
30 cd03361 TOPRIM_TopoIA_RevGyr T 100.0 3.5E-29 7.5E-34 236.8 12.3 143 7-163 2-170 (170)
31 cd03363 TOPRIM_TopoIA_TopoI TO 100.0 3.8E-29 8.2E-34 224.2 10.4 123 6-163 1-123 (123)
32 PF01751 Toprim: Toprim domain 99.8 6E-21 1.3E-25 165.3 3.5 98 7-151 1-100 (100)
33 cd01025 TOPRIM_recR TOPRIM_rec 97.9 4.1E-05 8.8E-10 67.3 8.5 38 106-148 56-93 (112)
34 smart00493 TOPRIM topoisomeras 97.9 2.1E-05 4.6E-10 64.0 5.5 72 6-132 1-72 (76)
35 PRK00076 recR recombination pr 96.6 0.019 4.1E-07 55.6 10.4 55 105-164 132-194 (196)
36 cd01027 TOPRIM_RNase_M5_like T 96.1 0.0079 1.7E-07 50.0 4.3 36 107-147 45-80 (81)
37 cd00188 TOPRIM Topoisomerase-p 95.8 0.041 8.9E-07 43.9 7.3 36 107-147 47-82 (83)
38 smart00437 TOP1Ac Bacterial DN 92.3 0.38 8.2E-06 48.9 7.1 109 219-330 126-244 (259)
39 PF13662 Toprim_4: Toprim doma 92.1 0.095 2.1E-06 43.2 2.1 35 107-146 46-80 (81)
40 PRK13844 recombination protein 91.5 0.62 1.3E-05 45.3 7.2 53 106-164 138-198 (200)
41 TIGR01057 topA_arch DNA topois 91.0 0.51 1.1E-05 54.0 7.2 131 403-542 196-331 (618)
42 PF01131 Topoisom_bac: DNA top 91.0 0.55 1.2E-05 50.8 7.1 114 217-332 228-351 (403)
43 TIGR00615 recR recombination p 90.5 0.46 1E-05 46.0 5.3 52 106-162 134-193 (195)
44 COG1658 Small primase-like pro 89.6 0.45 9.7E-06 42.9 4.1 68 96-164 45-120 (127)
45 TIGR00334 5S_RNA_mat_M5 ribonu 88.9 1.1 2.5E-05 42.4 6.4 69 96-165 37-110 (174)
46 COG4026 Uncharacterized protei 88.8 1.1 2.4E-05 43.7 6.3 56 102-162 53-114 (290)
47 PRK04031 DNA primase; Provisio 88.4 0.6 1.3E-05 49.9 4.7 70 97-170 201-270 (408)
48 PRK07220 DNA topoisomerase I; 88.3 1.4 3E-05 51.5 8.0 75 467-542 257-333 (740)
49 COG0353 RecR Recombinational D 86.0 1.5 3.2E-05 42.3 5.4 51 108-163 137-195 (198)
50 COG0550 TopA Topoisomerase IA 86.0 2 4.4E-05 48.5 7.4 127 406-536 179-311 (570)
51 cd00186 TOP1Ac DNA Topoisomera 85.8 1.7 3.6E-05 46.8 6.5 110 219-330 199-317 (381)
52 TIGR01051 topA_bact DNA topois 85.5 2.6 5.6E-05 48.2 8.1 118 220-342 372-505 (610)
53 PRK05776 DNA topoisomerase I; 85.5 2.2 4.8E-05 49.3 7.6 109 405-522 201-312 (670)
54 PRK07219 DNA topoisomerase I; 85.4 1.9 4.1E-05 51.1 7.1 119 219-342 394-520 (822)
55 PF14947 HTH_45: Winged helix- 84.4 0.87 1.9E-05 37.3 2.7 39 506-545 34-72 (77)
56 smart00529 HTH_DTXR Helix-turn 84.3 1.7 3.7E-05 36.6 4.6 44 498-542 7-50 (96)
57 COG3432 Predicted transcriptio 82.4 1.3 2.9E-05 37.8 3.1 37 509-545 49-88 (95)
58 TIGR01056 topB DNA topoisomera 81.6 4.2 9E-05 47.0 7.7 128 402-534 200-332 (660)
59 PRK08173 DNA topoisomerase III 81.2 3.6 7.7E-05 48.9 7.2 110 219-330 406-540 (862)
60 PF08259 Periviscerokin: Periv 80.8 0.69 1.5E-05 23.4 0.5 9 326-334 3-11 (11)
61 PRK11512 DNA-binding transcrip 80.6 2.1 4.5E-05 39.1 4.1 50 488-541 55-110 (144)
62 PRK14973 DNA topoisomerase I; 80.3 3.5 7.5E-05 49.4 6.7 110 219-330 385-502 (936)
63 PRK05582 DNA topoisomerase I; 80.3 4.8 0.0001 46.4 7.7 119 400-523 168-298 (650)
64 PF07848 PaaX: PaaX-like prote 80.3 1.6 3.4E-05 35.3 2.7 49 486-535 19-70 (70)
65 TIGR01889 Staph_reg_Sar staphy 79.6 3.9 8.4E-05 35.6 5.2 55 484-542 40-100 (109)
66 TIGR00373 conserved hypothetic 78.0 2 4.4E-05 40.3 3.1 35 296-334 29-63 (158)
67 PRK03573 transcriptional regul 77.6 2.6 5.7E-05 38.4 3.7 51 488-542 47-103 (144)
68 PRK04017 hypothetical protein; 77.1 2.4 5.3E-05 38.5 3.2 29 105-133 63-91 (132)
69 PRK07726 DNA topoisomerase III 76.8 5.7 0.00012 45.9 6.9 112 218-330 394-532 (658)
70 PRK07561 DNA topoisomerase I s 76.5 7.6 0.00016 46.3 8.0 117 402-522 183-305 (859)
71 PRK06599 DNA topoisomerase I; 76.2 7.1 0.00015 45.3 7.5 119 219-342 379-513 (675)
72 PRK06319 DNA topoisomerase I/S 75.4 13 0.00028 44.3 9.6 110 219-330 389-513 (860)
73 PRK03902 manganese transport t 75.0 3.5 7.5E-05 37.7 3.8 39 500-539 32-70 (142)
74 PF02002 TFIIE_alpha: TFIIE al 74.7 2.8 6.1E-05 36.2 2.9 32 303-334 31-62 (105)
75 PRK08780 DNA topoisomerase I; 73.5 11 0.00023 44.5 8.2 119 399-522 171-307 (780)
76 TIGR02277 PaaX_trns_reg phenyl 73.1 5.8 0.00013 40.8 5.2 54 487-541 17-73 (280)
77 PRK06266 transcription initiat 71.5 4 8.6E-05 39.1 3.3 29 305-333 42-70 (178)
78 PRK13777 transcriptional regul 71.2 4.5 9.7E-05 39.0 3.7 51 488-542 60-116 (185)
79 TIGR02647 DNA conserved hypoth 70.7 2.9 6.2E-05 34.0 1.8 44 296-342 17-60 (77)
80 PRK14165 winged helix-turn-hel 70.1 8.8 0.00019 38.0 5.5 53 485-541 19-74 (217)
81 PF13601 HTH_34: Winged helix 70.0 3.2 6.9E-05 34.3 2.0 44 498-542 22-72 (80)
82 TIGR02337 HpaR homoprotocatech 69.3 6 0.00013 34.7 3.8 41 501-542 53-99 (118)
83 PRK14724 DNA topoisomerase III 69.0 12 0.00026 45.2 7.4 112 218-330 415-559 (987)
84 COG1321 TroR Mn-dependent tran 67.1 6.3 0.00014 36.8 3.6 36 504-539 37-72 (154)
85 PRK10870 transcriptional repre 66.1 6 0.00013 37.7 3.3 54 485-542 69-128 (176)
86 COG1846 MarR Transcriptional r 66.0 5.6 0.00012 34.2 3.0 39 504-542 49-93 (126)
87 COG1675 TFA1 Transcription ini 65.2 6.2 0.00013 37.7 3.2 32 303-334 36-67 (176)
88 smart00347 HTH_MARR helix_turn 61.4 11 0.00023 31.3 3.8 51 488-542 25-81 (101)
89 PF13463 HTH_27: Winged helix 61.0 6.4 0.00014 30.6 2.1 31 505-535 32-68 (68)
90 PF02044 Bombesin: Bombesin-li 60.9 1.7 3.6E-05 23.5 -0.8 8 55-62 4-11 (14)
91 TIGR01054 rgy reverse gyrase. 60.5 20 0.00044 44.2 7.2 53 470-523 867-920 (1171)
92 PRK09416 lstR lineage-specific 59.7 23 0.00049 32.4 5.6 55 489-543 57-119 (135)
93 PRK14701 reverse gyrase; Provi 59.5 15 0.00033 46.7 6.0 65 469-536 838-903 (1638)
94 PF06969 HemN_C: HemN C-termin 58.7 7 0.00015 30.5 2.0 36 500-536 30-65 (66)
95 PF01325 Fe_dep_repress: Iron 58.5 13 0.00028 28.9 3.3 30 304-333 27-56 (60)
96 COG1321 TroR Mn-dependent tran 58.5 12 0.00026 35.0 3.7 39 303-341 28-66 (154)
97 PF13412 HTH_24: Winged helix- 58.0 14 0.0003 26.8 3.4 29 302-330 20-48 (48)
98 PF01047 MarR: MarR family; I 57.3 14 0.0003 27.9 3.4 32 303-334 21-52 (59)
99 PF09851 SHOCT: Short C-termin 54.5 8.4 0.00018 25.8 1.5 17 314-330 2-18 (31)
100 PF09114 MotA_activ: Transcrip 53.1 14 0.0003 31.1 2.9 29 511-540 52-80 (96)
101 smart00419 HTH_CRP helix_turn_ 52.3 23 0.00049 25.2 3.7 31 302-332 11-41 (48)
102 PTZ00407 DNA topoisomerase IA; 50.2 24 0.00052 41.6 5.2 62 278-342 561-624 (805)
103 PRK09401 reverse gyrase; Revie 49.8 32 0.00069 42.6 6.5 52 471-523 868-920 (1176)
104 PRK11050 manganese transport r 49.4 18 0.00039 33.5 3.4 41 501-542 62-102 (152)
105 PF01022 HTH_5: Bacterial regu 49.2 24 0.00051 25.7 3.3 27 305-331 21-47 (47)
106 COG1568 Predicted methyltransf 49.1 19 0.00041 36.9 3.7 34 509-543 52-85 (354)
107 cd07377 WHTH_GntR Winged helix 48.8 26 0.00056 26.6 3.8 29 304-332 30-58 (66)
108 cd03364 TOPRIM_DnaG_primases T 47.4 40 0.00086 27.2 4.8 27 107-133 43-69 (79)
109 smart00418 HTH_ARSR helix_turn 45.5 30 0.00065 25.7 3.7 29 304-332 15-43 (66)
110 cd01029 TOPRIM_primases TOPRIM 44.5 28 0.00061 27.9 3.5 26 107-132 43-68 (79)
111 COG1110 Reverse gyrase [DNA re 43.6 27 0.00058 41.8 4.3 71 468-539 878-949 (1187)
112 PF03962 Mnd1: Mnd1 family; I 42.0 25 0.00053 34.0 3.2 38 293-330 9-46 (188)
113 cd00092 HTH_CRP helix_turn_hel 41.5 41 0.0009 25.7 3.9 31 303-333 29-59 (67)
114 PF02037 SAP: SAP domain; Int 40.8 39 0.00084 23.2 3.2 31 487-517 3-33 (35)
115 PF04182 B-block_TFIIIC: B-blo 40.4 28 0.0006 28.2 2.8 30 301-330 20-49 (75)
116 PF01978 TrmB: Sugar-specific 40.3 37 0.00081 26.5 3.5 29 303-331 26-54 (68)
117 PF10281 Ish1: Putative stress 39.4 48 0.001 23.1 3.5 30 488-517 4-36 (38)
118 PF10087 DUF2325: Uncharacteri 38.8 87 0.0019 26.4 5.8 56 99-163 41-96 (97)
119 cd00092 HTH_CRP helix_turn_hel 38.5 56 0.0012 24.9 4.2 43 487-533 25-67 (67)
120 cd03365 TOPRIM_TopoIIA TOPRIM_ 38.2 32 0.0007 30.8 3.0 26 106-131 76-101 (120)
121 PF13730 HTH_36: Helix-turn-he 35.9 46 0.001 24.7 3.3 25 305-329 31-55 (55)
122 cd03366 TOPRIM_TopoIIA_GyrB TO 35.9 39 0.00084 30.0 3.1 27 106-132 71-97 (114)
123 PF14277 DUF4364: Domain of un 35.2 93 0.002 29.3 5.9 60 485-544 13-76 (163)
124 cd01030 TOPRIM_TopoIIA_like TO 35.0 38 0.00083 30.1 3.0 27 106-132 72-98 (115)
125 PF09339 HTH_IclR: IclR helix- 35.0 56 0.0012 24.2 3.5 33 295-331 18-50 (52)
126 COG4840 Uncharacterized protei 34.9 59 0.0013 25.8 3.6 28 297-324 40-67 (71)
127 smart00345 HTH_GNTR helix_turn 34.8 62 0.0013 23.8 3.9 29 303-331 24-52 (60)
128 PF09382 RQC: RQC domain; Int 34.7 67 0.0015 27.3 4.5 55 487-541 19-96 (106)
129 TIGR02719 repress_PhaQ poly-be 34.3 1.1E+02 0.0023 28.1 5.9 52 490-541 40-101 (138)
130 PRK14719 bifunctional RNAse/5- 34.3 42 0.0009 35.9 3.7 38 95-134 57-94 (360)
131 cd04449 DEP_DEPDC5-like DEP (D 34.2 1.4E+02 0.0031 24.6 6.2 62 267-330 3-66 (83)
132 PF03444 HrcA_DNA-bdg: Winged 34.0 64 0.0014 26.6 3.9 36 308-343 32-68 (78)
133 PF01726 LexA_DNA_bind: LexA D 33.6 46 0.00099 26.3 3.0 32 495-526 30-61 (65)
134 TIGR03433 padR_acidobact trans 33.4 69 0.0015 27.3 4.4 53 489-542 19-84 (100)
135 COG1695 Predicted transcriptio 33.2 84 0.0018 28.2 5.1 53 490-542 25-89 (138)
136 PRK06683 hypothetical protein; 33.2 1.5E+02 0.0031 24.6 6.0 55 94-162 17-71 (82)
137 PF10007 DUF2250: Uncharacteri 33.1 56 0.0012 27.8 3.6 28 304-331 26-53 (92)
138 COG4742 Predicted transcriptio 33.1 44 0.00096 34.0 3.5 37 505-542 40-76 (260)
139 PRK13601 putative L7Ae-like ri 33.0 1.5E+02 0.0031 24.7 6.0 53 95-161 15-67 (82)
140 PF01726 LexA_DNA_bind: LexA D 32.5 60 0.0013 25.6 3.5 30 303-332 29-59 (65)
141 smart00420 HTH_DEOR helix_turn 31.6 70 0.0015 22.8 3.6 35 295-333 14-48 (53)
142 PRK03902 manganese transport t 31.0 55 0.0012 29.7 3.5 40 303-342 26-65 (142)
143 smart00346 HTH_ICLR helix_turn 30.9 1.3E+02 0.0028 24.5 5.5 51 487-541 20-71 (91)
144 PF00325 Crp: Bacterial regula 30.9 77 0.0017 21.5 3.2 27 303-329 6-32 (32)
145 PRK13602 putative ribosomal pr 30.5 1.9E+02 0.004 23.9 6.3 54 95-162 18-71 (82)
146 PRK07714 hypothetical protein; 30.0 1.3E+02 0.0029 25.7 5.5 73 95-181 25-97 (100)
147 PF13545 HTH_Crp_2: Crp-like h 30.0 73 0.0016 25.1 3.7 38 293-334 26-63 (76)
148 TIGR01889 Staph_reg_Sar staphy 29.6 65 0.0014 27.8 3.6 32 302-333 46-77 (109)
149 PRK08208 coproporphyrinogen II 29.2 44 0.00095 36.5 2.9 45 508-556 378-422 (430)
150 PF03965 Penicillinase_R: Peni 28.5 51 0.0011 28.8 2.8 41 296-336 18-58 (115)
151 PRK13600 putative ribosomal pr 28.5 92 0.002 26.1 4.1 52 95-160 20-71 (84)
152 cd00090 HTH_ARSR Arsenical Res 28.5 70 0.0015 24.3 3.3 45 497-543 27-74 (78)
153 smart00550 Zalpha Z-DNA-bindin 28.4 84 0.0018 24.8 3.7 34 295-332 22-55 (68)
154 PF13155 Toprim_2: Toprim-like 28.4 70 0.0015 26.5 3.5 26 108-133 48-73 (96)
155 PF12802 MarR_2: MarR family; 28.0 77 0.0017 23.8 3.4 29 302-330 24-52 (62)
156 smart00540 LEM in nuclear memb 27.9 76 0.0016 23.2 3.0 32 486-517 4-39 (44)
157 PF02082 Rrf2: Transcriptional 27.5 69 0.0015 26.2 3.2 34 296-333 26-59 (83)
158 cd07377 WHTH_GntR Winged helix 27.0 71 0.0015 24.0 3.0 40 489-532 27-66 (66)
159 PF05402 PqqD: Coenzyme PQQ sy 27.0 1.2E+02 0.0025 23.5 4.3 36 295-330 29-68 (68)
160 PRK07283 hypothetical protein; 26.8 1.1E+02 0.0024 26.1 4.5 72 95-181 25-96 (98)
161 PF13463 HTH_27: Winged helix 26.3 97 0.0021 23.7 3.7 28 303-330 22-49 (68)
162 smart00513 SAP Putative DNA-bi 26.0 1.3E+02 0.0028 20.4 3.8 31 487-517 3-33 (35)
163 TIGR02698 CopY_TcrY copper tra 24.7 1.3E+02 0.0028 27.1 4.7 38 296-333 19-56 (130)
164 PF00376 MerR: MerR family reg 24.4 60 0.0013 22.7 1.9 31 303-338 3-35 (38)
165 PRK09391 fixK transcriptional 24.4 88 0.0019 30.7 3.9 32 302-333 182-213 (230)
166 PF01043 SecA_PP_bind: SecA pr 24.3 1.6E+02 0.0034 26.1 5.0 45 510-554 13-58 (113)
167 TIGR01884 cas_HTH CRISPR locus 23.9 45 0.00098 32.3 1.7 34 501-535 168-203 (203)
168 PF13362 Toprim_3: Toprim doma 23.6 2.2E+02 0.0047 23.7 5.7 27 107-133 41-69 (96)
169 TIGR01391 dnaG DNA primase, ca 22.9 2.9E+02 0.0063 30.0 7.9 47 106-157 299-346 (415)
170 TIGR03697 NtcA_cyano global ni 22.6 1E+02 0.0023 28.7 3.9 32 302-333 146-177 (193)
171 PRK08599 coproporphyrinogen II 22.5 74 0.0016 33.9 3.1 37 505-542 333-369 (377)
172 COG5204 SPT4 Transcription elo 22.3 65 0.0014 27.5 2.0 21 318-338 91-111 (112)
173 PF12840 HTH_20: Helix-turn-he 22.1 1.1E+02 0.0024 23.3 3.2 33 294-330 23-55 (61)
174 PRK12789 flgI flagellar basal 21.9 1.4E+02 0.0031 31.8 5.0 32 297-329 329-360 (367)
175 PF09012 FeoC: FeoC like trans 21.5 1.2E+02 0.0026 23.9 3.4 27 304-330 19-45 (69)
176 PF14178 YppF: YppF-like prote 21.4 1.5E+02 0.0033 23.2 3.7 34 297-330 2-38 (60)
177 PF10872 DUF2740: Protein of u 21.3 75 0.0016 22.6 1.9 27 394-420 3-30 (48)
178 PRK05799 coproporphyrinogen II 20.8 1.1E+02 0.0023 32.7 3.9 34 508-542 335-368 (374)
179 PF01638 HxlR: HxlR-like helix 20.5 83 0.0018 26.2 2.4 41 504-544 32-78 (90)
180 PF09105 SelB-wing_1: Elongati 20.5 1.2E+02 0.0027 22.5 2.9 34 304-337 22-55 (61)
181 PF09821 AAA_assoc_C: C-termin 20.4 99 0.0021 27.6 3.0 31 510-541 16-46 (120)
182 PRK13918 CRP/FNR family transc 20.3 1.2E+02 0.0026 28.7 3.8 32 302-333 152-183 (202)
183 PRK09057 coproporphyrinogen II 20.3 1.1E+02 0.0024 32.7 4.0 33 509-542 341-374 (380)
184 PF09857 DUF2084: Uncharacteri 20.1 1.3E+02 0.0027 25.2 3.2 32 510-541 49-80 (85)
185 COG1497 Predicted transcriptio 20.1 1.1E+02 0.0024 30.8 3.5 39 500-539 35-73 (260)
No 1
>PRK07220 DNA topoisomerase I; Validated
Probab=100.00 E-value=2.8e-131 Score=1118.92 Aligned_cols=532 Identities=30% Similarity=0.522 Sum_probs=469.0
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCC-------CceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNG-------ACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPL 78 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~-------~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~ 78 (562)
|+|||||| ||+|+.||+++|..+ .+++|+|. .+|+ .|+|+||.|||++|++|++|+.|..+++.
T Consensus 1 m~LiIaEK-----Ps~Ak~Ia~~Lg~~~~~~~~~~g~~~y~~~--~~g~--~~~v~~~~GHl~~l~~P~~y~~w~~~~~~ 71 (740)
T PRK07220 1 MHLIITEK-----NIAARRIAQILAPKKPKKTRVSGVDVYRYE--DNGD--DTVVVGLSGHIVNIDFPKEYNNWQKVDAR 71 (740)
T ss_pred CeEEEEeC-----HHHHHHHHHHhCCCCccccccCCcceeEEe--cCCC--CEEEEEeCcccccCCCCccccccCCCChh
Confidence 57999999 999999999998321 22234332 1354 48899999999999999999889887776
Q ss_pred CCCCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHH
Q psy8714 79 ELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKA 158 (562)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~ 158 (562)
.+|+.+.... ..+.++++.|++++++||+||||||||||||+|||||+++++.. +++++++|+|||++|+++|++
T Consensus 72 ~l~~~~~~~~--~~~~~~~~~lk~l~k~ad~viiAtD~DREGE~I~~~i~~~l~~~---~~~~~~~R~~fs~iT~~~I~~ 146 (740)
T PRK07220 72 DLIDAEIITT--PTQKKIVTALKKLGKEADRVTIATDYDREGELIGVEALNIIKKV---NPDIKFDRVRYSAITKKEIER 146 (740)
T ss_pred HcCCcceEec--CCHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHHHhc---CCCCceEEEEEccCCHHHHHH
Confidence 6664332211 23457889999999999999999999999999999999999753 345799999999999999999
Q ss_pred HHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEE
Q psy8714 159 AMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWL 238 (562)
Q Consensus 159 A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~ 238 (562)
||+||+++|.++++||+|||++||||||||||++|+.+++. + ++++|+||||||||+|||+||+||+||+|++||+
T Consensus 147 A~~n~~~~d~~l~~A~~aR~~~D~lvG~nlSr~~t~~~~~~-~---~~~lS~GRVQtptL~lIv~Re~eI~~F~p~~y~~ 222 (740)
T PRK07220 147 AFSNPVEVDFNLADAGHSRQVIDLVWGAALTRYISLAAGRL-G---KMFLSVGRVQSPTLALIVDREKEREAFVPTPYWE 222 (740)
T ss_pred HHhCCCCCChhHHHHHHHHHHHHHHhchhcCHHHHHHHHhh-C---CccccccccchhhhHHHHhhHHHHHhCCCCccEE
Confidence 99999999999999999999999999999999999877532 1 2369999999999999999999999999999999
Q ss_pred EEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHH
Q psy8714 239 LDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQ 318 (562)
Q Consensus 239 i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~ 318 (562)
|.+.+..++..|.+.|..++++|+++|+++++.+ + +.++|++|+.++++.+||+||||++||++||+ +||||++||+
T Consensus 223 i~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~-~-~~~~V~~v~~~~~~~~pP~pf~ts~Lq~~a~~-~g~s~~~tm~ 299 (740)
T PRK07220 223 IYATLENNGETFVAQHSTRRFWEKEEADRVFEKL-G-KTAEVTEVEKGTKTDKPPTPFNTTEFISAANS-IGFSAANAMR 299 (740)
T ss_pred EEEEEEcCCceEEEEeccCcCCCHHHHHHHHHhh-C-CCeEEEEEeeeeEecCCCCCcCHHHHHHHHHH-cCCCHHHHHH
Confidence 9999987778899999888999999999999998 3 47999999999999999999999999999995 8999999999
Q ss_pred HHHHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCC-CCCCCCCCCCccCCCcccCCCC
Q psy8714 319 IAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRK-GKDVGDHPPITPTKLATRTQLD 397 (562)
Q Consensus 319 iaQ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~H~AI~PT~~~~~~~L~ 397 (562)
+||+|||+||||||||||++||+++++..+++.+.. ..|+.++..++..+...|.. .++++||||||||...+.+.|+
T Consensus 300 iaQ~LYe~g~ITYPRTDs~~l~~~~~~~~~i~~l~~-~~~~~~~~~~l~~~~~~~~~~~~~~~~H~aI~PT~~~~~~~L~ 378 (740)
T PRK07220 300 IAESLYTNGYISYPRTDNTVYPESLDLREQIEIFAE-GPFGEYAQKLLEKGELVPTRGKKETTDHPPIYPASLAKKSELK 378 (740)
T ss_pred HHHHHHhCCceeecccCCeecCchhhHHHHHHHHHH-HHHHHHHHHhcccCCccCCCCCCCCCCCCCCCcccCCCcccCC
Confidence 999999999999999999999998888888887754 24666665555433223333 3456899999999986556899
Q ss_pred HHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEE
Q psy8714 398 GDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKM 477 (562)
Q Consensus 398 ~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i 477 (562)
++|++||+||||||||+||+||+|++|+|.++++++.|+++|++++++||++||+++..++..||.+++||.+.+.++.+
T Consensus 379 ~de~~lY~LI~rRfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~vy~~~~~~~~~LP~l~~Ge~~~~~~~~~ 458 (740)
T PRK07220 379 EDEWKVYELVVRRFFATFAGPAEWETMKLRFDIGGEEFRANGSRLTEPGWRWYYPYNAPEDRLLPELSEGEELKVKKKEM 458 (740)
T ss_pred HHHHHHHHHHHHHHHHHhCchheEEEEEEEEEECCeEEEEeeeEEeeCChHHHcCccccccccCCCCCCCCEeeeeeeee
Confidence 99999999999999999999999999999999999999999999999999999976544456799999999999999999
Q ss_pred eeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHH
Q psy8714 478 VERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSA 557 (562)
Q Consensus 478 ~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~ 557 (562)
.+++|+||+||||++||++||+.|||||||||+||++|++||||+ |+.|+||++|+.|+++|....+.|++|+|||.
T Consensus 459 ~ek~TkPP~ryTea~Li~~Me~~GIGTpATra~iI~~L~~R~Yi~---~k~l~pT~~G~~v~~~l~~~~~~i~~~~~Ta~ 535 (740)
T PRK07220 459 LDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYIH---GNPIQPTNTAFAVVDALEKYAPTITKPDMTSR 535 (740)
T ss_pred cccccCCCCCCCHHHHHHHHHhCCCCCCCcHHHHHHHHHhcCCcc---CCcccccHHHHHHHHHHHHhchhhcChhHHHH
Confidence 999999999999999999999999999999999999999999996 46899999999999999888889999999999
Q ss_pred HHhhC
Q psy8714 558 YRVQA 562 (562)
Q Consensus 558 ~E~~L 562 (562)
||.+|
T Consensus 536 ~E~~L 540 (740)
T PRK07220 536 LEEDM 540 (740)
T ss_pred HHHHH
Confidence 99876
No 2
>PRK08173 DNA topoisomerase III; Validated
Probab=100.00 E-value=5.8e-131 Score=1126.10 Aligned_cols=530 Identities=24% Similarity=0.386 Sum_probs=453.2
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCC----CCCccCCCCCCC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKY----NNWDKVDPLELF 81 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y----~~W~~~~p~~~~ 81 (562)
|+|||||| ||+|+.||.++|..+. -+|||+|++ |+||||+|||++|..|++| ++|+..++. ++
T Consensus 3 ~~LiIAEK-----Ps~Ak~Ia~~Lg~~~k-----~~gy~e~~~--~~Vtwa~GHL~el~~Pe~Y~~~~~~W~~~~LP-i~ 69 (862)
T PRK08173 3 KALIIAEK-----PSVANDIARALGGFTK-----HDEYFESDE--YVLSSAVGHLLEIAAPEEYEVKRGKWSFAHLP-VI 69 (862)
T ss_pred CEEEEEeC-----HHHHHHHHHHhCCCcC-----CCCeEeCCc--EEEEeeccccccCCCchhcccccccccccccC-CC
Confidence 46999999 9999999999976543 378999874 8999999999999877765 578765521 22
Q ss_pred CCCc---ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHH
Q psy8714 82 SCPT---EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKA 158 (562)
Q Consensus 82 ~~~~---~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~ 158 (562)
+.+. ......+|+++|+.|.+. ++||+||||||||||||+|+|+|+++++ +++||+|+||||||+++|++
T Consensus 70 p~~f~~~~~~~~~~q~~~ik~l~k~-~~~d~Ii~AtD~dREGElI~~~I~~~~~------~~kpv~Rlw~sslt~~aI~~ 142 (862)
T PRK08173 70 PPHFDLNPIAKTESRLKVLTKLIKR-KDVTRLINACDAGREGELIFRLIAQHAK------AKKPVKRLWLQSMTPQAIRD 142 (862)
T ss_pred CccccccccccHHHHHHHHHHHHhh-CCCCEEEECCCCChhHHHHHHHHHHHhC------CCCCeEEEEEccCCHHHHHH
Confidence 2111 112222344444444321 5799999999999999999999999994 46899999999999999999
Q ss_pred HHHhCCCCh--HhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcce
Q psy8714 159 AMWNLVKPN--IFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPY 236 (562)
Q Consensus 159 A~~nl~~~~--~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y 236 (562)
||+||++++ .++++||.||+++|||||||+||++|+..+.. |. ..++|+||||||||+|||+||++|+||+|++|
T Consensus 143 a~~nl~~~~~~~~L~~aa~aR~~aDwlvG~N~TR~~T~~~~~~-g~--~~~lSvGRVQTPtL~lVv~Re~eI~~F~p~~y 219 (862)
T PRK08173 143 GFANLRSDEDMQPLADAARCRSEADWLVGINGTRAMTAFNSKG-GG--FFLTTVGRVQTPTLSIVVEREEKIRRFVPRDY 219 (862)
T ss_pred HHhcCCCchhhHHHHHHHHHHHHHHHHhhHHHhHHHHHhHhhc-CC--ccccccccchhhHHHHHHHHHHHHHcCCCCcc
Confidence 999999987 48999999999999999999999999854432 21 24689999999999999999999999999999
Q ss_pred EEEEEEEeeCCeEEEEEee--------------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHH
Q psy8714 237 WLLDLTLNLNGVAVSVTWS--------------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELM 302 (562)
Q Consensus 237 ~~i~~~~~~~~~~~~~~~~--------------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq 302 (562)
|+|.+.+...++.|.+.|. .++++|+++|+.+++.|.+ ++++|++ +.+++++.||+||||++||
T Consensus 220 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~d~~~A~~i~~~~~~-~~~~V~~-~~k~~~~~pP~~f~Lt~LQ 297 (862)
T PRK08173 220 WEVRAEFVAAAGFYEGRWFDPKFKKDEFDPEKRASRLWSEAAAEAIVAACRG-KPGTVTE-ESKPSTQLSPLLFDLTSLQ 297 (862)
T ss_pred EEEEEEEecCCccEEEEEeccccccccccccccccccCCHHHHHHHHHHhcC-CCcEEEE-eeeEEecCCCCCCCHHHHH
Confidence 9999999877777888883 2589999999999999986 4789988 8899999999999999999
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhc-CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCC--CCCC--C
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQ-GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGI--SKPR--K 375 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~-glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~--~~~~--~ 375 (562)
++||++|||||++||++||+|||+ |+||||||||+|||+++ ++..+|+.+...+.+..++..++.... ...+ +
T Consensus 298 ~~A~~~~g~sa~~tL~iaQ~LYE~~k~iTYPRTDs~~l~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~r~~~ 377 (862)
T PRK08173 298 REANGRFGFSAKNTLGLAQALYEKHKVLTYPRTDSRALPEDYLGTVKQTLEMLKESNNYLPHAKQILDKGWVKPNKRIFD 377 (862)
T ss_pred HHHHHhcCCCHHHHHHHHHHHHhcCCEEEecCCCCccCCHHHHHHHHHHHHHHhCCcccHHHHHHhhcccccCCCCCcCC
Confidence 999999999999999999999996 89999999999999986 578888888654456655554443221 1223 2
Q ss_pred CCCCCCCCCCccCCCcccCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccc
Q psy8714 376 GKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSA 455 (562)
Q Consensus 376 ~~~~~~H~AI~PT~~~~~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~ 455 (562)
.++++||||||||...+ ..|+++|++||+||+|||||+|||||+|+.|+|.+.++++.|+++|++++++||+.||+.+.
T Consensus 378 ~~kv~dH~AIiPT~~~~-~~Ls~~E~~iY~lI~rRfla~f~~~a~~~~t~v~~~v~~~~F~a~G~~~~~~Gw~~vy~~~~ 456 (862)
T PRK08173 378 NSKISDHFAIIPTLQAP-KSLSEPEQKLYDLVVKRFLAVFFPAAEFLVTTRITEVAGHHFKTEGKVLVNPGWLAVYGKEA 456 (862)
T ss_pred CCCCCCCCCcCccCCCc-ccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCCcEEEEEEEEEeeCChHHHhCccc
Confidence 45578999999998765 46999999999999999999999999999999999999999999999999999999997543
Q ss_pred c-ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHH----------------hcCCCCcCchhHHHHHhhcC
Q psy8714 456 M-KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLME----------------KHGIGTDASIPVHINNICQR 518 (562)
Q Consensus 456 ~-~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me----------------~~GIGTpATra~iI~~L~~r 518 (562)
. ++..||.|++||.+.+.++.+.+++|+||+||||++||++|| +.|||||||||+||++|++|
T Consensus 457 ~~~~~~LP~l~~Ge~~~~~~~~~~e~~TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~~~~GIGTpATRA~IIe~L~~r 536 (862)
T PRK08173 457 QGADANLVPVQKGEKVKTDKIEAVALTTKPPARYNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGE 536 (862)
T ss_pred ccccccCCCcCCCCEeeeeeeeecccccCCCCCcCHHHHHHHHHhhhhccccHHHHhhhhcCCCCchhhHHHHHHHHHhC
Confidence 2 245699999999999999999999999999999999999998 57999999999999999999
Q ss_pred CeEEEcCCCeeecchhHHHHHHhhhcc-CccCCChhhHHHHHhhC
Q psy8714 519 NYVTVTSGRRLVPTSLGIVLVHGYQKI-DRELVEPTMRSAYRVQA 562 (562)
Q Consensus 519 ~Yi~~~~~k~l~~T~~G~~li~~l~~~-~~~l~~p~~Ta~~E~~L 562 (562)
|||++ +|+.|+||++|+.||++|... ++.|++|+|||.||.+|
T Consensus 537 ~Yi~~-~~k~l~pT~~G~~li~~l~~~~~~~l~~p~lTa~wE~~L 580 (862)
T PRK08173 537 KYLVR-EGRELIPTAKAFQLMTLLRGLGVEELTSPELTGEWEYKL 580 (862)
T ss_pred CcEEe-cCCEechhHHHHHHHHHHhhcCcccccChhHHHHHHHHH
Confidence 99997 678999999999999998653 56799999999999976
No 3
>PRK05776 DNA topoisomerase I; Provisional
Probab=100.00 E-value=2.7e-130 Score=1097.80 Aligned_cols=534 Identities=25% Similarity=0.410 Sum_probs=465.6
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCC-CceeeeeeeeEc----CCCcEEEEEEecccccccccccC-CCCCcc-CCCC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNG-ACSVHEWVGPLF----GDLVLFKMTSVCGHIMGLDFTSK-YNNWDK-VDPL 78 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~-~~~~~~~~g~~~----g~~~~~~Vt~~~GHl~~l~~~~~-y~~W~~-~~p~ 78 (562)
|.|||||| ||+|+.||+++|... .... ...|||+ |. .|+|+||.|||++|++|+. |..+.. +.|
T Consensus 2 ~~LiIaEK-----Ps~Ak~Ia~~Lg~~~~~~~~-~g~~~~e~~~~g~--~~~V~~~~GHl~~L~~~~~~~~~~~~~~~p- 72 (670)
T PRK05776 2 YILVIAEK-----PKAARKIAEALSEKPIRCRI-YGVPYWIVKRDGK--KIVVAPAAGHLFGLHTKSKGFPVFDYEWKP- 72 (670)
T ss_pred CEEEEEcC-----HHHHHHHHHHhCCCcccccc-CCCceEEEecCCC--CEEEEEecccCccCCCcccCCCCCCcCccc-
Confidence 68999999 999999999998321 1111 1124454 54 4899999999999987763 321110 112
Q ss_pred CCCCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHH
Q psy8714 79 ELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKA 158 (562)
Q Consensus 79 ~~~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~ 158 (562)
.|..... .....++++.|++++++||+||||||||||||+|||||+++++ +.++++|+|||++|+++|++
T Consensus 73 -~~~~~~~---~~~~~~~~~~lk~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~------~~~~v~R~~fs~iT~~~I~~ 142 (670)
T PRK05776 73 -LYEIDKG---SKYTKKYYELLSSLSKYADEFINACDYDIEGSVIGYLIIKYLG------DPKKAKRMKFSALTKSDIRR 142 (670)
T ss_pred -ceEeccC---cccHHHHHHHHHHHHhcCCEEEECCCCChhHHHHHHHHHHHhC------CCCCeeEEEEccCCHHHHHH
Confidence 2221111 0112368889999999999999999999999999999999995 25799999999999999999
Q ss_pred HHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEE
Q psy8714 159 AMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWL 238 (562)
Q Consensus 159 A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~ 238 (562)
||+||+++|.++++||+||+++|||||||+||++|+.++...|. ..++|+||||||||+|||+||+||++|+|++||.
T Consensus 143 A~~n~~~~d~~l~~A~~aR~~lD~lvG~nlSr~lt~~~~~~~g~--~~~lS~GRVQsptL~lVveRe~eI~~Fvp~~yw~ 220 (670)
T PRK05776 143 AFRNLETLDYEMINAGIARHELDWLWGINVSRALMSSVRDASGK--RVILSAGRVQSPTLKYVVEREIERNLFVPLPYFS 220 (670)
T ss_pred HHhCccccchhHHHHHHHHHHHHHHHhHHHhHHHHHHhhhhcCC--ccceecceecCchhhHhHhhHHHHHcCCCCcceE
Confidence 99999999999999999999999999999999999887643221 2479999999999999999999999999999999
Q ss_pred EEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHH
Q psy8714 239 LDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQ 318 (562)
Q Consensus 239 i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~ 318 (562)
|.+.+..++..|.+.|...++.|+++|+++++.+++.+.++|.+|+.++++.+||+||||++||++||++|||||++||+
T Consensus 221 i~~~~~~~~~~f~~~~~~~~~~~~~~a~~i~~~~~~~~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~As~~lg~sa~ktm~ 300 (670)
T PRK05776 221 VSIIIEKNGYEFTLKYENKKFETKEEAKEILEEIKKTGYLKVTKVEVKIEILEPPPPFNLGDLQVEAARIYGFSPYKTQS 300 (670)
T ss_pred EEEEEecCCceEEEEEcCCccCCHHHHHHHHHHhcCCCCEEEEEEEeeeEEcCCCCCCCHHHHHHHHHhhcCCCHHHHHH
Confidence 99999877888999998788999999999999997645799999999999999999999999999999999999999999
Q ss_pred HHHHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhC--CCCCCCCCCCC-CCCCCCccCCCcccCC
Q psy8714 319 IAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSN--GISKPRKGKDV-GDHPPITPTKLATRTQ 395 (562)
Q Consensus 319 iaQ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~--~~~~~~~~~~~-~~H~AI~PT~~~~~~~ 395 (562)
+||+|||+||||||||||++||+++++.++++.+...+.|+.++..++.. ...+|+++.+. +||||||||+..+ .+
T Consensus 301 iAQ~LYe~glISYPRTDs~~ls~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~k~~~aH~AI~PT~~~p-~~ 379 (670)
T PRK05776 301 IAEDLYLDGLISYPRTNSQKLPPTLNIRNILKGLSRSPQYRPLVNLLLKETKGVLKPVQGPKDDPAHPAIYPTGEPP-KN 379 (670)
T ss_pred HHHHHHhcCceecCCCccCCCChhhCHHHHHHHHhcchhHHHHHHHhhcccCCccccCCCCCCCCCCCCCCCCCCCc-cc
Confidence 99999999999999999999999988888999888777788877666542 23345555544 5899999998754 57
Q ss_pred CCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCe--EEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeee
Q psy8714 396 LDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADE--MFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQ 473 (562)
Q Consensus 396 L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~--~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~ 473 (562)
|+++|++||+||||||||+||+||+|++|+|.+.++++ .|+++|++++++||+.||+++++++..||.|++||.+.+.
T Consensus 380 L~~de~klY~LI~rRflA~~~~~a~~~~t~v~~~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~LP~l~~G~~~~~~ 459 (670)
T PRK05776 380 LSKDEFKLYDLIVRRFLASFAAPAVLSNTIVTLRVPGFPLVFSASGQRIEERGWLKYYPFHKFDEEELPLLKKGERVKIV 459 (670)
T ss_pred CCHHHHHHHHHHHHHHHHHhChhheEEEEEEEEEECCeEEEEEEEEEEEEECCceeecccCccccccCCCcCCCCEeEee
Confidence 99999999999999999999999999999999999999 9999999999999999997655445679999999999999
Q ss_pred eeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChh
Q psy8714 474 SVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPT 553 (562)
Q Consensus 474 ~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~ 553 (562)
++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.+ +|+.|+||++|+.|+++|...++.|++|+
T Consensus 460 ~~~~~~~~TkPP~ryTeasLi~~ME~~GIGtpATra~iI~~L~~R~Yv~~-~~k~l~pT~~G~~v~~~L~~~~~~l~~~~ 538 (670)
T PRK05776 460 DVKVRKSYTKPPSRYSKASLLKWMESVGIGTEATRARIIETLFKRGYLTS-NGKYIEVTPLGFGVAEVLEKYFPDIVSVE 538 (670)
T ss_pred eeeeeccccCCCCCCCHHHHHHHHhhCCCCCCccHHHHHHHHHhCCCEEe-eCCEEeECHHHHHHHHHHHHhccccCCHH
Confidence 99999999999999999999999999999999999999999999999997 67899999999999999988888999999
Q ss_pred hHHHHHhhC
Q psy8714 554 MRSAYRVQA 562 (562)
Q Consensus 554 ~Ta~~E~~L 562 (562)
|||.||.+|
T Consensus 539 ~Ta~~E~~L 547 (670)
T PRK05776 539 LTRDFEEKL 547 (670)
T ss_pred HHHHHHHHH
Confidence 999999876
No 4
>PRK14973 DNA topoisomerase I; Provisional
Probab=100.00 E-value=9.8e-130 Score=1117.15 Aligned_cols=532 Identities=31% Similarity=0.514 Sum_probs=462.1
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeee----eEcCCCcEEEEEEecccccccccccCCCCCccCC--CCC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVG----PLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD--PLE 79 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g----~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~--p~~ 79 (562)
|+|||||| ||+|+.||+++|...... ..-+| |++|+ ++||||.|||++|+|++.|++|+..+ |..
T Consensus 1 m~LiIAEK-----PSvAk~IA~~L~~~~~~~-~k~~g~~~~y~~~~---~~vt~~~GHLl~l~y~~~yk~W~~~~LPP~~ 71 (936)
T PRK14973 1 MHLIIAEK-----NIAANRIAQILAGKTKVQ-VKKDGGVSTYSFDD---TVVVGLRGHVVEVDFEPGYTNWRSEEHTPRS 71 (936)
T ss_pred CEEEEEcC-----HHHHHHHHHHhCCCCccc-cccCCCcceEEeCC---CEEEEEcccceecccCcccCCCccccCChhh
Confidence 57999999 999999999997542100 01133 55554 36999999999999999999998753 334
Q ss_pred CCCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHH
Q psy8714 80 LFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA 159 (562)
Q Consensus 80 ~~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A 159 (562)
+++.+.... ....++++.|++++++||.||||||||||||+|||||+++++.. +.+++|+|+|||++|+++|++|
T Consensus 72 l~~~~~~~~--~~~kk~~~~Ik~l~k~ad~IiiAtD~DREGE~I~~~i~e~~~~~---~~~~~v~R~~fs~iT~~~I~~A 146 (936)
T PRK14973 72 LIDADTIKK--PTEKKIVGLIQKLAKKADRVTIATDFDTEGELIGKEAYELVRAV---NPKVPIDRARFSAITKEEIVTA 146 (936)
T ss_pred ccCcceeec--CchHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHhhhc---cCCCceEEEEEccCCHHHHHHH
Confidence 554332111 22346888899999999999999999999999999999999743 3457999999999999999999
Q ss_pred HHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEE
Q psy8714 160 MWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLL 239 (562)
Q Consensus 160 ~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i 239 (562)
|+||++++.++++||+||+++|||||||+||++|+.++..+ ++++|+||||||||+|||+||+||+||+|++||+|
T Consensus 147 ~~nl~~~d~~l~~A~~aR~~~D~lvG~nlSr~lt~~~~~g~----~~~lS~GRVQTPtL~lIveRe~EI~~Fvp~~Yw~I 222 (936)
T PRK14973 147 FAEPTDLDFALAAAGEARQIIDLIWGASLTRFISLAAHRGG----DNILSVGRVQSPTLAMIVDREKEIEAFVPEKYWML 222 (936)
T ss_pred HhCCCCCcHHHHHHHHHHHHHHHHHHHHHhHHHHHHhhcCC----CcceeeccccchHHHHHHhHHHHHHcCCCCceEEE
Confidence 99999999999999999999999999999999999876321 34799999999999999999999999999999999
Q ss_pred EEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHH
Q psy8714 240 DLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQI 319 (562)
Q Consensus 240 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~i 319 (562)
.+.+..+|..|.+.|..++|+|+++|+.+++.+. .+++|++|++++++++||+||||++||++||+ |||||++||++
T Consensus 223 ~~~~~~~~~~~~a~~~~~r~~d~~~A~~i~~~~~--~~~~V~~v~~k~~~~~pP~Pf~ts~LQ~~ask-lg~Sa~kTm~i 299 (936)
T PRK14973 223 SLATEKDGEGIEARHTHGRFTDSAAAEAAYDATK--EPLVVTEVKEGHKVDRAPTPFDTTTFIVAASR-LGFSAANAMRI 299 (936)
T ss_pred EEEEecCCceEEEEEcCCCCCCHHHHHHHHHHcC--CCeEEEEEEeeeEeccCCCCccHHHHHHHHHH-cCCCHHHHHHH
Confidence 9999877788999999999999999999999884 46899999999999999999999999999885 99999999999
Q ss_pred HHHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCC-CCCCCCCccCCCcccCCCCH
Q psy8714 320 AERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKD-VGDHPPITPTKLATRTQLDG 398 (562)
Q Consensus 320 aQ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~H~AI~PT~~~~~~~L~~ 398 (562)
||+|||+||||||||||++||+++++.+++..+... .|+..+..+..+....|+++++ ++|||||+||...+...|++
T Consensus 300 AQ~LYE~glITYPRTDS~~l~~~~~~~~il~~l~~~-~~~~~~~~l~~~~~~~~~~~kk~~~aH~AI~PT~~~~~~~Ls~ 378 (936)
T PRK14973 300 AEDLYMNGYISYPRTDNTIYPKSLDLNGVLATLAKG-AFSKDVAWVKDNRRPVPTRGKKSSTDHPPIHPTGVATREELGD 378 (936)
T ss_pred HHHHHhCCeeeccCcccccCchhhhHHHHHHHHHHh-hhHHHHHHHhhcCCccCCCCCCCcCCcCCccCcCCcChhhCCH
Confidence 999999999999999999999987777777766532 2444333222221122444444 68899999998766568999
Q ss_pred HHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEe
Q psy8714 399 DAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMV 478 (562)
Q Consensus 399 ~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~ 478 (562)
+|++||+||||||||+||+||+|++|+|.++++++.|+++|++++++||+.||++++.++..||.+++||.+.+.++.+.
T Consensus 379 de~klY~LI~rRfLA~~~~~a~~~~t~v~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~LP~l~~Ge~~~~~~~~~~ 458 (936)
T PRK14973 379 DRWKLYELVVRRFLATLSPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEAKENILPAFALGEKLPILAVNLE 458 (936)
T ss_pred HHHHHHHHHHHHHHHHhChhheEEEEEEEEEECCEEEEEEEEEEeecCeeEeecccccccccCCCccCCCEEEeeeeEEe
Confidence 99999999999999999999999999999999999999999999999999999765444567999999999999999999
Q ss_pred eeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHH
Q psy8714 479 ERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAY 558 (562)
Q Consensus 479 e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~ 558 (562)
+++|+||+||||++||++||+.|||||||||+||++|++||||+ |+.|+||++|+.|+++|....+.|++|+|||.|
T Consensus 459 e~~T~PP~ryTEatLik~ME~~GIGTpATrA~II~~L~~R~Yve---~k~l~pT~~G~~li~~L~~~~~~l~~p~lTA~~ 535 (936)
T PRK14973 459 EKETQPPARYSQSRLIQRMEELGLGTKSTRHEVIGKLVSRKYIE---GNPLRPTLVGRAVTESLEEHAGTITEPDMTQTL 535 (936)
T ss_pred ecCCCCCCCCCHHHHHHHhccCCCCCcccHHHHHHHHHHccCee---CCceeEcHHHHHHHHHHHHhchhhcCHHHHHHH
Confidence 99999999999999999999999999999999999999999995 568999999999999998888899999999999
Q ss_pred HhhC
Q psy8714 559 RVQA 562 (562)
Q Consensus 559 E~~L 562 (562)
|.+|
T Consensus 536 E~~L 539 (936)
T PRK14973 536 EEHM 539 (936)
T ss_pred HHHH
Confidence 9876
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=4.8e-129 Score=1085.63 Aligned_cols=531 Identities=24% Similarity=0.380 Sum_probs=461.1
Q ss_pred EecccCcCCcchHHhhcccccCCCCceeeeeee--eEc----CCCcEEEEEEecccccccccccC--CCCCccCCCCCCC
Q psy8714 10 PASEIKLARPSLISLLTPLQRMNGACSVHEWVG--PLF----GDLVLFKMTSVCGHIMGLDFTSK--YNNWDKVDPLELF 81 (562)
Q Consensus 10 ~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g--~~~----g~~~~~~Vt~~~GHl~~l~~~~~--y~~W~~~~p~~~~ 81 (562)
|||| ||+|+.||+++|.... +...-+| ||+ |+ .|+||||.|||++|.+|++ |+.|+..+. +++
T Consensus 1 iAEK-----Ps~A~~ia~~l~~~~~-~~~~~~g~~y~~~~~~g~--~~~Vt~~~GHl~~l~~p~~~~~~~w~~~~l-P~~ 71 (618)
T TIGR01057 1 IAEK-----PKVAAKIAGALSDGRV-LKKSEYGVPYWEVRRDGK--KIIVASAVGHLFGLHPKSRGGYPVFDIEWV-PIF 71 (618)
T ss_pred CCCC-----hHHHHHHHHHhCCCCc-ccccCCCceEEEEecCCC--eEEEEEeccccccCCCccccCCCCCCcccC-cee
Confidence 6888 9999999999986521 0001245 665 54 5899999999999988764 666764321 222
Q ss_pred CCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714 82 SCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW 161 (562)
Q Consensus 82 ~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~ 161 (562)
+....+ ....++++.|++++++||+||||||||||||+|||+|+++++. .+||+|+|||++|+++|++||+
T Consensus 72 ~~~~~~---~~~~~~~~~ik~l~~~~d~ii~AtD~DREGE~I~~~i~~~~~~------~~~v~Rl~~~~lt~~~I~~a~~ 142 (618)
T TIGR01057 72 EFDKGK---GYVSKYIKALSKLAKGADEYINACDYDIEGEVIGFKALKYFCG------VERAKRMKFSTLTKQDIRRAYA 142 (618)
T ss_pred eecCCc---ccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhcc------CCCceEEEEccCCHHHHHHHHh
Confidence 211111 1113577888888899999999999999999999999999952 3789999999999999999999
Q ss_pred hCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEE
Q psy8714 162 NLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDL 241 (562)
Q Consensus 162 nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~ 241 (562)
||++.+.+++.||.||+++|||||||+||++|+.++...|. +.++|+||||||||+|||+||++|+||+|++||.|.+
T Consensus 143 nl~~~~~~l~~a~~aR~~~D~liG~n~Sr~~t~~~~~~~~~--~~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~ 220 (618)
T TIGR01057 143 NPEEIDYGMVDAGMARHILDWYWGINLSRALMEAIRAAAGR--WVILSAGRVQGPTLAFLVEREREINLFVPKPYWVIKA 220 (618)
T ss_pred CcccCCHhHHHHHHHHHHHHHHHhhhhhHHHHHHhhccCCC--cccccccccchhHHHHHHHhHHHHHcCcCCccEEEEE
Confidence 99999999999999999999999999999999887643221 3479999999999999999999999999999999999
Q ss_pred EEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHH
Q psy8714 242 TLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAE 321 (562)
Q Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ 321 (562)
.+..+++.|.+.|.+++++|+++|+++++.+++.+.++|+++++++++.+||+||||++||++||++|||||++||++||
T Consensus 221 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ 300 (618)
T TIGR01057 221 TLEKGGGVFDARPEKWKIWSEEEAKSIKEELKKSPWAAVEEVRSERSILKPPPPFDLGTLQREAYRIFGFSPKKTQSIAQ 300 (618)
T ss_pred EEecCCceEEEEEccCCcCCHHHHHHHHHHHhCCCCeEEEEEEeeeeeccCCCCccHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 99888888999999899999999999999998754799999999999999999999999999999999999999999999
Q ss_pred HhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCC-CCCCCCccCCCcccCCCCHHH
Q psy8714 322 RLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDV-GDHPPITPTKLATRTQLDGDA 400 (562)
Q Consensus 322 ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~H~AI~PT~~~~~~~L~~~e 400 (562)
+|||+||||||||||+|||+++++..+++.+...+.++.++..++.....+|++++++ +|||||+||...+...|+++|
T Consensus 301 ~LYe~g~ISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aH~aI~PT~~~~~~~L~~~e 380 (618)
T TIGR01057 301 ELYEEALISYPRTSSQKLPPSINYRAILDNLAKGPLYREAAERLLETGVLKPVEGKKEDPAHPAIHPTGEIPSQELSKDE 380 (618)
T ss_pred HHHhcCceeecCcccCccCHHHhHHHHHHHHhcccchHHHHHHhhcccccccCCCCCCCCCCCCcCccCCCccccCCHHH
Confidence 9999999999999999999988777888888765566665554433233456666666 489999999765434799999
Q ss_pred HHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEeee
Q psy8714 401 WRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVER 480 (562)
Q Consensus 401 ~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~ 480 (562)
++||+||+|||||+|||||+|++|+|.+.++++.|.++|++++++||+++|+.++.++..||.+++||.+.+.++.+.++
T Consensus 381 ~~iY~lI~~r~la~~~~~a~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~v~~~~~~~~~~lp~~~~gd~~~~~~~~~~e~ 460 (618)
T TIGR01057 381 KKVYDLIVRRFLAAFSEEAIREKSKVLLRIGQEKFRLSGLRVVKLGWLEYYHYSKFEEKELPPLDRGDKIKVVRVDVRVK 460 (618)
T ss_pred HHHHHHHHHHHHHHhChhhheeEEEEEEEECCeEEEEEEEEEEeCCcceeccCcccccccCCCCCCCCEeeeeeeeeccc
Confidence 99999999999999999999999999999999999999999999999999976544456699999999999999999999
Q ss_pred ecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHh
Q psy8714 481 KTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRV 560 (562)
Q Consensus 481 ~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~ 560 (562)
+|+||+||||++||++||+.|||||||||+||++|++||||+. + ++|+||++|+.|+++|....+.|++|+|||.||.
T Consensus 461 ~TkPP~~~Te~tLi~~Me~~GIGTpATra~iIe~L~~r~Yi~~-~-~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~E~ 538 (618)
T TIGR01057 461 ETQPPARYDKASLIREMESRGLGTKATRARIIETLYKRGYIEG-K-KSIKVTPLGEAVIETLQRYCPEIISEELTRRFES 538 (618)
T ss_pred ccCCCCCCCHHHHHHHHHhCCCCCCCcHHHHHHHHHhCCcEeE-C-CEEeeehHHHHHHHHHHHhchhhcChhhHHHHHH
Confidence 9999999999999999999999999999999999999999986 4 4799999999999999877778999999999998
Q ss_pred hC
Q psy8714 561 QA 562 (562)
Q Consensus 561 ~L 562 (562)
+|
T Consensus 539 ~L 540 (618)
T TIGR01057 539 KL 540 (618)
T ss_pred HH
Confidence 76
No 6
>PRK07219 DNA topoisomerase I; Validated
Probab=100.00 E-value=3.8e-129 Score=1114.57 Aligned_cols=540 Identities=30% Similarity=0.523 Sum_probs=467.8
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeee--eEc--CCCcEEEEEEecccccccccccCCCCCccCCCCCCC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVG--PLF--GDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELF 81 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g--~~~--g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~ 81 (562)
|.|||||| ||+|+.||+++|..+. +...-+| ||+ +++..|+|+|+.|||++|++|++|+.|+..+|..++
T Consensus 1 ~~LiIaEK-----ps~Ak~Ia~~L~~g~~-~~~~~~g~~~~~~~~~g~~~~v~~~~GHl~~l~~p~~y~~w~~~~l~~l~ 74 (822)
T PRK07219 1 TELIIAEK-----NNAARRIADILSGGKA-KKKRVNGVPYYEFERKGEKWIVIGLSGHIVTVDFPEEYGDWRDVDPAELI 74 (822)
T ss_pred CEEEEEeC-----HHHHHHHHHHhcCCCc-ccccCCCcceEEecCCCCeEEEEEecCcccccCCchhcCCcCcCChhhcc
Confidence 58999999 9999999999942211 0001123 444 222358999999999999999999999877654444
Q ss_pred CCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714 82 SCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW 161 (562)
Q Consensus 82 ~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~ 161 (562)
..+... ...+.++++.|++++++||+||||||||||||+|||+|++.+... ++++|+|+|||++|+++|++||+
T Consensus 75 ~~~~~~--~~~~~~~~~~lk~l~~~ad~iiiAtD~DREGE~I~~ei~~i~~~~----~~~~v~R~~fs~iT~~~I~~A~~ 148 (822)
T PRK07219 75 DADPVK--KITKQNYINALKKLAKDADEIIIATDYDREGELIGKEAYHILREV----CQVPVKRARFSSLTKKEIRKAFE 148 (822)
T ss_pred ccceee--cCCHHHHHHHHHHHHhcCCEEEEcCCCChhHHHHHHHHHHHHHhc----CCCceeEEEEccCCHHHHHHHHh
Confidence 322111 122446888999999999999999999999999997777666432 25899999999999999999999
Q ss_pred hCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEE
Q psy8714 162 NLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDL 241 (562)
Q Consensus 162 nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~ 241 (562)
||+++|.++++||+|||++|||||||+||++|+.+++. |. ..++|+||||||||+|||+||+||+||+|++||+|.+
T Consensus 149 n~~~~d~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~-g~--~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~yw~i~~ 225 (822)
T PRK07219 149 NPDEIDFNLADAGEARQIIDLYWGAALTRFLSLSVRQL-GR--WDFLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEA 225 (822)
T ss_pred CcccCCHHHHHHHHHHHHHHHHhhhhhCHHHHHHHHhc-cc--cCccccccccchhhHHHHHHHHHHHcCCCcccEEEEE
Confidence 99999999999999999999999999999999987643 21 2479999999999999999999999999999999999
Q ss_pred EEeeCCeEEEEEe----ecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHH
Q psy8714 242 TLNLNGVAVSVTW----SRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAM 317 (562)
Q Consensus 242 ~~~~~~~~~~~~~----~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl 317 (562)
.+..++..|.+.| ..++++|+++|+++++.+.+.+.++|.+|++++++.+||+||||++||++||++|||||++||
T Consensus 226 ~~~~~~~~~~~~~~~~~~~~r~~d~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~t~~Lq~~a~~~~g~sa~~tm 305 (822)
T PRK07219 226 LLDKEAQYFYRDLIGGHEAEKFWDEEEAEEIYEKLKGAKEATVSSVKKRERTISPPAPFNTTEFLREASKIFGISPKRAM 305 (822)
T ss_pred EEEecCcceeeecccccccCccCCHHHHHHHHHHhcCCCCeEEEEEEEeeEEccCCCCccHHHHHHHHHHHcCCCHHHHH
Confidence 9976555566655 456899999999999999864579999999999999999999999999999999999999999
Q ss_pred HHHHHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCC-CCCCCCCccCCCcccCCC
Q psy8714 318 QIAERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKD-VGDHPPITPTKLATRTQL 396 (562)
Q Consensus 318 ~iaQ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~H~AI~PT~~~~~~~L 396 (562)
++||+|||+||||||||||++||+++++.++++.+.....|+.++..++.....+|+++++ ++||||||||...+.+.|
T Consensus 306 ~iaQ~LYe~glITYpRTds~~l~~~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~~~aH~aI~PT~~~~~~~L 385 (822)
T PRK07219 306 EIAEKLYTAGYISYPRTDNTVYPDDLDPKELLKKLSKKKEYGPYAESILEQENIKPTEGKKETTDHPPIHPVDVPKREEL 385 (822)
T ss_pred HHHHHHHhCCceeccCcccccCCHHHHHHHHHHHhhcccchhhHhhhhcccCCcccCCCCCCCCCCCCCCCcCCCCcccC
Confidence 9999999999999999999999998877788888876666777665555433345666554 689999999997654689
Q ss_pred CHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeE
Q psy8714 397 DGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVK 476 (562)
Q Consensus 397 ~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~ 476 (562)
+++|++||+||+|||||+||+||+|++|+|.++++++.|+++|++++++||+++|+++..++..||.|++||.+.+.++.
T Consensus 386 ~~~e~~lY~LI~rrfla~~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~vy~~~~~~~~~lP~l~~G~~~~~~~~~ 465 (822)
T PRK07219 386 SDDEWKVYELIVRRFLATLADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEKFDEKELPDLEEGEKLKVNKIE 465 (822)
T ss_pred CHHHHHHHHHHHHHHHHHhCccceeeEEEEEEEeCCeEEEEEEEEEccCCcHhhcCccccccccCCCCCCCCEeeeeeeE
Confidence 99999999999999999999999999999999999999999999999999999997665445679999999999999999
Q ss_pred EeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHH
Q psy8714 477 MVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556 (562)
Q Consensus 477 i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta 556 (562)
+.+++|+||+||||++||++||+.|||||||||+||++|++|||| + +|+.|+||++|+.|+++|....+.|++|+|||
T Consensus 466 ~~~~~T~PP~rytea~Li~~Me~~GIGT~ATra~iI~~L~~R~Yv-~-~~~~l~pT~~G~~l~~~l~~~~~~l~~~~~Ta 543 (822)
T PRK07219 466 IEAKETQPPKRYTQSSLIKEMEKRGLGTKATRHDIIEKLYKRGYV-I-EGDPPRPTDLGIAVIEALEKYAPEIVSEEMTA 543 (822)
T ss_pred ecccccCCCCCCCHHHHHHHHHhCCCCCCccHHHHHHHHHhcCcE-e-cCCEeeecHHHHHHHHHHHHhchhhcChhHHH
Confidence 999999999999999999999999999999999999999999999 6 57799999999999999988888999999999
Q ss_pred HHHhhC
Q psy8714 557 AYRVQA 562 (562)
Q Consensus 557 ~~E~~L 562 (562)
.||..|
T Consensus 544 ~~E~~L 549 (822)
T PRK07219 544 QLEADM 549 (822)
T ss_pred HHHHHH
Confidence 999876
No 7
>PRK14724 DNA topoisomerase III; Provisional
Probab=100.00 E-value=1.8e-128 Score=1116.69 Aligned_cols=540 Identities=24% Similarity=0.343 Sum_probs=447.0
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCC----CCCccCCCCCCC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKY----NNWDKVDPLELF 81 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y----~~W~~~~p~~~~ 81 (562)
|+|||||| ||+|+.||.++|-+.... ...+|||+|++ |+||||+|||++|..|++| ++|+..++. ++
T Consensus 2 k~LiIAEK-----PSvAk~IA~aL~~~~g~~-~k~~gy~eg~~--~~Vtwa~GHL~eL~~Pe~y~~~~~~W~~~~LP-ii 72 (987)
T PRK14724 2 KTLVIAEK-----PSVAQDIVRALTPVAGKF-EKHDEHFESDS--YVVTSAVGHLVEIQAPEEFDVKRGKWSFANLP-VI 72 (987)
T ss_pred CEEEEEeC-----HHHHHHHHHHhhhccCCC-cCCCceecCCC--EEEEecccccccCCChhhcccccCCccccccc-cC
Confidence 57999999 999999999994211111 12478999874 8999999999999876665 568765421 22
Q ss_pred CCCcccccCCCCCchHHHHHhhc--ccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHH
Q psy8714 82 SCPTEKREATPKLKLPAFLANEA--KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAA 159 (562)
Q Consensus 82 ~~~~~~~~~~~~~~~i~~L~~~~--~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A 159 (562)
+.+..........++++.|++++ +++|+||||||||||||+|||+|+++++... .+.++||+|+||||||+++|++|
T Consensus 73 P~~f~~~~~~~~k~q~~~Ik~l~k~~~~~~II~AtD~DREGElI~~~I~~~~~~~~-~~~~kpv~Rlw~sslT~~aI~~a 151 (987)
T PRK14724 73 PPYFDLKPVDKTKTRLNAVVKLAKRKDVTELVNACDAGREGELIFRLIEQYAGGAK-GGLGKPVKRLWLQSMTPQAIRDG 151 (987)
T ss_pred CccceeeeccchHHHHHHHHHHHhhCCCCeEEECCCCCcchhHHHHHHHHHhCccc-ccCCCceEEEEEccCCHHHHHHH
Confidence 21111000111123444444444 5788999999999999999999999995210 01148999999999999999999
Q ss_pred HHhCCCChH--hHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceE
Q psy8714 160 MWNLVKPNI--FEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYW 237 (562)
Q Consensus 160 ~~nl~~~~~--~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~ 237 (562)
|+||++++. ++++||.||+++|||||||+||++|+..+...+ ..++|+||||||||+|||+||+||+||+|++||
T Consensus 152 f~nlr~~~~~~~L~~Aa~aR~~aDwLvG~N~SR~~T~~~~~~~~---~~~lSvGRVQTPtL~lVv~Re~eI~~F~p~~Y~ 228 (987)
T PRK14724 152 FDNLRSDAQMQGLASAARSRSEADWLVGINGTRAMTAFNSRDGG---FFLTTVGRVQTPTLSLVVEREEKIRKFVSRDYW 228 (987)
T ss_pred HhCCCCchhhhhHHHHHHHHHHHHHHhHHHHhHHHHHHHHhcCC---cceeccccchhHHHHHHHHHHHHHHhCCCCccE
Confidence 999999884 899999999999999999999999985432211 126899999999999999999999999999999
Q ss_pred EEEEEEeeCCeEEEEEee--------------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHH
Q psy8714 238 LLDLTLNLNGVAVSVTWS--------------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMR 303 (562)
Q Consensus 238 ~i~~~~~~~~~~~~~~~~--------------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~ 303 (562)
+|.+.|..+++.|.+.|. .++++++++|+++++.|.+ +.++|.+ +.+++++.||+||||++||+
T Consensus 229 ~i~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~A~~i~~~~~~-~~~~V~~-~~k~~~~~pP~pf~Lt~LQ~ 306 (987)
T PRK14724 229 EIHAGFHAEAGEYLGKWFDPQWKKASDDPEARADRVWSEREARAIADAVRG-KAATVTE-ESKPTTQASPLLFDLTSLQR 306 (987)
T ss_pred EEEEEEecCCCceeEEEeecccccccccccccccccCCHHHHHHHHHHhcC-CCeEEEE-eeeeEecCCCCCCcHHHHHH
Confidence 999999877777888772 2579999999999999986 4789988 89999999999999999999
Q ss_pred HHHhhCCCCHHHHHHHHHHhHhc-CceeecCCCCCCCCCcc--cHHHHHHHhccC--CchhHHHHHHhhCCC--CCCCC-
Q psy8714 304 VASSGLGMGPHHAMQIAERLYTQ-GYVSYPRTETTQYPENF--DLVAVLRQQESS--PDWGDHVREVLSNGI--SKPRK- 375 (562)
Q Consensus 304 ~a~~~~g~s~~~tl~iaQ~LYE~-glISYPRTds~~l~~~~--~~~~~l~~l~~~--~~~~~~~~~~~~~~~--~~~~~- 375 (562)
+||++|||||++||++||+|||+ ||||||||||+|||+++ .+..+|+.|... +.+..++...+.... ...+.
T Consensus 307 eA~~~~g~Sa~~TL~iAQ~LYE~~klITYPRTDS~~l~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~r~~ 386 (987)
T PRK14724 307 EANGKFGFSAKTTLALAQSLYERHKALTYPRTDSRALPEDYLPVAKQTFEMLATSGMRHLAPFAQQALDGNYVRPSKRIF 386 (987)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHcCCeEeecCcCCccCCHHHHHHHHHHHHHHhcccchhHHHHHHHHhcccccCCCCCcC
Confidence 99999999999999999999996 99999999999999986 477788777543 334444433333211 12222
Q ss_pred -CCCCCCCCCCccCCCcccCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccc
Q psy8714 376 -GKDVGDHPPITPTKLATRTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWS 454 (562)
Q Consensus 376 -~~~~~~H~AI~PT~~~~~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~ 454 (562)
.++++||||||||...+ ..|+++|++||+||+|||||+|||||+|++|+|.+.++++.|+++|++++++||+.||+.+
T Consensus 387 ~~~Kv~~H~AIiPT~~~p-~~Ls~~E~kiY~lI~rRfla~f~~~a~~~~t~v~~~~~~~~F~a~G~~i~~~GW~~vy~~~ 465 (987)
T PRK14724 387 DNSKVSDHFAIIPTTQAP-SGLSEAEQKLYDLVVRRFMAVFFPSAEYQVTTRISQVVGHSFKTEGKVLVKPGWLAIYGKE 465 (987)
T ss_pred CCCCCCCcCCcCCCCCCc-ccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEecCcEEEEEEEEECcCChHHHhCcc
Confidence 34568999999998765 6899999999999999999999999999999999999999999999999999999998643
Q ss_pred cc----------ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHH----------------hcCCCCcCch
Q psy8714 455 AM----------KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLME----------------KHGIGTDASI 508 (562)
Q Consensus 455 ~~----------~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me----------------~~GIGTpATr 508 (562)
.. ++..||.|++||.+.+.++.+.+++|+||+||||++||++|| +.||||||||
T Consensus 466 ~~~~~~~~~~~~~~~~LP~l~~Ge~v~~~~~~~~e~~TkPP~ryTEatLl~aME~~gk~v~d~el~~~~~~~GIGTpATR 545 (987)
T PRK14724 466 AANEVEDAKDGDKGQPLVPVKPGEMVRTEFAEAKGLKTKPPARYSEATLLGAMESAGKQIDDDELREAMQEKGLGTPATR 545 (987)
T ss_pred ccccccccccccccccCCCcCCCCEeeeeeccccccccCCCCCcCHHHHHHHHHhhhhcccchhhhhhhhcCCCCCcccH
Confidence 21 123599999999999999999999999999999999999998 5799999999
Q ss_pred hHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhcc-CccCCChhhHHHHHhhC
Q psy8714 509 PVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKI-DRELVEPTMRSAYRVQA 562 (562)
Q Consensus 509 a~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~-~~~l~~p~~Ta~~E~~L 562 (562)
|+||++|++||||++ +|+.|+||++|+.||++|... +++|++|+|||.||.+|
T Consensus 546 A~IIe~L~~r~Yi~~-~~k~l~pT~~G~~li~~L~~~~~~~l~~pelTa~wE~~L 599 (987)
T PRK14724 546 AAIIEGLLTEKYMLR-EGRELIPTAKAFQLMTLLRGLGVEELSRAELTGEWEYKL 599 (987)
T ss_pred HHHHHHHHhCCcEEe-cCCEEeEcHHHHHHHHHHHhcCchhhcChhHHHHHHHHH
Confidence 999999999999997 678999999999999998654 56799999999999976
No 8
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=100.00 E-value=4e-128 Score=1053.48 Aligned_cols=511 Identities=30% Similarity=0.451 Sum_probs=443.7
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~ 85 (562)
|.|||||| |+.|+.|++.+|.+ |+|+||+|||++|..|++++.|...+...+.+...
T Consensus 1 ~~LiIvEs-----PskAk~Ia~~Lg~~------------------~~V~as~GHi~dl~~~~~~~~~~~~~~~~~~~~~~ 57 (570)
T COG0550 1 KRLIIVES-----PSKAKTIAKYLGKG------------------YVVTASVGHLRDLPFPEEYKGWVDVDLPIFEPKYI 57 (570)
T ss_pred CeEEEEeC-----HHHHHHHHHhcCCC------------------cEEEEcccccccCCChhhccCCcCCccccccccee
Confidence 68999999 99999999655543 68999999999999988888898755332222111
Q ss_pred ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhCCC
Q psy8714 86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVK 165 (562)
Q Consensus 86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl~~ 165 (562)
..... +.++++.|+.++++||.||||||||||||+|||||+++++.. + ..+++|+|||+||+++|++||+|+++
T Consensus 58 ~~~~~--k~~~v~~lk~~ak~ad~v~lAtD~DREGE~I~~~i~~~l~~~---~-~~~~~R~~F~eiT~~aI~~A~~~p~~ 131 (570)
T COG0550 58 IKPGK--KKKVVKKLKKLAKKADEVYLATDPDREGEAIGWHILEVLKLK---N-PSKVKRVVFSEITKKAILSAFKNPRE 131 (570)
T ss_pred ccchh--hHHHHHHHHHHhccCCEEEECCCCCcchHHHHHHHHHHhCcc---C-CCceeEEEEecCCHHHHHHHHhCchh
Confidence 11110 446888999999999999999999999999999999999642 1 14699999999999999999999999
Q ss_pred ChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEee
Q psy8714 166 PNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL 245 (562)
Q Consensus 166 ~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~ 245 (562)
.|+++++||+||+++|||+|+|+||++|+.+++ +++|+||||||||+|||+||+||++|+|++||+|.+.+..
T Consensus 132 id~~lv~A~~aR~~lD~lvG~~lSr~l~~~~~~-------~~LSaGRVQSpaL~lVveRE~EI~~F~p~~yw~i~a~~~~ 204 (570)
T COG0550 132 IDMNLVDAQLARRILDRLVGYNLSRLLWKKLKR-------GVLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEK 204 (570)
T ss_pred hchHHHHHHHHHHHHHHHhhhhhhHHHHHhhcc-------CCCCCccccchhhhhhHhhHHHHHhCCCCcceEEEEEEec
Confidence 999999999999999999999999999987653 1599999999999999999999999999999999999988
Q ss_pred CCeEEEEEee------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHH
Q psy8714 246 NGVAVSVTWS------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQI 319 (562)
Q Consensus 246 ~~~~~~~~~~------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~i 319 (562)
+++.|.+.|. .+++.+...|.++++.+++ +.+.|.+++.++++..||+||+|++||++||++|||||++||++
T Consensus 205 ~~~~f~a~~~~~~~~~~~~~~~~~~a~~~~~~l~~-~~~~V~~ve~k~~~~~pp~Pf~tstLQq~As~~lgfs~kktm~i 283 (570)
T COG0550 205 GGGEFSARLTEIEGKKEGRLKDKDEAEEIVNKLKG-KPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDI 283 (570)
T ss_pred CCccEEEEEeccccccccccccHHHHHHHHHHccC-CceEEEEEeeeeeccCCCCCCcHHHHHHHHHHhCCCCHHHHHHH
Confidence 7766998886 3467888999999999985 57999999999999999999999999999999999999999999
Q ss_pred HHHhHhc-CceeecCCCCCCCCCccc--HHHHHHHhccCCchhHHHHHHhhC-CCCCCCCCC-CCCCCCCCccCC-Cccc
Q psy8714 320 AERLYTQ-GYVSYPRTETTQYPENFD--LVAVLRQQESSPDWGDHVREVLSN-GISKPRKGK-DVGDHPPITPTK-LATR 393 (562)
Q Consensus 320 aQ~LYE~-glISYPRTds~~l~~~~~--~~~~l~~l~~~~~~~~~~~~~~~~-~~~~~~~~~-~~~~H~AI~PT~-~~~~ 393 (562)
||+|||. ||||||||||++||+++. ....+.... |+. .++.. ....+.+++ +.+||||||||+ ..+
T Consensus 284 AQ~LYE~~glITYpRTDs~~ls~~~~~~~~~~i~~~~----yg~---~~l~~~~~~~~~~~~~~q~AHeAIrPT~~~~p- 355 (570)
T COG0550 284 AQKLYEGHGLITYPRTDSTRLSEEALAEARLYILAIA----YGK---EYLPLKPRRYPSKGKKAQEAHEAIRPTDFETP- 355 (570)
T ss_pred HHHHhcCCCcEEecCCCCCcCCHHHHHHHHHHHHhhc----cHH---hhcccccccCCCCCCCCcCCCCCcCCCCCCCc-
Confidence 9999997 999999999999999863 233333221 433 34432 122333433 348899999997 322
Q ss_pred CCCC-HHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccc--ccccCCCCCCCCCCee
Q psy8714 394 TQLD-GDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWS--AMKNESIPDFKPGDLI 470 (562)
Q Consensus 394 ~~L~-~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~--~~~~~~Lp~l~~G~~~ 470 (562)
..+. .||++||+|||||||||||+||+|++++|++.++++.|+++|++++++||+.||++. +.++..||.+++||.+
T Consensus 356 ~~~~~~de~klY~LI~rrflAs~m~~A~~~~~~v~l~~~~~~F~a~g~~~~~~Gw~~vy~~~~~~~~~~~lP~l~~gd~l 435 (570)
T COG0550 356 ESLKAYDELKLYDLIWRRFLASQMPDAIYEKTTVTLEVAGEKFKASGKVLKFDGWLKVYGEDKDEEEDKELPELKEGDEL 435 (570)
T ss_pred ccccchhHHHHHHHHHHHHHHHhCchhhheEEEEEEEecCcEEEEeeeEEecCcHHHhhcccccccccccCCCCCCCCee
Confidence 2333 799999999999999999999999999999999999999999999999999999865 2226789999999999
Q ss_pred eeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCC
Q psy8714 471 PIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELV 550 (562)
Q Consensus 471 ~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~ 550 (562)
.+.++++.+++|+||+||||++||++||+.|||||||||+||++|++||||.. +|+.|+||++|+.|++.|...++.++
T Consensus 436 ~~~~~~~~~~~T~PP~rytEasLvk~mE~~GIGrpSTyA~iI~~L~~RgYv~~-~~~~~~pT~~G~~v~~~L~~~f~~l~ 514 (570)
T COG0550 436 KVEKLEVEEHFTKPPPRYTEASLVKAMEKLGIGTPSTYASIIETLQKRGYVEK-KGKRLVPTELGEAVIELLEEYFPELV 514 (570)
T ss_pred EEeeeeecccccCCcCCCCHHHHHHHHHhCCCCCcccHHHHHHHHhcCCcEEe-cCCeeEEcHHHHHHHHHHHHhchhhc
Confidence 99999999999999999999999999999999999999999999999999998 67899999999999999999999999
Q ss_pred ChhhHHHHHhhC
Q psy8714 551 EPTMRSAYRVQA 562 (562)
Q Consensus 551 ~p~~Ta~~E~~L 562 (562)
+|+|||.||+.|
T Consensus 515 ~~~~Ta~mE~~L 526 (570)
T COG0550 515 DPDFTAKMEEKL 526 (570)
T ss_pred CHHHHHHHHHHH
Confidence 999999999986
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=2e-127 Score=1074.32 Aligned_cols=530 Identities=23% Similarity=0.334 Sum_probs=448.4
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEc-CCCcEEEEEEecccccccccc----cCCCCCccCCCCCC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLF-GDLVLFKMTSVCGHIMGLDFT----SKYNNWDKVDPLEL 80 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~-g~~~~~~Vt~~~GHl~~l~~~----~~y~~W~~~~p~~~ 80 (562)
|+|||||| ||+|+.|++++|..+. -+|||+ |.+ |+|+||+|||++|..| ++|++|+..++ ++
T Consensus 1 ~~LiIaEK-----Ps~Ak~Ia~~L~~~~~-----~~gy~e~g~~--~~V~~~~GHl~~L~~p~~~~~~~~~W~~~~l-p~ 67 (660)
T TIGR01056 1 MTLVLCEK-----PSQARDLATVLAKKKK-----GNGYLEIGVG--GFVTWAVGHLVELAEPEEYDEKYKNWRTYDL-PL 67 (660)
T ss_pred CeEEEEeC-----HHHHHHHHHHhCCCcC-----CCCcEEECCc--EEEEeCchhhhcCCChhhcccccCccccCCC-Cc
Confidence 68999999 9999999999986642 488999 874 7899999999999755 45668876442 11
Q ss_pred CCCCcccccCCCCCchHHHHHhhcc--cCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHH
Q psy8714 81 FSCPTEKREATPKLKLPAFLANEAK--DCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKA 158 (562)
Q Consensus 81 ~~~~~~~~~~~~~~~~i~~L~~~~~--~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~ 158 (562)
.+..........+.++++.|+++++ +||+||||||||||||+|||||+++++. +...+|+|+|||++|+++|++
T Consensus 68 ~p~~f~~~~~~~~~~~~~~ik~l~k~~~ad~Ii~AtDpDREGE~I~~~i~~~l~~----~~~~~v~Ri~f~~iT~~~I~~ 143 (660)
T TIGR01056 68 EPEDWQLVVSDKTKKQFNVIKRILKENKVDEVVIATDPDREGELIAREILDYLKV----TDKVTIKRLWISSLVDSSIRK 143 (660)
T ss_pred ccccceeeeccchHHHHHHHHHHhhhcCCCEEEECCCCCcchHHHHHHHHHHhCC----CCCCceEEEEeccCCHHHHHH
Confidence 1111000111223467888888888 9999999999999999999999999952 112399999999999999999
Q ss_pred HHHhCCCC--hHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcce
Q psy8714 159 AMWNLVKP--NIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPY 236 (562)
Q Consensus 159 A~~nl~~~--~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y 236 (562)
||+||+++ +.++++||.||+++|||||||+||++|+.++..+. +..+|+||||||||+|||+||+||+||+|++|
T Consensus 144 A~~n~~~~~~~~~l~~a~~aR~~~D~lvG~nlSr~lt~~~~~~g~---~~~lS~GRVQtptL~lIveRe~eI~~F~p~~y 220 (660)
T TIGR01056 144 AFKNLRPKSETEGLYKSGVARARADWLVGINLTRAFTKLGREAGN---DGVLSVGRVQTPTLAMVVKRENEIKNFVGKPF 220 (660)
T ss_pred HHHcCCCchhhhhHHHHHHHHHHHHHHHHHhHhHHHHHhhhhcCC---CCceecccchhhhhHHHHHHHHHHHcCCCCcc
Confidence 99999986 67899999999999999999999999987654311 24699999999999999999999999999999
Q ss_pred EEEEEEEeeCCeEEEEEeec-----ccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCC
Q psy8714 237 WLLDLTLNLNGVAVSVTWSR-----GHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGM 311 (562)
Q Consensus 237 ~~i~~~~~~~~~~~~~~~~~-----~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~ 311 (562)
|+|.+.+..++..|.+.|.. .+++|+++|+.+++.+.+ .+++|.+|+.++++.+||+||||++||++||++|||
T Consensus 221 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~~~~-~~~~V~~v~~k~~~~~pP~pf~ts~LQ~~as~~~g~ 299 (660)
T TIGR01056 221 YEVSATINKDEQEFTTEWQPYKDEEERELHEFLAENVVTDLTQ-KPALVTDIEKERKKTSAPLFYDLSALQEDANKRFGI 299 (660)
T ss_pred EEEEEEEEcCCceEEEEEeccCCcccCcCCHHHHHHHHHHhhC-CCeEEEEEEeeeeecCCCCCCCHHHHHHHHHHhcCC
Confidence 99999998777789999853 579999999999999976 468999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHhHhc-CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCC--CCCCCCCCCCCc
Q psy8714 312 GPHHAMQIAERLYTQ-GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPR--KGKDVGDHPPIT 386 (562)
Q Consensus 312 s~~~tl~iaQ~LYE~-glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~H~AI~ 386 (562)
||++||++||+|||+ ||||||||||++||+++ ++.++|+.+.... +......... ...+.+ +.++++||||||
T Consensus 300 s~~~tm~iAQ~LYE~~glITYpRTDS~~ls~~~~~~~~~~i~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~aH~AI~ 377 (660)
T TIGR01056 300 SAKRTLDIAQKLYETHKLITYPRTDSRYLPEDEKEMLLEVLDALKVIT-PALLPIKKRD-ELTNNRLWNDKKIEDHHAII 377 (660)
T ss_pred CHHHHHHHHHHHHHhCCEEEEecCCCccCCHHHHHHHHHHHHHhhccc-hhhhcccccc-cccccCcCCCCccCCcCCcc
Confidence 999999999999998 99999999999999986 4666776654321 1111100001 001111 223457899999
Q ss_pred cCCCcc-cCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccc----cCCC
Q psy8714 387 PTKLAT-RTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMK----NESI 461 (562)
Q Consensus 387 PT~~~~-~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~----~~~L 461 (562)
||...+ ...|+++|++||+||++||||+||+||+|++|+|.+.++++.|+++|++++++||+.+|+..+.+ +..|
T Consensus 378 PT~~~~~~~~L~~de~klY~LI~~Rflas~~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~~~L 457 (660)
T TIGR01056 378 PTGNDFNLSDLSEEERNVYKLIAQNYLMQFMPKEEYETTTIEIAIGKLMFEAKGKILQDNGWKALLGKQEEDEETEDTTL 457 (660)
T ss_pred ccCCccccccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECCEEEEEEEEEEcccCHHHHhcccccccccccccC
Confidence 998643 35899999999999999999999999999999999999999999999999999999999653322 2359
Q ss_pred CCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHH-----------------hcCCCCcCchhHHHHHhhcCCeEEEc
Q psy8714 462 PDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLME-----------------KHGIGTDASIPVHINNICQRNYVTVT 524 (562)
Q Consensus 462 p~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me-----------------~~GIGTpATra~iI~~L~~r~Yi~~~ 524 (562)
|.+++||.+.+.++.+.+++|+||+||||++||++|| +.|||||||||+||++|++||||+.
T Consensus 458 P~l~~G~~~~~~~~~~~~~~TkPP~ryTeasLi~~Me~~~k~v~d~~l~~~l~e~~GIGtpATrA~iI~~L~~R~Yv~~- 536 (660)
T TIGR01056 458 PAFQKGDELDVETLELLEKQTKPPARYTEGTLLSAMTNPAAFVQDKGLKKTLKETKGLGTEATRADIIENLFKRGFIQK- 536 (660)
T ss_pred CCCCCCCEeeeeecccccCcCCCCCCcCHHHHHHHHHhhhhcccCHHHHHHhhhccCCCCcccHHHHHHHHHhCCCEEe-
Confidence 9999999999999999999999999999999999999 7899999999999999999999997
Q ss_pred CCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 525 SGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 525 ~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
+|+.|+||++|+.|+++|. +.|++|+|||.||.+|
T Consensus 537 ~~k~l~pT~~G~~v~~~L~---~~i~~~~~Ta~~E~~L 571 (660)
T TIGR01056 537 KKNKIYITKNGKLLCLLLP---ELLTKPDLTAQWEQYL 571 (660)
T ss_pred eCCEEEEcHHHHHHHHHhH---HhcCChhHHHHHHHHH
Confidence 6789999999999999974 5799999999999876
No 10
>PRK07726 DNA topoisomerase III; Provisional
Probab=100.00 E-value=4.8e-127 Score=1074.28 Aligned_cols=528 Identities=25% Similarity=0.394 Sum_probs=454.3
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEeccccccccccc----CCCCCccCCCCCCC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTS----KYNNWDKVDPLELF 81 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~----~y~~W~~~~p~~~~ 81 (562)
|+|||||| ||+|+.||.++|..+ ..+|||+|++ |+||||.|||++|+.|+ +|+.|+..++ ++.
T Consensus 1 ~~LiIaEK-----Ps~Ak~Ia~~L~~~~-----~~~g~~~g~~--~~Vt~~~GHl~~L~~p~~y~~~~~~W~~~~l-pi~ 67 (658)
T PRK07726 1 MRLFIAEK-----PSVGRDIADVLKPHK-----KGDGYIEGNG--YIVTWAIGHLLELAEPEAYDERYKRWRLEDL-PII 67 (658)
T ss_pred CeEEEEeC-----HHHHHHHHHHhCCcc-----CCCCeEeCCC--EEEEechhhhccCCCchhcccccCccccccC-CCC
Confidence 68999999 999999999998543 2479999874 78999999999997655 5567876542 121
Q ss_pred CCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714 82 SCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW 161 (562)
Q Consensus 82 ~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~ 161 (562)
+............++++.|++++++||+||||||||||||+|||+|+++++ +++||+|+|||++|+++|++||+
T Consensus 68 p~~~~~~~~~~~~~~~~~ik~l~~~~d~Ii~AtD~DREGE~I~~~i~~~~~------~~~~v~Rl~~sslt~~~I~~A~~ 141 (658)
T PRK07726 68 PEKWKLVVKKKTAKQFNVVKKLLKQATEIVIATDADREGELIAREILDYCG------VRKPIKRLWISSLTDKAIKRAFA 141 (658)
T ss_pred cccceeeeccchHHHHHHHHHHHhhCCeEEEcCCCCccccHHHHHHHHHhC------CCCCeEEEEEccCCHHHHHHHHH
Confidence 111111111223467788888889999999999999999999999999994 36899999999999999999999
Q ss_pred hCCCCh--HhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEE
Q psy8714 162 NLVKPN--IFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLL 239 (562)
Q Consensus 162 nl~~~~--~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i 239 (562)
||++++ .+++.||.||+++|||||||+||++|+.+++.+. ++++|+||||||||+|||+||++|+||+|++||+|
T Consensus 142 nl~~~~~~~~l~~aa~aR~~~D~liG~nlSr~~t~~~~~~g~---~~~lS~GRVQTPtL~lVv~Re~eI~~F~p~~y~~i 218 (658)
T PRK07726 142 NLKPGKETIPLYYSALARSRADWLVGINMTRAYTLLGRKAGY---NGVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEV 218 (658)
T ss_pred hcCCchhhHHHHHHHHHHHHHHHHhhhhHhHHHHHHHhhcCC---CcceeecccccchhHHHHHHHHHHHcCCCcccEEE
Confidence 999975 5889999999999999999999999998764321 34799999999999999999999999999999999
Q ss_pred EEEEeeCCeEEEEEee--------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCC
Q psy8714 240 DLTLNLNGVAVSVTWS--------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGM 311 (562)
Q Consensus 240 ~~~~~~~~~~~~~~~~--------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~ 311 (562)
.+.+ .+|..|.+.|. +++++|++.|+.+++.+.+ +.++|.+|++++++++||+||||++||++||++|||
T Consensus 219 ~~~~-~~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~pP~pf~ls~Lq~~a~~~~g~ 296 (658)
T PRK07726 219 EAHL-TPGERFTAKWQPSEPYQDEEGRLLDRPLAEQVVARIQG-QPAKVTEVETKRKKEYAPLLYDLSELQIDANKRFGL 296 (658)
T ss_pred EEEE-cCCCeEEEEEeccccccccccccCCHHHHHHHHHHhcC-CCeEEEEEEeeEEecCCCCCCCHHHHHHHHHHhcCC
Confidence 9999 56678889995 3689999999999999975 479999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHhHhc-CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCC--CCCCCCCCCCc
Q psy8714 312 GPHHAMQIAERLYTQ-GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRK--GKDVGDHPPIT 386 (562)
Q Consensus 312 s~~~tl~iaQ~LYE~-glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~H~AI~ 386 (562)
||++||++||+|||+ ||||||||||++||+++ ++..+++.+.....|...+..++... .+.+. .++++||||||
T Consensus 297 s~~~tl~iaQ~LYE~~glITYPRTds~~ls~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~aH~AI~ 375 (658)
T PRK07726 297 SAKETLDIAQSLYETHKLITYPRTDSRYLPEDMVATLPEVLNAISKVDPYLLLAPPVLDPS-IRSRAWNDKKVTAHHAII 375 (658)
T ss_pred CHHHHHHHHHHHHHhcCEEEecCCCCccCCHHHHHHHHHHHHHHhccCcchhhhhhhhccc-cccCcCCCCcCCCCCCcC
Confidence 999999999999997 99999999999999986 57888888865555655444333221 12232 23458999999
Q ss_pred cCCCcc-cCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccc---cCCCC
Q psy8714 387 PTKLAT-RTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMK---NESIP 462 (562)
Q Consensus 387 PT~~~~-~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~---~~~Lp 462 (562)
||...+ ..+|+++|++||+||+|||||+|||||+|++|+|.+.++++.|.++|++++++||+.+|+.++.+ +..||
T Consensus 376 PT~~~~~~~~L~~~e~~iY~lI~~r~la~~~~~~~~~~t~v~~~~~~~~F~~~g~~i~~~Gw~~v~~~~~~~~~~~~~lp 455 (658)
T PRK07726 376 PTEQPPNLSKLSEDERKVYDLIARRYLAQFLPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEKEQPLP 455 (658)
T ss_pred ccCCCCCcccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECCEEEEEEEEEEccCCHHHHcccccccccccccCC
Confidence 998643 35799999999999999999999999999999999999999999999999999999999653322 23599
Q ss_pred CCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhc-----------------CCCCcCchhHHHHHhhcCCeEEEcC
Q psy8714 463 DFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKH-----------------GIGTDASIPVHINNICQRNYVTVTS 525 (562)
Q Consensus 463 ~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~-----------------GIGTpATra~iI~~L~~r~Yi~~~~ 525 (562)
.+++|+.+.+.++.+.+++|+||+||||++||++||+. |||||||||+||++|++||||.+ +
T Consensus 456 ~l~~g~~~~~~~~~~~e~~TkPP~~yTe~tLi~~Me~~~k~v~d~~~~~~l~e~~GIGTpATra~iIe~L~~R~Yi~~-~ 534 (658)
T PRK07726 456 VLAKGDELKVEKGEVKEGQTQPPKRFTEGTLLSAMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLEK-K 534 (658)
T ss_pred CcCCCCEeeecccccccccCCCCCCcCHHHHHHHHHhhhhhccCHHHHHhhcccCCCCccccHHHHHHHHHhCCCEEe-c
Confidence 99999999999999999999999999999999999875 99999999999999999999997 6
Q ss_pred CCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 526 GRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 526 ~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
|+.|+||++|+.|+++|. ..|++|+|||.||.+|
T Consensus 535 ~k~l~pT~~G~~li~~l~---~~l~~p~~Ta~~E~~L 568 (658)
T PRK07726 535 GKYIHATDKGKQLIDALP---EELTSPDMTAKWEQAL 568 (658)
T ss_pred CCEEEECHHHHHHHHHHH---HHcCChhhHHHHHHHH
Confidence 789999999999999874 4599999999999876
No 11
>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=6.9e-123 Score=1032.78 Aligned_cols=501 Identities=25% Similarity=0.385 Sum_probs=432.7
Q ss_pred EEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCccc
Q psy8714 8 LVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTEK 87 (562)
Q Consensus 8 l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~~~ 87 (562)
|||||| ||+|+.|+.++| + .|+||||.|||++|..|+.|.+|... |. |..
T Consensus 1 LiIaEk-----ps~a~~Ia~~lg----------------~--~~~Vt~~~GHl~~l~~~~~~~~~~~~-----~~-~~~- 50 (610)
T TIGR01051 1 LVIVES-----PAKAKTIKKYLG----------------D--EYEVEASMGHIRDLPKSRLGVDIEKD-----FE-PEY- 50 (610)
T ss_pred CEEEeC-----hHHHHHHHHHhC----------------C--CCEEEeccCeeccCCCcccCCChhhc-----Cc-eeE-
Confidence 799999 999999998775 1 25799999999999877666677542 11 111
Q ss_pred ccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcE-EEEEecccCHHHHHHHHHhCCCC
Q psy8714 88 REATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTV-WRARFSAITDKDIKAAMWNLVKP 166 (562)
Q Consensus 88 ~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v-~Rl~~sslt~~~I~~A~~nl~~~ 166 (562)
.....+.++++.|++++++||+||||||||||||+|||+|+++++ +++|+ +|+|||++|+++|++||+||+++
T Consensus 51 ~~~~~~~~~~~~i~~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~------~~~~~~~Rl~~s~lt~~~I~~a~~~l~~~ 124 (610)
T TIGR01051 51 VVSKGKKKVVKELKTLAKKADEVYLATDPDREGEAIAWHLAEVLK------PKDPVYKRIVFNEITKKAIRAALKNPREI 124 (610)
T ss_pred EEcccHHHHHHHHHHHHhcCCEEEECCCCCcchhHHHHHHHHHhC------CCCCCceEEEEccCCHHHHHHHHhCcccc
Confidence 111223467788888889999999999999999999999999995 34666 99999999999999999999999
Q ss_pred hHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEeeC
Q psy8714 167 NIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLN 246 (562)
Q Consensus 167 ~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~~ 246 (562)
+.++++||.||+++|||||||+||++|+.++ ..+|+||||||||+|||+||++|+||+|++||.|.+.+..+
T Consensus 125 ~~~l~~aa~aR~~~D~liG~n~Tr~~t~~~~--------~~lSvGRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~ 196 (610)
T TIGR01051 125 DMNLVNAQQARRILDRLVGYTLSPLLWKKVA--------KGLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKG 196 (610)
T ss_pred chhHHHHHHHHHHHHHHHhHhhhHHHHHhhc--------CCCCcceehHHHHHHHHHHHHHHHhcCCCceEEEEEEEecC
Confidence 9999999999999999999999999998543 13999999999999999999999999999999999999877
Q ss_pred CeEEEEEee--------cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHH
Q psy8714 247 GVAVSVTWS--------RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQ 318 (562)
Q Consensus 247 ~~~~~~~~~--------~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~ 318 (562)
++.|.+.|. .++++|+++|+++++.+.+ +.++|.+|+.++++++||+||||++||++||++|||||++||+
T Consensus 197 ~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~S~~~tl~ 275 (610)
T TIGR01051 197 EETFEALLTEVNGKKLKAGSDLDEAEATALKEQLKG-EELVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKTMM 275 (610)
T ss_pred CcceEEEEEecCCccccccccCCHHHHHHHHHHhcC-CCeEEEEEeeceeeeCCCCCcCHHHHHHHHHHhcCCCHHHHHH
Confidence 778888773 2478999999999999976 5789999999999999999999999999999999999999999
Q ss_pred HHHHhHhc--------CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCC-CCCCCCC-CCCCCCc
Q psy8714 319 IAERLYTQ--------GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISK-PRKGKDV-GDHPPIT 386 (562)
Q Consensus 319 iaQ~LYE~--------glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~-~~~~~~~-~~H~AI~ 386 (562)
+||+|||+ |+||||||||+|||+++ .+..+++.+.. . .++.....+ +...+.+ +|||||+
T Consensus 276 iaQ~LYe~~~~~~~~~g~iSYPRTds~~l~~~~~~~~~~~l~~~~~-----~---~~~~~~~~~~~~~~k~~~~~H~aI~ 347 (610)
T TIGR01051 276 IAQRLYEGVSTGDGTIGLITYMRTDSTRLSNQAVNEARNLIDKNYG-----K---EYLGPKPKRYKSKEKNAQEAHEAIR 347 (610)
T ss_pred HHHHHHhcccccCCceeEEeecCcCccccCHHHHHHHHHHHHHhhh-----H---hhccccCcccCCCCCCCCCCcCCCC
Confidence 99999999 99999999999999975 35555554321 1 112111111 2222324 7899999
Q ss_pred cCCCc--cc---CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEE--CCeEEEEEEEEEeecceeeeeccccc---
Q psy8714 387 PTKLA--TR---TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSV--ADEMFTMEAKYLLHPGFTGVMTWSAM--- 456 (562)
Q Consensus 387 PT~~~--~~---~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~--~~~~F~a~g~~~~~~Gw~~v~~~~~~--- 456 (562)
||... +. +.|+++|++||+||+|||||+|||||+|++|++.+.+ +++.|.++|++++++||+.+|+.+..
T Consensus 348 Pt~~~~~~~~~~~~Ls~~e~~iY~lI~rr~la~~~~~~~~~~t~v~~~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~ 427 (610)
T TIGR01051 348 PTSVFRTPEELKDYLKRDEFRLYELIWKRFVASQMADARYDSTSVRLTNEDGEYVFKATGRKLIFDGYYKVYVEGSDDPL 427 (610)
T ss_pred CCCCCcChhhhhccCCHHHHHHHHHHHHHHHHHhCccceEEEEEEEEEEcCCCeEEEEEEEEEEeCCHHHhccccccccc
Confidence 99763 22 4799999999999999999999999999999999999 99999999999999999999975422
Q ss_pred --ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchh
Q psy8714 457 --KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSL 534 (562)
Q Consensus 457 --~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~ 534 (562)
++..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.+ +|+.|+||++
T Consensus 428 ~~~~~~Lp~l~~g~~~~~~~~~~~~~~T~PP~~yTe~tLl~~Me~~GIGTpATra~iIe~L~~r~Yi~~-~~~~l~pT~~ 506 (610)
T TIGR01051 428 EEKDRILPPLKEGDAVKLVEVKPNQHFTQPPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKK-ENKRLYPTEL 506 (610)
T ss_pred ccccccCCCCCCCCEeEeeeeeeccccccCCCCCCHHHHHHHHhcCCCCccccHHHHHHHHhhCCeEEe-eCCEEeECHH
Confidence 1345999999999999999999999999999999999999999999999999999999999999997 6789999999
Q ss_pred HHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 535 GIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 535 G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
|+.|+++|....++|++|+|||.||..|
T Consensus 507 G~~li~~l~~~~~~l~~p~lTa~~E~~L 534 (610)
T TIGR01051 507 GFAVTDLLEKHFGDVVDYDFTAKMEKDL 534 (610)
T ss_pred HHHHHHHHHHhhhhhcCHHHHHHHHHHH
Confidence 9999999977667899999999999876
No 12
>PRK05582 DNA topoisomerase I; Validated
Probab=100.00 E-value=4.7e-121 Score=1026.49 Aligned_cols=499 Identities=23% Similarity=0.367 Sum_probs=429.0
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCC----CC-CccCCCCCC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKY----NN-WDKVDPLEL 80 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y----~~-W~~~~p~~~ 80 (562)
+.|||||| ||+|+.|++++|. .|+|+||.|||++|..+ .+ .. |. | .
T Consensus 3 ~~LiIaEk-----ps~a~~ia~~lg~------------------~~~V~~~~GHl~~l~~~-~~~~~~~~~~~---~--~ 53 (650)
T PRK05582 3 KKLVIVES-----PAKAKTIEKYLGK------------------NYKVVASMGHIRDLPKS-QLGIDIENNFE---P--K 53 (650)
T ss_pred CeEEEEeC-----HHHHHHHHHHcCC------------------CCEEEeccCchhcCCCc-cCCCCcccCCc---e--e
Confidence 46999999 9999999987752 26799999999999753 11 01 22 1 1
Q ss_pred CCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHH
Q psy8714 81 FSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM 160 (562)
Q Consensus 81 ~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~ 160 (562)
|.. .....++++.|++++++||+||||||||||||+|||||+++++. + .++++|+||||+|+++|++||
T Consensus 54 ~~~------~~~~~~~~~~ik~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~----~-~~~~~R~~~s~lt~~~I~~a~ 122 (650)
T PRK05582 54 YIT------IRGKGPVIKELKKAAKKAKKVYLATDPDREGEAIAWHLAHILGL----D-EKEKNRIVFNEITKDAIKNAF 122 (650)
T ss_pred eEE------CCcHHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhCC----C-CCCceEEEEcccCHHHHHHHH
Confidence 110 11223577888888899999999999999999999999999952 1 278899999999999999999
Q ss_pred HhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEE
Q psy8714 161 WNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD 240 (562)
Q Consensus 161 ~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~ 240 (562)
+||++++.++++||.||+++||+||||+||++|+.+++ .+|+||||||||+|||+||++|+||+|++||+|.
T Consensus 123 ~nl~~~~~~l~~a~~aR~~~D~liG~n~tr~~t~~~~~--------~ls~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~ 194 (650)
T PRK05582 123 KNPRKIDMNLVDAQQARRILDRLVGYKLSPLLWKKVKK--------GLSAGRVQSVALKLIIDREKEIRAFVPEEYWTID 194 (650)
T ss_pred hCcccccHHHHHHHHHHHHHHHHhhhhcCHHHHHhhcC--------CCccccchHhHHHHHHhHHHHHHhCCCCccEEEE
Confidence 99999999999999999999999999999999986431 3899999999999999999999999999999999
Q ss_pred EEEeeCCeEEEEEee-----cccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHH
Q psy8714 241 LTLNLNGVAVSVTWS-----RGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHH 315 (562)
Q Consensus 241 ~~~~~~~~~~~~~~~-----~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~ 315 (562)
+.+..++..|.+.|. .++++|+++|+++++.+.+ +.++|++|++++++.+||+||||++||++||++|||||++
T Consensus 195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~v~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~ 273 (650)
T PRK05582 195 AEFKKGKKKFEASFYGYKGKKIELKNEEDVKEILAELKK-KDFKVSKVKKKERKRNPPPPFTTSTLQQEAARKLNFSTKK 273 (650)
T ss_pred EEEecCCccEEEEEEecCCCccccCCHHHHHHHHHHhcC-CCeEEEEEeeeeeecCCCCCccHHHHHHHHHHHcCCCHHH
Confidence 999766666888763 4689999999999999976 5799999999999999999999999999999999999999
Q ss_pred HHHHHHHhHh---------cCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCC-CCCC
Q psy8714 316 AMQIAERLYT---------QGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDV-GDHP 383 (562)
Q Consensus 316 tl~iaQ~LYE---------~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~H~ 383 (562)
||++||+||| +||||||||||++||+++ .+..++..+. + ..++.....+..+.+++ +|||
T Consensus 274 tl~~aQ~LYe~~~~~~~~~~gliSYPRTds~~l~~~~~~~~~~~~~~~~-----~---~~~~~~~~~~~~~~~k~~~~H~ 345 (650)
T PRK05582 274 TMMIAQQLYEGIDLGKQGTVGLITYMRTDSTRISDTAQEEAREFIEEKY-----G---KEYLPKKPKVYKKKSGAQDAHE 345 (650)
T ss_pred HHHHHHHHhcccccCCCCceEEEEecCCCcccCCHHHHHHHHHHHHHHh-----H---HHhhccCCcccCCCcCCCCCCC
Confidence 9999999999 699999999999999975 2445444321 1 11121111112233345 5899
Q ss_pred CCccCCCc--cc---CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccccccc
Q psy8714 384 PITPTKLA--TR---TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKN 458 (562)
Q Consensus 384 AI~PT~~~--~~---~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~ 458 (562)
||+||... +. +.|+++|++||+||+|||||+|||||+|++|+|.++++++.|+++|++++++||+.+|+.++.++
T Consensus 346 aI~PT~~~~~p~~~~~~L~~~e~~iY~lI~~rfla~~~~~~~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~~~~~~~~~~ 425 (650)
T PRK05582 346 AIRPTSVFLTPESAKKYLTKDQLKLYKLIWNRFVASQMAPAVFDTVSVDLENNGVKFRASGSKVKFDGFMKVYVGDEEKD 425 (650)
T ss_pred CEeecCCCcChhHHhccCCHHHHHHHHHHHHHHHHHhCchhheeEEEEEEEeCCEEEEEEEEEEeeCChHhhcCCccccc
Confidence 99999862 22 47999999999999999999999999999999999999999999999999999999997433335
Q ss_pred CCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHH
Q psy8714 459 ESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVL 538 (562)
Q Consensus 459 ~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~l 538 (562)
..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.. +|+.|+||++|+.|
T Consensus 426 ~~lp~l~~g~~~~~~~~~~~~~~T~PP~~~Te~~Ll~~Me~~GIGT~ATra~iI~~L~~r~Yi~~-~~k~l~pT~~G~~l 504 (650)
T PRK05582 426 KMLPELEEGEKVKLKKIEPEQHFTQPPARYTEASLIKTLEELGIGRPSTYAPTISTIQKRGYVKL-EKKRLVPTELGEIV 504 (650)
T ss_pred ccCCCCCCCCEeEEEEeeecccccCCCCCCCHHHHHHHHHHcCCCCcccHHHHHHHHHhCCeEEe-eCCEEeecHHHHHH
Confidence 56999999999999999999999999999999999999999999999999999999999999997 67899999999999
Q ss_pred HHhhhccCccCCChhhHHHHHhhC
Q psy8714 539 VHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 539 i~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
+++|....++|++|+|||.||.+|
T Consensus 505 ~~~l~~~~~~l~~p~lTa~~E~~L 528 (650)
T PRK05582 505 NELLEEFFPDIVDVEFTAEMEEKL 528 (650)
T ss_pred HHHHHHhchhhcCHHHHHHHHHHH
Confidence 999987777899999999999876
No 13
>PRK08780 DNA topoisomerase I; Provisional
Probab=100.00 E-value=2.3e-120 Score=1032.28 Aligned_cols=507 Identities=22% Similarity=0.328 Sum_probs=430.6
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCC-C-CCccCCCCCCCCC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKY-N-NWDKVDPLELFSC 83 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y-~-~W~~~~p~~~~~~ 83 (562)
|.|||||| |+.|+.|++.+|. .|+|+||.|||++|..|+.+ . .|. +.| .|..
T Consensus 3 ~~LiIvEs-----PskAk~I~~~Lg~------------------~y~V~as~GHi~dL~~~~~~vd~~~~-f~~--~y~~ 56 (780)
T PRK08780 3 KHLVIVES-----PAKAKTINKYLGK------------------DFTVLASYGHVRDLVPKEGAVDPENG-FAM--RYDL 56 (780)
T ss_pred CeEEEEeC-----HHHHHHHHHHcCC------------------CCEEEeccCCcccCCCcccCCChhhC-Cce--EEEE
Confidence 67999999 9999999976552 26799999999999755443 2 111 111 1111
Q ss_pred CcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhC
Q psy8714 84 PTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163 (562)
Q Consensus 84 ~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl 163 (562)
...+.++++.|++++++||+||||||||||||+|||||+++|+.. +....++|+|+|||+||+++|++||+|+
T Consensus 57 ------~~~k~~~~~~lk~~~k~ad~vilAtD~DREGE~Ia~~i~~~l~~~-~~~~~~~v~Ri~f~eiT~~aI~~A~~n~ 129 (780)
T PRK08780 57 ------IDKNEKHVEAIAKAAKSADDLYLATDPDREGEAISWHLAEILKER-GLLKDKPMQRVVFTEITPRAIKEAMAKP 129 (780)
T ss_pred ------cCchHHHHHHHHHHHHhCCEEEECCCCCcccHHHHHHHHHHhccc-ccCCCCceEEEEEccCCHHHHHHHHhCC
Confidence 112346889999999999999999999999999999999999632 0011478999999999999999999999
Q ss_pred CCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEE
Q psy8714 164 VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL 243 (562)
Q Consensus 164 ~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~ 243 (562)
+++|+++++||+||+++|||||||+||++|..++ +.+|+||||||||+|||+||+||++|+|++||.|.+.+
T Consensus 130 r~~d~~l~~A~~aRr~lD~lvG~~lSr~l~~~~~--------~~lSaGRVQspaL~lIveRE~eI~~F~p~~yw~i~~~~ 201 (780)
T PRK08780 130 RDIASDLVDAQQARRALDYLVGFNLSPLLWRKIQ--------RGLSAGRVQSPALRMIVEREEEIEAFIAREYWSIEADC 201 (780)
T ss_pred CcCcHhHHHHHHHHHHHHHhcCeeecHHHHHhhC--------CCCcccccHHHHHHHHHHHHHHHHhCCCcceEEEEEEE
Confidence 9999999999999999999999999999997653 23899999999999999999999999999999999999
Q ss_pred eeCCeEEEEEeec--------ccccCHHHHHHHHHHhhh--cCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCH
Q psy8714 244 NLNGVAVSVTWSR--------GHIFDKSTCNVFFKAVEK--EKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGP 313 (562)
Q Consensus 244 ~~~~~~~~~~~~~--------~~~~~~~~a~~~~~~~~~--~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~ 313 (562)
..++..|.+.|.. .+++|+++|+++++.|.+ ...++|.+|++++++.+||+||+|++||++||++|||||
T Consensus 202 ~~~~~~f~a~~~~~~~~~~~~~~~~~~~~a~~i~~~~~~~~~~~~~V~~v~~k~~~~~pp~Pf~tstLQq~As~klg~s~ 281 (780)
T PRK08780 202 AHPSQPFNAKLIKLDGQKFEQFTITDGDTAEAARLRIQQAAQGTLHVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTT 281 (780)
T ss_pred ecCCceEEEEEEecCCccccccccCCHHHHHHHHHHHhhccCCCeEEEEEEeeeeecCCCCCccHHHHHHHHHHHcCCCH
Confidence 8767778877742 368999999999999974 247899999999999999999999999999999999999
Q ss_pred HHHHHHHHHhHhc---------CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCC-CCC-CCCCC
Q psy8714 314 HHAMQIAERLYTQ---------GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISK-PRK-GKDVG 380 (562)
Q Consensus 314 ~~tl~iaQ~LYE~---------glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~-~~~-~~~~~ 380 (562)
++||++||+|||. ||||||||||++||++. ++...|..+.... .+...... +.+ .+..+
T Consensus 282 ~~Tm~iAQ~LYE~~~~~~~~~~glITYpRTDS~~ls~~~~~~~~~~i~~~~g~~--------~~~~~~~~~~~~~~~~q~ 353 (780)
T PRK08780 282 RRTMQVAQKLYEGVDLGDEGSVGLITYMRTDSVNLSQDALAEIRDVIARDYGTA--------SLPDQPNTYKTKSKNAQE 353 (780)
T ss_pred HHHHHHHHHHHhhcccccCCceeEEEecccCCccCCHHHHHHHHHHHHHHhChh--------hhhhcccccCCCCCCCcC
Confidence 9999999999997 99999999999999875 3455554432211 11111111 112 22347
Q ss_pred CCCCCccCCCc--cc---CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECC-eEEEEEEEEEeecceeeeeccc
Q psy8714 381 DHPPITPTKLA--TR---TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVAD-EMFTMEAKYLLHPGFTGVMTWS 454 (562)
Q Consensus 381 ~H~AI~PT~~~--~~---~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~-~~F~a~g~~~~~~Gw~~v~~~~ 454 (562)
||||||||... +. ..|+++|++||+|||+||||+||+||+|++|+|.+.+++ +.|+++|++++++||+.+|...
T Consensus 354 aHeAI~PT~~~~~p~~~~~~L~~de~klY~LI~~R~lAs~m~~a~~~~t~v~~~~~~~~~F~a~G~~i~~~G~~~vy~~~ 433 (780)
T PRK08780 354 AHEAVRPTSALRTPAQVARFLSDDQRRLYELIWKRAVACQMIPATLNTVSVDLAAGSEHVFRATGSTVVVPGFLAVYEEG 433 (780)
T ss_pred CCCCCCCCCCCcChhhhhccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEeCCeeEEEEEEEEEeEcCeEEeeccc
Confidence 79999999753 21 479999999999999999999999999999999999987 7999999999999999999653
Q ss_pred cc----c--c--CCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCC
Q psy8714 455 AM----K--N--ESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSG 526 (562)
Q Consensus 455 ~~----~--~--~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~ 526 (562)
.. + + ..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.. +|
T Consensus 434 ~~~~~~~~~~~~~~LP~l~~G~~~~~~~~~~~~~~T~PP~ryTEasLik~mE~~GIGtpST~A~iI~~L~~R~Yv~~-~~ 512 (780)
T PRK08780 434 KDDKSAEDEDEGRKLPPMKEGDNVPLERIRAEQHFTEPPPRYTEASLVKALEEYGIGRPSTYASIISTLQFRKYVEM-EG 512 (780)
T ss_pred cccccccccchhccCCCcCCCCEeeeeeeeeeeeecCCCCCCCHHHHHHHHHhCCCCchhhHHHHHHHHHhCCcEec-cC
Confidence 21 1 1 45999999999999999999999999999999999999999999999999999999999999997 67
Q ss_pred CeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 527 RRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 527 k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
++|+||++|+.|+++|...++.|+||+|||.||.+|
T Consensus 513 k~l~pT~~G~~v~~~L~~~f~~l~~~~~Ta~~E~~L 548 (780)
T PRK08780 513 RRFRPTDVGRAVNKFLTGHFTRYVDYDFTARLEDDL 548 (780)
T ss_pred CEEeecHHHHHHHHHHHHhchhcCCHHHHHHHHHHH
Confidence 799999999999999988888999999999999876
No 14
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=100.00 E-value=4e-120 Score=1042.97 Aligned_cols=506 Identities=26% Similarity=0.400 Sum_probs=435.9
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEeccccccccc-----ccCCCC--Ccc--CC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDF-----TSKYNN--WDK--VD 76 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~-----~~~y~~--W~~--~~ 76 (562)
|.|||||| |+.|+.|++.+| . .|+|+||+|||++|.. |++|+. |.. .+
T Consensus 2 ~~LvIvEk-----P~kak~I~~~Lg----------------~--~~~V~~s~GHi~dL~~~~~~~~~~~k~~~w~~l~i~ 58 (859)
T PRK07561 2 KSLVIVES-----PAKAKTINKYLG----------------S--DYVVKASVGHIRDLPTSASSVPAKEKGALWARMGVD 58 (859)
T ss_pred CEEEEEeC-----HHHHHHHHHHcC----------------C--CCEEEeccCChhhCCCccccChhhhhhchHhhcCcC
Confidence 68999999 999999997665 2 2679999999999975 455653 431 22
Q ss_pred CCCCCCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHH
Q psy8714 77 PLELFSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDI 156 (562)
Q Consensus 77 p~~~~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I 156 (562)
|.+.|.... .....+.++++.|++++++||+||||||||||||+|||||+++++. ++++|+|+|||+||+++|
T Consensus 59 ~~~~f~~~y--~~~~~k~~~~~~lk~~~k~ad~iilAtD~DREGE~I~~~i~~~l~~-----~~~~v~Ri~f~~iT~~aI 131 (859)
T PRK07561 59 PDHDFEALY--EVLPGKEKVVSELKKAAKDADELYLATDPDREGEAIAWHLLEVLGG-----DDVPVKRVVFNEITKNAI 131 (859)
T ss_pred cccCcceeE--EECccHHHHHHHHHHHHhcCCEEEECCCCCccchHHHHHHHHHhCC-----CCCCeEEEEEccCCHHHH
Confidence 333332111 1112344789999999999999999999999999999999999952 368999999999999999
Q ss_pred HHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcce
Q psy8714 157 KAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPY 236 (562)
Q Consensus 157 ~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y 236 (562)
++||+|++++|.++++||+||+++|||||||+||++|..++ ..+|+||||||||+|||+||+||++|+|++|
T Consensus 132 ~~A~~n~~~~~~~l~~A~~aRr~lD~lvG~~lS~~l~~~~~--------~~lSaGRVQsp~L~lIv~Re~eI~~F~p~~y 203 (859)
T PRK07561 132 QEAFENPRELDINLVNAQQARRFLDRLVGYMVSPLLWKKIA--------RGLSAGRVQSVAVRLIVEREREIEAFVPEEY 203 (859)
T ss_pred HHHHhCcccCCHHHHHHHHHHHHHHHHhhhhcCHHHHHhhc--------cCCCcccchhhhhHHHHHHHHHHHhcCCCcc
Confidence 99999999999999999999999999999999999987643 2399999999999999999999999999999
Q ss_pred EEEEEEEee-CCeEEEEEeec--------ccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHh
Q psy8714 237 WLLDLTLNL-NGVAVSVTWSR--------GHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASS 307 (562)
Q Consensus 237 ~~i~~~~~~-~~~~~~~~~~~--------~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~ 307 (562)
|.|.+.+.. +|..|.+.|.. .+++|+++|+++++.+.+ ..++|.+|+.++++.+||+||+|++||++||+
T Consensus 204 w~i~~~~~~~~~~~f~a~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~pp~pf~ts~LQ~~As~ 282 (859)
T PRK07561 204 WDIHADLTTPRGDAFEARLTHLDGKKFAPVDLLNEAQAEAAVAALEG-ARYSVASVEDKPTTRKPSAPFTTSTLQQEASR 282 (859)
T ss_pred EEEEEEEEecCCCeEEEEEEeeCCceecccccCCHHHHHHHHHHhcC-CCeEEEEEEeceeEecCCCCccHHHHHHHHHH
Confidence 999999976 56678876631 247999999999999976 47899999999999999999999999999999
Q ss_pred hCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCCC--C-C--CC
Q psy8714 308 GLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKG--K-D--VG 380 (562)
Q Consensus 308 ~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~--~-~--~~ 380 (562)
+|||||++||++||+|||+||||||||||++||++. ++..+|..+ |+. .++. ..+|.+ + + .+
T Consensus 283 klg~s~~~tm~~aQ~LYE~glITYpRTDs~~ls~~~~~~~~~~i~~~-----~g~---~~~~---~~~r~~~~~~k~~q~ 351 (859)
T PRK07561 283 KLGFSVKKTMRIAQRLYEAGYITYMRTDSTNLSQEAINAARGYIGDN-----YGK---KYLP---EKPRQYSSKAKNAQE 351 (859)
T ss_pred hcCCCHHHHHHHHHHHHhCCeEEecCCCCCcCCHHHHHHHHHHHHHH-----hhh---hhcc---cCCccCCCcCCCCCC
Confidence 999999999999999999999999999999999874 355555543 221 1222 123332 1 2 26
Q ss_pred CCCCCccCCCc--cc--CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccccc
Q psy8714 381 DHPPITPTKLA--TR--TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAM 456 (562)
Q Consensus 381 ~H~AI~PT~~~--~~--~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~ 456 (562)
||||||||... +. ..|+++|++||+|||+||||+||+||+|++|+|.+.++++.|+++|++++++||+.+|..+..
T Consensus 352 aHeAI~Pt~~~~~~~~~~~L~~~e~~lY~LI~~R~lAs~m~~a~~~~~~v~~~~~~~~F~a~g~~i~~~G~~~vy~~~~~ 431 (859)
T PRK07561 352 AHEAIRPSDVFRTPDQLKGLEGDAQRLYELIWKRFVASQMAPARYDSTTVTIAAGDAELRATGRVLRFDGFLKVYVEGRD 431 (859)
T ss_pred CcCCcccCCCCcChhhhccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCCEEEEEEEEEEeeCCchheeccccc
Confidence 79999999652 21 469999999999999999999999999999999999999999999999999999999975432
Q ss_pred c-----cCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeec
Q psy8714 457 K-----NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVP 531 (562)
Q Consensus 457 ~-----~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~ 531 (562)
+ +..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.. +|+.|+|
T Consensus 432 ~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~T~PP~ryTeasLv~~me~~GIGtpsT~a~iI~~L~~R~Yv~~-~~~~l~p 510 (859)
T PRK07561 432 DALDDEDRRLPALKVGDALTLEKLDPTQHFTKPPARYSEASLVKELEKLGIGRPSTYASIISTIQDRGYVRL-ENRRFYP 510 (859)
T ss_pred cccccccccCCCCCCCCEeeeeeeEecccccCCCCCCCHHHHHHHHHhcCCCcchhHHHHHHHHhhcCeEEe-eCCEEee
Confidence 1 346999999999999999999999999999999999999999999999999999999999999997 6789999
Q ss_pred chhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 532 TSLGIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 532 T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
|++|+.|+++|...++.|++|+|||.||..|
T Consensus 511 T~~G~~v~~~l~~~f~~l~~~~~Ta~~E~~L 541 (859)
T PRK07561 511 EKMGRIVTDRLEEFFPRLVDYDFTARMEEEL 541 (859)
T ss_pred cHHHHHHHHHHHHhhhhhcCHHHHHHHHHHH
Confidence 9999999999988788999999999999876
No 15
>PRK06599 DNA topoisomerase I; Validated
Probab=100.00 E-value=1e-119 Score=1018.47 Aligned_cols=507 Identities=24% Similarity=0.367 Sum_probs=430.7
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~ 85 (562)
+.|||||| ||+|+.|+.++|. .|+|+||+|||++|. +.+..|...+| |. +.
T Consensus 3 ~~LiIaEK-----Ps~ak~Ia~~lg~------------------~~~V~~~~GHl~~l~--~~~~~~~~~~~---~~-~~ 53 (675)
T PRK06599 3 KKLVIVES-----PAKAKTIKKYLGK------------------DYKVLASFGHVRDLP--KKKGGVDPDND---FA-PK 53 (675)
T ss_pred CeEEEEeC-----HHHHHHHHHHcCC------------------CCEEEecccchhcCC--ccccCCCcccC---CC-ce
Confidence 46999999 9999999987752 267999999999994 33445654332 21 11
Q ss_pred ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhCCC
Q psy8714 86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVK 165 (562)
Q Consensus 86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl~~ 165 (562)
.. ....+.++++.|++++++||+||||||||||||+|||+|+++++.. .+.+++|+|+|||++|+++|++||+||++
T Consensus 54 ~~-~~~~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~--~~~~~~v~Rl~~s~lt~~~I~~a~~n~~~ 130 (675)
T PRK06599 54 YE-IIEGKEKVVDALKKAAKKADAVYLATDPDREGEAIAWHIAEVLKEA--KLKDKNVKRVVFNEITKKAVQEAIENPRD 130 (675)
T ss_pred EE-ECCcHHHHHHHHHHHHhhCCEEEECCCCCcchHHHHHHHHHHHHhh--cCCCCCeeEEEEccCCHHHHHHHHhCccc
Confidence 11 1122336788888888999999999999999999999999999521 02357999999999999999999999999
Q ss_pred ChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEee
Q psy8714 166 PNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL 245 (562)
Q Consensus 166 ~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~ 245 (562)
++.+++.||.||+++||+||||+||++|+.++ ..+|+||||||||+|||+||++|+||+|++||.|.+.+..
T Consensus 131 ~~~~l~~a~~aR~~~D~liG~n~tr~~t~~~~--------~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~ 202 (675)
T PRK06599 131 IDMDLVDAQQARRALDYLVGFKLSPLLWKKVR--------RGLSAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLAT 202 (675)
T ss_pred CCHHHHHHHHHHHHHHHHhhhhhCHHHHHhcc--------CCCccceeHHHHhHHHHHhHHHHHhcCCCceEEEEEEEEc
Confidence 99999999999999999999999999998763 2399999999999999999999999999999999999976
Q ss_pred -CCeEEEEEeec------c--cccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHH
Q psy8714 246 -NGVAVSVTWSR------G--HIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHA 316 (562)
Q Consensus 246 -~~~~~~~~~~~------~--~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~t 316 (562)
+|..|.+.|.. . +++|+++|+++++.+.+ ..++|+++++++++++||+||||++||++||++|||||++|
T Consensus 203 ~~~~~~~~~~~~~~~~~~~~~r~~~~~~a~~~~~~~~~-~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~t 281 (675)
T PRK06599 203 SNGEPFTAKLVEVNGKKLEKFSITNEEQAKALVKALEG-QAYTVDKIEKKERKRNPPPPFITSTLQQEASRKLGFSAKKT 281 (675)
T ss_pred CCCCeeEEEEEeccCccccccCCCCHHHHHHHHHHhcC-CCeEEEEEEeeEEecCCCCCCcHHHHHHHHHHHcCCCHHHH
Confidence 46678776531 1 69999999999999976 46899999999999999999999999999999999999999
Q ss_pred HHHHHHhHhc--------CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCC-CCCC-CCCCC
Q psy8714 317 MQIAERLYTQ--------GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRK-GKDV-GDHPP 384 (562)
Q Consensus 317 l~iaQ~LYE~--------glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~-~~H~A 384 (562)
|++||+|||+ ||||||||||+|||+++ ++..+++.+.. .. ++.......++ .+.+ +||||
T Consensus 282 l~~aQ~LYe~~~~~~~~~g~iSYPRTds~~l~~~~~~~~~~~l~~~~~-~~-------~~~~~~~~~~~~~~~~~~aH~a 353 (675)
T PRK06599 282 MRIAQKLYEGIDLGEGTVGLITYMRTDSVRLSNEALDEARKYITKKYG-KE-------YLPAKPRVYKKKSKNAQEAHEA 353 (675)
T ss_pred HHHHHHHHhccccccccceeEEeccCCCccCCHHHHHHHHHHHHHHhc-hh-------hccccCcccCCCCCCCCCCCCC
Confidence 9999999995 99999999999999875 35566655422 11 11101111112 2223 77999
Q ss_pred CccCCCc--cc---CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEE--CCeEEEEEEEEEeecceeeeecccccc
Q psy8714 385 ITPTKLA--TR---TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSV--ADEMFTMEAKYLLHPGFTGVMTWSAMK 457 (562)
Q Consensus 385 I~PT~~~--~~---~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~--~~~~F~a~g~~~~~~Gw~~v~~~~~~~ 457 (562)
|+||... +. +.|+++|++||+||+|||||+|||||+|++|+|.+.+ +++.|.++|++++++||+.+|++++.+
T Consensus 354 I~Pt~~~~~~~~~~~~l~~~e~~iY~lI~~rfla~~~~~~~~~~t~v~~~~~~~~~~F~a~g~~~~~~Gw~~~~~~~~~~ 433 (675)
T PRK06599 354 IRPTSINRTPESLKPYLTPDQFKLYELIWKRTVASQMAPAILDQTSVDIASENGKYVFRATGSVILFPGFLKVYGESKDD 433 (675)
T ss_pred CccCCCCCChhHhhccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEEcCCCeEEEEEEEEEEecCeeeeecccccc
Confidence 9999862 21 4799999999999999999999999999999999999 999999999999999999999764321
Q ss_pred -----cCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecc
Q psy8714 458 -----NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPT 532 (562)
Q Consensus 458 -----~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T 532 (562)
+..||.+++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.+ +|+.|+||
T Consensus 434 ~~~~~~~~lp~~~~g~~~~~~~~~~~~~~T~PP~r~te~tLi~~Me~~GIGT~ATra~iIe~L~~r~Yi~~-~~~~l~~T 512 (675)
T PRK06599 434 EEEDDEKLLPPLKEGEKLKLDELLPEQHFTEPPPRYSEASLVKKLEEYGIGRPSTYASIISTLQDREYVEL-EKKRFIPT 512 (675)
T ss_pred ccccccccCCCCCCCCEeeeeeeeecccccCCCCCCCHHHHHHHHhhCCCCccccHHHHHHHHhhCCeEEe-eCCEEeec
Confidence 345999999999999999999999999999999999999999999999999999999999999997 57799999
Q ss_pred hhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 533 SLGIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 533 ~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
++|+.|+++|....+.|++|+|||.||..|
T Consensus 513 ~~G~~l~~~l~~~~~~l~~p~lTa~~E~~L 542 (675)
T PRK06599 513 DLGRIVNDFLVEHFPKYVDYDFTAGLEDEL 542 (675)
T ss_pred HHHHHHHHHHHHhchhhCCHHHHHHHHHHH
Confidence 999999999876667899999999999875
No 16
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=100.00 E-value=2.4e-119 Score=1034.21 Aligned_cols=502 Identities=23% Similarity=0.334 Sum_probs=432.2
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~ 85 (562)
|.|||||| |+.|+.|++.+| . .|+|+|+.|||++| |+++..|...++ |. |.
T Consensus 3 ~~LvIvEs-----P~kak~I~~~Lg----------------~--~~~V~as~GHl~dL--p~~~~~~~~~~~---f~-p~ 53 (860)
T PRK06319 3 KSLIIVES-----PAKIKTLQKLLG----------------E--GFIFASSLGHIVDL--PAKEFGIDIEND---FE-PD 53 (860)
T ss_pred CeEEEEeC-----HHHHHHHHHHhC----------------C--CCEEEecccCcccC--CcccCCcCCCCC---CC-cc
Confidence 68999999 999999997665 2 26799999999999 666656765432 21 11
Q ss_pred ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhCCC
Q psy8714 86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVK 165 (562)
Q Consensus 86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl~~ 165 (562)
.. ....+.++++.|++++++||.||||||||||||+|+|||+++++ .+++|+|+|||++|+++|++||+|+++
T Consensus 54 y~-~~~~k~~~~~~ik~~~k~ad~iilAtDpDREGE~I~~~i~~~l~------~~~~v~Rv~f~~iT~~aI~~A~~~~~~ 126 (860)
T PRK06319 54 YQ-ILPDKEEVINKICKLAKKCDVVYLSPDPDREGEAIAWHIANQLP------KNTKIQRISFNAITKGAVTEALKHPRE 126 (860)
T ss_pred eE-ECccHHHHHHHHHHHHHhCCEEEECCCCCcchHHHHHHHHHHcC------CCCCeeEEEEccCCHHHHHHHHhCccc
Confidence 10 11223468899999999999999999999999999999999994 358999999999999999999999999
Q ss_pred ChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEee
Q psy8714 166 PNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL 245 (562)
Q Consensus 166 ~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~ 245 (562)
+|+++++||+||+++|||||||+||++|..++.. ..+|+||||||||+|||+||+||+||+|++||+|.+.+..
T Consensus 127 ~d~~l~~A~~aR~~lD~lvG~nlSr~l~~~~~~~------~~lSaGRVQsp~L~lIveRe~eI~~F~p~~yw~i~~~~~~ 200 (860)
T PRK06319 127 IDMALVNAQQARRLLDRIVGYKISPILSRKLQRR------SGVSAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHLKD 200 (860)
T ss_pred cCHHHHHHHHHHHHHHHHhhhhcCHHHHHhhccC------CCCcCCccchhhhHHHHHHHHHHHcCCCCceEEEEEEEec
Confidence 9999999999999999999999999999876532 2499999999999999999999999999999999999875
Q ss_pred C--CeEEEEEeec-------------------ccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHH
Q psy8714 246 N--GVAVSVTWSR-------------------GHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRV 304 (562)
Q Consensus 246 ~--~~~~~~~~~~-------------------~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~ 304 (562)
+ +..|.+.|.. .++.|+++|+++++.+++ ..++|++|++++++.+||+||+|++||++
T Consensus 201 ~~~~~~f~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~i~~~l~~-~~~~V~~v~~k~~~~~pp~pf~ts~LQ~~ 279 (860)
T PRK06319 201 PKTQKTFWAHLYSVDGKKWEKEIPEGKTEDEVLLINSKEKADHIVELLES-ATYTVTRVESKEKRRNAYPPFITSTLQQE 279 (860)
T ss_pred CCCCcceEEEeecccCcccccccccccccccccccCCHHHHHHHHHHhcC-CCeEEEEEEeeEeecCCCCCccHHHHHHH
Confidence 3 4568777631 137899999999999976 47999999999999999999999999999
Q ss_pred HHhhCCCCHHHHHHHHHHhHhc---------CceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCC
Q psy8714 305 ASSGLGMGPHHAMQIAERLYTQ---------GYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKP 373 (562)
Q Consensus 305 a~~~~g~s~~~tl~iaQ~LYE~---------glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~ 373 (562)
||++|||||++||++||+|||. ||||||||||++||++. ++..+|..+.. . .++. ..+
T Consensus 280 As~~~g~sa~~tm~iAQ~LYE~~~~~~~~~~glITYpRTDs~~ls~~~~~~~~~~i~~~~g-----~---~~~~---~~~ 348 (860)
T PRK06319 280 ASRHFRFSSSRTMNIAQTLYEGVDLDSEGATGLITYMRTDSVRTDPEALKQVRKYIEGTFG-----K---EFLP---SSP 348 (860)
T ss_pred HHHHcCCCHHHHHHHHHHHHhccccccCCceeEEeecCcCcccCCHHHHHHHHHHHHHhhh-----h---hhcc---cCC
Confidence 9999999999999999999994 99999999999999875 35555554321 1 1221 122
Q ss_pred CC--CCCC--CCCCCCccCCCc--cc---CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECC-eEEEEEEEEEe
Q psy8714 374 RK--GKDV--GDHPPITPTKLA--TR---TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVAD-EMFTMEAKYLL 443 (562)
Q Consensus 374 ~~--~~~~--~~H~AI~PT~~~--~~---~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~-~~F~a~g~~~~ 443 (562)
+. .+++ +||||||||... +. ..|+++|++||+|||+||||+||+||+|++|+|.+.+++ +.|+++|++++
T Consensus 349 ~~~~~~k~~q~aH~AI~PT~~~~~p~~~~~~L~~de~klY~LI~~RflAs~m~~a~~~~t~v~~~~~~~~~F~a~G~~i~ 428 (860)
T PRK06319 349 NVYTTKKMAQDAHEAIRPTDITLTPEKLRSKLTEDQYKLYSLIWKRFVASQMIPAIYDTLAIRITTNKGIDLRATGSLLK 428 (860)
T ss_pred cccCCCCCCCCCcCCCccCCCCcChhHhhccCCHHHHHHHHHHHHHHHHHhCchhheEEEEEEEEeCCeeEEEEEeEEEe
Confidence 22 2223 579999999853 22 479999999999999999999999999999999999987 68999999999
Q ss_pred ecceeeeeccccc------ccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhc
Q psy8714 444 HPGFTGVMTWSAM------KNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQ 517 (562)
Q Consensus 444 ~~Gw~~v~~~~~~------~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~ 517 (562)
++||++||..+.. ++..||.|++||.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++
T Consensus 429 ~~G~~~vy~~~~~~~~~~~~~~~LP~l~~Ge~~~~~~~~~~~~~T~PP~ryTeasLvk~me~~GIGtpsT~A~iI~~L~~ 508 (860)
T PRK06319 429 FKGFLAVYEEKRDDEGDEEENIHLPKLHEQDVLTKEELSAEQAFTKPLPRFTEASLVKELEKSGIGRPSTYATIMNKIQS 508 (860)
T ss_pred eCCHHHHhCccccccccccccccCCCCCCCCEeeeeeeeecccccCCCCCCCHHHHHHHHHhcCCCchhhHHHHHHHHhh
Confidence 9999999964321 1346999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 518 RNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 518 r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
||||.. +|++|+||++|+.|+++|...++.|++|+|||.||.+|
T Consensus 509 R~Yv~~-~~k~l~pT~~G~~v~~~L~~~f~~i~~~~~Ta~~E~~L 552 (860)
T PRK06319 509 REYTLK-ENQRLRPTELGKIISQFLETNFPRIMDIGFTALMEDEL 552 (860)
T ss_pred CCeEEc-cCCEEEECHHHHHHHHHHHHhchhhcChhHHHHHHHHH
Confidence 999997 57799999999999999988788999999999999876
No 17
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=100.00 E-value=3.7e-112 Score=947.12 Aligned_cols=531 Identities=20% Similarity=0.297 Sum_probs=412.7
Q ss_pred ceEEEEecccCcCCcchHHhhcccccCCCCceeeeee-eeEc----CCCcEEEEEEecccccccccccCCCCCccC--C-
Q psy8714 5 VKKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWV-GPLF----GDLVLFKMTSVCGHIMGLDFTSKYNNWDKV--D- 76 (562)
Q Consensus 5 ~~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~-g~~~----g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~--~- 76 (562)
.-+|+|+|+ |...=.+.-.++-.+-++-+.|. +++- |.. .-+..++-||+|.|..- .|... .
T Consensus 9 ~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~----~~~~~~~~~ 78 (805)
T PTZ00407 9 LEKLVIVES-----PNKVIKVEGLLSDPKVIPDWSFKQSHLRRIGTGAE-KAVAMATTGHFMALKEI----TWSPQASSP 78 (805)
T ss_pred hhheeEEec-----CCceEEEeecccCCCcCCCcccccccceeeccchH-HHHHHhhcccceeehhe----ecccCCCCC
Confidence 468999999 44433333333445555656663 2332 221 23466888999998521 23321 0
Q ss_pred ------CCCCCC--------CCcccccCCCC-CchHH-HHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCC
Q psy8714 77 ------PLELFS--------CPTEKREATPK-LKLPA-FLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP 140 (562)
Q Consensus 77 ------p~~~~~--------~~~~~~~~~~~-~~~i~-~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~ 140 (562)
+.+-|+ .|........+ .++|. .|++++++||+||+|||||||||+|+|||+++++... ..++
T Consensus 79 ~~~~~~~~~~~~~~~~~~~f~~~y~~~~~~~~~~~i~~~i~~~ak~ad~IIlATDpDREGE~Ia~hIle~l~~~~-~~~~ 157 (805)
T PTZ00407 79 ASVVGAGDEPFPSNGTLAEYTLEWELLPGRRIQETLERYIEEKADNVTEIILATDPDREGELIAVHALQTIKRLY-PKLK 157 (805)
T ss_pred cccCCCCCCCCCCCCceEEEEEEEEEcCCCchhHHHHHHHHHHHhcCCEEEECCCCCcchHHHHHHHHHHhchhc-cccC
Confidence 111122 01111111111 14565 6999999999999999999999999999999996420 0135
Q ss_pred CcEEEEEecccCHHHHHHHHHhC--CCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccch
Q psy8714 141 KTVWRARFSAITDKDIKAAMWNL--VKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTL 218 (562)
Q Consensus 141 ~~v~Rl~~sslt~~~I~~A~~nl--~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL 218 (562)
++++|+|||++|+++|++||+|+ ++++.++++|+.||+++|||||||+||+++... .+.+|+||||||||
T Consensus 158 k~v~Rv~FseITk~aI~~A~~nlkp~~~d~~L~~Aa~ARr~lD~LVG~nlS~~l~~~~--------~~~lSaGRVQTPtL 229 (805)
T PTZ00407 158 VPFSRAYMHSITEDGIRKAMRERHVEACDYDLANAAETRHAMDRIFGFLGSSVVRAAN--------SQMRSIGRVQTPAL 229 (805)
T ss_pred CcceEEEEccCCHHHHHHHHhCCCCCcccHhHHHHHHHHHHHHHHhhhhhhHHHHhhc--------cCceeecccchHHH
Confidence 78999999999999999999995 668889999999999999999999999987631 23699999999999
Q ss_pred hhhhhhhhhhhcccCc--ceEEEEEEEee---CCeEEEEEee--------cccccCHHHHHHHHHHhh--hcCceEEE-E
Q psy8714 219 GFCVERHDKIRTFKPE--PYWLLDLTLNL---NGVAVSVTWS--------RGHIFDKSTCNVFFKAVE--KEKHVTVV-D 282 (562)
Q Consensus 219 ~lIv~Re~eI~~F~p~--~y~~i~~~~~~---~~~~~~~~~~--------~~~~~~~~~a~~~~~~~~--~~~~~~V~-~ 282 (562)
+|||+||+||++|+|+ +||.|.+.+.. +|..|.+.|. +.++.|+++|+++++.++ +...++|. .
T Consensus 230 ~LIVeRE~EIe~Fkpee~~Yw~I~a~~~~~~~~g~~F~a~~~~~~~~~~~~~~~~~~~eA~~~~~~~~~~~~~~~~V~~~ 309 (805)
T PTZ00407 230 ILINEREDKIKAFLESNKSTFEVQAMCQFPSPHGTTFSQVVTITPDRKGGASHWATEAEARRCLEQWKLNNCTGFSVPLE 309 (805)
T ss_pred HHHHHHHHHHHhcCCccCceEEEEEEEeecCCCCcceeEEeeccccccccccccCCHHHHHHHHHHhhhccCCcEEEEEE
Confidence 9999999999999999 69999988752 3566776653 135778999999988764 22346664 4
Q ss_pred EEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhH
Q psy8714 283 VQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGD 360 (562)
Q Consensus 283 v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~ 360 (562)
+++++++++||+||||++||++||++|||||++||++||+|||.||||||||||++||+++ ++.+.|... ++.
T Consensus 310 v~~k~kk~~PP~PF~tstLQqeAsrkLG~Sa~kTM~iAQ~LYE~GlITYPRTDS~~l~~e~~~~i~~~I~~~-----~g~ 384 (805)
T PTZ00407 310 PKPQPSVVPPPQPFTMATAIAKANRQLKYSSEMVSGCLQDLFQLGHITYPRTDSTRIDESALPDIYAAVKKE-----FGK 384 (805)
T ss_pred EEEEEEEcCCCCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCceeccCCCCCcCCHHHHHHHHHHHHHh-----hhh
Confidence 6678999999999999999999999999999999999999999999999999999999986 344444431 221
Q ss_pred HHHHHh----------hCCCCCCC--------CC----C---CCC-CCCCCccCCCccc---CCCCHHHHHHHHHHHHHH
Q psy8714 361 HVREVL----------SNGISKPR--------KG----K---DVG-DHPPITPTKLATR---TQLDGDAWRLYDYIVRHF 411 (562)
Q Consensus 361 ~~~~~~----------~~~~~~~~--------~~----~---~~~-~H~AI~PT~~~~~---~~L~~~e~~vY~lI~rr~ 411 (562)
.++ ......++ .+ . +++ |||||+||+.... ..|+++|++||+||||||
T Consensus 385 ---~~l~~~~~~~~~~~~~~~~~k~~k~~~~~~k~~~d~~~~kvqeAHeAIrPT~~~~~~~~~~Ls~de~kLYdLI~rRf 461 (805)
T PTZ00407 385 ---EFLYRLEDRTVSAQEGKGSKKTGKKRSTKQKKGADTPVGNVEDAHEAIRPTNIDTTGESLSLSPPTRAVYDLVRRNT 461 (805)
T ss_pred ---hhhhhhcccccccccccccccccccccccccccccccccCCCCCcCCCCccCCCCChhhccCCHHHHHHHHHHHHHH
Confidence 111 10001111 11 1 444 7999999986432 269999999999999999
Q ss_pred HhhcccCceEEEEEEEEEEC-----CeEEEEEEEEEeecceeeeecccc----------c------c--cCCCCCCCCCC
Q psy8714 412 IGTLCGDLVYTQKVAKFSVA-----DEMFTMEAKYLLHPGFTGVMTWSA----------M------K--NESIPDFKPGD 468 (562)
Q Consensus 412 la~~~~~a~~~~t~v~~~~~-----~~~F~a~g~~~~~~Gw~~v~~~~~----------~------~--~~~Lp~l~~G~ 468 (562)
||+||+||+|++|++.+.+. ++.|+++|++++++||++||++.. . + +..||.+++||
T Consensus 462 LAs~m~~a~~e~t~v~i~~~~~~g~~~~F~asGk~v~~~Gw~~vy~~~~~~~~~~~~e~~e~~~~~~e~~~~LP~l~~Gd 541 (805)
T PTZ00407 462 LAVFMIPMKTEKIVATVKFTSGSGEKLEFELQGKRVVEPGWTRAFHKGDKGTTGPAEETDEDITAVEEGAPVVPSLSQEE 541 (805)
T ss_pred HHHhCchhEEEEEEEEEEEeccCCCceEEEEEEEEEeeCCHHHHhcccccccccccccccccccccccccccCCcccCCc
Confidence 99999999999999998873 358999999999999999996321 0 1 13599999998
Q ss_pred ------------------eeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeee
Q psy8714 469 ------------------LIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLV 530 (562)
Q Consensus 469 ------------------~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~ 530 (562)
.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|++||||.++.|++|+
T Consensus 542 ~~~~~~~~~~~g~~~~q~~~~i~~~~l~ek~TkPPpryTEAtLIk~ME~~GIGTPATrAsIIetL~~R~YV~~~~kkrl~ 621 (805)
T PTZ00407 542 FKAIMNLRSQLGSGVQKGFFELRSPQVRENRPVPPLPHSEGTLIEELKNNGVGRPSTYPMIVKTLLARGYIAVNPKGRCE 621 (805)
T ss_pred cccccccccccccccccceeecceeeeecccCCCCCCCCHHHHHHHHHhCCCCCcccHHHHHHHHHhcCCEEeccCceee
Confidence 35567889999999999999999999999999999999999999999999999983277899
Q ss_pred cchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 531 PTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 531 ~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
||++|+.|+++|...++.|++|+|||.||.+|
T Consensus 622 PT~lG~~Li~~L~~~fp~lv~p~~TA~~E~~L 653 (805)
T PTZ00407 622 TTPVGRMLVETAKSTFPSIVDIGFTAAFEKKL 653 (805)
T ss_pred ecHHHHHHHHHHHHhhhhhcChHHHHHHHHHH
Confidence 99999999999988888999999999999986
No 18
>PRK09401 reverse gyrase; Reviewed
Probab=100.00 E-value=4.8e-112 Score=994.95 Aligned_cols=504 Identities=22% Similarity=0.296 Sum_probs=421.6
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEc---CCCcEEEEEEecccccccccccCCCCCccCC-CC-CC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLF---GDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD-PL-EL 80 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~---g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~-p~-~~ 80 (562)
+.|||||| |++|+.||+++|....... ++-.+|+ |+. .++||||.|||++|..|++|..|...+ |. +.
T Consensus 602 ~~LiIaEk-----PskAk~IA~~lg~~~~r~~-g~~~~ye~~~~~~-~~~Vt~s~GHl~dL~~~~~y~g~~~~~~p~~P~ 674 (1176)
T PRK09401 602 TTLLIVES-----PTKARTIANFFGRPSRRRI-GGLVVYETVTGDR-ILTITASKGHVYDLTTEIGYYGVLVKDGGFVPV 674 (1176)
T ss_pred CEEEEEcC-----HHHHHHHHHHhCCCccccC-CCceeEEEecCCc-EEEEEEeccccccCCCccccCcccccCCcccce
Confidence 57999999 9999999999987532111 1111244 543 358999999999999999998898644 21 11
Q ss_pred CCC------------------Ccc-cccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCC
Q psy8714 81 FSC------------------PTE-KREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPK 141 (562)
Q Consensus 81 ~~~------------------~~~-~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~ 141 (562)
|.. |.. .....++.++++.|++++++||+||||||||||||+|||+|+++++. +++
T Consensus 675 y~~~k~c~~~g~~f~~~~~~~~~c~~~~~~~k~~~~~~Lr~l~~~~d~IiiAtDpDrEGE~Ia~~i~~~l~~-----~~~ 749 (1176)
T PRK09401 675 YDTIKRCRDCGYQFTDESDKCPRCGSTNIEDKEEIIEALRELALEVDEVLIATDPDTEGEKIAWDLYLLLSP-----YNS 749 (1176)
T ss_pred eeeeccccccccccccccccccccccccCCCHHHHHHHHHHHHhcCCEEEEccCcChhHHHHHHHHHHHhcc-----cCC
Confidence 210 000 00113345788999999999999999999999999999999999963 358
Q ss_pred cEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhh
Q psy8714 142 TVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFC 221 (562)
Q Consensus 142 ~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lI 221 (562)
+|+|+|||++|+++|++||+|++++|.+++.||.||+++||+||||+||++|+.+++ ..+|+||||||||+||
T Consensus 750 ~i~R~~f~eiT~~aI~~A~~n~r~~~~~l~~A~~aRr~~D~~iG~~lSr~l~~~~~~-------~~lSaGRVQTPtL~~I 822 (1176)
T PRK09401 750 NIKRIEFHEVTRKAILEALRNPRDVNENLVKAQIVRRIEDRWIGFELSQKLQKKFGK-------RNLSAGRVQTPVLGWI 822 (1176)
T ss_pred CEEEEEeecCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-------cCccccccccchhhhh
Confidence 999999999999999999999999999999999999999999999999999986542 2499999999999999
Q ss_pred hhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHH
Q psy8714 222 VERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVEL 301 (562)
Q Consensus 222 v~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~L 301 (562)
|+|++||++|++ ||.+ ... .+|..|.+.+ ++.+++.|+.+.+.+. +|.+++.++++.+||+||||++|
T Consensus 823 VeRe~ei~~f~~--~~~~-~~~-~~~~~~~~~~---~~~~~~~a~~~~~~l~-----~V~~v~~k~~~~~pP~Pf~t~~L 890 (1176)
T PRK09401 823 VERYKEYKKSKG--YVLV-IKL-ENGGGLELEG---EFSEKEEAEKFYNNLI-----EVEKVEEKEEELNPLPPYTTDTL 890 (1176)
T ss_pred hhhHHHhcccCC--EEEE-EEe-cCCceEEEEE---eeCCHHHHHHHHHhCC-----eeeEEEeeEEEecCCCCCccHHH
Confidence 999999999975 4444 332 3455566653 6889999999888774 78999999999999999999999
Q ss_pred HHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc-c-HHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCC
Q psy8714 302 MRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF-D-LVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDV 379 (562)
Q Consensus 302 q~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~-~-~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 (562)
|++||++|||||++||++||+|||+||||||||||+++|++. + +...+..+.. ....+||.+.++
T Consensus 891 q~~As~~lg~Sa~~tm~iAQ~LYE~glITYpRTDS~~ls~~~~~~a~~~l~~~~~-------------~~~~~~r~~~~~ 957 (1176)
T PRK09401 891 LSDASRKLRLSAQETMRIAQDLFELGLITYHRTDSTRVSDVGISVAKEYLEKRGG-------------EEYFVPRSWGEG 957 (1176)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHhCCceeecCCCCCcCCHHHHHHHHHHHHHhhC-------------ccccCCCCCCCC
Confidence 999999999999999999999999999999999999999864 2 3344443321 122467887778
Q ss_pred CCCCCCccCCCccc---------------CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEE-EEEEe
Q psy8714 380 GDHPPITPTKLATR---------------TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTME-AKYLL 443 (562)
Q Consensus 380 ~~H~AI~PT~~~~~---------------~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~-g~~~~ 443 (562)
+||||||||...+. ..|+++|++||+||+|||||+||+||+|++|++.+.++++.|.++ |++++
T Consensus 958 ~aH~AI~PT~~~~~~~l~~~~~~g~~~~~~~Lt~~e~~lY~LI~rRflAs~~~~a~~~~t~v~~~~~~~~f~~~~g~~i~ 1037 (1176)
T PRK09401 958 GAHEAIRPTRPLDAEELRQMIEEGILKLSEGLTKNHLRLYDLIFRRFMASQMKPAKVRYQKVLIKADGKELELELVVEIL 1037 (1176)
T ss_pred CCcCCcCccCCCCchhhhhhhccccccccccCCHHHHHHHHHHHHHHHHHhCchhEEEEEEEEEEECCEEEEEeeeeEEe
Confidence 99999999985331 468999999999999999999999999999999999999999999 99999
Q ss_pred ecceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEE
Q psy8714 444 HPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTV 523 (562)
Q Consensus 444 ~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~ 523 (562)
++||+.+|+.. .+|.++.|+.+.. ++.++|.||+||||++||++||+.|||||||||+||++|++||||..
T Consensus 1038 ~~Gw~~v~~~~-----~~p~~~~g~~~~~----~~~~~~~pp~~yTea~Li~~Me~~GIGtpAT~A~IIe~L~~R~YV~~ 1108 (1176)
T PRK09401 1038 EDGFNKVLPLK-----LYPLLEGKVKVKE----KKTYKKSKVPLYTQGDLISEMKERGIGRPSTYAKIVETLLRRGYVIE 1108 (1176)
T ss_pred eCChheeeccc-----cCCCCCCCCEeee----eccccCCCcCCCCHHHHHHHHHhCCCCCcCcHHHHHHHHhccCcEEE
Confidence 99999999643 3889999998864 45556666999999999999999999999999999999999999985
Q ss_pred cCC-CeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 524 TSG-RRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 524 ~~~-k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
.+| +.|+||++|+.++++|....+.+++|++||.||..|
T Consensus 1109 ~~~~k~l~pT~~G~~l~~~L~~~~~~l~s~e~Ta~~E~~l 1148 (1176)
T PRK09401 1109 SKGKKRLIPTKLGIKVYEYLSEKYKDLVSEERTRKLEEKM 1148 (1176)
T ss_pred cCCcceEeECHHHHHHHHHHHHhhhhcCCHHHHHHHHHHH
Confidence 344 589999999999999976667899999999999875
No 19
>KOG1956|consensus
Probab=100.00 E-value=2.6e-112 Score=894.43 Aligned_cols=553 Identities=38% Similarity=0.669 Sum_probs=513.1
Q ss_pred eEEEEecccCcCCcchHHh-----hcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCC
Q psy8714 6 KKLVPASEIKLARPSLISL-----LTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLEL 80 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~-----~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~ 80 (562)
+-|++|||.+ .+.++|.. .+.+.|.++++++|.|+..+.|++++.++|+..|||+++++|.+|..|..+.|..+
T Consensus 2 ~vl~vAekn~-~ak~va~il~~g~~~~re~rSk~~kiy~f~~~~~g~~~~~~mtsvsghl~~~~f~~~~s~w~s~~~~~l 80 (758)
T KOG1956|consen 2 RVLCVAEKNS-IAKSVASILSGGTVRRREGRSKYNKIYDFDFNLFGQNCDVTMTSVSGHLTEADFPSEYSKWQSCPPDEL 80 (758)
T ss_pred Ccccccccch-hhhhhhhhcCCCCcCCccchhhhhhhhhhhhhhcCCcceeEEeeccccccccCCcccccceeecCHHHH
Confidence 3589999932 22334443 56677889999999998888899999999999999999999999999999999999
Q ss_pred CCCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHH
Q psy8714 81 FSCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM 160 (562)
Q Consensus 81 ~~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~ 160 (562)
|..|..+.....+..+.+.|++++++||.+|||||||||||+|||||.+.|+.+ +....|.|+.||+||+.+|+.|.
T Consensus 81 f~a~~~~~~~~~~~~i~~~ir~eAr~ad~LviwtDcDREGE~Ig~eI~~v~~~~---~~~~~V~RA~Fs~it~~~I~sA~ 157 (758)
T KOG1956|consen 81 FDAPVIKSVPENAKDIAKTIREEARRADYLVIWTDCDREGENIGWEIIDVCRAV---KRLLQVRRARFSEITRSAIKSAA 157 (758)
T ss_pred hhhhhhhcCchhhhHHHHHHHHHHhhcceEEEeccCCccchhhhHHHHHHHHhh---CccceeehhhhhcccHHHHHHHH
Confidence 988877666666777889999999999999999999999999999999999876 55567999999999999999999
Q ss_pred HhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEE
Q psy8714 161 WNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD 240 (562)
Q Consensus 161 ~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~ 240 (562)
+||+++|+.+++|..||+++|++||..|||++|+.+++++.-+..+++|+|+||+|||++||||+++|++|+|+.||+|.
T Consensus 158 ~nlreid~~~v~AvdaR~ELDlrIGa~FTRlqT~~L~r~f~~~~~~viSyG~cQfpTLgfVvdR~~eIe~FvPEefWtl~ 237 (758)
T KOG1956|consen 158 RNLREIDEKLVHAVDARIELDLRIGAAFTRLQTLLLRRKFPILGEQVISYGPCQFPTLGFVVDRYKEIENFVPEEFWTLK 237 (758)
T ss_pred hCccccchHHHHHHHHHHHHHHHhhhhHHHHHhHHHHhhhhhhhccccccccccCcceeeeeehHHHHhccCCcceEEEE
Confidence 99999999999999999999999999999999999988776444689999999999999999999999999999999999
Q ss_pred EEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHH
Q psy8714 241 LTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIA 320 (562)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~ia 320 (562)
......++...+.|.+++++|...+--+.+.|...+.+.|+++.++++++.||+||+|.+||+.|+++|.||+++||+||
T Consensus 238 ~~~~~~~~~~~fnw~R~~lfdr~s~~~~~e~c~e~k~a~Vv~~~kkpktKyrP~pl~TvELqK~~s~~lrlSak~TM~iA 317 (758)
T KOG1956|consen 238 FKHTHKGGLTEFNWKRGHLFDRLSVVILYEICVEEKEATVVKVTKKPKTKYRPLPLDTVELQKLASRKLRLSAKHTMKIA 317 (758)
T ss_pred EEEeccCceeEEeecccccccHHHHHHHHHHHhcccceeEEecccCCccCCCCCcchHHHHHhhhhhheeccHHHHHHHH
Confidence 99988899999999999999999999999999888899999999999999999999999999999999999999999999
Q ss_pred HHhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCC-CCCCCCccCCCcc-cCCCCH
Q psy8714 321 ERLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDV-GDHPPITPTKLAT-RTQLDG 398 (562)
Q Consensus 321 Q~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~H~AI~PT~~~~-~~~L~~ 398 (562)
++||.+|+||||||++..+|.++++..+++.+...+.|+.+|..++..+...||++++. .||++|+||.... ...++.
T Consensus 318 E~ly~~gfisyprtetd~F~s~~~lk~lv~~qt~~~~wg~yA~~ll~~~~r~Prng~~~d~Ahppihp~k~~s~~~~~s~ 397 (758)
T KOG1956|consen 318 EKLYQKGFISYPRTETDNFPSDMDLKALVEKQTQDPAWGSYAQRLLQPENRNPRNGKHNDKAHPPIHPTKFTSREANLSG 397 (758)
T ss_pred HHHHhccceeccccccccCCCcCchHHHHHhhccCchhHHHHHHhhccCCCCCCCCccccccCCCccceeeccccccCCc
Confidence 99999999999999999999999999999999989999999999988655689998765 7899999998644 357999
Q ss_pred HHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEe
Q psy8714 399 DAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMV 478 (562)
Q Consensus 399 ~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~ 478 (562)
|+++||++|+||||||.+.||+-..|+|+++++.+.|.++|..+++.+|..||++++|++..||.++.|+.+.+..+++.
T Consensus 398 d~~~vye~v~rhflAc~S~dakg~et~vel~~~~E~F~asgl~vl~~NyldVy~yekwe~k~Lp~y~~ge~fq~~~lem~ 477 (758)
T KOG1956|consen 398 DHRKVYELVVRHFLACCSQDAKGAETTVELDIAQERFSASGLRVLERNYLDVYPYEKWEDKQLPVYEDGELFQPGELEMK 477 (758)
T ss_pred chHHHHHHHHHHHHHhhcccccccceEEEEeehhhhccccccchhhccccccccccccccccCcccccccccccceEEec
Confidence 99999999999999999999999999999999999999999999999999999999999889999999999999999999
Q ss_pred eeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEE-cCCCeeecchhHHHHHHhhhccCccCCChhhHHH
Q psy8714 479 ERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTV-TSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSA 557 (562)
Q Consensus 479 e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~-~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~ 557 (562)
++.|.||++|||++||+.|+++||||+||.|+||++|+.|+||.+ .+..+|.||.+|.+|+++|+.++-++++|.+||.
T Consensus 478 ~g~T~~P~~ltEaeLI~lMdk~GIGtdAT~aehi~kiq~R~Yv~~~~~~~~~~P~~lg~aLv~gyd~~g~e~sKp~lra~ 557 (758)
T KOG1956|consen 478 DGETSPPKYLTEAELISLMDKNGIGTDATIAEHIEKIQERGYVTKKNKVGRFVPTFLGVALVEGYDDMGLEMSKPFLRAE 557 (758)
T ss_pred cCccCCCCccCHHHHHHHHHHcCCCCchhHHHHHHHHHhhcceeeeccccccCchHHHHHHHHhHHhhhhhcCChHHHHH
Confidence 999999999999999999999999999999999999999999987 3334688999999999999999999999999999
Q ss_pred HHhhC
Q psy8714 558 YRVQA 562 (562)
Q Consensus 558 ~E~~L 562 (562)
||.+|
T Consensus 558 mE~~L 562 (758)
T KOG1956|consen 558 MEVDL 562 (758)
T ss_pred HHHHH
Confidence 99876
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=2.2e-109 Score=973.54 Aligned_cols=503 Identities=20% Similarity=0.272 Sum_probs=418.0
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCC-----CceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCC-CC-
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNG-----ACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD-PL- 78 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~-----~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~-p~- 78 (562)
..|||||| |+.|+.||.++|... ..++|+|.+ |+. .++||||.|||++|..|+.|..|...+ |.
T Consensus 602 ~~LiIvEs-----P~kAk~Ia~~lg~~~~r~~~g~~~yE~~~---g~~-~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~ 672 (1171)
T TIGR01054 602 TALLVVES-----PNKARTIARFFGKPSVRKIGGSVVYEVPV---GDL-ILMITASGGHVFDLVTDKGFHGVLVENGRYV 672 (1171)
T ss_pred ceEEEEcC-----hHHHHHHHHHhCCCcccccCCcceEEEec---CCe-eEEEEEeCceeeeCCCccccCcccccCCccc
Confidence 57999999 999999999998752 222333321 443 468999999999998887776776533 11
Q ss_pred CCCC------------------CCcc-cccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCC
Q psy8714 79 ELFS------------------CPTE-KREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININS 139 (562)
Q Consensus 79 ~~~~------------------~~~~-~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~ 139 (562)
+.|. +|.. .....++.++++.|++++++||+||||||||||||+|||+|++++++ +
T Consensus 673 P~y~~~k~~~~~~~~f~~~~~~~p~~~~~~~~~k~~~~~~lr~l~~~~d~ViiATDpDrEGE~Ia~~i~~~l~~-----~ 747 (1171)
T TIGR01054 673 PVYTSIKRCRDCGYQFTEDRESCPKCGSENIEDSKSIIEILRELAHEVDEVFIGTDPDTEGEKIGWDLALLLSP-----Y 747 (1171)
T ss_pred ccccccccCCchhhhccccccccccccccccccHHHHHHHHHHHHhcCCEEEECCCCCccHHHHHHHHHHHhcc-----c
Confidence 1111 0100 00113345788999999999999999999999999999999999863 3
Q ss_pred CCcEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchh
Q psy8714 140 PKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLG 219 (562)
Q Consensus 140 ~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~ 219 (562)
+++|+|+|||++|+++|++||+|++++|.++++||.||+++||+||||+||++|+.+++ +.+|+||||||||+
T Consensus 748 ~~~i~R~~f~eiT~~aI~~A~~n~r~~~~~L~~A~~aRr~~D~liG~~lSr~lt~~~~~-------~~lSaGRVQTPtL~ 820 (1171)
T TIGR01054 748 NPNVKRAEFHEVTRRAILEALESPRSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFNK-------RWLSAGRVQTPVLG 820 (1171)
T ss_pred CCCeEEEEEccCCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHhhhhCHHHHHhhcC-------CCcccceecchhhH
Confidence 67999999999999999999999999999999999999999999999999999975532 35999999999999
Q ss_pred hhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHH
Q psy8714 220 FCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTV 299 (562)
Q Consensus 220 lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~ 299 (562)
|||+|++||++|+ +||.+.+.. ++..+...| .+++.|+++.+.+. .++|.+++.++++.+||+||+|+
T Consensus 821 lIVeRe~ei~~~~--~~~~i~~~~--~~~~~~~~~-----~~~~~a~~~~~~~~---~~~V~~v~~k~~~~~pP~Pf~t~ 888 (1171)
T TIGR01054 821 WIIDRYRESREKR--GYLLIFALE--SDFRLGLEH-----DNRLEAKEFEKDLT---WLDVEDIAEREEERNPLPPYTTD 888 (1171)
T ss_pred HHHHHHHHHhCCC--ceEEEEEec--CCeEEEEEe-----CCHHHHHHHHHhCC---CcEEEEEEeeEEeccCCCCCCHH
Confidence 9999999999965 589887643 233344333 57888888888773 57899999999999999999999
Q ss_pred HHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCC
Q psy8714 300 ELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGK 377 (562)
Q Consensus 300 ~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 377 (562)
+||++||++|||||++||++||+|||+||||||||||+++|++. .+.+.+..+ +......||.+.
T Consensus 889 ~Lq~~As~~lg~sa~~tm~iAQ~LYE~GlITYpRTDS~~ls~~~~~~~~~~l~~~-------------~~~~~~~~r~~~ 955 (1171)
T TIGR01054 889 TMLEDANRKLGLSVKETMQIAQELFENGLITYHRTDSTRVSDVGMRVAKEYLASR-------------LGGEYFYPREWG 955 (1171)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHhCCEEEecCCCCCcCCHHHHHHHHHHHHHH-------------hcccccCCCCCC
Confidence 99999999999999999999999999999999999999999864 233333321 111123577777
Q ss_pred CCCCCCCCccCCCccc--------------CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECC-eEEEEEEEEE
Q psy8714 378 DVGDHPPITPTKLATR--------------TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVAD-EMFTMEAKYL 442 (562)
Q Consensus 378 ~~~~H~AI~PT~~~~~--------------~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~-~~F~a~g~~~ 442 (562)
+.+|||||+||...+. ..|+++|++||+||+|||||+||+||+|+++++.+.+++ +.|.++|+++
T Consensus 956 ~~~aHeAI~PT~~~~~~~l~~~~~~g~~~~~~Ls~~e~~lY~LI~rRflAs~~~~a~~~~t~v~~~~~~~~~f~~~g~~i 1035 (1171)
T TIGR01054 956 EGGAHECIRPTRPLDVDDLQRLILEGVIELEGLTREHLRLYDLIFRRFMASQMRPAKVDTKEITLKADGKEAEEEGIVEI 1035 (1171)
T ss_pred CCCCcCCcCCcCCCChhhhhhhhcccccccccCCHHHHHHHHHHHHHHHHHhCchheEEEEEEEEEeCCeeEEEEEEEEE
Confidence 7789999999986331 368999999999999999999999999999999999966 7999999999
Q ss_pred eecceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEE
Q psy8714 443 LHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVT 522 (562)
Q Consensus 443 ~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~ 522 (562)
+++||+.+|+.+. .+.+.+|+.+.+.+..+.++. ||+||||++||++||+.|||||||||+||++|++||||.
T Consensus 1036 ~~~Gw~~v~~~~~-----~~~~~~G~~~~~~~~~~~~~~--~~p~yTe~~Li~~Me~~GIGtpsT~A~II~~L~~R~YV~ 1108 (1171)
T TIGR01054 1036 VERGFELVYPLWR-----KNELEKGSTFIVKDKELRSVP--KVYPYTQGEIVQEMKERGIGRPSTYATIVEKLLRRGYVV 1108 (1171)
T ss_pred eeCCHHHHcCccc-----cccccCCCEeeeecceeeecC--CCCCCCHHHHHHHHHhCCCCCcccHHHHHHHhhccCcEE
Confidence 9999999997533 445788999988777776654 445999999999999999999999999999999999998
Q ss_pred EcCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 523 VTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 523 ~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
. +++.|+||++|+.|++.|....+.|++|++||.||..|
T Consensus 1109 ~-~~k~l~pT~lG~~v~~~L~~~~~~l~~~~~Ta~~E~~L 1147 (1171)
T TIGR01054 1109 E-SKGFLIPTKLGIEVYNYLTNRYPKLVSEDRTRELEEAM 1147 (1171)
T ss_pred e-eCCEEeECHHHHHHHHHHHhhhhhcCCHhHHHHHHHHH
Confidence 6 66799999999999999977667899999999999875
No 21
>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=2.8e-95 Score=777.77 Aligned_cols=380 Identities=31% Similarity=0.549 Sum_probs=301.8
Q ss_pred ChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEee
Q psy8714 166 PNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL 245 (562)
Q Consensus 166 ~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~ 245 (562)
.+.+++.||.||+++|||||||+||++| . .+++|+||||||||+|||+||++|+||+|++||.|.+.+..
T Consensus 2 ~~~~l~~a~~aR~~~D~liG~n~Sr~~t---~-------~~~ls~GRVQtp~L~li~~Re~ei~~f~~~~y~~i~~~~~~ 71 (403)
T PF01131_consen 2 EDKNLYNAAEARQEADWLIGMNLSRALT---G-------NGVLSVGRVQTPTLGLIVEREREIENFKPEPYYEIKAQFKK 71 (403)
T ss_dssp -GHHHHHHHHHHHHHHHHHHHHHHHHHH---H-------STT-TTHTTHHHHHHHHHHHHHHHHCEEEEEEEEEEEEEET
T ss_pred CCHhHHHHHHHHHHHHHhcChhcCHhhc---C-------CCccccCcccchHHHHHHHHHhhhhccCCCceEEEEEEecc
Confidence 5778999999999999999999999997 1 24799999999999999999999999999999999999876
Q ss_pred CCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHh
Q psy8714 246 NGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYT 325 (562)
Q Consensus 246 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE 325 (562)
++.. ...+.+.++.|+++|+.+++.+... .|.+++.++++.+||+||||++||++||++|||||++||++||+|||
T Consensus 72 ~~~~-~~~~~~~~~~~~~~a~~~~~~~~~~---~v~~~~~~~~~~~pP~p~~l~~Lq~~a~k~~g~s~~~tl~iaQ~LYE 147 (403)
T PF01131_consen 72 GGFE-FKNDDKKRFDDKEEAEQILEKLKNS---KVTEVEEKEKKKPPPLPFNLSTLQKEASKKLGFSAKETLDIAQKLYE 147 (403)
T ss_dssp CCS--EETTEES-CTSHHHHHHHHHHHHHC---EEEEEEEEEEEE----SB-HHHHHHHHHHHH---HHHHHHHHHHHHH
T ss_pred cccc-cccccccccccHHHHHHHhhcccCc---eEEEEEEEEeeecCCChHHHHHHHHHHHHHhhhhHHHHHHHHHHHHh
Confidence 5544 3445678999999999999999873 89999999999999999999999999999999999999999999999
Q ss_pred c-CceeecCCCCCCCCCcccHHHHHHHhccC-C-chhHHHHHHhhCCCCCCCCCCCCCCCCCCccCCCcc--cCCCCHHH
Q psy8714 326 Q-GYVSYPRTETTQYPENFDLVAVLRQQESS-P-DWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLAT--RTQLDGDA 400 (562)
Q Consensus 326 ~-glISYPRTds~~l~~~~~~~~~l~~l~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~~H~AI~PT~~~~--~~~L~~~e 400 (562)
+ ||||||||||++||++.++..+++.+... + .+...+...... .++++.++++|||||+||...+ ..+|+++|
T Consensus 148 ~~g~ISYPRTds~~l~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~--~~~~~~~kv~aH~AI~PT~~~~~~~~~Ls~~e 225 (403)
T PF01131_consen 148 KHGLISYPRTDSRYLPEDEDLKEILKYLKKHYGEDYFPEAPNLLKS--PKSKNDSKVTAHHAIIPTGKIPPDLSNLSEDE 225 (403)
T ss_dssp TTTSBS-SS-S---B-HHHGHHHHHHHHHHHTTGGGS-SS--TTSS--STTC-CCC-SSSS-B-BSSSTTHCGHHCHHHH
T ss_pred hhheeeeeccchhhhcchhhHHHHHHHHHHhccccccccchhhhhc--ccccCCccccCCCCccccccCccchhhcCHHH
Confidence 7 99999999999999987677777766542 1 122222111110 1112344568999999997654 36799999
Q ss_pred HHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeeccccccc--CCCCCCCCCCeeeeeeeEEe
Q psy8714 401 WRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKN--ESIPDFKPGDLIPIQSVKMV 478 (562)
Q Consensus 401 ~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~--~~Lp~l~~G~~~~~~~~~i~ 478 (562)
++||+||+|||||+|||||+|+++++.+.++++.|.++|++++++||+++|+....++ ..||.+++|+.+.+.++.+.
T Consensus 226 ~~vY~LI~rr~la~~~~~~~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~~~~~~~~~~~~~~lp~l~~g~~~~~~~~~~~ 305 (403)
T PF01131_consen 226 RKVYDLIARRFLAAFMPDAKYEKTTVTFEVGGEEFKASGKVIIDPGWKKVYPYEEEEDEEEDLPSLKEGDEIPIEDVEIK 305 (403)
T ss_dssp HHHHHHHHHHHHHHTS--EEEEEEEEEEEETTEEEEEEEEEEEEHGGGGCS-HCHCCTTSBB-----TTEEEEEEEEEEE
T ss_pred HHHHHHHHHHHHHHHHHHHheeeEEEEEEecCcEEEEEEeEEEECceeEEEEcccccccccccccccCCcEEeecccchh
Confidence 9999999999999999999999999999999999999999999999999997554432 36999999999999999999
Q ss_pred eeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHH
Q psy8714 479 ERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAY 558 (562)
Q Consensus 479 e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~ 558 (562)
+++|+||+||||++||++||+.|||||||||+||++|++||||++.+++.|+||++|+.|++.|... +.|++|++||.|
T Consensus 306 e~~TkPP~~~Te~~Ll~~Me~~GIGTpATra~iI~~L~~r~Yi~~~k~~~l~~T~~G~~li~~l~~~-~~l~~p~~Ta~~ 384 (403)
T PF01131_consen 306 EKKTKPPKRYTEASLLKAMEKAGIGTPATRASIIEKLIKRGYIERSKGKKLIPTPKGRALIEALPNF-PELISPEMTAQW 384 (403)
T ss_dssp EEEEESS--EBHHHHHHHHHHTTSS-TTTHHHHHHHHHHTTSEEE-ETTEEEEBHHHHHHHHHHHHC-CCCCSHHHHHHH
T ss_pred hhccCCCCCCCHHHHHhhhhhcCCCccccHHHHHHHhhccceeecccCceeeeehHHHHHHHHHHhh-HHhcCHHHHHHH
Confidence 9999999999999999999999999999999999999999999985568999999999999998554 789999999999
Q ss_pred HhhC
Q psy8714 559 RVQA 562 (562)
Q Consensus 559 E~~L 562 (562)
|..|
T Consensus 385 E~~L 388 (403)
T PF01131_consen 385 EEKL 388 (403)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 9875
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=5.9e-94 Score=761.40 Aligned_cols=348 Identities=32% Similarity=0.523 Sum_probs=307.6
Q ss_pred hHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEEEEeeCCe
Q psy8714 169 FEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGV 248 (562)
Q Consensus 169 ~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~ 248 (562)
++++||.||+++|||||||+||++|+.++. ++++|+||||||||+|||+||+||+||+|++||.|
T Consensus 2 ~l~~a~~aR~~~D~liG~n~sr~~t~~~~~------~~~lS~GRVQtPtL~liv~Re~ei~~F~p~~y~~i--------- 66 (381)
T cd00186 2 NLVNAQLARRILDRLVGFNLSRLLTKKLRR------KGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI--------- 66 (381)
T ss_pred cHHHHHHHHHHHHHHhhhhhhHHHHHHhCC------CCCCccccchhhHhHHHHHHHHHHHhCCCcceEEe---------
Confidence 688999999999999999999999987753 23699999999999999999999999999999998
Q ss_pred EEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCc
Q psy8714 249 AVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGY 328 (562)
Q Consensus 249 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~gl 328 (562)
+.++|+++++++++.+||+||||++||++||++|||||++||++||+|||+||
T Consensus 67 ---------------------------~~~~v~~~~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYe~gl 119 (381)
T cd00186 67 ---------------------------KEAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYEAGL 119 (381)
T ss_pred ---------------------------eeEEEEEEEeeeeecCCCCCcCHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCe
Confidence 24789999999999999999999999999999999999999999999999999
Q ss_pred eeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCCCCCCCCccCCCcc----cCCCCHHHHH
Q psy8714 329 VSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLAT----RTQLDGDAWR 402 (562)
Q Consensus 329 ISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~AI~PT~~~~----~~~L~~~e~~ 402 (562)
||||||||++||+++ .+..++..+.....+.. ..... ...+..+.++++|||||+||+..+ ...|+++|++
T Consensus 120 ISYPRTds~~ls~~~~~~~~~~~~~~~~~~~~~~--~~~~~-~~~~~~~~~~~~aH~AI~PT~~~~~~~~~~~l~~~e~~ 196 (381)
T cd00186 120 ITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYP--APLLG-RRNPKRGKKEQGAHEAIRPTKVAPTPELEANLSEDEFK 196 (381)
T ss_pred eeecCCCCccCCHHHHHHHHHHHHHhcCccccch--hhccc-cccccCCCCCcCCCCCCCcCCCCcCchhhccCCHHHHH
Confidence 999999999999986 34555555543221111 11111 111223445568999999998765 3689999999
Q ss_pred HHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccc-cCCCCCCCCCCeeeeeeeEEeeee
Q psy8714 403 LYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERK 481 (562)
Q Consensus 403 vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~-~~~Lp~l~~G~~~~~~~~~i~e~~ 481 (562)
||+||+|||||+||+||+|++++|.++++++.|.++|++++++||+.+|+.++.+ +..+|.+++|+.+.+.++.+.+++
T Consensus 197 iY~LI~rrfla~~~~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~p~l~~g~~~~~~~~~~~~~~ 276 (381)
T cd00186 197 LYELIWRRFLASQMADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKE 276 (381)
T ss_pred HHHHHHHHHHHHhCchhhEEEEEEEEEECCeEEEEEEEEEeeCCHHHHhCcccccccccCCCCCCCCEEeeeeeeeeecc
Confidence 9999999999999999999999999999999999999999999999999765443 345899999999999999999999
Q ss_pred cCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHHHHHhh
Q psy8714 482 TTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQ 561 (562)
Q Consensus 482 TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~ 561 (562)
|+||+||||++||++||+.|||||||||+||++|++||||.. +|+.|+||++|+.|+++|....+.|++|+|||.||.+
T Consensus 277 T~PP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~-~~k~l~pT~~G~~li~~l~~~~~~l~~p~lTa~~E~~ 355 (381)
T cd00186 277 TQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEK-EKKKLIPTELGFAVIELLEKHFPELVDPEFTAKLEEK 355 (381)
T ss_pred cCCCCCCCHHHHHHHHHhCCCCccccHHHHHHHHHhCCcEEe-eCCEEeECHHHHHHHHHHHHhchhccCHhHHHHHHHH
Confidence 999999999999999999999999999999999999999997 6779999999999999998777789999999999987
Q ss_pred C
Q psy8714 562 A 562 (562)
Q Consensus 562 L 562 (562)
|
T Consensus 356 L 356 (381)
T cd00186 356 L 356 (381)
T ss_pred H
Confidence 6
No 23
>PRK14701 reverse gyrase; Provisional
Probab=100.00 E-value=3.4e-91 Score=833.84 Aligned_cols=289 Identities=19% Similarity=0.234 Sum_probs=233.0
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCc-----eeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCC----
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGAC-----SVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVD---- 76 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~-----~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~---- 76 (562)
+.|||||| |++|+.||.++|....- ++|++ .++++.++||||.|||++|..|++|..|...+
T Consensus 581 ~~LiIaEk-----Ps~Ak~IA~~lg~~~~r~~g~~~~ye~----~~g~~~~~Vtas~GHl~dL~~~~~~~g~~~~~~~f~ 651 (1638)
T PRK14701 581 SALMIVES-----PNKARTIANFFGQPSVRKIGDLVAYEV----SIGDHMLIITASGGHVFDLVTNEGFHGVLINNNLFI 651 (1638)
T ss_pred CeEEEEeC-----hHHHHHHHHHhCCCccccCCCcceEEE----ecCCcEEEEEEecceeccCCCccccCccccccCccC
Confidence 67999999 99999999999864321 22222 12334689999999999998776665554322
Q ss_pred C-----------CCCCCC-------Ccc-cccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhccc
Q psy8714 77 P-----------LELFSC-------PTE-KREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI 137 (562)
Q Consensus 77 p-----------~~~~~~-------~~~-~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~ 137 (562)
| ..+|.. |.. ........++++.|++++++||+||||||||||||+|||+|++++..
T Consensus 652 P~y~~~k~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~lr~l~~~ad~viiatD~DrEGE~I~~~i~~~~~~---- 727 (1638)
T PRK14701 652 PIYDSIKRCRDCGHQFTDWEDKGVCPRCGSKNVDDAKENIKAMRELAHEVDEILIGTDPDTEGEKIAWDIRNVLAP---- 727 (1638)
T ss_pred CcccccccCCCchhhccccccccccccccccccccHHHHHHHHHHHHHhCCeEEECCCCChhhHHHHHHHHHHhcc----
Confidence 1 112211 000 00112234578889999999999999999999999999999999853
Q ss_pred CCCCcEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccc
Q psy8714 138 NSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPT 217 (562)
Q Consensus 138 ~~~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTpt 217 (562)
++++++|+|||++|+++|++||+||+++|.+++.||.||+++||+||||+||++|..+++ ..+|+|||||||
T Consensus 728 -~~~~i~R~~fs~lT~~aI~~A~~nlr~~d~~l~~A~~aRr~~D~~iG~nlSr~l~~~~~~-------~~lS~GRVQTPt 799 (1638)
T PRK14701 728 -YGPNIKRIEFHEVTRRAILKAIKEARDIDENRVKAQIVRRIEDRWIGFELSQKLWEVFED-------RNLSAGRVQTPV 799 (1638)
T ss_pred -CCCCeeEEEEccCCHHHHHHHHhCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhccC-------Cceeecccccch
Confidence 368999999999999999999999999999999999999999999999999999976542 359999999999
Q ss_pred hhhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCC
Q psy8714 218 LGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALN 297 (562)
Q Consensus 218 L~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~ 297 (562)
|+|||+|++||+| +|++||.+...+ + +.+.|.. +++ ...+.|.+++.++++.+||+|||
T Consensus 800 L~~Iv~Re~ei~~-~~~~~~~i~~~~---~--~~~~~~~----~~~-----------~~~~~V~~v~~k~~~~~pP~pf~ 858 (1638)
T PRK14701 800 LGWIIQRYKEFTE-SKVPFLGIILEN---D--LTVTIED----SKD-----------EVEVEVELVEEEEKERNPLPPYT 858 (1638)
T ss_pred hhhhHhhHHHHhc-CCCceEEEEEcC---c--eEEEecc----ccc-----------CCeEEEEEEEeeEEEccCCCCcC
Confidence 9999999999999 599999986543 2 3333321 111 02478999999999999999999
Q ss_pred HHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCC
Q psy8714 298 TVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTET 336 (562)
Q Consensus 298 l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds 336 (562)
|++||++||++|||||++||++||+|||+|++|||||..
T Consensus 859 t~~Lq~~As~~~g~s~~~tm~iAQ~LYE~g~~~~p~t~V 897 (1638)
T PRK14701 859 TDTMLRDASAFLKLSAKETMKLAQDLFEAGLCVTPDTYV 897 (1638)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHhCceeeCCCcee
Confidence 999999999999999999999999999999999999975
No 24
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.1e-77 Score=662.04 Aligned_cols=499 Identities=23% Similarity=0.333 Sum_probs=390.8
Q ss_pred EEEEecccCcCCcchHHhhcccccCCCCc-----eeeeeeeeEcCCCcEEEEEEecccccccccccCCC-------CCcc
Q psy8714 7 KLVPASEIKLARPSLISLLTPLQRMNGAC-----SVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYN-------NWDK 74 (562)
Q Consensus 7 ~l~~ae~~~~~~p~~a~~~~~~~g~~~~~-----~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~-------~W~~ 74 (562)
.|+|+|+ |..|++||..+|..... .+|+- .-|+. ...||++.||+++|-..+.+- +|-.
T Consensus 619 ~L~IVES-----PnKARTIA~FFgrPS~R~~~~~~vYEv---~~gD~-vL~ItAS~GHv~DLvt~~g~hGvl~~~~~~vP 689 (1187)
T COG1110 619 ALMIVES-----PNKARTIASFFGRPSVRRLGGGVVYEV---AIGDL-VLTITASGGHVFDLVTEPGVHGVLVKDGKYVP 689 (1187)
T ss_pred eEEEEeC-----ChHHHHHHHHhCCcceeeeCCeeEEEE---ecCCe-EEEEEecCCeeEEeecccccceeeccCCceEe
Confidence 4899999 88999999999974332 22221 12544 467999999999994322220 1111
Q ss_pred -------CC-CCCCC-----CCCcccc-cCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCC
Q psy8714 75 -------VD-PLELF-----SCPTEKR-EATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP 140 (562)
Q Consensus 75 -------~~-p~~~~-----~~~~~~~-~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~ 140 (562)
|. -...| .+|.... ...++..+|+.|++++-.+|+|+||||||.|||-|||+|..++.+ ++
T Consensus 690 vY~tIKrC~dcg~q~~~~~~~cP~Cgs~~v~d~~~~ve~lRelA~EvDeVlIgTDPDtEGEKIawDv~~~l~P-----y~ 764 (1187)
T COG1110 690 VYDTIKRCRDCGEQFVDSEDKCPRCGSRNVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFNYLRP-----YN 764 (1187)
T ss_pred hHHHHHHHhhcCceeccccccCCCCCCccccccHHHHHHHHHHHhhcCEEEEcCCCCCccchhHHHHHHhhCc-----CC
Confidence 11 00011 1333221 123456789999999999999999999999999999999999975 47
Q ss_pred CcEEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhh
Q psy8714 141 KTVWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGF 220 (562)
Q Consensus 141 ~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~l 220 (562)
..|+|+.||++|+.+|.+|++|+++.|.|++.||..|++.|++|||.||+.++..+. +.-+|+||||||+|++
T Consensus 765 ~nikR~eFHEVTrrAIleAl~n~r~vd~nlVkAQiVRRIeDRWIGF~LS~~Lw~~F~-------~~nLsAGRVQTPVLGW 837 (1187)
T COG1110 765 PNVKRIEFHEVTRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLWDVFN-------NKNLSAGRVQTPVLGW 837 (1187)
T ss_pred CceeEEEeeeecHHHHHHHHhCccccchhhhHHHhhhhhhhcccceeecHHHHHHhC-------ccCcccccccccccee
Confidence 889999999999999999999999999999999999999999999999998776553 2359999999999999
Q ss_pred hhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHH
Q psy8714 221 CVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVE 300 (562)
Q Consensus 221 Iv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~ 300 (562)
||+|+++-+.-+. |..+.. .+.. .+-+...++.+...+.. ....|.++..++...+||+||+|.+
T Consensus 838 IV~Ry~e~~~~~~--~~~~~~-------~~~~-----~~~~~~~~~~~~~~~~~-~~v~v~~~~e~ee~~~PlPPyTTDt 902 (1187)
T COG1110 838 IVNRYEEYKEKRG--YLVIQL-------DLDL-----PSGNREEVENVKRKLKL-IVVEVVDVVEREEEKNPLPPYTTDT 902 (1187)
T ss_pred ehhhHHHHhhccc--eeEeec-------ccee-----eccchhhhhhhhhhccc-ceEEEeehhhhhhccCCCCCcCcch
Confidence 9999998876444 443311 1111 22344555655555443 3466777666677789999999999
Q ss_pred HHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc-c-HHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCC
Q psy8714 301 LMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF-D-LVAVLRQQESSPDWGDHVREVLSNGISKPRKGKD 378 (562)
Q Consensus 301 Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~-~-~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 378 (562)
++.+||++||+|+++||++||.|+|.|+|||+||||+++|..- . ..+.|.. -+......||.|..
T Consensus 903 ~L~dAs~~L~lsa~~~M~iaQdLFE~GlITYHRTDSTrVS~~Gi~vAreyl~~-------------~~~e~~f~pR~Wge 969 (1187)
T COG1110 903 MLRDASRRLRLSADETMQIAQDLFEGGLITYHRTDSTRVSDVGIRVAREYLRK-------------EFGEEYFRPRSWGE 969 (1187)
T ss_pred HHHHHHHHhCCChhHHHHHHHHHHhccceEEeecCCcccchhhHHHHHHHHHH-------------hhccccccCCcccc
Confidence 9999999999999999999999999999999999999999742 1 1222211 11223468999988
Q ss_pred CCCCCCCccCCCcc---------------cCCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEEEE-EEE
Q psy8714 379 VGDHPPITPTKLAT---------------RTQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTMEA-KYL 442 (562)
Q Consensus 379 ~~~H~AI~PT~~~~---------------~~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a~g-~~~ 442 (562)
.+||+||+||...+ +..|+.++.+||+||.|||+|+||+|+++....+.+..++..-...+ ..+
T Consensus 970 ~GAHEaIRPtrPid~~eL~~~i~~G~i~~~~~Lt~~HlrvYdLIFrRFmASQm~pa~v~~~~~~i~~~~~~~~~e~~ve~ 1049 (1187)
T COG1110 970 EGAHEAIRPTRPIDVEELITLIEEGVIQLPIRLTKNHLRVYDLIFRRFMASQMRPAKVLKEKAEVKADGKDVELEALVEI 1049 (1187)
T ss_pred CCcccccCCCCCCCHHHHHHHHHcCCeeccchhhHHHHHHHHHHHHHHHHhhCCceeEEEEEEEEecCcceeeeeehhhh
Confidence 89999999998643 13489999999999999999999999999999999999875544444 445
Q ss_pred eecceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEE
Q psy8714 443 LHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVT 522 (562)
Q Consensus 443 ~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~ 522 (562)
...||..+|+. ..+|.+..|+ +.+....+...... ..||++++++.|++.|||+|||||.||++|.+||||.
T Consensus 1050 ~~~G~~~vy~~-----~~~p~l~~g~-l~v~~~~~~~~~kv--~lytqg~vi~~MKerGIGRPSTYAkive~L~~RgYvi 1121 (1187)
T COG1110 1050 LEDGFALVYPT-----RVLPELEKGT-LKVTEVEIRKVSKV--YLYTQGEVVEEMKERGIGRPSTYAKIVETLLRRGYVI 1121 (1187)
T ss_pred hccchhhhccc-----cccCccCCCc-eeeeeeEEEEcccc--cccccchHHHHHHhcCCCCCcHHHHHHHHHhcCCeEE
Confidence 68999999862 3478889998 77766665544433 4799999999999999999999999999999999998
Q ss_pred EcCCCe-eecchhHHHHHHhhhccCccCCChhhHHHHHhhC
Q psy8714 523 VTSGRR-LVPTSLGIVLVHGYQKIDRELVEPTMRSAYRVQA 562 (562)
Q Consensus 523 ~~~~k~-l~~T~~G~~li~~l~~~~~~l~~p~~Ta~~E~~L 562 (562)
-.+|++ ++||.+|+.+++.|..-.+.++|.+.|..+|+.|
T Consensus 1122 e~kg~~~lipTk~Gi~Vy~yL~~~~~~lVSEerTR~LEe~M 1162 (1187)
T COG1110 1122 ESKGRKKLIPTKLGIEVYEYLSEKYKKLVSEERTRRLEEIM 1162 (1187)
T ss_pred EecCceEeccccccHHHHHHHHHhcccccchhHHHHHHHHH
Confidence 756654 9999999999999988789999999999999864
No 25
>KOG1957|consensus
Probab=100.00 E-value=4.1e-74 Score=584.70 Aligned_cols=485 Identities=54% Similarity=0.845 Sum_probs=438.7
Q ss_pred EEEecccCcCCcchHHhhcccccC------CCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCC
Q psy8714 8 LVPASEIKLARPSLISLLTPLQRM------NGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELF 81 (562)
Q Consensus 8 l~~ae~~~~~~p~~a~~~~~~~g~------~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~ 81 (562)
|.+||| ||+|..||.+++. .+.+++.+|+|.|.|....|.||++.||+|.||||++|++|...||.+||
T Consensus 5 lmvaek-----psla~sia~ils~g~~s~~kg~csvhe~~g~f~g~~~~fk~tsvcghvmsldf~~kyn~w~~vdp~elf 79 (555)
T KOG1957|consen 5 LMVAEK-----PSLADSIANILSNGQASKRKGWCSVHEYDGQFRGRAARFKVTSVCGHVMSLDFPPKYNNWDKVDPAELF 79 (555)
T ss_pred eEeecC-----chHHHHHHHHhhCCccccccCceeeeeccccccCceeeEEEeeeeceeEeccCchhcCCccccCHHHHh
Confidence 779999 9999998877643 34588999999999999999999999999999999999999999999999
Q ss_pred CCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714 82 SCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW 161 (562)
Q Consensus 82 ~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~ 161 (562)
..|..+++++++.++.+.|..+++.||.+|+|.|||+|||+|.+||++..+.+|+.. ...++|+.||++|+++|.+|+.
T Consensus 80 ~apt~kkeanpk~~m~kfl~~eargcdy~vlwldcdkegenicfevidav~~~m~~~-~~~tyra~fsaitekdi~~am~ 158 (555)
T KOG1957|consen 80 SAPTEKKEANPKMNMNKFLASEARGCDYLVLWLDCDKEGENICFEVIDAVKCVMNRS-DFKTYRAHFSAITEKDIKKAMR 158 (555)
T ss_pred CCcchhcccCchhhHHHHHhhhccCCcEEEEEeecCCCcCeeehhhhhhhhhhhccC-cceEEeeeeccccHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999998888633 4567999999999999999999
Q ss_pred hCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhhhhhhhhhcccCcceEEEEE
Q psy8714 162 NLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDL 241 (562)
Q Consensus 162 nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv~Re~eI~~F~p~~y~~i~~ 241 (562)
||..+|.|.+.+..|||++|..| + .+..+|+|.||||||++.|+|...|+.|+|+.||.++.
T Consensus 159 ~lg~p~~nea~svdarqeldlri---------l---------ds~~isygpcqtptlgfcv~rhd~i~tfkpe~~w~l~~ 220 (555)
T KOG1957|consen 159 NLGEPDQNEALSVDARQELDLRI---------L---------DSSLISYGPCQTPTLGFCVTRHDQIQTFKPEQYWVLQT 220 (555)
T ss_pred hcCCCCcchhcccchhhhhhhhh---------h---------hhcceeecCCCCCcceeeeeehhhhhccCccceEEEee
Confidence 99999999999999999999987 1 13579999999999999999999999999999999999
Q ss_pred EEeeCCeEEEEEeecccccCHHHHHHHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHH
Q psy8714 242 TLNLNGVAVSVTWSRGHIFDKSTCNVFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAE 321 (562)
Q Consensus 242 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ 321 (562)
.+..++ +...|+++|++|.+.|.-+++.++..+++.|.+|.+|+..+..|..+||.+|.+-|
T Consensus 221 ~~~~~~--~~lew~r~rvfd~eia~~f~~~vk~~~~a~v~~vs~ke~~k~rp~alntvel~rv~---------------- 282 (555)
T KOG1957|consen 221 NFTTDD--LSLEWQRGRVFDAEIARVFLNRVKECKTALVEDVSKKEARKERPCALNTVELMRVA---------------- 282 (555)
T ss_pred ecCCCC--ccchhhhcchhhHHHHHHHHHHHHhhhhheehhhhhhHHhhcCCcccchhheeeee----------------
Confidence 987665 88999999999999999999999988999999999999999999999999998877
Q ss_pred HhHhcCceeecCCCCCCCCCcccHHHHHHHhccCCchhHHHHHHhhCCCCCCCCCCCCCCCCCCccCCCcccCCCCHHHH
Q psy8714 322 RLYTQGYVSYPRTETTQYPENFDLVAVLRQQESSPDWGDHVREVLSNGISKPRKGKDVGDHPPITPTKLATRTQLDGDAW 401 (562)
Q Consensus 322 ~LYE~glISYPRTds~~l~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~AI~PT~~~~~~~L~~~e~ 401 (562)
+|+++.+|+++|- +.. +.+++..++.+.++++|++|.|-+.......+.+-+
T Consensus 283 -----------itett~y~~nfd~--------si~---------~~D~L~~~s~gtdAgdgpPitpmr~~~R~m~~~dtk 334 (555)
T KOG1957|consen 283 -----------ITETTAYPANFDT--------SII---------LGDTLFEASFGTDAGDGPPITPMRKCNRYMKSGDTK 334 (555)
T ss_pred -----------EeecccCcccccc--------ccc---------cccccccccccCcCCCCCCcCcccccccccccccce
Confidence 4999999998851 110 112345566777788999999998766666777889
Q ss_pred HHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEE--EEEEEEeecceeeeecccc-------cccCCCCCCCC------
Q psy8714 402 RLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFT--MEAKYLLHPGFTGVMTWSA-------MKNESIPDFKP------ 466 (562)
Q Consensus 402 ~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~--a~g~~~~~~Gw~~v~~~~~-------~~~~~Lp~l~~------ 466 (562)
+||..++++|++.-+.+.+|..+++...++++.|. ..|+++.+.|+..+..... -++...|+.+.
T Consensus 335 RLY~~vCqhf~~tp~~~~~k~it~~k~slgdeqf~lw~~Gk~~~~~gft~fm~n~p~m~wgagcdECthPScq~slSmlg 414 (555)
T KOG1957|consen 335 RLYCYVCQHFYATPQFKCKKVITTVKCSLGDEQFILWCTGKRLREFGFTPFMPNNPKMPWGAGCDECTHPSCQQSLSMLG 414 (555)
T ss_pred eecchhhhhheeccCcCceEEEeeeeeccCCeeEEeccCcceeccCCccccccCCCccccccCCCccCCchHHhhhhccc
Confidence 99999999999999999999999999999999999 9999999999999975211 12455666555
Q ss_pred -CCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhcc
Q psy8714 467 -GDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKI 545 (562)
Q Consensus 467 -G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~ 545 (562)
|+.+.+.++.+.+..|.||-++|+..++..|+++||||.|.-+-+|..+-+|+|+.++.|+.+.||++|+.++.++..+
T Consensus 415 iG~~vEc~~v~Lv~~qTsPkwylTcnkcisvme~hgigtdasI~VhinsiceRnYv~Ve~gr~~~Pt~Lg~~l~~Gy~~~ 494 (555)
T KOG1957|consen 415 IGQCVECESVELVLDQTSPKWYLTCNKCISVMEKHGIGTDASIPVHINSICERNYVTVESGRALVPTPLGETLVRGYVKC 494 (555)
T ss_pred ceeEEEeccEEEEecCCCCCceeehhhhHHHHHhhcccceeeEEEeecchhhhheEeeecCcccCCCccchhhhcCceee
Confidence 9999999999999999999999999999999999999999999999999999999998999999999999999999989
Q ss_pred CccCCChhhHHHHHhhC
Q psy8714 546 DRELVEPTMRSAYRVQA 562 (562)
Q Consensus 546 ~~~l~~p~~Ta~~E~~L 562 (562)
+|++.-|.+.+..|.+|
T Consensus 495 DP~l~lpt~r~~~es~~ 511 (555)
T KOG1957|consen 495 DPELVLPTMRKEAESQL 511 (555)
T ss_pred CcceechhHHHHHHhhc
Confidence 99999999999999764
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=4.4e-68 Score=534.09 Aligned_cols=250 Identities=32% Similarity=0.538 Sum_probs=216.8
Q ss_pred cceeeccCCCCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCcc--cHHHHHHHhccCCchhHHH
Q psy8714 285 SSTKSKTKPQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPENF--DLVAVLRQQESSPDWGDHV 362 (562)
Q Consensus 285 ~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~~--~~~~~l~~l~~~~~~~~~~ 362 (562)
+++++.+||+||||++||++||++|||||++||++||+|||+|+||||||||+|||+++ ++..++..+.. +.|...+
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 46688999999999999999999999999999999999999999999999999999986 35566666543 2343322
Q ss_pred HHHhhCCCCCCC-CCCCCCCCCCCccCCCccc----CCCCHHHHHHHHHHHHHHHhhcccCceEEEEEEEEEECCeEEEE
Q psy8714 363 REVLSNGISKPR-KGKDVGDHPPITPTKLATR----TQLDGDAWRLYDYIVRHFIGTLCGDLVYTQKVAKFSVADEMFTM 437 (562)
Q Consensus 363 ~~~~~~~~~~~~-~~~~~~~H~AI~PT~~~~~----~~L~~~e~~vY~lI~rr~la~~~~~a~~~~t~v~~~~~~~~F~a 437 (562)
..... ...+. +.++++||||||||...+. .+|+++|++||+||+|||||+|||||+|++++|.+.++++.|.+
T Consensus 81 ~~~~~--~~~~~~~~~k~~~H~aI~PT~~~~~~~~~~~L~~~e~~iY~lI~rr~la~~~~~~~~~~t~v~~~~~~~~F~a 158 (259)
T smart00437 81 VSLLK--PRKPRWGKKEQGAHEAIRPTKPIPTPELEKELSEDEKKLYELIWRRFLASQMPDAKYEETKVIIKIGGEKFKA 158 (259)
T ss_pred hhhcc--CccccCCCCCCCCCCCCCccCCCCCchhhhhCCHHHHHHHHHHHHHHHHHhChhheEEEEEEEEEECCeEEEE
Confidence 11111 11222 3345689999999987542 47999999999999999999999999999999999999999999
Q ss_pred EEEEEeecceeeeecccccc-cCCCCCCCCCCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhh
Q psy8714 438 EAKYLLHPGFTGVMTWSAMK-NESIPDFKPGDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNIC 516 (562)
Q Consensus 438 ~g~~~~~~Gw~~v~~~~~~~-~~~Lp~l~~G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~ 516 (562)
+|++++++||+.||++++.+ +..||.+++|+.+.+.++.+.+++|+||+||||++||++||+.|||||||||+||++|+
T Consensus 159 ~g~~i~~~Gw~~v~~~~~~~~~~~lp~~~~g~~~~~~~~~~~e~~TkPP~~~Te~tLl~~Me~~GIGTpATra~iIe~L~ 238 (259)
T smart00437 159 KGKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKKTKPPARYTEASLIKLMEKRGIGRPSTYAEIIETLL 238 (259)
T ss_pred EEEEEeECCHHHhhcccccCccccCCCcCCCCEeeeeeeEEEecccCCCCCCCHHHHHHHHHHCCCCchhhHHHHHHHHH
Confidence 99999999999999765443 35699999999999999999999999999999999999999999999999999999999
Q ss_pred cCCeEEEcCCCeeecchhHHHH
Q psy8714 517 QRNYVTVTSGRRLVPTSLGIVL 538 (562)
Q Consensus 517 ~r~Yi~~~~~k~l~~T~~G~~l 538 (562)
+||||.+ +|+.|+||++|+.|
T Consensus 239 ~r~Yi~~-~~k~l~~T~~G~~l 259 (259)
T smart00437 239 DRGYVTK-EKKKLIPTELGIAV 259 (259)
T ss_pred hCCcEEe-eCCEEeEccceecC
Confidence 9999997 67899999999864
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=1.8e-33 Score=261.71 Aligned_cols=147 Identities=33% Similarity=0.400 Sum_probs=114.7
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceee--eeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCC--CC
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVH--EWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLE--LF 81 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~--~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~--~~ 81 (562)
|.|||||| ||+|+.||+++|....-... .+.++++|. .|+||||.|||++|++|++|..|....+.. ++
T Consensus 1 ~~LiIAEK-----Ps~Ak~ia~~L~~~~~~~~~~~~~~~~~~~~--~~~vt~~~GHl~~l~~p~~y~~~~~~~~~~~p~~ 73 (151)
T cd03362 1 MVLIIAEK-----PSVAKAIAKILGGGSKKKGKGRYYEFYGEGG--GYVVTWASGHLLELDFPEEYDPWDKVWPLEDPLF 73 (151)
T ss_pred CEEEEecC-----HHHHHHHHHHhCCCCccCCcccccceecCCC--CEEEEEEhhHhhcccChHHhccCCCCCccccCCc
Confidence 68999999 99999999999765432111 134466665 489999999999999999998776544322 33
Q ss_pred CCCcccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714 82 SCPTEKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW 161 (562)
Q Consensus 82 ~~~~~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~ 161 (562)
+............++++.|++++++||+||||||||||||+|||+|+++++.. .+++++|+|||++|+++|++||+
T Consensus 74 ~~~~~~~~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~~i~~~~~~~----~~~~v~R~~fsslT~~~I~~A~~ 149 (151)
T cd03362 74 PAPFKLKVDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKCV----KRKPVKRAWFSSLTPKAIRRAFK 149 (151)
T ss_pred CCceEEEECccHHHHHHHHHHHHhCCCeEEEccCCCccccHHHHHHHHHhCCC----CCCcEEEEEEccCCHHHHHHHHh
Confidence 32222222233456888899999999999999999999999999999999531 26899999999999999999999
Q ss_pred hC
Q psy8714 162 NL 163 (562)
Q Consensus 162 nl 163 (562)
||
T Consensus 150 nl 151 (151)
T cd03362 150 NL 151 (151)
T ss_pred cC
Confidence 86
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=7.3e-33 Score=255.07 Aligned_cols=142 Identities=34% Similarity=0.401 Sum_probs=111.9
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~ 85 (562)
|.|||||| ||+|+.|++++|..+... .++++|. .|+||||.|||++|++|++|..|....+..+++...
T Consensus 1 ~~LiIaEK-----Ps~a~~ia~~L~~~~~~~----~~~~~~~--~~~v~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~~ 69 (142)
T cd01028 1 KVLIIAEK-----PSKAKTIAKILGKGSKKK----GFYGEGG--GYVVTASVGHLLELPFPEEYVDWDKDWPLELFPFEP 69 (142)
T ss_pred CEEEEEeC-----HHHHHHHHHHhCCCcccC----CceecCC--CEEEEEEccccccCCCcccccccccCCchhhCCCCc
Confidence 68999999 999999999998765421 1466665 489999999999999999998765433322222111
Q ss_pred ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhC
Q psy8714 86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163 (562)
Q Consensus 86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl 163 (562)
.........++++.|++++++||+||||||||||||+|||+|+++++. .+++++|+|||++|+++|++||+||
T Consensus 70 ~~~~~~~~~~~~~~ik~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~-----~~~~v~R~~fsslT~~~I~~A~~nl 142 (142)
T cd01028 70 KYVVIPDKKKQLKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC-----DNKPVKRAWFSEITPKAIREAFKNL 142 (142)
T ss_pred eEEeCCcHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHhCC-----CCCCeEEEEEccCCHHHHHHHHhCc
Confidence 112223344678888888899999999999999999999999999953 1689999999999999999999986
No 29
>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=1.6e-32 Score=231.01 Aligned_cols=89 Identities=39% Similarity=0.558 Sum_probs=84.0
Q ss_pred EEEEEecccCHHHHHHHHHhCCCChHhHHHHHHHHHhHHhHhhccccHHhHHHhhcccCCCCCCccccCcccccchhhhh
Q psy8714 143 VWRARFSAITDKDIKAAMWNLVKPNIFEARSVDARQELDLRIGCAFTRYQTKFFQGKYGDLDASLISYGPCQTPTLGFCV 222 (562)
Q Consensus 143 v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~~aR~~~D~liG~nlSR~~t~~~~~~~~~~~~~~lS~GRVQTptL~lIv 222 (562)
|+|+|||++|+++|++||+|+++.+.++++||+||+++||++|||+||++|+.++. +.+|+||||||||+|||
T Consensus 1 v~R~~fs~lt~~~I~~a~~~l~~~~~~l~~a~~aR~~~D~l~G~n~Sr~~t~~~~~-------~~ls~GRVQtptL~lIv 73 (89)
T smart00436 1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRK-------GVLSAGRVQTPTLGLIV 73 (89)
T ss_pred CEEEEEecCCHHHHHHHHHCcccccHHHHHHHHHHHHHHHHHhHhhhHHHHHHhCC-------CCcceecchHHHHHHHH
Confidence 58999999999999999999999889999999999999999999999999987653 36999999999999999
Q ss_pred hhhhhhhcccCcceEE
Q psy8714 223 ERHDKIRTFKPEPYWL 238 (562)
Q Consensus 223 ~Re~eI~~F~p~~y~~ 238 (562)
+||+||+||+|++||.
T Consensus 74 ~R~~ei~~F~~~~y~~ 89 (89)
T smart00436 74 EREREIKNFVPKPYWE 89 (89)
T ss_pred HHHHHHHcCCCCCCCC
Confidence 9999999999999994
No 30
>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=99.96 E-value=3.5e-29 Score=236.82 Aligned_cols=143 Identities=23% Similarity=0.249 Sum_probs=108.3
Q ss_pred EEEEecccCcCCcchHHhhcccccCC-----CCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccC------
Q psy8714 7 KLVPASEIKLARPSLISLLTPLQRMN-----GACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKV------ 75 (562)
Q Consensus 7 ~l~~ae~~~~~~p~~a~~~~~~~g~~-----~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~------ 75 (562)
.|||||| ||+|+.||+++|.. +++++|+|. +++..|+|||+.|||++|++|+.|..|...
T Consensus 2 ~LiIaEK-----Ps~Ak~Ia~~L~~~~~~~~~~~~~~e~~----~~~~~~~Vt~~~GHl~~l~~~~~~~~~~~~~~~~~p 72 (170)
T cd03361 2 ALMIVES-----PNKARTIANFFGRPSVRRLGGLVVYEVS----TGDGVLMITASGGHVYDLVTKEGGHGVVEDDGRYVP 72 (170)
T ss_pred eEEEEeC-----hHHHHHHHHHhCCCcccccCCceeEEEe----cCCeEEEEEeCCCeeecCCCccCccCccccCCccee
Confidence 6999999 99999999999843 234445543 234467899999999999988877653321
Q ss_pred --------CCC-CCCC-----CCccc-ccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCC
Q psy8714 76 --------DPL-ELFS-----CPTEK-REATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSP 140 (562)
Q Consensus 76 --------~p~-~~~~-----~~~~~-~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~ 140 (562)
.|- .+|. +|... .....+.++++.|++++++||+||+|||||||||+|+|+|+++++.. +
T Consensus 73 ~~~~~~~c~pc~~lF~~~~~~cp~c~~~~~~~~~~~~~~l~~l~~~~~~iiiatD~drEGe~I~~~i~~~~~~~-----~ 147 (170)
T cd03361 73 VYDSIKRCRDCGYQFTEDSDKCPRCGSENIDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPY-----N 147 (170)
T ss_pred eeeEeeccCCcccccccccccCCcCCCcCCcchHHHHHHHHHHHhhCCEEEEecCCCccHHHHHHHHHHHhccC-----C
Confidence 110 1121 22211 11123457889999999999999999999999999999999999632 5
Q ss_pred CcEEEEEecccCHHHHHHHHHhC
Q psy8714 141 KTVWRARFSAITDKDIKAAMWNL 163 (562)
Q Consensus 141 ~~v~Rl~~sslt~~~I~~A~~nl 163 (562)
++++|+|||++|+++|++||+||
T Consensus 148 ~~v~R~~fs~it~~~I~~a~~n~ 170 (170)
T cd03361 148 KNIKRAEFHEVTRRAILEALRNP 170 (170)
T ss_pred CCeEEEEEecCCHHHHHHHHhCc
Confidence 78999999999999999999986
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=99.96 E-value=3.8e-29 Score=224.23 Aligned_cols=123 Identities=28% Similarity=0.283 Sum_probs=100.0
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~ 85 (562)
|+|||||| ||+|+.|++++|. .|+|+||.|||++|..|++|..|.. .|.. +..
T Consensus 1 ~~LiIaEK-----p~~a~~ia~~Lg~------------------~~~v~~~~GHl~~l~~p~~~~~~~~-~~~~-~~~-- 53 (123)
T cd03363 1 KKLVIVES-----PAKAKTIKKYLGK------------------EYEVLASVGHIRDLPKKGLGVDGED-DGFE-PKY-- 53 (123)
T ss_pred CEEEEEeC-----HHHHHHHHHHhCC------------------CcEEEeccCccccCCCcccCCChhc-cCcC-ceE--
Confidence 78999999 9999999988764 2679999999999998888865431 2211 111
Q ss_pred ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhC
Q psy8714 86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163 (562)
Q Consensus 86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl 163 (562)
. ....+.++++.|+++++++|+||||||||||||+|+|+|+++++ ++++|+|+|||++|+++|++||+||
T Consensus 54 -~-~~~~~~~~~~~ik~l~~~~~eiiiAtD~drEGe~i~~~i~~~~~------~~~~v~Rl~~sslt~~~I~~A~~n~ 123 (123)
T cd03363 54 -V-VIPGKKKVVKELKKLAKKADEIYLATDPDREGEAIAWHLAEVLK------LKKNVKRVVFNEITKEAIKEALKNP 123 (123)
T ss_pred -E-ECccHHHHHHHHHHHHhcCCEEEEcCCCCcchHHHHHHHHHHcC------CCCCeEEEEEccCCHHHHHHHHhCc
Confidence 0 11223467788888889999999999999999999999999995 3589999999999999999999985
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=99.81 E-value=6e-21 Score=165.30 Aligned_cols=98 Identities=24% Similarity=0.383 Sum_probs=81.4
Q ss_pred EEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCcc
Q psy8714 7 KLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPTE 86 (562)
Q Consensus 7 ~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~~ 86 (562)
+|||+|+ |+.|+.++++++ +. .+.|+|+.||++++..|+.|..
T Consensus 1 ~liIvE~-----ps~a~~i~~~l~---------------~~--~~~v~~~~Ghl~~~~~~~~~~~--------------- 43 (100)
T PF01751_consen 1 ELIIVEK-----PSDAKAIAKALG---------------GE--EYIVIATSGHLLELAKPEDYDP--------------- 43 (100)
T ss_dssp EEEEESS-----HHHHHHHHHHSS---------------TT--TEEEEEESSSSEESTTSSHHHC---------------
T ss_pred CEEEEeC-----HHHHHHHHHHcC---------------CC--CEEEEEeCCccccccccccccc---------------
Confidence 6999999 999999998777 22 2579999999999998887642
Q ss_pred cccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCc--EEEEEeccc
Q psy8714 87 KREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKT--VWRARFSAI 151 (562)
Q Consensus 87 ~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~--v~Rl~~ssl 151 (562)
..+.+.++.|+++++++|+||+|||||||||+|+|+|+++++.. .| ++|+||||+
T Consensus 44 ----~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i~~~~~~~------~~~~~~R~~~~~i 100 (100)
T PF01751_consen 44 ----KDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWEIIELLGKN------NPKLIKRVWFSSI 100 (100)
T ss_dssp ----HTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHHHHHHHHH------SHHHTTEEEEESS
T ss_pred ----ccccccchhhHHHhhhccEeeecCCCChHHHHHHHHHHHHHhHh------CCCcCCEEEEecC
Confidence 12346788888888899999999999999999999999999764 33 699999986
No 33
>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=97.95 E-value=4.1e-05 Score=67.31 Aligned_cols=38 Identities=16% Similarity=0.125 Sum_probs=32.8
Q ss_pred cCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe
Q psy8714 106 DCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF 148 (562)
Q Consensus 106 ~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~ 148 (562)
+.++||+|||||+|||.+++.|.+.++.. ..+|.|+-+
T Consensus 56 ~i~EVIlA~~pt~EGe~Ta~yi~~~l~~~-----~~kvsRlA~ 93 (112)
T cd01025 56 QVKEVILATNPTVEGEATALYIAKLLKDF-----GVKVTRLAQ 93 (112)
T ss_pred CCcEEEEecCCCchHHHHHHHHHHHHhHc-----CCCeEEEEE
Confidence 56899999999999999999999999753 567888854
No 34
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=97.89 E-value=2.1e-05 Score=63.97 Aligned_cols=72 Identities=24% Similarity=0.289 Sum_probs=50.5
Q ss_pred eEEEEecccCcCCcchHHhhcccccCCCCceeeeeeeeEcCCCcEEEEEEecccccccccccCCCCCccCCCCCCCCCCc
Q psy8714 6 KKLVPASEIKLARPSLISLLTPLQRMNGACSVHEWVGPLFGDLVLFKMTSVCGHIMGLDFTSKYNNWDKVDPLELFSCPT 85 (562)
Q Consensus 6 ~~l~~ae~~~~~~p~~a~~~~~~~g~~~~~~~~~~~g~~~g~~~~~~Vt~~~GHl~~l~~~~~y~~W~~~~p~~~~~~~~ 85 (562)
++|||+|. |.-|..+....+ . .+.+.++.||+...
T Consensus 1 ~~l~ivEg-----~~da~~~~~~~~----------------~--~~~~~~~~G~~~~~---------------------- 35 (76)
T smart00493 1 KVLIIVEG-----PADAIALEKAGG----------------F--GGNVVALGGHLLKK---------------------- 35 (76)
T ss_pred CEEEEEcC-----HHHHHHHHHhcC----------------C--CEEEEEEeeeecHH----------------------
Confidence 57999999 777777764222 0 13467888997210
Q ss_pred ccccCCCCCchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHh
Q psy8714 86 EKREATPKLKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVR 132 (562)
Q Consensus 86 ~~~~~~~~~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~ 132 (562)
+.++.|++...+ ++||+|+|+|+||+.+++++.+++.
T Consensus 36 ---------~~~~~l~~~~~~-~~Iii~~D~D~~G~~~~~~i~~~l~ 72 (76)
T smart00493 36 ---------EIIKLLKRLAKK-KEVILATDPDREGEAIAWKLAELLK 72 (76)
T ss_pred ---------HHHHHHHHHhcC-CEEEEEcCCChhHHHHHHHHHHHhh
Confidence 133344443334 7899999999999999999999885
No 35
>PRK00076 recR recombination protein RecR; Reviewed
Probab=96.57 E-value=0.019 Score=55.57 Aligned_cols=55 Identities=13% Similarity=0.099 Sum_probs=44.0
Q ss_pred ccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe--------cccCHHHHHHHHHhCC
Q psy8714 105 KDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF--------SAITDKDIKAAMWNLV 164 (562)
Q Consensus 105 ~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~--------sslt~~~I~~A~~nl~ 164 (562)
.++++||+||+|+.|||..++.|.+.++.. ...|.|+=. .=++.-.+.+||++-+
T Consensus 132 ~~v~EVIlA~~pt~EGe~Ta~yi~~~lk~~-----~ikvtRiA~GiP~G~~ley~D~~TL~~Al~~R~ 194 (196)
T PRK00076 132 GEVKEVILATNPTVEGEATAHYIARLLKPL-----GVKVTRLAHGVPVGGELEYVDEGTLSRALEGRR 194 (196)
T ss_pred CCCCEEEEeCCCCchHHHHHHHHHHHHHHc-----CCCeeeeeeCCCCCcceeeCCHHHHHHHHHhCc
Confidence 468999999999999999999999999753 467888753 3456777788887654
No 36
>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=96.09 E-value=0.0079 Score=49.97 Aligned_cols=36 Identities=22% Similarity=0.230 Sum_probs=29.2
Q ss_pred CCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEE
Q psy8714 107 CEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRAR 147 (562)
Q Consensus 107 ~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~ 147 (562)
.+.||++||+|+.|+.|.+.+.+.++. +...++|+.
T Consensus 45 ~~~VIiltD~D~aG~~i~~~~~~~l~~-----~~~~~~~~~ 80 (81)
T cd01027 45 YRGVIILTDPDRKGEKIRKKLSEYLSG-----PVPEIKRAF 80 (81)
T ss_pred CCEEEEEECCCHHHHHHHHHHHHHhcc-----cCCCeeecc
Confidence 689999999999999999999999853 234466653
No 37
>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=95.79 E-value=0.041 Score=43.92 Aligned_cols=36 Identities=28% Similarity=0.446 Sum_probs=28.7
Q ss_pred CCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEE
Q psy8714 107 CEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRAR 147 (562)
Q Consensus 107 ~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~ 147 (562)
+..|++++|+|.+|+.+++.+.+.+... ...+.|++
T Consensus 47 ~~~v~i~~D~D~~g~~~~~~~~~~~~~~-----~~~~~~~~ 82 (83)
T cd00188 47 AKEVIIATDADREGEAIALRLLELLKSL-----GKKVRRLL 82 (83)
T ss_pred CCEEEEEcCCChhHHHHHHHHHHHHHhc-----CCceEEee
Confidence 6799999999999999999999887531 35566654
No 38
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=92.30 E-value=0.38 Score=48.90 Aligned_cols=109 Identities=17% Similarity=0.306 Sum_probs=68.6
Q ss_pred hhhhhhhhhhhccc-CcceEEEEEEEeeCCeEEEEEee----cc--cccCH--HHHHHHHHHhhhcCceEEEEEEcceee
Q psy8714 219 GFCVERHDKIRTFK-PEPYWLLDLTLNLNGVAVSVTWS----RG--HIFDK--STCNVFFKAVEKEKHVTVVDVQSSTKS 289 (562)
Q Consensus 219 ~lIv~Re~eI~~F~-p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~--~~a~~~~~~~~~~~~~~V~~v~~~~~~ 289 (562)
.||+.|..+ +|= +..|-...+.+..++..|.+... .| .++.. .+.+..+-.+.....+.|.+++..++.
T Consensus 126 ~lI~rr~la--~~~~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~lp~~~~g~~~~~~~~~~~e~~ 203 (259)
T smart00437 126 ELIWRRFLA--SQMPDAKYEETKVIIKIGGEKFKAKGKTLLFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVEEKK 203 (259)
T ss_pred HHHHHHHHH--HhChhheEEEEEEEEEECCeEEEEEEEEEeECCHHHhhcccccCccccCCCcCCCCEeeeeeeEEEecc
Confidence 455555543 333 34455566667667777766532 11 12111 111111222333346788888889999
Q ss_pred ccCCCCCCHHHHHHHHHhhCCCCHHHH-HHHHHHhHhcCcee
Q psy8714 290 KTKPQALNTVELMRVASSGLGMGPHHA-MQIAERLYTQGYVS 330 (562)
Q Consensus 290 ~~pP~pf~l~~Lq~~a~~~~g~s~~~t-l~iaQ~LYE~glIS 330 (562)
+.||.+|+-++|...+-+ .|+.-.-| ..+.+.|.++|||.
T Consensus 204 TkPP~~~Te~tLl~~Me~-~GIGTpATra~iIe~L~~r~Yi~ 244 (259)
T smart00437 204 TKPPARYTEASLIKLMEK-RGIGRPSTYAEIIETLLDRGYVT 244 (259)
T ss_pred cCCCCCCCHHHHHHHHHH-CCCCchhhHHHHHHHHHhCCcEE
Confidence 999999999999999864 58764444 46699999999996
No 39
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=92.13 E-value=0.095 Score=43.17 Aligned_cols=35 Identities=20% Similarity=0.234 Sum_probs=23.4
Q ss_pred CCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEE
Q psy8714 107 CEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRA 146 (562)
Q Consensus 107 ~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl 146 (562)
..+||+|+|+|.+|+..+.++.+.+... ..+|+|+
T Consensus 46 ~~~Vii~~D~D~~G~~~a~~i~~~l~~~-----gi~v~~v 80 (81)
T PF13662_consen 46 VKEVIIAFDNDKAGEKAAQKIAKKLLPL-----GIRVTRV 80 (81)
T ss_dssp -SEEEEEEESSHHHHHHHHHHHHHHG--------------
T ss_pred CceEEEEeCcCHHHHHHHHHHHHHHHhh-----ccccccC
Confidence 5789999999999999999999977532 3556664
No 40
>PRK13844 recombination protein RecR; Provisional
Probab=91.50 E-value=0.62 Score=45.26 Aligned_cols=53 Identities=13% Similarity=0.167 Sum_probs=42.1
Q ss_pred cCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe--------cccCHHHHHHHHHhCC
Q psy8714 106 DCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF--------SAITDKDIKAAMWNLV 164 (562)
Q Consensus 106 ~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~--------sslt~~~I~~A~~nl~ 164 (562)
++++||+||.|+-|||.-+..|.+.++ + ...|.|+=. .=++...+.+||++-+
T Consensus 138 ~v~EVIlAt~~t~EGe~Ta~yi~~~lk-----~-~vkvtRlA~GiP~G~~ley~D~~TL~~Al~~R~ 198 (200)
T PRK13844 138 KIDEVILAISPTVEGETTAHFISQMIA-----K-DIKISRIGFGVPFGGELEYLDQQTLLHAFNART 198 (200)
T ss_pred CCcEEEEeCCCCccHHHHHHHHHHHhc-----C-CCcEEeeeecCcCCcceeecCHHHHHHHHHhCc
Confidence 689999999999999999999999885 2 466778742 3456777888887754
No 41
>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=91.03 E-value=0.51 Score=53.95 Aligned_cols=131 Identities=9% Similarity=0.120 Sum_probs=80.6
Q ss_pred HHHHHHHHHHh--hcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEeee
Q psy8714 403 LYDYIVRHFIG--TLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVER 480 (562)
Q Consensus 403 vY~lI~rr~la--~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~ 480 (562)
+-.+|+.|..+ .|- |..|=...+.+..++..|.+.... + .+...+.. +..+-.++..+...+.++.-+++
T Consensus 196 tL~lvv~Re~eI~~F~-p~~y~~i~~~~~~~~~~~~~~~~~----~--~~~~~~~a-~~~~~~~~~~~~~~V~~v~~~~~ 267 (618)
T TIGR01057 196 TLAFLVEREREINLFV-PKPYWVIKATLEKGGGVFDARPEK----W--KIWSEEEA-KSIKEELKKSPWAAVEEVRSERS 267 (618)
T ss_pred HHHHHHHhHHHHHcCc-CCccEEEEEEEecCCceEEEEEcc----C--CcCCHHHH-HHHHHHHhCCCCeEEEEEEeeee
Confidence 33567777665 444 444445556666666667665310 0 11111100 11112233333577888999999
Q ss_pred ecCCCCCCCHHHHHHHHH-hcCCCCcCchhHHHHHhhcCCeEEE-cCCCeeecchhH-HHHHHhh
Q psy8714 481 KTTPPDYLTESELISLME-KHGIGTDASIPVHINNICQRNYVTV-TSGRRLVPTSLG-IVLVHGY 542 (562)
Q Consensus 481 ~TkPP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~r~Yi~~-~~~k~l~~T~~G-~~li~~l 542 (562)
++.||.+|+-++|.+.|- +.|++..-|. .|.++|.+.|||.- ......+|.+.. ..+++.+
T Consensus 268 ~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~iaQ~LYe~g~ISYPRTds~~l~~~~~~~~~l~~l 331 (618)
T TIGR01057 268 ILKPPPPFDLGTLQREAYRIFGFSPKKTQ-SIAQELYEEALISYPRTSSQKLPPSINYRAILDNL 331 (618)
T ss_pred eccCCCCccHHHHHHHHHHhcCCCHHHHH-HHHHHHHhcCceeecCcccCccCHHHhHHHHHHHH
Confidence 999999999999999775 5699998888 79999999999973 122345555532 3344443
No 42
>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=91.02 E-value=0.55 Score=50.83 Aligned_cols=114 Identities=15% Similarity=0.278 Sum_probs=69.5
Q ss_pred chhhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeec----c--cccCHHHHHH---HHHHhhhcCceEEEEEEcce
Q psy8714 217 TLGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSR----G--HIFDKSTCNV---FFKAVEKEKHVTVVDVQSST 287 (562)
Q Consensus 217 tL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~----~--~~~~~~~a~~---~~~~~~~~~~~~V~~v~~~~ 287 (562)
+-.+|+.|..+. -+.|..|-...+.+..++..|.+.... | .+......+. .+..+.....+.+.++..++
T Consensus 228 vY~LI~rr~la~-~~~~~~~~~t~v~~~~~~~~F~~~g~~~~~~Gw~~~~~~~~~~~~~~~lp~l~~g~~~~~~~~~~~e 306 (403)
T PF01131_consen 228 VYDLIARRFLAA-FMPDAKYEKTTVTFEVGGEEFKASGKVIIDPGWKKVYPYEEEEDEEEDLPSLKEGDEIPIEDVEIKE 306 (403)
T ss_dssp HHHHHHHHHHHH-TS--EEEEEEEEEEEETTEEEEEEEEEEEEHGGGGCS-HCHCCTTSBB-----TTEEEEEEEEEEEE
T ss_pred HHHHHHHHHHHH-HHHHHheeeEEEEEEecCcEEEEEEeEEEECceeEEEEcccccccccccccccCCcEEeecccchhh
Confidence 345666665554 224455666778888888888876531 1 1222111111 23334444457788889999
Q ss_pred eeccCCCCCCHHHHHHHHHhhCCCCHHHH-HHHHHHhHhcCceeec
Q psy8714 288 KSKTKPQALNTVELMRVASSGLGMGPHHA-MQIAERLYTQGYVSYP 332 (562)
Q Consensus 288 ~~~~pP~pf~l~~Lq~~a~~~~g~s~~~t-l~iaQ~LYE~glISYP 332 (562)
+.+.||.+|+-++|...+- ..|+.-.-| ..|.+.|.++|||.--
T Consensus 307 ~~TkPP~~~Te~~Ll~~Me-~~GIGTpATra~iI~~L~~r~Yi~~~ 351 (403)
T PF01131_consen 307 KKTKPPKRYTEASLLKAME-KAGIGTPATRASIIEKLIKRGYIERS 351 (403)
T ss_dssp EEEESS--EBHHHHHHHHH-HTTSS-TTTHHHHHHHHHHTTSEEE-
T ss_pred hccCCCCCCCHHHHHhhhh-hcCCCccccHHHHHHHhhccceeecc
Confidence 9999999999999999884 568874444 5679999999999864
No 43
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=90.51 E-value=0.46 Score=45.99 Aligned_cols=52 Identities=13% Similarity=0.077 Sum_probs=40.6
Q ss_pred cCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe--------cccCHHHHHHHHHh
Q psy8714 106 DCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF--------SAITDKDIKAAMWN 162 (562)
Q Consensus 106 ~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~--------sslt~~~I~~A~~n 162 (562)
++++||+||+|+-|||.-+..|.+.++.. ..+|.|+=. .=++.-.+.+||++
T Consensus 134 ~v~EVIlAt~~tvEGe~Ta~yi~~~lk~~-----~ikvtRlA~GiP~G~~ley~D~~TL~~Al~~ 193 (195)
T TIGR00615 134 SVKEVILATNPTVEGEATALYIARLLQPF-----GVKVTRIASGLPVGGDLEYADEVTLARALEG 193 (195)
T ss_pred CCcEEEEeCCCCchHHHHHHHHHHHhhhc-----CCcEEeeeecCCCCcceeecCHHHHHHHHHc
Confidence 58999999999999999999999998742 467888742 33566667777765
No 44
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=89.60 E-value=0.45 Score=42.91 Aligned_cols=68 Identities=10% Similarity=0.136 Sum_probs=44.5
Q ss_pred hHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhccc----CCCCc---EEE-EEecccCHHHHHHHHHhCC
Q psy8714 96 LPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQINI----NSPKT---VWR-ARFSAITDKDIKAAMWNLV 164 (562)
Q Consensus 96 ~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~----~~~~~---v~R-l~~sslt~~~I~~A~~nl~ 164 (562)
.+..|+++ .+-..||+-||||+.||-|...+.+++.....- ....+ ..| +-+-++....++.|+.+..
T Consensus 45 ~ie~i~~~-~~~k~VIILTD~D~~Ge~Irk~l~~~l~~~~~~~id~~~~~~~~~~~~i~gVE~~~~~~~~~~l~~~~ 120 (127)
T COG1658 45 TIELIKKA-QKYKGVIILTDPDRKGERIRKKLKEYLPGAKGAFIDREIRNKLKINGKIIGVEEASSEALRKALKEVP 120 (127)
T ss_pred HHHHHHHh-hccCCEEEEeCCCcchHHHHHHHHHHhcccccccccHHHhhhcccccccccceecChHHHHHHHHhCC
Confidence 44455543 244579999999999999999999998652110 00111 222 2345788888888888765
No 45
>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=88.89 E-value=1.1 Score=42.45 Aligned_cols=69 Identities=14% Similarity=0.077 Sum_probs=44.5
Q ss_pred hHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhc----ccCCCCc-EEEEEecccCHHHHHHHHHhCCC
Q psy8714 96 LPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQI----NINSPKT-VWRARFSAITDKDIKAAMWNLVK 165 (562)
Q Consensus 96 ~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~----~~~~~~~-v~Rl~~sslt~~~I~~A~~nl~~ 165 (562)
.++.|+.+. +-.-||+-||||.-||.|=..|.+++.... .+....+ =.-+=+-..++++|++|+.+...
T Consensus 37 ~i~~i~~~~-~~rgVIIfTDpD~~GekIRk~i~~~vp~~khafi~~~~a~~~~~~iGVE~As~e~I~~AL~~~~~ 110 (174)
T TIGR00334 37 TINLIKKAQ-KKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPKHLAKPNKKKIGVEEASVEAIIAALENVHE 110 (174)
T ss_pred HHHHHHHHh-hcCCEEEEeCCCCchHHHHHHHHHHCCCCeEEeeeHHhcCcCCCCcccCCCCHHHHHHHHHHhcc
Confidence 455565544 334699999999999999888877763210 0000000 01134556789999999999875
No 46
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=88.76 E-value=1.1 Score=43.68 Aligned_cols=56 Identities=16% Similarity=0.293 Sum_probs=42.2
Q ss_pred hhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEec------ccCHHHHHHHHHh
Q psy8714 102 NEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFS------AITDKDIKAAMWN 162 (562)
Q Consensus 102 ~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~s------slt~~~I~~A~~n 162 (562)
..+..||.|+||||+||-|--+|....+-++.. -+.|.||.+. -++.+-|++-+.|
T Consensus 53 raaeGADlvlIATDaD~~GReLA~kf~eeLrg~-----VGhiERmK~PiGHDvEhiD~elvrkEl~n 114 (290)
T COG4026 53 RAAEGADLVLIATDADRVGRELAEKFFEELRGM-----VGHIERMKIPIGHDVEHIDVELVRKELKN 114 (290)
T ss_pred HhhccCCEEEEeecCcchhHHHHHHHHHHHHHh-----hhhhheeccCCCCCccccCHHHHHHHHHH
Confidence 446799999999999999999999888888654 3668888763 3455555555554
No 47
>PRK04031 DNA primase; Provisional
Probab=88.40 E-value=0.6 Score=49.85 Aligned_cols=70 Identities=21% Similarity=0.250 Sum_probs=48.9
Q ss_pred HHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhCCCChHhH
Q psy8714 97 PAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFE 170 (562)
Q Consensus 97 i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l 170 (562)
-..+.++++ .+.|++++|+|+-|+.|.+++++.++..+- .+.| .-.-.-++++++|.+|+.+..|..+.+
T Consensus 201 ~~~i~~l~k-~~~Vil~~DgD~aGe~I~k~l~~v~~~d~V--araP-~G~dVE~ls~eeI~kAL~~~~p~~~~l 270 (408)
T PRK04031 201 PETIIELSK-KKTVTAFLDGDRGGELILKELLQVADIDYV--ARAP-PGKEVEELTKKEIAKALRNKVPVEQYL 270 (408)
T ss_pred HHHHHHHhc-CCCEEEEECCCHHHHHHHHHHHhhcceeEE--ecCC-CCCChhhCCHHHHHHHHHhcCCHHHHH
Confidence 345556555 789999999999999999999875321100 0111 112356889999999999988877664
No 48
>PRK07220 DNA topoisomerase I; Validated
Probab=88.25 E-value=1.4 Score=51.53 Aligned_cols=75 Identities=17% Similarity=0.285 Sum_probs=54.8
Q ss_pred CCeeeeeeeEEeeeecCCCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEE-cCCCeeecchh-HHHHHHhh
Q psy8714 467 GDLIPIQSVKMVERKTTPPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTV-TSGRRLVPTSL-GIVLVHGY 542 (562)
Q Consensus 467 G~~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~-~~~k~l~~T~~-G~~li~~l 542 (562)
+..+.|.++..++++..||.+|+-++|..++-+.|+. |..-..|.+.|++.|||.- ......+|.+. ...+++.|
T Consensus 257 ~~~~~V~~v~~~~~~~~pP~pf~ts~Lq~~a~~~g~s-~~~tm~iaQ~LYe~g~ITYPRTDs~~l~~~~~~~~~i~~l 333 (740)
T PRK07220 257 GKTAEVTEVEKGTKTDKPPTPFNTTEFISAANSIGFS-AANAMRIAESLYTNGYISYPRTDNTVYPESLDLREQIEIF 333 (740)
T ss_pred CCCeEEEEEeeeeEecCCCCCcCHHHHHHHHHHcCCC-HHHHHHHHHHHHhCCceeecccCCeecCchhhHHHHHHHH
Confidence 3457788899999999999999999999999877773 4444579999999999973 12345556543 33344433
No 49
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=86.02 E-value=1.5 Score=42.30 Aligned_cols=51 Identities=14% Similarity=0.104 Sum_probs=38.0
Q ss_pred CeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEe--------cccCHHHHHHHHHhC
Q psy8714 108 EFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARF--------SAITDKDIKAAMWNL 163 (562)
Q Consensus 108 d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~--------sslt~~~I~~A~~nl 163 (562)
++||+||+|--|||.-+..|.+.+++. ..+|.|+=. -=+++-.+.+||.+-
T Consensus 137 ~EvIlAtnpTvEGeaTA~YI~~~l~~~-----~ikvtRlA~GiPvGg~lEyvD~~TL~~Al~~R 195 (198)
T COG0353 137 KEVILATNPTVEGEATALYIARLLKPL-----GLKVTRLAQGVPVGGELEYVDEGTLSRALEGR 195 (198)
T ss_pred ceEEEecCCCccchHHHHHHHHHHhhc-----CCeEEEEeecCccCCceecccHHHHHHHHhcC
Confidence 399999999999999999999999764 567888742 223455555555543
No 50
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=85.96 E-value=2 Score=48.49 Aligned_cols=127 Identities=17% Similarity=0.182 Sum_probs=77.6
Q ss_pred HHHHHHH--hhcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeecC
Q psy8714 406 YIVRHFI--GTLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKTT 483 (562)
Q Consensus 406 lI~rr~l--a~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~Tk 483 (562)
||+.|-- ..|- |..|-...+.+..++..|.+.-.......+..+...+.. ...+-.++ |+.+.|.+++-+.++..
T Consensus 179 lVveRE~EI~~F~-p~~yw~i~a~~~~~~~~f~a~~~~~~~~~~~~~~~~~~a-~~~~~~l~-~~~~~V~~ve~k~~~~~ 255 (570)
T COG0550 179 LVVEREREIEAFV-PEEYWEIKAIFEKGGGEFSARLTEIEGKKEGRLKDKDEA-EEIVNKLK-GKPAKVVSVEKKPKKRS 255 (570)
T ss_pred hhHhhHHHHHhCC-CCcceEEEEEEecCCccEEEEEeccccccccccccHHHH-HHHHHHcc-CCceEEEEEeeeeeccC
Confidence 3444433 3444 456667777777665557665443221111111110000 11122333 88888999999999999
Q ss_pred CCCCCCHHHHHHHHHh-cCCCCcCchhHHHHHhhcC-CeEEE--cCCCeeecchhHH
Q psy8714 484 PPDYLTESELISLMEK-HGIGTDASIPVHINNICQR-NYVTV--TSGRRLVPTSLGI 536 (562)
Q Consensus 484 PP~~~Te~~Li~~Me~-~GIGTpATra~iI~~L~~r-~Yi~~--~~~k~l~~T~~G~ 536 (562)
||++||-++|....-+ .|++..-|. .|-++|++. |||.- .....|-++-...
T Consensus 256 pp~Pf~tstLQq~As~~lgfs~kktm-~iAQ~LYE~~glITYpRTDs~~ls~~~~~~ 311 (570)
T COG0550 256 PPPPFTTSTLQQEASRKLGFSAKKTM-DIAQKLYEGHGLITYPRTDSTRLSEEALAE 311 (570)
T ss_pred CCCCCcHHHHHHHHHHhCCCCHHHHH-HHHHHHhcCCCcEEecCCCCCcCCHHHHHH
Confidence 9999999999988755 478877776 688999997 99973 3333444444443
No 51
>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=85.84 E-value=1.7 Score=46.75 Aligned_cols=110 Identities=17% Similarity=0.278 Sum_probs=68.5
Q ss_pred hhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEee----cc--cccC--HHHHHHHHHHhhhcCceEEEEEEcceeec
Q psy8714 219 GFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWS----RG--HIFD--KSTCNVFFKAVEKEKHVTVVDVQSSTKSK 290 (562)
Q Consensus 219 ~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~--~~~a~~~~~~~~~~~~~~V~~v~~~~~~~ 290 (562)
.||+.|....- ..+.-|=...+.+..++..|.+... .| .+.. +...+..+-.+.....+.+.+++..++.+
T Consensus 199 ~LI~rrfla~~-~~~~~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~p~l~~g~~~~~~~~~~~~~~T 277 (381)
T cd00186 199 ELIWRRFLASQ-MADAKYEETTVTLEIGGEKFKASGKVLLEDGWLEVYPEEKDDEEEEPPPLKEGDELKLEEVELEEKET 277 (381)
T ss_pred HHHHHHHHHHh-CchhhEEEEEEEEEECCeEEEEEEEEEeeCCHHHHhCcccccccccCCCCCCCCEEeeeeeeeeeccc
Confidence 46666665442 2344455566777666667766431 11 1111 11001111123333456778888889999
Q ss_pred cCCCCCCHHHHHHHHHhhCCCCHHHHH-HHHHHhHhcCcee
Q psy8714 291 TKPQALNTVELMRVASSGLGMGPHHAM-QIAERLYTQGYVS 330 (562)
Q Consensus 291 ~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~iaQ~LYE~glIS 330 (562)
.||.+|+-++|..++- ..|+.-.-|. .|.+.|.++|||.
T Consensus 278 ~PP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~r~Yi~ 317 (381)
T cd00186 278 QPPPRYTEASLIKLME-KRGIGRPSTYASIIETLLDRGYVE 317 (381)
T ss_pred CCCCCCCHHHHHHHHH-hCCCCccccHHHHHHHHHhCCcEE
Confidence 9999999999999885 4588755554 5699999999997
No 52
>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=85.50 E-value=2.6 Score=48.24 Aligned_cols=118 Identities=16% Similarity=0.287 Sum_probs=70.6
Q ss_pred hhhhhhhhhhccc-CcceEEEEEEEee--CCeEEEEEee----cc--ccc--C----HHHHHHHHHHhhhcCceEEEEEE
Q psy8714 220 FCVERHDKIRTFK-PEPYWLLDLTLNL--NGVAVSVTWS----RG--HIF--D----KSTCNVFFKAVEKEKHVTVVDVQ 284 (562)
Q Consensus 220 lIv~Re~eI~~F~-p~~y~~i~~~~~~--~~~~~~~~~~----~~--~~~--~----~~~a~~~~~~~~~~~~~~V~~v~ 284 (562)
||+.|... +|- |.-|-+..+.+.. ++..|.+... .| .++ + ++..+..+-.+.....+.+.+++
T Consensus 372 lI~rr~la--~~~~~~~~~~t~v~~~~~~~~~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~~~~Lp~l~~g~~~~~~~~~ 449 (610)
T TIGR01051 372 LIWKRFVA--SQMADARYDSTSVRLTNEDGEYVFKATGRKLIFDGYYKVYVEGSDDPLEEKDRILPPLKEGDAVKLVEVK 449 (610)
T ss_pred HHHHHHHH--HhCccceEEEEEEEEEEcCCCeEEEEEEEEEEeCCHHHhcccccccccccccccCCCCCCCCEeEeeeee
Confidence 45555543 343 4455556666665 5556765431 11 011 0 01111122233333456777888
Q ss_pred cceeeccCCCCCCHHHHHHHHHhhCCCCHHHHH-HHHHHhHhcCceeecCCCCCCCCCc
Q psy8714 285 SSTKSKTKPQALNTVELMRVASSGLGMGPHHAM-QIAERLYTQGYVSYPRTETTQYPEN 342 (562)
Q Consensus 285 ~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~iaQ~LYE~glISYPRTds~~l~~~ 342 (562)
..++.+.||.+|+-++|..+|-+ .|+...-|. .+.+.|.++|||. +-...-+|.+
T Consensus 450 ~~~~~T~PP~~yTe~tLl~~Me~-~GIGTpATra~iIe~L~~r~Yi~--~~~~~l~pT~ 505 (610)
T TIGR01051 450 PNQHFTQPPARYTEASLVKELEE-LGIGRPSTYASIISTIQDRGYVK--KENKRLYPTE 505 (610)
T ss_pred eccccccCCCCCCHHHHHHHHhc-CCCCccccHHHHHHHHhhCCeEE--eeCCEEeECH
Confidence 88899999999999999999854 587655554 5699999999998 3333344443
No 53
>PRK05776 DNA topoisomerase I; Provisional
Probab=85.46 E-value=2.2 Score=49.28 Aligned_cols=109 Identities=14% Similarity=0.154 Sum_probs=69.8
Q ss_pred HHHHHHHHh--hcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEeeeec
Q psy8714 405 DYIVRHFIG--TLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVERKT 482 (562)
Q Consensus 405 ~lI~rr~la--~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e~~T 482 (562)
.||+.|..+ .|-| ..|=...+.+..++..|.+.-. +++ +...+.. +..+-.++....+.|.++..++++.
T Consensus 201 ~lVveRe~eI~~Fvp-~~yw~i~~~~~~~~~~f~~~~~-----~~~-~~~~~~a-~~i~~~~~~~~~~~V~~v~~k~~~~ 272 (670)
T PRK05776 201 KYVVEREIERNLFVP-LPYFSVSIIIEKNGYEFTLKYE-----NKK-FETKEEA-KEILEEIKKTGYLKVTKVEVKIEIL 272 (670)
T ss_pred hHhHhhHHHHHcCCC-CcceEEEEEEecCCceEEEEEc-----CCc-cCCHHHH-HHHHHHhcCCCCEEEEEEEeeeEEc
Confidence 456666554 4443 3344455556556656766531 222 2111100 1111223322457788999999999
Q ss_pred CCCCCCCHHHHHHHHH-hcCCCCcCchhHHHHHhhcCCeEE
Q psy8714 483 TPPDYLTESELISLME-KHGIGTDASIPVHINNICQRNYVT 522 (562)
Q Consensus 483 kPP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~r~Yi~ 522 (562)
.||++|+-++|...+- +.|++..-|.. |.+.|.+.|||.
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 9999999999999885 45888877774 999999999997
No 54
>PRK07219 DNA topoisomerase I; Validated
Probab=85.37 E-value=1.9 Score=51.06 Aligned_cols=119 Identities=20% Similarity=0.363 Sum_probs=75.0
Q ss_pred hhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEee----cc--cccCHHHH-HHHHHHhhhcCceEEEEEEcceeecc
Q psy8714 219 GFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWS----RG--HIFDKSTC-NVFFKAVEKEKHVTVVDVQSSTKSKT 291 (562)
Q Consensus 219 ~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~~~a-~~~~~~~~~~~~~~V~~v~~~~~~~~ 291 (562)
.||+.|..... ..|..|=+..+.+..++..|.+... .| .++..+.. +..+-.+.....+.+.+++.+++.+.
T Consensus 394 ~LI~rrfla~~-~~~a~~~~t~v~~~~~~~~F~a~g~~i~~~Gw~~vy~~~~~~~~~lP~l~~G~~~~~~~~~~~~~~T~ 472 (822)
T PRK07219 394 ELIVRRFLATL-ADPAEWEYLKVELDVNGEIFKASGSRLVEEGWHEVYPYEKFDEKELPDLEEGEKLKVNKIEIEAKETQ 472 (822)
T ss_pred HHHHHHHHHHh-CccceeeEEEEEEEeCCeEEEEEEEEEccCCcHhhcCccccccccCCCCCCCCEeeeeeeEecccccC
Confidence 46777766553 2555666667777777777876542 11 11110000 11122233334567878888899999
Q ss_pred CCCCCCHHHHHHHHHhhCCCCHHHH-HHHHHHhHhcCceeecCCCCCCCCCc
Q psy8714 292 KPQALNTVELMRVASSGLGMGPHHA-MQIAERLYTQGYVSYPRTETTQYPEN 342 (562)
Q Consensus 292 pP~pf~l~~Lq~~a~~~~g~s~~~t-l~iaQ~LYE~glISYPRTds~~l~~~ 342 (562)
||.+|+-++|.+++-+ .|+.-.-| ..|.+.|+++||| +-.....|.+
T Consensus 473 PP~rytea~Li~~Me~-~GIGT~ATra~iI~~L~~R~Yv---~~~~~l~pT~ 520 (822)
T PRK07219 473 PPKRYTQSSLIKEMEK-RGLGTKATRHDIIEKLYKRGYV---IEGDPPRPTD 520 (822)
T ss_pred CCCCCCHHHHHHHHHh-CCCCCCccHHHHHHHHHhcCcE---ecCCEeeecH
Confidence 9999999999999854 58764444 5679999999999 4444444443
No 55
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=84.38 E-value=0.87 Score=37.26 Aligned_cols=39 Identities=5% Similarity=0.185 Sum_probs=31.3
Q ss_pred CchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhcc
Q psy8714 506 ASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKI 545 (562)
Q Consensus 506 ATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~ 545 (562)
.+-..+|+.|.++|+|.. .++.+..|++|..+++.++.+
T Consensus 34 ~~~~~yL~~L~~~gLI~~-~~~~Y~lTekG~~~l~~l~~~ 72 (77)
T PF14947_consen 34 STLKKYLKELEEKGLIKK-KDGKYRLTEKGKEFLEELEEL 72 (77)
T ss_dssp HHHHHHHHHHHHTTSEEE-ETTEEEE-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCcCeeC-CCCEEEECccHHHHHHHHHHH
Confidence 344569999999999986 567999999999999887543
No 56
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=84.27 E-value=1.7 Score=36.59 Aligned_cols=44 Identities=14% Similarity=0.198 Sum_probs=36.8
Q ss_pred HhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhh
Q psy8714 498 EKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGY 542 (562)
Q Consensus 498 e~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l 542 (562)
+..|| +++|-..++..|.+.|||.+..++.+.+|+.|..+++.+
T Consensus 7 ~~l~i-s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~ 50 (96)
T smart00529 7 ERLNV-SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRL 50 (96)
T ss_pred HHhCC-ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHH
Confidence 34577 788888999999999999986556899999999987554
No 57
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=82.43 E-value=1.3 Score=37.76 Aligned_cols=37 Identities=14% Similarity=0.183 Sum_probs=30.1
Q ss_pred hHHHHHhhcCCeEEEcCCC---eeecchhHHHHHHhhhcc
Q psy8714 509 PVHINNICQRNYVTVTSGR---RLVPTSLGIVLVHGYQKI 545 (562)
Q Consensus 509 a~iI~~L~~r~Yi~~~~~k---~l~~T~~G~~li~~l~~~ 545 (562)
..+|+-|.++|.+...+++ .+..|++|+.+++.+..+
T Consensus 49 ~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~~i 88 (95)
T COG3432 49 QKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYSEI 88 (95)
T ss_pred HHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHHHH
Confidence 4699999999977764443 699999999999988654
No 58
>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=81.59 E-value=4.2 Score=46.98 Aligned_cols=128 Identities=13% Similarity=0.149 Sum_probs=75.5
Q ss_pred HHHHHHHHHHHh--hcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEEee
Q psy8714 402 RLYDYIVRHFIG--TLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKMVE 479 (562)
Q Consensus 402 ~vY~lI~rr~la--~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i~e 479 (562)
-.-.||+.|..+ .| .|..|=...+.+..++..|.+.-.......++ +...+.. +..+-.+ .|..+.|.++..++
T Consensus 200 ptL~lIveRe~eI~~F-~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~a-~~i~~~~-~~~~~~V~~v~~k~ 275 (660)
T TIGR01056 200 PTLAMVVKRENEIKNF-VGKPFYEVSATINKDEQEFTTEWQPYKDEEER-ELHEFLA-ENVVTDL-TQKPALVTDIEKER 275 (660)
T ss_pred hhhHHHHHHHHHHHcC-CCCccEEEEEEEEcCCceEEEEEeccCCcccC-cCCHHHH-HHHHHHh-hCCCeEEEEEEeee
Confidence 344567777665 44 34444455566655555666653211111111 1100000 1111122 23457788899999
Q ss_pred eecCCCCCCCHHHHHHHHH-hcCCCCcCchhHHHHHhhcC-CeEEE-cCCCeeecchh
Q psy8714 480 RKTTPPDYLTESELISLME-KHGIGTDASIPVHINNICQR-NYVTV-TSGRRLVPTSL 534 (562)
Q Consensus 480 ~~TkPP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~r-~Yi~~-~~~k~l~~T~~ 534 (562)
++..||++|+-++|...+- +.|+...-|. .|.+.|++. |||.- ......+|.+.
T Consensus 276 ~~~~pP~pf~ts~LQ~~as~~~g~s~~~tm-~iAQ~LYE~~glITYpRTDS~~ls~~~ 332 (660)
T TIGR01056 276 KKTSAPLFYDLSALQEDANKRFGISAKRTL-DIAQKLYETHKLITYPRTDSRYLPEDE 332 (660)
T ss_pred eecCCCCCCCHHHHHHHHHHhcCCCHHHHH-HHHHHHHHhCCEEEEecCCCccCCHHH
Confidence 9999999999999999885 4588666666 799999997 99973 12234455544
No 59
>PRK08173 DNA topoisomerase III; Validated
Probab=81.18 E-value=3.6 Score=48.95 Aligned_cols=110 Identities=18% Similarity=0.328 Sum_probs=68.8
Q ss_pred hhhhhhhhhhhcccC-cceEEEEEEEeeCCeEEEEEee----cc--cccCH--HHHHHHHHHhhhcCceEEEEEEcceee
Q psy8714 219 GFCVERHDKIRTFKP-EPYWLLDLTLNLNGVAVSVTWS----RG--HIFDK--STCNVFFKAVEKEKHVTVVDVQSSTKS 289 (562)
Q Consensus 219 ~lIv~Re~eI~~F~p-~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~--~~a~~~~~~~~~~~~~~V~~v~~~~~~ 289 (562)
.||+.|..+. |=| .-|=...+.+..++..|.+... .| .++.. +..+..+-.+.....+.+.+++..++.
T Consensus 406 ~lI~rRfla~--f~~~a~~~~t~v~~~v~~~~F~a~G~~~~~~Gw~~vy~~~~~~~~~~LP~l~~Ge~~~~~~~~~~e~~ 483 (862)
T PRK08173 406 DLVVKRFLAV--FFPAAEFLVTTRITEVAGHHFKTEGKVLVNPGWLAVYGKEAQGADANLVPVQKGEKVKTDKIEAVALT 483 (862)
T ss_pred HHHHHHHHHH--hCchheEEEEEEEEEeCCcEEEEEEEEEeeCChHHHhCcccccccccCCCcCCCCEeeeeeeeecccc
Confidence 5666666544 444 4444455666677777776532 11 11110 001111222333345777888889999
Q ss_pred ccCCCCCCHHHHHHHHHh---------------hCCCC-HHHHHHHHHHhHhcCcee
Q psy8714 290 KTKPQALNTVELMRVASS---------------GLGMG-PHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 290 ~~pP~pf~l~~Lq~~a~~---------------~~g~s-~~~tl~iaQ~LYE~glIS 330 (562)
+.||.+|+=++|...|-. ..|+. |.-=-.|.+.|++.|||.
T Consensus 484 TkPP~ryTEatLl~aMe~~gk~v~D~el~~~~~~~GIGTpATRA~IIe~L~~r~Yi~ 540 (862)
T PRK08173 484 TKPPARYNEATLLSAMEGAGKLVEDDELREAMAEKGLGTPATRAAIIEGLLGEKYLV 540 (862)
T ss_pred cCCCCCcCHHHHHHHHHhhhhccccHHHHhhhhcCCCCchhhHHHHHHHHHhCCcEE
Confidence 999999999999988863 35665 444456799999999997
No 60
>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=80.79 E-value=0.69 Score=23.43 Aligned_cols=9 Identities=33% Similarity=1.025 Sum_probs=7.9
Q ss_pred cCceeecCC
Q psy8714 326 QGYVSYPRT 334 (562)
Q Consensus 326 ~glISYPRT 334 (562)
.|+|++|||
T Consensus 3 sGlI~fpR~ 11 (11)
T PF08259_consen 3 SGLIPFPRV 11 (11)
T ss_pred ccccccCCC
Confidence 489999997
No 61
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=80.58 E-value=2.1 Score=39.14 Aligned_cols=50 Identities=12% Similarity=0.205 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcC----C--CeeecchhHHHHHHh
Q psy8714 488 LTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS----G--RRLVPTSLGIVLVHG 541 (562)
Q Consensus 488 ~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~----~--k~l~~T~~G~~li~~ 541 (562)
.|.++|-..| |+ +++|-..+|+.|.++|||.+.. + ..|.+|++|+.+++.
T Consensus 55 ~t~~eLa~~l---~i-~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 55 ITPVELKKVL---SV-DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred CCHHHHHHHH---CC-CHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 4556665555 33 5788999999999999999731 1 359999999998755
No 62
>PRK14973 DNA topoisomerase I; Provisional
Probab=80.32 E-value=3.5 Score=49.36 Aligned_cols=110 Identities=14% Similarity=0.264 Sum_probs=69.3
Q ss_pred hhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEee----cc--cccCH-HHHHHHHHHhhhcCceEEEEEEcceeecc
Q psy8714 219 GFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWS----RG--HIFDK-STCNVFFKAVEKEKHVTVVDVQSSTKSKT 291 (562)
Q Consensus 219 ~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~-~~a~~~~~~~~~~~~~~V~~v~~~~~~~~ 291 (562)
.||+.|..+.. ..|.-|=+..+.+..++..|.+... .| .++.. +..+..+-.+.....+.+.+++..++.+.
T Consensus 385 ~LI~rRfLA~~-~~~a~~~~t~v~~~~~~~~F~a~G~~i~~~Gw~~vy~~~~~~~~~LP~l~~Ge~~~~~~~~~~e~~T~ 463 (936)
T PRK14973 385 ELVVRRFLATL-SPDAEWATMKVNFDAGGEPYTATGGRLLEAGWRTVYPYSEAKENILPAFALGEKLPILAVNLEEKETQ 463 (936)
T ss_pred HHHHHHHHHHh-ChhheEEEEEEEEEECCEEEEEEEEEEeecCeeEeecccccccccCCCccCCCEEEeeeeEEeecCCC
Confidence 46666665542 2445555666777766666765432 11 12110 11111222233334577778888899999
Q ss_pred CCCCCCHHHHHHHHHhhCCCCHHH-HHHHHHHhHhcCcee
Q psy8714 292 KPQALNTVELMRVASSGLGMGPHH-AMQIAERLYTQGYVS 330 (562)
Q Consensus 292 pP~pf~l~~Lq~~a~~~~g~s~~~-tl~iaQ~LYE~glIS 330 (562)
||..|+-++|.+.+-+ .|+.-.- =..|.+.|+++|||.
T Consensus 464 PP~ryTEatLik~ME~-~GIGTpATrA~II~~L~~R~Yve 502 (936)
T PRK14973 464 PPARYSQSRLIQRMEE-LGLGTKSTRHEVIGKLVSRKYIE 502 (936)
T ss_pred CCCCCCHHHHHHHhcc-CCCCCcccHHHHHHHHHHccCee
Confidence 9999999999999854 5876444 456799999999993
No 63
>PRK05582 DNA topoisomerase I; Validated
Probab=80.32 E-value=4.8 Score=46.43 Aligned_cols=119 Identities=16% Similarity=0.160 Sum_probs=73.1
Q ss_pred HHHHHHHHHHHHHh--hcccCceEEEEEEEEEECCeEEEEEEEEEeecceeeeecccccccCCCCCCCCCCeeeeeeeEE
Q psy8714 400 AWRLYDYIVRHFIG--TLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFTGVMTWSAMKNESIPDFKPGDLIPIQSVKM 477 (562)
Q Consensus 400 e~~vY~lI~rr~la--~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~i 477 (562)
+--+-.+|+.|..+ .|-|..-| ...+.+..++..|.+.-.......++ ++..+.. +..+-.+. |..+.+.++..
T Consensus 168 QtPtL~lvv~Re~eI~~F~p~~y~-~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~a-~~~~~~~~-~~~~~v~~v~~ 243 (650)
T PRK05582 168 QSVALKLIIDREKEIRAFVPEEYW-TIDAEFKKGKKKFEASFYGYKGKKIE-LKNEEDV-KEILAELK-KKDFKVSKVKK 243 (650)
T ss_pred hHhHHHHHHhHHHHHHhCCCCccE-EEEEEEecCCccEEEEEEecCCCccc-cCCHHHH-HHHHHHhc-CCCeEEEEEee
Confidence 33445678888854 55544444 44455555555566543111111111 1111000 11111222 34567778899
Q ss_pred eeeecCCCCCCCHHHHHHHHH-hcCCCCcCchhHHHHHhhc---------CCeEEE
Q psy8714 478 VERKTTPPDYLTESELISLME-KHGIGTDASIPVHINNICQ---------RNYVTV 523 (562)
Q Consensus 478 ~e~~TkPP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~---------r~Yi~~ 523 (562)
+++++.||.+|+-++|...|- +.|+...-|. .|.+.|++ .|||.-
T Consensus 244 ~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl-~~aQ~LYe~~~~~~~~~~gliSY 298 (650)
T PRK05582 244 KERKRNPPPPFTTSTLQQEAARKLNFSTKKTM-MIAQQLYEGIDLGKQGTVGLITY 298 (650)
T ss_pred eeeecCCCCCccHHHHHHHHHHHcCCCHHHHH-HHHHHHhcccccCCCCceEEEEe
Confidence 999999999999999998774 5699888888 79999999 699973
No 64
>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=80.31 E-value=1.6 Score=35.27 Aligned_cols=49 Identities=20% Similarity=0.388 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcC-CC--eeecchhH
Q psy8714 486 DYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS-GR--RLVPTSLG 535 (562)
Q Consensus 486 ~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~-~k--~l~~T~~G 535 (562)
....-++|+..|+..||+.+|+|.. +..|.++|.++..+ |+ .+.+|+.|
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 4456789999999999999999975 57999999999743 22 48888876
No 65
>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=79.63 E-value=3.9 Score=35.62 Aligned_cols=55 Identities=13% Similarity=0.132 Sum_probs=41.0
Q ss_pred CCCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEc----CC--CeeecchhHHHHHHhh
Q psy8714 484 PPDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVT----SG--RRLVPTSLGIVLVHGY 542 (562)
Q Consensus 484 PP~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~----~~--k~l~~T~~G~~li~~l 542 (562)
++...|..+|-..| |+- ++|-..+|+.|.++|||.+. .+ ..+.+|+.|+.+++.+
T Consensus 40 ~~~~~t~~eL~~~l---~~~-~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~ 100 (109)
T TIGR01889 40 NEGKLTLKEIIKEI---LIK-QSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESL 100 (109)
T ss_pred cCCcCcHHHHHHHH---CCC-HHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHH
Confidence 33456666666665 443 78889999999999999862 11 2599999999999764
No 66
>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=77.97 E-value=2 Score=40.29 Aligned_cols=35 Identities=23% Similarity=0.374 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCC
Q psy8714 296 LNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRT 334 (562)
Q Consensus 296 f~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRT 334 (562)
.+-.+|+ ..+|++...+-+++++|||.|+++|-|+
T Consensus 29 ~tdEeLa----~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~ 63 (158)
T TIGR00373 29 FTDEEIS----LELGIKLNEVRKALYALYDAGLADYKRR 63 (158)
T ss_pred CCHHHHH----HHHCCCHHHHHHHHHHHHHCCCceeeee
Confidence 4445544 4569999999999999999999999984
No 67
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=77.59 E-value=2.6 Score=38.36 Aligned_cols=51 Identities=14% Similarity=0.262 Sum_probs=38.4
Q ss_pred CCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcC----C--CeeecchhHHHHHHhh
Q psy8714 488 LTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS----G--RRLVPTSLGIVLVHGY 542 (562)
Q Consensus 488 ~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~----~--k~l~~T~~G~~li~~l 542 (562)
.|..+|.+.| |+ +++|-..+|+.|.++|||++.. + +.|.+|++|+.+++.+
T Consensus 47 ~t~~eLa~~l---~~-~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~ 103 (144)
T PRK03573 47 QSQIQLAKAI---GI-EQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEV 103 (144)
T ss_pred CCHHHHHHHh---CC-ChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHH
Confidence 3556666665 33 4568889999999999999731 1 3699999999988765
No 68
>PRK04017 hypothetical protein; Provisional
Probab=77.14 E-value=2.4 Score=38.49 Aligned_cols=29 Identities=17% Similarity=0.338 Sum_probs=25.8
Q ss_pred ccCCeEEEecCCCccchhHHHHHHHHHhh
Q psy8714 105 KDCEFLVLWLDCDKEGENICFEVMEAVRH 133 (562)
Q Consensus 105 ~~~d~Ii~AtD~DREGE~I~~~i~~~~~~ 133 (562)
.+...||+.||||.-||-|...+.+.+..
T Consensus 63 ~~~r~VIILTD~D~~GekIr~~l~~~l~~ 91 (132)
T PRK04017 63 SRGKEVIILTDFDRKGEELAKKLSEYLQG 91 (132)
T ss_pred hcCCeEEEEECCCcchHHHHHHHHHHHHh
Confidence 46678999999999999999999998864
No 69
>PRK07726 DNA topoisomerase III; Provisional
Probab=76.82 E-value=5.7 Score=45.91 Aligned_cols=112 Identities=15% Similarity=0.240 Sum_probs=70.0
Q ss_pred hhhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEeec----c--cccC----HHHHHHHHHHhhhcCceEEEEEEcce
Q psy8714 218 LGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWSR----G--HIFD----KSTCNVFFKAVEKEKHVTVVDVQSST 287 (562)
Q Consensus 218 L~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~----~--~~~~----~~~a~~~~~~~~~~~~~~V~~v~~~~ 287 (562)
-.||+.|....- ..|.-|-...+.+..++..|.+.... | .++. .++....+-.+.....+.+.+++..+
T Consensus 394 Y~lI~~r~la~~-~~~~~~~~t~v~~~~~~~~F~~~g~~i~~~Gw~~v~~~~~~~~~~~~~lp~l~~g~~~~~~~~~~~e 472 (658)
T PRK07726 394 YDLIARRYLAQF-LPPAEYDKTTIELEIAGGTFIAKGKQVVEAGWKALLGKKEEDEEKEQPLPVLAKGDELKVEKGEVKE 472 (658)
T ss_pred HHHHHHHHHHHh-CchhEEEEEEEEEEECCEEEEEEEEEEccCCHHHHcccccccccccccCCCcCCCCEeeeccccccc
Confidence 356777666543 35566666777777777777765321 1 1111 01101112223323346777888888
Q ss_pred eeccCCCCCCHHHHHHHHHhh----------------CCCCHHHH-HHHHHHhHhcCcee
Q psy8714 288 KSKTKPQALNTVELMRVASSG----------------LGMGPHHA-MQIAERLYTQGYVS 330 (562)
Q Consensus 288 ~~~~pP~pf~l~~Lq~~a~~~----------------~g~s~~~t-l~iaQ~LYE~glIS 330 (562)
+.+.||.+|+-++|.+.+-+. .|+.-.-| ..+.+.|.++|||.
T Consensus 473 ~~TkPP~~yTe~tLi~~Me~~~k~v~d~~~~~~l~e~~GIGTpATra~iIe~L~~R~Yi~ 532 (658)
T PRK07726 473 GQTQPPKRFTEGTLLSAMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLE 532 (658)
T ss_pred ccCCCCCCcCHHHHHHHHHhhhhhccCHHHHHhhcccCCCCccccHHHHHHHHHhCCCEE
Confidence 999999999999999988542 36654434 45689999999997
No 70
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=76.46 E-value=7.6 Score=46.31 Aligned_cols=117 Identities=15% Similarity=0.154 Sum_probs=71.7
Q ss_pred HHHHHHHHHHHh--hcccCceEEEEEEEEEE-CCeEEEEEEEEEeecc--eeeeecccccccCCCCCCCCCCeeeeeeeE
Q psy8714 402 RLYDYIVRHFIG--TLCGDLVYTQKVAKFSV-ADEMFTMEAKYLLHPG--FTGVMTWSAMKNESIPDFKPGDLIPIQSVK 476 (562)
Q Consensus 402 ~vY~lI~rr~la--~~~~~a~~~~t~v~~~~-~~~~F~a~g~~~~~~G--w~~v~~~~~~~~~~Lp~l~~G~~~~~~~~~ 476 (562)
-.-.||+.|... .|- +..|=...+.+.. ++..|.+.-...-... +..+...+.. +..+-.+. +..+.|.++.
T Consensus 183 p~L~lIv~Re~eI~~F~-p~~yw~i~~~~~~~~~~~f~a~~~~~~~~~~~~~~~~~~~~a-~~~~~~~~-~~~~~V~~v~ 259 (859)
T PRK07561 183 VAVRLIVEREREIEAFV-PEEYWDIHADLTTPRGDAFEARLTHLDGKKFAPVDLLNEAQA-EAAVAALE-GARYSVASVE 259 (859)
T ss_pred hhhHHHHHHHHHHHhcC-CCccEEEEEEEEecCCCeEEEEEEeeCCceecccccCCHHHH-HHHHHHhc-CCCeEEEEEE
Confidence 344567777765 444 4444455566654 4556776632211111 1112111100 11111232 4467788899
Q ss_pred EeeeecCCCCCCCHHHHHHHHH-hcCCCCcCchhHHHHHhhcCCeEE
Q psy8714 477 MVERKTTPPDYLTESELISLME-KHGIGTDASIPVHINNICQRNYVT 522 (562)
Q Consensus 477 i~e~~TkPP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~r~Yi~ 522 (562)
.++.+..||++||-++|...+- +.|+...-|. .|.+.|++.|||.
T Consensus 260 ~k~~~~~pp~pf~ts~LQ~~As~klg~s~~~tm-~~aQ~LYE~glIT 305 (859)
T PRK07561 260 DKPTTRKPSAPFTTSTLQQEASRKLGFSVKKTM-RIAQRLYEAGYIT 305 (859)
T ss_pred eceeEecCCCCccHHHHHHHHHHhcCCCHHHHH-HHHHHHHhCCeEE
Confidence 9999999999999999999885 4588777776 5889999999997
No 71
>PRK06599 DNA topoisomerase I; Validated
Probab=76.21 E-value=7.1 Score=45.26 Aligned_cols=119 Identities=13% Similarity=0.200 Sum_probs=70.7
Q ss_pred hhhhhhhhhhhccc-CcceEEEEEEEee--CCeEEEEEee----cc--ccc--CH----HHHHHHHHHhhhcCceEEEEE
Q psy8714 219 GFCVERHDKIRTFK-PEPYWLLDLTLNL--NGVAVSVTWS----RG--HIF--DK----STCNVFFKAVEKEKHVTVVDV 283 (562)
Q Consensus 219 ~lIv~Re~eI~~F~-p~~y~~i~~~~~~--~~~~~~~~~~----~~--~~~--~~----~~a~~~~~~~~~~~~~~V~~v 283 (562)
.||+.|..+ +|- |--|-+..+.+.. ++..|.+... .| .++ ++ ++.+..+-.+.....+.+.++
T Consensus 379 ~lI~~rfla--~~~~~~~~~~t~v~~~~~~~~~~F~a~g~~~~~~Gw~~~~~~~~~~~~~~~~~~lp~~~~g~~~~~~~~ 456 (675)
T PRK06599 379 ELIWKRTVA--SQMAPAILDQTSVDIASENGKYVFRATGSVILFPGFLKVYGESKDDEEEDDEKLLPPLKEGEKLKLDEL 456 (675)
T ss_pred HHHHHHHHH--HhCchheEEEEEEEEEEcCCCeEEEEEEEEEEecCeeeeeccccccccccccccCCCCCCCCEeeeeee
Confidence 355555543 344 3445556666666 6666765421 11 111 11 011111222333345677788
Q ss_pred EcceeeccCCCCCCHHHHHHHHHhhCCCCHHHH-HHHHHHhHhcCceeecCCCCCCCCCc
Q psy8714 284 QSSTKSKTKPQALNTVELMRVASSGLGMGPHHA-MQIAERLYTQGYVSYPRTETTQYPEN 342 (562)
Q Consensus 284 ~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~t-l~iaQ~LYE~glISYPRTds~~l~~~ 342 (562)
+..++.+.||..|+-++|...+-+ .|+.-.-| ..+.+.|.++|||. +.....+|.+
T Consensus 457 ~~~~~~T~PP~r~te~tLi~~Me~-~GIGT~ATra~iIe~L~~r~Yi~--~~~~~l~~T~ 513 (675)
T PRK06599 457 LPEQHFTEPPPRYSEASLVKKLEE-YGIGRPSTYASIISTLQDREYVE--LEKKRFIPTD 513 (675)
T ss_pred eecccccCCCCCCCHHHHHHHHhh-CCCCccccHHHHHHHHhhCCeEE--eeCCEEeecH
Confidence 888899999999999999998854 58765444 45699999999997 3344444443
No 72
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=75.36 E-value=13 Score=44.33 Aligned_cols=110 Identities=15% Similarity=0.283 Sum_probs=71.5
Q ss_pred hhhhhhhhhhhcccCcceEEEEEEEeeCC-eEEEEEee----cc--cccC-----HH--HHHHHHHHhhhcCceEEEEEE
Q psy8714 219 GFCVERHDKIRTFKPEPYWLLDLTLNLNG-VAVSVTWS----RG--HIFD-----KS--TCNVFFKAVEKEKHVTVVDVQ 284 (562)
Q Consensus 219 ~lIv~Re~eI~~F~p~~y~~i~~~~~~~~-~~~~~~~~----~~--~~~~-----~~--~a~~~~~~~~~~~~~~V~~v~ 284 (562)
.||++|..+.. ..|.-|-+..+.+..++ ..|.+... .| .++. .+ +.+..+-.+.....+.+.+++
T Consensus 389 ~LI~~RflAs~-m~~a~~~~t~v~~~~~~~~~F~a~G~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~Ge~~~~~~~~ 467 (860)
T PRK06319 389 SLIWKRFVASQ-MIPAIYDTLAIRITTNKGIDLRATGSLLKFKGFLAVYEEKRDDEGDEEENIHLPKLHEQDVLTKEELS 467 (860)
T ss_pred HHHHHHHHHHh-CchhheEEEEEEEEeCCeeEEEEEeEEEeeCCHHHHhCccccccccccccccCCCCCCCCEeeeeeee
Confidence 57777776653 36677777777777654 35665432 11 1111 01 111222223333456777888
Q ss_pred cceeeccCCCCCCHHHHHHHHHhhCCCC-HHHHHHHHHHhHhcCcee
Q psy8714 285 SSTKSKTKPQALNTVELMRVASSGLGMG-PHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 285 ~~~~~~~pP~pf~l~~Lq~~a~~~~g~s-~~~tl~iaQ~LYE~glIS 330 (562)
..++.+.||..|+-++|.+.+- .+|+. |+-=..|.+.|.++|||.
T Consensus 468 ~~~~~T~PP~ryTeasLvk~me-~~GIGtpsT~A~iI~~L~~R~Yv~ 513 (860)
T PRK06319 468 AEQAFTKPLPRFTEASLVKELE-KSGIGRPSTYATIMNKIQSREYTL 513 (860)
T ss_pred ecccccCCCCCCCHHHHHHHHH-hcCCCchhhHHHHHHHHhhCCeEE
Confidence 8889999999999999999985 47886 444456799999999996
No 73
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=75.00 E-value=3.5 Score=37.68 Aligned_cols=39 Identities=18% Similarity=0.226 Sum_probs=32.1
Q ss_pred cCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHH
Q psy8714 500 HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLV 539 (562)
Q Consensus 500 ~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li 539 (562)
.|+ +++|-..+|.+|.++|||.....+.+.+|+.|+.+.
T Consensus 32 l~v-s~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a 70 (142)
T PRK03902 32 LSV-HPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIG 70 (142)
T ss_pred hCC-ChhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHH
Confidence 467 588888899999999999854556899999997654
No 74
>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=74.68 E-value=2.8 Score=36.23 Aligned_cols=32 Identities=34% Similarity=0.586 Sum_probs=25.6
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhcCceeecCC
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQGYVSYPRT 334 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRT 334 (562)
.+.++.+|++++++-.+++.|++.|+|+|-|.
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 45677889999999999999999999999853
No 75
>PRK08780 DNA topoisomerase I; Provisional
Probab=73.45 E-value=11 Score=44.50 Aligned_cols=119 Identities=16% Similarity=0.125 Sum_probs=72.2
Q ss_pred HHHHHHHHHHHHHHh--hcccCceEEEEEEEEEECCeEEEEEEEEEeeccee----eeecccccccCCCCCCCC--CCee
Q psy8714 399 DAWRLYDYIVRHFIG--TLCGDLVYTQKVAKFSVADEMFTMEAKYLLHPGFT----GVMTWSAMKNESIPDFKP--GDLI 470 (562)
Q Consensus 399 ~e~~vY~lI~rr~la--~~~~~a~~~~t~v~~~~~~~~F~a~g~~~~~~Gw~----~v~~~~~~~~~~Lp~l~~--G~~~ 470 (562)
-|--.-.||+.|... .|- +..|=...+.+..++..|.+.-... .|-+ .+...+.. +..+-.++. +..+
T Consensus 171 VQspaL~lIveRE~eI~~F~-p~~yw~i~~~~~~~~~~f~a~~~~~--~~~~~~~~~~~~~~~a-~~i~~~~~~~~~~~~ 246 (780)
T PRK08780 171 VQSPALRMIVEREEEIEAFI-AREYWSIEADCAHPSQPFNAKLIKL--DGQKFEQFTITDGDTA-EAARLRIQQAAQGTL 246 (780)
T ss_pred cHHHHHHHHHHHHHHHHhCC-CcceEEEEEEEecCCceEEEEEEec--CCccccccccCCHHHH-HHHHHHHhhccCCCe
Confidence 344445678877765 444 4444455555655555677654211 1100 11110000 111111221 3457
Q ss_pred eeeeeEEeeeecCCCCCCCHHHHHHHH-HhcCCCCcCchhHHHHHhhcC---------CeEE
Q psy8714 471 PIQSVKMVERKTTPPDYLTESELISLM-EKHGIGTDASIPVHINNICQR---------NYVT 522 (562)
Q Consensus 471 ~~~~~~i~e~~TkPP~~~Te~~Li~~M-e~~GIGTpATra~iI~~L~~r---------~Yi~ 522 (562)
.|.++..++.+..||++||-++|...+ .+.|++..-|. .|.+.|++. |||.
T Consensus 247 ~V~~v~~k~~~~~pp~Pf~tstLQq~As~klg~s~~~Tm-~iAQ~LYE~~~~~~~~~~glIT 307 (780)
T PRK08780 247 HVTDVESKERKRNPAPPFTTSTLQQEASRKLGFTTRRTM-QVAQKLYEGVDLGDEGSVGLIT 307 (780)
T ss_pred EEEEEEeeeeecCCCCCccHHHHHHHHHHHcCCCHHHHH-HHHHHHHhhcccccCCceeEEE
Confidence 788899999999999999999999988 45688877776 488999996 8886
No 76
>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=73.15 E-value=5.8 Score=40.79 Aligned_cols=54 Identities=11% Similarity=0.104 Sum_probs=45.6
Q ss_pred CCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcC---CCeeecchhHHHHHHh
Q psy8714 487 YLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS---GRRLVPTSLGIVLVHG 541 (562)
Q Consensus 487 ~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~---~k~l~~T~~G~~li~~ 541 (562)
...-++|+..|+..||...+.| .++..|.++|+|+... .+.+.+|+.|+...+.
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 4567899999999999999999 5788999999998742 2579999999987754
No 77
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=71.48 E-value=4 Score=39.13 Aligned_cols=29 Identities=21% Similarity=0.353 Sum_probs=26.3
Q ss_pred HHhhCCCCHHHHHHHHHHhHhcCceeecC
Q psy8714 305 ASSGLGMGPHHAMQIAERLYTQGYVSYPR 333 (562)
Q Consensus 305 a~~~~g~s~~~tl~iaQ~LYE~glISYPR 333 (562)
++..+|++...+-+++++|||.||++|-|
T Consensus 42 LA~~Lgi~~~~VRk~L~~L~e~gLv~~~r 70 (178)
T PRK06266 42 IAEQTGIKLNTVRKILYKLYDARLADYKR 70 (178)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCeEEee
Confidence 44567999999999999999999999987
No 78
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=71.16 E-value=4.5 Score=39.01 Aligned_cols=51 Identities=16% Similarity=0.102 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcC----C--CeeecchhHHHHHHhh
Q psy8714 488 LTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTS----G--RRLVPTSLGIVLVHGY 542 (562)
Q Consensus 488 ~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~----~--k~l~~T~~G~~li~~l 542 (562)
.|..+|-+.| ++ +++|-..+|++|.++|||.+.. + +.+.+|++|+.+++-+
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 3555555543 23 5688889999999999999731 1 3599999999988654
No 79
>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=70.68 E-value=2.9 Score=34.04 Aligned_cols=44 Identities=16% Similarity=0.113 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCc
Q psy8714 296 LNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPEN 342 (562)
Q Consensus 296 f~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~ 342 (562)
|++++.|. .-|...=-+.++..++++|||+|+||=|-- .||++.
T Consensus 17 F~~~S~~~-GIKvH~dA~p~~i~a~~RLheKGLI~~pdG--gyLT~~ 60 (77)
T TIGR02647 17 FNLSSTQE-GIKVHSTASPAAVAAAARLHEKGLTTQPDG--GYLTSL 60 (77)
T ss_pred CCchhhhc-CccccccCCHHHHHHHHHHHHcCCccCCCC--CEecHH
Confidence 55554443 123333335677889999999999998854 499875
No 80
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=70.07 E-value=8.8 Score=37.99 Aligned_cols=53 Identities=17% Similarity=0.278 Sum_probs=42.4
Q ss_pred CCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEc---CCCeeecchhHHHHHHh
Q psy8714 485 PDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVT---SGRRLVPTSLGIVLVHG 541 (562)
Q Consensus 485 P~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~---~~k~l~~T~~G~~li~~ 541 (562)
|...|.++|-+.| |+ +++|-+.++..|.+.|||++. .+..+.+|++|+.+++.
T Consensus 19 ~~~IS~~eLA~~L---~i-S~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~ 74 (217)
T PRK14165 19 TVKISSSEFANHT---GT-SSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYN 74 (217)
T ss_pred CCCcCHHHHHHHH---Cc-CHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHH
Confidence 3456777777777 55 888999999999999999873 25679999999987643
No 81
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=69.98 E-value=3.2 Score=34.26 Aligned_cols=44 Identities=30% Similarity=0.488 Sum_probs=32.5
Q ss_pred HhcCCCCcCchhHHHHHhhcCCeEEEcC---CC----eeecchhHHHHHHhh
Q psy8714 498 EKHGIGTDASIPVHINNICQRNYVTVTS---GR----RLVPTSLGIVLVHGY 542 (562)
Q Consensus 498 e~~GIGTpATra~iI~~L~~r~Yi~~~~---~k----~l~~T~~G~~li~~l 542 (562)
+..|+ |+++-..|+.+|.+.|||..++ ++ .+..|++|+..++.+
T Consensus 22 ~~l~l-t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~ 72 (80)
T PF13601_consen 22 EELGL-TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERY 72 (80)
T ss_dssp HHTT---HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHH
T ss_pred HHhCc-CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHH
Confidence 34577 8889999999999999998732 22 389999999987654
No 82
>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=69.28 E-value=6 Score=34.73 Aligned_cols=41 Identities=17% Similarity=0.051 Sum_probs=33.1
Q ss_pred CCCCcCchhHHHHHhhcCCeEEEcC----C--CeeecchhHHHHHHhh
Q psy8714 501 GIGTDASIPVHINNICQRNYVTVTS----G--RRLVPTSLGIVLVHGY 542 (562)
Q Consensus 501 GIGTpATra~iI~~L~~r~Yi~~~~----~--k~l~~T~~G~~li~~l 542 (562)
|+-.+ |-..+|.+|.++|||.+.. + +.+.+|+.|+.+++.+
T Consensus 53 ~~~~~-tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~ 99 (118)
T TIGR02337 53 CILRP-SLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASL 99 (118)
T ss_pred CCCch-hHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHh
Confidence 55555 7889999999999999731 1 3699999999999765
No 83
>PRK14724 DNA topoisomerase III; Provisional
Probab=68.98 E-value=12 Score=45.23 Aligned_cols=112 Identities=19% Similarity=0.238 Sum_probs=68.5
Q ss_pred hhhhhhhhhhhhcccCcceEEEEEEEeeCCeEEEEEee----cc--cccCH------H-----HHHHHHHHhhhcCceEE
Q psy8714 218 LGFCVERHDKIRTFKPEPYWLLDLTLNLNGVAVSVTWS----RG--HIFDK------S-----TCNVFFKAVEKEKHVTV 280 (562)
Q Consensus 218 L~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~----~~--~~~~~------~-----~a~~~~~~~~~~~~~~V 280 (562)
-.||+.|..+.- +.|..|-...+.+..++..|.+... .| .+... + +-...+-.+.....+.+
T Consensus 415 Y~lI~rRfla~f-~~~a~~~~t~v~~~~~~~~F~a~G~~i~~~GW~~vy~~~~~~~~~~~~~~~~~~~LP~l~~Ge~v~~ 493 (987)
T PRK14724 415 YDLVVRRFMAVF-FPSAEYQVTTRISQVVGHSFKTEGKVLVKPGWLAIYGKEAANEVEDAKDGDKGQPLVPVKPGEMVRT 493 (987)
T ss_pred HHHHHHHHHHHh-CchhEEEEEEEEEEecCcEEEEEEEEECcCChHHHhCccccccccccccccccccCCCcCCCCEeee
Confidence 356777766542 2344454556666666777766431 11 11110 0 00011222333345677
Q ss_pred EEEEcceeeccCCCCCCHHHHHHHHHh---------------hCCCC-HHHHHHHHHHhHhcCcee
Q psy8714 281 VDVQSSTKSKTKPQALNTVELMRVASS---------------GLGMG-PHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 281 ~~v~~~~~~~~pP~pf~l~~Lq~~a~~---------------~~g~s-~~~tl~iaQ~LYE~glIS 330 (562)
.+++..++.+.||.+|+=++|.+.|-. ..|+. |.-=..|.+.|.+.|||.
T Consensus 494 ~~~~~~e~~TkPP~ryTEatLl~aME~~gk~v~d~el~~~~~~~GIGTpATRA~IIe~L~~r~Yi~ 559 (987)
T PRK14724 494 EFAEAKGLKTKPPARYSEATLLGAMESAGKQIDDDELREAMQEKGLGTPATRAAIIEGLLTEKYML 559 (987)
T ss_pred eeccccccccCCCCCcCHHHHHHHHHhhhhcccchhhhhhhhcCCCCCcccHHHHHHHHHhCCcEE
Confidence 788888999999999999999988852 34554 444456799999999996
No 84
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=67.09 E-value=6.3 Score=36.82 Aligned_cols=36 Identities=11% Similarity=0.036 Sum_probs=31.1
Q ss_pred CcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHH
Q psy8714 504 TDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLV 539 (562)
Q Consensus 504 TpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li 539 (562)
.|+|-..++++|.+.|||...+.+.+..|++|+.+.
T Consensus 37 sp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a 72 (154)
T COG1321 37 SPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKA 72 (154)
T ss_pred CcHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHH
Confidence 478889999999999999986667899999998544
No 85
>PRK10870 transcriptional repressor MprA; Provisional
Probab=66.06 E-value=6 Score=37.68 Aligned_cols=54 Identities=13% Similarity=0.139 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEc----CC--CeeecchhHHHHHHhh
Q psy8714 485 PDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVT----SG--RRLVPTSLGIVLVHGY 542 (562)
Q Consensus 485 P~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~----~~--k~l~~T~~G~~li~~l 542 (562)
+...|..+|-..|. + +++|-..+|++|.++|||++. .+ +.+.+|+.|+.+++.+
T Consensus 69 ~~~it~~eLa~~l~---l-~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i 128 (176)
T PRK10870 69 NHSIQPSELSCALG---S-SRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREV 128 (176)
T ss_pred CCCcCHHHHHHHHC---C-CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHH
Confidence 34456667777663 2 347778899999999999972 11 3599999999988664
No 86
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=66.03 E-value=5.6 Score=34.25 Aligned_cols=39 Identities=8% Similarity=0.094 Sum_probs=32.4
Q ss_pred CcCchhHHHHHhhcCCeEEEcC------CCeeecchhHHHHHHhh
Q psy8714 504 TDASIPVHINNICQRNYVTVTS------GRRLVPTSLGIVLVHGY 542 (562)
Q Consensus 504 TpATra~iI~~L~~r~Yi~~~~------~k~l~~T~~G~~li~~l 542 (562)
+++|-..+|+.|.++|||.+.. ...+.+|++|+.+++.+
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 5788889999999999999732 13599999999998664
No 87
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=65.23 E-value=6.2 Score=37.70 Aligned_cols=32 Identities=25% Similarity=0.426 Sum_probs=28.2
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhcCceeecCC
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQGYVSYPRT 334 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRT 334 (562)
.+.+..+|+....+.++++.|||.|+|+|.|.
T Consensus 36 eela~~l~i~~~~vrriL~~L~e~~li~~~k~ 67 (176)
T COG1675 36 EELAELLGIKKNEVRRILYALYEDGLISYRKK 67 (176)
T ss_pred HHHHHHhCccHHHHHHHHHHHHhCCceEEEee
Confidence 34567899999999999999999999999854
No 88
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=61.36 E-value=11 Score=31.27 Aligned_cols=51 Identities=16% Similarity=0.256 Sum_probs=37.1
Q ss_pred CCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCC------CeeecchhHHHHHHhh
Q psy8714 488 LTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSG------RRLVPTSLGIVLVHGY 542 (562)
Q Consensus 488 ~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~------k~l~~T~~G~~li~~l 542 (562)
.|-..|...| ++ +++|-..+|.+|.++|||..... ..+.+|+.|..++..+
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 4555555554 55 35667799999999999986322 3589999999988654
No 89
>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=60.98 E-value=6.4 Score=30.60 Aligned_cols=31 Identities=16% Similarity=0.269 Sum_probs=23.2
Q ss_pred cCchhHHHHHhhcCCeEEEc----CC--CeeecchhH
Q psy8714 505 DASIPVHINNICQRNYVTVT----SG--RRLVPTSLG 535 (562)
Q Consensus 505 pATra~iI~~L~~r~Yi~~~----~~--k~l~~T~~G 535 (562)
.+|-+.+|+.|.++|||+.. .+ +.+.+|+.|
T Consensus 32 ~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 32 KSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 45666899999999999752 12 369999988
No 90
>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=60.93 E-value=1.7 Score=23.55 Aligned_cols=8 Identities=50% Similarity=0.887 Sum_probs=5.6
Q ss_pred Eecccccc
Q psy8714 55 SVCGHIMG 62 (562)
Q Consensus 55 ~~~GHl~~ 62 (562)
|++||+|.
T Consensus 4 WAvGh~Mg 11 (14)
T PF02044_consen 4 WAVGHFMG 11 (14)
T ss_dssp CHHHCT--
T ss_pred cceeeeec
Confidence 89999985
No 91
>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=60.45 E-value=20 Score=44.17 Aligned_cols=53 Identities=11% Similarity=0.250 Sum_probs=45.8
Q ss_pred eeeeeeEEeeeecCCCCCCCHHHHHHHHH-hcCCCCcCchhHHHHHhhcCCeEEE
Q psy8714 470 IPIQSVKMVERKTTPPDYLTESELISLME-KHGIGTDASIPVHINNICQRNYVTV 523 (562)
Q Consensus 470 ~~~~~~~i~e~~TkPP~~~Te~~Li~~Me-~~GIGTpATra~iI~~L~~r~Yi~~ 523 (562)
+.+.++..++.+..||++||-++|++.+- +.|++..-|. .|.+.|++.|||.-
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 56777888999999999999999999885 4588888887 59999999999973
No 92
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=59.73 E-value=23 Score=32.38 Aligned_cols=55 Identities=20% Similarity=0.318 Sum_probs=43.0
Q ss_pred CHHHHHHHHHhcCCCC----cCchhHHHHHhhcCCeEEEc----CCCeeecchhHHHHHHhhh
Q psy8714 489 TESELISLMEKHGIGT----DASIPVHINNICQRNYVTVT----SGRRLVPTSLGIVLVHGYQ 543 (562)
Q Consensus 489 Te~~Li~~Me~~GIGT----pATra~iI~~L~~r~Yi~~~----~~k~l~~T~~G~~li~~l~ 543 (562)
.=-.|++.++..|.|. ++|-=.++..|.+.|||... ..+.+.+|+.|+...+...
T Consensus 57 yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~ 119 (135)
T PRK09416 57 TGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAE 119 (135)
T ss_pred CHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHH
Confidence 3456777787777765 78888999999999999851 2367999999999886653
No 93
>PRK14701 reverse gyrase; Provisional
Probab=59.48 E-value=15 Score=46.74 Aligned_cols=65 Identities=9% Similarity=0.123 Sum_probs=55.3
Q ss_pred eeeeeeeEEeeeecCCCCCCCHHHHHHHHHh-cCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHH
Q psy8714 469 LIPIQSVKMVERKTTPPDYLTESELISLMEK-HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGI 536 (562)
Q Consensus 469 ~~~~~~~~i~e~~TkPP~~~Te~~Li~~Me~-~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~ 536 (562)
.+.+.++..++++..||++||-.+|.+.+-+ .|++..-|. .|.+.|++.||+.- ....+.|+.|.
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--PDTYVSLHDGR 903 (1638)
T ss_pred eEEEEEEEeeEEEccCCCCcCHHHHHHHHHHhcCCCHHHHH-HHHHHHHhCceeeC--CCceeecCchH
Confidence 4667788889999999999999999999965 599888777 59999999999985 45777889896
No 94
>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=58.75 E-value=7 Score=30.48 Aligned_cols=36 Identities=19% Similarity=0.323 Sum_probs=25.6
Q ss_pred cCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHH
Q psy8714 500 HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGI 536 (562)
Q Consensus 500 ~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~ 536 (562)
.|.--.......|+.+.+.|+|+. .+..|.+|++|+
T Consensus 30 ~g~~~~~~~~~~l~~l~~~Gll~~-~~~~l~lT~~G~ 65 (66)
T PF06969_consen 30 FGIDFAEEFQKELEELQEDGLLEI-DGGRLRLTEKGR 65 (66)
T ss_dssp TT--THHH-HHHHHHHHHTTSEEE--SSEEEE-TTTG
T ss_pred HCcCHHHHHHHHHHHHHHCCCEEE-eCCEEEECcccC
Confidence 344434555778999999999998 567999999996
No 95
>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=58.46 E-value=13 Score=28.92 Aligned_cols=30 Identities=27% Similarity=0.485 Sum_probs=25.4
Q ss_pred HHHhhCCCCHHHHHHHHHHhHhcCceeecC
Q psy8714 304 VASSGLGMGPHHAMQIAERLYTQGYVSYPR 333 (562)
Q Consensus 304 ~a~~~~g~s~~~tl~iaQ~LYE~glISYPR 333 (562)
+.++.+|.|+.-+-+.+++|=++|||.|-+
T Consensus 27 ~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 27 DIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 456678999999999999999999999854
No 96
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=58.45 E-value=12 Score=35.01 Aligned_cols=39 Identities=21% Similarity=0.300 Sum_probs=32.5
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCC
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPE 341 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~ 341 (562)
++.++.++.||.-+.+.+++|.+.|||.|-+-.--.|++
T Consensus 28 ~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~ 66 (154)
T COG1321 28 KDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTE 66 (154)
T ss_pred HHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeEECh
Confidence 556788999999999999999999999995555555664
No 97
>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=57.98 E-value=14 Score=26.80 Aligned_cols=29 Identities=14% Similarity=0.288 Sum_probs=24.5
Q ss_pred HHHHHhhCCCCHHHHHHHHHHhHhcCcee
Q psy8714 302 MRVASSGLGMGPHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 302 q~~a~~~~g~s~~~tl~iaQ~LYE~glIS 330 (562)
|.+.++.+|+|...+-...++|-++|+|.
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 45677788999999999999999999984
No 98
>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=57.34 E-value=14 Score=27.92 Aligned_cols=32 Identities=22% Similarity=0.359 Sum_probs=26.1
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhcCceeecCC
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQGYVSYPRT 334 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRT 334 (562)
.+.++.+|+++..+-.++.+|.++|||+--+.
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 35667789999999999999999999986543
No 99
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=54.53 E-value=8.4 Score=25.81 Aligned_cols=17 Identities=24% Similarity=0.501 Sum_probs=14.9
Q ss_pred HHHHHHHHHhHhcCcee
Q psy8714 314 HHAMQIAERLYTQGYVS 330 (562)
Q Consensus 314 ~~tl~iaQ~LYE~glIS 330 (562)
.+.++.+++||++|.||
T Consensus 2 ~~~L~~L~~l~~~G~Is 18 (31)
T PF09851_consen 2 EDRLEKLKELYDKGEIS 18 (31)
T ss_pred hHHHHHHHHHHHcCCCC
Confidence 46788999999999997
No 100
>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=53.08 E-value=14 Score=31.10 Aligned_cols=29 Identities=24% Similarity=0.382 Sum_probs=24.0
Q ss_pred HHHHhhcCCeEEEcCCCeeecchhHHHHHH
Q psy8714 511 HINNICQRNYVTVTSGRRLVPTSLGIVLVH 540 (562)
Q Consensus 511 iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~ 540 (562)
=|-.|++.|||+. +|-.++.|..|..++.
T Consensus 52 NIGvLIKkglIEK-SGDGlv~T~~g~~Ii~ 80 (96)
T PF09114_consen 52 NIGVLIKKGLIEK-SGDGLVITEEGMDIII 80 (96)
T ss_dssp HHHHHHHTTSEEE-ETTEEEE-HHHHHHHH
T ss_pred hHHHHHHcCcccc-cCCceEEechHHHHHH
Confidence 4778999999997 6667999999999873
No 101
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=52.27 E-value=23 Score=25.16 Aligned_cols=31 Identities=19% Similarity=0.244 Sum_probs=26.9
Q ss_pred HHHHHhhCCCCHHHHHHHHHHhHhcCceeec
Q psy8714 302 MRVASSGLGMGPHHAMQIAERLYTQGYVSYP 332 (562)
Q Consensus 302 q~~a~~~~g~s~~~tl~iaQ~LYE~glISYP 332 (562)
+.+.++.+|+|...+.++.+.|-++|+|.+-
T Consensus 11 ~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 11 RQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4566778899999999999999999999864
No 102
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=50.21 E-value=24 Score=41.57 Aligned_cols=62 Identities=15% Similarity=0.184 Sum_probs=46.5
Q ss_pred eEEEEEEcceeeccCCCCCCHHHHHHHHHhhCCCCHHHH-HHHHHHhHhcCceeecCCCC-CCCCCc
Q psy8714 278 VTVVDVQSSTKSKTKPQALNTVELMRVASSGLGMGPHHA-MQIAERLYTQGYVSYPRTET-TQYPEN 342 (562)
Q Consensus 278 ~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~t-l~iaQ~LYE~glISYPRTds-~~l~~~ 342 (562)
..+.+++..++.+.||.+|+=++|.+.+- ..|+.-.-| -.|.+.|.++|||. +.+. +.+|.+
T Consensus 561 ~~i~~~~l~ek~TkPPpryTEAtLIk~ME-~~GIGTPATrAsIIetL~~R~YV~--~~~kkrl~PT~ 624 (805)
T PTZ00407 561 FELRSPQVRENRPVPPLPHSEGTLIEELK-NNGVGRPSTYPMIVKTLLARGYIA--VNPKGRCETTP 624 (805)
T ss_pred eecceeeeecccCCCCCCCCHHHHHHHHH-hCCCCCcccHHHHHHHHHhcCCEE--eccCceeeecH
Confidence 45667788888999999999999999885 468864444 45699999999997 3323 345554
No 103
>PRK09401 reverse gyrase; Reviewed
Probab=49.79 E-value=32 Score=42.57 Aligned_cols=52 Identities=13% Similarity=0.203 Sum_probs=45.2
Q ss_pred eeeeeEEeeeecCCCCCCCHHHHHHHHHh-cCCCCcCchhHHHHHhhcCCeEEE
Q psy8714 471 PIQSVKMVERKTTPPDYLTESELISLMEK-HGIGTDASIPVHINNICQRNYVTV 523 (562)
Q Consensus 471 ~~~~~~i~e~~TkPP~~~Te~~Li~~Me~-~GIGTpATra~iI~~L~~r~Yi~~ 523 (562)
.+.++..++.+..||++||-.+|.+.+-+ .|++..-|. .|.+.|++.|||.-
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 56678889999999999999999998854 699888887 58999999999974
No 104
>PRK11050 manganese transport regulator MntR; Provisional
Probab=49.41 E-value=18 Score=33.53 Aligned_cols=41 Identities=15% Similarity=0.256 Sum_probs=32.6
Q ss_pred CCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhh
Q psy8714 501 GIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGY 542 (562)
Q Consensus 501 GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l 542 (562)
||. ++|-+.+|..|.+.|||....++.+.+|+.|..++..+
T Consensus 62 ~is-~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~ 102 (152)
T PRK11050 62 GVS-QPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQES 102 (152)
T ss_pred CCC-HHHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHH
Confidence 554 56777899999999999875556799999999986544
No 105
>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=49.18 E-value=24 Score=25.68 Aligned_cols=27 Identities=19% Similarity=0.283 Sum_probs=23.2
Q ss_pred HHhhCCCCHHHHHHHHHHhHhcCceee
Q psy8714 305 ASSGLGMGPHHAMQIAERLYTQGYVSY 331 (562)
Q Consensus 305 a~~~~g~s~~~tl~iaQ~LYE~glISY 331 (562)
.++.+|+|...+-.-+..|.+.|+|+|
T Consensus 21 l~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 21 LAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHhccccchHHHHHHHHHHHCcCeeC
Confidence 455679999999999999999999986
No 106
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=49.15 E-value=19 Score=36.90 Aligned_cols=34 Identities=15% Similarity=0.139 Sum_probs=29.6
Q ss_pred hHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhh
Q psy8714 509 PVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQ 543 (562)
Q Consensus 509 a~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~ 543 (562)
++|++.|.+-|+|.+++| .+..|++|+.+++.+.
T Consensus 52 ~~i~~~l~~egiv~~~~g-~v~~TekG~E~~e~~g 85 (354)
T COG1568 52 ASILEILEDEGIVKIEEG-GVELTEKGEELAEELG 85 (354)
T ss_pred HHHHHHHHhcCcEEEecC-cEeehhhhHHHHHHhC
Confidence 579999999999999665 4999999999998763
No 107
>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=48.75 E-value=26 Score=26.57 Aligned_cols=29 Identities=17% Similarity=0.215 Sum_probs=25.2
Q ss_pred HHHhhCCCCHHHHHHHHHHhHhcCceeec
Q psy8714 304 VASSGLGMGPHHAMQIAERLYTQGYVSYP 332 (562)
Q Consensus 304 ~a~~~~g~s~~~tl~iaQ~LYE~glISYP 332 (562)
+.++.+|+|...+.+++..|-+.|+|++-
T Consensus 30 ~la~~~~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 30 ELAEELGVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 35567899999999999999999999853
No 108
>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=47.38 E-value=40 Score=27.25 Aligned_cols=27 Identities=19% Similarity=0.377 Sum_probs=23.5
Q ss_pred CCeEEEecCCCccchhHHHHHHHHHhh
Q psy8714 107 CEFLVLWLDCDKEGENICFEVMEAVRH 133 (562)
Q Consensus 107 ~d~Ii~AtD~DREGE~I~~~i~~~~~~ 133 (562)
...||+|+|.|..|..-+..+.+.+..
T Consensus 43 ~~~vii~~D~D~aG~~a~~~~~~~l~~ 69 (79)
T cd03364 43 AKEVILAFDGDEAGQKAALRALELLLK 69 (79)
T ss_pred CCeEEEEECCCHHHHHHHHHHHHHHHH
Confidence 478999999999999888888888754
No 109
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=45.54 E-value=30 Score=25.66 Aligned_cols=29 Identities=17% Similarity=0.192 Sum_probs=25.0
Q ss_pred HHHhhCCCCHHHHHHHHHHhHhcCceeec
Q psy8714 304 VASSGLGMGPHHAMQIAERLYTQGYVSYP 332 (562)
Q Consensus 304 ~a~~~~g~s~~~tl~iaQ~LYE~glISYP 332 (562)
++++.+|+|...+.++++.|.+.|+|+.-
T Consensus 15 ~i~~~l~is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 15 ELAEILGLSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 45566899999999999999999999854
No 110
>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=44.47 E-value=28 Score=27.86 Aligned_cols=26 Identities=19% Similarity=0.336 Sum_probs=22.4
Q ss_pred CCeEEEecCCCccchhHHHHHHHHHh
Q psy8714 107 CEFLVLWLDCDKEGENICFEVMEAVR 132 (562)
Q Consensus 107 ~d~Ii~AtD~DREGE~I~~~i~~~~~ 132 (562)
...||+|.|.|..|+.-+..+.+.+.
T Consensus 43 ~~~vii~~D~D~~G~~~~~~~~~~~~ 68 (79)
T cd01029 43 ARTVILAFDNDEAGKKAAARALELLL 68 (79)
T ss_pred CCEEEEEECCCHHHHHHHHHHHHHHH
Confidence 47899999999999988888877774
No 111
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=43.58 E-value=27 Score=41.82 Aligned_cols=71 Identities=11% Similarity=0.176 Sum_probs=47.2
Q ss_pred CeeeeeeeEEeeeecCCCCCCCHHHHHHHH-HhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHH
Q psy8714 468 DLIPIQSVKMVERKTTPPDYLTESELISLM-EKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLV 539 (562)
Q Consensus 468 ~~~~~~~~~i~e~~TkPP~~~Te~~Li~~M-e~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li 539 (562)
+.+.+.++..++..-.|||+||..|++..- .+.|++.+-|+ .|.+.|++-|+|.-..--.-..++.|+.+-
T Consensus 878 ~~v~v~~~~e~ee~~~PlPPyTTDt~L~dAs~~L~lsa~~~M-~iaQdLFE~GlITYHRTDSTrVS~~Gi~vA 949 (1187)
T COG1110 878 IVVEVVDVVEREEEKNPLPPYTTDTMLRDASRRLRLSADETM-QIAQDLFEGGLITYHRTDSTRVSDVGIRVA 949 (1187)
T ss_pred ceEEEeehhhhhhccCCCCCcCcchHHHHHHHHhCCChhHHH-HHHHHHHhccceEEeecCCcccchhhHHHH
Confidence 345665555556666788889988877654 45555555444 788999999999753223566777786654
No 112
>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=41.95 E-value=25 Score=34.02 Aligned_cols=38 Identities=18% Similarity=0.238 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCcee
Q psy8714 293 PQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 293 P~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glIS 330 (562)
.-.|++-+|-+.|.+.-|+++..+-++.|+|-+.|+|.
T Consensus 9 ~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~ 46 (188)
T PF03962_consen 9 KDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVH 46 (188)
T ss_pred CCcccHHHHHHHcccccCCchhhHHHHHHHHhccccch
Confidence 46899999999999977999999999999999999996
No 113
>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=41.55 E-value=41 Score=25.67 Aligned_cols=31 Identities=16% Similarity=0.206 Sum_probs=26.7
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhcCceeecC
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQGYVSYPR 333 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~glISYPR 333 (562)
.+.+..+|+|...+.++++.|=++|+|.+-+
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 4455678999999999999999999999865
No 114
>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=40.81 E-value=39 Score=23.16 Aligned_cols=31 Identities=23% Similarity=0.292 Sum_probs=26.7
Q ss_pred CCCHHHHHHHHHhcCCCCcCchhHHHHHhhc
Q psy8714 487 YLTESELISLMEKHGIGTDASIPVHINNICQ 517 (562)
Q Consensus 487 ~~Te~~Li~~Me~~GIGTpATra~iI~~L~~ 517 (562)
.+|-++|-+.+++.|+-+.-|++.+|+.|.+
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 4677899999999999999999999999864
No 115
>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=40.36 E-value=28 Score=28.20 Aligned_cols=30 Identities=20% Similarity=0.263 Sum_probs=26.9
Q ss_pred HHHHHHhhCCCCHHHHHHHHHHhHhcCcee
Q psy8714 301 LMRVASSGLGMGPHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 301 Lq~~a~~~~g~s~~~tl~iaQ~LYE~glIS 330 (562)
+|.+.++.+|.+|...-...++|.+.|||+
T Consensus 20 ~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~ 49 (75)
T PF04182_consen 20 TQSDLSKLLGIDPRSIFYRLKKLEKKGLIV 49 (75)
T ss_pred ehhHHHHHhCCCchHHHHHHHHHHHCCCEE
Confidence 567777889999999999999999999984
No 116
>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=40.30 E-value=37 Score=26.53 Aligned_cols=29 Identities=17% Similarity=0.252 Sum_probs=24.9
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhcCceee
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQGYVSY 331 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~glISY 331 (562)
.+.++.+|++...+-++..+|.++|+|.-
T Consensus 26 ~eIa~~l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 26 EEIAEELGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp HHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 34566789999999999999999999964
No 117
>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=39.38 E-value=48 Score=23.10 Aligned_cols=30 Identities=20% Similarity=0.256 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHhcCCCCc---CchhHHHHHhhc
Q psy8714 488 LTESELISLMEKHGIGTD---ASIPVHINNICQ 517 (562)
Q Consensus 488 ~Te~~Li~~Me~~GIGTp---ATra~iI~~L~~ 517 (562)
-|+..|-+.|+++||-.| .||...|+.+.+
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 489998877643
No 118
>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=38.75 E-value=87 Score=26.41 Aligned_cols=56 Identities=16% Similarity=0.228 Sum_probs=39.6
Q ss_pred HHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhC
Q psy8714 99 FLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNL 163 (562)
Q Consensus 99 ~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl 163 (562)
.|...+++||.||+-||+=- -...|.+.+.++.. .+|+....- -...+|.++++++
T Consensus 41 ~l~~~i~~aD~VIv~t~~vs--H~~~~~vk~~akk~-----~ip~~~~~~--~~~~~l~~~l~~~ 96 (97)
T PF10087_consen 41 RLPSKIKKADLVIVFTDYVS--HNAMWKVKKAAKKY-----GIPIIYSRS--RGVSSLERALERL 96 (97)
T ss_pred HHHHhcCCCCEEEEEeCCcC--hHHHHHHHHHHHHc-----CCcEEEECC--CCHHHHHHHHHhh
Confidence 35566789999999999753 45567888888642 567765533 4556899988764
No 119
>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=38.48 E-value=56 Score=24.92 Aligned_cols=43 Identities=12% Similarity=0.270 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecch
Q psy8714 487 YLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPTS 533 (562)
Q Consensus 487 ~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~ 533 (562)
..|..+|-+.+ |+ +++|-..++..|.+.|||.....+.+.+|+
T Consensus 25 ~~s~~ela~~~---g~-s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 25 PLTRQEIADYL---GL-TRETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred CcCHHHHHHHH---CC-CHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 35666665544 66 567778899999999999974325676653
No 120
>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=38.20 E-value=32 Score=30.76 Aligned_cols=26 Identities=19% Similarity=0.243 Sum_probs=22.2
Q ss_pred cCCeEEEecCCCccchhHHHHHHHHH
Q psy8714 106 DCEFLVLWLDCDKEGENICFEVMEAV 131 (562)
Q Consensus 106 ~~d~Ii~AtD~DREGE~I~~~i~~~~ 131 (562)
.-+.|||+||+|..|-.|.--++.++
T Consensus 76 rY~kiiimtDaD~DG~hI~~Llltff 101 (120)
T cd03365 76 RYGRLMIMTDQDHDGSHIKGLLINFI 101 (120)
T ss_pred CcCeEEEEeCCCCCccHHHHHHHHHH
Confidence 45689999999999999988877765
No 121
>PF13730 HTH_36: Helix-turn-helix domain
Probab=35.93 E-value=46 Score=24.66 Aligned_cols=25 Identities=16% Similarity=0.336 Sum_probs=21.5
Q ss_pred HHhhCCCCHHHHHHHHHHhHhcCce
Q psy8714 305 ASSGLGMGPHHAMQIAERLYTQGYV 329 (562)
Q Consensus 305 a~~~~g~s~~~tl~iaQ~LYE~glI 329 (562)
.++.+|+|...+.++...|-+.|+|
T Consensus 31 la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 31 LAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 3445699999999999999999987
No 122
>cd03366 TOPRIM_TopoIIA_GyrB TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. 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. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. 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 strand joining and as a general acid in strand cleava
Probab=35.87 E-value=39 Score=29.97 Aligned_cols=27 Identities=15% Similarity=0.215 Sum_probs=22.7
Q ss_pred cCCeEEEecCCCccchhHHHHHHHHHh
Q psy8714 106 DCEFLVLWLDCDKEGENICFEVMEAVR 132 (562)
Q Consensus 106 ~~d~Ii~AtD~DREGE~I~~~i~~~~~ 132 (562)
.-..|++.||+|..|-.|.--++.++-
T Consensus 71 rY~kiiimtDaD~DG~hI~~Llltff~ 97 (114)
T cd03366 71 RYHKIIIMTDADVDGAHIRTLLLTFFF 97 (114)
T ss_pred CcCeEEEEeCCCCCchHHHHHHHHHHH
Confidence 456899999999999999888877653
No 123
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=35.22 E-value=93 Score=29.33 Aligned_cols=60 Identities=12% Similarity=0.158 Sum_probs=50.1
Q ss_pred CCCCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEc----CCCeeecchhHHHHHHhhhc
Q psy8714 485 PDYLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVT----SGRRLVPTSLGIVLVHGYQK 544 (562)
Q Consensus 485 P~~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~----~~k~l~~T~~G~~li~~l~~ 544 (562)
..++|.+.|...+-..|.=+==|..+.|..|.+.|+|..+ ++..+..|+.|+...+.+..
T Consensus 13 ~~pltn~qit~~iL~~~~~nYF~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~F~~ 76 (163)
T PF14277_consen 13 KFPLTNSQITEFILENEYTNYFTLQQALSELVESGLITLETDSDNKTRYSITEKGKETLEFFEN 76 (163)
T ss_pred CCCCCHHHHHHHHHhcCcccHHHHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHHHHH
Confidence 3468889999988888888888999999999999999863 23579999999999887643
No 124
>cd01030 TOPRIM_TopoIIA_like TOPRIM_TopoIIA_like: 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). 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 cofactor required for full catalytic function.
Probab=35.01 E-value=38 Score=30.08 Aligned_cols=27 Identities=15% Similarity=0.220 Sum_probs=22.7
Q ss_pred cCCeEEEecCCCccchhHHHHHHHHHh
Q psy8714 106 DCEFLVLWLDCDKEGENICFEVMEAVR 132 (562)
Q Consensus 106 ~~d~Ii~AtD~DREGE~I~~~i~~~~~ 132 (562)
.-..|++.||+|..|-.|.--++.++-
T Consensus 72 rY~kiiimtDaD~DG~hI~~Llltff~ 98 (115)
T cd01030 72 RYGKIIIMTDADVDGSHIRTLLLTFFY 98 (115)
T ss_pred CcCeEEEEeCCCCCccHhHHHHHHHHH
Confidence 456899999999999999888877653
No 125
>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=34.99 E-value=56 Score=24.17 Aligned_cols=33 Identities=24% Similarity=0.456 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceee
Q psy8714 295 ALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSY 331 (562)
Q Consensus 295 pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISY 331 (562)
+.++++| ++.+|++...+..+++.|-+.||+..
T Consensus 18 ~~t~~ei----a~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 18 PLTLSEI----ARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp CEEHHHH----HHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCCHHHH----HHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 4566554 55679999999999999999999864
No 126
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.90 E-value=59 Score=25.85 Aligned_cols=28 Identities=14% Similarity=0.260 Sum_probs=24.9
Q ss_pred CHHHHHHHHHhhCCCCHHHHHHHHHHhH
Q psy8714 297 NTVELMRVASSGLGMGPHHAMQIAERLY 324 (562)
Q Consensus 297 ~l~~Lq~~a~~~~g~s~~~tl~iaQ~LY 324 (562)
+|+++....-++-.|||++...|||.|-
T Consensus 40 dLtdiy~mvkkkenfSpsEmqaiA~eL~ 67 (71)
T COG4840 40 DLTDIYDMVKKKENFSPSEMQAIADELG 67 (71)
T ss_pred HHHHHHHHHHHhccCCHHHHHHHHHHHH
Confidence 5788888888999999999999999984
No 127
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=34.85 E-value=62 Score=23.83 Aligned_cols=29 Identities=24% Similarity=0.334 Sum_probs=25.0
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhcCceee
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQGYVSY 331 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~glISY 331 (562)
.+.+..||+|..-+.++.+.|-+.|+|+.
T Consensus 24 ~~la~~~~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 24 RELAAQLGVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 44567889999999999999999999863
No 128
>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=34.72 E-value=67 Score=27.32 Aligned_cols=55 Identities=25% Similarity=0.384 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHH----------------hcCCCCcCchh---HHHHHhhcCCeEEEcCC----CeeecchhHHHHHHh
Q psy8714 487 YLTESELISLME----------------KHGIGTDASIP---VHINNICQRNYVTVTSG----RRLVPTSLGIVLVHG 541 (562)
Q Consensus 487 ~~Te~~Li~~Me----------------~~GIGTpATra---~iI~~L~~r~Yi~~~~~----k~l~~T~~G~~li~~ 541 (562)
+||-..++..+. ..|+|-.=++. .+|..|+..||+....+ ..|.+|++|..++..
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 677888877763 35888865555 47889999999976322 269999999999865
No 129
>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=34.29 E-value=1.1e+02 Score=28.12 Aligned_cols=52 Identities=15% Similarity=0.252 Sum_probs=38.3
Q ss_pred HHHHHHHHHhcCCC--CcCchhHHHHHhhcCCeEEEc-----CC---CeeecchhHHHHHHh
Q psy8714 490 ESELISLMEKHGIG--TDASIPVHINNICQRNYVTVT-----SG---RRLVPTSLGIVLVHG 541 (562)
Q Consensus 490 e~~Li~~Me~~GIG--TpATra~iI~~L~~r~Yi~~~-----~~---k~l~~T~~G~~li~~ 541 (562)
=-.|++.++..|+. ++.|--.++.+|.+.|||... .| +.+.+|+.|+..++.
T Consensus 40 GYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~ 101 (138)
T TIGR02719 40 GYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSM 101 (138)
T ss_pred HHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHH
Confidence 44677777776642 467888899999999999851 12 457799999986644
No 130
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=34.28 E-value=42 Score=35.87 Aligned_cols=38 Identities=18% Similarity=0.314 Sum_probs=29.5
Q ss_pred chHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhh
Q psy8714 95 KLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQ 134 (562)
Q Consensus 95 ~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~ 134 (562)
.+...|.+ .+..+||++||||+-|+-++..++++++..
T Consensus 57 ~cad~ii~--~gi~rVVi~~D~d~~G~~~~~~~~~~L~~a 94 (360)
T PRK14719 57 QIADDLIA--ENISEVILLTDFDRAGRVYAKNIMEEFQSR 94 (360)
T ss_pred HHHHHHHH--cCCCEEEEEECCCCCCCccchHHHHHHHHC
Confidence 35555654 366789999999999999998888888653
No 131
>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=34.24 E-value=1.4e+02 Score=24.57 Aligned_cols=62 Identities=11% Similarity=0.160 Sum_probs=44.4
Q ss_pred HHHHHhhhcCceEEEEEEcceeeccCCCCCCHHHHHHHHHhhCC--CCHHHHHHHHHHhHhcCcee
Q psy8714 267 VFFKAVEKEKHVTVVDVQSSTKSKTKPQALNTVELMRVASSGLG--MGPHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 267 ~~~~~~~~~~~~~V~~v~~~~~~~~pP~pf~l~~Lq~~a~~~~g--~s~~~tl~iaQ~LYE~glIS 330 (562)
++++.++......|.+ .......+|.-|.-+++-.=.-+.++ -|-.++..++|.|-+.|+|.
T Consensus 3 ~i~~~m~~~~~~~i~~--r~~~~~~~~~cF~G~e~VdWL~~~~~~~~~r~eAv~lgq~Ll~~g~I~ 66 (83)
T cd04449 3 EIAEAMRDPSGIGIFD--RSWHKGLPSNCFIGSEAVSWLINNFEDVDTREEAVELGQELMNEGLIE 66 (83)
T ss_pred HHHHHHhCCCCCceee--chhcCccCCcceEhHHHHHHHHHhCCCCCCHHHHHHHHHHHHHCCCEE
Confidence 3555555433323444 23457788899998888776666665 57889999999999999985
No 132
>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=33.99 E-value=64 Score=26.63 Aligned_cols=36 Identities=22% Similarity=0.290 Sum_probs=32.4
Q ss_pred hCCCCHHHHHHHHHHhHhcCcee-ecCCCCCCCCCcc
Q psy8714 308 GLGMGPHHAMQIAERLYTQGYVS-YPRTETTQYPENF 343 (562)
Q Consensus 308 ~~g~s~~~tl~iaQ~LYE~glIS-YPRTds~~l~~~~ 343 (562)
.++.||.-+-+.++.|-+-|||. =|=|.+.|+|.+.
T Consensus 32 ~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~ 68 (78)
T PF03444_consen 32 ELGRSPATIRNEMADLEELGLVESQPHPSGGRIPTDK 68 (78)
T ss_pred HHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHH
Confidence 47999999999999999999995 7999999999853
No 133
>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=33.57 E-value=46 Score=26.31 Aligned_cols=32 Identities=16% Similarity=0.483 Sum_probs=26.3
Q ss_pred HHHHhcCCCCcCchhHHHHHhhcCCeEEEcCC
Q psy8714 495 SLMEKHGIGTDASIPVHINNICQRNYVTVTSG 526 (562)
Q Consensus 495 ~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~ 526 (562)
+.++..|+--++|-..+++.|.++|||.+..|
T Consensus 30 EIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 30 EIAEALGLKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp HHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred HHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence 34455688889999999999999999998544
No 134
>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=33.45 E-value=69 Score=27.29 Aligned_cols=53 Identities=8% Similarity=0.141 Sum_probs=39.3
Q ss_pred CHHHHHHHHHhcC-----CCCcCchhHHHHHhhcCCeEEEc-----C---CCeeecchhHHHHHHhh
Q psy8714 489 TESELISLMEKHG-----IGTDASIPVHINNICQRNYVTVT-----S---GRRLVPTSLGIVLVHGY 542 (562)
Q Consensus 489 Te~~Li~~Me~~G-----IGTpATra~iI~~L~~r~Yi~~~-----~---~k~l~~T~~G~~li~~l 542 (562)
+--+|.+.+++.. |+ +.|--.++..|.+.|+|... . .+.+.+|+.|+.+++..
T Consensus 19 ~GYei~~~l~~~~~~~~~i~-~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~ 84 (100)
T TIGR03433 19 HGYGIAQRIQQISEDVLQVE-EGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAE 84 (100)
T ss_pred CHHHHHHHHHHHcCCccccC-CCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHH
Confidence 4556777776542 33 57788899999999999861 1 24699999999988654
No 135
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=33.24 E-value=84 Score=28.23 Aligned_cols=53 Identities=13% Similarity=0.113 Sum_probs=41.4
Q ss_pred HHHHHHHHHhcCCC----CcCchhHHHHHhhcCCeEEEc----C----CCeeecchhHHHHHHhh
Q psy8714 490 ESELISLMEKHGIG----TDASIPVHINNICQRNYVTVT----S----GRRLVPTSLGIVLVHGY 542 (562)
Q Consensus 490 e~~Li~~Me~~GIG----TpATra~iI~~L~~r~Yi~~~----~----~k~l~~T~~G~~li~~l 542 (562)
--+|.+.++..+-| .+.|-=.++.+|.+.|||... . .|.+.+|+.|+..+.-+
T Consensus 25 Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~ 89 (138)
T COG1695 25 GYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAEL 89 (138)
T ss_pred HHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHH
Confidence 44677778877666 578888999999999999851 1 36799999999877543
No 136
>PRK06683 hypothetical protein; Provisional
Probab=33.23 E-value=1.5e+02 Score=24.62 Aligned_cols=55 Identities=7% Similarity=0.033 Sum_probs=38.9
Q ss_pred CchHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHh
Q psy8714 94 LKLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWN 162 (562)
Q Consensus 94 ~~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~n 162 (562)
..+++.|++ .++..||+|.|++.. +-..|.+.|.. ++.|+. ++. |..++=.|+.-
T Consensus 17 ~~v~kaik~--gkaklViiA~Da~~~---~~~~i~~~~~~-----~~Vpv~--~~~--t~~eLG~A~G~ 71 (82)
T PRK06683 17 KRTLEAIKN--GIVKEVVIAEDADMR---LTHVIIRTALQ-----HNIPIT--KVE--SVRKLGKVAGI 71 (82)
T ss_pred HHHHHHHHc--CCeeEEEEECCCCHH---HHHHHHHHHHh-----cCCCEE--EEC--CHHHHHHHhCC
Confidence 346777775 688999999999865 77777777753 356773 222 77888777643
No 137
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=33.09 E-value=56 Score=27.83 Aligned_cols=28 Identities=14% Similarity=0.143 Sum_probs=25.1
Q ss_pred HHHhhCCCCHHHHHHHHHHhHhcCceee
Q psy8714 304 VASSGLGMGPHHAMQIAERLYTQGYVSY 331 (562)
Q Consensus 304 ~a~~~~g~s~~~tl~iaQ~LYE~glISY 331 (562)
..++.++++.+++..++++|-+.|||.+
T Consensus 26 ~ia~~l~~~~~~v~~~l~~Le~~GLler 53 (92)
T PF10007_consen 26 SIARRLKIPLEEVREALEKLEEMGLLER 53 (92)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 3567789999999999999999999985
No 138
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=33.07 E-value=44 Score=33.96 Aligned_cols=37 Identities=24% Similarity=0.396 Sum_probs=31.0
Q ss_pred cCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhh
Q psy8714 505 DASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGY 542 (562)
Q Consensus 505 pATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l 542 (562)
+++-...|++|.+.|.|.. +|+.+..|+.|+.+++-+
T Consensus 40 ~~ai~pqiKkL~~~~LV~~-~~~~Y~LS~~G~iiv~km 76 (260)
T COG4742 40 SSAILPQIKKLKDKGLVVQ-EGDRYSLSSLGKIIVEKM 76 (260)
T ss_pred cHHHHHHHHHHhhCCCEEe-cCCEEEecchHHHHHHHH
Confidence 4455678999999999997 688999999999888654
No 139
>PRK13601 putative L7Ae-like ribosomal protein; Provisional
Probab=33.02 E-value=1.5e+02 Score=24.69 Aligned_cols=53 Identities=11% Similarity=0.043 Sum_probs=39.1
Q ss_pred chHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHH
Q psy8714 95 KLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMW 161 (562)
Q Consensus 95 ~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~ 161 (562)
.+++.|++ .++..||+|.|++ +.+-..+.++|.. ++.|+. ..-|..++=.|+-
T Consensus 15 ~vlkaIk~--gkakLViiA~Da~---~~~~k~i~~~c~~-----~~Vpv~----~~~t~~eLG~A~G 67 (82)
T PRK13601 15 QTLKAITN--CNVLQVYIAKDAE---EHVTKKIKELCEE-----KSIKIV----YIDTMKELGVMCG 67 (82)
T ss_pred HHHHHHHc--CCeeEEEEeCCCC---HHHHHHHHHHHHh-----CCCCEE----EeCCHHHHHHHHC
Confidence 46677775 6888999999998 5788899888864 367883 2336677777764
No 140
>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=32.55 E-value=60 Score=25.62 Aligned_cols=30 Identities=20% Similarity=0.345 Sum_probs=24.5
Q ss_pred HHHHhhCCCC-HHHHHHHHHHhHhcCceeec
Q psy8714 303 RVASSGLGMG-PHHAMQIAERLYTQGYVSYP 332 (562)
Q Consensus 303 ~~a~~~~g~s-~~~tl~iaQ~LYE~glISYP 332 (562)
++..+.+|++ +.-+...++.|-++|||.-.
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 3445567886 99999999999999999853
No 141
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=31.64 E-value=70 Score=22.82 Aligned_cols=35 Identities=20% Similarity=0.213 Sum_probs=27.8
Q ss_pred CCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecC
Q psy8714 295 ALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPR 333 (562)
Q Consensus 295 pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPR 333 (562)
+++..+|.. .+|+|+..+....+.|.++|+|....
T Consensus 14 ~~s~~~l~~----~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 14 KVSVEELAE----LLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred CcCHHHHHH----HHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 356666554 46999999999999999999998643
No 142
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=30.95 E-value=55 Score=29.68 Aligned_cols=40 Identities=13% Similarity=0.267 Sum_probs=33.1
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCCCCCCc
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQGYVSYPRTETTQYPEN 342 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~~l~~~ 342 (562)
.+.++.+|+|+..+...+++|-++|||.|-|...-.|++.
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 5667789999999999999999999999876555556654
No 143
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=30.92 E-value=1.3e+02 Score=24.50 Aligned_cols=51 Identities=20% Similarity=0.203 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEc-CCCeeecchhHHHHHHh
Q psy8714 487 YLTESELISLMEKHGIGTDASIPVHINNICQRNYVTVT-SGRRLVPTSLGIVLVHG 541 (562)
Q Consensus 487 ~~Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~-~~k~l~~T~~G~~li~~ 541 (562)
..|-.+|-+.| |+ +.+|-..++..|.+.|||... .++.+.+++.+..+-..
T Consensus 20 ~~t~~~ia~~l---~i-~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~~~~~~ 71 (91)
T smart00346 20 GLTLAELAERL---GL-SKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVLELGQS 71 (91)
T ss_pred CcCHHHHHHHh---CC-CHHHHHHHHHHHHHCCCeeecCCCCceeecHHHHHHHHH
Confidence 46777776666 66 456666799999999999874 24567777766655433
No 144
>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=30.89 E-value=77 Score=21.52 Aligned_cols=27 Identities=22% Similarity=0.338 Sum_probs=22.8
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhcCce
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQGYV 329 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~glI 329 (562)
++.+..+|.|++-+-.+.-+|-++|+|
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 456678999999999999999999987
No 145
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=30.55 E-value=1.9e+02 Score=23.92 Aligned_cols=54 Identities=15% Similarity=0.037 Sum_probs=38.7
Q ss_pred chHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHh
Q psy8714 95 KLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWN 162 (562)
Q Consensus 95 ~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~n 162 (562)
.+++.|++ .++..||+|.|++. .+-.+|.+.|.. .+.|+. ++. |..++=.|+..
T Consensus 18 ~v~kai~~--gkaklViiA~D~~~---~~~~~i~~~c~~-----~~Vp~~--~~~--s~~eLG~a~G~ 71 (82)
T PRK13602 18 QTVKALKR--GSVKEVVVAEDADP---RLTEKVEALANE-----KGVPVS--KVD--SMKKLGKACGI 71 (82)
T ss_pred HHHHHHHc--CCeeEEEEECCCCH---HHHHHHHHHHHH-----cCCCEE--EEC--CHHHHHHHHCC
Confidence 46677775 68889999999987 477888888864 256663 333 77888777643
No 146
>PRK07714 hypothetical protein; Provisional
Probab=30.05 E-value=1.3e+02 Score=25.67 Aligned_cols=73 Identities=5% Similarity=-0.045 Sum_probs=46.7
Q ss_pred chHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhCCCChHhHHHHH
Q psy8714 95 KLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSV 174 (562)
Q Consensus 95 ~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~ 174 (562)
++.+.|++ .++..||+|.|++.. +..++...|.. .+.|+.. -.|.+++-.|+-...-.--...+.+
T Consensus 25 ~v~~al~~--g~~~lViiA~D~s~~---~~~ki~~~~~~-----~~vp~~~----~~sk~eLG~a~Gk~~~~~vai~d~g 90 (100)
T PRK07714 25 LVLKEVRS--GKAKLVLLSEDASVN---TTKKITDKCTY-----YNVPMRK----VENRQQLGHAIGKDERVVVAVLDEG 90 (100)
T ss_pred HHHHHHHh--CCceEEEEeCCCCHH---HHHHHHHHHHh-----cCCCEEE----eCCHHHHHHHhCCCcceEEEEeCch
Confidence 46677765 578899999999866 55677776643 2466632 2588999999975321122334556
Q ss_pred HHHHhHH
Q psy8714 175 DARQELD 181 (562)
Q Consensus 175 ~aR~~~D 181 (562)
.|+....
T Consensus 91 ~a~~l~~ 97 (100)
T PRK07714 91 FAKKLRS 97 (100)
T ss_pred hHHHHHH
Confidence 6665544
No 147
>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=30.01 E-value=73 Score=25.09 Aligned_cols=38 Identities=24% Similarity=0.350 Sum_probs=30.6
Q ss_pred CCCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCC
Q psy8714 293 PQALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRT 334 (562)
Q Consensus 293 P~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRT 334 (562)
|.|++.. +.+...|.|...+.+++..|=++|+|++-+.
T Consensus 26 ~~~lt~~----~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 26 PLPLTQE----EIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp EEESSHH----HHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred EecCCHH----HHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 5566654 4556679999999999999999999997554
No 148
>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=29.57 E-value=65 Score=27.82 Aligned_cols=32 Identities=19% Similarity=0.336 Sum_probs=26.4
Q ss_pred HHHHHhhCCCCHHHHHHHHHHhHhcCceeecC
Q psy8714 302 MRVASSGLGMGPHHAMQIAERLYTQGYVSYPR 333 (562)
Q Consensus 302 q~~a~~~~g~s~~~tl~iaQ~LYE~glISYPR 333 (562)
|.+.+..+++++..+..+...|+++|||+=-|
T Consensus 46 ~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 46 LKEIIKEILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 34456678999999999999999999998433
No 149
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=29.17 E-value=44 Score=36.50 Aligned_cols=45 Identities=20% Similarity=0.333 Sum_probs=36.1
Q ss_pred hhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhhhccCccCCChhhHH
Q psy8714 508 IPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTMRS 556 (562)
Q Consensus 508 ra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~Ta 556 (562)
....|+.|.+.|+|.. .+..+.+|++|+.+.+.+ ...+..|+..+
T Consensus 378 ~~~~l~~l~~~gll~~-~~~~l~lT~~G~~~~d~i---~~~~~~~~~~~ 422 (430)
T PRK08208 378 DFPELELLIDRGWLEQ-NGGRLRLTEEGLALSDAI---GPVFISPEVRA 422 (430)
T ss_pred HHHHHHHHHHCCCEEE-ECCEEEECcchhhHHHHH---HHHHcCHHHHH
Confidence 4568889999999998 567999999999999775 35566777654
No 150
>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=28.54 E-value=51 Score=28.79 Aligned_cols=41 Identities=10% Similarity=0.165 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecCCCC
Q psy8714 296 LNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPRTET 336 (562)
Q Consensus 296 f~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds 336 (562)
-+..++...+....+++..-++.++..|.++|+|+.-+..-
T Consensus 18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~gr 58 (115)
T PF03965_consen 18 ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIGR 58 (115)
T ss_dssp EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEETT
T ss_pred CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecCC
Confidence 56688888888888999999999999999999999876544
No 151
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=28.53 E-value=92 Score=26.07 Aligned_cols=52 Identities=12% Similarity=0.172 Sum_probs=33.9
Q ss_pred chHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHH
Q psy8714 95 KLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAM 160 (562)
Q Consensus 95 ~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~ 160 (562)
+.++.|++ ..+..||+|.|.|.. +-.+|...|... +.|+ .|+. |.+++=+|+
T Consensus 20 qt~Kai~k--g~~~~v~iA~Da~~~---vv~~l~~lceek-----~Ip~--v~V~--s~~~LGkAc 71 (84)
T PRK13600 20 ETLKALKK--DQVTSLIIAEDVEVY---LMTRVLSQINQK-----NIPV--SFFK--SKHALGKHV 71 (84)
T ss_pred HHHHHHhc--CCceEEEEeCCCCHH---HHHHHHHHHHHc-----CCCE--EEEC--CHHHHHHHh
Confidence 35666664 467899999999955 446998888642 3444 4554 345565555
No 152
>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=28.48 E-value=70 Score=24.33 Aligned_cols=45 Identities=16% Similarity=0.244 Sum_probs=32.5
Q ss_pred HHhcCCCCcCchhHHHHHhhcCCeEEEcC-C--CeeecchhHHHHHHhhh
Q psy8714 497 MEKHGIGTDASIPVHINNICQRNYVTVTS-G--RRLVPTSLGIVLVHGYQ 543 (562)
Q Consensus 497 Me~~GIGTpATra~iI~~L~~r~Yi~~~~-~--k~l~~T~~G~~li~~l~ 543 (562)
++..|++ .+|-..+++.|.+.|+|.... + +.+..|+ |..+++.++
T Consensus 27 ~~~~~i~-~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~~ 74 (78)
T cd00090 27 AERLGLS-QSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALLE 74 (78)
T ss_pred HHHHCcC-HhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHHH
Confidence 4455885 456667899999999998632 2 4578888 888887764
No 153
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=28.42 E-value=84 Score=24.84 Aligned_cols=34 Identities=15% Similarity=0.193 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeec
Q psy8714 295 ALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYP 332 (562)
Q Consensus 295 pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYP 332 (562)
.++.. +.++.+|++...+-.++.+|=+.|+|..-
T Consensus 22 ~~ta~----eLa~~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 22 TSTAL----QLAKNLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred CcCHH----HHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 46554 45667899999999999999999999863
No 154
>PF13155 Toprim_2: Toprim-like
Probab=28.39 E-value=70 Score=26.54 Aligned_cols=26 Identities=19% Similarity=0.348 Sum_probs=23.2
Q ss_pred CeEEEecCCCccchhHHHHHHHHHhh
Q psy8714 108 EFLVLWLDCDKEGENICFEVMEAVRH 133 (562)
Q Consensus 108 d~Ii~AtD~DREGE~I~~~i~~~~~~ 133 (562)
..|++|.|.|.-|..-...+.+.+..
T Consensus 48 ~~i~l~~DnD~aG~~~~~~~~~~l~~ 73 (96)
T PF13155_consen 48 KKIVLAFDNDEAGRKAAEKLQKELKE 73 (96)
T ss_pred CcEEEEeCCCHHHHHHHHHHHHHHHh
Confidence 67999999999999999999888754
No 155
>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=28.02 E-value=77 Score=23.83 Aligned_cols=29 Identities=24% Similarity=0.366 Sum_probs=24.0
Q ss_pred HHHHHhhCCCCHHHHHHHHHHhHhcCcee
Q psy8714 302 MRVASSGLGMGPHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 302 q~~a~~~~g~s~~~tl~iaQ~LYE~glIS 330 (562)
+.+.++.+|+++.-+..+...|=++|||.
T Consensus 24 ~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 24 QSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 34556678999999999999999999986
No 156
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=27.91 E-value=76 Score=23.21 Aligned_cols=32 Identities=22% Similarity=0.352 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHHHhcCCC----CcCchhHHHHHhhc
Q psy8714 486 DYLTESELISLMEKHGIG----TDASIPVHINNICQ 517 (562)
Q Consensus 486 ~~~Te~~Li~~Me~~GIG----TpATra~iI~~L~~ 517 (562)
..+|.++|.+.|.+.|+= |++||.-.+.+|.+
T Consensus 4 ~~LSd~eL~~~L~~~G~~~gPIt~sTR~vy~kkL~~ 39 (44)
T smart00540 4 DRLSDAELRAELKQYGLPPGPITDTTRKLYEKKLRK 39 (44)
T ss_pred hHcCHHHHHHHHHHcCCCCCCcCcchHHHHHHHHHH
Confidence 468899999999988753 79999999888864
No 157
>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=27.48 E-value=69 Score=26.17 Aligned_cols=34 Identities=24% Similarity=0.442 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecC
Q psy8714 296 LNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPR 333 (562)
Q Consensus 296 f~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPR 333 (562)
.+..+ .+..+|.|+..+-+++|.|-++|+|.=-|
T Consensus 26 ~s~~e----iA~~~~i~~~~l~kil~~L~~~Gli~s~~ 59 (83)
T PF02082_consen 26 VSSKE----IAERLGISPSYLRKILQKLKKAGLIESSR 59 (83)
T ss_dssp BEHHH----HHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CCHHH----HHHHHCcCHHHHHHHHHHHhhCCeeEecC
Confidence 55544 45578999999999999999999986544
No 158
>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=27.04 E-value=71 Score=24.04 Aligned_cols=40 Identities=18% Similarity=0.305 Sum_probs=27.5
Q ss_pred CHHHHHHHHHhcCCCCcCchhHHHHHhhcCCeEEEcCCCeeecc
Q psy8714 489 TESELISLMEKHGIGTDASIPVHINNICQRNYVTVTSGRRLVPT 532 (562)
Q Consensus 489 Te~~Li~~Me~~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T 532 (562)
|+.+|-. ..||. ..|-..++..|.+.|||....++.+.+|
T Consensus 27 ~~~~la~---~~~is-~~~v~~~l~~L~~~G~i~~~~~~~~~l~ 66 (66)
T cd07377 27 SERELAE---ELGVS-RTTVREALRELEAEGLVERRPGRGTFVA 66 (66)
T ss_pred CHHHHHH---HHCCC-HHHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence 4555444 44885 5666789999999999986555555543
No 159
>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=27.00 E-value=1.2e+02 Score=23.54 Aligned_cols=36 Identities=14% Similarity=0.300 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHhhCCCCHH----HHHHHHHHhHhcCcee
Q psy8714 295 ALNTVELMRVASSGLGMGPH----HAMQIAERLYTQGYVS 330 (562)
Q Consensus 295 pf~l~~Lq~~a~~~~g~s~~----~tl~iaQ~LYE~glIS 330 (562)
+.+..++.+.....|+.+++ .+....+.|.++|+|.
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 46778898888899999986 4566788888889874
No 160
>PRK07283 hypothetical protein; Provisional
Probab=26.82 E-value=1.1e+02 Score=26.08 Aligned_cols=72 Identities=10% Similarity=0.005 Sum_probs=46.4
Q ss_pred chHHHHHhhcccCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEecccCHHHHHHHHHhCCCChHhHHHHH
Q psy8714 95 KLPAFLANEAKDCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFSAITDKDIKAAMWNLVKPNIFEARSV 174 (562)
Q Consensus 95 ~~i~~L~~~~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~sslt~~~I~~A~~nl~~~~~~l~~a~ 174 (562)
++.+.|++ .++..||+|.|++..+- ..+.+.|.. ++.|+. .-.|.+++-.|+-..+.. -...+++
T Consensus 25 ~v~~aik~--gk~~lVi~A~Das~~~~---kk~~~~~~~-----~~Vp~~----~~~t~~eLG~a~Gk~~~v-vai~d~g 89 (98)
T PRK07283 25 LVVKAIQS--GQAKLVFLANDAGPNLT---KKVTDKSNY-----YQVEVS----TVFSTLELSAAVGKPRKV-LAVTDAG 89 (98)
T ss_pred HHHHHHHc--CCccEEEEeCCCCHHHH---HHHHHHHHH-----cCCCEE----EeCCHHHHHHHhCCCceE-EEEeChh
Confidence 46677775 57889999999986654 455555532 256773 223889999999863211 2344677
Q ss_pred HHHHhHH
Q psy8714 175 DARQELD 181 (562)
Q Consensus 175 ~aR~~~D 181 (562)
+|+...+
T Consensus 90 ~a~~l~~ 96 (98)
T PRK07283 90 FSKKMRS 96 (98)
T ss_pred HHHHHHH
Confidence 7776554
No 161
>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=26.28 E-value=97 Score=23.71 Aligned_cols=28 Identities=21% Similarity=0.342 Sum_probs=22.9
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHhcCcee
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE~glIS 330 (562)
.+.++.++++...+..+.++|-++|||.
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 4566789999999999999999999994
No 162
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=25.95 E-value=1.3e+02 Score=20.40 Aligned_cols=31 Identities=23% Similarity=0.336 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHhcCCCCcCchhHHHHHhhc
Q psy8714 487 YLTESELISLMEKHGIGTDASIPVHINNICQ 517 (562)
Q Consensus 487 ~~Te~~Li~~Me~~GIGTpATra~iI~~L~~ 517 (562)
.+|-++|-+.+...|+-|.-+++.+++.|.+
T Consensus 3 ~l~~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~ 33 (35)
T smart00513 3 KLKVSELKDELKKRGLSTSGTKAELVDRLLE 33 (35)
T ss_pred cCcHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 4678899999999999999999999998865
No 163
>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=24.69 E-value=1.3e+02 Score=27.08 Aligned_cols=38 Identities=11% Similarity=0.239 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCceeecC
Q psy8714 296 LNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVSYPR 333 (562)
Q Consensus 296 f~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glISYPR 333 (562)
-+..++...++...|++..-++.++..|.++|+|+.-+
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 164
>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=24.42 E-value=60 Score=22.72 Aligned_cols=31 Identities=26% Similarity=0.434 Sum_probs=20.7
Q ss_pred HHHHhhCCCCHHHHHHHHHHhHh-cCce-eecCCCCCC
Q psy8714 303 RVASSGLGMGPHHAMQIAERLYT-QGYV-SYPRTETTQ 338 (562)
Q Consensus 303 ~~a~~~~g~s~~~tl~iaQ~LYE-~glI-SYPRTds~~ 338 (562)
.++++.+|.|++. +. -|| .|+| +-.||++.|
T Consensus 3 ~e~A~~~gvs~~t-lR----~ye~~Gll~~~~r~~~g~ 35 (38)
T PF00376_consen 3 GEVAKLLGVSPRT-LR----YYEREGLLPPPERTEGGY 35 (38)
T ss_dssp HHHHHHHTS-HHH-HH----HHHHTTSS-SSEETTTS-
T ss_pred HHHHHHHCCCHHH-HH----HHHHCCCCCCCccCCCCe
Confidence 4567888988753 32 365 4999 888998764
No 165
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=24.36 E-value=88 Score=30.69 Aligned_cols=32 Identities=16% Similarity=0.209 Sum_probs=28.7
Q ss_pred HHHHHhhCCCCHHHHHHHHHHhHhcCceeecC
Q psy8714 302 MRVASSGLGMGPHHAMQIAERLYTQGYVSYPR 333 (562)
Q Consensus 302 q~~a~~~~g~s~~~tl~iaQ~LYE~glISYPR 333 (562)
|++.+..+|.|+..+-.+.++|.+.|+|+|-+
T Consensus 182 ~~~IA~~lGisretlsR~L~~L~~~GlI~~~~ 213 (230)
T PRK09391 182 RRDIADYLGLTIETVSRALSQLQDRGLIGLSG 213 (230)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCcEEecC
Confidence 56677889999999999999999999999864
No 166
>PF01043 SecA_PP_bind: SecA preprotein cross-linking domain; InterPro: IPR011130 The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain [].; GO: 0017038 protein import, 0016020 membrane; PDB: 3DIN_B 3JUX_A 3IQY_A 2IBM_A 3DL8_A 3JV2_B 3IQM_A 1TF2_A 1TF5_A 1M74_A ....
Probab=24.34 E-value=1.6e+02 Score=26.05 Aligned_cols=45 Identities=16% Similarity=0.138 Sum_probs=33.3
Q ss_pred HHHHHhhcC-CeEEEcCCCeeecchhHHHHHHhhhccCccCCChhh
Q psy8714 510 VHINNICQR-NYVTVTSGRRLVPTSLGIVLVHGYQKIDRELVEPTM 554 (562)
Q Consensus 510 ~iI~~L~~r-~Yi~~~~~k~l~~T~~G~~li~~l~~~~~~l~~p~~ 554 (562)
.++..|.+- .|..-++.+.+.+|+.|...++.+-.+++.+.++.-
T Consensus 13 ~~~~~L~~~~dy~vde~~~~v~LT~~G~~~~e~~~~~~~~l~~~~~ 58 (113)
T PF01043_consen 13 KFAKQLKEDEDYEVDEKQRTVELTEKGIEKAEKLLGISDNLYDEEN 58 (113)
T ss_dssp HHHHHSHTTTSECECTSTTEEEESHHHHHHHHHHHTSSSSTTSTTC
T ss_pred HHHHhCCCCCCEEEeCCCCeeeEhHHHHHHHHHHhhhccccccccc
Confidence 467778774 788766778999999999999865444456666544
No 167
>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=23.93 E-value=45 Score=32.31 Aligned_cols=34 Identities=26% Similarity=0.457 Sum_probs=26.9
Q ss_pred CCCCcCchhHHHHHhhcCCeEEEcC--CCeeecchhH
Q psy8714 501 GIGTDASIPVHINNICQRNYVTVTS--GRRLVPTSLG 535 (562)
Q Consensus 501 GIGTpATra~iI~~L~~r~Yi~~~~--~k~l~~T~~G 535 (562)
|+. ++|-..++..|.+.|||.+.. ++.+.+|++|
T Consensus 168 ~is-~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G 203 (203)
T TIGR01884 168 GKS-LSTISRHLRELEKKGLVEQKGRKGKRYSLTKLG 203 (203)
T ss_pred CcC-HHHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence 664 456669999999999999742 4679999987
No 168
>PF13362 Toprim_3: Toprim domain
Probab=23.57 E-value=2.2e+02 Score=23.68 Aligned_cols=27 Identities=19% Similarity=0.234 Sum_probs=22.5
Q ss_pred CCeEEEecCCCcc--chhHHHHHHHHHhh
Q psy8714 107 CEFLVLWLDCDKE--GENICFEVMEAVRH 133 (562)
Q Consensus 107 ~d~Ii~AtD~DRE--GE~I~~~i~~~~~~ 133 (562)
...||||.|.|.. |+.=+..+.+.+..
T Consensus 41 ~~~vii~~D~D~~~~G~~~a~~~~~~~~~ 69 (96)
T PF13362_consen 41 GRRVIIAADNDKANEGQKAAEKAAERLEA 69 (96)
T ss_pred CCeEEEEECCCCchhhHHHHHHHHHHHHh
Confidence 3568999999999 99888888887753
No 169
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=22.87 E-value=2.9e+02 Score=30.02 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=33.1
Q ss_pred cCCeEEEecCCCccchhHHHHHHHHHhhhcccCCCCcEEEEEec-ccCHHHHH
Q psy8714 106 DCEFLVLWLDCDKEGENICFEVMEAVRHQININSPKTVWRARFS-AITDKDIK 157 (562)
Q Consensus 106 ~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~~~~~~~v~Rl~~s-slt~~~I~ 157 (562)
.+.+||+|.|.|..|..=+..+++.+... ...++.+.+. ..+++++.
T Consensus 299 ~~~~vvl~~D~D~aG~~aa~r~~~~l~~~-----g~~v~v~~lp~gkDpdd~l 346 (415)
T TIGR01391 299 YADEIILCFDGDKAGRKAALRAIELLLPL-----GINVKVIKLPGGKDPDEYL 346 (415)
T ss_pred hCCeEEEEeCCCHHHHHHHHHHHHHHHHc-----CCeEEEEECCCCCCHHHHH
Confidence 35689999999999999998988887542 2445555443 45555553
No 170
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=22.56 E-value=1e+02 Score=28.73 Aligned_cols=32 Identities=9% Similarity=0.153 Sum_probs=28.6
Q ss_pred HHHHHhhCCCCHHHHHHHHHHhHhcCceeecC
Q psy8714 302 MRVASSGLGMGPHHAMQIAERLYTQGYVSYPR 333 (562)
Q Consensus 302 q~~a~~~~g~s~~~tl~iaQ~LYE~glISYPR 333 (562)
|.+.+..+|.|..-+-.+.++|=++|+|++-|
T Consensus 146 ~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~ 177 (193)
T TIGR03697 146 HQAIAEAIGSTRVTITRLLGDLRKKKLISIHK 177 (193)
T ss_pred HHHHHHHhCCcHHHHHHHHHHHHHCCCEEecC
Confidence 46667788999999999999999999999976
No 171
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=22.51 E-value=74 Score=33.93 Aligned_cols=37 Identities=11% Similarity=0.106 Sum_probs=30.5
Q ss_pred cCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhh
Q psy8714 505 DASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGY 542 (562)
Q Consensus 505 pATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l 542 (562)
.+.....++.|.+.|++.. .+..+.+|++|+.+++.+
T Consensus 333 ~~~~~~~~~~l~~~gl~~~-~~~~~~lt~~G~~~~~~i 369 (377)
T PRK08599 333 EDVFGETIQELQEQGLLEE-DDDHVRLTKKGKFLGNEV 369 (377)
T ss_pred HHHHHHHHHHHHHCCCEEE-ECCEEEECccHhHHHHHH
Confidence 3345668889999999998 567999999999998764
No 172
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=22.29 E-value=65 Score=27.51 Aligned_cols=21 Identities=33% Similarity=0.588 Sum_probs=17.2
Q ss_pred HHHHHhHhcCceeecCCCCCC
Q psy8714 318 QIAERLYTQGYVSYPRTETTQ 338 (562)
Q Consensus 318 ~iaQ~LYE~glISYPRTds~~ 338 (562)
++.+.|-.+|.|-||||.|..
T Consensus 91 dvve~L~~~g~~Y~pR~gs~~ 111 (112)
T COG5204 91 DVVEDLEQHGRIYYPRTGSFT 111 (112)
T ss_pred HHHHHHHHhCccccCCCCccc
Confidence 456778889999999999853
No 173
>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=22.11 E-value=1.1e+02 Score=23.34 Aligned_cols=33 Identities=18% Similarity=0.298 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCcee
Q psy8714 294 QALNTVELMRVASSGLGMGPHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 294 ~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glIS 330 (562)
.|.+.++|.. .+|+++..+..-.+.|-+.|+|+
T Consensus 23 ~~~t~~ela~----~l~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 23 GPMTVSELAE----ELGISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp STBEHHHHHH----HHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCHHHHHH----HHCCCHHHHHHHHHHHHHCCCeE
Confidence 4566666554 45899999999999999999986
No 174
>PRK12789 flgI flagellar basal body P-ring protein; Reviewed
Probab=21.86 E-value=1.4e+02 Score=31.80 Aligned_cols=32 Identities=22% Similarity=0.402 Sum_probs=27.2
Q ss_pred CHHHHHHHHHhhCCCCHHHHHHHHHHhHhcCce
Q psy8714 297 NTVELMRVASSGLGMGPHHAMQIAERLYTQGYV 329 (562)
Q Consensus 297 ~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE~glI 329 (562)
++.+|-...| .+|.+|.+.+.|+|.|.++|.+
T Consensus 329 tl~~lV~aLN-~lG~tp~DlIsILqalk~aGAL 360 (367)
T PRK12789 329 DLQTLVRGLN-QIGLKPSDIIAILQAIKTAGAL 360 (367)
T ss_pred CHHHHHHHHH-HcCCChHHHHHHHHHHHhcCcc
Confidence 6777766665 6899999999999999998865
No 175
>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=21.49 E-value=1.2e+02 Score=23.85 Aligned_cols=27 Identities=22% Similarity=0.518 Sum_probs=21.8
Q ss_pred HHHhhCCCCHHHHHHHHHHhHhcCcee
Q psy8714 304 VASSGLGMGPHHAMQIAERLYTQGYVS 330 (562)
Q Consensus 304 ~a~~~~g~s~~~tl~iaQ~LYE~glIS 330 (562)
+.++.||+|++.+...++.|-.+|+|-
T Consensus 19 eLa~~~~~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 19 ELAREFGISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHHHTT--HHHHHHHHHHHHCCTSCE
T ss_pred HHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 346789999999999999999999885
No 176
>PF14178 YppF: YppF-like protein
Probab=21.41 E-value=1.5e+02 Score=23.19 Aligned_cols=34 Identities=29% Similarity=0.384 Sum_probs=27.1
Q ss_pred CHHHHHHHHHhhCCCCH---HHHHHHHHHhHhcCcee
Q psy8714 297 NTVELMRVASSGLGMGP---HHAMQIAERLYTQGYVS 330 (562)
Q Consensus 297 ~l~~Lq~~a~~~~g~s~---~~tl~iaQ~LYE~glIS 330 (562)
++.+|++.-....++.| .+-|+-|+++|-.|-||
T Consensus 2 ~l~eLk~~F~~~k~y~p~~~NeLLDFar~~Yi~gei~ 38 (60)
T PF14178_consen 2 NLHELKQKFMQKKKYEPEDMNELLDFARKLYIQGEIS 38 (60)
T ss_pred CHHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCccc
Confidence 57788877776667665 67789999999999886
No 177
>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=21.27 E-value=75 Score=22.64 Aligned_cols=27 Identities=19% Similarity=0.162 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHHHHH-HHHhhcccCce
Q psy8714 394 TQLDGDAWRLYDYIVR-HFIGTLCGDLV 420 (562)
Q Consensus 394 ~~L~~~e~~vY~lI~r-r~la~~~~~a~ 420 (562)
..||+++-+|-.-|.| |||++|-.|..
T Consensus 3 kqlsp~qdk~hk~ilrdrflssfkqpgr 30 (48)
T PF10872_consen 3 KQLSPYQDKIHKHILRDRFLSSFKQPGR 30 (48)
T ss_pred cccCccHHHHHHHHHHHHHHHHhcCcch
Confidence 4688888888777664 89999976543
No 178
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=20.78 E-value=1.1e+02 Score=32.66 Aligned_cols=34 Identities=15% Similarity=0.119 Sum_probs=28.9
Q ss_pred hhHHHHHhhcCCeEEEcCCCeeecchhHHHHHHhh
Q psy8714 508 IPVHINNICQRNYVTVTSGRRLVPTSLGIVLVHGY 542 (562)
Q Consensus 508 ra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~l 542 (562)
....|+.|.+.|++.. ++..+.+|++|+.+.+.+
T Consensus 335 ~~~~l~~l~~~gl~~~-~~~~~~lT~~G~~~~~~i 368 (374)
T PRK05799 335 YGEVINKYIKLGLLIE-KEGRIYLSERGIEVSNSI 368 (374)
T ss_pred HHHHHHHHHHCCCEEE-ECCEEEEChhHHHHHHHH
Confidence 4567889999999997 566899999999998764
No 179
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=20.49 E-value=83 Score=26.18 Aligned_cols=41 Identities=10% Similarity=0.076 Sum_probs=30.3
Q ss_pred CcCchhHHHHHhhcCCeEEEc--C----CCeeecchhHHHHHHhhhc
Q psy8714 504 TDASIPVHINNICQRNYVTVT--S----GRRLVPTSLGIVLVHGYQK 544 (562)
Q Consensus 504 TpATra~iI~~L~~r~Yi~~~--~----~k~l~~T~~G~~li~~l~~ 544 (562)
++.+-+.-+..|.+.|.|.+. + ...+.+|++|..|...+..
T Consensus 32 s~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~~l~~ 78 (90)
T PF01638_consen 32 SPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLPVLEA 78 (90)
T ss_dssp -HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHHHHHH
Confidence 466777889999999999862 1 1248999999999977654
No 180
>PF09105 SelB-wing_1: Elongation factor SelB, winged helix ; InterPro: IPR015189 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 1". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; PDB: 2V9V_A 1LVA_A 2PLY_A.
Probab=20.49 E-value=1.2e+02 Score=22.50 Aligned_cols=34 Identities=15% Similarity=0.235 Sum_probs=26.6
Q ss_pred HHHhhCCCCHHHHHHHHHHhHhcCceeecCCCCC
Q psy8714 304 VASSGLGMGPHHAMQIAERLYTQGYVSYPRTETT 337 (562)
Q Consensus 304 ~a~~~~g~s~~~tl~iaQ~LYE~glISYPRTds~ 337 (562)
+|..+-.+|.++|-++.|++--.|-+|.-|.+..
T Consensus 22 eaatraslsleetrkllqsmaaagqvtllrvend 55 (61)
T PF09105_consen 22 EAATRASLSLEETRKLLQSMAAAGQVTLLRVEND 55 (61)
T ss_dssp HHHHHHT--HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred HHHHHhhccHHHHHHHHHHHHhcCceEEEEeccc
Confidence 3445567999999999999999999999887764
No 181
>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=20.38 E-value=99 Score=27.61 Aligned_cols=31 Identities=13% Similarity=0.107 Sum_probs=25.3
Q ss_pred HHHHHhhcCCeEEEcCCCeeecchhHHHHHHh
Q psy8714 510 VHINNICQRNYVTVTSGRRLVPTSLGIVLVHG 541 (562)
Q Consensus 510 ~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~ 541 (562)
.+++.+.--|+++. .++.+..|+.|+.++++
T Consensus 16 p~~eAaelLgf~~~-~~Gdi~LT~~G~~f~~a 46 (120)
T PF09821_consen 16 PIVEAAELLGFAEV-EEGDIRLTPLGRRFAEA 46 (120)
T ss_pred HHHHHHHHcCCeee-cCCcEEeccchHHHHHC
Confidence 36667777899998 46699999999999865
No 182
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=20.34 E-value=1.2e+02 Score=28.67 Aligned_cols=32 Identities=13% Similarity=0.204 Sum_probs=28.3
Q ss_pred HHHHHhhCCCCHHHHHHHHHHhHhcCceeecC
Q psy8714 302 MRVASSGLGMGPHHAMQIAERLYTQGYVSYPR 333 (562)
Q Consensus 302 q~~a~~~~g~s~~~tl~iaQ~LYE~glISYPR 333 (562)
|.+.+..+|.|+..+-.+..+|-+.|+|++.|
T Consensus 152 ~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~ 183 (202)
T PRK13918 152 HDELAAAVGSVRETVTKVIGELSREGYIRSGY 183 (202)
T ss_pred HHHHHHHhCccHHHHHHHHHHHHHCCCEEcCC
Confidence 45667789999999999999999999999765
No 183
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=20.28 E-value=1.1e+02 Score=32.70 Aligned_cols=33 Identities=18% Similarity=0.409 Sum_probs=27.8
Q ss_pred hHHHHHhhcCCeEEEcCCC-eeecchhHHHHHHhh
Q psy8714 509 PVHINNICQRNYVTVTSGR-RLVPTSLGIVLVHGY 542 (562)
Q Consensus 509 a~iI~~L~~r~Yi~~~~~k-~l~~T~~G~~li~~l 542 (562)
...|+.|.+.|++.. .+. .+.+|++|+.+.+.+
T Consensus 341 ~~~l~~l~~~gl~~~-~~~~~~~lT~~G~~~~d~i 374 (380)
T PRK09057 341 PERLADLIEEGLIER-DGGSRLRATPAGRLVLDAV 374 (380)
T ss_pred HHHHHHHHHCCCEEE-cCCCEEEECcchhHHHHHH
Confidence 357999999999997 344 899999999998764
No 184
>PF09857 DUF2084: Uncharacterized protein conserved in bacteria (DUF2084); InterPro: IPR018654 This domain is found in various hypothetical bacterial proteins that have no known function.
Probab=20.13 E-value=1.3e+02 Score=25.19 Aligned_cols=32 Identities=16% Similarity=0.267 Sum_probs=27.7
Q ss_pred HHHHHhhcCCeEEEcCCCeeecchhHHHHHHh
Q psy8714 510 VHINNICQRNYVTVTSGRRLVPTSLGIVLVHG 541 (562)
Q Consensus 510 ~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li~~ 541 (562)
.+..+|+.+++|...+|+.+..|..|...+.+
T Consensus 49 ~vF~kLK~krlI~S~~g~PYrIt~~Gl~~VR~ 80 (85)
T PF09857_consen 49 AVFRKLKRKRLIASKNGGPYRITRLGLRAVRA 80 (85)
T ss_pred HHHHHHhhccceeccCCCCeEEcHHHHHHhhh
Confidence 57789999999998778889999999998754
No 185
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=20.13 E-value=1.1e+02 Score=30.76 Aligned_cols=39 Identities=18% Similarity=0.237 Sum_probs=30.6
Q ss_pred cCCCCcCchhHHHHHhhcCCeEEEcCCCeeecchhHHHHH
Q psy8714 500 HGIGTDASIPVHINNICQRNYVTVTSGRRLVPTSLGIVLV 539 (562)
Q Consensus 500 ~GIGTpATra~iI~~L~~r~Yi~~~~~k~l~~T~~G~~li 539 (562)
.|| |+---..+|+.|.+-|||..+++..+..|.+|..++
T Consensus 35 lgi-T~QaVsehiK~Lv~eG~i~~~gR~~Y~iTkkG~e~l 73 (260)
T COG1497 35 LGI-TLQAVSEHIKELVKEGLIEKEGRGEYEITKKGAEWL 73 (260)
T ss_pred cCC-CHHHHHHHHHHHHhccceeecCCeeEEEehhHHHHH
Confidence 354 566677899999999999984334899999998744
Done!