Query psy17743
Match_columns 618
No_of_seqs 352 out of 658
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 21:48:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17743.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17743hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0981|consensus 100.0 1E-199 3E-204 1583.6 39.4 495 1-495 235-735 (759)
2 smart00435 TOPEUc DNA Topoisom 100.0 7E-136 2E-140 1072.2 33.4 366 121-491 1-391 (391)
3 cd00660 Topoisomer_IB_N Topois 100.0 8.7E-90 1.9E-94 670.9 18.6 191 1-191 25-215 (215)
4 cd03488 Topoisomer_IB_N_htopoI 100.0 9E-90 2E-94 670.8 18.6 191 1-191 25-215 (215)
5 cd03489 Topoisomer_IB_N_Ldtopo 100.0 6.4E-89 1.4E-93 663.7 18.5 190 1-191 23-212 (212)
6 cd03490 Topoisomer_IB_N_1 Topo 100.0 4.3E-88 9.4E-93 659.7 18.7 191 1-191 23-217 (217)
7 PF02919 Topoisom_I_N: Eukaryo 100.0 1.9E-88 4E-93 663.8 9.0 190 1-190 26-215 (215)
8 PHA03101 DNA topoisomerase typ 100.0 2.6E-64 5.7E-69 519.1 19.6 242 134-399 17-273 (314)
9 PF01028 Topoisom_I: Eukaryoti 100.0 2.6E-64 5.6E-69 504.5 13.3 230 193-427 2-234 (234)
10 cd00659 Topo_IB_C DNA topoisom 100.0 2.7E-57 5.9E-62 449.8 18.7 198 195-400 1-204 (218)
11 KOG0981|consensus 100.0 5.6E-49 1.2E-53 423.4 5.5 301 258-595 206-516 (759)
12 COG3569 Topoisomerase IB [DNA 100.0 1.5E-46 3.3E-51 385.9 -7.6 300 2-358 52-354 (354)
13 COG3569 Topoisomerase IB [DNA 100.0 7.1E-42 1.5E-46 351.5 12.8 269 97-406 13-306 (354)
14 smart00435 TOPEUc DNA Topoisom 100.0 1.6E-35 3.4E-40 313.1 4.5 109 481-589 48-156 (391)
15 PF14370 Topo_C_assoc: C-termi 99.8 1.7E-22 3.7E-27 168.9 -1.7 49 448-496 1-49 (71)
16 PF01028 Topoisom_I: Eukaryoti 99.8 9.4E-20 2E-24 183.6 -0.0 86 505-590 1-87 (234)
17 cd00659 Topo_IB_C DNA topoisom 99.6 2.7E-16 5.8E-21 157.2 2.6 77 514-590 1-84 (218)
18 PHA03101 DNA topoisomerase typ 98.6 1.6E-08 3.5E-13 106.2 2.2 78 512-589 79-158 (314)
19 cd03488 Topoisomer_IB_N_htopoI 97.4 6.2E-05 1.3E-09 75.6 1.7 24 481-504 192-215 (215)
20 cd00660 Topoisomer_IB_N Topois 97.4 6.2E-05 1.3E-09 75.6 1.7 24 481-504 192-215 (215)
21 cd03489 Topoisomer_IB_N_Ldtopo 97.4 6.4E-05 1.4E-09 75.4 1.8 24 481-504 189-212 (212)
22 cd03490 Topoisomer_IB_N_1 Topo 97.4 7E-05 1.5E-09 75.3 1.8 24 481-504 194-217 (217)
23 PF02919 Topoisom_I_N: Eukaryo 97.2 0.00012 2.7E-09 73.7 1.7 23 481-503 193-215 (215)
24 cd00397 DNA_BRE_C DNA breaking 96.5 0.0085 1.8E-07 53.7 7.0 123 233-395 14-156 (164)
25 TIGR02224 recomb_XerC tyrosine 95.7 0.033 7.2E-07 54.8 7.4 100 237-357 132-249 (295)
26 cd00801 INT_P4 Bacteriophage P 95.7 0.051 1.1E-06 55.4 9.0 122 237-396 202-333 (357)
27 cd01187 INT_SG4 INT_SG4, DNA b 95.6 0.14 3E-06 51.6 11.8 129 235-394 127-277 (299)
28 cd01193 INT_IntI IntI (E2) int 95.5 0.036 7.9E-07 53.3 6.8 100 237-356 89-213 (242)
29 PRK02436 xerD site-specific ty 95.4 0.039 8.5E-07 54.3 6.9 111 239-394 117-236 (245)
30 cd01192 INT_P22_C P22-like int 93.7 0.27 5.8E-06 45.8 7.8 119 237-394 24-151 (177)
31 PF00589 Phage_integrase: Phag 93.7 0.27 5.7E-06 44.7 7.6 105 235-358 22-142 (173)
32 PRK05084 xerS site-specific ty 93.6 0.15 3.3E-06 53.2 6.6 117 237-393 198-333 (357)
33 PRK09870 tyrosine recombinase; 93.6 0.26 5.5E-06 47.9 7.7 101 239-359 37-153 (200)
34 cd01188 INT_pAE1 pAE1 and rela 93.5 0.73 1.6E-05 43.5 10.5 97 239-355 30-144 (188)
35 PRK09692 integrase; Provisiona 93.4 0.41 9E-06 51.5 9.7 139 238-414 237-386 (413)
36 cd01190 INT_SG5 INT_SG5, DNA b 93.1 1.1 2.4E-05 43.8 11.4 85 237-341 98-190 (260)
37 cd01182 INT_REC_C DNA breaking 93.1 0.43 9.4E-06 41.8 7.7 123 235-396 16-155 (162)
38 cd01189 INT_phiLC3_C phiLC3 ph 92.8 0.82 1.8E-05 42.3 9.5 103 238-358 25-158 (191)
39 PRK00283 xerD site-specific ty 92.8 0.46 9.9E-06 47.3 8.2 118 237-394 137-273 (299)
40 cd00799 INT_Cre Cre recombinas 92.5 1 2.2E-05 45.2 10.4 123 237-394 119-265 (287)
41 TIGR02225 recomb_XerD tyrosine 92.3 1.4 2.9E-05 43.3 10.7 119 236-394 127-265 (291)
42 cd01194 INT_Tn554A_C Tn544A an 92.3 0.86 1.9E-05 42.5 8.9 120 237-394 19-164 (186)
43 cd01186 INT_SG3_C INT_SG3, DNA 92.1 0.57 1.2E-05 44.5 7.6 100 238-358 28-139 (180)
44 PRK00236 xerC site-specific ty 92.0 1.2 2.5E-05 43.9 9.9 98 237-355 139-251 (297)
45 PRK09871 tyrosine recombinase; 91.4 0.63 1.4E-05 44.9 7.2 118 238-394 30-164 (198)
46 cd01199 INT_Tn1545_C Tn1545-re 90.8 2.9 6.4E-05 39.3 11.0 124 236-395 23-183 (205)
47 cd00796 INT_Rci Rci recombinas 90.6 1.1 2.5E-05 42.9 8.1 101 236-358 66-171 (206)
48 PRK01287 xerC site-specific ty 90.4 1 2.2E-05 47.6 8.2 118 238-394 161-296 (358)
49 cd01184 INT_SG2_C INT_SG2, DNA 90.3 1.2 2.5E-05 41.7 7.6 122 238-396 28-173 (181)
50 TIGR02249 integrase_gron integ 89.9 1.2 2.7E-05 45.4 8.1 117 238-393 120-289 (315)
51 cd01197 INT_FimBE_C FimB and F 89.9 0.82 1.8E-05 42.9 6.3 116 239-393 29-160 (180)
52 PF14370 Topo_C_assoc: C-termi 89.6 0.099 2.1E-06 44.9 -0.1 25 593-618 47-71 (71)
53 cd00800 INT_Lambda_C Lambda in 89.2 1.1 2.3E-05 41.5 6.4 99 235-355 20-134 (162)
54 cd01185 INT_Tn4399 Tn4399 and 89.0 1 2.2E-05 45.4 6.6 112 245-394 160-277 (299)
55 PHA03397 vlf-1 very late expre 88.4 2 4.4E-05 47.1 8.8 130 209-358 165-312 (363)
56 cd01183 INT_SG1_C INT_SG1, DNA 87.3 1.4 3E-05 42.0 6.0 106 236-358 28-170 (196)
57 cd00798 INT_XerDC XerD and Xer 86.6 3.5 7.5E-05 40.1 8.5 97 238-355 131-245 (284)
58 cd01191 INT_phiCTX_C phiCTX ph 81.1 8.1 0.00018 37.0 8.4 120 238-394 24-184 (196)
59 cd01196 INT_VanD VanD integras 80.3 7.4 0.00016 39.0 8.1 115 238-394 111-238 (263)
60 cd01195 INT_Tn544B_C Tn544B an 79.5 6.6 0.00014 37.5 7.2 125 236-394 22-176 (195)
61 PF06476 DUF1090: Protein of u 79.4 16 0.00035 34.0 9.3 54 373-434 42-95 (115)
62 cd00797 HP1_INT_C Phage HP1 in 77.7 9 0.00019 35.2 7.2 94 238-357 20-117 (158)
63 cd01198 INT_ASSRA_C Archaeal s 75.9 15 0.00032 34.6 8.4 102 237-358 20-142 (186)
64 PF07106 TBPIP: Tat binding pr 74.0 12 0.00025 36.3 7.2 60 401-460 71-133 (169)
65 PF14282 FlxA: FlxA-like prote 64.7 21 0.00045 32.6 6.4 54 408-461 18-76 (106)
66 PRK15417 integrase/recombinase 60.5 24 0.00052 37.2 6.8 57 238-314 135-191 (337)
67 PRK01885 greB transcription el 58.4 40 0.00088 32.8 7.5 72 401-472 9-90 (157)
68 PRK05892 nucleoside diphosphat 58.1 48 0.001 32.3 7.9 69 401-472 10-87 (158)
69 PF07106 TBPIP: Tat binding pr 56.0 37 0.00081 32.8 6.8 22 328-349 30-53 (169)
70 KOG0804|consensus 54.7 12 0.00025 42.4 3.4 95 378-472 355-468 (493)
71 TIGR01461 greB transcription e 53.6 42 0.00092 32.6 6.7 72 401-472 7-88 (156)
72 PF05276 SH3BP5: SH3 domain-bi 53.4 47 0.001 34.8 7.4 70 375-457 147-226 (239)
73 TIGR01010 BexC_CtrB_KpsE polys 50.6 1.2E+02 0.0026 32.6 10.2 81 379-461 186-267 (362)
74 PF02388 FemAB: FemAB family; 49.8 28 0.00061 38.4 5.5 69 399-472 239-307 (406)
75 COG3883 Uncharacterized protei 49.1 23 0.0005 37.6 4.4 55 399-459 49-103 (265)
76 PF12835 Integrase_1: Integras 48.2 73 0.0016 31.7 7.6 135 234-393 31-175 (187)
77 PF01519 DUF16: Protein of unk 44.8 1.1E+02 0.0023 28.4 7.4 52 399-456 50-101 (102)
78 PF14282 FlxA: FlxA-like prote 43.0 1E+02 0.0022 28.1 7.1 58 400-458 17-80 (106)
79 PF02403 Seryl_tRNA_N: Seryl-t 41.3 1.1E+02 0.0023 27.3 6.9 58 401-461 35-92 (108)
80 PF09726 Macoilin: Transmembra 40.9 52 0.0011 39.3 6.1 32 438-469 540-571 (697)
81 PF13094 CENP-Q: CENP-Q, a CEN 39.4 3.5E+02 0.0076 25.9 11.6 107 411-536 36-143 (160)
82 PRK11637 AmiB activator; Provi 39.3 1.1E+02 0.0023 33.9 8.0 6 608-613 331-336 (428)
83 PF03962 Mnd1: Mnd1 family; I 38.9 1.1E+02 0.0023 30.8 7.1 16 328-343 27-42 (188)
84 PRK06342 transcription elongat 38.6 91 0.002 30.6 6.5 65 401-472 33-99 (160)
85 TIGR03007 pepcterm_ChnLen poly 37.8 2.1E+02 0.0045 32.0 10.0 24 268-293 109-132 (498)
86 PRK13182 racA polar chromosome 37.4 1.2E+02 0.0027 30.2 7.3 35 437-471 126-160 (175)
87 PHA02601 int integrase; Provis 36.4 88 0.0019 32.4 6.4 112 235-394 192-307 (333)
88 PF12718 Tropomyosin_1: Tropom 36.0 85 0.0018 30.2 5.7 60 400-459 33-96 (143)
89 PRK00226 greA transcription el 34.4 1.7E+02 0.0036 28.2 7.5 72 401-472 9-90 (157)
90 PRK13729 conjugal transfer pil 34.0 1E+02 0.0022 35.4 6.8 50 404-459 71-120 (475)
91 PF03449 GreA_GreB_N: Transcri 33.6 2.7E+02 0.0059 24.0 7.9 57 401-457 8-67 (74)
92 PF10498 IFT57: Intra-flagella 33.4 77 0.0017 35.0 5.6 25 436-460 328-352 (359)
93 COG1422 Predicted membrane pro 33.1 90 0.002 32.1 5.6 23 409-431 72-94 (201)
94 TIGR01462 greA transcription e 33.0 1.4E+02 0.0031 28.5 6.8 71 402-472 5-85 (151)
95 PF06810 Phage_GP20: Phage min 32.8 1.7E+02 0.0036 28.6 7.2 47 404-453 22-68 (155)
96 COG4787 FlgF Flagellar basal b 32.0 35 0.00076 35.6 2.6 62 99-161 85-151 (251)
97 KOG1962|consensus 31.7 1.2E+02 0.0025 31.6 6.2 62 400-461 149-211 (216)
98 COG3883 Uncharacterized protei 31.4 1.4E+02 0.003 32.0 6.8 26 438-463 75-100 (265)
99 PF05508 Ran-binding: RanGTP-b 31.2 1.3E+02 0.0028 32.7 6.7 30 381-413 27-56 (302)
100 PF09032 Siah-Interact_N: Siah 30.8 1.7E+02 0.0037 25.9 6.3 47 407-457 1-47 (79)
101 PF15290 Syntaphilin: Golgi-lo 30.1 71 0.0015 34.4 4.4 23 442-464 123-145 (305)
102 PF10779 XhlA: Haemolysin XhlA 29.0 2E+02 0.0044 24.3 6.3 47 404-456 1-47 (71)
103 PRK04406 hypothetical protein; 28.7 2.5E+02 0.0053 24.4 6.8 53 401-459 3-55 (75)
104 KOG0250|consensus 28.0 1.6E+02 0.0034 37.0 7.4 84 395-478 654-739 (1074)
105 PRK09039 hypothetical protein; 28.0 1.6E+02 0.0035 32.1 6.9 41 390-430 125-165 (343)
106 PF14257 DUF4349: Domain of un 27.3 1.5E+02 0.0032 30.6 6.2 85 390-480 120-204 (262)
107 PF06156 DUF972: Protein of un 27.2 1.9E+02 0.0042 26.7 6.3 45 400-457 13-57 (107)
108 COG5570 Uncharacterized small 27.1 2.1E+02 0.0046 23.8 5.7 50 411-460 7-57 (57)
109 TIGR02894 DNA_bind_RsfA transc 25.8 3.2E+02 0.0069 27.3 7.8 18 381-398 31-48 (161)
110 PF12329 TMF_DNA_bd: TATA elem 25.4 1.6E+02 0.0035 25.4 5.1 21 408-428 4-24 (74)
111 PF03961 DUF342: Protein of un 25.3 1.7E+02 0.0037 32.7 6.7 65 398-462 330-408 (451)
112 KOG0930|consensus 25.0 1.1E+02 0.0024 33.3 4.8 52 443-495 38-91 (395)
113 PF05529 Bap31: B-cell recepto 25.0 1.6E+02 0.0034 29.0 5.7 58 402-459 125-184 (192)
114 TIGR02338 gimC_beta prefoldin, 24.9 2.6E+02 0.0057 25.3 6.7 29 400-428 15-43 (110)
115 COG1382 GimC Prefoldin, chaper 24.8 2.3E+02 0.005 26.9 6.4 23 438-460 72-94 (119)
116 PRK11546 zraP zinc resistance 24.4 3E+02 0.0066 26.9 7.3 55 404-458 56-111 (143)
117 cd00632 Prefoldin_beta Prefold 24.1 3.6E+02 0.0078 24.2 7.3 28 400-427 11-38 (105)
118 PF11336 DUF3138: Protein of u 24.1 1.6E+02 0.0034 33.8 5.9 32 397-428 20-51 (514)
119 PF10458 Val_tRNA-synt_C: Valy 24.0 1.8E+02 0.0038 24.2 4.9 59 400-458 2-61 (66)
120 PLN02943 aminoacyl-tRNA ligase 23.4 1.4E+02 0.0029 37.1 5.9 67 401-467 888-955 (958)
121 PRK09343 prefoldin subunit bet 23.4 1.7E+02 0.0037 27.3 5.3 22 439-460 74-95 (121)
122 TIGR02680 conserved hypothetic 23.3 4.5E+02 0.0098 34.0 10.5 46 306-356 184-229 (1353)
123 PRK04325 hypothetical protein; 23.2 3.1E+02 0.0067 23.7 6.4 53 403-461 3-55 (74)
124 PF12329 TMF_DNA_bd: TATA elem 22.9 2.9E+02 0.0062 23.8 6.1 22 400-421 31-52 (74)
125 cd00890 Prefoldin Prefoldin is 22.6 2.7E+02 0.0059 25.0 6.4 32 396-427 81-112 (129)
126 PF00816 Histone_HNS: H-NS his 22.4 2E+02 0.0042 25.2 5.2 46 442-487 23-74 (93)
127 PF01920 Prefoldin_2: Prefoldi 22.3 4E+02 0.0087 23.0 7.2 22 439-460 65-86 (106)
128 PF13758 Prefoldin_3: Prefoldi 22.3 5.4E+02 0.012 23.8 8.0 82 347-428 5-94 (99)
129 PF11932 DUF3450: Protein of u 22.2 3E+02 0.0066 28.3 7.3 24 400-423 47-70 (251)
130 KOG4620|consensus 22.1 1.7E+02 0.0037 25.8 4.6 59 7-70 1-59 (80)
131 cd00632 Prefoldin_beta Prefold 21.9 3.4E+02 0.0075 24.3 6.8 46 397-455 58-103 (105)
132 KOG0804|consensus 21.8 1.6E+02 0.0035 33.7 5.5 19 376-394 384-402 (493)
133 PF07439 DUF1515: Protein of u 21.5 2.3E+02 0.0049 26.8 5.5 58 400-459 6-63 (112)
134 PF04102 SlyX: SlyX; InterPro 21.4 3.7E+02 0.0081 22.7 6.5 23 440-462 29-51 (69)
135 PRK09039 hypothetical protein; 21.3 3.3E+02 0.0071 29.8 7.7 43 380-422 59-101 (343)
136 PF11853 DUF3373: Protein of u 21.3 84 0.0018 36.2 3.3 27 399-426 22-48 (489)
137 TIGR02338 gimC_beta prefoldin, 21.0 3.7E+02 0.008 24.4 6.8 29 396-424 61-89 (110)
138 PF04508 Pox_A_type_inc: Viral 20.9 1.2E+02 0.0027 21.1 2.8 20 403-422 2-21 (23)
139 cd01390 HMGB-UBF_HMG-box HMGB- 20.9 2.7E+02 0.0059 21.9 5.3 52 39-100 11-62 (66)
140 PF10675 DUF2489: Protein of u 20.7 1.4E+02 0.0031 28.4 4.3 42 60-101 76-122 (131)
141 PF04065 Not3: Not1 N-terminal 20.7 3.1E+02 0.0067 28.8 7.0 62 402-463 122-190 (233)
142 COG4942 Membrane-bound metallo 20.5 2.7E+02 0.0059 31.7 6.9 23 437-459 88-110 (420)
143 PRK09841 cryptic autophosphory 20.4 1.1E+02 0.0024 36.3 4.2 22 404-425 341-362 (726)
144 PRK14720 transcript cleavage f 20.3 3.2E+02 0.0069 34.0 8.0 72 401-472 754-835 (906)
145 TIGR02132 phaR_Bmeg polyhydrox 20.1 6.3E+02 0.014 25.9 8.6 49 378-426 50-103 (189)
No 1
>KOG0981|consensus
Probab=100.00 E-value=1.2e-199 Score=1583.63 Aligned_cols=495 Identities=68% Similarity=1.088 Sum_probs=487.9
Q ss_pred CccCCeecCCChhhHHHHHHHHHHhCCCCCCchhHhhhhHHHHHHHcccccccccccccCCCcHHHHHHHHhhHHHHHcC
Q psy17743 1 MEAGGKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFRKMHAYFVQKSEERKAM 80 (618)
Q Consensus 1 ~~ydg~~v~L~~~~EEvA~f~a~~l~~~~~~~~~F~~NFf~d~~~~l~~~~~~~i~~~~kcDF~~i~~~~~~~~e~kk~~ 80 (618)
|||||+||+|||++||||||||+||+|+|+++|+||+|||+|||++|+.+++++|++|++|||++||+||++++|+||+|
T Consensus 235 ~~YdGkpv~L~~eaEEvAtfyA~mle~ey~tk~vF~~NFf~Dwrk~m~~~~~~~Ik~l~kCDFt~i~~yf~~~~E~rK~m 314 (759)
T KOG0981|consen 235 FYYDGKPVDLTPEAEEVATFYAAMLEHEYATKEVFRKNFFNDWRKVMTVEEREVIKDLSKCDFTPIFEYFKEQKEKRKQM 314 (759)
T ss_pred EEeCCccccCCHHHHHHHHHHHHHHhcchhccHHHHHHHHHHHHHHhhhhhhhhhccccccCCHHHHHHHHHHHHHHhhc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHhccccEEEEcCeeeeecccccCCCcccccCCCCCCCCCCCCCCCccchhhhccCCCCCCCCCCCC
Q psy17743 81 SKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGH 160 (618)
Q Consensus 81 t~eEK~~~k~~~~~~~~~y~~~~~DG~~ekvgnfrvepPGlfRgRG~hpk~G~~k~RI~pedv~iN~~k~a~IPpp~~Gh 160 (618)
|+|||+++|+|+++++++||||+||||+|+||||||||||||||||.||+||+||+||+|+||+||||+++|||+|||||
T Consensus 315 skEEK~~iKeEkek~ee~y~~cilDG~kEkigNFriEPPgLFRGRG~HPKmG~lKrRI~Pedi~iN~gkda~iP~pppGh 394 (759)
T KOG0981|consen 315 SKEEKLKIKEEKEKLEEKYGWCILDGHKEKIGNFRIEPPGLFRGRGEHPKMGKLKRRIMPEDITINCGKDAPIPEPPPGH 394 (759)
T ss_pred CHHHHHHHHHHHHHHHHHcCeEEecCcHhhhcccccCCCccccCCCCCCcccchhcccchhheEEecCCCCCCCCCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeeCCceeEEeeccCCcCCceeEEEecCCCccccccchHHHHHHHHHHHHHHHHHHHHHHhhcccccchhHHHHHH
Q psy17743 161 KWKEVRHDNQVTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVAL 240 (618)
Q Consensus 161 aWkdV~hdntvtWla~w~~hIqGr~QYvylh~~S~~k~~rD~~Kfe~ar~l~~~Lp~IR~~y~~dL~s~~~~~RqlA~Al 240 (618)
.|++|+|||||||||+|.++|||..+||||+|+|+++|++|++|||+||+|+.+|+.||++|++||+|++|..||+|||+
T Consensus 395 kWkEVrHDNTVTWLa~W~e~i~~~~KYi~L~~~SslKGesD~~KyE~ARrLk~~Id~IR~~Y~~d~ksk~m~~RQravAl 474 (759)
T KOG0981|consen 395 KWKEVRHDNTVTWLASWTENINGSFKYIMLNPSSSLKGESDKEKYETARRLKKYIDKIRATYTKDFKSKEMKVRQRAVAL 474 (759)
T ss_pred cccccccCCeeeeeeecccccCCceeEEEecCcccccCchhHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhccCC
Q psy17743 241 YFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVENKKG 320 (618)
Q Consensus 241 yLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~K~P 320 (618)
||||+||||+|||+++++||||||||||++||+|+|+++++..+|.|||||||||||+|+|+|+++||+||..|+++|.|
T Consensus 475 Y~IDklALRAGnEKdedeADTVGCCsLrvehV~l~p~~~~~e~vv~FDFLGKDSIrYyN~VeVek~VyKnl~~F~~~K~~ 554 (759)
T KOG0981|consen 475 YFIDKLALRAGNEKDEDEADTVGCCSLRVEHVTLHPPNKGKEFVVEFDFLGKDSIRYYNEVEVEKRVYKNLKIFMEGKKP 554 (759)
T ss_pred HHHHHHHHhccCcccccccccccceeeeeeeeEeeCccccccceEEeeccCccceeeeeeccccHHHHHHHHHHhcCCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CccccccCChhHHHHHHHHhcCCCeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHHHHHHHcCCCCCCCCch
Q psy17743 321 SDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSH 400 (618)
Q Consensus 321 gd~LF~~l~s~~LN~yLkelm~glTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr~VAilcNHqraV~K~~ 400 (618)
||+|||+|+|+.||+||+++|+|||||||||||||+|||++|..++.+.+++++|++.||+|||+|||||||||+|||+|
T Consensus 555 ~ddLFDrLdt~~LN~hL~~lM~GLTAKVFRTYNASiTlqeqL~~lt~p~~~v~~KIl~YnrANr~VAIlCNHQR~v~K~h 634 (759)
T KOG0981|consen 555 GDDLFDRLDTSSLNKHLQELMDGLTAKVFRTYNASITLQEQLDKLTNPDGNVAAKILSYNRANRTVAILCNHQRAVSKTH 634 (759)
T ss_pred cchhhhhhchHHHHHHHHHHhccchhhhhhhcchhhHHHHHHHhccCCCccHHHHHHHHhhccceeeeeecccccCCccH
Confidence 99999999999999999999999999999999999999999999999889999999999999999999999999999999
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC------CcccHHHHHHHHHHHHHHHHHhcccchhhccccceeeccCC
Q psy17743 401 DKSMGNLKEKISNKRKQVKDAERALKDAKKAGE------SKAMTDKKKTALGRLKEQLLKLEVQETDKEENKTIALGTSK 474 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k------~~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaLgTSk 474 (618)
++||++|+++|+++++||.+++.+|..++++.+ ..+.+|+++++++++++||++|++|++||||||+|||||||
T Consensus 635 ~~smekl~~kI~~~keql~e~~~~l~~ak~~~~~~~~~~~~k~~Ek~~k~~~~l~eqi~kl~~q~~dkeenK~vALGTSK 714 (759)
T KOG0981|consen 635 EKSMEKLAEKIKAKKEQLKEAEAELKSAKADEKKQEGSKEKKEVEKKEKKLERLEEQLKKLEIQMTDKEENKQVALGTSK 714 (759)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccHHHHHHHHHHHHHHHHHHhhhccchhhcceeeccccc
Confidence 999999999999999999999999999976533 34589999999999999999999999999999999999999
Q ss_pred cCCCCCccchhhhheeeccCC
Q psy17743 475 LNYLDPRISVTWLASWTENVQ 495 (618)
Q Consensus 475 ~NY~DPRitVtWlkkw~vpI~ 495 (618)
||||||||||+||++|+|||.
T Consensus 715 iNYiDPRitvawcKk~dVPiE 735 (759)
T KOG0981|consen 715 LNYIDPRITVAWCKKHDVPIE 735 (759)
T ss_pred ccccCCceeeeehhccCCcHH
Confidence 999999999999999999985
No 2
>smart00435 TOPEUc DNA Topoisomerase I (eukaryota). DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras
Probab=100.00 E-value=7.1e-136 Score=1072.21 Aligned_cols=366 Identities=67% Similarity=1.033 Sum_probs=349.8
Q ss_pred ccccCCCCCCCCCCCCCCCccchhhhccCCCCCCCCCCCCCcceeeeCCceeEEeeccCCcCCceeEEEecCCCcccccc
Q psy17743 121 LFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASWTENVQGQVKYIMLNPSSKLKGEK 200 (618)
Q Consensus 121 lfRgRG~hpk~G~~k~RI~pedv~iN~~k~a~IPpp~~GhaWkdV~hdntvtWla~w~~hIqGr~QYvylh~~S~~k~~r 200 (618)
||||||+||+||+||+||+|||||||||+++|||+|||||+|++|+|||||||||+|.++|+|+.|||||+|+|+|++++
T Consensus 1 lFrGRG~hpk~G~lK~Rv~pedv~iN~~k~a~vP~pp~gh~Wk~v~hd~~vtWLa~w~e~i~~~~KYv~l~a~S~wk~~r 80 (391)
T smart00435 1 LFRGRGEHPKTGKLKRRIMPEDITINIGKDAPVPEPPPGHKWKEVRHDNTVTWLASWKENINGSIKYVFLAASSSLKGQS 80 (391)
T ss_pred CCCCCCCCCCccccccccChhheEEecCCCCCCCccCCCCCcceeecCCCceEEEEeeccCCCceeEEEECCCchhhhhh
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCC
Q psy17743 201 DWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDG 280 (618)
Q Consensus 201 D~~Kfe~ar~l~~~Lp~IR~~y~~dL~s~~~~~RqlA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~ 280 (618)
|+.|||+|++|+.+||+||++|.+||+++++++||+|+|+||||.++||||||+|+++|+||||||||++||++++
T Consensus 81 D~~Kfera~~f~~~Lp~IR~~~~~dL~s~~~r~rqlAvav~LID~~alRvGnEkYa~en~T~Gl~TLR~eHV~l~~---- 156 (391)
T smart00435 81 DRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLALRAGNEKGEDEADTVGCCSLRVEHVTLKP---- 156 (391)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhHHHHHHHHHHHhcccCCChhhhhcCCCEeecccchhheEecC----
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999986
Q ss_pred CCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhccCCCccccccCChhHHHHHHHHhcCCCeeeeeccccchHHHHH
Q psy17743 281 KPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQQ 360 (618)
Q Consensus 281 ~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~K~Pgd~LF~~l~s~~LN~yLkelm~glTAKvFRTynASvt~~~ 360 (618)
+++|+|+|+|||||+|+++|.||++||+||+.|++++.||++||++|+|++||+||+++|||||||||||||||++|++
T Consensus 157 -~~~v~fdF~GKdgir~~~~v~vd~~l~k~L~~~~~~k~pg~~LF~~l~s~~lN~yLke~mgglTAKdFRTwnASvta~~ 235 (391)
T smart00435 157 -PNKVIFDFLGKDSIRYYNEVEVDKQVFKNLKIFMKPKKPGDDLFDRLNTSKLNKHLKELMPGLTAKVFRTYNASITLQE 235 (391)
T ss_pred -CCEEEEEEeCCCCcEEEEEEecCHHHHHHHHHHhcCCCChHHHHhhCCHHHHHHHHHHHcCCCeeeeeecChHHHHHHH
Confidence 3899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCccHHHHHHHHHHHHHHHHHHcCCCCCCCCchHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhc---------
Q psy17743 361 QLNELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAERALKDAKKA--------- 431 (618)
Q Consensus 361 ~L~~~~~~~~s~~ek~~~yn~Anr~VAilcNHqraV~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~--------- 431 (618)
+|.+++++.+++++++..||+||++||++|||||||||+|++||+||++||+++++|+.++++.|..++..
T Consensus 236 ~L~~~~~~~~s~~ek~~~yn~Anr~VAi~cnntraV~k~~~~~m~k~~~ki~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 315 (391)
T smart00435 236 QLKELTAKDGNVAEKILAYNRANREVAILCNHQRTVSKTHEKSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKRKLKS 315 (391)
T ss_pred HHHhCCCCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccchhhhhhh
Confidence 99998765578999999999999999999999999999999999999999999999999999888755310
Q ss_pred ----------------CCCcccHHHHHHHHHHHHHHHHHhcccchhhccccceeeccCCcCCCCCccchhhhheee
Q psy17743 432 ----------------GESKAMTDKKKTALGRLKEQLLKLEVQETDKEENKTIALGTSKLNYLDPRISVTWLASWT 491 (618)
Q Consensus 432 ----------------~k~~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaLgTSk~NY~DPRitVtWlkkw~ 491 (618)
.+....+++.+++|+++++||++|++|++||||||+|||||||||||||||||+||++|+
T Consensus 316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~i~k~~~q~~~ke~nk~vaLgTSk~NY~DPRitvawck~~~ 391 (391)
T smart00435 316 KFERDNEKLDAEVKEKKKEKKKEEKKKKQIERLEERIEKLEVQATDKEENKTVALGTSKINYIDPRITVAWCKKFD 391 (391)
T ss_pred hhhhhhhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCeeeecccchhhccCCcceeEeecccC
Confidence 001235577789999999999999999999999999999999999999999999999985
No 3
>cd00660 Topoisomer_IB_N Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I diffe
Probab=100.00 E-value=8.7e-90 Score=670.91 Aligned_cols=191 Identities=63% Similarity=1.108 Sum_probs=189.2
Q ss_pred CccCCeecCCChhhHHHHHHHHHHhCCCCCCchhHhhhhHHHHHHHcccccccccccccCCCcHHHHHHHHhhHHHHHcC
Q psy17743 1 MEAGGKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFRKMHAYFVQKSEERKAM 80 (618)
Q Consensus 1 ~~ydg~~v~L~~~~EEvA~f~a~~l~~~~~~~~~F~~NFf~d~~~~l~~~~~~~i~~~~kcDF~~i~~~~~~~~e~kk~~ 80 (618)
|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|+.++++.|++|++||||+||+||++++|+||+|
T Consensus 25 ~~YdG~pv~L~peaEEvAtf~a~ml~t~y~~~~~F~kNFf~Df~~~l~~~~~~~i~~f~kcDF~~i~~~~~~~~e~kK~~ 104 (215)
T cd00660 25 FYYDGKPVKLPPEAEEVATFFAVMLETDYATKEVFRKNFFKDFRKILTKEEKHIIKKLSKCDFTPIYQYFEEEKEKKKAM 104 (215)
T ss_pred EEECCEECcCCHHHHHHHHHHHHHcCCccccChHHHHHHHHHHHHHhccccCccccchhhCCCHHHHHHHHHHHHHHHcC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHhccccEEEEcCeeeeecccccCCCcccccCCCCCCCCCCCCCCCccchhhhccCCCCCCCCCCCC
Q psy17743 81 SKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGH 160 (618)
Q Consensus 81 t~eEK~~~k~~~~~~~~~y~~~~~DG~~ekvgnfrvepPGlfRgRG~hpk~G~~k~RI~pedv~iN~~k~a~IPpp~~Gh 160 (618)
|+|||+++|+++++++++||||+|||++|+||||||||||||||||+|||||+||+||+|||||||||++|+||+|||||
T Consensus 105 s~eEKk~~K~ek~~~e~~Y~~~~vDG~kekVgNfrvEPPgLFrGRG~HPK~G~lK~Rv~PedVtINigkda~vP~pp~Gh 184 (215)
T cd00660 105 SKEEKKAIKEEKEKLEEPYGYCLVDGHKEKVGNFRIEPPGLFRGRGEHPKMGKLKRRIMPEDITINIGKDAPVPEPPAGH 184 (215)
T ss_pred CHHHHHHHHHHHHhhhccCCEEEECCEEEeeCCcccCCCcccccCCCCCCCCccccccChhhEEEecCCCCCCCccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeeCCceeEEeeccCCcCCceeEEEec
Q psy17743 161 KWKEVRHDNQVTWLASWTENVQGQVKYIMLN 191 (618)
Q Consensus 161 aWkdV~hdntvtWla~w~~hIqGr~QYvylh 191 (618)
+|++|+|||||||||+|.++|||+.|||||+
T Consensus 185 ~WkeV~HDntVtWLA~W~enIn~~~KYV~La 215 (215)
T cd00660 185 KWKEVRHDNTVTWLASWKENINGQFKYVMLA 215 (215)
T ss_pred CcceeecCCCceEEEEeEeccCCceeEEEeC
Confidence 9999999999999999999999999999985
No 4
>cd03488 Topoisomer_IB_N_htopoI_like Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.
Probab=100.00 E-value=9e-90 Score=670.80 Aligned_cols=191 Identities=68% Similarity=1.186 Sum_probs=189.2
Q ss_pred CccCCeecCCChhhHHHHHHHHHHhCCCCCCchhHhhhhHHHHHHHcccccccccccccCCCcHHHHHHHHhhHHHHHcC
Q psy17743 1 MEAGGKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFRKMHAYFVQKSEERKAM 80 (618)
Q Consensus 1 ~~ydg~~v~L~~~~EEvA~f~a~~l~~~~~~~~~F~~NFf~d~~~~l~~~~~~~i~~~~kcDF~~i~~~~~~~~e~kk~~ 80 (618)
|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|+.++++.|++|++||||+||+||++++|+||+|
T Consensus 25 ~~YdG~pv~L~peaEEvAtf~a~ml~t~y~~~~~F~kNFf~Df~~~l~~~~~~~I~~f~kcDF~~i~~~~~~~~e~kK~~ 104 (215)
T cd03488 25 FYYDGKPVKLSPEAEEVATFYAKMLEHDYATKEIFQKNFFKDFKKVMTKEEKVIIKDFSKCDFTQMFAYFKAQKEEKKAM 104 (215)
T ss_pred EEECCEECcCCHHHHHHHHHHHHHcCCccccChHHHHHHHHHHHHHhccccCccccchhhCCCHHHHHHHHHHHHHHHcC
Confidence 68999999999999999999999999999999999999999999999999899999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHhccccEEEEcCeeeeecccccCCCcccccCCCCCCCCCCCCCCCccchhhhccCCCCCCCCCCCC
Q psy17743 81 SKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGH 160 (618)
Q Consensus 81 t~eEK~~~k~~~~~~~~~y~~~~~DG~~ekvgnfrvepPGlfRgRG~hpk~G~~k~RI~pedv~iN~~k~a~IPpp~~Gh 160 (618)
|+|||+++|+++++++++||||+|||++|+||||||||||||||||+|||||+||+||+|||||||||++|+||+|||||
T Consensus 105 tkeEKk~~K~ek~~~e~~Y~~~~vDG~kekVgNfrvEPPgLFrGRG~HPK~G~lK~Rv~PedVtINigkda~vP~pp~Gh 184 (215)
T cd03488 105 SKEEKKAIKAEKEKLEEEYGFCILDGHKEKVGNFRIEPPGLFRGRGAHPKTGKLKRRIMPEDIIINIGKDAKVPEPPPGH 184 (215)
T ss_pred CHHHHHHHHHHHHhhhccCCEEEECCEEEeeCCcccCCCccccCCCCCCCCCccccccChhhEEEecCCCCCCCccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeeCCceeEEeeccCCcCCceeEEEec
Q psy17743 161 KWKEVRHDNQVTWLASWTENVQGQVKYIMLN 191 (618)
Q Consensus 161 aWkdV~hdntvtWla~w~~hIqGr~QYvylh 191 (618)
+|++|+|||||||||+|.++|+|+.|||||+
T Consensus 185 ~WkeV~HDntVtWLA~W~enIn~~~KYV~La 215 (215)
T cd03488 185 KWKEVRHDNTVTWLASWTENINGSIKYVMLN 215 (215)
T ss_pred CcceeecCCCceEEEEeEeccCCceeEEEeC
Confidence 9999999999999999999999999999985
No 5
>cd03489 Topoisomer_IB_N_LdtopoI_like Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human
Probab=100.00 E-value=6.4e-89 Score=663.70 Aligned_cols=190 Identities=47% Similarity=0.914 Sum_probs=186.2
Q ss_pred CccCCeecCCChhhHHHHHHHHHHhCCCCCCchhHhhhhHHHHHHHcccccccccccccCCCcHHHHHHHHhhHHHHHcC
Q psy17743 1 MEAGGKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFRKMHAYFVQKSEERKAM 80 (618)
Q Consensus 1 ~~ydg~~v~L~~~~EEvA~f~a~~l~~~~~~~~~F~~NFf~d~~~~l~~~~~~~i~~~~kcDF~~i~~~~~~~~e~kk~~ 80 (618)
|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|+.. .+.|++|++||||+||+||++++|+||+|
T Consensus 23 ~~YdG~pv~L~pe~EEvAtf~a~ml~t~y~~~~~F~kNFf~df~~~l~~~-~~~I~~f~kcDF~~i~~~~~~~~e~kK~~ 101 (212)
T cd03489 23 ILYNGQPFDMTPEEEEVATMFAVMKEHDYYRKEVFRRNFFESWREILDKR-HHPIRKLELCDFTPIYEWHLREKEKKKSR 101 (212)
T ss_pred EeECCeECcCCHHHHHHHHHHHHHcCCccccchHHHHHHHHHHHHHhccc-CccccchhhCCCHHHHHHHHHHHHHHHhC
Confidence 68999999999999999999999999999999999999999999999765 34999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHhccccEEEEcCeeeeecccccCCCcccccCCCCCCCCCCCCCCCccchhhhccCCCCCCCCCCCC
Q psy17743 81 SKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGH 160 (618)
Q Consensus 81 t~eEK~~~k~~~~~~~~~y~~~~~DG~~ekvgnfrvepPGlfRgRG~hpk~G~~k~RI~pedv~iN~~k~a~IPpp~~Gh 160 (618)
|+|||+++|+++++++++||||+|||++|+||||||||||||||||+|||||+||+||+|||||||||++|+||+|||||
T Consensus 102 tkeEKk~~K~ek~~~e~~Y~~~~vDG~kekVgNFrvEPPgLFrGRG~HPK~G~lK~Rv~PedVtINigkda~vP~pp~Gh 181 (212)
T cd03489 102 TKEEKKALKEEKDKEAEPYMWCVWDGVKEQVANFRVEPPGLFRGRGEHPKMGKLKKRIQPEDITINIGKGAPIPECPAGH 181 (212)
T ss_pred CHHHHHHHHHHHHHhhccCCEEEECCEEEeeCCcccCCCcccccCCCCCCCcccccccChhheEEecCCCCCCCccCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeeCCceeEEeeccCCcCCceeEEEec
Q psy17743 161 KWKEVRHDNQVTWLASWTENVQGQVKYIMLN 191 (618)
Q Consensus 161 aWkdV~hdntvtWla~w~~hIqGr~QYvylh 191 (618)
+|++|+|||||||||+|.++|+|+.|||||+
T Consensus 182 ~WkeV~HDntVtWLA~W~enIn~~~KYV~La 212 (212)
T cd03489 182 KWKEVKHDNTVTWLAMWRDPIAGNFKYVMLA 212 (212)
T ss_pred CcceeecCCCceEEEEeEeccCCceeEEEeC
Confidence 9999999999999999999999999999985
No 6
>cd03490 Topoisomer_IB_N_1 Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB. Topo IB proteins include the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanoso
Probab=100.00 E-value=4.3e-88 Score=659.74 Aligned_cols=191 Identities=39% Similarity=0.675 Sum_probs=187.3
Q ss_pred CccCCeecCCChhhHHHHHHHHHHhCCCCCCchhHhhhhHHHHHHHccccc-ccccccccCCCcHHHHHHHHhhHHHHHc
Q psy17743 1 MEAGGKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKE-RAVITDLSKCDFRKMHAYFVQKSEERKA 79 (618)
Q Consensus 1 ~~ydg~~v~L~~~~EEvA~f~a~~l~~~~~~~~~F~~NFf~d~~~~l~~~~-~~~i~~~~kcDF~~i~~~~~~~~e~kk~ 79 (618)
|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|+.++ ++.|++|++||||+||+||++++|+||+
T Consensus 23 ~~YdG~pv~L~peaEEvAtf~a~ml~t~y~~~~~F~kNFf~df~~~l~~~~~~~~i~~f~kcDF~~i~~~~~~~ke~kK~ 102 (217)
T cd03490 23 IMYKGETIHLPPNLEEIATYWAQSMGTNYETKEKFCKNFWKVFVNSFEKDHKFIRRCKLSDADFSLIKNHLEEEKEKKKN 102 (217)
T ss_pred EeECCeECcCCHHHHHHHHHHHHHhCCccccchHHHHHHHHHHHHHhccccCcccccchhhCCCHHHHHHHHHHHHHHHh
Confidence 689999999999999999999999999999999999999999999998877 7789999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHhccccEEEEcCeeeeecccccCCCcccccCCCCCCCCCCCCCCCccchhhhccCCCCCCCCC--
Q psy17743 80 MSKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPP-- 157 (618)
Q Consensus 80 ~t~eEK~~~k~~~~~~~~~y~~~~~DG~~ekvgnfrvepPGlfRgRG~hpk~G~~k~RI~pedv~iN~~k~a~IPpp~-- 157 (618)
||+|||+++|+++++++++||||+|||++|+||||||||||||||||+|||||+||+||+|||||||||++|+||+||
T Consensus 103 ~tkeEKk~~K~ek~~~e~~Y~~~~vDG~kekVgNfriEPPgLFrGRG~HPK~G~lK~RV~PedVtINigkda~vP~~p~~ 182 (217)
T cd03490 103 LNKEEKEAKKKERAKREYPFNYALVDWIREKVSSNKLEPPGLFKGRGEHPKQGLLKSRIFPEDVILNISKDAPVPKVTNF 182 (217)
T ss_pred cCHHHHHHHHHHHHHhhccCCEEEECCEEEeeCCcccCCCcccccCCCCCCCCccccccChhheEEecCCCCCCCcCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred -CCCCcceeeeCCceeEEeeccCCcCCceeEEEec
Q psy17743 158 -PGHKWKEVRHDNQVTWLASWTENVQGQVKYIMLN 191 (618)
Q Consensus 158 -~GhaWkdV~hdntvtWla~w~~hIqGr~QYvylh 191 (618)
|||+|++|+|||||||||+|.++|||+.|||||+
T Consensus 183 ~~GH~WkeV~HDntVtWLA~W~enIn~~~KYV~Ls 217 (217)
T cd03490 183 MEGHSWKDIYHDNSVTWLAYYKDSINDQFKYMFLS 217 (217)
T ss_pred CCCCccceeecCCCceEEEEeecCCCCceeEEEeC
Confidence 9999999999999999999999999999999974
No 7
>PF02919 Topoisom_I_N: Eukaryotic DNA topoisomerase I, DNA binding fragment; InterPro: IPR008336 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the N-terminal DNA-binding domain found in eukaryotic topoisomerase I, which is a type IB enzymes. To cleave the DNA backbone, these enzymes must make a transient phosphotyrosine bond. The N-terminal domain of human topoisomerase I is thought to coordinate the restriction of free strand rotation during the topoisomerisation step of catalysis. A conserved tryptophan residue may be important for the DNA-interaction ability of the N-terminal domain []. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1TL8_A 1K4T_A 1A36_A 1RR8_C 1T8I_A 1SC7_A 1EJ9_A 1LPQ_A 1RRJ_A 1A31_A ....
Probab=100.00 E-value=1.9e-88 Score=663.83 Aligned_cols=190 Identities=61% Similarity=1.103 Sum_probs=156.3
Q ss_pred CccCCeecCCChhhHHHHHHHHHHhCCCCCCchhHhhhhHHHHHHHcccccccccccccCCCcHHHHHHHHhhHHHHHcC
Q psy17743 1 MEAGGKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFRKMHAYFVQKSEERKAM 80 (618)
Q Consensus 1 ~~ydg~~v~L~~~~EEvA~f~a~~l~~~~~~~~~F~~NFf~d~~~~l~~~~~~~i~~~~kcDF~~i~~~~~~~~e~kk~~ 80 (618)
|+|||+||+|||+|||||||||+||+|+|+++++||+|||+||+++|+++++..|++|++||||+||+||++++|+||+|
T Consensus 26 ~~YdGkpv~L~p~~EEvAtf~a~ml~t~y~~~~~F~~NFf~Df~~~l~~~~~~~i~~~~kcDF~~i~~~~~~~~e~kk~~ 105 (215)
T PF02919_consen 26 FYYDGKPVKLSPEAEEVATFYAKMLDTDYATKPVFNKNFFKDFRKVLTKEERKKIKDFDKCDFSPIYEYFEKEKEKKKNM 105 (215)
T ss_dssp EEETTEEE---HHHHHHHHHHHTTTTSGGGGSHHHHHHHHHHHHHHHCHCCHHH-S-GGGEETHHHHHHHHHHHHHHCTS
T ss_pred EEECCEEeecCHHHHHHHHHHHhhcCCcccccHHHHHHHHHHHHHHhhhccCcccCchhhCCCHHHHHHHHHHHHHHHhc
Confidence 68999999999999999999999999999999999999999999999999888999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHhccccEEEEcCeeeeecccccCCCcccccCCCCCCCCCCCCCCCccchhhhccCCCCCCCCCCCC
Q psy17743 81 SKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGH 160 (618)
Q Consensus 81 t~eEK~~~k~~~~~~~~~y~~~~~DG~~ekvgnfrvepPGlfRgRG~hpk~G~~k~RI~pedv~iN~~k~a~IPpp~~Gh 160 (618)
|+|||+++|+++++++++||||+|||++|+||||||||||||||||+|||||+||+||+|||||||||++|+||+|||||
T Consensus 106 skeEK~~~K~~k~~~~~~y~~~~vDG~~ekVGNfrvEPPGLFrGRG~HPK~G~lK~Ri~PedVtIN~~k~a~vP~pp~Gh 185 (215)
T PF02919_consen 106 SKEEKKALKEEKEELEEKYGYCLVDGRKEKVGNFRVEPPGLFRGRGEHPKMGMLKKRIYPEDVTINIGKDAPVPEPPPGH 185 (215)
T ss_dssp -CCHHHHHHHHHHHHHHHHSEEEETTEEEEBSS-B---SEE---SSS-TTTT-EE----GGGEEEE--TTS-----STT-
T ss_pred CHHHHHHHHHHHHHHHhhCcEEEECCcccccCceecCCCeeeecCCCCCCccccccccChhhEEEeCCCCCCCCcccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcceeeeCCceeEEeeccCCcCCceeEEEe
Q psy17743 161 KWKEVRHDNQVTWLASWTENVQGQVKYIML 190 (618)
Q Consensus 161 aWkdV~hdntvtWla~w~~hIqGr~QYvyl 190 (618)
+|++|+|||||||||+|.++|+|+.|||||
T Consensus 186 ~Wk~V~HDntvtWLA~W~enI~~~~KYV~L 215 (215)
T PF02919_consen 186 KWKEVVHDNTVTWLASWTENINGQFKYVML 215 (215)
T ss_dssp --SEEE--TTSS-SEEEEETTTTEEEEEEB
T ss_pred CcceeEeCCCceEEEEeEeccCCceeEEeC
Confidence 999999999999999999999999999996
No 8
>PHA03101 DNA topoisomerase type I; Provisional
Probab=100.00 E-value=2.6e-64 Score=519.11 Aligned_cols=242 Identities=19% Similarity=0.273 Sum_probs=225.4
Q ss_pred CCCCCCccchhhhccCCCCCCCCCCCCCcceeeeCCceeEEeec----cC-CcC-------CceeEEEecCCCccccccc
Q psy17743 134 LKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTWLASW----TE-NVQ-------GQVKYIMLNPSSKLKGEKD 201 (618)
Q Consensus 134 ~k~RI~pedv~iN~~k~a~IPpp~~GhaWkdV~hdntvtWla~w----~~-hIq-------Gr~QYvylh~~S~~k~~rD 201 (618)
..++|.+++-++.+++.++||| ||++| ||||+ ++ ||| ||+||+| || .|...||
T Consensus 17 ~~~~~~~~~~~~~RI~~LaIPP-----Aw~dV-------wI~p~~~e~~~~hlQAtG~Da~GRKQYrY-H~--~W~~~R~ 81 (314)
T PHA03101 17 FTNPVSDDNPTYEILKKVKIPP-----HLTDV-------VVYEQTYEEALTGLIFVGSDSKGRKQYFY-GK--LHVKNRN 81 (314)
T ss_pred hCCCCCCccHHHHHHHHcCCCC-----CcceE-------EEeeccccCCCCceEEEeecCCCCeeeee-CH--HHHHHHH
Confidence 4678888888999999999999 99999 99997 55 999 9999999 99 9999999
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhccccc-chhHHHHHHHHHhhh-ccccCCcccccccCccccccccccceEeecccC
Q psy17743 202 WQKYETARKLAKSINKIRENYQADWKSKEM-RIRQRAVALYFIDKL-ALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKD 279 (618)
Q Consensus 202 ~~Kfe~ar~l~~~Lp~IR~~y~~dL~s~~~-~~RqlA~AlyLID~l-aLRvGnEkya~endTvG~cTLR~eHV~l~~~~d 279 (618)
..||+++.+|+++||+||++|.+||+.+++ +++++|+++.|||.+ +||||||+|+++|+||||||||++||++++
T Consensus 82 ~~Kf~r~~~f~~~LP~iR~~v~~dL~~~~~~~~kvlAavv~LLd~~~~iRvGne~Ya~~N~SyGltTLr~rHv~v~g--- 158 (314)
T PHA03101 82 ANRDKIFVRVHNVIKKINCFIDKNIKIKKKNDVNFQLAVFLLMETSFFIRTGKMKYLKENETVGLLTLKNKHITISN--- 158 (314)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhccceecCCHhHHHhcCCccccccchhceEEEC---
Confidence 999999999999999999999999998888 899999999999999 799999999999999999999999999998
Q ss_pred CCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhccCCCccccccCChhHHHHHHHHhcCCCeeeeeccccchHHHH
Q psy17743 280 GKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITLQ 359 (618)
Q Consensus 280 ~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~K~Pgd~LF~~l~s~~LN~yLkelm~glTAKvFRTynASvt~~ 359 (618)
+.|+|+|+||||+++..+|..|++|+++|+.|++.+.||++||+|+++++||+||++. ||||||||||+||++++
T Consensus 159 ---~~i~f~F~GKsG~~~~~~i~dD~rL~~~v~~l~~~~~Pg~~LF~y~d~~~VN~Ylre~--~fTAKDFRTW~gTv~a~ 233 (314)
T PHA03101 159 ---DKILIKFVGKDKVSHEFVVHKSNRLYKPLLKLIDKTNPDDFLFNKLSERKVYKFMKQF--GIRLKDLRTYGVNYTFL 233 (314)
T ss_pred ---CEEEEEEECCCCcEEEEEecccHHHHHHHHHHHcCCCChHHHhhcCCHHHHHHHHHhC--CCcceeecCchHHHHHH
Confidence 8999999999999999999966999999999999888999999999999999999995 89999999999999999
Q ss_pred HHHhh-cCCCCccHHHHHHHHHHHHHHHHHHcCCCCCCCCc
Q psy17743 360 QQLNE-LMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKS 399 (618)
Q Consensus 360 ~~L~~-~~~~~~s~~ek~~~yn~Anr~VAilcNHqraV~K~ 399 (618)
..|.. +.. ..+..+.++.++.|+++||+.|||||||||+
T Consensus 234 ~~l~~~~~~-~~~~~~~kk~i~~~i~~vA~~LGNTPaV~R~ 273 (314)
T PHA03101 234 YNFWTNVKS-LDPLPSIKKLISLSIKQTAEIVGHTPSISKS 273 (314)
T ss_pred HHHHhhccc-cCChhHHHHHHHHHHHHHHHHhCCCHhhHHh
Confidence 99854 222 2334556678999999999999999999997
No 9
>PF01028 Topoisom_I: Eukaryotic DNA topoisomerase I, catalytic core; InterPro: IPR013500 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the catalytic core of eukaryotic and viral topoisomerase I (type IB) enzymes, which occurs near the C-terminal region of the protein. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity []. The crystal structures of human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes []. Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin. The crystal structure of an amino-terminal fragment of vaccinia virus DNA topoisomerase I shows that the fragment forms a five-stranded, antiparallel beta-sheet with two short alpha-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2F4Q_A 3M4A_A 3IGC_A 2H7G_X 2H7F_X 1A41_A 1VCC_A 1TL8_A 1K4T_A 1A36_A ....
Probab=100.00 E-value=2.6e-64 Score=504.51 Aligned_cols=230 Identities=35% Similarity=0.478 Sum_probs=208.9
Q ss_pred CCccccccchHHHHHHHHHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHhhhccccCCcccccccC-ccccccccccc
Q psy17743 193 SSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFIDKLALRAGNEKDEDQAD-TVGCCSLRVEH 271 (618)
Q Consensus 193 ~S~~k~~rD~~Kfe~ar~l~~~Lp~IR~~y~~dL~s~~~~~RqlA~AlyLID~laLRvGnEkya~end-TvG~cTLR~eH 271 (618)
+|+|++++|..||+++++|+++||+||++|.+||++..++++|+|+|+||||.++||||||+|+++|+ ||||||||++|
T Consensus 2 Ds~gRkQrd~~Kf~r~~~f~~~Lp~iR~~v~~dL~~~~~~~r~lA~a~~LlD~~~lRvGne~Y~~~n~ds~GltTLr~~H 81 (234)
T PF01028_consen 2 DSKGRKQRDEEKFDRARRFARALPKIRRRVRKDLRSGLPRERVLAVAVRLLDRTALRVGNEKYAEENGDSYGLTTLRVKH 81 (234)
T ss_dssp TTCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTCHHHHHHHHHHHHHHH------HHHHCCHHSHHHCCT-BGGG
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcchhHHHHHHHHHHhhheecCCcccccccCCCeeeCcCcHHH
Confidence 68999999999999999999999999999999997777799999999999999999999999999977 99999999999
Q ss_pred eEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhccCCCccccccCChhHHHHHHHHhcCCCeeeeecc
Q psy17743 272 IQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRT 351 (618)
Q Consensus 272 V~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~K~Pgd~LF~~l~s~~LN~yLkelm~glTAKvFRT 351 (618)
|++.+ ++.|+|+|+||||++|+.+|.||++|+++|+.|++++.||++||..|+|++||+||+++|+|||||||||
T Consensus 82 v~~~~-----~~~i~f~F~GK~g~~~~~~v~~d~~l~~~l~~~~~~~~pg~~LF~~v~s~~vN~yL~~~~~~~TaKdFRT 156 (234)
T PF01028_consen 82 VKLSG-----DNVIRFDFPGKSGVRQEITVRVDPRLAKNLKRLLRRKLPGDRLFHPVTSTDVNAYLREIMEDFTAKDFRT 156 (234)
T ss_dssp EEEET-----TCEEEEEEEEGGGEEEEEEEETTHHHHHHHHHHHTTTSTTSBTTTT--HHHHHHHHHHCTTTS-HHHHHH
T ss_pred eeecC-----CcEEEEEeeCCCCeEEEEEEecCHHHHHHHHHHHhCCCChhhccCCCCHHHHHHHHHHhcCCCceeeeee
Confidence 99999 3599999999999999999999999999999999889999999999999999999999998899999999
Q ss_pred ccchHHHHHHHhhcC--CCCccHHHHHHHHHHHHHHHHHHcCCCCCCCCchHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17743 352 YNASITLQQQLNELM--DPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAERALKD 427 (618)
Q Consensus 352 ynASvt~~~~L~~~~--~~~~s~~ek~~~yn~Anr~VAilcNHqraV~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~ 427 (618)
||||++|+++|.+.+ .+..+..+++++|+.||++||++|||||+|||+|.-.+..++..+++.++++++++++|++
T Consensus 157 w~at~~a~~~L~~~~~~~~~~~~~~~~~~~~~a~~~VA~~LgnTpaV~r~sYi~p~v~~~~~~~~~~~~~~~~~~~~~ 234 (234)
T PF01028_consen 157 WNATVLAAEALAKAPRVPPPESEKERKKAYNAAVKEVAELLGNTPAVCRKSYIHPRVLDLYIKELKEQIKELKKQLKE 234 (234)
T ss_dssp HHHHHHHHHHHHHHH--HHSSSHHHHHHHHHHHHHHHHHHHTSEHHHHHHHTSHHHHHHHTTSHHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHccCCCCCCCHHHHHHHHHHHHHHHHHHhCCCccccchhhhCHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999875 2346788899999999999999999999999999999999999999999999999998874
No 10
>cd00659 Topo_IB_C DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses and bacterial versions of Topo IB. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases.
Probab=100.00 E-value=2.7e-57 Score=449.83 Aligned_cols=198 Identities=56% Similarity=0.767 Sum_probs=188.3
Q ss_pred ccccccchHHHHHHHHHHHHHHHHHHHHHHhhccccc-chhHHHHHHHHHhhhccccCCcccccccCccccccccccceE
Q psy17743 195 KLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEM-RIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQ 273 (618)
Q Consensus 195 ~~k~~rD~~Kfe~ar~l~~~Lp~IR~~y~~dL~s~~~-~~RqlA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~ 273 (618)
+|+..++..||+++.+|+.+||+||++|.+||+++++ +++|+|+|+||||.++||||||+|+++|+||||||||++||+
T Consensus 1 ~w~~~r~~~K~~~~~~f~~~Lp~iR~~v~~dl~~~~~~~~~vlA~~~~Lld~~~iRvGne~Ya~~n~s~GltTLr~~Hv~ 80 (218)
T cd00659 1 DWKKYRKARKLKRLLAFGRALPKIRRRYTKDLKSKGMPRERQLATAVYLIDKFALRVGNEKYERENDTVGLCTLRKEHVT 80 (218)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchHhHHHHHHHHHHHhcccCCChhhhhcCCCEeecccchhhee
Confidence 5999999999999999999999999999999999999 999999999999999999999999999999999999999999
Q ss_pred eecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhccCCCccccc-----cCChhHHHHHHHHhcCCCeeee
Q psy17743 274 LHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVENKKGSDDLFD-----RLNTSVLNKHLSELMEGLTAKV 348 (618)
Q Consensus 274 l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~K~Pgd~LF~-----~l~s~~LN~yLkelm~glTAKv 348 (618)
+.+ +.|+|+|+||||++++.+|..|++|+++|+.|++ +.||++||+ .|+|++||+||+++|+||||||
T Consensus 81 ~~~------~~i~f~F~GK~g~~~~~~v~d~~~l~~~l~~~~~-k~pg~~LF~y~~~~~v~s~~vN~yl~e~~~~~TaKd 153 (218)
T cd00659 81 LKP------NVVRFDFLGKDSIRYENEVEVEPRLFKNLRKFLD-KLPGDDLFQYLQVDRLNSSKLNAYLREFMEGLTAKV 153 (218)
T ss_pred EeC------CEEEEEEECCCCcEEEEEECChHHHHHHHHHHHH-cCCcHHhhccCCCCcCCHHHHHHHHHHHhCCCChhh
Confidence 998 8999999999999999999933999999999998 799999995 4999999999999998899999
Q ss_pred eccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHHHHHHHcCCCCCCCCch
Q psy17743 349 FRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQRSVPKSH 400 (618)
Q Consensus 349 FRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr~VAilcNHqraV~K~~ 400 (618)
||||+||++++..|.+.++ ..+..++++.|+.|+++||++|||||+||++.
T Consensus 154 FRTw~at~~a~~~L~~~~~-~~~~~~~~~~i~~a~~~vA~~LgnTpav~r~s 204 (218)
T cd00659 154 FRTYNASLTALEQLARLPA-SLSLAEKKKAYNDANREVAILLNHTPAISKIN 204 (218)
T ss_pred cccchhHHHHHHHHHhcCC-CCCHHHHHHHHHHHHHHHHHHhCCCcchhHHH
Confidence 9999999999999987755 45788889999999999999999999999963
No 11
>KOG0981|consensus
Probab=100.00 E-value=5.6e-49 Score=423.41 Aligned_cols=301 Identities=37% Similarity=0.515 Sum_probs=187.2
Q ss_pred ccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhccCCCccccccCChhHHHHHH
Q psy17743 258 QADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVENKKGSDDLFDRLNTSVLNKHL 337 (618)
Q Consensus 258 endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~K~Pgd~LF~~l~s~~LN~yL 337 (618)
..|++--+||.-.-+-+.||-.--|..|.|-|-||- ...++. -..|+.-...+.+..----++|. -.=.|+|+
T Consensus 206 ~d~~~KW~tLeH~G~iFaPPYeplP~~Vk~~YdGkp---v~L~~e-aEEvAtfyA~mle~ey~tk~vF~---~NFf~Dwr 278 (759)
T KOG0981|consen 206 GDDGVKWTTLEHNGPIFAPPYEPLPSGVKFYYDGKP---VDLTPE-AEEVATFYAAMLEHEYATKEVFR---KNFFNDWR 278 (759)
T ss_pred CCCccceeeeeecCcccCCCCcCCCCCceEEeCCcc---ccCCHH-HHHHHHHHHHHHhcchhccHHHH---HHHHHHHH
Confidence 368888899988888888866556788999998874 222222 23454444444442222234444 34578888
Q ss_pred HHhc--CCCeeeeeccccchHHHHHHHhhcC-CCCccHHHHHHHHHHHHHHHH-----HHcCCCCCCCCchHHhHHHHHH
Q psy17743 338 SELM--EGLTAKVFRTYNASITLQQQLNELM-DPDFSEAEKILAYNRANRAVA-----VLCNHQRSVPKSHDKSMGNLKE 409 (618)
Q Consensus 338 kelm--~glTAKvFRTynASvt~~~~L~~~~-~~~~s~~ek~~~yn~Anr~VA-----ilcNHqraV~K~~~~~m~k~~~ 409 (618)
+.+. ++=-.|+|.-++-|-.+.-...+-. ....|..+|+..=....+..- ++=||+ +
T Consensus 279 k~m~~~~~~~Ik~l~kCDFt~i~~yf~~~~E~rK~mskEEK~~iKeEkek~ee~y~~cilDG~k---------------E 343 (759)
T KOG0981|consen 279 KVMTVEEREVIKDLSKCDFTPIFEYFKEQKEKRKQMSKEEKLKIKEEKEKLEEKYGWCILDGHK---------------E 343 (759)
T ss_pred HHhhhhhhhhhccccccCCHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHcCeEEecCcH---------------h
Confidence 8776 3344899999988876654433210 000111222210000000000 000110 0
Q ss_pred HHHHHHHHHHHHHHHHHHH-hhcCCCcccHHHHHHHHHHHHHHHHHhcccchhhccccc-eeeccCCcCCCCCccchhhh
Q psy17743 410 KISNKRKQVKDAERALKDA-KKAGESKAMTDKKKTALGRLKEQLLKLEVQETDKEENKT-IALGTSKLNYLDPRISVTWL 487 (618)
Q Consensus 410 ki~~~~~~~~~~~~~l~~~-~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~-vaLgTSk~NY~DPRitVtWl 487 (618)
| |...+-|=--+ ++.|.- +..-+ |+.||.--.+-+..-.+.+- -+.--++---+---+|||||
T Consensus 344 k-------igNFriEPPgLFRGRG~H-PKmG~-------lKrRI~Pedi~iN~gkda~iP~pppGhkWkEVrHDNTVTWL 408 (759)
T KOG0981|consen 344 K-------IGNFRIEPPGLFRGRGEH-PKMGK-------LKRRIMPEDITINCGKDAPIPEPPPGHKWKEVRHDNTVTWL 408 (759)
T ss_pred h-------hcccccCCCccccCCCCC-Ccccc-------hhcccchhheEEecCCCCCCCCCCCCCcccccccCCeeeee
Confidence 0 00000000000 111110 11112 22233222211111100000 01111111222235899999
Q ss_pred heeeccCCCceEEEEEcCCCcccCccchHhHHHHHHHhHHHHHHHHHHHhcccchhhhhhhheeeeeeeeehhhccCCCC
Q psy17743 488 ASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFIDKLALRAGNEK 567 (618)
Q Consensus 488 kkw~vpI~~~~Kyv~l~~~s~~k~~~d~~kye~ar~Lk~~i~~Ir~~y~~~~~s~~~~~rq~a~a~y~Id~lAlr~g~ek 567 (618)
+.|.+||+|++|||||||||+|||++||+|||+||+|++||+.||.+|++||+|++|.+|||||||||||+|||||||||
T Consensus 409 a~W~e~i~~~~KYi~L~~~SslKGesD~~KyE~ARrLk~~Id~IR~~Y~~d~ksk~m~~RQravAlY~IDklALRAGnEK 488 (759)
T KOG0981|consen 409 ASWTENINGSFKYIMLNPSSSLKGESDKEKYETARRLKKYIDKIRATYTKDFKSKEMKVRQRAVALYFIDKLALRAGNEK 488 (759)
T ss_pred eecccccCCceeEEEecCcccccCchhHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCceeeeeceeeeceeecccchhhH
Q psy17743 568 DEDQADTVGCCSLRVEHIQLHEEKDEKK 595 (618)
Q Consensus 568 ~~deadtvgccsLrvehi~l~~~~~~~~ 595 (618)
++||||||||||||||||+|+|++.+++
T Consensus 489 dedeADTVGCCsLrvehV~l~p~~~~~e 516 (759)
T KOG0981|consen 489 DEDEADTVGCCSLRVEHVTLHPPNKGKE 516 (759)
T ss_pred cccccccccceeeeeeeeEeeCcccccc
Confidence 9999999999999999999999998843
No 12
>COG3569 Topoisomerase IB [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.5e-46 Score=385.86 Aligned_cols=300 Identities=27% Similarity=0.301 Sum_probs=283.8
Q ss_pred ccCCeecCCChhhHHHHHHHHHHhCCCCCCchhHhhhhHHHHHHHcccc--cccccccccCCCcHHHHHHHHhhHHHHHc
Q psy17743 2 EAGGKEMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEK--ERAVITDLSKCDFRKMHAYFVQKSEERKA 79 (618)
Q Consensus 2 ~ydg~~v~L~~~~EEvA~f~a~~l~~~~~~~~~F~~NFf~d~~~~l~~~--~~~~i~~~~kcDF~~i~~~~~~~~e~kk~ 79 (618)
+|+|+||.|+|+.||| |+.|++++|.|++.| .|||.++-...+.- .+..||-|.+|||+.+..+|....++++.
T Consensus 52 ~~ri~~l~lPPay~dV---wi~ld~~gHlqatg~-DargRkqyryhpew~~~r~~~K~~~l~~F~kalp~lrr~~~~~~~ 127 (354)
T COG3569 52 LRRIAALALPPAYEDV---WICLDENGHLQATGR-DARGRKQYRYHPEWAALRDGIKYFSLVRFGKALPSLRRTIDADLR 127 (354)
T ss_pred HhcccccCCCcchhhh---eeecCccccccccch-hhhhhhhheeCchhhhcccchhHHHHHHHHHHhHHHHHHHHHhhc
Confidence 6899999999999999 999999999999999 99999998887642 24569999999999999999999999999
Q ss_pred CCHHHHHHHHHHHHHHhccccEEEEcCeeeeecccccCCCcccccCCCCCCCCCCCCCCCccchhhhccCCCCCCCCCCC
Q psy17743 80 MSKEEKKKIKDENEAITKEYGVCTIDGHKEKIGNFRIEPPGLFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPG 159 (618)
Q Consensus 80 ~t~eEK~~~k~~~~~~~~~y~~~~~DG~~ekvgnfrvepPGlfRgRG~hpk~G~~k~RI~pedv~iN~~k~a~IPpp~~G 159 (618)
++.++++++..+ .+|++||.+++|||| ++|||+|-||++|.+|++|.|++++||++...++ |
T Consensus 128 ~~~~~~~~v~a~--------~~~lLD~~~~rVGN~-----~y~r~ngsyg~TtllkRhV~~~~~ti~~~f~gk~-----G 189 (354)
T COG3569 128 LPGLPKEKVVAA--------KVCLLDGARIRVGNF-----AYARDNGSYGLTTLLKRHVDVEGSTIRFRFKGKS-----G 189 (354)
T ss_pred CCCccHHHHHHH--------HHHHhhhhHhhcccH-----HHhhccCCcCcccceeeeeccCCCEEEEEecCCc-----c
Confidence 999999999888 799999999999999 9999999999999999999999999999998755 9
Q ss_pred CCcceeeeCCceeEEeeccCCcCCceeEEEecCCCccccccchHHHHHHHHHHHHHHHHHHHHHHhhcccccchhHHHHH
Q psy17743 160 HKWKEVRHDNQVTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVA 239 (618)
Q Consensus 160 haWkdV~hdntvtWla~w~~hIqGr~QYvylh~~S~~k~~rD~~Kfe~ar~l~~~Lp~IR~~y~~dL~s~~~~~RqlA~A 239 (618)
|.|+++ .+|+.|++ .+++..|.- .+.|...|+.++..++.|+++..+-.||.+++
T Consensus 190 ~~~~~~-------------------l~~~rLaa--~L~~~~DLp----gr~Lf~y~D~~~~~~r~~s~~ln~ylr~~~g~ 244 (354)
T COG3569 190 KEWKER-------------------LKDPRLAA--ILRGQLDLP----GRKLFQYLDEDGRERRIDSKSLNAYLRQVTGA 244 (354)
T ss_pred hhhhhh-------------------hhhHHHHH--HHHHhhcCc----hHHHHHhhcccCCcccCCchhHHHHHHHhccc
Confidence 999999 78999999 999999987 99999999999999999999999999999999
Q ss_pred HHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhh-hcc
Q psy17743 240 LYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFV-ENK 318 (618)
Q Consensus 240 lyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~-~~K 318 (618)
.|++|.+++|.|+++-+++++|+||||++.+|+++.+ ...+.|+|++++++++| |+|+||++...++ ..+
T Consensus 245 ~~sak~Frtw~Gt~~a~~~a~t~g~~s~~~~~v~~~~-----~~A~~Lgnt~aisRr~Y----IhPqVf~~~~~~K~~~~ 315 (354)
T COG3569 245 PFSAKDFRTWGGTLLAEEEADTVGCCSEAPELVSLVA-----AVAAVLGNTPAISRRCY----IHPQVFDNYLIGKRLPK 315 (354)
T ss_pred ceehhHHHhccCchHHHHHHhhhcchhcchhhhhhcc-----chhhhccCCccccccce----ecHHHHhhhhhcccCcc
Confidence 9999999999999999999999999999999999988 48999999999999998 6999999999998 568
Q ss_pred CCCccccccCChhHHHHHHHHhcCCCeeeeeccccchHHH
Q psy17743 319 KGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASITL 358 (618)
Q Consensus 319 ~Pgd~LF~~l~s~~LN~yLkelm~glTAKvFRTynASvt~ 358 (618)
.+|+.+|++.... ||++++.+|.+|++|+|||||||.|+
T Consensus 316 ~~g~~lr~r~~~~-L~~ee~~Ll~~L~~~~~~~~~~~~t~ 354 (354)
T COG3569 316 KSGRQLRDRARLE-LNKEEQRLLRFLEAKVRRRYRASKTM 354 (354)
T ss_pred cchhHHHhhcccc-ccHHHHHHHhhhchhhhhhhhhhccC
Confidence 9999999999888 99999999999999999999999763
No 13
>COG3569 Topoisomerase IB [DNA replication, recombination, and repair]
Probab=100.00 E-value=7.1e-42 Score=351.49 Aligned_cols=269 Identities=20% Similarity=0.328 Sum_probs=239.5
Q ss_pred ccccEEEEcCeeeeecccccCCCcccc---cCCCCCCCCCCCCCCCccchhhhccCCCCCCCCCCCCCcceeeeCCceeE
Q psy17743 97 KEYGVCTIDGHKEKIGNFRIEPPGLFR---GRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHKWKEVRHDNQVTW 173 (618)
Q Consensus 97 ~~y~~~~~DG~~ekvgnfrvepPGlfR---gRG~hpk~G~~k~RI~pedv~iN~~k~a~IPpp~~GhaWkdV~hdntvtW 173 (618)
|+=|+|.|+- +-||+-| |+||. +.+-.+..+++.+ .|.+++.+.||| +|.|| |
T Consensus 13 e~~~l~yv~d----------~epgirr~~~gkgf~-y~~Pdg~l~sd~~-~~~ri~~l~lPP-----ay~dV-------w 68 (354)
T COG3569 13 EEAGLKYVSD----------EEPGIRREKTGKGFI-YRPPDGPLVSDAK-LLRRIAALALPP-----AYEDV-------W 68 (354)
T ss_pred hhhcceeecc----------cCcchhhhccCCceE-ecCCCCCCCccHH-HHhcccccCCCc-----chhhh-------e
Confidence 3456666665 4578877 66887 5566677888654 678889999999 99999 9
Q ss_pred EeeccC-CcC-------CceeEEEecCCCccccccchHHHHHHHHHHHHHHHHHHHHHHhhccccc-chhHHHHHHHHHh
Q psy17743 174 LASWTE-NVQ-------GQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEM-RIRQRAVALYFID 244 (618)
Q Consensus 174 la~w~~-hIq-------Gr~QYvylh~~S~~k~~rD~~Kfe~ar~l~~~Lp~IR~~y~~dL~s~~~-~~RqlA~AlyLID 244 (618)
||+.++ |+| ||+||+| || .|.+.++..||..+.+|+++||.||+.++.|++..+. .++++|..+.|||
T Consensus 69 i~ld~~gHlqatg~DargRkqyry-hp--ew~~~r~~~K~~~l~~F~kalp~lrr~~~~~~~~~~~~~~~v~a~~~~lLD 145 (354)
T COG3569 69 ICLDENGHLQATGRDARGRKQYRY-HP--EWAALRDGIKYFSLVRFGKALPSLRRTIDADLRLPGLPKEKVVAAKVCLLD 145 (354)
T ss_pred eecCccccccccchhhhhhhhhee-Cc--hhhhcccchhHHHHHHHHHHhHHHHHHHHHhhcCCCccHHHHHHHHHHHhh
Confidence 999999 999 9999999 99 9999999999999999999999999999999999888 7999999999999
Q ss_pred hhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhccCCCccc
Q psy17743 245 KLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVENKKGSDDL 324 (618)
Q Consensus 245 ~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~K~Pgd~L 324 (618)
-..+||||-.|++.|+|||+|||+.+||.+.+ ++|+|.|.||+|++|...+. +++++.+|+.+.+ .||..|
T Consensus 146 ~~~~rVGN~~y~r~ngsyg~TtllkRhV~~~~------~ti~~~f~gk~G~~~~~~l~-~~rLaa~L~~~~D--Lpgr~L 216 (354)
T COG3569 146 GARIRVGNFAYARDNGSYGLTTLLKRHVDVEG------STIRFRFKGKSGKEWKERLK-DPRLAAILRGQLD--LPGRKL 216 (354)
T ss_pred hhHhhcccHHHhhccCCcCcccceeeeeccCC------CEEEEEecCCcchhhhhhhh-hHHHHHHHHHhhc--CchHHH
Confidence 99999999999999999999999999999988 99999999999999999988 9999999999998 999999
Q ss_pred ccc---------CChhHHHHHHHHhcCC-CeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHHHHHHHcCCCC
Q psy17743 325 FDR---------LNTSVLNKHLSELMEG-LTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQR 394 (618)
Q Consensus 325 F~~---------l~s~~LN~yLkelm~g-lTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr~VAilcNHqr 394 (618)
|+| +++.++|.||++..+. +||||||||.||..+.+.+...... .++- ..+.+..+||..++|++
T Consensus 217 f~y~D~~~~~~r~~s~~ln~ylr~~~g~~~sak~Frtw~Gt~~a~~~a~t~g~~----s~~~-~~v~~~~~~A~~Lgnt~ 291 (354)
T COG3569 217 FQYLDEDGRERRIDSKSLNAYLRQVTGAPFSAKDFRTWGGTLLAEEEADTVGCC----SEAP-ELVSLVAAVAAVLGNTP 291 (354)
T ss_pred HHhhcccCCcccCCchhHHHHHHHhcccceehhHHHhccCchHHHHHHhhhcch----hcch-hhhhhccchhhhccCCc
Confidence 998 4799999999999995 9999999999999999998865432 2333 67889999999999999
Q ss_pred CCCCch---HHhHHH
Q psy17743 395 SVPKSH---DKSMGN 406 (618)
Q Consensus 395 aV~K~~---~~~m~k 406 (618)
+||..+ -+..++
T Consensus 292 aisRr~YIhPqVf~~ 306 (354)
T COG3569 292 AISRRCYIHPQVFDN 306 (354)
T ss_pred cccccceecHHHHhh
Confidence 999974 444444
No 14
>smart00435 TOPEUc DNA Topoisomerase I (eukaryota). DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras
Probab=100.00 E-value=1.6e-35 Score=313.07 Aligned_cols=109 Identities=67% Similarity=1.084 Sum_probs=107.2
Q ss_pred ccchhhhheeeccCCCceEEEEEcCCCcccCccchHhHHHHHHHhHHHHHHHHHHHhcccchhhhhhhheeeeeeeeehh
Q psy17743 481 RISVTWLASWTENVQGQVKYIMLNPSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFIDKLA 560 (618)
Q Consensus 481 RitVtWlkkw~vpI~~~~Kyv~l~~~s~~k~~~d~~kye~ar~Lk~~i~~Ir~~y~~~~~s~~~~~rq~a~a~y~Id~lA 560 (618)
.+|||||++|.+||+|++|||||+|||+++|++|+.|||+|++|+.+|+.||++|.+||+|+.|..||+|||+||||++|
T Consensus 48 d~~vtWLa~w~e~i~~~~KYv~l~a~S~wk~~rD~~Kfera~~f~~~Lp~IR~~~~~dL~s~~~r~rqlAvav~LID~~a 127 (391)
T smart00435 48 DNTVTWLASWKENINGSIKYVFLAASSSLKGQSDRKKYEKARKLKKHIDKIRKDYTKDLKSKEMKVRQRATALYLIDKLA 127 (391)
T ss_pred CCCceEEEEeeccCCCceeEEEECCCchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhhHHHHHHHHHHHhc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccCCCCCCCCCceeeeeceeeeceeecc
Q psy17743 561 LRAGNEKDEDQADTVGCCSLRVEHIQLHE 589 (618)
Q Consensus 561 lr~g~ek~~deadtvgccsLrvehi~l~~ 589 (618)
||||||+.++|+|||||||||+|||+|++
T Consensus 128 lRvGnEkYa~en~T~Gl~TLR~eHV~l~~ 156 (391)
T smart00435 128 LRAGNEKGEDEADTVGCCSLRVEHVTLKP 156 (391)
T ss_pred ccCCChhhhhcCCCEeecccchhheEecC
Confidence 99999999999999999999999999975
No 15
>PF14370 Topo_C_assoc: C-terminal topoisomerase domain; PDB: 1TL8_A 1K4T_A 1A36_A 1RR8_C 1T8I_A 1SC7_A 1EJ9_A 1LPQ_A 1RRJ_A 1A31_A ....
Probab=99.83 E-value=1.7e-22 Score=168.94 Aligned_cols=49 Identities=55% Similarity=0.878 Sum_probs=42.8
Q ss_pred HHHHHHHhcccchhhccccceeeccCCcCCCCCccchhhhheeeccCCC
Q psy17743 448 LKEQLLKLEVQETDKEENKTIALGTSKLNYLDPRISVTWLASWTENVQG 496 (618)
Q Consensus 448 ~~~~i~k~~~~~~~ke~nk~vaLgTSk~NY~DPRitVtWlkkw~vpI~~ 496 (618)
+++||+++++|+++||+||+|||||||||||||||||+||++|+|||+.
T Consensus 1 ~~~ri~k~~~~~~~k~~~K~vaLgTSKiNYlDPRItvAWck~~~VPieK 49 (71)
T PF14370_consen 1 IKERIKKLELQLKDKEDNKTVALGTSKINYLDPRITVAWCKRHEVPIEK 49 (71)
T ss_dssp -HHHHHHHHHHHHHHHHTSCE-SHHHHHHTS-HHHHHHHHHHTT--GGG
T ss_pred ChHHHHHHHHHHHHHhhcceeecchhhhhhcCcHHHHHHHHHhCCcHHH
Confidence 4689999999999999999999999999999999999999999999995
No 16
>PF01028 Topoisom_I: Eukaryotic DNA topoisomerase I, catalytic core; InterPro: IPR013500 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the catalytic core of eukaryotic and viral topoisomerase I (type IB) enzymes, which occurs near the C-terminal region of the protein. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity []. The crystal structures of human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes []. Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin. The crystal structure of an amino-terminal fragment of vaccinia virus DNA topoisomerase I shows that the fragment forms a five-stranded, antiparallel beta-sheet with two short alpha-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2F4Q_A 3M4A_A 3IGC_A 2H7G_X 2H7F_X 1A41_A 1VCC_A 1TL8_A 1K4T_A 1A36_A ....
Probab=99.75 E-value=9.4e-20 Score=183.59 Aligned_cols=86 Identities=38% Similarity=0.599 Sum_probs=75.2
Q ss_pred CCCcccCccchHhHHHHHHHhHHHHHHHHHHHhcccchhhhhhhheeeeeeeeehhhccCCCC-CCCCCceeeeeceeee
Q psy17743 505 PSSKLKGEKDWQKYETARKLAKSINKIRENYQADWKSKEMRIRQRAVALYFIDKLALRAGNEK-DEDQADTVGCCSLRVE 583 (618)
Q Consensus 505 ~~s~~k~~~d~~kye~ar~Lk~~i~~Ir~~y~~~~~s~~~~~rq~a~a~y~Id~lAlr~g~ek-~~deadtvgccsLrve 583 (618)
|+|+.++++|..|||.+++|..+|.+||+.|.++|.|..+..+|+|+|+||||.+|||+|||+ .++++||+||||||++
T Consensus 1 ~Ds~gRkQrd~~Kf~r~~~f~~~Lp~iR~~v~~dL~~~~~~~r~lA~a~~LlD~~~lRvGne~Y~~~n~ds~GltTLr~~ 80 (234)
T PF01028_consen 1 ADSKGRKQRDEEKFDRARRFARALPKIRRRVRKDLRSGLPRERVLAVAVRLLDRTALRVGNEKYAEENGDSYGLTTLRVK 80 (234)
T ss_dssp -TTCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTCHHHHHHHHHHHHHHH------HHHHCCHHSHHHCCT-BGG
T ss_pred CCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCcchhHHHHHHHHHHhhheecCCcccccccCCCeeeCcCcHH
Confidence 578999999999999999999999999999999999999999999999999999999999999 5778999999999999
Q ss_pred ceeeccc
Q psy17743 584 HIQLHEE 590 (618)
Q Consensus 584 hi~l~~~ 590 (618)
||++.++
T Consensus 81 Hv~~~~~ 87 (234)
T PF01028_consen 81 HVKLSGD 87 (234)
T ss_dssp GEEEETT
T ss_pred HeeecCC
Confidence 9999986
No 17
>cd00659 Topo_IB_C DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses and bacterial versions of Topo IB. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases.
Probab=99.60 E-value=2.7e-16 Score=157.23 Aligned_cols=77 Identities=57% Similarity=0.903 Sum_probs=73.2
Q ss_pred chHhHHHHHHHhH------HHHHHHHHHHhcccchhh-hhhhheeeeeeeeehhhccCCCCCCCCCceeeeeceeeecee
Q psy17743 514 DWQKYETARKLAK------SINKIRENYQADWKSKEM-RIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQ 586 (618)
Q Consensus 514 d~~kye~ar~Lk~------~i~~Ir~~y~~~~~s~~~-~~rq~a~a~y~Id~lAlr~g~ek~~deadtvgccsLrvehi~ 586 (618)
||.+++.++|+.. ++.+||+.|.+||+++.+ .++|+|+++||||+++||+|||+..++.+|+||||||++||+
T Consensus 1 ~w~~~r~~~K~~~~~~f~~~Lp~iR~~v~~dl~~~~~~~~~vlA~~~~Lld~~~iRvGne~Ya~~n~s~GltTLr~~Hv~ 80 (218)
T cd00659 1 DWKKYRKARKLKRLLAFGRALPKIRRRYTKDLKSKGMPRERQLATAVYLIDKFALRVGNEKYERENDTVGLCTLRKEHVT 80 (218)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcchHhHHHHHHHHHHHhcccCCChhhhhcCCCEeecccchhhee
Confidence 6888888888888 999999999999999998 999999999999999999999999999999999999999999
Q ss_pred eccc
Q psy17743 587 LHEE 590 (618)
Q Consensus 587 l~~~ 590 (618)
+.++
T Consensus 81 ~~~~ 84 (218)
T cd00659 81 LKPN 84 (218)
T ss_pred EeCC
Confidence 9873
No 18
>PHA03101 DNA topoisomerase type I; Provisional
Probab=98.59 E-value=1.6e-08 Score=106.16 Aligned_cols=78 Identities=23% Similarity=0.250 Sum_probs=66.5
Q ss_pred ccchHhHHHHHHHhHHHHHHHHHHHhccc--chhhhhhhheeeeeeeeehhhccCCCCCCCCCceeeeeceeeeceeecc
Q psy17743 512 EKDWQKYETARKLAKSINKIRENYQADWK--SKEMRIRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHE 589 (618)
Q Consensus 512 ~~d~~kye~ar~Lk~~i~~Ir~~y~~~~~--s~~~~~rq~a~a~y~Id~lAlr~g~ek~~deadtvgccsLrvehi~l~~ 589 (618)
..|-.||+..-.+...+..||+.+.+||. +......+.|+..+|.+.|++|+|||+-.++.+|+||||||.+||++.+
T Consensus 79 ~R~~~Kf~r~~~f~~~LP~iR~~v~~dL~~~~~~~~kvlAavv~LLd~~~~iRvGne~Ya~~N~SyGltTLr~rHv~v~g 158 (314)
T PHA03101 79 NRNANRDKIFVRVHNVIKKINCFIDKNIKIKKKNDVNFQLAVFLLMETSFFIRTGKMKYLKENETVGLLTLKNKHITISN 158 (314)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhccceecCCHhHHHhcCCccccccchhceEEEC
Confidence 45778999999999999999999999994 4555555666666555556999999999999999999999999999986
No 19
>cd03488 Topoisomer_IB_N_htopoI_like Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain.
Probab=97.41 E-value=6.2e-05 Score=75.61 Aligned_cols=24 Identities=67% Similarity=1.264 Sum_probs=23.0
Q ss_pred ccchhhhheeeccCCCceEEEEEc
Q psy17743 481 RISVTWLASWTENVQGQVKYIMLN 504 (618)
Q Consensus 481 RitVtWlkkw~vpI~~~~Kyv~l~ 504 (618)
.+|||||++|.++|+|++|||||+
T Consensus 192 DntVtWLA~W~enIn~~~KYV~La 215 (215)
T cd03488 192 DNTVTWLASWTENINGSIKYVMLN 215 (215)
T ss_pred CCCceEEEEeEeccCCceeEEEeC
Confidence 589999999999999999999996
No 20
>cd00660 Topoisomer_IB_N Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I diffe
Probab=97.41 E-value=6.2e-05 Score=75.60 Aligned_cols=24 Identities=63% Similarity=1.167 Sum_probs=23.0
Q ss_pred ccchhhhheeeccCCCceEEEEEc
Q psy17743 481 RISVTWLASWTENVQGQVKYIMLN 504 (618)
Q Consensus 481 RitVtWlkkw~vpI~~~~Kyv~l~ 504 (618)
.+|||||++|.++|+|++|||||+
T Consensus 192 DntVtWLA~W~enIn~~~KYV~La 215 (215)
T cd00660 192 DNTVTWLASWKENINGQFKYVMLA 215 (215)
T ss_pred CCCceEEEEeEeccCCceeEEEeC
Confidence 589999999999999999999996
No 21
>cd03489 Topoisomer_IB_N_LdtopoI_like Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human
Probab=97.40 E-value=6.4e-05 Score=75.35 Aligned_cols=24 Identities=46% Similarity=0.995 Sum_probs=23.0
Q ss_pred ccchhhhheeeccCCCceEEEEEc
Q psy17743 481 RISVTWLASWTENVQGQVKYIMLN 504 (618)
Q Consensus 481 RitVtWlkkw~vpI~~~~Kyv~l~ 504 (618)
.+|||||++|.++|+|++|||||+
T Consensus 189 DntVtWLA~W~enIn~~~KYV~La 212 (212)
T cd03489 189 DNTVTWLAMWRDPIAGNFKYVMLA 212 (212)
T ss_pred CCCceEEEEeEeccCCceeEEEeC
Confidence 589999999999999999999996
No 22
>cd03490 Topoisomer_IB_N_1 Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB. Topo IB proteins include the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanoso
Probab=97.38 E-value=7e-05 Score=75.34 Aligned_cols=24 Identities=42% Similarity=0.808 Sum_probs=22.8
Q ss_pred ccchhhhheeeccCCCceEEEEEc
Q psy17743 481 RISVTWLASWTENVQGQVKYIMLN 504 (618)
Q Consensus 481 RitVtWlkkw~vpI~~~~Kyv~l~ 504 (618)
.+|||||++|.+||+|++|||||+
T Consensus 194 DntVtWLA~W~enIn~~~KYV~Ls 217 (217)
T cd03490 194 DNSVTWLAYYKDSINDQFKYMFLS 217 (217)
T ss_pred CCCceEEEEeecCCCCceeEEEeC
Confidence 589999999999999999999996
No 23
>PF02919 Topoisom_I_N: Eukaryotic DNA topoisomerase I, DNA binding fragment; InterPro: IPR008336 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the N-terminal DNA-binding domain found in eukaryotic topoisomerase I, which is a type IB enzymes. To cleave the DNA backbone, these enzymes must make a transient phosphotyrosine bond. The N-terminal domain of human topoisomerase I is thought to coordinate the restriction of free strand rotation during the topoisomerisation step of catalysis. A conserved tryptophan residue may be important for the DNA-interaction ability of the N-terminal domain []. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1TL8_A 1K4T_A 1A36_A 1RR8_C 1T8I_A 1SC7_A 1EJ9_A 1LPQ_A 1RRJ_A 1A31_A ....
Probab=97.24 E-value=0.00012 Score=73.68 Aligned_cols=23 Identities=70% Similarity=1.256 Sum_probs=20.5
Q ss_pred ccchhhhheeeccCCCceEEEEE
Q psy17743 481 RISVTWLASWTENVQGQVKYIML 503 (618)
Q Consensus 481 RitVtWlkkw~vpI~~~~Kyv~l 503 (618)
.+|||||++|.++|+|++|||||
T Consensus 193 DntvtWLA~W~enI~~~~KYV~L 215 (215)
T PF02919_consen 193 DNTVTWLASWTENINGQFKYVML 215 (215)
T ss_dssp -TTSS-SEEEEETTTTEEEEEEB
T ss_pred CCCceEEEEeEeccCCceeEEeC
Confidence 58999999999999999999997
No 24
>cd00397 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site residues. The best-studied members of this diverse superfamily include human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl gener
Probab=96.47 E-value=0.0085 Score=53.74 Aligned_cols=123 Identities=24% Similarity=0.314 Sum_probs=85.3
Q ss_pred hhHHHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeec-CCceEEEEEeccchHHHHHH
Q psy17743 233 IRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLG-KDSIRYYNEVPVEKRVFKNL 311 (618)
Q Consensus 233 ~RqlA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlG-Kdsir~~~~V~vD~~v~knL 311 (618)
....+.++.|+-.+.+|+|. +|.|..+||.... .. +.+.+ |.|.. ..+++++.+...|
T Consensus 14 ~~~~~~~~~l~~~tG~R~~E-----------i~~l~~~~~~~~~------~~--~~i~~~K~~~~--~~i~i~~~~~~~l 72 (164)
T cd00397 14 PERLYLALLLLLATGLRISE-----------LCALRWSDIDLDK------RV--IHITGTKTKKE--RTVPLSEEALKLL 72 (164)
T ss_pred ccHHHHHHHHHHHhCCCHHH-----------HhCCchhhhcccc------CE--EEEecCCCCCe--eEEecCHHHHHHH
Confidence 34567778888889999985 7899999987643 33 45555 88744 4667777777777
Q ss_pred HHhhhcc----CCCcccccc--------CChhHHHHHHHHhcC-------CCeeeeeccccchHHHHHHHhhcCCCCccH
Q psy17743 312 QLFVENK----KGSDDLFDR--------LNTSVLNKHLSELME-------GLTAKVFRTYNASITLQQQLNELMDPDFSE 372 (618)
Q Consensus 312 ~~f~~~K----~Pgd~LF~~--------l~s~~LN~yLkelm~-------glTAKvFRTynASvt~~~~L~~~~~~~~s~ 372 (618)
....+.- .+++.||.. ++...++.+++.++. .+|+.+||...||.++.. ..+
T Consensus 73 ~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~R~t~~t~~~~~-----g~~---- 143 (164)
T cd00397 73 KEYLKKRRPANGDEEYLFPSRRGGPAATLSRRNVKRIFKAAGRRAGIDKEGLTPHSLRHTFASALLNA-----GLD---- 143 (164)
T ss_pred HHHHHHhccccCCCCceeecCCCCCccCCcHHHHHHHHHHHHHHcCCCCCCCCchHhHHHHHHHHHHc-----CCC----
Confidence 7766532 467788875 345578888888873 278888888777764431 111
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCC
Q psy17743 373 AEKILAYNRANRAVAVLCNHQRS 395 (618)
Q Consensus 373 ~ek~~~yn~Anr~VAilcNHqra 395 (618)
...+|.++||...
T Consensus 144 ----------~~~i~~~~gH~~~ 156 (164)
T cd00397 144 ----------LEAVQDLLGHSSI 156 (164)
T ss_pred ----------HHHHHHHhCCCcH
Confidence 4478888999653
No 25
>TIGR02224 recomb_XerC tyrosine recombinase XerC. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK.
Probab=95.67 E-value=0.033 Score=54.80 Aligned_cols=100 Identities=23% Similarity=0.306 Sum_probs=70.7
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhh
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVE 316 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~ 316 (618)
++++.|+-.+.+|+|. +|+|+.++|.+.+ +.+.+. ||.+..+ .|++.+.+...|..+++
T Consensus 132 ~~~~~l~~~tG~R~~E-----------l~~l~~~di~~~~------~~~~i~--~k~~~~r--~vpl~~~~~~~l~~~~~ 190 (295)
T TIGR02224 132 RAILELLYSSGLRVSE-----------LVGLDLDDLDLDS------GLVRVR--GKGNKER--IVPFGSYAKDALQAYLE 190 (295)
T ss_pred HHHHHHHHHhcchHHH-----------HhCCCchhcccCc------ceEEEe--cCCCcee--EEECCHHHHHHHHHHHH
Confidence 3556666678999986 8899999999876 566654 7776554 67778999999998875
Q ss_pred c-------cCCCccccc-----cCChhHHHHHHHHhc-----C-CCeeeeeccccchHH
Q psy17743 317 N-------KKGSDDLFD-----RLNTSVLNKHLSELM-----E-GLTAKVFRTYNASIT 357 (618)
Q Consensus 317 ~-------K~Pgd~LF~-----~l~s~~LN~yLkelm-----~-glTAKvFRTynASvt 357 (618)
. ..+++.||- .+++..+|..++.+. + ++|+.+||--.||..
T Consensus 191 ~~~~~~~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~~t~~ 249 (295)
T TIGR02224 191 ARREKLLASEGQDALFLNRRGGRLTPRGVQYRLQQLVAKAGLPKHVHPHALRHSFATHL 249 (295)
T ss_pred HhhhccchhcCCCeeEEeCCCCCCCHHHHHHHHHHHHHHcCCCCCcChHHHHHHHHHHH
Confidence 1 223336885 377888888888774 2 277788875444443
No 26
>cd00801 INT_P4 Bacteriophage P4 integrase. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. They share the same fold in their catalytic domain and the overall reaction mechanism with the superfamily of DNA breaking-rejoining enzymes. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes.
Probab=95.66 E-value=0.051 Score=55.42 Aligned_cols=122 Identities=20% Similarity=0.170 Sum_probs=87.7
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEe-ecCCceEEEEEeccchHHHHHHHHhh
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDF-LGKDSIRYYNEVPVEKRVFKNLQLFV 315 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdF-lGKdsir~~~~V~vD~~v~knL~~f~ 315 (618)
..++.|+=.+++|+|- +|.|+..||.+.. +.+.+.. .+|.+. ...|++.+.+...|....
T Consensus 202 ~~~~~l~~~tGlR~~E-----------i~~L~~~di~~~~------~~~~i~~~~~Kt~~--~r~vpl~~~~~~~l~~~~ 262 (357)
T cd00801 202 RLALKLLLLTGVRPGE-----------LRGARWSEIDLEN------ALWTIPAERMKTRR--PHRVPLSDQALALLEELR 262 (357)
T ss_pred HHHHHHHHHHCcChHh-----------HHcCcchhcccCC------CeEecchhhccCCC--CcccCCcHHHHHHHHHHH
Confidence 3444555559999985 8899999999865 5665533 367663 347788899999999887
Q ss_pred hccCCCccccc-------cCChhHHHHHHHHhc-CC-CeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHHHH
Q psy17743 316 ENKKGSDDLFD-------RLNTSVLNKHLSELM-EG-LTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAV 386 (618)
Q Consensus 316 ~~K~Pgd~LF~-------~l~s~~LN~yLkelm-~g-lTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr~V 386 (618)
....+++.||. .++...++..++.+. +. +|..+||-.-||.++. ...+ ...|
T Consensus 263 ~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRHt~at~~~~-----~g~~--------------~~~i 323 (357)
T cd00801 263 ELSGHSEYVFPSRRDRGKPLSENTLNKALKRMGYLGEWTPHGLRRTARTWLNE-----LGFP--------------PDVI 323 (357)
T ss_pred HHhCCCceEecCCCCCCCCCCHHHHHHHHHHcCCCCCcCcCchhHHHHHHHHH-----CCCC--------------HHHH
Confidence 65556788994 466788999999988 44 9999999877775543 1111 1357
Q ss_pred HHHcCCCCCC
Q psy17743 387 AVLCNHQRSV 396 (618)
Q Consensus 387 AilcNHqraV 396 (618)
+.++||.-..
T Consensus 324 ~~~lGHs~~~ 333 (357)
T cd00801 324 ERQLAHVLGG 333 (357)
T ss_pred HHHhCCCCCC
Confidence 8889998643
No 27
>cd01187 INT_SG4 INT_SG4, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 4, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases for which not much biochemical characterization is available.
Probab=95.61 E-value=0.14 Score=51.62 Aligned_cols=129 Identities=17% Similarity=0.149 Sum_probs=90.4
Q ss_pred HHHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHh
Q psy17743 235 QRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLF 314 (618)
Q Consensus 235 qlA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f 314 (618)
....++.|+-.+.+|+|- +|.|+.+||.+.. +.|.+. -+|.+..+ .|++.+.+...|..+
T Consensus 127 ~~~~~i~ll~~tGlR~~E-----------~~~L~~~did~~~------~~i~i~-~~K~~~~r--~vpl~~~l~~~l~~~ 186 (299)
T cd01187 127 TYRTLFGLLAVTGLRLGE-----------ALRLRLSDVDLDS------GILTVR-DSKFGKSR--LVPLHASTRAALRDY 186 (299)
T ss_pred HHHHHHHHHHHhCCcHHH-----------HHhCcHHhcCCCC------CeEEEE-ecCCCCcc--EEeCCHHHHHHHHHH
Confidence 344678888899999987 8999999998765 566553 37877654 688889999999876
Q ss_pred hhc------cCCCcccccc-----CChh---HHHHHHHHhcC------C--CeeeeeccccchHHHHHHHhhcCCCCccH
Q psy17743 315 VEN------KKGSDDLFDR-----LNTS---VLNKHLSELME------G--LTAKVFRTYNASITLQQQLNELMDPDFSE 372 (618)
Q Consensus 315 ~~~------K~Pgd~LF~~-----l~s~---~LN~yLkelm~------g--lTAKvFRTynASvt~~~~L~~~~~~~~s~ 372 (618)
... ..+++.||.. ++++ .++..++.+.. | +|..+||-.-||.++...+.. .. ++
T Consensus 187 ~~~~~~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRHt~at~~l~~~~~~-g~---~~ 262 (299)
T cd01187 187 LARRDRLLPAPDSSAFFVSSRGGRLSYGGHRVFYALSREIGLRGWAQRGRGPRLHDLRHRFAVTRLTRWYRA-GA---DV 262 (299)
T ss_pred HHHHHhhccCCCCcceeeCCCCCCCCcccchHHHHHHHHhCcccCCCCCCCCCcccccHHHHHHHHHHHHHc-CC---Ch
Confidence 431 2356788864 5556 78888888753 2 788999988888665433321 11 11
Q ss_pred HHHHHHHHHHHHHHHHHcCCCC
Q psy17743 373 AEKILAYNRANRAVAVLCNHQR 394 (618)
Q Consensus 373 ~ek~~~yn~Anr~VAilcNHqr 394 (618)
. .....|+.++||..
T Consensus 263 ~-------~~~~~v~~~lGH~~ 277 (299)
T cd01187 263 E-------RKLPVLATYLGHAN 277 (299)
T ss_pred h-------hhhHHHHHHcCCCC
Confidence 1 12368899999973
No 28
>cd01193 INT_IntI IntI (E2) integrases, site-specific tyrosine recombinases, DNA breaking-rejoining enzymes, N- and C-terminal domains. This CD includes integrases which are components of multiresistant integrons and mediate recombination between a proximal attI site and a secondary target called the attC (or 59-base element) present on various mobile gene cassettes. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group.
Probab=95.48 E-value=0.036 Score=53.33 Aligned_cols=100 Identities=21% Similarity=0.283 Sum_probs=71.7
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhh
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVE 316 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~ 316 (618)
.+++.|+=.+++|+|. ++.|+.+||.+.. +.+.+. .+|.+..+ .|++.+.+...|+...+
T Consensus 89 ~~~~~l~~~tG~R~~E-----------~~~L~~~di~~~~------~~~~i~-~~K~~~~~--~ipl~~~~~~~l~~~~~ 148 (242)
T cd01193 89 RLILSLLYGCGLRLSE-----------CLRLRVKDIDFDR------GQIRVR-QGKGGKDR--YVMLPEALLELLRAYWK 148 (242)
T ss_pred HHHHHHHHHcCCcHHH-----------HhcCCHHHcCCCC------CeEEEE-eCCCCCce--EEeccHHHHHHHHHHHH
Confidence 3555555568899987 7889999998865 677764 36776554 66677888888888765
Q ss_pred cc------CCCccccc-------------cCChhHHHHHHHHhcC------CCeeeeeccccchH
Q psy17743 317 NK------KGSDDLFD-------------RLNTSVLNKHLSELME------GLTAKVFRTYNASI 356 (618)
Q Consensus 317 ~K------~Pgd~LF~-------------~l~s~~LN~yLkelm~------glTAKvFRTynASv 356 (618)
.. .+++.||. .++++.+|..++.++. .+|...||-..||.
T Consensus 149 ~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~s~h~lRht~at~ 213 (242)
T cd01193 149 RARALGRERPWQWLFPSTRRSRDPVERRHHLSERTLQRALKKAVEQAGIDKRVTPHTLRHSFATH 213 (242)
T ss_pred HHHhcccCCCCceecccCCCCcccccccCCCCHHHHHHHHHHHHHHcCCCCCCCcCcchHHHHHH
Confidence 33 55667873 4678899999998753 27888888555554
No 29
>PRK02436 xerD site-specific tyrosine recombinase XerD-like protein; Reviewed
Probab=95.41 E-value=0.039 Score=54.32 Aligned_cols=111 Identities=18% Similarity=0.200 Sum_probs=77.7
Q ss_pred HHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhcc
Q psy17743 239 ALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVENK 318 (618)
Q Consensus 239 AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~K 318 (618)
+++|+-.+.||+|- +|.|+.+||.+.. +.|.+ +|.+..+ .|++++.+...|+...
T Consensus 117 ~~~ll~~tGlR~~E-----------l~~L~~~dId~~~------~~i~i---~k~~~~R--~vpl~~~l~~~L~~~~--- 171 (245)
T PRK02436 117 IALLILELGLTPSE-----------IAGLKVADIDLDF------QVLTI---EKAGGKR--VLTLPEALLPFLEAIL--- 171 (245)
T ss_pred HHHHHHHcCCCHHH-----------HhcCcHHHcCccC------CEEEE---cCCCcee--EEECCHHHHHHHHHHh---
Confidence 45566689999987 9999999998866 67766 3655443 6888899999998876
Q ss_pred CCCcccccc----CChhHHHHHHHHhc---C--CCeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHHHHHHH
Q psy17743 319 KGSDDLFDR----LNTSVLNKHLSELM---E--GLTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVAVL 389 (618)
Q Consensus 319 ~Pgd~LF~~----l~s~~LN~yLkelm---~--glTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr~VAil 389 (618)
++..||.. +++..++..++.++ | .+|..+||=--||.++. ... + ...|+.+
T Consensus 172 -~~~~lF~~~g~~~~~~~~~~~~~~~~~~~gi~~~t~H~lRHtfat~~~~-----~g~---~-----------~~~l~~~ 231 (245)
T PRK02436 172 -NQTYLFEHKGKPYSRQWFFNQLKSFVKSIGYPGLSAQKLREQFILKQKE-----AGK---S-----------IYELARL 231 (245)
T ss_pred -CCCeeecCCCCcccHHHHHHHHHHHHHHcCCCCCCcchhHHHHHHHHHH-----cCC---C-----------HHHHHHH
Confidence 45678853 56655666666553 2 38999998666665542 111 1 3469999
Q ss_pred cCCCC
Q psy17743 390 CNHQR 394 (618)
Q Consensus 390 cNHqr 394 (618)
+||+-
T Consensus 232 lGH~~ 236 (245)
T PRK02436 232 LGLKS 236 (245)
T ss_pred hCCCC
Confidence 99953
No 30
>cd01192 INT_P22_C P22-like integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial and phage integrases, including those similar to phage P22-like integrases, DLP12 and APSE-1.
Probab=93.73 E-value=0.27 Score=45.84 Aligned_cols=119 Identities=15% Similarity=0.081 Sum_probs=77.6
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEee-cCCceEEEEEeccchHHHHHHHHhh
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFL-GKDSIRYYNEVPVEKRVFKNLQLFV 315 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFl-GKdsir~~~~V~vD~~v~knL~~f~ 315 (618)
.+++.|+=.+.+|+|- ++.|+.++|.+.. +.+.+... +|.+..+ .|++.+.+...|+.+.
T Consensus 24 ~~~~~l~~~tG~R~~E-----------l~~l~~~did~~~------~~~~i~~~~~K~~~~r--~ipl~~~~~~~l~~~~ 84 (177)
T cd01192 24 KPAVLFALNTGLRRSE-----------ILGLEWSQVDLDN------RVAWVRPATSKGGRAI--RVPLNDEALQVLKRQK 84 (177)
T ss_pred HHHHHHHHHhCccHHH-----------HhcCchhhccccC------CEEEEeccCCCCCCee--EecCCHHHHHHHHHHh
Confidence 3455566678899887 8899999998765 66777653 5666544 5788899999999998
Q ss_pred hccCCCccccccCCh---hHHHHHHHHhc-----CCCeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHHHHH
Q psy17743 316 ENKKGSDDLFDRLNT---SVLNKHLSELM-----EGLTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVA 387 (618)
Q Consensus 316 ~~K~Pgd~LF~~l~s---~~LN~yLkelm-----~glTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr~VA 387 (618)
.. .++..||..... ...+..++.++ +++|...||-..||.++. ... + ...|+
T Consensus 85 ~~-~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~at~l~~-----~g~---~-----------~~~i~ 144 (177)
T cd01192 85 AG-AHKPWVFAGAGGDPRIDSKTAWRQALQRAGISDFRWHDLRHTWASWLVQ-----SGV---P-----------LYVLQ 144 (177)
T ss_pred cc-CCCCeEeecCCCCcccchHHHHHHHHHHcCCCCCcchhhhHHHHHHHHH-----cCC---C-----------HHHHH
Confidence 52 345678875321 12333344443 247888888776665432 111 1 23678
Q ss_pred HHcCCCC
Q psy17743 388 VLCNHQR 394 (618)
Q Consensus 388 ilcNHqr 394 (618)
.++||+.
T Consensus 145 ~~lGH~~ 151 (177)
T cd01192 145 ELLGHSS 151 (177)
T ss_pred HHhCCCC
Confidence 8899985
No 31
>PF00589 Phage_integrase: Phage integrase family; InterPro: IPR002104 Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The catalytic site residues in CRE recombinase (P06956 from SWISSPROT) are Arg-173, His-289, Arg-292 and Tyr-324.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration; PDB: 1A0P_A 1Z1G_B 1Z19_A 1AE9_A 1Z1B_A 1P7D_B 2A3V_C 1Q3V_E 1Q3U_A 1OUQ_F ....
Probab=93.72 E-value=0.27 Score=44.75 Aligned_cols=105 Identities=17% Similarity=0.263 Sum_probs=72.9
Q ss_pred HHHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEE-eecCCceEEEEEeccchHHHHHHHH
Q psy17743 235 QRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFD-FLGKDSIRYYNEVPVEKRVFKNLQL 313 (618)
Q Consensus 235 qlA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~Fd-FlGKdsir~~~~V~vD~~v~knL~~ 313 (618)
..++++.|+=.+++|+|. +++|+.+||.+.+ +.+.+. -.+|.+.. ..+.+.+.++..|+.
T Consensus 22 ~~~~~~~l~~~tG~R~~E-----------l~~l~~~~v~~~~------~~~~i~~~~~K~~~~--~~~~i~~~~~~~l~~ 82 (173)
T PF00589_consen 22 RNRLIILLLLYTGLRPSE-----------LLRLRWDDVDLEN------GEIYIPIRRTKTGKS--RTVPISPELAELLRE 82 (173)
T ss_dssp HHHHHHHHHHHHT--HHH-----------HHT-BGGGEETTT------TEEEEEEEECSSSEE--EEEECTHHHHHHHHH
T ss_pred HHHHHHHHHHHHccchhh-----------hhhhhhhhhhccc------ccccccccccccccc--ccccccccccccccc
Confidence 445667777788999976 8999999988766 666664 46676666 566667999999988
Q ss_pred hhhc----cCCCccccc-----cCChhHHHHHHHHhcC------CCeeeeeccccchHHH
Q psy17743 314 FVEN----KKGSDDLFD-----RLNTSVLNKHLSELME------GLTAKVFRTYNASITL 358 (618)
Q Consensus 314 f~~~----K~Pgd~LF~-----~l~s~~LN~yLkelm~------glTAKvFRTynASvt~ 358 (618)
.... ..+.+.||- .++...+|..++.+.. .+|..+||--.+|.++
T Consensus 83 ~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lR~t~~t~l~ 142 (173)
T PF00589_consen 83 YIKRRKRQNDDDDYLFPSSDGKPLSRQTINKIFRRIIKKAGIEKKFTPHSLRHTFATNLA 142 (173)
T ss_dssp HHHHHCHCHCCSSBSSBETTSSB--HHHHHHHHHHHHHHTT-SSCTCHHHHHHHHHHHHH
T ss_pred cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Confidence 7653 367788884 3789999999998862 3777777754445433
No 32
>PRK05084 xerS site-specific tyrosine recombinase XerS; Reviewed
Probab=93.63 E-value=0.15 Score=53.15 Aligned_cols=117 Identities=20% Similarity=0.248 Sum_probs=83.2
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhh
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVE 316 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~ 316 (618)
.+++.|+-.+.||+|- +|.|+.+||.+.. +.|.+ .+|.+..+ .|++.+.+...|.....
T Consensus 198 ~~i~~ll~~tGlR~~E-----------~~~L~~~did~~~------~~l~v--~~K~~~~r--~vpl~~~~~~~l~~~~~ 256 (357)
T PRK05084 198 LAIIALILGSGLRVSE-----------LVNLDLSDLNLKQ------MTIDV--TRKGGKRD--SVNIAPFALPYLEEYLK 256 (357)
T ss_pred HHHHHHHHHhCCCHHH-----------HHcCCHHHcCcCC------CEEEE--EecCCcee--EEEECHHHHHHHHHHHH
Confidence 3456677789999987 9999999998865 56555 47887765 56667888888877664
Q ss_pred cc-------CCCccccc--------cCChhHHHHHHHHhcC--C--CeeeeeccccchHHHHHHHhhcCCCCccHHHHHH
Q psy17743 317 NK-------KGSDDLFD--------RLNTSVLNKHLSELME--G--LTAKVFRTYNASITLQQQLNELMDPDFSEAEKIL 377 (618)
Q Consensus 317 ~K-------~Pgd~LF~--------~l~s~~LN~yLkelm~--g--lTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~ 377 (618)
.. .+.+.||- .++.+.++..++.+.. | +|..+||-..||.++.. +. +
T Consensus 257 ~~~~~~~~~~~~~~lF~~~~~~~~~~~~~~~i~~~~~~~~~~~gi~~~~H~lRHt~at~l~~~-----g~---~------ 322 (357)
T PRK05084 257 IRASRYKAEKQEKALFLTKYRGKPNRISARAIEKMVAKYSEAFGVRLTPHKLRHTLATRLYDA-----TK---D------ 322 (357)
T ss_pred HhhhhccCCCCCcceEeecCCCCCCCCCHHHHHHHHHHHHHHcCCCCCcccccHHHHHHHHHc-----CC---C------
Confidence 21 23456773 3777889999888753 3 88999998888865531 11 1
Q ss_pred HHHHHHHHHHHHcCCC
Q psy17743 378 AYNRANRAVAVLCNHQ 393 (618)
Q Consensus 378 ~yn~Anr~VAilcNHq 393 (618)
...|+.++||.
T Consensus 323 -----~~~i~~~lGH~ 333 (357)
T PRK05084 323 -----QVLVADQLGHT 333 (357)
T ss_pred -----HHHHHHHcCCC
Confidence 24788999996
No 33
>PRK09870 tyrosine recombinase; Provisional
Probab=93.63 E-value=0.26 Score=47.90 Aligned_cols=101 Identities=15% Similarity=0.180 Sum_probs=72.9
Q ss_pred HHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhc-
Q psy17743 239 ALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN- 317 (618)
Q Consensus 239 AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~- 317 (618)
++.|+-.+.+|+|. ++.|+.++|.+.. +.+.+. ..|.+.. ..|++.+.+...|..+...
T Consensus 37 ~~~l~~~tGlR~~E-----------i~~L~~~did~~~------~~l~i~-~~k~~~~--~~vpl~~~~~~~l~~~~~~~ 96 (200)
T PRK09870 37 LTLLCFIHGFRASE-----------ICRLRISDIDLKA------KCIYIH-RLKKGFS--TTHPLLNKEIQALKNWLSIR 96 (200)
T ss_pred HHHHHHHhCCcHHH-----------HHcccHHHcCCCC------CeEEEE-ECCCCcc--eEEECCHHHHHHHHHHHHhc
Confidence 45555678999988 8999999998865 566664 2344443 3567778888888777542
Q ss_pred ----cCCCccccc-----cCChhHHHHHHHHhc-----C-CCeeeeeccccchHHHH
Q psy17743 318 ----KKGSDDLFD-----RLNTSVLNKHLSELM-----E-GLTAKVFRTYNASITLQ 359 (618)
Q Consensus 318 ----K~Pgd~LF~-----~l~s~~LN~yLkelm-----~-glTAKvFRTynASvt~~ 359 (618)
..+++.||- .++.+.+|..++.+. + .+|..+||-..||.++.
T Consensus 97 ~~~~~~~~~~lf~~~~g~~~s~~~~~~~~k~~~~~~gi~~~~t~H~lRht~at~l~~ 153 (200)
T PRK09870 97 TSYPHAESEWVFLSRKGNPLSRQQFYHIISTSGGNAGLSLEIHPHMLRHSCGFALAN 153 (200)
T ss_pred ccCCCCCCCceeeCCCCCcCCHHHHHHHHHHHHHHcCCCCCCCCccccchHHHHHHH
Confidence 134567883 488899999998875 2 38899999988887553
No 34
>cd01188 INT_pAE1 pAE1 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal domain. This CD includes various bacterial integrases, including the predicted integrase of the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1.
Probab=93.53 E-value=0.73 Score=43.46 Aligned_cols=97 Identities=23% Similarity=0.342 Sum_probs=67.1
Q ss_pred HHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhc-
Q psy17743 239 ALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN- 317 (618)
Q Consensus 239 AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~- 317 (618)
++.|+-.+.+|.|. +|.|+..||.+.. +.+.+. .+|.+..+ .|.+.+.+...|..+.+.
T Consensus 30 ~~~l~~~tGlR~~E-----------l~~l~~~di~~~~------~~i~i~-~~K~~~~r--~vpl~~~~~~~l~~~~~~~ 89 (188)
T cd01188 30 ILLLLARLGLRAGE-----------VAALRLDDIDWRT------GTIRVR-QGKGGRVT--RLPLPAEVGAALADYLRDG 89 (188)
T ss_pred HHHHHHHHCCCHHH-----------HHhCcccccCCCC------CeEEEE-eCCCCcce--EEeCCHHHHHHHHHHHHhc
Confidence 45566668899987 8999999998754 555553 26776543 777889999888877642
Q ss_pred --cCCCcccccc--------CChhHHHHHHHHhcC--C-----Ceeeeeccccch
Q psy17743 318 --KKGSDDLFDR--------LNTSVLNKHLSELME--G-----LTAKVFRTYNAS 355 (618)
Q Consensus 318 --K~Pgd~LF~~--------l~s~~LN~yLkelm~--g-----lTAKvFRTynAS 355 (618)
..+++.||-. ++...+|.+++.++. | +|+.+||--.||
T Consensus 90 ~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at 144 (188)
T cd01188 90 RPATDSRRVFLRMRAPFRPFAGHSAVSNIVRRALRRAGISPRRGGAHLLRHSLAT 144 (188)
T ss_pred CCCCCCCceeeeccCCcCCcccHHHHHHHHHHHHHHcCCCcCCCCcHHHHHHHHH
Confidence 2345678842 478899999988884 2 355666643444
No 35
>PRK09692 integrase; Provisional
Probab=93.43 E-value=0.41 Score=51.51 Aligned_cols=139 Identities=13% Similarity=0.121 Sum_probs=89.6
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEe-ecCCceEEEEEeccchHHHHHHHHhhh
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDF-LGKDSIRYYNEVPVEKRVFKNLQLFVE 316 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdF-lGKdsir~~~~V~vD~~v~knL~~f~~ 316 (618)
.++.|+=.+.+|+|. +|.|+.++|.+.. +.+.+.= ..|.+.. ..|++.+.+...|+.+..
T Consensus 237 ~~~~lll~TG~R~gE-----------l~~l~W~diD~~~------~~~~I~~~~~K~~~~--r~VpL~~~~~~~L~~~~~ 297 (413)
T PRK09692 237 CLFMWQLLTITRPAE-----------AAEARWEEIDIEA------QEWKIPAARMKMNRD--HTVPLSDEALAILEMMKP 297 (413)
T ss_pred HHHHHHHHHCcchHH-----------HhcCchHHhccCC------CeEEechhhccCCCC--eeccChHHHHHHHHHHHH
Confidence 344555579999998 8999999998876 5666532 2343332 378888999999988865
Q ss_pred ccCCCcccccc-------CChhHHHHHHHHhc-CC-CeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHHHHH
Q psy17743 317 NKKGSDDLFDR-------LNTSVLNKHLSELM-EG-LTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVA 387 (618)
Q Consensus 317 ~K~Pgd~LF~~-------l~s~~LN~yLkelm-~g-lTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr~VA 387 (618)
...+++.||.. +++..+|..++.+- +. +|..+||--.||.++. ...+ ...|+
T Consensus 298 ~~~~~~~vF~~~~~~~~~~~~~~~~~~lk~~g~~~~~~~H~lRhT~aT~l~~-----~G~~--------------~~~i~ 358 (413)
T PRK09692 298 LSGNREFIFPSRIKPNQPMNSQTVNAALKRAGLGGVLVSHGLRSIASTALNE-----QGFP--------------PDVIE 358 (413)
T ss_pred hcCCCCeEecCCCCCCCCCCHHHHHHHHHHhCCCCCcCCCCcHHHHHHHHHh-----cCCC--------------HHHHH
Confidence 33456788843 56778999888753 23 5889999877775442 2211 23678
Q ss_pred HHcCCC-CCCCCchHHhHHHHHHHHHHH
Q psy17743 388 VLCNHQ-RSVPKSHDKSMGNLKEKISNK 414 (618)
Q Consensus 388 ilcNHq-raV~K~~~~~m~k~~~ki~~~ 414 (618)
.++||. .++...+-...+-+.++.+.+
T Consensus 359 ~~LGH~~~~~~~~~Y~r~~y~~err~~~ 386 (413)
T PRK09692 359 AALAHVDKNEVRRAYNRSDYLEQRRPMM 386 (413)
T ss_pred HHcCCCCCCchHHHHHHHHHHHHHHHHH
Confidence 899996 444333223344455554433
No 36
>cd01190 INT_SG5 INT_SG5, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 5, N- and C-terminal domains. The CD contains mainly predicted bacterial integrase/recombinases.
Probab=93.14 E-value=1.1 Score=43.81 Aligned_cols=85 Identities=18% Similarity=0.282 Sum_probs=62.1
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhh
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVE 316 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~ 316 (618)
.+++.|+=.+.+|.|. ++.|+.+||.+.. + ..+...||.+..+ +|++.+.+...|....+
T Consensus 98 ~~~~~l~~~tGlR~~E-----------i~~L~~~di~~~~------~-~~~~~~~k~~~~r--~vpl~~~~~~~l~~~~~ 157 (260)
T cd01190 98 RAMLLFLYNTGARVSE-----------ATGLKVDDLQLDP------P-AQVRLIGKGRKER--TVPLWRSTAAALRAWLR 157 (260)
T ss_pred HHHHHHHHHhCccHHH-----------HHcCCHHHhccCC------C-cEEEEecCCCcce--eEECCHHHHHHHHHHHH
Confidence 4577777889999987 7889999998754 2 2233457765543 67788999999988866
Q ss_pred ccC---CCcccccc-----CChhHHHHHHHHhc
Q psy17743 317 NKK---GSDDLFDR-----LNTSVLNKHLSELM 341 (618)
Q Consensus 317 ~K~---Pgd~LF~~-----l~s~~LN~yLkelm 341 (618)
... |.+.||-. ++...+|..++.+.
T Consensus 158 ~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~ 190 (260)
T cd01190 158 ERGLHAEDEPLFVNRRGEPMTRFGVTYLLRKHA 190 (260)
T ss_pred hcCCCCCCCeeeecCCCCcCcHHHHHHHHHHHH
Confidence 433 67788853 67778888887764
No 37
>cd01182 INT_REC_C DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family include the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many intergrase/recombinases also have N-terminal domains, which show little sequence or structure similarity.
Probab=93.10 E-value=0.43 Score=41.85 Aligned_cols=123 Identities=19% Similarity=0.183 Sum_probs=82.1
Q ss_pred HHHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHh
Q psy17743 235 QRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLF 314 (618)
Q Consensus 235 qlA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f 314 (618)
..+.++.|+=.+.+|.+. ++.|...||...+ ..+.+.- .|.+.. ..+.+++.++..|..+
T Consensus 16 ~~~~~~~l~~~~G~R~~e-----------i~~l~~~~v~~~~------~~~~i~~-~K~~~~--~~~~i~~~~~~~l~~~ 75 (162)
T cd01182 16 RDRALILLLLYTGLRVSE-----------LLALRWSDIDLDK------GTITVRR-TKTGKE--RTVPLSPELAELLREY 75 (162)
T ss_pred HHHHHHHHHHHhCCCHHH-----------HhhhehhcccCcC------CEEEEEe-cCCCCc--eEEecCHHHHHHHHHH
Confidence 445556666669999986 7888899998764 4444432 376644 4566677788888888
Q ss_pred hhc----cCCCccccccC-------ChhHHHHHHHHhcC------CCeeeeeccccchHHHHHHHhhcCCCCccHHHHHH
Q psy17743 315 VEN----KKGSDDLFDRL-------NTSVLNKHLSELME------GLTAKVFRTYNASITLQQQLNELMDPDFSEAEKIL 377 (618)
Q Consensus 315 ~~~----K~Pgd~LF~~l-------~s~~LN~yLkelm~------glTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~ 377 (618)
.+. ..++..||... +...++.+++.+.. ++|...||-..+|.++. ... +
T Consensus 76 ~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lR~~~~~~~~~-----~g~---~------ 141 (162)
T cd01182 76 LELRRPAPKPDDYLFPSRRGGPKRLTRRAVRRLLKKAGKRAGIPERLTPHDLRHTFATRLLE-----AGV---P------ 141 (162)
T ss_pred HHHhcccCCCCCeEEEcCCCCCcccchHHHHHHHHHHHHHcCCCcccCcchhHHHHHHHHHH-----CCC---C------
Confidence 764 25678889763 45667777777753 37888888777775443 111 1
Q ss_pred HHHHHHHHHHHHcCCCCCC
Q psy17743 378 AYNRANRAVAVLCNHQRSV 396 (618)
Q Consensus 378 ~yn~Anr~VAilcNHqraV 396 (618)
...||...||+...
T Consensus 142 -----~~~~~~~~gH~~~~ 155 (162)
T cd01182 142 -----LEVIQELLGHSSIS 155 (162)
T ss_pred -----HHHHHHHhCCCCHH
Confidence 44778888997643
No 38
>cd01189 INT_phiLC3_C phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus phage phiLC3, TPW22, Tuc2009, BK5-T, A2, bIL285, bIL286, bIL311, ul36 and phi g1e; Staphylococcus aureus phage phi13 and phi42; Oenococcus oeni phage fOg44; Streptococcus thermophilus phage O1205 and Sfi21; and Streptococcus pyogenes phage T12 and T270.
Probab=92.80 E-value=0.82 Score=42.34 Aligned_cols=103 Identities=19% Similarity=0.356 Sum_probs=66.5
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEE-----------ee-cCCceEEEEEeccch
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFD-----------FL-GKDSIRYYNEVPVEK 305 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~Fd-----------Fl-GKdsir~~~~V~vD~ 305 (618)
+++.|+=.+.+|.+. ++.|+..+|.... +.+.+. +. .|.+ .....|++.+
T Consensus 25 ~~~~l~~~~G~R~~E-----------i~~l~~~dv~~~~------~~~~~~~~~~~~~~~~~~~~~k~~-~~~~~v~i~~ 86 (191)
T cd01189 25 LLILLLAYTGLRIGE-----------ALALTWSDIDFEN------NTITINKTWDYKTGGYIFKPPKTK-SSIRTIPLDK 86 (191)
T ss_pred HHHHHHHHhccHHHH-----------HhhceecccCCcC------CEEEEEEEEEEcCCceEecCCccc-CcceeEecCH
Confidence 344444458888877 7788888876543 333222 21 1332 2334677888
Q ss_pred HHHHHHHHhhhc---------cCCCcccccc-----CChhHHHHHHHHhcC-----CCeeeeeccccchHHH
Q psy17743 306 RVFKNLQLFVEN---------KKGSDDLFDR-----LNTSVLNKHLSELME-----GLTAKVFRTYNASITL 358 (618)
Q Consensus 306 ~v~knL~~f~~~---------K~Pgd~LF~~-----l~s~~LN~yLkelm~-----glTAKvFRTynASvt~ 358 (618)
.+...|..+... ..+++.||.. ++...++..++.+.. ++|..+||-.-+|.++
T Consensus 87 ~~~~~l~~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~g~~~~s~h~lRht~~t~l~ 158 (191)
T cd01189 87 KTIAILKEYKKEQKKYLLGEINNDDELVFTNKGGKISTPSTINKRLKRICKKAGIPKITFHGLRHTHASLLL 158 (191)
T ss_pred HHHHHHHHHHHHHHHHhhcccCCCCCeEEeCCCCCCCCchhHHHHHHHHHHHcCCCCcceeccHHHHHHHHH
Confidence 888888887753 2467788886 456789999988752 3788888876666543
No 39
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=92.77 E-value=0.46 Score=47.28 Aligned_cols=118 Identities=22% Similarity=0.302 Sum_probs=79.7
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhh
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVE 316 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~ 316 (618)
.+++.|+=.+++|.|. +|.|+.++|.+.+ +.+.+. +|.+..+ .|++.+.+...|..+..
T Consensus 137 ~~~~~l~~~tGlR~~E-----------~~~L~~~di~~~~------~~~~i~--~k~~~~r--~vpl~~~~~~~l~~~~~ 195 (299)
T PRK00283 137 RAMLELLYATGLRVSE-----------LVGLTLDDVSLRQ------GVVRVT--GKGNKER--LVPLGEEAVYAIERYLE 195 (299)
T ss_pred HHHHHHHHHhCCcHHH-----------HHcCcHHHcCcCC------CEEEEe--ccCCCee--eeeCCHHHHHHHHHHHH
Confidence 4556666678999987 8899999998866 566654 7877654 56777888888888763
Q ss_pred c-------cCCCcccccc-----CChhHHHHHHHHhc-------CCCeeeeeccccchHHHHHHHhhcCCCCccHHHHHH
Q psy17743 317 N-------KKGSDDLFDR-----LNTSVLNKHLSELM-------EGLTAKVFRTYNASITLQQQLNELMDPDFSEAEKIL 377 (618)
Q Consensus 317 ~-------K~Pgd~LF~~-----l~s~~LN~yLkelm-------~glTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~ 377 (618)
. ..+++.||-. ++...++..++.+. +++|..+||--.||.++ +... +
T Consensus 196 ~~~~~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~gi~~~~~t~H~lRht~at~l~-----~~g~---~------ 261 (299)
T PRK00283 196 RGRPALLNGRSSDALFPSARGGQLTRQTFWHRIKHYAKRAGIDPKKLSPHVLRHAFATHLL-----NHGA---D------ 261 (299)
T ss_pred hcccccCCCCCCCceeecCCCCcCCHHHHHHHHHHHHHHhCCCccCCCchHHHHHHHHHHH-----HcCC---C------
Confidence 2 2345678853 56677888887763 23677777755555433 2211 1
Q ss_pred HHHHHHHHHHHHcCCCC
Q psy17743 378 AYNRANRAVAVLCNHQR 394 (618)
Q Consensus 378 ~yn~Anr~VAilcNHqr 394 (618)
...|+.++||+.
T Consensus 262 -----~~~i~~~lGH~~ 273 (299)
T PRK00283 262 -----LRVVQELLGHSD 273 (299)
T ss_pred -----HHHHHHHhCCCC
Confidence 247888899964
No 40
>cd00799 INT_Cre Cre recombinase, C-terminal catalytic domain. Cre-like recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region.
Probab=92.54 E-value=1 Score=45.23 Aligned_cols=123 Identities=17% Similarity=0.135 Sum_probs=81.5
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEee-cCCce---EEEEEecc-chHHHHHH
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFL-GKDSI---RYYNEVPV-EKRVFKNL 311 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFl-GKdsi---r~~~~V~v-D~~v~knL 311 (618)
.+++.|+-.+.+|+|- ++.|+.+||.+.. ++.+.+... +|.+. .....++. +..+...|
T Consensus 119 ~~~~~l~~~tGlR~~E-----------i~~L~~~did~~~-----~~~~~i~i~~~K~~~~~~~~~~~ip~~~~~~~~~l 182 (287)
T cd00799 119 LALLLLGFAGLLRRSE-----------LVRLRWEDLTFTD-----GGGLLVTLRRSKTDQSGLGVLKLIPPLTTCPVRAL 182 (287)
T ss_pred HHHHHHHHHhhhhHHH-----------HHhhhHhheEEcc-----CCCEEEEeccCCcCcCCCCeEEecCCcccCHHHHH
Confidence 4577777889999987 8899999999864 144555544 66633 44444442 12456666
Q ss_pred HHhhhc-cCCCcccccc-----------CChhHHHHHHHHhcC-------CCeeeeeccccchHHHHHHHhhcCCCCccH
Q psy17743 312 QLFVEN-KKGSDDLFDR-----------LNTSVLNKHLSELME-------GLTAKVFRTYNASITLQQQLNELMDPDFSE 372 (618)
Q Consensus 312 ~~f~~~-K~Pgd~LF~~-----------l~s~~LN~yLkelm~-------glTAKvFRTynASvt~~~~L~~~~~~~~s~ 372 (618)
+.+.+. ..+++.||.. +++..+|..++.+.. .+|...||-..||.++. ...+
T Consensus 183 ~~~~~~~~~~~~~lF~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~gi~~~~~~~H~lRht~at~l~~-----~g~~---- 253 (287)
T cd00799 183 ERWLEAARIPKGPLFRRIDRWGVLGPGALSDNSLNRILKRLAEAAGLRSGSWSGHSLRRGFATEAAR-----AGYS---- 253 (287)
T ss_pred HHHHHHhCCCCCceeEEecCCCCcCCCCCCHHHHHHHHHHHHHHcCCCcccccccccchhHHHHHHH-----cCCC----
Confidence 665542 3577888852 677889999998853 27888999877775543 1111
Q ss_pred HHHHHHHHHHHHHHHHHcCCCC
Q psy17743 373 AEKILAYNRANRAVAVLCNHQR 394 (618)
Q Consensus 373 ~ek~~~yn~Anr~VAilcNHqr 394 (618)
...|+.++||+.
T Consensus 254 ----------~~~i~~~lGH~~ 265 (287)
T cd00799 254 ----------LLEIMRQGRWRS 265 (287)
T ss_pred ----------HHHHHHHcCCCC
Confidence 246788999974
No 41
>TIGR02225 recomb_XerD tyrosine recombinase XerD. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK.
Probab=92.29 E-value=1.4 Score=43.31 Aligned_cols=119 Identities=26% Similarity=0.302 Sum_probs=79.2
Q ss_pred HHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhh
Q psy17743 236 RAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFV 315 (618)
Q Consensus 236 lA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~ 315 (618)
.++++.|+=.+++|+|. ++.|+..+|.... +.+. ..+|.+..+ .|++.+.+...|..+.
T Consensus 127 ~~~~~~l~~~tG~R~~E-----------~~~L~~~di~~~~------~~i~--~~~k~~~~r--~ipl~~~~~~~l~~~~ 185 (291)
T TIGR02225 127 DRAMLELLYATGLRVSE-----------LVGLRLEDVNLDE------GFVR--VRGKGNKER--LVPLGEEAIEALERYL 185 (291)
T ss_pred HHHHHHHHHHhCCCHHH-----------HHcCcHHHhCcCC------CeEE--EecCCCcce--EEecCHHHHHHHHHHH
Confidence 34556666678999987 8899999998765 4444 678887765 6777888888888765
Q ss_pred hcc---------CCCccccc-----cCChhHHHHHHHHhcC------CCeeeeeccccchHHHHHHHhhcCCCCccHHHH
Q psy17743 316 ENK---------KGSDDLFD-----RLNTSVLNKHLSELME------GLTAKVFRTYNASITLQQQLNELMDPDFSEAEK 375 (618)
Q Consensus 316 ~~K---------~Pgd~LF~-----~l~s~~LN~yLkelm~------glTAKvFRTynASvt~~~~L~~~~~~~~s~~ek 375 (618)
... .+++.||- .++.+.++..++.+.. ++|..+||-..|| .|....- +
T Consensus 186 ~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~h~lRht~~t-----~~~~~g~---~---- 253 (291)
T TIGR02225 186 KEARPLLLKKKVKESDALFLNRRGGPLSRQGVWKILKEYAKRAGIEKPISPHTLRHSFAT-----HLLENGA---D---- 253 (291)
T ss_pred HHhhhcccccccCCCCceeecCCCCcCCHHHHHHHHHHHHHHhCCCCCcCchHHHHHHHH-----HHHHcCC---C----
Confidence 321 15667884 3677788888888743 2567777743333 3332221 1
Q ss_pred HHHHHHHHHHHHHHcCCCC
Q psy17743 376 ILAYNRANRAVAVLCNHQR 394 (618)
Q Consensus 376 ~~~yn~Anr~VAilcNHqr 394 (618)
...++.++||+.
T Consensus 254 -------~~~i~~~~GH~~ 265 (291)
T TIGR02225 254 -------LRVVQELLGHAD 265 (291)
T ss_pred -------HHHHHHHhCCCC
Confidence 136788889964
No 42
>cd01194 INT_Tn554A_C Tn544A and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain. This CD includes various bacterial transposases similar to TnpA from transposon Tn554.
Probab=92.29 E-value=0.86 Score=42.46 Aligned_cols=120 Identities=22% Similarity=0.242 Sum_probs=79.8
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEee--------cCCceEEEEEeccchHHH
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFL--------GKDSIRYYNEVPVEKRVF 308 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFl--------GKdsir~~~~V~vD~~v~ 308 (618)
.+++.++-.+.+|.|. +|+|+.+||.+.+ +.+.+.-. +|.+. ...|++.+.+.
T Consensus 19 ~~~~~l~~~tglR~~E-----------i~~L~~~di~~~~------~~i~i~~~~~~~~~~~~K~~~--~r~v~l~~~~~ 79 (186)
T cd01194 19 KFLFALLYETGLRIGE-----------ALGLRIEDIDLAE------NQIWLVPREDNANGARAKSGR--ERRIPVSQYLI 79 (186)
T ss_pred HHHHHHHHHcCCChhh-----------hhccccceeecCC------CEEEEeecCCCcCcccccCCC--CceEEcCHHHH
Confidence 4556666688999987 8999999998865 55665532 24443 34667777877
Q ss_pred HHHHHhhh-----ccCCCccccc---------cCChhHHHHHHHHhcC----CCeeeeeccccchHHHHHHHhhcCCCCc
Q psy17743 309 KNLQLFVE-----NKKGSDDLFD---------RLNTSVLNKHLSELME----GLTAKVFRTYNASITLQQQLNELMDPDF 370 (618)
Q Consensus 309 knL~~f~~-----~K~Pgd~LF~---------~l~s~~LN~yLkelm~----glTAKvFRTynASvt~~~~L~~~~~~~~ 370 (618)
..|..... ...++..||- .++...++..++.++. .+|..+||-..+|..+. ...+
T Consensus 80 ~~l~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lR~t~~t~~~~-----~g~~-- 152 (186)
T cd01194 80 DLYVDYVTEIYYLEELESDYVFVNVKGGNQGKPLNYTDVYDLVRRLKKKTGIDFTPHMFRHTHATELIR-----AGWS-- 152 (186)
T ss_pred HHHHHHHHHHcccccCCCCEEEEcCCCCCCCcccCHHHHHHHHHHHHHHcCCCCCccccchHHHHHHHH-----cCCC--
Confidence 77776643 1355677874 2567778888887763 27888888777664332 2111
Q ss_pred cHHHHHHHHHHHHHHHHHHcCCCC
Q psy17743 371 SEAEKILAYNRANRAVAVLCNHQR 394 (618)
Q Consensus 371 s~~ek~~~yn~Anr~VAilcNHqr 394 (618)
...|+.++||+.
T Consensus 153 ------------~~~i~~~~gH~~ 164 (186)
T cd01194 153 ------------IEVVADRLGHAH 164 (186)
T ss_pred ------------HHHHHHHhCCCC
Confidence 136788999975
No 43
>cd01186 INT_SG3_C INT_SG3, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 3, catalytic domain. The CD contains various predicted bacterial and phage integrase/recombinase sequences for which not much experimental characterization is available.
Probab=92.10 E-value=0.57 Score=44.48 Aligned_cols=100 Identities=14% Similarity=0.215 Sum_probs=70.7
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhc
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN 317 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~ 317 (618)
+++.|+-.+.+|.|. ++.|+.++|...+ .+.+. .+|.|.. ..|++.+.+...|+.+...
T Consensus 28 ~~~~l~~~tGlR~~E-----------l~~l~~~di~~~~-------~i~i~-~~K~~~~--r~vpl~~~l~~~l~~~~~~ 86 (180)
T cd01186 28 LLFLIGINTGLRISD-----------ILALKVKDVRGDE-------RISIK-EKKTGKR--KRIYLNPILKEELLYYIKD 86 (180)
T ss_pred HHHHHHHHhhhHHHH-----------HHhcCHHHhCCCC-------ceEEE-EecCCce--EEEEECHHHHHHHHHHHHh
Confidence 457777789999987 8889999887642 23333 2566664 4677789999999988865
Q ss_pred cCCCcccccc-------CChhHHHHHHHHhcC--C---CeeeeeccccchHHH
Q psy17743 318 KKGSDDLFDR-------LNTSVLNKHLSELME--G---LTAKVFRTYNASITL 358 (618)
Q Consensus 318 K~Pgd~LF~~-------l~s~~LN~yLkelm~--g---lTAKvFRTynASvt~ 358 (618)
..+++.||.. ++.+.+|.+++.++. | +|..+||--.||.++
T Consensus 87 ~~~~~~lf~~~~~~~~~~~~~~~~~~~k~~~~~~gi~~~~~H~lRht~at~l~ 139 (180)
T cd01186 87 LEENEYLFQSRKGGNRPITRQQAYRILKKAAEQVGIDNIGTHTLRKTFGYHYY 139 (180)
T ss_pred CCCcCceEEecCCCCCCccHHHHHHHHHHHHHHcCCCcccccccHHHHHHHHH
Confidence 4567788864 677889999987763 2 566777765555443
No 44
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=91.99 E-value=1.2 Score=43.91 Aligned_cols=98 Identities=20% Similarity=0.313 Sum_probs=68.3
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhh
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVE 316 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~ 316 (618)
.+++.|+-.+.+|+|. +++|+.+||.+.. +.+.+ .+|.+..+ .|++.+.+...|.....
T Consensus 139 ~~~~~l~~~tG~R~~E-----------i~~L~~~~i~~~~------~~~~i--~~k~~~~r--~vpl~~~~~~~l~~~~~ 197 (297)
T PRK00236 139 RAILELLYGSGLRLSE-----------LVGLDIDDLDLAS------GTLRV--LGKGNKER--TVPLGRAAREALEAYLA 197 (297)
T ss_pred HHHHHHHHHccchHHH-----------HHhccHHHhccCC------ceEEE--EecCCceE--EEECcHHHHHHHHHHHH
Confidence 3455666678999987 8899999999754 55555 46766544 67778888888887765
Q ss_pred cc----CCCcccccc-----CChhHHHHHHHHhcC------CCeeeeeccccch
Q psy17743 317 NK----KGSDDLFDR-----LNTSVLNKHLSELME------GLTAKVFRTYNAS 355 (618)
Q Consensus 317 ~K----~Pgd~LF~~-----l~s~~LN~yLkelm~------glTAKvFRTynAS 355 (618)
.. .+++.||-. +++..+++.++.++. ++|..+||-.-||
T Consensus 198 ~~~~~~~~~~~lF~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~H~lRht~~t 251 (297)
T PRK00236 198 LRPLFLPDDDALFLGARGGRLSPRVVQRRVKKLGKKAGLPSHITPHKLRHSFAT 251 (297)
T ss_pred HccCcCccCCceeecCCCCCCChhHHHHHHHHHHHHcCCCCCcCcHHHHHHHHH
Confidence 32 367888843 677778888777752 3677777733334
No 45
>PRK09871 tyrosine recombinase; Provisional
Probab=91.44 E-value=0.63 Score=44.85 Aligned_cols=118 Identities=11% Similarity=0.118 Sum_probs=81.4
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhc
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN 317 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~ 317 (618)
+++.|+-.+.+|+|- ++.|+.++|.+.. +.|.+.- +|.+... .+++.+.+...|..+.+.
T Consensus 30 ~l~~l~~~tGlR~sE-----------l~~L~~~did~~~------~~i~i~~-~K~~~~~--~vpl~~~~~~~l~~~~~~ 89 (198)
T PRK09871 30 CLILLAYRHGMRISE-----------LLDLHYQDLDLNE------GRINIRR-LKNGFST--VHPLRFDEREAVERWTQE 89 (198)
T ss_pred HHHHHHHHhCCcHHH-----------HHcCCHHhcCccC------CeEEEEe-cCCCccc--eecCCHHHHHHHHHHHHh
Confidence 456677779999987 8899999998765 5666642 4655543 456678888888776532
Q ss_pred ------cCCCccccc-----cCChhHHHHHHHHhcC------CCeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHH
Q psy17743 318 ------KKGSDDLFD-----RLNTSVLNKHLSELME------GLTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYN 380 (618)
Q Consensus 318 ------K~Pgd~LF~-----~l~s~~LN~yLkelm~------glTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn 380 (618)
..+.+.||- .++++.+|..++.+.. .+|..+||-..||.++. .+. +
T Consensus 90 ~~~~~~~~~~~~lF~~~~g~~~~~~~~~~~lk~~~~~~~~~~~~~~H~LRHT~at~l~~-----~G~---~--------- 152 (198)
T PRK09871 90 RANWKGADRTDAIFISRRGSRLSRQQAYRIIRDAGIEAGTVTQTHPHMLRHACGYELAE-----RGA---D--------- 152 (198)
T ss_pred hhccCCCCCCCCeEecCCCCCccHHHHHHHHHHHHHhcCcCCCCCCcccchHHHHHHHH-----cCC---C---------
Confidence 134567884 4788889998888742 47889999888886542 111 1
Q ss_pred HHHHHHHHHcCCCC
Q psy17743 381 RANRAVAVLCNHQR 394 (618)
Q Consensus 381 ~Anr~VAilcNHqr 394 (618)
...|+.++||.-
T Consensus 153 --~~~i~~~lGH~s 164 (198)
T PRK09871 153 --TRLIQDYLGHRN 164 (198)
T ss_pred --HHHHHHHhCCCC
Confidence 236888899953
No 46
>cd01199 INT_Tn1545_C Tn1545-related conjugative transposon integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes bacterial (gram positive) and phage integrases, including those similar to Tn1545, Tn5252, and Tn5276 conjugative transposon integrases and Lactobacillus phage phi adh integrase.
Probab=90.84 E-value=2.9 Score=39.33 Aligned_cols=124 Identities=22% Similarity=0.282 Sum_probs=73.0
Q ss_pred HHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEee--------------cCCceEEEEEe
Q psy17743 236 RAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFL--------------GKDSIRYYNEV 301 (618)
Q Consensus 236 lA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFl--------------GKdsir~~~~V 301 (618)
..+++.|+-.+.+|+|. ++.|+.+||.+.. ..|.+.-. +.....-..+|
T Consensus 23 ~~~~~~l~~~tG~R~~E-----------i~~L~~~di~~~~------~~i~v~~~~~~~~~~~~~~~~~~~k~~~~~r~v 85 (205)
T cd01199 23 YADILEFLFLTGMRIGE-----------LLALQEKDIDFEN------KLINIDGTLDSHTGKEENGYKDTPKTKSSIRTI 85 (205)
T ss_pred HHHHHHHHHHhCChHHH-----------HhcCchhhccCCC------CEEEEEeeEeeccCCCCceeecCCCCCCCceEE
Confidence 34566677789999986 8889999988755 44444321 00000113478
Q ss_pred ccchHHHHHHHHhhhc---------cCCCcccccc-----CC-hhHHHHHHHHhc---C-----CCeeeeeccccchHHH
Q psy17743 302 PVEKRVFKNLQLFVEN---------KKGSDDLFDR-----LN-TSVLNKHLSELM---E-----GLTAKVFRTYNASITL 358 (618)
Q Consensus 302 ~vD~~v~knL~~f~~~---------K~Pgd~LF~~-----l~-s~~LN~yLkelm---~-----glTAKvFRTynASvt~ 358 (618)
++.+.+...|+..... ..+.+.||-. ++ +..++..++.+. + .+|...||-.-||.
T Consensus 86 ~l~~~~~~~l~~~~~~~~~~~~~~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~lRht~~t~-- 163 (205)
T cd01199 86 SLSERAVEIIKRFIKRNKFDKFNPDYKDSDFLFTNKKGNPLDLGPINSKILSKFLKDLGSQSKKHVTTHIFRHTHISF-- 163 (205)
T ss_pred ecCHHHHHHHHHHHHHHHhhhhcccCCCCceEEecCCCCEeccchHHHHHHHHHHHHcCCCcCCCcceecchHHHHHH--
Confidence 8889999999888763 2255677854 32 334555454432 1 36666777444443
Q ss_pred HHHHhhcCCCCccHHHHHHHHHHHHHHHHHHcCCCCC
Q psy17743 359 QQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQRS 395 (618)
Q Consensus 359 ~~~L~~~~~~~~s~~ek~~~yn~Anr~VAilcNHqra 395 (618)
+..... ....|+.++||+..
T Consensus 164 ---~~~~g~--------------~~~~i~~~lGH~~~ 183 (205)
T cd01199 164 ---LAEEGV--------------PLKAIMDRVGHSDG 183 (205)
T ss_pred ---HHHcCC--------------CHHHHHHHhCCCch
Confidence 222211 13467889999754
No 47
>cd00796 INT_Rci Rci recombinase, C-terminal catalytic domain. Rci enzymes are found in IncI1 incompatibility group plasmids such as R64. These recombinases belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The R64 Rci recombinase mediates site specific recombination at the highly mobile DNA segments called shufflon located in the C-terminal region of the pilV gene, which determines the recipient specificity in liquid mating. This gene encodes a thin pilus component that recognizes recipient's receptors required for liquid mating. The recombination occurs between any of the seven inverted repeats that separate four DNA segments of the shufflon. The segments can be inverted independently or in groups, resulting in a complex DNA rearrangement. The catalytic domain of Rci is linked to a variable N-terminal domain, whose function is unknown.
Probab=90.64 E-value=1.1 Score=42.85 Aligned_cols=101 Identities=22% Similarity=0.299 Sum_probs=70.7
Q ss_pred HHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhh
Q psy17743 236 RAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFV 315 (618)
Q Consensus 236 lA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~ 315 (618)
...+++|+=.+.+|.|. +|.|+.++|.+.. +.|.+. .+|.+.. ..|++.+.+...|+...
T Consensus 66 ~~~~~~l~~~tGlR~~E-----------~~~l~~~did~~~------~~i~i~-~~K~~~~--r~ipl~~~~~~~l~~~~ 125 (206)
T cd00796 66 LPVIILLALETAMRRGE-----------ILSLRWEQVDLKK------RVAHLP-DTKNGTS--RDVPLSKRAVALLQMLP 125 (206)
T ss_pred hHHHHHHHHHhcccHHH-----------HHcCcHHHcCccc------CEEEEe-cCcCCCc--ceecCCHHHHHHHHHhh
Confidence 35567777788999986 8999999998755 566654 2555543 36788888889998886
Q ss_pred hccCCCccccccCChhHHHHHHHHhcC-----CCeeeeeccccchHHH
Q psy17743 316 ENKKGSDDLFDRLNTSVLNKHLSELME-----GLTAKVFRTYNASITL 358 (618)
Q Consensus 316 ~~K~Pgd~LF~~l~s~~LN~yLkelm~-----glTAKvFRTynASvt~ 358 (618)
.. .+++.||. .+...++.+++.++. ++|..+||-..||.++
T Consensus 126 ~~-~~~~~lf~-~~~~~~~~~~~~~~~~~g~~~~~~H~lRht~~t~l~ 171 (206)
T cd00796 126 KV-PDDGPVFP-ITSDSVDAAFRRAKERAGLEDLHFHDLRHEATSRLF 171 (206)
T ss_pred hc-CCCCceec-CCCccHHHHHHHHHHHcCCCCCchHhhHhHHHHHHH
Confidence 53 46778886 355567878877764 3667777766665433
No 48
>PRK01287 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=90.44 E-value=1 Score=47.58 Aligned_cols=118 Identities=22% Similarity=0.321 Sum_probs=81.2
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhc
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN 317 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~ 317 (618)
+++.|+-.+.||+|. +|.|+..+|.+.. +.|.+. .||.+..+ .|.+.+.+...|+.+...
T Consensus 161 ~~~~ll~~tGlR~~E-----------~~~L~~~did~~~------~~i~i~-~~K~~~~R--~vpl~~~~~~~L~~~~~~ 220 (358)
T PRK01287 161 ALLELLWSTGIRRGE-----------LARLDLYDVDASR------GVVTVR-QGKGNKDR--VVPVGERALAWLQRYLQD 220 (358)
T ss_pred HHHHHHHHhCCCHHH-----------HHcCCHHhcCccC------CeEEEe-eCCCCCCC--cccCCHHHHHHHHHHHHH
Confidence 346666678899987 8999999998755 567664 47777654 577778888887776532
Q ss_pred -------cCCCcccccc-----CChhHHHHHHHHhcC--C----CeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHH
Q psy17743 318 -------KKGSDDLFDR-----LNTSVLNKHLSELME--G----LTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAY 379 (618)
Q Consensus 318 -------K~Pgd~LF~~-----l~s~~LN~yLkelm~--g----lTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~y 379 (618)
..+++.||-. +++..|+..++.+.. | +|..+||-..||.++. .+. +
T Consensus 221 ~r~~~~~~~~~~~lF~~~~g~~i~~~~i~~~~~~~~~~agi~~~~t~H~lRHt~at~l~~-----~G~---~-------- 284 (358)
T PRK01287 221 VRPQLAVRPDSGALFVAMDGDGLARNTLTNMVGRYIRAAGIEKAGACHLFRHAMATQMLE-----NGA---D-------- 284 (358)
T ss_pred hchhcccCCCCCceEEeCCCCcCCHHHHHHHHHHHHHHhCCCCCCCcccchHHHHHHHHH-----cCC---C--------
Confidence 1355678853 778889988887642 2 5677888777765332 111 1
Q ss_pred HHHHHHHHHHcCCCC
Q psy17743 380 NRANRAVAVLCNHQR 394 (618)
Q Consensus 380 n~Anr~VAilcNHqr 394 (618)
...|+.+|||..
T Consensus 285 ---~~~v~~~LGH~s 296 (358)
T PRK01287 285 ---TRHIQAILGHAK 296 (358)
T ss_pred ---HHHHHHHhCCCc
Confidence 237888999976
No 49
>cd01184 INT_SG2_C INT_SG2, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 2, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinases and phage-related integrases. Some have N-terminal domains, which show little sequence similarity to each other. Members of this subgroup are predominantly found in proteobacteria.
Probab=90.28 E-value=1.2 Score=41.75 Aligned_cols=122 Identities=20% Similarity=0.261 Sum_probs=74.0
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeec-------CCceEEEEEeccchHHHHH
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLG-------KDSIRYYNEVPVEKRVFKN 310 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlG-------Kdsir~~~~V~vD~~v~kn 310 (618)
.++.|+=.+.+|+|. +++|+.++|.+.. +.+.+.+.. |.+. -...|++.+.+...
T Consensus 28 ~~~~l~~~tGlR~~E-----------i~~l~~~di~~~~------~~~~i~~~~~~~~~~~K~~~-~~r~vpl~~~~~~~ 89 (181)
T cd01184 28 WLPLLGLYTGARVNE-----------IAQLQVDDIREED------GVPCIDITNDDEDQSLKNAA-SRRTIPVHPELIEL 89 (181)
T ss_pred HHHHHHHHHCCCHHH-----------HhcccHHHeeeeC------CeEEEEeecchhccCCCCCC-CcccccCCHHHHHc
Confidence 344455567899987 8889999998864 344444332 2222 14578888888887
Q ss_pred -HHHhhhc--cCCCccccccC-------ChhHHHHHHHHhc-------CCCeeeeeccccchHHHHHHHhhcCCCCccHH
Q psy17743 311 -LQLFVEN--KKGSDDLFDRL-------NTSVLNKHLSELM-------EGLTAKVFRTYNASITLQQQLNELMDPDFSEA 373 (618)
Q Consensus 311 -L~~f~~~--K~Pgd~LF~~l-------~s~~LN~yLkelm-------~glTAKvFRTynASvt~~~~L~~~~~~~~s~~ 373 (618)
|..+.+. ..+.+.||-.. ++..+++.++.++ .++|..+||--.||.++. ...
T Consensus 90 ~l~~~~~~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~t~H~lRht~at~~~~-----~g~------ 158 (181)
T cd01184 90 GFLDYVEARRAAGHKRLFPDLPAGKTGGYGSAVSKWFSRYLKKLGLKDKGKSFHSFRHTFITELRN-----AGV------ 158 (181)
T ss_pred cHHHHHHHHHccCCceecccccccCCCCchHHHHHHHHHHHHHhcCCCCccchhhhHHHHHHHHHH-----cCC------
Confidence 6555432 24567788752 3445555555553 237888888666664432 111
Q ss_pred HHHHHHHHHHHHHHHHcCCCCCC
Q psy17743 374 EKILAYNRANRAVAVLCNHQRSV 396 (618)
Q Consensus 374 ek~~~yn~Anr~VAilcNHqraV 396 (618)
-...|+.++||+...
T Consensus 159 --------~~~~i~~~lgHs~~~ 173 (181)
T cd01184 159 --------SRELIAAIMGHEEGT 173 (181)
T ss_pred --------CHHHHHHhcCCCCCC
Confidence 134678889997653
No 50
>TIGR02249 integrase_gron integron integrase. Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.
Probab=89.92 E-value=1.2 Score=45.40 Aligned_cols=117 Identities=21% Similarity=0.277 Sum_probs=78.0
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhc
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN 317 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~ 317 (618)
+++.|+=.+.+|+|- +|+|+.+||.+.. +.|.+. .+|.+.. .+|++.+.+...|+.....
T Consensus 120 ~~v~ll~~tGlR~~E-----------~~~L~~~did~~~------~~i~v~-~~K~~~~--r~vpl~~~~~~~L~~~~~~ 179 (315)
T TIGR02249 120 LIAKLLYGSGMRLME-----------CLRLRIQDIDFDY------GEIRIR-QGKGGKD--RTVTLPKELIPPLREQIEL 179 (315)
T ss_pred HHHHHHHHcCCCHHH-----------HHhccHHhcccCC------CeEEEE-eCCCCce--eEEecCHHHHHHHHHHHHH
Confidence 345566668899987 8999999999876 677775 4677654 4677778887777664321
Q ss_pred ------------------------cC-------CCccccc----------------cCChhHHHHHHHHhc-----CC-C
Q psy17743 318 ------------------------KK-------GSDDLFD----------------RLNTSVLNKHLSELM-----EG-L 344 (618)
Q Consensus 318 ------------------------K~-------Pgd~LF~----------------~l~s~~LN~yLkelm-----~g-l 344 (618)
+. +++.||- .+++..++..++.+. ++ +
T Consensus 180 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lf~~~~~~~~~~~g~~~~~~~~~~~~~~~~k~~~~~~gi~~~~ 259 (315)
T TIGR02249 180 ARAYHEADLAEGYGGVYLPHALARKYPNAPKEWGWQYLFPSHRLSRDPESGVIRRHHINETTIQRAVRRAVERAGIEKPV 259 (315)
T ss_pred HHhhhccchhhccccccchhhhhhcccccccCCCceeeeecccccccccccccccCCcCHHHHHHHHHHHHHHcCCCCCc
Confidence 01 1235663 256778888888874 23 7
Q ss_pred eeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHHHHHHHcCCC
Q psy17743 345 TAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQ 393 (618)
Q Consensus 345 TAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr~VAilcNHq 393 (618)
|..+||--.||.++. .+. + ...|+.++||.
T Consensus 260 ~~H~lRHt~at~l~~-----~g~---~-----------~~~i~~~LGH~ 289 (315)
T TIGR02249 260 TCHTLRHSFATHLLE-----SGA---D-----------IRTVQELLGHS 289 (315)
T ss_pred ccccccHHHHHHHHH-----cCC---C-----------HHHHHHHhCCC
Confidence 889999666665543 111 1 24688889996
No 51
>cd01197 INT_FimBE_C FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes those proteins similar to E.coli FimE and FimB regulatory proteins and Proteus mirabilis MrpI.
Probab=89.88 E-value=0.82 Score=42.90 Aligned_cols=116 Identities=17% Similarity=0.239 Sum_probs=79.4
Q ss_pred HHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhc-
Q psy17743 239 ALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN- 317 (618)
Q Consensus 239 AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~- 317 (618)
++.|+-.+.+|+|. +++|+.++|.+.. +.+.+.- +|.+..+ .+++.+.+...|+..+..
T Consensus 29 ~~~l~~~tGlR~~E-----------i~~L~~~did~~~------~~l~v~~-~K~~~~~--~~pi~~~~~~~l~~~~~~~ 88 (180)
T cd01197 29 LMLLMFRHGLRVSE-----------ACGLKLSDIDLES------RQIYIRR-LKGGFST--THPLRDDELEALKNWLEIR 88 (180)
T ss_pred HHHHHHHhCCcHHH-----------HHcCcHHHhCCCC------CeEEEEe-cCCCccc--eeECCHHHHHHHHHHHHHh
Confidence 45566678899987 8899999998765 5666653 3555433 567778888888887643
Q ss_pred ----cCCCccccc-----cCChhHHHHHHHHhcC--C----CeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHH
Q psy17743 318 ----KKGSDDLFD-----RLNTSVLNKHLSELME--G----LTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRA 382 (618)
Q Consensus 318 ----K~Pgd~LF~-----~l~s~~LN~yLkelm~--g----lTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~A 382 (618)
..+++.||- .++++.+++.++.+.. | +|..+||--.||.++ +...+
T Consensus 89 ~~~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~H~lRht~~t~l~-----~~g~~-------------- 149 (180)
T cd01197 89 AWKGLPDSDWIFLSRRGGPLSRQQVYKLIRRLGAQAGLSIKVHPHMLRHACGYALA-----NQGAD-------------- 149 (180)
T ss_pred ccCCCCCCCeEEeCCCCCcCCHHHHHHHHHHHHHHcCCCCCCCcchhhhHHHHHHH-----HcCCC--------------
Confidence 245667883 4788999999998852 2 567788876666443 22211
Q ss_pred HHHHHHHcCCC
Q psy17743 383 NRAVAVLCNHQ 393 (618)
Q Consensus 383 nr~VAilcNHq 393 (618)
...|+.++||+
T Consensus 150 ~~~i~~~lGH~ 160 (180)
T cd01197 150 TRLIQDYLGHR 160 (180)
T ss_pred HHHHHHHhCCC
Confidence 23688889997
No 52
>PF14370 Topo_C_assoc: C-terminal topoisomerase domain; PDB: 1TL8_A 1K4T_A 1A36_A 1RR8_C 1T8I_A 1SC7_A 1EJ9_A 1LPQ_A 1RRJ_A 1A31_A ....
Probab=89.59 E-value=0.099 Score=44.92 Aligned_cols=25 Identities=52% Similarity=0.966 Sum_probs=18.1
Q ss_pred hhHHHHHhhhhhhhhhhhhccccccC
Q psy17743 593 EKKIYNKTQRAKFRWAIDMATADFVF 618 (618)
Q Consensus 593 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 618 (618)
=.++|++++|.+|.||+|+ ..||.|
T Consensus 47 ieKifsktlr~KF~WA~~~-~~~~~F 71 (71)
T PF14370_consen 47 IEKIFSKTLREKFAWAMDV-DEDFKF 71 (71)
T ss_dssp GGGTS-HHHHHHTHHHCCS--TT---
T ss_pred HHHHhhHHHHHhhhHHHcC-CCCCCC
Confidence 3478999999999999999 899987
No 53
>cd00800 INT_Lambda_C Lambda integrase, C-terminal catalytic domain. Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites.
Probab=89.16 E-value=1.1 Score=41.49 Aligned_cols=99 Identities=13% Similarity=0.095 Sum_probs=69.4
Q ss_pred HHHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHh
Q psy17743 235 QRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLF 314 (618)
Q Consensus 235 qlA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f 314 (618)
....++.|+-.+.+|+|. +|.|+.+||.. +.+.+ -.+|.+.. ..|++.+.+...|..+
T Consensus 20 ~~~~~~~l~~~tGlR~~E-----------~~~l~~~di~~--------~~~~i-~~~K~~~~--r~vpl~~~~~~~l~~~ 77 (162)
T cd00800 20 WLRCAMDLALLTGQRVGD-----------VLRMKWSDIDD--------DGLHI-EQSKTGAK--LAIPLSPSLREVIERC 77 (162)
T ss_pred HHHHHHHHHHHHcCCHHH-----------HHhCcHHHccC--------CeEEE-EecCcCCe--eEEECCHHHHHHHHHH
Confidence 445667788889999987 88999998864 23433 24565443 3677889999999888
Q ss_pred hhccC-CCcccccc------CChhHHHHHHHHhc-----C----CCeeeeeccccch
Q psy17743 315 VENKK-GSDDLFDR------LNTSVLNKHLSELM-----E----GLTAKVFRTYNAS 355 (618)
Q Consensus 315 ~~~K~-Pgd~LF~~------l~s~~LN~yLkelm-----~----glTAKvFRTynAS 355 (618)
.+... +++.||.. ++...++..++.+. . .+|..+||...+|
T Consensus 78 ~~~~~~~~~~vf~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~H~lRht~~t 134 (162)
T cd00800 78 RDLSRVSSPYLVHTRPGGKQVSAKTLSRAFRKARKAAGVKWGGDPPTFHDIRAKAAS 134 (162)
T ss_pred HhhcccCCceEEEcCCCCCCcCcchHHHHHHHHHHhcccccCCCCCchhhHHHHHHH
Confidence 65332 56788853 67888999998874 1 3677788875444
No 54
>cd01185 INT_Tn4399 Tn4399 and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases, including cLV25, a Bacteroides fragilis chromosomal transfer factor integrase similar to the Bacteroides mobilizable transposon, Tn4399, integrase.
Probab=89.02 E-value=1 Score=45.39 Aligned_cols=112 Identities=20% Similarity=0.183 Sum_probs=77.8
Q ss_pred hhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhccCCCccc
Q psy17743 245 KLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVENKKGSDDL 324 (618)
Q Consensus 245 ~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~K~Pgd~L 324 (618)
.+.+|+|- +|.|+.+||..... +...|.+. .+|.+.. ..|++.+.+...|..+.. .+++.|
T Consensus 160 ~tGlR~~E-----------i~~L~~~did~~~~---g~~~i~~~-~~K~~~~--r~ipl~~~~~~~l~~~~~--~~~~~l 220 (299)
T cd01185 160 FTGLRYSD-----------IKKLTWEEIVEDSD---GEKWIRKR-RQKTKVE--VYIPLLDEALQILGKYPD--EKEGLV 220 (299)
T ss_pred HHcccHHH-----------HHhcCHHHceECCC---CCEEEEEe-ecccCCc--ccccCcHHHHHHHHHhcC--CCCCcC
Confidence 37899887 88999999988651 01233333 4666644 466777888899988875 267889
Q ss_pred cccCChhHHHHHHHHhcC------CCeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHHHHHHHcCCCC
Q psy17743 325 FDRLNTSVLNKHLSELME------GLTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQR 394 (618)
Q Consensus 325 F~~l~s~~LN~yLkelm~------glTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr~VAilcNHqr 394 (618)
|-.++...+|.+++.+.. ++|..+||--.||.++. ...+ ...|+.++||..
T Consensus 221 f~~~~~~~~~~~~~~~~~~~gi~~~~~~H~lRht~at~l~~-----~g~~--------------~~~i~~~lGH~~ 277 (299)
T cd01185 221 FPLLKNSNMNKPLKEWAKLAGIKKHITFHCARHTFATLQLL-----SGGP--------------IETVSKMLGHTN 277 (299)
T ss_pred cCCCCHHHHHHHHHHHHHHcCCCCCCccccchHHHHHHHHH-----cCCC--------------HHHHHHHhCCCc
Confidence 998888889999988863 36788888766665442 2111 135888899974
No 55
>PHA03397 vlf-1 very late expression factor 1; Provisional
Probab=88.41 E-value=2 Score=47.06 Aligned_cols=130 Identities=17% Similarity=0.083 Sum_probs=77.8
Q ss_pred HHHHHHHHHHHHHHHHhhc--cccc-c---hhHHHHHHHHHhhhccccCCcccccccCccccccccccceEe--ecccCC
Q psy17743 209 RKLAKSINKIRENYQADWK--SKEM-R---IRQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQL--HEEKDG 280 (618)
Q Consensus 209 r~l~~~Lp~IR~~y~~dL~--s~~~-~---~RqlA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l--~~~~d~ 280 (618)
..|...|.++...+..... .... . .---++++.|+-.+.||+|. +|+|+.+||.. ..
T Consensus 165 i~l~~~i~~ll~~i~~~~~~~~~~~~~~~~~~Rd~aif~lLl~TGLRISE-----------l~~Lk~eDId~~~~~---- 229 (363)
T PHA03397 165 IVLKDIIDPVLNYIEKKIKYLNSNYVHNRGLIRGAIVFCIILGTGLRITE-----------ARQITLDDLNKLIKK---- 229 (363)
T ss_pred hhHHHHHHHHHHHHHHHhhhccchhcccchhHHHHHHHHHHHHHHHHHHH-----------HHCCCHHHcchhhcC----
Confidence 3466777777777777555 2222 1 11235677888899999987 89999999985 44
Q ss_pred CCcEEEEE-eecCCceEEEEEeccchHHHHHHHHhhhc--cCCCccccccCCh----hHHHHHHHHhcC-C--Ceeeeec
Q psy17743 281 KPYVVCFD-FLGKDSIRYYNEVPVEKRVFKNLQLFVEN--KKGSDDLFDRLNT----SVLNKHLSELME-G--LTAKVFR 350 (618)
Q Consensus 281 ~~~~V~Fd-FlGKdsir~~~~V~vD~~v~knL~~f~~~--K~Pgd~LF~~l~s----~~LN~yLkelm~-g--lTAKvFR 350 (618)
+.+.+. ..||.+..+..-+. +.+.+.|+...+. +.| ..+|-..++ ..++.+++...- + +|+..||
T Consensus 230 --g~I~I~gi~tKg~K~R~VpLs--~~~~~~L~~~L~~y~~~~-~~~~is~~~~~~~~~~kki~kkAGI~~~~itpH~LR 304 (363)
T PHA03397 230 --GEHKVNNINLKRKKSRFNYLN--CIKKKPLELAREIYQKHP-TLLKISKNSSTPFKDFKRLLEEAGVEMDRPRSNMIR 304 (363)
T ss_pred --CEEEEecccCCCCceeEEEeC--hHHHHHHHHHHHHHhcCc-hhcccCCCchHHHHHHHHHHHHcCCCCCCCCCcccH
Confidence 677777 67888876655443 3333333333221 122 112211122 256666666642 2 7888888
Q ss_pred cccchHHH
Q psy17743 351 TYNASITL 358 (618)
Q Consensus 351 TynASvt~ 358 (618)
=..||.++
T Consensus 305 HTFAt~Ll 312 (363)
T PHA03397 305 HYLASNMY 312 (363)
T ss_pred HHHHHHHH
Confidence 66566544
No 56
>cd01183 INT_SG1_C INT_SG1, DNA breaking-rejoining enzymes, integrase/recombinases subgroup 1, C-terminal catalytic domain. The CD contains mainly predicted integrase/recombinase and site-specific XerD recombinases. The members of this CD are found predominantly in proteobacteria. These proteins have not been biochemically characerised as yet.
Probab=87.28 E-value=1.4 Score=42.00 Aligned_cols=106 Identities=16% Similarity=0.192 Sum_probs=69.9
Q ss_pred HHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEee-cCCceEEEEEeccchHHHHHHHHh
Q psy17743 236 RAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFL-GKDSIRYYNEVPVEKRVFKNLQLF 314 (618)
Q Consensus 236 lA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFl-GKdsir~~~~V~vD~~v~knL~~f 314 (618)
..+++.|+-.+.+|+|- +++|+.++|..... +....+... +|.+.. ..|++.+.+...|+..
T Consensus 28 ~~~l~~l~~~tGlR~~E-----------l~~L~~~did~~~~----~~~~~i~i~~~K~~~~--r~vpl~~~~~~~L~~~ 90 (196)
T cd01183 28 LLFLLALLYSTGLRISE-----------LAAATGPDLEAFVQ----GGGWWLYVPVGKGGKE--RRVPVSDELLAALARY 90 (196)
T ss_pred HHHHHHHHHHccChHHH-----------HHcccccccccccC----CCceEEEEecCCCCCc--eEEeCCHHHHHHHHHH
Confidence 34566777789999987 89999999987531 011233444 777654 4688889999999888
Q ss_pred hhcc--------CCCcccccc---------CChhHHHHHHHHhc-------------------CCCeeeeeccccchHHH
Q psy17743 315 VENK--------KGSDDLFDR---------LNTSVLNKHLSELM-------------------EGLTAKVFRTYNASITL 358 (618)
Q Consensus 315 ~~~K--------~Pgd~LF~~---------l~s~~LN~yLkelm-------------------~glTAKvFRTynASvt~ 358 (618)
.+.. .+++.||.. ++.+.++..++.++ ..+|..+||--.||.++
T Consensus 91 ~~~~~~~~~~~~~~~~~lF~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~ 170 (196)
T cd01183 91 RQARGLPPEPAAGEAVPLLGRHKSAGGGGGLSSAQLYRIVKRVFGAAADRLQADGFEEDAAQLRAASTHWLRHTHASHDL 170 (196)
T ss_pred HHHcCCCCCCCCCCCCceeeccccccCCCCCCHHHHHHHHHHHHHHHHHHHHhccChhHHHhhcccchHHHHHHHHHHHH
Confidence 6421 134568843 45677777776642 23677777766666544
No 57
>cd00798 INT_XerDC XerD and XerC integrases, DNA breaking-rejoining enzymes, N- and C-terminal domains. XerD-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequen
Probab=86.58 E-value=3.5 Score=40.09 Aligned_cols=97 Identities=24% Similarity=0.328 Sum_probs=65.3
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhc
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN 317 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~ 317 (618)
+++.|+=.+++|.|. +|.|+..||.+.+ +.+.+. +|.+..+ .|++.+.+...|+.+.+.
T Consensus 131 ~~~~l~~~tG~R~~E-----------i~~l~~~di~~~~------~~~~i~--~k~~~~~--~vpl~~~~~~~l~~~~~~ 189 (284)
T cd00798 131 ALLELLYSTGLRVSE-----------LVGLKLSDVDLSR------GLIRVR--GKGNKER--IVPLGETAVEALQRYLEV 189 (284)
T ss_pred HHHHHHHHhCchHHH-----------HHhCchHhhcccC------CeEEEE--ecCCCce--EEEeCHHHHHHHHHHHHH
Confidence 344455568999975 7889999998865 555554 8887655 566678888888887653
Q ss_pred c-------CCCccccc-----cCChhHHHHHHHHhcC------CCeeeeeccccch
Q psy17743 318 K-------KGSDDLFD-----RLNTSVLNKHLSELME------GLTAKVFRTYNAS 355 (618)
Q Consensus 318 K-------~Pgd~LF~-----~l~s~~LN~yLkelm~------glTAKvFRTynAS 355 (618)
. ..++.||- .+++..+|..++.+.. ++|..+||---||
T Consensus 190 ~~~~~~~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~g~~~~~~~h~lR~t~at 245 (284)
T cd00798 190 RRPLLLKVGDSDALFLNQRGKRLSRRGVWKILKEYARRAGIEKKISPHTLRHSFAT 245 (284)
T ss_pred cccccccCCCCCceeecCCCCCCCHHHHHHHHHHHHHHhCCCcCCChHHHHHHHHH
Confidence 2 23455763 3677788888877652 2677777754444
No 58
>cd01191 INT_phiCTX_C phiCTX phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various phage and bacterial integrases, including those similar to phage integrases: Bordetella and Pseudomonas phiCTX; E. coli Rac, Qin, and Shiga toxin 2 933W; and Salmonella typhimurium LT2 Gifsy-2 and Fels-1; and a putative pore-forming cytotoxin integrase from Vibrio parahaemolyticus O3:K6.
Probab=81.13 E-value=8.1 Score=36.99 Aligned_cols=120 Identities=16% Similarity=0.086 Sum_probs=71.3
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEe--------ecCCceEEEEEeccchHHHH
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDF--------LGKDSIRYYNEVPVEKRVFK 309 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdF--------lGKdsir~~~~V~vD~~v~k 309 (618)
.+++|+=.+.+|+|. |++|+.++|.+.. ..+.+.= .+|..- -...|.+.+++..
T Consensus 24 ~~~~l~~~tGlR~~E-----------~~~L~~~did~~~------~~~~i~~~~~~~~~~~~kt~~-~~r~vpl~~~~~~ 85 (196)
T cd01191 24 NLWEFAVFTGLRPSE-----------LIALAWEDVDLER------GTVYVRRALVRGIFKVPKTKA-GTRDVDLNPPALA 85 (196)
T ss_pred HHHHHHHHHCCCHHH-----------HHhCcHHhcCccC------CeEEEEeeeecccccCCCcCC-CeEEEeCCHHHHH
Confidence 456666668999987 8999999998765 4555431 123320 2335777888888
Q ss_pred HHHHhhhc--------------------cCCCcccccc------CC--hhHHHHHHHHhcC--C---CeeeeeccccchH
Q psy17743 310 NLQLFVEN--------------------KKGSDDLFDR------LN--TSVLNKHLSELME--G---LTAKVFRTYNASI 356 (618)
Q Consensus 310 nL~~f~~~--------------------K~Pgd~LF~~------l~--s~~LN~yLkelm~--g---lTAKvFRTynASv 356 (618)
.|...... +.+++.||.. ++ +..+|..++.++. | +|..+||--.||.
T Consensus 86 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lF~~~~~g~~~~~~~~~~~~~~~~~~~~~gi~~~~~H~lRht~at~ 165 (196)
T cd01191 86 ALKEQAKLTRLSRPHQITVLEREYGRTEKQKGTFVFHDPKTGEPWTYAVASRKSFWDPALKRAGIRYRNPYQMRHTFASW 165 (196)
T ss_pred HHHHHHHHhhcccccchhhcccccccccCCCceEEEecCCCCCcCCchhHHHHHHHHHHHHHcCCCcCCcccchHHHHHH
Confidence 88764321 1235667743 11 2335555555442 2 5777777766665
Q ss_pred HHHHHHhhcCCCCccHHHHHHHHHHHHHHHHHHcCCCC
Q psy17743 357 TLQQQLNELMDPDFSEAEKILAYNRANRAVAVLCNHQR 394 (618)
Q Consensus 357 t~~~~L~~~~~~~~s~~ek~~~yn~Anr~VAilcNHqr 394 (618)
++. ... ....|+.++||+.
T Consensus 166 l~~-----~g~--------------~~~~i~~~lGH~~ 184 (196)
T cd01191 166 MLT-----AGA--------------NPAFIADQMGHKS 184 (196)
T ss_pred HHH-----CCC--------------CHHHHHHHhCCCc
Confidence 542 111 1246888899986
No 59
>cd01196 INT_VanD VanD integrase, IntD, and related integrases, DNA breaking-rejoining enzymes, integrase/recombinases, N- and C-terminal domains. This CD includes various bacterial integrases including those similar to IntD, a putative integrase-like protein, a component of the vanD glycopeptide resistance cluster in Enterococcus faecium BM4339. Members of this CD are predominantly bacterial in origin.
Probab=80.34 E-value=7.4 Score=38.95 Aligned_cols=115 Identities=16% Similarity=0.178 Sum_probs=76.4
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhc
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN 317 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~ 317 (618)
++++|+-.+.+|+|. +|.|+.+||.+.. +.+ .+|.|..+ .|.+.+.+...|..+...
T Consensus 111 ~~~~l~~~tGlR~~E-----------~~~L~~~di~~~~--------~~i--~~K~~~~r--~i~l~~~~~~~l~~~~~~ 167 (263)
T cd01196 111 FVVWFLAATGARVSE-----------LIHIKVEHVQTGY--------ADI--YSKGGKIR--RLYIPKNLRVEALKWLKE 167 (263)
T ss_pred HHHHHHHHhCCCHHH-----------HhcCcHHHHhCCe--------eEE--eecCCcee--EEecCHHHHHHHHHHHHH
Confidence 467777788999987 9999999997632 223 36666543 567777777766666543
Q ss_pred c-CCCccccc-----cCChhHHHHHHHHhcC-------CCeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHH
Q psy17743 318 K-KGSDDLFD-----RLNTSVLNKHLSELME-------GLTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANR 384 (618)
Q Consensus 318 K-~Pgd~LF~-----~l~s~~LN~yLkelm~-------glTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr 384 (618)
. .+++.||. .++...++..++.+.. .+|..+||--.||.++. ... + ..
T Consensus 168 ~~~~~~~lf~~~~g~~~~~~~~~~~~~~~~~~~gi~~~~~~~H~lRHt~at~~~~-----~g~---~-----------~~ 228 (263)
T cd01196 168 LNLDSGYIFLNRFGKPITARGIAQQLKNYAAKYKMNPRVVYPHSFRHLFAKNFLA-----KYN---D-----------LA 228 (263)
T ss_pred cCCCCCceeeeCCCCcCcHHHHHHHHHHHHHHhCCCCCCCCchhhHHHHHHHHHH-----cCC---C-----------HH
Confidence 2 34567884 4788889999988742 26677788655564442 111 1 24
Q ss_pred HHHHHcCCCC
Q psy17743 385 AVAVLCNHQR 394 (618)
Q Consensus 385 ~VAilcNHqr 394 (618)
.|+.++||..
T Consensus 229 ~i~~~lGH~~ 238 (263)
T cd01196 229 LLADLMGHES 238 (263)
T ss_pred HHHHHhCCCC
Confidence 6888899863
No 60
>cd01195 INT_Tn544B_C Tn544B and related transposases, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes various bacterial transposases similar to TnpB from transposon Tn554.
Probab=79.48 E-value=6.6 Score=37.46 Aligned_cols=125 Identities=14% Similarity=0.181 Sum_probs=76.1
Q ss_pred HHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEe-ecCCceEEEEEeccchHHHHHHHHh
Q psy17743 236 RAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDF-LGKDSIRYYNEVPVEKRVFKNLQLF 314 (618)
Q Consensus 236 lA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdF-lGKdsir~~~~V~vD~~v~knL~~f 314 (618)
...++.|+-.+.+|+|- +++|+..++....+ ....+.+.- .+|.+ .-...|.+.+.+...|+..
T Consensus 22 ~~~~~~l~~~tGlR~~E-----------i~~L~~~~~~~~~~---~~~~~~~~~~~~K~~-~~~r~vpl~~~~~~~l~~~ 86 (195)
T cd01195 22 IIPMTMIVQETGMRISD-----------LLTLKKNCLLEDKD---GDFFYKYYQCIWKTK-IKEHIIPISKKVALLIKVR 86 (195)
T ss_pred HHHHHHHHHHhCCCHHH-----------HHcCCccccccCCC---CCceEEEEeecCcCC-CcCccccCCHHHHHHHHHH
Confidence 34566778888899986 66677665533221 012333322 35554 1234678889999998877
Q ss_pred hhc--------cCCCcccccc---------CChhHHHHHHHHhcC------------CCeeeeeccccchHHHHHHHhhc
Q psy17743 315 VEN--------KKGSDDLFDR---------LNTSVLNKHLSELME------------GLTAKVFRTYNASITLQQQLNEL 365 (618)
Q Consensus 315 ~~~--------K~Pgd~LF~~---------l~s~~LN~yLkelm~------------glTAKvFRTynASvt~~~~L~~~ 365 (618)
... ..|.+.||.. ++++.+|..++.+.. .+|..+||=..||.+++ .
T Consensus 87 ~~~~~~~~~~~~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~at~l~~-----~ 161 (195)
T cd01195 87 EDKTKELSTEDNNPSEYLFPRYDGKPKGQPTNKQAFRGELNKLAYEKNIVDKSGEIYHFHAHAFRHTVATRMIN-----N 161 (195)
T ss_pred HHHHHHHhccCCCCCceEeeccCCCCCCCcCcHHHHHHHHHHHHHHcCCccCCCCEeeccchhhhhHHHHHHHH-----c
Confidence 531 2456788853 677789998888753 24666777655554432 2
Q ss_pred CCCCccHHHHHHHHHHHHHHHHHHcCCCC
Q psy17743 366 MDPDFSEAEKILAYNRANRAVAVLCNHQR 394 (618)
Q Consensus 366 ~~~~~s~~ek~~~yn~Anr~VAilcNHqr 394 (618)
.- + ...|+.++||..
T Consensus 162 g~---~-----------~~~i~~~lGH~~ 176 (195)
T cd01195 162 GM---P-----------IHIIQKFLGHES 176 (195)
T ss_pred CC---C-----------HHHHHHHhCCCC
Confidence 11 1 136788999954
No 61
>PF06476 DUF1090: Protein of unknown function (DUF1090); InterPro: IPR009468 This family consists of several bacterial proteins of unknown function and is known as YqjC in Escherichia coli.
Probab=79.36 E-value=16 Score=34.04 Aligned_cols=54 Identities=24% Similarity=0.447 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHHHHcCCCCCCCCchHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC
Q psy17743 373 AEKILAYNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAERALKDAKKAGES 434 (618)
Q Consensus 373 ~ek~~~yn~Anr~VAilcNHqraV~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~ 434 (618)
..++.-...|..+|=..|.+ +.-....+.+|.+++.++.+.+.+|++|+..|..
T Consensus 42 ~~rv~GLe~AL~~v~~~Ctd--------~~l~~e~q~ki~~~~~kV~ere~eL~eA~~~G~~ 95 (115)
T PF06476_consen 42 QHRVAGLEKALEEVKAHCTD--------EGLKAERQQKIAEKQQKVAEREAELKEAQAKGDS 95 (115)
T ss_pred HHHHHHHHHHHHHHHhhcCC--------chhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCH
Confidence 34667788999999999987 3445667899999999999999999999877664
No 62
>cd00797 HP1_INT_C Phage HP1 integrase, C-terminal catalytic domain. Bacteriophage HP1 and related integrases are found in eubacteria, plasmids and temperate bacteriophages of the P2 family. They belong to the DNA breaking-rejoining enzyme superfamily, which includes tyrosine recombinases and type IB topoisomerases. These enzymes share the same fold in their C-terminal catalytic domain containing six conserved active site residues and the overall reaction mechanism. The HP1 recombinase controls phage replication by site-specific recombination between the HP1 genome and the chromosomal DNA. It is a heterobifunctional DNA-binding protein, which recognizes two different DNA sequence motifs (type I and type II binding sites). The C-terminal catalytic domain of the HP1 integrase binds to the type I site, while the less conserved N-terminal domain is largely responsible for binding to the type II site.
Probab=77.66 E-value=9 Score=35.22 Aligned_cols=94 Identities=22% Similarity=0.147 Sum_probs=64.2
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHhhhc
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLFVEN 317 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f~~~ 317 (618)
.++.|+=.+++|+|. ++.|+..+|.. +.+.+. .+|.+.. ..|++.+.+...|+...
T Consensus 20 ~~~~l~~~tG~R~~E-----------i~~l~~~di~~--------~~~~~~-~~K~~~~--r~ipl~~~~~~~l~~~~-- 75 (158)
T cd00797 20 DVAILCLDTGARWGE-----------ALGLKAEDIQE--------GRVTFW-KTKSGKS--RTVPISERVAAMLKRRR-- 75 (158)
T ss_pred HHHHHHHHhcCCHHH-----------HhcCCHHHccc--------CeEEEE-ecCCCCc--eEeeCCHHHHHHHHHHh--
Confidence 334444568889875 78888888742 334443 3676654 47778899988888764
Q ss_pred cCCCccccccCChhHHHHHHHHhcC----CCeeeeeccccchHH
Q psy17743 318 KKGSDDLFDRLNTSVLNKHLSELME----GLTAKVFRTYNASIT 357 (618)
Q Consensus 318 K~Pgd~LF~~l~s~~LN~yLkelm~----glTAKvFRTynASvt 357 (618)
+++.||-.++.+.++..++.+.. ++|..+||--.||.+
T Consensus 76 --~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~H~lRht~~t~l 117 (158)
T cd00797 76 --MRGGLFPDLYYESFRHIWKRAKIELPKGQATHILRHTFASHF 117 (158)
T ss_pred --hcCCCCCCcChHHHHHHHHHHHHHhCCCCccccchhHHHHHH
Confidence 35678877776778888888853 478888886555543
No 63
>cd01198 INT_ASSRA_C Archaeal site-specific recombinase A (ASSRA), DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain. Members of this CD are archael in origin. No biochemical characterization is available for the proteins of this subgroup at this point.
Probab=75.91 E-value=15 Score=34.61 Aligned_cols=102 Identities=17% Similarity=0.138 Sum_probs=59.8
Q ss_pred HHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEee-cCCceEEEEEeccchHHHHHHHHhh
Q psy17743 237 AVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFL-GKDSIRYYNEVPVEKRVFKNLQLFV 315 (618)
Q Consensus 237 A~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFl-GKdsir~~~~V~vD~~v~knL~~f~ 315 (618)
-++++|+=.+.+|+|. +++|+.+||.+.. ..|.+.-. +|.+.++ .+. ++.+...+....
T Consensus 20 ~~~~~ll~~tGlR~~E-----------l~~L~~~did~~~------~~i~i~~~k~k~~~r~--v~~-~~~~~~~~~~~~ 79 (186)
T cd01198 20 RAVIVGLAKTGIRRGE-----------LINLDRRDVNLDK------PTLYLKPASNKRSNRT--LFP-DLETELFRWLAI 79 (186)
T ss_pred HHHHHHHHHhCchHHH-----------HhCCeeccccccC------CEEEEcCCCCCCCcee--ecc-hHHHHHHHHHHh
Confidence 3667888889999987 8999999998865 56666654 2333332 122 444444444443
Q ss_pred hc--cCCCcccccc-----CChhH----HHHHHHHhc---------CCCeeeeeccccchHHH
Q psy17743 316 EN--KKGSDDLFDR-----LNTSV----LNKHLSELM---------EGLTAKVFRTYNASITL 358 (618)
Q Consensus 316 ~~--K~Pgd~LF~~-----l~s~~----LN~yLkelm---------~glTAKvFRTynASvt~ 358 (618)
.. ..+.+.||-. ++... ++.+++.+. +.+|..+||---||..+
T Consensus 80 ~~~~~~~~~~lF~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~H~lRHt~at~l~ 142 (186)
T cd01198 80 RPRTTSPADALFIGTQDGWGCRRLVYEMVTGMARRHGEHRPWGDLEENFTPHCFRHFFTTWLR 142 (186)
T ss_pred ccccCCCCCceEEecCCCcccchhHHHHHHHHHHHhcccccccccccCcCcccchhHHHHHHH
Confidence 22 1355678843 32333 445555542 13677777766666554
No 64
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=73.96 E-value=12 Score=36.28 Aligned_cols=60 Identities=15% Similarity=0.308 Sum_probs=32.7
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHhhc---CCCcccHHHHHHHHHHHHHHHHHhcccch
Q psy17743 401 DKSMGNLKEKISNKRKQVKDAERALKDAKKA---GESKAMTDKKKTALGRLKEQLLKLEVQET 460 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~---~k~~~~~e~~~~~~~~~~~~i~k~~~~~~ 460 (618)
...|..|...|..+++++.+++.+.+.+... -.+.++.+.+...|+.+++.+..|+..+.
T Consensus 71 ~eel~~ld~ei~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~ 133 (169)
T PF07106_consen 71 PEELAELDAEIKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLE 133 (169)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445556666666666666665555544321 11234556666666666666666655554
No 65
>PF14282 FlxA: FlxA-like protein
Probab=64.68 E-value=21 Score=32.56 Aligned_cols=54 Identities=17% Similarity=0.340 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCC-----cccHHHHHHHHHHHHHHHHHhcccchh
Q psy17743 408 KEKISNKRKQVKDAERALKDAKKAGES-----KAMTDKKKTALGRLKEQLLKLEVQETD 461 (618)
Q Consensus 408 ~~ki~~~~~~~~~~~~~l~~~~~~~k~-----~~~~e~~~~~~~~~~~~i~k~~~~~~~ 461 (618)
...|+.|+.||..|..+|+.+..+... ....+.+..+|..|..+|..+..+..-
T Consensus 18 ~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~q~~~ 76 (106)
T PF14282_consen 18 DSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQSQQAE 76 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555556666665555432111 112344556666666666666555443
No 66
>PRK15417 integrase/recombinase; Provisional
Probab=60.46 E-value=24 Score=37.19 Aligned_cols=57 Identities=14% Similarity=0.155 Sum_probs=41.2
Q ss_pred HHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHh
Q psy17743 238 VALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLF 314 (618)
Q Consensus 238 ~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f 314 (618)
+++.|+-.+.||+|- ++.|+.++|.+.. +.|.+. .||.+..+ .|.+.+.+...|+..
T Consensus 135 ~~~~ll~~TGlR~sE-----------l~~L~~~dId~~~------~~i~v~-~~K~~k~R--~vpl~~~~~~~L~~~ 191 (337)
T PRK15417 135 LFAQLLYGTGMRISE-----------GLQLRVKDLDFDH------GTIIVR-EGKGSKDR--ALMLPESLAPSLREQ 191 (337)
T ss_pred HHHHHHHHcCCcHHH-----------HHhcchhhccCCC------CeEEEE-eCCCCCce--eeeCCHHHHHHHHHH
Confidence 455677789999987 9999999998865 566653 37776654 466667777666543
No 67
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=58.37 E-value=40 Score=32.79 Aligned_cols=72 Identities=13% Similarity=0.213 Sum_probs=46.1
Q ss_pred HHhHHHHHHHHHHHHH-HHHHHHHHHHHHhhcCCCcc---------cHHHHHHHHHHHHHHHHHhcccchhhccccceee
Q psy17743 401 DKSMGNLKEKISNKRK-QVKDAERALKDAKKAGESKA---------MTDKKKTALGRLKEQLLKLEVQETDKEENKTIAL 470 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~-~~~~~~~~l~~~~~~~k~~~---------~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaL 470 (618)
...+++|++.++.++. ...++.++++.|+..|-.+. ....++.+|..|+.+|...++--........|++
T Consensus 9 ~~g~~~L~~EL~~L~~~~r~e~~~~i~~Ar~~GDl~ENaeY~aAk~~~~~~e~rI~~L~~~L~~A~iid~~~~~~~~V~~ 88 (157)
T PRK01885 9 REGYARLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIYGKKRLREIDRRVRFLTKRLENLKVVDYSPQQEGKVFF 88 (157)
T ss_pred HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHcCCcchhhcHHHHHHHHHHHHHHHHHHHHHHccCEEECCCCCCCCEEEe
Confidence 4578889999988876 56777777888865443221 2344566677777777666654333334467888
Q ss_pred cc
Q psy17743 471 GT 472 (618)
Q Consensus 471 gT 472 (618)
|+
T Consensus 89 Gs 90 (157)
T PRK01885 89 GA 90 (157)
T ss_pred CC
Confidence 86
No 68
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=58.15 E-value=48 Score=32.34 Aligned_cols=69 Identities=13% Similarity=0.157 Sum_probs=46.7
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcc---------cHHHHHHHHHHHHHHHHHhcccchhhccccceeec
Q psy17743 401 DKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKA---------MTDKKKTALGRLKEQLLKLEVQETDKEENKTIALG 471 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~---------~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaLg 471 (618)
.+.+++|++.++.|+....++-++++.|+..|-.+. ....++.+|..|+.+|...++- ..+...|++|
T Consensus 10 ~eg~~~L~~EL~~L~~~r~~i~~~i~~Ar~~GDlsENaey~aak~~q~~~e~RI~~L~~~L~~A~ii---~~~~~~V~~G 86 (158)
T PRK05892 10 PAARDHLEAELARLRARRDRLAVEVNDRGMIGDHGDQAEAIQRADELARLDDRINELDRRLRTGPTP---WSGSETLPGG 86 (158)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHhCCCcchhhhHHHHHHHHHHHHHHHHHHHHHHHhCEEe---cCCCCEEEcC
Confidence 456788999999998877777777877766543322 2234566777777777777663 2244678888
Q ss_pred c
Q psy17743 472 T 472 (618)
Q Consensus 472 T 472 (618)
+
T Consensus 87 s 87 (158)
T PRK05892 87 T 87 (158)
T ss_pred c
Confidence 6
No 69
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=56.02 E-value=37 Score=32.79 Aligned_cols=22 Identities=27% Similarity=0.584 Sum_probs=16.8
Q ss_pred CChhHHHHHHHHhcC-C-Ceeeee
Q psy17743 328 LNTSVLNKHLSELME-G-LTAKVF 349 (618)
Q Consensus 328 l~s~~LN~yLkelm~-g-lTAKvF 349 (618)
++=+.|-+.|..+.. | ++.|+|
T Consensus 30 ~~K~~v~k~Ld~L~~~g~i~~K~~ 53 (169)
T PF07106_consen 30 VGKTAVQKALDSLVEEGKIVEKEY 53 (169)
T ss_pred ccHHHHHHHHHHHHhCCCeeeeee
Confidence 455778888888875 5 999987
No 70
>KOG0804|consensus
Probab=54.75 E-value=12 Score=42.42 Aligned_cols=95 Identities=21% Similarity=0.225 Sum_probs=53.6
Q ss_pred HHHHHHHHHHH---HcCCCCCCCCchHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhc-----CCCc-------ccHHHHH
Q psy17743 378 AYNRANRAVAV---LCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAERALKDAKKA-----GESK-------AMTDKKK 442 (618)
Q Consensus 378 ~yn~Anr~VAi---lcNHqraV~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~-----~k~~-------~~~e~~~ 442 (618)
.|+....++-. ..+...+..|.-+.-|++++.|++...+++.+.+.+-+.+.++ ++.+ .....+.
T Consensus 355 ~~e~~~~e~~~l~~~~~~~e~~kk~~e~k~~q~q~k~~k~~kel~~~~E~n~~l~knq~vw~~kl~~~~e~~~~~~~s~d 434 (493)
T KOG0804|consen 355 YYELLITEADSLKQESSDLEAEKKIVERKLQQLQTKLKKCQKELKEEREENKKLIKNQDVWRGKLKELEEREKEALGSKD 434 (493)
T ss_pred HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444433 4566666777788889999999999888887776433322221 1111 1233445
Q ss_pred HHHHHHHHHHHHhcccchhhcccc----ceeecc
Q psy17743 443 TALGRLKEQLLKLEVQETDKEENK----TIALGT 472 (618)
Q Consensus 443 ~~~~~~~~~i~k~~~~~~~ke~nk----~vaLgT 472 (618)
.+|+-|+|||..|-..+....+.| +|.=||
T Consensus 435 ~~I~dLqEQlrDlmf~le~qqklk~dt~eIqegt 468 (493)
T KOG0804|consen 435 EKITDLQEQLRDLMFFLEAQQKLKSDTDEIQEGT 468 (493)
T ss_pred HHHHHHHHHHHhHheehhhhhhhhcchhhhcCce
Confidence 566666666666554444444433 455554
No 71
>TIGR01461 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB.
Probab=53.60 E-value=42 Score=32.60 Aligned_cols=72 Identities=13% Similarity=0.209 Sum_probs=47.2
Q ss_pred HHhHHHHHHHHHHHHH-HHHHHHHHHHHHhhcCCCcc---------cHHHHHHHHHHHHHHHHHhcccchhhccccceee
Q psy17743 401 DKSMGNLKEKISNKRK-QVKDAERALKDAKKAGESKA---------MTDKKKTALGRLKEQLLKLEVQETDKEENKTIAL 470 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~-~~~~~~~~l~~~~~~~k~~~---------~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaL 470 (618)
...+++|++.++.|+. ...++.++++.|+..|-.+. ....++.+|..|+.+|...++--.+......|++
T Consensus 7 ~~G~~~L~~El~~L~~~~r~~~~~~i~~Ar~~GDlsENaeY~aak~~~~~le~rI~~L~~~L~~A~iid~~~~~~~~V~~ 86 (156)
T TIGR01461 7 PEGYEKLKQELNYLWREERPEVTQKVTWAASLGDRSENADYQYGKKRLREIDRRVRFLTKRLENLKVVDYSPQQEGKVFF 86 (156)
T ss_pred HHHHHHHHHHHHHHHhcccHHHHHHHHHHHHcCCcchhhhhHHHHHHHHHHHHHHHHHHHHHhcCEEeCCCCCCCCEEec
Confidence 3567889999988874 56777777887765443221 2345566777777777777664333334567888
Q ss_pred cc
Q psy17743 471 GT 472 (618)
Q Consensus 471 gT 472 (618)
|+
T Consensus 87 Gs 88 (156)
T TIGR01461 87 GA 88 (156)
T ss_pred Ce
Confidence 87
No 72
>PF05276 SH3BP5: SH3 domain-binding protein 5 (SH3BP5); InterPro: IPR007940 The SH3 domain-binding protein inhibits the auto and transphophorylation of BTK and acts as a negative regulator of BTK-related signalling in B cells.
Probab=53.42 E-value=47 Score=34.78 Aligned_cols=70 Identities=24% Similarity=0.360 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHHHHHc-CCCCCCCCc---------hHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHH
Q psy17743 375 KILAYNRANRAVAVLC-NHQRSVPKS---------HDKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTA 444 (618)
Q Consensus 375 k~~~yn~Anr~VAilc-NHqraV~K~---------~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~ 444 (618)
....|+.|...|..|- -|.++|-|+ |...|+....+|..++.++..++..+..+ -+.
T Consensus 147 ~~~~~~~ae~~v~~Lek~lkr~I~KSrPYfe~K~~~~~~l~~~k~~v~~Le~~v~~aK~~Y~~A-------------Lrn 213 (239)
T PF05276_consen 147 RARIYNEAEQRVQQLEKKLKRAIKKSRPYFELKAKFNQQLEEQKEKVEELEAKVKQAKSRYSEA-------------LRN 213 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHH
Confidence 4567999999999875 899999665 44555555555555555555555444333 255
Q ss_pred HHHHHHHHHHhcc
Q psy17743 445 LGRLKEQLLKLEV 457 (618)
Q Consensus 445 ~~~~~~~i~k~~~ 457 (618)
+++|.++|..-..
T Consensus 214 LE~ISeeIH~~R~ 226 (239)
T PF05276_consen 214 LEQISEEIHEQRR 226 (239)
T ss_pred HHHHHHHHHHHHh
Confidence 6777777765543
No 73
>TIGR01010 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family. This family contains gamma proteobacterial proteins involved in capsule polysaccharide export.
Probab=50.63 E-value=1.2e+02 Score=32.63 Aligned_cols=81 Identities=9% Similarity=0.049 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHcCCCCCCCCchHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC-cccHHHHHHHHHHHHHHHHHhcc
Q psy17743 379 YNRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAERALKDAKKAGES-KAMTDKKKTALGRLKEQLLKLEV 457 (618)
Q Consensus 379 yn~Anr~VAilcNHqraV~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~-~~~~e~~~~~~~~~~~~i~k~~~ 457 (618)
+..|-.++...=+-...+. -+.+.......|..++.++.+++.+|..+...... .+.+-.++.+++.++.+|.+...
T Consensus 186 l~~ae~~l~~fr~~~~~~d--~~~~~~~~~~~i~~L~~~l~~~~~~l~~l~~~~~~~~P~v~~l~~~i~~l~~~i~~e~~ 263 (362)
T TIGR01010 186 LNATKAELLKYQIKNKVFD--PKAQSSAQLSLISTLEGELIRVQAQLAQLRSITPEQNPQVPSLQARIKSLRKQIDEQRN 263 (362)
T ss_pred HHHHHHHHHHHHHhCCCcC--hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCchHHHHHHHHHHHHHHHHHHH
Confidence 4445555555443333332 22334445566777888888888888777654333 56778888999999999888666
Q ss_pred cchh
Q psy17743 458 QETD 461 (618)
Q Consensus 458 ~~~~ 461 (618)
++..
T Consensus 264 ~i~~ 267 (362)
T TIGR01010 264 QLSG 267 (362)
T ss_pred Hhhc
Confidence 5554
No 74
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=49.79 E-value=28 Score=38.41 Aligned_cols=69 Identities=17% Similarity=0.276 Sum_probs=45.4
Q ss_pred chHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcccchhhccccceeecc
Q psy17743 399 SHDKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETDKEENKTIALGT 472 (618)
Q Consensus 399 ~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaLgT 472 (618)
+..+.++.++++|+.++.++++++..|.+.. |.......++.+++.++.+|..++.-+....+. |.|+.
T Consensus 239 ~~~~~~~~l~~~~~~~~~~i~~l~~~l~~~~---k~~~k~~~~~~q~~~~~k~~~~~~~~~~~~~~~--~~la~ 307 (406)
T PF02388_consen 239 NGKEYLESLQEKLEKLEKEIEKLEEKLEKNP---KKKNKLKELEEQLASLEKRIEEAEELIAEYGDE--IPLAG 307 (406)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHHHHHH-T---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SE--EEEEE
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc---chhhHHHHHHHHHHHHHHHHHHHHHHHHhcCCc--ceEEE
Confidence 4667788888888888888888887766544 222345667778888888888777654443333 55543
No 75
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.10 E-value=23 Score=37.62 Aligned_cols=55 Identities=13% Similarity=0.296 Sum_probs=28.7
Q ss_pred chHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcccc
Q psy17743 399 SHDKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQE 459 (618)
Q Consensus 399 ~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~ 459 (618)
+.+..++.|..+|+.+..++.+++++..+.+. ..++++++|+.++++|...+--+
T Consensus 49 ~~q~ei~~L~~qi~~~~~k~~~~~~~i~~~~~------eik~l~~eI~~~~~~I~~r~~~l 103 (265)
T COG3883 49 NIQNEIESLDNQIEEIQSKIDELQKEIDQSKA------EIKKLQKEIAELKENIVERQELL 103 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555555555555544443322 34455666666666665444333
No 76
>PF12835 Integrase_1: Integrase; InterPro: IPR024456 Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. This entry represents the catalytic domain from a family of putative prophage DNA-binding integrases.
Probab=48.22 E-value=73 Score=31.72 Aligned_cols=135 Identities=17% Similarity=0.124 Sum_probs=76.1
Q ss_pred hHHHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHH
Q psy17743 234 RQRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQL 313 (618)
Q Consensus 234 RqlA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~ 313 (618)
.-.|+++.|-..+.||.= | +++|+..+.+....++.+.+.+...+-+|.|..+...|.-.+.+...|..
T Consensus 31 ~~~a~~l~Lq~~fGLR~~------E-----a~~l~~~~~~w~~~l~~~~~~~~v~~gtKGGr~R~v~I~~~~~~~~~L~~ 99 (187)
T PF12835_consen 31 PRVAAALELQRAFGLRRE------E-----ALKLRPSLATWEKALERGDETLRVVVGTKGGRPREVPILDSEKQREALER 99 (187)
T ss_pred hhhHHHHHHHHHhCCCHH------H-----HHhccHhhhhHHHHHhcCCCceEEeecCCCCCcceecCCCcHHHHHHHHH
Confidence 346888899999999972 2 34444444422211222347888999999999998887524566666665
Q ss_pred hhhc-cCCCccccccCChhHHHHHHHHhc----C-C----CeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHH
Q psy17743 314 FVEN-KKGSDDLFDRLNTSVLNKHLSELM----E-G----LTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRAN 383 (618)
Q Consensus 314 f~~~-K~Pgd~LF~~l~s~~LN~yLkelm----~-g----lTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~An 383 (618)
-..- +..+..|+. ..+++.+++.+. . | .|+.-+|=.-| |+...++..... .+..|.
T Consensus 100 a~~~~~~~~~~li~---~~~l~~~~~~~~~~~~k~gl~~~~~~HGLRh~YA----qery~~l~~~G~-------~~~~a~ 165 (187)
T PF12835_consen 100 AAAVARERNGSLIP---KYSLKQALRRYRYALRKLGLTGSTGFHGLRHAYA----QERYEELQAQGF-------SYKEAL 165 (187)
T ss_pred HHHHhcccCCcccC---ccCHHHHHHHHHHHHHHcCCCcCCCchhHHHHHH----HHHHHHHHHCCC-------CHHHHH
Confidence 3221 123445555 233444443332 1 2 44455553333 344433322111 244688
Q ss_pred HHHHHHcCCC
Q psy17743 384 RAVAVLCNHQ 393 (618)
Q Consensus 384 r~VAilcNHq 393 (618)
..|+.-+||=
T Consensus 166 ~~VS~eLGHG 175 (187)
T PF12835_consen 166 AQVSQELGHG 175 (187)
T ss_pred HHHHHHhcCC
Confidence 8999999994
No 77
>PF01519 DUF16: Protein of unknown function DUF16; InterPro: IPR002862 Proteins that contain this domain are of unknown function. It appears to be confined to proteins from Mycoplasma pneumoniae [].; PDB: 2BA2_C.
Probab=44.84 E-value=1.1e+02 Score=28.45 Aligned_cols=52 Identities=19% Similarity=0.299 Sum_probs=42.5
Q ss_pred chHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhc
Q psy17743 399 SHDKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLE 456 (618)
Q Consensus 399 ~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~ 456 (618)
.+++++.++.++++..-+||+++..+.+.-- .+.+.+.+.+..+..||.+|+
T Consensus 50 ~qgeqI~kL~e~V~~QGEqIkel~~e~k~qg------ktL~~I~~~L~~inkRLD~~E 101 (102)
T PF01519_consen 50 AQGEQINKLTEKVDKQGEQIKELQVEQKAQG------KTLQLILKTLQSINKRLDKME 101 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHhhcc
Confidence 6888999999999999999999988776322 356778888899999998886
No 78
>PF14282 FlxA: FlxA-like protein
Probab=42.96 E-value=1e+02 Score=28.12 Aligned_cols=58 Identities=16% Similarity=0.248 Sum_probs=31.1
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHHH------HHHHhhcCCCcccHHHHHHHHHHHHHHHHHhccc
Q psy17743 400 HDKSMGNLKEKISNKRKQVKDAERA------LKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQ 458 (618)
Q Consensus 400 ~~~~m~k~~~ki~~~~~~~~~~~~~------l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~ 458 (618)
-+..++.|+.+|..|+++|.++... -+..+- .-.......++.+|.++..+......+
T Consensus 17 ~~~~I~~L~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~-q~Lq~QI~~LqaQI~qlq~q~~~~~~~ 80 (106)
T PF14282_consen 17 SDSQIEQLQKQIKQLQEQLQELSQDSDLDAEQKQQQI-QLLQAQIQQLQAQIAQLQSQQAEQQQQ 80 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcccCCCHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4666777777777777777666541 111100 001123456677777776666555433
No 79
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=41.30 E-value=1.1e+02 Score=27.32 Aligned_cols=58 Identities=24% Similarity=0.389 Sum_probs=30.8
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcccchh
Q psy17743 401 DKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETD 461 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~~~ 461 (618)
+.+.-.++.+++.++.+...+.+++..+++.+ ...+.+..++..++++|..++.++..
T Consensus 35 d~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~---~~~~~l~~e~~~lk~~i~~le~~~~~ 92 (108)
T PF02403_consen 35 DQERRELQQELEELRAERNELSKEIGKLKKAG---EDAEELKAEVKELKEEIKELEEQLKE 92 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTT---CCTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCc---ccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444455555555555555555555555443 33455555555555555555554443
No 80
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=40.88 E-value=52 Score=39.32 Aligned_cols=32 Identities=22% Similarity=0.214 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHHhcccchhhcccccee
Q psy17743 438 TDKKKTALGRLKEQLLKLEVQETDKEENKTIA 469 (618)
Q Consensus 438 ~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~va 469 (618)
-|.++.+...++..|.+|..+++.+||-....
T Consensus 540 ~e~~r~r~~~lE~E~~~lr~elk~kee~~~~~ 571 (697)
T PF09726_consen 540 AESCRQRRRQLESELKKLRRELKQKEEQIREL 571 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47788888999999999999998888865543
No 81
>PF13094 CENP-Q: CENP-Q, a CENPA-CAD centromere complex subunit
Probab=39.37 E-value=3.5e+02 Score=25.90 Aligned_cols=107 Identities=14% Similarity=0.181 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcccchhhccccceeeccCCcCCCCCccchhhhhee
Q psy17743 411 ISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETDKEENKTIALGTSKLNYLDPRISVTWLASW 490 (618)
Q Consensus 411 i~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaLgTSk~NY~DPRitVtWlkkw 490 (618)
+.....++..|+.++.+... ..++-.+.|+.++..+..++.+....+++..=.|.++-.+-......
T Consensus 36 L~~~~~~l~lLq~e~~~~e~------~le~d~~~L~~Le~~~~~~~~e~~~~~~~~~~vL~~~~~~~~~~~~~------- 102 (160)
T PF13094_consen 36 LAANLHQLELLQEEIEKEEA------ALERDYEYLQELEKNAKALEREREEEEKKAHPVLQLDDSGVLELPEL------- 102 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHhccchhhccccccccccccc-------
Confidence 33334444455555554422 23445566677777777776666666666333333322211110000
Q ss_pred eccCCCceEEEEEcCCCcccCcc-chHhHHHHHHHhHHHHHHHHHHH
Q psy17743 491 TENVQGQVKYIMLNPSSKLKGEK-DWQKYETARKLAKSINKIRENYQ 536 (618)
Q Consensus 491 ~vpI~~~~Kyv~l~~~s~~k~~~-d~~kye~ar~Lk~~i~~Ir~~y~ 536 (618)
..++. +-...|.+.+.- |-+-......|.+|++.|+..-.
T Consensus 103 ---~~~~~---~~~~~~~~~~~l~d~el~~l~~ql~~hl~s~~~n~~ 143 (160)
T PF13094_consen 103 ---PQKSL---LEASESRFAPTLCDEELLPLLKQLNKHLESMQNNLQ 143 (160)
T ss_pred ---ccccc---ccccccccCcccchHHHHHHHHHHHHHHHHHHccHH
Confidence 00000 333444455545 77888888999999999987643
No 82
>PRK11637 AmiB activator; Provisional
Probab=39.28 E-value=1.1e+02 Score=33.94 Aligned_cols=6 Identities=0% Similarity=0.207 Sum_probs=3.4
Q ss_pred hhhhcc
Q psy17743 608 AIDMAT 613 (618)
Q Consensus 608 ~~~~~~ 613 (618)
.||+++
T Consensus 331 Gi~i~~ 336 (428)
T PRK11637 331 GMVIGA 336 (428)
T ss_pred CEEeec
Confidence 566554
No 83
>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=38.93 E-value=1.1e+02 Score=30.79 Aligned_cols=16 Identities=13% Similarity=0.285 Sum_probs=13.3
Q ss_pred CChhHHHHHHHHhcCC
Q psy17743 328 LNTSVLNKHLSELMEG 343 (618)
Q Consensus 328 l~s~~LN~yLkelm~g 343 (618)
|++..|-++|+++.+.
T Consensus 27 I~~~~VKdvlq~LvDD 42 (188)
T PF03962_consen 27 IVSMSVKDVLQSLVDD 42 (188)
T ss_pred CchhhHHHHHHHHhcc
Confidence 7888899999998863
No 84
>PRK06342 transcription elongation factor regulatory protein; Validated
Probab=38.65 E-value=91 Score=30.61 Aligned_cols=65 Identities=11% Similarity=0.249 Sum_probs=39.6
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHH--HHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcccchhhccccceeecc
Q psy17743 401 DKSMGNLKEKISNKRKQVKDAER--ALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETDKEENKTIALGT 472 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~~~~~~~~--~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaLgT 472 (618)
...+++|++.++.|+..++++.. +|.+++ .....++.+|..|+.+|...++--. ......|.+|+
T Consensus 33 ~~G~~~L~~El~~L~~~i~~Ar~~GDlsEak------~~~~~~e~rI~~L~~~L~~A~Ii~~-~~~~d~V~~Gs 99 (160)
T PRK06342 33 EAGLKALEDQLAQARAAYEAAQAIEDVNERR------RQMARPLRDLRYLAARRRTAQLMPD-PASTDVVAFGS 99 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCChhHHH------HHHHHHHHHHHHHHHHHccCEEECC-CCCCCEEEeCc
Confidence 45677888887777655554432 122211 1223456778888888888877432 23556788887
No 85
>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily. Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene.
Probab=37.76 E-value=2.1e+02 Score=32.02 Aligned_cols=24 Identities=17% Similarity=0.311 Sum_probs=16.8
Q ss_pred cccceEeecccCCCCcEEEEEeecCC
Q psy17743 268 RVEHIQLHEEKDGKPYVVCFDFLGKD 293 (618)
Q Consensus 268 R~eHV~l~~~~d~~~~~V~FdFlGKd 293 (618)
..+++++.+ .++.+.|.++|.+.|
T Consensus 109 l~~~l~v~~--~~~s~vi~Is~~~~d 132 (498)
T TIGR03007 109 LRKNISISL--AGRDNLFTISYEDKD 132 (498)
T ss_pred HHhCcEEee--cCCCCeEEEEeeCCC
Confidence 356788876 344678888887764
No 86
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=37.44 E-value=1.2e+02 Score=30.18 Aligned_cols=35 Identities=20% Similarity=0.157 Sum_probs=26.0
Q ss_pred cHHHHHHHHHHHHHHHHHhcccchhhccccceeec
Q psy17743 437 MTDKKKTALGRLKEQLLKLEVQETDKEENKTIALG 471 (618)
Q Consensus 437 ~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaLg 471 (618)
-.|.+-++|++|+++|.+++......+...+++=+
T Consensus 126 e~ee~~~~l~~le~~~~~~e~~~~~~~~~~~~~~~ 160 (175)
T PRK13182 126 EMEEMLERLQKLEARLKKLEPIYITPDTEPTYERE 160 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccCCccccccccc
Confidence 45777889999999999988777666655555444
No 87
>PHA02601 int integrase; Provisional
Probab=36.41 E-value=88 Score=32.38 Aligned_cols=112 Identities=16% Similarity=0.160 Sum_probs=73.7
Q ss_pred HHHHHHHHHhhhccccCCcccccccCccccccccccceEeecccCCCCcEEEEEeecCCceEEEEEeccchHHHHHHHHh
Q psy17743 235 QRAVALYFIDKLALRAGNEKDEDQADTVGCCSLRVEHIQLHEEKDGKPYVVCFDFLGKDSIRYYNEVPVEKRVFKNLQLF 314 (618)
Q Consensus 235 qlA~AlyLID~laLRvGnEkya~endTvG~cTLR~eHV~l~~~~d~~~~~V~FdFlGKdsir~~~~V~vD~~v~knL~~f 314 (618)
.+.+++.|+=.+.+|.|- +|.|+.++|.. +.+.+. .+|.+- ...|++.+.+...|..
T Consensus 192 ~~~~~~~l~~~TG~R~~E-----------i~~L~~~did~--------~~~~~~-~~K~~~--~r~Vpl~~~~~~~L~~- 248 (333)
T PHA02601 192 DLGLIAKICLATGARWSE-----------AETLKRSQISP--------YKITFV-KTKGKK--NRTVPISEELYKMLPK- 248 (333)
T ss_pred hHHHHHHHHHHcCCCHHH-----------HHhCCHHHcCc--------CeEEEE-ECCCCc--eeEEECCHHHHHHHHh-
Confidence 345566677778899987 88898888742 334332 356553 3578888888887753
Q ss_pred hhccCCCccccccCChhHHHHHHHHhcC----CCeeeeeccccchHHHHHHHhhcCCCCccHHHHHHHHHHHHHHHHHHc
Q psy17743 315 VENKKGSDDLFDRLNTSVLNKHLSELME----GLTAKVFRTYNASITLQQQLNELMDPDFSEAEKILAYNRANRAVAVLC 390 (618)
Q Consensus 315 ~~~K~Pgd~LF~~l~s~~LN~yLkelm~----glTAKvFRTynASvt~~~~L~~~~~~~~s~~ek~~~yn~Anr~VAilc 390 (618)
..+.||... ...++.+++.+-- ++|..+||=-.||.+++. +. -...|+.++
T Consensus 249 -----~~~~~f~~~-~~~~~~~~~~~~~~~~~~~~~H~lRHt~at~l~~~-----G~--------------~~~~i~~~l 303 (333)
T PHA02601 249 -----RRGRLFKDA-YESFERAVKRAGIDLPEGQATHVLRHTFASHFMMN-----GG--------------NILVLQRIL 303 (333)
T ss_pred -----cCCCcChhH-HHHHHHHHHHhCCCCCCCCcCchhhHHHHHHHHHc-----CC--------------CHHHHHHHh
Confidence 234677543 5678888887632 478888988777766541 11 125788899
Q ss_pred CCCC
Q psy17743 391 NHQR 394 (618)
Q Consensus 391 NHqr 394 (618)
||..
T Consensus 304 GH~~ 307 (333)
T PHA02601 304 GHAT 307 (333)
T ss_pred CCCC
Confidence 9963
No 88
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=36.04 E-value=85 Score=30.16 Aligned_cols=60 Identities=20% Similarity=0.308 Sum_probs=39.9
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhc----CCCcccHHHHHHHHHHHHHHHHHhcccc
Q psy17743 400 HDKSMGNLKEKISNKRKQVKDAERALKDAKKA----GESKAMTDKKKTALGRLKEQLLKLEVQE 459 (618)
Q Consensus 400 ~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~----~k~~~~~e~~~~~~~~~~~~i~k~~~~~ 459 (618)
.+..+.-|+.|+..+..++..+...|..++.. .+...+.|.+.++|+.+++.+...+-.+
T Consensus 33 ~E~EI~sL~~K~~~lE~eld~~~~~l~~~k~~lee~~~~~~~~E~l~rriq~LEeele~ae~~L 96 (143)
T PF12718_consen 33 KEQEITSLQKKNQQLEEELDKLEEQLKEAKEKLEESEKRKSNAEQLNRRIQLLEEELEEAEKKL 96 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhHHHHHhhHHHHHHHHHHHHHHH
Confidence 56677777777777777777777777766431 1223355677777777777777665544
No 89
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=34.39 E-value=1.7e+02 Score=28.16 Aligned_cols=72 Identities=17% Similarity=0.305 Sum_probs=43.3
Q ss_pred HHhHHHHHHHHHHHHH-HHHHHHHHHHHHhhcCCC---------cccHHHHHHHHHHHHHHHHHhcccchhhccccceee
Q psy17743 401 DKSMGNLKEKISNKRK-QVKDAERALKDAKKAGES---------KAMTDKKKTALGRLKEQLLKLEVQETDKEENKTIAL 470 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~-~~~~~~~~l~~~~~~~k~---------~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaL 470 (618)
...+++|++.++.++. ..-++..+++.|...+-. +.....++.+|..+++.|...++--...-....|++
T Consensus 9 ~~g~~~L~~eL~~l~~~~r~~~~~~~~~A~~~gdl~En~~y~~a~~~~~~~~~ri~~l~~~L~~a~ii~~~~~~~~~V~~ 88 (157)
T PRK00226 9 QEGYEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHAAKEEQGFIEGRIRELEDKLSNAEVIDPSKLSGGKVKF 88 (157)
T ss_pred HHHHHHHHHHHHHHHhcccHHHHHHHHHHHHcCCccccccchHHHHHHHHHHHHHHHHHHHHHhCeecCcccCCCCEEec
Confidence 4566777777777765 344555555555433221 112244577788888888888764333324678888
Q ss_pred cc
Q psy17743 471 GT 472 (618)
Q Consensus 471 gT 472 (618)
|+
T Consensus 89 Gs 90 (157)
T PRK00226 89 GS 90 (157)
T ss_pred CC
Confidence 86
No 90
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=34.03 E-value=1e+02 Score=35.41 Aligned_cols=50 Identities=16% Similarity=0.197 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcccc
Q psy17743 404 MGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQE 459 (618)
Q Consensus 404 m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~ 459 (618)
++..|.+.++++++|+.+++++..... ..+..+.+|+.+++.+..|+.|+
T Consensus 71 LteqQ~kasELEKqLaaLrqElq~~sa------q~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 71 TTEMQVTAAQMQKQYEEIRRELDVLNK------QRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh------hhhhHHHHHHHHHHHHHHHHHHH
Confidence 444566777777777777766653321 12334556666666666666665
No 91
>PF03449 GreA_GreB_N: Transcription elongation factor, N-terminal; InterPro: IPR022691 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A 2ETN_C 2P4V_B.
Probab=33.60 E-value=2.7e+02 Score=24.00 Aligned_cols=57 Identities=12% Similarity=0.255 Sum_probs=36.4
Q ss_pred HHhHHHHHHHHHHHHH-HHHHHHHHHHHHhhcCCCcccH--HHHHHHHHHHHHHHHHhcc
Q psy17743 401 DKSMGNLKEKISNKRK-QVKDAERALKDAKKAGESKAMT--DKKKTALGRLKEQLLKLEV 457 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~-~~~~~~~~l~~~~~~~k~~~~~--e~~~~~~~~~~~~i~k~~~ 457 (618)
..++++|+..++.|+. ...++-+++..|+..|-.+.+. ..-+.....++.||..|+-
T Consensus 8 ~~g~~~L~~EL~~L~~~~rpe~~~~i~~Ar~~GDlsENaeY~aAke~q~~le~rI~~Le~ 67 (74)
T PF03449_consen 8 PEGYEKLQAELEHLKNVERPEIAEEIAEAREQGDLSENAEYHAAKERQAFLEARIRELEE 67 (74)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSSTSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHcCCcccchhHHHHHHHHHHHHHHHHHHHH
Confidence 3567889999988876 5677888888887766543332 3334444555555555543
No 92
>PF10498 IFT57: Intra-flagellar transport protein 57 ; InterPro: IPR019530 Eukaryotic cilia and flagella are specialised organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bi-directional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated []. This protein is known as Huntington-interacting protein-1 in humans.
Probab=33.35 E-value=77 Score=34.98 Aligned_cols=25 Identities=28% Similarity=0.351 Sum_probs=20.2
Q ss_pred ccHHHHHHHHHHHHHHHHHhcccch
Q psy17743 436 AMTDKKKTALGRLKEQLLKLEVQET 460 (618)
Q Consensus 436 ~~~e~~~~~~~~~~~~i~k~~~~~~ 460 (618)
..+-++++.|.+|++.|..|.+++-
T Consensus 328 sPlv~IKqAl~kLk~EI~qMdvrIG 352 (359)
T PF10498_consen 328 SPLVKIKQALTKLKQEIKQMDVRIG 352 (359)
T ss_pred CHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 4567888899999999998888764
No 93
>COG1422 Predicted membrane protein [Function unknown]
Probab=33.15 E-value=90 Score=32.06 Aligned_cols=23 Identities=22% Similarity=0.510 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Q psy17743 409 EKISNKRKQVKDAERALKDAKKA 431 (618)
Q Consensus 409 ~ki~~~~~~~~~~~~~l~~~~~~ 431 (618)
++.+++++..+|.+++.++|++.
T Consensus 72 ekm~~~qk~m~efq~e~~eA~~~ 94 (201)
T COG1422 72 EKMKELQKMMKEFQKEFREAQES 94 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 44445555556666666666543
No 94
>TIGR01462 greA transcription elongation factor GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein.
Probab=33.00 E-value=1.4e+02 Score=28.53 Aligned_cols=71 Identities=15% Similarity=0.318 Sum_probs=45.2
Q ss_pred HhHHHHHHHHHHHHH-HHHHHHHHHHHHhhcCCC---------cccHHHHHHHHHHHHHHHHHhcccchhhccccceeec
Q psy17743 402 KSMGNLKEKISNKRK-QVKDAERALKDAKKAGES---------KAMTDKKKTALGRLKEQLLKLEVQETDKEENKTIALG 471 (618)
Q Consensus 402 ~~m~k~~~ki~~~~~-~~~~~~~~l~~~~~~~k~---------~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaLg 471 (618)
..+++|++.++.|+. ..-++-.+++.|...+-. +.....++.+|..|+++|...++--........|++|
T Consensus 5 ~g~~~L~~el~~L~~~~r~~~~~~~~~a~~~gDl~Ena~y~aak~~~~~~e~ri~~L~~~L~~a~iv~~~~~~~~~V~~G 84 (151)
T TIGR01462 5 EGYEKLKEELEYLKTVKRPEISEEIAEAREHGDLSENAEYHAAKEEQGFNEGRIAELEDLLANAQVIDDSKLSTDVVGFG 84 (151)
T ss_pred HHHHHHHHHHHHHHhcccHHHHHHHHHHHHCCChhhccchHHHHHHHHHHHHHHHHHHHHHHhCcccCcccCCCCEEeeC
Confidence 467788888888874 355555666666433221 1233456777888888888888743333333688888
Q ss_pred c
Q psy17743 472 T 472 (618)
Q Consensus 472 T 472 (618)
+
T Consensus 85 s 85 (151)
T TIGR01462 85 S 85 (151)
T ss_pred C
Confidence 6
No 95
>PF06810 Phage_GP20: Phage minor structural protein GP20; InterPro: IPR009636 This family consists of several phage minor structural protein Gp20 sequences and prophage sequences of around 180 residues in length. The function of this family is unknown.; GO: 0005198 structural molecule activity
Probab=32.78 E-value=1.7e+02 Score=28.61 Aligned_cols=47 Identities=26% Similarity=0.397 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHH
Q psy17743 404 MGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLL 453 (618)
Q Consensus 404 m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~ 453 (618)
.....+.++.++.||.++.+.|+.+++. ...+|.++++|+.|+..+.
T Consensus 22 ~~~~~~e~~~~k~ql~~~d~~i~~Lk~~---~~d~eeLk~~i~~lq~~~~ 68 (155)
T PF06810_consen 22 VDKVKEERDNLKTQLKEADKQIKDLKKS---AKDNEELKKQIEELQAKNK 68 (155)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhc---cCCHHHHHHHHHHHHHHHH
Confidence 3445667777777777777777777652 2356778888888887777
No 96
>COG4787 FlgF Flagellar basal body rod protein [Cell motility and secretion]
Probab=32.03 E-value=35 Score=35.57 Aligned_cols=62 Identities=23% Similarity=0.402 Sum_probs=48.0
Q ss_pred ccEEEE---cCe--eeeecccccCCCcccccCCCCCCCCCCCCCCCccchhhhccCCCCCCCCCCCCC
Q psy17743 99 YGVCTI---DGH--KEKIGNFRIEPPGLFRGRGEHPKMGKLKRRVQAEDIIINCSKDSKVPPPPPGHK 161 (618)
Q Consensus 99 y~~~~~---DG~--~ekvgnfrvepPGlfRgRG~hpk~G~~k~RI~pedv~iN~~k~a~IPpp~~Gha 161 (618)
=||--| ||. --|-||++|.+-|+.-+-| ||-+|.=++-.-|++.++.|+.+-.|-.-+|||.
T Consensus 85 DGwlaVq~~dG~EaYTRnG~~qI~a~g~lTiqg-~pViG~ggpI~vPp~~~v~I~~DGtIsa~~~g~~ 151 (251)
T COG4787 85 DGWLAVQDADGSEAYTRNGNIQIDATGQLTIQG-HPVIGEGGPITVPPGAKVTIAADGTISALNPGDP 151 (251)
T ss_pred CceEEEEcCCCcchheecCceEECcccceecCC-CeeecCCCccccCCCceEEEecCceEEeccCCCC
Confidence 355444 554 2477999999999888988 8999997777779999999998887766555654
No 97
>KOG1962|consensus
Probab=31.70 E-value=1.2e+02 Score=31.57 Aligned_cols=62 Identities=19% Similarity=0.275 Sum_probs=41.2
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC-CcccHHHHHHHHHHHHHHHHHhcccchh
Q psy17743 400 HDKSMGNLKEKISNKRKQVKDAERALKDAKKAGE-SKAMTDKKKTALGRLKEQLLKLEVQETD 461 (618)
Q Consensus 400 ~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k-~~~~~e~~~~~~~~~~~~i~k~~~~~~~ 461 (618)
+++-+.++.++++.+++++++.+++|+.+.++.. ..+..|.+.....++-|.-.+|+-|+..
T Consensus 149 ~~~~~~~~~~~~~kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~~ 211 (216)
T KOG1962|consen 149 LEEENDKLKADLEKLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIES 211 (216)
T ss_pred hhhhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHhc
Confidence 7888888888888888888888888888764321 1233444455555555555566555543
No 98
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.41 E-value=1.4e+02 Score=32.00 Aligned_cols=26 Identities=15% Similarity=0.431 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHHhcccchhhc
Q psy17743 438 TDKKKTALGRLKEQLLKLEVQETDKE 463 (618)
Q Consensus 438 ~e~~~~~~~~~~~~i~k~~~~~~~ke 463 (618)
+++.+..|.+++.+|..++-.+..+.
T Consensus 75 i~~~~~eik~l~~eI~~~~~~I~~r~ 100 (265)
T COG3883 75 IDQSKAEIKKLQKEIAELKENIVERQ 100 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555554443
No 99
>PF05508 Ran-binding: RanGTP-binding protein; InterPro: IPR008812 The small Ras-like GTPase Ran plays an essential role in the transport of macromolecules in and out of the nucleus and has been implicated in spindle and nuclear envelope formation during mitosis in higher eukaryotes. The Saccharomyces cerevisiae ORF YGL164c encoding a novel RanGTP-binding protein, termed Yrb30p was identified. The protein competes with S. cerevisiae RanBP1 (Yrb1p) for binding to the GTP-bound form of S. cerevisiae Ran (Gsp1p) and is, like Yrb1p, able to form trimeric complexes with RanGTP and some of the karyopherins [].
Probab=31.22 E-value=1.3e+02 Score=32.71 Aligned_cols=30 Identities=13% Similarity=0.350 Sum_probs=19.0
Q ss_pred HHHHHHHHHcCCCCCCCCchHHhHHHHHHHHHH
Q psy17743 381 RANRAVAVLCNHQRSVPKSHDKSMGNLKEKISN 413 (618)
Q Consensus 381 ~Anr~VAilcNHqraV~K~~~~~m~k~~~ki~~ 413 (618)
-|+++|+.++-. ||+...+.+++++.+++.
T Consensus 27 yAikq~s~~l~~---ip~~~~~~l~~lq~~L~~ 56 (302)
T PF05508_consen 27 YAIKQCSRFLKK---IPDKDRKELEKLQRRLES 56 (302)
T ss_pred HHHHHHHHHHHh---CCHHHHHHHHHHHHHHHh
Confidence 377777777644 666666666666666543
No 100
>PF09032 Siah-Interact_N: Siah interacting protein, N terminal ; InterPro: IPR015120 The N-terminal domain of Siah interacting protein (SIP) adopts a helical hairpin structure with a hydrophobic core stabilised by a classic knobs-and-holes arrangement of side chains contributed by the two amphipathic helices. Little is known about this domain's function, except that it is crucial for interactions with Siah. It has also been hypothesised that SIP can dimerise through this N-terminal domain []. ; PDB: 1YSM_A 2A26_C 2A25_B 1X5M_A.
Probab=30.82 E-value=1.7e+02 Score=25.86 Aligned_cols=47 Identities=21% Similarity=0.384 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcc
Q psy17743 407 LKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEV 457 (618)
Q Consensus 407 ~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~ 457 (618)
|.++|++|+.+++|++.=|..++. ....+.+...|.+++..|.+++.
T Consensus 1 ~~~~i~eL~~Dl~El~~Ll~~a~R----~rVk~~L~~ei~klE~eI~~~~~ 47 (79)
T PF09032_consen 1 MSEQIEELQLDLEELKSLLEQAKR----KRVKDLLTNEIRKLETEIKKLKE 47 (79)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHTTT----CCHHHHHHHHHHHHHHHHHHCHH
T ss_pred ChhHHHHHHHHHHHHHHHHHHhhH----HHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788888888887776666532 23456778888888888888876
No 101
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=30.07 E-value=71 Score=34.44 Aligned_cols=23 Identities=13% Similarity=0.342 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHhcccchhhcc
Q psy17743 442 KTALGRLKEQLLKLEVQETDKEE 464 (618)
Q Consensus 442 ~~~~~~~~~~i~k~~~~~~~ke~ 464 (618)
.+.|.+|++-|+.++..+-+||.
T Consensus 123 RkEIkQLkQvieTmrssL~ekDk 145 (305)
T PF15290_consen 123 RKEIKQLKQVIETMRSSLAEKDK 145 (305)
T ss_pred HHHHHHHHHHHHHHHhhhchhhh
Confidence 35666777777777766666643
No 102
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=28.99 E-value=2e+02 Score=24.25 Aligned_cols=47 Identities=19% Similarity=0.379 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhc
Q psy17743 404 MGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLE 456 (618)
Q Consensus 404 m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~ 456 (618)
|+.+++++...+..++++...+..+.. ..+..++++..+.++|.+++
T Consensus 1 ~~~i~e~l~~ie~~l~~~~~~i~~lE~------~~~~~e~~i~~~~~~l~~I~ 47 (71)
T PF10779_consen 1 LQDIKEKLNRIETKLDNHEERIDKLEK------RDAANEKDIKNLNKQLEKIK 47 (71)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHH
Confidence 344556666665555555444333221 11233445555555555554
No 103
>PRK04406 hypothetical protein; Provisional
Probab=28.67 E-value=2.5e+02 Score=24.44 Aligned_cols=53 Identities=13% Similarity=0.286 Sum_probs=28.0
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcccc
Q psy17743 401 DKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQE 459 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~ 459 (618)
++.|..|.++|..|+.++.-.+.-+..++. .+-.-.++|+++..++..|.-++
T Consensus 3 ~~~~~~le~Ri~~LE~~lAfQE~tIe~LN~------~v~~Qq~~I~~L~~ql~~L~~rl 55 (75)
T PRK04406 3 EKTIEQLEERINDLECQLAFQEQTIEELND------ALSQQQLLITKMQDQMKYVVGKV 55 (75)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667777887777776554443333322 12233445555555555554433
No 104
>KOG0250|consensus
Probab=28.04 E-value=1.6e+02 Score=36.99 Aligned_cols=84 Identities=19% Similarity=0.225 Sum_probs=51.8
Q ss_pred CCCCchHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-CCcccHHHHHHHHHHHHHHHHHhcccchhhccc-cceeecc
Q psy17743 395 SVPKSHDKSMGNLKEKISNKRKQVKDAERALKDAKKAG-ESKAMTDKKKTALGRLKEQLLKLEVQETDKEEN-KTIALGT 472 (618)
Q Consensus 395 aV~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~-k~~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~n-k~vaLgT 472 (618)
-++.+++.+++.++.-+..++.++.++..++.+++..- +.......+..++.+++.+|.+....+++-..+ -.-++-|
T Consensus 654 ~~~~s~d~~ie~le~e~~~l~~~~~~l~~~~~~~e~~l~e~~~~~~~l~~~~~q~~~~~~~~~~em~el~n~~e~~~~~~ 733 (1074)
T KOG0250|consen 654 VDEFSFDDEIEDLEREASRLQKEILELENQRREAEKNLEELEKKLRELSEHIEQIKRRIRKKRAEMTELKNTAEEKQVDI 733 (1074)
T ss_pred ccchhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhcch
Confidence 44888999999998888888888888777766665321 011223445555555666666665555544333 3445566
Q ss_pred CCcCCC
Q psy17743 473 SKLNYL 478 (618)
Q Consensus 473 Sk~NY~ 478 (618)
|++|=+
T Consensus 734 ~~~~~l 739 (1074)
T KOG0250|consen 734 SKLEDL 739 (1074)
T ss_pred hhhHHH
Confidence 666644
No 105
>PRK09039 hypothetical protein; Validated
Probab=27.98 E-value=1.6e+02 Score=32.11 Aligned_cols=41 Identities=22% Similarity=0.302 Sum_probs=29.5
Q ss_pred cCCCCCCCCchHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy17743 390 CNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAERALKDAKK 430 (618)
Q Consensus 390 cNHqraV~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~ 430 (618)
+..+++....-..+++.|+.+|++++.|+..++.+|..++.
T Consensus 125 L~~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~ 165 (343)
T PRK09039 125 LDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASEK 165 (343)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444566888899999999999888888887754
No 106
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=27.32 E-value=1.5e+02 Score=30.56 Aligned_cols=85 Identities=14% Similarity=0.186 Sum_probs=56.4
Q ss_pred cCCCCCCCCchHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcccchhhcccccee
Q psy17743 390 CNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETDKEENKTIA 469 (618)
Q Consensus 390 cNHqraV~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~va 469 (618)
..++..-+.....++.-++.+|+.++.+.+.+..-|++++ ....+-+++.+|.+++.+|+.++.|+.. =...|+
T Consensus 120 v~~~~~~~~DvT~~y~D~~arl~~l~~~~~rl~~ll~ka~----~~~d~l~ie~~L~~v~~eIe~~~~~~~~--l~~~v~ 193 (262)
T PF14257_consen 120 VTSRNISSEDVTEQYVDLEARLKNLEAEEERLLELLEKAK----TVEDLLEIERELSRVRSEIEQLEGQLKY--LDDRVD 193 (262)
T ss_pred eeeeeccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcC----CHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHhhc
Confidence 3444445667777888888888888888877777766553 1123346788888888888888887655 334556
Q ss_pred eccCCcCCCCC
Q psy17743 470 LGTSKLNYLDP 480 (618)
Q Consensus 470 LgTSk~NY~DP 480 (618)
++|=-|++--|
T Consensus 194 ~sti~i~l~~~ 204 (262)
T PF14257_consen 194 YSTITISLYEP 204 (262)
T ss_pred eEEEEEEEEec
Confidence 66655554443
No 107
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=27.15 E-value=1.9e+02 Score=26.69 Aligned_cols=45 Identities=22% Similarity=0.361 Sum_probs=23.9
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcc
Q psy17743 400 HDKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEV 457 (618)
Q Consensus 400 ~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~ 457 (618)
++++|..|.+.|.+++.++.++-.|= ..++-.-+.+.++|.+++.
T Consensus 13 le~~l~~l~~~~~~LK~~~~~l~EEN-------------~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 13 LEQQLGQLLEELEELKKQLQELLEEN-------------ARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHhc
Confidence 45555555555555555555444331 2234445566666666655
No 108
>COG5570 Uncharacterized small protein [Function unknown]
Probab=27.13 E-value=2.1e+02 Score=23.84 Aligned_cols=50 Identities=26% Similarity=0.292 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCC-cccHHHHHHHHHHHHHHHHHhcccch
Q psy17743 411 ISNKRKQVKDAERALKDAKKAGES-KAMTDKKKTALGRLKEQLLKLEVQET 460 (618)
Q Consensus 411 i~~~~~~~~~~~~~l~~~~~~~k~-~~~~e~~~~~~~~~~~~i~k~~~~~~ 460 (618)
|.+++..-..++.++.++-..... ....-.++.+.-+++++|++|+.|++
T Consensus 7 l~eL~kkHg~le~ei~ea~n~Ps~dd~~i~eLKRrKL~lKeeIEkLka~~~ 57 (57)
T COG5570 7 LAELEKKHGNLEREIQEAMNSPSSDDLAIRELKRRKLRLKEEIEKLKAQMH 57 (57)
T ss_pred HHHHHHhhchHHHHHHHHhcCCCcchHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 334444334444455544322111 12334556666789999999988763
No 109
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=25.79 E-value=3.2e+02 Score=27.35 Aligned_cols=18 Identities=17% Similarity=-0.007 Sum_probs=15.0
Q ss_pred HHHHHHHHHcCCCCCCCC
Q psy17743 381 RANRAVAVLCNHQRSVPK 398 (618)
Q Consensus 381 ~Anr~VAilcNHqraV~K 398 (618)
+|..+||..||.|++.|-
T Consensus 31 ~AFeEvg~~L~RTsAACG 48 (161)
T TIGR02894 31 SAFEEVGRALNRTAAACG 48 (161)
T ss_pred HHHHHHHHHHcccHHHhc
Confidence 378899999999998875
No 110
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=25.41 E-value=1.6e+02 Score=25.35 Aligned_cols=21 Identities=14% Similarity=0.226 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy17743 408 KEKISNKRKQVKDAERALKDA 428 (618)
Q Consensus 408 ~~ki~~~~~~~~~~~~~l~~~ 428 (618)
..+|.++.++|+.|..|-..+
T Consensus 4 ~~~l~EKDe~Ia~L~eEGekL 24 (74)
T PF12329_consen 4 EKKLAEKDEQIAQLMEEGEKL 24 (74)
T ss_pred HHHHHhHHHHHHHHHHHHHHH
Confidence 445556666666666554443
No 111
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=25.28 E-value=1.7e+02 Score=32.74 Aligned_cols=65 Identities=22% Similarity=0.325 Sum_probs=35.8
Q ss_pred CchHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC--------------cccHHHHHHHHHHHHHHHHHhcccchhh
Q psy17743 398 KSHDKSMGNLKEKISNKRKQVKDAERALKDAKKAGES--------------KAMTDKKKTALGRLKEQLLKLEVQETDK 462 (618)
Q Consensus 398 K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~--------------~~~~e~~~~~~~~~~~~i~k~~~~~~~k 462 (618)
....+.++++.+.++.++.++.++++.+...++.++. .....++..+++++++++..|+.++...
T Consensus 330 ~~l~~~~~~l~~~~~~~~~~l~~l~~~l~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~l~~~l~~~ 408 (451)
T PF03961_consen 330 PELKEKLEELEEELEELKEELEKLKKNLKKLKKLKKQGKLPPEKKEQLKKLKEKKKELKEELKELKEELKELKEELERS 408 (451)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445666777777777777777777766665432111 1122344555555555555555544443
No 112
>KOG0930|consensus
Probab=24.96 E-value=1.1e+02 Score=33.30 Aligned_cols=52 Identities=27% Similarity=0.459 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHhcccc--hhhccccceeeccCCcCCCCCccchhhhheeeccCC
Q psy17743 443 TALGRLKEQLLKLEVQE--TDKEENKTIALGTSKLNYLDPRISVTWLASWTENVQ 495 (618)
Q Consensus 443 ~~~~~~~~~i~k~~~~~--~~ke~nk~vaLgTSk~NY~DPRitVtWlkkw~vpI~ 495 (618)
..|....++|..++..- +.++-||.|+.|--|.| |||---+.||...++--+
T Consensus 38 ~Ei~ev~~eid~~~~~e~skt~q~~k~~~~GRKKFN-mDP~Kgiq~l~e~~ll~~ 91 (395)
T KOG0930|consen 38 DEIAEVMEEIDNLESTEESKTKQRNKQVAMGRKKFN-MDPKKGIQFLIENDLLQN 91 (395)
T ss_pred HHHHHHHHHhhhhccccchhhHHHhHHHhhchhhcC-CChHHHhHHHHHcccccC
Confidence 33444444555554433 35678999999999999 899999999998876543
No 113
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=24.96 E-value=1.6e+02 Score=29.02 Aligned_cols=58 Identities=22% Similarity=0.263 Sum_probs=23.7
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHh--hcCCCcccHHHHHHHHHHHHHHHHHhcccc
Q psy17743 402 KSMGNLKEKISNKRKQVKDAERALKDAK--KAGESKAMTDKKKTALGRLKEQLLKLEVQE 459 (618)
Q Consensus 402 ~~m~k~~~ki~~~~~~~~~~~~~l~~~~--~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~ 459 (618)
.++.++++++++.+.|.+...+..++.. +..+....++++++++++.+..++.|+.|.
T Consensus 125 ~~l~~~~~~~~~~~kq~~~~~~~~~~~~~~~~~~~~~ei~~lk~el~~~~~~~~~LkkQ~ 184 (192)
T PF05529_consen 125 KELIKLEEKLEALKKQAESASEAAEKLLKEENKKLSEEIEKLKKELEKKEKEIEALKKQS 184 (192)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555555555443332222211 011112234444455555444444444443
No 114
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=24.88 E-value=2.6e+02 Score=25.34 Aligned_cols=29 Identities=21% Similarity=0.350 Sum_probs=17.0
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17743 400 HDKSMGNLKEKISNKRKQVKDAERALKDA 428 (618)
Q Consensus 400 ~~~~m~k~~~ki~~~~~~~~~~~~~l~~~ 428 (618)
+..+|+.+..++..+..++.+++.-++..
T Consensus 15 ~q~~~~~l~~q~~~le~~~~E~~~v~~eL 43 (110)
T TIGR02338 15 LQQQLQAVATQKQQVEAQLKEAEKALEEL 43 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556666666666666666666444443
No 115
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=24.78 E-value=2.3e+02 Score=26.93 Aligned_cols=23 Identities=26% Similarity=0.263 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHHhcccch
Q psy17743 438 TDKKKTALGRLKEQLLKLEVQET 460 (618)
Q Consensus 438 ~e~~~~~~~~~~~~i~k~~~~~~ 460 (618)
++.++++++.++-||..|+.|..
T Consensus 72 ~~eL~er~E~Le~ri~tLekQe~ 94 (119)
T COG1382 72 VDELEERKETLELRIKTLEKQEE 94 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555554443
No 116
>PRK11546 zraP zinc resistance protein; Provisional
Probab=24.36 E-value=3e+02 Score=26.90 Aligned_cols=55 Identities=15% Similarity=0.184 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC-cccHHHHHHHHHHHHHHHHHhccc
Q psy17743 404 MGNLKEKISNKRKQVKDAERALKDAKKAGES-KAMTDKKKTALGRLKEQLLKLEVQ 458 (618)
Q Consensus 404 m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~-~~~~e~~~~~~~~~~~~i~k~~~~ 458 (618)
.++-..+...|+.++..-+.||..+-...++ ...+.++.+.|..|..+|..+.++
T Consensus 56 ~~~f~~~t~~LRqqL~aKr~ELnALl~~~~pD~~kI~aL~kEI~~Lr~kL~e~r~~ 111 (143)
T PRK11546 56 HNDFYAQTSALRQQLVSKRYEYNALLTANPPDSSKINAVAKEMENLRQSLDELRVK 111 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455556666666666667666444333 345677888888888877755443
No 117
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=24.10 E-value=3.6e+02 Score=24.15 Aligned_cols=28 Identities=11% Similarity=0.222 Sum_probs=16.7
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17743 400 HDKSMGNLKEKISNKRKQVKDAERALKD 427 (618)
Q Consensus 400 ~~~~m~k~~~ki~~~~~~~~~~~~~l~~ 427 (618)
+.++++++..++..+..++.+++.-++.
T Consensus 11 l~~~~~~l~~~~~~l~~~~~E~~~v~~E 38 (105)
T cd00632 11 LQQQLQAYIVQRQKVEAQLNENKKALEE 38 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666666666666665544333
No 118
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=24.09 E-value=1.6e+02 Score=33.77 Aligned_cols=32 Identities=13% Similarity=0.236 Sum_probs=27.0
Q ss_pred CCchHHhHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17743 397 PKSHDKSMGNLKEKISNKRKQVKDAERALKDA 428 (618)
Q Consensus 397 ~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~ 428 (618)
+-+-..+|+.|+.++.+|+.|..||+++|...
T Consensus 20 a~a~a~~i~~L~~ql~aLq~~v~eL~~~laa~ 51 (514)
T PF11336_consen 20 AAATADQIKALQAQLQALQDQVNELRAKLAAK 51 (514)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 44566889999999999999999999988764
No 119
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=23.96 E-value=1.8e+02 Score=24.22 Aligned_cols=59 Identities=20% Similarity=0.369 Sum_probs=30.5
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHHHHHHHhh-cCCCcccHHHHHHHHHHHHHHHHHhccc
Q psy17743 400 HDKSMGNLKEKISNKRKQVKDAERALKDAKK-AGESKAMTDKKKTALGRLKEQLLKLEVQ 458 (618)
Q Consensus 400 ~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~-~~k~~~~~e~~~~~~~~~~~~i~k~~~~ 458 (618)
+++-.++|+.+++.++.++..+.+.|....= ...+...+++-+.+++.+..++.+++.+
T Consensus 2 ~~~E~~rL~Kel~kl~~~i~~~~~kL~n~~F~~kAP~eVve~er~kl~~~~~~~~~l~~~ 61 (66)
T PF10458_consen 2 VEAEIERLEKELEKLEKEIERLEKKLSNENFVEKAPEEVVEKEREKLEELEEELEKLEEA 61 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHHHHS-CCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCccccccCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455667777777766666666554432100 0012234455555566666666555443
No 120
>PLN02943 aminoacyl-tRNA ligase
Probab=23.44 E-value=1.4e+02 Score=37.08 Aligned_cols=67 Identities=7% Similarity=0.083 Sum_probs=28.8
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC-cccHHHHHHHHHHHHHHHHHhcccchhhccccc
Q psy17743 401 DKSMGNLKEKISNKRKQVKDAERALKDAKKAGES-KAMTDKKKTALGRLKEQLLKLEVQETDKEENKT 467 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~-~~~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~ 467 (618)
++..++|+.+|+.++.+++.+++.|....=..|. ...+++-+++++.++++|++++..+..-.++-+
T Consensus 888 ~~E~~rL~K~l~klekei~~~~~kLsN~~F~~KAP~evv~~e~~kl~~~~~~l~~~~~~l~~l~~~~~ 955 (958)
T PLN02943 888 SAEVERLSKRLSKMQTEYDALAARLSSPKFVEKAPEDVVRGVREKAAEAEEKIKLTKNRLAFLKSTSL 955 (958)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCchhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 3444444444444444444444333221101111 223445555555666666666555444333333
No 121
>PRK09343 prefoldin subunit beta; Provisional
Probab=23.43 E-value=1.7e+02 Score=27.26 Aligned_cols=22 Identities=27% Similarity=0.139 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHHhcccch
Q psy17743 439 DKKKTALGRLKEQLLKLEVQET 460 (618)
Q Consensus 439 e~~~~~~~~~~~~i~k~~~~~~ 460 (618)
..++++++-++.+|..++-+..
T Consensus 74 ~~l~~r~E~ie~~ik~lekq~~ 95 (121)
T PRK09343 74 KELKERKELLELRSRTLEKQEK 95 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555555555554443
No 122
>TIGR02680 conserved hypothetical protein TIGR02680. Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length.
Probab=23.30 E-value=4.5e+02 Score=33.95 Aligned_cols=46 Identities=13% Similarity=0.205 Sum_probs=31.8
Q ss_pred HHHHHHHHhhhccCCCccccccCChhHHHHHHHHhcCCCeeeeeccccchH
Q psy17743 306 RVFKNLQLFVENKKGSDDLFDRLNTSVLNKHLSELMEGLTAKVFRTYNASI 356 (618)
Q Consensus 306 ~v~knL~~f~~~K~Pgd~LF~~l~s~~LN~yLkelm~glTAKvFRTynASv 356 (618)
.+++.+..+..++.+ ..++++.|.++|++.++.++.=+.++-.-|+
T Consensus 184 ~l~~~l~~lr~P~Ls-----~~~~~~~l~~~l~~~l~~l~~~~i~~l~e~~ 229 (1353)
T TIGR02680 184 ALLDLLIQLRQPQLS-----KKPDEGVLSDALTEALPPLDDDELTDVADAL 229 (1353)
T ss_pred HHHHHHHHHcCCCCC-----CCCChHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 455666666554433 2477888999999999998877766655444
No 123
>PRK04325 hypothetical protein; Provisional
Probab=23.20 E-value=3.1e+02 Score=23.67 Aligned_cols=53 Identities=19% Similarity=0.246 Sum_probs=25.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcccchh
Q psy17743 403 SMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQETD 461 (618)
Q Consensus 403 ~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~~~ 461 (618)
+|..|+++|..|+..+.-.+.-+..+.. .+-.-.++|+++..++..|..++.+
T Consensus 3 ~~~~~e~Ri~~LE~klAfQE~tIe~LN~------vv~~Qq~~I~~L~~ql~~L~~rl~~ 55 (74)
T PRK04325 3 AVQEMEDRITELEIQLAFQEDLIDGLNA------TVARQQQTLDLLQAQLRLLYQQMRD 55 (74)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666666666655444433333221 1223345555555555555444433
No 124
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=22.86 E-value=2.9e+02 Score=23.82 Aligned_cols=22 Identities=27% Similarity=0.481 Sum_probs=9.0
Q ss_pred hHHhHHHHHHHHHHHHHHHHHH
Q psy17743 400 HDKSMGNLKEKISNKRKQVKDA 421 (618)
Q Consensus 400 ~~~~m~k~~~ki~~~~~~~~~~ 421 (618)
|..++.+|..++.+...++.++
T Consensus 31 ~~~~IKKLr~~~~e~e~~~~~l 52 (74)
T PF12329_consen 31 LNNTIKKLRAKIKELEKQIKEL 52 (74)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444443333
No 125
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=22.60 E-value=2.7e+02 Score=25.01 Aligned_cols=32 Identities=28% Similarity=0.461 Sum_probs=21.7
Q ss_pred CCCchHHhHHHHHHHHHHHHHHHHHHHHHHHH
Q psy17743 396 VPKSHDKSMGNLKEKISNKRKQVKDAERALKD 427 (618)
Q Consensus 396 V~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~ 427 (618)
|.++.+..+.-++.+++.++.++..+++.+.+
T Consensus 81 ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~ 112 (129)
T cd00890 81 VEKSLEEAIEFLKKRLETLEKQIEKLEKQLEK 112 (129)
T ss_pred EEecHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556677777788887777777777665543
No 126
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=22.39 E-value=2e+02 Score=25.22 Aligned_cols=46 Identities=15% Similarity=0.328 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHhcccchhh-----ccccceeeccCCcCCCCCcc-chhhh
Q psy17743 442 KTALGRLKEQLLKLEVQETDK-----EENKTIALGTSKLNYLDPRI-SVTWL 487 (618)
Q Consensus 442 ~~~~~~~~~~i~k~~~~~~~k-----e~nk~vaLgTSk~NY~DPRi-tVtWl 487 (618)
...|+.+.+.|...-+.+.+= .....-.-++...-|-||-. ..||.
T Consensus 23 ~~~~~~i~~~~~~~Gis~~el~~~~~~~~~~~~~~~~~~KYr~p~~~g~tWs 74 (93)
T PF00816_consen 23 EEAIAEIRELMAEYGISPEELAFGSAKKKKKRKRAKVPPKYRNPENPGETWS 74 (93)
T ss_dssp HHHHHHHHHHHHHTT--HHHCHHCCS-----EEEECSSESEEECSSSSEEEC
T ss_pred HHHHHHHHHHHHHhCCCHHHhhhhhhccccccccCCCCCeEeecCCCCCEee
Confidence 345566666666666555443 22334445566677888887 77775
No 127
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=22.35 E-value=4e+02 Score=23.04 Aligned_cols=22 Identities=23% Similarity=0.379 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHhcccch
Q psy17743 439 DKKKTALGRLKEQLLKLEVQET 460 (618)
Q Consensus 439 e~~~~~~~~~~~~i~k~~~~~~ 460 (618)
+.++..++.++..|.+++.+..
T Consensus 65 ~~L~~~~~~~~~~i~~l~~~~~ 86 (106)
T PF01920_consen 65 EELEERIEKLEKEIKKLEKQLK 86 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555555544443
No 128
>PF13758 Prefoldin_3: Prefoldin subunit
Probab=22.29 E-value=5.4e+02 Score=23.84 Aligned_cols=82 Identities=16% Similarity=0.364 Sum_probs=53.3
Q ss_pred eeeccccchHH-HHHHHhhcCCCCccHHHHHHHHHH-------HHHHHHHHcCCCCCCCCchHHhHHHHHHHHHHHHHHH
Q psy17743 347 KVFRTYNASIT-LQQQLNELMDPDFSEAEKILAYNR-------ANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQV 418 (618)
Q Consensus 347 KvFRTynASvt-~~~~L~~~~~~~~s~~ek~~~yn~-------Anr~VAilcNHqraV~K~~~~~m~k~~~ki~~~~~~~ 418 (618)
...|||.|=.- |-+.+..++...++..+..+.+.+ --++|-.++|..-.|+|+=++-+.-+.-+|+..++-+
T Consensus 5 ~hWq~w~aEYe~LKEEi~~l~~~~~~~~e~l~~i~r~f~g~lv~~kEi~~ilG~~~~i~Rt~~Qvv~~l~RRiDYV~~Ni 84 (99)
T PF13758_consen 5 YHWQTWEAEYEGLKEEIEALPEDDDATREDLLRIRRDFGGSLVTEKEIKEILGEGQGITRTREQVVDVLSRRIDYVQQNI 84 (99)
T ss_pred HHHHHHHHHHHHHHHHHHhccccCCCCHHHHHHHHHhcCcccccHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHHHH
Confidence 46789998863 345555553211222233322222 1357888999999999999999998999988888766
Q ss_pred HHHHHHHHHH
Q psy17743 419 KDAERALKDA 428 (618)
Q Consensus 419 ~~~~~~l~~~ 428 (618)
.-+++.|..|
T Consensus 85 ~tleKql~~a 94 (99)
T PF13758_consen 85 ETLEKQLEAA 94 (99)
T ss_pred HHHHHHHHHH
Confidence 6666555544
No 129
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=22.17 E-value=3e+02 Score=28.26 Aligned_cols=24 Identities=13% Similarity=0.219 Sum_probs=10.8
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHH
Q psy17743 400 HDKSMGNLKEKISNKRKQVKDAER 423 (618)
Q Consensus 400 ~~~~m~k~~~ki~~~~~~~~~~~~ 423 (618)
+..+.+.|...|+.++.+++.++.
T Consensus 47 ~~~e~~~L~~e~~~l~~e~e~L~~ 70 (251)
T PF11932_consen 47 WDDEKQELLAEYRQLEREIENLEV 70 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444443
No 130
>KOG4620|consensus
Probab=22.11 E-value=1.7e+02 Score=25.82 Aligned_cols=59 Identities=14% Similarity=0.230 Sum_probs=49.6
Q ss_pred ecCCChhhHHHHHHHHHHhCCCCCCchhHhhhhHHHHHHHcccccccccccccCCCcHHHHHHH
Q psy17743 7 EMKLSQDAEEIATFYARMIEHEYTTKEAFNTNFMKDWRKSMTEKERAVITDLSKCDFRKMHAYF 70 (618)
Q Consensus 7 ~v~L~~~~EEvA~f~a~~l~~~~~~~~~F~~NFf~d~~~~l~~~~~~~i~~~~kcDF~~i~~~~ 70 (618)
|..||--|-+|-.||-..|-+..+.-...+.||++--..++.+. ..+.+-||.-|--.+
T Consensus 1 ~~rlSgLQrqVlhlYR~~lraa~~Kp~~~~~~~m~fvh~EFrk~-----~~lpr~Df~~IEhLl 59 (80)
T KOG4620|consen 1 MSRLSGLQRQVLHLYRDLLRAARGKPGAEARRWMAFVHAEFRKH-----AGLPRSDFLRIEHLL 59 (80)
T ss_pred CcchhHHHHHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHh-----cCCcHhHHHHHHHHH
Confidence 45688889999999999999999999999999999888888664 457889999985444
No 131
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=21.92 E-value=3.4e+02 Score=24.27 Aligned_cols=46 Identities=20% Similarity=0.343 Sum_probs=25.6
Q ss_pred CCchHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHh
Q psy17743 397 PKSHDKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKL 455 (618)
Q Consensus 397 ~K~~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~ 455 (618)
..+.+..+..+.++++.+...++.+.+.+ +.+.+++..++.+|..+
T Consensus 58 ~~~~~ea~~~Le~~~e~le~~i~~l~~~~-------------~~l~~~~~elk~~l~~~ 103 (105)
T cd00632 58 KQEKEEARTELKERLETIELRIKRLERQE-------------EDLQEKLKELQEKIQQA 103 (105)
T ss_pred hccHHHHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHH
Confidence 45566666666666666665555555443 33445555555555544
No 132
>KOG0804|consensus
Probab=21.84 E-value=1.6e+02 Score=33.73 Aligned_cols=19 Identities=5% Similarity=0.034 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHcCCCC
Q psy17743 376 ILAYNRANRAVAVLCNHQR 394 (618)
Q Consensus 376 ~~~yn~Anr~VAilcNHqr 394 (618)
....+.-.+.++..++|.+
T Consensus 384 ~~q~q~k~~k~~kel~~~~ 402 (493)
T KOG0804|consen 384 LQQLQTKLKKCQKELKEER 402 (493)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344445555555555555
No 133
>PF07439 DUF1515: Protein of unknown function (DUF1515); InterPro: IPR010889 This family consists of several hypothetical bacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Rhizobium species. The function of this family is unknown.
Probab=21.48 E-value=2.3e+02 Score=26.78 Aligned_cols=58 Identities=14% Similarity=0.253 Sum_probs=30.5
Q ss_pred hHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcccHHHHHHHHHHHHHHHHHhcccc
Q psy17743 400 HDKSMGNLKEKISNKRKQVKDAERALKDAKKAGESKAMTDKKKTALGRLKEQLLKLEVQE 459 (618)
Q Consensus 400 ~~~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~k~~~~~e~~~~~~~~~~~~i~k~~~~~ 459 (618)
--+||+.++.+|+++++.+++-+ -+.+.+-.+.-...+.+.+.+..++..+..++-.+
T Consensus 6 ~~~q~~~l~~~v~~lRed~r~SE--drsa~SRa~mhrRlDElV~Rv~~lEs~~~~lk~dV 63 (112)
T PF07439_consen 6 LHQQLGTLNAEVKELREDIRRSE--DRSAASRASMHRRLDELVERVTTLESSVSTLKADV 63 (112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH--HHhhhhhHHHHHhHHHHHHHHHHHHHHHHHHHhhH
Confidence 34688888988888888776332 12221111111223445555555555555554443
No 134
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=21.44 E-value=3.7e+02 Score=22.65 Aligned_cols=23 Identities=22% Similarity=0.310 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHHHhcccchhh
Q psy17743 440 KKKTALGRLKEQLLKLEVQETDK 462 (618)
Q Consensus 440 ~~~~~~~~~~~~i~k~~~~~~~k 462 (618)
.-.++|++++.++..|..++.+-
T Consensus 29 ~Qq~~I~~L~~~l~~L~~rl~~~ 51 (69)
T PF04102_consen 29 EQQRQIDRLQRQLRLLRERLREL 51 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHT----
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 33455666666666655555443
No 135
>PRK09039 hypothetical protein; Validated
Probab=21.27 E-value=3.3e+02 Score=29.79 Aligned_cols=43 Identities=19% Similarity=0.203 Sum_probs=21.5
Q ss_pred HHHHHHHHHHcCCCCCCCCchHHhHHHHHHHHHHHHHHHHHHH
Q psy17743 380 NRANRAVAVLCNHQRSVPKSHDKSMGNLKEKISNKRKQVKDAE 422 (618)
Q Consensus 380 n~Anr~VAilcNHqraV~K~~~~~m~k~~~ki~~~~~~~~~~~ 422 (618)
+.-+.+.+.+++.-++-....+..+..++..+..++.+...++
T Consensus 59 ~~qIa~L~e~L~le~~~~~~l~~~l~~l~~~l~~a~~~r~~Le 101 (343)
T PRK09039 59 NSQIAELADLLSLERQGNQDLQDSVANLRASLSAAEAERSRLQ 101 (343)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444445555555555555556555555555444443333
No 136
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=21.26 E-value=84 Score=36.21 Aligned_cols=27 Identities=19% Similarity=0.286 Sum_probs=18.2
Q ss_pred chHHhHHHHHHHHHHHHHHHHHHHHHHH
Q psy17743 399 SHDKSMGNLKEKISNKRKQVKDAERALK 426 (618)
Q Consensus 399 ~~~~~m~k~~~ki~~~~~~~~~~~~~l~ 426 (618)
...+..+.+| ||++|+.||++|++++.
T Consensus 22 a~~~~~~~~q-kie~L~kql~~Lk~q~~ 48 (489)
T PF11853_consen 22 AMADDIDLLQ-KIEALKKQLEELKAQQD 48 (489)
T ss_pred hhhhhhHHHH-HHHHHHHHHHHHHHhhc
Confidence 3444455555 88888888888877654
No 137
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=20.98 E-value=3.7e+02 Score=24.39 Aligned_cols=29 Identities=28% Similarity=0.384 Sum_probs=17.8
Q ss_pred CCCchHHhHHHHHHHHHHHHHHHHHHHHH
Q psy17743 396 VPKSHDKSMGNLKEKISNKRKQVKDAERA 424 (618)
Q Consensus 396 V~K~~~~~m~k~~~ki~~~~~~~~~~~~~ 424 (618)
|.++.+..+..+.++|+.+...++.+++.
T Consensus 61 v~~~~~e~~~~l~~r~e~ie~~i~~lek~ 89 (110)
T TIGR02338 61 VKTDKEEAIQELKEKKETLELRVKTLQRQ 89 (110)
T ss_pred heecHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666677777776666555555443
No 138
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=20.91 E-value=1.2e+02 Score=21.13 Aligned_cols=20 Identities=25% Similarity=0.552 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHHHHHHHHHH
Q psy17743 403 SMGNLKEKISNKRKQVKDAE 422 (618)
Q Consensus 403 ~m~k~~~ki~~~~~~~~~~~ 422 (618)
.|+.++.+|..|+.||.++.
T Consensus 2 E~~rlr~rI~dLer~L~~C~ 21 (23)
T PF04508_consen 2 EMNRLRNRISDLERQLSECR 21 (23)
T ss_pred hHHHHHHHHHHHHHHHHHHh
Confidence 47888888888888887764
No 139
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=20.91 E-value=2.7e+02 Score=21.87 Aligned_cols=52 Identities=23% Similarity=0.416 Sum_probs=34.4
Q ss_pred hHHHHHHHcccccccccccccCCCcHHHHHHHHhhHHHHHcCCHHHHHHHHHHHHHHhcccc
Q psy17743 39 FMKDWRKSMTEKERAVITDLSKCDFRKMHAYFVQKSEERKAMSKEEKKKIKDENEAITKEYG 100 (618)
Q Consensus 39 Ff~d~~~~l~~~~~~~i~~~~kcDF~~i~~~~~~~~e~kk~~t~eEK~~~k~~~~~~~~~y~ 100 (618)
|+++++..+.... -.+.|+.|...+ .+.=++||.+||+.-.+..++..+.|.
T Consensus 11 f~~~~r~~~~~~~-------p~~~~~~i~~~~---~~~W~~ls~~eK~~y~~~a~~~~~~y~ 62 (66)
T cd01390 11 FSQEQRPKLKKEN-------PDASVTEVTKIL---GEKWKELSEEEKKKYEEKAEKDKERYE 62 (66)
T ss_pred HHHHHHHHHHHHC-------cCCCHHHHHHHH---HHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence 6677776664432 125677776554 455678999999888777666666664
No 140
>PF10675 DUF2489: Protein of unknown function (DUF2489); InterPro: IPR019617 This entry represents bacterial uncharacterised proteins.
Probab=20.74 E-value=1.4e+02 Score=28.38 Aligned_cols=42 Identities=26% Similarity=0.342 Sum_probs=36.5
Q ss_pred CCCcHHHHHHHHhh-----HHHHHcCCHHHHHHHHHHHHHHhccccE
Q psy17743 60 KCDFRKMHAYFVQK-----SEERKAMSKEEKKKIKDENEAITKEYGV 101 (618)
Q Consensus 60 kcDF~~i~~~~~~~-----~e~kk~~t~eEK~~~k~~~~~~~~~y~~ 101 (618)
.-||..||+.++.- -+++|+++|.|+-+.--++++.|..|.=
T Consensus 76 ~~~y~a~~~ly~~v~~mPtheaRk~L~k~ermk~D~eR~~~E~~~~~ 122 (131)
T PF10675_consen 76 DSDYPAFYELYEVVKHMPTHEARKALPKKERMKLDLEREKAEAELED 122 (131)
T ss_pred ccCChHHHHHHHHHccCCcHHHHHcCCHHHHHHHhHHHHHHHHHHHH
Confidence 77999999999885 5889999999999998889888887753
No 141
>PF04065 Not3: Not1 N-terminal domain, CCR4-Not complex component ; InterPro: IPR007207 The Ccr4-Not complex (Not1, Not2, Not3, Not4 and Not5) is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID []. This domain is the N-terminal region of the Not proteins.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.66 E-value=3.1e+02 Score=28.76 Aligned_cols=62 Identities=16% Similarity=0.208 Sum_probs=46.5
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-------CCcccHHHHHHHHHHHHHHHHHhcccchhhc
Q psy17743 402 KSMGNLKEKISNKRKQVKDAERALKDAKKAG-------ESKAMTDKKKTALGRLKEQLLKLEVQETDKE 463 (618)
Q Consensus 402 ~~m~k~~~ki~~~~~~~~~~~~~l~~~~~~~-------k~~~~~e~~~~~~~~~~~~i~k~~~~~~~ke 463 (618)
..++=|+.-|+.|..|+..++.++..+.... .....++.++..|++++-.|.+|+.-+..=+
T Consensus 122 e~~~wl~~~Id~L~~QiE~~E~E~E~L~~~~kKkk~~~~~~~r~~~l~~~ierhk~Hi~kLE~lLR~L~ 190 (233)
T PF04065_consen 122 EARDWLKDSIDELNRQIEQLEAEIESLSSQKKKKKKDSTKQERIEELESRIERHKFHIEKLELLLRLLD 190 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCccCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455588899999999999999988763211 1224568889999999999999998776543
No 142
>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]
Probab=20.51 E-value=2.7e+02 Score=31.68 Aligned_cols=23 Identities=35% Similarity=0.394 Sum_probs=19.3
Q ss_pred cHHHHHHHHHHHHHHHHHhcccc
Q psy17743 437 MTDKKKTALGRLKEQLLKLEVQE 459 (618)
Q Consensus 437 ~~e~~~~~~~~~~~~i~k~~~~~ 459 (618)
...++.+.|+.++.+|.+++.|.
T Consensus 88 ~l~~~~~~I~~~~~~l~~l~~q~ 110 (420)
T COG4942 88 DLKKLRKQIADLNARLNALEVQE 110 (420)
T ss_pred HHHHHHhhHHHHHHHHHHHHHHH
Confidence 45677888999999999998887
No 143
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=20.41 E-value=1.1e+02 Score=36.34 Aligned_cols=22 Identities=18% Similarity=0.176 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q psy17743 404 MGNLKEKISNKRKQVKDAERAL 425 (618)
Q Consensus 404 m~k~~~ki~~~~~~~~~~~~~l 425 (618)
|..++.++..++.++++++.++
T Consensus 341 v~~l~~~~~~L~~~~~~l~~~~ 362 (726)
T PRK09841 341 YRALLEKRQTLEQERKRLNKRV 362 (726)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444544444444444443
No 144
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=20.33 E-value=3.2e+02 Score=34.02 Aligned_cols=72 Identities=13% Similarity=0.358 Sum_probs=46.2
Q ss_pred HHhHHHHHHHHHHHHH-HHHHHHHHHHHHhhcCCCcc---------cHHHHHHHHHHHHHHHHHhcccchhhccccceee
Q psy17743 401 DKSMGNLKEKISNKRK-QVKDAERALKDAKKAGESKA---------MTDKKKTALGRLKEQLLKLEVQETDKEENKTIAL 470 (618)
Q Consensus 401 ~~~m~k~~~ki~~~~~-~~~~~~~~l~~~~~~~k~~~---------~~e~~~~~~~~~~~~i~k~~~~~~~ke~nk~vaL 470 (618)
..+.++|++.++.|+. ..-+.-++++.|+.-|-.+. ....++.+|..+++.|...++--........|.+
T Consensus 754 ~eg~~kL~~EL~~L~~v~Rpei~~~I~~Ar~~GDLsENaEY~aAKe~q~~le~RI~eLe~~L~~A~IId~~~~~~d~V~~ 833 (906)
T PRK14720 754 RRALNKKKKELEHLKDVEMPENSKDIGEAQELGDLRENAEYKAAKEKQQQLQAALKRLEAEIDSAKILDLTDVKTSKVGF 833 (906)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhCCCcccchhhHHHHHHHHHHHHHHHHHHHHHhcCEEeCcccCCCCEEEe
Confidence 4566777777777764 46666677777776554322 2345667777777777777774333334567888
Q ss_pred cc
Q psy17743 471 GT 472 (618)
Q Consensus 471 gT 472 (618)
|+
T Consensus 834 GS 835 (906)
T PRK14720 834 GT 835 (906)
T ss_pred CC
Confidence 86
No 145
>TIGR02132 phaR_Bmeg polyhydroxyalkanoic acid synthase, PhaR subunit. This model describes a protein, PhaR, localized to polyhydroxyalkanoic acid (PHA) inclusion granules in Bacillus cereus and related species. PhaR is required for PHA biosynthesis along with PhaC and may be a regulatory subunit.
Probab=20.05 E-value=6.3e+02 Score=25.87 Aligned_cols=49 Identities=22% Similarity=0.173 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHcCCCCCCCC-----chHHhHHHHHHHHHHHHHHHHHHHHHHH
Q psy17743 378 AYNRANRAVAVLCNHQRSVPK-----SHDKSMGNLKEKISNKRKQVKDAERALK 426 (618)
Q Consensus 378 ~yn~Anr~VAilcNHqraV~K-----~~~~~m~k~~~ki~~~~~~~~~~~~~l~ 426 (618)
.|.++..++....=++-.+|- .+.+-+-++..||+.+++++.++-..|.
T Consensus 50 ~yQKafnE~MekYLe~lNlPSr~DiarvA~lvinlE~kvD~lee~fdd~~d~l~ 103 (189)
T TIGR02132 50 FYQKALNDTTGNYLEQVNVPTKEDIANVASLVINLEEKVDLIEEFFDDKFDELE 103 (189)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444455443333333432 2445566778888888877766544443
Done!