Query gi|255764496|ref|YP_003065012.2| excinuclease ABC subunit C [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 616
No_of_seqs 192 out of 2410
Neff 6.8
Searched_HMMs 39220
Date Mon May 30 00:55:42 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 255764496.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00558 uvrC excinuclease ABC 100.0 0 0 1506.7 62.7 591 3-610 11-609 (609)
2 COG0322 UvrC Nuclease subunit 100.0 0 0 1318.8 57.1 569 3-607 9-581 (581)
3 PRK12306 uvrC excinuclease ABC 100.0 0 0 1313.8 54.1 512 1-553 2-517 (519)
4 TIGR00194 uvrC excinuclease AB 100.0 0 0 758.8 41.9 573 2-588 4-601 (601)
5 PRK07883 hypothetical protein; 100.0 0 0 584.8 28.5 335 3-345 220-564 (575)
6 pfam08459 UvrC_HhH_N UvrC Heli 100.0 0 0 401.2 16.7 154 369-542 1-154 (154)
7 PRK10545 nucleotide excision r 100.0 4.2E-45 0 344.5 17.8 182 3-192 28-214 (286)
8 LOAD_uvrC_endov consensus 100.0 6.8E-34 1.7E-38 264.0 12.3 121 369-506 1-122 (123)
9 smart00465 GIYc GIY-YIG type n 99.7 5.4E-17 1.4E-21 142.1 9.2 82 9-90 1-84 (84)
10 pfam01541 GIY-YIG GIY-YIG cata 99.4 9.3E-13 2.4E-17 111.6 5.7 76 9-85 1-77 (77)
11 PRK13766 Hef nuclease; Provisi 99.1 2.7E-10 6.9E-15 93.8 6.5 56 555-610 706-761 (764)
12 KOG2841 consensus 98.6 5.3E-08 1.3E-12 77.3 5.4 58 553-610 193-250 (254)
13 COG1948 MUS81 ERCC4-type nucle 98.6 9.7E-08 2.5E-12 75.3 5.9 131 461-611 98-238 (254)
14 TIGR00575 dnlj DNA ligase, NAD 98.6 8.1E-08 2.1E-12 75.9 4.9 56 558-613 524-590 (706)
15 PRK07956 ligA NAD-dependent DN 98.4 8.9E-07 2.3E-11 68.4 6.2 54 558-611 514-567 (668)
16 COG0272 Lig NAD-dependent DNA 98.3 1.3E-06 3.4E-11 67.2 5.4 54 558-611 514-567 (667)
17 TIGR00631 uvrb excinuclease AB 98.1 3E-06 7.6E-11 64.6 4.0 35 195-229 633-667 (667)
18 PRK00254 ski2-like helicase; P 98.1 2.2E-05 5.5E-10 58.4 8.2 84 529-612 596-702 (717)
19 TIGR02236 recomb_radA DNA repa 98.0 7.9E-06 2E-10 61.6 4.9 54 556-609 1-55 (333)
20 PRK01172 ski2-like helicase; P 97.8 0.00019 4.8E-09 51.6 9.2 53 556-608 613-666 (674)
21 PRK05298 excinuclease ABC subu 97.7 5.8E-05 1.5E-09 55.4 5.0 37 46-83 48-84 (657)
22 pfam02151 UVR UvrB/uvrC motif. 97.7 5.9E-05 1.5E-09 55.3 4.6 35 196-230 1-35 (36)
23 PRK13482 DNA integrity scannin 97.6 0.00017 4.4E-09 51.9 6.1 54 556-609 288-341 (352)
24 COG0556 UvrB Helicase subunit 97.6 0.00011 2.8E-09 53.3 5.0 35 536-572 559-593 (663)
25 PRK02362 ski2-like helicase; P 97.6 0.00062 1.6E-08 47.9 8.8 56 556-613 653-709 (736)
26 PRK00116 ruvA Holliday junctio 97.5 0.00013 3.3E-09 52.8 4.7 62 548-609 66-130 (198)
27 PRK08097 ligB NAD-dependent DN 97.5 0.00019 4.8E-09 51.7 5.0 51 558-611 495-545 (563)
28 TIGR00084 ruvA Holliday juncti 97.5 9.8E-05 2.5E-09 53.7 3.2 81 529-609 55-141 (217)
29 COG0632 RuvA Holliday junction 97.4 8.3E-05 2.1E-09 54.2 2.6 79 530-610 50-131 (201)
30 pfam04493 Endonuclease_5 Endon 97.4 0.00018 4.7E-09 51.7 4.1 115 367-501 3-126 (205)
31 COG1515 Nfi Deoxyinosine 3'end 97.3 0.00062 1.6E-08 47.9 6.1 104 378-501 27-133 (212)
32 PRK13901 ruvA Holliday junctio 97.3 0.00036 9.1E-09 49.6 4.6 60 550-609 67-129 (196)
33 TIGR01259 comE comEA protein; 97.3 0.00018 4.6E-09 51.8 2.9 53 551-608 68-123 (124)
34 PRK08609 hypothetical protein; 97.3 0.00041 1E-08 49.2 4.5 56 377-437 324-395 (570)
35 PRK07997 consensus 97.2 0.0005 1.3E-08 48.6 4.5 124 474-607 660-791 (928)
36 PRK07456 consensus 97.1 0.00095 2.4E-08 46.6 5.1 137 462-608 674-821 (975)
37 PRK06887 consensus 97.0 0.00077 2E-08 47.2 4.1 138 462-609 670-820 (954)
38 PRK08835 consensus 97.0 0.00099 2.5E-08 46.5 4.3 136 462-608 645-794 (931)
39 COG1623 Predicted nucleic-acid 96.9 0.0016 4.1E-08 44.9 5.0 54 556-609 294-347 (349)
40 TIGR00593 pola DNA polymerase 96.9 0.00049 1.3E-08 48.6 2.4 118 473-593 86-237 (1005)
41 PRK05797 consensus 96.9 0.0019 4.9E-08 44.4 5.3 137 462-609 584-734 (869)
42 PRK09482 xni exonuclease IX; P 96.9 0.0014 3.7E-08 45.3 4.6 62 538-606 161-226 (256)
43 TIGR00596 rad1 DNA repair prot 96.9 0.0012 3.1E-08 45.8 4.1 56 556-612 882-938 (939)
44 cd06559 Endonuclease_V Endonuc 96.9 0.0018 4.6E-08 44.6 4.9 104 377-500 23-130 (208)
45 PRK08786 consensus 96.8 0.0021 5.4E-08 44.1 4.9 136 462-607 642-790 (927)
46 smart00475 53EXOc 5'-3' exonuc 96.8 0.0021 5.4E-08 44.0 4.9 62 538-606 165-230 (259)
47 PRK04301 radA DNA repair and r 96.8 0.003 7.5E-08 43.0 5.6 12 214-225 68-79 (318)
48 pfam01367 5_3_exonuc 5'-3' exo 96.8 0.0025 6.2E-08 43.6 5.1 44 556-606 19-62 (100)
49 COG3880 Modulator of heat shoc 96.8 0.0023 5.9E-08 43.8 4.7 35 197-231 136-170 (176)
50 PRK07300 consensus 96.8 0.0024 6.1E-08 43.7 4.8 134 462-606 594-742 (880)
51 PRK08434 consensus 96.8 0.0022 5.7E-08 43.9 4.6 132 462-607 607-753 (887)
52 PRK07556 consensus 96.7 0.0029 7.4E-08 43.1 4.7 135 463-607 689-836 (977)
53 PRK05755 DNA polymerase I; Pro 96.7 0.0038 9.6E-08 42.2 5.1 136 462-607 605-753 (889)
54 TIGR01448 recD_rel helicase, R 96.7 0.0019 4.7E-08 44.5 3.5 145 317-500 357-520 (769)
55 PRK08928 consensus 96.7 0.003 7.5E-08 43.0 4.5 135 462-606 578-725 (861)
56 PRK07625 consensus 96.6 0.0028 7.2E-08 43.2 4.2 137 463-609 638-787 (922)
57 PRK05929 consensus 96.6 0.002 5.2E-08 44.2 3.4 136 462-607 586-735 (870)
58 PRK11617 endonuclease V; Provi 96.6 0.0061 1.6E-07 40.8 5.7 109 371-500 21-133 (223)
59 PRK08076 consensus 96.6 0.0041 1E-07 42.0 4.7 137 462-608 591-741 (877)
60 PRK07898 consensus 96.6 0.0032 8.2E-08 42.7 4.2 136 461-609 615-766 (902)
61 KOG0442 consensus 96.5 0.0044 1.1E-07 41.8 4.8 58 555-613 821-878 (892)
62 cd04657 Piwi_ago-like Piwi_ago 96.5 0.065 1.7E-06 33.3 10.7 114 377-514 196-328 (426)
63 cd00008 53EXOc 5'-3' exonuclea 96.4 0.0051 1.3E-07 41.3 4.5 62 538-606 162-227 (240)
64 smart00483 POLXc DNA polymeras 96.4 0.014 3.5E-07 38.2 6.6 22 212-233 21-42 (334)
65 PRK00024 radC DNA repair prote 96.3 0.0089 2.3E-07 39.6 5.2 44 361-408 105-148 (224)
66 PRK08609 hypothetical protein; 96.1 0.017 4.3E-07 37.6 5.9 19 427-445 439-457 (570)
67 PRK12766 50S ribosomal protein 96.1 0.0078 2E-07 40.0 3.9 50 556-605 11-61 (238)
68 TIGR00608 radc DNA repair prot 95.7 0.012 3.1E-07 38.6 3.7 38 568-605 39-81 (223)
69 PRK01216 DNA polymerase IV; Va 95.7 0.032 8.2E-07 35.5 5.8 12 216-227 123-134 (351)
70 pfam09517 RE_Eco29kI Eco29kI r 95.5 0.0088 2.3E-07 39.6 2.3 61 17-87 30-116 (170)
71 COG1555 ComEA DNA uptake prote 95.4 0.014 3.6E-07 38.1 3.2 51 555-607 97-147 (149)
72 TIGR00426 TIGR00426 competence 95.4 0.011 2.8E-07 38.9 2.6 51 552-607 14-68 (70)
73 cd00141 NT_POLXc Nucleotidyltr 95.4 0.068 1.7E-06 33.2 6.6 19 214-232 20-38 (307)
74 pfam00633 HHH Helix-hairpin-he 95.2 0.0084 2.2E-07 39.7 1.5 30 577-606 1-30 (30)
75 cd00080 HhH2_motif Helix-hairp 95.1 0.02 5.2E-07 37.0 3.3 30 556-585 23-52 (75)
76 PTZ00217 flap endonuclease-1; 95.1 0.034 8.6E-07 35.4 4.4 50 555-604 235-285 (394)
77 PRK03352 DNA polymerase IV; Va 95.1 0.072 1.8E-06 33.0 5.9 14 215-228 121-134 (345)
78 KOG4417 consensus 95.0 0.037 9.5E-07 35.1 4.2 117 375-506 38-158 (261)
79 PRK02406 DNA polymerase IV; Va 94.9 0.089 2.3E-06 32.4 5.9 25 475-499 316-340 (355)
80 COG1796 POL4 DNA polymerase IV 94.8 0.04 1E-06 34.9 3.9 18 217-234 28-45 (326)
81 cd01701 Pol_zeta Pol_zeta, a m 94.7 0.095 2.4E-06 32.1 5.7 11 217-227 170-180 (405)
82 COG0258 Exo 5'-3' exonuclease 94.7 0.059 1.5E-06 33.6 4.6 172 396-607 61-247 (310)
83 cd00128 XPG Xeroderma pigmento 94.7 0.063 1.6E-06 33.4 4.8 52 555-608 223-274 (316)
84 PRK03980 flap endonuclease-1; 94.3 0.062 1.6E-06 33.5 3.9 33 555-587 189-221 (295)
85 PRK10430 DNA-binding transcrip 94.3 0.25 6.3E-06 29.1 7.0 175 425-610 7-205 (239)
86 PRK01810 DNA polymerase IV; Va 94.2 0.15 3.7E-06 30.8 5.8 75 469-547 311-389 (410)
87 PRK07956 ligA NAD-dependent DN 94.2 0.097 2.5E-06 32.1 4.8 78 533-610 417-502 (668)
88 PRK08097 ligB NAD-dependent DN 94.2 0.12 3.1E-06 31.4 5.3 57 556-612 427-485 (563)
89 PRK03348 DNA polymerase IV; Pr 94.0 0.16 4.2E-06 30.5 5.6 29 471-499 312-340 (456)
90 PRK02794 DNA polymerase IV; Pr 93.9 0.19 4.8E-06 30.0 5.8 17 176-192 107-123 (417)
91 PRK00329 GIY-YIG nuclease supe 93.9 0.13 3.3E-06 31.2 5.0 63 12-77 9-71 (86)
92 TIGR01259 comE comEA protein; 93.7 0.046 1.2E-06 34.4 2.3 30 578-607 63-92 (124)
93 smart00483 POLXc DNA polymeras 93.6 0.074 1.9E-06 32.9 3.3 17 580-596 310-326 (334)
94 cd01700 Pol_V Pol V was discov 93.6 0.22 5.5E-06 29.6 5.6 10 427-436 255-264 (344)
95 cd01703 Pol_iota Pol iota is m 93.4 0.19 4.9E-06 29.9 5.2 54 557-612 212-267 (394)
96 TIGR03674 fen_arch flap struct 93.4 0.084 2.1E-06 32.5 3.4 48 555-610 236-283 (338)
97 cd01702 Pol_eta Pol eta is mem 93.2 0.12 3.1E-06 31.4 3.8 26 168-193 82-107 (358)
98 PRK07220 DNA topoisomerase I; 93.0 0.22 5.6E-06 29.5 5.0 48 554-601 685-733 (740)
99 cd00424 Pol_Y Y-family of DNA 92.9 0.26 6.6E-06 29.0 5.2 18 175-192 70-87 (341)
100 COG0272 Lig NAD-dependent DNA 92.8 0.28 7.1E-06 28.8 5.3 96 517-612 400-504 (667)
101 PRK03103 DNA polymerase IV; Re 92.7 0.4 1E-05 27.6 6.0 14 215-228 123-136 (410)
102 PRK03858 DNA polymerase IV; Va 92.3 0.41 1.1E-05 27.5 5.6 12 216-227 118-129 (398)
103 cd02826 Piwi-like Piwi-like: P 92.2 0.98 2.5E-05 24.9 10.5 115 378-514 170-300 (393)
104 COG1555 ComEA DNA uptake prote 91.8 0.12 3.1E-06 31.3 2.4 35 576-610 86-120 (149)
105 PRK12311 rpsB 30S ribosomal pr 91.8 1.1 2.7E-05 24.5 9.8 124 461-605 157-287 (332)
106 COG5241 RAD10 Nucleotide excis 91.1 0.18 4.7E-06 30.1 2.7 193 364-609 15-221 (224)
107 TIGR00375 TIGR00375 conserved 90.9 0.24 6.2E-06 29.2 3.2 60 545-606 295-366 (384)
108 COG3680 Uncharacterized protei 90.6 0.65 1.7E-05 26.1 5.1 84 2-87 2-107 (259)
109 pfam02171 Piwi Piwi domain. Th 90.4 1.5 3.7E-05 23.6 13.6 111 380-513 72-199 (296)
110 KOG2093 consensus 90.2 0.52 1.3E-05 26.8 4.4 76 537-614 525-607 (1016)
111 cd00141 NT_POLXc Nucleotidyltr 90.2 0.51 1.3E-05 26.9 4.3 13 583-595 287-299 (307)
112 cd04658 Piwi_piwi-like_Euk Piw 90.1 1.5 3.9E-05 23.4 14.8 113 378-514 227-356 (448)
113 TIGR01453 grpIintron_endo grou 89.4 1.7 4.2E-05 23.2 6.5 81 9-89 1-105 (281)
114 PRK10046 dpiA two-component re 89.0 1.9 4.7E-05 22.8 6.6 173 426-610 11-204 (225)
115 pfam02889 Sec63 Sec63 Brl doma 88.6 1.2 3E-05 24.2 5.3 22 47-68 33-54 (309)
116 TIGR01448 recD_rel helicase, R 88.6 0.78 2E-05 25.6 4.3 27 202-228 336-362 (769)
117 PRK03609 umuC DNA polymerase V 88.5 0.87 2.2E-05 25.2 4.5 29 472-500 319-348 (422)
118 COG2231 Uncharacterized protei 88.4 0.54 1.4E-05 26.7 3.4 46 392-438 124-172 (215)
119 COG1491 Predicted RNA-binding 88.2 1.5 3.9E-05 23.5 5.6 81 524-611 98-187 (202)
120 pfam04919 DUF655 Protein of un 88.0 0.99 2.5E-05 24.8 4.5 82 525-610 85-172 (181)
121 PTZ00035 Rad51; Provisional 87.7 1.3 3.3E-05 24.0 4.9 21 212-232 93-113 (350)
122 TIGR01011 rpsB_bact ribosomal 87.6 1.3 3.3E-05 23.9 4.9 70 435-527 137-207 (227)
123 smart00611 SEC63 Domain of unk 86.7 2.2 5.6E-05 22.3 5.6 11 466-476 249-259 (312)
124 pfam11731 Cdd1 Pathogenicity l 86.4 0.7 1.8E-05 25.9 3.0 40 552-591 9-49 (92)
125 COG1379 PHP family phosphoeste 86.4 1.3 3.3E-05 24.0 4.3 136 427-608 215-365 (403)
126 TIGR03491 RecB family nuclease 85.4 1.7 4.4E-05 23.1 4.6 14 214-227 249-262 (457)
127 PRK00377 cbiT cobalt-precorrin 85.2 2.9 7.5E-05 21.4 5.8 41 462-502 110-177 (198)
128 COG0177 Nth Predicted EndoIII- 83.7 1.5 3.8E-05 23.5 3.7 19 130-148 5-23 (211)
129 smart00279 HhH2 Helix-hairpin- 82.4 0.92 2.3E-05 25.1 2.2 19 557-575 18-36 (36)
130 pfam02371 Transposase_20 Trans 81.7 2 5.1E-05 22.6 3.7 42 556-599 3-44 (87)
131 PRK10702 endonuclease III; Pro 81.7 1.7 4.3E-05 23.1 3.3 21 128-148 3-23 (211)
132 COG2827 Predicted endonuclease 81.5 4.1 0.0001 20.4 5.3 67 7-76 2-68 (95)
133 pfam10391 DNA_pol_lambd_f Fing 80.7 1.7 4.3E-05 23.1 3.0 29 556-584 3-32 (52)
134 COG0758 Smf Predicted Rossmann 80.6 3.6 9.3E-05 20.7 4.7 40 71-110 63-102 (350)
135 pfam00633 HHH Helix-hairpin-he 79.6 0.86 2.2E-05 25.3 1.2 21 553-573 9-29 (30)
136 PRK13913 3-methyladenine DNA g 79.2 2.1 5.2E-05 22.5 3.1 25 220-250 118-142 (218)
137 TIGR01954 nusA_Cterm_rpt trans 78.9 2.6 6.7E-05 21.8 3.5 35 572-606 11-47 (52)
138 smart00278 HhH1 Helix-hairpin- 78.8 1.1 2.9E-05 24.4 1.6 20 556-575 2-21 (26)
139 pfam00318 Ribosomal_S2 Ribosom 77.7 5.3 0.00013 19.6 6.0 37 461-502 135-171 (205)
140 KOG1041 consensus 77.3 5.4 0.00014 19.5 10.6 107 377-502 603-729 (876)
141 COG1431 Argonaute homolog, imp 76.2 5.8 0.00015 19.3 6.3 100 380-503 475-579 (685)
142 PRK05299 rpsB 30S ribosomal pr 74.9 6.2 0.00016 19.1 6.5 53 461-527 155-207 (255)
143 TIGR00615 recR recombination p 73.8 1.9 4.8E-05 22.8 1.7 76 239-323 89-167 (205)
144 cd00056 ENDO3c endonuclease II 73.7 2.8 7.3E-05 21.5 2.6 15 557-571 85-99 (158)
145 KOG1921 consensus 73.5 4.9 0.00013 19.8 3.7 22 174-196 71-92 (286)
146 pfam08846 DUF1816 Domain of un 71.9 2.5 6.3E-05 21.9 1.9 19 119-137 22-40 (68)
147 TIGR03631 bact_S13 30S ribosom 69.9 3.4 8.7E-05 20.9 2.2 40 553-592 13-54 (113)
148 PRK05179 rpsM 30S ribosomal pr 69.1 3.5 9E-05 20.8 2.2 37 556-592 18-56 (122)
149 pfam11798 IMS_HHH IMS family H 68.9 3.4 8.6E-05 21.0 2.0 21 555-576 12-32 (33)
150 pfam00416 Ribosomal_S13 Riboso 68.5 3 7.7E-05 21.3 1.7 42 551-592 11-54 (106)
151 KOG2875 consensus 68.0 7.9 0.0002 18.3 3.8 50 159-220 58-107 (323)
152 TIGR02154 PhoB phosphate regul 67.8 7.1 0.00018 18.7 3.5 75 460-539 43-129 (226)
153 PRK10917 ATP-dependent DNA hel 67.3 4.3 0.00011 20.2 2.3 79 523-607 587-667 (677)
154 cd00758 MoCF_BD MoCF_BD: molyb 67.0 8.9 0.00023 17.9 3.9 75 402-499 17-95 (133)
155 TIGR00147 TIGR00147 conserved 66.5 9.3 0.00024 17.8 5.3 116 278-398 71-215 (316)
156 PRK02515 psbU photosystem II c 66.1 5.2 0.00013 19.6 2.5 53 556-614 74-126 (144)
157 pfam01949 DUF99 Protein of unk 65.9 9.5 0.00024 17.7 5.0 170 380-609 3-181 (185)
158 pfam01986 DUF123 Domain of unk 65.9 8.2 0.00021 18.2 3.5 25 18-42 5-32 (99)
159 PRK00766 hypothetical protein; 64.7 10 0.00026 17.6 4.6 167 380-608 9-187 (194)
160 COG1058 CinA Predicted nucleot 64.5 6.5 0.00017 18.9 2.8 36 465-502 181-217 (255)
161 PHA00439 exonuclease 63.9 4.1 0.00011 20.3 1.7 38 534-574 169-206 (288)
162 TIGR01083 nth endonuclease III 63.8 4.2 0.00011 20.3 1.7 18 131-148 4-21 (192)
163 KOG2518 consensus 63.2 7 0.00018 18.7 2.8 37 35-72 115-156 (556)
164 COG0099 RpsM Ribosomal protein 62.5 7.9 0.0002 18.3 2.9 37 556-592 18-56 (121)
165 pfam00730 HhH-GPD HhH-GPD supe 62.4 11 0.00028 17.3 4.4 15 557-571 83-97 (144)
166 TIGR02684 dnstrm_HI1420 probab 61.6 6.7 0.00017 18.8 2.4 36 426-490 53-88 (91)
167 pfam01645 Glu_synthase Conserv 61.1 12 0.00029 17.1 3.9 36 464-499 227-281 (367)
168 pfam03118 RNA_pol_A_CTD Bacter 60.2 12 0.0003 17.0 5.7 53 556-609 9-62 (62)
169 cd00686 Terpene_cyclase_cis_tr 59.9 12 0.00031 17.0 5.4 104 119-235 139-251 (357)
170 PRK08694 consensus 59.8 12 0.00031 17.0 3.8 37 463-499 330-378 (468)
171 COG4277 Predicted DNA-binding 59.1 6.3 0.00016 19.0 2.0 42 554-600 329-370 (404)
172 cd00885 cinA Competence-damage 58.7 11 0.00027 17.4 3.0 14 426-439 43-56 (170)
173 cd02808 GltS_FMN Glutamate syn 58.6 13 0.00032 16.8 4.1 34 464-497 239-291 (392)
174 CHL00137 rps13 ribosomal prote 57.8 6.3 0.00016 19.0 1.7 36 556-591 18-55 (122)
175 COG0389 DinP Nucleotidyltransf 56.6 14 0.00035 16.6 3.8 29 167-195 64-92 (354)
176 TIGR01317 GOGAT_sm_gam glutama 56.6 8.7 0.00022 18.0 2.3 30 132-178 85-116 (517)
177 COG4565 CitB Response regulato 55.7 14 0.00036 16.5 3.6 136 463-609 46-199 (224)
178 PRK01215 competence damage-ind 55.2 13 0.00034 16.7 3.0 35 466-502 184-218 (264)
179 COG1204 Superfamily II helicas 54.9 14 0.00037 16.4 4.3 60 552-611 672-733 (766)
180 PRK04053 rps13p 30S ribosomal 53.7 8.4 0.00022 18.1 1.8 11 333-343 88-98 (149)
181 TIGR02672 cas_csm6 CRISPR-asso 53.3 12 0.0003 17.1 2.5 43 461-504 251-297 (393)
182 COG3743 Uncharacterized conser 53.2 15 0.00039 16.2 3.3 40 555-595 67-108 (133)
183 TIGR02027 rpoA DNA-directed RN 53.0 15 0.00039 16.3 3.1 82 526-609 223-315 (324)
184 CHL00067 rps2 ribosomal protei 52.9 16 0.0004 16.2 7.4 36 461-501 155-190 (227)
185 PRK13844 recombination protein 52.5 10 0.00027 17.4 2.2 80 241-331 91-171 (200)
186 PRK00076 recR recombination pr 52.2 11 0.00027 17.4 2.2 31 240-272 86-116 (197)
187 COG0052 RpsB Ribosomal protein 52.0 16 0.00041 16.1 8.7 102 404-528 103-207 (252)
188 PRK02101 hypothetical protein; 51.9 16 0.00041 16.1 3.3 24 181-207 28-51 (257)
189 PRK10416 cell division protein 51.8 16 0.00041 16.1 3.2 128 362-518 335-479 (499)
190 cd01425 RPS2 Ribosomal protein 51.3 16 0.00042 16.0 8.2 37 461-502 125-161 (193)
191 PRK12278 50S ribosomal protein 50.5 17 0.00043 15.9 3.4 38 555-592 153-191 (216)
192 smart00852 MoCF_biosynth Proba 49.5 17 0.00044 15.8 3.7 55 425-502 41-97 (135)
193 pfam03883 DUF328 Protein of un 49.4 17 0.00045 15.8 3.7 12 300-311 156-167 (238)
194 TIGR01836 PHA_synth_III_C poly 49.4 9.7 0.00025 17.7 1.6 32 270-303 257-289 (367)
195 PRK13034 serine hydroxymethylt 49.3 18 0.00045 15.8 5.1 25 377-402 115-139 (422)
196 PRK11264 putative amino-acid A 48.8 12 0.00031 17.0 2.0 11 464-474 161-171 (248)
197 cd00886 MogA_MoaB MogA_MoaB fa 48.7 18 0.00045 15.8 2.8 31 425-475 43-73 (152)
198 pfam02906 Fe_hyd_lg_C Iron onl 48.5 16 0.0004 16.2 2.5 36 19-54 10-47 (286)
199 cd01141 TroA_d Periplasmic bin 47.8 18 0.00047 15.7 7.8 31 464-499 70-100 (186)
200 KOG4716 consensus 47.0 19 0.00048 15.6 3.2 11 221-231 113-123 (503)
201 PRK11411 fecB iron-dicitrate t 45.3 20 0.00051 15.4 4.0 11 299-309 101-111 (297)
202 pfam00464 SHMT Serine hydroxym 44.8 20 0.00052 15.3 5.4 25 377-402 104-128 (380)
203 PRK09202 nusA transcription el 44.6 21 0.00052 15.3 5.9 51 555-605 374-425 (428)
204 pfam03296 Pox_polyA_pol Poxvir 44.4 11 0.00029 17.2 1.3 31 26-56 49-79 (462)
205 TIGR00674 dapA dihydrodipicoli 43.9 21 0.00054 15.2 4.3 53 179-231 170-241 (288)
206 TIGR00600 rad2 DNA excision re 43.2 15 0.00037 16.4 1.7 27 557-583 954-982 (1127)
207 COG1031 Uncharacterized Fe-S o 42.9 19 0.00048 15.6 2.2 106 57-169 126-252 (560)
208 COG2183 Tex Transcriptional ac 42.8 18 0.00046 15.7 2.2 47 367-417 316-363 (780)
209 PRK13910 DNA glycosylase MutY; 42.4 22 0.00056 15.1 4.2 24 584-609 261-284 (290)
210 KOG3931 consensus 42.3 9.3 0.00024 17.8 0.6 40 161-203 163-202 (484)
211 KOG3182 consensus 42.3 22 0.00057 15.1 4.6 34 193-226 150-187 (212)
212 TIGR02667 moaB_proteo molybden 42.0 22 0.00057 15.0 2.7 30 425-474 45-74 (163)
213 COG0353 RecR Recombinational D 41.9 17 0.00045 15.8 1.9 27 240-268 87-113 (198)
214 PRK07945 hypothetical protein; 41.6 23 0.00058 15.0 3.3 31 204-234 114-161 (335)
215 cd06419 GH25_muramidase_2 Unch 41.5 12 0.00031 17.0 1.1 11 382-392 8-18 (190)
216 PRK04286 hypothetical protein; 41.3 21 0.00053 15.2 2.3 34 418-476 182-215 (294)
217 pfam05559 DUF763 Protein of un 41.1 16 0.0004 16.2 1.6 17 555-571 269-285 (319)
218 PRK03670 competence damage-ind 40.9 23 0.00059 14.9 2.9 35 465-502 184-219 (252)
219 pfam00994 MoCF_biosynth Probab 40.7 23 0.0006 14.9 2.6 41 425-487 40-82 (140)
220 COG4959 TraF Type IV secretory 40.5 17 0.00042 16.0 1.6 13 115-127 146-158 (173)
221 COG0061 nadF NAD kinase [Coenz 40.3 24 0.00061 14.9 4.3 26 265-291 85-110 (281)
222 PRK11823 DNA repair protein Ra 40.0 24 0.00061 14.8 3.5 16 425-440 330-345 (454)
223 cd01147 HemV-2 Metal binding p 39.8 24 0.00062 14.8 3.0 12 464-475 213-224 (262)
224 PRK05182 DNA-directed RNA poly 39.6 24 0.00062 14.8 3.0 44 567-610 255-300 (306)
225 KOG4825 consensus 39.5 24 0.00062 14.8 3.1 51 179-230 190-240 (666)
226 pfam07527 Hairy_orange Hairy O 39.4 24 0.00062 14.8 2.4 22 557-578 18-39 (43)
227 pfam03104 DNA_pol_B_exo DNA po 39.1 25 0.00063 14.7 5.2 95 378-489 84-193 (254)
228 PRK05636 replicative DNA helic 38.5 25 0.00064 14.7 3.5 38 464-501 378-427 (507)
229 cd00984 DnaB_C DnaB helicase C 38.0 26 0.00065 14.6 4.3 36 464-499 124-171 (242)
230 smart00696 DM9 Repeats found i 37.2 22 0.00055 15.1 1.8 14 16-29 21-34 (71)
231 PRK10880 adenine DNA glycosyla 37.2 26 0.00067 14.5 3.6 17 364-380 182-198 (350)
232 pfam06330 TRI5 Trichodiene syn 37.0 27 0.00068 14.5 6.2 106 119-235 139-251 (376)
233 COG2248 Predicted hydrolase (m 36.9 26 0.00066 14.6 2.2 34 418-476 181-214 (304)
234 PRK00260 cysS cysteinyl-tRNA s 36.8 27 0.00068 14.5 4.4 19 125-143 36-56 (460)
235 CHL00013 rpoA RNA polymerase a 36.6 27 0.00069 14.5 3.4 44 566-609 281-326 (333)
236 cd01139 TroA_f Periplasmic bin 36.5 27 0.00069 14.5 4.5 10 464-473 234-243 (342)
237 PRK03673 competence damage-ind 35.6 28 0.00071 14.4 2.9 17 188-204 147-163 (396)
238 KOG2379 consensus 35.6 28 0.00071 14.4 2.7 54 556-609 431-499 (501)
239 PRK07649 para-aminobenzoate/an 35.5 19 0.00048 15.6 1.3 37 256-293 152-188 (195)
240 PRK04020 rps2P 30S ribosomal p 34.9 29 0.00073 14.3 4.8 34 464-502 115-148 (204)
241 TIGR02042 sir sulfite reductas 33.4 30 0.00077 14.1 3.5 93 380-500 352-460 (583)
242 PRK07534 methionine synthase I 33.2 30 0.00077 14.1 2.1 16 556-571 274-289 (335)
243 pfam00072 Response_reg Respons 32.8 31 0.00078 14.0 3.6 73 426-501 5-80 (111)
244 COG1833 Uri superfamily endonu 32.4 31 0.00079 14.0 4.0 46 19-64 28-75 (132)
245 TIGR00088 trmD tRNA (guanine-N 32.1 23 0.0006 14.9 1.3 18 362-379 223-240 (247)
246 PRK09191 two-component respons 32.1 32 0.00081 14.0 3.7 36 463-502 182-221 (261)
247 PRK07758 hypothetical protein; 31.8 32 0.00081 13.9 3.9 45 565-609 45-89 (95)
248 TIGR01438 TGR thioredoxin and 31.7 32 0.00081 13.9 2.2 126 74-209 99-241 (513)
249 cd01744 GATase1_CPSase Small c 31.6 31 0.00079 14.0 1.9 34 256-290 144-178 (178)
250 PRK08506 replicative DNA helic 31.4 32 0.00082 13.9 3.9 37 464-500 304-352 (473)
251 PTZ00205 DNA polymerase kappa; 31.3 29 0.00075 14.2 1.7 30 163-192 189-218 (571)
252 pfam09597 IGR IGR protein moti 31.1 33 0.00083 13.9 3.7 46 562-609 7-52 (56)
253 TIGR01127 ilvA_1Cterm threonin 30.9 32 0.00081 13.9 1.9 122 391-541 257-380 (381)
254 PRK00011 glyA serine hydroxyme 30.8 33 0.00084 13.8 5.4 26 464-489 312-339 (415)
255 pfam06514 PsbU Photosystem II 30.6 27 0.00068 14.5 1.4 52 557-614 67-118 (135)
256 COG1628 Endonuclease V homolog 30.4 34 0.00086 13.8 3.9 153 380-580 9-168 (185)
257 TIGR02999 Sig-70_X6 RNA polyme 30.1 34 0.00086 13.7 2.0 14 281-294 88-101 (194)
258 COG1200 RecG RecG-like helicas 30.1 15 0.00039 16.2 0.1 31 54-92 61-91 (677)
259 cd07963 Anticodon_Ia_Cys Antic 29.6 35 0.00088 13.7 4.4 34 195-228 108-141 (156)
260 KOG2201 consensus 29.2 5.1 0.00013 19.7 -2.5 13 466-478 285-297 (371)
261 KOG0950 consensus 29.2 35 0.0009 13.6 3.7 54 554-607 893-949 (1008)
262 PRK05595 replicative DNA helic 29.2 35 0.0009 13.6 3.6 37 464-500 312-360 (444)
263 COG1415 Uncharacterized conser 29.1 23 0.0006 14.9 0.9 16 334-349 206-221 (373)
264 PRK06722 exonuclease; Provisio 28.9 3.8 9.7E-05 20.6 -3.2 19 169-187 77-95 (242)
265 PRK05920 aromatic acid decarbo 28.7 36 0.00091 13.6 3.5 26 377-402 71-101 (205)
266 pfam10551 MULE MULE transposas 28.6 36 0.00091 13.6 4.5 22 464-485 57-78 (93)
267 COG2205 KdpD Osmosensitive K+ 28.4 36 0.00092 13.5 3.0 133 464-608 719-858 (890)
268 COG2006 Uncharacterized conser 28.2 36 0.00093 13.5 2.8 12 464-475 194-205 (293)
269 pfam04679 DNA_ligase_A_C ATP d 27.8 37 0.00094 13.5 2.1 16 11-29 11-26 (95)
270 TIGR01163 rpe ribulose-phospha 27.8 37 0.00094 13.5 4.1 29 464-496 169-197 (216)
271 TIGR00140 hupD hydrogenase exp 27.7 36 0.00093 13.5 1.7 19 465-483 35-53 (156)
272 PRK09581 pleD response regulat 27.7 37 0.00095 13.5 3.4 25 56-84 25-49 (457)
273 PRK10867 signal recognition pa 27.1 38 0.00097 13.4 9.8 183 388-598 161-397 (453)
274 TIGR00528 gcvT glycine cleavag 27.0 21 0.00053 15.2 0.4 33 258-292 201-233 (394)
275 KOG2423 consensus 26.5 39 0.00099 13.3 3.4 75 61-140 85-159 (572)
276 smart00511 ORANGE Orange domai 25.3 40 0.001 13.2 1.6 23 556-578 17-39 (45)
277 COG4957 Predicted transcriptio 25.2 41 0.001 13.2 2.3 29 399-429 77-105 (148)
278 TIGR03600 phage_DnaB phage rep 25.2 41 0.001 13.1 4.5 37 464-500 306-353 (421)
279 pfam11901 DUF3421 Protein of u 25.1 41 0.001 13.1 1.8 15 16-30 4-18 (118)
280 KOG2747 consensus 24.8 12 0.00032 16.9 -1.1 96 117-246 140-235 (396)
281 COG0855 Ppk Polyphosphate kina 24.8 42 0.0011 13.1 2.5 15 486-500 578-592 (696)
282 TIGR02885 spore_sigF RNA polym 24.7 42 0.0011 13.1 2.0 11 508-518 145-155 (231)
283 KOG2520 consensus 24.5 42 0.0011 13.1 2.8 20 557-576 562-581 (815)
284 TIGR01684 viral_ppase viral ph 24.4 28 0.00071 14.4 0.6 50 272-321 66-116 (323)
285 KOG3206 consensus 24.4 42 0.0011 13.0 2.5 20 173-192 98-117 (234)
286 PRK05973 replicative DNA helic 24.3 43 0.0011 13.0 4.3 38 464-501 148-193 (237)
287 COG0837 Glk Glucokinase [Carbo 24.3 21 0.00054 15.2 -0.0 26 179-204 82-107 (320)
288 pfam03796 DnaB_C DnaB-like hel 24.1 43 0.0011 13.0 4.5 37 464-500 130-180 (186)
289 CHL00101 trpG anthranilate syn 24.1 43 0.0011 13.0 3.2 25 266-291 163-187 (190)
290 pfam01912 eIF-6 eIF-6 family. 24.0 43 0.0011 13.0 3.8 55 363-435 117-171 (198)
291 cd01142 TroA_e Periplasmic bin 23.8 43 0.0011 13.0 3.8 11 464-474 220-230 (289)
292 cd01825 SGNH_hydrolase_peri1 S 23.8 43 0.0011 13.0 5.1 49 381-439 137-185 (189)
293 PRK08840 replicative DNA helic 23.6 44 0.0011 12.9 4.0 36 464-499 330-377 (464)
294 cd00715 GPATase_N Glutamine am 23.1 45 0.0011 12.9 2.4 18 304-321 99-116 (252)
295 cd00156 REC Signal receiver do 23.0 45 0.0011 12.9 3.6 73 426-501 4-79 (113)
296 TIGR01627 A_thal_3515 uncharac 22.8 35 0.0009 13.6 0.9 16 460-476 145-160 (238)
297 KOG0190 consensus 22.5 17 0.00043 15.9 -0.8 134 56-228 24-184 (493)
298 KOG1795 consensus 22.5 46 0.0012 12.8 3.7 71 317-391 838-909 (2321)
299 PRK04885 ppnK inorganic polyph 22.2 46 0.0012 12.8 6.7 30 264-294 66-95 (265)
300 PRK03604 moaC bifunctional mol 22.0 47 0.0012 12.7 2.9 30 425-475 188-217 (301)
301 PRK12373 NADH dehydrogenase su 21.8 47 0.0012 12.7 3.3 39 555-594 326-366 (403)
302 pfam02638 DUF187 Uncharacteriz 21.5 48 0.0012 12.7 2.9 46 103-155 40-91 (394)
303 COG4231 Indolepyruvate ferredo 21.5 48 0.0012 12.7 5.3 27 57-85 58-84 (640)
304 smart00654 eIF6 translation in 21.5 48 0.0012 12.7 3.5 37 363-407 119-155 (200)
305 pfam11020 DUF2610 Protein of u 21.2 48 0.0012 12.7 1.3 31 316-348 35-65 (85)
306 COG4748 Uncharacterized conser 21.1 48 0.0012 12.6 1.3 47 182-228 127-174 (365)
307 PRK08857 para-aminobenzoate sy 21.0 46 0.0012 12.8 1.2 29 262-291 163-191 (192)
308 PRK07004 replicative DNA helic 20.9 49 0.0013 12.6 4.5 37 464-500 325-373 (460)
309 COG0303 MoeA Molybdopterin bio 20.9 49 0.0013 12.6 7.5 103 408-538 208-317 (404)
310 TIGR02775 TrbG_Ti P-type conju 20.8 38 0.00096 13.4 0.7 17 460-476 173-196 (220)
311 pfam05621 TniB Bacterial TniB 20.5 50 0.0013 12.5 6.7 82 400-501 98-190 (302)
312 KOG2383 consensus 20.5 29 0.00074 14.2 0.0 82 431-541 289-377 (467)
313 PRK07204 3-oxoacyl-(acyl carri 20.4 50 0.0013 12.5 2.3 66 318-389 34-113 (329)
314 COG0215 CysS Cysteinyl-tRNA sy 20.1 51 0.0013 12.5 4.3 42 194-235 84-132 (464)
315 pfam11202 DUF2983 Protein of u 20.1 51 0.0013 12.5 3.8 31 426-479 124-156 (353)
316 pfam02503 PP_kinase Polyphosph 20.0 51 0.0013 12.4 1.5 49 301-350 334-386 (678)
No 1
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=100.00 E-value=0 Score=1506.65 Aligned_cols=591 Identities=45% Similarity=0.767 Sum_probs=565.9
Q ss_pred HHHCCCCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCC-CCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHC
Q ss_conf 1258678862588869988889960125878887613788-778799999973444299982871999999998877618
Q gi|255764496|r 3 SEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSN-NHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLK 81 (616)
Q Consensus 3 ~~~lP~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~-~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~~ 81 (616)
.++||++||||+|+|++|+|||||||||||+||+|||+.. .+++||..||++|.+|||++|+||.||||||++|||+|+
T Consensus 11 l~~lP~~PGvY~~~d~~~~viYVGKAknLk~Rv~sYF~~~~~~~~kt~~mv~~i~~ie~ivt~sE~EALlLE~~LIK~~k 90 (609)
T PRK00558 11 LKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVSSYFRKKNDLSPKTRAMVSQIADIEYIVTRSETEALLLENNLIKKYK 90 (609)
T ss_pred HHHCCCCCEEEEEECCCCCEEEEECCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCEEEEEECCHHHHHHHHHHHHHHHC
T ss_conf 97689998558998899989998510526678898578988899789999998624789996998999999999986758
Q ss_pred CCCEECCCCCCCCCEEEEECCCCCCEEEEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCH
Q ss_conf 72003364689772699808899845999812356784377037887899999999997301100355421247886624
Q gi|255764496|r 82 PRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLL 161 (616)
Q Consensus 82 P~yNi~LkDdk~yPyi~it~~~~~p~l~~~r~~~~~~~~yfGPf~~~~~~~~~l~~l~~~f~lR~C~~~~~~~~~~pCl~ 161 (616)
|+|||+||||||||||+||.+|+|||+.++|+..++++.|||||||+++++.++++|+++||||+|+++++.++.||||+
T Consensus 91 P~YNilLkDDK~YPyi~it~~e~~Pri~~~R~~~~~~~~YfGPf~~~~~~~~~l~~l~k~F~lR~C~~~~~~~r~RPCL~ 170 (609)
T PRK00558 91 PRYNILLRDDKSYPYIKITTNEKFPRLAITRGAKKDKGRYFGPYPSAGAVRETLNLLQKLFPLRTCEDSVFKNRTRPCLL 170 (609)
T ss_pred CCCCCCCCCCCCCCEEEEECCCCCCEEEEEECCCCCCCEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHH
T ss_conf 98510124789983799977998730899957647897485786749999999999999835466774000347973224
Q ss_pred HHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--
Q ss_conf 455425866131220356655543234550387158999999999999863338888889999999986221100024--
Q gi|255764496|r 162 FQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIY-- 239 (616)
Q Consensus 162 y~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~G~~~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~i~~~q~v~~-- 239 (616)
||||+|+|||+|.||+++|++.|++++.||+|+++++++.|+++|+.||++|+||+||.+||+|++|+.++++|.+..
T Consensus 171 y~I~rC~aPC~g~Is~~~Y~~~V~~~~~fL~G~~~~l~~~L~~~M~~aS~~l~FE~Aa~~RD~i~aL~~i~~~Q~v~~~~ 250 (609)
T PRK00558 171 YQIGRCLAPCVGLVSKEEYAELVDEAKLFLQGKSDEVIKELEEKMEKASENLEFERAARLRDQIQALRRVQEKQKVSLAD 250 (609)
T ss_pred HHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEECCC
T ss_conf 43468566635757999999999999999827949999999999999997320667899999999999986356532588
Q ss_pred -CCCCHHHHCCCCCEEEEEEEEEECCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCC-CCCHHHEECCCCC-HHHHHH
Q ss_conf -5420111000188347889984247454101135667778997898887775432137-8981231026888-578766
Q gi|255764496|r 240 -NRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDK-PCPENILLSEEAE-ETSLLE 316 (616)
Q Consensus 240 -~d~Dvi~i~~~~~~~~I~vl~vR~G~i~g~~~f~~~~~~~~~~~eil~~fI~qyY~~~-~iP~~Iiv~~~~~-~~~~l~ 316 (616)
.|+||||++.+++.+||+|++||+|+++|+.+|+++...+.+.+|++++||.|||+++ .+|++|+++.+++ +.++++
T Consensus 251 ~~d~DVi~i~~~~~~~~i~v~~vR~G~i~g~~~~~~~~~~~~~~~eil~~fl~q~Y~~~~~~P~eIlv~~~~~~d~~~l~ 330 (609)
T PRK00558 251 LEDADVIAIAVDKGWACVQVFFIRGGKLLGRRSFFPKVPGDTELEEVLEAFIGQFYLDNRPIPKEILVPHELEIDKELLE 330 (609)
T ss_pred CCCCEEEEEEECCCEEEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCHHHHH
T ss_conf 76540799997198589999998788996005677046677998999999999998417899976883576785689999
Q ss_pred HHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCE
Q ss_conf 65432013433321256552667899999999986554323343389999999875156643516999707443775404
Q gi|255764496|r 317 ISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAV 396 (616)
Q Consensus 317 ~~L~~k~g~kV~i~~P~rG~kk~Ll~lA~~NA~~~l~~k~~~~~~~~~~l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~V 396 (616)
+||++++|.+|+|.+|++|++++|++||..||++.+.+++....+.+.+|++|++.|+|++.|+|||||||||+||+++|
T Consensus 331 ~~L~~~~~~kv~i~~PkrG~Kk~Ll~lA~~NA~~~l~~~~~~~~~~~~~l~~L~~~L~L~~~p~rIE~fDiSh~~G~~~V 410 (609)
T PRK00558 331 EALSEKAGRKVKIRVPQRGDKKELLELAEKNAREALERKLSDQSTQTAALEELAEALGLPTLPKRIECFDISHIQGTDTV 410 (609)
T ss_pred HHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCEE
T ss_conf 99985359946996188536899999999999999999987555699999999998388998878999824321687605
Q ss_pred EEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHH
Q ss_conf 88888516872803232110244445541168998999999997753131112333333334545798489980985899
Q gi|255764496|r 397 GCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQL 476 (616)
Q Consensus 397 as~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQl 476 (616)
||||||++|+|.|++||+|||+ +++++|||+||+|||+|||+++.++. .++|||||||||+|||
T Consensus 411 gsmVvf~~g~~~K~~YRkf~Ik--~~~~~DDy~~M~Evl~RR~~r~~~e~--------------~~lPDLilIDGGkgQL 474 (609)
T PRK00558 411 ASMVVFEDGGPDKSEYRRYNIK--GITGGDDYAAMREVLTRRFSRLLKEF--------------AKLPDLILIDGGKGQL 474 (609)
T ss_pred EEEEEEECCCCCHHHCCCCCCC--CCCCCCHHHHHHHHHHHHHHHHHHCC--------------CCCCCEEEECCCHHHH
T ss_conf 8999997897276764711369--99998659999999999998887538--------------9999889954977899
Q ss_pred HHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEE-CCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CC
Q ss_conf 99999999758877871899971877676634898-17983488579989999999887877887889899864321-47
Q gi|255764496|r 477 SAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFF-VKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKA-AY 554 (616)
Q Consensus 477 n~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~-~~~~~~i~l~~~~~~l~~Lq~iRDEaHRFAi~~hRk~r~k~-~~ 554 (616)
|+|.++|+++|++ .|||+||||+++|+++.|.++ ++.++++.|++++++|+|||+||||||||||+|||++|+|. +.
T Consensus 475 ~~a~~~l~~l~l~-~i~viglaK~~~r~~~~E~i~~~~~~~~i~l~~~s~~l~lLq~iRDEaHRFAi~~hR~~R~k~~~~ 553 (609)
T PRK00558 475 NAAKEVLEELGLD-DIPVIGLAKGDERKAGTEELFFPDGGEPFSLPPNSPALYLLQRIRDEAHRFAITFHRQKRSKARLT 553 (609)
T ss_pred HHHHHHHHHCCCC-CCCEEEEECCCCCCCCCEEEEECCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 9999999976999-860899971687777740899789982554499998999999998729887999999975020025
Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf 71004888798999999998088898993898888627899989999999985478
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616)
|.||+||||||+|+++||+||||+++|++||+|||++|+|||+++|++||++||+.
T Consensus 554 s~Ld~I~GIG~kr~~~Ll~~Fgs~~~i~~As~eeL~~v~Gi~~~~A~~I~~~l~~~ 609 (609)
T PRK00558 554 SRLDDIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISKKLAEKIYEALHKK 609 (609)
T ss_pred CCCCCCCCCCHHHHHHHHHHCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHCC
T ss_conf 71647899799999999997079999973899999648998999999999997059
No 2
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=100.00 E-value=0 Score=1318.83 Aligned_cols=569 Identities=44% Similarity=0.723 Sum_probs=539.7
Q ss_pred HHHCCCCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHCC
Q ss_conf 12586788625888699888899601258788876137887787999999734442999828719999999988776187
Q gi|255764496|r 3 SEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKP 82 (616)
Q Consensus 3 ~~~lP~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~~P 82 (616)
.+++|++||||+|+|.+|+|||||||||||+||+|||+.... +||..||+++.++||++|.||.|||+||+||||+|+|
T Consensus 9 l~~lP~~PGvY~~~d~~g~VlYVGKAknLr~Rv~sYF~~~~~-~kt~~lv~~i~~iE~ivt~~E~EALlLE~nLIK~~~P 87 (581)
T COG0322 9 LKNLPHSPGVYLMKDENGTVLYVGKAKNLRKRVSSYFRGRLD-PKTAALVENIADIEYIVTDTETEALLLENNLIKKHKP 87 (581)
T ss_pred HHHCCCCCCEEEEECCCCCEEEEEEHHHHHHHHHHHHCCCCC-HHHHHHHHHHCCEEEEEECCHHHHHHHHHHHHHHHCC
T ss_conf 964899980389988999889996445678888986167985-8999999744663699748877788889867776389
Q ss_pred CCEECCCCCCCCCEEEEECCCCCCEEEEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHH
Q ss_conf 20033646897726998088998459998123567843770378878999999999973011003554212478866244
Q gi|255764496|r 83 RFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLF 162 (616)
Q Consensus 83 ~yNi~LkDdk~yPyi~it~~~~~p~l~~~r~~~~~~~~yfGPf~~~~~~~~~l~~l~~~f~lR~C~~~~~~~~~~pCl~y 162 (616)
+|||+|||||+||||+||.+|+|||+.++|+...++++|||||++++++++++++|+++||||+|++..+++|.||||+|
T Consensus 88 rYNvlLkDdKsYp~i~it~~e~~Pri~i~R~~~~~~~~yFGPy~s~~a~~~~l~ll~rlfplR~C~~~~~~~r~rpCl~Y 167 (581)
T COG0322 88 RYNVLLKDDKSYPYIKITLHEEFPRIAITRGLRKDKGKYFGPYPSAGAVRETLNLLQRLFPLRTCSDSVKRNRRRPCLYY 167 (581)
T ss_pred CEEEECCCCCCCCEEEEECCCCCCCHHHHHHHHCCCCCEECCCCCHHHHHHHHHHHHHHHCCHHCCCCCCCCCCCCCHHH
T ss_conf 61377425897762896367666432453011016873689878634689999999976113316886433457864441
Q ss_pred HHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---
Q ss_conf 55425866131220356655543234550387158999999999999863338888889999999986221100024---
Q gi|255764496|r 163 QIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIY--- 239 (616)
Q Consensus 163 ~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~G~~~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~i~~~q~v~~--- 239 (616)
|||+|+|||++.+++++|.+.|+.++.||+|+++.+++.|+++|++||++++||+||.|||+|.+|..++++|.+..
T Consensus 168 ~i~rC~apC~~~is~e~Y~e~v~~~~~fL~G~~~~v~~~L~~~M~~As~~l~FE~Aa~~RD~i~al~~l~~~q~v~~~~~ 247 (581)
T COG0322 168 QIGRCLAPCVGLISEEEYREIVEEVKGFLKGKDDAVLQELEEKMEEASENLDFERAARLRDQIKALEKLQEKQAVSLFKL 247 (581)
T ss_pred HHCCCCCCEECCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 00255566005578999999999999997698899999999999999875147989999999999999974563356774
Q ss_pred CCCCHHHHCCCCCEEEEEEEEEECCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHEECCCCCHHHHHHHHH
Q ss_conf 54201110001883478899842474541011356677789978988877754321378981231026888578766654
Q gi|255764496|r 240 NRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAEETSLLEISF 319 (616)
Q Consensus 240 ~d~Dvi~i~~~~~~~~I~vl~vR~G~i~g~~~f~~~~~~~~~~~eil~~fI~qyY~~~~iP~~Iiv~~~~~~~~~l~~~L 319 (616)
.+.|||+++.+++.+||++|++|+|+++|+..++. ... +.+.+ +++||.|||..+..|++|+++..+++.. +++||
T Consensus 248 ~~~Dv~a~~~~~~~~~v~vf~~R~Gkllg~~~~f~-~~~-~~~~~-~~~fi~Q~Y~~~~~P~~Ill~~~~~~~~-l~~~l 323 (581)
T COG0322 248 QDLDVIAGAVDGGEACVQVFFVRGGKLLGRRAYFP-LEN-EAEEE-LEAFILQFYKSNEIPKEILLPQELPEEE-LEEAL 323 (581)
T ss_pred CCHHHHEEEECCCEEEEEEEEEECCHHCCCCCEEC-CCC-CCCHH-HHHHHHHHHCCCCCCCEEEECCCCCHHH-HHHHH
T ss_conf 11125023303986799987751431037754005-777-54057-9999999722788964578078877589-99999
Q ss_pred HHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCEEEE
Q ss_conf 32013433321256552667899999999986554323343389999999875156643516999707443775404888
Q gi|255764496|r 320 FKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCM 399 (616)
Q Consensus 320 ~~k~g~kV~i~~P~rG~kk~Ll~lA~~NA~~~l~~k~~~~~~~~~~l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~ 399 (616)
+...|. +|.+|++|++++|++||..||...+.+ +........++++|++.|+|+ .|+|||||||||++|+++||||
T Consensus 324 ~~~~~~--~i~~p~~G~kk~l~~~A~~NA~~~l~~-l~~~~~~~~~l~~l~~~l~l~-~p~rIE~~D~Sh~~g~~~V~sm 399 (581)
T COG0322 324 SEAAGL--EIRVPKRGEKKSLLELATKNAKEALEQ-LKERSDEKQALEALAALLGLP-APYRIECFDISHIQGEDTVGSM 399 (581)
T ss_pred HHHCCC--CCCCCCCCHHHHHHHHHHHHHHHHHHH-HHHCCCHHHHHHHHHHHHCCC-CCEEEEEEECCCCCCCCCEEEE
T ss_conf 861477--312688655889999999999999999-885133568999999985889-8616898516753566644579
Q ss_pred EEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHH
Q ss_conf 88516872803232110244445541168998999999997753131112333333334545798489980985899999
Q gi|255764496|r 400 VVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAA 479 (616)
Q Consensus 400 Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a 479 (616)
|||.+|+|.|++||+|||+ ++++|||+||+||++|||+++.++ +|||||+||||+||||+|
T Consensus 400 vvf~~g~~~k~~YRry~i~---~~~~dDya~m~evl~RR~~~~~~~----------------~~Pdli~iDGGkgQl~~a 460 (581)
T COG0322 400 VVFEDGGPSKKDYRRYNIK---ITGGDDYASMREVLTRRYSRLLKE----------------ELPDLILIDGGKGQLNAA 460 (581)
T ss_pred EEECCCCCCHHHCCCCCCC---CCCCCHHHHHHHHHHHHHHHCCCC----------------CCCCEEEEECCHHHHHHH
T ss_conf 9976898775436522446---789755999999999886511125----------------799779996978899999
Q ss_pred HHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-CCCCHH
Q ss_conf 9999975887787189997187767663489817983488579989999999887877887889899864321-477100
Q gi|255764496|r 480 QGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKA-AYSPLD 558 (616)
Q Consensus 480 ~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~iRDEaHRFAi~~hRk~r~k~-~~S~Ld 558 (616)
.+||+++|++ +|||||||+++ +.++++.++++.|++++|+|+|||+||||||||||||||++|.|. +.|.||
T Consensus 461 ~~vl~~l~~~--~~viglaK~~~-----~~~~~~~~~~~~l~~~~p~l~~lq~irDEaHrfAi~~hR~~R~k~~~~s~Ld 533 (581)
T COG0322 461 KEVLKELGLD--IPVIGLAKGEE-----ELLLPGPGEEFDLPPNSPALYLLQRIRDEAHRFAITYHRKKRSKAMLQSSLD 533 (581)
T ss_pred HHHHHHCCCC--CCEEEEEECCC-----EEEECCCCCEECCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 9999975998--61799971686-----0686699963127999889999999888999999998888766664027000
Q ss_pred CCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 4888798999999998088898993898888627899989999999985
Q gi|255764496|r 559 EINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 559 ~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
+|||||++|+++||+||||+++|+.||++||++| ||++++|++||++|
T Consensus 534 ~I~GiG~~r~~~LL~~Fgs~~~i~~As~eel~~v-gi~~~~a~~i~~~~ 581 (581)
T COG0322 534 DIPGIGPKRRKALLKHFGSLKGIKSASVEELAKV-GISKKLAEKIYEAL 581 (581)
T ss_pred CCCCCCHHHHHHHHHHHHCHHHHHHCCHHHHHHC-CCCHHHHHHHHHHC
T ss_conf 4888688999999998317888885599999874-99999999998529
No 3
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=100.00 E-value=0 Score=1313.79 Aligned_cols=512 Identities=37% Similarity=0.617 Sum_probs=482.5
Q ss_pred CCHHHCCCCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf 99125867886258886998888996012587888761378877879999997344429998287199999999887761
Q gi|255764496|r 1 MSSEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRL 80 (616)
Q Consensus 1 ~~~~~lP~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~ 80 (616)
|+.++||++||||+|+|++|+|||||||||||+||+|||+.+.+++||..||++|.+||||+|+||.||||||+||||+|
T Consensus 2 ~~L~~lP~~PGVY~~~d~~~~viYVGKAknLk~Rv~sYf~~~~~~~kt~~mv~~i~~ie~ivt~sE~EALlLE~nLIK~~ 81 (519)
T PRK12306 2 IDLSDIPKNPGCYLYKDEEGTIIYVGKAKNLKKRVSSYFQKKNHDPKTQSLVKAIRDIEFIVTDNEVEAFLLENTLIKKH 81 (519)
T ss_pred CCCCCCCCCCEEEEEECCCCCEEEEEEHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCEEEEEECCHHHHHHHHHHHHHHH
T ss_conf 77010989985389988999899996015377789985688899858999999873479999698899999999998674
Q ss_pred CCCCEECCCCCCCCCEEEEECCCCCCEEEEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 87200336468977269980889984599981235678437703788789999999999730110035542124788662
Q gi|255764496|r 81 KPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCL 160 (616)
Q Consensus 81 ~P~yNi~LkDdk~yPyi~it~~~~~p~l~~~r~~~~~~~~yfGPf~~~~~~~~~l~~l~~~f~lR~C~~~~~~~~~~pCl 160 (616)
+|+|||+|||||+||||+|| +|+|||+.++|+..+ .+.|||||||+++++.++++|+++||||+|++ .+.||||
T Consensus 82 kP~yNilLkDdK~YPyi~it-~e~~Pri~~~R~~~~-~g~YfGPf~~~~~~~~~l~~l~k~F~lR~C~~----~~~RpCL 155 (519)
T PRK12306 82 QPKYNIDLKDSKRYAYIYIS-EEKFPRIGIARNKSG-KGKFFGPFVSAKERDYVLDVLKKTFQLRSCKN----MPKRPCL 155 (519)
T ss_pred CCCCCEECCCCCCCCEEEEE-CCCCCCEEEEEECCC-CCEEECCCCCHHHHHHHHHHHHHHHCCCCCCC----CCCCCCH
T ss_conf 89862433679987279995-898873367751389-98188997987999999999999722264557----8998307
Q ss_pred HHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-
Q ss_conf 4455425866131220356655543234550387158999999999999863338888889999999986221100024-
Q gi|255764496|r 161 LFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIY- 239 (616)
Q Consensus 161 ~y~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~G~~~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~i~~~q~v~~- 239 (616)
+||||+|+|||+|.||+++|.+.|+++++||+|+++++++.|+++|..||++|+||+||.+||+|.+|+.++++|.+..
T Consensus 156 ~y~I~rC~aPCvg~is~e~Y~~~V~~~~~fL~Gk~~~~~~~L~~~M~~aS~~l~FE~AA~~RD~I~aL~~i~~~Q~v~~~ 235 (519)
T PRK12306 156 RYHIGNCTAPCTGNISSDEYLEQVKKAEEVLKGNIQELIEKLEEEMAEKAKNQQFERALVIRDEINAIENLQERQNVERQ 235 (519)
T ss_pred HHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 87862798087896899999999999999981796899999999999999744089999999999999999750511157
Q ss_pred --CCCCHHHHCCCCCEEEEEEEEEECCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHEECCCCCH-HHHHH
Q ss_conf --542011100018834788998424745410113566777899789888777543213789812310268885-78766
Q gi|255764496|r 240 --NRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAEE-TSLLE 316 (616)
Q Consensus 240 --~d~Dvi~i~~~~~~~~I~vl~vR~G~i~g~~~f~~~~~~~~~~~eil~~fI~qyY~~~~iP~~Iiv~~~~~~-~~~l~ 316 (616)
.|+||||++.+++.+||++|+||+|+++|+..|+++. .++++++||.|||+++.+|++|+++..+.+ .++++
T Consensus 236 ~~~d~Dvi~~~~~~~~~~i~v~~vR~G~l~g~~~~~~~~-----~e~il~~fl~qyY~~~~~P~~Iil~~~~~~~~~~l~ 310 (519)
T PRK12306 236 KKYDEDIINYIVKDGTVYLMVFNVLKGTLFDKKEFVFDY-----GENFFEEFLIQYYSENEPPSEIILSELPENLEEALL 310 (519)
T ss_pred CCCCCCEEEEEECCCEEEEEEEEEECCEEECCCCCCCCC-----CHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHHH
T ss_conf 765541578986288299999999899983575221576-----405799999999743799840342578876689999
Q ss_pred HHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCE
Q ss_conf 65432013433321256552667899999999986554323343389999999875156643516999707443775404
Q gi|255764496|r 317 ISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAV 396 (616)
Q Consensus 317 ~~L~~k~g~kV~i~~P~rG~kk~Ll~lA~~NA~~~l~~k~~~~~~~~~~l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~V 396 (616)
+||+++.|.+|+|.+|++|++++|++||..||+..+... ...+++|++.|+|+++|.+||||||||+||+++|
T Consensus 311 ~~L~~~~~~kv~i~~P~rG~kk~ll~lA~~Na~~~~~~~-------~~~l~~Lk~~L~L~~~p~rIEcfDiSh~~G~~~V 383 (519)
T PRK12306 311 EYLSHKKGSKVKITVPKQGEKKQLLDLALKNLEIYFFGD-------EIKLEELKNKLHLPKPPNVIECFDISHLSGTSTV 383 (519)
T ss_pred HHHHHHHCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCE
T ss_conf 999886099569975896489999999999999999866-------9999999998299987766999853111687747
Q ss_pred EEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHH
Q ss_conf 88888516872803232110244445541168998999999997753131112333333334545798489980985899
Q gi|255764496|r 397 GCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQL 476 (616)
Q Consensus 397 as~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQl 476 (616)
||||||++|+|.|++||+|||++ ++++|||+||+|||+|||+|+.+++. ++|||||||||+|||
T Consensus 384 asmVvF~~g~p~K~~YRkf~Ik~--~~~~DDy~~M~Evl~RR~~r~~~e~~--------------~lPDLilIDGGkgQl 447 (519)
T PRK12306 384 GSMVQFRNGKPDKKNYRRFKIKT--VEGIDDFASIAEVVKRRYSRLLEENS--------------ELPDLIIIDGGKGQL 447 (519)
T ss_pred EEEEEEECCCCCHHHHCCCCCCC--CCCCCHHHHHHHHHHHHHHHHHHCCC--------------CCCCEEEECCCHHHH
T ss_conf 99999978985857832722689--99985799999999999988775289--------------999989985999999
Q ss_pred HHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999758877871899971877676634898179834885799899999998878778878898998643214
Q gi|255764496|r 477 SAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKAA 553 (616)
Q Consensus 477 n~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~iRDEaHRFAi~~hRk~r~k~~ 553 (616)
|+|.+||+++|++ |||+||||+++ |+++++++.|+.|+++|++|+|||+||||||||||||||++|+|.+
T Consensus 448 ~~a~~vl~~l~~~--i~viglaK~~e-----~i~~~~~~~~i~l~~~s~~l~lLq~iRDEaHRFAIt~HR~~R~K~~ 517 (519)
T PRK12306 448 SSAFKELRKLKLK--IPIISIAKREE-----EIYVPGIKNPLPIKKNEKASLFIQEIRDEAHRFAITYNRLLRKKSL 517 (519)
T ss_pred HHHHHHHHHCCCC--CEEEEEEECCE-----EEECCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 9999999976999--32999980783-----8963899864565999989999999998798879998987515333
No 4
>TIGR00194 uvrC excinuclease ABC, C subunit; InterPro: IPR004791 Excinuclease ABC complex is involved in DNA replication, recombination and repair. This group defines the C subunit.; GO: 0009381 excinuclease ABC activity, 0006281 DNA repair, 0005737 cytoplasm, 0009380 excinuclease repair complex.
Probab=100.00 E-value=0 Score=758.75 Aligned_cols=573 Identities=39% Similarity=0.656 Sum_probs=525.2
Q ss_pred CHHHCCCCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCC--CCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf 912586788625888699888899601258788876137887--787999999734442999828719999999988776
Q gi|255764496|r 2 SSEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNN--HTHRITHMISQINNIRFTVTCTEVEALLLEANMIKR 79 (616)
Q Consensus 2 ~~~~lP~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~--~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~ 79 (616)
+.+++|+.||||+|+|.+++++|||||++|++||++||+... .+.++..|+.++.++|+++|.+|.+||+||+++|++
T Consensus 4 ~~~~~p~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~l~~~~~~~ 83 (601)
T TIGR00194 4 KLKKLPDEPGCYLWKDRNGKVLYVGKAKNLKKRVKSYFRENNPRASAKTELLVKQIADIEYILTSNENEALLLEANLIKQ 83 (601)
T ss_pred CHHHCCCCCCEEEEECCCCCEEEECCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHEEECCCHHHHHHHHHHHHH
T ss_conf 20216677761566327871688402367888888865103454137899999877542100213503567777667753
Q ss_pred HCCCCEECCCCCCCCCEEEEECCCCCCEEEEEE--CCCCCCCEEEECCC-CHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 187200336468977269980889984599981--23567843770378-878999999999973011003554212478
Q gi|255764496|r 80 LKPRFNILLRDDKSFPYILITDKHKIPALYKHR--DSSTIQGSYFGPFA-SVDAVEKTINSLQRTFFLRSCADSVFRHRT 156 (616)
Q Consensus 80 ~~P~yNi~LkDdk~yPyi~it~~~~~p~l~~~r--~~~~~~~~yfGPf~-~~~~~~~~l~~l~~~f~lR~C~~~~~~~~~ 156 (616)
|+|+||++|+||++|||+.+|..+.+|++.++| ....+.+.|||||+ +...++.++.++.++||+|.|...++..+.
T Consensus 84 ~~p~~~~~l~~~~~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~gp~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~ 163 (601)
T TIGR00194 84 YKPRYNVLLKDDKGYPYIYLTHSEKYPRLLLTRKKGLKKDKGKYFGPFPSNAFALRETLDLLLKLFPLRKCAKPVYHNRD 163 (601)
T ss_pred CCCCCCEEEECCCCCCEEEEECCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 07753236633776305886255432301111222201233320255544156789999999875545531001221257
Q ss_pred CCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 86624455425866131220356655543234550387158999999999999863338888889999999986221100
Q gi|255764496|r 157 RPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHND 236 (616)
Q Consensus 157 ~pCl~y~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~G~~~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~i~~~q~ 236 (616)
+||++|++|+|.|||.+.+++++|.+.++.+..|++|+..+++..|..+|..++++++||+|+.+||++.++..+...+.
T Consensus 164 ~pc~~~~~~~c~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (601)
T TIGR00194 164 RPCLYYQLGRCLGPCVGGITEEEYRELLEKVELFLNGGPDEVLKELEEKLEKASENLEFEEAARLRDQIKALLELNEKQK 243 (601)
T ss_pred CCEEHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 74110123334433431010467899999999986276568999999888876642127789999999999988766665
Q ss_pred CCC----CCCCHHHHCCCCCEEEEEEEEEECCEEEECC-CCCCCCCCCCCHHHHHHHHHHHHHCC----CCCCHHHEECC
Q ss_conf 024----5420111000188347889984247454101-13566777899789888777543213----78981231026
Q gi|255764496|r 237 SIY----NRMDCFSLYHNKNLACIQTCFFHFGQNRGTC-TFFLKTDSESTNAQILSYFLRQFYTD----KPCPENILLSE 307 (616)
Q Consensus 237 v~~----~d~Dvi~i~~~~~~~~I~vl~vR~G~i~g~~-~f~~~~~~~~~~~eil~~fI~qyY~~----~~iP~~Iiv~~ 307 (616)
+.. .+.|+++++..++..|+.++++|.|+++|.. .+.+......+..+++..|+.+||.. ..+|.+|+++.
T Consensus 244 ~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~ 323 (601)
T TIGR00194 244 VSLTKDLLDLDIIGYAFDGGVAAVVVLFIRDGKLLGKDGSFDFSLPGGTDLDELLETFLGQFYLSGYENRLLPSEILLPL 323 (601)
T ss_pred HHHHHHHCCCCEEEEECCCCCEEEEEEEEECCCEECCHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEECC
T ss_conf 54322100211124421676123454320045100000111101135551578999999987741000113640103112
Q ss_pred CCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHCCCCCCCEEEE
Q ss_conf 888578766654320134333212565526678999999999865543233433---89999999875156643516999
Q gi|255764496|r 308 EAEETSLLEISFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQKLSTEIS---HQMILKDFTKKFALPHIPKRIEI 384 (616)
Q Consensus 308 ~~~~~~~l~~~L~~k~g~kV~i~~P~rG~kk~Ll~lA~~NA~~~l~~k~~~~~~---~~~~l~~Lk~~L~L~~~p~rIE~ 384 (616)
...+..+++.|+++..|.++.+..|++|++..+++++..||...+..+...... ...++.++...|+++.+|.++||
T Consensus 324 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~ 403 (601)
T TIGR00194 324 SLEDLKLLEDLLSELRGRKVNVHLPKKGDKKKLLELAIKNAKLALKEKWSQFERNLDKTEALEDLAELLNLPELPKRLEG 403 (601)
T ss_pred CHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHEE
T ss_conf 10016789999875304401220265413789999988667888877653221035788899999997423333201000
Q ss_pred EECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCC--HHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCCCCC
Q ss_conf 70744377540488888516872803232110244445541--1689989999999977531-31112333333334545
Q gi|255764496|r 385 YDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQ--DDCAMMRMVLERRFSQLIK-NEENLNFHPKKQEYSFP 461 (616)
Q Consensus 385 fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~--DD~~~m~Evi~RR~~r~~~-~~~~l~~~~~~~~~~~~ 461 (616)
||+||+.|.++||+|++|.+|+|.+..||+|+++...+.++ |||++|.+++.|||..... +. ..
T Consensus 404 ~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~d~~~~~~~~~~~~~~~~~~g~~-------------~~ 470 (601)
T TIGR00194 404 FDISHLDGSNTVGSLVVFEDGKPLKASYRRYNLKNPSLTGGESDDYAALREVLRRRYSSILKGEN-------------NL 470 (601)
T ss_pred EEHHHCCCCCCHHEEEEEECCCCHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC-------------CC
T ss_conf 00000133210100123304530123322101367555676531578899999987655431423-------------47
Q ss_pred CCCCEEEEECCHHHHHHHHHHHHHCCC--CCCCCEEEEECCCCCCCCCEEEECCCCCEEEE--CCCCHHHHHHHHHHHHH
Q ss_conf 798489980985899999999997588--77871899971877676634898179834885--79989999999887877
Q gi|255764496|r 462 SWPDVVILDGGKGQLSAAQGVLKKLNV--ENRITIISIAKGPKRSAGMEKFFVKKGEALVL--NMRDPILYFIQRLRDEA 537 (616)
Q Consensus 462 ~~PDLilIDGGkgQln~a~~vl~~l~i--~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l--~~~~~~l~~Lq~iRDEa 537 (616)
+||||++||||+||++++..++..++. ...++++|++|+..+..+ ..+++.+..+..+ +++++.+.+++++|||+
T Consensus 471 p~~~~~~~dgg~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 549 (601)
T TIGR00194 471 PLPDLLLIDGGKGQLNAALEVLKSLGVWDLNKPPVIGLAKGAKRHEG-DILLLGDPEPVNLDLPPNSPALHLLQHLRDEA 549 (601)
T ss_pred CCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCC-CEEECCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 86643786176035789999986224444322102210012210024-30210255554433466641578888776665
Q ss_pred HHHHHHHHHHHHHHH-CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHH
Q ss_conf 887889899864321-477100488879899999999808889899389888
Q gi|255764496|r 538 HRFAITTHRKRRKKA-AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPET 588 (616)
Q Consensus 538 HRFAi~~hRk~r~k~-~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~ee 588 (616)
||||+.+||+++.+. ..+.|+.|+|+|+++.+.|+.+||+++.++.|+.++
T Consensus 550 ~~~~~~~~~~~~~~~~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~ 601 (601)
T TIGR00194 550 HRFAIGFHRKKRLKASLQSPLDKIPGVGEKRKKKLLKHFGSLDGIKEASVEE 601 (601)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 5565443455555555554433203554678999998741132333320249
No 5
>PRK07883 hypothetical protein; Validated
Probab=100.00 E-value=0 Score=584.77 Aligned_cols=335 Identities=23% Similarity=0.346 Sum_probs=275.3
Q ss_pred HHHCCCCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHCC
Q ss_conf 12586788625888699888899601258788876137887787999999734442999828719999999988776187
Q gi|255764496|r 3 SEQMPECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKP 82 (616)
Q Consensus 3 ~~~lP~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~~P 82 (616)
.+.||++||||+|+|..|+|||||||||||+||+|||+.+..++|+..||+++.+||||+|.||+||||||++|||+|+|
T Consensus 220 ~d~lP~~PGVY~f~d~~g~vlYVGKA~nLr~RV~sYF~~~~~r~r~~~mv~~~~~ve~i~t~te~EAlllE~rLIk~~~P 299 (575)
T PRK07883 220 AEGLPHAPGVYLFRGPSGEVLYVGTAVDLRRRVRSYFTAAEPRGRMKEMVALATRVDHVECAHELEAGVRELRLIAAHAP 299 (575)
T ss_pred HHCCCCCCEEEEEECCCCCEEEEEHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHEEEEEEECCHHHHHHHHHHHHHHHCC
T ss_conf 75399997469997799988985066789999999707778873899999975037999929888899999999988589
Q ss_pred CCEECCCCCCCCCEEEEECCCCCCEEEEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCC-CCCCCCCCH
Q ss_conf 2003364689772699808899845999812356784377037887899999999997301100355421-247886624
Q gi|255764496|r 83 RFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVF-RHRTRPCLL 161 (616)
Q Consensus 83 ~yNi~LkDdk~yPyi~it~~~~~p~l~~~r~~~~~~~~yfGPf~~~~~~~~~l~~l~~~f~lR~C~~~~~-~~~~~pCl~ 161 (616)
+||++|||||+||||+|| +|+|||+.++|....+++.|||||+|+++++.++++|+++||||+|++.+. ..+.+||++
T Consensus 300 ~YN~~lkddk~ypyi~lT-~e~fPRl~v~R~~~~d~a~yfGPf~s~~aa~~~~~~L~~~f~LR~Ct~~~~~~~~~rpCl~ 378 (575)
T PRK07883 300 PYNRRSKFPERWWWVTLT-DEPFPRLSVVRAPRDDDAEYLGPFRSRRAAELAAEALARAFPLRTCTDRLRPARHGPACPL 378 (575)
T ss_pred CCHHCCCCCCCCEEEEEC-CCCCCCEEEEECCCCCCCEEECCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH
T ss_conf 612205079985699977-9998727998553379984889969989999999999997388778897755568999804
Q ss_pred HHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--C
Q ss_conf 45542586613122035665554323455038715899999999999986333888888999999998622110002--4
Q gi|255764496|r 162 FQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSI--Y 239 (616)
Q Consensus 162 y~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~G~~~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~i~~~q~v~--~ 239 (616)
||||+|+||| +.++.++|.+.|+.+..||+|+.+++++.|.++|..+|++++||+||.+||+|.++.....+++-. +
T Consensus 379 ~~igrC~aPC-~~~s~~~Y~~~V~~a~~~L~G~~~~vl~~L~~rM~~aA~~~rFE~AA~lRDrl~Al~~~~~R~qrl~al 457 (575)
T PRK07883 379 AELGRCPAPC-DRVDAAAYAAAVARVRALLTGDDGAVLAALRRRIARLAAARRYEEAARLRDRLAALVRALWRGQRLAAL 457 (575)
T ss_pred HHHCCCCCCC-CCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 5526667786-899999999999999999679968999999999999987465999999999999999999999899986
Q ss_pred CCC-CHHHHCCCCCEEEEEEEEEECCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHEECCCCCHHHHHHHH
Q ss_conf 542-0111000188347889984247454101135667778997898887775432137898123102688857876665
Q gi|255764496|r 240 NRM-DCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAEETSLLEIS 318 (616)
Q Consensus 240 ~d~-Dvi~i~~~~~~~~I~vl~vR~G~i~g~~~f~~~~~~~~~~~eil~~fI~qyY~~~~iP~~Iiv~~~~~~~~~l~~~ 318 (616)
..+ .+++...+++. ...+..||.|++.+........ +...++.+....- ....++...+--..++|.++|..|
T Consensus 458 ~~~~elvaA~p~~~g-gwel~vvR~GRLa~a~~~~~g~----~~~~~v~al~a~a-e~v~~~~~~~~~a~~eE~~ll~rW 531 (575)
T PRK07883 458 AALPELVAARPDGEG-GWELAVVRHGRLAAAGVAPRGV----PPMPVVDALRAAA-ETVLPPPGPLPGALVEETELIARW 531 (575)
T ss_pred HCCHHHHEECCCCCC-CEEEEEEECCEEECCCCCCCCC----CCHHHHHHHHHHC-CCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf 406176344668999-8799998506120023368998----9349999999618-602799998888899999999999
Q ss_pred HHHHCCCCC----CCCCCCCCCH--HHHHHHHH
Q ss_conf 432013433----3212565526--67899999
Q gi|255764496|r 319 FFKQYGYKV----KITVPKQGEK--RKIIEQAL 345 (616)
Q Consensus 319 L~~k~g~kV----~i~~P~rG~k--k~Ll~lA~ 345 (616)
|..---+=| ....|..|.- ..|.+.|.
T Consensus 532 L~~pgvRlv~~~~~w~~p~~~a~~~~~~~~~~~ 564 (575)
T PRK07883 532 LEQPGVRLVRVDGGWASPARGAGRWAAWAATAR 564 (575)
T ss_pred HCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 769986899467886665432478999999999
No 6
>pfam08459 UvrC_HhH_N UvrC Helix-hairpin-helix N-terminal. This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyses nucleotide excision repair in a multi-step process. UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. The domain described here is found to the N-terminus of a helix hairpin helix (pfam00633) motif and also co-occurs with the pfam01541 catalytic domain which is found at the N-terminus of the same proteins.
Probab=100.00 E-value=0 Score=401.24 Aligned_cols=154 Identities=44% Similarity=0.748 Sum_probs=141.6
Q ss_pred HHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 98751566435169997074437754048888851687280323211024444554116899899999999775313111
Q gi|255764496|r 369 FTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEEN 448 (616)
Q Consensus 369 Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~ 448 (616)
|++.|+|++.|+|||||||||++|+++|||||||.+|+|.|+.||+|||++ . .+|||+||+||++|||+++.+++.
T Consensus 1 L~~~l~L~~~p~rIE~fDiSh~~G~~~V~s~Vvf~~g~~~K~~YRkf~Ik~--~-~~dD~~~m~evl~RR~~~~~~~~~- 76 (154)
T pfam08459 1 LAELLGLPKLPHRIECFDISHIQGTDTVGSMVVFEDGKPDKSEYRRYNIKG--T-PGDDYASMREVLTRRFSRLLKEKL- 76 (154)
T ss_pred CHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHCCCC--C-CCCHHHHHHHHHHHHHHHHHHCCC-
T ss_conf 967869899988899997875579773699999948975856624323789--9-997899999999999986541168-
Q ss_pred CCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHHH
Q ss_conf 23333333345457984899809858999999999975887787189997187767663489817983488579989999
Q gi|255764496|r 449 LNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILY 528 (616)
Q Consensus 449 l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~ 528 (616)
++|||||||||+||||+|.++|+++|++ |||+||||+++|++. ..++++..+++.|+.++++|+
T Consensus 77 -------------~~PDLilIDGGkgQl~~a~~~l~~~~~~--i~vi~iaK~~~~~~~-~i~~~~~~~~i~l~~~~~~~~ 140 (154)
T pfam08459 77 -------------PLPDLILIDGGKGQLNAAKEVLEELGLD--IPVIGLAKGEEHKTE-KLFLPGGPEPIPLPPDSPALH 140 (154)
T ss_pred -------------CCCCEEEECCCHHHHHHHHHHHHHCCCC--CEEEEEEECCCCCCC-EEEECCCCCEEECCCCCHHHH
T ss_conf -------------9998899759989999999999985999--529999735655541-477669983676599998999
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99988787788788
Q gi|255764496|r 529 FIQRLRDEAHRFAI 542 (616)
Q Consensus 529 ~Lq~iRDEaHRFAi 542 (616)
|||+||||||||||
T Consensus 141 ~Lq~iRDEaHRFAI 154 (154)
T pfam08459 141 LLQRIRDEAHRFAI 154 (154)
T ss_pred HHHHHHHHHHCCCC
T ss_conf 99999870752369
No 7
>PRK10545 nucleotide excision repair endonuclease; Provisional
Probab=100.00 E-value=4.2e-45 Score=344.51 Aligned_cols=182 Identities=27% Similarity=0.435 Sum_probs=157.5
Q ss_pred HHHCCCCCCEEEEECCCCCE-EEEEECHHHHHHHHHHCCCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHC
Q ss_conf 12586788625888699888-89960125878887613788778799999973444299982871999999998877618
Q gi|255764496|r 3 SEQMPECPGVYQMLDIAGRV-LYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLK 81 (616)
Q Consensus 3 ~~~lP~~pGvY~~~~~~~~i-iYvGKaknL~~Rv~syf~~~~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~~ 81 (616)
.++||++||||+|+|.+|.+ ||||||+|||+||+|||+ ++|..+|+.++.+|||++|+||++|||||++|||+++
T Consensus 28 l~~LP~~pGVY~f~~~~~~~plYVGKs~nlr~RV~shF~----~~~~~~l~~~v~~I~~~~T~~El~AlLlE~~lIK~~~ 103 (286)
T PRK10545 28 LNDLPTRPGVYLFHGESDTMPLYIGKSVNIRSRVLSHLR----TPDEAAMLRQSRRISWICTAGEIGALLLEARLIKEQQ 103 (286)
T ss_pred HHHCCCCCEEEEEECCCCCEEEEEECCHHHHHHHHHHHC----CCCHHHHHHHCCEEEEEEECCHHHHHHHHHHHHHHHC
T ss_conf 985799986899962899879997320868999999847----8138899974054899996999999999999998848
Q ss_pred CCCEECCCCCCCCCEEEEECCCCCCEEEEEECC-CCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCC--CCC-CCCC
Q ss_conf 720033646897726998088998459998123-567843770378878999999999973011003554--212-4788
Q gi|255764496|r 82 PRFNILLRDDKSFPYILITDKHKIPALYKHRDS-STIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADS--VFR-HRTR 157 (616)
Q Consensus 82 P~yNi~LkDdk~yPyi~it~~~~~p~l~~~r~~-~~~~~~yfGPf~~~~~~~~~l~~l~~~f~lR~C~~~--~~~-~~~~ 157 (616)
|+||++||+++.++.|.+..+ .|.+...+.. ......|||||+|...|+.+|..|.+.|.| |... +.+ .+.+
T Consensus 104 P~~Nr~lR~~~~l~si~l~~~--~~~~v~~~~~d~~~~~~lyG~F~S~r~A~~~L~~la~~~~L--C~kllGLE~~~~~~ 179 (286)
T PRK10545 104 PLFNKRLRRNRQLCSLQLNEG--RVDVVYAKEVDFSRAPNLFGLFANRRAALQALQRIADEQKL--CYGLLGLEPLSRGR 179 (286)
T ss_pred CCCCCCCCCCCCCEEEEEECC--CCCEEEECCCCCCCCCCEEEECCCHHHHHHHHHHHHHHHHH--HHHHCCCCCCCCCC
T ss_conf 865401247787527998569--76145300036432543232046899999999999999604--67752763578898
Q ss_pred CCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf 66244554258661312203566555432345503
Q gi|255764496|r 158 PCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLS 192 (616)
Q Consensus 158 pCl~y~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~ 192 (616)
||++||||+|.|+|+|++|+++|+..+..|..-++
T Consensus 180 pCF~yqIKrC~GACvGkEs~e~yN~RL~~AL~~~~ 214 (286)
T PRK10545 180 ACFRSALKRCAGACCGKESLEAHALRLRASLERLR 214 (286)
T ss_pred CCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf 60777864067550587798899999999998565
No 8
>LOAD_uvrC_endov consensus
Probab=100.00 E-value=6.8e-34 Score=263.96 Aligned_cols=121 Identities=35% Similarity=0.531 Sum_probs=107.9
Q ss_pred HHHHHCCC-CCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 98751566-43516999707443775404888885168728032321102444455411689989999999977531311
Q gi|255764496|r 369 FTKKFALP-HIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEE 447 (616)
Q Consensus 369 Lk~~L~L~-~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~ 447 (616)
|++.|+|+ ..|+|||||||||++|+++|||||||++|+|.|+.||+|||+..+. .+|||+||+||+.|||++..++
T Consensus 1 l~~~l~l~~~~p~rIe~~DiS~~~g~~~va~~Vvf~~g~~~k~~yR~~~i~~~~~-~~dD~~amrEv~~rr~~~~~~~-- 77 (123)
T LOAD_uvrC_endo 1 LAQLLNLPEDEPKRIEGFDISHLQGEDVVASMVVFEDGKPKKVEYRRYNIKRVTF-YIPDYLAFREVLTRRYASKKLE-- 77 (123)
T ss_pred CHHHHCCCCCCCCEEEEEECCCCCCCCEEEEEEEEECCCCEEEEEEEEEECCCCC-CCCHHHHHHHHHHHHHHHHHCC--
T ss_conf 9578695988978899998972589851899999988962378899997036678-8984999999999999987545--
Q ss_pred CCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCC
Q ss_conf 12333333334545798489980985899999999997588778718999718776766
Q gi|255764496|r 448 NLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAG 506 (616)
Q Consensus 448 ~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~ 506 (616)
.++|||||||||+||+++|.++++++|+. .||+|||||+..|.++
T Consensus 78 -------------~~~PDLilIDGg~~ql~~~~~~l~~lg~~-~ip~iglAK~~~~~~~ 122 (123)
T LOAD_uvrC_endo 78 -------------LKLPDLILVDGGGGQHPRALGVASHLGVL-GIPVIGVAKNLLHGTG 122 (123)
T ss_pred -------------CCCCCEEEECCCHHHHHHHHHHHHHCCCC-CCCEEEEEECCCCCCC
T ss_conf -------------88998999879677889999999986998-9858999808987779
No 9
>smart00465 GIYc GIY-YIG type nucleases (URI domain).
Probab=99.71 E-value=5.4e-17 Score=142.09 Aligned_cols=82 Identities=35% Similarity=0.530 Sum_probs=72.2
Q ss_pred CCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCC-CHHHHHHHHHCCCEEEEECCCHHH-HHHHHHHHHHHHCCCCEE
Q ss_conf 886258886998888996012587888761378877-879999997344429998287199-999999887761872003
Q gi|255764496|r 9 CPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNH-THRITHMISQINNIRFTVTCTEVE-ALLLEANMIKRLKPRFNI 86 (616)
Q Consensus 9 ~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~~-~~k~~~l~~~~~~ie~~~t~~e~e-AlilE~~lIk~~~P~yNi 86 (616)
.||||+|.|..|.++|||||+||++||+|||+.... +..+..|......++|+++.++.+ |+++|+.||++++|+||+
T Consensus 1 ~~gvY~~~~~~~~~~YVGka~nl~~R~~~h~~~~~~~~~~~~~l~~~~~~~~~~i~~~~~~~a~~~E~~lIk~~~p~~N~ 80 (84)
T smart00465 1 KPGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSRKGRLLIDALLKYGGNFEFIILESFDESALELEKYLIKEYKPKYNL 80 (84)
T ss_pred CCEEEEEECCCCCEEEEECHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCEEEEEECCCCHHHHHHHHHHHHHHHCCHHHH
T ss_conf 98789998599998999620019999999838778888799999997577999993987799999999999884982377
Q ss_pred CCCC
Q ss_conf 3646
Q gi|255764496|r 87 LLRD 90 (616)
Q Consensus 87 ~LkD 90 (616)
+++.
T Consensus 81 ~~~~ 84 (84)
T smart00465 81 LLKG 84 (84)
T ss_pred HHCC
T ss_conf 5169
No 10
>pfam01541 GIY-YIG GIY-YIG catalytic domain. This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.
Probab=99.36 E-value=9.3e-13 Score=111.56 Aligned_cols=76 Identities=33% Similarity=0.524 Sum_probs=64.1
Q ss_pred CCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHCC-CCE
Q ss_conf 88625888699888899601258788876137887787999999734442999828719999999988776187-200
Q gi|255764496|r 9 CPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKP-RFN 85 (616)
Q Consensus 9 ~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~~P-~yN 85 (616)
.||||+|.+.++.++|||+|+||++|+.+||+... ...+..+.....-+.+.++.++.+|+.+|..||++++| +||
T Consensus 1 ~~gVY~i~~~~~~~~YIG~t~nl~~R~~~H~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~a~~~E~~lI~~~~~~~yN 77 (77)
T pfam01541 1 KPGVYIITNKDNKVLYVGSTKNLKRRLKQHFSGKG-AKKTRNKAKPFELIILEEFPTKEEALELEKYLIKKYKPNKYN 77 (77)
T ss_pred CCEEEEEEECCCCEEEEEEECCHHHHHHHHHCCCC-CCCEEECCCEEEEEEEEEECCHHHHHHHHHHHHHHHCCCCCC
T ss_conf 99899999689899999873799999999975799-987872121389999999499999999999998986878999
No 11
>PRK13766 Hef nuclease; Provisional
Probab=99.08 E-value=2.7e-10 Score=93.78 Aligned_cols=56 Identities=32% Similarity=0.496 Sum_probs=53.1
Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf 71004888798999999998088898993898888627899989999999985478
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616)
..|..+|||||++.++||.||||+++|.+||++||.+|+|||++.|++|++.++.+
T Consensus 706 ~~l~~~pgvg~~~a~~ll~~fgsi~~i~~a~~~eL~~v~giG~~~A~~i~~~~~~~ 761 (764)
T PRK13766 706 YIVSSLPDVGPVLARNLLDHFGSVENVMTASEEELKAVEGIGEKTAKKIREVVTSE 761 (764)
T ss_pred HHHHHCCCCCHHHHHHHHHHCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHHHHCCC
T ss_conf 99983899999999999997199999965999999547496999999999985251
No 12
>KOG2841 consensus
Probab=98.63 E-value=5.3e-08 Score=77.26 Aligned_cols=58 Identities=28% Similarity=0.423 Sum_probs=54.4
Q ss_pred CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf 4771004888798999999998088898993898888627899989999999985478
Q gi|255764496|r 553 AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616)
Q Consensus 553 ~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616)
....|..|+||++.....||.+|||++.|-+||.+||++++|+|+..|++||++||.-
T Consensus 193 ~~~~Lt~i~~VnKtda~~LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~p 250 (254)
T KOG2841 193 LLGFLTTIPGVNKTDAQLLLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQP 250 (254)
T ss_pred HHHHHHHCCCCCCCCHHHHHHHCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHCC
T ss_conf 9999881789770018999885535999874177679867573789999999998451
No 13
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=98.60 E-value=9.7e-08 Score=75.34 Aligned_cols=131 Identities=25% Similarity=0.391 Sum_probs=83.7
Q ss_pred CCCCCEEEEEC------CHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHHHHHHHHH
Q ss_conf 57984899809------858999999999975887787189997187767663489817983488579989999999887
Q gi|255764496|r 461 PSWPDVVILDG------GKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLR 534 (616)
Q Consensus 461 ~~~PDLilIDG------GkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~iR 534 (616)
.+.|=|++.-. ++.+=|++..+|..+.++-.+ -.++..+... ...+++.|++..
T Consensus 98 y~rpvliVegd~~~~~~~~i~~~av~~al~s~~vdfg~---------------~vi~t~~~~~-----Ta~~i~~la~re 157 (254)
T COG1948 98 YERPVLIVEGDDSFSRRPKIHPNAVRGALASLAVDFGL---------------PVIWTRSPEE-----TAELIHELARRE 157 (254)
T ss_pred CCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHCCC---------------EEEEECCHHH-----HHHHHHHHHHHH
T ss_conf 78537999746454322446778999999998762485---------------1798488889-----999999999998
Q ss_pred HHHHHHHHHHHHHHHHHHCC----CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf 87788788989986432147----71004888798999999998088898993898888627899989999999985478
Q gi|255764496|r 535 DEAHRFAITTHRKRRKKAAY----SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616)
Q Consensus 535 DEaHRFAi~~hRk~r~k~~~----S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616)
.+.-.-.+.-|-+++.+... -.|..|||||++....||.+|||++++.+||.+||.+|.|||++.|..|+++|...
T Consensus 158 q~e~~r~v~~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~ 237 (254)
T COG1948 158 QEERKRSVNPHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLRTE 237 (254)
T ss_pred HHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHHCCCCHHHHHHHHHHHHCH
T ss_conf 77524555655432224557899999970899648999999998568887765599999774484688999999998344
Q ss_pred C
Q ss_conf 6
Q gi|255764496|r 611 T 611 (616)
Q Consensus 611 ~ 611 (616)
-
T Consensus 238 ~ 238 (254)
T COG1948 238 Y 238 (254)
T ss_pred H
T ss_conf 4
No 14
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=98.57 E-value=8.1e-08 Score=75.93 Aligned_cols=56 Identities=34% Similarity=0.529 Sum_probs=53.2
Q ss_pred HCCCCCCHHHHHHHHHHHCCHHHHHHCCHH-----------HHHHCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 048887989999999980888989938988-----------88627899989999999985478678
Q gi|255764496|r 558 DEINGIGPLRKRLLLQSFGTVKMISRSSPE-----------TLASIEGISKKIACKIYNHFHKNTSH 613 (616)
Q Consensus 558 d~I~GIG~k~~~~Ll~~Fgs~~~i~~As~e-----------eL~~v~gi~~~~A~~I~~~l~~~~~~ 613 (616)
.+|++||+.+.+.|-.||+|++++++||.| +|.+|+|||+++|..|+++||.+..-
T Consensus 524 LGIr~VG~~~A~~La~~f~tl~~L~~A~~e~~~~~~~f~~s~L~~~~g~G~~vA~~~~~~F~~~~~~ 590 (706)
T TIGR00575 524 LGIRHVGEVTAKLLAKHFGTLDKLKAASLETLESIYQFDRSELLSVEGVGPKVAESIVNFFHDPNNL 590 (706)
T ss_pred CCCHHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHHCCHHHHHCCCCHHHHHHHHHHHHHCCCCC
T ss_conf 2860357999999998558868998508216778875160556410140278999999987120001
No 15
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=98.38 E-value=8.9e-07 Score=68.42 Aligned_cols=54 Identities=28% Similarity=0.467 Sum_probs=51.4
Q ss_pred HCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf 048887989999999980888989938988886278999899999999854786
Q gi|255764496|r 558 DEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNT 611 (616)
Q Consensus 558 d~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~ 611 (616)
..|++||+.+.+.|.+||+|++++.+||.|+|.++.|||+.+|+.|.+||+.+.
T Consensus 514 LGI~~VG~~~Ak~La~~f~sl~~l~~as~e~L~~I~giG~~~A~si~~ff~~~~ 567 (668)
T PRK07956 514 LGIRHVGEKAAKALARHFGSLEALEAASEEELAAVEGIGEEVAQSIVEFFAVEH 567 (668)
T ss_pred CCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHCCHH
T ss_conf 278641299999999996689999708999985768844999999999970976
No 16
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=98.29 E-value=1.3e-06 Score=67.19 Aligned_cols=54 Identities=31% Similarity=0.450 Sum_probs=51.8
Q ss_pred HCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf 048887989999999980888989938988886278999899999999854786
Q gi|255764496|r 558 DEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNT 611 (616)
Q Consensus 558 d~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~ 611 (616)
.+|+.||+++.+.|-+||||++++..||.++|..++|||..+|+.|.+||+.+.
T Consensus 514 LGIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG~~vA~si~~ff~~~~ 567 (667)
T COG0272 514 LGIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVARSIIEFFANEE 567 (667)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCCHHHHHHHHHHHHHCCHH
T ss_conf 797114089999999876029999842999995066612899999999972777
No 17
>TIGR00631 uvrb excinuclease ABC, B subunit; InterPro: IPR004807 All proteins in this family for which functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0005737 cytoplasm, 0009380 excinuclease repair complex.
Probab=98.11 E-value=3e-06 Score=64.61 Aligned_cols=35 Identities=26% Similarity=0.394 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 15899999999999986333888888999999998
Q gi|255764496|r 195 NHNLKEKIARNMNQATLKEDYESAIIHRDRLAALS 229 (616)
Q Consensus 195 ~~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~ 229 (616)
-.++|++|+++|.+||++++||+||.+||+|..|+
T Consensus 633 ~~~~I~~Le~~M~~aA~~l~FE~AA~~RD~I~~L~ 667 (667)
T TIGR00631 633 LKKLIKQLEKEMKQAARNLEFEEAARLRDEIKELK 667 (667)
T ss_pred HHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCC
T ss_conf 99999999999999997526789999988886239
No 18
>PRK00254 ski2-like helicase; Provisional
Probab=98.10 E-value=2.2e-05 Score=58.41 Aligned_cols=84 Identities=29% Similarity=0.411 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHHHHHHH----------------HHHHHHH---CC---CCHHCCCCCCHHHHHHHHHH-HCCHHHHHHCC
Q ss_conf 99988787788788989----------------9864321---47---71004888798999999998-08889899389
Q gi|255764496|r 529 FIQRLRDEAHRFAITTH----------------RKRRKKA---AY---SPLDEINGIGPLRKRLLLQS-FGTVKMISRSS 585 (616)
Q Consensus 529 ~Lq~iRDEaHRFAi~~h----------------Rk~r~k~---~~---S~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As 585 (616)
.+|.+++-|+.||-... ...+.+. .. -+|-+|||||.+|.++|++. |.|++.|.+|+
T Consensus 596 ~lq~l~~~a~~~a~~~~~~~~~l~~~~~~~~~l~~l~~Rl~~Gv~~ELl~L~~I~gvgr~RAR~Ly~aGi~s~~~ia~A~ 675 (717)
T PRK00254 596 DIYRIVETAEWLVYSLKEIAKVLEASQDVVDYLETLRLRVKHGIREELIPLMELPMIGRKRARALYNAGFRDLEDIMNAK 675 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHCCCCCCCHHHHHHHHHCCCCCHHHHHCCC
T ss_conf 99999999999999999999983851889999999999998099765683564899898999999986999999996599
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf 888862789998999999998547867
Q gi|255764496|r 586 PETLASIEGISKKIACKIYNHFHKNTS 612 (616)
Q Consensus 586 ~eeL~~v~gi~~~~A~~I~~~l~~~~~ 612 (616)
+++|..++|+|+++|++|++.+.+.-.
T Consensus 676 p~~l~~i~g~g~~~a~~i~~~~~~~~~ 702 (717)
T PRK00254 676 PSELLAVEGIGAKIVEGIFKHLGKEVK 702 (717)
T ss_pred HHHEECCCCCCHHHHHHHHHHHCCEEE
T ss_conf 999030237278999999998386443
No 19
>TIGR02236 recomb_radA DNA repair and recombination protein RadA; InterPro: IPR011938 This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO), and archaeal RadB (IPR011939 from INTERPRO). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=98.03 E-value=7.9e-06 Score=61.59 Aligned_cols=54 Identities=31% Similarity=0.564 Sum_probs=49.5
Q ss_pred CHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 1004888798999999998-08889899389888862789998999999998547
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
.|+++|||||.|.+||-.. |.+++.|.-||+.||+.+.||++..|.+|-+.=++
T Consensus 1 ~ledLPGVGp~TA~KL~EaGy~t~~~iA~A~~~EL~~~~gI~E~~A~kiI~AAR~ 55 (333)
T TIGR02236 1 DLEDLPGVGPATAEKLREAGYDTLEAIAVASPKELSEIAGIGEGTAAKIIQAARK 55 (333)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 9665789757688998861078899984458579532037877789999999999
No 20
>PRK01172 ski2-like helicase; Provisional
Probab=97.84 E-value=0.00019 Score=51.61 Aligned_cols=53 Identities=40% Similarity=0.494 Sum_probs=49.2
Q ss_pred CHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf 1004888798999999998-0888989938988886278999899999999854
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYNHFH 608 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~ 608 (616)
+|-+|||||.+|.++|++. |.|++.|.+|++++|.+++|+|+++|++|.+.-+
T Consensus 613 ~L~~I~gigr~RAR~Ly~aG~~s~~dia~a~~~~L~~i~g~~~~~A~~Ii~~A~ 666 (674)
T PRK01172 613 DLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRAM 666 (674)
T ss_pred HHCCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf 771889999899999998699999999709998987641989999999999999
No 21
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=97.72 E-value=5.8e-05 Score=55.35 Aligned_cols=37 Identities=14% Similarity=0.264 Sum_probs=17.7
Q ss_pred HHHHHHHHHCCCEEEEECCCHHHHHHHHHHHHHHHCCC
Q ss_conf 79999997344429998287199999999887761872
Q gi|255764496|r 46 HRITHMISQINNIRFTVTCTEVEALLLEANMIKRLKPR 83 (616)
Q Consensus 46 ~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lIk~~~P~ 83 (616)
.-++..+.++.+=--|++.|-.-|--|-.. -|.+-|.
T Consensus 48 fTmAnvI~~~~rPtLVlahNKTLAAQLy~E-fk~fFP~ 84 (657)
T PRK05298 48 FTMANVIARVQRPTLVLAHNKTLAAQLYGE-FKEFFPE 84 (657)
T ss_pred HHHHHHHHHHCCCEEEECCCHHHHHHHHHH-HHHHCCC
T ss_conf 899999998689759976658899999999-9976888
No 22
>pfam02151 UVR UvrB/uvrC motif.
Probab=97.69 E-value=5.9e-05 Score=55.28 Aligned_cols=35 Identities=31% Similarity=0.509 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 58999999999999863338888889999999986
Q gi|255764496|r 196 HNLKEKIARNMNQATLKEDYESAIIHRDRLAALSH 230 (616)
Q Consensus 196 ~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~ 230 (616)
+.++..|+.+|..||++++||+||.+||+|..|+.
T Consensus 1 ~~~i~~l~~~m~~A~~~~dfE~Aa~lRD~i~~l~~ 35 (36)
T pfam02151 1 KKLIKELEEEMEEAAEEEDFEKAAKLRDQIKALEK 35 (36)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 96889999999999997538999998999999752
No 23
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=97.61 E-value=0.00017 Score=51.92 Aligned_cols=54 Identities=26% Similarity=0.319 Sum_probs=50.3
Q ss_pred CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 100488879899999999808889899389888862789998999999998547
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
.|-.||.+-..-..+|.++||++++|.+||.+||..|.|||+.-|+.|.+-|..
T Consensus 288 ~L~kiprlp~~vie~lV~~Fg~L~~ll~As~eeL~~VeGIGe~RAr~IregL~R 341 (352)
T PRK13482 288 ILAKIPRLPSAVIENLVKHFGTLQGLLEASIEDLDDVEGIGEVRARAIREGLSR 341 (352)
T ss_pred HHCCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf 860599999999999999852799998689988865679679999999999999
No 24
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=97.60 E-value=0.00011 Score=53.28 Aligned_cols=35 Identities=23% Similarity=0.349 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHCCCCCCHHHHHHHH
Q ss_conf 7788788989986432147710048887989999999
Q gi|255764496|r 536 EAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLL 572 (616)
Q Consensus 536 EaHRFAi~~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll 572 (616)
.+-+-||.-.-.||++.+ ..-.--||-|++.++=+
T Consensus 559 ~sM~~Ai~ET~RRR~iQ~--~yN~~hgItP~ti~K~i 593 (663)
T COG0556 559 DSMQKAIDETERRREIQM--AYNEEHGITPQTIKKKI 593 (663)
T ss_pred HHHHHHHHHHHHHHHHHH--HHHHHCCCCCCCHHHHH
T ss_conf 999999998888999999--99996699971220115
No 25
>PRK02362 ski2-like helicase; Provisional
Probab=97.59 E-value=0.00062 Score=47.92 Aligned_cols=56 Identities=23% Similarity=0.388 Sum_probs=50.4
Q ss_pred CHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 1004888798999999998-088898993898888627899989999999985478678
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSH 613 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~ 613 (616)
+|-+|||||.+|.++|++. |.|++.|..|++++|..+ +++++|++|++.+-...++
T Consensus 653 ~L~~I~gvgr~RAR~Ly~aGi~s~~dla~A~p~~l~~i--lg~~~a~~i~~~~~~~~~~ 709 (736)
T PRK02362 653 DLVGLRGIGRVRARRLYNAGITSRADLRAADKEVVAAI--LGPKIAERVLEQLGRRDPG 709 (736)
T ss_pred HHCCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHH--HHHHHHHHHHHHHCCCCCC
T ss_conf 77088999989999999879999999970999999999--7778999999983887898
No 26
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=97.54 E-value=0.00013 Score=52.79 Aligned_cols=62 Identities=19% Similarity=0.389 Sum_probs=52.3
Q ss_pred HHHHHCCCCHHCCCCCCHHHHHHHHHHHC---CHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 64321477100488879899999999808---889899389888862789998999999998547
Q gi|255764496|r 548 RRKKAAYSPLDEINGIGPLRKRLLLQSFG---TVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 548 ~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fg---s~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
+..+.++..|-+|.|||||+.-.+|..++ =+..|.+-..+.|+++||||+++|++|.-.|+.
T Consensus 66 ~~Er~~F~~Li~V~GIGpK~AL~ILs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~ELk~ 130 (198)
T PRK00116 66 KEERELFRLLISVSGVGPKLALAILSGLSPEELAQAIANGDIKALTKVPGVGKKTAERIVLELKD 130 (198)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHCCCCCCCHHHHHHHHHHHHH
T ss_conf 89999999985668857899998870299999999998589999706889788999999999998
No 27
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=97.49 E-value=0.00019 Score=51.65 Aligned_cols=51 Identities=12% Similarity=0.081 Sum_probs=45.8
Q ss_pred HCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf 048887989999999980888989938988886278999899999999854786
Q gi|255764496|r 558 DEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNT 611 (616)
Q Consensus 558 d~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~ 611 (616)
..|++||+.+.+.|-. ++.++.+||.+||..|+|||+.+|+.|.+||+.+.
T Consensus 495 LGI~~vG~~~a~~l~~---~~~~L~~as~e~l~~i~gIG~~~A~si~~fF~~~~ 545 (563)
T PRK08097 495 LGIPLTQAALNASLDR---SWQQLLSRTEQQWQQLPGIGEGRARQLIAFFDHPQ 545 (563)
T ss_pred CCCCCHHHHHHHHHHC---CHHHHHCCCHHHHHCCCCCCHHHHHHHHHHHCCHH
T ss_conf 6995089999999861---99999739998995579848999999999985988
No 28
>TIGR00084 ruvA Holliday junction DNA helicase RuvA; InterPro: IPR000085 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure . In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB.; GO: 0003678 DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=97.46 E-value=9.8e-05 Score=53.68 Aligned_cols=81 Identities=19% Similarity=0.293 Sum_probs=60.2
Q ss_pred HHHHHHHHHHHHHHH-HH-HHHHHHHCCCCHHCCCCCCHHHHHHHHHHHC--CHHH-HHHCCHHHHHHCCCCCHHHHHHH
Q ss_conf 999887877887889-89-9864321477100488879899999999808--8898-99389888862789998999999
Q gi|255764496|r 529 FIQRLRDEAHRFAIT-TH-RKRRKKAAYSPLDEINGIGPLRKRLLLQSFG--TVKM-ISRSSPETLASIEGISKKIACKI 603 (616)
Q Consensus 529 ~Lq~iRDEaHRFAi~-~h-Rk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~-i~~As~eeL~~v~gi~~~~A~~I 603 (616)
....+|..|-.--.. |- -.+..|.+++.|-++.|||||..-+||..+. .+.. |-+-.+..|+++||||+|+|+++
T Consensus 55 t~~~~RedaNQi~~~LfGF~~~~Er~lF~~Li~~nGvGpk~ALaiL~~~~~~~~~~ai~~~~~~~L~k~pGvGKK~A~~l 134 (217)
T TIGR00084 55 THLVVREDANQILHLLFGFNTLEERELFKELIKVNGVGPKLALAILSNMSPEEFVQAIETEEVKALVKIPGVGKKTAERL 134 (217)
T ss_pred EEEEEECCHHHHHHHHHCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf 87777604678999973479877899999985148802899999866788758988886410444204588573789999
Q ss_pred H-HHHCC
Q ss_conf 9-98547
Q gi|255764496|r 604 Y-NHFHK 609 (616)
Q Consensus 604 ~-~~l~~ 609 (616)
. -.|..
T Consensus 135 ~~leL~g 141 (217)
T TIGR00084 135 LALELKG 141 (217)
T ss_pred HHHHHHH
T ss_conf 8777545
No 29
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=97.44 E-value=8.3e-05 Score=54.22 Aligned_cols=79 Identities=24% Similarity=0.360 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHC---CHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 99887877887889899864321477100488879899999999808---889899389888862789998999999998
Q gi|255764496|r 530 IQRLRDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFG---TVKMISRSSPETLASIEGISKKIACKIYNH 606 (616)
Q Consensus 530 Lq~iRDEaHRFAi~~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fg---s~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616)
-+.+|..+|+. -.......+.++..|-+|.|||||..-++|..+. =.+.|.+..+.-|+++||||+++|++|.-.
T Consensus 50 ~~~vREd~~~L--yGF~~~~ER~lF~~LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivle 127 (201)
T COG0632 50 HLVVREDAHLL--YGFLTEEERELFRLLISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERIVLE 127 (201)
T ss_pred EEEEHHHHHHH--CCCCCHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHCCCCCCHHHHHHHHHH
T ss_conf 97522027887--0899889999999987118805899999984899999999998328676441898778899999999
Q ss_pred HCCC
Q ss_conf 5478
Q gi|255764496|r 607 FHKN 610 (616)
Q Consensus 607 l~~~ 610 (616)
|+..
T Consensus 128 Lk~K 131 (201)
T COG0632 128 LKGK 131 (201)
T ss_pred HHHH
T ss_conf 7605
No 30
>pfam04493 Endonuclease_5 Endonuclease V. Endonuclease V is specific for single-stranded DNA or for duplex DNA that contains uracil or that is damaged by a variety of agents.
Probab=97.42 E-value=0.00018 Score=51.72 Aligned_cols=115 Identities=19% Similarity=0.141 Sum_probs=68.4
Q ss_pred HHHHHHHCCCC------CCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHH--HHH
Q ss_conf 99987515664------3516999707443775404888885168728032321102444455411689989999--999
Q gi|255764496|r 367 KDFTKKFALPH------IPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVL--ERR 438 (616)
Q Consensus 367 ~~Lk~~L~L~~------~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi--~RR 438 (616)
++|++.+.+.. ..+.|-++|+|.-.|+..+|++||++-..... -|..+-....+.-..--|-|+||+- -.-
T Consensus 3 ~~l~~ki~~~~~~~~~~~l~~VaGvDvSf~~~~~~~aa~Vvl~~p~l~~-v~~~~~~~~~~fPYIPG~LaFRE~p~~l~a 81 (205)
T pfam04493 3 EELQKKISLSPDESEDSELRYVAGVDVSYDKETRAVAALVVLDFPSLEV-IEKKVIRGEISFPYIPGFLAFRELPLLLKA 81 (205)
T ss_pred HHHHHCEECCCCCCCCCCEEEEEEEEEEEECCCEEEEEEEEEECCCCCE-EEEEEEEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf 5742107736899997735699999973757984999999998899839-999999976236655403433101899999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEC-CHHHHHHHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf 977531311123333333345457984899809-858999999999975887787189997187
Q gi|255764496|r 439 FSQLIKNEENLNFHPKKQEYSFPSWPDVVILDG-GKGQLSAAQGVLKKLNVENRITIISIAKGP 501 (616)
Q Consensus 439 ~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDG-GkgQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616)
+.++. ..||++|+|| |..|=.-+- .-.-+|+..++|-||+||..
T Consensus 82 ~~~L~------------------~~PDvllvDG~Gi~HPR~~G-lAsHlGV~l~~PTIGVAK~~ 126 (205)
T pfam04493 82 LKKLY------------------DEPDVLLVDGNGIAHPRRFG-LATHAGVLLDKPTIGVAKKL 126 (205)
T ss_pred HHHCC------------------CCCCEEEECCCCCCCCCCCC-HHEEEEEECCCCCCCCCCCE
T ss_conf 99657------------------79999998787643762426-01035665287832301430
No 31
>COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair]
Probab=97.34 E-value=0.00062 Score=47.92 Aligned_cols=104 Identities=13% Similarity=0.118 Sum_probs=63.7
Q ss_pred CCCEEEEEECCCCCCCCCEEEEEEEE--CCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 35169997074437754048888851--6872803232110244445541168998999999997753131112333333
Q gi|255764496|r 378 IPKRIEIYDNSHIMGCSAVGCMVVVG--ENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKK 455 (616)
Q Consensus 378 ~p~rIE~fDiSh~~G~~~Vas~Vvf~--~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~ 455 (616)
.+..|-++|+|--.|...+||+|+.+ ++.+....+..=.+ ++-..--|-++||.- -+-++.+.
T Consensus 27 ~v~~vagvDvsy~~~~~~~aa~Vv~~~~~~~vie~~v~~~~~---~~PYIPGfLaFRE~p--~~l~a~~~---------- 91 (212)
T COG1515 27 EVRTVAGVDVSYEDGERGRAAAVVLDYPDLEVIETAVVRGPV---SFPYIPGFLAFRELP--LLLKALEK---------- 91 (212)
T ss_pred CCCEEEEEEEEECCCCEEEEEEEEEECCCCCEEEEEEEECCC---CCCCCCCHHHHHHHH--HHHHHHHH----------
T ss_conf 731689987776378807999999976877667789986330---047665045452028--89999986----------
Q ss_pred CCCCCCCCCCEEEEECC-HHHHHHHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf 33454579848998098-58999999999975887787189997187
Q gi|255764496|r 456 QEYSFPSWPDVVILDGG-KGQLSAAQGVLKKLNVENRITIISIAKGP 501 (616)
Q Consensus 456 ~~~~~~~~PDLilIDGG-kgQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616)
....||+++|||- ..|=.-+-=+ .-.|+-.++|.||+||..
T Consensus 92 ----l~~~~d~ilVDG~GiaHPR~~GlA-sH~Gv~l~~PtIGVAK~~ 133 (212)
T COG1515 92 ----LSVKPDLLLVDGHGIAHPRRLGLA-SHIGVLLDVPTIGVAKSR 133 (212)
T ss_pred ----CCCCCCEEEECCCCEECCCCCCHH-HEEEEEECCCCEEEEHHH
T ss_conf ----488888999868651457666732-113442078712576434
No 32
>PRK13901 ruvA Holliday junction DNA helicase motor protein; Provisional
Probab=97.32 E-value=0.00036 Score=49.65 Aligned_cols=60 Identities=25% Similarity=0.444 Sum_probs=51.5
Q ss_pred HHHCCCCHHCCCCCCHHHHHHHHHHHC---CHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 321477100488879899999999808---889899389888862789998999999998547
Q gi|255764496|r 550 KKAAYSPLDEINGIGPLRKRLLLQSFG---TVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 550 ~k~~~S~Ld~I~GIG~k~~~~Ll~~Fg---s~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
.+.++-.|-.|.|||||+.-.+|..+. =+..|.+-...-|.++||||+++|++|.-.|+.
T Consensus 67 Er~~F~~LisVsGIGpk~Al~iLs~~~~~~l~~aI~~~D~~~L~~vpGIG~KtA~rIi~ELk~ 129 (196)
T PRK13901 67 EREVFEELIGVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRG 129 (196)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf 999999987658826899999975799999999999289999831999589999999999976
No 33
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable . ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=97.29 E-value=0.00018 Score=51.80 Aligned_cols=53 Identities=26% Similarity=0.469 Sum_probs=42.7
Q ss_pred HHCCCCHHCCCCCCHHHHHHHHHHH---CCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf 2147710048887989999999980---888989938988886278999899999999854
Q gi|255764496|r 551 KAAYSPLDEINGIGPLRKRLLLQSF---GTVKMISRSSPETLASIEGISKKIACKIYNHFH 608 (616)
Q Consensus 551 k~~~S~Ld~I~GIG~k~~~~Ll~~F---gs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~ 608 (616)
++..-+|..||||||++.+.++.|= |-+ -|+|||.+|-|||++.-+++.+++.
T Consensus 68 ~As~~EL~~l~GiGP~kA~aIi~YRe~nG~F-----~SvddL~kVsGIG~k~~eKLk~~~~ 123 (124)
T TIGR01259 68 KASLEELQALPGIGPAKAKAIIEYREENGAF-----KSVDDLTKVSGIGEKSLEKLKDYVT 123 (124)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHHHHHCCCC-----CCHHHHHCCCCCCHHHHHHHHHCCC
T ss_conf 6789998636999813379999999856997-----7755500357885466874200037
No 34
>PRK08609 hypothetical protein; Provisional
Probab=97.26 E-value=0.00041 Score=49.21 Aligned_cols=56 Identities=11% Similarity=0.164 Sum_probs=24.1
Q ss_pred CCCCEEEEEECCCCCCCCCEEEEEEEECCCCC---------HHHHHHHHCCCC----CCCC---CHHHHHHHHHHHH
Q ss_conf 43516999707443775404888885168728---------032321102444----4554---1168998999999
Q gi|255764496|r 377 HIPKRIEIYDNSHIMGCSAVGCMVVVGENGFV---------KNQYRKFNLHPN----DVKT---QDDCAMMRMVLER 437 (616)
Q Consensus 377 ~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~---------K~~YR~f~Ik~~----~v~~---~DD~~~m~Evi~R 437 (616)
.+|..||-=|| -|+.-+-+ +|.+|... +..|.-.-|..- .+.+ .+++..+.+-|.+
T Consensus 324 ~lP~Li~~~di---~GdlH~Ht--~~SdG~~s~~ema~aa~~~G~~yl~itDHs~~~~~a~Gl~~~~~~~~~~~I~~ 395 (570)
T PRK08609 324 ELSNLIQLSDI---QGDLHMHT--TWSDGAFSIEEMVEACIAKGYKFMAITDHSQYLKVANGLTVERLRRQAEEIKA 395 (570)
T ss_pred CCCHHCCHHHH---CCEEEEEE--CCCCCCCHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 48331468774---62025520--12356253999999999859808998047643456789999999999999999
No 35
>PRK07997 consensus
Probab=97.21 E-value=0.0005 Score=48.57 Aligned_cols=124 Identities=23% Similarity=0.272 Sum_probs=64.1
Q ss_pred HHHHHHHHHHH--HCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEE-CCCCHHHHHHHHH-HHHHHHHHHH----HH
Q ss_conf 89999999999--758877871899971877676634898179834885-7998999999988-7877887889----89
Q gi|255764496|r 474 GQLSAAQGVLK--KLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVL-NMRDPILYFIQRL-RDEAHRFAIT----TH 545 (616)
Q Consensus 474 gQln~a~~vl~--~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l-~~~~~~l~~Lq~i-RDEaHRFAi~----~h 545 (616)
.|..+|-.-|. +=|+.+ ||+=+=- |.+ - ...|++..|..+.- |-++--|++|.++ .||+=-=|-. .|
T Consensus 660 ~Q~~t~TGRlSS~~PNLQN-IPir~~~-G~~--i-R~aFi~~~g~~l~saDYSQiELRilAh~s~d~~li~af~~~~DiH 734 (928)
T PRK07997 660 HQAVTATGRLSSTDPNLQN-IPVRNEE-GRR--I-RQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIH 734 (928)
T ss_pred HCCCCCCCCCCCCCCCCCC-CCCCCHH-HHH--H-HHHHCCCCCCEEEEECHHHHHHHHHHHHHCCHHHHHHHHCCCCCC
T ss_conf 1110212511258998675-8888622-578--9-987437899879970562899999999976876887751688834
Q ss_pred HHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 98643214771004888798999999998088898993898888627899989999999985
Q gi|255764496|r 546 RKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 546 Rk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
+.--.+...-++++|. ...|+++=--.||=+-+ .|.--|++-.||+.+-|+.+.+.+
T Consensus 735 ~~tA~~if~~~~~~v~--~~~R~~aK~vnfgi~YG---~s~~gLa~~l~i~~~eA~~~i~~y 791 (928)
T PRK07997 735 RATAAEVFGLPLEKVT--SEQRRSAKAINFGLIYG---MSAFGLARQLNIPRKEAQKYMDLY 791 (928)
T ss_pred HHHHHHHHCCCHHHCC--HHHHHHHHHHHHHHHHC---CCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 0117988299946579--88998868777664662---687789987099999999999999
No 36
>PRK07456 consensus
Probab=97.11 E-value=0.00095 Score=46.58 Aligned_cols=137 Identities=20% Similarity=0.230 Sum_probs=76.2
Q ss_pred CCCCEEEEECCHHH-----HHHHHHHH--HHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEE-ECCCCHHHHHHHHH
Q ss_conf 79848998098589-----99999999--975887787189997187767663489817983488-57998999999988
Q gi|255764496|r 462 SWPDVVILDGGKGQ-----LSAAQGVL--KKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALV-LNMRDPILYFIQRL 533 (616)
Q Consensus 462 ~~PDLilIDGGkgQ-----ln~a~~vl--~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~-l~~~~~~l~~Lq~i 533 (616)
.+|++|==|-|+=| ..+|-.-| .+=|+.+ ||+=+ ..| |+- ...|++..|..+. .|-+.--|++|.++
T Consensus 674 ~L~~~i~~~tgriht~f~Q~~t~TGRlSS~~PNLQN-IP~r~-~~g--~~i-R~~Fv~~~g~~l~saDySQiELRilAh~ 748 (975)
T PRK07456 674 ALPQLVEAETGRVHTDFNQAVTATGRLSSSNPNLQN-IPIRT-EFS--RRI-RKAFLPQEGWLLLSADYSQIELRILAHL 748 (975)
T ss_pred HHHHHHCCCCCEECCHHHHHCCCCCCCCCCCCCCCC-CCCCC-CCC--HHH-HEEECCCCCCEEEEECHHHHHHHHHHHH
T ss_conf 988752877587657555410665650478975135-77764-103--123-4124358998899963208799999998
Q ss_pred -HHHHHHHHHHHHHHHHHH-HCCCCHHCCCCCCH-HHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf -787788788989986432-14771004888798-9999999980888989938988886278999899999999854
Q gi|255764496|r 534 -RDEAHRFAITTHRKRRKK-AAYSPLDEINGIGP-LRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFH 608 (616)
Q Consensus 534 -RDEaHRFAi~~hRk~r~k-~~~S~Ld~I~GIG~-k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~ 608 (616)
.|++=-=| |....--. .+-|.+-+..-|.+ .|+++=--.||-+-++ |.--|++-.||+.+-|+...+.+.
T Consensus 749 s~d~~li~a--f~~~~DiH~~tA~~if~~~~v~~~~R~~AK~infgiiYG~---~~~gLa~~l~is~~eA~~~i~~yf 821 (975)
T PRK07456 749 SQEPVLLEA--YRSGDDVHTLTARLLFEKEEISSDERRLGKTINFGVIYGM---GAQRFARETGVSQSEAKEFLSRYK 821 (975)
T ss_pred HCCHHHHHH--HHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCC---CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 588899998--7179986899999863930199999999789887677646---877889885979999999999999
No 37
>PRK06887 consensus
Probab=97.04 E-value=0.00077 Score=47.23 Aligned_cols=138 Identities=25% Similarity=0.286 Sum_probs=79.1
Q ss_pred CCCCEEEEECCHH-----HHHHHHHHHH--HCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCC-HHHHHHHHH
Q ss_conf 7984899809858-----9999999999--7588778718999718776766348981798348857998-999999988
Q gi|255764496|r 462 SWPDVVILDGGKG-----QLSAAQGVLK--KLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRD-PILYFIQRL 533 (616)
Q Consensus 462 ~~PDLilIDGGkg-----Qln~a~~vl~--~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~-~~l~~Lq~i 533 (616)
.+|.+|==|-|+= |..++-.-|. +=|+++ ||+=+= -| |+- ...|++.+|..+.-...| --|++|.++
T Consensus 670 ~L~~~i~~~tgRiHt~f~q~~t~TGRlSS~~PNLQN-IPiRte-~G--r~i-R~aF~~~~g~~l~saDYSQIELRilAh~ 744 (954)
T PRK06887 670 KLPQMVNSKTGRVHTSYHQAVTATGRLSSSDPNLQN-IPIRNE-EG--RRI-RQAFIARDGYKIVAADYSQIELRIMAHL 744 (954)
T ss_pred HHHHHCCCCCCEECCCCCCCCCCCCCCCCCCCCCCC-CCCCCH-HH--HHH-HEEEECCCCCEEEEECHHHHHHHHHHHH
T ss_conf 887640778987777652011231201379986336-887860-22--233-4005438998899714528999999999
Q ss_pred -HHHHHHHHHHH----HHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf -78778878898----9986432147710048887989999999980888989938988886278999899999999854
Q gi|255764496|r 534 -RDEAHRFAITT----HRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFH 608 (616)
Q Consensus 534 -RDEaHRFAi~~----hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~ 608 (616)
.||+=.=|-.. |+.--.....-++++|. ...|+++=--.||=+-+ .|.--|++-.||+.+-|+...+.+.
T Consensus 745 s~d~~l~~af~~g~DiH~~tA~~vf~~~~~~v~--~~~R~~aK~vnfgi~YG---~~~~gLs~~l~i~~~eA~~~i~~yf 819 (954)
T PRK06887 745 SGDQGLINAFSEGKDIHRSTAAEIFGLSLDEVT--SEQRRSAKAINFGLIYG---MSAFGLSRQLGISRADAQKYMDLYF 819 (954)
T ss_pred HCCHHHHHHHHCCCCCHHHHHHHHHCCCHHHCC--HHHHHHHHHHHHHHHHC---CCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 668879999863888027789999499946689--88998768887665661---6877799870989999999999998
Q ss_pred C
Q ss_conf 7
Q gi|255764496|r 609 K 609 (616)
Q Consensus 609 ~ 609 (616)
.
T Consensus 820 ~ 820 (954)
T PRK06887 820 Q 820 (954)
T ss_pred H
T ss_conf 8
No 38
>PRK08835 consensus
Probab=97.00 E-value=0.00099 Score=46.46 Aligned_cols=136 Identities=21% Similarity=0.270 Sum_probs=69.6
Q ss_pred CCCCEEEEECCHH-----HHHHHHHHH--HHCCCCCCCCEEEEECCCC-CCCCCEEEECCCCCEEEE-CCCCHHHHHHHH
Q ss_conf 7984899809858-----999999999--9758877871899971877-676634898179834885-799899999998
Q gi|255764496|r 462 SWPDVVILDGGKG-----QLSAAQGVL--KKLNVENRITIISIAKGPK-RSAGMEKFFVKKGEALVL-NMRDPILYFIQR 532 (616)
Q Consensus 462 ~~PDLilIDGGkg-----Qln~a~~vl--~~l~i~~~i~viglaK~~~-r~~~~e~~~~~~~~~i~l-~~~~~~l~~Lq~ 532 (616)
.+|.+|=-+-|+= |..+|-.-| .+=|+.+ ||+= .++ |+- ...|++..|..+.- |-++--|++|.+
T Consensus 645 ~L~~~i~~~~gRiHt~f~Q~~t~TGRLSS~~PNLQN-IPiR----t~~G~~i-R~aFva~~g~~l~saDYSQIELRilAh 718 (931)
T PRK08835 645 KLPKMINPSTGRVHTSYHQAVTATGRLSSTDPNLQN-IPIR----NEEGRRI-RQAFVAPHGYKILAVDYSQIELRIMAH 718 (931)
T ss_pred HHHHHHCCCCCEECCHHHHCCCCCCCCCCCCCCCCC-CCCC----CHHHCCH-HHHEECCCCCEEEEECHHHHHHHHHHH
T ss_conf 557652867588787343101552452579963026-7888----6011100-053466998879970431899999999
Q ss_pred H-HHHHHHHHHH----HHHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 8-7877887889----8998643214771004888798999999998088898993898888627899989999999985
Q gi|255764496|r 533 L-RDEAHRFAIT----THRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 533 i-RDEaHRFAi~----~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
+ .|++=.=|-. -|+.--.....-++++|. ...|+++=--.||=+- ..|.--|++-.||+.+-|+.+.+.+
T Consensus 719 ~s~d~~li~af~~~~DiH~~tA~~if~v~~~~v~--~~~R~~AK~vnfgi~Y---G~~~~gLa~~l~i~~~eA~~~i~~y 793 (931)
T PRK08835 719 LSGDQALLDAFRDGKDIHAATAAEIMGVSIEQVS--SEQRRRAKAVNFGLIY---GMSAFGLAKQLGIPRGEAQAYMDKY 793 (931)
T ss_pred HCCCHHHHHHHHCCCCHHHHHHHHHHCCCHHHCC--HHHHHHHHHHHHHHHH---CCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 8299899999866998067899999599946689--9898775833311244---5787779987098999999999999
Q ss_pred C
Q ss_conf 4
Q gi|255764496|r 608 H 608 (616)
Q Consensus 608 ~ 608 (616)
.
T Consensus 794 f 794 (931)
T PRK08835 794 F 794 (931)
T ss_pred H
T ss_conf 8
No 39
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=96.94 E-value=0.0016 Score=44.93 Aligned_cols=54 Identities=28% Similarity=0.348 Sum_probs=50.4
Q ss_pred CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 100488879899999999808889899389888862789998999999998547
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
.|..||-+-..-..+|.+.||++++|.+||.|||.+|.|||+.-|+.|.+-|..
T Consensus 294 ~l~kIpRlp~~iv~nlV~~F~~l~~il~As~edL~~VeGIGe~rAr~i~~Gl~r 347 (349)
T COG1623 294 LLNKIPRLPFAIVENLVRAFGTLDGILEASAEDLDAVEGIGEARARAIKEGLSR 347 (349)
T ss_pred HHHCCCCCCHHHHHHHHHHHHHHHHHHHHCHHHHHHHCCHHHHHHHHHHHHHHH
T ss_conf 871176763789999999975289998714767766213669999999976753
No 40
>TIGR00593 pola DNA polymerase I; InterPro: IPR002298 DNA carries the biological information that instructs cells how to exist in an ordered fashion. Accurate replication is thus one of the most important events in the cell life cycle. This function is mediated by DNA-directed DNA polymerases, which add nucleotide triphosphate (dNTP) residues to the 5'-end of the growing DNA chain, using a complementary DNA as template. Small RNA molecules are generally used as primers for chain elongation, although terminal proteins may also be used. DNA-dependent DNA polymerases have been grouped into families, denoted A, B and X, on the basis of sequence similarities , . Members of family A, which includes bacterial and bacteriophage polymerases, share significant similarity to Escherichia coli polymerase I; hence family A is also known as the pol I family. The bacterial polymerases also contain an exonuclease activity, which is coded for in the N-terminal portion. Three motifs, A, B and C , are seen to be conserved across all DNA polymerases, with motifs A and C also seen in RNA polymerases. They are centred on invariant residues, and their structural significance was implied from the Klenow (E. coli) structure. Motif A contains a strictly-conserved aspartate at the junction of a beta-strand and an alpha-helix; motif B contains an alpha-helix with positive charges; and motif C has a doublet of negative charges, located in a beta-turn-beta secondary structure .; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication.
Probab=96.94 E-value=0.00049 Score=48.62 Aligned_cols=118 Identities=21% Similarity=0.309 Sum_probs=68.4
Q ss_pred HHHHHHHHHHHHHCCC----------CCCCCEEEEECCCCCCCCCEEEE-CCCCCEEEECCC-CHHHHHH----------
Q ss_conf 5899999999997588----------77871899971877676634898-179834885799-8999999----------
Q gi|255764496|r 473 KGQLSAAQGVLKKLNV----------ENRITIISIAKGPKRSAGMEKFF-VKKGEALVLNMR-DPILYFI---------- 530 (616)
Q Consensus 473 kgQln~a~~vl~~l~i----------~~~i~viglaK~~~r~~~~e~~~-~~~~~~i~l~~~-~~~l~~L---------- 530 (616)
.+|+..++++|..+|+ |+ | +.+|||..+. .|.++.+ ++|.+-+.|=.+ .-.....
T Consensus 86 ~~Qi~~i~e~l~algi~~~e~~GYEADD-~-IaTLA~~a~~-~G~~V~I~sgDrD~lQLvs~e~V~V~~~~~~~g~~~~~ 162 (1005)
T TIGR00593 86 IEQIPLIKELLEALGIPILEVEGYEADD-V-IATLAKQAEK-EGYEVRIISGDRDLLQLVSDENVKVLIPERKKGKTEFT 162 (1005)
T ss_pred HHHHHHHHHHHHHCCCEEEECCCCCHHH-H-HHHHHHHHHH-CCCEEEEEECCCCCCCCCCCCCEEEEECCCCCCCCCCE
T ss_conf 8768999999997198188228871012-8-9998887754-68548998378462112178614886435456754310
Q ss_pred -HHHHHHHHHHHHHHHHHHHHHHC---CC-CHHCCCCCCHHHHHHHHHHHCCHHHHHHCC-------HHHHHHCC
Q ss_conf -98878778878898998643214---77-100488879899999999808889899389-------88886278
Q gi|255764496|r 531 -QRLRDEAHRFAITTHRKRRKKAA---YS-PLDEINGIGPLRKRLLLQSFGTVKMISRSS-------PETLASIE 593 (616)
Q Consensus 531 -q~iRDEaHRFAi~~hRk~r~k~~---~S-~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As-------~eeL~~v~ 593 (616)
-....=.-+|.++=.+=.-=+++ .| =+=+||||||||..+||+.|||+++|.+++ .+.|.++.
T Consensus 163 ~~t~e~V~eKyGv~P~Q~~D~~AL~GD~SDNiPGV~GIGeKTA~kLL~~fgsLe~iy~~~ylkealr~~~~~~~k 237 (1005)
T TIGR00593 163 EITPEYVVEKYGVTPSQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENTYLKEALRLDNLDQIK 237 (1005)
T ss_pred ECCHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 117789875418674578876204688887859989737656899998721089999887788887477586228
No 41
>PRK05797 consensus
Probab=96.93 E-value=0.0019 Score=44.36 Aligned_cols=137 Identities=21% Similarity=0.250 Sum_probs=74.2
Q ss_pred CCCCEEEEECCHH-----HHHHHHHHH--HHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEE--EECCCCHHHHHHHH
Q ss_conf 7984899809858-----999999999--97588778718999718776766348981798348--85799899999998
Q gi|255764496|r 462 SWPDVVILDGGKG-----QLSAAQGVL--KKLNVENRITIISIAKGPKRSAGMEKFFVKKGEAL--VLNMRDPILYFIQR 532 (616)
Q Consensus 462 ~~PDLilIDGGkg-----Qln~a~~vl--~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i--~l~~~~~~l~~Lq~ 532 (616)
.+|.+|=-| |+= |..+|-.-| .+=|+++ ||+=+ .-|.+ -. ..|++.++... ..|-+.--|++|.+
T Consensus 584 ~L~~~i~~~-gRiHt~f~Q~~t~TGRLSS~~PNLQN-IP~r~-e~G~~--iR-~aFi~~~~~~~l~saDYSQIELRilAh 657 (869)
T PRK05797 584 GLKNVIDED-GRIHSNFNQTVTTTGRLSSTEPNLQN-IPIKY-EMGRE--IR-KVFIPNTEDSVILSADYSQIELRVLAH 657 (869)
T ss_pred HHHHHCCCC-CCCCCHHHHHHCCCCCCCCCCCCCCC-CCCCC-CCHHH--HH-HEEECCCCCCEEEECCHHHHHHHHHHH
T ss_conf 899742624-65054266543440211468986456-87765-20122--55-357147776158852277899999999
Q ss_pred H-HHHHHHHHH----HHHHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 8-787788788----98998643214771004888798999999998088898993898888627899989999999985
Q gi|255764496|r 533 L-RDEAHRFAI----TTHRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 533 i-RDEaHRFAi----~~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
+ .|++=-=|- --|+.--.....-++++|. ...|+++=--.||-+-+ .|.--|++-.||+.+-|+.+.+.+
T Consensus 658 ~s~d~~l~~af~~~~DiH~~tA~~vf~~~~~~v~--~~~R~~AK~infGiiYG---~~~~gLs~~l~i~~~eA~~~i~~y 732 (869)
T PRK05797 658 ISGDENLIDAFNHHEDIHTKTASEVFKVPIEEVT--PLMRSNAKAVNFGIVYG---IGDFSLSQDLNISRKEAKEYIDNY 732 (869)
T ss_pred HHCCHHHHHHHHCCCCHHHHHHHHHHCCCHHHCC--HHHHHHHHHHHHHHHHC---CCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 8468999998855997689999999598911179--88999988988566555---686778985298999999999999
Q ss_pred CC
Q ss_conf 47
Q gi|255764496|r 608 HK 609 (616)
Q Consensus 608 ~~ 609 (616)
..
T Consensus 733 f~ 734 (869)
T PRK05797 733 FE 734 (869)
T ss_pred HH
T ss_conf 99
No 42
>PRK09482 xni exonuclease IX; Provisional
Probab=96.93 E-value=0.0014 Score=45.28 Aligned_cols=62 Identities=23% Similarity=0.334 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHCC---C-CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 88788989986432147---7-100488879899999999808889899389888862789998999999998
Q gi|255764496|r 538 HRFAITTHRKRRKKAAY---S-PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNH 606 (616)
Q Consensus 538 HRFAi~~hRk~r~k~~~---S-~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616)
.+|.++-++=.--+++. | -+-.||||||||..+||++|||+++|.+.- ++ |++++.+++.++
T Consensus 161 ek~Gv~P~q~~d~~aL~GD~SDNIPGV~GIG~KtA~~LL~~fgsle~i~~n~-d~------i~~k~~~~l~~~ 226 (256)
T PRK09482 161 QEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLEGIYESL-DA------LPEKWRKKLEEH 226 (256)
T ss_pred HHCCCCHHHHHHEEEEECCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHH-HH------CCHHHHHHHHHC
T ss_conf 8528287353230247465436899999858889999999855099999837-75------568999999968
No 43
>TIGR00596 rad1 DNA repair protein (rad1); InterPro: IPR006167 All proteins in this family, for which functions are known, are components in a multiprotein endonuclease complex, usually made up of Rad1 and Rad10 homologues. This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologues of these genes, but the function of the Archaeal proteins is not known, so are not included in this family.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity, 0006281 DNA repair.
Probab=96.91 E-value=0.0012 Score=45.78 Aligned_cols=56 Identities=21% Similarity=0.377 Sum_probs=52.1
Q ss_pred CHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf 1004888798999999998-08889899389888862789998999999998547867
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTS 612 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~ 612 (616)
.|..+|||-+|=...|+.+ -+++.++.+.|.+||..+.| +...|++||++||.+-.
T Consensus 882 rLl~~PGV~~kN~rnl~~~G~k~~~el~~~S~~El~eL~g-~~e~a~~lY~Fl~~~~~ 938 (939)
T TIGR00596 882 RLLKLPGVTKKNIRNLLKKGVKSIRELAKLSQEELEELIG-DEEAAKRLYDFLRKELL 938 (939)
T ss_pred HHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CHHHHHHHHHHHHHHCC
T ss_conf 8557898560234555543155599999987999997507-97576689999876307
No 44
>cd06559 Endonuclease_V Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases. Endonuclease_V (EndoV) is an enzyme that can initiate repair of all possible deaminated DNA bases. EndoV cleaves the DNA strand containing lesions at the second phosphodiester bond 3' to the lesion using Mg2+ as a cofactor. EndoV homologs are conserved throughout all domains of life from bacteria to humans. EndoV is encoded by the nfi gene and nfi null mutant mice have a phenotype prone to cancer. The ability of endonuclease V to recognize mismatches and abnormal replicative DNA structures suggests that the enzyme plays an important role in DNA metabolism. The details of downstream processing for the EndoV pathway remain unknown.
Probab=96.89 E-value=0.0018 Score=44.56 Aligned_cols=104 Identities=18% Similarity=0.126 Sum_probs=61.3
Q ss_pred CCCCEEEEEECCCCC-CCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHH--HHHHHHHHCCCCCCCCCC
Q ss_conf 435169997074437-75404888885168728032321102444455411689989999--999977531311123333
Q gi|255764496|r 377 HIPKRIEIYDNSHIM-GCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVL--ERRFSQLIKNEENLNFHP 453 (616)
Q Consensus 377 ~~p~rIE~fDiSh~~-G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi--~RR~~r~~~~~~~l~~~~ 453 (616)
..++.|-++|+|... +...+|++|+++-... +--+..+-....+.-..--|-|+||+- ..-+.++.
T Consensus 23 ~~~~~VaGvDvsy~~~~~~~~a~~Vv~~~~~l-~~v~~~~~~~~~~fPYIPG~LaFRE~p~~l~a~~~l~---------- 91 (208)
T cd06559 23 GEVRLVAGVDVSYKKDGDLAVAAAVVLDYPDL-EVVETAVAVGEVTFPYIPGLLAFREGPPLLEALEKLK---------- 91 (208)
T ss_pred CCCEEEEEEEEEEECCCCEEEEEEEEEECCCC-EEEEEEEEEEEECCCCCCCHHHHCCCHHHHHHHHHCC----------
T ss_conf 98429999998787599889999999987997-4999999985304665540343301489999998557----------
Q ss_pred CCCCCCCCCCCCEEEEEC-CHHHHHHHHHHHHHCCCCCCCCEEEEECC
Q ss_conf 333345457984899809-85899999999997588778718999718
Q gi|255764496|r 454 KKQEYSFPSWPDVVILDG-GKGQLSAAQGVLKKLNVENRITIISIAKG 500 (616)
Q Consensus 454 ~~~~~~~~~~PDLilIDG-GkgQln~a~~vl~~l~i~~~i~viglaK~ 500 (616)
..|||+|+|| |..|=.-+- .-.-+|+..++|-||+||.
T Consensus 92 --------~~PdlllvDG~Gi~HPR~~G-lAsHlGv~l~~PtIGVAK~ 130 (208)
T cd06559 92 --------TKPDLLLVDGHGIAHPRRFG-LASHLGVLLDLPTIGVAKS 130 (208)
T ss_pred --------CCCCEEEECCCCCCCCCCCC-HHEEEEEECCCCCCCCCCC
T ss_conf --------79999998688752665547-0103455528783342154
No 45
>PRK08786 consensus
Probab=96.84 E-value=0.0021 Score=44.07 Aligned_cols=136 Identities=24% Similarity=0.278 Sum_probs=71.2
Q ss_pred CCCCEEEEECCHH-----HHHHHHHHHH--HCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCC-HHHHHHHHH
Q ss_conf 7984899809858-----9999999999--7588778718999718776766348981798348857998-999999988
Q gi|255764496|r 462 SWPDVVILDGGKG-----QLSAAQGVLK--KLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRD-PILYFIQRL 533 (616)
Q Consensus 462 ~~PDLilIDGGkg-----Qln~a~~vl~--~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~-~~l~~Lq~i 533 (616)
.+|++|-=+-|+= |..+|-.-|. +=|+.+ ||+=+ ..|.+ - ...|++..|..+.-...| --|++|.++
T Consensus 642 ~L~~~i~~~~gRiHt~f~Q~~t~TGRlSS~~PNLQN-IPirt-~~G~~--i-R~aFi~~~g~~l~saDYSQIELRilAh~ 716 (927)
T PRK08786 642 KLPEMIHPQSGRVHTSYHQAGAATGRLSSSDPNLQN-IPIRT-EDGRR--I-RRAFVAPAGRKLIACDYSQIELRIMAHL 716 (927)
T ss_pred HHHHHCCCCCCEECCCCHHHCCCCCEECCCCCCCCC-CCCCC-CCCCC--H-HHHEECCCCCEEEEECHHHHHHHHHHHH
T ss_conf 888740766576624216311454525279934114-88776-33302--2-6660258988799723648899999998
Q ss_pred -HHHHHHHHHHH----HHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf -78778878898----998643214771004888798999999998088898993898888627899989999999985
Q gi|255764496|r 534 -RDEAHRFAITT----HRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 534 -RDEaHRFAi~~----hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
.|++=-=|-.. |+.--.....-+.++|. ...|+++=--.||=+ ...|.--|++-.||+.+-|+...+..
T Consensus 717 s~d~~li~af~~~~DiH~~tA~~if~~~~~~v~--~~~R~~aK~infgii---YG~s~~gL~~~l~i~~~eA~~~i~~y 790 (927)
T PRK08786 717 SGDPGLVGAFESGADVHRATAAEVFGRTIDTVS--GDERRAAKAINFGLM---YGMSAFGLARQLGIGRGEAQDYIALY 790 (927)
T ss_pred HCCHHHHHHHCCCCCCCHHHHHHHHCCCHHHCC--HHHHHHHHEEEEEHH---HCCCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 288647777547867303268988299957669--778855152102003---33787779987099999999999999
No 46
>smart00475 53EXOc 5'-3' exonuclease.
Probab=96.83 E-value=0.0021 Score=44.04 Aligned_cols=62 Identities=26% Similarity=0.426 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHHCC---C-CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 88788989986432147---7-100488879899999999808889899389888862789998999999998
Q gi|255764496|r 538 HRFAITTHRKRRKKAAY---S-PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNH 606 (616)
Q Consensus 538 HRFAi~~hRk~r~k~~~---S-~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616)
.+|.++-..=---+++. | -+-.|||||+||..+||+.|||+++|.++. ++ + ++++.+++-++
T Consensus 165 e~~gv~P~q~~d~~aL~GD~sDnIpGV~GIG~KtA~kLL~~ygsle~i~~~~-d~---i---~~k~~~~l~~~ 230 (259)
T smart00475 165 EKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENL-DK---L---KKKLREKLLAH 230 (259)
T ss_pred HHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHH-HH---C---CHHHHHHHHHH
T ss_conf 8848998998637640464535899999847899999999839999999839-85---4---88999999977
No 47
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=96.83 E-value=0.003 Score=43.02 Aligned_cols=12 Identities=25% Similarity=0.385 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHH
Q ss_conf 388888899999
Q gi|255764496|r 214 DYESAIIHRDRL 225 (616)
Q Consensus 214 ~FE~Aa~~RD~I 225 (616)
.|..|..+-.+-
T Consensus 68 ~f~Ta~el~~~r 79 (318)
T PRK04301 68 GFETALEVLERR 79 (318)
T ss_pred CCCCHHHHHHHH
T ss_conf 982699999986
No 48
>pfam01367 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold.
Probab=96.82 E-value=0.0025 Score=43.61 Aligned_cols=44 Identities=25% Similarity=0.420 Sum_probs=34.1
Q ss_pred CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 100488879899999999808889899389888862789998999999998
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNH 606 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616)
-+-.|||||+||..+||.+|||+++|... .+++ +.++++++-++
T Consensus 19 nIPGv~GiG~KtA~~Ll~~~gsle~i~~n-~d~i------~~k~~~~l~~~ 62 (100)
T pfam01367 19 NIPGVPGIGEKTAAKLLKEYGSLENIYEN-LDKL------KGKLREKLLNG 62 (100)
T ss_pred CCCCCCCCCCHHHHHHHHHCCCHHHHHHH-HHHC------CHHHHHHHHHH
T ss_conf 88999998816899999981989999981-9871------79999999978
No 49
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=96.79 E-value=0.0023 Score=43.80 Aligned_cols=35 Identities=20% Similarity=0.310 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89999999999998633388888899999999862
Q gi|255764496|r 197 NLKEKIARNMNQATLKEDYESAIIHRDRLAALSHI 231 (616)
Q Consensus 197 ~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~i 231 (616)
.=|..|.+..+.+-+.++||+||.+||+|.+|+.-
T Consensus 136 ~~I~~L~e~Lq~~i~~EefEeAA~iRDqIr~Lk~k 170 (176)
T COG3880 136 RKIIALKEALQDLIEREEFEEAAVIRDQIRALKAK 170 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999888889999999999998854
No 50
>PRK07300 consensus
Probab=96.78 E-value=0.0024 Score=43.68 Aligned_cols=134 Identities=20% Similarity=0.179 Sum_probs=72.3
Q ss_pred CCCCEEEEECCHHHHHHHHHH-----H--HHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCE--EEECCCCHHHHHHHH
Q ss_conf 798489980985899999999-----9--9758877871899971877676634898179834--885799899999998
Q gi|255764496|r 462 SWPDVVILDGGKGQLSAAQGV-----L--KKLNVENRITIISIAKGPKRSAGMEKFFVKKGEA--LVLNMRDPILYFIQR 532 (616)
Q Consensus 462 ~~PDLilIDGGkgQln~a~~v-----l--~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~--i~l~~~~~~l~~Lq~ 532 (616)
.+|.+|-=| |+=|=+.-+.+ | .+=|+++ |||=+ ..|.+ - .+.|++..+.. +..|-+.--|++|.+
T Consensus 594 ~L~~~i~~~-gRIHTsf~Qt~TaTGRLSS~~PNLQN-IPiRt-e~Gr~--I-R~aFi~~~~~~~llsaDYSQIELRilAh 667 (880)
T PRK07300 594 GLQDYILAD-GKIHTRYVQDLTQTGRLSSVDPNLQN-IPVRL-EQGRL--I-RKAFVPSHEDAVLLSSDYSQIELRVLAH 667 (880)
T ss_pred HHHHHCCCC-CCCCCHHHHHHCCCCEECCCCCCCCC-CCCCC-CCCHH--H-HHEEECCCCCEEEEEECHHHHHHHHHHH
T ss_conf 899854754-61221356423133421147876346-88777-43520--4-4127327885599982322689999999
Q ss_pred H-HHHHHHHHHHHHHHHHHH-HCCCCHHCCC---CCC-HHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 8-787788788989986432-1477100488---879-899999999808889899389888862789998999999998
Q gi|255764496|r 533 L-RDEAHRFAITTHRKRRKK-AAYSPLDEIN---GIG-PLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNH 606 (616)
Q Consensus 533 i-RDEaHRFAi~~hRk~r~k-~~~S~Ld~I~---GIG-~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616)
+ .|++=-= .|....--. .+-|.+-.|| .|- ..|+++=--.||=+-+ .|.--|++-.||+.+-|+...+.
T Consensus 668 lS~D~~Li~--AF~~~~DIH~~TA~~if~v~~~~~Vt~~~Rr~AK~iNFGiiYG---~s~fgLs~~l~i~~~eA~~~I~~ 742 (880)
T PRK07300 668 ISGDEHLIA--AFKEGADIHTSTAMRVFGIEKAEDVTANDRRNAKAVNFGIVYG---ISDFGLSNNLGITRKQAKSYIDT 742 (880)
T ss_pred HHCCHHHHH--HHHCCCCHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHHHHC---CCHHHHHHHCCCCHHHHHHHHHH
T ss_conf 818888999--8715887789999999499732008999999986312111127---88677888649999999999999
No 51
>PRK08434 consensus
Probab=96.78 E-value=0.0022 Score=43.88 Aligned_cols=132 Identities=25% Similarity=0.307 Sum_probs=72.4
Q ss_pred CCCCEEEEEC-CHH-----HHHHHHHHH--HHCCCCCCCCEEEEECCCC-CCCCCEEEECCCCCEEE-ECCCCHHHHHHH
Q ss_conf 7984899809-858-----999999999--9758877871899971877-67663489817983488-579989999999
Q gi|255764496|r 462 SWPDVVILDG-GKG-----QLSAAQGVL--KKLNVENRITIISIAKGPK-RSAGMEKFFVKKGEALV-LNMRDPILYFIQ 531 (616)
Q Consensus 462 ~~PDLilIDG-Gkg-----Qln~a~~vl--~~l~i~~~i~viglaK~~~-r~~~~e~~~~~~~~~i~-l~~~~~~l~~Lq 531 (616)
.+|.++.-|. |+= |..+|-.-| .+=|+++ ||+=+ .-|.+ | ..|++.+|..+. .|-+.--|++|.
T Consensus 607 ~L~~~~~~d~tgRIHttfnQ~~t~TGRLSS~~PNLQN-IPirt-~~Gr~iR----~aFv~~~g~~l~~aDysQiElRilA 680 (887)
T PRK08434 607 PLLKLALKDKNSRIYTSFLQTGTATGRLSSKNPNLQN-IPARG-ELAKDIR----EAFVAKEGYSLISLDYSQIELRLLA 680 (887)
T ss_pred HHHHHCCCCCCCEECCHHHHHCCCCEEECCCCCCCCC-CCCCC-CCCHHHH----HHEEECCCCEEEEECHHHHHHHHHH
T ss_conf 8877514788870310115313221012368997567-87776-4215546----4434068877997057389999999
Q ss_pred HH-HHHHHHHHHH----HHHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 88-7877887889----899864321477100488879899999999808889899389888862789998999999998
Q gi|255764496|r 532 RL-RDEAHRFAIT----THRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNH 606 (616)
Q Consensus 532 ~i-RDEaHRFAi~----~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616)
++ .||+=-=|-. .|+.--.. .+. +++ -...|+++=--.||=+- ..|.--|++-.||+.+-|+...+.
T Consensus 681 h~s~d~~l~~af~~~~DiH~~tA~~-vf~--~~~--~~~~R~~aK~vnfgi~Y---G~~~~gLa~~l~i~~~eA~~~i~~ 752 (887)
T PRK08434 681 HFSKDEALLEAFKNDEDIHARTAIK-IFG--EEN--AKAKRAVAKSINFGLIY---GMGSKKLSETLGISAKEAKEYIES 752 (887)
T ss_pred HHCCCHHHHHHHHCCCCHHHHHHHH-HHC--CCC--CHHHHHHHHHHHHHHHH---CCCHHHHHHHCCCCHHHHHHHHHH
T ss_conf 9718899999984499848999999-837--778--88899897777756655---468777998709899999999999
Q ss_pred H
Q ss_conf 5
Q gi|255764496|r 607 F 607 (616)
Q Consensus 607 l 607 (616)
+
T Consensus 753 y 753 (887)
T PRK08434 753 Y 753 (887)
T ss_pred H
T ss_conf 9
No 52
>PRK07556 consensus
Probab=96.70 E-value=0.0029 Score=43.06 Aligned_cols=135 Identities=21% Similarity=0.283 Sum_probs=71.0
Q ss_pred CCCEEEEECCHHHHH-----HHHHHH--HHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEE-CCCCHHHHHHHHH-
Q ss_conf 984899809858999-----999999--9758877871899971877676634898179834885-7998999999988-
Q gi|255764496|r 463 WPDVVILDGGKGQLS-----AAQGVL--KKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVL-NMRDPILYFIQRL- 533 (616)
Q Consensus 463 ~PDLilIDGGkgQln-----~a~~vl--~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l-~~~~~~l~~Lq~i- 533 (616)
+|.+|-=|-|+=|=+ ++-.-| .+=|+++ ||+=+= -| |+- ...|++..|..+.- |-+.--|++|.++
T Consensus 689 L~~~i~~~~gRiHt~fnq~~t~TGRlSS~~PNLQN-IPir~e-~G--~~i-R~aFv~~~g~~l~saDYSQIELRilAh~s 763 (977)
T PRK07556 689 LPGYIHPQTGRVHTSYALAATTTGRLSSSDPNLQN-IPVRTE-EG--RKI-RTAFIATPGHKLVSADYSQIELRILAHIA 763 (977)
T ss_pred HHHHCCCCCCEECCCHHHHCEECCCCCCCCCCCCC-CCCCCC-CC--CHH-HEEECCCCCCEEEEECHHHHHHHHHHHHH
T ss_conf 88623789880777302323105764569986467-888763-23--032-32160499987998336688999999981
Q ss_pred HHHHHHHHHH----HHHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 7877887889----8998643214771004888798999999998088898993898888627899989999999985
Q gi|255764496|r 534 RDEAHRFAIT----THRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 534 RDEaHRFAi~----~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
+||+=-=|-. -|+.--.....-++++|. ...|+.+=--.||-+-+ .|.--|++-.||+.+-|+.+.+.+
T Consensus 764 ~d~~li~af~~~~DiH~~tA~~if~~~~~~v~--~~~R~~aK~iNfgi~YG---~~~~gL~~~l~i~~~eA~~~i~~y 836 (977)
T PRK07556 764 DIPALKQAFADGLDIHAMTASEMFGVPVEGMP--SEVRRRAKAINFGIIYG---ISAFGLANQLGIPREEAGAYIKRY 836 (977)
T ss_pred CCHHHHHHHCCCCCHHHHHHHHHHCCCHHHCC--HHHHHHHHEEEEHHHHC---CCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 78899987635987789999999599935489--99986526042034556---687779987198999999999999
No 53
>PRK05755 DNA polymerase I; Provisional
Probab=96.67 E-value=0.0038 Score=42.25 Aligned_cols=136 Identities=26% Similarity=0.339 Sum_probs=75.2
Q ss_pred CCCCEEEEECCHHH-----HHHHHHHH--HHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEE-CCCCHHHHHHHHH
Q ss_conf 79848998098589-----99999999--9758877871899971877676634898179834885-7998999999988
Q gi|255764496|r 462 SWPDVVILDGGKGQ-----LSAAQGVL--KKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVL-NMRDPILYFIQRL 533 (616)
Q Consensus 462 ~~PDLilIDGGkgQ-----ln~a~~vl--~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l-~~~~~~l~~Lq~i 533 (616)
.+|++|==|.|+=| ..+|-.-| .+=|+++ ||+=. ..|.+ -. ..|++..|..+.- |-++--|++|.++
T Consensus 605 ~L~~~i~~~tgRIHt~f~Q~~t~TGRLSS~~PNLQN-IPir~-e~Gr~--IR-~aFva~~g~~l~saDYSQIELRilAh~ 679 (889)
T PRK05755 605 GLPKMINPDTGRVHTSFNQAVTATGRLSSSDPNLQN-IPIRT-EEGRR--IR-QAFVAPEGYKLLSADYSQIELRILAHL 679 (889)
T ss_pred HHHHCCCCCCCEEECCHHHHHCCCCCCCCCCCCCCC-CCCCC-HHHHH--HH-HEEEECCCCEEEEECHHHHHHHHHHHH
T ss_conf 887524788984611001110320222479985346-87763-23044--55-227858998899951208999999998
Q ss_pred -HHHHHHHHHH----HHHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf -7877887889----8998643214771004888798999999998088898993898888627899989999999985
Q gi|255764496|r 534 -RDEAHRFAIT----THRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 534 -RDEaHRFAi~----~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
.||+=.=|-. .|+.--.....-+.++|. ...|+++=--.||-+ ...|.--|++-.||+.+-|+...+.+
T Consensus 680 S~D~~li~af~~g~DiH~~tA~~vf~v~~~~vt--~~~R~~AK~vnfGii---YG~s~~gLs~~l~is~~eA~~~i~~y 753 (889)
T PRK05755 680 SGDEGLIEAFAEGEDIHTATASEVFGVPLEEVT--SEQRRRAKAINFGLI---YGMSAFGLARQLGISRKEAKEYIDRY 753 (889)
T ss_pred HCCHHHHHHHHCCCCHHHHHHHHHHCCCHHHCC--HHHHHHHHHEEEHHH---HCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 089999999855998689999999399900189--999866261322144---46687789988199999999999999
No 54
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. .
Probab=96.66 E-value=0.0019 Score=44.48 Aligned_cols=145 Identities=21% Similarity=0.179 Sum_probs=77.2
Q ss_pred HHHHHHCCCCCCCCC--CCCCCH---HHHHHHHHHHHHHHHHHHHH--H------HHHHHHHHHHHHHHHCCCCC-CCEE
Q ss_conf 654320134333212--565526---67899999999986554323--3------43389999999875156643-5169
Q gi|255764496|r 317 ISFFKQYGYKVKITV--PKQGEK---RKIIEQALINAHRSHTQKLS--T------EISHQMILKDFTKKFALPHI-PKRI 382 (616)
Q Consensus 317 ~~L~~k~g~kV~i~~--P~rG~k---k~Ll~lA~~NA~~~l~~k~~--~------~~~~~~~l~~Lk~~L~L~~~-p~rI 382 (616)
++|....+.||-|.+ |=.|+- +-+++++..+.-..+..+-. . -...-++.+.|.+.=|+... ..|.
T Consensus 357 ~AL~~~~~~Kv~iLTGGPGTGKtT~t~~i~~~~~~~~gl~l~~~~~vndd~~v~LaAPTGrAAkRl~E~TG~~a~TIHRL 436 (769)
T TIGR01448 357 EALKTAIQDKVVILTGGPGTGKTTITKAIIELYEELKGLDLDKDDYVNDDLPVVLAAPTGRAAKRLAEVTGLEALTIHRL 436 (769)
T ss_pred HHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCHHHHHHCCCCCCCHHHHHHHH
T ss_conf 99999860948998577888616899999999987168775531245677648873774378885110026212347786
Q ss_pred EEEECCCCCCCCCEEEEEEEECCCCC-HHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 99707443775404888885168728-03232110244445541168998999999997753131112333333334545
Q gi|255764496|r 383 EIYDNSHIMGCSAVGCMVVVGENGFV-KNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFP 461 (616)
Q Consensus 383 E~fDiSh~~G~~~Vas~Vvf~~g~~~-K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~ 461 (616)
-+||-- +.+. |..=+.++- |.==.|..+||-+.|..+|-..
T Consensus 437 lG~~~~----------------~~~~~k~~~~~~~~---DL~IvDE~SM~Dt~L~~~lL~a------------------- 478 (769)
T TIGR01448 437 LGYGSD----------------TKSENKNLEDPIDA---DLLIVDESSMVDTWLASSLLAA------------------- 478 (769)
T ss_pred HCCCCC----------------CCCCCHHHCCCCCC---CEEEEECCCHHHHHHHHHHHHH-------------------
T ss_conf 368988----------------87321101134787---7699814621889999999861-------------------
Q ss_pred CCCC--EEEEECCHHHHHHH--HHHHHHCCCCCCCCEEEEECC
Q ss_conf 7984--89980985899999--999997588778718999718
Q gi|255764496|r 462 SWPD--VVILDGGKGQLSAA--QGVLKKLNVENRITIISIAKG 500 (616)
Q Consensus 462 ~~PD--LilIDGGkgQln~a--~~vl~~l~i~~~i~viglaK~ 500 (616)
+|| -||+=|=.-||=.| =.||++|=...-||++-|.|=
T Consensus 479 -~P~~a~lllVGD~DQLPSV~pG~VL~DLi~s~~iP~~~LT~v 520 (769)
T TIGR01448 479 -VPDHARLLLVGDADQLPSVGPGQVLKDLIQSKVIPVTRLTKV 520 (769)
T ss_pred -CCCCCEEEEECCCCCCCCCCCCHHHHHHHHCCCCCEEECCCE
T ss_conf -797777988837688898864408999984688661212111
No 55
>PRK08928 consensus
Probab=96.66 E-value=0.003 Score=43.02 Aligned_cols=135 Identities=22% Similarity=0.252 Sum_probs=72.3
Q ss_pred CCCCEEEEECCHH-----HHHHHHHHH--HHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEE-CCCCHHHHHHHHH
Q ss_conf 7984899809858-----999999999--9758877871899971877676634898179834885-7998999999988
Q gi|255764496|r 462 SWPDVVILDGGKG-----QLSAAQGVL--KKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVL-NMRDPILYFIQRL 533 (616)
Q Consensus 462 ~~PDLilIDGGkg-----Qln~a~~vl--~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l-~~~~~~l~~Lq~i 533 (616)
.+|.+|==.-|+= |..+|-.-| .+=|+++ ||+=+= .| |+- ...|++..|..+.- |-+.--|++|.++
T Consensus 578 ~L~~~i~~~tgRIHTsfnQt~taTGRLSS~~PNLQN-IPiRte-~G--r~i-R~aFva~~g~~l~saDYSQIELRilAhl 652 (861)
T PRK08928 578 SLPKQIDNNTGRVHTTFSQTSTTTGRLSSSNPNLQN-IPIRSE-EG--NKI-RQAFIAEKGYKLISADYSQIELRILAHI 652 (861)
T ss_pred HHHHHHCCCCCEECCCHHHHHHHCCEECCCCCCCCC-CCCCCC-CH--HHH-HEEECCCCCCEEEEECHHHHHHHHHHHH
T ss_conf 888874279985725210454311400036887356-777762-02--141-2403469998899853778899999998
Q ss_pred -HHHHHHHHHHHHH----HHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf -7877887889899----864321477100488879899999999808889899389888862789998999999998
Q gi|255764496|r 534 -RDEAHRFAITTHR----KRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNH 606 (616)
Q Consensus 534 -RDEaHRFAi~~hR----k~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616)
.||+=.=|-.... .--.....-++++|. ...|+++=--.||=+-+ .|.--|++-.||+.+-|+.+.+.
T Consensus 653 S~D~~Li~AF~~~~DIH~~TA~~vf~v~~~~vt--~~~Rr~AK~vNFGiiYG---~s~fgLs~~l~i~~~eA~~~i~~ 725 (861)
T PRK08928 653 ANVDAFKQAFINGDDIHTQTACQIFNLQKHELD--SELRRKAKSINFGIIYG---ISAFGLAKQLNITNSEASEYIKK 725 (861)
T ss_pred HCCHHHHHHHCCCCCHHHHHHHHHHCCCHHHCC--HHHHHHHHHHHHHHHHC---CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 178899998606886668888887389821189--88999999999998875---68888998829899999999999
No 56
>PRK07625 consensus
Probab=96.62 E-value=0.0028 Score=43.16 Aligned_cols=137 Identities=23% Similarity=0.260 Sum_probs=70.3
Q ss_pred CCCEEEEECCHHHHH-----HHHHHH--HHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCC-HHHHHHHHH-
Q ss_conf 984899809858999-----999999--97588778718999718776766348981798348857998-999999988-
Q gi|255764496|r 463 WPDVVILDGGKGQLS-----AAQGVL--KKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRD-PILYFIQRL- 533 (616)
Q Consensus 463 ~PDLilIDGGkgQln-----~a~~vl--~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~-~~l~~Lq~i- 533 (616)
+|.+|=-|.|+=|=+ +|-.-| .+=|+.+ ||+=+=- |.+ - ...|++..|..+.-...| --|++|.++
T Consensus 638 l~~~i~~~~gRiHt~f~Q~~t~TGRlSS~~PNLQN-IPir~~~-G~~--i-R~aFi~~~g~~l~~aDYSQiELRilAh~s 712 (922)
T PRK07625 638 LPRMVNPDTGRVHTNYAQAVAVTGRLASNDPNLQN-IPVRTEE-GRR--I-REAFIAPPGSKIVSADYSQIELRIMAHIS 712 (922)
T ss_pred HHHHCCCCCCEECCCHHEEECCCCCCCCCCCCCCC-CCCCCCC-CCH--H-HEEEECCCCCEEEEECHHHHHHHHHHHHH
T ss_conf 88850888787766200210233543579986336-8877622-401--3-34473189988998155388999999995
Q ss_pred HHHHHHHHHHH----HHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 78778878898----99864321477100488879899999999808889899389888862789998999999998547
Q gi|255764496|r 534 RDEAHRFAITT----HRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 534 RDEaHRFAi~~----hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
.|++=-=|-.. |+.--.....-+.++|. ...|+++=--.||=+ ...|.--|++-.||+.+-|+.+.+.+..
T Consensus 713 ~d~~l~~af~~~~DiH~~tA~~vf~v~~~~v~--~~~R~~AK~vnfgii---YG~s~~gLa~~l~i~~~eA~~~i~~yf~ 787 (922)
T PRK07625 713 GDESLLRAFAHGEDIHRATAAEVFGVTPLEVT--SDQRRIAKVINFGLI---YGMSAFGLASNLGITRDAAKLYIDRYFA 787 (922)
T ss_pred CCHHHHHHHHCCCCCCCCCHHHHHCCCHHHCC--HHHHHHHHEEEEHHH---HCCCHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf 78879999865998542426999698957689--999865170200236---5578677998719999999999999998
No 57
>PRK05929 consensus
Probab=96.60 E-value=0.002 Score=44.21 Aligned_cols=136 Identities=22% Similarity=0.288 Sum_probs=64.9
Q ss_pred CCCCEEEEECCHHH-----HHHHHHHH--HHCCCCCCCCEEEEECCCCCCCCCEEE-ECCCCCEE-EECCCCHHHHHHHH
Q ss_conf 79848998098589-----99999999--975887787189997187767663489-81798348-85799899999998
Q gi|255764496|r 462 SWPDVVILDGGKGQ-----LSAAQGVL--KKLNVENRITIISIAKGPKRSAGMEKF-FVKKGEAL-VLNMRDPILYFIQR 532 (616)
Q Consensus 462 ~~PDLilIDGGkgQ-----ln~a~~vl--~~l~i~~~i~viglaK~~~r~~~~e~~-~~~~~~~i-~l~~~~~~l~~Lq~ 532 (616)
.+|.+|=-+-|+=| ..+|-.-| .+=|+.+ ||+=+ .-|.+ -. ..| ++..|..+ .-|-+.--|++|.|
T Consensus 586 ~L~~~i~~~tgRIHTsfnQt~TaTGRLSSs~PNLQN-IPiRt-e~Gr~--IR-~aF~~~~~g~~llsaDYSQIELRilAH 660 (870)
T PRK05929 586 ALPKQIDSHTQRIHPTFNQVGTVTGRLACQDPNLQN-IPIRS-ERGRL--LR-KAFRLTKKNDYFLSADYSQIELRFLAH 660 (870)
T ss_pred HHHHHHCCCCCEECCEEECCCCCCCCCCCCCCCCCC-CCCCC-CCCHH--HH-HHEEECCCCCEEEEECHHHHHHHHHHH
T ss_conf 755422567687776233110111322468997653-67754-11156--78-751328999779961266889999999
Q ss_pred H-HHHHHHHHHH----HHHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 8-7877887889----8998643214771004888798999999998088898993898888627899989999999985
Q gi|255764496|r 533 L-RDEAHRFAIT----THRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 533 i-RDEaHRFAi~----~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
+ .|++=-=|-. -|+.--.....-++++|. ...|+++=--.||=+- ..|.--|++-.||+.+-|+.+.+..
T Consensus 661 lS~D~~Li~AF~~g~DIH~~tA~~if~v~~~~Vt--~~~Rr~AK~vNFGiiY---G~s~fgLa~~L~is~~eA~~~i~~Y 735 (870)
T PRK05929 661 LSQDESLKRAFESGEDIHAFTASQVFHVPLEQVT--KQQRMQAKTVNFGIVY---GQQAYGLSKILKISVSEAQGLIDAY 735 (870)
T ss_pred HHCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHCC--HHHHHHHHHHHHHHHH---CCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 8367868987505620766526988489812169--8789886883545675---6587889988498999999999999
No 58
>PRK11617 endonuclease V; Provisional
Probab=96.58 E-value=0.0061 Score=40.76 Aligned_cols=109 Identities=18% Similarity=0.167 Sum_probs=63.6
Q ss_pred HHHCCCCCCCEEEEEECCCCCC-CCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHH--HHHHHHHHCCCC
Q ss_conf 7515664351699970744377-5404888885168728032321102444455411689989999--999977531311
Q gi|255764496|r 371 KKFALPHIPKRIEIYDNSHIMG-CSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVL--ERRFSQLIKNEE 447 (616)
Q Consensus 371 ~~L~L~~~p~rIE~fDiSh~~G-~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi--~RR~~r~~~~~~ 447 (616)
+.++++ .|+.|-+.|+|...+ ...+|++||++-....-= |..+-....+.-..--|-|.||+- -.-+.++
T Consensus 21 d~~~~~-~~~~VaGvDvSf~~~~~~~~Aa~Vvl~~p~l~vv-~~~~~~~~~~fPYIPG~LaFRE~p~ll~a~~~L----- 93 (223)
T PRK11617 21 DRLDKD-PPDLIAGADVGFEQGGEVTRAAMVLLKYPSLELV-EYQVARIATTMPYIPGFLSFREYPALLAAWEQL----- 93 (223)
T ss_pred CCCCCC-CCCEEEEEEEEEECCCCEEEEEEEEEECCCCEEE-EEEEEEEECCCCCCCCHHHHCCHHHHHHHHHHC-----
T ss_conf 789988-7638999988685699779999999988993699-999999743688566146560349999999962-----
Q ss_pred CCCCCCCCCCCCCCCCCCEEEEEC-CHHHHHHHHHHHHHCCCCCCCCEEEEECC
Q ss_conf 123333333345457984899809-85899999999997588778718999718
Q gi|255764496|r 448 NLNFHPKKQEYSFPSWPDVVILDG-GKGQLSAAQGVLKKLNVENRITIISIAKG 500 (616)
Q Consensus 448 ~l~~~~~~~~~~~~~~PDLilIDG-GkgQln~a~~vl~~l~i~~~i~viglaK~ 500 (616)
...|||+++|| |..|=.-+ ..-.-+|+..++|-||+||.
T Consensus 94 -------------~~~PDvllvDG~Gi~HPRr~-GlAsHlGV~l~~PTIGVAK~ 133 (223)
T PRK11617 94 -------------SQKPDLVFVDGHGISHPRRL-GVASHFGLLVDVPTIGVAKK 133 (223)
T ss_pred -------------CCCCCEEEECCCCCCCCCCC-CHHHEEEEECCCCCCCCCCC
T ss_conf -------------77999999879754376241-61202455428783230053
No 59
>PRK08076 consensus
Probab=96.56 E-value=0.0041 Score=42.02 Aligned_cols=137 Identities=23% Similarity=0.249 Sum_probs=68.4
Q ss_pred CCCCEEEEECCHHHHH-----HHHHHH--HHCCCCCCCCEEEEECCCCCCCCCEEEECC-CCCEE-EECCCCHHHHHHHH
Q ss_conf 7984899809858999-----999999--975887787189997187767663489817-98348-85799899999998
Q gi|255764496|r 462 SWPDVVILDGGKGQLS-----AAQGVL--KKLNVENRITIISIAKGPKRSAGMEKFFVK-KGEAL-VLNMRDPILYFIQR 532 (616)
Q Consensus 462 ~~PDLilIDGGkgQln-----~a~~vl--~~l~i~~~i~viglaK~~~r~~~~e~~~~~-~~~~i-~l~~~~~~l~~Lq~ 532 (616)
++|.+|-=|-|+-|=+ +|-.-| .+=|+++ ||+=+= .|.+ - .+.|++. .|..+ ..|-+.--|++|.+
T Consensus 591 ~L~~~i~~~tgRiHt~fnQ~~t~TGRLSS~~PNLQN-IPirt~-~G~~--I-R~aFi~~~~g~~l~saDYSQIELRilAh 665 (877)
T PRK08076 591 GLLKVVHKDTHKVHTRFNQALTQTGRLSSTDPNLQN-IPIRLE-EGRK--I-RQAFVPSEEGWIMFAADYSQIELRVLAH 665 (877)
T ss_pred HHHHHHCCCCCEEECCCCHHCCCCCCCCCCCCCCCC-CCCCCH-HHHH--H-HHEEEECCCCCEEEEECHHHHHHHHHHH
T ss_conf 988741877545630100000455640257875236-777764-4577--8-7614307999679983266889999999
Q ss_pred H-HHHHHHHHHH----HHHHHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 8-7877887889----8998643214771004888798999999998088898993898888627899989999999985
Q gi|255764496|r 533 L-RDEAHRFAIT----THRKRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 533 i-RDEaHRFAi~----~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
+ .|++=-=|-. .|..--.....-++++|. -.-|+++=--.||=+ ...|.--|++-.||+.+-|+.+.+..
T Consensus 666 ~s~d~~l~~af~~~~DiH~~tA~~if~~~~~~vt--~~~R~~AK~infGii---YG~~~~gLs~~l~i~~~eA~~~i~~Y 740 (877)
T PRK08076 666 IAEDENLIEAFQHDMDIHTKTAMDVFHVEKDEVT--SNMRRQAKAVNFGIV---YGISDYGLSQNLGITRKEAAEFIERY 740 (877)
T ss_pred HHCCHHHHHHHHCCCCHHHHHHHHHHCCCCCCCC--HHHHHHHHHHHHHHH---HCCCHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 8278999998715975758888998489801089--999999889887787---65587889986298999999999999
Q ss_pred C
Q ss_conf 4
Q gi|255764496|r 608 H 608 (616)
Q Consensus 608 ~ 608 (616)
.
T Consensus 741 f 741 (877)
T PRK08076 741 F 741 (877)
T ss_pred H
T ss_conf 9
No 60
>PRK07898 consensus
Probab=96.56 E-value=0.0032 Score=42.74 Aligned_cols=136 Identities=23% Similarity=0.266 Sum_probs=73.5
Q ss_pred CCCCCEEEEECCHHHHHHHHHH-----H--HHCCCCCCCCEEEEECCCCCCCCCEEEECCCCC-EE-EECCCCHHHHHHH
Q ss_conf 5798489980985899999999-----9--975887787189997187767663489817983-48-8579989999999
Q gi|255764496|r 461 PSWPDVVILDGGKGQLSAAQGV-----L--KKLNVENRITIISIAKGPKRSAGMEKFFVKKGE-AL-VLNMRDPILYFIQ 531 (616)
Q Consensus 461 ~~~PDLilIDGGkgQln~a~~v-----l--~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~-~i-~l~~~~~~l~~Lq 531 (616)
..+|.+|--| |+=|=+.-+.+ | .+=|+.+ ||+=+= -|.+ - ...|++..|. .+ ..|-+.--|++|.
T Consensus 615 d~L~~~i~~~-gRIHtsfnQ~~T~TGRLSS~~PNLQN-IPir~~-~G~~--i-R~aFv~~~g~~~~~saDYSQiELRilA 688 (902)
T PRK07898 615 DGLIKAVADD-GRIHTTFNQTVAATGRLSSTDPNLQN-IPIRTE-AGRR--I-RDAFVVGEGYETLLTADYSQIEMRIMA 688 (902)
T ss_pred HHHHHHHCCC-CCCCCHHHHHHCCCCEECCCCCCCCC-CCCCCC-CHHH--H-HHEEECCCCCCEEEECCHHHHHHHHHH
T ss_conf 8889872657-72301265421211200258997667-777661-0155--6-760435899846774041367999999
Q ss_pred HH-HHHHHHHHHHHHHHH------HHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHH
Q ss_conf 88-787788788989986------43214771004888798999999998088898993898888627899989999999
Q gi|255764496|r 532 RL-RDEAHRFAITTHRKR------RKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIY 604 (616)
Q Consensus 532 ~i-RDEaHRFAi~~hRk~------r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~ 604 (616)
++ .||+= --.|.... -.....-+.++|. ...|+++=--.||- |...|.--|++-.||+.+-|+.+.
T Consensus 689 h~s~d~~l--~~af~~~~DiH~~tA~~if~v~~~~vt--~~~R~~AK~vNfgi---iYG~~~~gLs~~l~i~~~eA~~~i 761 (902)
T PRK07898 689 HLSGDEGL--IEAFNSGEDLHSFVASRVFGVPIDEVT--PELRRRVKAMSYGL---AYGLSAYGLSQQLKISTEEAKELM 761 (902)
T ss_pred HHCCCHHH--HHHHHCCCCHHHHHHHHHHCCCHHHCC--HHHHHHHHHHHHHH---HHCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 98088999--999844998889999998499925489--99998988877477---667588899987298999999999
Q ss_pred HHHCC
Q ss_conf 98547
Q gi|255764496|r 605 NHFHK 609 (616)
Q Consensus 605 ~~l~~ 609 (616)
+.+..
T Consensus 762 ~~yf~ 766 (902)
T PRK07898 762 DAYFA 766 (902)
T ss_pred HHHHH
T ss_conf 99998
No 61
>KOG0442 consensus
Probab=96.55 E-value=0.0044 Score=41.78 Aligned_cols=58 Identities=24% Similarity=0.377 Sum_probs=53.0
Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCC
Q ss_conf 71004888798999999998088898993898888627899989999999985478678
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSH 613 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~ 613 (616)
-.|..+|||-.+.-..+..+|+|++.+.+.|.++|+...|. ...|+.||+|||..-.+
T Consensus 821 ~fll~lPgVs~~n~~~l~~k~ks~~~La~sS~~el~el~~~-~~~a~~LYdFi~~~~~~ 878 (892)
T KOG0442 821 DFLLSLPGVSYINYRNLRHKFKSLKELANSSQEELSELLGV-HENAKLLYDFIHTEFAD 878 (892)
T ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCC-HHHHHHHHHHHHHHHHH
T ss_conf 88751898008889999998667999986739999999665-67799999999885143
No 62
>cd04657 Piwi_ago-like Piwi_ago-like: PIWI domain, Argonaute-like subfamily. Argonaute is the central component of the RNA-induced silencing complex (RISC) and related complexes. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing.
Probab=96.53 E-value=0.065 Score=33.35 Aligned_cols=114 Identities=22% Similarity=0.298 Sum_probs=61.3
Q ss_pred CCCCEEEEEECCCCC-C----CCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHH-HHHHHHHHHHHHHHCCCCCCC
Q ss_conf 435169997074437-7----5404888885168728032321102444455411689-989999999977531311123
Q gi|255764496|r 377 HIPKRIEIYDNSHIM-G----CSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCA-MMRMVLERRFSQLIKNEENLN 450 (616)
Q Consensus 377 ~~p~rIE~fDiSh~~-G----~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~-~m~Evi~RR~~r~~~~~~~l~ 450 (616)
..|--|-|+|++|-+ | .-.||++|.=-|..+ -..+-.+.+.....+-.+|.. +|.+.|...++ .
T Consensus 196 ~~~tMiiG~Dv~H~~~~~~~~~pSv~a~V~S~d~~~-~~y~~~~~~q~~~~e~i~~l~~~~~~~l~~~~~----~----- 265 (426)
T cd04657 196 KEPTMVLGADVTHPSPGDPAGAPSIAAVVASVDWHL-AQYPASVRLQSHRQEIIDDLESMVRELLRAFKK----A----- 265 (426)
T ss_pred CCCEEEEEEEEECCCCCCCCCCCEEEEEEEEECCCC-CEEEEEEEECCCCCEEHHHHHHHHHHHHHHHHH----H-----
T ss_conf 898799998604689888889962999999807997-768679998489868688899999999999999----7-----
Q ss_pred CCCCCCCCCCCCCCCEEEE--EC-CHHHHHHH--------HHHHHHCCCC--CCCCEEEEECCCCCCCCCEEEECCC
Q ss_conf 3333333454579848998--09-85899999--------9999975887--7871899971877676634898179
Q gi|255764496|r 451 FHPKKQEYSFPSWPDVVIL--DG-GKGQLSAA--------QGVLKKLNVE--NRITIISIAKGPKRSAGMEKFFVKK 514 (616)
Q Consensus 451 ~~~~~~~~~~~~~PDLilI--DG-GkgQln~a--------~~vl~~l~i~--~~i~viglaK~~~r~~~~e~~~~~~ 514 (616)
.+.+|+-||| || |.||+..+ ++++.+++-. -+|.+|-+.|..+ -++|+.+
T Consensus 266 ---------n~~~P~~IiiyRDGVsegq~~~v~~~Ev~~i~~a~~~~~~~~~pkit~ivv~Krh~-----~Rff~~~ 328 (426)
T cd04657 266 ---------TGKLPERIIYYRDGVSEGQFAQVLNEELPAIRKACAKLYPGYKPKITFIVVQKRHH-----TRFFPTD 328 (426)
T ss_pred ---------CCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECEE-----EEECCCC
T ss_conf ---------29998606898267780668999999999999999985578898679999820111-----2440367
No 63
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=96.42 E-value=0.0051 Score=41.32 Aligned_cols=62 Identities=23% Similarity=0.340 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHHHCC---C-CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 88788989986432147---7-100488879899999999808889899389888862789998999999998
Q gi|255764496|r 538 HRFAITTHRKRRKKAAY---S-PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNH 606 (616)
Q Consensus 538 HRFAi~~hRk~r~k~~~---S-~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616)
.+|.++-++-.--+++. | -+-.||||||||..+||+.|||+++|.++- + ++ +.++++++-++
T Consensus 162 ~~~gv~p~q~~d~~aL~GD~sDnIpGV~GiG~KtA~kLl~~~gsle~i~~~~-~---~~---~~k~~~~l~~~ 227 (240)
T cd00008 162 EKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENL-D---KI---KGKLREKLEEG 227 (240)
T ss_pred HHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHH-H---HC---CHHHHHHHHHC
T ss_conf 9609899999876997287646889999857899999999809999999829-8---52---78999999968
No 64
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=96.40 E-value=0.014 Score=38.22 Aligned_cols=22 Identities=14% Similarity=0.138 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3338888889999999986221
Q gi|255764496|r 212 KEDYESAIIHRDRLAALSHIQN 233 (616)
Q Consensus 212 ~l~FE~Aa~~RD~I~aL~~i~~ 233 (616)
..++=++.-||--+.+|+.+..
T Consensus 21 Gen~~k~~ay~~Aa~~i~~l~~ 42 (334)
T smart00483 21 GENKRKCSYFRKAASVLKSLPF 42 (334)
T ss_pred CCCHHHHHHHHHHHHHHHHCCC
T ss_conf 9977789999999999985983
No 65
>PRK00024 radC DNA repair protein RadC; Reviewed
Probab=96.29 E-value=0.0089 Score=39.57 Aligned_cols=44 Identities=5% Similarity=-0.118 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCCC
Q ss_conf 389999999875156643516999707443775404888885168728
Q gi|255764496|r 361 SHQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFV 408 (616)
Q Consensus 361 ~~~~~l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~ 408 (616)
+...+++-++..|.- ...|+|=+-.+.+.+.|-++.+-..|..+
T Consensus 105 s~~~v~~~~~~~l~~----~~~E~f~vl~Ld~~n~li~~~~i~~Gt~~ 148 (224)
T PRK00024 105 SPEDVADYLQAELRD----EEQEVFVVLFLDTKNRLIADEELFIGTLN 148 (224)
T ss_pred CHHHHHHHHHHHHCC----CCCCEEEEEEECCCCCEEEEEEEECCCCC
T ss_conf 999999999998656----67867999998787775568997047886
No 66
>PRK08609 hypothetical protein; Provisional
Probab=96.13 E-value=0.017 Score=37.56 Aligned_cols=19 Identities=11% Similarity=0.169 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHHHHCC
Q ss_conf 6899899999999775313
Q gi|255764496|r 427 DCAMMRMVLERRFSQLIKN 445 (616)
Q Consensus 427 D~~~m~Evi~RR~~r~~~~ 445 (616)
-|.+.++..++|+-+.+++
T Consensus 439 ~~~~~~~~~t~r~~~Ai~n 457 (570)
T PRK08609 439 SFSQSEEEIMKRLETACRN 457 (570)
T ss_pred CCCCCHHHHHHHHHHHHHC
T ss_conf 4579889999999999718
No 67
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=96.07 E-value=0.0078 Score=39.99 Aligned_cols=50 Identities=28% Similarity=0.565 Sum_probs=34.5
Q ss_pred CHHCCCCCCHHHHHHHHH-HHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 100488879899999999-80888989938988886278999899999999
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQ-SFGTVKMISRSSPETLASIEGISKKIACKIYN 605 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~-~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~ 605 (616)
.|.+|.|||+.+...|-. -|.|++.++.|+..+|+.|.||+-.+|-.|..
T Consensus 11 ~l~disgvg~~~a~~l~~ag~e~~~d~~~a~q~~l~~~~gignalaarika 61 (238)
T PRK12766 11 ELTDISGVGPSKAESLREAGFESVEDVRAADQSELADVDGIGNALAARIKA 61 (238)
T ss_pred HHHCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 764123668003678887040128989764277664201313899998741
No 68
>TIGR00608 radc DNA repair protein RadC; InterPro: IPR001405 RadC is a DNA repair protein found in many bacteria. They share a region of similarity at the C-terminus that contains two perfectly conserved histidine residues.; GO: 0006281 DNA repair.
Probab=95.74 E-value=0.012 Score=38.64 Aligned_cols=38 Identities=29% Similarity=0.547 Sum_probs=34.2
Q ss_pred HHHHHHHHC-----CHHHHHHCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 999999808-----88989938988886278999899999999
Q gi|255764496|r 568 KRLLLQSFG-----TVKMISRSSPETLASIEGISKKIACKIYN 605 (616)
Q Consensus 568 ~~~Ll~~Fg-----s~~~i~~As~eeL~~v~gi~~~~A~~I~~ 605 (616)
-+.||++|| ++..+++|+.++|++|+|||...|.+|.-
T Consensus 39 sk~lL~~fG~~~~d~l~~L~~~~~~~L~~v~GiG~ak~~qlka 81 (223)
T TIGR00608 39 SKELLKQFGQEELDSLDLLLSAEPEELSSVPGIGLAKAIQLKA 81 (223)
T ss_pred HHHHHHHHCHHCCCCHHHHHCCCHHHHHCCCCCHHHHHHHHHH
T ss_conf 9999987070001300143215857850468850889999999
No 69
>PRK01216 DNA polymerase IV; Validated
Probab=95.70 E-value=0.032 Score=35.54 Aligned_cols=12 Identities=17% Similarity=0.116 Sum_probs=5.3
Q ss_pred HHHHHHHHHHHH
Q ss_conf 888889999999
Q gi|255764496|r 216 ESAIIHRDRLAA 227 (616)
Q Consensus 216 E~Aa~~RD~I~a 227 (616)
|-|..+|+.|..
T Consensus 123 ~~a~~ir~~I~~ 134 (351)
T PRK01216 123 ELARKIKNEILE 134 (351)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999999
No 70
>pfam09517 RE_Eco29kI Eco29kI restriction endonuclease. This family includes the Eco29kI (recognizes and cleaves CCGC^GG ) restriction endonuclease.
Probab=95.48 E-value=0.0088 Score=39.59 Aligned_cols=61 Identities=30% Similarity=0.435 Sum_probs=37.0
Q ss_pred CCCCCEEEEEECHH-----------------HHHHHHHHCCCCCCCHHHHHHHHHCC-----C--EEEEECCCHHHHHH-
Q ss_conf 69988889960125-----------------87888761378877879999997344-----4--29998287199999-
Q gi|255764496|r 17 DIAGRVLYVGKAYN-----------------LQKRIKSYMHSNNHTHRITHMISQIN-----N--IRFTVTCTEVEALL- 71 (616)
Q Consensus 17 ~~~~~iiYvGKakn-----------------L~~Rv~syf~~~~~~~k~~~l~~~~~-----~--ie~~~t~~e~eAli- 71 (616)
...+.+||||||.- |-+|++-|.. =+..+. | .-|.|+....++.|
T Consensus 30 ~~~~~PIYVGKAvp~g~R~g~~~~~~~~g~~L~~Rl~EH~~----------SI~~~~~Ldi~DF~cR~lv~~~~~~~wI~ 99 (170)
T pfam09517 30 LSYTQPIYVGKAVPKGWRQGRGSDNAPPGNELFNRLREHAR----------SIAQVSDLDLEDFMCRFVIFELHGSDWIP 99 (170)
T ss_pred CCCCCCEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH----------HHHHHCCCCHHHEEEEEEEEECCCCCCHH
T ss_conf 36678817722468766557777787620999999999999----------88875289843627899997547664112
Q ss_pred -HHHHHHHHHCCCCEEC
Q ss_conf -9998877618720033
Q gi|255764496|r 72 -LEANMIKRLKPRFNIL 87 (616)
Q Consensus 72 -lE~~lIk~~~P~yNi~ 87 (616)
-|+-||++|+|-.|..
T Consensus 100 l~Ea~LI~~~~P~WN~~ 116 (170)
T pfam09517 100 LIEAALIKLFKPLWNTV 116 (170)
T ss_pred HHHHHHHHHHHHHHHHH
T ss_conf 68999999852777630
No 71
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=95.43 E-value=0.014 Score=38.09 Aligned_cols=51 Identities=24% Similarity=0.354 Sum_probs=40.3
Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 71004888798999999998088898993898888627899989999999985
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
..|..+||||+++.++++.+=-.-. .=.|+++|.+|+|||+++-+++..++
T Consensus 97 eeL~~lpgIG~~kA~aIi~yRe~~G--~f~sv~dL~~v~GiG~~~~ekl~~~i 147 (149)
T COG1555 97 EELQALPGIGPKKAQAIIDYREENG--PFKSVDDLAKVKGIGPKTLEKLKDYI 147 (149)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHHCC--CCCCHHHHCCCCCCCHHHHHHHHHHC
T ss_conf 9998867989999999999999739--97657887107777899999877561
No 72
>TIGR00426 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region; InterPro: IPR004509 This domain is found in competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This domain represents a region of two tandem copies of a helix-hairpin-helix domain, each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to this domain..
Probab=95.42 E-value=0.011 Score=38.88 Aligned_cols=51 Identities=24% Similarity=0.437 Sum_probs=42.5
Q ss_pred HCCCCHHC-CCCCCHHHHHHHHHH---HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 14771004-888798999999998---088898993898888627899989999999985
Q gi|255764496|r 552 AAYSPLDE-INGIGPLRKRLLLQS---FGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 552 ~~~S~Ld~-I~GIG~k~~~~Ll~~---Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
++.++|.. +.|||+++.+++..| +|.++ ++|+|.+|+||++++-+++...+
T Consensus 14 AtaeElq~~~~GvG~kKAeAIv~YREe~G~F~-----t~Edl~~V~GiG~~~~Ek~~~~i 68 (70)
T TIGR00426 14 ATAEELQKALSGVGAKKAEAIVAYREEYGRFK-----TVEDLKKVSGIGEKLLEKNKASI 68 (70)
T ss_pred HCHHHHHHHHCCCCHHHHHHHHHHHHCCCCCC-----CHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 04788887642887237899988753277957-----62223214787624555564430
No 73
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=95.41 E-value=0.068 Score=33.19 Aligned_cols=19 Identities=16% Similarity=0.029 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 3888888999999998622
Q gi|255764496|r 214 DYESAIIHRDRLAALSHIQ 232 (616)
Q Consensus 214 ~FE~Aa~~RD~I~aL~~i~ 232 (616)
|-=++.-||--+.+|+.+.
T Consensus 20 n~fr~rAY~~Aa~~l~~~~ 38 (307)
T cd00141 20 NPFRVRAYRKAARALESLP 38 (307)
T ss_pred CCHHHHHHHHHHHHHHHCC
T ss_conf 8266999999999998699
No 74
>pfam00633 HHH Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Probab=95.22 E-value=0.0084 Score=39.73 Aligned_cols=30 Identities=23% Similarity=0.301 Sum_probs=26.4
Q ss_pred CHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 889899389888862789998999999998
Q gi|255764496|r 577 TVKMISRSSPETLASIEGISKKIACKIYNH 606 (616)
Q Consensus 577 s~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616)
+++++..||.+||.++||||+++|+.|+.+
T Consensus 1 ~~~~~~~as~eeL~~lpGVG~~tA~~I~~~ 30 (30)
T pfam00633 1 SLEGLIPASREELLALPGVGPKTAEAILSY 30 (30)
T ss_pred CCCCCCCCCHHHHHHCCCCCHHHHHHHHCC
T ss_conf 964435235999972889776889988539
No 75
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=95.15 E-value=0.02 Score=36.97 Aligned_cols=30 Identities=23% Similarity=0.490 Sum_probs=27.4
Q ss_pred CHHCCCCCCHHHHHHHHHHHCCHHHHHHCC
Q ss_conf 100488879899999999808889899389
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFGTVKMISRSS 585 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As 585 (616)
-+-.|||||+||..+|++.|||+++|..+-
T Consensus 23 nipGV~GIG~ktA~~ll~~~~~l~~i~~~~ 52 (75)
T cd00080 23 NIPGVPGIGPKTALKLLKEYGSLENLLENL 52 (75)
T ss_pred CCCCCCCCCHHHHHHHHHHCCCHHHHHHHH
T ss_conf 887758637999999999909999999838
No 76
>PTZ00217 flap endonuclease-1; Provisional
Probab=95.15 E-value=0.034 Score=35.38 Aligned_cols=50 Identities=24% Similarity=0.367 Sum_probs=29.6
Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCC-CCHHHHHHHH
Q ss_conf 7100488879899999999808889899389888862789-9989999999
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEG-ISKKIACKIY 604 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~g-i~~~~A~~I~ 604 (616)
.-++.|+||||+|.-+|++.|||+++|...-...-..+|. .+-.-|..+|
T Consensus 235 DY~~~I~GIGpk~A~klIk~~~sie~il~~~~~~k~~~p~~~~~~~~r~~F 285 (394)
T PTZ00217 235 DYCDTIEGIGPKTAYELIKKYGSIEEILEHLDGTKYPVPENFPYKEARELF 285 (394)
T ss_pred CCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCCHHHHHHHH
T ss_conf 446899874889999999995999999987412467799879979999996
No 77
>PRK03352 DNA polymerase IV; Validated
Probab=95.07 E-value=0.072 Score=33.04 Aligned_cols=14 Identities=21% Similarity=-0.118 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 88888899999999
Q gi|255764496|r 215 YESAIIHRDRLAAL 228 (616)
Q Consensus 215 FE~Aa~~RD~I~aL 228 (616)
.+-|..+|+.|..-
T Consensus 121 ~~~a~~ir~~I~~~ 134 (345)
T PRK03352 121 EEVAEEIRAVVLEE 134 (345)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 99999999999998
No 78
>KOG4417 consensus
Probab=94.96 E-value=0.037 Score=35.07 Aligned_cols=117 Identities=20% Similarity=0.211 Sum_probs=60.3
Q ss_pred CCCCCCEEEEEECCCCCC-CCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHH--HHHHHHHHHCCCCCCCC
Q ss_conf 664351699970744377-540488888516872803232110244445541168998999--99999775313111233
Q gi|255764496|r 375 LPHIPKRIEIYDNSHIMG-CSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMV--LERRFSQLIKNEENLNF 451 (616)
Q Consensus 375 L~~~p~rIE~fDiSh~~G-~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Ev--i~RR~~r~~~~~~~l~~ 451 (616)
|+.+ +-+-+.|+|.--- +..+.+|+||.+-.--+--|.-|-++-..+...--|-+.||+ +---++++..|.-+.
T Consensus 38 L~ei-kyV~GiD~Sf~K~~S~~a~~~lv~~~lp~l~~v~~d~~~~~Le~pYvPgfLafREa~v~l~~L~~v~~erh~f-- 114 (261)
T KOG4417 38 LDEI-KYVAGIDTSFAKLNSDMAYISLVFWTLPDLKHVATDSDTRMLELPYVPGFLAFREAEVMLDFLKSVITERHEF-- 114 (261)
T ss_pred HHHE-EEEEEECCCHHHCCCCCEEEEEEEEECCCCEEEEEHHHHHHHCCCCCCCCEEEEHHHHHHHHHHHCCCCCCCC--
T ss_conf 0120-4664200102102798158999998633004642122466624676753102104589999998532235776--
Q ss_pred CCCCCCCCCCCCCCEEEEECCHHHHHH-HHHHHHHCCCCCCCCEEEEECCCCCCCC
Q ss_conf 333333454579848998098589999-9999997588778718999718776766
Q gi|255764496|r 452 HPKKQEYSFPSWPDVVILDGGKGQLSA-AQGVLKKLNVENRITIISIAKGPKRSAG 506 (616)
Q Consensus 452 ~~~~~~~~~~~~PDLilIDGGkgQln~-a~~vl~~l~i~~~i~viglaK~~~r~~~ 506 (616)
.||+|++||- |-+.- .-..-.-+|.-..+|.||+||+-.|..|
T Consensus 115 -----------r~dvilvDGn-G~lHprGfGlACHlGvL~~lp~iGVaKNlhH~~g 158 (261)
T KOG4417 115 -----------RPDVILVDGN-GELHPRGFGLACHLGVLSGLPSIGVAKNLHHTYG 158 (261)
T ss_pred -----------CCCEEEECCC-CEECCCCCCHHHHHHHHCCCCCCCHHCCHHHHHH
T ss_conf -----------6628998688-5474665443124567618972011000243430
No 79
>PRK02406 DNA polymerase IV; Validated
Probab=94.85 E-value=0.089 Score=32.36 Aligned_cols=25 Identities=8% Similarity=0.131 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 9999999999758877871899971
Q gi|255764496|r 475 QLSAAQGVLKKLNVENRITIISIAK 499 (616)
Q Consensus 475 Qln~a~~vl~~l~i~~~i~viglaK 499 (616)
=..+|.+.|+++.....|-++|+.=
T Consensus 316 i~~~a~~Ll~~~~~~~~iRliGV~l 340 (355)
T PRK02406 316 LEQLARQLLARRRGGRGVRLLGVGV 340 (355)
T ss_pred HHHHHHHHHHHHHCCCCEEEEEEEE
T ss_conf 9999999997400599778999997
No 80
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=94.77 E-value=0.04 Score=34.86 Aligned_cols=18 Identities=11% Similarity=0.145 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHHHHH
Q ss_conf 888899999999862211
Q gi|255764496|r 217 SAIIHRDRLAALSHIQNH 234 (616)
Q Consensus 217 ~Aa~~RD~I~aL~~i~~~ 234 (616)
++.-||+.=++|+..++.
T Consensus 28 k~~aYr~Aa~sle~~~e~ 45 (326)
T COG1796 28 KIRAYRKAAQSLENLTED 45 (326)
T ss_pred CHHHHHHHHHHHHHCCCC
T ss_conf 167899998755531354
No 81
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. Pol zeta has also been named Rev1; this subfamily is mainly present in eukaryotes.
Probab=94.72 E-value=0.095 Score=32.14 Aligned_cols=11 Identities=18% Similarity=0.139 Sum_probs=4.8
Q ss_pred HHHHHHHHHHH
Q ss_conf 88889999999
Q gi|255764496|r 217 SAIIHRDRLAA 227 (616)
Q Consensus 217 ~Aa~~RD~I~a 227 (616)
-|..+|.+|..
T Consensus 170 ~a~~Ir~~I~~ 180 (405)
T cd01701 170 LAETIRNEIKE 180 (405)
T ss_pred HHHHHHHHHHH
T ss_conf 99999999999
No 82
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=94.71 E-value=0.059 Score=33.65 Aligned_cols=172 Identities=15% Similarity=0.104 Sum_probs=78.9
Q ss_pred EEEEEEEECCCCC--HHHHHHHHCCCCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECC
Q ss_conf 4888885168728--032321102444455-4116899899999999775313111233333333454579848998098
Q gi|255764496|r 396 VGCMVVVGENGFV--KNQYRKFNLHPNDVK-TQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGG 472 (616)
Q Consensus 396 Vas~Vvf~~g~~~--K~~YR~f~Ik~~~v~-~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGG 472 (616)
+-.+|||..+.+. ...|..|+-.- -. .+++|..--..++.-...+...- -.....| .-=+-|+
T Consensus 61 ~~~~~vFD~~~~tfR~~~~~~yK~~R--~~~~p~~l~~q~~~i~~~~~~~~~~~-----------l~~~G~e-add~i~t 126 (310)
T COG0258 61 THPVVVFDGKPPTFRHELLEEYKANR--EKEMPDELAPQIPILTELLVALGIPL-----------LELMGIE-ADDPIET 126 (310)
T ss_pred CCEEEEECCCCCCHHHHHHHHHHHCC--CCCCHHHHHHHHHHHHHHHHHHCCHH-----------HHCCCCC-CCCCCCH
T ss_conf 61799976999622788899998468--95588999998899999999838255-----------3278968-3144408
Q ss_pred HHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCC-EEEE-CCCCHHHHHHHHHHHHHHHHHHHH-----H
Q ss_conf 58999999999975887787189997187767663489817983-4885-799899999998878778878898-----9
Q gi|255764496|r 473 KGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGE-ALVL-NMRDPILYFIQRLRDEAHRFAITT-----H 545 (616)
Q Consensus 473 kgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~-~i~l-~~~~~~l~~Lq~iRDEaHRFAi~~-----h 545 (616)
..|... ..| .++.|+-+++ +.+...... .+.. .+..+.. +.+...+.-.+ .
T Consensus 127 ~A~~a~------~~g-----~~~~I~S~Dk-----D~lql~~~~~~~~~~~~~~~~~------~~~~~~~~e~~~g~~p~ 184 (310)
T COG0258 127 LAQKAY------KKG-----DVVLIISGDK-----DLLQLVSPNVLVINGKKGEPEK------FLDLEEVEEKFKGLTPE 184 (310)
T ss_pred HHHHHH------HCC-----CCEEEEECCC-----CEEEECCCCEEEEECCCCCCCC------CCCHHHHHHHHCCCCHH
T ss_conf 999988------649-----9579997896-----7001148961786257788523------48999999985699989
Q ss_pred HHHHH-HHCC---C-CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 98643-2147---7-1004888798999999998088898993898888627899989999999985
Q gi|255764496|r 546 RKRRK-KAAY---S-PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 546 Rk~r~-k~~~---S-~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
+... ..+. | -+-.|+||||||..+||+.|||++.|...-. .+... ..+.+.+.+...|
T Consensus 185 -qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~-~~~~~--~~~~l~~~~~~af 247 (310)
T COG0258 185 -QLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLD-IIKKK--TREKLLEDKEKAF 247 (310)
T ss_pred -HHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHH-HCCCC--HHHHHHHHHHHHH
T ss_conf -988999982965357899998389999999998385999998775-21220--2566787799986
No 83
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=94.70 E-value=0.063 Score=33.44 Aligned_cols=52 Identities=17% Similarity=0.199 Sum_probs=36.3
Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf 710048887989999999980888989938988886278999899999999854
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFH 608 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~ 608 (616)
.-...||||||+|.-+|++.|||++++..+=......+|..-+ -+.+.++|.
T Consensus 223 Dy~~gi~giG~k~A~kli~~~~~~e~~~~~l~~~~~~~~~~~~--~~~~~~~f~ 274 (316)
T cd00128 223 DYTEGIPGIGPVTALKLIKKYGDIEKDIERLKKKLYRSPEDFP--LKEAREFFL 274 (316)
T ss_pred CCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCC--HHHHHHHHC
T ss_conf 8789999735999999999919999999999834876999999--799999857
No 84
>PRK03980 flap endonuclease-1; Provisional
Probab=94.27 E-value=0.062 Score=33.49 Aligned_cols=33 Identities=21% Similarity=0.351 Sum_probs=28.2
Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHH
Q ss_conf 710048887989999999980888989938988
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPE 587 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~e 587 (616)
.-.+.|+||||+|.-+|++.+||+++|..+--.
T Consensus 189 DY~~gI~gIGpk~Alklikk~~~ie~il~~~~~ 221 (295)
T PRK03980 189 DYNPGVKGIGPKTALKLIKKHGDLEKVLEAVGE 221 (295)
T ss_pred CCCCCCCCCCHHHHHHHHHHHCCHHHHHHHCCC
T ss_conf 899999984299999999996999999986376
No 85
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=94.26 E-value=0.25 Score=29.15 Aligned_cols=175 Identities=17% Similarity=0.130 Sum_probs=89.9
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCC--CCCC--CCCCCCCCCCCCCCEEEEECCHHHH---HHHHHHHHHCCCCCCCCEEEE
Q ss_conf 11689989999999977531311--1233--3333334545798489980985899---999999997588778718999
Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEE--NLNF--HPKKQEYSFPSWPDVVILDGGKGQL---SAAQGVLKKLNVENRITIISI 497 (616)
Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~--~l~~--~~~~~~~~~~~~PDLilIDGGkgQl---n~a~~vl~~l~i~~~i~vigl 497 (616)
.||-.++++++.+-..+...-.- .... .+..........|||||+|=--+.. .... .+.+.+.+ ++||-|
T Consensus 7 VEDD~~v~~~~~~~l~~~~gf~vv~~a~t~~eA~~~l~~~~~~~DLILLDi~mPd~~Glell~-~lR~~~~~--~~VI~I 83 (239)
T PRK10430 7 VDDDAMVAELNRRYVAQIPGFQCCGTASTLEKAKEIIFNSDTPIDLILLDIYMQQENGLDLLP-VLHEAGCK--SDVIVI 83 (239)
T ss_pred EECCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCCCEEEECCCCCCCCHHHHHH-HHHHHCCC--CEEEEE
T ss_conf 929899999999998518990899998999999999965799985899789999997899999-99985899--819999
Q ss_pred ECCCCCCCCCEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-C-CCCHHC---------------C
Q ss_conf 7187767663489817983488579989999999887877887889899864321-4-771004---------------8
Q gi|255764496|r 498 AKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKKA-A-YSPLDE---------------I 560 (616)
Q Consensus 498 aK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~iRDEaHRFAi~~hRk~r~k~-~-~S~Ld~---------------I 560 (616)
.--....+-.+-+-.+--+ ..+.+-+ +.++++--.||+- +++...... + .+.+|. =
T Consensus 84 Ta~~d~~~v~~Al~~Ga~D-YLiKPf~-----~~rl~~~L~~y~~-~~~~l~~~~~~~Q~~iD~l~~~~~~~~~~~~~lP 156 (239)
T PRK10430 84 SSAADAATIKDSLHYGVVD-YLIKPFQ-----ASRFEEALTGWRQ-KKMALEKRQYYDQAELDQLIHGSSSNEQDPRRLP 156 (239)
T ss_pred EECCCHHHHHHHHHCCCHH-HEECCCC-----HHHHHHHHHHHHH-HHHHHCCCCCCCHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 7268899999999839503-0489999-----9999999999999-9998545787899999999850578888766699
Q ss_pred CCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf 88798999999998088898993898888627899989999999985478
Q gi|255764496|r 561 NGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616)
Q Consensus 561 ~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616)
+||.+.|-+++...+....+ ...|.+|++...|||+.+|.+=.+||-..
T Consensus 157 KGl~~~TL~~i~~~l~~~~~-~~~sa~eva~~~giSRvTaRRYLe~L~~~ 205 (239)
T PRK10430 157 KGLTPQTLRTLCQWIDAHQD-YEFSTDELANEVNISRVSCRKYLIWLVNC 205 (239)
T ss_pred CCCCHHHHHHHHHHHHHCCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 99999999999999982799-98469999988585298899999999868
No 86
>PRK01810 DNA polymerase IV; Validated
Probab=94.22 E-value=0.15 Score=30.79 Aligned_cols=75 Identities=13% Similarity=0.180 Sum_probs=34.9
Q ss_pred EECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCC---CCCCCE-EEECCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8098589999999999758877871899971877---676634-898179834885799899999998878778878898
Q gi|255764496|r 469 LDGGKGQLSAAQGVLKKLNVENRITIISIAKGPK---RSAGME-KFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITT 544 (616)
Q Consensus 469 IDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~---r~~~~e-~~~~~~~~~i~l~~~~~~l~~Lq~iRDEaHRFAi~~ 544 (616)
.|=...=+++|.+.|++.--...+.++|+.=..= ...... .+|..+ + -.+...+...+-+|+..=-+.+|..
T Consensus 311 T~d~~~i~~~a~~L~~~~~~~~~~R~~GV~l~~L~~~~~~~~QldLFd~~-~---~~k~~~L~~aiD~In~rfG~~tI~~ 386 (410)
T PRK01810 311 IWEKRDIFQAASRLFKQHWDGDPVRLLGVTATELEWKTEAVKQLDLFSFE-E---DAKEEPLLAVIDQINDKYGTPLLQR 386 (410)
T ss_pred CCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCC-C---HHHHHHHHHHHHHHHHHHCHHHHHH
T ss_conf 58999999999999997507998699999984625487665577888985-2---1669999999999998757349999
Q ss_pred HHH
Q ss_conf 998
Q gi|255764496|r 545 HRK 547 (616)
Q Consensus 545 hRk 547 (616)
-+.
T Consensus 387 a~~ 389 (410)
T PRK01810 387 GSQ 389 (410)
T ss_pred HHC
T ss_conf 864
No 87
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=94.22 E-value=0.097 Score=32.10 Aligned_cols=78 Identities=19% Similarity=0.189 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHH-H-H-HHHHHH--CCC-CHHCCCCCCHHHHHHHHHHH--CCHHHHHHCCHHHHHHCCCCCHHHHHHHH
Q ss_conf 878778878898-9-9-864321--477-10048887989999999980--88898993898888627899989999999
Q gi|255764496|r 533 LRDEAHRFAITT-H-R-KRRKKA--AYS-PLDEINGIGPLRKRLLLQSF--GTVKMISRSSPETLASIEGISKKIACKIY 604 (616)
Q Consensus 533 iRDEaHRFAi~~-h-R-k~r~k~--~~S-~Ld~I~GIG~k~~~~Ll~~F--gs~~~i~~As~eeL~~v~gi~~~~A~~I~ 604 (616)
..||++-+...- + . +...+. ..| .-.+|.|+|+++..+|+..= .++..|...+.++|.+++|.+++.|++++
T Consensus 417 ~~~~~~~~C~N~~~Cpaq~~~~i~hF~Sr~amdI~GlG~~~i~~L~~~g~i~~~~Diy~L~~~~L~~l~gfgeKsa~nLl 496 (668)
T PRK07956 417 EEGEAVLRCTNGLSCPAQLKERLIHFVSRNAMDIDGLGEKIIEQLFEKGLIHTPADLFKLTEEDLLQLEGFGEKSAQNLL 496 (668)
T ss_pred ECCCEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHCCCHHHHHCCCCHHHHHHHHHH
T ss_conf 36963787789989989999988865244531646659999999987687665899972885454021235566999999
Q ss_pred HHHCCC
Q ss_conf 985478
Q gi|255764496|r 605 NHFHKN 610 (616)
Q Consensus 605 ~~l~~~ 610 (616)
+.+.+.
T Consensus 497 ~aIe~S 502 (668)
T PRK07956 497 DAIEKS 502 (668)
T ss_pred HHHHHH
T ss_conf 999985
No 88
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=94.18 E-value=0.12 Score=31.36 Aligned_cols=57 Identities=26% Similarity=0.282 Sum_probs=50.5
Q ss_pred CHHCCCCCCHHHHHHHHHHH--CCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf 10048887989999999980--8889899389888862789998999999998547867
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSF--GTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTS 612 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~F--gs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~ 612 (616)
.=.+|.|+|+++...|+..= .++..|...+.++|.+.+|++++.|+++.+.+.+...
T Consensus 427 ~amdI~GLGek~i~~L~~~gli~~~~Dly~L~~~~L~~l~g~geKsa~nLl~aIe~SK~ 485 (563)
T PRK08097 427 QGLGLDGIGEGTWRALHQTGRFEHLFSWLALTPEQLANTPGIGKARAAQLWHQFNLARQ 485 (563)
T ss_pred CCCCCCCCCHHHHHHHHHCCCCCCHHHHHHCCHHHHHCCCCHHHHHHHHHHHHHHHHCC
T ss_conf 41585676999999999758889979975089999855898578999999999999728
No 89
>PRK03348 DNA polymerase IV; Provisional
Probab=93.96 E-value=0.16 Score=30.46 Aligned_cols=29 Identities=14% Similarity=0.147 Sum_probs=16.6
Q ss_pred CCHHHHHHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 98589999999999758877871899971
Q gi|255764496|r 471 GGKGQLSAAQGVLKKLNVENRITIISIAK 499 (616)
Q Consensus 471 GGkgQln~a~~vl~~l~i~~~i~viglaK 499 (616)
--..=..+|.+.|.+......|-++|+.=
T Consensus 312 ~~~~i~~aA~~Ll~~~~~~~pvRLlGV~~ 340 (456)
T PRK03348 312 DAATLRAAARRLLPDPDEIGPIRLVGVGF 340 (456)
T ss_pred CHHHHHHHHHHHHHHHCCCCCEEEEEEEC
T ss_conf 98999999999997435489757997650
No 90
>PRK02794 DNA polymerase IV; Provisional
Probab=93.91 E-value=0.19 Score=29.99 Aligned_cols=17 Identities=24% Similarity=0.466 Sum_probs=7.5
Q ss_pred CHHHHHHHHHHHHHHHC
Q ss_conf 03566555432345503
Q gi|255764496|r 176 SSEKYMEFVHEAKKFLS 192 (616)
Q Consensus 176 s~~~Y~~~v~~~~~fL~ 192 (616)
..+-|.+.=..+.++|.
T Consensus 107 ~~~~Y~~~S~rv~~il~ 123 (417)
T PRK02794 107 DMEKYVRVGREVRAMMQ 123 (417)
T ss_pred CHHHHHHHHHHHHHHHH
T ss_conf 77999999999999999
No 91
>PRK00329 GIY-YIG nuclease superfamily protein; Validated
Probab=93.90 E-value=0.13 Score=31.22 Aligned_cols=63 Identities=17% Similarity=0.221 Sum_probs=42.3
Q ss_pred EEEEECCCCCEEEEEECHHHHHHHHHHCCCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHHH
Q ss_conf 258886998888996012587888761378877879999997344429998287199999999887
Q gi|255764496|r 12 VYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANMI 77 (616)
Q Consensus 12 vY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~lI 77 (616)
||+....+|. +|||-+.||..|+.+|-.+.. .|..+--.-..=+=+....+-.+|+-+|..+=
T Consensus 9 vYiL~~~dg~-lY~G~T~dl~rRl~~Hn~G~g--ak~Tr~~~p~~Lv~~e~~~~~~~A~~~E~~iK 71 (86)
T PRK00329 9 LYLLRCADGS-LYAGITTDVERRFAQHQSGKG--AKYTRGRPPLTLVYVEPVGDRSEALRAEYRFK 71 (86)
T ss_pred EEEEECCCCC-EEEEECCCHHHHHHHHHCCCC--CCCCCCCCCEEEEEEEECCCHHHHHHHHHHHH
T ss_conf 9999939999-999985799999999838899--87535789879999958989999999999997
No 92
>TIGR01259 comE comEA protein; InterPro: IPR004787 The comE locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. comEA and comEC are required for transformability, whereas the products of comEB and of the overlapping comER, which is transcribed in the reverse direction, are dispensable . ComEA has been shown to be an integral membrane protein, as predicted from hydropathy analysis, with its C-terminal domain outside the cytoplasmic membrane. This C-terminal domain possesses a sequence with similarity to those of several proteins known to be involved in nucleic acid transactions including UvrC and a human protein that binds to the replication origin of the Human herpesvirus 4 (Epstein-Barr virus) ..
Probab=93.66 E-value=0.046 Score=34.43 Aligned_cols=30 Identities=23% Similarity=0.226 Sum_probs=23.2
Q ss_pred HHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 898993898888627899989999999985
Q gi|255764496|r 578 VKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 578 ~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
.=+|-.||.+||..+|||||+-|+.|-+|=
T Consensus 63 ~VnlN~As~~EL~~l~GiGP~kA~aIi~YR 92 (124)
T TIGR01259 63 AVNLNKASLEELQALPGIGPAKAKAIIEYR 92 (124)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 134406789998636999813379999999
No 93
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=93.59 E-value=0.074 Score=32.94 Aligned_cols=17 Identities=18% Similarity=0.272 Sum_probs=10.1
Q ss_pred HHHHCCHHHHHHCCCCC
Q ss_conf 89938988886278999
Q gi|255764496|r 580 MISRSSPETLASIEGIS 596 (616)
Q Consensus 580 ~i~~As~eeL~~v~gi~ 596 (616)
.+.-+|++|+-...|++
T Consensus 310 ~~~~~sEedIf~~Lgl~ 326 (334)
T smart00483 310 FLKVESEEDIFDHLGLP 326 (334)
T ss_pred CCCCCCHHHHHHHCCCC
T ss_conf 37889999999974999
No 94
>cd01700 Pol_V Pol V was discovered in Escherichia coli as Umuc and UmuD proteins induced by UV. This branch of DNA polymerases is mostly found in bacteria. Pol V enables DNA replication to bypass covalently linked cys-sin T-T photo-dimers and 6-4 T-T or T-C photoproducts, which would otherwise stall the DNA replication fork.
Probab=93.57 E-value=0.22 Score=29.59 Aligned_cols=10 Identities=20% Similarity=0.195 Sum_probs=4.1
Q ss_pred HHHHHHHHHH
Q ss_conf 6899899999
Q gi|255764496|r 427 DCAMMRMVLE 436 (616)
Q Consensus 427 D~~~m~Evi~ 436 (616)
|+.-++++|.
T Consensus 255 d~~~i~~~l~ 264 (344)
T cd01700 255 TLDELREALA 264 (344)
T ss_pred CHHHHHHHHH
T ss_conf 9999999999
No 95
>cd01703 Pol_iota Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B. Unlike classic DNA polymerases,Y-family polymerases are induced by DNA damage. They can transverse normal replication-blocking DNA lesions. Unlike Pol eta, Pol iota is unable to replicate through a cis-syn T-T dimer. In human Pol iota, the base-pairing mode in the active site at the replicative end mat bee Hoogsteen instead of Watson-Click. Human Pol iota can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine. Pol iota prefers to insert Guanosine instead of Adenosine opposite Thymidine.
Probab=93.45 E-value=0.19 Score=29.94 Aligned_cols=54 Identities=26% Similarity=0.193 Sum_probs=20.6
Q ss_pred HHCCCCCCHHHHHHHHHHHC-CHHHHHHCC-HHHHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf 00488879899999999808-889899389-888862789998999999998547867
Q gi|255764496|r 557 LDEINGIGPLRKRLLLQSFG-TVKMISRSS-PETLASIEGISKKIACKIYNHFHKNTS 612 (616)
Q Consensus 557 Ld~I~GIG~k~~~~Ll~~Fg-s~~~i~~As-~eeL~~v~gi~~~~A~~I~~~l~~~~~ 612 (616)
+.+|+|||+|+.++|-..+. ++..+...+ .+.|.+.. |+..+..+|+..|..+.
T Consensus 212 i~ki~GIG~kt~~~L~~~gi~ti~dl~~~~~~~~l~~~f--G~~~g~~l~~~a~GiD~ 267 (394)
T cd01703 212 LRKIPGIGYKTAKKLEDHGISSVRDLQECSELLLLEKGF--GKGIAQRIWGLAHGRDD 267 (394)
T ss_pred HHHHCCCCHHHHHHHHHCCCEEHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHCCCCC
T ss_conf 055278179999999983892679876588799999987--88999999999569789
No 96
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=93.44 E-value=0.084 Score=32.55 Aligned_cols=48 Identities=17% Similarity=0.246 Sum_probs=34.1
Q ss_pred CCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf 71004888798999999998088898993898888627899989999999985478
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616)
.-.+.|+||||+|.-+|++.|||+++|.+.-. ..+- + .+.|.+.|.+.
T Consensus 236 DY~~gI~GIG~k~A~klIkk~~~ie~i~~~~~----~~~~-~---~~~~r~lF~~p 283 (338)
T TIGR03674 236 DYNEGVKGIGPKTALKLIKEHGDLEKVLKARG----EDIE-N---YDEIREFFLNP 283 (338)
T ss_pred CCCCCCCCCCHHHHHHHHHHHCCHHHHHHHCC----CCCC-C---HHHHHHHHCCC
T ss_conf 56789998568999999998599999998656----8877-8---99999984899
No 97
>cd01702 Pol_eta Pol eta is member of the DNA polimerase Y-family. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced cis-syn cyclobutane thymine-thumine (T-T) lesions. It synthesizes AA opposite a TT dimer. Pol eta is able to replicate through a variety of other distorting DNA lesion as well.
Probab=93.19 E-value=0.12 Score=31.40 Aligned_cols=26 Identities=19% Similarity=0.303 Sum_probs=17.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHCC
Q ss_conf 86613122035665554323455038
Q gi|255764496|r 168 SGPCTGEISSEKYMEFVHEAKKFLSG 193 (616)
Q Consensus 168 ~gpC~~~is~~~Y~~~v~~~~~fL~G 193 (616)
..|...+++-+-|.+.=..+.++|..
T Consensus 82 ~~~~~~~~~~~~Y~~~S~~i~~il~~ 107 (358)
T cd01702 82 PSPATHKVSLDPYRRASRKILNILKR 107 (358)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 44223556579999999999999998
No 98
>PRK07220 DNA topoisomerase I; Validated
Probab=93.02 E-value=0.22 Score=29.52 Aligned_cols=48 Identities=23% Similarity=0.275 Sum_probs=42.1
Q ss_pred CCCHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHH
Q ss_conf 771004888798999999998-088898993898888627899989999
Q gi|255764496|r 554 YSPLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIAC 601 (616)
Q Consensus 554 ~S~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v~gi~~~~A~ 601 (616)
-|.|++++|||+++.++|-.. --++..+..|..++|++..|++.+...
T Consensus 685 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 733 (740)
T PRK07220 685 PKSIKDIEGVGKATAGKLEEAGITTVEALAEADPIELAKAIKTSVKKIK 733 (740)
T ss_pred CCHHHCCCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHCCCHHHHH
T ss_conf 5201215565889999999768875999851898999987198889999
No 99
>cd00424 Pol_Y Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=92.93 E-value=0.26 Score=29.03 Aligned_cols=18 Identities=17% Similarity=0.300 Sum_probs=8.8
Q ss_pred CCHHHHHHHHHHHHHHHC
Q ss_conf 203566555432345503
Q gi|255764496|r 175 ISSEKYMEFVHEAKKFLS 192 (616)
Q Consensus 175 is~~~Y~~~v~~~~~fL~ 192 (616)
.+.+.|.+.-..+..+|.
T Consensus 70 ~~~~~Y~~~S~~i~~~l~ 87 (341)
T cd00424 70 YDLDLYRELSQRLLRLLK 87 (341)
T ss_pred CCHHHHHHHHHHHHHHHH
T ss_conf 988999999999999998
No 100
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=92.82 E-value=0.28 Score=28.79 Aligned_cols=96 Identities=19% Similarity=0.205 Sum_probs=70.5
Q ss_pred EEEECCCCHHHH-HHHHHHHHHHHHHHH-HH-HHHHH-HHC--CC-CHHCCCCCCHHHHHHHHHH--HCCHHHHHHCCHH
Q ss_conf 488579989999-999887877887889-89-98643-214--77-1004888798999999998--0888989938988
Q gi|255764496|r 517 ALVLNMRDPILY-FIQRLRDEAHRFAIT-TH-RKRRK-KAA--YS-PLDEINGIGPLRKRLLLQS--FGTVKMISRSSPE 587 (616)
Q Consensus 517 ~i~l~~~~~~l~-~Lq~iRDEaHRFAi~-~h-Rk~r~-k~~--~S-~Ld~I~GIG~k~~~~Ll~~--Fgs~~~i~~As~e 587 (616)
++.++..-|+-. -|.+.-+||+.|... .. ..++. +.. -| .=.+|.|+|+|....|+.+ ..++..+...+.+
T Consensus 400 ~~~~P~~CP~C~s~l~r~~~e~~~rC~n~~~C~aq~~e~l~hfvSr~AmdI~GLG~k~i~~L~e~~lI~~~~Dly~Lt~~ 479 (667)
T COG0272 400 PIPFPTHCPVCGSELVREEGEVVIRCTNGLNCPAQLKERLIHFVSRNALDIDGLGEKIIEQLFEKGLIKDIADLYTLTEE 479 (667)
T ss_pred CCCCCCCCCCCCCEEEECCCCEEEECCCCCCCHHHHHHHEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHCCHH
T ss_conf 88899979889997674267556866898788588862334674478657777679999999973753787987737898
Q ss_pred HHHHCCCCCHHHHHHHHHHHCCCCC
Q ss_conf 8862789998999999998547867
Q gi|255764496|r 588 TLASIEGISKKIACKIYNHFHKNTS 612 (616)
Q Consensus 588 eL~~v~gi~~~~A~~I~~~l~~~~~ 612 (616)
+|...+|++++.|+++++.+++.-.
T Consensus 480 ~l~~l~~~~~ks~~nLl~aIe~sK~ 504 (667)
T COG0272 480 DLLSLEGFGEKSAENLLNAIEKSKK 504 (667)
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHCC
T ss_conf 8841622446579999999998604
No 101
>PRK03103 DNA polymerase IV; Reviewed
Probab=92.73 E-value=0.4 Score=27.62 Aligned_cols=14 Identities=14% Similarity=-0.076 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 88888899999999
Q gi|255764496|r 215 YESAIIHRDRLAAL 228 (616)
Q Consensus 215 FE~Aa~~RD~I~aL 228 (616)
.|-|..+|+.|..=
T Consensus 123 ~~~a~~ir~~I~~~ 136 (410)
T PRK03103 123 REIAQKIQQAIMRE 136 (410)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 99999999999998
No 102
>PRK03858 DNA polymerase IV; Validated
Probab=92.35 E-value=0.41 Score=27.54 Aligned_cols=12 Identities=25% Similarity=0.202 Sum_probs=5.1
Q ss_pred HHHHHHHHHHHH
Q ss_conf 888889999999
Q gi|255764496|r 216 ESAIIHRDRLAA 227 (616)
Q Consensus 216 E~Aa~~RD~I~a 227 (616)
+-|..+|+.|..
T Consensus 118 ~~a~~ir~~I~~ 129 (398)
T PRK03858 118 QIAARLRARVRD 129 (398)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999999
No 103
>cd02826 Piwi-like Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism.
Probab=92.23 E-value=0.98 Score=24.86 Aligned_cols=115 Identities=16% Similarity=0.191 Sum_probs=60.2
Q ss_pred CCCEEEEEECCCCCCC--CCEEEEEEEECCCCCHHHHHHHH-CCCCCCCCCHHH-HHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 3516999707443775--40488888516872803232110-244445541168-9989999999977531311123333
Q gi|255764496|r 378 IPKRIEIYDNSHIMGC--SAVGCMVVVGENGFVKNQYRKFN-LHPNDVKTQDDC-AMMRMVLERRFSQLIKNEENLNFHP 453 (616)
Q Consensus 378 ~p~rIE~fDiSh~~G~--~~Vas~Vvf~~g~~~K~~YR~f~-Ik~~~v~~~DD~-~~m~Evi~RR~~r~~~~~~~l~~~~ 453 (616)
.|--|-|+|+||-+.. ...+|+|.|.........|..|. ..........|. .+|.|.|.-.++.-
T Consensus 170 ~~tmiiG~DV~H~~~~~~~~~~s~v~~~~~~~~~~~~~~~~~~q~~~~~~~~~l~~~~~~~l~~~~k~~----------- 238 (393)
T cd02826 170 KSDIFIGFDVSHPDRRTVNGGPSAVGFAANLSNHTFLGGFLYVQPSREVKLQDLGEVIKKCLDGFKKST----------- 238 (393)
T ss_pred CCEEEEEEEEECCCCCCCCCCCEEEEEEEECCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHHHHH-----------
T ss_conf 995999999365986778888869999973577630023899722533278899999999999999984-----------
Q ss_pred CCCCCCCCCCCCEEE--EEC-CHHHHHHHHHHHHH---------CCCCCCCCEEEEECCCCCCCCCEEEECCC
Q ss_conf 333345457984899--809-85899999999997---------58877871899971877676634898179
Q gi|255764496|r 454 KKQEYSFPSWPDVVI--LDG-GKGQLSAAQGVLKK---------LNVENRITIISIAKGPKRSAGMEKFFVKK 514 (616)
Q Consensus 454 ~~~~~~~~~~PDLil--IDG-GkgQln~a~~vl~~---------l~i~~~i~viglaK~~~r~~~~e~~~~~~ 514 (616)
...+|+-|+ =|| |.||+..+.+-... .+..-+|.+|-+.|+.+ .++|+.+
T Consensus 239 ------~~~lP~~IiiyRDGVseGQ~~~V~~ee~~~~~~~~~~~~~~~Pkit~Ivv~Krhh-----tRff~~~ 300 (393)
T cd02826 239 ------GEGLPEKIVIYRDGVSEGEFKRVKEEVEEIIKEACEIEESYRPKLVIIVVQKRHN-----TRFFPNE 300 (393)
T ss_pred ------CCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCC-----EEECCCC
T ss_conf ------6789825999946877266899999999999999985689998589999832322-----0124568
No 104
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=91.84 E-value=0.12 Score=31.35 Aligned_cols=35 Identities=29% Similarity=0.281 Sum_probs=23.2
Q ss_pred CCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf 88898993898888627899989999999985478
Q gi|255764496|r 576 GTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616)
Q Consensus 576 gs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616)
...-+|-.||.+||..+||||++.|+.|-++--++
T Consensus 86 ~~~vNiNtAs~eeL~~lpgIG~~kA~aIi~yRe~~ 120 (149)
T COG1555 86 EKKVNINTASAEELQALPGIGPKKAQAIIDYREEN 120 (149)
T ss_pred CCCCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHC
T ss_conf 54136661089999886798999999999999973
No 105
>PRK12311 rpsB 30S ribosomal protein S2; Provisional
Probab=91.83 E-value=1.1 Score=24.54 Aligned_cols=124 Identities=19% Similarity=0.180 Sum_probs=67.3
Q ss_pred CCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHH
Q ss_conf 57984899809858999999999975887787189997187767663489817983488579989999999887877887
Q gi|255764496|r 461 PSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRF 540 (616)
Q Consensus 461 ~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~iRDEaHRF 540 (616)
..+||+++|-.-.-.-.|+.++-+ + .||+|||+--.- .++.-.+.+|-|+.+.+-++-+=|-.-+=
T Consensus 157 ~~lPDlvfViD~~kE~iAV~EA~k-L----gIPvIaIvDTN~---------dP~~IdYpIPgNDDairsI~L~c~lia~A 222 (332)
T PRK12311 157 GGLPDLIFVIDTNKEDIAIQEAQR-L----GIPVAAIVDTNC---------DPKGITYLVPGNDDAGRAIALYCDLIARA 222 (332)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHH-C----CCCEEEEEECCC---------CCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 559998999689733899999998-0----979899973899---------98657756848655899999999999999
Q ss_pred HHHHHH-HHHHHH-CC--C---CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 889899-864321-47--7---10048887989999999980888989938988886278999899999999
Q gi|255764496|r 541 AITTHR-KRRKKA-AY--S---PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYN 605 (616)
Q Consensus 541 Ai~~hR-k~r~k~-~~--S---~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~ 605 (616)
++..-- ..-.-. -. + +-++.|-+-.. ..|..+.+=+.| .++|.++.|++++++++.-+
T Consensus 223 ~l~G~~~~~~~~g~d~g~~~~~~~~~~~~~~~~------~~~~~l~~p~g~-~ddl~ki~gvgp~~~~~ln~ 287 (332)
T PRK12311 223 AIDGISRAQGDLGIDIGASEAPLAEELPAAQAP------EGFQGLAGPRGA-PDDLKKLTGVSGAIEKKLND 287 (332)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCCHHHCCCCCCH------HHHHCCCCCCCC-CCHHHHHCCCCHHHHHHHHH
T ss_conf 999998752002667554346731125643333------454212478898-42577715767889998501
No 106
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=91.07 E-value=0.18 Score=30.10 Aligned_cols=193 Identities=16% Similarity=0.082 Sum_probs=109.9
Q ss_pred HHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEEC---CCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf 99999987515664351699970744377540488888516---872803232110244445541168998999999997
Q gi|255764496|r 364 MILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGE---NGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFS 440 (616)
Q Consensus 364 ~~l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~---g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~ 440 (616)
.++++.++.-+...-|..---.|+|-+|-.+++-+.+.=.+ +.+.+.+|- + +-..-|+|.+.+ |.
T Consensus 15 ~~~~~~~~ksg~~~~~s~s~~I~vsplQkgnp~l~~~~N~~w~y~~~i~Pd~~---~---~s~~~~lflslr------fh 82 (224)
T COG5241 15 GVAKLRKEKSGADTTGSQSLEIDVSPLQKGNPQLSRRINSNWVYNAFIKPDEW---T---DSKATDLFLSLR------FH 82 (224)
T ss_pred HHHHHHHHHCCCCCCCCEEEEEECCHHHCCCCCCCCCCCCCCEECCCCCCCHH---H---CCHHHHHHHHHH------HH
T ss_conf 99999886426567997135786476443897665431676233365586144---0---631899998876------40
Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEE
Q ss_conf 75313111233333333454579848998098589999999999758877871899971877676634898179834885
Q gi|255764496|r 441 QLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVL 520 (616)
Q Consensus 441 r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l 520 (616)
...-|. .. ......++...-|=|+.+|----|-. .++.+...++ +.+.+
T Consensus 83 s~~Pey--i~-~riSklKsYk~r~LL~hvd~~N~~as-IqElv~Tt~i---------------------------nti~l 131 (224)
T COG5241 83 STRPEY--IV-LRISKLKSYKERPLLNHVDSTNWRAS-IQELVSTTGI---------------------------NTIYL 131 (224)
T ss_pred CCCCCE--EE-EEEECCCCCCCCCEEEEECCCCHHHH-HHHHHHHCCC---------------------------CEEEH
T ss_conf 478753--78-76411455443521444446108999-9999875351---------------------------02311
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHH-HHH-------HHHC---CCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHH
Q ss_conf 79989999999887877887889899-864-------3214---771004888798999999998088898993898888
Q gi|255764496|r 521 NMRDPILYFIQRLRDEAHRFAITTHR-KRR-------KKAA---YSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETL 589 (616)
Q Consensus 521 ~~~~~~l~~Lq~iRDEaHRFAi~~hR-k~r-------~k~~---~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL 589 (616)
+- .-.|+-|+-.|+.- +++ +..+ .+.|-.|+||-+.--+.+|..||++..-..||.+|+
T Consensus 132 ~~----------svee~sry~~t~~~~~~~s~~iir~~~s~d~s~~fl~~i~~Vnksds~~~L~d~g~L~rf~gaSrdE~ 201 (224)
T COG5241 132 DY----------SVEERSRYFLTLTYHKLYSDYIIRRMQSLDRSNEFLILIFIVNKSDSEDTLNDIGKLCRFNGASRDEF 201 (224)
T ss_pred HH----------HHHHHHHHHHHHHHHHHCCHHHHHHCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 03----------16677899988579753278998734777656662588984446418989988878999856461588
Q ss_pred HHCCCCCHHHHHHHHHHHCC
Q ss_conf 62789998999999998547
Q gi|255764496|r 590 ASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 590 ~~v~gi~~~~A~~I~~~l~~ 609 (616)
+.+.|.|+.-|.++.++++-
T Consensus 202 e~l~g~g~~ka~~~ieyln~ 221 (224)
T COG5241 202 ELLLGFGFEKAAKYIEYLNL 221 (224)
T ss_pred HHHHCCCHHHHHHHHHHHCC
T ss_conf 99970088899999998546
No 107
>TIGR00375 TIGR00375 conserved hypothetical protein TIGR00375; InterPro: IPR005287 This family of conserved hypothetical proteins has no known function. .
Probab=90.92 E-value=0.24 Score=29.20 Aligned_cols=60 Identities=27% Similarity=0.364 Sum_probs=47.5
Q ss_pred HHHHHHHHC-CCCHHCCCCCCHHH----------HHHHHHHHC-CHHHHHHCCHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 998643214-77100488879899----------999999808-889899389888862789998999999998
Q gi|255764496|r 545 HRKRRKKAA-YSPLDEINGIGPLR----------KRLLLQSFG-TVKMISRSSPETLASIEGISKKIACKIYNH 606 (616)
Q Consensus 545 hRk~r~k~~-~S~Ld~I~GIG~k~----------~~~Ll~~Fg-s~~~i~~As~eeL~~v~gi~~~~A~~I~~~ 606 (616)
||+-|=.-. .=+|-.|+|+++++ -.+|.+.|| -++-+.+|.+|||++| .++++|..|-.+
T Consensus 295 ~p~~RPpYvhliPLae~ig~~~~kG~~TK~VQ~~wekl~k~fGtEi~VL~~A~~edla~~--~pPkvA~~i~~f 366 (384)
T TIGR00375 295 HPKFRPPYVHLIPLAEVIGLKIDKGVFTKAVQSLWEKLVKKFGTEIEVLLEAALEDLAKV--DPPKVAALIEKF 366 (384)
T ss_pred CCCCCCCCEEECCCEEECCCCCCCCEEEHHHHHHHHHHHHHHCCHHHHHHCCCHHHHHCC--CCCHHHHHHHHH
T ss_conf 875634850205630003534587313034677899986410415667642784587335--883588999986
No 108
>COG3680 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.58 E-value=0.65 Score=26.12 Aligned_cols=84 Identities=23% Similarity=0.347 Sum_probs=53.2
Q ss_pred CHHHCCCCC----C--EEEEECC-CCCEEEEEECHHHHHHHHHHC---CCCCC-----CHHHHHHHH-------HCCCEE
Q ss_conf 912586788----6--2588869-988889960125878887613---78877-----879999997-------344429
Q gi|255764496|r 2 SSEQMPECP----G--VYQMLDI-AGRVLYVGKAYNLQKRIKSYM---HSNNH-----THRITHMIS-------QINNIR 59 (616)
Q Consensus 2 ~~~~lP~~p----G--vY~~~~~-~~~iiYvGKaknL~~Rv~syf---~~~~~-----~~k~~~l~~-------~~~~ie 59 (616)
+.+++|.+. | ||+.-|. .+++.||||-+- |||-+|. ..... |.|.+.+-+ -+..|+
T Consensus 2 ~i~~fp~~v~~hLG~YVY~l~Dpr~~~ifYVGKG~G--nRVf~H~~~~sa~~d~~~~~srKlk~i~e~r~agl~iih~i~ 79 (259)
T COG3680 2 KIKKFPDSVLSHLGFYVYCLTDPRKDKIFYVGKGCG--NRVFEHEWVASASQDSGEIISRKLKAISECRKAGLYIIHLIE 79 (259)
T ss_pred CCCCCCHHHHHHHEEEEEEEECCCCCCEEEEECCCC--CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCEEEEEEH
T ss_conf 814188778755326899985478774799725876--315776654420156415778899999999973870223001
Q ss_pred EEECCCHHHHHHHHHHHHHHHCCCCEEC
Q ss_conf 9982871999999998877618720033
Q gi|255764496|r 60 FTVTCTEVEALLLEANMIKRLKPRFNIL 87 (616)
Q Consensus 60 ~~~t~~e~eAlilE~~lIk~~~P~yNi~ 87 (616)
.--...|.-|+-+|+.+|..+----|+.
T Consensus 80 ~hgl~dEktay~~eaa~id~~pgl~nv~ 107 (259)
T COG3680 80 VHGLADEKTAYKLEAAIIDHGPGLINVE 107 (259)
T ss_pred HHCCCCHHHHHHHHHHHHHCCCCHHHHH
T ss_conf 4047404678999998762177502566
No 109
>pfam02171 Piwi Piwi domain. This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA.
Probab=90.41 E-value=1.5 Score=23.60 Aligned_cols=111 Identities=20% Similarity=0.306 Sum_probs=60.5
Q ss_pred CEEEEEECCCCCCCC----CEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 169997074437754----0488888516872803232110244445541168998999999997753131112333333
Q gi|255764496|r 380 KRIEIYDNSHIMGCS----AVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKK 455 (616)
Q Consensus 380 ~rIE~fDiSh~~G~~----~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~ 455 (616)
.-|.|+|++|-.+.. .|+++|.--+..+. ..+-.+.+.... .+-...|.+++..++....+.
T Consensus 72 tmiiG~DV~h~~~~~~~~~Sv~~~vas~d~~~~-~~~~~~~~q~~~---~e~i~~l~~~~~~~L~~f~~~---------- 137 (296)
T pfam02171 72 DVIIGFDVSHPTGGTDDNPSVAGFVASMDKHPQ-KFAGGVRYQASG---QELIESLKDIIKESLRSFYKS---------- 137 (296)
T ss_pred CEEEEEEEECCCCCCCCCCEEEEEEEEECCCCC-EEEEEEEEECCC---CCHHHHHHHHHHHHHHHHHHH----------
T ss_conf 359999876799998999649999999569868-786799980799---583876999999999999997----------
Q ss_pred CCCCCCCCCCEEE--EEC-CHHHHHHH--------HHHHHHCCCC--CCCCEEEEECCCCCCCCCEEEECC
Q ss_conf 3345457984899--809-85899999--------9999975887--787189997187767663489817
Q gi|255764496|r 456 QEYSFPSWPDVVI--LDG-GKGQLSAA--------QGVLKKLNVE--NRITIISIAKGPKRSAGMEKFFVK 513 (616)
Q Consensus 456 ~~~~~~~~PDLil--IDG-GkgQln~a--------~~vl~~l~i~--~~i~viglaK~~~r~~~~e~~~~~ 513 (616)
.+.+|+=|+ =|| |.||+..+ +++.++++-+ -+|.+|-+.|+.+ -++++.
T Consensus 138 ----~~~~P~~IiiyRDGvsegq~~~v~~~Ev~~ik~a~~~~~~~~~pkit~Ivv~Krh~-----~Rff~~ 199 (296)
T pfam02171 138 ----RKKKPERIIIYRDGVSEGQFPQVLNYEVNQIKEACKELGEDYNPKLTVIVVQKRHH-----TRFFAS 199 (296)
T ss_pred ----CCCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCC-----EEECCC
T ss_conf ----08998459999368880458999999999999999985678899789999952432-----143247
No 110
>KOG2093 consensus
Probab=90.16 E-value=0.52 Score=26.80 Aligned_cols=76 Identities=21% Similarity=0.232 Sum_probs=56.3
Q ss_pred HHHHHHH---HHHHHHHH-H-CCC-CHHCCCCCCHHHHHHHHHHH-CCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 7887889---89986432-1-477-10048887989999999980-8889899389888862789998999999998547
Q gi|255764496|r 537 AHRFAIT---THRKRRKK-A-AYS-PLDEINGIGPLRKRLLLQSF-GTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 537 aHRFAi~---~hRk~r~k-~-~~S-~Ld~I~GIG~k~~~~Ll~~F-gs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
|-|-|.- ||-...+. . +.+ .+++.||||-....+|-..| .+...+..-+.+.|.++ .+++++++||...+.
T Consensus 525 ATr~AKP~Gq~~l~a~~veeFis~~~v~~LPGVG~sm~~kL~s~~i~tCgdLq~~T~~kl~k~--~G~Klgq~i~~~CrG 602 (1016)
T KOG2093 525 ATRVAKPNGQFYLSAEKVEEFISQLKVDDLPGVGSSMKSKLVSQFIQTCGDLQLITLIKLRKV--FGPKLGQKIYRGCRG 602 (1016)
T ss_pred HHHHCCCCCEEEECHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHH--HCCCHHHHHHHHCCC
T ss_conf 873058886166358899998610555668774289999999852424688999999987765--352077999986278
Q ss_pred CCCCC
Q ss_conf 86789
Q gi|255764496|r 610 NTSHT 614 (616)
Q Consensus 610 ~~~~~ 614 (616)
=+..+
T Consensus 603 ~Dd~P 607 (1016)
T KOG2093 603 IDDDP 607 (1016)
T ss_pred CCCCH
T ss_conf 76770
No 111
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=90.15 E-value=0.51 Score=26.86 Aligned_cols=13 Identities=15% Similarity=0.263 Sum_probs=6.4
Q ss_pred HCCHHHHHHCCCC
Q ss_conf 3898888627899
Q gi|255764496|r 583 RSSPETLASIEGI 595 (616)
Q Consensus 583 ~As~eeL~~v~gi 595 (616)
.+|++++-...|+
T Consensus 287 ~~sE~~If~~Lgl 299 (307)
T cd00141 287 GETEEEIFEALGL 299 (307)
T ss_pred CCCHHHHHHHCCC
T ss_conf 9999999998599
No 112
>cd04658 Piwi_piwi-like_Euk Piwi_piwi-like_Euk: PIWI domain, Piwi-like subfamily found in eukaryotes. This domain is found in Piwi and closely related proteins, where it is believed to perform a crucial role in germline cells, via RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The mechanism in Piwi is believed to be similar to that in Argonaute, the central component of the RNA-induced silencing complex (RISC). The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing.
Probab=90.08 E-value=1.5 Score=23.41 Aligned_cols=113 Identities=20% Similarity=0.245 Sum_probs=59.8
Q ss_pred CCCEEEEEECCCCC--CCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCC-CHHH-HHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf 35169997074437--754048888851687280323211024444554-1168-9989999999977531311123333
Q gi|255764496|r 378 IPKRIEIYDNSHIM--GCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKT-QDDC-AMMRMVLERRFSQLIKNEENLNFHP 453 (616)
Q Consensus 378 ~p~rIE~fDiSh~~--G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~-~DD~-~~m~Evi~RR~~r~~~~~~~l~~~~ 453 (616)
.|--|-|+|++|-. +...|+++|.=. +...-+.|-.+.+.....+. .++. .+|.+.|...++.
T Consensus 227 ~~tmiiG~DV~H~~~~~~~Sv~a~vaS~-~~~~~~~~s~~~~q~~~~~~~~~~l~~~~~~~L~~f~~~------------ 293 (448)
T cd04658 227 KNTMIVGIDVYHDTITKKKSVVGFVASL-NKSITKWFSKYISQVRGQEEIIDSLGKSMKKALKAYKKE------------ 293 (448)
T ss_pred CCEEEEEEEEECCCCCCCCCEEEEEEEE-CCCCCEEHEEEEECCCCEEEHHHHHHHHHHHHHHHHHHH------------
T ss_conf 8639998887868988997589999882-576561000689826982662756999999999999997------------
Q ss_pred CCCCCCCCCCCCEEEE--EC-CHHHHHHHHH--------HHHHCCCC--CCCCEEEEECCCCCCCCCEEEECCC
Q ss_conf 3333454579848998--09-8589999999--------99975887--7871899971877676634898179
Q gi|255764496|r 454 KKQEYSFPSWPDVVIL--DG-GKGQLSAAQG--------VLKKLNVE--NRITIISIAKGPKRSAGMEKFFVKK 514 (616)
Q Consensus 454 ~~~~~~~~~~PDLilI--DG-GkgQln~a~~--------vl~~l~i~--~~i~viglaK~~~r~~~~e~~~~~~ 514 (616)
.+.+|+-|+| || |.||+..+.+ ++..+.-. -+|.+|-+.|+.+ -+++..+
T Consensus 294 ------~~~~P~~IiiyRDGVSegq~~~v~~~E~~~i~~a~~~~~~~~~pkit~ivv~Krh~-----tRff~~~ 356 (448)
T cd04658 294 ------NKKLPSRIIIYRDGVGDGQLKKVKEYEVPQIKKAIKQYSENYSPKLAYIVVNKRIN-----TRFFNQG 356 (448)
T ss_pred ------CCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCC-----CEEEECC
T ss_conf ------29998448999467673568999999999999999984689998489999833432-----2211157
No 113
>TIGR01453 grpIintron_endo group I intron endonuclease; InterPro: IPR006350 These sequences represent a subfamily of endonucleases containing the N-terminal endo/excinuclease amino terminal domain, IPR000305 from INTERPRO. Sequences containing this domain are often termed often termed GIY-YIG endonucleases after a conserved sequence motif. The sequences are encoded by open reading frames found in group I introns in both phage and mitochondria. The closely related endonucleases of Bacteriophage T4: segA, segB, segC, segD and segE, are not included in this family. I-TevI (P13299 from SWISSPROT) from Bacteriophage T4 consists of an N-terminal catalytic GIY-YIG domain, a flexible linker region and a C-terminal DNA-binding domain , . The GIY-YIG domain forms a novel alpha/beta fold, with the putative catalytic residues and a putative metal-binding site located on a concave surface. The C-terminal DNA-binding region forms three subdomains - a zinc-finger, a DNA minor-groove binding alpha helix and a helix-turn helix region. Multiple DNA-protein contacts over an extended region of the DNA substrate molecule are thought to contribute to the high site specificity of this protein. .
Probab=89.42 E-value=1.7 Score=23.18 Aligned_cols=81 Identities=25% Similarity=0.411 Sum_probs=53.1
Q ss_pred CCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCCC-H-----HHHH-HHHHC-CCEEEEECC---------CHHHHHH
Q ss_conf 8862588869988889960125878887613788778-7-----9999-99734-442999828---------7199999
Q gi|255764496|r 9 CPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHT-H-----RITH-MISQI-NNIRFTVTC---------TEVEALL 71 (616)
Q Consensus 9 ~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~~~-~-----k~~~-l~~~~-~~ie~~~t~---------~e~eAli 71 (616)
..|||.|.+....-.|||-+.++..|...|+...... . .... +...- ..+.+.+.. +..+...
T Consensus 1 ~~g~y~~~~~~~~~~y~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~f~~~~~~~~~~~~~~~~~~~~~~ 80 (281)
T TIGR01453 1 KSGIYLLTNLINGKLYVGSSVDLSKRLKEHLNLSKKKNRSNENSLLSKALLKYGLSNFSFEILEYYGGTDKICNLDDLIE 80 (281)
T ss_pred CCCEEEEEECCCCCEEECCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHH
T ss_conf 96247775415762220320357888887532100110012456676777650521015788751165200100467777
Q ss_pred H---HHHHHHHHCC----CCEECCC
Q ss_conf 9---9988776187----2003364
Q gi|255764496|r 72 L---EANMIKRLKP----RFNILLR 89 (616)
Q Consensus 72 l---E~~lIk~~~P----~yNi~Lk 89 (616)
. |.-+|+...| .||++--
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~n~~~~ 105 (281)
T TIGR01453 81 RLLDETYYIKLLNPLFPLLYNILKI 105 (281)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 8877677776520001211112210
No 114
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=88.96 E-value=1.9 Score=22.85 Aligned_cols=173 Identities=13% Similarity=0.069 Sum_probs=86.5
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCC--CCCCCCCCCCCCCCCCCEEEEECCHHHHHH---HHHHHHHCCCCCCCCEEEEECC
Q ss_conf 16899899999999775313111--233333333454579848998098589999---9999997588778718999718
Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEEN--LNFHPKKQEYSFPSWPDVVILDGGKGQLSA---AQGVLKKLNVENRITIISIAKG 500 (616)
Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~--l~~~~~~~~~~~~~~PDLilIDGGkgQln~---a~~vl~~l~i~~~i~viglaK~ 500 (616)
||=.++++++.+.+.++..-..- ...+......-...-|||||.|=.-+..+- +.+ +.+.+.. ++||-|.=-
T Consensus 11 EDd~~v~~~l~~~L~~~~gf~~V~~A~~~~eA~~~l~~~~pDLvLLDi~LPd~~Glell~~-lr~~~~~--~~VI~iTA~ 87 (225)
T PRK10046 11 EDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIERFKPGLILLDNYLPDGRGINLLHE-LVQAHYP--GDVVFTTAA 87 (225)
T ss_pred ECCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHH-HHHHCCC--CCEEEEECC
T ss_conf 5989999999999972899549999899999999997359999998289899979999999-9964879--988999689
Q ss_pred CCCCCCCEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HC-CCCHH--------------CCCCCC
Q ss_conf 776766348981798348857998999999988787788788989986432-14-77100--------------488879
Q gi|255764496|r 501 PKRSAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFAITTHRKRRKK-AA-YSPLD--------------EINGIG 564 (616)
Q Consensus 501 ~~r~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~iRDEaHRFAi~~hRk~r~k-~~-~S~Ld--------------~I~GIG 564 (616)
....+..+-+-.+--+ ..+++-+ +.++++--.||+-.+ +....+ .. ...+| -=+||.
T Consensus 88 ~d~~~~~~Al~~Ga~D-YLvKPf~-----~erl~~~L~~y~~~~-~~l~~~~~~~Q~~iD~~~~~~~~~~~~~~lpKGl~ 160 (225)
T PRK10046 88 SDMETVSEAVRCGVFD-YLIKPIA-----YERLGQTLTRFRQRK-HMLESIDSASQKQIDEMFNAYARGEPKDELPTGID 160 (225)
T ss_pred CCHHHHHHHHHCCCCC-CEECCCC-----HHHHHHHHHHHHHHH-HHHCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf 9999999999749983-1028999-----999999999999999-98635776899999999623356888565899999
Q ss_pred HHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf 8999999998088898993898888627899989999999985478
Q gi|255764496|r 565 PLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616)
Q Consensus 565 ~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616)
+.|-+++...+.. .-...|.+|++...|||+.+|.+=.+||-..
T Consensus 161 ~~Tl~~v~~~l~~--~~~~~ta~eva~~~giSrvTaRRYLe~L~~~ 204 (225)
T PRK10046 161 PLTLNAVRKLFKE--PGVQHTAETVAQALTISRTTARRYLEYCASR 204 (225)
T ss_pred HHHHHHHHHHHHC--CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 8999999999971--7998689999998585199999999999868
No 115
>pfam02889 Sec63 Sec63 Brl domain. This domain (also known as the Brl domain) is required for assembly of functional endoplasmic reticulum translocons.
Probab=88.62 E-value=1.2 Score=24.23 Aligned_cols=22 Identities=9% Similarity=0.093 Sum_probs=10.3
Q ss_pred HHHHHHHHCCCEEEEECCCHHH
Q ss_conf 9999997344429998287199
Q gi|255764496|r 47 RITHMISQINNIRFTVTCTEVE 68 (616)
Q Consensus 47 k~~~l~~~~~~ie~~~t~~e~e 68 (616)
....++..+.-++-+.+..+-+
T Consensus 33 ~lL~il~~a~EF~~i~vR~~E~ 54 (309)
T pfam02889 33 DLLEILSSASEFEEIPVREEEK 54 (309)
T ss_pred HHHHHHHCCHHHHCCCCCCCHH
T ss_conf 9999984876462198482279
No 116
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. .
Probab=88.59 E-value=0.78 Score=25.57 Aligned_cols=27 Identities=7% Similarity=0.119 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999998633388888899999999
Q gi|255764496|r 202 IARNMNQATLKEDYESAIIHRDRLAAL 228 (616)
Q Consensus 202 L~~~M~~aS~~l~FE~Aa~~RD~I~aL 228 (616)
|++-...--+..+++-+..-|.-|..+
T Consensus 336 ~Q~hi~eve~~~~~~l~~~Qk~AL~~~ 362 (769)
T TIGR01448 336 LQKHILEVEKKLRLKLSEEQKEALKTA 362 (769)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999868750677068899999998
No 117
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=88.50 E-value=0.87 Score=25.23 Aligned_cols=29 Identities=17% Similarity=0.260 Sum_probs=14.5
Q ss_pred CHHHHHHHHHHHHHCCCC-CCCCEEEEECC
Q ss_conf 858999999999975887-78718999718
Q gi|255764496|r 472 GKGQLSAAQGVLKKLNVE-NRITIISIAKG 500 (616)
Q Consensus 472 GkgQln~a~~vl~~l~i~-~~i~viglaK~ 500 (616)
..--+.+|...|+++=.. ..+..+|+.=.
T Consensus 319 t~~i~~~a~~ll~~i~~~g~~~rkiGV~ls 348 (422)
T PRK03609 319 SRDIINAATRALDAIWRDGHRYQKAGVMLG 348 (422)
T ss_pred HHHHHHHHHHHHHHHCCCCCCEEEEEEEEE
T ss_conf 999999999999975158971689978940
No 118
>COG2231 Uncharacterized protein related to Endonuclease III [DNA replication, recombination, and repair]
Probab=88.39 E-value=0.54 Score=26.73 Aligned_cols=46 Identities=11% Similarity=0.255 Sum_probs=22.5
Q ss_pred CCCCEEEEEEEECCCCC--HHHH-HHHHCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 75404888885168728--0323-21102444455411689989999999
Q gi|255764496|r 392 GCSAVGCMVVVGENGFV--KNQY-RKFNLHPNDVKTQDDCAMMRMVLERR 438 (616)
Q Consensus 392 G~~~Vas~Vvf~~g~~~--K~~Y-R~f~Ik~~~v~~~DD~~~m~Evi~RR 438 (616)
|..|.-|+..|--++|. .+.| |++==+-..+.+ ++|..|++.++.-
T Consensus 124 G~ETaDsILlYa~~rp~FVvD~YtrR~l~rlg~i~~-k~ydeik~~fe~~ 172 (215)
T COG2231 124 GKETADSILLYALDRPVFVVDKYTRRLLSRLGGIEE-KKYDEIKELFEEN 172 (215)
T ss_pred CHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCC-CCHHHHHHHHHHC
T ss_conf 622399999998048644632999999999455102-5499999999853
No 119
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=88.20 E-value=1.5 Score=23.46 Aligned_cols=81 Identities=19% Similarity=0.394 Sum_probs=55.2
Q ss_pred CHHHHHHHHH-HHHHHHHHHHHHHHHHHHHCCCCHHCCCCCCHHHHHHHHHH-----HCCHHHHHHCCHHHHHHCCCC--
Q ss_conf 8999999988-78778878898998643214771004888798999999998-----088898993898888627899--
Q gi|255764496|r 524 DPILYFIQRL-RDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQS-----FGTVKMISRSSPETLASIEGI-- 595 (616)
Q Consensus 524 ~~~l~~Lq~i-RDEaHRFAi~~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~-----Fgs~~~i~~As~eeL~~v~gi-- 595 (616)
+.+-+.+-.| +..-.||.--|+-..--......|+-.||||+|+...+|.. |.|++.|++ .|+|+
T Consensus 98 ~eLpyvve~iV~~~E~rFV~FFN~A~PIt~RLH~LELLpGiGkK~m~~IleERkkkpFeSFeDi~~-------Rv~~~~~ 170 (202)
T COG1491 98 SELPYVVEKIVKENEDRFVKFFNEAEPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE-------RVKGLHD 170 (202)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCHHHHHH-------HHCCCCC
T ss_conf 551899999998615678887335676338788887531204999999999874288866899998-------8056777
Q ss_pred -CHHHHHHHHHHHCCCC
Q ss_conf -9899999999854786
Q gi|255764496|r 596 -SKKIACKIYNHFHKNT 611 (616)
Q Consensus 596 -~~~~A~~I~~~l~~~~ 611 (616)
-+-+|++|.+.+...+
T Consensus 171 p~~~I~~RIl~El~~~~ 187 (202)
T COG1491 171 PAKMIAERILDELKDED 187 (202)
T ss_pred HHHHHHHHHHHHHCCCC
T ss_conf 89999999999960877
No 120
>pfam04919 DUF655 Protein of unknown function, DUF655. This family includes several uncharacterized archaeal proteins.
Probab=88.03 E-value=0.99 Score=24.81 Aligned_cols=82 Identities=16% Similarity=0.286 Sum_probs=54.1
Q ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHCCCCHHCCCCCCHHHHHHHHHH-----HCCHHHHHHCCHHHHHHCCCCCHH
Q ss_conf 999999988-78778878898998643214771004888798999999998-----088898993898888627899989
Q gi|255764496|r 525 PILYFIQRL-RDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQS-----FGTVKMISRSSPETLASIEGISKK 598 (616)
Q Consensus 525 ~~l~~Lq~i-RDEaHRFAi~~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~-----Fgs~~~i~~As~eeL~~v~gi~~~ 598 (616)
.+-+.++.| .+...||.--|++.---......|+-+||||+|+...++.. |.|++.|.+.- ..++..-+-
T Consensus 85 eL~~vi~~iV~~nE~~FV~FfN~A~pit~rlH~leLLPGIGkK~~~~ileeR~~~~FeSFedi~~Rv----~~l~dp~~~ 160 (181)
T pfam04919 85 ELPYVVEEIVKENEDRFVKFFNEAEPITTRLHQLELLPGIGKKMMWAILEERKKKPFESFEDIKERV----KGLHDPVKI 160 (181)
T ss_pred HHHHHHHHHHHHCHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHH----CCCCCHHHH
T ss_conf 9999999999968467667651368744878888753340389999999996559988999999883----578999999
Q ss_pred HHHHHHHHHCCC
Q ss_conf 999999985478
Q gi|255764496|r 599 IACKIYNHFHKN 610 (616)
Q Consensus 599 ~A~~I~~~l~~~ 610 (616)
+|++|.+.+...
T Consensus 161 i~~Ri~~El~~~ 172 (181)
T pfam04919 161 IVERIIEELRDP 172 (181)
T ss_pred HHHHHHHHHCCC
T ss_conf 999999996498
No 121
>PTZ00035 Rad51; Provisional
Probab=87.68 E-value=1.3 Score=23.98 Aligned_cols=21 Identities=19% Similarity=0.165 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 333888888999999998622
Q gi|255764496|r 212 KEDYESAIIHRDRLAALSHIQ 232 (616)
Q Consensus 212 ~l~FE~Aa~~RD~I~aL~~i~ 232 (616)
.+.|..|..+-++-+.+-++.
T Consensus 93 ~~gF~ta~~~~~~R~~~~~it 113 (350)
T PTZ00035 93 NSGFCNAIDYHDARQNLIKFT 113 (350)
T ss_pred CCCCCCHHHHHHHHHHCEEEC
T ss_conf 777711999999986460357
No 122
>TIGR01011 rpsB_bact ribosomal protein S2; InterPro: IPR005706 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This family describes the bacterial, mitochondrial and chloroplast forms of ribosomal protein S2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=87.55 E-value=1.3 Score=23.92 Aligned_cols=70 Identities=20% Similarity=0.238 Sum_probs=36.3
Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC-EEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECC
Q ss_conf 9999977531311123333333345457984-899809858999999999975887787189997187767663489817
Q gi|255764496|r 435 LERRFSQLIKNEENLNFHPKKQEYSFPSWPD-VVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVK 513 (616)
Q Consensus 435 i~RR~~r~~~~~~~l~~~~~~~~~~~~~~PD-LilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~ 513 (616)
|.|+..||.+.-.. -..-..+|| |++||=.+=|+.+ .||- .| .|||+||+=-. =.+
T Consensus 137 L~Re~~KL~k~LgG--------Ik~M~~lPd~l~viD~~~E~IAv-~EA~-kL----gIPvvA~vDTN---------CdP 193 (227)
T TIGR01011 137 LSREKEKLEKNLGG--------IKDMKKLPDLLFVIDPRKEKIAV-AEAR-KL----GIPVVAIVDTN---------CDP 193 (227)
T ss_pred HHHHHHHHHHHHHH--------HHHHHCCCCEEEEECCCCCHHHH-HHHH-HC----CCCEEEEECCC---------CCC
T ss_conf 78999998655300--------25453169708997482106899-9973-37----99789870478---------888
Q ss_pred CCCEEEECCCCHHH
Q ss_conf 98348857998999
Q gi|255764496|r 514 KGEALVLNMRDPIL 527 (616)
Q Consensus 514 ~~~~i~l~~~~~~l 527 (616)
+.=-+.+|-|+-+.
T Consensus 194 d~vD~~IPgNDDai 207 (227)
T TIGR01011 194 DVVDYPIPGNDDAI 207 (227)
T ss_pred CCCCCCCCCCCCHH
T ss_conf 86650257973058
No 123
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=86.67 E-value=2.2 Score=22.34 Aligned_cols=11 Identities=36% Similarity=0.456 Sum_probs=6.6
Q ss_pred EEEEECCHHHH
Q ss_conf 89980985899
Q gi|255764496|r 466 VVILDGGKGQL 476 (616)
Q Consensus 466 LilIDGGkgQl 476 (616)
+++-|+-.+.+
T Consensus 249 i~v~d~~~~~l 259 (312)
T smart00611 249 LVIGDSDGNEL 259 (312)
T ss_pred EEEEECCCCEE
T ss_conf 99998899979
No 124
>pfam11731 Cdd1 Pathogenicity locus. Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=86.40 E-value=0.7 Score=25.90 Aligned_cols=40 Identities=18% Similarity=0.245 Sum_probs=32.0
Q ss_pred HCCCCHHCCCCCCHHHHHHHHH-HHCCHHHHHHCCHHHHHH
Q ss_conf 1477100488879899999999-808889899389888862
Q gi|255764496|r 552 AAYSPLDEINGIGPLRKRLLLQ-SFGTVKMISRSSPETLAS 591 (616)
Q Consensus 552 ~~~S~Ld~I~GIG~k~~~~Ll~-~Fgs~~~i~~As~eeL~~ 591 (616)
...+.|.+|||||+++.+-|.. -+-+++.++.++.+||-.
T Consensus 9 ~~l~~L~~lPnIG~a~a~DL~~LGi~~~~~L~g~dp~elY~ 49 (92)
T pfam11731 9 SALKELTDLPNIGKATAKDLRLLGINSPAQLAGRDPLELYE 49 (92)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHCCCCHHHHHCCCHHHHHH
T ss_conf 99998741897469999999991899899991799999999
No 125
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=86.38 E-value=1.3 Score=24.00 Aligned_cols=136 Identities=24% Similarity=0.303 Sum_probs=80.9
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCC
Q ss_conf 68998999999997753131112333333334545798489980985899999999997588778718999718776766
Q gi|255764496|r 427 DCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAG 506 (616)
Q Consensus 427 D~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~ 506 (616)
+|..++-+|.++=.+-+- ...+--|-| ||=++.|+.+.-....+.. |+.-+
T Consensus 215 sF~~~r~Ai~~~~g~~iv-------------aNyGLdP~L-----GKY~~TAC~rC~t~y~le~-------A~~~~---- 265 (403)
T COG1379 215 SFEELRKAIKGKDGCKIV-------------ANYGLDPRL-----GKYHLTACSRCYTRYSLEE-------AKSLR---- 265 (403)
T ss_pred CHHHHHHHHHCCCCCEEE-------------EECCCCCCC-----CCHHHHHHHHHHHCCCCCH-------HHHHC----
T ss_conf 889999997158996178-------------733767111-----3064788987600467554-------55406----
Q ss_pred CEEEECC-CCCEEEECCCCHHHHHHHHHHHHHHHHHHHH-HH-HHHHHHC-CCCHHCCC----CCC------HHHHHHHH
Q ss_conf 3489817-9834885799899999998878778878898-99-8643214-77100488----879------89999999
Q gi|255764496|r 507 MEKFFVK-KGEALVLNMRDPILYFIQRLRDEAHRFAITT-HR-KRRKKAA-YSPLDEIN----GIG------PLRKRLLL 572 (616)
Q Consensus 507 ~e~~~~~-~~~~i~l~~~~~~l~~Lq~iRDEaHRFAi~~-hR-k~r~k~~-~S~Ld~I~----GIG------~k~~~~Ll 572 (616)
+-+. =|..+ . .-++|-+--.|-+. +| +-|---+ .-+|..|+ |.| +.+-.+|.
T Consensus 266 ---wrCpkCGg~i--k---------KGV~dRv~ELad~~~~~p~~RPPYlhliPLaeIi~~~~g~gi~tK~V~~~we~lv 331 (403)
T COG1379 266 ---WRCPKCGGKI--K---------KGVSDRVLELADTEPEHPKHRPPYLHLIPLAEIISMALGKGITTKAVKRTWERLV 331 (403)
T ss_pred ---CCCCCCCCCH--H---------HHHHHHHHHHHCCCCCCCCCCCCCEECCCHHHHHHHHHCCCEECHHHHHHHHHHH
T ss_conf ---4686236601--0---------3088999986205733689999822206499888877346600026899999999
Q ss_pred HHHCC-HHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf 98088-8989938988886278999899999999854
Q gi|255764496|r 573 QSFGT-VKMISRSSPETLASIEGISKKIACKIYNHFH 608 (616)
Q Consensus 573 ~~Fgs-~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~ 608 (616)
+.||| ++-+-.|.+|+|+.| -+++|+.|..+=+
T Consensus 332 ~~FGtEi~vLi~a~~e~La~V---~~~vA~aI~~~R~ 365 (403)
T COG1379 332 RAFGTEIDVLIDAPIEELARV---DPKVAEAIVAFRN 365 (403)
T ss_pred HHHCCHHHHHHCCCHHHHHHH---HHHHHHHHHHHHC
T ss_conf 984213156752898999664---5899999999845
No 126
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=85.36 E-value=1.7 Score=23.06 Aligned_cols=14 Identities=14% Similarity=-0.111 Sum_probs=5.5
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 38888889999999
Q gi|255764496|r 214 DYESAIIHRDRLAA 227 (616)
Q Consensus 214 ~FE~Aa~~RD~I~a 227 (616)
..|.|+.++.|-++
T Consensus 249 ~~~~~~~l~~qA~a 262 (457)
T TIGR03491 249 GLGVAEQLVQQARA 262 (457)
T ss_pred CHHHHHHHHHHHHH
T ss_conf 66999999999998
No 127
>PRK00377 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Probab=85.17 E-value=2.9 Score=21.39 Aligned_cols=41 Identities=32% Similarity=0.429 Sum_probs=26.9
Q ss_pred CCCCEEEEECCHHHHHH---------------------------HHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf 79848998098589999---------------------------999999758877871899971877
Q gi|255764496|r 462 SWPDVVILDGGKGQLSA---------------------------AQGVLKKLNVENRITIISIAKGPK 502 (616)
Q Consensus 462 ~~PDLilIDGGkgQln~---------------------------a~~vl~~l~i~~~i~viglaK~~~ 502 (616)
+-||-++|+||.||+.. +.+.|++++....+--+.++++..
T Consensus 110 p~pD~vFIGG~~g~l~~il~~~~~~L~~gGriVinaVtlet~~~~~~~l~~~~~~~ev~qv~vsr~~~ 177 (198)
T PRK00377 110 PKSDRYFIGGGGEELPEIIQAALEKIGKGGRIVADAILLESLNKALSALEELGYKYEVTEVIIAKGMK 177 (198)
T ss_pred CCCCEEEEECCCCCHHHHHHHHHHHCCCCCEEEEEEECHHHHHHHHHHHHHCCCCCEEEEEEEEECCC
T ss_conf 98898999788777899999999857999899998362988999999999769981499999464732
No 128
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=83.70 E-value=1.5 Score=23.50 Aligned_cols=19 Identities=5% Similarity=0.074 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHHCCC
Q ss_conf 9999999999730110035
Q gi|255764496|r 130 AVEKTINSLQRTFFLRSCA 148 (616)
Q Consensus 130 ~~~~~l~~l~~~f~lR~C~ 148 (616)
.+.++++.+...||--.|.
T Consensus 5 ~~~~i~~~l~~~~p~~~~~ 23 (211)
T COG0177 5 KALEILDRLRELYPEPKTE 23 (211)
T ss_pred HHHHHHHHHHHHCCCCCCC
T ss_conf 6999999999878887675
No 129
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=82.39 E-value=0.92 Score=25.06 Aligned_cols=19 Identities=37% Similarity=0.697 Sum_probs=16.6
Q ss_pred HHCCCCCCHHHHHHHHHHH
Q ss_conf 0048887989999999980
Q gi|255764496|r 557 LDEINGIGPLRKRLLLQSF 575 (616)
Q Consensus 557 Ld~I~GIG~k~~~~Ll~~F 575 (616)
+-.|||||+|+..+||+.|
T Consensus 18 ipGV~GIG~ktA~~ll~~~ 36 (36)
T smart00279 18 IPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CCCCCCCCHHHHHHHHHHC
T ss_conf 8999974789999999859
No 130
>pfam02371 Transposase_20 Transposase IS116/IS110/IS902 family. Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. This region is often found with pfam01548. The exact function of this region is uncertain. This family contains a HHH motif suggesting a DNA-binding function.
Probab=81.75 E-value=2 Score=22.62 Aligned_cols=42 Identities=31% Similarity=0.487 Sum_probs=33.7
Q ss_pred CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHH
Q ss_conf 10048887989999999980888989938988886278999899
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKI 599 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~ 599 (616)
.|..|||||+.+.-.|+...|.+. .=.|.+++.+..|+.+..
T Consensus 3 ~L~sipGiG~~~a~~l~aeigd~~--rF~~~~~~~s~~Gl~P~~ 44 (87)
T pfam02371 3 LLLSIPGIGPITAAALLAEIGDIS--RFKSARQLAAYAGLAPRE 44 (87)
T ss_pred HHHCCCCCCHHHHHHHHHHHCCHH--HCCCHHHHHHHCCCCCCC
T ss_conf 342699952999999999929853--278999999983999985
No 131
>PRK10702 endonuclease III; Provisional
Probab=81.66 E-value=1.7 Score=23.15 Aligned_cols=21 Identities=5% Similarity=-0.100 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHCCC
Q ss_conf 789999999999730110035
Q gi|255764496|r 128 VDAVEKTINSLQRTFFLRSCA 148 (616)
Q Consensus 128 ~~~~~~~l~~l~~~f~lR~C~ 148 (616)
...+.++++.|.+.||=..|.
T Consensus 3 ~~~~~~i~~~l~~~~p~~~~~ 23 (211)
T PRK10702 3 KAKRLEILTRLRDNNPHPTTE 23 (211)
T ss_pred HHHHHHHHHHHHHHCCCCCCC
T ss_conf 899999999999878699998
No 132
>COG2827 Predicted endonuclease containing a URI domain [DNA replication, recombination, and repair]
Probab=81.49 E-value=4.1 Score=20.39 Aligned_cols=67 Identities=18% Similarity=0.189 Sum_probs=47.1
Q ss_pred CCCCCEEEEECCCCCEEEEEECHHHHHHHHHHCCCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHHHHHH
Q ss_conf 6788625888699888899601258788876137887787999999734442999828719999999988
Q gi|255764496|r 7 PECPGVYQMLDIAGRVLYVGKAYNLQKRIKSYMHSNNHTHRITHMISQINNIRFTVTCTEVEALLLEANM 76 (616)
Q Consensus 7 P~~pGvY~~~~~~~~iiYvGKaknL~~Rv~syf~~~~~~~k~~~l~~~~~~ie~~~t~~e~eAlilE~~l 76 (616)
|+..=||++... +.-+|+|=+.|+..|+..|=.+. ..|-.+=-.-+.=|=+....+-.+|+-.|..+
T Consensus 2 ~~~~~vYil~c~-dgtlY~GvT~D~~rR~~~H~~Gk--gakyT~~~~~~~Lv~~e~~~~~~~A~~~E~~i 68 (95)
T COG2827 2 ANNWYVYILRCA-DGTLYTGVTTDLERRLAEHNSGK--GAKYTRRYGPVRLVWYEEFDDKSEALRREKRI 68 (95)
T ss_pred CCCEEEEEEEEC-CCCEEEEECCCHHHHHHHHHCCC--CCCHHCCCCCEEEEEEEECCCHHHHHHHHHHH
T ss_conf 964699999807-99889973188999999985465--53411127866999986329989999999999
No 133
>pfam10391 DNA_pol_lambd_f Fingers domain of DNA polymerase lambda. DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone.
Probab=80.68 E-value=1.7 Score=23.14 Aligned_cols=29 Identities=21% Similarity=0.371 Sum_probs=23.8
Q ss_pred CHHCCCCCCHHHHHHHHHH-HCCHHHHHHC
Q ss_conf 1004888798999999998-0888989938
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQS-FGTVKMISRS 584 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~A 584 (616)
.|..|-||||++.++++.. +.|++++++.
T Consensus 3 ~f~~I~GvGp~~A~~~~~~G~~ti~dL~~~ 32 (52)
T pfam10391 3 LFTNIWGVGPKTARKWYRQGIRTLEDLREN 32 (52)
T ss_pred HHHHCCCCCHHHHHHHHHHCCCCHHHHHHC
T ss_conf 366354406999999999478889999746
No 134
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=80.55 E-value=3.6 Score=20.73 Aligned_cols=40 Identities=30% Similarity=0.458 Sum_probs=20.7
Q ss_pred HHHHHHHHHHCCCCEECCCCCCCCCEEEEECCCCCCEEEE
Q ss_conf 9999887761872003364689772699808899845999
Q gi|255764496|r 71 LLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYK 110 (616)
Q Consensus 71 ilE~~lIk~~~P~yNi~LkDdk~yPyi~it~~~~~p~l~~ 110 (616)
.+|..+..-.+|.-.+...+|+.||-..-...++.|-|++
T Consensus 63 ~~~~~le~~~~~~~~~i~~~d~~YP~~Lk~i~~pP~vLf~ 102 (350)
T COG0758 63 LLELELEKIEKPGIKIITLGDEDYPKLLKEINDPPPVLFY 102 (350)
T ss_pred HHHHHHHHHHHCCCEEECCCCCCCHHHHHHCCCCCEEEEE
T ss_conf 8999999999549768426874354999845599938998
No 135
>pfam00633 HHH Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain.
Probab=79.64 E-value=0.86 Score=25.27 Aligned_cols=21 Identities=24% Similarity=0.450 Sum_probs=17.7
Q ss_pred CCCCHHCCCCCCHHHHHHHHH
Q ss_conf 477100488879899999999
Q gi|255764496|r 553 AYSPLDEINGIGPLRKRLLLQ 573 (616)
Q Consensus 553 ~~S~Ld~I~GIG~k~~~~Ll~ 573 (616)
...+|.++||||+++...++.
T Consensus 9 s~eeL~~lpGVG~~tA~~I~~ 29 (30)
T pfam00633 9 SREELLALPGVGPKTAEAILS 29 (30)
T ss_pred CHHHHHHCCCCCHHHHHHHHC
T ss_conf 599997288977688998853
No 136
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=79.20 E-value=2.1 Score=22.52 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCHHHHCCC
Q ss_conf 8999999998622110002454201110001
Q gi|255764496|r 220 IHRDRLAALSHIQNHNDSIYNRMDCFSLYHN 250 (616)
Q Consensus 220 ~~RD~I~aL~~i~~~q~v~~~d~Dvi~i~~~ 250 (616)
..|+.+-+++-+-. .-+|+|-++.-
T Consensus 118 ~~Re~LL~lkGIG~------ETADsILlYa~ 142 (218)
T PRK13913 118 VTREWLLDQKGIGK------ESADAILCYVC 142 (218)
T ss_pred HHHHHHHCCCCCCH------HHHHHHHHHHC
T ss_conf 58999974898663------33999999974
No 137
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication; InterPro: IPR010214 NusA, or N utilisation substance protein A, is a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents an acidic 50-residue region found in two copies toward the C terminus of most proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic ; GO: 0030528 transcription regulator activity.
Probab=78.85 E-value=2.6 Score=21.77 Aligned_cols=35 Identities=29% Similarity=0.413 Sum_probs=31.1
Q ss_pred HHHHCCHHHHHHCCHHHHHH--CCCCCHHHHHHHHHH
Q ss_conf 99808889899389888862--789998999999998
Q gi|255764496|r 572 LQSFGTVKMISRSSPETLAS--IEGISKKIACKIYNH 606 (616)
Q Consensus 572 l~~Fgs~~~i~~As~eeL~~--v~gi~~~~A~~I~~~ 606 (616)
-.=|-|++.|...+++||.. |.|++..+|+.+...
T Consensus 11 ~eGf~t~EdlAy~~~~EL~~fGIeG~~Ee~A~~L~~~ 47 (52)
T TIGR01954 11 EEGFTTVEDLAYVPVDELLSFGIEGLDEETAKELINR 47 (52)
T ss_pred HHCCCHHHHHHCCCHHHHHHHCCCCCCHHHHHHHHHH
T ss_conf 7367317887504556688635899887889999999
No 138
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=78.77 E-value=1.1 Score=24.38 Aligned_cols=20 Identities=30% Similarity=0.549 Sum_probs=10.5
Q ss_pred CHHCCCCCCHHHHHHHHHHH
Q ss_conf 10048887989999999980
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSF 575 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~F 575 (616)
.|.+|+|||+++.++|+.+.
T Consensus 2 ~L~~v~GIG~k~A~~ll~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred CCCCCCCCCCHHHHHHHHHH
T ss_conf 21017998811599999976
No 139
>pfam00318 Ribosomal_S2 Ribosomal protein S2.
Probab=77.68 E-value=5.3 Score=19.57 Aligned_cols=37 Identities=24% Similarity=0.245 Sum_probs=27.7
Q ss_pred CCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf 579848998098589999999999758877871899971877
Q gi|255764496|r 461 PSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616)
Q Consensus 461 ~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616)
..+||+++|-+....-.|+.|+.. ..||++|++=-+-
T Consensus 135 ~~~Pd~vii~d~~~~~~ai~Ea~~-----l~IP~I~ivDTn~ 171 (205)
T pfam00318 135 KKLPDLVIVVDPNKEHIAIKEASK-----LGIPVIAIVDTNC 171 (205)
T ss_pred HHCCCEEEEECCCCCHHHHHHHHH-----CCCCEEEECCCCC
T ss_conf 008986998578645389999987-----5997565405999
No 140
>KOG1041 consensus
Probab=77.25 E-value=5.4 Score=19.48 Aligned_cols=107 Identities=24% Similarity=0.263 Sum_probs=61.4
Q ss_pred CCCCEEEEEECCCCCCC-----CCEEEEEEEECCCCCHHHHHHHHC-CCCCCCCC-HHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 43516999707443775-----404888885168728032321102-44445541-168998999999997753131112
Q gi|255764496|r 377 HIPKRIEIYDNSHIMGC-----SAVGCMVVVGENGFVKNQYRKFNL-HPNDVKTQ-DDCAMMRMVLERRFSQLIKNEENL 449 (616)
Q Consensus 377 ~~p~rIE~fDiSh~~G~-----~~Vas~Vvf~~g~~~K~~YR~f~I-k~~~v~~~-DD~~~m~Evi~RR~~r~~~~~~~l 449 (616)
..|..|-|||+||-.+. ++..+.||+.-.. ....|+-+-. -....+-. ||-.+++|.|.--++.
T Consensus 603 ~~ptl~IG~dVsHp~~~~~~~~~PSia~vv~s~~~-~~~~y~g~~~~Q~~r~e~i~~~~~~~~e~l~~f~~~-------- 673 (876)
T KOG1041 603 DSPTLFIGFDVSHPAAGTSFDGNPSIVGVVYNLDW-HPQKFAGFVRFQKSRQEVIQDLGEMIRELLRSFRKS-------- 673 (876)
T ss_pred CCCEEEEEEEEECCCCCCCCCCCCCEEEEEECCCC-CCHHHCCEEEEECCCCEECCCHHHHHHHHHHHHHHH--------
T ss_conf 88759999870079877777899718999960776-715327468970587100144678999999999986--------
Q ss_pred CCCCCCCCCCCCCCCCEEEE--EC-CHHH--------HHHHHHHHHHCC--CCCCCCEEEEECCCC
Q ss_conf 33333333454579848998--09-8589--------999999999758--877871899971877
Q gi|255764496|r 450 NFHPKKQEYSFPSWPDVVIL--DG-GKGQ--------LSAAQGVLKKLN--VENRITIISIAKGPK 502 (616)
Q Consensus 450 ~~~~~~~~~~~~~~PDLilI--DG-GkgQ--------ln~a~~vl~~l~--i~~~i~viglaK~~~ 502 (616)
....|+=|+| || +.|| |.+++++...+. ..-.|.+|-+-|+.+
T Consensus 674 ----------t~~~P~rIIiYRdGvSEGqf~~Vl~~El~~ir~ac~~~~~~y~P~it~IVvqKrHh 729 (876)
T KOG1041 674 ----------TRKLPDRIVIYRDGVSEGQFSMVLEEELRAIKEACKKLQEGYNPKITVIVAQKRHH 729 (876)
T ss_pred ----------CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCC
T ss_conf ----------06699759999578783218899999999999999860736698769999823544
No 141
>COG1431 Argonaute homolog, implicated in RNA metabolism [Translation, ribosomal structure and biogenesis]
Probab=76.21 E-value=5.8 Score=19.29 Aligned_cols=100 Identities=18% Similarity=0.141 Sum_probs=63.9
Q ss_pred CEEEEEECCCCC-CCCCE-EEEEEEECCCCCHHHHHHHHCCC-CCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 169997074437-75404-88888516872803232110244-4455411689989999999977531311123333333
Q gi|255764496|r 380 KRIEIYDNSHIM-GCSAV-GCMVVVGENGFVKNQYRKFNLHP-NDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQ 456 (616)
Q Consensus 380 ~rIE~fDiSh~~-G~~~V-as~Vvf~~g~~~K~~YR~f~Ik~-~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~ 456 (616)
.-|.+.|+|-.. |.-+| |+|+||...|---..|+.+.--. .-.....||.+.-+=+-++++.
T Consensus 475 DaivGlDvsr~~~gn~tV~gct~~f~seg~l~eyy~t~tpa~GErl~~~g~yle~~~~~gfe~~n--------------- 539 (685)
T COG1431 475 DAIVGLDVSRVSEGNWTVEGCTSCFVSEGGLEEYYHTVTPALGERLETSGRYLEKMNWRGFESRN--------------- 539 (685)
T ss_pred CCEEEEEEEEEEECCEEEEEEEEEEECCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCC---------------
T ss_conf 41331135677408807720268986068438961024678532003378999998864021067---------------
Q ss_pred CCCCCCCCCEEEEECC--HHHHHHHHHHHHHCCCCCCCCEEEEECCCCC
Q ss_conf 3454579848998098--5899999999997588778718999718776
Q gi|255764496|r 457 EYSFPSWPDVVILDGG--KGQLSAAQGVLKKLNVENRITIISIAKGPKR 503 (616)
Q Consensus 457 ~~~~~~~PDLilIDGG--kgQln~a~~vl~~l~i~~~i~viglaK~~~r 503 (616)
. =+.+=||- .+-+++++++=.++|. ++.|+.+-|+..+
T Consensus 540 ------~-iV~lRDG~l~~~E~aavkeyg~elgs--n~ev~~i~knNp~ 579 (685)
T COG1431 540 ------L-IVTLRDGKLVAGEIAAVKEYGGELGS--NPEVNRILKNNPW 579 (685)
T ss_pred ------E-EEEEECCCCCHHHHHHHHHHHHHCCC--CHHHHEECCCCCE
T ss_conf ------4-69984684416889999997320377--7456201105871
No 142
>PRK05299 rpsB 30S ribosomal protein S2; Provisional
Probab=74.86 E-value=6.2 Score=19.05 Aligned_cols=53 Identities=17% Similarity=0.198 Sum_probs=34.5
Q ss_pred CCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHH
Q ss_conf 5798489980985899999999997588778718999718776766348981798348857998999
Q gi|255764496|r 461 PSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPIL 527 (616)
Q Consensus 461 ~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l 527 (616)
..+||+++|=+-.-.-+|+.++.+ + .||+|||+=-+- .++.-.+.+|-|+.+.
T Consensus 155 ~~lPd~viv~d~~~e~~AV~EA~k-l----~IPvI~ivDTn~---------dP~~idypIP~NDDs~ 207 (255)
T PRK05299 155 GGLPDALFVVDPNKEHIAVKEARK-L----GIPVVAIVDTNC---------DPDGVDYPIPGNDDAI 207 (255)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHH-C----CCCEEEEECCCC---------CCCCCCEEECCCCCHH
T ss_conf 319987998478533799999997-5----998887624899---------9665865533775289
No 143
>TIGR00615 recR recombination protein RecR; InterPro: IPR000093 The bacterial protein recR seems to play a role in a recombinational process of DNA repair . It may act with recF and recO. RecR is a protein of about 200 amino acid residues. This protein contains a putative C4-type zinc finger in the N-terminal section.; GO: 0006281 DNA repair, 0006310 DNA recombination.
Probab=73.76 E-value=1.9 Score=22.78 Aligned_cols=76 Identities=13% Similarity=0.123 Sum_probs=32.6
Q ss_pred CCCCCHHHHCCCCCEEEEEEEEEECCEEEECCCCCCCC--CCCCCHHHHHHHHHHHHHCCCCCCHHHEECCCCC-HHHHH
Q ss_conf 45420111000188347889984247454101135667--7789978988877754321378981231026888-57876
Q gi|255764496|r 239 YNRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKT--DSESTNAQILSYFLRQFYTDKPCPENILLSEEAE-ETSLL 315 (616)
Q Consensus 239 ~~d~Dvi~i~~~~~~~~I~vl~vR~G~i~g~~~f~~~~--~~~~~~~eil~~fI~qyY~~~~iP~~Iiv~~~~~-~~~~l 315 (616)
.+..||+++..-+..- ...||=+|.+. .++. +.+....++++..=.. ....-|+|||+-..+. |-+..
T Consensus 89 ~~p~Dv~a~E~~~~f~--G~YhVL~G~is-----Pl~Gigp~~~~i~~L~~riGeR--l~~~~~~EVIlA~nPt~EGeaT 159 (205)
T TIGR00615 89 EDPKDVFALEKTKEFR--GRYHVLGGLIS-----PLDGIGPEDLKIAALLKRIGER--LQEESVKEVILATNPTVEGEAT 159 (205)
T ss_pred CCHHHHHHHHHHHHHC--CCEEEECCEEC-----CCCCCCCCCCCHHHHHHHHHCC--CCCCCCCEEEEECCCCCHHHHH
T ss_conf 4726799987654216--60143156417-----6457683221468899886000--0005797788607898413479
Q ss_pred HHHHHHHC
Q ss_conf 66543201
Q gi|255764496|r 316 EISFFKQY 323 (616)
Q Consensus 316 ~~~L~~k~ 323 (616)
..++.+..
T Consensus 160 a~Yi~~~l 167 (205)
T TIGR00615 160 ALYIARLL 167 (205)
T ss_pred HHHHHHHH
T ss_conf 99999998
No 144
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=73.73 E-value=2.8 Score=21.50 Aligned_cols=15 Identities=20% Similarity=0.412 Sum_probs=5.1
Q ss_pred HHCCCCCCHHHHHHH
Q ss_conf 004888798999999
Q gi|255764496|r 557 LDEINGIGPLRKRLL 571 (616)
Q Consensus 557 Ld~I~GIG~k~~~~L 571 (616)
|..|||||++|....
T Consensus 85 L~~l~GIG~~TA~~v 99 (158)
T cd00056 85 LLALPGVGRKTANVV 99 (158)
T ss_pred HHCCCCCCHHHHHHH
T ss_conf 875898289999999
No 145
>KOG1921 consensus
Probab=73.52 E-value=4.9 Score=19.79 Aligned_cols=22 Identities=14% Similarity=0.003 Sum_probs=11.0
Q ss_pred CCCHHHHHHHHHHHHHHHCCCCH
Q ss_conf 22035665554323455038715
Q gi|255764496|r 174 EISSEKYMEFVHEAKKFLSGGNH 196 (616)
Q Consensus 174 ~is~~~Y~~~v~~~~~fL~G~~~ 196 (616)
..++.++.-+|--. ..|+.-++
T Consensus 71 ~~~pk~~RfqvLv~-lmLSSQTK 92 (286)
T KOG1921 71 KADPKERRFQVLVG-LMLSSQTK 92 (286)
T ss_pred CCCHHHHHHHHHHH-HHHHCCHH
T ss_conf 57805675999999-99701007
No 146
>pfam08846 DUF1816 Domain of unknown function (DUF1816). CpcD phycobilisome linker-like from Crocosphaera watsonii WH 8501 is associated with the pfam01383 domain, suggesting this presumed domain could have a role in phycobilisomes.
Probab=71.90 E-value=2.5 Score=21.94 Aligned_cols=19 Identities=26% Similarity=0.641 Sum_probs=14.2
Q ss_pred CEEEECCCCHHHHHHHHHH
Q ss_conf 4377037887899999999
Q gi|255764496|r 119 GSYFGPFASVDAVEKTINS 137 (616)
Q Consensus 119 ~~yfGPf~~~~~~~~~l~~ 137 (616)
--|||||.+...|...+.-
T Consensus 22 tYyFGPF~t~~ea~~~~~~ 40 (68)
T pfam08846 22 TYWFGPFLTREEAEAALPG 40 (68)
T ss_pred EEEECCCCCHHHHHHHHCC
T ss_conf 8896884898999987302
No 147
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=69.91 E-value=3.4 Score=20.94 Aligned_cols=40 Identities=33% Similarity=0.396 Sum_probs=26.0
Q ss_pred CCCCHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHC
Q ss_conf 477100488879899999999808--8898993898888627
Q gi|255764496|r 553 AYSPLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLASI 592 (616)
Q Consensus 553 ~~S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~v 592 (616)
+...|..|.|||+.+...+....| .-..+.+.|.+|+.++
T Consensus 13 v~~ALt~I~GIG~~~A~~Ic~~lgId~~~k~g~Ls~~qi~~I 54 (113)
T TIGR03631 13 VEIALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAI 54 (113)
T ss_pred HHHHHHCEECCCHHHHHHHHHHCCCCCCCCHHHCCHHHHHHH
T ss_conf 460652002758999999999929998778644999999999
No 148
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=69.07 E-value=3.5 Score=20.81 Aligned_cols=37 Identities=27% Similarity=0.386 Sum_probs=18.7
Q ss_pred CHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHC
Q ss_conf 100488879899999999808--8898993898888627
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLASI 592 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~v 592 (616)
.|..|.|||+.+...+++.+| .-..+.+.|.+|+.++
T Consensus 18 ALt~I~GIG~~~A~~Ic~~lgId~~~k~g~Ls~~qi~~I 56 (122)
T PRK05179 18 ALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKL 56 (122)
T ss_pred HHHHHCCCCHHHHHHHHHHCCCCCCCCHHHCCHHHHHHH
T ss_conf 773002758999999999829997668876569999999
No 149
>pfam11798 IMS_HHH IMS family HHH motif. These proteins are involved in UV protection, eg.
Probab=68.88 E-value=3.4 Score=20.98 Aligned_cols=21 Identities=33% Similarity=0.642 Sum_probs=17.3
Q ss_pred CCHHCCCCCCHHHHHHHHHHHC
Q ss_conf 7100488879899999999808
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFG 576 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fg 576 (616)
-++.+|+|||+++.++ |+.+|
T Consensus 12 lpi~~i~GIG~~~~~~-L~~~g 32 (33)
T pfam11798 12 LPISKIPGIGRKTAEK-LEALG 32 (33)
T ss_pred CCCCCCCCCCHHHHHH-HHHCC
T ss_conf 7622168866678999-99826
No 150
>pfam00416 Ribosomal_S13 Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.
Probab=68.54 E-value=3 Score=21.34 Aligned_cols=42 Identities=26% Similarity=0.343 Sum_probs=29.5
Q ss_pred HHCCCCHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHC
Q ss_conf 21477100488879899999999808--8898993898888627
Q gi|255764496|r 551 KAAYSPLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLASI 592 (616)
Q Consensus 551 k~~~S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~v 592 (616)
|.+...|..|.|||+.+...+....| .-..+.+.|.+|+.++
T Consensus 11 K~v~~ALt~I~GIG~~~A~~Ic~~lgi~~~~k~~~Lt~~qi~~l 54 (106)
T pfam00416 11 KKIEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRI 54 (106)
T ss_pred CEEEEEECCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHH
T ss_conf 68644411210528999999999919597757154999999999
No 151
>KOG2875 consensus
Probab=68.04 E-value=7.9 Score=18.32 Aligned_cols=50 Identities=6% Similarity=0.178 Sum_probs=21.7
Q ss_pred CCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 62445542586613122035665554323455038715899999999999986333888888
Q gi|255764496|r 159 CLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAII 220 (616)
Q Consensus 159 Cl~y~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~G~~~~ii~~L~~~M~~aS~~l~FE~Aa~ 220 (616)
|..|-.+ |+++|- ..++ ++.+..||+-+.+ +..|.+. --|..-.|-+-|.
T Consensus 58 ~~~y~~~-~s~~~p----~~de---l~~i~~yf~ldv~--L~~l~~~--W~~~D~~F~~la~ 107 (323)
T KOG2875 58 CTVYRGD-KSASRP----TPDE---LEAISKYFQLDVT--LAQLYHH--WGSVDDHFQELAQ 107 (323)
T ss_pred EEEEEEE-CCCCCC----CHHH---HHHHHHHHHHEEE--HHHHHHH--HCCCCHHHHHHHH
T ss_conf 4899841-488999----8579---9999998821102--9998887--3757737888867
No 152
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB; InterPro: IPR011879 PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself . It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006817 phosphate transport.
Probab=67.81 E-value=7.1 Score=18.66 Aligned_cols=75 Identities=24% Similarity=0.386 Sum_probs=42.7
Q ss_pred CCCCCCEEEEEC---CHHHHHHHHHHHHHCCCCCCCCEEEE-ECCCCC--CCCCEEEECCCCCEEEECCCCHH------H
Q ss_conf 457984899809---85899999999997588778718999-718776--76634898179834885799899------9
Q gi|255764496|r 460 FPSWPDVVILDG---GKGQLSAAQGVLKKLNVENRITIISI-AKGPKR--SAGMEKFFVKKGEALVLNMRDPI------L 527 (616)
Q Consensus 460 ~~~~PDLilIDG---GkgQln~a~~vl~~l~i~~~i~vigl-aK~~~r--~~~~e~~~~~~~~~i~l~~~~~~------l 527 (616)
.-.+|||||.|= |.-=+..|+..-++ ....+||||=| |||++. -.|+|+ +- +-+.-++-||. .
T Consensus 43 ~E~~PDLILLDWMLPG~SGIel~R~Lr~~-~~Tr~iPIIMLTARGeE~Drv~GLet---GA-DDYvtKPFSp~EL~ARik 117 (226)
T TIGR02154 43 NERLPDLILLDWMLPGTSGIELARRLRRE-PETRAIPIIMLTARGEEEDRVRGLET---GA-DDYVTKPFSPRELLARIK 117 (226)
T ss_pred HCCCCCEEEECCCCCCCCHHHHHHHHCCC-CCCCCCCEEEEECCCCCCCCCCCCCC---CC-CCEEECCCCHHHHHHHHH
T ss_conf 60799889961478997569999873476-33148881774055560001131136---88-750367886588999999
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999988787788
Q gi|255764496|r 528 YFIQRLRDEAHR 539 (616)
Q Consensus 528 ~~Lq~iRDEaHR 539 (616)
-+|.|++-++--
T Consensus 118 AVLRR~~P~~~~ 129 (226)
T TIGR02154 118 AVLRRIRPELSD 129 (226)
T ss_pred HHHHCCCHHHHC
T ss_conf 998316712420
No 153
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=67.34 E-value=4.3 Score=20.18 Aligned_cols=79 Identities=11% Similarity=0.196 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHH-HHHHH-HCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHH
Q ss_conf 989999999887877887889899-86432-1477100488879899999999808889899389888862789998999
Q gi|255764496|r 523 RDPILYFIQRLRDEAHRFAITTHR-KRRKK-AAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIA 600 (616)
Q Consensus 523 ~~~~l~~Lq~iRDEaHRFAi~~hR-k~r~k-~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A 600 (616)
++.+..=|.-+.+..+=|.|.-.- +.|.- .+... .=.|...=+.-.|.+...=++..+....+=|.. .+.++
T Consensus 587 ~~~~~~Rl~~~~~~~dGf~iae~Dl~lRg~G~~~G~--~QsG~~~f~~adl~~D~~il~~Ar~~A~~il~~----dp~l~ 660 (677)
T PRK10917 587 SETARERLKIMRETNDGFEIAEKDLELRGPGELLGT--RQSGLPEFKVADLVRDQELLEEARKEARELLER----DPELA 660 (677)
T ss_pred CHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCC--CCCCCCCCEEEEHHHHHHHHHHHHHHHHHHHHH----CHHHH
T ss_conf 978999999999858749999999961588566887--666988744740887799999999999999987----97989
Q ss_pred HHHHHHH
Q ss_conf 9999985
Q gi|255764496|r 601 CKIYNHF 607 (616)
Q Consensus 601 ~~I~~~l 607 (616)
+.+...+
T Consensus 661 ~~~~~~~ 667 (677)
T PRK10917 661 EALLERW 667 (677)
T ss_pred HHHHHHH
T ss_conf 9999988
No 154
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=67.04 E-value=8.9 Score=17.93 Aligned_cols=75 Identities=19% Similarity=0.211 Sum_probs=45.9
Q ss_pred EECCCCC-HHHHHHHHCCCCCC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHH--HHH
Q ss_conf 5168728-03232110244445-5411689989999999977531311123333333345457984899809858--999
Q gi|255764496|r 402 VGENGFV-KNQYRKFNLHPNDV-KTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKG--QLS 477 (616)
Q Consensus 402 f~~g~~~-K~~YR~f~Ik~~~v-~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkg--Qln 477 (616)
++.+++. ...-+.+....... --+||...+++++.+...+ .|||++-||-+ .-.
T Consensus 17 ~dsn~~~l~~~l~~~G~~v~~~~iv~Dd~~~i~~~l~~~~~~----------------------~DlIIttGG~s~g~~D 74 (133)
T cd00758 17 EDTNGPALEALLEDLGCEVIYAGVVPDDADSIRAALIEASRE----------------------ADLVLTTGGTGVGRRD 74 (133)
T ss_pred EEHHHHHHHHHHHHCCCEEEEEEEECCCHHHHHHHHHHHHHC----------------------CCEEEECCCCCCCCCC
T ss_conf 973799999999988997989889897999999999998614----------------------9999993886679885
Q ss_pred HHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 9999999758877871899971
Q gi|255764496|r 478 AAQGVLKKLNVENRITIISIAK 499 (616)
Q Consensus 478 ~a~~vl~~l~i~~~i~viglaK 499 (616)
...+++.+++-. .++.-+++=
T Consensus 75 ~t~~~l~~~g~~-~~~~~~v~~ 95 (133)
T cd00758 75 VTPEALAELGER-EAHGKGVAL 95 (133)
T ss_pred CHHHHHHHHCCC-EEEEEEEEE
T ss_conf 189999985392-888876545
No 155
>TIGR00147 TIGR00147 conserved hypothetical protein TIGR00147; InterPro: IPR005218 Although the proteins in this group all contain the diacylglycerol kinase catalytic domain, their function is, as yet, unknown..
Probab=66.46 E-value=9.3 Score=17.79 Aligned_cols=116 Identities=19% Similarity=0.220 Sum_probs=52.7
Q ss_pred CCCCHHHHHHHHHHHHHCCCCCCHHHEECCCC----------CHHHHHHHHHHHHCCCCCCCCCCCCCCHHH------HH
Q ss_conf 78997898887775432137898123102688----------857876665432013433321256552667------89
Q gi|255764496|r 278 SESTNAQILSYFLRQFYTDKPCPENILLSEEA----------EETSLLEISFFKQYGYKVKITVPKQGEKRK------II 341 (616)
Q Consensus 278 ~~~~~~eil~~fI~qyY~~~~iP~~Iiv~~~~----------~~~~~l~~~L~~k~g~kV~i~~P~rG~kk~------Ll 341 (616)
.+.+..|++.... +. .+..+|..=++|.-- +-.++++..=.-..|.+..|.+-+-..... .+
T Consensus 71 GDGTi~ev~naL~-~~-d~~diP~lg~~P~Gt~NDFsr~lgIp~~~L~ka~~~~~~G~~~~~d~gqvN~~~~ksqilyF~ 148 (316)
T TIGR00147 71 GDGTIHEVVNALK-DL-DDKDIPALGILPVGTANDFSRALGIPKEDLIKAAKKVIAGKARAIDLGQVNKQYDKSQILYFI 148 (316)
T ss_pred CCCCHHHHHHHHH-HH-CCCCCCEEEEECCCCCCCHHHHCCCCHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHH
T ss_conf 8984899988887-51-257788245435765550333138758999999999838897346642226720046787777
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-----HH-------HHHHHHHHCCCCCCCEEEE-EECCCCCCCCCEEE
Q ss_conf 9999999986554323343389-----99-------9999875156643516999-70744377540488
Q gi|255764496|r 342 EQALINAHRSHTQKLSTEISHQ-----MI-------LKDFTKKFALPHIPKRIEI-YDNSHIMGCSAVGC 398 (616)
Q Consensus 342 ~lA~~NA~~~l~~k~~~~~~~~-----~~-------l~~Lk~~L~L~~~p~rIE~-fDiSh~~G~~~Vas 398 (616)
+++----... ..+.+.+.... .. +..|...=.+ -|.++|| +|..+++|...+=.
T Consensus 149 N~~GiG~day-~~~~~~~~p~~rvflk~~LG~~~Y~~~~L~~~~s~--~p~~~~~~~d~~~~~~~~~~~~ 215 (316)
T TIGR00147 149 NIAGIGFDAY-VTELTTEVPEKRVFLKALLGKLSYFLSGLEALASL--KPFELEIKIDGEEIQGEAVLFL 215 (316)
T ss_pred HHHHHHHHHH-HHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCC--CCCEEEEEECCCEEECCEEEEE
T ss_conf 5443115567-76565315407889999742565787577432246--8855899765823300146887
No 156
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=66.06 E-value=5.2 Score=19.62 Aligned_cols=53 Identities=13% Similarity=0.187 Sum_probs=35.9
Q ss_pred CHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCCC
Q ss_conf 10048887989999999980888989938988886278999899999999854786789
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSHT 614 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~~ 614 (616)
.+-+.||.+|.-..++..+=- =.|+||+-.+||++.+-.+.+..++.+=+-.+
T Consensus 74 ~f~q~pGmYPtlA~kIv~~~P------Y~sVeDvl~ipgLse~qK~~l~k~~~~Ftvt~ 126 (144)
T PRK02515 74 AFRQFPGMYPTLAGKIVKNAP------YDSVEDVLNLPGLSERQKELLEANLENFTVTE 126 (144)
T ss_pred HHHHCCCCCHHHHHHHHHCCC------CCCHHHHHHCCCCCHHHHHHHHHHHCCCEECC
T ss_conf 998688846799999984799------78799997178999999999998653663468
No 157
>pfam01949 DUF99 Protein of unknown function DUF99. The function of this archaebacterial protein family is unknown.
Probab=65.89 E-value=9.5 Score=17.72 Aligned_cols=170 Identities=15% Similarity=0.175 Sum_probs=88.7
Q ss_pred CEEEEEECCCCC--CCCCEEEEEEEECCCC-CHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 169997074437--7540488888516872-8032321102444455411689989999999977531311123333333
Q gi|255764496|r 380 KRIEIYDNSHIM--GCSAVGCMVVVGENGF-VKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQ 456 (616)
Q Consensus 380 ~rIE~fDiSh~~--G~~~Vas~Vvf~~g~~-~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~ 456 (616)
-|+-+||=|-+. +..++-..|||..+.. .--.++.. ++.|.|=...|.+++.+++..
T Consensus 3 iRvlGidDs~F~~~~~~~~lvGvv~r~~~~idGv~~~~i-----tvdG~DaT~~i~~mv~~~~~~--------------- 62 (185)
T pfam01949 3 IRVLGIDDSPFPRRDGKSILAGVVMRGDLVIDGVAFGEI-----TVDGDDATDAIIDLVKGKFRP--------------- 62 (185)
T ss_pred EEEEEEECCCCCCCCCCEEEEEEEEECCCEEEEEEEEEE-----EECCCCHHHHHHHHHHHCCCC---------------
T ss_conf 179998568766899858999999978918978999899-----877952799999999843556---------------
Q ss_pred CCCCCCCCCEEEEECC-HHHHHHH--HHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHHHHHHHH
Q ss_conf 3454579848998098-5899999--999997588778718999718776766348981798348857998999999988
Q gi|255764496|r 457 EYSFPSWPDVVILDGG-KGQLSAA--QGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRL 533 (616)
Q Consensus 457 ~~~~~~~PDLilIDGG-kgQln~a--~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~i 533 (616)
-=.+|++||= -|=.|.+ .+.-+++| +||+++.-.. ++-+.+ ..+ +-.+.
T Consensus 63 ------~i~~V~L~Git~aGFNvvD~~~l~~~tg----~PVI~V~~~~-----------p~~~~i-----e~A--L~khf 114 (185)
T pfam01949 63 ------DIRVILLDGITFGGFNIIDIEELYEETG----LPVIVVMRKE-----------PDLEGI-----ESA--LRKHF 114 (185)
T ss_pred ------CCEEEEECCEEEEEEEEECHHHHHHHHC----CCEEEEEEEC-----------CCHHHH-----HHH--HHHHC
T ss_conf ------6229998776253148845999999879----9889999737-----------986899-----999--99878
Q ss_pred HHHHHHHHHHHHHHHHHHHC---CCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 78778878898998643214---77100488879899999999808889899389888862789998999999998547
Q gi|255764496|r 534 RDEAHRFAITTHRKRRKKAA---YSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 534 RDEaHRFAi~~hRk~r~k~~---~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
-|...|.++-..-..+.... ....-+--|+.+.....+++.|--.. ++|- +-.+|+-|-..+..
T Consensus 115 ~d~~~R~~~i~~~g~~~~~~~~~~~iyvq~~Gi~~~~A~~ii~~~t~~g-----------~iPE-PLRvAhlIA~~v~~ 181 (185)
T pfam01949 115 PDDEERLKIIRKLGPIEPLPTRGGPVYIQAAGIDPEEAKELIERTTIRG-----------KIPE-PLRVAHLIASGVMR 181 (185)
T ss_pred CCHHHHHHHHHHCCCCEEEECCCCCEEEEECCCCHHHHHHHHHHHHHCC-----------CCCC-HHHHHHHHHHHHCC
T ss_conf 9989999999857996783038976999986999999999999971169-----------9971-27999999888602
No 158
>pfam01986 DUF123 Domain of unknown function DUF123. This archaebacterial domain has no known function. It is attached to an endonuclease domain in the putative endonuclease MJ0613. The domain contains several conserved cysteines and histidines. This suggests that the domain may be a zinc binding nucleic acid interaction domain (Bateman A unpubl.).
Probab=65.88 E-value=8.2 Score=18.20 Aligned_cols=25 Identities=36% Similarity=0.473 Sum_probs=20.6
Q ss_pred CCCCEEEEEEC---HHHHHHHHHHCCCC
Q ss_conf 99888899601---25878887613788
Q gi|255764496|r 18 IAGRVLYVGKA---YNLQKRIKSYMHSN 42 (616)
Q Consensus 18 ~~~~iiYvGKa---knL~~Rv~syf~~~ 42 (616)
+.|-.+|||-| .+|.+||.-|++..
T Consensus 5 ~~G~Y~YvGSA~G~~~L~~Ri~RHl~~~ 32 (99)
T pfam01986 5 PAGYYVYVGSALGPGGLAARIARHLRRS 32 (99)
T ss_pred CCEEEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf 8762999853677886189999986544
No 159
>PRK00766 hypothetical protein; Provisional
Probab=64.72 E-value=10 Score=17.57 Aligned_cols=167 Identities=14% Similarity=0.164 Sum_probs=87.1
Q ss_pred CEEEEEECCCCC---CCCCEEEEEEEECCCC-CHHHHHHHHCCCCCCCCCHHHHHHHHHHHH-HHHHHHCCCCCCCCCCC
Q ss_conf 169997074437---7540488888516872-803232110244445541168998999999-99775313111233333
Q gi|255764496|r 380 KRIEIYDNSHIM---GCSAVGCMVVVGENGF-VKNQYRKFNLHPNDVKTQDDCAMMRMVLER-RFSQLIKNEENLNFHPK 454 (616)
Q Consensus 380 ~rIE~fDiSh~~---G~~~Vas~Vvf~~g~~-~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~R-R~~r~~~~~~~l~~~~~ 454 (616)
-|+-+||=|-+. +..++-..|||..+.. .-=.+++.. +.|.|=...|-+++.+ +|.
T Consensus 9 iRvlGiDDs~F~~~~~~~~~LvGvv~r~~~~idGv~~~~it-----vDG~DaT~~i~~mv~~~~~r-------------- 69 (194)
T PRK00766 9 IRVLGIDDGTFLFKSGEKVILVGVVMRGGQWVDGVLSRWIT-----VDGLDATEAIIDMINSSRHR-------------- 69 (194)
T ss_pred CEEEEEECCCCCCCCCCCEEEEEEEEECCEEEEEEEEEEEE-----ECCCCHHHHHHHHHHCCCCC--------------
T ss_conf 58999855866678999569999999789389999998898-----78952799999999706556--------------
Q ss_pred CCCCCCCCCCCE--EEEECC-HHHHHHH--HHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHHHH
Q ss_conf 333454579848--998098-5899999--99999758877871899971877676634898179834885799899999
Q gi|255764496|r 455 KQEYSFPSWPDV--VILDGG-KGQLSAA--QGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYF 529 (616)
Q Consensus 455 ~~~~~~~~~PDL--ilIDGG-kgQln~a--~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~~ 529 (616)
||+ |++||= -|=.|.+ .+.-+++| +||+++.-.. | +-+.+ ..+ +
T Consensus 70 ---------~~i~~VlL~Git~aGFNvvD~~~l~~~tg----~PVI~V~~~~----------P-~~~~i-----~~A--L 118 (194)
T PRK00766 70 ---------GQLRVIMLDGITYAGFNVVDIEELHRETG----LPVIVVVRKK----------P-DFEAI-----ESA--L 118 (194)
T ss_pred ---------CCEEEEEECCEEEEEEEEECHHHHHHHHC----CCEEEEEEEC----------C-CHHHH-----HHH--H
T ss_conf ---------65479998775352147836999999879----9989999637----------9-76899-----999--9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH--CCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 99887877887889899864321--4771004888798999999998088898993898888627899989999999985
Q gi|255764496|r 530 IQRLRDEAHRFAITTHRKRRKKA--AYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHF 607 (616)
Q Consensus 530 Lq~iRDEaHRFAi~~hRk~r~k~--~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l 607 (616)
-.+.-|-..|.++-..-...... -....-+--|+.+.....+++.|--.. ++|- +-.+|+-|-..+
T Consensus 119 ~khf~d~e~R~~~~~~~g~~~~~~~~~~iyvq~~Gi~~~~A~~ii~~~t~~g-----------~iPE-PLRvAhlIA~av 186 (194)
T PRK00766 119 RKHFSDGEERWKLIKKAGPIVELIPGKNLYIQAAGIEPETAAEVIRVTSIRS-----------LIPE-PLRLAHLIASGV 186 (194)
T ss_pred HHHCCCHHHHHHHHHHCCCCEECCCCCCEEEEECCCCHHHHHHHHHHHCCCC-----------CCCC-HHHHHHHHHHHH
T ss_conf 9868988999999985699676368982799985999999999999970079-----------9971-279999998775
Q ss_pred C
Q ss_conf 4
Q gi|255764496|r 608 H 608 (616)
Q Consensus 608 ~ 608 (616)
-
T Consensus 187 ~ 187 (194)
T PRK00766 187 M 187 (194)
T ss_pred H
T ss_conf 1
No 160
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=64.49 E-value=6.5 Score=18.93 Aligned_cols=36 Identities=22% Similarity=0.195 Sum_probs=24.0
Q ss_pred CEEEEE-CCHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf 489980-98589999999999758877871899971877
Q gi|255764496|r 465 DVVILD-GGKGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616)
Q Consensus 465 DLilID-GGkgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616)
..+.+- -|..+|..-.+-+..-. ..+.+.+.+|.-+
T Consensus 181 ~~~~~~gi~ES~la~~L~~i~~~~--~~~~i~s~p~~~~ 217 (255)
T COG1058 181 RVLRVFGIGESSLAPTLKDLQDEQ--PNVTIASYPKDGE 217 (255)
T ss_pred EEEEECCCCHHHHHHHHHHHHHCC--CCCEEEECCCCCC
T ss_conf 999986877578789999998508--9977982588773
No 161
>PHA00439 exonuclease
Probab=63.90 E-value=4.1 Score=20.33 Aligned_cols=38 Identities=21% Similarity=0.312 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHCCCCCCHHHHHHHHHH
Q ss_conf 78778878898998643214771004888798999999998
Q gi|255764496|r 534 RDEAHRFAITTHRKRRKKAAYSPLDEINGIGPLRKRLLLQS 574 (616)
Q Consensus 534 RDEaHRFAi~~hRk~r~k~~~S~Ld~I~GIG~k~~~~Ll~~ 574 (616)
..||+||-.. +--.-....-.-.|||||+||.++||..
T Consensus 169 ~~~ad~~~~~---QtL~GD~tDgy~GvpGiG~ktA~klL~~ 206 (288)
T PHA00439 169 PETADRWHLF---QTIKGDSTDGYSGIPGWGPDTAEAFLNN 206 (288)
T ss_pred HHHHHHHHHH---HHHCCCCCCCCCCCCCCCHHHHHHHHCC
T ss_conf 6568898888---8624747689789988488999998637
No 162
>TIGR01083 nth endonuclease III; InterPro: IPR005759 The spectrum of DNA damage caused by reactive oxygen species includes a wide variety of modifications of purine and pyrimidine bases. Among these modified bases, 7,8-dihydro-8-oxoguanine (8-oxoG) is an important mutagenic lesion. Base excision repair is a critical mechanism for preventing mutations by removing the oxidative lesion from the DNA. Escherichia coli Nth protein (endonuclease III) has an 8-oxoG DNA glycosylase/AP lyase activity which removes 8-oxoG preferentially from 8-oxoG/G mispairs. Human hNTH1 protein, a homolog of E. coli Nth protein, has similar DNA glycosylase/AP lyase activity that removes 8-oxoG from 8-oxoG/G mispairs . ; GO: 0003906 DNA-(apurinic or apyrimidinic site) lyase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=63.84 E-value=4.2 Score=20.29 Aligned_cols=18 Identities=6% Similarity=0.230 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHCCC
Q ss_conf 999999999730110035
Q gi|255764496|r 131 VEKTINSLQRTFFLRSCA 148 (616)
Q Consensus 131 ~~~~l~~l~~~f~lR~C~ 148 (616)
+.++++.|.+.||=-+|.
T Consensus 4 ~~~il~~L~~~yP~p~tE 21 (192)
T TIGR01083 4 AQEILERLRKLYPHPTTE 21 (192)
T ss_pred HHHHHHHHHHHCCCCEEE
T ss_conf 789999999738997254
No 163
>KOG2518 consensus
Probab=63.21 E-value=7 Score=18.67 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=22.1
Q ss_pred HHHHCCCCC-CC----HHHHHHHHHCCCEEEEECCCHHHHHHH
Q ss_conf 876137887-78----799999973444299982871999999
Q gi|255764496|r 35 IKSYMHSNN-HT----HRITHMISQINNIRFTVTCTEVEALLL 72 (616)
Q Consensus 35 v~syf~~~~-~~----~k~~~l~~~~~~ie~~~t~~e~eAlil 72 (616)
-+.||+... -+ .++.++++.. .|||||..=|.+|.+-
T Consensus 115 A~~~fqr~VdIT~~ma~~lI~~~r~~-nVe~IVAPyEADAQla 156 (556)
T KOG2518 115 ARECFQRCVDITPEMAHKLIQYLRSQ-NVEYIVAPYEADAQLA 156 (556)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHC-CCCEEECCCCCCCHHH
T ss_conf 99999876117699999999999976-9755865762321237
No 164
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=62.50 E-value=7.9 Score=18.29 Aligned_cols=37 Identities=24% Similarity=0.363 Sum_probs=26.8
Q ss_pred CHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHC
Q ss_conf 100488879899999999808--8898993898888627
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLASI 592 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~v 592 (616)
.|..|.|||..+-+.++..-| --..+...|.||+.++
T Consensus 18 ALt~IyGIG~~~a~~I~~~~gi~~~~r~~~Lteeei~~i 56 (121)
T COG0099 18 ALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL 56 (121)
T ss_pred HHHHHCCCCHHHHHHHHHHCCCCHHHHHCCCCHHHHHHH
T ss_conf 046303536999999999919886676452999999999
No 165
>pfam00730 HhH-GPD HhH-GPD superfamily base excision DNA repair protein. This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family.
Probab=62.42 E-value=11 Score=17.28 Aligned_cols=15 Identities=20% Similarity=0.379 Sum_probs=5.8
Q ss_pred HHCCCCCCHHHHHHH
Q ss_conf 004888798999999
Q gi|255764496|r 557 LDEINGIGPLRKRLL 571 (616)
Q Consensus 557 Ld~I~GIG~k~~~~L 571 (616)
|..+||||+++..-.
T Consensus 83 L~~l~GIG~~ta~~~ 97 (144)
T pfam00730 83 LLALPGVGRWTAEAV 97 (144)
T ss_pred HHCCCCCCHHHHHHH
T ss_conf 860889769999999
No 166
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057 Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=61.58 E-value=6.7 Score=18.80 Aligned_cols=36 Identities=22% Similarity=0.308 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCC
Q ss_conf 16899899999999775313111233333333454579848998098589999999999758877
Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQGVLKKLNVEN 490 (616)
Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~vl~~l~i~~ 490 (616)
-+.+.=||.|+|=|| |||.+++.++.+|++-|||..
T Consensus 53 ~~tGlsREsLYkALs-----------------------------~~GnP~f~T~lkV~~ALG~~L 88 (91)
T TIGR02684 53 KKTGLSRESLYKALS-----------------------------GGGNPTFDTILKVTKALGLKL 88 (91)
T ss_pred HHHCCCHHHHHHHHC-----------------------------CCCCCCHHHHHHHHHHCCCEE
T ss_conf 982876788788735-----------------------------688956688899998408602
No 167
>pfam01645 Glu_synthase Conserved region in glutamate synthase. This family represents a region of the glutamate synthase protein. This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster.
Probab=61.09 E-value=12 Score=17.12 Aligned_cols=36 Identities=19% Similarity=0.473 Sum_probs=23.3
Q ss_pred CCEEEEECCHHHH-------------------HHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 8489980985899-------------------99999999758877871899971
Q gi|255764496|r 464 PDVVILDGGKGQL-------------------SAAQGVLKKLNVENRITIISIAK 499 (616)
Q Consensus 464 PDLilIDGGkgQl-------------------n~a~~vl~~l~i~~~i~viglaK 499 (616)
||.|.|||+.|=- ..|.++|.+.|+.++|.|++=-|
T Consensus 227 ~D~I~IdG~eGGTGAaP~~~~d~~GlP~~~~L~~~~~~L~~~glR~~V~liasGg 281 (367)
T pfam01645 227 ADIILIDGHDGGTGASPKTSIKHAGLPWELALAEVHQTLVENGLRDRVSLIADGG 281 (367)
T ss_pred CCEEEECCCCCCCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCC
T ss_conf 8889971789867755488997442469999999999998706757649997699
No 168
>pfam03118 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal.
Probab=60.19 E-value=12 Score=17.01 Aligned_cols=53 Identities=23% Similarity=0.279 Sum_probs=41.2
Q ss_pred CHHCCCCCCHHHHHHHH-HHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 10048887989999999-9808889899389888862789998999999998547
Q gi|255764496|r 556 PLDEINGIGPLRKRLLL-QSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll-~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
++++. ++.......|- ....++..+.+-|.+||.++|++|++..+.|.+.|++
T Consensus 9 ~I~~L-~LS~R~~N~Lk~~~I~tv~dL~~~s~~dLl~i~N~G~kSl~EI~~~L~~ 62 (62)
T pfam03118 9 PIEEL-ELSVRSYNCLKRAGINTVGDLLSKSEEDLLKIKNFGKKSLEEIKEKLEE 62 (62)
T ss_pred CHHHH-CCCHHHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
T ss_conf 89981-6868999999894996799998589999974889868579999999829
No 169
>cd00686 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function as homodimers and are found in several genera of fungi.
Probab=59.92 E-value=12 Score=16.98 Aligned_cols=104 Identities=19% Similarity=0.313 Sum_probs=62.3
Q ss_pred CEEEECCCCHHHHHHHHHHHHHHHHHHCCC--CCCCCC----CCCCCCHHHHHHCCCCCCCCC--CHHHHHHHHHHHHHH
Q ss_conf 437703788789999999999730110035--542124----788662445542586613122--035665554323455
Q gi|255764496|r 119 GSYFGPFASVDAVEKTINSLQRTFFLRSCA--DSVFRH----RTRPCLLFQIKRCSGPCTGEI--SSEKYMEFVHEAKKF 190 (616)
Q Consensus 119 ~~yfGPf~~~~~~~~~l~~l~~~f~lR~C~--~~~~~~----~~~pCl~y~i~~C~gpC~~~i--s~~~Y~~~v~~~~~f 190 (616)
-+|||||-+-.-+|.++++.+- |= ..-|.+ ..-|-+.--| .|+|-|+|.- ..+.+ +.-..|
T Consensus 139 Lrhyg~FCslniiRsTlDfFeG------CWIEQ~NF~GypGs~~yPgFLRRl-NgLG~~vg~sl~P~~~f----dE~~~F 207 (357)
T cd00686 139 LRHFGPFCSLNLIRSTLDFFEG------CWIEQYNFGGFPGSHDYPQFLRRM-NGLGHCVGASLWPKEQF----NERSLF 207 (357)
T ss_pred HHHCCCCHHHHHHHHHHHHHCC------CCEEECCCCCCCCCCCCHHHHHHH-CCCCCCCCCCCCCHHHC----CHHHHH
T ss_conf 9760763144779977776512------010332568988854360899984-26544025453765652----778889
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH
Q ss_conf 0387158999999999999863338888-88999999998622110
Q gi|255764496|r 191 LSGGNHNLKEKIARNMNQATLKEDYESA-IIHRDRLAALSHIQNHN 235 (616)
Q Consensus 191 L~G~~~~ii~~L~~~M~~aS~~l~FE~A-a~~RD~I~aL~~i~~~q 235 (616)
++ ....+.+++.-|.-.-+-+-|=+- -.-|||+..+++.....
T Consensus 208 ~e--itsaiAqme~~m~~~NDLmSFYKE~d~~rDq~~LV~N~~~~~ 251 (357)
T cd00686 208 LE--ITSAIAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVVSD 251 (357)
T ss_pred HH--HHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHEEEEC
T ss_conf 99--999999751418899999999997178056788875212355
No 170
>PRK08694 consensus
Probab=59.79 E-value=12 Score=16.96 Aligned_cols=37 Identities=24% Similarity=0.469 Sum_probs=25.5
Q ss_pred CCCEEEEE-------CCHH-----HHHHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 98489980-------9858-----9999999999758877871899971
Q gi|255764496|r 463 WPDVVILD-------GGKG-----QLSAAQGVLKKLNVENRITIISIAK 499 (616)
Q Consensus 463 ~PDLilID-------GGkg-----Qln~a~~vl~~l~i~~~i~viglaK 499 (616)
.+|||+|| .|++ ++..+-+.|+.+-.+.+|||+.|+-
T Consensus 330 kl~~vvIDYLqLi~~~~~~~~r~~~i~~isr~LK~lAkel~ipvi~LsQ 378 (468)
T PRK08694 330 KLGLIVIDYLQLMAGSGRSDNRASELGEISRSLKALAKELQVPIIALSQ 378 (468)
T ss_pred CCCEEEEEHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECC
T ss_conf 8738997367541688876559999999999999999997998999632
No 171
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=59.14 E-value=6.3 Score=18.99 Aligned_cols=42 Identities=29% Similarity=0.415 Sum_probs=23.5
Q ss_pred CCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHH
Q ss_conf 77100488879899999999808889899389888862789998999
Q gi|255764496|r 554 YSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIA 600 (616)
Q Consensus 554 ~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A 600 (616)
...|..|||||+|....++.. ........|.|.++ |+.-+-|
T Consensus 329 ~~~llRVPGiG~ksa~rIv~~----Rr~~rl~~e~Lkk~-GvvlkRa 370 (404)
T COG4277 329 YKELLRVPGIGVKSARRIVMT----RRRTRLTLEDLKKL-GVVLKRA 370 (404)
T ss_pred HHHHCCCCCCCHHHHHHHHHH----HHHCCCCHHHHHHH-CEEEECC
T ss_conf 778211688773788999887----42302679898653-3032214
No 172
>cd00885 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin.
Probab=58.69 E-value=11 Score=17.38 Aligned_cols=14 Identities=29% Similarity=0.242 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 16899899999999
Q gi|255764496|r 426 DDCAMMRMVLERRF 439 (616)
Q Consensus 426 DD~~~m~Evi~RR~ 439 (616)
||...+.+.+.+-.
T Consensus 43 D~~~~I~~al~~~~ 56 (170)
T cd00885 43 DDEDRIAEALRRAS 56 (170)
T ss_pred CCHHHHHHHHHHHH
T ss_conf 88999999999997
No 173
>cd02808 GltS_FMN Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast and bacterial pathway for ammonia assimilation. It is a multifunctional enzyme that functions through three distinct active centers, carrying out L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor.
Probab=58.56 E-value=13 Score=16.82 Aligned_cols=34 Identities=26% Similarity=0.526 Sum_probs=17.5
Q ss_pred CCEEEEECCHHHH-------------------HHHHHHHHHCCCCCCCCEEEE
Q ss_conf 8489980985899-------------------999999997588778718999
Q gi|255764496|r 464 PDVVILDGGKGQL-------------------SAAQGVLKKLNVENRITIISI 497 (616)
Q Consensus 464 PDLilIDGGkgQl-------------------n~a~~vl~~l~i~~~i~vigl 497 (616)
||.|.|||+.|=- ..|.++|.+.|+.++|.|++=
T Consensus 239 ~DfItIDG~eGGTGAaP~~~~d~~GlP~~~~l~~~~~~L~~~glr~~i~lias 291 (392)
T cd02808 239 ADFITIDGAEGGTGAAPLTFIDHVGLPTELGLARAHQALVKNGLRDRVSLIAS 291 (392)
T ss_pred CCEEEEECCCCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEC
T ss_conf 99999607998754142999974997389999999999997699676379963
No 174
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=57.77 E-value=6.3 Score=19.02 Aligned_cols=36 Identities=22% Similarity=0.249 Sum_probs=15.0
Q ss_pred CHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHH
Q ss_conf 100488879899999999808--889899389888862
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLAS 591 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~ 591 (616)
.|..|.|||+.+...+....| .-..+.+.|.+|+.+
T Consensus 18 aLt~I~GIG~~~A~~Ic~~lgi~~~~k~~~Ls~~qi~~ 55 (122)
T CHL00137 18 ALTYIYGIGLTSAKKILEKANIDPDTRTKDLTDEQIVS 55 (122)
T ss_pred HHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHH
T ss_conf 11100061899999999984989885526299999999
No 175
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=56.63 E-value=14 Score=16.60 Aligned_cols=29 Identities=14% Similarity=0.119 Sum_probs=12.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 58661312203566555432345503871
Q gi|255764496|r 167 CSGPCTGEISSEKYMEFVHEAKKFLSGGN 195 (616)
Q Consensus 167 C~gpC~~~is~~~Y~~~v~~~~~fL~G~~ 195 (616)
|...++-.-.-+.|...=..+..+++.-+
T Consensus 64 cp~~~~~~~~~~~y~~~s~~i~~i~~~~~ 92 (354)
T COG0389 64 CPRAIVAPPNFAAYRLASAEIRAILERYT 92 (354)
T ss_pred CCCEEEECCCHHHHHHHHHHHHHHHHCCC
T ss_conf 89809978807999999999999875012
No 176
>TIGR01317 GOGAT_sm_gam glutamate synthases, NADH/NADPH, small subunit; InterPro: IPR006005 One pathway for the assimilation of ammonia and glutamate biosynthesis involves glutamate synthase (1.4.1.13 from EC) which transfers the amide group of glutamine to 2-oxoglutarate to yield two molecules of glutamate. 2 L-glutamate + NADP^+ = L-glutamine + 2-oxoglutarate + NADPH + H^+. This describes a family in several archaeal and deeply branched bacterial lineages of a homotetrameric form of the NADPH-dependent or NADH-dependent glutamate synthase (1.4.1.13 from EC and 1.4.1.14 from EC respectively) small subunit. There is no corresponding large subunit. ; GO: 0016639 oxidoreductase activity acting on the CH-NH2 group of donors NAD or NADP as acceptor, 0006537 glutamate biosynthetic process.
Probab=56.63 E-value=8.7 Score=18.02 Aligned_cols=30 Identities=30% Similarity=0.723 Sum_probs=17.3
Q ss_pred HHHHHHHHHH--HHHHCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCHH
Q ss_conf 9999999973--0110035542124788662445542586613122035
Q gi|255764496|r 132 EKTINSLQRT--FFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSE 178 (616)
Q Consensus 132 ~~~l~~l~~~--f~lR~C~~~~~~~~~~pCl~y~i~~C~gpC~~~is~~ 178 (616)
|.+|+-|+++ || -|..|- |+|||.+..+-.
T Consensus 85 k~ALdrLh~TNNFP-------EFTGRv----------CPAPCEgaCtLg 116 (517)
T TIGR01317 85 KEALDRLHKTNNFP-------EFTGRV----------CPAPCEGACTLG 116 (517)
T ss_pred HHHHHHHHHHCCCC-------CCCCCC----------CCCCCCCCCCCC
T ss_conf 89999987646786-------567764----------878863000055
No 177
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=55.72 E-value=14 Score=16.50 Aligned_cols=136 Identities=20% Similarity=0.311 Sum_probs=75.7
Q ss_pred CCCEEEEE----CCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCC----CEEEECCCCHHHHHHHHHH
Q ss_conf 98489980----985899999999997588778718999718776766348981798----3488579989999999887
Q gi|255764496|r 463 WPDVVILD----GGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKG----EALVLNMRDPILYFIQRLR 534 (616)
Q Consensus 463 ~PDLilID----GGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~----~~i~l~~~~~~l~~Lq~iR 534 (616)
-|||||.| +|.| +.... .+..-+....|-+++=|++-+.-. |.+..+-- +|+..++-..+ |+ |
T Consensus 46 ~pDLILLDiYmPd~~G-i~lL~-~ir~~~~~~DVI~iTAA~d~~tI~--~alr~Gv~DYLiKPf~~eRl~~a---L~--~ 116 (224)
T COG4565 46 KPDLILLDIYMPDGNG-IELLP-ELRSQHYPVDVIVITAASDMETIK--EALRYGVVDYLIKPFTFERLQQA---LT--R 116 (224)
T ss_pred CCCEEEEEECCCCCCC-HHHHH-HHHHCCCCCCEEEEECCCHHHHHH--HHHHCCCHHHEECCEEHHHHHHH---HH--H
T ss_conf 8997999602679850-77999-998468997889995344378999--99965823220563409999999---99--9
Q ss_pred HHHHHHHHHHHHHHHHH---HCC---C---CHHCC-CCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHH
Q ss_conf 87788788989986432---147---7---10048-88798999999998088898993898888627899989999999
Q gi|255764496|r 535 DEAHRFAITTHRKRRKK---AAY---S---PLDEI-NGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIY 604 (616)
Q Consensus 535 DEaHRFAi~~hRk~r~k---~~~---S---~Ld~I-~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~ 604 (616)
=.-+|-+...|+....+ .++ + .-++. +||-+.|-+++...|. ..=..-|-|||++..|||+..|.+=.
T Consensus 117 y~~~r~~l~~~~~~sQ~~lD~l~~~~~k~~~~~~LPkGi~~~Tl~~i~~~~~--~~~~~~Taeela~~~giSRvTaRRYL 194 (224)
T COG4565 117 YRQKRHALESHQQLSQKELDQLFNIQSKEQPPDDLPKGLDELTLQKVREALK--EPDQELTAEELAQALGISRVTARRYL 194 (224)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHH--CCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999862010279999999832254567554787767999999999986--75776479999988372199999999
Q ss_pred HHHCC
Q ss_conf 98547
Q gi|255764496|r 605 NHFHK 609 (616)
Q Consensus 605 ~~l~~ 609 (616)
+++-.
T Consensus 195 eyl~~ 199 (224)
T COG4565 195 EYLVS 199 (224)
T ss_pred HHHHH
T ss_conf 99984
No 178
>PRK01215 competence damage-inducible protein A; Provisional
Probab=55.17 E-value=13 Score=16.70 Aligned_cols=35 Identities=17% Similarity=0.157 Sum_probs=21.7
Q ss_pred EEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf 8998098589999999999758877871899971877
Q gi|255764496|r 466 VVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616)
Q Consensus 466 LilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616)
|.+..=|..+|.....-+.+-. . .+.+.+.+|+-+
T Consensus 184 l~~~Gi~ES~la~~L~~l~~~~-p-~v~i~syP~~~~ 218 (264)
T PRK01215 184 ILVRGVPESDLAPYIKEVMKEY-P-RVYVKSHPKGIE 218 (264)
T ss_pred EEECCCCHHHHHHHHHHHHHHC-C-CCEEECCCCCCC
T ss_conf 9988999799999999999878-9-974865897541
No 179
>COG1204 Superfamily II helicase [General function prediction only]
Probab=54.93 E-value=14 Score=16.41 Aligned_cols=60 Identities=22% Similarity=0.454 Sum_probs=51.9
Q ss_pred HCCCCHHCCCCCCHHHHHHHHHH-HCCHHHHH-HCCHHHHHHCCCCCHHHHHHHHHHHCCCC
Q ss_conf 14771004888798999999998-08889899-38988886278999899999999854786
Q gi|255764496|r 552 AAYSPLDEINGIGPLRKRLLLQS-FGTVKMIS-RSSPETLASIEGISKKIACKIYNHFHKNT 611 (616)
Q Consensus 552 ~~~S~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~-~As~eeL~~v~gi~~~~A~~I~~~l~~~~ 611 (616)
.....|..|+|+|-++..+++.. +.+++.+. .|...++....|++.+++..|.+.+....
T Consensus 672 e~~~~l~~i~~~grvrar~ly~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~ 733 (766)
T COG1204 672 EELLELVEIRGVGRVRARKLYNAGYKSLEDLRLIADPAELLPLTGIGERLVEAILESLGRDV 733 (766)
T ss_pred HHHCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 66222110012316678998873200088887406746540131157989999999740444
No 180
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=53.66 E-value=8.4 Score=18.10 Aligned_cols=11 Identities=27% Similarity=0.501 Sum_probs=4.4
Q ss_pred CCCCHHHHHHH
Q ss_conf 65526678999
Q gi|255764496|r 333 KQGEKRKIIEQ 343 (616)
Q Consensus 333 ~rG~kk~Ll~l 343 (616)
..|+...|++.
T Consensus 88 ~tG~~~hli~~ 98 (149)
T PRK04053 88 ETGEDLHLIGS 98 (149)
T ss_pred CCCCCEEEEHH
T ss_conf 56851021248
No 181
>TIGR02672 cas_csm6 CRISPR-associated protein, Csm6 family; InterPro: IPR013489 Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognizable features . This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins..
Probab=53.34 E-value=12 Score=17.11 Aligned_cols=43 Identities=21% Similarity=0.374 Sum_probs=26.9
Q ss_pred CCCCCEEEEECCHHHHHH----HHHHHHHCCCCCCCCEEEEECCCCCC
Q ss_conf 579848998098589999----99999975887787189997187767
Q gi|255764496|r 461 PSWPDVVILDGGKGQLSA----AQGVLKKLNVENRITIISIAKGPKRS 504 (616)
Q Consensus 461 ~~~PDLilIDGGkgQln~----a~~vl~~l~i~~~i~viglaK~~~r~ 504 (616)
..||.|++.|||+|.||- +..+|++. +...-..=++-+..++.
T Consensus 251 kh~p~li~~dd~~p~ln~sfPdCeail~d~-l~~~~k~r~~l~~~~~~ 297 (393)
T TIGR02672 251 KHLPELIVLDDNLPKLNDSFPDCEAILDDK-LEKVKKIRLLLEKEKKS 297 (393)
T ss_pred HCCCCCEEEECCCCCCCCCCCCHHHHHHHH-HHHHHHHHHHHHCCCCC
T ss_conf 138643664178886587653068887545-55567765444236667
No 182
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=53.23 E-value=15 Score=16.23 Aligned_cols=40 Identities=30% Similarity=0.499 Sum_probs=32.2
Q ss_pred CCHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHCCCC
Q ss_conf 7100488879899999999808--8898993898888627899
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLASIEGI 595 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~v~gi 595 (616)
+.|-.|.||||+--+.| +..| ++..|...|..|+..+.+.
T Consensus 67 DDLt~I~GIGPk~e~~L-n~~GI~tfaQIAAwt~~di~~id~~ 108 (133)
T COG3743 67 DDLTRISGIGPKLEKVL-NELGIFTFAQIAAWTRADIAWIDDY 108 (133)
T ss_pred CCCHHHCCCCHHHHHHH-HHCCCCCHHHHHHCCHHHHHHHHHH
T ss_conf 54211004378899899-8747763999974489999999854
No 183
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit; InterPro: IPR011773 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins , .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription DNA-dependent.
Probab=53.00 E-value=15 Score=16.27 Aligned_cols=82 Identities=18% Similarity=0.244 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---------HHHCCCCHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHCCC
Q ss_conf 999999887877887889899864---------321477100488879899999999808--889899389888862789
Q gi|255764496|r 526 ILYFIQRLRDEAHRFAITTHRKRR---------KKAAYSPLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLASIEG 594 (616)
Q Consensus 526 ~l~~Lq~iRDEaHRFAi~~hRk~r---------~k~~~S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~v~g 594 (616)
-|.++..+.+++--|-+.-.+... .+.+....|++. + -+|--.=|+.=| |+.++..-|.+||.+++.
T Consensus 223 hl~~f~~~~~~~~~~~~~~~~~~ee~~~~~~~~~~~l~~~IeeLd-L-SVRs~NCLk~~gI~t~geL~~~~e~eLl~i~N 300 (324)
T TIGR02027 223 HLEPFVEIEEEIEELEESQEEEKEEDFDIKLEKSKLLSIKIEELD-L-SVRSYNCLKRAGIHTLGELVSKSEEELLKIKN 300 (324)
T ss_pred HHHHHHCCCCHHHHCCHHHHHCCCCCCCCCHHHHHHHCCCCHHHH-H-HHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCC
T ss_conf 888851577104421211120587644567257787517800324-5-48988646460354178888603898841788
Q ss_pred CCHHHHHHHHHHHCC
Q ss_conf 998999999998547
Q gi|255764496|r 595 ISKKIACKIYNHFHK 609 (616)
Q Consensus 595 i~~~~A~~I~~~l~~ 609 (616)
+|+|-...|.+.|++
T Consensus 301 fGkKSl~EI~ekL~~ 315 (324)
T TIGR02027 301 FGKKSLDEIKEKLAE 315 (324)
T ss_pred CCHHHHHHHHHHHHH
T ss_conf 573338999999887
No 184
>CHL00067 rps2 ribosomal protein S2
Probab=52.85 E-value=16 Score=16.19 Aligned_cols=36 Identities=28% Similarity=0.429 Sum_probs=27.3
Q ss_pred CCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf 57984899809858999999999975887787189997187
Q gi|255764496|r 461 PSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGP 501 (616)
Q Consensus 461 ~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616)
..+||+|+|=+-..--+|+.|+.+ + .||+|||+=-.
T Consensus 155 ~~lPd~iii~d~~~e~~ai~Ea~k---L--~IPvIaivDTn 190 (227)
T CHL00067 155 TKLPDIVIIVDQQEEYTALRECIK---L--GIPTISIVDTN 190 (227)
T ss_pred HCCCCEEEEECCCCCHHHHHHHHH---C--CCCEEEEEECC
T ss_conf 208976999677533799999987---5--99989996389
No 185
>PRK13844 recombination protein RecR; Provisional
Probab=52.46 E-value=10 Score=17.42 Aligned_cols=80 Identities=14% Similarity=0.083 Sum_probs=33.2
Q ss_pred CCCHHHHCCCCCEEEEEEEEEECCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHEECCCCC-HHHHHHHHH
Q ss_conf 4201110001883478899842474541011356677789978988877754321378981231026888-578766654
Q gi|255764496|r 241 RMDCFSLYHNKNLACIQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQFYTDKPCPENILLSEEAE-ETSLLEISF 319 (616)
Q Consensus 241 d~Dvi~i~~~~~~~~I~vl~vR~G~i~g~~~f~~~~~~~~~~~eil~~fI~qyY~~~~iP~~Iiv~~~~~-~~~~l~~~L 319 (616)
..|++++...+.+- .+.||=+|.+.-.....++ +...+ .|.+.-.+. -.+|||+-..+. |-+.-..++
T Consensus 91 ~~Dl~aiE~s~~y~--G~YhVL~G~iSpl~gigp~---~l~i~-----~L~~ri~~~-~i~EVIlA~~~t~EGe~Ta~yi 159 (200)
T PRK13844 91 MLDMIAIEEAGIYR--GKYFVLNGRISPLDGIGPS---ELKLD-----ILQQIIADR-KIDEVILAISPTVEGETTAHFI 159 (200)
T ss_pred HHHHHHHHHHCCCC--EEEEECCCCCCCCCCCCHH---HHCHH-----HHHHHHCCC-CCCEEEEECCCCCCHHHHHHHH
T ss_conf 89999999744106--6888748744732388822---30679-----999886379-9747999679996509999999
Q ss_pred HHHCCCCCCCCC
Q ss_conf 320134333212
Q gi|255764496|r 320 FKQYGYKVKITV 331 (616)
Q Consensus 320 ~~k~g~kV~i~~ 331 (616)
.+.....|+|..
T Consensus 160 ~~~l~~~ikitr 171 (200)
T PRK13844 160 SQMIAKDIKISR 171 (200)
T ss_pred HHHHCCCCCEEE
T ss_conf 998449972776
No 186
>PRK00076 recR recombination protein RecR; Reviewed
Probab=52.20 E-value=11 Score=17.37 Aligned_cols=31 Identities=6% Similarity=-0.070 Sum_probs=14.4
Q ss_pred CCCCHHHHCCCCCEEEEEEEEEECCEEEECCCC
Q ss_conf 542011100018834788998424745410113
Q gi|255764496|r 240 NRMDCFSLYHNKNLACIQTCFFHFGQNRGTCTF 272 (616)
Q Consensus 240 ~d~Dvi~i~~~~~~~~I~vl~vR~G~i~g~~~f 272 (616)
+..|++++...+.+- ...||=+|.+.-....
T Consensus 86 ~~~Dl~~iE~s~~y~--G~YhVLgG~lSpl~gi 116 (197)
T PRK00076 86 SPADVLAIERTGEYR--GLYHVLGGLLSPLDGI 116 (197)
T ss_pred CHHHHHHHHCCCCEE--EEEEECCCCCCCCCCC
T ss_conf 899999997579454--7835856624821289
No 187
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=52.00 E-value=16 Score=16.09 Aligned_cols=102 Identities=16% Similarity=0.175 Sum_probs=52.1
Q ss_pred CCCCCHHHHHHHH-CCCCCCCCCHHHHHHHHHHH--HHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHH
Q ss_conf 6872803232110-24444554116899899999--99977531311123333333345457984899809858999999
Q gi|255764496|r 404 ENGFVKNQYRKFN-LHPNDVKTQDDCAMMRMVLE--RRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQ 480 (616)
Q Consensus 404 ~g~~~K~~YR~f~-Ik~~~v~~~DD~~~m~Evi~--RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~ 480 (616)
|-.+.++.+++|+ +......+ -|.-.=+|++. |...+|.+.-. ....-..+||+++|..-...-.|++
T Consensus 103 N~~ti~~si~rl~~lE~~~~~~-~~~~tKkE~l~l~re~~kL~k~lg--------GIk~m~~~Pd~l~ViDp~~e~iAv~ 173 (252)
T COG0052 103 NFKTIRKSIKRLKELEKMEEDG-FDGLTKKEALMLTRELEKLEKSLG--------GIKDMKGLPDVLFVIDPRKEKIAVK 173 (252)
T ss_pred CCHHHHHHHHHHHHHHHHHHCC-CCCCCHHHHHHHHHHHHHHHHHHC--------CHHHCCCCCCEEEEECCCHHHHHHH
T ss_conf 7405888999999999876414-321007888877778999987401--------4111267999899968817689999
Q ss_pred HHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHHH
Q ss_conf 999975887787189997187767663489817983488579989999
Q gi|255764496|r 481 GVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILY 528 (616)
Q Consensus 481 ~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~ 528 (616)
++-+ + .|||+||+--.. .++.-.+.+|-|+.+.+
T Consensus 174 EA~k-l----gIPVvAlvDTn~---------dpd~VD~~IP~Ndda~r 207 (252)
T COG0052 174 EANK-L----GIPVVALVDTNC---------DPDGVDYVIPGNDDAIR 207 (252)
T ss_pred HHHH-C----CCCEEEEECCCC---------CCCCCCEEECCCCHHHH
T ss_conf 9997-5----999899841899---------97657655228870898
No 188
>PRK02101 hypothetical protein; Validated
Probab=51.94 E-value=16 Score=16.09 Aligned_cols=24 Identities=13% Similarity=0.084 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf 555432345503871589999999999
Q gi|255764496|r 181 MEFVHEAKKFLSGGNHNLKEKIARNMN 207 (616)
Q Consensus 181 ~~~v~~~~~fL~G~~~~ii~~L~~~M~ 207 (616)
.+....+...|+.-+. ++|.+-|.
T Consensus 28 ~~~t~~l~~~Lk~~s~---~el~~lm~ 51 (257)
T PRK02101 28 LDQSQALIDELRQLSP---DQLASLMK 51 (257)
T ss_pred HHHHHHHHHHHHHCCH---HHHHHHHC
T ss_conf 7999999999983799---99999978
No 189
>PRK10416 cell division protein FtsY; Provisional
Probab=51.78 E-value=16 Score=16.07 Aligned_cols=128 Identities=15% Similarity=0.208 Sum_probs=63.5
Q ss_pred HHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCC--CCCCHHHHHHHHHHHHHH
Q ss_conf 899999998751566435169997074437754048888851687280323211024444--554116899899999999
Q gi|255764496|r 362 HQMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPND--VKTQDDCAMMRMVLERRF 439 (616)
Q Consensus 362 ~~~~l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~--v~~~DD~~~m~Evi~RR~ 439 (616)
+.-+.++|+.+-.-.. +.+ +++-.|.++.+ |+|.-- ....-|.|.+---| ..-.+|-..|.|.-. .
T Consensus 335 RaAAieQL~~w~~r~~----v~v--i~~~~g~Dpa~--V~~dai--~~a~~~~~DvviiDTAGRl~~~~~LM~EL~k--i 402 (499)
T PRK10416 335 RAAAVEQLQVWGQRNN----IPV--IAQHTGADSAS--VIFDAI--QAAKARNVDVLIADTAGRLQNKSHLMEELKK--I 402 (499)
T ss_pred CHHHHHHHHHHHCCCC----CEE--EECCCCCCHHH--HHHHHH--HHHHHCCCCEEEEECCCCCCCCHHHHHHHHH--H
T ss_conf 5689999999842457----369--83689999799--999999--9999729998998577643260999999999--9
Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCC--EEEEECCHHHH--HHHHHHHHHCCCCCCCCEEEEECCCC-----------CC
Q ss_conf 77531311123333333345457984--89980985899--99999999758877871899971877-----------67
Q gi|255764496|r 440 SQLIKNEENLNFHPKKQEYSFPSWPD--VVILDGGKGQL--SAAQGVLKKLNVENRITIISIAKGPK-----------RS 504 (616)
Q Consensus 440 ~r~~~~~~~l~~~~~~~~~~~~~~PD--LilIDGGkgQl--n~a~~vl~~l~i~~~i~viglaK~~~-----------r~ 504 (616)
.|.++... ..-|+ |+++|+..||= +.|+.--+.++++ -+-|.|=+. +.
T Consensus 403 ~rvi~k~~-------------~~aP~e~lLVlDa~tGQna~~qak~F~e~~~lt----GiIlTKlDGtAKGG~~lsi~~~ 465 (499)
T PRK10416 403 VRVMKKLD-------------VEAPHEVMLTIDASTGQNAVSQAKLFHEAVGLT----GITLTKLDGTAKGGVIFSVADQ 465 (499)
T ss_pred HHHHHHCC-------------CCCCCEEEEEEECCCCHHHHHHHHHHHHCCCCC----EEEEECCCCCCCCHHHHHHHHH
T ss_conf 99997237-------------899974899977876778999999984427997----5999656778852599999999
Q ss_pred CCCEEEECCCCCEE
Q ss_conf 66348981798348
Q gi|255764496|r 505 AGMEKFFVKKGEAL 518 (616)
Q Consensus 505 ~~~e~~~~~~~~~i 518 (616)
++.-+.|.+-|+.+
T Consensus 466 ~~~PI~fiG~GE~i 479 (499)
T PRK10416 466 FGIPIRYIGVGERI 479 (499)
T ss_pred HCCCEEEEECCCCH
T ss_conf 88395998679882
No 190
>cd01425 RPS2 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane an
Probab=51.31 E-value=16 Score=16.02 Aligned_cols=37 Identities=24% Similarity=0.239 Sum_probs=27.9
Q ss_pred CCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf 579848998098589999999999758877871899971877
Q gi|255764496|r 461 PSWPDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616)
Q Consensus 461 ~~~PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616)
...||+|+|=+..-.-+++.|+-. ..||++|++=-+.
T Consensus 125 ~~~Pdliiv~d~~~~~~ai~Ea~~-----l~IPvI~i~Dtn~ 161 (193)
T cd01425 125 FRLPDLVIVLDPRKEHQAIREASK-----LGIPVIAIVDTNC 161 (193)
T ss_pred CCCCCEEEEECCCCCHHHHHHHHH-----HCCCEEEEECCCC
T ss_conf 669998999889841689999986-----1875578850899
No 191
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=50.47 E-value=17 Score=15.93 Aligned_cols=38 Identities=29% Similarity=0.459 Sum_probs=30.6
Q ss_pred CCHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHC
Q ss_conf 71004888798999999998-088898993898888627
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASI 592 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v 592 (616)
..|-.|+||||+-.++|-.- .-++..|..-|.+|+..+
T Consensus 153 DDLk~I~GIGP~~e~~Ln~~GI~~F~QIA~~t~~dia~i 191 (216)
T PRK12278 153 DDLTKITGVGPALAKKLNEAGITTFAQIAALTDEDIAAI 191 (216)
T ss_pred CCCCEECCCCHHHHHHHHHHCCCHHHHHHCCCHHHHHHH
T ss_conf 654360265889999999818723999855999999998
No 192
>smart00852 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Probab=49.55 E-value=17 Score=15.83 Aligned_cols=55 Identities=20% Similarity=0.281 Sum_probs=38.7
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHH--HHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf 11689989999999977531311123333333345457984899809858--9999999999758877871899971877
Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKG--QLSAAQGVLKKLNVENRITIISIAKGPK 502 (616)
Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkg--Qln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616)
.||...+.+.+.+-..+ .|+|++=||-| .-....+++.+++-. .++..++|=...
T Consensus 41 ~Dd~~~i~~~l~~~~~~----------------------~DlIittGG~g~g~~D~t~~al~~~~~~-~~~~~~~a~~Pg 97 (135)
T smart00852 41 PDDKEAIKEALREALER----------------------ADLVITTGGTGPGPDDVTPEAVAEALGK-ELPGFGEAMRPG 97 (135)
T ss_pred CCCHHHHHHHHHHHHHC----------------------CCEEEECCCCCCCCCCCHHHHHHHHCCC-CCCCEEEEEEEC
T ss_conf 99999999999998414----------------------8999982887899986589999997398-204549999959
No 193
>pfam03883 DUF328 Protein of unknown function (DUF328). Members of this family are functionally uncharacterized. They are about 250 amino acids in length.
Probab=49.43 E-value=17 Score=15.82 Aligned_cols=12 Identities=17% Similarity=0.437 Sum_probs=5.0
Q ss_pred CHHHEECCCCCH
Q ss_conf 812310268885
Q gi|255764496|r 300 PENILLSEEAEE 311 (616)
Q Consensus 300 P~~Iiv~~~~~~ 311 (616)
++++|++.-..+
T Consensus 156 ~~~~iinLaS~e 167 (238)
T pfam03883 156 EDEVLVNLASNE 167 (238)
T ss_pred CCCEEEECCCHH
T ss_conf 788388725088
No 194
>TIGR01836 PHA_synth_III_C poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit; InterPro: IPR010125 This entry represents the PhaC subunit of a heterodimeric form of polyhydroxyalkanoic acid (PHA) synthase. Excepting the PhaC of Bacillus megaterium (which needs PhaR), all members require PhaE (IPR010123 from INTERPRO) for activity and are designated class III. This enzyme builds ester polymers for carbon and energy storage that accumulate in inclusions, and both this enzyme and the depolymerase associate with the inclusions. Class III enzymes polymerise short-chain-length hydroxyalkanoates.; GO: 0008415 acyltransferase activity, 0042619 poly-hydroxybutyrate biosynthetic process.
Probab=49.41 E-value=9.7 Score=17.67 Aligned_cols=32 Identities=9% Similarity=0.386 Sum_probs=23.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCCC-CCHHH
Q ss_conf 11356677789978988877754321378-98123
Q gi|255764496|r 270 CTFFLKTDSESTNAQILSYFLRQFYTDKP-CPENI 303 (616)
Q Consensus 270 ~~f~~~~~~~~~~~eil~~fI~qyY~~~~-iP~~I 303 (616)
+.|.|+++.. ..|++++||.+||+.|. +-.++
T Consensus 257 EKWifDsPd~--AGEafRQf~kdFYQ~N~li~G~~ 289 (367)
T TIGR01836 257 EKWIFDSPDQ--AGEAFRQFVKDFYQQNGLINGEV 289 (367)
T ss_pred HHHHCCCCCC--CHHHHHHHHHHHHHHCCCEECEE
T ss_conf 2232178883--21358999999987166142407
No 195
>PRK13034 serine hydroxymethyltransferase; Reviewed
Probab=49.27 E-value=18 Score=15.80 Aligned_cols=25 Identities=16% Similarity=-0.001 Sum_probs=11.1
Q ss_pred CCCCEEEEEECCCCCCCCCEEEEEEE
Q ss_conf 43516999707443775404888885
Q gi|255764496|r 377 HIPKRIEIYDNSHIMGCSAVGCMVVV 402 (616)
Q Consensus 377 ~~p~rIE~fDiSh~~G~~~Vas~Vvf 402 (616)
++-.+|-+.|.+| +|--+-|+.|.|
T Consensus 115 ~PGD~im~l~l~~-GGHltHG~~~~~ 139 (422)
T PRK13034 115 KPGDTILGMSLDA-GGHLTHGAKVAL 139 (422)
T ss_pred CCCCEEEECCCCC-CCCCCCCCCCCC
T ss_conf 8998688436777-762557887553
No 196
>PRK11264 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional
Probab=48.79 E-value=12 Score=16.99 Aligned_cols=11 Identities=27% Similarity=0.739 Sum_probs=5.8
Q ss_pred CCEEEEECCHH
Q ss_conf 84899809858
Q gi|255764496|r 464 PDVVILDGGKG 474 (616)
Q Consensus 464 PDLilIDGGkg 474 (616)
|+++|.|==-+
T Consensus 161 P~iLllDEPTs 171 (248)
T PRK11264 161 PEVILFDEPTS 171 (248)
T ss_pred CCEEEECCCCC
T ss_conf 99999879876
No 197
>cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.
Probab=48.69 E-value=18 Score=15.81 Aligned_cols=31 Identities=26% Similarity=0.362 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHH
Q ss_conf 116899899999999775313111233333333454579848998098589
Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQ 475 (616)
Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQ 475 (616)
+||...+++.+.+...+ .-+||||.=||-|-
T Consensus 43 pDd~~~I~~~l~~~~~~--------------------~~~DlIittGGTG~ 73 (152)
T cd00886 43 PDDKDEIREALIEWADE--------------------DGVDLILTTGGTGL 73 (152)
T ss_pred CCCHHHHHHHHHHHHHC--------------------CCCCEEEECCCCCC
T ss_conf 99989999999999853--------------------69888996685558
No 198
>pfam02906 Fe_hyd_lg_C Iron only hydrogenase large subunit, C-terminal domain.
Probab=48.54 E-value=16 Score=16.19 Aligned_cols=36 Identities=6% Similarity=0.050 Sum_probs=20.0
Q ss_pred CCCEEEEEECHHHHHHHHHHCCCCC-CC-HHHHHHHHH
Q ss_conf 9888899601258788876137887-78-799999973
Q gi|255764496|r 19 AGRVLYVGKAYNLQKRIKSYMHSNN-HT-HRITHMISQ 54 (616)
Q Consensus 19 ~~~iiYvGKaknL~~Rv~syf~~~~-~~-~k~~~l~~~ 54 (616)
.|+.+|+.=|-.-+.=...+|.-.. .. .+....++.
T Consensus 10 ~gk~vvasiaP~~~~~f~~~~~~~~~~~~~kl~~aLk~ 47 (286)
T pfam02906 10 DGKKVVAQIAPAVRVAFGEEFGLPPGTVTGKLVAALRK 47 (286)
T ss_pred CCCEEEEEECCHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 89989999796889999898599810578999999998
No 199
>cd01141 TroA_d Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=47.83 E-value=18 Score=15.65 Aligned_cols=31 Identities=29% Similarity=0.534 Sum_probs=20.2
Q ss_pred CCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 848998098589999999999758877871899971
Q gi|255764496|r 464 PDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAK 499 (616)
Q Consensus 464 PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK 499 (616)
|||||..++-.+-. ..+.|+++|+ +++.+.-
T Consensus 70 PDlVi~~~~~~~~~-~~~~L~~~gI----~v~~~~~ 100 (186)
T cd01141 70 PDLVILYGGFQAQT-ILDKLEQLGI----PVLYVNE 100 (186)
T ss_pred CCEEEEECCCCCHH-HHHHHHHCCC----CEEEEEC
T ss_conf 99999958878678-9999996499----5799606
No 200
>KOG4716 consensus
Probab=47.01 E-value=19 Score=15.56 Aligned_cols=11 Identities=9% Similarity=0.166 Sum_probs=5.9
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999862
Q gi|255764496|r 221 HRDRLAALSHI 231 (616)
Q Consensus 221 ~RD~I~aL~~i 231 (616)
..|.|.++++.
T Consensus 113 VqnhI~s~NW~ 123 (503)
T KOG4716 113 VQNHIKSLNWG 123 (503)
T ss_pred HHHHHHHCCCE
T ss_conf 98776623525
No 201
>PRK11411 fecB iron-dicitrate transporter substrate-binding subunit; Provisional
Probab=45.34 E-value=20 Score=15.39 Aligned_cols=11 Identities=18% Similarity=0.317 Sum_probs=6.8
Q ss_pred CCHHHEECCCC
Q ss_conf 98123102688
Q gi|255764496|r 299 CPENILLSEEA 309 (616)
Q Consensus 299 iP~~Iiv~~~~ 309 (616)
-|+.|+.....
T Consensus 101 kPDLII~~~~~ 111 (297)
T PRK11411 101 KPDLIIADSSR 111 (297)
T ss_pred CCCEEEEECCC
T ss_conf 99999970765
No 202
>pfam00464 SHMT Serine hydroxymethyltransferase.
Probab=44.84 E-value=20 Score=15.34 Aligned_cols=25 Identities=28% Similarity=0.150 Sum_probs=12.2
Q ss_pred CCCCEEEEEECCCCCCCCCEEEEEEE
Q ss_conf 43516999707443775404888885
Q gi|255764496|r 377 HIPKRIEIYDNSHIMGCSAVGCMVVV 402 (616)
Q Consensus 377 ~~p~rIE~fDiSh~~G~~~Vas~Vvf 402 (616)
++-.+|-+.|.+| +|-.+-|+.|-|
T Consensus 104 ~PGD~il~l~l~~-GGHltHg~~~~~ 128 (380)
T pfam00464 104 NPGDRIMGLDLPH-GGHLTHGYPVNF 128 (380)
T ss_pred CCCCEEEECCCCC-CCCCCCCCCCCE
T ss_conf 7999899536777-754567986562
No 203
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=44.55 E-value=21 Score=15.31 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=45.3
Q ss_pred CCHHCCCCCCHHHHHHHHHH-HCCHHHHHHCCHHHHHHCCCCCHHHHHHHHH
Q ss_conf 71004888798999999998-0888989938988886278999899999999
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQS-FGTVKMISRSSPETLASIEGISKKIACKIYN 605 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~-Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~ 605 (616)
..|.+++|+.+.....|-.. |.+++.+..++.++|..++|++...|..|..
T Consensus 374 ~~l~~~~~~~~~~~~~l~~~g~~~~edl~~~~~del~~~~~~~~e~a~~li~ 425 (428)
T PRK09202 374 DDLLNLEGLDPELAFKLAEKGVKTLEDLAELAVDELIDIEGLDEEEAGELIM 425 (428)
T ss_pred HHHHHCCCCCHHHHHHHHHCCCCCHHHHHCCCHHHHHHCCCCCHHHHHHHHH
T ss_conf 7786456999999999998699879999657988896377989999999998
No 204
>pfam03296 Pox_polyA_pol Poxvirus poly(A) polymerase catalytic subunit.
Probab=44.36 E-value=11 Score=17.20 Aligned_cols=31 Identities=19% Similarity=0.424 Sum_probs=24.9
Q ss_pred EECHHHHHHHHHHCCCCCCCHHHHHHHHHCC
Q ss_conf 6012587888761378877879999997344
Q gi|255764496|r 26 GKAYNLQKRIKSYMHSNNHTHRITHMISQIN 56 (616)
Q Consensus 26 GKaknL~~Rv~syf~~~~~~~k~~~l~~~~~ 56 (616)
|....++.||.+||++.....|+.++..-+.
T Consensus 49 ~s~~eIk~ri~~YFsKQ~~~~kiG~i~tIie 79 (462)
T pfam03296 49 SSDSEIKRRILEYFSKQRTTYKIGKILTIIE 79 (462)
T ss_pred CCHHHHHHHHHHHHHHCCCHHHHHHEEEEEE
T ss_conf 9879999999998753443443300111305
No 205
>TIGR00674 dapA dihydrodipicolinate synthase; InterPro: IPR005263 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta-semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue . Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC, IPR005264 from INTERPRO) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Sinorhizobium meliloti protein mosA , which is involved in the biosynthesis of the rhizopine 3-O-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry . Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel. This family represents a subclass of dihydrodipicolinate synthase. ; GO: 0008840 dihydrodipicolinate synthase activity, 0019877 diaminopimelate biosynthetic process.
Probab=43.94 E-value=21 Score=15.24 Aligned_cols=53 Identities=21% Similarity=0.300 Sum_probs=39.3
Q ss_pred HHHHHHH-HHHHHHCCCC------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6655543-2345503871------------------589999999999998633388888899999999862
Q gi|255764496|r 179 KYMEFVH-EAKKFLSGGN------------------HNLKEKIARNMNQATLKEDYESAIIHRDRLAALSHI 231 (616)
Q Consensus 179 ~Y~~~v~-~~~~fL~G~~------------------~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~i 231 (616)
++...+. +=-.+|.|++ .++..++-++|-+++.+.+|++|.++..++.-|=+.
T Consensus 170 ~i~~~~p~~dF~vlsGDD~l~l~~~~~Gg~GVISV~~N~~P~~~~emv~~a~~G~~~~A~EIh~kL~~L~~~ 241 (288)
T TIGR00674 170 EIKAITPDDDFVVLSGDDALTLPILALGGKGVISVTSNVAPKLMKEMVENALEGDFAEAREIHQKLMPLFKA 241 (288)
T ss_pred HHHHHCCCCCEEEEECCCCHHHHHHHHCCCEEEEHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 999866898538884786113699981896167300555689999999998538978999999878889887
No 206
>TIGR00600 rad2 DNA excision repair protein (rad2); InterPro: IPR001044 Xeroderma pigmentosum (XP) is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair , . XP-G can be corrected by a 133 Kd nuclear protein, XPGC . XPGC is an acidic protein that confers normal UV resistance in expressing cells . It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms , . XPGC cleaves one strand of the duplex at the border with the single-stranded region . XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases , ; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C-terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents XPGC, an acidic protein that confers normal UV resistance in expressing cells, can correct XP-G. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms. XPGC cleaves one strand of the duplex at the border with the single-stranded region , .; GO: 0003697 single-stranded DNA binding, 0004519 endonuclease activity, 0006289 nucleotide-excision repair, 0005634 nucleus.
Probab=43.16 E-value=15 Score=16.39 Aligned_cols=27 Identities=15% Similarity=0.389 Sum_probs=19.2
Q ss_pred HHCCCCCCHHHHHHHHHHHC--CHHHHHH
Q ss_conf 00488879899999999808--8898993
Q gi|255764496|r 557 LDEINGIGPLRKRLLLQSFG--TVKMISR 583 (616)
Q Consensus 557 Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~ 583 (616)
=.+||+||+++...+|..|+ +++.+.+
T Consensus 954 T~Gl~~vG~V~A~EiL~EFPG~gLe~L~~ 982 (1127)
T TIGR00600 954 TEGLPTVGPVSAMEILNEFPGDGLEPLLK 982 (1127)
T ss_pred HCCCCCCCHHHHHHHHHCCCCCCCHHHHH
T ss_conf 35788664044665552387864013445
No 207
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=42.94 E-value=19 Score=15.59 Aligned_cols=106 Identities=12% Similarity=0.199 Sum_probs=52.7
Q ss_pred CEEEEECCCHHHHHHHHH-----------------HHHHHHCCCCEECCCCCCCCC-EEEEECC--CCCCEEEEEECCCC
Q ss_conf 429998287199999999-----------------887761872003364689772-6998088--99845999812356
Q gi|255764496|r 57 NIRFTVTCTEVEALLLEA-----------------NMIKRLKPRFNILLRDDKSFP-YILITDK--HKIPALYKHRDSST 116 (616)
Q Consensus 57 ~ie~~~t~~e~eAlilE~-----------------~lIk~~~P~yNi~LkDdk~yP-yi~it~~--~~~p~l~~~r~~~~ 116 (616)
.+|+++ ..+.||++.+. ++|.++.|+=-...|.--.|| |+..-.+ -.-||-.. -.-+-
T Consensus 126 ~fD~va-~gD~Ea~~~dl~~eG~~~~~~~~r~rd~~el~~~A~~GA~vv~qHP~yp~~vi~EiETyRGC~r~~~-ggCSF 203 (560)
T COG1031 126 GFDVVA-SGDVEAFVYDLFSEGVERAIDPDRFRDYEELDAYAPLGAEVVKQHPNYPEYVICEIETYRGCPRRVS-GGCSF 203 (560)
T ss_pred CEEEEE-ECCHHHHHHHHHHCCCCCCCCHHHHCCHHHHHHHHHCCCHHHHHCCCCCCEEEEEEEECCCCCCCCC-CCCCC
T ss_conf 304898-4569999999986477545880533028988766524335877388995307999851368732036-88754
Q ss_pred C-CCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHCCC
Q ss_conf 7-8437703788789999999999730110035542124788662445542586
Q gi|255764496|r 117 I-QGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSG 169 (616)
Q Consensus 117 ~-~~~yfGPf~~~~~~~~~l~~l~~~f~lR~C~~~~~~~~~~pCl~y~i~~C~g 169 (616)
. +-.| |+ +.......+++-+.-+|. |--..|+-.-.||+...++--.|
T Consensus 204 CtEp~~-g~-~~~R~~e~Vv~EVkaLY~---~GvrhFRlGRQ~difsy~~~~~g 252 (560)
T COG1031 204 CTEPVR-GR-PEFRPPEDVVEEVKALYR---AGVRHFRLGRQADIFSYGADDNG 252 (560)
T ss_pred CCCCCC-CC-CCCCCHHHHHHHHHHHHH---HCCCEEEECCCCCEEEECCCCCC
T ss_conf 167576-88-465898999999999997---06030561565410112156568
No 208
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=42.83 E-value=18 Score=15.69 Aligned_cols=47 Identities=19% Similarity=0.227 Sum_probs=23.1
Q ss_pred HHHHHHH-CCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHC
Q ss_conf 9998751-56643516999707443775404888885168728032321102
Q gi|255764496|r 367 KDFTKKF-ALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNL 417 (616)
Q Consensus 367 ~~Lk~~L-~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~I 417 (616)
+.|+..| .-+-.|+.+-+||=----| +-+-|.++-|..-..++-|--
T Consensus 316 ~nL~~lLl~aP~~~~~~lglDPg~rtG----~k~Avvd~tGk~l~~~~Iyp~ 363 (780)
T COG2183 316 ENLKDLLLAAPAKPKATLGLDPGFRTG----CKVAVVDDTGKLLDTATIYPH 363 (780)
T ss_pred HHHHHHHHCCCCCCCCEEECCCCCCCC----CEEEEECCCCCEECEEEEECC
T ss_conf 988998724888886012048763013----079998378855531699727
No 209
>PRK13910 DNA glycosylase MutY; Provisional
Probab=42.37 E-value=22 Score=15.08 Aligned_cols=24 Identities=25% Similarity=0.387 Sum_probs=12.4
Q ss_pred CCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 89888862789998999999998547
Q gi|255764496|r 584 SSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 584 As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
.+.+||.+++ + ++..++|++.|.+
T Consensus 261 ~~l~el~~l~-l-ps~~kKIL~~Lk~ 284 (290)
T PRK13910 261 YSLKDLETLP-I-SSMTLKILNFLKQ 284 (290)
T ss_pred EEHHHHHHCC-C-CCHHHHHHHHHHH
T ss_conf 1677752088-9-8289999999977
No 210
>KOG3931 consensus
Probab=42.31 E-value=9.3 Score=17.81 Aligned_cols=40 Identities=23% Similarity=0.370 Sum_probs=27.2
Q ss_pred HHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 4455425866131220356655543234550387158999999
Q gi|255764496|r 161 LFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIA 203 (616)
Q Consensus 161 ~y~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~G~~~~ii~~L~ 203 (616)
.-|++||.|||...- -|--.|+.+.+=--|-.+.....-+
T Consensus 163 r~HwWRC~GpCr~R~---Pf~GYVKR~~NRaPgpnD~WW~~HQ 202 (484)
T KOG3931 163 RRHWWRCNGPCRHRP---PFYGYVKRATNRAPGPNDYWWAEHQ 202 (484)
T ss_pred HHHHHHCCCCCCCCC---CCHHHHHCCCCCCCCCCCHHHHHHH
T ss_conf 766542577466788---7311000003689897437899876
No 211
>KOG3182 consensus
Probab=42.31 E-value=22 Score=15.07 Aligned_cols=34 Identities=24% Similarity=0.187 Sum_probs=12.5
Q ss_pred CCCHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHH
Q ss_conf 87158999999999999----86333888888999999
Q gi|255764496|r 193 GGNHNLKEKIARNMNQA----TLKEDYESAIIHRDRLA 226 (616)
Q Consensus 193 G~~~~ii~~L~~~M~~a----S~~l~FE~Aa~~RD~I~ 226 (616)
|.+-+.+-.|++-|.+. -+.--||-++..|.++.
T Consensus 150 G~N~eYLf~La~am~~l~p~~~D~hl~eL~~~Vrk~l~ 187 (212)
T KOG3182 150 GPNREYLFNLAKAMRQLFPGAEDEHLFELENEVRKYLV 187 (212)
T ss_pred CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 98689999999999970897304899999999999873
No 212
>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B; InterPro: IPR013484 MoaB is thought to be involved in molybdopterin biosynthesis, though its exact role is not known. Structural studies of this polypeptide suggest that it may play a role in substrate-shuttling during biosynthesis . MoaB was capable of binding GTP, and it was suggested that the putative active site could also bind precursor Z and/or molybdenum. Potential protein interaction domains were also found, implying that MoaB may play a transport and/or storage role in molybdopterin biosynthesis. .
Probab=42.04 E-value=22 Score=15.04 Aligned_cols=30 Identities=23% Similarity=0.482 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHH
Q ss_conf 11689989999999977531311123333333345457984899809858
Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKG 474 (616)
Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkg 474 (616)
.||...||.+|..|... +-=|.||+=||-|
T Consensus 45 ~DD~y~iRA~Vs~WIAd--------------------~~VqVil~TGGTG 74 (163)
T TIGR02667 45 KDDIYQIRAQVSEWIAD--------------------PAVQVILITGGTG 74 (163)
T ss_pred HHHHHHHHHHHHHHCCC--------------------CCCCEEEECCCCC
T ss_conf 74489999999873489--------------------8655688718823
No 213
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=41.88 E-value=17 Score=15.82 Aligned_cols=27 Identities=11% Similarity=0.006 Sum_probs=10.8
Q ss_pred CCCCHHHHCCCCCEEEEEEEEEECCEEEE
Q ss_conf 54201110001883478899842474541
Q gi|255764496|r 240 NRMDCFSLYHNKNLACIQTCFFHFGQNRG 268 (616)
Q Consensus 240 ~d~Dvi~i~~~~~~~~I~vl~vR~G~i~g 268 (616)
+..||+++...+..- ...||=+|.+.-
T Consensus 87 ~p~Dv~a~E~~~~f~--G~YhVL~G~lsp 113 (198)
T COG0353 87 EPKDVLALEKTGEFR--GLYHVLGGLLSP 113 (198)
T ss_pred CHHHHHHHHHHCCCC--EEEEEECCCCCC
T ss_conf 649999999745257--278884573373
No 214
>PRK07945 hypothetical protein; Provisional
Probab=41.63 E-value=23 Score=15.00 Aligned_cols=31 Identities=13% Similarity=0.139 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHH-----------------HHHHHHHHHHHHHHHHH
Q ss_conf 99999986333888-----------------88899999999862211
Q gi|255764496|r 204 RNMNQATLKEDYES-----------------AIIHRDRLAALSHIQNH 234 (616)
Q Consensus 204 ~~M~~aS~~l~FE~-----------------Aa~~RD~I~aL~~i~~~ 234 (616)
++|..++..+-||- +..++.|+..|..++++
T Consensus 114 eeMa~aA~~lGyeYlaITDHS~~l~vA~GLs~erL~~Q~~eI~~ln~~ 161 (335)
T PRK07945 114 EEMMATAAALGHEYCALTDHSPRLTVANGLSPERLRKQLDVIAELNER 161 (335)
T ss_pred HHHHHHHHHCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 999999998398279980488534566897999999999999999854
No 215
>cd06419 GH25_muramidase_2 Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain. Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues.
Probab=41.46 E-value=12 Score=16.98 Aligned_cols=11 Identities=18% Similarity=-0.124 Sum_probs=4.0
Q ss_pred EEEEECCCCCC
Q ss_conf 99970744377
Q gi|255764496|r 382 IEIYDNSHIMG 392 (616)
Q Consensus 382 IE~fDiSh~~G 392 (616)
|.+.||||.||
T Consensus 8 i~GIDVS~~qg 18 (190)
T cd06419 8 VLGVQLSQDDG 18 (190)
T ss_pred CEEEEECCCCC
T ss_conf 45279579889
No 216
>PRK04286 hypothetical protein; Provisional
Probab=41.27 E-value=21 Score=15.25 Aligned_cols=34 Identities=29% Similarity=0.494 Sum_probs=24.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHH
Q ss_conf 44445541168998999999997753131112333333334545798489980985899
Q gi|255764496|r 418 HPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQL 476 (616)
Q Consensus 418 k~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQl 476 (616)
-+.|++|+-|-.++..++... ||+++|||=-+-|
T Consensus 182 ~~SDvqG~~~~e~v~~il~~~-------------------------P~ivii~GPPtYL 215 (294)
T PRK04286 182 FASDVQGPLNDEAVEFILEKK-------------------------PTVVIIGGPPTYL 215 (294)
T ss_pred ECCCCCCCCCHHHHHHHHHCC-------------------------CCEEEECCCCHHH
T ss_conf 805566768789999998639-------------------------9989967984565
No 217
>pfam05559 DUF763 Protein of unknown function (DUF763). This family consists of several uncharacterized bacterial and archaeal proteins of unknown function.
Probab=41.06 E-value=16 Score=16.18 Aligned_cols=17 Identities=35% Similarity=0.540 Sum_probs=9.7
Q ss_pred CCHHCCCCCCHHHHHHH
Q ss_conf 71004888798999999
Q gi|255764496|r 555 SPLDEINGIGPLRKRLL 571 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~L 571 (616)
.+|..|+||||+|.++|
T Consensus 269 eeLLl~~GvGp~TlRAL 285 (319)
T pfam05559 269 EELLLLKGVGPSTLRAL 285 (319)
T ss_pred HHHHHCCCCCHHHHHHH
T ss_conf 99971479888999999
No 218
>PRK03670 competence damage-inducible protein A; Provisional
Probab=40.95 E-value=23 Score=14.93 Aligned_cols=35 Identities=14% Similarity=0.042 Sum_probs=21.0
Q ss_pred CEEEEEC-CHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf 4899809-8589999999999758877871899971877
Q gi|255764496|r 465 DVVILDG-GKGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616)
Q Consensus 465 DLilIDG-GkgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616)
..++..| |.+.+....+-+.+- .++.|-+..|...
T Consensus 184 ~~~~~~~~~Es~ia~~L~~~~~~---~~v~igsYPk~~~ 219 (252)
T PRK03670 184 KKYLAEITDESKLAPILEETIER---FNVRIHSSPKGFG 219 (252)
T ss_pred EEEEECCCCHHHHHHHHHHHHHH---HCCEEEECCCCCC
T ss_conf 99997899888999999999886---2986993878889
No 219
>pfam00994 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Probab=40.71 E-value=23 Score=14.90 Aligned_cols=41 Identities=29% Similarity=0.417 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHH--HHHHHHHHHHHCC
Q ss_conf 11689989999999977531311123333333345457984899809858--9999999999758
Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKG--QLSAAQGVLKKLN 487 (616)
Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkg--Qln~a~~vl~~l~ 487 (616)
+||.+.+++++.+-..+ -|+|++-||-| .-....+++.+++
T Consensus 40 ~Dd~~~i~~~l~~~~~~----------------------~DliittGG~g~g~~D~t~~al~~~~ 82 (140)
T pfam00994 40 PDDPEAIKEALAAAADE----------------------ADVVITTGGTGPGPDDVTPEALAELG 82 (140)
T ss_pred CCCHHHHHHHHHHHHCC----------------------CCEEEECCCCCCCCCCCHHHHHHHHH
T ss_conf 88999999999997326----------------------99999878877898985599999985
No 220
>COG4959 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=40.49 E-value=17 Score=16.00 Aligned_cols=13 Identities=31% Similarity=0.935 Sum_probs=7.9
Q ss_pred CCCCCEEEECCCC
Q ss_conf 5678437703788
Q gi|255764496|r 115 STIQGSYFGPFAS 127 (616)
Q Consensus 115 ~~~~~~yfGPf~~ 127 (616)
.+-.++||||++.
T Consensus 146 ~SfDsRYfGpipa 158 (173)
T COG4959 146 TSFDSRYFGPIPA 158 (173)
T ss_pred CCCCCCEECCCCH
T ss_conf 6554422056677
No 221
>COG0061 nadF NAD kinase [Coenzyme metabolism]
Probab=40.26 E-value=24 Score=14.86 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=9.3
Q ss_pred EEEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 454101135667778997898887775
Q gi|255764496|r 265 QNRGTCTFFLKTDSESTNAQILSYFLR 291 (616)
Q Consensus 265 ~i~g~~~f~~~~~~~~~~~eil~~fI~ 291 (616)
...|+..|..+.. .++.++++..++.
T Consensus 85 in~G~lGFLt~~~-~~~~~~~~~~~~~ 110 (281)
T COG0061 85 INLGHLGFLTDFE-PDELEKALDALLE 110 (281)
T ss_pred EECCCCCCCCCCC-HHHHHHHHHHHHC
T ss_conf 9889830036768-7899999999864
No 222
>PRK11823 DNA repair protein RadA; Provisional
Probab=39.97 E-value=24 Score=14.82 Aligned_cols=16 Identities=44% Similarity=0.636 Sum_probs=12.1
Q ss_pred CHHHHHHHHHHHHHHH
Q ss_conf 1168998999999997
Q gi|255764496|r 425 QDDCAMMRMVLERRFS 440 (616)
Q Consensus 425 ~DD~~~m~Evi~RR~~ 440 (616)
.+-.+|+--|+.+|..
T Consensus 330 ~~Rl~mllAVlek~~~ 345 (454)
T PRK11823 330 QNRLAMLLAVLEKRLG 345 (454)
T ss_pred HHHHHHHHHHHHHHHC
T ss_conf 8999999999999849
No 223
>cd01147 HemV-2 Metal binding protein HemV-2. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=39.76 E-value=24 Score=14.80 Aligned_cols=12 Identities=50% Similarity=0.755 Sum_probs=8.3
Q ss_pred CCEEEEECCHHH
Q ss_conf 848998098589
Q gi|255764496|r 464 PDVVILDGGKGQ 475 (616)
Q Consensus 464 PDLilIDGGkgQ 475 (616)
||.|++..+-+.
T Consensus 213 PDvI~~~~~~~~ 224 (262)
T cd01147 213 PDVIFLDTGSFY 224 (262)
T ss_pred CCEEEEECCCCC
T ss_conf 998999278753
No 224
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=39.60 E-value=24 Score=14.79 Aligned_cols=44 Identities=18% Similarity=0.160 Sum_probs=33.4
Q ss_pred HHHHHHHHH--CCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCC
Q ss_conf 999999980--88898993898888627899989999999985478
Q gi|255764496|r 567 RKRLLLQSF--GTVKMISRSSPETLASIEGISKKIACKIYNHFHKN 610 (616)
Q Consensus 567 ~~~~Ll~~F--gs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 610 (616)
|-..-|+.= .++.++.+-|.+||.++++.|++-.+.|.+.|..-
T Consensus 255 Rs~NcLk~a~I~tI~dLv~~se~dLl~ikNfGkKSl~EI~~kL~~~ 300 (306)
T PRK05182 255 RSYNCLKRAGINTIGDLVQRTEEELLKTPNLGKKSLEEIKEKLAEL 300 (306)
T ss_pred HHHHHHHHCCCCCHHHHHHCCHHHHHHCCCCCCCCHHHHHHHHHHC
T ss_conf 8875587859936999874799999618997620399999999972
No 225
>KOG4825 consensus
Probab=39.50 E-value=24 Score=14.78 Aligned_cols=51 Identities=20% Similarity=0.165 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 6655543234550387158999999999999863338888889999999986
Q gi|255764496|r 179 KYMEFVHEAKKFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAALSH 230 (616)
Q Consensus 179 ~Y~~~v~~~~~fL~G~~~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~ 230 (616)
+|.+..+.|+.=|+ +..+-...|+..--.|.++++|..|...+|+|.+++.
T Consensus 190 dlAKkaklAiaDLk-KsgeeleelEndKgcAVadEDfdlAkdkkdeiealRa 240 (666)
T KOG4825 190 DLAKKAKLAIADLK-KSGEELEELENDKGCAVADEDFDLAKDKKDEIEALRA 240 (666)
T ss_pred HHHHHHHHHHHHHH-HHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 58999999999999-8889998775013651110246677777999999999
No 226
>pfam07527 Hairy_orange Hairy Orange. The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute.
Probab=39.38 E-value=24 Score=14.76 Aligned_cols=22 Identities=23% Similarity=0.486 Sum_probs=16.9
Q ss_pred HHCCCCCCHHHHHHHHHHHCCH
Q ss_conf 0048887989999999980888
Q gi|255764496|r 557 LDEINGIGPLRKRLLLQSFGTV 578 (616)
Q Consensus 557 Ld~I~GIG~k~~~~Ll~~Fgs~ 578 (616)
|...+|+.+..+..|+.|+++.
T Consensus 18 L~~~~~~~~~~~~rLl~HL~~~ 39 (43)
T pfam07527 18 LSSVEGVDPDVRARLLSHLASC 39 (43)
T ss_pred HCCCCCCCHHHHHHHHHHHHHH
T ss_conf 6258999868999999999998
No 227
>pfam03104 DNA_pol_B_exo DNA polymerase family B, exonuclease domain. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold.
Probab=39.09 E-value=25 Score=14.73 Aligned_cols=95 Identities=15% Similarity=0.109 Sum_probs=49.6
Q ss_pred CCCEEEEEECCCCCCC--------CCE--EEEEEEECCCCCHHHHHHHHCCCCC-CC-CC--HHHHHHHHHHHHHHHHHH
Q ss_conf 3516999707443775--------404--8888851687280323211024444-55-41--168998999999997753
Q gi|255764496|r 378 IPKRIEIYDNSHIMGC--------SAV--GCMVVVGENGFVKNQYRKFNLHPND-VK-TQ--DDCAMMRMVLERRFSQLI 443 (616)
Q Consensus 378 ~p~rIE~fDiSh~~G~--------~~V--as~Vvf~~g~~~K~~YR~f~Ik~~~-v~-~~--DD~~~m~Evi~RR~~r~~ 443 (616)
+|.+|-+|||--.++. ++| -|+|++..|.+.+..=.-|-+.+.+ +. +. --|..=+|+|.+.+.-+.
T Consensus 84 pplrilsfDIEc~~~~g~FP~~~~d~IiqIs~~~~~~g~~~~~~~~~~tl~~~~~i~~~~~V~~f~~E~~ll~~f~~~i~ 163 (254)
T pfam03104 84 PPLRVLSFDIECTSLKGKFPENEKDPIIQISCMLYREGEPDPIEDKLFTLKSCALIEIGGEVYIFPSEKELLRRFFEFIR 163 (254)
T ss_pred CCCEEEEEEEEECCCCCCCCCCCCCEEEEEEEEEEECCCCCCCCEEEEEECCCCCCCCCCEEEEECCHHHHHHHHHHHHH
T ss_conf 88539999889588899999878983899998988567898632069980787767789779995999999999999987
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEECCHHH-HHHHHHHHHHCCCC
Q ss_conf 13111233333333454579848998098589-99999999975887
Q gi|255764496|r 444 KNEENLNFHPKKQEYSFPSWPDVVILDGGKGQ-LSAAQGVLKKLNVE 489 (616)
Q Consensus 444 ~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQ-ln~a~~vl~~l~i~ 489 (616)
+.+ ||+|+==-+-|= +-...+-.+.+++.
T Consensus 164 ~~d-----------------pdii~gyNi~~FD~~yl~~Ra~~l~~~ 193 (254)
T pfam03104 164 QYD-----------------PDIITGYNGDNFDWPYILNRAKILGLK 193 (254)
T ss_pred HCC-----------------CCEEEECCCCCCCHHHHHHHHHHHCCC
T ss_conf 519-----------------989996678778889999999996896
No 228
>PRK05636 replicative DNA helicase; Provisional
Probab=38.50 E-value=25 Score=14.67 Aligned_cols=38 Identities=26% Similarity=0.375 Sum_probs=25.8
Q ss_pred CCEEEEE------CCH------HHHHHHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf 8489980------985------8999999999975887787189997187
Q gi|255764496|r 464 PDVVILD------GGK------GQLSAAQGVLKKLNVENRITIISIAKGP 501 (616)
Q Consensus 464 PDLilID------GGk------gQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616)
.|||+|| +|. .++..+-+.|+.+-.+.+|||+.|+-=.
T Consensus 378 l~livVDYLQLm~~~~~~~~R~~ev~~ISr~LK~lAkel~vpVi~LsQLn 427 (507)
T PRK05636 378 LKMIVVDYLQLMSSGKRVESRQQEVSEFSRQLKLLAKELDVPLIAISQLN 427 (507)
T ss_pred CCEEEEEHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf 99899845884568888766899999999999999999799889971268
No 229
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=38.03 E-value=26 Score=14.62 Aligned_cols=36 Identities=19% Similarity=0.386 Sum_probs=18.3
Q ss_pred CCEEEEE-------CCH-----HHHHHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 8489980-------985-----89999999999758877871899971
Q gi|255764496|r 464 PDVVILD-------GGK-----GQLSAAQGVLKKLNVENRITIISIAK 499 (616)
Q Consensus 464 PDLilID-------GGk-----gQln~a~~vl~~l~i~~~i~viglaK 499 (616)
||+|+|| ++. -++..+.+.|+.+-.+.+|||+.++-
T Consensus 124 ~~~vvvDylql~~~~~~~~~~~~~i~~i~~~Lk~lA~e~~v~Vi~~sQ 171 (242)
T cd00984 124 LGLIVIDYLQLMSGSKKKGNRQQEVAEISRSLKLLAKELNVPVIALSQ 171 (242)
T ss_pred CCEEEEEHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCEEEEEEC
T ss_conf 989998269854677766579999999999999999997993999846
No 230
>smart00696 DM9 Repeats found in Drosophila proteins.
Probab=37.23 E-value=22 Score=15.15 Aligned_cols=14 Identities=57% Similarity=0.980 Sum_probs=8.3
Q ss_pred ECCCCCEEEEEECH
Q ss_conf 86998888996012
Q gi|255764496|r 16 LDIAGRVLYVGKAY 29 (616)
Q Consensus 16 ~~~~~~iiYvGKak 29 (616)
.|.+|+.||||.|.
T Consensus 21 ~~~~Ge~lYvgR~~ 34 (71)
T smart00696 21 TDSDGEPLYVGRAY 34 (71)
T ss_pred ECCCCCEEEEEEEE
T ss_conf 07999999999999
No 231
>PRK10880 adenine DNA glycosylase; Provisional
Probab=37.16 E-value=26 Score=14.53 Aligned_cols=17 Identities=18% Similarity=0.204 Sum_probs=6.7
Q ss_pred HHHHHHHHHHCCCCCCC
Q ss_conf 99999987515664351
Q gi|255764496|r 364 MILKDFTKKFALPHIPK 380 (616)
Q Consensus 364 ~~l~~Lk~~L~L~~~p~ 380 (616)
.++=+|-.....++.|.
T Consensus 182 QAlMDLGA~vCtp~~P~ 198 (350)
T PRK10880 182 QAMMDLGAMVCTRSKPK 198 (350)
T ss_pred HHHHHHHHHHCCCCCCC
T ss_conf 99999734102799998
No 232
>pfam06330 TRI5 Trichodiene synthase (TRI5). This family consists of several fungal trichodiene synthase proteins (EC:4.2.3.6). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyse the first step in the trichothecene pathways of Fusarium and Trichothecium species.
Probab=36.98 E-value=27 Score=14.51 Aligned_cols=106 Identities=20% Similarity=0.276 Sum_probs=62.0
Q ss_pred CEEEECCCCHHHHHHHHHHHHHHHHHHCCC--CCCCCC-C---CCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf 437703788789999999999730110035--542124-7---8866244554258661312203566555432345503
Q gi|255764496|r 119 GSYFGPFASVDAVEKTINSLQRTFFLRSCA--DSVFRH-R---TRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLS 192 (616)
Q Consensus 119 ~~yfGPf~~~~~~~~~l~~l~~~f~lR~C~--~~~~~~-~---~~pCl~y~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~ 192 (616)
-+|||||-+-.-+|.++++.+- |= ..-|.+ + .-|-+.--| .|+|-|+|.---- .+..+.-+.|++
T Consensus 139 Lrhyg~FCslniiRsTlDfFeG------CWIEQ~NF~G~pGs~~yPgFLRRl-NgLG~~vg~sl~P--~~~fDE~~~F~e 209 (376)
T pfam06330 139 LRHFGPFCSLNLIRSTLDFFEG------CWIEQYNFGGFPGSDDYPQFLRRM-NGLGHCVGGSLWP--KELFDEQKLFLE 209 (376)
T ss_pred HHHCCCCHHHHHHHHHHHHHCC------CCEEECCCCCCCCCCCCHHHHHHH-CCCCCCCCCCCCC--HHHCCHHHHHHH
T ss_conf 9750764144779877766512------010332568988854353899983-3655412545476--565276778999
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH
Q ss_conf 87158999999999999863338888-88999999998622110
Q gi|255764496|r 193 GGNHNLKEKIARNMNQATLKEDYESA-IIHRDRLAALSHIQNHN 235 (616)
Q Consensus 193 G~~~~ii~~L~~~M~~aS~~l~FE~A-a~~RD~I~aL~~i~~~q 235 (616)
....+.+++.-|.-.-+-+-|=+- -.-||++..+++.....
T Consensus 210 --itsaiAqme~~m~~~NDLmSFYKE~d~~rDq~sLV~N~~~~~ 251 (376)
T pfam06330 210 --ITSAVAQMENWMVWVNDLMSFYKEFDDERDQISLVKNYVTCD 251 (376)
T ss_pred --HHHHHHHHCCHHHHHHHHHHHHHHHCCCHHHHHHHHHEEEEC
T ss_conf --999999751418899999999997178056788875224455
No 233
>COG2248 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]
Probab=36.88 E-value=26 Score=14.59 Aligned_cols=34 Identities=32% Similarity=0.557 Sum_probs=23.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHH
Q ss_conf 44445541168998999999997753131112333333334545798489980985899
Q gi|255764496|r 418 HPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQL 476 (616)
Q Consensus 418 k~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQl 476 (616)
-..|++|+.--.++...+.+| ||+++|||--+-+
T Consensus 181 faSDvqGp~~~~~l~~i~e~~-------------------------P~v~ii~GPpty~ 214 (304)
T COG2248 181 FASDVQGPINDEALEFILEKR-------------------------PDVLIIGGPPTYL 214 (304)
T ss_pred ECCCCCCCCCCHHHHHHHHCC-------------------------CCEEEECCCCHHH
T ss_conf 713666888608889998518-------------------------9889966982667
No 234
>PRK00260 cysS cysteinyl-tRNA synthetase; Validated
Probab=36.82 E-value=27 Score=14.49 Aligned_cols=19 Identities=16% Similarity=0.343 Sum_probs=11.7
Q ss_pred CCCHHHHHHHH--HHHHHHHH
Q ss_conf 78878999999--99997301
Q gi|255764496|r 125 FASVDAVEKTI--NSLQRTFF 143 (616)
Q Consensus 125 f~~~~~~~~~l--~~l~~~f~ 143 (616)
+++.+.+|..+ ++|.++..
T Consensus 36 ~~HiG~~r~~v~~D~l~R~l~ 56 (460)
T PRK00260 36 YAHIGHARSFVVFDVLRRYLR 56 (460)
T ss_pred CCCHHCCCHHHHHHHHHHHHH
T ss_conf 732000308999999999999
No 235
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=36.62 E-value=27 Score=14.47 Aligned_cols=44 Identities=20% Similarity=0.206 Sum_probs=35.3
Q ss_pred HHHHHHHHHH--CCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 9999999980--8889899389888862789998999999998547
Q gi|255764496|r 566 LRKRLLLQSF--GTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 566 k~~~~Ll~~F--gs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
.|--.-|+.= .++.++.+-|.+||.++.+.|++-.+.|.+.|++
T Consensus 281 vRs~NCLKra~I~tvgdLv~~se~dLl~ikNfGkKSl~EI~ekL~e 326 (333)
T CHL00013 281 VRAYNCLKRANIHTLLDLLNYSQEDLLKIKNFGQKSVKQVLDALEK 326 (333)
T ss_pred HHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHH
T ss_conf 8877436373893799986389999941899863029999999988
No 236
>cd01139 TroA_f Periplasmic binding protein TroA_f. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=36.54 E-value=27 Score=14.46 Aligned_cols=10 Identities=40% Similarity=1.109 Sum_probs=8.5
Q ss_pred CCEEEEECCH
Q ss_conf 8489980985
Q gi|255764496|r 464 PDVVILDGGK 473 (616)
Q Consensus 464 PDLilIDGGk 473 (616)
||+|++.|+-
T Consensus 234 PDvIii~~~~ 243 (342)
T cd01139 234 PEIIIATGGN 243 (342)
T ss_pred CCEEEEECCC
T ss_conf 8889996775
No 237
>PRK03673 competence damage-inducible protein A; Provisional
Probab=35.64 E-value=28 Score=14.36 Aligned_cols=17 Identities=18% Similarity=0.217 Sum_probs=8.2
Q ss_pred HHHHCCCCHHHHHHHHH
Q ss_conf 45503871589999999
Q gi|255764496|r 188 KKFLSGGNHNLKEKIAR 204 (616)
Q Consensus 188 ~~fL~G~~~~ii~~L~~ 204 (616)
.-||-|=..|+...+++
T Consensus 147 ~~~LPGvP~Emk~M~~~ 163 (396)
T PRK03673 147 MFFTPGVPSEFKVMVEQ 163 (396)
T ss_pred EEEECCCHHHHHHHHHH
T ss_conf 99918984999999999
No 238
>KOG2379 consensus
Probab=35.56 E-value=28 Score=14.35 Aligned_cols=54 Identities=17% Similarity=0.350 Sum_probs=40.4
Q ss_pred CHHCCCCCCHHHHHHHHHHHCCHHHHHHCC----HHHHHHC-----------CCCCHHHHHHHHHHHCC
Q ss_conf 100488879899999999808889899389----8888627-----------89998999999998547
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFGTVKMISRSS----PETLASI-----------EGISKKIACKIYNHFHK 609 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As----~eeL~~v-----------~gi~~~~A~~I~~~l~~ 609 (616)
.|.+|+||+.-+.-+|..+|.|+..+..|= .+++... ..|++++..+|+.+|-+
T Consensus 431 qLMqvkg~S~erAiAI~d~YpTl~sLl~AY~~s~~~k~~~l~ln~~~~~~~~rn~~~~Ls~~l~~~F~~ 499 (501)
T KOG2379 431 QLMQVKGMSLERAIAIADRYPTLRSLLSAYEVSADDKLRLLLLNPIKCGPGSRNIGPALSAKLYEFFLP 499 (501)
T ss_pred HHHHCCCCCHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf 998434754888999999656899999998616837888325565535641024307778889976515
No 239
>PRK07649 para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II; Validated
Probab=35.54 E-value=19 Score=15.58 Aligned_cols=37 Identities=19% Similarity=0.246 Sum_probs=19.1
Q ss_pred EEEEEEECCEEEECCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 88998424745410113566777899789888777543
Q gi|255764496|r 256 IQTCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQF 293 (616)
Q Consensus 256 I~vl~vR~G~i~g~~~f~~~~~~~~~~~eil~~fI~qy 293 (616)
|.-+.-+.-.+.|.+ |-++....+....++.+||..+
T Consensus 152 i~ai~h~~~pi~GVQ-FHPEs~~T~~G~~il~NFl~k~ 188 (195)
T PRK07649 152 IMAIRHKTLPIEGVQ-FHPESIMTSHGKELLQNFIRKY 188 (195)
T ss_pred EEEEEECCCCEEEEE-ECCCCCCCCCHHHHHHHHHHHH
T ss_conf 899993899889998-6898889977689999999861
No 240
>PRK04020 rps2P 30S ribosomal protein S2; Provisional
Probab=34.94 E-value=29 Score=14.29 Aligned_cols=34 Identities=18% Similarity=0.527 Sum_probs=24.0
Q ss_pred CCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf 848998098589999999999758877871899971877
Q gi|255764496|r 464 PDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616)
Q Consensus 464 PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616)
|||++|=--.-.-+|+.++.+ + .||+|||+=-+.
T Consensus 115 PdlliV~Dp~~e~~AV~EA~~---l--~IPvIaivDTn~ 148 (204)
T PRK04020 115 PDVLVVTDPRGDAQAVKEAIE---I--GIPVVALCDTDN 148 (204)
T ss_pred CCEEEEECCCCCHHHHHHHHH---C--CCCEEEEECCCC
T ss_conf 998999788630489999987---6--999899827998
No 241
>TIGR02042 sir sulfite reductase, ferredoxin dependent; InterPro: IPR011787 Distantly related to the iron-sulphur hemoprotein of sulphite reductase (NADPH) found in Proteobacteria and Eubacteria, sulphite reductase (ferredoxin) is a cyanobacterial and plant monomeric enzyme that also catalyzes the reduction of sulphite to sulphide.; GO: 0020037 heme binding, 0050311 sulfite reductase (ferredoxin) activity, 0051539 4 iron 4 sulfur cluster binding.
Probab=33.36 E-value=30 Score=14.11 Aligned_cols=93 Identities=14% Similarity=0.123 Sum_probs=57.3
Q ss_pred CEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 16999707443775404888885168728032321102444455411689989999999977531311123333333345
Q gi|255764496|r 380 KRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYS 459 (616)
Q Consensus 380 ~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~ 459 (616)
.+---|===|=+|+=..=.-+...+|+-. .+ =.|.+| .++||||.|+=-.+.
T Consensus 352 f~y~~yLGWHE~GDG~~F~Gl~~d~GRvk-~~-G~~~lk----------~aLRE~v~~~~l~~~---------------- 403 (583)
T TIGR02042 352 FEYKDYLGWHEQGDGKLFLGLHIDSGRVK-DE-GAFQLK----------KALREIVEKYNLPVR---------------- 403 (583)
T ss_pred CCCCCCCCCEECCCCCEEEEEEEECCEEC-CC-HHHHHH----------HHHHHHHHHHCCCEE----------------
T ss_conf 32102466403178855720663065244-73-017889----------999998876335436----------------
Q ss_pred CCCCCCEEEEECCHHHHHHHHHHHHHC-CCCCC---------------CCEEEEECC
Q ss_conf 457984899809858999999999975-88778---------------718999718
Q gi|255764496|r 460 FPSWPDVVILDGGKGQLSAAQGVLKKL-NVENR---------------ITIISIAKG 500 (616)
Q Consensus 460 ~~~~PDLilIDGGkgQln~a~~vl~~l-~i~~~---------------i~viglaK~ 500 (616)
..+-=|+||-|=-.+.=.+...+|+.. ++... +|+||||=-
T Consensus 404 lTp~Qn~~~~~i~~~~k~~I~~~L~~~~g~~~~~~~dpL~~~AMACPAlP~CgLAIT 460 (583)
T TIGR02042 404 LTPNQNIILYDIKPEWKRAITTVLAQANGVLQPEAIDPLNRYAMACPALPLCGLAIT 460 (583)
T ss_pred ECCCCCEEEEECCCCHHHHHHHHHHHCCCCCCCCEECHHHHHHHCCCCCCCCCCHHH
T ss_conf 548851799725720024899999632321464000226666410677676631243
No 242
>PRK07534 methionine synthase I; Validated
Probab=33.23 E-value=30 Score=14.10 Aligned_cols=16 Identities=13% Similarity=0.073 Sum_probs=6.4
Q ss_pred CHHCCCCCCHHHHHHH
Q ss_conf 1004888798999999
Q gi|255764496|r 556 PLDEINGIGPLRKRLL 571 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~L 571 (616)
.+=.==|+||.-.+.|
T Consensus 274 IIGGCCGttPeHIkai 289 (335)
T PRK07534 274 IIGGCCGTMPEHLAAM 289 (335)
T ss_pred EEEECCCCCHHHHHHH
T ss_conf 9988889987999999
No 243
>pfam00072 Response_reg Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
Probab=32.79 E-value=31 Score=14.05 Aligned_cols=73 Identities=14% Similarity=0.141 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH---HHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf 1689989999999977531311123333333345457984899809858999---999999975887787189997187
Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLS---AAQGVLKKLNVENRITIISIAKGP 501 (616)
Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln---~a~~vl~~l~i~~~i~viglaK~~ 501 (616)
||-..+++++.+-+.+.--+-.....+...-..-....||||++|=.-+.++ .+.+ +++.+- .+|++.+.-..
T Consensus 5 DD~~~~~~~l~~~L~~~g~~v~~a~~g~~al~~~~~~~~dlvi~Di~mP~~dG~el~~~-ir~~~~--~~piI~~T~~~ 80 (111)
T pfam00072 5 DDDPLIRELLRQLLEKEGYVVAEADDGEEALELLKEKRPDLILLDIRMPGMDGLELLRR-IRRRPP--TTPVIVLTAHG 80 (111)
T ss_pred ECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHH-HHHCCC--CCEEEEEECCC
T ss_conf 89899999999999988999999899999999998479989999536899501579999-973599--98099997508
No 244
>COG1833 Uri superfamily endonuclease [Replication, recombination, and repair]
Probab=32.41 E-value=31 Score=14.01 Aligned_cols=46 Identities=22% Similarity=0.338 Sum_probs=32.4
Q ss_pred CCCEEEEEECHH-HHHHHHHHCCCCC-CCHHHHHHHHHCCCEEEEECC
Q ss_conf 988889960125-8788876137887-787999999734442999828
Q gi|255764496|r 19 AGRVLYVGKAYN-LQKRIKSYMHSNN-HTHRITHMISQINNIRFTVTC 64 (616)
Q Consensus 19 ~~~iiYvGKakn-L~~Rv~syf~~~~-~~~k~~~l~~~~~~ie~~~t~ 64 (616)
.|=..|||-|-+ +.+||.-||.... ..+-+--|..++.-+..++++
T Consensus 28 ~G~YaYvGSa~~~~~~RV~RH~~~~kk~hWHIDyLl~~~~~~~a~~~~ 75 (132)
T COG1833 28 RGYYAYVGSAMGSLEKRVKRHFSRKKKKHWHIDYLLCKAEVLGAIIFP 75 (132)
T ss_pred CEEEEEECCCCCHHHHHHHHHHCCCCCCCCCHHHHHCCCEEEEEEEEC
T ss_conf 706999876340066777877465545431067662576063799835
No 245
>TIGR00088 trmD tRNA (guanine-N1)-methyltransferase; InterPro: IPR002649 In transfer RNA many different modified nucleosides are found, especially in the anticodon region. tRNA (guanine-N1-)-methyltransferase 2.1.1.31 from EC is one of several nucleases operating together with the tRNA-modifying enzymes before the formation of the mature tRNA. It catalyses the reaction: S-adenosyl-L-methionine + tRNA -> S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine methylating guanosine(G) to N1-methylguanine (1-methylguanosine (m1G)) at position 37 of tRNAs that read CUN (leucine), CCN(proline), and CGG (arginine) codons. The presence of m1G improves the cellular growth rate and the polypeptide steptime and also prevents the tRNA from shifting the reading frame . The mechanism of the trmD3-induced frameshift involving mutant tRNA(Pro) and tRNA(Leu) species has been investigated . It has been suggested that the conformation of the anticodon loop may be a major determining element for the formation of m1G37 in vivo . ; GO: 0003723 RNA binding, 0008175 tRNA methyltransferase activity, 0008033 tRNA processing.
Probab=32.08 E-value=23 Score=14.90 Aligned_cols=18 Identities=17% Similarity=0.028 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHCCCCCC
Q ss_conf 899999998751566435
Q gi|255764496|r 362 HQMILKDFTKKFALPHIP 379 (616)
Q Consensus 362 ~~~~l~~Lk~~L~L~~~p 379 (616)
..+..+-+++.+.+...+
T Consensus 223 ~~~RpDL~~~~~~~~~e~ 240 (247)
T TIGR00088 223 KLRRPDLYKKYLALTEEQ 240 (247)
T ss_pred HHCCHHHHHHHHHCCCCC
T ss_conf 311667899987506731
No 246
>PRK09191 two-component response regulator; Provisional
Probab=32.05 E-value=32 Score=13.96 Aligned_cols=36 Identities=25% Similarity=0.556 Sum_probs=27.8
Q ss_pred CCCEEEEE----CCHHHHHHHHHHHHHCCCCCCCCEEEEECCCC
Q ss_conf 98489980----98589999999999758877871899971877
Q gi|255764496|r 463 WPDVVILD----GGKGQLSAAQGVLKKLNVENRITIISIAKGPK 502 (616)
Q Consensus 463 ~PDLilID----GGkgQln~a~~vl~~l~i~~~i~viglaK~~~ 502 (616)
.|||+|+| ||..=+.+|.+++.+.+ ||||=|.=-.+
T Consensus 182 ~PDlvL~DI~L~d~~sGIdaa~~I~~~~~----iPvIFiTAype 221 (261)
T PRK09191 182 RPGLILADIQLADGSSGIDAVNDILKTFD----VPVIFITAFPE 221 (261)
T ss_pred CCCEEEEEEECCCCCCHHHHHHHHHHHCC----CCEEEECCCHH
T ss_conf 98989995347999879999999998289----99899777846
No 247
>PRK07758 hypothetical protein; Provisional
Probab=31.81 E-value=32 Score=13.94 Aligned_cols=45 Identities=20% Similarity=0.316 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 899999999808889899389888862789998999999998547
Q gi|255764496|r 565 PLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 565 ~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
|.|+-..-.-.-+++.+..-|..||.+.-|||++.-...-+.+.+
T Consensus 45 PARRAL~~~GI~TLedLskytEkELL~LHGmGP~ai~~L~~aLke 89 (95)
T PRK07758 45 PARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEE 89 (95)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 889999982811499998851999999848688889999999998
No 248
>TIGR01438 TGR thioredoxin and glutathione reductase; InterPro: IPR006338 This homodimeric, FAD-containing member of the pyridine nucleotide disulphide oxidoreductase family contains a C-terminal motif Cys-SeCys-Gly, where SeCys is selenocysteine encoded by TGA (in some sequence reports interpreted as a stop codon). In some members of this subfamily, Cys-SeCys-Gly is replaced by Cys-Cys-Gly. The reach of the selenium atom at the C-terminal arm of the protein is proposed to allow broad substrate specificity , .; GO: 0016654 oxidoreductase activity acting on NADH or NADPH disulfide as acceptor, 0050660 FAD binding, 0050661 NADP binding, 0006118 electron transport.
Probab=31.74 E-value=32 Score=13.93 Aligned_cols=126 Identities=16% Similarity=0.220 Sum_probs=66.6
Q ss_pred HHHHHHHCCCCEECCCCCCC-CC--EEEEECCCCCCEEEEEEC-CCCCCCEEEEC-----------CC-CHHHHHHHHHH
Q ss_conf 98877618720033646897-72--699808899845999812-35678437703-----------78-87899999999
Q gi|255764496|r 74 ANMIKRLKPRFNILLRDDKS-FP--YILITDKHKIPALYKHRD-SSTIQGSYFGP-----------FA-SVDAVEKTINS 137 (616)
Q Consensus 74 ~~lIk~~~P~yNi~LkDdk~-yP--yi~it~~~~~p~l~~~r~-~~~~~~~yfGP-----------f~-~~~~~~~~l~~ 137 (616)
++-|+...=-|-+.||..|- |- |-.+-+++. -++..|.+ ..+.+..|=|| || +...++++==.
T Consensus 99 q~hi~slNw~Yrv~Lr~kKv~Y~Nayaefvdk~k-i~i~~t~kGd~~ke~~~sa~~~lIaTG~RP~yp~~ipGaKEl~It 177 (513)
T TIGR01438 99 QDHIKSLNWSYRVALREKKVKYINAYAEFVDKDK-IVIKATDKGDKKKEEILSAKRVLIATGLRPKYPDDIPGAKELSIT 177 (513)
T ss_pred HHHHHHCCHHEEEEHHCCCCEEEEEEEEEECCCE-EEEEEEECCCCCCCEEEECCEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf 6455540032000010154026630024427846-899986067876320450363698047888888888884011013
Q ss_pred HHHHHHHHCCCCCCC-CCCCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Q ss_conf 997301100355421-247886624455425866131220356655543234550387158999999999999
Q gi|255764496|r 138 LQRTFFLRSCADSVF-RHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNHNLKEKIARNMNQA 209 (616)
Q Consensus 138 l~~~f~lR~C~~~~~-~~~~~pCl~y~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~G~~~~ii~~L~~~M~~a 209 (616)
=-.+|-|..|.--.+ -..+=--|+ |.|-.+.-.|+-.|.-=-=.|+|=..........=|+..
T Consensus 178 SDDlFsL~~~PGKTLvVGasYVALE---------CaGFL~~~g~dV~V~VRSI~LrGFDqdca~kv~ehm~e~ 241 (513)
T TIGR01438 178 SDDLFSLKKVPGKTLVVGASYVALE---------CAGFLAALGLDVTVLVRSILLRGFDQDCAVKVKEHMKEQ 241 (513)
T ss_pred CHHHCCCCCCCCCEEEECCCHHHHH---------HHHHHHHCCCCEEEEEEEEECCCCCHHHHHHHHHHHHCC
T ss_conf 0122036688686578776142357---------788986339964999988523475778999999886408
No 249
>cd01744 GATase1_CPSase Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II. This group of sequences represents the small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II. CPSase II catalyzes the production of carbomyl phosphate (CP) from bicarbonate, glutamine and two molecules of MgATP. The reaction is believed to proceed by a series of four biochemical reactions involving a minimum of three discrete highly reactive intermediates. The synthesis of CP is critical for the initiation of two separate biosynthetic pathways. In one CP is coupled to aspartate, its carbon and nitrogen nuclei ultimately incorporated into the aromatic moieties of pyrimidine nucleotides. In the second pathway CP is condensed with ornithine at the start of the urea cycle and is utilized for the detoxification of ammonia and biosynthesis of arginine. CPSases may be encoded by one or by several genes, depending on the species. The E.coli enzyme is
Probab=31.56 E-value=31 Score=14.04 Aligned_cols=34 Identities=6% Similarity=-0.064 Sum_probs=14.2
Q ss_pred EEEEEEECCEEEECCCCCCCCC-CCCCHHHHHHHHH
Q ss_conf 8899842474541011356677-7899789888777
Q gi|255764496|r 256 IQTCFFHFGQNRGTCTFFLKTD-SESTNAQILSYFL 290 (616)
Q Consensus 256 I~vl~vR~G~i~g~~~f~~~~~-~~~~~~eil~~fI 290 (616)
+.-+.-+.-.+.|.+-+ ++.. ...+...++.+||
T Consensus 144 i~ai~h~~~~i~GVQFH-PEs~~~~~~~~~if~nFl 178 (178)
T cd01744 144 VEGIRHKDLPVFSVQFH-PEASPGPHDTEYLFDEFL 178 (178)
T ss_pred EEEEEECCCCEEEEEEC-CCCCCCCCCCHHHHHHHC
T ss_conf 79999899999999859-979999977489897239
No 250
>PRK08506 replicative DNA helicase; Provisional
Probab=31.44 E-value=32 Score=13.90 Aligned_cols=37 Identities=32% Similarity=0.361 Sum_probs=23.7
Q ss_pred CCEEEEE------CCH------HHHHHHHHHHHHCCCCCCCCEEEEECC
Q ss_conf 8489980------985------899999999997588778718999718
Q gi|255764496|r 464 PDVVILD------GGK------GQLSAAQGVLKKLNVENRITIISIAKG 500 (616)
Q Consensus 464 PDLilID------GGk------gQln~a~~vl~~l~i~~~i~viglaK~ 500 (616)
.|||+|| |+. .+++..-+.|+.+-.+.+||||+|+-=
T Consensus 304 l~livIDYLQLm~~~~~~~~R~~ev~~ISr~LK~lAkEl~vPViaLSQL 352 (473)
T PRK08506 304 IGLAVIDYLQLMSGSKNFKDRHLQISEISRGLKLLARELDIPIIALSQL 352 (473)
T ss_pred CCEEEEEHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 8789963675546888753088999999999999999969979997036
No 251
>PTZ00205 DNA polymerase kappa; Provisional
Probab=31.31 E-value=29 Score=14.18 Aligned_cols=30 Identities=13% Similarity=0.208 Sum_probs=14.3
Q ss_pred HHHHCCCCCCCCCCHHHHHHHHHHHHHHHC
Q ss_conf 554258661312203566555432345503
Q gi|255764496|r 163 QIKRCSGPCTGEISSEKYMEFVHEAKKFLS 192 (616)
Q Consensus 163 ~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~ 192 (616)
..+.|+---+=...-+.|.+.-..+..+|.
T Consensus 189 AkkLCP~LI~vp~~f~kYr~vS~~Ir~If~ 218 (571)
T PTZ00205 189 ALKICPNLLILPPDFDAYNEESNTVRRIVA 218 (571)
T ss_pred HHHHCCCEEEECCCCHHHHHHHHHHHHHHH
T ss_conf 998699719989961899999999999999
No 252
>pfam09597 IGR IGR protein motif. This domain is found in fungal proteins and contains a conserved IGR motif. Its function is unknown.
Probab=31.10 E-value=33 Score=13.86 Aligned_cols=46 Identities=22% Similarity=0.175 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCC
Q ss_conf 879899999999808889899389888862789998999999998547
Q gi|255764496|r 562 GIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHK 609 (616)
Q Consensus 562 GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~ 609 (616)
+||.-..+. ...|-|++++-.+|-.+|... ||+.+.-+=|..+.|+
T Consensus 7 ~IGR~~~~~-~~kfe~w~~Lf~~~s~~lK~~-GIp~r~RryiL~~~~k 52 (56)
T pfam09597 7 LIGRGCSEH-ADKFESWEKLFETSSKQLKEL-GIPVKQRRYILRWREK 52 (56)
T ss_pred HHCCCHHHH-HHHCCCHHHHHHHCHHHHHHC-CCCHHHHHHHHHHHHH
T ss_conf 885269988-875157999976177999885-9988999999999999
No 253
>TIGR01127 ilvA_1Cterm threonine dehydratase; InterPro: IPR005789 Serine and threonine dehydratases , are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue. A form of threonine dehydratase with two copies of the C-terminal domain is described by . This model describes a phylogenetically distinct which branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any domain. Many members of this model are found in species with other isoleucine biosynthetic enzymes.; GO: 0004794 L-threonine ammonia-lyase activity.
Probab=30.91 E-value=32 Score=13.93 Aligned_cols=122 Identities=17% Similarity=0.157 Sum_probs=69.4
Q ss_pred CCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf 77540488888516872803232110244445541168998999999997753131112333333334545798489980
Q gi|255764496|r 391 MGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILD 470 (616)
Q Consensus 391 ~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilID 470 (616)
+|.-.||+. . +++.+..+-|+=-|=-. -|+=|..||..||.|=+-+.=+- - .=.-+|.|
T Consensus 257 AGA~gvAA~--L-~~K~~~~kG~K~~~v~S--GGNID~~~l~~iI~kGL~~~GR~---------------v-~I~~~~~D 315 (381)
T TIGR01127 257 AGAVGVAAV--L-EDKVDYVKGKKVAVVVS--GGNIDLNLLEKIILKGLVKSGRK---------------V-RIETVIPD 315 (381)
T ss_pred CHHHHHHHH--H-HHHCCCCCCCEEEEEEE--CCCCCHHHHHHHHHHHHHCCCCE---------------E-EEEEEEEC
T ss_conf 458999999--9-75403689828999985--47768667778865522205836---------------9-99999823
Q ss_pred CCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCH--HHHHHHHHHHHHHHHH
Q ss_conf 9858999999999975887787189997187767663489817983488579989--9999998878778878
Q gi|255764496|r 471 GGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDP--ILYFIQRLRDEAHRFA 541 (616)
Q Consensus 471 GGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~--~l~~Lq~iRDEaHRFA 541 (616)
--|||+-..+++++.+- .|+.+-=+.-++ ++=+-...=.+.|+..++ +..++..+||++-.|-
T Consensus 316 -~PG~L~~ll~~~A~~~a----Ni~~i~hDR~~~---~~~~G~a~v~~~LEt~g~~H~~ei~~~L~~~Gy~f~ 380 (381)
T TIGR01127 316 -RPGALYKLLEVIAEERA----NIVKIEHDRLSK---EIPPGFAKVELELETRGKEHLDEILKVLRDKGYEFK 380 (381)
T ss_pred -CCCCHHHHHHHHHHHCC----CEEEEEECCCCC---CCCCCCEEEEEEEEECCHHHHHHHHHHHHHCCCEEC
T ss_conf -89866999999998169----789999737577---778675389999840886899999999976375442
No 254
>PRK00011 glyA serine hydroxymethyltransferase; Reviewed
Probab=30.83 E-value=33 Score=13.83 Aligned_cols=26 Identities=27% Similarity=0.391 Sum_probs=15.3
Q ss_pred CCEEEEEC-CHH-HHHHHHHHHHHCCCC
Q ss_conf 84899809-858-999999999975887
Q gi|255764496|r 464 PDVVILDG-GKG-QLSAAQGVLKKLNVE 489 (616)
Q Consensus 464 PDLilIDG-Gkg-Qln~a~~vl~~l~i~ 489 (616)
--|++||= .+| -=..|.++|++.||.
T Consensus 312 nHlvlvdl~~~g~~G~~a~~~Le~~gI~ 339 (415)
T PRK00011 312 NHLVLVDLRKKGLTGKDAEAALEEANIT 339 (415)
T ss_pred CCEEEEECCCCCCCHHHHHHHHHHCCEE
T ss_conf 7447764564568899999999985908
No 255
>pfam06514 PsbU Photosystem II 12 kDa extrinsic protein (PsbU). This family consists of several photosystem II 12 kDa extrinsic protein (PsbU) proteins from cyanobacteria and algae. PsbU is an extrinsic protein of the photosystem II complex of cyanobacteria and red algae. PsbU is known to stabilize the oxygen-evolving machinery of the photosystem II complex against heat-induced inactivation.
Probab=30.63 E-value=27 Score=14.51 Aligned_cols=52 Identities=15% Similarity=0.216 Sum_probs=33.9
Q ss_pred HHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHCCCCCCC
Q ss_conf 0048887989999999980888989938988886278999899999999854786789
Q gi|255764496|r 557 LDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFHKNTSHT 614 (616)
Q Consensus 557 Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~~~~~~~ 614 (616)
+-+.||..|.-..++..+=- =.|+||+..+||++.+-.+.+..++.+=+-.+
T Consensus 67 f~q~pGmYPtlA~kIv~~~P------Y~~v~Dvl~ipgLse~qk~~l~~~~~~Ftvt~ 118 (135)
T pfam06514 67 FRQLPGMYPTLAGKIVKNAP------YKSVEDVLNIPGLSERQKALLKKYLDNFTVTE 118 (135)
T ss_pred HHHCCCCCHHHHHHHHHCCC------CCCHHHHHCCCCCCHHHHHHHHHHHCCCEECC
T ss_conf 98688846789999973799------67799997188989999999998660562468
No 256
>COG1628 Endonuclease V homolog [Replication, recombination, and repair]
Probab=30.38 E-value=34 Score=13.77 Aligned_cols=153 Identities=14% Similarity=0.150 Sum_probs=77.4
Q ss_pred CEEEEEECCCCCC---CCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf 1699970744377---5404888885168728032321102444455411689989999999977531311123333333
Q gi|255764496|r 380 KRIEIYDNSHIMG---CSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQ 456 (616)
Q Consensus 380 ~rIE~fDiSh~~G---~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~ 456 (616)
-|+-+||-|.+.- ...++++|...++--..=.|+...+ .|.|=...+..++.|- ++
T Consensus 9 irvlG~DD~~f~~~~~~~~~vG~v~r~~~~v~gv~~~~i~v-----DG~D~T~~i~~~v~~~-~~--------------- 67 (185)
T COG1628 9 IRVLGIDDGPFSRGDDKVTLVGVVMRGDRVVDGVAFSLITV-----DGLDVTDAISDMVNRS-KR--------------- 67 (185)
T ss_pred EEEEEEECCCCCCCCCEEEEEEEEEECCEEEEEEEEEEEEE-----CCCHHHHHHHHHHHHH-HC---------------
T ss_conf 39999715766777860899999998886887667789986-----6823889999999985-25---------------
Q ss_pred CCCCCCCCCEEEEECCH-HHHHHH--HHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHHHHHHHH
Q ss_conf 34545798489980985-899999--999997588778718999718776766348981798348857998999999988
Q gi|255764496|r 457 EYSFPSWPDVVILDGGK-GQLSAA--QGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPILYFIQRL 533 (616)
Q Consensus 457 ~~~~~~~PDLilIDGGk-gQln~a--~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~i 533 (616)
.. -++|+.||=. |--|.+ ..+-++.| +||+.+.... ++.+.+.. + +..+.
T Consensus 68 ----~~-~rvVlLdGIt~aGFNivDi~~l~~~tg----~PVi~V~~k~-----------P~~e~i~~-----A--l~k~f 120 (185)
T COG1628 68 ----RD-LRVVLLDGITFAGFNIVDIEALYKETG----LPVIVVYRKK-----------PDIERIES-----A--LRKHF 120 (185)
T ss_pred ----CC-CCEEEECCEEECCCEEECHHHHHHHHC----CCEEEEEECC-----------CCHHHHHH-----H--HHHHC
T ss_conf ----56-118998772030524842899887619----9689999637-----------98789999-----9--99758
Q ss_pred HHHHHHHHHHHHHHHHHHHC-CCCHHCCCCCCHHHHHHHHHHHCCHHH
Q ss_conf 78778878898998643214-771004888798999999998088898
Q gi|255764496|r 534 RDEAHRFAITTHRKRRKKAA-YSPLDEINGIGPLRKRLLLQSFGTVKM 580 (616)
Q Consensus 534 RDEaHRFAi~~hRk~r~k~~-~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~ 580 (616)
+|-.-|..+--.=....+.. .-.--+--||++...+.+++.|....+
T Consensus 121 ~d~e~R~rii~~~g~~~~~~~~~iy~q~~Gi~~~~A~~ii~~~t~~gk 168 (185)
T COG1628 121 DDAEERIRIIESAGEIEKVITGPIYIQAAGIEPSEAERIIRKTTIRGK 168 (185)
T ss_pred CCHHHHHHHHHHCCCCEEECCCCEEEEEECCCHHHHHHHHHHHCCCCC
T ss_conf 879999999985787526048977999942798999999998632678
No 257
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=30.11 E-value=34 Score=13.74 Aligned_cols=14 Identities=14% Similarity=0.140 Sum_probs=10.3
Q ss_pred CHHHHHHHHHHHHH
Q ss_conf 97898887775432
Q gi|255764496|r 281 TNAQILSYFLRQFY 294 (616)
Q Consensus 281 ~~~eil~~fI~qyY 294 (616)
-.+..+.+.|..++
T Consensus 88 ~AA~aMRrIL~D~A 101 (194)
T TIGR02999 88 AAAKAMRRILVDHA 101 (194)
T ss_pred HHHHHHHHHHHHHH
T ss_conf 99999999999999
No 258
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=30.09 E-value=15 Score=16.20 Aligned_cols=31 Identities=23% Similarity=0.139 Sum_probs=17.8
Q ss_pred HCCCEEEEECCCHHHHHHHHHHHHHHHCCCCEECCCCCC
Q ss_conf 344429998287199999999887761872003364689
Q gi|255764496|r 54 QINNIRFTVTCTEVEALLLEANMIKRLKPRFNILLRDDK 92 (616)
Q Consensus 54 ~~~~ie~~~t~~e~eAlilE~~lIk~~~P~yNi~LkDdk 92 (616)
+...++..|+..+.-+ ..-+..+-+.+.|+.
T Consensus 61 ~~vti~g~V~~~~~~~--------~~~~~~l~v~~~d~~ 91 (677)
T COG1200 61 EIVTIEGTVLSHEKFP--------FGKRKLLKVTLSDGT 91 (677)
T ss_pred CEEEEEEEEEEEECCC--------CCCCCEEEEEEECCC
T ss_conf 6699999997640257--------788734999996296
No 259
>cd07963 Anticodon_Ia_Cys Anticodon-binding domain of cysteinyl tRNA synthetases. This domain is found in cysteinyl tRNA synthetases (CysRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. CysRS catalyzes the transfer of cysteine to the 3'-end of its tRNA.
Probab=29.57 E-value=35 Score=13.68 Aligned_cols=34 Identities=32% Similarity=0.244 Sum_probs=26.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 1589999999999998633388888899999999
Q gi|255764496|r 195 NHNLKEKIARNMNQATLKEDYESAIIHRDRLAAL 228 (616)
Q Consensus 195 ~~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL 228 (616)
....+..|-++=..|=.+-+|++|-.+||+|..+
T Consensus 108 ~~~~I~~Li~~R~~AR~~Kdf~~AD~IRd~L~~~ 141 (156)
T cd07963 108 SVAEIEALIAQRNQARKAKDWAEADRIRDELAAQ 141 (156)
T ss_pred CHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 7999999999999999839978999999999987
No 260
>KOG2201 consensus
Probab=29.21 E-value=5.1 Score=19.69 Aligned_cols=13 Identities=15% Similarity=0.394 Sum_probs=5.6
Q ss_pred EEEEECCHHHHHH
Q ss_conf 8998098589999
Q gi|255764496|r 466 VVILDGGKGQLSA 478 (616)
Q Consensus 466 LilIDGGkgQln~ 478 (616)
|+.|---.||+..
T Consensus 285 L~mIsnNIGqiAy 297 (371)
T KOG2201 285 LRMISNNIGQIAY 297 (371)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999721899999
No 261
>KOG0950 consensus
Probab=29.18 E-value=35 Score=13.63 Aligned_cols=54 Identities=30% Similarity=0.363 Sum_probs=44.1
Q ss_pred CCCHHCCCCCCHHHHHHHHH-HHCCHHHHHHCCHHHHHHCCC--CCHHHHHHHHHHH
Q ss_conf 77100488879899999999-808889899389888862789--9989999999985
Q gi|255764496|r 554 YSPLDEINGIGPLRKRLLLQ-SFGTVKMISRSSPETLASIEG--ISKKIACKIYNHF 607 (616)
Q Consensus 554 ~S~Ld~I~GIG~k~~~~Ll~-~Fgs~~~i~~As~eeL~~v~g--i~~~~A~~I~~~l 607 (616)
..+|..|+|+-..|...|+. -|.|+..|.+|+.++|++..+ |+-+.|..|...-
T Consensus 893 L~~Lmrv~~~~~~RAr~lf~Agf~tv~~iA~a~p~klvkel~~si~~~~a~~i~~s~ 949 (1008)
T KOG0950 893 LIPLMRVPDVKAERARQLFKAGFTSVGSIANATPEKLVKELPISISMKQATQIVASA 949 (1008)
T ss_pred HHHHHCCCHHHHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 454525743678999999984453358885588277898751445187765577555
No 262
>PRK05595 replicative DNA helicase; Provisional
Probab=29.16 E-value=35 Score=13.63 Aligned_cols=37 Identities=24% Similarity=0.387 Sum_probs=24.1
Q ss_pred CCEEEEEC------CH------HHHHHHHHHHHHCCCCCCCCEEEEECC
Q ss_conf 84899809------85------899999999997588778718999718
Q gi|255764496|r 464 PDVVILDG------GK------GQLSAAQGVLKKLNVENRITIISIAKG 500 (616)
Q Consensus 464 PDLilIDG------Gk------gQln~a~~vl~~l~i~~~i~viglaK~ 500 (616)
+|||+||- .. -++..+-+.|+.+-.+.+|||+.|+-=
T Consensus 312 ~~liiiDYlqLi~~~~~~~~r~~ev~~isr~LK~lAkel~ipvi~lsQL 360 (444)
T PRK05595 312 IDLILIDYLQLMSGGKSSESRQQEVSEISRSIKALAKEMECPVIALSQL 360 (444)
T ss_pred CCEEEEEHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 9989982376357898888899999999999999999969979997026
No 263
>COG1415 Uncharacterized conserved protein [Function unknown]
Probab=29.10 E-value=23 Score=14.91 Aligned_cols=16 Identities=6% Similarity=0.198 Sum_probs=9.3
Q ss_pred CCCHHHHHHHHHHHHH
Q ss_conf 5526678999999999
Q gi|255764496|r 334 QGEKRKIIEQALINAH 349 (616)
Q Consensus 334 rG~kk~Ll~lA~~NA~ 349 (616)
++.++-+++++..++.
T Consensus 206 ~~~r~~~ldl~reg~~ 221 (373)
T COG1415 206 RDNRKLILDLVREGPS 221 (373)
T ss_pred HHHHHHHHHHHHHCCH
T ss_conf 5557889999985738
No 264
>PRK06722 exonuclease; Provisional
Probab=28.86 E-value=3.8 Score=20.58 Aligned_cols=19 Identities=26% Similarity=0.461 Sum_probs=8.4
Q ss_pred CCCCCCCCHHHHHHHHHHH
Q ss_conf 6613122035665554323
Q gi|255764496|r 169 GPCTGEISSEKYMEFVHEA 187 (616)
Q Consensus 169 gpC~~~is~~~Y~~~v~~~ 187 (616)
.||....+.-+-+..|-++
T Consensus 77 ~P~~~~~~~~dl~k~v~~~ 95 (242)
T PRK06722 77 CPCMEKERRIDLQKFVFQA 95 (242)
T ss_pred CCCCCCHHHHHHHHHHHHC
T ss_conf 9998421088899998631
No 265
>PRK05920 aromatic acid decarboxylase; Validated
Probab=28.67 E-value=36 Score=13.57 Aligned_cols=26 Identities=15% Similarity=0.196 Sum_probs=20.4
Q ss_pred CCCCEEEEEECCCC-----CCCCCEEEEEEE
Q ss_conf 43516999707443-----775404888885
Q gi|255764496|r 377 HIPKRIEIYDNSHI-----MGCSAVGCMVVV 402 (616)
Q Consensus 377 ~~p~rIE~fDiSh~-----~G~~~Vas~Vvf 402 (616)
..+..|.+||++.+ +|++.+-+|||-
T Consensus 71 ~~~~~i~~~~~~d~~A~iASGS~~~dgMvV~ 101 (205)
T PRK05920 71 ANAGQLRVHGKDDWGAPIASGSFATDGMVIA 101 (205)
T ss_pred CCCCCEEECCHHHCCCCCCCCCCCCCCEEEE
T ss_conf 5677447837764278656677665836994
No 266
>pfam10551 MULE MULE transposase domain. This domain was identified by Babu and colleagues.
Probab=28.61 E-value=36 Score=13.57 Aligned_cols=22 Identities=36% Similarity=0.542 Sum_probs=20.0
Q ss_pred CCEEEEECCHHHHHHHHHHHHH
Q ss_conf 8489980985899999999997
Q gi|255764496|r 464 PDVVILDGGKGQLSAAQGVLKK 485 (616)
Q Consensus 464 PDLilIDGGkgQln~a~~vl~~ 485 (616)
|.+|+.||.+|-.+|+.+++-+
T Consensus 57 p~~iisD~~~~l~~Ai~~vfP~ 78 (93)
T pfam10551 57 PVTIITDGDKGLKKAIKEVFPD 78 (93)
T ss_pred CEEEEECCCHHHHHHHHHHCCC
T ss_conf 7599964975599999998898
No 267
>COG2205 KdpD Osmosensitive K+ channel histidine kinase [Signal transduction mechanisms]
Probab=28.39 E-value=36 Score=13.54 Aligned_cols=133 Identities=16% Similarity=0.167 Sum_probs=80.6
Q ss_pred CCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCHHH-HHHHHHHHHHHHHHH
Q ss_conf 8489980985899999999997588778718999718776766348981798348857998999-999988787788788
Q gi|255764496|r 464 PDVVILDGGKGQLSAAQGVLKKLNVENRITIISIAKGPKRSAGMEKFFVKKGEALVLNMRDPIL-YFIQRLRDEAHRFAI 542 (616)
Q Consensus 464 PDLilIDGGkgQln~a~~vl~~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~~i~l~~~~~~l-~~Lq~iRDEaHRFAi 542 (616)
=|+-=|+.|--+++..-..++|+= . =.+-.+.|..- +..+.+....+-..+..+++++ +.|.++=|-|++||=
T Consensus 719 LdmTRi~sG~~~l~~~~~~veEvV-g--~Al~r~~k~~~---~~~i~v~~~~dl~li~~D~~LieQVLiNLleNA~Kyap 792 (890)
T COG2205 719 LDMTRLQSGGVNLKLDWVLVEEVV-G--EALQRLRKRFT---GHKIVVSVPVDLPLIHVDSPLIEQVLINLLENALKYAP 792 (890)
T ss_pred HHHHHHHCCCCCCCCCHHHHHHHH-H--HHHHHHHHHCC---CCEEEEECCCCCCEEECCHHHHHHHHHHHHHHHHHHCC
T ss_conf 767777137864144520399999-9--99998663047---83589955888716764788999999999987874289
Q ss_pred HHHH------HHHHHHCCCCHHCCCCCCHHHHHHHHHHHCCHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHC
Q ss_conf 9899------86432147710048887989999999980888989938988886278999899999999854
Q gi|255764496|r 543 TTHR------KRRKKAAYSPLDEINGIGPLRKRLLLQSFGTVKMISRSSPETLASIEGISKKIACKIYNHFH 608 (616)
Q Consensus 543 ~~hR------k~r~k~~~S~Ld~I~GIG~k~~~~Ll~~Fgs~~~i~~As~eeL~~v~gi~~~~A~~I~~~l~ 608 (616)
..-+ ..+++..++..|.=|||-+...+++...|-+..+... ..=.|.|-.+++.|.+.-.
T Consensus 793 ~~s~I~I~~~~~~~~v~~~V~DeGpGIP~~~~~~IFD~F~r~~~~~~------~~G~GLGLsIc~~iv~ahg 858 (890)
T COG2205 793 PGSEIRINAGVERENVVFSVIDEGPGIPEGELERIFDKFYRGNKESA------TRGVGLGLAICRGIVEAHG 858 (890)
T ss_pred CCCEEEEEEEEECCEEEEEEEECCCCCCHHHHHHHHHHHHCCCCCCC------CCCCCCCHHHHHHHHHHCC
T ss_conf 99769999998245699999718999885678876465414888778------8876622999999999748
No 268
>COG2006 Uncharacterized conserved protein [Function unknown]
Probab=28.20 E-value=36 Score=13.52 Aligned_cols=12 Identities=50% Similarity=0.866 Sum_probs=10.0
Q ss_pred CCEEEEECCHHH
Q ss_conf 848998098589
Q gi|255764496|r 464 PDVVILDGGKGQ 475 (616)
Q Consensus 464 PDLilIDGGkgQ 475 (616)
|||-|+||=+|.
T Consensus 194 P~ltI~Dgi~G~ 205 (293)
T COG2006 194 PDLTIMDGIIGM 205 (293)
T ss_pred CCEEEEEEEEEC
T ss_conf 867988316752
No 269
>pfam04679 DNA_ligase_A_C ATP dependent DNA ligase C terminal region. This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase.
Probab=27.84 E-value=37 Score=13.48 Aligned_cols=16 Identities=63% Similarity=1.049 Sum_probs=11.5
Q ss_pred CEEEEECCCCCEEEEEECH
Q ss_conf 6258886998888996012
Q gi|255764496|r 11 GVYQMLDIAGRVLYVGKAY 29 (616)
Q Consensus 11 GvY~~~~~~~~iiYvGKak 29 (616)
||| |.+|+..||||.-
T Consensus 11 g~~---~~~g~l~~vgkVg 26 (95)
T pfam04679 11 GVY---DDDGRLVYVGKVG 26 (95)
T ss_pred EEE---CCCCCEEEEEEEC
T ss_conf 999---8999999998766
No 270
>TIGR01163 rpe ribulose-phosphate 3-epimerase; InterPro: IPR000056 Ribulose-phosphate 3-epimerase (5.1.3.1 from EC) (also known as pentose-5-phosphate 3-epimerase or PPE) is the enzyme that converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. In Alcaligenes eutrophus two copies of the gene coding for PPE are known , one is chromosomally encoded P40117 from SWISSPROT, the other one is on a plasmid Q04539 from SWISSPROT. PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure.; GO: 0004750 ribulose-phosphate 3-epimerase activity, 0005975 carbohydrate metabolic process.
Probab=27.80 E-value=37 Score=13.47 Aligned_cols=29 Identities=17% Similarity=0.336 Sum_probs=22.2
Q ss_pred CCEEEEECCHHHHHHHHHHHHHCCCCCCCCEEE
Q ss_conf 848998098589999999999758877871899
Q gi|255764496|r 464 PDVVILDGGKGQLSAAQGVLKKLNVENRITIIS 496 (616)
Q Consensus 464 PDLilIDGGkgQln~a~~vl~~l~i~~~i~vig 496 (616)
+=+|-||||..+-|++. +.+.|-+ +-|.|
T Consensus 169 ~~~ieVDGGv~~~ni~~--~~~AGAD--~~VaG 197 (216)
T TIGR01163 169 SILIEVDGGVNEDNIAE--VAEAGAD--ILVAG 197 (216)
T ss_pred CEEEEECCCCCHHHHHH--HHHCCCC--EEEEE
T ss_conf 55899717989767999--9975898--99983
No 271
>TIGR00140 hupD hydrogenase expression/formation protein; InterPro: IPR004419 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of metallopeptidases belong to the MEROPS peptidase family A31 (HybD endopeptidase family, clan AE). The family contains the HyaD and HybD endopeptidases and their homologues. ; GO: 0046872 metal ion binding, 0016485 protein processing.
Probab=27.72 E-value=36 Score=13.53 Aligned_cols=19 Identities=32% Similarity=0.405 Sum_probs=11.8
Q ss_pred CEEEEECCHHHHHHHHHHH
Q ss_conf 4899809858999999999
Q gi|255764496|r 465 DVVILDGGKGQLSAAQGVL 483 (616)
Q Consensus 465 DLilIDGGkgQln~a~~vl 483 (616)
.+=|+|||-.=+.-...+-
T Consensus 35 ~V~~lDGGT~G~~L~~~~~ 53 (156)
T TIGR00140 35 NVTLLDGGTQGLYLLGLIE 53 (156)
T ss_pred EEEEEECHHHHHHHHHHHH
T ss_conf 2489835357889999987
No 272
>PRK09581 pleD response regulator PleD; Reviewed
Probab=27.72 E-value=37 Score=13.46 Aligned_cols=25 Identities=16% Similarity=0.307 Sum_probs=16.2
Q ss_pred CCEEEEECCCHHHHHHHHHHHHHHHCCCC
Q ss_conf 44299982871999999998877618720
Q gi|255764496|r 56 NNIRFTVTCTEVEALLLEANMIKRLKPRF 84 (616)
Q Consensus 56 ~~ie~~~t~~e~eAlilE~~lIk~~~P~y 84 (616)
...+.+...|-.||| .++.+++|-.
T Consensus 25 ~~y~v~~a~~G~eAL----~~~~~~~PDL 49 (457)
T PRK09581 25 EYYTVLTASSGAEAI----EICEREQPDI 49 (457)
T ss_pred CCCEEEEECCHHHHH----HHHHHCCCCE
T ss_conf 899999989999999----9997189998
No 273
>PRK10867 signal recognition particle protein; Provisional
Probab=27.05 E-value=38 Score=13.38 Aligned_cols=183 Identities=20% Similarity=0.239 Sum_probs=83.9
Q ss_pred CCCCCCCCEEEEEEEECCCCCHH-HHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC-
Q ss_conf 44377540488888516872803-2321102444455411689989999999977531311123333333345457984-
Q gi|255764496|r 388 SHIMGCSAVGCMVVVGENGFVKN-QYRKFNLHPNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPD- 465 (616)
Q Consensus 388 Sh~~G~~~Vas~Vvf~~g~~~K~-~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PD- 465 (616)
++-.|.+||. |++.--...++ .|----|-+ ...-..|-.+|.|.-. ..+..+ ||
T Consensus 161 ~~~~~~dp~~--ia~~a~~~ak~~~~DvvivDT-AGRl~~d~~Lm~El~~--i~~~~~-------------------P~e 216 (453)
T PRK10867 161 PSDVGQKPVD--IVNAALKEAKLKFYDVLLVDT-AGRLHVDEAMMDEIKQ--VHASIN-------------------PVE 216 (453)
T ss_pred CCCCCCCHHH--HHHHHHHHHHHCCCCEEEEEC-CCCHHCCHHHHHHHHH--HHHHHC-------------------CCC
T ss_conf 6788998899--999999999977999999978-7601210888999999--987637-------------------871
Q ss_pred -EEEEECCHHHH--HHHHHHHHHCCCCCCCCEEEEECCCCC-----------CCCCEEEECCCCCEE-EECCCCH-----
Q ss_conf -89980985899--999999997588778718999718776-----------766348981798348-8579989-----
Q gi|255764496|r 466 -VVILDGGKGQL--SAAQGVLKKLNVENRITIISIAKGPKR-----------SAGMEKFFVKKGEAL-VLNMRDP----- 525 (616)
Q Consensus 466 -LilIDGGkgQl--n~a~~vl~~l~i~~~i~viglaK~~~r-----------~~~~e~~~~~~~~~i-~l~~~~~----- 525 (616)
|+++|+-.||= +.|..--+.++++. +=|.|=+.. .++.-+.|.+.|+.+ .|..-+|
T Consensus 217 ~llV~Da~~GQ~a~~~a~~F~~~~~~~g----vIlTKlDgdarGG~alS~~~~t~~PI~FiG~GEk~ddle~F~p~r~as 292 (453)
T PRK10867 217 TLFVVDAMTGQDAANTAKAFNEALPLTG----VVLTKVDGDARGGAALSIRHITGKPIKFLGVGEKTDALEPFHPDRIAS 292 (453)
T ss_pred EEEEEECCCCHHHHHHHHHHHHHCCCCE----EEEECCCCCCCCHHHHHHHHHHCCCCEEEECCCCCCCCCCCCHHHHHH
T ss_conf 3797432235668999999998559870----787504678761389899999786967886699824588768489999
Q ss_pred -------HHHHHHHHHHH-----HH----------HHHHHHHH-HHH--HHH--CCCCHHCCCCCCHHHHHHHH----HH
Q ss_conf -------99999988787-----78----------87889899-864--321--47710048887989999999----98
Q gi|255764496|r 526 -------ILYFIQRLRDE-----AH----------RFAITTHR-KRR--KKA--AYSPLDEINGIGPLRKRLLL----QS 574 (616)
Q Consensus 526 -------~l~~Lq~iRDE-----aH----------RFAi~~hR-k~r--~k~--~~S~Ld~I~GIG~k~~~~Ll----~~ 574 (616)
+.-|+.++++. +. +|-..-.+ +.+ +|+ +.+.|.-|||+|........ +.
T Consensus 293 RILGmGDi~~Lvek~~~~~d~~~~~~~~~k~~~g~~F~l~D~~~Q~~~i~kmG~l~~il~miPG~~~~~~~~~~~~~~~~ 372 (453)
T PRK10867 293 RILGMGDVLSLIEDIESKVDRAQAEKLASKLKKGDGFDLNDFLEQLKQMKNMGGMASLMGKLPGMGQLPDNVKSQMDDKV 372 (453)
T ss_pred HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCHHHHHCCCHHH
T ss_conf 86189878999999998750889999999987069856999999999997457799999758896533455561321778
Q ss_pred HCCHH-HHHHCCHHHHHHCCCCCHH
Q ss_conf 08889-8993898888627899989
Q gi|255764496|r 575 FGTVK-MISRSSPETLASIEGISKK 598 (616)
Q Consensus 575 Fgs~~-~i~~As~eeL~~v~gi~~~ 598 (616)
|.-++ =|...+.+|+..-.=|+..
T Consensus 373 ~~~~~aii~SMT~~Er~~p~il~~S 397 (453)
T PRK10867 373 LVRMEAIINSMTLKERAKPEIIKGS 397 (453)
T ss_pred HHHHHHHHHCCCHHHHHCCCCCCHH
T ss_conf 9889999964899987395011335
No 274
>TIGR00528 gcvT glycine cleavage system T protein; InterPro: IPR006223 This is a subfamily of glycine cleavage T proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase 2.1.2.10 from EC that catalyses the following reaction: (6S)-tetrahydrofolate + S-aminomethyldihydrolipoylprotein = (6R)-5,10-methylenetetrahydrofolate + NH_3 + dihydrolipoylprotein ; GO: 0004047 aminomethyltransferase activity, 0006546 glycine catabolic process.
Probab=26.96 E-value=21 Score=15.25 Aligned_cols=33 Identities=9% Similarity=0.137 Sum_probs=17.9
Q ss_pred EEEEECCEEEECCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 99842474541011356677789978988877754
Q gi|255764496|r 258 TCFFHFGQNRGTCTFFLKTDSESTNAQILSYFLRQ 292 (616)
Q Consensus 258 vl~vR~G~i~g~~~f~~~~~~~~~~~eil~~fI~q 292 (616)
|+.-|.|. +|...|.+.... +...++-+.|+..
T Consensus 201 v~IArtGY-TGEdGfEI~~~~-e~A~~~w~~l~~~ 233 (394)
T TIGR00528 201 VFIARTGY-TGEDGFEIAVAN-EKAVEFWKKLVEA 233 (394)
T ss_pred EEEECCCC-CCCCCEEEECCC-HHHHHHHHHHHHC
T ss_conf 99825777-664541586187-3689999999862
No 275
>KOG2423 consensus
Probab=26.50 E-value=39 Score=13.31 Aligned_cols=75 Identities=27% Similarity=0.410 Sum_probs=47.6
Q ss_pred EECCCHHHHHHHHHHHHHHHCCCCEECCCCCCCCCEEEEECCCCCCEEEEEECCCCCCCEEEECCCCHHHHHHHHHHHHH
Q ss_conf 98287199999999887761872003364689772699808899845999812356784377037887899999999997
Q gi|255764496|r 61 TVTCTEVEALLLEANMIKRLKPRFNILLRDDKSFPYILITDKHKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQR 140 (616)
Q Consensus 61 ~~t~~e~eAlilE~~lIk~~~P~yNi~LkDdk~yPyi~it~~~~~p~l~~~r~~~~~~~~yfGPf~~~~~~~~~l~~l~~ 140 (616)
+|..+++++|-- .|=++.+-.|||+||-.| -||-.+.....-||+.+...-.- ..-|||=+..+..+....-+..
T Consensus 85 vI~q~~Lq~Fr~--e~g~~~~dpyqVllk~~K-lPmSLL~e~~k~~rvhvldtesF--~~tFG~KsqRKRp~L~~s~le~ 159 (572)
T KOG2423 85 VISQTELQKFRE--ELGKKLKDPYQVLLKQSK-LPMSLLQEKTKTPRVHVLDTESF--EDTFGPKSQRKRPKLTASSLEE 159 (572)
T ss_pred EECHHHHHHHHH--HHHHHHCCHHHHEEECCC-CCHHHHHCCCCCCCEEEECCCCH--HHHHCCHHHHCCCCCCHHHHHH
T ss_conf 416899999999--987563572662000577-77566531555760464125526--6541836440376641644999
No 276
>smart00511 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family.
Probab=25.27 E-value=40 Score=13.19 Aligned_cols=23 Identities=26% Similarity=0.312 Sum_probs=17.7
Q ss_pred CHHCCCCCCHHHHHHHHHHHCCH
Q ss_conf 10048887989999999980888
Q gi|255764496|r 556 PLDEINGIGPLRKRLLLQSFGTV 578 (616)
Q Consensus 556 ~Ld~I~GIG~k~~~~Ll~~Fgs~ 578 (616)
.|...||+-+..+.+|+.|+++-
T Consensus 17 fLs~~~~~~~~~~~rLl~HL~~~ 39 (45)
T smart00511 17 FLSQLPGTDPDVRARLLSHLQTH 39 (45)
T ss_pred HHHCCCCCCHHHHHHHHHHHHHH
T ss_conf 99628999869999999999999
No 277
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=25.23 E-value=41 Score=13.15 Aligned_cols=29 Identities=17% Similarity=0.297 Sum_probs=20.4
Q ss_pred EEEEECCCCCHHHHHHHHCCCCCCCCCHHHH
Q ss_conf 8885168728032321102444455411689
Q gi|255764496|r 399 MVVVGENGFVKNQYRKFNLHPNDVKTQDDCA 429 (616)
Q Consensus 399 ~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~ 429 (616)
.||+++|+..|+.=|+..-+- +. .+|+|.
T Consensus 77 IicLEDGkkfKSLKRHL~t~~-gm-TPd~YR 105 (148)
T COG4957 77 IICLEDGKKFKSLKRHLTTHY-GL-TPDEYR 105 (148)
T ss_pred EEEECCCCCHHHHHHHHHCCC-CC-CHHHHH
T ss_conf 877026852278999873225-99-979999
No 278
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=25.17 E-value=41 Score=13.15 Aligned_cols=37 Identities=22% Similarity=0.330 Sum_probs=24.7
Q ss_pred CCEEEEE------CCH-----HHHHHHHHHHHHCCCCCCCCEEEEECC
Q ss_conf 8489980------985-----899999999997588778718999718
Q gi|255764496|r 464 PDVVILD------GGK-----GQLSAAQGVLKKLNVENRITIISIAKG 500 (616)
Q Consensus 464 PDLilID------GGk-----gQln~a~~vl~~l~i~~~i~viglaK~ 500 (616)
+|||+|| |.. -++..+-+.|+.+-.+.+|||++|+-=
T Consensus 306 l~livIDYLqLi~~~~~~~r~~ei~~Isr~LK~lAkel~ipVi~lsQL 353 (421)
T TIGR03600 306 LDLIVVDYIQLMAPTRGRDRNEELGGISRGLKALAKELDVPVVLLAQL 353 (421)
T ss_pred CCEEEECHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 869997578653788888889999999999999999979978997057
No 279
>pfam11901 DUF3421 Protein of unknown function (DUF3421). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 119 to 296 amino acids in length.
Probab=25.13 E-value=41 Score=13.14 Aligned_cols=15 Identities=40% Similarity=0.700 Sum_probs=12.4
Q ss_pred ECCCCCEEEEEECHH
Q ss_conf 869988889960125
Q gi|255764496|r 16 LDIAGRVLYVGKAYN 30 (616)
Q Consensus 16 ~~~~~~iiYvGKakn 30 (616)
.|.+|..||||.|..
T Consensus 4 ~d~dG~~iYVgRa~~ 18 (118)
T pfam11901 4 HDSDGATIYVGRAKH 18 (118)
T ss_pred CCCCCCEEEEEEEEE
T ss_conf 679999989999997
No 280
>KOG2747 consensus
Probab=24.82 E-value=12 Score=16.89 Aligned_cols=96 Identities=18% Similarity=0.320 Sum_probs=50.8
Q ss_pred CCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCH
Q ss_conf 78437703788789999999999730110035542124788662445542586613122035665554323455038715
Q gi|255764496|r 117 IQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAKKFLSGGNH 196 (616)
Q Consensus 117 ~~~~yfGPf~~~~~~~~~l~~l~~~f~lR~C~~~~~~~~~~pCl~y~i~~C~gpC~~~is~~~Y~~~v~~~~~fL~G~~~ 196 (616)
...-||-|||- -+.-+..+|- |.-.+.--+.+-||..|+..|.--+- =..|-|...- .+|++=+..
T Consensus 140 i~~WY~SPyP~------e~~~~~~lYi---CEfCLkY~~s~~~l~rH~~kC~~rhP--PG~EIYR~~~---iSvfEVDG~ 205 (396)
T KOG2747 140 IKTWYFSPYPE------EYAKLDKLYI---CEFCLKYMKSRTSLQRHLKKCKLRHP--PGNEIYRKGN---ISVFEVDGR 205 (396)
T ss_pred EEEEECCCCCH------HHCCCCEEEE---EHHHHHHHCCHHHHHHHHHHCCCCCC--CCCEEEECCC---EEEEEECCC
T ss_conf 66544489855------6546883998---44466562516899999985688799--9650034598---679996586
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH
Q ss_conf 89999999999998633388888899999999862211000245420111
Q gi|255764496|r 197 NLKEKIARNMNQATLKEDYESAIIHRDRLAALSHIQNHNDSIYNRMDCFS 246 (616)
Q Consensus 197 ~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL~~i~~~q~v~~~d~Dvi~ 246 (616)
. + ..|=..|=.|.++.=.....+-|.|-|-
T Consensus 206 ~--~------------------k~YCQnLCLlaKLFLdhKTLYyDvdpFl 235 (396)
T KOG2747 206 K--Q------------------KLYCQNLCLLAKLFLDHKTLYYDVDPFL 235 (396)
T ss_pred C--C------------------HHHHHHHHHHHHHHHHCCEEEEECCCEE
T ss_conf 1--1------------------4999999999998860752566147638
No 281
>COG0855 Ppk Polyphosphate kinase [Inorganic ion transport and metabolism]
Probab=24.81 E-value=42 Score=13.10 Aligned_cols=15 Identities=20% Similarity=0.224 Sum_probs=11.6
Q ss_pred CCCCCCCCEEEEECC
Q ss_conf 588778718999718
Q gi|255764496|r 486 LNVENRITIISIAKG 500 (616)
Q Consensus 486 l~i~~~i~viglaK~ 500 (616)
-|++++|.|.||+-+
T Consensus 578 ~glSeNIrV~SIVGR 592 (696)
T COG0855 578 PGLSENIRVRSIVGR 592 (696)
T ss_pred CCCCCCEEEEEEHHH
T ss_conf 876745589870022
No 282
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=24.70 E-value=42 Score=13.09 Aligned_cols=11 Identities=9% Similarity=0.434 Sum_probs=4.4
Q ss_pred EEEECCCCCEE
Q ss_conf 48981798348
Q gi|255764496|r 508 EKFFVKKGEAL 518 (616)
Q Consensus 508 e~~~~~~~~~i 518 (616)
|++|-++|.||
T Consensus 145 ~tvh~dDGdPi 155 (231)
T TIGR02885 145 DTVHEDDGDPI 155 (231)
T ss_pred CEEECCCCCHH
T ss_conf 01141794644
No 283
>KOG2520 consensus
Probab=24.50 E-value=42 Score=13.06 Aligned_cols=20 Identities=30% Similarity=0.624 Sum_probs=16.1
Q ss_pred HHCCCCCCHHHHHHHHHHHC
Q ss_conf 00488879899999999808
Q gi|255764496|r 557 LDEINGIGPLRKRLLLQSFG 576 (616)
Q Consensus 557 Ld~I~GIG~k~~~~Ll~~Fg 576 (616)
-+.|+||||++...+|..|+
T Consensus 562 t~Gl~giGpV~AlEil~Efp 581 (815)
T KOG2520 562 TEGLKGIGPVSALEILAEFP 581 (815)
T ss_pred CCCCCCCCCHHHHHHHHHCC
T ss_conf 56777656068999998747
No 284
>TIGR01684 viral_ppase viral phosphatase; InterPro: IPR007827 This family contains uncharacterised baculoviral proteins..
Probab=24.45 E-value=28 Score=14.35 Aligned_cols=50 Identities=12% Similarity=0.016 Sum_probs=29.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHEEC-CCCCHHHHHHHHHHH
Q ss_conf 35667778997898887775432137898123102-688857876665432
Q gi|255764496|r 272 FFLKTDSESTNAQILSYFLRQFYTDKPCPENILLS-EEAEETSLLEISFFK 321 (616)
Q Consensus 272 f~~~~~~~~~~~eil~~fI~qyY~~~~iP~~Iiv~-~~~~~~~~l~~~L~~ 321 (616)
|.+..-...++-.-+..-+.+-|.-...=..=+++ +.++--+.|.+|+-.
T Consensus 66 Yk~~~f~c~Ddm~dlR~~lk~~fK~~~lG~~fVl~R~k~~~y~cLnEW~V~ 116 (323)
T TIGR01684 66 YKLQVFSCADDMKDLRAHLKTAFKLSYLGHVFVLFRHKPAMYACLNEWLVL 116 (323)
T ss_pred EEEEEEECCHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCHHHHHCCCCCE
T ss_conf 025565324146898887313125210326999735898857851210000
No 285
>KOG3206 consensus
Probab=24.37 E-value=42 Score=13.04 Aligned_cols=20 Identities=30% Similarity=0.506 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHHHHHHHHC
Q ss_conf 12203566555432345503
Q gi|255764496|r 173 GEISSEKYMEFVHEAKKFLS 192 (616)
Q Consensus 173 ~~is~~~Y~~~v~~~~~fL~ 192 (616)
-.||+++|.+.-+.+..|++
T Consensus 98 y~iSee~Y~qRtdSvr~~kk 117 (234)
T KOG3206 98 YEISEEDYLQRTDSVRRFKK 117 (234)
T ss_pred EECCHHHHHHHHHHHHHHHH
T ss_conf 44278888665589999999
No 286
>PRK05973 replicative DNA helicase; Provisional
Probab=24.30 E-value=43 Score=13.03 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=24.3
Q ss_pred CCEEEEE--------CCHHHHHHHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf 8489980--------9858999999999975887787189997187
Q gi|255764496|r 464 PDVVILD--------GGKGQLSAAQGVLKKLNVENRITIISIAKGP 501 (616)
Q Consensus 464 PDLilID--------GGkgQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616)
.+||+|| .....++.....|+.+.-+..+||++|+-=.
T Consensus 148 ~~LIVIDYLQLM~~~r~~~eiseisRsLK~lAkEl~vPVvaLSQLn 193 (237)
T PRK05973 148 GTLVVIDYLQLLDQRREKPDLSVQVRALKSFARKRGVILVFISQID 193 (237)
T ss_pred CCEEEEECHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEECCC
T ss_conf 9689997677526677886689999999999998699399940036
No 287
>COG0837 Glk Glucokinase [Carbohydrate transport and metabolism]
Probab=24.26 E-value=21 Score=15.21 Aligned_cols=26 Identities=12% Similarity=0.083 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf 66555432345503871589999999
Q gi|255764496|r 179 KYMEFVHEAKKFLSGGNHNLKEKIAR 204 (616)
Q Consensus 179 ~Y~~~v~~~~~fL~G~~~~ii~~L~~ 204 (616)
+|.-..+....-|.=+.-.+++.++.
T Consensus 82 ~W~~s~~~~r~~Lgl~~v~liNDF~A 107 (320)
T COG0837 82 DWVFSIARMRAELGLDHLSLINDFAA 107 (320)
T ss_pred CCEECHHHHHHHCCCCCEEEECHHHH
T ss_conf 51105999997549881798613888
No 288
>pfam03796 DnaB_C DnaB-like helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=24.13 E-value=43 Score=13.01 Aligned_cols=37 Identities=22% Similarity=0.363 Sum_probs=25.5
Q ss_pred CCEEEEE-------CC-------HHHHHHHHHHHHHCCCCCCCCEEEEECC
Q ss_conf 8489980-------98-------5899999999997588778718999718
Q gi|255764496|r 464 PDVVILD-------GG-------KGQLSAAQGVLKKLNVENRITIISIAKG 500 (616)
Q Consensus 464 PDLilID-------GG-------kgQln~a~~vl~~l~i~~~i~viglaK~ 500 (616)
+|+|+|| .+ ..++....+-|+.+-.+.++||+.++-=
T Consensus 130 ~~~vvvDyl~l~~~~~~~~~~~r~~~v~~i~~~Lk~lA~e~~i~ii~~sQl 180 (186)
T pfam03796 130 LGLIVIDYLQLMQGSKASKSENRQQEISEISRSLKALAKELNIPVIALSQL 180 (186)
T ss_pred CCEEEEEHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEECC
T ss_conf 988997489863677888775599999999999999999979918997225
No 289
>CHL00101 trpG anthranilate synthase component 2
Probab=24.06 E-value=43 Score=13.00 Aligned_cols=25 Identities=28% Similarity=0.340 Sum_probs=12.4
Q ss_pred EEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 54101135667778997898887775
Q gi|255764496|r 266 NRGTCTFFLKTDSESTNAQILSYFLR 291 (616)
Q Consensus 266 i~g~~~f~~~~~~~~~~~eil~~fI~ 291 (616)
+.|.+ |-++....+....+|.+||.
T Consensus 163 i~GVQ-FHPEs~~T~~G~~il~NFl~ 187 (190)
T CHL00101 163 LRGIQ-FHPESILTEHGQQLLRNFLS 187 (190)
T ss_pred EEEEE-ECCCCCCCCCHHHHHHHHHH
T ss_conf 79999-74866999486999999998
No 290
>pfam01912 eIF-6 eIF-6 family. This family includes eukaryotic translation initiation factor 6 as well as presumed archaebacterial homologues.
Probab=24.01 E-value=43 Score=13.00 Aligned_cols=55 Identities=18% Similarity=0.283 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf 9999999875156643516999707443775404888885168728032321102444455411689989999
Q gi|255764496|r 363 QMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVL 435 (616)
Q Consensus 363 ~~~l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi 435 (616)
....+.+++.|+.+-.+..| .|..+|||+.|+.|.|.- +.+. ...+|...+++++
T Consensus 117 ~e~~e~I~dvLgVev~~~~i--------ag~~~VGS~~v~tN~G~L--------vhP~--~s~eE~~~l~~~l 171 (198)
T pfam01912 117 RETEEIIADVLGVEVFRGTI--------AGNKTVGSAGVATNKGGL--------VHPD--ATEEELEELSELL 171 (198)
T ss_pred HHHHHHHHHHHCCEEEEEEE--------CCCCCCEEEEEEECCEEE--------ECCC--CCHHHHHHHHHHH
T ss_conf 89999998863963999985--------685762278999577178--------8899--8999999999987
No 291
>cd01142 TroA_e Periplasmic binding protein TroA_e. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=23.83 E-value=43 Score=12.97 Aligned_cols=11 Identities=36% Similarity=0.758 Sum_probs=8.9
Q ss_pred CCEEEEECCHH
Q ss_conf 84899809858
Q gi|255764496|r 464 PDVVILDGGKG 474 (616)
Q Consensus 464 PDLilIDGGkg 474 (616)
||.|++.++.+
T Consensus 220 PDvI~~~~~~~ 230 (289)
T cd01142 220 PDVIIVGNADT 230 (289)
T ss_pred CCEEEECCCCC
T ss_conf 98899847643
No 292
>cd01825 SGNH_hydrolase_peri1 SGNH_peri1; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=23.77 E-value=43 Score=12.97 Aligned_cols=49 Identities=18% Similarity=0.288 Sum_probs=24.9
Q ss_pred EEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 69997074437754048888851687280323211024444554116899899999999
Q gi|255764496|r 381 RIEIYDNSHIMGCSAVGCMVVVGENGFVKNQYRKFNLHPNDVKTQDDCAMMRMVLERRF 439 (616)
Q Consensus 381 rIE~fDiSh~~G~~~Vas~Vvf~~g~~~K~~YR~f~Ik~~~v~~~DD~~~m~Evi~RR~ 439 (616)
.+-.+|.-..+|.. +||-.|.+.+...++|=||+-+ =|.-|.+.+..-+
T Consensus 137 ~~~f~D~~~~MGG~--~s~~~w~~~~L~~~D~vH~t~~--------Gy~~~a~~l~~aL 185 (189)
T cd01825 137 GIAFWDLYAAMGGE--GGIWQWAEPGLARKDYVHLTPR--------GYERLANLLYEAL 185 (189)
T ss_pred CCEEEEHHHHHCCC--CHHHHHHHCCCCCCCCCCCCHH--------HHHHHHHHHHHHH
T ss_conf 98598668964884--1577763124357998772867--------9999999999999
No 293
>PRK08840 replicative DNA helicase; Provisional
Probab=23.58 E-value=44 Score=12.94 Aligned_cols=36 Identities=14% Similarity=0.315 Sum_probs=23.3
Q ss_pred CCEEEEEC-------CHH-----HHHHHHHHHHHCCCCCCCCEEEEEC
Q ss_conf 84899809-------858-----9999999999758877871899971
Q gi|255764496|r 464 PDVVILDG-------GKG-----QLSAAQGVLKKLNVENRITIISIAK 499 (616)
Q Consensus 464 PDLilIDG-------Gkg-----Qln~a~~vl~~l~i~~~i~viglaK 499 (616)
.|||+||- |++ |+..+-..|+.+-.+.+|||+.|+-
T Consensus 330 l~lvvIDYLqL~~~~~~~~~r~~~i~~isr~lK~lAkel~vpVv~lsQ 377 (464)
T PRK08840 330 LSMIMVDYLQLMRVPALQDNRTLEIAEISRSLKALAKELNVPVVALSQ 377 (464)
T ss_pred CCEEEEEHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEECC
T ss_conf 878996188660678864036789999999999999996998999631
No 294
>cd00715 GPATase_N Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP, resulting in phosphoribosylamine, pyrophosphate and glutamate. GPATase crystalizes as a homotetramer, but can also exist as a homdimer.
Probab=23.09 E-value=45 Score=12.87 Aligned_cols=18 Identities=6% Similarity=-0.093 Sum_probs=10.4
Q ss_pred EECCCCCHHHHHHHHHHH
Q ss_conf 102688857876665432
Q gi|255764496|r 304 LLSEEAEETSLLEISFFK 321 (616)
Q Consensus 304 iv~~~~~~~~~l~~~L~~ 321 (616)
.-+-.+.+...|.+.|.+
T Consensus 99 vHNG~I~N~~eL~~~l~~ 116 (252)
T cd00715 99 AHNGNLVNAKELREELEE 116 (252)
T ss_pred EEEEEECCHHHHHHHHHH
T ss_conf 995388899999999985
No 295
>cd00156 REC Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers
Probab=22.96 E-value=45 Score=12.86 Aligned_cols=73 Identities=18% Similarity=0.150 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHH---HHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf 1689989999999977531311123333333345457984899809858999---999999975887787189997187
Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLS---AAQGVLKKLNVENRITIISIAKGP 501 (616)
Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln---~a~~vl~~l~i~~~i~viglaK~~ 501 (616)
||-..+++.+.+-+.+.--+-.....+...-..-....|||||+|-.-+.++ .+.++ ++.+- .+||+-+.-..
T Consensus 4 DD~~~~~~~l~~~L~~~g~~v~~a~~g~~al~~~~~~~~dlvi~D~~mP~~~G~el~~~i-r~~~~--~~pvI~lT~~~ 79 (113)
T cd00156 4 DDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLAEEKPDLILLDIMMPGMDGLELLRRI-RKRGP--DIPIIFLTAHG 79 (113)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCCEEEECCCCCCCCCHHHHHHH-HHHCC--CCCEEEEECCC
T ss_conf 272999999999999889999998999999999875799999977999898726999999-98589--99599997878
No 296
>TIGR01627 A_thal_3515 uncharacterized plant-specific domain TIGR01627; InterPro: IPR006514 These sequences contain an uncharacterised domain found in both Arabidopsis thaliana (at least 10 copies) and Oryza sativa. Most member proteins have only a short stretch of sequence N-terminal to this domain, but one has a long N-terminal extension that includes a protein kinase domain (IPR000719 from INTERPRO). .
Probab=22.75 E-value=35 Score=13.61 Aligned_cols=16 Identities=38% Similarity=0.873 Sum_probs=11.7
Q ss_pred CCCCCCEEEEECCHHHH
Q ss_conf 45798489980985899
Q gi|255764496|r 460 FPSWPDVVILDGGKGQL 476 (616)
Q Consensus 460 ~~~~PDLilIDGGkgQl 476 (616)
...| |||+|||=.|.=
T Consensus 145 ~tkW-DvI~VDgPrGd~ 160 (238)
T TIGR01627 145 DTKW-DVIVVDGPRGDD 160 (238)
T ss_pred CCCC-CEEEEECCCCCC
T ss_conf 3654-278861888987
No 297
>KOG0190 consensus
Probab=22.52 E-value=17 Score=15.90 Aligned_cols=134 Identities=19% Similarity=0.272 Sum_probs=76.4
Q ss_pred CCEEEEECCCHHHHHHHHHHH------------HHHHCCCCE---ECCCCC-CCCCEEEEECC-----------CCCCEE
Q ss_conf 442999828719999999988------------776187200---336468-97726998088-----------998459
Q gi|255764496|r 56 NNIRFTVTCTEVEALLLEANM------------IKRLKPRFN---ILLRDD-KSFPYILITDK-----------HKIPAL 108 (616)
Q Consensus 56 ~~ie~~~t~~e~eAlilE~~l------------Ik~~~P~yN---i~LkDd-k~yPyi~it~~-----------~~~p~l 108 (616)
...=.++|..-++-+|-.+.+ +|++.|.|- -.|+.. -.=+.-+|... -.||.|
T Consensus 24 ~~~Vl~Lt~dnf~~~i~~~~~vlVeFYAPWCghck~LaPey~kAA~~Lke~~s~i~LakVDat~~~~~~~~y~v~gyPTl 103 (493)
T KOG0190 24 EEDVLVLTKDNFKETINGHEFVLVEFYAPWCGHCKALAPEYEKAATELKEEGSPVKLAKVDATEESDLASKYEVRGYPTL 103 (493)
T ss_pred CCCEEEECCCCHHHHHCCCCEEEEEEECHHHHHHHHHCCHHHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHCCCCCCEE
T ss_conf 66179971755887751684489998722234445308278999987530489753687406433546766057888737
Q ss_pred EEEECCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 99812356784377037887899999999997301100355421247886624455425866131220356655543234
Q gi|255764496|r 109 YKHRDSSTIQGSYFGPFASVDAVEKTINSLQRTFFLRSCADSVFRHRTRPCLLFQIKRCSGPCTGEISSEKYMEFVHEAK 188 (616)
Q Consensus 109 ~~~r~~~~~~~~yfGPf~~~~~~~~~l~~l~~~f~lR~C~~~~~~~~~~pCl~y~i~~C~gpC~~~is~~~Y~~~v~~~~ 188 (616)
.+.|+-.. ...|-||+..-+ ++..+++. +||-+ ..-..++.+.
T Consensus 104 kiFrnG~~-~~~Y~G~r~adg----IV~wl~kq--------------------------~gPa~------~~l~~~~~a~ 146 (493)
T KOG0190 104 KIFRNGRS-AQDYNGPREADG----IVKWLKKQ--------------------------SGPAS------KTLKTVDEAE 146 (493)
T ss_pred EEEECCCC-CEECCCCCCHHH----HHHHHHHC--------------------------CCCCC------EECCCHHHHH
T ss_conf 99865975-431268211789----99999862--------------------------28885------1523388887
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 5503871589999999999998633388888899999999
Q gi|255764496|r 189 KFLSGGNHNLKEKIARNMNQATLKEDYESAIIHRDRLAAL 228 (616)
Q Consensus 189 ~fL~G~~~~ii~~L~~~M~~aS~~l~FE~Aa~~RD~I~aL 228 (616)
.|+.++..-++--.+..|..+ .--|..|+.+||.+.-.
T Consensus 147 ~~l~~~~~~vig~F~d~~~~~--~~~~~~a~~l~~d~~F~ 184 (493)
T KOG0190 147 EFLSKKDVVVIGFFKDLESLA--ESFFDAASKLRDDYKFA 184 (493)
T ss_pred HHCCCCCEEEEEEECCCCCCH--HHHHHHHHHCCCCCEEE
T ss_conf 443678638998744455525--89999998402444132
No 298
>KOG1795 consensus
Probab=22.45 E-value=46 Score=12.79 Aligned_cols=71 Identities=21% Similarity=0.306 Sum_probs=43.5
Q ss_pred HHHHHHCCCCCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCC
Q ss_conf 654320134333212565-526678999999999865543233433899999998751566435169997074437
Q gi|255764496|r 317 ISFFKQYGYKVKITVPKQ-GEKRKIIEQALINAHRSHTQKLSTEISHQMILKDFTKKFALPHIPKRIEIYDNSHIM 391 (616)
Q Consensus 317 ~~L~~k~g~kV~i~~P~r-G~kk~Ll~lA~~NA~~~l~~k~~~~~~~~~~l~~Lk~~L~L~~~p~rIE~fDiSh~~ 391 (616)
+-|.+.+ .+++..|+. -+...|++.|..|-.+.+.+ +.+..-.++++++..-.+- ...-..|+||+++|+-
T Consensus 838 E~lke~y--s~k~rlnqsqrEEl~lieqAydnphe~l~r-IKr~LLTqR~FKeVgi~~m-d~y~~lipvY~v~plE 909 (2321)
T KOG1795 838 ERLKEAY--SVKVRLNQSQREELGLIEQAYDNPHEALSR-IKRHLLTQRSFKEVGIEFM-DLYSHLIPVYSVEPLE 909 (2321)
T ss_pred HHHHHHC--CCCCCCCHHHHHHHHHHHHHHHCHHHHHHH-HHHHHHHHHHHHHHCEEHH-HHCCCCEEEEECCHHH
T ss_conf 9987624--401257766788998999885086989999-9998876620254074276-6427730245245798
No 299
>PRK04885 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional
Probab=22.22 E-value=46 Score=12.76 Aligned_cols=30 Identities=10% Similarity=0.125 Sum_probs=13.0
Q ss_pred CEEEECCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 7454101135667778997898887775432
Q gi|255764496|r 264 GQNRGTCTFFLKTDSESTNAQILSYFLRQFY 294 (616)
Q Consensus 264 G~i~g~~~f~~~~~~~~~~~eil~~fI~qyY 294 (616)
|...|+..|.-+... ++.++.+..++..-|
T Consensus 66 GIN~G~lGFLt~~~~-~~~~~~l~~i~~~~~ 95 (265)
T PRK04885 66 GVHTGHLGFYTDWRD-FEVDKLVIALAKDPG 95 (265)
T ss_pred EEECCCEEEECCCCH-HHHHHHHHHHHCCCC
T ss_conf 873585257614787-899999999982996
No 300
>PRK03604 moaC bifunctional molybdenum cofactor biosynthesis protein C/molybdopterin-binding protein; Provisional
Probab=21.99 E-value=47 Score=12.72 Aligned_cols=30 Identities=17% Similarity=0.349 Sum_probs=23.9
Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHH
Q ss_conf 116899899999999775313111233333333454579848998098589
Q gi|255764496|r 425 QDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQ 475 (616)
Q Consensus 425 ~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQ 475 (616)
+||.+.+++.|.++... -+||||.-||-|=
T Consensus 188 PDd~~~I~~~l~~~~~~---------------------~~dlIlTtGGTG~ 217 (301)
T PRK03604 188 PDEPEEIAAAVQAWIAE---------------------GVELIITTGGTGL 217 (301)
T ss_pred CCCHHHHHHHHHHHHHC---------------------CCCEEEEECCCCC
T ss_conf 89889999999999977---------------------9979997089778
No 301
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=21.84 E-value=47 Score=12.70 Aligned_cols=39 Identities=26% Similarity=0.426 Sum_probs=29.6
Q ss_pred CCHHCCCCCCHHHHHHHHHHHC--CHHHHHHCCHHHHHHCCC
Q ss_conf 7100488879899999999808--889899389888862789
Q gi|255764496|r 555 SPLDEINGIGPLRKRLLLQSFG--TVKMISRSSPETLASIEG 594 (616)
Q Consensus 555 S~Ld~I~GIG~k~~~~Ll~~Fg--s~~~i~~As~eeL~~v~g 594 (616)
..|-.|+|||||-.+ +|+..| -++.|..=+.+|++=|.+
T Consensus 326 DDLk~ikGvGPkle~-~ln~lG~~hfdQiA~W~~~evaWvd~ 366 (403)
T PRK12373 326 DDLKLISGVGPKIEG-TLNELGIFTFDQVASWKKAERAWVDG 366 (403)
T ss_pred CHHHHHCCCCHHHHH-HHHHHCCEEHHHHHCCCHHHHHHHHH
T ss_conf 355664175878999-98862626489865268999999874
No 302
>pfam02638 DUF187 Uncharacterized BCR, COG1649.
Probab=21.50 E-value=48 Score=12.66 Aligned_cols=46 Identities=9% Similarity=0.140 Sum_probs=22.5
Q ss_pred CCCCEEEEEECCCCCCCEEEECCCCHHHHHHHHHHHHHH------HHHHCCCCCCCCCC
Q ss_conf 998459998123567843770378878999999999973------01100355421247
Q gi|255764496|r 103 HKIPALYKHRDSSTIQGSYFGPFASVDAVEKTINSLQRT------FFLRSCADSVFRHR 155 (616)
Q Consensus 103 ~~~p~l~~~r~~~~~~~~yfGPf~~~~~~~~~l~~l~~~------f~lR~C~~~~~~~~ 155 (616)
+++--+.+|-.... . +++.....++++.|.++ |..|.+.+.+....
T Consensus 40 ~EiRGVWlt~v~~~---~----~~~~~q~~e~i~~L~~lnfNtV~~qVr~~gdalYpS~ 91 (394)
T pfam02638 40 NEIRGVWLTNVDSN---D----WPDPVQLQEAIALLDDLNFNTVYPQVWNDGHALYPSA 91 (394)
T ss_pred CCEEEEEEECCCCC---C----CCCHHHHHHHHHHHHHCCCCEEEEEEECCCCEEECCC
T ss_conf 34067999415877---6----5898999999999998699879999957855230664
No 303
>COG4231 Indolepyruvate ferredoxin oxidoreductase, alpha and beta subunits [Energy production and conversion]
Probab=21.47 E-value=48 Score=12.65 Aligned_cols=27 Identities=15% Similarity=0.069 Sum_probs=15.5
Q ss_pred CEEEEECCCHHHHHHHHHHHHHHHCCCCE
Q ss_conf 42999828719999999988776187200
Q gi|255764496|r 57 NIRFTVTCTEVEALLLEANMIKRLKPRFN 85 (616)
Q Consensus 57 ~ie~~~t~~e~eAlilE~~lIk~~~P~yN 85 (616)
+|.+.-..||. +-+|.-+=-.|-+.+-
T Consensus 58 ~vy~e~s~NEk--vA~e~a~GA~~~G~ra 84 (640)
T COG4231 58 DVYFEWSLNEK--VALETAAGASYAGVRA 84 (640)
T ss_pred CEEEEECCCHH--HHHHHHHHHHHCCCEE
T ss_conf 38997065489--9999998765337002
No 304
>smart00654 eIF6 translation initiation factor 6.
Probab=21.46 E-value=48 Score=12.65 Aligned_cols=37 Identities=19% Similarity=0.191 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCEEEEEEEECCCC
Q ss_conf 999999987515664351699970744377540488888516872
Q gi|255764496|r 363 QMILKDFTKKFALPHIPKRIEIYDNSHIMGCSAVGCMVVVGENGF 407 (616)
Q Consensus 363 ~~~l~~Lk~~L~L~~~p~rIE~fDiSh~~G~~~Vas~Vvf~~g~~ 407 (616)
....+.+++.|+.+-.... +.|..+|||+.|+.|.|.
T Consensus 119 ~e~~e~I~dvL~Vev~~~~--------iag~~~VGs~~v~tN~G~ 155 (200)
T smart00654 119 KETEEIISDVLGVEVFRGT--------IAGNITVGSYCVVTNKGG 155 (200)
T ss_pred HHHHHHHHHHHCCEEEEEE--------ECCCCCCCEEEEEECCEE
T ss_conf 8999999874093599998--------778165323799987848
No 305
>pfam11020 DUF2610 Protein of unknown function (DUF2610). This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=21.20 E-value=48 Score=12.68 Aligned_cols=31 Identities=23% Similarity=0.087 Sum_probs=21.2
Q ss_pred HHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf 665432013433321256552667899999999
Q gi|255764496|r 316 EISFFKQYGYKVKITVPKQGEKRKIIEQALINA 348 (616)
Q Consensus 316 ~~~L~~k~g~kV~i~~P~rG~kk~Ll~lA~~NA 348 (616)
..||++.+|..|.=.+ ...-.+|-++|.+|-
T Consensus 35 ~~WLs~eRGG~Ip~~V--m~Sl~kL~~LA~kn~ 65 (85)
T pfam11020 35 ATWLSKERGGVIPEKV--MDSLSKLHELAKKNG 65 (85)
T ss_pred HHHHHHHHCCCCCHHH--HHHHHHHHHHHHHCC
T ss_conf 8898872189886999--999999999998739
No 306
>COG4748 Uncharacterized conserved protein [Function unknown]
Probab=21.07 E-value=48 Score=12.64 Aligned_cols=47 Identities=15% Similarity=0.069 Sum_probs=25.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHH
Q ss_conf 5543234550387158999999999999863-3388888899999999
Q gi|255764496|r 182 EFVHEAKKFLSGGNHNLKEKIARNMNQATLK-EDYESAIIHRDRLAAL 228 (616)
Q Consensus 182 ~~v~~~~~fL~G~~~~ii~~L~~~M~~aS~~-l~FE~Aa~~RD~I~aL 228 (616)
..+.+.+-|+.-+-.++....-.....+|.+ .+-|.++..---+.-+
T Consensus 127 ~N~MD~kPFm~~nL~~i~~~~~~eLkkfsk~~fN~E~~~~~A~elkYt 174 (365)
T COG4748 127 PNKMDNKPFMEFNLEDIKEKQFNELKKFSKESFNVEELASFALELKYT 174 (365)
T ss_pred CCCCCCCCCEEEEHHHCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 555567862697753364555699999766149999999899876679
No 307
>PRK08857 para-aminobenzoate synthase component II; Provisional
Probab=21.03 E-value=46 Score=12.78 Aligned_cols=29 Identities=17% Similarity=0.145 Sum_probs=12.2
Q ss_pred ECCEEEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf 247454101135667778997898887775
Q gi|255764496|r 262 HFGQNRGTCTFFLKTDSESTNAQILSYFLR 291 (616)
Q Consensus 262 R~G~i~g~~~f~~~~~~~~~~~eil~~fI~ 291 (616)
+...+.|.+ |-++....+....+|.+||.
T Consensus 163 ~~~~i~GVQ-FHPEs~~T~~G~~il~NFl~ 191 (192)
T PRK08857 163 KTLPIEAVQ-FHPESIKTEQGHQLLANFLA 191 (192)
T ss_pred CCCCEEEEE-ECCCCCCCCCHHHHHHHHHC
T ss_conf 899989998-77977998474899999726
No 308
>PRK07004 replicative DNA helicase; Provisional
Probab=20.92 E-value=49 Score=12.58 Aligned_cols=37 Identities=22% Similarity=0.336 Sum_probs=25.0
Q ss_pred CCEEEEEC-------CH-----HHHHHHHHHHHHCCCCCCCCEEEEECC
Q ss_conf 84899809-------85-----899999999997588778718999718
Q gi|255764496|r 464 PDVVILDG-------GK-----GQLSAAQGVLKKLNVENRITIISIAKG 500 (616)
Q Consensus 464 PDLilIDG-------Gk-----gQln~a~~vl~~l~i~~~i~viglaK~ 500 (616)
+|||+||- ++ .++..+-+.|+.+-.+.+|||+.||-=
T Consensus 325 l~lvviDYlqli~~~~~~~~r~~ei~~isr~lK~lAkel~ipvi~lsQL 373 (460)
T PRK07004 325 LGLIIIDYLQLMSGSSQGENRATEISEISRSLKSLAKELDVPVIALSQL 373 (460)
T ss_pred CCEEEEEHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 8899850775447888888899999999999999999969978997046
No 309
>COG0303 MoeA Molybdopterin biosynthesis enzyme [Coenzyme metabolism]
Probab=20.87 E-value=49 Score=12.57 Aligned_cols=103 Identities=21% Similarity=0.290 Sum_probs=62.0
Q ss_pred CHHHHHHHHCCCCC-CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCH--HHHHHHHHHHH
Q ss_conf 80323211024444-5541168998999999997753131112333333334545798489980985--89999999999
Q gi|255764496|r 408 VKNQYRKFNLHPND-VKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGK--GQLSAAQGVLK 484 (616)
Q Consensus 408 ~K~~YR~f~Ik~~~-v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGk--gQln~a~~vl~ 484 (616)
-...-+.+...... ---.||...+++++.+=... -|+|++=||- |--..+.++++
T Consensus 208 l~a~l~~~G~e~~~~giv~Dd~~~l~~~i~~a~~~----------------------~DviItsGG~SvG~~D~v~~~l~ 265 (404)
T COG0303 208 LAALLERAGGEVVDLGIVPDDPEALREAIEKALSE----------------------ADVIITSGGVSVGDADYVKAALE 265 (404)
T ss_pred HHHHHHHCCCCEEECCCCCCCHHHHHHHHHHHHHC----------------------CCEEEEECCCCCCCHHHHHHHHH
T ss_conf 99999975992453353599989999999977524----------------------99999969866761466999998
Q ss_pred -HCCCCCCCCEEEEECCCCCCCCCEEEECCCCC-EEEECCCC--HHHHHHHHHHHHHH
Q ss_conf -75887787189997187767663489817983-48857998--99999998878778
Q gi|255764496|r 485 -KLNVENRITIISIAKGPKRSAGMEKFFVKKGE-ALVLNMRD--PILYFIQRLRDEAH 538 (616)
Q Consensus 485 -~l~i~~~i~viglaK~~~r~~~~e~~~~~~~~-~i~l~~~~--~~l~~Lq~iRDEaH 538 (616)
++| + |.+-|++=+..+-++. =..++. -+-|+-+. ....|..-+|+=-.
T Consensus 266 ~~lG-~--v~~~gia~kPGkP~~~---g~~~~~~v~gLPGnPvSalv~f~~~v~p~l~ 317 (404)
T COG0303 266 RELG-E--VLFHGVAMKPGKPTGL---GRLGGKPVFGLPGNPVSALVNFELFVRPLLR 317 (404)
T ss_pred HCCC-C--EEEEEEEECCCCCEEE---EEECCCEEEECCCCHHHHHHHHHHHHHHHHH
T ss_conf 4389-3--7997666069984599---9989978998988779999999999999999
No 310
>TIGR02775 TrbG_Ti P-type conjugative transfer protein TrbG; InterPro: IPR014142 The TrbG protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbG is a homologue of the F-type TraK protein (which is believed to be an outer membrane pore-forming secretin, IPR014126 from INTERPRO) as well as the vir system VirB9 protein , ..
Probab=20.82 E-value=38 Score=13.40 Aligned_cols=17 Identities=29% Similarity=0.671 Sum_probs=13.6
Q ss_pred CCCCCCEEEE--ECC-----HHHH
Q ss_conf 4579848998--098-----5899
Q gi|255764496|r 460 FPSWPDVVIL--DGG-----KGQL 476 (616)
Q Consensus 460 ~~~~PDLilI--DGG-----kgQl 476 (616)
.+++|=|++| ||| ++||
T Consensus 173 q~elP~LfVv~~~GGlftdd~~~L 196 (220)
T TIGR02775 173 QGELPPLFVVGPDGGLFTDDENEL 196 (220)
T ss_pred CCCCCEEEEEECCCCEEECCCCCE
T ss_conf 444870168826886456378636
No 311
>pfam05621 TniB Bacterial TniB protein. This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein which is involved in Tn5053 mercury resistance transposition.
Probab=20.53 E-value=50 Score=12.52 Aligned_cols=82 Identities=13% Similarity=0.137 Sum_probs=54.7
Q ss_pred EEEECCCCCHHHHHHHHC--C--CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEE-----
Q ss_conf 885168728032321102--4--4445541168998999999997753131112333333334545798489980-----
Q gi|255764496|r 400 VVVGENGFVKNQYRKFNL--H--PNDVKTQDDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILD----- 470 (616)
Q Consensus 400 Vvf~~g~~~K~~YR~f~I--k--~~~v~~~DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilID----- 470 (616)
|++..-.|.++.-|.|.- . ..-....|+.+.++..+-+=+.++. +-+++||
T Consensus 98 Vl~vq~P~~p~~~~lY~~IL~~l~aP~~~~~~~~~~~~~~~~ll~~~~--------------------vrmLIIDEiHnl 157 (302)
T pfam05621 98 VLVVQMPSEPSVIRFYVALLAAMGAPLRPRPRLPEMEQLALALLRKVG--------------------VRMLVIDELHNV 157 (302)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCC--------------------CCEEEEECHHHH
T ss_conf 899976999886899999999837877888778999999999999749--------------------878998543656
Q ss_pred --CCHHHHHHHHHHHHHCCCCCCCCEEEEECCC
Q ss_conf --9858999999999975887787189997187
Q gi|255764496|r 471 --GGKGQLSAAQGVLKKLNVENRITIISIAKGP 501 (616)
Q Consensus 471 --GGkgQln~a~~vl~~l~i~~~i~viglaK~~ 501 (616)
|+--+..++..+|+.++-+.+||++++--.+
T Consensus 158 L~Gs~~~qr~~ln~LK~L~Nel~IpiV~vGt~e 190 (302)
T pfam05621 158 LAGNSVNRREFLNLLRFLGNELRIPLVGVGTRD 190 (302)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCEEEECCHH
T ss_conf 048688999999999998636587869953199
No 312
>KOG2383 consensus
Probab=20.45 E-value=29 Score=14.24 Aligned_cols=82 Identities=21% Similarity=0.272 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEECCHHHHHHHHH-----HHHHCCCC--CCCCEEEEECCCCC
Q ss_conf 899999999775313111233333333454579848998098589999999-----99975887--78718999718776
Q gi|255764496|r 431 MRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDGGKGQLSAAQG-----VLKKLNVE--NRITIISIAKGPKR 503 (616)
Q Consensus 431 m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDGGkgQln~a~~-----vl~~l~i~--~~i~viglaK~~~r 503 (616)
..-++.++|+.+..++.+. ..|.++.|=|-+=+++-|.. .+++|=-. .-.+-++|||+-
T Consensus 289 ~~~~l~~~fk~~~~dq~d~------------~~~~~l~v~GR~l~vpk~cg~VA~ftFeeLC~rPlgAaDYL~lak~f-- 354 (467)
T KOG2383 289 VETVLKEWFKLLAADQNDG------------TRQRTLVVFGRKLIVPKACGGVADFTFEELCGRPLGAADYLGLAKNF-- 354 (467)
T ss_pred HHHHHHHHHHHHHCCCCCC------------CCCCCEEEECCEEEECCCCCCCCCCCHHHHCCCCCCHHHHHHHHHHC--
T ss_conf 7899999999974358887------------77742267522677025578703122998708954247799997642--
Q ss_pred CCCCEEEECCCCCEEEECCCCHHHHHHHHHHHHHHHHH
Q ss_conf 76634898179834885799899999998878778878
Q gi|255764496|r 504 SAGMEKFFVKKGEALVLNMRDPILYFIQRLRDEAHRFA 541 (616)
Q Consensus 504 ~~~~e~~~~~~~~~i~l~~~~~~l~~Lq~iRDEaHRFA 541 (616)
++++..+- | .|=+.+||++|||-
T Consensus 355 ----hti~v~dI-P----------~lsl~~r~~~rRFI 377 (467)
T KOG2383 355 ----HTIIVRDI-P----------QLSLENRDQARRFI 377 (467)
T ss_pred ----CEEEEECC-C----------HHHHHHHHHHHHHH
T ss_conf ----45776065-1----------11057788776787
No 313
>PRK07204 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed
Probab=20.38 E-value=50 Score=12.50 Aligned_cols=66 Identities=15% Similarity=0.132 Sum_probs=30.3
Q ss_pred HHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH-HHH-------------HHHHHHHHHHHHHHHCCCCCCCEEE
Q ss_conf 54320134333212565526678999999999865543-233-------------4338999999987515664351699
Q gi|255764496|r 318 SFFKQYGYKVKITVPKQGEKRKIIEQALINAHRSHTQK-LST-------------EISHQMILKDFTKKFALPHIPKRIE 383 (616)
Q Consensus 318 ~L~~k~g~kV~i~~P~rG~kk~Ll~lA~~NA~~~l~~k-~~~-------------~~~~~~~l~~Lk~~L~L~~~p~rIE 383 (616)
|+.++.|-+-+ +.+ .+ ..-.+||..=|+..|.+- +.. .......--.+++.|++++. .+.
T Consensus 34 ~i~~~tGI~~R-~~a-~~--e~~sdma~~Aa~~aL~~agi~~~dIdliI~~s~t~d~~~P~~A~~v~~~LGl~~~--~~~ 107 (329)
T PRK07204 34 WTLKKAGVKTR-YFV-DG--ETSSYMGAEAAKKAVEDAKLTWDDIDCIICGSGTIQQAIPSTASLIQEQLGLQHS--GIP 107 (329)
T ss_pred HHHHCCCCEEE-EEC-CC--CCHHHHHHHHHHHHHHHCCCCHHHCCEEEEECCCCCCCCCCHHHHHHHHHCCCCC--CCE
T ss_conf 99762386168-557-99--9859999999999999759898888499992578998898099999999647888--835
Q ss_pred EEECCC
Q ss_conf 970744
Q gi|255764496|r 384 IYDNSH 389 (616)
Q Consensus 384 ~fDiSh 389 (616)
|||++.
T Consensus 108 afDi~~ 113 (329)
T PRK07204 108 CFDINS 113 (329)
T ss_pred EEEHHH
T ss_conf 500301
No 314
>COG0215 CysS Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=20.12 E-value=51 Score=12.46 Aligned_cols=42 Identities=5% Similarity=-0.005 Sum_probs=19.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHH------HHH-HHHHHHHHHHHHHHH
Q ss_conf 715899999999999986333888------888-999999998622110
Q gi|255764496|r 194 GNHNLKEKIARNMNQATLKEDYES------AII-HRDRLAALSHIQNHN 235 (616)
Q Consensus 194 ~~~~ii~~L~~~M~~aS~~l~FE~------Aa~-~RD~I~aL~~i~~~q 235 (616)
...++-+...+.|..-.+.|+-.. |-. +-+.|..|+.+.++.
T Consensus 84 ~~~ev~~~~i~~f~~D~~aL~v~~p~~~PraTe~I~~iI~~I~~Li~kG 132 (464)
T COG0215 84 SIREVAERYIAAFFEDMDALNVLPPDIEPRATEHIDEIIEFIEKLIEKG 132 (464)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHCHHHHHHHHHHHHHCC
T ss_conf 9999999999999999998299998655747647999999999999779
No 315
>pfam11202 DUF2983 Protein of unknown function (DUF2983). This bacterial family of proteins has no known function.
Probab=20.08 E-value=51 Score=12.45 Aligned_cols=31 Identities=32% Similarity=0.565 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEEEEC--CHHHHHHH
Q ss_conf 1689989999999977531311123333333345457984899809--85899999
Q gi|255764496|r 426 DDCAMMRMVLERRFSQLIKNEENLNFHPKKQEYSFPSWPDVVILDG--GKGQLSAA 479 (616)
Q Consensus 426 DD~~~m~Evi~RR~~r~~~~~~~l~~~~~~~~~~~~~~PDLilIDG--GkgQln~a 479 (616)
=|..+|+.++.|+ +.-++++||| |||-++--
T Consensus 124 ID~~AL~~Il~~H-----------------------~~~~ivFVDGWTGKGaI~~E 156 (353)
T pfam11202 124 IDENALRYILARH-----------------------PPESIVFVDGWTGKGAITRE 156 (353)
T ss_pred CCHHHHHHHHHHC-----------------------CCCCEEEEECCCCCHHHHHH
T ss_conf 5899999999868-----------------------98774997078772188999
No 316
>pfam02503 PP_kinase Polyphosphate kinase. Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules.
Probab=20.00 E-value=51 Score=12.44 Aligned_cols=49 Identities=22% Similarity=0.234 Sum_probs=23.2
Q ss_pred HHHEECCCCCHHHHHHHHHHHHC-CCC---CCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf 12310268885787666543201-343---332125655266789999999998
Q gi|255764496|r 301 ENILLSEEAEETSLLEISFFKQY-GYK---VKITVPKQGEKRKIIEQALINAHR 350 (616)
Q Consensus 301 ~~Iiv~~~~~~~~~l~~~L~~k~-g~k---V~i~~P~rG~kk~Ll~lA~~NA~~ 350 (616)
+.|++.++.+.-+.+-++|.+-. +.+ |++..=..+....+++ |+.+|.+
T Consensus 334 ~DiLlhhPY~SF~~vv~fl~~AA~DP~V~aIK~TLYR~a~~S~Iv~-aLi~AA~ 386 (678)
T pfam02503 334 KDILLHHPYESFDPVVDFLRQAAADPDVLAIKQTLYRTSKDSPIVD-ALIEAAE 386 (678)
T ss_pred CCEEEECCHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCHHHH-HHHHHHH
T ss_conf 6968847765612799999998379985378778985279888999-9999998
Done!