Query 006771
Match_columns 632
No_of_seqs 229 out of 688
Neff 5.9
Searched_HMMs 46136
Date Thu Mar 28 14:15:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006771.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006771hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2379 Endonuclease MUS81 [Re 100.0 9.9E-72 2.2E-76 598.6 27.4 471 7-628 1-496 (501)
2 COG1948 MUS81 ERCC4-type nucle 100.0 8.3E-36 1.8E-40 301.2 22.3 207 375-631 26-236 (254)
3 PRK13766 Hef nuclease; Provisi 99.9 8E-27 1.7E-31 273.1 21.4 207 373-629 559-767 (773)
4 TIGR00596 rad1 DNA repair prot 99.9 1E-25 2.3E-30 261.9 20.3 210 374-630 584-809 (814)
5 PF02732 ERCC4: ERCC4 domain; 99.9 1.1E-23 2.4E-28 195.7 15.4 133 381-518 1-143 (143)
6 KOG0442 Structure-specific end 99.8 2.5E-18 5.4E-23 194.6 16.2 209 373-629 649-872 (892)
7 PF14716 HHH_8: Helix-hairpin- 98.2 5.4E-06 1.2E-10 68.9 6.9 67 20-88 1-68 (68)
8 KOG2534 DNA polymerase IV (fam 97.2 0.001 2.3E-08 70.0 7.9 73 17-92 9-81 (353)
9 KOG2841 Structure-specific end 97.0 0.0064 1.4E-07 61.8 11.2 133 460-629 113-247 (254)
10 smart00483 POLXc DNA polymeras 96.6 0.0056 1.2E-07 66.1 7.9 73 18-92 1-73 (334)
11 PF12826 HHH_2: Helix-hairpin- 95.8 0.0088 1.9E-07 49.2 3.3 51 567-629 5-55 (64)
12 cd00141 NT_POLXc Nucleotidyltr 95.4 0.027 5.9E-07 60.1 6.4 47 46-92 24-70 (307)
13 PRK08609 hypothetical protein; 93.9 0.12 2.5E-06 59.9 7.0 71 20-92 3-73 (570)
14 TIGR00084 ruvA Holliday juncti 92.5 0.3 6.5E-06 48.8 6.6 37 560-598 68-104 (191)
15 PRK13901 ruvA Holliday junctio 92.4 0.29 6.4E-06 49.1 6.3 58 560-627 68-125 (196)
16 PRK14602 ruvA Holliday junctio 92.2 0.34 7.3E-06 48.9 6.5 57 560-626 70-126 (203)
17 PRK14605 ruvA Holliday junctio 92.1 0.38 8.3E-06 48.2 6.7 56 560-625 69-124 (194)
18 PRK14601 ruvA Holliday junctio 92.0 0.35 7.6E-06 48.1 6.2 58 560-627 69-126 (183)
19 PRK14603 ruvA Holliday junctio 91.8 0.36 7.9E-06 48.5 6.2 57 560-626 68-124 (197)
20 PRK14604 ruvA Holliday junctio 91.8 0.35 7.5E-06 48.6 6.0 58 560-627 69-126 (195)
21 PRK14600 ruvA Holliday junctio 91.5 0.32 7E-06 48.4 5.5 57 560-627 69-125 (186)
22 PRK14606 ruvA Holliday junctio 91.5 0.42 9E-06 47.7 6.2 57 560-626 69-125 (188)
23 COG1948 MUS81 ERCC4-type nucle 91.4 0.087 1.9E-06 54.7 1.3 57 541-600 193-249 (254)
24 TIGR03433 padR_acidobact trans 91.1 1.1 2.3E-05 39.9 7.9 74 125-221 6-86 (100)
25 PF14520 HHH_5: Helix-hairpin- 91.1 0.57 1.2E-05 37.7 5.5 51 565-627 5-56 (60)
26 TIGR02337 HpaR homoprotocatech 91.0 0.64 1.4E-05 42.2 6.5 70 122-221 27-101 (118)
27 PF13463 HTH_27: Winged helix 89.4 0.22 4.8E-06 40.3 1.8 59 125-212 5-68 (68)
28 PF14947 HTH_45: Winged helix- 89.2 0.25 5.5E-06 41.9 2.2 39 181-221 33-71 (77)
29 PF01638 HxlR: HxlR-like helix 89.2 0.55 1.2E-05 40.9 4.3 36 186-221 38-78 (90)
30 PF00633 HHH: Helix-hairpin-he 89.1 0.32 7E-06 34.2 2.2 22 64-85 8-29 (30)
31 PRK14671 uvrC excinuclease ABC 88.1 0.83 1.8E-05 53.5 6.1 53 563-629 567-619 (621)
32 PF00633 HHH: Helix-hairpin-he 87.7 0.63 1.4E-05 32.7 2.9 19 565-583 11-29 (30)
33 PRK14669 uvrC excinuclease ABC 87.6 0.9 2E-05 53.2 5.9 55 561-629 548-602 (624)
34 PF09114 MotA_activ: Transcrip 87.4 0.5 1.1E-05 41.5 2.7 63 125-218 18-81 (96)
35 cd00080 HhH2_motif Helix-hairp 86.5 0.79 1.7E-05 38.9 3.5 32 567-598 24-55 (75)
36 PRK00116 ruvA Holliday junctio 85.0 2.3 5.1E-05 42.4 6.6 36 560-597 69-104 (192)
37 PF13601 HTH_34: Winged helix 84.6 0.77 1.7E-05 39.4 2.6 64 126-219 3-72 (80)
38 PF12826 HHH_2: Helix-hairpin- 84.3 0.63 1.4E-05 38.2 1.9 48 40-89 10-57 (64)
39 PRK14667 uvrC excinuclease ABC 82.6 1.4 3.1E-05 51.0 4.5 54 565-631 514-567 (567)
40 TIGR02719 repress_PhaQ poly-be 82.5 1.7 3.7E-05 41.4 4.2 38 184-221 60-104 (138)
41 PF11313 DUF3116: Protein of u 82.3 1.2 2.7E-05 38.9 2.9 32 190-221 50-83 (85)
42 PF03551 PadR: Transcriptional 82.3 1.1 2.4E-05 37.4 2.6 32 186-217 36-74 (75)
43 PF14277 DUF4364: Domain of un 82.0 2.8 6.2E-05 40.9 5.7 72 129-222 3-77 (163)
44 PRK03902 manganese transport t 81.9 1.7 3.7E-05 40.9 4.0 38 184-222 38-76 (142)
45 PRK00558 uvrC excinuclease ABC 81.7 2 4.3E-05 50.2 5.2 55 563-629 541-595 (598)
46 PF07848 PaaX: PaaX-like prote 81.2 1.1 2.4E-05 37.7 2.2 66 125-212 2-70 (70)
47 COG1695 Predicted transcriptio 80.8 8 0.00017 36.0 8.1 75 124-221 10-91 (138)
48 PF14338 Mrr_N: Mrr N-terminal 80.6 4.4 9.5E-05 35.4 5.9 81 127-217 8-89 (92)
49 COG1555 ComEA DNA uptake prote 80.6 2.8 6.2E-05 40.3 5.0 48 36-87 100-147 (149)
50 COG1733 Predicted transcriptio 80.5 2 4.4E-05 39.8 3.9 36 186-221 56-96 (120)
51 PRK13777 transcriptional regul 80.4 4.9 0.00011 40.1 6.8 70 122-221 44-118 (185)
52 PRK09482 flap endonuclease-lik 80.4 2.2 4.7E-05 44.7 4.5 32 568-599 185-216 (256)
53 smart00347 HTH_MARR helix_turn 79.8 2 4.4E-05 36.7 3.5 68 125-222 12-84 (101)
54 PRK11512 DNA-binding transcrip 79.7 2.1 4.6E-05 40.2 3.8 70 122-221 39-113 (144)
55 PRK13482 DNA integrity scannin 79.5 3 6.4E-05 45.5 5.3 32 564-595 286-317 (352)
56 PRK07945 hypothetical protein; 79.3 1.7 3.7E-05 47.0 3.5 100 46-163 24-131 (335)
57 PF07381 DUF1495: Winged helix 79.1 1.2 2.6E-05 39.4 1.7 34 185-218 53-89 (90)
58 PRK14666 uvrC excinuclease ABC 79.0 3.4 7.4E-05 48.8 6.0 55 562-628 634-688 (694)
59 TIGR01259 comE comEA protein. 78.8 4.1 9E-05 37.7 5.4 28 60-87 91-118 (120)
60 TIGR02702 SufR_cyano iron-sulf 78.8 2.2 4.7E-05 42.7 3.8 62 126-217 4-72 (203)
61 smart00529 HTH_DTXR Helix-turn 78.5 2.7 5.9E-05 36.3 3.9 36 185-221 17-52 (96)
62 PRK09416 lstR lineage-specific 77.5 11 0.00023 35.9 7.7 39 183-221 79-120 (135)
63 PRK14670 uvrC excinuclease ABC 76.8 3.2 7E-05 48.2 4.9 52 566-629 515-566 (574)
64 PF03501 S10_plectin: Plectin/ 76.8 1.9 4.1E-05 38.5 2.3 36 184-219 40-77 (95)
65 COG1796 POL4 DNA polymerase IV 76.6 5.5 0.00012 42.8 6.2 74 18-93 3-79 (326)
66 smart00278 HhH1 Helix-hairpin- 76.1 2.8 6.1E-05 28.1 2.6 20 566-585 2-21 (26)
67 COG1846 MarR Transcriptional r 75.9 2.6 5.7E-05 37.1 3.1 36 186-221 55-95 (126)
68 TIGR01889 Staph_reg_Sar staphy 75.5 3.6 7.9E-05 36.9 4.0 74 122-221 24-102 (109)
69 PF12836 HHH_3: Helix-hairpin- 74.9 2.7 5.9E-05 34.4 2.7 45 39-87 20-64 (65)
70 smart00475 53EXOc 5'-3' exonuc 74.5 4.2 9.2E-05 42.5 4.7 32 568-599 189-220 (259)
71 COG5045 Ribosomal protein S10E 74.3 2.3 4.9E-05 37.5 2.2 34 185-218 43-78 (105)
72 cd00008 53EXOc 5'-3' exonuclea 73.8 4.7 0.0001 41.6 4.8 32 568-599 186-217 (240)
73 smart00278 HhH1 Helix-hairpin- 73.4 2.7 5.8E-05 28.3 1.9 20 68-87 2-21 (26)
74 TIGR02277 PaaX_trns_reg phenyl 72.4 3.2 6.9E-05 44.0 3.2 69 128-218 2-73 (280)
75 PRK10870 transcriptional repre 71.9 4.3 9.3E-05 39.9 3.8 70 124-221 56-130 (176)
76 COG3432 Predicted transcriptio 71.2 5.7 0.00012 35.5 4.0 38 183-220 47-86 (95)
77 PRK03573 transcriptional regul 69.9 5.7 0.00012 37.1 4.0 70 123-221 31-105 (144)
78 PF14520 HHH_5: Helix-hairpin- 69.3 3.4 7.3E-05 33.2 2.0 49 38-88 10-59 (60)
79 PRK14976 5'-3' exonuclease; Pr 69.1 6.6 0.00014 41.6 4.7 32 568-599 194-225 (281)
80 PRK14668 uvrC excinuclease ABC 68.5 9.3 0.0002 44.6 6.1 54 563-628 523-576 (577)
81 PTZ00034 40S ribosomal protein 67.0 2.7 5.9E-05 39.1 1.1 37 184-220 43-81 (124)
82 COG0632 RuvA Holliday junction 66.5 14 0.00031 37.3 6.2 58 560-627 69-126 (201)
83 PRK02515 psbU photosystem II c 65.8 6.6 0.00014 37.1 3.4 38 556-593 52-91 (132)
84 COG0322 UvrC Nuclease subunit 65.6 6.2 0.00014 45.9 3.9 56 560-628 525-580 (581)
85 COG1497 Predicted transcriptio 65.1 5.7 0.00012 41.2 3.1 31 187-218 45-75 (260)
86 COG4742 Predicted transcriptio 64.9 6 0.00013 41.5 3.3 61 127-220 17-77 (260)
87 TIGR01259 comE comEA protein. 64.7 6.6 0.00014 36.3 3.2 32 556-587 59-90 (120)
88 TIGR00575 dnlj DNA ligase, NAD 64.7 9.1 0.0002 45.3 5.1 51 567-629 500-550 (652)
89 TIGR01884 cas_HTH CRISPR locus 64.5 3.3 7.1E-05 41.4 1.3 30 183-212 173-203 (203)
90 PRK02515 psbU photosystem II c 64.3 9.3 0.0002 36.1 4.1 33 60-92 80-112 (132)
91 PRK07956 ligA NAD-dependent DN 64.1 8.1 0.00018 45.8 4.6 49 569-629 515-563 (665)
92 PRK14672 uvrC excinuclease ABC 64.0 8 0.00017 45.8 4.4 52 565-628 608-659 (691)
93 PRK14351 ligA NAD-dependent DN 62.5 11 0.00024 44.8 5.3 62 554-629 519-580 (689)
94 COG1321 TroR Mn-dependent tran 60.5 11 0.00023 36.6 3.9 36 186-222 43-78 (154)
95 TIGR00426 competence protein C 60.4 11 0.00023 31.1 3.4 28 60-87 40-67 (69)
96 PRK07758 hypothetical protein; 58.8 9 0.00019 34.2 2.8 43 50-92 44-92 (95)
97 PRK12766 50S ribosomal protein 58.8 7.9 0.00017 39.9 2.8 29 566-594 4-33 (232)
98 TIGR00194 uvrC excinuclease AB 58.7 10 0.00023 44.1 4.2 34 562-595 538-571 (574)
99 PRK00254 ski2-like helicase; P 56.9 13 0.00029 44.3 4.7 51 566-628 646-697 (720)
100 cd00090 HTH_ARSR Arsenical Res 56.6 8.5 0.00018 30.5 2.2 38 183-221 36-75 (78)
101 PF02371 Transposase_20: Trans 55.2 6.2 0.00013 34.1 1.2 27 565-591 2-28 (87)
102 PTZ00217 flap endonuclease-1; 52.9 15 0.00032 40.9 4.0 29 569-597 239-267 (393)
103 PF00570 HRDC: HRDC domain Blo 52.8 26 0.00057 28.2 4.6 57 22-82 3-59 (68)
104 TIGR00426 competence protein C 52.6 15 0.00032 30.3 3.0 21 564-584 15-36 (69)
105 PRK03980 flap endonuclease-1; 52.1 14 0.0003 39.5 3.5 27 569-595 193-219 (292)
106 smart00279 HhH2 Helix-hairpin- 52.1 12 0.00027 27.4 2.1 18 568-585 19-36 (36)
107 TIGR00637 ModE_repress ModE mo 52.0 16 0.00034 32.7 3.3 39 183-221 32-76 (99)
108 PF01978 TrmB: Sugar-specific 51.9 6.5 0.00014 32.1 0.8 45 141-210 21-66 (68)
109 PF06969 HemN_C: HemN C-termin 51.6 7.2 0.00016 31.5 1.0 31 181-213 34-65 (66)
110 PF01367 5_3_exonuc: 5'-3' exo 51.3 0.55 1.2E-05 42.3 -6.1 34 567-600 20-53 (101)
111 COG2345 Predicted transcriptio 51.3 9 0.00019 39.2 1.8 31 184-214 42-79 (218)
112 PRK10308 3-methyl-adenine DNA 49.7 26 0.00056 37.2 5.1 47 40-86 173-226 (283)
113 PRK14165 winged helix-turn-hel 49.7 18 0.00039 37.0 3.7 38 183-220 37-76 (217)
114 PRK09834 DNA-binding transcrip 49.6 17 0.00038 37.7 3.7 39 183-221 42-80 (263)
115 smart00346 HTH_ICLR helix_turn 47.9 26 0.00056 29.7 3.9 68 126-222 8-75 (91)
116 TIGR00593 pola DNA polymerase 47.0 27 0.00059 42.9 5.3 32 569-600 189-220 (887)
117 PRK04172 pheS phenylalanyl-tRN 47.0 15 0.00033 41.8 3.1 33 186-218 39-72 (489)
118 TIGR03674 fen_arch flap struct 46.7 19 0.00041 39.2 3.5 28 569-596 240-267 (338)
119 COG0272 Lig NAD-dependent DNA 46.3 18 0.00039 42.6 3.5 51 567-629 513-563 (667)
120 PRK05755 DNA polymerase I; Pro 46.2 25 0.00055 43.1 4.9 33 567-599 189-221 (880)
121 smart00418 HTH_ARSR helix_turn 45.8 21 0.00045 27.4 2.8 36 183-218 26-64 (66)
122 KOG3344 40s ribosomal protein 45.8 8.8 0.00019 36.4 0.7 34 186-219 44-79 (150)
123 PF12836 HHH_3: Helix-hairpin- 45.8 11 0.00024 30.8 1.2 21 564-584 13-33 (65)
124 cd00128 XPG Xeroderma pigmento 45.0 23 0.00049 37.9 3.8 29 569-597 227-255 (316)
125 COG1555 ComEA DNA uptake prote 44.2 27 0.00058 33.6 3.8 29 564-592 96-130 (149)
126 KOG2379 Endonuclease MUS81 [Re 43.9 18 0.00038 41.2 2.8 46 110-155 61-114 (501)
127 TIGR00738 rrf2_super rrf2 fami 43.6 29 0.00062 31.8 3.8 66 125-215 8-74 (132)
128 cd00056 ENDO3c endonuclease II 42.0 48 0.001 31.3 5.1 44 44-87 55-103 (158)
129 PRK05638 threonine synthase; V 40.9 20 0.00043 40.2 2.8 36 183-218 402-440 (442)
130 PF04079 DUF387: Putative tran 40.8 17 0.00036 35.4 1.8 30 185-214 111-146 (159)
131 smart00550 Zalpha Z-DNA-bindin 40.7 20 0.00043 29.6 2.0 26 185-210 40-66 (68)
132 COG0632 RuvA Holliday junction 39.5 32 0.00069 34.9 3.6 54 28-83 69-124 (201)
133 TIGR01448 recD_rel helicase, p 39.1 59 0.0013 39.1 6.4 27 560-586 77-105 (720)
134 COG0258 Exo 5'-3' exonuclease 38.7 41 0.00089 35.9 4.6 28 569-596 202-229 (310)
135 PRK13913 3-methyladenine DNA g 37.9 43 0.00093 34.3 4.3 50 38-87 86-141 (218)
136 TIGR00281 segregation and cond 37.5 20 0.00044 35.8 1.9 29 186-214 117-151 (186)
137 TIGR02647 DNA conserved hypoth 37.5 41 0.00089 28.9 3.4 34 184-220 36-69 (77)
138 smart00478 ENDO3c endonuclease 33.8 24 0.00052 33.1 1.6 24 64-87 69-92 (149)
139 TIGR01083 nth endonuclease III 33.5 66 0.0014 31.9 4.8 49 39-87 76-126 (191)
140 PRK14350 ligA NAD-dependent DN 33.0 54 0.0012 39.1 4.7 67 555-629 494-561 (669)
141 PRK00558 uvrC excinuclease ABC 32.9 69 0.0015 37.7 5.5 62 13-88 503-564 (598)
142 PRK11050 manganese transport r 31.7 59 0.0013 31.1 4.0 35 186-221 70-104 (152)
143 PF02295 z-alpha: Adenosine de 31.6 35 0.00077 28.3 2.1 22 190-211 43-65 (66)
144 PRK14600 ruvA Holliday junctio 31.1 54 0.0012 32.8 3.7 50 37-88 77-132 (186)
145 PRK13347 coproporphyrinogen II 31.0 28 0.0006 39.3 1.8 39 181-221 398-436 (453)
146 KOG2875 8-oxoguanine DNA glyco 31.0 40 0.00087 35.9 2.8 23 48-83 212-234 (323)
147 PF13814 Replic_Relax: Replica 30.2 51 0.0011 32.0 3.3 58 140-219 7-73 (191)
148 PRK14601 ruvA Holliday junctio 29.7 33 0.00071 34.2 1.9 20 64-83 105-124 (183)
149 PRK14602 ruvA Holliday junctio 29.3 34 0.00073 34.6 1.9 51 37-88 78-134 (203)
150 PRK14604 ruvA Holliday junctio 29.2 34 0.00073 34.4 1.9 53 29-83 70-124 (195)
151 COG0122 AlkA 3-methyladenine D 28.6 31 0.00068 36.7 1.6 22 66-87 197-218 (285)
152 PRK14603 ruvA Holliday junctio 28.3 36 0.00077 34.3 1.9 58 29-88 69-132 (197)
153 KOG2518 5'-3' exonuclease [Rep 27.9 57 0.0012 37.5 3.5 37 559-595 211-255 (556)
154 PTZ00326 phenylalanyl-tRNA syn 27.8 41 0.00089 38.6 2.5 34 184-217 38-72 (494)
155 PLN02853 Probable phenylalanyl 27.5 42 0.00092 38.4 2.5 34 184-217 35-69 (492)
156 PRK13901 ruvA Holliday junctio 27.4 38 0.00082 34.2 1.9 57 30-88 70-132 (196)
157 PRK14605 ruvA Holliday junctio 27.2 52 0.0011 33.0 2.9 59 29-88 70-133 (194)
158 PRK05799 coproporphyrinogen II 26.8 67 0.0015 35.0 3.9 33 187-221 338-370 (374)
159 PRK14606 ruvA Holliday junctio 25.5 43 0.00093 33.5 1.9 53 29-83 70-124 (188)
160 PRK00116 ruvA Holliday junctio 25.5 1.2E+02 0.0026 30.3 5.0 50 37-88 77-129 (192)
161 PF11731 Cdd1: Pathogenicity l 25.2 37 0.00079 30.3 1.2 22 63-84 8-29 (93)
162 PRK11242 DNA-binding transcrip 25.0 57 0.0012 33.4 2.8 37 183-221 31-70 (296)
163 PF09202 Rio2_N: Rio2, N-termi 24.8 1.1E+02 0.0025 26.5 4.1 65 125-215 8-73 (82)
164 PRK10702 endonuclease III; Pro 23.8 1.1E+02 0.0023 31.2 4.4 52 31-83 69-125 (211)
165 PRK14670 uvrC excinuclease ABC 23.5 1.3E+02 0.0028 35.3 5.5 60 13-88 476-535 (574)
166 COG1414 IclR Transcriptional r 23.4 1.8E+02 0.0039 30.0 6.1 70 125-223 6-75 (246)
167 PF15516 BpuSI_N: BpuSI N-term 23.3 2.1E+02 0.0045 27.5 5.8 71 398-476 19-99 (159)
168 PF10391 DNA_pol_lambd_f: Fing 23.2 1.1E+02 0.0024 24.2 3.5 28 565-592 2-30 (52)
169 TIGR03252 uncharacterized HhH- 23.2 67 0.0014 32.0 2.7 22 67-88 115-136 (177)
170 cd04466 S1_YloQ_GTPase S1_YloQ 23.1 78 0.0017 25.4 2.7 29 413-443 37-65 (68)
171 PRK00135 scpB segregation and 22.7 56 0.0012 32.7 2.1 61 120-213 87-153 (188)
172 TIGR00084 ruvA Holliday juncti 22.5 53 0.0012 32.9 1.9 52 30-83 70-123 (191)
173 smart00341 HRDC Helicase and R 22.1 2.4E+02 0.0051 23.3 5.5 56 22-82 6-62 (81)
174 COG3743 Uncharacterized conser 22.0 51 0.0011 31.3 1.5 19 67-85 67-85 (133)
175 PRK09249 coproporphyrinogen II 21.7 74 0.0016 35.8 3.1 36 184-221 401-436 (453)
176 PF11798 IMS_HHH: IMS family H 21.7 75 0.0016 22.5 2.0 18 68-85 12-29 (32)
177 COG3451 VirB4 Type IV secretor 21.5 1.9E+02 0.0042 35.3 6.6 74 15-88 495-580 (796)
178 PRK07956 ligA NAD-dependent DN 21.4 1E+02 0.0022 36.8 4.2 47 40-88 518-564 (665)
179 PF10987 DUF2806: Protein of u 21.1 2.6E+02 0.0056 28.6 6.6 62 23-88 40-101 (219)
180 PF00126 HTH_1: Bacterial regu 21.0 63 0.0014 25.7 1.7 29 183-213 29-60 (60)
181 TIGR00194 uvrC excinuclease AB 20.9 1.8E+02 0.0039 34.1 6.0 62 13-88 501-562 (574)
182 COG1386 scpB Chromosome segreg 20.8 82 0.0018 31.5 2.8 29 187-215 123-157 (184)
183 PRK12766 50S ribosomal protein 20.5 66 0.0014 33.3 2.1 49 38-88 8-57 (232)
184 COG3453 Uncharacterized protei 20.3 95 0.0021 29.2 2.9 33 121-156 94-126 (130)
185 PRK15090 DNA-binding transcrip 20.1 1.2E+02 0.0027 31.1 4.1 40 183-222 44-83 (257)
186 PRK08898 coproporphyrinogen II 20.0 1.1E+02 0.0023 33.9 3.8 33 187-221 358-390 (394)
187 PF03832 WSK: WSK motif; Inte 20.0 40 0.00087 24.2 0.3 12 183-194 5-16 (31)
No 1
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=100.00 E-value=9.9e-72 Score=598.64 Aligned_cols=471 Identities=36% Similarity=0.472 Sum_probs=348.9
Q ss_pred ccccccccccCCCCHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchH-HHHHHHHH
Q 006771 7 MENHSKRRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGK-WILKLMQE 85 (632)
Q Consensus 7 ~~~~~~~~~~~~~N~~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~-~i~~~L~~ 85 (632)
|+|+. +.+....++ + .+.+|.....++++|...+..++|.||+++||+||.|+-+.+++++++|||+ ||++.++.
T Consensus 1 m~~~~-~~~~~s~~g-~--~~~~~~~~~~~~~~~~~~~~~~s~~ka~r~l~~~~~~l~tl~dl~~ikG~G~~~~~k~~~~ 76 (501)
T KOG2379|consen 1 MENPS-LQLTSSLRG-R--TFRRKVNRLDHKPKGESRKSEYSLKKALRNLCKAKDPLMTLPDLSSIKGFGKKWIVKLMEA 76 (501)
T ss_pred CCccc-cccccCCCC-c--hhhhhhhhhhhcccccchhhcccHHHHHHHhhcccCcccchhhcccccCccchhHHHHHhH
Confidence 66663 444445555 2 5666666667777888889999999999999999999999999999999999 88888776
Q ss_pred H---hhcCCCC-CCCchhhhhcccccccccCCCcccccCCCchHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCC
Q 006771 86 F---FETDSGG-SEPEDLTAKSKKSKAVKTKGTKRYMPQRNSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTP 161 (632)
Q Consensus 86 ~---~~~~~~~-~p~~~~~~~~~~~~~kk~r~~k~YvP~~rSGaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~ 161 (632)
| |.++... .-|. +..|+ +.....+|+|+++|-.|+.+..+++....+.. ..++.
T Consensus 77 ~~~~~~~~~e~~~~~~--n~~gk-----~~~~~ee~~~~R~s~~~~~~~~~~r~~~~~~~------------r~~l~--- 134 (501)
T KOG2379|consen 77 YSVLCVENNEQLSLPT--NRSGK-----KALDDEEYRPQRYSVEDAGVTDGHRLPTKDKA------------RSGLE--- 134 (501)
T ss_pred HHHHhhcccccccccc--ccccc-----cccccchhhhhhhhhcccccccccccCccchh------------hcccC---
Confidence 5 4444332 1111 22333 67778999999999999999888776554332 11111
Q ss_pred CCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecCCCceecChhHHHHHHHHHhhcCCCCCcc-cccCCCCCCC
Q 006771 162 IMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLSRSGFADSIE-NVVNGKDSDK 240 (632)
Q Consensus 162 ~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~~~~~~~~~~-~~~~~~~~~~ 240 (632)
|+ ... ++-|..+..++..|++.+++.|..+..|+.+....-. ..+.+ ..+..-. +
T Consensus 135 --~~------------~~~-~~~~~~~n~~~~~G~~~~~~~~~~~~~~~~~~n~~~~-------~~~~~r~q~~~~~-~- 190 (501)
T KOG2379|consen 135 --PQ------------ERT-GTHQIMANLLIREGLSKDEIAPLPRNYTDALLNSVPV-------ESPRSRMQSLVPK-G- 190 (501)
T ss_pred --cc------------ccc-cchHHHHHHhhcCccccccccccchhccchhhccCCc-------CCcHHHhhccCcc-c-
Confidence 11 011 3449999999999999999999999999999883322 11111 1111000 0
Q ss_pred cccchhhhhccCCCCCCCcccccccCccCCCCCCCCchhhhhhhhcCcchhHHhhhcccccccccccccccchhhhhhhc
Q 006771 241 NELSELDLVLAHPDSNGEVTECFVPLSRKEKSTDVPFESLERFTRMGYSKEQVLRAFGEVSETSQHKEISSLWPAVLCRL 320 (632)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~s~~~~~~~~~ 320 (632)
..... ...... . ++ | ..+++...|..
T Consensus 191 ----s~~~~-------~~~~~q-------~--~d-~---------------------------------~e~r~~~~~~~ 216 (501)
T KOG2379|consen 191 ----SHLLS-------EVSNQQ-------T--LD-P---------------------------------LEKRLLKTCRY 216 (501)
T ss_pred ----hhhhe-------eccccc-------c--cC-h---------------------------------hhcCccccccc
Confidence 00000 000000 0 00 0 00000000000
Q ss_pred chhhhhhhccccccccccccccccccccCCCCCCcccccccCCCCCcCCCCCCceeEEEEEeCcccccccCCchHHHHHH
Q 006771 321 QEDEVYALHSELHSVREDYDAASRTCISTNDDPKTRVNLLSVPPLSFGERFEDAYEVVLILDDREQFAVQGSRSRRIIEN 400 (632)
Q Consensus 321 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~pp~~~~~~~~~~y~V~LvVD~RE~~s~~~~~~r~~i~~ 400 (632)
++ .....+- .|+.++. |+|+||+++ .. .+.++.+
T Consensus 217 -----------------------------~~-----~~~~~~c--------~d~~e~~-~~d~~~iks-~~--~~l~~~~ 250 (501)
T KOG2379|consen 217 -----------------------------SN-----QPTELVC--------SDNREVF-IIDTREIKS-LL--RRLFFGE 250 (501)
T ss_pred -----------------------------cc-----cceeEEe--------cCCceee-eccCccccc-cc--hhhhhhh
Confidence 00 0000000 2456888 999999984 22 3567777
Q ss_pred HHhhCCCcEEEEeccCCCEEEEeeccCCCcceeeceeEEEechhHHHhhhccchHHHHHHHHHHcCCCceEEEEeCC--C
Q 006771 401 VCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLVRCGLKKLIYLVEGD--P 478 (632)
Q Consensus 401 ~l~~~gV~~evr~L~vGD~iWvar~k~~~~E~VLd~IVERKrldDL~~SI~DGRf~eQK~RLk~sG~~~~iYLVEg~--~ 478 (632)
.+...||+++||+|+||||||||+|+..|.|+||||||||||+|||++||+||||+|||+||++||++++||||||+ .
T Consensus 251 ~~~~~~v~~evR~L~vGD~lWVa~~k~~g~E~VLd~IVERKr~DDl~SSIrDgRf~EQK~RLq~sGik~~iYlvE~~~~~ 330 (501)
T KOG2379|consen 251 YFELEGVKHEVRSLEVGDFLWVARHKYDGTELVLDFIVERKRLDDLVSSIRDGRFKEQKNRLQRSGIKRIIYLVEEDGNP 330 (501)
T ss_pred hhhhccceeeEEEecccceEEEecccCCCceEeeeeheeecchHHHHHHHhccchHHHHHHHHhcCcceEEEEEeccCCc
Confidence 78889999999999999999999999999999999999999999999999999999999999999999999999998 5
Q ss_pred CCchhHHHHHHHHHHhhhhcCceEEEcCCHHHHHHHHHHHHHHHHHhhhhcCCc--------cccc-----cCcCCCChh
Q 006771 479 NSSEAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVELPE--------DQLK-----CAAVCPPFD 545 (632)
Q Consensus 479 ~~~~~~e~i~tAl~~tqv~~gf~V~rT~~~~eT~~~L~~lt~~i~~~y~~~~~~--------~~~~-----~~~~~~~f~ 545 (632)
+.+.+.++|++|+++|+|.+||+|+||.|+.||+++|+++|+.+.+.|.....+ ++.. +...|++|+
T Consensus 331 n~~~~~eslktA~~~t~v~~GF~V~RT~~l~et~s~l~y~tr~~~~~~~~~~~~~~d~~~~~~q~~~~~~~p~~~~~~f~ 410 (501)
T KOG2379|consen 331 NQSKPAESLKTAVTNTLVLEGFDVIRTRDLGETVSKLAYLTRGLLQIYASLLLDKEDYRERDDQLKGAMTVPSETELSFS 410 (501)
T ss_pred ccccHHHHHHHHHHHHhhhcceEEEEecChhHHHHHHHHHhHHHHHHHHHhhccccccccchhhhhcccCCCCcccccHH
Confidence 566789999999999999999999999999999999999999999998775432 1111 123457899
Q ss_pred hhhhhhcccccccchHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhc----CCcccHHH
Q 006771 546 EFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQS----NNAVSASA 621 (632)
Q Consensus 546 ~f~~~~~K~~~~Tv~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~----~~~IG~~l 621 (632)
+|++.++|++.+||+|+|++|||+|+|||.++|.||+++||||.+|+.||+.++. .+++..||..+. .+.||++|
T Consensus 411 ~F~~~~~K~~~~TV~evf~~qLMqvkg~S~erAiAI~d~YpTl~sLl~AY~~s~~-~k~~~l~ln~~~~~~~~rn~~~~L 489 (501)
T KOG2379|consen 411 AFQERLSKGKALTVGEVFARQLMQVKGMSLERAIAIADRYPTLRSLLSAYEVSAD-DKLRLLLLNPIKCGPGSRNIGPAL 489 (501)
T ss_pred HHHHHhhhcccccHHHHHHHHHHhccCccHHHHHHHHHhccCHHHHHHHHhccCc-HHHHhccccccccccccccccHHH
Confidence 9999999999999999999999999999999999999999999999999997654 566666666653 35699999
Q ss_pred Hhhhhhh
Q 006771 622 SRNIFQL 628 (632)
Q Consensus 622 Sr~Iy~~ 628 (632)
|.+||.+
T Consensus 490 s~~l~~~ 496 (501)
T KOG2379|consen 490 SAKLYEF 496 (501)
T ss_pred HHHHHHh
Confidence 9999973
No 2
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=8.3e-36 Score=301.18 Aligned_cols=207 Identities=24% Similarity=0.325 Sum_probs=174.3
Q ss_pred eeEEEEEeCcccccccCCchHHHHHHHHhhCCCcEEEEeccCCCEEEEeeccCCCcceeeceeEEEechhHHHhhhccch
Q 006771 375 YEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNR 454 (632)
Q Consensus 375 y~V~LvVD~RE~~s~~~~~~r~~i~~~l~~~gV~~evr~L~vGD~iWvar~k~~~~E~VLd~IVERKrldDL~~SI~DGR 454 (632)
..+++|||+||+++ -+...|...||++++++|+||||||++ ++|||||+++||++||+|||
T Consensus 26 ~~~~viVD~RE~rs--------~v~~~L~~~gv~v~~~~LevGDYvvs~-----------~v~VERKs~~Dfv~Si~dgR 86 (254)
T COG1948 26 FEVVVIVDSRELRS--------EVPRLLKRLGVKVEVRTLEVGDYVVSD-----------DVIVERKSISDFVSSIIDGR 86 (254)
T ss_pred cceEEEEecchhcc--------cchHHHHhCCCeEEEEecccccEEeec-----------CeeEEeccHHHHHHHHhcch
Confidence 69999999999984 244567799999999999999999998 79999999999999999999
Q ss_pred HHHHHHHHHHcCCCceEEEEeCCCC---Cc-hhHHHHHHHHHHhhhhcCceEEEcCCHHHHHHHHHHHHHHHHHhhhhcC
Q 006771 455 YRDQKLRLVRCGLKKLIYLVEGDPN---SS-EAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVEL 530 (632)
Q Consensus 455 f~eQK~RLk~sG~~~~iYLVEg~~~---~~-~~~e~i~tAl~~tqv~~gf~V~rT~~~~eT~~~L~~lt~~i~~~y~~~~ 530 (632)
|++|+.||+++|. +++++|||+.+ .. ..+++|++|++++++..||.|++|.|.++|+.+|..|++..+.. ..
T Consensus 87 lfeQ~~rL~~~y~-rpvliVegd~~~~~~~~i~~~av~~al~s~~vdfg~~vi~t~~~~~Ta~~i~~la~req~e--~~- 162 (254)
T COG1948 87 LFEQAKRLKKSYE-RPVLIVEGDDSFSRRPKIHPNAVRGALASLAVDFGLPVIWTRSPEETAELIHELARREQEE--RK- 162 (254)
T ss_pred HHHHHHHHHhcCC-ccEEEEEcccccccccccCHHHHHHHHHHHHhhcCceEEEeCCHHHHHHHHHHHHHHHHHh--cc-
Confidence 9999999999954 77788888732 22 47899999999999999999999999999999999999998752 10
Q ss_pred CccccccCcCCCChhhhhhhhcccccccchHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhh
Q 006771 531 PEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLW 610 (632)
Q Consensus 531 ~~~~~~~~~~~~~f~~f~~~~~K~~~~Tv~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~ 610 (632)
+. .. ...+.+..|+++....+|++||||+...|..++.+|+|+.++++|-. ++|.+
T Consensus 163 ---r~----v~--------~~~~~~~~t~~e~q~~il~s~pgig~~~a~~ll~~fgS~~~~~tas~---------~eL~~ 218 (254)
T COG1948 163 ---RS----VN--------PHGKKKAKTLKELQLYILESIPGIGPKLAERLLKKFGSVEDVLTASE---------EELMK 218 (254)
T ss_pred ---cc----cc--------ccccccccchHHHHHHHHHcCCCccHHHHHHHHHHhcCHHHHhhcCH---------HHHHH
Confidence 00 00 12345678999999999999999999999999999999999998753 12222
Q ss_pred hhcCCcccHHHHhhhhhhhcc
Q 006771 611 KQSNNAVSASASRNIFQLVWG 631 (632)
Q Consensus 611 ~~~~~~IG~~lSr~Iy~~vwg 631 (632)
. .-||+..++.||.++|.
T Consensus 219 v---~gig~k~A~~I~~~~~t 236 (254)
T COG1948 219 V---KGIGEKKAREIYRFLRT 236 (254)
T ss_pred h---cCccHHHHHHHHHHHhc
Confidence 2 23999999999998874
No 3
>PRK13766 Hef nuclease; Provisional
Probab=99.95 E-value=8e-27 Score=273.12 Aligned_cols=207 Identities=21% Similarity=0.269 Sum_probs=164.5
Q ss_pred CceeEEEEEeCcccccccCCchHHHHHHHHhhCCCcEEEEeccCCCEEEEeeccCCCcceeeceeEEEechhHHHhhhcc
Q 006771 373 DAYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRD 452 (632)
Q Consensus 373 ~~y~V~LvVD~RE~~s~~~~~~r~~i~~~l~~~gV~~evr~L~vGD~iWvar~k~~~~E~VLd~IVERKrldDL~~SI~D 452 (632)
+++.+.+|||+||+++ .+.+.|.+.||++++++|+||||++.. +++||||+++||++||+|
T Consensus 559 ~~~~~~i~vD~RE~~~--------~~~~~l~~~g~~~~~~~L~~gDy~~~~-----------~~~vERK~~~Dl~~s~~~ 619 (773)
T PRK13766 559 EPEGPKIIVDSRELRS--------NVARHLKRLGAEVELKTLEVGDYVVSD-----------RVAVERKTAEDFVDSIID 619 (773)
T ss_pred CCCCcEEEEeCCCccc--------hhhHHHHhCCCEEEEEecCCCCEEccC-----------CeEEEeCcHHHHHHHhhc
Confidence 4589999999999873 366688899999999999999999765 599999999999999999
Q ss_pred chHHHHHHHHHHcCCCceEEEEeCCCC--CchhHHHHHHHHHHhhhhcCceEEEcCCHHHHHHHHHHHHHHHHHhhhhcC
Q 006771 453 NRYRDQKLRLVRCGLKKLIYLVEGDPN--SSEAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVEL 530 (632)
Q Consensus 453 GRf~eQK~RLk~sG~~~~iYLVEg~~~--~~~~~e~i~tAl~~tqv~~gf~V~rT~~~~eT~~~L~~lt~~i~~~y~~~~ 530 (632)
|||++|+.||+++ +.+++|||||+.. ....++++++||+.+++.+||.|++|.|.++|+.+|..|++..+.
T Consensus 620 ~r~~~q~~~l~~~-~~~~~lliE~~~~~~~~~~~~~i~~~l~~l~~~~~~~ii~~~~~~eta~~l~~l~~~~~~------ 692 (773)
T PRK13766 620 RRLFEQVKDLKRA-YERPVLIIEGDLYTIRNIHPNAIRGALASIAVDFGIPILFTRDEEETADLLKVIAKREQE------ 692 (773)
T ss_pred CcHHHHHHHHHhc-CCCcEEEEEcCchhhcccCHHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHHHHHhhccc------
Confidence 9999999999999 6788999999731 223678999999999999999999999999999999999764321
Q ss_pred CccccccCcCCCChhhhhhhhcccccccchHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhh
Q 006771 531 PEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLW 610 (632)
Q Consensus 531 ~~~~~~~~~~~~~f~~f~~~~~K~~~~Tv~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~ 610 (632)
.++.. .. ...+.+.++..+.....|.+|||||+..|..|+++|+|+..+++|-. ++ |.
T Consensus 693 ~~~~~------~~------~~~~~~~~~~~~~~~~~L~~ipgig~~~a~~Ll~~fgs~~~i~~as~---------~~-L~ 750 (773)
T PRK13766 693 EEKRE------VS------VHGEKKAMTLKEQQEYIVESLPDVGPVLARNLLEHFGSVEAVMTASE---------EE-LM 750 (773)
T ss_pred cCCCC------cc------cccCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCH---------HH-HH
Confidence 01110 11 01122346666666667999999999999999999999999886531 12 22
Q ss_pred hhcCCcccHHHHhhhhhhh
Q 006771 611 KQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 611 ~~~~~~IG~~lSr~Iy~~v 629 (632)
.+ .+ ||+..+++|++++
T Consensus 751 ~i-~G-ig~~~a~~i~~~~ 767 (773)
T PRK13766 751 EV-EG-IGEKTAKRIREVV 767 (773)
T ss_pred hC-CC-CCHHHHHHHHHHH
Confidence 21 12 8899999998754
No 4
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=99.94 E-value=1e-25 Score=261.86 Aligned_cols=210 Identities=19% Similarity=0.191 Sum_probs=164.2
Q ss_pred ceeEEEEEeCcccccccCCchHHHHHHHHhhCCCcEEEEeccCCCEEEEeeccCCCcceeeceeEEEechhHHHhhhccc
Q 006771 374 AYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDN 453 (632)
Q Consensus 374 ~y~V~LvVD~RE~~s~~~~~~r~~i~~~l~~~gV~~evr~L~vGD~iWvar~k~~~~E~VLd~IVERKrldDL~~SI~DG 453 (632)
...+.+|||.||+++ .++.+|.+.|+.+++++|+|||||... +++||||+++||++||.||
T Consensus 584 ~~~~~IiVD~REfrS--------~lp~~L~~~G~~v~p~tL~VGDYilS~-----------~i~VERKSi~Dli~Sl~~g 644 (814)
T TIGR00596 584 LTQPKVIVDMREFRS--------SLPSLLHRRGIRVIPCMLTVGDYILTP-----------DICVERKSISDLIGSLNNG 644 (814)
T ss_pred CCCceEEEecCcccc--------hhHHHHHHCCCEEEEEecCcccEEecC-----------CeEEEeCcHHHHHHHHhcc
Confidence 356789999999973 477789999999999999999999987 7999999999999999999
Q ss_pred hHHHHHHHHHHcCCCceEEEEeCCCCCc------------hhH--HHHHHHHHHhhhhc-CceEEEcCCHHHHHHHHHHH
Q 006771 454 RYRDQKLRLVRCGLKKLIYLVEGDPNSS------------EAA--ESIKTACFTTEILE-GFDVQRTSGLADTLRKYGYI 518 (632)
Q Consensus 454 Rf~eQK~RLk~sG~~~~iYLVEg~~~~~------------~~~--e~i~tAl~~tqv~~-gf~V~rT~~~~eT~~~L~~l 518 (632)
|+++|+.+|.++ |+++++||||+.+.. ..+ .+|+++++.+.+.. |+.|+||.++.+|+.+|..|
T Consensus 645 RL~~Q~~~m~~~-Y~~PvLLIE~d~~~~f~l~~~~~~~~~~~~~~~~i~~~L~~L~l~fP~l~IiwS~s~~~TA~i~~~L 723 (814)
T TIGR00596 645 RLYNQCEKMLRY-YAYPVLLIEFDQNKSFSLEPRNDLSQEISSVNNDIQQKLALLTLHFPKLRIIWSSSPYATAEIFEEL 723 (814)
T ss_pred hHHHHHHHHHHh-cCCcEEEEEecCCcccccccccccccccCccHHHHHHHHHHHHHhcCCceEEecCCHHHHHHHHHHH
Confidence 999999999999 999999999985321 134 79999999988887 99999999999999999999
Q ss_pred HHHHHHhhhhcCCccccccCcCCCChhhhhhhhcccccccchHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhc
Q 006771 519 TQAITEYYKVELPEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSIL 598 (632)
Q Consensus 519 t~~i~~~y~~~~~~~~~~~~~~~~~f~~f~~~~~K~~~~Tv~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~ 598 (632)
++..++ ++... .+....=.....| ...+ ....+.+|.+|||||+..|..|+.+|+|+++|++|-.
T Consensus 724 k~~e~e-------pd~~~----~v~i~~~~~~~~k-~~~~-~~~~q~~L~~lPgI~~~~a~~ll~~f~si~~l~~as~-- 788 (814)
T TIGR00596 724 KLGKEE-------PDPAT----AAALGSDENTTAE-GLKF-NDGPQDFLLKLPGVTKKNYRNLRKKVKSIRELAKLSQ-- 788 (814)
T ss_pred HhcCCC-------CCccc----ceecCcccccccc-cccc-cHHHHHHHHHCCCCCHHHHHHHHHHcCCHHHHHhCCH--
Confidence 876321 11111 1111000000111 1223 3344566889999999999999999999999997652
Q ss_pred cccHHHHHHHhhhhcCCccc-HHHHhhhhhhhc
Q 006771 599 EGDVCAQEEMLWKQSNNAVS-ASASRNIFQLVW 630 (632)
Q Consensus 599 ~~~~~~~e~mL~~~~~~~IG-~~lSr~Iy~~vw 630 (632)
++|.. .|| +..+++||+|+-
T Consensus 789 -------eeL~~-----~iG~~~~A~~i~~fl~ 809 (814)
T TIGR00596 789 -------NELNE-----LIGDEEAAKRLYDFLR 809 (814)
T ss_pred -------HHHHH-----HhCCHHHHHHHHHHhc
Confidence 23333 288 999999999764
No 5
>PF02732 ERCC4: ERCC4 domain; InterPro: IPR006166 This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases (3.1.22 from EC) [], and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006259 DNA metabolic process; PDB: 2BHN_D 2BGW_B 1J22_A 1J25_A 1J24_A 1J23_A 2ZIU_A 2ZIW_A 2ZIV_A 2ZIX_A ....
Probab=99.91 E-value=1.1e-23 Score=195.74 Aligned_cols=133 Identities=32% Similarity=0.448 Sum_probs=111.0
Q ss_pred EeCcccccccCCchHHHHHHHHhhCCCcEEEEeccCCCEEEEeeccCCCcceeeceeEEEechhHHHhhhccchHHHHHH
Q 006771 381 LDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKL 460 (632)
Q Consensus 381 VD~RE~~s~~~~~~r~~i~~~l~~~gV~~evr~L~vGD~iWvar~k~~~~E~VLd~IVERKrldDL~~SI~DGRf~eQK~ 460 (632)
||+||.+++ .++.+...|...||++++++||+|||+|.. ......|.++++|||||+++||++||+||||.+|+.
T Consensus 1 VD~re~~~~----~~~~l~~~l~~~gv~~~~~~l~~gd~~~~~-~~~~~~e~~~~~iverk~~~dl~~si~~~rl~~q~~ 75 (143)
T PF02732_consen 1 VDSRELRSS----GGEQLLEALRELGVKVEVRQLPVGDYIWWR-INQISEETMVPVIVERKTLDDLVASIKDGRLEEQVQ 75 (143)
T ss_dssp EEGGGCTSS----CHHHHHHHHHCTTSEEEEE--SSSSEEEEE-S----BESSECEEEEEEEHHHHHHHHHTTHHHHHHH
T ss_pred CCchHhCcc----cHHHHHHHHHHCCCEEEEEECCCCCEEEEC-CCCCccccceEEEEEhhHHHHHHhhhcCCchHHHHH
Confidence 899998732 256788899999999999999999999965 334456666799999999999999999999999999
Q ss_pred HHHH-cCCCceEEEEeCCCCCc---------hhHHHHHHHHHHhhhhcCceEEEcCCHHHHHHHHHHH
Q 006771 461 RLVR-CGLKKLIYLVEGDPNSS---------EAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYI 518 (632)
Q Consensus 461 RLk~-sG~~~~iYLVEg~~~~~---------~~~e~i~tAl~~tqv~~gf~V~rT~~~~eT~~~L~~l 518 (632)
||++ +|+++++|||||..... ..+++|.+|+..+|+..||.|++|.+..||++||+.|
T Consensus 76 rl~~~~~~~~~~~lVEg~~~~~~~~~~~~~~~~~~~i~~~L~~lq~~~~~~v~~~~~~~et~~~l~~f 143 (143)
T PF02732_consen 76 RLKRASPFKRVILLVEGLDSYLRKNKNYRRQQSPSAIEEALVELQLRYGISVIFTESWEETADWLASF 143 (143)
T ss_dssp HHHCCHCSSEEEEEEESCSSTCCC-----HSSTHHHHHHHHHHHHHCSS-EEEEESSHHHHHHHHHHH
T ss_pred HHhhcCCCCeEEEEEEccCccccccchhcccCCHHHHHHHHHHHHHHcCeEEEEECCHHHHHHHhhhC
Confidence 9997 78999999999975422 2357999999999999999999999999999999865
No 6
>KOG0442 consensus Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair]
Probab=99.78 E-value=2.5e-18 Score=194.63 Aligned_cols=209 Identities=20% Similarity=0.211 Sum_probs=151.8
Q ss_pred CceeEEEEEeCcccccccCCchHHHHHHHHhhCCCcEEEEeccCCCEEEEeeccCCCcceeeceeEEEechhHHHhhhcc
Q 006771 373 DAYEVVLILDDREQFAVQGSRSRRIIENVCSQFKIQMEVRRLPVGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRD 452 (632)
Q Consensus 373 ~~y~V~LvVD~RE~~s~~~~~~r~~i~~~l~~~gV~~evr~L~vGD~iWvar~k~~~~E~VLd~IVERKrldDL~~SI~D 452 (632)
.+-+..+|||.||+++ -++.+|+++|+++++.+|+|||||... ++|||||+++||++|+..
T Consensus 649 ~t~e~pVIVDmREf~S--------sLP~~Lh~~G~~Vip~tL~vGDYIlSP-----------~icVERKSIsDLi~SLns 709 (892)
T KOG0442|consen 649 ATKETPVIVDMREFRS--------SLPSLLHRKGLRVIPCTLEVGDYILSP-----------DICVERKSISDLIQSLNS 709 (892)
T ss_pred cccccceEeehHHHHh--------hchHHHHhCCceEEEEeecccCEEccc-----------cceeeeccHHHHHHhhhc
Confidence 3445669999999984 478899999999999999999999998 899999999999999999
Q ss_pred chHHHHHHHHHHcCCCceEEEEeCCCCCc-------h-----hHHHHHHHHHHhhhhc--CceEEEcCCHHHHHHHHHHH
Q 006771 453 NRYRDQKLRLVRCGLKKLIYLVEGDPNSS-------E-----AAESIKTACFTTEILE--GFDVQRTSGLADTLRKYGYI 518 (632)
Q Consensus 453 GRf~eQK~RLk~sG~~~~iYLVEg~~~~~-------~-----~~e~i~tAl~~tqv~~--gf~V~rT~~~~eT~~~L~~l 518 (632)
|||+.|+..|.+. |..+++|||.+.+.. . ....|.+-+. +.+.. .+.++|+.++..|++++..|
T Consensus 710 gRly~Q~~~M~~~-Y~~pvLLIEfd~~k~fs~~~~~~ls~e~sk~~i~skL~-lLil~fP~LRilWS~Sp~~Ta~if~eL 787 (892)
T KOG0442|consen 710 GRLYNQCEMMQRY-YERPVLLIEFDQEKSFSLQPRSDLSQELSKNDIVSKLT-LLILAFPKLRILWSSSPLATAEIFEEL 787 (892)
T ss_pred chHHHHHHHHHHh-ccCcEEEEEecCCCCcCCCCccchhhhhhHHHHHHHHH-HHHhcCCceEEEecCchhHHHHHHHHH
Confidence 9999999999999 999999999885421 1 2234555544 45544 49999999999999998777
Q ss_pred HHHHHHhhhhcCCccccccCcCCCChhhhhhhhcccccccchHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhc
Q 006771 519 TQAITEYYKVELPEDQLKCAAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSIL 598 (632)
Q Consensus 519 t~~i~~~y~~~~~~~~~~~~~~~~~f~~f~~~~~K~~~~Tv~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~ 598 (632)
...- ..+|........ +=++++. ...+.+..-...|+.+|||+...+..+..+|.++..|..-..
T Consensus 788 Kl~~-------~epD~~~Ai~lg-~~~~~~~-----~~~~~n~~~~~fll~lPgVs~~n~~~l~~k~ks~~~La~sS~-- 852 (892)
T KOG0442|consen 788 KLSE-------PEPDPARAISLG-TDEEGNS-----ESESYNSSALDFLLSLPGVSYINYRNLRHKFKSLKELANSSQ-- 852 (892)
T ss_pred hhcC-------CCCCcchheeec-ccccccc-----cccccCchHHHHHhcCCCccHHHHHHHHHHhhHHHHHHhCcH--
Confidence 5431 112211110000 1001111 123445555677999999999999999999999988874321
Q ss_pred cccHHHHHHHhhhhcCCccc-HHHHhhhhhhh
Q 006771 599 EGDVCAQEEMLWKQSNNAVS-ASASRNIFQLV 629 (632)
Q Consensus 599 ~~~~~~~e~mL~~~~~~~IG-~~lSr~Iy~~v 629 (632)
++ |+. ++| ...++.||+||
T Consensus 853 -------~e-l~e----l~~~~~~a~~LYdFi 872 (892)
T KOG0442|consen 853 -------EE-LSE----LLGVHENAKLLYDFI 872 (892)
T ss_pred -------HH-HHH----HhcchHHHHHHHHHH
Confidence 11 111 133 57888999876
No 7
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=98.16 E-value=5.4e-06 Score=68.89 Aligned_cols=67 Identities=24% Similarity=0.258 Sum_probs=55.4
Q ss_pred CHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhh-hhccccchHHHHHHHHHHhh
Q 006771 20 NEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKD-LSQVKGVGKWILKLMQEFFE 88 (632)
Q Consensus 20 N~~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~-l~~lkG~G~~i~~~L~~~~~ 88 (632)
|..+..-|.+..+...-. |-..--..+|++|..+|+++|.|+.+.+| ++.|+|||++|+..++++++
T Consensus 1 N~~i~~~L~~la~~~~~~--~~~~~r~~aY~~Aa~~i~~l~~~i~~~~~~~~~l~gIG~~ia~kI~E~le 68 (68)
T PF14716_consen 1 NQEIADALEELADLYELQ--GGDPFRARAYRRAAAAIKALPYPITSGEEDLKKLPGIGKSIAKKIDEILE 68 (68)
T ss_dssp THHHHHHHHHHHHHHHHT--STSHHHHHHHHHHHHHHHHSSS-HHSHHHHHCTSTTTTHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHh--hCCcHHHHHHHHHHHHHHhCCHhHhhHHHHHhhCCCCCHHHHHHHHHHHC
Confidence 778888888876665554 22346678999999999999999999998 99999999999999998863
No 8
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=97.18 E-value=0.001 Score=69.99 Aligned_cols=73 Identities=21% Similarity=0.233 Sum_probs=57.6
Q ss_pred CCCCHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHhhcCCC
Q 006771 17 CAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFETDSG 92 (632)
Q Consensus 17 ~~~N~~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~~~~~ 92 (632)
-+-|..+-.-+ |-+-++.+- .|- +--+.+|.+|...|++||.||.+.+||..|+|||++|++.+++++..+-+
T Consensus 9 t~~N~~~~~al-eiLa~~~ev-~g~-~~r~~~y~~Aasvlk~~p~~I~S~~ea~~lP~iG~kia~ki~EiletG~l 81 (353)
T KOG2534|consen 9 TNNNQIFTEAL-EILAEAYEV-EGE-EDRARAYRRAASVLKSLPFPITSGEEAEKLPGIGPKIAEKIQEILETGVL 81 (353)
T ss_pred ccccHHHHHHH-HHHHHhhcc-ccc-HHHHHHHHHHHHHHHhCCCCcccHHHhcCCCCCCHHHHHHHHHHHHcCCc
Confidence 45566555443 445666662 132 35578999999999999999999999999999999999999999987755
No 9
>KOG2841 consensus Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair]
Probab=97.00 E-value=0.0064 Score=61.80 Aligned_cols=133 Identities=14% Similarity=0.128 Sum_probs=83.8
Q ss_pred HHHHHcC--CCceEEEEeCCCCCchhHHHHHHHHHHhhhhcCceEEEcCCHHHHHHHHHHHHHHHHHhhhhcCCcccccc
Q 006771 460 LRLVRCG--LKKLIYLVEGDPNSSEAAESIKTACFTTEILEGFDVQRTSGLADTLRKYGYITQAITEYYKVELPEDQLKC 537 (632)
Q Consensus 460 ~RLk~sG--~~~~iYLVEg~~~~~~~~e~i~tAl~~tqv~~gf~V~rT~~~~eT~~~L~~lt~~i~~~y~~~~~~~~~~~ 537 (632)
.|++.-| +++.|+|+-=+... ....+ .-++.+..+++|.+.-.-+++|.++||-.+. .|+++..+ -
T Consensus 113 ~Ri~~l~k~yk~~VLl~~vd~~e--~~~~l-~el~k~~~l~~~Tl~lA~s~EeaaryIE~~k-----~~ek~p~d-l--- 180 (254)
T KOG2841|consen 113 RRIRKLGKNYKLRVLLVHVDMEE--PYKPL-LELTKTCDLNDVTLVLAWSMEEAARYIETYK-----EYEKKPID-L--- 180 (254)
T ss_pred HHHHHhcccccceEEEEEecCcc--hHHHH-HHHHHHHHhhceeeeeeccHHHHHHHHHHHH-----HhhcCCch-h---
Confidence 4555443 66777766544322 11222 2345566788999999999999999985443 23332110 0
Q ss_pred CcCCCChhhhhhhhcccccccchHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcc
Q 006771 538 AAVCPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAV 617 (632)
Q Consensus 538 ~~~~~~f~~f~~~~~K~~~~Tv~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~I 617 (632)
...+. ....-.--+..|.+||||+--.|..|+.+|||+.+|+.|.+. +|-.-+ + +
T Consensus 181 ------------i~~~~-~~d~ls~~~~~Lt~i~~VnKtda~~LL~~FgsLq~~~~AS~~---------ele~~~--G-~ 235 (254)
T KOG2841|consen 181 ------------IMERK-DRDLLSSLLGFLTTIPGVNKTDAQLLLQKFGSLQQISNASEG---------ELEQCP--G-L 235 (254)
T ss_pred ------------hhhcc-cccHHHHHHHHHHhCCCCCcccHHHHHHhcccHHHHHhcCHh---------HHHhCc--C-c
Confidence 00000 011111346689999999999999999999999999988642 222221 2 8
Q ss_pred cHHHHhhhhhhh
Q 006771 618 SASASRNIFQLV 629 (632)
Q Consensus 618 G~~lSr~Iy~~v 629 (632)
|+.-+++||+++
T Consensus 236 G~~kak~l~~~l 247 (254)
T KOG2841|consen 236 GPAKAKRLHKFL 247 (254)
T ss_pred CHHHHHHHHHHH
Confidence 999999999865
No 10
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=96.61 E-value=0.0056 Score=66.11 Aligned_cols=73 Identities=22% Similarity=0.228 Sum_probs=58.7
Q ss_pred CCCHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHhhcCCC
Q 006771 18 AENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFETDSG 92 (632)
Q Consensus 18 ~~N~~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~~~~~ 92 (632)
|.|.++...|.+-.+-+.-. |-...-...|.+|.++|++.|.|+.++++++.|+|||++|++.+++++.++..
T Consensus 1 ~~N~~I~~~L~~la~l~el~--gen~~k~~ay~~Aa~~i~~l~~~i~~~~~l~~lpgIG~~ia~kI~Eil~tG~~ 73 (334)
T smart00483 1 NLNRGIIDALEILAENYEVF--GENKRKCSYFRKAASVLKSLPFPINSMKDLKGLPGIGDKIKKKIEEIIETGKS 73 (334)
T ss_pred CCcHHHHHHHHHHHHHHHHh--cccHHHHHHHHHHHHHHHhCCCCCCCHHHHhcCCCccHHHHHHHHHHHHhCcH
Confidence 45888888888865544422 32223356899999999999999999999999999999999999999887654
No 11
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=95.79 E-value=0.0088 Score=49.16 Aligned_cols=51 Identities=20% Similarity=0.313 Sum_probs=35.3
Q ss_pred HhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhh
Q 006771 567 LMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 567 Lm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~v 629 (632)
-+.||||+...|..|.++|+|+..|.+|.. ++|..- .-||+.+++.|+.+|
T Consensus 5 aLGI~~VG~~~ak~L~~~f~sl~~l~~a~~---------e~L~~i---~gIG~~~A~si~~ff 55 (64)
T PF12826_consen 5 ALGIPGVGEKTAKLLAKHFGSLEALMNASV---------EELSAI---PGIGPKIAQSIYEFF 55 (64)
T ss_dssp HCTSTT--HHHHHHHHHCCSCHHHHCC--H---------HHHCTS---TT--HHHHHHHHHHH
T ss_pred eCCCCCccHHHHHHHHHHcCCHHHHHHcCH---------HHHhcc---CCcCHHHHHHHHHHH
Confidence 358999999999999999999999987732 233222 239999999999854
No 12
>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=95.44 E-value=0.027 Score=60.11 Aligned_cols=47 Identities=26% Similarity=0.377 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHhhcCCC
Q 006771 46 DMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFETDSG 92 (632)
Q Consensus 46 ~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~~~~~ 92 (632)
..+|++|.++|++.|.|+.+..++..|+|||++|++.++++..++..
T Consensus 24 ~~aY~~Aa~~l~~l~~~i~~~~~~~~ipgiG~~ia~kI~E~~~tG~~ 70 (307)
T cd00141 24 VRAYRKAARALESLPEPIESLEEAKKLPGIGKKIAEKIEEILETGKL 70 (307)
T ss_pred HHHHHHHHHHHHhCCcccCCHHHhcCCCCccHHHHHHHHHHHHcCCH
Confidence 56999999999999999999999999999999999999999887543
No 13
>PRK08609 hypothetical protein; Provisional
Probab=93.93 E-value=0.12 Score=59.94 Aligned_cols=71 Identities=20% Similarity=0.277 Sum_probs=55.4
Q ss_pred CHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHhhcCCC
Q 006771 20 NEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFETDSG 92 (632)
Q Consensus 20 N~~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~~~~~ 92 (632)
|.++...|.+-.+ +.|. +|-..--..+|++|.++|++.|.|+.+..++..|+|||+.|++.+++++.++.+
T Consensus 3 n~~ia~~l~~~A~-~le~-~g~n~fr~~aYr~Aa~~i~~l~~~i~~~~~l~~ipgIG~~ia~kI~Eil~tG~~ 73 (570)
T PRK08609 3 KKDVIKLLETIAT-YMEL-KGENPFKISAFRKAAQALELDERSLSEIDDFTKLKGIGKGTAEVIQEYRETGES 73 (570)
T ss_pred hHHHHHHHHHHHH-HHHh-cCCCcHHHHHHHHHHHHHHhCchhhhhhhhhccCCCcCHHHHHHHHHHHHhCCh
Confidence 6677777777544 3331 132112356899999999999999999999999999999999999999887654
No 14
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=92.55 E-value=0.3 Score=48.81 Aligned_cols=37 Identities=19% Similarity=0.300 Sum_probs=31.7
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhc
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSIL 598 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~ 598 (632)
+++|. +|+.|+||++.+|.+|+..| ++.+|++|-.+-
T Consensus 68 r~lF~-~L~~V~GIGpK~Al~iL~~~-~~~el~~aI~~~ 104 (191)
T TIGR00084 68 RELFK-ELIKVNGVGPKLALAILSNM-SPEEFVYAIETE 104 (191)
T ss_pred HHHHH-HHhCCCCCCHHHHHHHHhcC-CHHHHHHHHHhC
Confidence 66776 77899999999999999987 699999988753
No 15
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.41 E-value=0.29 Score=49.11 Aligned_cols=58 Identities=21% Similarity=0.270 Sum_probs=43.5
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQ 627 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~ 627 (632)
+++|. +|..|.|||+..|.+|++.+ +|.+|++|-.+-+. ..|..+ .+ ||+..++||.-
T Consensus 68 r~lF~-~LisVsGIGPK~ALaILs~~-~~~el~~aI~~~D~------~~L~~v-pG-IGkKtAeRIIl 125 (196)
T PRK13901 68 REVFE-ELIGVDGIGPRAALRVLSGI-KYNEFRDAIDREDI------ELISKV-KG-IGNKMAGKIFL 125 (196)
T ss_pred HHHHH-HHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCH------HHHhhC-CC-CCHHHHHHHHH
Confidence 56665 78899999999999999998 89999999865432 334432 23 78888887763
No 16
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.21 E-value=0.34 Score=48.93 Aligned_cols=57 Identities=16% Similarity=0.285 Sum_probs=41.3
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIF 626 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy 626 (632)
+++|. +|..|+||++..|.+|++.+ +|.+|++|-.+-+. ..|..+ .+ ||+-.++||.
T Consensus 70 r~lF~-~Li~V~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~------~~L~~i-pG-IGkKtAerIi 126 (203)
T PRK14602 70 RQTFI-VLISISKVGAKTALAILSQF-RPDDLRRLVAEEDV------AALTRV-SG-IGKKTAQHIF 126 (203)
T ss_pred HHHHH-HHhCCCCcCHHHHHHHHhhC-CHHHHHHHHHhCCH------HHHhcC-CC-cCHHHHHHHH
Confidence 56665 88999999999999999997 78899998765432 223331 22 6666666664
No 17
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.08 E-value=0.38 Score=48.18 Aligned_cols=56 Identities=18% Similarity=0.256 Sum_probs=39.6
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNI 625 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~I 625 (632)
+++|. +|..|+||++..|.+|++.|+ |..|++|-..-+. ..|..+ .+ ||+..++||
T Consensus 69 r~lF~-~Li~V~GIGpK~Al~ILs~~~-~~~l~~aI~~~D~------~~L~~v-pG-IGkKtAerI 124 (194)
T PRK14605 69 LSLFE-TLIDVSGIGPKLGLAMLSAMN-AEALASAIISGNA------ELLSTI-PG-IGKKTASRI 124 (194)
T ss_pred HHHHH-HHhCCCCCCHHHHHHHHHhCC-HHHHHHHHHhCCH------HHHHhC-CC-CCHHHHHHH
Confidence 56665 889999999999999999995 8899988754322 223321 12 666666664
No 18
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.98 E-value=0.35 Score=48.09 Aligned_cols=58 Identities=19% Similarity=0.288 Sum_probs=43.9
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQ 627 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~ 627 (632)
+++|. +|..|.||++..|.+|++.+ +|.+|+.|-.+-+. ..|..+ .+ ||+..++||.-
T Consensus 69 r~lF~-~Li~VsGIGpK~Al~ILs~~-~~~el~~aI~~~D~------~~L~~v-pG-IGkKtAeRIil 126 (183)
T PRK14601 69 QKMFE-MLLKVNGIGANTAMAVCSSL-DVNSFYKALSLGDE------SVLKKV-PG-IGPKSAKRIIA 126 (183)
T ss_pred HHHHH-HHhccCCccHHHHHHHHcCC-CHHHHHHHHHhCCH------HHHhhC-CC-CCHHHHHHHHH
Confidence 56665 78899999999999999997 89999999876433 334431 23 88888888763
No 19
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.78 E-value=0.36 Score=48.48 Aligned_cols=57 Identities=21% Similarity=0.246 Sum_probs=41.2
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIF 626 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy 626 (632)
+++|. +|..|.||++..|.+|++.+ +|..|++|-.+-+. ..|..+ .. ||+-.++||.
T Consensus 68 r~lF~-~L~~V~GIGpK~AL~iLs~~-~~~~l~~aI~~~D~------~~L~kv-pG-IGkKtAerIi 124 (197)
T PRK14603 68 LELFE-LLLGVSGVGPKLALALLSAL-PPALLARALLEGDA------RLLTSA-SG-VGKKLAERIA 124 (197)
T ss_pred HHHHH-HHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCH------HHHhhC-CC-CCHHHHHHHH
Confidence 56665 78899999999999999987 89999999765432 223331 22 6666666665
No 20
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.78 E-value=0.35 Score=48.55 Aligned_cols=58 Identities=19% Similarity=0.137 Sum_probs=42.5
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQ 627 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~ 627 (632)
+++|. +|..|.||++..|.+|++.+ +|.+|+.|-.+-+. ..|..+ .. ||+..++||.-
T Consensus 69 r~lF~-~Li~V~GIGpK~Al~iLs~~-~~~el~~aI~~~D~------~~L~kv-pG-IGkKtAerIil 126 (195)
T PRK14604 69 RQLFE-LLIGVSGVGPKAALNLLSSG-TPDELQLAIAGGDV------ARLARV-PG-IGKKTAERIVL 126 (195)
T ss_pred HHHHH-HHhCcCCcCHHHHHHHHcCC-CHHHHHHHHHhCCH------HHHhhC-CC-CCHHHHHHHHH
Confidence 56665 88899999999999999986 89999999866432 233331 23 77777777653
No 21
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.55 E-value=0.32 Score=48.42 Aligned_cols=57 Identities=23% Similarity=0.239 Sum_probs=45.0
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQ 627 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~ 627 (632)
+++|. +|..|.||++..|.+|++.+ +|.+|++|-.+-+. ..| . -.+ ||+..++||.-
T Consensus 69 r~lF~-~LisV~GIGpK~Al~iLs~~-~~~~l~~aI~~~D~------~~L-~-vpG-IGkKtAerIil 125 (186)
T PRK14600 69 QDCLR-MLVKVSGVNYKTAMSILSKL-TPEQLFSAIVNEDK------AAL-K-VNG-IGEKLINRIIT 125 (186)
T ss_pred HHHHH-HHhCcCCcCHHHHHHHHccC-CHHHHHHHHHcCCH------hhe-E-CCC-CcHHHHHHHHH
Confidence 56665 78899999999999999997 89999999876432 334 3 234 88888888874
No 22
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.49 E-value=0.42 Score=47.72 Aligned_cols=57 Identities=18% Similarity=0.224 Sum_probs=42.9
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIF 626 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy 626 (632)
+++|. +|..|.||++..|.+|++.+ +|.+|++|-.+-+. ..|..+ .+ ||+..++||.
T Consensus 69 r~lF~-~Li~V~GIGpK~AL~iLs~~-~~~el~~aI~~~D~------~~L~~v-pG-IGkKtAerIi 125 (188)
T PRK14606 69 KELFL-SLTKVSRLGPKTALKIISNE-DAETLVTMIASQDV------EGLSKL-PG-ISKKTAERIV 125 (188)
T ss_pred HHHHH-HHhccCCccHHHHHHHHcCC-CHHHHHHHHHhCCH------HHHhhC-CC-CCHHHHHHHH
Confidence 56665 78899999999999999997 88999999876533 334432 23 7777777775
No 23
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=91.40 E-value=0.087 Score=54.68 Aligned_cols=57 Identities=21% Similarity=0.095 Sum_probs=46.7
Q ss_pred CCChhhhhhhhcccccccchHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccc
Q 006771 541 CPPFDEFLKRCQDLDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEG 600 (632)
Q Consensus 541 ~~~f~~f~~~~~K~~~~Tv~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~ 600 (632)
+..+..|....++.+.+|+.+ ..||.+.|||+++|.+|.+.|+|+..+.++|+.+..
T Consensus 193 ~~a~~ll~~fgS~~~~~tas~---~eL~~v~gig~k~A~~I~~~~~t~~~~~~~~~~~~~ 249 (254)
T COG1948 193 KLAERLLKKFGSVEDVLTASE---EELMKVKGIGEKKAREIYRFLRTEYKLIEALETDSS 249 (254)
T ss_pred HHHHHHHHHhcCHHHHhhcCH---HHHHHhcCccHHHHHHHHHHHhchhhhhcccCCccc
Confidence 344555555556666777777 799999999999999999999999999999987754
No 24
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=91.12 E-value=1.1 Score=39.91 Aligned_cols=74 Identities=18% Similarity=0.182 Sum_probs=46.7
Q ss_pred HHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeee----
Q 006771 125 AYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKS---- 200 (632)
Q Consensus 125 aYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~---- 200 (632)
.|+||..|... .++=-||++.-+.+...-..+. +. |--.-++.|.++|||...
T Consensus 6 ~~~iL~~L~~~------~~~GYei~~~l~~~~~~~~~i~--------------~g---tlY~~L~rLe~~GlI~~~~~~~ 62 (100)
T TIGR03433 6 DLLILKTLSLG------PLHGYGIAQRIQQISEDVLQVE--------------EG---SLYPALHRLERRGWIAAEWGES 62 (100)
T ss_pred HHHHHHHHhcC------CCCHHHHHHHHHHHcCCccccC--------------CC---cHHHHHHHHHHCCCeEEEeeec
Confidence 57777777532 2455566666555422112221 11 334568899999999862
Q ss_pred --cCCC-ceecChhHHHHHHHHHh
Q 006771 201 --SCPA-KYMLTPGGREAARECLS 221 (632)
Q Consensus 201 --grP~-rY~LTdeG~elA~~l~~ 221 (632)
++|. .|.|||.|+++-..+..
T Consensus 63 ~~~~~rk~y~iT~~Gr~~l~~~~~ 86 (100)
T TIGR03433 63 ENNRRAKFYRLTAAGRKQLAAETE 86 (100)
T ss_pred CCCCCceEEEECHHHHHHHHHHHH
Confidence 4444 49999999999887664
No 25
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=91.06 E-value=0.57 Score=37.72 Aligned_cols=51 Identities=22% Similarity=0.283 Sum_probs=39.9
Q ss_pred HHHhcCCCCCHHHHHHHHHh-cCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhh
Q 006771 565 VQLMQVPQVTEEIAITVLDL-YPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQ 627 (632)
Q Consensus 565 ~mLm~IpGVs~ekA~~I~~~-ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~ 627 (632)
.-|+.||||++..|..|.+. |.|+.+|.+|- .+++..- .+ ||+..+++|..
T Consensus 5 ~~L~~I~Gig~~~a~~L~~~G~~t~~~l~~a~---------~~~L~~i--~G-ig~~~a~~i~~ 56 (60)
T PF14520_consen 5 DDLLSIPGIGPKRAEKLYEAGIKTLEDLANAD---------PEELAEI--PG-IGEKTAEKIIE 56 (60)
T ss_dssp HHHHTSTTCHHHHHHHHHHTTCSSHHHHHTSH---------HHHHHTS--TT-SSHHHHHHHHH
T ss_pred HhhccCCCCCHHHHHHHHhcCCCcHHHHHcCC---------HHHHhcC--CC-CCHHHHHHHHH
Confidence 36889999999999999999 99999998642 2233332 23 89999999875
No 26
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=90.99 E-value=0.64 Score=42.16 Aligned_cols=70 Identities=19% Similarity=0.146 Sum_probs=50.7
Q ss_pred CchHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeec
Q 006771 122 NSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSS 201 (632)
Q Consensus 122 rSGaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~g 201 (632)
...-|.||..|+.. .+++-.||-+. .+.+ + -+.+.-++.|.++|||.+.-
T Consensus 27 t~~q~~iL~~l~~~-----~~~t~~ela~~---~~~~-----~-----------------~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 27 TEQQWRILRILAEQ-----GSMEFTQLANQ---ACIL-----R-----------------PSLTGILARLERDGLVTRLK 76 (118)
T ss_pred CHHHHHHHHHHHHc-----CCcCHHHHHHH---hCCC-----c-----------------hhHHHHHHHHHHCCCEEecc
Confidence 44568899888753 35776666653 2211 1 15678899999999999876
Q ss_pred CC-----CceecChhHHHHHHHHHh
Q 006771 202 CP-----AKYMLTPGGREAARECLS 221 (632)
Q Consensus 202 rP-----~rY~LTdeG~elA~~l~~ 221 (632)
.| ..|.||++|.++...+..
T Consensus 77 ~~~D~R~~~v~LT~~G~~~~~~~~~ 101 (118)
T TIGR02337 77 ASNDQRRVYISLTPKGQALYASLSP 101 (118)
T ss_pred CCCCCCeeEEEECHhHHHHHHHhhH
Confidence 54 359999999999988764
No 27
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=89.35 E-value=0.22 Score=40.28 Aligned_cols=59 Identities=32% Similarity=0.429 Sum_probs=38.6
Q ss_pred HHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecCC-
Q 006771 125 AYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCP- 203 (632)
Q Consensus 125 aYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~grP- 203 (632)
-|.+|..|+ ...+.++-.+|.+.-. +.. =+.=..|+.|+.+|||.+...|
T Consensus 5 q~~vL~~l~----~~~~~~t~~~l~~~~~--------~~~-----------------~~vs~~i~~L~~~glv~~~~~~~ 55 (68)
T PF13463_consen 5 QWQVLRALA----HSDGPMTQSDLAERLG--------ISK-----------------STVSRIIKKLEEKGLVEKERDPH 55 (68)
T ss_dssp HHHHHHHHT------TS-BEHHHHHHHTT----------H-----------------HHHHHHHHHHHHTTSEEEEEESS
T ss_pred HHHHHHHHH----ccCCCcCHHHHHHHHC--------cCH-----------------HHHHHHHHHHHHCCCEEecCCCC
Confidence 367788886 2246788888887421 110 1233567999999999877666
Q ss_pred ----CceecChhH
Q 006771 204 ----AKYMLTPGG 212 (632)
Q Consensus 204 ----~rY~LTdeG 212 (632)
..|.|||+|
T Consensus 56 d~R~~~~~LT~~G 68 (68)
T PF13463_consen 56 DKRSKRYRLTPAG 68 (68)
T ss_dssp CTTSEEEEE-HHH
T ss_pred cCCeeEEEeCCCC
Confidence 469999998
No 28
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=89.22 E-value=0.25 Score=41.93 Aligned_cols=39 Identities=33% Similarity=0.355 Sum_probs=31.0
Q ss_pred ccccchhhHHHHhcCcEeeecCCCceecChhHHHHHHHHHh
Q 006771 181 WYSGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 181 fYtaWsSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~ 221 (632)
+.+...-++.|+++|||-+ ....|.|||.|.++.+.+..
T Consensus 33 ~~~~~~yL~~L~~~gLI~~--~~~~Y~lTekG~~~l~~l~~ 71 (77)
T PF14947_consen 33 YSTLKKYLKELEEKGLIKK--KDGKYRLTEKGKEFLEELEE 71 (77)
T ss_dssp HHHHHHHHHHHHHTTSEEE--ETTEEEE-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCcCeeC--CCCEEEECccHHHHHHHHHH
Confidence 3467788899999999933 44589999999999998764
No 29
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=89.16 E-value=0.55 Score=40.90 Aligned_cols=36 Identities=31% Similarity=0.412 Sum_probs=28.2
Q ss_pred hhhHHHHhcCcEeee---cCCC--ceecChhHHHHHHHHHh
Q 006771 186 SCMKTLITKGLVVKS---SCPA--KYMLTPGGREAARECLS 221 (632)
Q Consensus 186 sSmktLi~k~LV~~~---grP~--rY~LTdeG~elA~~l~~ 221 (632)
..++.|+..|||.+. +.|. .|.||+.|.+++..+..
T Consensus 38 ~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~~l~~ 78 (90)
T PF01638_consen 38 QRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLPVLEA 78 (90)
T ss_dssp HHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHHHHHH
T ss_pred HHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHHHHHH
Confidence 467899999999764 4565 59999999999987654
No 30
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=89.07 E-value=0.32 Score=34.22 Aligned_cols=22 Identities=14% Similarity=0.368 Sum_probs=18.0
Q ss_pred CChhhhhccccchHHHHHHHHH
Q 006771 64 KTLKDLSQVKGVGKWILKLMQE 85 (632)
Q Consensus 64 ~~~k~l~~lkG~G~~i~~~L~~ 85 (632)
.+.+||.+|+|||++++..+-.
T Consensus 8 as~eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 8 ASIEELMKLPGIGPKTANAILS 29 (30)
T ss_dssp SSHHHHHTSTT-SHHHHHHHHH
T ss_pred CCHHHHHhCCCcCHHHHHHHHh
Confidence 4688999999999999998644
No 31
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=88.14 E-value=0.83 Score=53.52 Aligned_cols=53 Identities=19% Similarity=0.326 Sum_probs=42.6
Q ss_pred HHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhh
Q 006771 563 FAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 563 f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~v 629 (632)
+-..|..|||||+..|..|+++|+|+..|.+| + .++ |..+ ||+.++++|+.+|
T Consensus 567 ~~s~L~~I~GIG~k~a~~Ll~~Fgs~~~i~~A-----s----~ee-L~~v----ig~k~A~~I~~~~ 619 (621)
T PRK14671 567 LQTELTDIAGIGEKTAEKLLEHFGSVEKVAKA-----S----LEE-LAAV----AGPKTAETIYRYY 619 (621)
T ss_pred hhhhhhcCCCcCHHHHHHHHHHcCCHHHHHhC-----C----HHH-HHHH----hCHHHHHHHHHHh
Confidence 34678899999999999999999999999876 1 223 3332 9999999999854
No 32
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=87.69 E-value=0.63 Score=32.74 Aligned_cols=19 Identities=26% Similarity=0.490 Sum_probs=16.2
Q ss_pred HHHhcCCCCCHHHHHHHHH
Q 006771 565 VQLMQVPQVTEEIAITVLD 583 (632)
Q Consensus 565 ~mLm~IpGVs~ekA~~I~~ 583 (632)
..|+.||||++..|.+|++
T Consensus 11 eeL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 11 EELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHHTSTT-SHHHHHHHHH
T ss_pred HHHHhCCCcCHHHHHHHHh
Confidence 4699999999999999986
No 33
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=87.56 E-value=0.9 Score=53.16 Aligned_cols=55 Identities=16% Similarity=0.221 Sum_probs=43.2
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhh
Q 006771 561 DVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 561 e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~v 629 (632)
..+--.|..|||||+.++.+|+++|+|+..+.+|-. +++.+ .||+.++++|+.++
T Consensus 548 ~~~~S~L~~IpGIG~kr~~~LL~~FgSi~~I~~As~---------eeL~~-----vi~~k~A~~I~~~l 602 (624)
T PRK14669 548 RDRTSELLEIPGVGAKTVQRLLKHFGSLERVRAATE---------TQLAA-----VVGRAAAEAIIAHF 602 (624)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCH---------HHHHH-----HhCHHHHHHHHHHh
Confidence 344557889999999999999999999999997652 23322 18889999998854
No 34
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=87.38 E-value=0.5 Score=41.48 Aligned_cols=63 Identities=24% Similarity=0.347 Sum_probs=43.0
Q ss_pred HHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchh-hHHHHhcCcEeeecCC
Q 006771 125 AYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSC-MKTLITKGLVVKSSCP 203 (632)
Q Consensus 125 aYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsS-mktLi~k~LV~~~grP 203 (632)
+-.||+-+++. .|+|-.|+-++-. ++. . -+.=+| +.+||+||||-++|-.
T Consensus 18 ~~~ilI~v~Kk-----~Fit~~ev~e~l~----------~~~----------~----~~~V~SNIGvLIKkglIEKSGDG 68 (96)
T PF09114_consen 18 AANILIQVAKK-----NFITASEVREALA----------TEM----------N----KASVNSNIGVLIKKGLIEKSGDG 68 (96)
T ss_dssp HHHHHHHHHHS-----TTB-HHHHHH-T-----------TTS---------------HHHHHHHHHHHHHTTSEEEETTE
T ss_pred HHHHHHHHHHH-----ccCCHHHHHHHHH----------HHh----------h----hhHHHHhHHHHHHcCcccccCCc
Confidence 34678888776 5889888888421 110 0 123344 9999999999999985
Q ss_pred CceecChhHHHHHHH
Q 006771 204 AKYMLTPGGREAARE 218 (632)
Q Consensus 204 ~rY~LTdeG~elA~~ 218 (632)
|.+|++|.++-..
T Consensus 69 --lv~T~~g~~Ii~~ 81 (96)
T PF09114_consen 69 --LVITEEGMDIIIQ 81 (96)
T ss_dssp --EEE-HHHHHHHHH
T ss_pred --eEEechHHHHHHH
Confidence 9999999998554
No 35
>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=86.54 E-value=0.79 Score=38.87 Aligned_cols=32 Identities=22% Similarity=0.357 Sum_probs=28.4
Q ss_pred HhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhc
Q 006771 567 LMQVPQVTEEIAITVLDLYPTLLSLAHAYSIL 598 (632)
Q Consensus 567 Lm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~ 598 (632)
+..||||++.+|..|+..|+++..++.+.+..
T Consensus 24 i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~~ 55 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEYGSLENLLENLDKI 55 (75)
T ss_pred CCCCCcccHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 34699999999999999999999999987654
No 36
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=85.03 E-value=2.3 Score=42.41 Aligned_cols=36 Identities=19% Similarity=0.241 Sum_probs=27.7
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSI 597 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~ 597 (632)
+++ ...|..|||||+..|..|+++|+. ..|.+|-.+
T Consensus 69 k~~-f~~L~~i~GIGpk~A~~il~~fg~-~~l~~~i~~ 104 (192)
T PRK00116 69 REL-FRLLISVSGVGPKLALAILSGLSP-EELVQAIAN 104 (192)
T ss_pred HHH-HHHHhcCCCCCHHHHHHHHHhCCH-HHHHHHHHh
Confidence 445 457889999999999999999987 445555443
No 37
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=84.59 E-value=0.77 Score=39.42 Aligned_cols=64 Identities=28% Similarity=0.250 Sum_probs=43.5
Q ss_pred HHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEee-----e
Q 006771 126 YALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVK-----S 200 (632)
Q Consensus 126 YAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~-----~ 200 (632)
.+||..|+.. +.++=.||.+.-.- . . -+-+.-|++|.+.|||-. .
T Consensus 3 l~Il~~L~~~-----~~~~f~~L~~~l~l--------t------------~-----g~Ls~hL~~Le~~GyV~~~k~~~~ 52 (80)
T PF13601_consen 3 LAILALLYAN-----EEATFSELKEELGL--------T------------D-----GNLSKHLKKLEEAGYVEVEKEFEG 52 (80)
T ss_dssp HHHHHHHHHH-----SEEEHHHHHHHTT----------------------H-----HHHHHHHHHHHHTTSEEEEEE-SS
T ss_pred HHHHHHHhhc-----CCCCHHHHHHHhCc--------C------------H-----HHHHHHHHHHHHCCCEEEEEeccC
Confidence 3678888764 45777888885221 1 0 157889999999999962 3
Q ss_pred cCCC-ceecChhHHHHHHHH
Q 006771 201 SCPA-KYMLTPGGREAAREC 219 (632)
Q Consensus 201 grP~-rY~LTdeG~elA~~l 219 (632)
++|. -|.|||+|++.-...
T Consensus 53 ~~p~t~~~lT~~Gr~~~~~~ 72 (80)
T PF13601_consen 53 RRPRTWYSLTDKGREAFERY 72 (80)
T ss_dssp S--EEEEEE-HHHHHHHHHH
T ss_pred CCCeEEEEECHHHHHHHHHH
Confidence 4586 599999999987654
No 38
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=84.34 E-value=0.63 Score=38.19 Aligned_cols=48 Identities=27% Similarity=0.520 Sum_probs=30.9
Q ss_pred CCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHhhc
Q 006771 40 GLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFET 89 (632)
Q Consensus 40 g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~~ 89 (632)
++++..+..+-+.|.++.+--.. +..++.+++|||+.+++-+.+||.+
T Consensus 10 ~VG~~~ak~L~~~f~sl~~l~~a--~~e~L~~i~gIG~~~A~si~~ff~~ 57 (64)
T PF12826_consen 10 GVGEKTAKLLAKHFGSLEALMNA--SVEELSAIPGIGPKIAQSIYEFFQD 57 (64)
T ss_dssp T--HHHHHHHHHCCSCHHHHCC----HHHHCTSTT--HHHHHHHHHHHH-
T ss_pred CccHHHHHHHHHHcCCHHHHHHc--CHHHHhccCCcCHHHHHHHHHHHCC
Confidence 45555566666666665543322 7889999999999999999999874
No 39
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=82.64 E-value=1.4 Score=50.99 Aligned_cols=54 Identities=19% Similarity=0.208 Sum_probs=42.7
Q ss_pred HHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhhcc
Q 006771 565 VQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLVWG 631 (632)
Q Consensus 565 ~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~vwg 631 (632)
-.|..|||||+.+..+|+++|+|+..+-.|-. |++ +.+ + ||+.++++|++.+=|
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~As~---------eeL-~~v--g-i~~~~A~~I~~~l~~ 567 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYRNFKTLYDFLKADD---------EEL-KKL--G-IPPSVKQEVKKYLSG 567 (567)
T ss_pred CccccCCCCCHHHHHHHHHHhCCHHHHHhCCH---------HHH-HHc--C-CCHHHHHHHHHHhcC
Confidence 35789999999999999999999999997752 222 222 2 899999999986643
No 40
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=82.53 E-value=1.7 Score=41.37 Aligned_cols=38 Identities=18% Similarity=0.364 Sum_probs=28.2
Q ss_pred cchhhHHHHhcCcEeee------cCCCc-eecChhHHHHHHHHHh
Q 006771 184 GWSCMKTLITKGLVVKS------SCPAK-YMLTPGGREAARECLS 221 (632)
Q Consensus 184 aWsSmktLi~k~LV~~~------grP~r-Y~LTdeG~elA~~l~~ 221 (632)
--..++.|.+.|||..+ |+|.| |.|||.|++.-..+..
T Consensus 60 LYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~ 104 (138)
T TIGR02719 60 VYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCAN 104 (138)
T ss_pred HHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHH
Confidence 34578999999999742 34444 8899999997776554
No 41
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=82.26 E-value=1.2 Score=38.86 Aligned_cols=32 Identities=25% Similarity=0.365 Sum_probs=27.3
Q ss_pred HHHhcCcEeee--cCCCceecChhHHHHHHHHHh
Q 006771 190 TLITKGLVVKS--SCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 190 tLi~k~LV~~~--grP~rY~LTdeG~elA~~l~~ 221 (632)
-|..+|+|.+. +++.||+||+.|.++=++++.
T Consensus 50 WLE~ngyI~R~~~~~~~rY~~T~kG~~ll~~~~~ 83 (85)
T PF11313_consen 50 WLEENGYIFRDNNNNEKRYSLTEKGKELLAEIKN 83 (85)
T ss_pred HHhhcCeeEeecCCCcceeEEeccHHHHHHHHHh
Confidence 48899999975 678899999999999888763
No 42
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=82.26 E-value=1.1 Score=37.43 Aligned_cols=32 Identities=34% Similarity=0.518 Sum_probs=23.6
Q ss_pred hhhHHHHhcCcEeee-----cCC-Cc-eecChhHHHHHH
Q 006771 186 SCMKTLITKGLVVKS-----SCP-AK-YMLTPGGREAAR 217 (632)
Q Consensus 186 sSmktLi~k~LV~~~-----grP-~r-Y~LTdeG~elA~ 217 (632)
..++.|.++|||... ++| .| |.|||+|++..+
T Consensus 36 ~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~ 74 (75)
T PF03551_consen 36 PALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELR 74 (75)
T ss_dssp HHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHH
T ss_pred HHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhc
Confidence 357889999999632 333 43 999999998654
No 43
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=81.99 E-value=2.8 Score=40.91 Aligned_cols=72 Identities=15% Similarity=0.247 Sum_probs=52.9
Q ss_pred HHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeee---cCCCc
Q 006771 129 LITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKS---SCPAK 205 (632)
Q Consensus 129 LlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~---grP~r 205 (632)
||-||-.+.- ...+|+.||.+..-... -..|++==.++.-|+..|||... .+-.+
T Consensus 3 LlILYiL~~v-~~pltn~qit~~iL~~~---------------------~~nYF~lqq~l~eL~es~~i~~~~~~~~~~~ 60 (163)
T PF14277_consen 3 LLILYILKKV-KFPLTNSQITEFILENE---------------------YTNYFTLQQALSELVESGLITLETDSDNKTR 60 (163)
T ss_pred hhHhHHHHhC-CCCCCHHHHHHHHHhcC---------------------cccHHHHHHHHHHHHHCCCEEEeeccCCCcE
Confidence 4556665544 45699999999644321 12456777888999999999843 34468
Q ss_pred eecChhHHHHHHHHHhh
Q 006771 206 YMLTPGGREAARECLSR 222 (632)
Q Consensus 206 Y~LTdeG~elA~~l~~~ 222 (632)
|.||++|.+++..+..+
T Consensus 61 y~iTe~G~~tl~~F~~~ 77 (163)
T PF14277_consen 61 YSITEKGKETLEFFENR 77 (163)
T ss_pred EEECHhhHHHHHHHHHh
Confidence 99999999999998754
No 44
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=81.89 E-value=1.7 Score=40.91 Aligned_cols=38 Identities=16% Similarity=0.256 Sum_probs=28.8
Q ss_pred cchh-hHHHHhcCcEeeecCCCceecChhHHHHHHHHHhh
Q 006771 184 GWSC-MKTLITKGLVVKSSCPAKYMLTPGGREAARECLSR 222 (632)
Q Consensus 184 aWsS-mktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~~ 222 (632)
+++. ++.|.++|||.... ...|.||+.|+++|..+..+
T Consensus 38 svs~~l~~L~~~Gli~~~~-~~~i~LT~~G~~~a~~~~~~ 76 (142)
T PRK03902 38 SVTKMVQKLDKDEYLIYEK-YRGLVLTPKGKKIGKRLVYR 76 (142)
T ss_pred HHHHHHHHHHHCCCEEEec-CceEEECHHHHHHHHHHHHH
Confidence 3444 48999999997542 23699999999999987543
No 45
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=81.66 E-value=2 Score=50.21 Aligned_cols=55 Identities=18% Similarity=0.307 Sum_probs=42.2
Q ss_pred HHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhh
Q 006771 563 FAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 563 f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~v 629 (632)
+.-.|..|||||+..+..|+++|+|+..+.+|-. +++ .. ..+ ||+.+++.|+.++
T Consensus 541 ~~s~L~~IpGIG~k~~k~Ll~~FgS~~~i~~As~---------eeL-~~-v~G-ig~~~A~~I~~~l 595 (598)
T PRK00558 541 LTSALDDIPGIGPKRRKALLKHFGSLKAIKEASV---------EEL-AK-VPG-ISKKLAEAIYEAL 595 (598)
T ss_pred hhhhHhhCCCcCHHHHHHHHHHcCCHHHHHhCCH---------HHH-hh-cCC-cCHHHHHHHHHHh
Confidence 3456889999999999999999999999987632 122 22 112 8999999999854
No 46
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=81.20 E-value=1.1 Score=37.68 Aligned_cols=66 Identities=21% Similarity=0.292 Sum_probs=47.5
Q ss_pred HHHHHHHHHhcCCC-CCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeee--c
Q 006771 125 AYALLITLYRGTTN-GNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKS--S 201 (632)
Q Consensus 125 aYAiLlaL~~~~~~-~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~--g 201 (632)
|-.+|++||-.... ....+.=.+||+..++++ +.+ .++=.++.-|.++|++..+ |
T Consensus 2 a~Sli~tl~Gdy~~~~g~~i~~~~Li~ll~~~G-----v~e-----------------~avR~alsRl~~~G~L~~~r~G 59 (70)
T PF07848_consen 2 ARSLIVTLLGDYLRPRGGWIWVASLIRLLAAFG-----VSE-----------------SAVRTALSRLVRRGWLESERRG 59 (70)
T ss_dssp HHHHHHHHHHHHCCTTTS-EEHHHHHHHHCCTT-------H-----------------HHHHHHHHHHHHTTSEEEECCC
T ss_pred cceehHHHHHHHhccCCCceeHHHHHHHHHHcC-----CCh-----------------HHHHHHHHHHHHcCceeeeecC
Confidence 45788999854432 235589999999988876 322 2466789999999999855 7
Q ss_pred CCCceecChhH
Q 006771 202 CPAKYMLTPGG 212 (632)
Q Consensus 202 rP~rY~LTdeG 212 (632)
|-..|.|||.|
T Consensus 60 r~~~Y~Lt~~g 70 (70)
T PF07848_consen 60 RRSYYRLTERG 70 (70)
T ss_dssp TEEEEEE-HHH
T ss_pred ccceEeeCCCC
Confidence 77789999987
No 47
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=80.80 E-value=8 Score=36.02 Aligned_cols=75 Identities=25% Similarity=0.268 Sum_probs=48.2
Q ss_pred hHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeee---
Q 006771 124 VAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKS--- 200 (632)
Q Consensus 124 GaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~--- 200 (632)
-.|.||.-|... -++--||+..-+.++.--+.+ ++.-.|. .++.|.++|||..+
T Consensus 10 l~~~iL~~L~~~------~~~Gyei~k~~~~~~~~~~~~--------------s~gtiYp---~L~~Le~~Gli~~~~~~ 66 (138)
T COG1695 10 LELLILSLLSEK------PSHGYEIIKELEELSGGLWEP--------------SPGTIYP---LLKRLEKEGLIESRWEE 66 (138)
T ss_pred HHHHHHHHHhcC------CchHHHHHHHHHHHcCCCCcC--------------CCCcHHH---HHHHHHHCCCeEEEecc
Confidence 356666666443 366678888777765432222 2233454 56788999999742
Q ss_pred ---cCCCc-eecChhHHHHHHHHHh
Q 006771 201 ---SCPAK-YMLTPGGREAARECLS 221 (632)
Q Consensus 201 ---grP~r-Y~LTdeG~elA~~l~~ 221 (632)
|.|.| |.|||.|++..+..++
T Consensus 67 ~~~g~~rk~Y~lTe~G~~~l~~~~~ 91 (138)
T COG1695 67 SGGGPPRKYYRLTEKGKEELAELRE 91 (138)
T ss_pred cCCCCCceEEEECHHHHHHHHHHHH
Confidence 23444 9999999999887653
No 48
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=80.63 E-value=4.4 Score=35.40 Aligned_cols=81 Identities=20% Similarity=0.238 Sum_probs=45.9
Q ss_pred HHHHHHHhcCCCCCCCCCHHHHHHHHHhc-CCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecCCCc
Q 006771 127 ALLITLYRGTTNGNEFMRKQDLIDAAEAS-GLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCPAK 205 (632)
Q Consensus 127 AiLlaL~~~~~~~~~~mtK~eLi~~Aq~~-~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~grP~r 205 (632)
.||-+|... .+.++..||++....+ ..+.-... .-.+.+-+...-++.-+| +...|.+-|||.+-+| ..
T Consensus 8 piL~~L~~~----g~~~~~~ei~~~v~~~~~ls~e~~~----~~~~sg~~~~~~~~ri~W-a~~~L~~aGli~~~~r-G~ 77 (92)
T PF14338_consen 8 PILEALKDL----GGSASRKEIYERVAERFGLSDEERN----ERLPSGQGYSRFKNRIRW-ARSYLKKAGLIERPKR-GI 77 (92)
T ss_pred HHHHHHHHc----CCCcCHHHHHHHHHHHhCCCHHHHH----HHcccCCcchhHHHhHHH-HHHHHHHCCCccCCCC-Cc
Confidence 466666443 3569999999976665 32211000 000000011112333445 5689999999955443 26
Q ss_pred eecChhHHHHHH
Q 006771 206 YMLTPGGREAAR 217 (632)
Q Consensus 206 Y~LTdeG~elA~ 217 (632)
|.||++|.++-.
T Consensus 78 ~~iT~~G~~~l~ 89 (92)
T PF14338_consen 78 WRITEKGRKALA 89 (92)
T ss_pred eEECHhHHHHHh
Confidence 999999998754
No 49
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=80.56 E-value=2.8 Score=40.30 Aligned_cols=48 Identities=23% Similarity=0.511 Sum_probs=37.1
Q ss_pred hCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHh
Q 006771 36 ETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFF 87 (632)
Q Consensus 36 e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~ 87 (632)
+...|++.+. -+|+-.-+.--+||++..||++++|||+++.++|++++
T Consensus 100 ~~lpgIG~~k----A~aIi~yRe~~G~f~sv~dL~~v~GiG~~~~ekl~~~i 147 (149)
T COG1555 100 QALPGIGPKK----AQAIIDYREENGPFKSVDDLAKVKGIGPKTLEKLKDYI 147 (149)
T ss_pred HHCCCCCHHH----HHHHHHHHHHcCCCCcHHHHHhccCCCHHHHHHHHhhc
Confidence 4456777533 35555556666799999999999999999999998774
No 50
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=80.50 E-value=2 Score=39.81 Aligned_cols=36 Identities=33% Similarity=0.455 Sum_probs=28.8
Q ss_pred hhhHHHHhcCcEeeec---CCCc--eecChhHHHHHHHHHh
Q 006771 186 SCMKTLITKGLVVKSS---CPAK--YMLTPGGREAARECLS 221 (632)
Q Consensus 186 sSmktLi~k~LV~~~g---rP~r--Y~LTdeG~elA~~l~~ 221 (632)
...|.|.+.|||.+.- .|.| |+|||-|.+|..-|..
T Consensus 56 ~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~~vl~~ 96 (120)
T COG1733 56 RRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLLPVLLA 96 (120)
T ss_pred HHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHHHHHHH
Confidence 3468999999999763 3544 9999999999987764
No 51
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=80.40 E-value=4.9 Score=40.08 Aligned_cols=70 Identities=21% Similarity=0.206 Sum_probs=49.9
Q ss_pred CchHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeec
Q 006771 122 NSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSS 201 (632)
Q Consensus 122 rSGaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~g 201 (632)
.-+-|.+|..|+.. .++|=.||.+. +..+. + |.=..++.|.++|||.+.-
T Consensus 44 t~~q~~iL~~L~~~-----~~itq~eLa~~----l~l~~----------------s-----Tvtr~l~rLE~kGlI~R~~ 93 (185)
T PRK13777 44 NINEHHILWIAYHL-----KGASISEIAKF----GVMHV----------------S-----TAFNFSKKLEERGYLTFSK 93 (185)
T ss_pred CHHHHHHHHHHHhC-----CCcCHHHHHHH----HCCCH----------------h-----hHHHHHHHHHHCCCEEecC
Confidence 34568999999765 46777776662 21110 1 2334678999999999887
Q ss_pred CCC-----ceecChhHHHHHHHHHh
Q 006771 202 CPA-----KYMLTPGGREAARECLS 221 (632)
Q Consensus 202 rP~-----rY~LTdeG~elA~~l~~ 221 (632)
+|. ...||++|.++...+..
T Consensus 94 ~~~DrR~~~I~LTekG~~l~~~l~~ 118 (185)
T PRK13777 94 KEDDKRNTYIELTEKGEELLLETME 118 (185)
T ss_pred CCCCCCeeEEEECHHHHHHHHHHHH
Confidence 773 38899999999998764
No 52
>PRK09482 flap endonuclease-like protein; Provisional
Probab=80.40 E-value=2.2 Score=44.73 Aligned_cols=32 Identities=16% Similarity=0.223 Sum_probs=29.2
Q ss_pred hcCCCCCHHHHHHHHHhcCCHHHHHHHHhhcc
Q 006771 568 MQVPQVTEEIAITVLDLYPTLLSLAHAYSILE 599 (632)
Q Consensus 568 m~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~ 599 (632)
-.|||||+..|..|++.|+|+..++++.+++.
T Consensus 185 pGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~ 216 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQFRSLENIYESLDALP 216 (256)
T ss_pred CCCCCcChHHHHHHHHHhCCHHHHHHhHHHhh
Confidence 47899999999999999999999999987763
No 53
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=79.81 E-value=2 Score=36.66 Aligned_cols=68 Identities=24% Similarity=0.286 Sum_probs=47.0
Q ss_pred HHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeec---
Q 006771 125 AYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSS--- 201 (632)
Q Consensus 125 aYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~g--- 201 (632)
.+.||..|+.. ..++-.||.+... +.+ -+.=..++.|.++|+|.+..
T Consensus 12 ~~~il~~l~~~-----~~~~~~~la~~~~--------~s~-----------------~~i~~~l~~L~~~g~v~~~~~~~ 61 (101)
T smart00347 12 QFLVLRILYEE-----GPLSVSELAKRLG--------VSP-----------------STVTRVLDRLEKKGLIRRLPSPE 61 (101)
T ss_pred HHHHHHHHHHc-----CCcCHHHHHHHHC--------CCc-----------------hhHHHHHHHHHHCCCeEecCCCC
Confidence 46777777654 3588888876532 111 12346789999999998552
Q ss_pred -CCC-ceecChhHHHHHHHHHhh
Q 006771 202 -CPA-KYMLTPGGREAARECLSR 222 (632)
Q Consensus 202 -rP~-rY~LTdeG~elA~~l~~~ 222 (632)
++. .|.||+.|+++.+.+...
T Consensus 62 ~~r~~~~~lT~~g~~~~~~~~~~ 84 (101)
T smart00347 62 DRRSVLVSLTEEGRELIEELLEA 84 (101)
T ss_pred CCCeEEEEECHhHHHHHHHHHHH
Confidence 233 599999999999987653
No 54
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=79.69 E-value=2.1 Score=40.22 Aligned_cols=70 Identities=16% Similarity=0.230 Sum_probs=49.6
Q ss_pred CchHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeec
Q 006771 122 NSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSS 201 (632)
Q Consensus 122 rSGaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~g 201 (632)
..+-|.||..|+.. +++|=.||.+... +.+ -|.=..++.|+++|||.+.-
T Consensus 39 t~~q~~vL~~l~~~-----~~~t~~eLa~~l~--------i~~-----------------~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 39 TAAQFKVLCSIRCA-----ACITPVELKKVLS--------VDL-----------------GALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred CHHHHHHHHHHHHc-----CCCCHHHHHHHHC--------CCH-----------------HHHHHHHHHHHHCCCEEecc
Confidence 34568899998743 4688888877532 211 02234568999999999876
Q ss_pred CCC-----ceecChhHHHHHHHHHh
Q 006771 202 CPA-----KYMLTPGGREAARECLS 221 (632)
Q Consensus 202 rP~-----rY~LTdeG~elA~~l~~ 221 (632)
.|. ...||++|.++..++..
T Consensus 89 ~~~DrR~~~l~LT~~G~~~~~~~~~ 113 (144)
T PRK11512 89 NPNDKRGVLVKLTTSGAAICEQCHQ 113 (144)
T ss_pred CcccCCeeEeEEChhHHHHHHHHHH
Confidence 663 48999999999887653
No 55
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=79.52 E-value=3 Score=45.53 Aligned_cols=32 Identities=16% Similarity=0.287 Sum_probs=30.3
Q ss_pred HHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHH
Q 006771 564 AVQLMQVPQVTEEIAITVLDLYPTLLSLAHAY 595 (632)
Q Consensus 564 ~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay 595 (632)
.|+|..||+|+...|..|+++|+|+..+++|-
T Consensus 286 yRiLs~IPrl~k~iAk~Ll~~FGSL~~Il~As 317 (352)
T PRK13482 286 YRLLSKIPRLPSAVIENLVEHFGSLQGLLAAS 317 (352)
T ss_pred HHHHhcCCCCCHHHHHHHHHHcCCHHHHHcCC
Confidence 68999999999999999999999999999874
No 56
>PRK07945 hypothetical protein; Provisional
Probab=79.30 E-value=1.7 Score=47.05 Aligned_cols=100 Identities=13% Similarity=0.076 Sum_probs=70.6
Q ss_pred HHHHHHHHHHHhccCCC-CCChh---hhhccccchHHHHHHHHHHhhcCCCCCCCchhhhhcccccccccCCCcccccCC
Q 006771 46 DMTLSKAYNNICDAKNP-IKTLK---DLSQVKGVGKWILKLMQEFFETDSGGSEPEDLTAKSKKSKAVKTKGTKRYMPQR 121 (632)
Q Consensus 46 ~~ty~kA~~sl~~~p~~-~~~~k---~l~~lkG~G~~i~~~L~~~~~~~~~~~p~~~~~~~~~~~~~kk~r~~k~YvP~~ 121 (632)
..+|++|.++|...+.+ +.... +|..|+|||+.++..+.++.+++..+ .=+.+. . ..=|.
T Consensus 24 v~ayr~aa~~~~~~~~~~~~~~~~~g~l~~~~giG~~~a~~i~e~~~tg~~~-~l~~l~--~------------~~~~~- 87 (335)
T PRK07945 24 VRAFRRAADVVEALDAAERARRARAGSLTSLPGIGPKTAKVIAQALAGRVPD-YLAELR--A------------DAEPL- 87 (335)
T ss_pred HHHHHHHHHHHHhcChhHHHHHHhcCCcccCCCcCHHHHHHHHHHHhcCCHH-HHHHHH--H------------hhcCC-
Confidence 46999999999999988 76554 89999999999999999999866431 001110 0 11122
Q ss_pred CchHHHHHHHHHh----cCCCCCCCCCHHHHHHHHHhcCCCCCCCC
Q 006771 122 NSVAYALLITLYR----GTTNGNEFMRKQDLIDAAEASGLSHTPIM 163 (632)
Q Consensus 122 rSGaYAiLlaL~~----~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~ 163 (632)
||-+|.-.+.- ++.-+.+..+=+|.+++|..-+...+.+.
T Consensus 88 --~g~~l~~~~~~D~H~HT~~Sdg~~~~ee~v~~Ai~~Gl~~i~~T 131 (335)
T PRK07945 88 --GGGALRAALRGDLHTHSDWSDGGSPIEEMARTAAALGHEYCALT 131 (335)
T ss_pred --ccHHHHHHHhhhcccccCCCCCCCCHHHHHHHHHHCCCCEEEEe
Confidence 57777777753 22234566788999999999877766654
No 57
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=79.06 E-value=1.2 Score=39.41 Aligned_cols=34 Identities=26% Similarity=0.318 Sum_probs=27.1
Q ss_pred chhhHHHHhcCcE-ee--ecCCCceecChhHHHHHHH
Q 006771 185 WSCMKTLITKGLV-VK--SSCPAKYMLTPGGREAARE 218 (632)
Q Consensus 185 WsSmktLi~k~LV-~~--~grP~rY~LTdeG~elA~~ 218 (632)
.+...+|+.-||| .+ .++.+-|.|||+|..+|..
T Consensus 53 Y~~e~SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~~~~ 89 (90)
T PF07381_consen 53 YNKEDSLVGLGLVEEEEEKGGFKYYRLTEKGKRIAEM 89 (90)
T ss_pred cCcchhHHHcCCeeEeeecCCeeEEEeChhhhhHHhc
Confidence 4566789999999 43 3556689999999999864
No 58
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=78.99 E-value=3.4 Score=48.81 Aligned_cols=55 Identities=15% Similarity=0.172 Sum_probs=42.4
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhh
Q 006771 562 VFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQL 628 (632)
Q Consensus 562 ~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~ 628 (632)
.+.-.|..|||||+.++..|+++|+|+..+..|-. ++ |..+ .-||+.+.++|++.
T Consensus 634 ~~~s~L~~IPGIGpkr~k~LL~~FGSle~I~~AS~---------eE-La~V--~Gig~k~Ae~I~~~ 688 (694)
T PRK14666 634 ALTGELQRVEGIGPATARLLWERFGSLQAMAAAGE---------EG-LAAV--PGIGPARAAALHEH 688 (694)
T ss_pred hhHhHHhhCCCCCHHHHHHHHHHhCCHHHHHhcCH---------HH-HHhc--CCcCHHHHHHHHHH
Confidence 33456899999999999999999999999997642 12 2322 23899999999874
No 59
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=78.81 E-value=4.1 Score=37.67 Aligned_cols=28 Identities=25% Similarity=0.593 Sum_probs=22.7
Q ss_pred CCCCCChhhhhccccchHHHHHHHHHHh
Q 006771 60 KNPIKTLKDLSQVKGVGKWILKLMQEFF 87 (632)
Q Consensus 60 p~~~~~~k~l~~lkG~G~~i~~~L~~~~ 87 (632)
..+|.+..||+.++|||+++.++|.+|+
T Consensus 91 ~g~f~s~eeL~~V~GIg~k~~~~i~~~l 118 (120)
T TIGR01259 91 NGAFKSVDDLTKVSGIGEKSLEKLKDYA 118 (120)
T ss_pred cCCcCCHHHHHcCCCCCHHHHHHHHhce
Confidence 4678888888888888888888887764
No 60
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=78.77 E-value=2.2 Score=42.71 Aligned_cols=62 Identities=27% Similarity=0.312 Sum_probs=45.1
Q ss_pred HHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeee-----
Q 006771 126 YALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKS----- 200 (632)
Q Consensus 126 YAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~----- 200 (632)
.+||..|... +.+|-.||-+.- + +.+ =|.+.-++.|.++|||.+.
T Consensus 4 ~~IL~~L~~~-----~~~t~~eLA~~l---g-----is~-----------------~tV~~~L~~Le~~GlV~r~~~~~~ 53 (203)
T TIGR02702 4 EDILSYLLKQ-----GQATAAALAEAL---A-----ISP-----------------QAVRRHLKDLETEGLIEYEAVVQG 53 (203)
T ss_pred HHHHHHHHHc-----CCCCHHHHHHHH---C-----cCH-----------------HHHHHHHHHHHHCCCeEEeecccC
Confidence 5788888654 348888887752 2 222 1678889999999999753
Q ss_pred -cCCCc-eecChhHHHHHH
Q 006771 201 -SCPAK-YMLTPGGREAAR 217 (632)
Q Consensus 201 -grP~r-Y~LTdeG~elA~ 217 (632)
|||.. |.||+.|.++..
T Consensus 54 ~gRp~~~y~LT~~G~~~~~ 72 (203)
T TIGR02702 54 MGRPQYHYQLSRQGREQFP 72 (203)
T ss_pred CCCCceEEEECcchhhhcc
Confidence 67874 899999998643
No 61
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=78.50 E-value=2.7 Score=36.33 Aligned_cols=36 Identities=33% Similarity=0.333 Sum_probs=30.3
Q ss_pred chhhHHHHhcCcEeeecCCCceecChhHHHHHHHHHh
Q 006771 185 WSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 185 WsSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~ 221 (632)
=..++.|.++|||.+..++ .|.||+.|..++..+..
T Consensus 17 s~~l~~L~~~glI~r~~~~-~~~lT~~g~~~~~~~~~ 52 (96)
T smart00529 17 TQMLKKLEKDGLVEYEPYR-GITLTEKGRRLARRLLR 52 (96)
T ss_pred HHHHHHHHHCCCEEEcCCC-ceEechhHHHHHHHHHH
Confidence 3467899999999997764 79999999999988764
No 62
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=77.53 E-value=11 Score=35.88 Aligned_cols=39 Identities=23% Similarity=0.250 Sum_probs=29.3
Q ss_pred ccchhhHHHHhcCcEeee--cCCC-ceecChhHHHHHHHHHh
Q 006771 183 SGWSCMKTLITKGLVVKS--SCPA-KYMLTPGGREAARECLS 221 (632)
Q Consensus 183 taWsSmktLi~k~LV~~~--grP~-rY~LTdeG~elA~~l~~ 221 (632)
+-..-.+.|.++|||... |++. -|.|||.|++.-+....
T Consensus 79 tIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~ 120 (135)
T PRK09416 79 SLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEK 120 (135)
T ss_pred cHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHh
Confidence 345578899999999753 3333 39999999998877654
No 63
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=76.81 E-value=3.2 Score=48.22 Aligned_cols=52 Identities=13% Similarity=0.174 Sum_probs=40.7
Q ss_pred HHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhh
Q 006771 566 QLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 566 mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~v 629 (632)
.|-.|||||+.+..+++++|+|+..+.+|-. |++.+- .+ |++.++++|++.+
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~~I~~As~---------eeL~~v--~g-i~~~~A~~I~~~l 566 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYKDILLLNE---------DEIAEK--MK-INIKMAKKIKKFA 566 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhCCH---------HHHHhC--CC-CCHHHHHHHHHHH
Confidence 5789999999999999999999999997752 233222 12 7888999998754
No 64
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=76.77 E-value=1.9 Score=38.49 Aligned_cols=36 Identities=28% Similarity=0.271 Sum_probs=27.4
Q ss_pred cchhhHHHHhcCcEeeec--CCCceecChhHHHHHHHH
Q 006771 184 GWSCMKTLITKGLVVKSS--CPAKYMLTPGGREAAREC 219 (632)
Q Consensus 184 aWsSmktLi~k~LV~~~g--rP~rY~LTdeG~elA~~l 219 (632)
-.-.|++|..+|+|-+.= |---|.||+||.|-=+..
T Consensus 40 V~k~mqSL~SrgyVke~faWrh~Yw~LT~eGIeyLR~y 77 (95)
T PF03501_consen 40 VIKAMQSLKSRGYVKEQFAWRHYYWYLTNEGIEYLREY 77 (95)
T ss_dssp HHHHHHHHHHCTSEEEEECTTEEEEEE-HHHHHHHHHH
T ss_pred HHHHHhcccchhhhcCeecceEEEEEEcchhHHHHHHH
Confidence 467789999999998763 334699999999975554
No 65
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=76.64 E-value=5.5 Score=42.82 Aligned_cols=74 Identities=16% Similarity=0.227 Sum_probs=56.5
Q ss_pred CCCHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhh--h-ccccchHHHHHHHHHHhhcCCCC
Q 006771 18 AENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDL--S-QVKGVGKWILKLMQEFFETDSGG 93 (632)
Q Consensus 18 ~~N~~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l--~-~lkG~G~~i~~~L~~~~~~~~~~ 93 (632)
..|.++...+.+-.+-+--. |-.+=-..+|++|-+||-.+...+...-+. . .|+|||+.|+..|++|.+.+...
T Consensus 3 ~~n~~ia~~le~iA~~me~~--Gen~fk~~aYr~Aa~sle~~~e~~~ei~e~~~~t~l~gIGk~ia~~I~e~l~tG~~~ 79 (326)
T COG1796 3 MNNHDIARLLERIADYMELE--GENPFKIRAYRKAAQSLENLTEDLEEIEERGRLTELPGIGKGIAEKISEYLDTGEVK 79 (326)
T ss_pred cchHHHHHHHHHHHHHHHhc--CCCccchHHHHHHHHhhhhcccchHHHHhhcccCCCCCccHHHHHHHHHHHHcCccH
Confidence 45677888888765555432 221123579999999999999999888887 4 89999999999999998876553
No 66
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=76.06 E-value=2.8 Score=28.14 Aligned_cols=20 Identities=25% Similarity=0.511 Sum_probs=17.7
Q ss_pred HHhcCCCCCHHHHHHHHHhc
Q 006771 566 QLMQVPQVTEEIAITVLDLY 585 (632)
Q Consensus 566 mLm~IpGVs~ekA~~I~~~y 585 (632)
.|+.|||||.+.|..|++..
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 58899999999999999744
No 67
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=75.87 E-value=2.6 Score=37.09 Aligned_cols=36 Identities=33% Similarity=0.397 Sum_probs=29.8
Q ss_pred hhhHHHHhcCcEeeecCCC-----ceecChhHHHHHHHHHh
Q 006771 186 SCMKTLITKGLVVKSSCPA-----KYMLTPGGREAARECLS 221 (632)
Q Consensus 186 sSmktLi~k~LV~~~grP~-----rY~LTdeG~elA~~l~~ 221 (632)
.-++.|+++|||.+.-.|. .+.||++|.++...+..
T Consensus 55 ~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~ 95 (126)
T COG1846 55 RLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP 95 (126)
T ss_pred HHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc
Confidence 4568999999999876663 49999999999998754
No 68
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=75.54 E-value=3.6 Score=36.95 Aligned_cols=74 Identities=15% Similarity=0.102 Sum_probs=51.5
Q ss_pred CchHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeec
Q 006771 122 NSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSS 201 (632)
Q Consensus 122 rSGaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~g 201 (632)
...-|.+|..|+....+ .++++=.||.+...- .+ -+.=-.++.|+++|||.+.-
T Consensus 24 s~~q~~vL~~l~~~~~~-~~~~t~~eL~~~l~~--------~~-----------------stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 24 SLEELLILYYLGKLENN-EGKLTLKEIIKEILI--------KQ-----------------SALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred CHHHHHHHHHHHhhhcc-CCcCcHHHHHHHHCC--------CH-----------------HHHHHHHHHHHHCCCEeccC
Confidence 44457888888842222 356888888775332 11 12334678999999999887
Q ss_pred CCC-----ceecChhHHHHHHHHHh
Q 006771 202 CPA-----KYMLTPGGREAARECLS 221 (632)
Q Consensus 202 rP~-----rY~LTdeG~elA~~l~~ 221 (632)
.|. .+.||++|.++...+..
T Consensus 78 ~~~D~R~~~i~lT~~G~~~~~~~~~ 102 (109)
T TIGR01889 78 SEDDERKVIISINKEQRSKIESLIS 102 (109)
T ss_pred CcccCCeEEEEECHHHHHHHHHHHH
Confidence 774 38899999999988764
No 69
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=74.91 E-value=2.7 Score=34.43 Aligned_cols=45 Identities=24% Similarity=0.489 Sum_probs=29.1
Q ss_pred CCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHh
Q 006771 39 KGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFF 87 (632)
Q Consensus 39 ~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~ 87 (632)
.|++. ..-+++-..+.--+||.+..||+.+.|||+...++|+.|+
T Consensus 20 pgi~~----~~A~~Iv~~R~~~G~f~s~~dL~~v~gi~~~~~~~l~~~l 64 (65)
T PF12836_consen 20 PGIGP----KQAKAIVEYREKNGPFKSLEDLKEVPGIGPKTYEKLKPYL 64 (65)
T ss_dssp TT--H----HHHHHHHHHHHHH-S-SSGGGGGGSTT--HHHHHHHCCCE
T ss_pred CCCCH----HHHHHHHHHHHhCcCCCCHHHHhhCCCCCHHHHHHHHhhc
Confidence 36654 3444555555555899999999999999999999987664
No 70
>smart00475 53EXOc 5'-3' exonuclease.
Probab=74.54 E-value=4.2 Score=42.54 Aligned_cols=32 Identities=22% Similarity=0.318 Sum_probs=29.0
Q ss_pred hcCCCCCHHHHHHHHHhcCCHHHHHHHHhhcc
Q 006771 568 MQVPQVTEEIAITVLDLYPTLLSLAHAYSILE 599 (632)
Q Consensus 568 m~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~ 599 (632)
-.|||||+..|..|+++|+|+..++++.+++.
T Consensus 189 pGV~GIG~KtA~~Ll~~ygsle~i~~~~~~~~ 220 (259)
T smart00475 189 PGVPGIGEKTAAKLLKEFGSLENILENLDKLK 220 (259)
T ss_pred CCCCCCCHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 36899999999999999999999999988764
No 71
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=74.34 E-value=2.3 Score=37.55 Aligned_cols=34 Identities=38% Similarity=0.467 Sum_probs=25.7
Q ss_pred chhhHHHHhcCcEeeecCC--CceecChhHHHHHHH
Q 006771 185 WSCMKTLITKGLVVKSSCP--AKYMLTPGGREAARE 218 (632)
Q Consensus 185 WsSmktLi~k~LV~~~grP--~rY~LTdeG~elA~~ 218 (632)
=-.|+||+++|+|-....= .-|.||+||.|--+.
T Consensus 43 ika~qsl~S~GYvkt~~~W~~~YytLT~eGveyLRE 78 (105)
T COG5045 43 IKAMQSLISYGYVKTIHVWRHSYYTLTPEGVEYLRE 78 (105)
T ss_pred HHHHHHHhhcceeEEEeeeeeeEEEecHHHHHHHHH
Confidence 3468999999999754331 469999999996544
No 72
>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=73.83 E-value=4.7 Score=41.59 Aligned_cols=32 Identities=22% Similarity=0.328 Sum_probs=29.1
Q ss_pred hcCCCCCHHHHHHHHHhcCCHHHHHHHHhhcc
Q 006771 568 MQVPQVTEEIAITVLDLYPTLLSLAHAYSILE 599 (632)
Q Consensus 568 m~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~ 599 (632)
-.|||||+..|..|+++|+|+..++++.++..
T Consensus 186 pGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~ 217 (240)
T cd00008 186 PGVPGIGEKTAAKLLKEYGSLEGILENLDKIK 217 (240)
T ss_pred CCCCccCHHHHHHHHHHhCCHHHHHHhHHHHh
Confidence 36899999999999999999999999988763
No 73
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=73.43 E-value=2.7 Score=28.26 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=17.1
Q ss_pred hhhccccchHHHHHHHHHHh
Q 006771 68 DLSQVKGVGKWILKLMQEFF 87 (632)
Q Consensus 68 ~l~~lkG~G~~i~~~L~~~~ 87 (632)
+|..|+|||++++++|-.|.
T Consensus 2 ~L~~i~GiG~k~A~~il~~~ 21 (26)
T smart00278 2 ELLKVPGIGPKTAEKILEAX 21 (26)
T ss_pred hhhhCCCCCHHHHHHHHHhc
Confidence 67899999999999987643
No 74
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=72.40 E-value=3.2 Score=43.95 Aligned_cols=69 Identities=22% Similarity=0.306 Sum_probs=48.2
Q ss_pred HHHHHHhcCCCCC-CCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecC--CC
Q 006771 128 LLITLYRGTTNGN-EFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSC--PA 204 (632)
Q Consensus 128 iLlaL~~~~~~~~-~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~gr--P~ 204 (632)
+|++||-.....+ .-+.=..||+.++.++-+ . . +-=.+++.|.++|+|....+ -+
T Consensus 2 li~T~~Gd~~~~~gg~i~~~~Li~l~~~~gi~-----~--------------~---~vr~al~RL~~~G~l~~~~~grr~ 59 (280)
T TIGR02277 2 LIVTLYGDAIRPRGGAIWLGSLIEFLAGLGIN-----E--------------R---LVRTAVSRLVAQGWLQSERKGRRS 59 (280)
T ss_pred eEEEehhhhccCCCCceeHHHHHHHHHhcCCC-----c--------------c---hHHHHHHHHHHCCCEEeeecCCCC
Confidence 4556665554322 348889999999987522 1 1 23457889999999976644 35
Q ss_pred ceecChhHHHHHHH
Q 006771 205 KYMLTPGGREAARE 218 (632)
Q Consensus 205 rY~LTdeG~elA~~ 218 (632)
.|.||+.|.+..+.
T Consensus 60 ~Y~LT~~g~~~l~~ 73 (280)
T TIGR02277 60 FYSLTDKGRRRFAA 73 (280)
T ss_pred EEEECHHHHHHHHH
Confidence 69999999987665
No 75
>PRK10870 transcriptional repressor MprA; Provisional
Probab=71.92 E-value=4.3 Score=39.85 Aligned_cols=70 Identities=26% Similarity=0.281 Sum_probs=49.5
Q ss_pred hHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecCC
Q 006771 124 VAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCP 203 (632)
Q Consensus 124 GaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~grP 203 (632)
+-|.||+.|+... ..++|=.||-+. .+.+. .|.=.-++.|+++|||.+..+|
T Consensus 56 ~q~~iL~~L~~~~---~~~it~~eLa~~---l~l~~----------------------~tvsr~v~rLe~kGlV~R~~~~ 107 (176)
T PRK10870 56 TLFMALITLESQE---NHSIQPSELSCA---LGSSR----------------------TNATRIADELEKRGWIERRESD 107 (176)
T ss_pred HHHHHHHHHhcCC---CCCcCHHHHHHH---HCCCH----------------------HHHHHHHHHHHHCCCEEecCCC
Confidence 4688999997532 356776776664 33221 1233456899999999988777
Q ss_pred C-----ceecChhHHHHHHHHHh
Q 006771 204 A-----KYMLTPGGREAARECLS 221 (632)
Q Consensus 204 ~-----rY~LTdeG~elA~~l~~ 221 (632)
. ...||++|.++...+..
T Consensus 108 ~DrR~~~v~LT~~G~~~~~~i~~ 130 (176)
T PRK10870 108 NDRRCLHLQLTEKGHEFLREVLP 130 (176)
T ss_pred CCCCeeEEEECHHHHHHHHHHHH
Confidence 4 48899999999998754
No 76
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=71.22 E-value=5.7 Score=35.50 Aligned_cols=38 Identities=24% Similarity=0.364 Sum_probs=28.1
Q ss_pred ccchhhHHHHhcCcEeeecCCC--ceecChhHHHHHHHHH
Q 006771 183 SGWSCMKTLITKGLVVKSSCPA--KYMLTPGGREAARECL 220 (632)
Q Consensus 183 taWsSmktLi~k~LV~~~grP~--rY~LTdeG~elA~~l~ 220 (632)
.|=+=++-|.++|||...-++. .|.|||.|..+-+.+.
T Consensus 47 ~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~ 86 (95)
T COG3432 47 RAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYS 86 (95)
T ss_pred HHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHH
Confidence 4444566789999888765544 5999999999866554
No 77
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=69.95 E-value=5.7 Score=37.11 Aligned_cols=70 Identities=19% Similarity=0.241 Sum_probs=47.9
Q ss_pred chHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecC
Q 006771 123 SVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSC 202 (632)
Q Consensus 123 SGaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~gr 202 (632)
.+-|.+|..|+... .++|-.||.+ ..+.+.- |-=..++.|+++|||.+.-.
T Consensus 31 ~~q~~vL~~l~~~~----~~~t~~eLa~---~l~~~~~----------------------tvt~~v~~Le~~GlV~r~~~ 81 (144)
T PRK03573 31 QTHWVTLHNIHQLP----PEQSQIQLAK---AIGIEQP----------------------SLVRTLDQLEEKGLISRQTC 81 (144)
T ss_pred HHHHHHHHHHHHcC----CCCCHHHHHH---HhCCChh----------------------hHHHHHHHHHHCCCEeeecC
Confidence 34678888887642 3566555555 3332211 12246789999999998866
Q ss_pred CC-----ceecChhHHHHHHHHHh
Q 006771 203 PA-----KYMLTPGGREAARECLS 221 (632)
Q Consensus 203 P~-----rY~LTdeG~elA~~l~~ 221 (632)
|. ...|||+|.++...+..
T Consensus 82 ~~DrR~~~l~LT~~G~~~~~~~~~ 105 (144)
T PRK03573 82 ASDRRAKRIKLTEKAEPLISEVEA 105 (144)
T ss_pred CCCcCeeeeEEChHHHHHHHHHHH
Confidence 63 48999999999988764
No 78
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=69.35 E-value=3.4 Score=33.20 Aligned_cols=49 Identities=16% Similarity=0.214 Sum_probs=33.4
Q ss_pred CCCCchhHHHHHHHH-HHHHhccCCCCCChhhhhccccchHHHHHHHHHHhh
Q 006771 38 PKGLSENIDMTLSKA-YNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFE 88 (632)
Q Consensus 38 ~~g~~~~~~~ty~kA-~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~ 88 (632)
-.|++.+.+..+..+ +.++.+- ---++.+|..++|||++.++.|.++++
T Consensus 10 I~Gig~~~a~~L~~~G~~t~~~l--~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 10 IPGIGPKRAEKLYEAGIKTLEDL--ANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp STTCHHHHHHHHHHTTCSSHHHH--HTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHhcCCCcHHHH--HcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 347777766666665 4444321 112678899999999999999877664
No 79
>PRK14976 5'-3' exonuclease; Provisional
Probab=69.10 E-value=6.6 Score=41.62 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=28.7
Q ss_pred hcCCCCCHHHHHHHHHhcCCHHHHHHHHhhcc
Q 006771 568 MQVPQVTEEIAITVLDLYPTLLSLAHAYSILE 599 (632)
Q Consensus 568 m~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~ 599 (632)
-.|||||+..|..|++.|+|+..+++...++.
T Consensus 194 pGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~ 225 (281)
T PRK14976 194 KGVKGIGPKTAIKLLNKYGNIENIYENIDKIK 225 (281)
T ss_pred CCCCcccHHHHHHHHHHcCCHHHHHHhHHHHh
Confidence 36999999999999999999999998877763
No 80
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=68.54 E-value=9.3 Score=44.58 Aligned_cols=54 Identities=17% Similarity=0.140 Sum_probs=40.9
Q ss_pred HHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhh
Q 006771 563 FAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQL 628 (632)
Q Consensus 563 f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~ 628 (632)
+.-.|..|||||+.++..|+++|+|+..+.+|-.+ ++.+- .+ ||+.++++|++.
T Consensus 523 ~~~~L~~IpGIG~kr~~~LL~~FGS~~~I~~As~e---------eL~~v--pG-i~~~~A~~I~~~ 576 (577)
T PRK14668 523 VSTVLDDVPGVGPETRKRLLRRFGSVEGVREASVE---------DLRDV--PG-VGEKTAETIRER 576 (577)
T ss_pred HHhHHhcCCCCCHHHHHHHHHHcCCHHHHHhCCHH---------HHHhC--CC-CCHHHHHHHHHh
Confidence 44578899999999999999999999999977532 22111 12 778888888763
No 81
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=67.00 E-value=2.7 Score=39.11 Aligned_cols=37 Identities=32% Similarity=0.348 Sum_probs=28.9
Q ss_pred cchhhHHHHhcCcEeeecC--CCceecChhHHHHHHHHH
Q 006771 184 GWSCMKTLITKGLVVKSSC--PAKYMLTPGGREAARECL 220 (632)
Q Consensus 184 aWsSmktLi~k~LV~~~gr--P~rY~LTdeG~elA~~l~ 220 (632)
-+-.|++|.++|+|-+.=. =--|.||+||.|--+...
T Consensus 43 Vik~mqSL~Srg~Vke~f~WrhyYw~LT~eGieyLR~yL 81 (124)
T PTZ00034 43 VMMLMRSLKSRGLVKEQFAWQHYYYYLTDEGIEYLRTYL 81 (124)
T ss_pred HHHHHHccccCCceEEEEeeEEEEEEEchHHHHHHHHHh
Confidence 5778999999999987633 236999999999766543
No 82
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=66.50 E-value=14 Score=37.35 Aligned_cols=58 Identities=19% Similarity=0.233 Sum_probs=40.5
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQ 627 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~ 627 (632)
+++|. .|..|.|||+..|.+|++- -++..|++|-..-+- ..|..+ .. ||+-.++||.-
T Consensus 69 R~lF~-~LisVnGIGpK~ALaiLs~-~~~~~l~~aI~~~d~------~~L~k~-PG-IGkKtAerivl 126 (201)
T COG0632 69 RELFR-LLISVNGIGPKLALAILSN-LDPEELAQAIANEDV------KALSKI-PG-IGKKTAERIVL 126 (201)
T ss_pred HHHHH-HHHccCCccHHHHHHHHcC-CCHHHHHHHHHhcCh------HhhhcC-CC-CCHHHHHHHHH
Confidence 56664 7889999999999999985 468889988765432 233331 22 67777776653
No 83
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=65.79 E-value=6.6 Score=37.06 Aligned_cols=38 Identities=13% Similarity=0.241 Sum_probs=29.5
Q ss_pred cccchHHHHHHHhcCCCCCHHHHHHHHH--hcCCHHHHHH
Q 006771 556 KMTVSDVFAVQLMQVPQVTEEIAITVLD--LYPTLLSLAH 593 (632)
Q Consensus 556 ~~Tv~e~f~~mLm~IpGVs~ekA~~I~~--~ypTp~~L~~ 593 (632)
...+...-.+.|+++|||++.+|.+|+. -|.++.+|.+
T Consensus 52 kIdiN~A~~~el~~lpGigP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 52 KIDLNNSSVRAFRQFPGMYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred cccCCccCHHHHHHCCCCCHHHHHHHHHCCCCCCHHHHHc
Confidence 3444445556688999999999999998 4888888863
No 84
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=65.63 E-value=6.2 Score=45.95 Aligned_cols=56 Identities=18% Similarity=0.268 Sum_probs=43.0
Q ss_pred hHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhh
Q 006771 560 SDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQL 628 (632)
Q Consensus 560 ~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~ 628 (632)
+..+..-|-.|||||+....+|++||+|...+..|..+ + ++.+ + |++.++++||..
T Consensus 525 k~~~~s~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~As~e---------e-l~~v--g-i~~~~a~~i~~~ 580 (581)
T COG0322 525 KAMLQSSLDDIPGIGPKRRKALLKHFGSLKGIKSASVE---------E-LAKV--G-ISKKLAEKIYEA 580 (581)
T ss_pred hhhhcCccccCCCcCHHHHHHHHHHhhCHHHHHhcCHH---------H-HHHc--C-CCHHHHHHHHhh
Confidence 34444557899999999999999999999999977532 2 2222 3 889999999863
No 85
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=65.08 E-value=5.7 Score=41.18 Aligned_cols=31 Identities=32% Similarity=0.468 Sum_probs=28.0
Q ss_pred hhHHHHhcCcEeeecCCCceecChhHHHHHHH
Q 006771 187 CMKTLITKGLVVKSSCPAKYMLTPGGREAARE 218 (632)
Q Consensus 187 SmktLi~k~LV~~~grP~rY~LTdeG~elA~~ 218 (632)
-||.|++-|||-++|| .+|.+|++|.|...+
T Consensus 45 hiK~Lv~eG~i~~~gR-~~Y~iTkkG~e~l~~ 75 (260)
T COG1497 45 HIKELVKEGLIEKEGR-GEYEITKKGAEWLLE 75 (260)
T ss_pred HHHHHHhccceeecCC-eeEEEehhHHHHHHH
Confidence 4899999999999998 699999999998764
No 86
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=64.91 E-value=6 Score=41.51 Aligned_cols=61 Identities=25% Similarity=0.278 Sum_probs=45.8
Q ss_pred HHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecCCCce
Q 006771 127 ALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCPAKY 206 (632)
Q Consensus 127 AiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~grP~rY 206 (632)
.||+.|-. +..|=+||.+.-...+ + +-=..+|-|+..|||.+.|+ .|
T Consensus 17 ~lLllL~e------gPkti~EI~~~l~vs~--------------------~-----ai~pqiKkL~~~~LV~~~~~--~Y 63 (260)
T COG4742 17 DLLLLLKE------GPKTIEEIKNELNVSS--------------------S-----AILPQIKKLKDKGLVVQEGD--RY 63 (260)
T ss_pred HHHHHHHh------CCCCHHHHHHHhCCCc--------------------H-----HHHHHHHHHhhCCCEEecCC--EE
Confidence 67777733 3578888888532211 0 23456899999999999987 89
Q ss_pred ecChhHHHHHHHHH
Q 006771 207 MLTPGGREAARECL 220 (632)
Q Consensus 207 ~LTdeG~elA~~l~ 220 (632)
.||+.|.-++.++.
T Consensus 64 ~LS~~G~iiv~km~ 77 (260)
T COG4742 64 SLSSLGKIIVEKME 77 (260)
T ss_pred EecchHHHHHHHHH
Confidence 99999999999876
No 87
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=64.71 E-value=6.6 Score=36.34 Aligned_cols=32 Identities=9% Similarity=0.200 Sum_probs=25.0
Q ss_pred cccchHHHHHHHhcCCCCCHHHHHHHHHhcCC
Q 006771 556 KMTVSDVFAVQLMQVPQVTEEIAITVLDLYPT 587 (632)
Q Consensus 556 ~~Tv~e~f~~mLm~IpGVs~ekA~~I~~~ypT 587 (632)
.+.+...-...|+.|||||+.+|..|++.+.+
T Consensus 59 ~iniNtA~~~eL~~lpGIG~~~A~~Ii~~R~~ 90 (120)
T TIGR01259 59 AVNINAASLEELQALPGIGPAKAKAIIEYREE 90 (120)
T ss_pred CEeCCcCCHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 34444455668999999999999999998643
No 88
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=64.67 E-value=9.1 Score=45.31 Aligned_cols=51 Identities=24% Similarity=0.258 Sum_probs=38.2
Q ss_pred HhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhh
Q 006771 567 LMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 567 Lm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~v 629 (632)
.+.|||||...|..|.++|+|+..|.+|- .+++..- .-||+..+++|+.+|
T Consensus 500 aLgIpgVG~~~ak~L~~~f~sl~~l~~As---------~eeL~~i---~GIG~~~A~~I~~ff 550 (652)
T TIGR00575 500 ALGIRHVGEVTAKNLAKHFGTLDKLKAAS---------LEELLSV---EGVGPKVAESIVNFF 550 (652)
T ss_pred hccCCCcCHHHHHHHHHHhCCHHHHHhCC---------HHHHhcC---CCcCHHHHHHHHHHH
Confidence 44899999999999999999999988652 1133221 228888888888754
No 89
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=64.54 E-value=3.3 Score=41.44 Aligned_cols=30 Identities=30% Similarity=0.320 Sum_probs=27.5
Q ss_pred ccchhhHHHHhcCcEeeec-CCCceecChhH
Q 006771 183 SGWSCMKTLITKGLVVKSS-CPAKYMLTPGG 212 (632)
Q Consensus 183 taWsSmktLi~k~LV~~~g-rP~rY~LTdeG 212 (632)
|.+.-++.|.++|||.+.+ |+.+|.||+.|
T Consensus 173 tv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G 203 (203)
T TIGR01884 173 TISRHLRELEKKGLVEQKGRKGKRYSLTKLG 203 (203)
T ss_pred HHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence 6889999999999999887 88899999987
No 90
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=64.28 E-value=9.3 Score=36.10 Aligned_cols=33 Identities=12% Similarity=0.291 Sum_probs=27.8
Q ss_pred CCCCCChhhhhccccchHHHHHHHHHHhhcCCC
Q 006771 60 KNPIKTLKDLSQVKGVGKWILKLMQEFFETDSG 92 (632)
Q Consensus 60 p~~~~~~k~l~~lkG~G~~i~~~L~~~~~~~~~ 92 (632)
-.||++..|+.+|+|||++..+.|++|...--.
T Consensus 80 nGpf~sveDL~~V~GIgekqk~~l~k~~~~ftV 112 (132)
T PRK02515 80 NAPYDSVEDVLNLPGLSERQKELLEANLDNFTV 112 (132)
T ss_pred CCCCCCHHHHHcCCCCCHHHHHHHHHhhcceee
Confidence 679999999999999999988888887654433
No 91
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=64.10 E-value=8.1 Score=45.82 Aligned_cols=49 Identities=20% Similarity=0.269 Sum_probs=37.6
Q ss_pred cCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhh
Q 006771 569 QVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 569 ~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~v 629 (632)
.|||||...|..|+++|+|+..|.+|- .+++..- .=||+..+++|+.+|
T Consensus 515 gi~~IG~~~ak~L~~~f~sl~~l~~As---------~eeL~~i---~GIG~~~A~sI~~ff 563 (665)
T PRK07956 515 GIRHVGEKAAKALARHFGSLEALRAAS---------EEELAAV---EGVGEVVAQSIVEFF 563 (665)
T ss_pred hccCcCHHHHHHHHHHcCCHHHHHhCC---------HHHHhcc---CCcCHHHHHHHHHHH
Confidence 899999999999999999999988652 1233322 228888999888754
No 92
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=64.00 E-value=8 Score=45.77 Aligned_cols=52 Identities=15% Similarity=0.225 Sum_probs=39.6
Q ss_pred HHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhh
Q 006771 565 VQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQL 628 (632)
Q Consensus 565 ~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~ 628 (632)
-.|-.|||||+.++.+|+++|+|+..+..|-.+ ++.+- .-||+.++++|+..
T Consensus 608 s~L~~IpGiG~kr~~~LL~~FgS~~~i~~As~e---------el~~v---~gi~~~~A~~i~~~ 659 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAHFGSFRSLQSATPQ---------DIATA---IHIPLTQAHTILHA 659 (691)
T ss_pred cccccCCCCCHHHHHHHHHHhcCHHHHHhCCHH---------HHHhC---CCCCHHHHHHHHHH
Confidence 357799999999999999999999999977521 22221 12788888888863
No 93
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=62.47 E-value=11 Score=44.82 Aligned_cols=62 Identities=15% Similarity=0.202 Sum_probs=42.7
Q ss_pred cccccchHHHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhh
Q 006771 554 LDKMTVSDVFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 554 ~~~~Tv~e~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~v 629 (632)
++..++..+ + .=+.|||||...|..|.++|+|+..|.+|- .+++..- .-||+..++.|+++|
T Consensus 519 sk~~~l~r~-l-~ALgIpgIG~~~ak~L~~~F~si~~L~~As---------~eeL~~i---~GIG~k~A~sI~~ff 580 (689)
T PRK14351 519 SREPPLADF-L-VALGIPEVGPTTARNLAREFGTFEAIMDAD---------EEALRAV---DDVGPTVAEEIREFF 580 (689)
T ss_pred HccCCHHHH-H-HHcCCCCcCHHHHHHHHHHhCCHHHHHhCC---------HHHHhcc---CCcCHHHHHHHHHHH
Confidence 345555543 2 235899999999999999999999888753 1222221 228888888888743
No 94
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=60.53 E-value=11 Score=36.56 Aligned_cols=36 Identities=36% Similarity=0.418 Sum_probs=28.7
Q ss_pred hhhHHHHhcCcEeeecCCCceecChhHHHHHHHHHhh
Q 006771 186 SCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLSR 222 (632)
Q Consensus 186 sSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~~ 222 (632)
.-++-|.+.|||-...+ ..|.|||.|.++|..+...
T Consensus 43 ~ml~rL~~~GlV~~~~y-~gi~LT~~G~~~a~~~~r~ 78 (154)
T COG1321 43 EMLKRLERLGLVEYEPY-GGVTLTEKGREKAKELLRK 78 (154)
T ss_pred HHHHHHHHCCCeEEecC-CCeEEChhhHHHHHHHHHH
Confidence 34578899999976544 3799999999999987654
No 95
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include 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 model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=60.44 E-value=11 Score=31.09 Aligned_cols=28 Identities=32% Similarity=0.533 Sum_probs=25.0
Q ss_pred CCCCCChhhhhccccchHHHHHHHHHHh
Q 006771 60 KNPIKTLKDLSQVKGVGKWILKLMQEFF 87 (632)
Q Consensus 60 p~~~~~~k~l~~lkG~G~~i~~~L~~~~ 87 (632)
-.+|+++.|+.++.|||+++.++|..|.
T Consensus 40 ~g~~~s~~dL~~v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 40 YGPFKTVEDLKQVPGIGNSLVEKNLAVI 67 (69)
T ss_pred cCCcCCHHHHHcCCCCCHHHHHHHHhhc
Confidence 4589999999999999999999998764
No 96
>PRK07758 hypothetical protein; Provisional
Probab=58.80 E-value=9 Score=34.23 Aligned_cols=43 Identities=14% Similarity=0.136 Sum_probs=34.0
Q ss_pred HHHHHHHhccCC------CCCChhhhhccccchHHHHHHHHHHhhcCCC
Q 006771 50 SKAYNNICDAKN------PIKTLKDLSQVKGVGKWILKLMQEFFETDSG 92 (632)
Q Consensus 50 ~kA~~sl~~~p~------~~~~~k~l~~lkG~G~~i~~~L~~~~~~~~~ 92 (632)
.+|++.|+++.+ .=.+..||.+|+|||++-++.|++.+.+.|+
T Consensus 44 vRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIkekL~E~GL 92 (95)
T PRK07758 44 APARRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKALEESGL 92 (95)
T ss_pred HHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHHHHcCC
Confidence 456777766543 3467788999999999999999998888775
No 97
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=58.78 E-value=7.9 Score=39.92 Aligned_cols=29 Identities=14% Similarity=0.195 Sum_probs=27.2
Q ss_pred HHhcCCCCCHHHHHHHHHh-cCCHHHHHHH
Q 006771 566 QLMQVPQVTEEIAITVLDL-YPTLLSLAHA 594 (632)
Q Consensus 566 mLm~IpGVs~ekA~~I~~~-ypTp~~L~~A 594 (632)
.|..|||||..+|..|+++ |.|+.+|..|
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 4789999999999999999 9999999887
No 98
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=58.74 E-value=10 Score=44.12 Aligned_cols=34 Identities=21% Similarity=0.371 Sum_probs=30.0
Q ss_pred HHHHHHhcCCCCCHHHHHHHHHhcCCHHHHHHHH
Q 006771 562 VFAVQLMQVPQVTEEIAITVLDLYPTLLSLAHAY 595 (632)
Q Consensus 562 ~f~~mLm~IpGVs~ekA~~I~~~ypTp~~L~~Ay 595 (632)
++.-.|..|||||+.+..+|+++|+|+..+.+|-
T Consensus 538 ~~~S~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~As 571 (574)
T TIGR00194 538 SLQSPLLKIPGVGEKRVQKLLKYFGSLKGIKKAS 571 (574)
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHcCCHHHHHhCC
Confidence 3445688999999999999999999999998774
No 99
>PRK00254 ski2-like helicase; Provisional
Probab=56.87 E-value=13 Score=44.30 Aligned_cols=51 Identities=20% Similarity=0.376 Sum_probs=38.8
Q ss_pred HHhcCCCCCHHHHHHHHHh-cCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhh
Q 006771 566 QLMQVPQVTEEIAITVLDL-YPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQL 628 (632)
Q Consensus 566 mLm~IpGVs~ekA~~I~~~-ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~ 628 (632)
-|.+||||+.++|..+.++ |.|+.++..|- .+++.+- .-||+.++++|++.
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s~~~i~~a~---------~~el~~~---~gi~~~~a~~i~~~ 697 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRSIEDIVNAK---------PSELLKV---EGIGAKIVEGIFKH 697 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCCHHHHHhCC---------HHHHhcC---CCCCHHHHHHHHHH
Confidence 4679999999999999999 99999999643 1233222 12888888888874
No 100
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=56.60 E-value=8.5 Score=30.46 Aligned_cols=38 Identities=24% Similarity=0.118 Sum_probs=30.0
Q ss_pred ccchhhHHHHhcCcEeee--cCCCceecChhHHHHHHHHHh
Q 006771 183 SGWSCMKTLITKGLVVKS--SCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 183 taWsSmktLi~k~LV~~~--grP~rY~LTdeG~elA~~l~~ 221 (632)
+....++.|.++|++... +++..|.+|+ |.++...+..
T Consensus 36 ~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~~~ 75 (78)
T cd00090 36 TVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALLES 75 (78)
T ss_pred HHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHHHH
Confidence 577889999999999865 3335799998 8888887653
No 101
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=55.18 E-value=6.2 Score=34.14 Aligned_cols=27 Identities=19% Similarity=0.187 Sum_probs=21.2
Q ss_pred HHHhcCCCCCHHHHHHHHHhcCCHHHH
Q 006771 565 VQLMQVPQVTEEIAITVLDLYPTLLSL 591 (632)
Q Consensus 565 ~mLm~IpGVs~ekA~~I~~~ypTp~~L 591 (632)
..|++||||+.-.|..|+...+.+..|
T Consensus 2 ~~l~sipGig~~~a~~llaeigd~~rF 28 (87)
T PF02371_consen 2 ELLTSIPGIGPITAATLLAEIGDISRF 28 (87)
T ss_pred chhcCCCCccHHHHHHHHHHHcCchhc
Confidence 358999999999999999755555444
No 102
>PTZ00217 flap endonuclease-1; Provisional
Probab=52.93 E-value=15 Score=40.93 Aligned_cols=29 Identities=7% Similarity=0.196 Sum_probs=27.0
Q ss_pred cCCCCCHHHHHHHHHhcCCHHHHHHHHhh
Q 006771 569 QVPQVTEEIAITVLDLYPTLLSLAHAYSI 597 (632)
Q Consensus 569 ~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~ 597 (632)
.|||||+.+|..|++.|+++..+++..+.
T Consensus 239 gi~GIG~ktA~~Li~~~gsle~il~~~~~ 267 (393)
T PTZ00217 239 TIKGIGPKTAYKLIKKYKSIEEILEHLDK 267 (393)
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHHHHh
Confidence 69999999999999999999999988765
No 103
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=52.81 E-value=26 Score=28.23 Aligned_cols=57 Identities=21% Similarity=0.327 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHH
Q 006771 22 ELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKL 82 (632)
Q Consensus 22 ~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~ 82 (632)
.++.=+.+|+++.+... +.. .....=..++..|... .| .+..++.++.|+|++.+++
T Consensus 3 ~~~~~L~~~R~~~A~~~-~~~-~~~Il~~~~L~~ia~~-~P-~s~~~L~~i~g~~~~~~~~ 59 (68)
T PF00570_consen 3 ALLKALKEWREELAREE-DVP-PYRILSDEALLEIAKR-LP-TSIEELLQIPGMGKRKVRK 59 (68)
T ss_dssp HHHHHHHHHHHHHHHHH-TS--HHHHS-HHHHHHHHHH----SSHHHHHTSTTCGHHHHHH
T ss_pred HHHHHHHHHHHHHHHHc-CcC-cccccCHHHHHHHHHh-CC-CCHHHHHHccCCCHHHHHH
Confidence 46677899999999742 332 3333446778888765 23 5899999999999998886
No 104
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include 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 model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=52.64 E-value=15 Score=30.27 Aligned_cols=21 Identities=19% Similarity=0.172 Sum_probs=18.3
Q ss_pred HHHHhc-CCCCCHHHHHHHHHh
Q 006771 564 AVQLMQ-VPQVTEEIAITVLDL 584 (632)
Q Consensus 564 ~~mLm~-IpGVs~ekA~~I~~~ 584 (632)
...|.. +||||...|.+|+++
T Consensus 15 ~~~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 15 AEELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHHHhHCCCCCHHHHHHHHHH
Confidence 346777 999999999999998
No 105
>PRK03980 flap endonuclease-1; Provisional
Probab=52.11 E-value=14 Score=39.49 Aligned_cols=27 Identities=7% Similarity=0.096 Sum_probs=25.1
Q ss_pred cCCCCCHHHHHHHHHhcCCHHHHHHHH
Q 006771 569 QVPQVTEEIAITVLDLYPTLLSLAHAY 595 (632)
Q Consensus 569 ~IpGVs~ekA~~I~~~ypTp~~L~~Ay 595 (632)
.|||||+.+|..|++.|+|+..+++..
T Consensus 193 GI~GIG~ktA~kLi~~~~sle~i~~~~ 219 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHGDLEKVLEER 219 (292)
T ss_pred CCCCccHHHHHHHHHHCCCHHHHHHhc
Confidence 689999999999999999999999854
No 106
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=52.08 E-value=12 Score=27.36 Aligned_cols=18 Identities=17% Similarity=0.253 Sum_probs=16.2
Q ss_pred hcCCCCCHHHHHHHHHhc
Q 006771 568 MQVPQVTEEIAITVLDLY 585 (632)
Q Consensus 568 m~IpGVs~ekA~~I~~~y 585 (632)
-.||||++..|..++++|
T Consensus 19 ~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 19 PGVKGIGPKTALKLLREF 36 (36)
T ss_pred CCCCcccHHHHHHHHHhC
Confidence 379999999999999987
No 107
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=52.03 E-value=16 Score=32.69 Aligned_cols=39 Identities=18% Similarity=0.225 Sum_probs=30.6
Q ss_pred ccchhhHHHHhc---CcEeeecC---CCceecChhHHHHHHHHHh
Q 006771 183 SGWSCMKTLITK---GLVVKSSC---PAKYMLTPGGREAARECLS 221 (632)
Q Consensus 183 taWsSmktLi~k---~LV~~~gr---P~rY~LTdeG~elA~~l~~ 221 (632)
+.|..|+.|.+. -|+.+..+ +..+.||++|.+++..+..
T Consensus 32 tvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~~~~~~ 76 (99)
T TIGR00637 32 SAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLIQLYDL 76 (99)
T ss_pred HHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHHHHHHH
Confidence 689999999754 67777643 6689999999999766543
No 108
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=51.95 E-value=6.5 Score=32.07 Aligned_cols=45 Identities=20% Similarity=0.312 Sum_probs=34.2
Q ss_pred CCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeee-cCCCceecCh
Q 006771 141 EFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKS-SCPAKYMLTP 210 (632)
Q Consensus 141 ~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~-grP~rY~LTd 210 (632)
+.+|-+||.+...- +. -+....++.|.++|||.+. |+|..|..+|
T Consensus 21 ~~~t~~eIa~~l~i--------~~-----------------~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~~ 66 (68)
T PF01978_consen 21 GPATAEEIAEELGI--------SR-----------------STVYRALKSLEEKGLVEREEGRPKVYRAVP 66 (68)
T ss_dssp CHEEHHHHHHHHTS--------SH-----------------HHHHHHHHHHHHTTSEEEEEECCEEEEEE-
T ss_pred CCCCHHHHHHHHCc--------CH-----------------HHHHHHHHHHHHCCCEEEEcCceEEEEEeC
Confidence 56888888876432 11 3789999999999999875 7888898654
No 109
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=51.58 E-value=7.2 Score=31.52 Aligned_cols=31 Identities=23% Similarity=0.353 Sum_probs=23.5
Q ss_pred ccccchh-hHHHHhcCcEeeecCCCceecChhHH
Q 006771 181 WYSGWSC-MKTLITKGLVVKSSCPAKYMLTPGGR 213 (632)
Q Consensus 181 fYtaWsS-mktLi~k~LV~~~grP~rY~LTdeG~ 213 (632)
|...|.. ++.|++.|||...++ ++.||++|+
T Consensus 34 ~~~~~~~~l~~l~~~Gll~~~~~--~l~lT~~G~ 65 (66)
T PF06969_consen 34 FAEEFQKELEELQEDGLLEIDGG--RLRLTEKGR 65 (66)
T ss_dssp THHH-HHHHHHHHHTTSEEE-SS--EEEE-TTTG
T ss_pred HHHHHHHHHHHHHHCCCEEEeCC--EEEECcccC
Confidence 4456666 789999999998886 899999996
No 110
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=51.31 E-value=0.55 Score=42.33 Aligned_cols=34 Identities=21% Similarity=0.352 Sum_probs=26.0
Q ss_pred HhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccc
Q 006771 567 LMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEG 600 (632)
Q Consensus 567 Lm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~ 600 (632)
+-.|||||+..|..++++|+|+..++.+.+....
T Consensus 20 IPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~~~ 53 (101)
T PF01367_consen 20 IPGVPGIGPKTAAKLLQEYGSLENILANLDEIKG 53 (101)
T ss_dssp B---TTSTCHCCCCCHHHHTSCHCCCCC-SSS-T
T ss_pred CCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhccc
Confidence 3479999999999999999999999987766643
No 111
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=51.29 E-value=9 Score=39.25 Aligned_cols=31 Identities=39% Similarity=0.461 Sum_probs=25.5
Q ss_pred cchhhHHHHhcCcEe------eecCCC-ceecChhHHH
Q 006771 184 GWSCMKTLITKGLVV------KSSCPA-KYMLTPGGRE 214 (632)
Q Consensus 184 aWsSmktLi~k~LV~------~~grP~-rY~LTdeG~e 214 (632)
+=-=|..|+.+|||. ..|||+ .|.||+.|.+
T Consensus 42 vR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 42 VRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred HHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence 344588999999996 249998 5999999988
No 112
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=49.74 E-value=26 Score=37.23 Aligned_cols=47 Identities=19% Similarity=0.369 Sum_probs=32.9
Q ss_pred CCchhHHHHHHHHHHHHhccCCCCCC-------hhhhhccccchHHHHHHHHHH
Q 006771 40 GLSENIDMTLSKAYNNICDAKNPIKT-------LKDLSQVKGVGKWILKLMQEF 86 (632)
Q Consensus 40 g~~~~~~~ty~kA~~sl~~~p~~~~~-------~k~l~~lkG~G~~i~~~L~~~ 86 (632)
|.+.+-+.+...+.+.+.+-.+++.. .++|.+|+|||+|+++.+--+
T Consensus 173 Gl~~~Ra~~L~~lA~~i~~g~l~l~~~~~~~~~~~~L~~LpGIGpwTA~~vllr 226 (283)
T PRK10308 173 GMPLKRAEALIHLANAALEGTLPLTIPGDVEQAMKTLQTFPGIGRWTANYFALR 226 (283)
T ss_pred CCCHHHHHHHHHHHHHHHcCCCCccccCCHHHHHHHHhcCCCcCHHHHHHHHHH
Confidence 55544455666677777665666542 468999999999999986544
No 113
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=49.71 E-value=18 Score=37.02 Aligned_cols=38 Identities=16% Similarity=0.239 Sum_probs=30.5
Q ss_pred ccchhhHHHHhcCcEeeecCCC--ceecChhHHHHHHHHH
Q 006771 183 SGWSCMKTLITKGLVVKSSCPA--KYMLTPGGREAARECL 220 (632)
Q Consensus 183 taWsSmktLi~k~LV~~~grP~--rY~LTdeG~elA~~l~ 220 (632)
|+=.-++.|.++|||.+...|. .+.||+.|.++.+++.
T Consensus 37 Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~ 76 (217)
T PRK14165 37 TAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEY 76 (217)
T ss_pred HHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHH
Confidence 3445678999999999886653 6999999999987654
No 114
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=49.57 E-value=17 Score=37.66 Aligned_cols=39 Identities=21% Similarity=0.210 Sum_probs=34.1
Q ss_pred ccchhhHHHHhcCcEeeecCCCceecChhHHHHHHHHHh
Q 006771 183 SGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 183 taWsSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~ 221 (632)
|.-.-++||.++|||.+...+.+|.||..+++++..+..
T Consensus 42 tv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~~~l~~~~~~ 80 (263)
T PRK09834 42 TVRRLLETLQEEGYVRRSASDDSFRLTLKVRQLSEGFRD 80 (263)
T ss_pred HHHHHHHHHHHCCCEEEecCCCcEEEcHHHHHHHHhhhc
Confidence 566778999999999998888899999999999987654
No 115
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=47.91 E-value=26 Score=29.71 Aligned_cols=68 Identities=21% Similarity=0.208 Sum_probs=48.5
Q ss_pred HHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecCCCc
Q 006771 126 YALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCPAK 205 (632)
Q Consensus 126 YAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~grP~r 205 (632)
..||-.|... ...++-.||.+... ++. =|...-+++|.++|+|.+.+.-.+
T Consensus 8 ~~Il~~l~~~----~~~~t~~~ia~~l~--------i~~-----------------~tv~r~l~~L~~~g~l~~~~~~~~ 58 (91)
T smart00346 8 LAVLRALAEE----PGGLTLAELAERLG--------LSK-----------------STAHRLLNTLQELGYVEQDGQNGR 58 (91)
T ss_pred HHHHHHHHhC----CCCcCHHHHHHHhC--------CCH-----------------HHHHHHHHHHHHCCCeeecCCCCc
Confidence 4455555432 24688888887642 221 167888999999999988654457
Q ss_pred eecChhHHHHHHHHHhh
Q 006771 206 YMLTPGGREAARECLSR 222 (632)
Q Consensus 206 Y~LTdeG~elA~~l~~~ 222 (632)
|.|+...++++......
T Consensus 59 y~l~~~~~~~~~~~~~~ 75 (91)
T smart00346 59 YRLGPKVLELGQSYLSS 75 (91)
T ss_pred eeecHHHHHHHHHHHhc
Confidence 99999999999987643
No 116
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=47.04 E-value=27 Score=42.91 Aligned_cols=32 Identities=16% Similarity=0.245 Sum_probs=29.1
Q ss_pred cCCCCCHHHHHHHHHhcCCHHHHHHHHhhccc
Q 006771 569 QVPQVTEEIAITVLDLYPTLLSLAHAYSILEG 600 (632)
Q Consensus 569 ~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~ 600 (632)
.|||||+..|..|++.|+|+..++...+++.+
T Consensus 189 GVpGIG~KtA~kLL~~ygsle~i~~~~~~i~~ 220 (887)
T TIGR00593 189 GVKGIGEKTAAKLLQEFGSLENIYENLDQIKS 220 (887)
T ss_pred CCCCcCHHHHHHHHHHcCCHHHHHHHHHHhcc
Confidence 59999999999999999999999998887743
No 117
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=47.02 E-value=15 Score=41.81 Aligned_cols=33 Identities=33% Similarity=0.368 Sum_probs=26.9
Q ss_pred hhhHHHHhcCcEeeecCC-CceecChhHHHHHHH
Q 006771 186 SCMKTLITKGLVVKSSCP-AKYMLTPGGREAARE 218 (632)
Q Consensus 186 sSmktLi~k~LV~~~grP-~rY~LTdeG~elA~~ 218 (632)
..++.|.+||||...-+- ..|.||++|+++++.
T Consensus 39 ~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~~~ 72 (489)
T PRK04172 39 RAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAEE 72 (489)
T ss_pred HHHHHHHhCCCEEEEeeeEEEEEECHHHHHHHHh
Confidence 347899999999976542 359999999999984
No 118
>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=46.65 E-value=19 Score=39.20 Aligned_cols=28 Identities=14% Similarity=0.124 Sum_probs=25.9
Q ss_pred cCCCCCHHHHHHHHHhcCCHHHHHHHHh
Q 006771 569 QVPQVTEEIAITVLDLYPTLLSLAHAYS 596 (632)
Q Consensus 569 ~IpGVs~ekA~~I~~~ypTp~~L~~Ay~ 596 (632)
.|||||+.+|..|++.|+|+..+++..+
T Consensus 240 Gv~GIG~ktA~kli~~~gsie~il~~~~ 267 (338)
T TIGR03674 240 GVKGIGPKTALKLIKEHGDLEKVLKARG 267 (338)
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHhhc
Confidence 7999999999999999999999998743
No 119
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=46.32 E-value=18 Score=42.64 Aligned_cols=51 Identities=22% Similarity=0.247 Sum_probs=38.3
Q ss_pred HhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhh
Q 006771 567 LMQVPQVTEEIAITVLDLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 567 Lm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~v 629 (632)
=+.||.|+...|..|.++|+|+..|+.|-.+ + |.. ... ||..+++.|+.+|
T Consensus 513 aLGIr~VG~~~Ak~La~~f~sl~~l~~a~~e---------~-l~~-i~g-iG~~vA~si~~ff 563 (667)
T COG0272 513 ALGIRHVGETTAKSLARHFGTLEALLAASEE---------E-LAS-IPG-IGEVVARSIIEFF 563 (667)
T ss_pred HcCCchhhHHHHHHHHHHhhhHHHHHhcCHH---------H-Hhh-ccc-hhHHHHHHHHHHH
Confidence 4589999999999999999999999977422 1 111 122 8888888888743
No 120
>PRK05755 DNA polymerase I; Provisional
Probab=46.23 E-value=25 Score=43.05 Aligned_cols=33 Identities=24% Similarity=0.347 Sum_probs=29.5
Q ss_pred HhcCCCCCHHHHHHHHHhcCCHHHHHHHHhhcc
Q 006771 567 LMQVPQVTEEIAITVLDLYPTLLSLAHAYSILE 599 (632)
Q Consensus 567 Lm~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~~~ 599 (632)
+-.|||||+..|..|+++|+|+..++++..++.
T Consensus 189 ipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~ 221 (880)
T PRK05755 189 IPGVPGIGEKTAAKLLQEYGSLEGLYENLDEIK 221 (880)
T ss_pred CCCCCCccHHHHHHHHHHcCCHHHHHHhHHHhc
Confidence 347999999999999999999999999887764
No 121
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=45.85 E-value=21 Score=27.35 Aligned_cols=36 Identities=25% Similarity=0.176 Sum_probs=28.9
Q ss_pred ccchhhHHHHhcCcEeee--cCCCceecCh-hHHHHHHH
Q 006771 183 SGWSCMKTLITKGLVVKS--SCPAKYMLTP-GGREAARE 218 (632)
Q Consensus 183 taWsSmktLi~k~LV~~~--grP~rY~LTd-eG~elA~~ 218 (632)
+.|.-++.|.++|+|... |+...|.+|+ .|.++...
T Consensus 26 ~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~ 64 (66)
T smart00418 26 TVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLEE 64 (66)
T ss_pred HHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence 689999999999999854 4445799999 88776654
No 122
>KOG3344 consensus 40s ribosomal protein s10 [Translation, ribosomal structure and biogenesis]
Probab=45.84 E-value=8.8 Score=36.42 Aligned_cols=34 Identities=29% Similarity=0.362 Sum_probs=25.8
Q ss_pred hhhHHHHhcCcEeeecC--CCceecChhHHHHHHHH
Q 006771 186 SCMKTLITKGLVVKSSC--PAKYMLTPGGREAAREC 219 (632)
Q Consensus 186 sSmktLi~k~LV~~~gr--P~rY~LTdeG~elA~~l 219 (632)
..|++|+++|+|-+.-. =--|.||.||.+--+.-
T Consensus 44 kaMQSl~SrgYvkeqfaWrH~Yw~LTneGi~yLR~Y 79 (150)
T KOG3344|consen 44 KAMQSLKSRGYVKEQFAWRHFYWYLTNEGIEYLREY 79 (150)
T ss_pred HHHHHHhhhhhHHhhhhhheeeeeechhHHHHHHHH
Confidence 56999999999976532 13689999999865543
No 123
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=45.81 E-value=11 Score=30.84 Aligned_cols=21 Identities=19% Similarity=0.362 Sum_probs=16.6
Q ss_pred HHHHhcCCCCCHHHHHHHHHh
Q 006771 564 AVQLMQVPQVTEEIAITVLDL 584 (632)
Q Consensus 564 ~~mLm~IpGVs~ekA~~I~~~ 584 (632)
...|+++||+|...|.+|++.
T Consensus 13 ~~eL~~lpgi~~~~A~~Iv~~ 33 (65)
T PF12836_consen 13 AEELQALPGIGPKQAKAIVEY 33 (65)
T ss_dssp HHHHHTSTT--HHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHH
Confidence 456999999999999999974
No 124
>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=44.98 E-value=23 Score=37.90 Aligned_cols=29 Identities=10% Similarity=0.178 Sum_probs=25.4
Q ss_pred cCCCCCHHHHHHHHHhcCCHHHHHHHHhh
Q 006771 569 QVPQVTEEIAITVLDLYPTLLSLAHAYSI 597 (632)
Q Consensus 569 ~IpGVs~ekA~~I~~~ypTp~~L~~Ay~~ 597 (632)
.|||||+.+|..|++.|+++...++.+..
T Consensus 227 gv~giG~k~A~~li~~~~~~~~~~~~l~~ 255 (316)
T cd00128 227 GIPGIGPVTALKLIKKYGDIEKDIERLKK 255 (316)
T ss_pred CCCCccHHHHHHHHHHcCChHHHHHHHHH
Confidence 79999999999999999998887776643
No 125
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=44.19 E-value=27 Score=33.65 Aligned_cols=29 Identities=24% Similarity=0.393 Sum_probs=21.9
Q ss_pred HHHHhcCCCCCHHHHHHHHH------hcCCHHHHH
Q 006771 564 AVQLMQVPQVTEEIAITVLD------LYPTLLSLA 592 (632)
Q Consensus 564 ~~mLm~IpGVs~ekA~~I~~------~ypTp~~L~ 592 (632)
...|..+||||+.+|.+|++ .|.++.+|.
T Consensus 96 ~eeL~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~ 130 (149)
T COG1555 96 AEELQALPGIGPKKAQAIIDYREENGPFKSVDDLA 130 (149)
T ss_pred HHHHHHCCCCCHHHHHHHHHHHHHcCCCCcHHHHH
Confidence 44578999999999999996 345555544
No 126
>KOG2379 consensus Endonuclease MUS81 [Replication, recombination and repair]
Probab=43.88 E-value=18 Score=41.22 Aligned_cols=46 Identities=13% Similarity=0.131 Sum_probs=36.4
Q ss_pred ccCCCcccccCCCchHHHHHHHHHhcCC------CCCCCCCHHHH--HHHHHhc
Q 006771 110 KTKGTKRYMPQRNSVAYALLITLYRGTT------NGNEFMRKQDL--IDAAEAS 155 (632)
Q Consensus 110 k~r~~k~YvP~~rSGaYAiLlaL~~~~~------~~~~~mtK~eL--i~~Aq~~ 155 (632)
+.|+-..|++.+-+|+|-.++.++...+ .|+..++++|. +..++.+
T Consensus 61 ~ikG~G~~~~~k~~~~~~~~~~~~~e~~~~~~n~~gk~~~~~ee~~~~R~s~~~ 114 (501)
T KOG2379|consen 61 SIKGFGKKWIVKLMEAYSVLCVENNEQLSLPTNRSGKKALDDEEYRPQRYSVED 114 (501)
T ss_pred cccCccchhHHHHHhHHHHHhhccccccccccccccccccccchhhhhhhhhcc
Confidence 6778888999999999999999997765 36777878877 4555554
No 127
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=43.60 E-value=29 Score=31.81 Aligned_cols=66 Identities=21% Similarity=0.165 Sum_probs=47.9
Q ss_pred HHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeee-cCC
Q 006771 125 AYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKS-SCP 203 (632)
Q Consensus 125 aYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~-grP 203 (632)
-|||.+-+|-....+...++-+||-+. .+ +++ -+.+.-+.+|.+.|||... |..
T Consensus 8 ~~al~~l~~la~~~~~~~~s~~eia~~---~~-----i~~-----------------~~v~~il~~L~~~gli~~~~g~~ 62 (132)
T TIGR00738 8 EYALRALLDLALNPDEGPVSVKEIAER---QG-----ISR-----------------SYLEKILRTLRRAGLVESVRGPG 62 (132)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHH---HC-----cCH-----------------HHHHHHHHHHHHCCcEEeccCCC
Confidence 477777776654455567888888653 22 332 2679999999999999764 665
Q ss_pred CceecChhHHHH
Q 006771 204 AKYMLTPGGREA 215 (632)
Q Consensus 204 ~rY~LTdeG~el 215 (632)
-.|.|+....++
T Consensus 63 ggy~l~~~~~~i 74 (132)
T TIGR00738 63 GGYRLARPPEEI 74 (132)
T ss_pred CCccCCCCHHHC
Confidence 579999888876
No 128
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=41.99 E-value=48 Score=31.34 Aligned_cols=44 Identities=16% Similarity=0.200 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHHHhccCCCC-----CChhhhhccccchHHHHHHHHHHh
Q 006771 44 NIDMTLSKAYNNICDAKNPI-----KTLKDLSQVKGVGKWILKLMQEFF 87 (632)
Q Consensus 44 ~~~~ty~kA~~sl~~~p~~~-----~~~k~l~~lkG~G~~i~~~L~~~~ 87 (632)
+-+.+...+.+.+.+..+.+ .--++|.+|+|||+|++..+--|+
T Consensus 55 ~kA~~i~~~a~~~~~~~~~~~~~~~~~~~~L~~l~GIG~~tA~~~l~~~ 103 (158)
T cd00056 55 RKAKYLKELARAIVEGFGGLVLDDPDAREELLALPGVGRKTANVVLLFA 103 (158)
T ss_pred HHHHHHHHHHHHHHHHcCCccCCCcccHHHHHcCCCCCHHHHHHHHHHH
Confidence 34445555555554433332 356788999999999999976554
No 129
>PRK05638 threonine synthase; Validated
Probab=40.94 E-value=20 Score=40.25 Aligned_cols=36 Identities=25% Similarity=0.333 Sum_probs=29.0
Q ss_pred ccchhhHHHHhcCcEee---ecCCCceecChhHHHHHHH
Q 006771 183 SGWSCMKTLITKGLVVK---SSCPAKYMLTPGGREAARE 218 (632)
Q Consensus 183 taWsSmktLi~k~LV~~---~grP~rY~LTdeG~elA~~ 218 (632)
+.+.-++.|.+.|||.. +|+...|.||++|+++...
T Consensus 402 ~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~ 440 (442)
T PRK05638 402 AVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLEN 440 (442)
T ss_pred hHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHh
Confidence 56788999999999963 4654559999999998765
No 130
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=40.75 E-value=17 Score=35.43 Aligned_cols=30 Identities=33% Similarity=0.328 Sum_probs=21.6
Q ss_pred chhhHHHHhcCcEeeec------CCCceecChhHHH
Q 006771 185 WSCMKTLITKGLVVKSS------CPAKYMLTPGGRE 214 (632)
Q Consensus 185 WsSmktLi~k~LV~~~g------rP~rY~LTdeG~e 214 (632)
=+.+++|+++|||.+.| ||..|..|+.=.+
T Consensus 111 ~~~i~~L~e~glI~~~gr~~~~Grp~ly~tT~~Fl~ 146 (159)
T PF04079_consen 111 DSVIKTLLERGLIEEVGRKDTPGRPILYGTTDKFLE 146 (159)
T ss_dssp HCHHHHHHHTTSEEEEEE-TTTT--EEEEE-HHHHH
T ss_pred HHHHHHHHHCCCEEecCcCCCCCCCeEeehhHHHHH
Confidence 45789999999998655 7888999986433
No 131
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=40.73 E-value=20 Score=29.64 Aligned_cols=26 Identities=31% Similarity=0.367 Sum_probs=21.3
Q ss_pred chhhHHHHhcCcEeeec-CCCceecCh
Q 006771 185 WSCMKTLITKGLVVKSS-CPAKYMLTP 210 (632)
Q Consensus 185 WsSmktLi~k~LV~~~g-rP~rY~LTd 210 (632)
=--+.+|+++|||...+ +|.+|.|+.
T Consensus 40 ~r~L~~L~~~G~V~~~~~~~~~W~i~~ 66 (68)
T smart00550 40 NRVLYSLEKKGKVCKQGGTPPLWKLTD 66 (68)
T ss_pred HHHHHHHHHCCCEEecCCCCCceEeec
Confidence 34578999999999875 888999875
No 132
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=39.46 E-value=32 Score=34.90 Aligned_cols=54 Identities=15% Similarity=0.268 Sum_probs=35.4
Q ss_pred HHHHHHHHhCCCCCchhHHHHHHHH--HHHHhccCCCCCChhhhhccccchHHHHHHH
Q 006771 28 LQKRQEMAETPKGLSENIDMTLSKA--YNNICDAKNPIKTLKDLSQVKGVGKWILKLM 83 (632)
Q Consensus 28 ~ew~~e~~e~~~g~~~~~~~ty~kA--~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L 83 (632)
++|-..+.. -.|++.|+++.-=.+ ...++.+- .-.+-+-|.+++|||+|+++||
T Consensus 69 R~lF~~Lis-VnGIGpK~ALaiLs~~~~~~l~~aI-~~~d~~~L~k~PGIGkKtAeri 124 (201)
T COG0632 69 RELFRLLIS-VNGIGPKLALAILSNLDPEELAQAI-ANEDVKALSKIPGIGKKTAERI 124 (201)
T ss_pred HHHHHHHHc-cCCccHHHHHHHHcCCCHHHHHHHH-HhcChHhhhcCCCCCHHHHHHH
Confidence 345555555 348888887654433 23333332 3456778899999999999994
No 133
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. 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=39.13 E-value=59 Score=39.08 Aligned_cols=27 Identities=11% Similarity=0.233 Sum_probs=21.4
Q ss_pred hHHHHHHHhc--CCCCCHHHHHHHHHhcC
Q 006771 560 SDVFAVQLMQ--VPQVTEEIAITVLDLYP 586 (632)
Q Consensus 560 ~e~f~~mLm~--IpGVs~ekA~~I~~~yp 586 (632)
.+..++-|.+ |+||++..|..|.++|+
T Consensus 77 ~~~i~~yL~s~~~~GIG~~~A~~iv~~fg 105 (720)
T TIGR01448 77 KEGIVAYLSSRSIKGVGKKLAQRIVKTFG 105 (720)
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHHHhC
Confidence 4444556654 99999999999999997
No 134
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=38.67 E-value=41 Score=35.91 Aligned_cols=28 Identities=21% Similarity=0.285 Sum_probs=25.4
Q ss_pred cCCCCCHHHHHHHHHhcCCHHHHHHHHh
Q 006771 569 QVPQVTEEIAITVLDLYPTLLSLAHAYS 596 (632)
Q Consensus 569 ~IpGVs~ekA~~I~~~ypTp~~L~~Ay~ 596 (632)
.|+|||+++|..|++.|++...+.+..+
T Consensus 202 GV~GIG~ktA~~Ll~~~gs~e~i~~~~~ 229 (310)
T COG0258 202 GVKGIGPKTALKLLQEYGSLEGLYENLD 229 (310)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHHhhh
Confidence 3999999999999999999999998765
No 135
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=37.88 E-value=43 Score=34.34 Aligned_cols=50 Identities=22% Similarity=0.186 Sum_probs=29.4
Q ss_pred CCCCchhHHHHHHHHHHHHhc-cCC-----CCCChhhhhccccchHHHHHHHHHHh
Q 006771 38 PKGLSENIDMTLSKAYNNICD-AKN-----PIKTLKDLSQVKGVGKWILKLMQEFF 87 (632)
Q Consensus 38 ~~g~~~~~~~ty~kA~~sl~~-~p~-----~~~~~k~l~~lkG~G~~i~~~L~~~~ 87 (632)
+.|...+=+...+...+.+.+ +.. .-..-++|.+|+|||+|+++.+=-|+
T Consensus 86 p~Gf~~~KA~~Lk~la~~i~~~~g~~~~~~~~~~re~Ll~l~GIG~kTAd~iLlya 141 (218)
T PRK13913 86 PSGFYNQKAKRLIDLSENILKDFGSFENFKQEVTREWLLDQKGIGKESADAILCYV 141 (218)
T ss_pred hcCCHHHHHHHHHHHHHHHHHHcCCchhccCchHHHHHHcCCCccHHHHHHHHHHH
Confidence 446654344444444444432 111 01344789999999999999965553
No 136
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=37.49 E-value=20 Score=35.79 Aligned_cols=29 Identities=31% Similarity=0.361 Sum_probs=23.7
Q ss_pred hhhHHHHhcCcEeee------cCCCceecChhHHH
Q 006771 186 SCMKTLITKGLVVKS------SCPAKYMLTPGGRE 214 (632)
Q Consensus 186 sSmktLi~k~LV~~~------grP~rY~LTdeG~e 214 (632)
+.+++|+.+|||... |||..|..|+.=.+
T Consensus 117 ~~l~~L~ergLI~~~Gr~~~~Grp~ly~TT~~Fl~ 151 (186)
T TIGR00281 117 QIVDDLVEKGLVVELGRKDTPGRSFIYETTPKFYD 151 (186)
T ss_pred HHHHHHHHCCCeEecCcCCCCCCCeeehhhHHHHH
Confidence 578999999999765 78888999986444
No 137
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=37.49 E-value=41 Score=28.92 Aligned_cols=34 Identities=32% Similarity=0.279 Sum_probs=25.7
Q ss_pred cchhhHHHHhcCcEeeecCCCceecChhHHHHHHHHH
Q 006771 184 GWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECL 220 (632)
Q Consensus 184 aWsSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~ 220 (632)
.=+.++.|-+|||+- +|.-=+|||+|.+.|...+
T Consensus 36 ~i~a~~RLheKGLI~---~pdGgyLT~~G~~~aEhaq 69 (77)
T TIGR02647 36 AVAAAARLHEKGLTT---QPDGGYLTSLGLEAAEHAQ 69 (77)
T ss_pred HHHHHHHHHHcCCcc---CCCCCEecHHHHHHHHHHH
Confidence 456678899999995 4431189999999998654
No 138
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=33.78 E-value=24 Score=33.11 Aligned_cols=24 Identities=21% Similarity=0.353 Sum_probs=19.6
Q ss_pred CChhhhhccccchHHHHHHHHHHh
Q 006771 64 KTLKDLSQVKGVGKWILKLMQEFF 87 (632)
Q Consensus 64 ~~~k~l~~lkG~G~~i~~~L~~~~ 87 (632)
...++|.+|+|||+|.++.+--++
T Consensus 69 ~~~~~L~~l~GIG~~tA~~~l~~~ 92 (149)
T smart00478 69 DDREELLKLPGVGRKTANAVLSFA 92 (149)
T ss_pred HHHHHHHcCCCCcHHHHHHHHHHH
Confidence 456788999999999999866554
No 139
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=33.50 E-value=66 Score=31.88 Aligned_cols=49 Identities=14% Similarity=0.226 Sum_probs=29.2
Q ss_pred CCCchhHHHHHHHHHHHHhc-cCCCC-CChhhhhccccchHHHHHHHHHHh
Q 006771 39 KGLSENIDMTLSKAYNNICD-AKNPI-KTLKDLSQVKGVGKWILKLMQEFF 87 (632)
Q Consensus 39 ~g~~~~~~~ty~kA~~sl~~-~p~~~-~~~k~l~~lkG~G~~i~~~L~~~~ 87 (632)
-|...+-+...+++.+.+.. +...+ ..-++|.+|+|||+|++..+--|+
T Consensus 76 ~G~~~~Ka~~i~~~a~~i~~~~~~~~~~~~~~L~~l~GIG~ktA~~ill~~ 126 (191)
T TIGR01083 76 IGLYRNKAKNIIALCRILVERYGGEVPEDREELVKLPGVGRKTANVVLNVA 126 (191)
T ss_pred cCChHHHHHHHHHHHHHHHHHcCCCCchHHHHHHhCCCCcHHHHHHHHHHH
Confidence 36543344444444444432 22211 346789999999999999865443
No 140
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=33.01 E-value=54 Score=39.08 Aligned_cols=67 Identities=13% Similarity=0.174 Sum_probs=42.4
Q ss_pred ccccchHHHHHHHhcCCCCCHHHHHHHH-HhcCCHHHHHHHHhhccccHHHHHHHhhhhcCCcccHHHHhhhhhhh
Q 006771 555 DKMTVSDVFAVQLMQVPQVTEEIAITVL-DLYPTLLSLAHAYSILEGDVCAQEEMLWKQSNNAVSASASRNIFQLV 629 (632)
Q Consensus 555 ~~~Tv~e~f~~mLm~IpGVs~ekA~~I~-~~ypTp~~L~~Ay~~~~~~~~~~e~mL~~~~~~~IG~~lSr~Iy~~v 629 (632)
+..++.. |+. =+.||+|+...|..|. ++|.|+..|.++-.... ...++++.- .. ||+.++..|+.+|
T Consensus 494 k~~~l~r-~l~-ALGI~~vG~~~ak~La~~~f~~~~~l~~~~~~~~---~~~e~l~~i--~g-iG~~~a~si~~ff 561 (669)
T PRK14350 494 KKRPFSK-LLL-SMGIKDLGENTILLLINNNLNSFDKISTLCQDRE---FALSKLLKI--KG-IGEKIALNIIEAF 561 (669)
T ss_pred hCCCHHH-HHH-HcCCCchhHHHHHHHHHHhhCCHHHHHhhhhccC---CCHHHHhhC--CC-ccHHHHHHHHHHH
Confidence 3445543 232 2369999999999999 89999998876421100 112334432 23 8888888888744
No 141
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=32.88 E-value=69 Score=37.66 Aligned_cols=62 Identities=13% Similarity=0.229 Sum_probs=40.4
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHhh
Q 006771 13 RRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFE 88 (632)
Q Consensus 13 ~~~~~~~N~~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~ 88 (632)
.++.++.|..++.+|..-+||+-. .+.||.+-.++=... -..|..|+|||++.++.|-.+|.
T Consensus 503 ~~~~l~~~~~~l~llq~irDEaHR--------FAi~~hR~~R~k~~~------~s~L~~IpGIG~k~~k~Ll~~Fg 564 (598)
T PRK00558 503 EPIILPPDSPALYLLQRIRDEAHR--------FAITFHRKKRSKARL------TSALDDIPGIGPKRRKALLKHFG 564 (598)
T ss_pred ceEecCCCCHHHHHHHHHHHHhhh--------hhhhhhccccccchh------hhhHhhCCCcCHHHHHHHHHHcC
Confidence 578889999999999998888754 234555544432221 14455677777777777666554
No 142
>PRK11050 manganese transport regulator MntR; Provisional
Probab=31.67 E-value=59 Score=31.07 Aligned_cols=35 Identities=31% Similarity=0.416 Sum_probs=27.8
Q ss_pred hhhHHHHhcCcEeeecCCCceecChhHHHHHHHHHh
Q 006771 186 SCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 186 sSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~ 221 (632)
..++.|.++|||..... ..+.||+.|..++..+..
T Consensus 70 r~l~~Le~~GlI~r~~~-~~v~LT~~G~~l~~~~~~ 104 (152)
T PRK11050 70 KMLKRLARDGLVEMRPY-RGVFLTPEGEKLAQESRE 104 (152)
T ss_pred HHHHHHHHCCCEEEecC-CceEECchHHHHHHHHHH
Confidence 35688999999986432 369999999999887764
No 143
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=31.62 E-value=35 Score=28.30 Aligned_cols=22 Identities=36% Similarity=0.495 Sum_probs=17.9
Q ss_pred HHHhcCcEeee-cCCCceecChh
Q 006771 190 TLITKGLVVKS-SCPAKYMLTPG 211 (632)
Q Consensus 190 tLi~k~LV~~~-grP~rY~LTde 211 (632)
.|.++|+|.+. |+|.+|+||++
T Consensus 43 ~L~k~g~v~k~~~~PP~W~l~~~ 65 (66)
T PF02295_consen 43 RLEKQGKVCKEGGTPPKWSLTEK 65 (66)
T ss_dssp HHHHTTSEEEECSSSTEEEE-HC
T ss_pred HHHHCCCEeeCCCCCCceEeccC
Confidence 57889999976 78999999974
No 144
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.09 E-value=54 Score=32.79 Aligned_cols=50 Identities=16% Similarity=0.223 Sum_probs=32.1
Q ss_pred CCCCCchhHHHHHHHH--HHHHhccCCCCCChhhhhccccchHHHHHHH----HHHhh
Q 006771 37 TPKGLSENIDMTLSKA--YNNICDAKNPIKTLKDLSQVKGVGKWILKLM----QEFFE 88 (632)
Q Consensus 37 ~~~g~~~~~~~ty~kA--~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L----~~~~~ 88 (632)
+-+|++.|.++..=.. .+.+..+-. =...+-| +++|||+|+++|| ++.+.
T Consensus 77 sV~GIGpK~Al~iLs~~~~~~l~~aI~-~~D~~~L-~vpGIGkKtAerIilELk~K~~ 132 (186)
T PRK14600 77 KVSGVNYKTAMSILSKLTPEQLFSAIV-NEDKAAL-KVNGIGEKLINRIITELQYKVS 132 (186)
T ss_pred CcCCcCHHHHHHHHccCCHHHHHHHHH-cCCHhhe-ECCCCcHHHHHHHHHHHHHHhh
Confidence 4458887776654443 333333322 2567888 9999999999994 55553
No 145
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=31.00 E-value=28 Score=39.28 Aligned_cols=39 Identities=23% Similarity=0.358 Sum_probs=33.4
Q ss_pred ccccchhhHHHHhcCcEeeecCCCceecChhHHHHHHHHHh
Q 006771 181 WYSGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 181 fYtaWsSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~ 221 (632)
|...|..++.|+.+|||...++ ++.||++|+-++..+..
T Consensus 398 ~~~~~~~l~~l~~~gl~~~~~~--~~~lT~~G~~~~~~i~~ 436 (453)
T PRK13347 398 FLDELARLEPLAADGLVTIDGG--GIRVTPEGRPLIRAVAA 436 (453)
T ss_pred HHHHHHHHHHHHHCCCEEEECC--EEEECcchhHHHHHHHH
Confidence 3445888999999999998876 89999999999998764
No 146
>KOG2875 consensus 8-oxoguanine DNA glycosylase [Replication, recombination and repair]
Probab=30.98 E-value=40 Score=35.88 Aligned_cols=23 Identities=22% Similarity=0.518 Sum_probs=17.9
Q ss_pred HHHHHHHHHhccCCCCCChhhhhccccchHHHHHHH
Q 006771 48 TLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLM 83 (632)
Q Consensus 48 ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L 83 (632)
-|.+|.+.|| .|+|||+|+++-+
T Consensus 212 ~yeear~~L~-------------~lpGVG~KVADCI 234 (323)
T KOG2875|consen 212 SYEEAREALC-------------SLPGVGPKVADCI 234 (323)
T ss_pred cHHHHHHHHh-------------cCCCCcchHhhhh
Confidence 4777887776 5779999998853
No 147
>PF13814 Replic_Relax: Replication-relaxation
Probab=30.16 E-value=51 Score=31.98 Aligned_cols=58 Identities=28% Similarity=0.347 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeee---------cCCCceecCh
Q 006771 140 NEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKS---------SCPAKYMLTP 210 (632)
Q Consensus 140 ~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~---------grP~rY~LTd 210 (632)
..+||.+||....-+.+.+ ++ ++=.-|+.|.+.|||-.. +.|.-|.||+
T Consensus 7 ~r~lt~~Qi~~l~~~~~~~-------------------~~---~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~ 64 (191)
T PF13814_consen 7 HRFLTTDQIARLLFPSSKS-------------------ER---TARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTP 64 (191)
T ss_pred hcCcCHHHHHHHHcCCCcc-------------------hH---HHHHHHHHHhhCCcEEeecccccccCCCcceEEEECH
Confidence 3789999998864443211 01 455678999999999643 2345799999
Q ss_pred hHHHHHHHH
Q 006771 211 GGREAAREC 219 (632)
Q Consensus 211 eG~elA~~l 219 (632)
.|.+++..+
T Consensus 65 ~G~~~l~~~ 73 (191)
T PF13814_consen 65 AGARLLADL 73 (191)
T ss_pred HHHHHHHhc
Confidence 999998653
No 148
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.74 E-value=33 Score=34.23 Aligned_cols=20 Identities=25% Similarity=0.242 Sum_probs=17.8
Q ss_pred CChhhhhccccchHHHHHHH
Q 006771 64 KTLKDLSQVKGVGKWILKLM 83 (632)
Q Consensus 64 ~~~k~l~~lkG~G~~i~~~L 83 (632)
.+.+-|.+++|||+|+++||
T Consensus 105 ~D~~~L~~vpGIGkKtAeRI 124 (183)
T PRK14601 105 GDESVLKKVPGIGPKSAKRI 124 (183)
T ss_pred CCHHHHhhCCCCCHHHHHHH
Confidence 56788999999999999994
No 149
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.25 E-value=34 Score=34.64 Aligned_cols=51 Identities=10% Similarity=0.184 Sum_probs=32.6
Q ss_pred CCCCCchhHHHHHHHH--HHHHhccCCCCCChhhhhccccchHHHHHH----HHHHhh
Q 006771 37 TPKGLSENIDMTLSKA--YNNICDAKNPIKTLKDLSQVKGVGKWILKL----MQEFFE 88 (632)
Q Consensus 37 ~~~g~~~~~~~ty~kA--~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~----L~~~~~ 88 (632)
+-+|++.|+++..=.+ .+.++.+ +-=.+.+.|.+++|||+|+++| |++.+.
T Consensus 78 ~V~GIGpK~Al~iLs~~~~~~l~~a-I~~~D~~~L~~ipGIGkKtAerIilELkdK~~ 134 (203)
T PRK14602 78 SISKVGAKTALAILSQFRPDDLRRL-VAEEDVAALTRVSGIGKKTAQHIFLELKYKLK 134 (203)
T ss_pred CCCCcCHHHHHHHHhhCCHHHHHHH-HHhCCHHHHhcCCCcCHHHHHHHHHHHHHhhc
Confidence 3458887766654332 2222222 1235788899999999999999 456554
No 150
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.20 E-value=34 Score=34.45 Aligned_cols=53 Identities=17% Similarity=0.172 Sum_probs=31.5
Q ss_pred HHHHHHHhCCCCCchhHHHHHHHH--HHHHhccCCCCCChhhhhccccchHHHHHHH
Q 006771 29 QKRQEMAETPKGLSENIDMTLSKA--YNNICDAKNPIKTLKDLSQVKGVGKWILKLM 83 (632)
Q Consensus 29 ew~~e~~e~~~g~~~~~~~ty~kA--~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L 83 (632)
+|-..+.. -.|++.|+++..=.. .+.++.+ +.=.+.+.|.+++|||+|+++||
T Consensus 70 ~lF~~Li~-V~GIGpK~Al~iLs~~~~~el~~a-I~~~D~~~L~kvpGIGkKtAerI 124 (195)
T PRK14604 70 QLFELLIG-VSGVGPKAALNLLSSGTPDELQLA-IAGGDVARLARVPGIGKKTAERI 124 (195)
T ss_pred HHHHHHhC-cCCcCHHHHHHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHH
Confidence 34444444 458875555443332 2222222 12356788999999999999994
No 151
>COG0122 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=28.56 E-value=31 Score=36.69 Aligned_cols=22 Identities=27% Similarity=0.729 Sum_probs=17.3
Q ss_pred hhhhhccccchHHHHHHHHHHh
Q 006771 66 LKDLSQVKGVGKWILKLMQEFF 87 (632)
Q Consensus 66 ~k~l~~lkG~G~~i~~~L~~~~ 87 (632)
-+.|.+|+|||+|+++++--|+
T Consensus 197 ~e~L~~i~GIG~WTAe~~llf~ 218 (285)
T COG0122 197 IEELTALKGIGPWTAEMFLLFG 218 (285)
T ss_pred HHHHHcCCCcCHHHHHHHHHHc
Confidence 3567789999999999965543
No 152
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.33 E-value=36 Score=34.31 Aligned_cols=58 Identities=16% Similarity=0.139 Sum_probs=33.8
Q ss_pred HHHHHHHhCCCCCchhHHHHHHHH--HHHHhccCCCCCChhhhhccccchHHHHHH----HHHHhh
Q 006771 29 QKRQEMAETPKGLSENIDMTLSKA--YNNICDAKNPIKTLKDLSQVKGVGKWILKL----MQEFFE 88 (632)
Q Consensus 29 ew~~e~~e~~~g~~~~~~~ty~kA--~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~----L~~~~~ 88 (632)
+|-+.+.. -+|++.|+++..=.. .+.++.+ +.=.+.+-|.+++|||+|+++| |++.+.
T Consensus 69 ~lF~~L~~-V~GIGpK~AL~iLs~~~~~~l~~a-I~~~D~~~L~kvpGIGkKtAerIilELkdK~~ 132 (197)
T PRK14603 69 ELFELLLG-VSGVGPKLALALLSALPPALLARA-LLEGDARLLTSASGVGKKLAERIALELKGKVP 132 (197)
T ss_pred HHHHHHhC-cCCcCHHHHHHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHHHHhh
Confidence 34444444 358876665543221 1112211 1235678899999999999999 455554
No 153
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=27.93 E-value=57 Score=37.54 Aligned_cols=37 Identities=22% Similarity=0.180 Sum_probs=30.1
Q ss_pred chHHHHHH--------HhcCCCCCHHHHHHHHHhcCCHHHHHHHH
Q 006771 559 VSDVFAVQ--------LMQVPQVTEEIAITVLDLYPTLLSLAHAY 595 (632)
Q Consensus 559 v~e~f~~m--------Lm~IpGVs~ekA~~I~~~ypTp~~L~~Ay 595 (632)
-.|.|.+| |..|||||..+|..++.+|+++...+-.|
T Consensus 211 ~~ekfr~mciLSGCDYl~slpGvGl~tA~k~l~k~~~~d~vi~~~ 255 (556)
T KOG2518|consen 211 TEEKFRRMCILSGCDYLSSLPGVGLATAHKLLSKYNTPDRVIISH 255 (556)
T ss_pred CHHHHHHHHHhcCCcccccCccccHHHHHHHHHhcCcHHHHHHHH
Confidence 34666666 44799999999999999999999997543
No 154
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=27.75 E-value=41 Score=38.58 Aligned_cols=34 Identities=15% Similarity=0.222 Sum_probs=27.5
Q ss_pred cchhhHHHHhcCcEeeecCCC-ceecChhHHHHHH
Q 006771 184 GWSCMKTLITKGLVVKSSCPA-KYMLTPGGREAAR 217 (632)
Q Consensus 184 aWsSmktLi~k~LV~~~grP~-rY~LTdeG~elA~ 217 (632)
.=+.++.|..||||--.-+-. .|.||+||.+.++
T Consensus 38 v~~~~~~L~~kg~v~~~~~~~~~~~LT~eG~~~~~ 72 (494)
T PTZ00326 38 VVGAIKSLESANYITTEMKKSNTWTLTEEGEDYLK 72 (494)
T ss_pred HHHHHHHHHhCCCEEEEEEEEEEEEECHHHHHHHH
Confidence 345588999999997665544 7999999999987
No 155
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=27.46 E-value=42 Score=38.43 Aligned_cols=34 Identities=21% Similarity=0.175 Sum_probs=27.6
Q ss_pred cchhhHHHHhcCcEeeecCCC-ceecChhHHHHHH
Q 006771 184 GWSCMKTLITKGLVVKSSCPA-KYMLTPGGREAAR 217 (632)
Q Consensus 184 aWsSmktLi~k~LV~~~grP~-rY~LTdeG~elA~ 217 (632)
.=+.++.|..||||--.-+-. .|.||+||.+.++
T Consensus 35 v~~~~~~L~~kg~v~~~~~~~~~~~LT~eG~~~l~ 69 (492)
T PLN02853 35 VVGVIKSLHGFRYVDAQDIKRETWVLTEEGKKYAA 69 (492)
T ss_pred HHHHHHHHHhCCCEEEEEEEEEEEEECHHHHHHHH
Confidence 345589999999997665554 7999999999987
No 156
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.39 E-value=38 Score=34.21 Aligned_cols=57 Identities=19% Similarity=0.293 Sum_probs=33.8
Q ss_pred HHHHHHhCCCCCchhHHHHHHHH--HHHHhccCCCCCChhhhhccccchHHHHHHH----HHHhh
Q 006771 30 KRQEMAETPKGLSENIDMTLSKA--YNNICDAKNPIKTLKDLSQVKGVGKWILKLM----QEFFE 88 (632)
Q Consensus 30 w~~e~~e~~~g~~~~~~~ty~kA--~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L----~~~~~ 88 (632)
|-+.+. +-+|++.|+++..=-+ .+.+..+ +.-...+.|.+++|||+|+++|| ++.+.
T Consensus 70 lF~~Li-sVsGIGPK~ALaILs~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAeRIIlELkdKl~ 132 (196)
T PRK13901 70 VFEELI-GVDGIGPRAALRVLSGIKYNEFRDA-IDREDIELISKVKGIGNKMAGKIFLKLRGKLV 132 (196)
T ss_pred HHHHHh-CcCCcCHHHHHHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHHHhhc
Confidence 333344 3458876666544321 1112221 13457788999999999999994 55553
No 157
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.18 E-value=52 Score=33.00 Aligned_cols=59 Identities=14% Similarity=0.181 Sum_probs=35.9
Q ss_pred HHHHHHHhCCCCCchhHHHHHHHHHHHHh-ccCCCCCChhhhhccccchHHHHHH----HHHHhh
Q 006771 29 QKRQEMAETPKGLSENIDMTLSKAYNNIC-DAKNPIKTLKDLSQVKGVGKWILKL----MQEFFE 88 (632)
Q Consensus 29 ew~~e~~e~~~g~~~~~~~ty~kA~~sl~-~~p~~~~~~k~l~~lkG~G~~i~~~----L~~~~~ 88 (632)
+|-+.+. +-+|++.++++..-.++..=. ..-+--..++.|.+++|||+|.++| |++.+.
T Consensus 70 ~lF~~Li-~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~Ki~ 133 (194)
T PRK14605 70 SLFETLI-DVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIVLELKDKIA 133 (194)
T ss_pred HHHHHHh-CCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence 3334444 445888777766554422111 0011136889999999999999999 455553
No 158
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=26.81 E-value=67 Score=35.00 Aligned_cols=33 Identities=21% Similarity=0.401 Sum_probs=27.7
Q ss_pred hhHHHHhcCcEeeecCCCceecChhHHHHHHHHHh
Q 006771 187 CMKTLITKGLVVKSSCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 187 SmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~ 221 (632)
.++.|+++|||...+. ++.||++|+-++..+..
T Consensus 338 ~l~~l~~~gl~~~~~~--~~~lT~~G~~~~~~i~~ 370 (374)
T PRK05799 338 VINKYIKLGLLIEKEG--RIYLSERGIEVSNSIMS 370 (374)
T ss_pred HHHHHHHCCCEEEECC--EEEEChhHHHHHHHHHH
Confidence 3568899999998765 89999999999987653
No 159
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.52 E-value=43 Score=33.49 Aligned_cols=53 Identities=9% Similarity=0.156 Sum_probs=31.8
Q ss_pred HHHHHHHhCCCCCchhHHHHHHH--HHHHHhccCCCCCChhhhhccccchHHHHHHH
Q 006771 29 QKRQEMAETPKGLSENIDMTLSK--AYNNICDAKNPIKTLKDLSQVKGVGKWILKLM 83 (632)
Q Consensus 29 ew~~e~~e~~~g~~~~~~~ty~k--A~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L 83 (632)
+|-+.+.. -+|++.|+++..=- ..+.++.+ +.-...+-|.+++|||+|+++||
T Consensus 70 ~lF~~Li~-V~GIGpK~AL~iLs~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAerI 124 (188)
T PRK14606 70 ELFLSLTK-VSRLGPKTALKIISNEDAETLVTM-IASQDVEGLSKLPGISKKTAERI 124 (188)
T ss_pred HHHHHHhc-cCCccHHHHHHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHH
Confidence 34444443 45887666554331 12222222 13356788999999999999994
No 160
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=25.47 E-value=1.2e+02 Score=30.29 Aligned_cols=50 Identities=14% Similarity=0.237 Sum_probs=33.7
Q ss_pred CCCCCchhHHHHHHHHHHH---HhccCCCCCChhhhhccccchHHHHHHHHHHhh
Q 006771 37 TPKGLSENIDMTLSKAYNN---ICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFE 88 (632)
Q Consensus 37 ~~~g~~~~~~~ty~kA~~s---l~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~ 88 (632)
+-+|++.+.+...-+.+.+ ..+ .--.++++|.+++|||++.++++-..++
T Consensus 77 ~i~GIGpk~A~~il~~fg~~~l~~~--i~~~d~~~L~~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSPEELVQA--IANGDVKALTKVPGIGKKTAERIVLELK 129 (192)
T ss_pred cCCCCCHHHHHHHHHhCCHHHHHHH--HHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 4568888777666544332 100 1124789999999999999999765544
No 161
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 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=25.24 E-value=37 Score=30.35 Aligned_cols=22 Identities=23% Similarity=0.353 Sum_probs=19.2
Q ss_pred CCChhhhhccccchHHHHHHHH
Q 006771 63 IKTLKDLSQVKGVGKWILKLMQ 84 (632)
Q Consensus 63 ~~~~k~l~~lkG~G~~i~~~L~ 84 (632)
....++|+.|+|||+.+.+.|.
T Consensus 8 ~~~~~~L~~iP~IG~a~a~DL~ 29 (93)
T PF11731_consen 8 RAGLSDLTDIPNIGKATAEDLR 29 (93)
T ss_pred HHHHHHHhcCCCccHHHHHHHH
Confidence 3468899999999999999875
No 162
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=25.02 E-value=57 Score=33.45 Aligned_cols=37 Identities=19% Similarity=0.064 Sum_probs=30.9
Q ss_pred ccchhhHHHHhc---CcEeeecCCCceecChhHHHHHHHHHh
Q 006771 183 SGWSCMKTLITK---GLVVKSSCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 183 taWsSmktLi~k---~LV~~~grP~rY~LTdeG~elA~~l~~ 221 (632)
+.+..|+.|.+. .|+.++|| ++.||++|..++..+..
T Consensus 31 avS~~i~~LE~~lg~~Lf~R~~~--~~~lT~~G~~l~~~~~~ 70 (296)
T PRK11242 31 TLSQQIRQLEESLGVQLFDRSGR--TVRLTDAGEVYLRYARR 70 (296)
T ss_pred HHHHHHHHHHHHhCCeeEeEcCC--ceeechhHHHHHHHHHH
Confidence 467889999765 78888877 69999999999998764
No 163
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=24.79 E-value=1.1e+02 Score=26.47 Aligned_cols=65 Identities=22% Similarity=0.201 Sum_probs=47.0
Q ss_pred HHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecCCC
Q 006771 125 AYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCPA 204 (632)
Q Consensus 125 aYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~grP~ 204 (632)
-|.||.|+-....+ ++++.-+.|...|.-.. -..=-+++.|.+++||.....|-
T Consensus 8 d~rvL~aiE~gmk~-hE~VP~~~I~~~s~l~~-------------------------~~~~~~L~~L~~~kLv~~~~~~Y 61 (82)
T PF09202_consen 8 DFRVLRAIEMGMKN-HEWVPLELIEKISGLSE-------------------------GEVEKRLKRLVKLKLVSRRNKPY 61 (82)
T ss_dssp HHHHHHHHHTTTTT--SSEEHHHHHHHHT--H-------------------------HHHHHHHHHHHHTTSEEEE-SSS
T ss_pred HHHHHHHHHHcccC-CccCCHHHHHHHhCcCH-------------------------HHHHHHHHHHHhcCCccccCCCc
Confidence 47899999887776 88899888888665420 01234789999999999987775
Q ss_pred -ceecChhHHHH
Q 006771 205 -KYMLTPGGREA 215 (632)
Q Consensus 205 -rY~LTdeG~el 215 (632)
-|.||=.|-..
T Consensus 62 ~GYrLT~~GYD~ 73 (82)
T PF09202_consen 62 DGYRLTFLGYDY 73 (82)
T ss_dssp -EEEE-HHHHHH
T ss_pred ceEEEeecchhH
Confidence 59999999874
No 164
>PRK10702 endonuclease III; Provisional
Probab=23.85 E-value=1.1e+02 Score=31.18 Aligned_cols=52 Identities=15% Similarity=0.243 Sum_probs=0.0
Q ss_pred HHHHHh--CCCCCchhHHHHHHHHHHHHhcc---CCCCCChhhhhccccchHHHHHHH
Q 006771 31 RQEMAE--TPKGLSENIDMTLSKAYNNICDA---KNPIKTLKDLSQVKGVGKWILKLM 83 (632)
Q Consensus 31 ~~e~~e--~~~g~~~~~~~ty~kA~~sl~~~---p~~~~~~k~l~~lkG~G~~i~~~L 83 (632)
.++..+ ++-|...+-+..+.++.+-+.+- +.| ...++|..|+|||+|++.-+
T Consensus 69 ~~~l~~~i~~~G~y~~kA~~l~~~a~~i~~~~~~~~p-~~~~~Ll~lpGVG~ktA~~i 125 (211)
T PRK10702 69 VEGVKTYIKTIGLYNSKAENVIKTCRILLEQHNGEVP-EDRAALEALPGVGRKTANVV 125 (211)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHcCCCCC-chHHHHhcCCcccHHHHHHH
No 165
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=23.51 E-value=1.3e+02 Score=35.32 Aligned_cols=60 Identities=13% Similarity=0.159 Sum_probs=48.0
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHhh
Q 006771 13 RRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFE 88 (632)
Q Consensus 13 ~~~~~~~N~~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~ 88 (632)
.++..+.+..++.||..-+||+-. .+.||.+-.++= + -+.|..|+|||++-.+.|=.||.
T Consensus 476 ~~~~l~~~s~~l~lLq~iRDEaHR--------FAit~hRk~R~k------~--~s~L~~I~GiG~kr~~~LL~~Fg 535 (574)
T PRK14670 476 QGIKLPKGNPALRILQNVRDEAHR--------KANGFNKKLREN------I--KLNYTKIKGIGEKKAKKILKSLG 535 (574)
T ss_pred ceeecCCCCHHHHHHHHHHHHHHH--------HHHHHHHHhhcc------c--ccccccCCCCCHHHHHHHHHHhC
Confidence 578889999999999998888754 456787766654 2 25888999999999999887775
No 166
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=23.39 E-value=1.8e+02 Score=30.04 Aligned_cols=70 Identities=23% Similarity=0.219 Sum_probs=51.8
Q ss_pred HHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEeeecCCC
Q 006771 125 AYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVKSSCPA 204 (632)
Q Consensus 125 aYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~~grP~ 204 (632)
|-+||-.|.. +..+|+=.||.+... +++ =|++.-+.||+.+|||...+.-.
T Consensus 6 al~iL~~l~~----~~~~l~l~ela~~~g--------lpk-----------------sT~~RlL~tL~~~G~v~~d~~~g 56 (246)
T COG1414 6 ALAILDLLAE----GPGGLSLAELAERLG--------LPK-----------------STVHRLLQTLVELGYVEQDPEDG 56 (246)
T ss_pred HHHHHHHHHh----CCCCCCHHHHHHHhC--------cCH-----------------HHHHHHHHHHHHCCCEEEcCCCC
Confidence 3456666655 234578777776422 222 17899999999999999998877
Q ss_pred ceecChhHHHHHHHHHhhc
Q 006771 205 KYMLTPGGREAARECLSRS 223 (632)
Q Consensus 205 rY~LTdeG~elA~~l~~~~ 223 (632)
+|.|+..=.+++.......
T Consensus 57 ~Y~Lg~~~~~lg~~~l~~~ 75 (246)
T COG1414 57 RYRLGPRLLELGAAALSSL 75 (246)
T ss_pred cEeehHHHHHHHHHHHhcC
Confidence 9999999999999866543
No 167
>PF15516 BpuSI_N: BpuSI N-terminal domain
Probab=23.29 E-value=2.1e+02 Score=27.47 Aligned_cols=71 Identities=25% Similarity=0.409 Sum_probs=44.2
Q ss_pred HHHHHhhCCCcEEEEec---c----CCCEEEEeeccCCCcceeeceeEEEechhHHHhhhccchHHHHHHHHH-Hc--CC
Q 006771 398 IENVCSQFKIQMEVRRL---P----VGDGIWIARHRQTQSEYVLDFIVERKKVDDLRSSIRDNRYRDQKLRLV-RC--GL 467 (632)
Q Consensus 398 i~~~l~~~gV~~evr~L---~----vGD~iWvar~k~~~~E~VLd~IVERKrldDL~~SI~DGRf~eQK~RLk-~s--G~ 467 (632)
+...|...|+.-+-.-+ + +.||++..+ ..+.+|| +||=||--|-++| -||+.|..--- .+ .+
T Consensus 19 lnqAL~~~GLd~~yeviHH~~vgsi~~DFvl~~k---~t~k~vL--~iEvKR~~~~V~S---TRY~~QA~SYv~Ea~~~l 90 (159)
T PF15516_consen 19 LNQALKNLGLDTQYEVIHHEPVGSIVPDFVLRRK---STNKYVL--IIEVKRTKSAVSS---TRYRMQAQSYVQEANQKL 90 (159)
T ss_pred HHHHHHHcCCccceeEEEeccCCccccceEEEec---CCceEEE--EEEEecchhhhhh---hHHHHHHHHHHHHhcccc
Confidence 33455566664433322 2 357877653 3456666 6788888887777 79999987654 33 45
Q ss_pred CceEEEEeC
Q 006771 468 KKLIYLVEG 476 (632)
Q Consensus 468 ~~~iYLVEg 476 (632)
..++|.|-.
T Consensus 91 e~pYy~itN 99 (159)
T PF15516_consen 91 ESPYYAITN 99 (159)
T ss_pred cCceEEEec
Confidence 677787754
No 168
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 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. This entry represents 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 []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=23.24 E-value=1.1e+02 Score=24.21 Aligned_cols=28 Identities=18% Similarity=-0.052 Sum_probs=20.3
Q ss_pred HHHhcCCCCCHHHHHHHHH-hcCCHHHHH
Q 006771 565 VQLMQVPQVTEEIAITVLD-LYPTLLSLA 592 (632)
Q Consensus 565 ~mLm~IpGVs~ekA~~I~~-~ypTp~~L~ 592 (632)
+.++.|.||++.+|....+ -|.|+.+|.
T Consensus 2 ~~f~~I~GVG~~tA~~w~~~G~rtl~Dl~ 30 (52)
T PF10391_consen 2 KLFTGIWGVGPKTARKWYAKGIRTLEDLR 30 (52)
T ss_dssp HHHHTSTT--HHHHHHHHHTT--SHHHHH
T ss_pred cchhhcccccHHHHHHHHHhCCCCHHHHh
Confidence 5688999999999999876 578888884
No 169
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=23.17 E-value=67 Score=31.99 Aligned_cols=22 Identities=23% Similarity=0.413 Sum_probs=18.1
Q ss_pred hhhhccccchHHHHHHHHHHhh
Q 006771 67 KDLSQVKGVGKWILKLMQEFFE 88 (632)
Q Consensus 67 k~l~~lkG~G~~i~~~L~~~~~ 88 (632)
++|..|+|||++.+...=.+|.
T Consensus 115 e~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 115 RRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred HHHHcCCCCCHHHHHHHHHHHH
Confidence 6899999999999998544544
No 170
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=23.11 E-value=78 Score=25.36 Aligned_cols=29 Identities=28% Similarity=0.382 Sum_probs=19.5
Q ss_pred eccCCCEEEEeeccCCCcceeeceeEEEech
Q 006771 413 RLPVGDGIWIARHRQTQSEYVLDFIVERKKV 443 (632)
Q Consensus 413 ~L~vGD~iWvar~k~~~~E~VLd~IVERKrl 443 (632)
.+-|||.|++.. ..+++.+..-|.|||+.
T Consensus 37 ~~~VGD~V~~~~--~~~~~~~I~~vl~R~s~ 65 (68)
T cd04466 37 PPAVGDRVEFEP--EDDGEGVIEEILPRKNL 65 (68)
T ss_pred CCCCCcEEEEEE--CCCCcEEEEEEeccceE
Confidence 457899998853 22344566677899873
No 171
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=22.70 E-value=56 Score=32.71 Aligned_cols=61 Identities=16% Similarity=0.184 Sum_probs=42.3
Q ss_pred CCCchHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcCCCCCCCCCCCCCCCCCCCCCCCCcccccchhhHHHHhcCcEee
Q 006771 120 QRNSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASGLSHTPIMPEKGKGKPRQFGSSPRDWYSGWSCMKTLITKGLVVK 199 (632)
Q Consensus 120 ~~rSGaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~~ss~~~~p~~~~~~~~~~~~~~~~fYtaWsSmktLi~k~LV~~ 199 (632)
+...++.-+|-.++.. ..+|+.||.+.-. .+ .=+-+++|+.+|||.+
T Consensus 87 ~LS~aaLEtLaiIay~-----qPiTr~eI~~irG----------------------v~------~~~ii~~L~~~gLI~e 133 (188)
T PRK00135 87 SLSQAALEVLAIIAYK-----QPITRIEIDEIRG----------------------VN------SDGALQTLLAKGLIKE 133 (188)
T ss_pred CCCHHHHHHHHHHHHc-----CCcCHHHHHHHHC----------------------CC------HHHHHHHHHHCCCeEE
Confidence 4555666666666443 5799999998521 22 1345799999999985
Q ss_pred ------ecCCCceecChhHH
Q 006771 200 ------SSCPAKYMLTPGGR 213 (632)
Q Consensus 200 ------~grP~rY~LTdeG~ 213 (632)
.|||..|.+|+.=.
T Consensus 134 ~gr~~~~Grp~ly~tT~~F~ 153 (188)
T PRK00135 134 VGRKEVPGRPILYGTTDEFL 153 (188)
T ss_pred cCcCCCCCCCeeeehhHHHH
Confidence 47788899998733
No 172
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=22.52 E-value=53 Score=32.86 Aligned_cols=52 Identities=17% Similarity=0.289 Sum_probs=31.5
Q ss_pred HHHHHHhCCCCCchhHHHHHHHHH--HHHhccCCCCCChhhhhccccchHHHHHHH
Q 006771 30 KRQEMAETPKGLSENIDMTLSKAY--NNICDAKNPIKTLKDLSQVKGVGKWILKLM 83 (632)
Q Consensus 30 w~~e~~e~~~g~~~~~~~ty~kA~--~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L 83 (632)
|-..+.. -+|+..|.+...-..+ +.+..+ .-=.+++.+.+|+|||+|+++++
T Consensus 70 lF~~L~~-V~GIGpK~Al~iL~~~~~~el~~a-I~~~d~~~L~~ipGiGkKtAerI 123 (191)
T TIGR00084 70 LFKELIK-VNGVGPKLALAILSNMSPEEFVYA-IETEEVKALVKIPGVGKKTAERL 123 (191)
T ss_pred HHHHHhC-CCCCCHHHHHHHHhcCCHHHHHHH-HHhCCHHHHHhCCCCCHHHHHHH
Confidence 3344443 4588877776663221 111110 01146788999999999999995
No 173
>smart00341 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease.
Probab=22.06 E-value=2.4e+02 Score=23.26 Aligned_cols=56 Identities=20% Similarity=0.272 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHH-hCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHH
Q 006771 22 ELAMYMLQKRQEMA-ETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKL 82 (632)
Q Consensus 22 ~l~~~~~ew~~e~~-e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~ 82 (632)
.++.=|.+|+++.+ +. +..... ..=.+++..|+... | .+..++..+.|+|++.+++
T Consensus 6 ~~~~~L~~wR~~~A~~~--~~~~~~-I~~~~~L~~ia~~~-P-~~~~~L~~i~g~~~~~~~~ 62 (81)
T smart00341 6 RLLRRLRQWRDEIARRE--DVPPYF-VLPDETLIKMAAAL-P-TNVSELLAIDGVGEEKARR 62 (81)
T ss_pred HHHHHHHHHHHHHHHHc--CCCCeE-EECHHHHHHHHHHC-C-CCHHHHhcCCCCCHHHHHH
Confidence 45667888999855 43 332111 12236777776543 2 2789999999999876654
No 174
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=22.04 E-value=51 Score=31.27 Aligned_cols=19 Identities=32% Similarity=0.697 Sum_probs=17.7
Q ss_pred hhhhccccchHHHHHHHHH
Q 006771 67 KDLSQVKGVGKWILKLMQE 85 (632)
Q Consensus 67 k~l~~lkG~G~~i~~~L~~ 85 (632)
.||+-|.||||++-..|.+
T Consensus 67 DDLt~I~GIGPk~e~~Ln~ 85 (133)
T COG3743 67 DDLTRISGIGPKLEKVLNE 85 (133)
T ss_pred ccchhhcccCHHHHHHHHH
Confidence 7999999999999999975
No 175
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=21.73 E-value=74 Score=35.83 Aligned_cols=36 Identities=25% Similarity=0.261 Sum_probs=30.0
Q ss_pred cchhhHHHHhcCcEeeecCCCceecChhHHHHHHHHHh
Q 006771 184 GWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 184 aWsSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~ 221 (632)
.|..++.|+.+|||...+. ++.||++|+-++..+..
T Consensus 401 ~~~~l~~l~~~gll~~~~~--~~~lT~~G~~~~d~i~~ 436 (453)
T PRK09249 401 ELERLAPLEADGLVELDEN--GITVTPKGRLLVRNIAM 436 (453)
T ss_pred HHHHHHHHHHCCCEEEECC--EEEECccchHHHHHHHH
Confidence 3556789999999998764 89999999999988764
No 176
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=21.68 E-value=75 Score=22.52 Aligned_cols=18 Identities=22% Similarity=0.372 Sum_probs=14.0
Q ss_pred hhhccccchHHHHHHHHH
Q 006771 68 DLSQVKGVGKWILKLMQE 85 (632)
Q Consensus 68 ~l~~lkG~G~~i~~~L~~ 85 (632)
.+..+.|||+++.++|..
T Consensus 12 pi~~~~GIG~kt~~kL~~ 29 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKLNK 29 (32)
T ss_dssp BGGGSTTS-HHHHHHHHC
T ss_pred CHHhhCCccHHHHHHHHH
Confidence 356899999999999864
No 177
>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]
Probab=21.47 E-value=1.9e+02 Score=35.26 Aligned_cols=74 Identities=19% Similarity=0.195 Sum_probs=58.7
Q ss_pred ccCCCCHHH--------HHHHHHHHHHHHh-CCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchH---HHHHH
Q 006771 15 VVCAENEEL--------AMYMLQKRQEMAE-TPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGK---WILKL 82 (632)
Q Consensus 15 ~~~~~N~~l--------~~~~~ew~~e~~e-~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~---~i~~~ 82 (632)
++++=||+- ..|+.+|+.-+.. .....++....+...|+.++-..|--.+..+++..+-++.+ -|..+
T Consensus 495 ~~~~~NPf~~l~~t~~n~~fl~~~~~~ll~~~~~~~~~~~~~~i~~~~~~~~~~~~~~r~~~~l~~~l~~~~~~~~l~sr 574 (796)
T COG3451 495 VPSGFNPFEILEDTDENREFLAEWLVKLLAHEGISLSPAEERAISAAINNLATAPKEDRTFSDLIELLGIKERPNSLASR 574 (796)
T ss_pred CCcccCchhccCCchhhHHHHHHHHHHHhhcccccccHHHHHHHHHHHHHhccCccccCcHHHHHHHhccCCCchhHHHH
Confidence 455667776 7889999888887 34455666677888999999887777788888888888884 79999
Q ss_pred HHHHhh
Q 006771 83 MQEFFE 88 (632)
Q Consensus 83 L~~~~~ 88 (632)
|+.||.
T Consensus 575 L~~~~~ 580 (796)
T COG3451 575 LAPWCE 580 (796)
T ss_pred HHHHhc
Confidence 999997
No 178
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=21.43 E-value=1e+02 Score=36.78 Aligned_cols=47 Identities=21% Similarity=0.456 Sum_probs=26.2
Q ss_pred CCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHhh
Q 006771 40 GLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFE 88 (632)
Q Consensus 40 g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~ 88 (632)
|++++.+..+-+.+.|+.+-.. -+..++.+++|||++++..|.+||.
T Consensus 518 ~IG~~~ak~L~~~f~sl~~l~~--As~eeL~~i~GIG~~~A~sI~~ff~ 564 (665)
T PRK07956 518 HVGEKAAKALARHFGSLEALRA--ASEEELAAVEGVGEVVAQSIVEFFA 564 (665)
T ss_pred CcCHHHHHHHHHHcCCHHHHHh--CCHHHHhccCCcCHHHHHHHHHHHh
Confidence 4444444444444443332111 2456777777777777777777765
No 179
>PF10987 DUF2806: Protein of unknown function (DUF2806); InterPro: IPR021254 This bacterial family of proteins has no known function.
Probab=21.10 E-value=2.6e+02 Score=28.59 Aligned_cols=62 Identities=13% Similarity=0.124 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHhh
Q 006771 23 LAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFE 88 (632)
Q Consensus 23 l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~ 88 (632)
=-+|+..|.+.|.+-+ .+.++..+.|.+-.=...|+.| +.+-|..|+.+-++-++.++.+|.
T Consensus 40 D~DWl~~f~~~A~~is---n~~mQ~LWakILa~Ei~~PGs~-SlrtL~~Lk~mt~~eA~lf~k~~~ 101 (219)
T PF10987_consen 40 DPDWLYRFFDMAEDIS---NEEMQELWAKILAGEIKNPGSF-SLRTLQTLKQMTKKEAQLFQKACS 101 (219)
T ss_pred ChHHHHHHHHHHHhcC---cHHHHHHHHHHHHHHhcCCCCC-CHHHHHHHHhCCHHHHHHHHHHHH
Confidence 3589999999999842 3589999999999999999876 689999999999999999998765
No 180
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=20.96 E-value=63 Score=25.66 Aligned_cols=29 Identities=24% Similarity=0.167 Sum_probs=21.4
Q ss_pred ccchhhHHHHhc---CcEeeecCCCceecChhHH
Q 006771 183 SGWSCMKTLITK---GLVVKSSCPAKYMLTPGGR 213 (632)
Q Consensus 183 taWsSmktLi~k---~LV~~~grP~rY~LTdeG~ 213 (632)
+.|..|+.|.+. .|+.+.++ .+.||++|.
T Consensus 29 ~vs~~i~~LE~~lg~~Lf~r~~~--~~~lT~~G~ 60 (60)
T PF00126_consen 29 AVSRQIKQLEEELGVPLFERSGR--GLRLTEAGE 60 (60)
T ss_dssp HHHHHHHHHHHHHTS-SEEECSS--SEEE-HHHH
T ss_pred HHHHHHHHHHHHhCCeEEEECCC--CeeEChhhC
Confidence 578888888644 78888887 599999995
No 181
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=20.88 E-value=1.8e+02 Score=34.13 Aligned_cols=62 Identities=13% Similarity=0.222 Sum_probs=48.8
Q ss_pred ccccCCCCHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHhccCCCCCChhhhhccccchHHHHHHHHHHhh
Q 006771 13 RRVVCAENEELAMYMLQKRQEMAETPKGLSENIDMTLSKAYNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFE 88 (632)
Q Consensus 13 ~~~~~~~N~~l~~~~~ew~~e~~e~~~g~~~~~~~ty~kA~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~ 88 (632)
.++.++.|..++.||..-+||+-. .+.+|-+-.++=.... +.|..|+|||++-.+.|=.||.
T Consensus 501 ~~i~l~~~s~~l~lLq~irDEaHR--------FAi~~hR~~r~k~~~~------S~Ld~I~GIG~kr~~~LL~~Fg 562 (574)
T TIGR00194 501 QGINIDLNSPALQLLQHIRDEAHR--------FAISFHRKKRLKASLQ------SPLLKIPGVGEKRVQKLLKYFG 562 (574)
T ss_pred ceeecCCCCHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHH------HHHhcCCCCCHHHHHHHHHHcC
Confidence 567888899999999999888754 4568877777654332 6778999999999999877775
No 182
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=20.82 E-value=82 Score=31.48 Aligned_cols=29 Identities=24% Similarity=0.288 Sum_probs=24.5
Q ss_pred hhHHHHhcCcEeeec------CCCceecChhHHHH
Q 006771 187 CMKTLITKGLVVKSS------CPAKYMLTPGGREA 215 (632)
Q Consensus 187 SmktLi~k~LV~~~g------rP~rY~LTdeG~el 215 (632)
-|+||+.+|||.+.| ||.-|-.|+.-.+.
T Consensus 123 ~i~~L~e~glI~~~g~~~~~Grp~ly~tT~~Fl~~ 157 (184)
T COG1386 123 VISTLLERGLIREVGRRDTPGRPYLYGTTEKFLDY 157 (184)
T ss_pred HHHHHHHCCCeEecCCCCCCCCceeeeccHHHHHH
Confidence 689999999998665 67789999988764
No 183
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=20.55 E-value=66 Score=33.35 Aligned_cols=49 Identities=16% Similarity=0.295 Sum_probs=38.4
Q ss_pred CCCCchhHHHHHHHH-HHHHhccCCCCCChhhhhccccchHHHHHHHHHHhh
Q 006771 38 PKGLSENIDMTLSKA-YNNICDAKNPIKTLKDLSQVKGVGKWILKLMQEFFE 88 (632)
Q Consensus 38 ~~g~~~~~~~ty~kA-~~sl~~~p~~~~~~k~l~~lkG~G~~i~~~L~~~~~ 88 (632)
..|++.+....+.++ +.|+.+- .--++.+|.+++|||++++..+.+++.
T Consensus 8 IpGIG~krakkLl~~GF~Sve~I--k~AS~eEL~~V~GIg~k~AekI~e~l~ 57 (232)
T PRK12766 8 ISGVGPSKAEALREAGFESVEDV--RAADQSELAEVDGIGNALAARIKADVG 57 (232)
T ss_pred CCCcCHHHHHHHHHcCCCCHHHH--HhCCHHHHHHccCCCHHHHHHHHHHhc
Confidence 457887777777777 6666542 234689999999999999999999886
No 184
>COG3453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.29 E-value=95 Score=29.21 Aligned_cols=33 Identities=15% Similarity=0.091 Sum_probs=26.0
Q ss_pred CCchHHHHHHHHHhcCCCCCCCCCHHHHHHHHHhcC
Q 006771 121 RNSVAYALLITLYRGTTNGNEFMRKQDLIDAAEASG 156 (632)
Q Consensus 121 ~rSGaYAiLlaL~~~~~~~~~~mtK~eLi~~Aq~~~ 156 (632)
=|||+.++.|=...+ . .++|.++||++.+|.++
T Consensus 94 CrsGtRs~~ly~~~~-~--~~gm~~de~~a~g~a~G 126 (130)
T COG3453 94 CRSGTRSLNLYGLGE-L--DGGMSRDEIEALGQAAG 126 (130)
T ss_pred ecCCchHHHHHHHHH-H--hcCCCHHHHHHHHHhhC
Confidence 379999987665555 2 47899999999999874
No 185
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=20.12 E-value=1.2e+02 Score=31.10 Aligned_cols=40 Identities=25% Similarity=0.272 Sum_probs=34.2
Q ss_pred ccchhhHHHHhcCcEeeecCCCceecChhHHHHHHHHHhh
Q 006771 183 SGWSCMKTLITKGLVVKSSCPAKYMLTPGGREAARECLSR 222 (632)
Q Consensus 183 taWsSmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~~ 222 (632)
|...=++||.++|||.+.....+|.|+..=.+++......
T Consensus 44 tv~Rll~tL~~~G~l~~~~~~~~Y~lG~~~~~lg~~~~~~ 83 (257)
T PRK15090 44 TVYRFLQTMKTLGYVAQEGESEKYSLTLKLFELGAKALQN 83 (257)
T ss_pred HHHHHHHHHHHCCCEEEcCCCCcEEecHHHHHHHHHHHhh
Confidence 6788899999999999876667899999999999876543
No 186
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=20.05 E-value=1.1e+02 Score=33.95 Aligned_cols=33 Identities=15% Similarity=0.216 Sum_probs=27.4
Q ss_pred hhHHHHhcCcEeeecCCCceecChhHHHHHHHHHh
Q 006771 187 CMKTLITKGLVVKSSCPAKYMLTPGGREAARECLS 221 (632)
Q Consensus 187 SmktLi~k~LV~~~grP~rY~LTdeG~elA~~l~~ 221 (632)
-++.|+++|||...+. ++.||++|+-++..+..
T Consensus 358 ~l~~l~~~gll~~~~~--~~~LT~~G~~~~d~i~~ 390 (394)
T PRK08898 358 QLAAAEQRGLLERDHT--RIRPTPLGQRFLNDLQE 390 (394)
T ss_pred HHHHHHHCCCEEEECC--EEEEChhHhHHHHHHHH
Confidence 4567889999998765 89999999999887653
No 187
>PF03832 WSK: WSK motif; InterPro: IPR001573 Cell signalling mediated via GPCRs (G-protein-coupled receptors) involves the assembly of receptors, G-proteins, effectors and downstream elements into complexes that approach in design 'solid-state' signalling devices. Scaffold molecules, such as the AKAPs (A-kinase anchoring proteins), were discovered more than a decade ago and represent dynamic platforms, enabling multivalent signalling []. This family of functionally related proteins is classified on the basis of their ability to associate with the PKA holoenzyme inside cells. A shared property of most, if not all, AKAPs is the ability to form multivalent signal transduction complexes. Each anchoring protein contains at least two functional motifs []. The conserved PKA binding motif forms an amphipathic helix of 14-18 residues that interacts with hydrophobic determinants located in the extreme N terminus of the regulatory subunit dimmer. The subcellular address of each AKAP is encoded by a unique targeting motif. Gravin, an autoantigen recognised by serum from myasthenia gravis patients contains 3 repeats of this domain []. The WSK motif is short motif, named after three conserved residues found in the WXSXK motif, found in protein kinase A anchoring proteins. ; GO: 0006605 protein targeting, 0007165 signal transduction
Probab=20.05 E-value=40 Score=24.15 Aligned_cols=12 Identities=42% Similarity=0.836 Sum_probs=10.0
Q ss_pred ccchhhHHHHhc
Q 006771 183 SGWSCMKTLITK 194 (632)
Q Consensus 183 taWsSmktLi~k 194 (632)
++|.|+|-|+..
T Consensus 5 ~~W~S~KrlVt~ 16 (31)
T PF03832_consen 5 STWASFKRLVTP 16 (31)
T ss_pred chhHHHHhhcCc
Confidence 589999999854
Done!