Query 038397
Match_columns 1102
No_of_seqs 220 out of 350
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 10:36:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038397.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038397hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1513 Nuclear helicase MOP-3 100.0 3E-292 6E-297 2472.2 55.9 892 159-1099 209-1143(1300)
2 PF13872 AAA_34: P-loop contai 100.0 3E-118 6E-123 976.0 23.4 299 181-484 2-303 (303)
3 PF13871 Helicase_C_4: Helicas 100.0 7.7E-97 2E-101 804.5 28.2 275 751-1040 1-278 (278)
4 PRK04914 ATP-dependent helicas 99.4 4.6E-10 9.9E-15 141.8 33.5 188 219-433 155-345 (956)
5 PLN03142 Probable chromatin-re 99.3 4.9E-10 1.1E-14 142.1 27.8 239 215-485 168-418 (1033)
6 PF00176 SNF2_N: SNF2 family N 99.2 4.9E-10 1.1E-14 122.2 16.5 240 221-484 2-260 (299)
7 PRK13766 Hef nuclease; Provisi 99.1 6.6E-09 1.4E-13 129.8 25.5 76 806-891 417-492 (773)
8 cd00046 DEXDc DEAD-like helica 98.9 2.4E-09 5.1E-14 101.1 8.8 141 243-401 2-144 (144)
9 smart00487 DEXDc DEAD-like hel 98.6 1.1E-07 2.4E-12 95.4 8.0 167 215-409 7-178 (201)
10 PF04851 ResIII: Type III rest 98.5 2.8E-07 6E-12 93.1 9.2 163 217-401 4-182 (184)
11 TIGR00603 rad25 DNA repair hel 98.5 0.00013 2.9E-09 90.7 31.7 157 216-404 255-414 (732)
12 PF00270 DEAD: DEAD/DEAH box h 98.4 2.1E-07 4.5E-12 93.5 5.5 165 219-408 2-169 (169)
13 cd00268 DEADc DEAD-box helicas 98.2 4E-06 8.6E-11 87.4 8.0 164 216-408 21-191 (203)
14 PF07652 Flavi_DEAD: Flaviviru 97.9 6.9E-05 1.5E-09 76.4 9.5 125 250-403 13-138 (148)
15 PHA02558 uvsW UvsW helicase; P 97.8 9.8E-05 2.1E-09 88.8 12.5 147 214-402 112-260 (501)
16 KOG0390 DNA repair protein, SN 97.7 0.0012 2.5E-08 82.5 19.5 116 750-891 601-720 (776)
17 TIGR00348 hsdR type I site-spe 97.5 0.00041 8.9E-09 86.4 11.5 160 219-403 241-404 (667)
18 KOG1244 Predicted transcriptio 97.5 1.9E-05 4.1E-10 86.1 -0.2 50 662-711 283-332 (336)
19 KOG1000 Chromatin remodeling p 97.5 0.00094 2E-08 78.6 12.7 181 217-437 199-382 (689)
20 KOG0387 Transcription-coupled 97.4 0.0011 2.3E-08 81.7 13.1 246 204-485 195-477 (923)
21 PRK02362 ski2-like helicase; P 97.4 0.00068 1.5E-08 85.3 12.0 158 216-401 23-181 (737)
22 COG1111 MPH1 ERCC4-like helica 97.4 0.0026 5.6E-08 75.6 15.2 201 245-497 33-241 (542)
23 COG1061 SSL2 DNA or RNA helica 97.3 0.0015 3.3E-08 77.6 11.8 126 214-366 34-160 (442)
24 PRK00254 ski2-like helicase; P 97.2 0.0018 4E-08 81.3 11.8 155 216-401 23-179 (720)
25 PF00271 Helicase_C: Helicase 97.1 0.00046 9.9E-09 61.6 4.1 52 806-865 27-78 (78)
26 PRK01172 ski2-like helicase; P 97.1 0.0024 5.2E-08 79.6 10.8 155 217-401 23-179 (674)
27 KOG0825 PHD Zn-finger protein 97.0 0.00059 1.3E-08 83.0 4.7 53 658-710 213-266 (1134)
28 PRK01297 ATP-dependent RNA hel 97.0 0.0023 5E-08 76.4 9.3 159 216-404 109-283 (475)
29 PRK11776 ATP-dependent RNA hel 96.9 0.0019 4E-08 76.8 7.9 157 216-401 26-188 (460)
30 cd00079 HELICc Helicase superf 96.9 0.0009 1.9E-08 64.0 4.3 59 805-872 71-129 (131)
31 PRK11448 hsdR type I restricti 96.9 0.0038 8.3E-08 81.8 11.2 175 217-402 414-595 (1123)
32 KOG1924 RhoA GTPase effector D 96.8 0.0022 4.8E-08 78.4 7.5 31 750-783 1040-1070(1102)
33 TIGR00643 recG ATP-dependent D 96.8 0.0043 9.2E-08 77.0 10.2 153 216-401 235-396 (630)
34 TIGR01587 cas3_core CRISPR-ass 96.8 0.0042 9.1E-08 70.9 9.4 142 245-400 3-164 (358)
35 PTZ00424 helicase 45; Provisio 96.8 0.0029 6.3E-08 73.2 7.6 153 216-400 50-210 (401)
36 smart00490 HELICc helicase sup 96.6 0.0028 6E-08 55.6 4.6 53 805-865 30-82 (82)
37 PRK00398 rpoP DNA-directed RNA 96.6 0.0014 3.1E-08 54.3 2.4 32 16-47 2-33 (46)
38 PRK10590 ATP-dependent RNA hel 96.5 0.0044 9.6E-08 73.7 7.2 76 806-893 289-364 (456)
39 PRK04537 ATP-dependent RNA hel 96.4 0.006 1.3E-07 74.9 7.8 155 216-401 31-202 (572)
40 TIGR00595 priA primosomal prot 96.4 0.0062 1.3E-07 73.8 7.1 132 246-400 3-138 (505)
41 PRK11192 ATP-dependent RNA hel 96.4 0.0093 2E-07 70.2 8.4 74 806-891 289-362 (434)
42 KOG0385 Chromatin remodeling c 96.3 0.4 8.7E-06 60.0 21.9 233 209-483 160-414 (971)
43 TIGR03817 DECH_helic helicase/ 96.3 0.017 3.6E-07 73.2 10.7 162 216-402 36-205 (742)
44 PRK00398 rpoP DNA-directed RNA 96.2 0.003 6.5E-08 52.4 2.4 33 96-128 3-35 (46)
45 PRK10917 ATP-dependent DNA hel 96.1 0.01 2.2E-07 74.5 7.5 152 216-401 261-419 (681)
46 KOG0354 DEAD-box like helicase 96.1 0.025 5.4E-07 70.6 10.6 158 217-404 63-224 (746)
47 PRK05580 primosome assembly pr 96.1 0.016 3.6E-07 72.6 9.2 157 215-400 143-303 (679)
48 TIGR00614 recQ_fam ATP-depende 96.1 0.033 7.2E-07 66.7 11.1 156 216-401 11-172 (470)
49 PLN00206 DEAD-box ATP-dependen 96.0 0.018 3.8E-07 70.0 8.5 80 806-897 412-491 (518)
50 KOG1002 Nucleotide excision re 96.0 0.0071 1.5E-07 71.4 4.8 141 219-388 187-345 (791)
51 PRK11634 ATP-dependent RNA hel 95.9 0.018 3.9E-07 71.6 8.5 156 216-402 28-191 (629)
52 PRK11131 ATP-dependent RNA hel 95.9 0.019 4.2E-07 75.7 8.7 160 198-401 64-228 (1294)
53 PRK11057 ATP-dependent DNA hel 95.9 0.023 4.9E-07 70.4 8.8 169 216-417 25-199 (607)
54 PTZ00110 helicase; Provisional 95.9 0.014 3E-07 71.4 6.8 78 806-895 421-498 (545)
55 PRK14714 DNA polymerase II lar 95.9 0.0061 1.3E-07 78.6 3.9 29 97-126 693-721 (1337)
56 PRK04837 ATP-dependent RNA hel 95.8 0.017 3.6E-07 68.0 6.7 155 216-401 30-200 (423)
57 TIGR01967 DEAH_box_HrpA ATP-de 95.7 0.022 4.8E-07 75.3 8.3 159 198-401 57-221 (1283)
58 COG1205 Distinct helicase fami 95.6 0.069 1.5E-06 68.7 11.6 162 219-403 73-244 (851)
59 TIGR00580 mfd transcription-re 95.5 0.027 5.8E-07 72.9 7.8 152 216-401 451-609 (926)
60 TIGR01053 LSD1 zinc finger dom 95.4 0.011 2.4E-07 45.6 2.3 29 17-45 1-29 (31)
61 KOG1015 Transcription regulato 95.3 1.2 2.6E-05 57.0 20.3 251 216-486 668-961 (1567)
62 KOG0389 SNF2 family DNA-depend 95.1 0.41 9E-06 60.0 15.3 283 216-540 399-711 (941)
63 PHA02653 RNA helicase NPH-II; 95.0 0.082 1.8E-06 66.4 9.4 68 809-878 443-514 (675)
64 PRK13767 ATP-dependent helicas 94.9 0.1 2.2E-06 67.5 10.4 161 215-401 31-217 (876)
65 TIGR01053 LSD1 zinc finger dom 94.9 0.016 3.4E-07 44.8 1.9 28 96-123 1-28 (31)
66 KOG0384 Chromodomain-helicase 94.9 0.91 2E-05 59.4 18.1 343 212-599 366-752 (1373)
67 COG4096 HsdR Type I site-speci 94.9 0.072 1.6E-06 66.9 8.3 122 219-364 168-297 (875)
68 PF13401 AAA_22: AAA domain; P 94.8 0.1 2.2E-06 50.4 7.8 118 240-402 4-127 (131)
69 PRK11192 ATP-dependent RNA hel 94.7 0.026 5.7E-07 66.5 4.1 157 216-401 23-188 (434)
70 PTZ00110 helicase; Provisional 94.6 0.064 1.4E-06 65.7 7.0 154 216-401 152-318 (545)
71 PRK10689 transcription-repair 94.5 0.063 1.4E-06 71.0 7.3 156 216-403 600-760 (1147)
72 PLN00206 DEAD-box ATP-dependen 94.4 0.068 1.5E-06 65.0 6.8 155 216-401 143-310 (518)
73 PRK11776 ATP-dependent RNA hel 94.2 0.071 1.5E-06 63.5 6.1 76 806-893 286-361 (460)
74 PF00628 PHD: PHD-finger; Int 94.2 0.0072 1.6E-07 50.5 -1.6 47 663-709 2-50 (51)
75 KOG4439 RNA polymerase II tran 94.0 0.57 1.2E-05 58.2 13.0 237 241-502 345-608 (901)
76 KOG4299 PHD Zn-finger protein 93.9 0.029 6.2E-07 68.2 2.0 49 662-710 255-305 (613)
77 TIGR01970 DEAH_box_HrpB ATP-de 93.5 0.38 8.3E-06 61.8 11.2 147 220-403 5-158 (819)
78 PRK01297 ATP-dependent RNA hel 93.4 0.076 1.6E-06 63.7 4.4 63 805-876 378-440 (475)
79 PRK10590 ATP-dependent RNA hel 93.3 0.13 2.7E-06 61.6 6.2 155 216-401 23-190 (456)
80 PRK14559 putative protein seri 93.2 0.086 1.9E-06 65.8 4.6 35 98-139 29-63 (645)
81 COG0610 Type I site-specific r 93.0 0.21 4.5E-06 65.2 7.7 142 239-404 271-416 (962)
82 TIGR03158 cas3_cyano CRISPR-as 92.9 0.45 9.7E-06 55.3 9.6 46 244-293 17-62 (357)
83 PF09788 Tmemb_55A: Transmembr 92.9 0.26 5.6E-06 54.7 7.0 89 10-128 99-191 (256)
84 PRK04837 ATP-dependent RNA hel 92.8 0.069 1.5E-06 62.9 3.0 54 806-867 299-352 (423)
85 cd04718 BAH_plant_2 BAH, or Br 92.7 0.067 1.4E-06 55.1 2.2 27 684-710 1-27 (148)
86 PRK11664 ATP-dependent RNA hel 92.6 0.52 1.1E-05 60.6 10.5 141 220-402 8-160 (812)
87 TIGR01389 recQ ATP-dependent D 92.3 0.76 1.6E-05 56.9 11.0 155 216-402 13-173 (591)
88 PRK09751 putative ATP-dependen 91.9 0.29 6.3E-06 66.1 7.2 134 249-402 4-170 (1490)
89 PRK04023 DNA polymerase II lar 91.7 0.12 2.7E-06 65.9 3.2 24 97-126 652-675 (1121)
90 TIGR00614 recQ_fam ATP-depende 91.6 0.22 4.9E-06 59.7 5.4 56 806-869 270-325 (470)
91 TIGR02098 MJ0042_CXXC MJ0042 f 91.6 0.12 2.7E-06 40.9 2.1 29 16-44 1-34 (38)
92 PF13604 AAA_30: AAA domain; P 91.6 1 2.3E-05 48.0 9.7 63 217-289 2-65 (196)
93 COG1643 HrpA HrpA-like helicas 91.5 0.53 1.2E-05 60.4 8.7 152 200-401 42-205 (845)
94 COG0513 SrmB Superfamily II DN 91.2 0.3 6.5E-06 59.6 5.9 80 806-896 317-396 (513)
95 COG2888 Predicted Zn-ribbon RN 91.1 0.11 2.4E-06 45.6 1.5 31 97-127 10-40 (61)
96 PF07754 DUF1610: Domain of un 91.1 0.12 2.7E-06 37.8 1.4 24 99-122 1-24 (24)
97 KOG1924 RhoA GTPase effector D 91.0 0.44 9.6E-06 59.3 6.9 25 339-363 862-887 (1102)
98 PF04810 zf-Sec23_Sec24: Sec23 90.9 0.071 1.5E-06 43.3 0.1 33 18-50 3-39 (40)
99 PRK04537 ATP-dependent RNA hel 90.7 0.22 4.8E-06 61.5 4.2 54 806-867 301-354 (572)
100 PRK10917 ATP-dependent DNA hel 90.7 0.84 1.8E-05 57.6 9.3 99 806-919 525-640 (681)
101 PTZ00424 helicase 45; Provisio 90.6 0.18 4E-06 58.4 3.2 53 806-866 311-363 (401)
102 PRK09401 reverse gyrase; Revie 90.4 1.6 3.4E-05 58.4 11.8 126 218-366 82-215 (1176)
103 COG1996 RPC10 DNA-directed RNA 90.2 0.11 2.5E-06 44.1 0.7 34 15-48 4-37 (49)
104 TIGR01587 cas3_core CRISPR-ass 90.1 0.51 1.1E-05 54.1 6.1 63 805-878 271-336 (358)
105 PF06943 zf-LSD1: LSD1 zinc fi 89.7 0.26 5.6E-06 36.5 2.2 24 20-43 1-24 (25)
106 KOG0957 PHD finger protein [Ge 89.6 2.8 6E-05 50.4 11.5 48 660-707 544-595 (707)
107 PF07754 DUF1610: Domain of un 89.5 0.21 4.5E-06 36.6 1.5 23 20-43 1-24 (24)
108 KOG0341 DEAD-box protein abstr 89.0 0.3 6.5E-06 56.9 3.2 55 805-867 464-518 (610)
109 PRK11057 ATP-dependent DNA hel 88.9 0.38 8.2E-06 59.9 4.2 54 806-867 280-333 (607)
110 TIGR00643 recG ATP-dependent D 88.9 1.1 2.5E-05 55.9 8.4 61 806-877 502-563 (630)
111 smart00249 PHD PHD zinc finger 88.7 0.14 3.1E-06 40.7 0.3 43 665-707 4-47 (47)
112 KOG0920 ATP-dependent RNA heli 88.7 2.1 4.6E-05 55.4 10.5 173 219-433 175-361 (924)
113 PF10122 Mu-like_Com: Mu-like 88.2 0.21 4.6E-06 42.7 0.9 36 16-51 3-40 (51)
114 COG1203 CRISPR-associated heli 88.1 1.7 3.8E-05 55.4 9.4 148 243-400 216-379 (733)
115 PRK11634 ATP-dependent RNA hel 88.1 0.82 1.8E-05 57.3 6.3 72 806-889 289-360 (629)
116 KOG1000 Chromatin remodeling p 88.0 0.49 1.1E-05 56.8 4.1 89 805-902 535-626 (689)
117 TIGR02621 cas3_GSU0051 CRISPR- 87.8 0.73 1.6E-05 59.2 5.7 69 218-295 17-87 (844)
118 COG2888 Predicted Zn-ribbon RN 87.8 0.32 6.9E-06 42.9 1.8 24 19-42 11-34 (61)
119 PRK09694 helicase Cas3; Provis 87.6 2.2 4.7E-05 55.5 9.8 70 320-401 411-480 (878)
120 TIGR01054 rgy reverse gyrase. 87.2 1.6 3.4E-05 58.5 8.5 125 218-366 80-213 (1171)
121 COG1996 RPC10 DNA-directed RNA 87.2 0.29 6.2E-06 41.7 1.2 32 95-126 5-36 (49)
122 COG4581 Superfamily II RNA hel 87.0 2.4 5.2E-05 55.5 9.7 159 196-400 109-269 (1041)
123 KOG1245 Chromatin remodeling c 86.8 0.16 3.4E-06 68.2 -0.9 49 662-710 1110-1158(1404)
124 TIGR01384 TFS_arch transcripti 86.7 0.71 1.5E-05 44.4 3.7 27 19-47 2-28 (104)
125 smart00659 RPOLCX RNA polymera 86.6 0.56 1.2E-05 39.1 2.6 31 16-47 1-31 (44)
126 PF13719 zinc_ribbon_5: zinc-r 86.5 0.48 1E-05 37.9 2.0 28 16-43 1-33 (37)
127 TIGR03817 DECH_helic helicase/ 86.4 1.2 2.6E-05 56.9 6.6 135 806-971 323-457 (742)
128 PF11023 DUF2614: Protein of u 86.4 0.31 6.7E-06 48.0 1.1 36 14-51 66-101 (114)
129 PRK00415 rps27e 30S ribosomal 86.3 0.82 1.8E-05 40.4 3.5 38 10-47 4-42 (59)
130 PF13240 zinc_ribbon_2: zinc-r 86.3 0.29 6.4E-06 35.4 0.6 22 19-44 1-22 (23)
131 KOG0350 DEAD-box ATP-dependent 86.3 1.1 2.3E-05 54.2 5.5 76 805-891 476-551 (620)
132 PRK14890 putative Zn-ribbon RN 86.2 0.5 1.1E-05 41.7 2.1 33 97-129 8-40 (59)
133 TIGR01389 recQ ATP-dependent D 86.1 0.76 1.7E-05 56.8 4.6 54 806-867 268-321 (591)
134 TIGR02098 MJ0042_CXXC MJ0042 f 86.1 0.39 8.4E-06 38.1 1.3 32 95-126 1-37 (38)
135 cd01121 Sms Sms (bacterial rad 85.9 7.2 0.00016 46.1 12.1 86 245-365 86-171 (372)
136 TIGR01206 lysW lysine biosynth 85.5 0.5 1.1E-05 41.1 1.8 31 17-47 2-34 (54)
137 smart00661 RPOL9 RNA polymeras 85.2 0.53 1.2E-05 39.5 1.8 32 19-50 2-35 (52)
138 cd00009 AAA The AAA+ (ATPases 85.0 14 0.00031 34.9 11.9 37 243-280 21-57 (151)
139 KOG0922 DEAH-box RNA helicase 84.9 2.1 4.5E-05 53.3 7.3 131 223-400 57-204 (674)
140 PF13248 zf-ribbon_3: zinc-rib 84.6 0.45 9.8E-06 35.2 1.0 25 96-124 2-26 (26)
141 PRK13700 conjugal transfer pro 84.4 2.9 6.3E-05 53.0 8.4 254 240-558 184-458 (732)
142 PRK15483 type III restriction- 84.2 3.6 7.8E-05 53.8 9.3 156 241-410 59-260 (986)
143 PF13717 zinc_ribbon_4: zinc-r 84.1 0.76 1.6E-05 36.7 2.1 28 16-43 1-33 (36)
144 TIGR00580 mfd transcription-re 84.0 2.1 4.6E-05 56.0 7.2 82 806-900 706-788 (926)
145 PLN03137 ATP-dependent DNA hel 83.9 1 2.2E-05 59.5 4.2 55 806-868 724-778 (1195)
146 smart00834 CxxC_CXXC_SSSS Puta 83.5 0.74 1.6E-05 36.7 1.9 27 17-43 5-34 (41)
147 KOG0386 Chromatin remodeling c 83.4 0.8 1.7E-05 58.8 3.0 118 212-368 390-531 (1157)
148 COG1201 Lhr Lhr-like helicases 82.8 29 0.00063 45.1 16.3 159 216-402 22-194 (814)
149 PRK01172 ski2-like helicase; P 82.7 0.87 1.9E-05 57.2 3.0 61 806-866 305-365 (674)
150 PF09538 FYDLN_acid: Protein o 82.7 0.84 1.8E-05 45.0 2.3 33 15-48 7-39 (108)
151 PF08271 TF_Zn_Ribbon: TFIIB z 82.7 0.75 1.6E-05 37.7 1.6 27 18-44 1-28 (43)
152 COG1202 Superfamily II helicas 82.6 5.2 0.00011 49.3 9.1 138 245-400 236-381 (830)
153 PF13086 AAA_11: AAA domain; P 82.4 1.9 4.1E-05 45.2 5.0 67 216-292 1-75 (236)
154 PF14353 CpXC: CpXC protein 82.1 0.99 2.1E-05 45.0 2.6 31 17-47 1-50 (128)
155 COG1198 PriA Primosomal protei 81.7 1.1 2.4E-05 56.8 3.4 23 96-123 462-484 (730)
156 PRK10689 transcription-repair 81.6 2.2 4.7E-05 57.1 6.1 82 806-901 855-938 (1147)
157 KOG1512 PHD Zn-finger protein 81.5 0.61 1.3E-05 52.3 0.9 45 662-708 316-361 (381)
158 PF13240 zinc_ribbon_2: zinc-r 81.4 0.7 1.5E-05 33.5 0.9 23 98-124 1-23 (23)
159 PF03833 PolC_DP2: DNA polymer 80.9 0.5 1.1E-05 59.8 0.0 24 96-125 680-703 (900)
160 COG3421 Uncharacterized protei 80.8 6.3 0.00014 48.9 9.0 148 250-411 6-175 (812)
161 PF09297 zf-NADH-PPase: NADH p 80.8 0.86 1.9E-05 35.2 1.3 26 19-44 5-30 (32)
162 TIGR01206 lysW lysine biosynth 80.8 1.2 2.6E-05 38.8 2.3 31 96-126 2-34 (54)
163 PF03604 DNA_RNApol_7kD: DNA d 79.8 0.95 2.1E-05 35.4 1.2 27 19-46 2-28 (32)
164 PF13824 zf-Mss51: Zinc-finger 79.7 0.98 2.1E-05 39.5 1.4 23 19-44 1-23 (55)
165 COG1204 Superfamily II helicas 79.4 6.9 0.00015 50.4 9.3 141 242-400 48-189 (766)
166 PRK08727 hypothetical protein; 79.2 9.5 0.00021 41.8 9.2 125 243-435 43-173 (233)
167 PRK14701 reverse gyrase; Provi 78.9 7 0.00015 54.2 9.6 124 218-366 81-214 (1638)
168 PRK05642 DNA replication initi 78.7 46 0.00099 36.6 14.3 72 355-435 100-177 (234)
169 smart00659 RPOLCX RNA polymera 78.5 1.4 3.1E-05 36.7 1.9 29 97-126 3-31 (44)
170 KOG4684 Uncharacterized conser 77.7 4 8.6E-05 44.5 5.4 85 10-126 114-201 (275)
171 PF01155 HypA: Hydrogenase exp 77.3 0.95 2.1E-05 44.6 0.7 30 14-45 67-96 (113)
172 PF06733 DEAD_2: DEAD_2; Inte 76.9 2.1 4.5E-05 44.5 3.2 43 317-368 117-161 (174)
173 TIGR00373 conserved hypothetic 76.8 0.92 2E-05 47.3 0.5 33 96-128 109-142 (158)
174 PRK13767 ATP-dependent helicas 76.8 3.2 6.9E-05 54.1 5.4 62 806-875 334-395 (876)
175 smart00531 TFIIE Transcription 76.5 1.1 2.3E-05 46.1 0.9 37 94-130 97-139 (147)
176 PRK02935 hypothetical protein; 76.4 1.5 3.2E-05 42.9 1.7 36 14-51 67-102 (110)
177 PRK06266 transcription initiat 76.4 1 2.3E-05 47.9 0.7 34 95-128 116-150 (178)
178 PLN00162 transport protein sec 76.1 3 6.4E-05 53.6 4.8 35 17-51 53-91 (761)
179 COG1198 PriA Primosomal protei 76.0 1.9 4.1E-05 54.8 3.0 26 18-43 445-470 (730)
180 PRK14714 DNA polymerase II lar 75.6 1.9 4E-05 57.0 2.8 26 97-127 680-705 (1337)
181 COG2051 RPS27A Ribosomal prote 75.4 2.5 5.4E-05 38.3 2.7 39 10-48 12-51 (67)
182 PRK06067 flagellar accessory p 75.1 11 0.00024 40.9 8.3 105 244-364 28-132 (234)
183 PF06943 zf-LSD1: LSD1 zinc fi 75.0 2.3 4.9E-05 31.7 1.9 24 99-122 1-24 (25)
184 PF13717 zinc_ribbon_4: zinc-r 74.9 1.7 3.8E-05 34.6 1.4 17 35-51 2-18 (36)
185 TIGR02621 cas3_GSU0051 CRISPR- 74.8 4 8.6E-05 52.8 5.4 47 813-870 337-383 (844)
186 KOG2462 C2H2-type Zn-finger pr 74.6 1.8 3.8E-05 48.8 2.0 81 19-135 132-235 (279)
187 PLN00209 ribosomal protein S27 74.3 2.9 6.3E-05 39.6 3.0 37 11-47 30-67 (86)
188 PRK00411 cdc6 cell division co 74.3 38 0.00083 39.4 13.0 71 201-278 22-93 (394)
189 PRK14890 putative Zn-ribbon RN 74.3 1.8 3.8E-05 38.4 1.5 25 19-43 9-33 (59)
190 PRK02362 ski2-like helicase; P 74.0 2.4 5.2E-05 54.0 3.2 62 806-867 323-385 (737)
191 PRK03681 hypA hydrogenase nick 73.5 2.1 4.6E-05 42.4 2.0 30 14-44 67-96 (114)
192 PRK03824 hypA hydrogenase nick 73.2 2.3 5.1E-05 43.3 2.3 28 16-43 69-115 (135)
193 PF11023 DUF2614: Protein of u 72.9 1.8 3.9E-05 42.8 1.3 36 92-129 65-100 (114)
194 PTZ00083 40S ribosomal protein 72.6 3.3 7.1E-05 39.2 2.9 37 11-47 29-66 (85)
195 smart00531 TFIIE Transcription 72.2 1.4 3E-05 45.3 0.5 32 16-47 98-135 (147)
196 PF12773 DZR: Double zinc ribb 72.0 3 6.5E-05 34.8 2.3 28 97-125 13-40 (50)
197 PRK12380 hydrogenase nickel in 72.0 2.1 4.6E-05 42.3 1.6 28 14-43 67-94 (113)
198 KOG0948 Nuclear exosomal RNA h 71.7 5.8 0.00013 50.2 5.5 151 197-400 120-275 (1041)
199 PHA02653 RNA helicase NPH-II; 71.4 5 0.00011 50.9 5.1 39 354-402 293-332 (675)
200 PHA00626 hypothetical protein 71.3 2.6 5.6E-05 37.0 1.7 28 18-45 1-33 (59)
201 PRK11823 DNA repair protein Ra 71.2 63 0.0014 39.2 14.0 87 245-366 84-170 (446)
202 smart00834 CxxC_CXXC_SSSS Puta 71.1 3 6.4E-05 33.3 2.0 28 96-123 5-35 (41)
203 PF03604 DNA_RNApol_7kD: DNA d 71.0 3.1 6.7E-05 32.6 2.0 27 98-125 2-28 (32)
204 PF13248 zf-ribbon_3: zinc-rib 71.0 1.9 4.2E-05 31.9 0.8 24 17-44 2-25 (26)
205 KOG4443 Putative transcription 70.9 1.6 3.5E-05 53.9 0.6 48 661-708 69-116 (694)
206 PRK13826 Dtr system oriT relax 70.5 19 0.00042 48.1 10.2 53 216-279 381-434 (1102)
207 PF09297 zf-NADH-PPase: NADH p 70.1 2.5 5.4E-05 32.6 1.3 27 97-123 4-30 (32)
208 TIGR00100 hypA hydrogenase nic 70.0 2.8 6.1E-05 41.6 2.0 29 14-44 67-95 (115)
209 PRK08181 transposase; Validate 69.9 19 0.00041 40.9 8.7 55 217-278 88-142 (269)
210 PF01155 HypA: Hydrogenase exp 69.7 1.8 4E-05 42.7 0.7 28 95-124 69-96 (113)
211 KOG0328 Predicted ATP-dependen 69.4 4.7 0.0001 45.9 3.8 156 218-404 51-213 (400)
212 PF06221 zf-C2HC5: Putative zi 69.2 2.7 5.8E-05 37.1 1.5 29 97-126 19-47 (57)
213 TIGR02300 FYDLN_acid conserved 69.1 3.9 8.5E-05 41.4 2.8 32 16-48 8-39 (129)
214 PRK14559 putative protein seri 69.0 3.3 7.1E-05 52.2 2.8 24 97-126 16-39 (645)
215 PRK09751 putative ATP-dependen 68.9 7.9 0.00017 53.1 6.3 51 806-864 321-371 (1490)
216 PHA00012 I assembly protein 68.8 29 0.00062 40.8 9.9 23 249-271 9-31 (361)
217 PLN03137 ATP-dependent DNA hel 68.7 26 0.00056 47.1 10.6 159 216-402 460-627 (1195)
218 TIGR00100 hypA hydrogenase nic 68.5 3.4 7.4E-05 41.0 2.3 28 94-123 68-95 (115)
219 PF13719 zinc_ribbon_5: zinc-r 67.7 3.1 6.8E-05 33.3 1.5 28 96-123 2-34 (37)
220 KOG2907 RNA polymerase I trans 67.5 1.6 3.4E-05 43.2 -0.3 27 19-45 9-35 (116)
221 PRK12380 hydrogenase nickel in 66.5 3.9 8.5E-05 40.5 2.2 28 94-123 68-95 (113)
222 KOG1546 Metacaspase involved i 66.3 5.1 0.00011 46.3 3.3 28 18-47 5-32 (362)
223 PF09848 DUF2075: Uncharacteri 66.3 8.9 0.00019 44.5 5.4 49 244-292 4-53 (352)
224 COG1111 MPH1 ERCC4-like helica 66.1 16 0.00034 44.7 7.4 76 806-891 419-494 (542)
225 COG0553 HepA Superfamily II DN 66.0 9.3 0.0002 48.7 6.0 71 806-884 755-828 (866)
226 PF14803 Nudix_N_2: Nudix N-te 65.7 3.2 7E-05 32.9 1.1 24 20-43 3-30 (34)
227 PF05191 ADK_lid: Adenylate ki 65.5 4.9 0.00011 32.2 2.1 30 97-126 2-33 (36)
228 smart00661 RPOL9 RNA polymeras 65.2 3.6 7.9E-05 34.5 1.5 30 98-127 2-33 (52)
229 PRK00762 hypA hydrogenase nick 65.1 3.1 6.8E-05 41.8 1.2 29 14-43 67-100 (124)
230 PF01667 Ribosomal_S27e: Ribos 65.0 3.7 8E-05 36.0 1.5 34 13-46 3-37 (55)
231 TIGR00686 phnA alkylphosphonat 64.9 3.6 7.8E-05 40.5 1.6 27 19-46 4-30 (109)
232 PRK03681 hypA hydrogenase nick 64.5 4.3 9.4E-05 40.2 2.1 28 95-123 69-96 (114)
233 PRK06526 transposase; Provisio 64.3 17 0.00036 40.8 6.8 33 244-278 102-134 (254)
234 PRK04296 thymidine kinase; Pro 64.3 13 0.00028 39.5 5.8 31 244-276 6-36 (190)
235 TIGR02605 CxxC_CxxC_SSSS putat 63.9 4.5 9.8E-05 34.1 1.8 27 17-43 5-34 (52)
236 PF12340 DUF3638: Protein of u 63.8 14 0.0003 41.1 6.0 118 245-367 45-187 (229)
237 PF00931 NB-ARC: NB-ARC domain 63.8 34 0.00074 37.7 9.2 118 238-399 17-137 (287)
238 TIGR00595 priA primosomal prot 63.5 4.8 0.0001 49.4 2.6 26 18-43 223-248 (505)
239 PRK08084 DNA replication initi 63.2 32 0.00069 37.8 8.7 36 243-279 47-82 (235)
240 COG2093 DNA-directed RNA polym 62.2 3.5 7.7E-05 36.9 0.9 23 97-123 5-27 (64)
241 PRK10220 hypothetical protein; 62.2 5.1 0.00011 39.6 2.0 27 19-46 5-31 (111)
242 PRK11827 hypothetical protein; 62.1 5.7 0.00012 35.4 2.2 30 18-47 9-38 (60)
243 PRK00564 hypA hydrogenase nick 61.6 3.9 8.5E-05 40.7 1.2 30 14-44 68-97 (117)
244 PF09723 Zn-ribbon_8: Zinc rib 61.6 5.2 0.00011 32.8 1.7 27 17-43 5-34 (42)
245 PRK02935 hypothetical protein; 61.1 4.8 0.0001 39.5 1.6 36 92-130 66-102 (110)
246 KOG1923 Rac1 GTPase effector F 60.8 17 0.00037 46.2 6.5 64 2-98 280-353 (830)
247 PF09788 Tmemb_55A: Transmembr 60.7 8.7 0.00019 43.1 3.7 44 4-47 144-189 (256)
248 PRK00420 hypothetical protein; 60.3 5 0.00011 39.9 1.7 34 96-130 23-56 (112)
249 PF10571 UPF0547: Uncharacteri 60.3 4.4 9.5E-05 30.3 0.9 22 19-44 2-23 (26)
250 PF04810 zf-Sec23_Sec24: Sec23 60.2 4.2 9E-05 33.1 0.9 31 97-127 3-37 (40)
251 cd00350 rubredoxin_like Rubred 59.5 6.9 0.00015 30.5 2.0 25 97-123 2-26 (33)
252 PRK03824 hypA hydrogenase nick 59.4 6.5 0.00014 40.2 2.3 29 95-123 69-116 (135)
253 PHA02558 uvsW UvsW helicase; P 59.1 17 0.00036 44.5 6.2 55 806-868 388-443 (501)
254 KOG1132 Helicase of the DEAD s 58.5 4.6 9.9E-05 51.8 1.3 47 318-372 221-267 (945)
255 PRK09376 rho transcription ter 58.3 31 0.00067 41.5 7.9 88 180-281 120-209 (416)
256 PF08274 PhnA_Zn_Ribbon: PhnA 58.1 3.5 7.7E-05 31.9 0.1 25 19-44 4-28 (30)
257 PRK00564 hypA hydrogenase nick 57.6 5.9 0.00013 39.5 1.7 29 94-123 69-97 (117)
258 COG0556 UvrB Helicase subunit 57.4 10 0.00022 46.7 3.8 48 353-402 332-397 (663)
259 cd00729 rubredoxin_SM Rubredox 57.3 9.2 0.0002 30.2 2.3 26 96-123 2-27 (34)
260 COG0553 HepA Superfamily II DN 56.9 19 0.0004 46.0 6.4 167 216-411 338-518 (866)
261 PF05707 Zot: Zonular occluden 56.4 8.8 0.00019 40.8 2.8 28 342-369 69-96 (193)
262 cd01128 rho_factor Transcripti 56.4 24 0.00052 39.6 6.3 49 239-290 16-68 (249)
263 PF05876 Terminase_GpA: Phage 56.2 6.4 0.00014 48.9 2.0 28 17-44 200-238 (557)
264 PRK14086 dnaA chromosomal repl 55.8 53 0.0012 41.5 9.7 71 355-434 380-456 (617)
265 TIGR00373 conserved hypothetic 55.8 3.5 7.6E-05 43.1 -0.3 29 17-45 109-138 (158)
266 PRK06266 transcription initiat 55.7 4.3 9.4E-05 43.3 0.4 29 17-45 117-146 (178)
267 TIGR00596 rad1 DNA repair prot 55.4 75 0.0016 41.6 11.2 53 837-891 475-527 (814)
268 PF04710 Pellino: Pellino; In 54.4 4.2 9E-05 48.0 0.0 43 93-135 359-411 (416)
269 PF04216 FdhE: Protein involve 54.3 4.8 0.0001 45.7 0.5 26 94-123 195-220 (290)
270 TIGR00376 DNA helicase, putati 54.3 14 0.00031 46.6 4.6 57 216-282 157-213 (637)
271 KOG0331 ATP-dependent RNA heli 54.0 29 0.00062 42.9 6.9 147 241-409 128-289 (519)
272 TIGR01562 FdhE formate dehydro 53.8 10 0.00022 43.8 3.0 26 94-123 208-233 (305)
273 TIGR00622 ssl1 transcription f 53.5 14 0.00031 36.8 3.5 83 20-127 4-94 (112)
274 TIGR00767 rho transcription te 53.2 32 0.0007 41.4 7.0 47 242-290 170-220 (415)
275 KOG3507 DNA-directed RNA polym 53.2 12 0.00025 33.3 2.5 42 5-47 6-49 (62)
276 PRK14873 primosome assembly pr 53.0 9.1 0.0002 48.6 2.6 27 17-43 392-418 (665)
277 CHL00095 clpC Clp protease ATP 53.0 50 0.0011 43.1 9.3 57 339-400 258-314 (821)
278 PRK09694 helicase Cas3; Provis 52.9 22 0.00047 46.7 6.0 62 806-878 611-682 (878)
279 PRK05580 primosome assembly pr 52.9 8.6 0.00019 48.9 2.4 26 18-43 391-416 (679)
280 cd01120 RecA-like_NTPases RecA 52.5 68 0.0015 31.4 8.3 37 246-284 5-41 (165)
281 KOG0336 ATP-dependent RNA heli 52.3 14 0.0003 44.1 3.7 54 806-867 509-562 (629)
282 TIGR02639 ClpA ATP-dependent C 52.3 50 0.0011 42.5 9.0 76 322-401 241-319 (731)
283 KOG0391 SNF2 family DNA-depend 52.2 12 0.00026 49.6 3.4 203 245-485 638-871 (1958)
284 KOG0955 PHD finger protein BR1 51.4 5.3 0.00011 52.6 0.3 46 660-708 219-267 (1051)
285 COG2824 PhnA Uncharacterized Z 51.3 9.3 0.0002 37.7 1.8 26 19-45 5-30 (112)
286 PF07295 DUF1451: Protein of u 51.2 12 0.00025 39.0 2.6 33 14-46 109-141 (146)
287 PRK00762 hypA hydrogenase nick 50.9 8.6 0.00019 38.7 1.6 28 95-123 69-101 (124)
288 KOG0331 ATP-dependent RNA heli 50.2 19 0.00042 44.3 4.7 53 807-867 386-438 (519)
289 PRK10865 protein disaggregatio 50.2 38 0.00083 44.4 7.6 88 322-414 237-333 (857)
290 KOG0333 U5 snRNP-like RNA heli 50.0 13 0.00029 45.5 3.2 54 806-867 561-614 (673)
291 PF07282 OrfB_Zn_ribbon: Putat 49.8 11 0.00024 33.5 2.0 29 16-44 27-55 (69)
292 PF09538 FYDLN_acid: Protein o 49.8 15 0.00033 36.4 3.0 37 97-135 10-48 (108)
293 PRK00254 ski2-like helicase; P 49.7 18 0.00039 46.2 4.5 59 806-866 315-375 (720)
294 COG4416 Com Mu-like prophage p 49.5 4 8.7E-05 35.6 -0.8 31 17-47 4-36 (60)
295 PRK12496 hypothetical protein; 49.4 9.7 0.00021 40.1 1.8 28 97-126 128-155 (164)
296 PRK00432 30S ribosomal protein 49.0 8.5 0.00018 33.0 1.1 25 19-44 22-46 (50)
297 PF14803 Nudix_N_2: Nudix N-te 48.3 8.1 0.00018 30.7 0.8 25 98-122 2-30 (34)
298 COG4889 Predicted helicase [Ge 48.2 1.1E+02 0.0023 40.4 10.4 135 217-370 162-322 (1518)
299 PRK14873 primosome assembly pr 48.0 46 0.00099 42.5 7.6 128 251-401 170-303 (665)
300 COG1439 Predicted nucleic acid 47.5 10 0.00022 40.6 1.5 29 94-126 137-165 (177)
301 cd00729 rubredoxin_SM Rubredox 47.1 15 0.00033 29.0 2.1 27 17-45 2-28 (34)
302 PRK05298 excinuclease ABC subu 47.0 36 0.00078 43.2 6.5 62 806-878 490-556 (652)
303 PLN03086 PRLI-interacting fact 47.0 11 0.00025 46.7 2.1 11 114-124 504-514 (567)
304 COG1545 Predicted nucleic-acid 46.8 11 0.00024 38.7 1.6 27 94-124 27-53 (140)
305 smart00382 AAA ATPases associa 46.7 31 0.00066 32.1 4.6 38 244-283 6-43 (148)
306 cd00561 CobA_CobO_BtuR ATP:cor 46.6 1E+02 0.0023 32.5 8.8 29 248-277 9-37 (159)
307 PF12773 DZR: Double zinc ribb 46.5 8.7 0.00019 32.1 0.7 27 17-44 12-38 (50)
308 KOG1123 RNA polymerase II tran 46.4 22 0.00047 43.5 4.2 125 316-482 387-511 (776)
309 PRK12422 chromosomal replicati 46.3 95 0.0021 37.8 9.7 72 355-435 205-282 (445)
310 cd00350 rubredoxin_like Rubred 46.3 14 0.00031 28.8 1.9 25 18-44 2-26 (33)
311 KOG0383 Predicted helicase [Ge 45.7 6.8 0.00015 49.6 -0.0 49 657-708 44-92 (696)
312 TIGR00963 secA preprotein tran 45.3 11 0.00024 48.3 1.7 125 250-400 78-214 (745)
313 PF00004 AAA: ATPase family as 45.2 45 0.00097 31.8 5.5 32 337-368 42-74 (132)
314 PRK00241 nudC NADH pyrophospha 45.0 11 0.00024 42.3 1.5 25 19-43 101-125 (256)
315 PF05729 NACHT: NACHT domain 44.6 91 0.002 30.8 7.8 54 347-402 76-131 (166)
316 PF07295 DUF1451: Protein of u 44.4 16 0.00035 38.0 2.4 30 94-123 110-139 (146)
317 PF08792 A2L_zn_ribbon: A2L zi 44.4 15 0.00032 29.1 1.6 29 17-45 3-31 (33)
318 PF14353 CpXC: CpXC protein 44.2 13 0.00028 37.1 1.6 32 96-127 1-51 (128)
319 TIGR03714 secA2 accessory Sec 43.8 35 0.00076 44.1 5.7 105 250-364 92-207 (762)
320 KOG0925 mRNA splicing factor A 43.7 17 0.00037 44.3 2.7 42 353-401 160-201 (699)
321 PRK08533 flagellar accessory p 43.6 90 0.002 34.3 8.2 57 236-296 21-77 (230)
322 KOG2462 C2H2-type Zn-finger pr 43.2 33 0.00072 39.1 4.7 68 26-124 121-197 (279)
323 COG3877 Uncharacterized protei 42.8 14 0.0003 36.5 1.5 10 34-43 19-28 (122)
324 PRK03564 formate dehydrogenase 42.7 21 0.00045 41.5 3.2 26 93-122 209-234 (309)
325 PRK14892 putative transcriptio 42.6 15 0.00032 36.0 1.7 30 96-126 21-54 (99)
326 KOG0921 Dosage compensation co 42.6 66 0.0014 42.1 7.6 174 194-404 344-538 (1282)
327 PF09082 DUF1922: Domain of un 42.5 11 0.00024 34.5 0.8 29 17-47 3-31 (68)
328 smart00488 DEXDc2 DEAD-like he 42.4 20 0.00043 40.9 3.0 33 322-363 214-247 (289)
329 smart00489 DEXDc3 DEAD-like he 42.4 20 0.00043 40.9 3.0 33 322-363 214-247 (289)
330 PRK07952 DNA replication prote 42.4 40 0.00086 37.8 5.3 37 241-278 99-135 (244)
331 COG1571 Predicted DNA-binding 42.2 18 0.00039 43.5 2.7 28 17-45 350-377 (421)
332 TIGR02562 cas3_yersinia CRISPR 42.1 45 0.00097 44.5 6.3 46 344-400 586-633 (1110)
333 KOG3842 Adaptor protein Pellin 42.1 11 0.00024 43.3 0.9 32 104-135 391-424 (429)
334 KOG4451 Uncharacterized conser 42.0 11 0.00024 41.5 0.9 24 96-123 249-272 (286)
335 PF00301 Rubredoxin: Rubredoxi 41.9 20 0.00044 30.5 2.2 27 97-123 2-43 (47)
336 PF14369 zf-RING_3: zinc-finge 41.6 20 0.00043 28.6 2.0 23 20-42 5-28 (35)
337 KOG2907 RNA polymerase I trans 41.4 8.3 0.00018 38.3 -0.1 31 97-127 8-38 (116)
338 TIGR00515 accD acetyl-CoA carb 41.2 9.6 0.00021 43.6 0.3 35 13-47 22-57 (285)
339 PF06745 KaiC: KaiC; InterPro 41.1 40 0.00086 36.3 5.0 50 245-296 23-73 (226)
340 COG5178 PRP8 U5 snRNP spliceos 40.9 21 0.00046 47.0 3.1 22 738-759 1019-1040(2365)
341 cd00730 rubredoxin Rubredoxin; 40.7 21 0.00046 30.7 2.2 27 97-123 2-43 (50)
342 CHL00174 accD acetyl-CoA carbo 40.7 9.7 0.00021 43.8 0.2 35 13-47 34-69 (296)
343 PF08271 TF_Zn_Ribbon: TFIIB z 40.6 16 0.00034 30.0 1.4 29 97-125 1-30 (43)
344 COG4820 EutJ Ethanolamine util 40.6 45 0.00098 36.8 5.1 55 1028-1082 134-191 (277)
345 PRK11664 ATP-dependent RNA hel 40.6 24 0.00051 46.0 3.6 69 806-876 259-337 (812)
346 KOG0388 SNF2 family DNA-depend 40.4 29 0.00062 44.1 4.0 70 806-883 1088-1159(1185)
347 KOG1016 Predicted DNA helicase 40.3 1.4E+02 0.0031 38.7 9.8 69 806-883 781-853 (1387)
348 COG0513 SrmB Superfamily II DN 40.2 77 0.0017 39.1 7.8 154 216-401 51-215 (513)
349 PRK09752 adhesin; Provisional 40.1 26 0.00055 46.8 3.7 13 241-253 1031-1043(1250)
350 KOG2906 RNA polymerase III sub 40.0 17 0.00037 35.4 1.7 33 19-51 3-37 (105)
351 TIGR00604 rad3 DNA repair heli 39.8 20 0.00044 45.7 2.8 42 318-368 194-236 (705)
352 COG1594 RPB9 DNA-directed RNA 39.3 23 0.00049 35.3 2.5 31 19-49 4-36 (113)
353 PF07282 OrfB_Zn_ribbon: Putat 38.9 11 0.00024 33.5 0.2 34 95-128 27-60 (69)
354 TIGR03743 SXT_TraD conjugative 38.7 48 0.001 42.1 5.8 53 243-296 178-232 (634)
355 PRK06393 rpoE DNA-directed RNA 38.7 14 0.00031 33.4 0.9 21 97-123 6-26 (64)
356 PF02150 RNA_POL_M_15KD: RNA p 38.3 8.8 0.00019 30.5 -0.4 29 20-48 4-33 (35)
357 COG5047 SEC23 Vesicle coat com 37.7 18 0.00039 44.7 1.8 35 17-51 53-92 (755)
358 PF14319 Zn_Tnp_IS91: Transpos 37.5 23 0.00051 35.0 2.3 30 94-123 40-69 (111)
359 PF12172 DUF35_N: Rubredoxin-l 37.4 16 0.00036 28.9 1.0 25 95-123 10-34 (37)
360 PRK14973 DNA topoisomerase I; 37.4 40 0.00087 44.6 5.0 25 98-122 637-665 (936)
361 COG2816 NPY1 NTP pyrophosphohy 37.4 18 0.00038 41.4 1.6 24 20-43 114-137 (279)
362 COG1998 RPS31 Ribosomal protei 37.2 14 0.00031 31.8 0.6 28 20-47 22-49 (51)
363 PRK12377 putative replication 37.0 67 0.0015 36.1 6.0 42 242-285 102-143 (248)
364 KOG1001 Helicase-like transcri 36.9 22 0.00048 45.3 2.5 78 809-894 587-665 (674)
365 TIGR02880 cbbX_cfxQ probable R 36.6 2E+02 0.0044 32.7 9.8 30 241-270 58-87 (284)
366 KOG4323 Polycomb-like PHD Zn-f 36.3 7.3 0.00016 47.1 -1.7 42 670-711 180-225 (464)
367 COG0003 ArsA Predicted ATPase 36.3 46 0.001 38.9 4.7 57 241-300 3-59 (322)
368 KOG1779 40s ribosomal protein 36.0 23 0.00049 33.3 1.7 36 13-48 30-66 (84)
369 PF02591 DUF164: Putative zinc 35.9 17 0.00038 31.4 1.0 25 19-43 24-54 (56)
370 PF01695 IstB_IS21: IstB-like 35.9 36 0.00078 36.0 3.5 42 242-285 48-89 (178)
371 PRK08351 DNA-directed RNA poly 35.7 20 0.00043 32.2 1.3 21 98-124 5-25 (61)
372 TIGR01970 DEAH_box_HrpB ATP-de 35.3 34 0.00073 44.7 3.8 68 806-875 256-333 (819)
373 TIGR00708 cobA cob(I)alamin ad 35.2 1.9E+02 0.0041 31.0 8.7 26 247-272 11-36 (173)
374 PRK00241 nudC NADH pyrophospha 34.5 20 0.00043 40.4 1.4 27 97-123 100-126 (256)
375 PRK05654 acetyl-CoA carboxylas 34.4 12 0.00025 43.1 -0.4 36 12-47 22-58 (292)
376 TIGR03158 cas3_cyano CRISPR-as 34.3 37 0.0008 39.7 3.6 41 811-862 317-357 (357)
377 PF10058 DUF2296: Predicted in 34.3 26 0.00057 30.6 1.8 31 14-44 19-53 (54)
378 PRK05986 cob(I)alamin adenolsy 33.8 2.6E+02 0.0057 30.5 9.6 138 244-409 25-163 (191)
379 TIGR03346 chaperone_ClpB ATP-d 33.8 1.2E+02 0.0027 39.8 8.5 88 339-433 252-345 (852)
380 PF09334 tRNA-synt_1g: tRNA sy 33.7 27 0.00059 41.5 2.5 36 97-135 150-185 (391)
381 PRK00415 rps27e 30S ribosomal 33.5 28 0.0006 31.1 1.8 34 95-128 10-44 (59)
382 PRK07219 DNA topoisomerase I; 33.5 34 0.00073 44.7 3.4 32 96-127 708-746 (822)
383 PF01783 Ribosomal_L32p: Ribos 33.1 26 0.00055 30.7 1.6 21 18-43 27-47 (56)
384 PTZ00407 DNA topoisomerase IA; 33.1 5.3E+02 0.012 34.1 13.6 156 423-595 578-770 (805)
385 PRK14892 putative transcriptio 32.9 32 0.0007 33.7 2.3 30 14-44 18-51 (99)
386 KOG1986 Vesicle coat complex C 32.9 24 0.00051 44.6 1.8 36 16-51 52-91 (745)
387 COG1110 Reverse gyrase [DNA re 32.8 1.3E+02 0.0028 40.2 8.1 51 243-294 99-149 (1187)
388 COG4098 comFA Superfamily II D 32.7 6.1E+02 0.013 30.6 12.7 148 214-403 95-245 (441)
389 PF13453 zf-TFIIB: Transcripti 32.7 32 0.0007 27.9 2.0 24 19-42 1-26 (41)
390 PLN00162 transport protein sec 32.6 66 0.0014 41.7 5.7 31 218-248 136-166 (761)
391 CHL00181 cbbX CbbX; Provisiona 31.9 4E+02 0.0087 30.5 11.3 13 353-365 123-135 (287)
392 PRK00432 30S ribosomal protein 31.4 25 0.00055 30.2 1.2 27 96-123 20-46 (50)
393 PF05605 zf-Di19: Drought indu 31.4 20 0.00044 30.7 0.7 12 114-125 2-13 (54)
394 PRK13130 H/ACA RNA-protein com 31.4 30 0.00065 30.6 1.7 25 96-126 5-29 (56)
395 TIGR00631 uvrb excinuclease AB 31.3 1.1E+02 0.0024 39.2 7.2 51 806-864 486-541 (655)
396 PRK09200 preprotein translocas 31.1 79 0.0017 41.2 6.0 132 225-364 67-211 (790)
397 PRK05398 formyl-coenzyme A tra 31.0 52 0.0011 39.5 4.2 93 287-402 23-127 (416)
398 TIGR00310 ZPR1_znf ZPR1 zinc f 30.9 22 0.00047 38.6 0.9 27 18-44 1-39 (192)
399 PRK11032 hypothetical protein; 30.8 34 0.00073 36.3 2.3 29 95-123 123-151 (160)
400 COG2051 RPS27A Ribosomal prote 30.8 33 0.00071 31.4 1.8 35 94-128 17-52 (67)
401 cd01124 KaiC KaiC is a circadi 30.7 1E+02 0.0022 31.6 5.9 50 245-296 3-52 (187)
402 PF10058 DUF2296: Predicted in 30.6 36 0.00077 29.8 2.0 30 93-122 19-52 (54)
403 TIGR02768 TraA_Ti Ti-type conj 30.5 63 0.0014 41.8 5.1 54 216-280 352-406 (744)
404 PRK00464 nrdR transcriptional 30.1 33 0.00072 36.0 2.1 26 18-43 1-36 (154)
405 PRK06450 threonine synthase; V 30.1 24 0.00051 41.2 1.1 30 16-48 2-31 (338)
406 PHA03368 DNA packaging termina 30.1 1.8E+02 0.004 37.4 8.6 122 244-404 259-393 (738)
407 PF02662 FlpD: Methyl-viologen 30.0 55 0.0012 32.9 3.6 45 339-391 40-88 (124)
408 TIGR01384 TFS_arch transcripti 29.9 26 0.00055 33.8 1.1 27 98-126 2-28 (104)
409 PF14599 zinc_ribbon_6: Zinc-r 29.8 34 0.00074 30.7 1.8 30 14-43 27-56 (61)
410 PRK08939 primosomal protein Dn 29.7 97 0.0021 35.8 5.9 39 240-279 155-193 (306)
411 COG2835 Uncharacterized conser 29.7 35 0.00077 30.6 1.8 30 18-47 9-38 (60)
412 PRK07764 DNA polymerase III su 29.6 1E+02 0.0022 40.5 6.6 51 354-417 122-174 (824)
413 KOG1830 Wiskott Aldrich syndro 29.5 2.7E+02 0.0059 33.8 9.4 28 258-291 489-517 (518)
414 PRK07220 DNA topoisomerase I; 29.4 61 0.0013 41.9 4.7 27 18-44 590-622 (740)
415 PRK15319 AIDA autotransporter- 29.4 77 0.0017 44.4 5.6 60 3-93 1671-1730(2039)
416 PRK06835 DNA replication prote 29.3 88 0.0019 36.6 5.5 37 242-279 184-220 (329)
417 COG1799 Uncharacterized protei 29.2 65 0.0014 34.4 4.0 30 538-567 88-117 (167)
418 COG0777 AccD Acetyl-CoA carbox 29.0 29 0.00062 39.6 1.5 35 14-48 25-60 (294)
419 TIGR02639 ClpA ATP-dependent C 28.7 3.4E+02 0.0073 35.2 11.0 23 344-366 545-567 (731)
420 TIGR01967 DEAH_box_HrpA ATP-de 28.6 1.6E+02 0.0035 40.6 8.3 115 807-932 324-459 (1283)
421 PRK12722 transcriptional activ 28.4 38 0.00082 36.7 2.2 29 94-122 132-162 (187)
422 COG1326 Uncharacterized archae 28.0 22 0.00049 38.5 0.4 29 94-123 4-39 (201)
423 PF05191 ADK_lid: Adenylate ki 28.0 25 0.00053 28.3 0.5 26 19-44 3-30 (36)
424 PF12846 AAA_10: AAA-like doma 28.0 95 0.0021 34.0 5.3 52 243-300 4-55 (304)
425 PRK07219 DNA topoisomerase I; 27.9 73 0.0016 41.7 5.0 33 17-49 602-640 (822)
426 PHA02942 putative transposase; 27.9 36 0.00078 40.5 2.1 27 17-44 325-351 (383)
427 PF13245 AAA_19: Part of AAA d 27.8 88 0.0019 28.7 4.2 47 244-290 13-62 (76)
428 KOG1546 Metacaspase involved i 27.7 83 0.0018 36.9 4.8 23 7-30 11-33 (362)
429 KOG2593 Transcription initiati 27.6 25 0.00055 42.2 0.8 36 96-131 128-170 (436)
430 PF13824 zf-Mss51: Zinc-finger 27.5 39 0.00086 29.8 1.7 23 99-124 2-24 (55)
431 PRK07591 threonine synthase; V 27.5 32 0.0007 41.3 1.6 31 15-48 16-46 (421)
432 KOG1925 Rac1 GTPase effector F 27.4 1.1E+02 0.0023 37.7 5.7 32 102-135 290-327 (817)
433 PRK12860 transcriptional activ 27.3 45 0.00097 36.2 2.5 29 93-121 131-161 (189)
434 KOG0344 ATP-dependent RNA heli 27.3 59 0.0013 40.6 3.8 65 804-878 430-494 (593)
435 PF00290 Trp_syntA: Tryptophan 27.1 45 0.00097 37.8 2.6 120 281-407 24-180 (259)
436 PF00301 Rubredoxin: Rubredoxi 27.1 47 0.001 28.3 2.1 27 18-44 2-43 (47)
437 PF13500 AAA_26: AAA domain; P 27.1 70 0.0015 33.8 3.9 131 243-400 3-138 (199)
438 PHA01732 proline-rich protein 26.9 80 0.0017 30.3 3.7 9 103-111 64-72 (94)
439 COG1998 RPS31 Ribosomal protei 26.7 30 0.00065 29.9 0.9 30 94-123 17-46 (51)
440 TIGR02605 CxxC_CxxC_SSSS putat 26.7 45 0.00097 28.1 1.9 28 96-123 5-35 (52)
441 CHL00095 clpC Clp protease ATP 26.7 3.7E+02 0.0079 35.4 11.0 51 344-404 603-665 (821)
442 PRK00423 tfb transcription ini 26.5 38 0.00082 39.1 1.9 31 14-44 8-39 (310)
443 PF03811 Zn_Tnp_IS1: InsA N-te 26.5 42 0.00091 27.1 1.6 29 14-42 2-36 (36)
444 TIGR01031 rpmF_bact ribosomal 26.4 38 0.00083 29.7 1.5 21 18-43 27-47 (55)
445 PRK00420 hypothetical protein; 26.2 41 0.00088 33.7 1.8 28 18-47 24-52 (112)
446 KOG2302 T-type voltage-gated C 26.1 3.1E+02 0.0067 36.7 9.5 11 116-126 544-554 (1956)
447 PF14446 Prok-RING_1: Prokaryo 26.0 39 0.00085 29.7 1.5 27 16-44 4-30 (54)
448 PRK13889 conjugal transfer rel 26.0 79 0.0017 42.3 4.8 53 216-279 346-399 (988)
449 KOG1246 DNA-binding protein ju 25.6 33 0.00071 45.2 1.3 49 660-709 155-203 (904)
450 PRK06260 threonine synthase; V 25.6 38 0.00083 40.2 1.8 30 96-127 3-32 (397)
451 PRK07591 threonine synthase; V 25.5 36 0.00079 40.8 1.6 31 94-127 16-46 (421)
452 PF03966 Trm112p: Trm112p-like 25.4 39 0.00084 30.4 1.4 16 29-44 47-62 (68)
453 PF14319 Zn_Tnp_IS91: Transpos 25.3 57 0.0012 32.4 2.6 30 14-43 39-68 (111)
454 PF00367 PTS_EIIB: phosphotran 25.2 53 0.0011 26.3 1.9 19 755-773 3-21 (35)
455 PF01485 IBR: IBR domain; Int 25.1 38 0.00083 29.0 1.3 25 19-43 20-48 (64)
456 PRK09710 lar restriction allev 25.1 54 0.0012 29.8 2.2 26 19-44 8-36 (64)
457 PF09548 Spore_III_AB: Stage I 25.1 1.6E+02 0.0034 31.1 6.1 127 885-1031 19-146 (170)
458 PRK06260 threonine synthase; V 25.0 34 0.00073 40.7 1.2 29 17-47 3-31 (397)
459 PF08996 zf-DNA_Pol: DNA Polym 24.8 51 0.0011 35.4 2.4 30 14-43 15-53 (188)
460 COG3809 Uncharacterized protei 24.7 51 0.0011 31.1 2.0 25 18-42 2-28 (88)
461 TIGR00155 pqiA_fam integral me 24.6 49 0.0011 39.8 2.4 31 96-126 13-45 (403)
462 COG1645 Uncharacterized Zn-fin 24.4 40 0.00087 34.6 1.4 31 19-51 30-60 (131)
463 KOG0342 ATP-dependent RNA heli 24.4 80 0.0017 38.9 4.1 71 806-890 374-446 (543)
464 PF00448 SRP54: SRP54-type pro 24.4 87 0.0019 33.7 4.1 33 244-278 5-37 (196)
465 KOG3214 Uncharacterized Zn rib 24.0 26 0.00057 34.3 0.0 28 108-135 41-68 (109)
466 PRK14974 cell division protein 24.0 3E+02 0.0066 32.4 8.6 35 241-277 141-175 (336)
467 TIGR02782 TrbB_P P-type conjug 23.9 75 0.0016 36.5 3.7 44 210-262 110-153 (299)
468 TIGR03029 EpsG chain length de 23.8 2.4E+02 0.0051 31.4 7.5 37 241-278 104-140 (274)
469 PRK13111 trpA tryptophan synth 23.1 4.5E+02 0.0097 29.8 9.5 40 321-365 91-135 (258)
470 COG2816 NPY1 NTP pyrophosphohy 23.1 42 0.00091 38.5 1.4 27 97-123 112-138 (279)
471 TIGR00570 cdk7 CDK-activating 23.1 32 0.00069 39.9 0.5 27 97-126 29-55 (309)
472 KOG1984 Vesicle coat complex C 23.0 39 0.00085 43.7 1.3 38 14-51 335-376 (1007)
473 PRK12722 transcriptional activ 22.9 47 0.001 36.0 1.7 24 19-42 136-161 (187)
474 PF14835 zf-RING_6: zf-RING of 22.9 36 0.00077 31.0 0.7 38 97-134 8-60 (65)
475 PRK12898 secA preprotein trans 22.7 2.1E+02 0.0045 36.8 7.4 83 807-892 516-600 (656)
476 smart00647 IBR In Between Ring 22.7 72 0.0016 27.3 2.5 25 19-43 20-48 (64)
477 KOG0954 PHD finger protein [Ge 22.5 21 0.00045 45.2 -1.1 46 661-708 272-319 (893)
478 PF02374 ArsA_ATPase: Anion-tr 22.3 1.1E+02 0.0024 35.3 4.6 37 243-281 4-40 (305)
479 TIGR03253 oxalate_frc formyl-C 22.1 94 0.002 37.3 4.2 92 287-401 22-125 (415)
480 PLN02610 probable methionyl-tR 22.0 48 0.001 43.2 1.8 36 97-135 171-206 (801)
481 PF05280 FlhC: Flagellar trans 21.9 57 0.0012 35.0 2.0 31 93-123 131-163 (175)
482 PRK06893 DNA replication initi 21.9 86 0.0019 34.3 3.5 36 243-279 41-76 (229)
483 PHA00626 hypothetical protein 21.8 51 0.0011 29.3 1.4 31 97-127 1-36 (59)
484 COG5243 HRD1 HRD ubiquitin lig 21.8 33 0.0007 40.5 0.2 42 89-130 308-350 (491)
485 PRK04023 DNA polymerase II lar 21.7 46 0.00099 43.9 1.5 26 92-123 622-647 (1121)
486 PHA00350 putative assembly pro 21.6 43 0.00093 40.2 1.2 23 249-271 9-32 (399)
487 KOG0383 Predicted helicase [Ge 21.5 1.2E+02 0.0026 39.1 5.0 246 214-492 293-568 (696)
488 TIGR03499 FlhF flagellar biosy 21.4 1.1E+02 0.0023 34.8 4.3 35 244-278 197-232 (282)
489 PF06221 zf-C2HC5: Putative zi 21.4 45 0.00099 29.6 1.0 25 19-44 20-44 (57)
490 PF13173 AAA_14: AAA domain 21.3 95 0.0021 30.6 3.4 35 353-398 62-96 (128)
491 PRK03525 crotonobetainyl-CoA:c 21.3 96 0.0021 37.2 4.0 87 288-402 31-126 (405)
492 PRK12286 rpmF 50S ribosomal pr 21.2 60 0.0013 28.7 1.7 21 18-43 28-48 (57)
493 PRK13833 conjugal transfer pro 21.2 89 0.0019 36.6 3.6 46 210-264 122-167 (323)
494 PRK12860 transcriptional activ 21.1 54 0.0012 35.6 1.7 25 18-42 135-161 (189)
495 CHL00200 trpA tryptophan synth 21.0 98 0.0021 35.1 3.8 37 321-362 93-130 (263)
496 COG1096 Predicted RNA-binding 20.9 49 0.0011 35.9 1.3 27 95-123 148-174 (188)
497 TIGR03754 conj_TOL_TraD conjug 20.8 1.4E+02 0.003 38.2 5.4 50 244-295 184-235 (643)
498 PF01667 Ribosomal_S27e: Ribos 20.8 66 0.0014 28.4 1.9 31 95-125 6-37 (55)
499 PRK09200 preprotein translocas 20.8 1.7E+02 0.0038 38.3 6.3 82 805-896 471-559 (790)
500 TIGR00730 conserved hypothetic 20.7 55 0.0012 35.0 1.7 126 394-528 4-149 (178)
No 1
>KOG1513 consensus Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription; Signal transduction mechanisms]
Probab=100.00 E-value=2.7e-292 Score=2472.17 Aligned_cols=892 Identities=48% Similarity=0.793 Sum_probs=771.7
Q ss_pred cccCCccccccccccCCCCcCCCCCCCcccccccCCCCCCCCCCccCcccccccccCCcccchhhHHHHHHhhccccCCC
Q 038397 159 EDEGGMVGETFTDYRPPKLSIGPAHPDPIVETSSLSAVHPPEPTYDLLIKYDLESSKSLSCLQIETLVYASQRHLQHLPN 238 (1102)
Q Consensus 159 ~~~~~~~~~~~~~y~p~~~~~~~~hP~~lve~~~l~sv~pP~~~y~~~lp~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~ 238 (1102)
+.|+.++++||++|+|+|+++|+.|||+|||||+|+||+|||++|.|.||. |++|.||++|||||+||||+|++.||+
T Consensus 209 d~EelG~aeTya~Y~PsKlk~GkaHPD~VVEtatLSSV~ppdi~YqlalP~--i~sg~lSALQLEav~YAcQ~He~llPs 286 (1300)
T KOG1513|consen 209 DYEELGVAETYADYWPSKLKIGKAHPDRVVETATLSSVEPPDITYQLALPS--IDSGHLSALQLEAVTYACQAHEVLLPS 286 (1300)
T ss_pred cHHhhchhhhhhhhchhhhhccccCCccceeeeeccccCCCCceEEEeccc--CcccchhHHHHHHHHHHHhhhhhcCCC
Confidence 445668999999999999999999999999999999999999999999998 899999999999999999999999999
Q ss_pred CCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCccc-
Q 038397 239 SARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSVG- 317 (1102)
Q Consensus 239 g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~- 317 (1102)
|.|+|||||||+||||||+|||||+||||+||+|++|||||+||+|||+|||+|||+..|.||+||||||++|++++++
T Consensus 287 G~RaGfLiGDGAGVGKGRTvAgiIfeNyLkGRKrAlW~SVSsDLKfDAERDL~DigA~~I~V~alnK~KYakIss~en~n 366 (1300)
T KOG1513|consen 287 GQRAGFLIGDGAGVGKGRTVAGIIFENYLKGRKRALWFSVSSDLKFDAERDLRDIGATGIAVHALNKFKYAKISSKENTN 366 (1300)
T ss_pred CccceeeeccCcccCCCceeEEEEehhhhcccceeEEEEeccccccchhhchhhcCCCCccceehhhcccccccccccCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999886
Q ss_pred cccceEEeehhhhhhccc----cccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCcc
Q 038397 318 IREGVVFLTYSSLIASSE----KGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEAR 393 (1102)
Q Consensus 318 ~~~GvlF~TYs~L~~~~~----~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~AR 393 (1102)
.++||||+||+.||++++ |++||+.||++|||+||+|||||||||||||+++.++.+|||||++||+||++||+||
T Consensus 367 ~krGViFaTYtaLIGEs~~~~~kyrtR~rQllqW~Ge~feGvIvfDECHkAKNL~p~~~~k~TKtG~tVLdLQk~LP~AR 446 (1300)
T KOG1513|consen 367 TKRGVIFATYTALIGESQGKGGKYRTRFRQLLQWCGEDFEGVIVFDECHKAKNLVPTAGAKSTKTGKTVLDLQKKLPNAR 446 (1300)
T ss_pred ccceeEEEeeHhhhhhccccCchHHHHHHHHHHHhhhccceeEEehhhhhhcccccccCCCcCcccHhHHHHHHhCCCce
Confidence 899999999999999975 4689999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEecCCCCCCCccchhhhccccCCCCCCCCHHHHHHHHhccChhHHHHHHHHHHhccceeeeccCCCCceeEEEeccC
Q 038397 394 VVYCSATGASEPRNMGYMVRLGLWGAGTCFKDFQIFLGALDKGGVGALELVAMDMKARGMYVCRTLSYKGAEFEVIEAPL 473 (1102)
Q Consensus 394 vvY~SATgasep~Nl~ym~RLGLWg~gt~f~~~~~f~~a~~~gGv~amE~va~dlK~~G~yiaR~LSf~gvef~i~e~~l 473 (1102)
|||+||||||||+||+||+||||||+||+|++|.+|++|+|++|||||||||||||.+||||||||||+||+|+|+|++|
T Consensus 447 VVYASATGAsEPrNMaYM~RLGlWGegtaf~eF~eFi~AvEkRGvGAMEIVAMDMK~rGmYiARQLSFkgVsFrieEv~l 526 (1300)
T KOG1513|consen 447 VVYASATGASEPRNMAYMVRLGLWGEGTAFPEFEEFIHAVEKRGVGAMEIVAMDMKLRGMYIARQLSFKGVSFRIEEVPL 526 (1300)
T ss_pred EEEeeccCCCCcchhhhhhhhccccCCCcCccHHHHHHHHHhcCCceeeeeehhhhhhhhhhhhhccccCceEEEEeccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHhhhhhhHHHHHHHHhcCchHHHHHHHHHHHCCCeEEEE
Q 038397 474 EAEMTDMYKKAAEFWAELRVELLSASAFLANDKPNSSQLWRLYWSGHQRFFRHMCMSAKVPATVRLAKKALAEGKCVVIG 553 (1102)
Q Consensus 474 ~~~~~~~Yd~~a~~w~~~~~~~~~a~e~~~~~~~~~~~~~~~FwsahQrFFk~l~~a~Kv~~~V~~a~eal~~Gk~vVIg 553 (1102)
+++|+++||++|+||+++++.|++|+++|+.+.+..|.+|+|||++|||||||||||+||.++|++|+|+++.|||||||
T Consensus 527 s~eF~k~Yn~a~~LW~ea~~kFq~a~e~m~~E~R~~Kt~wgQFWsaHQRFFKyLCIAaKV~~~V~laReaik~~KcVVIG 606 (1300)
T KOG1513|consen 527 SKEFRKVYNRAAELWAEALNKFQQAAELMDLESRTCKTLWGQFWSAHQRFFKYLCIAAKVNHLVELAREAIKRGKCVVIG 606 (1300)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHhhhHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCceEEEe
Confidence 99999999999999999999999999999998888899999999999999999999999999999999999999999999
Q ss_pred EecchhHHHHHHHHhcCCCcCccccChHHHHHHHHHhhCCCCCCCCCCCCchhhHHHhhhcccCCCCCCccccc--cccc
Q 038397 554 LQSTGEARTEEAVTKYGLELDDFISGPRELLLKFVEENYPLPEKPEPLPGEESVKELQRKRHSASPGVSFKGRV--RKAA 631 (1102)
Q Consensus 554 LqSTGEA~~~~~l~~~~~~l~dfvst~r~il~~~v~~~FP~~~~~~~~~~~~~~~~~~r~r~~~~~~~s~kGR~--RK~a 631 (1102)
|||||||+|+|.|++.+|+|++||||+|+||++||+||||++++...- +......|. +.+.+||. .+..
T Consensus 607 LQSTGEsrTle~Le~~~G~Ln~FVStAk~v~~s~iekHFPa~~r~~~~-----~tt~~G~r~----g~~~~~Rs~e~~~~ 677 (1300)
T KOG1513|consen 607 LQSTGESRTLEVLEENDGELNCFVSTAKGVFQSLIEKHFPAPKRKSDR-----VTTGAGSRR----GRRPRGRSNEAKAP 677 (1300)
T ss_pred eccccchhHHHHHHhcCCchhHHHHHHHHHHHHHHHHhCCCccccccc-----ccccccccc----ccCcccCCCccccc
Confidence 999999999999999999999999999999999999999999763211 000000000 01111221 1111
Q ss_pred ccC---cCCCCCCCCCC---cc--ccc----CCCCC-Cccc-------cccccccCcHHHHhhhhhccccCCccccCCCC
Q 038397 632 KWK---PASDGESDEES---ET--DSA----HESTE-SDDE-------FQICEICNSEEERKKLLQCSCCGQLVHSGCLV 691 (1102)
Q Consensus 632 k~~---~~sd~~~DeeS---es--dSd----~~Ssd-SDDE-------f~~ce~cgsed~k~kLL~cs~cgk~~H~~cL~ 691 (1102)
+.. +-.+|++|+++ ++ ++| +|+-+ +||+ +...+.-.++++..+ ..|+.- -.
T Consensus 678 k~~~~tdg~~~~~d~d~~~sd~~~~~d~~sa~ee~~~~~d~~~~~~~~~~~sd~~~~ee~~~e-~lc~~~--------~d 748 (1300)
T KOG1513|consen 678 KLACETDGVIDISDDDSTESDPGLDSDFNSAPEELVGQDDDVVIVDAVALPSDDRGSEEEFNE-FLCLLQ--------RD 748 (1300)
T ss_pred chhcccccccccccccccccCcccccccccchHhhhccccceeccccccCCccchhhhhhhhh-hhhhcc--------cC
Confidence 111 11112222111 00 011 11100 0110 000111111111111 223210 01
Q ss_pred CCcccCCCCCCccccchhhhHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC--CCCCChHHHHHHhhCCCceeeee
Q 038397 692 PPITDVIPSDWSCHSCKEKTEEYLQSRHAYLTELLKRYEAALERKSKILDIIRSM--DFPNNPLDDIVDQLGGPDKVAEM 769 (1102)
Q Consensus 692 PP~~di~~~dW~c~sCkek~eE~~~~r~~~~~e~~~~~~~a~~~r~~LL~~i~~L--~LP~n~LD~LId~LGGp~~VAEm 769 (1102)
|++.+ ++ -..++ ...+++..... ..++..+||++||++|+.| .||||+||||||+||||+.||||
T Consensus 749 ~~~~~---e~---t~~~d---n~~kkrk~~e~----~~er~~~mkeeLL~kverLg~~LP~NTLDqLIdelGGp~~VAEM 815 (1300)
T KOG1513|consen 749 PHGPG---ED---TLQKD---NKAKKRKRDEE----EAERVERMKEELLDKVERLGRELPPNTLDQLIDELGGPQRVAEM 815 (1300)
T ss_pred CCCCC---cc---hhhhh---hhhhhhcccHH----HHHHHHHHHHHHHHHHHHhcccCCcchHHHHHHHhCCchhHHHh
Confidence 12211 00 00010 01111211111 1245667999999999999 89999999999999999999999
Q ss_pred cCCcceEEEcCCCCeEEEEecCCccchhhccchHHHhhhcCCcceEEEEecccccccccccccccccccceeEEEecCCC
Q 038397 770 TGRRGMLVRASSGKGVTYQARNTKEVTMEMVNMHEKQLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPW 849 (1102)
Q Consensus 770 TGRkgRvVr~~dG~~v~ye~R~~~d~~~~~~N~~Ek~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpW 849 (1102)
|||+||||+++||. |.||+|.+.|+++|.+|++|||+||+|+|+|||||||||+|||||+||||.||||||||||||||
T Consensus 816 TGRrGrvV~te~g~-v~ye~R~e~dvsld~vN~~EKqrFM~GeK~vAIISEAaSSGiSLQsDrRv~NqRRRvHiTLELPW 894 (1300)
T KOG1513|consen 816 TGRRGRVVSTEDGT-VAYESRAEQDVSLDLVNLREKQRFMDGEKLVAIISEAASSGISLQSDRRVQNQRRRVHITLELPW 894 (1300)
T ss_pred hccCceeEecCCCc-eeeecccccCCChhhcchHHHhhhccccceeeeeehhhccCceeecchhhhhhhheEEEEEECCc
Confidence 99999999999997 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHhHHHHhhcccccCCCCCCCeEEEeecCccchhhhHHHHHHHHhhcCCccccccccCC--CCCcCCcCChHHHHHHHHH
Q 038397 850 SADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRFASIVAKRLESLGALTQGDRRAGL--SLSAYNYDSAFGKKALMMM 927 (1102)
Q Consensus 850 sADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRFaS~VAkRLeSLGALT~GdRra~~--~ls~fNldn~YGr~AL~~~ 927 (1102)
|||+||||||||||||||++|+|+||||||+|||||||+||||||||||||||||||++ |||+|||||+|||.||+.+
T Consensus 895 SADrAIQQFGRTHRSNQVsaPEYvFlIseLAGErRFAS~VAKRLESLGALThGDRRATetRDLSqfNidNkyGr~ALe~v 974 (1300)
T KOG1513|consen 895 SADRAIQQFGRTHRSNQVSAPEYVFLISELAGERRFASIVAKRLESLGALTHGDRRATETRDLSQFNIDNKYGRRALETV 974 (1300)
T ss_pred chhHHHHHhcccccccccCCCeEEEEehhhccchHHHHHHHHHHHhhccccccccccccccchhhhcccchhhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999975 8999999999999999999
Q ss_pred HHHHhccCccCCCCCCCCCCCcch-HHHHHHHHHHHhhhccceeccccCCCCCCCCCCcc-cccCCcccHHHHHHHHhCC
Q 038397 928 YRGIMEQDVLPVVPPGCSSEKPET-IQDFMTKAKAALVSVGIVRDTVLGNGKDYGKLSGR-IIDSDMHDVGRFLNRLLGL 1005 (1102)
Q Consensus 928 ~~~i~~~~~~p~~p~~~~~~~~~~-~~~f~~~~~~~L~~vGl~~~~~~~~~~~~~~~~g~-~~~~d~~~i~~FLNRlLgl 1005 (1102)
|+.|+++. .|.+|++. +| .++||.||+.+|.+|||+..+ + .+|. ..+||.++|+|||||||||
T Consensus 975 l~ti~~~~-~~~v~~Pq-----~Yk~g~Ff~D~~~~m~gVGi~~r~-----e----~~g~~tveKd~~nIsKFLNRILGl 1039 (1300)
T KOG1513|consen 975 LTTILSQT-EPLVPVPQ-----DYKVGEFFRDMKQAMLGVGIGVRE-----E----RNGVLTVEKDCNNISKFLNRILGL 1039 (1300)
T ss_pred HHHHhccc-CCCCCCCC-----CCcchHHHHHHHHHHhceeeeeec-----c----cCceeEeecchhhHHHHHHHHhCC
Confidence 99999887 68888764 45 569999999999999987541 1 1243 4689999999999999999
Q ss_pred ChhhHHHHHHHHHHHHHHHHHHHHHcCCCCCCccccccceEEEeccceEEE--ecCCCCceEEEEEEEeccccChhhhcc
Q 038397 1006 PPDIQNRLFELFISILDLLVQNARIEGNLDSGIVDMKANIIELQGTPKTVH--VDNMSGASTMLFTFTLDRGITWEGLGF 1083 (1102)
Q Consensus 1006 ~v~~Qn~lF~~F~~~l~~~i~~ak~~G~~d~Gi~dl~~~~~~~~~~~~~~~--~~~~~ga~t~l~~~~~drGmswe~A~~ 1083 (1102)
+|+.||+||+||++++.++|+++|++|+||+||+||+++..+|++....++ .+..+.+.|++|||.||||||||+|++
T Consensus 1040 ~Vh~QNaLFqYFsDtm~~lI~q~Kr~GryDmGILDLgag~e~Vrk~~~~~Fl~~~~tgs~~vElhtIsVERGmsWEeA~~ 1119 (1300)
T KOG1513|consen 1040 EVHKQNALFQYFSDTMTALIQQAKREGRYDMGILDLGAGDEEVRKESLQVFLRPGATGSGQVELHTISVERGMSWEEAFA 1119 (1300)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHhhhcCccccceeecccccchhhhhhhheeeccCCCCcceeEEEEEEeccCccHHHHHH
Confidence 999999999999999999999999999999999999998877775443333 445556799999999999999999999
Q ss_pred ccc--------cceeeeeecCCcc
Q 038397 1084 KTS--------MLTSVTIRYQPKV 1099 (1102)
Q Consensus 1084 k~~--------~~~~~~~~~~~~~ 1099 (1102)
||. ||-+.|+|||||+
T Consensus 1120 k~~elt~~~dGFYls~k~RnnKks 1143 (1300)
T KOG1513|consen 1120 KYKELTGPDDGFYLSHKVRNNKKS 1143 (1300)
T ss_pred HHHhhcCCCCceEEeehhhCCCcc
Confidence 997 7788999999997
No 2
>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1
Probab=100.00 E-value=2.8e-118 Score=975.98 Aligned_cols=299 Identities=61% Similarity=1.062 Sum_probs=290.6
Q ss_pred CCCCCcccccccCCCCCCCCCCccCcccccccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHH
Q 038397 181 PAHPDPIVETSSLSAVHPPEPTYDLLIKYDLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAG 260 (1102)
Q Consensus 181 ~~hP~~lve~~~l~sv~pP~~~y~~~lp~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~Ag 260 (1102)
.+|||+||||++|+||+||+++|.|+||+.++++|.||++|||||+||||+|+++||+|+|+|||+||||||||||||||
T Consensus 2 ~~HP~~vvEs~~lasv~~P~~~y~~~lp~~~~~~g~LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAg 81 (303)
T PF13872_consen 2 KPHPDPVVESASLASVAPPDPTYRLHLPEEVIDSGLLSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAG 81 (303)
T ss_pred CCCCchHhhhhhhhcCCCCCCCcccCCCHHHHhcccccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCccccccceEEeehhhhhhccc---cc
Q 038397 261 LIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASSE---KG 337 (1102)
Q Consensus 261 iI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~---~~ 337 (1102)
||+|||++||+|+||||+|+||++||+|||+|||+..|.|+||+++++++ .+.+++||||+|||+|+++++ ++
T Consensus 82 iI~~n~l~Gr~r~vwvS~s~dL~~Da~RDl~DIG~~~i~v~~l~~~~~~~----~~~~~~GvlF~TYs~L~~~~~~~~~~ 157 (303)
T PF13872_consen 82 IILENWLRGRKRAVWVSVSNDLKYDAERDLRDIGADNIPVHPLNKFKYGD----IIRLKEGVLFSTYSTLISESQSGGKY 157 (303)
T ss_pred HHHHHHHcCCCceEEEECChhhhhHHHHHHHHhCCCcccceechhhccCc----CCCCCCCccchhHHHHHhHHhccCCc
Confidence 99999999999999999999999999999999999999999999999984 467899999999999999864 56
Q ss_pred cchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCCCCCccchhhhcccc
Q 038397 338 RSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGASEPRNMGYMVRLGLW 417 (1102)
Q Consensus 338 ~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~ym~RLGLW 417 (1102)
+|||+||++|||+||||||||||||+|||+.. +++++||+|.+|++||++||+||||||||||||||+||+||+|||||
T Consensus 158 ~sRl~ql~~W~g~dfdgvivfDEcH~akn~~~-~~~~~sk~g~avl~LQ~~LP~ARvvY~SATgasep~NmaYm~RLGLW 236 (303)
T PF13872_consen 158 RSRLDQLVDWCGEDFDGVIVFDECHKAKNLSS-GSKKPSKTGIAVLELQNRLPNARVVYASATGASEPRNMAYMSRLGLW 236 (303)
T ss_pred cchHHHHHHHHhcCCCceEEeccchhcCCCCc-cCccccHHHHHHHHHHHhCCCCcEEEecccccCCCceeeeeeecccc
Confidence 89999999999999999999999999999964 44789999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCHHHHHHHHhccChhHHHHHHHHHHhccceeeeccCCCCceeEEEeccCcHHHHHHHHHH
Q 038397 418 GAGTCFKDFQIFLGALDKGGVGALELVAMDMKARGMYVCRTLSYKGAEFEVIEAPLEAEMTDMYKKA 484 (1102)
Q Consensus 418 g~gt~f~~~~~f~~a~~~gGv~amE~va~dlK~~G~yiaR~LSf~gvef~i~e~~l~~~~~~~Yd~~ 484 (1102)
|+||||++|++|+++|++|||++|||||||||++|+||||+|||+||||+++||+|+++|++|||+|
T Consensus 237 G~gtpf~~~~~f~~a~~~gGv~amE~vA~dlKa~G~yiaR~LSf~gvef~~~e~~l~~~~~~~Yd~~ 303 (303)
T PF13872_consen 237 GPGTPFPDFDDFLEAMEKGGVGAMEMVAMDLKARGMYIARQLSFEGVEFEIEEVPLTPEQIKMYDAY 303 (303)
T ss_pred CCCCCCCCHHHHHHHHHhcCchHHHHHHHHHHhcchheeeecccCCceEEEEEecCCHHHHHHhcCC
Confidence 9999999999999999999999999999999999999999999999999999999999999999975
No 3
>PF13871 Helicase_C_4: Helicase_C-like
Probab=100.00 E-value=7.7e-97 Score=804.52 Aligned_cols=275 Identities=58% Similarity=0.962 Sum_probs=254.4
Q ss_pred ChHHHHHHhhCCCceeeeecCCcceEEEcCCCCeEEEEecCCccchhhccchHHHhhhcCCcceEEEEeccccccccccc
Q 038397 751 NPLDDIVDQLGGPDKVAEMTGRRGMLVRASSGKGVTYQARNTKEVTMEMVNMHEKQLFMDGKKLVAIISEAGSAGVSLQA 830 (1102)
Q Consensus 751 n~LD~LId~LGGp~~VAEmTGRkgRvVr~~dG~~v~ye~R~~~d~~~~~~N~~Ek~~Fm~G~K~VAIISeAaSTGISLhA 830 (1102)
||||+|||+||||++|||||||++|||++++|+ ++||.|++.+++++++|++||++||+|+|+|||||+||||||||||
T Consensus 1 n~LD~li~~lGg~~~VAEiTGR~~r~v~~~~G~-~~~e~R~~~~~~~~~~N~~e~~~F~~g~k~v~iis~AgstGiSlHA 79 (278)
T PF13871_consen 1 NPLDQLIDRLGGPDKVAEITGRSGRVVRDNDGR-VRYESRSASDVSLDSINIAEKQAFMDGEKDVAIISDAGSTGISLHA 79 (278)
T ss_pred CcHHHHHHHcCCCCeEEEccCCceeEEEeCCCc-EEEEEccCCCCchhhccHHHHHHHhCCCceEEEEecccccccchhc
Confidence 899999999999999999999999999999997 8899999999999999999999999999999999999999999999
Q ss_pred ccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhhHHHHHHHHhhcCCccccccccCC--
Q 038397 831 DRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRFASIVAKRLESLGALTQGDRRAGL-- 908 (1102)
Q Consensus 831 Drr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRFaS~VAkRLeSLGALT~GdRra~~-- 908 (1102)
|++++|||||||||||+|||||+|||||||||||||+++|+|++++|||+||+||+|+|||||+||||||+|||+++.
T Consensus 80 d~~~~nqr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE~Rfas~va~rL~sLgAlt~gdr~~~~~~ 159 (278)
T PF13871_consen 80 DRRVKNQRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGERRFASTVARRLESLGALTRGDRRAGGAL 159 (278)
T ss_pred cccCCCCCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHHHHHHHHHHHHHhhccccccCcccccccc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999964
Q ss_pred CCCcCCcCChHHHHHHHHHHHHHhccCccCCCCCCCCCCCcchHHHHHHHHHHHhhhccceeccccCCCCCCCCCCccc-
Q 038397 909 SLSAYNYDSAFGKKALMMMYRGIMEQDVLPVVPPGCSSEKPETIQDFMTKAKAALVSVGIVRDTVLGNGKDYGKLSGRI- 987 (1102)
Q Consensus 909 ~ls~fNldn~YGr~AL~~~~~~i~~~~~~p~~p~~~~~~~~~~~~~f~~~~~~~L~~vGl~~~~~~~~~~~~~~~~g~~- 987 (1102)
++++|||||+||+.||+.||+.|++....++.||+|+ .++.+|+.+|+.+|.+|||+..+ +. +|..
T Consensus 160 ~~~~~n~~~~yg~~aL~~~~~~~~~~~~~~~~~~~~~----~~~~~F~~~~~~~L~~VGL~~~~----~~-----~g~~~ 226 (278)
T PF13871_consen 160 DLSEFNLDNKYGRKALRRMYQAIPGGKSPPVPPPGYP----GSLGEFFEDMRTALEGVGLLSED----DE-----SGGLK 226 (278)
T ss_pred cccccccchHHHHHHHHHHHHHHhcccCCccCCCCcc----ccHHHHHHHHHHHHhhccccccc----cc-----CCccc
Confidence 6999999999999999999999997665334344553 35789999999999999998641 11 2322
Q ss_pred ccCCcccHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHcCCCCCCccc
Q 038397 988 IDSDMHDVGRFLNRLLGLPPDIQNRLFELFISILDLLVQNARIEGNLDSGIVD 1040 (1102)
Q Consensus 988 ~~~d~~~i~~FLNRlLgl~v~~Qn~lF~~F~~~l~~~i~~ak~~G~~d~Gi~d 1040 (1102)
.+++. +|++||||||||||++||+||+||+++|+++|++||++|+||+||+|
T Consensus 227 ~~k~~-~V~kFLNRLLGL~V~~Qn~LF~yF~~~l~~~I~~AK~~G~yD~GI~d 278 (278)
T PF13871_consen 227 LDKDP-SVPKFLNRLLGLPVEMQNALFKYFTDTLDAIIEQAKAEGRYDEGIED 278 (278)
T ss_pred ccccc-cHHHHHHHhhCCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCC
Confidence 34555 99999999999999999999999999999999999999999999987
No 4
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=99.37 E-value=4.6e-10 Score=141.78 Aligned_cols=188 Identities=21% Similarity=0.271 Sum_probs=124.9
Q ss_pred cchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhh-hCCCc
Q 038397 219 CLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDD-VGATC 297 (1102)
Q Consensus 219 ~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~d-iG~~~ 297 (1102)
.=|++.+....+++ ...++|+|-+|.||+-+.+.||.+-+++|+.+.+-|=+...|.+-....+.. .+-.
T Consensus 155 pHQl~~~~~vl~~~--------~~R~LLADEvGLGKTIeAglil~~l~~~g~~~rvLIVvP~sL~~QW~~El~~kF~l~- 225 (956)
T PRK04914 155 PHQLYIAHEVGRRH--------APRVLLADEVGLGKTIEAGMIIHQQLLTGRAERVLILVPETLQHQWLVEMLRRFNLR- 225 (956)
T ss_pred HHHHHHHHHHhhcc--------CCCEEEEeCCcCcHHHHHHHHHHHHHHcCCCCcEEEEcCHHHHHHHHHHHHHHhCCC-
Confidence 56888755555554 4568999999999999988888888999997677788888998887776632 2211
Q ss_pred ccccccCCCCCCcCCCCccc-cccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCch
Q 038397 298 IEVHALNKLPYSKLDSRSVG-IREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPT 376 (1102)
Q Consensus 298 i~v~~l~~~~~~~~~~~~~~-~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s 376 (1102)
..++.-.......-+ .... ....++.+||..|... ..+++++++. +|| +||+||||+++|.. .++|
T Consensus 226 ~~i~~~~~~~~~~~~-~~~pf~~~~~vI~S~~~l~~~----~~~~~~l~~~---~wd-lvIvDEAH~lk~~~----~~~s 292 (956)
T PRK04914 226 FSLFDEERYAEAQHD-ADNPFETEQLVICSLDFLRRN----KQRLEQALAA---EWD-LLVVDEAHHLVWSE----EAPS 292 (956)
T ss_pred eEEEcCcchhhhccc-ccCccccCcEEEEEHHHhhhC----HHHHHHHhhc---CCC-EEEEechhhhccCC----CCcC
Confidence 111111111000000 1112 2567999999999753 2356665543 677 77889999999752 2457
Q ss_pred hHHHHHHHHhhhCCCccEEEEecCCCCCCCccc-hhhhccccCCCCCCCCHHHHHHHH
Q 038397 377 RTGEAVLELQARLPEARVVYCSATGASEPRNMG-YMVRLGLWGAGTCFKDFQIFLGAL 433 (1102)
Q Consensus 377 ~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~-ym~RLGLWg~gt~f~~~~~f~~a~ 433 (1102)
+.-+++..|..+.| .++..|||..- .|+. +..+|-|--|+. |.++++|....
T Consensus 293 ~~y~~v~~La~~~~--~~LLLTATP~q--~~~~e~falL~lLdP~~-f~~~~~F~~e~ 345 (956)
T PRK04914 293 REYQVVEQLAEVIP--GVLLLTATPEQ--LGQESHFARLRLLDPDR-FHDYEAFVEEQ 345 (956)
T ss_pred HHHHHHHHHhhccC--CEEEEEcCccc--CCcHHHHHhhhhhCCCc-CCCHHHHHHHH
Confidence 77777777766543 68889999764 2232 567777776654 88999998643
No 5
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=99.30 E-value=4.9e-10 Score=142.13 Aligned_cols=239 Identities=13% Similarity=0.111 Sum_probs=143.2
Q ss_pred CCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHH-hccCceEEEEEcCCchhhhHHhhhhhh
Q 038397 215 KSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENW-HHGRRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 215 g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~-l~Gr~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
|.|=+=|+++|.+....++. ..|-+|+|-+|.||+.|+.++|.+-. .+|....+-|=+...|+.-..+.+...
T Consensus 168 ~~Lr~YQleGlnWLi~l~~~------g~gGILADEMGLGKTlQaIalL~~L~~~~~~~gp~LIVvP~SlL~nW~~Ei~kw 241 (1033)
T PLN03142 168 GKMRDYQLAGLNWLIRLYEN------GINGILADEMGLGKTLQTISLLGYLHEYRGITGPHMVVAPKSTLGNWMNEIRRF 241 (1033)
T ss_pred cchHHHHHHHHHHHHHHHhc------CCCEEEEeCCCccHHHHHHHHHHHHHHhcCCCCCEEEEeChHHHHHHHHHHHHH
Confidence 67889999999999876542 34558899999999999888876543 356555555556666777677776554
Q ss_pred CCCcccccccCCCCCC--cCCCC-ccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCC
Q 038397 294 GATCIEVHALNKLPYS--KLDSR-SVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPE 370 (1102)
Q Consensus 294 G~~~i~v~~l~~~~~~--~~~~~-~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~ 370 (1102)
- ..+.++-+..-+.. .+... ...-+.+||.+||..++... ..|.. + .| .+||+||||+.||..
T Consensus 242 ~-p~l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~----~~L~k-~-----~W-~~VIvDEAHrIKN~~-- 307 (1033)
T PLN03142 242 C-PVLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEK----TALKR-F-----SW-RYIIIDEAHRIKNEN-- 307 (1033)
T ss_pred C-CCCceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHH----HHhcc-C-----CC-CEEEEcCccccCCHH--
Confidence 2 12222211110000 00000 00124579999999997531 12221 1 23 389999999999974
Q ss_pred CCCCchhHHHHHHHHhhhCCCccEEEEecCCCCCCCccc-hhhhccccCCCCCCCCHHHHHHHHhccC-hhHHHHHHHHH
Q 038397 371 AGSQPTRTGEAVLELQARLPEARVVYCSATGASEPRNMG-YMVRLGLWGAGTCFKDFQIFLGALDKGG-VGALELVAMDM 448 (1102)
Q Consensus 371 ~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~-ym~RLGLWg~gt~f~~~~~f~~a~~~gG-v~amE~va~dl 448 (1102)
|+..+++..|+. -+.+-.|+|...+ |+. +++-|.+--++ .|.+...|-......+ ....+++..--
T Consensus 308 -----Sklskalr~L~a----~~RLLLTGTPlqN--nl~ELwsLL~FL~P~-~f~s~~~F~~~f~~~~~~~~~e~i~~L~ 375 (1033)
T PLN03142 308 -----SLLSKTMRLFST----NYRLLITGTPLQN--NLHELWALLNFLLPE-IFSSAETFDEWFQISGENDQQEVVQQLH 375 (1033)
T ss_pred -----HHHHHHHHHhhc----CcEEEEecCCCCC--CHHHHHHHHhcCCCC-cCCCHHHHHHHHccccccchHHHHHHHH
Confidence 778888776643 3457788998754 443 22222222232 4667777766655433 22333333222
Q ss_pred Hhccce-eeec-----cCCCCceeEEEeccCcHHHHHHHHHHH
Q 038397 449 KARGMY-VCRT-----LSYKGAEFEVIEAPLEAEMTDMYKKAA 485 (1102)
Q Consensus 449 K~~G~y-iaR~-----LSf~gvef~i~e~~l~~~~~~~Yd~~a 485 (1102)
+...-| ++|. .++-.-...++.+.|++.++++|+...
T Consensus 376 ~~L~pf~LRR~KsdV~~~LPpK~e~iv~v~LS~~Qk~lY~~ll 418 (1033)
T PLN03142 376 KVLRPFLLRRLKSDVEKGLPPKKETILKVGMSQMQKQYYKALL 418 (1033)
T ss_pred HHhhHHHhhhhHHHHhhhCCCceeEEEeeCCCHHHHHHHHHHH
Confidence 223333 3442 255666778888999999999998763
No 6
>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1) [, ]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. Proteins that contain this domain appear to be distantly related to the DEAX box helicases IPR001410 from INTERPRO, however no helicase activity has ever been demonstrated for these proteins. ; GO: 0003677 DNA binding, 0005524 ATP binding; PDB: 1Z63_B 1Z3I_X 3DMQ_A 3MWY_W.
Probab=99.17 E-value=4.9e-10 Score=122.21 Aligned_cols=240 Identities=20% Similarity=0.180 Sum_probs=144.3
Q ss_pred hhhHHHHHHhhc---cccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCc----eEEEEEcCCchhhhHHhhhhhh
Q 038397 221 QIETLVYASQRH---LQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRR----KALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 221 Qle~v~ya~q~h---~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~----~~~w~s~s~~L~~Da~RDl~di 293 (1102)
|+++|.+...+- ...-......|++++|.+|.||+-++.++|...+..++. +++.+.-+ .+..-..+.+...
T Consensus 2 Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~~~~l~~~~~~~~~~~~LIv~P~-~l~~~W~~E~~~~ 80 (299)
T PF00176_consen 2 QLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIALISYLKNEFPQRGEKKTLIVVPS-SLLSQWKEEIEKW 80 (299)
T ss_dssp HHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHHHHHHHHCCTTSS-S-EEEEE-T-TTHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhhhhhhhhccccccccceeEeecc-chhhhhhhhhccc
Confidence 899998888775 112223457899999999999999998888866665554 48887666 7777777888877
Q ss_pred CCC-cccccccCCCCCCcCCCCccccccceEEeehhhhhhcc-ccccchHHHHHHHhccCCCceEEeecchhccccCCCC
Q 038397 294 GAT-CIEVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASS-EKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEA 371 (1102)
Q Consensus 294 G~~-~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~-~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~ 371 (1102)
... .+.++...................+|+.+||+.+.... .....-|.+ . + -++||+||+|.++|..
T Consensus 81 ~~~~~~~v~~~~~~~~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~----~--~-~~~vIvDEaH~~k~~~--- 150 (299)
T PF00176_consen 81 FDPDSLRVIIYDGDSERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLKQ----I--K-WDRVIVDEAHRLKNKD--- 150 (299)
T ss_dssp SGT-TS-EEEESSSCHHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHT----S--E-EEEEEETTGGGGTTTT---
T ss_pred cccccccccccccccccccccccccccceeeecccccccccccccccccccc----c--c-ceeEEEeccccccccc---
Confidence 732 45555544332000001122346789999999998211 111122222 1 2 3588999999998664
Q ss_pred CCCchhHHHHHHHHhhhCCCccEEEEecCCCCC-CCccchhhhccccCCCCCCCCHHHHHHHHhc----cChhHHHHHHH
Q 038397 372 GSQPTRTGEAVLELQARLPEARVVYCSATGASE-PRNMGYMVRLGLWGAGTCFKDFQIFLGALDK----GGVGALELVAM 446 (1102)
Q Consensus 372 ~~~~s~~g~avl~LQ~~lP~ARvvY~SATgase-p~Nl~ym~RLGLWg~gt~f~~~~~f~~a~~~----gGv~amE~va~ 446 (1102)
|+...++..|+ .-+++..|||...+ +..+.-+.++ |++ .+|.+...|.+.+.. .....++.+..
T Consensus 151 ----s~~~~~l~~l~----~~~~~lLSgTP~~n~~~dl~~~l~~-L~~--~~~~~~~~f~~~~~~~~~~~~~~~~~~L~~ 219 (299)
T PF00176_consen 151 ----SKRYKALRKLR----ARYRWLLSGTPIQNSLEDLYSLLRF-LNP--DPFSDRRSFKKWFYRPDKENSYENIERLRE 219 (299)
T ss_dssp ----SHHHHHHHCCC----ECEEEEE-SS-SSSGSHHHHHHHHH-HCT--TTCSSHHHHHHHTHHHHHTHHHHHHHHHHH
T ss_pred ----ccccccccccc----cceEEeeccccccccccccccchhe-eec--cccccchhhhhhhhhhcccccccccccccc
Confidence 78888887766 34566789998764 4444444444 222 356688888887532 23444444444
Q ss_pred HHHhccceeeec-----cCCCCceeEEEeccCcHHHHHHHHHH
Q 038397 447 DMKARGMYVCRT-----LSYKGAEFEVIEAPLEAEMTDMYKKA 484 (1102)
Q Consensus 447 dlK~~G~yiaR~-----LSf~gvef~i~e~~l~~~~~~~Yd~~ 484 (1102)
-|+ ..+++|. ..+......++.++|+++++++|+..
T Consensus 220 ~l~--~~~~r~~~~d~~~~lp~~~~~~~~~~ls~~q~~~Y~~~ 260 (299)
T PF00176_consen 220 LLS--EFMIRRTKKDVEKELPPKIEHVINVELSPEQRELYNEL 260 (299)
T ss_dssp HHC--CCEECHCGGGGCTTSTCEEEEEEEEGG-HHHHHHHHHH
T ss_pred ccc--hhhhhhhcccccccCCceEEEEEEeCCCHHHHHHHHHH
Confidence 443 2333332 24556778888899999999999943
No 7
>PRK13766 Hef nuclease; Provisional
Probab=99.12 E-value=6.6e-09 Score=129.85 Aligned_cols=76 Identities=24% Similarity=0.210 Sum_probs=64.7
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRF 885 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRF 885 (1102)
++|.+|+..|+|-+++++.|+.++ .-++=|..++|||..+.||++||++|.++.. .|.++..+=.-|.+|
T Consensus 417 ~~F~~g~~~vLvaT~~~~eGldi~--------~~~~VI~yd~~~s~~r~iQR~GR~gR~~~~~--v~~l~~~~t~ee~~y 486 (773)
T PRK13766 417 DKFRAGEFNVLVSTSVAEEGLDIP--------SVDLVIFYEPVPSEIRSIQRKGRTGRQEEGR--VVVLIAKGTRDEAYY 486 (773)
T ss_pred HHHHcCCCCEEEECChhhcCCCcc--------cCCEEEEeCCCCCHHHHHHHhcccCcCCCCE--EEEEEeCCChHHHHH
Confidence 489999999999999999999995 4555577899999999999999999988854 688888888888888
Q ss_pred HHHHHH
Q 038397 886 ASIVAK 891 (1102)
Q Consensus 886 aS~VAk 891 (1102)
.+.+.|
T Consensus 487 ~~~~~k 492 (773)
T PRK13766 487 WSSRRK 492 (773)
T ss_pred HHhhHH
Confidence 766544
No 8
>cd00046 DEXDc DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Probab=98.95 E-value=2.4e-09 Score=101.15 Aligned_cols=141 Identities=19% Similarity=0.112 Sum_probs=96.6
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhc-cCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCC-CCcCCCCcccccc
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHH-GRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLP-YSKLDSRSVGIRE 320 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~-Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~-~~~~~~~~~~~~~ 320 (1102)
++++...||.||+.++...+.+.+.. ..++.+|+.-+..|.......+.+.....+.+.-+.... .... ........
T Consensus 2 ~~~i~~~~G~GKT~~~~~~~~~~~~~~~~~~~lv~~p~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~ 80 (144)
T cd00046 2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQVAERLKELFGEGIKVGYLIGGTSIKQQ-EKLLSGKT 80 (144)
T ss_pred CEEEECCCCCchhHHHHHHHHHHHhcccCCCEEEEcCcHHHHHHHHHHHHHHhhCCcEEEEEecCcchhHH-HHHhcCCC
Confidence 57889999999999999999999986 557899999999999998888888775322222221111 0000 00113467
Q ss_pred ceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecC
Q 038397 321 GVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSAT 400 (1102)
Q Consensus 321 GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SAT 400 (1102)
.|+|+||.++........ + ......+||+||||...+.. .........+...++.++++.|||
T Consensus 81 ~i~i~t~~~~~~~~~~~~--~-------~~~~~~~iiiDE~h~~~~~~--------~~~~~~~~~~~~~~~~~~i~~saT 143 (144)
T cd00046 81 DIVVGTPGRLLDELERLK--L-------SLKKLDLLILDEAHRLLNQG--------FGLLGLKILLKLPKDRQVLLLSAT 143 (144)
T ss_pred CEEEECcHHHHHHHHcCC--c-------chhcCCEEEEeCHHHHhhcc--------hHHHHHHHHhhCCccceEEEEecc
Confidence 799999999875322111 0 11345699999999998752 122224455667889999999999
Q ss_pred C
Q 038397 401 G 401 (1102)
Q Consensus 401 g 401 (1102)
.
T Consensus 144 p 144 (144)
T cd00046 144 P 144 (144)
T ss_pred C
Confidence 3
No 9
>smart00487 DEXDc DEAD-like helicases superfamily.
Probab=98.59 E-value=1.1e-07 Score=95.38 Aligned_cols=167 Identities=19% Similarity=0.173 Sum_probs=109.1
Q ss_pred CCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhcc-CceEEEEEcCCchhhhHHhhhhhh
Q 038397 215 KSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHG-RRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 215 g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~G-r~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
..+.+.|.+++....+.. ..+++..++|.||+..++..+++.+.++ .++++|++-+..+.......+...
T Consensus 7 ~~~~~~Q~~~~~~~~~~~---------~~~~i~~~~GsGKT~~~~~~~~~~~~~~~~~~~l~~~p~~~~~~~~~~~~~~~ 77 (201)
T smart00487 7 EPLRPYQKEAIEALLSGL---------RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQWAEELKKL 77 (201)
T ss_pred CCCCHHHHHHHHHHHcCC---------CcEEEECCCCCchhHHHHHHHHHHhcccCCCcEEEEeCCHHHHHHHHHHHHHH
Confidence 346789999987766432 4667888899999999999999999876 467999999999999888888777
Q ss_pred CCCc--ccccccCCCCCCcCCCCcccccc-ceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCC
Q 038397 294 GATC--IEVHALNKLPYSKLDSRSVGIRE-GVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPE 370 (1102)
Q Consensus 294 G~~~--i~v~~l~~~~~~~~~~~~~~~~~-GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~ 370 (1102)
+... ..+.-+....... .-..+.... +|+++||..|.....+..... ..-.+||+||||...+.
T Consensus 78 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~v~~~t~~~l~~~~~~~~~~~---------~~~~~iIiDE~h~~~~~--- 144 (201)
T smart00487 78 GPSLGLKVVGLYGGDSKRE-QLRKLESGKTDILVTTPGRLLDLLENDLLEL---------SNVDLVILDEAHRLLDG--- 144 (201)
T ss_pred hccCCeEEEEEeCCcchHH-HHHHHhcCCCCEEEeChHHHHHHHHcCCcCH---------hHCCEEEEECHHHHhcC---
Confidence 6431 1111111111000 000011223 899999999986543322111 12358999999999863
Q ss_pred CCCCchhHHHHHHHHhhhC-CCccEEEEecCCCCCCCccc
Q 038397 371 AGSQPTRTGEAVLELQARL-PEARVVYCSATGASEPRNMG 409 (1102)
Q Consensus 371 ~~~~~s~~g~avl~LQ~~l-P~ARvvY~SATgasep~Nl~ 409 (1102)
........+.+.+ ++.+++..|||...+..|.+
T Consensus 145 ------~~~~~~~~~~~~~~~~~~~v~~saT~~~~~~~~~ 178 (201)
T smart00487 145 ------GFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLL 178 (201)
T ss_pred ------CcHHHHHHHHHhCCccceEEEEecCCchhHHHHH
Confidence 1122222333333 68899999999987766665
No 10
>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3.1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) [, , ].; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 2Y3T_B 2W74_B 2FWR_A 2FZ4_A 3UWX_B 3H1T_A 3B6E_A 2FDC_A 1D9Z_A 1T5L_B ....
Probab=98.54 E-value=2.8e-07 Score=93.06 Aligned_cols=163 Identities=20% Similarity=0.172 Sum_probs=100.2
Q ss_pred cccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCC
Q 038397 217 LSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGAT 296 (1102)
Q Consensus 217 LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~ 296 (1102)
|.+-|.|+|.-.....+.. ...+. +++--.||.||+..++.+|.+-+. +++|+.-+.+|..-...++.+++..
T Consensus 4 lr~~Q~~ai~~i~~~~~~~--~~~~~-~ll~~~tGsGKT~~~~~~~~~l~~----~~l~~~p~~~l~~Q~~~~~~~~~~~ 76 (184)
T PF04851_consen 4 LRPYQQEAIARIINSLENK--KEERR-VLLNAPTGSGKTIIALALILELAR----KVLIVAPNISLLEQWYDEFDDFGSE 76 (184)
T ss_dssp E-HHHHHHHHHHHHHHHTT--SGCSE-EEEEESTTSSHHHHHHHHHHHHHC----EEEEEESSHHHHHHHHHHHHHHSTT
T ss_pred CCHHHHHHHHHHHHHHHhc--CCCCC-EEEEECCCCCcChhhhhhhhcccc----ceeEecCHHHHHHHHHHHHHHhhhh
Confidence 5577888877666543322 11233 445557999999999999988887 8999999999999999999888876
Q ss_pred cccccccCC-----CC-----CCcCC--CCccccccceEEeehhhhhhccccc-cch---HHHHHHHhccCCCceEEeec
Q 038397 297 CIEVHALNK-----LP-----YSKLD--SRSVGIREGVVFLTYSSLIASSEKG-RSR---LQQLVQWCGSGYDGLVIFDE 360 (1102)
Q Consensus 297 ~i~v~~l~~-----~~-----~~~~~--~~~~~~~~GvlF~TYs~L~~~~~~~-~sR---l~Ql~~W~g~dfdgvivfDE 360 (1102)
...+...+. .. ..... .........++|+||..|....... ... ....-.|. +...+|||||
T Consensus 77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~--~~~~~vI~DE 154 (184)
T PF04851_consen 77 KYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLK--NKFDLVIIDE 154 (184)
T ss_dssp SEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGG--GSESEEEEET
T ss_pred hhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhcc--ccCCEEEEeh
Confidence 554321111 00 00000 0001245669999999998763221 111 01111233 2345999999
Q ss_pred chhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCC
Q 038397 361 CHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 361 cH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATg 401 (1102)
||++.+.. . =..+.+ .+.+.+|+.|||.
T Consensus 155 aH~~~~~~--------~-~~~i~~----~~~~~~l~lTATp 182 (184)
T PF04851_consen 155 AHHYPSDS--------S-YREIIE----FKAAFILGLTATP 182 (184)
T ss_dssp GGCTHHHH--------H-HHHHHH----SSCCEEEEEESS-
T ss_pred hhhcCCHH--------H-HHHHHc----CCCCeEEEEEeCc
Confidence 99987441 1 223332 7889999999994
No 11
>TIGR00603 rad25 DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.47 E-value=0.00013 Score=90.72 Aligned_cols=157 Identities=18% Similarity=0.189 Sum_probs=94.2
Q ss_pred CcccchhhHHHHHHhhccccCCCC-CcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNS-ARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVG 294 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g-~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG 294 (1102)
.|=+=|.++|.-... +| .|.|.+.-. ||.||+.+..++|.. + +++++.+--+..|.+=..+.+....
T Consensus 255 ~LRpYQ~eAl~~~~~-------~gr~r~GIIvLP-tGaGKTlvai~aa~~-l---~k~tLILvps~~Lv~QW~~ef~~~~ 322 (732)
T TIGR00603 255 QIRPYQEKSLSKMFG-------NGRARSGIIVLP-CGAGKSLVGVTAACT-V---KKSCLVLCTSAVSVEQWKQQFKMWS 322 (732)
T ss_pred CcCHHHHHHHHHHHh-------cCCCCCcEEEeC-CCCChHHHHHHHHHH-h---CCCEEEEeCcHHHHHHHHHHHHHhc
Confidence 455779999754432 22 257776654 999999998777653 2 3568988888888877777776542
Q ss_pred C-CcccccccCCCCCCcCCCCcc-ccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCC
Q 038397 295 A-TCIEVHALNKLPYSKLDSRSV-GIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAG 372 (1102)
Q Consensus 295 ~-~~i~v~~l~~~~~~~~~~~~~-~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~ 372 (1102)
. ....|.-+. |. .+.. .-..+|+.+||+++.....+. .-..++++|+....=|+|||||||...+
T Consensus 323 ~l~~~~I~~~t----g~--~k~~~~~~~~VvVtTYq~l~~~~~r~-~~~~~~l~~l~~~~~gLII~DEvH~lpA------ 389 (732)
T TIGR00603 323 TIDDSQICRFT----SD--AKERFHGEAGVVVSTYSMVAHTGKRS-YESEKVMEWLTNREWGLILLDEVHVVPA------ 389 (732)
T ss_pred CCCCceEEEEe----cC--cccccccCCcEEEEEHHHhhcccccc-hhhhHHHHHhccccCCEEEEEccccccH------
Confidence 1 222221110 10 0111 113679999999987542221 1234567888654347999999999742
Q ss_pred CCchhHHHHHHHHhhhCCCccEEEEecCCCCC
Q 038397 373 SQPTRTGEAVLELQARLPEARVVYCSATGASE 404 (1102)
Q Consensus 373 ~~~s~~g~avl~LQ~~lP~ARvvY~SATgase 404 (1102)
.+=+.++ ..+...+.+-.|||--.+
T Consensus 390 ----~~fr~il---~~l~a~~RLGLTATP~Re 414 (732)
T TIGR00603 390 ----AMFRRVL---TIVQAHCKLGLTATLVRE 414 (732)
T ss_pred ----HHHHHHH---HhcCcCcEEEEeecCccc
Confidence 2222222 233344678888887654
No 12
>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3RRM_A 3RRN_A 3PEW_A 2KBE_A 3PEY_A 3FHO_A 2ZJA_A 2ZJ8_A 2ZJ5_A 2ZJ2_A ....
Probab=98.44 E-value=2.1e-07 Score=93.45 Aligned_cols=165 Identities=18% Similarity=0.172 Sum_probs=111.6
Q ss_pred cchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccC-ceEEEEEcCCchhhhHHhhhhhhCCC-
Q 038397 219 CLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGR-RKALWISVGSDLKFDARRDLDDVGAT- 296 (1102)
Q Consensus 219 ~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr-~~~~w~s~s~~L~~Da~RDl~diG~~- 296 (1102)
+.|.+++....+. .-+++.-+||.||+......++..+.++. .+++++.-...|..+..+++..++..
T Consensus 2 ~~Q~~~~~~i~~~----------~~~li~aptGsGKT~~~~~~~l~~~~~~~~~~~lii~P~~~l~~q~~~~~~~~~~~~ 71 (169)
T PF00270_consen 2 PLQQEAIEAIISG----------KNVLISAPTGSGKTLAYILPALNRLQEGKDARVLIIVPTRALAEQQFERLRKFFSNT 71 (169)
T ss_dssp HHHHHHHHHHHTT----------SEEEEECSTTSSHHHHHHHHHHHHHHTTSSSEEEEEESSHHHHHHHHHHHHHHTTTT
T ss_pred HHHHHHHHHHHcC----------CCEEEECCCCCccHHHHHHHHHhhhccCCCceEEEEeeccccccccccccccccccc
Confidence 5688887766632 23788999999999999999999999982 38999999999999999999999886
Q ss_pred cccccccCC-CCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCc
Q 038397 297 CIEVHALNK-LPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQP 375 (1102)
Q Consensus 297 ~i~v~~l~~-~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~ 375 (1102)
.+.+..+.. .+...-....+..+..||++|+..|...-..++..+ .. -++|||||+|..-... -
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~~~--------~~-~~~iViDE~h~l~~~~------~ 136 (169)
T PF00270_consen 72 NVRVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKINI--------SR-LSLIVIDEAHHLSDET------F 136 (169)
T ss_dssp TSSEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSSTG--------TT-ESEEEEETHHHHHHTT------H
T ss_pred ccccccccccccccccccccccccccccccCcchhhcccccccccc--------cc-ceeeccCccccccccc------H
Confidence 344433321 110000000111246799999999986522211112 12 3699999999988531 1
Q ss_pred hhHHHHHHHHhhhCCCccEEEEecCCCCCCCcc
Q 038397 376 TRTGEAVLELQARLPEARVVYCSATGASEPRNM 408 (1102)
Q Consensus 376 s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl 408 (1102)
...-..+++.....++.+++++|||-.++++||
T Consensus 137 ~~~~~~i~~~~~~~~~~~~i~~SAT~~~~~~~~ 169 (169)
T PF00270_consen 137 RAMLKSILRRLKRFKNIQIILLSATLPSNVEKL 169 (169)
T ss_dssp HHHHHHHHHHSHTTTTSEEEEEESSSTHHHHHH
T ss_pred HHHHHHHHHHhcCCCCCcEEEEeeCCChhHhhC
Confidence 234445555555566899999999987665553
No 13
>cd00268 DEADc DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region.
Probab=98.18 E-value=4e-06 Score=87.44 Aligned_cols=164 Identities=18% Similarity=0.210 Sum_probs=104.7
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhcc----CceEEEEEcCCchhhhHHhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHG----RRKALWISVGSDLKFDARRDLD 291 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~G----r~~~~w~s~s~~L~~Da~RDl~ 291 (1102)
.++..|.+++....+ + ..+++.-.||.||+-..+-.+++.+... +.+++++.-...|..+...+++
T Consensus 21 ~~~~~Q~~~~~~~~~-~---------~~~li~~~TG~GKT~~~~~~~l~~~~~~~~~~~~~viii~p~~~L~~q~~~~~~ 90 (203)
T cd00268 21 KPTPIQARAIPPLLS-G---------RDVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQIAEVAR 90 (203)
T ss_pred CCCHHHHHHHHHHhc-C---------CcEEEECCCCCcHHHHHHHHHHHHHHhhcccCCceEEEEcCCHHHHHHHHHHHH
Confidence 467899999755543 2 3577888899999988766666666654 5679999999999999999999
Q ss_pred hhCCC-cccccccCC-CCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCC
Q 038397 292 DVGAT-CIEVHALNK-LPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVP 369 (1102)
Q Consensus 292 diG~~-~i~v~~l~~-~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~ 369 (1102)
+++.. .+.+.-+.. .+..+ +.+...-...|+++|...|...-.++...++. -.+||+||||.+.+.
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~iiv~T~~~l~~~l~~~~~~~~~---------l~~lIvDE~h~~~~~-- 158 (203)
T cd00268 91 KLGKHTNLKVVVIYGGTSIDK-QIRKLKRGPHIVVATPGRLLDLLERGKLDLSK---------VKYLVLDEADRMLDM-- 158 (203)
T ss_pred HHhccCCceEEEEECCCCHHH-HHHHhcCCCCEEEEChHHHHHHHHcCCCChhh---------CCEEEEeChHHhhcc--
Confidence 88642 333322211 11000 00011124579999987765432222222221 258999999998743
Q ss_pred CCCCCchhHHHHHHHHhhhCC-CccEEEEecCCCCCCCcc
Q 038397 370 EAGSQPTRTGEAVLELQARLP-EARVVYCSATGASEPRNM 408 (1102)
Q Consensus 370 ~~~~~~s~~g~avl~LQ~~lP-~ARvvY~SATgasep~Nl 408 (1102)
..+.....+.+.++ +.+++.+|||.-.+..++
T Consensus 159 -------~~~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~ 191 (203)
T cd00268 159 -------GFEDQIREILKLLPKDRQTLLFSATMPKEVRDL 191 (203)
T ss_pred -------ChHHHHHHHHHhCCcccEEEEEeccCCHHHHHH
Confidence 24455555556666 578999999977554443
No 14
>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain. The domain is related to the DEAD/DEAH box helicase domain which is found in a large family of ATPases.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity, 0019079 viral genome replication; PDB: 2QEQ_A 2V6J_A 2V6I_A 8OHM_A 4A92_B 1JR6_A 1HEI_A 1ONB_A 1A1V_A 1YMF_A ....
Probab=97.85 E-value=6.9e-05 Score=76.44 Aligned_cols=125 Identities=20% Similarity=0.245 Sum_probs=77.9
Q ss_pred CCCCcchh-hHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCccccccceEEeehh
Q 038397 250 AGVGKGRT-IAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSVGIREGVVFLTYS 328 (1102)
Q Consensus 250 ~GvGKGR~-~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs 328 (1102)
.|.||+|. +.-+|.++..++.| ++-+--+--+..-+.+=|++.. +.++. +-. .. ...-++.|=-.||+
T Consensus 13 pGaGKTr~vlp~~~~~~i~~~~r-vLvL~PTRvva~em~~aL~~~~---~~~~t-~~~-~~-----~~~g~~~i~vMc~a 81 (148)
T PF07652_consen 13 PGAGKTRRVLPEIVREAIKRRLR-VLVLAPTRVVAEEMYEALKGLP---VRFHT-NAR-MR-----THFGSSIIDVMCHA 81 (148)
T ss_dssp TTSSTTTTHHHHHHHHHHHTT---EEEEESSHHHHHHHHHHTTTSS---EEEES-TTS-S---------SSSSEEEEEHH
T ss_pred CCCCCcccccHHHHHHHHHccCe-EEEecccHHHHHHHHHHHhcCC---cccCc-eee-ec-----cccCCCcccccccH
Confidence 68899996 78889999888876 7877777778888888886553 33321 111 00 01123456678999
Q ss_pred hhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCC
Q 038397 329 SLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGAS 403 (1102)
Q Consensus 329 ~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgas 403 (1102)
++-..-..+.. + .+|| +||+||||-+= ..|-.++..+.-+.....++|||+|||...
T Consensus 82 t~~~~~~~p~~-~--------~~yd-~II~DEcH~~D--------p~sIA~rg~l~~~~~~g~~~~i~mTATPPG 138 (148)
T PF07652_consen 82 TYGHFLLNPCR-L--------KNYD-VIIMDECHFTD--------PTSIAARGYLRELAESGEAKVIFMTATPPG 138 (148)
T ss_dssp HHHHHHHTSSC-T--------TS-S-EEEECTTT--S--------HHHHHHHHHHHHHHHTTS-EEEEEESS-TT
T ss_pred HHHHHhcCccc-c--------cCcc-EEEEeccccCC--------HHHHhhheeHHHhhhccCeeEEEEeCCCCC
Confidence 88643111111 1 2344 99999999843 225667777777777777899999999653
No 15
>PHA02558 uvsW UvsW helicase; Provisional
Probab=97.85 E-value=9.8e-05 Score=88.81 Aligned_cols=147 Identities=16% Similarity=0.163 Sum_probs=95.1
Q ss_pred cCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhh
Q 038397 214 SKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 214 ~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
.+.|.+-|.++|.-+. +| +.|.+. -.||-||+..++.++..-..+++.+++++.-+.+|..-..+.++..
T Consensus 112 ~~~~r~~Q~~av~~~l-~~--------~~~il~-apTGsGKT~i~~~l~~~~~~~~~~~vLilvpt~eL~~Q~~~~l~~~ 181 (501)
T PHA02558 112 KIEPHWYQYDAVYEGL-KN--------NRRLLN-LPTSAGKSLIQYLLSRYYLENYEGKVLIIVPTTSLVTQMIDDFVDY 181 (501)
T ss_pred cCCCCHHHHHHHHHHH-hc--------CceEEE-eCCCCCHHHHHHHHHHHHHhcCCCeEEEEECcHHHHHHHHHHHHHh
Confidence 3578899999965443 33 346444 5599999998777655433344448999999999999999999887
Q ss_pred CCCc-ccccccCCCCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCC
Q 038397 294 GATC-IEVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAG 372 (1102)
Q Consensus 294 G~~~-i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~ 372 (1102)
+... ..+..+. .+.....+.-|+++||-+|.... -.|+. +| ++||+||||++...
T Consensus 182 ~~~~~~~~~~i~-------~g~~~~~~~~I~VaT~qsl~~~~----------~~~~~-~~-~~iIvDEaH~~~~~----- 237 (501)
T PHA02558 182 RLFPREAMHKIY-------SGTAKDTDAPIVVSTWQSAVKQP----------KEWFD-QF-GMVIVDECHLFTGK----- 237 (501)
T ss_pred ccccccceeEEe-------cCcccCCCCCEEEeeHHHHhhch----------hhhcc-cc-CEEEEEchhcccch-----
Confidence 6421 1111110 01111123459999999986321 13542 45 59999999998621
Q ss_pred CCchhHHHHHHHHhhhCCCcc-EEEEecCCC
Q 038397 373 SQPTRTGEAVLELQARLPEAR-VVYCSATGA 402 (1102)
Q Consensus 373 ~~~s~~g~avl~LQ~~lP~AR-vvY~SATga 402 (1102)
+ ...+-..+|+++ ++..|||--
T Consensus 238 -----~---~~~il~~~~~~~~~lGLTATp~ 260 (501)
T PHA02558 238 -----S---LTSIITKLDNCKFKFGLTGSLR 260 (501)
T ss_pred -----h---HHHHHHhhhccceEEEEeccCC
Confidence 1 223336677775 799999973
No 16
>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]
Probab=97.75 E-value=0.0012 Score=82.45 Aligned_cols=116 Identities=22% Similarity=0.334 Sum_probs=83.3
Q ss_pred CChHHHHHHhhCCCceeeeecCCcceEEEcCCCCeEEEEecCCccchhhccchHHHhhhcCCc---ceEEEEeccccccc
Q 038397 750 NNPLDDIVDQLGGPDKVAEMTGRRGMLVRASSGKGVTYQARNTKEVTMEMVNMHEKQLFMDGK---KLVAIISEAGSAGV 826 (1102)
Q Consensus 750 ~n~LD~LId~LGGp~~VAEmTGRkgRvVr~~dG~~v~ye~R~~~d~~~~~~N~~Ek~~Fm~G~---K~VAIISeAaSTGI 826 (1102)
.+++=+++|.| +++-.+.|++ +-+=||+ .....|.. . -+.|++=+ +-.+.=|-|||-||
T Consensus 601 Isny~~tldl~---e~~~~~~g~~---~~rLdG~-~~~~qRq~------~-----vd~FN~p~~~~~vfLlSsKAgg~Gi 662 (776)
T KOG0390|consen 601 ISNYTQTLDLF---EQLCRWRGYE---VLRLDGK-TSIKQRQK------L-----VDTFNDPESPSFVFLLSSKAGGEGL 662 (776)
T ss_pred eccHHHHHHHH---HHHHhhcCce---EEEEcCC-CchHHHHH------H-----HHhccCCCCCceEEEEecccccCce
Confidence 34555666665 4444565554 3444776 43444532 1 25787644 44556689999999
Q ss_pred ccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCC-CeEEEeecCccchhhhHHHHHH
Q 038397 827 SLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASA-PEYRIIFTNLGGERRFASIVAK 891 (1102)
Q Consensus 827 SLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsa-P~Y~~l~T~l~GErRFaS~VAk 891 (1102)
||=.-.|+ |.+...|+.-.-.|-+.|.+|-+|.-+ =+|++|+|+-.-|+-|--..-|
T Consensus 663 nLiGAsRl--------il~D~dWNPa~d~QAmaR~~RdGQKk~v~iYrLlatGtiEEk~~qrq~~K 720 (776)
T KOG0390|consen 663 NLIGASRL--------ILFDPDWNPAVDQQAMARAWRDGQKKPVYIYRLLATGTIEEKIYQRQTHK 720 (776)
T ss_pred eecccceE--------EEeCCCCCchhHHHHHHHhccCCCcceEEEEEeecCCCchHHHHHHHHHh
Confidence 99987764 899999999999999999999999853 4799999999999988655444
No 17
>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family. Members of this family are assumed to differ from each other in DNA site specificity.
Probab=97.53 E-value=0.00041 Score=86.40 Aligned_cols=160 Identities=18% Similarity=0.249 Sum_probs=102.0
Q ss_pred cchhhHHHHHHhhccc-cCCCCCcceeEeecCCCCCcchhhHHHHHHHHh-ccCceEEEEEcCCchhhhHHhhhhhhCCC
Q 038397 219 CLQIETLVYASQRHLQ-HLPNSARAGFFIGDGAGVGKGRTIAGLIWENWH-HGRRKALWISVGSDLKFDARRDLDDVGAT 296 (1102)
Q Consensus 219 ~~Qle~v~ya~q~h~~-~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l-~Gr~~~~w~s~s~~L~~Da~RDl~diG~~ 296 (1102)
..|.+||.=+..+-.. ..+.|.|.|.+.- -||.||+.+++.++..-.. .+..|+|++.-..+|..=+...+...|..
T Consensus 241 ~~Q~~av~~~~~~~~~~~~~~~~~~gli~~-~TGsGKT~t~~~la~~l~~~~~~~~vl~lvdR~~L~~Q~~~~f~~~~~~ 319 (667)
T TIGR00348 241 YMQYRAVKKIVESITRKTWGKDERGGLIWH-TQGSGKTLTMLFAARKALELLKNPKVFFVVDRRELDYQLMKEFQSLQKD 319 (667)
T ss_pred HHHHHHHHHHHHHHHhcccCCCCceeEEEE-ecCCCccHHHHHHHHHHHhhcCCCeEEEEECcHHHHHHHHHHHHhhCCC
Confidence 4477776544444322 2234566777665 5999999999988765432 23467999999999999999999998854
Q ss_pred ccc-ccccCCCCCCcCCCCccccccceEEeehhhhhhccccccchHHHHH-HHhccCCCceEEeecchhccccCCCCCCC
Q 038397 297 CIE-VHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLV-QWCGSGYDGLVIFDECHKAKNLVPEAGSQ 374 (1102)
Q Consensus 297 ~i~-v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~-~W~g~dfdgvivfDEcH~akn~~~~~~~~ 374 (1102)
... +.....++ +.+ .....+|+|+|+-+|... ++..+ .+.-..++-+||+||||+..
T Consensus 320 ~~~~~~s~~~L~-~~l----~~~~~~iivtTiQk~~~~-------~~~~~~~~~~~~~~~lvIvDEaHrs~--------- 378 (667)
T TIGR00348 320 CAERIESIAELK-RLL----EKDDGGIIITTIQKFDKK-------LKEEEEKFPVDRKEVVVIFDEAHRSQ--------- 378 (667)
T ss_pred CCcccCCHHHHH-HHH----hCCCCCEEEEEhHHhhhh-------HhhhhhccCCCCCCEEEEEEcCcccc---------
Confidence 221 11100010 000 012467999999999641 21111 11112456699999999843
Q ss_pred chhHHHHHHHHhhhCCCccEEEEecCCCC
Q 038397 375 PTRTGEAVLELQARLPEARVVYCSATGAS 403 (1102)
Q Consensus 375 ~s~~g~avl~LQ~~lP~ARvvY~SATgas 403 (1102)
.|.....|.+.+|+|..+=-+||...
T Consensus 379 ---~~~~~~~l~~~~p~a~~lGfTaTP~~ 404 (667)
T TIGR00348 379 ---YGELAKNLKKALKNASFFGFTGTPIF 404 (667)
T ss_pred ---chHHHHHHHhhCCCCcEEEEeCCCcc
Confidence 33344556689999999999999864
No 18
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=97.52 E-value=1.9e-05 Score=86.09 Aligned_cols=50 Identities=38% Similarity=0.885 Sum_probs=45.8
Q ss_pred cccccCcHHHHhhhhhccccCCccccCCCCCCcccCCCCCCccccchhhh
Q 038397 662 ICEICNSEEERKKLLQCSCCGQLVHSGCLVPPITDVIPSDWSCHSCKEKT 711 (1102)
Q Consensus 662 ~ce~cgsed~k~kLL~cs~cgk~~H~~cL~PP~~di~~~dW~c~sCkek~ 711 (1102)
-|.+|++.++...||.|+.|++++|+.||.||++.-|.++|+|++|-+.+
T Consensus 283 ~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG~~~ 332 (336)
T KOG1244|consen 283 YCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCLEEL 332 (336)
T ss_pred eeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHHHHH
Confidence 47889988888899999999999999999999999999999999998544
No 19
>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]
Probab=97.48 E-value=0.00094 Score=78.64 Aligned_cols=181 Identities=23% Similarity=0.259 Sum_probs=108.7
Q ss_pred cccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhh-CC
Q 038397 217 LSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDV-GA 295 (1102)
Q Consensus 217 LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~di-G~ 295 (1102)
|=.-|.|.|++|..|+-+ .|++|-+|.||+-|.-+|.+.-...+ ++-|-....|+++...-+.-- +.
T Consensus 199 LlPFQreGv~faL~RgGR---------~llADeMGLGKTiQAlaIA~yyraEw---plliVcPAsvrftWa~al~r~lps 266 (689)
T KOG1000|consen 199 LLPFQREGVIFALERGGR---------ILLADEMGLGKTIQALAIARYYRAEW---PLLIVCPASVRFTWAKALNRFLPS 266 (689)
T ss_pred hCchhhhhHHHHHhcCCe---------EEEecccccchHHHHHHHHHHHhhcC---cEEEEecHHHhHHHHHHHHHhccc
Confidence 336799999999988632 58999999999998877766554433 334456667777655444322 22
Q ss_pred -CcccccccCCCCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCC
Q 038397 296 -TCIEVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQ 374 (1102)
Q Consensus 296 -~~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~ 374 (1102)
..|-|+--++-+.. .+....-|.-..|-.|..- .-+ +-...=+||||||||..|+.-
T Consensus 267 ~~pi~vv~~~~D~~~-----~~~t~~~v~ivSye~ls~l--------~~~---l~~~~~~vvI~DEsH~Lk~sk------ 324 (689)
T KOG1000|consen 267 IHPIFVVDKSSDPLP-----DVCTSNTVAIVSYEQLSLL--------HDI---LKKEKYRVVIFDESHMLKDSK------ 324 (689)
T ss_pred ccceEEEecccCCcc-----ccccCCeEEEEEHHHHHHH--------HHH---HhcccceEEEEechhhhhccc------
Confidence 11212111110000 0112233677788888642 111 112223799999999999874
Q ss_pred chhHHHHHHHHhhhCCCccEEEEecCCC-CCCCccchhhhccccCCCCCCCCHHHHHHHHhccC
Q 038397 375 PTRTGEAVLELQARLPEARVVYCSATGA-SEPRNMGYMVRLGLWGAGTCFKDFQIFLGALDKGG 437 (1102)
Q Consensus 375 ~s~~g~avl~LQ~~lP~ARvvY~SATga-sep~Nl~ym~RLGLWg~gt~f~~~~~f~~a~~~gG 437 (1102)
|+.-++++.|-+. --||+.-|.|.| |.|..|---.|+ -..|=|++|.+|--..=.+|
T Consensus 325 -tkr~Ka~~dllk~--akhvILLSGTPavSRP~elytqi~a---vd~tlfp~f~efa~rYCd~k 382 (689)
T KOG1000|consen 325 -TKRTKAATDLLKV--AKHVILLSGTPAVSRPSELYTQIRA---VDHTLFPNFHEFAIRYCDGK 382 (689)
T ss_pred -hhhhhhhhhHHHH--hhheEEecCCcccCCchhhhhhhhh---hcccccccHHHHHHHhcCcc
Confidence 3333444444343 247999999988 777666443333 23466899999987665554
No 20
>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]
Probab=97.45 E-value=0.0011 Score=81.69 Aligned_cols=246 Identities=22% Similarity=0.256 Sum_probs=148.4
Q ss_pred cCcccccccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccC-ceEEEEEcCCch
Q 038397 204 DLLIKYDLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGR-RKALWISVGSDL 282 (1102)
Q Consensus 204 ~~~lp~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr-~~~~w~s~s~~L 282 (1102)
...+|..+. -.|=.-|-|.|.|-=.-|.+ |+|=+|||-+|.||+-||-..+.--+-.|+ .++.-|=-..++
T Consensus 195 ~~~vPg~I~--~~Lf~yQreGV~WL~~L~~q------~~GGILgDeMGLGKTIQiisFLaaL~~S~k~~~paLIVCP~Ti 266 (923)
T KOG0387|consen 195 GFKVPGFIW--SKLFPYQREGVQWLWELYCQ------RAGGILGDEMGLGKTIQIISFLAALHHSGKLTKPALIVCPATI 266 (923)
T ss_pred cccccHHHH--HHhhHHHHHHHHHHHHHHhc------cCCCeecccccCccchhHHHHHHHHhhcccccCceEEEccHHH
Confidence 356676553 13447789998876555543 788899999999999999765544444432 112223334455
Q ss_pred hhhHHhhhhhhCCC-cccc-cccCC-CCC---------CcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhcc
Q 038397 283 KFDARRDLDDVGAT-CIEV-HALNK-LPY---------SKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGS 350 (1102)
Q Consensus 283 ~~Da~RDl~diG~~-~i~v-~~l~~-~~~---------~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~ 350 (1102)
..-..+.|.--+.. .+.+ |+-+. ..| +++--.......||+.+||+.++-....= .. +.|
T Consensus 267 i~qW~~E~~~w~p~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~~d~l-~~----~~W--- 338 (923)
T KOG0387|consen 267 IHQWMKEFQTWWPPFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQGDDL-LG----ILW--- 338 (923)
T ss_pred HHHHHHHHHHhCcceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhcccCccc-cc----ccc---
Confidence 55555555555443 2211 22211 011 11000112346679999999998543211 11 236
Q ss_pred CCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCC----CCCccchhhhccccCCCCCCCCH
Q 038397 351 GYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGAS----EPRNMGYMVRLGLWGAGTCFKDF 426 (1102)
Q Consensus 351 dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgas----ep~Nl~ym~RLGLWg~gt~f~~~ 426 (1102)
+++|+||-|+-+|-. |+..+++.+|+.. -||+. |.|..- |-=||--.++-|..|.-+-|.
T Consensus 339 ---~y~ILDEGH~IrNpn-------s~islackki~T~---~RiIL-SGTPiQNnL~ELwsLfDFv~PG~Lgt~~~F~-- 402 (923)
T KOG0387|consen 339 ---DYVILDEGHRIRNPN-------SKISLACKKIRTV---HRIIL-SGTPIQNNLTELWSLFDFVFPGKLGTLPVFQ-- 402 (923)
T ss_pred ---cEEEecCcccccCCc-------cHHHHHHHhcccc---ceEEe-eCccccchHHHHHHHhhhccCCcccchHHHH--
Confidence 599999999999985 8999999987765 46654 667653 333333355666666444453
Q ss_pred HHHHHHHhccChh-H-------------------HHHHHHHHHhccceeeeccCCCCceeEEEeccCcHHHHHHHHHHH
Q 038397 427 QIFLGALDKGGVG-A-------------------LELVAMDMKARGMYVCRTLSYKGAEFEVIEAPLEAEMTDMYKKAA 485 (1102)
Q Consensus 427 ~~f~~a~~~gGv~-a-------------------mE~va~dlK~~G~yiaR~LSf~gvef~i~e~~l~~~~~~~Yd~~a 485 (1102)
++|-.-|..||-+ | +=.+=+-||+.=.- |...+-+-.++-+.||+.|+++|.+.-
T Consensus 403 ~~f~~pI~~GgyaNAs~~qv~~aykca~~Lr~lI~PylLRR~K~dv~~----~~Lp~K~E~VlfC~LT~~QR~~Y~~fl 477 (923)
T KOG0387|consen 403 QNFEHPINRGGYANASPRQVQTAYKCAVALRDLISPYLLRRMKSDVKG----LKLPKKEEIVLFCRLTKLQRRLYQRFL 477 (923)
T ss_pred hhhhhheeccccCCCCHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhh----ccCCCccceEEEEeccHHHHHHHHHHh
Confidence 5566677777743 1 11233344443221 677788888888999999999998764
No 21
>PRK02362 ski2-like helicase; Provisional
Probab=97.44 E-value=0.00068 Score=85.28 Aligned_cols=158 Identities=19% Similarity=0.152 Sum_probs=99.8
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGA 295 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~ 295 (1102)
.|.+-|.+++.-.... ..-+++.=.||-||+-...-.|+..+.+|. |+|++.-.-.|-.+-.++|+.++.
T Consensus 23 ~l~p~Q~~ai~~~~~~---------g~nvlv~APTGSGKTlia~lail~~l~~~~-kal~i~P~raLa~q~~~~~~~~~~ 92 (737)
T PRK02362 23 ELYPPQAEAVEAGLLD---------GKNLLAAIPTASGKTLIAELAMLKAIARGG-KALYIVPLRALASEKFEEFERFEE 92 (737)
T ss_pred cCCHHHHHHHHHHHhC---------CCcEEEECCCcchHHHHHHHHHHHHHhcCC-cEEEEeChHHHHHHHHHHHHHhhc
Confidence 4778899996432222 234677788999998766556788888766 599999999999999999998753
Q ss_pred CcccccccCCCCCCcCCCCc-cccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCC
Q 038397 296 TCIEVHALNKLPYSKLDSRS-VGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQ 374 (1102)
Q Consensus 296 ~~i~v~~l~~~~~~~~~~~~-~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~ 374 (1102)
-.+.|.-+. |..+... .--...||.+|+-.+..-..++ ..|+.. =++||+||+|...+.. .|
T Consensus 93 ~g~~v~~~t----Gd~~~~~~~l~~~~IiV~Tpek~~~llr~~-------~~~l~~--v~lvViDE~H~l~d~~--rg-- 155 (737)
T PRK02362 93 LGVRVGIST----GDYDSRDEWLGDNDIIVATSEKVDSLLRNG-------APWLDD--ITCVVVDEVHLIDSAN--RG-- 155 (737)
T ss_pred CCCEEEEEe----CCcCccccccCCCCEEEECHHHHHHHHhcC-------hhhhhh--cCEEEEECccccCCCc--ch--
Confidence 233332221 1111111 1123469999987654332221 135432 2799999999876421 11
Q ss_pred chhHHHHHHHHhhhCCCccEEEEecCC
Q 038397 375 PTRTGEAVLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 375 ~s~~g~avl~LQ~~lP~ARvvY~SATg 401 (1102)
...-..+..|....|+.|||..|||-
T Consensus 156 -~~le~il~rl~~~~~~~qii~lSATl 181 (737)
T PRK02362 156 -PTLEVTLAKLRRLNPDLQVVALSATI 181 (737)
T ss_pred -HHHHHHHHHHHhcCCCCcEEEEcccC
Confidence 12223344555666899999999994
No 22
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=97.40 E-value=0.0026 Score=75.58 Aligned_cols=201 Identities=19% Similarity=0.214 Sum_probs=120.9
Q ss_pred EeecCCCCCcchhhHHHHHHHHhccCc-eEEEEEcCCchhhhHHhhhhh-hCCCcccccccCCCCCCcCCCCc---cccc
Q 038397 245 FIGDGAGVGKGRTIAGLIWENWHHGRR-KALWISVGSDLKFDARRDLDD-VGATCIEVHALNKLPYSKLDSRS---VGIR 319 (1102)
Q Consensus 245 ~~gDg~GvGKGR~~AgiI~~n~l~Gr~-~~~w~s~s~~L~~Da~RDl~d-iG~~~i~v~~l~~~~~~~~~~~~---~~~~ 319 (1102)
|+.==||.||+ .||.++..|+++-.. |+|++.-+.-|..-=.+=++. .|...-++..|. |+++.+. .-.+
T Consensus 33 LvvlPTGLGKT-~IA~~V~~~~l~~~~~kvlfLAPTKPLV~Qh~~~~~~v~~ip~~~i~~lt----Gev~p~~R~~~w~~ 107 (542)
T COG1111 33 LVVLPTGLGKT-FIAAMVIANRLRWFGGKVLFLAPTKPLVLQHAEFCRKVTGIPEDEIAALT----GEVRPEEREELWAK 107 (542)
T ss_pred EEEecCCccHH-HHHHHHHHHHHHhcCCeEEEecCCchHHHHHHHHHHHHhCCChhheeeec----CCCChHHHHHHHhh
Confidence 34444899997 577888888776443 599999988887654444433 355444445553 3333221 1134
Q ss_pred cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEec
Q 038397 320 EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSA 399 (1102)
Q Consensus 320 ~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SA 399 (1102)
.-|+|+|==++-..=..| |++- .|| -+|||||||+|-+-+ .=+..+...++ .--+-+|+=.+|
T Consensus 108 ~kVfvaTPQvveNDl~~G--rid~------~dv-~~lifDEAHRAvGny-----AYv~Va~~y~~---~~k~~~ilgLTA 170 (542)
T COG1111 108 KKVFVATPQVVENDLKAG--RIDL------DDV-SLLIFDEAHRAVGNY-----AYVFVAKEYLR---SAKNPLILGLTA 170 (542)
T ss_pred CCEEEeccHHHHhHHhcC--ccCh------HHc-eEEEechhhhccCcc-----hHHHHHHHHHH---hccCceEEEEec
Confidence 558888865553221222 2210 123 299999999986543 22334444331 222447888888
Q ss_pred CCCCCCCccchhhhccccCCCCCCCCHHHHHHHHhccChhHHHHHH---HHHHhccceeeeccCCCCceeEEEeccCcHH
Q 038397 400 TGASEPRNMGYMVRLGLWGAGTCFKDFQIFLGALDKGGVGALELVA---MDMKARGMYVCRTLSYKGAEFEVIEAPLEAE 476 (1102)
Q Consensus 400 Tgasep~Nl~ym~RLGLWg~gt~f~~~~~f~~a~~~gGv~amE~va---~dlK~~G~yiaR~LSf~gvef~i~e~~l~~~ 476 (1102)
|.+|+ .+.+.+-+++-||.-.|+-- +|. .-|+ ..++++.+.++|+++
T Consensus 171 SPGs~---------------------~ekI~eV~~nLgIe~vevrTE~d~DV---~~Yv------~~~kve~ikV~lp~e 220 (542)
T COG1111 171 SPGSD---------------------LEKIQEVVENLGIEKVEVRTEEDPDV---RPYV------KKIKVEWIKVDLPEE 220 (542)
T ss_pred CCCCC---------------------HHHHHHHHHhCCcceEEEecCCCccH---HHhh------ccceeEEEeccCcHH
Confidence 85554 56777777777877665311 111 1132 467899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 038397 477 MTDMYKKAAEFWAELRVELLS 497 (1102)
Q Consensus 477 ~~~~Yd~~a~~w~~~~~~~~~ 497 (1102)
+.++=|...++.....+.+.+
T Consensus 221 ~~~ir~~l~~~l~~~Lk~L~~ 241 (542)
T COG1111 221 IKEIRDLLRDALKPRLKPLKE 241 (542)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 999888887776665554443
No 23
>COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair]
Probab=97.28 E-value=0.0015 Score=77.65 Aligned_cols=126 Identities=22% Similarity=0.198 Sum_probs=83.0
Q ss_pred cCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhh
Q 038397 214 SKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 214 ~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
...|-+-|-|+ +-|..++ +.. .++|.++-= ||.||+-..+.+|.+-..+ ++++.-...|..-+..++..-
T Consensus 34 ~~~lr~yQ~~a-l~a~~~~---~~~-~~~gvivlp-TGaGKT~va~~~~~~~~~~----~Lvlv~~~~L~~Qw~~~~~~~ 103 (442)
T COG1061 34 EFELRPYQEEA-LDALVKN---RRT-ERRGVIVLP-TGAGKTVVAAEAIAELKRS----TLVLVPTKELLDQWAEALKKF 103 (442)
T ss_pred CCCCcHHHHHH-HHHHHhh---ccc-CCceEEEeC-CCCCHHHHHHHHHHHhcCC----EEEEECcHHHHHHHHHHHHHh
Confidence 34566889888 5555553 333 477877766 8999999998888765443 999999999999998777655
Q ss_pred CCCcccccccCCCCCCcCCCCccccc-cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccc
Q 038397 294 GATCIEVHALNKLPYSKLDSRSVGIR-EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKN 366 (1102)
Q Consensus 294 G~~~i~v~~l~~~~~~~~~~~~~~~~-~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn 366 (1102)
...... .|.+.+....+. .+|.|+||.++.... -+..-.+..| ++|||||||++..
T Consensus 104 ~~~~~~--------~g~~~~~~~~~~~~~i~vat~qtl~~~~--------~l~~~~~~~~-~liI~DE~Hh~~a 160 (442)
T COG1061 104 LLLNDE--------IGIYGGGEKELEPAKVTVATVQTLARRQ--------LLDEFLGNEF-GLIIFDEVHHLPA 160 (442)
T ss_pred cCCccc--------cceecCceeccCCCcEEEEEhHHHhhhh--------hhhhhccccc-CEEEEEccccCCc
Confidence 544311 122222223334 479999999997531 1112222233 5999999999773
No 24
>PRK00254 ski2-like helicase; Provisional
Probab=97.19 E-value=0.0018 Score=81.28 Aligned_cols=155 Identities=19% Similarity=0.144 Sum_probs=95.3
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGA 295 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~ 295 (1102)
.|..-|.+++.-.... ..-+++.=.||-||+-..--.|+.++++...++|++.-...|-.+..++|..++.
T Consensus 23 ~l~~~Q~~ai~~~~~~---------g~nvlv~apTGsGKT~~~~l~il~~l~~~~~~~l~l~P~~aLa~q~~~~~~~~~~ 93 (720)
T PRK00254 23 ELYPPQAEALKSGVLE---------GKNLVLAIPTASGKTLVAEIVMVNKLLREGGKAVYLVPLKALAEEKYREFKDWEK 93 (720)
T ss_pred CCCHHHHHHHHHHHhC---------CCcEEEECCCCcHHHHHHHHHHHHHHHhcCCeEEEEeChHHHHHHHHHHHHHHhh
Confidence 4778898886532222 2346788899999987665567888886666899999999999999999887543
Q ss_pred CcccccccCCCCCCcCCCCc-cccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCC
Q 038397 296 TCIEVHALNKLPYSKLDSRS-VGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQ 374 (1102)
Q Consensus 296 ~~i~v~~l~~~~~~~~~~~~-~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~ 374 (1102)
-.+.|.-+. |..+... .--...||++|+-.+..-...+ . .|+.. =++||+||+|......
T Consensus 94 ~g~~v~~~~----Gd~~~~~~~~~~~~IiV~Tpe~~~~ll~~~-~------~~l~~--l~lvViDE~H~l~~~~------ 154 (720)
T PRK00254 94 LGLRVAMTT----GDYDSTDEWLGKYDIIIATAEKFDSLLRHG-S------SWIKD--VKLVVADEIHLIGSYD------ 154 (720)
T ss_pred cCCEEEEEe----CCCCCchhhhccCCEEEEcHHHHHHHHhCC-c------hhhhc--CCEEEEcCcCccCCcc------
Confidence 233332221 1111111 1113469999976654322111 1 25432 2699999999975321
Q ss_pred chhHHHHHHHH-hhhCCCccEEEEecCC
Q 038397 375 PTRTGEAVLEL-QARLPEARVVYCSATG 401 (1102)
Q Consensus 375 ~s~~g~avl~L-Q~~lP~ARvvY~SATg 401 (1102)
.|.....+ .+..++.|+|..|||-
T Consensus 155 ---rg~~le~il~~l~~~~qiI~lSATl 179 (720)
T PRK00254 155 ---RGATLEMILTHMLGRAQILGLSATV 179 (720)
T ss_pred ---chHHHHHHHHhcCcCCcEEEEEccC
Confidence 12222222 2233568999999995
No 25
>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....
Probab=97.14 E-value=0.00046 Score=61.61 Aligned_cols=52 Identities=29% Similarity=0.466 Sum_probs=46.5
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSN 865 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSN 865 (1102)
+.|.+|+..|+|-|++++.||.++.-. +-|.+++|||...-+|..||+||-+
T Consensus 27 ~~f~~~~~~vli~t~~~~~Gid~~~~~--------~vi~~~~~~~~~~~~Q~~GR~~R~g 78 (78)
T PF00271_consen 27 KKFNSGEIRVLIATDILGEGIDLPDAS--------HVIFYDPPWSPEEYIQRIGRAGRIG 78 (78)
T ss_dssp HHHHTTSSSEEEESCGGTTSSTSTTES--------EEEESSSESSHHHHHHHHTTSSTTT
T ss_pred HHhhccCceEEEeeccccccccccccc--------cccccccCCCHHHHHHHhhcCCCCC
Confidence 699999999999999999999997543 3477889999999999999999964
No 26
>PRK01172 ski2-like helicase; Provisional
Probab=97.06 E-value=0.0024 Score=79.59 Aligned_cols=155 Identities=22% Similarity=0.204 Sum_probs=92.4
Q ss_pred cccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCC
Q 038397 217 LSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGAT 296 (1102)
Q Consensus 217 LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~ 296 (1102)
|..-|.+++. +...+ .-+++.-.||-||+-..--.|++.+.+|. ++|++.-...|-.+-.++|+.+...
T Consensus 23 l~~~Q~~ai~-~l~~~---------~nvlv~apTGSGKTl~a~lail~~l~~~~-k~v~i~P~raLa~q~~~~~~~l~~~ 91 (674)
T PRK01172 23 LYDHQRMAIE-QLRKG---------ENVIVSVPTAAGKTLIAYSAIYETFLAGL-KSIYIVPLRSLAMEKYEELSRLRSL 91 (674)
T ss_pred CCHHHHHHHH-HHhcC---------CcEEEECCCCchHHHHHHHHHHHHHHhCC-cEEEEechHHHHHHHHHHHHHHhhc
Confidence 5678888854 33222 34677888999999876666888888875 5999999889988888888765432
Q ss_pred cccccccCCCCCCcCCCCc-cccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCc
Q 038397 297 CIEVHALNKLPYSKLDSRS-VGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQP 375 (1102)
Q Consensus 297 ~i~v~~l~~~~~~~~~~~~-~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~ 375 (1102)
.+.|.-+ .|..+... .--...|+++|+-.+..-...... |+.. + ++||+||+|...+.. .|
T Consensus 92 g~~v~~~----~G~~~~~~~~~~~~dIiv~Tpek~~~l~~~~~~-------~l~~-v-~lvViDEaH~l~d~~--rg--- 153 (674)
T PRK01172 92 GMRVKIS----IGDYDDPPDFIKRYDVVILTSEKADSLIHHDPY-------IIND-V-GLIVADEIHIIGDED--RG--- 153 (674)
T ss_pred CCeEEEE----eCCCCCChhhhccCCEEEECHHHHHHHHhCChh-------HHhh-c-CEEEEecchhccCCC--cc---
Confidence 2222211 11111111 011346999998654432211111 2211 2 699999999875421 11
Q ss_pred hhHHHHHH-HHhhhCCCccEEEEecCC
Q 038397 376 TRTGEAVL-ELQARLPEARVVYCSATG 401 (1102)
Q Consensus 376 s~~g~avl-~LQ~~lP~ARvvY~SATg 401 (1102)
.+-..++ .+...-++.|||..|||-
T Consensus 154 -~~le~ll~~~~~~~~~~riI~lSATl 179 (674)
T PRK01172 154 -PTLETVLSSARYVNPDARILALSATV 179 (674)
T ss_pred -HHHHHHHHHHHhcCcCCcEEEEeCcc
Confidence 1112222 233344688999999993
No 27
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=97.02 E-value=0.00059 Score=83.03 Aligned_cols=53 Identities=28% Similarity=0.738 Sum_probs=48.3
Q ss_pred cccccccccCcHHHHhhhhhccccCCc-cccCCCCCCcccCCCCCCccccchhh
Q 038397 658 DEFQICEICNSEEERKKLLQCSCCGQL-VHSGCLVPPITDVIPSDWSCHSCKEK 710 (1102)
Q Consensus 658 DEf~~ce~cgsed~k~kLL~cs~cgk~-~H~~cL~PP~~di~~~dW~c~sCkek 710 (1102)
.|-..|++|..-+..+-||+|+.|.++ +|++||.|++..++.+.|.|+.|.+.
T Consensus 213 ~E~~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 213 QEEVKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSLL 266 (1134)
T ss_pred cccccceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchhh
Confidence 345789999999988999999999998 99999999999999999999999853
No 28
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=96.97 E-value=0.0023 Score=76.40 Aligned_cols=159 Identities=16% Similarity=0.154 Sum_probs=94.1
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhcc---------CceEEEEEcCCchhhhH
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHG---------RRKALWISVGSDLKFDA 286 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~G---------r~~~~w~s~s~~L~~Da 286 (1102)
.++.-|.+++-+..+.+ -.++.-.||-||+-.-.--|++..++. ..+++++.-...|-.|.
T Consensus 109 ~~~~iQ~~ai~~~~~G~----------dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~~~aLil~PtreLa~Q~ 178 (475)
T PRK01297 109 YCTPIQAQVLGYTLAGH----------DAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIAPTRELVVQI 178 (475)
T ss_pred CCCHHHHHHHHHHhCCC----------CEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCCceEEEEeCcHHHHHHH
Confidence 57788988876554432 234555799999844333356665543 46799999999999999
Q ss_pred HhhhhhhCCC-cccccccCCCCCCcCCCCcccc---ccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecch
Q 038397 287 RRDLDDVGAT-CIEVHALNKLPYSKLDSRSVGI---REGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECH 362 (1102)
Q Consensus 287 ~RDl~diG~~-~i~v~~l~~~~~~~~~~~~~~~---~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH 362 (1102)
.+.++.+... .+.+..+..- ...+.....+ .-.||++|.-.|.....++.. |+. .+ .+||+||||
T Consensus 179 ~~~~~~l~~~~~~~v~~~~gg--~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~~~~-------~l~-~l-~~lViDEah 247 (475)
T PRK01297 179 AKDAAALTKYTGLNVMTFVGG--MDFDKQLKQLEARFCDILVATPGRLLDFNQRGEV-------HLD-MV-EVMVLDEAD 247 (475)
T ss_pred HHHHHHhhccCCCEEEEEEcc--CChHHHHHHHhCCCCCEEEECHHHHHHHHHcCCc-------ccc-cC-ceEEechHH
Confidence 9999988642 3443332110 0000000011 235999998887532111111 111 11 489999999
Q ss_pred hccccCCCCCCCchhHHHHHHHHhhhCCC---ccEEEEecCCCCC
Q 038397 363 KAKNLVPEAGSQPTRTGEAVLELQARLPE---ARVVYCSATGASE 404 (1102)
Q Consensus 363 ~akn~~~~~~~~~s~~g~avl~LQ~~lP~---ARvvY~SATgase 404 (1102)
...+.. ....+..+-+.+|. .+++.+|||-..+
T Consensus 248 ~l~~~~---------~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~ 283 (475)
T PRK01297 248 RMLDMG---------FIPQVRQIIRQTPRKEERQTLLFSATFTDD 283 (475)
T ss_pred HHHhcc---------cHHHHHHHHHhCCCCCCceEEEEEeecCHH
Confidence 976431 22234455566653 4799999995443
No 29
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=96.93 E-value=0.0019 Score=76.77 Aligned_cols=157 Identities=16% Similarity=0.195 Sum_probs=93.6
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccC--ceEEEEEcCCchhhhHHhhhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGR--RKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr--~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
.++.-|.+++-...+.. -.++.-.||.||+-...-.|++....++ .+++++.-+-.|-......++.+
T Consensus 26 ~~t~iQ~~ai~~~l~g~----------dvi~~a~TGsGKT~a~~lpil~~l~~~~~~~~~lil~PtreLa~Q~~~~~~~~ 95 (460)
T PRK11776 26 EMTPIQAQSLPAILAGK----------DVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQVAKEIRRL 95 (460)
T ss_pred CCCHHHHHHHHHHhcCC----------CEEEECCCCCcHHHHHHHHHHHHhhhccCCceEEEEeCCHHHHHHHHHHHHHH
Confidence 36788999977665422 2556667999999544444666554443 36899999999999888888887
Q ss_pred CCC--cccccccCC-CCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCC
Q 038397 294 GAT--CIEVHALNK-LPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPE 370 (1102)
Q Consensus 294 G~~--~i~v~~l~~-~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~ 370 (1102)
+.. .+.|..+.. .+.+. .-....-.-.||.+|...|...-.++.-.|+. + ++|||||||++.+..
T Consensus 96 ~~~~~~~~v~~~~Gg~~~~~-~~~~l~~~~~IvV~Tp~rl~~~l~~~~~~l~~--------l-~~lViDEad~~l~~g-- 163 (460)
T PRK11776 96 ARFIPNIKVLTLCGGVPMGP-QIDSLEHGAHIIVGTPGRILDHLRKGTLDLDA--------L-NTLVLDEADRMLDMG-- 163 (460)
T ss_pred HhhCCCcEEEEEECCCChHH-HHHHhcCCCCEEEEChHHHHHHHHcCCccHHH--------C-CEEEEECHHHHhCcC--
Confidence 642 344433321 11100 00001112359999998776432222212221 1 489999999987542
Q ss_pred CCCCchhHHHHHHHHhhhCC-CccEEEEecCC
Q 038397 371 AGSQPTRTGEAVLELQARLP-EARVVYCSATG 401 (1102)
Q Consensus 371 ~~~~~s~~g~avl~LQ~~lP-~ARvvY~SATg 401 (1102)
-...+.++-..+| +.+++..|||-
T Consensus 164 -------~~~~l~~i~~~~~~~~q~ll~SAT~ 188 (460)
T PRK11776 164 -------FQDAIDAIIRQAPARRQTLLFSATY 188 (460)
T ss_pred -------cHHHHHHHHHhCCcccEEEEEEecC
Confidence 1233444445555 45689999994
No 30
>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
Probab=96.93 E-value=0.0009 Score=63.97 Aligned_cols=59 Identities=27% Similarity=0.507 Sum_probs=50.2
Q ss_pred HhhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeE
Q 038397 805 KQLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEY 872 (1102)
Q Consensus 805 k~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y 872 (1102)
.+.|.+|...|+|-+.+++.|+.+.. -..-|.+.+||+...-+|+.||+||.+| ....|
T Consensus 71 ~~~f~~~~~~ili~t~~~~~G~d~~~--------~~~vi~~~~~~~~~~~~Q~~GR~~R~~~-~~~~~ 129 (131)
T cd00079 71 LKDFREGEIVVLVATDVIARGIDLPN--------VSVVINYDLPWSPSSYLQRIGRAGRAGQ-KGTAI 129 (131)
T ss_pred HHHHHcCCCcEEEEcChhhcCcChhh--------CCEEEEeCCCCCHHHheecccccccCCC-CceEE
Confidence 36899999999999999999999862 3455788899999999999999999999 44433
No 31
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=96.92 E-value=0.0038 Score=81.78 Aligned_cols=175 Identities=19% Similarity=0.184 Sum_probs=100.6
Q ss_pred cccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccC-ceEEEEEcCCchhhhHHhhhhhhCC
Q 038397 217 LSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGR-RKALWISVGSDLKFDARRDLDDVGA 295 (1102)
Q Consensus 217 LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr-~~~~w~s~s~~L~~Da~RDl~diG~ 295 (1102)
|=+-|.+||.-...+- ..|.| +.++-=-||.||+++++++|+.-+..++ +|++|+.-..+|..=+...++..+.
T Consensus 414 lR~YQ~~AI~ai~~a~----~~g~r-~~Ll~maTGSGKT~tai~li~~L~~~~~~~rVLfLvDR~~L~~Qa~~~F~~~~~ 488 (1123)
T PRK11448 414 LRYYQEDAIQAVEKAI----VEGQR-EILLAMATGTGKTRTAIALMYRLLKAKRFRRILFLVDRSALGEQAEDAFKDTKI 488 (1123)
T ss_pred CCHHHHHHHHHHHHHH----HhccC-CeEEEeCCCCCHHHHHHHHHHHHHhcCccCeEEEEecHHHHHHHHHHHHHhccc
Confidence 5578999975544432 23444 4555577999999999998877665543 6899999999999999999998875
Q ss_pred Ccc-cccccCCCCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCC--CC
Q 038397 296 TCI-EVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPE--AG 372 (1102)
Q Consensus 296 ~~i-~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~--~~ 372 (1102)
... .+..+.... .+.........+|+|+||-+|.+.-..... ..-.-++ ..|| +||+||||+...+... .+
T Consensus 489 ~~~~~~~~i~~i~--~L~~~~~~~~~~I~iaTiQtl~~~~~~~~~--~~~~~~~-~~fd-lIIiDEaHRs~~~d~~~~~~ 562 (1123)
T PRK11448 489 EGDQTFASIYDIK--GLEDKFPEDETKVHVATVQGMVKRILYSDD--PMDKPPV-DQYD-CIIVDEAHRGYTLDKEMSEG 562 (1123)
T ss_pred ccccchhhhhchh--hhhhhcccCCCCEEEEEHHHHHHhhhcccc--ccccCCC-Cccc-EEEEECCCCCCccccccccc
Confidence 432 111111110 011111233568999999998753110000 0000133 2466 8999999997433210 00
Q ss_pred C-CchhHHHHHHHHhhh--CCCccEEEEecCCC
Q 038397 373 S-QPTRTGEAVLELQAR--LPEARVVYCSATGA 402 (1102)
Q Consensus 373 ~-~~s~~g~avl~LQ~~--lP~ARvvY~SATga 402 (1102)
. .--.+.......++. .++|.+|=.+||..
T Consensus 563 ~~~~~~~~~~~~~yr~iL~yFdA~~IGLTATP~ 595 (1123)
T PRK11448 563 ELQFRDQLDYVSKYRRVLDYFDAVKIGLTATPA 595 (1123)
T ss_pred hhccchhhhHHHHHHHHHhhcCccEEEEecCCc
Confidence 0 000111112222232 34788888899986
No 32
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=96.84 E-value=0.0022 Score=78.38 Aligned_cols=31 Identities=26% Similarity=0.441 Sum_probs=16.4
Q ss_pred CChHHHHHHhhCCCceeeeecCCcceEEEcCCCC
Q 038397 750 NNPLDDIVDQLGGPDKVAEMTGRRGMLVRASSGK 783 (1102)
Q Consensus 750 ~n~LD~LId~LGGp~~VAEmTGRkgRvVr~~dG~ 783 (1102)
...+|.|++.|-. =|----|+.|+-|..+|+
T Consensus 1040 ~GVmDslLeaLqs---gaafr~rrk~~prq~~~r 1070 (1102)
T KOG1924|consen 1040 TGVMDSLLEALQS---GAAFRTRRKRLPRQTRGR 1070 (1102)
T ss_pred hhhHHHHHHHHHh---hccccCcccccCCCCccc
Confidence 4678888887731 111122455555555554
No 33
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=96.83 E-value=0.0043 Score=77.00 Aligned_cols=153 Identities=22% Similarity=0.166 Sum_probs=92.5
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGA 295 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~ 295 (1102)
.|+..|.++|.-..+.-....| ....+.|| ||.||+-..+-.|+..+.+|.+ ++++.-...|-....+.++.+..
T Consensus 235 ~lt~~Q~~ai~~I~~~~~~~~~---~~~Ll~g~-TGSGKT~va~l~il~~~~~g~q-vlilaPT~~LA~Q~~~~~~~l~~ 309 (630)
T TIGR00643 235 KLTRAQKRVVKEILQDLKSDVP---MNRLLQGD-VGSGKTLVAALAMLAAIEAGYQ-VALMAPTEILAEQHYNSLRNLLA 309 (630)
T ss_pred CCCHHHHHHHHHHHHHhccCCC---ccEEEECC-CCCcHHHHHHHHHHHHHHcCCc-EEEECCHHHHHHHHHHHHHHHhc
Confidence 3678999997654433211111 12345565 9999998776678888888875 99999999999999988888754
Q ss_pred C-cccccccCC-CCCCcCCCCcc-ccc---cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCC
Q 038397 296 T-CIEVHALNK-LPYSKLDSRSV-GIR---EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVP 369 (1102)
Q Consensus 296 ~-~i~v~~l~~-~~~~~~~~~~~-~~~---~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~ 369 (1102)
. .+.+.-+.. .+...- .... .+. -.||++|.+.|... -.++ + =++||+||+|+..
T Consensus 310 ~~gi~v~lltg~~~~~~r-~~~~~~i~~g~~~IiVgT~~ll~~~-----~~~~--------~-l~lvVIDEaH~fg---- 370 (630)
T TIGR00643 310 PLGIEVALLTGSLKGKRR-KELLETIASGQIHLVVGTHALIQEK-----VEFK--------R-LALVIIDEQHRFG---- 370 (630)
T ss_pred ccCcEEEEEecCCCHHHH-HHHHHHHhCCCCCEEEecHHHHhcc-----cccc--------c-cceEEEechhhcc----
Confidence 3 344433321 110000 0000 122 35999998877421 1111 1 2699999999853
Q ss_pred CCCCCchhHHHHHHHHhhhCC---CccEEEEecCC
Q 038397 370 EAGSQPTRTGEAVLELQARLP---EARVVYCSATG 401 (1102)
Q Consensus 370 ~~~~~~s~~g~avl~LQ~~lP---~ARvvY~SATg 401 (1102)
.++-.. |....+ +.+++.+|||.
T Consensus 371 ------~~qr~~---l~~~~~~~~~~~~l~~SATp 396 (630)
T TIGR00643 371 ------VEQRKK---LREKGQGGFTPHVLVMSATP 396 (630)
T ss_pred ------HHHHHH---HHHhcccCCCCCEEEEeCCC
Confidence 122222 223343 67899999994
No 34
>TIGR01587 cas3_core CRISPR-associated helicase Cas3. This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Probab=96.82 E-value=0.0042 Score=70.94 Aligned_cols=142 Identities=15% Similarity=0.125 Sum_probs=82.9
Q ss_pred EeecCCCCCcchhhHHHHHHHHhcc-CceEEEEEcCCchhhhHHhhhhhh-CCCcccccccCCC---C-CCc---CC---
Q 038397 245 FIGDGAGVGKGRTIAGLIWENWHHG-RRKALWISVGSDLKFDARRDLDDV-GATCIEVHALNKL---P-YSK---LD--- 312 (1102)
Q Consensus 245 ~~gDg~GvGKGR~~AgiI~~n~l~G-r~~~~w~s~s~~L~~Da~RDl~di-G~~~i~v~~l~~~---~-~~~---~~--- 312 (1102)
++.-.||-||+-...-.|++...++ ..|++++.-.-.|..|..+.|.++ |......|.-..+ . .+. ..
T Consensus 3 vi~apTGsGKT~~~~~~~l~~~~~~~~~~ii~v~P~~~L~~q~~~~l~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (358)
T TIGR01587 3 VIEAPTGYGKTEAALLWALHSIKSQKADRVIIALPTRATINAMYRRAKELFGSNLGLLHSSSSFKRIKEMGDSEEFEHLF 82 (358)
T ss_pred EEEeCCCCCHHHHHHHHHHHHHhhCCCCeEEEEeehHHHHHHHHHHHHHHhCcccEEeeccHHHHHHhccCCchhHHHHH
Confidence 4555699999988877888887544 367898888889999999999998 6422111111100 0 000 00
Q ss_pred -----CCccccccceEEeehhhhhhcccc-ccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHh
Q 038397 313 -----SRSVGIREGVVFLTYSSLIASSEK-GRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQ 386 (1102)
Q Consensus 313 -----~~~~~~~~GvlF~TYs~L~~~~~~-~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ 386 (1102)
+...-....|+++|.-++...-.. ...+.-.+... -..+|||||+|.+... ..+. ...+.
T Consensus 83 ~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~----~~~~iViDE~h~~~~~---------~~~~-l~~~l 148 (358)
T TIGR01587 83 PLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASI----ANSLLIFDEVHFYDEY---------TLAL-ILAVL 148 (358)
T ss_pred HHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHh----cCCEEEEeCCCCCCHH---------HHHH-HHHHH
Confidence 000113456999999887643211 11111111111 1268999999997632 1111 33333
Q ss_pred hhC--CCccEEEEecC
Q 038397 387 ARL--PEARVVYCSAT 400 (1102)
Q Consensus 387 ~~l--P~ARvvY~SAT 400 (1102)
..+ .+.+++.+|||
T Consensus 149 ~~l~~~~~~~i~~SAT 164 (358)
T TIGR01587 149 EVLKDNDVPILLMSAT 164 (358)
T ss_pred HHHHHcCCCEEEEecC
Confidence 333 37899999999
No 35
>PTZ00424 helicase 45; Provisional
Probab=96.76 E-value=0.0029 Score=73.17 Aligned_cols=153 Identities=17% Similarity=0.127 Sum_probs=88.1
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhc--cCceEEEEEcCCchhhhHHhhhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHH--GRRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~--Gr~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
.++..|.+++....... -.++--.||-||+-...-.|++.... ...+++.+.-...|.....+-+..+
T Consensus 50 ~~~~~Q~~ai~~i~~~~----------d~ii~apTGsGKT~~~~l~~l~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~ 119 (401)
T PTZ00424 50 KPSAIQQRGIKPILDGY----------DTIGQAQSGTGKTATFVIAALQLIDYDLNACQALILAPTRELAQQIQKVVLAL 119 (401)
T ss_pred CCCHHHHHHHHHHhCCC----------CEEEECCCCChHHHHHHHHHHHHhcCCCCCceEEEECCCHHHHHHHHHHHHHH
Confidence 46788988865544322 23455669999997555455555542 3356999999999998888888877
Q ss_pred CCC-cccccccCCCCCCcCC-CCcc-ccc--cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccC
Q 038397 294 GAT-CIEVHALNKLPYSKLD-SRSV-GIR--EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLV 368 (1102)
Q Consensus 294 G~~-~i~v~~l~~~~~~~~~-~~~~-~~~--~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~ 368 (1102)
+.. .+.+..+ .|... ...+ .+. ..|+++|.-.|...-.++.-.+ +.=++||+||||.+....
T Consensus 120 ~~~~~~~~~~~----~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~l---------~~i~lvViDEah~~~~~~ 186 (401)
T PTZ00424 120 GDYLKVRCHAC----VGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDKRHLRV---------DDLKLFILDEADEMLSRG 186 (401)
T ss_pred hhhcCceEEEE----ECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHhCCccc---------ccccEEEEecHHHHHhcc
Confidence 642 1111111 11000 0000 112 2599999877653311111111 112589999999976421
Q ss_pred CCCCCCchhHHHHHHH-HhhhCCCccEEEEecC
Q 038397 369 PEAGSQPTRTGEAVLE-LQARLPEARVVYCSAT 400 (1102)
Q Consensus 369 ~~~~~~~s~~g~avl~-LQ~~lP~ARvvY~SAT 400 (1102)
-.+ .+.+ +...-++.++|..|||
T Consensus 187 --------~~~-~~~~i~~~~~~~~~~i~~SAT 210 (401)
T PTZ00424 187 --------FKG-QIYDVFKKLPPDVQVALFSAT 210 (401)
T ss_pred --------hHH-HHHHHHhhCCCCcEEEEEEec
Confidence 111 2223 3344467899999999
No 36
>smart00490 HELICc helicase superfamily c-terminal domain.
Probab=96.60 E-value=0.0028 Score=55.58 Aligned_cols=53 Identities=30% Similarity=0.544 Sum_probs=45.9
Q ss_pred HhhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCC
Q 038397 805 KQLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSN 865 (1102)
Q Consensus 805 k~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSN 865 (1102)
.+.|.+|+..|.|-+.++++|+.++.- +.-|.+.+||+....+|..||+||.+
T Consensus 30 ~~~f~~~~~~vli~t~~~~~Gi~~~~~--------~~vi~~~~~~~~~~~~Q~~gR~~R~g 82 (82)
T smart00490 30 LEKFNNGKIKVLVATDVAERGLDLPGV--------DLVIIYDLPWSPASYIQRIGRAGRAG 82 (82)
T ss_pred HHHHHcCCCeEEEECChhhCCcChhcC--------CEEEEeCCCCCHHHHHHhhcccccCC
Confidence 367999999999999999999998742 24567888999999999999999974
No 37
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.58 E-value=0.0014 Score=54.27 Aligned_cols=32 Identities=19% Similarity=0.390 Sum_probs=28.9
Q ss_pred ceeecCCcceEEEeCCCcceecCCCCCCCCCC
Q 038397 16 VQVRCAGCHIILTVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l 47 (1102)
+..+|.+||+.+.+.+..+.+.||+||.+..+
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 46789999999999999999999999987665
No 38
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=96.53 E-value=0.0044 Score=73.75 Aligned_cols=76 Identities=18% Similarity=0.329 Sum_probs=58.5
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRF 885 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRF 885 (1102)
+.|.+|+..|+|-+++++-||-+..-. +=|-.++|++...-||+.|||+|.++. .--+.+++. .|.++
T Consensus 289 ~~F~~g~~~iLVaTdv~~rGiDip~v~--------~VI~~~~P~~~~~yvqR~GRaGR~g~~-G~ai~l~~~---~d~~~ 356 (456)
T PRK10590 289 ADFKSGDIRVLVATDIAARGLDIEELP--------HVVNYELPNVPEDYVHRIGRTGRAAAT-GEALSLVCV---DEHKL 356 (456)
T ss_pred HHHHcCCCcEEEEccHHhcCCCcccCC--------EEEEeCCCCCHHHhhhhccccccCCCC-eeEEEEecH---HHHHH
Confidence 579999999999999999999876443 335679999999999999999998863 334444443 47776
Q ss_pred HHHHHHHH
Q 038397 886 ASIVAKRL 893 (1102)
Q Consensus 886 aS~VAkRL 893 (1102)
...+.+.|
T Consensus 357 ~~~ie~~l 364 (456)
T PRK10590 357 LRDIEKLL 364 (456)
T ss_pred HHHHHHHh
Confidence 66666554
No 39
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=96.44 E-value=0.006 Score=74.92 Aligned_cols=155 Identities=18% Similarity=0.155 Sum_probs=94.3
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhcc---------CceEEEEEcCCchhhhH
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHG---------RRKALWISVGSDLKFDA 286 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~G---------r~~~~w~s~s~~L~~Da 286 (1102)
.++.-|-++|-.+.+. .-.++-=-||.||+-...-.|++.++.- ..++|++.-+-.|-...
T Consensus 31 ~ptpiQ~~~ip~~l~G----------~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~raLIl~PTreLa~Qi 100 (572)
T PRK04537 31 RCTPIQALTLPVALPG----------GDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAPTRELAIQI 100 (572)
T ss_pred CCCHHHHHHHHHHhCC----------CCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceEEEEeCcHHHHHHH
Confidence 4667888887655432 2355666699999876655567766531 24799999999999999
Q ss_pred HhhhhhhCCC-cccccccCC-CCCCcCCCCccccc--cceEEeehhhhhhccc-cccchHHHHHHHhccCCCceEEeecc
Q 038397 287 RRDLDDVGAT-CIEVHALNK-LPYSKLDSRSVGIR--EGVVFLTYSSLIASSE-KGRSRLQQLVQWCGSGYDGLVIFDEC 361 (1102)
Q Consensus 287 ~RDl~diG~~-~i~v~~l~~-~~~~~~~~~~~~~~--~GvlF~TYs~L~~~~~-~~~sRl~Ql~~W~g~dfdgvivfDEc 361 (1102)
..++..++.. .+.+..+.. ..+. .....+. -.||++|--.|...-. .+.-.| .--.+||||||
T Consensus 101 ~~~~~~l~~~~~i~v~~l~Gg~~~~---~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l---------~~v~~lViDEA 168 (572)
T PRK04537 101 HKDAVKFGADLGLRFALVYGGVDYD---KQRELLQQGVDVIIATPGRLIDYVKQHKVVSL---------HACEICVLDEA 168 (572)
T ss_pred HHHHHHHhccCCceEEEEECCCCHH---HHHHHHhCCCCEEEECHHHHHHHHHhccccch---------hheeeeEecCH
Confidence 9999888754 343332211 1110 0000122 2499999877653211 110111 11247999999
Q ss_pred hhccccCCCCCCCchhHHHHHHHHhhhCC---CccEEEEecCC
Q 038397 362 HKAKNLVPEAGSQPTRTGEAVLELQARLP---EARVVYCSATG 401 (1102)
Q Consensus 362 H~akn~~~~~~~~~s~~g~avl~LQ~~lP---~ARvvY~SATg 401 (1102)
|.+.... ....+..|...+| +.+++..|||-
T Consensus 169 h~lld~g---------f~~~i~~il~~lp~~~~~q~ll~SATl 202 (572)
T PRK04537 169 DRMFDLG---------FIKDIRFLLRRMPERGTRQTLLFSATL 202 (572)
T ss_pred HHHhhcc---------hHHHHHHHHHhcccccCceEEEEeCCc
Confidence 9986431 2334455667777 46799999994
No 40
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.36 E-value=0.0062 Score=73.80 Aligned_cols=132 Identities=23% Similarity=0.169 Sum_probs=83.2
Q ss_pred eecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCcc-cc---ccc
Q 038397 246 IGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSV-GI---REG 321 (1102)
Q Consensus 246 ~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~-~~---~~G 321 (1102)
.|+ ||-||+-..--+|.+...+|++ ++.+.-.-.|-.+..+.++..-...+.+.. ++...++- .+.+ .+ +..
T Consensus 3 ~g~-TGsGKT~v~l~~i~~~l~~g~~-vLvlvP~i~L~~Q~~~~l~~~f~~~v~vlh-s~~~~~er-~~~~~~~~~g~~~ 78 (505)
T TIGR00595 3 FGV-TGSGKTEVYLQAIEKVLALGKS-VLVLVPEIALTPQMIQRFKYRFGSQVAVLH-SGLSDSEK-LQAWRKVKNGEIL 78 (505)
T ss_pred cCC-CCCCHHHHHHHHHHHHHHcCCe-EEEEeCcHHHHHHHHHHHHHHhCCcEEEEE-CCCCHHHH-HHHHHHHHcCCCC
Confidence 354 8999998776666666666764 999998989999999999864333332211 11110000 0000 11 234
Q ss_pred eEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecC
Q 038397 322 VVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSAT 400 (1102)
Q Consensus 322 vlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SAT 400 (1102)
||+.|.++|.. .+ .++ |+||+||.|...--- ...|.-.++-+..+..++.++.||+.|||
T Consensus 79 IVVGTrsalf~-------p~--------~~l-~lIIVDEeh~~sykq---~~~p~y~ar~~a~~ra~~~~~~vil~SAT 138 (505)
T TIGR00595 79 VVIGTRSALFL-------PF--------KNL-GLIIVDEEHDSSYKQ---EEGPRYHARDVAVYRAKKFNCPVVLGSAT 138 (505)
T ss_pred EEECChHHHcC-------cc--------cCC-CEEEEECCCcccccc---ccCCCCcHHHHHHHHHHhcCCCEEEEeCC
Confidence 99999998742 11 123 899999999755221 11244455666677788899999999999
No 41
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=96.36 E-value=0.0093 Score=70.25 Aligned_cols=74 Identities=18% Similarity=0.421 Sum_probs=55.5
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRF 885 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRF 885 (1102)
+.|.+|+..|+|-++.++.||.+..-.-| |-+.+|+|++.-||+.|||+|.+.... -+.++ + ..|.++
T Consensus 289 ~~f~~G~~~vLVaTd~~~~GiDip~v~~V--------I~~d~p~s~~~yiqr~GR~gR~g~~g~-ai~l~-~--~~d~~~ 356 (434)
T PRK11192 289 KRLTDGRVNVLVATDVAARGIDIDDVSHV--------INFDMPRSADTYLHRIGRTGRAGRKGT-AISLV-E--AHDHLL 356 (434)
T ss_pred HHHhCCCCcEEEEccccccCccCCCCCEE--------EEECCCCCHHHHhhcccccccCCCCce-EEEEe-c--HHHHHH
Confidence 58999999999999999999998644333 457899999999999999999876421 22222 2 356666
Q ss_pred HHHHHH
Q 038397 886 ASIVAK 891 (1102)
Q Consensus 886 aS~VAk 891 (1102)
...+.+
T Consensus 357 ~~~i~~ 362 (434)
T PRK11192 357 LGKIER 362 (434)
T ss_pred HHHHHH
Confidence 655554
No 42
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=96.34 E-value=0.4 Score=59.98 Aligned_cols=233 Identities=19% Similarity=0.207 Sum_probs=127.9
Q ss_pred ccccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCce-----EEEEEcC--Cc
Q 038397 209 YDLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRK-----ALWISVG--SD 281 (1102)
Q Consensus 209 ~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~-----~~w~s~s--~~ 281 (1102)
.+.+..|.|-+-|+|.|.|-.+.|+- .-+-+++|.+|.||+-|--++ =.|++|++. .|-...| .+
T Consensus 160 P~~v~~g~lr~YQveGlnWLi~l~en------gingILaDEMGLGKTlQtIs~--l~yl~~~~~~~GPfLVi~P~StL~N 231 (971)
T KOG0385|consen 160 PSYVKGGELRDYQLEGLNWLISLYEN------GINGILADEMGLGKTLQTISL--LGYLKGRKGIPGPFLVIAPKSTLDN 231 (971)
T ss_pred chhhcCCccchhhhccHHHHHHHHhc------CcccEeehhcccchHHHHHHH--HHHHHHhcCCCCCeEEEeeHhhHHH
Confidence 35567899999999999999999863 334579999999999886443 344544431 1111111 11
Q ss_pred hhhhHHhhhhhhCCCcccccccCCCCCCcCC------CCc-cccccceEEeehhhhhhccccccchHHHHHHHhccCCCc
Q 038397 282 LKFDARRDLDDVGATCIEVHALNKLPYSKLD------SRS-VGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDG 354 (1102)
Q Consensus 282 L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~------~~~-~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdg 354 (1102)
......|=. ..+.+.-+ +|.-. .+. ..-.-+|+.|||=-.+.. ++=|++ +.| -
T Consensus 232 W~~Ef~rf~-----P~l~~~~~----~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d----k~~lk~-~~W------~ 291 (971)
T KOG0385|consen 232 WMNEFKRFT-----PSLNVVVY----HGDKEERAALRRDIMLPGRFDVCITSYEIAIKD----KSFLKK-FNW------R 291 (971)
T ss_pred HHHHHHHhC-----CCcceEEE----eCCHHHHHHHHHHhhccCCCceEeehHHHHHhh----HHHHhc-CCc------e
Confidence 111111100 11111000 11000 000 012567999999887754 333433 356 4
Q ss_pred eEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCCCCCccch-hhhccccCCCCCCCCHHHHHHHH
Q 038397 355 LVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGASEPRNMGY-MVRLGLWGAGTCFKDFQIFLGAL 433 (1102)
Q Consensus 355 vivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~y-m~RLGLWg~gt~f~~~~~f~~a~ 433 (1102)
.||.||+|+.||-. |+-...+.++ .-.-|.+ - ||.-=-.||.- .+=|.+-=|. =|.+.++|-+.+
T Consensus 292 ylvIDEaHRiKN~~-------s~L~~~lr~f---~~~nrLL-l--TGTPLQNNL~ELWaLLnFllPd-iF~~~e~F~swF 357 (971)
T KOG0385|consen 292 YLVIDEAHRIKNEK-------SKLSKILREF---KTDNRLL-L--TGTPLQNNLHELWALLNFLLPD-IFNSAEDFDSWF 357 (971)
T ss_pred EEEechhhhhcchh-------hHHHHHHHHh---cccceeE-e--eCCcccccHHHHHHHHHhhchh-hccCHHHHHHHH
Confidence 89999999999984 4444333322 1122333 2 45555568773 1212111232 378888888888
Q ss_pred hcc-ChhHHHHHHHHHHhccceeeecc------CCCCceeEEEeccCcHHHHHHHHH
Q 038397 434 DKG-GVGALELVAMDMKARGMYVCRTL------SYKGAEFEVIEAPLEAEMTDMYKK 483 (1102)
Q Consensus 434 ~~g-Gv~amE~va~dlK~~G~yiaR~L------Sf~gvef~i~e~~l~~~~~~~Yd~ 483 (1102)
..- -.+-.|++..-=+-.+-|+-|.+ |.---.--++.+.|+.-|++.|-+
T Consensus 358 ~~~~~~~~~e~v~~Lh~vL~pFlLRR~K~dVe~sLppKkE~~iyvgms~mQkk~Y~~ 414 (971)
T KOG0385|consen 358 DFTNCEGDQELVSRLHKVLRPFLLRRIKSDVEKSLPPKKELIIYVGMSSMQKKWYKA 414 (971)
T ss_pred cccccccCHHHHHHHHhhhhHHHHHHHHHhHhhcCCCcceeeEeccchHHHHHHHHH
Confidence 764 34556655544444455554433 222222334557999999999987
No 43
>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase. A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.
Probab=96.30 E-value=0.017 Score=73.21 Aligned_cols=162 Identities=15% Similarity=0.153 Sum_probs=98.0
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccC-ceEEEEEcCCchhhhHHhhhhhhC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGR-RKALWISVGSDLKFDARRDLDDVG 294 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr-~~~~w~s~s~~L~~Da~RDl~diG 294 (1102)
.|+.-|.+++..+.+- .-.++-=+||-||+-.-.=-|++..++.. -++|.++-...|-.|-.+.++.++
T Consensus 36 ~p~~~Q~~ai~~il~G----------~nvvv~apTGSGKTla~~LPiL~~l~~~~~~~aL~l~PtraLa~q~~~~l~~l~ 105 (742)
T TIGR03817 36 RPWQHQARAAELAHAG----------RHVVVATGTASGKSLAYQLPVLSALADDPRATALYLAPTKALAADQLRAVRELT 105 (742)
T ss_pred cCCHHHHHHHHHHHCC----------CCEEEECCCCCcHHHHHHHHHHHHHhhCCCcEEEEEcChHHHHHHHHHHHHHhc
Confidence 3778899997766532 23567778999997544334677776644 579999999999999999999997
Q ss_pred CCcccccccCCCCCCcCCC---CccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCC
Q 038397 295 ATCIEVHALNKLPYSKLDS---RSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEA 371 (1102)
Q Consensus 295 ~~~i~v~~l~~~~~~~~~~---~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~ 371 (1102)
...+.+..+. |.... ..+.-+-.||++|--.|...--....|+..+++-+ .+||+||+|.+.+..
T Consensus 106 ~~~i~v~~~~----Gdt~~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l-----~~vViDEah~~~g~f--- 173 (742)
T TIGR03817 106 LRGVRPATYD----GDTPTEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRL-----RYVVIDECHSYRGVF--- 173 (742)
T ss_pred cCCeEEEEEe----CCCCHHHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcC-----CEEEEeChhhccCcc---
Confidence 4334332221 11100 01112235899997555421111122333333322 589999999986532
Q ss_pred CCCchhHHHHHHHHhhh---CC-CccEEEEecCCC
Q 038397 372 GSQPTRTGEAVLELQAR---LP-EARVVYCSATGA 402 (1102)
Q Consensus 372 ~~~~s~~g~avl~LQ~~---lP-~ARvvY~SATga 402 (1102)
.+.......+|++. ++ +-+++.+|||-.
T Consensus 174 ---g~~~~~il~rL~ri~~~~g~~~q~i~~SATi~ 205 (742)
T TIGR03817 174 ---GSHVALVLRRLRRLCARYGASPVFVLASATTA 205 (742)
T ss_pred ---HHHHHHHHHHHHHHHHhcCCCCEEEEEecCCC
Confidence 13444444445433 22 357899999954
No 44
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.24 E-value=0.003 Score=52.40 Aligned_cols=33 Identities=18% Similarity=0.466 Sum_probs=29.9
Q ss_pred eecCCCccceeeccCCCccccCCCCCccccccc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVELAVDM 128 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~~ 128 (1102)
...|.+||+.+.+++....+.||+||.++...+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRILFKE 35 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEEEcc
Confidence 478999999999999998999999999988753
No 45
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=96.15 E-value=0.01 Score=74.48 Aligned_cols=152 Identities=21% Similarity=0.184 Sum_probs=93.8
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGA 295 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~ 295 (1102)
.|+..|.+++.-..+....-.| ..-.+.|| ||-||+-..+-.|+.....|.+ ++++.-...|-.+..+.++.+..
T Consensus 261 ~lt~~Q~~ai~~I~~d~~~~~~---~~~Ll~~~-TGSGKT~va~~~il~~~~~g~q-~lilaPT~~LA~Q~~~~l~~l~~ 335 (681)
T PRK10917 261 ELTGAQKRVVAEILADLASPKP---MNRLLQGD-VGSGKTVVAALAALAAIEAGYQ-AALMAPTEILAEQHYENLKKLLE 335 (681)
T ss_pred CCCHHHHHHHHHHHHhhhccCC---ceEEEECC-CCCcHHHHHHHHHHHHHHcCCe-EEEEeccHHHHHHHHHHHHHHHh
Confidence 3779999997654443221111 22355566 9999998887778888888765 99999999999999999888764
Q ss_pred C-cccccccCC-CCCCcCCCCcc--ccc---cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccC
Q 038397 296 T-CIEVHALNK-LPYSKLDSRSV--GIR---EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLV 368 (1102)
Q Consensus 296 ~-~i~v~~l~~-~~~~~~~~~~~--~~~---~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~ 368 (1102)
. .+.|.-+.. .+... .+.+ .+. -.||.+|.+.|... -.++ -=++||+||+|+..
T Consensus 336 ~~~i~v~ll~G~~~~~~--r~~~~~~l~~g~~~IvVgT~~ll~~~-----v~~~---------~l~lvVIDE~Hrfg--- 396 (681)
T PRK10917 336 PLGIRVALLTGSLKGKE--RREILEAIASGEADIVIGTHALIQDD-----VEFH---------NLGLVIIDEQHRFG--- 396 (681)
T ss_pred hcCcEEEEEcCCCCHHH--HHHHHHHHhCCCCCEEEchHHHhccc-----chhc---------ccceEEEechhhhh---
Confidence 3 344433321 11000 0000 122 34999998766421 1111 12689999999963
Q ss_pred CCCCCCchhHHHHHHHHhhhCCCccEEEEecCC
Q 038397 369 PEAGSQPTRTGEAVLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 369 ~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATg 401 (1102)
.++-. .|...-.+..++..|||.
T Consensus 397 -------~~qr~---~l~~~~~~~~iL~~SATp 419 (681)
T PRK10917 397 -------VEQRL---ALREKGENPHVLVMTATP 419 (681)
T ss_pred -------HHHHH---HHHhcCCCCCEEEEeCCC
Confidence 12222 233444467899999994
No 46
>KOG0354 consensus DEAD-box like helicase [General function prediction only]
Probab=96.13 E-value=0.025 Score=70.57 Aligned_cols=158 Identities=22% Similarity=0.203 Sum_probs=87.3
Q ss_pred cccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCc--eEEEEEcCCchhhhHHhhhhhhC
Q 038397 217 LSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRR--KALWISVGSDLKFDARRDLDDVG 294 (1102)
Q Consensus 217 LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~--~~~w~s~s~~L~~Da~RDl~diG 294 (1102)
|=+=|.|-|.-|- -+.. ++.==||.||++ ||+.|..|+++.+. |+|++.-+--|..==. +---+=
T Consensus 63 lR~YQ~eivq~AL-gkNt----------ii~lPTG~GKTf-IAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~-a~~~~~ 129 (746)
T KOG0354|consen 63 LRNYQEELVQPAL-GKNT----------IIALPTGSGKTF-IAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQI-ACFSIY 129 (746)
T ss_pred ccHHHHHHhHHhh-cCCe----------EEEeecCCCccc-hHHHHHHHHHhcCCcceEEEeeCCchHHHHHH-HHHhhc
Confidence 4467888777666 2222 344448889987 66788888887774 4676665555554222 111110
Q ss_pred CCcccccccC--CCCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCC
Q 038397 295 ATCIEVHALN--KLPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAG 372 (1102)
Q Consensus 295 ~~~i~v~~l~--~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~ 372 (1102)
...-.+..+. ..+-.. -..+--..-|+|+|=-.|...=..+ .... + .+| -+|||||||+|..-.
T Consensus 130 ~~~~~~T~~l~~~~~~~~--r~~i~~s~~vff~TpQil~ndL~~~-~~~~-----l-s~f-s~iv~DE~Hra~kn~---- 195 (746)
T KOG0354|consen 130 LIPYSVTGQLGDTVPRSN--RGEIVASKRVFFRTPQILENDLKSG-LHDE-----L-SDF-SLIVFDECHRTSKNH---- 195 (746)
T ss_pred cCcccceeeccCccCCCc--hhhhhcccceEEeChHhhhhhcccc-cccc-----c-ceE-EEEEEcccccccccc----
Confidence 0000010000 000000 0011235679999988776542222 1110 1 123 499999999987543
Q ss_pred CCchhHHHHHHHHhhhCCCccEEEEecCCCCC
Q 038397 373 SQPTRTGEAVLELQARLPEARVVYCSATGASE 404 (1102)
Q Consensus 373 ~~~s~~g~avl~LQ~~lP~ARvvY~SATgase 404 (1102)
.=++.-+.++++-+..+ ||+=-+||-+|+
T Consensus 196 -~Y~~Vmr~~l~~k~~~~--qILgLTASpG~~ 224 (746)
T KOG0354|consen 196 -PYNNIMREYLDLKNQGN--QILGLTASPGSK 224 (746)
T ss_pred -cHHHHHHHHHHhhhccc--cEEEEecCCCcc
Confidence 23567778888777754 999999997743
No 47
>PRK05580 primosome assembly protein PriA; Validated
Probab=96.12 E-value=0.016 Score=72.57 Aligned_cols=157 Identities=24% Similarity=0.218 Sum_probs=97.0
Q ss_pred CCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhh-
Q 038397 215 KSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDV- 293 (1102)
Q Consensus 215 g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~di- 293 (1102)
..|+..|.+++.... .+. +.+. +++---||-||+-....+|.+...+|++ ++++.-.-.|-.+..+.++..
T Consensus 143 ~~Lt~~Q~~ai~~i~-~~~-----~~~~-~Ll~~~TGSGKT~v~l~~i~~~l~~g~~-vLvLvPt~~L~~Q~~~~l~~~f 214 (679)
T PRK05580 143 PTLNPEQAAAVEAIR-AAA-----GFSP-FLLDGVTGSGKTEVYLQAIAEVLAQGKQ-ALVLVPEIALTPQMLARFRARF 214 (679)
T ss_pred CCCCHHHHHHHHHHH-hcc-----CCCc-EEEECCCCChHHHHHHHHHHHHHHcCCe-EEEEeCcHHHHHHHHHHHHHHh
Confidence 358899998866543 331 2223 4444449999998887788888888864 999999999999999888763
Q ss_pred CCCcccccccCCCCCCc-CCC-Cccc-cccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCC
Q 038397 294 GATCIEVHALNKLPYSK-LDS-RSVG-IREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPE 370 (1102)
Q Consensus 294 G~~~i~v~~l~~~~~~~-~~~-~~~~-~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~ 370 (1102)
|.....+|.- ....+ ... ..+. -.-.||..|.+.+.. .+ .++ ++||+||+|...-..
T Consensus 215 g~~v~~~~s~--~s~~~r~~~~~~~~~g~~~IVVgTrsal~~--------------p~-~~l-~liVvDEeh~~s~~~-- 274 (679)
T PRK05580 215 GAPVAVLHSG--LSDGERLDEWRKAKRGEAKVVIGARSALFL--------------PF-KNL-GLIIVDEEHDSSYKQ-- 274 (679)
T ss_pred CCCEEEEECC--CCHHHHHHHHHHHHcCCCCEEEeccHHhcc--------------cc-cCC-CEEEEECCCcccccc--
Confidence 4321111211 10000 000 0000 123589999877631 11 122 699999999744221
Q ss_pred CCCCchhHHHHHHHHhhhCCCccEEEEecC
Q 038397 371 AGSQPTRTGEAVLELQARLPEARVVYCSAT 400 (1102)
Q Consensus 371 ~~~~~s~~g~avl~LQ~~lP~ARvvY~SAT 400 (1102)
...|.--.+.+..+..+..++.+|+.|||
T Consensus 275 -~~~p~y~~r~va~~ra~~~~~~~il~SAT 303 (679)
T PRK05580 275 -QEGPRYHARDLAVVRAKLENIPVVLGSAT 303 (679)
T ss_pred -CcCCCCcHHHHHHHHhhccCCCEEEEcCC
Confidence 12334445566666677889999999999
No 48
>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.06 E-value=0.033 Score=66.74 Aligned_cols=156 Identities=21% Similarity=0.163 Sum_probs=92.6
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcch--hhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGR--TIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR--~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
.|-.-|.++|....+.+ -.++--.||-||+- ++..+ ..+. .+|+++-.-.|..|-.+.|...
T Consensus 11 ~~r~~Q~~ai~~~l~g~----------dvlv~apTGsGKTl~y~lp~l-----~~~~-~~lVi~P~~~L~~dq~~~l~~~ 74 (470)
T TIGR00614 11 SFRPVQLEVINAVLLGR----------DCFVVMPTGGGKSLCYQLPAL-----CSDG-ITLVISPLISLMEDQVLQLKAS 74 (470)
T ss_pred CCCHHHHHHHHHHHcCC----------CEEEEcCCCCcHhHHHHHHHH-----HcCC-cEEEEecHHHHHHHHHHHHHHc
Confidence 35578999977766432 24566679999984 22222 2333 4899999999999999999887
Q ss_pred CCCcccccccCCCCCCc----CCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCC
Q 038397 294 GATCIEVHALNKLPYSK----LDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVP 369 (1102)
Q Consensus 294 G~~~i~v~~l~~~~~~~----~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~ 369 (1102)
|.... -++.-.... +-.....-.-.+|++|.-.|... .|+.+.+++. ..=.+||+||||.....
T Consensus 75 gi~~~---~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~-----~~~~~~l~~~--~~i~~iViDEaH~i~~~-- 142 (470)
T TIGR00614 75 GIPAT---FLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSAS-----NRLLQTLEER--KGITLIAVDEAHCISQW-- 142 (470)
T ss_pred CCcEE---EEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCc-----hhHHHHHHhc--CCcCEEEEeCCcccCcc--
Confidence 75422 221110000 00000011234899999887532 2343434333 22359999999997532
Q ss_pred CCCCCchhHHHHHHHHhhhCCCccEEEEecCC
Q 038397 370 EAGSQPTRTGEAVLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 370 ~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATg 401 (1102)
|..--..=.....|...+|+++++..|||.
T Consensus 143 --g~~fr~~~~~l~~l~~~~~~~~~l~lTAT~ 172 (470)
T TIGR00614 143 --GHDFRPDYKALGSLKQKFPNVPIMALTATA 172 (470)
T ss_pred --ccccHHHHHHHHHHHHHcCCCceEEEecCC
Confidence 110011112344577889999999999994
No 49
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=96.00 E-value=0.018 Score=69.97 Aligned_cols=80 Identities=23% Similarity=0.330 Sum_probs=61.2
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRF 885 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRF 885 (1102)
+.|-+|+..|+|-+++++-||-+..-+ .-|...+|.|.+.-||+.|||+|.++- +=-|.|+ + ..++++
T Consensus 412 ~~Fr~G~~~ILVaTdvl~rGiDip~v~--------~VI~~d~P~s~~~yihRiGRaGR~g~~-G~ai~f~-~--~~~~~~ 479 (518)
T PLN00206 412 KSFLVGEVPVIVATGVLGRGVDLLRVR--------QVIIFDMPNTIKEYIHQIGRASRMGEK-GTAIVFV-N--EEDRNL 479 (518)
T ss_pred HHHHCCCCCEEEEecHhhccCCcccCC--------EEEEeCCCCCHHHHHHhccccccCCCC-eEEEEEE-c--hhHHHH
Confidence 579999999999999999999885443 445578999999999999999999862 3234433 3 256777
Q ss_pred HHHHHHHHhhcC
Q 038397 886 ASIVAKRLESLG 897 (1102)
Q Consensus 886 aS~VAkRLeSLG 897 (1102)
+.-+.+.|+..|
T Consensus 480 ~~~l~~~l~~~~ 491 (518)
T PLN00206 480 FPELVALLKSSG 491 (518)
T ss_pred HHHHHHHHHHcC
Confidence 777777776543
No 50
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=95.99 E-value=0.0071 Score=71.44 Aligned_cols=141 Identities=22% Similarity=0.292 Sum_probs=84.4
Q ss_pred cchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCC---chhhhHHhhhhhhCC
Q 038397 219 CLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGS---DLKFDARRDLDDVGA 295 (1102)
Q Consensus 219 ~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~---~L~~Da~RDl~diG~ 295 (1102)
.-|.|.+.|+..+-+-. =+|=+++|-+|+||+-|.-++++-..-+-. ++-+--.- .-+....|--. |+
T Consensus 187 ~fQkE~l~Wl~~QE~Ss-----~~GGiLADEMGMGKTIQtIaLllae~~ra~--tLVvaP~VAlmQW~nEI~~~T~--gs 257 (791)
T KOG1002|consen 187 PFQKEGLAWLTSQEESS-----VAGGILADEMGMGKTIQTIALLLAEVDRAP--TLVVAPTVALMQWKNEIERHTS--GS 257 (791)
T ss_pred hhhHHHHHHHHHhhhhh-----hccceehhhhccchHHHHHHHHHhccccCC--eeEEccHHHHHHHHHHHHHhcc--Cc
Confidence 56999999998776533 355579999999999998777776433222 22111100 11111122111 33
Q ss_pred CcccccccCCCCCCcCCCCcc--ccccceEEeehhhhhhcccc-------------ccchHHHHHHHhccCCCceEEeec
Q 038397 296 TCIEVHALNKLPYSKLDSRSV--GIREGVVFLTYSSLIASSEK-------------GRSRLQQLVQWCGSGYDGLVIFDE 360 (1102)
Q Consensus 296 ~~i~v~~l~~~~~~~~~~~~~--~~~~GvlF~TYs~L~~~~~~-------------~~sRl~Ql~~W~g~dfdgvivfDE 360 (1102)
..+-++.-.+- .+.+ -+...|+.+||+.+-+.-.| .+|=|.+| +| --||+||
T Consensus 258 lkv~~YhG~~R------~~nikel~~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi-~~------~RiIlDE 324 (791)
T KOG1002|consen 258 LKVYIYHGAKR------DKNIKELMNYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSI-KF------YRIILDE 324 (791)
T ss_pred eEEEEEecccc------cCCHHHhhcCcEEEEecHHHHHHHHhccccccccCCcccccchhhhc-ee------eeeehhh
Confidence 33322221110 1122 15678999999998765211 15666664 44 3689999
Q ss_pred chhccccCCCCCCCchhHHHHHHHHhhh
Q 038397 361 CHKAKNLVPEAGSQPTRTGEAVLELQAR 388 (1102)
Q Consensus 361 cH~akn~~~~~~~~~s~~g~avl~LQ~~ 388 (1102)
+|.-|+-. |+|++||..|...
T Consensus 325 AH~IK~R~-------snTArAV~~L~tt 345 (791)
T KOG1002|consen 325 AHNIKDRQ-------SNTARAVFALETT 345 (791)
T ss_pred hccccccc-------ccHHHHHHhhHhh
Confidence 99999774 8999999876543
No 51
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=95.95 E-value=0.018 Score=71.59 Aligned_cols=156 Identities=19% Similarity=0.180 Sum_probs=92.2
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhcc--CceEEEEEcCCchhhhHHhhhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHG--RRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~G--r~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
.+|.-|.++|-...+.+ -+++-=.||.||+-..+--|++..... ..++|.+.-.-.|.......+..+
T Consensus 28 ~ptpiQ~~ai~~ll~g~----------dvl~~ApTGsGKT~af~lpll~~l~~~~~~~~~LIL~PTreLa~Qv~~~l~~~ 97 (629)
T PRK11634 28 KPSPIQAECIPHLLNGR----------DVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQVAEAMTDF 97 (629)
T ss_pred CCCHHHHHHHHHHHcCC----------CEEEEcCCCCcHHHHHHHHHHHHhhhccCCCeEEEEeCcHHHHHHHHHHHHHH
Confidence 36678888866554322 234444699999876554466665433 346899999989988887777776
Q ss_pred CCC--cccccccCCC-CCCcCCCCccccc--cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccC
Q 038397 294 GAT--CIEVHALNKL-PYSKLDSRSVGIR--EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLV 368 (1102)
Q Consensus 294 G~~--~i~v~~l~~~-~~~~~~~~~~~~~--~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~ 368 (1102)
... .+.+..+..- ++. .....+. -.||.+|...|...-..+.-.|+. =.+|||||||.+.+..
T Consensus 98 ~~~~~~i~v~~~~gG~~~~---~q~~~l~~~~~IVVgTPgrl~d~l~r~~l~l~~---------l~~lVlDEAd~ml~~g 165 (629)
T PRK11634 98 SKHMRGVNVVALYGGQRYD---VQLRALRQGPQIVVGTPGRLLDHLKRGTLDLSK---------LSGLVLDEADEMLRMG 165 (629)
T ss_pred HhhcCCceEEEEECCcCHH---HHHHHhcCCCCEEEECHHHHHHHHHcCCcchhh---------ceEEEeccHHHHhhcc
Confidence 532 3333333210 000 0000122 349999988876432222222222 1479999999987542
Q ss_pred CCCCCCchhHHHHHHHHhhhCCC-ccEEEEecCCC
Q 038397 369 PEAGSQPTRTGEAVLELQARLPE-ARVVYCSATGA 402 (1102)
Q Consensus 369 ~~~~~~~s~~g~avl~LQ~~lP~-ARvvY~SATga 402 (1102)
....+..+...+|. .+++.+|||-.
T Consensus 166 ---------f~~di~~Il~~lp~~~q~llfSAT~p 191 (629)
T PRK11634 166 ---------FIEDVETIMAQIPEGHQTALFSATMP 191 (629)
T ss_pred ---------cHHHHHHHHHhCCCCCeEEEEEccCC
Confidence 12335555667765 46899999953
No 52
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=95.91 E-value=0.019 Score=75.71 Aligned_cols=160 Identities=24% Similarity=0.296 Sum_probs=84.5
Q ss_pred CCCCCccCcccccccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEE
Q 038397 198 PPEPTYDLLIKYDLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWIS 277 (1102)
Q Consensus 198 pP~~~y~~~lp~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s 277 (1102)
.|.+.|.-.||-+ ...+.|..+.+.|... ++.-.||.||+-|+--++++.. .|....|-++
T Consensus 64 ~p~~~~~~~LPi~---------~~r~~Il~ai~~~~Vv---------iI~GeTGSGKTTqlPq~lle~g-~g~~g~I~~T 124 (1294)
T PRK11131 64 RPEITYPENLPVS---------QKKQDILEAIRDHQVV---------IVAGETGSGKTTQLPKICLELG-RGVKGLIGHT 124 (1294)
T ss_pred CcccCCCCCCCHH---------HHHHHHHHHHHhCCeE---------EEECCCCCCHHHHHHHHHHHcC-CCCCCceeeC
Confidence 5789999999953 3447778888877432 3433499999999998988863 2322234333
Q ss_pred cCCch--hhhHHhhhhhhCCCcccccccCC-CCCC-cCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCC
Q 038397 278 VGSDL--KFDARRDLDDVGATCIEVHALNK-LPYS-KLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYD 353 (1102)
Q Consensus 278 ~s~~L--~~Da~RDl~diG~~~i~v~~l~~-~~~~-~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfd 353 (1102)
-.--+ .+=|.|=-..+|.. +.. +.|+ ..+ +.++-..-|+|+|--.|...-..+.. | .++
T Consensus 125 QPRRlAArsLA~RVA~El~~~------lG~~VGY~vrf~-~~~s~~t~I~v~TpG~LL~~l~~d~~-L--------s~~- 187 (1294)
T PRK11131 125 QPRRLAARTVANRIAEELETE------LGGCVGYKVRFN-DQVSDNTMVKLMTDGILLAEIQQDRL-L--------MQY- 187 (1294)
T ss_pred CCcHHHHHHHHHHHHHHHhhh------hcceeceeecCc-cccCCCCCEEEEChHHHHHHHhcCCc-c--------ccC-
Confidence 22111 01111111111110 100 1111 000 11122345899998887654221110 1 112
Q ss_pred ceEEeecchh-ccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCC
Q 038397 354 GLVIFDECHK-AKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 354 gvivfDEcH~-akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATg 401 (1102)
.+||+||+|. +-|.. ---| .+.++..+-|+.++|.+|||-
T Consensus 188 ~~IIIDEAHERsLn~D-------fLLg-~Lk~lL~~rpdlKvILmSATi 228 (1294)
T PRK11131 188 DTIIIDEAHERSLNID-------FILG-YLKELLPRRPDLKVIITSATI 228 (1294)
T ss_pred cEEEecCccccccccc-------hHHH-HHHHhhhcCCCceEEEeeCCC
Confidence 3899999994 65542 1122 123333344778999999996
No 53
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=95.87 E-value=0.023 Score=70.39 Aligned_cols=169 Identities=22% Similarity=0.253 Sum_probs=94.3
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcch--hhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGR--TIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR--~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
.+.+-|.++|..... + +-.++++ -||-||+- ++.+++ ..| .+|.++-.-.|..|-.+.|+..
T Consensus 25 ~~r~~Q~~ai~~il~-g--------~dvlv~a-pTGsGKTl~y~lpal~----~~g--~tlVisPl~sL~~dqv~~l~~~ 88 (607)
T PRK11057 25 QFRPGQQEIIDAVLS-G--------RDCLVVM-PTGGGKSLCYQIPALV----LDG--LTLVVSPLISLMKDQVDQLLAN 88 (607)
T ss_pred CCCHHHHHHHHHHHc-C--------CCEEEEc-CCCchHHHHHHHHHHH----cCC--CEEEEecHHHHHHHHHHHHHHc
Confidence 466889999765543 2 2334444 59999986 333332 233 4888998899999999999888
Q ss_pred CCCcccccccCCCCCCcCCCCcc-ccc---cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCC
Q 038397 294 GATCIEVHALNKLPYSKLDSRSV-GIR---EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVP 369 (1102)
Q Consensus 294 G~~~i~v~~l~~~~~~~~~~~~~-~~~---~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~ 369 (1102)
|....- ++............ .+. --+|++|--.|... .-++++..| + =++||+||||......
T Consensus 89 gi~~~~---~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~-----~~~~~l~~~---~-l~~iVIDEaH~i~~~G- 155 (607)
T PRK11057 89 GVAAAC---LNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMD-----NFLEHLAHW---N-PALLAVDEAHCISQWG- 155 (607)
T ss_pred CCcEEE---EcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcCh-----HHHHHHhhC---C-CCEEEEeCcccccccc-
Confidence 754322 21110000000000 112 23788887777531 122222222 2 3689999999975321
Q ss_pred CCCCCchhHHHHHHHHhhhCCCccEEEEecCCCCCCCccchhhhcccc
Q 038397 370 EAGSQPTRTGEAVLELQARLPEARVVYCSATGASEPRNMGYMVRLGLW 417 (1102)
Q Consensus 370 ~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~ym~RLGLW 417 (1102)
..-.| .=.....|...+|+.++|..|||.-...++ .++.+|++.
T Consensus 156 -~~fr~--~y~~L~~l~~~~p~~~~v~lTAT~~~~~~~-di~~~l~l~ 199 (607)
T PRK11057 156 -HDFRP--EYAALGQLRQRFPTLPFMALTATADDTTRQ-DIVRLLGLN 199 (607)
T ss_pred -CcccH--HHHHHHHHHHhCCCCcEEEEecCCChhHHH-HHHHHhCCC
Confidence 01111 113445677889999999999995433222 234444443
No 54
>PTZ00110 helicase; Provisional
Probab=95.87 E-value=0.014 Score=71.44 Aligned_cols=78 Identities=22% Similarity=0.402 Sum_probs=58.7
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRF 885 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRF 885 (1102)
+.|.+|+..|+|-+++++.||-...=. +-|-..+|++.+.-||+.|||+|.+.. .--|.|+.. .+.+.
T Consensus 421 ~~F~~G~~~ILVaTdv~~rGIDi~~v~--------~VI~~d~P~s~~~yvqRiGRtGR~G~~-G~ai~~~~~---~~~~~ 488 (545)
T PTZ00110 421 NEFKTGKSPIMIATDVASRGLDVKDVK--------YVINFDFPNQIEDYVHRIGRTGRAGAK-GASYTFLTP---DKYRL 488 (545)
T ss_pred HHHhcCCCcEEEEcchhhcCCCcccCC--------EEEEeCCCCCHHHHHHHhcccccCCCC-ceEEEEECc---chHHH
Confidence 589999999999999999999876443 345578999999999999999999874 334555543 35666
Q ss_pred HHHHHHHHhh
Q 038397 886 ASIVAKRLES 895 (1102)
Q Consensus 886 aS~VAkRLeS 895 (1102)
+..+.+-|+.
T Consensus 489 ~~~l~~~l~~ 498 (545)
T PTZ00110 489 ARDLVKVLRE 498 (545)
T ss_pred HHHHHHHHHH
Confidence 5555554433
No 55
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=95.86 E-value=0.0061 Score=78.65 Aligned_cols=29 Identities=34% Similarity=0.732 Sum_probs=23.6
Q ss_pred ecCCCccceeeccCCCccccCCCCCccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
..|.+||+.+...... +-.||+||.++.-
T Consensus 693 y~CPsCGaev~~des~-a~~CP~CGtplv~ 721 (1337)
T PRK14714 693 YVCPDCGAEVPPDESG-RVECPRCDVELTP 721 (1337)
T ss_pred eeCccCCCccCCCccc-cccCCCCCCcccc
Confidence 5899999988766555 6689999999765
No 56
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=95.76 E-value=0.017 Score=68.04 Aligned_cols=155 Identities=17% Similarity=0.146 Sum_probs=92.7
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhcc---------CceEEEEEcCCchhhhH
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHG---------RRKALWISVGSDLKFDA 286 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~G---------r~~~~w~s~s~~L~~Da 286 (1102)
.++.-|-+++-...+.+ -.++--.||.||+-...--|++.+++. ..+++.+.-.-.|-...
T Consensus 30 ~pt~iQ~~aip~il~g~----------dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~~~~lil~PtreLa~Qi 99 (423)
T PRK04837 30 NCTPIQALALPLTLAGR----------DVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQPRALIMAPTRELAVQI 99 (423)
T ss_pred CCCHHHHHHHHHHhCCC----------cEEEECCCCchHHHHHHHHHHHHHHhcccccccccCCceEEEECCcHHHHHHH
Confidence 45678888876665432 356666799999876555566666532 24689999999999999
Q ss_pred HhhhhhhCCC-cccccccCC-CCCCcCCCCcccccc--ceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecch
Q 038397 287 RRDLDDVGAT-CIEVHALNK-LPYSKLDSRSVGIRE--GVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECH 362 (1102)
Q Consensus 287 ~RDl~diG~~-~i~v~~l~~-~~~~~~~~~~~~~~~--GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH 362 (1102)
..++..++.. .+.+..+.. ..+. .....+.+ .||++|...|...-..+.-.| +-=.+||+||||
T Consensus 100 ~~~~~~l~~~~~~~v~~~~gg~~~~---~~~~~l~~~~~IlV~TP~~l~~~l~~~~~~l---------~~v~~lViDEad 167 (423)
T PRK04837 100 HADAEPLAQATGLKLGLAYGGDGYD---KQLKVLESGVDILIGTTGRLIDYAKQNHINL---------GAIQVVVLDEAD 167 (423)
T ss_pred HHHHHHHhccCCceEEEEECCCCHH---HHHHHhcCCCCEEEECHHHHHHHHHcCCccc---------ccccEEEEecHH
Confidence 9888888653 344332211 0000 00001222 499999887754321111111 112489999999
Q ss_pred hccccCCCCCCCchhHHHHHHHHhhhCCCc---cEEEEecCC
Q 038397 363 KAKNLVPEAGSQPTRTGEAVLELQARLPEA---RVVYCSATG 401 (1102)
Q Consensus 363 ~akn~~~~~~~~~s~~g~avl~LQ~~lP~A---RvvY~SATg 401 (1102)
++.+.. -...+..+-+.+|.. ..+..|||-
T Consensus 168 ~l~~~~---------f~~~i~~i~~~~~~~~~~~~~l~SAT~ 200 (423)
T PRK04837 168 RMFDLG---------FIKDIRWLFRRMPPANQRLNMLFSATL 200 (423)
T ss_pred HHhhcc---------cHHHHHHHHHhCCCccceeEEEEeccC
Confidence 986541 123344455667743 357889994
No 57
>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=95.74 E-value=0.022 Score=75.28 Aligned_cols=159 Identities=23% Similarity=0.307 Sum_probs=86.9
Q ss_pred CCCCCccCcccccccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEE
Q 038397 198 PPEPTYDLLIKYDLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWIS 277 (1102)
Q Consensus 198 pP~~~y~~~lp~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s 277 (1102)
.|.+.|...||- ....+.|..+...|... ++.|. ||.||+-|+--+++++.. |.+..|.++
T Consensus 57 ~~~~~~~~~LPi---------~~~~~~Il~~l~~~~vv--------ii~g~-TGSGKTTqlPq~lle~~~-~~~~~I~~t 117 (1283)
T TIGR01967 57 VPEIRYPDNLPV---------SAKREDIAEAIAENQVV--------IIAGE-TGSGKTTQLPKICLELGR-GSHGLIGHT 117 (1283)
T ss_pred cccccCCCCCCH---------HHHHHHHHHHHHhCceE--------EEeCC-CCCCcHHHHHHHHHHcCC-CCCceEecC
Confidence 477889888985 34457788888877433 33344 999999999999998642 333234333
Q ss_pred cCCch--hhhHHhhhhhhCCCcccccccCC-CCCC-cCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCC
Q 038397 278 VGSDL--KFDARRDLDDVGATCIEVHALNK-LPYS-KLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYD 353 (1102)
Q Consensus 278 ~s~~L--~~Da~RDl~diG~~~i~v~~l~~-~~~~-~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfd 353 (1102)
-.--+ ..=|+|=-..+|.. +.. +-|. ..++ .++-..-|+|+|.--|...-... + .+ .++
T Consensus 118 QPRRlAA~svA~RvA~elg~~------lG~~VGY~vR~~~-~~s~~T~I~~~TdGiLLr~l~~d--~------~L-~~~- 180 (1283)
T TIGR01967 118 QPRRLAARTVAQRIAEELGTP------LGEKVGYKVRFHD-QVSSNTLVKLMTDGILLAETQQD--R------FL-SRY- 180 (1283)
T ss_pred CccHHHHHHHHHHHHHHhCCC------cceEEeeEEcCCc-ccCCCceeeeccccHHHHHhhhC--c------cc-ccC-
Confidence 32211 11122222222321 110 1111 0011 11223348888887776432111 0 01 122
Q ss_pred ceEEeecchh-ccccCCCCCCCchhHHHH-HHHHhhhCCCccEEEEecCC
Q 038397 354 GLVIFDECHK-AKNLVPEAGSQPTRTGEA-VLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 354 gvivfDEcH~-akn~~~~~~~~~s~~g~a-vl~LQ~~lP~ARvvY~SATg 401 (1102)
.+|||||+|. +-|.. .... +.++....|+.++|.+|||-
T Consensus 181 ~~IIIDEaHERsL~~D---------~LL~lLk~il~~rpdLKlIlmSATl 221 (1283)
T TIGR01967 181 DTIIIDEAHERSLNID---------FLLGYLKQLLPRRPDLKIIITSATI 221 (1283)
T ss_pred cEEEEcCcchhhccch---------hHHHHHHHHHhhCCCCeEEEEeCCc
Confidence 4899999994 66542 2222 34445566899999999996
No 58
>COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only]
Probab=95.57 E-value=0.069 Score=68.67 Aligned_cols=162 Identities=16% Similarity=0.171 Sum_probs=103.8
Q ss_pred cchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCc-eEEEEEcCCchhhhHHhhhhhhCCCc
Q 038397 219 CLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRR-KALWISVGSDLKFDARRDLDDVGATC 297 (1102)
Q Consensus 219 ~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~-~~~w~s~s~~L~~Da~RDl~diG~~~ 297 (1102)
.=|.||..++-. ..-.++.-|||-||+=.--==|+++.+++.+ +++.|.-.+.|-.|=..=++.+..+.
T Consensus 73 ~HQ~~A~~~~~~----------G~~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~~rl~~~~~~~ 142 (851)
T COG1205 73 SHQVDALRLIRE----------GRNVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQAERLRELISDL 142 (851)
T ss_pred HHHHHHHHHHHC----------CCCEEEECCCCCchhHHHHHHHHHHHhhCcCccEEEEechhhhHhhHHHHHHHHHHhC
Confidence 456677554332 1447899999999987666669999998874 57999999999999776666655432
Q ss_pred ccccccCCCCC-CcCCCCc----cccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCC
Q 038397 298 IEVHALNKLPY-SKLDSRS----VGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAG 372 (1102)
Q Consensus 298 i~v~~l~~~~~-~~~~~~~----~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~ 372 (1102)
-. .++-..| |+..... +.-+-.||||+|.-|-..--....+. -|+-.. =-.||+||+|--.+.
T Consensus 143 ~~--~v~~~~y~Gdt~~~~r~~~~~~pp~IllTNpdMLh~~llr~~~~~----~~~~~~-Lk~lVvDElHtYrGv----- 210 (851)
T COG1205 143 PG--KVTFGRYTGDTPPEERRAIIRNPPDILLTNPDMLHYLLLRNHDAW----LWLLRN-LKYLVVDELHTYRGV----- 210 (851)
T ss_pred CC--cceeeeecCCCChHHHHHHHhCCCCEEEeCHHHHHHHhccCcchH----HHHHhc-CcEEEEecceecccc-----
Confidence 10 1111111 2111111 13345699999998764311111111 122111 138999999998866
Q ss_pred CCchhHHHHHHHHhhhCC----CccEEEEecCCCC
Q 038397 373 SQPTRTGEAVLELQARLP----EARVVYCSATGAS 403 (1102)
Q Consensus 373 ~~~s~~g~avl~LQ~~lP----~ARvvY~SATgas 403 (1102)
..|..+.-+.+|.+++- +-.+|.+|||-+.
T Consensus 211 -~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~n 244 (851)
T COG1205 211 -QGSEVALLLRRLLRRLRRYGSPLQIICTSATLAN 244 (851)
T ss_pred -chhHHHHHHHHHHHHHhccCCCceEEEEeccccC
Confidence 45899999999998875 4578999999543
No 59
>TIGR00580 mfd transcription-repair coupling factor (mfd). All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.
Probab=95.52 E-value=0.027 Score=72.86 Aligned_cols=152 Identities=15% Similarity=0.148 Sum_probs=93.5
Q ss_pred CcccchhhHHHHHHhhccccCCCCC-cceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSA-RAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVG 294 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~-R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG 294 (1102)
.++.-|..||.-..+.-+ .+. .--.+.|| ||-||+-...-.++....+|. +++++.-...|-..-...++.+.
T Consensus 451 ~~T~~Q~~aI~~I~~d~~----~~~~~d~Ll~ad-TGsGKT~val~a~l~al~~g~-qvlvLvPT~~LA~Q~~~~f~~~~ 524 (926)
T TIGR00580 451 EETPDQLKAIEEIKADME----SPRPMDRLVCGD-VGFGKTEVAMRAAFKAVLDGK-QVAVLVPTTLLAQQHFETFKERF 524 (926)
T ss_pred CCCHHHHHHHHHHHhhhc----ccCcCCEEEECC-CCccHHHHHHHHHHHHHHhCC-eEEEEeCcHHHHHHHHHHHHHHh
Confidence 467899998664443221 121 12345566 999999877767888888885 59999999999999888888764
Q ss_pred CC-cccccccCCCCCCcCCCCc-c-cccc---ceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccC
Q 038397 295 AT-CIEVHALNKLPYSKLDSRS-V-GIRE---GVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLV 368 (1102)
Q Consensus 295 ~~-~i~v~~l~~~~~~~~~~~~-~-~~~~---GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~ 368 (1102)
.. .+.|.-|+.+..++- .+. . .+.. .||.+|...|.. .-.++ +. ++||+||+|+..-
T Consensus 525 ~~~~i~v~~Lsg~~~~~e-~~~~~~~l~~g~~dIVIGTp~ll~~-----~v~f~--------~L-~llVIDEahrfgv-- 587 (926)
T TIGR00580 525 ANFPVTIELLSRFRSAKE-QNEILKELASGKIDILIGTHKLLQK-----DVKFK--------DL-GLLIIDEEQRFGV-- 587 (926)
T ss_pred ccCCcEEEEEeccccHHH-HHHHHHHHHcCCceEEEchHHHhhC-----CCCcc--------cC-CEEEeecccccch--
Confidence 42 444444443311100 000 0 1223 489999854421 11111 11 6999999999521
Q ss_pred CCCCCCchhHHHHHHHHhhhCCCccEEEEecCC
Q 038397 369 PEAGSQPTRTGEAVLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 369 ~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATg 401 (1102)
++ -..|+...++..|+.+|||-
T Consensus 588 --------~~---~~~L~~~~~~~~vL~~SATp 609 (926)
T TIGR00580 588 --------KQ---KEKLKELRTSVDVLTLSATP 609 (926)
T ss_pred --------hH---HHHHHhcCCCCCEEEEecCC
Confidence 11 12344555678999999995
No 60
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=95.38 E-value=0.011 Score=45.55 Aligned_cols=29 Identities=31% Similarity=0.714 Sum_probs=26.6
Q ss_pred eeecCCcceEEEeCCCcceecCCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLTEFICGTCNLPQ 45 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~ 45 (1102)
|+.|.+|+..|.|++|-+.|.|..|++..
T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~vt 29 (31)
T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQTVN 29 (31)
T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCeEe
Confidence 57899999999999999999999998743
No 61
>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]
Probab=95.34 E-value=1.2 Score=57.02 Aligned_cols=251 Identities=20% Similarity=0.276 Sum_probs=144.8
Q ss_pred CcccchhhHHHH----HHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHH---hccCceEEEEEcCCchhh---h
Q 038397 216 SLSCLQIETLVY----ASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENW---HHGRRKALWISVGSDLKF---D 285 (1102)
Q Consensus 216 ~LS~~Qle~v~y----a~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~---l~Gr~~~~w~s~s~~L~~---D 285 (1102)
.|-.-|+..|.+ +|+.-... -+....|.+++-=+|.||+-|+-.+.+.-. --|-++++-|+--+.+.. .
T Consensus 668 kLKpHQv~GvqFMwd~~~eSlkr~-~~~~GsGcILAHcMGLGKTlQVvtflhTvL~c~klg~ktaLvV~PlNt~~NW~~E 746 (1567)
T KOG1015|consen 668 KLKPHQVDGVQFMWDCCCESLKRT-KKSPGSGCILAHCMGLGKTLQVVTFLHTVLLCDKLGFKTALVVCPLNTALNWMNE 746 (1567)
T ss_pred hcCcccccchhHHHHHHHHHHHhh-cCCCCcchHHHHhhcccceehhhHHHHHHHHhhccCCceEEEEcchHHHHHHHHH
Confidence 566778888774 56655443 334478999999999999999988655444 456777887776665543 1
Q ss_pred HHhhhhhhCC-CcccccccCCCCCCcCC---CCccccccceEEeehhhhhhcccc--ccchH--HHHHHHh-ccCCCceE
Q 038397 286 ARRDLDDVGA-TCIEVHALNKLPYSKLD---SRSVGIREGVVFLTYSSLIASSEK--GRSRL--QQLVQWC-GSGYDGLV 356 (1102)
Q Consensus 286 a~RDl~diG~-~~i~v~~l~~~~~~~~~---~~~~~~~~GvlF~TYs~L~~~~~~--~~sRl--~Ql~~W~-g~dfdgvi 356 (1102)
.+.=+.++-- ..|+|+-|..++.-.-- -+.+.-+.||+..-|-.++--+.. .++|= +++..-+ .+.+| ++
T Consensus 747 FekWm~~~e~~~~leV~eL~~vkr~e~R~~~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD-~v 825 (1567)
T KOG1015|consen 747 FEKWMEGLEDDEKLEVSELATVKRPEERSYMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPD-FV 825 (1567)
T ss_pred HHHhcccccccccceeehhhhccChHHHHHHHHHHHhcCCEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCC-eE
Confidence 1111121222 35667666665431000 011233558999999887743321 11221 2223333 23333 79
Q ss_pred EeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCCCCCccc-h-----hhhccccCCCCCCCCHHHHH
Q 038397 357 IFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGASEPRNMG-Y-----MVRLGLWGAGTCFKDFQIFL 430 (1102)
Q Consensus 357 vfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~-y-----m~RLGLWg~gt~f~~~~~f~ 430 (1102)
|.||.|..||-. |-+.+|+..+.-+ -||+. ||.-=-.||. | .++-||.|.-+-|. .-|+
T Consensus 826 VCDE~HiLKNek-------sa~Skam~~irtk---RRI~L---TGTPLQNNLmEY~CMVnFVKe~lLGs~~Efr--NRFv 890 (1567)
T KOG1015|consen 826 VCDEGHILKNEK-------SAVSKAMNSIRTK---RRIIL---TGTPLQNNLMEYHCMVNFVKENLLGSIKEFR--NRFV 890 (1567)
T ss_pred Eecchhhhccch-------HHHHHHHHHHHhh---eeEEe---ecCchhhhhHHHHHHHHhcccccccCcHHHH--Hhhc
Confidence 999999999985 5566666654443 56765 5555556655 3 47889999776675 4588
Q ss_pred HHHhccCh--hHHHHHHHHHHhccce--------eeeccCCCCc--------eeEEEeccCcHHHHHHHHHHHH
Q 038397 431 GALDKGGV--GALELVAMDMKARGMY--------VCRTLSYKGA--------EFEVIEAPLEAEMTDMYKKAAE 486 (1102)
Q Consensus 431 ~a~~~gGv--~amE~va~dlK~~G~y--------iaR~LSf~gv--------ef~i~e~~l~~~~~~~Yd~~a~ 486 (1102)
+-|++|-- +-|+=| +-||.+--. |-| .+|.=+ +| ++-+.||+-|..+|..+-+
T Consensus 891 NpI~nGq~~dST~~DV-r~Mk~RsHILye~LkgcVqR-kDy~Vltk~LPPK~ey-Vi~vrltelQ~~LYq~yL~ 961 (1567)
T KOG1015|consen 891 NPIQNGQCADSTMVDV-RVMKKRSHILYEMLKGCVQR-KDYTVLTKFLPPKHEY-VIAVRLTELQCKLYQYYLD 961 (1567)
T ss_pred CccccCccCCCcHHHH-HHHHHHHHHHHHHHHHHHhh-hhhhhhcccCCCceeE-EEEEeccHHHHHHHHHHHh
Confidence 88887732 112211 222322111 101 122211 22 3456899999999998843
No 62
>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]
Probab=95.06 E-value=0.41 Score=60.00 Aligned_cols=283 Identities=17% Similarity=0.181 Sum_probs=154.0
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHH---hccCceEEEEEcCCchhhhHHhhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENW---HHGRRKALWISVGSDLKFDARRDLDD 292 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~---l~Gr~~~~w~s~s~~L~~Da~RDl~d 292 (1102)
.|-+=|+-.|.|=+-=|..-|. | +++|-+|.||+-|+-+..-+-. .+|.+-+| |...-++-..|.+.-
T Consensus 399 ~LkdYQlvGvNWL~Llyk~~l~-----g-ILADEMGLGKTiQvIaFlayLkq~g~~gpHLVV---vPsSTleNWlrEf~k 469 (941)
T KOG0389|consen 399 QLKDYQLVGVNWLLLLYKKKLN-----G-ILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVV---VPSSTLENWLREFAK 469 (941)
T ss_pred cccchhhhhHHHHHHHHHcccc-----c-eehhhccCcchhHHHHHHHHHHHcCCCCCcEEE---ecchhHHHHHHHHHH
Confidence 4668888898888877766543 4 7999999999999976544333 35554222 333344556666533
Q ss_pred hCCCcccccccCCCCCCcCC--------CCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhc
Q 038397 293 VGATCIEVHALNKLPYSKLD--------SRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKA 364 (1102)
Q Consensus 293 iG~~~i~v~~l~~~~~~~~~--------~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~a 364 (1102)
- |..+.|-+- ||..+ .+....+..||.+||....+.+ ..++ .+-.| .|| ++||||.|..
T Consensus 470 w-CPsl~Ve~Y----yGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~k-dDRs---flk~~---~~n-~viyDEgHmL 536 (941)
T KOG0389|consen 470 W-CPSLKVEPY----YGSQDERRELRERIKKNKDDYDVLLTTYNLAASSK-DDRS---FLKNQ---KFN-YVIYDEGHML 536 (941)
T ss_pred h-CCceEEEec----cCcHHHHHHHHHHHhccCCCccEEEEEeecccCCh-HHHH---HHHhc---ccc-EEEecchhhh
Confidence 2 333443322 23110 0112236679999999876432 1122 23333 566 8899999999
Q ss_pred cccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCCCCCccch-hhhccccCCCCCCC-CHHHHHHHHhccCh----
Q 038397 365 KNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGASEPRNMGY-MVRLGLWGAGTCFK-DFQIFLGALDKGGV---- 438 (1102)
Q Consensus 365 kn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~y-m~RLGLWg~gt~f~-~~~~f~~a~~~gGv---- 438 (1102)
||.. |.. ---|..---|-|++. ||.-=-.||-- |+=|-+-=+.. |. +.+++-.-++..+-
T Consensus 537 KN~~-------SeR---y~~LM~I~An~RlLL---TGTPLQNNL~ELiSLL~FvlP~v-F~~~~~dl~~if~~k~~~d~d 602 (941)
T KOG0389|consen 537 KNRT-------SER---YKHLMSINANFRLLL---TGTPLQNNLKELISLLAFVLPKV-FDSSMEDLDVIFKAKKTSDGD 602 (941)
T ss_pred hccc-------hHH---HHHhccccccceEEe---eCCcccccHHHHHHHHHHHhhHh-hhccchHHHHHHhccCCccch
Confidence 9985 221 112223323446654 44444456552 33221111111 11 23333333333331
Q ss_pred -----hHHHHHHHHHHhccceeeecc------CCCCceeEEEeccCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCC
Q 038397 439 -----GALELVAMDMKARGMYVCRTL------SYKGAEFEVIEAPLEAEMTDMYKKAAEFWAELRVELLSASAFLANDKP 507 (1102)
Q Consensus 439 -----~amE~va~dlK~~G~yiaR~L------Sf~gvef~i~e~~l~~~~~~~Yd~~a~~w~~~~~~~~~a~e~~~~~~~ 507 (1102)
=+.|-+++.=--.+=||=|.+ +.---.=.|+.+.|++.|..+||.++++...-..+..+- .+ +
T Consensus 603 ~e~~~l~qerIsrAK~im~PFILRR~K~qVL~~LPpK~~~Ie~c~mse~Q~~~Y~~~~~~~~~~~~~~~~n-----s~-~ 676 (941)
T KOG0389|consen 603 IENALLSQERISRAKTIMKPFILRRLKSQVLKQLPPKIQRIEYCEMSEKQKQLYDELIELYDVKLNEVSKN-----SE-L 676 (941)
T ss_pred hhHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcCCccceeEeeecchHHHHHHHHHHHHHhhhccccccc-----cc-c
Confidence 124444444333455665554 333334567778999999999999998873222211111 01 1
Q ss_pred ChhHHHHHhh--hhhhHHHHHHHHhcCchHHHHHH
Q 038397 508 NSSQLWRLYW--SGHQRFFRHMCMSAKVPATVRLA 540 (1102)
Q Consensus 508 ~~~~~~~~Fw--sahQrFFk~l~~a~Kv~~~V~~a 540 (1102)
..+.+.+|+- +.|.-.||+.-..-|+....++.
T Consensus 677 ~~~~vlmqlRK~AnHPLL~R~~Y~de~L~~mak~i 711 (941)
T KOG0389|consen 677 KSGNVLMQLRKAANHPLLFRSIYTDEKLRKMAKRI 711 (941)
T ss_pred ccchHHHHHHHHhcChhHHHHhccHHHHHHHHHHH
Confidence 1122444554 78999999988777766655554
No 63
>PHA02653 RNA helicase NPH-II; Provisional
Probab=94.97 E-value=0.082 Score=66.36 Aligned_cols=68 Identities=12% Similarity=0.012 Sum_probs=40.4
Q ss_pred cCCcceEEEEecccccccccccccccccc----cceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecC
Q 038397 809 MDGKKLVAIISEAGSAGVSLQADRRAANQ----KRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTN 878 (1102)
Q Consensus 809 m~G~K~VAIISeAaSTGISLhADrr~~NQ----RRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~ 878 (1102)
-+|+..|.|-++-|++||-..-=.-|-|- ..+.+.-.|.+.|...++|+-|||+|. ..+--|++...+
T Consensus 443 ~~gk~kILVATdIAERGIDIp~V~~VID~G~~k~p~~~~g~~~~iSkasa~QRaGRAGR~--~~G~c~rLyt~~ 514 (675)
T PHA02653 443 SSKNPSIIISTPYLESSVTIRNATHVYDTGRVYVPEPFGGKEMFISKSMRTQRKGRVGRV--SPGTYVYFYDLD 514 (675)
T ss_pred ccCceeEEeccChhhccccccCeeEEEECCCccCCCcccCcccccCHHHHHHhccCcCCC--CCCeEEEEECHH
Confidence 35555566666666665554322222111 001111235677999999999999999 467777777654
No 64
>PRK13767 ATP-dependent helicase; Provisional
Probab=94.93 E-value=0.1 Score=67.50 Aligned_cols=161 Identities=18% Similarity=0.116 Sum_probs=93.2
Q ss_pred CCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhc--------cCceEEEEEcCCchhhhH
Q 038397 215 KSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHH--------GRRKALWISVGSDLKFDA 286 (1102)
Q Consensus 215 g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~--------Gr~~~~w~s~s~~L~~Da 286 (1102)
+.|...|.+++--. .++ .-+++.=.||-||+-...--|++.++. ...+++||+-...|-.|.
T Consensus 31 ~~~tpiQ~~Ai~~i-l~g---------~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtraLa~di 100 (876)
T PRK13767 31 GTFTPPQRYAIPLI-HEG---------KNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRALNNDI 100 (876)
T ss_pred CCCCHHHHHHHHHH-HcC---------CCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHHHHHHH
Confidence 35889999996543 332 125677779999976544346666653 134699999999999998
Q ss_pred Hhhhhh----h-------CCC--cccccccCCCCCCcCCCC----ccccccceEEeehhhhhhccccccchHHHHHHHhc
Q 038397 287 RRDLDD----V-------GAT--CIEVHALNKLPYSKLDSR----SVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCG 349 (1102)
Q Consensus 287 ~RDl~d----i-------G~~--~i~v~~l~~~~~~~~~~~----~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g 349 (1102)
.+.|.. | |.. .+.|.-+ .|..... ...-.-.||.+|.=+|..--... ++ ..|+.
T Consensus 101 ~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~----~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~--~~---~~~l~ 171 (876)
T PRK13767 101 HRNLEEPLTEIREIAKERGEELPEIRVAIR----TGDTSSYEKQKMLKKPPHILITTPESLAILLNSP--KF---REKLR 171 (876)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcCCeeEEEE----cCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcCh--hH---HHHHh
Confidence 876542 1 221 2222111 1111000 01123469999987764321111 11 22332
Q ss_pred cCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhC-CCccEEEEecCC
Q 038397 350 SGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARL-PEARVVYCSATG 401 (1102)
Q Consensus 350 ~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~l-P~ARvvY~SATg 401 (1102)
. =.+||+||||...+.. ..........+|.... ++.+++..|||-
T Consensus 172 ~--l~~VVIDE~H~l~~~~-----RG~~l~~~L~rL~~l~~~~~q~IglSATl 217 (876)
T PRK13767 172 T--VKWVIVDEIHSLAENK-----RGVHLSLSLERLEELAGGEFVRIGLSATI 217 (876)
T ss_pred c--CCEEEEechhhhccCc-----cHHHHHHHHHHHHHhcCCCCeEEEEeccc
Confidence 2 2579999999987431 1233444555666666 677889999993
No 65
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=94.92 E-value=0.016 Score=44.77 Aligned_cols=28 Identities=29% Similarity=0.777 Sum_probs=25.9
Q ss_pred eecCCCccceeeccCCCccccCCCCCcc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
|+.|++|+..|..|.|-.+|+|..|.+-
T Consensus 1 q~~C~~C~t~L~yP~gA~~vrCs~C~~v 28 (31)
T TIGR01053 1 QVVCGGCRTLLMYPRGASSVRCALCQTV 28 (31)
T ss_pred CcCcCCCCcEeecCCCCCeEECCCCCeE
Confidence 5899999999999999999999999863
No 66
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=94.88 E-value=0.91 Score=59.37 Aligned_cols=343 Identities=17% Similarity=0.226 Sum_probs=182.3
Q ss_pred cccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCce---EEEEEcCC-chhhhHH
Q 038397 212 ESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRK---ALWISVGS-DLKFDAR 287 (1102)
Q Consensus 212 ~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~---~~w~s~s~-~L~~Da~ 287 (1102)
+..+.|=+-|||.|.+-..... .+.-.+++|-+|.||+-|--..+.+-+..++-. .|-+..|. .-...-.
T Consensus 366 ~~g~~LRdyQLeGlNWl~~~W~------~~~n~ILADEmgLgktvqti~fl~~l~~~~~~~gpflvvvplst~~~W~~ef 439 (1373)
T KOG0384|consen 366 KGGNELRDYQLEGLNWLLYSWY------KRNNCILADEMGLGKTVQTITFLSYLFHSLQIHGPFLVVVPLSTITAWEREF 439 (1373)
T ss_pred cccchhhhhhcccchhHHHHHH------hcccceehhhcCCCcchHHHHHHHHHHHhhhccCCeEEEeehhhhHHHHHHH
Confidence 4457888999999997765542 255568999999999999877777666555432 12222221 0011111
Q ss_pred hhhhhhCCCc----c---cccccCCCCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeec
Q 038397 288 RDLDDVGATC----I---EVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDE 360 (1102)
Q Consensus 288 RDl~diG~~~----i---~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDE 360 (1102)
+=|.|+.+-. + .+.-...|-+. +..-.++-.+|.|||-.+... +.=|.+ +.| .++++||
T Consensus 440 ~~w~~mn~i~y~g~~~sr~~i~~ye~~~~---~~~~~lkf~~lltTye~~LkD----k~~L~~-i~w------~~~~vDe 505 (1373)
T KOG0384|consen 440 ETWTDMNVIVYHGNLESRQLIRQYEFYHS---SNTKKLKFNALLTTYEIVLKD----KAELSK-IPW------RYLLVDE 505 (1373)
T ss_pred HHHhhhceeeeecchhHHHHHHHHHheec---CCccccccceeehhhHHHhcc----Hhhhcc-CCc------ceeeecH
Confidence 2233222210 0 01111222111 112246788999999998754 233333 345 5899999
Q ss_pred chhccccCCCCCCCchhHHHH--HHHHhhhCCCccEEEEecCCCCCCCccchhhhc-cccCCCCCCCCHHHHHHHHhcc-
Q 038397 361 CHKAKNLVPEAGSQPTRTGEA--VLELQARLPEARVVYCSATGASEPRNMGYMVRL-GLWGAGTCFKDFQIFLGALDKG- 436 (1102)
Q Consensus 361 cH~akn~~~~~~~~~s~~g~a--vl~LQ~~lP~ARvvY~SATgasep~Nl~ym~RL-GLWg~gt~f~~~~~f~~a~~~g- 436 (1102)
+|+.||.. ++--.. -..+ +-|++ =||.-=-+|+--.--| .+--|| -|.+.++|.......
T Consensus 506 ahrLkN~~-------~~l~~~l~~f~~-----~~rll---itgTPlQNsikEL~sLl~Fl~P~-kf~~~~~f~~~~~~~~ 569 (1373)
T KOG0384|consen 506 AHRLKNDE-------SKLYESLNQFKM-----NHRLL---ITGTPLQNSLKELWSLLHFLMPG-KFDSWDEFLEEFDEET 569 (1373)
T ss_pred HhhcCchH-------HHHHHHHHHhcc-----cceee---ecCCCccccHHHHHHHhcccCCC-CCCcHHHHHHhhcchh
Confidence 99999984 222222 1122 22343 3444444455432222 112333 489999998877222
Q ss_pred --ChhHHHHHHHHHHhccceeee-----ccCCCCceeEEEeccCcHHHHHHHHHHHHH---------------HHHHHHH
Q 038397 437 --GVGALELVAMDMKARGMYVCR-----TLSYKGAEFEVIEAPLEAEMTDMYKKAAEF---------------WAELRVE 494 (1102)
Q Consensus 437 --Gv~amE~va~dlK~~G~yiaR-----~LSf~gvef~i~e~~l~~~~~~~Yd~~a~~---------------w~~~~~~ 494 (1102)
||..+. .. ..=+.++| +-|..--+-.|++|.||.-|.+-|...-.- +--|..+
T Consensus 570 e~~~~~L~---~~--L~P~~lRr~kkdvekslp~k~E~IlrVels~lQk~yYk~ILtkN~~~LtKG~~g~~~~lLNimmE 644 (1373)
T KOG0384|consen 570 EEQVRKLQ---QI--LKPFLLRRLKKDVEKSLPPKEETILRVELSDLQKQYYKAILTKNFSALTKGAKGSTPSLLNIMME 644 (1373)
T ss_pred HHHHHHHH---HH--hhHHHHHHHHhhhccCCCCCcceEEEeehhHHHHHHHHHHHHhhHHHHhccCCCCCchHHHHHHH
Confidence 222211 11 11222333 236777778899999999999998754210 1112222
Q ss_pred HHHHHhhhcCCCCChhHHHHHhhhhhhH--HHHHHHHh-cCchHHHHHHHHHHHCCCeEEEEEecchhHHHHHHHHhc--
Q 038397 495 LLSASAFLANDKPNSSQLWRLYWSGHQR--FFRHMCMS-AKVPATVRLAKKALAEGKCVVIGLQSTGEARTEEAVTKY-- 569 (1102)
Q Consensus 495 ~~~a~e~~~~~~~~~~~~~~~FwsahQr--FFk~l~~a-~Kv~~~V~~a~eal~~Gk~vVIgLqSTGEA~~~~~l~~~-- 569 (1102)
|.+++..--.-++.-..+...|-. |.+ -.+.|+++ -|+--+=++--..-+.||.|.|==|=+ |+++.|+++
T Consensus 645 LkKccNHpyLi~gaee~~~~~~~~-~~~d~~L~~lI~sSGKlVLLDKLL~rLk~~GHrVLIFSQMV---RmLDIL~eYL~ 720 (1373)
T KOG0384|consen 645 LKKCCNHPYLIKGAEEKILGDFRD-KMRDEALQALIQSSGKLVLLDKLLPRLKEGGHRVLIFSQMV---RMLDILAEYLS 720 (1373)
T ss_pred HHHhcCCccccCcHHHHHHHhhhh-cchHHHHHHHHHhcCcEEeHHHHHHHHhcCCceEEEhHHHH---HHHHHHHHHHH
Confidence 333222110001111123344443 111 23455554 477666666666666789999976654 677777664
Q ss_pred --CCCcCccccChHHHHHHHHHhhCCCCCCCC
Q 038397 570 --GLELDDFISGPRELLLKFVEENYPLPEKPE 599 (1102)
Q Consensus 570 --~~~l~dfvst~r~il~~~v~~~FP~~~~~~ 599 (1102)
+-...-++-+-|.=|..---.||=.|+.++
T Consensus 721 ~r~ypfQRLDGsvrgelRq~AIDhFnap~Sdd 752 (1373)
T KOG0384|consen 721 LRGYPFQRLDGSVRGELRQQAIDHFNAPDSDD 752 (1373)
T ss_pred HcCCcceeccCCcchHHHHHHHHhccCCCCCc
Confidence 222222333456667777778898887765
No 67
>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=94.86 E-value=0.072 Score=66.90 Aligned_cols=122 Identities=21% Similarity=0.330 Sum_probs=79.4
Q ss_pred cchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccC-ceEEEEEcCCchhhhHH---hhhhhhC
Q 038397 219 CLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGR-RKALWISVGSDLKFDAR---RDLDDVG 294 (1102)
Q Consensus 219 ~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr-~~~~w~s~s~~L~~Da~---RDl~diG 294 (1102)
.=|.+||.=-+.+.. .|.++ .|+-=-||.||+|+.=+||+--|..|+ +|++|+.-.+.|..=|. .|..=-|
T Consensus 168 yyQ~~AI~rv~Eaf~----~g~~r-aLlvMATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA~~af~~~~P~~ 242 (875)
T COG4096 168 YYQIIAIRRVIEAFS----KGQNR-ALLVMATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQAYGAFEDFLPFG 242 (875)
T ss_pred HHHHHHHHHHHHHHh----cCCce-EEEEEecCCCcceeHHHHHHHHHhcchhheeeEEechHHHHHHHHHHHHHhCCCc
Confidence 557788776666553 45555 677777889999999999999999998 88999988888876554 3332112
Q ss_pred CCcccccccCCCCCCcCCCCccccccceEEeehhhhhhcc-cc--ccchHHHHHHHhcc-CCCceEEeecchhc
Q 038397 295 ATCIEVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASS-EK--GRSRLQQLVQWCGS-GYDGLVIFDECHKA 364 (1102)
Q Consensus 295 ~~~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~-~~--~~sRl~Ql~~W~g~-dfdgvivfDEcH~a 364 (1102)
.. .|+.. .+.+.-..-|.++||-++.+.- ++ ..-|+ +. .|| +||.||||+-
T Consensus 243 ~~------~n~i~-----~~~~~~s~~i~lsTyqt~~~~~~~~~~~~~~f-------~~g~FD-lIvIDEaHRg 297 (875)
T COG4096 243 TK------MNKIE-----DKKGDTSSEIYLSTYQTMTGRIEQKEDEYRRF-------GPGFFD-LIVIDEAHRG 297 (875)
T ss_pred cc------eeeee-----cccCCcceeEEEeehHHHHhhhhccccccccC-------CCCcee-EEEechhhhh
Confidence 11 12111 1111113459999999998752 11 12222 33 355 9999999994
No 68
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=94.79 E-value=0.1 Score=50.43 Aligned_cols=118 Identities=16% Similarity=0.145 Sum_probs=67.6
Q ss_pred CcceeEeecCCCCCcchhhHHHHHHHHhc----cCceEEEEEcCCch-hhhHHhhhhh-hCCCcccccccCCCCCCcCCC
Q 038397 240 ARAGFFIGDGAGVGKGRTIAGLIWENWHH----GRRKALWISVGSDL-KFDARRDLDD-VGATCIEVHALNKLPYSKLDS 313 (1102)
Q Consensus 240 ~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~----Gr~~~~w~s~s~~L-~~Da~RDl~d-iG~~~i~v~~l~~~~~~~~~~ 313 (1102)
.+..++.|. +|+||+..+.-++.+.-.. +....+|++....- ..+..+.+.+ +|.. ..
T Consensus 4 ~~~~~i~G~-~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~------~~--------- 67 (131)
T PF13401_consen 4 QRILVISGP-PGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLP------LK--------- 67 (131)
T ss_dssp ---EEEEE--TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-S------SS---------
T ss_pred CcccEEEcC-CCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCcc------cc---------
Confidence 467788888 9999999998887776543 25668888876543 2222222211 1111 00
Q ss_pred CccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCcc
Q 038397 314 RSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEAR 393 (1102)
Q Consensus 314 ~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~AR 393 (1102)
. ......-++++.+++......+||+||+|... . ...-.....|.+ -++..
T Consensus 68 ---~----------------~~~~~~l~~~~~~~l~~~~~~~lviDe~~~l~--~-------~~~l~~l~~l~~-~~~~~ 118 (131)
T PF13401_consen 68 ---S----------------RQTSDELRSLLIDALDRRRVVLLVIDEADHLF--S-------DEFLEFLRSLLN-ESNIK 118 (131)
T ss_dssp ---S----------------TS-HHHHHHHHHHHHHHCTEEEEEEETTHHHH--T-------HHHHHHHHHHTC-SCBEE
T ss_pred ---c----------------cCCHHHHHHHHHHHHHhcCCeEEEEeChHhcC--C-------HHHHHHHHHHHh-CCCCe
Confidence 0 01112334677888876555799999999974 0 334445555656 45667
Q ss_pred EEEEecCCC
Q 038397 394 VVYCSATGA 402 (1102)
Q Consensus 394 vvY~SATga 402 (1102)
||.++-...
T Consensus 119 vvl~G~~~l 127 (131)
T PF13401_consen 119 VVLVGTPEL 127 (131)
T ss_dssp EEEEESSTT
T ss_pred EEEEEChhh
Confidence 787766543
No 69
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=94.71 E-value=0.026 Score=66.48 Aligned_cols=157 Identities=14% Similarity=0.196 Sum_probs=87.9
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHh------ccCceEEEEEcCCchhhhHHhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWH------HGRRKALWISVGSDLKFDARRD 289 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l------~Gr~~~~w~s~s~~L~~Da~RD 289 (1102)
.++..|.++|-.+.+. + .+++-=.||.||+-...-.|+...+ .|..++++++-+..|-....+.
T Consensus 23 ~p~~iQ~~ai~~~~~g---------~-d~l~~apTGsGKT~~~~lp~l~~l~~~~~~~~~~~~~lil~Pt~eLa~Q~~~~ 92 (434)
T PRK11192 23 RPTAIQAEAIPPALDG---------R-DVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELAMQVADQ 92 (434)
T ss_pred CCCHHHHHHHHHHhCC---------C-CEEEECCCCChHHHHHHHHHHHHHhhccccCCCCceEEEECCcHHHHHHHHHH
Confidence 3567899997666642 1 2556666999998654333444433 2346799999999999888888
Q ss_pred hhhhCCC-cccccccCC-CCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhcccc
Q 038397 290 LDDVGAT-CIEVHALNK-LPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNL 367 (1102)
Q Consensus 290 l~diG~~-~i~v~~l~~-~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~ 367 (1102)
++.++.. .+.+..+.. ..+... ...+.-.-.||++|.-.|...-.++. + .+ .++ .+|||||||.+...
T Consensus 93 ~~~l~~~~~~~v~~~~gg~~~~~~-~~~l~~~~~IlV~Tp~rl~~~~~~~~--~-----~~-~~v-~~lViDEah~~l~~ 162 (434)
T PRK11192 93 ARELAKHTHLDIATITGGVAYMNH-AEVFSENQDIVVATPGRLLQYIKEEN--F-----DC-RAV-ETLILDEADRMLDM 162 (434)
T ss_pred HHHHHccCCcEEEEEECCCCHHHH-HHHhcCCCCEEEEChHHHHHHHHcCC--c-----Cc-ccC-CEEEEECHHHHhCC
Confidence 8877642 333322211 111000 00011123499999876653211110 0 00 112 37999999998643
Q ss_pred CCCCCCCchhHHHHHHHHhhhCCC-ccEEEEecCC
Q 038397 368 VPEAGSQPTRTGEAVLELQARLPE-ARVVYCSATG 401 (1102)
Q Consensus 368 ~~~~~~~~s~~g~avl~LQ~~lP~-ARvvY~SATg 401 (1102)
. .+..+..+...++. .+++..|||-
T Consensus 163 ~---------~~~~~~~i~~~~~~~~q~~~~SAT~ 188 (434)
T PRK11192 163 G---------FAQDIETIAAETRWRKQTLLFSATL 188 (434)
T ss_pred C---------cHHHHHHHHHhCccccEEEEEEeec
Confidence 1 22333344444443 4688999993
No 70
>PTZ00110 helicase; Provisional
Probab=94.59 E-value=0.064 Score=65.73 Aligned_cols=154 Identities=15% Similarity=0.165 Sum_probs=88.4
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhc------c-CceEEEEEcCCchhhhHHh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHH------G-RRKALWISVGSDLKFDARR 288 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~------G-r~~~~w~s~s~~L~~Da~R 288 (1102)
.++.-|.+++-.+.+.+ -.++--.||-||+-.-.--++...+. | ...+|++.-.-.|-.+...
T Consensus 152 ~pt~iQ~~aip~~l~G~----------dvI~~ApTGSGKTlaylLP~l~~i~~~~~~~~~~gp~~LIL~PTreLa~Qi~~ 221 (545)
T PTZ00110 152 EPTPIQVQGWPIALSGR----------DMIGIAETGSGKTLAFLLPAIVHINAQPLLRYGDGPIVLVLAPTRELAEQIRE 221 (545)
T ss_pred CCCHHHHHHHHHHhcCC----------CEEEEeCCCChHHHHHHHHHHHHHHhcccccCCCCcEEEEECChHHHHHHHHH
Confidence 46788999876665432 33555679999986432212333222 1 2358999999999999888
Q ss_pred hhhhhCCC-cccccccCCCCCCcCCC--Ccccc--ccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchh
Q 038397 289 DLDDVGAT-CIEVHALNKLPYSKLDS--RSVGI--REGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHK 363 (1102)
Q Consensus 289 Dl~diG~~-~i~v~~l~~~~~~~~~~--~~~~~--~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~ 363 (1102)
-+..++.. .+.+..+ ||.... ....+ .-.||++|.-.|...-..+...|.. =.+||+||||.
T Consensus 222 ~~~~~~~~~~i~~~~~----~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~~~~~l~~---------v~~lViDEAd~ 288 (545)
T PTZ00110 222 QCNKFGASSKIRNTVA----YGGVPKRGQIYALRRGVEILIACPGRLIDFLESNVTNLRR---------VTYLVLDEADR 288 (545)
T ss_pred HHHHHhcccCccEEEE----eCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHcCCCChhh---------CcEEEeehHHh
Confidence 88888753 3332221 111100 00112 2359999988776432222222221 14899999999
Q ss_pred ccccCCCCCCCchhHHHHHHHHhhhC-CCccEEEEecCC
Q 038397 364 AKNLVPEAGSQPTRTGEAVLELQARL-PEARVVYCSATG 401 (1102)
Q Consensus 364 akn~~~~~~~~~s~~g~avl~LQ~~l-P~ARvvY~SATg 401 (1102)
+.... -...+..+-..+ |+.+++..|||.
T Consensus 289 mld~g---------f~~~i~~il~~~~~~~q~l~~SAT~ 318 (545)
T PTZ00110 289 MLDMG---------FEPQIRKIVSQIRPDRQTLMWSATW 318 (545)
T ss_pred hhhcc---------hHHHHHHHHHhCCCCCeEEEEEeCC
Confidence 87541 112233333333 677899999993
No 71
>PRK10689 transcription-repair coupling factor; Provisional
Probab=94.55 E-value=0.063 Score=70.99 Aligned_cols=156 Identities=15% Similarity=0.147 Sum_probs=91.2
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGA 295 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~ 295 (1102)
.+|.-|.++|.-.-+.-+. +.....++--.||.||+-+..-.++....+|. +++.+.-...|-....+.++....
T Consensus 600 ~~T~~Q~~aI~~il~d~~~----~~~~d~Ll~a~TGsGKT~val~aa~~~~~~g~-qvlvLvPT~eLA~Q~~~~f~~~~~ 674 (1147)
T PRK10689 600 ETTPDQAQAINAVLSDMCQ----PLAMDRLVCGDVGFGKTEVAMRAAFLAVENHK-QVAVLVPTTLLAQQHYDNFRDRFA 674 (1147)
T ss_pred CCCHHHHHHHHHHHHHhhc----CCCCCEEEEcCCCcCHHHHHHHHHHHHHHcCC-eEEEEeCcHHHHHHHHHHHHHhhc
Confidence 4778999996643332111 11233455555999999865544555556665 499999999998888888887543
Q ss_pred C-cccccccCCCCCCcCCCCcc-ccc---cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCC
Q 038397 296 T-CIEVHALNKLPYSKLDSRSV-GIR---EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPE 370 (1102)
Q Consensus 296 ~-~i~v~~l~~~~~~~~~~~~~-~~~---~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~ 370 (1102)
. .+.+.-++.+...+-....+ .++ -.||.+|...|.. . +.|- + =++||+||+|++. .
T Consensus 675 ~~~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL~~-----~------v~~~--~-L~lLVIDEahrfG-~--- 736 (1147)
T PRK10689 675 NWPVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLLQS-----D------VKWK--D-LGLLIVDEEHRFG-V--- 736 (1147)
T ss_pred cCCceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHHhC-----C------CCHh--h-CCEEEEechhhcc-h---
Confidence 2 34444443321100000001 122 2499999865531 1 1121 1 2689999999972 1
Q ss_pred CCCCchhHHHHHHHHhhhCCCccEEEEecCCCC
Q 038397 371 AGSQPTRTGEAVLELQARLPEARVVYCSATGAS 403 (1102)
Q Consensus 371 ~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgas 403 (1102)
++ ...|....++.+|+..|||-..
T Consensus 737 ------~~---~e~lk~l~~~~qvLl~SATpip 760 (1147)
T PRK10689 737 ------RH---KERIKAMRADVDILTLTATPIP 760 (1147)
T ss_pred ------hH---HHHHHhcCCCCcEEEEcCCCCH
Confidence 11 1234455568899999999643
No 72
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=94.44 E-value=0.068 Score=64.98 Aligned_cols=155 Identities=15% Similarity=0.140 Sum_probs=90.0
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhc---------cCceEEEEEcCCchhhhH
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHH---------GRRKALWISVGSDLKFDA 286 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~---------Gr~~~~w~s~s~~L~~Da 286 (1102)
.++.-|.+++-.+.+ + .-.++--.||-||+-.----|+.+.+. ...++|+++-...|-...
T Consensus 143 ~ptpiQ~~aip~il~-g---------~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~~aLIL~PTreLa~Qi 212 (518)
T PLN00206 143 FPTPIQMQAIPAALS-G---------RSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNPLAMVLTPTRELCVQV 212 (518)
T ss_pred CCCHHHHHHHHHHhc-C---------CCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCceEEEEeCCHHHHHHH
Confidence 477889999766653 2 234566679999985322223443321 234699999999998776
Q ss_pred HhhhhhhCCC-cccccccCCCCCCc-CCCCccccc--cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecch
Q 038397 287 RRDLDDVGAT-CIEVHALNKLPYSK-LDSRSVGIR--EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECH 362 (1102)
Q Consensus 287 ~RDl~diG~~-~i~v~~l~~~~~~~-~~~~~~~~~--~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH 362 (1102)
.+-++.++.. .+.+..+.. |. .......+. --||.+|.-.|..--.++...|+. =.+|||||||
T Consensus 213 ~~~~~~l~~~~~~~~~~~~g---G~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~~~~~l~~---------v~~lViDEad 280 (518)
T PLN00206 213 EDQAKVLGKGLPFKTALVVG---GDAMPQQLYRIQQGVELIVGTPGRLIDLLSKHDIELDN---------VSVLVLDEVD 280 (518)
T ss_pred HHHHHHHhCCCCceEEEEEC---CcchHHHHHHhcCCCCEEEECHHHHHHHHHcCCccchh---------eeEEEeecHH
Confidence 6666666532 222211100 00 000001122 349999987765431111111211 1489999999
Q ss_pred hccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCC
Q 038397 363 KAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 363 ~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATg 401 (1102)
.+.... -...+.++-..+|+.+++..|||-
T Consensus 281 ~ml~~g---------f~~~i~~i~~~l~~~q~l~~SATl 310 (518)
T PLN00206 281 CMLERG---------FRDQVMQIFQALSQPQVLLFSATV 310 (518)
T ss_pred HHhhcc---------hHHHHHHHHHhCCCCcEEEEEeeC
Confidence 986431 223456677788999999999994
No 73
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=94.17 E-value=0.071 Score=63.53 Aligned_cols=76 Identities=18% Similarity=0.287 Sum_probs=59.3
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRF 885 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRF 885 (1102)
+.|.+|+..|+|-++.++.||-+..-. +=|-..+|.+++.-||+.|||+|.++. +--|.++.. .|.+.
T Consensus 286 ~~F~~g~~~vLVaTdv~~rGiDi~~v~--------~VI~~d~p~~~~~yiqR~GRtGR~g~~-G~ai~l~~~---~e~~~ 353 (460)
T PRK11776 286 VRFANRSCSVLVATDVAARGLDIKALE--------AVINYELARDPEVHVHRIGRTGRAGSK-GLALSLVAP---EEMQR 353 (460)
T ss_pred HHHHcCCCcEEEEecccccccchhcCC--------eEEEecCCCCHhHhhhhcccccCCCCc-ceEEEEEch---hHHHH
Confidence 689999999999999999999988654 344578999999999999999999874 445555443 36666
Q ss_pred HHHHHHHH
Q 038397 886 ASIVAKRL 893 (1102)
Q Consensus 886 aS~VAkRL 893 (1102)
...+.+.+
T Consensus 354 ~~~i~~~~ 361 (460)
T PRK11776 354 ANAIEDYL 361 (460)
T ss_pred HHHHHHHh
Confidence 66665543
No 74
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=94.15 E-value=0.0072 Score=50.49 Aligned_cols=47 Identities=28% Similarity=0.970 Sum_probs=36.8
Q ss_pred ccccCcHHHHhhhhhccccCCccccCCCCCCcc--cCCCCCCccccchh
Q 038397 663 CEICNSEEERKKLLQCSCCGQLVHSGCLVPPIT--DVIPSDWSCHSCKE 709 (1102)
Q Consensus 663 ce~cgsed~k~kLL~cs~cgk~~H~~cL~PP~~--di~~~dW~c~sCke 709 (1102)
|.+|+..++...++.|+.|++.+|..|+.|+.. ..+.+.|.|+.|+.
T Consensus 2 C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 2 CPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp BTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred CcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 455666555667899999999999999999875 44455999999974
No 75
>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=93.98 E-value=0.57 Score=58.21 Aligned_cols=237 Identities=20% Similarity=0.252 Sum_probs=131.8
Q ss_pred cceeEeecCCCCCcchhhHHHHHHHHhccCce------EEE--EEcCCchhhhHHhhhhh-hCCCcccc--cccCCCCCC
Q 038397 241 RAGFFIGDGAGVGKGRTIAGLIWENWHHGRRK------ALW--ISVGSDLKFDARRDLDD-VGATCIEV--HALNKLPYS 309 (1102)
Q Consensus 241 R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~------~~w--~s~s~~L~~Da~RDl~d-iG~~~i~v--~~l~~~~~~ 309 (1102)
..|=++||-.|.||+-++-.+|++.-..-+.+ +-| |=....|.+-.+-...+ +....+.| |+-++. -
T Consensus 345 ~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~PaSli~qW~~Ev~~rl~~n~LsV~~~HG~n~--r 422 (901)
T KOG4439|consen 345 PSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPASLIHQWEAEVARRLEQNALSVYLYHGPNK--R 422 (901)
T ss_pred CCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcHHHHHHHHHHHHHHHhhcceEEEEecCCcc--c
Confidence 34557999999999998777777654321110 001 00111122211111100 11122222 222222 1
Q ss_pred cCCCCccccccceEEeehhhhhh----cc--ccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHH
Q 038397 310 KLDSRSVGIREGVVFLTYSSLIA----SS--EKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVL 383 (1102)
Q Consensus 310 ~~~~~~~~~~~GvlF~TYs~L~~----~~--~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl 383 (1102)
.|+.+.. -+..||.+||...-. +. .+..|=|.+ |.|- -|||||+|.-+|.- |++..||-
T Consensus 423 ~i~~~~L-~~YDvViTTY~lva~~~~~e~~~~~~~spL~~-I~W~------RVILDEAH~IrN~~-------tq~S~AVC 487 (901)
T KOG4439|consen 423 EISAKEL-RKYDVVITTYNLVANKPDDELEEGKNSSPLAR-IAWS------RVILDEAHNIRNSN-------TQCSKAVC 487 (901)
T ss_pred cCCHHHH-hhcceEEEeeeccccCCchhhhcccCccHHHH-hhHH------Hhhhhhhhhhcccc-------hhHHHHHH
Confidence 1211111 367899999987654 11 122455655 6894 79999999999985 89999999
Q ss_pred HHhhhCCCccEEEEecCCCCCCCccchhhhccccCCCCCCCCHHHHHHHHhccChhHHHHHHHHHHhccceeeec-----
Q 038397 384 ELQARLPEARVVYCSATGASEPRNMGYMVRLGLWGAGTCFKDFQIFLGALDKGGVGALELVAMDMKARGMYVCRT----- 458 (1102)
Q Consensus 384 ~LQ~~lP~ARvvY~SATgasep~Nl~ym~RLGLWg~gt~f~~~~~f~~a~~~gGv~amE~va~dlK~~G~yiaR~----- 458 (1102)
.|+.. .|= -.|+|..- .|+--+--|=.|=.-.||-++..+.+.|...--+..+-+. |+-.-++++|+
T Consensus 488 ~L~a~---~RW-clTGTPiq--Nn~~DvysLlrFLr~~pF~D~~~Wke~i~~~s~~g~~rln--ll~K~LmLRRTKdQl~ 559 (901)
T KOG4439|consen 488 KLSAK---SRW-CLTGTPIQ--NNLWDVYSLLRFLRCPPFGDLKQWKENIDNMSKGGANRLN--LLTKSLMLRRTKDQLQ 559 (901)
T ss_pred HHhhc---cee-ecccCccc--cchhHHHHHHHHhcCCCcchHHHHHHhccCccccchhhhh--hhhhhHHhhhhHHhhc
Confidence 99877 232 12444443 3433222222232335787777777776644333333332 23334566661
Q ss_pred -----cCCCCceeEEEeccCcHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 038397 459 -----LSYKGAEFEVIEAPLEAEMTDMYKKAAEFWAELRVELLSASAFL 502 (1102)
Q Consensus 459 -----LSf~gvef~i~e~~l~~~~~~~Yd~~a~~w~~~~~~~~~a~e~~ 502 (1102)
-..-.-.+++.++.|+.+-..+|+-..++=..+.+.|....+-.
T Consensus 560 a~~klv~Lp~k~i~l~~leLs~~E~~vY~i~~~askk~~kq~L~~~e~~ 608 (901)
T KOG4439|consen 560 ANGKLVNLPEKNIELHELELSGDEAKVYQIMMEASKKLFKQFLLQREDR 608 (901)
T ss_pred cccccccCcccceEEEEEeecchHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 14455678888899999999999987777666666665555544
No 76
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=93.89 E-value=0.029 Score=68.19 Aligned_cols=49 Identities=33% Similarity=0.883 Sum_probs=42.2
Q ss_pred cccccCcHHHHhhhhhccccCCccccCCCCCCc--ccCCCCCCccccchhh
Q 038397 662 ICEICNSEEERKKLLQCSCCGQLVHSGCLVPPI--TDVIPSDWSCHSCKEK 710 (1102)
Q Consensus 662 ~ce~cgsed~k~kLL~cs~cgk~~H~~cL~PP~--~di~~~dW~c~sCkek 710 (1102)
.|..|+....-..++.|++|.+.+|+.||.||+ ..+|.++|+|+.|+.+
T Consensus 255 fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k 305 (613)
T KOG4299|consen 255 FCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIK 305 (613)
T ss_pred HHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence 588888776666678999999999999999995 4689999999999854
No 77
>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB. This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=93.52 E-value=0.38 Score=61.81 Aligned_cols=147 Identities=22% Similarity=0.267 Sum_probs=77.5
Q ss_pred chhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhh-hhCCCc-
Q 038397 220 LQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLD-DVGATC- 297 (1102)
Q Consensus 220 ~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~-diG~~~- 297 (1102)
..++.|..+.+.|... ++---||.||+-++-=.|+++...+ .+++-+.-.-.+-.-+.+-+. .+|...
T Consensus 5 ~~~~~i~~~l~~~~~v---------Ii~a~TGSGKTT~vpl~lL~~~~~~-~~ilvlqPrR~aA~qiA~rva~~~~~~~g 74 (819)
T TIGR01970 5 AVLPALRDALAAHPQV---------VLEAPPGAGKSTAVPLALLDAPGIG-GKIIMLEPRRLAARSAAQRLASQLGEAVG 74 (819)
T ss_pred HHHHHHHHHHHcCCcE---------EEECCCCCCHHHHHHHHHHHhhccC-CeEEEEeCcHHHHHHHHHHHHHHhCCCcC
Confidence 4456777777777432 3333399999999998899886433 235444434333333333332 222110
Q ss_pred ccccccCCCCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCC--ceEEeecchh-ccccCCCCCCC
Q 038397 298 IEVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYD--GLVIFDECHK-AKNLVPEAGSQ 374 (1102)
Q Consensus 298 i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfd--gvivfDEcH~-akn~~~~~~~~ 374 (1102)
..| . ..+.. + ....-+.-|+|+|.-.|... ++ . ..++. ++|||||+|. .-+.
T Consensus 75 ~~V-G-y~vr~---~-~~~s~~t~I~v~T~G~Llr~-------l~---~--d~~L~~v~~VIiDEaHER~L~~------- 129 (819)
T TIGR01970 75 QTV-G-YRVRG---E-NKVSRRTRLEVVTEGILTRM-------IQ---D--DPELDGVGALIFDEFHERSLDA------- 129 (819)
T ss_pred cEE-E-EEEcc---c-cccCCCCcEEEECCcHHHHH-------Hh---h--CcccccCCEEEEeccchhhhcc-------
Confidence 001 0 00000 0 01122345889988666421 11 1 01122 4999999995 5443
Q ss_pred chhHHHHH-HHHhhhC-CCccEEEEecCCCC
Q 038397 375 PTRTGEAV-LELQARL-PEARVVYCSATGAS 403 (1102)
Q Consensus 375 ~s~~g~av-l~LQ~~l-P~ARvvY~SATgas 403 (1102)
..+.+. .+++..+ ++.++|.+|||-..
T Consensus 130 --Dl~L~ll~~i~~~lr~dlqlIlmSATl~~ 158 (819)
T TIGR01970 130 --DLGLALALDVQSSLREDLKILAMSATLDG 158 (819)
T ss_pred --chHHHHHHHHHHhcCCCceEEEEeCCCCH
Confidence 233333 3455544 57899999999543
No 78
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=93.37 E-value=0.076 Score=63.66 Aligned_cols=63 Identities=21% Similarity=0.316 Sum_probs=51.2
Q ss_pred HhhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEee
Q 038397 805 KQLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIF 876 (1102)
Q Consensus 805 k~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~ 876 (1102)
-+.|.+|+.+|+|-+++++-||-+..= ++=|.+.+|+|.+..+|+.||++|.|+- +--|.|+.
T Consensus 378 ~~~Fr~G~~~vLvaT~~l~~GIDi~~v--------~~VI~~~~P~s~~~y~Qr~GRaGR~g~~-g~~i~~~~ 440 (475)
T PRK01297 378 LEGFREGKIRVLVATDVAGRGIHIDGI--------SHVINFTLPEDPDDYVHRIGRTGRAGAS-GVSISFAG 440 (475)
T ss_pred HHHHhCCCCcEEEEccccccCCcccCC--------CEEEEeCCCCCHHHHHHhhCccCCCCCC-ceEEEEec
Confidence 478999999999999999999987543 2445678999999999999999999984 33454443
No 79
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=93.33 E-value=0.13 Score=61.58 Aligned_cols=155 Identities=14% Similarity=0.164 Sum_probs=91.0
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccC--------ceEEEEEcCCchhhhHH
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGR--------RKALWISVGSDLKFDAR 287 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr--------~~~~w~s~s~~L~~Da~ 287 (1102)
.++.-|.++|-...+. .-.++-=.||.||+-...--|++.+..+. .++|++.-.-.|-.+..
T Consensus 23 ~pt~iQ~~ai~~il~g----------~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLil~PtreLa~Qi~ 92 (456)
T PRK10590 23 EPTPIQQQAIPAVLEG----------RDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTRELAAQIG 92 (456)
T ss_pred CCCHHHHHHHHHHhCC----------CCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEEEeCcHHHHHHHH
Confidence 4678899997665532 23566667999998776555677665422 36999999999998888
Q ss_pred hhhhhhCCC-cccccccC-CCCCCcCCCCcccc--ccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchh
Q 038397 288 RDLDDVGAT-CIEVHALN-KLPYSKLDSRSVGI--REGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHK 363 (1102)
Q Consensus 288 RDl~diG~~-~i~v~~l~-~~~~~~~~~~~~~~--~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~ 363 (1102)
+.++.+... .+.+..+. .... +.....+ .-.||++|.-.|........-.|+ -=.+||+||||.
T Consensus 93 ~~~~~~~~~~~~~~~~~~gg~~~---~~~~~~l~~~~~IiV~TP~rL~~~~~~~~~~l~---------~v~~lViDEah~ 160 (456)
T PRK10590 93 ENVRDYSKYLNIRSLVVFGGVSI---NPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLD---------QVEILVLDEADR 160 (456)
T ss_pred HHHHHHhccCCCEEEEEECCcCH---HHHHHHHcCCCcEEEEChHHHHHHHHcCCcccc---------cceEEEeecHHH
Confidence 888876432 22222110 0000 0000011 235999998777543211111111 124899999999
Q ss_pred ccccCCCCCCCchhHHHHHHHHhhhCCCc-cEEEEecCC
Q 038397 364 AKNLVPEAGSQPTRTGEAVLELQARLPEA-RVVYCSATG 401 (1102)
Q Consensus 364 akn~~~~~~~~~s~~g~avl~LQ~~lP~A-RvvY~SATg 401 (1102)
+.... ....+..+-+.+|.- ++++.|||-
T Consensus 161 ll~~~---------~~~~i~~il~~l~~~~q~l~~SAT~ 190 (456)
T PRK10590 161 MLDMG---------FIHDIRRVLAKLPAKRQNLLFSATF 190 (456)
T ss_pred Hhccc---------cHHHHHHHHHhCCccCeEEEEeCCC
Confidence 86431 122333344556655 589999994
No 80
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=93.19 E-value=0.086 Score=65.76 Aligned_cols=35 Identities=23% Similarity=0.600 Sum_probs=24.4
Q ss_pred cCCCccceeeccCCCccccCCCCCcccccccccccccCCCCC
Q 038397 98 PCANCKAILNVPHGLVRFSCPQCAVELAVDMSKVKQFFPPPP 139 (1102)
Q Consensus 98 ~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~~~~~~~~~~~~~ 139 (1102)
+|.+||+.+ |.+ .--||.||..+.- ....+|.+++
T Consensus 29 ~Cp~CG~~~--~~~--~~fC~~CG~~~~~---~~~~~~~~~~ 63 (645)
T PRK14559 29 PCPQCGTEV--PVD--EAHCPNCGAETGT---IWWAIIAQAS 63 (645)
T ss_pred cCCCCCCCC--Ccc--cccccccCCcccc---hhhhhccccc
Confidence 699999984 333 4489999999765 3555664443
No 81
>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=92.95 E-value=0.21 Score=65.22 Aligned_cols=142 Identities=20% Similarity=0.201 Sum_probs=96.8
Q ss_pred CCcceeEeecCCCCCcchhh---HHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCc
Q 038397 239 SARAGFFIGDGAGVGKGRTI---AGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRS 315 (1102)
Q Consensus 239 g~R~Gf~~gDg~GvGKGR~~---AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~ 315 (1102)
|.+.|.+|-==+|-||+-++ |+.++++ .+-.++++|+-..||-+=....+..++-...... .......+. +.
T Consensus 271 ~~~~~G~IWHtqGSGKTlTm~~~A~~l~~~--~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~--~~~s~~~Lk-~~ 345 (962)
T COG0610 271 GDGKGGYIWHTQGSGKTLTMFKLARLLLEL--PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP--KAESTSELK-EL 345 (962)
T ss_pred CcCCceEEEeecCCchHHHHHHHHHHHHhc--cCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc--cccCHHHHH-HH
Confidence 78888899888999999886 6778888 6777899999998888877777777776533221 111111100 01
Q ss_pred c-ccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccE
Q 038397 316 V-GIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARV 394 (1102)
Q Consensus 316 ~-~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARv 394 (1102)
+ ..+.||||||==-|...-.+. ..|.-..-+=|||+||||+ |+.|...-.+...+|+|..
T Consensus 346 l~~~~~~ii~TTIQKf~~~~~~~-------~~~~~~~~~ivvI~DEaHR------------SQ~G~~~~~~~~~~~~a~~ 406 (962)
T COG0610 346 LEDGKGKIIVTTIQKFNKAVKED-------ELELLKRKNVVVIIDEAHR------------SQYGELAKLLKKALKKAIF 406 (962)
T ss_pred HhcCCCcEEEEEecccchhhhcc-------cccccCCCcEEEEEechhh------------ccccHHHHHHHHHhccceE
Confidence 1 126799999976665432221 1122234566999999999 8889999999999999766
Q ss_pred EEEecCCCCC
Q 038397 395 VYCSATGASE 404 (1102)
Q Consensus 395 vY~SATgase 404 (1102)
.=-++|....
T Consensus 407 ~gFTGTPi~~ 416 (962)
T COG0610 407 IGFTGTPIFK 416 (962)
T ss_pred EEeeCCcccc
Confidence 6666665543
No 82
>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type. subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.
Probab=92.88 E-value=0.45 Score=55.35 Aligned_cols=46 Identities=15% Similarity=0.200 Sum_probs=33.6
Q ss_pred eEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhh
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
+|++=.||-||+-...-.|+. ...+++++.-...|..|-.+.|+..
T Consensus 17 ~~i~apTGsGKT~~~~~~~l~----~~~~~~~~~P~~aL~~~~~~~~~~~ 62 (357)
T TIGR03158 17 IFNTAPTGAGKTLAWLTPLLH----GENDTIALYPTNALIEDQTEAIKEF 62 (357)
T ss_pred EEEECCCCCCHHHHHHHHHHH----cCCCEEEEeChHHHHHHHHHHHHHH
Confidence 577888999997543222332 3346899998999999988888876
No 83
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=92.85 E-value=0.26 Score=54.71 Aligned_cols=89 Identities=21% Similarity=0.398 Sum_probs=64.6
Q ss_pred CCCCccceeecCCcceEEEeCCCcceecCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCC
Q 038397 10 PPPNVGVQVRCAGCHIILTVGPGLTEFICGT--CNLPQMLPPELMPASTGGSVPNNTTSSNTTNSTRPTHMKAASSHVPA 87 (1102)
Q Consensus 10 ~~~~~~~~~~C~~C~a~l~~~pg~~~~~Cp~--C~~~~~l~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a 87 (1102)
.|||++--|||+ |.+.|--.--.+...||- |.....|.|.. . .|. .+++
T Consensus 99 ~aPpGKKYVRCP-CNCLLICk~sS~rIaCPRp~CkRiI~L~~~~------~-~p~--~~~~------------------- 149 (256)
T PF09788_consen 99 NAPPGKKYVRCP-CNCLLICKSSSQRIACPRPNCKRIINLGPSH------Q-GPV--TPPV------------------- 149 (256)
T ss_pred CCCCCCeeEecC-CceEEEeecccccccCCCCCCcceEEeCCcc------C-CCC--CCCC-------------------
Confidence 567899999996 999999999999999987 99999886653 1 010 0000
Q ss_pred CCCCCccceecCCCccceeeccCCC-ccc-cCCCCCccccccc
Q 038397 88 LGIDPTKIQLPCANCKAILNVPHGL-VRF-SCPQCAVELAVDM 128 (1102)
Q Consensus 88 ~~~~~t~~~~~C~~C~A~~~vp~~~-~~f-~Cp~C~~~L~v~~ 128 (1102)
-..|.-.++-|++|.-.+-.+.-. ..+ +||.|..--.|-.
T Consensus 150 -~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSVG~ 191 (256)
T PF09788_consen 150 -PTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSVGP 191 (256)
T ss_pred -CCCCCceeEECCCCCCcEeccCCCCCccccCCCCceeccccc
Confidence 012233469999999999988655 355 9999997666653
No 84
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=92.85 E-value=0.069 Score=62.93 Aligned_cols=54 Identities=19% Similarity=0.370 Sum_probs=48.3
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQA 867 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQv 867 (1102)
+.|.+|+..|+|-+++++.||-+..- ++-|-+.+|+|.+.-+|+.|||+|.++.
T Consensus 299 ~~F~~g~~~vLVaTdv~~rGiDip~v--------~~VI~~d~P~s~~~yiqR~GR~gR~G~~ 352 (423)
T PRK04837 299 EEFTRGDLDILVATDVAARGLHIPAV--------THVFNYDLPDDCEDYVHRIGRTGRAGAS 352 (423)
T ss_pred HHHHcCCCcEEEEechhhcCCCcccc--------CEEEEeCCCCchhheEeccccccCCCCC
Confidence 68999999999999999999998753 3456788999999999999999999975
No 85
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=92.67 E-value=0.067 Score=55.10 Aligned_cols=27 Identities=37% Similarity=0.855 Sum_probs=24.9
Q ss_pred ccccCCCCCCcccCCCCCCccccchhh
Q 038397 684 LVHSGCLVPPITDVIPSDWSCHSCKEK 710 (1102)
Q Consensus 684 ~~H~~cL~PP~~di~~~dW~c~sCkek 710 (1102)
++|..||.||+..+|.++|+|+.|..+
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~~ 27 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEVE 27 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcCC
Confidence 589999999999999999999999854
No 86
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=92.62 E-value=0.52 Score=60.63 Aligned_cols=141 Identities=21% Similarity=0.245 Sum_probs=73.0
Q ss_pred chhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHH-hccCceEEEEEcCC-chhhhHHhhhh-hhCCC
Q 038397 220 LQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENW-HHGRRKALWISVGS-DLKFDARRDLD-DVGAT 296 (1102)
Q Consensus 220 ~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~-l~Gr~~~~w~s~s~-~L~~Da~RDl~-diG~~ 296 (1102)
..++.|.-+.+.|.. .++-=.||.||+-++--.|+++. .+| +++ +.... .+-.-+.+-+. .+|..
T Consensus 8 ~~~~~i~~~l~~~~~---------vvv~A~TGSGKTt~~pl~lL~~~~~~~--~il-vlqPrR~aA~qia~rva~~l~~~ 75 (812)
T PRK11664 8 AVLPELLTALKTAPQ---------VLLKAPTGAGKSTWLPLQLLQHGGING--KII-MLEPRRLAARNVAQRLAEQLGEK 75 (812)
T ss_pred HHHHHHHHHHHhCCC---------EEEEcCCCCCHHHHHHHHHHHcCCcCC--eEE-EECChHHHHHHHHHHHHHHhCcc
Confidence 345666777777633 23333499999999988888764 333 333 44432 33332223232 12221
Q ss_pred c-ccccccCCCCCCcCCC-CccccccceEEeehhhhhhccccccchHHHHHHHhcc--CCC--ceEEeecchhc-cccCC
Q 038397 297 C-IEVHALNKLPYSKLDS-RSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGS--GYD--GLVIFDECHKA-KNLVP 369 (1102)
Q Consensus 297 ~-i~v~~l~~~~~~~~~~-~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~--dfd--gvivfDEcH~a-kn~~~ 369 (1102)
. ..| -| .+.. ....-..-|+|+|.-.|.. ++.. +++ ++|||||+|+- -+.
T Consensus 76 ~g~~V------Gy-~vr~~~~~~~~t~I~v~T~G~Llr--------------~l~~d~~L~~v~~IIlDEaHER~l~~-- 132 (812)
T PRK11664 76 PGETV------GY-RMRAESKVGPNTRLEVVTEGILTR--------------MIQRDPELSGVGLVILDEFHERSLQA-- 132 (812)
T ss_pred cCceE------EE-EecCccccCCCCcEEEEChhHHHH--------------HHhhCCCcCcCcEEEEcCCCcccccc--
Confidence 0 000 00 0000 0111223588999866642 2221 223 49999999982 221
Q ss_pred CCCCCchhHHHH-HHHHhhhC-CCccEEEEecCCC
Q 038397 370 EAGSQPTRTGEA-VLELQARL-PEARVVYCSATGA 402 (1102)
Q Consensus 370 ~~~~~~s~~g~a-vl~LQ~~l-P~ARvvY~SATga 402 (1102)
....+ ..++++.+ ++.++|.+|||--
T Consensus 133 -------Dl~L~ll~~i~~~lr~~lqlilmSATl~ 160 (812)
T PRK11664 133 -------DLALALLLDVQQGLRDDLKLLIMSATLD 160 (812)
T ss_pred -------chHHHHHHHHHHhCCccceEEEEecCCC
Confidence 22222 23455544 6789999999953
No 87
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=92.28 E-value=0.76 Score=56.85 Aligned_cols=155 Identities=18% Similarity=0.145 Sum_probs=90.4
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchh--hHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRT--IAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~--~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
.|.+-|.++|....+.+ -.++-=.||-||+-. +.++ +++. .++.++-.-.|..|-.+.|+..
T Consensus 13 ~fr~~Q~~~i~~il~g~----------dvlv~~PTG~GKTl~y~lpal-----~~~g-~~lVisPl~sL~~dq~~~l~~~ 76 (591)
T TIGR01389 13 DFRPGQEEIISHVLDGR----------DVLVVMPTGGGKSLCYQVPAL-----LLKG-LTVVISPLISLMKDQVDQLRAA 76 (591)
T ss_pred CCCHHHHHHHHHHHcCC----------CEEEEcCCCccHhHHHHHHHH-----HcCC-cEEEEcCCHHHHHHHHHHHHHc
Confidence 35678999965554322 245666799999864 3333 3343 3788888889999998999988
Q ss_pred CCCcccccccCC-CCCCcCCC--Ccc-ccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCC
Q 038397 294 GATCIEVHALNK-LPYSKLDS--RSV-GIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVP 369 (1102)
Q Consensus 294 G~~~i~v~~l~~-~~~~~~~~--~~~-~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~ 369 (1102)
|.. +.-++. ........ ..+ .-.-.+|++|.-.|.+. ++...+. ..-=++||+||||.....
T Consensus 77 gi~---~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~------~~~~~l~---~~~l~~iViDEaH~i~~~-- 142 (591)
T TIGR01389 77 GVA---AAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQD------YFLNMLQ---RIPIALVAVDEAHCVSQW-- 142 (591)
T ss_pred CCc---EEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcCh------HHHHHHh---cCCCCEEEEeCCcccccc--
Confidence 743 222221 11100000 000 01235899988877532 2222222 222368999999987532
Q ss_pred CCCCCchhHHHHHHHHhhhCCCccEEEEecCCC
Q 038397 370 EAGSQPTRTGEAVLELQARLPEARVVYCSATGA 402 (1102)
Q Consensus 370 ~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATga 402 (1102)
|..--..=..+..|.+.+|+..|+-.|||..
T Consensus 143 --g~~frp~y~~l~~l~~~~~~~~vi~lTAT~~ 173 (591)
T TIGR01389 143 --GHDFRPEYQRLGSLAERFPQVPRIALTATAD 173 (591)
T ss_pred --cCccHHHHHHHHHHHHhCCCCCEEEEEeCCC
Confidence 1110111134556778899999999999954
No 88
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=91.88 E-value=0.29 Score=66.09 Aligned_cols=134 Identities=22% Similarity=0.215 Sum_probs=81.5
Q ss_pred CCCCCcchhhHHH--HHHHHhc------------cCceEEEEEcCCchhhhHHhhhhh----hC-------CC--ccccc
Q 038397 249 GAGVGKGRTIAGL--IWENWHH------------GRRKALWISVGSDLKFDARRDLDD----VG-------AT--CIEVH 301 (1102)
Q Consensus 249 g~GvGKGR~~Agi--I~~n~l~------------Gr~~~~w~s~s~~L~~Da~RDl~d----iG-------~~--~i~v~ 301 (1102)
.||-|| +.|+. |+++.++ ...++|+||-...|-.|..+.|+. |. .. .|.|.
T Consensus 4 PTGSGK--TLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V~ 81 (1490)
T PRK09751 4 PTGSGK--TLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRVG 81 (1490)
T ss_pred CCCcHH--HHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEEE
Confidence 366666 45553 6677653 135799999999999999999874 32 11 12221
Q ss_pred ccCCCCCCcCCCCc----cccccceEEeehhhhhhc-cccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCch
Q 038397 302 ALNKLPYSKLDSRS----VGIREGVVFLTYSSLIAS-SEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPT 376 (1102)
Q Consensus 302 ~l~~~~~~~~~~~~----~~~~~GvlF~TYs~L~~~-~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s 376 (1102)
.+ .|....+. +.-+-.||.+|.-+|..- +.+. | .|+.. =..||+||+|.+.+.. ..+
T Consensus 82 vr----tGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~--r-----~~L~~--Vr~VIVDE~H~L~g~k-----RG~ 143 (1490)
T PRK09751 82 IR----TGDTPAQERSKLTRNPPDILITTPESLYLMLTSRA--R-----ETLRG--VETVIIDEVHAVAGSK-----RGA 143 (1490)
T ss_pred EE----ECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhh--h-----hhhcc--CCEEEEecHHHhcccc-----ccc
Confidence 11 12111111 112347999999988542 1111 1 13321 1489999999987531 225
Q ss_pred hHHHHHHHHhhhCC-CccEEEEecCCC
Q 038397 377 RTGEAVLELQARLP-EARVVYCSATGA 402 (1102)
Q Consensus 377 ~~g~avl~LQ~~lP-~ARvvY~SATga 402 (1102)
.....+.+|...++ +.++|-.|||=.
T Consensus 144 ~Lel~LeRL~~l~~~~~QrIgLSATI~ 170 (1490)
T PRK09751 144 HLALSLERLDALLHTSAQRIGLSATVR 170 (1490)
T ss_pred HHHHHHHHHHHhCCCCCeEEEEEeeCC
Confidence 56667778887775 579999999953
No 89
>PRK04023 DNA polymerase II large subunit; Validated
Probab=91.66 E-value=0.12 Score=65.89 Aligned_cols=24 Identities=21% Similarity=0.517 Sum_probs=19.5
Q ss_pred ecCCCccceeeccCCCccccCCCCCccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
..|..||...+. ..||-||.++..
T Consensus 652 ~fCP~CG~~~~~------y~CPKCG~El~~ 675 (1121)
T PRK04023 652 YRCPRCGIEVEE------DECEKCGREPTP 675 (1121)
T ss_pred eeCccccCcCCC------CcCCCCCCCCCc
Confidence 689999887663 459999999765
No 90
>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.65 E-value=0.22 Score=59.74 Aligned_cols=56 Identities=25% Similarity=0.265 Sum_probs=48.5
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASA 869 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsa 869 (1102)
+.|.+|+..|.|-++|.+.||-+-.- |+=|-..+|.|...-+|+.||++|.++...
T Consensus 270 ~~F~~g~~~vLVaT~~~~~GID~p~V--------~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~ 325 (470)
T TIGR00614 270 HKFQRDEIQVVVATVAFGMGINKPDV--------RFVIHYSLPKSMESYYQESGRAGRDGLPSE 325 (470)
T ss_pred HHHHcCCCcEEEEechhhccCCcccc--------eEEEEeCCCCCHHHHHhhhcCcCCCCCCce
Confidence 68999999999999999999987642 345666899999999999999999988654
No 91
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=91.65 E-value=0.12 Score=40.93 Aligned_cols=29 Identities=21% Similarity=0.587 Sum_probs=23.6
Q ss_pred ceeecCCcceEEEeCCC-----cceecCCCCCCC
Q 038397 16 VQVRCAGCHIILTVGPG-----LTEFICGTCNLP 44 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~pg-----~~~~~Cp~C~~~ 44 (1102)
+.+.|++|++.+.+++. ...+.||.||..
T Consensus 1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 35789999999998853 347999999964
No 92
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=91.55 E-value=1 Score=48.00 Aligned_cols=63 Identities=21% Similarity=0.254 Sum_probs=42.3
Q ss_pred cccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHh-ccCceEEEEEcCCchhhhHHhh
Q 038397 217 LSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWH-HGRRKALWISVGSDLKFDARRD 289 (1102)
Q Consensus 217 LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l-~Gr~~~~w~s~s~~L~~Da~RD 289 (1102)
|++.|.++|.+..... .|--++.|. +|.||+..++.++ +.|. +| .++++++-++....+...+
T Consensus 2 L~~~Q~~a~~~~l~~~-------~~~~~l~G~-aGtGKT~~l~~~~-~~~~~~g-~~v~~~apT~~Aa~~L~~~ 65 (196)
T PF13604_consen 2 LNEEQREAVRAILTSG-------DRVSVLQGP-AGTGKTTLLKALA-EALEAAG-KRVIGLAPTNKAAKELREK 65 (196)
T ss_dssp S-HHHHHHHHHHHHCT-------CSEEEEEES-TTSTHHHHHHHHH-HHHHHTT---EEEEESSHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHhcC-------CeEEEEEEC-CCCCHHHHHHHHH-HHHHhCC-CeEEEECCcHHHHHHHHHh
Confidence 7899999999886543 233334455 9999999887754 4444 45 6699999887766665444
No 93
>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]
Probab=91.55 E-value=0.53 Score=60.44 Aligned_cols=152 Identities=20% Similarity=0.211 Sum_probs=84.5
Q ss_pred CCCccCcccccccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcC
Q 038397 200 EPTYDLLIKYDLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVG 279 (1102)
Q Consensus 200 ~~~y~~~lp~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s 279 (1102)
...|...||- ....+.|.+|.++|...+- .|. ||.||+-|+--+++|....+.. .|=+
T Consensus 42 ~~~~~~~LPv---------~~~~~~i~~ai~~~~vvii--------~ge-tGsGKTTqlP~~lle~g~~~~g-~I~~--- 99 (845)
T COG1643 42 ILEYRSGLPV---------TAVRDEILKAIEQNQVVII--------VGE-TGSGKTTQLPQFLLEEGLGIAG-KIGC--- 99 (845)
T ss_pred hhhccccCCc---------HHHHHHHHHHHHhCCEEEE--------eCC-CCCChHHHHHHHHHhhhcccCC-eEEe---
Confidence 3566777775 4556888999999966533 333 9999999999999999873332 3322
Q ss_pred CchhhhHHhhhhhhCCC-cccccccCCCCCCcCCCCccccccceEEeehhhhhhccccccchHH-----HHHHHhccCCC
Q 038397 280 SDLKFDARRDLDDVGAT-CIEVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQ-----QLVQWCGSGYD 353 (1102)
Q Consensus 280 ~~L~~Da~RDl~diG~~-~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~-----Ql~~W~g~dfd 353 (1102)
.+-+| +.++... .+. .-++ .+.|+ .++ .-|-|-.- ...+||++ .|+.||..|+.
T Consensus 100 ----tQPRR-lAArsvA~RvA-eel~-~~~G~----~VG--Y~iRfe~~-------~s~~Trik~mTdGiLlrei~~D~~ 159 (845)
T COG1643 100 ----TQPRR-LAARSVAERVA-EELG-EKLGE----TVG--YSIRFESK-------VSPRTRIKVMTDGILLREIQNDPL 159 (845)
T ss_pred ----cCchH-HHHHHHHHHHH-HHhC-CCcCc----eee--EEEEeecc-------CCCCceeEEeccHHHHHHHhhCcc
Confidence 23334 4333322 110 0010 01111 011 00111100 01123332 35677765433
Q ss_pred ----ceEEeecchhccccCCCCCCCchhHHHHHH-HHhhhCC-CccEEEEecCC
Q 038397 354 ----GLVIFDECHKAKNLVPEAGSQPTRTGEAVL-ELQARLP-EARVVYCSATG 401 (1102)
Q Consensus 354 ----gvivfDEcH~akn~~~~~~~~~s~~g~avl-~LQ~~lP-~ARvvY~SATg 401 (1102)
++|||||+|.=. -.|-.+++.+ ++|.++| +-|||-+|||-
T Consensus 160 Ls~ys~vIiDEaHERS--------l~tDilLgllk~~~~~rr~DLKiIimSATl 205 (845)
T COG1643 160 LSGYSVVIIDEAHERS--------LNTDILLGLLKDLLARRRDDLKLIIMSATL 205 (845)
T ss_pred cccCCEEEEcchhhhh--------HHHHHHHHHHHHHHhhcCCCceEEEEeccc
Confidence 499999999833 1144444444 3367777 69999999994
No 94
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=91.22 E-value=0.3 Score=59.57 Aligned_cols=80 Identities=23% Similarity=0.346 Sum_probs=65.1
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRF 885 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRF 885 (1102)
+.|++|+..|+|-+|.|+=||...-=..| |-..+|.+.|.-|++.|||+|.| ....=..+++. .+|.++
T Consensus 317 ~~F~~g~~~vLVaTDvaaRGiDi~~v~~V--------inyD~p~~~e~yvHRiGRTgRaG--~~G~ai~fv~~-~~e~~~ 385 (513)
T COG0513 317 EKFKDGELRVLVATDVAARGLDIPDVSHV--------INYDLPLDPEDYVHRIGRTGRAG--RKGVAISFVTE-EEEVKK 385 (513)
T ss_pred HHHHcCCCCEEEEechhhccCCcccccee--------EEccCCCCHHHheeccCccccCC--CCCeEEEEeCc-HHHHHH
Confidence 69999999999999999999987644333 77899999999999999999999 44555555555 568888
Q ss_pred HHHHHHHHhhc
Q 038397 886 ASIVAKRLESL 896 (1102)
Q Consensus 886 aS~VAkRLeSL 896 (1102)
...+.+.+..-
T Consensus 386 l~~ie~~~~~~ 396 (513)
T COG0513 386 LKRIEKRLERK 396 (513)
T ss_pred HHHHHHHHhcc
Confidence 88888886544
No 95
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.09 E-value=0.11 Score=45.62 Aligned_cols=31 Identities=23% Similarity=0.535 Sum_probs=27.4
Q ss_pred ecCCCccceeeccCCCccccCCCCCcccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAVD 127 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~ 127 (1102)
-.|.+||.++.+-++.+.|.||.||...+.-
T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~R 40 (61)
T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCGEVEIYR 40 (61)
T ss_pred ceeccCCCEeccCCceeEeeCCCCCceeeeh
Confidence 4799999999999999999999999765553
No 96
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=91.08 E-value=0.12 Score=37.76 Aligned_cols=24 Identities=29% Similarity=0.833 Sum_probs=19.9
Q ss_pred CCCccceeeccCCCccccCCCCCc
Q 038397 99 CANCKAILNVPHGLVRFSCPQCAV 122 (1102)
Q Consensus 99 C~~C~A~~~vp~~~~~f~Cp~C~~ 122 (1102)
|.+||+.+.--.-.++|.||-||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 889999998444477999999984
No 97
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=91.04 E-value=0.44 Score=59.35 Aligned_cols=25 Identities=24% Similarity=0.219 Sum_probs=11.1
Q ss_pred chHHHHHHHhcc-CCCceEEeecchh
Q 038397 339 SRLQQLVQWCGS-GYDGLVIFDECHK 363 (1102)
Q Consensus 339 sRl~Ql~~W~g~-dfdgvivfDEcH~ 363 (1102)
|=|..|++-|.+ +.|-+=+-||-|+
T Consensus 862 TLLHfLae~~e~kypd~l~F~ddl~h 887 (1102)
T KOG1924|consen 862 TLLHFLAEICEEKYPDILKFPDDLEH 887 (1102)
T ss_pred HHHHHHHHHHHHhChhhhcchhhHHH
Confidence 444555555543 3333334444443
No 98
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=90.90 E-value=0.071 Score=43.26 Aligned_cols=33 Identities=36% Similarity=0.803 Sum_probs=22.7
Q ss_pred eecCCcceEE----EeCCCcceecCCCCCCCCCCCCC
Q 038397 18 VRCAGCHIIL----TVGPGLTEFICGTCNLPQMLPPE 50 (1102)
Q Consensus 18 ~~C~~C~a~l----~~~pg~~~~~Cp~C~~~~~l~p~ 50 (1102)
+||..|+|.| ++..+...+.|+.|+..+.||++
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp~~ 39 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLPPH 39 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--EEE--GG
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCcCCCCCC
Confidence 6999999999 78899999999999998888764
No 99
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=90.73 E-value=0.22 Score=61.49 Aligned_cols=54 Identities=19% Similarity=0.446 Sum_probs=46.2
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQA 867 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQv 867 (1102)
+.|.+|+..|+|-+++++.||-+..=. +-|-..+|||.+.-||+.|||+|.+.-
T Consensus 301 ~~Fr~G~~~VLVaTdv~arGIDip~V~--------~VInyd~P~s~~~yvqRiGRaGR~G~~ 354 (572)
T PRK04537 301 NRFQKGQLEILVATDVAARGLHIDGVK--------YVYNYDLPFDAEDYVHRIGRTARLGEE 354 (572)
T ss_pred HHHHcCCCeEEEEehhhhcCCCccCCC--------EEEEcCCCCCHHHHhhhhcccccCCCC
Confidence 689999999999999999999765322 335568999999999999999999873
No 100
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=90.73 E-value=0.84 Score=57.63 Aligned_cols=99 Identities=19% Similarity=0.301 Sum_probs=67.2
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCC-cHhHHHHhhcccccCCCCCCCeEEEeecCcc----
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPW-SADRAIQQFGRTHRSNQASAPEYRIIFTNLG---- 880 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpW-sADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~---- 880 (1102)
+.|.+|+.+|+|-++..+.||....- ++.|....|. ....-+|+.||++|.++ +-|.+++++-+
T Consensus 525 ~~F~~g~~~ILVaT~vie~GiDip~v--------~~VIi~~~~r~gls~lhQ~~GRvGR~g~---~g~~ill~~~~~~~~ 593 (681)
T PRK10917 525 AAFKAGEIDILVATTVIEVGVDVPNA--------TVMVIENAERFGLAQLHQLRGRVGRGAA---QSYCVLLYKDPLSET 593 (681)
T ss_pred HHHHcCCCCEEEECcceeeCcccCCC--------cEEEEeCCCCCCHHHHHHHhhcccCCCC---ceEEEEEECCCCChh
Confidence 68999999999999999999987532 4556666664 56778899999999875 57888888533
Q ss_pred chhhhHHHHHH------------HHhhcCCccccccccCCCCCcCCcCChH
Q 038397 881 GERRFASIVAK------------RLESLGALTQGDRRAGLSLSAYNYDSAF 919 (1102)
Q Consensus 881 GErRFaS~VAk------------RLeSLGALT~GdRra~~~ls~fNldn~Y 919 (1102)
..+|+- ++++ +|+--|-+. |.|++| ++.|.+-+-+
T Consensus 594 ~~~rl~-~~~~~~dgf~iae~dl~~rg~g~~~-g~~q~g--~~~~~~~~~~ 640 (681)
T PRK10917 594 ARERLK-IMRETNDGFVIAEKDLELRGPGELL-GTRQSG--LPEFKVADLV 640 (681)
T ss_pred HHHHHH-HHHHhcchHHHHHHhHhhCCCcccc-CceecC--CCCeeEeeHh
Confidence 223332 3322 334444444 677776 4555555443
No 101
>PTZ00424 helicase 45; Provisional
Probab=90.61 E-value=0.18 Score=58.44 Aligned_cols=53 Identities=26% Similarity=0.407 Sum_probs=46.9
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQ 866 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQ 866 (1102)
+.|.+|+.+|+|-++.++-||-+..-.-+ |-+.+|.|....+|+.||++|.+.
T Consensus 311 ~~f~~g~~~vLvaT~~l~~GiDip~v~~V--------I~~~~p~s~~~y~qr~GRagR~g~ 363 (401)
T PTZ00424 311 REFRSGSTRVLITTDLLARGIDVQQVSLV--------INYDLPASPENYIHRIGRSGRFGR 363 (401)
T ss_pred HHHHcCCCCEEEEcccccCCcCcccCCEE--------EEECCCCCHHHEeecccccccCCC
Confidence 68999999999999999999998765443 557799999999999999999875
No 102
>PRK09401 reverse gyrase; Reviewed
Probab=90.44 E-value=1.6 Score=58.42 Aligned_cols=126 Identities=17% Similarity=0.066 Sum_probs=72.7
Q ss_pred ccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHh-ccCceEEEEEcCCchhhhHHhhhhhhCCC
Q 038397 218 SCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWH-HGRRKALWISVGSDLKFDARRDLDDVGAT 296 (1102)
Q Consensus 218 S~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l-~Gr~~~~w~s~s~~L~~Da~RDl~diG~~ 296 (1102)
+..|.+++-.+.+. .-|++--.||.||+-. +++.-.++ ....+++.+.-+-.|-......++.++..
T Consensus 82 t~iQ~~~i~~il~g----------~dv~i~ApTGsGKT~f--~l~~~~~l~~~g~~alIL~PTreLa~Qi~~~l~~l~~~ 149 (1176)
T PRK09401 82 WSLQRTWAKRLLLG----------ESFAIIAPTGVGKTTF--GLVMSLYLAKKGKKSYIIFPTRLLVEQVVEKLEKFGEK 149 (1176)
T ss_pred cHHHHHHHHHHHCC----------CcEEEEcCCCCCHHHH--HHHHHHHHHhcCCeEEEEeccHHHHHHHHHHHHHHhhh
Confidence 35676666555432 2456666899999953 33322333 22356999999999999999999999863
Q ss_pred -cccccccC---CCCCCcCCCCcccc---ccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccc
Q 038397 297 -CIEVHALN---KLPYSKLDSRSVGI---REGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKN 366 (1102)
Q Consensus 297 -~i~v~~l~---~~~~~~~~~~~~~~---~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn 366 (1102)
.+.+..+. ..+..........+ ...||.+|.-.|.. .++.+..+.=.+||+||||++..
T Consensus 150 ~~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~-----------~~~~l~~~~~~~lVvDEaD~~L~ 215 (1176)
T PRK09401 150 VGCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSK-----------NFDELPKKKFDFVFVDDVDAVLK 215 (1176)
T ss_pred cCceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHH-----------HHHhccccccCEEEEEChHHhhh
Confidence 33322221 11000000000011 23599999866642 23334333235899999999874
No 103
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=90.19 E-value=0.11 Score=44.12 Aligned_cols=34 Identities=15% Similarity=0.366 Sum_probs=29.4
Q ss_pred cceeecCCcceEEEeCCCcceecCCCCCCCCCCC
Q 038397 15 GVQVRCAGCHIILTVGPGLTEFICGTCNLPQMLP 48 (1102)
Q Consensus 15 ~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~ 48 (1102)
.+.-+|+.||+.++..-.+....|||||....+.
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSRILVK 37 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcEEEEe
Confidence 3456799999999888899999999999977763
No 104
>TIGR01587 cas3_core CRISPR-associated helicase Cas3. This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model.
Probab=90.07 E-value=0.51 Score=54.11 Aligned_cols=63 Identities=29% Similarity=0.394 Sum_probs=48.7
Q ss_pred HhhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCC---CeEEEeecC
Q 038397 805 KQLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASA---PEYRIIFTN 878 (1102)
Q Consensus 805 k~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsa---P~Y~~l~T~ 878 (1102)
.+.|.+|+..|+|-+++++.||.+..| ++|..-.| .+.-||+.||++|.+.-.. -.|++...+
T Consensus 271 ~~~f~~~~~~ilvaT~~~~~GiDi~~~---------~vi~~~~~--~~~~iqr~GR~gR~g~~~~~~~~~~v~~~~~ 336 (358)
T TIGR01587 271 LEEMKKNEKFVIVATQVIEASLDISAD---------VMITELAP--IDSLIQRLGRLHRYGRKNGENFEVYIITIAP 336 (358)
T ss_pred HHHhcCCCCeEEEECcchhceeccCCC---------EEEEcCCC--HHHHHHHhccccCCCCCCCCCCeEEEEeecC
Confidence 468999999999999999999998533 44554444 8899999999999877544 556655444
No 105
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=89.74 E-value=0.26 Score=36.47 Aligned_cols=24 Identities=29% Similarity=0.819 Sum_probs=23.0
Q ss_pred cCCcceEEEeCCCcceecCCCCCC
Q 038397 20 CAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 20 C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
|.+|+..|.|++|-+...|.-|++
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 899999999999999999999985
No 106
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=89.64 E-value=2.8 Score=50.36 Aligned_cols=48 Identities=35% Similarity=0.882 Sum_probs=42.8
Q ss_pred cccccccCcHHHHhhhhhccccCCccccCCCCCCcccCCCC----CCccccc
Q 038397 660 FQICEICNSEEERKKLLQCSCCGQLVHSGCLVPPITDVIPS----DWSCHSC 707 (1102)
Q Consensus 660 f~~ce~cgsed~k~kLL~cs~cgk~~H~~cL~PP~~di~~~----dW~c~sC 707 (1102)
...|-+|....+...+++||.|-..||-+||.||+...|.. .|.|+.|
T Consensus 544 ~ysCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsEC 595 (707)
T KOG0957|consen 544 NYSCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSEC 595 (707)
T ss_pred ceeeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeeccc
Confidence 46799999888888899999999999999999999987654 5999999
No 107
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=89.46 E-value=0.21 Score=36.61 Aligned_cols=23 Identities=22% Similarity=0.648 Sum_probs=18.7
Q ss_pred cCCcceEEEeCCC-cceecCCCCCC
Q 038397 20 CAGCHIILTVGPG-LTEFICGTCNL 43 (1102)
Q Consensus 20 C~~C~a~l~~~pg-~~~~~Cp~C~~ 43 (1102)
|..||..|. +.+ -+.|.||.||.
T Consensus 1 C~sC~~~i~-~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIA-PREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCccc-CcccCceEeCCCCCC
Confidence 788998887 444 78999999983
No 108
>KOG0341 consensus DEAD-box protein abstrakt [RNA processing and modification]
Probab=89.03 E-value=0.3 Score=56.90 Aligned_cols=55 Identities=25% Similarity=0.443 Sum_probs=49.7
Q ss_pred HhhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCC
Q 038397 805 KQLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQA 867 (1102)
Q Consensus 805 k~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQv 867 (1102)
-.+|-.|+|+|++-+|-||-|...+.-..|.| ...|-.++.-++++|||+|||-.
T Consensus 464 i~afr~gkKDVLVATDVASKGLDFp~iqHVIN--------yDMP~eIENYVHRIGRTGRsg~~ 518 (610)
T KOG0341|consen 464 IEAFRAGKKDVLVATDVASKGLDFPDIQHVIN--------YDMPEEIENYVHRIGRTGRSGKT 518 (610)
T ss_pred HHHHhcCCCceEEEecchhccCCCccchhhcc--------CCChHHHHHHHHHhcccCCCCCc
Confidence 36999999999999999999999998877766 57899999999999999999964
No 109
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=88.91 E-value=0.38 Score=59.85 Aligned_cols=54 Identities=17% Similarity=0.278 Sum_probs=46.0
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQA 867 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQv 867 (1102)
+.|++|+..|.|-++|.+.||.+..-+-| |-..+|.|.+.-+|+.||++|.++-
T Consensus 280 ~~F~~g~~~VLVaT~a~~~GIDip~V~~V--------I~~d~P~s~~~y~Qr~GRaGR~G~~ 333 (607)
T PRK11057 280 EAFQRDDLQIVVATVAFGMGINKPNVRFV--------VHFDIPRNIESYYQETGRAGRDGLP 333 (607)
T ss_pred HHHHCCCCCEEEEechhhccCCCCCcCEE--------EEeCCCCCHHHHHHHhhhccCCCCC
Confidence 68999999999999999999987644333 3356899999999999999998853
No 110
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=88.87 E-value=1.1 Score=55.94 Aligned_cols=61 Identities=16% Similarity=0.256 Sum_probs=49.1
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCC-cHhHHHHhhcccccCCCCCCCeEEEeec
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPW-SADRAIQQFGRTHRSNQASAPEYRIIFT 877 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpW-sADkAIQqfGRTHRSNQvsaP~Y~~l~T 877 (1102)
++|.+|+.+|+|-++..+.||.+..- ++.|....|. +....+|..||++|.++ +-|.++++
T Consensus 502 ~~F~~g~~~ILVaT~vie~GvDiP~v--------~~VIi~~~~r~gls~lhQ~~GRvGR~g~---~g~~il~~ 563 (630)
T TIGR00643 502 EEFREGEVDILVATTVIEVGVDVPNA--------TVMVIEDAERFGLSQLHQLRGRVGRGDH---QSYCLLVY 563 (630)
T ss_pred HHHHcCCCCEEEECceeecCcccCCC--------cEEEEeCCCcCCHHHHHHHhhhcccCCC---CcEEEEEE
Confidence 68999999999999999999987532 3455556664 67888999999999875 46777776
No 111
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG0920 consensus ATP-dependent RNA helicase A [RNA processing and modification]
Probab=88.65 E-value=2.1 Score=55.42 Aligned_cols=173 Identities=18% Similarity=0.250 Sum_probs=94.0
Q ss_pred cchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCce-EEEEEcCCchhhhHHhhhhhhCCCc
Q 038397 219 CLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRK-ALWISVGSDLKFDARRDLDDVGATC 297 (1102)
Q Consensus 219 ~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~-~~w~s~s~~L~~Da~RDl~diG~~~ 297 (1102)
..+-++|.=|.++|...+ |--.||+||+-|+=-.|+|++..+... .|-++-. |=+.+|...+
T Consensus 175 ~~~r~~Il~~i~~~qVvv---------IsGeTGcGKTTQvpQfiLd~~~~~~~~~~IicTQP--------RRIsAIsvAe 237 (924)
T KOG0920|consen 175 YKMRDTILDAIEENQVVV---------ISGETGCGKTTQVPQFILDEAIESGAACNIICTQP--------RRISAISVAE 237 (924)
T ss_pred HHHHHHHHHHHHhCceEE---------EeCCCCCCchhhhhHHHHHHHHhcCCCCeEEecCC--------chHHHHHHHH
Confidence 456688888888886554 433499999999999999999665521 1211111 3333333211
Q ss_pred cccc----ccC-CCCCC-cCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCC
Q 038397 298 IEVH----ALN-KLPYS-KLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEA 371 (1102)
Q Consensus 298 i~v~----~l~-~~~~~-~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~ 371 (1102)
-.-. +++ .+-|. .+.+ ..+...=++|||+-.|-..-+.+.+ | .-.+.||.||.|.=- .
T Consensus 238 RVa~ER~~~~g~~VGYqvrl~~-~~s~~t~L~fcTtGvLLr~L~~~~~-l---------~~vthiivDEVHER~-i---- 301 (924)
T KOG0920|consen 238 RVAKERGESLGEEVGYQVRLES-KRSRETRLLFCTTGVLLRRLQSDPT-L---------SGVTHIIVDEVHERS-I---- 301 (924)
T ss_pred HHHHHhccccCCeeeEEEeeec-ccCCceeEEEecHHHHHHHhccCcc-c---------ccCceeeeeeEEEcc-C----
Confidence 1000 011 11110 0111 1122234899999998643111111 1 134699999999832 1
Q ss_pred CCCchhHHHHHHHHhhhCCCccEEEEecCCCCCCCccchhhhccccC-------CCCCCCCHHHHHHHH
Q 038397 372 GSQPTRTGEAVLELQARLPEARVVYCSATGASEPRNMGYMVRLGLWG-------AGTCFKDFQIFLGAL 433 (1102)
Q Consensus 372 ~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~ym~RLGLWg-------~gt~f~~~~~f~~a~ 433 (1102)
.+--.=..+..|..+-|+-+|+-+|||.- ..-.++- +| +|..|+-..-|++-+
T Consensus 302 --~~DflLi~lk~lL~~~p~LkvILMSAT~d-----ae~fs~Y--F~~~pvi~i~grtfpV~~~fLEDi 361 (924)
T KOG0920|consen 302 --NTDFLLILLKDLLPRNPDLKVILMSATLD-----AELFSDY--FGGCPVITIPGRTFPVKEYFLEDI 361 (924)
T ss_pred --CcccHHHHHHHHhhhCCCceEEEeeeecc-----hHHHHHH--hCCCceEeecCCCcchHHHHHHHH
Confidence 11112234444555569999999999964 2211221 22 566688777777743
No 113
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=88.17 E-value=0.21 Score=42.71 Aligned_cols=36 Identities=19% Similarity=0.485 Sum_probs=28.4
Q ss_pred ceeecCCcceEEEeCCCc--ceecCCCCCCCCCCCCCC
Q 038397 16 VQVRCAGCHIILTVGPGL--TEFICGTCNLPQMLPPEL 51 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~pg~--~~~~Cp~C~~~~~l~p~~ 51 (1102)
.++||.+|+..|--.-+. -+.+||-|++-+.+....
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~ 40 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATS 40 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccceEeccC
Confidence 478999999999664333 599999999988885444
No 114
>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]
Probab=88.07 E-value=1.7 Score=55.36 Aligned_cols=148 Identities=17% Similarity=0.073 Sum_probs=79.7
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhcc---CceEEEEEcCCchhhhHHhhhhhhCCCcccccc--cCCCC-CCcCCCCcc
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHHG---RRKALWISVGSDLKFDARRDLDDVGATCIEVHA--LNKLP-YSKLDSRSV 316 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~G---r~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~--l~~~~-~~~~~~~~~ 316 (1102)
=+++-.-||.||+-..+.+.+.+...+ ..|.+.+---..+..|..+=++.++.....+.. .++.. +.....+.
T Consensus 216 ~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie~~~~r~~~~~~~~~~~~~~~h~~~~~~~~~~~~~- 294 (733)
T COG1203 216 LVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIEDMYRRAKEIFGLFSVIGKSLHSSSKEPLLLEPDQ- 294 (733)
T ss_pred cEEEEeCCCCChHHHHHHHHHHHhhccccccceEEEEccHHHHHHHHHHHHHhhhcccccccccccccccchhhhcccc-
Confidence 356788899999887777777766663 566777777778888888877776654332211 11111 11000000
Q ss_pred ccccceEEeehhhhhhcc-ccccchHHHHHHH-h-ccCC-------CceEEeecchhccccCCCCCCCchhHHHHHHHHh
Q 038397 317 GIREGVVFLTYSSLIASS-EKGRSRLQQLVQW-C-GSGY-------DGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQ 386 (1102)
Q Consensus 317 ~~~~GvlF~TYs~L~~~~-~~~~sRl~Ql~~W-~-g~df-------dgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ 386 (1102)
...+.-+|+.+....- .--.+.+.|++-- . +..| ..++||||.|-..--. .+....++++++
T Consensus 295 --~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h~~~~~~------~~~~l~~~i~~l 366 (733)
T COG1203 295 --DILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVHLYADET------MLAALLALLEAL 366 (733)
T ss_pred --ccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHHhhcccc------hHHHHHHHHHHH
Confidence 1112222222211100 0000111111110 0 0112 3699999999977331 255666777766
Q ss_pred hhCCCccEEEEecC
Q 038397 387 ARLPEARVVYCSAT 400 (1102)
Q Consensus 387 ~~lP~ARvvY~SAT 400 (1102)
... +++||.+|||
T Consensus 367 ~~~-g~~ill~SAT 379 (733)
T COG1203 367 AEA-GVPVLLMSAT 379 (733)
T ss_pred HhC-CCCEEEEecC
Confidence 664 7899999999
No 115
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=88.06 E-value=0.82 Score=57.30 Aligned_cols=72 Identities=18% Similarity=0.384 Sum_probs=54.7
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRF 885 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRF 885 (1102)
+.|.+|+.+|+|-++.++.||-+..=.-| |-+.+|.+.+.-||+.|||+|.+.. .--+.+ ++ ..|+++
T Consensus 289 ~~Fr~G~~~ILVATdv~arGIDip~V~~V--------I~~d~P~~~e~yvqRiGRtGRaGr~-G~ai~~-v~--~~e~~~ 356 (629)
T PRK11634 289 ERLKDGRLDILIATDVAARGLDVERISLV--------VNYDIPMDSESYVHRIGRTGRAGRA-GRALLF-VE--NRERRL 356 (629)
T ss_pred HHHhCCCCCEEEEcchHhcCCCcccCCEE--------EEeCCCCCHHHHHHHhccccCCCCc-ceEEEE-ec--hHHHHH
Confidence 68999999999999999999987643333 4578999999999999999999864 333333 33 356666
Q ss_pred HHHH
Q 038397 886 ASIV 889 (1102)
Q Consensus 886 aS~V 889 (1102)
...+
T Consensus 357 l~~i 360 (629)
T PRK11634 357 LRNI 360 (629)
T ss_pred HHHH
Confidence 5544
No 116
>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]
Probab=88.03 E-value=0.49 Score=56.79 Aligned_cols=89 Identities=25% Similarity=0.366 Sum_probs=69.2
Q ss_pred HhhhcC-CcceEEEEe-cccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCe-EEEeecCccc
Q 038397 805 KQLFMD-GKKLVAIIS-EAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPE-YRIIFTNLGG 881 (1102)
Q Consensus 805 k~~Fm~-G~K~VAIIS-eAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~-Y~~l~T~l~G 881 (1102)
.|.|+- .+-.|||+| +|||+|+-|-|- ++-+-+||+|+.-.-||-=-|.||-+|.|+=- |.++.-+-+.
T Consensus 535 ~qsFQ~seev~VAvlsItA~gvGLt~tAa--------~~VVFaEL~wnPgvLlQAEDRaHRiGQkssV~v~ylvAKgT~D 606 (689)
T KOG1000|consen 535 CQSFQTSEEVRVAVLSITAAGVGLTLTAA--------SVVVFAELHWNPGVLLQAEDRAHRIGQKSSVFVQYLVAKGTAD 606 (689)
T ss_pred HHHhccccceEEEEEEEeecccceeeecc--------ceEEEEEecCCCceEEechhhhhhccccceeeEEEEEecCchH
Confidence 478885 567899999 899999999987 45688999999999999999999999998764 4445555555
Q ss_pred hhhhHHHHHHHHhhcCCcccc
Q 038397 882 ERRFASIVAKRLESLGALTQG 902 (1102)
Q Consensus 882 ErRFaS~VAkRLeSLGALT~G 902 (1102)
|.=. -++.++|.-||-++-|
T Consensus 607 dy~W-p~l~~KL~vl~s~gl~ 626 (689)
T KOG1000|consen 607 DYMW-PMLQQKLDVLGSVGLS 626 (689)
T ss_pred HHHH-HHHHHHHHHHhhcccC
Confidence 5543 4567777777766543
No 117
>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype. This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.
Probab=87.82 E-value=0.73 Score=59.22 Aligned_cols=69 Identities=12% Similarity=0.078 Sum_probs=38.9
Q ss_pred ccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHH--hccCceEEEEEcCCchhhhHHhhhhhhCC
Q 038397 218 SCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENW--HHGRRKALWISVGSDLKFDARRDLDDVGA 295 (1102)
Q Consensus 218 S~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~--l~Gr~~~~w~s~s~~L~~Da~RDl~diG~ 295 (1102)
+.-|.++|-....-+ --.++.=.||-||+-.+|..++-.. ...-++.|++.-.-.|-......++.+|.
T Consensus 17 tpiQ~~~i~~il~G~---------~~v~~~apTGSGKTaa~aafll~~~~~~~~~~rLv~~vPtReLa~Qi~~~~~~~~k 87 (844)
T TIGR02621 17 FPWQLSLAERFVAGQ---------PPESCSTPTGLGKTSIIAAWLLAVEIGAKVPRRLVYVVNRRTVVDQVTEEAEKIGE 87 (844)
T ss_pred CHHHHHHHHHHHcCC---------CcceEecCCCCcccHHHHHhhccccccccccceEEEeCchHHHHHHHHHHHHHHHH
Confidence 366777766544221 1123345799999976653333221 12224566676677777766666666664
No 118
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=87.82 E-value=0.32 Score=42.89 Aligned_cols=24 Identities=25% Similarity=0.678 Sum_probs=23.1
Q ss_pred ecCCcceEEEeCCCcceecCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCN 42 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~ 42 (1102)
.|..||..|...-+-+.|.||.||
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCG 34 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCG 34 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCC
Confidence 699999999999999999999999
No 119
>PRK09694 helicase Cas3; Provisional
Probab=87.61 E-value=2.2 Score=55.53 Aligned_cols=70 Identities=26% Similarity=0.207 Sum_probs=40.0
Q ss_pred cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEec
Q 038397 320 EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSA 399 (1102)
Q Consensus 320 ~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SA 399 (1102)
.-|+.+|.-|+...--+.+-+. +..+|= -..||||||+|..=.. -+..=..+++.+.+ ...+||++||
T Consensus 411 api~V~TiDQlL~a~l~~kh~~---lR~~~L-a~svvIiDEVHAyD~y-------m~~lL~~~L~~l~~-~g~~vIllSA 478 (878)
T PRK09694 411 GQIGVCTIDQVLISVLPVKHRF---IRGFGL-GRSVLIVDEVHAYDAY-------MYGLLEAVLKAQAQ-AGGSVILLSA 478 (878)
T ss_pred CCEEEcCHHHHHHHHHccchHH---HHHHhh-ccCeEEEechhhCCHH-------HHHHHHHHHHHHHh-cCCcEEEEeC
Confidence 4588888887774321111111 122210 2359999999985211 12233455555544 3689999999
Q ss_pred CC
Q 038397 400 TG 401 (1102)
Q Consensus 400 Tg 401 (1102)
|=
T Consensus 479 TL 480 (878)
T PRK09694 479 TL 480 (878)
T ss_pred CC
Confidence 94
No 120
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=87.23 E-value=1.6 Score=58.46 Aligned_cols=125 Identities=14% Similarity=0.121 Sum_probs=70.1
Q ss_pred ccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCC-
Q 038397 218 SCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGAT- 296 (1102)
Q Consensus 218 S~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~- 296 (1102)
+..|.+++-.+.+. .-|++-=.||.||+-.... +.........+++.+.-...|-.+..+.++.++..
T Consensus 80 ~~iQ~~~i~~il~G----------~d~vi~ApTGsGKT~f~l~-~~~~l~~~g~~vLIL~PTreLa~Qi~~~l~~l~~~~ 148 (1171)
T TIGR01054 80 WSIQKMWAKRVLRG----------DSFAIIAPTGVGKTTFGLA-MSLFLAKKGKRCYIILPTTLLVIQVAEKISSLAEKA 148 (1171)
T ss_pred cHHHHHHHHHHhCC----------CeEEEECCCCCCHHHHHHH-HHHHHHhcCCeEEEEeCHHHHHHHHHHHHHHHHHhc
Confidence 34566665444432 2345555699999963322 22223332356999999999999999999888642
Q ss_pred cccccc---c-CCCCCCcCCCCcc-cc---ccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccc
Q 038397 297 CIEVHA---L-NKLPYSKLDSRSV-GI---REGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKN 366 (1102)
Q Consensus 297 ~i~v~~---l-~~~~~~~~~~~~~-~~---~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn 366 (1102)
.+.++. + +.+++.+- .... .+ .-.||.+|...|... +++ +...|+ +||+||||++..
T Consensus 149 ~i~~~~i~~~~Gg~~~~e~-~~~~~~l~~~~~dIlV~Tp~rL~~~-------~~~----l~~~~~-~iVvDEaD~~L~ 213 (1171)
T TIGR01054 149 GVGTVNIGAYHSRLPTKEK-KEFMERIENGDFDILITTTMFLSKN-------YDE----LGPKFD-FIFVDDVDALLK 213 (1171)
T ss_pred CCceeeeeeecCCCCHHHH-HHHHHHHhcCCCCEEEECHHHHHHH-------HHH----hcCCCC-EEEEeChHhhhh
Confidence 222221 1 11111100 0000 11 235999998776421 222 222343 899999999976
No 121
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=87.23 E-value=0.29 Score=41.74 Aligned_cols=32 Identities=22% Similarity=0.619 Sum_probs=28.7
Q ss_pred ceecCCCccceeeccCCCccccCCCCCccccc
Q 038397 95 IQLPCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
..-.|.+||+.+..+.....-.||+||.-+.+
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~ 36 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSRILV 36 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcEEEE
Confidence 34689999999999999999999999998877
No 122
>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]
Probab=87.03 E-value=2.4 Score=55.54 Aligned_cols=159 Identities=23% Similarity=0.225 Sum_probs=95.6
Q ss_pred CCCCCCCccCcccccccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEE
Q 038397 196 VHPPEPTYDLLIKYDLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALW 275 (1102)
Q Consensus 196 v~pP~~~y~~~lp~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w 275 (1102)
+++|.-.|+..|+ +-|-+| +|+..+.+.. |+.==||-||+-..=--|.....+|.| ++.
T Consensus 109 ~~~~~~~~~F~LD----------~fQ~~a-~~~Ler~esV---------lV~ApTssGKTvVaeyAi~~al~~~qr-viY 167 (1041)
T COG4581 109 LAPPAREYPFELD----------PFQQEA-IAILERGESV---------LVCAPTSSGKTVVAEYAIALALRDGQR-VIY 167 (1041)
T ss_pred cCcHHHhCCCCcC----------HHHHHH-HHHHhCCCcE---------EEEccCCCCcchHHHHHHHHHHHcCCc-eEe
Confidence 4555555555554 668899 8888887543 455558888876665567777788877 777
Q ss_pred EEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCccccccc-eEEeehhhhhhccccccchHHHHHHHhccCCCc
Q 038397 276 ISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSVGIREG-VVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDG 354 (1102)
Q Consensus 276 ~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~G-vlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdg 354 (1102)
.|-=..|-.=-.||+...=.+..++..|-+ |+. .|.-+.. ++++| =-|+.---.| .+||.+ .-
T Consensus 168 TsPIKALsNQKyrdl~~~fgdv~~~vGL~T---GDv---~IN~~A~clvMTT-EILRnMlyrg-------~~~~~~--i~ 231 (1041)
T COG4581 168 TSPIKALSNQKYRDLLAKFGDVADMVGLMT---GDV---SINPDAPCLVMTT-EILRNMLYRG-------SESLRD--IE 231 (1041)
T ss_pred ccchhhhhhhHHHHHHHHhhhhhhhcccee---cce---eeCCCCceEEeeH-HHHHHHhccC-------cccccc--cc
Confidence 776555555555777654333211222221 110 1111222 56666 4444322122 356644 45
Q ss_pred eEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCc-cEEEEecC
Q 038397 355 LVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEA-RVVYCSAT 400 (1102)
Q Consensus 355 vivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~A-RvvY~SAT 400 (1102)
-|||||+|-+.... -|-+=.+.--.||++ ++|+-|||
T Consensus 232 ~ViFDEvHyi~D~e---------RG~VWEE~Ii~lP~~v~~v~LSAT 269 (1041)
T COG4581 232 WVVFDEVHYIGDRE---------RGVVWEEVIILLPDHVRFVFLSAT 269 (1041)
T ss_pred eEEEEeeeeccccc---------cchhHHHHHHhcCCCCcEEEEeCC
Confidence 79999999988553 344445555678888 99999999
No 123
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=86.75 E-value=0.16 Score=68.16 Aligned_cols=49 Identities=35% Similarity=0.925 Sum_probs=44.8
Q ss_pred cccccCcHHHHhhhhhccccCCccccCCCCCCcccCCCCCCccccchhh
Q 038397 662 ICEICNSEEERKKLLQCSCCGQLVHSGCLVPPITDVIPSDWSCHSCKEK 710 (1102)
Q Consensus 662 ~ce~cgsed~k~kLL~cs~cgk~~H~~cL~PP~~di~~~dW~c~sCkek 710 (1102)
.|..|.......+|+.|+.|.+++|..|++|-+..++.++|.|+.|...
T Consensus 1110 ~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~e 1158 (1404)
T KOG1245|consen 1110 LCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRKE 1158 (1404)
T ss_pred hhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccchh
Confidence 4788888888888999999999999999999999999999999999853
No 124
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=86.66 E-value=0.71 Score=44.44 Aligned_cols=27 Identities=19% Similarity=0.562 Sum_probs=22.0
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l 47 (1102)
-|+.||..|.... ..|.|+.|++....
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccCC--CeEECcCCCCcccc
Confidence 4999999996543 47999999987665
No 125
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.65 E-value=0.56 Score=39.11 Aligned_cols=31 Identities=13% Similarity=0.299 Sum_probs=25.6
Q ss_pred ceeecCCcceEEEeCCCcceecCCCCCCCCCC
Q 038397 16 VQVRCAGCHIILTVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l 47 (1102)
+.-.|+.||+.++..+ ...+.||+||.....
T Consensus 1 ~~Y~C~~Cg~~~~~~~-~~~irC~~CG~rIly 31 (44)
T smart00659 1 MIYICGECGRENEIKS-KDVVRCRECGYRILY 31 (44)
T ss_pred CEEECCCCCCEeecCC-CCceECCCCCceEEE
Confidence 3468999999999985 578999999986654
No 126
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=86.47 E-value=0.48 Score=37.89 Aligned_cols=28 Identities=21% Similarity=0.576 Sum_probs=23.4
Q ss_pred ceeecCCcceEEEeCC-----CcceecCCCCCC
Q 038397 16 VQVRCAGCHIILTVGP-----GLTEFICGTCNL 43 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~p-----g~~~~~Cp~C~~ 43 (1102)
+.++|++|++.+.+++ +-..+.||.|+.
T Consensus 1 M~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred CEEECCCCCceEEcCHHHcccCCcEEECCCCCc
Confidence 3578999999997765 467999999996
No 127
>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase. A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.
Probab=86.36 E-value=1.2 Score=56.86 Aligned_cols=135 Identities=16% Similarity=0.184 Sum_probs=85.1
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRF 885 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRF 885 (1102)
++|.+|+.+|.|-+++++-||-.-. -.+=|...+|=+.+.-+||.|||+|.++.+- -+.++++=+.+..+
T Consensus 323 ~~f~~G~i~vLVaTd~lerGIDI~~--------vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~--ai~v~~~~~~d~~~ 392 (742)
T TIGR03817 323 RALRDGELLGVATTNALELGVDISG--------LDAVVIAGFPGTRASLWQQAGRAGRRGQGAL--VVLVARDDPLDTYL 392 (742)
T ss_pred HHHHcCCceEEEECchHhccCCccc--------ccEEEEeCCCCCHHHHHHhccccCCCCCCcE--EEEEeCCChHHHHH
Confidence 6899999999999999999998863 1244667899999999999999999998653 34555555666666
Q ss_pred HHHHHHHHhhcCCccccccccCCCCCcCCcCChHHHHHHHHHHHHHhccCccCCCCCCCCCCCcchHHHHHHHHHHHhhh
Q 038397 886 ASIVAKRLESLGALTQGDRRAGLSLSAYNYDSAFGKKALMMMYRGIMEQDVLPVVPPGCSSEKPETIQDFMTKAKAALVS 965 (1102)
Q Consensus 886 aS~VAkRLeSLGALT~GdRra~~~ls~fNldn~YGr~AL~~~~~~i~~~~~~p~~p~~~~~~~~~~~~~f~~~~~~~L~~ 965 (1102)
.....+.++. ...-...|.+|.| .|..-+..... +.|+-+. ..+.++..+.++...|.+
T Consensus 393 ~~~~~~~~~~-----------~~e~~~~~~~n~~---il~~hl~~aa~--e~~l~~~-----~~~~~~~~~~~~~~~l~~ 451 (742)
T TIGR03817 393 VHHPEALFDR-----------PVEATVFDPDNPY---VLGPHLCCAAA--ELPLTEA-----DLELFGPAAAEVLDQLVE 451 (742)
T ss_pred HhCHHHHhcC-----------CCccceeCCCcHH---HHHHHHHHHHh--cCCCChH-----HHHhhchhHHHHHHHHHH
Confidence 5544333221 0011246788888 33333322221 2343211 112222224566777888
Q ss_pred ccceec
Q 038397 966 VGIVRD 971 (1102)
Q Consensus 966 vGl~~~ 971 (1102)
-|++..
T Consensus 452 ~g~l~~ 457 (742)
T TIGR03817 452 QGLLRR 457 (742)
T ss_pred CCcEEe
Confidence 887753
No 128
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=86.36 E-value=0.31 Score=47.99 Aligned_cols=36 Identities=33% Similarity=0.621 Sum_probs=29.3
Q ss_pred ccceeecCCcceEEEeCCCcceecCCCCCCCCCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLTEFICGTCNLPQMLPPEL 51 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~p~~ 51 (1102)
.++++.|++|+..-.+- |-++ .|.+|+.+..|+|++
T Consensus 66 kav~V~CP~C~K~TKmL-Gr~D-~CM~C~~pLTLd~~l 101 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKML-GRVD-ACMHCKEPLTLDPSL 101 (114)
T ss_pred cceeeECCCCCChHhhh-chhh-ccCcCCCcCccCchh
Confidence 56899999999876543 3334 999999999998887
No 129
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=86.34 E-value=0.82 Score=40.45 Aligned_cols=38 Identities=18% Similarity=0.287 Sum_probs=31.7
Q ss_pred CCCCccceeecCCcceEE-EeCCCcceecCCCCCCCCCC
Q 038397 10 PPPNVGVQVRCAGCHIIL-TVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 10 ~~~~~~~~~~C~~C~a~l-~~~pg~~~~~Cp~C~~~~~l 47 (1102)
.|-.-++.++|++|+.+- .|.+..+...|+.||..+.-
T Consensus 4 ~p~S~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 4 QPRSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred CCCCeEEEEECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 344578999999999765 89999999999999975544
No 130
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=86.26 E-value=0.29 Score=35.36 Aligned_cols=22 Identities=27% Similarity=0.760 Sum_probs=16.6
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
.|++||+.+.- ...| ||+||++
T Consensus 1 ~Cp~CG~~~~~---~~~f-C~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIED---DAKF-CPNCGTP 22 (23)
T ss_pred CCcccCCCCCC---cCcc-hhhhCCc
Confidence 49999999852 3444 9999975
No 131
>KOG0350 consensus DEAD-box ATP-dependent RNA helicase [RNA processing and modification]
Probab=86.25 E-value=1.1 Score=54.19 Aligned_cols=76 Identities=26% Similarity=0.364 Sum_probs=63.5
Q ss_pred HhhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhh
Q 038397 805 KQLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERR 884 (1102)
Q Consensus 805 k~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErR 884 (1102)
-..|..|+..|+|-|||-+-||-+--=- +-|-.++|-|+-.-|++-|||.|.||.- |.+-.-+=.++|+
T Consensus 476 l~~f~~g~i~vLIcSD~laRGiDv~~v~--------~VINYd~P~~~ktyVHR~GRTARAgq~G---~a~tll~~~~~r~ 544 (620)
T KOG0350|consen 476 LEKFAKGDINVLICSDALARGIDVNDVD--------NVINYDPPASDKTYVHRAGRTARAGQDG---YAITLLDKHEKRL 544 (620)
T ss_pred HHHHhcCCceEEEehhhhhcCCcccccc--------eEeecCCCchhhHHHHhhcccccccCCc---eEEEeeccccchH
Confidence 4689999999999999999999874322 3467899999999999999999999974 5555556688999
Q ss_pred hHHHHHH
Q 038397 885 FASIVAK 891 (1102)
Q Consensus 885 FaS~VAk 891 (1102)
|.-++.+
T Consensus 545 F~klL~~ 551 (620)
T KOG0350|consen 545 FSKLLKK 551 (620)
T ss_pred HHHHHHH
Confidence 9988776
No 132
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=86.23 E-value=0.5 Score=41.73 Aligned_cols=33 Identities=21% Similarity=0.544 Sum_probs=26.4
Q ss_pred ecCCCccceeeccCCCccccCCCCCcccccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAVDMS 129 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~~~ 129 (1102)
..|.+||+.+.--...+.|.||.||..++.--.
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~ 40 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCE 40 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCeeEeech
Confidence 469999999965565889999999998665333
No 133
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=86.09 E-value=0.76 Score=56.83 Aligned_cols=54 Identities=20% Similarity=0.263 Sum_probs=45.9
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQA 867 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQv 867 (1102)
+.|++|+..|.|-++|.+.||-...- |.-|...+|+|.+.-+|+.||++|.++-
T Consensus 268 ~~F~~g~~~vlVaT~a~~~GID~p~v--------~~VI~~~~p~s~~~y~Q~~GRaGR~G~~ 321 (591)
T TIGR01389 268 EDFLYDDVKVMVATNAFGMGIDKPNV--------RFVIHYDMPGNLESYYQEAGRAGRDGLP 321 (591)
T ss_pred HHHHcCCCcEEEEechhhccCcCCCC--------CEEEEcCCCCCHHHHhhhhccccCCCCC
Confidence 68999999999999999999986533 2344567899999999999999998853
No 134
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=86.05 E-value=0.39 Score=38.10 Aligned_cols=32 Identities=22% Similarity=0.542 Sum_probs=25.4
Q ss_pred ceecCCCccceeeccCC-----CccccCCCCCccccc
Q 038397 95 IQLPCANCKAILNVPHG-----LVRFSCPQCAVELAV 126 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~~-----~~~f~Cp~C~~~L~v 126 (1102)
+.+.|.+|++...++.. -..+.||.||..+.+
T Consensus 1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 35889999999999864 236899999988653
No 135
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=85.88 E-value=7.2 Score=46.11 Aligned_cols=86 Identities=21% Similarity=0.301 Sum_probs=48.6
Q ss_pred EeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCccccccceEE
Q 038397 245 FIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSVGIREGVVF 324 (1102)
Q Consensus 245 ~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~GvlF 324 (1102)
+++=..|+||+-.+.-+..+.-.+| .+++|+|-.... ....+....+|... +.+.+
T Consensus 86 LI~G~pG~GKStLllq~a~~~a~~g-~~VlYvs~EEs~-~qi~~Ra~rlg~~~----------------------~~l~l 141 (372)
T cd01121 86 LIGGDPGIGKSTLLLQVAARLAKRG-GKVLYVSGEESP-EQIKLRADRLGIST----------------------ENLYL 141 (372)
T ss_pred EEEeCCCCCHHHHHHHHHHHHHhcC-CeEEEEECCcCH-HHHHHHHHHcCCCc----------------------ccEEE
Confidence 3344499999987766655444444 469999875433 22222233344221 11111
Q ss_pred eehhhhhhccccccchHHHHHHHhccCCCceEEeecchhcc
Q 038397 325 LTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAK 365 (1102)
Q Consensus 325 ~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~ak 365 (1102)
.. .+.+++|++++...--.+||+|+.+.+.
T Consensus 142 ~~-----------e~~le~I~~~i~~~~~~lVVIDSIq~l~ 171 (372)
T cd01121 142 LA-----------ETNLEDILASIEELKPDLVIIDSIQTVY 171 (372)
T ss_pred Ec-----------cCcHHHHHHHHHhcCCcEEEEcchHHhh
Confidence 11 2346777777754333489999998874
No 136
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=85.50 E-value=0.5 Score=41.10 Aligned_cols=31 Identities=19% Similarity=0.444 Sum_probs=26.2
Q ss_pred eeecCCcceEEEeCCCc--ceecCCCCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGL--TEFICGTCNLPQML 47 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~--~~~~Cp~C~~~~~l 47 (1102)
...|+.||+.++++... .-+.||.||...++
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELEV 34 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEEE
Confidence 45899999999997644 46899999998887
No 137
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=85.24 E-value=0.53 Score=39.50 Aligned_cols=32 Identities=22% Similarity=0.591 Sum_probs=25.9
Q ss_pred ecCCcceEEEeCCCc--ceecCCCCCCCCCCCCC
Q 038397 19 RCAGCHIILTVGPGL--TEFICGTCNLPQMLPPE 50 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~--~~~~Cp~C~~~~~l~p~ 50 (1102)
-|+.||..|....+- ..+.||.||+...+.+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEECCCc
Confidence 499999999777653 38999999998877554
No 138
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=85.01 E-value=14 Score=34.87 Aligned_cols=37 Identities=14% Similarity=0.199 Sum_probs=20.7
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCC
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGS 280 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~ 280 (1102)
.+++--.+|+||+..+. .|...+.+-....+|++.+.
T Consensus 21 ~v~i~G~~G~GKT~l~~-~i~~~~~~~~~~v~~~~~~~ 57 (151)
T cd00009 21 NLLLYGPPGTGKTTLAR-AIANELFRPGAPFLYLNASD 57 (151)
T ss_pred eEEEECCCCCCHHHHHH-HHHHHhhcCCCCeEEEehhh
Confidence 44444449999996554 44444433334466665543
No 139
>KOG0922 consensus DEAH-box RNA helicase [RNA processing and modification]
Probab=84.93 E-value=2.1 Score=53.28 Aligned_cols=131 Identities=21% Similarity=0.300 Sum_probs=72.7
Q ss_pred hHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCc---cc
Q 038397 223 ETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATC---IE 299 (1102)
Q Consensus 223 e~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~---i~ 299 (1102)
+-|.|+.++|... .++|+ ||.||+-||--..+|.-...+-+ ||+.+ +.
T Consensus 57 ~~il~~ve~nqvl--------IviGe-TGsGKSTQipQyL~eaG~~~~g~--------------------I~~TQPRRVA 107 (674)
T KOG0922|consen 57 DQILYAVEDNQVL--------IVIGE-TGSGKSTQIPQYLAEAGFASSGK--------------------IACTQPRRVA 107 (674)
T ss_pred HHHHHHHHHCCEE--------EEEcC-CCCCccccHhHHHHhcccccCCc--------------------EEeecCchHH
Confidence 5578999988543 45677 99999999977776665444432 23321 11
Q ss_pred ccccCC-------CCCCcCCCCcc------ccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccc
Q 038397 300 VHALNK-------LPYSKLDSRSV------GIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKN 366 (1102)
Q Consensus 300 v~~l~~-------~~~~~~~~~~~------~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn 366 (1102)
...|.+ .++|..-+-.| +-+.-|.|.|=--|..+--.. .-| .. =.|||+||+|.=-=
T Consensus 108 avslA~RVAeE~~~~lG~~VGY~IRFed~ts~~TrikymTDG~LLRE~l~D-p~L--------sk-YsvIIlDEAHERsl 177 (674)
T KOG0922|consen 108 AVSLAKRVAEEMGCQLGEEVGYTIRFEDSTSKDTRIKYMTDGMLLREILKD-PLL--------SK-YSVIILDEAHERSL 177 (674)
T ss_pred HHHHHHHHHHHhCCCcCceeeeEEEecccCCCceeEEEecchHHHHHHhcC-Ccc--------cc-ccEEEEechhhhhh
Confidence 122211 12332111111 113337777776665442111 111 11 24999999998431
Q ss_pred cCCCCCCCchhHHHHHH-HHhhhCCCccEEEEecC
Q 038397 367 LVPEAGSQPTRTGEAVL-ELQARLPEARVVYCSAT 400 (1102)
Q Consensus 367 ~~~~~~~~~s~~g~avl-~LQ~~lP~ARvvY~SAT 400 (1102)
.|-.=..+| .++.+-|.-||+-+|||
T Consensus 178 --------~TDiLlGlLKki~~~R~~LklIimSAT 204 (674)
T KOG0922|consen 178 --------HTDILLGLLKKILKKRPDLKLIIMSAT 204 (674)
T ss_pred --------HHHHHHHHHHHHHhcCCCceEEEEeee
Confidence 133333333 36666678899999999
No 140
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=84.58 E-value=0.45 Score=35.18 Aligned_cols=25 Identities=32% Similarity=0.772 Sum_probs=18.6
Q ss_pred eecCCCccceeeccCCCccccCCCCCccc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVEL 124 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L 124 (1102)
.+.|.+||+.+ +.+ .--||.||++|
T Consensus 2 ~~~Cp~Cg~~~--~~~--~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEI--DPD--AKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcC--Ccc--cccChhhCCCC
Confidence 47899999943 333 44799999986
No 141
>PRK13700 conjugal transfer protein TraD; Provisional
Probab=84.41 E-value=2.9 Score=53.00 Aligned_cols=254 Identities=15% Similarity=0.202 Sum_probs=132.6
Q ss_pred CcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccc-----cccCCCCC----Cc
Q 038397 240 ARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEV-----HALNKLPY----SK 310 (1102)
Q Consensus 240 ~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v-----~~l~~~~~----~~ 310 (1102)
..++|++--.||.||+-.+-.+|..-..+|.| +|-+..+++......|--+|+---..+- .+.+.++. ..
T Consensus 184 E~~H~li~GttGSGKS~~i~~LL~~ir~RGdr-AIIyD~~GeFv~~FY~p~~DiILNPfDaRs~~Ws~f~Ei~~~~D~~~ 262 (732)
T PRK13700 184 EIQNFCLHGTVGAGKSEVIRRLANYARQRGDM-VVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDN 262 (732)
T ss_pred hhcceEEeCCCCCCHHHHHHHHHHHHHHcCCe-EEEEeCCCchHHHhcCCccceeeCCCCccCCCCchHHhhcCHHHHHH
Confidence 36788888889999999998888877778775 9989999988766665433443222211 01111100 00
Q ss_pred CCCCcc--ccccceEEeehhhhhhc------cccccchHHHHHHHhccCCCceEEeecchhccccCCCC---CCCchhHH
Q 038397 311 LDSRSV--GIREGVVFLTYSSLIAS------SEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEA---GSQPTRTG 379 (1102)
Q Consensus 311 ~~~~~~--~~~~GvlF~TYs~L~~~------~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~---~~~~s~~g 379 (1102)
+...-| +-++.=.|..|+..+=. ...+..-...|++|+-. .-+||-|..-.-.+.. +.+..|++
T Consensus 263 iA~sLIP~~~~~dpFW~~aAR~Ifa~~~~~L~~~~~~s~~~L~~~Ll~-----~~~e~L~~~L~~T~aa~lv~~~~ekta 337 (732)
T PRK13700 263 TANTLIPMGTKEDPFWQGSGRTIFAEAAYLMRNDPNRSYSKLVDTLLS-----IKIEKLRTYLRNSPAANLVEEKIEKTA 337 (732)
T ss_pred HHHHhCCCCCCCChhHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHh-----CCHHHHHHHHhcCchhhcccccchHHH
Confidence 000001 11222344444443311 11222234556677643 1124444433222111 12223444
Q ss_pred HHHHHHhhhCCCccEEEEecCCCCCCCccchhhhccccCCCCCCCCHHHHHHHHhcc-ChhHHHHHHHHHHhccceeeec
Q 038397 380 EAVLELQARLPEARVVYCSATGASEPRNMGYMVRLGLWGAGTCFKDFQIFLGALDKG-GVGALELVAMDMKARGMYVCRT 458 (1102)
Q Consensus 380 ~avl~LQ~~lP~ARvvY~SATgasep~Nl~ym~RLGLWg~gt~f~~~~~f~~a~~~g-Gv~amE~va~dlK~~G~yiaR~ 458 (1102)
..+.- |-++..+-+-|+. |++..|.+| ++.+++....+. ..+
T Consensus 338 ~SIra---------------vL~~yi~~lr~L~--~~~~~g~~F-SIRdWi~~~~~~~~~g------------------- 380 (732)
T PRK13700 338 ISIRA---------------VLTNYVKAIRYLQ--GIEHNGEPF-TIRDWMRGVREDQKNG------------------- 380 (732)
T ss_pred HHHHH---------------HHHHHHHHHHhhh--hcccCCCCc-cHHHHHhhccccCCCc-------------------
Confidence 33221 1111222345555 457666678 777887653221 111
Q ss_pred cCCCCceeEEEeccCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCChhHHHHHhhhhhhHHHHHHHHhcCchHHHH
Q 038397 459 LSYKGAEFEVIEAPLEAEMTDMYKKAAEFWAELRVELLSASAFLANDKPNSSQLWRLYWSGHQRFFRHMCMSAKVPATVR 538 (1102)
Q Consensus 459 LSf~gvef~i~e~~l~~~~~~~Yd~~a~~w~~~~~~~~~a~e~~~~~~~~~~~~~~~FwsahQrFFk~l~~a~Kv~~~V~ 538 (1102)
.+-+...+++...+.-...+|-.+- +...+. ++.. .. +.+|- |+-.|-.--|+|.+++
T Consensus 381 ---------~LFIt~~~~~~~~LrPLISlwld~A--i~~LLs-l~~~-~~-rRlw~--------~lDElpsLgkLp~L~~ 438 (732)
T PRK13700 381 ---------WLFISSNADTHASLKPVISMWLSIA--IRGLLA-MGEN-RN-RRVWF--------FCDELPTLHKLPDLVE 438 (732)
T ss_pred ---------eEEEeeCHHHHHHHHHHHHHHHHHH--HHHHhc-CCCC-CC-CcEEE--------EEECccccccchhHHH
Confidence 1223456777777777777886652 222222 1111 11 12221 1223333349999999
Q ss_pred HHHHHHHCCCeEEEEEecch
Q 038397 539 LAKKALAEGKCVVIGLQSTG 558 (1102)
Q Consensus 539 ~a~eal~~Gk~vVIgLqSTG 558 (1102)
..-++-+.|.|+|||+||..
T Consensus 439 ~La~~Rk~G~~~vlGiQs~a 458 (732)
T PRK13700 439 ILPEARKFGGCYVFGIQSYA 458 (732)
T ss_pred HHHHHHhcCCEEEEEeCCHH
Confidence 99999999999999999983
No 142
>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional
Probab=84.19 E-value=3.6 Score=53.78 Aligned_cols=156 Identities=20% Similarity=0.156 Sum_probs=88.2
Q ss_pred cceeEeecCCCCCcchhhHHHHHHHHhc-cCceEEEEEcCCchhh--------hHHhhh-h-hhCCCcccccccCC---C
Q 038397 241 RAGFFIGDGAGVGKGRTIAGLIWENWHH-GRRKALWISVGSDLKF--------DARRDL-D-DVGATCIEVHALNK---L 306 (1102)
Q Consensus 241 R~Gf~~gDg~GvGKGR~~AgiI~~n~l~-Gr~~~~w~s~s~~L~~--------Da~RDl-~-diG~~~i~v~~l~~---~ 306 (1102)
-..|.+-=.||.||+.+.++.|++-+.+ |.++.|.+--|...++ |.-+++ + ..+...+.++..+. -
T Consensus 59 ~~n~~~~M~TGtGKT~~~~~~i~~l~~~~~~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~~ 138 (986)
T PRK15483 59 KANIDIKMETGTGKTYVYTRLMYELHQKYGLFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDKK 138 (986)
T ss_pred cceEEEEeCCCCCHHHHHHHHHHHHHHHcCCcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCccc
Confidence 3788888889999999999999998877 8888887665533322 222221 1 24444455444431 1
Q ss_pred CCCc------CCCCccc--c---ccceEEeehhhhhhccccccchHHHH--------HHHhccCCCceEEeecchhcccc
Q 038397 307 PYSK------LDSRSVG--I---REGVVFLTYSSLIASSEKGRSRLQQL--------VQWCGSGYDGLVIFDECHKAKNL 367 (1102)
Q Consensus 307 ~~~~------~~~~~~~--~---~~GvlF~TYs~L~~~~~~~~sRl~Ql--------~~W~g~dfdgvivfDEcH~akn~ 367 (1102)
+-|+ +..-... . .=-|+++|-..|.+......-. +|. ++.+. +-.-+||.||.|++...
T Consensus 139 k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~-D~~l~~g~~~p~~~i~-~~~PivIiDEPh~~~~~ 216 (986)
T PRK15483 139 KSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDY-DQTLLGGFTSPVDALA-ATRPVVIIDEPHRFPRD 216 (986)
T ss_pred ccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchh-hhhhccCCCChHHHHH-hCCCEEEEECCCCCCcc
Confidence 1111 0000000 1 1139999999987642210000 222 12221 34569999999998642
Q ss_pred CCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCC-------------CCCccch
Q 038397 368 VPEAGSQPTRTGEAVLELQARLPEARVVYCSATGAS-------------EPRNMGY 410 (1102)
Q Consensus 368 ~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgas-------------ep~Nl~y 410 (1102)
.-|. ..|.+.-|.-.+- =|||--. +..||.|
T Consensus 217 ------~k~~-----~~i~~lnpl~~lr-ysAT~~~~~~~~g~~~~~~~d~~NlvY 260 (986)
T PRK15483 217 ------NKFY-----QAIEALKPQMIIR-FGATFPDITEGKGKNKCTRKDYYNLQF 260 (986)
T ss_pred ------hHHH-----HHHHhcCcccEEE-EeeecCCccccccccccccccccCcee
Confidence 1123 2334444555444 5999976 4789998
No 143
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=84.05 E-value=0.76 Score=36.65 Aligned_cols=28 Identities=18% Similarity=0.581 Sum_probs=23.2
Q ss_pred ceeecCCcceEEEe-----CCCcceecCCCCCC
Q 038397 16 VQVRCAGCHIILTV-----GPGLTEFICGTCNL 43 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~-----~pg~~~~~Cp~C~~ 43 (1102)
+.+.|++|++.+.+ +++...+.|+.||.
T Consensus 1 M~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred CEEECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 36789999999964 56678999999996
No 144
>TIGR00580 mfd transcription-repair coupling factor (mfd). All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.
Probab=83.95 E-value=2.1 Score=55.95 Aligned_cols=82 Identities=18% Similarity=0.259 Sum_probs=54.9
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCC-CcHhHHHHhhcccccCCCCCCCeEEEeecCccchhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELP-WSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERR 884 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElp-WsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErR 884 (1102)
++|.+|+.+|+|=++..+.||-..-=. +.|....| .+...-+|+.|||+|+|+ .-|.+++.+-. +.
T Consensus 706 ~~F~~Gk~~ILVaT~iie~GIDIp~v~--------~VIi~~a~~~gls~l~Qr~GRvGR~g~---~g~aill~~~~--~~ 772 (926)
T TIGR00580 706 LEFYKGEFQVLVCTTIIETGIDIPNAN--------TIIIERADKFGLAQLYQLRGRVGRSKK---KAYAYLLYPHQ--KA 772 (926)
T ss_pred HHHHcCCCCEEEECChhhcccccccCC--------EEEEecCCCCCHHHHHHHhcCCCCCCC---CeEEEEEECCc--cc
Confidence 589999999999999999999886322 22333332 234466899999999987 45777665421 12
Q ss_pred hHHHHHHHHhhcCCcc
Q 038397 885 FASIVAKRLESLGALT 900 (1102)
Q Consensus 885 FaS~VAkRLeSLGALT 900 (1102)
+...-.+||+.|-..+
T Consensus 773 l~~~~~~RL~~~~~~~ 788 (926)
T TIGR00580 773 LTEDAQKRLEAIQEFS 788 (926)
T ss_pred CCHHHHHHHHHHHHhh
Confidence 3344556666654443
No 145
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=83.86 E-value=1 Score=59.47 Aligned_cols=55 Identities=24% Similarity=0.222 Sum_probs=46.8
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQAS 868 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvs 868 (1102)
++|++|+..|.|-++|.+.||-.-.=+ +=|-..+|-|.+.-+|+.||++|-++-+
T Consensus 724 e~F~~Gei~VLVATdAFGMGIDkPDVR--------~VIHydlPkSiEsYyQriGRAGRDG~~g 778 (1195)
T PLN03137 724 KQWSKDEINIICATVAFGMGINKPDVR--------FVIHHSLPKSIEGYHQECGRAGRDGQRS 778 (1195)
T ss_pred HHHhcCCCcEEEEechhhcCCCccCCc--------EEEEcCCCCCHHHHHhhhcccCCCCCCc
Confidence 689999999999999999999765332 3344789999999999999999998743
No 146
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=83.53 E-value=0.74 Score=36.70 Aligned_cols=27 Identities=22% Similarity=0.491 Sum_probs=22.7
Q ss_pred eeecCCcceEEEeCCCcc---eecCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLT---EFICGTCNL 43 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~---~~~Cp~C~~ 43 (1102)
..+|..||..+++..+.. ...||.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 568999999998777654 688999996
No 147
>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]
Probab=83.43 E-value=0.8 Score=58.82 Aligned_cols=118 Identities=24% Similarity=0.336 Sum_probs=69.6
Q ss_pred cccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhh
Q 038397 212 ESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLD 291 (1102)
Q Consensus 212 ~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~ 291 (1102)
.-.|.|=.=|+..+.+-.. |+++.=-| +++|-+|+||+-|.-..|.+=+=+-
T Consensus 390 l~GG~Lk~YQl~GLqWmVS-----LyNNnLNG-ILADEMGLGKTIQtIsLitYLmE~K---------------------- 441 (1157)
T KOG0386|consen 390 LQGGELKEYQLHGLQWMVS-----LYNNNLNG-ILADEMGLGKTIQTISLITYLMEHK---------------------- 441 (1157)
T ss_pred hcCCCCchhhhhhhHHHhh-----ccCCCccc-ccchhcccchHHHHHHHHHHHHHHc----------------------
Confidence 3456666777777665543 33333222 3899999999888877776554211
Q ss_pred hhCCCcccccccCCCCCC------------cCC--C----------CccccccceEEeehhhhhhccccccchHHHHHHH
Q 038397 292 DVGATCIEVHALNKLPYS------------KLD--S----------RSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQW 347 (1102)
Q Consensus 292 diG~~~i~v~~l~~~~~~------------~~~--~----------~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W 347 (1102)
.+-+..+.|+|++.++-. +|. + .....+..||.+||=-++.. +.=| +=|+|
T Consensus 442 ~~~GP~LvivPlstL~NW~~Ef~kWaPSv~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiikd----k~lL-sKI~W 516 (1157)
T KOG0386|consen 442 QMQGPFLIIVPLSTLVNWSSEFPKWAPSVQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIKD----KALL-SKISW 516 (1157)
T ss_pred ccCCCeEEeccccccCCchhhccccccceeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcCC----HHHH-hccCC
Confidence 112233344555554311 000 0 01135677999999988853 2223 23567
Q ss_pred hccCCCceEEeecchhccccC
Q 038397 348 CGSGYDGLVIFDECHKAKNLV 368 (1102)
Q Consensus 348 ~g~dfdgvivfDEcH~akn~~ 368 (1102)
--+|+||-|++||..
T Consensus 517 ------~yMIIDEGHRmKNa~ 531 (1157)
T KOG0386|consen 517 ------KYMIIDEGHRMKNAI 531 (1157)
T ss_pred ------cceeecccccccchh
Confidence 368999999999985
No 148
>COG1201 Lhr Lhr-like helicases [General function prediction only]
Probab=82.82 E-value=29 Score=45.09 Aligned_cols=159 Identities=22% Similarity=0.161 Sum_probs=99.0
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHH--HHHHHhcc-------CceEEEEEcCCchhhhH
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGL--IWENWHHG-------RRKALWISVGSDLKFDA 286 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~Agi--I~~n~l~G-------r~~~~w~s~s~~L~~Da 286 (1102)
.+.+.|.+|+-- ..+++. .|+-==||-|| +.||+ |++..+.. .-.+++||--..|-.|.
T Consensus 22 ~~t~~Q~~a~~~-i~~G~n---------vLiiAPTGsGK--TeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkALn~Di 89 (814)
T COG1201 22 SLTPPQRYAIPE-IHSGEN---------VLIIAPTGSGK--TEAAFLPVINELLSLGKGKLEDGIYALYISPLKALNNDI 89 (814)
T ss_pred CCCHHHHHHHHH-HhCCCc---------eEEEcCCCCCh--HHHHHHHHHHHHHhccCCCCCCceEEEEeCcHHHHHHHH
Confidence 577899999543 334432 33444477777 57775 45544433 35789999999999999
Q ss_pred HhhhhhhCCC-cccccccCCCCCCcCCC----CccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecc
Q 038397 287 RRDLDDVGAT-CIEVHALNKLPYSKLDS----RSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDEC 361 (1102)
Q Consensus 287 ~RDl~diG~~-~i~v~~l~~~~~~~~~~----~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEc 361 (1102)
+|-|...|.. .++| + ..-|+... +-..-+-.||-+|==+|.---.. .++.+.+. +- -.+|.||.
T Consensus 90 ~~rL~~~~~~~G~~v-~---vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~--~~~r~~l~----~v-r~VIVDEi 158 (814)
T COG1201 90 RRRLEEPLRELGIEV-A---VRHGDTPQSEKQKMLKNPPHILITTPESLAILLNS--PKFRELLR----DV-RYVIVDEI 158 (814)
T ss_pred HHHHHHHHHHcCCcc-c---eecCCCChHHhhhccCCCCcEEEeChhHHHHHhcC--HHHHHHhc----CC-cEEEeehh
Confidence 9999998863 4444 1 11121110 11123456899887666433111 14444332 11 16889999
Q ss_pred hhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCC
Q 038397 362 HKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGA 402 (1102)
Q Consensus 362 H~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATga 402 (1102)
|+.++. +...+-.....+|++..++.+=+=-|||-.
T Consensus 159 Hel~~s-----KRG~~Lsl~LeRL~~l~~~~qRIGLSATV~ 194 (814)
T COG1201 159 HALAES-----KRGVQLALSLERLRELAGDFQRIGLSATVG 194 (814)
T ss_pred hhhhcc-----ccchhhhhhHHHHHhhCcccEEEeehhccC
Confidence 999865 355788889999999987666667788844
No 149
>PRK01172 ski2-like helicase; Provisional
Probab=82.75 E-value=0.87 Score=57.24 Aligned_cols=61 Identities=21% Similarity=0.110 Sum_probs=45.7
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQ 866 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQ 866 (1102)
+.|.+|...|.|-++.++.|+.+.+.+=+-..-.|.--..-.|+|.....|+.||++|.+.
T Consensus 305 ~~f~~g~i~VLvaT~~la~Gvnipa~~VII~~~~~~~~~~~~~~s~~~~~Qm~GRAGR~g~ 365 (674)
T PRK01172 305 EMFRNRYIKVIVATPTLAAGVNLPARLVIVRDITRYGNGGIRYLSNMEIKQMIGRAGRPGY 365 (674)
T ss_pred HHHHcCCCeEEEecchhhccCCCcceEEEEcCceEeCCCCceeCCHHHHHHHhhcCCCCCC
Confidence 6799999999999999999999988432222222221112246899999999999999885
No 150
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=82.70 E-value=0.84 Score=44.98 Aligned_cols=33 Identities=15% Similarity=0.328 Sum_probs=23.6
Q ss_pred cceeecCCcceEEEeCCCcceecCCCCCCCCCCC
Q 038397 15 GVQVRCAGCHIILTVGPGLTEFICGTCNLPQMLP 48 (1102)
Q Consensus 15 ~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~ 48 (1102)
..+-.|+.||+-|.== +-.-..|||||..+.+.
T Consensus 7 GtKR~Cp~CG~kFYDL-nk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 7 GTKRTCPSCGAKFYDL-NKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCcccCCCCcchhccC-CCCCccCCCCCCccCcc
Confidence 4456699999998321 11557799999977765
No 151
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=82.68 E-value=0.75 Score=37.72 Aligned_cols=27 Identities=26% Similarity=0.770 Sum_probs=22.5
Q ss_pred eecCCcceE-EEeCCCcceecCCCCCCC
Q 038397 18 VRCAGCHII-LTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 18 ~~C~~C~a~-l~~~pg~~~~~Cp~C~~~ 44 (1102)
++|+.||.. +.+.+...++.|+.||+-
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BB
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCE
Confidence 479999997 477889999999999974
No 152
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=82.57 E-value=5.2 Score=49.34 Aligned_cols=138 Identities=22% Similarity=0.317 Sum_probs=85.5
Q ss_pred EeecCCCCCcchh--hHHHHHHHHhccCceEEEEEc----CCchhhhHHhhhhhhCCCc-ccccccCCCCCCc-CCCCcc
Q 038397 245 FIGDGAGVGKGRT--IAGLIWENWHHGRRKALWISV----GSDLKFDARRDLDDVGATC-IEVHALNKLPYSK-LDSRSV 316 (1102)
Q Consensus 245 ~~gDg~GvGKGR~--~AgiI~~n~l~Gr~~~~w~s~----s~~L~~Da~RDl~diG~~~-i~v~~l~~~~~~~-~~~~~~ 316 (1102)
|+---|+-||+-. +||| .|.+.|.+|.+|+.- -|.-+.|.++--+-+|-.. |+| ..+.++... .-....
T Consensus 236 lVVSaTasGKTLIgElAGi--~~~l~~g~KmlfLvPLVALANQKy~dF~~rYs~LglkvairV-G~srIk~~~~pv~~~t 312 (830)
T COG1202 236 LVVSATASGKTLIGELAGI--PRLLSGGKKMLFLVPLVALANQKYEDFKERYSKLGLKVAIRV-GMSRIKTREEPVVVDT 312 (830)
T ss_pred EEEeccCCCcchHHHhhCc--HHHHhCCCeEEEEehhHHhhcchHHHHHHHhhcccceEEEEe-chhhhcccCCccccCC
Confidence 4555688889865 4564 688887788998764 3555667777777788753 554 333332110 000112
Q ss_pred ccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEE
Q 038397 317 GIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVY 396 (1102)
Q Consensus 317 ~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY 396 (1102)
+.+..||--||-..---=..| -+| | -=|++|.||.|-....-- .+---| -+-+|....|.|..+|
T Consensus 313 ~~dADIIVGTYEGiD~lLRtg-~~l-------g--diGtVVIDEiHtL~deER----G~RLdG-LI~RLr~l~~~AQ~i~ 377 (830)
T COG1202 313 SPDADIIVGTYEGIDYLLRTG-KDL-------G--DIGTVVIDEIHTLEDEER----GPRLDG-LIGRLRYLFPGAQFIY 377 (830)
T ss_pred CCCCcEEEeechhHHHHHHcC-Ccc-------c--ccceEEeeeeeeccchhc----ccchhh-HHHHHHHhCCCCeEEE
Confidence 456779999997532110011 122 1 138999999998875421 122233 4567899999999999
Q ss_pred EecC
Q 038397 397 CSAT 400 (1102)
Q Consensus 397 ~SAT 400 (1102)
-|||
T Consensus 378 LSAT 381 (830)
T COG1202 378 LSAT 381 (830)
T ss_pred EEee
Confidence 9999
No 153
>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A.
Probab=82.43 E-value=1.9 Score=45.16 Aligned_cols=67 Identities=24% Similarity=0.210 Sum_probs=48.4
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcce-eEeecCCCCCcchhhHHHHHHHH-------hccCceEEEEEcCCchhhhHH
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAG-FFIGDGAGVGKGRTIAGLIWENW-------HHGRRKALWISVGSDLKFDAR 287 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~G-f~~gDg~GvGKGR~~AgiI~~n~-------l~Gr~~~~w~s~s~~L~~Da~ 287 (1102)
.|+..|.+||.++... .+ +++--..|.||+.+++.+|..-+ ....++.+|++.++.-..++.
T Consensus 1 ~ln~~Q~~Ai~~~~~~----------~~~~~i~GpPGTGKT~~l~~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~ 70 (236)
T PF13086_consen 1 KLNESQREAIQSALSS----------NGITLIQGPPGTGKTTTLASIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNIL 70 (236)
T ss_dssp ---HHHHHHHHHHCTS----------SE-EEEE-STTSSHHHHHHHHHHHH-------HCCCSS-EEEEESSHHHHHHHH
T ss_pred CCCHHHHHHHHHHHcC----------CCCEEEECCCCCChHHHHHHHHHHhccchhhhhhhccccceeecCCchhHHHHH
Confidence 4788999998877643 23 34444469999999999988874 566677999999998888888
Q ss_pred hhhhh
Q 038397 288 RDLDD 292 (1102)
Q Consensus 288 RDl~d 292 (1102)
.-|..
T Consensus 71 ~~l~~ 75 (236)
T PF13086_consen 71 ERLKK 75 (236)
T ss_dssp HHHHC
T ss_pred HHHHh
Confidence 77766
No 154
>PF14353 CpXC: CpXC protein
Probab=82.14 E-value=0.99 Score=44.99 Aligned_cols=31 Identities=19% Similarity=0.542 Sum_probs=23.8
Q ss_pred eeecCCcceEEE------eCCCcc-------------eecCCCCCCCCCC
Q 038397 17 QVRCAGCHIILT------VGPGLT-------------EFICGTCNLPQML 47 (1102)
Q Consensus 17 ~~~C~~C~a~l~------~~pg~~-------------~~~Cp~C~~~~~l 47 (1102)
++.|++||..+. |..... .|.||.||....+
T Consensus 1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceec
Confidence 578999999884 344433 7999999986666
No 155
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=81.71 E-value=1.1 Score=56.80 Aligned_cols=23 Identities=39% Similarity=0.796 Sum_probs=17.1
Q ss_pred eecCCCccceeeccCCCccccCCCCCcc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
++.|--||..-.+ .++||.||.+
T Consensus 462 ~L~CH~Cg~~~~~-----p~~Cp~Cgs~ 484 (730)
T COG1198 462 QLRCHYCGYQEPI-----PQSCPECGSE 484 (730)
T ss_pred eeEeCCCCCCCCC-----CCCCCCCCCC
Confidence 4788888876444 4589999998
No 156
>PRK10689 transcription-repair coupling factor; Provisional
Probab=81.63 E-value=2.2 Score=57.07 Aligned_cols=82 Identities=21% Similarity=0.283 Sum_probs=55.5
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecC--CCcHhHHHHhhcccccCCCCCCCeEEEeecCccchh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLEL--PWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGER 883 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLEl--pWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GEr 883 (1102)
++|.+|+.+|+|-++.++.||-.-.=. |+.++- .++...-+|+.|||+|+|+. -|.++++.-...
T Consensus 855 ~~Fr~Gk~~VLVaTdIierGIDIP~v~---------~VIi~~ad~fglaq~~Qr~GRvGR~g~~---g~a~ll~~~~~~- 921 (1147)
T PRK10689 855 NDFHHQRFNVLVCTTIIETGIDIPTAN---------TIIIERADHFGLAQLHQLRGRVGRSHHQ---AYAWLLTPHPKA- 921 (1147)
T ss_pred HHHHhcCCCEEEECchhhcccccccCC---------EEEEecCCCCCHHHHHHHhhccCCCCCc---eEEEEEeCCCcc-
Confidence 689999999999999999999884222 222221 13445679999999999885 488887754321
Q ss_pred hhHHHHHHHHhhcCCccc
Q 038397 884 RFASIVAKRLESLGALTQ 901 (1102)
Q Consensus 884 RFaS~VAkRLeSLGALT~ 901 (1102)
......+||+.+-.+|.
T Consensus 922 -~~~~~~~rl~~~~~~~~ 938 (1147)
T PRK10689 922 -MTTDAQKRLEAIASLED 938 (1147)
T ss_pred -cCHHHHHHHHHHHHhcC
Confidence 22234466666555554
No 157
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=81.51 E-value=0.61 Score=52.29 Aligned_cols=45 Identities=27% Similarity=0.753 Sum_probs=37.4
Q ss_pred cccccCcHHHHhhhhhccccCCccccCCCCCCcccCCCCCCcccc-ch
Q 038397 662 ICEICNSEEERKKLLQCSCCGQLVHSGCLVPPITDVIPSDWSCHS-CK 708 (1102)
Q Consensus 662 ~ce~cgsed~k~kLL~cs~cgk~~H~~cL~PP~~di~~~dW~c~s-Ck 708 (1102)
.|.+|+......+++.||-|++++|+.|.- +-++|.+.|.|+- |.
T Consensus 316 lC~IC~~P~~E~E~~FCD~CDRG~HT~CVG--L~~lP~G~WICD~~C~ 361 (381)
T KOG1512|consen 316 LCRICLGPVIESEHLFCDVCDRGPHTLCVG--LQDLPRGEWICDMRCR 361 (381)
T ss_pred hhhccCCcccchheeccccccCCCCccccc--cccccCccchhhhHHH
Confidence 367899888888899999999999999963 3467889999993 44
No 158
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=81.37 E-value=0.7 Score=33.46 Aligned_cols=23 Identities=39% Similarity=0.969 Sum_probs=17.4
Q ss_pred cCCCccceeeccCCCccccCCCCCccc
Q 038397 98 PCANCKAILNVPHGLVRFSCPQCAVEL 124 (1102)
Q Consensus 98 ~C~~C~A~~~vp~~~~~f~Cp~C~~~L 124 (1102)
.|.+||+.+.... .| ||.||.+|
T Consensus 1 ~Cp~CG~~~~~~~---~f-C~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIEDDA---KF-CPNCGTPL 23 (23)
T ss_pred CCcccCCCCCCcC---cc-hhhhCCcC
Confidence 3889999886443 34 99999886
No 159
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=80.90 E-value=0.5 Score=59.82 Aligned_cols=24 Identities=25% Similarity=0.714 Sum_probs=0.0
Q ss_pred eecCCCccceeeccCCCccccCCCCCcccc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVELA 125 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~ 125 (1102)
...|..|+..++-. .||-|+.+..
T Consensus 680 ~~~Cp~C~~~~~~~------~C~~C~~~~~ 703 (900)
T PF03833_consen 680 VYVCPDCGIEVEED------ECPKCGRETT 703 (900)
T ss_dssp ------------------------------
T ss_pred ceeccccccccCcc------ccccccccCc
Confidence 37899999977644 9999999943
No 160
>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.83 E-value=6.3 Score=48.88 Aligned_cols=148 Identities=22% Similarity=0.286 Sum_probs=86.6
Q ss_pred CCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhh-------------hCCCcccccccCCCCCCcCCCCcc
Q 038397 250 AGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDD-------------VGATCIEVHALNKLPYSKLDSRSV 316 (1102)
Q Consensus 250 ~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~d-------------iG~~~i~v~~l~~~~~~~~~~~~~ 316 (1102)
||-||+-.+||+|++-|-+|.|+-+++--+....+-..-...| +|...|++--+|.+..
T Consensus 6 tgsgkt~~ma~lil~~y~kgyr~flffvnq~nilekt~~nftd~~s~kylf~e~i~~~d~~i~ikkvn~fse-------- 77 (812)
T COG3421 6 TGSGKTLVMAGLILECYKKGYRNFLFFVNQANILEKTKLNFTDSVSSKYLFSENININDENIEIKKVNNFSE-------- 77 (812)
T ss_pred cCCChhhHHHHHHHHHHHhchhhEEEEecchhHHHHHHhhcccchhhhHhhhhhhhcCCceeeeeeecccCc--------
Confidence 7899999999999999999999999987777666655544433 3344444433333321
Q ss_pred cccc--ceEEeehhhhhhc--ccc-ccchHHHHHHHhccCCCceEEeecchhccccCCCCCC---CchhHHHHHHHH-hh
Q 038397 317 GIRE--GVVFLTYSSLIAS--SEK-GRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGS---QPTRTGEAVLEL-QA 387 (1102)
Q Consensus 317 ~~~~--GvlF~TYs~L~~~--~~~-~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~---~~s~~g~avl~L-Q~ 387 (1102)
..+ -|.|+|--.|-+. +.+ -..-|+-+ ++-.-|.+=||+|+.....-.+.. +.-.-=.+++.| -+
T Consensus 78 -hnd~iei~fttiq~l~~d~~~~ken~itledl-----~~~klvfl~deahhln~~tkkk~~de~~~~~~we~~v~la~~ 151 (812)
T COG3421 78 -HNDAIEIYFTTIQGLFSDFTRAKENAITLEDL-----KDQKLVFLADEAHHLNTETKKKLNDEASEKRNWESVVKLALE 151 (812)
T ss_pred -cCCceEEEEeehHHHHHHHHhhccccccHhhH-----hhCceEEEechhhhhhhhhhhhcccHHHHHhhHHHHHHHHHh
Confidence 122 3889995554432 111 12223322 244568888999997655422211 000011123322 34
Q ss_pred hCCCccEEEEecCCCCCCCccchh
Q 038397 388 RLPEARVVYCSATGASEPRNMGYM 411 (1102)
Q Consensus 388 ~lP~ARvvY~SATgasep~Nl~ym 411 (1102)
.-|+--++--|||.-.+-...+-|
T Consensus 152 ~nkd~~~lef~at~~k~k~v~~ky 175 (812)
T COG3421 152 QNKDNLLLEFSATIPKEKSVEDKY 175 (812)
T ss_pred cCCCceeehhhhcCCccccHHHHh
Confidence 556667888889888665555533
No 161
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=80.79 E-value=0.86 Score=35.15 Aligned_cols=26 Identities=23% Similarity=0.432 Sum_probs=18.6
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
-|+.||+.....++-....||.||..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 49999999999999999999999964
No 162
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=80.78 E-value=1.2 Score=38.81 Aligned_cols=31 Identities=29% Similarity=0.684 Sum_probs=26.3
Q ss_pred eecCCCccceeeccCCCc--cccCCCCCccccc
Q 038397 96 QLPCANCKAILNVPHGLV--RFSCPQCAVELAV 126 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~--~f~Cp~C~~~L~v 126 (1102)
+..|..||+.+.||.... -..||.||++|-|
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELEV 34 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEEE
Confidence 468999999999988654 3599999999988
No 163
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=79.75 E-value=0.95 Score=35.40 Aligned_cols=27 Identities=22% Similarity=0.616 Sum_probs=21.1
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLPQM 46 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~~~ 46 (1102)
.|+.||+.....++ ....|++||....
T Consensus 2 ~C~~Cg~~~~~~~~-~~irC~~CG~RIl 28 (32)
T PF03604_consen 2 ICGECGAEVELKPG-DPIRCPECGHRIL 28 (32)
T ss_dssp BESSSSSSE-BSTS-STSSBSSSS-SEE
T ss_pred CCCcCCCeeEcCCC-CcEECCcCCCeEE
Confidence 49999999998887 4689999998654
No 164
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=79.71 E-value=0.98 Score=39.46 Aligned_cols=23 Identities=35% Similarity=0.871 Sum_probs=20.2
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
.|+.|+..+ |+-..|.||+||.+
T Consensus 1 ~Cpv~~~~~---~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 1 LCPVCKKDL---PAHVNFECPDCGIP 23 (55)
T ss_pred CCCCCcccc---ccccCCcCCCCCCc
Confidence 488999887 99999999999964
No 165
>COG1204 Superfamily II helicase [General function prediction only]
Probab=79.36 E-value=6.9 Score=50.41 Aligned_cols=141 Identities=21% Similarity=0.170 Sum_probs=88.4
Q ss_pred ceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCC-Ccccccc
Q 038397 242 AGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDS-RSVGIRE 320 (1102)
Q Consensus 242 ~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~-~~~~~~~ 320 (1102)
.=+++.==||-||+-..==.|+.-.++|+.|+|++---..|-+--.+-++++-.-.|+|...- |+.+. ..--.+.
T Consensus 48 ~N~li~aPTgsGKTlIA~lai~~~l~~~~~k~vYivPlkALa~Ek~~~~~~~~~~GirV~~~T----gD~~~~~~~l~~~ 123 (766)
T COG1204 48 ENVLISAPTGSGKTLIALLAILSTLLEGGGKVVYIVPLKALAEEKYEEFSRLEELGIRVGIST----GDYDLDDERLARY 123 (766)
T ss_pred CcEEEEcCCCCchHHHHHHHHHHHHHhcCCcEEEEeChHHHHHHHHHHhhhHHhcCCEEEEec----CCcccchhhhccC
Confidence 345666679999988776678888888888899998888887766666653322223332221 11111 1112467
Q ss_pred ceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecC
Q 038397 321 GVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSAT 400 (1102)
Q Consensus 321 GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SAT 400 (1102)
+||-+||=.+-+--.+..+ |... . ++||.||.|....-.-+.. --..+-++...-++.|+|=.|||
T Consensus 124 ~ViVtT~EK~Dsl~R~~~~-------~~~~-V-~lvViDEiH~l~d~~RG~~-----lE~iv~r~~~~~~~~rivgLSAT 189 (766)
T COG1204 124 DVIVTTPEKLDSLTRKRPS-------WIEE-V-DLVVIDEIHLLGDRTRGPV-----LESIVARMRRLNELIRIVGLSAT 189 (766)
T ss_pred CEEEEchHHhhHhhhcCcc-------hhhc-c-cEEEEeeeeecCCcccCce-----ehhHHHHHHhhCcceEEEEEeee
Confidence 8999999777654333333 4433 2 5899999999875521111 11234455566667999999999
No 166
>PRK08727 hypothetical protein; Validated
Probab=79.18 E-value=9.5 Score=41.82 Aligned_cols=125 Identities=16% Similarity=0.171 Sum_probs=73.6
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCccccccce
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSVGIREGV 322 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~Gv 322 (1102)
.+++--++|+||+.-+.++..+-..+|. ++++++... ..+.+
T Consensus 43 ~l~l~G~~G~GKThL~~a~~~~~~~~~~-~~~y~~~~~-----~~~~~-------------------------------- 84 (233)
T PRK08727 43 WLYLSGPAGTGKTHLALALCAAAEQAGR-SSAYLPLQA-----AAGRL-------------------------------- 84 (233)
T ss_pred eEEEECCCCCCHHHHHHHHHHHHHHcCC-cEEEEeHHH-----hhhhH--------------------------------
Confidence 3566666999999999988877666675 588887421 00000
Q ss_pred EEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCC--CccEEEEecC
Q 038397 323 VFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLP--EARVVYCSAT 400 (1102)
Q Consensus 323 lF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP--~ARvvY~SAT 400 (1102)
.++++.+. .. -+||+||.|...+- ...-.+...|-+.+- ...||++|-.
T Consensus 85 -------------------~~~~~~l~-~~-dlLiIDDi~~l~~~--------~~~~~~lf~l~n~~~~~~~~vI~ts~~ 135 (233)
T PRK08727 85 -------------------RDALEALE-GR-SLVALDGLESIAGQ--------REDEVALFDFHNRARAAGITLLYTARQ 135 (233)
T ss_pred -------------------HHHHHHHh-cC-CEEEEeCcccccCC--------hHHHHHHHHHHHHHHHcCCeEEEECCC
Confidence 00111111 11 38999999976632 123345566666543 3459998887
Q ss_pred CCCCCCcc--chhhhccccCCCCCCC--CHHHHHHHHhc
Q 038397 401 GASEPRNM--GYMVRLGLWGAGTCFK--DFQIFLGALDK 435 (1102)
Q Consensus 401 gasep~Nl--~ym~RLGLWg~gt~f~--~~~~f~~a~~~ 435 (1102)
..++-..+ ...+|| -||.-..|+ +.++....+++
T Consensus 136 ~p~~l~~~~~dL~SRl-~~~~~~~l~~~~~e~~~~iL~~ 173 (233)
T PRK08727 136 MPDGLALVLPDLRSRL-AQCIRIGLPVLDDVARAAVLRE 173 (233)
T ss_pred ChhhhhhhhHHHHHHH-hcCceEEecCCCHHHHHHHHHH
Confidence 66665433 456887 255444454 55666555544
No 167
>PRK14701 reverse gyrase; Provisional
Probab=78.91 E-value=7 Score=54.15 Aligned_cols=124 Identities=13% Similarity=0.126 Sum_probs=70.3
Q ss_pred ccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHH--hccCceEEEEEcCCchhhhHHhhhhhhCC
Q 038397 218 SCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENW--HHGRRKALWISVGSDLKFDARRDLDDVGA 295 (1102)
Q Consensus 218 S~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~--l~Gr~~~~w~s~s~~L~~Da~RDl~diG~ 295 (1102)
+..|.+++--+.+.+ -|++-=.||.||+-. +++.-.+ .+|. +++.++-...|-.+....++.++.
T Consensus 81 t~iQ~~~i~~il~G~----------d~li~APTGsGKTl~--~~~~al~~~~~g~-~aLVl~PTreLa~Qi~~~l~~l~~ 147 (1638)
T PRK14701 81 WSIQKTWAKRILRGK----------SFSIVAPTGMGKSTF--GAFIALFLALKGK-KCYIILPTTLLVKQTVEKIESFCE 147 (1638)
T ss_pred CHHHHHHHHHHHcCC----------CEEEEEcCCCCHHHH--HHHHHHHHHhcCC-eEEEEECHHHHHHHHHHHHHHHHh
Confidence 467777766555532 234555599999973 2222223 2554 599999999999999999998765
Q ss_pred C---cccccccCC-CCCCcCCCCcc-ccc---cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccc
Q 038397 296 T---CIEVHALNK-LPYSKLDSRSV-GIR---EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKN 366 (1102)
Q Consensus 296 ~---~i~v~~l~~-~~~~~~~~~~~-~~~---~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn 366 (1102)
. .+.+..++. +...+- .... .+. -.||.+|--.|.. .++++.. .++ .+||+||||.+..
T Consensus 148 ~~~~~v~v~~~~g~~s~~e~-~~~~~~l~~g~~dILV~TPgrL~~-------~~~~l~~---~~i-~~iVVDEAD~ml~ 214 (1638)
T PRK14701 148 KANLDVRLVYYHSNLRKKEK-EEFLERIENGDFDILVTTAQFLAR-------NFPEMKH---LKF-DFIFVDDVDAFLK 214 (1638)
T ss_pred hcCCceeEEEEeCCCCHHHH-HHHHHHHhcCCCCEEEECCchhHH-------hHHHHhh---CCC-CEEEEECceeccc
Confidence 3 223323321 111000 0000 122 2488888554431 2333221 334 4899999999864
No 168
>PRK05642 DNA replication initiation factor; Validated
Probab=78.73 E-value=46 Score=36.63 Aligned_cols=72 Identities=21% Similarity=0.133 Sum_probs=45.3
Q ss_pred eEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCC--ccEEEEecCCCCCCCc--cchhhhccccCCCCCC--CCHHH
Q 038397 355 LVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPE--ARVVYCSATGASEPRN--MGYMVRLGLWGAGTCF--KDFQI 428 (1102)
Q Consensus 355 vivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~--ARvvY~SATgasep~N--l~ym~RLGLWg~gt~f--~~~~~ 428 (1102)
++|+|+.|...+. .++-.....|=|.+.. -++|++|-|..++-.. =...+|++ ||.-..+ ++.++
T Consensus 100 ~LiiDDi~~~~~~--------~~~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~-~gl~~~l~~~~~e~ 170 (234)
T PRK05642 100 LVCLDDLDVIAGK--------ADWEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLT-LALVFQMRGLSDED 170 (234)
T ss_pred EEEEechhhhcCC--------hHHHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHh-cCeeeecCCCCHHH
Confidence 7889999976432 2233445666665544 4688888877766543 34679986 7754433 36777
Q ss_pred HHHHHhc
Q 038397 429 FLGALDK 435 (1102)
Q Consensus 429 f~~a~~~ 435 (1102)
.+..+++
T Consensus 171 ~~~il~~ 177 (234)
T PRK05642 171 KLRALQL 177 (234)
T ss_pred HHHHHHH
Confidence 7776653
No 169
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=78.52 E-value=1.4 Score=36.75 Aligned_cols=29 Identities=14% Similarity=0.406 Sum_probs=24.8
Q ss_pred ecCCCccceeeccCCCccccCCCCCccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
..|+.||+.+++. ......||.||..+..
T Consensus 3 Y~C~~Cg~~~~~~-~~~~irC~~CG~rIly 31 (44)
T smart00659 3 YICGECGRENEIK-SKDVVRCRECGYRILY 31 (44)
T ss_pred EECCCCCCEeecC-CCCceECCCCCceEEE
Confidence 5799999999987 4467899999999765
No 170
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=77.68 E-value=4 Score=44.48 Aligned_cols=85 Identities=22% Similarity=0.459 Sum_probs=59.1
Q ss_pred CCCCccceeecCCcceEEEeCCCcceecCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCC
Q 038397 10 PPPNVGVQVRCAGCHIILTVGPGLTEFICG--TCNLPQMLPPELMPASTGGSVPNNTTSSNTTNSTRPTHMKAASSHVPA 87 (1102)
Q Consensus 10 ~~~~~~~~~~C~~C~a~l~~~pg~~~~~Cp--~C~~~~~l~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a 87 (1102)
..||++--|||+ |.+.|--.---+...|| +|.....|.|-. + . .+.
T Consensus 114 nAPpGKKYVRCP-CNCLLICK~sSqRIACPRpnCkRiInL~p~~----------~------~---------------p~~ 161 (275)
T KOG4684|consen 114 NAPPGKKYVRCP-CNCLLICKASSQRIACPRPNCKRIINLDPLI----------E------K---------------PRD 161 (275)
T ss_pred CCCCCCceeecC-CcEEEEEecccceeccCCCCcceeeecCCCC----------C------C---------------CCC
Confidence 355789999997 88888888888999996 788877764332 1 0 011
Q ss_pred CCCCCccceecCCCccceeeccCCCccc-cCCCCCccccc
Q 038397 88 LGIDPTKIQLPCANCKAILNVPHGLVRF-SCPQCAVELAV 126 (1102)
Q Consensus 88 ~~~~~t~~~~~C~~C~A~~~vp~~~~~f-~Cp~C~~~L~v 126 (1102)
++-.|+.-++.|+.|.-.+-+..-.... +||.|..--.|
T Consensus 162 P~~~P~gcRV~CgHC~~tFLfnt~tnaLArCPHCrKvSsv 201 (275)
T KOG4684|consen 162 PGTAPTGCRVKCGHCNETFLFNTLTNALARCPHCRKVSSV 201 (275)
T ss_pred CCCCCcceEEEecCccceeehhhHHHHHhcCCcccchhhh
Confidence 2234556689999999987665544454 89999765444
No 171
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=77.31 E-value=0.95 Score=44.65 Aligned_cols=30 Identities=27% Similarity=0.535 Sum_probs=20.5
Q ss_pred ccceeecCCcceEEEeCCCcceecCCCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLTEFICGTCNLPQ 45 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~ 45 (1102)
.+...+|..||..+.+..-. +.||.||-..
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~ 96 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFD--FSCPRCGSPD 96 (113)
T ss_dssp E--EEEETTTS-EEECHHCC--HH-SSSSSS-
T ss_pred cCCcEECCCCCCEEecCCCC--CCCcCCcCCC
Confidence 34578899999988776655 8999999753
No 172
>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.
Probab=76.91 E-value=2.1 Score=44.52 Aligned_cols=43 Identities=30% Similarity=0.481 Sum_probs=27.6
Q ss_pred ccccceEEeehhhhhhccccccchHHHHHHHh-ccCC-CceEEeecchhccccC
Q 038397 317 GIREGVVFLTYSSLIASSEKGRSRLQQLVQWC-GSGY-DGLVIFDECHKAKNLV 368 (1102)
Q Consensus 317 ~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~-g~df-dgvivfDEcH~akn~~ 368 (1102)
...-.|||++|+-|..... | ..+ |-++ +.+|||||+|+.-+.+
T Consensus 117 ~~~adivi~~y~yl~~~~~----~-----~~~~~~~~~~~ivI~DEAHNL~~~~ 161 (174)
T PF06733_consen 117 AKNADIVICNYNYLFDPSI----R-----KSLFGIDLKDNIVIFDEAHNLEDAA 161 (174)
T ss_dssp GGG-SEEEEETHHHHSHHH----H-----HHHCT--CCCEEEEETTGGGCGGGC
T ss_pred cccCCEEEeCHHHHhhHHH----H-----hhhccccccCcEEEEecccchHHHH
Confidence 3456799999999986521 1 122 2233 4599999999876654
No 173
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=76.84 E-value=0.92 Score=47.32 Aligned_cols=33 Identities=21% Similarity=0.455 Sum_probs=28.2
Q ss_pred eecCCCccceeeccCCCc-cccCCCCCccccccc
Q 038397 96 QLPCANCKAILNVPHGLV-RFSCPQCAVELAVDM 128 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~-~f~Cp~C~~~L~v~~ 128 (1102)
--.|.+|+...++..-+. .|.||.||.+|.-++
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAMELNFTCPRCGAMLDYLD 142 (158)
T ss_pred eEECCCCCcEeeHHHHHHcCCcCCCCCCEeeecc
Confidence 478999999998877666 699999999998765
No 174
>PRK13767 ATP-dependent helicase; Provisional
Probab=76.84 E-value=3.2 Score=54.11 Aligned_cols=62 Identities=19% Similarity=0.224 Sum_probs=49.4
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEe
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRII 875 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l 875 (1102)
++|.+|+..|+|-+++.+-||.+-.-. +-|.+..|.|....+|+.||++|.-...+.-+.+.
T Consensus 334 ~~fk~G~i~vLVaTs~Le~GIDip~Vd--------~VI~~~~P~sv~~ylQRiGRaGR~~g~~~~g~ii~ 395 (876)
T PRK13767 334 EKLKRGELKVVVSSTSLELGIDIGYID--------LVVLLGSPKSVSRLLQRIGRAGHRLGEVSKGRIIV 395 (876)
T ss_pred HHHHcCCCeEEEECChHHhcCCCCCCc--------EEEEeCCCCCHHHHHHhcccCCCCCCCCCcEEEEE
Confidence 679999999999999999999985432 44568899999999999999999743333444444
No 175
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=76.50 E-value=1.1 Score=46.10 Aligned_cols=37 Identities=27% Similarity=0.582 Sum_probs=28.0
Q ss_pred cceecCCCccceeeccCC------CccccCCCCCccccccccc
Q 038397 94 KIQLPCANCKAILNVPHG------LVRFSCPQCAVELAVDMSK 130 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~------~~~f~Cp~C~~~L~v~~~~ 130 (1102)
.....|.+||...++-.- .+.|.||.||.+|..++..
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~ 139 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDNS 139 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCch
Confidence 346899999998876322 2349999999999887643
No 176
>PRK02935 hypothetical protein; Provisional
Probab=76.39 E-value=1.5 Score=42.91 Aligned_cols=36 Identities=31% Similarity=0.417 Sum_probs=28.8
Q ss_pred ccceeecCCcceEEEeCCCcceecCCCCCCCCCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLTEFICGTCNLPQMLPPEL 51 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~p~~ 51 (1102)
.++||.|++|+..-++--- .-.|.+|+.+..|+|++
T Consensus 67 kavqV~CP~C~K~TKmLGr--vD~CM~C~~PLTLd~~l 102 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLGR--VDACMHCNQPLTLDRSL 102 (110)
T ss_pred cceeeECCCCCchhhhccc--eeecCcCCCcCCcCccc
Confidence 5789999999987654322 23899999999998887
No 177
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=76.38 E-value=1 Score=47.87 Aligned_cols=34 Identities=26% Similarity=0.572 Sum_probs=28.7
Q ss_pred ceecCCCccceeeccCCCc-cccCCCCCccccccc
Q 038397 95 IQLPCANCKAILNVPHGLV-RFSCPQCAVELAVDM 128 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~~~~-~f~Cp~C~~~L~v~~ 128 (1102)
.--.|.+|+...++..-+. .|.||.||.+|.-++
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEYD 150 (178)
T ss_pred CEEECCCCCcEEeHHHHhhcCCcCCCCCCCCeecc
Confidence 3478999999998877665 699999999998765
No 178
>PLN00162 transport protein sec23; Provisional
Probab=76.13 E-value=3 Score=53.60 Aligned_cols=35 Identities=29% Similarity=0.642 Sum_probs=31.7
Q ss_pred eeecCCcceEE----EeCCCcceecCCCCCCCCCCCCCC
Q 038397 17 QVRCAGCHIIL----TVGPGLTEFICGTCNLPQMLPPEL 51 (1102)
Q Consensus 17 ~~~C~~C~a~l----~~~pg~~~~~Cp~C~~~~~l~p~~ 51 (1102)
-+||..|++.| .|..+-..+.||.|+..+.+|++-
T Consensus 53 pvRC~~CraylNPf~~~d~~~~~W~C~~C~~~N~~P~~Y 91 (761)
T PLN00162 53 PLRCRTCRAVLNPYCRVDFQAKIWICPFCFQRNHFPPHY 91 (761)
T ss_pred CCccCCCcCEECCceEEecCCCEEEccCCCCCCCCchHh
Confidence 48999999999 678888999999999999998875
No 179
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=75.98 E-value=1.9 Score=54.82 Aligned_cols=26 Identities=23% Similarity=0.590 Sum_probs=23.9
Q ss_pred eecCCcceEEEeCCCcceecCCCCCC
Q 038397 18 VRCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
..|++|...|++--....+.|.|||+
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~ 470 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGY 470 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCC
Confidence 35999999999999999999999996
No 180
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=75.60 E-value=1.9 Score=57.03 Aligned_cols=26 Identities=27% Similarity=0.763 Sum_probs=17.3
Q ss_pred ecCCCccceeeccCCCccccCCCCCcccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAVD 127 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~ 127 (1102)
.-|..||+.++. .+.||.||+++.-|
T Consensus 680 ~fCP~CGs~te~-----vy~CPsCGaev~~d 705 (1337)
T PRK14714 680 NRCPDCGTHTEP-----VYVCPDCGAEVPPD 705 (1337)
T ss_pred ccCcccCCcCCC-----ceeCccCCCccCCC
Confidence 367777777643 35777777776554
No 181
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=75.45 E-value=2.5 Score=38.26 Aligned_cols=39 Identities=21% Similarity=0.387 Sum_probs=32.2
Q ss_pred CCCCccceeecCCcceE-EEeCCCcceecCCCCCCCCCCC
Q 038397 10 PPPNVGVQVRCAGCHII-LTVGPGLTEFICGTCNLPQMLP 48 (1102)
Q Consensus 10 ~~~~~~~~~~C~~C~a~-l~~~pg~~~~~Cp~C~~~~~l~ 48 (1102)
.|.--++.|+|++|+-+ ..|.+..+...|+.||....-|
T Consensus 12 ~p~s~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 12 EPRSRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred CCCceEEEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 45557899999999865 5899999999999999865543
No 182
>PRK06067 flagellar accessory protein FlaH; Validated
Probab=75.06 E-value=11 Score=40.85 Aligned_cols=105 Identities=15% Similarity=0.234 Sum_probs=62.5
Q ss_pred eEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCccccccceE
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSVGIREGVV 323 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~Gvl 323 (1102)
.++.-+.|+||+-....++++...+|++ ++|++..... .+..+++..+|.+-.+.+.-.+++.-.+ . .+++.
T Consensus 28 ~~i~G~~GsGKt~l~~~~~~~~~~~g~~-~~y~~~e~~~-~~~~~~~~~~g~~~~~~~~~g~l~i~~~-----~-~~~~~ 99 (234)
T PRK06067 28 ILIEGDHGTGKSVLSQQFVYGALKQGKK-VYVITTENTS-KSYLKQMESVKIDISDFFLWGYLRIFPL-----N-TEGFE 99 (234)
T ss_pred EEEECCCCCChHHHHHHHHHHHHhCCCE-EEEEEcCCCH-HHHHHHHHHCCCChhHHHhCCCceEEec-----c-ccccc
Confidence 3445579999999998898888888765 9999998765 5677888888754322111111111000 0 00110
Q ss_pred EeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhc
Q 038397 324 FLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKA 364 (1102)
Q Consensus 324 F~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~a 364 (1102)
+. +..-...++.|.+...+.--.+||+||--..
T Consensus 100 ~~--------~~~~~~ll~~l~~~i~~~~~~~iviDs~t~~ 132 (234)
T PRK06067 100 WN--------STLANKLLELIIEFIKSKREDVIIIDSLTIF 132 (234)
T ss_pred cC--------cchHHHHHHHHHHHHHhcCCCEEEEecHHHH
Confidence 00 1111346777777776522349999998854
No 183
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=75.00 E-value=2.3 Score=31.67 Aligned_cols=24 Identities=29% Similarity=0.865 Sum_probs=22.6
Q ss_pred CCCccceeeccCCCccccCCCCCc
Q 038397 99 CANCKAILNVPHGLVRFSCPQCAV 122 (1102)
Q Consensus 99 C~~C~A~~~vp~~~~~f~Cp~C~~ 122 (1102)
|++|...|..|.|-.+-+|..|..
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~ 24 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHT 24 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCc
Confidence 899999999999999999999974
No 184
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=74.85 E-value=1.7 Score=34.63 Aligned_cols=17 Identities=18% Similarity=0.348 Sum_probs=14.7
Q ss_pred eecCCCCCCCCCCCCCC
Q 038397 35 EFICGTCNLPQMLPPEL 51 (1102)
Q Consensus 35 ~~~Cp~C~~~~~l~p~~ 51 (1102)
.+.||.|+..-.|+.+.
T Consensus 2 ~i~Cp~C~~~y~i~d~~ 18 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEK 18 (36)
T ss_pred EEECCCCCCEEeCCHHH
Confidence 46899999999998876
No 185
>TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype. This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs.
Probab=74.79 E-value=4 Score=52.79 Aligned_cols=47 Identities=28% Similarity=0.395 Sum_probs=36.9
Q ss_pred ceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCC
Q 038397 813 KLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAP 870 (1102)
Q Consensus 813 K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP 870 (1102)
..|+|-++.+..||-+..| +.|+--.| .|.-||++|||||-+.....
T Consensus 337 ~~ILVATdVaerGLDId~d---------~VI~d~aP--~esyIQRiGRtgR~G~~~~~ 383 (844)
T TIGR02621 337 TVYLVCTSAGEVGVNISAD---------HLVCDLAP--FESMQQRFGRVNRFGELQAC 383 (844)
T ss_pred ceEEeccchhhhcccCCcc---------eEEECCCC--HHHHHHHhcccCCCCCCCCc
Confidence 6799999999999999765 33332245 58999999999999996555
No 186
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=74.64 E-value=1.8 Score=48.82 Aligned_cols=81 Identities=25% Similarity=0.551 Sum_probs=53.9
Q ss_pred ecCCcceEEEeCCC-------------cceecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCC
Q 038397 19 RCAGCHIILTVGPG-------------LTEFICGTCNLPQMLPPELMPASTGGSVPNNTTSSNTTNSTRPTHMKAASSHV 85 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg-------------~~~~~Cp~C~~~~~l~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (1102)
.|.-||..+.-..| ...|.|++|+....==|+| .-|++++.
T Consensus 132 ~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpAL----------------kMHirTH~---------- 185 (279)
T KOG2462|consen 132 KCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPAL----------------KMHIRTHT---------- 185 (279)
T ss_pred eccccccccccccccchhhcccccccccccccCCCCCceeeehHHH----------------hhHhhccC----------
Confidence 39999999977777 5678999999654432222 01111111
Q ss_pred CCCCCCCccceecCCCccceeecc----------CCCccccCCCCCcccccccccccccC
Q 038397 86 PALGIDPTKIQLPCANCKAILNVP----------HGLVRFSCPQCAVELAVDMSKVKQFF 135 (1102)
Q Consensus 86 ~a~~~~~t~~~~~C~~C~A~~~vp----------~~~~~f~Cp~C~~~L~v~~~~~~~~~ 135 (1102)
....|.=||..++=| -|.+.|.||-|+...+ |.+-||.-+
T Consensus 186 ---------l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFA-DRSNLRAHm 235 (279)
T KOG2462|consen 186 ---------LPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFA-DRSNLRAHM 235 (279)
T ss_pred ---------CCcccccccccccchHHhhcccccccCCCCccCCcccchhc-chHHHHHHH
Confidence 247899999998843 4677899999998865 356555444
No 187
>PLN00209 ribosomal protein S27; Provisional
Probab=74.35 E-value=2.9 Score=39.62 Aligned_cols=37 Identities=27% Similarity=0.603 Sum_probs=30.7
Q ss_pred CCCccceeecCCcceEE-EeCCCcceecCCCCCCCCCC
Q 038397 11 PPNVGVQVRCAGCHIIL-TVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 11 ~~~~~~~~~C~~C~a~l-~~~pg~~~~~Cp~C~~~~~l 47 (1102)
|-.-++.|+|++|+.+- .|.+..+...|..||....-
T Consensus 30 PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 30 PNSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred CCCEEEEEECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 44478999999999765 89999999999999975443
No 188
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=74.33 E-value=38 Score=39.44 Aligned_cols=71 Identities=20% Similarity=0.172 Sum_probs=38.6
Q ss_pred CCccCcccccccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhcc-CceEEEEEc
Q 038397 201 PTYDLLIKYDLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHG-RRKALWISV 278 (1102)
Q Consensus 201 ~~y~~~lp~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~G-r~~~~w~s~ 278 (1102)
+...-++|+.++.. +.|++.+.-+...+-. -...+..++.|. .|+||+-.+--+..+.-.++ .-..+|++.
T Consensus 22 ~l~~~~~P~~l~~R----e~e~~~l~~~l~~~~~--~~~~~~~lI~G~-~GtGKT~l~~~v~~~l~~~~~~~~~v~in~ 93 (394)
T PRK00411 22 VLEPDYVPENLPHR----EEQIEELAFALRPALR--GSRPLNVLIYGP-PGTGKTTTVKKVFEELEEIAVKVVYVYINC 93 (394)
T ss_pred hCCCCCcCCCCCCH----HHHHHHHHHHHHHHhC--CCCCCeEEEECC-CCCCHHHHHHHHHHHHHHhcCCcEEEEEEC
Confidence 33333456655533 6677776666544311 011234556666 99999988876665544444 233444443
No 189
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=74.32 E-value=1.8 Score=38.41 Aligned_cols=25 Identities=24% Similarity=0.732 Sum_probs=20.9
Q ss_pred ecCCcceEEEeCCCcceecCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
.|..||..|.-...-+.|.||.||.
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCCCC
Confidence 5999999996555469999999994
No 190
>PRK02362 ski2-like helicase; Provisional
Probab=73.96 E-value=2.4 Score=54.00 Aligned_cols=62 Identities=24% Similarity=0.133 Sum_probs=49.2
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEE-ecCCCcHhHHHHhhcccccCCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHIT-LELPWSADRAIQQFGRTHRSNQA 867 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHit-LElpWsADkAIQqfGRTHRSNQv 867 (1102)
+.|.+|+..|.|-++..+.||.+.+.+=+-+.-+|..-. --.|.+...-+|+.||++|-++-
T Consensus 323 ~~Fr~G~i~VLvaT~tla~GvnlPa~~VVI~~~~~yd~~~g~~~~s~~~y~Qm~GRAGR~g~d 385 (737)
T PRK02362 323 DAFRDRLIKVISSTPTLAAGLNLPARRVIIRDYRRYDGGAGMQPIPVLEYHQMAGRAGRPGLD 385 (737)
T ss_pred HHHHcCCCeEEEechhhhhhcCCCceEEEEecceeecCCCCceeCCHHHHHHHhhcCCCCCCC
Confidence 689999999999999999999999876555432222100 12688999999999999998864
No 191
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=73.47 E-value=2.1 Score=42.42 Aligned_cols=30 Identities=17% Similarity=0.304 Sum_probs=21.2
Q ss_pred ccceeecCCcceEEEeCCCcceecCCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
.+...+|..||..+... ....+.||.||-.
T Consensus 67 ~p~~~~C~~Cg~~~~~~-~~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQYVTLL-TQRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCCeeecC-CccCCcCcCcCCC
Confidence 34578899999866553 2234789999953
No 192
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=73.20 E-value=2.3 Score=43.29 Aligned_cols=28 Identities=18% Similarity=0.498 Sum_probs=21.3
Q ss_pred ceeecCCcceEEEeC-----------------CC--cceecCCCCCC
Q 038397 16 VQVRCAGCHIILTVG-----------------PG--LTEFICGTCNL 43 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~-----------------pg--~~~~~Cp~C~~ 43 (1102)
...+|.+||.+..+. |- -..+.||+||-
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs 115 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGS 115 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCC
Confidence 578899999988776 11 34477999995
No 193
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=72.86 E-value=1.8 Score=42.84 Aligned_cols=36 Identities=25% Similarity=0.478 Sum_probs=27.4
Q ss_pred CccceecCCCccceeeccCCCccccCCCCCcccccccc
Q 038397 92 PTKIQLPCANCKAILNVPHGLVRFSCPQCAVELAVDMS 129 (1102)
Q Consensus 92 ~t~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~~~ 129 (1102)
....++.|.+|+..+-+--- ...|.+|+.||..|.+
T Consensus 65 tkav~V~CP~C~K~TKmLGr--~D~CM~C~~pLTLd~~ 100 (114)
T PF11023_consen 65 TKAVQVECPNCGKQTKMLGR--VDACMHCKEPLTLDPS 100 (114)
T ss_pred ccceeeECCCCCChHhhhch--hhccCcCCCcCccCch
Confidence 34468999999998765322 2599999999999754
No 194
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=72.56 E-value=3.3 Score=39.18 Aligned_cols=37 Identities=27% Similarity=0.588 Sum_probs=30.7
Q ss_pred CCCccceeecCCcceEE-EeCCCcceecCCCCCCCCCC
Q 038397 11 PPNVGVQVRCAGCHIIL-TVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 11 ~~~~~~~~~C~~C~a~l-~~~pg~~~~~Cp~C~~~~~l 47 (1102)
|-.-++.|+|++|+.+- .|.+..+...|..||..+.-
T Consensus 29 PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 29 PNSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred CCCeEEEEECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 44478999999999765 88999999999999975443
No 195
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=72.18 E-value=1.4 Score=45.29 Aligned_cols=32 Identities=19% Similarity=0.338 Sum_probs=23.7
Q ss_pred ceeecCCcceEEEeCCC------cceecCCCCCCCCCC
Q 038397 16 VQVRCAGCHIILTVGPG------LTEFICGTCNLPQML 47 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~pg------~~~~~Cp~C~~~~~l 47 (1102)
....|++|+..+++.-. ...|.||.||.....
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 45679999999976333 334999999986554
No 196
>PF12773 DZR: Double zinc ribbon
Probab=71.98 E-value=3 Score=34.84 Aligned_cols=28 Identities=29% Similarity=0.631 Sum_probs=19.6
Q ss_pred ecCCCccceeeccCCCccccCCCCCcccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELA 125 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~ 125 (1102)
.-|.+||+.|. ........||.||..+.
T Consensus 13 ~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 13 KFCPHCGTPLP-PPDQSKKICPNCGAENP 40 (50)
T ss_pred cCChhhcCChh-hccCCCCCCcCCcCCCc
Confidence 67888888888 33333567888888743
No 197
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=71.97 E-value=2.1 Score=42.34 Aligned_cols=28 Identities=18% Similarity=0.434 Sum_probs=21.6
Q ss_pred ccceeecCCcceEEEeCCCcceecCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
.+...+|..||..+.+. -..|.||.||-
T Consensus 67 vp~~~~C~~Cg~~~~~~--~~~~~CP~Cgs 94 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIH--QHDAQCPHCHG 94 (113)
T ss_pred eCcEEEcccCCCEEecC--CcCccCcCCCC
Confidence 35678899999777665 35677999995
No 198
>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]
Probab=71.69 E-value=5.8 Score=50.19 Aligned_cols=151 Identities=24% Similarity=0.320 Sum_probs=81.5
Q ss_pred CCCCCCccCcccccccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEE
Q 038397 197 HPPEPTYDLLIKYDLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWI 276 (1102)
Q Consensus 197 ~pP~~~y~~~lp~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~ 276 (1102)
.||..+|...| -+-|-+| +--..+.+-.|. ---|-.||+- +|--..---|+-+.|+|+-
T Consensus 120 ~~pAk~YPF~L----------DpFQ~~a-I~Cidr~eSVLV---------SAHTSAGKTV-VAeYAIA~sLr~kQRVIYT 178 (1041)
T KOG0948|consen 120 KPPAKTYPFTL----------DPFQSTA-IKCIDRGESVLV---------SAHTSAGKTV-VAEYAIAMSLREKQRVIYT 178 (1041)
T ss_pred CCcccCCCccc----------CchHhhh-hhhhcCCceEEE---------EeecCCCcch-HHHHHHHHHHHhcCeEEee
Confidence 35556666544 3566677 334455544444 3348889975 4444444557788889998
Q ss_pred EcCCch----hhhHHhhhhhhCCCcccccccCCCCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCC
Q 038397 277 SVGSDL----KFDARRDLDDVGATCIEVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGY 352 (1102)
Q Consensus 277 s~s~~L----~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~df 352 (1102)
|-=..| +.+..-...|+|-..=+| .|.....+|-.|-=-|++---+|..=+.. |.|
T Consensus 179 SPIKALSNQKYREl~~EF~DVGLMTGDV--------------TInP~ASCLVMTTEILRsMLYRGSEvmrE-VaW----- 238 (1041)
T KOG0948|consen 179 SPIKALSNQKYRELLEEFKDVGLMTGDV--------------TINPDASCLVMTTEILRSMLYRGSEVMRE-VAW----- 238 (1041)
T ss_pred ChhhhhcchhHHHHHHHhcccceeecce--------------eeCCCCceeeeHHHHHHHHHhccchHhhe-eee-----
Confidence 864444 333334445555432111 12234456666656666543333222222 445
Q ss_pred CceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCC-ccEEEEecC
Q 038397 353 DGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPE-ARVVYCSAT 400 (1102)
Q Consensus 353 dgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~-ARvvY~SAT 400 (1102)
|||||.|-|..--- |.-.-.|- =.||+ .|.||-|||
T Consensus 239 ---VIFDEIHYMRDkER--GVVWEETI-------IllP~~vr~VFLSAT 275 (1041)
T KOG0948|consen 239 ---VIFDEIHYMRDKER--GVVWEETI-------ILLPDNVRFVFLSAT 275 (1041)
T ss_pred ---EEeeeehhcccccc--ceeeeeeE-------EeccccceEEEEecc
Confidence 89999999986532 21111110 13444 488888888
No 199
>PHA02653 RNA helicase NPH-II; Provisional
Probab=71.43 E-value=5 Score=50.93 Aligned_cols=39 Identities=26% Similarity=0.291 Sum_probs=24.6
Q ss_pred ceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCC-ccEEEEecCCC
Q 038397 354 GLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPE-ARVVYCSATGA 402 (1102)
Q Consensus 354 gvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~-ARvvY~SATga 402 (1102)
++|||||+|+.-.. +....+++. +.+++ .+++.+|||--
T Consensus 293 ~~VVIDEaHEr~~~--------~DllL~llk--~~~~~~rq~ILmSATl~ 332 (675)
T PHA02653 293 GTVIIDEVHEHDQI--------GDIIIAVAR--KHIDKIRSLFLMTATLE 332 (675)
T ss_pred CEEEccccccCccc--------hhHHHHHHH--HhhhhcCEEEEEccCCc
Confidence 58999999997533 233333332 22222 37999999953
No 200
>PHA00626 hypothetical protein
Probab=71.26 E-value=2.6 Score=37.01 Aligned_cols=28 Identities=14% Similarity=0.485 Sum_probs=21.7
Q ss_pred eecCCcceEEEeCCCc-----ceecCCCCCCCC
Q 038397 18 VRCAGCHIILTVGPGL-----TEFICGTCNLPQ 45 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~-----~~~~Cp~C~~~~ 45 (1102)
+.|+.||-.-.+.-|+ +.|.||.||+.-
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 3699999965556554 899999999843
No 201
>PRK11823 DNA repair protein RadA; Provisional
Probab=71.16 E-value=63 Score=39.23 Aligned_cols=87 Identities=18% Similarity=0.317 Sum_probs=50.8
Q ss_pred EeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCccccccceEE
Q 038397 245 FIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSVGIREGVVF 324 (1102)
Q Consensus 245 ~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~GvlF 324 (1102)
+++-..|+||+-.+--+..+.-.+|. +++|+|..... ....+....+|.+. + . ++
T Consensus 84 lI~G~pG~GKTtL~lq~a~~~a~~g~-~vlYvs~Ees~-~qi~~ra~rlg~~~------~----------------~-l~ 138 (446)
T PRK11823 84 LIGGDPGIGKSTLLLQVAARLAAAGG-KVLYVSGEESA-SQIKLRAERLGLPS------D----------------N-LY 138 (446)
T ss_pred EEECCCCCCHHHHHHHHHHHHHhcCC-eEEEEEccccH-HHHHHHHHHcCCCh------h----------------c-EE
Confidence 34445999998776655554333554 59999975543 33333444455321 0 0 11
Q ss_pred eehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccc
Q 038397 325 LTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKN 366 (1102)
Q Consensus 325 ~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn 366 (1102)
. .. .+.+++|++++.+.--.+||+|+.+.+..
T Consensus 139 ~-----~~-----e~~l~~i~~~i~~~~~~lVVIDSIq~l~~ 170 (446)
T PRK11823 139 L-----LA-----ETNLEAILATIEEEKPDLVVIDSIQTMYS 170 (446)
T ss_pred E-----eC-----CCCHHHHHHHHHhhCCCEEEEechhhhcc
Confidence 1 00 23477888888653334999999987754
No 202
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=71.13 E-value=3 Score=33.26 Aligned_cols=28 Identities=21% Similarity=0.698 Sum_probs=23.0
Q ss_pred eecCCCccceeeccCCCc---cccCCCCCcc
Q 038397 96 QLPCANCKAILNVPHGLV---RFSCPQCAVE 123 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~---~f~Cp~C~~~ 123 (1102)
...|..||..+.+..... .-.||.||++
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 578999999998877654 4589999995
No 203
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=71.01 E-value=3.1 Score=32.64 Aligned_cols=27 Identities=26% Similarity=0.736 Sum_probs=20.5
Q ss_pred cCCCccceeeccCCCccccCCCCCcccc
Q 038397 98 PCANCKAILNVPHGLVRFSCPQCAVELA 125 (1102)
Q Consensus 98 ~C~~C~A~~~vp~~~~~f~Cp~C~~~L~ 125 (1102)
.|+.||+...+..+ ..-+|+.||--+.
T Consensus 2 ~C~~Cg~~~~~~~~-~~irC~~CG~RIl 28 (32)
T PF03604_consen 2 ICGECGAEVELKPG-DPIRCPECGHRIL 28 (32)
T ss_dssp BESSSSSSE-BSTS-STSSBSSSS-SEE
T ss_pred CCCcCCCeeEcCCC-CcEECCcCCCeEE
Confidence 49999999998865 4679999997654
No 204
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=70.97 E-value=1.9 Score=31.85 Aligned_cols=24 Identities=21% Similarity=0.663 Sum_probs=17.9
Q ss_pred eeecCCcceEEEeCCCcceecCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
++.|++||+.+ .++ .--||+||..
T Consensus 2 ~~~Cp~Cg~~~--~~~--~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEI--DPD--AKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcC--Ccc--cccChhhCCC
Confidence 57899999954 333 5679999975
No 205
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=70.86 E-value=1.6 Score=53.91 Aligned_cols=48 Identities=33% Similarity=0.835 Sum_probs=43.3
Q ss_pred ccccccCcHHHHhhhhhccccCCccccCCCCCCcccCCCCCCccccch
Q 038397 661 QICEICNSEEERKKLLQCSCCGQLVHSGCLVPPITDVIPSDWSCHSCK 708 (1102)
Q Consensus 661 ~~ce~cgsed~k~kLL~cs~cgk~~H~~cL~PP~~di~~~dW~c~sCk 708 (1102)
..|+.|+...++.+++.|+.|+-.||-.|..||...++.+.|+|.-|.
T Consensus 69 rvCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~ 116 (694)
T KOG4443|consen 69 RVCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCT 116 (694)
T ss_pred eeeeeccccCCcccccccccccccccccccCCccccccCcccccHHHH
Confidence 468889988889999999999999999999999999999999988653
No 206
>PRK13826 Dtr system oriT relaxase; Provisional
Probab=70.54 E-value=19 Score=48.08 Aligned_cols=53 Identities=26% Similarity=0.332 Sum_probs=34.9
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHH-hccCceEEEEEcC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENW-HHGRRKALWISVG 279 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~-l~Gr~~~~w~s~s 279 (1102)
.||+.|.++|.+... +.|-.++.|. +|.||+-.+..++ +-| ..|.+ ++.+..+
T Consensus 381 ~Ls~eQ~~Av~~i~~--------~~r~~~v~G~-AGTGKTt~l~~~~-~~~e~~G~~-V~g~ApT 434 (1102)
T PRK13826 381 RLSDEQKTAIEHVAG--------PARIAAVVGR-AGAGKTTMMKAAR-EAWEAAGYR-VVGGALA 434 (1102)
T ss_pred CCCHHHHHHHHHHhc--------cCCeEEEEeC-CCCCHHHHHHHHH-HHHHHcCCe-EEEEcCc
Confidence 699999999877642 2355566665 9999999986653 445 34443 5544333
No 207
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=70.11 E-value=2.5 Score=32.62 Aligned_cols=27 Identities=30% Similarity=0.518 Sum_probs=18.4
Q ss_pred ecCCCccceeeccCCCccccCCCCCcc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
--|+.||+.+..-++--...||.||.+
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred cccCcCCccccCCCCcCEeECCCCcCE
Confidence 469999999999999778899999975
No 208
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=69.98 E-value=2.8 Score=41.59 Aligned_cols=29 Identities=17% Similarity=0.383 Sum_probs=21.9
Q ss_pred ccceeecCCcceEEEeCCCcceecCCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
.++..+|..||....+.. ..|.||.||-.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~--~~~~CP~Cgs~ 95 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEI--DLYRCPKCHGI 95 (115)
T ss_pred eCcEEEcccCCCEEecCC--cCccCcCCcCC
Confidence 345788999997776643 36889999964
No 209
>PRK08181 transposase; Validated
Probab=69.90 E-value=19 Score=40.86 Aligned_cols=55 Identities=20% Similarity=0.229 Sum_probs=36.5
Q ss_pred cccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEc
Q 038397 217 LSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISV 278 (1102)
Q Consensus 217 LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~ 278 (1102)
++..|+.++.+ |+.+ +. .+.++++--.+|+||+.-..+|..+-..+|++ ++|++.
T Consensus 88 ~~~~~~~~L~~-~~~~---~~--~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~-v~f~~~ 142 (269)
T PRK08181 88 VSKAQVMAIAA-GDSW---LA--KGANLLLFGPPGGGKSHLAAAIGLALIENGWR-VLFTRT 142 (269)
T ss_pred CCHHHHHHHHH-HHHH---Hh--cCceEEEEecCCCcHHHHHHHHHHHHHHcCCc-eeeeeH
Confidence 45677777544 3222 11 12345554449999999999998887778865 788875
No 210
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=69.70 E-value=1.8 Score=42.65 Aligned_cols=28 Identities=25% Similarity=0.554 Sum_probs=21.9
Q ss_pred ceecCCCccceeeccCCCccccCCCCCccc
Q 038397 95 IQLPCANCKAILNVPHGLVRFSCPQCAVEL 124 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L 124 (1102)
.+..|..||....+.... |.||.||..-
T Consensus 69 ~~~~C~~Cg~~~~~~~~~--~~CP~Cgs~~ 96 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFD--FSCPRCGSPD 96 (113)
T ss_dssp -EEEETTTS-EEECHHCC--HH-SSSSSS-
T ss_pred CcEECCCCCCEEecCCCC--CCCcCCcCCC
Confidence 468999999999998885 9999999983
No 211
>KOG0328 consensus Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis]
Probab=69.40 E-value=4.7 Score=45.91 Aligned_cols=156 Identities=21% Similarity=0.206 Sum_probs=88.6
Q ss_pred ccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCc--eEEEEEcCCchhhhHHhhhhhhCC
Q 038397 218 SCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRR--KALWISVGSDLKFDARRDLDDVGA 295 (1102)
Q Consensus 218 S~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~--~~~w~s~s~~L~~Da~RDl~diG~ 295 (1102)
|+-|-.||..-+.-|.. +.--+.|.||+-+.+--++.|.--+-| .++-+|-+-.|-.-.+.=+.+||.
T Consensus 51 S~IQqrAi~~IlkGrdV----------iaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi~~vi~alg~ 120 (400)
T KOG0328|consen 51 SAIQQRAIPQILKGRDV----------IAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQIQKVILALGD 120 (400)
T ss_pred hHHHhhhhhhhhcccce----------EEEecCCCCceEEEEeeeeeecccccceeeEEEecChHHHHHHHHHHHHHhcc
Confidence 45555555555544433 344567888988887667777644443 577788888899988999999997
Q ss_pred C-cccccccCCCCCCcCCCCccc-cccc--eEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCC
Q 038397 296 T-CIEVHALNKLPYSKLDSRSVG-IREG--VVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEA 371 (1102)
Q Consensus 296 ~-~i~v~~l~~~~~~~~~~~~~~-~~~G--vlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~ 371 (1102)
. ++.+|+.-.-+. + ++.+. +..| |+-.|=-....--+++.-|- .-=-+|||||+..+.|-.
T Consensus 121 ~mnvq~hacigg~n--~-gedikkld~G~hvVsGtPGrv~dmikr~~L~t---------r~vkmlVLDEaDemL~kg--- 185 (400)
T KOG0328|consen 121 YMNVQCHACIGGKN--L-GEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRT---------RAVKMLVLDEADEMLNKG--- 185 (400)
T ss_pred cccceEEEEecCCc--c-chhhhhhcccceEeeCCCchHHHHHHhccccc---------cceeEEEeccHHHHHHhh---
Confidence 4 777776532110 0 01111 1222 22222111100000111111 011389999999998761
Q ss_pred CCCchhHHHHHHHHhhhCC-CccEEEEecCCCCC
Q 038397 372 GSQPTRTGEAVLELQARLP-EARVVYCSATGASE 404 (1102)
Q Consensus 372 ~~~~s~~g~avl~LQ~~lP-~ARvvY~SATgase 404 (1102)
.+...-++-+.|| ++.||+.|||-..+
T Consensus 186 ------fk~Qiydiyr~lp~~~Qvv~~SATlp~e 213 (400)
T KOG0328|consen 186 ------FKEQIYDIYRYLPPGAQVVLVSATLPHE 213 (400)
T ss_pred ------HHHHHHHHHHhCCCCceEEEEeccCcHH
Confidence 2223344456777 99999999995433
No 212
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=69.20 E-value=2.7 Score=37.10 Aligned_cols=29 Identities=31% Similarity=0.590 Sum_probs=25.4
Q ss_pred ecCCCccceeeccCCCccccCCCCCccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
-.|-+||-|+=.-+|+ ..+|+|||.+|..
T Consensus 19 ~NCl~CGkIiC~~Eg~-~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 19 PNCLNCGKIICEQEGP-LGPCPFCGTPLLS 47 (57)
T ss_pred ccccccChhhcccccC-cCcCCCCCCcccC
Confidence 5899999999999997 6699999988655
No 213
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=69.12 E-value=3.9 Score=41.39 Aligned_cols=32 Identities=3% Similarity=-0.180 Sum_probs=23.4
Q ss_pred ceeecCCcceEEEeCCCcceecCCCCCCCCCCC
Q 038397 16 VQVRCAGCHIILTVGPGLTEFICGTCNLPQMLP 48 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~ 48 (1102)
.+--|++||+-|.= =+-.-..|||||..+.+.
T Consensus 8 tKr~Cp~cg~kFYD-Lnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPNTGSKFYD-LNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCCcCccccc-cCCCCccCCCcCCccCcc
Confidence 34559999999832 223678899999987654
No 214
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=69.02 E-value=3.3 Score=52.17 Aligned_cols=24 Identities=38% Similarity=0.802 Sum_probs=19.2
Q ss_pred ecCCCccceeeccCCCccccCCCCCccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
--|.+||+.+.. -.||.||.++..
T Consensus 16 kFC~~CG~~l~~------~~Cp~CG~~~~~ 39 (645)
T PRK14559 16 RFCQKCGTSLTH------KPCPQCGTEVPV 39 (645)
T ss_pred ccccccCCCCCC------CcCCCCCCCCCc
Confidence 589999999853 269999999554
No 215
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=68.94 E-value=7.9 Score=53.06 Aligned_cols=51 Identities=20% Similarity=0.315 Sum_probs=44.7
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRS 864 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRS 864 (1102)
+.|.+|+..|.|-|++..-||.+-+=.-| |-++.|.|+...+|+.||++|.
T Consensus 321 ~~fK~G~LrvLVATssLELGIDIg~VDlV--------Iq~gsP~sVas~LQRiGRAGR~ 371 (1490)
T PRK09751 321 QALKSGELRCVVATSSLELGIDMGAVDLV--------IQVATPLSVASGLQRIGRAGHQ 371 (1490)
T ss_pred HHHHhCCceEEEeCcHHHccCCcccCCEE--------EEeCCCCCHHHHHHHhCCCCCC
Confidence 68999999999999999999998654333 4478999999999999999996
No 216
>PHA00012 I assembly protein
Probab=68.78 E-value=29 Score=40.83 Aligned_cols=23 Identities=22% Similarity=0.192 Sum_probs=20.3
Q ss_pred CCCCCcchhhHHHHHHHHhccCc
Q 038397 249 GAGVGKGRTIAGLIWENWHHGRR 271 (1102)
Q Consensus 249 g~GvGKGR~~AgiI~~n~l~Gr~ 271 (1102)
--|-||+-...+-|.+-..+||+
T Consensus 9 kPGSGKSl~aV~~I~~~L~~Gr~ 31 (361)
T PHA00012 9 KLGAGKTLVAVSRIQDKLVKGCI 31 (361)
T ss_pred CCCCCchHHHHHHHHHHHHcCCE
Confidence 37889999988899999999985
No 217
>PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional
Probab=68.71 E-value=26 Score=47.05 Aligned_cols=159 Identities=18% Similarity=0.160 Sum_probs=85.2
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcch--hhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGR--TIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR--~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~di 293 (1102)
.|..-|.++|..+.+ + + =.|+-=.||-||+- |+.+++ .+. .+|+||-.-.|..|-...|...
T Consensus 460 sFRp~Q~eaI~aiL~-G--------r-DVLVimPTGSGKSLcYQLPAL~-----~~G-iTLVISPLiSLmqDQV~~L~~~ 523 (1195)
T PLN03137 460 SFRPNQREIINATMS-G--------Y-DVFVLMPTGGGKSLTYQLPALI-----CPG-ITLVISPLVSLIQDQIMNLLQA 523 (1195)
T ss_pred CCCHHHHHHHHHHHc-C--------C-CEEEEcCCCccHHHHHHHHHHH-----cCC-cEEEEeCHHHHHHHHHHHHHhC
Confidence 466777777554432 2 1 13444568889975 343332 343 4999999999999988888776
Q ss_pred CCCcccccccCC-CCCCcCCCCcc-c-----cccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccc
Q 038397 294 GATCIEVHALNK-LPYSKLDSRSV-G-----IREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKN 366 (1102)
Q Consensus 294 G~~~i~v~~l~~-~~~~~~~~~~~-~-----~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn 366 (1102)
|... ..|+. ...... .+.+ . -+-.||++|--.|..... -...|+. +.+. ..=..||+||||....
T Consensus 524 GI~A---a~L~s~~s~~eq-~~ilr~l~s~~g~~~ILyvTPERL~~~d~-ll~~L~~-L~~~--~~LslIVIDEAHcVSq 595 (1195)
T PLN03137 524 NIPA---ASLSAGMEWAEQ-LEILQELSSEYSKYKLLYVTPEKVAKSDS-LLRHLEN-LNSR--GLLARFVIDEAHCVSQ 595 (1195)
T ss_pred CCeE---EEEECCCCHHHH-HHHHHHHHhcCCCCCEEEEChHHhhcchH-HHHHHHh-hhhc--cccceeccCcchhhhh
Confidence 6432 22221 100000 0000 0 122488888766642100 0011111 1121 1125789999999754
Q ss_pred cCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCC
Q 038397 367 LVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGA 402 (1102)
Q Consensus 367 ~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATga 402 (1102)
.. -.-.+.-. .+..|...+|+..++-.|||.-
T Consensus 596 WG--hDFRpdYr--~L~~Lr~~fp~vPilALTATAT 627 (1195)
T PLN03137 596 WG--HDFRPDYQ--GLGILKQKFPNIPVLALTATAT 627 (1195)
T ss_pred cc--cchHHHHH--HHHHHHHhCCCCCeEEEEecCC
Confidence 31 00112222 2334678899999999999953
No 218
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=68.54 E-value=3.4 Score=40.97 Aligned_cols=28 Identities=18% Similarity=0.609 Sum_probs=22.8
Q ss_pred cceecCCCccceeeccCCCccccCCCCCcc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
..+..|.+||....+... .|.||.||.+
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~ 95 (115)
T TIGR00100 68 PVECECEDCSEEVSPEID--LYRCPKCHGI 95 (115)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCcCC
Confidence 346899999988877654 5889999986
No 219
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=67.68 E-value=3.1 Score=33.28 Aligned_cols=28 Identities=29% Similarity=0.791 Sum_probs=23.0
Q ss_pred eecCCCccceeeccCC-----CccccCCCCCcc
Q 038397 96 QLPCANCKAILNVPHG-----LVRFSCPQCAVE 123 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~-----~~~f~Cp~C~~~ 123 (1102)
.+.|.+|++...||.. -....||.|+..
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 4789999999999876 346799999864
No 220
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=67.47 E-value=1.6 Score=43.19 Aligned_cols=27 Identities=19% Similarity=0.548 Sum_probs=24.2
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLPQ 45 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~~ 45 (1102)
-|..||..|..+..-..+.|+.|....
T Consensus 9 FC~~CG~ll~~~~~~~~~~C~~Ck~~~ 35 (116)
T KOG2907|consen 9 FCSDCGSLLEEPSAQSTVLCIRCKIEY 35 (116)
T ss_pred hhhhhhhhcccccccCceEeccccccC
Confidence 499999999999999999999999744
No 221
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=66.52 E-value=3.9 Score=40.47 Aligned_cols=28 Identities=25% Similarity=0.632 Sum_probs=21.9
Q ss_pred cceecCCCccceeeccCCCccccCCCCCcc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
..+..|..||....+... .|.||.||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQVVEIHQH--DAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCEEecCCc--CccCcCCCCC
Confidence 346899999977777653 6679999975
No 222
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=66.31 E-value=5.1 Score=46.26 Aligned_cols=28 Identities=25% Similarity=0.618 Sum_probs=14.4
Q ss_pred eecCCcceEEEeCCCcceecCCCCCCCCCC
Q 038397 18 VRCAGCHIILTVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l 47 (1102)
+.|. |+-.+..+||..- .|-.|++.+-|
T Consensus 5 ~~~~-~~~p~~~pp~ar~-q~~~~~~~~~~ 32 (362)
T KOG1546|consen 5 VGCN-CQRPMAPPPGARY-QCAGCHAVTQI 32 (362)
T ss_pred ccCC-CCCCCCCCCCCcc-cccccceeeee
Confidence 3444 5555555555555 55555554444
No 223
>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function. It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].
Probab=66.26 E-value=8.9 Score=44.52 Aligned_cols=49 Identities=27% Similarity=0.320 Sum_probs=34.3
Q ss_pred eEeecCCCCCcchhhHHHHHHH-HhccCceEEEEEcCCchhhhHHhhhhh
Q 038397 244 FFIGDGAGVGKGRTIAGLIWEN-WHHGRRKALWISVGSDLKFDARRDLDD 292 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n-~l~Gr~~~~w~s~s~~L~~Da~RDl~d 292 (1102)
||+--|+|.||+-..--+..+. -.....+++.++.+..|..-.+.-+..
T Consensus 4 ~~I~G~aGTGKTvla~~l~~~l~~~~~~~~~~~l~~n~~l~~~l~~~l~~ 53 (352)
T PF09848_consen 4 ILITGGAGTGKTVLALNLAKELQNSEEGKKVLYLCGNHPLRNKLREQLAK 53 (352)
T ss_pred EEEEecCCcCHHHHHHHHHHHhhccccCCceEEEEecchHHHHHHHHHhh
Confidence 5666679999987665555555 133445589999999988766666643
No 224
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=66.15 E-value=16 Score=44.74 Aligned_cols=76 Identities=24% Similarity=0.232 Sum_probs=65.0
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRF 885 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRF 885 (1102)
+.|..|+-+|+|-+--|=-|+-.-.= =+-|-.|+=-|+=+.||+.|||+|. ..+=.|++++.+-.-|.+|
T Consensus 419 ~~Fr~Ge~nVLVaTSVgEEGLDIp~v--------DlVifYEpvpSeIR~IQR~GRTGR~--r~Grv~vLvt~gtrdeayy 488 (542)
T COG1111 419 DQFRKGEYNVLVATSVGEEGLDIPEV--------DLVIFYEPVPSEIRSIQRKGRTGRK--RKGRVVVLVTEGTRDEAYY 488 (542)
T ss_pred HHHhcCCceEEEEcccccccCCCCcc--------cEEEEecCCcHHHHHHHhhCccccC--CCCeEEEEEecCchHHHHH
Confidence 68999999999999888888876532 1457789999999999999999997 8899999999999999999
Q ss_pred HHHHHH
Q 038397 886 ASIVAK 891 (1102)
Q Consensus 886 aS~VAk 891 (1102)
=|+.-|
T Consensus 489 ~~s~rk 494 (542)
T COG1111 489 YSSRRK 494 (542)
T ss_pred HHHHHH
Confidence 887543
No 225
>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]
Probab=65.97 E-value=9.3 Score=48.66 Aligned_cols=71 Identities=25% Similarity=0.384 Sum_probs=57.2
Q ss_pred hhhcCC-cceEEEEe-cccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCC-CCeEEEeecCccch
Q 038397 806 QLFMDG-KKLVAIIS-EAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQAS-APEYRIIFTNLGGE 882 (1102)
Q Consensus 806 ~~Fm~G-~K~VAIIS-eAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvs-aP~Y~~l~T~l~GE 882 (1102)
+.|+++ +..|.++| .||++||.|..-. ..|.++..|+-..-.|-..|.||-+|.. --.|++++.|---|
T Consensus 755 ~~f~~~~~~~v~lls~kagg~glnLt~a~--------~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~i~~~tiEe 826 (866)
T COG0553 755 DRFNADEEEKVFLLSLKAGGLGLNLTGAD--------TVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGTIEE 826 (866)
T ss_pred HHhhcCCCCceEEEEecccccceeecccc--------eEEEeccccChHHHHHHHHHHHHhcCcceeEEEEeecCCcHHH
Confidence 599997 45666666 5999999998432 4688999999999999999999999984 46777777776666
Q ss_pred hh
Q 038397 883 RR 884 (1102)
Q Consensus 883 rR 884 (1102)
+=
T Consensus 827 ~i 828 (866)
T COG0553 827 KI 828 (866)
T ss_pred HH
Confidence 53
No 226
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=65.70 E-value=3.2 Score=32.94 Aligned_cols=24 Identities=21% Similarity=0.571 Sum_probs=14.6
Q ss_pred cCCcceEEEe--C--CCcceecCCCCCC
Q 038397 20 CAGCHIILTV--G--PGLTEFICGTCNL 43 (1102)
Q Consensus 20 C~~C~a~l~~--~--pg~~~~~Cp~C~~ 43 (1102)
|+.||..|+. + .+-..+.||.||.
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred cccccChhhhhcCCCCCccceECCCCCC
Confidence 9999999854 5 5778899999996
No 227
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=65.54 E-value=4.9 Score=32.24 Aligned_cols=30 Identities=23% Similarity=0.495 Sum_probs=23.5
Q ss_pred ecCCCccceeeccCCCcc--ccCCCCCccccc
Q 038397 97 LPCANCKAILNVPHGLVR--FSCPQCAVELAV 126 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~--f~Cp~C~~~L~v 126 (1102)
.-|..||++.|+..+... --|..||.+|+-
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCeeEe
Confidence 469999999999776553 489999999864
No 228
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=65.18 E-value=3.6 Score=34.47 Aligned_cols=30 Identities=30% Similarity=0.709 Sum_probs=24.0
Q ss_pred cCCCccceeeccCCCc--cccCCCCCcccccc
Q 038397 98 PCANCKAILNVPHGLV--RFSCPQCAVELAVD 127 (1102)
Q Consensus 98 ~C~~C~A~~~vp~~~~--~f~Cp~C~~~L~v~ 127 (1102)
-|..||.+|..+..-. ++.||.||...-++
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEECC
Confidence 4999999998886543 79999999876554
No 229
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=65.07 E-value=3.1 Score=41.80 Aligned_cols=29 Identities=21% Similarity=0.474 Sum_probs=20.0
Q ss_pred ccceeecCCcceEEEeC-CCc--c--eecCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVG-PGL--T--EFICGTCNL 43 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~-pg~--~--~~~Cp~C~~ 43 (1102)
.+...+| .||..+... ..+ . .+.||.||-
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCC
Confidence 3457889 999887654 222 2 267999994
No 230
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=65.00 E-value=3.7 Score=36.02 Aligned_cols=34 Identities=24% Similarity=0.414 Sum_probs=23.2
Q ss_pred CccceeecCCcceEE-EeCCCcceecCCCCCCCCC
Q 038397 13 NVGVQVRCAGCHIIL-TVGPGLTEFICGTCNLPQM 46 (1102)
Q Consensus 13 ~~~~~~~C~~C~a~l-~~~pg~~~~~Cp~C~~~~~ 46 (1102)
.-++.|+|++|+.+- .|.+..+...|..||..+.
T Consensus 3 S~Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 3 SYFMDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp --EEEEE-TTT-SEEEEETT-SS-EE-SSSTSEEE
T ss_pred ccEEEEECCCCCCeeEEEecCCeEEEcccCCCEec
Confidence 457899999999765 8999999999999997543
No 231
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=64.87 E-value=3.6 Score=40.53 Aligned_cols=27 Identities=26% Similarity=0.533 Sum_probs=23.9
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLPQM 46 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~~~ 46 (1102)
.|+.|+...+|+.|-. |.||.|+++-.
T Consensus 4 ~CP~C~seytY~dg~~-~iCpeC~~EW~ 30 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQ-LICPSCLYEWN 30 (109)
T ss_pred cCCcCCCcceEecCCe-eECcccccccc
Confidence 5999999999999985 99999998543
No 232
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=64.52 E-value=4.3 Score=40.24 Aligned_cols=28 Identities=21% Similarity=0.519 Sum_probs=20.9
Q ss_pred ceecCCCccceeeccCCCccccCCCCCcc
Q 038397 95 IQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
.+..|..||....++.. ..|.||.||..
T Consensus 69 ~~~~C~~Cg~~~~~~~~-~~~~CP~Cgs~ 96 (114)
T PRK03681 69 AECWCETCQQYVTLLTQ-RVRRCPQCHGD 96 (114)
T ss_pred cEEEcccCCCeeecCCc-cCCcCcCcCCC
Confidence 46899999976665533 23789999976
No 233
>PRK06526 transposase; Provisional
Probab=64.31 E-value=17 Score=40.84 Aligned_cols=33 Identities=30% Similarity=0.530 Sum_probs=26.1
Q ss_pred eEeecCCCCCcchhhHHHHHHHHhccCceEEEEEc
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISV 278 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~ 278 (1102)
+|+| .+|+||+....+|..+-..+|++ ++|++.
T Consensus 102 ll~G-p~GtGKThLa~al~~~a~~~g~~-v~f~t~ 134 (254)
T PRK06526 102 VFLG-PPGTGKTHLAIGLGIRACQAGHR-VLFATA 134 (254)
T ss_pred EEEe-CCCCchHHHHHHHHHHHHHCCCc-hhhhhH
Confidence 4445 58999999999999888888875 677555
No 234
>PRK04296 thymidine kinase; Provisional
Probab=64.29 E-value=13 Score=39.48 Aligned_cols=31 Identities=19% Similarity=0.326 Sum_probs=21.4
Q ss_pred eEeecCCCCCcchhhHHHHHHHHhccCceEEEE
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENWHHGRRKALWI 276 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~ 276 (1102)
++.|+ +|.||+-.+-+++.....+|++ ++.+
T Consensus 6 litG~-~GsGKTT~~l~~~~~~~~~g~~-v~i~ 36 (190)
T PRK04296 6 FIYGA-MNSGKSTELLQRAYNYEERGMK-VLVF 36 (190)
T ss_pred EEECC-CCCHHHHHHHHHHHHHHHcCCe-EEEE
Confidence 44555 6888997777777766667754 6655
No 235
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=63.94 E-value=4.5 Score=34.13 Aligned_cols=27 Identities=22% Similarity=0.481 Sum_probs=20.6
Q ss_pred eeecCCcceEEEeCCCcc---eecCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLT---EFICGTCNL 43 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~---~~~Cp~C~~ 43 (1102)
+.+|..||.++++--... ...||.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 578999999887654333 457999996
No 236
>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length. There are two conserved sequence motifs: LLE and NMG.
Probab=63.83 E-value=14 Score=41.11 Aligned_cols=118 Identities=18% Similarity=0.240 Sum_probs=78.1
Q ss_pred EeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhh-CC---CcccccccCCCCCCcCCCCc-----
Q 038397 245 FIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDV-GA---TCIEVHALNKLPYSKLDSRS----- 315 (1102)
Q Consensus 245 ~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~di-G~---~~i~v~~l~~~~~~~~~~~~----- 315 (1102)
..==.+|-||+..|.=|+.-.+..|.+ .+-+-+-..|..-+..+|+.- |+ ..|--.|++.- -+++...
T Consensus 45 v~QlnMGeGKTsVI~Pmla~~LAdg~~-LvrviVpk~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~--~~~~~~~~~~~~ 121 (229)
T PF12340_consen 45 VMQLNMGEGKTSVIVPMLALALADGSR-LVRVIVPKALLEQMRQMLRSRLGGLLNRRIYHLPFSRS--TPLTPETLEKIR 121 (229)
T ss_pred EeeecccCCccchHHHHHHHHHcCCCc-EEEEEcCHHHHHHHHHHHHHHHHHHhCCeeEEecccCC--CCCCHHHHHHHH
Confidence 444458999999999999998889886 888889999999999998764 33 22223344442 1121110
Q ss_pred -----cccccceEEeehhhhhhccc-------cc----cchHHHHHHHhccCCCceEEeecchhcccc
Q 038397 316 -----VGIREGVVFLTYSSLIASSE-------KG----RSRLQQLVQWCGSGYDGLVIFDECHKAKNL 367 (1102)
Q Consensus 316 -----~~~~~GvlF~TYs~L~~~~~-------~~----~sRl~Ql~~W~g~dfdgvivfDEcH~akn~ 367 (1102)
..-..|||-+|=..+.+-.= .+ ...|..+.+|+.+ ...=|+|||+..-+.
T Consensus 122 ~l~~~~~~~~gill~~PEhilSf~L~~le~l~~~~~~~~~~l~~~q~~l~~--~~rdilDEsDe~L~~ 187 (229)
T PF12340_consen 122 QLLEECMRSGGILLATPEHILSFKLKGLERLQDGKPEEARELLKIQKWLDE--HSRDILDESDEILSV 187 (229)
T ss_pred HHHHHHHHcCCEEEeChHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHh--cCCeEeECchhccCc
Confidence 12367899888777654321 11 2456777889975 234599999997654
No 237
>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []. This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.
Probab=63.82 E-value=34 Score=37.67 Aligned_cols=118 Identities=14% Similarity=0.229 Sum_probs=61.9
Q ss_pred CCCcceeEeecCCCCCcchhhHHHHHHHHhccC-ceEEEEEcCCchh-hhHHhhh-hhhCCCcccccccCCCCCCcCCCC
Q 038397 238 NSARAGFFIGDGAGVGKGRTIAGLIWENWHHGR-RKALWISVGSDLK-FDARRDL-DDVGATCIEVHALNKLPYSKLDSR 314 (1102)
Q Consensus 238 ~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr-~~~~w~s~s~~L~-~Da~RDl-~diG~~~i~v~~l~~~~~~~~~~~ 314 (1102)
++.+.-.+.|- .|+||+..+..+..+-..+.+ ...+|++.+.... .+..+++ ..++...-.+
T Consensus 17 ~~~~~v~I~G~-~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~-------------- 81 (287)
T PF00931_consen 17 NEVRVVAIVGM-GGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSI-------------- 81 (287)
T ss_dssp TSSEEEEEEES-TTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STS--------------
T ss_pred CCeEEEEEEcC-CcCCcceeeeeccccccccccccccccccccccccccccccccccccccccccc--------------
Confidence 34566666777 799999888777655444333 4689999976432 2222222 2223221100
Q ss_pred ccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccE
Q 038397 315 SVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARV 394 (1102)
Q Consensus 315 ~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARv 394 (1102)
.....-....++|.+|+... .-+||||......... .-...+...-++.+|
T Consensus 82 -----------------~~~~~~~~~~~~l~~~L~~~-~~LlVlDdv~~~~~~~-----------~l~~~~~~~~~~~ki 132 (287)
T PF00931_consen 82 -----------------SDPKDIEELQDQLRELLKDK-RCLLVLDDVWDEEDLE-----------ELREPLPSFSSGSKI 132 (287)
T ss_dssp -----------------SCCSSHHHHHHHHHHHHCCT-SEEEEEEEE-SHHHH------------------HCHHSS-EE
T ss_pred -----------------ccccccccccccchhhhccc-cceeeeeeeccccccc-----------ccccccccccccccc
Confidence 00011123567778888765 8899999876654221 001112223346789
Q ss_pred EEEec
Q 038397 395 VYCSA 399 (1102)
Q Consensus 395 vY~SA 399 (1102)
+.+|=
T Consensus 133 lvTTR 137 (287)
T PF00931_consen 133 LVTTR 137 (287)
T ss_dssp EEEES
T ss_pred ccccc
Confidence 99873
No 238
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=63.48 E-value=4.8 Score=49.36 Aligned_cols=26 Identities=23% Similarity=0.568 Sum_probs=23.3
Q ss_pred eecCCcceEEEeCCCcceecCCCCCC
Q 038397 18 VRCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
++|++|...|+|--....+.|.|||.
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGY 248 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcC
Confidence 46999999999988888999999997
No 239
>PRK08084 DNA replication initiation factor; Provisional
Probab=63.16 E-value=32 Score=37.80 Aligned_cols=36 Identities=14% Similarity=0.260 Sum_probs=25.6
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcC
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVG 279 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s 279 (1102)
.+++--..|+||+.-+.++..+-..+|. ++++++.+
T Consensus 47 ~l~l~Gp~G~GKThLl~a~~~~~~~~~~-~v~y~~~~ 82 (235)
T PRK08084 47 YIYLWSREGAGRSHLLHAACAELSQRGR-AVGYVPLD 82 (235)
T ss_pred eEEEECCCCCCHHHHHHHHHHHHHhCCC-eEEEEEHH
Confidence 4444445999999999887776666664 47777763
No 240
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=62.22 E-value=3.5 Score=36.90 Aligned_cols=23 Identities=30% Similarity=0.736 Sum_probs=19.9
Q ss_pred ecCCCccceeeccCCCccccCCCCCcc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
..|.+|+.+++.... .||.||++
T Consensus 5 kAC~~Ck~l~~~d~e----~CP~Cgs~ 27 (64)
T COG2093 5 KACKNCKRLTPEDTE----ICPVCGST 27 (64)
T ss_pred HHHhhccccCCCCCc----cCCCCCCc
Confidence 579999999887655 79999998
No 241
>PRK10220 hypothetical protein; Provisional
Probab=62.16 E-value=5.1 Score=39.60 Aligned_cols=27 Identities=22% Similarity=0.465 Sum_probs=23.7
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLPQM 46 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~~~ 46 (1102)
.|+.|....+|+.|-. |.||.|+.+-.
T Consensus 5 ~CP~C~seytY~d~~~-~vCpeC~hEW~ 31 (111)
T PRK10220 5 HCPKCNSEYTYEDNGM-YICPECAHEWN 31 (111)
T ss_pred cCCCCCCcceEcCCCe-EECCcccCcCC
Confidence 4999999999999986 99999998543
No 242
>PRK11827 hypothetical protein; Provisional
Probab=62.06 E-value=5.7 Score=35.42 Aligned_cols=30 Identities=30% Similarity=0.406 Sum_probs=26.0
Q ss_pred eecCCcceEEEeCCCcceecCCCCCCCCCC
Q 038397 18 VRCAGCHIILTVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l 47 (1102)
+.|+.|+..|.+..+..+|.|..|+..--|
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~laYPI 38 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNLAFPL 38 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCeeccc
Confidence 569999999999999999999999965444
No 243
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.60 E-value=3.9 Score=40.72 Aligned_cols=30 Identities=20% Similarity=0.544 Sum_probs=20.2
Q ss_pred ccceeecCCcceEEEeCCCcceecCCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
.+...+|..||..+.+. ....+.||.||-+
T Consensus 68 vp~~~~C~~Cg~~~~~~-~~~~~~CP~Cgs~ 97 (117)
T PRK00564 68 EKVELECKDCSHVFKPN-ALDYGVCEKCHSK 97 (117)
T ss_pred cCCEEEhhhCCCccccC-CccCCcCcCCCCC
Confidence 45678899999665443 2233459999963
No 244
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=61.59 E-value=5.2 Score=32.84 Aligned_cols=27 Identities=22% Similarity=0.534 Sum_probs=21.1
Q ss_pred eeecCCcceEEEeCCCcc---eecCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLT---EFICGTCNL 43 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~---~~~Cp~C~~ 43 (1102)
+.+|..||..+++-...+ ...||.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 578999998886654444 589999996
No 245
>PRK02935 hypothetical protein; Provisional
Probab=61.09 E-value=4.8 Score=39.51 Aligned_cols=36 Identities=28% Similarity=0.550 Sum_probs=28.8
Q ss_pred CccceecCCCccceeeccCCCcc-ccCCCCCccccccccc
Q 038397 92 PTKIQLPCANCKAILNVPHGLVR-FSCPQCAVELAVDMSK 130 (1102)
Q Consensus 92 ~t~~~~~C~~C~A~~~vp~~~~~-f~Cp~C~~~L~v~~~~ 130 (1102)
....|+.|.+|+..+.+ ++| ..|.+|+.||..|.+.
T Consensus 66 tkavqV~CP~C~K~TKm---LGrvD~CM~C~~PLTLd~~l 102 (110)
T PRK02935 66 TKAVQVICPSCEKPTKM---LGRVDACMHCNQPLTLDRSL 102 (110)
T ss_pred ccceeeECCCCCchhhh---ccceeecCcCCCcCCcCccc
Confidence 34568999999998876 454 5999999999998643
No 246
>KOG1923 consensus Rac1 GTPase effector FRL [Signal transduction mechanisms; Cytoskeleton]
Probab=60.77 E-value=17 Score=46.16 Aligned_cols=64 Identities=14% Similarity=0.237 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCccceeecCCcceEEEeCCCcceecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--------
Q 038397 2 TQPPVPPPPPPNVGVQVRCAGCHIILTVGPGLTEFICGTCNLPQMLPPELMPASTGGSVPNNTTSSNTTNST-------- 73 (1102)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~p~~~p~~~~~~~~~~~~~~~~~~~~-------- 73 (1102)
++||.|+|.| +..+.-. ||+|||.+..+||||+++|..+
T Consensus 280 s~ppppap~p-~~~~~~a--------------------------------~p~p~~~~~~pPppp~~ppv~~ln~~~s~~ 326 (830)
T KOG1923|consen 280 SGPPPPAPLP-HTAQSDA--------------------------------APSPLRLRCSPPPPPPFPPVGPLNSNLSSG 326 (830)
T ss_pred CCCCCCCCCC-CcccccC--------------------------------CCCCCCCCCCCCCCCCCCCCCCCCCCCcCC
Q ss_pred --CCCCcccccCCCCCCCCCCccceec
Q 038397 74 --RPTHMKAASSHVPALGIDPTKIQLP 98 (1102)
Q Consensus 74 --~~~~~~~~~~~~~a~~~~~t~~~~~ 98 (1102)
.|++.++.+...+.++-.++..+.+
T Consensus 327 ~p~pp~~p~l~~~~espvpp~~~~~~~ 353 (830)
T KOG1923|consen 327 APQPPGVPFLLTFPESPVPPPQRLMIP 353 (830)
T ss_pred CCCCCCCCcccCCCCCCCCCCcccccc
No 247
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=60.71 E-value=8.7 Score=43.07 Aligned_cols=44 Identities=23% Similarity=0.400 Sum_probs=31.6
Q ss_pred CCCCCCCCCCccceeecCCcceEEEeCCCc--ceecCCCCCCCCCC
Q 038397 4 PPVPPPPPPNVGVQVRCAGCHIILTVGPGL--TEFICGTCNLPQML 47 (1102)
Q Consensus 4 ~~~~~~~~~~~~~~~~C~~C~a~l~~~pg~--~~~~Cp~C~~~~~l 47 (1102)
|..|+++..|....|.|+||..++-+.-=. +--.||.|...-++
T Consensus 144 p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrKvSSV 189 (256)
T PF09788_consen 144 PVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRKVSSV 189 (256)
T ss_pred CCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCceeccc
Confidence 333344445788899999999999887544 45599999974444
No 248
>PRK00420 hypothetical protein; Validated
Probab=60.26 E-value=5 Score=39.93 Aligned_cols=34 Identities=18% Similarity=0.175 Sum_probs=26.4
Q ss_pred eecCCCccceeeccCCCccccCCCCCccccccccc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVELAVDMSK 130 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~~~~ 130 (1102)
.-+|..||+.|.=. .-+...||.||..+.|...+
T Consensus 23 ~~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~~~v~~~e 56 (112)
T PRK00420 23 SKHCPVCGLPLFEL-KDGEVVCPVHGKVYIVKSDE 56 (112)
T ss_pred cCCCCCCCCcceec-CCCceECCCCCCeeeeccHH
Confidence 36899999887753 23378999999999986644
No 249
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=60.25 E-value=4.4 Score=30.34 Aligned_cols=22 Identities=18% Similarity=0.554 Sum_probs=17.5
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
.|+.|++++. ++.-.||.||+.
T Consensus 2 ~CP~C~~~V~----~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVP----ESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCch----hhcCcCCCCCCC
Confidence 5999999883 456789999974
No 250
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=60.20 E-value=4.2 Score=33.11 Aligned_cols=31 Identities=26% Similarity=0.596 Sum_probs=16.9
Q ss_pred ecCCCccceeec----cCCCccccCCCCCcccccc
Q 038397 97 LPCANCKAILNV----PHGLVRFSCPQCAVELAVD 127 (1102)
Q Consensus 97 ~~C~~C~A~~~v----p~~~~~f~Cp~C~~~L~v~ 127 (1102)
+.|.+|+|.+|- ..+-..+.|++|+..=.++
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp 37 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLP 37 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--EEE--
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCcCCCC
Confidence 689999999974 4455578999999865443
No 251
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=59.52 E-value=6.9 Score=30.54 Aligned_cols=25 Identities=24% Similarity=0.664 Sum_probs=19.6
Q ss_pred ecCCCccceeeccCCCccccCCCCCcc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
-.|..||-+..-.. ..+.||.||++
T Consensus 2 ~~C~~CGy~y~~~~--~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIYDGEE--APWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEECCCc--CCCcCcCCCCc
Confidence 46999998876433 67899999985
No 252
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=59.42 E-value=6.5 Score=40.15 Aligned_cols=29 Identities=24% Similarity=0.613 Sum_probs=22.0
Q ss_pred ceecCCCccceeeccC-----------------C--CccccCCCCCcc
Q 038397 95 IQLPCANCKAILNVPH-----------------G--LVRFSCPQCAVE 123 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~-----------------~--~~~f~Cp~C~~~ 123 (1102)
....|.+||....+.. . ...+.||.||..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 4689999999988861 0 234689999975
No 253
>PHA02558 uvsW UvsW helicase; Provisional
Probab=59.08 E-value=17 Score=44.45 Aligned_cols=55 Identities=22% Similarity=0.246 Sum_probs=43.3
Q ss_pred hhhcCCcceEEEEe-cccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCC
Q 038397 806 QLFMDGKKLVAIIS-EAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQAS 868 (1102)
Q Consensus 806 ~~Fm~G~K~VAIIS-eAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvs 868 (1102)
+.|.+|+..|.|.| +-.++||..- +-..-|..-++-|...-+|+.||+||.+.-.
T Consensus 388 ~~~~~~~~~vLvaT~~~l~eG~Dip--------~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K 443 (501)
T PHA02558 388 KIAEGGKGIIIVASYGVFSTGISIK--------NLHHVIFAHPSKSKIIVLQSIGRVLRKHGSK 443 (501)
T ss_pred HHHhCCCCeEEEEEcceeccccccc--------cccEEEEecCCcchhhhhhhhhccccCCCCC
Confidence 56888888899998 8999999774 2223455677778888999999999987643
No 254
>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]
Probab=58.51 E-value=4.6 Score=51.79 Aligned_cols=47 Identities=26% Similarity=0.510 Sum_probs=32.6
Q ss_pred cccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCC
Q 038397 318 IREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAG 372 (1102)
Q Consensus 318 ~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~ 372 (1102)
-...|||+-|+-|+...-++..- |+| -+.||||||+|++-..+..++
T Consensus 221 edAdIIF~PYnYLiDp~iR~~~~----v~L----knsIVIfDEAHNiEdic~esa 267 (945)
T KOG1132|consen 221 EDADIIFCPYNYLIDPKIRRSHK----VDL----KNSIVIFDEAHNIEDICRESA 267 (945)
T ss_pred ccCcEEEechhhhcCHhhhcccc----ccc----cccEEEEeccccHHHHHhhcc
Confidence 45679999999999652211111 344 356999999999888776544
No 255
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=58.32 E-value=31 Score=41.49 Aligned_cols=88 Identities=11% Similarity=0.117 Sum_probs=54.0
Q ss_pred CCCCCCcccccccCCCCCCCCCCccCcccccccccCCcccchhhHHHHHHhhccccCCCCC-cceeEeecCCCCCcchhh
Q 038397 180 GPAHPDPIVETSSLSAVHPPEPTYDLLIKYDLESSKSLSCLQIETLVYASQRHLQHLPNSA-RAGFFIGDGAGVGKGRTI 258 (1102)
Q Consensus 180 ~~~hP~~lve~~~l~sv~pP~~~y~~~lp~~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~-R~Gf~~gDg~GvGKGR~~ 258 (1102)
....|+...+........|+.|.-++.|-.... . .+....-+-.+|=|. -+|.++|+ .|+||+ ++
T Consensus 120 ng~~~~~~~~r~~f~~l~p~~p~~R~~le~~~~--~----------~~~~rvID~l~PIGkGQR~lIvgp-pGvGKT-TL 185 (416)
T PRK09376 120 NGEDPEKARNRPLFENLTPLYPNERLRLETGNP--E----------DLSTRIIDLIAPIGKGQRGLIVAP-PKAGKT-VL 185 (416)
T ss_pred CCCCHHHhcCCCCcccCCCCChhhcccccCCCC--c----------ccceeeeeeecccccCceEEEeCC-CCCChh-HH
Confidence 356677777777778888888887776643110 0 111222333445332 23444565 899999 67
Q ss_pred HHHHHHHHhcc-CceEEEEEcCCc
Q 038397 259 AGLIWENWHHG-RRKALWISVGSD 281 (1102)
Q Consensus 259 AgiI~~n~l~G-r~~~~w~s~s~~ 281 (1102)
|.-|+.+..+. .--.+|+.++.+
T Consensus 186 aK~Ian~I~~nhFDv~~~VvLIgE 209 (416)
T PRK09376 186 LQNIANSITTNHPEVHLIVLLIDE 209 (416)
T ss_pred HHHHHHHHHhhcCCeEEEEEEeCC
Confidence 77787777654 234579988877
No 256
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=58.07 E-value=3.5 Score=31.90 Aligned_cols=25 Identities=20% Similarity=0.452 Sum_probs=14.3
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
+|+.|+...++ ..-..|.||.|+.+
T Consensus 4 ~Cp~C~se~~y-~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY-EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E-E-SSSEEETTTTEE
T ss_pred CCCCCCCccee-ccCCEEeCCccccc
Confidence 59999999999 55567999999964
No 257
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=57.58 E-value=5.9 Score=39.48 Aligned_cols=29 Identities=21% Similarity=0.531 Sum_probs=20.9
Q ss_pred cceecCCCccceeeccCCCccccCCCCCcc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
..+..|..||....++.. .-+.||.||.+
T Consensus 69 p~~~~C~~Cg~~~~~~~~-~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHVFKPNAL-DYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCccccCCc-cCCcCcCCCCC
Confidence 346899999977666532 22369999986
No 258
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=57.35 E-value=10 Score=46.66 Aligned_cols=48 Identities=31% Similarity=0.488 Sum_probs=31.6
Q ss_pred CceEEeecchhccccCCC--CCCCchhHHHHHHHHhhhCCCc----------------cEEEEecCCC
Q 038397 353 DGLVIFDECHKAKNLVPE--AGSQPTRTGEAVLELQARLPEA----------------RVVYCSATGA 402 (1102)
Q Consensus 353 dgvivfDEcH~akn~~~~--~~~~~s~~g~avl~LQ~~lP~A----------------RvvY~SATga 402 (1102)
|.++|.||+|-.--...+ +|..+-|+ ...+.-=+||.| .+||+|||..
T Consensus 332 d~Ll~IDESHvTvPQi~gMynGDrsRK~--~LVeyGFRLPSAlDNRPL~feEf~~~~~q~i~VSATPg 397 (663)
T COG0556 332 DFLLFIDESHVTVPQIGGMYNGDRSRKQ--TLVEYGFRLPSALDNRPLKFEEFEAKIPQTIYVSATPG 397 (663)
T ss_pred ceEEEEeccccchHhhhchhcccHHHHH--HHHHhcCcCcccccCCCCCHHHHHHhcCCEEEEECCCC
Confidence 569999999987655433 33333332 233444567776 7999999965
No 259
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=57.32 E-value=9.2 Score=30.22 Aligned_cols=26 Identities=23% Similarity=0.483 Sum_probs=19.6
Q ss_pred eecCCCccceeeccCCCccccCCCCCcc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
.-.|..||-+..-.+ ....||.||++
T Consensus 2 ~~~C~~CG~i~~g~~--~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEE--APEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCc--CCCcCcCCCCc
Confidence 357999999876432 34599999986
No 260
>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]
Probab=56.94 E-value=19 Score=45.99 Aligned_cols=167 Identities=23% Similarity=0.243 Sum_probs=89.4
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCc--eEEEEEcCCchhhhHHhhhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRR--KALWISVGSDLKFDARRDLDDV 293 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~--~~~w~s~s~~L~~Da~RDl~di 293 (1102)
.|-+-|++.+.+-.. .|.. ...|=+++|.+|.||+.|.-..+...+..+.. ...-+.+...+..-..+.+ .-
T Consensus 338 ~lr~yq~~g~~wl~~----~l~~-~~~~~ilaD~mglGKTiq~i~~l~~~~~~~~~~~~~~liv~p~s~~~nw~~e~-~k 411 (866)
T COG0553 338 ELRPYQLEGVNWLSE----LLRS-NLLGGILADDMGLGKTVQTIALLLSLLESIKVYLGPALIVVPASLLSNWKREF-EK 411 (866)
T ss_pred hhHHHHHHHHHHHHH----HHHh-ccCCCcccccccchhHHHHHHHHHhhhhcccCCCCCeEEEecHHHHHHHHHHH-hh
Confidence 344568888766552 1111 12334578999999999887777665555553 2444555555665555555 22
Q ss_pred CCCccc-c--cccCCCC-CCcCCCCcc--------ccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecc
Q 038397 294 GATCIE-V--HALNKLP-YSKLDSRSV--------GIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDEC 361 (1102)
Q Consensus 294 G~~~i~-v--~~l~~~~-~~~~~~~~~--------~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEc 361 (1102)
-+..+. + +...+.. ..+. ... .+...|+-+||..|.... ....-|.. ++| ..+|+||+
T Consensus 412 ~~~~~~~~~~~~g~~~~~~~~~--~~~~~~~~~~~~~~~~v~itty~~l~~~~-~~~~~l~~-~~~------~~~v~DEa 481 (866)
T COG0553 412 FAPDLRLVLVYHGEKSELDKKR--EALRDLLKLHLVIIFDVVITTYELLRRFL-VDHGGLKK-IEW------DRVVLDEA 481 (866)
T ss_pred hCccccceeeeeCCcccccHHH--HHHHHHhhhcccceeeEEechHHHHHHhh-hhHHHHhh-cee------eeeehhhH
Confidence 222222 2 1111110 0000 000 112568999999998621 00111211 122 48999999
Q ss_pred hhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCCCCCccchh
Q 038397 362 HKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGASEPRNMGYM 411 (1102)
Q Consensus 362 H~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~ym 411 (1102)
|..||.. |+.++++..++.. .-+=.|.|- =..||.-+
T Consensus 482 ~~ikn~~-------s~~~~~l~~~~~~----~~~~LtgTP--len~l~eL 518 (866)
T COG0553 482 HRIKNDQ-------SSEGKALQFLKAL----NRLDLTGTP--LENRLGEL 518 (866)
T ss_pred HHHhhhh-------hHHHHHHHHHhhc----ceeeCCCCh--HhhhHHHH
Confidence 9999885 6777776644433 224445555 35666533
No 261
>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.
Probab=56.39 E-value=8.8 Score=40.77 Aligned_cols=28 Identities=14% Similarity=0.179 Sum_probs=18.8
Q ss_pred HHHHHHhccCCCceEEeecchhccccCC
Q 038397 342 QQLVQWCGSGYDGLVIFDECHKAKNLVP 369 (1102)
Q Consensus 342 ~Ql~~W~g~dfdgvivfDEcH~akn~~~ 369 (1102)
+++-+|..-+-+++||+||||..-|...
T Consensus 69 ~~~~~~~~~~~~~liviDEa~~~~~~r~ 96 (193)
T PF05707_consen 69 DDPDDWRKLPKGSLIVIDEAQNFFPSRS 96 (193)
T ss_dssp GGHHHHTTSGTT-EEEETTGGGTSB---
T ss_pred hhhhhhcccCCCcEEEEECChhhcCCCc
Confidence 3456788755678999999999776643
No 262
>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.
Probab=56.37 E-value=24 Score=39.56 Aligned_cols=49 Identities=16% Similarity=0.141 Sum_probs=29.9
Q ss_pred CCcceeEeecCCCCCcchhhHHHHHHHHhccC-ceEEEEEcCCc---hhhhHHhhh
Q 038397 239 SARAGFFIGDGAGVGKGRTIAGLIWENWHHGR-RKALWISVGSD---LKFDARRDL 290 (1102)
Q Consensus 239 g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr-~~~~w~s~s~~---L~~Da~RDl 290 (1102)
|.|.+ ++|+ .|+||+ +++..|+.+..+.. ...+|+.++.+ =..|..+++
T Consensus 16 Gqr~~-I~G~-~G~GKT-TLlr~I~n~l~~~~fdv~~~v~vI~er~~ev~el~~~I 68 (249)
T cd01128 16 GQRGL-IVAP-PKAGKT-TLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSV 68 (249)
T ss_pred CCEEE-EECC-CCCCHH-HHHHHHHhccccccCCeEEEEEEccCCCccHHHHHHHh
Confidence 44444 4565 899999 56677777765542 23569886655 344444554
No 263
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=56.25 E-value=6.4 Score=48.86 Aligned_cols=28 Identities=21% Similarity=0.549 Sum_probs=22.3
Q ss_pred eeecCCcceEE-------EeC----CCcceecCCCCCCC
Q 038397 17 QVRCAGCHIIL-------TVG----PGLTEFICGTCNLP 44 (1102)
Q Consensus 17 ~~~C~~C~a~l-------~~~----pg~~~~~Cp~C~~~ 44 (1102)
.++|++||... .++ |.+..|.||.||..
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~ 238 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCE 238 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCC
Confidence 56799999864 343 66999999999973
No 264
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=55.83 E-value=53 Score=41.55 Aligned_cols=71 Identities=15% Similarity=0.237 Sum_probs=41.7
Q ss_pred eEEeecchhccccCCCCCCCchhHHHHHHHHhhhCC--CccEEEEecCCCCCCCcc--chhhhccccCCCCC--CCCHHH
Q 038397 355 LVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLP--EARVVYCSATGASEPRNM--GYMVRLGLWGAGTC--FKDFQI 428 (1102)
Q Consensus 355 vivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP--~ARvvY~SATgasep~Nl--~ym~RLGLWg~gt~--f~~~~~ 428 (1102)
|||+|+.|...+. ..++ .....|-|.+- +..||++|-...++-.++ ...+|| .||--.. =++.+.
T Consensus 380 LLlIDDIq~l~gk------e~tq--eeLF~l~N~l~e~gk~IIITSd~~P~eL~~l~~rL~SRf-~~GLvv~I~~PD~Et 450 (617)
T PRK14086 380 ILLVDDIQFLEDK------ESTQ--EEFFHTFNTLHNANKQIVLSSDRPPKQLVTLEDRLRNRF-EWGLITDVQPPELET 450 (617)
T ss_pred EEEEehhccccCC------HHHH--HHHHHHHHHHHhcCCCEEEecCCChHhhhhccHHHHhhh-hcCceEEcCCCCHHH
Confidence 8899999987643 1223 33344444443 356999887776666655 356787 5765332 245665
Q ss_pred HHHHHh
Q 038397 429 FLGALD 434 (1102)
Q Consensus 429 f~~a~~ 434 (1102)
-+..|+
T Consensus 451 R~aIL~ 456 (617)
T PRK14086 451 RIAILR 456 (617)
T ss_pred HHHHHH
Confidence 554443
No 265
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=55.79 E-value=3.5 Score=43.06 Aligned_cols=29 Identities=17% Similarity=0.429 Sum_probs=22.6
Q ss_pred eeecCCcceEEEeCCCcc-eecCCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLT-EFICGTCNLPQ 45 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~-~~~Cp~C~~~~ 45 (1102)
.--|++|+..+++.-.+. .|.||.||...
T Consensus 109 ~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAMELNFTCPRCGAML 138 (158)
T ss_pred eEECCCCCcEeeHHHHHHcCCcCCCCCCEe
Confidence 445999999997665553 79999999754
No 266
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=55.66 E-value=4.3 Score=43.27 Aligned_cols=29 Identities=28% Similarity=0.596 Sum_probs=22.7
Q ss_pred eeecCCcceEEEeCCCcc-eecCCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLT-EFICGTCNLPQ 45 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~-~~~Cp~C~~~~ 45 (1102)
.-.|++|+..+++.-.+. .|.||.||...
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCGEML 146 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCCCCC
Confidence 445999999997765553 79999999754
No 267
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=55.44 E-value=75 Score=41.60 Aligned_cols=53 Identities=15% Similarity=0.147 Sum_probs=42.8
Q ss_pred ccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhhHHHHHH
Q 038397 837 QKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRFASIVAK 891 (1102)
Q Consensus 837 QRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRFaS~VAk 891 (1102)
-+.+.=|..|+--+.=+.||.+-++|+..+ .-.|.++..+---|.||.+++-|
T Consensus 475 ~~P~~VImYEP~~sfIR~IEvyra~r~~r~--~rVyfL~y~~S~EEq~yl~sirr 527 (814)
T TIGR00596 475 LMPRYVIMYEPDISFIRQLEVYKASRPLRP--LRVYFLYYGGSIEEQRYLTSLRR 527 (814)
T ss_pred hCCCEEEEECCChHHHHHHHHHHccCCCCC--cEEEEEEECCcHHHHHHHHHHHH
Confidence 366888999999999999994444333333 55899999999999999999987
No 268
>PF04710 Pellino: Pellino; InterPro: IPR006800 Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase [, , ].; PDB: 3EGB_B 3EGA_A.
Probab=54.37 E-value=4.2 Score=48.02 Aligned_cols=43 Identities=33% Similarity=0.658 Sum_probs=0.0
Q ss_pred ccceecCCCcc--------ceeeccCCCccc--cCCCCCcccccccccccccC
Q 038397 93 TKIQLPCANCK--------AILNVPHGLVRF--SCPQCAVELAVDMSKVKQFF 135 (1102)
Q Consensus 93 t~~~~~C~~C~--------A~~~vp~~~~~f--~Cp~C~~~L~v~~~~~~~~~ 135 (1102)
|-.-.||+.=- +.+.+|||...| .||||.++|.-+..++|.+|
T Consensus 359 thaF~PCGHv~SekTa~yWs~i~lPhGt~~f~a~CPFCa~~L~g~~g~vrLiF 411 (416)
T PF04710_consen 359 THAFNPCGHVCSEKTAKYWSQIPLPHGTHAFHAACPFCATPLDGEQGYVRLIF 411 (416)
T ss_dssp -----------------------------------------------------
T ss_pred ceeecccccccchhhhhhhhcCCCCCCcccccccCCcccCcccCCCCceEEEE
Confidence 33346666533 567899999998 89999999999888998887
No 269
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=54.30 E-value=4.8 Score=45.71 Aligned_cols=26 Identities=31% Similarity=0.650 Sum_probs=15.7
Q ss_pred cceecCCCccceeeccCCCccccCCCCCcc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
+-.+.|+-|+..=++. |..||+||..
T Consensus 195 ~R~L~Cs~C~t~W~~~----R~~Cp~Cg~~ 220 (290)
T PF04216_consen 195 KRYLHCSLCGTEWRFV----RIKCPYCGNT 220 (290)
T ss_dssp EEEEEETTT--EEE------TTS-TTT---
T ss_pred cEEEEcCCCCCeeeec----CCCCcCCCCC
Confidence 4579999999998876 6699999987
No 270
>TIGR00376 DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.
Probab=54.27 E-value=14 Score=46.60 Aligned_cols=57 Identities=26% Similarity=0.293 Sum_probs=43.6
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCch
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDL 282 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L 282 (1102)
.|...|.+||..|..+. .-+++=-..|.||+.+++.+|..-..+|. +++.++-|+.-
T Consensus 157 ~ln~~Q~~Av~~~l~~~---------~~~lI~GpPGTGKT~t~~~ii~~~~~~g~-~VLv~a~sn~A 213 (637)
T TIGR00376 157 NLNESQKEAVSFALSSK---------DLFLIHGPPGTGKTRTLVELIRQLVKRGL-RVLVTAPSNIA 213 (637)
T ss_pred CCCHHHHHHHHHHhcCC---------CeEEEEcCCCCCHHHHHHHHHHHHHHcCC-CEEEEcCcHHH
Confidence 57899999998876432 12344445999999999999999888888 58888876633
No 271
>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=54.04 E-value=29 Score=42.93 Aligned_cols=147 Identities=18% Similarity=0.251 Sum_probs=86.6
Q ss_pred cceeEeecCCCCCcch--hhHHHHHHHHh-----cc-CceEEEEEcCCchhhhHHhhhhhhCCC-cccccccCCCCCCcC
Q 038397 241 RAGFFIGDGAGVGKGR--TIAGLIWENWH-----HG-RRKALWISVGSDLKFDARRDLDDVGAT-CIEVHALNKLPYSKL 311 (1102)
Q Consensus 241 R~Gf~~gDg~GvGKGR--~~AgiI~~n~l-----~G-r~~~~w~s~s~~L~~Da~RDl~diG~~-~i~v~~l~~~~~~~~ 311 (1102)
++..+....||-||+- .+-+|++=+-. +| ..+++-++-.-+|-.=.+++.+++|.. .+.. .+-||-.
T Consensus 128 GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTRELA~QV~~~~~~~~~~~~~~~----~cvyGG~ 203 (519)
T KOG0331|consen 128 GRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTRELAVQVQAEAREFGKSLRLRS----TCVYGGA 203 (519)
T ss_pred CCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEEEEcCcHHHHHHHHHHHHHHcCCCCccE----EEEeCCC
Confidence 3566777889999964 34455554431 23 244777777778888888888888875 3222 2223311
Q ss_pred C--CCccccccc--eEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhh
Q 038397 312 D--SRSVGIREG--VVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQA 387 (1102)
Q Consensus 312 ~--~~~~~~~~G--vlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~ 387 (1102)
. .....++.| |+-+|=--|+..-+.+..-|.++ ..+|+||+..|-... -.-.+..+-+
T Consensus 204 ~~~~Q~~~l~~gvdiviaTPGRl~d~le~g~~~l~~v---------~ylVLDEADrMldmG---------Fe~qI~~Il~ 265 (519)
T KOG0331|consen 204 PKGPQLRDLERGVDVVIATPGRLIDLLEEGSLNLSRV---------TYLVLDEADRMLDMG---------FEPQIRKILS 265 (519)
T ss_pred CccHHHHHHhcCCcEEEeCChHHHHHHHcCCccccce---------eEEEeccHHhhhccc---------cHHHHHHHHH
Confidence 1 111124444 56555444443322222222221 479999999998763 2234555667
Q ss_pred hC-CCcc-EEEEecCCCCCCCccc
Q 038397 388 RL-PEAR-VVYCSATGASEPRNMG 409 (1102)
Q Consensus 388 ~l-P~AR-vvY~SATgasep~Nl~ 409 (1102)
++ |..| .+.-|||+-+++++|+
T Consensus 266 ~i~~~~rQtlm~saTwp~~v~~lA 289 (519)
T KOG0331|consen 266 QIPRPDRQTLMFSATWPKEVRQLA 289 (519)
T ss_pred hcCCCcccEEEEeeeccHHHHHHH
Confidence 77 4444 8999999777766666
No 272
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=53.80 E-value=10 Score=43.81 Aligned_cols=26 Identities=23% Similarity=0.542 Sum_probs=21.9
Q ss_pred cceecCCCccceeeccCCCccccCCCCCcc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
.-.++|+-|+..=++. |-.||+||..
T Consensus 208 ~RyL~CslC~teW~~~----R~~C~~Cg~~ 233 (305)
T TIGR01562 208 LRYLSCSLCATEWHYV----RVKCSHCEES 233 (305)
T ss_pred ceEEEcCCCCCccccc----CccCCCCCCC
Confidence 4479999999988776 7799999974
No 273
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=53.54 E-value=14 Score=36.82 Aligned_cols=83 Identities=24% Similarity=0.422 Sum_probs=47.4
Q ss_pred cCCcceEEEeCCCcceecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCccceecC
Q 038397 20 CAGCHIILTVGPGLTEFICGTCNLPQMLPPELMPASTGGSVPNNTTSSNTTNSTRPTHMKAASSHVPALGIDPTKIQLPC 99 (1102)
Q Consensus 20 C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~t~~~~~C 99 (1102)
|+.|++-.---| ..||-||..+-+++-| .++.- |+ -| ++++...+-. .....-.|
T Consensus 4 CPrC~skvC~LP----~~CpiCgLtLVss~HL-----ARSyH--------HL--fP--l~~f~ev~~~----~~~~~~~C 58 (112)
T TIGR00622 4 CPQCRAKVCELP----VECPICGLTLILSTHL-----ARSYH--------HL--FP--LKAFQEIPLE----EYNGSRFC 58 (112)
T ss_pred CCCCCCCccCCC----CcCCcCCCEEeccchH-----HHhhh--------cc--CC--Cccccccccc----ccCCCCcc
Confidence 778887663333 6799999888777777 11100 01 01 1122111101 11112359
Q ss_pred CCccceeecc--------CCCccccCCCCCcccccc
Q 038397 100 ANCKAILNVP--------HGLVRFSCPQCAVELAVD 127 (1102)
Q Consensus 100 ~~C~A~~~vp--------~~~~~f~Cp~C~~~L~v~ 127 (1102)
.+|+..+.-+ ....+|+|+.|....=+|
T Consensus 59 ~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~d 94 (112)
T TIGR00622 59 FGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVD 94 (112)
T ss_pred cCcCCCCCCcccccccccccccceeCCCCCCccccc
Confidence 9999988654 235689999999877665
No 274
>TIGR00767 rho transcription termination factor Rho. Members of this family differ in the specificity of RNA binding.
Probab=53.19 E-value=32 Score=41.39 Aligned_cols=47 Identities=15% Similarity=0.189 Sum_probs=30.5
Q ss_pred ceeEeecCCCCCcchhhHHHHHHHHhcc-CceEEEEEcCCc---hhhhHHhhh
Q 038397 242 AGFFIGDGAGVGKGRTIAGLIWENWHHG-RRKALWISVGSD---LKFDARRDL 290 (1102)
Q Consensus 242 ~Gf~~gDg~GvGKGR~~AgiI~~n~l~G-r~~~~w~s~s~~---L~~Da~RDl 290 (1102)
++-++|+ +|+||+ +++..|..++.+. ..-.+|+-++.+ =..|.+|.+
T Consensus 170 ~~~IvG~-~g~GKT-tL~~~i~~~I~~nhfdv~v~VlLIgER~~EVtDLqrsI 220 (415)
T TIGR00767 170 RGLIVAP-PKAGKT-VLLQKIAQAITRNHPEVELIVLLIDERPEEVTDMQRSV 220 (415)
T ss_pred EEEEECC-CCCChh-HHHHHHHHhhcccCCceEEEEEEcCCCCccHHHHHHHh
Confidence 3445666 899999 5677788887765 233679888855 334444544
No 275
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=53.16 E-value=12 Score=33.34 Aligned_cols=42 Identities=17% Similarity=0.313 Sum_probs=31.1
Q ss_pred CCCCCCCCC--ccceeecCCcceEEEeCCCcceecCCCCCCCCCC
Q 038397 5 PVPPPPPPN--VGVQVRCAGCHIILTVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 5 ~~~~~~~~~--~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l 47 (1102)
+..+++.+| ..+---|+.||+..+..+|- -+.|-.||+....
T Consensus 6 s~~~~aa~~r~~~miYiCgdC~~en~lk~~D-~irCReCG~RIly 49 (62)
T KOG3507|consen 6 SLGDPAAGPRTATMIYICGDCGQENTLKRGD-VIRCRECGYRILY 49 (62)
T ss_pred CCCCccCCCCcccEEEEeccccccccccCCC-cEehhhcchHHHH
Confidence 334444334 66777799999999999884 5899999986543
No 276
>PRK14873 primosome assembly protein PriA; Provisional
Probab=53.04 E-value=9.1 Score=48.60 Aligned_cols=27 Identities=22% Similarity=0.336 Sum_probs=23.7
Q ss_pred eeecCCcceEEEeCCCcceecCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
..+|++|...|++--+...+.|.+||+
T Consensus 392 ~~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 392 PARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred eeECCCCCCceeEecCCCeeECCCCcC
Confidence 357999999999977778999999996
No 277
>CHL00095 clpC Clp protease ATP binding subunit
Probab=53.03 E-value=50 Score=43.07 Aligned_cols=57 Identities=19% Similarity=0.243 Sum_probs=35.6
Q ss_pred chHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecC
Q 038397 339 SRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSAT 400 (1102)
Q Consensus 339 sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SAT 400 (1102)
.||+++++.+-..-..+|++||.|..-+.....| +. .+..-|...|-+..+...-||
T Consensus 258 ~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g---~~--~~a~lLkp~l~rg~l~~IgaT 314 (821)
T CHL00095 258 ERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEG---AI--DAANILKPALARGELQCIGAT 314 (821)
T ss_pred HHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCC---cc--cHHHHhHHHHhCCCcEEEEeC
Confidence 5899999988655456899999998764432111 11 122334566656666666666
No 278
>PRK09694 helicase Cas3; Provisional
Probab=52.86 E-value=22 Score=46.67 Aligned_cols=62 Identities=24% Similarity=0.394 Sum_probs=46.3
Q ss_pred hhh-cCCc---ceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCC------CCeEEEe
Q 038397 806 QLF-MDGK---KLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQAS------APEYRII 875 (1102)
Q Consensus 806 ~~F-m~G~---K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvs------aP~Y~~l 875 (1102)
+.| .+|+ ..|+|-+...-.|+-+-.| +.||--.| +|.-||+.||+||.+-.. .|.+..+
T Consensus 611 ~~fgk~g~r~~~~ILVaTQViE~GLDId~D---------vlItdlaP--idsLiQRaGR~~R~~~~~rp~~~~~p~~~V~ 679 (878)
T PRK09694 611 ENFGKNGKRNQGRILVATQVVEQSLDLDFD---------WLITQLCP--VDLLFQRLGRLHRHHRKYRPAGFEIPVATVL 679 (878)
T ss_pred HHHHhcCCcCCCeEEEECcchhheeecCCC---------eEEECCCC--HHHHHHHHhccCCCCCCCCCCCCcCceEEEE
Confidence 456 5666 3799999999999999665 46665566 899999999999998642 4555555
Q ss_pred ecC
Q 038397 876 FTN 878 (1102)
Q Consensus 876 ~T~ 878 (1102)
..+
T Consensus 680 ~p~ 682 (878)
T PRK09694 680 LPD 682 (878)
T ss_pred ecc
Confidence 443
No 279
>PRK05580 primosome assembly protein PriA; Validated
Probab=52.86 E-value=8.6 Score=48.86 Aligned_cols=26 Identities=23% Similarity=0.525 Sum_probs=23.0
Q ss_pred eecCCcceEEEeCCCcceecCCCCCC
Q 038397 18 VRCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
.+|++|...|++--....+.|.|||.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~ 416 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGY 416 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcC
Confidence 46889999999988888999999997
No 280
>cd01120 RecA-like_NTPases RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.
Probab=52.46 E-value=68 Score=31.37 Aligned_cols=37 Identities=16% Similarity=0.342 Sum_probs=28.1
Q ss_pred eecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhh
Q 038397 246 IGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKF 284 (1102)
Q Consensus 246 ~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~ 284 (1102)
.|. +|+||+..+..++...-.+|.+ ++|++....+..
T Consensus 5 ~G~-~G~GKT~l~~~i~~~~~~~~~~-v~~~~~e~~~~~ 41 (165)
T cd01120 5 FGP-TGSGKTTLALQLALNIATKGGK-VVYVDIEEEIEE 41 (165)
T ss_pred eCC-CCCCHHHHHHHHHHHHHhcCCE-EEEEECCcchHH
Confidence 444 8999999998888777666654 999998766543
No 281
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=52.26 E-value=14 Score=44.08 Aligned_cols=54 Identities=17% Similarity=0.375 Sum_probs=47.4
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQA 867 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQv 867 (1102)
+.|-+|+-.|+|-+|-||-|+-+|---.|- -...|-+++.-+++.|||+|.+-.
T Consensus 509 ~~~ksG~vrILvaTDlaSRGlDv~DiTHV~--------NyDFP~nIeeYVHRvGrtGRaGr~ 562 (629)
T KOG0336|consen 509 EDFKSGEVRILVATDLASRGLDVPDITHVY--------NYDFPRNIEEYVHRVGRTGRAGRT 562 (629)
T ss_pred HhhhcCceEEEEEechhhcCCCchhcceee--------ccCCCccHHHHHHHhcccccCCCC
Confidence 689999999999999999999998655443 467899999999999999998753
No 282
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=52.26 E-value=50 Score=42.46 Aligned_cols=76 Identities=20% Similarity=0.287 Sum_probs=43.7
Q ss_pred eEEeehhhhhhcc-ccc--cchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEe
Q 038397 322 VVFLTYSSLIASS-EKG--RSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCS 398 (1102)
Q Consensus 322 vlF~TYs~L~~~~-~~~--~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~S 398 (1102)
++....++|.... ..| ..||+++++.+...-+.+|++||.|..-+...+.++ +..... -|...|-+..|...-
T Consensus 241 ~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~--~~~~~~--~L~~~l~~g~i~~Ig 316 (731)
T TIGR02639 241 IYSLDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGG--SMDASN--LLKPALSSGKLRCIG 316 (731)
T ss_pred EEEecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCc--cHHHHH--HHHHHHhCCCeEEEE
Confidence 4444555665422 112 368999998775545679999999987654221111 121112 234556666777766
Q ss_pred cCC
Q 038397 399 ATG 401 (1102)
Q Consensus 399 ATg 401 (1102)
||-
T Consensus 317 aTt 319 (731)
T TIGR02639 317 STT 319 (731)
T ss_pred ecC
Confidence 664
No 283
>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]
Probab=52.23 E-value=12 Score=49.56 Aligned_cols=203 Identities=18% Similarity=0.315 Sum_probs=108.9
Q ss_pred EeecCCCCCcchhhHHHHHHHH-hccC--ceEEEEEcCCchhhhHH-hhhhhhCCCcccccccCCCCCC-----cCCCCc
Q 038397 245 FIGDGAGVGKGRTIAGLIWENW-HHGR--RKALWISVGSDLKFDAR-RDLDDVGATCIEVHALNKLPYS-----KLDSRS 315 (1102)
Q Consensus 245 ~~gDg~GvGKGR~~AgiI~~n~-l~Gr--~~~~w~s~s~~L~~Da~-RDl~diG~~~i~v~~l~~~~~~-----~~~~~~ 315 (1102)
+++|-+|.||+-|.-.+..+-- -.|. -+.|-+..|.-|...++ .-| |..++|. . =|| +...+.
T Consensus 638 ILADEmGLGKTIQtISllAhLACeegnWGPHLIVVpTsviLnWEMElKRw----cPglKIL--T--YyGs~kErkeKRqg 709 (1958)
T KOG0391|consen 638 ILADEMGLGKTIQTISLLAHLACEEGNWGPHLIVVPTSVILNWEMELKRW----CPGLKIL--T--YYGSHKERKEKRQG 709 (1958)
T ss_pred eehhhhcccchhHHHHHHHHHHhcccCCCCceEEeechhhhhhhHHHhhh----CCcceEe--e--ecCCHHHHHHHhhc
Confidence 5899999999998855443211 1111 23555666666665544 111 1111110 0 012 000011
Q ss_pred cc--cccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCcc
Q 038397 316 VG--IREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEAR 393 (1102)
Q Consensus 316 ~~--~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~AR 393 (1102)
+. ...-|-.+.|-+....-. -+++ ..| -.+|+||+|+-||.. |+-=.|++.++.+ -|
T Consensus 710 W~kPnaFHVCItSYklv~qd~~----AFkr-krW------qyLvLDEaqnIKnfk-------sqrWQAllnfnsq---rR 768 (1958)
T KOG0391|consen 710 WAKPNAFHVCITSYKLVFQDLT----AFKR-KRW------QYLVLDEAQNIKNFK-------SQRWQALLNFNSQ---RR 768 (1958)
T ss_pred ccCCCeeEEeehhhHHHHhHHH----HHHh-hcc------ceeehhhhhhhcchh-------HHHHHHHhccchh---he
Confidence 11 122377788887764321 1221 246 489999999999995 6777777766554 23
Q ss_pred EEEEecCCCCCCCccchhhhccccC-----CCCCCCCHHHHHHHHhccChhHHH--------HHHHHHHhccceeeeccC
Q 038397 394 VVYCSATGASEPRNMGYMVRLGLWG-----AGTCFKDFQIFLGALDKGGVGALE--------LVAMDMKARGMYVCRTLS 460 (1102)
Q Consensus 394 vvY~SATgasep~Nl~ym~RLGLWg-----~gt~f~~~~~f~~a~~~gGv~amE--------~va~dlK~~G~yiaR~LS 460 (1102)
.+. ||.-=-+||. -||. --+-|.+.++|..-+.+==-|.|| +|++-=|-.--||=|.|-
T Consensus 769 LLL---tgTPLqNslm-----ELWSLmhFLmP~~f~shd~fk~wfsnPltgmiEgsqeyn~klV~RLHkVlrPfiLRRlK 840 (1958)
T KOG0391|consen 769 LLL---TGTPLQNSLM-----ELWSLMHFLMPQTFASHDIFKPWFSNPLTGMIEGSQEYNHKLVIRLHKVLRPFILRRLK 840 (1958)
T ss_pred eee---cCCchhhHHH-----HHHHHHHHhhchhhhhhhhHHHHhcCcchhhcccchhhchHHHHHHHHHhHHHHHHHHH
Confidence 333 3322223332 2353 112377777777665543223333 566665666666655542
Q ss_pred CCCce-------eEEEeccCcHHHHHHHHHHH
Q 038397 461 YKGAE-------FEVIEAPLEAEMTDMYKKAA 485 (1102)
Q Consensus 461 f~gve-------f~i~e~~l~~~~~~~Yd~~a 485 (1102)
.+|| -+|+.+.|+..|+-+||...
T Consensus 841 -~dVEKQlpkKyEHvv~CrLSkRQR~LYDDfm 871 (1958)
T KOG0391|consen 841 -RDVEKQLPKKYEHVVKCRLSKRQRALYDDFM 871 (1958)
T ss_pred -HHHHHhcchhhhhheeeehhhhHHHHHHHHh
Confidence 1222 24567799999999999764
No 284
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=51.37 E-value=5.3 Score=52.58 Aligned_cols=46 Identities=28% Similarity=0.702 Sum_probs=36.7
Q ss_pred cccccccCcHHHH--hhhhhccccCCccccCCCC-CCcccCCCCCCccccch
Q 038397 660 FQICEICNSEEER--KKLLQCSCCGQLVHSGCLV-PPITDVIPSDWSCHSCK 708 (1102)
Q Consensus 660 f~~ce~cgsed~k--~kLL~cs~cgk~~H~~cL~-PP~~di~~~dW~c~sCk 708 (1102)
+..|.+|...+-. ..++.||.|+..+|+.|.. |+ ++.+.|.|-.|-
T Consensus 219 D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~---ipeg~WlCr~Cl 267 (1051)
T KOG0955|consen 219 DAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPF---IPEGQWLCRRCL 267 (1051)
T ss_pred CccceeecccccCCCceEEEcCCCcchhhhhccCCCC---CCCCcEeehhhc
Confidence 4568887766554 5688999999999999986 43 567899999986
No 285
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=51.34 E-value=9.3 Score=37.66 Aligned_cols=26 Identities=27% Similarity=0.561 Sum_probs=23.6
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLPQ 45 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~~ 45 (1102)
.|+.|.-...|..|+ .|.||.|+++-
T Consensus 5 ~cp~c~sEytYed~~-~~~cpec~~ew 30 (112)
T COG2824 5 PCPKCNSEYTYEDGG-QLICPECAHEW 30 (112)
T ss_pred CCCccCCceEEecCc-eEeCchhcccc
Confidence 499999999999999 99999999743
No 286
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=51.24 E-value=12 Score=39.02 Aligned_cols=33 Identities=12% Similarity=0.200 Sum_probs=27.2
Q ss_pred ccceeecCCcceEEEeCCCcceecCCCCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLTEFICGTCNLPQM 46 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~ 46 (1102)
+.-.+.|-+||..+.+..-..=-+||.||..+.
T Consensus 109 g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F 141 (146)
T PF07295_consen 109 GPGTLVCENCGHEVELTHPERLPPCPKCGHTEF 141 (146)
T ss_pred cCceEecccCCCEEEecCCCcCCCCCCCCCCee
Confidence 445678999999999988777779999997654
No 287
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=50.88 E-value=8.6 Score=38.71 Aligned_cols=28 Identities=21% Similarity=0.612 Sum_probs=19.9
Q ss_pred ceecCCCccceeecc-CCC----ccccCCCCCcc
Q 038397 95 IQLPCANCKAILNVP-HGL----VRFSCPQCAVE 123 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp-~~~----~~f~Cp~C~~~ 123 (1102)
.+..| .||...++. ..+ ..+.||.||..
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~ 101 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNK 101 (124)
T ss_pred eeEEe-eCcCcccccccchhccccCCcCcCCCCC
Confidence 46899 999887665 222 23689999954
No 288
>KOG0331 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=50.25 E-value=19 Score=44.34 Aligned_cols=53 Identities=21% Similarity=0.439 Sum_probs=45.1
Q ss_pred hhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCC
Q 038397 807 LFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQA 867 (1102)
Q Consensus 807 ~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQv 867 (1102)
.|-+|+-.|+|-++=|+=|+-.-- =++=|-..+|-+.+.=|++.|||+|+||.
T Consensus 386 ~FreG~~~vLVATdVAaRGLDi~d--------V~lVInydfP~~vEdYVHRiGRTGRa~~~ 438 (519)
T KOG0331|consen 386 GFREGKSPVLVATDVAARGLDVPD--------VDLVINYDFPNNVEDYVHRIGRTGRAGKK 438 (519)
T ss_pred hcccCCcceEEEcccccccCCCcc--------ccEEEeCCCCCCHHHHHhhcCccccCCCC
Confidence 599999999999999999886532 23557789999999999999999997765
No 289
>PRK10865 protein disaggregation chaperone; Provisional
Probab=50.19 E-value=38 Score=44.39 Aligned_cols=88 Identities=20% Similarity=0.237 Sum_probs=51.9
Q ss_pred eEEeehhhhhhcc-ccc--cchHHHHHHHhcc-CCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEE
Q 038397 322 VVFLTYSSLIASS-EKG--RSRLQQLVQWCGS-GYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYC 397 (1102)
Q Consensus 322 vlF~TYs~L~~~~-~~~--~sRl~Ql~~W~g~-dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~ 397 (1102)
+++...+.|.... .+| ..||+++++.+.. .-..+|++||.|...+.-.+.| + ..+..-|...|-+..+...
T Consensus 237 ~~~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~---~--~d~~~~lkp~l~~g~l~~I 311 (857)
T PRK10865 237 VLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADG---A--MDAGNMLKPALARGELHCV 311 (857)
T ss_pred EEEEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCcc---c--hhHHHHhcchhhcCCCeEE
Confidence 4555555554322 122 3589999988743 3345999999999865432111 1 1122334566667777777
Q ss_pred ecCCCCCC-----Cccchhhhc
Q 038397 398 SATGASEP-----RNMGYMVRL 414 (1102)
Q Consensus 398 SATgasep-----~Nl~ym~RL 414 (1102)
-||--.+- .+.+...|+
T Consensus 312 gaTt~~e~r~~~~~d~al~rRf 333 (857)
T PRK10865 312 GATTLDEYRQYIEKDAALERRF 333 (857)
T ss_pred EcCCCHHHHHHhhhcHHHHhhC
Confidence 77766553 456666665
No 290
>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]
Probab=49.97 E-value=13 Score=45.50 Aligned_cols=54 Identities=17% Similarity=0.323 Sum_probs=44.9
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQA 867 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQv 867 (1102)
+.|-.|.++|+|-+|+|+-||-..-=.- -|-...+=|++--++++|||+|.+|.
T Consensus 561 ~~fr~~t~dIlVaTDvAgRGIDIpnVSl--------VinydmaksieDYtHRIGRTgRAGk~ 614 (673)
T KOG0333|consen 561 ADFREGTGDILVATDVAGRGIDIPNVSL--------VINYDMAKSIEDYTHRIGRTGRAGKS 614 (673)
T ss_pred HHHHhcCCCEEEEecccccCCCCCccce--------eeecchhhhHHHHHHHhccccccccC
Confidence 6899999999999999999996542211 24456788999999999999999995
No 291
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=49.84 E-value=11 Score=33.46 Aligned_cols=29 Identities=17% Similarity=0.374 Sum_probs=24.9
Q ss_pred ceeecCCcceEEEeCCCcceecCCCCCCC
Q 038397 16 VQVRCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
-...|+.||....-...-..|.||.||..
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 34569999999988888899999999974
No 292
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=49.82 E-value=15 Score=36.37 Aligned_cols=37 Identities=22% Similarity=0.486 Sum_probs=25.4
Q ss_pred ecCCCccceee-ccCCCccccCCCCCcccccc-cccccccC
Q 038397 97 LPCANCKAILN-VPHGLVRFSCPQCAVELAVD-MSKVKQFF 135 (1102)
Q Consensus 97 ~~C~~C~A~~~-vp~~~~~f~Cp~C~~~L~v~-~~~~~~~~ 135 (1102)
--|.+||+.+- +.. ..-.||+||....++ ..+.+...
T Consensus 10 R~Cp~CG~kFYDLnk--~PivCP~CG~~~~~~~~~k~r~~~ 48 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNK--DPIVCPKCGTEFPPEPPLKSRRPR 48 (108)
T ss_pred ccCCCCcchhccCCC--CCccCCCCCCccCccccccccccc
Confidence 67999999763 222 234799999998887 44444444
No 293
>PRK00254 ski2-like helicase; Provisional
Probab=49.67 E-value=18 Score=46.24 Aligned_cols=59 Identities=25% Similarity=0.217 Sum_probs=41.9
Q ss_pred hhhcCCcceEEEEeccccccccccccccccc-ccceeEEEecCCC-cHhHHHHhhcccccCCC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAAN-QKRRVHITLELPW-SADRAIQQFGRTHRSNQ 866 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~N-QRRRvHitLElpW-sADkAIQqfGRTHRSNQ 866 (1102)
+.|.+|...|.|-+.+.+.|+.+-|.+-+-. .++.-. .-.|+ +...-+|+.||++|.+.
T Consensus 315 ~~F~~G~i~VLvaT~tLa~Gvnipa~~vVI~~~~~~~~--~~~~~~~~~~~~Qm~GRAGR~~~ 375 (720)
T PRK00254 315 DAFREGLIKVITATPTLSAGINLPAFRVIIRDTKRYSN--FGWEDIPVLEIQQMMGRAGRPKY 375 (720)
T ss_pred HHHHCCCCeEEEeCcHHhhhcCCCceEEEECCceEcCC--CCceeCCHHHHHHhhhccCCCCc
Confidence 6899999999999999999999987655432 111100 11111 35567999999999754
No 294
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=49.52 E-value=4 Score=35.55 Aligned_cols=31 Identities=29% Similarity=0.627 Sum_probs=25.0
Q ss_pred eeecCCcceEEEeCCC--cceecCCCCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPG--LTEFICGTCNLPQML 47 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg--~~~~~Cp~C~~~~~l 47 (1102)
.+||+.|+..|.=+-| --+.+||.|-.-+.+
T Consensus 4 tiRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 4 TIRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred eeehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 5899999999955444 468899999987776
No 295
>PRK12496 hypothetical protein; Provisional
Probab=49.44 E-value=9.7 Score=40.13 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=20.9
Q ss_pred ecCCCccceeeccCCCccccCCCCCccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
..|.+||...+. ++..--||.||.+|--
T Consensus 128 ~~C~gC~~~~~~--~~~~~~C~~CG~~~~r 155 (164)
T PRK12496 128 KVCKGCKKKYPE--DYPDDVCEICGSPVKR 155 (164)
T ss_pred EECCCCCccccC--CCCCCcCCCCCChhhh
Confidence 569999977654 3345589999999743
No 296
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=49.04 E-value=8.5 Score=33.03 Aligned_cols=25 Identities=24% Similarity=0.606 Sum_probs=19.9
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
-|+.||.. -..+....|.|..||+.
T Consensus 22 fCP~Cg~~-~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 22 FCPRCGSG-FMAEHLDRWHCGKCGYT 46 (50)
T ss_pred cCcCCCcc-hheccCCcEECCCcCCE
Confidence 49999997 44444589999999975
No 297
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=48.33 E-value=8.1 Score=30.72 Aligned_cols=25 Identities=32% Similarity=0.808 Sum_probs=13.3
Q ss_pred cCCCccceeec--c--CCCccccCCCCCc
Q 038397 98 PCANCKAILNV--P--HGLVRFSCPQCAV 122 (1102)
Q Consensus 98 ~C~~C~A~~~v--p--~~~~~f~Cp~C~~ 122 (1102)
-|..||..|.. | .+..|+-||-||.
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCC
Confidence 38888887654 6 5555788999884
No 298
>COG4889 Predicted helicase [General function prediction only]
Probab=48.21 E-value=1.1e+02 Score=40.41 Aligned_cols=135 Identities=23% Similarity=0.230 Sum_probs=75.8
Q ss_pred cccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCC
Q 038397 217 LSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGAT 296 (1102)
Q Consensus 217 LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~ 296 (1102)
+-.-|-+||.-|..-+. +..|--.+.+=|| ||+-+. -=|-|...+ .|.+++--|-.|+.--.|.|..--..
T Consensus 162 ~R~hQq~Aid~a~~~F~----~n~RGkLIMAcGT--GKTfTs-LkisEala~--~~iL~LvPSIsLLsQTlrew~~~~~l 232 (1518)
T COG4889 162 PRPHQQTAIDAAKEGFS----DNDRGKLIMACGT--GKTFTS-LKISEALAA--ARILFLVPSISLLSQTLREWTAQKEL 232 (1518)
T ss_pred CChhHHHHHHHHHhhcc----cccCCcEEEecCC--CccchH-HHHHHHHhh--hheEeecchHHHHHHHHHHHhhccCc
Confidence 33678888655544332 2233334445444 576654 235666665 67999999999999999999765444
Q ss_pred ccccc---ccCCC------------CCCcC-CCCcc---------ccccceEEeehhhhhhccccccchHHHHHHHhc-c
Q 038397 297 CIEVH---ALNKL------------PYSKL-DSRSV---------GIREGVVFLTYSSLIASSEKGRSRLQQLVQWCG-S 350 (1102)
Q Consensus 297 ~i~v~---~l~~~------------~~~~~-~~~~~---------~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g-~ 350 (1102)
.+... .=.|. ++..- +++.| ..+--|||+||-+|-.-.+ -+=.| +
T Consensus 233 ~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFsTYQSl~~i~e---------AQe~G~~ 303 (1518)
T COG4889 233 DFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFSTYQSLPRIKE---------AQEAGLD 303 (1518)
T ss_pred cceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEEcccchHHHHH---------HHHcCCC
Confidence 33211 11111 11100 00111 1122399999988853211 01123 2
Q ss_pred CCCceEEeecchhccccCCC
Q 038397 351 GYDGLVIFDECHKAKNLVPE 370 (1102)
Q Consensus 351 dfdgvivfDEcH~akn~~~~ 370 (1102)
.|| +||.||+|+.-++...
T Consensus 304 ~fD-liicDEAHRTtGa~~a 322 (1518)
T COG4889 304 EFD-LIICDEAHRTTGATLA 322 (1518)
T ss_pred Ccc-EEEecchhccccceec
Confidence 465 8999999998877543
No 299
>PRK14873 primosome assembly protein PriA; Provisional
Probab=47.95 E-value=46 Score=42.53 Aligned_cols=128 Identities=19% Similarity=0.087 Sum_probs=84.3
Q ss_pred CCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCC-Ccccc-cccCCCCCCcCCCCc-ccccc---ceEE
Q 038397 251 GVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGA-TCIEV-HALNKLPYSKLDSRS-VGIRE---GVVF 324 (1102)
Q Consensus 251 GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~-~~i~v-~~l~~~~~~~~~~~~-~~~~~---GvlF 324 (1102)
|-||+...+-+|-+...+||. ++-+=-.-.|-....+.++..-. ..+.+ |+ ++.-++- -.. ..+.+ .||-
T Consensus 170 GSGKTevyl~~i~~~l~~Gk~-vLvLvPEi~lt~q~~~rl~~~f~~~~v~~lhS--~l~~~~R-~~~w~~~~~G~~~IVi 245 (665)
T PRK14873 170 GEDWARRLAAAAAATLRAGRG-ALVVVPDQRDVDRLEAALRALLGAGDVAVLSA--GLGPADR-YRRWLAVLRGQARVVV 245 (665)
T ss_pred CCcHHHHHHHHHHHHHHcCCe-EEEEecchhhHHHHHHHHHHHcCCCcEEEECC--CCCHHHH-HHHHHHHhCCCCcEEE
Confidence 679999999999999999998 77777777788888888876654 44433 21 1110000 000 01223 3888
Q ss_pred eehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCC
Q 038397 325 LTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 325 ~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATg 401 (1102)
.|.|.+-..- .. =|+||.||=|...-. ....|---++-|..+..+.-++.||+.|||-
T Consensus 246 GtRSAvFaP~----~~------------LgLIIvdEEhd~syk---q~~~p~yhaRdvA~~Ra~~~~~~lvLgSaTP 303 (665)
T PRK14873 246 GTRSAVFAPV----ED------------LGLVAIWDDGDDLLA---EPRAPYPHAREVALLRAHQHGCALLIGGHAR 303 (665)
T ss_pred EcceeEEecc----CC------------CCEEEEEcCCchhhc---CCCCCCccHHHHHHHHHHHcCCcEEEECCCC
Confidence 8888875431 11 289999999976533 2334444667677777778899999999993
No 300
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=47.47 E-value=10 Score=40.60 Aligned_cols=29 Identities=38% Similarity=0.795 Sum_probs=24.5
Q ss_pred cceecCCCccceeeccCCCccccCCCCCccccc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
+-+..|-+|+.+++-|++ -||.||.++..
T Consensus 137 ~w~~rC~GC~~~f~~~~~----~Cp~CG~~~~~ 165 (177)
T COG1439 137 KWRLRCHGCKRIFPEPKD----FCPICGSPLKR 165 (177)
T ss_pred eeeEEEecCceecCCCCC----cCCCCCCceEE
Confidence 457899999999996655 89999999765
No 301
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=47.08 E-value=15 Score=29.00 Aligned_cols=27 Identities=22% Similarity=0.401 Sum_probs=18.8
Q ss_pred eeecCCcceEEEeCCCcceecCCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLTEFICGTCNLPQ 45 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~ 45 (1102)
.-+|..||-+..... .--.||.||.+.
T Consensus 2 ~~~C~~CG~i~~g~~--~p~~CP~Cg~~~ 28 (34)
T cd00729 2 VWVCPVCGYIHEGEE--APEKCPICGAPK 28 (34)
T ss_pred eEECCCCCCEeECCc--CCCcCcCCCCch
Confidence 357999998876431 223999999743
No 302
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=47.04 E-value=36 Score=43.24 Aligned_cols=62 Identities=16% Similarity=0.088 Sum_probs=45.8
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEecC-----CCcHhHHHHhhcccccCCCCCCCeEEEeecC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLEL-----PWSADRAIQQFGRTHRSNQASAPEYRIIFTN 878 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLEl-----pWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~ 878 (1102)
+.|.+|+..|.|-++..+-|+.+..-. +-|..+. |-+...-||+.|||+|.+ .-..+++++.
T Consensus 490 ~~f~~g~i~vlV~t~~L~rGfdlp~v~--------lVii~d~eifG~~~~~~~yiqr~GR~gR~~---~G~~i~~~~~ 556 (652)
T PRK05298 490 RDLRLGEFDVLVGINLLREGLDIPEVS--------LVAILDADKEGFLRSERSLIQTIGRAARNV---NGKVILYADK 556 (652)
T ss_pred HHHHcCCceEEEEeCHHhCCccccCCc--------EEEEeCCcccccCCCHHHHHHHhccccCCC---CCEEEEEecC
Confidence 579999999998899999999877543 3344443 678889999999999952 2344444443
No 303
>PLN03086 PRLI-interacting factor K; Provisional
Probab=46.98 E-value=11 Score=46.70 Aligned_cols=11 Identities=18% Similarity=0.522 Sum_probs=6.5
Q ss_pred cccCCCCCccc
Q 038397 114 RFSCPQCAVEL 124 (1102)
Q Consensus 114 ~f~Cp~C~~~L 124 (1102)
.+.|+||+...
T Consensus 504 pi~C~fC~~~v 514 (567)
T PLN03086 504 LITCRFCGDMV 514 (567)
T ss_pred ceeCCCCCCcc
Confidence 45666666554
No 304
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=46.81 E-value=11 Score=38.75 Aligned_cols=27 Identities=26% Similarity=0.721 Sum_probs=23.5
Q ss_pred cceecCCCccceeeccCCCccccCCCCCccc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVEL 124 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L 124 (1102)
.+-..|.+||.+..-|+. -||.|+.+-
T Consensus 27 l~g~kC~~CG~v~~PPr~----~Cp~C~~~~ 53 (140)
T COG1545 27 LLGTKCKKCGRVYFPPRA----YCPKCGSET 53 (140)
T ss_pred EEEEEcCCCCeEEcCCcc----cCCCCCCCC
Confidence 456799999999998877 899999994
No 305
>smart00382 AAA ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Probab=46.67 E-value=31 Score=32.11 Aligned_cols=38 Identities=24% Similarity=0.300 Sum_probs=23.3
Q ss_pred eEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchh
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLK 283 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~ 283 (1102)
+|+|. +|+||+-.+..++..-...+ ...++++.+....
T Consensus 6 ~l~G~-~G~GKTtl~~~l~~~~~~~~-~~~~~~~~~~~~~ 43 (148)
T smart00382 6 LIVGP-PGSGKTTLARALARELGPPG-GGVIYIDGEDILE 43 (148)
T ss_pred EEECC-CCCcHHHHHHHHHhccCCCC-CCEEEECCEEccc
Confidence 34455 99999988866655544443 3466666554433
No 306
>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.
Probab=46.63 E-value=1e+02 Score=32.46 Aligned_cols=29 Identities=31% Similarity=0.430 Sum_probs=24.0
Q ss_pred cCCCCCcchhhHHHHHHHHhccCceEEEEE
Q 038397 248 DGAGVGKGRTIAGLIWENWHHGRRKALWIS 277 (1102)
Q Consensus 248 Dg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s 277 (1102)
-|.|.||+-.+.|+.+..+-+|++ ++++-
T Consensus 9 ~g~G~Gkt~~a~g~~~ra~~~g~~-v~~vQ 37 (159)
T cd00561 9 TGNGKGKTTAALGLALRALGHGYR-VGVVQ 37 (159)
T ss_pred CCCCCCHHHHHHHHHHHHHHCCCe-EEEEE
Confidence 456888999999999999999986 76643
No 307
>PF12773 DZR: Double zinc ribbon
Probab=46.47 E-value=8.7 Score=32.07 Aligned_cols=27 Identities=26% Similarity=0.554 Sum_probs=21.7
Q ss_pred eeecCCcceEEEeCCCcceecCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
...|.+||..|. .+......||.||..
T Consensus 12 ~~fC~~CG~~l~-~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLP-PPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChh-hccCCCCCCcCCcCC
Confidence 456999999998 556667889999973
No 308
>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]
Probab=46.35 E-value=22 Score=43.53 Aligned_cols=125 Identities=22% Similarity=0.268 Sum_probs=72.8
Q ss_pred cccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEE
Q 038397 316 VGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVV 395 (1102)
Q Consensus 316 ~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvv 395 (1102)
....-||+-+|||-+--. .+..---+++.+|+..-==|+||+||.|- -|.++=+-|+-+-...-+ +
T Consensus 387 ~~~~~gvvvsTYsMva~t-~kRS~eaek~m~~l~~~EWGllllDEVHv----------vPA~MFRRVlsiv~aHcK---L 452 (776)
T KOG1123|consen 387 FPSGAGVVVTTYSMVAYT-GKRSHEAEKIMDFLRGREWGLLLLDEVHV----------VPAKMFRRVLSIVQAHCK---L 452 (776)
T ss_pred CCCCCcEEEEeeehhhhc-ccccHHHHHHHHHHhcCeeeeEEeehhcc----------chHHHHHHHHHHHHHHhh---c
Confidence 346779999999987532 22223357789999865569999999996 346666667655443111 1
Q ss_pred EEecCCCCCCCccchhhhccccCCCCCCCCHHHHHHHHhccChhHHHHHHHHHHhccceeeeccCCCCceeEEEeccCcH
Q 038397 396 YCSATGASEPRNMGYMVRLGLWGAGTCFKDFQIFLGALDKGGVGALELVAMDMKARGMYVCRTLSYKGAEFEVIEAPLEA 475 (1102)
Q Consensus 396 Y~SATgasep~Nl~ym~RLGLWg~gt~f~~~~~f~~a~~~gGv~amE~va~dlK~~G~yiaR~LSf~gvef~i~e~~l~~ 475 (1102)
=-.||=..|-.-.. --+|+= |--.-|.==|||.+.| |||+ |.---+-++||+
T Consensus 453 GLTATLvREDdKI~----------------DLNFLI-----GPKlYEAnWmdL~~kG-hIA~------VqCaEVWCpMt~ 504 (776)
T KOG1123|consen 453 GLTATLVREDDKIT----------------DLNFLI-----GPKLYEANWMDLQKKG-HIAK------VQCAEVWCPMTP 504 (776)
T ss_pred cceeEEeecccccc----------------ccceee-----cchhhhccHHHHHhCC-ceeE------EeeeeeecCCCH
Confidence 11344333322211 112221 3444555566766665 5654 344445569999
Q ss_pred HHHHHHH
Q 038397 476 EMTDMYK 482 (1102)
Q Consensus 476 ~~~~~Yd 482 (1102)
+|-+-|=
T Consensus 505 eFy~eYL 511 (776)
T KOG1123|consen 505 EFYREYL 511 (776)
T ss_pred HHHHHHH
Confidence 8865553
No 309
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=46.35 E-value=95 Score=37.76 Aligned_cols=72 Identities=13% Similarity=0.201 Sum_probs=41.7
Q ss_pred eEEeecchhccccCCCCCCCchhHHHHHHHHhhhC--CCccEEEEecCCCCCCCccc--hhhhccccCCCCCC--CCHHH
Q 038397 355 LVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARL--PEARVVYCSATGASEPRNMG--YMVRLGLWGAGTCF--KDFQI 428 (1102)
Q Consensus 355 vivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~l--P~ARvvY~SATgasep~Nl~--ym~RLGLWg~gt~f--~~~~~ 428 (1102)
|+++||.|...+- ..++.. ...+=+.+ .+..||.+|-+..++..+|. .-+|+. ||--..+ +++++
T Consensus 205 vLiIDDiq~l~~k------~~~qee--lf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~-~Gl~~~l~~pd~e~ 275 (445)
T PRK12422 205 ALFIEDIEVFSGK------GATQEE--FFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFE-WGIAIPLHPLTKEG 275 (445)
T ss_pred EEEEcchhhhcCC------hhhHHH--HHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhc-CCeEEecCCCCHHH
Confidence 8999999986532 123332 22232222 35678888877666666663 567773 6654444 46666
Q ss_pred HHHHHhc
Q 038397 429 FLGALDK 435 (1102)
Q Consensus 429 f~~a~~~ 435 (1102)
...-+++
T Consensus 276 r~~iL~~ 282 (445)
T PRK12422 276 LRSFLER 282 (445)
T ss_pred HHHHHHH
Confidence 5554443
No 310
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=46.32 E-value=14 Score=28.76 Aligned_cols=25 Identities=24% Similarity=0.650 Sum_probs=19.4
Q ss_pred eecCCcceEEEeCCCcceecCCCCCCC
Q 038397 18 VRCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
-+|..||-+. .+......||.||..
T Consensus 2 ~~C~~CGy~y--~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 YVCPVCGYIY--DGEEAPWVCPVCGAP 26 (33)
T ss_pred EECCCCCCEE--CCCcCCCcCcCCCCc
Confidence 3699999654 456688999999963
No 311
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=45.72 E-value=6.8 Score=49.62 Aligned_cols=49 Identities=35% Similarity=0.786 Sum_probs=40.4
Q ss_pred ccccccccccCcHHHHhhhhhccccCCccccCCCCCCcccCCCCCCccccch
Q 038397 657 DDEFQICEICNSEEERKKLLQCSCCGQLVHSGCLVPPITDVIPSDWSCHSCK 708 (1102)
Q Consensus 657 DDEf~~ce~cgsed~k~kLL~cs~cgk~~H~~cL~PP~~di~~~dW~c~sCk 708 (1102)
+.+...|.+|... ..++.|+.|..-+|..|+.+|....+.++|.|+.|.
T Consensus 44 ~~~~e~c~ic~~~---g~~l~c~tC~~s~h~~cl~~pl~~~p~~~~~c~Rc~ 92 (696)
T KOG0383|consen 44 DAEQEACRICADG---GELLWCDTCPASFHASCLGPPLTPQPNGEFICPRCF 92 (696)
T ss_pred hhhhhhhhhhcCC---CcEEEeccccHHHHHHccCCCCCcCCccceeeeeec
Confidence 3345678887654 347779999999999999999999999899999884
No 312
>TIGR00963 secA preprotein translocase, SecA subunit. The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus.
Probab=45.28 E-value=11 Score=48.26 Aligned_cols=125 Identities=18% Similarity=0.179 Sum_probs=0.0
Q ss_pred CCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhC--CCcccccccCCCCCCcCCCCccccccceEEeeh
Q 038397 250 AGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVG--ATCIEVHALNKLPYSKLDSRSVGIREGVVFLTY 327 (1102)
Q Consensus 250 ~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG--~~~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TY 327 (1102)
||-||+-..+=-++-|.+.|+. +.-++++. |=|.||...++ ...+.+...--..-.....+.....-.|++.|-
T Consensus 78 TGeGKTLva~lpa~l~aL~G~~-V~VvTpt~---~LA~qdae~~~~l~~~LGLsv~~i~g~~~~~~r~~~y~~dIvyGT~ 153 (745)
T TIGR00963 78 TGEGKTLTATLPAYLNALTGKG-VHVVTVND---YLAQRDAEWMGQVYRFLGLSVGLILSGMSPEERREAYACDITYGTN 153 (745)
T ss_pred CCCccHHHHHHHHHHHHHhCCC-EEEEcCCH---HHHHHHHHHHHHHhccCCCeEEEEeCCCCHHHHHHhcCCCEEEECC
Q ss_pred hhh----------hhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEE
Q 038397 328 SSL----------IASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYC 397 (1102)
Q Consensus 328 s~L----------~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~ 397 (1102)
+.| ..........+ +++|+||+|++. --.++.-+.+.-.-+..-.+|.
T Consensus 154 ~rlgfDyLrd~~~~~~~~~~~r~l------------~~aIIDEaDs~L----------IDeaRtpLiisg~~~~~~~ly~ 211 (745)
T TIGR00963 154 NELGFDYLRDNMAHSKEEKVQRPF------------HFAIIDEVDSIL----------IDEARTPLIISGPAEKSTELYL 211 (745)
T ss_pred CchhhHHHhcccccchhhhhcccc------------ceeEeecHHHHh----------HHhhhhHHhhcCCCCCchHHHH
Q ss_pred ecC
Q 038397 398 SAT 400 (1102)
Q Consensus 398 SAT 400 (1102)
+||
T Consensus 212 ~a~ 214 (745)
T TIGR00963 212 QAN 214 (745)
T ss_pred HHH
No 313
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=45.17 E-value=45 Score=31.82 Aligned_cols=32 Identities=9% Similarity=0.126 Sum_probs=26.1
Q ss_pred ccchHHHHHHHhccCC-CceEEeecchhccccC
Q 038397 337 GRSRLQQLVQWCGSGY-DGLVIFDECHKAKNLV 368 (1102)
Q Consensus 337 ~~sRl~Ql~~W~g~df-dgvivfDEcH~akn~~ 368 (1102)
...++.++++.+...- ..||+|||+|+.....
T Consensus 42 ~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~ 74 (132)
T PF00004_consen 42 SEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKS 74 (132)
T ss_dssp HHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHC
T ss_pred cccccccccccccccccceeeeeccchhccccc
Confidence 3568888888887655 6899999999988776
No 314
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=45.02 E-value=11 Score=42.30 Aligned_cols=25 Identities=16% Similarity=0.351 Sum_probs=23.3
Q ss_pred ecCCcceEEEeCCCcceecCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
-|+.||..+....+-....|+.||.
T Consensus 101 fC~~CG~~~~~~~~~~~~~C~~c~~ 125 (256)
T PRK00241 101 FCGYCGHPMHPSKTEWAMLCPHCRE 125 (256)
T ss_pred cccccCCCCeecCCceeEECCCCCC
Confidence 3999999999999999999999995
No 315
>PF05729 NACHT: NACHT domain
Probab=44.56 E-value=91 Score=30.84 Aligned_cols=54 Identities=15% Similarity=0.140 Sum_probs=28.5
Q ss_pred HhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhh--CCCccEEEEecCCC
Q 038397 347 WCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQAR--LPEARVVYCSATGA 402 (1102)
Q Consensus 347 W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~--lP~ARvvY~SATga 402 (1102)
++.....-+||+|=...........+ ....-.....|-.. +|+.+++.+|-+..
T Consensus 76 ~~~~~~~~llilDglDE~~~~~~~~~--~~~~~~~l~~l~~~~~~~~~~liit~r~~~ 131 (166)
T PF05729_consen 76 LLEKNKRVLLILDGLDELEEQDQSQE--RQRLLDLLSQLLPQALPPGVKLIITSRPRA 131 (166)
T ss_pred HHHcCCceEEEEechHhcccchhhhH--HHHHHHHHHHHhhhccCCCCeEEEEEcCCh
Confidence 33344556788876665553321100 11222233344444 88999999986643
No 316
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=44.41 E-value=16 Score=37.99 Aligned_cols=30 Identities=27% Similarity=0.538 Sum_probs=24.3
Q ss_pred cceecCCCccceeeccCCCccccCCCCCcc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
...+.|.+||..+.+.+.-.=-+||.||-.
T Consensus 110 ~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred CceEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 446999999999999985433499999964
No 317
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=44.39 E-value=15 Score=29.07 Aligned_cols=29 Identities=17% Similarity=0.186 Sum_probs=24.7
Q ss_pred eeecCCcceEEEeCCCcceecCCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLTEFICGTCNLPQ 45 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~ 45 (1102)
..+|.+|+..+.+..--....|+.||...
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 35799999999998888899999999643
No 318
>PF14353 CpXC: CpXC protein
Probab=44.17 E-value=13 Score=37.14 Aligned_cols=32 Identities=22% Similarity=0.773 Sum_probs=23.3
Q ss_pred eecCCCccceeeccC-------------------CCccccCCCCCcccccc
Q 038397 96 QLPCANCKAILNVPH-------------------GLVRFSCPQCAVELAVD 127 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~-------------------~~~~f~Cp~C~~~L~v~ 127 (1102)
++.|.+||....+.. .+-.|.||.||....++
T Consensus 1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 368999998766532 23478999999986664
No 319
>TIGR03714 secA2 accessory Sec system translocase SecA2. Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii.
Probab=43.75 E-value=35 Score=44.07 Aligned_cols=105 Identities=20% Similarity=0.185 Sum_probs=0.0
Q ss_pred CCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhh----hhhCCCcccccccCCCCCCcCCCCccccccceEEe
Q 038397 250 AGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDL----DDVGATCIEVHALNKLPYSKLDSRSVGIREGVVFL 325 (1102)
Q Consensus 250 ~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl----~diG~~~i~v~~l~~~~~~~~~~~~~~~~~GvlF~ 325 (1102)
||-||+-..+--++.|.+.|+. ++-++++..|-..-...+ +-+|-+...++.-+....-.-..+.....-.|+++
T Consensus 92 TGeGKTLta~Lpa~l~aL~g~~-V~VVTpn~yLA~Rdae~m~~l~~~LGLsv~~~~~~s~~~~~~~~~rr~~y~~dIvyg 170 (762)
T TIGR03714 92 TGEGKTLTATMPLYLNALTGKG-AMLVTTNDYLAKRDAEEMGPVYEWLGLTVSLGVVDDPDEEYDANEKRKIYNSDIVYT 170 (762)
T ss_pred CCcchHHHHHHHHHHHhhcCCc-eEEeCCCHHHHHHHHHHHHHHHhhcCCcEEEEECCCCccccCHHHHHHhCCCCEEEE
Q ss_pred ehhhhhhccccccchHHHHHHHhccCCCce-------EEeecchhc
Q 038397 326 TYSSLIASSEKGRSRLQQLVQWCGSGYDGL-------VIFDECHKA 364 (1102)
Q Consensus 326 TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgv-------ivfDEcH~a 364 (1102)
|-+.|- ++-|.+=+..+.+.. +|+||+|.+
T Consensus 171 Tp~~Lg---------fDyLrD~l~~~~~~~~~r~l~~~IVDEaDsI 207 (762)
T TIGR03714 171 TNSALG---------FDYLIDNLASNKEGKFLRPFNYVIVDEVDSV 207 (762)
T ss_pred Cchhhh---------hhHHHHHhhcchhhcccccCcEEEEecHhhH
No 320
>KOG0925 consensus mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification]
Probab=43.70 E-value=17 Score=44.34 Aligned_cols=42 Identities=29% Similarity=0.347 Sum_probs=29.4
Q ss_pred CceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCC
Q 038397 353 DGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 353 dgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATg 401 (1102)
=||||+||+|.---+ .-.-+|.---.+.++ |+-+||-+|||-
T Consensus 160 y~viiLDeahERtlA------TDiLmGllk~v~~~r-pdLk~vvmSatl 201 (699)
T KOG0925|consen 160 YGVIILDEAHERTLA------TDILMGLLKEVVRNR-PDLKLVVMSATL 201 (699)
T ss_pred ccEEEechhhhhhHH------HHHHHHHHHHHHhhC-CCceEEEeeccc
Confidence 389999999985432 123455544444455 999999999993
No 321
>PRK08533 flagellar accessory protein FlaH; Reviewed
Probab=43.65 E-value=90 Score=34.34 Aligned_cols=57 Identities=16% Similarity=0.238 Sum_probs=40.1
Q ss_pred CCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCC
Q 038397 236 LPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGAT 296 (1102)
Q Consensus 236 l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~ 296 (1102)
+|.|+ .-.++|+ .|+||+-...-+++....+|. +.++++... -..|..|.+..+|.+
T Consensus 21 i~~g~-~~~i~G~-~G~GKTtl~~~~~~~~~~~g~-~~~yi~~e~-~~~~~~~~~~~~g~~ 77 (230)
T PRK08533 21 IPAGS-LILIEGD-ESTGKSILSQRLAYGFLQNGY-SVSYVSTQL-TTTEFIKQMMSLGYD 77 (230)
T ss_pred CCCCc-EEEEECC-CCCCHHHHHHHHHHHHHhCCC-cEEEEeCCC-CHHHHHHHHHHhCCc
Confidence 45454 3344455 999999887777777666774 589999444 457888888888864
No 322
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=43.16 E-value=33 Score=39.08 Aligned_cols=68 Identities=16% Similarity=0.392 Sum_probs=41.4
Q ss_pred EEEeCCCcceecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccCCCCCCCCCCccceecCCCccce
Q 038397 26 ILTVGPGLTEFICGTCNLPQMLPPELMPASTGGSVPNNTTSSNTTNSTRPTHMKAASSHVPALGIDPTKIQLPCANCKAI 105 (1102)
Q Consensus 26 ~l~~~pg~~~~~Cp~C~~~~~l~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~t~~~~~C~~C~A~ 105 (1102)
...-+-.-..+.|+.||..-.....| ...-|.+-++ | ++....|..|+..
T Consensus 121 ~~~~~~~~~r~~c~eCgk~ysT~snL--------------------------srHkQ~H~~~---~-s~ka~~C~~C~K~ 170 (279)
T KOG2462|consen 121 ATASAAKHPRYKCPECGKSYSTSSNL--------------------------SRHKQTHRSL---D-SKKAFSCKYCGKV 170 (279)
T ss_pred cccccccCCceecccccccccccccc--------------------------chhhcccccc---c-ccccccCCCCCce
Confidence 33336677899999999765554444 1111222111 1 1556899999976
Q ss_pred eec---------cCCCccccCCCCCccc
Q 038397 106 LNV---------PHGLVRFSCPQCAVEL 124 (1102)
Q Consensus 106 ~~v---------p~~~~~f~Cp~C~~~L 124 (1102)
..= .|+ -++.|++||...
T Consensus 171 YvSmpALkMHirTH~-l~c~C~iCGKaF 197 (279)
T KOG2462|consen 171 YVSMPALKMHIRTHT-LPCECGICGKAF 197 (279)
T ss_pred eeehHHHhhHhhccC-CCcccccccccc
Confidence 532 233 378999999864
No 323
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.84 E-value=14 Score=36.49 Aligned_cols=10 Identities=40% Similarity=0.982 Sum_probs=4.7
Q ss_pred ceecCCCCCC
Q 038397 34 TEFICGTCNL 43 (1102)
Q Consensus 34 ~~~~Cp~C~~ 43 (1102)
|++.|+.|++
T Consensus 19 TeL~c~~~et 28 (122)
T COG3877 19 TELKCSNCET 28 (122)
T ss_pred EEEecCCCCc
Confidence 4444444444
No 324
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=42.65 E-value=21 Score=41.47 Aligned_cols=26 Identities=27% Similarity=0.571 Sum_probs=21.9
Q ss_pred ccceecCCCccceeeccCCCccccCCCCCc
Q 038397 93 TKIQLPCANCKAILNVPHGLVRFSCPQCAV 122 (1102)
Q Consensus 93 t~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~ 122 (1102)
..-.++|+-|+..=+++ |-.||+||.
T Consensus 209 G~RyL~CslC~teW~~~----R~~C~~Cg~ 234 (309)
T PRK03564 209 GLRYLHCNLCESEWHVV----RVKCSNCEQ 234 (309)
T ss_pred CceEEEcCCCCCccccc----CccCCCCCC
Confidence 34579999999988876 669999996
No 325
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=42.64 E-value=15 Score=35.97 Aligned_cols=30 Identities=13% Similarity=0.583 Sum_probs=21.9
Q ss_pred eecCCCccceeecc----CCCccccCCCCCccccc
Q 038397 96 QLPCANCKAILNVP----HGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp----~~~~~f~Cp~C~~~L~v 126 (1102)
.+.|.+||+ ..|+ .|.+.-.|+.||.----
T Consensus 21 ~f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 21 IFECPRCGK-VSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred EeECCCCCC-eEeeeecCCCcceEECCCCCCccCE
Confidence 489999995 4554 45556799999986433
No 326
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=42.59 E-value=66 Score=42.13 Aligned_cols=174 Identities=21% Similarity=0.223 Sum_probs=90.7
Q ss_pred CCCCCCCCCccCcccc----------cccccCCcccchhhHHHHHH-hhccccCCCCCcceeEeecCCCCCcchhhHHHH
Q 038397 194 SAVHPPEPTYDLLIKY----------DLESSKSLSCLQIETLVYAS-QRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLI 262 (1102)
Q Consensus 194 ~sv~pP~~~y~~~lp~----------~~~~~g~LS~~Qle~v~ya~-q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI 262 (1102)
+.+.++.+.|...+|+ .+-..+.|+-+|....+|-. +.| +--.+.|. +|+||..|+|-.|
T Consensus 344 a~~~~~s~~q~~~~~~~~~~d~e~~~~~a~re~lpva~~~~~i~q~v~dn--------~v~~I~ge-tgcgk~tq~aq~i 414 (1282)
T KOG0921|consen 344 AFMSMESISQRIMEKERFKRDEALDKITAQREELPVAQYRSEILQAVAEN--------RVVIIKGE-TGCGKSTQVAQFL 414 (1282)
T ss_pred ccccccCcccchhhhhhhhcccchhhhhhhhhhCcHHHHHHHHHHHHhcC--------ceeeEeec-ccccchhHHHHHH
Confidence 4566666776665553 34455678888888877744 444 33333444 9999999999999
Q ss_pred HHHHhccCceEEE-EEcCC-------chhhhHH-hhhhhhCCCcccccccCCCCCCcCCCCccccccc-eEEeehhhhhh
Q 038397 263 WENWHHGRRKALW-ISVGS-------DLKFDAR-RDLDDVGATCIEVHALNKLPYSKLDSRSVGIREG-VVFLTYSSLIA 332 (1102)
Q Consensus 263 ~~n~l~Gr~~~~w-~s~s~-------~L~~Da~-RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~G-vlF~TYs~L~~ 332 (1102)
+|.|++.-.-.++ ..++. -|.+|.. .|-..+|-. +-|..--.......+| ++|+|---|.+
T Consensus 415 Le~~~~ns~g~~~na~v~qprrisaisiaerva~er~e~~g~t---------vgy~vRf~Sa~prpyg~i~fctvgvllr 485 (1282)
T KOG0921|consen 415 LESFLENSNGASFNAVVSQPRRISAISLAERVANERGEEVGET---------CGYNVRFDSATPRPYGSIMFCTVGVLLR 485 (1282)
T ss_pred HHHHhhccccccccceeccccccchHHHHHHHHHhhHHhhccc---------ccccccccccccccccceeeeccchhhh
Confidence 9999764332111 11111 1222222 222222221 1111000012234555 77888666553
Q ss_pred ccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCCC
Q 038397 333 SSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGASE 404 (1102)
Q Consensus 333 ~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgase 404 (1102)
.-..+ |.- --.++.||.|.---. + --.=....++..-.|.-+|+..|||=-++
T Consensus 486 ~~e~g---lrg---------~sh~i~deiherdv~----~---dfll~~lr~m~~ty~dl~v~lmsatIdTd 538 (1282)
T KOG0921|consen 486 MMENG---LRG---------ISHVIIDEIHERDVD----T---DFVLIVLREMISTYRDLRVVLMSATIDTD 538 (1282)
T ss_pred hhhhc---ccc---------cccccchhhhhhccc----h---HHHHHHHHhhhccchhhhhhhhhcccchh
Confidence 32211 100 126788999874311 0 01111222344566788999999996554
No 327
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=42.49 E-value=11 Score=34.48 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=22.7
Q ss_pred eeecCCcceEEEeCCCcceecCCCCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l 47 (1102)
-.|| .||..|...-+..-=.| .||....|
T Consensus 3 ifrC-~Cgr~lya~e~~kTkkC-~CG~~l~v 31 (68)
T PF09082_consen 3 IFRC-DCGRYLYAKEGAKTKKC-VCGKTLKV 31 (68)
T ss_dssp EEEE-TTS--EEEETT-SEEEE-TTTEEEE-
T ss_pred EEEe-cCCCEEEecCCcceeEe-cCCCeeee
Confidence 4699 89999999999999999 99987766
No 328
>smart00488 DEXDc2 DEAD-like helicases superfamily.
Probab=42.42 E-value=20 Score=40.87 Aligned_cols=33 Identities=36% Similarity=0.543 Sum_probs=0.0
Q ss_pred eEEeehhhhhhccccccchHHHHHHHhccCCCc-eEEeecchh
Q 038397 322 VVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDG-LVIFDECHK 363 (1102)
Q Consensus 322 vlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdg-vivfDEcH~ 363 (1102)
||+++|+-|.... +.+-+|.+++. +|||||+|+
T Consensus 214 ivi~ny~yll~~~---------~r~~~~~~l~~~~lIiDEAHn 247 (289)
T smart00488 214 VVVLPYQYLLDPK---------IRQALSIELKDSIVIFDEAHN 247 (289)
T ss_pred EEEECHHHHhcHH---------HHHHhcccccccEEEEeCccC
No 329
>smart00489 DEXDc3 DEAD-like helicases superfamily.
Probab=42.42 E-value=20 Score=40.87 Aligned_cols=33 Identities=36% Similarity=0.543 Sum_probs=0.0
Q ss_pred eEEeehhhhhhccccccchHHHHHHHhccCCCc-eEEeecchh
Q 038397 322 VVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDG-LVIFDECHK 363 (1102)
Q Consensus 322 vlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdg-vivfDEcH~ 363 (1102)
||+++|+-|.... +.+-+|.+++. +|||||+|+
T Consensus 214 ivi~ny~yll~~~---------~r~~~~~~l~~~~lIiDEAHn 247 (289)
T smart00489 214 VVVLPYQYLLDPK---------IRQALSIELKDSIVIFDEAHN 247 (289)
T ss_pred EEEECHHHHhcHH---------HHHHhcccccccEEEEeCccC
No 330
>PRK07952 DNA replication protein DnaC; Validated
Probab=42.36 E-value=40 Score=37.76 Aligned_cols=37 Identities=30% Similarity=0.403 Sum_probs=30.3
Q ss_pred cceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEc
Q 038397 241 RAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISV 278 (1102)
Q Consensus 241 R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~ 278 (1102)
..||++--++|+||+..+++|..+-..+|+ +++++++
T Consensus 99 ~~~~~l~G~~GtGKThLa~aia~~l~~~g~-~v~~it~ 135 (244)
T PRK07952 99 IASFIFSGKPGTGKNHLAAAICNELLLRGK-SVLIITV 135 (244)
T ss_pred CceEEEECCCCCCHHHHHHHHHHHHHhcCC-eEEEEEH
Confidence 358888888999999999999988777775 4788865
No 331
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=42.22 E-value=18 Score=43.48 Aligned_cols=28 Identities=18% Similarity=0.376 Sum_probs=21.5
Q ss_pred eeecCCcceEEEeCCCcceecCCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLTEFICGTCNLPQ 45 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~ 45 (1102)
.-+|+-||..++=+=-. .|.|+.||+.-
T Consensus 350 ~p~Cp~Cg~~m~S~G~~-g~rC~kCg~~~ 377 (421)
T COG1571 350 NPVCPRCGGRMKSAGRN-GFRCKKCGTRA 377 (421)
T ss_pred CCCCCccCCchhhcCCC-CcccccccccC
Confidence 33699999999644333 99999999853
No 332
>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3. The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc.
Probab=42.15 E-value=45 Score=44.48 Aligned_cols=46 Identities=26% Similarity=0.229 Sum_probs=29.9
Q ss_pred HHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhh--hCCCccEEEEecC
Q 038397 344 LVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQA--RLPEARVVYCSAT 400 (1102)
Q Consensus 344 l~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~--~lP~ARvvY~SAT 400 (1102)
++-++|= ...+|||||.|..- ..+-.+++.|-+ ....++|+.+|||
T Consensus 586 ~l~ll~L-a~svlVlDEVHaYD----------~~~~~~L~rlL~w~~~lG~~VlLmSAT 633 (1110)
T TIGR02562 586 IAPMLRL-MSSDLILDEPDDYE----------PEDLPALLRLVQLAGLLGSRVLLSSAT 633 (1110)
T ss_pred HHHHHHh-cCCCEEEECCccCC----------HHHHHHHHHHHHHHHHcCCCEEEEeCC
Confidence 3344442 35699999999854 233334444444 4558999999999
No 333
>KOG3842 consensus Adaptor protein Pellino [Signal transduction mechanisms]
Probab=42.13 E-value=11 Score=43.27 Aligned_cols=32 Identities=38% Similarity=0.783 Sum_probs=28.1
Q ss_pred ceeeccCCCccc--cCCCCCcccccccccccccC
Q 038397 104 AILNVPHGLVRF--SCPQCAVELAVDMSKVKQFF 135 (1102)
Q Consensus 104 A~~~vp~~~~~f--~Cp~C~~~L~v~~~~~~~~~ 135 (1102)
+.+.+|||.-+| .||||+..|+-+...++.+|
T Consensus 391 s~iplPhGT~~f~a~CPFC~~~L~ge~~~ikliF 424 (429)
T KOG3842|consen 391 SQIPLPHGTHAFHAACPFCATQLAGEQGYIKLIF 424 (429)
T ss_pred hcCcCCCccccccccCcchhhhhccCCceEEEEE
Confidence 456789999999 89999999999988888766
No 334
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=41.97 E-value=11 Score=41.51 Aligned_cols=24 Identities=21% Similarity=0.599 Sum_probs=18.2
Q ss_pred eecCCCccceeeccCCCccccCCCCCcc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
+-.|-+|++..+-..- -||+|.+-
T Consensus 249 MK~ClsChqqIHRNAP----iCPlCKaK 272 (286)
T KOG4451|consen 249 MKVCLSCHQQIHRNAP----ICPLCKAK 272 (286)
T ss_pred chHHHHHHHHHhcCCC----CCcchhhc
Confidence 4679999998764433 79999864
No 335
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=41.92 E-value=20 Score=30.49 Aligned_cols=27 Identities=26% Similarity=0.746 Sum_probs=18.1
Q ss_pred ecCCCccceeeccCC--------------C-ccccCCCCCcc
Q 038397 97 LPCANCKAILNVPHG--------------L-VRFSCPQCAVE 123 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~--------------~-~~f~Cp~C~~~ 123 (1102)
..|..||-+-+-..| | ..+.||.|+++
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 468888887765554 2 36799999986
No 336
>PF14369 zf-RING_3: zinc-finger
Probab=41.64 E-value=20 Score=28.62 Aligned_cols=23 Identities=22% Similarity=0.769 Sum_probs=18.2
Q ss_pred cCCcceEEEeCCCcceec-CCCCC
Q 038397 20 CAGCHIILTVGPGLTEFI-CGTCN 42 (1102)
Q Consensus 20 C~~C~a~l~~~pg~~~~~-Cp~C~ 42 (1102)
|=.|...+.+.+.....+ ||.|+
T Consensus 5 Ch~C~~~V~~~~~~~~~~~CP~C~ 28 (35)
T PF14369_consen 5 CHQCNRFVRIAPSPDSDVACPRCH 28 (35)
T ss_pred CccCCCEeEeCcCCCCCcCCcCCC
Confidence 889999999876444445 99998
No 337
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=41.40 E-value=8.3 Score=38.33 Aligned_cols=31 Identities=26% Similarity=0.643 Sum_probs=28.3
Q ss_pred ecCCCccceeeccCCCccccCCCCCcccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAVD 127 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~ 127 (1102)
.-|.-||++|..|.--..+-|++|+....|+
T Consensus 8 ~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v~ 38 (116)
T KOG2907|consen 8 DFCSDCGSLLEEPSAQSTVLCIRCKIEYPVS 38 (116)
T ss_pred chhhhhhhhcccccccCceEeccccccCCHH
Confidence 6799999999999999999999999987774
No 338
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=41.20 E-value=9.6 Score=43.62 Aligned_cols=35 Identities=20% Similarity=0.390 Sum_probs=26.2
Q ss_pred CccceeecCCcceEEEeCCC-cceecCCCCCCCCCC
Q 038397 13 NVGVQVRCAGCHIILTVGPG-LTEFICGTCNLPQML 47 (1102)
Q Consensus 13 ~~~~~~~C~~C~a~l~~~pg-~~~~~Cp~C~~~~~l 47 (1102)
|...=.+|++|+..+....= -....||.||+...|
T Consensus 22 ~~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 22 PEGVWTKCPKCGQVLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred CCCCeeECCCCcchhhHHHHHhhCCCCCCCCCcCcC
Confidence 56677889999999855421 123799999998776
No 339
>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....
Probab=41.15 E-value=40 Score=36.31 Aligned_cols=50 Identities=16% Similarity=0.351 Sum_probs=37.8
Q ss_pred EeecCCCCCcchhhHHHHHHHHhc-cCceEEEEEcCCchhhhHHhhhhhhCCC
Q 038397 245 FIGDGAGVGKGRTIAGLIWENWHH-GRRKALWISVGSDLKFDARRDLDDVGAT 296 (1102)
Q Consensus 245 ~~gDg~GvGKGR~~AgiI~~n~l~-Gr~~~~w~s~s~~L~~Da~RDl~diG~~ 296 (1102)
++.=.+|.||+-..--+++++..+ |.+ ++|||.... ..+..+.++.+|.+
T Consensus 23 li~G~~GsGKT~l~~q~l~~~~~~~ge~-vlyvs~ee~-~~~l~~~~~s~g~d 73 (226)
T PF06745_consen 23 LISGPPGSGKTTLALQFLYNGLKNFGEK-VLYVSFEEP-PEELIENMKSFGWD 73 (226)
T ss_dssp EEEESTTSSHHHHHHHHHHHHHHHHT---EEEEESSS--HHHHHHHHHTTTS-
T ss_pred EEEeCCCCCcHHHHHHHHHHhhhhcCCc-EEEEEecCC-HHHHHHHHHHcCCc
Confidence 333349999999998999999999 776 999998544 47788888888875
No 340
>COG5178 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]
Probab=40.90 E-value=21 Score=46.96 Aligned_cols=22 Identities=18% Similarity=0.277 Sum_probs=16.2
Q ss_pred HHHHHHhcCCCCCChHHHHHHh
Q 038397 738 KILDIIRSMDFPNNPLDDIVDQ 759 (1102)
Q Consensus 738 ~LL~~i~~L~LP~n~LD~LId~ 759 (1102)
.||.++-+|-|-||--|.||..
T Consensus 1019 tLLnrLl~Lv~DpnlAdYi~ak 1040 (2365)
T COG5178 1019 TLLNRLLKLVLDPNLADYIIAK 1040 (2365)
T ss_pred HHHHHHHHHHhCchHHHHHhhc
Confidence 5677777777778888888754
No 341
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=40.74 E-value=21 Score=30.72 Aligned_cols=27 Identities=30% Similarity=0.752 Sum_probs=19.5
Q ss_pred ecCCCccceeeccC---------C-----Cc-cccCCCCCcc
Q 038397 97 LPCANCKAILNVPH---------G-----LV-RFSCPQCAVE 123 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~---------~-----~~-~f~Cp~C~~~ 123 (1102)
..|..||-+-+-.. | |. .|.||.|+++
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 46888998877433 2 33 5899999986
No 342
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=40.69 E-value=9.7 Score=43.80 Aligned_cols=35 Identities=17% Similarity=0.205 Sum_probs=26.5
Q ss_pred CccceeecCCcceEEEeCCC-cceecCCCCCCCCCC
Q 038397 13 NVGVQVRCAGCHIILTVGPG-LTEFICGTCNLPQML 47 (1102)
Q Consensus 13 ~~~~~~~C~~C~a~l~~~pg-~~~~~Cp~C~~~~~l 47 (1102)
|...=.+|++|+..+....= -....||.||+...|
T Consensus 34 p~~lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rl 69 (296)
T CHL00174 34 YKHLWVQCENCYGLNYKKFLKSKMNICEQCGYHLKM 69 (296)
T ss_pred CCCCeeECCCccchhhHHHHHHcCCCCCCCCCCcCC
Confidence 56678899999999865442 123699999997777
No 343
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=40.63 E-value=16 Score=30.01 Aligned_cols=29 Identities=24% Similarity=0.590 Sum_probs=21.6
Q ss_pred ecCCCcccee-eccCCCccccCCCCCcccc
Q 038397 97 LPCANCKAIL-NVPHGLVRFSCPQCAVELA 125 (1102)
Q Consensus 97 ~~C~~C~A~~-~vp~~~~~f~Cp~C~~~L~ 125 (1102)
+.|.+||+.. ...+..+-+-|+.||.-|.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEee
Confidence 4699999964 5677778889999987543
No 344
>COG4820 EutJ Ethanolamine utilization protein, possible chaperonin [Amino acid transport and metabolism]
Probab=40.61 E-value=45 Score=36.77 Aligned_cols=55 Identities=24% Similarity=0.304 Sum_probs=42.3
Q ss_pred HHHcCCCCCCccccccc--eEEEeccceEEEe-cCCCCceEEEEEEEeccccChhhhc
Q 038397 1028 ARIEGNLDSGIVDMKAN--IIELQGTPKTVHV-DNMSGASTMLFTFTLDRGITWEGLG 1082 (1102)
Q Consensus 1028 ak~~G~~d~Gi~dl~~~--~~~~~~~~~~~~~-~~~~ga~t~l~~~~~drGmswe~A~ 1082 (1102)
|---+--|-|+.||+++ .|.+.+.-+++|+ |..||.+---+++.=.+|+|+|+|.
T Consensus 134 a~vL~l~dg~VVDiGGGTTGIsi~kkGkViy~ADEpTGGtHmtLvlAG~ygi~~EeAE 191 (277)
T COG4820 134 ADVLQLDDGGVVDIGGGTTGISIVKKGKVIYSADEPTGGTHMTLVLAGNYGISLEEAE 191 (277)
T ss_pred HHHhccCCCcEEEeCCCcceeEEEEcCcEEEeccCCCCceeEEEEEecccCcCHhHHH
Confidence 33344558899999986 6777766788887 5567776666788889999999994
No 345
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=40.61 E-value=24 Score=45.99 Aligned_cols=69 Identities=13% Similarity=0.139 Sum_probs=51.2
Q ss_pred hhhcCCcceEEEEeccccccccccccccccc----------ccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEe
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAAN----------QKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRII 875 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~N----------QRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l 875 (1102)
+.|-+|+..|.|=++-|.|||..---+=|.| .+...--+...+=|-..|+|+-||++|+ + .+--|++.
T Consensus 259 ~~~~~G~rkVlvATnIAErsLtIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRaGR~-~-~G~cyrL~ 336 (812)
T PRK11664 259 LPAPAGRRKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGRAGRL-E-PGICLHLY 336 (812)
T ss_pred ccccCCCeEEEEecchHHhcccccCceEEEECCCcccccccccCCcceeEEEeechhhhhhhccccCCC-C-CcEEEEec
Confidence 5688999999999999999988765444444 2233344455566889999999999998 3 55666665
Q ss_pred e
Q 038397 876 F 876 (1102)
Q Consensus 876 ~ 876 (1102)
+
T Consensus 337 t 337 (812)
T PRK11664 337 S 337 (812)
T ss_pred C
Confidence 4
No 346
>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]
Probab=40.41 E-value=29 Score=44.11 Aligned_cols=70 Identities=26% Similarity=0.418 Sum_probs=59.1
Q ss_pred hhhcCCcceEEEEe-cccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCC-CCCeEEEeecCccchh
Q 038397 806 QLFMDGKKLVAIIS-EAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQA-SAPEYRIIFTNLGGER 883 (1102)
Q Consensus 806 ~~Fm~G~K~VAIIS-eAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQv-saP~Y~~l~T~l~GEr 883 (1102)
..|+.-++-|-++| +||+-||.|-|--.| |-.+..|+...-.|-+-|.||=+|. .--.|++++-+---||
T Consensus 1088 rDwQ~sdiFvFLLSTRAGGLGINLTAADTV--------iFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~rgTvEEk 1159 (1185)
T KOG0388|consen 1088 RDWQASDIFVFLLSTRAGGLGINLTAADTV--------IFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITRGTVEEK 1159 (1185)
T ss_pred hhccCCceEEEEEecccCcccccccccceE--------EEecCCCCcchhhHHHHHHHhccCccceeeeeecccccHHHH
Confidence 58898888887665 799999999987654 7889999999999999999999998 4578999887766665
No 347
>KOG1016 consensus Predicted DNA helicase, DEAD-box superfamily [General function prediction only]
Probab=40.30 E-value=1.4e+02 Score=38.71 Aligned_cols=69 Identities=23% Similarity=0.340 Sum_probs=51.8
Q ss_pred hhhcCCcc---eEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEE-eecCccc
Q 038397 806 QLFMDGKK---LVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRI-IFTNLGG 881 (1102)
Q Consensus 806 ~~Fm~G~K---~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~-l~T~l~G 881 (1102)
+.|++--- ++.|-..||+.||.|-+-.| .|..-.=|+.---.|-..|+=|-+|.. |.|++ |+-|---
T Consensus 781 nqfN~e~~lsWlfllstrag~lGinLIsanr--------~~ifda~wnpchdaqavcRvyrYGQ~K-pcfvYRlVmD~~l 851 (1387)
T KOG1016|consen 781 NQFNSEPGLSWLFLLSTRAGSLGINLISANR--------CIIFDACWNPCHDAQAVCRVYRYGQQK-PCFVYRLVMDNSL 851 (1387)
T ss_pred HhccCCCCceeeeeehhccccccceeeccce--------EEEEEeecCccccchhhhhhhhhcCcC-ceeEEeehhhhhh
Confidence 47876543 66777999999999975433 567788899988899999999999965 55443 4556666
Q ss_pred hh
Q 038397 882 ER 883 (1102)
Q Consensus 882 Er 883 (1102)
||
T Consensus 852 Ek 853 (1387)
T KOG1016|consen 852 EK 853 (1387)
T ss_pred HH
Confidence 76
No 348
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=40.16 E-value=77 Score=39.11 Aligned_cols=154 Identities=15% Similarity=0.214 Sum_probs=89.2
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhc-cC-ce--EEEEEcCCchhhhHHhhhh
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHH-GR-RK--ALWISVGSDLKFDARRDLD 291 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~-Gr-~~--~~w~s~s~~L~~Da~RDl~ 291 (1102)
..|.-|..+|-.+.+. .-.+.-..||.||+=--.-=|+++... .. .. ++-+.-.-.|-.-...++.
T Consensus 51 ~pt~IQ~~~IP~~l~g----------~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~~~~~~aLil~PTRELA~Qi~~~~~ 120 (513)
T COG0513 51 EPTPIQLAAIPLILAG----------RDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQIAEELR 120 (513)
T ss_pred CCCHHHHHHHHHHhCC----------CCEEEECCCCChHHHHHHHHHHHHHhcccccCCCceEEECCCHHHHHHHHHHHH
Confidence 3455666666665544 335678889999933222237777552 23 22 6777778889988899999
Q ss_pred hhCCCc--ccccccCCCCCCcCC--CCccccc--cceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhcc
Q 038397 292 DVGATC--IEVHALNKLPYSKLD--SRSVGIR--EGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAK 365 (1102)
Q Consensus 292 diG~~~--i~v~~l~~~~~~~~~--~~~~~~~--~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~ak 365 (1102)
.++... +.+..+ +|-.+ .....++ -.||.+|=--|...-+.+.-.|.+ =..+|+||+.+|.
T Consensus 121 ~~~~~~~~~~~~~i----~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~~l~l~~---------v~~lVlDEADrmL 187 (513)
T COG0513 121 KLGKNLGGLRVAVV----YGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLSG---------VETLVLDEADRML 187 (513)
T ss_pred HHHhhcCCccEEEE----ECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcCCcchhh---------cCEEEeccHhhhh
Confidence 998753 443322 11000 0001123 237777655554221111111211 1389999999999
Q ss_pred ccCCCCCCCchhHHHHHHHHhhhCCC-ccEEEEecCC
Q 038397 366 NLVPEAGSQPTRTGEAVLELQARLPE-ARVVYCSATG 401 (1102)
Q Consensus 366 n~~~~~~~~~s~~g~avl~LQ~~lP~-ARvvY~SATg 401 (1102)
+.. -...+..+-..+|. -.++..|||-
T Consensus 188 d~G---------f~~~i~~I~~~~p~~~qtllfSAT~ 215 (513)
T COG0513 188 DMG---------FIDDIEKILKALPPDRQTLLFSATM 215 (513)
T ss_pred cCC---------CHHHHHHHHHhCCcccEEEEEecCC
Confidence 882 22344455567764 7889999993
No 349
>PRK09752 adhesin; Provisional
Probab=40.05 E-value=26 Score=46.84 Aligned_cols=13 Identities=23% Similarity=0.251 Sum_probs=7.3
Q ss_pred cceeEeecCCCCC
Q 038397 241 RAGFFIGDGAGVG 253 (1102)
Q Consensus 241 R~Gf~~gDg~GvG 253 (1102)
+.|.+.|-|..-+
T Consensus 1031 ~lGVMaGYG~a~s 1043 (1250)
T PRK09752 1031 MLGIVGGYSDNQG 1043 (1250)
T ss_pred EEEEEEEEecccc
Confidence 5667766554433
No 350
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=40.03 E-value=17 Score=35.44 Aligned_cols=33 Identities=30% Similarity=0.607 Sum_probs=28.7
Q ss_pred ecCCcceEEEeCCCcc--eecCCCCCCCCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLT--EFICGTCNLPQMLPPEL 51 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~--~~~Cp~C~~~~~l~p~~ 51 (1102)
-|+.||-.|.|+-|-. +|.|+.|.+.-.|..+.
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~~ei 37 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFPISREI 37 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceeeEeeee
Confidence 4999999999998875 99999999987776655
No 351
>TIGR00604 rad3 DNA repair helicase (rad3). All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.76 E-value=20 Score=45.66 Aligned_cols=42 Identities=31% Similarity=0.464 Sum_probs=28.6
Q ss_pred cccceEEeehhhhhhccccccchHHHHHHHhccC-CCceEEeecchhccccC
Q 038397 318 IREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSG-YDGLVIFDECHKAKNLV 368 (1102)
Q Consensus 318 ~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~d-fdgvivfDEcH~akn~~ 368 (1102)
-.-.|||+.|.-|.... .| + -++.+ -|-+|||||+|+.-+.+
T Consensus 194 ~~advIi~pYnyl~dp~----~r--~---~~~~~l~~~ivI~DEAHNL~d~~ 236 (705)
T TIGR00604 194 PFANIVLLPYQYLLDPK----IR--S---AVSIELKDSIVIFDEAHNLDNVC 236 (705)
T ss_pred hcCCEEEechHHhcCHH----HH--H---HhhcccccCEEEEECccchHHHH
Confidence 45679999999998642 22 1 11222 35699999999976554
No 352
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=39.34 E-value=23 Score=35.32 Aligned_cols=31 Identities=16% Similarity=0.401 Sum_probs=25.8
Q ss_pred ecCCcceEEEeCC--CcceecCCCCCCCCCCCC
Q 038397 19 RCAGCHIILTVGP--GLTEFICGTCNLPQMLPP 49 (1102)
Q Consensus 19 ~C~~C~a~l~~~p--g~~~~~Cp~C~~~~~l~p 49 (1102)
-|+.||..|...- +-..|+|+.||+...+.+
T Consensus 4 FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 4 FCPKCGSLLYPKKDDEGGKLVCRKCGYEEEASN 36 (113)
T ss_pred ccCCccCeeEEeEcCCCcEEECCCCCcchhccc
Confidence 3999999998743 455999999999988865
No 353
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=38.91 E-value=11 Score=33.53 Aligned_cols=34 Identities=24% Similarity=0.550 Sum_probs=26.9
Q ss_pred ceecCCCccceeeccCCCccccCCCCCccccccc
Q 038397 95 IQLPCANCKAILNVPHGLVRFSCPQCAVELAVDM 128 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~~ 128 (1102)
..--|..||....-+.....|.||.||...-=|.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD~ 60 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRDV 60 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEECcHH
Confidence 3457999999998866667899999998865544
No 354
>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily. Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.
Probab=38.70 E-value=48 Score=42.06 Aligned_cols=53 Identities=26% Similarity=0.303 Sum_probs=40.9
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCc--hhhhHHhhhhhhCCC
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSD--LKFDARRDLDDVGAT 296 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~--L~~Da~RDl~diG~~ 296 (1102)
..++--.||+||++..+.+|.....+|. .+|+|...+| |+...+.-.+..|..
T Consensus 178 H~lv~G~TGsGKT~l~~~l~~q~i~~g~-~viv~DpKgD~~l~~~~~~~~~~~G~~ 232 (634)
T TIGR03743 178 HTLVLGTTGVGKTRLAELLITQDIRRGD-VVIVIDPKGDADLKRRMRAEAKRAGRP 232 (634)
T ss_pred cEEEECCCCCCHHHHHHHHHHHHHHcCC-eEEEEeCCCchHHHHHHHHHHHHhCCC
Confidence 3444445999999998666666666676 5888988877 888888888888875
No 355
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=38.66 E-value=14 Score=33.43 Aligned_cols=21 Identities=29% Similarity=0.654 Sum_probs=18.0
Q ss_pred ecCCCccceeeccCCCccccCCCCCcc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
.-|.+|+.+++.. .||.||..
T Consensus 6 ~AC~~C~~i~~~~------~Cp~Cgs~ 26 (64)
T PRK06393 6 RACKKCKRLTPEK------TCPVHGDE 26 (64)
T ss_pred hhHhhCCcccCCC------cCCCCCCC
Confidence 6799999999533 99999996
No 356
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=38.34 E-value=8.8 Score=30.54 Aligned_cols=29 Identities=21% Similarity=0.519 Sum_probs=20.4
Q ss_pred cCCcceEEEeCCCcce-ecCCCCCCCCCCC
Q 038397 20 CAGCHIILTVGPGLTE-FICGTCNLPQMLP 48 (1102)
Q Consensus 20 C~~C~a~l~~~pg~~~-~~Cp~C~~~~~l~ 48 (1102)
|+.||-.|.+..+... ..|+.|++.+.+.
T Consensus 4 Cp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 4 CPECGNLLYPKEDKEKRVACRTCGYEEPIS 33 (35)
T ss_dssp ETTTTSBEEEEEETTTTEEESSSS-EEE-S
T ss_pred CCCCCccceEcCCCccCcCCCCCCCccCCC
Confidence 9999999976655433 2799999977663
No 357
>COG5047 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]
Probab=37.74 E-value=18 Score=44.67 Aligned_cols=35 Identities=31% Similarity=0.805 Sum_probs=31.1
Q ss_pred eeecCC-cceEE----EeCCCcceecCCCCCCCCCCCCCC
Q 038397 17 QVRCAG-CHIIL----TVGPGLTEFICGTCNLPQMLPPEL 51 (1102)
Q Consensus 17 ~~~C~~-C~a~l----~~~pg~~~~~Cp~C~~~~~l~p~~ 51 (1102)
-|.|.+ |++.| ++-++-....||.|+-.+.|||+-
T Consensus 53 pv~C~~pC~avlnpyC~id~r~~~W~CpfCnqrn~lp~qy 92 (755)
T COG5047 53 PVKCTAPCKAVLNPYCHIDERNQSWICPFCNQRNTLPPQY 92 (755)
T ss_pred CceecccchhhcCcceeeccCCceEecceecCCCCCChhh
Confidence 366999 99999 788999999999999999998776
No 358
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=37.53 E-value=23 Score=35.02 Aligned_cols=30 Identities=20% Similarity=0.427 Sum_probs=27.4
Q ss_pred cceecCCCccceeeccCCCccccCCCCCcc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
..+..|.+||...-++++=+.-.||.|+.-
T Consensus 40 ~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 40 FHRYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred cceeecCCCCceEEecCcccCcCCCCCCCh
Confidence 357899999999999999998899999986
No 359
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=37.45 E-value=16 Score=28.89 Aligned_cols=25 Identities=24% Similarity=0.779 Sum_probs=14.8
Q ss_pred ceecCCCccceeeccCCCccccCCCCCcc
Q 038397 95 IQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
+.-.|..||.+...|.. .||.|++.
T Consensus 10 ~~~rC~~Cg~~~~pPr~----~Cp~C~s~ 34 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPRP----VCPHCGSD 34 (37)
T ss_dssp EEEE-TTT--EEES--S----EETTTT--
T ss_pred EEEEcCCCCCEecCCCc----CCCCcCcc
Confidence 44689999999887764 89999864
No 360
>PRK14973 DNA topoisomerase I; Provisional
Probab=37.40 E-value=40 Score=44.62 Aligned_cols=25 Identities=20% Similarity=0.425 Sum_probs=17.8
Q ss_pred cCCCccc--eeeccCCCc-cc-cCCCCCc
Q 038397 98 PCANCKA--ILNVPHGLV-RF-SCPQCAV 122 (1102)
Q Consensus 98 ~C~~C~A--~~~vp~~~~-~f-~Cp~C~~ 122 (1102)
.|.-||+ ++.+..|-- -| .||.|.-
T Consensus 637 ~Cp~CG~p~~~~~r~Gr~g~fl~CP~C~~ 665 (936)
T PRK14973 637 VCPIHHLNHVRLIRKGARPWDIGCPLCSH 665 (936)
T ss_pred CCCCCCCCceEEeecCCCcccccCccccc
Confidence 7999998 666666633 24 7999943
No 361
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=37.36 E-value=18 Score=41.36 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=23.5
Q ss_pred cCCcceEEEeCCCcceecCCCCCC
Q 038397 20 CAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 20 C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
|++||.......|-....||.||.
T Consensus 114 Cg~CG~~~~~~~~g~~~~C~~cg~ 137 (279)
T COG2816 114 CGRCGTKTYPREGGWARVCPKCGH 137 (279)
T ss_pred CCCCCCcCccccCceeeeCCCCCC
Confidence 999999999999999999999996
No 362
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=37.23 E-value=14 Score=31.80 Aligned_cols=28 Identities=18% Similarity=0.547 Sum_probs=21.9
Q ss_pred cCCcceEEEeCCCcceecCCCCCCCCCC
Q 038397 20 CAGCHIILTVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 20 C~~C~a~l~~~pg~~~~~Cp~C~~~~~l 47 (1102)
|+.||...-.+.=.-.+.|..||+.+..
T Consensus 22 CPrCG~gvfmA~H~dR~~CGkCgyTe~~ 49 (51)
T COG1998 22 CPRCGPGVFMADHKDRWACGKCGYTEFK 49 (51)
T ss_pred CCCCCCcchhhhcCceeEeccccceEee
Confidence 9999986555555569999999987643
No 363
>PRK12377 putative replication protein; Provisional
Probab=37.04 E-value=67 Score=36.06 Aligned_cols=42 Identities=21% Similarity=0.303 Sum_probs=32.2
Q ss_pred ceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhh
Q 038397 242 AGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFD 285 (1102)
Q Consensus 242 ~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~D 285 (1102)
.++++--.+|+||+..+.+|..+-..+|+. ++++++. +|..+
T Consensus 102 ~~l~l~G~~GtGKThLa~AIa~~l~~~g~~-v~~i~~~-~l~~~ 143 (248)
T PRK12377 102 TNFVFSGKPGTGKNHLAAAIGNRLLAKGRS-VIVVTVP-DVMSR 143 (248)
T ss_pred CeEEEECCCCCCHHHHHHHHHHHHHHcCCC-eEEEEHH-HHHHH
Confidence 566665569999999999998888778875 8998884 45443
No 364
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=36.88 E-value=22 Score=45.31 Aligned_cols=78 Identities=23% Similarity=0.299 Sum_probs=58.6
Q ss_pred cCCcceEEEEe-cccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchhhhHH
Q 038397 809 MDGKKLVAIIS-EAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGERRFAS 887 (1102)
Q Consensus 809 m~G~K~VAIIS-eAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GErRFaS 887 (1102)
.++...|.++| .||+.|+.|-+--++ |.+++=||.-.-=|=+=|.||=+|-..=....++.-=--|-|+..
T Consensus 587 ~~~~~~vll~Slkag~~glnlt~a~~v--------~~~d~~wnp~~eeQaidR~hrigq~k~v~v~r~~i~dtveer~l~ 658 (674)
T KOG1001|consen 587 CDPLVTALLMSLKAGKVGLNLTAASHV--------LLMDPWWNPAVEEQAIDRAHRIGQTKPVKVSRFIIKDTVEERILK 658 (674)
T ss_pred cCccHHHHHHHHHHhhhhhchhhhhHH--------HhhchhcChHHHHHHHHHHHHhcccceeeeeeehhhhccHHHHHH
Confidence 34556666666 589999999876554 567888999888899999999999876665444444456778888
Q ss_pred HHHHHHh
Q 038397 888 IVAKRLE 894 (1102)
Q Consensus 888 ~VAkRLe 894 (1102)
+..|++.
T Consensus 659 iq~~K~~ 665 (674)
T KOG1001|consen 659 IQEKKRE 665 (674)
T ss_pred HHHHHHH
Confidence 8888764
No 365
>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX. Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.
Probab=36.63 E-value=2e+02 Score=32.71 Aligned_cols=30 Identities=13% Similarity=0.059 Sum_probs=18.6
Q ss_pred cceeEeecCCCCCcchhhHHHHHHHHhccC
Q 038397 241 RAGFFIGDGAGVGKGRTIAGLIWENWHHGR 270 (1102)
Q Consensus 241 R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr 270 (1102)
+.++++---+|+||+-..-++...-...|.
T Consensus 58 ~~~vll~G~pGTGKT~lA~~ia~~l~~~g~ 87 (284)
T TIGR02880 58 TLHMSFTGNPGTGKTTVALRMAQILHRLGY 87 (284)
T ss_pred CceEEEEcCCCCCHHHHHHHHHHHHHHcCC
Confidence 456777555999998766454444443444
No 366
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=36.26 E-value=7.3 Score=47.09 Aligned_cols=42 Identities=31% Similarity=0.692 Sum_probs=33.6
Q ss_pred HHHhhhhhccccCCccccCCCCCCcccC----CCCCCccccchhhh
Q 038397 670 EERKKLLQCSCCGQLVHSGCLVPPITDV----IPSDWSCHSCKEKT 711 (1102)
Q Consensus 670 d~k~kLL~cs~cgk~~H~~cL~PP~~di----~~~dW~c~sCkek~ 711 (1102)
-.+.+|++|++|.+-+|+.|--|++.+. +...|+|.-|.-..
T Consensus 180 ~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~ 225 (464)
T KOG4323|consen 180 GAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGP 225 (464)
T ss_pred CccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccch
Confidence 3445899999999999999999987653 44569999997543
No 367
>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=36.26 E-value=46 Score=38.86 Aligned_cols=57 Identities=32% Similarity=0.423 Sum_probs=40.3
Q ss_pred cceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccc
Q 038397 241 RAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEV 300 (1102)
Q Consensus 241 R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v 300 (1102)
|-=||.|-| ||||+-+.|++-+.-=..|+ |++=+|+-+.+--.=-.|. +||.+.-+|
T Consensus 3 riv~f~GKG-GVGKTT~aaA~A~~lA~~g~-kvLlvStDPAhsL~d~f~~-elg~~~~~I 59 (322)
T COG0003 3 RIVFFTGKG-GVGKTTIAAATAVKLAESGK-KVLLVSTDPAHSLGDVFDL-ELGHDPRKV 59 (322)
T ss_pred EEEEEecCC-cccHHHHHHHHHHHHHHcCC-cEEEEEeCCCCchHhhhcc-ccCCchhhc
Confidence 445677775 99999999998888888885 4999988765544323444 567665544
No 368
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=36.00 E-value=23 Score=33.31 Aligned_cols=36 Identities=25% Similarity=0.531 Sum_probs=29.5
Q ss_pred CccceeecCCcceEE-EeCCCcceecCCCCCCCCCCC
Q 038397 13 NVGVQVRCAGCHIIL-TVGPGLTEFICGTCNLPQMLP 48 (1102)
Q Consensus 13 ~~~~~~~C~~C~a~l-~~~pg~~~~~Cp~C~~~~~l~ 48 (1102)
.-++-|+|+||..+- .|.+.-|-..|+.|+...-.|
T Consensus 30 syFm~VkC~gc~~iT~vfSHaqtvVvc~~c~~il~~~ 66 (84)
T KOG1779|consen 30 SYFMDVKCPGCFKITTVFSHAQTVVVCEGCSTILCQP 66 (84)
T ss_pred ceEEEEEcCCceEEEEEeecCceEEEcCCCceEEEEe
Confidence 357889999998776 789999999999999755443
No 369
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=35.87 E-value=17 Score=31.36 Aligned_cols=25 Identities=32% Similarity=0.836 Sum_probs=20.3
Q ss_pred ecCCcceEE------EeCCCcceecCCCCCC
Q 038397 19 RCAGCHIIL------TVGPGLTEFICGTCNL 43 (1102)
Q Consensus 19 ~C~~C~a~l------~~~pg~~~~~Cp~C~~ 43 (1102)
.|.||+..| .+.-+-.-..||+||.
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 499999988 4556666789999996
No 370
>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif. They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.
Probab=35.86 E-value=36 Score=36.01 Aligned_cols=42 Identities=21% Similarity=0.316 Sum_probs=30.6
Q ss_pred ceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhh
Q 038397 242 AGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFD 285 (1102)
Q Consensus 242 ~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~D 285 (1102)
.|+++--.+|+||+...++|..+-..+|++ ++|++.+ +|+..
T Consensus 48 ~~l~l~G~~G~GKThLa~ai~~~~~~~g~~-v~f~~~~-~L~~~ 89 (178)
T PF01695_consen 48 ENLILYGPPGTGKTHLAVAIANEAIRKGYS-VLFITAS-DLLDE 89 (178)
T ss_dssp -EEEEEESTTSSHHHHHHHHHHHHHHTT---EEEEEHH-HHHHH
T ss_pred eEEEEEhhHhHHHHHHHHHHHHHhccCCcc-eeEeecC-ceecc
Confidence 466654469999999999999998888876 8888865 35443
No 371
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=35.66 E-value=20 Score=32.25 Aligned_cols=21 Identities=29% Similarity=0.757 Sum_probs=17.8
Q ss_pred cCCCccceeeccCCCccccCCCCCccc
Q 038397 98 PCANCKAILNVPHGLVRFSCPQCAVEL 124 (1102)
Q Consensus 98 ~C~~C~A~~~vp~~~~~f~Cp~C~~~L 124 (1102)
-|.+|+.+++.. .||.||...
T Consensus 5 AC~~C~~i~~~~------~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYITTED------RCPVCGSRD 25 (61)
T ss_pred hhhhCCcccCCC------cCCCCcCCc
Confidence 799999999533 699999975
No 372
>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB. This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=35.33 E-value=34 Score=44.66 Aligned_cols=68 Identities=18% Similarity=0.225 Sum_probs=48.2
Q ss_pred hhhcCCcceEEEEeccccccccccccccccc----------ccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEe
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAAN----------QKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRII 875 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~N----------QRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l 875 (1102)
+.|.+|+..|.|=++-|.|||-.--=+-|-| -+..+-.+...+=|-..|+|+-||++|+ ...=-|++.
T Consensus 256 ~~~~~G~rkVlVATnIAErgItIp~V~~VID~Gl~r~~~yd~~~g~~~L~~~~iSkasa~QR~GRAGR~--~~G~cyrL~ 333 (819)
T TIGR01970 256 KPDPQGRRKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGRAGRL--EPGVCYRLW 333 (819)
T ss_pred hhcccCCeEEEEecchHhhcccccCceEEEEcCcccccccccccCCceeeEEEECHHHHHhhhhhcCCC--CCCEEEEeC
Confidence 4688999999999999999988765444433 2223333444566888899999999998 244445544
No 373
>TIGR00708 cobA cob(I)alamin adenosyltransferase. Alternate name: corrinoid adenosyltransferase.
Probab=35.25 E-value=1.9e+02 Score=31.03 Aligned_cols=26 Identities=27% Similarity=0.488 Sum_probs=22.0
Q ss_pred ecCCCCCcchhhHHHHHHHHhccCce
Q 038397 247 GDGAGVGKGRTIAGLIWENWHHGRRK 272 (1102)
Q Consensus 247 gDg~GvGKGR~~AgiI~~n~l~Gr~~ 272 (1102)
=-|.|.||+-.+.|+.+...-+|.+-
T Consensus 11 ~~g~GkGKtt~a~g~a~ra~~~g~~v 36 (173)
T TIGR00708 11 HTGNGKGKTTAAFGMALRALGHGKKV 36 (173)
T ss_pred ECCCCCChHHHHHHHHHHHHHCCCeE
Confidence 44578889999999999999999873
No 374
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=34.48 E-value=20 Score=40.38 Aligned_cols=27 Identities=19% Similarity=0.457 Sum_probs=23.6
Q ss_pred ecCCCccceeeccCCCccccCCCCCcc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
--|+.||..+.+-++-.+..|+.|+..
T Consensus 100 ~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 100 RFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred ccccccCCCCeecCCceeEECCCCCCE
Confidence 479999999998888888999999954
No 375
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=34.42 E-value=12 Score=43.09 Aligned_cols=36 Identities=17% Similarity=0.328 Sum_probs=26.3
Q ss_pred CCccceeecCCcceEEEeCCCc-ceecCCCCCCCCCC
Q 038397 12 PNVGVQVRCAGCHIILTVGPGL-TEFICGTCNLPQML 47 (1102)
Q Consensus 12 ~~~~~~~~C~~C~a~l~~~pg~-~~~~Cp~C~~~~~l 47 (1102)
-|...=.+|+.|+..+.-..=- ....||.||+...|
T Consensus 22 ~~~~~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 58 (292)
T PRK05654 22 VPEGLWTKCPSCGQVLYRKELEANLNVCPKCGHHMRI 58 (292)
T ss_pred CCCCCeeECCCccchhhHHHHHhcCCCCCCCCCCeeC
Confidence 3566788999999988443311 23699999997777
No 376
>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type. subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system.
Probab=34.34 E-value=37 Score=39.69 Aligned_cols=41 Identities=20% Similarity=0.178 Sum_probs=33.7
Q ss_pred CcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccc
Q 038397 811 GKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTH 862 (1102)
Q Consensus 811 G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTH 862 (1102)
++..|+|-++.++.||.+-.| .+| .+ |-+++.-||++|||+
T Consensus 317 ~~~~iLVaTdv~~rGiDi~~~---------~vi-~~-p~~~~~yiqR~GR~g 357 (357)
T TIGR03158 317 MQFDILLGTSTVDVGVDFKRD---------WLI-FS-ARDAAAFWQRLGRLG 357 (357)
T ss_pred ccCCEEEEecHHhcccCCCCc---------eEE-EC-CCCHHHHhhhcccCC
Confidence 377899999999999988543 233 45 889999999999985
No 377
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=34.30 E-value=26 Score=30.59 Aligned_cols=31 Identities=13% Similarity=0.235 Sum_probs=22.4
Q ss_pred ccceeecCCcceE----EEeCCCcceecCCCCCCC
Q 038397 14 VGVQVRCAGCHII----LTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 14 ~~~~~~C~~C~a~----l~~~pg~~~~~Cp~C~~~ 44 (1102)
....+-|.+|... +...+.-.+|.||+||..
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred CceeEECcccchhhcccccccCCceEEEcCCCCCc
Confidence 3345559999754 356667779999999974
No 378
>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated
Probab=33.79 E-value=2.6e+02 Score=30.49 Aligned_cols=138 Identities=22% Similarity=0.245 Sum_probs=67.3
Q ss_pred eEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcC-CchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCccccccce
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVG-SDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSVGIREGV 322 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s-~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~Gv 322 (1102)
..+=.|.|.||+--+-|+.+...-+|.+ ++.+-.- +...+.=..=++.++ .+.++. ...|.
T Consensus 25 v~v~~g~GkGKtt~a~g~a~ra~g~G~~-V~ivQFlKg~~~~GE~~~l~~l~--~v~~~~---------------~g~~~ 86 (191)
T PRK05986 25 LIVHTGNGKGKSTAAFGMALRAVGHGKK-VGVVQFIKGAWSTGERNLLEFGG--GVEFHV---------------MGTGF 86 (191)
T ss_pred EEEECCCCCChHHHHHHHHHHHHHCCCe-EEEEEEecCCCccCHHHHHhcCC--CcEEEE---------------CCCCC
Confidence 3446667888999999999999999987 4433221 111221111111111 122111 12232
Q ss_pred EEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCC
Q 038397 323 VFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGA 402 (1102)
Q Consensus 323 lF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATga 402 (1102)
.|.+ .........-+.-|+...+++..+--.+|||||.=-|-+..- -......--|+++-++-.||. ||-
T Consensus 87 ~~~~-~~~~e~~~~~~~~~~~a~~~l~~~~ydlvVLDEi~~Al~~gl------i~~eevi~~L~~rp~~~evVl---TGR 156 (191)
T PRK05986 87 TWET-QDRERDIAAAREGWEEAKRMLADESYDLVVLDELTYALKYGY------LDVEEVLEALNARPGMQHVVI---TGR 156 (191)
T ss_pred cccC-CCcHHHHHHHHHHHHHHHHHHhCCCCCEEEEehhhHHHHCCC------ccHHHHHHHHHcCCCCCEEEE---ECC
Confidence 2322 000000011123345555555443334999999988877632 112233334555655667776 455
Q ss_pred CCCCccc
Q 038397 403 SEPRNMG 409 (1102)
Q Consensus 403 sep~Nl~ 409 (1102)
.-|..|.
T Consensus 157 ~~p~~Li 163 (191)
T PRK05986 157 GAPRELI 163 (191)
T ss_pred CCCHHHH
Confidence 4444443
No 379
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=33.77 E-value=1.2e+02 Score=39.78 Aligned_cols=88 Identities=16% Similarity=0.074 Sum_probs=47.2
Q ss_pred chHHHHHHHhcc-CCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCCCC-----Cccchhh
Q 038397 339 SRLQQLVQWCGS-GYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGASEP-----RNMGYMV 412 (1102)
Q Consensus 339 sRl~Ql~~W~g~-dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep-----~Nl~ym~ 412 (1102)
.||+++++=+.. +-..+|++||.|...+...+.+ +. .+...|...+-+.++...-||--.+- .|.+...
T Consensus 252 ~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~---~~--d~~~~Lk~~l~~g~i~~IgaTt~~e~r~~~~~d~al~r 326 (852)
T TIGR03346 252 ERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEG---AM--DAGNMLKPALARGELHCIGATTLDEYRKYIEKDAALER 326 (852)
T ss_pred HHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcc---hh--HHHHHhchhhhcCceEEEEeCcHHHHHHHhhcCHHHHh
Confidence 578888876643 3356999999998765421111 11 12233455566667766666644432 2455555
Q ss_pred hccccCCCCCCCCHHHHHHHH
Q 038397 413 RLGLWGAGTCFKDFQIFLGAL 433 (1102)
Q Consensus 413 RLGLWg~gt~f~~~~~f~~a~ 433 (1102)
|.-.- -.+=++.++.+..+
T Consensus 327 Rf~~i--~v~~p~~~~~~~iL 345 (852)
T TIGR03346 327 RFQPV--FVDEPTVEDTISIL 345 (852)
T ss_pred cCCEE--EeCCCCHHHHHHHH
Confidence 55321 01223555555544
No 380
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=33.71 E-value=27 Score=41.53 Aligned_cols=36 Identities=28% Similarity=0.618 Sum_probs=27.2
Q ss_pred ecCCCccceeeccCCCccccCCCCCcccccccccccccC
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAVDMSKVKQFF 135 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~~~~~~~~~ 135 (1102)
-.|.+||..+. |..+..-.|..||.+..+ .+.++|+
T Consensus 150 ~~Ce~cG~~~~-~~~l~~p~~~~~g~~~~~--r~e~~~f 185 (391)
T PF09334_consen 150 DQCENCGRPLE-PEELINPVCKICGSPPEV--REEENYF 185 (391)
T ss_dssp TEETTTSSBEE-CCCSECEEETTTS-B-EE--EEEEEEE
T ss_pred CcccCCCCCcc-cccccCCccccccccCcc--ccceEEE
Confidence 58999999998 888999999999999755 2344554
No 381
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=33.52 E-value=28 Score=31.15 Aligned_cols=34 Identities=21% Similarity=0.392 Sum_probs=26.9
Q ss_pred ceecCCCccceeeccC-CCccccCCCCCccccccc
Q 038397 95 IQLPCANCKAILNVPH-GLVRFSCPQCAVELAVDM 128 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~-~~~~f~Cp~C~~~L~v~~ 128 (1102)
+.+.|..|+.++.|=. --..-.|+.||..|+-+-
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~Pt 44 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPT 44 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCCcccCC
Confidence 5699999999986643 333569999999998864
No 382
>PRK07219 DNA topoisomerase I; Validated
Probab=33.46 E-value=34 Score=44.68 Aligned_cols=32 Identities=34% Similarity=0.723 Sum_probs=23.1
Q ss_pred eecCCC---ccceeeccCC----CccccCCCCCcccccc
Q 038397 96 QLPCAN---CKAILNVPHG----LVRFSCPQCAVELAVD 127 (1102)
Q Consensus 96 ~~~C~~---C~A~~~vp~~----~~~f~Cp~C~~~L~v~ 127 (1102)
-+.|.+ |+....+|.. ...-.||.||.+++.-
T Consensus 708 F~~Cs~yp~C~~~~~l~~~~~~~~~~~~CpkCg~~l~~~ 746 (822)
T PRK07219 708 FLGCTNYPKCKYTLPLPRRGKITVTDEKCPECGLPLLRV 746 (822)
T ss_pred eeeCCCCCCCCceeecccccccccccCCCCCCCCeEEEE
Confidence 477876 9888877753 1235899999988763
No 383
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=33.14 E-value=26 Score=30.69 Aligned_cols=21 Identities=24% Similarity=0.727 Sum_probs=16.0
Q ss_pred eecCCcceEEEeCCCcceecCCCCCC
Q 038397 18 VRCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
+.|+.||+ +..++ ..|+.||+
T Consensus 27 ~~c~~cg~-~~~~H----~vc~~cG~ 47 (56)
T PF01783_consen 27 VKCPNCGE-PKLPH----RVCPSCGY 47 (56)
T ss_dssp EESSSSSS-EESTT----SBCTTTBB
T ss_pred eeeccCCC-Eeccc----EeeCCCCe
Confidence 67999994 44444 78999985
No 384
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=33.10 E-value=5.3e+02 Score=34.07 Aligned_cols=156 Identities=17% Similarity=0.271 Sum_probs=82.4
Q ss_pred CCCHHHHHHHHhccChhH---HHHHHHHHHhccceeeeccCCCCceeEEEeccCcHHHHHHHHHHHHHHH-----HHHHH
Q 038397 423 FKDFQIFLGALDKGGVGA---LELVAMDMKARGMYVCRTLSYKGAEFEVIEAPLEAEMTDMYKKAAEFWA-----ELRVE 494 (1102)
Q Consensus 423 f~~~~~f~~a~~~gGv~a---mE~va~dlK~~G~yiaR~LSf~gvef~i~e~~l~~~~~~~Yd~~a~~w~-----~~~~~ 494 (1102)
.-+-..++.+||+.|||- .--+---|+.+| ||.+. .+=. ++ -|+.=+.+++.+-+.+. ++...
T Consensus 578 ryTEAtLIk~ME~~GIGTPATrAsIIetL~~R~-YV~~~---~kkr--l~---PT~lG~~Li~~L~~~fp~lv~p~~TA~ 648 (805)
T PTZ00407 578 PHSEGTLIEELKNNGVGRPSTYPMIVKTLLARG-YIAVN---PKGR--CE---TTPVGRMLVETAKSTFPSIVDIGFTAA 648 (805)
T ss_pred CCCHHHHHHHHHhCCCCCcccHHHHHHHHHhcC-CEEec---cCce--ee---ecHHHHHHHHHHHHhhhhhcChHHHHH
Confidence 447899999999999972 222335667777 66553 0111 22 23334455555444332 23456
Q ss_pred HHHHHhhhcCCCCChh-------------HHHHHhhhhhhHHHHHHHHhc-CchHHHHHHHHHHH--CCCeEEEEEecch
Q 038397 495 LLSASAFLANDKPNSS-------------QLWRLYWSGHQRFFRHMCMSA-KVPATVRLAKKALA--EGKCVVIGLQSTG 558 (1102)
Q Consensus 495 ~~~a~e~~~~~~~~~~-------------~~~~~FwsahQrFFk~l~~a~-Kv~~~V~~a~eal~--~Gk~vVIgLqSTG 558 (1102)
+++.++.+..++.... .+...||+. |.+.+-.+ ++-. ++.....++ +.+.. -.+|+
T Consensus 649 ~E~~Ld~Ia~G~~~~~~~~~~~~~~~~~~~vl~~F~~~----F~~~v~~a~~~~~-~~~~~~~~~~~~~~~~---~~~~~ 720 (805)
T PTZ00407 649 FEKKLDRIAKPGPAKRPALLRPTNVSQADYVLSMFLST----FLNYVTEATKAQR-AAIVERSMRLKQEQEG---GSGTD 720 (805)
T ss_pred HHHHHHHHHcCCcchhhhccccccchhHHHHHHHHHHH----HHHHHhhhhhhhH-HHHHHhhhhhhHhhhc---CCCCC
Confidence 6667777754422211 367889976 33333333 3322 333333332 33332 23456
Q ss_pred hHHHHHHHHhcC----CCcCccccChH---------HHHHHHHHhhCCCC
Q 038397 559 EARTEEAVTKYG----LELDDFISGPR---------ELLLKFVEENYPLP 595 (1102)
Q Consensus 559 EA~~~~~l~~~~----~~l~dfvst~r---------~il~~~v~~~FP~~ 595 (1102)
-+-.++-+.... ....|.|--|| .-|.+||.+|||-.
T Consensus 721 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 770 (805)
T PTZ00407 721 DAEFEESVVKAKKKVALAVPDLVDLPKTYRNFTALQRSLNDYLRRNFPPS 770 (805)
T ss_pred chHHHHHHHHHHhhhhhcCchhhhchhhhhhHHHHHHHHHHHHHhcCChh
Confidence 555555444322 23456665554 34788999999943
No 385
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=32.93 E-value=32 Score=33.68 Aligned_cols=30 Identities=20% Similarity=0.595 Sum_probs=22.6
Q ss_pred ccceeecCCcceEEEe----CCCcceecCCCCCCC
Q 038397 14 VGVQVRCAGCHIILTV----GPGLTEFICGTCNLP 44 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~----~pg~~~~~Cp~C~~~ 44 (1102)
...-+.|++||+ ..+ ..|.....|+.||+-
T Consensus 18 lpt~f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 18 LPKIFECPRCGK-VSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred CCcEeECCCCCC-eEeeeecCCCcceEECCCCCCc
Confidence 345677999994 333 468899999999973
No 386
>KOG1986 consensus Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.91 E-value=24 Score=44.60 Aligned_cols=36 Identities=31% Similarity=0.691 Sum_probs=30.2
Q ss_pred ceeecCCcceEE----EeCCCcceecCCCCCCCCCCCCCC
Q 038397 16 VQVRCAGCHIIL----TVGPGLTEFICGTCNLPQMLPPEL 51 (1102)
Q Consensus 16 ~~~~C~~C~a~l----~~~pg~~~~~Cp~C~~~~~l~p~~ 51 (1102)
--++|-.|||.| .|-.+-....||.|.-.+.+||+-
T Consensus 52 ~P~~C~~C~AvlNPyc~vd~~a~~W~CpfC~qrN~~p~~Y 91 (745)
T KOG1986|consen 52 DPLRCSKCGAVLNPYCSVDFRAKSWICPFCNQRNPFPPHY 91 (745)
T ss_pred CCchhccchhhcCcceeecccCceEeccccccCCCCChhh
Confidence 347899999999 688888899999999877776665
No 387
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=32.84 E-value=1.3e+02 Score=40.18 Aligned_cols=51 Identities=20% Similarity=0.117 Sum_probs=38.4
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhC
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVG 294 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG 294 (1102)
-|-+-==|||||+-..+-+-+.+-.+|+ |+.-|=-...|..-+..=|..++
T Consensus 99 SFaiiAPTGvGKTTfg~~~sl~~a~kgk-r~yii~PT~~Lv~Q~~~kl~~~~ 149 (1187)
T COG1110 99 SFAIIAPTGVGKTTFGLLMSLYLAKKGK-RVYIIVPTTTLVRQVYERLKKFA 149 (1187)
T ss_pred ceEEEcCCCCchhHHHHHHHHHHHhcCC-eEEEEecCHHHHHHHHHHHHHHH
Confidence 3445455999999999888888888895 47777667778877777776665
No 388
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=32.68 E-value=6.1e+02 Score=30.56 Aligned_cols=148 Identities=25% Similarity=0.253 Sum_probs=76.6
Q ss_pred cCCcccchhhHH---HHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhh
Q 038397 214 SKSLSCLQIETL---VYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDL 290 (1102)
Q Consensus 214 ~g~LS~~Qle~v---~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl 290 (1102)
.|.||.-|-.+- +-+.++++.. ++--=||.||+-.|=-.|-....+|-+ +.-.|-.-|..-...--|
T Consensus 95 ~G~Ls~~Q~~as~~l~q~i~~k~~~---------lv~AV~GaGKTEMif~~i~~al~~G~~-vciASPRvDVclEl~~Rl 164 (441)
T COG4098 95 KGTLSPGQKKASNQLVQYIKQKEDT---------LVWAVTGAGKTEMIFQGIEQALNQGGR-VCIASPRVDVCLELYPRL 164 (441)
T ss_pred ccccChhHHHHHHHHHHHHHhcCcE---------EEEEecCCCchhhhHHHHHHHHhcCCe-EEEecCcccchHHHHHHH
Confidence 677887776543 3344455443 344458999999988777777788876 333333333222221111
Q ss_pred hhhCCCcccccccCCCCCCcCCCCccccccceEEeehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCC
Q 038397 291 DDVGATCIEVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPE 370 (1102)
Q Consensus 291 ~diG~~~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~ 370 (1102)
++- ...+++..| ||. |+.. ...-+|-+|--||. |++| .|| +||.||...---..
T Consensus 165 k~a-F~~~~I~~L----yg~--S~~~-fr~plvVaTtHQLl--------rFk~-------aFD-~liIDEVDAFP~~~-- 218 (441)
T COG4098 165 KQA-FSNCDIDLL----YGD--SDSY-FRAPLVVATTHQLL--------RFKQ-------AFD-LLIIDEVDAFPFSD-- 218 (441)
T ss_pred HHh-hccCCeeeE----ecC--Cchh-ccccEEEEehHHHH--------HHHh-------hcc-EEEEeccccccccC--
Confidence 110 011111122 221 1111 22346666666665 4555 587 77789987643221
Q ss_pred CCCCchhHHHHHHHHhhhCCCccEEEEecCCCC
Q 038397 371 AGSQPTRTGEAVLELQARLPEARVVYCSATGAS 403 (1102)
Q Consensus 371 ~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgas 403 (1102)
.++- -.||. +.+=+++-.+|.|||...
T Consensus 219 ---d~~L-~~Av~--~ark~~g~~IylTATp~k 245 (441)
T COG4098 219 ---DQSL-QYAVK--KARKKEGATIYLTATPTK 245 (441)
T ss_pred ---CHHH-HHHHH--HhhcccCceEEEecCChH
Confidence 1111 11222 234456778999999543
No 389
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=32.67 E-value=32 Score=27.95 Aligned_cols=24 Identities=21% Similarity=0.519 Sum_probs=18.7
Q ss_pred ecCCcceEE--EeCCCcceecCCCCC
Q 038397 19 RCAGCHIIL--TVGPGLTEFICGTCN 42 (1102)
Q Consensus 19 ~C~~C~a~l--~~~pg~~~~~Cp~C~ 42 (1102)
.|+.|+..| .--+++.-..||.|+
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCC
Confidence 489999887 222778888899997
No 390
>PLN00162 transport protein sec23; Provisional
Probab=32.60 E-value=66 Score=41.73 Aligned_cols=31 Identities=19% Similarity=0.161 Sum_probs=24.4
Q ss_pred ccchhhHHHHHHhhccccCCCCCcceeEeec
Q 038397 218 SCLQIETLVYASQRHLQHLPNSARAGFFIGD 248 (1102)
Q Consensus 218 S~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gD 248 (1102)
.+.+++.+.-+.++--..||++.+-||+.=|
T Consensus 136 ~~~~l~~lk~sl~~~L~~LP~~a~VGlITF~ 166 (761)
T PLN00162 136 IEEELGALKSALLQAIALLPENALVGLITFG 166 (761)
T ss_pred hHHHHHHHHHHHHHHHHhCCCCCEEEEEEEC
Confidence 3567788877777766779999999998865
No 391
>CHL00181 cbbX CbbX; Provisional
Probab=31.95 E-value=4e+02 Score=30.46 Aligned_cols=13 Identities=23% Similarity=0.347 Sum_probs=11.3
Q ss_pred CceEEeecchhcc
Q 038397 353 DGLVIFDECHKAK 365 (1102)
Q Consensus 353 dgvivfDEcH~ak 365 (1102)
.|||++||+|...
T Consensus 123 ggVLfIDE~~~l~ 135 (287)
T CHL00181 123 GGVLFIDEAYYLY 135 (287)
T ss_pred CCEEEEEccchhc
Confidence 5899999999864
No 392
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=31.45 E-value=25 Score=30.22 Aligned_cols=27 Identities=22% Similarity=0.523 Sum_probs=19.9
Q ss_pred eecCCCccceeeccCCCccccCCCCCcc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
.--|.+||+-+-.+|. .+|.|+-||-.
T Consensus 20 ~~fCP~Cg~~~m~~~~-~r~~C~~Cgyt 46 (50)
T PRK00432 20 NKFCPRCGSGFMAEHL-DRWHCGKCGYT 46 (50)
T ss_pred cCcCcCCCcchheccC-CcEECCCcCCE
Confidence 4589999995333444 79999999864
No 393
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=31.43 E-value=20 Score=30.67 Aligned_cols=12 Identities=33% Similarity=1.063 Sum_probs=9.5
Q ss_pred cccCCCCCcccc
Q 038397 114 RFSCPQCAVELA 125 (1102)
Q Consensus 114 ~f~Cp~C~~~L~ 125 (1102)
.|.||+|+..+.
T Consensus 2 ~f~CP~C~~~~~ 13 (54)
T PF05605_consen 2 SFTCPYCGKGFS 13 (54)
T ss_pred CcCCCCCCCccC
Confidence 589999999544
No 394
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=31.37 E-value=30 Score=30.59 Aligned_cols=25 Identities=20% Similarity=0.454 Sum_probs=20.4
Q ss_pred eecCCCccceeeccCCCccccCCCCCccccc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
...|.+||.-+- .-.||.||.++.+
T Consensus 5 mr~C~~CgvYTL------k~~CP~CG~~t~~ 29 (56)
T PRK13130 5 IRKCPKCGVYTL------KEICPVCGGKTKN 29 (56)
T ss_pred ceECCCCCCEEc------cccCcCCCCCCCC
Confidence 367999998765 5589999999766
No 395
>TIGR00631 uvrb excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
Probab=31.28 E-value=1.1e+02 Score=39.16 Aligned_cols=51 Identities=22% Similarity=0.173 Sum_probs=41.2
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEec-----CCCcHhHHHHhhcccccC
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLE-----LPWSADRAIQQFGRTHRS 864 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLE-----lpWsADkAIQqfGRTHRS 864 (1102)
+.|.+|+..|+|-++..+.|+-+-.-. +-+.++ .|-|...-||+.|||+|.
T Consensus 486 ~~fr~G~i~VLV~t~~L~rGfDiP~v~--------lVvi~DadifG~p~~~~~~iqriGRagR~ 541 (655)
T TIGR00631 486 RDLRLGEFDVLVGINLLREGLDLPEVS--------LVAILDADKEGFLRSERSLIQTIGRAARN 541 (655)
T ss_pred HHHhcCCceEEEEcChhcCCeeeCCCc--------EEEEeCcccccCCCCHHHHHHHhcCCCCC
Confidence 589999999999899999999876443 223344 577888999999999996
No 396
>PRK09200 preprotein translocase subunit SecA; Reviewed
Probab=31.08 E-value=79 Score=41.22 Aligned_cols=132 Identities=18% Similarity=0.122 Sum_probs=0.0
Q ss_pred HHHHHhhccccCCCCC--------cceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCC
Q 038397 225 LVYASQRHLQHLPNSA--------RAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGAT 296 (1102)
Q Consensus 225 v~ya~q~h~~~l~~g~--------R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~ 296 (1102)
|.-|+.|.-...|..- ..|-+.-=.||-||+-..+=-++.|.+.|+. +.-++++..|-..-...+..+...
T Consensus 67 vrea~~R~~g~~p~~vQl~~~~~l~~G~Iaem~TGeGKTL~a~lp~~l~al~G~~-v~VvTpt~~LA~qd~e~~~~l~~~ 145 (790)
T PRK09200 67 VREAAKRVLGMRPYDVQLIGALVLHEGNIAEMQTGEGKTLTATMPLYLNALEGKG-VHLITVNDYLAKRDAEEMGQVYEF 145 (790)
T ss_pred HHHHHHHHhCCCCchHHHHhHHHHcCCceeeecCCCcchHHHHHHHHHHHHcCCC-eEEEeCCHHHHHHHHHHHHHHHhh
Q ss_pred cccccccCCCCCCcCCCCccccccceEEeehhhh-----hhccccccchHHHHHHHhccCCCceEEeecchhc
Q 038397 297 CIEVHALNKLPYSKLDSRSVGIREGVVFLTYSSL-----IASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKA 364 (1102)
Q Consensus 297 ~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L-----~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~a 364 (1102)
----+.+..-.......+.....-.|+++|-+.| +..-......+-| ..--++|+||+|.+
T Consensus 146 lGl~v~~i~g~~~~~~~r~~~y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~-------r~~~~~IvDEaDsi 211 (790)
T PRK09200 146 LGLTVGLNFSDIDDASEKKAIYEADIIYTTNSELGFDYLRDNLADSKEDKVQ-------RPLNYAIIDEIDSI 211 (790)
T ss_pred cCCeEEEEeCCCCcHHHHHHhcCCCEEEECCccccchhHHhccccchhhhcc-------cccceEEEeccccc
No 397
>PRK05398 formyl-coenzyme A transferase; Provisional
Probab=30.95 E-value=52 Score=39.50 Aligned_cols=93 Identities=22% Similarity=0.298 Sum_probs=51.7
Q ss_pred HhhhhhhCCCcccccccCCCCCCcCCCCcc-ccc--cceEEeehhhhhhc---------cccccchHHHHHHHhccCCCc
Q 038397 287 RRDLDDVGATCIEVHALNKLPYSKLDSRSV-GIR--EGVVFLTYSSLIAS---------SEKGRSRLQQLVQWCGSGYDG 354 (1102)
Q Consensus 287 ~RDl~diG~~~i~v~~l~~~~~~~~~~~~~-~~~--~GvlF~TYs~L~~~---------~~~~~sRl~Ql~~W~g~dfdg 354 (1102)
-+=|.|+||+-|+|-|... |+...... ... .+..|. ++... +..|+..|..|++++ |
T Consensus 23 ~~lLAdlGA~VIKVE~p~~---GD~~R~~~~~~~~~~s~~f~---~~NrgKrsi~lDLk~~eGr~~l~~Lv~~A----D- 91 (416)
T PRK05398 23 TQLLAWFGADVIKVERPGV---GDVTRNQLRDIPDVDSLYFT---MLNSNKRSITLDTKTPEGKEVLEKLIREA----D- 91 (416)
T ss_pred HHHHHHcCCCEEEecCCCC---CCcccccCCCCCCcccHHHH---HcCCCCeEEEeeCCCHHHHHHHHHHHhcC----C-
Confidence 3668899999999987531 21100000 011 122232 22211 123578899999886 4
Q ss_pred eEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCC
Q 038397 355 LVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGA 402 (1102)
Q Consensus 355 vivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATga 402 (1102)
|+|- |.-++ .-.+-|+---.|...- -|+||||-||-
T Consensus 92 Vvie-------n~rpg---~~~rlGl~~e~L~~~n--P~LI~~sisg~ 127 (416)
T PRK05398 92 VLVE-------NFGPG---ALDRMGFTWERIQEIN--PRLIVASIKGF 127 (416)
T ss_pred EEEE-------CCCcc---hHHHcCCCHHHHHhhC--cCEEEEEEeeC
Confidence 3331 23221 2245677777777774 47999999983
No 398
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=30.92 E-value=22 Score=38.63 Aligned_cols=27 Identities=30% Similarity=0.518 Sum_probs=18.0
Q ss_pred eecCCcceEEE-----e--CCC-----cceecCCCCCCC
Q 038397 18 VRCAGCHIILT-----V--GPG-----LTEFICGTCNLP 44 (1102)
Q Consensus 18 ~~C~~C~a~l~-----~--~pg-----~~~~~Cp~C~~~ 44 (1102)
+.|++||.... + -|. +..|.|+.||+.
T Consensus 1 ~~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr 39 (192)
T TIGR00310 1 IDCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYR 39 (192)
T ss_pred CcCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCc
Confidence 36999985432 1 243 357899999984
No 399
>PRK11032 hypothetical protein; Provisional
Probab=30.85 E-value=34 Score=36.26 Aligned_cols=29 Identities=28% Similarity=0.511 Sum_probs=24.7
Q ss_pred ceecCCCccceeeccCCCccccCCCCCcc
Q 038397 95 IQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
..+.|.+||-.+++-+--.=-+||-||..
T Consensus 123 G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 123 GNLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred ceEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 45999999999999877666699999975
No 400
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=30.81 E-value=33 Score=31.38 Aligned_cols=35 Identities=20% Similarity=0.359 Sum_probs=27.6
Q ss_pred cceecCCCccceeeccCCCc-cccCCCCCccccccc
Q 038397 94 KIQLPCANCKAILNVPHGLV-RFSCPQCAVELAVDM 128 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~-~f~Cp~C~~~L~v~~ 128 (1102)
-+.+.|..|+-.+.|=.--. .-.|..||.-|+-+.
T Consensus 17 Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~PT 52 (67)
T COG2051 17 FLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEPT 52 (67)
T ss_pred EEEEECCCCCCEEEEeccCceEEEecccccEEEecC
Confidence 35699999999987754433 459999999999865
No 401
>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs. A related protein is found in archaea.
Probab=30.74 E-value=1e+02 Score=31.61 Aligned_cols=50 Identities=14% Similarity=0.371 Sum_probs=37.6
Q ss_pred EeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCC
Q 038397 245 FIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGAT 296 (1102)
Q Consensus 245 ~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~ 296 (1102)
++.-.+|+||+-...-++++.-.+|.+ ++|+|...+ ..+..+.+..+|.+
T Consensus 3 li~G~~G~GKT~l~~~~~~~~~~~g~~-v~~~s~e~~-~~~~~~~~~~~g~~ 52 (187)
T cd01124 3 LLSGGPGTGKTTFALQFLYAGLARGEP-GLYVTLEES-PEELIENAESLGWD 52 (187)
T ss_pred EEEcCCCCCHHHHHHHHHHHHHHCCCc-EEEEECCCC-HHHHHHHHHHcCCC
Confidence 444459999999888888888888865 999998643 55666667777654
No 402
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=30.55 E-value=36 Score=29.79 Aligned_cols=30 Identities=20% Similarity=0.606 Sum_probs=20.7
Q ss_pred ccceecCCCccceee----ccCCCccccCCCCCc
Q 038397 93 TKIQLPCANCKAILN----VPHGLVRFSCPQCAV 122 (1102)
Q Consensus 93 t~~~~~C~~C~A~~~----vp~~~~~f~Cp~C~~ 122 (1102)
.+..+-|++|...-- ..-...+|.||+||.
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred CceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 355689999976432 223334899999996
No 403
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=30.54 E-value=63 Score=41.79 Aligned_cols=54 Identities=20% Similarity=0.242 Sum_probs=37.4
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHh-ccCceEEEEEcCC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWH-HGRRKALWISVGS 280 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l-~Gr~~~~w~s~s~ 280 (1102)
.||+.|.+||.++...+ + =++|-.++|+||+-.+.+|+ +-|. +|. +++++..++
T Consensus 352 ~Ls~~Q~~Av~~i~~s~--------~-~~il~G~aGTGKTtll~~i~-~~~~~~g~-~V~~~ApTg 406 (744)
T TIGR02768 352 RLSEEQYEAVRHVTGSG--------D-IAVVVGRAGTGKSTMLKAAR-EAWEAAGY-RVIGAALSG 406 (744)
T ss_pred CCCHHHHHHHHHHhcCC--------C-EEEEEecCCCCHHHHHHHHH-HHHHhCCC-eEEEEeCcH
Confidence 58999999998876422 2 34566779999999888865 4443 454 366665543
No 404
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=30.14 E-value=33 Score=36.03 Aligned_cols=26 Identities=23% Similarity=0.438 Sum_probs=17.0
Q ss_pred eecCCcceEE-------EeCCC--cc-eecCCCCCC
Q 038397 18 VRCAGCHIIL-------TVGPG--LT-EFICGTCNL 43 (1102)
Q Consensus 18 ~~C~~C~a~l-------~~~pg--~~-~~~Cp~C~~ 43 (1102)
++|+.||-.- ..+|| +. ...||.||.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~ 36 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGK 36 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCC
Confidence 5789998422 34566 22 378999986
No 405
>PRK06450 threonine synthase; Validated
Probab=30.13 E-value=24 Score=41.21 Aligned_cols=30 Identities=23% Similarity=0.423 Sum_probs=23.0
Q ss_pred ceeecCCcceEEEeCCCcceecCCCCCCCCCCC
Q 038397 16 VQVRCAGCHIILTVGPGLTEFICGTCNLPQMLP 48 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~ 48 (1102)
|.++|..||.+. ++ ...+.||.||-+..+.
T Consensus 2 ~~~~C~~Cg~~~--~~-~~~~~C~~cg~~l~~~ 31 (338)
T PRK06450 2 VKEVCMKCGKER--ES-IYEIRCKKCGGPFEIL 31 (338)
T ss_pred ceeEECCcCCcC--CC-cccccCCcCCCEeEEe
Confidence 568999999985 45 4468999999665553
No 406
>PHA03368 DNA packaging terminase subunit 1; Provisional
Probab=30.07 E-value=1.8e+02 Score=37.39 Aligned_cols=122 Identities=14% Similarity=0.250 Sum_probs=64.2
Q ss_pred eEeecCCCCCcchhhHHHHHHHH--hccCceEEEEEcC----CchhhhHHhhhhhhCCCcccccccCCCCCCcCCCCcc-
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENW--HHGRRKALWISVG----SDLKFDARRDLDDVGATCIEVHALNKLPYSKLDSRSV- 316 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~--l~Gr~~~~w~s~s----~~L~~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~- 316 (1102)
|+++=. .||+-.+.++|+--. ..|.+ .+|+.-. ...+.....=+........ +..+ .| +.+
T Consensus 259 flVPRR--~GKTwivv~iI~~ll~s~~Gi~-IgytAH~~~ts~~vF~eI~~~le~~f~~~~-v~~v----kG----e~I~ 326 (738)
T PHA03368 259 FLVPRR--HGKTWFLVPLIALALATFRGIK-IGYTAHIRKATEPVFEEIGARLRQWFGASR-VDHV----KG----ETIS 326 (738)
T ss_pred EEeccc--CCchhhHHHHHHHHHHhCCCCE-EEEEcCcHHHHHHHHHHHHHHHhhhcchhh-eeee----cC----cEEE
Confidence 444443 379999988888776 45765 7776533 3333333332222211111 1111 11 233
Q ss_pred -ccccc----eEEe-ehhhhhhccccccchHHHHHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCC
Q 038397 317 -GIREG----VVFL-TYSSLIASSEKGRSRLQQLVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLP 390 (1102)
Q Consensus 317 -~~~~G----vlF~-TYs~L~~~~~~~~sRl~Ql~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP 390 (1102)
.++.| ++|. ++.+ .+-+ |.+|| ++|+||+|-.+.. +=.+++-+.+.-
T Consensus 327 i~f~nG~kstI~FaSarnt---NsiR------------GqtfD-LLIVDEAqFIk~~----------al~~ilp~l~~~- 379 (738)
T PHA03368 327 FSFPDGSRSTIVFASSHNT---NGIR------------GQDFN-LLFVDEANFIRPD----------AVQTIMGFLNQT- 379 (738)
T ss_pred EEecCCCccEEEEEeccCC---CCcc------------CCccc-EEEEechhhCCHH----------HHHHHHHHHhcc-
Confidence 34433 5664 3221 1111 34577 8899999987732 222333333333
Q ss_pred CccEEEEecCCCCC
Q 038397 391 EARVVYCSATGASE 404 (1102)
Q Consensus 391 ~ARvvY~SATgase 404 (1102)
++.++|+|.|..++
T Consensus 380 n~k~I~ISS~Ns~~ 393 (738)
T PHA03368 380 NCKIIFVSSTNTGK 393 (738)
T ss_pred CccEEEEecCCCCc
Confidence 89999999997765
No 407
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=29.99 E-value=55 Score=32.95 Aligned_cols=45 Identities=22% Similarity=0.338 Sum_probs=32.4
Q ss_pred chHHHHHHHhccCCCceEE----eecchhccccCCCCCCCchhHHHHHHHHhhhCCC
Q 038397 339 SRLQQLVQWCGSGYDGLVI----FDECHKAKNLVPEAGSQPTRTGEAVLELQARLPE 391 (1102)
Q Consensus 339 sRl~Ql~~W~g~dfdgviv----fDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ 391 (1102)
=....|++-+...+|||+| .+|||.-... .++...|..+++.|..
T Consensus 40 v~~~~il~Af~~GADGV~V~gC~~g~Ch~~~Gn--------~~a~~Rv~~~k~~L~~ 88 (124)
T PF02662_consen 40 VDPEFILRAFEKGADGVLVAGCHPGDCHYREGN--------YRAEKRVERLKKLLEE 88 (124)
T ss_pred cCHHHHHHHHHcCCCEEEEeCCCCCCCCcchhh--------HHHHHHHHHHHHHHHH
Confidence 3456688888888999999 5899985433 5667777777766543
No 408
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=29.86 E-value=26 Score=33.78 Aligned_cols=27 Identities=22% Similarity=0.667 Sum_probs=21.3
Q ss_pred cCCCccceeeccCCCccccCCCCCccccc
Q 038397 98 PCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 98 ~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
-|.+||.+|.... ..+.|+.|+.....
T Consensus 2 fC~~Cg~~l~~~~--~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPKN--GVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccCC--CeEECcCCCCcccc
Confidence 5999999996543 37999999987444
No 409
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=29.84 E-value=34 Score=30.72 Aligned_cols=30 Identities=20% Similarity=0.372 Sum_probs=18.8
Q ss_pred ccceeecCCcceEEEeCCCcceecCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
..|.+.|..|++.-+|+=-.-.++|+.|+-
T Consensus 27 ~~v~IlCNDC~~~s~v~fH~lg~KC~~C~S 56 (61)
T PF14599_consen 27 KKVWILCNDCNAKSEVPFHFLGHKCSHCGS 56 (61)
T ss_dssp -EEEEEESSS--EEEEE--TT----TTTS-
T ss_pred CEEEEECCCCCCccceeeeHhhhcCCCCCC
Confidence 568899999999999999999999999983
No 410
>PRK08939 primosomal protein DnaI; Reviewed
Probab=29.74 E-value=97 Score=35.80 Aligned_cols=39 Identities=21% Similarity=0.272 Sum_probs=31.5
Q ss_pred CcceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcC
Q 038397 240 ARAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVG 279 (1102)
Q Consensus 240 ~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s 279 (1102)
...|+++--..|+||+..++||..+-..+|.+ +++++++
T Consensus 155 ~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~-v~~~~~~ 193 (306)
T PRK08939 155 KVKGLYLYGDFGVGKSYLLAAIANELAKKGVS-STLLHFP 193 (306)
T ss_pred CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCC-EEEEEHH
Confidence 34677664459999999999999998888876 8888875
No 411
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=29.74 E-value=35 Score=30.60 Aligned_cols=30 Identities=27% Similarity=0.544 Sum_probs=26.8
Q ss_pred eecCCcceEEEeCCCcceecCCCCCCCCCC
Q 038397 18 VRCAGCHIILTVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l 47 (1102)
+-|+-|+..|.+-.-..+|.|+.|+.+-.|
T Consensus 9 LaCP~~kg~L~~~~~~~~L~c~~~~~aYpI 38 (60)
T COG2835 9 LACPVCKGPLVYDEEKQELICPRCKLAYPI 38 (60)
T ss_pred eeccCcCCcceEeccCCEEEecccCceeec
Confidence 459999999999999999999999976655
No 412
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=29.59 E-value=1e+02 Score=40.51 Aligned_cols=51 Identities=25% Similarity=0.351 Sum_probs=29.8
Q ss_pred ceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCCCCCccc--hhhhcccc
Q 038397 354 GLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGASEPRNMG--YMVRLGLW 417 (1102)
Q Consensus 354 gvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~--ym~RLGLW 417 (1102)
.|||+||+|++-. ....+.|++-+..|. .+++.=+| +++..|. .-+|.-++
T Consensus 122 KV~IIDEad~lt~----------~a~NaLLK~LEEpP~-~~~fIl~t--t~~~kLl~TIrSRc~~v 174 (824)
T PRK07764 122 KIFIIDEAHMVTP----------QGFNALLKIVEEPPE-HLKFIFAT--TEPDKVIGTIRSRTHHY 174 (824)
T ss_pred eEEEEechhhcCH----------HHHHHHHHHHhCCCC-CeEEEEEe--CChhhhhHHHHhheeEE
Confidence 5999999999852 234466666666554 34333344 5665554 34555444
No 413
>KOG1830 consensus Wiskott Aldrich syndrome proteins [Cytoskeleton]
Probab=29.53 E-value=2.7e+02 Score=33.79 Aligned_cols=28 Identities=25% Similarity=0.119 Sum_probs=14.9
Q ss_pred hHHHHHHHHhccCceEEEEEcCCchh-hhHHhhhh
Q 038397 258 IAGLIWENWHHGRRKALWISVGSDLK-FDARRDLD 291 (1102)
Q Consensus 258 ~AgiI~~n~l~Gr~~~~w~s~s~~L~-~Da~RDl~ 291 (1102)
+|.||. ||.+|=+|-|.|=- ++=+-||.
T Consensus 489 vatiLs------RRiaveysdseDdssefDe~dW~ 517 (518)
T KOG1830|consen 489 VATILS------RRIAVEYSDSEDDSSEFDEDDWS 517 (518)
T ss_pred HHHHHH------HHHHHHhccCccccccccccccc
Confidence 555554 35566666666544 33344553
No 414
>PRK07220 DNA topoisomerase I; Validated
Probab=29.44 E-value=61 Score=41.89 Aligned_cols=27 Identities=26% Similarity=0.461 Sum_probs=18.0
Q ss_pred eecCCcceEEEeCC---CcceecC---CCCCCC
Q 038397 18 VRCAGCHIILTVGP---GLTEFIC---GTCNLP 44 (1102)
Q Consensus 18 ~~C~~C~a~l~~~p---g~~~~~C---p~C~~~ 44 (1102)
..|+.||..+.... |-..+.| |.|...
T Consensus 590 ~~CP~Cg~~l~~r~~r~g~~f~gCs~yp~C~~~ 622 (740)
T PRK07220 590 GKCPLCGSDLMVRRSKRGSRFIGCEGYPECTFS 622 (740)
T ss_pred cccccCCCeeeEEecCCCceEEEcCCCCCCCce
Confidence 47999998876533 3335678 568753
No 415
>PRK15319 AIDA autotransporter-like protein ShdA; Provisional
Probab=29.40 E-value=77 Score=44.42 Aligned_cols=60 Identities=5% Similarity=-0.109 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCccceeecCCcceEEEeCCCcceecCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccccc
Q 038397 3 QPPVPPPPPPNVGVQVRCAGCHIILTVGPGLTEFICGTCNLPQMLPPELMPASTGGSVPNNTTSSNTTNSTRPTHMKAAS 82 (1102)
Q Consensus 3 ~~~~~~~~~~~~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~p~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (1102)
.|+++|+++||..+ .|-.-|.||++|.+.||+.||+|....+.+.||..
T Consensus 1671 pp~~~~~~~P~~~~-------------------------------d~~~~~~PP~~p~~~~~v~Pp~p~~~~~~~tPP~~ 1719 (2039)
T PRK15319 1671 DDDSGGDDTPSDGG-------------------------------DDGGNVTPPDDGGDGGNVTPPDDGGDGGDVTPPDH 1719 (2039)
T ss_pred CCccccccCCCCcc-------------------------------ccccCCCCCccccccccCCCCCccccccCCCCCCc
Q ss_pred CCCCCCCCCCc
Q 038397 83 SHVPALGIDPT 93 (1102)
Q Consensus 83 ~~~~a~~~~~t 93 (1102)
...+.+-+-|+
T Consensus 1720 ~g~~~P~YRPE 1730 (2039)
T PRK15319 1720 GGDVAPQYRAD 1730 (2039)
T ss_pred CCCCcccccCc
No 416
>PRK06835 DNA replication protein DnaC; Validated
Probab=29.31 E-value=88 Score=36.59 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=29.6
Q ss_pred ceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcC
Q 038397 242 AGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVG 279 (1102)
Q Consensus 242 ~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s 279 (1102)
.++++--.+|+||+..+.+|..+-.-+|++ +++++..
T Consensus 184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~-V~y~t~~ 220 (329)
T PRK06835 184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKS-VIYRTAD 220 (329)
T ss_pred CcEEEECCCCCcHHHHHHHHHHHHHHCCCe-EEEEEHH
Confidence 566664469999999999998888878864 8988873
No 417
>COG1799 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.23 E-value=65 Score=34.39 Aligned_cols=30 Identities=30% Similarity=0.308 Sum_probs=26.0
Q ss_pred HHHHHHHHCCCeEEEEEecchhHHHHHHHH
Q 038397 538 RLAKKALAEGKCVVIGLQSTGEARTEEAVT 567 (1102)
Q Consensus 538 ~~a~eal~~Gk~vVIgLqSTGEA~~~~~l~ 567 (1102)
..+-..|++||||||=||.-+.+-.++.++
T Consensus 88 ~~ia~~lk~~k~Vvinl~~m~~~qArRivD 117 (167)
T COG1799 88 QEIADYLKNRKAVVINLQRMDPAQARRIVD 117 (167)
T ss_pred HHHHHHHhcCceEEEEeeeCCHHHHHHHHH
Confidence 345678999999999999999999998884
No 418
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=28.99 E-value=29 Score=39.65 Aligned_cols=35 Identities=17% Similarity=0.393 Sum_probs=27.0
Q ss_pred ccceeecCCcceEEEeCC-CcceecCCCCCCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGP-GLTEFICGTCNLPQMLP 48 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~p-g~~~~~Cp~C~~~~~l~ 48 (1102)
..+=.+|+.|+..+..+. +.....||.|++..+|.
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~ 60 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRIS 60 (294)
T ss_pred CCceeECCCccceeeHHHHHhhhhcccccCcccccC
Confidence 666788999999886544 33468999999988774
No 419
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=28.67 E-value=3.4e+02 Score=35.18 Aligned_cols=23 Identities=22% Similarity=0.239 Sum_probs=17.0
Q ss_pred HHHHhccCCCceEEeecchhccc
Q 038397 344 LVQWCGSGYDGLVIFDECHKAKN 366 (1102)
Q Consensus 344 l~~W~g~dfdgvivfDEcH~akn 366 (1102)
|.+.+.....+||+|||.|||-.
T Consensus 545 l~~~~~~~p~~VvllDEieka~~ 567 (731)
T TIGR02639 545 LTEAVRKHPHCVLLLDEIEKAHP 567 (731)
T ss_pred HHHHHHhCCCeEEEEechhhcCH
Confidence 44455455678999999999863
No 420
>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=28.58 E-value=1.6e+02 Score=40.56 Aligned_cols=115 Identities=15% Similarity=0.107 Sum_probs=67.5
Q ss_pred hhcCCc-ceEEEEeccccccccccccccccc----------ccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEe
Q 038397 807 LFMDGK-KLVAIISEAGSAGVSLQADRRAAN----------QKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRII 875 (1102)
Q Consensus 807 ~Fm~G~-K~VAIISeAaSTGISLhADrr~~N----------QRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l 875 (1102)
.|..+. ..|.|-++-|.|||..--=+-|.| -+..+.-...-|=|-..|+|+-||++|.+ .+-.|++.
T Consensus 324 vf~~~~~rkIVLATNIAEtSLTIpgV~yVIDsGl~r~~~yd~~~~~~~L~~~~ISkasa~QRaGRAGR~~--~G~cyRLy 401 (1283)
T TIGR01967 324 VFQPHSGRRIVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRVA--PGICIRLY 401 (1283)
T ss_pred HhCCCCCceEEEeccHHHhccccCCeeEEEeCCCccccccccccCccccCCccCCHHHHHHHhhhhCCCC--CceEEEec
Confidence 455443 578899999999988765554444 22233322233448999999999999996 55566665
Q ss_pred ecCcc---------chhh-hHHHHHHHHhhcCCccccccccCCCCCcCCcCChHHHHHHHHHHHHHh
Q 038397 876 FTNLG---------GERR-FASIVAKRLESLGALTQGDRRAGLSLSAYNYDSAFGKKALMMMYRGIM 932 (1102)
Q Consensus 876 ~T~l~---------GErR-FaS~VAkRLeSLGALT~GdRra~~~ls~fNldn~YGr~AL~~~~~~i~ 932 (1102)
+-+-- -=.| -++.|.=+|.++|. .++..|.|=.+=...+++.-++.+.
T Consensus 402 te~~~~~~~~~~~PEIlR~~L~~viL~l~~lg~---------~di~~f~fldpP~~~~i~~A~~~L~ 459 (1283)
T TIGR01967 402 SEEDFNSRPEFTDPEILRTNLASVILQMLALRL---------GDIAAFPFIEAPDPRAIRDGFRLLE 459 (1283)
T ss_pred CHHHHHhhhhccCcccccccHHHHHHHHHhcCC---------CCcccccCCCCCCHHHHHHHHHHHH
Confidence 43211 0011 14455556767663 1244555555555555555555443
No 421
>PRK12722 transcriptional activator FlhC; Provisional
Probab=28.40 E-value=38 Score=36.72 Aligned_cols=29 Identities=21% Similarity=0.387 Sum_probs=21.1
Q ss_pred cceecCCCccceeecc-CCC-ccccCCCCCc
Q 038397 94 KIQLPCANCKAILNVP-HGL-VRFSCPQCAV 122 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp-~~~-~~f~Cp~C~~ 122 (1102)
....+|..||-..-+- +.+ .+|.||+|.-
T Consensus 132 L~l~~C~~Cgg~fv~~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 132 LQLSSCNCCGGHFVTHAHDPVGSFVCGLCQP 162 (187)
T ss_pred EeeccCCCCCCCeeccccccCCCCcCCCCCC
Confidence 4457899999875533 333 3899999987
No 422
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=28.03 E-value=22 Score=38.52 Aligned_cols=29 Identities=24% Similarity=0.696 Sum_probs=23.5
Q ss_pred cceecCCCccceeeccCCCccc-------cCCCCCcc
Q 038397 94 KIQLPCANCKAILNVPHGLVRF-------SCPQCAVE 123 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f-------~Cp~C~~~ 123 (1102)
.+-+.|.+|| ...++|.+.++ +|.-||.-
T Consensus 4 ~iy~~Cp~Cg-~eev~hEVik~~g~~~lvrC~eCG~V 39 (201)
T COG1326 4 EIYIECPSCG-SEEVSHEVIKERGREPLVRCEECGTV 39 (201)
T ss_pred eEEEECCCCC-cchhhHHHHHhcCCceEEEccCCCcE
Confidence 4568999999 88888876654 89999964
No 423
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=28.00 E-value=25 Score=28.33 Aligned_cols=26 Identities=27% Similarity=0.574 Sum_probs=20.0
Q ss_pred ecCCcceEEE--eCCCcceecCCCCCCC
Q 038397 19 RCAGCHIILT--VGPGLTEFICGTCNLP 44 (1102)
Q Consensus 19 ~C~~C~a~l~--~~pg~~~~~Cp~C~~~ 44 (1102)
-|..||++.+ +.|-..+-.|..||-+
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~ 30 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGE 30 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEB
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCe
Confidence 4999999984 5778888899999963
No 424
>PF12846 AAA_10: AAA-like domain
Probab=27.97 E-value=95 Score=33.96 Aligned_cols=52 Identities=19% Similarity=0.332 Sum_probs=34.4
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchhhhHHhhhhhhCCCcccc
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLKFDARRDLDDVGATCIEV 300 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~~Da~RDl~diG~~~i~v 300 (1102)
.+++|. ||.||+..+..++.+.+..|.. .++|...++... -.+..|+..+.+
T Consensus 4 ~~i~G~-tGsGKT~~~~~l~~~~~~~g~~-~~i~D~~g~~~~----~~~~~~~~~i~~ 55 (304)
T PF12846_consen 4 TLILGK-TGSGKTTLLKNLLEQLIRRGPR-VVIFDPKGDYSP----LARALGGQYIDI 55 (304)
T ss_pred EEEECC-CCCcHHHHHHHHHHHHHHcCCC-EEEEcCCchHHH----HHHhcCceEEEe
Confidence 355665 9999999999888888888865 777744433322 233345555543
No 425
>PRK07219 DNA topoisomerase I; Validated
Probab=27.88 E-value=73 Score=41.69 Aligned_cols=33 Identities=24% Similarity=0.340 Sum_probs=22.5
Q ss_pred eeecCCcceEEEeC---CCcceecC---CCCCCCCCCCC
Q 038397 17 QVRCAGCHIILTVG---PGLTEFIC---GTCNLPQMLPP 49 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~---pg~~~~~C---p~C~~~~~l~p 49 (1102)
..+|+.||..+.+. .|...+.| |.|.....||.
T Consensus 602 ~~~CP~Cg~~l~~r~~~~g~~F~gCs~yp~C~~t~~lp~ 640 (822)
T PRK07219 602 IGKCPECGGDLIIIRTDKGSRFVGCSGYPDCRNTFPLPS 640 (822)
T ss_pred cCcCCCCCCcceeeeccCCceeeecCCCcCCCCeeecCC
Confidence 35799999877543 34345789 55997766654
No 426
>PHA02942 putative transposase; Provisional
Probab=27.88 E-value=36 Score=40.53 Aligned_cols=27 Identities=22% Similarity=0.527 Sum_probs=21.0
Q ss_pred eeecCCcceEEEeCCCcceecCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
...|+.||.... ..+.-.|.||.||+.
T Consensus 325 Sq~Cs~CG~~~~-~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 325 SVSCPKCGHKMV-EIAHRYFHCPSCGYE 351 (383)
T ss_pred CccCCCCCCccC-cCCCCEEECCCCCCE
Confidence 467999998753 445568999999984
No 427
>PF13245 AAA_19: Part of AAA domain
Probab=27.84 E-value=88 Score=28.72 Aligned_cols=47 Identities=23% Similarity=0.263 Sum_probs=36.4
Q ss_pred eEeecCCCCCcchhhHHHHHHHHhc---cCceEEEEEcCCchhhhHHhhh
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENWHH---GRRKALWISVGSDLKFDARRDL 290 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~l~---Gr~~~~w~s~s~~L~~Da~RDl 290 (1102)
|++--+.|-||+.+++.+|.+.+.. +.++.+.++-++.......+-+
T Consensus 13 ~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t~~aa~~l~~rl 62 (76)
T PF13245_consen 13 FVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPTRAAADELRERL 62 (76)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCCHHHHHHHHHHH
Confidence 3446679999999999999998864 1345899999988777776666
No 428
>KOG1546 consensus Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=27.70 E-value=83 Score=36.87 Aligned_cols=23 Identities=35% Similarity=0.818 Sum_probs=18.3
Q ss_pred CCCCCCCccceeecCCcceEEEeC
Q 038397 7 PPPPPPNVGVQVRCAGCHIILTVG 30 (1102)
Q Consensus 7 ~~~~~~~~~~~~~C~~C~a~l~~~ 30 (1102)
+|-.|||.++- +|++|.+.-.++
T Consensus 11 ~p~~~pp~ar~-q~~~~~~~~~~~ 33 (362)
T KOG1546|consen 11 RPMAPPPGARY-QCAGCHAVTQIA 33 (362)
T ss_pred CCCCCCCCCcc-cccccceeeeec
Confidence 34567788888 999999988665
No 429
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=27.56 E-value=25 Score=42.18 Aligned_cols=36 Identities=28% Similarity=0.581 Sum_probs=27.8
Q ss_pred eecCCCccceee-------ccCCCccccCCCCCcccccccccc
Q 038397 96 QLPCANCKAILN-------VPHGLVRFSCPQCAVELAVDMSKV 131 (1102)
Q Consensus 96 ~~~C~~C~A~~~-------vp~~~~~f~Cp~C~~~L~v~~~~~ 131 (1102)
--.|.+|+...+ +...-..|+|-+|+.+|+.|.+++
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~ 170 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKL 170 (436)
T ss_pred cccCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccC
Confidence 478999998733 233345999999999999987665
No 430
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=27.50 E-value=39 Score=29.82 Aligned_cols=23 Identities=39% Similarity=0.953 Sum_probs=16.2
Q ss_pred CCCccceeeccCCCccccCCCCCccc
Q 038397 99 CANCKAILNVPHGLVRFSCPQCAVEL 124 (1102)
Q Consensus 99 C~~C~A~~~vp~~~~~f~Cp~C~~~L 124 (1102)
|--|+..+ .+...|.||.||.+.
T Consensus 2 Cpv~~~~~---~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 2 CPVCKKDL---PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCcccc---ccccCCcCCCCCCcC
Confidence 44455544 556789999999874
No 431
>PRK07591 threonine synthase; Validated
Probab=27.50 E-value=32 Score=41.29 Aligned_cols=31 Identities=23% Similarity=0.539 Sum_probs=23.3
Q ss_pred cceeecCCcceEEEeCCCcceecCCCCCCCCCCC
Q 038397 15 GVQVRCAGCHIILTVGPGLTEFICGTCNLPQMLP 48 (1102)
Q Consensus 15 ~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~ 48 (1102)
...++|..||.++. +... +.||.||-...+-
T Consensus 16 ~~~l~C~~Cg~~~~--~~~~-~~C~~cg~~l~~~ 46 (421)
T PRK07591 16 AVALKCRECGAEYP--LGPI-HVCEECFGPLEVA 46 (421)
T ss_pred eeEEEeCCCCCcCC--CCCC-ccCCCCCCeEEEE
Confidence 34689999999864 4555 9999999655553
No 432
>KOG1925 consensus Rac1 GTPase effector FHOS [Signal transduction mechanisms; Cytoskeleton]
Probab=27.37 E-value=1.1e+02 Score=37.67 Aligned_cols=32 Identities=25% Similarity=0.468 Sum_probs=19.6
Q ss_pred ccceeeccCCCccccCCCCCc------ccccccccccccC
Q 038397 102 CKAILNVPHGLVRFSCPQCAV------ELAVDMSKVKQFF 135 (1102)
Q Consensus 102 C~A~~~vp~~~~~f~Cp~C~~------~L~v~~~~~~~~~ 135 (1102)
=-+.+.-|||+.+. -+|+. +.++|-.++.++|
T Consensus 290 r~~~~~~~~Gv~~~--r~~~t~W~s~D~~~~D~~r~~~LF 327 (817)
T KOG1925|consen 290 RDVKLAGGHGVSAS--RPCATLWASLDPVSVDTARLEHLF 327 (817)
T ss_pred ecceecCCCCCccc--cccchhhhccCcceecHHHHHHHH
Confidence 34556678887754 24443 2346667777777
No 433
>PRK12860 transcriptional activator FlhC; Provisional
Probab=27.32 E-value=45 Score=36.24 Aligned_cols=29 Identities=17% Similarity=0.358 Sum_probs=21.6
Q ss_pred ccceecCCCccceeeccCC--CccccCCCCC
Q 038397 93 TKIQLPCANCKAILNVPHG--LVRFSCPQCA 121 (1102)
Q Consensus 93 t~~~~~C~~C~A~~~vp~~--~~~f~Cp~C~ 121 (1102)
.....+|..||-..-+-.. ..+|.||+|.
T Consensus 131 ~L~l~~C~~Cgg~fv~~~~e~~~~f~CplC~ 161 (189)
T PRK12860 131 MLQLARCCRCGGKFVTHAHDLRHNFVCGLCQ 161 (189)
T ss_pred CeeeccCCCCCCCeeccccccCCCCcCCCCC
Confidence 4567899999987554333 3389999999
No 434
>KOG0344 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=27.27 E-value=59 Score=40.56 Aligned_cols=65 Identities=23% Similarity=0.324 Sum_probs=54.5
Q ss_pred HHhhhcCCcceEEEEecccccccccccccccccccceeEEEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecC
Q 038397 804 EKQLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTN 878 (1102)
Q Consensus 804 Ek~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~ 878 (1102)
+-++|-.|++.|+|-++--+-||-+|=-.-+.| --+|-|.-.-|.++|||+|-.+-.- -..+.||
T Consensus 430 ~~~~FR~g~IwvLicTdll~RGiDf~gvn~VIn--------yD~p~s~~syihrIGRtgRag~~g~--Aitfytd 494 (593)
T KOG0344|consen 430 TMERFRIGKIWVLICTDLLARGIDFKGVNLVIN--------YDFPQSDLSYIHRIGRTGRAGRSGK--AITFYTD 494 (593)
T ss_pred HHHHHhccCeeEEEehhhhhccccccCcceEEe--------cCCCchhHHHHHHhhccCCCCCCcc--eEEEecc
Confidence 347999999999999999999999997777777 6799999999999999999988642 2344455
No 435
>PF00290 Trp_syntA: Tryptophan synthase alpha chain; InterPro: IPR002028 Tryptophan synthase (4.2.1.20 from EC) catalyzes the last step in the biosynthesis of tryptophan [, ]: L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O It has two functional domains, each found in bacteria and plants on a separate subunit. In Escherichia coli, the 2 subunits, A and B, are encoded by the trpA and trpB genes respectively. The alpha chain is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and the beta chain IPR006653 from INTERPRO is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together in a single multifunctional protein, in the order: (NH2-A-B-COOH) [, ]. The two domains of the Neurospora crassa polypeptide are linked by a connector of 54-amino acid residues that has less than 25% identity to the 45-residue connector of the Saccharomyces cerevisiae (Baker's yeast) polypeptide. Two acidic residues are believed to serve as proton donors/acceptors in the enzyme's catalytic mechanism.; GO: 0004834 tryptophan synthase activity, 0006568 tryptophan metabolic process; PDB: 1TJR_B 1RD5_B 1K8X_A 1QOQ_A 1KFE_A 1KFB_A 2CLO_A 1TTP_A 2RH9_A 1K7F_A ....
Probab=27.15 E-value=45 Score=37.81 Aligned_cols=120 Identities=20% Similarity=0.374 Sum_probs=61.8
Q ss_pred chhhhHHhhhhhhCCCcccc-cccCCCCC-CcC---------CC-----------Cccc---cccceEEeehhhhhhccc
Q 038397 281 DLKFDARRDLDDVGATCIEV-HALNKLPY-SKL---------DS-----------RSVG---IREGVVFLTYSSLIASSE 335 (1102)
Q Consensus 281 ~L~~Da~RDl~diG~~~i~v-~~l~~~~~-~~~---------~~-----------~~~~---~~~GvlF~TYs~L~~~~~ 335 (1102)
+-..++-+-|.+=|++-|++ +|.+.=.+ |.+ .. +.+. .+.-+++.||...+-..
T Consensus 24 ~~~~~~~~~l~~~GaD~iEiGiPfSDP~ADGpvIq~A~~rAL~~G~~~~~~~~~~~~ir~~~~~~pivlm~Y~N~i~~~- 102 (259)
T PF00290_consen 24 ETTLEILKALEEAGADIIEIGIPFSDPVADGPVIQKASQRALKNGFTLEKIFELVKEIRKKEPDIPIVLMTYYNPIFQY- 102 (259)
T ss_dssp HHHHHHHHHHHHTTBSSEEEE--SSSCTTSSHHHHHHHHHHHHTT--HHHHHHHHHHHHHHCTSSEEEEEE-HHHHHHH-
T ss_pred HHHHHHHHHHHHcCCCEEEECCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHHHHHHHHhccCCCCCEEEEeeccHHhcc-
Confidence 45667777888888887775 34443110 100 00 0111 34459999999887421
Q ss_pred cccchHHHHHHHhcc-CCCceEEee----cchhccccCCCCC------CCchhHHHHHHHHhhhCCCccEEEE-ecCCCC
Q 038397 336 KGRSRLQQLVQWCGS-GYDGLVIFD----ECHKAKNLVPEAG------SQPTRTGEAVLELQARLPEARVVYC-SATGAS 403 (1102)
Q Consensus 336 ~~~sRl~Ql~~W~g~-dfdgvivfD----EcH~akn~~~~~~------~~~s~~g~avl~LQ~~lP~ARvvY~-SATgas 403 (1102)
-++..++.|.+ .+|||||-| |.+..++.....| ..|+-.-.-+..+.+. ....||+ |-+|.|
T Consensus 103 ----G~e~F~~~~~~aGvdGlIipDLP~ee~~~~~~~~~~~gl~~I~lv~p~t~~~Ri~~i~~~--a~gFiY~vs~~GvT 176 (259)
T PF00290_consen 103 ----GIERFFKEAKEAGVDGLIIPDLPPEESEELREAAKKHGLDLIPLVAPTTPEERIKKIAKQ--ASGFIYLVSRMGVT 176 (259)
T ss_dssp -----HHHHHHHHHHHTEEEEEETTSBGGGHHHHHHHHHHTT-EEEEEEETTS-HHHHHHHHHH---SSEEEEESSSSSS
T ss_pred ----chHHHHHHHHHcCCCEEEEcCCChHHHHHHHHHHHHcCCeEEEEECCCCCHHHHHHHHHh--CCcEEEeeccCCCC
Confidence 25666777764 799999987 4444443322222 1222222233333333 2345664 777776
Q ss_pred CCCc
Q 038397 404 EPRN 407 (1102)
Q Consensus 404 ep~N 407 (1102)
..++
T Consensus 177 G~~~ 180 (259)
T PF00290_consen 177 GSRT 180 (259)
T ss_dssp STTS
T ss_pred CCcc
Confidence 6544
No 436
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=27.07 E-value=47 Score=28.34 Aligned_cols=27 Identities=22% Similarity=0.754 Sum_probs=17.5
Q ss_pred eecCCcceEEEeCCC---------c------ceecCCCCCCC
Q 038397 18 VRCAGCHIILTVGPG---------L------TEFICGTCNLP 44 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg---------~------~~~~Cp~C~~~ 44 (1102)
-+|..||-+-.-..| | ..+.||.|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 579999987754444 3 35789999974
No 437
>PF13500 AAA_26: AAA domain; PDB: 3OF5_A 2IOJ_A 4A0G_B 4A0R_A 4A0H_B 4A0F_B 3FMI_C 3FPA_D 3FMF_C 3FGN_A ....
Probab=27.05 E-value=70 Score=33.80 Aligned_cols=131 Identities=18% Similarity=0.187 Sum_probs=68.0
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCchh--hhHHhhhhhhCCCcccccccCCCCCCcCCCCcccccc
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSDLK--FDARRDLDDVGATCIEVHALNKLPYSKLDSRSVGIRE 320 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~L~--~Da~RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~ 320 (1102)
=|+.|.+||+||+-..+|++..-..+|.+-..|=.+..... .|++.=-+-.|.. . ......
T Consensus 3 i~I~~t~t~vGKT~vslgL~~~l~~~g~~v~~~KPi~~~~~~d~d~~~~~~~~~~~-----------~------~~~~~~ 65 (199)
T PF13500_consen 3 IFITGTDTGVGKTVVSLGLARALRRRGIKVGYFKPIQTGPEDDEDAELIRELFGLS-----------E------PPDDPS 65 (199)
T ss_dssp EEEEESSSSSSHHHHHHHHHHHHHHTTSEEEEEEEEEESCCCSSHHHHHHHHCCTC-----------C------CHHHHE
T ss_pred EEEEeCCCCCCHHHHHHHHHHHHHhCCCceEEEeeeEecCCCCchHHHHHHHhCCC-----------c------cccccc
Confidence 37789999999999999999999999998666655544333 2222211111110 0 111124
Q ss_pred ceEEeeh-hhhhhccccc-cchHHHHH-HHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEE
Q 038397 321 GVVFLTY-SSLIASSEKG-RSRLQQLV-QWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYC 397 (1102)
Q Consensus 321 GvlF~TY-s~L~~~~~~~-~sRl~Ql~-~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~ 397 (1102)
++.|... +........+ .-.+++++ +.+..+.|-|||= ++.+ -..|.-.+....+|-+.| +|.||-+
T Consensus 66 ~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~l~~~~D~vlVE-------Gag~--~~~~~~~~~~n~dia~~L-~a~vIlV 135 (199)
T PF13500_consen 66 PYTFDEPASPHLAAELEGVDIDLERIIYKELAEEYDVVLVE-------GAGG--LMVPIFSGDLNADIAKAL-GAPVILV 135 (199)
T ss_dssp CEEESSSS-HHHHHHHHT----HHHHHHHHCHTTTCEEEEE-------ESSS--TTSECCTTEEHHHHHHHH-T-EEEEE
T ss_pred ccccCcccCHHHHhhccCCcccHHHHHHHHHhhcCCEEEEe-------CCcc--cCcccccChHHHHHHHHc-CCCEEEE
Confidence 5556543 3333222222 22277774 5666667766553 1100 012222333444555555 7888888
Q ss_pred ecC
Q 038397 398 SAT 400 (1102)
Q Consensus 398 SAT 400 (1102)
+..
T Consensus 136 ~~~ 138 (199)
T PF13500_consen 136 ASG 138 (199)
T ss_dssp EES
T ss_pred eCC
Confidence 764
No 438
>PHA01732 proline-rich protein
Probab=26.95 E-value=80 Score=30.33 Aligned_cols=9 Identities=33% Similarity=0.567 Sum_probs=3.8
Q ss_pred cceeeccCC
Q 038397 103 KAILNVPHG 111 (1102)
Q Consensus 103 ~A~~~vp~~ 111 (1102)
-|.|.+|-+
T Consensus 64 TasLrIpkq 72 (94)
T PHA01732 64 TASLRIPKQ 72 (94)
T ss_pred cceeEeecc
Confidence 344444433
No 439
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=26.71 E-value=30 Score=29.93 Aligned_cols=30 Identities=17% Similarity=0.443 Sum_probs=21.6
Q ss_pred cceecCCCccceeeccCCCccccCCCCCcc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
...--|.+||+-+-.-+-..|.+|.-||--
T Consensus 17 rk~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 17 RKNRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred EccccCCCCCCcchhhhcCceeEeccccce
Confidence 334579999985555555569999999854
No 440
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=26.70 E-value=45 Score=28.10 Aligned_cols=28 Identities=25% Similarity=0.665 Sum_probs=20.8
Q ss_pred eecCCCccceeeccCCCc---cccCCCCCcc
Q 038397 96 QLPCANCKAILNVPHGLV---RFSCPQCAVE 123 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~---~f~Cp~C~~~ 123 (1102)
...|..||....+-.... .-.||.||..
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGGE 35 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCCC
Confidence 578999999777764433 2379999984
No 441
>CHL00095 clpC Clp protease ATP binding subunit
Probab=26.66 E-value=3.7e+02 Score=35.37 Aligned_cols=51 Identities=20% Similarity=0.209 Sum_probs=30.7
Q ss_pred HHHHhccCCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhh------------CCCccEEEEecCCCCC
Q 038397 344 LVQWCGSGYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQAR------------LPEARVVYCSATGASE 404 (1102)
Q Consensus 344 l~~W~g~dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~------------lP~ARvvY~SATgase 404 (1102)
|.+.+-.....||+|||.+||-.. .-.+.+.+-+. +.++-+|.+|--|+..
T Consensus 603 l~~~~~~~p~~VvllDeieka~~~----------v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~g~~~ 665 (821)
T CHL00095 603 LTEAVRKKPYTVVLFDEIEKAHPD----------IFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKV 665 (821)
T ss_pred HHHHHHhCCCeEEEECChhhCCHH----------HHHHHHHHhccCceecCCCcEEecCceEEEEeCCcchHH
Confidence 334444455689999999997522 22233332221 4567788888877753
No 442
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=26.53 E-value=38 Score=39.10 Aligned_cols=31 Identities=23% Similarity=0.462 Sum_probs=25.0
Q ss_pred ccceeecCCcce-EEEeCCCcceecCCCCCCC
Q 038397 14 VGVQVRCAGCHI-ILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 14 ~~~~~~C~~C~a-~l~~~pg~~~~~Cp~C~~~ 44 (1102)
+..+..|+.||. .+.+.....+..|..||+-
T Consensus 8 ~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 8 EEEKLVCPECGSDKLIYDYERGEIVCADCGLV 39 (310)
T ss_pred cccCCcCcCCCCCCeeEECCCCeEeecccCCc
Confidence 344568999998 6666788899999999973
No 443
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=26.48 E-value=42 Score=27.10 Aligned_cols=29 Identities=21% Similarity=0.609 Sum_probs=22.7
Q ss_pred ccceeecCCcceEE-EeC-----CCcceecCCCCC
Q 038397 14 VGVQVRCAGCHIIL-TVG-----PGLTEFICGTCN 42 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l-~~~-----pg~~~~~Cp~C~ 42 (1102)
+.|.|.|+.|+..- .+. .|.+.|.|..|.
T Consensus 2 a~i~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 2 AKIDVHCPRCQSTEGVKKNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred CcEeeeCCCCCCCCcceeCCCCCCCCEeEecCcCC
Confidence 46889999999988 444 466789999984
No 444
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=26.36 E-value=38 Score=29.69 Aligned_cols=21 Identities=29% Similarity=0.695 Sum_probs=16.8
Q ss_pred eecCCcceEEEeCCCcceecCCCCCC
Q 038397 18 VRCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
+.|++||+ +=+.-..||.||+
T Consensus 27 ~~C~~cG~-----~~~~H~vc~~cG~ 47 (55)
T TIGR01031 27 VVCPNCGE-----FKLPHRVCPSCGY 47 (55)
T ss_pred eECCCCCC-----cccCeeECCccCe
Confidence 45999997 4566789999996
No 445
>PRK00420 hypothetical protein; Validated
Probab=26.17 E-value=41 Score=33.71 Aligned_cols=28 Identities=21% Similarity=0.440 Sum_probs=20.3
Q ss_pred eecCCcceEEEe-CCCcceecCCCCCCCCCC
Q 038397 18 VRCAGCHIILTV-GPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 18 ~~C~~C~a~l~~-~pg~~~~~Cp~C~~~~~l 47 (1102)
-.|+-||..|.= ..| +..||.||.....
T Consensus 24 ~~CP~Cg~pLf~lk~g--~~~Cp~Cg~~~~v 52 (112)
T PRK00420 24 KHCPVCGLPLFELKDG--EVVCPVHGKVYIV 52 (112)
T ss_pred CCCCCCCCcceecCCC--ceECCCCCCeeee
Confidence 359999988854 555 7789999975443
No 446
>KOG2302 consensus T-type voltage-gated Ca2+ channel, pore-forming alpha1I subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=26.15 E-value=3.1e+02 Score=36.72 Aligned_cols=11 Identities=36% Similarity=0.709 Sum_probs=8.7
Q ss_pred cCCCCCccccc
Q 038397 116 SCPQCAVELAV 126 (1102)
Q Consensus 116 ~Cp~C~~~L~v 126 (1102)
+||+|.-...-
T Consensus 544 scpyc~ra~~~ 554 (1956)
T KOG2302|consen 544 SCPYCQRADGR 554 (1956)
T ss_pred CCcchhhcCCC
Confidence 89999877554
No 447
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=26.03 E-value=39 Score=29.74 Aligned_cols=27 Identities=22% Similarity=0.564 Sum_probs=21.3
Q ss_pred ceeecCCcceEEEeCCCcceecCCCCCCC
Q 038397 16 VQVRCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 16 ~~~~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
..-+|..||..| .++-.-..||.||++
T Consensus 4 ~~~~C~~Cg~~~--~~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 4 EGCKCPVCGKKF--KDGDDIVVCPECGAP 30 (54)
T ss_pred cCccChhhCCcc--cCCCCEEECCCCCCc
Confidence 356899999865 567778899999963
No 448
>PRK13889 conjugal transfer relaxase TraA; Provisional
Probab=26.01 E-value=79 Score=42.25 Aligned_cols=53 Identities=23% Similarity=0.282 Sum_probs=34.5
Q ss_pred CcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHh-ccCceEEEEEcC
Q 038397 216 SLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWH-HGRRKALWISVG 279 (1102)
Q Consensus 216 ~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l-~Gr~~~~w~s~s 279 (1102)
.||+.|.+||.+++..+ +-.+ +--++|.||+-.+..+ .+-|- .|.+ ++.+.-+
T Consensus 346 ~Ls~eQr~Av~~il~s~--------~v~v-v~G~AGTGKTT~l~~~-~~~~e~~G~~-V~~~ApT 399 (988)
T PRK13889 346 VLSGEQADALAHVTDGR--------DLGV-VVGYAGTGKSAMLGVA-REAWEAAGYE-VRGAALS 399 (988)
T ss_pred CCCHHHHHHHHHHhcCC--------CeEE-EEeCCCCCHHHHHHHH-HHHHHHcCCe-EEEecCc
Confidence 59999999999887543 2334 4445999999988654 44443 3543 5544433
No 449
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=25.62 E-value=33 Score=45.23 Aligned_cols=49 Identities=37% Similarity=0.900 Sum_probs=40.6
Q ss_pred cccccccCcHHHHhhhhhccccCCccccCCCCCCcccCCCCCCccccchh
Q 038397 660 FQICEICNSEEERKKLLQCSCCGQLVHSGCLVPPITDVIPSDWSCHSCKE 709 (1102)
Q Consensus 660 f~~ce~cgsed~k~kLL~cs~cgk~~H~~cL~PP~~di~~~dW~c~sCke 709 (1102)
...|..|+.++....+ +|+.|.+.+|..|+.||...++.++|.|+.|..
T Consensus 155 ~~~~~~~~k~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 203 (904)
T KOG1246|consen 155 YPQCNTCSKGKEEKLL-LCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIP 203 (904)
T ss_pred chhhhccccCCCccce-ecccccCcccccccCCCCCcCCcCcccCCcccc
Confidence 3456777776655444 999999999999999999999999999998863
No 450
>PRK06260 threonine synthase; Validated
Probab=25.58 E-value=38 Score=40.21 Aligned_cols=30 Identities=27% Similarity=0.637 Sum_probs=23.3
Q ss_pred eecCCCccceeeccCCCccccCCCCCcccccc
Q 038397 96 QLPCANCKAILNVPHGLVRFSCPQCAVELAVD 127 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~ 127 (1102)
.+.|.+||....... ..+.||.||-.|.+.
T Consensus 3 ~~~C~~cg~~~~~~~--~~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 3 WLKCIECGKEYDPDE--IIYTCPECGGLLEVI 32 (397)
T ss_pred EEEECCCCCCCCCCC--ccccCCCCCCeEEEE
Confidence 489999999875443 357899999887764
No 451
>PRK07591 threonine synthase; Validated
Probab=25.52 E-value=36 Score=40.82 Aligned_cols=31 Identities=26% Similarity=0.560 Sum_probs=24.6
Q ss_pred cceecCCCccceeeccCCCccccCCCCCcccccc
Q 038397 94 KIQLPCANCKAILNVPHGLVRFSCPQCAVELAVD 127 (1102)
Q Consensus 94 ~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~ 127 (1102)
...+.|.+||...... .. +.||-||..|.+.
T Consensus 16 ~~~l~C~~Cg~~~~~~--~~-~~C~~cg~~l~~~ 46 (421)
T PRK07591 16 AVALKCRECGAEYPLG--PI-HVCEECFGPLEVA 46 (421)
T ss_pred eeEEEeCCCCCcCCCC--CC-ccCCCCCCeEEEE
Confidence 3459999999987643 33 9999999988775
No 452
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=25.40 E-value=39 Score=30.37 Aligned_cols=16 Identities=31% Similarity=0.447 Sum_probs=13.0
Q ss_pred eCCCcceecCCCCCCC
Q 038397 29 VGPGLTEFICGTCNLP 44 (1102)
Q Consensus 29 ~~pg~~~~~Cp~C~~~ 44 (1102)
+..--..|.||.||.+
T Consensus 47 ~~i~eg~L~Cp~c~r~ 62 (68)
T PF03966_consen 47 VEIVEGELICPECGRE 62 (68)
T ss_dssp EETTTTEEEETTTTEE
T ss_pred ccccCCEEEcCCCCCE
Confidence 6677788999999964
No 453
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=25.27 E-value=57 Score=32.36 Aligned_cols=30 Identities=20% Similarity=0.269 Sum_probs=27.1
Q ss_pred ccceeecCCcceEEEeCCCcceecCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
+....+|.+||..-.+...--.-.||.||.
T Consensus 39 G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKIVYNSCKNRHCPSCQA 68 (111)
T ss_pred CcceeecCCCCceEEecCcccCcCCCCCCC
Confidence 667888999999999999888889999996
No 454
>PF00367 PTS_EIIB: phosphotransferase system, EIIB; InterPro: IPR018113 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) [, ] is a major carbohydrate transport system in bacteria. The PTS catalyzes the phosphorylation of incoming sugar substrates concomitant with their translocation across the cell membrane. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred to enzyme-I (EI) of PTS which in turn transfers it to a phosphoryl carrier protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease which consists of at least three structurally distinct domains (IIA, IIB, and IIC) [] which can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA) carries the first permease-specific phoshorylation site, a histidine, which is phosphorylated by phospho-HPr. The second domain (IIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the permease. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate in a process catalyzed by the IIC domain; this process is coupled to the transmembrane transport of the sugar. This entry covers the phosphorylation site of EIIB domains. ; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity; PDB: 3IPJ_B 3BP3_A 1O2F_B 3BP8_C 1IBA_A.
Probab=25.15 E-value=53 Score=26.31 Aligned_cols=19 Identities=26% Similarity=0.595 Sum_probs=15.5
Q ss_pred HHHHhhCCCceeeeecCCc
Q 038397 755 DIVDQLGGPDKVAEMTGRR 773 (1102)
Q Consensus 755 ~LId~LGGp~~VAEmTGRk 773 (1102)
+||+.|||.+++.+++-=-
T Consensus 3 ~il~~lGG~~NI~~v~~C~ 21 (35)
T PF00367_consen 3 QILEALGGKENIKSVTNCA 21 (35)
T ss_dssp HHHHHCTTCCCEEEEEE-S
T ss_pred HHHHHhCCHHHHHHHhcCc
Confidence 6899999999999986433
No 455
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=25.14 E-value=38 Score=28.95 Aligned_cols=25 Identities=24% Similarity=0.713 Sum_probs=17.3
Q ss_pred ecCC--cceEEEeCCCcce--ecCCCCCC
Q 038397 19 RCAG--CHIILTVGPGLTE--FICGTCNL 43 (1102)
Q Consensus 19 ~C~~--C~a~l~~~pg~~~--~~Cp~C~~ 43 (1102)
.|++ |+..+.+..+... +.|+.|++
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~ 48 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGT 48 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCS
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCC
Confidence 6966 9999999999998 99999996
No 456
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=25.13 E-value=54 Score=29.82 Aligned_cols=26 Identities=19% Similarity=0.347 Sum_probs=19.8
Q ss_pred ecCCcceEE---EeCCCcceecCCCCCCC
Q 038397 19 RCAGCHIIL---TVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 19 ~C~~C~a~l---~~~pg~~~~~Cp~C~~~ 44 (1102)
+|+.||..- ...-|.-.|.|..|++.
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 599999765 44555566999999974
No 457
>PF09548 Spore_III_AB: Stage III sporulation protein AB (spore_III_AB); InterPro: IPR014198 This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=25.07 E-value=1.6e+02 Score=31.11 Aligned_cols=127 Identities=16% Similarity=0.156 Sum_probs=73.5
Q ss_pred hHHHHHHHHhhcCCccccccccCCCCCcCCcCChHHHHHHHHHHHHHhccCccCCCCCCCCCCCcchHHHHHHHHHHHhh
Q 038397 885 FASIVAKRLESLGALTQGDRRAGLSLSAYNYDSAFGKKALMMMYRGIMEQDVLPVVPPGCSSEKPETIQDFMTKAKAALV 964 (1102)
Q Consensus 885 FaS~VAkRLeSLGALT~GdRra~~~ls~fNldn~YGr~AL~~~~~~i~~~~~~p~~p~~~~~~~~~~~~~f~~~~~~~L~ 964 (1102)
++.-..+|+.-|..|.+. |...+=|=.||..-|...+..+-... ...+..||.++...|.
T Consensus 19 ~a~~~~~R~~~L~~l~~~-------L~~L~~EI~y~~tpL~eal~~i~~~~-------------~~~~~~~f~~~a~~L~ 78 (170)
T PF09548_consen 19 YARRLKRRVRQLRELRRA-------LQLLETEIRYGATPLPEALERISRRS-------------EGPIGEFFERVAERLE 78 (170)
T ss_pred HHHHHHHHHHHHHHHHHH-------HHHHHHHHHHcCCCHHHHHHHHHhcc-------------cchHHHHHHHHHHHHH
Confidence 444455555555544332 22333344556655666665554221 1227889988887776
Q ss_pred hccceeccccCCC-CCCCCCCcccccCCcccHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHc
Q 038397 965 SVGIVRDTVLGNG-KDYGKLSGRIIDSDMHDVGRFLNRLLGLPPDIQNRLFELFISILDLLVQNARIE 1031 (1102)
Q Consensus 965 ~vGl~~~~~~~~~-~~~~~~~g~~~~~d~~~i~~FLNRlLgl~v~~Qn~lF~~F~~~l~~~i~~ak~~ 1031 (1102)
.-.-.+-...+.. -.....+..+.++|..-+..|-+-|-...+++|...|+.+...|+..+++|+++
T Consensus 79 ~~~~~~~~~~w~~~~~~~~~~~~L~~~d~e~L~~lg~~LG~~D~~~Q~k~i~l~~~~L~~~~~~a~~~ 146 (170)
T PF09548_consen 79 KNEGESFAEAWEEAVEKLLKESALKKEDKEILLELGKSLGYSDREMQEKHIELYLEQLEQQLEEAREE 146 (170)
T ss_pred cCCCCCHHHHHHHHHHhhhhcCCCCHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2210000000000 000001233445666678888888889999999999999999999999999864
No 458
>PRK06260 threonine synthase; Validated
Probab=24.97 E-value=34 Score=40.66 Aligned_cols=29 Identities=17% Similarity=0.419 Sum_probs=21.8
Q ss_pred eeecCCcceEEEeCCCcceecCCCCCCCCCC
Q 038397 17 QVRCAGCHIILTVGPGLTEFICGTCNLPQML 47 (1102)
Q Consensus 17 ~~~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l 47 (1102)
.++|..||.++ ++....+.||.||-...+
T Consensus 3 ~~~C~~cg~~~--~~~~~~~~Cp~cg~~l~~ 31 (397)
T PRK06260 3 WLKCIECGKEY--DPDEIIYTCPECGGLLEV 31 (397)
T ss_pred EEEECCCCCCC--CCCCccccCCCCCCeEEE
Confidence 58999999985 455556889999954443
No 459
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=24.82 E-value=51 Score=35.39 Aligned_cols=30 Identities=13% Similarity=0.430 Sum_probs=18.1
Q ss_pred ccceeecCCcceEEEeCCCcc---------eecCCCCCC
Q 038397 14 VGVQVRCAGCHIILTVGPGLT---------EFICGTCNL 43 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l~~~pg~~---------~~~Cp~C~~ 43 (1102)
....++|++|+....++.-.. .+.||.|+.
T Consensus 15 ~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~ 53 (188)
T PF08996_consen 15 EPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST 53 (188)
T ss_dssp --EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred CceEeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence 456889999999998876655 789999996
No 460
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.71 E-value=51 Score=31.10 Aligned_cols=25 Identities=28% Similarity=0.635 Sum_probs=21.6
Q ss_pred eecCCcceEE--EeCCCcceecCCCCC
Q 038397 18 VRCAGCHIIL--TVGPGLTEFICGTCN 42 (1102)
Q Consensus 18 ~~C~~C~a~l--~~~pg~~~~~Cp~C~ 42 (1102)
+-|+.|++.| .+-.|+--=-||.|+
T Consensus 2 llCP~C~v~l~~~~rs~vEiD~CPrCr 28 (88)
T COG3809 2 LLCPICGVELVMSVRSGVEIDYCPRCR 28 (88)
T ss_pred cccCcCCceeeeeeecCceeeeCCccc
Confidence 3599999999 677898888999996
No 461
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=24.60 E-value=49 Score=39.75 Aligned_cols=31 Identities=26% Similarity=0.799 Sum_probs=24.8
Q ss_pred eecCCCccceeeccCCCc--cccCCCCCccccc
Q 038397 96 QLPCANCKAILNVPHGLV--RFSCPQCAVELAV 126 (1102)
Q Consensus 96 ~~~C~~C~A~~~vp~~~~--~f~Cp~C~~~L~v 126 (1102)
.+-|..|+.+.++|.--. +-.||-||..|.-
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTLTV 45 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCCcC
Confidence 467999999999986333 4579999999965
No 462
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=24.39 E-value=40 Score=34.59 Aligned_cols=31 Identities=26% Similarity=0.560 Sum_probs=23.4
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCCCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLPQMLPPEL 51 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~~~l~p~~ 51 (1102)
-|+-||..|-=..| ...||.||+...+-.+.
T Consensus 30 hCp~Cg~PLF~KdG--~v~CPvC~~~~~~v~~e 60 (131)
T COG1645 30 HCPKCGTPLFRKDG--EVFCPVCGYREVVVEEE 60 (131)
T ss_pred hCcccCCcceeeCC--eEECCCCCceEEEeecc
Confidence 39999999966655 56899999776664444
No 463
>KOG0342 consensus ATP-dependent RNA helicase pitchoune [RNA processing and modification]
Probab=24.38 E-value=80 Score=38.86 Aligned_cols=71 Identities=15% Similarity=0.279 Sum_probs=55.9
Q ss_pred hhhcCCcceEEEEecccccccccccccccccccceeEEEec--CCCcHhHHHHhhcccccCCCCCCCeEEEeecCccchh
Q 038397 806 QLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVHITLE--LPWSADRAIQQFGRTHRSNQASAPEYRIIFTNLGGER 883 (1102)
Q Consensus 806 ~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvHitLE--lpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~l~GEr 883 (1102)
..|+.-+.-|++-||-|.=|.-+-+ ||..+| +|-+-+.=|+++|||.|+|-- .=-|-+| ++-|.
T Consensus 374 ~~F~kaesgIL~cTDVaARGlD~P~----------V~~VvQ~~~P~d~~~YIHRvGRTaR~gk~-G~alL~l---~p~El 439 (543)
T KOG0342|consen 374 FEFCKAESGILVCTDVAARGLDIPD----------VDWVVQYDPPSDPEQYIHRVGRTAREGKE-GKALLLL---APWEL 439 (543)
T ss_pred HHHhhcccceEEecchhhccCCCCC----------ceEEEEeCCCCCHHHHHHHhccccccCCC-ceEEEEe---ChhHH
Confidence 5899999999999999999987753 565554 799999999999999997753 3334444 36788
Q ss_pred hhHHHHH
Q 038397 884 RFASIVA 890 (1102)
Q Consensus 884 RFaS~VA 890 (1102)
=|.+-+-
T Consensus 440 ~Flr~LK 446 (543)
T KOG0342|consen 440 GFLRYLK 446 (543)
T ss_pred HHHHHHh
Confidence 8887765
No 464
>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....
Probab=24.36 E-value=87 Score=33.74 Aligned_cols=33 Identities=36% Similarity=0.449 Sum_probs=25.0
Q ss_pred eEeecCCCCCcchhhHHHHHHHHhccCceEEEEEc
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISV 278 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~ 278 (1102)
+|+|- +||||+-++|=+-..--++|++ +..+|.
T Consensus 5 ~lvGp-tGvGKTTt~aKLAa~~~~~~~~-v~lis~ 37 (196)
T PF00448_consen 5 ALVGP-TGVGKTTTIAKLAARLKLKGKK-VALISA 37 (196)
T ss_dssp EEEES-TTSSHHHHHHHHHHHHHHTT---EEEEEE
T ss_pred EEECC-CCCchHhHHHHHHHHHhhcccc-ceeecC
Confidence 45666 9999999999998888888554 666664
No 465
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=24.02 E-value=26 Score=34.30 Aligned_cols=28 Identities=14% Similarity=0.369 Sum_probs=17.0
Q ss_pred ccCCCccccCCCCCcccccccccccccC
Q 038397 108 VPHGLVRFSCPQCAVELAVDMSKVKQFF 135 (1102)
Q Consensus 108 vp~~~~~f~Cp~C~~~L~v~~~~~~~~~ 135 (1102)
-.++++--+|-.|+.....+..+|..-|
T Consensus 41 k~~~iG~~sC~iC~esFqt~it~LsepI 68 (109)
T KOG3214|consen 41 KKHNIGKASCRICEESFQTTITALSEPI 68 (109)
T ss_pred hhcCcceeeeeehhhhhccchHhhccch
Confidence 3455556677777777666555554443
No 466
>PRK14974 cell division protein FtsY; Provisional
Probab=23.96 E-value=3e+02 Score=32.41 Aligned_cols=35 Identities=29% Similarity=0.321 Sum_probs=22.8
Q ss_pred cceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEE
Q 038397 241 RAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWIS 277 (1102)
Q Consensus 241 R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s 277 (1102)
+.-.|+| -+|+||+-++|-+...--.+|. +++.++
T Consensus 141 ~vi~~~G-~~GvGKTTtiakLA~~l~~~g~-~V~li~ 175 (336)
T PRK14974 141 VVIVFVG-VNGTGKTTTIAKLAYYLKKNGF-SVVIAA 175 (336)
T ss_pred eEEEEEc-CCCCCHHHHHHHHHHHHHHcCC-eEEEec
Confidence 4455667 6999999999988853223343 455543
No 467
>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB. The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.
Probab=23.89 E-value=75 Score=36.52 Aligned_cols=44 Identities=23% Similarity=0.305 Sum_probs=36.2
Q ss_pred cccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHH
Q 038397 210 DLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLI 262 (1102)
Q Consensus 210 ~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI 262 (1102)
.++..|.||..|.+.+.-+.+. +..+++.-+||.||+-.+.+++
T Consensus 110 ~l~~~g~~~~~~~~~L~~~v~~---------~~~ilI~G~tGSGKTTll~al~ 153 (299)
T TIGR02782 110 DYVEAGIMTAAQRDVLREAVLA---------RKNILVVGGTGSGKTTLANALL 153 (299)
T ss_pred HHHhcCCCCHHHHHHHHHHHHc---------CCeEEEECCCCCCHHHHHHHHH
Confidence 4567899999998887776653 5688899999999999998876
No 468
>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG. The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF).
Probab=23.78 E-value=2.4e+02 Score=31.38 Aligned_cols=37 Identities=24% Similarity=0.194 Sum_probs=25.2
Q ss_pred cceeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEc
Q 038397 241 RAGFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISV 278 (1102)
Q Consensus 241 R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~ 278 (1102)
|.=-+.+=..|+||+-..+.+-+.--..|+ |++.|..
T Consensus 104 ~vi~vts~~~g~Gktt~a~nLA~~la~~g~-~VllID~ 140 (274)
T TIGR03029 104 KALAVVSAKSGEGCSYIAANLAIVFSQLGE-KTLLIDA 140 (274)
T ss_pred eEEEEECCCCCCCHHHHHHHHHHHHHhcCC-eEEEEeC
Confidence 333444666899999988877666445565 5887765
No 469
>PRK13111 trpA tryptophan synthase subunit alpha; Provisional
Probab=23.11 E-value=4.5e+02 Score=29.83 Aligned_cols=40 Identities=28% Similarity=0.456 Sum_probs=27.8
Q ss_pred ceEEeehhhhhhccccccchHHHHHHHhcc-CCCceEEee----cchhcc
Q 038397 321 GVVFLTYSSLIASSEKGRSRLQQLVQWCGS-GYDGLVIFD----ECHKAK 365 (1102)
Q Consensus 321 GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~-dfdgvivfD----EcH~ak 365 (1102)
-+++.||...+-. -.++.+++.|-+ ..||+||=| |+....
T Consensus 91 p~vlm~Y~N~i~~-----~G~e~f~~~~~~aGvdGviipDLp~ee~~~~~ 135 (258)
T PRK13111 91 PIVLMTYYNPIFQ-----YGVERFAADAAEAGVDGLIIPDLPPEEAEELR 135 (258)
T ss_pred CEEEEecccHHhh-----cCHHHHHHHHHHcCCcEEEECCCCHHHHHHHH
Confidence 4788888887632 135666777764 799999987 555544
No 470
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=23.07 E-value=42 Score=38.46 Aligned_cols=27 Identities=26% Similarity=0.485 Sum_probs=24.5
Q ss_pred ecCCCccceeeccCCCccccCCCCCcc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
--|++||..+..-++--...||.||..
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~ 138 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHE 138 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCc
Confidence 369999999999999889999999976
No 471
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.06 E-value=32 Score=39.93 Aligned_cols=27 Identities=30% Similarity=0.534 Sum_probs=14.2
Q ss_pred ecCCCccceeeccCCCccccCCCCCccccc
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAV 126 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v 126 (1102)
.-|.+|=-.+- ..++.+||.|+.+|--
T Consensus 29 ~~C~sCv~~l~---~~~~~~CP~C~~~lrk 55 (309)
T TIGR00570 29 TLCESCVDLLF---VRGSGSCPECDTPLRK 55 (309)
T ss_pred cccHHHHHHHh---cCCCCCCCCCCCccch
Confidence 45666655542 1123467777766543
No 472
>KOG1984 consensus Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.99 E-value=39 Score=43.72 Aligned_cols=38 Identities=26% Similarity=0.578 Sum_probs=33.2
Q ss_pred ccceeecCCcceEE----EeCCCcceecCCCCCCCCCCCCCC
Q 038397 14 VGVQVRCAGCHIIL----TVGPGLTEFICGTCNLPQMLPPEL 51 (1102)
Q Consensus 14 ~~~~~~C~~C~a~l----~~~pg~~~~~Cp~C~~~~~l~p~~ 51 (1102)
...-+||..|++.. .+--|...|.|..|+.....|++-
T Consensus 335 ~sgPvRC~RCkaYinPFmqF~~~gr~f~Cn~C~~~n~vp~~y 376 (1007)
T KOG1984|consen 335 ESGPVRCNRCKAYINPFMQFIDGGRKFICNFCGSKNQVPDDY 376 (1007)
T ss_pred CCCCcchhhhhhhcCcceEEecCCceEEecCCCccccCChhh
Confidence 55589999999987 789999999999999988887665
No 473
>PRK12722 transcriptional activator FlhC; Provisional
Probab=22.90 E-value=47 Score=36.01 Aligned_cols=24 Identities=25% Similarity=0.721 Sum_probs=19.0
Q ss_pred ecCCcceEEEeCCC--cceecCCCCC
Q 038397 19 RCAGCHIILTVGPG--LTEFICGTCN 42 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg--~~~~~Cp~C~ 42 (1102)
+|..||..+.+... ...|+||-|+
T Consensus 136 ~C~~Cgg~fv~~~~e~~~~f~CplC~ 161 (187)
T PRK12722 136 SCNCCGGHFVTHAHDPVGSFVCGLCQ 161 (187)
T ss_pred cCCCCCCCeeccccccCCCCcCCCCC
Confidence 49999999853332 5699999999
No 474
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=22.85 E-value=36 Score=31.02 Aligned_cols=38 Identities=26% Similarity=0.482 Sum_probs=15.6
Q ss_pred ecCCCccceeeccCCCcc---------------ccCCCCCccccccccccccc
Q 038397 97 LPCANCKAILNVPHGLVR---------------FSCPQCAVELAVDMSKVKQF 134 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~---------------f~Cp~C~~~L~v~~~~~~~~ 134 (1102)
+.|.+|..++..|+-++. -.||.|.+|-.+-+-+....
T Consensus 8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~~~Nrq 60 (65)
T PF14835_consen 8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDIQINRQ 60 (65)
T ss_dssp TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS----HH
T ss_pred cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHHHhhhh
Confidence 789999999999975331 26999999987766555443
No 475
>PRK12898 secA preprotein translocase subunit SecA; Reviewed
Probab=22.70 E-value=2.1e+02 Score=36.83 Aligned_cols=83 Identities=17% Similarity=0.141 Sum_probs=51.5
Q ss_pred hhcCCcceEEEEecccccccccccccccccccceeE-EEecCCCcHhHHHHhhcccccCCCCCCCeEEEeecC-ccchhh
Q 038397 807 LFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVH-ITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFTN-LGGERR 884 (1102)
Q Consensus 807 ~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvH-itLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T~-l~GErR 884 (1102)
.|..+...|.|-++.|+=|+-.-....+. ..==.| |-.++|=|.+.-+|..|||+|-+.- =..++++|. =.-=++
T Consensus 516 ~~ag~~g~VlVATdmAgRGtDI~l~~~V~-~~GGLhVI~~d~P~s~r~y~hr~GRTGRqG~~--G~s~~~is~eD~l~~~ 592 (656)
T PRK12898 516 ARAGQRGRITVATNMAGRGTDIKLEPGVA-ARGGLHVILTERHDSARIDRQLAGRCGRQGDP--GSYEAILSLEDDLLQS 592 (656)
T ss_pred HHcCCCCcEEEEccchhcccCcCCccchh-hcCCCEEEEcCCCCCHHHHHHhcccccCCCCC--eEEEEEechhHHHHHh
Confidence 34444446999999999998775432111 000013 6679999999999999999998753 234455542 111145
Q ss_pred hHHHHHHH
Q 038397 885 FASIVAKR 892 (1102)
Q Consensus 885 FaS~VAkR 892 (1102)
|++-..++
T Consensus 593 ~~~~~~~~ 600 (656)
T PRK12898 593 FLGSRGLA 600 (656)
T ss_pred hhhHHHHH
Confidence 66554444
No 476
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=22.69 E-value=72 Score=27.29 Aligned_cols=25 Identities=24% Similarity=0.712 Sum_probs=21.6
Q ss_pred ecC--CcceEEEeC--CCcceecCCCCCC
Q 038397 19 RCA--GCHIILTVG--PGLTEFICGTCNL 43 (1102)
Q Consensus 19 ~C~--~C~a~l~~~--pg~~~~~Cp~C~~ 43 (1102)
.|+ +|+..+... ++...+.||.|+.
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~~ 48 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCGF 48 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCCC
Confidence 499 999999886 4889999999986
No 477
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=22.48 E-value=21 Score=45.20 Aligned_cols=46 Identities=35% Similarity=0.884 Sum_probs=22.5
Q ss_pred ccccccCcH--HHHhhhhhccccCCccccCCCCCCcccCCCCCCccccch
Q 038397 661 QICEICNSE--EERKKLLQCSCCGQLVHSGCLVPPITDVIPSDWSCHSCK 708 (1102)
Q Consensus 661 ~~ce~cgse--d~k~kLL~cs~cgk~~H~~cL~PP~~di~~~dW~c~sCk 708 (1102)
+.|+.|-+. ++-.+|..|+.|..-+|+.|.- +..+|++.|+|..|.
T Consensus 272 viCDvCrspD~e~~neMVfCd~Cn~cVHqaCyG--Ile~p~gpWlCr~Ca 319 (893)
T KOG0954|consen 272 VICDVCRSPDSEEANEMVFCDKCNICVHQACYG--ILEVPEGPWLCRTCA 319 (893)
T ss_pred ceeceecCCCccccceeEEeccchhHHHHhhhc--eeecCCCCeeehhcc
Confidence 444444433 2223455566666666666641 122344566666553
No 478
>PF02374 ArsA_ATPase: Anion-transporting ATPase; PDB: 2WOO_A 3IBG_B 3SJA_A 3H84_B 3SJD_A 3ZS9_A 3A37_A 2WOJ_A 3SJC_B 3A36_B ....
Probab=22.35 E-value=1.1e+02 Score=35.34 Aligned_cols=37 Identities=38% Similarity=0.540 Sum_probs=29.0
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCc
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSD 281 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~ 281 (1102)
=||.|-| ||||+-..|+.-+.-=.+|+| ++=+|..+.
T Consensus 4 ~~~~GKG-GVGKTT~aaA~A~~~A~~G~r-tLlvS~Dpa 40 (305)
T PF02374_consen 4 LFFGGKG-GVGKTTVAAALALALARRGKR-TLLVSTDPA 40 (305)
T ss_dssp EEEEEST-TSSHHHHHHHHHHHHHHTTS--EEEEESSTT
T ss_pred EEEecCC-CCCcHHHHHHHHHHHhhCCCC-eeEeecCCC
Confidence 3667774 999999999998888888876 888887553
No 479
>TIGR03253 oxalate_frc formyl-CoA transferase. This enzyme, formyl-CoA transferase, transfers coenzyme A from formyl-CoA to oxalate. It forms a pathway, together with oxalyl-CoA decarboxylase, for oxalate degradation; decarboxylation by the latter gene regenerates formyl-CoA. The two enzymes typically are encoded by a two-gene operon.
Probab=22.10 E-value=94 Score=37.33 Aligned_cols=92 Identities=23% Similarity=0.354 Sum_probs=51.7
Q ss_pred HhhhhhhCCCcccccccCCCCCCcCCCCcc-ccc--cceEEeehhhhhhc---------cccccchHHHHHHHhccCCCc
Q 038397 287 RRDLDDVGATCIEVHALNKLPYSKLDSRSV-GIR--EGVVFLTYSSLIAS---------SEKGRSRLQQLVQWCGSGYDG 354 (1102)
Q Consensus 287 ~RDl~diG~~~i~v~~l~~~~~~~~~~~~~-~~~--~GvlF~TYs~L~~~---------~~~~~sRl~Ql~~W~g~dfdg 354 (1102)
-+=|.|+||+-|+|-|... |+...... ... .+..| .++... +.+|+..|.+|+.++ |-
T Consensus 22 ~~lLAdlGAeVIKVE~p~~---GD~~R~~~~~~~~~~s~~f---~~~nr~Krsi~lDLk~~~g~~~l~~Lv~~A----DV 91 (415)
T TIGR03253 22 TQMLAWLGADVIKIERPGV---GDITRGQLRDIPDVDSLYF---TMLNCNKRSITLNTKTPEGKEVLEELIKKA----DV 91 (415)
T ss_pred HHHHHHcCCcEEEeCCCCC---CccccccCCCCCCcccHHH---HHhCCCCeEEEeeCCCHHHHHHHHHHHhhC----CE
Confidence 3668899999999986531 21100000 001 12222 223221 123578899999875 53
Q ss_pred eEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCC
Q 038397 355 LVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATG 401 (1102)
Q Consensus 355 vivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATg 401 (1102)
|| | |.-+ ....+-|+---.|...-| ++||||-||
T Consensus 92 vi-----e---n~rp---g~~~rlGL~~~~L~~~nP--~LV~~sisg 125 (415)
T TIGR03253 92 MV-----E---NFGP---GALDRMGFTWEYIQEINP--RLILASIKG 125 (415)
T ss_pred EE-----E---CCCC---ChHHHcCCCHHHHHHhCC--CeEEEEeee
Confidence 33 1 2322 223567777778888855 699999997
No 480
>PLN02610 probable methionyl-tRNA synthetase
Probab=22.00 E-value=48 Score=43.20 Aligned_cols=36 Identities=22% Similarity=0.555 Sum_probs=25.3
Q ss_pred ecCCCccceeeccCCCccccCCCCCcccccccccccccC
Q 038397 97 LPCANCKAILNVPHGLVRFSCPQCAVELAVDMSKVKQFF 135 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~~~f~Cp~C~~~L~v~~~~~~~~~ 135 (1102)
-.|.+||+.++.-. +.--.|..||.+... .+.++|+
T Consensus 171 d~Ce~Cg~~~~p~e-Li~p~c~~~g~~~~~--~~~~~~f 206 (801)
T PLN02610 171 DQCEKCGKLLNPTE-LIDPKCKVCKNTPRI--RDTDHLF 206 (801)
T ss_pred chhhhccccCChhh-hcCCcccCCCCcceE--EEcceEE
Confidence 47999998877644 444469999998654 4455555
No 481
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=21.92 E-value=57 Score=35.00 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=13.5
Q ss_pred ccceecCCCccceeecc-CCC-ccccCCCCCcc
Q 038397 93 TKIQLPCANCKAILNVP-HGL-VRFSCPQCAVE 123 (1102)
Q Consensus 93 t~~~~~C~~C~A~~~vp-~~~-~~f~Cp~C~~~ 123 (1102)
.....+|..||....+- +.+ ..|.||+|.-+
T Consensus 131 ~l~l~~C~~C~~~fv~~~~~~~~~~~Cp~C~~p 163 (175)
T PF05280_consen 131 MLQLAPCRRCGGHFVTHAHDPRHSFVCPFCQPP 163 (175)
T ss_dssp SEEEEE-TTT--EEEEESS--SS----TT----
T ss_pred CccccCCCCCCCCeECcCCCCCcCcCCCCCCCc
Confidence 45678999999987774 442 37999999953
No 482
>PRK06893 DNA replication initiation factor; Validated
Probab=21.89 E-value=86 Score=34.31 Aligned_cols=36 Identities=22% Similarity=0.357 Sum_probs=28.5
Q ss_pred eeEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcC
Q 038397 243 GFFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVG 279 (1102)
Q Consensus 243 Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s 279 (1102)
.+++--..|+||+.-+-+|..+-..+|++ ++|++.+
T Consensus 41 ~l~l~G~~G~GKThL~~ai~~~~~~~~~~-~~y~~~~ 76 (229)
T PRK06893 41 FFYIWGGKSSGKSHLLKAVSNHYLLNQRT-AIYIPLS 76 (229)
T ss_pred eEEEECCCCCCHHHHHHHHHHHHHHcCCC-eEEeeHH
Confidence 34454459999999999999888888864 8888874
No 483
>PHA00626 hypothetical protein
Probab=21.80 E-value=51 Score=29.28 Aligned_cols=31 Identities=16% Similarity=0.395 Sum_probs=22.7
Q ss_pred ecCCCccceeeccCCC-----ccccCCCCCcccccc
Q 038397 97 LPCANCKAILNVPHGL-----VRFSCPQCAVELAVD 127 (1102)
Q Consensus 97 ~~C~~C~A~~~vp~~~-----~~f~Cp~C~~~L~v~ 127 (1102)
+.|.+||....+--++ .+|.|+-||-...-|
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeechh
Confidence 4699999976665443 478999999875554
No 484
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=21.76 E-value=33 Score=40.51 Aligned_cols=42 Identities=31% Similarity=0.554 Sum_probs=29.6
Q ss_pred CCCCccceecCCCccceeeccCCCcc-ccCCCCCccccccccc
Q 038397 89 GIDPTKIQLPCANCKAILNVPHGLVR-FSCPQCAVELAVDMSK 130 (1102)
Q Consensus 89 ~~~~t~~~~~C~~C~A~~~vp~~~~~-f~Cp~C~~~L~v~~~~ 130 (1102)
+.+-+-+++||+.|=-.--+--...| ..||.|..|++-|.+.
T Consensus 308 ~~~~~pKrLpCGHilHl~CLknW~ERqQTCPICr~p~ifd~~~ 350 (491)
T COG5243 308 GLDMTPKRLPCGHILHLHCLKNWLERQQTCPICRRPVIFDQSS 350 (491)
T ss_pred cccCCcccccccceeeHHHHHHHHHhccCCCcccCccccccCC
Confidence 34455557999988554444455555 5899999999998655
No 485
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.70 E-value=46 Score=43.91 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=20.7
Q ss_pred CccceecCCCccceeeccCCCccccCCCCCcc
Q 038397 92 PTKIQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 92 ~t~~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
.+...-.|..||+.+ ..|.||.||..
T Consensus 622 VEVg~RfCpsCG~~t------~~frCP~CG~~ 647 (1121)
T PRK04023 622 VEIGRRKCPSCGKET------FYRRCPFCGTH 647 (1121)
T ss_pred ecccCccCCCCCCcC------CcccCCCCCCC
Confidence 444556899999985 57899999987
No 486
>PHA00350 putative assembly protein
Probab=21.57 E-value=43 Score=40.24 Aligned_cols=23 Identities=22% Similarity=0.182 Sum_probs=18.7
Q ss_pred CCCCCcchhhHH-HHHHHHhccCc
Q 038397 249 GAGVGKGRTIAG-LIWENWHHGRR 271 (1102)
Q Consensus 249 g~GvGKGR~~Ag-iI~~n~l~Gr~ 271 (1102)
-.|-||+--+.. .|+....+||+
T Consensus 9 ~pGSGKT~~aV~~~i~palk~GR~ 32 (399)
T PHA00350 9 RPGSYKSYEAVVYHIIPALKDGRK 32 (399)
T ss_pred CCCCchhHHHHHHHHHHHHHCCCE
Confidence 378899988776 68899999974
No 487
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=21.52 E-value=1.2e+02 Score=39.05 Aligned_cols=246 Identities=18% Similarity=0.189 Sum_probs=115.6
Q ss_pred cCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHHHHhccCc-eEEEEEcCCchhhhHHhhhhh
Q 038397 214 SKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWENWHHGRR-KALWISVGSDLKFDARRDLDD 292 (1102)
Q Consensus 214 ~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~n~l~Gr~-~~~w~s~s~~L~~Da~RDl~d 292 (1102)
.|.|+..|+|.+.|+......--+ -+++|-.|+||+-+....++.-+-.+.+ .+.=++++.--.--++|-..-
T Consensus 293 ~g~L~~~qleGln~L~~~ws~~~~------~ilADEmgLgktVqsi~fl~sl~~~~~~~~P~Lv~ap~sT~~nwe~e~~~ 366 (696)
T KOG0383|consen 293 GGTLHPYQLEGLNWLRISWSPGVD------AILADEMGLGKTVQSIVFLYSLPKEIHSPGPPLVVAPLSTIVNWEREFEL 366 (696)
T ss_pred CccccccchhhhhhhhcccccCCC------cccchhhcCCceeeEEEEEeecccccCCCCCceeeccCccccCCCCchhc
Confidence 589999999999998876533211 2578999999987763333332222222 111111111100001111100
Q ss_pred hCCCcccc------------cccCCC---CCC-----cCCC--CccccccceEEeehhhhhhccccccchHHHHHHHhcc
Q 038397 293 VGATCIEV------------HALNKL---PYS-----KLDS--RSVGIREGVVFLTYSSLIASSEKGRSRLQQLVQWCGS 350 (1102)
Q Consensus 293 iG~~~i~v------------~~l~~~---~~~-----~~~~--~~~~~~~GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~ 350 (1102)
. +..+.| ...+.+ ++. +++. +.-.++.-|+|++|+...-. . -+-.-++|
T Consensus 367 w-ap~~~vv~~~G~~k~r~iirepe~s~ed~~~~~~~~i~~~~~~s~~k~~vl~~s~~~~~~~-~----~il~~v~w--- 437 (696)
T KOG0383|consen 367 W-APSFYVVPYPGTAKSRAIIREPEFSFEDSSIKSSPKISEMKTESSAKFHVLLPSYETIEID-Q----SILFSVQW--- 437 (696)
T ss_pred c-CCCcccccCCCCccchhhhhcccccccccccccCCccccccchhhcccccCCCchhhcccC-H----HHHhhhhc---
Confidence 0 000000 000111 000 0110 11125667888888875432 1 12234567
Q ss_pred CCCceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCCCCCCccchhhhccccCCCCCCCCHHHHH
Q 038397 351 GYDGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGASEPRNMGYMVRLGLWGAGTCFKDFQIFL 430 (1102)
Q Consensus 351 dfdgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATgasep~Nl~ym~RLGLWg~gt~f~~~~~f~ 430 (1102)
|++|.||.|+.||--. .--..|+...=.-+++ -||---=.|+.|+.-|=-++.-..|.+...|.
T Consensus 438 ---~~livde~~rlkn~~s----------~~f~~l~~~~~~~~~l---ltgtPlqnn~~el~~ll~flt~~~~~~~~~f~ 501 (696)
T KOG0383|consen 438 ---GLLIVDEAHRLKNKQS----------KRFRVLTAYPIDSKLL---LTGTPLQNNLEELFNLLNFLTPGRFNSLEWFL 501 (696)
T ss_pred ---ceeEeechhhcccchh----------hhhhhccccccchhhh---ccCCcchhhhHHhhhcccccCcccccchhhhh
Confidence 8999999999998731 1112222221122222 25555556777777763344333466555555
Q ss_pred HHHhccChhHHHHHHHH-HHhccceeeecc--CCCC---ceeEEEeccCcHHHHHHHHHHH-HHHHHHH
Q 038397 431 GALDKGGVGALELVAMD-MKARGMYVCRTL--SYKG---AEFEVIEAPLEAEMTDMYKKAA-EFWAELR 492 (1102)
Q Consensus 431 ~a~~~gGv~amE~va~d-lK~~G~yiaR~L--Sf~g---vef~i~e~~l~~~~~~~Yd~~a-~~w~~~~ 492 (1102)
+.... +.--|-+-+- +-..|.+++|-. =+++ -...|..+.|++-|.++|.+-- .=|.-++
T Consensus 502 e~~~d--~~~~~~~~~l~~l~~p~~lrr~k~d~l~~~P~Kte~i~~~~~~~~Q~~~yk~~~t~n~~~l~ 568 (696)
T KOG0383|consen 502 EEFHD--ISCEEQIKKLHLLLCPHMLRRLKLDVLKPMPLKTELIGRVELSPCQKKYYKKILTRNWQGLL 568 (696)
T ss_pred hhcch--hhHHHHHHhhccccCchhhhhhhhhhccCCCccceeEEEEecCHHHHHHHHHHHcCChHHHh
Confidence 43322 1111111110 001122333322 1233 4556777899999999987532 2355544
No 488
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=21.40 E-value=1.1e+02 Score=34.82 Aligned_cols=35 Identities=29% Similarity=0.304 Sum_probs=26.9
Q ss_pred eEeecCCCCCcchhhHHHHHHHHhc-cCceEEEEEc
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENWHH-GRRKALWISV 278 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~l~-Gr~~~~w~s~ 278 (1102)
+++.-.+|+||+-+++.++.....+ |.+++..|+.
T Consensus 197 i~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~ 232 (282)
T TIGR03499 197 IALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITT 232 (282)
T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEEC
Confidence 3334459999999999998877776 7677887774
No 489
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=21.39 E-value=45 Score=29.61 Aligned_cols=25 Identities=28% Similarity=0.554 Sum_probs=21.5
Q ss_pred ecCCcceEEEeCCCcceecCCCCCCC
Q 038397 19 RCAGCHIILTVGPGLTEFICGTCNLP 44 (1102)
Q Consensus 19 ~C~~C~a~l~~~pg~~~~~Cp~C~~~ 44 (1102)
-|-+||.++=..-|. .-+|++||.+
T Consensus 20 NCl~CGkIiC~~Eg~-~~pC~fCg~~ 44 (57)
T PF06221_consen 20 NCLNCGKIICEQEGP-LGPCPFCGTP 44 (57)
T ss_pred cccccChhhcccccC-cCcCCCCCCc
Confidence 599999999887777 8899999954
No 490
>PF13173 AAA_14: AAA domain
Probab=21.33 E-value=95 Score=30.55 Aligned_cols=35 Identities=14% Similarity=0.242 Sum_probs=25.6
Q ss_pred CceEEeecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEe
Q 038397 353 DGLVIFDECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCS 398 (1102)
Q Consensus 353 dgvivfDEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~S 398 (1102)
..+|||||.|+..+. ...+..|-+.-|+.+||.++
T Consensus 62 ~~~i~iDEiq~~~~~-----------~~~lk~l~d~~~~~~ii~tg 96 (128)
T PF13173_consen 62 KKYIFIDEIQYLPDW-----------EDALKFLVDNGPNIKIILTG 96 (128)
T ss_pred CcEEEEehhhhhccH-----------HHHHHHHHHhccCceEEEEc
Confidence 468999999999765 34555555666888887754
No 491
>PRK03525 crotonobetainyl-CoA:carnitine CoA-transferase; Provisional
Probab=21.25 E-value=96 Score=37.18 Aligned_cols=87 Identities=14% Similarity=0.133 Sum_probs=50.9
Q ss_pred hhhhhhCCCcccccccCCCCCCcCCCCccccccceEEeehhhhhhc---------cccccchHHHHHHHhccCCCceEEe
Q 038397 288 RDLDDVGATCIEVHALNKLPYSKLDSRSVGIREGVVFLTYSSLIAS---------SEKGRSRLQQLVQWCGSGYDGLVIF 358 (1102)
Q Consensus 288 RDl~diG~~~i~v~~l~~~~~~~~~~~~~~~~~GvlF~TYs~L~~~---------~~~~~sRl~Ql~~W~g~dfdgvivf 358 (1102)
+=|.|+||+-|+|-+... |+ ..+- .+..| ..+... +..|+..|..|+.++ |-||
T Consensus 31 ~lLAdlGAeVIKVE~p~~---GD----~~R~-~~~~~---~~~NrgKrsi~LDLk~~~Gr~~l~~Li~~A----DVvi-- 93 (405)
T PRK03525 31 QMFAEWGAEVIWIENVAW---AD----TIRV-QPNYP---QLSRRNLHALSLNIFKDEGREAFLKLMETT----DIFI-- 93 (405)
T ss_pred HHHHHcCCcEEEECCCCC---CC----cccc-ccchh---hhccCCCeeEEEeCCCHHHHHHHHHHHHhC----CEEE--
Confidence 668899999999987532 21 1110 01122 222211 134578899999876 4333
Q ss_pred ecchhccccCCCCCCCchhHHHHHHHHhhhCCCccEEEEecCCC
Q 038397 359 DECHKAKNLVPEAGSQPTRTGEAVLELQARLPEARVVYCSATGA 402 (1102)
Q Consensus 359 DEcH~akn~~~~~~~~~s~~g~avl~LQ~~lP~ARvvY~SATga 402 (1102)
| |.-++ .--+-|+---.|+... =++||||-||-
T Consensus 94 ---e---n~rpg---~~~rlGl~~e~L~~~n--P~LIy~sisgf 126 (405)
T PRK03525 94 ---E---ASKGP---AFARRGITDEVLWEHN--PKLVIAHLSGF 126 (405)
T ss_pred ---E---CCCcc---HHHHcCCCHHHHHHhC--CCeEEEEeeEC
Confidence 1 23221 2246677777788884 46999999974
No 492
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=21.24 E-value=60 Score=28.73 Aligned_cols=21 Identities=29% Similarity=0.752 Sum_probs=16.4
Q ss_pred eecCCcceEEEeCCCcceecCCCCCC
Q 038397 18 VRCAGCHIILTVGPGLTEFICGTCNL 43 (1102)
Q Consensus 18 ~~C~~C~a~l~~~pg~~~~~Cp~C~~ 43 (1102)
+.|++||.. =+.-..||.||+
T Consensus 28 ~~C~~CG~~-----~~~H~vC~~CG~ 48 (57)
T PRK12286 28 VECPNCGEP-----KLPHRVCPSCGY 48 (57)
T ss_pred eECCCCCCc-----cCCeEECCCCCc
Confidence 459999974 345788999996
No 493
>PRK13833 conjugal transfer protein TrbB; Provisional
Probab=21.23 E-value=89 Score=36.55 Aligned_cols=46 Identities=28% Similarity=0.328 Sum_probs=36.9
Q ss_pred cccccCCcccchhhHHHHHHhhccccCCCCCcceeEeecCCCCCcchhhHHHHHH
Q 038397 210 DLESSKSLSCLQIETLVYASQRHLQHLPNSARAGFFIGDGAGVGKGRTIAGLIWE 264 (1102)
Q Consensus 210 ~~~~~g~LS~~Qle~v~ya~q~h~~~l~~g~R~Gf~~gDg~GvGKGR~~AgiI~~ 264 (1102)
..+..|.||..|.+.+.-+... |..+++.-+||.||+-.+.+++.+
T Consensus 122 ~lv~~g~~~~~~~~~L~~~v~~---------~~nilI~G~tGSGKTTll~aL~~~ 167 (323)
T PRK13833 122 DYVTSKIMTEAQASVIRSAIDS---------RLNIVISGGTGSGKTTLANAVIAE 167 (323)
T ss_pred HHHHcCCCCHHHHHHHHHHHHc---------CCeEEEECCCCCCHHHHHHHHHHH
Confidence 3568999999998886665553 567899999999999999887654
No 494
>PRK12860 transcriptional activator FlhC; Provisional
Probab=21.11 E-value=54 Score=35.63 Aligned_cols=25 Identities=28% Similarity=0.711 Sum_probs=19.8
Q ss_pred eecCCcceEEEeCC--CcceecCCCCC
Q 038397 18 VRCAGCHIILTVGP--GLTEFICGTCN 42 (1102)
Q Consensus 18 ~~C~~C~a~l~~~p--g~~~~~Cp~C~ 42 (1102)
.+|..||..+.+.. -...|+||-|.
T Consensus 135 ~~C~~Cgg~fv~~~~e~~~~f~CplC~ 161 (189)
T PRK12860 135 ARCCRCGGKFVTHAHDLRHNFVCGLCQ 161 (189)
T ss_pred ccCCCCCCCeeccccccCCCCcCCCCC
Confidence 45999999985443 35699999999
No 495
>CHL00200 trpA tryptophan synthase alpha subunit; Provisional
Probab=21.01 E-value=98 Score=35.14 Aligned_cols=37 Identities=22% Similarity=0.342 Sum_probs=26.2
Q ss_pred ceEEeehhhhhhccccccchHHHHHHHhcc-CCCceEEeecch
Q 038397 321 GVVFLTYSSLIASSEKGRSRLQQLVQWCGS-GYDGLVIFDECH 362 (1102)
Q Consensus 321 GvlF~TYs~L~~~~~~~~sRl~Ql~~W~g~-dfdgvivfDEcH 362 (1102)
-+++.||...+-. -.++..++.|-+ ..|||||-|+-+
T Consensus 93 p~vlm~Y~N~i~~-----~G~e~F~~~~~~aGvdgviipDLP~ 130 (263)
T CHL00200 93 PIVIFTYYNPVLH-----YGINKFIKKISQAGVKGLIIPDLPY 130 (263)
T ss_pred CEEEEecccHHHH-----hCHHHHHHHHHHcCCeEEEecCCCH
Confidence 4789999988742 135556677754 799999999544
No 496
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=20.88 E-value=49 Score=35.87 Aligned_cols=27 Identities=30% Similarity=0.610 Sum_probs=21.2
Q ss_pred ceecCCCccceeeccCCCccccCCCCCcc
Q 038397 95 IQLPCANCKAILNVPHGLVRFSCPQCAVE 123 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~~~~~f~Cp~C~~~ 123 (1102)
+.--|.+|++.|.. .-....||-||..
T Consensus 148 I~A~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 148 IYARCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEEEccCCCcceEE--cCcEEECCCCCCE
Confidence 34579999999998 3336799999964
No 497
>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family. Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.
Probab=20.82 E-value=1.4e+02 Score=38.20 Aligned_cols=50 Identities=22% Similarity=0.274 Sum_probs=39.3
Q ss_pred eEeecCCCCCcchhhHHHHHHHHhccCceEEEEEcCCc--hhhhHHhhhhhhCC
Q 038397 244 FFIGDGAGVGKGRTIAGLIWENWHHGRRKALWISVGSD--LKFDARRDLDDVGA 295 (1102)
Q Consensus 244 f~~gDg~GvGKGR~~AgiI~~n~l~Gr~~~~w~s~s~~--L~~Da~RDl~diG~ 295 (1102)
+++|- ||+||++.+..+|..-..+|. .+++|...+| |+...+.-.+..|-
T Consensus 184 lV~Gt-TGsGKT~l~~~li~q~i~~g~-~vi~fDpkgD~el~~~~~~~~~~~GR 235 (643)
T TIGR03754 184 LVLGT-TRVGKTRLAELLITQDIRRGD-VVIVFDPKGDADLLKRMYAEAKRAGR 235 (643)
T ss_pred EEECC-CCCCHHHHHHHHHHHHHHcCC-eEEEEeCCCCHHHHHHHHHHHHHhCC
Confidence 44555 999999999988888888887 4899988774 67777777777776
No 498
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=20.80 E-value=66 Score=28.44 Aligned_cols=31 Identities=26% Similarity=0.525 Sum_probs=0.0
Q ss_pred ceecCCCccceeeccCCCccc-cCCCCCcccc
Q 038397 95 IQLPCANCKAILNVPHGLVRF-SCPQCAVELA 125 (1102)
Q Consensus 95 ~~~~C~~C~A~~~vp~~~~~f-~Cp~C~~~L~ 125 (1102)
+.+.|.+|+.++.|=.--..- .|..||.-|+
T Consensus 6 m~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS-EE-SSSTSEEE
T ss_pred EEEECCCCCCeeEEEecCCeEEEcccCCCEec
No 499
>PRK09200 preprotein translocase subunit SecA; Reviewed
Probab=20.79 E-value=1.7e+02 Score=38.25 Aligned_cols=82 Identities=21% Similarity=0.191 Sum_probs=0.0
Q ss_pred HhhhcCCcceEEEEecccccccccccccccccccceeE-------EEecCCCcHhHHHHhhcccccCCCCCCCeEEEeec
Q 038397 805 KQLFMDGKKLVAIISEAGSAGVSLQADRRAANQKRRVH-------ITLELPWSADRAIQQFGRTHRSNQASAPEYRIIFT 877 (1102)
Q Consensus 805 k~~Fm~G~K~VAIISeAaSTGISLhADrr~~NQRRRvH-------itLElpWsADkAIQqfGRTHRSNQvsaP~Y~~l~T 877 (1102)
.++|..| .|.|-++-||=|+-...+ ..|+ |-.++|=|...-+|..|||+|-++- +--+-|+..
T Consensus 471 ~~ag~~g--~VlIATdmAgRG~DI~l~-------~~V~~~GGL~VI~~d~p~s~r~y~qr~GRtGR~G~~-G~s~~~is~ 540 (790)
T PRK09200 471 AEAGQKG--AVTVATNMAGRGTDIKLG-------EGVHELGGLAVIGTERMESRRVDLQLRGRSGRQGDP-GSSQFFISL 540 (790)
T ss_pred HHcCCCC--eEEEEccchhcCcCCCcc-------cccccccCcEEEeccCCCCHHHHHHhhccccCCCCC-eeEEEEEcc
Q ss_pred CccchhhhHHHHHHHHhhc
Q 038397 878 NLGGERRFASIVAKRLESL 896 (1102)
Q Consensus 878 ~l~GErRFaS~VAkRLeSL 896 (1102)
+=.-=++|.+--.+++-++
T Consensus 541 eD~l~~~~~~~~~~~~~~~ 559 (790)
T PRK09200 541 EDDLLKRFAPEELEKLKKK 559 (790)
T ss_pred hHHHHHhhccHHHHHHHHH
No 500
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=20.73 E-value=55 Score=34.95 Aligned_cols=126 Identities=17% Similarity=0.207 Sum_probs=0.0
Q ss_pred EEEEecCCCCCCCccchhhhcccc--CCCCCCCCHHHHHHHHhccC-hhHHHHHHHHHHhcccee---------eeccCC
Q 038397 394 VVYCSATGASEPRNMGYMVRLGLW--GAGTCFKDFQIFLGALDKGG-VGALELVAMDMKARGMYV---------CRTLSY 461 (1102)
Q Consensus 394 vvY~SATgasep~Nl~ym~RLGLW--g~gt~f~~~~~f~~a~~~gG-v~amE~va~dlK~~G~yi---------aR~LSf 461 (1102)
.|||||-...+|........||-| -.| ..-+--|| .|.|+.+|+.-+..|-++ .++...
T Consensus 4 ~V~~~s~~~~~~~~~~~A~~lG~~la~~g---------~~lV~GGg~~GlM~a~a~ga~~~gG~viGi~p~~l~~~~~~~ 74 (178)
T TIGR00730 4 CVYCGSSPGGNAAYKELAAELGAYLAGQG---------WGLVYGGGRVGLMGAIADAAMENGGTAVGVNPSGLFSGEVVH 74 (178)
T ss_pred EEECcCCCCCCcHHHHHHHHHHHHHHHCC---------CEEEECCChHhHHHHHHHHHHhcCCeEEEecchhhhhhhccC
Q ss_pred CCceeEEEeccCcHHHHHHHHHHHHHHHH-----HHHHHHHHHhhhcCCCCChhHHH---HHhhhhhhHHHHHHH
Q 038397 462 KGAEFEVIEAPLEAEMTDMYKKAAEFWAE-----LRVELLSASAFLANDKPNSSQLW---RLYWSGHQRFFRHMC 528 (1102)
Q Consensus 462 ~gvef~i~e~~l~~~~~~~Yd~~a~~w~~-----~~~~~~~a~e~~~~~~~~~~~~~---~~FwsahQrFFk~l~ 528 (1102)
..++-.+....+..+...|...+-.+-.. -..++-.++.+...+...+.-+. ..||.....|+++|.
T Consensus 75 ~~~~~~i~~~~~~~Rk~~m~~~sda~I~lPGG~GTL~El~e~~~~~qlg~~~kPiil~n~~g~~~~l~~~l~~~~ 149 (178)
T TIGR00730 75 QNLTELIEVNGMHERKAMMAELADAFIAMPGGFGTLEELFEVLTWAQLGIHQKPIILFNVNGHFDGLVEWLKYSI 149 (178)
T ss_pred CCCCceEEECCHHHHHHHHHHhCCEEEEcCCCcchHHHHHHHHHHHHcCCCCCCEEEECCcchHHHHHHHHHHHH
Done!