Query gi|254781187|ref|YP_003065600.1| putative phage terminase, large subunit [Candidatus Liberibacter asiaticus str. psy62] Match_columns 367 No_of_seqs 184 out of 358 Neff 7.3 Searched_HMMs 39220 Date Mon May 30 07:52:43 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781187.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam03237 Terminase_6 Terminas 100.0 2.6E-28 6.6E-33 192.6 19.9 247 82-350 2-261 (380) 2 pfam04466 Terminase_3 Phage te 99.9 3.3E-25 8.5E-30 173.5 19.2 253 77-350 3-264 (387) 3 pfam03354 Terminase_1 Phage Te 99.8 3.1E-18 7.9E-23 130.8 18.7 261 53-336 1-298 (473) 4 COG5323 Uncharacterized conser 99.4 2.3E-13 6E-18 100.9 6.8 238 80-345 39-281 (410) 5 COG4626 Phage terminase-like p 99.4 3.2E-10 8.1E-15 81.7 19.9 306 1-338 7-364 (546) 6 COG1783 XtmB Phage terminase l 99.2 6.3E-10 1.6E-14 79.8 14.6 233 79-336 27-273 (414) 7 TIGR01547 phage_term_2 phage t 99.1 7E-09 1.8E-13 73.4 15.8 248 80-340 4-304 (462) 8 pfam05876 Terminase_GpA Phage 98.9 4.9E-07 1.2E-11 62.1 16.1 166 52-242 18-192 (552) 9 COG4373 Mu-like prophage FluMu 98.8 2.5E-07 6.3E-12 64.0 14.2 236 79-336 31-332 (509) 10 COG1061 SSL2 DNA or RNA helica 98.7 1E-06 2.6E-11 60.1 13.9 162 48-242 34-196 (442) 11 COG1444 Predicted P-loop ATPas 98.6 3.6E-06 9.1E-11 56.8 14.4 149 54-236 215-364 (758) 12 smart00487 DEXDc DEAD-like hel 98.6 1E-06 2.6E-11 60.1 10.8 173 46-240 4-180 (201) 13 PRK10875 recD exonuclease V su 98.5 1.6E-05 4E-10 52.9 14.1 156 52-241 149-312 (607) 14 PRK13766 Hef nuclease; Provisi 98.4 5.9E-06 1.5E-10 55.5 11.7 159 48-231 13-173 (764) 15 TIGR01448 recD_rel helicase, R 98.4 4.2E-06 1.1E-10 56.4 10.3 138 52-243 352-509 (769) 16 pfam04851 ResIII Type III rest 98.3 6.8E-06 1.7E-10 55.1 10.0 100 50-232 3-103 (103) 17 TIGR01447 recD exodeoxyribonuc 98.2 3.8E-05 9.6E-10 50.5 11.4 156 52-232 229-395 (753) 18 pfam02562 PhoH PhoH-like prote 98.2 1.4E-05 3.5E-10 53.2 9.0 56 51-118 5-60 (205) 19 PRK10536 hypothetical protein; 98.2 5.5E-05 1.4E-09 49.6 12.1 184 51-273 60-261 (262) 20 PRK02362 ski2-like helicase; P 98.2 8.7E-05 2.2E-09 48.3 12.8 158 47-237 20-187 (736) 21 PRK01172 ski2-like helicase; P 98.2 0.0001 2.6E-09 47.9 13.1 160 50-239 22-187 (674) 22 COG1111 MPH1 ERCC4-like helica 98.2 5.4E-05 1.4E-09 49.6 11.3 167 48-241 13-183 (542) 23 PRK00254 ski2-like helicase; P 98.1 0.00022 5.6E-09 45.9 13.2 143 48-223 21-173 (717) 24 KOG0354 consensus 98.1 8.1E-05 2.1E-09 48.5 10.5 156 50-233 62-224 (746) 25 smart00488 DEXDc2 DEAD-like he 98.0 4.9E-05 1.3E-09 49.8 9.1 80 33-132 2-85 (289) 26 smart00489 DEXDc3 DEAD-like he 98.0 4.9E-05 1.3E-09 49.8 9.1 80 33-132 2-85 (289) 27 pfam00270 DEAD DEAD/DEAH box h 98.0 9.5E-05 2.4E-09 48.1 10.5 69 52-133 1-70 (167) 28 PRK10590 ATP-dependent RNA hel 98.0 0.00016 4.1E-09 46.7 10.9 138 45-204 18-162 (457) 29 KOG2036 consensus 97.9 0.00037 9.5E-09 44.5 11.5 145 52-211 255-399 (1011) 30 PRK11192 ATP-dependent RNA hel 97.9 0.00049 1.2E-08 43.7 11.9 75 46-133 21-100 (417) 31 PRK04837 ATP-dependent RNA hel 97.9 0.00017 4.4E-09 46.5 9.3 76 45-133 26-109 (423) 32 PRK11634 ATP-dependent RNA hel 97.8 0.00045 1.2E-08 43.9 10.8 76 45-133 23-99 (629) 33 cd00268 DEADc DEAD-box helicas 97.8 0.00041 1E-08 44.2 9.9 74 46-132 17-93 (203) 34 PRK04537 ATP-dependent RNA hel 97.7 0.0008 2E-08 42.4 10.9 79 44-135 25-111 (574) 35 PTZ00110 helicase; Provisional 97.7 0.00074 1.9E-08 42.6 10.6 159 45-227 199-368 (602) 36 cd00046 DEXDc DEAD-like helica 97.7 0.00027 6.9E-09 45.3 8.3 53 79-132 2-54 (144) 37 PRK01297 ATP-dependent RNA hel 97.7 0.00052 1.3E-08 43.6 9.7 77 43-132 99-183 (472) 38 COG1204 Superfamily II helicas 97.7 0.0023 5.8E-08 39.7 12.7 158 57-239 31-198 (766) 39 PRK11776 ATP-dependent RNA hel 97.6 0.00097 2.5E-08 41.9 10.4 78 45-135 21-99 (459) 40 PRK06305 DNA polymerase III su 97.6 0.0029 7.4E-08 39.0 12.2 138 54-229 21-159 (462) 41 PRK13709 conjugal transfer nic 97.5 0.0016 4.1E-08 40.5 10.4 159 10-229 938-1099(1756) 42 COG1203 CRISPR-associated heli 97.5 0.0052 1.3E-07 37.5 12.0 171 50-231 195-381 (733) 43 COG4096 HsdR Type I site-speci 97.4 0.0021 5.4E-08 39.8 9.7 74 44-124 159-232 (875) 44 COG0513 SrmB Superfamily II DN 97.4 0.0032 8E-08 38.8 10.2 159 46-226 47-212 (513) 45 PRK09112 DNA polymerase III su 97.3 0.0096 2.5E-07 35.8 11.9 159 45-230 13-180 (352) 46 PRK04914 ATP-dependent helicas 97.3 0.013 3.4E-07 35.0 13.9 176 40-238 137-324 (955) 47 PRK05896 DNA polymerase III su 97.3 0.011 2.8E-07 35.4 12.0 138 54-229 20-157 (613) 48 PRK05563 DNA polymerase III su 97.3 0.0089 2.3E-07 36.0 11.5 136 54-227 20-155 (541) 49 pfam00176 SNF2_N SNF2 family N 97.3 0.0051 1.3E-07 37.5 10.1 137 81-233 20-160 (295) 50 PRK08058 DNA polymerase III su 97.3 0.013 3.2E-07 35.1 12.0 123 50-228 6-147 (329) 51 COG4581 Superfamily II RNA hel 97.3 0.015 3.8E-07 34.7 13.1 159 47-244 116-283 (1041) 52 PRK06647 DNA polymerase III su 97.3 0.012 3.1E-07 35.2 11.9 137 54-229 20-157 (560) 53 PRK06674 DNA polymerase III su 97.2 0.013 3.4E-07 34.9 12.0 138 54-229 20-157 (563) 54 PRK08769 DNA polymerase III su 97.2 0.0062 1.6E-07 37.0 10.0 147 51-229 5-151 (319) 55 PRK08451 DNA polymerase III su 97.2 0.016 4.2E-07 34.4 12.0 136 55-228 19-154 (523) 56 COG1484 DnaC DNA replication p 97.2 0.0083 2.1E-07 36.2 10.5 71 35-113 69-139 (254) 57 PRK11448 hsdR type I restricti 97.2 0.018 4.6E-07 34.1 13.1 72 44-122 410-484 (1126) 58 PRK08074 bifunctional ATP-depe 97.1 0.0078 2E-07 36.4 9.9 72 50-130 258-332 (932) 59 TIGR02782 TrbB_P P-type conjug 97.1 0.0018 4.5E-08 40.3 6.6 56 52-118 125-181 (315) 60 PRK11747 dinG ATP-dependent DN 97.1 0.01 2.6E-07 35.7 10.4 68 50-123 25-92 (697) 61 PRK07133 DNA polymerase III su 97.1 0.021 5.3E-07 33.8 11.9 129 54-227 22-154 (718) 62 PRK05707 DNA polymerase III su 97.1 0.012 3.1E-07 35.2 10.6 36 194-229 109-144 (328) 63 PRK07270 DNA polymerase III su 97.1 0.021 5.4E-07 33.7 12.1 138 54-229 19-156 (557) 64 KOG0390 consensus 97.1 0.021 5.4E-07 33.7 11.8 173 52-242 240-424 (776) 65 pfam07652 Flavi_DEAD Flaviviru 97.1 0.008 2E-07 36.3 9.5 131 81-240 6-144 (146) 66 PRK00440 rfc replication facto 97.1 0.022 5.7E-07 33.5 11.8 119 55-230 21-140 (318) 67 PRK06871 DNA polymerase III su 97.1 0.02 5E-07 33.9 11.3 140 54-229 5-144 (324) 68 PRK07994 DNA polymerase III su 97.0 0.012 3.2E-07 35.1 10.2 134 54-225 20-153 (643) 69 TIGR03015 pepcterm_ATPase puta 97.0 0.021 5.3E-07 33.7 11.3 152 38-231 6-166 (269) 70 PRK06645 DNA polymerase III su 97.0 0.02 5.1E-07 33.8 11.2 142 54-229 25-166 (507) 71 PRK07471 DNA polymerase III su 96.9 0.0075 1.9E-07 36.5 8.4 160 47-230 9-178 (363) 72 pfam05970 DUF889 PIF1 helicase 96.9 0.002 5.2E-08 39.9 5.5 97 85-216 2-99 (418) 73 PRK13826 Dtr system oriT relax 96.9 0.013 3.3E-07 35.0 9.6 114 81-240 401-520 (1102) 74 COG1875 NYN ribonuclease and A 96.9 0.0015 3.9E-08 40.7 4.8 156 53-237 231-394 (436) 75 PRK06090 DNA polymerase III su 96.9 0.03 7.7E-07 32.8 11.5 134 60-229 13-146 (319) 76 PRK08181 transposase; Validate 96.9 0.024 6.2E-07 33.3 10.5 128 50-244 87-220 (269) 77 TIGR01054 rgy reverse gyrase; 96.8 0.015 3.8E-07 34.6 9.3 200 80-286 102-375 (1843) 78 PRK13889 conjugal transfer rel 96.8 0.018 4.6E-07 34.1 9.3 131 53-241 349-486 (992) 79 pfam05127 DUF699 Putative ATPa 96.7 0.043 1.1E-06 31.8 12.2 85 106-212 12-96 (160) 80 PRK05564 DNA polymerase III su 96.7 0.036 9.1E-07 32.3 10.5 121 54-229 8-131 (313) 81 KOG1805 consensus 96.7 0.0085 2.2E-07 36.1 7.0 130 78-230 687-829 (1100) 82 PRK07246 bifunctional ATP-depe 96.7 0.035 8.8E-07 32.4 10.1 74 50-134 245-318 (820) 83 COG1205 Distinct helicase fami 96.7 0.02 5.1E-07 33.9 8.8 74 51-137 71-144 (851) 84 PRK12323 DNA polymerase III su 96.6 0.05 1.3E-06 31.4 11.4 140 54-226 20-159 (721) 85 PRK12377 putative replication 96.6 0.051 1.3E-06 31.4 13.3 60 45-113 73-135 (248) 86 COG1199 DinG Rad3-related DNA 96.6 0.023 5.8E-07 33.5 8.9 67 49-124 14-80 (654) 87 PRK07764 DNA polymerase III su 96.6 0.025 6.3E-07 33.3 9.0 137 55-227 20-156 (775) 88 PRK08691 DNA polymerase III su 96.6 0.052 1.3E-06 31.3 11.4 134 54-225 20-153 (704) 89 COG1201 Lhr Lhr-like helicases 96.6 0.023 5.7E-07 33.5 8.6 78 46-136 18-101 (814) 90 KOG0952 consensus 96.5 0.023 6E-07 33.4 8.5 139 53-213 113-263 (1230) 91 PRK10917 ATP-dependent DNA hel 96.5 0.061 1.6E-06 30.9 11.8 83 42-137 253-335 (677) 92 COG1110 Reverse gyrase [DNA re 96.5 0.018 4.7E-07 34.1 7.7 109 79-200 99-212 (1187) 93 PRK12402 replication factor C 96.5 0.063 1.6E-06 30.8 11.8 35 193-227 127-161 (337) 94 TIGR02397 dnaX_nterm DNA polym 96.4 0.067 1.7E-06 30.7 11.0 119 54-230 18-154 (363) 95 KOG0338 consensus 96.3 0.012 3E-07 35.3 6.0 197 44-267 197-404 (691) 96 PRK08699 DNA polymerase III su 96.3 0.071 1.8E-06 30.5 9.9 127 79-229 23-151 (325) 97 KOG0335 consensus 96.3 0.038 9.6E-07 32.2 8.4 167 43-233 89-273 (482) 98 COG3972 Superfamily I DNA and 96.3 0.018 4.7E-07 34.1 6.7 134 82-224 181-327 (660) 99 PRK07003 DNA polymerase III su 96.3 0.085 2.2E-06 30.0 11.7 135 54-226 20-154 (816) 100 TIGR00345 arsA arsenite-activa 96.2 0.0057 1.4E-07 37.2 3.9 44 87-130 7-51 (330) 101 PRK11057 ATP-dependent DNA hel 96.1 0.021 5.3E-07 33.8 6.4 62 46-124 21-82 (607) 102 PRK05703 flhF flagellar biosyn 96.1 0.054 1.4E-06 31.2 8.4 68 51-118 184-252 (412) 103 PRK13767 ATP-dependent helicas 96.0 0.043 1.1E-06 31.8 7.6 89 7-124 6-101 (878) 104 TIGR03499 FlhF flagellar biosy 96.0 0.037 9.5E-07 32.2 7.1 70 50-119 165-237 (282) 105 TIGR02525 plasmid_TraJ plasmid 96.0 0.0086 2.2E-07 36.1 3.8 35 80-114 152-186 (374) 106 PRK06872 DNA polymerase III su 96.0 0.067 1.7E-06 30.6 8.4 135 54-226 20-154 (696) 107 TIGR03346 chaperone_ClpB ATP-d 96.0 0.12 3E-06 29.2 10.3 48 54-101 569-619 (852) 108 pfam01695 IstB IstB-like ATP b 96.0 0.08 2E-06 30.2 8.7 55 50-115 29-83 (178) 109 KOG0330 consensus 95.9 0.028 7E-07 33.0 6.2 156 47-224 80-240 (476) 110 PRK09183 transposase/IS protei 95.9 0.12 3E-06 29.2 9.4 68 35-114 66-136 (258) 111 PRK06526 transposase; Provisio 95.9 0.13 3.2E-06 29.0 9.3 127 50-244 80-212 (254) 112 PRK08853 DNA polymerase III su 95.8 0.14 3.5E-06 28.8 11.1 134 54-225 20-153 (717) 113 TIGR02621 cas3_GSU0051 CRISPR- 95.8 0.03 7.6E-07 32.8 6.0 158 45-216 11-215 (975) 114 KOG0331 consensus 95.7 0.035 8.8E-07 32.4 6.1 260 45-331 108-407 (519) 115 PRK07952 DNA replication prote 95.7 0.15 3.8E-06 28.5 12.9 65 45-115 68-133 (242) 116 PRK13833 conjugal transfer pro 95.7 0.036 9.2E-07 32.3 6.1 55 52-117 130-184 (323) 117 KOG0949 consensus 95.7 0.057 1.5E-06 31.1 7.1 167 50-242 511-682 (1330) 118 KOG0333 consensus 95.7 0.034 8.6E-07 32.4 5.8 144 38-203 247-408 (673) 119 PRK09111 DNA polymerase III su 95.6 0.16 4E-06 28.3 12.0 139 54-226 27-166 (600) 120 PRK08770 DNA polymerase III su 95.4 0.17 4.3E-06 28.2 8.5 135 54-226 20-154 (663) 121 KOG0391 consensus 95.3 0.11 2.8E-06 29.3 7.5 167 49-242 614-785 (1958) 122 COG1200 RecG RecG-like helicas 95.3 0.2 5.2E-06 27.7 9.5 82 42-136 258-339 (677) 123 PRK05648 DNA polymerase III su 95.3 0.19 4.9E-06 27.8 8.5 135 54-226 20-154 (705) 124 KOG0340 consensus 95.2 0.15 3.8E-06 28.5 7.9 158 37-218 16-184 (442) 125 TIGR03117 cas_csf4 CRISPR-asso 95.2 0.23 5.9E-06 27.3 9.1 45 80-124 19-63 (636) 126 PRK07993 DNA polymerase III su 95.1 0.25 6.3E-06 27.2 10.4 134 61-229 13-146 (334) 127 PRK13894 conjugal transfer ATP 94.9 0.077 2E-06 30.2 5.8 55 53-118 136-190 (320) 128 TIGR02768 TraA_Ti Ti-type conj 94.7 0.28 7.2E-06 26.8 8.2 122 53-231 417-539 (888) 129 KOG0350 consensus 94.7 0.17 4.4E-06 28.1 7.1 149 54-214 163-318 (620) 130 PRK07399 DNA polymerase III su 94.7 0.2 5.2E-06 27.7 7.3 41 189-230 123-163 (314) 131 TIGR00643 recG ATP-dependent D 94.7 0.3 7.5E-06 26.7 8.1 81 42-135 303-383 (721) 132 COG0470 HolB ATPase involved i 94.6 0.32 8.2E-06 26.5 11.8 103 79-229 26-147 (325) 133 PRK13342 recombination factor 94.6 0.32 8.2E-06 26.5 10.2 112 78-254 38-149 (417) 134 CHL00095 clpC Clp protease ATP 94.6 0.33 8.5E-06 26.4 9.0 127 54-222 513-647 (823) 135 KOG2170 consensus 94.5 0.34 8.7E-06 26.3 10.1 126 52-232 88-226 (344) 136 PRK06964 DNA polymerase III su 94.4 0.35 9E-06 26.2 10.4 37 193-229 134-170 (342) 137 KOG0389 consensus 94.4 0.19 4.8E-06 27.9 6.7 144 81-233 422-565 (941) 138 COG4889 Predicted helicase [Ge 94.3 0.37 9.5E-06 26.1 8.9 91 23-127 134-225 (1518) 139 PRK12723 flagellar biosynthesi 94.3 0.33 8.5E-06 26.4 7.7 73 49-121 145-221 (388) 140 PRK07132 DNA polymerase III su 94.3 0.39 9.9E-06 26.0 11.9 119 56-229 4-130 (303) 141 pfam05894 Podovirus_Gp16 Podov 94.2 0.39 1E-05 25.9 13.3 145 78-243 19-173 (333) 142 PRK07276 DNA polymerase III su 94.2 0.41 1E-05 25.8 11.5 136 53-228 5-141 (290) 143 PRK05917 DNA polymerase III su 94.1 0.41 1E-05 25.8 11.2 166 52-271 4-169 (290) 144 KOG0342 consensus 94.1 0.42 1.1E-05 25.7 8.0 168 45-234 99-276 (543) 145 PRK07940 DNA polymerase III su 94.0 0.44 1.1E-05 25.6 11.7 138 55-229 10-158 (395) 146 pfam00580 UvrD-helicase UvrD/R 93.9 0.1 2.6E-06 29.5 4.5 45 79-123 15-61 (494) 147 KOG1015 consensus 93.7 0.21 5.3E-06 27.6 5.8 160 80-242 699-871 (1567) 148 TIGR00631 uvrb excinuclease AB 93.7 0.48 1.2E-05 25.4 7.6 189 55-302 14-215 (667) 149 PRK11034 clpA ATP-dependent Cl 93.7 0.5 1.3E-05 25.3 8.2 47 54-100 462-511 (758) 150 PHA00149 DNA encapsidation pro 93.6 0.51 1.3E-05 25.2 10.5 143 77-243 18-172 (331) 151 PRK12724 flagellar biosynthesi 93.6 0.51 1.3E-05 25.2 7.6 42 79-120 225-266 (432) 152 PRK00411 cdc6 cell division co 93.5 0.53 1.4E-05 25.1 11.6 70 57-128 37-110 (394) 153 COG4962 CpaF Flp pilus assembl 93.4 0.18 4.5E-06 28.1 4.9 51 53-117 160-210 (355) 154 KOG0339 consensus 93.3 0.54 1.4E-05 25.1 7.3 158 48-230 243-410 (731) 155 PRK10416 cell division protein 93.3 0.58 1.5E-05 24.9 10.4 106 74-214 294-402 (499) 156 KOG0334 consensus 93.0 0.45 1.1E-05 25.6 6.6 75 48-135 385-465 (997) 157 pfam02456 Adeno_IVa2 Adenoviru 92.9 0.21 5.3E-06 27.6 4.7 84 52-138 58-145 (370) 158 PRK06731 flhF flagellar biosyn 92.9 0.67 1.7E-05 24.5 13.8 69 50-120 45-117 (270) 159 smart00382 AAA ATPases associa 92.7 0.68 1.7E-05 24.5 7.1 40 79-120 4-43 (148) 160 TIGR03158 cas3_cyano CRISPR-as 92.7 0.7 1.8E-05 24.4 7.8 65 55-135 2-66 (357) 161 TIGR01074 rep ATP-dependent DN 92.7 0.26 6.7E-06 27.0 5.0 89 55-158 8-98 (677) 162 PRK00149 dnaA chromosomal repl 92.7 0.66 1.7E-05 24.5 7.0 56 53-115 128-183 (447) 163 COG0593 DnaA ATPase involved i 92.6 0.63 1.6E-05 24.7 6.9 36 80-115 116-151 (408) 164 COG1702 PhoH Phosphate starvat 92.6 0.17 4.3E-06 28.2 3.9 150 50-232 128-281 (348) 165 PRK10919 ATP-dependent DNA hel 92.6 0.25 6.3E-06 27.2 4.7 45 80-124 18-64 (672) 166 PRK12727 flagellar biosynthesi 92.5 0.74 1.9E-05 24.2 10.1 40 80-119 351-391 (557) 167 TIGR01420 pilT_fam twitching m 92.5 0.18 4.6E-06 28.0 3.9 27 79-105 129-155 (350) 168 TIGR03345 VI_ClpV1 type VI sec 92.4 0.76 1.9E-05 24.2 9.4 48 54-101 570-620 (852) 169 PRK08116 hypothetical protein; 92.3 0.8 2E-05 24.0 12.5 33 80-114 111-143 (262) 170 PRK06835 DNA replication prote 92.3 0.61 1.6E-05 24.7 6.4 82 25-115 138-220 (330) 171 COG2812 DnaX DNA polymerase II 92.2 0.82 2.1E-05 24.0 7.3 134 54-225 20-153 (515) 172 KOG0352 consensus 92.2 0.82 2.1E-05 24.0 7.2 166 53-243 23-223 (641) 173 cd01130 VirB11-like_ATPase Typ 92.1 0.46 1.2E-05 25.5 5.6 51 53-117 12-62 (186) 174 PRK06995 flhF flagellar biosyn 92.1 0.3 7.8E-06 26.6 4.7 41 80-120 179-220 (404) 175 PRK06696 uridine kinase; Valid 92.0 0.74 1.9E-05 24.2 6.6 54 55-113 7-60 (227) 176 cd01128 rho_factor Transcripti 91.9 0.43 1.1E-05 25.7 5.3 35 79-113 18-52 (249) 177 PRK11054 helD DNA helicase IV; 91.6 0.43 1.1E-05 25.7 5.0 46 79-124 211-258 (684) 178 PRK10865 protein disaggregatio 91.5 0.97 2.5E-05 23.5 8.5 48 54-101 572-622 (857) 179 PRK04195 replication factor C 91.1 1.1 2.7E-05 23.3 12.0 22 79-100 42-63 (403) 180 KOG0328 consensus 91.1 0.17 4.2E-06 28.2 2.5 151 47-221 46-202 (400) 181 PRK09270 frcK putative fructos 91.0 0.85 2.2E-05 23.9 6.1 38 76-113 33-70 (230) 182 COG5525 Bacteriophage tail ass 90.9 0.21 5.3E-06 27.6 2.8 152 52-231 49-207 (611) 183 TIGR03305 alt_F1F0_F1_bet alte 90.8 0.78 2E-05 24.1 5.7 51 79-130 140-191 (449) 184 COG5410 Uncharacterized protei 90.8 0.84 2.2E-05 23.9 5.9 187 5-223 3-203 (305) 185 COG0003 ArsA Predicted ATPase 90.5 0.38 9.8E-06 26.0 3.9 47 81-128 6-52 (322) 186 COG0514 RecQ Superfamily II DN 90.5 0.69 1.7E-05 24.4 5.2 61 47-124 14-74 (590) 187 pfam02374 ArsA_ATPase Anion-tr 90.4 0.64 1.6E-05 24.6 5.0 42 81-124 5-47 (304) 188 KOG0947 consensus 90.3 1.3 3.2E-05 22.8 8.1 68 50-132 297-364 (1248) 189 KOG0332 consensus 90.3 0.22 5.7E-06 27.4 2.5 72 43-124 105-177 (477) 190 KOG0781 consensus 90.2 1.3 3.3E-05 22.8 9.5 137 55-230 362-506 (587) 191 pfam03308 ArgK ArgK protein. T 90.2 1.3 3.3E-05 22.8 6.7 54 55-118 15-70 (267) 192 pfam05496 RuvB_N Holliday junc 90.0 1.3 3.4E-05 22.6 9.5 26 193-218 103-128 (234) 193 TIGR01978 sufC FeS assembly AT 89.8 0.25 6.3E-06 27.2 2.5 72 192-272 166-243 (248) 194 pfam00437 GSPII_E Type II/IV s 89.8 1.4 3.5E-05 22.6 6.8 37 79-117 141-177 (283) 195 KOG4284 consensus 89.8 0.68 1.7E-05 24.5 4.7 137 47-208 44-185 (980) 196 PRK11889 flhF flagellar biosyn 89.7 1.4 3.6E-05 22.5 13.0 60 58-120 223-283 (436) 197 pfam00448 SRP54 SRP54-type pro 89.3 1.5 3.8E-05 22.4 12.0 52 80-135 4-55 (196) 198 KOG0991 consensus 89.3 1.1 2.9E-05 23.1 5.5 94 74-216 45-138 (333) 199 PRK08939 primosomal protein Dn 89.2 1.5 3.9E-05 22.3 7.7 70 45-117 127-196 (306) 200 PRK10037 cell division protein 89.2 0.73 1.9E-05 24.3 4.5 43 77-121 1-45 (250) 201 TIGR00580 mfd transcription-re 89.2 1.5 3.9E-05 22.3 7.0 60 51-117 509-571 (997) 202 PRK11773 uvrD DNA-dependent he 89.1 0.34 8.5E-06 26.3 2.7 44 80-123 25-70 (722) 203 KOG0989 consensus 88.8 1.7 4.2E-05 22.1 9.7 172 54-274 40-221 (346) 204 cd02025 PanK Pantothenate kina 88.7 0.9 2.3E-05 23.7 4.7 34 80-113 2-35 (220) 205 COG1703 ArgK Putative periplas 88.6 1.5 3.8E-05 22.4 5.7 75 25-117 13-91 (323) 206 PRK09401 reverse gyrase; Revie 88.6 1.7 4.3E-05 22.0 17.0 110 79-201 95-209 (1176) 207 PRK11664 ATP-dependent RNA hel 88.4 1.7 4.5E-05 21.9 14.7 145 79-243 22-170 (812) 208 TIGR00678 holB DNA polymerase 88.3 1.8 4.5E-05 21.9 7.5 132 79-230 16-158 (216) 209 COG1239 ChlI Mg-chelatase subu 88.3 1.8 4.5E-05 21.9 7.2 161 48-233 19-199 (423) 210 cd02035 ArsA ArsA ATPase funct 88.3 0.67 1.7E-05 24.5 3.8 31 82-114 4-34 (217) 211 PRK13900 type IV secretion sys 88.3 1.5 3.9E-05 22.3 5.6 37 78-117 161-197 (332) 212 cd03115 SRP The signal recogni 88.3 1.1 2.7E-05 23.2 4.8 52 80-135 3-54 (173) 213 pfam01637 Arch_ATPase Archaeal 88.1 1.8 4.6E-05 21.8 10.8 52 57-116 6-57 (223) 214 cd01983 Fer4_NifH The Fer4_Nif 88.1 1.2 3.1E-05 22.9 5.0 33 80-114 2-34 (99) 215 cd02036 MinD Bacterial cell di 88.0 1.1 2.7E-05 23.3 4.7 32 80-113 2-34 (179) 216 TIGR01425 SRP54_euk signal rec 87.9 1.7 4.3E-05 22.0 5.7 94 84-209 128-223 (453) 217 cd00550 ArsA_ATPase Oxyanion-t 87.9 0.74 1.9E-05 24.2 3.8 40 82-123 5-45 (254) 218 PRK13851 type IV secretion sys 87.8 1.2 3.2E-05 22.9 4.9 101 78-220 163-263 (343) 219 KOG0337 consensus 87.8 1.2 3.1E-05 23.0 4.8 74 45-131 38-113 (529) 220 PRK08233 hypothetical protein; 87.7 0.96 2.4E-05 23.6 4.3 32 79-114 5-36 (182) 221 KOG1123 consensus 87.7 0.57 1.5E-05 24.9 3.1 147 41-210 293-441 (776) 222 KOG1002 consensus 87.6 1.9 5E-05 21.7 7.0 216 3-233 119-357 (791) 223 PRK07667 uridine kinase; Provi 87.6 0.63 1.6E-05 24.7 3.3 27 75-101 12-38 (190) 224 TIGR00750 lao LAO/AO transport 87.6 2 5E-05 21.7 5.9 58 50-117 17-78 (333) 225 PTZ00301 uridine kinase; Provi 87.5 1.3 3.4E-05 22.7 4.9 26 79-104 5-30 (210) 226 KOG0923 consensus 87.3 2 5.2E-05 21.6 10.0 160 54-243 269-431 (902) 227 cd02034 CooC The accessory pro 87.1 1.5 3.8E-05 22.4 5.0 37 79-117 1-37 (116) 228 pfam07517 SecA_DEAD SecA DEAD- 87.1 2.1 5.3E-05 21.5 7.9 143 79-242 93-235 (381) 229 COG2842 Uncharacterized ATPase 87.0 2.1 5.4E-05 21.5 6.5 107 80-231 97-203 (297) 230 pfam07570 consensus 86.6 0.79 2E-05 24.1 3.3 28 78-106 14-41 (45) 231 TIGR03029 EpsG chain length de 86.3 2.3 5.9E-05 21.2 7.1 77 37-117 63-142 (274) 232 KOG0347 consensus 86.0 0.64 1.6E-05 24.6 2.6 265 45-336 198-538 (731) 233 COG2607 Predicted ATPase (AAA+ 85.7 2.5 6.3E-05 21.0 12.9 92 33-135 36-137 (287) 234 pfam02500 DNA_pack_N Probable 85.6 1.3 3.2E-05 22.8 4.0 51 83-134 186-236 (276) 235 cd02028 UMPK_like Uridine mono 85.4 1.8 4.5E-05 21.9 4.7 38 80-117 2-39 (179) 236 cd01135 V_A-ATPase_B V/A-type 85.2 1.4 3.6E-05 22.5 4.1 44 79-122 71-115 (276) 237 TIGR01969 minD_arch cell divis 84.9 0.95 2.4E-05 23.6 3.1 191 80-285 3-207 (258) 238 PRK06921 hypothetical protein; 84.8 2.7 6.9E-05 20.8 9.0 59 51-114 94-152 (265) 239 pfam03205 MobB Molybdopterin g 84.8 2.3 5.8E-05 21.2 5.0 34 78-113 1-34 (122) 240 pfam10236 DAP3 Mitochondrial r 84.7 2.4 6.2E-05 21.1 5.1 27 77-103 23-49 (274) 241 KOG0348 consensus 84.6 2.8 7.1E-05 20.7 7.7 139 45-204 154-300 (708) 242 TIGR02562 cas3_yersinia CRISPR 84.6 1.3 3.3E-05 22.8 3.6 262 53-326 423-776 (1153) 243 pfam09848 DUF2075 Uncharacteri 84.6 2.8 7.1E-05 20.7 8.0 39 80-118 4-42 (348) 244 CHL00060 atpB ATP synthase CF1 84.6 2.8 7.1E-05 20.7 6.2 50 79-129 157-207 (480) 245 CHL00081 chlI Mg-protoporyphyr 84.5 2.8 7.2E-05 20.7 9.1 52 179-233 130-194 (347) 246 cd01133 F1-ATPase_beta F1 ATP 84.4 2.8 7.2E-05 20.7 5.8 33 79-111 71-103 (274) 247 TIGR00959 ffh signal recogniti 84.2 1.1 2.9E-05 23.1 3.2 112 80-225 105-227 (439) 248 PRK13407 bchI magnesium chelat 84.2 2.9 7.4E-05 20.6 8.1 54 177-233 117-183 (334) 249 KOG3022 consensus 84.2 2 5.2E-05 21.5 4.5 34 78-113 48-82 (300) 250 cd01134 V_A-ATPase_A V/A-type 84.1 2.9 7.5E-05 20.6 5.5 37 79-120 159-195 (369) 251 cd02042 ParA ParA and ParB of 84.0 1.6 4.1E-05 22.2 3.9 28 86-115 9-36 (104) 252 PRK12597 F0F1 ATP synthase sub 83.9 3 7.6E-05 20.5 6.4 44 79-122 143-187 (459) 253 pfam05673 DUF815 Protein of un 83.9 3 7.6E-05 20.5 11.2 52 79-136 55-106 (248) 254 PRK05298 excinuclease ABC subu 83.9 3 7.6E-05 20.5 7.9 68 51-131 14-81 (657) 255 COG3640 CooC CO dehydrogenase 83.8 2.8 7.1E-05 20.7 5.1 34 79-113 2-35 (255) 256 pfam00308 Bac_DnaA Bacterial d 83.7 3 7.7E-05 20.5 7.0 36 80-115 37-72 (219) 257 pfam06564 YhjQ YhjQ protein. T 83.7 2.2 5.7E-05 21.3 4.6 36 77-114 1-37 (244) 258 PRK11670 putative ATPase; Prov 83.6 2.4 6.1E-05 21.1 4.7 34 79-114 109-143 (369) 259 PRK08118 topology modulation p 83.3 1.2 3E-05 23.0 3.0 26 77-102 1-26 (167) 260 PRK11131 ATP-dependent RNA hel 83.3 3.2 8.1E-05 20.4 14.2 161 53-244 77-240 (1295) 261 PRK13341 recombination factor 83.2 3.2 8.1E-05 20.4 10.0 41 78-123 53-93 (726) 262 KOG1803 consensus 82.9 2.6 6.6E-05 20.9 4.6 45 80-126 204-248 (649) 263 PRK04220 2-phosphoglycerate ki 82.9 2.5 6.4E-05 21.0 4.5 89 10-124 42-131 (306) 264 PRK07568 aspartate aminotransf 82.8 3.3 8.4E-05 20.3 7.6 64 51-122 64-127 (396) 265 cd02038 FleN-like FleN is a me 82.8 2.7 6.9E-05 20.8 4.7 33 80-114 2-35 (139) 266 COG1373 Predicted ATPase (AAA+ 82.5 3.4 8.7E-05 20.2 10.4 16 79-94 39-54 (398) 267 cd04169 RF3 RF3 subfamily. Pe 82.4 3.4 8.7E-05 20.2 5.4 140 78-243 3-146 (267) 268 COG1149 MinD superfamily P-loo 82.3 1.3 3.3E-05 22.7 2.9 72 192-275 164-240 (284) 269 TIGR00603 rad25 DNA repair hel 82.3 1.4 3.6E-05 22.5 3.1 148 41-211 260-411 (756) 270 TIGR01587 cas3_core CRISPR-ass 82.3 3.3 8.4E-05 20.3 5.0 50 80-130 2-54 (424) 271 cd01120 RecA-like_NTPases RecA 82.3 3.4 8.8E-05 20.1 6.2 42 80-123 2-45 (165) 272 cd02024 NRK1 Nicotinamide ribo 82.2 2 5.2E-05 21.5 3.9 21 80-100 2-22 (187) 273 cd01869 Rab1_Ypt1 Rab1/Ypt1 su 82.1 1.6 4.1E-05 22.2 3.3 23 76-98 1-23 (166) 274 cd03110 Fer4_NifH_child This p 82.0 1.3 3.3E-05 22.8 2.8 36 190-232 91-126 (179) 275 TIGR02788 VirB11 P-type DNA tr 81.9 1.3 3.2E-05 22.8 2.7 94 78-191 159-270 (328) 276 KOG0345 consensus 81.9 3.6 9.1E-05 20.0 8.6 122 79-208 45-174 (567) 277 KOG2228 consensus 81.8 3.6 9.2E-05 20.0 7.9 81 43-134 24-105 (408) 278 PRK09280 F0F1 ATP synthase sub 81.5 3.7 9.4E-05 20.0 6.8 34 79-112 147-180 (466) 279 COG1643 HrpA HrpA-like helicas 81.5 3.7 9.4E-05 20.0 13.1 161 53-244 53-217 (845) 280 cd01886 EF-G Elongation factor 81.4 0.78 2E-05 24.1 1.5 133 79-242 1-138 (270) 281 pfam01935 DUF87 Domain of unkn 81.4 3.2 8.2E-05 20.3 4.7 39 79-118 25-63 (218) 282 PRK02731 histidinol-phosphate 81.3 2.5 6.4E-05 21.0 4.1 58 51-121 65-122 (367) 283 TIGR01075 uvrD DNA helicase II 81.2 3.7 9.5E-05 19.9 4.9 55 79-136 19-73 (741) 284 COG0210 UvrD Superfamily I DNA 81.1 3.8 9.7E-05 19.9 6.0 45 79-123 17-63 (655) 285 KOG0742 consensus 80.9 3.9 9.9E-05 19.8 11.5 77 57-135 365-441 (630) 286 PRK06793 fliI flagellum-specif 80.8 3.2 8.2E-05 20.3 4.5 41 79-122 158-199 (432) 287 pfam00931 NB-ARC NB-ARC domain 80.7 3.9 0.0001 19.8 10.7 48 76-123 18-66 (285) 288 TIGR01407 dinG_rel DnaQ family 80.7 3.9 0.0001 19.8 7.4 76 51-133 261-339 (944) 289 COG4240 Predicted kinase [Gene 80.7 3.9 0.0001 19.8 5.1 52 56-114 34-86 (300) 290 cd01868 Rab11_like Rab11-like. 80.4 2 5.1E-05 21.6 3.3 23 76-98 2-24 (165) 291 COG0610 Type I site-specific r 80.3 4 0.0001 19.7 12.4 138 51-203 249-388 (962) 292 CHL00175 minD septum-site dete 80.3 3.5 9E-05 20.1 4.6 36 76-113 11-48 (279) 293 pfam00155 Aminotran_1_2 Aminot 79.8 4.2 0.00011 19.6 6.0 69 49-124 35-104 (351) 294 COG1074 RecB ATP-dependent exo 79.7 4.2 0.00011 19.6 6.4 47 184-231 372-419 (1139) 295 pfam05729 NACHT NACHT domain. 79.6 2.5 6.5E-05 21.0 3.6 27 79-105 2-28 (165) 296 TIGR01968 minD_bact septum sit 79.6 2.6 6.6E-05 20.9 3.7 123 80-214 4-136 (272) 297 PRK06067 flagellar accessory p 79.6 4.3 0.00011 19.6 6.2 40 79-120 34-75 (241) 298 TIGR02545 ATP_syn_fliI flagell 78.9 1.4 3.7E-05 22.5 2.2 46 79-134 160-205 (439) 299 KOG4181 consensus 78.8 2.8 7.2E-05 20.7 3.7 62 55-123 171-232 (491) 300 COG4178 ABC-type uncharacteriz 78.6 4.6 0.00012 19.4 5.9 49 183-231 525-574 (604) 301 PRK05480 uridine kinase; Provi 78.6 2.3 5.9E-05 21.2 3.2 24 78-101 7-30 (209) 302 PRK10818 cell division inhibit 78.6 4.4 0.00011 19.5 4.6 32 80-113 5-37 (270) 303 PRK08149 ATP synthase SpaL; Va 78.4 2.8 7.1E-05 20.7 3.6 38 79-121 152-189 (427) 304 KOG0385 consensus 78.4 4.6 0.00012 19.3 9.5 172 36-241 159-336 (971) 305 TIGR03496 FliI_clade1 flagella 78.2 4.7 0.00012 19.3 5.2 36 79-119 139-174 (411) 306 COG0455 flhG Antiactivator of 78.2 4.7 0.00012 19.3 4.9 35 78-112 3-38 (262) 307 PRK10689 transcription-repair 78.1 4.7 0.00012 19.3 8.0 59 54-120 604-662 (1148) 308 cd01863 Rab18 Rab18 subfamily. 78.0 2.2 5.7E-05 21.3 2.9 21 78-98 1-21 (161) 309 TIGR02868 CydC ABC transporter 78.0 2.5 6.3E-05 21.0 3.1 72 55-141 373-447 (566) 310 PRK08927 fliI flagellum-specif 78.0 3.3 8.4E-05 20.3 3.8 39 79-122 160-198 (441) 311 TIGR02746 TraC-F-type type-IV 77.9 4.8 0.00012 19.3 5.5 47 78-124 490-536 (900) 312 PRK07960 fliI flagellum-specif 77.9 2.7 6.8E-05 20.8 3.3 39 79-122 177-215 (455) 313 PRK13235 nifH nitrogenase redu 77.9 4.8 0.00012 19.3 4.9 43 77-121 1-45 (274) 314 pfam00485 PRK Phosphoribulokin 77.9 2.1 5.3E-05 21.5 2.8 22 80-101 2-23 (196) 315 PRK07721 fliI flagellum-specif 77.9 3.6 9.2E-05 20.0 4.0 38 79-121 158-195 (435) 316 PRK03321 putative aminotransfe 77.9 4.8 0.00012 19.3 5.2 58 51-121 55-112 (352) 317 PRK05688 fliI flagellum-specif 77.9 2.2 5.6E-05 21.3 2.9 46 79-134 170-215 (451) 318 PRK03158 histidinol-phosphate 77.8 2.9 7.3E-05 20.6 3.5 59 51-122 62-120 (359) 319 cd01131 PilT Pilus retraction 77.7 3.8 9.7E-05 19.9 4.1 35 80-115 4-38 (198) 320 PRK09435 arginine/ornithine tr 77.7 4.9 0.00012 19.2 7.1 59 53-121 33-93 (325) 321 PRK07594 type III secretion sy 77.6 3.3 8.5E-05 20.2 3.7 38 79-121 157-194 (433) 322 COG1419 FlhF Flagellar GTP-bin 77.6 4.9 0.00013 19.2 9.3 62 55-118 183-245 (407) 323 cd02023 UMPK Uridine monophosp 77.6 2.2 5.6E-05 21.3 2.8 22 80-101 2-23 (198) 324 COG0556 UvrB Helicase subunit 77.5 4.9 0.00013 19.2 7.0 69 51-132 13-81 (663) 325 pfam03266 DUF265 Protein of un 77.5 4.9 0.00013 19.2 7.1 60 191-255 95-157 (168) 326 PRK12289 ribosome-associated G 77.4 2.5 6.4E-05 21.0 3.1 16 82-97 176-191 (351) 327 cd01864 Rab19 Rab19 subfamily. 77.4 2.8 7.1E-05 20.7 3.3 23 76-98 2-24 (165) 328 PRK12422 chromosomal replicati 77.4 5 0.00013 19.2 6.2 53 57-115 124-177 (455) 329 cd00009 AAA The AAA+ (ATPases 77.4 5 0.00013 19.2 11.8 35 79-115 21-55 (151) 330 cd01892 Miro2 Miro2 subfamily. 77.2 3.1 7.9E-05 20.4 3.5 23 76-98 3-25 (169) 331 PRK10263 DNA translocase FtsK; 77.2 3.4 8.6E-05 20.2 3.7 47 70-116 1003-1051(1355) 332 PRK08972 fliI flagellum-specif 77.1 3.8 9.7E-05 19.9 3.9 38 79-121 162-199 (440) 333 cd01867 Rab8_Rab10_Rab13_like 77.0 2.9 7.5E-05 20.6 3.3 23 76-98 2-24 (167) 334 PRK08533 flagellar accessory p 77.0 5.1 0.00013 19.1 6.4 44 75-120 22-67 (230) 335 cd01865 Rab3 Rab3 subfamily. 77.0 2.6 6.6E-05 20.9 3.1 23 77-99 1-23 (165) 336 pfam02367 UPF0079 Uncharacteri 76.9 4.1 0.00011 19.7 4.1 49 57-118 3-51 (123) 337 PRK06002 fliI flagellum-specif 76.8 2.3 5.9E-05 21.2 2.7 21 79-99 167-187 (450) 338 pfam01580 FtsK_SpoIIIE FtsK/Sp 76.7 5.2 0.00013 19.0 4.6 41 77-117 38-80 (202) 339 PRK00741 prfC peptide chain re 76.7 2.6 6.5E-05 20.9 2.9 137 77-241 10-152 (526) 340 PHA02518 ParA-like protein; Pr 76.6 3.1 8E-05 20.4 3.4 28 85-114 9-36 (211) 341 PRK08472 fliI flagellum-specif 76.6 3.1 8E-05 20.4 3.4 22 79-100 160-181 (435) 342 PRK13909 putative recombinatio 76.6 5.2 0.00013 19.0 6.4 40 191-231 325-371 (911) 343 cd04122 Rab14 Rab14 subfamily. 76.5 2.9 7.5E-05 20.6 3.2 24 76-99 1-24 (166) 344 PRK06217 hypothetical protein; 76.4 2.7 6.8E-05 20.8 3.0 28 77-104 1-28 (185) 345 pfam07726 AAA_3 ATPase family 76.4 5.3 0.00013 19.0 7.5 24 194-217 65-88 (131) 346 COG0552 FtsY Signal recognitio 76.3 5.3 0.00014 19.0 9.7 124 75-234 139-272 (340) 347 TIGR02784 addA_alphas double-s 76.3 2.9 7.4E-05 20.6 3.1 24 192-215 397-420 (1190) 348 KOG0327 consensus 76.2 3.7 9.5E-05 19.9 3.7 67 46-124 44-111 (397) 349 COG0563 Adk Adenylate kinase a 76.2 3.5 9E-05 20.1 3.5 29 79-107 2-30 (178) 350 PRK03566 consensus 76.2 1.5 3.7E-05 22.4 1.6 54 55-121 69-122 (365) 351 PRK13231 nitrogenase reductase 76.0 5.4 0.00014 18.9 4.6 45 77-124 2-48 (264) 352 cd04138 H_N_K_Ras_like H-Ras/N 75.9 3 7.8E-05 20.5 3.2 22 78-99 2-23 (162) 353 cd04110 Rab35 Rab35 subfamily. 75.8 3.2 8.2E-05 20.3 3.3 24 75-98 4-27 (199) 354 PRK06820 type III secretion sy 75.8 4.3 0.00011 19.6 3.9 35 79-118 165-199 (445) 355 PRK07196 fliI flagellum-specif 75.7 5.5 0.00014 18.9 5.8 38 79-121 157-194 (434) 356 TIGR00958 3a01208 antigen pept 75.6 2.5 6.3E-05 21.0 2.6 23 79-101 561-583 (770) 357 CHL00059 atpA ATP synthase CF1 75.6 5.6 0.00014 18.9 4.9 22 79-100 165-186 (501) 358 cd01866 Rab2 Rab2 subfamily. 75.6 3.2 8.2E-05 20.3 3.2 23 76-98 3-25 (168) 359 pfam07728 AAA_5 AAA domain (dy 75.5 5.6 0.00014 18.8 7.7 25 193-217 68-92 (139) 360 PRK07324 transaminase; Validat 75.5 5.6 0.00014 18.8 6.2 60 53-124 62-121 (373) 361 cd04116 Rab9 Rab9 subfamily. 75.4 3.4 8.8E-05 20.2 3.3 23 76-98 4-26 (170) 362 smart00175 RAB Rab subfamily o 75.4 2.9 7.3E-05 20.6 2.9 21 78-98 1-21 (164) 363 PRK06315 type III secretion sy 75.2 2.6 6.5E-05 20.9 2.6 22 79-100 166-187 (442) 364 cd04114 Rab30 Rab30 subfamily. 75.1 4.1 0.0001 19.7 3.7 24 75-98 5-28 (169) 365 PRK11331 5-methylcytosine-spec 75.1 5.7 0.00015 18.8 4.4 40 79-118 196-237 (459) 366 pfam00735 Septin Septin. Membe 74.8 3.3 8.4E-05 20.3 3.1 23 77-99 4-26 (280) 367 cd04136 Rap_like Rap-like subf 74.8 3.3 8.5E-05 20.2 3.1 22 78-99 2-23 (163) 368 KOG0920 consensus 74.8 5.8 0.00015 18.7 14.1 186 53-273 176-365 (924) 369 PRK00081 coaE dephospho-CoA ki 74.6 3.1 8E-05 20.4 3.0 31 77-113 2-32 (199) 370 PRK04863 mukB cell division pr 74.6 4.1 0.0001 19.7 3.5 36 79-117 29-64 (1486) 371 cd04107 Rab32_Rab38 Rab38/Rab3 74.5 3.2 8.2E-05 20.3 3.0 21 78-98 1-21 (201) 372 PRK07261 topology modulation p 74.5 3.3 8.4E-05 20.3 3.0 22 79-100 2-23 (171) 373 PRK13705 plasmid-partitioning 74.4 6 0.00015 18.7 7.5 87 23-114 50-142 (388) 374 TIGR00955 3a01204 Pigment prec 74.4 2 5E-05 21.6 1.9 233 55-305 44-325 (671) 375 KOG1133 consensus 74.3 6 0.00015 18.7 5.5 47 50-104 15-62 (821) 376 PRK09265 aminotransferase AlaT 74.3 6 0.00015 18.7 8.9 61 51-119 70-131 (404) 377 PRK06936 type III secretion sy 74.1 6.1 0.00015 18.6 6.0 36 79-119 164-199 (439) 378 cd04127 Rab27A Rab27a subfamil 74.0 3.9 9.9E-05 19.8 3.3 23 76-98 3-25 (180) 379 TIGR03497 FliI_clade2 flagella 74.0 6.1 0.00016 18.6 5.4 41 79-122 139-180 (413) 380 PRK13768 GTPase; Provisional 73.9 6.2 0.00016 18.6 4.9 36 78-113 3-38 (253) 381 PRK13230 nitrogenase reductase 73.8 6.2 0.00016 18.6 5.0 35 77-113 1-35 (292) 382 COG0572 Udk Uridine kinase [Nu 73.8 3.2 8.1E-05 20.4 2.8 23 77-99 8-30 (218) 383 cd04125 RabA_like RabA-like su 73.8 3.4 8.6E-05 20.2 2.9 22 78-99 1-22 (188) 384 cd04123 Rab21 Rab21 subfamily. 73.6 3.5 8.9E-05 20.1 3.0 22 78-99 1-22 (162) 385 TIGR01166 cbiO cobalt ABC tran 73.4 3.3 8.4E-05 20.2 2.8 43 179-222 133-180 (190) 386 PRK13634 cbiO cobalt transport 73.4 0.53 1.3E-05 25.1 -1.3 37 55-99 6-42 (276) 387 cd02037 MRP-like MRP (Multiple 73.4 6.3 0.00016 18.5 4.5 32 80-113 2-34 (169) 388 COG0396 sufC Cysteine desulfur 73.3 2.9 7.3E-05 20.6 2.5 81 182-272 154-238 (251) 389 smart00173 RAS Ras subfamily o 73.3 3.6 9.2E-05 20.0 3.0 21 78-98 1-21 (164) 390 COG2805 PilT Tfp pilus assembl 73.3 6.4 0.00016 18.5 5.5 34 79-113 127-160 (353) 391 cd04113 Rab4 Rab4 subfamily. 73.3 3.5 8.9E-05 20.1 2.9 21 78-98 1-21 (161) 392 cd04175 Rap1 Rap1 subgroup. T 73.2 3.8 9.7E-05 19.9 3.1 22 78-99 2-23 (164) 393 cd03277 ABC_SMC5_euk Eukaryoti 73.2 3 7.7E-05 20.5 2.6 21 79-100 26-46 (213) 394 COG3421 Uncharacterized protei 73.1 6.4 0.00016 18.5 5.0 33 85-118 5-37 (812) 395 KOG0344 consensus 72.8 6.5 0.00017 18.4 6.2 74 46-132 154-233 (593) 396 KOG4439 consensus 72.8 6.5 0.00017 18.4 6.8 138 81-235 349-506 (901) 397 PRK04196 V-type ATP synthase s 72.7 5.8 0.00015 18.8 3.9 45 79-123 145-193 (460) 398 pfam04665 Pox_A32 Poxvirus A32 72.7 5.1 0.00013 19.1 3.7 43 78-122 14-56 (241) 399 cd04148 RGK RGK subfamily. Th 72.6 3.6 9.3E-05 20.0 2.9 21 78-98 1-21 (221) 400 COG2256 MGS1 ATPase related to 72.6 6.6 0.00017 18.4 7.4 40 79-123 50-89 (436) 401 cd01860 Rab5_related Rab5-rela 72.6 4 0.0001 19.7 3.1 22 78-99 2-23 (163) 402 cd00154 Rab Rab family. Rab G 72.5 3.8 9.7E-05 19.9 3.0 22 78-99 1-22 (159) 403 PRK10751 molybdopterin-guanine 72.4 6.7 0.00017 18.4 4.5 38 79-118 4-41 (170) 404 cd01850 CDC_Septin CDC/Septin. 72.3 4.1 0.0001 19.7 3.1 24 76-99 3-26 (276) 405 KOG0336 consensus 72.3 4.6 0.00012 19.4 3.4 149 80-243 260-421 (629) 406 cd04103 Centaurin_gamma Centau 72.1 4 0.0001 19.8 3.0 22 78-99 1-22 (158) 407 TIGR03498 FliI_clade3 flagella 72.0 3.7 9.3E-05 20.0 2.8 35 79-118 142-176 (418) 408 PRK09099 type III secretion sy 72.0 3.8 9.7E-05 19.9 2.9 23 79-101 165-187 (441) 409 cd01870 RhoA_like RhoA-like su 71.8 4.1 0.0001 19.7 3.0 22 78-99 2-23 (175) 410 cd04177 RSR1 RSR1 subgroup. R 71.7 4.3 0.00011 19.5 3.1 22 78-99 2-23 (168) 411 TIGR03324 alt_F1F0_F1_al alter 71.7 6.9 0.00018 18.3 4.3 21 79-99 164-184 (497) 412 pfam00071 Ras Ras family. Incl 71.7 3.7 9.4E-05 20.0 2.7 20 79-98 1-20 (162) 413 cd01136 ATPase_flagellum-secre 71.5 5 0.00013 19.1 3.4 36 79-119 71-106 (326) 414 PRK05922 type III secretion sy 71.4 6.2 0.00016 18.6 3.8 35 79-118 159-193 (434) 415 cd04121 Rab40 Rab40 subfamily. 71.4 5 0.00013 19.2 3.3 23 76-98 5-27 (189) 416 cd02040 NifH NifH gene encodes 71.4 7 0.00018 18.2 4.8 35 77-113 1-35 (270) 417 PRK13764 ATPase; Provisional 71.2 7.1 0.00018 18.2 5.0 26 79-104 261-286 (605) 418 COG1197 Mfd Transcription-repa 71.2 7.1 0.00018 18.2 7.1 75 53-136 597-671 (1139) 419 KOG0346 consensus 71.0 7.2 0.00018 18.2 6.6 77 47-136 38-121 (569) 420 COG1157 FliI Flagellar biosynt 70.9 4.1 0.0001 19.7 2.8 47 79-135 165-211 (441) 421 KOG0979 consensus 70.8 3.2 8.2E-05 20.3 2.3 18 82-99 47-64 (1072) 422 cd03116 MobB Molybdenum is an 70.7 7.3 0.00019 18.1 4.8 39 79-119 3-41 (159) 423 COG3973 Superfamily I DNA and 70.5 7.4 0.00019 18.1 5.2 51 79-134 228-282 (747) 424 PRK13721 conjugal transfer ATP 70.5 7.4 0.00019 18.1 5.4 42 78-121 475-518 (864) 425 cd03289 ABCC_CFTR2 The CFTR su 70.5 4.6 0.00012 19.4 3.0 31 79-112 32-62 (275) 426 pfam04310 MukB MukB N-terminal 70.3 4.2 0.00011 19.6 2.8 36 79-117 29-64 (227) 427 TIGR01526 nadR_NMN_Atrans nico 70.2 4.9 0.00012 19.2 3.1 35 65-101 165-199 (346) 428 PRK10636 putative ABC transpor 70.2 3.7 9.5E-05 19.9 2.5 34 189-222 165-199 (638) 429 pfam07015 VirC1 VirC1 protein. 70.2 7.5 0.00019 18.1 6.1 100 80-212 4-104 (231) 430 COG1674 FtsK DNA segregation A 70.1 6.5 0.00017 18.4 3.7 50 67-116 520-571 (858) 431 cd04139 RalA_RalB RalA/RalB su 70.1 4.7 0.00012 19.3 3.0 22 78-99 1-22 (164) 432 cd04145 M_R_Ras_like M-Ras/R-R 70.1 5.1 0.00013 19.1 3.2 22 77-98 2-23 (164) 433 TIGR02546 III_secr_ATP type II 70.0 7 0.00018 18.3 3.8 129 79-243 155-321 (430) 434 PRK13646 cbiO cobalt transport 69.9 1.3 3.2E-05 22.8 0.0 37 54-98 18-54 (286) 435 cd04168 TetM_like Tet(M)-like 69.8 7.6 0.00019 18.0 5.6 135 79-244 1-140 (237) 436 cd04176 Rap2 Rap2 subgroup. T 69.8 5.1 0.00013 19.1 3.1 22 78-99 2-23 (163) 437 KOG1802 consensus 69.8 5 0.00013 19.1 3.1 37 80-117 428-464 (935) 438 cd00157 Rho Rho (Ras homology) 69.7 4.7 0.00012 19.3 2.9 21 78-98 1-21 (171) 439 TIGR00150 TIGR00150 conserved 69.7 5.2 0.00013 19.1 3.1 38 79-121 29-67 (147) 440 pfam03029 ATP_bind_1 Conserved 69.7 6.8 0.00017 18.3 3.7 35 82-116 1-35 (234) 441 PRK11147 ABC transporter ATPas 69.6 4.2 0.00011 19.6 2.7 42 185-228 168-210 (632) 442 PRK06851 hypothetical protein; 69.4 1.7 4.3E-05 22.1 0.6 51 79-129 33-83 (368) 443 TIGR03371 cellulose_yhjQ cellu 69.2 7.8 0.0002 18.0 4.6 36 77-114 1-37 (246) 444 PRK13695 putative NTPase; Prov 69.2 7.8 0.0002 18.0 6.7 164 77-268 3-169 (174) 445 pfam01656 CbiA CobQ/CobB/MinD/ 69.2 7.9 0.0002 17.9 4.1 31 81-113 2-33 (212) 446 cd01124 KaiC KaiC is a circadi 69.1 7.9 0.0002 17.9 6.2 34 80-115 2-35 (187) 447 TIGR02030 BchI-ChlI magnesium 68.9 8 0.0002 17.9 4.5 138 73-218 21-161 (340) 448 cd04170 EF-G_bact Elongation f 68.6 4.7 0.00012 19.3 2.7 134 79-243 1-139 (268) 449 PRK13343 F0F1 ATP synthase sub 68.6 8.1 0.00021 17.9 4.1 21 79-99 164-184 (502) 450 TIGR00064 ftsY signal recognit 68.6 8.1 0.00021 17.9 7.0 130 70-235 77-218 (284) 451 COG5008 PilU Tfp pilus assembl 68.4 7.1 0.00018 18.2 3.6 29 80-108 130-158 (375) 452 cd01122 GP4d_helicase GP4d_hel 68.4 8.2 0.00021 17.8 7.0 44 80-124 33-78 (271) 453 TIGR01281 DPOR_bchL light-inde 68.3 4.6 0.00012 19.4 2.6 42 80-123 3-46 (275) 454 cd04140 ARHI_like ARHI subfami 68.2 5.6 0.00014 18.8 3.1 22 78-99 2-23 (165) 455 cd04141 Rit_Rin_Ric Rit/Rin/Ri 68.2 5.9 0.00015 18.7 3.2 22 78-99 3-24 (172) 456 cd01129 PulE-GspE PulE/GspE Th 68.1 8.3 0.00021 17.8 6.6 54 50-115 63-116 (264) 457 pfam09140 MipZ ATPase MipZ. Mi 68.1 7.2 0.00018 18.2 3.6 30 86-117 10-39 (261) 458 KOG0388 consensus 68.0 8.3 0.00021 17.8 8.0 163 53-234 570-737 (1185) 459 TIGR00486 TIGR00486 conserved 67.9 8.3 0.00021 17.8 4.5 75 45-128 193-278 (325) 460 cd04117 Rab15 Rab15 subfamily. 67.9 5.3 0.00013 19.0 2.9 22 78-99 1-22 (161) 461 PRK03333 coaE dephospho-CoA ki 67.9 5 0.00013 19.1 2.7 23 77-99 1-23 (394) 462 cd03291 ABCC_CFTR1 The CFTR su 67.8 5.4 0.00014 19.0 2.9 33 58-98 52-84 (282) 463 PRK13873 conjugal transfer ATP 67.8 8.4 0.00021 17.8 4.7 33 79-112 443-475 (815) 464 cd04115 Rab33B_Rab33A Rab33B/R 67.6 6.4 0.00016 18.5 3.3 23 77-99 2-24 (170) 465 cd00877 Ran Ran (Ras-related n 67.6 5.7 0.00015 18.8 3.0 21 78-98 1-21 (166) 466 cd04119 RJL RJL (RabJ-Like) su 67.5 5.6 0.00014 18.9 2.9 20 79-98 2-21 (168) 467 cd03247 ABCC_cytochrome_bd The 67.4 5.4 0.00014 18.9 2.8 21 79-99 30-50 (178) 468 cd04111 Rab39 Rab39 subfamily. 67.3 6.6 0.00017 18.4 3.3 24 76-99 1-24 (211) 469 PRK13637 cbiO cobalt transport 67.2 1.1 2.7E-05 23.3 -0.8 37 54-98 18-54 (287) 470 cd03246 ABCC_Protease_Secretio 67.1 5.7 0.00015 18.8 2.9 21 79-99 30-50 (173) 471 KOG1969 consensus 67.1 8.7 0.00022 17.7 9.1 107 51-217 306-413 (877) 472 cd03369 ABCC_NFT1 Domain 2 of 67.0 6.1 0.00016 18.6 3.1 22 79-100 36-57 (207) 473 pfam02689 Herpes_Helicase Heli 67.0 8.7 0.00022 17.7 4.5 37 73-117 57-93 (801) 474 PRK09694 hypothetical protein; 66.8 8.8 0.00022 17.6 8.7 76 47-135 285-360 (878) 475 cd03249 ABC_MTABC3_MDL1_MDL2 M 66.5 6 0.00015 18.7 2.9 21 79-99 31-51 (238) 476 cd04129 Rho2 Rho2 subfamily. 66.3 6.5 0.00017 18.4 3.1 22 78-99 2-23 (187) 477 PRK11819 putative ABC transpor 66.3 5.7 0.00015 18.8 2.8 39 188-228 178-217 (556) 478 cd00984 DnaB_C DnaB helicase C 66.3 9 0.00023 17.6 6.7 35 80-115 16-50 (242) 479 PRK13233 nifH nitrogenase redu 66.2 9 0.00023 17.6 5.0 44 78-122 3-48 (275) 480 PRK13645 cbiO cobalt transport 66.1 1.1 2.7E-05 23.2 -1.0 38 53-98 21-58 (289) 481 PRK13640 cbiO cobalt transport 66.1 5.7 0.00015 18.8 2.8 34 58-99 23-56 (283) 482 cd03114 ArgK-like The function 66.0 9.1 0.00023 17.6 4.7 36 80-117 2-37 (148) 483 COG1341 Predicted GTPase or GT 66.0 9.1 0.00023 17.6 6.0 56 47-104 45-100 (398) 484 cd01862 Rab7 Rab7 subfamily. 66.0 6.3 0.00016 18.5 3.0 21 78-98 1-21 (172) 485 COG1136 SalX ABC-type antimicr 65.9 5.7 0.00015 18.8 2.7 33 79-114 33-65 (226) 486 cd01861 Rab6 Rab6 subfamily. 65.9 6.3 0.00016 18.5 2.9 21 79-99 2-22 (161) 487 cd00615 Orn_deC_like Ornithine 65.9 9.2 0.00023 17.5 6.1 31 94-124 86-116 (294) 488 PRK00080 ruvB Holliday junctio 65.8 9.2 0.00023 17.5 8.1 94 55-217 30-128 (328) 489 cd04112 Rab26 Rab26 subfamily. 65.7 6.5 0.00017 18.5 3.0 21 78-98 1-21 (191) 490 cd00876 Ras Ras family. The R 65.6 5.9 0.00015 18.7 2.7 21 79-99 1-21 (160) 491 cd03248 ABCC_TAP TAP, the Tran 65.1 6.4 0.00016 18.5 2.9 22 79-100 42-63 (226) 492 PRK07367 consensus 65.0 9.5 0.00024 17.4 7.0 64 51-122 63-127 (385) 493 COG0542 clpA ATP-binding subun 64.9 9.6 0.00024 17.4 11.2 134 54-229 495-642 (786) 494 cd03240 ABC_Rad50 The catalyti 64.8 6.5 0.00016 18.5 2.8 20 79-98 24-43 (204) 495 PTZ00132 GTP-binding nuclear p 64.8 7.5 0.00019 18.1 3.1 56 221-277 110-169 (209) 496 PRK10790 putative multidrug tr 64.8 6.6 0.00017 18.4 2.9 18 80-97 370-387 (593) 497 cd03223 ABCD_peroxisomal_ALDP 64.8 5.9 0.00015 18.7 2.6 37 190-228 108-145 (166) 498 TIGR01082 murC UDP-N-acetylmur 64.4 9.8 0.00025 17.4 5.2 52 55-119 96-148 (491) 499 PRK13886 conjugal transfer pro 64.4 8.5 0.00022 17.7 3.4 30 87-116 13-42 (241) 500 cd01875 RhoG RhoG subfamily. 64.2 8 0.0002 17.9 3.2 21 78-98 4-24 (191) No 1 >pfam03237 Terminase_6 Terminase-like family. This family represents a group of terminase proteins. Probab=99.97 E-value=2.6e-28 Score=192.55 Aligned_cols=247 Identities=16% Similarity=0.084 Sum_probs=183.6 Q ss_pred EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 61488678899999999999970899779997153799999999999999986231211233332100012333221111 Q gi|254781187|r 82 ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQS 161 (367) Q Consensus 82 v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 161 (367) +.+|||+|||++++..++++++.+++.+++++++|..|++.++++.+..++...... .+....... T Consensus 2 ~~ggr~~GKT~~~~~~~~~~a~~~~~~~~~i~~~t~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~ 67 (380) T pfam03237 2 ILGSRQSGKTFAFAREALRHALGNGPKNQIILSASKAQARLEFKKGIIEIAGDLLEI--------------TFEEKNGNP 67 (380) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHHHHHCCC--------------CEEECCCCE T ss_conf 426452528399999999999858997289997999999999999999966886387--------------167278873 Q ss_pred CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHH-HHH-HHHHHCCCCCEEEEEEECCCCCCCHHHH Q ss_conf 34577612662101354455652101135862899975455998899-998-9874069882589998078999876887 Q gi|254781187|r 162 MGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIIN-KSI-LGFFTELNPNRFWIMTSNTRRLNGWFYD 239 (367) Q Consensus 162 ~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~-e~i-~g~Lt~~~~~~~~i~igNP~r~~g~Fye 239 (367) +...+|+.+.... .+++.+.++++|....++++||++.+++..+ ..+ .+.++....+ .+.++||+.+.++||+ T Consensus 68 i~~~nGs~i~~~~---~~~~~~~~~~rG~~~~~i~~DE~a~~~~~~~~~~~~~~~~~~~~~~--~~~~stp~~~~~~~~~ 142 (380) T pfam03237 68 IILPNGAKLYFLG---LESETTAQGYRGASIAGIYFDEATWLPKFQESELVRRLRATKGKWR--KTFFSTPPSPGHWVYD 142 (380) T ss_pred EEECCCCEEEEEE---CCCCCCHHHCCCCCCCEEEEEEHHHCCCHHHHHHHHHHHCCCCCCC--EEEEECCCCCCCCHHH T ss_conf 9915998899962---5776643103485455499830453662789999864410479975--7999889899851989 Q ss_pred HHHCCC-------CCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEECHHHHHHHHCCCCCC Q ss_conf 541122-------3504675233328888988999999621688000268886443277898078299986443157777 Q gi|254781187|r 240 IFNIPL-------EDWKRYQIDTRTVEGIDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFIPHNYIEEAMSREAID 312 (367) Q Consensus 240 ~~~~~~-------~~w~~~~~~~~d~p~~~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~d~~ip~~~ie~a~~~~~~~ 312 (367) .|.... ..|..++++..++|..++++++++++.|++. .|+++++|+|. .+++++|+..+++.+......+ T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~t~~d~~~~~~~~~e~l~~~~~~~--~~~qe~~g~f~-~~~g~if~~~~~~~~~~~~~~~ 219 (380) T pfam03237 143 FWTGWLDDKGKRTFIPADVEVTIEDARALGPEYKEELRALYSDE--EFARLLMGEWV-DTSGSIFKRFELERCDVDEERP 219 (380) T ss_pred HHHHHCCCCCCCCEEEEEEECCHHHHCCCCHHHHHHHHHHCCHH--HHHHHHCCCEE-CCCCCEECHHHHHHCCCCCCCC T ss_conf 98554016777520220674566871326889999998768999--99998588666-5788571478885464675568 Q ss_pred CCCCCEEEEEECCC-CCCCEEEEEEE---CCCEEEEEHHHCH Q ss_conf 88984899996387-78810899997---0883687042030 Q gi|254781187|r 313 DLYAPLIMGCDIAG-EGGDKTVVVFR---RGNIIEHIFDWSA 350 (367) Q Consensus 313 ~~~~p~viGvDvAr-~G~D~Tvi~~r---~G~~v~~i~~~~~ 350 (367) ....++++|+|+|. .++|+|++++. .++....+.++.. T Consensus 220 p~~~~~~~g~D~~~~~~~D~t~~~v~~~~~~~~~~~~~~~~~ 261 (380) T pfam03237 220 PEHREVIGGVDPAASRGGDYAALVVIAEVDGDKFYVLAREHE 261 (380) T ss_pred CCCCEEEEEECCCCCCCCCCEEEEEEEECCCCEEEEEEEEEE T ss_conf 888559999867888889966999999657985999999983 No 2 >pfam04466 Terminase_3 Phage terminase large subunit. Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit. This region is found on the large subunit and possess an endonuclease and ATPase activity that require Mg2+ and a neutral or slightly basic reaction. This region is also found in bacterial sequences. Probab=99.94 E-value=3.3e-25 Score=173.49 Aligned_cols=253 Identities=18% Similarity=0.153 Sum_probs=185.9 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 12477614886788999999999999708997799971537999999999999999862312112333321000123332 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAE 156 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 (367) +|+++. +|||+|||..+|..++-.++.+| .+++|++.+.+++++.+|+++++.++.+...+.+..+...+.. T Consensus 3 r~~v~~-GGrgsgKS~~~a~~~i~~~~~~~-~~~l~~r~~~~slr~sv~~~~~~~i~~~~~~~~~~~~~s~~~i------ 74 (387) T pfam04466 3 RYKVAK-GGRGSGKSYHIALKLVLKLLMHP-RTNLVIREVKNTIEDSVFTQLQEALSMLGLDHEFKISKSPIEI------ 74 (387) T ss_pred CEEEEE-ECCCCHHHHHHHHHHHHHHHHCC-CEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEE------ T ss_conf 689999-08886799999999999998789-8699997556889999999999999976997348973761489------ Q ss_pred CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCH Q ss_conf 21111345776126621013544556521011358628999754559988999989874069882589998078999876 Q gi|254781187|r 157 LLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRLNGW 236 (367) Q Consensus 157 ~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~ 236 (367) ....+|+.+.+. +. ++|+++.|+.+ ..++++|||+.++...|+.+.++++.......+++..||.....| T Consensus 75 -----~~~~~gs~i~f~-G~--d~~~~iks~~~--i~~~~~eEa~~~~~~~~~~l~~~~r~~~~~~~i~~~~NP~~~~~w 144 (387) T pfam04466 75 -----TVKINGSKFLFY-GM--DDPAKIKSIKD--VSDAWIEEAAEFKTEDFDQLIPTIRRPKPGSEIFMSFNPVNKLNW 144 (387) T ss_pred -----EECCCCCEEEEE-EC--CCHHHHHCCCC--CEEEEEECHHHCCHHHHHHHHHHHCCCCCCEEEEEECCCCCCCCH T ss_conf -----987899699998-57--89688416366--149999412447998999999885317887199998289998774 Q ss_pred HHHHHHCC-----CCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEECHHHHHHHHCCCCC Q ss_conf 88754112-----2350467523332888898899999962168800026888644327789807829998644315777 Q gi|254781187|r 237 FYDIFNIP-----LEDWKRYQIDTRTVEGIDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFIPHNYIEEAMSREAI 311 (367) Q Consensus 237 Fye~~~~~-----~~~w~~~~~~~~d~p~~~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~d~~ip~~~ie~a~~~~~~ 311 (367) .|+.|-+. ..++..++....|||++++++++++++.+..++..|++.++|+|.. .++.+|+.-.+ ........ T Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~ty~DNp~L~~~~i~~~e~~k~~dp~~y~~~~lGe~~~-~~g~V~~~~~~-~~~~~~~~ 222 (387) T pfam04466 145 TYKRFFKNDKSELDDDTYIHHSTYRDNPFLPEVDIREIEELKRRNPDYYRIEYLGEFGG-LGTLVLPNFEI-KPLWVEAA 222 (387) T ss_pred HHHHHHCCCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCEEE-CCCEEEECCEE-EECCCCCH T ss_conf 88997417754677885999999616998999999999998703999989977571563-48779735445-55232640 Q ss_pred CCCCCCEEEEEECCCCCCCEEEEEE----ECCCEEEEEHHHCH Q ss_conf 7889848999963877881089999----70883687042030 Q gi|254781187|r 312 DDLYAPLIMGCDIAGEGGDKTVVVF----RRGNIIEHIFDWSA 350 (367) Q Consensus 312 ~~~~~p~viGvDvAr~G~D~Tvi~~----r~G~~v~~i~~~~~ 350 (367) .+....+.+|+|. |+-.|.|+++. ..|+.+....++.+ T Consensus 223 ~~~~~~~~~G~D~-G~~~dpta~v~~~~~~~~~~lyi~~e~y~ 264 (387) T pfam04466 223 EDAHIKLGFKRDF-GFDESATASVRGALDVKKKVIYLYDEYYD 264 (387) T ss_pred HHHHCCCCCCEEC-CCCCCCCEEEEEEEECCCCEEEEEEEEEC T ss_conf 2200033421354-64378877999999779989999999984 No 3 >pfam03354 Terminase_1 Phage Terminase. The majority of the members of this family are bacteriophage proteins, several of which are thought to be terminase large subunit proteins. There are also a number of bacterial proteins of unknown function. Probab=99.82 E-value=3.1e-18 Score=130.78 Aligned_cols=261 Identities=15% Similarity=0.147 Sum_probs=159.3 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEE-EEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 899999998888751245555541124-77614886788999999999999708--997799971537999999999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFK-CAISAGRGIGKTTLNAWMMLWLISTR--PGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~-~~v~sgrg~GKS~~~a~~~lw~~~~~--~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) +||.-++..|.-.-.. ...-+|| +.+.-|||.|||.++|+++++.++.. ++..++++|++.+|++ ++|.+++ T Consensus 1 PwQ~f~i~~ifGw~~~----~g~Rrfr~~~i~v~RkNGKS~l~a~i~ly~~~~~ge~~~ei~~~A~~~~QA~-~~f~~~~ 75 (473) T pfam03354 1 PWQKFILGLMFGWRKG----CGVRRFREAYVSVGRKNGKSYLMAIRVLYELLLGGKSNQEILVAATTFKQAE-KLFKYVK 75 (473) T ss_pred CCHHHHHHHEEEEEEC----CCCEEEEEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEEEEECCHHHHH-HHHHHHH T ss_conf 9461562514418928----9988999999998268602699999999999709983874999979899999-9999999 Q ss_pred HHHHHCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC-HHH Q ss_conf 99986231211-2333321000123332211113457761266210135445565210113586289997545599-889 Q gi|254781187|r 130 KWLSMLPHRHW-FEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP-DII 207 (367) Q Consensus 130 k~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~-d~i 207 (367) ++++..|...- +... ... ..+..+........+...++ ++++..| .+..++|+||..-.+ +.+ T Consensus 76 ~mi~~~p~l~~~~~~~-------~~~--~~~~~i~~~~t~s~~~~ls~---~~~~~dG---~~~~~~i~DE~h~~~~~~~ 140 (473) T pfam03354 76 NQVKLSPFLSIANENK-------LLK--SQKDGIEMKINNNVFKALSN---NGDQYDG---GNPSLAIFDEMHEFKDREL 140 (473) T ss_pred HHHHCCHHHHHHHHCC-------CCC--CCCEEEEECCCCCEEEEEEC---CCCCCCC---CCCCEEEEEECCCCCCHHH T ss_conf 9997398777553011-------013--10015898078968999857---8987669---9872899872230488278 Q ss_pred HHHHHHHHHCCCCCEEEEEEECC-CCCCCHHHHHHHCCC---------CC--E--EEEEECCC-----------CCCCC- Q ss_conf 99989874069882589998078-999876887541122---------35--0--46752333-----------28888- Q gi|254781187|r 208 NKSILGFFTELNPNRFWIMTSNT-RRLNGWFYDIFNIPL---------ED--W--KRYQIDTR-----------TVEGI- 261 (367) Q Consensus 208 ~e~i~g~Lt~~~~~~~~i~igNP-~r~~g~Fye~~~~~~---------~~--w--~~~~~~~~-----------d~p~~- 261 (367) +++++..+......++ +.|+|. +...+.+++.+...+ ++ . ..+..+.. -||.+ T Consensus 141 ~~~l~sg~~~r~~~l~-~~ITTag~~~~~~~~~~~~~~~~vl~g~~~~~d~~~f~~i~~~d~~dd~~D~~~W~kANP~lg 219 (473) T pfam03354 141 VSTIVTGMRKQDNPQT-IQITTAGPNRGGPYDEEREYIKRILEGDVERDDDSYFGLIYELDNDDEVKDPAKWIKANPLLG 219 (473) T ss_pred HHHHHHHHHCCCCCEE-EEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCCCCCCCHHHHHHHCCCCC T ss_conf 9999876316888719-997677889887189999999999708777678766999971698877689899998596767 Q ss_pred ---CHHHHHHHHH-HCCCC--CCEEEEEEEEEECCCCCCEEECHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCCEEEEE Q ss_conf ---9889999996-21688--00026888644327789807829998644315777788984899996387788108999 Q gi|254781187|r 262 ---DSGFHEGIIS-RYGLD--SDVARIEILGQFPQQEVNNFIPHNYIEEAMSREAIDDLYAPLIMGCDIAGEGGDKTVVV 335 (367) Q Consensus 262 ---~~~~i~~~~~-~~ged--S~~~r~ev~G~Fp~~~~d~~ip~~~ie~a~~~~~~~~~~~p~viGvDvAr~G~D~Tvi~ 335 (367) +.+.+.+..+ ..... -+.|+...+.++...+++++++.+.+++|.. +...-.+.++++|+|+|.. +|-|+++ T Consensus 220 ~~~~~~~l~~~~~~a~~~p~~~~~f~~k~lN~w~~~~~~~wl~~~~w~~~~~-~~~~~~g~~~~~G~DlS~~-~Dlta~~ 297 (473) T pfam03354 220 SSLTRDNLLKGLIDAIGSPLKMNKFLTKNFNLWMGQDTDSWLTLQDWEQAVF-PPFDINGRRVYIGVDLSMK-GDVTALV 297 (473) T ss_pred CCCCHHHHHHHHHHHHHCHHHHHHHHHHHCCCEECCCCCCCCCHHHHHHCCC-CHHHHCCCEEEEEEEECCC-CCCCEEE T ss_conf 8879999999999986493768999997238634454465789999974789-8578479969999840357-7641379 Q ss_pred E Q ss_conf 9 Q gi|254781187|r 336 F 336 (367) Q Consensus 336 ~ 336 (367) + T Consensus 298 ~ 298 (473) T pfam03354 298 F 298 (473) T ss_pred E T ss_conf 9 No 4 >COG5323 Uncharacterized conserved protein [Function unknown] Probab=99.44 E-value=2.3e-13 Score=100.87 Aligned_cols=238 Identities=17% Similarity=0.187 Sum_probs=170.2 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 77614886788999999999999708997799971537999999999999999862312112333321000123332211 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLE 159 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (367) -.+..|||+|||..-|-++.|.++-.|. +..+++|.+.+++++..-...+....- .+...+++. + T Consensus 39 WL~~GGRGsGKTrAGAeWv~~~AlgkpS--iALvgeTl~DaREVMidGpSGi~~~~~-~~RPr~EaS------------R 103 (410) T COG5323 39 WLMLGGRGSGKTRAGAEWVTWNALGKPS--IALVGETLHDAREVMIDGPSGIMYHAG-ASRPRLEAS------------R 103 (410) T ss_pred EEEECCCCCCCCCCCCEEEEEHHCCCCC--HHHHHCCCCCHHHHHHCCCHHHHHHHH-CCCCHHHHH------------H T ss_conf 6676365677655553002211026840--655401001146763148278887630-147214545------------5 Q ss_pred CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC--CHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHH Q ss_conf 11345776126621013544556521011358628999754559--9889999898740698825899980789998768 Q gi|254781187|r 160 QSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT--PDIINKSILGFFTELNPNRFWIMTSNTRRLNGWF 237 (367) Q Consensus 160 ~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI--~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~F 237 (367) ..+.-++| +.+..+|.+.|+++.| ..+++.+.||.... |++.|+.++=.|.-+..+... . .+++++.... T Consensus 104 RRL~WpNG---AvA~~FSsEDPeSLRG---PQFh~AW~DEl~kWk~PqETw~MLqFGLRLGe~PRqv-V-TTTPrp~plL 175 (410) T COG5323 104 RRLDWPNG---AVAYAFSSEDPDSLRG---PQFHLAWTDELLKWKEPQETWAMLQFGLRLGEDPRQV-V-TTTPRPIPLL 175 (410) T ss_pred HHHCCCCC---CEEEEECCCCHHHCCC---CCCCHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHH-E-ECCCCCCHHH T ss_conf 63036885---0144303588032048---5200677788744798488999998766516784010-2-0599862789 Q ss_pred HHHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEECHHHHHHHHCCCCCCCCCCC Q ss_conf 87541122350467523332888898899999962168800026888644327789807829998644315777788984 Q gi|254781187|r 238 YDIFNIPLEDWKRYQIDTRTVEGIDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFIPHNYIEEAMSREAIDDLYAP 317 (367) Q Consensus 238 ye~~~~~~~~w~~~~~~~~d~p~~~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~d~~ip~~~ie~a~~~~~~~~~~~p 317 (367) --+..++. --..+.-.+.+..++.+.|++.+.+.||- ...-|||+.|+..+. ++.++..+.++.|++ ..|.|-+. T Consensus 176 KaLl~dpt-v~~trm~Ta~NAgNLapgFl~t~a~rYgG-TRLgrQEldGelvee-~GaLw~r~dle~c~e--a~p~pL~R 250 (410) T COG5323 176 KALLADPT-VALTRMGTAANAGNLAPGFLRTLASRYGG-TRLGRQELDGELVEE-DGALWRREDLERCRE--ARPAPLDR 250 (410) T ss_pred HHHHCCCC-HHHHHCCCCCCCCCCCHHHHHHHHHHHCC-CCHHHHHCCCEEECC-CCCCCCHHHHHHHHH--CCCCCCCE T ss_conf 98842861-25450543224456577999999998454-411355528778636-773002878999986--18987023 Q ss_pred EEEEEECC-CCCCCEEEEEE--ECCCEEEEE Q ss_conf 89999638-77881089999--708836870 Q gi|254781187|r 318 LIMGCDIA-GEGGDKTVVVF--RRGNIIEHI 345 (367) Q Consensus 318 ~viGvDvA-r~G~D~Tvi~~--r~G~~v~~i 345 (367) +++.||+- ..|+|++-|.+ +...+.+.+ T Consensus 251 iVVAVDPPA~~g~~sCGIVVaG~~~gr~~VL 281 (410) T COG5323 251 IVVAVDPPATAGGDSCGIVVAGRRDGRAFVL 281 (410) T ss_pred EEEEECCCCCCCCCCEEEEEEEEECCCEEEE T ss_conf 7997269876778751169988505816996 No 5 >COG4626 Phage terminase-like protein, large subunit [General function prediction only] Probab=99.39 E-value=3.2e-10 Score=81.66 Aligned_cols=306 Identities=15% Similarity=0.116 Sum_probs=171.5 Q ss_pred CCCCCCCCCCCHHHHHHHHCCCCCC--CCHH--HHHHHHHCCCCC---------CCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 9755545723378999975232012--5988--885543014668---------88443666842899999998888751 Q gi|254781187|r 1 MPRLISTDQKLEQELHEMLMHAECV--LSFK--NFVMRFFPWGIK---------GKPLEHFSQPHRWQLEFMEAVDVHCH 67 (367) Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~--~f~~~~~~w~~~---------~~~~~~~~~p~~wq~~~l~~~~~~~~ 67 (367) +++.+.+-+...|.+.-.+ .++. .++. .|+..+|. ++ |.|+ .-.+||.-++-.|.-... T Consensus 7 ~dg~~~a~~~~k~a~kr~~--~DL~~~~~~e~~~~~i~~~e--~~~~~~~~~~~~~p~----~l~PwQkFiia~l~G~~~ 78 (546) T COG4626 7 IDGWITACKDWKQAAKRHL--SDLPAPIYPEQAERAIAIFE--QLRIVDGPGSPGFPE----SLEPWQKFIVAALFGFYD 78 (546) T ss_pred CCCCCCCCHHHHHHHHHHH--HHHHCCCCHHHHHHHHHHHH--HCCCCCCCCCCCCCC----CCCCHHHHHHHHHHHEEE T ss_conf 4773125788999999777--74104247555236665544--002103677789863----435189999998760350 Q ss_pred CCCCCCCCCEEEE-EEECCCCCCHHHHHHHHHHHHHHHCC--CCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC Q ss_conf 2455555411247-76148867889999999999997089--97799971537999999999999999862312112333 Q gi|254781187|r 68 SNVNNSNPTIFKC-AISAGRGIGKTTLNAWMMLWLISTRP--GMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQ 144 (367) Q Consensus 68 ~~~~~~~~~~~~~-~v~sgrg~GKS~~~a~~~lw~~~~~~--~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~ 144 (367) .+... -+|+. .|.-+|+-|||+++|.+++..++... +..+.++||+..|+.+ +|.+++..+...+.. T Consensus 79 k~T~~---rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~~~~~~~~i~A~s~~qa~~-~F~~ar~mv~~~~~l------ 148 (546) T COG4626 79 KQTGI---RRFKEAFIFIPRKNGKSTLAAGIMMTALLLNWRSGAGIYILAPSVEQAAN-SFNPARDMVKRDDDL------ 148 (546) T ss_pred CCCCE---EEEEEEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHH-HHHHHHHHHHHCCCH------ T ss_conf 57870---68889999974578557899999999987653047608998342899988-768999998737213------ Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH--HHHHHHHHHHHCCCCCE Q ss_conf 3210001233322111134577612662101354455652101135862899975455998--89999898740698825 Q gi|254781187|r 145 SLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD--IINKSILGFFTELNPNR 222 (367) Q Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d--~i~e~i~g~Lt~~~~~~ 222 (367) +.... ....+..+........+-+.++ ++....|.| ..++|+||-.-..+ +.+.++.+.|-..-+. T Consensus 149 --~~~~~---~~~~s~~i~~~~~~s~ik~~aa---~~~~~Dg~~---~~~~I~DEih~f~~~~~~~~~~~~g~~ar~~~- 216 (546) T COG4626 149 --RDLCN---VQTHSRTITHRKTDSTIKAVAA---DPNTVDGLN---SVGAIIDELHLFGKQEDMYSEAKGGLGARPEG- 216 (546) T ss_pred --HHHCC---CCCCEEEEEECCCCEEEEEHHC---CCCCCCCCC---CCEEEEEHHHHHCCHHHHHHHHHHHHCCCCCC- T ss_conf --33206---5454048986155111330104---887556787---65488763754167899999997420157676- Q ss_pred EEEEEECC-CCCCCHHHHHHHCCC---CC-------EE-EEEECCC-----------CCCCCC----HHHHHH-HHHHCC Q ss_conf 89998078-999876887541122---35-------04-6752333-----------288889----889999-996216 Q gi|254781187|r 223 FWIMTSNT-RRLNGWFYDIFNIPL---ED-------WK-RYQIDTR-----------TVEGID----SGFHEG-IISRYG 274 (367) Q Consensus 223 ~~i~igNP-~r~~g~Fye~~~~~~---~~-------w~-~~~~~~~-----------d~p~~~----~~~i~~-~~~~~g 274 (367) +++.|+|- .-..|+|++..+..+ ++ .. ....+.. .||++. .+++.. .++... T Consensus 217 l~~~ITT~g~~~~g~~~q~~~y~k~vl~g~~~d~~~f~~i~e~Dd~~e~~dpe~w~kaNPnlg~sv~~~~l~s~~~ka~~ 296 (546) T COG4626 217 LVVYITTSGDPPAGVFKQKLQYAKDVLDGKIKDPHFFPVIYELDEEGEHDDPENWAKANPNLGVSVDEAFLYSEYRKARN 296 (546) T ss_pred EEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCCCCCEEEHHHHHHHHHHHHC T ss_conf 39999668988741899999999998669878821079999768820003867774308876514207777769998731 Q ss_pred CC--CCEEEEEEEEEECCCCCCEEECHHHHHHHHCC--CCCCCCCCCEEEEEECCCCCCCEEEEEE--EC Q ss_conf 88--00026888644327789807829998644315--7777889848999963877881089999--70 Q gi|254781187|r 275 LD--SDVARIEILGQFPQQEVNNFIPHNYIEEAMSR--EAIDDLYAPLIMGCDIAGEGGDKTVVVF--RR 338 (367) Q Consensus 275 ed--S~~~r~ev~G~Fp~~~~d~~ip~~~ie~a~~~--~~~~~~~~p~viGvDvAr~G~D~Tvi~~--r~ 338 (367) .. -..|..+-+..|... .+.+++.+.+++|..+ +.....+..++.|+|.|+. .|-|.+++ |. T Consensus 297 ~~q~~~dF~tK~lNi~~~~-~~~~~~~~~w~~~~~~~lde~~~~gq~c~~G~Dls~~-~D~ts~al~f~~ 364 (546) T COG4626 297 APQEARDFMTKHLNIWIGA-SDAWFGADFWEQQGRTVLDEILLRGQVCYGGIDLSGL-DDLTSMALVGRY 364 (546) T ss_pred CCHHCHHHHHCCCCEEECH-HHCCCCHHHHHHHCCCCCCHHHHCCCEEEEEECCCCC-CCCCCEEEEEEC T ss_conf 8111227775123315100-1024686899973144565355148668997332345-555410688753 No 6 >COG1783 XtmB Phage terminase large subunit [General function prediction only] Probab=99.24 E-value=6.3e-10 Score=79.85 Aligned_cols=233 Identities=18% Similarity=0.150 Sum_probs=163.6 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 47761488678899999999999970899779997153799999999999999986231211233332100012333221 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL 158 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (367) .+ +.+|||++||..+|--++--++..|+..++|+....+..++.+|.+++-.++.+-..+.|..... . T Consensus 27 ~i-~~G~rGS~KSy~~alk~i~kl~~~~~~d~lvIR~v~nt~k~St~~~~~e~l~e~gv~~~f~~~~s-----------~ 94 (414) T COG1783 27 FI-AKGGRGSSKSYATALKNIEKLLSEPGIDVLVIREVENTHKQSTYALFKEALSELGVTKFFKISKS-----------S 94 (414) T ss_pred EE-EECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECC-----------C T ss_conf 99-98267775008889999999970778757999972354412089999999998384011577417-----------8 Q ss_pred CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC-HHHHHHHHHH-HHCCCCCEEEEEEECCCCCCCH Q ss_conf 1113457761266210135445565210113586289997545599-8899998987-4069882589998078999876 Q gi|254781187|r 159 EQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP-DIINKSILGF-FTELNPNRFWIMTSNTRRLNGW 236 (367) Q Consensus 159 ~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~-d~i~e~i~g~-Lt~~~~~~~~i~igNP~r~~g~ 236 (367) ...+..++|..+++.. ...|..+.+++......+|+.||+.++ ..-.|.+..+ ......+ +++.+||-.-.+| T Consensus 95 pe~i~~~~G~ri~F~G---~ddp~klKSi~~~~~s~~WfEE~~e~s~e~~~e~l~~l~~~~~~~~--~~~~snpv~~~pw 169 (414) T COG1783 95 PEIILKDTGQRIIFKG---LDDPAKLKSIAVNWISDLWFEEASEFSYEDDIELLVELRRRELKGH--IILSSNPVSFNPW 169 (414) T ss_pred HHHEECCCCCEEEEEC---CCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--CEEECCCCCCCCC T ss_conf 6660212586789945---8987885230100433555787763303456888777641223777--2463264345885 Q ss_pred HHHHHHC------CCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEE------CHHHHHH Q ss_conf 8875411------223504675233328888988999999621688000268886443277898078------2999864 Q gi|254781187|r 237 FYDIFNI------PLEDWKRYQIDTRTVEGIDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFI------PHNYIEE 304 (367) Q Consensus 237 Fye~~~~------~~~~w~~~~~~~~d~p~~~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~d~~i------p~~~ie~ 304 (367) -|..|-. .+.+...++-...|+++++...+++.+....-+.+.||.-+.|+|-- ...-++ |.+++.. T Consensus 170 ~~~~w~~~~~Dek~~~dt~~hhtT~~dn~fL~~~~v~~~ed~k~~d~d~yri~~~gev~v-~~~~v~~~~e~~~~d~v~~ 248 (414) T COG1783 170 TYKHWLEFAVDEKKKADTYIHHTTYRDNLFLGFDDVDELEDLKKNDPDLYRIVRDGEVGV-KNGDVFDQFEVKPFDAVKF 248 (414) T ss_pred CHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEEEE-CCCEECCHHHCCCHHHHHH T ss_conf 388888887443557866888620135666777899999876412854123899778986-0752546321577288776 Q ss_pred HHCCCCCCCCCCCEEEEEECCCCCCCEEEEEE Q ss_conf 43157777889848999963877881089999 Q gi|254781187|r 305 AMSREAIDDLYAPLIMGCDIAGEGGDKTVVVF 336 (367) Q Consensus 305 a~~~~~~~~~~~p~viGvDvAr~G~D~Tvi~~ 336 (367) |.++-..+ ..|+|. |+-.+.++|+. T Consensus 249 ~i~~i~~~------s~gm~~-Gf~~~~n~l~~ 273 (414) T COG1783 249 AIDNISRP------STGMDF-GFTAKFNRLLK 273 (414) T ss_pred HHHHHCCC------CCCCEE-EEEECCCEEEE T ss_conf 67761556------554024-25740757788 No 7 >TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family; InterPro: IPR006437 This group of sequences represent a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from the phage terminase family represented by IPR005021 from INTERPRO.; GO: 0006323 DNA packaging. Probab=99.14 E-value=7e-09 Score=73.43 Aligned_cols=248 Identities=16% Similarity=0.155 Sum_probs=170.9 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHC-----CCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCC-CCCCCCCCCCCCCCC Q ss_conf 77614886788999999999999708-----997799971537999999999999999862312-112333321000123 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTR-----PGMSIICIANSETQLKNTLWAEVSKWLSMLPHR-HWFEMQSLSLHPSGW 153 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~-----~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~-~~~~~~~~~~~~~~~ 153 (367) ....+|+++|||+.++..++-.++.. ++..++++..+....++.++..+...+...-.. +.+....... T Consensus 4 ~~~~G~~~sgk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~g~~~~~~~~~~~~~----- 78 (462) T TIGR01547 4 IIAKGGRGSGKTFAIALKLVLKLLANKDLYGKPRNILAARKVQNSIRDSVFKDIEDLLSDLGLNLYEFKKSKSPM----- 78 (462) T ss_pred EEECCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCC----- T ss_conf 663266653157899999999998764531488406887402335665668889999987064022132036662----- Q ss_pred CCCCCCCCCCCCC---CCEEEEECCCCCCCCCCCCCCCCC--------CCCEEEEECCCCCCHHHHHHHHHHHHCCCCC- Q ss_conf 3322111134577---612662101354455652101135--------8628999754559988999989874069882- Q gi|254781187|r 154 YAELLEQSMGIDS---KHYTITCRTYSEERPDTFVGPHNT--------HGMAVFNDEASGTPDIINKSILGFFTELNPN- 221 (367) Q Consensus 154 ~~~~~~~~~~~~~---~~~~~~a~~~~~~~~ea~~g~h~~--------~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~- 221 (367) ..+..+ +..++.. +...+.+..+.+..+. ....++++||+.++...++.+.++++..+.+ T Consensus 79 -------~~~~~~~~~~~~~~f~-G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ee~~~~~~~~~~~~~~~~r~~~~~~ 150 (462) T TIGR01547 79 -------EIKILNTGGGAYFIFK-GLNSDKPEKLKSGAGLGFTLWEVGLLADLWFEEASELTKEDIKELIPRLREPGGKN 150 (462) T ss_pred -------EEEECCCCCCEEEEEE-CCCCCCHHHHHHCCCCCEEEEHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCE T ss_conf -------5776157886179960-65756246643104664100014455656555444301446888887640577750 Q ss_pred EEEEEEECCCCCCCHHHHHHHCC--C--CCEE---------------EEEECCCCCCCCC----HHHHHHHHHHCCCCCC Q ss_conf 58999807899987688754112--2--3504---------------6752333288889----8899999962168800 Q gi|254781187|r 222 RFWIMTSNTRRLNGWFYDIFNIP--L--EDWK---------------RYQIDTRTVEGID----SGFHEGIISRYGLDSD 278 (367) Q Consensus 222 ~~~i~igNP~r~~g~Fye~~~~~--~--~~w~---------------~~~~~~~d~p~~~----~~~i~~~~~~~gedS~ 278 (367) ..+++-.||.....++++.|... . .... .++....|+|+++ ..++++....+..+.. T Consensus 151 ~~~~~~~nP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dn~~~~~~~~~~~~~~~~~~~~~~~~ 230 (462) T TIGR01547 151 KFIIFSSNPESPLHWVYKDFIENLGEDEFRICDKPPYEYGVVDKKLYILHSTYRDNPFLSGGDVEEYIQELEKLKDRDPA 230 (462) T ss_pred EEEEEEECCCCCCCHHHHHHHHCCCCCCHHHHCCCCHHHHHEEECEEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCHH T ss_conf 69998408898553056665430477601221011013220000002567420346567611589999999986315613 Q ss_pred EEEEEEEEEECCCCCCEEECHHHH------HHHHC---CCCCCCCCCCE--EEEEECCCC-CCCEEEEEEECCC Q ss_conf 026888644327789807829998------64431---57777889848--999963877-8810899997088 Q gi|254781187|r 279 VARIEILGQFPQQEVNNFIPHNYI------EEAMS---REAIDDLYAPL--IMGCDIAGE-GGDKTVVVFRRGN 340 (367) Q Consensus 279 ~~r~ev~G~Fp~~~~d~~ip~~~i------e~a~~---~~~~~~~~~p~--viGvDvAr~-G~D~Tvi~~r~G~ 340 (367) .||..++|+|...++-+.+...+. ....+ ..+...+..+. +.|.|.+.. |...++++..... T Consensus 231 ~~~~~~~G~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~ 304 (462) T TIGR01547 231 LYRRILLGEWVSAADVWSLGLPVLTSEGILFKKLDVKAAYIKELPNDPSDFVGGIDAGGVDGNSPSAYVLLGIE 304 (462) T ss_pred HHHHHHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHEEEECCCCCCCCCCEEEEEEEEE T ss_conf 43344423510122332204444344411121110022123431232100013201476666530367887200 No 8 >pfam05876 Terminase_GpA Phage terminase large subunit (GpA). This family 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=98.86 E-value=4.9e-07 Score=62.12 Aligned_cols=166 Identities=10% Similarity=0.053 Sum_probs=102.9 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH Q ss_conf 28999999988887512455555411247761488678899999999999970899779997153799999999999999 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW 131 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~ 131 (367) .++|.++++.+.+. .+.+|.+..+-|+|||.+.-.++-|.+...| ..++++-||...+++..=..|... T Consensus 18 ~Py~~eimd~l~~~----------~v~~V~~~k~aQ~GkT~~~~n~igy~i~~~P-~p~l~v~Pt~~~a~~~s~~rl~Pm 86 (552) T pfam05876 18 TPYLREIMDALSPP----------SVERVVFMKSAQVGKTELLLNWIGYFIDHDP-APMLVVQPTDDDAKRFSKDRLDPM 86 (552) T ss_pred CCHHHHHHHHCCCC----------CCEEEEEEECCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCHHHHHHHHHHHHHHH T ss_conf 80769999854887----------8449999957870388999999988663089-887999418999999999989999 Q ss_pred HHHCCCCCC-CCCCCCCCCCCCCCCCCCCCCCC-CCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHH--- Q ss_conf 986231211-23333210001233322111134-5776126621013544556521011358628999754559988--- Q gi|254781187|r 132 LSMLPHRHW-FEMQSLSLHPSGWYAELLEQSMG-IDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDI--- 206 (367) Q Consensus 132 ~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~--- 206 (367) ++..|.-.. +... . .....+....+ +.+|.....+ +.+..++++...-++++||....+.. T Consensus 87 i~~sP~L~~~~~~~----~---~r~~~nt~~~K~f~gg~l~~~g-------a~S~~~L~s~~~r~l~~DEvD~~~~~~~~ 152 (552) T pfam05876 87 IRASPALRERLAPA----R---SRDSDNTLLSKRFPGGSLLLIG-------ANSPANLRSRPVRYVILDEVDAYPEDVDG 152 (552) T ss_pred HHCCHHHHHHHCCC----C---CCCCCCCEEEEEECCCEEEEEE-------CCCCHHHHCCCCCEEEECCHHHCCCCCCC T ss_conf 86198999750755----5---6566774124760783799955-------79961430486355885134436545677 Q ss_pred ---HHHHHHHHHHCCCCCEEEEEEECCCCC-CCHHHHHHH Q ss_conf ---999989874069882589998078999-876887541 Q gi|254781187|r 207 ---INKSILGFFTELNPNRFWIMTSNTRRL-NGWFYDIFN 242 (367) Q Consensus 207 ---i~e~i~g~Lt~~~~~~~~i~igNP~r~-~g~Fye~~~ 242 (367) ..+-++.-.++...+.+.+..|+|+.. ++.-...|. T Consensus 153 eGdP~~La~~R~~tf~~~~K~~~~STPt~~g~s~I~~~~~ 192 (552) T pfam05876 153 EGDPISLAEKRTETFGSRRKILAGSTPTIKGTSRIEALYE 192 (552) T ss_pred CCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHHHHH T ss_conf 8798999999987530285799983899999668999986 No 9 >COG4373 Mu-like prophage FluMu protein gp28 [General function prediction only] Probab=98.84 E-value=2.5e-07 Score=63.96 Aligned_cols=236 Identities=19% Similarity=0.238 Sum_probs=144.4 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHH---CCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC Q ss_conf 47761488678899999999999970---899779997153799999999999999986231211233332100012333 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLIST---RPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYA 155 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~---~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (367) ++|-.| |.+|-|+..|.--+--+.. .-|..|.++......+++-+ .....|.+.+-. -++.+....... T Consensus 31 kIAEKS-RRtGlTwaeA~~dV~~Aak~k~eGG~dVfy~gs~~emArEyI-~acamwar~fN~------~A~d~~E~~f~d 102 (509) T COG4373 31 KIAEKS-RRTGLTWAEAYEDVRDAAKPKREGGMDVFYSGSDLEMAREYI-RACAMWARIFNV------VATDLGEVVFED 102 (509) T ss_pred EHHHHC-CCCCCCHHHHHHHHHHHHCCCCCCCCEEEEECCCHHHHHHHH-HHHHHHHHHHHH------HHHHHHHHHHCC T ss_conf 153530-102642888777898752112258852588447489999999-999999999988------877777876447 Q ss_pred C---CCCCC-CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC--HHHHHHHHHHHHCCCCCEEEEEEEC Q ss_conf 2---21111-3457761266210135445565210113586289997545599--8899998987406988258999807 Q gi|254781187|r 156 E---LLEQS-MGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP--DIINKSILGFFTELNPNRFWIMTSN 229 (367) Q Consensus 156 ~---~~~~~-~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~--d~i~e~i~g~Lt~~~~~~~~i~igN 229 (367) . ...++ +.+.+|. -+.+ -..||.++.|..|. +++|||++-. ++++.++.+ ++-=+.++- .||+ T Consensus 103 ~dk~~Iltyvi~FasGf-kI~A---LSSnPknlRg~qG~----VviDEaAFHE~ldEllkAA~a-ltmWGa~vR--viSt 171 (509) T COG4373 103 SDKSAILTYVIAFASGF-KITA---LSSNPKNLRGKQGK----VVIDEAAFHEDLDELLKAAAA-LTMWGAPVR--VIST 171 (509) T ss_pred CCHHHHHHHHEEECCCC-EEEE---CCCCCCCCCCCCCC----EEEEHHHHHHHHHHHHHHHHH-HHHCCCCEE--EEEC T ss_conf 87565567303204774-6766---04797455467884----886236656539999998778-765177248--9962 Q ss_pred CCCCCCHHHHHHHC---CCCCEEEEEECCCC------------------CCCCCHHHHHHHHHHCCCCCCEEEEEEEEEE Q ss_conf 89998768875411---22350467523332------------------8888988999999621688000268886443 Q gi|254781187|r 230 TRRLNGWFYDIFNI---PLEDWKRYQIDTRT------------------VEGIDSGFHEGIISRYGLDSDVARIEILGQF 288 (367) Q Consensus 230 P~r~~g~Fye~~~~---~~~~w~~~~~~~~d------------------~p~~~~~~i~~~~~~~gedS~~~r~ev~G~F 288 (367) -++..+.|+++-.. +++.|.++.+.-.| .|..-..|..+..+.-|.+ +-+..|+.|. T Consensus 172 HNGvDnlFnQ~iQear~grk~ysvH~iTldDAiadGLy~RIc~v~~~~w~pE~Ea~w~a~l~~~a~t~-eda~eEy~C~- 249 (509) T COG4373 172 HNGVDNLFNQMIQEARQGRKKYSVHSITLDDAIADGLYERICNVDRPAWAPEVEAKWLAELRAIAGTD-EDAQEEYMCN- 249 (509) T ss_pred CCCHHHHHHHHHHHHHCCCCCCEEEEEEHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC-HHHHHHHCCC- T ss_conf 68701789999999870255531788865777777899999826774567567889999888656981-4457762877- Q ss_pred CCCCCCEEECHHHHHHHHCCCCCC------------------------------------CCCCCEEEEEECCCCCCCEE Q ss_conf 277898078299986443157777------------------------------------88984899996387788108 Q gi|254781187|r 289 PQQEVNNFIPHNYIEEAMSREAID------------------------------------DLYAPLIMGCDIAGEGGDKT 332 (367) Q Consensus 289 p~~~~d~~ip~~~ie~a~~~~~~~------------------------------------~~~~p~viGvDvAr~G~D~T 332 (367) |..+.+++||..+|++++-+++.. .|......|||.||. +|-| T Consensus 250 Pk~s~gAYIphalie~a~~~~vp~l~fe~~~~f~~~~~~~r~~~~~~~cl~~l~P~Lqalnp~~r~~fGvDfaR~-~DLs 328 (509) T COG4373 250 PKDSTGAYIPHALIEAAVAAEVPDLIFELGSEFHDIPAWLRESEVLTWCLPDLRPALQALNPGGRLYFGVDFARK-RDLS 328 (509) T ss_pred CCCCCCCCCCHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEECCCCCCC-CCCE T ss_conf 566776646678999887547985179757455423566424566665344356898732999716521220225-6734 Q ss_pred EEEE Q ss_conf 9999 Q gi|254781187|r 333 VVVF 336 (367) Q Consensus 333 vi~~ 336 (367) |+++ T Consensus 329 v~~v 332 (509) T COG4373 329 VLWV 332 (509) T ss_pred EEEE T ss_conf 9998 No 10 >COG1061 SSL2 DNA or RNA helicases of superfamily II [Transcription / DNA replication, recombination, and repair] Probab=98.71 E-value=1e-06 Score=60.14 Aligned_cols=162 Identities=18% Similarity=0.143 Sum_probs=97.7 Q ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH Q ss_conf 66842899999998888751245555541124776148867889999999999997089977999715379999999999 Q gi|254781187|r 48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAE 127 (367) Q Consensus 48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~e 127 (367) .-.|+.+|.+.++++-.+... .. |..|..+-|.|||.+++..+-..- .++++++|+..-+.+-- .. T Consensus 34 ~~~lr~yQ~~al~a~~~~~~~-~~-------~gvivlpTGaGKT~va~~~~~~~~-----~~~Lvlv~~~~L~~Qw~-~~ 99 (442) T COG1061 34 EFELRPYQEEALDALVKNRRT-ER-------RGVIVLPTGAGKTVVAAEAIAELK-----RSTLVLVPTKELLDQWA-EA 99 (442) T ss_pred CCCCHHHHHHHHHHHHHHCCC-CC-------CEEEEECCCCCHHHHHHHHHHHHC-----CCEEEEECCHHHHHHHH-HH T ss_conf 788859999999999962225-78-------679996799988999999999826-----98899978299999999-99 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHH Q ss_conf 99999862312112333321000123332211113457761266210135445565210113586289997545599889 Q gi|254781187|r 128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDII 207 (367) Q Consensus 128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i 207 (367) +.+....... + ............ ....+++-++..... .+.-+.+.++.|+|+||+..++... T Consensus 100 ~~~~~~~~~~----------~----g~~~~~~~~~~~-~~i~vat~qtl~~~~--~l~~~~~~~~~liI~DE~Hh~~a~~ 162 (442) T COG1061 100 LKKFLLLNDE----------I----GIYGGGEKELEP-AKVTVATVQTLARRQ--LLDEFLGNEFGLIIFDEVHHLPAPS 162 (442) T ss_pred HHHHCCCCCC----------C----CEECCCCCCCCC-CCEEEEEEHHHHHHH--HHHHHCCCCCCEEEEECCCCCCCHH T ss_conf 9973488676----------6----033687233577-748999838976415--5554035666759997524578477 Q ss_pred HHHHHHHHHCCCCCEEEEEEECCCCCC-CHHHHHHH Q ss_conf 999898740698825899980789998-76887541 Q gi|254781187|r 208 NKSILGFFTELNPNRFWIMTSNTRRLN-GWFYDIFN 242 (367) Q Consensus 208 ~e~i~g~Lt~~~~~~~~i~igNP~r~~-g~Fye~~~ 242 (367) +..+...++.... ..-++.+|.|.. +...+.+. T Consensus 163 ~~~~~~~~~~~~~--~LGLTATp~R~D~~~~~~l~~ 196 (442) T COG1061 163 YRRILELLSAAYP--RLGLTATPEREDGGRIGDLFD 196 (442) T ss_pred HHHHHHHHHCCCE--EEEEECCCCCCCCCCHHHHHH T ss_conf 9999997510310--467714872448775248774 No 11 >COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only] Probab=98.62 E-value=3.6e-06 Score=56.83 Aligned_cols=149 Identities=19% Similarity=0.143 Sum_probs=84.1 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089-97799971537999999999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) =|.+++..+....+.+.. -++|.|.||=|||++....+ ..+...- ..+|+||||+...+. .++.-+.+-+ T Consensus 215 dQ~~~l~~~~~l~~~~~~-------~~vlTAdRGRGKSA~lGi~~-~~~~~~~~~~~iiVTAP~~~nv~-~Lf~fa~~~l 285 (758) T COG1444 215 DQAEALEILERLLDAPKR-------ALVLTADRGRGKSAALGIAL-AAAARLAGSVRIIVTAPTPANVQ-TLFEFAGKGL 285 (758) T ss_pred HHHHHHHHHHHHHCCCCC-------EEEEECCCCCCHHHHHHHHH-HHHHHHCCCCEEEEECCCHHHHH-HHHHHHHHHH T ss_conf 189999999999708983-------59998677874768874999-99997337720899679778899-9999998769 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH Q ss_conf 86231211233332100012333221111345776126621013544556521011358628999754559988999989 Q gi|254781187|r 133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL 212 (367) Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~ 212 (367) +.+-.++....+..- ++....+..+. ..=.+|..-+ .. ..++++||||+||=.+...+. T Consensus 286 ~~lg~~~~v~~~~~g-------------~~~~~~~~~~~----i~y~~P~~a~--~~--~DllvVDEAAaIplplL~~l~ 344 (758) T COG1444 286 EFLGYKRKVAPDALG-------------EIREVSGDGFR----IEYVPPDDAQ--EE--ADLLVVDEAAAIPLPLLHKLL 344 (758) T ss_pred HHHCCCCCCCCCCCC-------------CEEEECCCCEE----EEEECCHHHC--CC--CCEEEEEHHHCCCHHHHHHHH T ss_conf 982774555634424-------------40000477425----7751750012--56--888998103128869999998 Q ss_pred HHHHCCCCCEEEEEEECCCCCCCH Q ss_conf 874069882589998078999876 Q gi|254781187|r 213 GFFTELNPNRFWIMTSNTRRLNGW 236 (367) Q Consensus 213 g~Lt~~~~~~~~i~igNP~r~~g~ 236 (367) ..-.+.++..+.+=..++|. T Consensus 345 ----~~~~rv~~sTTIhGYEGtGR 364 (758) T COG1444 345 ----RRFPRVLFSTTIHGYEGTGR 364 (758) T ss_pred ----HHCCCEEEEEEECCCCCCCH T ss_conf ----64481699974024466771 No 12 >smart00487 DEXDc DEAD-like helicases superfamily. Probab=98.58 E-value=1e-06 Score=60.14 Aligned_cols=173 Identities=13% Similarity=0.023 Sum_probs=92.5 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHH Q ss_conf 36668428999999988887512455555411247761488678899999999999970899779997153799999999 Q gi|254781187|r 46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLW 125 (367) Q Consensus 46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw 125 (367) ..+..|+++|.++++.+.... ..+.|.++-|+|||..++.+++..+......++++++|+...+.+. . T Consensus 4 ~~~~~~~~~Q~~~~~~~~~~~-----------~~~~i~~~tGsGKT~~~~~~~~~~~~~~~~~~~li~~P~~~l~~q~-~ 71 (201) T smart00487 4 FGFEPLRPYQKEAIEALLSGL-----------RDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAEQW-A 71 (201) T ss_pred CCCCCCCHHHHHHHHHHHCCC-----------CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHH-H T ss_conf 379999988999999998389-----------9889989999609999999999986338997599990859999999-9 Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC Q ss_conf 99999998623121123333210001233322111134577-61266210135445565210113586289997545599 Q gi|254781187|r 126 AEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDS-KHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP 204 (367) Q Consensus 126 ~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~ 204 (367) .++.++........-........ ........... ...+.+-..... ...... .......++|+|||..+. T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~i~i~t~~~l~~-~~~~~~-~~~~~~~~vIiDE~H~~~ 142 (201) T smart00487 72 EELKKLGPSLGLKVVGLYGGDSK-------REQLRKLESGKTDILVTTPGRLLD-LLENDL-LELSNVDLVILDEAHRLL 142 (201) T ss_pred HHHHHCCCCCEEEEEEEECCCCH-------HHHHHHHHCCCCCEEEECHHHHHH-HHHHCC-CCCCCCEEEEEECHHHHH T ss_conf 88601021020445565247737-------999999975999899955899999-997275-452543199998967751 Q ss_pred H-HHHHHHHHHHH--CCCCCEEEEEEECCCCCCCHHHHH Q ss_conf 8-89999898740--698825899980789998768875 Q gi|254781187|r 205 D-IINKSILGFFT--ELNPNRFWIMTSNTRRLNGWFYDI 240 (367) Q Consensus 205 d-~i~e~i~g~Lt--~~~~~~~~i~igNP~r~~g~Fye~ 240 (367) + .....+...+. ..+.+ ++++.+||+...-.+... T Consensus 143 ~~~~~~~~~~~~~~~~~~~~-~i~lSAT~~~~~~~~~~~ 180 (201) T smart00487 143 DGGFGDQLEKLLKLLPKNVQ-LLLLSATPPEEIENLLEL 180 (201) T ss_pred CCCCHHHHHHHHHHCCCCCC-EEEECCCCCHHHHHHHHH T ss_conf 25709999999996799997-899924898689999999 No 13 >PRK10875 recD exonuclease V subunit alpha; Provisional Probab=98.45 E-value=1.6e-05 Score=52.92 Aligned_cols=156 Identities=20% Similarity=0.154 Sum_probs=83.7 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEE-EEECCCCCCHHHHHHHHHHHH--HHHCCCCEEEEECCCHHHHHHHHHHHH Q ss_conf 28999999988887512455555411247-761488678899999999999--970899779997153799999999999 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKC-AISAGRGIGKTTLNAWMMLWL--ISTRPGMSIICIANSETQLKNTLWAEV 128 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~-~v~sgrg~GKS~~~a~~~lw~--~~~~~~~~v~~~A~t~~Q~~~~lw~ei 128 (367) ..||+.+... -+++ ++ .|.+|=|+|||+.++.++.-+ +...++.+|..+|||.+-+.... .-+ T Consensus 149 ~dwQk~A~a~---Al~~----------~~~vIsGGPGTGKTttV~~lLa~l~~~~~~~~l~I~LaAPTGKAAaRL~-Esi 214 (607) T PRK10875 149 VNWQKVAAAV---ALTR----------RISVISGGPGTGKTTTVAKLLAALIQLADGERCRIRLAAPTGKAAARLT-ESL 214 (607) T ss_pred CCHHHHHHHH---HHHC----------CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHH-HHH T ss_conf 5189999999---8755----------7789967999877889999999999964589970899882289999999-999 Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHH Q ss_conf 99998623121123333210001233322111134577612662101354455652101135862899975455998899 Q gi|254781187|r 129 SKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIIN 208 (367) Q Consensus 129 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~ 208 (367) .+.+..++..... ....+....-.-.-++..+++.. .....+||- ...++||||||.|+-..+ T Consensus 215 ~~~~~~l~~~~~~------~~~~p~~a~TiHRLLg~~p~~~~---f~~~~~nPL--------~~DvlIVDEASMVDl~Lm 277 (607) T PRK10875 215 GKALRQLPLTDEQ------KKRIPEDASTLHRLLGAQPGSQR---LRYHAGNPL--------HLDVLVVDEASMIDLPMM 277 (607) T ss_pred HHHHHHCCCCHHH------HHCCCCCCEEHHHHCCCCCCCCC---CCCCCCCCC--------CCCEEEEECCHHHHHHHH T ss_conf 8787534766566------63376556658975296789876---565779999--------889899907336659999 Q ss_pred HHHHHHHHCCCCCEEEEEEECCC-----CCCCHHHHHH Q ss_conf 99898740698825899980789-----9987688754 Q gi|254781187|r 209 KSILGFFTELNPNRFWIMTSNTR-----RLNGWFYDIF 241 (367) Q Consensus 209 e~i~g~Lt~~~~~~~~i~igNP~-----r~~g~Fye~~ 241 (367) ..+.-++.. +.++ +++|.|. +.+..|.|+. T Consensus 278 ~~LL~Alp~-~aRL--ILvGD~dQLpSVgaGaVL~DL~ 312 (607) T PRK10875 278 SRLIDALPD-HARV--IFLGDRDQLASVEAGAVLGDIC 312 (607) T ss_pred HHHHHHCCC-CCEE--EEECCHHHCCCCCCCCCHHHHH T ss_conf 999982899-9889--9965623247888882179999 No 14 >PRK13766 Hef nuclease; Provisional Probab=98.44 E-value=5.9e-06 Score=55.47 Aligned_cols=159 Identities=11% Similarity=0.068 Sum_probs=80.7 Q ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH Q ss_conf 66842899999998888751245555541124776148867889999999999997089977999715379999999999 Q gi|254781187|r 48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAE 127 (367) Q Consensus 48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~e 127 (367) .-.+|.+|.++++.--. + ++.|+.+.|+|||.+++.++..++- .++.|++.+|||-.-+.+-. .. T Consensus 13 ~ie~R~YQ~el~~~Al~---~----------NtiVvLPTG~GKT~IA~lvi~~~l~-~~~gKilFLaPT~pLV~Qq~-~~ 77 (764) T PRK13766 13 TIEARLYQQLLAAKALK---G----------NTLVVLPTGLGKTAIALLVIAERLQ-KYGGKVLILAPTKPLVEQHA-EF 77 (764) T ss_pred CCCCCHHHHHHHHHHHH---C----------CEEEEECCCCCHHHHHHHHHHHHHH-HCCCEEEEECCCHHHHHHHH-HH T ss_conf 77653879999999985---8----------9899959986689999999999997-48988999858888999999-99 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC-CHH Q ss_conf 9999986231211233332100012333221111345776126621013544556521011358628999754559-988 Q gi|254781187|r 128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT-PDI 206 (367) Q Consensus 128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI-~d~ 206 (367) +++.......+-. ..+ +...+ ..+...-......+++.+.....-..+ -+.-..+.|+|+|||... .+. T Consensus 78 ~~~~l~i~~~~i~-~lt-G~~~~------~~r~~~w~~~~Viv~TPQvl~ndL~~g--~i~l~dv~lLVfDEaHha~Gnh 147 (764) T PRK13766 78 FRKFLNIDPEKIV-VLT-GEISP------EKRAALWEKAKVIVATPQVIENDLLAG--RISLEDVSLLIFDEAHRAVGNY 147 (764) T ss_pred HHHHCCCCCCEEE-EEE-CCCCH------HHHHHHHCCCCEEEECCHHHHHHHHHC--CCCHHHCCEEEEECCCCCCCCC T ss_conf 9997099955289-998-88782------768998607999999908999999829--8678882289997466666776 Q ss_pred HH-HHHHHHHHCCCCCEEEEEEECCC Q ss_conf 99-99898740698825899980789 Q gi|254781187|r 207 IN-KSILGFFTELNPNRFWIMTSNTR 231 (367) Q Consensus 207 i~-e~i~g~Lt~~~~~~~~i~igNP~ 231 (367) .+ .++.-.+.......+.-++.+|. T Consensus 148 ~Y~~I~~~y~~~~~~PrILGLTASPG 173 (764) T PRK13766 148 AYVFIAERYHEDAKNPLVLGLTASPG 173 (764) T ss_pred CHHHHHHHHHHCCCCCEEEEECCCCC T ss_conf 28999999985377855885036887 No 15 >TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. . Probab=98.41 E-value=4.2e-06 Score=56.37 Aligned_cols=138 Identities=17% Similarity=0.205 Sum_probs=89.9 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEE-EECCCCCCHHHHHHHHHHHHHHHC-----------CCCEEEEECCCHHH Q ss_conf 289999999888875124555554112477-614886788999999999999708-----------99779997153799 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCA-ISAGRGIGKTTLNAWMMLWLISTR-----------PGMSIICIANSETQ 119 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~-v~sgrg~GKS~~~a~~~lw~~~~~-----------~~~~v~~~A~t~~Q 119 (367) ..=|+++|..+..+ ||. +.+|=|+|||+++-..+-.+.... .+.+|+..|||.+= T Consensus 352 ~~~Qk~AL~~~~~~-------------Kv~iLTGGPGTGKtT~t~~i~~~~~~~~gl~l~~~~~vndd~~v~LaAPTGrA 418 (769) T TIGR01448 352 SEEQKEALKTAIQD-------------KVVILTGGPGTGKTTITKAIIELYEELKGLDLDKDDYVNDDLPVVLAAPTGRA 418 (769) T ss_pred HHHHHHHHHHHHCC-------------CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCHHH T ss_conf 68899999998609-------------48998577888616899999999987168775531245677648873774378 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCC-CCC--CCCCEEE Q ss_conf 9999999999999862312112333321000123332211113457761266210135445565210-113--5862899 Q gi|254781187|r 120 LKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVG-PHN--THGMAVF 196 (367) Q Consensus 120 ~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g-~h~--~~~~l~i 196 (367) +|.. .|+---...-++++ ++.+.. +.-.+ .|- -++.|+| T Consensus 419 AkRl--~E~TG~~a~TIHRL----------------------lG~~~~--------------~~~~~k~~~~~~~~DL~I 460 (769) T TIGR01448 419 AKRL--AEVTGLEALTIHRL----------------------LGYGSD--------------TKSENKNLEDPIDADLLI 460 (769) T ss_pred HHHC--CCCCCCHHHHHHHH----------------------HCCCCC--------------CCCCCHHHCCCCCCCEEE T ss_conf 8851--10026212347786----------------------368988--------------873211011347877699 Q ss_pred EECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC-----CCCCCCHHHHHHHC Q ss_conf 975455998899998987406988258999807-----89998768875411 Q gi|254781187|r 197 NDEASGTPDIINKSILGFFTELNPNRFWIMTSN-----TRRLNGWFYDIFNI 243 (367) Q Consensus 197 vDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igN-----P~r~~g~Fye~~~~ 243 (367) |||.|.|++-.+..+..++.+ +++++ ++|- |-.++..|-|+-+. T Consensus 461 vDE~SM~Dt~L~~~lL~a~P~-~a~ll--lVGD~DQLPSV~pG~VL~DLi~s 509 (769) T TIGR01448 461 VDESSMVDTWLASSLLAAVPD-HARLL--LVGDADQLPSVGPGQVLKDLIQS 509 (769) T ss_pred EECCCHHHHHHHHHHHHHCCC-CCEEE--EECCCCCCCCCCCCHHHHHHHHC T ss_conf 814621889999999861797-77798--88376888988644089999846 No 16 >pfam04851 ResIII Type III restriction enzyme, res subunit. Probab=98.34 E-value=6.8e-06 Score=55.12 Aligned_cols=100 Identities=20% Similarity=0.295 Sum_probs=69.1 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537999999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) ..|+||.++++++.++- |..|.++-|+|||.+++.++.++. .++.++++++|+..-+.+. T Consensus 3 ~LR~yQ~~a~~~~~~~~------------~~~i~~pTGsGKT~~~~~~i~~~~--~~~~~~lvlvp~~~L~~Q~------ 62 (103) T pfam04851 3 ELRPYQIEAIRNLLEKK------------RGLIVMATGSGKTLTAAKLIARLL--KGKKKVLFLVPRKDLLEQA------ 62 (103) T ss_pred CCCHHHHHHHHHHHHCC------------CEEEEECCCCCHHHHHHHHHHHHH--HCCCCEEEEECCHHHHHHH------ T ss_conf 87299999999999639------------869995899987999999999998--4699299990829999999------ Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHH-HH Q ss_conf 99986231211233332100012333221111345776126621013544556521011358628999754559988-99 Q gi|254781187|r 130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDI-IN 208 (367) Q Consensus 130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~-i~ 208 (367) .+. .++|+|||...+.. .| T Consensus 63 --~~~----------------------------------------------------------~lii~DE~H~~~a~~~~ 82 (103) T pfam04851 63 --LEE----------------------------------------------------------FVIIIDEAHHSSAKTKY 82 (103) T ss_pred --HHH----------------------------------------------------------HHHHHHHHHHCCCHHHH T ss_conf --996----------------------------------------------------------56460163523537899 Q ss_pred HHHHHHHHCCCCCEEEEEEECCCC Q ss_conf 998987406988258999807899 Q gi|254781187|r 209 KSILGFFTELNPNRFWIMTSNTRR 232 (367) Q Consensus 209 e~i~g~Lt~~~~~~~~i~igNP~r 232 (367) ..+...+. ....+-++.+|.| T Consensus 83 ~~l~~~~~---~~~~lGlTATP~R 103 (103) T pfam04851 83 RKILEYFK---PAFLLGLTATPER 103 (103) T ss_pred HHHHHHCC---CCEEEEEEECCCC T ss_conf 99999577---2608998008889 No 17 >TIGR01447 recD exodeoxyribonuclease V, alpha subunit; InterPro: IPR006344 This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. C-terminal part of the protein matches a domain found in viral RNA helicase, superfamily 1, IPR000606 from INTERPRO. ; GO: 0008854 exodeoxyribonuclease V activity, 0009338 exodeoxyribonuclease V complex. Probab=98.21 E-value=3.8e-05 Score=50.55 Aligned_cols=156 Identities=19% Similarity=0.161 Sum_probs=86.6 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-----CEEEEECCCHHHHHHHHHH Q ss_conf 28999999988887512455555411247761488678899999999999970899-----7799971537999999999 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-----MSIICIANSETQLKNTLWA 126 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-----~~v~~~A~t~~Q~~~~lw~ 126 (367) +.||.=++...-. ++ | ..|.+|=|+|||+.++-+++=....-+. .+|.++|||++=+. .+-. T Consensus 229 ~D~Q~~a~~~aL~---~~--------f-~li~GGPGTGKTTTv~~LL~al~~~~~~~G~~~~~I~l~APTGKAa~-RL~e 295 (753) T TIGR01447 229 TDWQKVAVALALK---SN--------F-SLITGGPGTGKTTTVARLLLALIKQSPKQGKPRLRIALAAPTGKAAA-RLAE 295 (753) T ss_pred HHHHHHHHHHHHH---CC--------E-EEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHH-HHHH T ss_conf 3799999999860---87--------6-89987988977899999999999989864997404788668447999-9999 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHH Q ss_conf 99999986231211233332100012333221111345776126621013544556521011358628999754559988 Q gi|254781187|r 127 EVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDI 206 (367) Q Consensus 127 ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~ 206 (367) -|.+....+....- .+. +...........+ +.---|...+....++.+.... -....+||||||.|+=. T Consensus 296 sl~~~~~~L~~~~~-aid--~~~~~~~~~~~~T--iHrLLG~~~I~~~~fr~h~~N~------L~~DVLvvDEaSMVdl~ 364 (753) T TIGR01447 296 SLRKAVKKLAAENM-AID--EDLIAALPSEATT--IHRLLGIKPIDTKRFRHHERNP------LPLDVLVVDEASMVDLP 364 (753) T ss_pred HHHHHHHHHHHHCC-CCC--HHHHCCCCHHHHH--HHHHHCCCCCCCCCCCCCCCCC------CCCCEEEECCCHHCCHH T ss_conf 99988632234236-658--7985487204568--8886166147876776777788------98552787060022679 Q ss_pred HHHHHHHHHHCCCCC------EEEEEEECCCC Q ss_conf 999989874069882------58999807899 Q gi|254781187|r 207 INKSILGFFTELNPN------RFWIMTSNTRR 232 (367) Q Consensus 207 i~e~i~g~Lt~~~~~------~~~i~igNP~r 232 (367) .+..+.-++.... | .-+|++|-++- T Consensus 365 lm~kL~~A~~~~~-k~~KLy~~~LIllGD~nQ 395 (753) T TIGR01447 365 LMAKLLKALPPNT-KDKKLYADRLILLGDKNQ 395 (753) T ss_pred HHHHHHHHCCCCC-CCCCHHHCCCCEECCCCC T ss_conf 9999997226300-132010102001226788 No 18 >pfam02562 PhoH PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation. Probab=98.21 E-value=1.4e-05 Score=53.24 Aligned_cols=56 Identities=18% Similarity=0.025 Sum_probs=46.2 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH Q ss_conf 42899999998888751245555541124776148867889999999999997089977999715379 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET 118 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~ 118 (367) -++-|+.+++.+.++. -+.+.++-|+|||++++..++..+......+++++.|.-. T Consensus 5 ~~~~Q~~~~~~l~~~~------------iv~~~GpAGtGKT~la~~~al~~l~~~~~~kiii~Rp~v~ 60 (205) T pfam02562 5 KTLGQKRYVEAIRKND------------IVFGIGPAGTGKTYLAVAAAVDALKDGKVKRIILTRPAVE 60 (205) T ss_pred CCHHHHHHHHHHHCCC------------EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCC T ss_conf 9888999999971798------------0799899986099999999999997189437999757712 No 19 >PRK10536 hypothetical protein; Provisional Probab=98.20 E-value=5.5e-05 Score=49.56 Aligned_cols=184 Identities=16% Similarity=0.121 Sum_probs=95.3 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH--------- Q ss_conf 42899999998888751245555541124776148867889999999999997089977999715379999--------- Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK--------- 121 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~--------- 121 (367) -++-|.+.++.|.++. -+-..++-|+|||++++.+++-.+....-.++++|.|.-.--+ T Consensus 60 kt~~Q~~yi~~i~~~~------------ivf~~GpAGTGKT~lA~a~Al~~l~~~~~~kIIltRP~V~~ge~lGfLPGdl 127 (262) T PRK10536 60 RNEAQLHYLKAIESKQ------------LIFATGEAGCGKTWISAAKAAEALIHKDVDRIIVTRPVLQADEDLGFLPGDI 127 (262) T ss_pred CCHHHHHHHHHHHHCC------------EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCH T ss_conf 9864999999986198------------3999899987589999999999998588868999667875676667698987 Q ss_pred -HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC Q ss_conf -9999999999986231211233332100012333221111345776126621013544556521011358628999754 Q gi|254781187|r 122 -NTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA 200 (367) Q Consensus 122 -~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEA 200 (367) +.+.+.+.-.+..+-.. +. ....+..+....|..-+ .|-++---+..+-.++|+||| T Consensus 128 ~EK~~Pyl~Pi~D~L~~~-----------lg---~~~~~~~~~~e~G~Iei--------~PlafmRGrTf~na~IIvDEa 185 (262) T PRK10536 128 AEKFAPYFRPVYDVLVRR-----------LG---ASFMQYCLRPEIGKVEI--------APFAYMRGRTFENAVVILDEA 185 (262) T ss_pred HHHHHHHHHHHHHHHHHH-----------HC---HHHHHHHHHHHCCCEEE--------EEHHHHCCCCCCCEEEEEEHH T ss_conf 998878887899999999-----------68---59999998730594899--------875874477514428998412 Q ss_pred CCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCC------CCHHHHHHHCCC--CCEEEEEECCCCCCCCCHHHHHHHHHH Q ss_conf 559988999989874069882589998078999------876887541122--350467523332888898899999962 Q gi|254781187|r 201 SGTPDIINKSILGFFTELNPNRFWIMTSNTRRL------NGWFYDIFNIPL--EDWKRYQIDTRTVEGIDSGFHEGIISR 272 (367) Q Consensus 201 sgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~------~g~Fye~~~~~~--~~w~~~~~~~~d~p~~~~~~i~~~~~~ 272 (367) +-....-...+. |--+....+++.|.+.-. .+-+.+...... +....+.++..| .+....+.+.... T Consensus 186 QN~T~~qmk~iL---TRiG~~SKiVi~GD~~Q~Dl~~~~~SGL~~~~~~l~~~~~i~~i~F~~~D--IVRs~lVk~Il~a 260 (262) T PRK10536 186 QNVTAAQMKMFL---TRLGENVTVIVNGDITQCDLPRGVKSGLSDALERFEEDEMVGIVRFGKED--CVRSALCQRTLHA 260 (262) T ss_pred HCCCHHHHHHHH---HHCCCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHCCCCCEEEEECCCCC--CCCCHHHHHHHHH T ss_conf 128999998898---54259968999688202269999987399999995699965899836444--0167899999996 Q ss_pred C Q ss_conf 1 Q gi|254781187|r 273 Y 273 (367) Q Consensus 273 ~ 273 (367) | T Consensus 261 Y 261 (262) T PRK10536 261 Y 261 (262) T ss_pred C T ss_conf 2 No 20 >PRK02362 ski2-like helicase; Provisional Probab=98.19 E-value=8.7e-05 Score=48.31 Aligned_cols=158 Identities=16% Similarity=0.032 Sum_probs=83.6 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH Q ss_conf 66684289999999888875124555554112477614886788999999999999708997799971537999999999 Q gi|254781187|r 47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWA 126 (367) Q Consensus 47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ 126 (367) +++.--+||.++++. .+..+. ++.|+++.|+|||.++-..++-.+. .+.|+++++|...=+.+.. . T Consensus 20 gI~~Lyp~Q~eal~~---gl~~g~--------NlvvsaPTgsGKTlvAElail~~l~--~g~k~vYi~P~kALa~EK~-~ 85 (736) T PRK02362 20 GIEELYPPQAEAVEA---GLLEGK--------NLLAAIPTASGKTLLAELAMLKAIA--EGGKALYIVPLRALASEKF-E 85 (736) T ss_pred CCCCCCHHHHHHHHH---HHCCCC--------CEEEECCCCCCHHHHHHHHHHHHHH--HCCEEEEECCHHHHHHHHH-H T ss_conf 997578999999986---435698--------1899799998589999999999998--3997999858799999999-9 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCC------CCCCCEEEEECC Q ss_conf 99999986231211233332100012333221111345776126621013544556521011------358628999754 Q gi|254781187|r 127 EVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPH------NTHGMAVFNDEA 200 (367) Q Consensus 127 ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h------~~~~~l~ivDEA 200 (367) +++++...-.. ............-...... ++.+. ||.+..+- -.+.-++|+||. T Consensus 86 ~~~~~~~~gi~------------V~~~tGd~~~~~~~l~~~d-IiV~T------~EK~dsl~r~~~~~l~~v~lVViDEi 146 (736) T PRK02362 86 EFSEFSELGLR------------VGISTGDYDRRDEYLGRND-IIVAT------SEKTDSLLRNGAPWIDDISCVVADEV 146 (736) T ss_pred HHHHHHCCCCE------------EEEEECCCCCCHHHCCCCC-EEEEC------HHHHHHHHHCCCHHHHCCCEEEEECC T ss_conf 99987457998------------9998089887831436899-99999------79999998448167650898998176 Q ss_pred CCCCH----HHHHHHHHHHHCCCCCEEEEEEECCCCCCCHH Q ss_conf 55998----89999898740698825899980789998768 Q gi|254781187|r 201 SGTPD----IINKSILGFFTELNPNRFWIMTSNTRRLNGWF 237 (367) Q Consensus 201 sgI~d----~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~F 237 (367) ..|.| .++|++...+..-+...-.+..|.+-.+...+ T Consensus 147 Hli~d~~RG~~lE~~lskl~~~~~~iqiIgLSATl~N~~~l 187 (736) T PRK02362 147 HLIDSPNRGPTLEVTLAKLRRLNPDMQVIALSATIGNADEL 187 (736) T ss_pred EEECCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHH T ss_conf 78668872499999999997338774389862455899999 No 21 >PRK01172 ski2-like helicase; Provisional Probab=98.18 E-value=0.0001 Score=47.92 Aligned_cols=160 Identities=12% Similarity=-0.023 Sum_probs=81.9 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537999999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) .+.+||++.+..+.++- ++.|+++.|.|||.++-..++-.+. .+.|+++++|...=+.+.. .+++ T Consensus 22 ~l~p~Q~ea~~~~~~gk------------NllvsaPTgsGKTlvAe~ai~~~l~--~~~k~iyi~P~kAL~~EK~-~~~~ 86 (674) T PRK01172 22 ELYDHQRMAIEQLRKGE------------NVIVSVPTAAGKTLIAYSAIYETFL--AGLKSIYIVPLRSLAMEKY-EELS 86 (674) T ss_pred CCCHHHHHHHHHHHCCC------------CEEEECCCCCCHHHHHHHHHHHHHH--HCCCEEEECCHHHHHHHHH-HHHH T ss_conf 88989999999997799------------5999789998699999999999998--5897999877899999999-9999 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---- Q ss_conf 9998623121123333210001233322111134577612662101354455652101135862899975455998---- Q gi|254781187|r 130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---- 205 (367) Q Consensus 130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---- 205 (367) ++.... . .+. ..........-...... ++.+..-..++--+-+.-.-.+..++|+||...|.| T Consensus 87 ~~~~~g-~----~v~-------~~tGd~~~~~~~~~~~~-I~V~T~Ek~~sl~~~~~~~l~~v~~vViDEiH~i~d~~RG 153 (674) T PRK01172 87 RLRSLG-M----RVK-------ISIGDYDDPPDFIKRYD-VVILTSEKADSLIHHDPYIINDVGLIVADEIHIIGDEDRG 153 (674) T ss_pred HHHCCC-C----EEE-------EEECCCCCCCCCCCCCC-EEEECHHHHHHHHHCCCHHHCCCCEEEEECCEECCCCCCH T ss_conf 887379-8----277-------88538889801025589-9998789999998649502213698998265250687724 Q ss_pred HHHHHHHHHHH--CCCCCEEEEEEECCCCCCCHHHH Q ss_conf 89999898740--69882589998078999876887 Q gi|254781187|r 206 IINKSILGFFT--ELNPNRFWIMTSNTRRLNGWFYD 239 (367) Q Consensus 206 ~i~e~i~g~Lt--~~~~~~~~i~igNP~r~~g~Fye 239 (367) .+||.+...+. .++.++ +..|-+-.+...+.+ T Consensus 154 ~~lE~~l~kl~~l~~~~qi--IgLSATi~N~~~la~ 187 (674) T PRK01172 154 PTLETVLSSARYVNPDARI--LALSATVSNANELAQ 187 (674) T ss_pred HHHHHHHHHHHHCCCCEEE--EEECCCCCCHHHHHH T ss_conf 9999999999853866079--971578689999998 No 22 >COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair] Probab=98.16 E-value=5.4e-05 Score=49.61 Aligned_cols=167 Identities=13% Similarity=0.075 Sum_probs=88.6 Q ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH Q ss_conf 66842899999998888751245555541124776148867889999999999997089977999715379999999999 Q gi|254781187|r 48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAE 127 (367) Q Consensus 48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~e 127 (367) ...||.+|..+....-. + ++.|+-+.|.|||+++++.+..++--.++ +++.+|||..-+-+-. .- T Consensus 13 ~ie~R~YQ~~i~a~al~---~----------NtLvvlPTGLGKT~IA~~V~~~~l~~~~~-kvlfLAPTKPLV~Qh~-~~ 77 (542) T COG1111 13 TIEPRLYQLNIAAKALF---K----------NTLVVLPTGLGKTFIAAMVIANRLRWFGG-KVLFLAPTKPLVLQHA-EF 77 (542) T ss_pred CCCHHHHHHHHHHHHHH---C----------CEEEEECCCCCHHHHHHHHHHHHHHHCCC-EEEEECCCCHHHHHHH-HH T ss_conf 32588999999999864---4----------83899528750799999999999874588-4899658951799999-99 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEEECCCCCCCCCCCCC-CCCCCCCEEEEECCC-CCC Q ss_conf 9999986231211233332100012333221111345776-1266210135445565210-113586289997545-599 Q gi|254781187|r 128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSK-HYTITCRTYSEERPDTFVG-PHNTHGMAVFNDEAS-GTP 204 (367) Q Consensus 128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~a~~~~~~~~ea~~g-~h~~~~~l~ivDEAs-gI~ 204 (367) +++.....++. -...+ +.+.+ .+.......+ ..+++-++.. | +=..| +--+...|+|+|||. .+- T Consensus 78 ~~~v~~ip~~~-i~~lt-Gev~p-------~~R~~~w~~~kVfvaTPQvve--N-Dl~~Grid~~dv~~lifDEAHRAvG 145 (542) T COG1111 78 CRKVTGIPEDE-IAALT-GEVRP-------EEREELWAKKKVFVATPQVVE--N-DLKAGRIDLDDVSLLIFDEAHRAVG 145 (542) T ss_pred HHHHHCCCHHH-EEEEC-CCCCH-------HHHHHHHHHCCEEEECCHHHH--H-HHHCCCCCHHHCEEEEECHHHHCCC T ss_conf 99985898433-23111-77786-------889998751778995638777--6-8761766767805898623554137 Q ss_pred HHHH-HHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHH Q ss_conf 8899-998987406988258999807899987688754 Q gi|254781187|r 205 DIIN-KSILGFFTELNPNRFWIMTSNTRRLNGWFYDIF 241 (367) Q Consensus 205 d~i~-e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~ 241 (367) +..| .++.--+....+..+.-++.+|-......-+.. T Consensus 146 nyAYv~Va~~y~~~~k~~~ilgLTASPGs~~ekI~eV~ 183 (542) T COG1111 146 NYAYVFVAKEYLRSAKNPLILGLTASPGSDLEKIQEVV 183 (542) T ss_pred CCHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHH T ss_conf 60699999999982568437987238999879999999 No 23 >PRK00254 ski2-like helicase; Provisional Probab=98.08 E-value=0.00022 Score=45.87 Aligned_cols=143 Identities=13% Similarity=0.041 Sum_probs=80.9 Q ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH Q ss_conf 66842899999998888751245555541124776148867889999999999997089977999715379999999999 Q gi|254781187|r 48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAE 127 (367) Q Consensus 48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~e 127 (367) ++.--+||.++|+. ++..+. ++.|+++.|.|||.++-..++-.+.. .+.++++++|...=+.+.. .+ T Consensus 21 I~~l~p~Q~e~l~~---g~~~g~--------NllvsaPT~sGKTlvAElail~~~l~-~~~k~iyi~P~kALa~EK~-~~ 87 (717) T PRK00254 21 IEELYPPQAEALTS---GVLEGK--------NLLIAIPTASGKTLIAEIAMVNKLLR-EGGKAVYLVPLKALAEEKF-RE 87 (717) T ss_pred CCCCCHHHHHHHHH---HHCCCC--------CEEEECCCCCCHHHHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHH-HH T ss_conf 87268999999874---233698--------18998998874899999999999985-2992999926799999999-99 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCC------CCCCCEEEEECCC Q ss_conf 9999986231211233332100012333221111345776126621013544556521011------3586289997545 Q gi|254781187|r 128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPH------NTHGMAVFNDEAS 201 (367) Q Consensus 128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h------~~~~~l~ivDEAs 201 (367) +++|-..-. + ............-... ..-++.+. +|.+..+- -.+.-++|+||+. T Consensus 88 f~~~~~~g~-~-----------V~~~tGd~~~~~~~l~-~~dIiV~T------~Ek~dsl~r~~~~~l~~i~lvViDEiH 148 (717) T PRK00254 88 FKDWEVLGL-R-----------VAMATGDYDSKDEWLG-KYDIIIAT------AEKFDSLLRHGSSWIKDVKLLVADEIH 148 (717) T ss_pred HHHHHHCCC-E-----------EEEEECCCCCCCCCCC-CCCEEEEC------HHHHHHHHHCCHHHHHCCCEEEEECEE T ss_conf 987774498-8-----------9897489888701046-89999988------899999997162565326989997607 Q ss_pred CCCH----HHHHHHHHHHHCCCCCEE Q ss_conf 5998----899998987406988258 Q gi|254781187|r 202 GTPD----IINKSILGFFTELNPNRF 223 (367) Q Consensus 202 gI~d----~i~e~i~g~Lt~~~~~~~ 223 (367) .|.| .+||.+..-+.. ..+++ T Consensus 149 ~igD~~RG~~lE~~l~~l~~-~~qiI 173 (717) T PRK00254 149 LIGSRDRGATLEFILTHMLG-RAQII 173 (717) T ss_pred ECCCCCCHHHHHHHHHHHHC-CCEEE T ss_conf 88898740999999995100-36699 No 24 >KOG0354 consensus Probab=98.05 E-value=8.1e-05 Score=48.51 Aligned_cols=156 Identities=14% Similarity=0.096 Sum_probs=84.9 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537999999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) .+|.+|.++... |=+ -++.|+++.|.|||+++|..+.-++-.+|..||+.+||+.--+..-. +.++ T Consensus 62 ~lR~YQ~eivq~-ALg------------kNtii~lPTG~GKTfIAa~Vm~nh~rw~p~~KiVF~aP~~pLv~QQ~-a~~~ 127 (746) T KOG0354 62 ELRNYQEELVQP-ALG------------KNTIIALPTGSGKTFIAAVIMKNHFEWRPKGKVVFLAPTRPLVNQQI-ACFS 127 (746) T ss_pred CCCHHHHHHHHH-HHC------------CCEEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHH-HHHH T ss_conf 560789998678-626------------87699953599861047999999972377643899607711788889-8876 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCC---CCCEEEEECCCCC-CH Q ss_conf 9998623121123333210001233322111134577612662101354455652101135---8628999754559-98 Q gi|254781187|r 130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNT---HGMAVFNDEASGT-PD 205 (367) Q Consensus 130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~---~~~l~ivDEAsgI-~d 205 (367) ..... +-....-+..-+. ....++-......+.+.+.-. ..++..... .+.|+|+|||..- .+ T Consensus 128 ~~~~~----~~~T~~l~~~~~~-----~~r~~i~~s~~vff~TpQil~----ndL~~~~~~~ls~fs~iv~DE~Hra~kn 194 (746) T KOG0354 128 IYLIP----YSVTGQLGDTVPR-----SNRGEIVASKRVFFRTPQILE----NDLKSGLHDELSDFSLIVFDECHRTSKN 194 (746) T ss_pred HCCCC----CCCEEECCCCCCC-----CCHHHHHCCCCEEEECHHHHH----HHCCCCCCCCCCEEEEEEECCCCCCCCC T ss_conf 20676----0104550575688-----762453102635896727634----3325433454551799997222445556 Q ss_pred HHH-HHHHHHH--HCCCCCEEEEEEECCCCC Q ss_conf 899-9989874--069882589998078999 Q gi|254781187|r 206 IIN-KSILGFF--TELNPNRFWIMTSNTRRL 233 (367) Q Consensus 206 ~i~-e~i~g~L--t~~~~~~~~i~igNP~r~ 233 (367) ..| .++.--+ ...+.+++ .++.+|-.. T Consensus 195 ~~Y~~Vmr~~l~~k~~~~qIL-gLTASpG~~ 224 (746) T KOG0354 195 HPYNNIMREYLDLKNQGNQIL-GLTASPGSK 224 (746) T ss_pred CCHHHHHHHHHHHHHCCCCEE-EEECCCCCC T ss_conf 617999999998651466179-985588845 No 25 >smart00488 DEXDc2 DEAD-like helicases superfamily. Probab=98.03 E-value=4.9e-05 Score=49.84 Aligned_cols=80 Identities=24% Similarity=0.431 Sum_probs=57.9 Q ss_pred HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHH-HHHHHHHHHHHC---CCC Q ss_conf 5430146688844366684289999999888875124555554112477614886788999-999999999708---997 Q gi|254781187|r 33 MRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTL-NAWMMLWLISTR---PGM 108 (367) Q Consensus 33 ~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~-~a~~~lw~~~~~---~~~ 108 (367) .|.||. .|++.|.++++.|.+.++++. .+.+-||.|+|||.. .+..+-|..... ... T Consensus 2 ~~~FPy-----------~py~~Q~e~m~~v~~~l~~~~--------~~llEaPTGtGKTlalL~~al~~~~~~~~~~~~~ 62 (289) T smart00488 2 LFYFPY-----------EPYPIQYEFMEELKRVLDRGK--------IGILESPTGTGKTLSLLCLTLTWLRSFPERIQKI 62 (289) T ss_pred EECCCC-----------CCCHHHHHHHHHHHHHHHCCC--------EEEEECCCCHHHHHHHHHHHHHHHHHCHHCCCCC T ss_conf 327899-----------999899999999999997499--------7999899965189999999999999670102456 Q ss_pred EEEEECCCHHHHHHHHHHHHHHHH Q ss_conf 799971537999999999999999 Q gi|254781187|r 109 SIICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 109 ~v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) ++++...|.+|....+ .|+++.. T Consensus 63 ki~~~t~t~~~~~~~~-~elr~~~ 85 (289) T smart00488 63 KLIYLSRTVSEIEKRL-EELRKLM 85 (289) T ss_pred EEEEEECCHHHHHHHH-HHHHHHC T ss_conf 1687615378899999-9998632 No 26 >smart00489 DEXDc3 DEAD-like helicases superfamily. Probab=98.03 E-value=4.9e-05 Score=49.84 Aligned_cols=80 Identities=24% Similarity=0.431 Sum_probs=57.9 Q ss_pred HHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHH-HHHHHHHHHHHC---CCC Q ss_conf 5430146688844366684289999999888875124555554112477614886788999-999999999708---997 Q gi|254781187|r 33 MRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTL-NAWMMLWLISTR---PGM 108 (367) Q Consensus 33 ~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~-~a~~~lw~~~~~---~~~ 108 (367) .|.||. .|++.|.++++.|.+.++++. .+.+-||.|+|||.. .+..+-|..... ... T Consensus 2 ~~~FPy-----------~py~~Q~e~m~~v~~~l~~~~--------~~llEaPTGtGKTlalL~~al~~~~~~~~~~~~~ 62 (289) T smart00489 2 LFYFPY-----------EPYPIQYEFMEELKRVLDRGK--------IGILESPTGTGKTLSLLCLTLTWLRSFPERIQKI 62 (289) T ss_pred EECCCC-----------CCCHHHHHHHHHHHHHHHCCC--------EEEEECCCCHHHHHHHHHHHHHHHHHCHHCCCCC T ss_conf 327899-----------999899999999999997499--------7999899965189999999999999670102456 Q ss_pred EEEEECCCHHHHHHHHHHHHHHHH Q ss_conf 799971537999999999999999 Q gi|254781187|r 109 SIICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 109 ~v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) ++++...|.+|....+ .|+++.. T Consensus 63 ki~~~t~t~~~~~~~~-~elr~~~ 85 (289) T smart00489 63 KLIYLSRTVSEIEKRL-EELRKLM 85 (289) T ss_pred EEEEEECCHHHHHHHH-HHHHHHC T ss_conf 1687615378899999-9998632 No 27 >pfam00270 DEAD DEAD/DEAH box helicase. 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. Probab=98.03 E-value=9.5e-05 Score=48.11 Aligned_cols=69 Identities=20% Similarity=0.149 Sum_probs=48.6 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHHHH Q ss_conf 2899999998888751245555541124776148867889999999999997089-977999715379999999999999 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) ++.|.+++..+..+. .+.|.++.|+|||......++-.+.... +.++++++|+..-+.+.. ..+++ T Consensus 1 ~~~Q~~~i~~~~~g~------------~~iv~~pTGsGKT~~~~~~~l~~~~~~~~~~~~v~l~Pt~aL~~q~~-~~~~~ 67 (167) T pfam00270 1 TPIQAEAIPAILEGK------------DVLVQAPTGSGKTLAFLLPALQALLKNPDGPQALVLAPTRELAEQIY-EELKK 67 (167) T ss_pred CHHHHHHHHHHHCCC------------CEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHH-HHHHH T ss_conf 945999999997699------------78998899975899999999999874778987999906088888999-88643 Q ss_pred HHH Q ss_conf 998 Q gi|254781187|r 131 WLS 133 (367) Q Consensus 131 ~~~ 133 (367) ... T Consensus 68 ~~~ 70 (167) T pfam00270 68 LGK 70 (167) T ss_pred HHH T ss_conf 210 No 28 >PRK10590 ATP-dependent RNA helicase RhlE; Provisional Probab=97.98 E-value=0.00016 Score=46.67 Aligned_cols=138 Identities=16% Similarity=0.053 Sum_probs=77.8 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-------CCEEEEECCCH Q ss_conf 43666842899999998888751245555541124776148867889999999999997089-------97799971537 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-------GMSIICIANSE 117 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-------~~~v~~~A~t~ 117 (367) -.+|..|++-|.+.+-.+-+.. -+.+.|..|+|||.....=++-.+.... +.+++|++||. T Consensus 18 ~~G~~~PTpIQ~~aIP~iL~Gr------------Dvl~~A~TGSGKTlAflLPil~~l~~~~~~~~~~~~~~aLIL~PTR 85 (457) T PRK10590 18 EQGYREPTPIQQQAIPAVLEGR------------DLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALILTPTR 85 (457) T ss_pred HCCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCHH T ss_conf 7799999999999999997799------------8899889811899999999999986367654456882499976879 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEE Q ss_conf 99999999999999986231211233332100012333221111345776126621013544556521011358628999 Q gi|254781187|r 118 TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFN 197 (367) Q Consensus 118 ~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~iv 197 (367) .-+.++ ..+++++...+..+. ..+. ..............+.-++.+.+-+...-..-..+.-.+.-++|+ T Consensus 86 ELA~Qi-~~~~~~l~~~~~~~~------~~~~---Gg~~~~~q~~~l~~~~dIlVaTPGRLldl~~~~~~~l~~v~~lVl 155 (457) T PRK10590 86 ELAAQI-GENVRDYSKYLNIRS------LVVF---GGVSINPQMMKLRGGVDVLVATPGRLLDLEHQNAVKLDQVEILVL 155 (457) T ss_pred HHHHHH-HHHHHHHCCCCCCEE------EEEE---CCCCHHHHHHHHCCCCCEEEECCHHHHHHHHCCCCCCCCCEEEEE T ss_conf 999999-999997425589459------9997---997775999986189998998928889888626776575239998 Q ss_pred ECCCCCC Q ss_conf 7545599 Q gi|254781187|r 198 DEASGTP 204 (367) Q Consensus 198 DEAsgI~ 204 (367) |||--+= T Consensus 156 DEAD~mL 162 (457) T PRK10590 156 DEADRML 162 (457) T ss_pred ECCHHHH T ss_conf 3705651 No 29 >KOG2036 consensus Probab=97.90 E-value=0.00037 Score=44.46 Aligned_cols=145 Identities=14% Similarity=0.054 Sum_probs=77.6 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH Q ss_conf 28999999988887512455555411247761488678899999999999970899779997153799999999999999 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW 131 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~ 131 (367) +.-|.+++-...+.+..... ..-+++.||||-|||+.....+. .+..+-...|.+|+|+-..+++. |--+-|= T Consensus 255 T~dQakav~~f~dai~eK~l-----r~~vsLtA~RGRGKSAALGlsiA-~AVa~GysnIyvtSPspeNlkTl-FeFv~kG 327 (1011) T KOG2036 255 TLDQAKAVLTFFDAIVEKTL-----RSTVSLTASRGRGKSAALGLSIA-GAVAFGYSNIYVTSPSPENLKTL-FEFVFKG 327 (1011) T ss_pred HHHHHHHHHHHHHHHHHHHH-----CCEEEEEECCCCCCHHHHHHHHH-HHHHCCCCEEEECCCCHHHHHHH-HHHHHCC T ss_conf 17789999999999987540-----56278985477870055647899-99863750378748983888999-9999803 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHH Q ss_conf 98623121123333210001233322111134577612662101354455652101135862899975455998899998 Q gi|254781187|r 132 LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSI 211 (367) Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i 211 (367) ...+-.+....++...-....+.....+..+..+-+ ++..--+|..-+-+. ...|+++|||+.||=.+--.+ T Consensus 328 fDaL~Yqeh~Dy~iI~s~np~fkkaivRInifr~hr------QtIQYi~P~D~~kl~--q~eLlVIDEAAAIPLplvk~L 399 (1011) T KOG2036 328 FDALEYQEHVDYDIIQSTNPDFKKAIVRINIFREHR------QTIQYISPHDHQKLG--QAELLVIDEAAAIPLPLVKKL 399 (1011) T ss_pred HHHHCCHHHCCHHHHHHCCHHHHHHEEEEEEECCCC------CEEEEECCCHHHHCC--CCCEEEECHHHCCCHHHHHHH T ss_conf 123131443251146542823140279998742640------136755630054406--774898600202777899985 No 30 >PRK11192 ATP-dependent RNA helicase SrmB; Provisional Probab=97.89 E-value=0.00049 Score=43.74 Aligned_cols=75 Identities=15% Similarity=0.079 Sum_probs=53.7 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH----CC-CCEEEEECCCHHHH Q ss_conf 36668428999999988887512455555411247761488678899999999999970----89-97799971537999 Q gi|254781187|r 46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST----RP-GMSIICIANSETQL 120 (367) Q Consensus 46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~----~~-~~~v~~~A~t~~Q~ 120 (367) .+|..|++-|.+.+-.+-++. -+.+.|..|+|||.....=++-.+.- .+ ..++++++||..=+ T Consensus 21 ~g~~~pT~IQ~~aIp~il~g~------------dvl~~A~TGSGKTlaylLPil~~l~~~~~~~~~~~~~LIl~PTrELa 88 (417) T PRK11192 21 KGYTRPTAIQAEAIPPALDGR------------DVLGSAPTGTGKTAAFLLPALQHLLDFPRRKSGPPRILILTPTRELA 88 (417) T ss_pred CCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECHHHHH T ss_conf 799999999999999997799------------88998999867999999999999875210368996499994719999 Q ss_pred HHHHHHHHHHHHH Q ss_conf 9999999999998 Q gi|254781187|r 121 KNTLWAEVSKWLS 133 (367) Q Consensus 121 ~~~lw~ei~k~~~ 133 (367) .++ ..+++++.. T Consensus 89 ~Qi-~~~~~~l~~ 100 (417) T PRK11192 89 MQV-ADQARELAK 100 (417) T ss_pred HHH-HHHHHHHHC T ss_conf 999-999998640 No 31 >PRK04837 ATP-dependent RNA helicase RhlB; Provisional Probab=97.86 E-value=0.00017 Score=46.51 Aligned_cols=76 Identities=14% Similarity=0.031 Sum_probs=54.4 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC--------CEEEEECCC Q ss_conf 436668428999999988887512455555411247761488678899999999999970899--------779997153 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG--------MSIICIANS 116 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~--------~~v~~~A~t 116 (367) -.+|..|++-|...+-.+-++. -+.+.|..|+|||.....-++-.++..+. .+++|++|| T Consensus 26 ~~g~~~pTpIQ~~aIP~il~G~------------Dvi~~A~TGSGKTlAfllPil~~ll~~~~~~~~~~~~p~aLIL~PT 93 (423) T PRK04837 26 KKGFEYCTPIQALALPLTLAGR------------DVAGQAQTGTGKTMAFLTATFHHLLSHPAPEGRKVNQPRALIMAPT 93 (423) T ss_pred HCCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECC T ss_conf 7799999999999999996799------------8899899987499999999999998374533455678618999388 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 79999999999999998 Q gi|254781187|r 117 ETQLKNTLWAEVSKWLS 133 (367) Q Consensus 117 ~~Q~~~~lw~ei~k~~~ 133 (367) ..=+.++ ..+++.+.. T Consensus 94 RELa~Qi-~~~~~~l~~ 109 (423) T PRK04837 94 RELAVQI-HADAEPLAQ 109 (423) T ss_pred HHHHHHH-HHHHHHHHC T ss_conf 9999999-999999743 No 32 >PRK11634 ATP-dependent RNA helicase DeaD; Provisional Probab=97.81 E-value=0.00045 Score=43.94 Aligned_cols=76 Identities=14% Similarity=0.100 Sum_probs=55.5 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHH Q ss_conf 4366684289999999888875124555554112477614886788999999999999708-997799971537999999 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTR-PGMSIICIANSETQLKNT 123 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~-~~~~v~~~A~t~~Q~~~~ 123 (367) -.+|..|++-|.+.+-.+-+. . -+.+.|-.|+|||...+.-++-.+... ....++|++||..-+.++ T Consensus 23 ~~Gf~~PTpIQ~~aIP~iL~G----k--------Dvi~~AqTGSGKTlAFlLPiL~~l~~~~~~pqaLIL~PTRELA~QV 90 (629) T PRK11634 23 DLGYEKPSPIQAECIPHLLNG----R--------DVLGMAQTGSGKTAAFSLPLLHNLDPELKAPQILVLAPTRELAVQV 90 (629) T ss_pred HCCCCCCCHHHHHHHHHHHCC----C--------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHHHH T ss_conf 879999999999999999679----9--------8899788847899999999999866236898689978998999999 Q ss_pred HHHHHHHHHH Q ss_conf 9999999998 Q gi|254781187|r 124 LWAEVSKWLS 133 (367) Q Consensus 124 lw~ei~k~~~ 133 (367) ..+++++.. T Consensus 91 -~~~~~~l~~ 99 (629) T PRK11634 91 -AEAMTDFSK 99 (629) T ss_pred -HHHHHHHHH T ss_conf -999999972 No 33 >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=97.76 E-value=0.00041 Score=44.21 Aligned_cols=74 Identities=18% Similarity=0.088 Sum_probs=53.7 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC---CCEEEEECCCHHHHHH Q ss_conf 3666842899999998888751245555541124776148867889999999999997089---9779997153799999 Q gi|254781187|r 46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP---GMSIICIANSETQLKN 122 (367) Q Consensus 46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~---~~~v~~~A~t~~Q~~~ 122 (367) .+|..|++-|.+.+..+-++ . .+.+.|..|+|||.....-++-.+...+ +.++++++||..-+.+ T Consensus 17 ~g~~~pt~IQ~~~ip~il~g----~--------dvi~~a~TGSGKTlay~lpil~~l~~~~~~~~~~alil~PTrELa~Q 84 (203) T cd00268 17 LGFEKPTPIQARAIPPLLSG----R--------DVIGQAQTGSGKTAAFLIPILEKLDPSPKKDGPQALILAPTRELALQ 84 (203) T ss_pred CCCCCCCHHHHHHHHHHHCC----C--------CEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHH T ss_conf 79999999999999999779----9--------88997579972228888699999861667689669999687999999 Q ss_pred HHHHHHHHHH Q ss_conf 9999999999 Q gi|254781187|r 123 TLWAEVSKWL 132 (367) Q Consensus 123 ~lw~ei~k~~ 132 (367) + ..++++.. T Consensus 85 i-~~~~~~l~ 93 (203) T cd00268 85 I-AEVARKLG 93 (203) T ss_pred H-HHHHHHHC T ss_conf 9-99999850 No 34 >PRK04537 ATP-dependent RNA helicase RhlB; Provisional Probab=97.73 E-value=0.0008 Score=42.42 Aligned_cols=79 Identities=16% Similarity=0.063 Sum_probs=57.9 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC--------CCEEEEECC Q ss_conf 443666842899999998888751245555541124776148867889999999999997089--------977999715 Q gi|254781187|r 44 PLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP--------GMSIICIAN 115 (367) Q Consensus 44 ~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~--------~~~v~~~A~ 115 (367) .-.+|..|++-|.+.+-.+-+. . .+.+.|..|+|||.....-++-.+...+ +.+++|++| T Consensus 25 ~~~Gf~~PTpIQ~~aIP~iL~G----k--------Dvi~~A~TGSGKTLAYlLPiL~~Ll~~~~l~~~~~~~p~aLILvP 92 (574) T PRK04537 25 ESAGFTRCTPIQALTLPVALPG----G--------DVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRALILAP 92 (574) T ss_pred HHCCCCCCCHHHHHHHHHHHCC----C--------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEECC T ss_conf 9779998999999999999579----9--------889984898889999999999999837443457789961999779 Q ss_pred CHHHHHHHHHHHHHHHHHHC Q ss_conf 37999999999999999862 Q gi|254781187|r 116 SETQLKNTLWAEVSKWLSML 135 (367) Q Consensus 116 t~~Q~~~~lw~ei~k~~~~~ 135 (367) |..-+.++ ..++.++...+ T Consensus 93 TRELA~QI-~~~~~~l~~~~ 111 (574) T PRK04537 93 TRELAIQI-HKDAVKFGADL 111 (574) T ss_pred CHHHHHHH-HHHHHHHHCCC T ss_conf 89999999-99999986458 No 35 >PTZ00110 helicase; Provisional Probab=97.72 E-value=0.00074 Score=42.63 Aligned_cols=159 Identities=12% Similarity=-0.022 Sum_probs=84.1 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC------CCEEEEECCCHH Q ss_conf 43666842899999998888751245555541124776148867889999999999997089------977999715379 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP------GMSIICIANSET 118 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~------~~~v~~~A~t~~ 118 (367) -.+|+.|++-|.+.+=.+-. . + -+...|-.|+|||.....=++-.+...+ +..++|+|||.. T Consensus 199 ~~GF~~PTPIQ~qaIPiaLs---G---r------DvIgiAqTGSGKTLAFlLP~l~hi~~q~~~~~~~gP~aLILaPTRE 266 (602) T PTZ00110 199 AAGFTEPTPIQVQGWPIALS---G---R------DMIGIAETGSGKTLAFLLPAIVHINAQPLLRPGDGPIVLVLAPTRE 266 (602) T ss_pred HCCCCCCCHHHHHHHHHHHC---C---C------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHH T ss_conf 76999999899999879856---9---8------6799878978899999999999985163436789976999738399 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEE Q ss_conf 99999999999999862312112333321000123332211113457761266210135445565210113586289997 Q gi|254781187|r 119 QLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFND 198 (367) Q Consensus 119 Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivD 198 (367) =+.++ ..++.++......+ ...++ ..............+.-++.|.+-|...--.-..+.-..+.++|+| T Consensus 267 LA~QI-~~e~~~~~~~~~ir------~~~i~---GG~~~~~Q~~~L~~G~dIvVATPGRLiDlL~~~~~~L~~v~yLVLD 336 (602) T PTZ00110 267 LAEQI-REQALQFGRSSKLK------NSVAY---GGVPKRFQTYALRRGVEILIACPGRLIDFLESNVTNLRRVTYLVLD 336 (602) T ss_pred HHHHH-HHHHHHHHCCCCCE------EEEEE---CCCCHHHHHHHHCCCCCEEEECCHHHHHHHHCCCCCCCCEEEEEEE T ss_conf 99999-99999971547854------99997---9968799999871699999979238999996499874310289987 Q ss_pred CCCCCCH-----HHHHHHHHHHHCCCCCEEEEEE Q ss_conf 5455998-----8999989874069882589998 Q gi|254781187|r 199 EASGTPD-----IINKSILGFFTELNPNRFWIMT 227 (367) Q Consensus 199 EAsgI~d-----~i~e~i~g~Lt~~~~~~~~i~i 227 (367) ||--.=| .+-..+ ..+ ..+..++++.. T Consensus 337 EADRMLDmGFe~qI~~Il-~~i-~pdRQTlLFSA 368 (602) T PTZ00110 337 EADRMLDMGFEPQIRKIV-SQI-RPDRQTLMWSA 368 (602) T ss_pred CHHHHHCCCCHHHHHHHH-HHC-CCCCEEEEEEC T ss_conf 577663546299999999-858-97877999955 No 36 >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=97.71 E-value=0.00027 Score=45.31 Aligned_cols=53 Identities=17% Similarity=0.236 Sum_probs=41.5 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHH Q ss_conf 477614886788999999999999708997799971537999999999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) .+.|.++-|+|||..+...++-.+....+.++++++|+..-+.+. ..++.+.. T Consensus 2 ~~lv~~ptGsGKT~~~~~~~~~~~~~~~~~~~lil~Pt~~L~~q~-~~~~~~~~ 54 (144) T cd00046 2 DVLLAAPTGSGKTLAALLPILELLDSLKGGQVLVLAPTRELANQV-AERLKELF 54 (144) T ss_pred CEEEECCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHH-HHHHHHHC T ss_conf 999988997179999999999999756897699974679999999-99999974 No 37 >PRK01297 ATP-dependent RNA helicase RhlB; Provisional Probab=97.70 E-value=0.00052 Score=43.58 Aligned_cols=77 Identities=13% Similarity=0.013 Sum_probs=56.0 Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC--------CCEEEEEC Q ss_conf 8443666842899999998888751245555541124776148867889999999999997089--------97799971 Q gi|254781187|r 43 KPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP--------GMSIICIA 114 (367) Q Consensus 43 ~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~--------~~~v~~~A 114 (367) +.-.+|..|++-|.+.+-.+-.+ . -+.+.|..|+|||.....=++-.+...+ ..+++|++ T Consensus 99 L~~~Gf~~PTpIQ~~aIP~iL~G----k--------Dvi~~A~TGSGKTlAyLLPil~~ll~~~~~~~~~~~~p~aLIL~ 166 (472) T PRK01297 99 IHDLGFPYCTPIQAQVLGYTLAG----H--------DAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPRALIIA 166 (472) T ss_pred HHHCCCCCCCHHHHHHHHHHHCC----C--------CEEEECCCCCHHHHHHHHHHHHHHHHCCCCHHCCCCCCEEEEEC T ss_conf 99779999999999999999769----9--------88998999867999999999999971775101136895299987 Q ss_pred CCHHHHHHHHHHHHHHHH Q ss_conf 537999999999999999 Q gi|254781187|r 115 NSETQLKNTLWAEVSKWL 132 (367) Q Consensus 115 ~t~~Q~~~~lw~ei~k~~ 132 (367) ||..=+.++. ..++... T Consensus 167 PTRELa~QI~-~~~~~L~ 183 (472) T PRK01297 167 PTRELVVQIA-KDAAALT 183 (472) T ss_pred CCHHHHHHHH-HHHHHHH T ss_conf 9999999999-9999974 No 38 >COG1204 Superfamily II helicase [General function prediction only] Probab=97.68 E-value=0.0023 Score=39.66 Aligned_cols=158 Identities=16% Similarity=0.060 Sum_probs=85.3 Q ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 99998888751245555541124776148867889999999999997089977999715379999999999999998623 Q gi|254781187|r 57 EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLP 136 (367) Q Consensus 57 ~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~ 136 (367) +++-.++.+...+... . -++.|+++.|+|||.++-..++=.+.-+ +.++++++|+..=+.++. .++++|-..-+ T Consensus 31 el~~~qq~av~~~~~~-~---~N~li~aPTgsGKTlIA~lai~~~l~~~-~~k~vYivPlkALa~Ek~-~~~~~~~~~Gi 104 (766) T COG1204 31 ELFNPQQEAVEKGLLS-D---ENVLISAPTGSGKTLIALLAILSTLLEG-GGKVVYIVPLKALAEEKY-EEFSRLEELGI 104 (766) T ss_pred HHHHHHHHHHHCCCCC-C---CCEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEECHHHHHHHHH-HHHHHHHHCCC T ss_conf 7557899874111257-9---8679976788866999999999999855-983899907599999999-98666886597 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCC------CCCCCEEEEECCCCCCHH---- Q ss_conf 1211233332100012333221111345776126621013544556521011------358628999754559988---- Q gi|254781187|r 137 HRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPH------NTHGMAVFNDEASGTPDI---- 206 (367) Q Consensus 137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h------~~~~~l~ivDEAsgI~d~---- 206 (367) +...........+-...... ++.+ .||.+..+- .....|+|+||+.-+.|. T Consensus 105 ------------rV~~~TgD~~~~~~~l~~~~-ViVt------T~EK~Dsl~R~~~~~~~~V~lvViDEiH~l~d~~RG~ 165 (766) T COG1204 105 ------------RVGISTGDYDLDDERLARYD-VIVT------TPEKLDSLTRKRPSWIEEVDLVVIDEIHLLGDRTRGP 165 (766) T ss_pred ------------EEEEECCCCCCCHHHHCCCC-EEEE------CHHHHHHHHHCCCCHHHCCCEEEEEEEEECCCCCCCC T ss_conf ------------79996488655533414588-7997------4678667650675333401689994210148756586 Q ss_pred HHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHH Q ss_conf 999989874069882589998078999876887 Q gi|254781187|r 207 INKSILGFFTELNPNRFWIMTSNTRRLNGWFYD 239 (367) Q Consensus 207 i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye 239 (367) +.|++..-+...+...-.+..|-+-.+.+-+.+ T Consensus 166 ~lE~iv~r~~~~~~~~rivgLSATlpN~~evA~ 198 (766) T COG1204 166 VLESIVARMRRLNELIRIVGLSATLPNAEEVAD 198 (766) T ss_pred EEHHHHHHHHHHCCCEEEEEEEEECCCHHHHHH T ss_conf 402279888852755179887311688899999 No 39 >PRK11776 ATP-dependent RNA helicase DbpA; Provisional Probab=97.65 E-value=0.00097 Score=41.90 Aligned_cols=78 Identities=12% Similarity=0.101 Sum_probs=56.7 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHHHH Q ss_conf 4366684289999999888875124555554112477614886788999999999999708-997799971537999999 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTR-PGMSIICIANSETQLKNT 123 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~-~~~~v~~~A~t~~Q~~~~ 123 (367) -.+|..|++-|.+.+-.+-++. -+.+.|..|+|||.....-++-.+-.. ....+++++||..=+.++ T Consensus 21 ~~G~~~pTpIQ~~aIP~il~G~------------Dvi~~A~TGSGKTlAfllPil~~l~~~~~~~qaLIL~PTRELa~QV 88 (459) T PRK11776 21 ELGYTEMTPIQAQSLPAILAGK------------DVIAQAKTGSGKTAAFGLGLLQKLDVKRFRVQALVLCPTRELADQV 88 (459) T ss_pred HCCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEECHHHHHHHH T ss_conf 7799999989999999997799------------8899889985899999999998411367898599996759999999 Q ss_pred HHHHHHHHHHHC Q ss_conf 999999999862 Q gi|254781187|r 124 LWAEVSKWLSML 135 (367) Q Consensus 124 lw~ei~k~~~~~ 135 (367) ..+++++.+.+ T Consensus 89 -~~~~~~l~~~~ 99 (459) T PRK11776 89 -AKEIRRLARFI 99 (459) T ss_pred -HHHHHHHHHHC T ss_conf -99999998505 No 40 >PRK06305 DNA polymerase III subunits gamma and tau; Validated Probab=97.59 E-value=0.0029 Score=38.98 Aligned_cols=138 Identities=17% Similarity=0.100 Sum_probs=71.9 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE-EEECCCHHHHHHHHHHHHHHHH Q ss_conf 999999988887512455555411247761488678899999999999970899779-9971537999999999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSI-ICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v-~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) .|..+.+.+...+..+.. .+. ..-.+.||+|||+++-.++-...|.++.... -|-.- .. +.+|.. T Consensus 21 GQ~~vv~~L~nai~~~ri-~HA----yLF~GprGtGKTT~ArilAkaLnC~~~~~~~~pCg~C------~~-C~~I~~-- 86 (462) T PRK06305 21 GQDAVVTVLKNALRFNRA-AHA----YLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQC------AI-CKEISS-- 86 (462) T ss_pred CCHHHHHHHHHHHHCCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCC------HH-HHHHHC-- T ss_conf 909999999999984997-623----4303899859999999999996799998888988766------88-899863-- Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH Q ss_conf 86231211233332100012333221111345776126621013544556521011358628999754559988999989 Q gi|254781187|r 133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL 212 (367) Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~ 212 (367) -.....++..+ ...+| .-..+-..+ .-.+....+.+. .+|+||+...+...|.+++ T Consensus 87 --g~~~DViEiDa-----------------As~~g--VddIRel~e--~v~~~P~~~~yK-VyIIDEvhmLs~~AfNALL 142 (462) T PRK06305 87 --GTSLDVIEIDG-----------------ASHRG--IEDIRQINE--TVLFTPSKSQYK-IYIIDEVHMLTKEAFNSLL 142 (462) T ss_pred --CCCCCEEEECC-----------------CCCCC--HHHHHHHHH--HHCCCCCCCCEE-EEEEECHHHCCHHHHHHHH T ss_conf --89998686435-----------------53446--689999997--710088677505-9998152117999999999 Q ss_pred HHHHCCCCCEEEEEEEC Q ss_conf 87406988258999807 Q gi|254781187|r 213 GFFTELNPNRFWIMTSN 229 (367) Q Consensus 213 g~Lt~~~~~~~~i~igN 229 (367) .+|-.+-...+.+++.| T Consensus 143 KtLEEPP~~v~FILaTT 159 (462) T PRK06305 143 KTLEEPPQHVKFFLATT 159 (462) T ss_pred HHHHCCCCCEEEEEEEC T ss_conf 98618987749999818 No 41 >PRK13709 conjugal transfer nickase/helicase TraI; Provisional Probab=97.55 E-value=0.0016 Score=40.53 Aligned_cols=159 Identities=16% Similarity=0.184 Sum_probs=89.7 Q ss_pred CCHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCC Q ss_conf 33789999752320125988885543014668884436668428999999988887512455555411247761488678 Q gi|254781187|r 10 KLEQELHEMLMHAECVLSFKNFVMRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIG 89 (367) Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~f~~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~G 89 (367) ++|+.+...+-..+--.-| |+.-+ |-....+-+..|.+..+-|.+. +.+| ++|.+-=|+| T Consensus 938 etEK~IL~~i~~GK~tv~P--L~~~v--------~~s~l~~LT~GQK~At~LIltT---------~DRF-vaIQGyAGVG 997 (1756) T PRK13709 938 EAEKSILRHILEGKEAVTP--LMERV--------PGELMEKLTSGQRAATRMILET---------SDRF-TVVQGYAGVG 997 (1756) T ss_pred HHHHHHHHHHHCCCCCCCC--CHHHC--------CHHHHCCCCHHHHHHHHHHHCC---------CCCE-EEEEECCCCC T ss_conf 9999999999747665686--02327--------5566635785778777563247---------8725-9987035566 Q ss_pred HHHHHHHHHHHHHHHCCC---CEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 899999999999970899---77999715379999999999999998623121123333210001233322111134577 Q gi|254781187|r 90 KTTLNAWMMLWLISTRPG---MSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDS 166 (367) Q Consensus 90 KS~~~a~~~lw~~~~~~~---~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (367) ||+..-..+- .+-+-|. .+|+=.|||.+.++++==.-| ..+.+.-++. +. T Consensus 998 KTTql~avi~-ai~tl~~~~rpqViGLAPTH~AV~EL~~~GV-------------~AQTlaSfL~-------------d~ 1050 (1756) T PRK13709 998 KTTQFRAVMS-AVNMLPESERPRVVGLGPTHRAVGEMRSAGV-------------DAQTLASFLH-------------DT 1050 (1756) T ss_pred HHHHHHHHHH-HHHHCCCCCCCCEEEECCHHHHHHHHHHCCC-------------CHHHHHHHHH-------------HH T ss_conf 6778999999-9972551358726756751789999996496-------------0789999986-------------20 Q ss_pred CCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC Q ss_conf 612662101354455652101135862899975455998899998987406988258999807 Q gi|254781187|r 167 KHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSN 229 (367) Q Consensus 167 ~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igN 229 (367) . ......+.|+ + ...|+++||+|.|.+.=+..+...+..+++|. ++.|- T Consensus 1051 ~-----~~~~~ge~~d-y------~nTLFllDESSMVgN~dma~~~~lV~asggRA--V~~GD 1099 (1756) T PRK13709 1051 Q-----LQQRSGETPD-F------SNTLFLLDESSMVGNTDMARAYALIAAGGGRA--VASGD 1099 (1756) T ss_pred H-----HHHHCCCCCC-C------CCEEEEEEHHHCCCHHHHHHHHHHHHHCCCCE--EEECC T ss_conf 2-----3441489876-5------54289983043147088999999997059837--97277 No 42 >COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms] Probab=97.46 E-value=0.0052 Score=37.46 Aligned_cols=171 Identities=13% Similarity=0.049 Sum_probs=87.4 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708--9977999715379999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTR--PGMSIICIANSETQLKNTLWAE 127 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~--~~~~v~~~A~t~~Q~~~~lw~e 127 (367) ++.+||.++++.+-....+.. -+.+.++.|.|||.+++.+++..+.-. -..+++.+-|+..-+. .+... T Consensus 195 ~~~~~~~~~~~~~~~~~~~~~--------~~vl~aPTG~GKT~asl~~a~~~~~~~~~~~~r~i~vlP~~t~ie-~~~~r 265 (733) T COG1203 195 EGYELQEKALELILRLEKRSL--------LVVLEAPTGYGKTEASLILALALLDEKIKLKSRVIYVLPFRTIIE-DMYRR 265 (733) T ss_pred CHHHHHHHHHHHHHHCCCCCC--------EEEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHH-HHHHH T ss_conf 113556799999873225575--------189991688871999999999975311354562899655899999-99999 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCEEE---EECCCCCCCCCCCCCCC-----CCCCCEEEE Q ss_conf 99999862312112333321000123332--211113457761266---21013544556521011-----358628999 Q gi|254781187|r 128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAE--LLEQSMGIDSKHYTI---TCRTYSEERPDTFVGPH-----NTHGMAVFN 197 (367) Q Consensus 128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~---~a~~~~~~~~ea~~g~h-----~~~~~l~iv 197 (367) ++.+....-.................... ............... ...+.+-.+ ....+.+ .-...++|+ T Consensus 266 ~~~~~~~~~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~S~vIl 344 (733) T COG1203 266 AKEIFGLFSVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILI-FSVKGFKFEFLALLLTSLVIL 344 (733) T ss_pred HHHHHCCCCCCCCCCCCCCHHHHHHCCCCCCCEEEEECCCCCCCCCCCEEECHHHHHH-HHHCCCCCHHHHHHHHCCEEE T ss_conf 9875123554331001310255651701002258881242236204522206999855-740466725778876467787 Q ss_pred ECCCCCCHH-HHHHHHHHH---HCCCCCEEEEEEECCC Q ss_conf 754559988-999989874---0698825899980789 Q gi|254781187|r 198 DEASGTPDI-INKSILGFF---TELNPNRFWIMTSNTR 231 (367) Q Consensus 198 DEAsgI~d~-i~e~i~g~L---t~~~~~~~~i~igNP~ 231 (367) ||+...++. .+.++.+++ ...|.+++ ++..|.| T Consensus 345 DE~h~~~~~~~~~~l~~~i~~l~~~g~~il-l~SATlP 381 (733) T COG1203 345 DEVHLYADETMLAALLALLEALAEAGVPVL-LMSATLP 381 (733) T ss_pred ECHHHCCCCCHHHHHHHHHHHHHHCCCCEE-EEECCCC T ss_conf 427541654308999999999996899789-9927899 No 43 >COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms] Probab=97.43 E-value=0.0021 Score=39.85 Aligned_cols=74 Identities=15% Similarity=0.167 Sum_probs=55.2 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH Q ss_conf 44366684289999999888875124555554112477614886788999999999999708997799971537999999 Q gi|254781187|r 44 PLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT 123 (367) Q Consensus 44 ~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~ 123 (367) +-....+||.+|..+.+.+.++..++..+ -+.|. ..|+|||..+-.++--++-+.--++|+-.|-.-.++.+. T Consensus 159 ~~~s~i~~RyyQ~~AI~rv~Eaf~~g~~r------aLlvM-ATGTGKTrTAiaii~rL~r~~~~KRVLFLaDR~~Lv~QA 231 (875) T COG4096 159 DIDSAIGPRYYQIIAIRRVIEAFSKGQNR------ALLVM-ATGTGKTRTAIAIIDRLIKSGWVKRVLFLADRNALVDQA 231 (875) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCCCE------EEEEE-ECCCCCCEEHHHHHHHHHHCCHHHEEEEEECHHHHHHHH T ss_conf 63223362278899999999998668744------89997-058885231999999999614143056761267899999 Q ss_pred H Q ss_conf 9 Q gi|254781187|r 124 L 124 (367) Q Consensus 124 l 124 (367) . T Consensus 232 ~ 232 (875) T COG4096 232 Y 232 (875) T ss_pred H T ss_conf 9 No 44 >COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis] Probab=97.39 E-value=0.0032 Score=38.77 Aligned_cols=159 Identities=14% Similarity=-0.023 Sum_probs=87.3 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHH--HCCCCE-EEEECCCHHHHHH Q ss_conf 3666842899999998888751245555541124776148867889999999999997--089977-9997153799999 Q gi|254781187|r 46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIS--TRPGMS-IICIANSETQLKN 122 (367) Q Consensus 46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~--~~~~~~-v~~~A~t~~Q~~~ 122 (367) .+|..|++-|...+-.+-.. .-+.+.|-.|+|||.....=++-.+. ...... .++++||..=+.+ T Consensus 47 ~gf~~pt~IQ~~~iP~~l~g------------~Dvi~~A~TGsGKT~Af~lP~l~~i~~~~~~~~~~aLil~PTRELA~Q 114 (513) T COG0513 47 LGFEEPTPIQLAAIPLILAG------------RDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVSALILAPTRELAVQ 114 (513) T ss_pred CCCCCCCHHHHHHCHHHHCC------------CCEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCHHHHHH T ss_conf 59899898999658776369------------997998689871789999999999740045577756997799999999 Q ss_pred HHHHHHHHHHHHCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC Q ss_conf 99999999998623-12112333321000123332211113457761266210135445565210113586289997545 Q gi|254781187|r 123 TLWAEVSKWLSMLP-HRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS 201 (367) Q Consensus 123 ~lw~ei~k~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs 201 (367) + ..++.++....+ .+ ...+. .......+. .....+.-++.+.+-+...--....++..+.-.+|+|||. T Consensus 115 i-~~~~~~~~~~~~~~~------~~~i~--GG~~~~~q~-~~l~~g~~ivVaTPGRllD~i~~~~l~l~~v~~lVlDEAD 184 (513) T COG0513 115 I-AEELRKLGKNLGGLR------VAVVY--GGVSIRKQI-EALKRGVDIVVATPGRLLDLIKRGKLDLSGVETLVLDEAD 184 (513) T ss_pred H-HHHHHHHHHHCCCCE------EEEEE--CCCCHHHHH-HHHHCCCCEEEECCCHHHHHHHCCCCCCCCEEEEEECCHH T ss_conf 9-999999986245842------99998--998989999-9872499899979608999986488554650189967617 Q ss_pred CCCH-HHHHHHHHHHH--CCCCCEEEEE Q ss_conf 5998-89999898740--6988258999 Q gi|254781187|r 202 GTPD-IINKSILGFFT--ELNPNRFWIM 226 (367) Q Consensus 202 gI~d-~i~e~i~g~Lt--~~~~~~~~i~ 226 (367) -+=| .+.+.++..+. ..+..++++. T Consensus 185 rmld~gf~~~i~~I~~~~p~~~qtllfS 212 (513) T COG0513 185 RMLDMGFIDDIEKILKALPPDRQTLLFS 212 (513) T ss_pred HHCCCCCHHHHHHHHHHCCCCCEEEEEE T ss_conf 6638876899999997389774899998 No 45 >PRK09112 DNA polymerase III subunit delta'; Validated Probab=97.30 E-value=0.0096 Score=35.79 Aligned_cols=159 Identities=14% Similarity=0.186 Sum_probs=78.2 Q ss_pred CCCCCCCHH-----HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE--EEECCCH Q ss_conf 436668428-----999999988887512455555411247761488678899999999999970899779--9971537 Q gi|254781187|r 45 LEHFSQPHR-----WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSI--ICIANSE 117 (367) Q Consensus 45 ~~~~~~p~~-----wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v--~~~A~t~ 117 (367) +++..+|+. .|.++.+.+..-.+.+...+ -....+.+|+||++++=.++-+.++...+... -+..|-. T Consensus 13 ~~g~p~Pr~~~~liGq~~~~~~L~~a~~~gRl~H-----A~Lf~GP~GiGKaTlA~~~A~~Ll~~~~~~~~~~~~~~pd~ 87 (352) T PRK09112 13 IDGVPSPSENNRLFGHEEARAFLAQAYREGRLHH-----ALLFEGPEGIGKATLAFHLANHILSHPDPNEAPETLADPDP 87 (352) T ss_pred CCCCCCCCCHHHHCCHHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCC T ss_conf 8999896446462786999999999998499652-----46535899808999999999998669986668655678887 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEE Q ss_conf 999999999999999862312112333321000123332--211113457761266210135445565210113586289 Q gi|254781187|r 118 TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAE--LLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAV 195 (367) Q Consensus 118 ~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ 195 (367) + ...++.+.. ...|+ .+.+. +++... ..+..+..+. .+.... --+.....+.+ -.+ T Consensus 88 ~---~~~~r~i~~--g~hpd--l~~i~------r~~d~k~~~~~~~I~vd~------iR~l~~--~~~~~~~~~~~-kv~ 145 (352) T PRK09112 88 A---SPLWRQIAQ--GAHPN--LLHLT------RPFDEKTGKFKTAITVDE------IRRVTH--FLSQTSGDGNW-RIV 145 (352) T ss_pred C---CHHHHHHHC--CCCCC--EEEEE------CCCCHHHHHHHCCCCHHH------HHHHHH--HHCCCCCCCCE-EEE T ss_conf 8---778999974--89999--56553------432202145433577799------999999--84548866880-699 Q ss_pred EEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECC Q ss_conf 99754559988999989874069882589998078 Q gi|254781187|r 196 FNDEASGTPDIINKSILGFFTELNPNRFWIMTSNT 230 (367) Q Consensus 196 ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP 230 (367) |+|||.......+.++..+|-.+-.+.+.+++++- T Consensus 146 Iid~ad~m~~~aaNALLK~LEEPp~~~~fiLit~~ 180 (352) T PRK09112 146 IIDPADDMNRNAANAILKTLEEPPARALFILISHS 180 (352) T ss_pred EECCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECC T ss_conf 98187874699999999985348987489988699 No 46 >PRK04914 ATP-dependent helicase HepA; Validated Probab=97.30 E-value=0.013 Score=34.97 Aligned_cols=176 Identities=13% Similarity=0.134 Sum_probs=90.4 Q ss_pred CCCCCCCCCCCCH----HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 6888443666842----899999998888751245555541124776148867889999999999997089977999715 Q gi|254781187|r 40 IKGKPLEHFSQPH----RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 40 ~~~~~~~~~~~p~----~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) ....|+.++-||+ +-|.-+.+++... +. +|+.++=-=|.|||.-+..++--.+....-.+|+|+.| T Consensus 137 ~~~~~~~gl~g~r~~l~pHQ~~ia~~v~~r-------~~---PRvLLADEVGLGKTIEAGLIl~ell~rgra~RvLIvvP 206 (955) T PRK04914 137 QFQSPLRGLRGARAGLIPHQLYIAHEVGRR-------HA---PRVLLADEVGLGKTIEAGLIIHQQLLTGRAERVLIIVP 206 (955) T ss_pred HHCCCCCCCCCCCCCCCCHHHHHHHHHHHC-------CC---CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEECC T ss_conf 726951132233246563799999999714-------58---84897058888689999999999997487777999927 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEE Q ss_conf 37999999999999999862312112333321000123332211113457761266210135445565210113586289 Q gi|254781187|r 116 SETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAV 195 (367) Q Consensus 116 t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ 195 (367) .. +..-.-.|+..-.+.. |..-............. .-+......+.+.-+-..++....-+......|+ T Consensus 207 ~~--L~~QW~~EL~~KF~L~-----f~i~D~~r~~~~~~~~~----NpF~~~~~vI~Sld~l~~~~~~~e~l~~a~WDLV 275 (955) T PRK04914 207 ET--LQHQWLVEMLRRFNLR-----FSLFDEERCAEAQADAD----NPFETEQLVICSLDFLRKNKKRLEQALDAEWDLL 275 (955) T ss_pred HH--HHHHHHHHHHHHCCCC-----CEEECCHHHHHHHCCCC----CCCCCCCEEEEEHHHHCCCHHHHHHHHCCCCCEE T ss_conf 79--9899999999983998-----09955188887533579----9754589799878996039678998733898889 Q ss_pred EEECCCCC------CHHHHHHHHHHHHCCCCCEEEEEEECCCC--CCCHHH Q ss_conf 99754559------98899998987406988258999807899--987688 Q gi|254781187|r 196 FNDEASGT------PDIINKSILGFFTELNPNRFWIMTSNTRR--LNGWFY 238 (367) Q Consensus 196 ivDEAsgI------~d~i~e~i~g~Lt~~~~~~~~i~igNP~r--~~g~Fy 238 (367) |||||..+ +..-+..++. |+... +.+.+++.||-. ..+.|. T Consensus 276 IVDEAHhL~~~~~~~s~~y~lve~-La~~~-~~lLLLTATP~QlG~e~~Fa 324 (955) T PRK04914 276 VVDEAHHLVWSEEAPSREYQVVEQ-LAEVI-PGVLLLTATPEQLGQESHFA 324 (955) T ss_pred EEHHHHHHCCCCCCCCHHHHHHHH-HHHHC-CCEEEEECCCCCCCCHHHHH T ss_conf 971344530588788879999999-98515-97699847998898666898 No 47 >PRK05896 DNA polymerase III subunits gamma and tau; Validated Probab=97.28 E-value=0.011 Score=35.43 Aligned_cols=138 Identities=14% Similarity=0.093 Sum_probs=71.2 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|..+.+.+..-++++... |. ....++||+||++++-.++-...|..+...-.|-.-. ..+ .+.. . T Consensus 20 GQe~iv~~L~nAI~~~Ria-HA----YLFsGPrGvGKTTlArifAkaLnC~~~~~~dpCg~C~--sC~-----~I~~--g 85 (613) T PRK05896 20 GQELIKKILVNAILNNKLT-HA----YIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCS--VCE-----SINT--N 85 (613) T ss_pred CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCH--HHH-----HHHC--C T ss_conf 8299999999999849976-22----7755899848899999999996699999999888887--899-----9856--9 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..|.- .+.. .....| .-..+..... -++....|.+. .+|+|||.......|.+++- T Consensus 86 ~h~Dv--iEId-----------------aasn~g--IDeIReLie~--~~~~P~~gkyK-V~IIDEah~Ln~~AaNALLK 141 (613) T PRK05896 86 QSVDI--VELD-----------------AASNNG--VDEIRNIIDN--INYLPTTFKYK-VYIIDEAHMLSTSAWNALLK 141 (613) T ss_pred CCCCE--EEEE-----------------CCCCCC--HHHHHHHHHH--HCCCCCCCCCE-EEEECCHHHCCHHHHHHHHH T ss_conf 99986--8840-----------------655578--8999999997--08587579945-99981622179999999998 Q ss_pred HHHCCCCCEEEEEEEC Q ss_conf 7406988258999807 Q gi|254781187|r 214 FFTELNPNRFWIMTSN 229 (367) Q Consensus 214 ~Lt~~~~~~~~i~igN 229 (367) +|-.+-...+.+++++ T Consensus 142 tLEEPP~~viFIL~Tt 157 (613) T PRK05896 142 TLEEPPKHVVFIFATT 157 (613) T ss_pred HCCCCCCCCEEEEEEC T ss_conf 5348987837999828 No 48 >PRK05563 DNA polymerase III subunits gamma and tau; Validated Probab=97.28 E-value=0.0089 Score=35.99 Aligned_cols=136 Identities=14% Similarity=0.107 Sum_probs=67.4 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|..+.+.+...+..+... |. ..-++.||+|||+++-+++--.-|.++..---|- + ...+ .++.. T Consensus 20 gQ~~v~~~L~n~i~~~~i~-ha----yLf~GprG~GKTs~Ari~akalnc~~~~~~~pC~-----~-C~~C-~~i~~--- 84 (541) T PRK05563 20 GQEHITTTLKNQIINNRIA-HA----YLFCGTRGTGKTSTAKIFAKAVNCLNPQDGEPCN-----E-CEIC-KKINE--- 84 (541) T ss_pred CCHHHHHHHHHHHHCCCCC-EE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCC-----C-CHHH-HHHHC--- T ss_conf 8499999999999849932-04----5303879958999999999995799988898575-----1-4889-99856--- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) .. ...+.+ +........-..+-.++.. .+.-..+.+ -.+|+||+...+...|.+++- T Consensus 85 ----g~--------------~~Dv~E--idaas~~gvd~iR~~~~~~--~~~p~~~~~-Kv~IiDEvhmls~~a~nallK 141 (541) T PRK05563 85 ----GL--------------LMDVIE--IDAASNNGVDDIREIIENV--KYPPQEGKY-KVYIMDEVHMLSQGAVNAFLK 141 (541) T ss_pred ----CC--------------CCCEEE--ECCCCCCCHHHHHHHHHHC--EECCCCCCE-EEEEEECCCCCCHHHHHHHHH T ss_conf ----89--------------887366--2444447889999999761--048767870-599997723389999999999 Q ss_pred HHHCCCCCEEEEEE Q ss_conf 74069882589998 Q gi|254781187|r 214 FFTELNPNRFWIMT 227 (367) Q Consensus 214 ~Lt~~~~~~~~i~i 227 (367) +|-.+-.....++. T Consensus 142 tlEePp~~~~Fila 155 (541) T PRK05563 142 TLEEPPSNVIFILA 155 (541) T ss_pred HHHCCCCCCEEEEE T ss_conf 98548777569997 No 49 >pfam00176 SNF2_N SNF2 family N-terminal domain. 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). Probab=97.26 E-value=0.0051 Score=37.46 Aligned_cols=137 Identities=16% Similarity=0.167 Sum_probs=68.3 Q ss_pred EEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 761488678899999999999970899-7799971537999999999999999862312112333321000123332211 Q gi|254781187|r 81 AISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLE 159 (367) Q Consensus 81 ~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (367) ..+=-=|.|||.-+-.++.......+. .+++|++|.. +....-.|+++|...............+. .... T Consensus 20 iLaDeMGLGKTiq~ia~l~~~~~~~~~~~~~LIV~P~s--l~~~W~~Ei~~~~~~~~~~~~~~~~~~r~-------~~~~ 90 (295) T pfam00176 20 ILADEMGLGKTLQTISLLAYLKELKPLAGPHLVVCPLS--TLDNWLNEFEKWAPDLNIVVYYGDGDSRS-------ELLR 90 (295) T ss_pred EEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEECHH--HHHHHHHHHHHHCCCCCEEEEEECHHHHH-------HHHH T ss_conf 97227875799999999999998388999889997578--88767889998679970799984707689-------9988 Q ss_pred CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHH---HHHHHHHHHCCCCCEEEEEEECCCCC Q ss_conf 113457761266210135445565210113586289997545599889---99989874069882589998078999 Q gi|254781187|r 160 QSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDII---NKSILGFFTELNPNRFWIMTSNTRRL 233 (367) Q Consensus 160 ~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i---~e~i~g~Lt~~~~~~~~i~igNP~r~ 233 (367) .......-...+.....-.... .-++......+|+|||..|.+.- +.++. .| ..+..|+++|||-.+ T Consensus 91 ~~~~~~~~~ivitsY~~~~~~~---~~l~~~~w~~vI~DEaH~iKN~~s~~~~a~~-~l---~~~~r~~LTGTPiqN 160 (295) T pfam00176 91 NVLRTGKFDVLITSYEYIRRDK---DELHKANWRYVILDEGHRIKNAKSKLSLALK-SL---KTNNRLLLTGTPIQN 160 (295) T ss_pred HHHHCCCCCEEEECHHHHHHHH---HHHHCCCCCEEEEECCCCCCCHHHHHHHHHH-HC---CCCCEEEEECCCCCC T ss_conf 6774168859993099999759---9984087658998762012587889999999-52---358189986874558 No 50 >PRK08058 DNA polymerase III subunit delta'; Validated Probab=97.25 E-value=0.013 Score=35.06 Aligned_cols=123 Identities=14% Similarity=0.160 Sum_probs=75.9 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC-------------------EE Q ss_conf 84289999999888875124555554112477614886788999999999999708997-------------------79 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGM-------------------SI 110 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~-------------------~v 110 (367) ....-|..+.+.+..-+++|... | .....+.+|+||+.++-.++-+.+|..+.. .+ T Consensus 6 ~~~~~Q~~i~~~L~~~i~~~rl~-H----A~Lf~Gp~G~GK~~~A~~~A~~LlC~~~~~~~~Cg~C~~C~~~~~~~HPD~ 80 (329) T PRK08058 6 QLTALQPIVVKMLQNSIAKNRLA-H----AYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIESGNHPDV 80 (329) T ss_pred HHHHHHHHHHHHHHHHHHCCCCC-C----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCCCE T ss_conf 88831899999999999859966-1----565578999889999999999973999999998878889999876999976 Q ss_pred EEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCC Q ss_conf 99715379999999999999998623121123333210001233322111134577612662101354455652101135 Q gi|254781187|r 111 ICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNT 190 (367) Q Consensus 111 ~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~ 190 (367) ..+.|...+.+- ..|+...+.+ +.....|. T Consensus 81 ~~i~p~~~~i~i---dqiR~L~~~~-----------------------------------------------~~~p~~g~ 110 (329) T PRK08058 81 HLVAPDGQSIKK---DQIRYLKEEF-----------------------------------------------SKSGVESN 110 (329) T ss_pred EEECCCCCCCCH---HHHHHHHHHH-----------------------------------------------CCCCCCCC T ss_conf 774566140779---9999999996-----------------------------------------------43875788 Q ss_pred CCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEE Q ss_conf 86289997545599889999898740698825899980 Q gi|254781187|r 191 HGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTS 228 (367) Q Consensus 191 ~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~ig 228 (367) +. .+|+|||.........++..+|-.+-..+++++++ T Consensus 111 ~K-V~II~~Ae~m~~~AaNALLKtLEEPp~~t~fIL~t 147 (329) T PRK08058 111 KK-VYIIEHADKMTASAANSLLKFLEEPSGDTTAILLT 147 (329) T ss_pred CE-EEEEECHHHHCHHHHHHHHHHHHCCCCCCEEEEEE T ss_conf 67-99973477629999999999864689786799872 No 51 >COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair] Probab=97.25 E-value=0.015 Score=34.67 Aligned_cols=159 Identities=13% Similarity=0.064 Sum_probs=87.1 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH Q ss_conf 66684289999999888875124555554112477614886788999999999999708997799971537999999999 Q gi|254781187|r 47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWA 126 (367) Q Consensus 47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ 126 (367) +.-.+++||.+.+..|.... .|-|+|..|.|||.+ |-+++..++.+ +.++++|+|...-..+. ++ T Consensus 116 ~~F~LD~fQ~~a~~~Ler~e------------sVlV~ApTssGKTvV-aeyAi~~al~~-~qrviYTsPIKALsNQK-yr 180 (1041) T COG4581 116 YPFELDPFQQEAIAILERGE------------SVLVCAPTSSGKTVV-AEYAIALALRD-GQRVIYTSPIKALSNQK-YR 180 (1041) T ss_pred CCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCCCCHH-HHHHHHHHHHC-CCCEEECCCHHHHHHHH-HH T ss_conf 89896789999999984799------------579973378985559-99999999871-89448616306642067-99 Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECC-----CCCCCCCCCCCCCCCCCCEEEEECCC Q ss_conf 9999998623121123333210001233322111134577612662101-----35445565210113586289997545 Q gi|254781187|r 127 EVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRT-----YSEERPDTFVGPHNTHGMAVFNDEAS 201 (367) Q Consensus 127 ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~-----~~~~~~ea~~g~h~~~~~l~ivDEAs 201 (367) ++..-.... ...|-..| .+....+...+..-.| +--...+..+ ....+|+||.. T Consensus 181 dl~~~fgdv-~~~vGL~T---------------GDv~IN~~A~clvMTTEILRnMlyrg~~~~~-----~i~~ViFDEvH 239 (1041) T COG4581 181 DLLAKFGDV-ADMVGLMT---------------GDVSINPDAPCLVMTTEILRNMLYRGSESLR-----DIEWVVFDEVH 239 (1041) T ss_pred HHHHHHHHH-HHHCCCEE---------------CCEEECCCCCEEEEEHHHHHHHHCCCCCCCC-----CCCEEEEEEEE T ss_conf 999986005-65404010---------------5434279996688609999998625861013-----53068887666 Q ss_pred CCCH----HHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCC Q ss_conf 5998----899998987406988258999807899987688754112 Q gi|254781187|r 202 GTPD----IINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIP 244 (367) Q Consensus 202 gI~d----~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~ 244 (367) .|.| .+||-..-.+-.. -+ ++++|-+..+.-.|.+....- T Consensus 240 yi~D~eRG~VWEE~Ii~lP~~-v~--~v~LSATv~N~~EF~~Wi~~~ 283 (1041) T COG4581 240 YIGDRERGVVWEEVIILLPDH-VR--FVFLSATVPNAEEFAEWIQRV 283 (1041) T ss_pred ECCCCCCCHHHHHHHHHCCCC-CC--EEEEECCCCCHHHHHHHHHHC T ss_conf 504632212578999866777-76--899967889879999999740 No 52 >PRK06647 DNA polymerase III subunits gamma and tau; Validated Probab=97.25 E-value=0.012 Score=35.19 Aligned_cols=137 Identities=18% Similarity=0.112 Sum_probs=71.0 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCHHHHHHHHHHHHHHHH Q ss_conf 9999999888875124555554112477614886788999999999999708997799971-537999999999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA-NSETQLKNTLWAEVSKWL 132 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A-~t~~Q~~~~lw~ei~k~~ 132 (367) .|..+.+.+...++.+... |. ..-++.||+|||+++-+++-...|..++.---|-. ++- .++.. T Consensus 20 GQe~vv~~L~nai~~~rl~-HA----yLFsGprG~GKTt~ArilAk~LnC~~~~~~~PCg~C~sC--------~~i~~-- 84 (560) T PRK06647 20 GQDFVVETLKHSIEKNKIA-NA----YIFSGPRGVGKTSSARAFARCLNCVNGPTIMPCGECFSC--------KSIDN-- 84 (560) T ss_pred CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHH--------HHHHC-- T ss_conf 9499999999999749977-43----663289987899999999999659999998888788788--------88745-- Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH Q ss_conf 86231211233332100012333221111345776126621013544556521011358628999754559988999989 Q gi|254781187|r 133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL 212 (367) Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~ 212 (367) ...++ .++..+ .........+-... .-.+....+.+ -.+|+|||...+...|.+++ T Consensus 85 g~~~D--viEida-------------------asn~~VddIR~l~e--~v~~~P~~~~y-KV~IIDEahmLt~~A~NALL 140 (560) T PRK06647 85 DSSLD--VIEIDG-------------------ASNTSVQDVRQIKE--EIMFPPASSRY-RVYIIDEVHMLSNSAFNALL 140 (560) T ss_pred CCCCC--EEEECC-------------------CCCCCHHHHHHHHH--HHCCCCCCCCE-EEEEECCHHHCCHHHHHHHH T ss_conf 99987--576436-------------------45488899999999--86328766870-69996465655999999999 Q ss_pred HHHHCCCCCEEEEEEEC Q ss_conf 87406988258999807 Q gi|254781187|r 213 GFFTELNPNRFWIMTSN 229 (367) Q Consensus 213 g~Lt~~~~~~~~i~igN 229 (367) -+|-.+-...+.+++.| T Consensus 141 KtLEEPP~~~~FILaTt 157 (560) T PRK06647 141 KTIEEPPPYIVFIFATT 157 (560) T ss_pred HHHHCCCCCEEEEEECC T ss_conf 98634887559999779 No 53 >PRK06674 DNA polymerase III subunits gamma and tau; Validated Probab=97.24 E-value=0.013 Score=34.92 Aligned_cols=138 Identities=12% Similarity=0.086 Sum_probs=71.4 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|..+.+.+..-+..+.. .|. ..-.+.||+|||.++-.++-...|.+++..--|- . ...+ ..+.. . T Consensus 20 GQ~~v~~~L~nai~~~ri-~HA----yLF~GprGtGKts~Ari~AkaLnC~~~~~~~pC~--~----C~~C-~~i~~--g 85 (563) T PRK06674 20 GQEHVTKTLQNALLQEKV-SHA----YLFSGPRGTGKTSIAKVFAKAVNCEHAPVAEPCN--E----CPSC-LGITN--G 85 (563) T ss_pred CHHHHHHHHHHHHHCCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCC--C----CHHH-HHHHC--C T ss_conf 809999999999984996-503----4312899868999999999985799999988776--6----8789-99855--8 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..+. ..+. +....+| ....+-.+.. -.+....+.+ -.+|+||+...+...|.+++. T Consensus 86 ~~~D--viEi-----------------Daasn~g--Vd~IR~i~~~--v~~~P~~~~y-KV~IIDeah~Lt~~A~NALLK 141 (563) T PRK06674 86 SISD--VLEI-----------------DAASNNG--VDEIRDIRDK--VKFAPSAVEY-KVYIIDEVHMLSIGAFNALLK 141 (563) T ss_pred CCCC--EEEE-----------------CCCCCCC--HHHHHHHHHH--HCCCCCCCCE-EEEEEECHHHCCHHHHHHHHH T ss_conf 9987--7985-----------------2555578--7999999998--2648867873-799985456379999999999 Q ss_pred HHHCCCCCEEEEEEEC Q ss_conf 7406988258999807 Q gi|254781187|r 214 FFTELNPNRFWIMTSN 229 (367) Q Consensus 214 ~Lt~~~~~~~~i~igN 229 (367) +|-.+-...+.+++.| T Consensus 142 tLEEPP~~viFILaTt 157 (563) T PRK06674 142 TLEEPPGHVIFILATT 157 (563) T ss_pred HHHCCCCCEEEEEECC T ss_conf 8638875649999659 No 54 >PRK08769 DNA polymerase III subunit delta'; Validated Probab=97.21 E-value=0.0062 Score=36.97 Aligned_cols=147 Identities=13% Similarity=0.162 Sum_probs=77.4 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH Q ss_conf 42899999998888751245555541124776148867889999999999997089977999715379999999999999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) -.+||.+..+.+...+++|...+ ...+.+..|+||+.++-.++-+.+|..++....+-. ... +. T Consensus 5 ~~PWq~~~~~~L~~~i~~~rl~H-----A~Lf~Gp~G~GK~~~A~~~A~~llc~~~~~~~~~~~------~~~----i~- 68 (319) T PRK08769 5 FSPWQQRAFDQTVAALDAGRLGH-----GLLICGPEGLGKRAVALALAEHVLASGPDPALAQRT------RQL----IA- 68 (319) T ss_pred CCCCCHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCHH------HHH----HH- T ss_conf 58776899999999997699420-----687589998789999999999983799797654338------899----96- Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHH Q ss_conf 99862312112333321000123332211113457761266210135445565210113586289997545599889999 Q gi|254781187|r 131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKS 210 (367) Q Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~ 210 (367) ....|+-+..... +... ....+.+++.+.-.-.+.. -+.....|.+ -.+|+|||.........+ T Consensus 69 -~g~HPD~~~i~~~-----~~~~-~~k~k~~I~IdqiR~l~~~--------~~~~p~~g~~-KV~IId~Ad~mn~~AaNa 132 (319) T PRK08769 69 -AGTHPDLQLVSFI-----PNRT-GDKLRTEIVIEQVREISQK--------LALTPQYGIA-QVVIVDPADAINRSACNA 132 (319) T ss_pred -CCCCCCEEEEECC-----CCCC-CCCCCCCCCHHHHHHHHHH--------HHHCCCCCCC-EEEEECCHHHCCHHHHHH T ss_conf -6899896877534-----4445-4311234869999999999--------6137202795-699980667528999999 Q ss_pred HHHHHHCCCCCEEEEEEEC Q ss_conf 8987406988258999807 Q gi|254781187|r 211 ILGFFTELNPNRFWIMTSN 229 (367) Q Consensus 211 i~g~Lt~~~~~~~~i~igN 229 (367) +..+|-.+....+++++++ T Consensus 133 lLK~LEEPp~~~~~iL~~~ 151 (319) T PRK08769 133 LLKTLEEPSPGRYLWLISA 151 (319) T ss_pred HHHHHCCCCCCEEEEEEEC T ss_conf 9998227998848999869 No 55 >PRK08451 DNA polymerase III subunits gamma and tau; Validated Probab=97.19 E-value=0.016 Score=34.37 Aligned_cols=136 Identities=15% Similarity=0.082 Sum_probs=69.5 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH Q ss_conf 99999988887512455555411247761488678899999999999970899779997153799999999999999986 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM 134 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~ 134 (367) |..+.+.+..-++++... | -....++||+||++++-.++-...|..++..--|-. -. .+ ..+.. .. T Consensus 19 Qe~iv~~L~nAi~~~Rl~-H----AYLFsGPrGvGKTt~ArifAkaLnC~~~~~~~PCg~--C~----sC-~~i~~--g~ 84 (523) T PRK08451 19 QESVSKTLSLALDNNRLA-H----AYLFSGLRGSGKTSSARIFSRALVCEQGPSSTPCGT--CA----QC-QAALE--GR 84 (523) T ss_pred CHHHHHHHHHHHHCCCCC-C----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CH----HH-HHHHC--CC T ss_conf 499999999999859967-1----587578998688999999999975999999898887--88----89-99864--89 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHH Q ss_conf 23121123333210001233322111134577612662101354455652101135862899975455998899998987 Q gi|254781187|r 135 LPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGF 214 (367) Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~ 214 (367) .|+ ..+..+. .....-..+..... -.+....+.+. .+|+|||.......+.+++-+ T Consensus 85 hpD--ViEiDaa-------------------sn~gID~IReLie~--~~~~P~~gryK-V~IIDEah~Lt~~A~NALLKT 140 (523) T PRK08451 85 HID--IIEMDAA-------------------SNRGIDDIRNLIEQ--TKYKPSMARFK-IFIIDEVHMLTKEAFNALLKT 140 (523) T ss_pred CCC--EEEECCC-------------------CCCCHHHHHHHHHH--HCCCCCCCCEE-EEEEECCCCCCHHHHHHHHHH T ss_conf 998--5510553-------------------33689999999997--23588679727-999826030489999999997 Q ss_pred HHCCCCCEEEEEEE Q ss_conf 40698825899980 Q gi|254781187|r 215 FTELNPNRFWIMTS 228 (367) Q Consensus 215 Lt~~~~~~~~i~ig 228 (367) |-.+-...+.+++. T Consensus 141 LEEPP~~vvFILaT 154 (523) T PRK08451 141 LEEPPSYVKFILAT 154 (523) T ss_pred CCCCCCCCEEEEEC T ss_conf 03898783799975 No 56 >COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair] Probab=97.18 E-value=0.0083 Score=36.18 Aligned_cols=71 Identities=20% Similarity=0.129 Sum_probs=52.8 Q ss_pred HHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 3014668884436668428999999988887512455555411247761488678899999999999970899779997 Q gi|254781187|r 35 FFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 35 ~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) .+|.. +...+..|..+..-+.+++..+....+.-. ....+.+.++-|+|||++++++..-.+ ..+..|+++ T Consensus 69 ~~p~~-k~~~~~d~~~~~~~~~~~l~~~~~~~~~~~-----~~~nl~l~G~~G~GKthLa~Ai~~~l~--~~g~sv~f~ 139 (254) T COG1484 69 SFPAK-KTFEEFDFEFQPGIDKKALEDLASLVEFFE-----RGENLVLLGPPGVGKTHLAIAIGNELL--KAGISVLFI 139 (254) T ss_pred CCCCC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHC-----CCCCEEEECCCCCCHHHHHHHHHHHHH--HCCCEEEEE T ss_conf 68755-785430235885566999999999998732-----588289989999879999999999999--839849998 No 57 >PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional Probab=97.17 E-value=0.018 Score=34.11 Aligned_cols=72 Identities=17% Similarity=0.221 Sum_probs=52.4 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH---HHH Q ss_conf 44366684289999999888875124555554112477614886788999999999999708997799971537---999 Q gi|254781187|r 44 PLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE---TQL 120 (367) Q Consensus 44 ~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~---~Q~ 120 (367) |...-.+-|.+|.++.+++.+.+..+.. |..+.=..|+|||..+..++--++-+.--.+|+..+-.. +|+ T Consensus 410 ~~~~~i~lR~YQ~~AI~~v~~a~~~~~r-------raLl~MATGTGKTrtaial~~rLlk~~~~kRILFLvDR~~L~~QA 482 (1126) T PRK11448 410 PFDYELGLRYYQEDAIQAVEKALANGQR-------EILLAMATGTGKTRTAIALMYRLLKAKRFKRILFLVDRRALGEQA 482 (1126) T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHCCCC-------CEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHH T ss_conf 9877777868899999999999980985-------468872488858989999999999658767257985658999999 Q ss_pred HH Q ss_conf 99 Q gi|254781187|r 121 KN 122 (367) Q Consensus 121 ~~ 122 (367) .+ T Consensus 483 ~~ 484 (1126) T PRK11448 483 LD 484 (1126) T ss_pred HH T ss_conf 99 No 58 >PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Probab=97.14 E-value=0.0078 Score=36.38 Aligned_cols=72 Identities=21% Similarity=0.190 Sum_probs=49.9 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH---HHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537---999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE---TQLKNTLWA 126 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~---~Q~~~~lw~ 126 (367) .+|+-|.+|...|++.+..+. .+.|-||.|+|||..--.-++.++..+ +.+|++..+|. +|+-..-.+ T Consensus 258 e~R~~Q~~ma~~V~~al~~~~--------~l~iEApTGtGKTlaYLlPai~~A~~~-~~~vvIST~T~~LQ~QL~~kdlp 328 (932) T PRK08074 258 EKREGQQEMMKEVYTALRDSR--------HALIEAGTGTGKTLAYLLPAAYFAKKK-EEPVIISTYTVQLQQQLLEKDIP 328 (932) T ss_pred CCCHHHHHHHHHHHHHHHCCC--------CEEEECCCCCCCHHHHHHHHHHHHHHC-CCCEEEEECCHHHHHHHHHHHHH T ss_conf 758789999999999985388--------479986888871368799999999975-99099991628899999986899 Q ss_pred HHHH Q ss_conf 9999 Q gi|254781187|r 127 EVSK 130 (367) Q Consensus 127 ei~k 130 (367) .+++ T Consensus 329 ~L~~ 332 (932) T PRK08074 329 LLQK 332 (932) T ss_pred HHHH T ss_conf 9999 No 59 >TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB; InterPro: IPR014149 This entry represents TrbB, a protein, which is encoded 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 homologue of the vir system VirB11 ATPase , and the Flp pilus system ATPase TadA .. Probab=97.12 E-value=0.0018 Score=40.30 Aligned_cols=56 Identities=18% Similarity=0.261 Sum_probs=45.8 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHH-HCCCCEEEEECCCHH Q ss_conf 2899999998888751245555541124776148867889999999999997-089977999715379 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIS-TRPGMSIICIANSET 118 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~-~~~~~~v~~~A~t~~ 118 (367) +.-|.++|.+--. .+ .++.|.+|.|+|||+|+-+++--... +.|+-|++++.-|.. T Consensus 125 taaQ~d~l~~Av~-ar----------~NIlv~GGTGSGKTTLaNAlla~I~~l~~P~dR~vIiEDT~E 181 (315) T TIGR02782 125 TAAQRDVLREAVA-AR----------KNILVVGGTGSGKTTLANALLAEIAKLNDPDDRVVIIEDTAE 181 (315) T ss_pred CHHHHHHHHHHHH-HC----------CCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEECCHH T ss_conf 5789999999997-12----------988998145885799999999988521699961899854713 No 60 >PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional Probab=97.12 E-value=0.01 Score=35.69 Aligned_cols=68 Identities=13% Similarity=0.131 Sum_probs=44.3 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT 123 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~ 123 (367) .||+-|.+|..+|++.+...... -.+.|-||.|+|||..--.-++.++.. .+.+|+|..+|..--..+ T Consensus 25 e~R~~Q~~Ma~~V~~al~~~~~~-----~~l~iEAgTGtGKTlaYL~Pai~~a~~-~~~~vvIST~T~~LQeQL 92 (697) T PRK11747 25 IPRAGQRQMIAEVAKTLAGEYGR-----HILVIEAGTGVGKSLAYLLAGIPIARA-EKKKLVISTATVALQEQL 92 (697) T ss_pred CCCHHHHHHHHHHHHHHHCCCCC-----CEEEEECCCCCHHHHHHHHHHHHHHHH-CCCCEEEECCCHHHHHHH T ss_conf 71878999999999996166678-----669998999720899999999999998-299799988988999999 No 61 >PRK07133 DNA polymerase III subunits gamma and tau; Validated Probab=97.11 E-value=0.021 Score=33.77 Aligned_cols=129 Identities=16% Similarity=0.106 Sum_probs=70.5 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC----EEEEECCCHHHHHHHHHHHHH Q ss_conf 9999999888875124555554112477614886788999999999999708997----799971537999999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGM----SIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~----~v~~~A~t~~Q~~~~lw~ei~ 129 (367) .|..+.+.+..-++++... | ...-+++||+|||+++-.++-...|.++.. ...|.+... T Consensus 22 GQe~Vv~tL~nAI~~gRIa-H----AYLF~GPRGvGKTT~ARIfAKaLNC~~~~d~~~pC~~C~~~~~------------ 84 (718) T PRK07133 22 GQDHIIETLKNIIKSGKIS-H----AYLFSGPHGTGKTSVAKIFANALNCSHKTDLIEPCQNCIENFN------------ 84 (718) T ss_pred CCHHHHHHHHHHHHCCCCC-C----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHCCC------------ T ss_conf 8599999999999749975-0----5862389986889999999999679999999997702143047------------ Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHH Q ss_conf 99986231211233332100012333221111345776126621013544556521011358628999754559988999 Q gi|254781187|r 130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINK 209 (367) Q Consensus 130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e 209 (367) .+ ... .++........-..+...+. -.+....|.+. .+|+|||...+...|. T Consensus 85 --------~s---------------~DV--iEIDAASn~gVDdIReLie~--v~y~P~~gkYK-VyIIDEvHMLS~~AfN 136 (718) T PRK07133 85 --------NN---------------LDI--IEMDAASNNGVDEIRELREN--VKNLPQISKYK-IYIIDEVHMLSKSAFN 136 (718) T ss_pred --------CC---------------CCE--EEECCCCCCCHHHHHHHHHH--HCCCCCCCCEE-EEEEECCCCCCHHHHH T ss_conf --------89---------------873--77545566888999999998--25588778724-9999662007999999 Q ss_pred HHHHHHHCCCCCEEEEEE Q ss_conf 989874069882589998 Q gi|254781187|r 210 SILGFFTELNPNRFWIMT 227 (367) Q Consensus 210 ~i~g~Lt~~~~~~~~i~i 227 (367) +++-+|-.+-..++.++. T Consensus 137 ALLKtLEEPP~hvvFILa 154 (718) T PRK07133 137 ALLKTLEEPPKHVIFILA 154 (718) T ss_pred HHHHHHCCCCCCCEEEEE T ss_conf 999850279878279997 No 62 >PRK05707 DNA polymerase III subunit delta'; Validated Probab=97.10 E-value=0.012 Score=35.20 Aligned_cols=36 Identities=14% Similarity=0.168 Sum_probs=30.4 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC Q ss_conf 899975455998899998987406988258999807 Q gi|254781187|r 194 AVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSN 229 (367) Q Consensus 194 l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igN 229 (367) .+|+|+|.........++..+|-.+-..++++++++ T Consensus 109 V~iI~~Ae~m~~~AaNALLKtLEEPp~~t~fiL~t~ 144 (328) T PRK05707 109 VVLIEPAEAMNRNAANALLKSLEEPSGQTVLLLISH 144 (328) T ss_pred EEEEEHHHHHCHHHHHHHHHHHHCCCCCEEEEEEEC T ss_conf 999502877389999999998507898759998609 No 63 >PRK07270 DNA polymerase III subunits gamma and tau; Validated Probab=97.09 E-value=0.021 Score=33.68 Aligned_cols=138 Identities=14% Similarity=0.093 Sum_probs=69.5 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|..+.+.+..-++++... |. ..-.++||+|||.++-.++-...|.++...--|-. -..-+.+. . . T Consensus 19 GQe~i~~~L~nal~~~ri~-HA----yLF~GP~GtGKts~ArifAkaLnC~~~~~~~pC~~--C~~C~~i~-----~--g 84 (557) T PRK07270 19 GQEVVATTLKQAVESGKIS-HA----YLFSGPRGTGKTSAAKIFAKAMNCPNQVDGEPCNN--CDICRDIT-----N--G 84 (557) T ss_pred CHHHHHHHHHHHHHCCCCC-EE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC--CHHHHHHH-----C--C T ss_conf 8199999999999859954-04----42108998689999999999957999899998887--77999987-----5--8 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..++ .++..+. ...| .-..+-.+. --++....+.+ -.+|+|||...+...+.+++- T Consensus 85 ~~~D--viEidaa-----------------s~~g--Vd~IRei~~--~~~~~P~~~~y-KV~IIDEah~Ls~~A~NALLK 140 (557) T PRK07270 85 SLED--VIEIDAA-----------------SNNG--VDEIRDIRD--KSTYAPSRATY-KVYIIDEVHMLSTGAFNALLK 140 (557) T ss_pred CCCC--EEEECCC-----------------CCCC--HHHHHHHHH--HHCCCCCCCCE-EEEEECCHHHCCHHHHHHHHH T ss_conf 9997--4873477-----------------7678--899999999--84238777883-899971445349999998999 Q ss_pred HHHCCCCCEEEEEEEC Q ss_conf 7406988258999807 Q gi|254781187|r 214 FFTELNPNRFWIMTSN 229 (367) Q Consensus 214 ~Lt~~~~~~~~i~igN 229 (367) +|-.+-...+.+++.| T Consensus 141 tLEEPP~~~vFIL~Tt 156 (557) T PRK07270 141 TLEEPTENVVFILATT 156 (557) T ss_pred HHHCCCCCEEEEEEEC T ss_conf 8528998769999849 No 64 >KOG0390 consensus Probab=97.09 E-value=0.021 Score=33.72 Aligned_cols=173 Identities=20% Similarity=0.119 Sum_probs=94.1 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-----CEEEEECCCHHHHHHHHHH Q ss_conf 28999999988887512455555411247761488678899999999999970899-----7799971537999999999 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-----MSIICIANSETQLKNTLWA 126 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-----~~v~~~A~t~~Q~~~~lw~ 126 (367) ++-|.|.++=+.+.+-.......+ .-..++-.=|+|||.++-.++.-++..+|+ .+.+|++|+. +-...-+ T Consensus 240 rPHQ~EG~~FL~knl~g~~~~~~~--~GCImAd~~GlGKTlq~IsflwtlLrq~P~~~~~~~k~lVV~P~s--Lv~nWkk 315 (776) T KOG0390 240 RPHQREGFEFLYKNLAGLIRPKNS--GGCIMADEPGLGKTLQCISFIWTLLRQFPQAKPLINKPLVVAPSS--LVNNWKK 315 (776) T ss_pred CCHHHHHHHHHHHHHHCCCCCCCC--CCEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEECCHH--HHHHHHH T ss_conf 815787789978641131115888--754720788764078889999999986867554446607984588--8878999 Q ss_pred HHHHHHHH-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE---EEEECCCCCCCCCCCCCCCCCCCCEEEEECCCC Q ss_conf 99999986-23121123333210001233322111134577612---662101354455652101135862899975455 Q gi|254781187|r 127 EVSKWLSM-LPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHY---TITCRTYSEERPDTFVGPHNTHGMAVFNDEASG 202 (367) Q Consensus 127 ei~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg 202 (367) |+.||... .++...+.......|++ ..-...+.+..-+. .+..-+++ ...+-+......++|+||..- T Consensus 316 EF~KWl~~~~i~~l~~~~~~~~~w~~----~~sil~~~~~~~~~~vli~sye~~~----~~~~~il~~~~glLVcDEGHr 387 (776) T KOG0390 316 EFGKWLGNHRINPLDFYSTKKSSWIK----LKSILFLGYKQFTTPVLIISYETAS----DYCRKILLIRPGLLVCDEGHR 387 (776) T ss_pred HHHHHCCCCCCCEEEEECCCCHHHHH----HHHHHHHHHHHEEEEEEECCHHHHH----HHHHHHHCCCCCEEEECCCCC T ss_conf 99874253555404542345256666----6789886221125787863699999----999998547898699779888 Q ss_pred CCH---HHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHH Q ss_conf 998---8999989874069882589998078999876887541 Q gi|254781187|r 203 TPD---IINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFN 242 (367) Q Consensus 203 I~d---~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~ 242 (367) -.+ .+|.++- .-..+.-.++.|||-- |-|-|.|+ T Consensus 388 lkN~~s~~~kaL~----~l~t~rRVLLSGTp~Q--Ndl~EyFn 424 (776) T KOG0390 388 LKNSDSLTLKALS----SLKTPRRVLLTGTPIQ--NDLKEYFN 424 (776) T ss_pred CCCHHHHHHHHHH----HCCCCCEEEEECCCCC--CCHHHHHH T ss_conf 5622458999997----4687736996077533--46999978 No 65 >pfam07652 Flavi_DEAD Flavivirus DEAD domain. Probab=97.07 E-value=0.008 Score=36.29 Aligned_cols=131 Identities=18% Similarity=0.090 Sum_probs=74.7 Q ss_pred EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 76148867889999999999997089977999715379999999999999998623121123333210001233322111 Q gi|254781187|r 81 AISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQ 160 (367) Q Consensus 81 ~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (367) .+--.=|.|||.-.---++-. +.....++++.|||. ++-+|+.+.++..+.+.....-.. T Consensus 6 ~ld~HPGaGKTr~vLP~~v~~-~i~~~lRtlVLaPTR-----VV~~Em~eAL~g~~vr~~t~a~~~-------------- 65 (146) T pfam07652 6 VLDLHPGAGKTRKVLPELVRE-CIDRRLRTLVLAPTR-----VVLAEMEEALRGLPIRYHTPAVSS-------------- 65 (146) T ss_pred EEECCCCCCCCCHHHHHHHHH-HHHCCCEEEEECCHH-----HHHHHHHHHHCCCCCEEECHHHHC-------------- T ss_conf 985389999702248999999-997286189977279-----999999999758994675234313-------------- Q ss_pred CCCCCCCCEEEE-----ECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHH---HCCCCCEEEEEEECCCC Q ss_conf 134577612662-----1013544556521011358628999754559988999989874---06988258999807899 Q gi|254781187|r 161 SMGIDSKHYTIT-----CRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFF---TELNPNRFWIMTSNTRR 232 (367) Q Consensus 161 ~~~~~~~~~~~~-----a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~L---t~~~~~~~~i~igNP~r 232 (367) ...+...+. ..+-+. +.+.+.-+..++|+|||.+.+.....+ .|-+ ...+.-.+.+++.+|++ T Consensus 66 ---~~~~~~ivdvmCHAT~t~r~-----l~~~~~~ny~viIMDE~H~~DP~SIAa-rG~~~~~~~~g~~a~i~mTATPPG 136 (146) T pfam07652 66 ---EHTGREIVDVMCHATFTQRL-----LSPVRVPNYEVIIMDEAHFTDPASIAA-RGYISTLVELGEAAAIFMTATPPG 136 (146) T ss_pred ---CCCCCCEEEEECHHHHHHHH-----HCCCCCCCEEEEEEECCCCCCHHHHHH-HHHHHHHHHCCCEEEEEEECCCCC T ss_conf ---66888418897159888897-----368885644799985122389899998-899998854386579999568999 Q ss_pred CCCHHHHH Q ss_conf 98768875 Q gi|254781187|r 233 LNGWFYDI 240 (367) Q Consensus 233 ~~g~Fye~ 240 (367) .++.|-++ T Consensus 137 ~~~~fp~S 144 (146) T pfam07652 137 TSDPFPES 144 (146) T ss_pred CCCCCCCC T ss_conf 89989888 No 66 >PRK00440 rfc replication factor C small subunit; Reviewed Probab=97.07 E-value=0.022 Score=33.55 Aligned_cols=119 Identities=16% Similarity=0.170 Sum_probs=61.6 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHHHHHHHHHHHHHH Q ss_conf 99999988887512455555411247761488678899999999999970899779997-15379999999999999998 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-ANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~~Q~~~~lw~ei~k~~~ 133 (367) |.++...+...++.+. .| .+.+.++.|+|||+++-.++--..+-.....++-. |...+.+. ++-..++...+ T Consensus 21 ~~~~~~~L~~~i~~~~---~p---hlLf~GppG~GKTt~a~~la~~l~~~~~~~~~lelnasd~r~id-~vr~~i~~~~~ 93 (318) T PRK00440 21 QEEIVERLKSFVKEKN---MP---HLLFAGPPGTGKTTAALALARELYGEYWRENFLELNASDERGID-VIRNKIKEFAR 93 (318) T ss_pred CHHHHHHHHHHHHCCC---CC---EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCHH-HHHHHHHHHHH T ss_conf 6999999999998799---86---69888959988999999999997698643476895164566717-89999999997 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..+ +. +...-++|+|||.+.......++.. T Consensus 94 ~~~-----------------------------------------------~~---~~~~kiiiiDE~d~l~~~aq~aL~~ 123 (318) T PRK00440 94 TAP-----------------------------------------------VG---GAPFKIIFLDEADNLTSDAQQALRR 123 (318) T ss_pred HCC-----------------------------------------------CC---CCCEEEEEEECCCCCCHHHHHHHHH T ss_conf 267-----------------------------------------------78---9973899986855322556788876 Q ss_pred HHHCCCCCEEEEEEECC Q ss_conf 74069882589998078 Q gi|254781187|r 214 FFTELNPNRFWIMTSNT 230 (367) Q Consensus 214 ~Lt~~~~~~~~i~igNP 230 (367) +|-........+++.|. T Consensus 124 ~mE~~~~~~~fil~~n~ 140 (318) T PRK00440 124 TMEMYSQTTRFILSCNY 140 (318) T ss_pred HHHCCCCCCEEEEECCC T ss_conf 43105666258863488 No 67 >PRK06871 DNA polymerase III subunit delta'; Validated Probab=97.05 E-value=0.02 Score=33.91 Aligned_cols=140 Identities=16% Similarity=0.288 Sum_probs=72.8 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) ||....+.+....+.+...+ ...+.+.+|+||+.++-.++-|.+|..|+...-|-.-..=++ +. .. T Consensus 5 Wl~~~~~~l~~~~~~~r~~H-----A~L~~G~~G~Gk~~la~~~a~~llC~~~~~~~~Cg~C~sC~l-------~~--~g 70 (324) T PRK06871 5 WLQPIYQQITQTFLQGRGHH-----ALLFKADSGLGTEQLIRALAQWLMCQAPGDEQPCGQCHSCHL-------FQ--AG 70 (324) T ss_pred CCHHHHHHHHHHHHCCCCCE-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHH-------HH--CC T ss_conf 65799999999998699543-----787689999789999999999982899999998888989999-------97--38 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) .-|+-++..... ..+++.+.-..... .-+-.+.+| .+ -.+|+|+|.........++.. T Consensus 71 ~HPD~~~i~~~~-------------~k~I~vd~IR~l~~-----~~~~~~~~g---~~-KV~iI~~ae~m~~~AaNALLK 128 (324) T PRK06871 71 NHPDFHILEPID-------------GKDIGVDQVREINE-----KVSQFAQQG---GN-KVVYIQGAERLTEAAANALLK 128 (324) T ss_pred CCCCEEEEECCC-------------CCCCCHHHHHHHHH-----HHHHCCCCC---CC-EEEEECCHHHHHHHHHHHHHH T ss_conf 999879984678-------------88788999999999-----986462205---96-699975888857999999999 Q ss_pred HHHCCCCCEEEEEEEC Q ss_conf 7406988258999807 Q gi|254781187|r 214 FFTELNPNRFWIMTSN 229 (367) Q Consensus 214 ~Lt~~~~~~~~i~igN 229 (367) +|-.+...++.+++++ T Consensus 129 tLEEPp~~~~fiL~t~ 144 (324) T PRK06871 129 TLEEPRPNTYFLLQAD 144 (324) T ss_pred HHCCCCCCEEEEEEEC T ss_conf 8338987838999878 No 68 >PRK07994 DNA polymerase III subunits gamma and tau; Validated Probab=97.04 E-value=0.012 Score=35.11 Aligned_cols=134 Identities=15% Similarity=0.144 Sum_probs=72.5 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|..+++.+...+..+.. ++. ....+.||+|||+++-.++-.+-|.....-.-| . + ... ..+|.. T Consensus 20 GQ~~v~~~l~na~~~~r~-~ha----ylf~G~rG~GKtt~ari~ak~lnc~~~~~~~pc----g-~-c~~-c~~i~~--- 84 (643) T PRK07994 20 GQEHVLTALANGLSLGRI-HHA----YLFSGTRGVGKTSIARLLAKGLNCETGITATPC----G-V-CDN-CREIEQ--- 84 (643) T ss_pred CCHHHHHHHHHHHHHCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCC----C-C-CHH-HHHHHC--- T ss_conf 879999999999982986-634----874589988888999999999679999999978----7-6-776-898865--- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..+....+.+ ...+...-..+-..+ --.+.-.+|.+. .+|+||....+...|.+++. T Consensus 85 ------------------g~~~d~~eid--aas~~~vd~~rel~~--~~~y~p~~~r~k-vyiidEvhmls~~afnalLK 141 (643) T PRK07994 85 ------------------GRFVDLIEID--AASRTKVEDTRDLLD--NVQYAPARGRFK-VYLIDEVHMLSRHSFNALLK 141 (643) T ss_pred ------------------CCCCCEEEEE--CCCCCCHHHHHHHHH--HCCCCCCCCCEE-EEEEECHHHCCHHHHHHHHH T ss_conf ------------------8988758863--677788899999998--446688778536-99972210158999999998 Q ss_pred HHHCCCCCEEEE Q ss_conf 740698825899 Q gi|254781187|r 214 FFTELNPNRFWI 225 (367) Q Consensus 214 ~Lt~~~~~~~~i 225 (367) +|-.+-...+.+ T Consensus 142 tlEePp~hv~fi 153 (643) T PRK07994 142 TLEEPPAHVKFL 153 (643) T ss_pred HHCCCCHHCEEE T ss_conf 623786100899 No 69 >TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems. Probab=97.03 E-value=0.021 Score=33.73 Aligned_cols=152 Identities=14% Similarity=0.142 Sum_probs=72.5 Q ss_pred CCCCCCCCCCCCCCH-----HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEE Q ss_conf 466888443666842-----899999998888751245555541124776148867889999999999997089-97799 Q gi|254781187|r 38 WGIKGKPLEHFSQPH-----RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSII 111 (367) Q Consensus 38 w~~~~~~~~~~~~p~-----~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~ 111 (367) ||-+..|+..-..|+ +-..++|..+.-.++.... + +.|.+.=|+|||++.-.++-.. .+ ...++ T Consensus 6 fgl~~~PF~~~pd~~~~y~s~~h~~al~~L~~~l~~~~g------~-~lltGe~GtGKTtllr~l~~~l---~~~~~~~~ 75 (269) T TIGR03015 6 FGFTTKPFQLLPDPDFFYPSKGHKRAMAYLEYGLSQREG------F-ILITGEVGAGKTTLIRNLLKRL---DQERVVAA 75 (269) T ss_pred CCCCCCCCCCCCCHHHCCCCHHHHHHHHHHHHHHHCCCC------E-EEEECCCCCCHHHHHHHHHHHC---CCCCEEEE T ss_conf 499989999999845414786699999999999964896------5-9997299898899999999845---93454899 Q ss_pred EECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCC Q ss_conf 97153799999999999999986231211233332100012333221111345776126621013544556521011358 Q gi|254781187|r 112 CIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTH 191 (367) Q Consensus 112 ~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~ 191 (367) .+.++.-...+.+ ..|..-+..-+... ...... .. +.... . + ....+.. T Consensus 76 ~i~~~~l~~~~ll-~~i~~~lg~~~~~~----~~~~~~----------~~---------l~~~L----~-~--~~~~g~~ 124 (269) T TIGR03015 76 KLVNTRVDAEDLL-RMVAADFGLETEGR----DKAALL----------RE---------LEDFL----I-E--QFAAGKR 124 (269) T ss_pred EECCCCCCHHHHH-HHHHHHCCCCCCCC----CHHHHH----------HH---------HHHHH----H-H--HHHCCCC T ss_conf 9769999999999-99999859898898----999999----------99---------99999----9-9--9966994 Q ss_pred CCEEEEECCCCCCHHHHHHHHHHH---HCCCCCEEEEEEECCC Q ss_conf 628999754559988999989874---0698825899980789 Q gi|254781187|r 192 GMAVFNDEASGTPDIINKSILGFF---TELNPNRFWIMTSNTR 231 (367) Q Consensus 192 ~~l~ivDEAsgI~d~i~e~i~g~L---t~~~~~~~~i~igNP~ 231 (367) .++|+|||..+++++.+.+.-.+ ++..+-.-.+++|.|. T Consensus 125 -~vliIDEAq~L~~~~Le~Lr~L~n~e~~~~~ll~iiL~Gqpe 166 (269) T TIGR03015 125 -ALLVVDEAQNLTPELLEELRMLSNFQTDNAKLLQIFLVGQPE 166 (269) T ss_pred -EEEEEECHHHCCHHHHHHHHHHHCCCCCCCCCEEEEEECCHH T ss_conf -699972422199999999999970135888704899957867 No 70 >PRK06645 DNA polymerase III subunits gamma and tau; Validated Probab=97.02 E-value=0.02 Score=33.83 Aligned_cols=142 Identities=15% Similarity=0.096 Sum_probs=68.2 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|..+.+.+...+..+... + ...-.+.||+|||+.+-.++--.-|..+...--...|-.. ...+ ..+.. T Consensus 25 GQ~~~~~~l~n~i~~~~~~-~----aylf~G~rG~GKTt~Ari~ak~lnc~~~~~~~~~~~~c~~--c~~c-~~i~~--- 93 (507) T PRK06645 25 GQEVLVKVLSYTILNDRLA-G----GYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEK--CTNC-ISFNN--- 93 (507) T ss_pred CCHHHHHHHHHHHHCCCCC-C----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCC--CHHH-HHHHC--- T ss_conf 9399999999999739966-3----4774587997889999999999679998888998888888--7678-99865--- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) .....+.+.+ .......-..+...+. -.+.-..+.+ -.+|+||+...+...|.+++- T Consensus 94 ------------------~~~~dv~EiD--aas~~gv~~ir~l~~~--~~~~p~~~~~-kv~iidE~hmls~~a~nallk 150 (507) T PRK06645 94 ------------------HNHPDIIEID--AASKTSVDDIRRIIES--AEYKPLQGKH-KIFIIDEVHMLSKGAFNALLK 150 (507) T ss_pred ------------------CCCCCEEEEE--CCCCCCHHHHHHHHHH--CCCCCCCCCE-EEEEECCHHHCCHHHHHHHHH T ss_conf ------------------8999859963--7888888999999863--5517876743-589952142248999999999 Q ss_pred HHHCCCCCEEEEEEEC Q ss_conf 7406988258999807 Q gi|254781187|r 214 FFTELNPNRFWIMTSN 229 (367) Q Consensus 214 ~Lt~~~~~~~~i~igN 229 (367) +|-.+-.....++..| T Consensus 151 tlEepp~~~~Fi~att 166 (507) T PRK06645 151 TLEEPPPHIIFIFATT 166 (507) T ss_pred HHHCCCCCEEEEEECC T ss_conf 7427864438999748 No 71 >PRK07471 DNA polymerase III subunit delta'; Validated Probab=96.95 E-value=0.0075 Score=36.47 Aligned_cols=160 Identities=16% Similarity=0.169 Sum_probs=79.8 Q ss_pred CCCCCHH-----HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH-HH Q ss_conf 6668428-----99999998888751245555541124776148867889999999999997089977999715379-99 Q gi|254781187|r 47 HFSQPHR-----WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET-QL 120 (367) Q Consensus 47 ~~~~p~~-----wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~-Q~ 120 (367) +..+|+. .|.++...+..-.+.+...+ -....+.+|+||++++=.++-+.+|+.++....+...... .+ T Consensus 9 ~~p~P~~~~~liGqe~~~~~L~~a~~~grl~H-----A~Lf~Gp~GiGK~tlA~~~A~~ll~~~~~~~~~~~~~~~~l~~ 83 (363) T PRK07471 9 ADPHPRETTALFGHAAAEAALLDAYRSGRLHH-----AWLIGGPQGIGKATLAYRMARFLLATPPPGGDAVFPPPASLAV 83 (363) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC-----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHCC T ss_conf 99599982731681999999999998599764-----5876799981889999999999857999777776787053125 Q ss_pred --HHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEE Q ss_conf --9999999999998623121123333210001233322--111134577612662101354455652101135862899 Q gi|254781187|r 121 --KNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL--LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVF 196 (367) Q Consensus 121 --~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~i 196 (367) ..-.++.+. .......+.+. +.+.... .+..+..+. .+.. ..--++....|.+. .+| T Consensus 84 ~~~~p~~r~i~----~~~hpdl~~i~------r~~d~k~~~~~~~I~Vd~------iR~l--~~~~~~~p~~g~~k-V~I 144 (363) T PRK07471 84 DPDHPVARRIA----AGAHGGLLTLE------RSWNEKGKRLRTVITVDE------VRET--IGFFGLTAAEGGWR-VVI 144 (363) T ss_pred CCCCCHHHHHH----CCCCCCEEEEE------CCCCCCCCCCCCCCCHHH------HHHH--HHHHCCCCCCCCCE-EEE T ss_conf 87772899995----26999846676------200113332124453999------9999--99972485248966-999 Q ss_pred EECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECC Q ss_conf 9754559988999989874069882589998078 Q gi|254781187|r 197 NDEASGTPDIINKSILGFFTELNPNRFWIMTSNT 230 (367) Q Consensus 197 vDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP 230 (367) +|||.......+.+++.+|-.+-.+++++++++- T Consensus 145 Id~ad~mn~~aaNALLK~LEEPP~~t~fiLit~~ 178 (363) T PRK07471 145 VDTADEMNANAANALLKVLEEPPARSLLLLVSHA 178 (363) T ss_pred EECHHHHCHHHHHHHHHHHCCCCCCEEEEEEECC T ss_conf 8687873889999999972158988389986399 No 72 >pfam05970 DUF889 PIF1 helicase. The PIF1 helicase inhibits telomerase activity and is cell cycle regulated. Probab=96.95 E-value=0.002 Score=39.94 Aligned_cols=97 Identities=14% Similarity=-0.003 Sum_probs=54.0 Q ss_pred CCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH-HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 886788999999999999708997799971537999999-9999999998623121123333210001233322111134 Q gi|254781187|r 85 GRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT-LWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMG 163 (367) Q Consensus 85 grg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~-lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (367) +=|+|||++.-.++-++- ..+..+++||||.--|..+ --.-+-.|.. .. +. T Consensus 2 ~AGTGKS~ll~~i~~~l~--~~~~~v~vtA~TGiAA~~i~gG~TiHs~~g--------------------i~------~~ 53 (418) T pfam05970 2 YGGTGKTFLWNALSARIR--SRGKIVLNVASSGIAALLLPGGRTAHSRFG--------------------IP------LD 53 (418) T ss_pred CCCCCHHHHHHHHHHHHH--HCCCEEEEECCHHHHHHCCCCCEEHHHCCC--------------------CC------CC T ss_conf 798879999999999997--689889998968999851699873985269--------------------89------88 Q ss_pred CCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 57761266210135445565210113586289997545599889999898740 Q gi|254781187|r 164 IDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFT 216 (367) Q Consensus 164 ~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt 216 (367) .......-. .. +.....-++ +..++|+||.|.|+...|+.+.-.|. T Consensus 54 ~~~~~~~~~--~~---~~~~~~~~~--~~~vLIIDEiSMv~~~lfd~id~~lr 99 (418) T pfam05970 54 IDEDSTCKI--KR---GSKLAELLK--KASLIIWDEAPMTHRHCFEALDRTLR 99 (418) T ss_pred CCCCCCEEE--CC---CHHHHHHHH--HCCEEEEECCCCCCHHHHHHHHHHHH T ss_conf 774201121--33---778899874--08799985411357899999999999 No 73 >PRK13826 Dtr system oriT relaxase; Provisional Probab=96.94 E-value=0.013 Score=35.01 Aligned_cols=114 Identities=16% Similarity=0.123 Sum_probs=64.6 Q ss_pred EEECCCCCCHHHHHHH-HHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 7614886788999999-999999708997799971537999999999999999862312112333321000123332211 Q gi|254781187|r 81 AISAGRGIGKTTLNAW-MMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLE 159 (367) Q Consensus 81 ~v~sgrg~GKS~~~a~-~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (367) +|.+-=|.|||++... --.|-. .|.+|+=.|++...+... =.+- . .... .+..|... T Consensus 401 ~VvG~AGaGKStmL~aAReawEa---~GyrV~GaALsGkAAegL-e~~s-G----------I~Sr----TlAs~e~~--- 458 (1102) T PRK13826 401 AVIGRAGAGKTTMMKAAREAWEA---AGYRVVGGALAGKAAEGL-EKEA-G----------IASR----TLSSWELR--- 458 (1102) T ss_pred EEEECCCCCHHHHHHHHHHHHHH---CCCEEEEECCCHHHHHHH-HHCC-C----------CCCH----HHHHHHHH--- T ss_conf 99842888788999999999997---797798015007899977-5346-9----------5303----38999987--- Q ss_pred CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECC-----CCCC Q ss_conf 11345776126621013544556521011358628999754559988999989874069882589998078-----9998 Q gi|254781187|r 160 QSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNT-----RRLN 234 (367) Q Consensus 160 ~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP-----~r~~ 234 (367) .. + +. .-+ ....++|+|||+.|....+.-+.......|.+++ +.|-| -..+ T Consensus 459 ----w~--------------~-gr-~~L--~~~dVlVIDEAGMVgsrqmarvl~~ae~aGAKvV--LVGD~~QLQpIeAG 514 (1102) T PRK13826 459 ----WN--------------Q-GR-DQL--DNKTVFVLDEAGMVSSRQMALFVEAVTRAGAKLV--LVGDPEQLQPIEAG 514 (1102) T ss_pred ----HC--------------C-CC-CCC--CCCCEEEEECCCCCCHHHHHHHHHHHHHCCCEEE--EECCHHHHCCCCCC T ss_conf ----43--------------5-86-556--7873899845556557999999999997599899--96887882761046 Q ss_pred CHHHHH Q ss_conf 768875 Q gi|254781187|r 235 GWFYDI 240 (367) Q Consensus 235 g~Fye~ 240 (367) +.|-.+ T Consensus 515 aaFrai 520 (1102) T PRK13826 515 AAFRAI 520 (1102) T ss_pred HHHHHH T ss_conf 889999 No 74 >COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only] Probab=96.94 E-value=0.0015 Score=40.71 Aligned_cols=156 Identities=13% Similarity=0.042 Sum_probs=82.6 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHHHHH Q ss_conf 899999998888751245555541124776148867889999999999997089-9779997153799999999999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLWAEVSKW 131 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw~ei~k~ 131 (367) ..|+=.|+.+-+ +.+-=|...+--|+|||.++-+..+.-..-+. ..|++++.|+..--+++-| T Consensus 231 ~eQ~~ALdlLld----------~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~y~KiiVtRp~vpvG~dIGf------ 294 (436) T COG1875 231 AEQRVALDLLLD----------DDIDLVSLGGKAGTGKTLLALAAGLEQVLERKRYRKIIVTRPTVPVGEDIGF------ 294 (436) T ss_pred HHHHHHHHHHCC----------CCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHCEEEEECCCCCCCCCCCC------ T ss_conf 888888998638----------7778488633577667699999899999877543027883377677531376------ Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEEEEECCC-CCCCCCCCCCCCCCC--CCEEEEECCCCCC Q ss_conf 98623121123333210001233322----1111345776126621013-544556521011358--6289997545599 Q gi|254781187|r 132 LSMLPHRHWFEMQSLSLHPSGWYAEL----LEQSMGIDSKHYTITCRTY-SEERPDTFVGPHNTH--GMAVFNDEASGTP 204 (367) Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~a~~~-~~~~~ea~~g~h~~~--~~l~ivDEAsgI~ 204 (367) +| -....+|.||.-.. .........++........ ..-.-+++--+||.+ -.++|+|||+... T Consensus 295 ---LP-------G~eEeKm~PWmq~i~DnLE~L~~~~~~~~~~l~~~l~~~~iev~alt~IRGRSl~~~FiIIDEaQNLT 364 (436) T COG1875 295 ---LP-------GTEEEKMGPWMQAIFDNLEVLFSPNEPGDRALEEILSRGRIEVEALTYIRGRSLPDSFIIIDEAQNLT 364 (436) T ss_pred ---CC-------CCHHHHCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCEEEEEEEEECCCCCCCCEEEEEHHHCCC T ss_conf ---88-------84366506157676667998726665536789988741542566520131665553069971212178 Q ss_pred HHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHH Q ss_conf 889999898740698825899980789998768 Q gi|254781187|r 205 DIINKSILGFFTELNPNRFWIMTSNTRRLNGWF 237 (367) Q Consensus 205 d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~F 237 (367) ....-.|.- -.+.+++ .+++|||.-..+++ T Consensus 365 pheikTilt-R~G~GsK--IVl~gd~aQiD~~y 394 (436) T COG1875 365 PHELKTILT-RAGEGSK--IVLTGDPAQIDTPY 394 (436) T ss_pred HHHHHHHHH-HHCCCCE--EEEECCHHHCCCCC T ss_conf 888899987-6069977--99808988827754 No 75 >PRK06090 DNA polymerase III subunit delta'; Validated Probab=96.92 E-value=0.03 Score=32.75 Aligned_cols=134 Identities=10% Similarity=0.118 Sum_probs=68.7 Q ss_pred HHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 98888751245555541124776148867889999999999997089977999715379999999999999998623121 Q gi|254781187|r 60 EAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRH 139 (367) Q Consensus 60 ~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~ 139 (367) +.+....+.+... + .+.+.+.+|+||+.++-.++-|.+|..+... .|-.-.. + ..+. ...-|+-+ T Consensus 13 ~~l~~~~~~~rl~-H----A~L~~g~~G~Gk~~la~~la~~LlC~~~~~~-~Cg~C~s------C-~l~~--~g~HPD~~ 77 (319) T PRK06090 13 QNWKSGLDAERIP-G----ALLLQSDEGLGVESLVELFSHALLCQNYQSE-ACGFCHS------C-ELMK--SGNHPDLH 77 (319) T ss_pred HHHHHHHHCCCCC-C----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCC-CCCCCHH------H-HHHH--CCCCCCCE T ss_conf 9999999869963-0----6766799985799999999999808999999-8877877------9-9987--58999823 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCC Q ss_conf 12333321000123332211113457761266210135445565210113586289997545599889999898740698 Q gi|254781187|r 140 WFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELN 219 (367) Q Consensus 140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~ 219 (367) +...+. ....++.+.-.... +.....+.+| -+ -.+|+|+|.........++..+|-++. T Consensus 78 ~i~pe~------------~~k~I~vd~IR~l~-----~~~~~~~~~g---~~-KV~iI~~ae~m~~~AaNALLKtLEEPp 136 (319) T PRK06090 78 VIKPEK------------EGKSITVEQIRQCN-----RLAQESSQLG---GY-RLFVIEPADAMNESASNALLKTLEEPA 136 (319) T ss_pred EEECCC------------CCCCCCHHHHHHHH-----HHHHHCCCCC---CC-EEEEECCHHHCCHHHHHHHHHHHCCCC T ss_conf 661233------------56768799999999-----9975452106---93-699981444349999999999842899 Q ss_pred CCEEEEEEEC Q ss_conf 8258999807 Q gi|254781187|r 220 PNRFWIMTSN 229 (367) Q Consensus 220 ~~~~~i~igN 229 (367) .+++.+++++ T Consensus 137 ~~t~fiL~t~ 146 (319) T PRK06090 137 PNCLFLLVTH 146 (319) T ss_pred CCEEEEEEEC T ss_conf 8838998768 No 76 >PRK08181 transposase; Validated Probab=96.86 E-value=0.024 Score=33.31 Aligned_cols=128 Identities=14% Similarity=0.107 Sum_probs=68.9 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537999999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) ++.+-|..-|..--.+++++. ++.+.++-|+|||+++.++..- .++.|.+|..+.-.. +..++. T Consensus 87 ~i~~~~i~~L~~~~~fi~~~~--------Nvil~Gp~GtGKThLA~Alg~~--A~~~G~~V~f~~~~~------L~~~L~ 150 (269) T PRK08181 87 MISKAQVMALAAGDSWLAKGA--------NLLLFGPPGGGKSHLAAAIGLA--LIENGWRVLFTRTTD------LVQKLQ 150 (269) T ss_pred CCCHHHHHHHHCCCHHHHCCC--------EEEEECCCCCCHHHHHHHHHHH--HHHCCCEEEEEEHHH------HHHHHH T ss_conf 989999999965675886487--------0899899998788999999999--998799399978999------999999 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC----- Q ss_conf 999862312112333321000123332211113457761266210135445565210113586289997545599----- Q gi|254781187|r 130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP----- 204 (367) Q Consensus 130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~----- 204 (367) ...... .. ...+.-+ ....|+|+||...+| T Consensus 151 ~a~~~~--------------------------------~~-----------~~~~~~l--~~~dLLIiDe~G~~~~~~~~ 185 (269) T PRK08181 151 VARREL--------------------------------QL-----------ESAIAKL--DKFDLLILDDLAYVTKDQAE 185 (269) T ss_pred HHHHCC--------------------------------CH-----------HHHHHHH--HCCCEEEEHHCCCCCCCHHH T ss_conf 977558--------------------------------39-----------9999997--44460122010566799899 Q ss_pred -HHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCC Q ss_conf -8899998987406988258999807899987688754112 Q gi|254781187|r 205 -DIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIP 244 (367) Q Consensus 205 -d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~ 244 (367) +..|+.+..-- +.+. .+++ .+.+.+..++.|.++ T Consensus 186 ~~~lf~lI~~Ry---e~~S-~IIT--Sn~~~~~W~~~f~D~ 220 (269) T PRK08181 186 TSVLFELISARY---ERRS-ILIT--ANQPFGEWNRVFPDP 220 (269) T ss_pred HHHHHHHHHHHH---CCCC-EEEE--CCCCHHHHHHHCCCH T ss_conf 999999999985---7888-8998--899977887753868 No 77 >TIGR01054 rgy reverse gyrase; InterPro: IPR005736 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=96.85 E-value=0.015 Score=34.62 Aligned_cols=200 Identities=18% Similarity=0.101 Sum_probs=104.7 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCC--CCCCCCCCCCCCC Q ss_conf 77614886788999999999999708997799971537999999999999999862312112333--3210001233322 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQ--SLSLHPSGWYAEL 157 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~--~~~~~~~~~~~~~ 157 (367) -|+.|+.|+|||++...+.+++++- .|.++.++=||..=++++- ..|++...+.- .... ....+.+....+. T Consensus 102 Fai~APTGVGKttFG~~mslflA~k-KGkR~y~ilPT~lLv~Qv~-~kl~~~~~k~g----~~~~~l~~~yhS~L~~~~k 175 (1843) T TIGR01054 102 FAIVAPTGVGKTTFGLVMSLFLAKK-KGKRSYIILPTTLLVKQVA-EKLSSLAEKEG----VGIVRLLGAYHSKLSTKEK 175 (1843) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHH-CCCEEEEEECHHHHHHHHH-HHHHHHCCCCC----CCCEEEEEEEECCCCHHHH T ss_conf 4898058876779999999998654-2987899947078899999-99875200257----5000022210112654567 Q ss_pred CCCCCCCCCCCEEEEECCCCCCCCCCCCCCC-CCCCCEEEEECCCCC----------------CH----HHHHHH----- Q ss_conf 1111345776126621013544556521011-358628999754559----------------98----899998----- Q gi|254781187|r 158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPH-NTHGMAVFNDEASGT----------------PD----IINKSI----- 211 (367) Q Consensus 158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h-~~~~~l~ivDEAsgI----------------~d----~i~e~i----- 211 (367) ...--++.+|.+-+.-.| +..-.=++.-++ +.++.|++||---.+ +. ..|+.| T Consensus 176 ke~~Eri~~GDfdilitT-~~FL~K~~~~L~~~y~F~liFVDDVDa~Lk~skNVD~~L~LlGF~eE~i~~a~~~i~L~~k 254 (1843) T TIGR01054 176 KEVKERIENGDFDILITT-SMFLSKNFDKLKNQYKFDLIFVDDVDALLKASKNVDKILKLLGFSEELIEKAYELIKLKLK 254 (1843) T ss_pred HHHHHHHHCCCEEEEHHH-HHHHHHHHHHCCCCCEEEEEEEECHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 889998731891786122-4688876651789851448997153676316555667775517889999999999999887 Q ss_pred ---------------------------------HHHHHCCCCCEEEEEEECCC-CCCCHHHHHHHCCC-------CCE-E Q ss_conf ---------------------------------98740698825899980789-99876887541122-------350-4 Q gi|254781187|r 212 ---------------------------------LGFFTELNPNRFWIMTSNTR-RLNGWFYDIFNIPL-------EDW-K 249 (367) Q Consensus 212 ---------------------------------~g~Lt~~~~~~~~i~igNP~-r~~g~Fye~~~~~~-------~~w-~ 249 (367) +.......++.-++++|+-| ++-|-=..+|+..- ... - T Consensus 255 ~~k~~~~~~~~~~~~R~E~~~~~LE~~~r~~~~~a~~~~krGr~g~LivsSATG~prG~r~~LFR~LL~FevG~~~~~GL 334 (1843) T TIGR01054 255 ENKLEEDLAREKIVVRLEARKKLLEAKRRLEKLEAEIKKKRGRKGVLIVSSATGKPRGKRVKLFRELLGFEVGKGSDTGL 334 (1843) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCCHHHHHHHHCCCCCCCCCCCCC T ss_conf 64357788888886467888999999999898776474324886469998514888761336536552710057642233 Q ss_pred EEEECCCCCCCC-CHHHHHH---HHHHCCCCCCEEEEEEEE Q ss_conf 675233328888-9889999---996216880002688864 Q gi|254781187|r 250 RYQIDTRTVEGI-DSGFHEG---IISRYGLDSDVARIEILG 286 (367) Q Consensus 250 ~~~~~~~d~p~~-~~~~i~~---~~~~~gedS~~~r~ev~G 286 (367) .--++..+++.- =.+-+.+ ..+.+|..--+|=.--+| T Consensus 335 RnvvD~y~~~~d~v~E~~~~sve~v~~LG~GGlVyvs~~yG 375 (1843) T TIGR01054 335 RNVVDVYEEDEDGVKEKLLESVELVKKLGKGGLVYVSIDYG 375 (1843) T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCC T ss_conf 21388511488844688999999999847943999712225 No 78 >PRK13889 conjugal transfer relaxase TraA; Provisional Probab=96.78 E-value=0.018 Score=34.14 Aligned_cols=131 Identities=12% Similarity=0.019 Sum_probs=72.6 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEE-EECCCCCCHHHHHHH-HHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH Q ss_conf 89999999888875124555554112477-614886788999999-9999997089977999715379999999999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCA-ISAGRGIGKTTLNAW-MMLWLISTRPGMSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~-v~sgrg~GKS~~~a~-~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) .=|++.++.|... . +++ |.+-=|.|||++... --.|- ..|.+|+=.|++..-+...- .+- T Consensus 349 ~EQ~~A~~hiT~~----------~--~iavVvG~AGtGKStmL~aAReawE---a~GyrV~GaALsGkAAegLe-~~s-- 410 (992) T PRK13889 349 GEQADALAHVTDG----------R--DLGVVVGYAGTGKSAMLGVAREAWE---AAGYEVRGAALSGIAAENLE-GGS-- 410 (992) T ss_pred HHHHHHHHHHCCC----------C--CEEEEEECCCCCHHHHHHHHHHHHH---HCCCEEEEECCCHHHHHHHH-HCC-- T ss_conf 9999999986478----------9--7589983388878899999999999---77988981150068999765-347-- Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHH Q ss_conf 99862312112333321000123332211113457761266210135445565210113586289997545599889999 Q gi|254781187|r 131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKS 210 (367) Q Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~ 210 (367) -+ ... .+..|... + . .....+. ....+|||||+.|+...+.- T Consensus 411 ----GI-----~Sr----TlAs~e~~-------------------w--~--~g~~~L~--~~dVlVVDEAGMVgSRqMar 452 (992) T PRK13889 411 ----GI-----ASR----TIASLEHG-------------------W--G--QGRDLLT--ARDVLVIDEAGMVGTRQLER 452 (992) T ss_pred ----CC-----CCH----HHHHHHHH-------------------H--H--CCCCCCC--CCCEEEEECCCCCCHHHHHH T ss_conf ----94-----316----79999998-------------------7--4--6733478--98589996765577499999 Q ss_pred HHHHHHCCCCCEEEEEEECC-----CCCCCHHHHHH Q ss_conf 89874069882589998078-----99987688754 Q gi|254781187|r 211 ILGFFTELNPNRFWIMTSNT-----RRLNGWFYDIF 241 (367) Q Consensus 211 i~g~Lt~~~~~~~~i~igNP-----~r~~g~Fye~~ 241 (367) +.......+.+++ ++|-| ...++.|-.+. T Consensus 453 ll~~Ae~AGAKVV--LVGD~~QLq~IeAGaaFral~ 486 (992) T PRK13889 453 VLSHAADAGAKVV--LVGDPQQLQAIEAGAAFRSIH 486 (992) T ss_pred HHHHHHHCCCEEE--EECCHHHCCCCCCCHHHHHHH T ss_conf 9999998499899--948877718864688999999 No 79 >pfam05127 DUF699 Putative ATPase (DUF699). This putative domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase. This domain is often associated with pfam00583. This domain is found in isolation in the uncharacterized protein HI1254 from Haemophilus influenzae. Probab=96.73 E-value=0.043 Score=31.82 Aligned_cols=85 Identities=21% Similarity=0.153 Sum_probs=47.0 Q ss_pred CCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCC Q ss_conf 99779997153799999999999999986231211233332100012333221111345776126621013544556521 Q gi|254781187|r 106 PGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFV 185 (367) Q Consensus 106 ~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~ 185 (367) -..+|+||||+...+. .+|.-+.+-++.+..... . .......+.... +..+-..|+..- T Consensus 12 ~~~~I~VTAP~~~nv~-~lf~~~~~~L~~lg~~~~--------~-----~~~~~~~~~~~~-------~~i~f~~Pd~l~ 70 (160) T pfam05127 12 GYSRILVTAPSPANVQ-TLFEFAIKGLDALGYKPK--------K-----REGIIASLRGNG-------QRIRFIAPDELL 70 (160) T ss_pred CCCEEEEECCCHHHHH-HHHHHHHHHHHHCCCCCC--------C-----CCCCEEEEECCC-------EEEEEECCHHHH T ss_conf 9973999799989999-999999999986386434--------5-----655047875287-------689996808986 Q ss_pred CCCCCCCCEEEEECCCCCCHHHHHHHH Q ss_conf 011358628999754559988999989 Q gi|254781187|r 186 GPHNTHGMAVFNDEASGTPDIINKSIL 212 (367) Q Consensus 186 g~h~~~~~l~ivDEAsgI~d~i~e~i~ 212 (367) ... ....+++|||||.||-.+...+. T Consensus 71 ~~~-~~~DllvVDEAAaIP~p~L~~ll 96 (160) T pfam05127 71 KLP-PQADLLVVDEAAAIPLPLLKQLL 96 (160) T ss_pred HCC-CCCCEEEEEHHHCCCHHHHHHHH T ss_conf 167-87768997324218889999998 No 80 >PRK05564 DNA polymerase III subunit delta'; Validated Probab=96.73 E-value=0.036 Score=32.32 Aligned_cols=121 Identities=12% Similarity=0.067 Sum_probs=71.4 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC---EEEEECCCHHHHHHHHHHHHHH Q ss_conf 9999999888875124555554112477614886788999999999999708997---7999715379999999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGM---SIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~---~v~~~A~t~~Q~~~~lw~ei~k 130 (367) .|.++.+.+...++.+.. .|. ....+.+|+||+.++-.++-..+|...+. -++...+...+. +--..|+. T Consensus 8 Gq~~i~~~L~~~i~~~rl-~HA----yLF~Gp~G~GK~~~A~~~A~~ll~~~~~~~~~D~~~~~~~~~~~--I~vd~IR~ 80 (313) T PRK05564 8 GHENIKNRIDNSIIKGKF-SHA----SLIVGEDGIGKSILAKEIANKILGKSEQREYVDIIEYKPINKKS--IGVDDIRN 80 (313) T ss_pred CHHHHHHHHHHHHHCCCC-CCE----EEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCC--CCHHHHHH T ss_conf 829999999999987998-750----43279998509999999999982899778898658863322569--99899999 Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHH Q ss_conf 99862312112333321000123332211113457761266210135445565210113586289997545599889999 Q gi|254781187|r 131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKS 210 (367) Q Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~ 210 (367) .++.+ ++....|.+ -.+|+|||.........+ T Consensus 81 l~~~~-----------------------------------------------~~~p~~g~~-KV~II~~ae~m~~~AaNA 112 (313) T PRK05564 81 IIEEV-----------------------------------------------NKKPYEGDK-KVIIIYKSEKMTEQAQNA 112 (313) T ss_pred HHHHH-----------------------------------------------HHCCCCCCC-EEEEECCHHHHCHHHHHH T ss_conf 99998-----------------------------------------------408625895-699980777758999999 Q ss_pred HHHHHHCCCCCEEEEEEEC Q ss_conf 8987406988258999807 Q gi|254781187|r 211 ILGFFTELNPNRFWIMTSN 229 (367) Q Consensus 211 i~g~Lt~~~~~~~~i~igN 229 (367) +..+|-.+-..++.+++.+ T Consensus 113 LLKtLEEPP~~t~fIL~t~ 131 (313) T PRK05564 113 FLKTIEEPPKGVFIILLCE 131 (313) T ss_pred HHHCCCCCCCCEEEEEEEC T ss_conf 8455036899858998649 No 81 >KOG1805 consensus Probab=96.68 E-value=0.0085 Score=36.12 Aligned_cols=130 Identities=17% Similarity=0.107 Sum_probs=70.0 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 24776148867889999999999997089977999715379999999999999998623121123333210001233322 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL 157 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (367) |++ |.+=-|+|||++++.++--++.+ +++|+.|+-|..-+.+++-+..+--+..+ ++......++. T Consensus 687 y~L-I~GMPGTGKTTtI~~LIkiL~~~--gkkVLLtsyThsAVDNILiKL~~~~i~~l-----------RLG~~~kih~~ 752 (1100) T KOG1805 687 YAL-ILGMPGTGKTTTISLLIKILVAL--GKKVLLTSYTHSAVDNILIKLKGFGIYIL-----------RLGSEEKIHPD 752 (1100) T ss_pred HHE-EECCCCCCCHHHHHHHHHHHHHC--CCEEEEEEHHHHHHHHHHHHHHCCCCCEE-----------ECCCCCCCCHH T ss_conf 220-32699898122599999999973--88189985056788999998750671103-----------44872224468 Q ss_pred CCCCC-------------CCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEE Q ss_conf 11113-------------45776126621013544556521011358628999754559988999989874069882589 Q gi|254781187|r 158 LEQSM-------------GIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFW 224 (367) Q Consensus 158 ~~~~~-------------~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~ 224 (367) .+... +.-.+..-+.|.|.-.-+ +-+-.- ..+.++|+|||+.|+..+ ..|.|.-.+ + . T Consensus 753 v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~-~plf~~--R~FD~cIiDEASQI~lP~---~LgPL~~s~-k--F 823 (1100) T KOG1805 753 VEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGIN-HPLFVN--RQFDYCIIDEASQILLPL---CLGPLSFSN-K--F 823 (1100) T ss_pred HHHHHCCCCCCHHHHHHHHHHHCCCCEEEEECCCCC-CHHHHC--CCCCEEEECCCCCCCCCH---HHHHHHHCC-E--E T ss_conf 998712344545339999997289767999715788-655521--426789986511114342---121021123-5--8 Q ss_pred EEEECC Q ss_conf 998078 Q gi|254781187|r 225 IMTSNT 230 (367) Q Consensus 225 i~igNP 230 (367) ++.|-+ T Consensus 824 VLVGDh 829 (1100) T KOG1805 824 VLVGDH 829 (1100) T ss_pred EEECCC T ss_conf 996463 No 82 >PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated Probab=96.67 E-value=0.035 Score=32.39 Aligned_cols=74 Identities=23% Similarity=0.205 Sum_probs=48.0 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537999999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) .+|+-|.+|.+.|++.+..+. .+.|-||.|+|||..--.-+ +....+.+|++..+|..--.+.+.+++. T Consensus 245 E~R~~Q~~Ma~~V~~al~~~~--------~l~IEAgTGtGKTlaYLlPa---ia~~~~~~vVIST~T~~LQeQL~~kDlp 313 (820) T PRK07246 245 EERPKQEQFAQLVDEDYHDGV--------ASFIEAQTGIGKTYGYLLPL---LAQSDQNQIIVSVPTKLLQDQIMAGEVK 313 (820) T ss_pred CCCHHHHHHHHHHHHHHCCCC--------CEEEECCCCCCHHHHHHHHH---HHHCCCCEEEEEECCHHHHHHHHHHHHH T ss_conf 618899999999999980588--------38998899964799999999---9843798399990869999999997899 Q ss_pred HHHHH Q ss_conf 99986 Q gi|254781187|r 130 KWLSM 134 (367) Q Consensus 130 k~~~~ 134 (367) ...+. T Consensus 314 ~L~~~ 318 (820) T PRK07246 314 AIQEQ 318 (820) T ss_pred HHHHH T ss_conf 99998 No 83 >COG1205 Distinct helicase family with a unique C-terminal domain including a metal-binding cysteine cluster [General function prediction only] Probab=96.67 E-value=0.02 Score=33.88 Aligned_cols=74 Identities=15% Similarity=0.192 Sum_probs=64.6 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH Q ss_conf 42899999998888751245555541124776148867889999999999997089977999715379999999999999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) +-.-|.+.++.+.+.. .+.|.+|.|+|||-..-.-+++.++..+..+.+++-||-.=+.|-. ..+++ T Consensus 71 lY~HQ~~A~~~~~~G~------------~vvVtTgTgSGKTe~FllPIld~~l~~~~a~AL~lYPtnALa~DQ~-~rl~~ 137 (851) T COG1205 71 LYSHQVDALRLIREGR------------NVVVTTGTGSGKTESFLLPILDHLLRDPSARALLLYPTNALANDQA-ERLRE 137 (851) T ss_pred CCHHHHHHHHHHHCCC------------CEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHH-HHHHH T ss_conf 0077999999997799------------8899789988545898999999983086650899804377676699-99999 Q ss_pred HHHHCCC Q ss_conf 9986231 Q gi|254781187|r 131 WLSMLPH 137 (367) Q Consensus 131 ~~~~~~~ 137 (367) +.+.++. T Consensus 138 ~~~~~~~ 144 (851) T COG1205 138 LISDLPG 144 (851) T ss_pred HHHHCCC T ss_conf 9984787 No 84 >PRK12323 DNA polymerase III subunits gamma and tau; Provisional Probab=96.64 E-value=0.05 Score=31.41 Aligned_cols=140 Identities=17% Similarity=0.159 Sum_probs=73.6 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|.-+++.+..-+..+... +. ..-.+.||+|||+++-.++--+-|.+++...-+++.--.+- .. +.+|.. T Consensus 20 GQ~~v~~~l~na~~~~r~~-ha----ylf~G~rGvGKTt~ari~Ak~lnc~~~~~~~g~~~~pcg~C-~~-C~~i~~--- 89 (721) T PRK12323 20 GQEHVVRALTHALEQQRLH-HA----YLFTGTRGVGKTTLSRILAKSLNCTGPDGEGGITAQPCGQC-RA-CTEIDA--- 89 (721) T ss_pred CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC-HH-HHHHHC--- T ss_conf 8599999999999719975-44----75027998889899999999976899866789878878776-54-687756--- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..+..+. ++....++..-..+-..+.. .+.-..|.+. .+|+||....+...|.+++. T Consensus 90 ------------------g~~~d~~--EiDaas~~~v~~~r~l~~~~--~y~P~~~~~K-vyiiDevhmls~~afnalLK 146 (721) T PRK12323 90 ------------------GRFVDYI--EMDAASNRGVDEMAQLLDQA--VYAPTAGRFK-VYMIDEVHMLTNHAFNAMLK 146 (721) T ss_pred ------------------CCCCCEE--EEECCCCCCHHHHHHHHHHC--CCCCCCCCEE-EEEEECCCCCCHHHHHHHHH T ss_conf ------------------8987647--74367678889999999854--5588766446-99985400058999999998 Q ss_pred HHHCCCCCEEEEE Q ss_conf 7406988258999 Q gi|254781187|r 214 FFTELNPNRFWIM 226 (367) Q Consensus 214 ~Lt~~~~~~~~i~ 226 (367) +|-..=...+.++ T Consensus 147 tlEePP~hv~Fil 159 (721) T PRK12323 147 TLEEPPPHVKFIL 159 (721) T ss_pred HHCCCCCCEEEEE T ss_conf 4017975538999 No 85 >PRK12377 putative replication protein; Provisional Probab=96.63 E-value=0.051 Score=31.36 Aligned_cols=60 Identities=18% Similarity=0.217 Sum_probs=39.2 Q ss_pred CCCCCCCHHHHHHHHH---HHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 4366684289999999---88887512455555411247761488678899999999999970899779997 Q gi|254781187|r 45 LEHFSQPHRWQLEFME---AVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~---~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) ++++.--.+-|++++. .++++...+ .-.+...++-|+|||++++++..-.+- .|.+|+.+ T Consensus 73 f~ny~~~~~~~~~a~~~a~~~~~~F~~~-------~~NlIf~G~pGtGKTHLA~AIg~~a~~--~G~sVlF~ 135 (248) T PRK12377 73 FANYQVQNDGQRYALSQAKSIADELMTG-------CTNFVFSGKPGTGKNHLAAAIGNRLLA--KGRSVIVV 135 (248) T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHCC-------CCEEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEE T ss_conf 3456457878999999999999987318-------860899899998788999999999998--79969998 No 86 >COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair] Probab=96.62 E-value=0.023 Score=33.51 Aligned_cols=67 Identities=22% Similarity=0.143 Sum_probs=51.7 Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH Q ss_conf 6842899999998888751245555541124776148867889999999999997089977999715379999999 Q gi|254781187|r 49 SQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL 124 (367) Q Consensus 49 ~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l 124 (367) -.||+.|.++...|++-+.++. .+.|-||-|+|||...-..++-+..... .++++..+|..+....+ T Consensus 14 ~~~r~~Q~~~~~~v~~a~~~~~--------~~~iEapTGtGKTl~yL~~al~~~~~~~-~~viist~t~~lq~q~~ 80 (654) T COG1199 14 FEPRPEQREMAEAVAEALKGGE--------GLLIEAPTGTGKTLAYLLPALAYAREEG-KKVIISTRTKALQEQLL 80 (654) T ss_pred CCCCHHHHHHHHHHHHHHHCCC--------EEEEECCCCCCHHHHHHHHHHHHHHHCC-CEEEEECCCHHHHHHHH T ss_conf 9989899999999999981687--------1899889985175999999998677529-75999899576888987 No 87 >PRK07764 DNA polymerase III subunits gamma and tau; Validated Probab=96.62 E-value=0.025 Score=33.31 Aligned_cols=137 Identities=17% Similarity=0.100 Sum_probs=69.4 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH Q ss_conf 99999988887512455555411247761488678899999999999970899779997153799999999999999986 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM 134 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~ 134 (367) |..+.+.+..-++.+.. .|. ..-++.||+|||+++=+++--+.|.+....--|-. ...+ ..|.. .. T Consensus 20 Qe~v~~~L~~Ai~~gri-~HA----YLFsGprG~GKTt~ARilAkaLNC~~~~~~~PCg~------C~sC-~~i~~--g~ 85 (775) T PRK07764 20 QEHVTEPLSTALDSGRI-NHA----YLFSGPRGCGKTSSARILARSLNCAQGPTSTPCGV------CDSC-VALAP--GG 85 (775) T ss_pred CHHHHHHHHHHHHCCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC------CHHH-HHHHC--CC T ss_conf 59999999999981997-633----76237888788899999999966899999898888------7637-88863--89 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHH Q ss_conf 23121123333210001233322111134577612662101354455652101135862899975455998899998987 Q gi|254781187|r 135 LPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGF 214 (367) Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~ 214 (367) ..+-...++. ...+..+...+-.++ --.+.-..+.+. .+|+||+..++...|++++.+ T Consensus 86 ~~~~DviEiD-------------------AAS~~gVddiReL~e--~~~y~P~~~ryK-VyIIDEaHmls~~afNALLKt 143 (775) T PRK07764 86 PGSLDVVEID-------------------AASHGGVDDARELRE--RAFFAPAQSRYR-IFIIDEAHMVTTAGFNALLKI 143 (775) T ss_pred CCCCCEEEEC-------------------CCCCCCHHHHHHHHH--HCCCCCCCCCEE-EEEEECHHHHCHHHHHHHHHH T ss_conf 8888668731-------------------565568899999998--547687678635-999853544079999999886 Q ss_pred HHCCCCCEEEEEE Q ss_conf 4069882589998 Q gi|254781187|r 215 FTELNPNRFWIMT 227 (367) Q Consensus 215 Lt~~~~~~~~i~i 227 (367) |-..-...++|+. T Consensus 144 LEEPP~hvvFIla 156 (775) T PRK07764 144 VEEPPEHLIFIFA 156 (775) T ss_pred HCCCCCCEEEEEE T ss_conf 2278646279995 No 88 >PRK08691 DNA polymerase III subunits gamma and tau; Validated Probab=96.61 E-value=0.052 Score=31.30 Aligned_cols=134 Identities=16% Similarity=0.126 Sum_probs=68.8 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|.-+++.+..-+..|.. .+. ..-.+.||+|||+++-.++.-+-|..+..---|-. ... +.+|.. T Consensus 20 GQ~~v~~~L~nal~~~rl-~ha----ylf~G~rGvGKTt~Ari~Ak~lNC~~~~~~~pCg~------C~~-C~~i~~--- 84 (704) T PRK08691 20 GQEHVVKALQNALDEGRL-HHA----YLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGV------CQS-CTQIDA--- 84 (704) T ss_pred CCHHHHHHHHHHHHHCCC-CCE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC------CHH-HHHHHC--- T ss_conf 869999999999981997-523----75027898788899999999967999999997877------776-787855--- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) . .+..+...+ ...+...-..+-..+. -.+.-..|.+. .+|+||+...+...|.+++. T Consensus 85 -g-----------------~~~D~~EiD--aAs~~~vdd~R~l~~~--~~y~P~~~~yK-VyiiDEvhmLs~~afNAlLK 141 (704) T PRK08691 85 -G-----------------RYVDLLEID--AASNTGIDNIREVLEN--AQYAPTAGKYK-VYIIDEVHMLSKSAFNAMLK 141 (704) T ss_pred -C-----------------CCCCEEEEE--CCCCCCHHHHHHHHHH--CCCCCCCCCEE-EEEEECHHHCCHHHHHHHHH T ss_conf -8-----------------998747742--4544588999999985--34688678535-99983154438999999998 Q ss_pred HHHCCCCCEEEE Q ss_conf 740698825899 Q gi|254781187|r 214 FFTELNPNRFWI 225 (367) Q Consensus 214 ~Lt~~~~~~~~i 225 (367) +|-.+=...+.+ T Consensus 142 tLEEPP~~v~Fi 153 (704) T PRK08691 142 TLEEPPEHVKFI 153 (704) T ss_pred HHCCCCCCEEEE T ss_conf 614797560899 No 89 >COG1201 Lhr Lhr-like helicases [General function prediction only] Probab=96.58 E-value=0.023 Score=33.53 Aligned_cols=78 Identities=15% Similarity=0.071 Sum_probs=60.6 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC------CCEEEEECCCHHH Q ss_conf 3666842899999998888751245555541124776148867889999999999997089------9779997153799 Q gi|254781187|r 46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP------GMSIICIANSETQ 119 (367) Q Consensus 46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~------~~~v~~~A~t~~Q 119 (367) +.|..|++-|+.++..|.+.. .+.|.|+.|+|||-.+=.-++-.+.... +..+++++|-..- T Consensus 18 ~~~~~~t~~Q~~a~~~i~~G~------------nvLiiAPTGsGKTeAAfLpil~~l~~~~~~~~~~~i~~lYIsPLkAL 85 (814) T COG1201 18 RKFTSLTPPQRYAIPEIHSGE------------NVLIIAPTGSGKTEAAFLPVINELLSLGKGKLEDGIYALYISPLKAL 85 (814) T ss_pred HHCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHH T ss_conf 850899878999999985898------------46998689997379999999999986068888885699995707888 Q ss_pred HHHHHHHHHHHHHHHCC Q ss_conf 99999999999998623 Q gi|254781187|r 120 LKNTLWAEVSKWLSMLP 136 (367) Q Consensus 120 ~~~~lw~ei~k~~~~~~ 136 (367) .+|+. .-+..|.+.+- T Consensus 86 n~Di~-~rL~~~~~~~G 101 (814) T COG1201 86 NNDIR-RRLEEPLRELG 101 (814) T ss_pred HHHHH-HHHHHHHHHCC T ss_conf 78999-99999999759 No 90 >KOG0952 consensus Probab=96.55 E-value=0.023 Score=33.43 Aligned_cols=139 Identities=19% Similarity=0.189 Sum_probs=74.6 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH--------CCCCEEEEECCCHHHHHHHH Q ss_conf 8999999988887512455555411247761488678899999999999970--------89977999715379999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST--------RPGMSIICIANSETQLKNTL 124 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~--------~~~~~v~~~A~t~~Q~~~~l 124 (367) .-|-++....+.- +. +..|+|+.|.|||.++-.-+|-.+-. ..+.||+++||...-+.++ T Consensus 113 ~iQS~vFp~aY~S--------ne---NMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPmKALa~Em- 180 (1230) T KOG0952 113 RIQSEVFPVAYKS--------NE---NMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPMKALAAEM- 180 (1230) T ss_pred HHHHHHHHHHHCC--------CC---CEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECHHHHHHHH- T ss_conf 7787741465147--------88---77997778997167899999999985014554346871399992568899999- Q ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC Q ss_conf 999999998623121123333210001233322111134-5776126621013544556521011358628999754559 Q gi|254781187|r 125 WAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMG-IDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT 203 (367) Q Consensus 125 w~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI 203 (367) +.+|-.++--... .+....--+.....+...+++. ..++.|=+..+-+... .++.+. .-|+|+||-.-+ T Consensus 181 ---~~~~~kkl~~~gi-~v~ELTGD~ql~~tei~~tqiiVTTPEKwDvvTRk~~~d--~~l~~~----V~LviIDEVHlL 250 (1230) T KOG0952 181 ---VDKFSKKLAPLGI-SVRELTGDTQLTKTEIADTQIIVTTPEKWDVVTRKSVGD--SALFSL----VRLVIIDEVHLL 250 (1230) T ss_pred ---HHHHHHHCCCCCC-EEEEECCCCHHHHHHHHHCCEEEECCCCEEEEEEEECCC--HHHHHH----EEEEEEEEEHHH T ss_conf ---9998664242462-588841754566778774377970634000466541262--655554----204885300121 Q ss_pred CHH---HHHHHHH Q ss_conf 988---9999898 Q gi|254781187|r 204 PDI---INKSILG 213 (367) Q Consensus 204 ~d~---i~e~i~g 213 (367) .|+ +.|+|-. T Consensus 251 hd~RGpvlEtiVa 263 (1230) T KOG0952 251 HDDRGPVLETIVA 263 (1230) T ss_pred CCCCCCHHHHHHH T ss_conf 5766406999999 No 91 >PRK10917 ATP-dependent DNA helicase RecG; Provisional Probab=96.50 E-value=0.061 Score=30.86 Aligned_cols=83 Identities=19% Similarity=0.241 Sum_probs=62.7 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 88443666842899999998888751245555541124776148867889999999999997089977999715379999 Q gi|254781187|r 42 GKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 42 ~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) .+|. .++.-|.+++++|...+..+. .|.|+ +.+-=|+|||.++...++- ...-|..++++|||+==++ T Consensus 253 ~LPF----~LT~~Q~~~~~ei~~dl~~~~-----~m~rl-lqGDVGsGKT~va~~a~~~--~~~~g~q~a~maPTeiLa~ 320 (677) T PRK10917 253 SLPF----ELTGAQKRVVAEILADLASPK-----PMNRL-LQGDVGSGKTVVAALAALA--AIEAGYQAALMAPTEILAE 320 (677) T ss_pred HCCC----CCCHHHHHHHHHHHHHHCCCC-----CCHHH-HCCCCCCCHHHHHHHHHHH--HHHHCCEEEEECCCHHHHH T ss_conf 0999----889889999999998765995-----42777-3287678889999999999--9981994899876799999 Q ss_pred HHHHHHHHHHHHHCCC Q ss_conf 9999999999986231 Q gi|254781187|r 122 NTLWAEVSKWLSMLPH 137 (367) Q Consensus 122 ~~lw~ei~k~~~~~~~ 137 (367) + -+..+++++..+.. T Consensus 321 Q-h~~~~~~~~~~~~i 335 (677) T PRK10917 321 Q-HYRNLKKWLEPLGI 335 (677) T ss_pred H-HHHHHHHHHHHCCC T ss_conf 9-99999987763498 No 92 >COG1110 Reverse gyrase [DNA replication, recombination, and repair] Probab=96.50 E-value=0.018 Score=34.07 Aligned_cols=109 Identities=22% Similarity=0.225 Sum_probs=64.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 47761488678899999999999970899779997153799999999999999986231211233332100012333221 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL 158 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (367) -.|+.|+.|+|||+..+.+.+|++.-. .+++++-||..-+++.. ..++++.+..-.. ...+. |+...- T Consensus 99 SFaiiAPTGvGKTTfg~~~sl~~a~kg--kr~yii~PT~~Lv~Q~~-~kl~~~~e~~~~~--------~~~~~-yh~~l~ 166 (1187) T COG1110 99 SFAIIAPTGVGKTTFGLLMSLYLAKKG--KRVYIIVPTTTLVRQVY-ERLKKFAEDAGSL--------DVLVV-YHSALP 166 (1187) T ss_pred CEEEECCCCCCHHHHHHHHHHHHHHCC--CEEEEEECCHHHHHHHH-HHHHHHHHHCCCC--------CEEEE-ECCCCC T ss_conf 448982788765479999999987558--74999966789999999-9999988653785--------24665-312366 Q ss_pred -----CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC Q ss_conf -----111345776126621013544556521011358628999754 Q gi|254781187|r 159 -----EQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA 200 (367) Q Consensus 159 -----~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEA 200 (367) ..--.+.+|.+-+ -.+.+..-+-++.-++.-++.|+++|-. T Consensus 167 ~~ekee~le~i~~gdfdI-litTs~FL~k~~e~L~~~kFdfifVDDV 212 (1187) T COG1110 167 TKEKEEALERIESGDFDI-LITTSQFLSKRFEELSKLKFDFIFVDDV 212 (1187) T ss_pred HHHHHHHHHHHHCCCCCE-EEEEHHHHHHHHHHHCCCCCCEEEECCH T ss_conf 577999999986599639-9974787886699840457778998047 No 93 >PRK12402 replication factor C small subunit 2; Reviewed Probab=96.49 E-value=0.063 Score=30.81 Aligned_cols=35 Identities=9% Similarity=0.154 Sum_probs=26.5 Q ss_pred CEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEE Q ss_conf 28999754559988999989874069882589998 Q gi|254781187|r 193 MAVFNDEASGTPDIINKSILGFFTELNPNRFWIMT 227 (367) Q Consensus 193 ~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~i 227 (367) -++|+|||..+......++..+|-........+++ T Consensus 127 KiiIlDEad~lt~~Aq~aLlk~lEe~~~~~~fIl~ 161 (337) T PRK12402 127 KLILFDNAEALREDAQQALRRIMERYSETCRFIFS 161 (337) T ss_pred EEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEE T ss_conf 49997071317999999999887408876699872 No 94 >TIGR02397 dnaX_nterm DNA polymerase III, subunits gamma and tau; InterPro: IPR012763 This entry represents the well-conserved first N-terminal domain of DnaX, approx. 365 aa. The full-length product of the dnaX gene in Escherichia coli encodes the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the extreme thermophile Thermus thermophilis.; GO: 0003887 DNA-directed DNA polymerase activity, 0005524 ATP binding, 0006260 DNA replication, 0009360 DNA polymerase III complex. Probab=96.44 E-value=0.067 Score=30.65 Aligned_cols=119 Identities=13% Similarity=0.101 Sum_probs=72.2 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC----C--EEEEECCCHHHHHHHH--- Q ss_conf 999999988887512455555411247761488678899999999999970899----7--7999715379999999--- Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG----M--SIICIANSETQLKNTL--- 124 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~----~--~v~~~A~t~~Q~~~~l--- 124 (367) .|.=+.+.+..-+..+.- .|.+ .=++.||+|||+++=.++-=+=|. +. | --.|.+-+..+.-|++ T Consensus 18 GQ~~iv~tL~NAi~~~ri-~HAY----LF~GpRGtGKTS~ARIfAKaLNC~-~~~~~PCn~C~~C~~i~~g~~~DviEiD 91 (363) T TIGR02397 18 GQEHIVKTLKNAIKNGRI-AHAY----LFSGPRGTGKTSIARIFAKALNCQ-GPDGEPCNECESCKEINSGSSLDVIEID 91 (363) T ss_pred CCHHHHHHHHHHHHHCCC-CCEE----EECCCCCCCHHHHHHHHHHHHCCC-CCCCCCCCCCCHHHHHHCCCCCCEEEEC T ss_conf 517999999999971896-6234----502859976355899999986588-7877877775022776528986668864 Q ss_pred ------H---HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEE Q ss_conf ------9---9999999862312112333321000123332211113457761266210135445565210113586289 Q gi|254781187|r 125 ------W---AEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAV 195 (367) Q Consensus 125 ------w---~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ 195 (367) - ++|..-+. +.-..+.+.+ + T Consensus 92 AASN~gVD~IR~l~e~v~--------------------------------------------------y~P~~~kYKv-Y 120 (363) T TIGR02397 92 AASNNGVDDIRELRENVK--------------------------------------------------YAPSKGKYKV-Y 120 (363) T ss_pred CCCCCCHHHHHHHHHHHC--------------------------------------------------CCCCCCCCCE-E T ss_conf 865687889999987303--------------------------------------------------6875544335-8 Q ss_pred EEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECC Q ss_conf 99754559988999989874069882589998078 Q gi|254781187|r 196 FNDEASGTPDIINKSILGFFTELNPNRFWIMTSNT 230 (367) Q Consensus 196 ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP 230 (367) |+||+...+...|.|++-||=.+=...+.+ +-|| T Consensus 121 IIDEVHMLS~~AFNALLKTLEEPP~hV~FI-lATT 154 (363) T TIGR02397 121 IIDEVHMLSKSAFNALLKTLEEPPEHVVFI-LATT 154 (363) T ss_pred EEECCCCCCHHHHHHHHHHHCCCCCCEEEE-EECC T ss_conf 873230286568999876522798762888-7348 No 95 >KOG0338 consensus Probab=96.33 E-value=0.012 Score=35.25 Aligned_cols=197 Identities=14% Similarity=0.103 Sum_probs=94.6 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC----CEEEEECCCHHH Q ss_conf 4436668428999999988887512455555411247761488678899999999999970899----779997153799 Q gi|254781187|r 44 PLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG----MSIICIANSETQ 119 (367) Q Consensus 44 ~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~----~~v~~~A~t~~Q 119 (367) ...+|..|++.|...+- -.+.. . -+.-+|..|+|||+..+.=+|-.|+.+|- .+|+|.-||..- T Consensus 197 ~~lGy~~PTpIQ~a~IP---vallg---k------DIca~A~TGsGKTAAF~lPiLERLlYrPk~~~~TRVLVL~PTREL 264 (691) T KOG0338 197 STLGYKKPTPIQVATIP---VALLG---K------DICACAATGSGKTAAFALPILERLLYRPKKVAATRVLVLVPTREL 264 (691) T ss_pred HHCCCCCCCCHHHHCCC---HHHHC---C------HHHHEECCCCCCHHHHHHHHHHHHHCCCCCCCCEEEEEEECCHHH T ss_conf 74387888740331012---77522---2------256401146871145678899998527356761269998350899 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEEC Q ss_conf 99999999999998623121123333210001233322111134577612662101354455652101135862899975 Q gi|254781187|r 120 LKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDE 199 (367) Q Consensus 120 ~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDE 199 (367) +-++ ....++.....-...-+...-+.++.. ...++..+...+++--..-. ---|..+++-++.-.+|+|| T Consensus 265 aiQv-~sV~~qlaqFt~I~~~L~vGGL~lk~Q-------E~~LRs~PDIVIATPGRlID-HlrNs~sf~ldsiEVLvlDE 335 (691) T KOG0338 265 AIQV-HSVTKQLAQFTDITVGLAVGGLDLKAQ-------EAVLRSRPDIVIATPGRLID-HLRNSPSFNLDSIEVLVLDE 335 (691) T ss_pred HHHH-HHHHHHHHHHCCCEEEEEECCCCHHHH-------HHHHHHCCCEEEECCHHHHH-HHCCCCCCCCCCEEEEEECH T ss_conf 9999-999999876604024445247457889-------99983089879946505888-75158876534325777333 Q ss_pred CCCCC-----HHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCC-EEEEEEC-CCCCCCCCHHHHH Q ss_conf 45599-----8899998987406988258999807899987688754112235-0467523-3328888988999 Q gi|254781187|r 200 ASGTP-----DIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLED-WKRYQID-TRTVEGIDSGFHE 267 (367) Q Consensus 200 AsgI~-----d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~-w~~~~~~-~~d~p~~~~~~i~ 267 (367) |.-.= +.+-|.|. |+..+...+ +||- | .+.-.-++-.--.+. ...+--+ -...|.+.++|+. T Consensus 336 ADRMLeegFademnEii~--lcpk~RQTm--LFSA-T-MteeVkdL~slSL~kPvrifvd~~~~~a~~LtQEFiR 404 (691) T KOG0338 336 ADRMLEEGFADEMNEIIR--LCPKNRQTM--LFSA-T-MTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQEFIR 404 (691) T ss_pred HHHHHHHHHHHHHHHHHH--HCCCCCCCE--EEHH-H-HHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHE T ss_conf 888999999999999998--551023001--2112-2-5788999997551798589857865444044477810 No 96 >PRK08699 DNA polymerase III subunit delta'; Validated Probab=96.33 E-value=0.071 Score=30.47 Aligned_cols=127 Identities=15% Similarity=0.135 Sum_probs=61.4 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEEEC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 4776148867889999999999997089977-99971-537999999999999999862312112333321000123332 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMS-IICIA-NSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAE 156 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~-v~~~A-~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 (367) -....+..|+||..++-.++-+++|..|... .-|-. ++=+.... ..-|+-++....... .. .. T Consensus 23 A~L~~Gp~G~Gk~~~A~~~A~~llC~~~~~~~~~Cg~C~sC~~~~~----------g~HPD~~~i~p~~~~--~~---~g 87 (325) T PRK08699 23 AWLFVGKKGTGKTAFARFAAKALLCETPAPGCKPCGECMSCHLFGQ----------GSHPDFYEITPLADE--PE---NG 87 (325) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHC----------CCCCCEEEEECCCCC--CC---CC T ss_conf 7975799997899999999999828999888998988888999865----------999996885134453--00---16 Q ss_pred CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC Q ss_conf 2111134577612662101354455652101135862899975455998899998987406988258999807 Q gi|254781187|r 157 LLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSN 229 (367) Q Consensus 157 ~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igN 229 (367) .....++.+.- +-.... -+.....|.+ -.+|+|+|.......-.++..+|-.+-..++.+++++ T Consensus 88 ~~~~~I~idqi------R~l~~~--~~~~~~~~~~-kV~ii~~ae~mn~~aaNaLLK~LEEPp~~~~fiL~t~ 151 (325) T PRK08699 88 RKLLQIKIDAV------REIIDN--VYLTSVRGGL-RVILIHPAESMNVQAANSLLKVLEEPPPQVVFLLVSH 151 (325) T ss_pred CCCCCCCHHHH------HHHHHH--HCCCCCCCCC-EEEEECCHHHHCHHHHHHHHHHHCCCCCCEEEEEEEC T ss_conf 65566769999------999999--7108656894-6999857777589999999998417888848999879 No 97 >KOG0335 consensus Probab=96.30 E-value=0.038 Score=32.17 Aligned_cols=167 Identities=13% Similarity=-0.020 Sum_probs=85.4 Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC-C----------CCEEE Q ss_conf 844366684289999999888875124555554112477614886788999999999999708-9----------97799 Q gi|254781187|r 43 KPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTR-P----------GMSII 111 (367) Q Consensus 43 ~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~-~----------~~~v~ 111 (367) ....++..|++.|.-.+-.|.+. .-+.++|-.|+|||...-.=++=.+.-. + ...++ T Consensus 89 ~~~~~~~~ptpvQk~sip~i~~G------------rdlmacAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~P~~l 156 (482) T KOG0335 89 IKRSGYTKPTPVQKYSIPIISGG------------RDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVYPRAL 156 (482) T ss_pred CCCCCCCCCCCCEECCCCEEECC------------CCEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEE T ss_conf 23356668986156042244258------------842788257885137888889999986486566656778897259 Q ss_pred EECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCC Q ss_conf 97153799999999999999986231211233332100012333221111345776126621013544556521011358 Q gi|254781187|r 112 CIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTH 191 (367) Q Consensus 112 ~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~ 191 (367) +.|||..-+. -++.|.+|....+-.+.-.-+. .............+.-++.+..-+...-..-.-+--.+ T Consensus 157 IlapTReL~~-Qi~nea~k~~~~s~~~~~~~yg---------g~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~g~i~l~~ 226 (482) T KOG0335 157 ILAPTRELVD-QIYNEARKFSYLSGMKSVVVYG---------GTDLGAQLRFIKRGCDILVATPGRLKDLIERGKISLDN 226 (482) T ss_pred EEECCHHHHH-HHHHHHHHHCCCCCCEEEEEEC---------CCCHHHHHHHHCCCCCEEEECCCHHHHHHHCCEEEHHH T ss_conf 9817378766-7888887640221220330057---------84454422333257557885575056455415112623 Q ss_pred CCEEEEECCC-------CCCHHHHHHHHHHHHCCCCCEEEEEEECCCCC Q ss_conf 6289997545-------59988999989874069882589998078999 Q gi|254781187|r 192 GMAVFNDEAS-------GTPDIINKSILGFFTELNPNRFWIMTSNTRRL 233 (367) Q Consensus 192 ~~l~ivDEAs-------gI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~ 233 (367) +-++++|||- |.|+.=+-+....+...+.+.- ++|+ ++-+ T Consensus 227 ~k~~vLDEADrMlD~mgF~p~Ir~Iv~~~~~~~~~~~qt-~mFS-Atfp 273 (482) T KOG0335 227 CKFLVLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQT-LLFS-ATFP 273 (482) T ss_pred CCEEEECCHHHHHHHCCCCHHHHHHHCCCCCCCCCCEEE-EEEE-CCCC T ss_conf 858995236776663266620799962558887466137-8873-5577 No 98 >COG3972 Superfamily I DNA and RNA helicases [General function prediction only] Probab=96.29 E-value=0.018 Score=34.08 Aligned_cols=134 Identities=15% Similarity=0.120 Sum_probs=66.7 Q ss_pred EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH---HHHHHHHHHHHH-H-------HHHHCCCCCCCCCCCCCCCC Q ss_conf 614886788999999999999708997799971537---999999999999-9-------99862312112333321000 Q gi|254781187|r 82 ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE---TQLKNTLWAEVS-K-------WLSMLPHRHWFEMQSLSLHP 150 (367) Q Consensus 82 v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~---~Q~~~~lw~ei~-k-------~~~~~~~~~~~~~~~~~~~~ 150 (367) |++=-|+|||.+.|..+.....++|+.+|++|--|. +|.|+.+ ++.- . |-+++....|...+....+- T Consensus 181 IrGLAGSGKT~~La~Kaa~lh~knPd~~I~~Tfftk~L~s~~r~lv-~~F~f~~~e~~pdW~~~l~~h~wgG~t~~g~y~ 259 (660) T COG3972 181 IRGLAGSGKTELLAHKAAELHSKNPDSRIAFTFFTKILASTMRTLV-PEFFFMRVEKQPDWGTKLFCHNWGGLTKEGFYG 259 (660) T ss_pred HHCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEEHHHHHHHHHHHH-HHHHHHHHHCCCCCCCEEEEECCCCCCCCCCHH T ss_conf 2002478730298877789744799863899866678889999999-999998862488724268884357878886038 Q ss_pred -CCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCC-CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEE Q ss_conf -123332211113457761266210135445565210113-58628999754559988999989874069882589 Q gi|254781187|r 151 -SGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHN-THGMAVFNDEASGTPDIINKSILGFFTELNPNRFW 224 (367) Q Consensus 151 -~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~-~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~ 224 (367) ..+...+.+......+ ..++..-.|.++...+ .....+++||++..|+..++-..-..+ .-+++.| T Consensus 260 ~~~~~~~~~~~~fsg~g-------~~F~~aC~eli~~~~~~~~yD~ilIDE~QDFP~~F~~Lcf~~tk-d~Krlvy 327 (660) T COG3972 260 MYRYICHYYEIPFSGFG-------NGFDAACKELIADINNKKAYDYILIDESQDFPQSFIDLCFMVTK-DKKRLVY 327 (660) T ss_pred HHHHHHCCCCCCCCCCC-------CCHHHHHHHHHHHHHCCCCCCEEEECCCCCCCHHHHHHHHHHHC-CCCEEEE T ss_conf 89998426654547877-------40679999999864256423179942455477899999999824-7543898 No 99 >PRK07003 DNA polymerase III subunits gamma and tau; Validated Probab=96.25 E-value=0.085 Score=29.98 Aligned_cols=135 Identities=17% Similarity=0.159 Sum_probs=66.3 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|.-+++.+..-+..+... +. ..-.+.||+|||+++-.++--+-|......--| . + ... +.+|.. T Consensus 20 GQ~~v~~~l~nal~~~rl~-ha----ylf~G~rGvGKTt~aRi~Ak~lnC~~~~~~~pc----g-~-C~~-C~~i~~--- 84 (816) T PRK07003 20 GQEHVVRALTHALDGGRLH-HA----YLFTGTRGVGKTTLSRIFAKALNCETGVTSQPC----G-V-CRA-CREIDE--- 84 (816) T ss_pred CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCC----C-C-CHH-HHHHHC--- T ss_conf 8499999999999709863-14----751178988888999999998678999998978----7-7-555-787755--- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..+..+.+.+- ..+...-..+-..+.. .+.-..|.+ -.+|+||....+...|.+++. T Consensus 85 ------------------g~~~d~iEiDa--AS~~~vd~~r~l~~~~--~y~p~~~r~-KvyiiDEvHmls~~afnalLK 141 (816) T PRK07003 85 ------------------GRFVDYVEMDA--ASNRGVDEMAALLERA--VYAPVDARF-KVYMIDEVHMLTNHAFNAMLK 141 (816) T ss_pred ------------------CCCCCEEEEEC--CCCCCHHHHHHHHHHC--CCCCCCCCE-EEEEEECHHHCCHHHHHHHHH T ss_conf ------------------88775478635--5435768999999862--247866744-799984154339999999998 Q ss_pred HHHCCCCCEEEEE Q ss_conf 7406988258999 Q gi|254781187|r 214 FFTELNPNRFWIM 226 (367) Q Consensus 214 ~Lt~~~~~~~~i~ 226 (367) +|-..=...+.++ T Consensus 142 tlEepP~hv~Fil 154 (816) T PRK07003 142 TLEEPPPHVKFIL 154 (816) T ss_pred HHCCCCCCEEEEE T ss_conf 4037986648999 No 100 >TIGR00345 arsA arsenite-activated ATPase (arsA); InterPro: IPR003348 This ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell. In Escherichia coli an anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773. This ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance . The ArsA and ArsB proteins form a membrane-bound pump that functions as an oxyanion-translocating ATPase. The ArsC protein is an arsenate reductase that reduces arsenate to arsenite, which is subsequently pumped out of the cell .; GO: 0005524 ATP binding, 0006820 anion transport, 0016020 membrane. Probab=96.24 E-value=0.0057 Score=37.21 Aligned_cols=44 Identities=25% Similarity=0.489 Sum_probs=34.8 Q ss_pred CCCHHHHHHHHHHHHHHHCCCCEEEEECCC-HHHHHHHHHHHHHH Q ss_conf 678899999999999970899779997153-79999999999999 Q gi|254781187|r 87 GIGKTTLNAWMMLWLISTRPGMSIICIANS-ETQLKNTLWAEVSK 130 (367) Q Consensus 87 g~GKS~~~a~~~lw~~~~~~~~~v~~~A~t-~~Q~~~~lw~ei~k 130 (367) |||||+++|+.++|++--.||.|+++++.- .+.+.|++=.|+.+ T Consensus 7 GVGKTt~SaAtA~~lAe~qPGkkvLl~STDPAHsL~D~F~~e~G~ 51 (330) T TIGR00345 7 GVGKTTISAATAIRLAEQQPGKKVLLVSTDPAHSLSDVFEQELGH 51 (330) T ss_pred CCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHCC T ss_conf 823888999999999851899779998408600278861132177 No 101 >PRK11057 ATP-dependent DNA helicase RecQ; Provisional Probab=96.13 E-value=0.021 Score=33.75 Aligned_cols=62 Identities=16% Similarity=0.102 Sum_probs=44.0 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH Q ss_conf 3666842899999998888751245555541124776148867889999999999997089977999715379999999 Q gi|254781187|r 46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL 124 (367) Q Consensus 46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l 124 (367) .+++..++-|.+++.++-..- -+.+..+.|.|||.+--.=++- . +..++|++|..+-++|-+ T Consensus 21 FG~~~Fr~~Q~e~i~~~l~g~------------D~l~~mpTG~GKSlcyQlPal~----~-~g~tiVisPLisLm~DQv 82 (607) T PRK11057 21 FGYQQFRPGQEEIIDTVLSGR------------DCLVVMPTGGGKSLCYQIPALV----L-DGLTLVVSPLISLMKDQV 82 (607) T ss_pred CCCCCCCHHHHHHHHHHHCCC------------CEEEECCCCCHHHHHHHHHHHH----C-CCCEEEECCHHHHHHHHH T ss_conf 698434576999999998699------------8899878995597999999987----7-998899868799999999 No 102 >PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated Probab=96.12 E-value=0.054 Score=31.21 Aligned_cols=68 Identities=15% Similarity=0.027 Sum_probs=43.0 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHH Q ss_conf 428999999988887512455555411247761488678899999999999970899-77999715379 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSET 118 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~ 118 (367) +..-...++..+.+.+.-..........-+++.++-|+|||+.+|=++..+.+.+.. ...++|+.|++ T Consensus 184 ~~~~~~~l~~~L~~~l~~~~~~~~~~~~vvalVGPTGVGKTTTiAKLAA~~~l~~~~~kV~lIT~DtyR 252 (412) T PRK05703 184 PREAWRYLLELLANMLPTRVEDILEQGGVVALVGPTGVGKTTTLAKLAARYALEEGKDKVALITLDTYR 252 (412) T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCC T ss_conf 799999999999975788876654567369998888875676999999999997299817999837677 No 103 >PRK13767 ATP-dependent helicase; Provisional Probab=96.03 E-value=0.043 Score=31.82 Aligned_cols=89 Identities=15% Similarity=0.066 Sum_probs=56.5 Q ss_pred CCCCCHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCC Q ss_conf 57233789999752320125988885543014668884436668428999999988887512455555411247761488 Q gi|254781187|r 7 TDQKLEQELHEMLMHAECVLSFKNFVMRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGR 86 (367) Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgr 86 (367) |..+++++.++++ +|.- .- |= -..|..|++.|+++...|.+.- .+.|.|+. T Consensus 6 ~~~~~~~~~~~~l-------~p~v--~~---wf-----~~~~~~p~~~Q~~a~~~i~~G~------------~~Li~ApT 56 (878) T PRK13767 6 TKEYSDEEILSLL-------HPYV--AE---WF-----KRKFGTFTPPQRYAIPLIHEGK------------NVLISSPT 56 (878) T ss_pred HCCCCHHHHHHHC-------CHHH--HH---HH-----HHCCCCCCHHHHHHHHHHHCCC------------CEEEECCC T ss_conf 1026757677627-------9899--99---99-----8537999989999999996799------------88998999 Q ss_pred CCCHHHHHHHHHHHHHHH-------CCCCEEEEECCCHHHHHHHH Q ss_conf 678899999999999970-------89977999715379999999 Q gi|254781187|r 87 GIGKTTLNAWMMLWLIST-------RPGMSIICIANSETQLKNTL 124 (367) Q Consensus 87 g~GKS~~~a~~~lw~~~~-------~~~~~v~~~A~t~~Q~~~~l 124 (367) |+|||..+-.-++-.+.. ..+..+++++|...=++|+. T Consensus 57 GsGKTlAaflp~l~~l~~~~~~~~~~~~~~~LyIsPLkAL~~D~~ 101 (878) T PRK13767 57 GSGKTLAAFLGIIDELFRLAEEGELEDSVYCIYVSPLRALNNDIH 101 (878) T ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCHHHHHHHHH T ss_conf 813999999999999985000367788728999684798899999 No 104 >TIGR03499 FlhF flagellar biosynthetic protein FlhF. Probab=95.99 E-value=0.037 Score=32.18 Aligned_cols=70 Identities=13% Similarity=0.013 Sum_probs=45.3 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCC--CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEEECCCHHH Q ss_conf 8428999999988887512455555--41124776148867889999999999997089977-9997153799 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSN--PTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMS-IICIANSETQ 119 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~--~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~-v~~~A~t~~Q 119 (367) .++.....+...+++.+........ ....-+++.++.|+|||+.+|-++..+...+...+ .++|.-|++- T Consensus 165 ~~~~~~~~l~~~L~~~i~~~~~~~~~~~~~~vi~lvGPTGVGKTTTiAKLAa~~~l~~~~~~V~lIT~DtyRi 237 (282) T TIGR03499 165 DAESAWRWLREALENMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLAKLAARFVLEHGKKKVALITTDTYRI 237 (282) T ss_pred CHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCH T ss_conf 9789999999999964777887655445672799977888757889999999999973899679998077767 No 105 >TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ; InterPro: IPR013364 Proteins in this entry are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase (IPR013363 from INTERPRO) of a type-IV secretion-like system of the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii.. Probab=95.98 E-value=0.0086 Score=36.08 Aligned_cols=35 Identities=29% Similarity=0.335 Sum_probs=32.1 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 77614886788999999999999708997799971 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) -.|++-.|+|||+++|.+=-+.+-|+|+.||+++. T Consensus 152 GLiCG~TGSGKSTl~AaiY~~~l~t~pdRKivT~E 186 (374) T TIGR02525 152 GLICGETGSGKSTLAAAIYRHCLETYPDRKIVTYE 186 (374) T ss_pred EEECCCCCCCHHHHHHHHHHHHCCCCCCCEEEEEE T ss_conf 02217789728999999999850748897079865 No 106 >PRK06872 DNA polymerase III subunits gamma and tau; Provisional Probab=95.98 E-value=0.067 Score=30.62 Aligned_cols=135 Identities=15% Similarity=0.140 Sum_probs=70.6 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|.-+++.+..-+..+... +. ....+.||+|||+++-.++--+-|......--|-. ... +.+|.. T Consensus 20 gq~~v~~~l~~a~~~~r~~-ha----ylf~g~rg~gktt~ari~ak~lnc~~~~~~~pcg~------c~~-c~~i~~--- 84 (696) T PRK06872 20 GQEHILTALSNGLKENRLH-HA----YLFSGTRGVGKTSIARLFAKGLNCVHGVTATPCGE------CEN-CKAIEE--- 84 (696) T ss_pred CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC------CHH-HHHHHC--- T ss_conf 8599999999999719863-04----75117898888899999999867899999997888------622-576744--- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..+..+.+ +....++..-..+-..+. -.+.-.+|.+. .+|+||....+...|.+++. T Consensus 85 ------------------g~~~d~~e--idaas~~~v~~~r~l~~~--~~~~p~~~~~k-vy~idevhmls~~~fnallk 141 (696) T PRK06872 85 ------------------GNFIDLIE--IDAASRTKVEDTRELLDN--VQYKPVVGRFK-VYLIDEVHMLSRHSFNALLK 141 (696) T ss_pred ------------------CCCCCEEE--EECCCCCCHHHHHHHHHH--CCCCCCCCCEE-EEEEEHHHHCCHHHHHHHHH T ss_conf ------------------78775467--505655788999999984--54577677547-99970054438999999987 Q ss_pred HHHCCCCCEEEEE Q ss_conf 7406988258999 Q gi|254781187|r 214 FFTELNPNRFWIM 226 (367) Q Consensus 214 ~Lt~~~~~~~~i~ 226 (367) +|-..=...+.++ T Consensus 142 tleepp~~v~f~l 154 (696) T PRK06872 142 TLEEPPEYVKFLL 154 (696) T ss_pred HHCCCCCCEEEEE T ss_conf 5027975448998 No 107 >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=95.98 E-value=0.12 Score=29.16 Aligned_cols=48 Identities=29% Similarity=0.259 Sum_probs=29.1 Q ss_pred HHHHHHHHHHHHHHCC-CCCCCCC--EEEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 9999999888875124-5555541--1247761488678899999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSN-VNNSNPT--IFKCAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 54 wq~~~l~~~~~~~~~~-~~~~~~~--~~~~~v~sgrg~GKS~~~a~~~lw~ 101 (367) .|.++++.|++.+++. ..-..|. +--....++-|+|||.++-.++-.+ T Consensus 569 GQd~AI~~I~~aI~~sraGL~dp~rP~GsFlf~GptGvGKTELAKaLAe~L 619 (852) T TIGR03346 569 GQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFL 619 (852) T ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHH T ss_conf 709999999999999971888899974589986788776899999999998 No 108 >pfam01695 IstB IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function. Probab=95.97 E-value=0.08 Score=30.17 Aligned_cols=55 Identities=16% Similarity=0.118 Sum_probs=34.9 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 842899999998888751245555541124776148867889999999999997089977999715 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) +.+++|..-|.. .+.+.++ .++.+.++-|+|||++++++..-. + ..+.+|..+.- T Consensus 29 ~~~~~~i~~L~~-~~~i~~~--------~Nlll~G~~GtGKThLA~Ai~~~~-~-~~g~~v~f~~~ 83 (178) T pfam01695 29 GLDRRLIAELAG-LDWIEQA--------ENLLLLGPPGVGKTHLACALGHQA-C-RAGYSVLFTRT 83 (178) T ss_pred CCCHHHHHHHHC-CCCHHCC--------CCEEEECCCCCCHHHHHHHHHHHH-H-HCCCEEEEEEC T ss_conf 989999998855-9742158--------768998999987899999999999-9-86985999961 No 109 >KOG0330 consensus Probab=95.93 E-value=0.028 Score=33.00 Aligned_cols=156 Identities=15% Similarity=0.056 Sum_probs=83.6 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHHHHHHHHH Q ss_conf 6668428999999988887512455555411247761488678899999999999970899-779997153799999999 Q gi|254781187|r 47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSETQLKNTLW 125 (367) Q Consensus 47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~Q~~~~lw 125 (367) +++.|++-|.+.+-. -++. . -+..+|-.|+|||...+.=++-.|+-.|. ..++|.+||..-+.++ T Consensus 80 ~~~~PT~IQ~~aiP~---~L~g-~--------dvIglAeTGSGKT~afaLPIl~~LL~~p~~~~~lVLtPtRELA~QI-- 145 (476) T KOG0330 80 GWKKPTKIQSEAIPV---ALGG-R--------DVIGLAETGSGKTGAFALPILQRLLQEPKLFFALVLTPTRELAQQI-- 145 (476) T ss_pred CCCCCCHHHHHHCCH---HHCC-C--------CEEEEECCCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHH-- T ss_conf 767874444520655---4379-8--------5799943588840231799999997198774489964828999999-- Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCC-CCCCCCCCCCCCCCCCEEEEECCCCCC Q ss_conf 9999999862312112333321000123332211113457761266210135-445565210113586289997545599 Q gi|254781187|r 126 AEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYS-EERPDTFVGPHNTHGMAVFNDEASGTP 204 (367) Q Consensus 126 ~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~-~~~~ea~~g~h~~~~~l~ivDEAsgI~ 204 (367) +|.-..+...+.- .+. -.... ......-.-...+..++.|.+-+ -+--++-.|++-+..-++++|||.-+= T Consensus 146 ~e~fe~Lg~~igl---r~~----~lvGG-~~m~~q~~~L~kkPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlL 217 (476) T KOG0330 146 AEQFEALGSGIGL---RVA----VLVGG-MDMMLQANQLSKKPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLL 217 (476) T ss_pred HHHHHHHCCCCCE---EEE----EEECC-CHHHHHHHHHHCCCCEEEECCHHHHHHHHHCCCCCHHHHHHHHHCHHHHHH T ss_conf 9999875356672---799----98658-329999887624898798370789999874368408875787633177662 Q ss_pred HHHHH-HHHHHHH--CCCCCEEE Q ss_conf 88999-9898740--69882589 Q gi|254781187|r 205 DIINK-SILGFFT--ELNPNRFW 224 (367) Q Consensus 205 d~i~e-~i~g~Lt--~~~~~~~~ 224 (367) |.-|+ .+.-.|. ....+++. T Consensus 218 d~dF~~~ld~ILk~ip~erqt~L 240 (476) T KOG0330 218 DMDFEEELDYILKVIPRERQTFL 240 (476) T ss_pred HHHHHHHHHHHHHHCCCCCEEEE T ss_conf 11568999999874674414899 No 110 >PRK09183 transposase/IS protein; Provisional Probab=95.91 E-value=0.12 Score=29.15 Aligned_cols=68 Identities=21% Similarity=0.194 Sum_probs=38.6 Q ss_pred HHCCCCCCCCCCCCC---CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 301466888443666---84289999999888875124555554112477614886788999999999999708997799 Q gi|254781187|r 35 FFPWGIKGKPLEHFS---QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSII 111 (367) Q Consensus 35 ~~~w~~~~~~~~~~~---~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~ 111 (367) -||+. +..+-..|+ +..+.|..-|.. .++++++ .++.+.++-|+|||++++++.. ..++.|.+|. T Consensus 66 ~fp~~-ktle~fDf~~~~~l~~~~i~~La~-~~fi~~~--------~Nvil~G~~GtGKThLA~Alg~--~A~~~G~~v~ 133 (258) T PRK09183 66 AFPAV-KTFEEYDFTFATGAPQKQLQSLRS-LSFIERN--------ENIVLLGPSGVGKTHLAIALGY--EAVRAGIKVR 133 (258) T ss_pred CCCCC-CCHHHCCCCCCCCCCHHHHHHHHC-CCHHHCC--------CCEEEECCCCCCHHHHHHHHHH--HHHHCCCEEE T ss_conf 99998-777555654688623899998825-8166558--------8679989999868999999999--9998799399 Q ss_pred EEC Q ss_conf 971 Q gi|254781187|r 112 CIA 114 (367) Q Consensus 112 ~~A 114 (367) .+. T Consensus 134 f~~ 136 (258) T PRK09183 134 FTT 136 (258) T ss_pred EEE T ss_conf 978 No 111 >PRK06526 transposase; Provisional Probab=95.86 E-value=0.13 Score=28.96 Aligned_cols=127 Identities=14% Similarity=0.139 Sum_probs=66.3 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537999999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) +..+-|.+-|.. .+++.++. ++.+.++-|+|||++++++..- + |+.|.+|.++.-.. +..++. T Consensus 80 ~l~~~~i~~La~-~~fi~~~~--------Nvil~G~~GtGKThLA~Alg~~-A-~~~G~~v~f~~~~~------L~~~L~ 142 (254) T PRK06526 80 SLKRDTIAHLGT-LDFVTGKE--------NVVFLGPPGTGKTHLAIGLGIR-A-CQAGHRVLFATAAQ------WVARLA 142 (254) T ss_pred CCCHHHHHHHHC-CCHHHCCC--------CEEEECCCCCCHHHHHHHHHHH-H-HHCCCCEEEEEHHH------HHHHHH T ss_conf 989999999863-71776588--------7899899998689999999999-9-98699679987799------999999 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC----- Q ss_conf 999862312112333321000123332211113457761266210135445565210113586289997545599----- Q gi|254781187|r 130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP----- 204 (367) Q Consensus 130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~----- 204 (367) ..... +. -...+.-+ ....|+|+||....| T Consensus 143 ~a~~~--------------------------------g~-----------~~~~~~~l--~~~dLLIiDe~g~~~~~~~~ 177 (254) T PRK06526 143 AAHHA--------------------------------GR-----------LQDELVKL--GRIPLLIVDEVGYIPFEAEA 177 (254) T ss_pred HHHHC--------------------------------CC-----------HHHHHHHH--HCCCEEEEECCCCCCCCHHH T ss_conf 98855--------------------------------80-----------99999985--13687765021364478899 Q ss_pred -HHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCC Q ss_conf -8899998987406988258999807899987688754112 Q gi|254781187|r 205 -DIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIP 244 (367) Q Consensus 205 -d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~ 244 (367) +..|+++..-- +.+. .++++ +.+....++.|.++ T Consensus 178 a~~lf~li~~Ry---e~~S-~IiTS--n~~~~~W~~~f~D~ 212 (254) T PRK06526 178 ANLFFQLVSSRY---ERAS-LIVTS--NKPFGRWGEVFGDD 212 (254) T ss_pred HHHHHHHHHHHH---CCCC-EEEEC--CCCHHHHHHHCCCH T ss_conf 999999999997---4588-67665--89866888864868 No 112 >PRK08853 DNA polymerase III subunits gamma and tau; Validated Probab=95.82 E-value=0.14 Score=28.75 Aligned_cols=134 Identities=19% Similarity=0.159 Sum_probs=67.8 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|.-+++.+..-+..+... +. ..-.+.||+|||+++-.++--+-|......--|.- ... +.+|.. T Consensus 20 GQ~~v~~~L~nal~~~rl~-ha----ylf~G~rGvGKTt~ARi~Ak~lNC~~~~~~~pcg~------C~~-C~~i~~--- 84 (717) T PRK08853 20 GQSHVLTALENALAHNRLH-HA----YLFSGTRGVGKTTIGRLFAKGLNCETGITSTPCGQ------CAT-CKEIDE--- 84 (717) T ss_pred CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCC------CCC-HHHHHC--- T ss_conf 8599999999999709974-05----76108898889899999999867899999997888------702-676744--- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..+..+.+.+ ...+...-..+-..+ + -.+.-.+|.+. .+|+||....+...|.+++. T Consensus 85 ------------------g~~~d~~EiD--aAs~~~vdd~rel~~-~-~~y~p~~~~yK-vyiiDEvHmls~~afnAlLK 141 (717) T PRK08853 85 ------------------GRFVDLLEID--AASRTKVEDTRELLD-N-VQYKPARGRFK-VYLIDEVHMLSRHSFNALLK 141 (717) T ss_pred ------------------CCCCCEEEEC--CCCCCCHHHHHHHHH-H-CCCCCCCCCEE-EEEEECHHHCCHHHHHHHHH T ss_conf ------------------7877524540--565678899999998-5-55488778547-99983054438999999987 Q ss_pred HHHCCCCCEEEE Q ss_conf 740698825899 Q gi|254781187|r 214 FFTELNPNRFWI 225 (367) Q Consensus 214 ~Lt~~~~~~~~i 225 (367) +|-.+=...+.+ T Consensus 142 tlEEPP~hv~Fi 153 (717) T PRK08853 142 TLEEPPEYVKFL 153 (717) T ss_pred HHCCCCCCEEEE T ss_conf 603787564899 No 113 >TIGR02621 cas3_GSU0051 CRISPR-associated helicase Cas3, Anaes-subtype; InterPro: IPR013444 This entry represents a CRISPR-associated putative DEAH-box helicase, or Cas3, subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. The proteins include both DEAH and HD motifs.. Probab=95.80 E-value=0.03 Score=32.78 Aligned_cols=158 Identities=17% Similarity=0.138 Sum_probs=81.3 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHH-HHHHHHHHHHHHHC-----------CCCEEEE Q ss_conf 43666842899999998888751245555541124776148867889-99999999999708-----------9977999 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKT-TLNAWMMLWLISTR-----------PGMSIIC 112 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS-~~~a~~~lw~~~~~-----------~~~~v~~ 112 (367) +.+.+||.+||.++.+.+.+. ..|+ ++.-+.|+||| .+++.+++-...-. -+.+-++ T Consensus 11 ~~G~~GPfpwQ~~L~~r~~~G-------~~P~----~~s~PTg~GKTlavi~~WlyAl~~~a~~~Grrr~~~~vP~RL~y 79 (975) T TIGR02621 11 LTGYSGPFPWQLRLAERFVAG-------EPPE----SCSVPTGLGKTLAVIAVWLYALAIDAEQVGRRRRRRKVPRRLVY 79 (975) T ss_pred HCCCCCCCHHHHHHHHHHHCC-------CCCC----CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEECCCEEEE T ss_conf 358988865899999998548-------9887----66787532368999999999987400036732421336831378 Q ss_pred ECCCHHHHHHHHHHHHHHHHHHCCCCCCCC------CCCCCC-------------CCCCCCCCCC--CCCCCCCCC-CEE Q ss_conf 715379999999999999998623121123------333210-------------0012333221--111345776-126 Q gi|254781187|r 113 IANSETQLKNTLWAEVSKWLSMLPHRHWFE------MQSLSL-------------HPSGWYAELL--EQSMGIDSK-HYT 170 (367) Q Consensus 113 ~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~------~~~~~~-------------~~~~~~~~~~--~~~~~~~~~-~~~ 170 (367) +-+- +.+=|-.+.+..|+.+.|+...... +..... .++..+.... -++...++. ..+ T Consensus 80 vVdR-R~vVD~~te~a~~i~~aL~~~pe~~Av~~vl~slr~~~~~Pa~a~pl~v~~LRGg~ad~~rDltew~~~P~rPav 158 (975) T TIGR02621 80 VVDR-RTVVDQSTEEAEKIREALGEAPELPAVRYVLESLRSAFAIPAEAEPLAVSTLRGGFADNDRDLTEWTRDPSRPAV 158 (975) T ss_pred EEEC-CEEECCHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCCCEE T ss_conf 8714-245343278999999854688877899999997323678776566523311167553022323345317899669 Q ss_pred EEE-------------CCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 621-------------0135445565210113586289997545599889999898740 Q gi|254781187|r 171 ITC-------------RTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFT 216 (367) Q Consensus 171 ~~a-------------~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt 216 (367) |.+ .+.+-.+.-=-+|+-|.. .|+++||| +++..+-|.+.-..+ T Consensus 159 ivgTvDm~gSRLLFrGYg~spk~rpihAal~G~D-Al~VlDEA-Hl~~~f~e~L~~i~~ 215 (975) T TIGR02621 159 IVGTVDMIGSRLLFRGYGCSPKSRPIHAALLGQD-ALIVLDEA-HLSPAFQETLKQIRS 215 (975) T ss_pred EEECCCCHHHHHHHHCCCCCCCCCCHHHHHHHCH-HHHHHHHH-HCCHHHHHHHHHHHH T ss_conf 9834420234354413456766551122213110-66543343-058789999999851 No 114 >KOG0331 consensus Probab=95.74 E-value=0.035 Score=32.39 Aligned_cols=260 Identities=11% Similarity=0.014 Sum_probs=118.9 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH------CC-CCEEEEECCCH Q ss_conf 436668428999999988887512455555411247761488678899999999999970------89-97799971537 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST------RP-GMSIICIANSE 117 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~------~~-~~~v~~~A~t~ 117 (367) ..+|..|++-|+...--+-+ + .-+...|..|+|||.....=++-++.. +. +.+++|.+||. T Consensus 108 ~~g~~~PtpIQaq~wp~~l~----G--------rD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vLVL~PTR 175 (519) T KOG0331 108 EQGFEKPTPIQAQGWPIALS----G--------RDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVLVLAPTR 175 (519) T ss_pred HCCCCCCCHHHHCCCCEECC----C--------CCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEECCCH T ss_conf 53999885344144651126----8--------86577823578620555557999987004443479998699976859 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEE Q ss_conf 99999999999999986231211233332100012333221111345776126621013544556521011358628999 Q gi|254781187|r 118 TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFN 197 (367) Q Consensus 118 ~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~iv 197 (367) .-+..+ -.+..++...+..+.--.....+..+... ....|.-.+.+.+-+-..--....+.-..+.++++ T Consensus 176 ELA~QV-~~~~~~~~~~~~~~~~cvyGG~~~~~Q~~---------~l~~gvdiviaTPGRl~d~le~g~~~l~~v~ylVL 245 (519) T KOG0331 176 ELAVQV-QAEAREFGKSLRLRSTCVYGGAPKGPQLR---------DLERGVDVVIATPGRLIDLLEEGSLNLSRVTYLVL 245 (519) T ss_pred HHHHHH-HHHHHHHCCCCCCCEEEEECCCCCCHHHH---------HHHCCCCEEEECCHHHHHHHHCCCCCCCCEEEEEE T ss_conf 999999-99999970777740799868988637889---------87559818980771789999748856453039996 Q ss_pred ECCCCCCHHHH-HHHHHHHHC---CCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCC----CCC-------C- Q ss_conf 75455998899-998987406---9882589998078999876887541122350467523332----888-------8- Q gi|254781187|r 198 DEASGTPDIIN-KSILGFFTE---LNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRT----VEG-------I- 261 (367) Q Consensus 198 DEAsgI~d~i~-e~i~g~Lt~---~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d----~p~-------~- 261 (367) |||--.-|.=| +.++-.+.. ....++|... +-++..-.+.+.|.. +...+.+-..+ +.. . T Consensus 246 DEADrMldmGFe~qI~~Il~~i~~~~rQtlm~sa-Twp~~v~~lA~~fl~---~~~~i~ig~~~~~~a~~~i~qive~~~ 321 (519) T KOG0331 246 DEADRMLDMGFEPQIRKILSQIPRPDRQTLMFSA-TWPKEVRQLAEDFLN---NPIQINVGNKKELKANHNIRQIVEVCD 321 (519) T ss_pred CCHHHHHCCCCHHHHHHHHHHCCCCCCCEEEEEE-ECCHHHHHHHHHHHC---CCEEEEECCHHHHHHHCCHHHHHHHCC T ss_conf 3477663135379999998755897522788865-464889999999845---964899612145544333146511268 Q ss_pred ---CHHHHHHHHHHCCCCCCEEEEEEEEEECCCCC------------CEEECHHHHHHHHCC--CCCCCCCCCEEEEEEC Q ss_conf ---98899999962168800026888644327789------------807829998644315--7777889848999963 Q gi|254781187|r 262 ---DSGFHEGIISRYGLDSDVARIEILGQFPQQEV------------NNFIPHNYIEEAMSR--EAIDDLYAPLIMGCDI 324 (367) Q Consensus 262 ---~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~------------d~~ip~~~ie~a~~~--~~~~~~~~p~viGvDv 324 (367) ...-+.+.++.+.. ...-++.+.|+--+..+ ..-|..+.-+.-.+. .......-|+.+.=|| T Consensus 322 ~~~K~~~l~~lL~~~~~-~~~~KvIIFc~tkr~~~~l~~~l~~~~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdV 400 (519) T KOG0331 322 ETAKLRKLGKLLEDISS-DSEGKVIIFCETKRTCDELARNLRRKGWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDV 400 (519) T ss_pred HHHHHHHHHHHHHHHHC-CCCCCEEEEECCHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHCCCCCCCEEEECCC T ss_conf 78898879999999735-68986899964336499999887751766155006664889999997502688546988153 Q ss_pred CCCCCCE Q ss_conf 8778810 Q gi|254781187|r 325 AGEGGDK 331 (367) Q Consensus 325 Ar~G~D~ 331 (367) |..|=|= T Consensus 401 AaRGLDi 407 (519) T KOG0331 401 AARGLDV 407 (519) T ss_pred CCCCCCC T ss_conf 1256887 No 115 >PRK07952 DNA replication protein DnaC; Validated Probab=95.72 E-value=0.15 Score=28.50 Aligned_cols=65 Identities=18% Similarity=0.187 Sum_probs=39.9 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECC Q ss_conf 43666842899999998888751245555541124776148867889999999999997089977999-715 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IAN 115 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~ 115 (367) ++++.-..+-|.++|..--.+.++- ....--+...++-|+|||+++++++.-.+. .+..|++ +++ T Consensus 68 Feny~~~~~~q~~al~~a~~y~enf----~~~~~gLlF~G~~GTGKThLA~aIan~Li~--~G~sVlf~t~~ 133 (242) T PRK07952 68 FENYRVECEGQMNALSKARQYVEEF----DGNIASFIFSGKPGTGKNHLAAAICNELLL--RGKSVLIITVA 133 (242) T ss_pred EECEECCCHHHHHHHHHHHHHHHHH----CCCCCEEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEEHH T ss_conf 2120158777899999999999865----438871799789999789999999999998--79949997799 No 116 >PRK13833 conjugal transfer protein TrbB; Provisional Probab=95.71 E-value=0.036 Score=32.29 Aligned_cols=55 Identities=20% Similarity=0.295 Sum_probs=42.7 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 289999999888875124555554112477614886788999999999999708997799971537 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) .+.|.++|+..-.. ..++.|++|.|+|||++..+++-......|+.+++++-.+. T Consensus 130 t~~~~~~L~~aV~~-----------r~nilVsGgTGSGKTTllnaL~~~i~~~~p~eRivtIEDt~ 184 (323) T PRK13833 130 TEAQASTIRSAISS-----------RLNIVISGGTGSGKTTLANAVIAEIVASAPEDRLVILEDTA 184 (323) T ss_pred CHHHHHHHHHHHHC-----------CCCEEEECCCCCCHHHHHHHHHHHHCCCCCHHEEEEECCCC T ss_conf 99999999999981-----------89689991777756899999998640289323399945750 No 117 >KOG0949 consensus Probab=95.70 E-value=0.057 Score=31.05 Aligned_cols=167 Identities=14% Similarity=0.113 Sum_probs=78.5 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537999999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) -|+.||.+.|..+.-. . .+.|.|++-.|||++.=-.+=-.+-......|+.+||+..-+..+. +.+. T Consensus 511 ~Pd~WQ~elLDsvDr~------e------SavIVAPTSaGKTfisfY~iEKVLResD~~VVIyvaPtKaLVnQvs-a~Vy 577 (1330) T KOG0949 511 CPDEWQRELLDSVDRN------E------SAVIVAPTSAGKTFISFYAIEKVLRESDSDVVIYVAPTKALVNQVS-ANVY 577 (1330) T ss_pred CCCHHHHHHHHHHHCC------C------CEEEEEECCCCCEECCHHHHHHHHHHCCCCEEEEECCHHHHHHHHH-HHHH T ss_conf 9838888776655056------6------2599820467861005899999985427987999664587766666-7788 Q ss_pred H-HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC----C Q ss_conf 9-9986231211233332100012333221111345776126621013544556521011358628999754559----9 Q gi|254781187|r 130 K-WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT----P 204 (367) Q Consensus 130 k-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI----~ 204 (367) - .-...++...+.+.. ..+.|-......+..+.-.. +.... -.+|-.-+++- +..-.+|+||-.-| . T Consensus 578 aRF~~~t~~rg~sl~g~---ltqEYsinp~nCQVLITvPe-clesl---Llspp~~q~~c-erIRyiIfDEVH~iG~~ed 649 (1330) T KOG0949 578 ARFDTKTFLRGVSLLGD---LTQEYSINPWNCQVLITVPE-CLESL---LLSPPHHQKFC-ERIRYIIFDEVHLIGNEED 649 (1330) T ss_pred HHHCCCCCCCCHHHHHH---HHHHHCCCCHHCEEEEECHH-HHHHH---HCCCHHHHHHH-HCCEEEEECHHHHCCCCCC T ss_conf 76336765631346766---66773578411359997467-89988---63856653022-4005897112332465243 Q ss_pred HHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHH Q ss_conf 88999989874069882589998078999876887541 Q gi|254781187|r 205 DIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFN 242 (367) Q Consensus 205 d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~ 242 (367) ..+||-+.-..+- .--.+-..+|||. .|+.-.+ T Consensus 650 ~l~~Eqll~li~C-P~L~LSATigN~~----l~qkWln 682 (1330) T KOG0949 650 GLLWEQLLLLIPC-PFLVLSATIGNPN----LFQKWLN 682 (1330) T ss_pred CHHHHHHHHHCCC-CEEEEECCCCCHH----HHHHHHH T ss_conf 4189987774578-7068741338888----9999999 No 118 >KOG0333 consensus Probab=95.67 E-value=0.034 Score=32.44 Aligned_cols=144 Identities=19% Similarity=0.149 Sum_probs=82.1 Q ss_pred CCCCCCCCC--------CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHH-HHHHHHHHHCC-- Q ss_conf 466888443--------6668428999999988887512455555411247761488678899999-99999997089-- Q gi|254781187|r 38 WGIKGKPLE--------HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNA-WMMLWLISTRP-- 106 (367) Q Consensus 38 w~~~~~~~~--------~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a-~~~lw~~~~~~-- 106 (367) |.+.+.|++ ++..|++-|+.+ |.-.+|+.. =+-| +-.|+|||...- -+++|...+-| T Consensus 247 wEE~~~P~e~l~~I~~~~y~eptpIqR~a---ipl~lQ~rD--------~igv-aETgsGktaaf~ipLl~~IsslP~~~ 314 (673) T KOG0333 247 WEESGFPLELLSVIKKPGYKEPTPIQRQA---IPLGLQNRD--------PIGV-AETGSGKTAAFLIPLLIWISSLPPMA 314 (673) T ss_pred HHHCCCCHHHHHHHHHCCCCCCCHHHHHH---CCCHHCCCC--------EEEE-EECCCCCCCCCHHHHHHHHHCCCCCC T ss_conf 32238988999999734899984678863---110101477--------2368-73167753200015889987089841 Q ss_pred -------CCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCC Q ss_conf -------9779997153799999999999999986231211233332100012333221111345776126621013544 Q gi|254781187|r 107 -------GMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEE 179 (367) Q Consensus 107 -------~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ 179 (367) |...+++|||..-+ ..+..|..|+...+-++ ..............+....|.-+..|.+.+.. T Consensus 315 ~~en~~~gpyaiilaptReLa-qqIeeEt~kf~~~lg~r---------~vsvigg~s~EEq~fqls~gceiviatPgrLi 384 (673) T KOG0333 315 RLENNIEGPYAIILAPTRELA-QQIEEETNKFGKPLGIR---------TVSVIGGLSFEEQGFQLSMGCEIVIATPGRLI 384 (673) T ss_pred HHHHCCCCCEEEEECHHHHHH-HHHHHHHHHHCCCCCCE---------EEEEECCCCHHHHHHHHHCCCEEEECCCHHHH T ss_conf 444234686001203379999-99999998750301432---------89985463366530246415414424740788 Q ss_pred CCCCCCCCCCCCCCEEEEECCCCC Q ss_conf 556521011358628999754559 Q gi|254781187|r 180 RPDTFVGPHNTHGMAVFNDEASGT 203 (367) Q Consensus 180 ~~ea~~g~h~~~~~l~ivDEAsgI 203 (367) ..--=.-+-...+..+++|||.-. T Consensus 385 d~Lenr~lvl~qctyvvldeadrm 408 (673) T KOG0333 385 DSLENRYLVLNQCTYVVLDEADRM 408 (673) T ss_pred HHHHHHHHHHCCCCEEECCCHHHH T ss_conf 877778887505846762406665 No 119 >PRK09111 DNA polymerase III subunits gamma and tau; Validated Probab=95.65 E-value=0.16 Score=28.34 Aligned_cols=139 Identities=15% Similarity=0.094 Sum_probs=69.3 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEEECCCHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977-99971537999999999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMS-IICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~-v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) .|.-+.+.+..-+..|... |. ....+.||+|||+++-.++--+-|..|+.. .....|-.. ... +.+|.. T Consensus 27 gq~~~~~~l~~~~~~~~~~-~a----~l~~g~rg~gktt~ari~a~~lnc~~~~~~~~~~~~~c~~--c~~-c~~i~~-- 96 (600) T PRK09111 27 GQEAMVRTLRNAFETGRIA-QA----FMLTGVRGVGKTTTARILARALNYKGPDGVGGPTIDPCGV--GEH-CQAIME-- 96 (600) T ss_pred CCHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--CHH-HHHHHC-- T ss_conf 8599999999999729842-04----7645789878999999999996698876668998898998--865-898866-- Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH Q ss_conf 86231211233332100012333221111345776126621013544556521011358628999754559988999989 Q gi|254781187|r 133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL 212 (367) Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~ 212 (367) ..+..+. ++....++..-..+-..+.. .+.-..+.+. .+|+||....+...|.+++ T Consensus 97 -------------------~~~~d~~--e~daas~~~v~~~r~~~~~~--~~~p~~~~~k-v~iidevhmls~~afnall 152 (600) T PRK09111 97 -------------------GRHVDVI--EMDAASHTGVDDIREIIESV--RYRPVSARYK-VYIIDEVHMLSTAAFNALL 152 (600) T ss_pred -------------------CCCCCEE--EEECCCCCCHHHHHHHHHHH--CCCCCCCCEE-EEEEECCCCCCHHHHHHHH T ss_conf -------------------8998758--85155457888999999860--5388777546-9996001105799999999 Q ss_pred HHHHCCCCCEEEEE Q ss_conf 87406988258999 Q gi|254781187|r 213 GFFTELNPNRFWIM 226 (367) Q Consensus 213 g~Lt~~~~~~~~i~ 226 (367) .+|-.+=...+.++ T Consensus 153 ktleepp~~~~fi~ 166 (600) T PRK09111 153 KTLEEPPPHVKFIF 166 (600) T ss_pred HHHHCCCCCEEEEE T ss_conf 87625986549999 No 120 >PRK08770 DNA polymerase III subunits gamma and tau; Validated Probab=95.37 E-value=0.17 Score=28.19 Aligned_cols=135 Identities=19% Similarity=0.186 Sum_probs=70.1 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|.-+++.+..-+..+... +. ..-.+-||+|||+++-.++--+-|.. |.+. .|-. + ... +.+|.. T Consensus 20 gq~~~~~~l~~~~~~~~~~-~a----~lf~g~rg~gkt~~ar~~a~~lnc~~-~~~~---~pc~-~-c~~-c~~i~~--- 84 (663) T PRK08770 20 GQEHVVRALSNALDSGRVH-HA----FLFTGTRGVGKTTIARIFAKSLNCET-GTSA---DPCG-Q-CPA-CLDIDA--- 84 (663) T ss_pred CCHHHHHHHHHHHHCCCCC-EE----EEEECCCCCCHHHHHHHHHHHHCCCC-CCCC---CCCC-C-CHH-HHHHHC--- T ss_conf 8599999999999709974-04----76227998888899999999867899-9999---9787-7-877-898854--- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..+..+.+.+ ...+...-..+-..+. -.+.-.+|.+. .+|+||....+...|.+++. T Consensus 85 ------------------~~~~d~~e~d--aas~~~v~~~r~~~~~--~~~~p~~~~~k-vy~idevhmls~~~fna~lk 141 (663) T PRK08770 85 ------------------GRYIDLLEID--AASNTGVDDVREVIEN--AQYMPSRGKFK-VYLIDEVHMLSKAAFNALLK 141 (663) T ss_pred ------------------CCCCCEEEEE--CCCCCCHHHHHHHHHH--CCCCCCCCCEE-EEEEECHHHCCHHHHHHHHH T ss_conf ------------------8988658864--6765888999999984--43588777436-99970043328999999987 Q ss_pred HHHCCCCCEEEEE Q ss_conf 7406988258999 Q gi|254781187|r 214 FFTELNPNRFWIM 226 (367) Q Consensus 214 ~Lt~~~~~~~~i~ 226 (367) +|-.+=...+.++ T Consensus 142 tleepp~~v~f~~ 154 (663) T PRK08770 142 TLEEPPEHVKFLL 154 (663) T ss_pred HHCCCCCCEEEEE T ss_conf 4027864428998 No 121 >KOG0391 consensus Probab=95.34 E-value=0.11 Score=29.32 Aligned_cols=167 Identities=14% Similarity=0.159 Sum_probs=89.4 Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHHHHHHHHHHH Q ss_conf 68428999999988887512455555411247761488678899999999999970899-77999715379999999999 Q gi|254781187|r 49 SQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSETQLKNTLWAE 127 (367) Q Consensus 49 ~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~Q~~~~lw~e 127 (367) ..-|.+|.-=|.=++.--++|.+ -..+---|.|||.-+-.++.+++|..-+ .--+++-||..-+.- ==| T Consensus 614 GqLReYQkiGLdWLatLYeknlN--------GILADEmGLGKTIQtISllAhLACeegnWGPHLIVVpTsviLnW--EME 683 (1958) T KOG0391 614 GQLREYQKIGLDWLATLYEKNLN--------GILADEMGLGKTIQTISLLAHLACEEGNWGPHLIVVPTSVILNW--EME 683 (1958) T ss_pred HHHHHHHHHHHHHHHHHHHHCCC--------CEEHHHHCCCCHHHHHHHHHHHHHCCCCCCCCEEEEECHHHHHH--HHH T ss_conf 77888887517999999873344--------32223314651457999999987504577873698513221133--678 Q ss_pred HHHHHHHCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH- Q ss_conf 9999986231-21123333210001233322111134577612662101354455652101135862899975455998- Q gi|254781187|r 128 VSKWLSMLPH-RHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD- 205 (367) Q Consensus 128 i~k~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d- 205 (367) +|+|.-.+.. -+.-.....+.+-+.|... ..|-.+.++=...--....+.....-++|+|||..|.+ T Consensus 684 lKRwcPglKILTYyGs~kErkeKRqgW~kP-----------naFHVCItSYklv~qd~~AFkrkrWqyLvLDEaqnIKnf 752 (1958) T KOG0391 684 LKRWCPGLKILTYYGSHKERKEKRQGWAKP-----------NAFHVCITSYKLVFQDLTAFKRKRWQYLVLDEAQNIKNF 752 (1958) T ss_pred HHHHCCCCEEEEECCCHHHHHHHHHCCCCC-----------CEEEEEEHHHHHHHHHHHHHHHHCCCEEEHHHHHHHCCH T ss_conf 865277535765217788888875144688-----------804886310688873778887641122321455542300 Q ss_pred --HHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHH Q ss_conf --8999989874069882589998078999876887541 Q gi|254781187|r 206 --IINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFN 242 (367) Q Consensus 206 --~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~ 242 (367) .-|+++...-+. .+ .+++|+|-. |-|-++|. T Consensus 753 ksqrWQAllnfnsq--rR--LLLtgTPLq--NslmELWS 785 (1958) T KOG0391 753 KSQRWQALLNFNSQ--RR--LLLTGTPLQ--NSLMELWS 785 (1958) T ss_pred HHHHHHHHHCCCHH--HE--EEECCCCHH--HHHHHHHH T ss_conf 67889998530012--00--221187204--67999999 No 122 >COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription] Probab=95.33 E-value=0.2 Score=27.67 Aligned_cols=82 Identities=21% Similarity=0.277 Sum_probs=61.0 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 88443666842899999998888751245555541124776148867889999999999997089977999715379999 Q gi|254781187|r 42 GKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 42 ~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) .+|+ .++..|..++++|...+.++. .|-|+ +.+-=|+|||..++..++-. . .-|..+..+|||+==|+ T Consensus 258 ~LPF----~LT~aQ~~vi~EI~~Dl~~~~-----~M~RL-lQGDVGSGKTvVA~laml~a-i-~~G~Q~ALMAPTEILA~ 325 (677) T COG1200 258 ALPF----KLTNAQKRVIKEILADLASPV-----PMNRL-LQGDVGSGKTVVALLAMLAA-I-EAGYQAALMAPTEILAE 325 (677) T ss_pred HCCC----CCCHHHHHHHHHHHHHHCCCH-----HHHHH-HCCCCCCCHHHHHHHHHHHH-H-HCCCEEEEECCHHHHHH T ss_conf 5899----767899999999986644866-----66787-52676777899999999999-8-72881688663799999 Q ss_pred HHHHHHHHHHHHHCC Q ss_conf 999999999998623 Q gi|254781187|r 122 NTLWAEVSKWLSMLP 136 (367) Q Consensus 122 ~~lw~ei~k~~~~~~ 136 (367) + -+..+++|+..+- T Consensus 326 Q-H~~~~~~~l~~~~ 339 (677) T COG1200 326 Q-HYESLRKWLEPLG 339 (677) T ss_pred H-HHHHHHHHHHHCC T ss_conf 9-9999998766519 No 123 >PRK05648 DNA polymerase III subunits gamma and tau; Reviewed Probab=95.26 E-value=0.19 Score=27.83 Aligned_cols=135 Identities=16% Similarity=0.205 Sum_probs=69.6 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|.-+++.+..-+..+... |. ..-.+.||+|||+++-.++--+-| ..|... .|-. + ... +.+|.. T Consensus 20 gq~~~~~~l~~~~~~~~~~-~a----~l~~g~rg~gkt~~ar~~ak~lnc-~~~~~~---~pc~-~-c~~-c~~i~~--- 84 (705) T PRK05648 20 GQTHVLKALINALDNQRLH-HA----YLFTGTRGVGKTTIARIIAKCLNC-ETGVSS---TPCG-E-CSV-CREIDE--- 84 (705) T ss_pred CHHHHHHHHHHHHHCCCCC-CE----EEEECCCCCCHHHHHHHHHHHHCC-CCCCCC---CCCC-C-CHH-HHHHHC--- T ss_conf 8199999999999709863-04----650078988898999999998677-899988---9787-7-600-466624--- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) ..+..+.+.+ ...+...-..+-..+. -.+.-.+|.+. .+|+||....+...|.+++. T Consensus 85 ------------------~~~~d~~e~d--~as~~~v~~~r~~~~~--~~~~p~~~~~k-v~~idevhmls~~~fnallk 141 (705) T PRK05648 85 ------------------GRFVDLIEVD--AASRTKVEDTRELLDN--VQYAPTRGRYK-VYLIDEVHMLSSHSFNALLK 141 (705) T ss_pred ------------------CCCCCEEEEC--CCCCCCHHHHHHHHHH--CCCCCCCCCEE-EEEEEHHHHCCHHHHHHHHH T ss_conf ------------------8977634451--5544788999999985--55177677457-99984265417999999987 Q ss_pred HHHCCCCCEEEEE Q ss_conf 7406988258999 Q gi|254781187|r 214 FFTELNPNRFWIM 226 (367) Q Consensus 214 ~Lt~~~~~~~~i~ 226 (367) +|-.+=...+.++ T Consensus 142 tleepp~~v~f~~ 154 (705) T PRK05648 142 TLEEPPPHVKFLL 154 (705) T ss_pred HCCCCCCCEEEEE T ss_conf 4047975459998 No 124 >KOG0340 consensus Probab=95.24 E-value=0.15 Score=28.50 Aligned_cols=158 Identities=15% Similarity=0.015 Sum_probs=84.3 Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEEECC Q ss_conf 1466888443666842899999998888751245555541124776148867889999999999997089977-999715 Q gi|254781187|r 37 PWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMS-IICIAN 115 (367) Q Consensus 37 ~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~-v~~~A~ 115 (367) ||=.+-+--.+..+|++-|....-.|-+.. -+.=+|-.|+|||+..|.-++-.+.-+|... .++..| T Consensus 16 ~Wlve~l~~l~i~~pTpiQ~~cIpkILeGr------------dcig~AkTGsGKT~AFaLPil~rLsedP~giFalvlTP 83 (442) T KOG0340 16 PWLVEQLKALGIKKPTPIQQACIPKILEGR------------DCIGCAKTGSGKTAAFALPILNRLSEDPYGIFALVLTP 83 (442) T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHCCC------------CCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCEEEEECC T ss_conf 899999998358899826765248785466------------31031346887411222787776133887606999545 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCC------CCCCCCCC Q ss_conf 379999999999999998623121123333210001233322111134577612662101354455------65210113 Q gi|254781187|r 116 SETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERP------DTFVGPHN 189 (367) Q Consensus 116 t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~------ea~~g~h~ 189 (367) |..-+-.+ +|--..+.++.+..-- .................+...+.+..-+...+ +..-++ T Consensus 84 TrELA~Qi--aEQF~alGk~l~lK~~--------vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~-- 151 (442) T KOG0340 84 TRELALQI--AEQFIALGKLLNLKVS--------VIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIF-- 151 (442) T ss_pred HHHHHHHH--HHHHHHHCCCCCCEEE--------EEECCHHHHHHHHHCCCCCCEEECCCCCCCCCCCCCCCCCHHHH-- T ss_conf 28888888--8999984564563279--------99756887645444266987575176333541126876552555-- Q ss_pred CCCCEEEEECCCCCC----HHHHHHHHHHHHCC Q ss_conf 586289997545599----88999989874069 Q gi|254781187|r 190 THGMAVFNDEASGTP----DIINKSILGFFTEL 218 (367) Q Consensus 190 ~~~~l~ivDEAsgI~----d~i~e~i~g~Lt~~ 218 (367) ...-++++|||.-+= ++..+.++-.+-.. T Consensus 152 ~rlkflVlDEADrvL~~~f~d~L~~i~e~lP~~ 184 (442) T KOG0340 152 QRLKFLVLDEADRVLAGCFPDILEGIEECLPKP 184 (442) T ss_pred HCEEEEEECCHHHHHCCCHHHHHHHHHCCCCCC T ss_conf 300467741302654156056776665048876 No 125 >TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome. Probab=95.16 E-value=0.23 Score=27.34 Aligned_cols=45 Identities=20% Similarity=0.248 Sum_probs=35.4 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH Q ss_conf 776148867889999999999997089977999715379999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL 124 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l 124 (367) ..|-||.|+|||..--.-++.++.-+++.+|+|..+|..--.+.+ T Consensus 19 ~lVEAGTGTGKSLAYLvPAl~~a~~~~g~rVVISTaT~aLQeQL~ 63 (636) T TIGR03117 19 GMLEASTGVGKTLAMIMAALTMLKERPDQKIAIAVPTLALMGQLW 63 (636) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHH T ss_conf 999899971088999999999998579998899798799999997 No 126 >PRK07993 DNA polymerase III subunit delta'; Validated Probab=95.07 E-value=0.25 Score=27.17 Aligned_cols=134 Identities=13% Similarity=0.113 Sum_probs=68.9 Q ss_pred HHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 88887512455555411247761488678899999999999970899779997153799999999999999986231211 Q gi|254781187|r 61 AVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHW 140 (367) Q Consensus 61 ~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~ 140 (367) .+....+.+...+ .+.+.+..|+||+.++-.++-+.+|..|...--|-.-.. -+ .+. ...-|+-++ T Consensus 13 ~l~~~~~~~rl~H-----A~L~~G~~G~Gk~~la~~~a~~llC~~~~~~~~Cg~C~~--C~-----l~~--~~~HPD~~~ 78 (334) T PRK07993 13 KLVGSYQAGRGHH-----ALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRG--CQ-----LMQ--AGTHPDYYT 78 (334) T ss_pred HHHHHHHCCCCCE-----EEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHH--HH-----HHH--CCCCCCEEE T ss_conf 9999998598104-----675479999889999999999981899999999999978--99-----986--689998477 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCC Q ss_conf 23333210001233322111134577612662101354455652101135862899975455998899998987406988 Q gi|254781187|r 141 FEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNP 220 (367) Q Consensus 141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~ 220 (367) ...+. ....++.+.-.-.. . --+.....|.+. .+|+|+|.......-.++..+|-.+.. T Consensus 79 i~pe~------------~~~~I~IdqIR~l~------~--~~~~~~~~g~~k-V~iI~~Ae~mn~~AaNaLLKtLEEPp~ 137 (334) T PRK07993 79 LTPEK------------GKSSLGVDAVREVT------E--KLYEHARLGGAK-VVWLPDAALLTDAAANALLKTLEEPPE 137 (334) T ss_pred ECCCC------------CCCCCCHHHHHHHH------H--HHHHCCCCCCCE-EEEECCHHHHCHHHHHHHHHHHCCCCC T ss_conf 53422------------34559999999999------9--984366569947-999766777599999999986127998 Q ss_pred CEEEEEEEC Q ss_conf 258999807 Q gi|254781187|r 221 NRFWIMTSN 229 (367) Q Consensus 221 ~~~~i~igN 229 (367) .++.+++++ T Consensus 138 ~t~~iL~t~ 146 (334) T PRK07993 138 KTWFFLACR 146 (334) T ss_pred CEEEEEECC T ss_conf 849998669 No 127 >PRK13894 conjugal transfer ATPase TrbB; Provisional Probab=94.95 E-value=0.077 Score=30.25 Aligned_cols=55 Identities=22% Similarity=0.171 Sum_probs=41.0 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH Q ss_conf 899999998888751245555541124776148867889999999999997089977999715379 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET 118 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~ 118 (367) +-|.++|+..-.. ..++.|++|.|+|||++..+++-......|..+++++..+.. T Consensus 136 ~~~a~~L~~~V~~-----------r~nilI~G~TgsGKTTll~all~~i~~~~p~eRivtIED~~E 190 (320) T PRK13894 136 AEQREAIIAAVRA-----------HRNILVIGGTGSGKTTLVNAIINEMVIQDPTERVFIIEDTGE 190 (320) T ss_pred HHHHHHHHHHHHC-----------CCCEEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCHHH T ss_conf 9999999999972-----------875899858886568999999863202695201775258788 No 128 >TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA; InterPro: IPR014136 This entry represents the Ti-type conjugative transfer relaxase TraA. TraA contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, IPR005053 from INTERPRO) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, IPR014129 from INTERPRO). 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=94.74 E-value=0.28 Score=26.79 Aligned_cols=122 Identities=18% Similarity=0.019 Sum_probs=67.7 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH Q ss_conf 8999999988887512455555411247761488-678899999999999970899779997153799999999999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW 131 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~ 131 (367) .=|.++++.|...- ++||.-|+ |.|||++...+=..|-.-. -+|+=-|=+.+-++ -|-++ T Consensus 417 ~EQ~~Av~hvt~s~------------~iavVvG~AGtGKSt~L~aAR~AWe~~G--y~V~GAALsGKAAe-gLe~~---- 477 (888) T TIGR02768 417 EEQKEAVRHVTGSG------------DIAVVVGRAGTGKSTMLKAAREAWEAAG--YRVIGAALSGKAAE-GLEAE---- 477 (888) T ss_pred HHHHHHHHHHCCCC------------CEEEEECCCCCCHHHHHHHHHHHHHHCC--CEEEEHHHHHHHHH-HHHCC---- T ss_conf 89999987532899------------6489974899876678999999998739--77871545558988-73002---- Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHH Q ss_conf 98623121123333210001233322111134577612662101354455652101135862899975455998899998 Q gi|254781187|r 132 LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSI 211 (367) Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i 211 (367) +-.....++-|... + .....-++.. ..+|+|||..|.-.-+.=+ T Consensus 478 -----------sGI~SRTLASle~a-------------W----------~~G~d~L~~~--dvLviDEAGMV~S~Qm~r~ 521 (888) T TIGR02768 478 -----------SGIESRTLASLEYA-------------W----------ANGRDLLEDK--DVLVIDEAGMVGSRQMARV 521 (888) T ss_pred -----------CCCCHHHHHHHHHH-------------H----------HCCCCCCCCC--CEEEEECCCCHHHHHHHHH T ss_conf -----------68750478879999-------------8----------7387522477--6689851544146778899 Q ss_pred HHHHHCCCCCEEEEEEECCC Q ss_conf 98740698825899980789 Q gi|254781187|r 212 LGFFTELNPNRFWIMTSNTR 231 (367) Q Consensus 212 ~g~Lt~~~~~~~~i~igNP~ 231 (367) ...-...+.|+ +++|-|. T Consensus 522 l~~A~~AGaKv--VLvGD~~ 539 (888) T TIGR02768 522 LKEAEEAGAKV--VLVGDPE 539 (888) T ss_pred HHHHHHCCCCE--EEECCHH T ss_conf 99998727605--9848857 No 129 >KOG0350 consensus Probab=94.73 E-value=0.17 Score=28.12 Aligned_cols=149 Identities=15% Similarity=0.041 Sum_probs=75.2 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCC-EEEEEEECCCCCCHHHHHHHHHHHHHHHCCC--CEEEEECCCHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541-1247761488678899999999999970899--77999715379999999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPT-IFKCAISAGRGIGKTTLNAWMMLWLISTRPG--MSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~-~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~--~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) -|.-+|--+-+.++. ..|. -.-++|.|+.|+|||-.-+.=|+=.+..+|- .+++++-||..-+-++ ...+++ T Consensus 163 VQ~aVlp~ll~~~~~----p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ~L~~R~v~~LRavVivPtr~L~~QV-~~~f~~ 237 (620) T KOG0350 163 VQYAVLPSLLEEIRS----PPPSRPRDICVNAPTGSGKTLAYVIPIVQLLSSRPVKRLRAVVIVPTRELALQV-YDTFKR 237 (620) T ss_pred HHHHHHHHHHHHHCC----CCCCCCCCEEEECCCCCCCEEEEHHHHHHHHCCCCCCCEEEEEEEEHHHHHHHH-HHHHHH T ss_conf 588888899986147----999887754775578988456651378999703873405799995479999999-999998 Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CEEEEECCCCC-CCCCCCCCCCCCCCCEEEEECCCCCCHH Q ss_conf 9986231211233332100012333221111345776---12662101354-4556521011358628999754559988 Q gi|254781187|r 131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSK---HYTITCRTYSE-ERPDTFVGPHNTHGMAVFNDEASGTPDI 206 (367) Q Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~a~~~~~-~~~ea~~g~h~~~~~l~ivDEAsgI~d~ 206 (367) |....-. .-+... ...-.+.....+..+.. .-+..+.+.|. .--.+..|+--.+.-++|+|||.-+=+. T Consensus 238 ~~~~tgL---~V~~~s----gq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~LrfLVIDEADRll~q 310 (620) T KOG0350 238 LNSGTGL---AVCSLS----GQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKHLRFLVIDEADRLLDQ 310 (620) T ss_pred HCCCCCE---EEEECC----CCCCHHHHHHHHHCCCCCCCCCEEECCCHHHHHHCCCCCCCCHHHCEEEEECHHHHHHHH T ss_conf 5668865---988601----454057899997259976543669737268888604898756445357775257789999 Q ss_pred HHHHHHHH Q ss_conf 99998987 Q gi|254781187|r 207 INKSILGF 214 (367) Q Consensus 207 i~e~i~g~ 214 (367) .|+-=.++ T Consensus 311 sfQ~Wl~~ 318 (620) T KOG0350 311 SFQEWLDT 318 (620) T ss_pred HHHHHHHH T ss_conf 99988999 No 130 >PRK07399 DNA polymerase III subunit delta'; Validated Probab=94.69 E-value=0.2 Score=27.69 Aligned_cols=41 Identities=10% Similarity=0.179 Sum_probs=30.3 Q ss_pred CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECC Q ss_conf 358628999754559988999989874069882589998078 Q gi|254781187|r 189 NTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNT 230 (367) Q Consensus 189 ~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP 230 (367) |.+ -.+|+|+|.........++..+|-.+.+.++.++..+| T Consensus 123 ~~~-kVvII~~ae~m~~~AaNaLLKtLEEP~~~~fILit~~~ 163 (314) T PRK07399 123 APR-KVVVIEDAETMNEAAANALLKTLEEPGNGTLILIAPSP 163 (314) T ss_pred CCC-EEEEECCHHHCCHHHHHHHHHHHCCCCCCEEEEEECCH T ss_conf 884-79998897871999999999861478785699997993 No 131 >TIGR00643 recG ATP-dependent DNA helicase RecG; InterPro: IPR004609 The ATP-dependent DNA helicase RecG 3.6.1 from EC plays a critical role in recombination and DNA repair. It helps to process Holliday junction intermediates to mature products by catalysing branch migration. RecG has DNA unwinding activity characteristic of a DNA helicase with 3' to 5' polarity.; GO: 0004003 ATP-dependent DNA helicase activity, 0006281 DNA repair, 0006310 DNA recombination. Probab=94.67 E-value=0.3 Score=26.68 Aligned_cols=81 Identities=22% Similarity=0.295 Sum_probs=60.9 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 88443666842899999998888751245555541124776148867889999999999997089977999715379999 Q gi|254781187|r 42 GKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 42 ~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) .+|. .+|.-|...+.+|...+.++. .|-|+ |.+==|+|||..++..++-.+ .-|-++..+|||+==|+ T Consensus 303 ~LPF----~LT~aQ~r~v~EI~~DL~~~~-----pMnRL-lQGDVGSGKT~VA~la~l~~i--~~GYQ~ALMAPTEiLA~ 370 (721) T TIGR00643 303 SLPF----ELTRAQKRVVKEILQDLKSDV-----PMNRL-LQGDVGSGKTLVAALAMLAAI--ESGYQVALMAPTEILAE 370 (721) T ss_pred CCCC----CCCHHHHHHHHHHHHHHCCCC-----CCCCC-CCCCCCCHHHHHHHHHHHHHH--HCCCEEEEECCHHHHHH T ss_conf 2888----776778999999998614787-----53222-110106638999999999998--46980999177689999 Q ss_pred HHHHHHHHHHHHHC Q ss_conf 99999999999862 Q gi|254781187|r 122 NTLWAEVSKWLSML 135 (367) Q Consensus 122 ~~lw~ei~k~~~~~ 135 (367) + -...+.+|+..+ T Consensus 371 Q-Hy~~~~~~l~p~ 383 (721) T TIGR00643 371 Q-HYDSLRNLLAPL 383 (721) T ss_pred H-HHHHHHHHHCCC T ss_conf 9-999999962354 No 132 >COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair] Probab=94.63 E-value=0.32 Score=26.47 Aligned_cols=103 Identities=18% Similarity=0.165 Sum_probs=64.3 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCC-------------------EEEEECCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 477614886788999999999999708997-------------------7999715379999999999999998623121 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGM-------------------SIICIANSETQLKNTLWAEVSKWLSMLPHRH 139 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~-------------------~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~ 139 (367) .+.+.+..|+|||+++-+++-++.+..+.. .++-+.|+.....++.-..+++..+... T Consensus 26 alL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~--- 102 (325) T COG0470 26 ALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKIDIIVEQVRELAEFLS--- 102 (325) T ss_pred CEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHCC--- T ss_conf 10037999997899999999996586643345520022444320256886599773213333006999999998604--- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCC Q ss_conf 12333321000123332211113457761266210135445565210113586289997545599889999898740698 Q gi|254781187|r 140 WFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELN 219 (367) Q Consensus 140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~ 219 (367) ..+..+. .-++|+|||..+....-.+++.++-.+. T Consensus 103 --------------------------------------------~~~~~~~-~kviiidead~mt~~A~nallk~lEep~ 137 (325) T COG0470 103 --------------------------------------------ESPLEGG-YKVVIIDEADKLTEDAANALLKTLEEPP 137 (325) T ss_pred --------------------------------------------CCCCCCC-CEEEEEECCCCCCHHHHHHHHHHCCCCC T ss_conf --------------------------------------------4656677-2699973203269888876754332488 Q ss_pred CCEEEEEEEC Q ss_conf 8258999807 Q gi|254781187|r 220 PNRFWIMTSN 229 (367) Q Consensus 220 ~~~~~i~igN 229 (367) .+...+++.| T Consensus 138 ~~~~~il~~n 147 (325) T COG0470 138 KNTRFILITN 147 (325) T ss_pred CCEEEEEEEC T ss_conf 8716999749 No 133 >PRK13342 recombination factor protein RarA; Reviewed Probab=94.62 E-value=0.32 Score=26.46 Aligned_cols=112 Identities=12% Similarity=0.117 Sum_probs=64.4 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 24776148867889999999999997089977999715379999999999999998623121123333210001233322 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL 157 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (367) +.+..-++.|+|||+++-.++--. +...+-...+.+.+++ +++.++.... T Consensus 38 ~s~Il~GPPG~GKTTlA~iiA~~~-----~~~f~~lnA~~~gv~d-----ir~ii~~a~~-------------------- 87 (417) T PRK13342 38 SSMILWGPPGTGKTTLARIIAGAT-----DAEFEALSAVTSGVKD-----LREVIEEAKQ-------------------- 87 (417) T ss_pred CEEEEECCCCCCHHHHHHHHHHHH-----CCCEEEEECCCCCHHH-----HHHHHHHHHH-------------------- T ss_conf 759988969998999999999986-----8988996141038899-----9999999886-------------------- Q ss_pred CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHH Q ss_conf 11113457761266210135445565210113586289997545599889999898740698825899980789998768 Q gi|254781187|r 158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRLNGWF 237 (367) Q Consensus 158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~F 237 (367) ... +.. .++++||..-..-...+++++.+-.+ . .++||.+|. |++ T Consensus 88 -------------------------~~~---~~~-tilfiDEIHRfnK~QQD~LLp~vE~g--~--iiLIgATTE--NP~ 132 (417) T PRK13342 88 -------------------------SRL---GRR-TILFIDEIHRFNKAQQDALLPHVEDG--T--ITLIGATTE--NPS 132 (417) T ss_pred -------------------------HHC---CCC-EEEEEECHHHCCHHHHHHHHHHHHCC--C--EEEEEECCC--CCH T ss_conf -------------------------314---896-59999782005889999998751126--5--699974157--922 Q ss_pred HHHHHCCCCCEEEEEEC Q ss_conf 87541122350467523 Q gi|254781187|r 238 YDIFNIPLEDWKRYQID 254 (367) Q Consensus 238 ye~~~~~~~~w~~~~~~ 254 (367) +..-..-.++-.++.+. T Consensus 133 f~in~aLlSRc~vf~l~ 149 (417) T PRK13342 133 FEVNPALLSRAQVFELK 149 (417) T ss_pred HHCCHHHHHHHHHEECC T ss_conf 53489898565700205 No 134 >CHL00095 clpC Clp protease ATP binding subunit Probab=94.56 E-value=0.33 Score=26.37 Aligned_cols=127 Identities=20% Similarity=0.178 Sum_probs=62.9 Q ss_pred HHHHHHHHHHHHHHCC-CCCCCCCEE--EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH Q ss_conf 9999999888875124-555554112--4776148867889999999999997089977999715379999999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSN-VNNSNPTIF--KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 54 wq~~~l~~~~~~~~~~-~~~~~~~~~--~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) .|.++++.|++.+++. ..-..|..+ -..-+++-|+|||.++-.++-.+.-......-+=++..... ..+.+ T Consensus 513 GQd~AI~~vs~ai~rsraGl~~~~rPigsFlf~GPTGvGKTElAK~LA~~LFg~e~~liR~DMSEy~E~------hsvsr 586 (823) T CHL00095 513 GQDEAVVAVSKAIRRARVGLKNPNRPIASFIFCGPTGVGKTELTKALASYFFGSEEAMIRLDMSEYMEK------HTVSK 586 (823) T ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCC------CCHHH T ss_conf 769999999999999970899899974689987899887799999999997478202588535101554------20767 Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHH Q ss_conf 99862312112333321000123332211113457761266210135445565210113586289997545599889999 Q gi|254781187|r 131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKS 210 (367) Q Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~ 210 (367) .+...| . +.+++.|.. -.|+.. +..+ ..+++||-..-.+++|+. T Consensus 587 LIGaPP-----------------G------YVGy~eGG~----------LTeaVr--r~Py-sVvLfDEIEKAHpdV~ni 630 (823) T CHL00095 587 LIGSPP-----------------G------YVGYNEGGQ----------LTEAVR--KKPY-TVVLFDEIEKAHPDIFNL 630 (823) T ss_pred HCCCCC-----------------C------CCCCCCCCC----------HHHHHH--CCCC-EEEEECHHHHCCHHHHHH T ss_conf 458998-----------------7------667787882----------019887--1998-699862131138899998 Q ss_pred HH-----HHHHCCCCCE Q ss_conf 89-----8740698825 Q gi|254781187|r 211 IL-----GFFTELNPNR 222 (367) Q Consensus 211 i~-----g~Lt~~~~~~ 222 (367) +. |.||++.++. T Consensus 631 lLQvlDdG~LtD~~Gr~ 647 (823) T CHL00095 631 LLQILDDGRLTDSKGRT 647 (823) T ss_pred HHHHCCCCCCCCCCCCE T ss_conf 87651688434899998 No 135 >KOG2170 consensus Probab=94.51 E-value=0.34 Score=26.31 Aligned_cols=126 Identities=13% Similarity=0.089 Sum_probs=70.8 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE--EEE----CCCHHHHHHHHH Q ss_conf 28999999988887512455555411247761488678899999999999970899779--997----153799999999 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSI--ICI----ANSETQLKNTLW 125 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v--~~~----A~t~~Q~~~~lw 125 (367) ..-+.-+++.|-.|..+.. ...|- -+|.-++-|+||++.+-.++--+..-.-.+.. ..+ =|..+-+. -.- T Consensus 88 Hla~~~Vv~alk~~~~n~~-p~KPL--vLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~ie-~Yk 163 (344) T KOG2170 88 HLAKQLVVNALKSHWANPN-PRKPL--VLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKIE-DYK 163 (344) T ss_pred HHHHHHHHHHHHHHHCCCC-CCCCE--EEEECCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHH-HHH T ss_conf 8799999999999862899-99875--8983089987564899999999875112562688765541599767899-999 Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH Q ss_conf 99999998623121123333210001233322111134577612662101354455652101135862899975455998 Q gi|254781187|r 126 AEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD 205 (367) Q Consensus 126 ~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d 205 (367) .++++|++. +.+ +-...++|+||+...|. T Consensus 164 ~eL~~~v~~------------------------------------------------~v~---~C~rslFIFDE~DKmp~ 192 (344) T KOG2170 164 EELKNRVRG------------------------------------------------TVQ---ACQRSLFIFDEVDKLPP 192 (344) T ss_pred HHHHHHHHH------------------------------------------------HHH---HCCCCEEEECHHHHCCH T ss_conf 999999999------------------------------------------------998---55775487310543587 Q ss_pred HHHHHHHHHHH-------CCCCCEEEEEEECCCC Q ss_conf 89999898740-------6988258999807899 Q gi|254781187|r 206 IINKSILGFFT-------ELNPNRFWIMTSNTRR 232 (367) Q Consensus 206 ~i~e~i~g~Lt-------~~~~~~~~i~igNP~r 232 (367) ...++|.|.|- ....+.+.+..||..+ T Consensus 193 gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg 226 (344) T KOG2170 193 GLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGG 226 (344) T ss_pred HHHHHHHHHHCCCCCCCCCCCCCEEEEEECCCCC T ss_conf 6999876663046321355455148999717861 No 136 >PRK06964 DNA polymerase III subunit delta'; Validated Probab=94.44 E-value=0.35 Score=26.21 Aligned_cols=37 Identities=16% Similarity=0.152 Sum_probs=30.2 Q ss_pred CEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC Q ss_conf 2899975455998899998987406988258999807 Q gi|254781187|r 193 MAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSN 229 (367) Q Consensus 193 ~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igN 229 (367) -.+|+|.|.......-.++..+|-.+...++.+++++ T Consensus 134 kVviI~~Ae~mn~~aaNalLK~LEEPp~~~~~iL~~~ 170 (342) T PRK06964 134 RVVVLYPAEALNVAAANALLKTLEEPPPGVVFLLVSA 170 (342) T ss_pred EEEEECCHHHHCHHHHHHHHHHHCCCCCCEEEEEEEC T ss_conf 4999827787389999999997237987848999869 No 137 >KOG0389 consensus Probab=94.43 E-value=0.19 Score=27.89 Aligned_cols=144 Identities=14% Similarity=0.102 Sum_probs=79.0 Q ss_pred EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 76148867889999999999997089977999715379999999999999998623121123333210001233322111 Q gi|254781187|r 81 AISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQ 160 (367) Q Consensus 81 ~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (367) ..+--=|.|||.=+-++..++.--.-+.--+|+.|+. .+. -+-+|+.||.-.+.......-+..+..++..... . T Consensus 422 ILADEMGLGKTiQvIaFlayLkq~g~~gpHLVVvPsS-Tle-NWlrEf~kwCPsl~Ve~YyGSq~ER~~lR~~i~~---~ 496 (941) T KOG0389 422 ILADEMGLGKTIQVIAFLAYLKQIGNPGPHLVVVPSS-TLE-NWLREFAKWCPSLKVEPYYGSQDERRELRERIKK---N 496 (941) T ss_pred EEHHHCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCH-HHH-HHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHC---C T ss_conf 5322205763348999999999729999837992031-688-8999999759752877415768999999999861---6 Q ss_pred CCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCC Q ss_conf 1345776126621013544556521011358628999754559988999989874069882589998078999 Q gi|254781187|r 161 SMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRL 233 (367) Q Consensus 161 ~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~ 233 (367) ...+ ....+.-..-..+.+.-.-++..++.++|.||+....+..-+-....|+-..+..+ +++|+|--+ T Consensus 497 ~~~y---dVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~SeRy~~LM~I~An~Rl-LLTGTPLQN 565 (941) T KOG0389 497 KDDY---DVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRTSERYKHLMSINANFRL-LLTGTPLQN 565 (941) T ss_pred CCCC---CEEEEEEECCCCCHHHHHHHHHCCCCEEEECCHHHHHCCCHHHHHHHCCCCCCCEE-EEECCCCCC T ss_conf 8885---28998721103886778999866666799613265421334988875064655358-851874201 No 138 >COG4889 Predicted helicase [General function prediction only] Probab=94.34 E-value=0.37 Score=26.07 Aligned_cols=91 Identities=23% Similarity=0.137 Sum_probs=60.1 Q ss_pred CCCCCHHHHHHHHHC-CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 012598888554301-4668884436668428999999988887512455555411247761488678899999999999 Q gi|254781187|r 23 ECVLSFKNFVMRFFP-WGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 23 ~~~~~~~~f~~~~~~-w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~ 101 (367) ++..+|...-.+ .| =-+.++||.....||+.|-.+..+.-+|.+.|. +-++..+ -|+|||+.+--+.--. T Consensus 134 ei~es~IDW~~f-~p~e~~~nl~l~~~kk~R~hQq~Aid~a~~~F~~n~------RGkLIMA--cGTGKTfTsLkisEal 204 (1518) T COG4889 134 EIAESPIDWDIF-DPTELQDNLPLKKPKKPRPHQQTAIDAAKEGFSDND------RGKLIMA--CGTGKTFTSLKISEAL 204 (1518) T ss_pred HHHCCCCCHHHC-CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCC------CCCEEEE--CCCCCCCHHHHHHHHH T ss_conf 873288775434-953266565647878998367899999986255166------7758983--3788621378899998 Q ss_pred HHHCCCCEEEEECCCHHHHHHHHHHH Q ss_conf 97089977999715379999999999 Q gi|254781187|r 102 ISTRPGMSIICIANSETQLKNTLWAE 127 (367) Q Consensus 102 ~~~~~~~~v~~~A~t~~Q~~~~lw~e 127 (367) +. .+++..+|+.+-+.+.+ +| T Consensus 205 a~----~~iL~LvPSIsLLsQTl-re 225 (1518) T COG4889 205 AA----ARILFLVPSISLLSQTL-RE 225 (1518) T ss_pred HH----HHEEEECCHHHHHHHHH-HH T ss_conf 64----02365435189999999-98 No 139 >PRK12723 flagellar biosynthesis regulator FlhF; Provisional Probab=94.28 E-value=0.33 Score=26.36 Aligned_cols=73 Identities=10% Similarity=-0.060 Sum_probs=42.4 Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCCCCEEE-EEEECCCCCCHHHHHHHHHHHHHHHCCCC---EEEEECCCHHHHH Q ss_conf 6842899999998888751245555541124-77614886788999999999999708997---7999715379999 Q gi|254781187|r 49 SQPHRWQLEFMEAVDVHCHSNVNNSNPTIFK-CAISAGRGIGKTTLNAWMMLWLISTRPGM---SIICIANSETQLK 121 (367) Q Consensus 49 ~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~-~~v~sgrg~GKS~~~a~~~lw~~~~~~~~---~v~~~A~t~~Q~~ 121 (367) +..++-+..++..+.+.+..........-.| ++..++.|+|||+.+|=++..+.+..... ..++|+.|++-+. T Consensus 145 ~~~~~v~~~l~~~i~~~i~~~~~~~~~~k~~vi~lVGPTGvGKTTTiAKLAa~~~l~~~~k~~~V~lit~DtyRigA 221 (388) T PRK12723 145 DDYDKVRDSVIIYIAKTIKCSGSIIDNLKKRIFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGA 221 (388) T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHH T ss_conf 40879999999999976223666533557628999899887578799999999998626767737999807875889 No 140 >PRK07132 DNA polymerase III subunit delta'; Validated Probab=94.26 E-value=0.39 Score=25.96 Aligned_cols=119 Identities=10% Similarity=0.051 Sum_probs=66.3 Q ss_pred HHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC--------CHHHHHHHHHHH Q ss_conf 999998888751245555541124776148867889999999999997089977999715--------379999999999 Q gi|254781187|r 56 LEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN--------SETQLKNTLWAE 127 (367) Q Consensus 56 ~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~--------t~~Q~~~~lw~e 127 (367) +.+.+.+..-++++.. .|.+ ...+.||+||+.++..++-...|+..+....+..+ ....++. .. T Consensus 4 e~iv~~L~nai~~~kl-sHAY----LF~G~~G~Gk~~~a~~~a~~l~~~~~~~~~~~~~~~~~~~id~~~~~i~~---~~ 75 (303) T PRK07132 4 NNIIKSLDNLAKQNKI-SHSF----LLKSNYNNDLDESILYFLNKFNNLQSLNLNLEELPYNIFLFDIFDEDLSK---EE 75 (303) T ss_pred HHHHHHHHHHHHCCCC-CEEE----EEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCCHHH---HH T ss_conf 3899999999984997-6168----86789986799999999999729987888754565323041332220016---88 Q ss_pred HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHH Q ss_conf 99999862312112333321000123332211113457761266210135445565210113586289997545599889 Q gi|254781187|r 128 VSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDII 207 (367) Q Consensus 128 i~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i 207 (367) +...++. .....++ + |.+ -.+|+|||....... T Consensus 76 i~~~i~~-----------------------------------------~~~~~~~--~---~~~-Kv~IIdea~~lt~~A 108 (303) T PRK07132 76 FLSAIEK-----------------------------------------FSFSSFV--S---NQK-KILIIKNIEKTSNSS 108 (303) T ss_pred HHHHHHH-----------------------------------------HHHCCCC--C---CCE-EEEEEECHHHCCHHH T ss_conf 9999999-----------------------------------------9736655--6---870-699981655339999 Q ss_pred HHHHHHHHHCCCCCEEEEEEEC Q ss_conf 9998987406988258999807 Q gi|254781187|r 208 NKSILGFFTELNPNRFWIMTSN 229 (367) Q Consensus 208 ~e~i~g~Lt~~~~~~~~i~igN 229 (367) +.+++-+|-.+....+.+++.+ T Consensus 109 ~NaLLKtLEEPp~~~~fil~t~ 130 (303) T PRK07132 109 LNALLKTIEEPSKNTYFLLTTK 130 (303) T ss_pred HHHHHHHCCCCCCCEEEEEEEC T ss_conf 9999987038986848999728 No 141 >pfam05894 Podovirus_Gp16 Podovirus DNA encapsidation protein (Gp16). This family consists of several DNA encapsidation protein (Gp16) sequences from the phi-29-like viruses. Gene product 16 catalyses the in vivo and in vitro genome-encapsidation reaction. Probab=94.21 E-value=0.39 Score=25.91 Aligned_cols=145 Identities=19% Similarity=0.192 Sum_probs=74.7 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 24776148867889999999999997089977999715379999999999999998623121123333210001233322 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL 157 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (367) .+..| +|||+|||+.+--.++--++.. |.+.+...-...-++..-=.-........|+.. |. ... T Consensus 19 lnfvI-G~RGiGKTya~k~~~ikd~i~k-GeqFiYLRr~k~El~k~~n~~F~di~~~fpn~e-f~------------Vkg 83 (333) T pfam05894 19 LNFVI-GARGIGKTYALKERVIKDFIKK-GEQFIYLRRYKTELKKLANEFFNDVAHEFPNNE-FY------------VKG 83 (333) T ss_pred EEEEE-ECCCCCHHHHHHHHHHHHHHHC-CCEEEEEEECCHHHHHHHHHHHHHHHHHCCCCE-EE------------EEC T ss_conf 79998-2465540246778889999862-967999991206888777775551665378980-79------------975 Q ss_pred CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC-------CCCCHHHHH---HHHHHHHCCCCCEEEEEE Q ss_conf 1111345776126621013544556521011358628999754-------559988999---989874069882589998 Q gi|254781187|r 158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA-------SGTPDIINK---SILGFFTELNPNRFWIMT 227 (367) Q Consensus 158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEA-------sgI~d~i~e---~i~g~Lt~~~~~~~~i~i 227 (367) ++..+...--.+++.-.+| .+..+..=.+..-+++||. ..+|+++-. .+.-..+. .....+++. T Consensus 84 nki~~~~k~igy~i~LS~~-----q~lKS~~Yp~V~~I~fDEfi~ek~~~~Y~pNev~~llnl~~tV~R~-Re~vr~~~l 157 (333) T pfam05894 84 NKFYIKGELIGYAIPLSNW-----QALKSLAYPNVSTIFFDEFVREKDYGSYDPNEVRNFLNLMDTVFRA-RERVRCICL 157 (333) T ss_pred CEEEECCEEEEEEEEHHHH-----HHHHCCCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHH-CCCEEEEEE T ss_conf 4899878289999863245-----5631347985589983511244544578943899999999998750-377389996 Q ss_pred ECCCCCCCHHHHHHHC Q ss_conf 0789998768875411 Q gi|254781187|r 228 SNTRRLNGWFYDIFNI 243 (367) Q Consensus 228 gNP~r~~g~Fye~~~~ 243 (367) ||--...|+.+..|+- T Consensus 158 sNAv~i~NPYF~~f~~ 173 (333) T pfam05894 158 SNAVSIVNPYFLLFHI 173 (333) T ss_pred CCHHHCCCHHHEEEEC T ss_conf 4704204725515511 No 142 >PRK07276 DNA polymerase III subunit delta'; Validated Probab=94.15 E-value=0.41 Score=25.83 Aligned_cols=136 Identities=11% Similarity=0.099 Sum_probs=69.7 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC-CHHHHHHHHHHHHHHH Q ss_conf 899999998888751245555541124776148867889999999999997089977999715-3799999999999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN-SETQLKNTLWAEVSKW 131 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~-t~~Q~~~~lw~ei~k~ 131 (367) +.|-++...+..-++++.. .|.+.| +| |+||..++-+++-+.+|..+....-|-.- .-+++.. T Consensus 5 ~~Qp~i~~~l~~~i~~~rl-~HAyLf-----~G-~~Gk~~~A~~~A~~l~C~~~~~~~pCg~C~~C~~i~~--------- 68 (290) T PRK07276 5 QKQPKLFQRFQTILEQDRL-NHAYLF-----SG-DFASFEMALFLAQSLFCEQKEDVLPCGHCRSCRLIEQ--------- 68 (290) T ss_pred HHHHHHHHHHHHHHHCCCC-CEEEEC-----CC-CCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHC--------- T ss_conf 8789999999999984996-505421-----69-8687999999999981899999898988999999876--------- Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHH Q ss_conf 98623121123333210001233322111134577612662101354455652101135862899975455998899998 Q gi|254781187|r 132 LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSI 211 (367) Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i 211 (367) ...|+-+....+. ..++.+. ..-... .-+..+..|.+ -.+|+|+|.........++ T Consensus 69 -~~hpDv~~i~~~~--------------~~I~vd~--IR~l~~------~~~~~~~~g~~-KV~II~~Ad~mt~~AaNaL 124 (290) T PRK07276 69 -GDFSDVTVIEPQG--------------QVIKTDT--IRELTA------NFSQSGYEGKR-QVFIIKDADKMHVNAANSL 124 (290) T ss_pred -CCCCCCEEECCCC--------------CCCCHHH--HHHHHH------HHHHCCCCCCE-EEEEECCHHHCCHHHHHHH T ss_conf -9998713771677--------------7576889--999999------98445613782-7999776565299999999 Q ss_pred HHHHHCCCCCEEEEEEE Q ss_conf 98740698825899980 Q gi|254781187|r 212 LGFFTELNPNRFWIMTS 228 (367) Q Consensus 212 ~g~Lt~~~~~~~~i~ig 228 (367) ..+|-.+....+++++. T Consensus 125 LK~LEEPp~~t~~iLlt 141 (290) T PRK07276 125 LKVIEEPQSEIYIFLLT 141 (290) T ss_pred HHHHCCCCCCCEEEEEE T ss_conf 99703898883799887 No 143 >PRK05917 DNA polymerase III subunit delta'; Validated Probab=94.14 E-value=0.41 Score=25.83 Aligned_cols=166 Identities=10% Similarity=-0.008 Sum_probs=80.8 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH Q ss_conf 28999999988887512455555411247761488678899999999999970899779997153799999999999999 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW 131 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~ 131 (367) ..||. +...++++.. .| .....+..|+||+.++-.++-..+|...+.. ..+ +.. T Consensus 4 ~~We~-----L~~~i~~~Rl-~H----AyLf~Gp~G~GK~~~A~~~A~~LLc~~~p~~-------~~~--------i~~- 57 (290) T PRK05917 4 AAWEA-----LLQRVRDQKV-PS----AILLHGQDLSNLSQYAYELASLILLESSPEA-------QYK--------ISQ- 57 (290) T ss_pred HHHHH-----HHHHHHCCCC-CE----EEEEECCCCCCHHHHHHHHHHHHHCCCCCCH-------HHH--------HHH- T ss_conf 49999-----9999983996-60----6876899986599999999999857899616-------889--------874- Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHH Q ss_conf 98623121123333210001233322111134577612662101354455652101135862899975455998899998 Q gi|254781187|r 132 LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSI 211 (367) Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i 211 (367) ..-|+-+++...... .. .+.+. .+.... --++....|.+ -.+|+|||.........++ T Consensus 58 -~~HPD~~~i~pe~k~--------~~----~~Id~------iR~l~~--~i~~~p~~g~~-KV~IId~Ad~Mn~~AaNAL 115 (290) T PRK05917 58 -KIHPDIHEFFPEGKG--------RL----HSIET------PRAIKK--QIWIHPYEANY-KIYIIHEADRMTLDAISAF 115 (290) T ss_pred -CCCCCEEEECCCCCC--------CC----CCHHH------HHHHHH--HHCCCCCCCCC-EEEEECCHHHHCHHHHHHH T ss_conf -689985996157778--------87----86789------999999--96418646882-6999756776389999999 Q ss_pred HHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHH Q ss_conf 987406988258999807899987688754112235046752333288889889999996 Q gi|254781187|r 212 LGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRTVEGIDSGFHEGIIS 271 (367) Q Consensus 212 ~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d~p~~~~~~i~~~~~ 271 (367) ..+|-.+...++.+++.+-+ . ..-.-=+.+=..++++-.+-...+++.++.+.+ T Consensus 116 LKtLEEPP~~tvfILit~~~--~----~lLpTI~SRCQ~I~i~~~e~~~i~~e~~~~l~~ 169 (290) T PRK05917 116 LKVLEDPPKHSVIILTSAKP--Q----RLPPTIRSRSLSIHIPGEEKTLPSKEDIAYLIR 169 (290) T ss_pred HHHHCCCCCCEEEEEEECCH--H----HCCHHHHHCCCEEECCCCCCCCCCHHHHHHHHH T ss_conf 99734798785999986992--5----482377633511677762013478899999999 No 144 >KOG0342 consensus Probab=94.08 E-value=0.42 Score=25.74 Aligned_cols=168 Identities=13% Similarity=0.061 Sum_probs=85.9 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHH---H--CCCCEEEEECCCHHH Q ss_conf 43666842899999998888751245555541124776148867889999999999997---0--899779997153799 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIS---T--RPGMSIICIANSETQ 119 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~---~--~~~~~v~~~A~t~~Q 119 (367) -++|..=+.-|.+.+..+-+.. .+.++|-.|+|||...-.-++-++. + +++..+++++||..- T Consensus 99 ~~GF~~MT~VQ~~ti~pll~gk------------Dvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r~~~~vlIi~PTREL 166 (543) T KOG0342 99 EMGFETMTPVQQKTIPPLLEGK------------DVLAAAKTGTGKTLAFLLPAIELLRKLKFKPRNGTGVLIICPTREL 166 (543) T ss_pred HCCCCCCHHHHHHHCCCCCCCC------------CCEEEECCCCCCEEEEHHHHHHHHHHCCCCCCCCEEEEEECCCHHH T ss_conf 3585300288874267667984------------3124512688741010468999998536577787148996562899 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCC-CCCCCCCCCCCCCCCEEEEE Q ss_conf 99999999999998623121123333210001233322111134577612662101354-45565210113586289997 Q gi|254781187|r 120 LKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSE-ERPDTFVGPHNTHGMAVFND 198 (367) Q Consensus 120 ~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~ea~~g~h~~~~~l~ivD 198 (367) +.++ ++|+++.+.-.+. .+.. +-+-+........ +...+.....|.+-+. +--++-.|+-..+.-++|+| T Consensus 167 A~Q~-~~eak~Ll~~h~~-~~v~-----~viGG~~~~~e~~--kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~lvlD 237 (543) T KOG0342 167 AMQI-FAEAKELLKYHES-ITVG-----IVIGGNNFSVEAD--KLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCLVLD 237 (543) T ss_pred HHHH-HHHHHHHHHHCCC-CCEE-----EEECCCCCHHHHH--HHHCCCCEEEECCCHHHHHHHCCCCCHHHCCCEEEEE T ss_conf 9989-9999999972767-7347-----8767741058999--7515552788678417767655784122122035750 Q ss_pred CCCCCCHHHH----HHHHHHHHCCCCCEEEEEEECCCCCC Q ss_conf 5455998899----99898740698825899980789998 Q gi|254781187|r 199 EASGTPDIIN----KSILGFFTELNPNRFWIMTSNTRRLN 234 (367) Q Consensus 199 EAsgI~d~i~----e~i~g~Lt~~~~~~~~i~igNP~r~~ 234 (367) ||.-+-|.-| +-|...+.. ..+.+++...-|++-. T Consensus 238 EADrlLd~GF~~di~~Ii~~lpk-~rqt~LFSAT~~~kV~ 276 (543) T KOG0342 238 EADRLLDIGFEEDVEQIIKILPK-QRQTLLFSATQPSKVK 276 (543) T ss_pred CCHHHHHCCCHHHHHHHHHHCCC-CCCEEEEECCCCHHHH T ss_conf 20356652518889999875235-5304676478968899 No 145 >PRK07940 DNA polymerase III subunit delta'; Validated Probab=93.98 E-value=0.44 Score=25.63 Aligned_cols=138 Identities=15% Similarity=0.190 Sum_probs=72.1 Q ss_pred HHHHHHHHHHHHHCCC-----------CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH Q ss_conf 9999998888751245-----------55554112477614886788999999999999708997799971537999999 Q gi|254781187|r 55 QLEFMEAVDVHCHSNV-----------NNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT 123 (367) Q Consensus 55 q~~~l~~~~~~~~~~~-----------~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~ 123 (367) |+.+.+.+..-++.+. ...|.+ ...+++|+||+.++-+++--++|.+++..- |- .-. . T Consensus 10 Qe~v~~~L~~A~~~~R~~~~~~~~~~~~~~HAy----LF~Gp~G~Gk~~~A~~~A~~l~C~~~~~~~-cg--~C~----~ 78 (395) T PRK07940 10 QDAVVAELRAAARAARADSAHSAAAGSGMTHAW----LFTGPPGSGRSNAARAFAAALQCTDPGVPG-CG--ECR----A 78 (395) T ss_pred CHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEE----EEECCCCCCHHHHHHHHHHHHCCCCCCCCC-CC--CCH----H T ss_conf 299999999999836343443333468766037----636899878899999999996699999999-98--787----8 Q ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC Q ss_conf 99999999986231211233332100012333221111345776126621013544556521011358628999754559 Q gi|254781187|r 124 LWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT 203 (367) Q Consensus 124 lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI 203 (367) + ..+. ....|+-++....... ++.+. .+-.. ..-++....|.+. .+|+|||... T Consensus 79 C-~~i~--~g~hpDv~~i~p~~~~--------------i~id~------iR~l~--~~~~~~p~~~~~k-v~ii~~a~~m 132 (395) T PRK07940 79 C-RTVL--AGTHPDVRVVVPEGLS--------------IGVDE------VREIV--QIAARRPTTGRWR-IVVIEDADRL 132 (395) T ss_pred H-HHHH--CCCCCCEEEEECCCCC--------------CCHHH------HHHHH--HHHHHCCCCCCCE-EEEEECHHHH T ss_conf 9-9987--6899871898268776--------------88999------99999--9985273037955-9998077874 Q ss_pred CHHHHHHHHHHHHCCCCCEEEEEEEC Q ss_conf 98899998987406988258999807 Q gi|254781187|r 204 PDIINKSILGFFTELNPNRFWIMTSN 229 (367) Q Consensus 204 ~d~i~e~i~g~Lt~~~~~~~~i~igN 229 (367) .....+++..+|-.+-...++++..+ T Consensus 133 ~~~a~NalLKtLEEPp~~~~fiL~t~ 158 (395) T PRK07940 133 TERAANALLKAVEEPPPRTVWLLCAP 158 (395) T ss_pred CHHHHHHHHHHHCCCCCCEEEEEEEC T ss_conf 89999999985217888869998739 No 146 >pfam00580 UvrD-helicase UvrD/REP helicase. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Bacillus subtilis addA and Escherichia coli exodeoxyribonuclease V beta have large insertions near to the carboxy-terminus relative to other members of the family. Probab=93.92 E-value=0.1 Score=29.53 Aligned_cols=45 Identities=20% Similarity=0.266 Sum_probs=36.3 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHH Q ss_conf 477614886788999999999999708--997799971537999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTR--PGMSIICIANSETQLKNT 123 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~--~~~~v~~~A~t~~Q~~~~ 123 (367) .+.|.||=|+|||+....-+++++... ++.+|+++.-|.+-+.++ T Consensus 15 ~llV~AgAGSGKT~~L~~Ri~~li~~~~~~p~~IL~lTFT~kAA~Em 61 (494) T pfam00580 15 PLLVLAGAGTGKTRVLTERIAYLILEGGIDPEEILAVTFTNKAAREM 61 (494) T ss_pred CEEEEEECCHHHHHHHHHHHHHHHHHCCCCHHHEEEEECHHHHHHHH T ss_conf 97999718706899999999999981899974787670289999999 No 147 >KOG1015 consensus Probab=93.73 E-value=0.21 Score=27.61 Aligned_cols=160 Identities=16% Similarity=0.127 Sum_probs=78.7 Q ss_pred EEEECCCCCCHHHHHHHHH-HHHHHHCCC-CEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC-------- Q ss_conf 7761488678899999999-999970899-779997153799999999999999986231211233332100-------- Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMM-LWLISTRPG-MSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLH-------- 149 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~-lw~~~~~~~-~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~-------- 149 (367) ..++-+-|.|||.-+-.++ .-++|..-+ .+++|+.|. +.+- -.+.|+.+|...+.+..-+++..+..+ T Consensus 699 cILAHcMGLGKTlQVvtflhTvL~c~klg~ktaLvV~Pl-Nt~~-NW~~EFekWm~~~e~~~~leV~eL~~vkr~e~R~~ 776 (1567) T KOG1015 699 CILAHCMGLGKTLQVVTFLHTVLLCDKLGFKTALVVCPL-NTAL-NWMNEFEKWMEGLEDDEKLEVSELATVKRPEERSY 776 (1567) T ss_pred HHHHHHHCCCCEEHHHHHHHHHHHHHCCCCCEEEEECCH-HHHH-HHHHHHHHHCCCCCCCCCCEEEHHHHCCCHHHHHH T ss_conf 177875045640014678889987420478568997235-9988-99999998612422246621202120267488999 Q ss_pred -CCCCCCCCCCCCCCCCCCCEEEEECCC--CCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEE Q ss_conf -012333221111345776126621013--54455652101135862899975455998899998987406988258999 Q gi|254781187|r 150 -PSGWYAELLEQSMGIDSKHYTITCRTY--SEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIM 226 (367) Q Consensus 150 -~~~~~~~~~~~~~~~~~~~~~~~a~~~--~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~ 226 (367) +..|....-..-++++.=...+.++.- +.....-.+.+-.....+++.|||.-+.++--.+...+..-...+.+ |+ T Consensus 777 ~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKNeksa~Skam~~irtkRRI-~L 855 (1567) T KOG1015 777 MLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKNEKSAVSKAMNSIRTKRRI-IL 855 (1567) T ss_pred HHHHHHHCCCEEEEEHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCEEEECCHHHHCCCHHHHHHHHHHHHHHEEE-EE T ss_conf 99999752977997368888775145603567999999860578997687242122135247899999987764047-75 Q ss_pred EECCCCCCCHHHHHHH Q ss_conf 8078999876887541 Q gi|254781187|r 227 TSNTRRLNGWFYDIFN 242 (367) Q Consensus 227 igNP~r~~g~Fye~~~ 242 (367) +|+|--+.=.-|-|+- T Consensus 856 TGTPLQNNLmEY~CMV 871 (1567) T KOG1015 856 TGTPLQNNLMEYHCMV 871 (1567) T ss_pred ECCCHHHHHHHHHHHH T ss_conf 2671133248887888 No 148 >TIGR00631 uvrb excinuclease ABC, B subunit; InterPro: IPR004807 All proteins in this family for which functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0005737 cytoplasm, 0009380 excinuclease repair complex. Probab=93.72 E-value=0.48 Score=25.38 Aligned_cols=189 Identities=15% Similarity=0.138 Sum_probs=104.3 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH Q ss_conf 99999988887512455555411247761488678899999999999970899779997153799999999999999986 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM 134 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~ 134 (367) |=++.+.+.+.++.|.. +.+ ..+-.|+|||+.+|++|-= -+.=.+|+|+.. .|.--|..|+|.+ T Consensus 14 QP~AI~~L~~~l~~G~~------~Qt-LLGvTGsGKTFT~AnVIa~-----~~rPTLV~aHNK-TLAAQLY~EfKef--- 77 (667) T TIGR00631 14 QPKAIAKLVEGLEAGEK------EQT-LLGVTGSGKTFTMANVIAQ-----VQRPTLVLAHNK-TLAAQLYNEFKEF--- 77 (667) T ss_pred HHHHHHHHHHHHHCCCC------CEE-EEEEECCCHHHHHHHHHHH-----HCCCEEEECCCH-HHHHHHHHHHHHH--- T ss_conf 18999999999856887------147-8532148627889899998-----479849985777-6799999999863--- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHH---HHH Q ss_conf 23121123333210001233322111134577612662101354455652101135862899975455998899---998 Q gi|254781187|r 135 LPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIIN---KSI 211 (367) Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~---e~i 211 (367) .|+. + - +++..+ .+=.+|||+=--. .+.| +==|.|-|+|- =.+ T Consensus 78 FPeN------A-----V----EYFvSY--------------YDYYQPEAYvP~~----DtyI-EKdaSINdeIerlR~SA 123 (667) T TIGR00631 78 FPEN------A-----V----EYFVSY--------------YDYYQPEAYVPSK----DTYI-EKDASINDEIERLRLSA 123 (667) T ss_pred CCCC------C-----E----EEEEEC--------------CCCCCCCCCCCCC----CCEE-ECCCCHHHHHHHHHHHH T ss_conf 8677------2-----4----525520--------------3237873214798----8413-04553004676778898 Q ss_pred HHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHHH---------CCCCCCEEEE Q ss_conf 9874069882589998078999876887541122350467523332888898899999962---------1688000268 Q gi|254781187|r 212 LGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRTVEGIDSGFHEGIISR---------YGLDSDVARI 282 (367) Q Consensus 212 ~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d~p~~~~~~i~~~~~~---------~gedS~~~r~ 282 (367) .-+|.+..--+...++|.=-+. .....|..+.++-.-...++.+.+.+..-. +..++..+|= T Consensus 124 T~SLl~RrDVIVVASVScIYGL---------G~P~~Y~~~~~~l~vG~~~~~~~ll~~LV~lqY~RNd~~f~RG~FRvrG 194 (667) T TIGR00631 124 TKSLLERRDVIVVASVSCIYGL---------GSPEEYLKMVLHLEVGKEIDRRELLRRLVELQYERNDVDFQRGTFRVRG 194 (667) T ss_pred HHHHCCCCCEEEEEEEEEECCC---------CCCHHHHCCEEEEEECCCCCHHHHHHHHHHHCEEECCEECCCCCEEEEE T ss_conf 8864237878999875520688---------8825564227865407855889999886340305712340577125763 Q ss_pred EEEEEEC-CCCCCEEECHHHH Q ss_conf 8864432-7789807829998 Q gi|254781187|r 283 EILGQFP-QQEVNNFIPHNYI 302 (367) Q Consensus 283 ev~G~Fp-~~~~d~~ip~~~i 302 (367) .|-=.|| ..+++-.+-.++. T Consensus 195 DVvEIfP~~~~~~~~~RiEfF 215 (667) T TIGR00631 195 DVVEIFPAAYEDEFAVRIEFF 215 (667) T ss_pred EEEEEECCCCCCCCEEEEEEE T ss_conf 189863477677724899852 No 149 >PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional Probab=93.68 E-value=0.5 Score=25.29 Aligned_cols=47 Identities=15% Similarity=0.094 Sum_probs=26.4 Q ss_pred HHHHHHHHHHHHHHCC-CCCCCC--CEEEEEEECCCCCCHHHHHHHHHHH Q ss_conf 9999999888875124-555554--1124776148867889999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSN-VNNSNP--TIFKCAISAGRGIGKTTLNAWMMLW 100 (367) Q Consensus 54 wq~~~l~~~~~~~~~~-~~~~~~--~~~~~~v~sgrg~GKS~~~a~~~lw 100 (367) .|.+++..+++.+++. ..-..| .+--..-.++.|+|||.++-.++-. T Consensus 462 GQ~~Ai~~v~~ai~~~raGL~~~~rPigsFlf~GPTGVGKTElak~LA~~ 511 (758) T PRK11034 462 GQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKA 511 (758) T ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHH T ss_conf 54999999999999986388899997058999789987779999999999 No 150 >PHA00149 DNA encapsidation protein Probab=93.62 E-value=0.51 Score=25.23 Aligned_cols=143 Identities=20% Similarity=0.241 Sum_probs=76.1 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH--HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 1247761488678899999999999970899779997153799999--99999999998623121123333210001233 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN--TLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWY 154 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~--~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~ 154 (367) +.+..| ++||+|||+.+--.++--++.. |.+.+...-...-++. ..++.+ ....|+ +-|.. T Consensus 18 ~l~fvi-G~RgiGKTya~k~~~~k~~i~k-geqfiyLRr~k~El~~k~~Ff~d~---~~~~~~-~ef~V----------- 80 (331) T PHA00149 18 ILNFVI-GARGIGKTYALKKYLIKRFIKK-GEQFIYLRRYKSELKKKSKFFADI---AQEFPN-TEFEV----------- 80 (331) T ss_pred EEEEEE-ECCCCCHHHHHHHHHHHHHHHC-CCEEEEEEECCHHHHHHHHHHHHH---HHHCCC-CCEEE----------- T ss_conf 469998-2465440357778899999862-967999993243452021056789---975789-74599----------- Q ss_pred CCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC-------CCCCHHHH---HHHHHHHHCCCCCEEE Q ss_conf 3221111345776126621013544556521011358628999754-------55998899---9989874069882589 Q gi|254781187|r 155 AELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA-------SGTPDIIN---KSILGFFTELNPNRFW 224 (367) Q Consensus 155 ~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEA-------sgI~d~i~---e~i~g~Lt~~~~~~~~ 224 (367) ..++..+...--.+.+.-+ +..++.|..=.+..-+++||. ..+|+++- ..+.-..+.. ....+ T Consensus 81 -k~~ki~~~~k~igy~i~lS-----~~q~~Ks~~Yp~V~~I~fDEfi~~k~n~~Ylpne~~allnli~tV~R~R-e~i~~ 153 (331) T PHA00149 81 -KGRKIYIKGKLIGYAIPLS-----TWQALKSSAYPNVSTIFFDEFIREKDNKRYLPNEVDALLNLIDTVFRAR-ERVRC 153 (331) T ss_pred -EEEEEEECCEEEEEEEEHH-----HHHHHCCCCCCCEEEEEEEHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH-CCEEE T ss_conf -7008998680799997044-----6776325689955899712233305433568850899999999987753-57599 Q ss_pred EEEECCCCCCCHHHHHHHC Q ss_conf 9980789998768875411 Q gi|254781187|r 225 IMTSNTRRLNGWFYDIFNI 243 (367) Q Consensus 225 i~igNP~r~~g~Fye~~~~ 243 (367) +++||-.-..|+++.-|+- T Consensus 154 ~~lsNa~~~~NPyF~yf~~ 172 (331) T PHA00149 154 ICLSNAVSIVNPYFLYFGL 172 (331) T ss_pred EEECCCCCCCCCHHHEEEE T ss_conf 9975854303604423421 No 151 >PRK12724 flagellar biosynthesis regulator FlhF; Provisional Probab=93.59 E-value=0.51 Score=25.22 Aligned_cols=42 Identities=14% Similarity=-0.036 Sum_probs=34.0 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH Q ss_conf 477614886788999999999999708997799971537999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQL 120 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~ 120 (367) -++..++.|+|||+.+|=++.-+.+.+.....++|+.|++=+ T Consensus 225 vi~lVGPTGVGKTTTiAKLAA~~~l~~~kkVaLIT~DTYRIg 266 (432) T PRK12724 225 VVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDNYRIA 266 (432) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCCHH T ss_conf 999989999888999999999999974992799952665377 No 152 >PRK00411 cdc6 cell division control protein 6; Reviewed Probab=93.51 E-value=0.53 Score=25.11 Aligned_cols=70 Identities=17% Similarity=0.156 Sum_probs=36.9 Q ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE----CCCHHHHHHHHHHHH Q ss_conf 999988887512455555411247761488678899999999999970899779997----153799999999999 Q gi|254781187|r 57 EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI----ANSETQLKNTLWAEV 128 (367) Q Consensus 57 ~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~----A~t~~Q~~~~lw~ei 128 (367) +-++.|+.+++.-.....| .++.|.+.-|+|||..+-..+-.+--...+..++.+ .+|..|+-..++..+ T Consensus 37 ~Ei~~l~~~l~~~l~g~~~--~n~~I~G~pGTGKT~~vk~v~~~l~~~~~~~~~vyINc~~~~t~~~i~~~i~~~L 110 (394) T PRK00411 37 EQIEELAFALRPALRGSRP--SNVLILGPPGTGKTTTVKKVFEELEEAALKVVYVYINCQIDRTRYAILSEIARSL 110 (394) T ss_pred HHHHHHHHHHHHHHCCCCC--CCEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHH T ss_conf 9999999999999759999--8479988999989999999999999746896599996966898999999999995 No 153 >COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion] Probab=93.37 E-value=0.18 Score=28.06 Aligned_cols=51 Identities=25% Similarity=0.274 Sum_probs=38.2 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 89999999888875124555554112477614886788999999999999708997799971537 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) .=|.++|+.+... +.++.|++|.|+|||++..++... --++.+++|+-.|. T Consensus 160 ~~~a~~L~~av~~-----------r~NILisGGTGSGKTTlLNal~~~---i~~~eRvItiEDta 210 (355) T COG4962 160 RRAAKFLRRAVGI-----------RCNILISGGTGSGKTTLLNALSGF---IDSDERVITIEDTA 210 (355) T ss_pred HHHHHHHHHHHHH-----------CEEEEEECCCCCCHHHHHHHHHHC---CCCCCEEEEEEEHH T ss_conf 8999999999862-----------015999678788799999999715---79765089981236 No 154 >KOG0339 consensus Probab=93.31 E-value=0.54 Score=25.07 Aligned_cols=158 Identities=18% Similarity=0.133 Sum_probs=82.8 Q ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC------CCEEEEECCCHHHHH Q ss_conf 66842899999998888751245555541124776148867889999999999997089------977999715379999 Q gi|254781187|r 48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP------GMSIICIANSETQLK 121 (367) Q Consensus 48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~------~~~v~~~A~t~~Q~~ 121 (367) |..|+.-|+.+|-... ....+ +-| |-.|+||+...+|-++-++.-.| +.-.++++||..-+. T Consensus 243 y~kptpiq~qalptal---------sgrdv--igI-AktgSgktaAfi~pm~~himdq~eL~~g~gPi~vilvPTrela~ 310 (731) T KOG0339 243 YEKPTPIQCQALPTAL---------SGRDV--IGI-AKTGSGKTAAFIWPMIVHIMDQPELKPGEGPIGVILVPTRELAS 310 (731) T ss_pred CCCCCCCCCCCCCCCC---------CCCCC--HHE-EECCCCCHHHHHHHHHHHHCCHHHHCCCCCCEEEEEECCHHHHH T ss_conf 0467752334355224---------66521--111-21157505677777777741405206899976999806389999 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC Q ss_conf 99999999999862312112333321000123332211113457761266210135445565210113586289997545 Q gi|254781187|r 122 NTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS 201 (367) Q Consensus 122 ~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs 201 (367) ++ +.|.|++-...-...-..+.-...| ...-....|.-++.|.+-|.-.--.+.+..-.+..++++|||. T Consensus 311 Qi-~~eaKkf~K~ygl~~v~~ygGgsk~---------eQ~k~Lk~g~EivVaTPgRlid~VkmKatn~~rvS~LV~DEad 380 (731) T KOG0339 311 QI-FSEAKKFGKAYGLRVVAVYGGGSKW---------EQSKELKEGAEIVVATPGRLIDMVKMKATNLSRVSYLVLDEAD 380 (731) T ss_pred HH-HHHHHHHHHHCCCEEEEEECCCCHH---------HHHHHHHCCCEEEEECHHHHHHHHHHHCCCCEEEEEEEEECHH T ss_conf 99-9999986311264278863687488---------8777650277289966288899988603331003578871111 Q ss_pred CCCHHHHH----HHHHHHHCCCCCEEEEEEECC Q ss_conf 59988999----989874069882589998078 Q gi|254781187|r 202 GTPDIINK----SILGFFTELNPNRFWIMTSNT 230 (367) Q Consensus 202 gI~d~i~e----~i~g~Lt~~~~~~~~i~igNP 230 (367) -.=+.=|+ .|-..++. +... ++|+++ T Consensus 381 rmfdmGfe~qVrSI~~hirp-drQt--llFsaT 410 (731) T KOG0339 381 RMFDMGFEPQVRSIKQHIRP-DRQT--LLFSAT 410 (731) T ss_pred HHHCCCCHHHHHHHHHHCCC-CCEE--EEEECC T ss_conf 13126547989999864488-6427--986031 No 155 >PRK10416 cell division protein FtsY; Provisional Probab=93.28 E-value=0.58 Score=24.89 Aligned_cols=106 Identities=15% Similarity=0.165 Sum_probs=56.8 Q ss_pred CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC Q ss_conf 5411247761488678899999999999970899779997-153799999999999999986231211233332100012 Q gi|254781187|r 74 NPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-ANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSG 152 (367) Q Consensus 74 ~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~ 152 (367) .|.+ +.+.+=.|+|||+.++=++.|+.- .+.+|++. +-|++-+- ...++.|.++.-. T Consensus 294 ~P~V--Il~vGvNG~GKTTTigKLA~~~~~--~gkkVllaA~DTfRaAA---ieQL~~w~~r~~v--------------- 351 (499) T PRK10416 294 TPFV--ILMVGVNGVGKTTTIGKLARQFEQ--QGKSVMLAAGDTFRAAA---VEQLQVWGQRNNI--------------- 351 (499) T ss_pred CCEE--EEEECCCCCCHHHHHHHHHHHHHH--CCCCEEEEEECCCCHHH---HHHHHHHHCCCCC--------------- T ss_conf 9879--999747878789899999999997--79953788406675689---9999998424573--------------- Q ss_pred CCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC--HHHHHHHHHH Q ss_conf 3332211113457761266210135445565210113586289997545599--8899998987 Q gi|254781187|r 153 WYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP--DIINKSILGF 214 (367) Q Consensus 153 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~--d~i~e~i~g~ 214 (367) .......+.++.... -++++.....+...+|+|-|.-.. ...++-+... T Consensus 352 ---~vi~~~~g~Dpa~V~----------~dai~~a~~~~~DvviiDTAGRl~~~~~LM~EL~ki 402 (499) T PRK10416 352 ---PVIAQHTGADSASVI----------FDAIQAAKARNVDVLIADTAGRLQNKSHLMEELKKI 402 (499) T ss_pred ---EEEECCCCCCHHHHH----------HHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHH T ss_conf ---698368999979999----------999999997299989985776432609999999999 No 156 >KOG0334 consensus Probab=93.03 E-value=0.45 Score=25.57 Aligned_cols=75 Identities=24% Similarity=0.252 Sum_probs=47.6 Q ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH-HHHCC-----CCEEEEECCCHHHHH Q ss_conf 668428999999988887512455555411247761488678899999999999-97089-----977999715379999 Q gi|254781187|r 48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWL-ISTRP-----GMSIICIANSETQLK 121 (367) Q Consensus 48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~-~~~~~-----~~~v~~~A~t~~Q~~ 121 (367) +..|+..|..++-.|-.. .-|...|=-|+|||...-..++=+ ...++ |...+++|||..++. T Consensus 385 y~k~~~IQ~qAiP~ImsG------------rdvIgvakTgSGKT~af~LPmirhi~dQr~~~~gdGPi~li~aPtrela~ 452 (997) T KOG0334 385 YEKPTPIQAQAIPAIMSG------------RDVIGVAKTGSGKTLAFLLPMIRHIKDQRPLEEGDGPIALILAPTRELAM 452 (997) T ss_pred CCCCCCHHHHHCCHHCCC------------CCEEEEECCCCCCCHHHHHHHHHHHCCCCCHHCCCCCEEEEECCCHHHHH T ss_conf 899875566430122257------------74587732688620344211555420479711078864799737778999 Q ss_pred HHHHHHHHHHHHHC Q ss_conf 99999999999862 Q gi|254781187|r 122 NTLWAEVSKWLSML 135 (367) Q Consensus 122 ~~lw~ei~k~~~~~ 135 (367) ++ .++++++...+ T Consensus 453 QI-~r~~~kf~k~l 465 (997) T KOG0334 453 QI-HREVRKFLKLL 465 (997) T ss_pred HH-HHHHHHHHHHC T ss_conf 99-99999987741 No 157 >pfam02456 Adeno_IVa2 Adenovirus IVa2 protein. IVa2 protein can interact with the adenoviral packaging signal and that this interaction involves DNA sequences that have previously been demonstrated to be required for packaging. During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter. Probab=92.88 E-value=0.21 Score=27.62 Aligned_cols=84 Identities=11% Similarity=0.033 Sum_probs=56.0 Q ss_pred HHHHHHHHHHHHHHHHCCCC----CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH Q ss_conf 28999999988887512455----55541124776148867889999999999997089977999715379999999999 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVN----NSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAE 127 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~----~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~e 127 (367) ..-..+++..-..+++.+.. ++.-.=+=..|-++.|.|||.+.-.++---++.-++.+|+.++|+...+- -.| T Consensus 58 ~~~~~~~~n~~~~~L~~dG~~~SLNy~~qP~I~vVYGPTG~GKSQLlRNlis~~lI~P~PETVfFItPq~~mIp---p~E 134 (370) T pfam02456 58 MEAVHGQLNEASRYLRPDGELPSLNYGLQPVIGVVYGPTGCGKSQLLRNLLSCQLIQPIPETVFFITPQKDMIP---PQE 134 (370) T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCC---HHH T ss_conf 99999999863154066896575546787449999889987789999998734667799972899767778679---899 Q ss_pred HHHHHHHCCCC Q ss_conf 99999862312 Q gi|254781187|r 128 VSKWLSMLPHR 138 (367) Q Consensus 128 i~k~~~~~~~~ 138 (367) +.-|-..+-.. T Consensus 135 ~~aWe~Ql~EG 145 (370) T pfam02456 135 QTAWELQLCEG 145 (370) T ss_pred HHHHHHHHHHC T ss_conf 99999998735 No 158 >PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated Probab=92.88 E-value=0.67 Score=24.52 Aligned_cols=69 Identities=17% Similarity=0.117 Sum_probs=41.7 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCC---CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEE-EEECCCHHHH Q ss_conf 84289999999888875124555---55411247761488678899999999999970899779-9971537999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNN---SNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSI-ICIANSETQL 120 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~---~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v-~~~A~t~~Q~ 120 (367) +...++.++++.+.+.+...... ......-+.+.+..|+|||+.+|=++.|+. .+ +.++ ++++-|++-+ T Consensus 45 ~~~~~~~~vi~~l~~~l~~~~~~~~~~~~~~~vI~lvG~~G~GKTTT~AKLA~~~~-~~-~~kV~lia~DtyR~a 117 (270) T PRK06731 45 NATMITEEVIEYILEDMSSHFNTENVFEKEVQTIALIGPTGVGKTTTLAKMAWQFH-GK-KKTVGFITTDHSRIG 117 (270) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHH-HC-CCEEEEEEECCCCHH T ss_conf 45532999999999999875076654679981899988898988999999999998-67-990899983888888 No 159 >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=92.73 E-value=0.68 Score=24.47 Aligned_cols=40 Identities=25% Similarity=0.137 Sum_probs=26.5 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH Q ss_conf 477614886788999999999999708997799971537999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQL 120 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~ 120 (367) .+.+.++-|+|||+++..++.-..... ..++.++...... T Consensus 4 ~ill~G~~GsGKTtl~~~la~~~~~~~--~~v~~~~~~~~~~ 43 (148) T smart00382 4 VILIVGPPGSGKTTLARALARELGPPG--GGVIYIDGEDILE 43 (148) T ss_pred EEEEECCCCHHHHHHHHHHHHHHCCCC--CCEEEEEHHHHHH T ss_conf 899999997029999999998726689--9689987599898 No 160 >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=92.71 E-value=0.7 Score=24.38 Aligned_cols=65 Identities=15% Similarity=0.175 Sum_probs=45.0 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH Q ss_conf 99999988887512455555411247761488678899999999999970899779997153799999999999999986 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM 134 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~ 134 (367) |.|+++++.+.. .+ =+.+.|+.|+|||..+-.-++ ..+.+++++.|+..-+.|.. ..++++++. T Consensus 2 q~~~~~~~~~~~-------~~---~ivitAPTgsGKT~Aa~lp~l-----~~~~~~lyi~P~kAL~~Dq~-~~l~~~~~~ 65 (357) T TIGR03158 2 QVATFEALQSKD-------AD---IIFNTAPTGAGKTLAWLTPLL-----HGENDTIALYPTNALIEDQT-EAIKEFVDV 65 (357) T ss_pred HHHHHHHHHCCC-------CC---EEEEECCCCCCHHHHHHHHHH-----HCCCCEEEECCHHHHHHHHH-HHHHHHHHH T ss_conf 689999997689-------98---699989998569999999997-----38987999777899999999-999999987 Q ss_pred C Q ss_conf 2 Q gi|254781187|r 135 L 135 (367) Q Consensus 135 ~ 135 (367) + T Consensus 66 ~ 66 (357) T TIGR03158 66 F 66 (357) T ss_pred H T ss_conf 4 No 161 >TIGR01074 rep ATP-dependent DNA helicase Rep; InterPro: IPR005752 RepA hexameric DNA helicase contain ATP-binding domains similar to those seen in monomeric helicases but which are arranged in a ring. There is compelling evidence to suggest that a single ssDNA molecule passes through the centre of the hexameric ring. Activity of the enzyme is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilizing the duplex and separating the two strands in an active process ; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm. Probab=92.70 E-value=0.26 Score=27.01 Aligned_cols=89 Identities=21% Similarity=0.120 Sum_probs=63.8 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH--HHCCCCEEEEECCCHHHHHHHHHHHHHHHH Q ss_conf 999999888875124555554112477614886788999999999999--708997799971537999999999999999 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLI--STRPGMSIICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~--~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) |.++.+.+.= | +.|.||=|+|||.++--.|.+++ |+.++.+|+.+.=|=+-|+++= -.|++.+ T Consensus 8 Q~~AV~Y~~G----------P----lLVLAGAGSGKT~VI~~KIayLi~~cgY~a~~IaAvTFTNKAA~EMk-ERVA~~L 72 (677) T TIGR01074 8 QQEAVEYVGG----------P----LLVLAGAGSGKTRVITNKIAYLIQNCGYKAKNIAAVTFTNKAAREMK-ERVAKTL 72 (677) T ss_pred HHHHHHHHCC----------C----CEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHH-HHHHHHC T ss_conf 7999986158----------7----14651777786357888999987515878761689735237779999-9998522 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 86231211233332100012333221 Q gi|254781187|r 133 SMLPHRHWFEMQSLSLHPSGWYAELL 158 (367) Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (367) .+.-.+.+.-+|...+-+.....+.+ T Consensus 73 ~~~~~~GL~isTFH~LGL~Ii~~E~~ 98 (677) T TIGR01074 73 GKGQAKGLTISTFHTLGLKIIRREHN 98 (677) T ss_pred CCCCCCCCEEECCHHHHHHHHHHHHH T ss_conf 65455854475205733899999998 No 162 >PRK00149 dnaA chromosomal replication initiation protein; Reviewed Probab=92.68 E-value=0.66 Score=24.54 Aligned_cols=56 Identities=23% Similarity=0.315 Sum_probs=41.9 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 899999998888751245555541124776148867889999999999997089977999715 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) +.=..+.+++++. +...++| +-|-++-|+|||+|..++....+-.+|+.+|+++.. T Consensus 128 ~lA~aAA~~Va~~---pg~~yNP----LfIyG~~GlGKTHLl~AIgn~~~~~~p~~~v~Y~ta 183 (447) T PRK00149 128 RLAHAAALAVAEN---PGKAYNP----LFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVSS 183 (447) T ss_pred HHHHHHHHHHHHC---CCCCCCC----EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEH T ss_conf 9999999999837---6767785----589779988788999999999998589972899549 No 163 >COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair] Probab=92.63 E-value=0.63 Score=24.68 Aligned_cols=36 Identities=22% Similarity=0.307 Sum_probs=32.5 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 776148867889999999999997089977999715 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) +-+.+|-|+|||++..++....+...|..++++... T Consensus 116 lfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~s 151 (408) T COG0593 116 LFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTS 151 (408) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCH T ss_conf 799879999789999999999986299864885048 No 164 >COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms] Probab=92.60 E-value=0.17 Score=28.17 Aligned_cols=150 Identities=18% Similarity=0.117 Sum_probs=75.6 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537999999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) .-+.-|..-+++|.+|.- +..+ +.=|+|||+++...++-.+-...=.+|+.|.|.- .+- T Consensus 128 ~kt~~Q~~y~eai~~~di-----------~fGi-GpAGTGKTyLava~av~al~~~~v~rIiLtRPaV-EAG-------- 186 (348) T COG1702 128 PKTPGQNMYPEAIEEHDI-----------VFGI-GPAGTGKTYLAVAKAVDALGAGQVRRIILTRPAV-EAG-------- 186 (348) T ss_pred ECCHHHHHHHHHHHHCCE-----------EEEE-CCCCCCCCHHHHHHHHHHHHCCCHHEEECCCCCH-HCC-------- T ss_conf 668458788999874273-----------6641-5645697111277665265406412010068313-036-------- Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCEEEEECCCCCCCCCCCCCCCCCC--CCEEEEECCCCCCH Q ss_conf 99986231211233332100012333221111345--776126621013544556521011358--62899975455998 Q gi|254781187|r 130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGI--DSKHYTITCRTYSEERPDTFVGPHNTH--GMAVFNDEASGTPD 205 (367) Q Consensus 130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~a~~~~~~~~ea~~g~h~~~--~~l~ivDEAsgI~d 205 (367) ++ --|..-+.+.+..||.-+........ .........++.-+-.|-++ .+|++ -.++|+|||+--. T Consensus 187 ---Ek----lGfLPGdl~eKvdPylRPLyDAl~d~l~~~~~~~~~e~~vIEiAPlAy--MRGRTL~dAfVIlDEaQNtT- 256 (348) T COG1702 187 ---EK----LGFLPGDLREKVDPYLRPLYDALYDILGAERVEALDERGVIEIAPLAY--MRGRTLNDAFVILDEAQNTT- 256 (348) T ss_pred ---CC----CCCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCEEEECHHH--HHCCCCCCEEEEEECCCCCC- T ss_conf ---42----370788234324611041789999986489773055509487602456--53587787289985510050- Q ss_pred HHHHHHHHHHHCCCCCEEEEEEECCCC Q ss_conf 899998987406988258999807899 Q gi|254781187|r 206 IINKSILGFFTELNPNRFWIMTSNTRR 232 (367) Q Consensus 206 ~i~e~i~g~Lt~~~~~~~~i~igNP~r 232 (367) -+-+.=.||--+..+.|+.+|.++- T Consensus 257 --~~QmKMfLTRiGf~skmvItGD~tQ 281 (348) T COG1702 257 --VGQMKMFLTRIGFESKMVITGDITQ 281 (348) T ss_pred --HHHHCEEEEEECCCCEEEEECCCCC T ss_conf --6451340033137742699757521 No 165 >PRK10919 ATP-dependent DNA helicase Rep; Provisional Probab=92.59 E-value=0.25 Score=27.17 Aligned_cols=45 Identities=22% Similarity=0.307 Sum_probs=36.2 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEECCCHHHHHHHH Q ss_conf 7761488678899999999999970--89977999715379999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLIST--RPGMSIICIANSETQLKNTL 124 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~--~~~~~v~~~A~t~~Q~~~~l 124 (367) +.|.||=|+|||.....-+.|++.. -++.+|+++.=|.+-+.++- T Consensus 18 ~lVlAGaGSGKT~tLt~Ria~Li~~~~v~P~~ILalTFT~kAA~Emk 64 (672) T PRK10919 18 CLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTNKAAREMK 64 (672) T ss_pred EEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCHHHHHHHHH T ss_conf 89997385587999999999998668989333854421799999999 No 166 >PRK12727 flagellar biosynthesis regulator FlhF; Provisional Probab=92.51 E-value=0.74 Score=24.22 Aligned_cols=40 Identities=18% Similarity=0.169 Sum_probs=31.8 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHH Q ss_conf 776148867889999999999997089-9779997153799 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQ 119 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q 119 (367) ++..++.|+|||+.+|-++.-++..+- .+..++|..|++- T Consensus 351 ~AlvGpTGvGKTTT~aKlAa~~~~~~g~~~valit~DtyRi 391 (557) T PRK12727 351 IALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRV 391 (557) T ss_pred EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCCCH T ss_conf 78743777673117999999999973998189997266408 No 167 >TIGR01420 pilT_fam twitching motility protein; InterPro: IPR006321 These represent the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction . Members of this family may be found in some species that do not have type IV pili but have related structures for DNA uptake and natural transformation. ; GO: 0005524 ATP binding, 0006810 transport. Probab=92.48 E-value=0.18 Score=27.99 Aligned_cols=27 Identities=22% Similarity=0.279 Sum_probs=19.8 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHC Q ss_conf 477614886788999999999999708 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTR 105 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~ 105 (367) =+.|.++-|+|||+..|.+|=+.=-+. T Consensus 129 LiLVTGPTGSGKSTTlAsmIDyIN~~~ 155 (350) T TIGR01420 129 LILVTGPTGSGKSTTLASMIDYINKNK 155 (350) T ss_pred CEEEECCCCCCHHHHHHHHHHHHHCCC T ss_conf 389876889867899999997874038 No 168 >TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system. Probab=92.43 E-value=0.76 Score=24.16 Aligned_cols=48 Identities=17% Similarity=0.151 Sum_probs=27.7 Q ss_pred HHHHHHHHHHHHHHCC---CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 9999999888875124---55555411247761488678899999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSN---VNNSNPTIFKCAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 54 wq~~~l~~~~~~~~~~---~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~ 101 (367) .|.++++.|++.+++. .....-..--..-.++.|+|||.++-.++-.+ T Consensus 570 GQ~~Av~~v~~ai~~sraGl~d~~rPigsFLFlGPTGVGKTElAK~LA~~L 620 (852) T TIGR03345 570 GQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELL 620 (852) T ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHH T ss_conf 849999999999999871799999985689987899877899999999997 No 169 >PRK08116 hypothetical protein; Validated Probab=92.26 E-value=0.8 Score=24.03 Aligned_cols=33 Identities=27% Similarity=0.359 Sum_probs=23.7 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 77614886788999999999999708997799971 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) +...++-|+|||+++++++...+ .+ +..|+++. T Consensus 111 Lll~G~~GtGKThLa~aIa~~l~-~~-g~~V~~~~ 143 (262) T PRK08116 111 LLLWGSPGNGKTYLAAAIANELI-EK-GVPVVFVN 143 (262) T ss_pred EEEECCCCCCHHHHHHHHHHHHH-HC-CCEEEEEE T ss_conf 89989899989999999999999-87-99399988 No 170 >PRK06835 DNA replication protein DnaC; Validated Probab=92.25 E-value=0.61 Score=24.73 Aligned_cols=82 Identities=16% Similarity=0.169 Sum_probs=50.1 Q ss_pred CCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH Q ss_conf 25988885543014668884436668428999999988887512455555411247761488678899999999999970 Q gi|254781187|r 25 VLSFKNFVMRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST 104 (367) Q Consensus 25 ~~~~~~f~~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~ 104 (367) ..+|.+|=+-.|+- +.+ | .....|++-=.+++...-++.++ +...--.+...++-|+|||+++++++.-.+-. T Consensus 138 ~enF~~F~~~~ys~-~~~-~-~~~~sprenm~~i~~~~~~fi~~----F~~~~~nLlf~G~~G~GKTfLa~~IA~ell~~ 210 (330) T PRK06835 138 ENNFSNFNLNYYSD-EKD-G-DEPISPRENMENILEKCLNFIKN----FDKNNENLLFYGNTGTGKTFLSNCIAKELLDR 210 (330) T ss_pred HCCCCCCCHHHCCC-CCC-C-CCCCCHHHHHHHHHHHHHHHHHH----CCCCCCCEEEECCCCCCHHHHHHHHHHHHHHC T ss_conf 61431178865399-878-8-88989899999999999999872----47888866988999998899999999999987 Q ss_pred CCCCEEEE-ECC Q ss_conf 89977999-715 Q gi|254781187|r 105 RPGMSIIC-IAN 115 (367) Q Consensus 105 ~~~~~v~~-~A~ 115 (367) . ..|++ +|+ T Consensus 211 g--~sViy~ta~ 220 (330) T PRK06835 211 G--KTVIYRTSD 220 (330) T ss_pred C--CEEEEEEHH T ss_conf 9--949996299 No 171 >COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair] Probab=92.16 E-value=0.82 Score=23.96 Aligned_cols=134 Identities=15% Similarity=0.104 Sum_probs=65.6 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999998 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLS 133 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~ 133 (367) .|+-+.+.+..-+..+.. .+.+ .-++.||+|||+++-.++--+-|.+...--.| .+.. .+ .+|..= T Consensus 20 GQe~v~~~L~nal~~~ri-~hAY----lfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC-----~~C~-~C-k~I~~g-- 85 (515) T COG2812 20 GQEHVVKTLSNALENGRI-AHAY----LFSGPRGVGKTTIARILAKALNCENGPTAEPC-----GKCI-SC-KEINEG-- 85 (515) T ss_pred CCHHHHHHHHHHHHHCCC-HHHH----HHCCCCCCCCHHHHHHHHHHHCCCCCCCCCCC-----HHHH-HH-HHHHCC-- T ss_conf 648999999999980842-3336----51377776710499999999568898777722-----5316-66-865148-- Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHH Q ss_conf 62312112333321000123332211113457761266210135445565210113586289997545599889999898 Q gi|254781187|r 134 MLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILG 213 (367) Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g 213 (367) .. ..+ +++........-.-+-..+. -.+.-..+.+. .+|+||+...+...|.++.. T Consensus 86 ~~-------------------~Dv--iEiDaASn~gVddiR~i~e~--v~y~P~~~ryK-VyiIDEvHMLS~~afNALLK 141 (515) T COG2812 86 SL-------------------IDV--IEIDAASNTGVDDIREIIEK--VNYAPSEGRYK-VYIIDEVHMLSKQAFNALLK 141 (515) T ss_pred CC-------------------CCC--HHHHHHHCCCHHHHHHHHHH--HCCCCCCCCCE-EEEEECHHHHHHHHHHHHHC T ss_conf 86-------------------410--11364445486799999987--24688666641-89983187643788888751 Q ss_pred HHHCCCCCEEEE Q ss_conf 740698825899 Q gi|254781187|r 214 FFTELNPNRFWI 225 (367) Q Consensus 214 ~Lt~~~~~~~~i 225 (367) +|-.+=...+.+ T Consensus 142 TLEEPP~hV~FI 153 (515) T COG2812 142 TLEEPPSHVKFI 153 (515) T ss_pred CCCCCCCCEEEE T ss_conf 113686674899 No 172 >KOG0352 consensus Probab=92.16 E-value=0.82 Score=23.95 Aligned_cols=166 Identities=15% Similarity=0.114 Sum_probs=75.6 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH- Q ss_conf 8999999988887512455555411247761488678899999999999970899779997153799999999999999- Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW- 131 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~- 131 (367) +-|+.....+...-+ -|-|+-+.|.|||-+.-.-.| ...+ -.||++|-..-+++.+ ..+.+. T Consensus 23 ~LQE~A~~c~VK~k~-----------DVyVsMPTGaGKSLCyQLPaL----~~~g-ITIV~SPLiALIkDQi-DHL~~LK 85 (641) T KOG0352 23 RLQEQAINCIVKRKC-----------DVYVSMPTGAGKSLCYQLPAL----VHGG-ITIVISPLIALIKDQI-DHLKRLK 85 (641) T ss_pred HHHHHHHHHHHHCCC-----------CEEEECCCCCCHHHHHHCHHH----HHCC-EEEEECHHHHHHHHHH-HHHHHHC T ss_conf 578998999883467-----------379964688760145426587----7288-1899307899999998-7787405 Q ss_pred --HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEC-CCCCCCCCCCCCCCCCCCC-EEEEECCCCCCH-- Q ss_conf --9862312112333321000123332211113457761266210-1354455652101135862-899975455998-- Q gi|254781187|r 132 --LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCR-TYSEERPDTFVGPHNTHGM-AVFNDEASGTPD-- 205 (367) Q Consensus 132 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~-~~~~~~~ea~~g~h~~~~~-l~ivDEAsgI~d-- 205 (367) .+. .|......+ +..........+..++ ..+|+-- .++..=-.-++++|..+.+ +++||||.-|++ T Consensus 86 Vp~~S-LNSKlSt~E---R~ri~~DL~~ekp~~K----~LYITPE~AAt~~FQ~lLn~L~~r~~L~Y~vVDEAHCVSQWG 157 (641) T KOG0352 86 VPCES-LNSKLSTVE---RSRIMGDLAKEKPTIK----MLYITPEGAATDGFQKLLNGLANRDVLRYIVVDEAHCVSQWG 157 (641) T ss_pred CCHHH-HHCHHHHHH---HHHHHHHHHHCCCCEE----EEEECHHHHHHHHHHHHHHHHHHHCEEEEEEECHHHHHHHHC T ss_conf 61666-401210788---9999888874377514----899763155566689999988741402247733466677626 Q ss_pred -H--HHHHHHHHHHCCCCCEEEEE-------------------------EECCCCCCCHHHHHHHC Q ss_conf -8--99998987406988258999-------------------------80789998768875411 Q gi|254781187|r 206 -I--INKSILGFFTELNPNRFWIM-------------------------TSNTRRLNGWFYDIFNI 243 (367) Q Consensus 206 -~--i~e~i~g~Lt~~~~~~~~i~-------------------------igNP~r~~g~Fye~~~~ 243 (367) + .-.--+|.|++.-.-..|++ +.+|.-..|.|||...+ T Consensus 158 HDFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~FR~NLFYD~~~K 223 (641) T KOG0352 158 HDFRPDYLTLGSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPTFRDNLFYDNHMK 223 (641) T ss_pred CCCCCCHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHCCCCHHHHCCCCHHHHHHHHHHHH T ss_conf 666820444666774469996698543467767799999976058544405741454445788888 No 173 >cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase. Probab=92.09 E-value=0.46 Score=25.49 Aligned_cols=51 Identities=27% Similarity=0.330 Sum_probs=36.8 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 89999999888875124555554112477614886788999999999999708997799971537 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) +=|.++|+.....- .++.|+++.|+|||++...++-+. .+..+++++..+. T Consensus 12 ~~~~~~L~~~v~~~-----------~nIlIsG~tGSGKTTll~al~~~i---~~~~rivtiEd~~ 62 (186) T cd01130 12 PLQAAYLWLAVEAR-----------KNILISGGTGSGKTTLLNALLAFI---PPDERIITIEDTA 62 (186) T ss_pred HHHHHHHHHHHHCC-----------CCEEEECCCCCCHHHHHHHHHHHC---CCCCCEEEECCCH T ss_conf 99999999999859-----------989998999998999999999613---3456459841535 No 174 >PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated Probab=92.07 E-value=0.3 Score=26.60 Aligned_cols=41 Identities=20% Similarity=0.138 Sum_probs=33.3 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHH Q ss_conf 776148867889999999999997089-97799971537999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQL 120 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~ 120 (367) ++..++.|+|||+.+|=++..+.+.+- ....++|..|++-. T Consensus 179 ~alVGPTGVGKTTTiAKLAAr~~l~~g~~kVaLIT~DTYRIg 220 (404) T PRK06995 179 FALVGPTGVGKTTTTAKLAARCVMRHGASKVALLTTDSYRIG 220 (404) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHH T ss_conf 898668887637589999999999838983799976875478 No 175 >PRK06696 uridine kinase; Validated Probab=92.01 E-value=0.74 Score=24.24 Aligned_cols=54 Identities=17% Similarity=0.129 Sum_probs=37.1 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 99999988887512455555411247761488678899999999999970899779997 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) ...++.+|++++....- .-.++|+|.++=|+|||+++..++--+-. .+..++++ T Consensus 7 r~~~~~~~~~~i~~~~p---~rpl~VgIdG~~gSGKTTlA~~La~~L~~--~G~~V~~v 60 (227) T PRK06696 7 RKQVVKEIANHILTLNL---TRPLRVAIDGITASGKTTFANELAEEIKK--RGRPVIRA 60 (227) T ss_pred HHHHHHHHHHHHHHCCC---CCCEEEEEECCCCCCHHHHHHHHHHHHHH--CCCCEEEE T ss_conf 87899999999983599---98689997789987879999999999974--69948997 No 176 >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=91.91 E-value=0.43 Score=25.70 Aligned_cols=35 Identities=26% Similarity=0.263 Sum_probs=26.9 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 47761488678899999999999970899779997 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) |..|-+|+|+|||++...++.-....+++..+++. T Consensus 18 R~gI~g~~gvGKT~Ll~~i~~~~~~~~~~~~~v~~ 52 (249) T cd01128 18 RGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVL 52 (249) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEE T ss_conf 77887899988999999999999985898499999 No 177 >PRK11054 helD DNA helicase IV; Provisional Probab=91.59 E-value=0.43 Score=25.67 Aligned_cols=46 Identities=22% Similarity=0.260 Sum_probs=38.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHHH Q ss_conf 477614886788999999999999708--9977999715379999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTR--PGMSIICIANSETQLKNTL 124 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~--~~~~v~~~A~t~~Q~~~~l 124 (367) ++.|.||=|+|||..+..-+.|++... ++.+|++++=|.+-+.++- T Consensus 211 ~~LVLAGAGSGKT~vLt~RiayLI~~g~~~P~~ILaLTFT~kAA~EMr 258 (684) T PRK11054 211 SLLVLAGAGSGKTSVLVARAGWLLARGQAQPEQILLLAFGRKAAEEMD 258 (684) T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHCCCCCHHHEEEEECCHHHHHHHH T ss_conf 648983389970779999999999759998667786863499999999 No 178 >PRK10865 protein disaggregation chaperone; Provisional Probab=91.53 E-value=0.97 Score=23.53 Aligned_cols=48 Identities=25% Similarity=0.206 Sum_probs=30.2 Q ss_pred HHHHHHHHHHHHHHCC-CCCCCCCE--EEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 9999999888875124-55555411--247761488678899999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSN-VNNSNPTI--FKCAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 54 wq~~~l~~~~~~~~~~-~~~~~~~~--~~~~v~sgrg~GKS~~~a~~~lw~ 101 (367) .|.++++.|++.+++. ..-..|.. --....++-|+|||.++-.++-.+ T Consensus 572 GQd~AI~~v~~aI~~sraGL~dp~rPiGsFLFlGPTGVGKTElAK~LA~~L 622 (857) T PRK10865 572 GQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFM 622 (857) T ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH T ss_conf 809999999999999863899999973899986898788899999999998 No 179 >PRK04195 replication factor C large subunit; Provisional Probab=91.11 E-value=1.1 Score=23.27 Aligned_cols=22 Identities=23% Similarity=0.191 Sum_probs=17.4 Q ss_pred EEEEECCCCCCHHHHHHHHHHH Q ss_conf 4776148867889999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLW 100 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw 100 (367) -+.+.++.|+|||+++-+++-- T Consensus 42 ~lLL~GPpGvGKTT~a~~lAk~ 63 (403) T PRK04195 42 ALLLYGPPGVGKTSLAHALAND 63 (403) T ss_pred EEEEECCCCCCHHHHHHHHHHH T ss_conf 6998893998799999999998 No 180 >KOG0328 consensus Probab=91.11 E-value=0.17 Score=28.21 Aligned_cols=151 Identities=13% Similarity=-0.006 Sum_probs=74.2 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHH Q ss_conf 666842899999998888751245555541124776148867889999999999997089-9779997153799999999 Q gi|254781187|r 47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLW 125 (367) Q Consensus 47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw 125 (367) +|..|-.-|..++-.|-. + ..|.+.|--|+|||...+.-++=-+-... ...+++.+||..-+..+ T Consensus 46 GfekPS~IQqrAi~~Ilk----G--------rdViaQaqSGTGKTa~~si~vlq~~d~~~r~tQ~lilsPTRELa~Qi-- 111 (400) T KOG0328 46 GFEKPSAIQQRAIPQILK----G--------RDVIAQAQSGTGKTATFSISVLQSLDISVRETQALILSPTRELAVQI-- 111 (400) T ss_pred CCCCCHHHHHHHHHHHHC----C--------CCEEEEECCCCCCEEEEEEEEEEECCCCCCEEEEEEECCHHHHHHHH-- T ss_conf 257816777610245633----6--------61478704788844789866314034342003578954708999999-- Q ss_pred HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC---- Q ss_conf 9999999862312112333321000123332211113457761266210135445565210113586289997545---- Q gi|254781187|r 126 AEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS---- 201 (367) Q Consensus 126 ~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs---- 201 (367) .++-..+...-+-.-+.|.. ....-..--+.+-|...+.+.+-+...--..+.++-...-++++|||. T Consensus 112 ~~vi~alg~~mnvq~hacig--------g~n~gedikkld~G~hvVsGtPGrv~dmikr~~L~tr~vkmlVLDEaDemL~ 183 (400) T KOG0328 112 QKVILALGDYMNVQCHACIG--------GKNLGEDIKKLDYGQHVVSGTPGRVLDMIKRRSLRTRAVKMLVLDEADEMLN 183 (400) T ss_pred HHHHHHHCCCCCCEEEEEEC--------CCCCCHHHHHHCCCCEEEECCCCHHHHHHHHCCCCCCCEEEEEECCHHHHHH T ss_conf 99999832423644898735--------7751034565325614750798159999986231011426898545899987 Q ss_pred -CCCHHHHHHHHHHHHCCCCC Q ss_conf -59988999989874069882 Q gi|254781187|r 202 -GTPDIINKSILGFFTELNPN 221 (367) Q Consensus 202 -gI~d~i~e~i~g~Lt~~~~~ 221 (367) |..+.+|++..- -.++.. T Consensus 184 kgfk~Qiydiyr~--lp~~~Q 202 (400) T KOG0328 184 KGFKEQIYDIYRY--LPPGAQ 202 (400) T ss_pred HHHHHHHHHHHHH--CCCCCE T ss_conf 5677889999984--799866 No 181 >PRK09270 frcK putative fructose transport system kinase; Reviewed Probab=91.03 E-value=0.85 Score=23.88 Aligned_cols=38 Identities=24% Similarity=0.244 Sum_probs=27.2 Q ss_pred CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 11247761488678899999999999970899779997 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) .++-++|+++=|+|||+++..++--+-...+...++++ T Consensus 33 rR~lIgIaG~pGSGKSTlA~~l~~~L~~~~~~~~~~~v 70 (230) T PRK09270 33 RRTVVGIAGPPGAGKSTLAETLWEALSQQGPELPAIQV 70 (230) T ss_pred CEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEE T ss_conf 71899998999889999999999998623799857997 No 182 >COG5525 Bacteriophage tail assembly protein [General function prediction only] Probab=90.92 E-value=0.21 Score=27.64 Aligned_cols=152 Identities=12% Similarity=0.080 Sum_probs=83.3 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH Q ss_conf 28999999988887512455555411247761488678899999999999970899779997153799999999999999 Q gi|254781187|r 52 HRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKW 131 (367) Q Consensus 52 ~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~ 131 (367) .+.|.++...+ ...+..+|.+..+-++|||.+.-..+.+++.+.| ..-+++.||...+++-+-..+..- T Consensus 49 ~p~~~~~~n~~----------~~~~~~~V~f~k~ArvG~T~m~~gw~~Y~I~~~p-~~mlv~qpt~~~a~~~~k~k~~pt 117 (611) T COG5525 49 LPFQIAIMNAM----------GSDEIRAVNFVKSARVGKTKMLLGWIGYFIEHKP-RNMLVVQPTDEKAREHSKTKVEPT 117 (611) T ss_pred CHHHHHHHHCC----------CCCCCEEEEEEECCCCCCEEEECCEEEEEEEECC-CCCEEECCCHHHHHHHHHHHCCCC T ss_conf 26899987536----------9864168999740203622454225899998657-652333365557799888750750 Q ss_pred HHHCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHH- Q ss_conf 986231-211233332100012333221111345776126621013544556521011358628999754559988999- Q gi|254781187|r 132 LSMLPH-RHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINK- 209 (367) Q Consensus 132 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e- 209 (367) ++-.|. .+. +.+.....+...-.+..|..+..+- .+....++.+..++.+||-+.++.++-. T Consensus 118 i~~~p~l~~~---------ls~~~~dNn~~~K~f~~G~~l~~g~-------~s~~~~r~~s~~~v~lde~d~fpedv~~E 181 (611) T COG5525 118 IRDVPSLVSL---------LSPSRNDNNLTDKRFPGGVFLMIGW-------KSAKNYRSISVDVVVLDELDRFPEDVEGE 181 (611) T ss_pred HHCCHHHHHH---------CCCCCCCCCEECCCCCCCEEEEECC-------CCCCCCCCCCHHHHHHHHHHCCCHHHCCC T ss_conf 2006337865---------2765678731102334772797256-------54565667644565666774365122268 Q ss_pred -----HHHHHHHCCCCCEEEEEEECCC Q ss_conf -----9898740698825899980789 Q gi|254781187|r 210 -----SILGFFTELNPNRFWIMTSNTR 231 (367) Q Consensus 210 -----~i~g~Lt~~~~~~~~i~igNP~ 231 (367) .+..-+++ ....+.+..|+|+ T Consensus 182 Gs~~sl~~kR~~t-~~~~~~l~~stP~ 207 (611) T COG5525 182 GSATSLASKRITT-MSWGKSLVESTPT 207 (611) T ss_pred CCHHHHHHHHHCC-CCCCCEEEECCCC T ss_conf 8876778876024-5566224413787 No 183 >TIGR03305 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase. Probab=90.83 E-value=0.78 Score=24.08 Aligned_cols=51 Identities=29% Similarity=0.526 Sum_probs=35.4 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHHHHHHHHHH Q ss_conf 4776148867889999999999997089977999-715379999999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKNTLWAEVSK 130 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~~lw~ei~k 130 (367) |+.+-+|+|+|||.++..++.-....+.+..|++ +....+.+.+ ++.++++ T Consensus 140 r~gIfggaGvGKT~Ll~e~i~n~~~~~~~v~V~~~IGER~rE~~e-~~~el~~ 191 (449) T TIGR03305 140 KAGLFGGAGVGKTVLLTEMIHNMVGQHQGVSIFCGIGERCREGEE-LYREMKE 191 (449) T ss_pred EEEEECCCCCCCCCHHHHHHHHHHHHCCCEEEEEEEEEEHHHHHH-HHHHHHH T ss_conf 656652799984101899998656414886899997452167999-9999875 No 184 >COG5410 Uncharacterized protein conserved in bacteria [Function unknown] Probab=90.83 E-value=0.84 Score=23.89 Aligned_cols=187 Identities=15% Similarity=0.089 Sum_probs=88.0 Q ss_pred CCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEC Q ss_conf 54572337899997523201259888855430146688844366684289999999888875124555554112477614 Q gi|254781187|r 5 ISTDQKLEQELHEMLMHAECVLSFKNFVMRFFPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISA 84 (367) Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~s 84 (367) .++|.-+++.|..+| |.++-+.|.+++|-....+ .- + | -|-.+++-+.-+|.+.+. .-++.+-- T Consensus 3 ~~~~~~~~EaL~~~L----~~~~h~f~~r~f~T~~~~~-~Y-~---~-~~H~~iI~~~L~~Vi~G~------~k~~Iin~ 66 (305) T COG5410 3 RSTEQAQEEALIKAL----CEADHLFFTRYFFTQRQQL-RY-R---V-NWHHHVIAGVLDDVIAGR------RKDVIINV 66 (305) T ss_pred CCHHHHHHHHHHHHH----HHHHHHHHHHHHHEECCCC-EE-C---C-HHHHHHHHHHHHHHHCCC------CEEEEEEC T ss_conf 203777799999999----9999988867652116653-00-2---1-155799998888886363------10489966 Q ss_pred CCCCCHHHHHHH-HHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH-HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 886788999999-9999997089977999715379999999999999-99862312112333321000123332211113 Q gi|254781187|r 85 GRGIGKTTLNAW-MMLWLISTRPGMSIICIANSETQLKNTLWAEVSK-WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSM 162 (367) Q Consensus 85 grg~GKS~~~a~-~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (367) +-+.-||.+++. +-.++|..+|.+++++++.+. +-.+.+.+-.+ .+++-....+|..+.. +..+....-.+ T Consensus 67 PP~~skS~~Vs~~~PaY~L~~NP~KR~~~~SYSd--~La~~~s~~~r~ii~sd~y~~LFp~~I~-----~~~~~~k~w~i 139 (305) T COG5410 67 PPGSSKSELVAINVPAYGLALNPYKRFLHISYSD--DLALLNSETAREIVQSDEYRALFPLEIA-----DDAKSKKRWNV 139 (305) T ss_pred CCCCCCCEEEEEECCHHEEEECCCCEEEEEEHHH--HHHHHHCHHHHHHHHCCCHHHCCCEEEC-----CCCCCCCCEEE T ss_conf 9852323478850541125507633189854767--8998834467898722103320763204-----67667632368 Q ss_pred CCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCC--------CCHHHHHHHHHHH----HCCCCCEE Q ss_conf 4577612662101354455652101135862899975455--------9988999989874----06988258 Q gi|254781187|r 163 GIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASG--------TPDIINKSILGFF----TELNPNRF 223 (367) Q Consensus 163 ~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg--------I~d~i~e~i~g~L----t~~~~~~~ 223 (367) ..++|..+++..+ .+.-|+...++|+|.--. |-++++.-.+.++ ..++..++ T Consensus 140 ~~~gGg~yaTs~g---------G~ATG~GaD~LIIDDP~k~e~a~SktIR~K~Yr~~~st~~sr~~~~~s~ii 203 (305) T COG5410 140 VVDGGGVYATSLG---------GQATGFGADALIIDDPLKVEDAYSKTIRSKAYRKLVSTVKSRKASPDTPII 203 (305) T ss_pred EEECCEEEEEECC---------CCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEE T ss_conf 9428878887305---------654577874698659988777545689999999999998753038997189 No 185 >COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning] Probab=90.54 E-value=0.38 Score=25.98 Aligned_cols=47 Identities=19% Similarity=0.254 Sum_probs=29.2 Q ss_pred EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHH Q ss_conf 761488678899999999999970899779997153799999999999 Q gi|254781187|r 81 AISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEV 128 (367) Q Consensus 81 ~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei 128 (367) .+.+==|+|||+++|+.++|.+.-... ..++.....+.+.+++=-++ T Consensus 6 ~f~GKGGVGKTT~aaA~A~~lA~~g~k-vLlvStDPAhsL~d~f~~el 52 (322) T COG0003 6 FFTGKGGVGKTTIAAATAVKLAESGKK-VLLVSTDPAHSLGDVFDLEL 52 (322) T ss_pred EEECCCCCCHHHHHHHHHHHHHHCCCC-EEEEEECCCCCHHHHHCCCC T ss_conf 993688545899999999999975990-79998489874476542304 No 186 >COG0514 RecQ Superfamily II DNA helicase [DNA replication, recombination, and repair] Probab=90.53 E-value=0.69 Score=24.44 Aligned_cols=61 Identities=16% Similarity=0.151 Sum_probs=40.9 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH Q ss_conf 666842899999998888751245555541124776148867889999999999997089977999715379999999 Q gi|254781187|r 47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL 124 (367) Q Consensus 47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l 124 (367) ++++.|+-|.++++.+.+.. ++.|.=+.|.|||-+.-.-++-. +| -++|++|-.+=.+|-+ T Consensus 14 Gy~~FR~gQ~evI~~~l~g~------------d~lvvmPTGgGKSlCyQiPAll~----~G-~TLVVSPLiSLM~DQV 74 (590) T COG0514 14 GYASFRPGQQEIIDALLSGK------------DTLVVMPTGGGKSLCYQIPALLL----EG-LTLVVSPLISLMKDQV 74 (590) T ss_pred CCCCCCCCHHHHHHHHHCCC------------CEEEECCCCCCCCHHHHHHHHHC----CC-CEEEECCHHHHHHHHH T ss_conf 91303888899999996588------------67998538987106743678865----99-7899785688899999 No 187 >pfam02374 ArsA_ATPase Anion-transporting ATPase. This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell. Probab=90.40 E-value=0.64 Score=24.62 Aligned_cols=42 Identities=19% Similarity=0.389 Sum_probs=26.5 Q ss_pred EEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCHHHHHHHH Q ss_conf 7614886788999999999999708997799971-5379999999 Q gi|254781187|r 81 AISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA-NSETQLKNTL 124 (367) Q Consensus 81 ~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A-~t~~Q~~~~l 124 (367) -+.+-=|+|||+++|+++++.+- .|.|+++++ .-.+.+.+++ T Consensus 5 ~~~GKGGVGKTT~AaA~A~~~A~--~G~rvLlvStDPAhsL~D~~ 47 (304) T pfam02374 5 FFGGKGGVGKTTVSCATAVRLSE--QGKKVLLVSTDPAHSLSDSF 47 (304) T ss_pred EEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEECCCCCHHHHHH T ss_conf 99579857489999999999995--89929999469721488984 No 188 >KOG0947 consensus Probab=90.34 E-value=1.3 Score=22.84 Aligned_cols=68 Identities=13% Similarity=0.165 Sum_probs=46.6 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999999999999708997799971537999999999999 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) .|+..|+++...+--+. -|-|+|..-.|||.++- +++ -++.....+.++|+|-. -+.+-=|+..+ T Consensus 297 elD~FQk~Ai~~lerg~------------SVFVAAHTSAGKTvVAE-YAi-alaq~h~TR~iYTSPIK-ALSNQKfRDFk 361 (1248) T KOG0947 297 ELDTFQKEAIYHLERGD------------SVFVAAHTSAGKTVVAE-YAI-ALAQKHMTRTIYTSPIK-ALSNQKFRDFK 361 (1248) T ss_pred CCCHHHHHHHHHHHCCC------------EEEEEECCCCCCCHHHH-HHH-HHHHHHCCCEEECCHHH-HHCCCHHHHHH T ss_conf 76678999999997278------------17997137788436999-999-99886355157526346-54001578887 Q ss_pred HHH Q ss_conf 999 Q gi|254781187|r 130 KWL 132 (367) Q Consensus 130 k~~ 132 (367) .-. T Consensus 362 ~tF 364 (1248) T KOG0947 362 ETF 364 (1248) T ss_pred HHC T ss_conf 742 No 189 >KOG0332 consensus Probab=90.26 E-value=0.22 Score=27.43 Aligned_cols=72 Identities=18% Similarity=0.122 Sum_probs=44.6 Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHC-CCCEEEEECCCHHHHH Q ss_conf 844366684289999999888875124555554112477614886788999999999999708-9977999715379999 Q gi|254781187|r 43 KPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTR-PGMSIICIANSETQLK 121 (367) Q Consensus 43 ~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~-~~~~v~~~A~t~~Q~~ 121 (367) +-.+.|+-|.+.|+..|--+-.+-- . ++.-.|--|+|||+....-+|-.+--. .-..++|+|||..-++ T Consensus 105 ly~M~F~kPskIQe~aLPlll~~Pp---------~-nlIaQsqsGtGKTaaFvL~MLsRvd~~~~~PQ~iCLaPtrELA~ 174 (477) T KOG0332 105 LYAMKFQKPSKIQETALPLLLAEPP---------Q-NLIAQSQSGTGKTAAFVLTMLSRVDPDVVVPQCICLAPTRELAP 174 (477) T ss_pred HHHHCCCCCCHHHHHHCCHHHCCCC---------H-HHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCEEECCHHHHHH T ss_conf 8875268832577752125305982---------6-56655017886058999999873483335877405476177799 Q ss_pred HHH Q ss_conf 999 Q gi|254781187|r 122 NTL 124 (367) Q Consensus 122 ~~l 124 (367) .++ T Consensus 175 Q~~ 177 (477) T KOG0332 175 QTG 177 (477) T ss_pred HHH T ss_conf 898 No 190 >KOG0781 consensus Probab=90.20 E-value=1.3 Score=22.77 Aligned_cols=137 Identities=15% Similarity=0.267 Sum_probs=74.9 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCH-----HHHHHHHHHHH Q ss_conf 999999888875124555554112477614886788999999999999708997799971-537-----99999999999 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA-NSE-----TQLKNTLWAEV 128 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A-~t~-----~Q~~~~lw~ei 128 (367) -.++||+|..--++. -|++ ++..+=.|+|||+-.|-++.|++-.. .+|++.| .|. .|++.- + T Consensus 362 sVDlLrdI~~ar~~k----rPYv--i~fvGVNGVGKSTNLAKIayWLlqNk--frVlIAACDTFRsGAvEQLrtH----v 429 (587) T KOG0781 362 SVDLLRDIMSARRRK----RPYV--ISFVGVNGVGKSTNLAKIAYWLLQNK--FRVLIAACDTFRSGAVEQLRTH----V 429 (587) T ss_pred HHHHHHHHHHHHHCC----CCEE--EEEEEECCCCCCCHHHHHHHHHHHCC--CEEEEEECCCHHHHHHHHHHHH----H T ss_conf 066999999987468----9759--99982147665132999999998578--3699986243124478999999----9 Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH--H Q ss_conf 99998623121123333210001233322111134577612662101354455652101135862899975455998--8 Q gi|254781187|r 129 SKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD--I 206 (367) Q Consensus 129 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d--~ 206 (367) ++...+.+ +.-.++.+.|. ++ .+.-+ -++++-.+..++..+++|-|.-..+ . T Consensus 430 ~rl~~l~~-------~~v~lfekGYg------------kd---~a~va----k~AI~~a~~~gfDvvLiDTAGRmhn~~~ 483 (587) T KOG0781 430 ERLSALHG-------TMVELFEKGYG------------KD---AAGVA----KEAIQEARNQGFDVVLIDTAGRMHNNAP 483 (587) T ss_pred HHHHHHCC-------CHHHHHHHHCC------------CC---HHHHH----HHHHHHHHHCCCCEEEEECCCCCCCCHH T ss_conf 99987455-------20488861047------------78---28999----9999999866987899835443347806 Q ss_pred HHHHHHHHHHCCCCCEEEEEEECC Q ss_conf 999989874069882589998078 Q gi|254781187|r 207 INKSILGFFTELNPNRFWIMTSNT 230 (367) Q Consensus 207 i~e~i~g~Lt~~~~~~~~i~igNP 230 (367) .+.++.. |...+.+-+.+..|-- T Consensus 484 LM~~L~k-l~~~n~pD~i~~VgEA 506 (587) T KOG0781 484 LMTSLAK-LIKVNKPDLILFVGEA 506 (587) T ss_pred HHHHHHH-HHHCCCCCEEEEEHHH T ss_conf 7899999-9744798659985055 No 191 >pfam03308 ArgK ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems. Probab=90.20 E-value=1.3 Score=22.77 Aligned_cols=54 Identities=19% Similarity=0.191 Sum_probs=40.2 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHH Q ss_conf 99999988887512455555411247761488678899999999999970899779997--15379 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSET 118 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~ 118 (367) -.++|+.+..+.. ...++-|...-|+|||+++..++..+.-. +.+|.|+ -|+.. T Consensus 15 ~~~ll~~~~~~~g--------~a~~iGiTG~PGaGKStli~~l~~~~~~~--g~~vaVlAvDPSS~ 70 (267) T pfam03308 15 ARELLRRLMPLTG--------RAHRVGITGVPGAGKSTLIEALGMELRRR--GHRVAVLAVDPSSP 70 (267) T ss_pred HHHHHHHHHHHCC--------CCEEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEEECCCCC T ss_conf 9999999874359--------95599876899887999999999999968--98689999789998 No 192 >pfam05496 RuvB_N Holliday junction DNA helicase ruvB N-terminus. The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein. Probab=89.95 E-value=1.3 Score=22.64 Aligned_cols=26 Identities=12% Similarity=0.189 Sum_probs=21.4 Q ss_pred CEEEEECCCCCCHHHHHHHHHHHHCC Q ss_conf 28999754559988999989874069 Q gi|254781187|r 193 MAVFNDEASGTPDIINKSILGFFTEL 218 (367) Q Consensus 193 ~l~ivDEAsgI~d~i~e~i~g~Lt~~ 218 (367) .++++||..-......++++|.+-++ T Consensus 103 ~ILFIDEIHr~nK~qqd~Llp~vE~g 128 (234) T pfam05496 103 DVLFIDEIHRLNRAVEEILYPAMEDF 128 (234) T ss_pred CEEEEECHHHCCHHHHHHCCCCCCCC T ss_conf 88999665435876887445533461 No 193 >TIGR01978 sufC FeS assembly ATPase SufC; InterPro: IPR010230 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents SufC, which acts as an ATPase in the SUF system. SufC belongs to the ATP-binding cassette transporter family (IPR003439 from INTERPRO) but is no longer thought to be part of a transporter. The complex is reported as cytosolic or associated with the membrane.; GO: 0005524 ATP binding, 0006810 transport. Probab=89.83 E-value=0.25 Score=27.17 Aligned_cols=72 Identities=19% Similarity=0.228 Sum_probs=47.0 Q ss_pred CCEEEEECC-CCCC-HH---HHHHHHHHHHCCC-CCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCHHH Q ss_conf 628999754-5599-88---9999898740698-8258999807899987688754112235046752333288889889 Q gi|254781187|r 192 GMAVFNDEA-SGTP-DI---INKSILGFFTELN-PNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRTVEGIDSGF 265 (367) Q Consensus 192 ~~l~ivDEA-sgI~-d~---i~e~i~g~Lt~~~-~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d~p~~~~~~ 265 (367) +.|+|+||- ||.+ |. |.+.+. .+++.. .+.++ +++ ++-+++..=+.++..+-++-+-+..=+.+. T Consensus 166 P~laiLDE~DSGLDiDALk~V~~~in-~lr~~~P~~~~l-iiT-------HY~rlL~~I~PD~VhVl~~GrIV~sGd~~L 236 (248) T TIGR01978 166 PKLAILDEIDSGLDIDALKIVAEGIN-RLREEHPDRAFL-IIT-------HYQRLLNYIKPDVVHVLVDGRIVKSGDVEL 236 (248) T ss_pred CCEEEEECCCCCCCHHHHHHHHHHHH-HHHCCCCCCEEE-EEE-------CHHHHHHHCCCCEEEEEECCEEEEECCHHH T ss_conf 95798606888763788899999999-873068980089-987-------517884131898899974675876489899 Q ss_pred HHHHHHH Q ss_conf 9999962 Q gi|254781187|r 266 HEGIISR 272 (367) Q Consensus 266 i~~~~~~ 272 (367) ..+..++ T Consensus 237 a~~le~~ 243 (248) T TIGR01978 237 AKELEEK 243 (248) T ss_pred HHHHHHH T ss_conf 9999860 No 194 >pfam00437 GSPII_E Type II/IV secretion system protein. This family contains both type II and type IV pathway secretion proteins from bacteria. VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection. Probab=89.79 E-value=1.4 Score=22.56 Aligned_cols=37 Identities=27% Similarity=0.321 Sum_probs=25.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 477614886788999999999999708997799971537 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) .+.|+++.|+|||++..+++-.. -.++.+++++..+. T Consensus 141 ~ilIsG~TGSGKTT~l~all~~i--~~~~~riitiED~~ 177 (283) T pfam00437 141 NILVSGGTGSGKTTLLYALLNEI--NTDDERIVTIEDPV 177 (283) T ss_pred EEEEECCCCCCHHHHHHHHHHHC--CCCCCCEEEECCCC T ss_conf 59998899998899999999840--87776278733785 No 195 >KOG4284 consensus Probab=89.78 E-value=0.68 Score=24.46 Aligned_cols=137 Identities=15% Similarity=0.094 Sum_probs=69.6 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHH---HHHH Q ss_conf 6668428999999988887512455555411247761488678899999999999970899-77999715379---9999 Q gi|254781187|r 47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSET---QLKN 122 (367) Q Consensus 47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~---Q~~~ 122 (367) .|--|++-|..++-.+...+ -+.|.|--|+|||-+.+.+++--+-.+-. ..+++++||.. |+++ T Consensus 44 ~f~~ptkiQaaAIP~~~~km------------DliVQaKSGTGKTlVfsv~av~sl~~~~~~~q~~Iv~PTREiaVQI~~ 111 (980) T KOG4284 44 AFALPTKIQAAAIPAIFSKM------------DLIVQAKSGTGKTLVFSVLAVESLDSRSSHIQKVIVTPTREIAVQIKE 111 (980) T ss_pred CCCCCCCHHHHHHHHHHCCC------------CEEEEECCCCCCEEEEEEEEEHHCCCCCCCCEEEEEECCHHHHHHHHH T ss_conf 34578701343211443155------------358981378885589985430222756676206997143566457999 Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCC Q ss_conf 99999999998623121123333210001233322111134577612662101354455652101135862899975455 Q gi|254781187|r 123 TLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASG 202 (367) Q Consensus 123 ~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg 202 (367) .+++. +|.-..++|. .+...-.+..+.+.+ +.+.++.+.+-+-..---+..+.--+.-|+|+|||.. T Consensus 112 tv~~v-------~~sf~g~~cs---vfIGGT~~~~d~~rl---k~~rIvIGtPGRi~qL~el~~~n~s~vrlfVLDEADk 178 (980) T KOG4284 112 TVRKV-------APSFTGARCS---VFIGGTAHKLDLIRL---KQTRIVIGTPGRIAQLVELGAMNMSHVRLFVLDEADK 178 (980) T ss_pred HHHHH-------CCCCCCCCEE---EEECCCHHHHHHHHH---HHCEEEECCCHHHHHHHHHCCCCCCCEEEEEECCHHH T ss_conf 99986-------5244576058---996685435556665---4023784383588999870677711026888431776 Q ss_pred CCH-HHH Q ss_conf 998-899 Q gi|254781187|r 203 TPD-IIN 208 (367) Q Consensus 203 I~d-~i~ 208 (367) .=+ ..| T Consensus 179 L~~t~sf 185 (980) T KOG4284 179 LMDTESF 185 (980) T ss_pred HHCHHHH T ss_conf 6320247 No 196 >PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional Probab=89.67 E-value=1.4 Score=22.51 Aligned_cols=60 Identities=18% Similarity=0.108 Sum_probs=38.7 Q ss_pred HHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC-EEEEECCCHHHH Q ss_conf 999888875124555554112477614886788999999999999708997-799971537999 Q gi|254781187|r 58 FMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGM-SIICIANSETQL 120 (367) Q Consensus 58 ~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~-~v~~~A~t~~Q~ 120 (367) +|+++.-|... .+.+.-++--+|..++.|+|||+.+|=++..+. ..+. ..++|..|++-+ T Consensus 223 ~~~~~~~~~~~-~~~~~~~~q~IALVGPTGVGKTTTIAKLAArf~--~~~KkVALITtDTYRIG 283 (436) T PRK11889 223 ILEDMRSHFNT-ENVFEKEVQTIALIGPTGVGKTTTLAKMAWQFH--GKKKTVGFITTDHSRIG 283 (436) T ss_pred HHHHHHHHCCH-HHHHHHHCEEEEEECCCCCCHHHHHHHHHHHHH--CCCCEEEEEECCCCHHH T ss_conf 99998874031-013364171799989999888999999999986--16980899980663476 No 197 >pfam00448 SRP54 SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins. Probab=89.34 E-value=1.5 Score=22.35 Aligned_cols=52 Identities=17% Similarity=0.155 Sum_probs=33.9 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC Q ss_conf 77614886788999999999999708997799971537999999999999999862 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSML 135 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~ 135 (367) +++.++.|+|||+.+|-++.|+.. +.....++++.|++-.- ...++.+.+.+ T Consensus 4 i~lvGptGvGKTTTiaKLAa~~~~-~~~~V~lit~Dt~R~gA---~eQL~~ya~~l 55 (196) T pfam00448 4 ILLVGLQGSGKTTTIAKLAAYLKK-QGKKVLLVAADTFRAAA---IEQLKQLAERL 55 (196) T ss_pred EEEECCCCCCHHHHHHHHHHHHHH-CCCEEEEEECCCCCHHH---HHHHHHHHHHC T ss_conf 999899999889999999999997-79928999758776889---99999999863 No 198 >KOG0991 consensus Probab=89.29 E-value=1.1 Score=23.13 Aligned_cols=94 Identities=15% Similarity=0.115 Sum_probs=52.4 Q ss_pred CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC Q ss_conf 54112477614886788999999999999708997799971537999999999999999862312112333321000123 Q gi|254781187|r 74 NPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGW 153 (367) Q Consensus 74 ~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~ 153 (367) ..+|+.+.+++.-|+|||+.+-.++--++-.....-++-.-.+...--+++-..||.+..+-. T Consensus 45 ~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRGIDvVRn~IK~FAQ~kv----------------- 107 (333) T KOG0991 45 EGNMPNLIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERGIDVVRNKIKMFAQKKV----------------- 107 (333) T ss_pred CCCCCCEEEECCCCCCHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHC----------------- T ss_conf 289986675279998616489999999838066657632057655460899999999987203----------------- Q ss_pred CCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 332211113457761266210135445565210113586289997545599889999898740 Q gi|254781187|r 154 YAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFT 216 (367) Q Consensus 154 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt 216 (367) .-..| ++ -.+|+|||....+..-.+++-+|- T Consensus 108 ----------------------------~lp~g---rh-KIiILDEADSMT~gAQQAlRRtME 138 (333) T KOG0991 108 ----------------------------TLPPG---RH-KIIILDEADSMTAGAQQALRRTME 138 (333) T ss_pred ----------------------------CCCCC---CE-EEEEEECCCHHHHHHHHHHHHHHH T ss_conf ----------------------------48998---52-489961522020689999999999 No 199 >PRK08939 primosomal protein DnaI; Reviewed Probab=89.23 E-value=1.5 Score=22.30 Aligned_cols=70 Identities=16% Similarity=-0.003 Sum_probs=43.5 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 4366684289999999888875124555554112477614886788999999999999708997799971537 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) |..+.--+.-..+++.++.+++..-. ..+...-+-+.+.-|+|||+++++++--++ ..--..+++..|+. T Consensus 127 ~~d~~~~d~~R~~a~~~a~~F~~~y~--~~~~~kGlyl~G~~G~GKTyL~~aian~La-~~g~~v~~v~~p~~ 196 (306) T PRK08939 127 LADIDLDDLDRLDALMAALDFLEAYK--PGEKVKGLYLYGDFGVGKTYLLAAIANELA-KKGVSSTLVHFPEF 196 (306) T ss_pred HHHCCCCCHHHHHHHHHHHHHHHHHC--CCCCCCEEEEECCCCCCHHHHHHHHHHHHH-HCCCEEEEEEHHHH T ss_conf 98648897789999999999999737--698887788989999989999999999999-86992999875999 No 200 >PRK10037 cell division protein; Provisional Probab=89.22 E-value=0.73 Score=24.27 Aligned_cols=43 Identities=19% Similarity=0.323 Sum_probs=28.7 Q ss_pred EEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEECC-CHHHHH Q ss_conf 1247761488-67889999999999997089977999715-379999 Q gi|254781187|r 77 IFKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIAN-SETQLK 121 (367) Q Consensus 77 ~~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A~-t~~Q~~ 121 (367) |..++|.|.| |+|||+++|.++. ++..-+.+|+++=- -++.++ T Consensus 1 M~iial~s~kGGVGkTTltAnLA~--aL~~~g~~VlaID~dpqN~Lr 45 (250) T PRK10037 1 MAILGLQGVRGGVGTTSITAALAW--SLQMLGENVLVIDACPDNLLR 45 (250) T ss_pred CCEEEEEECCCCCCHHHHHHHHHH--HHHHCCCCEEEEECCHHHHHH T ss_conf 937999607888768999999999--999779918999578256678 No 201 >TIGR00580 mfd transcription-repair coupling factor; InterPro: IPR004576 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 transcribed 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. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by TcrF, which releases RNAP and the truncated transcript. The TcrF may replace RNAP at the lesion site and then recruit the UvrA/B/C repair system.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair. Probab=89.18 E-value=1.5 Score=22.28 Aligned_cols=60 Identities=13% Similarity=0.144 Sum_probs=48.0 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC---CEEEEECCCH Q ss_conf 428999999988887512455555411247761488678899999999999970899---7799971537 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG---MSIICIANSE 117 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~---~~v~~~A~t~ 117 (367) +|+=|.++..+|-..+++....| |+ ||+==|.|||-++...+. .+.+.-. ..|+++.||- T Consensus 509 eT~DQ~~AI~eik~Dm~~~~~MD-----RL-~CGDVGfGKTEVAmRAaF-kAv~~gneylKQVavLVPTT 571 (997) T TIGR00580 509 ETPDQLKAIEEIKADMESPRPMD-----RL-VCGDVGFGKTEVAMRAAF-KAVLDGNEYLKQVAVLVPTT 571 (997) T ss_pred CCHHHHHHHHHHHHHHCCCCCCC-----EE-EECCCCCCHHHHHHHHHH-HHHCCCCCEECEEEEECCHH T ss_conf 97789999999999740689873-----46-524548853688887888-76338782201168962704 No 202 >PRK11773 uvrD DNA-dependent helicase II; Provisional Probab=89.15 E-value=0.34 Score=26.35 Aligned_cols=44 Identities=23% Similarity=0.394 Sum_probs=33.7 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHH--CCCCEEEEECCCHHHHHHH Q ss_conf 7761488678899999999999970--8997799971537999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLIST--RPGMSIICIANSETQLKNT 123 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~--~~~~~v~~~A~t~~Q~~~~ 123 (367) +.|.||=|+|||.....-+.|++.. -++.+|+++.=|.+-+.++ T Consensus 25 ~lV~AGaGSGKT~vL~~Ria~Li~~~gv~p~~ILalTFTnkAA~Em 70 (722) T PRK11773 25 MLVLAGAGSGKTRVLVHRIAWLMQVENASPYSILAVTFTNKAAAEM 70 (722) T ss_pred EEEEECCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH T ss_conf 7999738715999999999999982999878828984589999999 No 203 >KOG0989 consensus Probab=88.76 E-value=1.7 Score=22.10 Aligned_cols=172 Identities=12% Similarity=0.054 Sum_probs=80.9 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHHHHHH Q ss_conf 99999998888751245555541124776148867889999999999997089-97799971537999999999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) .|..+...+-.-+.+ +.+|. ..--+++|+|||..+-+++--..+-.. +++++-.-.+...-..+.-..++.+. T Consensus 40 gQe~vV~~L~~a~~~---~~lp~---~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~lnaSderGisvvr~Kik~fa 113 (346) T KOG0989 40 GQEHVVQVLKNALLR---RILPH---YLFYGPPGTGKTSTALAFARALNCEQLFPCRVLELNASDERGISVVREKIKNFA 113 (346) T ss_pred CHHHHHHHHHHHHHH---CCCCE---EEEECCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHCCCCCCCCCCHHHHHCCHH T ss_conf 159999999999860---68860---786689998676899999998557423555424313660014310066523799 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH Q ss_conf 86231211233332100012333221111345776126621013544556521011358628999754559988999989 Q gi|254781187|r 133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL 212 (367) Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~ 212 (367) ... .... ...+.-..-+-.+|+|||...+.+.|.++. T Consensus 114 kl~-----------------------------------------~~~~--~~~~~~~~~fKiiIlDEcdsmtsdaq~aLr 150 (346) T KOG0989 114 KLT-----------------------------------------VLLK--RSDGYPCPPFKIIILDECDSMTSDAQAALR 150 (346) T ss_pred HHH-----------------------------------------HCCC--CCCCCCCCCCEEEEEECHHHHHHHHHHHHH T ss_conf 875-----------------------------------------0255--656788986328997416453099999999 Q ss_pred HHHHCCCCCEEEEEEECC-CCCCCHHH-H--HHH-CCCCC----EEEEEECCCCCCCCCHHHHHHHHHHCC Q ss_conf 874069882589998078-99987688-7--541-12235----046752333288889889999996216 Q gi|254781187|r 213 GFFTELNPNRFWIMTSNT-RRLNGWFY-D--IFN-IPLED----WKRYQIDTRTVEGIDSGFHEGIISRYG 274 (367) Q Consensus 213 g~Lt~~~~~~~~i~igNP-~r~~g~Fy-e--~~~-~~~~~----w~~~~~~~~d~p~~~~~~i~~~~~~~g 274 (367) -+|-.....+-.|++.|- .+--.+.- + -|+ ++-++ -....+.+.++=-++++-++.+...-+ T Consensus 151 r~mE~~s~~trFiLIcnylsrii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d~~al~~I~~~S~ 221 (346) T KOG0989 151 RTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASKEGVDIDDDALKLIAKISD 221 (346) T ss_pred HHHHCCCCCEEEEEECCCHHHCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCC T ss_conf 99862546659999738856477287746777128876447899999999888589978789999999738 No 204 >cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis. Probab=88.72 E-value=0.9 Score=23.72 Aligned_cols=34 Identities=18% Similarity=0.128 Sum_probs=21.6 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 7761488678899999999999970899779997 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) +.|++|-|+|||+++..+.--+.....+.+|.++ T Consensus 2 IGIaG~sgSGKST~a~~l~~~l~~~~~~~~v~ii 35 (220) T cd02025 2 IGIAGSVAVGKSTTARVLQALLSRWPDHPNVELI 35 (220) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEE T ss_conf 8978899877999999999986002699948999 No 205 >COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism] Probab=88.60 E-value=1.5 Score=22.38 Aligned_cols=75 Identities=19% Similarity=0.154 Sum_probs=48.8 Q ss_pred CCCHHHHHHHHHCCCCCCCCCCCCCCCHH--HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH Q ss_conf 25988885543014668884436668428--9999999888875124555554112477614886788999999999999 Q gi|254781187|r 25 VLSFKNFVMRFFPWGIKGKPLEHFSQPHR--WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLI 102 (367) Q Consensus 25 ~~~~~~f~~~~~~w~~~~~~~~~~~~p~~--wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~ 102 (367) +.|-..-.+.+. |..-..|+. --.++|+.++.+.- ...++-|.+.=|+|||+++-.++.-+ T Consensus 13 ~GdrrAlARaIT--------lvEs~~~~h~~~a~~ll~~l~p~tG--------~a~viGITG~PGaGKSTli~~L~~~l- 75 (323) T COG1703 13 AGDRRALARAIT--------LVESRRPDHRALARELLRALYPRTG--------NAHVIGITGVPGAGKSTLIEALGREL- 75 (323) T ss_pred CCCHHHHHHHHH--------HHHCCCCHHHHHHHHHHHHHHHCCC--------CCCEEEECCCCCCCHHHHHHHHHHHH- T ss_conf 479989999989--------9764795024679999999731179--------98378731799886688999999999- Q ss_pred HHCCCCEEEEEC--CCH Q ss_conf 708997799971--537 Q gi|254781187|r 103 STRPGMSIICIA--NSE 117 (367) Q Consensus 103 ~~~~~~~v~~~A--~t~ 117 (367) .+.+.+|.|+| |+. T Consensus 76 -~~~G~rVaVlAVDPSS 91 (323) T COG1703 76 -RERGHRVAVLAVDPSS 91 (323) T ss_pred -HHCCCEEEEEEECCCC T ss_conf -9779678999988999 No 206 >PRK09401 reverse gyrase; Reviewed Probab=88.60 E-value=1.7 Score=22.04 Aligned_cols=110 Identities=21% Similarity=0.198 Sum_probs=62.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC- Q ss_conf 4776148867889999999999997089977999715379999999999999998623121123333210001233322- Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL- 157 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~- 157 (367) ..|+.|+.|+|||++...+.+|++. .+.|++++-||..-++++. ..+..+.++.-.. +....++... T Consensus 95 SFaiiAPTG~GKTtfgl~~sly~a~--kgkks~~i~PT~~Lv~Q~~-~kl~~~~~~~~~~---------~~~~~y~~~~~ 162 (1176) T PRK09401 95 SFAIIAPTGVGKTTFGLVMALYLAK--KGKKSYIIFPTRLLVEQVV-EKLRKLAEKVGVK---------VRLLYYHSSLK 162 (1176) T ss_pred CEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEECCHHHHHHHH-HHHHHHHHHHCCC---------CEEEEEECCCC T ss_conf 7489888998888999999999986--5983999968889999999-9999999970998---------40899856776 Q ss_pred ----CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC Q ss_conf ----11113457761266210135445565210113586289997545 Q gi|254781187|r 158 ----LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS 201 (367) Q Consensus 158 ----~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs 201 (367) .+..-....|..-+. .+.+..-+-++.-+....+.++.||-.- T Consensus 163 ~~~kee~~~~~~~gdfdIl-itT~~fl~kn~~~l~~~~f~fifvDDVD 209 (1176) T PRK09401 163 KKEKEEFLERLEEGDFDIL-VTTSQFLSKNFDELPKDRFDFVFVDDVD 209 (1176) T ss_pred HHHHHHHHHHHHCCCCCEE-EEEHHHHHHHHHHCCCCCCCEEEEECHH T ss_conf 6678999988655998689-9856767654876035688889993418 No 207 >PRK11664 ATP-dependent RNA helicase HrpB; Provisional Probab=88.38 E-value=1.7 Score=21.95 Aligned_cols=145 Identities=16% Similarity=0.072 Sum_probs=64.9 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 47761488678899999999999970899779997153799999999999999986231211233332100012333221 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL 158 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (367) .+.|.+.-|+|||+.+--+++-.... ..+|+||-|-.=-++.+ -..++....... ....++.... T Consensus 22 ~~vl~a~tGsGKtTqvP~~ll~~~~~--~g~I~~~qPRR~AA~s~-A~RvA~e~~e~~------------G~~VGY~vR~ 86 (812) T PRK11664 22 QVLLKAPTGAGKSTWLPLQLLQQGGI--NGKIIMLEPRRLAARNV-AQRLAEQLGEKP------------GETVGYRMRA 86 (812) T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCC--CCCEEEECCHHHHHHHH-HHHHHHHHCCCC------------CCEEEEEECC T ss_conf 79999089999899999999964688--99389938839999999-999999729999------------9867578256 Q ss_pred CCCCCCCCCCEEEE-ECCCCCCCCCCCCCCCCCCCCEEEEECCC--CCCHHH-HHHHHHHHHCCCCCEEEEEEECCCCCC Q ss_conf 11134577612662-10135445565210113586289997545--599889-999898740698825899980789998 Q gi|254781187|r 159 EQSMGIDSKHYTIT-CRTYSEERPDTFVGPHNTHGMAVFNDEAS--GTPDII-NKSILGFFTELNPNRFWIMTSNTRRLN 234 (367) Q Consensus 159 ~~~~~~~~~~~~~~-a~~~~~~~~ea~~g~h~~~~~l~ivDEAs--gI~d~i-~e~i~g~Lt~~~~~~~~i~igNP~r~~ 234 (367) .......+...|++ +...+....+ ..+ ..+.++|+||+. .+.-++ +-.+.-...........++.| -|-.. T Consensus 87 e~~~s~~Tri~~~T~GiLlr~l~~d--p~L--~~~~~vI~DE~HER~l~~Dl~l~l~~~~~~~~r~dLklvvMS-ATld~ 161 (812) T PRK11664 87 ESKVGPNTRLEVVTEGILTRMIQRD--PEL--SGVGLVILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMS-ATLDN 161 (812) T ss_pred CCCCCCCCEEEEECHHHHHHHHHHC--CCC--CCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEC-CCCCH T ss_conf 7788998579997558999997249--776--778889995754687518999999999998618982899984-78884 Q ss_pred CHHHHHHHC Q ss_conf 768875411 Q gi|254781187|r 235 GWFYDIFNI 243 (367) Q Consensus 235 g~Fye~~~~ 243 (367) ..|.+.|.. T Consensus 162 ~~~~~~~~~ 170 (812) T PRK11664 162 DRLQQLLPD 170 (812) T ss_pred HHHHHHCCC T ss_conf 889975899 No 208 >TIGR00678 holB DNA polymerase III, delta' subunit; InterPro: IPR004622 DNA-directed DNA polymerase (2.7.7.7 from EC) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. DNA polymerase III is a complex, multi-chain enzyme responsible for most of the replicative synthesis in bacteria. The enzyme also has 3' to 5' exonuclease activity. It has a core composed of alpha, epsilon and theta chains, that associate with a tau subunit which allows the core dimerisation to form the PolIII' complex. PolIII' associates with the gamma complex (gamma, delta, delta', psi and chi chains) and with the beta chain. This domain is the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tightly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classified as delta'. The noise cut-off is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits.; GO: 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication. Probab=88.35 E-value=1.8 Score=21.93 Aligned_cols=132 Identities=16% Similarity=0.160 Sum_probs=70.5 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC--------- Q ss_conf 47761488678899999999999970899779997153799999999999999986231211233332100--------- Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLH--------- 149 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~--------- 149 (367) -....+..|+||..++-+++-|++|..+....-|-.-..-+.-. ...-|+-+++..+..... T Consensus 16 A~LF~G~~G~Gk~~~A~~~A~~l~C~~~~~~~~Cg~C~~C~~~~---------~G~HPD~~~~~P~~~~~~~~~de~~~~ 86 (216) T TIGR00678 16 AYLFTGPEGVGKELLALALAKALLCEPRGGGEPCGECHSCRLIE---------AGNHPDLHRLEPEGQSKSLTADEAAEG 86 (216) T ss_pred CEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHH---------HCCCCCEEEEEEECCCCCCCHHHHHHH T ss_conf 12544488874899999999998077857788888588899987---------079982378742347777776458976 Q ss_pred --CCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEE Q ss_conf --012333221111345776126621013544556521011358628999754559988999989874069882589998 Q gi|254781187|r 150 --PSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMT 227 (367) Q Consensus 150 --~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~i 227 (367) .. .. ...+..++.+.=-.. ...=+..+..+.+. .+|+|.|.-.....=.+++.+|=.+..+++++++ T Consensus 87 ~~g~-a~-~~~~~~Ik~dq~R~l--------~~~~~~~~~~~~~r-VviI~~Ae~mn~~AANALLKtLEEPp~~t~fiL~ 155 (216) T TIGR00678 87 EEGS-AK-RRALPQIKVDQVREL--------VEFLSLTPQESGRR-VVIIEDAERMNEAAANALLKTLEEPPPNTLFILI 155 (216) T ss_pred HCCC-CC-CCCCCCCCHHHHHHH--------HHHHHHCCCCCCCE-EEEECCHHHCCHHHHHHHHHHEECCCCCEEEEEE T ss_conf 2564-21-136787872789999--------99986064214751-7997673232589898651010127987079885 Q ss_pred ECC Q ss_conf 078 Q gi|254781187|r 228 SNT 230 (367) Q Consensus 228 gNP 230 (367) +.- T Consensus 156 ~~~ 158 (216) T TIGR00678 156 THS 158 (216) T ss_pred CCC T ss_conf 088 No 209 >COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism] Probab=88.32 E-value=1.8 Score=21.92 Aligned_cols=161 Identities=14% Similarity=0.068 Sum_probs=73.5 Q ss_pred CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-----CCCHHHHHH Q ss_conf 668428999999988887512455555411247761488678899999999999970899779997-----153799999 Q gi|254781187|r 48 FSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-----ANSETQLKN 122 (367) Q Consensus 48 ~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-----A~t~~Q~~~ 122 (367) ..|-++|-.=++.+ .-.|.+-.+.|++-+|+|||+++=+++- .-|+..++.- -|+..- T Consensus 19 ivGqd~lk~aL~l~----------av~P~iggvLI~G~kGtaKSt~~Rala~----LLp~~~~V~gc~f~cdP~~P~--- 81 (423) T COG1239 19 IVGQDPLKLALGLN----------AVDPQIGGALIAGEKGTAKSTLARALAD----LLPEIEVVIGCPFNCDPDDPE--- 81 (423) T ss_pred HCCCHHHHHHHHHH----------HCCCCCCEEEEECCCCCCHHHHHHHHHH----HCCCCCEECCCCCCCCCCCHH--- T ss_conf 43753777887653----------0263104268766887527799999998----679633216887889988705--- Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC-C-CCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECC Q ss_conf 99999999998623121123333210001233322111-1-345776126621013544556521011358628999754 Q gi|254781187|r 123 TLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQ-S-MGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEA 200 (367) Q Consensus 123 ~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEA 200 (367) .+..+.++-.... .|..... +++..-..+...+ + +-++-....+....-....|.-+.-.| .-.++|||- T Consensus 82 ~~c~~c~~k~~e~---~~~~~~~--r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~An---RGIlYvDEv 153 (423) T COG1239 82 EMCDECRAKGDEL---EWLPREK--RKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARAN---RGILYVDEV 153 (423) T ss_pred HHHHHHHHHCCCC---CCCCCCC--EECCEECCCCCCCHHHHCCCCCHHHHHHCCCCCCCCCCHHHCC---CCEEEEECC T ss_conf 5519998620232---4454221--0031223887630433004567999972683002775110035---887987233 Q ss_pred CCCCHHHHHHHHHHHHCC-------------CCCEEEEEEECCCCC Q ss_conf 559988999989874069-------------882589998078999 Q gi|254781187|r 201 SGTPDIINKSILGFFTEL-------------NPNRFWIMTSNTRRL 233 (367) Q Consensus 201 sgI~d~i~e~i~g~Lt~~-------------~~~~~~i~igNP~r~ 233 (367) .-++|.+-+++.-.+..+ -.+.+++.+.||-.+ T Consensus 154 nlL~d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeG 199 (423) T COG1239 154 NLLDDHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEG 199 (423) T ss_pred CCCCHHHHHHHHHHHHHCCCEEEECCEEECCCCCEEEEEECCCCCC T ss_conf 4351899999999997177403357503136761799964485446 No 210 >cd02035 ArsA ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence. Probab=88.31 E-value=0.67 Score=24.49 Aligned_cols=31 Identities=26% Similarity=0.461 Sum_probs=23.6 Q ss_pred EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 614886788999999999999708997799971 Q gi|254781187|r 82 ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 82 v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) +.+==|+|||++++.+++.++-. |.|++++. T Consensus 4 ~sGKGGVGKTTvAaalA~~lA~~--G~rvLlvs 34 (217) T cd02035 4 FTGKGGVGKTTIAAATAVRLAEE--GKKVLLVS 34 (217) T ss_pred EECCCCCCHHHHHHHHHHHHHHC--CCEEEEEE T ss_conf 97899661999999999999968--99499995 No 211 >PRK13900 type IV secretion system ATPase VirB11; Provisional Probab=88.26 E-value=1.5 Score=22.28 Aligned_cols=37 Identities=22% Similarity=0.206 Sum_probs=27.7 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 2477614886788999999999999708997799971537 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) .++.|++|.|+|||++..+++-. .-++.+++++-.+. T Consensus 161 ~NilI~G~TgSGKTTll~aL~~~---ip~~eRiitIEDt~ 197 (332) T PRK13900 161 KNIIISGGTSTGKTTFTNAALRE---IPAIERLITVEDAR 197 (332) T ss_pred CCEEEECCCCCCHHHHHHHHHHC---CCCCCCEEEECCCH T ss_conf 71999888898899999999835---89535356631406 No 212 >cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain. Probab=88.26 E-value=1.1 Score=23.24 Aligned_cols=52 Identities=17% Similarity=0.198 Sum_probs=32.8 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC Q ss_conf 77614886788999999999999708997799971537999999999999999862 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSML 135 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~ 135 (367) +++.+..|+|||+.+|-++.++. .+.....++++.|++-.- ...++.+.+.+ T Consensus 3 i~lvGptGvGKTTTiaKLA~~~~-~~~~kV~lit~Dt~R~gA---~eQL~~~a~~l 54 (173) T cd03115 3 ILLVGLQGVGKTTTAAKLALYLK-KKGKKVLLVAADTYRPAA---IEQLRVLGEQV 54 (173) T ss_pred EEEECCCCCCHHHHHHHHHHHHH-HCCCEEEEEECCCCCHHH---HHHHHHHHHHC T ss_conf 99989999988999999999999-769928999748875779---99999999974 No 213 >pfam01637 Arch_ATPase Archaeal ATPase. This family contain a conserved P-loop motif that is involved in binding ATP. This family is almost exclusively found in archaebacteria and particularly in Methanococcus jannaschii that encodes sixteen members of this family. Probab=88.12 E-value=1.8 Score=21.85 Aligned_cols=52 Identities=13% Similarity=0.082 Sum_probs=28.2 Q ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC Q ss_conf 999988887512455555411247761488678899999999999970899779997153 Q gi|254781187|r 57 EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANS 116 (367) Q Consensus 57 ~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t 116 (367) +-|+.+.+.++++... -++|-+.|++|||.++-..+-= .-.++..++..... T Consensus 6 ~EL~~L~~~~~~~~~~------~ivi~G~RR~GKTsLi~~~~~~--~~~~~~~~i~~~~~ 57 (223) T pfam01637 6 KELKELEEWAERGTYP------IIVVYGPRRCGKTALLREFLEE--LRELGYRVIYYDPL 57 (223) T ss_pred HHHHHHHHHHHCCCCC------EEEEECCCCCCHHHHHHHHHHH--CCCCCCEEEEEECH T ss_conf 9999999999669971------8999868878799999999986--33468528999514 No 214 >cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion. Probab=88.10 E-value=1.2 Score=22.90 Aligned_cols=33 Identities=30% Similarity=0.423 Sum_probs=26.4 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 77614886788999999999999708997799971 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) +++.+--|+|||++++.++..+.. .+.+++++- T Consensus 2 i~~~~~kGvGKTT~a~~La~~la~--~g~~Vl~vD 34 (99) T cd01983 2 IVVTGKGGVGKTTLAANLAAALAK--RGKRVLLID 34 (99) T ss_pred EEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEC T ss_conf 898589977689999999999998--899699986 No 215 >cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer. Probab=88.01 E-value=1.1 Score=23.27 Aligned_cols=32 Identities=31% Similarity=0.503 Sum_probs=25.0 Q ss_pred EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 7761488-678899999999999970899779997 Q gi|254781187|r 80 CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 80 ~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) ++|+||. |+|||++++.++..++.. +.+++++ T Consensus 2 Iav~s~KGGVGKTT~a~NLA~aLa~~--g~~vllv 34 (179) T cd02036 2 IVVTSGKGGVGKTTTTANLGTALAQL--GYKVVLI 34 (179) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEE T ss_conf 89973999870999999999999977--9918999 No 216 >TIGR01425 SRP54_euk signal recognition particle protein SRP54; InterPro: IPR006325 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. 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. This entry represents 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.; GO: 0005525 GTP binding, 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle. Probab=87.94 E-value=1.7 Score=22.03 Aligned_cols=94 Identities=11% Similarity=0.090 Sum_probs=56.3 Q ss_pred CCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 48867889999999999997089977999715379999999999999998623121123333210001233322111134 Q gi|254781187|r 84 AGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMG 163 (367) Q Consensus 84 sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 163 (367) +=.|+|||+.+.=|++|+=--. ...++|+|-|. |-.-|..+++-..+.. -|++.. +.+ T Consensus 128 GLQGaGKTTtctKLA~YYk~rG-fK~~lvCADTF---RAGAFdQLkqNA~kA~--------------iPFYGs----y~E 185 (453) T TIGR01425 128 GLQGAGKTTTCTKLAYYYKRRG-FKPALVCADTF---RAGAFDQLKQNATKAK--------------IPFYGS----YLE 185 (453) T ss_pred ECCCCCHHHHHHHHHHHHHCCC-CCEEEECCCCC---CCCHHHHHHHHHHHCC--------------CCCCCC----CCC T ss_conf 2148871566878777763266-43256517754---2324899987476448--------------971201----048 Q ss_pred CCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC--CHHHHH Q ss_conf 5776126621013544556521011358628999754559--988999 Q gi|254781187|r 164 IDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT--PDIINK 209 (367) Q Consensus 164 ~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI--~d~i~e 209 (367) .|+ ..+. .|..+-++.|+..++|||-..-= .+..|+ T Consensus 186 ~DP--VkiA--------~EGv~~Fk~E~~diIivDTSGRHkQe~~LF~ 223 (453) T TIGR01425 186 SDP--VKIA--------SEGVEKFKKEKFDIIIVDTSGRHKQEEELFE 223 (453) T ss_pred CCC--EEEE--------CCCHHHHHCCCCCEEEEECCCCCHHHHHHHH T ss_conf 987--0780--------0201132212784799837987322588889 No 217 >cd00550 ArsA_ATPase Oxyanion-translocating ATPase (ArsA). This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life. ArsA contains a highly conserved AAA motif present in the AAA+ ATPase superfamily associated with a variety of cellular activities. To form a functional ATP-driven pump, ArsA interacts with the permease ArsB, which is a channel-forming integral membrane protein. One of the most interesting features of ArsA is the allosteric activation by its transport substrates. A divalent cation, typically Mg2+, is required for its enzymatic activity. Probab=87.91 E-value=0.74 Score=24.24 Aligned_cols=40 Identities=23% Similarity=0.432 Sum_probs=26.6 Q ss_pred EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC-HHHHHHH Q ss_conf 61488678899999999999970899779997153-7999999 Q gi|254781187|r 82 ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANS-ETQLKNT 123 (367) Q Consensus 82 v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t-~~Q~~~~ 123 (367) +.+==|+|||+++|.+++..+-. |.|+++++-. .+.+.++ T Consensus 5 ~~GKGGVGKTT~AaalA~~lA~~--G~kVLlvstDPahsLsd~ 45 (254) T cd00550 5 FGGKGGVGKTTISAATAVRLAEQ--GKKVLLVSTDPAHSLSDS 45 (254) T ss_pred EECCCCCCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCHHHH T ss_conf 96898554899999999999968--994999958986448898 No 218 >PRK13851 type IV secretion system protein VirB11; Provisional Probab=87.80 E-value=1.2 Score=22.86 Aligned_cols=101 Identities=13% Similarity=0.084 Sum_probs=54.4 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 24776148867889999999999997089977999715379999999999999998623121123333210001233322 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL 157 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (367) .++.|++|.|+|||++..+++-. .-++.+++++-.+..- . ++..++.... + T Consensus 163 ~NIlIsGgTGSGKTTllnALl~~---IP~~eRIvtIEDt~EL---------~-----l~~~n~V~l~----~-------- 213 (343) T PRK13851 163 LTMLLCGPTGSGKTTMSKTLISA---IPPQERLITIEDTLEL---------V-----IPHENHVRLL----Y-------- 213 (343) T ss_pred CCEEEECCCCCCHHHHHHHHHHC---CCCCCCEEEECCCCCC---------C-----CCCCCEEEEE----E-------- T ss_conf 88999888986199999999962---8965527996115002---------5-----8999968999----6-------- Q ss_pred CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCC Q ss_conf 111134577612662101354455652101135862899975455998899998987406988 Q gi|254781187|r 158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNP 220 (367) Q Consensus 158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~ 220 (367) .+...+.. ..+.......+ +| .+..-+|+-|.-| ++.|+-+...-|+..+ T Consensus 214 ----~~~~~g~~---~vt~~~Ll~~a---LR-mrPDRIivGEvRG--~EA~d~L~A~nTGH~G 263 (343) T PRK13851 214 ----SKNGAGLG---AVTAEHLLQAS---LR-MRPDRILLGEMRD--DAAWAYLSEVVSGHPG 263 (343) T ss_pred ----CCCCCCCC---CCCHHHHHHHH---HC-CCCCEEEEEEECC--HHHHHHHHHHHCCCCC T ss_conf ----58988858---39799999998---60-7998289985266--9999999998469998 No 219 >KOG0337 consensus Probab=87.77 E-value=1.2 Score=22.95 Aligned_cols=74 Identities=16% Similarity=0.128 Sum_probs=46.7 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC--CCEEEEECCCHHHHHH Q ss_conf 43666842899999998888751245555541124776148867889999999999997089--9779997153799999 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP--GMSIICIANSETQLKN 122 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~--~~~v~~~A~t~~Q~~~ 122 (367) -++|..|++-|++-.-. +++. .-+.-.|--|+|||...-+=++-.|..+- +.+.++..||..-+-. T Consensus 38 kkg~~~ptpiqRKTipl---iLe~---------~dvv~martgsgktaaf~ipm~e~Lk~~s~~g~RalilsptreLa~q 105 (529) T KOG0337 38 KKGFNTPTPIQRKTIPL---ILEG---------RDVVGMARTGSGKTAAFLIPMIEKLKSHSQTGLRALILSPTRELALQ 105 (529) T ss_pred HHHCCCCCCHHCCCCCC---EEEC---------CCCCEEEECCCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCHHHHHH T ss_conf 86238998411034420---0314---------52100552278610467889999986136446202432670889999 Q ss_pred HHHHHHHHH Q ss_conf 999999999 Q gi|254781187|r 123 TLWAEVSKW 131 (367) Q Consensus 123 ~lw~ei~k~ 131 (367) . +.-++.. T Consensus 106 t-lkvvkdl 113 (529) T KOG0337 106 T-LKVVKDL 113 (529) T ss_pred H-HHHHHHH T ss_conf 9-9999985 No 220 >PRK08233 hypothetical protein; Provisional Probab=87.74 E-value=0.96 Score=23.55 Aligned_cols=32 Identities=25% Similarity=0.174 Sum_probs=24.2 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 477614886788999999999999708997799971 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) =++|++|.|+|||+++-.++-- .|+..++..- T Consensus 5 IIgIaGgSgSGKTtla~~l~~~----l~~~~~~~~D 36 (182) T PRK08233 5 IITIAAVSGGGKTTLTERLTHK----LKNSKALYFD 36 (182) T ss_pred EEEEECCCCCCHHHHHHHHHHH----CCCCEEEEEC T ss_conf 9999688867899999999997----4677589966 No 221 >KOG1123 consensus Probab=87.70 E-value=0.57 Score=24.93 Aligned_cols=147 Identities=13% Similarity=0.081 Sum_probs=73.4 Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH Q ss_conf 88844366684289999999888875124555554112477614886788999999999999708997799971537999 Q gi|254781187|r 41 KGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQL 120 (367) Q Consensus 41 ~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~ 120 (367) ++..|--...+|++|++-|+.+.-.-+- ++ -+.|. +-|.|||-..- -++|.-..+++|.+++.-.+ T Consensus 293 l~idLKPst~iRpYQEksL~KMFGNgRA---RS-----GiIVL-PCGAGKtLVGv-----TAa~tikK~clvLcts~VSV 358 (776) T KOG1123 293 LDIDLKPSTQIRPYQEKSLSKMFGNGRA---RS-----GIIVL-PCGAGKTLVGV-----TAACTIKKSCLVLCTSAVSV 358 (776) T ss_pred CCCCCCCCCCCCCHHHHHHHHHHCCCCC---CC-----CEEEE-ECCCCCCEEEE-----EEEEEECCCEEEEECCCCCH T ss_conf 8867685455575378789997378854---47-----61898-56998742545-----55545514279995575669 Q ss_pred HHHHHHH-HHHHHHHCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEE Q ss_conf 9999999-9999986231211233332100012333-2211113457761266210135445565210113586289997 Q gi|254781187|r 121 KNTLWAE-VSKWLSMLPHRHWFEMQSLSLHPSGWYA-ELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFND 198 (367) Q Consensus 121 ~~~lw~e-i~k~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivD 198 (367) .+ |+. .+.|...-+. ..-..+....-..+... ....++ +..+....-+-+......-+++...-|+++| T Consensus 359 eQ--WkqQfk~wsti~d~-~i~rFTsd~Ke~~~~~~gvvvsTY------sMva~t~kRS~eaek~m~~l~~~EWGllllD 429 (776) T KOG1123 359 EQ--WKQQFKQWSTIQDD-QICRFTSDAKERFPSGAGVVVTTY------SMVAYTGKRSHEAEKIMDFLRGREWGLLLLD 429 (776) T ss_pred HH--HHHHHHHHHCCCCC-CEEEEECCCCCCCCCCCCEEEEEE------EHHHHCCCCCHHHHHHHHHHHCCEEEEEEEE T ss_conf 99--99998745016855-457720244545789885799873------1311056642779999999843710168842 Q ss_pred CCCCCCHHHHHH Q ss_conf 545599889999 Q gi|254781187|r 199 EASGTPDIINKS 210 (367) Q Consensus 199 EAsgI~d~i~e~ 210 (367) |..-||...|-- T Consensus 430 EVHvvPA~MFRR 441 (776) T KOG1123 430 EVHVVPAKMFRR 441 (776) T ss_pred HHCCCHHHHHHH T ss_conf 111126999999 No 222 >KOG1002 consensus Probab=87.65 E-value=1.9 Score=21.67 Aligned_cols=216 Identities=13% Similarity=0.058 Sum_probs=92.7 Q ss_pred CCCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHH-------CCCCCC----CCCCCCCCCH-------HHHHHHHHHHHH Q ss_conf 5554572337899997523201259888855430-------146688----8443666842-------899999998888 Q gi|254781187|r 3 RLISTDQKLEQELHEMLMHAECVLSFKNFVMRFF-------PWGIKG----KPLEHFSQPH-------RWQLEFMEAVDV 64 (367) Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~-------~w~~~~----~~~~~~~~p~-------~wq~~~l~~~~~ 64 (367) |..++--+.-..++...|.++..-.-.|..++.- -|..++ -..+...+|. ++|.|.|.=... T Consensus 119 rrk~~ark~k~~~s~~k~q~k~~p~er~~~rl~eh~pE~~~v~~dlde~~p~i~e~aeqP~dlii~LL~fQkE~l~Wl~~ 198 (791) T KOG1002 119 RRKPTARKKKKKTSTEKKQPKVTPYERNTLRLYEHHPELRNVFTDLDEANPVIAERAEQPDDLIIPLLPFQKEGLAWLTS 198 (791) T ss_pred CCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHCCCCCCCCEECCHHHHHHHHHHHHH T ss_conf 45752355554333554276558410003556541803444453231237401220369601342131446777888877 Q ss_pred HHHCCCCCCCCCEEEEE-EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCC--CCCC Q ss_conf 75124555554112477-61488678899999999999970899779997153799999999999999986231--2112 Q gi|254781187|r 65 HCHSNVNNSNPTIFKCA-ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPH--RHWF 141 (367) Q Consensus 65 ~~~~~~~~~~~~~~~~~-v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~--~~~~ 141 (367) +.+. .++-- .+---|.|||.-+-.+++- --.....+|+||+-.-. ..-.||.+.-+..-. -+.- T Consensus 199 QE~S--------s~~GGiLADEMGMGKTIQtIaLlla---e~~ra~tLVvaP~VAlm--QW~nEI~~~T~gslkv~~YhG 265 (791) T KOG1002 199 QEES--------SVAGGILADEMGMGKTIQTIALLLA---EVDRAPTLVVAPTVALM--QWKNEIERHTSGSLKVYIYHG 265 (791) T ss_pred HHHH--------HHCCCEEHHHHCCCHHHHHHHHHHH---CCCCCCEEEECCHHHHH--HHHHHHHHHCCCCEEEEEEEC T ss_conf 3554--------3124311243146417999999986---23568706975489999--999999876257647999726 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCC--CCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCC Q ss_conf 33332100012333221111345776126621013544--5565210113586289997545599889999898740698 Q gi|254781187|r 142 EMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEE--RPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELN 219 (367) Q Consensus 142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~--~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~ 219 (367) ......+.....+..+..++....+.. .-.-.+++.. .-....-+|+-.+.-+|+|||.+|.+..-..+.....-.. T Consensus 266 ~~R~~nikel~~YDvVLTty~vvEs~y-Rk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~IK~R~snTArAV~~L~t 344 (791) T KOG1002 266 AKRDKNIKELMNYDVVLTTYAVVESVY-RKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNIKDRQSNTARAVFALET 344 (791) T ss_pred CCCCCCHHHHHCCCEEEEECHHHHHHH-HHCCCCCCCCCCCCCCCCHHHHCEEEEEEHHHHCCCCCCCCCHHHHHHHHHH T ss_conf 423577888606767997018788898-7402342113774245323331010235221202531013327888876676 Q ss_pred CCEEEEEEECCCCC Q ss_conf 82589998078999 Q gi|254781187|r 220 PNRFWIMTSNTRRL 233 (367) Q Consensus 220 ~~~~~i~igNP~r~ 233 (367) ... ||+-|+|-.+ T Consensus 345 t~r-w~LSGTPLQN 357 (791) T KOG1002 345 TYR-WCLSGTPLQN 357 (791) T ss_pred HHH-HHCCCCCCHH T ss_conf 653-2205883011 No 223 >PRK07667 uridine kinase; Provisional Probab=87.64 E-value=0.63 Score=24.65 Aligned_cols=27 Identities=26% Similarity=0.129 Sum_probs=22.7 Q ss_pred CCEEEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 411247761488678899999999999 Q gi|254781187|r 75 PTIFKCAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 75 ~~~~~~~v~sgrg~GKS~~~a~~~lw~ 101 (367) .++|-++|++|-|+|||+++.-++--+ T Consensus 12 ~~r~iIgIaG~sgSGKTTla~~L~~~l 38 (190) T PRK07667 12 ENRFILGIDGLSRSGKTTFVANLKENM 38 (190) T ss_pred CCEEEEEEECCCCCCHHHHHHHHHHHH T ss_conf 986999977989788999999999998 No 224 >TIGR00750 lao LAO/AO transport system ATPase; InterPro: IPR005129 Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.. Probab=87.60 E-value=2 Score=21.65 Aligned_cols=58 Identities=24% Similarity=0.341 Sum_probs=42.2 Q ss_pred CCH--HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC--CCH Q ss_conf 842--89999999888875124555554112477614886788999999999999708997799971--537 Q gi|254781187|r 50 QPH--RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA--NSE 117 (367) Q Consensus 50 ~p~--~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A--~t~ 117 (367) +|+ .-=.++|+.|...+ .+.-++=|.+-=|+|||++...++- .+-+.|.+|.|+| ||. T Consensus 17 ~p~H~~~a~~ll~~i~p~~--------GnA~~vG~TG~PGaGKSTl~~~l~~--~lrRrG~~VaViAvDP~S 78 (333) T TIGR00750 17 EPEHRELAKELLERILPKT--------GNAHVVGITGVPGAGKSTLVEKLIM--ELRRRGLKVAVIAVDPSS 78 (333) T ss_pred CCHHHHHHHHHHHHHHHHC--------CCCEEEEEECCCCCCHHHHHHHHHH--HHHHCCCEEEEEEECCCC T ss_conf 9704799999999862432--------7907876646888857779999989--997659768999887975 No 225 >PTZ00301 uridine kinase; Provisional Probab=87.49 E-value=1.3 Score=22.68 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=20.0 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHH Q ss_conf 47761488678899999999999970 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLIST 104 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~ 104 (367) =+.|++|-|+|||+++..++--+... T Consensus 5 iIgIaGgSgSGKTT~a~~i~~~l~~~ 30 (210) T PTZ00301 5 VIGISGASGSGKSSLSTNIVSELMAH 30 (210) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHH T ss_conf 99996887678999999999998761 No 226 >KOG0923 consensus Probab=87.34 E-value=2 Score=21.56 Aligned_cols=160 Identities=17% Similarity=0.062 Sum_probs=80.9 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH-HH Q ss_conf 99999998888751245555541124776148867889999999999997089977999715379999999999999-99 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK-WL 132 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k-~~ 132 (367) +..++|.+|.+|. -+.|.+-.|+|||+-+--++.---.|.-+.+|.||-|-.--+..+- +.+++ +- T Consensus 269 ykdell~av~e~Q------------VLiI~GeTGSGKTTQiPQyL~EaGytk~gk~IgcTQPRRVAAmSVA-aRVA~EMg 335 (902) T KOG0923 269 YKDELLKAVKEHQ------------VLIIVGETGSGKTTQIPQYLYEAGYTKGGKKIGCTQPRRVAAMSVA-ARVAEEMG 335 (902) T ss_pred HHHHHHHHHHHCC------------EEEEECCCCCCCCCCCCHHHHHCCCCCCCCEEEECCCCHHHHHHHH-HHHHHHHC T ss_conf 3999999998670------------8999757889864456289885421358946740685068877799-99999857 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCC--CCHHHHHH Q ss_conf 8623121123333210001233322111134577612662101354455652101135862899975455--99889999 Q gi|254781187|r 133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASG--TPDIINKS 210 (367) Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg--I~d~i~e~ 210 (367) -++-+ ...++. .+ -.....++-+++ ...+-..++...|-. -.+...+|+|||.- ...+|.=. T Consensus 336 vkLG~--eVGYsI--RF---EdcTSekTvlKY-----MTDGmLlREfL~epd----LasYSViiiDEAHERTL~TDILfg 399 (902) T KOG0923 336 VKLGH--EVGYSI--RF---EDCTSEKTVLKY-----MTDGMLLREFLSEPD----LASYSVIIVDEAHERTLHTDILFG 399 (902) T ss_pred CCCCC--CCCEEE--EE---CCCCCCCEEEEE-----ECCHHHHHHHHCCCC----CCCEEEEEEEHHHHHHHHHHHHHH T ss_conf 40143--144488--85---035674122432-----243067998714634----223359996024320034567999 Q ss_pred HHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHC Q ss_conf 898740698825899980789998768875411 Q gi|254781187|r 211 ILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNI 243 (367) Q Consensus 211 i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~ 243 (367) +..-+......+. +++++-|...--|-..|-. T Consensus 400 LvKDIar~RpdLK-llIsSAT~DAekFS~fFDd 431 (902) T KOG0923 400 LVKDIARFRPDLK-LLISSATMDAEKFSAFFDD 431 (902) T ss_pred HHHHHHHHCCCCE-EEEECCCCCHHHHHHHCCC T ss_conf 8788875087604-7732222678999876168 No 227 >cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function. Probab=87.13 E-value=1.5 Score=22.41 Aligned_cols=37 Identities=32% Similarity=0.541 Sum_probs=28.0 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 477614886788999999999999708997799971537 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) |++|+.==|+|||++++.++.+++-. +.+++++-.-- T Consensus 1 kia~~GKGGvGKtt~~~~la~~l~~~--g~~vl~iD~Dp 37 (116) T cd02034 1 KIAITGKGGVGKTTIAALLARYLAEK--GKPVLAIDADP 37 (116) T ss_pred CEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEECCC T ss_conf 97898899774999999999999978--99699998989 No 228 >pfam07517 SecA_DEAD SecA DEAD-like domain. SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the pfam00270. Probab=87.12 E-value=2.1 Score=21.48 Aligned_cols=143 Identities=11% Similarity=-0.034 Sum_probs=63.5 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 47761488678899999999999970899779997153799999999999999986231211233332100012333221 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL 158 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (367) ++|=.. .|=|||-.++..+.-.+++..+.- +||.|.+=--|+. ..+...++.+-...-.-....... -..... T Consensus 93 ~IaEM~-TGEGKTL~atl~a~l~AL~Gk~Vh-vvTvNdYLA~RDa--e~m~~vy~~LGLsvg~i~~~~~~~---err~aY 165 (381) T pfam07517 93 KIAEMK-TGEGKTLTATLPAYLNALSGKGVH-VVTVNDYLAKRDA--EWMGPLYEFLGLSVGVITSDMSPE---ERREAY 165 (381) T ss_pred CEEEEE-CCCCCHHHHHHHHHHHHCCCCCCE-EEECCHHHHHHHH--HHHHHHHHHHCCEEEECCCCCCHH---HHHHHH T ss_conf 725887-699811999999999973799748-9975888868899--997999998486054227889848---889875 Q ss_pred CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHH Q ss_conf 11134577612662101354455652101135862899975455998899998987406988258999807899987688 Q gi|254781187|r 159 EQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRLNGWFY 238 (367) Q Consensus 159 ~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fy 238 (367) ..++-+...+-+.+-..-. .-..+....-.....++||||+-.| |-+....-+ ++|.|......+| T Consensus 166 ~~DItYgTn~e~gFDYLRD-nm~~~~~~~vqR~~~~aIVDEvDSi-----------LIDEArtPL--IISg~~~~~~~~y 231 (381) T pfam07517 166 NCDITYGTNSELGFDYLRD-NMALSKEDKVQRGLNFAIVDEVDSI-----------LIDEARTPL--IISGPVEDESELY 231 (381) T ss_pred HCCCEECCHHHHHHHHHHH-HHHCCHHHHCCCCCCEEEEECCCHH-----------EEECCCCCC--EECCCCCCCCHHH T ss_conf 1660550322321445323-4415825434577776999745112-----------120467863--5407887630589 Q ss_pred HHHH Q ss_conf 7541 Q gi|254781187|r 239 DIFN 242 (367) Q Consensus 239 e~~~ 242 (367) ..+. T Consensus 232 ~~~~ 235 (381) T pfam07517 232 LIAD 235 (381) T ss_pred HHHH T ss_conf 9999 No 229 >COG2842 Uncharacterized ATPase, putative transposase [General function prediction only] Probab=87.03 E-value=2.1 Score=21.45 Aligned_cols=107 Identities=10% Similarity=0.046 Sum_probs=60.6 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 77614886788999999999999708997799971537999999999999999862312112333321000123332211 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLE 159 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (367) ++|-+.+|+||+...-.+ +-.+ +...++.++....+...+-.+....... +.+.+. T Consensus 97 ~~vyg~~g~gKt~a~~~y----~~s~-p~~~l~~~~p~~~a~~~i~~i~~~~~~~---------~~~~~~---------- 152 (297) T COG2842 97 VVVYGYAGLGKTQAAKNY----APSN-PNALLIEADPSYTALVLILIICAAAFGA---------TDGTIN---------- 152 (297) T ss_pred EEEECCCCCHHHHHHHHH----CCCC-CCCEEECCCHHHHHHHHHHHHHHHHHCC---------CCHHHH---------- T ss_conf 788633220068999865----3358-6413615881367889999999987401---------421688---------- Q ss_pred CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCC Q ss_conf 113457761266210135445565210113586289997545599889999898740698825899980789 Q gi|254781187|r 160 QSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTR 231 (367) Q Consensus 160 ~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~ 231 (367) . .+ ++.........-++++|||...+-..++.++-.....+-- ++.+|+|. T Consensus 153 -----------d--~~------~~~~~~l~~~~~~iivDEA~~L~~~ale~lr~i~d~~Gi~--~vLvG~pr 203 (297) T COG2842 153 -----------D--LT------ERLMIRLRDTVRLIIVDEADRLPYRALEELRRIHDKTGIG--VVLVGMPR 203 (297) T ss_pred -----------H--HH------HHHHHHHCCCCCEEEEEHHHCCCHHHHHHHHHHHHHHCCE--EEEECCHH T ss_conf -----------8--89------9999997157652665032125868999999988750815--99836768 No 230 >pfam07570 consensus Probab=86.57 E-value=0.79 Score=24.06 Aligned_cols=28 Identities=25% Similarity=0.478 Sum_probs=22.6 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCC Q ss_conf 24776148867889999999999997089 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRP 106 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~ 106 (367) +++ +.+|||++||..+|..++..+.-.| T Consensus 14 y~v-~kGgrgS~KS~~~a~~~i~~~~kyp 41 (45) T pfam07570 14 YIV-AKGGRGSGKSSVIALKIILKLLKYP 41 (45) T ss_pred EEE-EECCCCCCCHHHHHHHHHHHHHHCC T ss_conf 077-5457676602789999999998342 No 231 >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=86.33 E-value=2.3 Score=21.22 Aligned_cols=77 Identities=17% Similarity=0.055 Sum_probs=49.7 Q ss_pred CCCCCCC--CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 1466888--44366684289999999888875124555554112477614-88678899999999999970899779997 Q gi|254781187|r 37 PWGIKGK--PLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISA-GRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 37 ~w~~~~~--~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~s-grg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) ++|+-+. +|--.-.|.-=|.|.+|.+...+--.--.. ...-++|.| ..|-|||+++|.+++-++-. |.|++.+ T Consensus 63 ~~~~~~~~~~l~aa~~P~s~~~Ea~R~lRs~l~~~~~~~--~~~~LaItS~~pGEGKS~vAaNLA~~~Aq~--G~RvLLV 138 (274) T TIGR03029 63 PPNDGSFSPDLIAAYQPFSPQVEALRALRSQLMLRWFSE--GRKALAVVSAKSGEGCSYIAANLAIVFSQL--GEKTLLI 138 (274) T ss_pred CCCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC--CCCEEEEECCCCCCCHHHHHHHHHHHHHHC--CCEEEEE T ss_conf 845578898998773899889999999999999984578--883899968999998999999999999967--9919999 Q ss_pred CCCH Q ss_conf 1537 Q gi|254781187|r 114 ANSE 117 (367) Q Consensus 114 A~t~ 117 (367) -.-. T Consensus 139 DaDL 142 (274) T TIGR03029 139 DANL 142 (274) T ss_pred ECCC T ss_conf 5888 No 232 >KOG0347 consensus Probab=85.99 E-value=0.64 Score=24.61 Aligned_cols=265 Identities=14% Similarity=0.100 Sum_probs=118.4 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH--------------HHCCCCEE Q ss_conf 4366684289999999888875124555554112477614886788999999999999--------------70899779 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLI--------------STRPGMSI 110 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~--------------~~~~~~~v 110 (367) -.+|+.|++.|...|-+. ++... -+.=+|-.|+|||-..+.=++-.+ .-++-.-. T Consensus 198 ~~gFs~Pt~IQsl~lp~a---i~gk~--------DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~k~~k~~~ 266 (731) T KOG0347 198 NLGFSRPTEIQSLVLPAA---IRGKV--------DILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSAKYVKPIA 266 (731) T ss_pred HCCCCCCCCCHHHCCCHH---HCCCH--------HCCCCCCCCCCCEEEECCHHHHHHHHCCCHHHHHHHHHHCCCCCEE T ss_conf 647899861044116676---54630--------0003334688742441232545433036537654467760576403 Q ss_pred EEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCEEEEE---CCCCCCCCCCCCC Q ss_conf 9971537999999999999999862312112333321000123332211-11345776126621---0135445565210 Q gi|254781187|r 111 ICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLE-QSMGIDSKHYTITC---RTYSEERPDTFVG 186 (367) Q Consensus 111 ~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~a---~~~~~~~~ea~~g 186 (367) +|++||..-+-.+. ..++.+.+.. .. ....+ ..+....-+ +-+...+ -++.| +.|...+..+.-- T Consensus 267 LV~tPTRELa~QV~-~Hl~ai~~~t----~i--~v~si--~GGLavqKQqRlL~~~p--~IVVATPGRlweli~e~n~~l 335 (731) T KOG0347 267 LVVTPTRELAHQVK-QHLKAIAEKT----QI--RVASI--TGGLAVQKQQRLLNQRP--DIVVATPGRLWELIEEDNTHL 335 (731) T ss_pred EEECCHHHHHHHHH-HHHHHHCCCC----CE--EEEEE--ECHHHHHHHHHHHHCCC--CEEEECCHHHHHHHHHHHHHH T ss_conf 89637099999999-9999861346----72--78875--23057999999985299--879936628999997510666 Q ss_pred CCCCCCCEEEEECCCCC-CHHHHHHHHHHH---HC----CCCCEEEEEEECCCCCCCHHHHHHHCCCCC-----E----- Q ss_conf 11358628999754559-988999989874---06----988258999807899987688754112235-----0----- Q gi|254781187|r 187 PHNTHGMAVFNDEASGT-PDIINKSILGFF---TE----LNPNRFWIMTSNTRRLNGWFYDIFNIPLED-----W----- 248 (367) Q Consensus 187 ~h~~~~~l~ivDEAsgI-~d~i~e~i~g~L---t~----~~~~~~~i~igNP~r~~g~Fye~~~~~~~~-----w----- 248 (367) ..-....|+++|||.-. .+..|+-+.-.| -+ .....+ .+| -|-.-+.+.......++. . T Consensus 336 ~~~k~vkcLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTl--VFS-ATlt~~~~~~~~~~~k~~~k~~~~~~kiq 412 (731) T KOG0347 336 GNFKKVKCLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTL--VFS-ATLTLVLQQPLSSSRKKKDKEDELNAKIQ 412 (731) T ss_pred HHHHHCEEEEECCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCEE--EEE-EEEEHHHCCHHHHHHHCCCHHHHHHHHHH T ss_conf 423324078873477775511099999999986031105101258--998-77633321705776542211455667999 Q ss_pred ----------EEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCCEEECH--HHHH------------- Q ss_conf ----------467523332888898899999962168800026888644327789807829--9986------------- Q gi|254781187|r 249 ----------KRYQIDTRTVEGIDSGFHEGIISRYGLDSDVARIEILGQFPQQEVNNFIPH--NYIE------------- 303 (367) Q Consensus 249 ----------~~~~~~~~d~p~~~~~~i~~~~~~~gedS~~~r~ev~G~Fp~~~~d~~ip~--~~ie------------- 303 (367) ...-++..-...+.....+..+..-.-.-+.|-+.++-.||.. +-+|.- +.+. T Consensus 413 ~Lmk~ig~~~kpkiiD~t~q~~ta~~l~Es~I~C~~~eKD~ylyYfl~ryPGr--TlVF~NsId~vKRLt~~L~~L~i~p 490 (731) T KOG0347 413 HLMKKIGFRGKPKIIDLTPQSATASTLTESLIECPPLEKDLYLYYFLTRYPGR--TLVFCNSIDCVKRLTVLLNNLDIPP 490 (731) T ss_pred HHHHHHCCCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCEEEEEEEEECCCC--EEEEECHHHHHHHHHHHHHHCCCCC T ss_conf 99998475689826766820447888887763588544540689988636983--5998411889999999974169997 Q ss_pred ----HHHC-----CCC--CCCCCCCEEEEEECCCCCCC----EEEEEE Q ss_conf ----4431-----577--77889848999963877881----089999 Q gi|254781187|r 304 ----EAMS-----REA--IDDLYAPLIMGCDIAGEGGD----KTVVVF 336 (367) Q Consensus 304 ----~a~~-----~~~--~~~~~~p~viGvDvAr~G~D----~Tvi~~ 336 (367) ++|. .+. .-.....+.+.-|||-.|=| ..||+. T Consensus 491 ~~LHA~M~QKqRLknLEkF~~~~~~VLiaTDVAARGLDIp~V~HVIHY 538 (731) T KOG0347 491 LPLHASMIQKQRLKNLEKFKQSPSGVLIATDVAARGLDIPGVQHVIHY 538 (731) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCEEEEEEHHHHCCCCCCCCCEEEEE T ss_conf 102577889999876998744888179962344425888786367896 No 233 >COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only] Probab=85.69 E-value=2.5 Score=21.02 Aligned_cols=92 Identities=15% Similarity=0.139 Sum_probs=53.0 Q ss_pred HHHHCCCCCCCCCCCCCCCHH----------HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH Q ss_conf 543014668884436668428----------9999999888875124555554112477614886788999999999999 Q gi|254781187|r 33 MRFFPWGIKGKPLEHFSQPHR----------WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLI 102 (367) Q Consensus 33 ~~~~~w~~~~~~~~~~~~p~~----------wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~ 102 (367) .++|-|+..+.-|.....|.. =|.++|-+=....-.+.-. -.|..-+.||+|||.++-++..-+. T Consensus 36 a~~f~~~~~~~~L~pv~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~G~pA-----NnVLLwGaRGtGKSSLVKA~~~e~~ 110 (287) T COG2607 36 ALAFRWRPAIGYLEPVPDPDPIDLADLVGVDRQKEALVRNTEQFAEGLPA-----NNVLLWGARGTGKSSLVKALLNEYA 110 (287) T ss_pred HHHHHCCCCCCCCCCCCCCCCCCHHHHHCCHHHHHHHHHHHHHHHCCCCC-----CCEEEECCCCCCHHHHHHHHHHHHH T ss_conf 55773133568666889899767898727318999999989999728865-----2367763777774799999999987 Q ss_pred HHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC Q ss_conf 708997799971537999999999999999862 Q gi|254781187|r 103 STRPGMSIICIANSETQLKNTLWAEVSKWLSML 135 (367) Q Consensus 103 ~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~ 135 (367) ...+ + .+.-+.+++.+ .+.+-..++.. T Consensus 111 ~~gl--r--LVEV~k~dl~~--Lp~l~~~Lr~~ 137 (287) T COG2607 111 DEGL--R--LVEVDKEDLAT--LPDLVELLRAR 137 (287) T ss_pred HCCC--E--EEEECHHHHHH--HHHHHHHHHCC T ss_conf 4177--0--79976888865--79999999618 No 234 >pfam02500 DNA_pack_N Probable DNA packing protein, N-terminus. This family includes proteins that are probably involved in DNA packing in herpesvirus. This domain is normally found at the N-terminus of the protein. Probab=85.55 E-value=1.3 Score=22.79 Aligned_cols=51 Identities=22% Similarity=0.285 Sum_probs=43.1 Q ss_pred ECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH Q ss_conf 1488678899999999999970899779997153799999999999999986 Q gi|254781187|r 83 SAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM 134 (367) Q Consensus 83 ~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~ 134 (367) .-+|.=|||++.-.+|--.|....|.+|-+||. ++-+.+-+|.||..-+++ T Consensus 186 LVPRRHGKTWfvVpiIsllL~s~egI~IGYvAH-qkhvs~~VF~EI~~rl~r 236 (276) T pfam02500 186 LVPRRHGKTWFVVPIISLLLSSFEGIHIGYVAH-QKHVSEPVFTEIINRLRR 236 (276) T ss_pred EEECCCCCEEEHHHHHHHHHHHCCCCEEEEHHH-HHHHHHHHHHHHHHHHHH T ss_conf 731578973553999999997315855542688-887438999999999998 No 235 >cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK). Probab=85.44 E-value=1.8 Score=21.92 Aligned_cols=38 Identities=24% Similarity=0.225 Sum_probs=25.8 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 77614886788999999999999708997799971537 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) ++|++|-|+|||+++..+.--+-.....+.++.+-.-+ T Consensus 2 IgIaG~SgSGKTT~a~~L~~~l~~~~~~~~vis~D~yy 39 (179) T cd02028 2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDDYY 39 (179) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC T ss_conf 89989897789999999999984648853999546664 No 236 >cd01135 V_A-ATPase_B V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit. Probab=85.20 E-value=1.4 Score=22.49 Aligned_cols=44 Identities=16% Similarity=0.116 Sum_probs=29.2 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHH Q ss_conf 4776148867889999999999997089-9779997153799999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKN 122 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~ 122 (367) |+.|-+|+|+|||++.+.++.--..... ...+++.+-.....++ T Consensus 71 R~gIfgg~GvGKs~L~~~i~~~~~~~~~~~~~v~V~~~IGer~re 115 (276) T cd01135 71 KIPIFSGSGLPHNELAAQIARQAGVVGEEENFAVVFAAMGITMED 115 (276) T ss_pred EEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEEEECCEEHHH T ss_conf 633205788636789999999877513688735999615553257 No 237 >TIGR01969 minD_arch cell division ATPase MinD; InterPro: IPR010224 Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. Several members of this family are found in archaeal genomes but their function is uncharacterised. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. This entry represents the archaeal MinD family. The exact roles of the various archaeal MinD homologs are unknown. . Probab=84.90 E-value=0.95 Score=23.58 Aligned_cols=191 Identities=13% Similarity=0.060 Sum_probs=94.1 Q ss_pred EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 7761488-678899999999999970899779997153799999999999999986231211233332100012333221 Q gi|254781187|r 80 CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL 158 (367) Q Consensus 80 ~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (367) ++|+||- |+||||++|.+.+-+.-+ |.+|+++=.--..+.=.+ |=.+=.+-+.-|-.....-.+..+.|.+... T Consensus 3 I~iASGKGGtGKTT~tANLgVALA~~--Gk~V~~~DADI~MANL~L---iLgmE~~~VTLhDVLAGeA~i~DAIY~gp~G 77 (258) T TIGR01969 3 ITIASGKGGTGKTTITANLGVALAKL--GKKVLVLDADITMANLEL---ILGMEDKPVTLHDVLAGEADIKDAIYEGPEG 77 (258) T ss_pred EEEEECCCCCCHHHEEEHHHHHHHHC--CCEEEEEECCHHHHHHHH---HHCCCCCCCCCCCCCCCCCCHHHHCCCCCCC T ss_conf 89997788986140000077889860--976899946766776898---8446888967522134456100110028898 Q ss_pred CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHH Q ss_conf 11134577612662101354455652101135862899975455998899998987406988258999807899987688 Q gi|254781187|r 159 EQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRLNGWFY 238 (367) Q Consensus 159 ~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fy 238 (367) ..+.--..=++--.-+.--+.-+|-...++.. ..++++|==||+--+...++. .. .+.+ +.-||-= + --- T Consensus 78 nV~V~PagvSLEg~rKA~~~~L~dV~~~i~~~-~D~lLIDAPAGL~~~a~~Al~----~a-~elL--LVvNPEi-~-SIt 147 (258) T TIGR01969 78 NVKVIPAGVSLEGLRKADPDKLEDVLKEIIDD-TDFLLIDAPAGLERDAVTALA----AA-DELL--LVVNPEI-S-SIT 147 (258) T ss_pred CEEEECCCCCHHHCCCCCHHHHHHHHHHHHCC-CCEEEEECCCCCCHHHHHHHH----HC-CCCE--EEECCCH-H-HHH T ss_conf 44785061221000126833328999987204-377887478983378999998----61-8664--8667654-4-677 Q ss_pred HHHH---CCCC-CE----EEEEECCCCCCCCCHHHHHHHHHH-----CCCCCCEEEEEEE Q ss_conf 7541---1223-50----467523332888898899999962-----1688000268886 Q gi|254781187|r 239 DIFN---IPLE-DW----KRYQIDTRTVEGIDSGFHEGIISR-----YGLDSDVARIEIL 285 (367) Q Consensus 239 e~~~---~~~~-~w----~~~~~~~~d~p~~~~~~i~~~~~~-----~gedS~~~r~ev~ 285 (367) |... -+++ +- -..---.++.-.++++.+|...+- -.||+.+-|.=.. T Consensus 148 DaLK~k~va~~lGt~ilG~vlNRv~~~~tel~~~eiE~iLevPVl~~vPEDP~VR~AAa~ 207 (258) T TIGR01969 148 DALKVKIVAEKLGTAILGVVLNRVTRDKTELGREEIEAILEVPVLGVVPEDPEVRRAAAF 207 (258) T ss_pred HHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCHHHHHHHHCCCEEEEECCCHHHHHHHHC T ss_conf 788999998760883246899602366663788899988479738985698434456424 No 238 >PRK06921 hypothetical protein; Provisional Probab=84.84 E-value=2.7 Score=20.78 Aligned_cols=59 Identities=19% Similarity=0.068 Sum_probs=34.3 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 4289999999888875124555554112477614886788999999999999708997799971 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) +.+.-..+++.+.++.+--..+.+ .+...+.-|+|||+++++++-.++-. .+..|+++. T Consensus 94 ~k~a~~~a~eY~~~F~~i~~~~~~----~l~f~G~~G~GKThLa~aIa~~Ll~~-~~~~Vly~~ 152 (265) T PRK06921 94 IKDAYECAVEYVKDFEKIQGCRKN----SIALLGQPGSGKTHLLTAAANELMRK-KGVPVLYFP 152 (265) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCC----CEEEECCCCCCHHHHHHHHHHHHHHH-CCCEEEEEE T ss_conf 999999999999977876077766----27997289898899999999999996-297199988 No 239 >pfam03205 MobB Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop. Probab=84.77 E-value=2.3 Score=21.23 Aligned_cols=34 Identities=21% Similarity=0.262 Sum_probs=26.1 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 247761488678899999999999970899779997 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) +|+.|.+..++|||+++..++-+.+-. +.++++. T Consensus 1 p~v~i~G~~~sGKttl~~~L~~~~~~~--g~~~~~~ 34 (122) T pfam03205 1 PIVLVVGPKDSGKTTLIRKLLNYLKRR--GYRVAVV 34 (122) T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHC--CCCEEEE T ss_conf 979999489998999999999999987--9944899 No 240 >pfam10236 DAP3 Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29). Probab=84.72 E-value=2.4 Score=21.09 Aligned_cols=27 Identities=26% Similarity=0.498 Sum_probs=22.2 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHH Q ss_conf 124776148867889999999999997 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLIS 103 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~ 103 (367) ..|+.+-+.+|+|||.+.+-++.|-.. T Consensus 23 ~~r~vL~G~~GsGKS~~L~q~v~~A~~ 49 (274) T pfam10236 23 VVRFVLTGERGSGKSVLLAQAMAYALT 49 (274) T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHH T ss_conf 518998897997799999999999985 No 241 >KOG0348 consensus Probab=84.61 E-value=2.8 Score=20.72 Aligned_cols=139 Identities=13% Similarity=0.026 Sum_probs=78.8 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-------CCEEEEECCCH Q ss_conf 43666842899999998888751245555541124776148867889999999999997089-------97799971537 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-------GMSIICIANSE 117 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-------~~~v~~~A~t~ 117 (367) ...+..|+--|...+-.|-+ ++ -+.|.|-.|+|||-.-+.=++-.+...+ |.-.+|++||. T Consensus 154 ~m~i~~pTsVQkq~IP~lL~------gr------D~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs~G~~ALVivPTR 221 (708) T KOG0348 154 KMKISAPTSVQKQAIPVLLE------GR------DALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRSDGPYALVIVPTR 221 (708) T ss_pred HHCCCCCCHHHHCCHHHHHC------CC------CEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECHH T ss_conf 74557640676502035525------86------3478857788621799999999997268655556883489980419 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCC-CCCCCCCCCCCCCCCEEE Q ss_conf 9999999999999998623121123333210001233322111134577612662101354-455652101135862899 Q gi|254781187|r 118 TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSE-ERPDTFVGPHNTHGMAVF 196 (367) Q Consensus 118 ~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~-~~~ea~~g~h~~~~~l~i 196 (367) .-+-.+ +.-+.|.+. ..+|.-. -.-.+....-+-..+...|..+..+.+-|. +--.+-..+|-...-.+| T Consensus 222 EL~~Q~-y~~~qKLl~---~~hWIVP-----g~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LRwlV 292 (708) T KOG0348 222 ELALQI-YETVQKLLK---PFHWIVP-----GVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLRWLV 292 (708) T ss_pred HHHHHH-HHHHHHHHC---CCEEEEE-----CEEECCCCCCCHHHHHHCCCEEEECCCHHHHHHHHCCCHHEEEEEEEEE T ss_conf 999999-999998725---7437730-----2122363310178887548548975842788987430022100356898 Q ss_pred EECCCCCC Q ss_conf 97545599 Q gi|254781187|r 197 NDEASGTP 204 (367) Q Consensus 197 vDEAsgI~ 204 (367) +|||.-|= T Consensus 293 lDEaDrll 300 (708) T KOG0348 293 LDEADRLL 300 (708) T ss_pred ECCHHHHH T ss_conf 53436787 No 242 >TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3, Yersinia-type; InterPro: IPR013395 The helicase encoded in many CRISPR-associated (cas) gene clusters is designated Cas3. The Yersinia-type helicase Cas3 proteins differ from the more common Cas3 proteins by being considerably larger, though they still share a number of motifs, 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=84.60 E-value=1.3 Score=22.78 Aligned_cols=262 Identities=15% Similarity=0.121 Sum_probs=116.0 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC-------CH-------- Q ss_conf 899999998888751245555541124776148867889999999999997089977999715-------37-------- Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN-------SE-------- 117 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~-------t~-------- 117 (367) .||-++......-.++- ......++++ ||.|+|||..-|.++--+---.+|+++.+-=+ |+ T Consensus 423 ~WQ~kA~~~a~~~~~~~-~~~G~f~vN~---AsTGcGKT~aNar~~yaL~~~~~G~R~a~ALgLR~LTLQTG~ALk~~L~ 498 (1153) T TIGR02562 423 RWQNKAFNLAQKLRQKS-EEQGAFGVNM---ASTGCGKTLANARLMYALRDDKQGLRFAIALGLRSLTLQTGSALKKRLN 498 (1153) T ss_pred HHHHHHHHHHHHHHHHH-HHCCCEEEEC---CCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC T ss_conf 67889999999988735-4279469862---6468437999999986177888874001343224678888899997417 Q ss_pred -----------HHHHHHHHHHHHHHHHHC------CCCCCCCCCC---CCCCCCCCCCCCCCCCCCCCCCC--------- Q ss_conf -----------999999999999999862------3121123333---21000123332211113457761--------- Q gi|254781187|r 118 -----------TQLKNTLWAEVSKWLSML------PHRHWFEMQS---LSLHPSGWYAELLEQSMGIDSKH--------- 168 (367) Q Consensus 118 -----------~Q~~~~lw~ei~k~~~~~------~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~--------- 168 (367) .++...+|..-+.-++.. +...|+.... ...+..+.........+-.+.+. T Consensus 499 L~d~~lAv~iG~~~~~~Lf~~~~ek~e~~~~~gs~s~~~f~~~~~~~~~~~~~~~~~~~~~~~~ls~d~k~~~lL~aP~l 578 (1153) T TIGR02562 499 LSDDDLAVLIGGTAVKKLFDLSKEKIEQVDEDGSESAEKFLEEGQDCNLVDYDGALDTEELLSRLSKDDKLKKLLAAPVL 578 (1153) T ss_pred CCCCCEEEEECCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCHHHHHHHCCCHHHHHHHHCCHH T ss_conf 88576367865288899999877652020035688615550432116863236775414675431025455466525126 Q ss_pred -EEEEECCCCCCCCCCCCCCCCCCCCE------EEEECCCCCCHHHHHHH-----HHHHHCCCCCEEEEEEECC---CCC Q ss_conf -26621013544556521011358628------99975455998899998-----9874069882589998078---999 Q gi|254781187|r 169 -YTITCRTYSEERPDTFVGPHNTHGMA------VFNDEASGTPDIINKSI-----LGFFTELNPNRFWIMTSNT---RRL 233 (367) Q Consensus 169 -~~~~a~~~~~~~~ea~~g~h~~~~~l------~ivDEAsgI~d~i~e~i-----~g~Lt~~~~~~~~i~igNP---~r~ 233 (367) ..+.--. --.|+.+|-|-=..|| +|+||--+-+.+-.-++ ...| -|.+.++ |+- +.- T Consensus 579 vcTiDhLi---~A~Es~rgG~~i~p~LRllsSDLiLDE~Ddy~~~dLpAl~RLV~lAgL--~GsrVll---SSATL~p~l 650 (1153) T TIGR02562 579 VCTIDHLI---PATESVRGGHHIAPMLRLLSSDLILDEPDDYEREDLPALLRLVQLAGL--LGSRVLL---SSATLPPAL 650 (1153) T ss_pred HHHHHHCC---CCCCCCCCCEEHHHHHHHHHHHHEECCCCCCCHHHHHHHHHHHHHHHH--HCCHHHH---HCCCCCHHH T ss_conf 65543200---467754456107889987532320048888871234899999999998--4441422---213660889 Q ss_pred CCHHHHHHHCCC----------CCEEEEEECCCCCCCCC--------------HHHHHHHHHHCCCCCCEEEEEEEE--E Q ss_conf 876887541122----------35046752333288889--------------889999996216880002688864--4 Q gi|254781187|r 234 NGWFYDIFNIPL----------EDWKRYQIDTRTVEGID--------------SGFHEGIISRYGLDSDVARIEILG--Q 287 (367) Q Consensus 234 ~g~Fye~~~~~~----------~~w~~~~~~~~d~p~~~--------------~~~i~~~~~~~gedS~~~r~ev~G--~ 287 (367) -.-.|+.|..++ +.-..+++.|.|-+.+- .+|+..+...+...+..-+.+++. + T Consensus 651 v~~lF~AY~aGr~~y~~~~G~~~~~~~~cc~w~de~~~~~~~~~q~~~F~~~h~~F~~~r~~~L~~~p~~R~AeLLsLS~ 730 (1153) T TIGR02562 651 VKTLFKAYEAGRKIYQALKGQPKKPLNICCAWVDEPQVVQADCNQKEEFIQRHQDFVRKRAEKLAKKPVRRLAELLSLSS 730 (1153) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHCCCCCC T ss_conf 99999999999999997467988860556532464679998642169999998889999999862676223020036888 Q ss_pred E-CCCCCCEEECH---HHHHHH---HCCCCCCCCCCCEEEEEECCC Q ss_conf 3-27789807829---998644---315777788984899996387 Q gi|254781187|r 288 F-PQQEVNNFIPH---NYIEEA---MSREAIDDLYAPLIMGCDIAG 326 (367) Q Consensus 288 F-p~~~~d~~ip~---~~ie~a---~~~~~~~~~~~p~viGvDvAr 326 (367) - |+.++.++++. .+.+.+ +.-...-+|.....+.|-+=| T Consensus 731 ~kpr~Gn~s~~~~la~~ll~~~~~LH~~h~~t~p~~~K~vSvGLiR 776 (1153) T TIGR02562 731 LKPRKGNESVYLALAESLLEGALRLHQLHAQTDPKSEKKVSVGLIR 776 (1153) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEEE T ss_conf 8865650567999999999999999860266777678778886154 No 243 >pfam09848 DUF2075 Uncharacterized conserved protein (DUF2075). This domain, found in various prokaryotic proteins (including putative ATP/GTP binding proteins), has no known function. Probab=84.59 E-value=2.8 Score=20.71 Aligned_cols=39 Identities=18% Similarity=0.325 Sum_probs=24.7 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH Q ss_conf 776148867889999999999997089977999715379 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET 118 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~ 118 (367) +.|.++=|+|||.+..-++.-......+...+....... T Consensus 4 ~~V~G~pGtGKTvv~l~l~~~l~~~~~~~~~~~l~~N~~ 42 (348) T pfam09848 4 FLVTGGPGTGKTVVALNLFAELSDSDLGRTAVFLSGNHP 42 (348) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCHH T ss_conf 999777993899999999999864402682089957866 No 244 >CHL00060 atpB ATP synthase CF1 beta subunit Probab=84.58 E-value=2.8 Score=20.71 Aligned_cols=50 Identities=22% Similarity=0.383 Sum_probs=30.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHHHHHHHHH Q ss_conf 4776148867889999999999997089977999-71537999999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKNTLWAEVS 129 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~~lw~ei~ 129 (367) |+.+-+|+|+|||+++..++.-..-.+.+..|++ +-...+.+++ ++.|++ T Consensus 157 RigIfggaGvGKTvLl~eli~niak~~~~v~V~a~IGER~RE~~e-~~~e~~ 207 (480) T CHL00060 157 KIGLFGGAGVGKTVLIMELINNIAKAHGGVSVFGGVGERTREGND-LYMEMK 207 (480) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHH-HHHHHH T ss_conf 887656899887899999996120037988999996677367999-999998 No 245 >CHL00081 chlI Mg-protoporyphyrin IX chelatase Probab=84.48 E-value=2.8 Score=20.68 Aligned_cols=52 Identities=13% Similarity=0.026 Sum_probs=32.8 Q ss_pred CCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCC-------------CCEEEEEEECCCCC Q ss_conf 45565210113586289997545599889999898740698-------------82589998078999 Q gi|254781187|r 179 ERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELN-------------PNRFWIMTSNTRRL 233 (367) Q Consensus 179 ~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~-------------~~~~~i~igNP~r~ 233 (367) ..|.-++..| .-++++||.--.+|.+-+++.-++..+. .+.+.+++.||-.+ T Consensus 130 f~pGlLa~A~---rGiLyvDEINll~d~~v~~LLda~a~G~~~VEReG~S~~~Pa~F~liaT~NPeEg 194 (347) T CHL00081 130 FEPGLLAKAN---RGILYVDEVNLLDDHLVDILLDSAASGWNTVEREGISIRHPARFVLIGSGNPEEG 194 (347) T ss_pred CCCCHHHHCC---CCEEEEEHHHHHHHHHHHHHHHHHHCCEEEECCCCEEECCCCCEEEEECCCCCCC T ss_conf 5653122203---8858861454323799999999985580898046423305750068855786556 No 246 >cd01133 F1-ATPase_beta F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic. Probab=84.44 E-value=2.8 Score=20.67 Aligned_cols=33 Identities=27% Similarity=0.409 Sum_probs=24.2 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEE Q ss_conf 477614886788999999999999708997799 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSII 111 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~ 111 (367) |+.|-+++|+|||++.+.++.-....+.+..|+ T Consensus 71 R~~I~~~~g~GKt~ll~~ii~~~~~~~~~v~V~ 103 (274) T cd01133 71 KIGLFGGAGVGKTVLIMELINNIAKAHGGYSVF 103 (274) T ss_pred EEEEECCCCCCCCHHHHHHHHHHHHCCCCEEEE T ss_conf 778757999982368999999998508987999 No 247 >TIGR00959 ffh signal recognition particle protein; InterPro: IPR004780 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. 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. This entry represents various SRP subunits.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle. Probab=84.20 E-value=1.1 Score=23.10 Aligned_cols=112 Identities=14% Similarity=0.160 Sum_probs=62.8 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH------HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC Q ss_conf 77614886788999999999999708997799971537------999999999999999862312112333321000123 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE------TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGW 153 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~------~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~ 153 (367) +-.++=.|+||||.+|=++.|.+.-..+.+++.+|--- +||+.. .+.+. . T Consensus 105 ilmvGLQGsGKTTt~gKLA~~ll~kk~~~kvLLva~D~yRPAA~~QL~~L-----g~Q~g-----------------V-- 160 (439) T TIGR00959 105 ILMVGLQGSGKTTTAGKLALYLLKKKEGKKVLLVACDLYRPAAIEQLKVL-----GEQVG-----------------V-- 160 (439) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEHHCCCHHHHHHHHHH-----HHHCC-----------------C-- T ss_conf 99731378857889999999999986389703403210347899999997-----67528-----------------8-- Q ss_pred CCCCCC-CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC--CCCHHHHHHHH--HHHHCCCCCEEEE Q ss_conf 332211-113457761266210135445565210113586289997545--59988999989--8740698825899 Q gi|254781187|r 154 YAELLE-QSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS--GTPDIINKSIL--GFFTELNPNRFWI 225 (367) Q Consensus 154 ~~~~~~-~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs--gI~d~i~e~i~--g~Lt~~~~~~~~i 225 (367) +++. ...+.++-+ . .-++ ..+.+-+...++..+|+|-|. .|++..++=+. -..+.++ +++.+ T Consensus 161 --pvf~h~~~~~~p~~--P-v~ia----~~Al~~Ak~~~~D~vI~DTAGRL~ID~~LM~EL~~iK~~~nP~-EiLlV 227 (439) T TIGR00959 161 --PVFAHLGKGQSPDD--P-VEIA----RQALEEAKENGFDVVIVDTAGRLQIDEELMEELAEIKEILNPD-EILLV 227 (439) T ss_pred --CCCCCCCCCCCCCC--H-HHHH----HHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHCCC-EEEEC T ss_conf --71100478889887--7-8999----9999999974897899726751255599999999998886887-05412 No 248 >PRK13407 bchI magnesium chelatase subunit I; Provisional Probab=84.17 E-value=2.9 Score=20.60 Aligned_cols=54 Identities=13% Similarity=0.054 Sum_probs=35.4 Q ss_pred CCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCC-------------CCCEEEEEEECCCCC Q ss_conf 544556521011358628999754559988999989874069-------------882589998078999 Q gi|254781187|r 177 SEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTEL-------------NPNRFWIMTSNTRRL 233 (367) Q Consensus 177 ~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~-------------~~~~~~i~igNP~r~ 233 (367) +...|.-++-.|+ -.+++||..-.++.+-+++.-.+.++ -.+...+++.||-.+ T Consensus 117 ~~~~PGlLa~Ah~---GVLylDEinll~~~vld~Ll~~~e~G~~~IeReg~s~~~ParF~LVatmNPeEg 183 (334) T PRK13407 117 KAFEPGLLARANR---GYLYIDEVNLLEDHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEG 183 (334) T ss_pred CCCCCCHHHHCCC---CEEEEECHHHCCHHHHHHHHHHHHCCCEEEEECCEEEECCCCCEEEEEECCCCC T ss_conf 7788605434028---867872053333889999998871695799977634603662658982088877 No 249 >KOG3022 consensus Probab=84.16 E-value=2 Score=21.54 Aligned_cols=34 Identities=26% Similarity=0.411 Sum_probs=26.3 Q ss_pred EEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 247761488-678899999999999970899779997 Q gi|254781187|r 78 FKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 78 ~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) -.++|+||- |+|||+.++.+++-++. ++.++.+. T Consensus 48 ~iI~VlSGKGGVGKSTvt~nla~~La~--~g~~vglL 82 (300) T KOG3022 48 HIILVLSGKGGVGKSTVTVNLALALAS--EGKKVGLL 82 (300) T ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHC--CCCCEEEE T ss_conf 589998678877616899999999861--79717997 No 250 >cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. Probab=84.08 E-value=2.9 Score=20.58 Aligned_cols=37 Identities=19% Similarity=0.239 Sum_probs=24.8 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH Q ss_conf 477614886788999999999999708997799971537999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQL 120 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~ 120 (367) |..|-+++|+|||.+...++-| .+..+++.+.-.+.. T Consensus 159 r~~I~g~~g~GKT~l~~~i~k~-----~~~dv~Vyv~iGeRg 195 (369) T cd01134 159 TAAIPGPFGCGKTVIQQSLSKY-----SNSDIVIYVGCGERG 195 (369) T ss_pred EEEEECCCCCCHHHHHHHHHHC-----CCCCEEEEEEEECCH T ss_conf 4677668776899999999853-----799889999971141 No 251 >cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition. Probab=84.04 E-value=1.6 Score=22.16 Aligned_cols=28 Identities=29% Similarity=0.334 Sum_probs=22.3 Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 867889999999999997089977999715 Q gi|254781187|r 86 RGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 86 rg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) =|+|||+++..++..+.. .+.+++++-- T Consensus 9 GGvGKtt~~~~la~~~a~--~g~~vl~iD~ 36 (104) T cd02042 9 GGVGKTTTAVNLAAALAR--RGKRVLLIDL 36 (104) T ss_pred CCCCHHHHHHHHHHHHHH--CCCEEEEEEC T ss_conf 987689999999999997--7992999977 No 252 >PRK12597 F0F1 ATP synthase subunit beta; Provisional Probab=83.93 E-value=3 Score=20.54 Aligned_cols=44 Identities=20% Similarity=0.370 Sum_probs=29.4 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHH Q ss_conf 4776148867889999999999997089977999-7153799999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKN 122 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~ 122 (367) |+.+-+|.|+|||.++..++.-....+.+..|++ +-...+.+++ T Consensus 143 rigIfggaGvGKTvL~~~ii~n~~~~~~~v~V~~~iGER~rEv~e 187 (459) T PRK12597 143 KTGLFGGAGVGKTVLMMELIFNISKRHQGSSVFAGVGERSREGHE 187 (459) T ss_pred EEEEECCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHH T ss_conf 777436899982157899999877551783688862454688999 No 253 >pfam05673 DUF815 Protein of unknown function (DUF815). This family consists of several bacterial proteins of unknown function. Probab=83.89 E-value=3 Score=20.53 Aligned_cols=52 Identities=19% Similarity=0.326 Sum_probs=32.0 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 4776148867889999999999997089977999715379999999999999998623 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLP 136 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~ 136 (367) .+.+-+.||+|||.++-+++.-+. ..+.++|=+. .+++.+. +.|-..++..| T Consensus 55 nvLLwG~RGtGKSSlVKall~~~~--~~gLrlIEv~--k~~L~~L--p~i~~~l~~~~ 106 (248) T pfam05673 55 NVLLWGARGTGKSSLVKALLNEYA--DQGLRLIEVD--KDDLGDL--PDIVDLLRGRP 106 (248) T ss_pred CEEEECCCCCCHHHHHHHHHHHHH--HCCCEEEEEC--HHHHCCH--HHHHHHHHCCC T ss_conf 367676898988899999999863--1495699987--8887219--99999996499 No 254 >PRK05298 excinuclease ABC subunit B; Provisional Probab=83.88 E-value=3 Score=20.52 Aligned_cols=68 Identities=18% Similarity=0.162 Sum_probs=48.2 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH Q ss_conf 42899999998888751245555541124776148867889999999999997089977999715379999999999999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) |.-=|-++...+.+++++|.. +.+ +.+-.|+|||+.+|..+-- -..-.+++|+...-| .-++.|++. T Consensus 14 P~GDQP~AI~~L~~gi~~g~~------~Q~-LlGvTGSGKTfTmAnvI~~-----~~rPtLVlahNKTLA-AQLy~Efk~ 80 (657) T PRK05298 14 PAGDQPQAIAELVEGIESGEK------HQT-LLGVTGSGKTFTMANVIAR-----VQRPTLVLAHNKTLA-AQLYGEFKE 80 (657) T ss_pred CCCCCHHHHHHHHHHHHCCCC------EEE-EECCCCCCHHHHHHHHHHH-----HCCCEEEECCCHHHH-HHHHHHHHH T ss_conf 999879999999989974996------369-9703678566899999998-----689759976658899-999999997 Q ss_pred H Q ss_conf 9 Q gi|254781187|r 131 W 131 (367) Q Consensus 131 ~ 131 (367) + T Consensus 81 f 81 (657) T PRK05298 81 F 81 (657) T ss_pred H T ss_conf 6 No 255 >COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning] Probab=83.84 E-value=2.8 Score=20.70 Aligned_cols=34 Identities=32% Similarity=0.542 Sum_probs=26.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 47761488678899999999999970899779997 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) ++||++=-|+|||+++|.++.-++..+. .+|+++ T Consensus 2 kIaI~GKGG~GKTtiaalll~~l~~~~~-~~VLvV 35 (255) T COG3640 2 KIAITGKGGVGKTTIAALLLKRLLSKGG-YNVLVV 35 (255) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHCCC-CEEEEE T ss_conf 6999659976589999999999986489-549999 No 256 >pfam00308 Bac_DnaA Bacterial dnaA protein. Probab=83.74 E-value=3 Score=20.49 Aligned_cols=36 Identities=22% Similarity=0.379 Sum_probs=30.4 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 776148867889999999999997089977999715 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) +-|-+.-|+|||++..+++.-..-..++.+++++.. T Consensus 37 l~i~G~~G~GKTHLLqA~~~~~~~~~~~~~v~yl~~ 72 (219) T pfam00308 37 LFIYGGVGLGKTHLLHAIGNYALRNFPNLRVVYLTS 72 (219) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEH T ss_conf 699889999888999999999998499982888439 No 257 >pfam06564 YhjQ YhjQ protein. This family consists of several bacterial YhjQ proteins. The function of this family is unknown. However, the family does contain a P-loop sequence motif suggesting a nucleotide binding function. Probab=83.71 E-value=2.2 Score=21.29 Aligned_cols=36 Identities=31% Similarity=0.396 Sum_probs=26.5 Q ss_pred EEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 1247761488-6788999999999999708997799971 Q gi|254781187|r 77 IFKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 77 ~~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) |..++|+++. |+|||++++.+..-+ ...|.+|+++= T Consensus 1 MkiIai~s~KGGVGKTT~t~nLa~aL--a~~G~rVLlID 37 (244) T pfam06564 1 MAVLALQGVRGGVGTTSLTAALGWAL--QQLGESVLVID 37 (244) T ss_pred CEEEEEECCCCCCCHHHHHHHHHHHH--HHCCCCEEEEE T ss_conf 92999966999861999999999999--97799589996 No 258 >PRK11670 putative ATPase; Provisional Probab=83.56 E-value=2.4 Score=21.10 Aligned_cols=34 Identities=26% Similarity=0.438 Sum_probs=26.0 Q ss_pred EEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 47761488-6788999999999999708997799971 Q gi|254781187|r 79 KCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 79 ~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) -++|+||- |+|||+.++.+++-+.. .|.+|.+.= T Consensus 109 vIAVaSGKGGVGKSTvavNLA~ALA~--~G~kVgllD 143 (369) T PRK11670 109 IIAVSSGKGGVGKSSTAVNLALALAA--EGAKVGILD 143 (369) T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHH--CCCCEEEEE T ss_conf 99998589988899999999999996--699378982 No 259 >PRK08118 topology modulation protein; Reviewed Probab=83.31 E-value=1.2 Score=23.00 Aligned_cols=26 Identities=27% Similarity=0.189 Sum_probs=21.5 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHH Q ss_conf 12477614886788999999999999 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLI 102 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~ 102 (367) |-|+.|-++-|+|||+++..+.--.- T Consensus 1 M~rI~IiG~~GsGKSTlAr~L~~~~~ 26 (167) T PRK08118 1 MKKIILIGSGGSGKSTLARQLGEKLN 26 (167) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHC T ss_conf 96799988999879999999999889 No 260 >PRK11131 ATP-dependent RNA helicase HrpA; Provisional Probab=83.28 E-value=3.2 Score=20.37 Aligned_cols=161 Identities=15% Similarity=0.007 Sum_probs=77.4 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHH Q ss_conf 89999999888875124555554112477614886788999999999999708997799971537999999999999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) ....+++..|.+|. =+.|++-.|+|||+=+-=+++- +.....++|+||-|-.=-+..+ -..+..-. T Consensus 77 ~~r~~i~~~i~~nq------------Vvii~GeTGsGKTTQiPq~~le-~g~g~~~~I~~TQPRRiAA~sv-A~RVA~E~ 142 (1295) T PRK11131 77 QKKQDILEAIRDHQ------------VVIVAGETGSGKTTQLPKICLE-LGRGIKGLIGHTQPRRLAARTV-ANRIAEEL 142 (1295) T ss_pred HHHHHHHHHHHHCC------------EEEEECCCCCCHHHHHHHHHHH-CCCCCCCEEEECCCHHHHHHHH-HHHHHHHH T ss_conf 89999999999799------------6999768999878899999996-2799999899779659999999-99999981 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE-EEECCCCCCCCCCCCCCCCCCCCEEEEECCCC--CCHHHHH Q ss_conf 86231211233332100012333221111345776126-62101354455652101135862899975455--9988999 Q gi|254781187|r 133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYT-ITCRTYSEERPDTFVGPHNTHGMAVFNDEASG--TPDIINK 209 (367) Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg--I~d~i~e 209 (367) ... ... ..++...+.......+...+ -.+...++-..+ ..+ .....+|+|||.- +.-++.- T Consensus 143 ~~~-lG~-----------~VGY~VRf~~~~s~~t~i~~~TdGiLL~e~~~d--~~L--~~y~~iIiDEaHERsl~~D~LL 206 (1295) T PRK11131 143 ETE-LGG-----------CVGYKVRFNDQVSDNTMVKLMTDGILLAEIQQD--RLL--MQYDTIIIDEAHERSLNIDFIL 206 (1295) T ss_pred CCC-CCC-----------EEEEEECCCCCCCCCCEEEEECCHHHHHHHHHC--CCC--CCCCEEEEECCCCCCCHHHHHH T ss_conf 999-899-----------888894569887999779997656999986209--987--8877799868556880199999 Q ss_pred HHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCC Q ss_conf 98987406988258999807899987688754112 Q gi|254781187|r 210 SILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIP 244 (367) Q Consensus 210 ~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~ 244 (367) .+.-.+-........+++ +-|-....|-+.|... T Consensus 207 g~Lk~ll~~R~dLKvIim-SATid~e~fs~yF~~a 240 (1295) T PRK11131 207 GYLKELLPRRPDLKVIIT-SATIDPERFSRHFNNA 240 (1295) T ss_pred HHHHHHHHHCCCCEEEEE-CCCCCHHHHHHHCCCC T ss_conf 999999833999889995-5868979999657999 No 261 >PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed Probab=83.23 E-value=3.2 Score=20.36 Aligned_cols=41 Identities=17% Similarity=0.138 Sum_probs=26.3 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH Q ss_conf 2477614886788999999999999708997799971537999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT 123 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~ 123 (367) ..+..-++=|+|||+++-.++-- -+...+....+...++++ T Consensus 53 ~S~Il~GPPGtGKTTLA~iIA~~-----t~~~F~~lsAv~sgvkdl 93 (726) T PRK13341 53 GSLILYGPPGVGKTTLARIIANH-----TRAHFSSLNAVLAGVKDL 93 (726) T ss_pred CEEEEECCCCCCHHHHHHHHHHH-----HCCCEEEEECCCCCHHHH T ss_conf 82788897999999999999887-----488679985620377999 No 262 >KOG1803 consensus Probab=82.91 E-value=2.6 Score=20.90 Aligned_cols=45 Identities=20% Similarity=0.190 Sum_probs=36.9 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH Q ss_conf 77614886788999999999999708997799971537999999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWA 126 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ 126 (367) ..|.++-|+|||+...-++.=.+.- +.+|+|+|||--.+.+++=+ T Consensus 204 ~~I~GPPGTGKT~TlvEiI~qlvk~--~k~VLVcaPSn~AVdNiver 248 (649) T KOG1803 204 LIIHGPPGTGKTRTLVEIISQLVKQ--KKRVLVCAPSNVAVDNIVER 248 (649) T ss_pred EEEECCCCCCCEEEHHHHHHHHHHC--CCEEEEECCCHHHHHHHHHH T ss_conf 5755799888404399999999972--88599976736789999987 No 263 >PRK04220 2-phosphoglycerate kinase; Provisional Probab=82.86 E-value=2.5 Score=20.98 Aligned_cols=89 Identities=12% Similarity=0.134 Sum_probs=46.8 Q ss_pred CCHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCHHHHH-HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCC Q ss_conf 33789999752320125988885543014668884436668428999-99998888751245555541124776148867 Q gi|254781187|r 10 KLEQELHEMLMHAECVLSFKNFVMRFFPWGIKGKPLEHFSQPHRWQL-EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGI 88 (367) Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~f~~~~~~w~~~~~~~~~~~~p~~wq~-~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~ 88 (367) +.|+.|.+.....-.+++....|+.. |....+|..-++ ++.+.+. + ...|. =+.|.+.-|+ T Consensus 42 ei~~~L~~~~~~~i~~~el~~~v~~~---------l~~~~~~~~a~rY~~~r~~r-~------~~~pl--iILigGtsGv 103 (306) T PRK04220 42 EIEEELKKEGITKITKEELRRRVYYK---------LIEKDYEEIAEKYLLWRRIR-K------SKEPI--IILIGGASGV 103 (306) T ss_pred HHHHHHHHCCCEEECHHHHHHHHHHH---------HHHHCCHHHHHHHHHHHHHH-C------CCCCE--EEEEECCCCC T ss_conf 99999986577163599999999999---------99844099999999999985-3------69987--9998589988 Q ss_pred CHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH Q ss_conf 889999999999997089977999715379999999 Q gi|254781187|r 89 GKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL 124 (367) Q Consensus 89 GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l 124 (367) |||++++-++-- -+-+.++-. +.+|.++ T Consensus 104 GKSTlA~~LA~r-----LgI~~visT---D~IREVm 131 (306) T PRK04220 104 GTSTIAFELASR-----LGIRSVIGT---DSIREVM 131 (306) T ss_pred CHHHHHHHHHHH-----HCCCEEECC---HHHHHHH T ss_conf 789999999997-----098834222---1699999 No 264 >PRK07568 aspartate aminotransferase; Provisional Probab=82.81 E-value=3.3 Score=20.26 Aligned_cols=64 Identities=14% Similarity=0.093 Sum_probs=39.7 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH Q ss_conf 428999999988887512455555411247761488678899999999999970899779997153799999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN 122 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~ 122 (367) |...-.++-++|+++.++-.....|+ ++.|.+| ++ .|..++..++++||-.|++..|++..... T Consensus 64 ~~~G~~~LReaia~~~~~~g~~~~~d--~I~iT~G---a~---~al~~~~~~l~~pGD~Vlv~~P~y~~y~~ 127 (396) T PRK07568 64 HSAGIDSLREAFSKYYKRFNIDFDKD--EIIVTNG---GS---EAILFALMAICDPGDEIIVPEPFYANYNG 127 (396) T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCHH--EEEECCC---HH---HHHHHHHHHHCCCCCEEEEECCCCCCHHH T ss_conf 98671999999999999868898822--2898578---06---99999999727998989993897532599 No 265 >cd02038 FleN-like FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by influencing FleQ activity. Probab=82.77 E-value=2.7 Score=20.80 Aligned_cols=33 Identities=30% Similarity=0.562 Sum_probs=23.7 Q ss_pred EEEECC-CCCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 776148-86788999999999999708997799971 Q gi|254781187|r 80 CAISAG-RGIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 80 ~~v~sg-rg~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) ++|+|| -|+|||++++.+..-+. +.|.+++++= T Consensus 2 i~v~sgKgGvGkt~~~~nLa~~la--~~G~~vll~D 35 (139) T cd02038 2 IAVTSGKGGVGKTNISANLALALA--KLGKRVLLLD 35 (139) T ss_pred EEEECCCCCCCHHHHHHHHHHHHH--HCCCCEEEEE T ss_conf 899649999839999999999999--7899699998 No 266 >COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only] Probab=82.47 E-value=3.4 Score=20.18 Aligned_cols=16 Identities=44% Similarity=0.397 Sum_probs=14.5 Q ss_pred EEEEECCCCCCHHHHH Q ss_conf 4776148867889999 Q gi|254781187|r 79 KCAISAGRGIGKTTLN 94 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~ 94 (367) -+.|.+.||+|||++. T Consensus 39 i~~i~GpR~~GKTtll 54 (398) T COG1373 39 IILILGPRQVGKTTLL 54 (398) T ss_pred EEEEECCCCCCHHHHH T ss_conf 4999888647789999 No 267 >cd04169 RF3 RF3 subfamily. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts. Probab=82.39 E-value=3.4 Score=20.16 Aligned_cols=140 Identities=14% Similarity=0.048 Sum_probs=67.7 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 24776148867889999999999997089977999715379999999999999998623121123333210001233322 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL 157 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (367) +++++.+..|.|||+++=+++.---....-.+|--=....+.+.|-.=-|.++-+.....-..+.|.. T Consensus 3 Rniai~gH~gaGKTtL~EalL~~~G~i~r~G~V~~~~~~g~t~~D~~~eE~~R~iSi~~~~~~~~w~~------------ 70 (267) T cd04169 3 RTFAIISHPDAGKTTLTEKLLLFGGAIREAGAVKARKSRKHATSDWMEIEKQRGISVTSSVMQFEYRD------------ 70 (267) T ss_pred CEEEEECCCCCCHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCHHHHHHCCCEEECCEEEEEECC------------ T ss_conf 17999847999989999999986686333854630368886046887999865944863637887899------------ Q ss_pred CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---HHHHHHHHHHHCCCCCEEEEEEECCC-CC Q ss_conf 111134577612662101354455652101135862899975455998---89999898740698825899980789-99 Q gi|254781187|r 158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---IINKSILGFFTELNPNRFWIMTSNTR-RL 233 (367) Q Consensus 158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---~i~e~i~g~Lt~~~~~~~~i~igNP~-r~ 233 (367) .+..++.+-+......|...+++.-...++++|=.+||.- .+|+.+. ..+-+.+ + +-|=- +. T Consensus 71 --------~kinliDTPG~~DF~~e~~~al~v~D~AviVv~a~~GVe~~T~~~w~~a~----~~~iP~i-i-fINKmDr~ 136 (267) T cd04169 71 --------CVINLLDTPGHEDFSEDTYRTLTAVDSAVMVIDAAKGVEPQTRKLFEVCR----LRGIPII-T-FINKLDRE 136 (267) T ss_pred --------EEEEEEECCCCHHHHHHHHHHHHHHHCEEEEEECCCCCCHHHHHHHHHHH----HCCCCEE-E-EEECCCCC T ss_conf --------89999979697789999999998864547995256665355899999999----7299979-9-98534567 Q ss_pred CCHHHHHHHC Q ss_conf 8768875411 Q gi|254781187|r 234 NGWFYDIFNI 243 (367) Q Consensus 234 ~g~Fye~~~~ 243 (367) ..-|.++... T Consensus 137 ~adf~~~l~~ 146 (267) T cd04169 137 GRDPLELLDE 146 (267) T ss_pred CCCHHHHHHH T ss_conf 8987899999 No 268 >COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion] Probab=82.35 E-value=1.3 Score=22.74 Aligned_cols=72 Identities=18% Similarity=0.077 Sum_probs=38.0 Q ss_pred CCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHC--CC---CCEEEEEECCCCCCCCCHHHH Q ss_conf 6289997545599889999898740698825899980789998768875411--22---350467523332888898899 Q gi|254781187|r 192 GMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNI--PL---EDWKRYQIDTRTVEGIDSGFH 266 (367) Q Consensus 192 ~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~--~~---~~w~~~~~~~~d~p~~~~~~i 266 (367) .-++|+|-|+|+.-.+..++.+ .+. .+++.-|| +.| ++|+-+- .. +--..+-++-. ++..+ .+ T Consensus 164 ~~~~IIDsaaG~gCpVi~sl~~----aD~---ai~VTEPT-p~g-lhD~kr~~el~~~f~ip~~iViNr~-~~g~s--~i 231 (284) T COG1149 164 ADLLIIDSAAGTGCPVIASLKG----ADL---AILVTEPT-PFG-LHDLKRALELVEHFGIPTGIVINRY-NLGDS--EI 231 (284) T ss_pred CCEEEEECCCCCCCHHHHHHCC----CCE---EEEEECCC-CCC-HHHHHHHHHHHHHHCCCEEEEEECC-CCCCH--HH T ss_conf 2125885799789717776416----877---99981688-523-6689999999998399549999667-77720--89 Q ss_pred HHHHHHCCC Q ss_conf 999962168 Q gi|254781187|r 267 EGIISRYGL 275 (367) Q Consensus 267 ~~~~~~~ge 275 (367) ++.-+.+|- T Consensus 232 e~~~~e~gi 240 (284) T COG1149 232 EEYCEEEGI 240 (284) T ss_pred HHHHHHCCC T ss_conf 998887399 No 269 >TIGR00603 rad25 DNA repair helicase rad25; InterPro: IPR001161 Xeroderma pigmentosum (XP) is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair , . XP-G can be corrected by a 133 Kd nuclear protein, XPGC . XPGC is an acidic protein that confers normal UV resistance in expressing cells . It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms , . XPGC cleaves one strand of the duplex at the border with the single-stranded region . XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases , ; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C-terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents XP group B (XP-B) give rise to both XP and Cockayne syndrome . The DNA/RNA helicase domain IPR001650 from INTERPRO is also present in this group of proteins.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006289 nucleotide-excision repair, 0005634 nucleus. Probab=82.34 E-value=1.4 Score=22.52 Aligned_cols=148 Identities=11% Similarity=0.084 Sum_probs=76.1 Q ss_pred CCCCCCCCCCCHHHHHHHHH-HHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH Q ss_conf 88844366684289999999-88887512455555411247761488678899999999999970899779997153799 Q gi|254781187|r 41 KGKPLEHFSQPHRWQLEFME-AVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ 119 (367) Q Consensus 41 ~~~~~~~~~~p~~wq~~~l~-~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q 119 (367) ++..|==...+|++|+|=|+ .+.=.=| =|+ =|.|. +=|.|||-.-- -++|.--++|+|.+++.=. T Consensus 260 L~IDLKP~t~~RPYQEKSLrsKMFGNGR---ARS-----GiIVL-PCGAGKsLVGv-----TAACTvkKs~lVLctS~VS 325 (756) T TIGR00603 260 LNIDLKPTTVLRPYQEKSLRSKMFGNGR---ARS-----GIIVL-PCGAGKSLVGV-----TAACTVKKSVLVLCTSAVS 325 (756) T ss_pred CCCCCCCCCCCCCCHHHHCCCCCCCCCC---CCC-----CCEEC-CCCCCCCHHHH-----HHHEEEEEEEEEEECCCHH T ss_conf 6745587778897511104445667861---105-----51776-77888311225-----4420231007897267100 Q ss_pred HHHHHHHHH-HHHHHHCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEE Q ss_conf 999999999-9999862312112333321000123-33221111345776126621013544556521011358628999 Q gi|254781187|r 120 LKNTLWAEV-SKWLSMLPHRHWFEMQSLSLHPSGW-YAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFN 197 (367) Q Consensus 120 ~~~~lw~ei-~k~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~iv 197 (367) +.+ |+.- +.|-+.-+ ..--..|....-.... -....+ +=+..+.+.--|.+..--+.=+++...=|+|+ T Consensus 326 V~Q--W~~QFk~WSti~d-~~IcrFTSD~Ke~~~~~~gv~vs------TYsMva~t~kRS~es~k~m~~l~~rEWGl~~L 396 (756) T TIGR00603 326 VEQ--WKQQFKLWSTIDD-SQICRFTSDAKEKFHGEAGVVVS------TYSMVAHTGKRSYESEKVMEWLTNREWGLILL 396 (756) T ss_pred HHH--HHHHHHHCCCCCC-CCCCCCCCCCCCCCCCCCCEEEE------CCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEE T ss_conf 889--9988752268873-55110252135762665335887------33000247543188999999970687317986 Q ss_pred ECCCCCCHHHH-HHH Q ss_conf 75455998899-998 Q gi|254781187|r 198 DEASGTPDIIN-KSI 211 (367) Q Consensus 198 DEAsgI~d~i~-e~i 211 (367) ||-.-||...| -|+ T Consensus 397 DEVHvvPA~mFRrVl 411 (756) T TIGR00603 397 DEVHVVPAAMFRRVL 411 (756) T ss_pred CCCCCCCCCCCCCHH T ss_conf 110103500166010 No 270 >TIGR01587 cas3_core CRISPR-associated helicase Cas3; InterPro: IPR006474 This entry represents a highly conserved core region of the Cas3 sequences. The proteins are found in association with CRISPR repeat elements in a broad range of bacteria and Archaea . Cas3 appears to be a helicase, containing a DEAD/DEAH box region and conserved C-terminal domain. Some but not all members have an N-terminal HD domain region (IPR006674 from INTERPRO), these sequences are not included within this group.. Probab=82.30 E-value=3.3 Score=20.26 Aligned_cols=50 Identities=20% Similarity=0.232 Sum_probs=36.3 Q ss_pred EEEECCCCCCHHHHHHHHHHH---HHHHCCCCEEEEECCCHHHHHHHHHHHHHH Q ss_conf 776148867889999999999---997089977999715379999999999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLW---LISTRPGMSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw---~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) +.|.|+-|-|||.++..++.. ..-...-.|++.+=|+...+.++. ..++. T Consensus 2 ~v~~APTG~GKTe~aL~~A~~sah~~k~~~~~~~I~alP~r~~~na~~-~r~~~ 54 (424) T TIGR01587 2 LVIEAPTGYGKTEAALLWALKSAHLIKKQKADKVIFALPTRVTINAMY-RRLKE 54 (424) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCEEEECCHHHHHHHHH-HHHHH T ss_conf 688617899878999999986366642244401012202688899999-99998 No 271 >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=82.30 E-value=3.4 Score=20.14 Aligned_cols=42 Identities=21% Similarity=0.274 Sum_probs=29.3 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC--CHHHHHHH Q ss_conf 776148867889999999999997089977999715--37999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN--SETQLKNT 123 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~--t~~Q~~~~ 123 (367) +.|.++.|+|||+++..++..... ++.++++++- +.+|++.. T Consensus 2 ~li~g~~g~GKttl~~~~~~~~~~--~~~~~~~~~~ee~~~q~~~~ 45 (165) T cd01120 2 ILVFGPTGSGKTTLALQLALNIAT--KGGKVVYVDIEEEIEELTER 45 (165) T ss_pred EEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEEECCCCHHHHHHH T ss_conf 899989999899999999999876--39979999866644899999 No 272 >cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside. Probab=82.16 E-value=2 Score=21.53 Aligned_cols=21 Identities=33% Similarity=0.279 Sum_probs=17.9 Q ss_pred EEEECCCCCCHHHHHHHHHHH Q ss_conf 776148867889999999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLW 100 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw 100 (367) ++|++|-|+|||+++..+.-- T Consensus 2 IgIaG~S~SGKTTla~~L~~~ 22 (187) T cd02024 2 VGISGVTNSGKTTLAKLLQRI 22 (187) T ss_pred EEEECCCCCCHHHHHHHHHHH T ss_conf 899688887599999999998 No 273 >cd01869 Rab1_Ypt1 Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to t Probab=82.14 E-value=1.6 Score=22.20 Aligned_cols=23 Identities=26% Similarity=0.427 Sum_probs=20.1 Q ss_pred CEEEEEEECCCCCCHHHHHHHHH Q ss_conf 11247761488678899999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) ++||+++.+..|+|||.++-.++ T Consensus 1 y~~Kiv~vGd~~vGKTsli~r~~ 23 (166) T cd01869 1 YLFKLLLIGDSGVGKSCLLLRFA 23 (166) T ss_pred CEEEEEEECCCCCCHHHHHHHHH T ss_conf 96999999999978999999994 No 274 >cd03110 Fer4_NifH_child This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion. Probab=82.00 E-value=1.3 Score=22.79 Aligned_cols=36 Identities=8% Similarity=0.097 Sum_probs=23.1 Q ss_pred CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEEEEECCCC Q ss_conf 5862899975455998899998987406988258999807899 Q gi|254781187|r 190 THGMAVFNDEASGTPDIINKSILGFFTELNPNRFWIMTSNTRR 232 (367) Q Consensus 190 ~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~r 232 (367) +.+.++|+|=.+|+.+.+..++. ..+ .. +...+|.. T Consensus 91 ~~~D~viiD~Ppg~~~~~~~al~----~ad-~~--iiVttP~~ 126 (179) T cd03110 91 EGAELIIIDGPPGIGCPVIASLT----GAD-AA--LLVTEPTP 126 (179) T ss_pred CCCCEEEEECCCCCCHHHHHHHH----CCC-EE--EEECCCCH T ss_conf 37998998189997578999997----399-49--99819947 No 275 >TIGR02788 VirB11 P-type DNA transfer ATPase VirB11; InterPro: IPR014155 This entry contains VirB11, a protein that is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer . VirB11 is believed to be an ATPase and is a homologue of the P-like conjugation system TrbB protein and the Flp pilus system protein TadA .. Probab=81.87 E-value=1.3 Score=22.80 Aligned_cols=94 Identities=18% Similarity=0.146 Sum_probs=51.0 Q ss_pred EEEEEECCCCCCHHHHHHHHHHH---------------HHHHC-CCCEEEEECCC-HHHHHHHHHHHH-HHHHHHCCCCC Q ss_conf 24776148867889999999999---------------99708-99779997153-799999999999-99998623121 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLW---------------LISTR-PGMSIICIANS-ETQLKNTLWAEV-SKWLSMLPHRH 139 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw---------------~~~~~-~~~~v~~~A~t-~~Q~~~~lw~ei-~k~~~~~~~~~ 139 (367) ..+.|++|-|+|||++.-+++-. ..+-+ |+..-+.-+-. .+|...+.-+.+ +-.+++-| T Consensus 159 knIii~GGTgSGKTTf~kal~~~IP~~ER~iTIED~~E~~~~hhpN~V~L~ysk~v~~g~~~vt~~~Ll~scLRMrP--- 235 (328) T TIGR02788 159 KNIIISGGTGSGKTTFLKALVKEIPKDERLITIEDTRELFLPHHPNKVHLFYSKGVGQGSAKVTPKDLLESCLRMRP--- 235 (328) T ss_pred CEEEEEECCCCHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHCCCC--- T ss_conf 91999906897189999999732762252788852011478889864565534642344356898999999711774--- Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCC Q ss_conf 1233332100012333221111345776126621013544556521011358 Q gi|254781187|r 140 WFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTH 191 (367) Q Consensus 140 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~ 191 (367) .++.+.. ++.+ ..|.+-+-...+-|.++-.+|+.+ T Consensus 236 ------DRI~LgE---------LRG~--Eaf~F~~~~nsGHpGsiTT~HA~s 270 (328) T TIGR02788 236 ------DRILLGE---------LRGD--EAFDFIRAVNSGHPGSITTVHAGS 270 (328) T ss_pred ------CHHHHHH---------HCCH--HHHHHHHHHCCCCCCCEEEEEECC T ss_conf ------0576743---------0332--578888752059886056787189 No 276 >KOG0345 consensus Probab=81.86 E-value=3.6 Score=20.04 Aligned_cols=122 Identities=15% Similarity=-0.020 Sum_probs=59.0 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHC----CCC--EEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC Q ss_conf 477614886788999999999999708----997--79997153799999999999999986231211233332100012 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTR----PGM--SIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSG 152 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~----~~~--~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~ 152 (367) -|+|-|..|+|||...-.=++-.+.-+ |+. -.++++||..-+++| ..-+..+++.+++-....+.- T Consensus 45 DVvveavTGSGKTlAFllP~le~i~rr~~~~~~~~vgalIIsPTRELa~QI-~~V~~~F~~~l~~l~~~l~vG------- 116 (567) T KOG0345 45 DVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPGQVGALIISPTRELARQI-REVAQPFLEHLPNLNCELLVG------- 116 (567) T ss_pred CEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHHH-HHHHHHHHHHCCCCCEEEEEC------- T ss_conf 568985678871066899999999861157896512479965719999999-999999998503654599976------- Q ss_pred CCCCCCCCCCCCCCCCEEEEECCCCCCCCCC--CCCCCCCCCCEEEEECCCCCCHHHH Q ss_conf 3332211113457761266210135445565--2101135862899975455998899 Q gi|254781187|r 153 WYAELLEQSMGIDSKHYTITCRTYSEERPDT--FVGPHNTHGMAVFNDEASGTPDIIN 208 (367) Q Consensus 153 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea--~~g~h~~~~~l~ivDEAsgI~d~i~ 208 (367) ...........-..+..+..+.+-+...--. ...+...+..++|+|||.-.=|--| T Consensus 117 G~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~LVLDEADrLldmgF 174 (567) T KOG0345 117 GRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEILVLDEADRLLDMGF 174 (567) T ss_pred CCCHHHHHHHHHHHCCCEEEECCHHHHHHHHCHHHCCCCCCCCEEEECCHHHHHCCCH T ss_conf 8647779999997099589947624999984530003613311577514676744327 No 277 >KOG2228 consensus Probab=81.79 E-value=3.6 Score=20.02 Aligned_cols=81 Identities=20% Similarity=0.187 Sum_probs=44.1 Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHH Q ss_conf 84436668428999999988887512455555411247761488678899999999999970899779997-15379999 Q gi|254781187|r 43 KPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-ANSETQLK 121 (367) Q Consensus 43 ~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~~Q~~ 121 (367) ++|.+.+.-++=-.++++.-..|-+. --+++.++||+|||.+.+-.+.- .-..+.+.+++ =|-.=|.. T Consensus 24 ~~l~g~~~~~~~l~~~lkqt~~~gEs---------nsviiigprgsgkT~li~~~Ls~--~q~~~E~~l~v~Lng~~~~d 92 (408) T KOG2228 24 INLFGVQDEQKHLSELLKQTILHGES---------NSVIIIGPRGSGKTILIDTRLSD--IQENGENFLLVRLNGELQTD 92 (408) T ss_pred CCEEEHHHHHHHHHHHHHHHHHHCCC---------CCEEEECCCCCCCEEEEHHHHHH--HHHCCCEEEEEEECCCCHHH T ss_conf 65000587899999999999984477---------72699814778816740778766--77517727999878500155 Q ss_pred HHHHHHHHHHHHH Q ss_conf 9999999999986 Q gi|254781187|r 122 NTLWAEVSKWLSM 134 (367) Q Consensus 122 ~~lw~ei~k~~~~ 134 (367) .+...+|.+.++. T Consensus 93 k~al~~I~rql~~ 105 (408) T KOG2228 93 KIALKGITRQLAL 105 (408) T ss_pred HHHHHHHHHHHHH T ss_conf 8999999999999 No 278 >PRK09280 F0F1 ATP synthase subunit beta; Validated Probab=81.52 E-value=3.7 Score=19.97 Aligned_cols=34 Identities=26% Similarity=0.395 Sum_probs=26.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 4776148867889999999999997089977999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC 112 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~ 112 (367) |+.+-+|.|+|||.+...++.-....+.+..|++ T Consensus 147 rigIfggaGvGKTvLl~eli~n~a~~~~~v~V~a 180 (466) T PRK09280 147 KIGLFGGAGVGKTVLIMELINNIAKEHGGYSVFA 180 (466) T ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE T ss_conf 7985579999800899999999998659909999 No 279 >COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair] Probab=81.47 E-value=3.7 Score=19.95 Aligned_cols=161 Identities=15% Similarity=0.043 Sum_probs=77.4 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHH Q ss_conf 89999999888875124555554112477614886788999999999999708997799971537999999999999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) .-..+++..|..|. .+.|.+.-|+|||+-.--+++-.-. .-+.+|+||-|-.=-++++ .++.. T Consensus 53 ~~~~~i~~ai~~~~------------vvii~getGsGKTTqlP~~lle~g~-~~~g~I~~tQPRRlAArsv----A~RvA 115 (845) T COG1643 53 AVRDEILKAIEQNQ------------VVIIVGETGSGKTTQLPQFLLEEGL-GIAGKIGCTQPRRLAARSV----AERVA 115 (845) T ss_pred HHHHHHHHHHHHCC------------EEEEECCCCCCHHHHHHHHHHHHHC-CCCCEEEECCCHHHHHHHH----HHHHH T ss_conf 88999999998697------------8998679988758788999996001-6687599658438999999----99999 Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-EEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCC--CCHHHHH Q ss_conf 862312112333321000123332211113457761-2662101354455652101135862899975455--9988999 Q gi|254781187|r 133 SMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKH-YTITCRTYSEERPDTFVGPHNTHGMAVFNDEASG--TPDIINK 209 (367) Q Consensus 133 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsg--I~d~i~e 209 (367) +.+-.+. ...-++...+.......... ..-.+...+.-.-+. .-....++|+|||.- +..++-- T Consensus 116 eel~~~~---------G~~VGY~iRfe~~~s~~Trik~mTdGiLlrei~~D~----~Ls~ys~vIiDEaHERSl~tDilL 182 (845) T COG1643 116 EELGEKL---------GETVGYSIRFESKVSPRTRIKVMTDGILLREIQNDP----LLSGYSVVIIDEAHERSLNTDILL 182 (845) T ss_pred HHHCCCC---------CCEEEEEEEEECCCCCCCEEEEECCHHHHHHHHHCC----CCCCCCEEEEECHHHHHHHHHHHH T ss_conf 9838986---------765437999622678771468951479999984380----204587799701335568889999 Q ss_pred HHHHH-HHCCCCCEEEEEEECCCCCCCHHHHHHHCC Q ss_conf 98987-406988258999807899987688754112 Q gi|254781187|r 210 SILGF-FTELNPNRFWIMTSNTRRLNGWFYDIFNIP 244 (367) Q Consensus 210 ~i~g~-Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~ 244 (367) .+..- +........ +++.+-|-+...|...|..+ T Consensus 183 gllk~~~~~rr~DLK-iIimSATld~~rfs~~f~~a 217 (845) T COG1643 183 GLLKDLLARRRDDLK-LIIMSATLDAERFSAYFGNA 217 (845) T ss_pred HHHHHHHHHCCCCCE-EEEEECCCCHHHHHHHCCCC T ss_conf 999999864688705-99972535889999762899 No 280 >cd01886 EF-G Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group conta Probab=81.42 E-value=0.78 Score=24.09 Aligned_cols=133 Identities=13% Similarity=0.094 Sum_probs=65.2 Q ss_pred EEEEECCCCCCHHHHHHHHHHHH-HHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 47761488678899999999999-97089977999715379999999999999998623121123333210001233322 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWL-ISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL 157 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~-~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (367) +++|.+..|.|||+++-.++.-- +..+.|. | ...+.+.+-.=-|.++-+.....-..+.|+.. T Consensus 1 Niai~gH~gaGKTtL~EalL~~ag~i~r~G~-v----~~g~tv~D~~~eE~~R~isi~~~~~~~~w~~~----------- 64 (270) T cd01886 1 NIGIIAHIDAGKTTTTERILYYTGRIHKIGE-V----HGGGATMDFMEQERERGITIQSAATTCFWKDH----------- 64 (270) T ss_pred CEEEEECCCCCHHHHHHHHHHHCCCCCCCCE-E----CCCCCCCCCCHHHHHCCCEEECCEEEEEECCE----------- T ss_conf 9899968999988999999986687355815-5----38975566848898768707336689998998----------- Q ss_pred CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC---HHHHHHHHHHHHCCCCCEEEEEEECC-CCC Q ss_conf 11113457761266210135445565210113586289997545599---88999989874069882589998078-999 Q gi|254781187|r 158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP---DIINKSILGFFTELNPNRFWIMTSNT-RRL 233 (367) Q Consensus 158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~---d~i~e~i~g~Lt~~~~~~~~i~igNP-~r~ 233 (367) +..++.+-+......|...+++.-...++++|=++||. ..+|+.+. ..+-+.+ .+-|= .|. T Consensus 65 ---------~inliDTPG~~DF~~e~~~aL~~~D~AviVv~a~~GVe~~T~~~w~~~~----~~~lP~i--~fINKmDre 129 (270) T cd01886 65 ---------RINIIDTPGHVDFTIEVERSLRVLDGAVAVFDAVAGVEPQTETVWRQAD----RYNVPRI--AFVNKMDRT 129 (270) T ss_pred ---------EEEEEECCCCHHHHHHHHHHHHHHCEEEEEEECCCCHHHHHHHHHHHHH----HCCCCEE--EEEECCCCC T ss_conf ---------9999869696788999999987755599998467644263699998899----8499989--999887877 Q ss_pred CCHHHHHHH Q ss_conf 876887541 Q gi|254781187|r 234 NGWFYDIFN 242 (367) Q Consensus 234 ~g~Fye~~~ 242 (367) ..-|.+... T Consensus 130 ~ad~~~~l~ 138 (270) T cd01886 130 GADFFRVVE 138 (270) T ss_pred CCCCHHHHH T ss_conf 887166899 No 281 >pfam01935 DUF87 Domain of unknown function DUF87. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands. Probab=81.39 E-value=3.2 Score=20.31 Aligned_cols=39 Identities=18% Similarity=0.269 Sum_probs=29.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH Q ss_conf 4776148867889999999999997089977999715379 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET 118 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~ 118 (367) .++|.+-.|+|||++++.++- .+.-.++..+++.=|... T Consensus 25 H~aIlg~TGsGKS~tv~vLl~-~l~~~~~~~vlVfDpHgE 63 (218) T pfam01935 25 HFAILGSTGSGKSNTVAVLLE-ELLEKKGATVLIFDPHGE 63 (218) T ss_pred HEEEECCCCCCHHHHHHHHHH-HHHHCCCCCEEEECCCCC T ss_conf 147872699976999999999-998547997899828863 No 282 >PRK02731 histidinol-phosphate aminotransferase; Validated Probab=81.30 E-value=2.5 Score=21.01 Aligned_cols=58 Identities=16% Similarity=0.182 Sum_probs=34.5 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 42899999998888751245555541124776148867889999999999997089977999715379999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) |+.-..++-++|+++..=+. + ++.| |.| =+ .+..++..+++.|+.+|++..|++..-. T Consensus 65 Pd~~~~~Lr~aiA~~~~v~~--~-----~Ilv--~nG--s~--e~i~l~~~a~~~pgd~Vl~~~P~f~~Y~ 122 (367) T PRK02731 65 PDGSGFELKAALAEKFGVDP--E-----QIIL--GNG--SD--EILELLARAYLGPGDEVIYSEHAFAVYP 122 (367) T ss_pred CCCCHHHHHHHHHHHHCCCH--H-----HEEE--CCC--HH--HHHHHHHHHHHCCCCEEEECCCCHHHHH T ss_conf 59878999999999978581--1-----1998--578--99--9999999998479986444798626899 No 283 >TIGR01075 uvrD DNA helicase II; InterPro: IPR005753 The SOS response is required for efficient nucleotide excision repair (NER) of the major ultraviolet light (UV) induced DNA lesions. The expression of three NER genes, uvrA, uvrB, and uvrD, is upregulated as part of the SOS response. UvrD differs from the others in that it is not involved in lesion recognition but rather in promoting the post-incision steps of NER, including turnover of the UvrBC incision complex . The form of the UvrD helicase with optimal helicase activity is oligomeric with at least two sites for binding the DNA substrate, where one site contacts regions of the 3'-ssDNA tail that are distal from the single-stranded/double-stranded DNA junction.; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm. Probab=81.20 E-value=3.7 Score=19.93 Aligned_cols=55 Identities=27% Similarity=0.317 Sum_probs=40.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 4776148867889999999999997089977999715379999999999999998623 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLP 136 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~ 136 (367) ...|.||=|+|||-+..-=|.|++....=+.-=++|-|.. +.--+|++.-+..+. T Consensus 19 ~~LvLAGAGSGKTRVL~hRIaWL~~v~~~s~~SiMAVTFT---NKAA~Em~~Ri~~~~ 73 (741) T TIGR01075 19 NLLVLAGAGSGKTRVLTHRIAWLLSVENASPHSIMAVTFT---NKAAAEMRHRIEALL 73 (741) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECHH---HHHHHHHHHHHHHHH T ss_conf 5548730688850247888998874078998535632003---478999999999986 No 284 >COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair] Probab=81.12 E-value=3.8 Score=19.88 Aligned_cols=45 Identities=22% Similarity=0.270 Sum_probs=35.2 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHC--CCCEEEEECCCHHHHHHH Q ss_conf 477614886788999999999999708--997799971537999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTR--PGMSIICIANSETQLKNT 123 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~--~~~~v~~~A~t~~Q~~~~ 123 (367) .+.|.||.|+|||.....-+.|++... .+..|+++.=|-+-++.+ T Consensus 17 p~lV~AGaGsGKT~vlt~Ria~li~~~~v~p~~Il~vTFTnkAA~em 63 (655) T COG0210 17 PLLVLAGAGSGKTRVLTERIAYLIAAGGVDPEQILAITFTNKAAAEM 63 (655) T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHCCCCCHHHEEEEEEEHHHHHHH T ss_conf 86999579986189999999999873895757717789676999999 No 285 >KOG0742 consensus Probab=80.88 E-value=3.9 Score=19.83 Aligned_cols=77 Identities=13% Similarity=0.069 Sum_probs=48.6 Q ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC Q ss_conf 9999888875124555554112477614886788999999999999708997799971537999999999999999862 Q gi|254781187|r 57 EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSML 135 (367) Q Consensus 57 ~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~ 135 (367) +-++.|+.-- .|.+.++...+++..-++-|+|||..+--++..--+-+.=.+.-=+||-..|+-+.+ .++-+|..++ T Consensus 365 ~Rie~lA~aT-aNTK~h~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAPlG~qaVTki-H~lFDWakkS 441 (630) T KOG0742 365 KRIEDLAIAT-ANTKKHQAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGAQAVTKI-HKLFDWAKKS 441 (630) T ss_pred HHHHHHHHHH-CCCCCCCCHHHHEEEECCCCCCHHHHHHHHHHHCCCCEEHHCCCCCCCCHHHHHHHH-HHHHHHHHHC T ss_conf 9999998874-043002430440032479998604999999885287410013787555217889999-9987887515 No 286 >PRK06793 fliI flagellum-specific ATP synthase; Validated Probab=80.78 E-value=3.2 Score=20.33 Aligned_cols=41 Identities=27% Similarity=0.465 Sum_probs=26.0 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHHH Q ss_conf 47761488678899999999999970899779997-153799999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-ANSETQLKN 122 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~~Q~~~ 122 (367) |+.|-+|+|+|||++.++++..- .-+..|++. ....+-+++ T Consensus 158 R~gIfg~sGvGKstLl~~i~~~~---~adv~Vi~lIGeRgrEv~e 199 (432) T PRK06793 158 KIGIFAGSGVGKSTLLGMIAKNA---KADINVISLVGERGREVKD 199 (432) T ss_pred EEEEECCCCCCHHHHHHHHHHHC---CCCCEEEEEEEEECHHHHH T ss_conf 66663268987899999998724---5786579998886279999 No 287 >pfam00931 NB-ARC NB-ARC domain. Probab=80.73 E-value=3.9 Score=19.80 Aligned_cols=48 Identities=15% Similarity=0.006 Sum_probs=29.9 Q ss_pred CEEEEEEECCCCCCHHHHHHHHHHHH-HHHCCCCEEEEECCCHHHHHHH Q ss_conf 11247761488678899999999999-9708997799971537999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMMLWL-ISTRPGMSIICIANSETQLKNT 123 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~lw~-~~~~~~~~v~~~A~t~~Q~~~~ 123 (367) ++.-++|.+--|+|||+++..+.-.. .-.+.+.++.++........++ T Consensus 18 ~~~vI~I~G~gGiGKTtLA~~v~~~~~i~~~F~~~~wv~vs~~~~~~~i 66 (285) T pfam00931 18 NLGVVGIVGMGGVGKTTLAKQIYNDDSVGGHFDSVAWVVVSKTYTEFRL 66 (285) T ss_pred CCEEEEEECCCCCCHHHHHHHHHCCHHHHHCCCEEEEEEECCCCCHHHH T ss_conf 9539998899956399999999716556505983899997976668999 No 288 >TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative; InterPro: IPR006310 These are a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of Escherichia coli. . Probab=80.67 E-value=3.9 Score=19.79 Aligned_cols=76 Identities=21% Similarity=0.187 Sum_probs=49.8 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH---HHHHHHHHHH Q ss_conf 4289999999888875124555554112477614886788999999999999708997799971537---9999999999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE---TQLKNTLWAE 127 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~---~Q~~~~lw~e 127 (367) =|.=|.++...|.+++.+|... .+-|-||-|+|||..==--++ +....++..|++-.+|. +|+-+.-.+. T Consensus 261 ~R~~Q~~la~~v~~~l~~Gt~~------~~lIEA~tG~GKtlgYLLPal-~~~~~~~~~vviST~Tk~LQ~QL~E~d~P~ 333 (944) T TIGR01407 261 YREEQLKLAELVEDELTHGTEE------KSLIEAPTGTGKTLGYLLPAL-YLAKEEEKPVVISTATKVLQSQLLEKDIPL 333 (944) T ss_pred HHHHHHHHHHHHHHHHCCCCCH------HHHEECCCCCCHHHHHHHHHH-HHCCCCCCCEEEEECCHHHHHHHHHHHHHH T ss_conf 1388999999999984157661------133023766432589999999-731378885699836366565656888898 Q ss_pred HHHHHH Q ss_conf 999998 Q gi|254781187|r 128 VSKWLS 133 (367) Q Consensus 128 i~k~~~ 133 (367) +++.+. T Consensus 334 l~~~~~ 339 (944) T TIGR01407 334 LNKILN 339 (944) T ss_pred HHHHCC T ss_conf 886518 No 289 >COG4240 Predicted kinase [General function prediction only] Probab=80.65 E-value=3.9 Score=19.78 Aligned_cols=52 Identities=21% Similarity=0.312 Sum_probs=30.8 Q ss_pred HHHHHHHHHH-HHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 9999988887-5124555554112477614886788999999999999708997799971 Q gi|254781187|r 56 LEFMEAVDVH-CHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 56 ~~~l~~~~~~-~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) .+++..|+.. .+++ .| +=+-|+++.|+|||++++.+...+....- .++...+ T Consensus 34 Lpll~Kiap~~qe~g----rP--li~gisGpQGSGKStls~~i~~~L~~kg~-ert~~lS 86 (300) T COG4240 34 LPLLAKIAPWAQERG----RP--LIVGISGPQGSGKSTLSALIVRLLAAKGL-ERTATLS 86 (300) T ss_pred HHHHHHHHHHHHHCC----CC--EEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEE T ss_conf 788986445442127----96--39985268887653599999999997365-3068866 No 290 >cd01868 Rab11_like Rab11-like. Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP Probab=80.43 E-value=2 Score=21.59 Aligned_cols=23 Identities=26% Similarity=0.501 Sum_probs=20.0 Q ss_pred CEEEEEEECCCCCCHHHHHHHHH Q ss_conf 11247761488678899999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) +.||+.|.+..|+|||.++..++ T Consensus 2 y~~Kiv~iGd~~VGKTsli~r~~ 24 (165) T cd01868 2 YLFKIVLIGDSGVGKSNLLSRFT 24 (165) T ss_pred EEEEEEEECCCCCCHHHHHHHHH T ss_conf 35899999999978999999997 No 291 >COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms] Probab=80.34 E-value=4 Score=19.72 Aligned_cols=138 Identities=13% Similarity=0.060 Sum_probs=68.5 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH Q ss_conf 42899999998888751245555541124776148867889999999999997089977999715379999999999999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) ++.-|..++....+-....... ...-+-.|=--.|+|||..+.+++-+.+-.-...+|+++-- ..-+.+-+..++++ T Consensus 249 ~~~~q~~a~~~~i~~~~~~~~~--~~~~~G~IWHtqGSGKTltm~~~A~~l~~~~~~~~v~fvvD-R~dLd~Q~~~~f~~ 325 (962) T COG0610 249 QRYAQYRAVQKAIKRILKASNP--GDGKGGYIWHTQGSGKTLTMFKLARLLLELPKNPKVLFVVD-RKDLDDQTSDEFQS 325 (962) T ss_pred HHHHHHHHHHHHHHHHHHHCCC--CCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEC-HHHHHHHHHHHHHH T ss_conf 7889999999999999971267--87772389840698378999999999983659996999967-28899999999999 Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCEEEEECCCCCCCCCC-CCCCCCCCCCEEEEECCCCC Q ss_conf 9986231211233332100012333221111345-7761266210135445565-21011358628999754559 Q gi|254781187|r 131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGI-DSKHYTITCRTYSEERPDT-FVGPHNTHGMAVFNDEASGT 203 (367) Q Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~a~~~~~~~~ea-~~g~h~~~~~l~ivDEAsgI 203 (367) .-......+ ..... ...+..++. ..+..+.+-+.+.....+. .....+.+ ..+|+|||.-- T Consensus 326 ~~~~~~~~~--~~~s~---------~~Lk~~l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~-ivvI~DEaHRS 388 (962) T COG0610 326 FGKVAFNDP--KAEST---------SELKELLEDGKGKIIVTTIQKFNKAVKEDELELLKRKN-VVVIIDEAHRS 388 (962) T ss_pred HHHHHHCCC--CCCCH---------HHHHHHHHCCCCCEEEEEECCCCHHHHCCCCCCCCCCC-EEEEEECCCCC T ss_conf 887632044--44579---------99999986589848999710264333333200047876-79998640103 No 292 >CHL00175 minD septum-site determining protein; Validated Probab=80.33 E-value=3.5 Score=20.07 Aligned_cols=36 Identities=31% Similarity=0.484 Sum_probs=26.2 Q ss_pred CEEE-EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 1124-7761488-678899999999999970899779997 Q gi|254781187|r 76 TIFK-CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 76 ~~~~-~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) .|-| ++|++|. |+|||++++.+..-++. .+.||+++ T Consensus 11 ~m~kiIaV~s~KGGVGKTT~a~NLa~aLA~--~G~kVlli 48 (279) T CHL00175 11 TMTRIIVITSGKGGVGKTTTTANLGMSIAR--LGYRVALI 48 (279) T ss_pred CCCEEEEEECCCCCCCHHHHHHHHHHHHHH--CCCCEEEE T ss_conf 988699997489984489999999999997--89988999 No 293 >pfam00155 Aminotran_1_2 Aminotransferase class I and II. Probab=79.83 E-value=4.2 Score=19.62 Aligned_cols=69 Identities=14% Similarity=0.085 Sum_probs=42.7 Q ss_pred CCCHHHHHHHHHHHHHHHHCCCCCC-CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH Q ss_conf 6842899999998888751245555-541124776148867889999999999997089977999715379999999 Q gi|254781187|r 49 SQPHRWQLEFMEAVDVHCHSNVNNS-NPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL 124 (367) Q Consensus 49 ~~p~~wq~~~l~~~~~~~~~~~~~~-~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l 124 (367) -+|..--.++-++|+++.++..... .|+ -.+.+.+| . + .+..++-.+++.|+-.|++-.|++......+ T Consensus 35 Y~~~~G~~~LR~aia~~~~~~~~~~~~~e-~~I~~t~G--~--~--~~l~~~~~~l~~~gd~Vli~~P~y~~~~~~~ 104 (351) T pfam00155 35 YGPTDGLPELREALAKFLGRSPVLKLDRE-AAVVFGSG--A--G--ANIEALIFLLANPGDAILVPAPTYASYIRIA 104 (351) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCCCCC-CEEEECCC--H--H--HHHHHHHHHHCCCCCEEEECCCCCHHHHHHH T ss_conf 79818789999999998601029999947-48998113--9--9--9999999996699499998899868899999 No 294 >COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair] Probab=79.72 E-value=4.2 Score=19.59 Aligned_cols=47 Identities=13% Similarity=0.128 Sum_probs=29.9 Q ss_pred CCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCC-CEEEEEEECCC Q ss_conf 2101135862899975455998899998987406988-25899980789 Q gi|254781187|r 184 FVGPHNTHGMAVFNDEASGTPDIINKSILGFFTELNP-NRFWIMTSNTR 231 (367) Q Consensus 184 ~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~~~-~~~~i~igNP~ 231 (367) ...++.. +-.+++||++--+..-|.++....++... ....+++|-|- T Consensus 372 ~~~lr~~-~~~iLIDEfQDT~~~Q~~Il~~l~~~~~~~~~~lF~VGD~K 419 (1139) T COG1074 372 AESLREQ-YPHILIDEFQDTDPQQWRILSRLFAGFKAGNRTLFLVGDPK 419 (1139) T ss_pred HHHHHHC-CCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCCH T ss_conf 9999847-98588740345998899999999725667785079974734 No 295 >pfam05729 NACHT NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931. Probab=79.62 E-value=2.5 Score=20.96 Aligned_cols=27 Identities=26% Similarity=0.298 Sum_probs=21.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHC Q ss_conf 477614886788999999999999708 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTR 105 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~ 105 (367) ++.|.+.-|+|||+++..+++-|+--. T Consensus 2 ~i~i~G~aG~GKTtll~kl~~~wa~g~ 28 (165) T pfam05729 2 TVILQGEAGSGKTTLLQKLALLWAQGK 28 (165) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHCCC T ss_conf 899982798989999999999998698 No 296 >TIGR01968 minD_bact septum site-determining protein MinD; InterPro: IPR010223 This entry describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE . MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD . The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.; GO: 0016887 ATPase activity, 0000918 selection of site for barrier septum formation. Probab=79.61 E-value=2.6 Score=20.92 Aligned_cols=123 Identities=19% Similarity=0.179 Sum_probs=59.2 Q ss_pred EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCH-HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 7761488-678899999999999970899779997-1537-999999999999999862312112333321000123332 Q gi|254781187|r 80 CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI-ANSE-TQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAE 156 (367) Q Consensus 80 ~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~-~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 (367) +.|.||- |+||||.+|.+-.=++.. |.||+++ +-.. +-| |++-..=.+.+.-+.+----.|+ ... T Consensus 4 iViTSGKGGVGKTTtTANlG~aLA~l--G~kVvliD~DiGLRNL-D~~lGLEnRivYt~vDVveG~C~---------l~q 71 (272) T TIGR01968 4 IVITSGKGGVGKTTTTANLGTALARL--GKKVVLIDADIGLRNL-DLLLGLENRIVYTLVDVVEGECR---------LQQ 71 (272) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEECCCCCHHH-HHHHCCCHHHHHHHHHHHCCCCC---------CCC T ss_conf 99981788977358989999999961--9828999547570345-77742310354535543248421---------100 Q ss_pred CCCCCCCCCCCCEEEEECCCCCCC--CCCC----CCCCCC-CCCEEEEECCCCCCHHHHHHHHHH Q ss_conf 211113457761266210135445--5652----101135-862899975455998899998987 Q gi|254781187|r 157 LLEQSMGIDSKHYTITCRTYSEER--PDTF----VGPHNT-HGMAVFNDEASGTPDIINKSILGF 214 (367) Q Consensus 157 ~~~~~~~~~~~~~~~~a~~~~~~~--~ea~----~g~h~~-~~~l~ivDEAsgI~d~i~e~i~g~ 214 (367) +...+-+..+=..-+.+|+.+.+. +|.+ +.+..+ ++.++|+|==|||..-+-.|+.|+ T Consensus 72 ALikDKr~~NL~LLpAsQ~rdK~~~~~E~~~~lv~~Lk~~~~FDYviIDcPAGIE~GF~nAv~~A 136 (272) T TIGR01968 72 ALIKDKRLENLYLLPASQTRDKDAVTPEQMKKLVNELKEEEHFDYVIIDCPAGIESGFRNAVAPA 136 (272) T ss_pred CCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHHHHC T ss_conf 10012675235663653023613469778999999985437930799737877435689987526 No 297 >PRK06067 flagellar accessory protein FlaH; Validated Probab=79.59 E-value=4.3 Score=19.57 Aligned_cols=40 Identities=18% Similarity=0.202 Sum_probs=26.8 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC--CCHHHH Q ss_conf 477614886788999999999999708997799971--537999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA--NSETQL 120 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A--~t~~Q~ 120 (367) -+.|.++.|+|||.++.-++. ..+.+ +.++++++ .+.+|+ T Consensus 34 ~~li~G~~G~GKt~~~~~f~~-~~~~~-g~~~~~~~~ee~~~~~ 75 (241) T PRK06067 34 LILIEGENDTGKSVLSQQFVW-GALNQ-GKRGLAITTENTSKSY 75 (241) T ss_pred EEEEECCCCCCHHHHHHHHHH-HHHHC-CCEEEEEEECCCHHHH T ss_conf 899980799887999999999-99867-9829999942899999 No 298 >TIGR02545 ATP_syn_fliI flagellar protein export ATPase FliI; InterPro: IPR013379 FliI proteins are involved in bacterial flagellum systems, acting to drive protein export for flagellar biosynthesis. The most closely related proteins are the YscN proteins of bacterial type III secretion systems.; GO: 0016887 ATPase activity, 0001539 ciliary or flagellar motility, 0009296 flagellum biogenesis, 0009288 flagellin-based flagellum. Probab=78.94 E-value=1.4 Score=22.47 Aligned_cols=46 Identities=26% Similarity=0.348 Sum_probs=30.0 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH Q ss_conf 47761488678899999999999970899779997153799999999999999986 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM 134 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~ 134 (367) |+-|-||=|+|||+|.++++-+ -..-|+|+|=-..-= +|++.+++. T Consensus 160 R~GIFAGSGVGKSTLLGMiAr~-----t~ADV~VIALIGERG-----REV~EFiE~ 205 (439) T TIGR02545 160 RLGIFAGSGVGKSTLLGMIARY-----TEADVNVIALIGERG-----REVKEFIED 205 (439) T ss_pred EEEEECCCCHHHHHHHHHHHCC-----CCCCEEEEEEECCCC-----CCCHHHHHH T ss_conf 0266337744478898887506-----658878998444656-----643135543 No 299 >KOG4181 consensus Probab=78.82 E-value=2.8 Score=20.66 Aligned_cols=62 Identities=15% Similarity=0.112 Sum_probs=34.6 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH Q ss_conf 999999888875124555554112477614886788999999999999708997799971537999999 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT 123 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~ 123 (367) |..+..++.+.+. +.+++--+.|.+|.|+|||++.+.++.= ..+.+.+..+-.|...-+++. T Consensus 171 ~g~~~d~a~~ll~-----~~tdf~VIgvlG~QgsGKStllslLaan--s~~~dyr~yvFRpvS~Ea~E~ 232 (491) T KOG4181 171 NGIFNDNARKLLH-----KTTDFTVIGVLGGQGSGKSTLLSLLAAN--SLDYDYRQYVFRPVSPEADEC 232 (491) T ss_pred CCCHHHHHHHHHH-----CCCCEEEEEEECCCCCCHHHHHHHHHCC--CHHHHHHHHHCCCCCHHHHHH T ss_conf 5512368999961-----4898169974047775488999998426--847766777303578556665 No 300 >COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only] Probab=78.64 E-value=4.6 Score=19.39 Aligned_cols=49 Identities=20% Similarity=0.164 Sum_probs=22.2 Q ss_pred CCCCCCCCCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCEEEEEEECCC Q ss_conf 521011358628999754-5599889999898740698825899980789 Q gi|254781187|r 183 TFVGPHNTHGMAVFNDEA-SGTPDIINKSILGFFTELNPNRFWIMTSNTR 231 (367) Q Consensus 183 a~~g~h~~~~~l~ivDEA-sgI~d~i~e~i~g~Lt~~~~~~~~i~igNP~ 231 (367) +|+-+--.....+++||| +.++++.-..+.-++.+.=.....+.+|-.+ T Consensus 525 afARilL~kP~~v~LDEATsALDe~~e~~l~q~l~~~lp~~tvISV~Hr~ 574 (604) T COG4178 525 AFARLLLHKPKWVFLDEATSALDEETEDRLYQLLKEELPDATVISVGHRP 574 (604) T ss_pred HHHHHHHCCCCEEEEECCHHCCCHHHHHHHHHHHHHHCCCCEEEEECCCH T ss_conf 99999970999899806011259578999999998548997899955600 No 301 >PRK05480 uridine kinase; Provisional Probab=78.63 E-value=2.3 Score=21.18 Aligned_cols=24 Identities=33% Similarity=0.393 Sum_probs=19.7 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 247761488678899999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~ 101 (367) +-++|++|-|+|||+++..+.--+ T Consensus 7 ~iIgIaG~SgSGKTT~a~~L~~~l 30 (209) T PRK05480 7 IIIGIAGGSGSGKTTVASTIYEEL 30 (209) T ss_pred EEEEEECCCCCCHHHHHHHHHHHC T ss_conf 899998999778999999999980 No 302 >PRK10818 cell division inhibitor MinD; Provisional Probab=78.62 E-value=4.4 Score=19.48 Aligned_cols=32 Identities=31% Similarity=0.492 Sum_probs=25.1 Q ss_pred EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 7761488-678899999999999970899779997 Q gi|254781187|r 80 CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 80 ~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) ++|++|. |+|||+++..++.-++. .+.+++++ T Consensus 5 IaV~s~KGGVGKTT~avNLA~aLA~--~G~kVlli 37 (270) T PRK10818 5 IVVTSGKGGVGKTTSSAAIATGLAQ--KGKKTVVI 37 (270) T ss_pred EEEECCCCCCCHHHHHHHHHHHHHH--CCCCEEEE T ss_conf 9997899984189999999999997--79968999 No 303 >PRK08149 ATP synthase SpaL; Validated Probab=78.45 E-value=2.8 Score=20.70 Aligned_cols=38 Identities=21% Similarity=0.238 Sum_probs=26.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 4776148867889999999999997089977999715379999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) |+.|-+|.|+|||++.++++-+ -+..++|.|--...-+ T Consensus 152 R~gIf~gsGvGKs~Ll~~i~~~-----~~adv~Via~IGeRgr 189 (427) T PRK08149 152 RMGIFASAGCGKTMLMNMLIEH-----TEADVFVIGLIGERGR 189 (427) T ss_pred EEECCCCCCCCHHHHHHHHHHH-----CCCCEEEEEEECCCHH T ss_conf 4000278998677999988863-----5899899997023378 No 304 >KOG0385 consensus Probab=78.42 E-value=4.6 Score=19.35 Aligned_cols=172 Identities=16% Similarity=0.138 Sum_probs=86.4 Q ss_pred HCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH-CCCCEEEEEC Q ss_conf 014668884436668428999999988887512455555411247761488678899999999999970-8997799971 Q gi|254781187|r 36 FPWGIKGKPLEHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST-RPGMSIICIA 114 (367) Q Consensus 36 ~~w~~~~~~~~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~-~~~~~v~~~A 114 (367) -||+.++.. .+.+|.+=|.=+.---+++.+ ...+---|.|||.-+-.++.++... .-+.-.+|++ T Consensus 159 sP~~v~~g~------lr~YQveGlnWLi~l~engin--------gILaDEMGLGKTlQtIs~l~yl~~~~~~~GPfLVi~ 224 (971) T KOG0385 159 SPSYVKGGE------LRDYQLEGLNWLISLYENGIN--------GILADEMGLGKTLQTISLLGYLKGRKGIPGPFLVIA 224 (971) T ss_pred CCHHHCCCC------CCHHHHCCHHHHHHHHHCCCC--------CEEEHHCCCCHHHHHHHHHHHHHHHCCCCCCEEEEE T ss_conf 832214785------543320337999999865766--------584231045338999999999998517999849981 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCC---CCCCCCCCCCCCC Q ss_conf 5379999999999999998623121123333210001233322111134577612662101354---4556521011358 Q gi|254781187|r 115 NSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSE---ERPDTFVGPHNTH 191 (367) Q Consensus 115 ~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~---~~~ea~~g~h~~~ 191 (367) |.. .+. -...|+++|.-.++.-....-...+.. ...++.. .+ .+....|+=+ .....+. ..+ T Consensus 225 P~S-tL~-NW~~Ef~rf~P~l~~~~~~Gdk~eR~~--------~~r~~~~-~~-~fdV~iTsYEi~i~dk~~lk---~~~ 289 (971) T KOG0385 225 PKS-TLD-NWMNEFKRFTPSLNVVVYHGDKEERAA--------LRRDIML-PG-RFDVCITSYEIAIKDKSFLK---KFN 289 (971) T ss_pred EHH-HHH-HHHHHHHHHCCCCCEEEEECCHHHHHH--------HHHHHHC-CC-CCCEEEEHHHHHHHHHHHHH---CCC T ss_conf 276-678-999999976898634988479999999--------9998531-57-87668640788986688986---199 Q ss_pred CCEEEEECCCCCCHHH--HHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHH Q ss_conf 6289997545599889--9998987406988258999807899987688754 Q gi|254781187|r 192 GMAVFNDEASGTPDII--NKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIF 241 (367) Q Consensus 192 ~~l~ivDEAsgI~d~i--~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~ 241 (367) .-++|+|||.-|.+.- ...+.--+.. .+++ +++|+|--+ -.+++| T Consensus 290 W~ylvIDEaHRiKN~~s~L~~~lr~f~~-~nrL--LlTGTPLQN--NL~ELW 336 (971) T KOG0385 290 WRYLVIDEAHRIKNEKSKLSKILREFKT-DNRL--LLTGTPLQN--NLHELW 336 (971) T ss_pred CEEEEECHHHHHCCHHHHHHHHHHHHCC-CCEE--EEECCCCCC--CHHHHH T ss_conf 3499952365414624489999998566-5526--752785436--499999 No 305 >TIGR03496 FliI_clade1 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively. Probab=78.24 E-value=4.7 Score=19.32 Aligned_cols=36 Identities=22% Similarity=0.407 Sum_probs=25.3 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH Q ss_conf 47761488678899999999999970899779997153799 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ 119 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q 119 (367) |+.|-+|.|+|||++.++++-+ -+..++|++--... T Consensus 139 R~gIf~g~GvGKs~Ll~~ia~~-----~~adv~VialIGeR 174 (411) T TIGR03496 139 RIGIFAGSGVGKSVLLGMMARY-----TEADVVVVGLIGER 174 (411) T ss_pred EEEECCCCCCCHHHHHHHHHHC-----CCCCEEEEECCCCC T ss_conf 3132279998677999999753-----48988999532530 No 306 >COG0455 flhG Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility] Probab=78.17 E-value=4.7 Score=19.30 Aligned_cols=35 Identities=26% Similarity=0.328 Sum_probs=24.6 Q ss_pred EEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 247761488-67889999999999997089977999 Q gi|254781187|r 78 FKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIIC 112 (367) Q Consensus 78 ~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~ 112 (367) ..++|.||. |+|||+++|.+....+.......+++ T Consensus 3 ~~Iav~SgKGGvGKTtitanlga~~~~~~~k~V~~i 38 (262) T COG0455 3 KVIAVVSGKGGVGKTTITANLGAALAALGGKVVLLI 38 (262) T ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEE T ss_conf 899998458875689899869999996489769999 No 307 >PRK10689 transcription-repair coupling factor; Provisional Probab=78.12 E-value=4.7 Score=19.29 Aligned_cols=59 Identities=12% Similarity=0.131 Sum_probs=37.2 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHH Q ss_conf 9999999888875124555554112477614886788999999999999708997799971537999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQL 120 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~ 120 (367) =|.++..+|-+..+++. .|=|+ ||+==|.|||-++...+. .+...|..|.+.+||.==+ T Consensus 604 DQl~AI~eV~~DMes~~-----PMDRL-iCGDVGfGKTEVA~RAAF--kav~~gkQVavlvPTTiLA 662 (1148) T PRK10689 604 DQAQAINAVLSDMCQPL-----AMDRL-VCGDVGFGKTEVAMRAAF--LAVENHKQVAVLVPTTLLA 662 (1148) T ss_pred HHHHHHHHHHHHHHCCC-----CCCEE-EECCCCCCHHHHHHHHHH--HHHHCCCEEEEEECCCCCH T ss_conf 89999999987763886-----77415-676888877999999999--9996398089983662237 No 308 >cd01863 Rab18 Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of mos Probab=77.99 E-value=2.2 Score=21.31 Aligned_cols=21 Identities=24% Similarity=0.414 Sum_probs=18.5 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) +|++|.+..|+|||.++..++ T Consensus 1 ~KivvvG~~~vGKTsli~r~~ 21 (161) T cd01863 1 LKILLIGDSGVGKSSLLLRFT 21 (161) T ss_pred CEEEEECCCCCCHHHHHHHHH T ss_conf 989999979957999999996 No 309 >TIGR02868 CydC ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC; InterPro: IPR014223 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents CydC, a member of a heterodimeric ATP-binding cassette-type transporter (ABC transporter). It is involved in the export of glutathione from the cytoplasm to the periplasm and is required for the assembly of both cytochrome c and cytochrome bd , , .; GO: 0042626 ATPase activity coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane. Probab=77.96 E-value=2.5 Score=21.05 Aligned_cols=72 Identities=21% Similarity=0.200 Sum_probs=41.1 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCE--EEEECCCHHHHHHHHHHHHHHHH Q ss_conf 9999998888751245555541124776148867889999999999997089977--99971537999999999999999 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMS--IICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~--v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) |..+|+.|.=++. .-.|++|.+.=|+|||++.+.+.= ..|+.+ +.+.--.-.++. -.|+.+.+ T Consensus 373 ~~~vl~~V~L~l~--------~G~r~Ai~G~SG~GKsTLL~~L~G----~l~P~~G~vtl~G~~~~~~~---~~evrr~v 437 (566) T TIGR02868 373 PPNVLDGVSLDLP--------PGERVAILGPSGSGKSTLLATLAG----LLDPLQGEVTLDGVPVSSLS---EDEVRRRV 437 (566) T ss_pred CHHHHCCCCCCCC--------CCCCEEEECCCCCCHHHHHHHHHH----HCCCCCCCEEECCCCHHHCC---CCHHEHHE T ss_conf 3465427864113--------886089866887657899999984----02899991787773243257---31100000 Q ss_pred HHCCC-CCCC Q ss_conf 86231-2112 Q gi|254781187|r 133 SMLPH-RHWF 141 (367) Q Consensus 133 ~~~~~-~~~~ 141 (367) ..++- -|.| T Consensus 438 ~~~aQ~aHlF 447 (566) T TIGR02868 438 SVFAQDAHLF 447 (566) T ss_pred EECCCCCCCC T ss_conf 3127886211 No 310 >PRK08927 fliI flagellum-specific ATP synthase; Validated Probab=77.96 E-value=3.3 Score=20.26 Aligned_cols=39 Identities=21% Similarity=0.266 Sum_probs=27.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH Q ss_conf 47761488678899999999999970899779997153799999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN 122 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~ 122 (367) |+.|-+|.|+|||++.++++-. -...++|.|--...-++ T Consensus 160 RigIfagsGvGKs~Ll~~i~r~-----~~adv~VialIGeRgrE 198 (441) T PRK08927 160 RLGIFAGSGVGKSVLLSMLARN-----TDADVSVIGLIGERGRE 198 (441) T ss_pred EEEECCCCCCCHHHHHHHHHHH-----CCCCCEEEEECCCCHHH T ss_conf 6663168999878999999864-----16773787522651899 No 311 >TIGR02746 TraC-F-type type-IV secretion system protein TraC; InterPro: IPR014117 The proteins in this entry are found in the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The proteins contain the Walker A and B motifs and so are putative nucleotide triphosphatases.. Probab=77.93 E-value=4.8 Score=19.26 Aligned_cols=47 Identities=21% Similarity=0.326 Sum_probs=37.1 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH Q ss_conf 24776148867889999999999997089977999715379999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL 124 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l 124 (367) |+++|.++=|.|||+++-.+++=.+...-..-|+=+--++..+...+ T Consensus 490 YN~~~~g~sG~GKSf~~Q~~~~~~L~~G~kv~viDvG~Sy~KLC~~l 536 (900) T TIGR02746 490 YNIAVVGGSGAGKSFFMQELIVSVLSRGGKVWVIDVGRSYKKLCEML 536 (900) T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHH T ss_conf 14899728898716879899999851798489996078848887651 No 312 >PRK07960 fliI flagellum-specific ATP synthase; Validated Probab=77.92 E-value=2.7 Score=20.82 Aligned_cols=39 Identities=21% Similarity=0.366 Sum_probs=26.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH Q ss_conf 47761488678899999999999970899779997153799999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN 122 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~ 122 (367) |+.|-+|.|+|||++.++++-. ....++|++--...-++ T Consensus 177 RigIfagsGvGKs~Ll~~iar~-----~~adv~Vi~lIGERgrE 215 (455) T PRK07960 177 RMGLFAGSGVGKSVLLGMMARY-----TRADVIVVGLIGERGRE 215 (455) T ss_pred EEECCCCCCCCHHHHHHHHHHH-----HCCCEEEEEEECEEHHH T ss_conf 7632489988499999999886-----08985899720406289 No 313 >PRK13235 nifH nitrogenase reductase; Reviewed Probab=77.91 E-value=4.8 Score=19.26 Aligned_cols=43 Identities=23% Similarity=0.298 Sum_probs=31.8 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHH Q ss_conf 1247761488678899999999999970899779997--15379999 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSETQLK 121 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~Q~~ 121 (367) |.++||-.==|+|||+.++.+...++-. |.||+++ =|..+..+ T Consensus 1 m~~iaiyGKGGVGKSTtt~NLaAALA~~--GkkVl~IgcDPk~dsT~ 45 (274) T PRK13235 1 MRKVAIYGKGGIGKSTTTQNTVAGLAEM--GKKVMVVGCDPKADSTR 45 (274) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEECCCCCCCHHH T ss_conf 9679997998554767899999999978--99799989898453667 No 314 >pfam00485 PRK Phosphoribulokinase / Uridine kinase family. In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain. Probab=77.90 E-value=2.1 Score=21.49 Aligned_cols=22 Identities=23% Similarity=0.359 Sum_probs=18.6 Q ss_pred EEEECCCCCCHHHHHHHHHHHH Q ss_conf 7761488678899999999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~ 101 (367) +.|++|-|+|||+++..+.--+ T Consensus 2 IgIaG~SgSGKTT~a~~L~~~l 23 (196) T pfam00485 2 IGVAGSSGAGKTTVARTFVSIF 23 (196) T ss_pred EEEECCCCCCHHHHHHHHHHHH T ss_conf 8998998571999999999996 No 315 >PRK07721 fliI flagellum-specific ATP synthase; Validated Probab=77.88 E-value=3.6 Score=20.02 Aligned_cols=38 Identities=26% Similarity=0.302 Sum_probs=26.2 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 4776148867889999999999997089977999715379999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) |+.|-+|.|+|||++.++++-+- ...++|.+--...-+ T Consensus 158 RigIf~gsGvGKs~Ll~~iar~~-----~adv~V~~liGeR~r 195 (435) T PRK07721 158 RVGIFAGSGVGKSTLMGMIARQT-----SADLNVIALIGERGR 195 (435) T ss_pred EEEECCCCCCCHHHHHHHHHHHH-----CCCEEEEEEECCCHH T ss_conf 41002689987899999998874-----488258999332028 No 316 >PRK03321 putative aminotransferase; Provisional Probab=77.87 E-value=4.8 Score=19.25 Aligned_cols=58 Identities=21% Similarity=0.230 Sum_probs=35.2 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 42899999998888751245555541124776148867889999999999997089977999715379999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) |+....++-++|+++..-... ++.| |.|+ +.+ ...+-.+++.|+.+|++..|++..-. T Consensus 55 Pd~~~~~Lr~aiA~~~~v~~~-------~I~v--~nGs--~e~--i~~~~~~~~~~gd~Vl~p~P~f~~Y~ 112 (352) T PRK03321 55 PDNGAVELRAALAEHLGVAPE-------HVAV--GCGS--VAL--CQQLVQATAGPGDEVVFAWRSFEAYP 112 (352) T ss_pred CCCCHHHHHHHHHHHHCCCHH-------HEEE--CCCH--HHH--HHHHHHHHHCCCCEEEECCCCHHHHH T ss_conf 899869999999998787858-------7998--7469--999--99999998179798998888532689 No 317 >PRK05688 fliI flagellum-specific ATP synthase; Validated Probab=77.86 E-value=2.2 Score=21.33 Aligned_cols=46 Identities=24% Similarity=0.380 Sum_probs=28.4 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHH Q ss_conf 47761488678899999999999970899779997153799999999999999986 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSM 134 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~ 134 (367) |+.|-+|+|+|||++.++++-+ -...++|++--.... +|++.+++. T Consensus 170 R~gIfggsGvGKS~Ll~~i~r~-----~~adv~Vi~lIGERg-----rEv~efi~~ 215 (451) T PRK05688 170 RLGLFAGTGVGKSVLLGMMTRF-----TEADIIVVGLIGERG-----REVKEFIEH 215 (451) T ss_pred EEEECCCCCCCHHHHHHHHHHH-----HCCCEEEEEEEEEEH-----HHHHHHHHH T ss_conf 6421048898689999999885-----279869999612775-----999999999 No 318 >PRK03158 histidinol-phosphate aminotransferase; Provisional Probab=77.85 E-value=2.9 Score=20.62 Aligned_cols=59 Identities=14% Similarity=0.219 Sum_probs=36.5 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH Q ss_conf 428999999988887512455555411247761488678899999999999970899779997153799999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN 122 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~ 122 (367) |+.-..++-+.|+++..-... .+.| |. |=+- +..++..+++.|+.+|++.+|++..-.. T Consensus 62 Pd~~~~~Lr~~iA~~~gv~~~-------~I~v--~n--Gs~e--~i~~~~~~~~~~g~~vvi~~P~f~~Y~~ 120 (359) T PRK03158 62 PDGYAFELRTKVAKHLGVKEE-------QLIF--GN--GSDE--VIQIISRALLHEGTNTVMANPTFSQYRH 120 (359) T ss_pred CCCCHHHHHHHHHHHHCCCHH-------HEEE--CC--CHHH--HHHHHHHHHHCCCCEEECCCCEEEHHHH T ss_conf 698889999999998684867-------7998--47--8899--9999999980799811137982055599 No 319 >cd01131 PilT Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility. Probab=77.74 E-value=3.8 Score=19.87 Aligned_cols=35 Identities=23% Similarity=0.339 Sum_probs=25.7 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 776148867889999999999997089977999715 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) +.|+++-|+|||+..+.++-+. ..+.+.+++.+.. T Consensus 4 iLitG~TGSGKTTtl~all~~i-~~~~~~~IiTiED 38 (198) T cd01131 4 VLVTGPTGSGKSTTLAAMIDYI-NKNKTHHILTIED 38 (198) T ss_pred EEEECCCCCCHHHHHHHHHHHH-CCCCCCEEEEECC T ss_conf 9998999997999999999853-6378836999647 No 320 >PRK09435 arginine/ornithine transport system ATPase; Provisional Probab=77.72 E-value=4.9 Score=19.22 Aligned_cols=59 Identities=22% Similarity=0.330 Sum_probs=40.4 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE--ECCCHHHHH Q ss_conf 899999998888751245555541124776148867889999999999997089977999--715379999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC--IANSETQLK 121 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~--~A~t~~Q~~ 121 (367) ..-.++|+.+..|. ...+++-|.+.-|+|||+++..++..+... +.+|.| +-|+..-.. T Consensus 33 ~~~~~ll~~l~~~~--------g~a~~iGiTG~pG~GKStli~~l~~~~~~~--g~~v~vlavDPsS~~sg 93 (325) T PRK09435 33 ALAQELLDALLPHT--------GNALRIGITGVPGVGKSTFIEALGMHLIEQ--GHKVAVLAVDPSSTRTG 93 (325) T ss_pred HHHHHHHHHHHHCC--------CCCEEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEEECCCCCCCC T ss_conf 99999999863017--------982599742799986889999999999967--98589999789999888 No 321 >PRK07594 type III secretion system ATPase; Validated Probab=77.61 E-value=3.3 Score=20.23 Aligned_cols=38 Identities=21% Similarity=0.258 Sum_probs=25.2 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 4776148867889999999999997089977999715379999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) |+.|-+|+|+|||++.++++. +....+.|.+--...-+ T Consensus 157 R~gIfgg~GvGKTtLl~~i~~-----~~~adv~V~~lIGERgr 194 (433) T PRK07594 157 RVGIFSAPGVGKSTLLAMLCN-----APDADSNVLVLIGERGR 194 (433) T ss_pred EEEECCCCCCCHHHHHHHHHH-----CCCCCCEEEEEECCCHH T ss_conf 742047899985589999984-----24798159999410048 No 322 >COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion] Probab=77.61 E-value=4.9 Score=19.20 Aligned_cols=62 Identities=16% Similarity=0.061 Sum_probs=37.4 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHH Q ss_conf 9999998888751245555541124776148867889999999999997089-977999715379 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSET 118 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~ 118 (367) -.+.++.+-.+.-.+....+ -.-++..++.|+|||+..|=++.-+..... ....++|-.|++ T Consensus 183 ~~~~l~~~~~~~~~~~~~~~--~~vi~LVGPTGVGKTTTlAKLAar~~~~~~~~kVaiITtDtYR 245 (407) T COG1419 183 FSEKLRKLLLSLIENLIVEQ--KRVIALVGPTGVGKTTTLAKLAARYVMLKKKKKVAIITTDTYR 245 (407) T ss_pred HHHHHHHHHHHHCCCCCCCC--CCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCH T ss_conf 79999998876441111246--8579998998875887999999999753257606899714411 No 323 >cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine. Probab=77.60 E-value=2.2 Score=21.32 Aligned_cols=22 Identities=36% Similarity=0.481 Sum_probs=18.3 Q ss_pred EEEECCCCCCHHHHHHHHHHHH Q ss_conf 7761488678899999999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~ 101 (367) ++|+++-|+|||+++..+.--+ T Consensus 2 IgI~G~sgsGKTT~a~~L~~~l 23 (198) T cd02023 2 IGIAGGSGSGKTTVAEEIIEQL 23 (198) T ss_pred EEEECCCCCCHHHHHHHHHHHH T ss_conf 8988999885999999999980 No 324 >COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair] Probab=77.55 E-value=4.9 Score=19.19 Aligned_cols=69 Identities=17% Similarity=0.184 Sum_probs=47.9 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH Q ss_conf 42899999998888751245555541124776148867889999999999997089977999715379999999999999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) |.-=|-++.+.+.+.++++.. +.+ ..+-.|+|||+.+|..+-- -..-.+|+|+...-+ .-++.|+|. T Consensus 13 PaGDQP~AI~~Lv~gi~~g~~------~Qt-LLGvTGSGKTfT~AnVI~~-----~~rPtLV~AhNKTLA-aQLy~Efk~ 79 (663) T COG0556 13 PAGDQPEAIAELVEGIENGLK------HQT-LLGVTGSGKTFTMANVIAK-----VQRPTLVLAHNKTLA-AQLYSEFKE 79 (663) T ss_pred CCCCCHHHHHHHHHHHHCCCE------EEE-EEEECCCCCHHHHHHHHHH-----HCCCEEEEECCHHHH-HHHHHHHHH T ss_conf 999867999999988863860------258-8620368831079999998-----689719982555479-999999997 Q ss_pred HH Q ss_conf 99 Q gi|254781187|r 131 WL 132 (367) Q Consensus 131 ~~ 132 (367) +. T Consensus 80 fF 81 (663) T COG0556 80 FF 81 (663) T ss_pred HC T ss_conf 68 No 325 >pfam03266 DUF265 Protein of unknown function, DUF265. Probab=77.50 E-value=4.9 Score=19.19 Aligned_cols=60 Identities=13% Similarity=0.120 Sum_probs=35.4 Q ss_pred CCCEEEEECCCCC---CHHHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECC Q ss_conf 8628999754559---9889999898740698825899980789998768875411223504675233 Q gi|254781187|r 191 HGMAVFNDEASGT---PDIINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDT 255 (367) Q Consensus 191 ~~~l~ivDEAsgI---~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~ 255 (367) +..++++||-... +..+.++++..|.+ +.+.+ ++- |.+....|-+...+ +.+...+.++. T Consensus 95 ~~dlivIDEIG~mEl~s~~F~~~v~~~l~~-~~~vl--~ti-~~~~~~~~v~~i~~-~~d~~i~~vt~ 157 (168) T pfam03266 95 EADLIIIDEIGPMELKSPKFREAIEEVLSS-NKPVL--AVV-HRRSDSPLVERIRR-RPDVKIFVVTE 157 (168) T ss_pred CCCEEEEECCCHHHHHHHHHHHHHHHHHCC-CCCEE--EEE-EECCCCHHHHHHHC-CCCCEEEEECH T ss_conf 898999976314533149999999999669-99799--999-72589838999741-79938999786 No 326 >PRK12289 ribosome-associated GTPase; Reviewed Probab=77.44 E-value=2.5 Score=20.97 Aligned_cols=16 Identities=25% Similarity=0.574 Sum_probs=8.9 Q ss_pred EECCCCCCHHHHHHHH Q ss_conf 6148867889999999 Q gi|254781187|r 82 ISAGRGIGKTTLNAWM 97 (367) Q Consensus 82 v~sgrg~GKS~~~a~~ 97 (367) +++.-|+|||+++-.+ T Consensus 176 ~~G~SGVGKSSLIN~L 191 (351) T PRK12289 176 VAGPSGVGKSSLINRL 191 (351) T ss_pred EECCCCCCHHHHHHHH T ss_conf 9817988788988763 No 327 >cd01864 Rab19 Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet chracterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Probab=77.44 E-value=2.8 Score=20.70 Aligned_cols=23 Identities=22% Similarity=0.343 Sum_probs=20.3 Q ss_pred CEEEEEEECCCCCCHHHHHHHHH Q ss_conf 11247761488678899999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) ++||+.+.+..|+|||.++..++ T Consensus 2 ~~~Kiv~lGd~~vGKTsli~r~~ 24 (165) T cd01864 2 FLFKIILIGDSNVGKTCVVQRFK 24 (165) T ss_pred EEEEEEEECCCCCCHHHHHHHHH T ss_conf 58999999999958999999996 No 328 >PRK12422 chromosomal replication initiation protein; Provisional Probab=77.42 E-value=5 Score=19.17 Aligned_cols=53 Identities=19% Similarity=0.188 Sum_probs=35.1 Q ss_pred HHHHHHHHHHHCC-CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 9999888875124-5555541124776148867889999999999997089977999715 Q gi|254781187|r 57 EFMEAVDVHCHSN-VNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 57 ~~l~~~~~~~~~~-~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) .+..+++.....+ ...++| +-|-++-|.|||+|.-++.... ..++.+|+++.. T Consensus 124 ~aa~~va~~~~~~~g~~yNP----LfIyG~~GlGKTHLL~AIgn~i--~~~~~kV~Yvta 177 (455) T PRK12422 124 RILQEFAKVSEQGKGFPFNP----IYLFGPEGSGKTHLMQAAVSAL--RESGGKILYVSS 177 (455) T ss_pred HHHHHHHHCCCCCCCCCCCC----EEEECCCCCCHHHHHHHHHHHH--HCCCCEEEEECH T ss_conf 99999983755358876787----5887899997899999999985--379986999749 No 329 >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=77.36 E-value=5 Score=19.16 Aligned_cols=35 Identities=26% Similarity=0.358 Sum_probs=23.3 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 4776148867889999999999997089977999715 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) .+.+.+.-|+|||+++..++- .+. +.+..++.+.. T Consensus 21 ~ill~GppGtGKT~la~~ia~-~~~-~~~~~~~~~~~ 55 (151) T cd00009 21 NLLLYGPPGTGKTTLARAIAN-ELF-RPGAPFLYLNA 55 (151) T ss_pred EEEEECCCCCCHHHHHHHHHH-HHC-CCCCCEEEEEH T ss_conf 089989999886599999999-712-13798278547 No 330 >cd01892 Miro2 Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. Probab=77.23 E-value=3.1 Score=20.44 Aligned_cols=23 Identities=26% Similarity=0.585 Sum_probs=20.3 Q ss_pred CEEEEEEECCCCCCHHHHHHHHH Q ss_conf 11247761488678899999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) ++|++.|.+-.|+|||.++-.++ T Consensus 3 ~vfk~~VlG~~~VGKTsLi~rf~ 25 (169) T cd01892 3 NVFLCFVLGAKGSGKSALLRAFL 25 (169) T ss_pred EEEEEEEECCCCCCHHHHHHHHH T ss_conf 08999999999988999999996 No 331 >PRK10263 DNA translocase FtsK; Provisional Probab=77.21 E-value=3.4 Score=20.21 Aligned_cols=47 Identities=17% Similarity=0.156 Sum_probs=34.4 Q ss_pred CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC--CEEEEECCC Q ss_conf 55555411247761488678899999999999970899--779997153 Q gi|254781187|r 70 VNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG--MSIICIANS 116 (367) Q Consensus 70 ~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~--~~v~~~A~t 116 (367) ...++..|.-+.|++..|+|||.++-.+|+=+|....+ .|.|.+-|+ T Consensus 1003 vv~DLaKMPHLLIAGtTGSGKSV~iNsmI~SlLyk~~PdevrlImIDPK 1051 (1355) T PRK10263 1003 VVADLAKMPHLLVAGTTGSGKSVGVNAMILSMLYKAQPEDVRFIMIDPK 1051 (1355) T ss_pred EEEEHHHCCCEEEECCCCCCCHHHHHHHHHHHHHCCCHHHEEEEEECCC T ss_conf 7747421971134046788830439999999984388879479986687 No 332 >PRK08972 fliI flagellum-specific ATP synthase; Validated Probab=77.06 E-value=3.8 Score=19.88 Aligned_cols=38 Identities=21% Similarity=0.330 Sum_probs=26.6 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 4776148867889999999999997089977999715379999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) |+.|-+|.|+|||++.++++- +....++|++--...-+ T Consensus 162 RigIf~gsGvGKS~Ll~~i~r-----~~~advvVi~lIGERgr 199 (440) T PRK08972 162 RMGLFAGSGVGKSVLLGMMTR-----GTTADVIVVGLVGERGR 199 (440) T ss_pred EEEECCCCCCCHHHHHHHHHH-----CCCCCEEEEEEECEEHH T ss_conf 666315789758999988875-----14787899986231369 No 333 >cd01867 Rab8_Rab10_Rab13_like Rab8/Sec4/Ypt2. Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhi Probab=77.02 E-value=2.9 Score=20.58 Aligned_cols=23 Identities=26% Similarity=0.417 Sum_probs=20.1 Q ss_pred CEEEEEEECCCCCCHHHHHHHHH Q ss_conf 11247761488678899999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) +.+|+.+.+..|+|||.++..++ T Consensus 2 y~~KivlvGd~~vGKTsli~r~~ 24 (167) T cd01867 2 YLFKLLLIGDSGVGKSCLLLRFS 24 (167) T ss_pred EEEEEEEECCCCCCHHHHHHHHH T ss_conf 68999999999978899999996 No 334 >PRK08533 flagellar accessory protein FlaH; Reviewed Probab=77.02 E-value=5.1 Score=19.10 Aligned_cols=44 Identities=18% Similarity=0.192 Sum_probs=27.8 Q ss_pred CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHH Q ss_conf 411247761488678899999999999970899779997--1537999 Q gi|254781187|r 75 PTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSETQL 120 (367) Q Consensus 75 ~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~Q~ 120 (367) |.-.-+.|.+..|+|||.++.-++. ..+. .+.+++++ ..|.++. T Consensus 22 p~gs~~li~G~~GtGKsi~~~~~~~-~~l~-~g~~~~yis~e~t~~~~ 67 (230) T PRK08533 22 PFGSIILIEGDESTGKSILSQRLAY-GFLQ-NGYSVSYVSSQLTTTEF 67 (230) T ss_pred CCCCEEEEECCCCCCHHHHHHHHHH-HHHH-CCCEEEEEEECCCHHHH T ss_conf 8984899986899878999999999-9987-89869999943899999 No 335 >cd01865 Rab3 Rab3 subfamily. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promot Probab=77.00 E-value=2.6 Score=20.89 Aligned_cols=23 Identities=26% Similarity=0.297 Sum_probs=19.2 Q ss_pred EEEEEEECCCCCCHHHHHHHHHH Q ss_conf 12477614886788999999999 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~l 99 (367) +||+.+.+..|+|||.++..++- T Consensus 1 ~~KivllGd~~VGKTsli~r~~~ 23 (165) T cd01865 1 MFKLLIIGNSSVGKTSFLFRYAD 23 (165) T ss_pred CEEEEEECCCCCCHHHHHHHHHC T ss_conf 98999999999688999999924 No 336 >pfam02367 UPF0079 Uncharacterized P-loop hydrolase UPF0079. This uncharacterized family contains a P-loop. Probab=76.90 E-value=4.1 Score=19.65 Aligned_cols=49 Identities=18% Similarity=0.105 Sum_probs=34.8 Q ss_pred HHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH Q ss_conf 99998888751245555541124776148867889999999999997089977999715379 Q gi|254781187|r 57 EFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET 118 (367) Q Consensus 57 ~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~ 118 (367) ++-+.++..++.+. -+...+.=|+|||+++-.++--+ +...-|++||+. T Consensus 3 ~lg~~ia~~l~~G~--------vi~L~G~LGaGKTtfvr~i~~~l-----g~~~~V~SPTF~ 51 (123) T pfam02367 3 NLGKRLAQLLKAGD--------VVLLSGDLGAGKTTFVRGLAKGL-----GITGNVTSPTFT 51 (123) T ss_pred HHHHHHHHHCCCCC--------EEEEECCCCCCHHHHHHHHHHHC-----CCCCCCCCCCEE T ss_conf 99999997689997--------99998887788999999999985-----998873799558 No 337 >PRK06002 fliI flagellum-specific ATP synthase; Validated Probab=76.76 E-value=2.3 Score=21.22 Aligned_cols=21 Identities=43% Similarity=0.602 Sum_probs=18.0 Q ss_pred EEEEECCCCCCHHHHHHHHHH Q ss_conf 477614886788999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~l 99 (367) |+.|-+|+|+|||++.++++- T Consensus 167 R~gIfgg~GvGKTtLl~~i~~ 187 (450) T PRK06002 167 RIGIFAGSGVGKSTLLAMLAR 187 (450) T ss_pred EEEECCCCCCCHHHHHHHHHH T ss_conf 777426899987599999986 No 338 >pfam01580 FtsK_SpoIIIE FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from E. coli and the stage III sporulation protein E SpoIIIE which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer. Probab=76.71 E-value=5.2 Score=19.05 Aligned_cols=41 Identities=20% Similarity=0.245 Sum_probs=31.6 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCC--CEEEEECCCH Q ss_conf 1247761488678899999999999970899--7799971537 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPG--MSIICIANSE 117 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~--~~v~~~A~t~ 117 (367) ...+.|.+.-|+|||.+.-.++..++..+.+ .+++++-++. T Consensus 38 ~pH~Lv~G~tGsGKS~~l~~li~sl~~~~~p~~v~l~liD~K~ 80 (202) T pfam01580 38 MPHLLIAGATGSGKSTFLNTLILSLAARHSPEEVRLYLIDPKG 80 (202) T ss_pred CCCEEEECCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEECCCC T ss_conf 8868996589998009999999999873796206999974896 No 339 >PRK00741 prfC peptide chain release factor 3; Provisional Probab=76.68 E-value=2.6 Score=20.94 Aligned_cols=137 Identities=13% Similarity=0.066 Sum_probs=67.4 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC--HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 1247761488678899999999999970899779997153--79999999999999998623121123333210001233 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANS--ETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWY 154 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t--~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~ 154 (367) +++++|.|.-|.|||+++-.+++.--..+.-.+| -+.+ .+...| |-++.+-....+...... ..|. T Consensus 10 ~RniaIi~H~dAGKTTLtE~lL~~~GaI~~~G~V--~~~~~~~~~~sD--~~~~E~~RgiSI~ssv~~--------~e~~ 77 (526) T PRK00741 10 RRTFAIISHPDAGKTTLTEKLLLFGGAIQEAGTV--KGRKSGRHATSD--WMEMEKQRGISVTSSVMQ--------FPYR 77 (526) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCEE--ECCCCCCCCCCC--CCHHHHHCCCEEECCEEE--------EEEC T ss_conf 1779999378989899999999746752448466--314678864678--858899759648615177--------8678 Q ss_pred CCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCC---HHHHHHHHHHHHCCCCCEEEEEEECCC Q ss_conf 32211113457761266210135445565210113586289997545599---889999898740698825899980789 Q gi|254781187|r 155 AELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTP---DIINKSILGFFTELNPNRFWIMTSNTR 231 (367) Q Consensus 155 ~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~---d~i~e~i~g~Lt~~~~~~~~i~igNP~ 231 (367) . . ...++..-+......|...+++.-...++++|=++||. ..+|+++. ..+-+.+ ++-|=- T Consensus 78 ~--~--------~iNliDTPGh~DF~~e~~raL~a~D~Av~Vida~~GVe~qTe~~w~~~~----~~~iP~i--~FINKm 141 (526) T PRK00741 78 D--C--------LINLLDTPGHEDFSEDTYRTLTAVDSALMVIDAAKGVEPQTRKLMEVCR----LRDTPIF--TFINKL 141 (526) T ss_pred C--E--------EEEEEECCCCHHHHHHHHHHHHHHCEEEEEEECCCCCCHHHHHHHHHHH----HCCCCEE--EEEECC T ss_conf 9--8--------9999909894677899999998737599999777552333689999988----6399889--999656 Q ss_pred C-CCCHHHHHH Q ss_conf 9-987688754 Q gi|254781187|r 232 R-LNGWFYDIF 241 (367) Q Consensus 232 r-~~g~Fye~~ 241 (367) . ..--|.++. T Consensus 142 DR~~ad~~~~l 152 (526) T PRK00741 142 DRDGREPLELL 152 (526) T ss_pred CCCCCCHHHHH T ss_conf 76789878988 No 340 >PHA02518 ParA-like protein; Provisional Probab=76.63 E-value=3.1 Score=20.40 Aligned_cols=28 Identities=29% Similarity=0.548 Sum_probs=21.2 Q ss_pred CCCCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 886788999999999999708997799971 Q gi|254781187|r 85 GRGIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 85 grg~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) ==|+|||+++..++.++.. .+.+|+++= T Consensus 9 KGGvGKTT~a~nLA~~la~--~G~~VlliD 36 (211) T PHA02518 9 KGGAGKTTVATNLASWLHA--DGHKVLLVD 36 (211) T ss_pred CCCCHHHHHHHHHHHHHHH--CCCCEEEEE T ss_conf 9997499999999999997--899489997 No 341 >PRK08472 fliI flagellum-specific ATP synthase; Validated Probab=76.59 E-value=3.1 Score=20.39 Aligned_cols=22 Identities=41% Similarity=0.531 Sum_probs=19.6 Q ss_pred EEEEECCCCCCHHHHHHHHHHH Q ss_conf 4776148867889999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLW 100 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw 100 (367) |+.|-+|+|+|||++.+.++.+ T Consensus 160 R~gIf~g~GvGKt~Ll~~i~~~ 181 (435) T PRK08472 160 KLGIFAGSGVGKSTLMGMIVKG 181 (435) T ss_pred EEECCCCCCCCCCHHHHHHHHH T ss_conf 6512358999833578888776 No 342 >PRK13909 putative recombination protein RecB; Provisional Probab=76.57 E-value=5.2 Score=19.02 Aligned_cols=40 Identities=13% Similarity=0.146 Sum_probs=26.2 Q ss_pred CCCEEEEECCCCCCHHHHHHHHHHHH----C---CCCCEEEEEEECCC Q ss_conf 86289997545599889999898740----6---98825899980789 Q gi|254781187|r 191 HGMAVFNDEASGTPDIINKSILGFFT----E---LNPNRFWIMTSNTR 231 (367) Q Consensus 191 ~~~l~ivDEAsgI~d~i~e~i~g~Lt----~---~~~~~~~i~igNP~ 231 (367) .+-.++|||++-.+..-|+.+.+.+. + .+.+. .+++|-|. T Consensus 325 ~~~~ilVDEFQDTn~~Q~~il~~L~~~~~~g~~~~~~~~-lf~VGD~K 371 (911) T PRK13909 325 KISHILIDEFQDTSLLQYKILLPLIDEIKSGEGQSKNRS-FFYVGDVK 371 (911) T ss_pred CCCEEEEEHHCCCCHHHHHHHHHHHHHHHCCCCCCCCCC-EEEECCCC T ss_conf 576899640024899999999999987623555678872-79973773 No 343 >cd04122 Rab14 Rab14 subfamily. Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GT Probab=76.47 E-value=2.9 Score=20.56 Aligned_cols=24 Identities=33% Similarity=0.394 Sum_probs=20.7 Q ss_pred CEEEEEEECCCCCCHHHHHHHHHH Q ss_conf 112477614886788999999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~l 99 (367) +.||+.+.+-.|+|||.++..++- T Consensus 1 y~~KivlvGd~~VGKTsli~r~~~ 24 (166) T cd04122 1 YIFKYIIIGDMGVGKSCLLHQFTE 24 (166) T ss_pred CEEEEEEECCCCCCHHHHHHHHHC T ss_conf 949999999999579999999912 No 344 >PRK06217 hypothetical protein; Validated Probab=76.43 E-value=2.7 Score=20.83 Aligned_cols=28 Identities=29% Similarity=0.297 Sum_probs=21.9 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHH Q ss_conf 1247761488678899999999999970 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLIST 104 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~ 104 (367) |.|+.|.+.-|+|||+++..+.--.-+. T Consensus 1 m~rI~i~G~sGsGkSTla~~La~~l~~~ 28 (185) T PRK06217 1 MMRIHITGASGSGTTTLGAALAEALDLP 28 (185) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHCCC T ss_conf 9679997899887899999999975989 No 345 >pfam07726 AAA_3 ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Probab=76.42 E-value=5.3 Score=19.00 Aligned_cols=24 Identities=21% Similarity=0.371 Sum_probs=20.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHC Q ss_conf 899975455998899998987406 Q gi|254781187|r 194 AVFNDEASGTPDIINKSILGFFTE 217 (367) Q Consensus 194 l~ivDEAsgI~d~i~e~i~g~Lt~ 217 (367) ++++||....++.+..++...|.+ T Consensus 65 vl~lDEin~a~~~v~~~Ll~~l~e 88 (131) T pfam07726 65 VLLADEINRAPPKTQSALLEAMQE 88 (131) T ss_pred CEEEEHHHCCCHHHHHHHHHHHHC T ss_conf 056401203998999999976326 No 346 >COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion] Probab=76.30 E-value=5.3 Score=18.98 Aligned_cols=124 Identities=17% Similarity=0.150 Sum_probs=65.9 Q ss_pred CCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC Q ss_conf 4112477614886788999999999999708997799971-537999999999999999862312112333321000123 Q gi|254781187|r 75 PTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA-NSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGW 153 (367) Q Consensus 75 ~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A-~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~ 153 (367) |++ +.+.+=.|+|||+.+|=++-|+.. .+.+|++.| -|.+-+- -..++-|.+++-.. T Consensus 139 p~V--il~vGVNG~GKTTTIaKLA~~l~~--~g~~VllaA~DTFRAaA---iEQL~~w~er~gv~--------------- 196 (340) T COG0552 139 PFV--ILFVGVNGVGKTTTIAKLAKYLKQ--QGKSVLLAAGDTFRAAA---IEQLEVWGERLGVP--------------- 196 (340) T ss_pred CEE--EEEEECCCCCHHHHHHHHHHHHHH--CCCEEEEEECCHHHHHH---HHHHHHHHHHHCCE--------------- T ss_conf 679--999934888637179999999997--89869998233478999---99999999995992--------------- Q ss_pred CCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH--HHHHHH-------HHHHHCCCCCEEE Q ss_conf 3322111134577612662101354455652101135862899975455998--899998-------9874069882589 Q gi|254781187|r 154 YAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD--IINKSI-------LGFFTELNPNRFW 224 (367) Q Consensus 154 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d--~i~e~i-------~g~Lt~~~~~~~~ 224 (367) ..+...+.|+-+.. -++.+...+.+...+++|-|.-..+ ..++-+ .+.+.+.--++++ T Consensus 197 ---vI~~~~G~DpAaVa----------fDAi~~Akar~~DvvliDTAGRLhnk~nLM~EL~KI~rV~~k~~~~ap~e~ll 263 (340) T COG0552 197 ---VISGKEGADPAAVA----------FDAIQAAKARGIDVVLIDTAGRLHNKKNLMDELKKIVRVIKKDDPDAPHEILL 263 (340) T ss_pred ---EECCCCCCCCHHHH----------HHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEE T ss_conf ---78259999808999----------99999999769999999675544573668999999999846456899842899 Q ss_pred EEEECCCCCC Q ss_conf 9980789998 Q gi|254781187|r 225 IMTSNTRRLN 234 (367) Q Consensus 225 i~igNP~r~~ 234 (367) + +-..++.. T Consensus 264 v-lDAttGqn 272 (340) T COG0552 264 V-LDATTGQN 272 (340) T ss_pred E-EECCCCHH T ss_conf 9-77564756 No 347 >TIGR02784 addA_alphas double-strand break repair helicase AddA; InterPro: IPR014151 AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologues between the alphaproteobacteria and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.. Probab=76.26 E-value=2.9 Score=20.61 Aligned_cols=24 Identities=21% Similarity=0.025 Sum_probs=19.7 Q ss_pred CCEEEEECCCCCCHHHHHHHHHHH Q ss_conf 628999754559988999989874 Q gi|254781187|r 192 GMAVFNDEASGTPDIINKSILGFF 215 (367) Q Consensus 192 ~~l~ivDEAsgI~d~i~e~i~g~L 215 (367) +..++||||+--++.-|++|+-.- T Consensus 397 iDHILvDEAQDTSP~QW~iI~~LA 420 (1190) T TIGR02784 397 IDHILVDEAQDTSPEQWEIIQALA 420 (1190) T ss_pred CCEEEECCHHCCCHHHHHHHHHHH T ss_conf 043771220048865899999998 No 348 >KOG0327 consensus Probab=76.19 E-value=3.7 Score=19.93 Aligned_cols=67 Identities=16% Similarity=0.106 Sum_probs=41.4 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CEEEEECCCHHHHHHHH Q ss_conf 36668428999999988887512455555411247761488678899999999999970899-77999715379999999 Q gi|254781187|r 46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MSIICIANSETQLKNTL 124 (367) Q Consensus 46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~v~~~A~t~~Q~~~~l 124 (367) ++|..|.--|-.+ |..-+.. + .+-+.+--|+||+...+..++-.+.+... +.+++.||+...+..+. T Consensus 44 ~GFekPSaIQqrA---I~p~i~G------~---dv~~qaqsgTgKt~af~i~ilq~iD~~~ke~qalilaPtreLa~q~~ 111 (397) T KOG0327 44 YGFEKPSAIQQRA---ILPCIKG------H---DVIAQAQSGTGKTAAFLISILQQIDMSVKETQALILAPTRELAQQIQ 111 (397) T ss_pred HCCCCCHHHHHCC---CCCCCCC------C---CEEEEEECCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHH T ss_conf 0368822777634---3553468------7---44676302544114667888751374167777988613278889899 No 349 >COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism] Probab=76.16 E-value=3.5 Score=20.07 Aligned_cols=29 Identities=24% Similarity=0.141 Sum_probs=22.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCC Q ss_conf 47761488678899999999999970899 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPG 107 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~ 107 (367) |+.|.++=|+|||+++..++-.+=+.|-+ T Consensus 2 riiilG~pGaGK~T~A~~La~~~~i~hls 30 (178) T COG0563 2 RILILGPPGAGKSTLAKKLAKKLGLPHLD 30 (178) T ss_pred EEEEECCCCCCHHHHHHHHHHHCCCCEEC T ss_conf 79998999998899999999976997855 No 350 >PRK03566 consensus Probab=76.16 E-value=1.5 Score=22.43 Aligned_cols=54 Identities=17% Similarity=0.134 Sum_probs=31.8 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 9999998888751245555541124776148867889999999999997089977999715379999 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) ..++-++|+++..-.. + ++.| |. |=+. +..++..+++.|+.+|++..|++..-. T Consensus 69 ~~~Lr~aiA~~~gv~~-----~--~I~v--~~--Gs~e--~i~l~~~a~~~pGd~Vl~~~P~y~~Y~ 122 (365) T PRK03566 69 GFELKAALAEKLGVPP-----E--QITL--GN--GSND--LLELLARAFLGPGDEIIYSQYAFAVYP 122 (365) T ss_pred HHHHHHHHHHHHCCCH-----H--HEEE--CC--CHHH--HHHHHHHHHCCCCCEEEECCCCHHHHH T ss_conf 8999999999978486-----6--7998--77--8999--999999985589987676688668999 No 351 >PRK13231 nitrogenase reductase-like protein; Reviewed Probab=75.97 E-value=5.4 Score=18.93 Aligned_cols=45 Identities=24% Similarity=0.217 Sum_probs=32.2 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHHHHH Q ss_conf 1247761488678899999999999970899779997--15379999999 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSETQLKNTL 124 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~Q~~~~l 124 (367) |.++||-.==|+|||+.++.+..-++ . +.||+.+ -|+.+..+..+ T Consensus 2 m~~iAiyGKGGIGKSTt~~NlaaalA-~--g~rVl~igcDpk~dst~~L~ 48 (264) T PRK13231 2 LKKIAIYGKGGIGKSTTVSNMAAAYS-S--DNSTLVIGCDPKADTTRTLV 48 (264) T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHH-C--CCCEEEECCCCCCCHHHHHH T ss_conf 42899978985478889999999998-7--99779985688850246761 No 352 >cd04138 H_N_K_Ras_like H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1. Probab=75.91 E-value=3 Score=20.47 Aligned_cols=22 Identities=23% Similarity=0.536 Sum_probs=19.4 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.+.+..|+|||.++..++- T Consensus 2 ~KvvlvGd~~VGKTsli~r~~~ 23 (162) T cd04138 2 YKLVVVGAGGVGKSALTIQLIQ 23 (162) T ss_pred EEEEEECCCCCCHHHHHHHHHH T ss_conf 3999989999889999999983 No 353 >cd04110 Rab35 Rab35 subfamily. Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is Probab=75.84 E-value=3.2 Score=20.32 Aligned_cols=24 Identities=29% Similarity=0.466 Sum_probs=20.9 Q ss_pred CCEEEEEEECCCCCCHHHHHHHHH Q ss_conf 411247761488678899999999 Q gi|254781187|r 75 PTIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 75 ~~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) ...||+.+.+..|+|||.++-.++ T Consensus 4 d~~~KIvlvGd~~VGKTSli~r~~ 27 (199) T cd04110 4 DHLFKLLIIGDSGVGKSSLLLRFA 27 (199) T ss_pred CEEEEEEEECCCCCCHHHHHHHHH T ss_conf 757799999979988899999995 No 354 >PRK06820 type III secretion system ATPase; Validated Probab=75.84 E-value=4.3 Score=19.57 Aligned_cols=35 Identities=23% Similarity=0.302 Sum_probs=24.0 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH Q ss_conf 4776148867889999999999997089977999715379 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET 118 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~ 118 (367) |+.|-+|+|+|||++.+.++.+ -...++|.+--.. T Consensus 165 R~gIfgg~GvGKT~Ll~~i~~~-----~~adv~V~~~IGe 199 (445) T PRK06820 165 RIGIFAAAGVGKSTLLSMLCAD-----SAADVMVLALIGE 199 (445) T ss_pred CCEEECCCCCCCCHHHHHHHHH-----CCCCEEEEEEEEE T ss_conf 4211068999812234456530-----6788799998744 No 355 >PRK07196 fliI flagellum-specific ATP synthase; Validated Probab=75.65 E-value=5.5 Score=18.87 Aligned_cols=38 Identities=16% Similarity=0.365 Sum_probs=25.8 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 4776148867889999999999997089977999715379999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) |+.|-+|.|+|||++.++++-. ....++|.+--...-+ T Consensus 157 RigIfggsGvGKs~Ll~~I~r~-----~~advvVi~lIGeRgr 194 (434) T PRK07196 157 RVGLMAGSGVGKSVLLGMITRY-----TQADVVVVGLIGERGR 194 (434) T ss_pred EEEECCCCCCCHHHHHHHHHHH-----HCCCEEEEEECCEEHH T ss_conf 4210147899789999999897-----3799899974222349 No 356 >TIGR00958 3a01208 antigen peptide transporter 2; InterPro: IPR005293 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Proteins of this family are involved in the transport of antigens from the cytoplasm to a membrane-bound compartment for association with MHC class I molecules.; GO: 0005215 transporter activity, 0006810 transport. Probab=75.63 E-value=2.5 Score=21.05 Aligned_cols=23 Identities=26% Similarity=0.307 Sum_probs=19.2 Q ss_pred EEEEECCCCCCHHHHHHHHHHHH Q ss_conf 47761488678899999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~ 101 (367) =+|+.++-|.|||+++|.+-..+ T Consensus 561 vvALVGPsGsGKStvaaLL~n~Y 583 (770) T TIGR00958 561 VVALVGPSGSGKSTVAALLQNLY 583 (770) T ss_pred EEEEECCCCCCHHHHHHHHHHCC T ss_conf 59986589983999999998557 No 357 >CHL00059 atpA ATP synthase CF1 alpha subunit Probab=75.58 E-value=5.6 Score=18.86 Aligned_cols=22 Identities=27% Similarity=0.252 Sum_probs=17.9 Q ss_pred EEEEECCCCCCHHHHHHHHHHH Q ss_conf 4776148867889999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLW 100 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw 100 (367) |..|-++||+|||+++.-.++- T Consensus 165 R~lI~Gd~gvGKTtl~~d~Iin 186 (501) T CHL00059 165 RELIIGDRQTGKTAVATDTILN 186 (501) T ss_pred EEEEECCCCCCHHHHHHHHHHH T ss_conf 6677557884477999999985 No 358 >cd01866 Rab2 Rab2 subfamily. Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key featur Probab=75.56 E-value=3.2 Score=20.31 Aligned_cols=23 Identities=30% Similarity=0.450 Sum_probs=20.3 Q ss_pred CEEEEEEECCCCCCHHHHHHHHH Q ss_conf 11247761488678899999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) +.||+.+.+..|+|||.++..++ T Consensus 3 y~~KivlvGd~~VGKTsli~r~~ 25 (168) T cd01866 3 YLFKYIIIGDTGVGKSCLLLQFT 25 (168) T ss_pred EEEEEEEECCCCCCHHHHHHHHH T ss_conf 88899999989978899999991 No 359 >pfam07728 AAA_5 AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Probab=75.49 E-value=5.6 Score=18.85 Aligned_cols=25 Identities=20% Similarity=0.201 Sum_probs=20.4 Q ss_pred CEEEEECCCCCCHHHHHHHHHHHHC Q ss_conf 2899975455998899998987406 Q gi|254781187|r 193 MAVFNDEASGTPDIINKSILGFFTE 217 (367) Q Consensus 193 ~l~ivDEAsgI~d~i~e~i~g~Lt~ 217 (367) -.+++||....+..+..++...|-+ T Consensus 68 ~vl~lDEin~a~~~v~~~L~~~le~ 92 (139) T pfam07728 68 EIAVLDEINRANPDVLNSLLSLLDE 92 (139) T ss_pred CEEEECCHHHCCHHHHHHHHHHHCC T ss_conf 6899634344899999999999748 No 360 >PRK07324 transaminase; Validated Probab=75.46 E-value=5.6 Score=18.84 Aligned_cols=60 Identities=23% Similarity=0.231 Sum_probs=39.0 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHH Q ss_conf 899999998888751245555541124776148867889999999999997089977999715379999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTL 124 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l 124 (367) +.--++-++|+..-+ +...+ ++.|.+| ...|..++-.+++.||-.|++..|++.+...+. T Consensus 62 ~G~~~LR~~Ia~~y~-~v~~d-----~IlvT~G------a~~Al~l~~~~l~~pGD~Viv~~P~Y~~~~~~~ 121 (373) T PRK07324 62 EGSPEFKEAVASLYQ-NVKPD-----NILQTNG------ATGANHLVLYALIEPGDHVISVYPTYQQLYDIP 121 (373) T ss_pred CCCHHHHHHHHHHHC-CCCHH-----HEEECCC------HHHHHHHHHHHHCCCCCEEEECCCCCHHHHHHH T ss_conf 898999999999866-99867-----8898687------899999999997599998998899857799999 No 361 >cd04116 Rab9 Rab9 subfamily. Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CX Probab=75.44 E-value=3.4 Score=20.15 Aligned_cols=23 Identities=22% Similarity=0.476 Sum_probs=20.5 Q ss_pred CEEEEEEECCCCCCHHHHHHHHH Q ss_conf 11247761488678899999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) .++|+.|.+..|+|||.++..++ T Consensus 4 ~~~KivvlGd~~VGKTsli~r~~ 26 (170) T cd04116 4 SLLKVILLGDGGVGKSSLMNRYV 26 (170) T ss_pred EEEEEEEECCCCCCHHHHHHHHH T ss_conf 08999999999978999999997 No 362 >smart00175 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking. Probab=75.41 E-value=2.9 Score=20.62 Aligned_cols=21 Identities=29% Similarity=0.536 Sum_probs=18.8 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) ||+.|.+..|+|||.++..++ T Consensus 1 ~Ki~vvG~~~vGKTsli~r~~ 21 (164) T smart00175 1 FKIILIGDSGVGKSSLLSRFT 21 (164) T ss_pred CEEEEECCCCCCHHHHHHHHH T ss_conf 989999989977999999994 No 363 >PRK06315 type III secretion system ATPase; Provisional Probab=75.17 E-value=2.6 Score=20.93 Aligned_cols=22 Identities=32% Similarity=0.466 Sum_probs=19.5 Q ss_pred EEEEECCCCCCHHHHHHHHHHH Q ss_conf 4776148867889999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLW 100 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw 100 (367) |+.|-+|+|+|||++.++++.. T Consensus 166 R~gIfagsGvGKs~Ll~~i~~~ 187 (442) T PRK06315 166 RIGIFAGAGVGKSSLLGMIARN 187 (442) T ss_pred EEECCCCCCCCHHHHHHHHHHH T ss_conf 7640389999888999999974 No 364 >cd04114 Rab30 Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Probab=75.10 E-value=4.1 Score=19.67 Aligned_cols=24 Identities=29% Similarity=0.452 Sum_probs=20.6 Q ss_pred CCEEEEEEECCCCCCHHHHHHHHH Q ss_conf 411247761488678899999999 Q gi|254781187|r 75 PTIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 75 ~~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) ...||+.+.+..|+|||.++..++ T Consensus 5 d~~~KivllGd~~VGKTsli~r~~ 28 (169) T cd04114 5 DFLFKIVLIGNAGVGKTCLVRRFT 28 (169) T ss_pred CEEEEEEEECCCCCCHHHHHHHHH T ss_conf 779899999989979999999998 No 365 >PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional Probab=75.09 E-value=5.7 Score=18.79 Aligned_cols=40 Identities=15% Similarity=0.233 Sum_probs=30.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHH Q ss_conf 47761488678899999999999970899779997--15379 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSET 118 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~ 118 (367) .+...+.-|+|||+++-+++-+.+....+.++..+ .|+++ T Consensus 196 nvIL~G~pGtGKT~lAk~lA~~l~g~~~~~rv~~Vqfhpsys 237 (459) T PRK11331 196 NIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYS 237 (459) T ss_pred CEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECCCCC T ss_conf 279658999887899999999970788778468998358866 No 366 >pfam00735 Septin Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerize to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis. Probab=74.82 E-value=3.3 Score=20.26 Aligned_cols=23 Identities=35% Similarity=0.475 Sum_probs=19.2 Q ss_pred EEEEEEECCCCCCHHHHHHHHHH Q ss_conf 12477614886788999999999 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~l 99 (367) -|.+-|++.+|+|||+++--+.- T Consensus 4 ~fnimvvG~sGlGKTTfiNtL~~ 26 (280) T pfam00735 4 DFTLMVVGESGLGKTTLINTLFL 26 (280) T ss_pred EEEEEEECCCCCCHHHHHHHHHC T ss_conf 78999977999978999999857 No 367 >cd04136 Rap_like Rap-like subfamily. The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Probab=74.81 E-value=3.3 Score=20.23 Aligned_cols=22 Identities=23% Similarity=0.522 Sum_probs=19.2 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.+.+..|+|||.++..++- T Consensus 2 fKivllGd~~VGKTsli~r~~~ 23 (163) T cd04136 2 YKVVVLGSGGVGKSALTVQFVQ 23 (163) T ss_pred EEEEEECCCCCCHHHHHHHHHH T ss_conf 1999989999889999999971 No 368 >KOG0920 consensus Probab=74.80 E-value=5.8 Score=18.74 Aligned_cols=186 Identities=19% Similarity=0.156 Sum_probs=89.0 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHHHHH Q ss_conf 89999999888875124555554112477614886788999999999999-70899779997153799999999999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLI-STRPGMSIICIANSETQLKNTLWAEVSKW 131 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~-~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~ 131 (367) +-++++|..|.++. -+.|++..|.|||+-+--+++-.. ...+.++|+||-|-.-.|-.+ -..+++- T Consensus 176 ~~r~~Il~~i~~~q------------VvvIsGeTGcGKtTQvpQfiLd~~~~~~~~~~IicTQPRRIsAIsv-AeRVa~E 242 (924) T KOG0920 176 KMRDTILDAIEENQ------------VVVISGETGCGKTTQVPQFILDEAIESGAACNIICTQPRRISAISV-AERVAKE 242 (924) T ss_pred HHHHHHHHHHHHCC------------EEEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCHHHHHHH-HHHHHHH T ss_conf 78999999997496------------6999578898712246699999998628997388667751778999-9999887 Q ss_pred HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCC--CCCHHHH Q ss_conf 986231211233332100012333221111345776-1266210135445565210113586289997545--5998899 Q gi|254781187|r 132 LSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSK-HYTITCRTYSEERPDTFVGPHNTHGMAVFNDEAS--GTPDIIN 208 (367) Q Consensus 132 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAs--gI~d~i~ 208 (367) ....+. ....|-.... ........ ....++...+....+ .. ..+...+|+||.. .+..+.. T Consensus 243 R~~~~g-----------~~VGYqvrl~-~~~s~~t~L~fcTtGvLLr~L~~~--~~--l~~~thiivDEVHER~i~~Dfl 306 (924) T KOG0920 243 RGESLG-----------EEVGYQVRLE-SKRSRETRLLFCTTGVLLRRLQSD--PT--LSGVTHIIVDEVHERSINTDFL 306 (924) T ss_pred HCCCCC-----------CEEEEEEEEE-CCCCCCEEEEEECHHHHHHHHCCC--CC--CCCCCEEEEEEEEECCCCCCCH T ss_conf 546668-----------7136898620-136775168984068999875468--62--1458665442279716775217 Q ss_pred HHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHHHC Q ss_conf 99898740698825899980789998768875411223504675233328888988999999621 Q gi|254781187|r 209 KSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRTVEGIDSGFHEGIISRY 273 (367) Q Consensus 209 e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d~p~~~~~~i~~~~~~~ 273 (367) -.+.--+-..+.....++.| -|-+.-.|-+-|. .-.+++++.+.-| +..-++++..+.. T Consensus 307 Li~lk~lL~~~p~LkvILMS-AT~dae~fs~YF~----~~pvi~i~grtfp-V~~~fLEDil~~~ 365 (924) T KOG0920 307 LILLKDLLPRNPDLKVILMS-ATLDAELFSDYFG----GCPVITIPGRTFP-VKEYFLEDILSKT 365 (924) T ss_pred HHHHHHHHHHCCCCEEEEEE-EECCHHHHHHHHC----CCCEEEECCCCCC-HHHHHHHHHHHHH T ss_conf 99999886228885699862-1126288898718----9935864687864-5887899999875 No 369 >PRK00081 coaE dephospho-CoA kinase; Reviewed Probab=74.59 E-value=3.1 Score=20.39 Aligned_cols=31 Identities=23% Similarity=0.392 Sum_probs=24.0 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 1247761488678899999999999970899779997 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) |..+.|.+|-|+|||+++..+-- .|..++.. T Consensus 2 m~~IgiTG~igsGKStv~~~l~~------~G~~vida 32 (199) T PRK00081 2 MLIIGLTGGIGSGKSTVANIFAE------LGVPVIDA 32 (199) T ss_pred CEEEEEECCCCCCHHHHHHHHHH------CCCCEEEH T ss_conf 78999578887779999999998------89939963 No 370 >PRK04863 mukB cell division protein MukB; Provisional Probab=74.59 E-value=4.1 Score=19.70 Aligned_cols=36 Identities=25% Similarity=0.392 Sum_probs=27.4 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 477614886788999999999999708997799971537 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) =++.++|.|.|||+++++++.- .-||.+-+-..||. T Consensus 29 VttLsGgNGAGKSTtMaAf~ta---LIPD~tlLhfrntt 64 (1486) T PRK04863 29 VTTLSGGNGAGKSTTMAAFVTA---LIPDLTLLHFRNTT 64 (1486) T ss_pred EEEEECCCCCCHHHHHHHHHHH---HCCCCCEEECCCCC T ss_conf 0330058886579899999999---67643023114666 No 371 >cd04107 Rab32_Rab38 Rab38/Rab32 subfamily. Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Probab=74.52 E-value=3.2 Score=20.32 Aligned_cols=21 Identities=24% Similarity=0.423 Sum_probs=18.7 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) ||+.+.+..|+|||.++-.++ T Consensus 1 fKvvllGd~gVGKTsLi~rf~ 21 (201) T cd04107 1 LKVLVIGDLGVGKTSIIKRYV 21 (201) T ss_pred CEEEEECCCCCCHHHHHHHHH T ss_conf 979999999978999999998 No 372 >PRK07261 topology modulation protein; Provisional Probab=74.47 E-value=3.3 Score=20.28 Aligned_cols=22 Identities=36% Similarity=0.383 Sum_probs=19.0 Q ss_pred EEEEECCCCCCHHHHHHHHHHH Q ss_conf 4776148867889999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLW 100 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw 100 (367) |+.|-++=|+|||+++..+.-- T Consensus 2 rI~IiG~sGsGKSTlAr~L~~~ 23 (171) T PRK07261 2 KIAIIGYSGSGKSTLARFLGQH 23 (171) T ss_pred EEEEECCCCCCHHHHHHHHHHH T ss_conf 8999889998689999999998 No 373 >PRK13705 plasmid-partitioning protein SopA; Provisional Probab=74.44 E-value=6 Score=18.68 Aligned_cols=87 Identities=10% Similarity=0.090 Sum_probs=45.6 Q ss_pred CCCCCHHHHHHHHHCCCCCCCCCCCCCCC---HH-HHHHHHHHHHHHHHCCCCCCCCCEE-EEEEEC-CCCCCHHHHHHH Q ss_conf 01259888855430146688844366684---28-9999999888875124555554112-477614-886788999999 Q gi|254781187|r 23 ECVLSFKNFVMRFFPWGIKGKPLEHFSQP---HR-WQLEFMEAVDVHCHSNVNNSNPTIF-KCAISA-GRGIGKTTLNAW 96 (367) Q Consensus 23 ~~~~~~~~f~~~~~~w~~~~~~~~~~~~p---~~-wq~~~l~~~~~~~~~~~~~~~~~~~-~~~v~s-grg~GKS~~~a~ 96 (367) .+..+ +++-...-|.+-.|.....|- |. |-.+-+.++.+.+.....+...+.. -+||+- ==|+|||+.+.. T Consensus 50 gvs~~---~lr~~~~~g~~P~p~~~~~gr~~~R~~Ytl~~i~~lR~~~~~~p~R~~g~~~~VIAVaNqKGGvGKTTTavn 126 (388) T PRK13705 50 GVSSQ---AIRDAEKAGRLPHPDMEMRGRVEQRVGYTIEQINHMRDVFGTRLRRAEDEFPPVIGVAAHKGGVYKTSVSVH 126 (388) T ss_pred CCCHH---HHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHH T ss_conf 99999---999786468999997687776554551069999999999643889999998728999527888559999999 Q ss_pred HHHHHHHHCCCCEEEEEC Q ss_conf 999999708997799971 Q gi|254781187|r 97 MMLWLISTRPGMSIICIA 114 (367) Q Consensus 97 ~~lw~~~~~~~~~v~~~A 114 (367) ++-.++. .|.||+++= T Consensus 127 LA~~LAl--~G~RVLlID 142 (388) T PRK13705 127 LAQDLAL--KGLRVLLVE 142 (388) T ss_pred HHHHHHH--CCCEEEEEE T ss_conf 9999997--799089995 No 374 >TIGR00955 3a01204 Pigment precourser permease; InterPro: IPR005284 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family includes different parts of a membrane-spanning permease system necessary for the transport of pigment precursor into pigment cells responsible for eye color. White protein dimerises with brown protein for the transport of guanine and with scarlet protein for the transport of tryptophan.; GO: 0006810 transport. Probab=74.43 E-value=2 Score=21.65 Aligned_cols=233 Identities=11% Similarity=0.005 Sum_probs=103.2 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCC-CE-EEE--ECCCHHHHHHHHHHHHHH Q ss_conf 99999988887512455555411247761488678899999999999970899-77-999--715379999999999999 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPG-MS-IIC--IANSETQLKNTLWAEVSK 130 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~-~~-v~~--~A~t~~Q~~~~lw~ei~k 130 (367) +..+|..+.=+.+.|. =+||.++=|.|||+|..+++---.---.. .. |++ ..-..++.+.+. +.+.+ T Consensus 44 ~K~lL~~vSG~a~~Ge--------LlA~mGsSGAGKTTLmn~La~R~~~g~~~~g~~v~lNG~~~~~~~~~~~s-aYvqQ 114 (671) T TIGR00955 44 RKHLLKNVSGVAKPGE--------LLAIMGSSGAGKTTLMNALAFRSPKGLKVSGSVVLLNGRPIDAKEMRAIS-AYVQQ 114 (671) T ss_pred CHHHHHCCCEEECCCE--------EEEEECCCCCCHHHHHHHHHCCCCCCCEECCCEEEECCEECCHHHHHHHH-CHHEE T ss_conf 2011103520210670--------68984787662689999985337478614683678758375868998540-12201 Q ss_pred ---HHHHCCCCCCCCCCCCCCCCCCCCCCCCC-----------------CCCCCCCCCEEEEECCCCCCCCCCCCCCCCC Q ss_conf ---99862312112333321000123332211-----------------1134577612662101354455652101135 Q gi|254781187|r 131 ---WLSMLPHRHWFEMQSLSLHPSGWYAELLE-----------------QSMGIDSKHYTITCRTYSEERPDTFVGPHNT 190 (367) Q Consensus 131 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~ 190 (367) .+..+=....+..++.-+-.+-......+ ....+.+|..-..+-+-++--+=|..-+ . T Consensus 115 ~Dlf~~~LTv~E~L~f~A~lRm~~~~~~~~~k~~rV~~vl~~l~L~~ca~T~IG~pg~~KGlSGGErKRLafA~E~l--t 192 (671) T TIGR00955 115 DDLFIPTLTVREHLMFQAHLRMKRRVTKKHEKRERVDEVLQALGLRKCADTRIGIPGRVKGLSGGERKRLAFASELL--T 192 (671) T ss_pred HHHCCCCCCHHEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCHHHHCCCCCCCCCEEEECCCHHHHHHHHHHHH--H T ss_conf 10048851030000101223347667605799999999998604211211343799964552011367899887887--1 Q ss_pred CCCEEEEEC-CCCCCH----HHHHHHHHHHHCCCCCEEEEEEECCCCCCCHHHHHHHCC----CC-------------CE Q ss_conf 862899975-455998----899998987406988258999807899987688754112----23-------------50 Q gi|254781187|r 191 HGMAVFNDE-ASGTPD----IINKSILGFFTELNPNRFWIMTSNTRRLNGWFYDIFNIP----LE-------------DW 248 (367) Q Consensus 191 ~~~l~ivDE-AsgI~d----~i~e~i~g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~----~~-------------~w 248 (367) ++.++++|| -||.|- .+-.++. .|+..|+ ++.+.|=.|. ...|+.|.+= .+ .+ T Consensus 193 dP~~LFcDEPTSGLDSfmA~~Vv~~L~-~LA~~G~-tiI~tIHQPS---s~lF~lFd~i~lla~Grvvy~G~p~~a~~FF 267 (671) T TIGR00955 193 DPIILFCDEPTSGLDSFMAYSVVQVLK-GLAQKGK-TIICTIHQPS---SELFELFDKIILLAEGRVVYLGSPDQAVPFF 267 (671) T ss_pred CCCEEEECCCCCHHHHHHHHHHHHHHH-HHHCCCC-EEEEEEECCC---HHHHHHHCCEEEEECCEEEEECCCHHHHHHH T ss_conf 894265038895345999999999999-9850897-9999830561---8898511716775277279827810368989 Q ss_pred EEEE--ECCCCCCCCCHHHHHHHHHHCCCCCCE-EEEEEEEEECCCCCCEEECHHHHHHH Q ss_conf 4675--233328888988999999621688000-26888644327789807829998644 Q gi|254781187|r 249 KRYQ--IDTRTVEGIDSGFHEGIISRYGLDSDV-ARIEILGQFPQQEVNNFIPHNYIEEA 305 (367) Q Consensus 249 ~~~~--~~~~d~p~~~~~~i~~~~~~~gedS~~-~r~ev~G~Fp~~~~d~~ip~~~ie~a 305 (367) ..+- ..+..+ +.+.||+.+..+.-..+... -|.+..... +.....-+..+..... T Consensus 268 ~~~Gpd~~cP~~-yNPADF~~~~la~~p~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 325 (671) T TIGR00955 268 SELGPDFPCPEN-YNPADFYLQVLAVIPGSENERSRETIEKIC-DAFAVSDIGRSMLVNT 325 (671) T ss_pred HHCCCCCCCCCC-CCCHHHHHHHHHCCCCCCHHHHHHHHHHHH-HHHHCCHHHHHHHHHH T ss_conf 844888789788-888889999973155520034799999998-7651450246789988 No 375 >KOG1133 consensus Probab=74.32 E-value=6 Score=18.67 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=34.5 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHH-HHHHHHHHHHH Q ss_conf 84289999999888875124555554112477614886788999-99999999970 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTL-NAWMMLWLIST 104 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~-~a~~~lw~~~~ 104 (367) .|-..|.+++++++-.+..+.. -..-|+.|+|||-. +++.+-|+-.. T Consensus 15 ~PYdIQ~~lM~elyrvLe~GkI--------gIfESPTGTGKSLSLiCaaltWL~~~ 62 (821) T KOG1133 15 TPYDIQEDLMRELYRVLEEGKI--------GIFESPTGTGKSLSLICAALTWLRDF 62 (821) T ss_pred CCHHHHHHHHHHHHHHHHCCCE--------EEEECCCCCCCHHHHHHHHHHHHHHH T ss_conf 8236999999999999853762--------46757998881178999898998876 No 376 >PRK09265 aminotransferase AlaT; Validated Probab=74.30 E-value=6 Score=18.66 Aligned_cols=61 Identities=10% Similarity=-0.006 Sum_probs=38.3 Q ss_pred CHHHHHHHHHHHHHHHHCCCC-CCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH Q ss_conf 428999999988887512455-555411247761488678899999999999970899779997153799 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVN-NSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ 119 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~-~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q 119 (367) |...-.++-++|+++.++... ...|+ ++.|.. |-+. |...+-.++++||-.|++-+|.+.. T Consensus 70 ~~~G~~eLReaIA~~~~~~~~~~~~p~--~I~vT~----Ga~~--al~~~~~all~pGDeVlvp~P~Yp~ 131 (404) T PRK09265 70 DSKGLFSARKAIMQYYQQKGIPDVDVD--DIYIGN----GVSE--LIVMAMQALLNNGDEVLVPAPDYPL 131 (404) T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCHH--HEEECC----CHHH--HHHHHHHHHCCCCCEEEEECCCCCH T ss_conf 888889999999999997569998889--978758----8899--9999999964998989994688730 No 377 >PRK06936 type III secretion system ATPase; Provisional Probab=74.10 E-value=6.1 Score=18.63 Aligned_cols=36 Identities=25% Similarity=0.228 Sum_probs=24.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH Q ss_conf 47761488678899999999999970899779997153799 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ 119 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q 119 (367) |+.|-+|.|+|||++.++++.. +..+ ++|.+--... T Consensus 164 R~gIfagsGvGKs~Ll~~i~r~---~~ad--v~V~alIGER 199 (439) T PRK06936 164 RMGIFAAAGGGKSTLLASLIRS---AEVD--VTVLALIGER 199 (439) T ss_pred EEECCCCCCCCHHHHHHHHHHH---HCCC--CEEEEEECCC T ss_conf 0102369999889999999764---3269--5799980730 No 378 >cd04127 Rab27A Rab27a subfamily. The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated Probab=74.04 E-value=3.9 Score=19.81 Aligned_cols=23 Identities=22% Similarity=0.254 Sum_probs=19.9 Q ss_pred CEEEEEEECCCCCCHHHHHHHHH Q ss_conf 11247761488678899999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) +.+|+.|.+..|+|||.++..++ T Consensus 3 ~~~KivvvGd~~VGKTsli~r~~ 25 (180) T cd04127 3 YLIKFLALGDSGVGKTSFLYQYT 25 (180) T ss_pred EEEEEEEECCCCCCHHHHHHHHH T ss_conf 78899999999988899999996 No 379 >TIGR03497 FliI_clade2 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively. Probab=73.99 E-value=6.1 Score=18.62 Aligned_cols=41 Identities=24% Similarity=0.478 Sum_probs=25.9 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHH Q ss_conf 4776148867889999999999997089977999-7153799999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKN 122 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~ 122 (367) |+.+-+|.|+|||++.++++-+- ..+..|++ +....+.+++ T Consensus 139 RigIfag~GvGKt~Ll~~ia~~~---~adv~Vi~liGERgrEv~e 180 (413) T TIGR03497 139 RVGIFAGSGVGKSTLLGMIARNA---KADINVIALIGERGREVRD 180 (413) T ss_pred EEEECCCCCCCHHHHHHHHHHHH---CCCCCEEEEEEEECHHHHH T ss_conf 44210589987769999999874---3785238886332289999 No 380 >PRK13768 GTPase; Provisional Probab=73.87 E-value=6.2 Score=18.60 Aligned_cols=36 Identities=25% Similarity=0.340 Sum_probs=27.7 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 247761488678899999999999970899779997 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) +-+.|.+.-|+|||+..+.+--|.........++=. T Consensus 3 ~~~~ViGpaGSGKsT~~~~l~~~l~~~~r~~~vvNL 38 (253) T PRK13768 3 YIVFFLGTAGSGKTTLVGALSDWLEEQGYDVAIVNL 38 (253) T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEC T ss_conf 189998999998899999999999976997599978 No 381 >PRK13230 nitrogenase reductase-like protein; Reviewed Probab=73.84 E-value=6.2 Score=18.59 Aligned_cols=35 Identities=26% Similarity=0.324 Sum_probs=28.2 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 1247761488678899999999999970899779997 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) |.++||-.==|+|||+.+..+..-++.. |.||+++ T Consensus 1 m~~ia~yGKGGVGKTTTavNLAaALA~~--GkkVLlI 35 (292) T PRK13230 1 MKQIAFYGKGGIGKSTTVCNLAAALSKS--GKKVIVV 35 (292) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEE T ss_conf 9679991799857898999999999987--9959997 No 382 >COG0572 Udk Uridine kinase [Nucleotide transport and metabolism] Probab=73.82 E-value=3.2 Score=20.36 Aligned_cols=23 Identities=30% Similarity=0.413 Sum_probs=18.9 Q ss_pred EEEEEEECCCCCCHHHHHHHHHH Q ss_conf 12477614886788999999999 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~l 99 (367) ++=+.|++|.|+|||+++-.+.- T Consensus 8 ~iiIgIaG~SgSGKTTv~~~l~~ 30 (218) T COG0572 8 VIIIGIAGGSGSGKTTVAKELSE 30 (218) T ss_pred EEEEEEECCCCCCHHHHHHHHHH T ss_conf 69999867987788999999999 No 383 >cd04125 RabA_like RabA-like subfamily. RabA was first identified in D. discoideum, where its expression levels were compared to other Rabs in growing and developing cells. The RabA mRNA levels were below the level of detection by Northern blot analysis, suggesting a very low level of expression. The function of RabA remains unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Probab=73.77 E-value=3.4 Score=20.19 Aligned_cols=22 Identities=32% Similarity=0.471 Sum_probs=19.0 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.|.+..|+|||.++..++- T Consensus 1 ~KivvvGd~~VGKTsli~r~~~ 22 (188) T cd04125 1 FKVVIIGDYGVGKSSLLKRFTE 22 (188) T ss_pred CEEEEECCCCCCHHHHHHHHHH T ss_conf 9799999999789999999951 No 384 >cd04123 Rab21 Rab21 subfamily. The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site Probab=73.56 E-value=3.5 Score=20.10 Aligned_cols=22 Identities=27% Similarity=0.353 Sum_probs=19.2 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||++|.+..|+|||.++..++- T Consensus 1 ~Ki~vvG~~~vGKTsli~r~~~ 22 (162) T cd04123 1 FKVVLLGEGRVGKTSLVLRYVE 22 (162) T ss_pred CEEEEECCCCCCHHHHHHHHHH T ss_conf 9899999999679999999983 No 385 >TIGR01166 cbiO cobalt ABC transporter, ATP-binding protein; InterPro: IPR005876 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. This superfamily includes two groups, one which catalyses the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drives both the process of uptake and efflux.; GO: 0006824 cobalt ion transport, 0009276 1-2nm peptidoglycan-based cell wall. Probab=73.45 E-value=3.3 Score=20.25 Aligned_cols=43 Identities=9% Similarity=0.071 Sum_probs=27.6 Q ss_pred CCCCCCCCCCCCCCCEEEEEC-CCCCCHH----HHHHHHHHHHCCCCCE Q ss_conf 455652101135862899975-4559988----9999898740698825 Q gi|254781187|r 179 ERPDTFVGPHNTHGMAVFNDE-ASGTPDI----INKSILGFFTELNPNR 222 (367) Q Consensus 179 ~~~ea~~g~h~~~~~l~ivDE-AsgI~d~----i~e~i~g~Lt~~~~~~ 222 (367) ...-|++|+=+.+...+|+|| .||++.. +.+.|. -|+..++.+ T Consensus 133 kkRvAIAGAvAM~Pd~l~LDEPTAGLDp~G~~q~~~~l~-~L~~~G~tv 180 (190) T TIGR01166 133 KKRVAIAGAVAMRPDVLLLDEPTAGLDPAGAEQLLAILR-RLRAEGTTV 180 (190) T ss_pred HHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHH-HHHHCCCEE T ss_conf 357777758861663466427888978747999999988-787239989 No 386 >PRK13634 cbiO cobalt transporter ATP-binding subunit; Provisional Probab=73.41 E-value=0.53 Score=25.14 Aligned_cols=37 Identities=27% Similarity=0.198 Sum_probs=25.0 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHH Q ss_conf 999999888875124555554112477614886788999999999 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~l 99 (367) +.++|++|.=.++.+. .++|.+..|+|||++.-.+.- T Consensus 6 e~~AL~~Vsl~i~~Ge--------~vaiiG~sGsGKSTLl~~l~G 42 (276) T PRK13634 6 ERRALYDVNVSIPSGS--------YVAIIGHTGSGKSTLLQHLNG 42 (276) T ss_pred CCEEEECCEEEECCCC--------EEEEECCCCCHHHHHHHHHHC T ss_conf 7666514477998998--------999999999699999999974 No 387 >cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter. Probab=73.37 E-value=6.3 Score=18.52 Aligned_cols=32 Identities=28% Similarity=0.478 Sum_probs=22.7 Q ss_pred EEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 7761488-678899999999999970899779997 Q gi|254781187|r 80 CAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 80 ~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) ++|.||. |+|||++++.+++-+... +.++.+. T Consensus 2 i~v~s~kggvgkst~~~~la~~l~~~--g~~v~~~ 34 (169) T cd02037 2 IAVMSGKGGVGKSTVAVNLALALAKL--GYKVGLL 34 (169) T ss_pred EEEECCCCCCCHHHHHHHHHHHHHHC--CCCEEEE T ss_conf 89974999881999999999999987--9978999 No 388 >COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones] Probab=73.29 E-value=2.9 Score=20.63 Aligned_cols=81 Identities=16% Similarity=0.059 Sum_probs=40.5 Q ss_pred CCCCCCCCCCCCEEEEECC-CCCCHHHHH-HHH--HHHHCCCCCEEEEEEECCCCCCCHHHHHHHCCCCCEEEEEECCCC Q ss_conf 6521011358628999754-559988999-989--874069882589998078999876887541122350467523332 Q gi|254781187|r 182 DTFVGPHNTHGMAVFNDEA-SGTPDIINK-SIL--GFFTELNPNRFWIMTSNTRRLNGWFYDIFNIPLEDWKRYQIDTRT 257 (367) Q Consensus 182 ea~~g~h~~~~~l~ivDEA-sgI~d~i~e-~i~--g~Lt~~~~~~~~i~igNP~r~~g~Fye~~~~~~~~w~~~~~~~~d 257 (367) |-+|-.- -..-++|+||- ||++=+... +.. ..|.+.+.-.+ + | | +.-+....-..+...+-.+-+- T Consensus 154 EilQ~~~-lePkl~ILDE~DSGLDIdalk~V~~~i~~lr~~~~~~l-i-I-T------Hy~rll~~i~pD~vhvl~~GrI 223 (251) T COG0396 154 EILQLLL-LEPKLAILDEPDSGLDIDALKIVAEGINALREEGRGVL-I-I-T------HYQRLLDYIKPDKVHVLYDGRI 223 (251) T ss_pred HHHHHHH-CCCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCEEE-E-E-E------CHHHHHHHCCCCEEEEEECCEE T ss_conf 9999984-59988995588767558999999999999865897299-9-9-5------5799984268887999988889 Q ss_pred CCCCCHHHHHHHHHH Q ss_conf 888898899999962 Q gi|254781187|r 258 VEGIDSGFHEGIISR 272 (367) Q Consensus 258 ~p~~~~~~i~~~~~~ 272 (367) +-.-+++..++.+++ T Consensus 224 v~sG~~el~~~le~~ 238 (251) T COG0396 224 VKSGDPELAEELEEK 238 (251) T ss_pred EECCCHHHHHHHHHH T ss_conf 832998999999971 No 389 >smart00173 RAS Ras subfamily of RAS small GTPases. Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades Probab=73.29 E-value=3.6 Score=20.03 Aligned_cols=21 Identities=24% Similarity=0.534 Sum_probs=18.5 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) ||+.|.+..|+|||.++-.++ T Consensus 1 fKiv~vGd~~vGKTsli~r~~ 21 (164) T smart00173 1 YKLVVLGSGGVGKSALTIQFV 21 (164) T ss_pred CEEEEECCCCCCHHHHHHHHH T ss_conf 989999999978999999997 No 390 >COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion] Probab=73.28 E-value=6.4 Score=18.51 Aligned_cols=34 Identities=24% Similarity=0.300 Sum_probs=22.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 47761488678899999999999970899779997 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) -+.|.++.|+|||+..|.++-+.=-+.+ ..|+.+ T Consensus 127 LILVTGpTGSGKSTTlAamId~iN~~~~-~HIlTI 160 (353) T COG2805 127 LILVTGPTGSGKSTTLAAMIDYINKHKA-KHILTI 160 (353) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHCCCC-CCEEEE T ss_conf 6998679999678799999999841477-516872 No 391 >cd04113 Rab4 Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to p Probab=73.25 E-value=3.5 Score=20.10 Aligned_cols=21 Identities=33% Similarity=0.479 Sum_probs=18.8 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) ||+.+.+..|+|||.++..++ T Consensus 1 ~Kivl~Gd~~vGKTsli~r~~ 21 (161) T cd04113 1 FKFIIIGSSGTGKSCLLHRFV 21 (161) T ss_pred CEEEEECCCCCCHHHHHHHHH T ss_conf 989999949967999999997 No 392 >cd04175 Rap1 Rap1 subgroup. The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the n Probab=73.21 E-value=3.8 Score=19.88 Aligned_cols=22 Identities=23% Similarity=0.499 Sum_probs=19.3 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.+.+..|+|||.++..++- T Consensus 2 fKIvllGd~~VGKTsli~r~~~ 23 (164) T cd04175 2 YKLVVLGSGGVGKSALTVQFVQ 23 (164) T ss_pred EEEEEECCCCCCHHHHHHHHHH T ss_conf 2999989999759999999970 No 393 >cd03277 ABC_SMC5_euk Eukaryotic SMC5 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for Probab=73.16 E-value=3 Score=20.49 Aligned_cols=21 Identities=24% Similarity=0.287 Sum_probs=17.5 Q ss_pred EEEEECCCCCCHHHHHHHHHHH Q ss_conf 4776148867889999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLW 100 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw 100 (367) ++ |.+..|+|||++++++++= T Consensus 26 N~-IiGpNGSGKSsIv~AI~lg 46 (213) T cd03277 26 NM-IIGPNGSGKSSIVCAICLG 46 (213) T ss_pred EE-EECCCCCCHHHHHHHHHHH T ss_conf 79-9889988789999999988 No 394 >COG3421 Uncharacterized protein conserved in bacteria [Function unknown] Probab=73.13 E-value=6.4 Score=18.49 Aligned_cols=33 Identities=21% Similarity=0.203 Sum_probs=20.2 Q ss_pred CCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH Q ss_conf 8867889999999999997089977999715379 Q gi|254781187|r 85 GRGIGKTTLNAWMMLWLISTRPGMSIICIANSET 118 (367) Q Consensus 85 grg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~ 118 (367) ..|+|||.++|.+||...--. ..+.+.--|..+ T Consensus 5 atgsgkt~~ma~lil~~y~kg-yr~flffvnq~n 37 (812) T COG3421 5 ATGSGKTLVMAGLILECYKKG-YRNFLFFVNQAN 37 (812) T ss_pred CCCCCHHHHHHHHHHHHHHHC-HHHEEEEECCHH T ss_conf 358870059999999999734-041899852116 No 395 >KOG0344 consensus Probab=72.80 E-value=6.5 Score=18.44 Aligned_cols=74 Identities=18% Similarity=0.213 Sum_probs=48.5 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC------CCEEEEECCCHHH Q ss_conf 3666842899999998888751245555541124776148867889999999999997089------9779997153799 Q gi|254781187|r 46 EHFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP------GMSIICIANSETQ 119 (367) Q Consensus 46 ~~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~------~~~v~~~A~t~~Q 119 (367) -.|++|.+-|+.+ |.-.+++ ..+..++.-|.|||.....=++=.+.-+- +-+.++++|+..- T Consensus 154 ~~F~~Pt~iq~~a---ipvfl~~---------r~~lAcapTGsgKtlaf~~Pil~~L~~~~~~~~~~gl~a~Il~ptreL 221 (593) T KOG0344 154 LGFDEPTPIQKQA---IPVFLEK---------RDVLACAPTGSGKTLAFNLPILQHLKDLSQEKHKVGLRALILSPTREL 221 (593) T ss_pred CCCCCCCCCCCHH---HHHHHCC---------CCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCHHHH T ss_conf 7888877310011---5666413---------305886357886205655699999987520357654278884444999 Q ss_pred HHHHHHHHHHHHH Q ss_conf 9999999999999 Q gi|254781187|r 120 LKNTLWAEVSKWL 132 (367) Q Consensus 120 ~~~~lw~ei~k~~ 132 (367) +.++ ..|..++- T Consensus 222 a~Qi-~re~~k~~ 233 (593) T KOG0344 222 AAQI-YREMRKYS 233 (593) T ss_pred HHHH-HHHHHHCC T ss_conf 9999-99998557 No 396 >KOG4439 consensus Probab=72.76 E-value=6.5 Score=18.43 Aligned_cols=138 Identities=17% Similarity=0.149 Sum_probs=61.8 Q ss_pred EEECCCCCCHHHHHHHHHHHHHHHCC-------C-CEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC Q ss_conf 76148867889999999999997089-------9-779997153799999999999999986231211233332100012 Q gi|254781187|r 81 AISAGRGIGKTTLNAWMMLWLISTRP-------G-MSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSG 152 (367) Q Consensus 81 ~v~sgrg~GKS~~~a~~~lw~~~~~~-------~-~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~ 152 (367) .++--+|.|||..+-.+++.--..+. . .+.++++|.. -+ --.-+|+++-++..... .++. T Consensus 349 ILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~PaS-li-~qW~~Ev~~rl~~n~Ls---------V~~~- 416 (901) T KOG4439 349 ILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPAS-LI-HQWEAEVARRLEQNALS---------VYLY- 416 (901) T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEECCHH-HH-HHHHHHHHHHHHHCCEE---------EEEE- T ss_conf 502133455306799999988999875414456557728867399-99-98899999998635007---------9986- Q ss_pred CCCCCCCCCCCCCC--C-CEEEEECCCCCCCCCCCCCCCCCC-------CCEEEEECCCCCCHHHHHHHHH--HHHCCCC Q ss_conf 33322111134577--6-126621013544556521011358-------6289997545599889999898--7406988 Q gi|254781187|r 153 WYAELLEQSMGIDS--K-HYTITCRTYSEERPDTFVGPHNTH-------GMAVFNDEASGTPDIINKSILG--FFTELNP 220 (367) Q Consensus 153 ~~~~~~~~~~~~~~--~-~~~~~a~~~~~~~~ea~~g~h~~~-------~~l~ivDEAsgI~d~i~e~i~g--~Lt~~~~ 220 (367) +.-++.++.... . ...++....-...|.+-.+.++.. ..-+|+|||.-|.+.--..... .|+... T Consensus 417 --HG~n~r~i~~~~L~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN~~tq~S~AVC~L~a~~- 493 (901) T KOG4439 417 --HGPNKREISAKELRKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRNSNTQCSKAVCKLSAKS- 493 (901) T ss_pred --CCCCCCCCCHHHHHHCCEEEEEEECCCCCCCHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCC- T ss_conf --17861547888873256699852110157730333156742777756777534245541366306788988776204- Q ss_pred CEEEEEEECCCCCCC Q ss_conf 258999807899987 Q gi|254781187|r 221 NRFWIMTSNTRRLNG 235 (367) Q Consensus 221 ~~~~i~igNP~r~~g 235 (367) -||.+|+|-.+.. T Consensus 494 --RWclTGTPiqNn~ 506 (901) T KOG4439 494 --RWCLTGTPIQNNL 506 (901) T ss_pred --EEECCCCCCCCCH T ss_conf --1331267544441 No 397 >PRK04196 V-type ATP synthase subunit B; Provisional Probab=72.72 E-value=5.8 Score=18.76 Aligned_cols=45 Identities=13% Similarity=0.054 Sum_probs=29.4 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCE-EEE---ECCCHHHHHHH Q ss_conf 4776148867889999999999997089977-999---71537999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMS-IIC---IANSETQLKNT 123 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~-v~~---~A~t~~Q~~~~ 123 (367) |+.|-+|.|+|||.+++.++........+.. ++| +....+.+.+. T Consensus 145 r~~If~gsGvgks~l~~~i~~qa~~~~~~~~~~vV~~~iGeR~~E~~e~ 193 (460) T PRK04196 145 KLPIFSGSGLPHNELAAQIARQAKVLGSEEKFAVVFAAMGITFEEANFF 193 (460) T ss_pred EEEEECCCCCCCCHHHHHHHHHHHHCCCCCCCEEEEEECCEECHHHHHH T ss_conf 7655338998811699999998775057888159997320760689999 No 398 >pfam04665 Pox_A32 Poxvirus A32 protein. The A32 protein is thought to be involved in viral DNA packaging. Probab=72.68 E-value=5.1 Score=19.10 Aligned_cols=43 Identities=26% Similarity=0.280 Sum_probs=28.7 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH Q ss_conf 247761488678899999999999970899779997153799999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN 122 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~ 122 (367) ||+|+.+|-|+|||+..--+..-+..-. .-|....|..+.+.+ T Consensus 14 FrmaivGgSGSGKT~yLlsLf~tlv~ky--khIfLfTpv~N~~Yd 56 (241) T pfam04665 14 FRMAIVGGSGSGKTTYLLSLLRTLVRKF--KHIFLFTPVYNNAYD 56 (241) T ss_pred CEEEEEECCCCCHHHHHHHHHHHHHHHH--EEEEEECCCCCCCCC T ss_conf 3599981588756699999999997741--589996244673236 No 399 >cd04148 RGK RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ra Probab=72.61 E-value=3.6 Score=19.99 Aligned_cols=21 Identities=19% Similarity=0.539 Sum_probs=18.8 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) ||+.+.+..|+|||.++..++ T Consensus 1 yKVvllGd~gVGKTSLi~rf~ 21 (221) T cd04148 1 YRVVMLGSPGVGKSSLASQFT 21 (221) T ss_pred CEEEEECCCCCHHHHHHHHHH T ss_conf 979999989970999999998 No 400 >COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair] Probab=72.60 E-value=6.6 Score=18.41 Aligned_cols=40 Identities=18% Similarity=0.182 Sum_probs=27.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH Q ss_conf 477614886788999999999999708997799971537999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNT 123 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~ 123 (367) ....=++=|+|||+++..++-- -+..+.-++.+.+.++++ T Consensus 50 SmIl~GPPG~GKTTlA~liA~~-----~~~~f~~~sAv~~gvkdl 89 (436) T COG2256 50 SMILWGPPGTGKTTLARLIAGT-----TNAAFEALSAVTSGVKDL 89 (436) T ss_pred EEEEECCCCCCHHHHHHHHHHH-----HCCCEEEECCCCCCHHHH T ss_conf 0577789998888999999876-----177669951523467999 No 401 >cd01860 Rab5_related Rab5-related subfamily. This subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence mo Probab=72.57 E-value=4 Score=19.75 Aligned_cols=22 Identities=23% Similarity=0.400 Sum_probs=19.4 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.|.+..|+|||.++..++- T Consensus 2 ~KivviGd~~vGKTsli~r~~~ 23 (163) T cd01860 2 FKLVLLGDSSVGKSSLVLRFVK 23 (163) T ss_pred EEEEEECCCCCCHHHHHHHHHH T ss_conf 7999999599689999999943 No 402 >cd00154 Rab Rab family. Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide di Probab=72.51 E-value=3.8 Score=19.89 Aligned_cols=22 Identities=32% Similarity=0.478 Sum_probs=19.0 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) +|+.|.+..|+|||.++..++- T Consensus 1 ~Ki~vvG~~~vGKTsli~~~~~ 22 (159) T cd00154 1 FKIVLIGDSGVGKTSLLLRFVD 22 (159) T ss_pred CEEEEECCCCCCHHHHHHHHHH T ss_conf 9899999699689999999970 No 403 >PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional Probab=72.37 E-value=6.7 Score=18.38 Aligned_cols=38 Identities=32% Similarity=0.248 Sum_probs=29.9 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH Q ss_conf 4776148867889999999999997089977999715379 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET 118 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~ 118 (367) =++|.+-.|+|||+++..++-.+ +..|.+|.++-.+.. T Consensus 4 ii~ivG~s~SGKTTLi~kli~~l--~~~G~rV~~IKH~~H 41 (170) T PRK10751 4 LLAIAAWSGTGKTTLLKKLIPAL--CARGIRPGLIKHTHH 41 (170) T ss_pred EEEEEECCCCCHHHHHHHHHHHH--HHCCCEEEEEECCCC T ss_conf 79999469999999999999999--987984999945777 No 404 >cd01850 CDC_Septin CDC/Septin. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities. Probab=72.35 E-value=4.1 Score=19.71 Aligned_cols=24 Identities=21% Similarity=0.328 Sum_probs=20.0 Q ss_pred CEEEEEEECCCCCCHHHHHHHHHH Q ss_conf 112477614886788999999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~l 99 (367) .-|.+-|++.+|+|||+++--+.. T Consensus 3 ~~fnimVvG~sGlGKsTfiNtLf~ 26 (276) T cd01850 3 FQFNIMVVGESGLGKSTFINTLFN 26 (276) T ss_pred CEEEEEEECCCCCCHHHHHHHHHC T ss_conf 579999976899988999999747 No 405 >KOG0336 consensus Probab=72.31 E-value=4.6 Score=19.37 Aligned_cols=149 Identities=16% Similarity=0.038 Sum_probs=65.2 Q ss_pred EEEECCCCCCHHHHHHHHHHHH-------HHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC Q ss_conf 7761488678899999999999-------970899779997153799999999999999986231211233332100012 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWL-------ISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSG 152 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~-------~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~ 152 (367) +...|-.|.||+-..-.-.+-+ .-.+++..+++.+||..-+-. +=.|.++....-- ....++-.. T Consensus 260 liGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~p~~lvl~ptreLalq-ie~e~~kysyng~-------ksvc~yggg 331 (629) T KOG0336 260 LIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNGPGVLVLTPTRELALQ-IEGEVKKYSYNGL-------KSVCVYGGG 331 (629) T ss_pred EEEEEECCCCCCHHHHCCCEEEEECCCHHHHCCCCCCEEEEECCHHHHHH-HHHHHHHHHHCCC-------CEEEEECCC T ss_conf 47787448984778750540145146111203689854998333888998-8767767643584-------328875487 Q ss_pred CCCCCCCCCCCCCCCCEEEEECCCCCCC--CCCCCCCCCCCCCEEEEECCCCCCHHHHH-HHHHHHHC--CCCCEEEEEE Q ss_conf 3332211113457761266210135445--56521011358628999754559988999-98987406--9882589998 Q gi|254781187|r 153 WYAELLEQSMGIDSKHYTITCRTYSEER--PDTFVGPHNTHGMAVFNDEASGTPDIINK-SILGFFTE--LNPNRFWIMT 227 (367) Q Consensus 153 ~~~~~~~~~~~~~~~~~~~~a~~~~~~~--~ea~~g~h~~~~~l~ivDEAsgI~d~i~e-~i~g~Lt~--~~~~~~~i~i 227 (367) ..+...-....|.-.+.+.+-+... -+++-.+ .+..++++|||...=|.=|| .|...|-+ ++..+. ++ T Consensus 332 ---nR~eqie~lkrgveiiiatPgrlndL~~~n~i~l--~siTYlVlDEADrMLDMgFEpqIrkilldiRPDRqtv--mT 404 (629) T KOG0336 332 ---NRNEQIEDLKRGVEIIIATPGRLNDLQMDNVINL--ASITYLVLDEADRMLDMGFEPQIRKILLDIRPDRQTV--MT 404 (629) T ss_pred ---CCHHHHHHHHCCCEEEEECCCHHHHHHHCCEEEE--EEEEEEEECCHHHHHCCCCCHHHHHHHHHCCCCCEEE--EE T ss_conf ---8546899874574177607851765553172001--1258898612666644566288898865227762255--31 Q ss_pred EC-CCCCCCHHHHHHHC Q ss_conf 07-89998768875411 Q gi|254781187|r 228 SN-TRRLNGWFYDIFNI 243 (367) Q Consensus 228 gN-P~r~~g~Fye~~~~ 243 (367) |- -+.+.-...+.|.+ T Consensus 405 SATWP~~VrrLa~sY~K 421 (629) T KOG0336 405 SATWPEGVRRLAQSYLK 421 (629) T ss_pred CCCCCHHHHHHHHHHHH T ss_conf 05586689999998640 No 406 >cd04103 Centaurin_gamma Centaurin gamma. The centaurins (alpha, beta, gamma, and delta) are large, multi-domain proteins that all contain an ArfGAP domain and ankyrin repeats, and in some cases, numerous additional domains. Centaurin gamma contains an additional GTPase domain near its N-terminus. The specific function of this GTPase domain has not been well characterized, but centaurin gamma 2 (CENTG2) may play a role in the development of autism. Centaurin gamma 1 is also called PIKE (phosphatidyl inositol (PI) 3-kinase enhancer) and centaurin gamma 2 is also known as AGAP (ArfGAP protein with a GTPase-like domain, ankyrin repeats and a Pleckstrin homology domain) or GGAP. Three isoforms of PIKE have been identified. PIKE-S (short) and PIKE-L (long) are brain-specific isoforms, with PIKE-S restricted to the nucleus and PIKE-L found in multiple cellular compartments. A third isoform, PIKE-A was identified in human glioblastoma brain cancers and has been found in various tissues. Probab=72.10 E-value=4 Score=19.76 Aligned_cols=22 Identities=23% Similarity=0.240 Sum_probs=19.2 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) +|++|.+..|+|||.++..++- T Consensus 1 ~KivllGd~~VGKTsl~~Rf~~ 22 (158) T cd04103 1 LKLGIVGNLQSGKSALVHRYLT 22 (158) T ss_pred CEEEEECCCCCCHHHHHHHHHH T ss_conf 9999999699879999999980 No 407 >TIGR03498 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively. Probab=72.02 E-value=3.7 Score=19.99 Aligned_cols=35 Identities=29% Similarity=0.385 Sum_probs=24.5 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH Q ss_conf 4776148867889999999999997089977999715379 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET 118 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~ 118 (367) |+.+-+|.|+|||++.+.++-+ -+..++|.+--.. T Consensus 142 RigIfgg~GvGKt~Ll~~i~~~-----~~adv~V~aliGe 176 (418) T TIGR03498 142 RLGIFAGSGVGKSTLLSMLARN-----TDADVVVIALVGE 176 (418) T ss_pred EEECCCCCCCCHHHHHHHHHHH-----CCCCEEEEEEEEE T ss_conf 6411378999888999999875-----0798689988302 No 408 >PRK09099 type III secretion system ATPase; Provisional Probab=71.96 E-value=3.8 Score=19.87 Aligned_cols=23 Identities=30% Similarity=0.319 Sum_probs=19.9 Q ss_pred EEEEECCCCCCHHHHHHHHHHHH Q ss_conf 47761488678899999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~ 101 (367) |+.|-+|+|+|||++.++++-+. T Consensus 165 R~gIf~gsGvGKstLl~~iar~~ 187 (441) T PRK09099 165 RMGIFAPAGVGKSTLMGMFARGT 187 (441) T ss_pred EEEEECCCCCCHHHHHHHHHHHH T ss_conf 33001589887899999898751 No 409 >cd01870 RhoA_like RhoA-like subfamily. The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranyl Probab=71.79 E-value=4.1 Score=19.69 Aligned_cols=22 Identities=27% Similarity=0.123 Sum_probs=19.0 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) .|+++.+..|+|||.++..++- T Consensus 2 ~Ki~liGd~~VGKTsli~r~~~ 23 (175) T cd01870 2 KKLVIVGDGACGKTCLLIVFSK 23 (175) T ss_pred CEEEEECCCCCCHHHHHHHHHC T ss_conf 0999999899669999999970 No 410 >cd04177 RSR1 RSR1 subgroup. RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key featu Probab=71.74 E-value=4.3 Score=19.55 Aligned_cols=22 Identities=23% Similarity=0.507 Sum_probs=19.6 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.+.+..|+|||.++..++- T Consensus 2 fKivlvGd~~VGKTsli~rf~~ 23 (168) T cd04177 2 YKIVVLGAGGVGKSALTVQFVQ 23 (168) T ss_pred EEEEEECCCCCCHHHHHHHHHH T ss_conf 1999989999779999999961 No 411 >TIGR03324 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase. Probab=71.70 E-value=6.9 Score=18.28 Aligned_cols=21 Identities=29% Similarity=0.310 Sum_probs=16.9 Q ss_pred EEEEECCCCCCHHHHHHHHHH Q ss_conf 477614886788999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~l 99 (367) |..|-++||+|||+++...++ T Consensus 164 RelIigdrgtGKTtla~dtIi 184 (497) T TIGR03324 164 RELILGDRQTGKTAIAIDTIL 184 (497) T ss_pred EEEEECCCCCCHHHHHHHHHH T ss_conf 677645888880088999997 No 412 >pfam00071 Ras Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices. Probab=71.69 E-value=3.7 Score=19.96 Aligned_cols=20 Identities=25% Similarity=0.423 Sum_probs=17.9 Q ss_pred EEEEECCCCCCHHHHHHHHH Q ss_conf 47761488678899999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~ 98 (367) |++|.+..|+|||.++..++ T Consensus 1 Ki~vvG~~~vGKTsli~r~~ 20 (162) T pfam00071 1 KLVLVGDGGVGKSSLLIRFT 20 (162) T ss_pred CEEEECCCCCCHHHHHHHHH T ss_conf 98999979977999999996 No 413 >cd01136 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway. Probab=71.54 E-value=5 Score=19.14 Aligned_cols=36 Identities=28% Similarity=0.303 Sum_probs=24.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH Q ss_conf 47761488678899999999999970899779997153799 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ 119 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q 119 (367) |+.|-+|+|+|||++.+.++.. ....++|.+--... T Consensus 71 R~~Ifg~~g~GKt~Ll~~i~~~-----~~~~v~V~~~IGer 106 (326) T cd01136 71 RLGIFAGSGVGKSTLLGMIARG-----TTADVNVIALIGER 106 (326) T ss_pred EEEEECCCCCCCCHHHHHHHHC-----CCCCEEEEEEECCC T ss_conf 7874369999846678768641-----46775999960533 No 414 >PRK05922 type III secretion system ATPase; Validated Probab=71.43 E-value=6.2 Score=18.58 Aligned_cols=35 Identities=20% Similarity=0.145 Sum_probs=24.3 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHH Q ss_conf 4776148867889999999999997089977999715379 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSET 118 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~ 118 (367) |+.+-+|.|+|||++.+.++.. ....+.|++--.. T Consensus 159 R~gIf~g~GvGKt~Ll~~ia~~-----~~~~v~V~alIGe 193 (434) T PRK05922 159 RIGVFSEPGSGKSSLLSTIAKG-----SKSTINVIALIGE 193 (434) T ss_pred EEEECCCCCCCHHHHHHHHHHC-----CCCCEEEEEEEEE T ss_conf 7773079999789999867653-----6787599984551 No 415 >cd04121 Rab40 Rab40 subfamily. This subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide d Probab=71.37 E-value=5 Score=19.17 Aligned_cols=23 Identities=17% Similarity=0.274 Sum_probs=20.0 Q ss_pred CEEEEEEECCCCCCHHHHHHHHH Q ss_conf 11247761488678899999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) +.+|+.|.+..|+|||.++..++ T Consensus 5 y~~KivllGd~~VGKTsl~~r~~ 27 (189) T cd04121 5 YLLKFLLVGDSDVGKGEILASLQ 27 (189) T ss_pred EEEEEEEECCCCCCHHHHHHHHH T ss_conf 89999999989978999999997 No 416 >cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia. Probab=71.37 E-value=7 Score=18.24 Aligned_cols=35 Identities=26% Similarity=0.315 Sum_probs=27.5 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 1247761488678899999999999970899779997 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) |+.+||..==|+|||+.++.++.-++. -|.||+++ T Consensus 1 ~r~Iai~GKGGVGKTTtavNLA~aLa~--~GkkVlli 35 (270) T cd02040 1 MRQIAIYGKGGIGKSTTTQNLSAALAE--MGKKVMIV 35 (270) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHH--CCCEEEEE T ss_conf 958999799857789999999999998--79949998 No 417 >PRK13764 ATPase; Provisional Probab=71.25 E-value=7.1 Score=18.22 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=22.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHH Q ss_conf 47761488678899999999999970 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLIST 104 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~ 104 (367) -+.|++.-|.|||+++.+++-++... T Consensus 261 GilIaG~PGaGKsTfaqalA~~~~~~ 286 (605) T PRK13764 261 GILIAGAPGAGKSTFAQALAEFYADM 286 (605) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHC T ss_conf 49997799997789999999999847 No 418 >COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription] Probab=71.19 E-value=7.1 Score=18.21 Aligned_cols=75 Identities=16% Similarity=0.192 Sum_probs=48.2 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHH Q ss_conf 89999999888875124555554112477614886788999999999999708997799971537999999999999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWL 132 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~ 132 (367) +=|...+.+|-...+.+.-. =|+ |++-=|+|||-++...+. .....|..|.+..||-==+.+= +.-+++-. T Consensus 597 ~DQl~AI~eVk~DM~~~kpM-----DRL-iCGDVGFGKTEVAmRAAF--kAV~~GKQVAvLVPTTlLA~QH-y~tFkeRF 667 (1139) T COG1197 597 PDQLKAIEEVKRDMESGKPM-----DRL-ICGDVGFGKTEVAMRAAF--KAVMDGKQVAVLVPTTLLAQQH-YETFKERF 667 (1139) T ss_pred HHHHHHHHHHHHHHCCCCCC-----HHE-EECCCCCCHHHHHHHHHH--HHHCCCCEEEEECCCHHHHHHH-HHHHHHHH T ss_conf 78999999999886069866-----102-565768759999999999--9863797499992607868998-99999873 Q ss_pred HHCC Q ss_conf 8623 Q gi|254781187|r 133 SMLP 136 (367) Q Consensus 133 ~~~~ 136 (367) .-.| T Consensus 668 ~~fP 671 (1139) T COG1197 668 AGFP 671 (1139) T ss_pred CCCC T ss_conf 3898 No 419 >KOG0346 consensus Probab=71.00 E-value=7.2 Score=18.19 Aligned_cols=77 Identities=14% Similarity=0.165 Sum_probs=51.1 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-------CCEEEEECCCHHH Q ss_conf 666842899999998888751245555541124776148867889999999999997089-------9779997153799 Q gi|254781187|r 47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-------GMSIICIANSETQ 119 (367) Q Consensus 47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-------~~~v~~~A~t~~Q 119 (367) +++.|+.-|..++--+ ++. . .+..+|-.|+|||..-+.=++=.++... +...++.+||..- T Consensus 38 G~ekpTlIQs~aIpla---LEg-K--------DvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~iLvPTkEL 105 (569) T KOG0346 38 GWEKPTLIQSSAIPLA---LEG-K--------DVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAVILVPTKEL 105 (569) T ss_pred CCCCCCHHHHCCCCHH---HCC-C--------CEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECHHHH T ss_conf 7677623443221243---248-6--------314652268871378899999999976403643246306999250999 Q ss_pred HHHHHHHHHHHHHHHCC Q ss_conf 99999999999998623 Q gi|254781187|r 120 LKNTLWAEVSKWLSMLP 136 (367) Q Consensus 120 ~~~~lw~ei~k~~~~~~ 136 (367) +.++ ..++.+....++ T Consensus 106 ~qQv-y~viekL~~~c~ 121 (569) T KOG0346 106 AQQV-YKVIEKLVEYCS 121 (569) T ss_pred HHHH-HHHHHHHHHHHH T ss_conf 9999-999999999878 No 420 >COG1157 FliI Flagellar biosynthesis/type III secretory pathway ATPase [Cell motility and secretion / Intracellular trafficking and secretion] Probab=70.88 E-value=4.1 Score=19.68 Aligned_cols=47 Identities=26% Similarity=0.298 Sum_probs=31.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHC Q ss_conf 477614886788999999999999708997799971537999999999999999862 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSML 135 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~ 135 (367) |+-|=||-|+|||++.++++- +....++|+|=-...- +|++.+++.. T Consensus 165 RiGIFAgsGVGKStLLgMiar-----~t~aDv~ViaLIGERG-----REVrEFIE~~ 211 (441) T COG1157 165 RIGIFAGSGVGKSTLLGMIAR-----NTEADVNVIALIGERG-----REVREFIEKD 211 (441) T ss_pred EEEEEECCCCCHHHHHHHHHC-----CCCCCEEEEEEEECCC-----HHHHHHHHHH T ss_conf 678871699868999999962-----4669879999760664-----0599999986 No 421 >KOG0979 consensus Probab=70.76 E-value=3.2 Score=20.32 Aligned_cols=18 Identities=28% Similarity=0.410 Sum_probs=9.7 Q ss_pred EECCCCCCHHHHHHHHHH Q ss_conf 614886788999999999 Q gi|254781187|r 82 ISAGRGIGKTTLNAWMML 99 (367) Q Consensus 82 v~sgrg~GKS~~~a~~~l 99 (367) |.++.|+|||.++++++| T Consensus 47 IiGpNGSGKSSiVcAIcL 64 (1072) T KOG0979 47 IIGPNGSGKSSIVCAICL 64 (1072) T ss_pred EECCCCCCCHHHHHHHHH T ss_conf 877898970488999999 No 422 >cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin. Probab=70.68 E-value=7.3 Score=18.14 Aligned_cols=39 Identities=23% Similarity=0.278 Sum_probs=30.5 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH Q ss_conf 47761488678899999999999970899779997153799 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ 119 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q 119 (367) =++|.+-.++|||+++..++-.+ +..|.+|.++=...+. T Consensus 3 ii~ivG~snSGKTTLi~kli~~l--~~~G~~V~~iKH~~H~ 41 (159) T cd03116 3 VIGFVGYSGSGKTTLLEKLIPAL--SARGLRVAVIKHDHHD 41 (159) T ss_pred EEEEEECCCCCHHHHHHHHHHHH--HHCCCEEEEEEECCCC T ss_conf 99999679999999999999999--9779859899734767 No 423 >COG3973 Superfamily I DNA and RNA helicases [General function prediction only] Probab=70.51 E-value=7.4 Score=18.12 Aligned_cols=51 Identities=18% Similarity=0.301 Sum_probs=37.8 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCC----CEEEEECCCHHHHHHHHHHHHHHHHHH Q ss_conf 47761488678899999999999970899----779997153799999999999999986 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPG----MSIICIANSETQLKNTLWAEVSKWLSM 134 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~----~~v~~~A~t~~Q~~~~lw~ei~k~~~~ 134 (367) -+.|.++-|+|||+++--=+.|++..+.+ .-|++.+|.. ++-..++..+-. T Consensus 228 ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l~~k~vlvl~PN~-----vFleYis~VLPe 282 (747) T COG3973 228 ILVVQGAAGSGKTTIALHRVAYLLYGYRGPLQAKPVLVLGPNR-----VFLEYISRVLPE 282 (747) T ss_pred EEEEECCCCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEECCCH-----HHHHHHHHHCHH T ss_conf 4899558888713588999999985356624668659982838-----999999875544 No 424 >PRK13721 conjugal transfer ATP-binding protein TraC; Provisional Probab=70.47 E-value=7.4 Score=18.12 Aligned_cols=42 Identities=19% Similarity=0.277 Sum_probs=30.7 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHH Q ss_conf 247761488678899999999999970899779997--15379999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSETQLK 121 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~Q~~ 121 (367) |+++|.++-|.|||+++-.++.=++.. |.+|+++ -.++..+. T Consensus 475 ~N~~I~g~SGsGKSf~~q~l~~~~~~~--G~~V~IID~G~SY~~lc 518 (864) T PRK13721 475 YNMAVCGTSGAGKTGLIQPLIRSVLDS--GGFAVVFDMGDGYKSLC 518 (864) T ss_pred CCEEEECCCCCCHHHHHHHHHHHHHHC--CCEEEEEECCCCHHHHH T ss_conf 006998289986899999999999857--99799996997899999 No 425 >cd03289 ABCC_CFTR2 The CFTR subfamily domain 2. The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2. Probab=70.46 E-value=4.6 Score=19.36 Aligned_cols=31 Identities=19% Similarity=0.228 Sum_probs=22.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 4776148867889999999999997089977999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC 112 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~ 112 (367) +++|.+.-|+|||+++..++- +.. +...|.+ T Consensus 32 ~vaIvG~sGsGKSTLl~lL~g--l~~-~~G~I~i 62 (275) T cd03289 32 RVGLLGRTGSGKSTLLSAFLR--LLN-TEGDIQI 62 (275) T ss_pred EEEEECCCCCCHHHHHHHHHH--HCC-CCCEEEE T ss_conf 999999999979999999960--357-8953999 No 426 >pfam04310 MukB MukB N-terminal. This family represents the N-terminal region of MukB, one of a group of bacterial proteins essential for the movement of nucleoids from mid-cell towards the cell quarters (i.e. chromosome partitioning). The structure of the N-terminal domain consists of an antiparallel six-stranded beta sheet surrounded by one helix on one side and by five helices on the other side. It contains an exposed Walker A loop in an unexpected helix-loop-helix motif (in other proteins, Walker A motifs generally adopt a P loop conformation as part of a strand-loop-helix motif embedded in a conserved topology of alternating helices and (parallel) beta strands). Probab=70.31 E-value=4.2 Score=19.60 Aligned_cols=36 Identities=28% Similarity=0.407 Sum_probs=27.6 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 477614886788999999999999708997799971537 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) -++..+|.|.|||++.++++.- .-|+.+-+-..||. T Consensus 29 vttLsG~NGAGKsT~m~Af~ta---lIPDl~~l~frntt 64 (227) T pfam04310 29 VTTLSGGNGAGKSTTMAAFITA---LIPDLSLLHFRNTT 64 (227) T ss_pred EEEEECCCCCCHHHHHHHHHHH---HCCCCEEEEECCCC T ss_conf 6886447876548799999998---66664388621556 No 427 >TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase; InterPro: IPR006417 The NadR protein of Escherichia coli and closely related bacteria is both enzyme and regulatory protein. The first 60 or so amino acids, N-terminal region is a DNA-binding helix-turn-helix domain (IPR001387 from INTERPRO) responsible for repressing the nadAB genes of NAD de novo biosynthesis. The NadR homologs in Mycobacterium tuberculosis, Haemophilus influenzae, and others appear to lack the repressor domain. NadR has recently been shown to act as an enzyme of the salvage pathway of NAD biosynthesis, nicotinamide-nucleotide adenylyltransferase; members of this family are presumed to share this activity. E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this family share that activity. ; GO: 0003677 DNA binding, 0030528 transcription regulator activity, 0006810 transport, 0019363 pyridine nucleotide biosynthetic process, 0045449 regulation of transcription. Probab=70.24 E-value=4.9 Score=19.22 Aligned_cols=35 Identities=29% Similarity=0.244 Sum_probs=26.0 Q ss_pred HHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHH Q ss_conf 7512455555411247761488678899999999999 Q gi|254781187|r 65 HCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWL 101 (367) Q Consensus 65 ~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~ 101 (367) |+.+-..++ .+.+|||.+|--+|||+|+-.++--+ T Consensus 165 hIpr~~rp~--F~k~V~ilG~eStGKstLv~~lA~~~ 199 (346) T TIGR01526 165 HIPREVRPF--FVKTVAILGGESTGKSTLVNKLAEKL 199 (346) T ss_pred HCCCEECCC--EEEEEEEECCCCCCHHHHHHHHHHHH T ss_conf 147202322--04588885588863689999999984 No 428 >PRK10636 putative ABC transporter ATP-binding protein; Provisional Probab=70.20 E-value=3.7 Score=19.92 Aligned_cols=34 Identities=6% Similarity=-0.130 Sum_probs=22.3 Q ss_pred CCCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCE Q ss_conf 358628999754-5599889999898740698825 Q gi|254781187|r 189 NTHGMAVFNDEA-SGTPDIINKSILGFFTELNPNR 222 (367) Q Consensus 189 ~~~~~l~ivDEA-sgI~d~i~e~i~g~Lt~~~~~~ 222 (367) .....++++||- ++.+-.....++..|...+.-+ T Consensus 165 ~~~PdlLLLDEPTnhLD~~~i~~L~~~L~~~~gtv 199 (638) T PRK10636 165 ICRSDLLLLDEPTNHLDLDAVIWLEKWLKSYQGTL 199 (638) T ss_pred CCCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCEE T ss_conf 58999899708888899899999999999769819 No 429 >pfam07015 VirC1 VirC1 protein. This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon which enhances T-DNA processing probably does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA. Probab=70.15 E-value=7.5 Score=18.07 Aligned_cols=100 Identities=15% Similarity=0.112 Sum_probs=49.1 Q ss_pred EEEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 77614-88678899999999999970899779997153799999999999999986231211233332100012333221 Q gi|254781187|r 80 CAISA-GRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL 158 (367) Q Consensus 80 ~~v~s-grg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (367) +++++ -=|+|||+++..++..+. ..|.+|.++-.--++ .-.-|.+...-..... T Consensus 4 i~~~~~KGG~GKtT~a~~la~~~~--~~g~~V~liD~Dpq~-s~~~W~~~a~~~~~~~---------------------- 58 (231) T pfam07015 4 ITFCSFKGGAGKTTALMGLCSALA--SDGKRVALFEADENR-PLTKWRENALRKGTWD---------------------- 58 (231) T ss_pred EEEEECCCCCCHHHHHHHHHHHHH--HCCCEEEEEECCCCC-CHHHHHHHHHHCCCCC---------------------- T ss_conf 999617998659999999999999--689959999689986-8899999876468888---------------------- Q ss_pred CCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHH Q ss_conf 111345776126621013544556521011358628999754559988999989 Q gi|254781187|r 159 EQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSIL 212 (367) Q Consensus 159 ~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~ 212 (367) +......... ...-.......+...+.++|+|-+..+++.+-.++. T Consensus 59 -------~~~~v~~~~~-~~~l~~~~~~~~~~~yD~VIIDtpg~~s~~~~~AI~ 104 (231) T pfam07015 59 -------PACEIFNADE-LPLLEQAYEHAEGSGFDYALADTHGGSSELNNTIIA 104 (231) T ss_pred -------CCCCEECCCC-HHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHH T ss_conf -------7652220566-015899999886579998998399857589999999 No 430 >COG1674 FtsK DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning] Probab=70.10 E-value=6.5 Score=18.44 Aligned_cols=50 Identities=18% Similarity=0.113 Sum_probs=35.9 Q ss_pred HCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCC--EEEEECCC Q ss_conf 124555554112477614886788999999999999708997--79997153 Q gi|254781187|r 67 HSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGM--SIICIANS 116 (367) Q Consensus 67 ~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~--~v~~~A~t 116 (367) +....-+...+..+.|++..|+|||+..-.+++=++.++.+. +.+++-|. T Consensus 520 ~~~~~~dlak~~hlli~G~tgsGKSv~lnt~i~Sll~~~~P~ev~~~~iD~k 571 (858) T COG1674 520 QEPIVIDLAKAGHLLIAGATGSGKSVALNTMILSLLYTHSPEEVRFYIIDPK 571 (858) T ss_pred CCCEEEECCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCHHEEEEEECCC T ss_conf 8813855356888788248886515589999999875189068499997478 No 431 >cd04139 RalA_RalB RalA/RalB subfamily. The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exo Probab=70.09 E-value=4.7 Score=19.32 Aligned_cols=22 Identities=27% Similarity=0.572 Sum_probs=19.1 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.+.+.-|+|||.++..++- T Consensus 1 fKvvlvGd~~VGKTsli~r~~~ 22 (164) T cd04139 1 YKVIVVGAGGVGKSALTLQFMY 22 (164) T ss_pred CEEEEECCCCCCHHHHHHHHHH T ss_conf 9799999999889999999971 No 432 >cd04145 M_R_Ras_like M-Ras/R-Ras-like subfamily. This subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an ali Probab=70.08 E-value=5.1 Score=19.09 Aligned_cols=22 Identities=27% Similarity=0.625 Sum_probs=19.0 Q ss_pred EEEEEEECCCCCCHHHHHHHHH Q ss_conf 1247761488678899999999 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~ 98 (367) -||+.|.+.-|+|||.++..++ T Consensus 2 t~Kiv~lGd~~VGKTsli~r~~ 23 (164) T cd04145 2 TYKLVVVGGGGVGKSALTIQFI 23 (164) T ss_pred CEEEEEECCCCCCHHHHHHHHH T ss_conf 3799999999978899999998 No 433 >TIGR02546 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase; InterPro: IPR013380 Proteins in this entry are found in a variety of bacteria, and are predicted to be ATPases involved in type III secretion systems. One example is YscN (P40290 from SWISSPROT) from Yersinia enterocolitica, which is thought to energise the YOP (Yersinia outer protein) secretion system .; GO: 0046961 hydrogen ion transporting ATPase activity rotational mechanism, 0030254 protein secretion by the type III secretion system. Probab=69.95 E-value=7 Score=18.26 Aligned_cols=129 Identities=16% Similarity=0.164 Sum_probs=67.7 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 47761488678899999999999970899779997153799999999999999986231211233332100012333221 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAELL 158 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (367) |+=|=|+=|+|||+|.++++ -...+.|+|+|=-..-= +|++.+++..--. T Consensus 155 RiGIFA~aG~GKSTLL~~i~-----~g~~ADv~V~ALIGERG-----REVREFiE~~lg~-------------------- 204 (430) T TIGR02546 155 RIGIFAGAGVGKSTLLGMIA-----RGASADVNVIALIGERG-----REVREFIEHLLGE-------------------- 204 (430) T ss_pred EEEEEECCCCCHHHHHHHHH-----CCCCCCEEEEEECCCCC-----HHHHHHHHHCCCH-------------------- T ss_conf 05787088861668999986-----18988789986027876-----0478887520783-------------------- Q ss_pred CCCCCCCCCCEEEEECCCCCCCCCCCCCCC------------CCCCCEEEEEC--------------------CCCCCHH Q ss_conf 111345776126621013544556521011------------35862899975--------------------4559988 Q gi|254781187|r 159 EQSMGIDSKHYTITCRTYSEERPDTFVGPH------------NTHGMAVFNDE--------------------ASGTPDI 206 (367) Q Consensus 159 ~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h------------~~~~~l~ivDE--------------------AsgI~d~ 206 (367) + ...-..+.+.|++.-..|..+..+ |.+ +|+++|= +.|.|+- T Consensus 205 ----e-~~~RsVlVvsTSDrss~eR~~AAy~ATaIAEYFRDQGk~-VlLmmDSlTRfARA~REiGLAaGEP~aR~GyPPS 278 (430) T TIGR02546 205 ----E-GRKRSVLVVSTSDRSSLERLKAAYTATAIAEYFRDQGKR-VLLMMDSLTRFARALREIGLAAGEPPARRGYPPS 278 (430) T ss_pred ----H-HCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCE-EEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCC T ss_conf ----0-524248996079866799999987887999999973990-7988402779999987788753784002577873 Q ss_pred HHHHHHHHH--HCCCCCEEEEEEEC----CCCCCCHHHHHHHC Q ss_conf 999989874--06988258999807----89998768875411 Q gi|254781187|r 207 INKSILGFF--TELNPNRFWIMTSN----TRRLNGWFYDIFNI 243 (367) Q Consensus 207 i~e~i~g~L--t~~~~~~~~i~igN----P~r~~g~Fye~~~~ 243 (367) +|..+=-.| ++.+.+..+-++.| ++..+.++.|--+. T Consensus 279 VF~~LPRLLERaG~~e~GSITA~YTVLvEgDd~~dP~ADEvRS 321 (430) T TIGR02546 279 VFSSLPRLLERAGNSEKGSITALYTVLVEGDDMNDPIADEVRS 321 (430) T ss_pred HHHHCCHHHCCCCCCCCCCEEEEEEEEECCCCCCCCHHHHHHH T ss_conf 6650750122786112962534567876277799843665544 No 434 >PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional Probab=69.86 E-value=1.3 Score=22.82 Aligned_cols=37 Identities=24% Similarity=0.270 Sum_probs=25.6 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHH Q ss_conf 999999988887512455555411247761488678899999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) .+.++|++|.=.+.++. .++|.+..|+|||++.-.+. T Consensus 18 ~~~~aL~~vsl~I~~Ge--------~~aiiG~nGsGKSTLl~~l~ 54 (286) T PRK13646 18 YQHQAIHDVNTEFEQGK--------YYAIVGQTGSGKSTLIQNIN 54 (286) T ss_pred CCCCEEECEEEEECCCC--------EEEEECCCCCHHHHHHHHHH T ss_conf 70506624177986998--------99999999981999999997 No 435 >cd04168 TetM_like Tet(M)-like subfamily. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB. Probab=69.83 E-value=7.6 Score=18.03 Aligned_cols=135 Identities=16% Similarity=0.124 Sum_probs=67.4 Q ss_pred EEEEECCCCCCHHHHHHHHHHH-HHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 4776148867889999999999-997089977999715379999999999999998623121123333210001233322 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLW-LISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL 157 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw-~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (367) ++++.+..|.|||+++-.++.- ....+.|. |- ..+...+..=-|.++-+.....-..+.|.. T Consensus 1 Niai~gH~~~GKTtL~e~lL~~~g~i~r~G~-v~----~g~t~~D~~~eE~~r~isi~~~~~~~~~~~------------ 63 (237) T cd04168 1 NIGILAHVDAGKTTLTESLLYTSGAIRKLGS-VD----KGTTRTDTMELERQRGITIFSAVASFQWED------------ 63 (237) T ss_pred CEEEECCCCCCHHHHHHHHHHHCCHHHHCCC-EE----CCCCCCCCHHHHHHHCCEEEEEEEEEEECC------------ T ss_conf 9899938998999999999996571222663-30----683037854998984870310589999899------------ Q ss_pred CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---HHHHHHHHHHHCCCCCEEEEEEECC-CCC Q ss_conf 111134577612662101354455652101135862899975455998---8999989874069882589998078-999 Q gi|254781187|r 158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---IINKSILGFFTELNPNRFWIMTSNT-RRL 233 (367) Q Consensus 158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---~i~e~i~g~Lt~~~~~~~~i~igNP-~r~ 233 (367) ....++.+-+......+...+++.-...++++|=.+||.. .+|..+. ..+-+.+ +. -|= .|. T Consensus 64 --------~~~n~iDtPG~~dF~~e~~~al~~~D~av~Vv~a~~Gv~~~t~~~~~~~~----~~~~P~i-if-iNKmDre 129 (237) T cd04168 64 --------TKVNLIDTPGHMDFIAEVERSLSVLDGAILVISAVEGVQAQTRILWRLLR----KLNIPTI-IF-VNKIDRA 129 (237) T ss_pred --------EEEEEEECCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHHHH----HCCCCEE-EE-EECCCCC T ss_conf --------87999889884656668988976348169999658882234499999999----8599859-98-6244578 Q ss_pred CCHHHHHHHCC Q ss_conf 87688754112 Q gi|254781187|r 234 NGWFYDIFNIP 244 (367) Q Consensus 234 ~g~Fye~~~~~ 244 (367) .--|.+....- T Consensus 130 ~adf~~~l~~i 140 (237) T cd04168 130 GADLEKVYQEI 140 (237) T ss_pred CCCHHHHHHHH T ss_conf 99999999999 No 436 >cd04176 Rap2 Rap2 subgroup. The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, incl Probab=69.80 E-value=5.1 Score=19.08 Aligned_cols=22 Identities=23% Similarity=0.514 Sum_probs=19.2 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.+.+.-|+|||.++..++- T Consensus 2 ~KivllGd~~VGKTsli~r~~~ 23 (163) T cd04176 2 YKVVVLGSGGVGKSALTVQFVS 23 (163) T ss_pred EEEEEECCCCCCHHHHHHHHHH T ss_conf 3999989999789999999970 No 437 >KOG1802 consensus Probab=69.80 E-value=5 Score=19.13 Aligned_cols=37 Identities=22% Similarity=0.281 Sum_probs=29.6 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 77614886788999999999999708997799971537 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) ..|.++-|+|||..+|.++. .+..+....|+|+||+- T Consensus 428 sLIQGPPGTGKTvtsa~IVy-hl~~~~~~~VLvcApSN 464 (935) T KOG1802 428 SLIQGPPGTGKTVTSATIVY-HLARQHAGPVLVCAPSN 464 (935) T ss_pred EEEECCCCCCCEEHHHHHHH-HHHHHCCCCEEEECCCC T ss_conf 15546999883311689999-99985289569981650 No 438 >cd00157 Rho Rho (Ras homology) family. Members of the Rho family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho protein Probab=69.74 E-value=4.7 Score=19.30 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=18.3 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) +|+.+.+..|+|||.++..++ T Consensus 1 iKi~llGd~~VGKTsli~r~~ 21 (171) T cd00157 1 IKIVVVGDGAVGKTCLLISYT 21 (171) T ss_pred CEEEEECCCCCCHHHHHHHHH T ss_conf 989999999966999999996 No 439 >TIGR00150 TIGR00150 conserved hypothetical protein TIGR00150; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements . . Probab=69.65 E-value=5.2 Score=19.06 Aligned_cols=38 Identities=21% Similarity=0.214 Sum_probs=28.7 Q ss_pred EEEE-ECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHH Q ss_conf 4776-148867889999999999997089977999715379999 Q gi|254781187|r 79 KCAI-SAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLK 121 (367) Q Consensus 79 ~~~v-~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~ 121 (367) .|.+ .+==|.|||+++-+++. +-|....+++||++=+. T Consensus 29 ~v~~L~GDlGaGKTtl~~G~~~-----~LG~~~~~~SPTftlv~ 67 (147) T TIGR00150 29 TVVLLKGDLGAGKTTLVKGLLQ-----GLGITGNVTSPTFTLVN 67 (147) T ss_pred EEEEEECCCCCCHHHHHHHHHH-----HCCCEEEEECCCCCEEE T ss_conf 3899732346665899999998-----37922688579321010 No 440 >pfam03029 ATP_bind_1 Conserved hypothetical ATP binding protein. Members of this family are found in a range of archaea and eukaryotes and have hypothesized ATP binding activity. Probab=69.65 E-value=6.8 Score=18.33 Aligned_cols=35 Identities=20% Similarity=0.250 Sum_probs=25.5 Q ss_pred EECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC Q ss_conf 61488678899999999999970899779997153 Q gi|254781187|r 82 ISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANS 116 (367) Q Consensus 82 v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t 116 (367) |.++-|+|||+..+.+.-|.-..+....++=.=|- T Consensus 1 ViGpaGSGKTT~~~~l~~~l~~~~r~~~vvNLDPA 35 (234) T pfam03029 1 VVGGAGSGKTTFVGALSEILPLRGRSVYVVNLDPA 35 (234) T ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC T ss_conf 98989898899999999999977997599978986 No 441 >PRK11147 ABC transporter ATPase component; Reviewed Probab=69.63 E-value=4.2 Score=19.60 Aligned_cols=42 Identities=14% Similarity=0.088 Sum_probs=27.4 Q ss_pred CCCCCCCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCEEEEEEE Q ss_conf 1011358628999754-5599889999898740698825899980 Q gi|254781187|r 185 VGPHNTHGMAVFNDEA-SGTPDIINKSILGFFTELNPNRFWIMTS 228 (367) Q Consensus 185 ~g~h~~~~~l~ivDEA-sgI~d~i~e~i~g~Lt~~~~~~~~i~ig 228 (367) +..-..+..++|+||- ++.+-...+.++..|...+.-+ ++++ T Consensus 168 A~aL~~~PdlLlLDEPTn~LD~~~~~~L~~~L~~~~gtv--liIS 210 (632) T PRK11147 168 ARALVSNPDVLLLDEPTNHLDIETIEWLEGFLKTFQGSI--IFIS 210 (632) T ss_pred HHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCCEE--EEEE T ss_conf 998568999999848876589999999999999759849--9997 No 442 >PRK06851 hypothetical protein; Provisional Probab=69.42 E-value=1.7 Score=22.07 Aligned_cols=51 Identities=16% Similarity=0.228 Sum_probs=41.1 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHH Q ss_conf 477614886788999999999999708997799971537999999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVS 129 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~ 129 (367) -..+.+|-|+|||+++-.+.--++....+...+.++.--+.+.-++.++++ T Consensus 33 i~ilKGGpGtGKStlmK~ig~~~~~~GydVE~~hcssD~~SlDGvvip~lk 83 (368) T PRK06851 33 IFILKGGPGTGKSTLMKKIGEEFLEKGYDVEFLHCSSDNDSLDGVIIPELK 83 (368) T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCEEEECCCC T ss_conf 999968999778999999999999689837999758998864359975787 No 443 >TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PMID:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined. Probab=69.23 E-value=7.8 Score=17.95 Aligned_cols=36 Identities=31% Similarity=0.341 Sum_probs=25.0 Q ss_pred EEEEEEECCC-CCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 1247761488-6788999999999999708997799971 Q gi|254781187|r 77 IFKCAISAGR-GIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 77 ~~~~~v~sgr-g~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) |..++|.++. |+|||++++.++.-+. ..|.+|+++= T Consensus 1 MkiIav~n~KGGVGKTT~avNLA~~La--~~G~rVLlID 37 (246) T TIGR03371 1 MKVIAIVGIKGGVGRTTLTAALASALK--LLGEPVLAID 37 (246) T ss_pred CEEEEEECCCCCCCHHHHHHHHHHHHH--HCCCCEEEEE T ss_conf 939999759998549999999999999--6899789997 No 444 >PRK13695 putative NTPase; Provisional Probab=69.22 E-value=7.8 Score=17.95 Aligned_cols=164 Identities=11% Similarity=0.043 Sum_probs=69.5 Q ss_pred EEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 12477614886788999999999999708997799971537999999999999999862312112333321000123332 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAE 156 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 (367) ..|+-+.+--|+|||+++.-++--+-.-......++|.+....-+.+- |.+-...-....+... T Consensus 3 ~~kI~iTG~PGvGKTTli~Kv~~~L~~~g~~v~GF~T~Evre~G~R~G----------------F~vv~l~~g~~~~lA~ 66 (174) T PRK13695 3 ALRIGITGMPGVGKTTLVLKIAELLAREGYKVGGFITEEVREGGKRIG----------------FKIIDLDTGEEGILAR 66 (174) T ss_pred CCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCEEEE----------------EEEEECCCCCEEEEEE T ss_conf 429998789998899999999999863696174699525603882850----------------5999905885687675 Q ss_pred CCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC---CHHHHHHHHHHHHCCCCCEEEEEEECCCCC Q ss_conf 21111345776126621013544556521011358628999754559---988999989874069882589998078999 Q gi|254781187|r 157 LLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGT---PDIINKSILGFFTELNPNRFWIMTSNTRRL 233 (367) Q Consensus 157 ~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI---~d~i~e~i~g~Lt~~~~~~~~i~igNP~r~ 233 (367) ... .....-|.+.+....+....-.+++-.. .+..++++||-... +..+.++++..|.+ +.+.+ ..+ | + T Consensus 67 ~~~-~~~~~VgkY~V~~~~~e~~~~~~l~~a~-~~~dlivIDEIG~MEl~s~~F~~~V~~~L~s-~kpvl-~ti--h-~- 138 (174) T PRK13695 67 VGA-VSRPRVGKYVVNLEDLERIAIPAISRAL-READLIIIDEIGPMELKSKKFVSAVEEVLKS-EKPVI-ATV--H-R- 138 (174) T ss_pred CCC-CCCCCCCCEEEEHHHHHHHHHHHHHHCC-CCCCEEEEECCCHHHHHHHHHHHHHHHHHCC-CCCEE-EEE--C-H- T ss_conf 378-8985545668716897899899998353-5787999963103311049999999999738-99899-997--7-5- Q ss_pred CCHHHHHHHCCCCCEEEEEECCCCCCCCCHHHHHH Q ss_conf 87688754112235046752333288889889999 Q gi|254781187|r 234 NGWFYDIFNIPLEDWKRYQIDTRTVEGIDSGFHEG 268 (367) Q Consensus 234 ~g~Fye~~~~~~~~w~~~~~~~~d~p~~~~~~i~~ 268 (367) .|-+.... ++ -..+.++-.+-..+..+-++. T Consensus 139 --p~v~~ik~-~~-~~v~~vT~~NRd~l~~~Il~~ 169 (174) T PRK13695 139 --PVVQRIRS-LG-GEVFWLTPENRNILPEEILNR 169 (174) T ss_pred --HHHHHHHC-CC-CEEEEECHHHHHHHHHHHHHH T ss_conf --88898633-79-899998934677559999999 No 445 >pfam01656 CbiA CobQ/CobB/MinD/ParA nucleotide binding domain. This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family. Probab=69.19 E-value=7.9 Score=17.95 Aligned_cols=31 Identities=39% Similarity=0.498 Sum_probs=22.7 Q ss_pred EEEC-CCCCCHHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 7614-88678899999999999970899779997 Q gi|254781187|r 81 AISA-GRGIGKTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 81 ~v~s-grg~GKS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) +|.+ -=|+|||++++.++..+.- .+.+|+++ T Consensus 2 av~s~KGGVGKTT~a~nLA~~la~--~G~rVlli 33 (212) T pfam01656 2 AIAGTKGGVGKTTLAANLARALAK--RGYRVLLI 33 (212) T ss_pred EEECCCCCHHHHHHHHHHHHHHHH--CCCCEEEE T ss_conf 897689980699999999999997--89978998 No 446 >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=69.08 E-value=7.9 Score=17.93 Aligned_cols=34 Identities=24% Similarity=0.305 Sum_probs=25.5 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 776148867889999999999997089977999715 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) +.|.++-|+|||.++.-++.-.+. .+.++++++- T Consensus 2 tLi~G~pGsGKT~~a~qfl~~~a~--~ge~~lyis~ 35 (187) T cd01124 2 TLLSGGPGTGKTTFALQFLYAGLA--RGEPGLYVTL 35 (187) T ss_pred EEEEECCCCCHHHHHHHHHHHHHH--CCCCEEEEEE T ss_conf 158768999999999999999987--6997899995 No 447 >TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I; InterPro: IPR011775 This entry represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll . This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. It is also found in certain archaea not known to make chlorins.; GO: 0005524 ATP binding, 0016851 magnesium chelatase activity, 0006779 porphyrin biosynthetic process. Probab=68.85 E-value=8 Score=17.90 Aligned_cols=138 Identities=12% Similarity=0.036 Sum_probs=68.0 Q ss_pred CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH--HHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCC Q ss_conf 554112477614886788999999999999708997799971537--999999999999999862-31211233332100 Q gi|254781187|r 73 SNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE--TQLKNTLWAEVSKWLSML-PHRHWFEMQSLSLH 149 (367) Q Consensus 73 ~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~--~Q~~~~lw~ei~k~~~~~-~~~~~~~~~~~~~~ 149 (367) -+|..==|-|.+-||+|||+.+=+|+- .-|.-+++---|.- -..+..+..|.+-..... ..+... +-..+.. T Consensus 21 idP~IGGVmvmGdRGTgKSTavRALAa----lLP~IkaVagcP~n~~Ps~~~~~c~e~r~~~~~~Gkt~~~~-~i~~pvp 95 (340) T TIGR02030 21 IDPKIGGVMVMGDRGTGKSTAVRALAA----LLPEIKAVAGCPFNSAPSDREELCEEVRILEDSSGKTKKLA-VIEKPVP 95 (340) T ss_pred ECCCCCEEEEECCCCCCHHHHHHHHHH----HCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCE-EEECCCC T ss_conf 068856288867789835689999997----49940786176878888886135767777531268656751-5515765 Q ss_pred CCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCC Q ss_conf 012333221111345776126621013544556521011358628999754559988999989874069 Q gi|254781187|r 150 PSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKSILGFFTEL 218 (367) Q Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~i~g~Lt~~ 218 (367) +-.......+.-.-+.--.-.+-+++-....|.=++- .|+=++++||---..|++-++++=.-.++ T Consensus 96 vVDLPLGaTEDRVcGtlDIerALt~GvkAFePGLLAr---ANRG~LYiDEVNLLeDHlVDvLLDvAasG 161 (340) T TIGR02030 96 VVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLAR---ANRGYLYIDEVNLLEDHLVDVLLDVAASG 161 (340) T ss_pred EEECCCCCCCCCEECHHHHHHHHHCCCCCCCCCCHHH---HCCCCEEEEEEHHHHHHHHHHHHHHCCCC T ss_conf 3647988621313440247677504721036630466---61784255210001245665665220478 No 448 >cd04170 EF-G_bact Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group Probab=68.63 E-value=4.7 Score=19.33 Aligned_cols=134 Identities=19% Similarity=0.111 Sum_probs=67.5 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHH-HHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 477614886788999999999999-7089977999715379999999999999998623121123333210001233322 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLI-STRPGMSIICIANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSLHPSGWYAEL 157 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~-~~~~~~~v~~~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (367) ++++.+.-|.|||+++-.++..-- ..+.|. | ...+.+.|-+=-|.++-+.....-..+.|+. T Consensus 1 Ni~iigH~~aGKTtL~E~lL~~~g~i~~~G~-V----~~g~t~~D~~~~E~~RgiSi~s~~~~~~w~~------------ 63 (268) T cd04170 1 NIALVGHSGSGKTTLAEALLYATGAIDRLGS-V----EDGTTVSDYDPEEIKRKMSISTSVAPLEWKG------------ 63 (268) T ss_pred CEEEEECCCCCHHHHHHHHHHHCCCCCCCCC-C----CCCCCCCCCCHHHHHCCCCEECCEEEEEECC------------ T ss_conf 9899908999989999999996699665765-4----5897357787889867967513557888899------------ Q ss_pred CCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---HHHHHHHHHHHCCCCCEEEEEEECCC-CC Q ss_conf 111134577612662101354455652101135862899975455998---89999898740698825899980789-99 Q gi|254781187|r 158 LEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---IINKSILGFFTELNPNRFWIMTSNTR-RL 233 (367) Q Consensus 158 ~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---~i~e~i~g~Lt~~~~~~~~i~igNP~-r~ 233 (367) ....++..-+......|...+++.-...++++|=.+||.. .+|+.+. ..+-+.+ ++-|=- |. T Consensus 64 --------~~inliDTPG~~DF~~e~~~aL~v~D~Av~Vida~~GVe~~T~~~w~~~~----~~~iP~i--~fINKmDr~ 129 (268) T cd04170 64 --------HKINLIDTPGYADFVGETRAALRAADAALVVVSAQSGVEVGTEKLWEFAD----EAGIPRI--IFINKMDRE 129 (268) T ss_pred --------EEEEEEECCCCHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHH----HCCCCEE--EEEECCCCC T ss_conf --------79999869897579999999840478399994187547687999999999----8599989--999787878 Q ss_pred CCHHHHHHHC Q ss_conf 8768875411 Q gi|254781187|r 234 NGWFYDIFNI 243 (367) Q Consensus 234 ~g~Fye~~~~ 243 (367) .--|.++... T Consensus 130 ~ad~~~~l~~ 139 (268) T cd04170 130 RADFDKTLAA 139 (268) T ss_pred CCCHHHHHHH T ss_conf 9964779999 No 449 >PRK13343 F0F1 ATP synthase subunit alpha; Provisional Probab=68.62 E-value=8.1 Score=17.87 Aligned_cols=21 Identities=24% Similarity=0.294 Sum_probs=17.1 Q ss_pred EEEEECCCCCCHHHHHHHHHH Q ss_conf 477614886788999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~l 99 (367) |+.|-+|+|+|||+++.-.++ T Consensus 164 R~gIfg~~GvGKT~L~~~~I~ 184 (502) T PRK13343 164 RELIIGDRQTGKTAIAIDAII 184 (502) T ss_pred EEECCCCCCCCCCHHHHHHHH T ss_conf 775136788880489999999 No 450 >TIGR00064 ftsY signal recognition particle-docking protein FtsY; InterPro: IPR004390 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family includes the cell division ABC transporter and the periplasmic substrate-binding protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In Escherichia coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.; GO: 0005525 GTP binding. Probab=68.61 E-value=8.1 Score=17.87 Aligned_cols=130 Identities=17% Similarity=0.198 Sum_probs=72.7 Q ss_pred CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 5555541124776148867889999999999997089977999-715379999999999999998623121123333210 Q gi|254781187|r 70 VNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKNTLWAEVSKWLSMLPHRHWFEMQSLSL 148 (367) Q Consensus 70 ~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~~lw~ei~k~~~~~~~~~~~~~~~~~~ 148 (367) .....|+++ .+.+=.|+|||+.+|=++-++.--. .+|++ -+-|.+=+- -..+..|.+++-. T Consensus 77 ~~~~kp~Vi--l~VGVNG~GKTTTIaKLA~~l~~~G--k~V~laAgDTFRAAA---~EQL~~Wa~R~gv----------- 138 (284) T TIGR00064 77 PEEKKPNVI--LFVGVNGVGKTTTIAKLANKLKKQG--KSVLLAAGDTFRAAA---IEQLEVWAKRLGV----------- 138 (284) T ss_pred CCCCCCEEE--EEEEEECCCHHHHHHHHHHHHHHCC--CEEEEECCCHHHHHH---HHHHHHHHHHHCC----------- T ss_conf 147897799--9984408860102889999998749--908998275247999---9999998988387----------- Q ss_pred CCCCCCCCCCCCCCC-CCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---------HHHHHHHHHHH-C Q ss_conf 001233322111134-577612662101354455652101135862899975455998---------89999898740-6 Q gi|254781187|r 149 HPSGWYAELLEQSMG-IDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---------IINKSILGFFT-E 217 (367) Q Consensus 149 ~~~~~~~~~~~~~~~-~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---------~i~e~i~g~Lt-~ 217 (367) ...+...+ .|+-+..- ++.+...+.+...+++|-|.-... +|.-++.-... + T Consensus 139 -------~vi~~~~gn~DPAaV~f----------DAi~~Ak~~niDvvliDTAGRLqnk~NLm~EL~KI~RV~~k~~~~~ 201 (284) T TIGR00064 139 -------DVIKQKEGNADPAAVIF----------DAIQAAKARNIDVVLIDTAGRLQNKVNLMDELKKIKRVIKKVDPVD 201 (284) T ss_pred -------EEEECCCCCCCCHHHHH----------HHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCC T ss_conf -------55407889887178999----------9899998749978997347545466203999999999873210257 Q ss_pred CCCCEEEEEEECCCCCCC Q ss_conf 988258999807899987 Q gi|254781187|r 218 LNPNRFWIMTSNTRRLNG 235 (367) Q Consensus 218 ~~~~~~~i~igNP~r~~g 235 (367) .-...+ +.+-..++.++ T Consensus 202 aP~e~l-LVlDAt~Gqna 218 (284) T TIGR00064 202 APDEVL-LVLDATTGQNA 218 (284) T ss_pred CCCEEE-EEEHHHHHHHH T ss_conf 875575-42202220308 No 451 >COG5008 PilU Tfp pilus assembly protein, ATPase PilU [Cell motility and secretion / Intracellular trafficking and secretion] Probab=68.39 E-value=7.1 Score=18.20 Aligned_cols=29 Identities=28% Similarity=0.280 Sum_probs=18.4 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCC Q ss_conf 77614886788999999999999708997 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGM 108 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~ 108 (367) +.|.++.|+|||+..|.++-+.--..++. T Consensus 130 viiVGaTGSGKSTtmAaMi~yRN~~s~gH 158 (375) T COG5008 130 VIIVGATGSGKSTTMAAMIGYRNKNSTGH 158 (375) T ss_pred EEEECCCCCCCHHHHHHHHCCCCCCCCCC T ss_conf 99987788884016899860134688773 No 452 >cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands. Probab=68.37 E-value=8.2 Score=17.84 Aligned_cols=44 Identities=30% Similarity=0.396 Sum_probs=29.1 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC--CCHHHHHHHH Q ss_conf 77614886788999999999999708997799971--5379999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA--NSETQLKNTL 124 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A--~t~~Q~~~~l 124 (367) +.|+|.-|+|||+++.-+++..+. ..+.+|++.+ -+..|+...+ T Consensus 33 ~viaarpg~GKT~f~~~~a~~~~~-~~g~~vl~~SlEm~~~~~~~Rl 78 (271) T cd01122 33 IILTAGTGVGKTTFLREYALDLIT-QHGVRVGTISLEEPVVRTARRL 78 (271) T ss_pred EEEEECCCCCHHHHHHHHHHHHHH-HCCCEEEEEECCCCHHHHHHHH T ss_conf 999968998699999999999999-7699089997049999999999 No 453 >TIGR01281 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein; InterPro: IPR005971 Synonym: dark protochlorophyllide reductase Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite. The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulphur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase . ; GO: 0005524 ATP binding, 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction. Probab=68.30 E-value=4.6 Score=19.38 Aligned_cols=42 Identities=19% Similarity=0.230 Sum_probs=29.7 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE--ECCCHHHHHHH Q ss_conf 776148867889999999999997089977999--71537999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC--IANSETQLKNT 123 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~--~A~t~~Q~~~~ 123 (367) +||=.==|+|||+.+|.+.+-++ +.|+||+= +=|+.+...++ T Consensus 3 lAvYGKGGiGKSTTssNLSvA~A--~~GkkVlQIGCDPKhDSTFTL 46 (275) T TIGR01281 3 LAVYGKGGIGKSTTSSNLSVALA--KKGKKVLQIGCDPKHDSTFTL 46 (275) T ss_pred EEEECCCCCCCHHHHHHHHHHHH--HCCCEEEEECCCCCCCCCCCC T ss_conf 88863888770046789999998--469918985257888877454 No 454 >cd04140 ARHI_like ARHI subfamily. ARHI (A Ras homolog member I) is a member of the Ras family with several unique structural and functional properties. ARHI is expressed in normal human ovarian and breast tissue, but its expression is decreased or eliminated in breast and ovarian cancer. ARHI contains an N-terminal extension of 34 residues (human) that is required to retain its tumor suppressive activity. Unlike most other Ras family members, ARHI is maintained in the constitutively active (GTP-bound) state in resting cells and has modest GTPase activity. ARHI inhibits STAT3 (signal transducers and activators of transcription 3), a latent transcription factor whose abnormal activation plays a critical role in oncogenesis. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to Probab=68.21 E-value=5.6 Score=18.83 Aligned_cols=22 Identities=18% Similarity=0.468 Sum_probs=19.5 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.|.+--|+|||.++..++- T Consensus 2 ~KivllGd~~VGKTsli~r~~~ 23 (165) T cd04140 2 YRVVVFGAGGVGKSSLVLRFVK 23 (165) T ss_pred EEEEEECCCCCCHHHHHHHHHH T ss_conf 0999989999769999999964 No 455 >cd04141 Rit_Rin_Ric Rit/Rin/Ric subfamily. Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to sign Probab=68.20 E-value=5.9 Score=18.73 Aligned_cols=22 Identities=18% Similarity=0.459 Sum_probs=19.5 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.|.+..|+|||.++..++- T Consensus 3 ~Kiv~lGd~~VGKTsli~r~~~ 24 (172) T cd04141 3 YKIVMLGAGGVGKSAVTMQFIS 24 (172) T ss_pred EEEEEECCCCCCHHHHHHHHHH T ss_conf 6999999999779999999970 No 456 >cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB. Probab=68.12 E-value=8.3 Score=17.81 Aligned_cols=54 Identities=20% Similarity=0.153 Sum_probs=34.8 Q ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 842899999998888751245555541124776148867889999999999997089977999715 Q gi|254781187|r 50 QPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 50 ~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) |..+-|.+.|+.+....+. -+.|++.-|+|||+....++-. +..++.+|+.+.. T Consensus 63 G~~~~~~~~l~~~~~~~~G----------lilitGptGSGKtTtl~a~l~~--~~~~~~~i~tiEd 116 (264) T cd01129 63 GLKPENLEIFRKLLEKPHG----------IILVTGPTGSGKTTTLYSALSE--LNTPEKNIITVED 116 (264) T ss_pred CCCHHHHHHHHHHHHCCCC----------EEEEECCCCCCHHHHHHHHHHH--HCCCCCEEEEEEC T ss_conf 7999999999999708998----------8999789999779999999986--4368850899867 No 457 >pfam09140 MipZ ATPase MipZ. MipZ is an ATPase that forms a complex with the chromosome partitioning protein ParB near the chromosomal origin of replication. It is responsible for the temporal and spatial regulation of FtsZ ring formation. Probab=68.09 E-value=7.2 Score=18.19 Aligned_cols=30 Identities=23% Similarity=0.267 Sum_probs=22.3 Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 86788999999999999708997799971537 Q gi|254781187|r 86 RGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 86 rg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) =|+|||+.+..++..++.. |.+|+++=-.- T Consensus 10 GGvGKTTtavnLA~aLA~~--G~rVllIDlDp 39 (261) T pfam09140 10 GGSGKSTTAVHVAVALLYL--GARVATIDLDL 39 (261) T ss_pred CCCCHHHHHHHHHHHHHHC--CCCEEEEECCC T ss_conf 9872999999999999988--99789997999 No 458 >KOG0388 consensus Probab=67.96 E-value=8.3 Score=17.79 Aligned_cols=163 Identities=15% Similarity=0.144 Sum_probs=78.1 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCC-CCEEEEECCCHHHHHHHHHHHHHHH Q ss_conf 899999998888751245555541124776148867889999999999997089-9779997153799999999999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRP-GMSIICIANSETQLKNTLWAEVSKW 131 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~-~~~v~~~A~t~~Q~~~~lw~ei~k~ 131 (367) ++|.+=|.=++.--..+.+ -..+---|.|||.-+-.++.+++-++. ..-.+|++|. +.+. -.-.||.++ T Consensus 570 EYQlkGLnWLvnlYdqGiN--------GILADeMGLGKTVQsisvlAhLaE~~nIwGPFLVVtpa-StL~-NWaqEisrF 639 (1185) T KOG0388 570 EYQLKGLNWLVNLYDQGIN--------GILADEMGLGKTVQSISVLAHLAETHNIWGPFLVVTPA-STLH-NWAQEISRF 639 (1185) T ss_pred HHHHCCHHHHHHHHHCCCC--------CEEHHHHCCCHHHHHHHHHHHHHHHCCCCCCEEEEEHH-HHHH-HHHHHHHHH T ss_conf 8765007899999870344--------12133304532688999999998744588763896027-8776-799999985 Q ss_pred HHHCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCH---HH Q ss_conf 986231-21123333210001233322111134577612662101354455652101135862899975455998---89 Q gi|254781187|r 132 LSMLPH-RHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPD---II 207 (367) Q Consensus 132 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d---~i 207 (367) +-.+.. .+|-..+...+--+.|..... +-+..+-...++.--.-.....=++.. ..-+.|+|||+.|.. .- T Consensus 640 lP~~k~lpywGs~~eRkiLrKfw~rKnm--Y~rna~fhVviTSYQlvVtDeky~qkv---KWQYMILDEAQAIKSSsS~R 714 (1185) T KOG0388 640 LPSFKVLPYWGSPSERKILRKFWNRKNM--YRRNAPFHVVITSYQLVVTDEKYLQKV---KWQYMILDEAQAIKSSSSSR 714 (1185) T ss_pred CCCCEEECCCCCHHHHHHHHHHCCHHHH--HCCCCCCEEEEEEEEEEECHHHHHHHH---HHHHEEHHHHHHHHHHHHHH T ss_conf 8654243476880266899974044444--304799528997531111159999863---34520055787764322567 Q ss_pred HHHHHHHHHCCCCCEEEEEEECCCCCC Q ss_conf 999898740698825899980789998 Q gi|254781187|r 208 NKSILGFFTELNPNRFWIMTSNTRRLN 234 (367) Q Consensus 208 ~e~i~g~Lt~~~~~~~~i~igNP~r~~ 234 (367) |..+...-+ .+++ +++|+|-.++ T Consensus 715 WKtLLsF~c--RNRL--LLTGTPIQNs 737 (1185) T KOG0388 715 WKTLLSFKC--RNRL--LLTGTPIQNS 737 (1185) T ss_pred HHHHHHHHC--CCEE--EECCCCCCHH T ss_conf 887740210--3404--5318853017 No 459 >TIGR00486 TIGR00486 conserved hypothetical protein TIGR00486; InterPro: IPR002678 This family contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown .. Probab=67.94 E-value=8.3 Score=17.79 Aligned_cols=75 Identities=13% Similarity=0.186 Sum_probs=49.8 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHCC----CCCCC------CCEEEEEEECCCCCC-HHHHHHHHHHHHHHHCCCCEEEEE Q ss_conf 4366684289999999888875124----55555------411247761488678-899999999999970899779997 Q gi|254781187|r 45 LEHFSQPHRWQLEFMEAVDVHCHSN----VNNSN------PTIFKCAISAGRGIG-KTTLNAWMMLWLISTRPGMSIICI 113 (367) Q Consensus 45 ~~~~~~p~~wq~~~l~~~~~~~~~~----~~~~~------~~~~~~~v~sgrg~G-KS~~~a~~~lw~~~~~~~~~v~~~ 113 (367) +..+..+..- .+++..+...+.++ ..... ..+.||||+||-|.+ ||++...+. .+.-+.+| T Consensus 193 ~~~~~~~~~~-~~~~~~~~~~L~v~~~~~~~~~~PsaWnq~~v~kvA~vsG~G~s~ks~~~~a~~-------~gvd~yiT 264 (325) T TIGR00486 193 VGELKASIES-KEEVLEIKKKLNVKPLLVVKKGEPSAWNQEKVKKVAVVSGSGLSDKSFIMKALR-------EGVDLYIT 264 (325) T ss_pred EEEECCCCCH-HHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHH-------CCCCEEEC T ss_conf 6753455105-788888887449971788506887523102166389995578752789999997-------08968971 Q ss_pred CCCHHHHHHHHHHHH Q ss_conf 153799999999999 Q gi|254781187|r 114 ANSETQLKNTLWAEV 128 (367) Q Consensus 114 A~t~~Q~~~~lw~ei 128 (367) -....|.. .+|+|+ T Consensus 265 Gd~~h~~~-~~A~e~ 278 (325) T TIGR00486 265 GDLSHHTA-HLAREL 278 (325) T ss_pred CCCHHHHH-HHHHHC T ss_conf 65406678-876438 No 460 >cd04117 Rab15 Rab15 subfamily. Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to Probab=67.87 E-value=5.3 Score=19.01 Aligned_cols=22 Identities=27% Similarity=0.407 Sum_probs=19.0 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) ||+.+.+..|+|||.++..++- T Consensus 1 ~KIvllGd~~VGKTsli~r~~~ 22 (161) T cd04117 1 FRLLLIGDSGVGKTCLLCRFTD 22 (161) T ss_pred CEEEEECCCCCCHHHHHHHHHC T ss_conf 9899999499858999999942 No 461 >PRK03333 coaE dephospho-CoA kinase/unknown domain fusion protein; Provisional Probab=67.87 E-value=5 Score=19.15 Aligned_cols=23 Identities=26% Similarity=0.541 Sum_probs=18.3 Q ss_pred EEEEEEECCCCCCHHHHHHHHHH Q ss_conf 12477614886788999999999 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~l 99 (367) |+++.+.+|=|+|||+.+.++.- T Consensus 1 M~~IGLTGGIgsGKStv~~~l~~ 23 (394) T PRK03333 1 MLRIGLTGGIGAGKSTVSATLAQ 23 (394) T ss_pred CEEEEEECCCCCCHHHHHHHHHH T ss_conf 94998306755579999999998 No 462 >cd03291 ABCC_CFTR1 The CFTR subfamily domain 1. The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits, or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2. Probab=67.82 E-value=5.4 Score=18.97 Aligned_cols=33 Identities=21% Similarity=0.391 Sum_probs=24.7 Q ss_pred HHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHH Q ss_conf 99988887512455555411247761488678899999999 Q gi|254781187|r 58 FMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 58 ~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) +|+.|.=.+..+. +++|.+.-|+|||+++..++ T Consensus 52 VLk~Isf~I~~Ge--------~vaIVG~sGSGKSTLl~lL~ 84 (282) T cd03291 52 VLKNINLKIEKGE--------MLAITGSTGSGKTSLLMLIL 84 (282) T ss_pred EEECEEEEECCCC--------EEEEECCCCCHHHHHHHHHH T ss_conf 1416489984999--------99999999981999999995 No 463 >PRK13873 conjugal transfer ATPase TrbE; Provisional Probab=67.77 E-value=8.4 Score=17.77 Aligned_cols=33 Identities=27% Similarity=0.413 Sum_probs=19.6 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE Q ss_conf 4776148867889999999999997089977999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC 112 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~ 112 (367) ...|.++-|.|||++.+.++.= ..-+++.+|++ T Consensus 443 HtlI~GpTGsGKTvll~~l~~q-~~ry~~~~vf~ 475 (815) T PRK13873 443 HTLVVGPTGAGKSVLLALMALQ-FRRYPGSQVFA 475 (815) T ss_pred CEEEECCCCCCHHHHHHHHHHH-HHHCCCCCEEE T ss_conf 4389788999899999999999-86448984899 No 464 >cd04115 Rab33B_Rab33A Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine Probab=67.65 E-value=6.4 Score=18.49 Aligned_cols=23 Identities=30% Similarity=0.429 Sum_probs=19.2 Q ss_pred EEEEEEECCCCCCHHHHHHHHHH Q ss_conf 12477614886788999999999 Q gi|254781187|r 77 IFKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 77 ~~~~~v~sgrg~GKS~~~a~~~l 99 (367) .||+.+.+..|+|||.++-.++- T Consensus 2 ~~Kiv~lGd~~VGKTsli~r~~~ 24 (170) T cd04115 2 IFKIIVIGDSNVGKTCLTYRFCA 24 (170) T ss_pred EEEEEEECCCCCCHHHHHHHHHC T ss_conf 69999999799779999999953 No 465 >cd00877 Ran Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases. Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is Probab=67.55 E-value=5.7 Score=18.79 Aligned_cols=21 Identities=33% Similarity=0.482 Sum_probs=18.1 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) ||+.+.+..|+|||.++-.++ T Consensus 1 ~KivlvGd~~VGKTsli~r~~ 21 (166) T cd00877 1 FKLVLVGDGGTGKTTFVKRHL 21 (166) T ss_pred CEEEEECCCCCCHHHHHHHHH T ss_conf 989999999988899999998 No 466 >cd04119 RJL RJL (RabJ-Like) subfamily. RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Probab=67.52 E-value=5.6 Score=18.87 Aligned_cols=20 Identities=20% Similarity=0.290 Sum_probs=17.9 Q ss_pred EEEEECCCCCCHHHHHHHHH Q ss_conf 47761488678899999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~ 98 (367) |+.|.+..|+|||.++..++ T Consensus 2 KivvvG~~~vGKTSLi~r~~ 21 (168) T cd04119 2 KVISMGNSGVGKSCIIKRYC 21 (168) T ss_pred EEEEECCCCCCHHHHHHHHH T ss_conf 89999959956899999996 No 467 >cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism. Probab=67.41 E-value=5.4 Score=18.94 Aligned_cols=21 Identities=33% Similarity=0.335 Sum_probs=18.4 Q ss_pred EEEEECCCCCCHHHHHHHHHH Q ss_conf 477614886788999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~l 99 (367) +++|.+.-|+|||++...++= T Consensus 30 ~~aivG~sGsGKSTLl~~l~G 50 (178) T cd03247 30 KIALLGRSGSGKSTLLQLLTG 50 (178) T ss_pred EEEEECCCCCHHHHHHHHHHH T ss_conf 999999998759999999986 No 468 >cd04111 Rab39 Rab39 subfamily. Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Probab=67.32 E-value=6.6 Score=18.39 Aligned_cols=24 Identities=17% Similarity=0.242 Sum_probs=20.6 Q ss_pred CEEEEEEECCCCCCHHHHHHHHHH Q ss_conf 112477614886788999999999 Q gi|254781187|r 76 TIFKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 76 ~~~~~~v~sgrg~GKS~~~a~~~l 99 (367) +.||+.+.+.-|+|||.++..++- T Consensus 1 y~fKivllGd~~VGKTsL~~rf~~ 24 (211) T cd04111 1 YQFRLIVIGDSTVGKSSLLKRFTE 24 (211) T ss_pred CEEEEEEECCCCCCHHHHHHHHHH T ss_conf 979999999999619999999981 No 469 >PRK13637 cbiO cobalt transporter ATP-binding subunit; Provisional Probab=67.16 E-value=1.1 Score=23.30 Aligned_cols=37 Identities=19% Similarity=0.300 Sum_probs=26.0 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHH Q ss_conf 999999988887512455555411247761488678899999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 54 wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) ++..+|++|.=.++.+. .+++.+..|+|||++...+. T Consensus 18 ~~~~aL~~isl~i~~GE--------~v~iiG~nGsGKSTLl~~l~ 54 (287) T PRK13637 18 FEKKALDNVNIEIEDGE--------FVALIGHTGSGKSTLIQHLN 54 (287) T ss_pred CCCEEEECEEEEECCCC--------EEEEECCCCCHHHHHHHHHH T ss_conf 73817532076987998--------99999999939999999997 No 470 >cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra Probab=67.10 E-value=5.7 Score=18.79 Aligned_cols=21 Identities=33% Similarity=0.379 Sum_probs=18.6 Q ss_pred EEEEECCCCCCHHHHHHHHHH Q ss_conf 477614886788999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~l 99 (367) .++|.+.-|+|||++...++= T Consensus 30 ~vaIvG~sGsGKSTLl~ll~g 50 (173) T cd03246 30 SLAIIGPSGSGKSTLARLILG 50 (173) T ss_pred EEEEECCCCCHHHHHHHHHHC T ss_conf 999999999809999999966 No 471 >KOG1969 consensus Probab=67.05 E-value=8.7 Score=17.68 Aligned_cols=107 Identities=18% Similarity=0.226 Sum_probs=59.9 Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE-CCCHHHHHHHHHHHHH Q ss_conf 428999999988887512455555411247761488678899999999999970899779997-1537999999999999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI-ANSETQLKNTLWAEVS 129 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~-A~t~~Q~~~~lw~ei~ 129 (367) +-+|-.|++...-+.++|.... -+..++.-|.|||+++-.++- +-|-+|+=+ |-.++.+. . ++ T Consensus 306 ~~~~~ke~~~~~~~~s~RP~kK------ilLL~GppGlGKTTLAHViAk-----qaGYsVvEINASDeRt~~-~----v~ 369 (877) T KOG1969 306 KGPTEKEVLDMELDPSKRPPKK------ILLLCGPPGLGKTTLAHVIAK-----QAGYSVVEINASDERTAP-M----VK 369 (877) T ss_pred CCCCHHHHHHCCCCCCCCCCCC------EEEEECCCCCCHHHHHHHHHH-----HCCCEEEEECCCCCCCHH-H----HH T ss_conf 4664345563246866798400------687536887872479999998-----628548873255543478-8----99 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHH Q ss_conf 99986231211233332100012333221111345776126621013544556521011358628999754559988999 Q gi|254781187|r 130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINK 209 (367) Q Consensus 130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e 209 (367) +-++.+. . + ++.-+. +....|+|+||--|-+....+ T Consensus 370 ~kI~~av------------q----------------~---------------~s~l~a-dsrP~CLViDEIDGa~~~~Vd 405 (877) T KOG1969 370 EKIENAV------------Q----------------N---------------HSVLDA-DSRPVCLVIDEIDGAPRAAVD 405 (877) T ss_pred HHHHHHH------------H----------------H---------------CCCCCC-CCCCCEEEEECCCCCCHHHHH T ss_conf 9999988------------6----------------4---------------112256-888635998424687289999 Q ss_pred HHHHHHHC Q ss_conf 98987406 Q gi|254781187|r 210 SILGFFTE 217 (367) Q Consensus 210 ~i~g~Lt~ 217 (367) +|+..+.. T Consensus 406 vilslv~a 413 (877) T KOG1969 406 VILSLVKA 413 (877) T ss_pred HHHHHHHH T ss_conf 99999974 No 472 >cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1). NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate. Probab=67.02 E-value=6.1 Score=18.61 Aligned_cols=22 Identities=32% Similarity=0.406 Sum_probs=18.8 Q ss_pred EEEEECCCCCCHHHHHHHHHHH Q ss_conf 4776148867889999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLW 100 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw 100 (367) +++|.+.-|+|||+++..+.=. T Consensus 36 ~v~ivG~sGsGKSTLl~ll~g~ 57 (207) T cd03369 36 KIGIVGRTGAGKSTLILALFRF 57 (207) T ss_pred EEEEECCCCCCHHHHHHHHHHH T ss_conf 9999999998799999999987 No 473 >pfam02689 Herpes_Helicase Helicase. This family consists of Helicases from the Herpes viruses. Helicases are responsible for the unwinding of DNA and are essential for replication and completion of the viral life cycle. Probab=66.96 E-value=8.7 Score=17.67 Aligned_cols=37 Identities=16% Similarity=0.161 Sum_probs=24.3 Q ss_pred CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 554112477614886788999999999999708997799971537 Q gi|254781187|r 73 SNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 73 ~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) .+|.. -..|.+--|.|||+.+..+.- ...+++|..|. T Consensus 57 ~LPFs-~ylITGtAGaGKSTsIq~L~~-------~LdCvITGaT~ 93 (801) T pfam02689 57 ELPFS-AYLITGTAGAGKSTSIQTLNE-------NLDCLITGATR 93 (801) T ss_pred CCCCE-EEEEECCCCCCCHHHHHHHHH-------HCCEEEECCHH T ss_conf 67725-899953788870518999997-------53928956158 No 474 >PRK09694 hypothetical protein; Provisional Probab=66.77 E-value=8.8 Score=17.65 Aligned_cols=76 Identities=22% Similarity=0.205 Sum_probs=48.7 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHH Q ss_conf 66684289999999888875124555554112477614886788999999999999708997799971537999999999 Q gi|254781187|r 47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWA 126 (367) Q Consensus 47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ 126 (367) ....|++-|..+ .++.. .|- =+.|-+.-|.|||-.+-+++.-++...-...+++.-||...+. -||. T Consensus 285 ~~~~PrplQ~~~-~~l~~---------~Pg--L~IiEAptG~GKTEAAL~~A~~L~~~~~~~Gl~faLPT~ATaN-aMf~ 351 (878) T PRK09694 285 NGYQPRQLQTLV-DALPL---------APG--LTVIEAPTGSGKTETALAYAWKLIDQQLADSVIFALPTQATAN-AMLS 351 (878) T ss_pred CCCCCCHHHHHH-HHCCC---------CCC--EEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHH-HHHH T ss_conf 899996799999-84567---------998--7999758999758999999999997348983699774798899-9999 Q ss_pred HHHHHHHHC Q ss_conf 999999862 Q gi|254781187|r 127 EVSKWLSML 135 (367) Q Consensus 127 ei~k~~~~~ 135 (367) .+.++++.+ T Consensus 352 Rv~~~~~~~ 360 (878) T PRK09694 352 RMEAAASKL 360 (878) T ss_pred HHHHHHHHH T ss_conf 999999973 No 475 >cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another. Probab=66.54 E-value=6 Score=18.66 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=18.1 Q ss_pred EEEEECCCCCCHHHHHHHHHH Q ss_conf 477614886788999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~l 99 (367) +++|.+.-|+|||+++..++- T Consensus 31 ~iaIvG~sGsGKSTLl~ll~g 51 (238) T cd03249 31 TVALVGSSGCGKSTVVSLLER 51 (238) T ss_pred EEEEECCCCCCHHHHHHHHHH T ss_conf 999999999989999999823 No 476 >cd04129 Rho2 Rho2 subfamily. Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors). Probab=66.32 E-value=6.5 Score=18.44 Aligned_cols=22 Identities=32% Similarity=0.288 Sum_probs=19.0 Q ss_pred EEEEEECCCCCCHHHHHHHHHH Q ss_conf 2477614886788999999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~l 99 (367) .|+.+.+..|+|||.++..++- T Consensus 2 ~KivllGd~~VGKTsLi~r~~~ 23 (187) T cd04129 2 RKLVIVGDGACGKTSLLSVFTL 23 (187) T ss_pred EEEEEECCCCCCHHHHHHHHHH T ss_conf 1999999899768999999982 No 477 >PRK11819 putative ABC transporter ATP-binding protein; Reviewed Probab=66.29 E-value=5.7 Score=18.79 Aligned_cols=39 Identities=8% Similarity=-0.011 Sum_probs=25.3 Q ss_pred CCCCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCEEEEEEE Q ss_conf 1358628999754-5599889999898740698825899980 Q gi|254781187|r 188 HNTHGMAVFNDEA-SGTPDIINKSILGFFTELNPNRFWIMTS 228 (367) Q Consensus 188 h~~~~~l~ivDEA-sgI~d~i~e~i~g~Lt~~~~~~~~i~ig 228 (367) -.....++|+||- +..+...-+.++..|......+ ++++ T Consensus 178 L~~~PdlLlLDEPTn~LD~~~i~~L~~~L~~~~gtv--ivVS 217 (556) T PRK11819 178 LLSKPDMLLLDEPTNHLDAESVAWLEQFLHDYPGTV--VAVT 217 (556) T ss_pred HHCCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCCE--EEEE T ss_conf 846999899848877789778999999976337877--9999 No 478 >cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. Probab=66.28 E-value=9 Score=17.59 Aligned_cols=35 Identities=17% Similarity=0.251 Sum_probs=26.5 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECC Q ss_conf 776148867889999999999997089977999715 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIAN 115 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~ 115 (367) +.|+|+-|+|||+++.-+++..+. +.+.+|++.+. T Consensus 16 ~vi~a~~g~GKS~~~~~la~~~a~-~~g~~V~~~Sl 50 (242) T cd00984 16 IIIAARPSMGKTAFALNIAENIAK-KQGKPVLFFSL 50 (242) T ss_pred EEEEECCCCCHHHHHHHHHHHHHH-HCCCCEEEEEC T ss_conf 999968999999999999999999-77995999933 No 479 >PRK13233 nifH nitrogenase reductase; Reviewed Probab=66.23 E-value=9 Score=17.58 Aligned_cols=44 Identities=18% Similarity=0.086 Sum_probs=32.6 Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHHH Q ss_conf 247761488678899999999999970899779997--153799999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICI--ANSETQLKN 122 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~--A~t~~Q~~~ 122 (367) .++||-.==|+|||+.++.+...++-. .+.||+++ =|..+..+. T Consensus 3 ~~iaiyGKGGIGKSTTt~NLaaALA~l-~GkrVl~IgcDPk~dST~~ 48 (275) T PRK13233 3 RKIAIYGKGGIGKSTTTQNTAAAMAHF-HDKKVFIHGCDPKADSTRL 48 (275) T ss_pred CEEEEECCCCCCHHHHHHHHHHHHHHH-CCCEEEEECCCCCCCHHHH T ss_conf 389998998544654599999999964-7988999797887613677 No 480 >PRK13645 cbiO cobalt transporter ATP-binding subunit; Provisional Probab=66.10 E-value=1.1 Score=23.24 Aligned_cols=38 Identities=13% Similarity=0.233 Sum_probs=25.0 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHH Q ss_conf 8999999988887512455555411247761488678899999999 Q gi|254781187|r 53 RWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 53 ~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~ 98 (367) +|..++|++|.=.+.++. .++|.+..|+|||+++-.+. T Consensus 21 ~~~~~AL~~vsl~i~~Ge--------~~aIiG~nGsGKSTL~~~l~ 58 (289) T PRK13645 21 PFEFKALNNTSLTFKKNK--------VTCVIGTTGSGKSTMIQLTN 58 (289) T ss_pred CCCCEEEECCEEEECCCC--------EEEEECCCCCHHHHHHHHHH T ss_conf 883658653288988998--------99999999957999999996 No 481 >PRK13640 cbiO cobalt transporter ATP-binding subunit; Provisional Probab=66.09 E-value=5.7 Score=18.79 Aligned_cols=34 Identities=18% Similarity=0.180 Sum_probs=23.3 Q ss_pred HHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHH Q ss_conf 999888875124555554112477614886788999999999 Q gi|254781187|r 58 FMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 58 ~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~l 99 (367) +|+.|.=.+.++. .++|.+..|+|||++...+.= T Consensus 23 aL~~vsl~I~~Ge--------~vaiiG~nGsGKSTL~~~l~G 56 (283) T PRK13640 23 ALKDVSFSIPRGS--------WTALIGHNGSGKSTISKLING 56 (283) T ss_pred EEECCEEEECCCC--------EEEEECCCCCHHHHHHHHHHC T ss_conf 7877186998999--------999999999879999999964 No 482 >cd03114 ArgK-like The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems. Probab=66.00 E-value=9.1 Score=17.55 Aligned_cols=36 Identities=25% Similarity=0.286 Sum_probs=27.1 Q ss_pred EEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCH Q ss_conf 77614886788999999999999708997799971537 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSE 117 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~ 117 (367) +-|...=|+|||+++..++..+.-. +.++.++|.-- T Consensus 2 iGitG~pGaGKStLi~~l~~~~~~~--g~~VaVlavDP 37 (148) T cd03114 2 IGITGVPGAGKSTLIDALITALRAR--GKRVAVLAIDP 37 (148) T ss_pred EEECCCCCCCHHHHHHHHHHHHHHC--CCEEEEEEECC T ss_conf 7625899787899999999999978--98379999688 No 483 >COG1341 Predicted GTPase or GTP-binding protein [General function prediction only] Probab=65.99 E-value=9.1 Score=17.55 Aligned_cols=56 Identities=18% Similarity=0.168 Sum_probs=36.4 Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHH Q ss_conf 6668428999999988887512455555411247761488678899999999999970 Q gi|254781187|r 47 HFSQPHRWQLEFMEAVDVHCHSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLIST 104 (367) Q Consensus 47 ~~~~p~~wq~~~l~~~~~~~~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~ 104 (367) ....|..| .+.++.|.+.-.+ .........++.|.++-.+|||+++++++.-++.- T Consensus 45 ~ve~P~d~-~~~~e~i~~~~~~-~~~~~~~~~~vmvvG~vDSGKSTLt~~LaN~~l~r 100 (398) T COG1341 45 LVEVPEDR-SEPLEEIADTWES-KSESAGKVGVVMVVGPVDSGKSTLTTYLANKLLAR 100 (398) T ss_pred CCCCCHHH-HHHHHHHHHCCCC-CCHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHC T ss_conf 42281676-3178997632244-20120687389998986767889999999887644 No 484 >cd01862 Rab7 Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C- Probab=65.99 E-value=6.3 Score=18.54 Aligned_cols=21 Identities=33% Similarity=0.483 Sum_probs=18.3 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) +|+.+.+.-|+|||.++..++ T Consensus 1 ~KivlvGd~~VGKTsli~r~~ 21 (172) T cd01862 1 LKVIILGDSGVGKTSLMNQYV 21 (172) T ss_pred CEEEEECCCCCCHHHHHHHHH T ss_conf 989999989978999999995 No 485 >COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms] Probab=65.94 E-value=5.7 Score=18.81 Aligned_cols=33 Identities=27% Similarity=0.233 Sum_probs=22.8 Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEC Q ss_conf 477614886788999999999999708997799971 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIA 114 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A 114 (367) -++|.+.-|+|||++...+. .+-.|..-.+.+. T Consensus 33 ~vaI~GpSGSGKSTLLniig---~ld~pt~G~v~i~ 65 (226) T COG1136 33 FVAIVGPSGSGKSTLLNLLG---GLDKPTSGEVLIN 65 (226) T ss_pred EEEEECCCCCCHHHHHHHHH---CCCCCCCCEEEEC T ss_conf 99998999998999999996---4667888469999 No 486 >cd01861 Rab6 Rab6 subfamily. Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Probab=65.86 E-value=6.3 Score=18.54 Aligned_cols=21 Identities=24% Similarity=0.398 Sum_probs=18.2 Q ss_pred EEEEECCCCCCHHHHHHHHHH Q ss_conf 477614886788999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~l 99 (367) |+.|.+..|+|||.++..++- T Consensus 2 Ki~vvG~~~vGKTsli~r~~~ 22 (161) T cd01861 2 KLVFLGDQSVGKTSIITRFMY 22 (161) T ss_pred EEEEECCCCCCHHHHHHHHHH T ss_conf 799999799789999999931 No 487 >cd00615 Orn_deC_like Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine decarboxylase (LDC). ODC is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. ADC catalyzes the decarboxylation of arginine and LDC catalyzes the decarboxylation of lysine. Members of this family are widely found in all three forms of life. Probab=65.86 E-value=9.2 Score=17.54 Aligned_cols=31 Identities=23% Similarity=0.223 Sum_probs=23.9 Q ss_pred HHHHHHHHHHHCCCCEEEEECCCHHHHHHHH Q ss_conf 9999999997089977999715379999999 Q gi|254781187|r 94 NAWMMLWLISTRPGMSIICIANSETQLKNTL 124 (367) Q Consensus 94 ~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~l 124 (367) .+..+.-+.+++|+.+|++-.|..+.+-..+ T Consensus 86 ~g~~a~i~a~~~~gd~vlv~RN~HkSv~~gl 116 (294) T cd00615 86 SSNKAVILAVCGPGDKILIDRNCHKSVINGL 116 (294) T ss_pred HHHHHHHHHHCCCCCEEEEECCCHHHHHHHH T ss_conf 9999999983289998998265189999999 No 488 >PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed Probab=65.80 E-value=9.2 Score=17.53 Aligned_cols=94 Identities=16% Similarity=0.175 Sum_probs=54.0 Q ss_pred HHHHHHHHHHHH----HCCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEE-ECCCHHHHHHHHHHHHH Q ss_conf 999999888875----1245555541124776148867889999999999997089977999-71537999999999999 Q gi|254781187|r 55 QLEFMEAVDVHC----HSNVNNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIIC-IANSETQLKNTLWAEVS 129 (367) Q Consensus 55 q~~~l~~~~~~~----~~~~~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~-~A~t~~Q~~~~lw~ei~ 129 (367) |.++.+.+.-.+ +|+..-+ -+...++-|.|||+++..++--+ +.++-+ .+|......|.. +. T Consensus 30 Q~~i~~~L~v~i~Aak~r~e~ld-----H~Ll~GPPGlGKTTLA~iiA~E~-----~~~~~~tsGP~lek~~DL~-~i-- 96 (328) T PRK00080 30 QEKVKENLKIFIEAAKKRGEALD-----HVLLYGPPGLGKTTLANIIANEM-----GVNIRITSGPALEKAGDLA-AL-- 96 (328) T ss_pred HHHHHHHHHHHHHHHHHCCCCCC-----CEEEECCCCCCHHHHHHHHHHHH-----CCCCEECCCCCCCCHHHHH-HH-- T ss_conf 59999999999999996499988-----05765889988999999999986-----8881562450016747899-99-- Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHH Q ss_conf 99986231211233332100012333221111345776126621013544556521011358628999754559988999 Q gi|254781187|r 130 KWLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINK 209 (367) Q Consensus 130 k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e 209 (367) +. .+. ++ ..+.+||..-++..+-| T Consensus 97 --Lt----------------------------------------------------~l~-~~-dvLFIDEIHRl~~~vEE 120 (328) T PRK00080 97 --LT----------------------------------------------------NLE-EG-DVLFIDEIHRLSPVVEE 120 (328) T ss_pred --HH----------------------------------------------------HCC-CC-CEEEEHHHHHCCHHHHH T ss_conf --96----------------------------------------------------088-78-76765065324888998 Q ss_pred HHHHHHHC Q ss_conf 98987406 Q gi|254781187|r 210 SILGFFTE 217 (367) Q Consensus 210 ~i~g~Lt~ 217 (367) .+.++|-+ T Consensus 121 ~LY~AMED 128 (328) T PRK00080 121 ILYPAMED 128 (328) T ss_pred HHHHHHHH T ss_conf 85798775 No 489 >cd04112 Rab26 Rab26 subfamily. First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation. Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Probab=65.68 E-value=6.5 Score=18.45 Aligned_cols=21 Identities=33% Similarity=0.506 Sum_probs=17.9 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) ||+.|.+-.|+|||.++..++ T Consensus 1 ~KIv~vGd~~VGKTsli~r~~ 21 (191) T cd04112 1 FKVMLLGDSGVGKTCLLVRFK 21 (191) T ss_pred CEEEEECCCCCCHHHHHHHHH T ss_conf 989999949987999999999 No 490 >cd00876 Ras Ras family. The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of m Probab=65.56 E-value=5.9 Score=18.72 Aligned_cols=21 Identities=19% Similarity=0.427 Sum_probs=17.7 Q ss_pred EEEEECCCCCCHHHHHHHHHH Q ss_conf 477614886788999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMML 99 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~l 99 (367) |++|.+..|+|||.++..++- T Consensus 1 Ki~ivG~~~vGKTsli~r~~~ 21 (160) T cd00876 1 KVVVLGAGGVGKSAITIQFVK 21 (160) T ss_pred CEEEECCCCCCHHHHHHHHHH T ss_conf 999999699679999999961 No 491 >cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules. Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes. Probab=65.09 E-value=6.4 Score=18.49 Aligned_cols=22 Identities=27% Similarity=0.335 Sum_probs=18.8 Q ss_pred EEEEECCCCCCHHHHHHHHHHH Q ss_conf 4776148867889999999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMMLW 100 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~lw 100 (367) +++|.+.-|+|||+++..+.=. T Consensus 42 ~vaIvG~sGsGKSTL~~ll~gl 63 (226) T cd03248 42 VTALVGPSGSGKSTVVALLENF 63 (226) T ss_pred EEEEECCCCCHHHHHHHHHHCC T ss_conf 9999999998499999999645 No 492 >PRK07367 consensus Probab=65.00 E-value=9.5 Score=17.43 Aligned_cols=64 Identities=14% Similarity=0.114 Sum_probs=36.9 Q ss_pred CHHHHHHHHHHHHHHHHCCC-CCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH Q ss_conf 42899999998888751245-5555411247761488678899999999999970899779997153799999 Q gi|254781187|r 51 PHRWQLEFMEAVDVHCHSNV-NNSNPTIFKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKN 122 (367) Q Consensus 51 p~~wq~~~l~~~~~~~~~~~-~~~~~~~~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~ 122 (367) |..--.++.++|+++.++.. ....|+ .+.|..|= ..|...+-.+++.||-+|++..|++..-.. T Consensus 63 ~~~G~~~lR~aia~~~~~~~g~~~~~d--~I~it~G~------~~al~~~~~~l~~pGD~Vlv~~P~y~~y~~ 127 (385) T PRK07367 63 PAAGEPALREAIAHKLRRENGLDYQAE--NILVTNGG------KQSLYNLMMALIDPGDEVIIPAPYWLSYPE 127 (385) T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCCHH--EEEECCCH------HHHHHHHHHHHCCCCCEEEECCCCCCCCHH T ss_conf 999989999999999999858999850--49990898------999999999974899989990698777199 No 493 >COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones] Probab=64.86 E-value=9.6 Score=17.42 Aligned_cols=134 Identities=23% Similarity=0.191 Sum_probs=69.5 Q ss_pred HHHHHHHHHHHHHHCC-CCCCCCCEE--EEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHH Q ss_conf 9999999888875124-555554112--4776148867889999999999997089977999715379999999999999 Q gi|254781187|r 54 WQLEFMEAVDVHCHSN-VNNSNPTIF--KCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQLKNTLWAEVSK 130 (367) Q Consensus 54 wq~~~l~~~~~~~~~~-~~~~~~~~~--~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q~~~~lw~ei~k 130 (367) .|.+++.+|++.+++. .+-..|.++ -..-+++-|+|||.++-.++-.+. ......+-.=-++=|-+-. +.+ T Consensus 495 GQd~AV~~v~~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lf--g~e~aliR~DMSEy~EkHs----VSr 568 (786) T COG0542 495 GQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALF--GDEQALIRIDMSEYMEKHS----VSR 568 (786) T ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHC--CCCCCCEEECHHHHHHHHH----HHH T ss_conf 7399999999999998569999998735788667886569999999999965--9974445545687777877----998 Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHH Q ss_conf 99862312112333321000123332211113457761266210135445565210113586289997545599889999 Q gi|254781187|r 131 WLSMLPHRHWFEMQSLSLHPSGWYAELLEQSMGIDSKHYTITCRTYSEERPDTFVGPHNTHGMAVFNDEASGTPDIINKS 210 (367) Q Consensus 131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~ea~~g~h~~~~~l~ivDEAsgI~d~i~e~ 210 (367) .+...| + +.+++.|.. -.|+.. +..+ ..+++||-..-.++|++. T Consensus 569 LIGaPP----------------G-------YVGyeeGG~----------LTEaVR--r~Py-SViLlDEIEKAHpdV~ni 612 (786) T COG0542 569 LIGAPP----------------G-------YVGYEEGGQ----------LTEAVR--RKPY-SVILLDEIEKAHPDVFNL 612 (786) T ss_pred HHCCCC----------------C-------CCEECCCCC----------HHHHHH--CCCC-EEEEECHHHHCCHHHHHH T ss_conf 727999----------------8-------720065540----------037660--6998-688841264408899999 Q ss_pred HH-----HHHHCCCCCE------EEEEEEC Q ss_conf 89-----8740698825------8999807 Q gi|254781187|r 211 IL-----GFFTELNPNR------FWIMTSN 229 (367) Q Consensus 211 i~-----g~Lt~~~~~~------~~i~igN 229 (367) +. |.||++.++. +.+++|| T Consensus 613 lLQVlDdGrLTD~~Gr~VdFrNtiIImTSN 642 (786) T COG0542 613 LLQVLDDGRLTDGQGRTVDFRNTIIIMTSN 642 (786) T ss_pred HHHHHCCCCEECCCCCEEECCEEEEEEECC T ss_conf 999846780554899888430028998450 No 494 >cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence. Probab=64.85 E-value=6.5 Score=18.47 Aligned_cols=20 Identities=30% Similarity=0.292 Sum_probs=16.7 Q ss_pred EEEEECCCCCCHHHHHHHHH Q ss_conf 47761488678899999999 Q gi|254781187|r 79 KCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 79 ~~~v~sgrg~GKS~~~a~~~ 98 (367) -+++.+..|+|||++..++. T Consensus 24 itaivG~NGaGKSTLl~~i~ 43 (204) T cd03240 24 LTLIVGQNGAGKTTIIEALK 43 (204) T ss_pred EEEEECCCCCCHHHHHHHHH T ss_conf 89999899999999999986 No 495 >PTZ00132 GTP-binding nuclear protein; Provisional Probab=64.84 E-value=7.5 Score=18.09 Aligned_cols=56 Identities=11% Similarity=0.029 Sum_probs=33.2 Q ss_pred CEEEEEEECCCCCCCH---HH-HHHHCCCCCEEEEEECCCCCCCCCHHHHHHHHHHCCCCC Q ss_conf 2589998078999876---88-754112235046752333288889889999996216880 Q gi|254781187|r 221 NRFWIMTSNTRRLNGW---FY-DIFNIPLEDWKRYQIDTRTVEGIDSGFHEGIISRYGLDS 277 (367) Q Consensus 221 ~~~~i~igNP~r~~g~---Fy-e~~~~~~~~w~~~~~~~~d~p~~~~~~i~~~~~~~gedS 277 (367) ....+++||=...... -. ..|. ...+..-+..++.++-++..-|..-.++-+|... T Consensus 110 ~ipivLVGNK~DL~~r~V~~~~~~~a-~~~~~~f~EtSAKtg~NV~e~F~~Lar~il~~~~ 169 (209) T PTZ00132 110 NIPIVLVGNKVDVKDRQVKAKQITFH-RKKNLQYYDISAKSNYNFEKPFLWLARRLANDPN 169 (209) T ss_pred CCCEEEEEECCCCCCCCCCHHHHHHH-HHCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCC T ss_conf 98789997623224135579999999-9879989997268993979999999999847999 No 496 >PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional Probab=64.80 E-value=6.6 Score=18.39 Aligned_cols=18 Identities=33% Similarity=0.530 Sum_probs=6.9 Q ss_pred EEEECCCCCCHHHHHHHH Q ss_conf 776148867889999999 Q gi|254781187|r 80 CAISAGRGIGKTTLNAWM 97 (367) Q Consensus 80 ~~v~sgrg~GKS~~~a~~ 97 (367) +++.+.-|+|||+++..+ T Consensus 370 vaIVG~SGsGKSTL~~LL 387 (593) T PRK10790 370 VALVGHTGSGKSTLASLL 387 (593) T ss_pred EEEECCCCCCHHHHHHHH T ss_conf 998799988689999999 No 497 >cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt Probab=64.78 E-value=5.9 Score=18.72 Aligned_cols=37 Identities=24% Similarity=0.231 Sum_probs=23.6 Q ss_pred CCCCEEEEECC-CCCCHHHHHHHHHHHHCCCCCEEEEEEE Q ss_conf 58628999754-5599889999898740698825899980 Q gi|254781187|r 190 THGMAVFNDEA-SGTPDIINKSILGFFTELNPNRFWIMTS 228 (367) Q Consensus 190 ~~~~l~ivDEA-sgI~d~i~e~i~g~Lt~~~~~~~~i~ig 228 (367) .+..++++||+ +.++...-..+.-.+...+.- +++++ T Consensus 108 ~~p~iliLDEpTs~LD~~~~~~l~~~l~~~~~T--vi~Vt 145 (166) T cd03223 108 HKPKFVFLDEATSALDEESEDRLYQLLKELGIT--VISVG 145 (166) T ss_pred CCCCEEEECCCCCCCCHHHHHHHHHHHHHCCCE--EEEEE T ss_conf 499999975853328999999999999977998--99994 No 498 >TIGR01082 murC UDP-N-acetylmuramate--alanine ligase; InterPro: IPR005758 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC) and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales . This entry represents UDP-N-acetylmuramate-alanine ligase (MurC). MurC is an essential, cytoplasmic peptidoglycan biosynthetic enzyme, catalyzes the ATP-dependent ligation of L-alanine (Ala) and UDP-N-acetylmuramic acid (UNAM) to form UDP-N-acetylmuramyl-L-alanine (UNAM-Ala). The enzyme is a nonribosomal peptide ligase which utilises ATP to form an amide bond between L-alanine and UNAM.1 Mechanistic studies on the Escherichia coli MurC enzyme using oxygen isotope analyses demonstrated that the enzyme-catalyzed reaction proceeds through an acyl phosphate UNAM intermediate prior to L-alanine addition.; GO: 0005524 ATP binding, 0008763 UDP-N-acetylmuramate-L-alanine ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm. Probab=64.44 E-value=9.8 Score=17.37 Aligned_cols=52 Identities=17% Similarity=0.160 Sum_probs=39.8 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCE-EEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCHHH Q ss_conf 99999988887512455555411-247761488678899999999999970899779997153799 Q gi|254781187|r 55 QLEFMEAVDVHCHSNVNNSNPTI-FKCAISAGRGIGKTTLNAWMMLWLISTRPGMSIICIANSETQ 119 (367) Q Consensus 55 q~~~l~~~~~~~~~~~~~~~~~~-~~~~v~sgrg~GKS~~~a~~~lw~~~~~~~~~v~~~A~t~~Q 119 (367) ..++|.++-.. . .-++|++-| |||+.+|+++.-+--+..+.++++-....+- T Consensus 96 R~~~Lael~~~-----------~k~~iaVaGtH--GKTTTTamia~~~~~aGLdPt~~~GG~~~~~ 148 (491) T TIGR01082 96 RAEMLAELMRK-----------RKESIAVAGTH--GKTTTTAMIAVILKEAGLDPTVIVGGEVKEA 148 (491) T ss_pred HHHHHHHHHHH-----------HCCEEEEECCC--CCHHHHHHHHHHHHHCCCCCCEEECCCCCCC T ss_conf 78999999862-----------08707998368--7256899999999844999768986643665 No 499 >PRK13886 conjugal transfer protein TraL; Provisional Probab=64.38 E-value=8.5 Score=17.75 Aligned_cols=30 Identities=17% Similarity=0.155 Sum_probs=0.0 Q ss_pred CCCHHHHHHHHHHHHHHHCCCCEEEEECCC Q ss_conf 678899999999999970899779997153 Q gi|254781187|r 87 GIGKTTLNAWMMLWLISTRPGMSIICIANS 116 (367) Q Consensus 87 g~GKS~~~a~~~lw~~~~~~~~~v~~~A~t 116 (367) |+|||.+++.++=+++....+..++=|=|+ T Consensus 13 GVGKS~va~~LaQY~~~~~~~~~~iDTDpv 42 (241) T PRK13886 13 GVGKSMIAATIAQYKAGKGQKPLCIDTDPV 42 (241) T ss_pred CCHHHHHHHHHHHHHHHCCCCCCEEECCCC T ss_conf 630999999999999835999855608999 No 500 >cd01875 RhoG RhoG subfamily. RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding. However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif. Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology. RhoG has also been shown to play a role in caveolar trafficking and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists. Most Rho proteins contain a lipid modification site at the C-termin Probab=64.15 E-value=8 Score=17.91 Aligned_cols=21 Identities=29% Similarity=0.498 Sum_probs=0.0 Q ss_pred EEEEEECCCCCCHHHHHHHHH Q ss_conf 247761488678899999999 Q gi|254781187|r 78 FKCAISAGRGIGKTTLNAWMM 98 (367) Q Consensus 78 ~~~~v~sgrg~GKS~~~a~~~ 98 (367) +|+.+.+..|+|||.++..++ T Consensus 4 ~KivlvGd~~VGKTsli~r~~ 24 (191) T cd01875 4 IKCVVVGDGAVGKTCLLICYT 24 (191) T ss_pred EEEEEECCCCCCHHHHHHHHH T ss_conf 899999999989999999997 Done!