Query gi|254780182|ref|YP_003064595.1| DNA gyrase subunit A [Candidatus Liberibacter asiaticus str. psy62] Match_columns 910 No_of_seqs 225 out of 2407 Neff 5.8 Searched_HMMs 39220 Date Mon May 23 08:20:21 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780182.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01063 gyrA DNA gyrase, A s 100.0 0 0 2802.2 67.8 854 16-899 1-864 (864) 2 PRK05560 DNA gyrase subunit A; 100.0 0 0 2463.1 86.2 814 11-909 4-817 (822) 3 PRK13979 DNA topoisomerase IV 100.0 0 0 2378.2 84.1 855 9-902 7-912 (959) 4 PRK05561 DNA topoisomerase IV 100.0 0 0 2157.7 74.7 734 8-842 3-743 (745) 5 COG0188 GyrA Type IIA topoisom 100.0 0 0 2119.5 77.0 794 16-900 8-803 (804) 6 TIGR01061 parC_Gpos DNA topois 100.0 0 0 1906.9 38.1 729 16-831 1-738 (745) 7 TIGR01062 parC_Gneg DNA topois 100.0 0 0 1568.0 55.9 683 16-745 1-704 (747) 8 PRK09631 DNA topoisomerase IV 100.0 0 0 1402.8 54.5 609 20-726 2-615 (626) 9 PRK09630 DNA topoisomerase IV 100.0 0 0 1299.6 44.3 468 19-539 2-479 (479) 10 smart00434 TOP4c DNA Topoisome 100.0 0 0 1187.1 42.3 439 19-497 1-444 (445) 11 cd00187 TOP4c DNA Topoisomeras 100.0 0 0 1149.0 43.1 443 39-508 2-445 (445) 12 pfam00521 DNA_topoisoIV DNA gy 100.0 0 0 1084.0 43.2 423 40-499 1-424 (428) 13 PRK12758 DNA topoisomerase IV 100.0 0 0 887.3 55.4 695 8-830 14-729 (879) 14 PTZ00108 DNA topoisomerase II; 100.0 2.8E-45 0 423.6 31.5 468 12-512 721-1208(1506) 15 KOG0355 consensus 100.0 2.6E-42 0 397.7 -38.0 752 11-883 71-830 (842) 16 PRK13979 DNA topoisomerase IV 99.9 4.9E-24 1.3E-28 234.1 22.3 240 536-833 622-948 (959) 17 PRK05560 DNA gyrase subunit A; 99.9 7.2E-23 1.8E-27 223.7 22.3 199 535-745 608-809 (822) 18 TIGR01063 gyrA DNA gyrase, A s 99.9 3.9E-22 1E-26 217.1 19.1 192 538-741 636-862 (864) 19 KOG0355 consensus 99.9 1.5E-21 3.7E-26 212.0 8.2 185 17-251 645-831 (842) 20 PRK05561 DNA topoisomerase IV 99.8 9.9E-19 2.5E-23 186.7 21.3 188 646-901 509-700 (745) 21 COG0188 GyrA Type IIA topoisom 99.7 1.5E-15 3.9E-20 158.1 18.3 81 648-729 653-736 (804) 22 TIGR01061 parC_Gpos DNA topois 99.5 4.9E-14 1.2E-18 144.7 8.5 199 647-901 499-705 (745) 23 TIGR01062 parC_Gneg DNA topois 98.7 1.1E-06 2.8E-11 78.9 14.1 186 648-900 508-703 (747) 24 PRK09631 DNA topoisomerase IV 98.1 0.0034 8.6E-08 47.7 22.7 68 653-725 458-527 (626) 25 pfam03989 DNA_gyraseA_C DNA gy 98.0 3.3E-05 8.3E-10 65.7 7.0 47 851-897 2-48 (50) 26 pfam03989 DNA_gyraseA_C DNA gy 97.9 6.2E-05 1.6E-09 63.2 7.0 48 693-741 1-48 (50) 27 PRK09630 DNA topoisomerase IV 97.6 0.0059 1.5E-07 45.5 13.4 112 357-491 308-427 (479) 28 KOG1240 consensus 96.7 0.095 2.4E-06 34.7 16.6 153 646-863 1062-1220(1431) 29 KOG3863 consensus 87.3 2.4 6E-05 22.2 6.6 64 394-489 458-532 (604) 30 KOG1920 consensus 87.0 2.5 6.3E-05 22.1 12.3 16 307-324 649-664 (1265) 31 TIGR02895 spore_sigI RNA polym 85.7 2.5 6.5E-05 21.9 5.6 100 360-521 64-163 (225) 32 pfam11197 DUF2835 Protein of u 84.8 2.9 7.5E-05 21.4 5.6 45 692-738 19-66 (68) 33 KOG4212 consensus 82.4 1.9 5E-05 23.0 3.8 63 265-331 46-110 (608) 34 pfam04201 TPD52 Tumour protein 81.2 3.1 8E-05 21.1 4.5 49 465-520 26-74 (162) 35 pfam05133 Phage_prot_Gp6 Phage 80.0 4.3 0.00011 19.8 6.2 12 121-132 140-151 (435) 36 COG5207 UBP14 Isopeptidase T [ 77.1 0.67 1.7E-05 27.1 0.0 14 89-102 162-175 (749) 37 KOG4010 consensus 76.6 5.3 0.00014 19.1 4.8 43 463-505 39-81 (208) 38 pfam12395 DUF3658 Protein of u 75.6 1.5 3.7E-05 24.1 1.5 53 67-132 57-110 (111) 39 PRK03992 proteasome-activating 72.0 6.6 0.00017 18.2 7.7 130 471-616 5-136 (390) 40 pfam10977 DUF2797 Protein of u 71.6 4.4 0.00011 19.8 3.1 25 591-616 76-100 (233) 41 pfam03982 DAGAT Diacylglycerol 71.5 1 2.6E-05 25.5 -0.2 67 30-113 13-99 (297) 42 TIGR02515 IV_pilus_PilQ type I 70.3 5.5 0.00014 19.0 3.4 36 820-865 385-420 (464) 43 TIGR00909 2A0306 amino acid tr 69.4 4.1 0.0001 20.1 2.6 35 52-98 316-350 (451) 44 cd04793 LanC LanC is the cycla 68.4 7.7 0.0002 17.6 3.8 70 175-244 103-188 (382) 45 TIGR00019 prfA peptide chain r 67.3 8.1 0.00021 17.4 9.9 46 469-514 48-96 (373) 46 cd06461 M2_ACE Peptidase famil 63.9 6.8 0.00017 18.1 2.8 55 99-157 149-206 (477) 47 KOG2264 consensus 62.9 9.5 0.00024 16.8 4.9 46 214-260 256-310 (907) 48 pfam04799 Fzo_mitofusin fzo-li 62.4 9.7 0.00025 16.7 6.8 54 461-514 113-169 (171) 49 PRK03298 hypothetical protein; 61.8 8.4 0.00021 17.3 3.0 34 678-711 119-154 (224) 50 KOG0640 consensus 61.5 10 0.00025 16.6 8.6 24 874-897 382-405 (430) 51 PRK10834 hypothetical protein; 61.4 3.6 9.3E-05 20.5 1.0 125 78-207 47-192 (239) 52 KOG1764 consensus 60.4 8.5 0.00022 17.3 2.8 17 235-252 85-101 (381) 53 COG3953 SLT domain proteins [G 60.3 3.6 9.3E-05 20.5 0.9 23 113-136 66-89 (235) 54 KOG0243 consensus 60.1 11 0.00027 16.4 8.6 25 177-201 220-244 (1041) 55 COG1579 Zn-ribbon protein, pos 60.0 11 0.00027 16.4 10.7 63 455-517 83-145 (239) 56 cd07925 LigA_like_1 The A subu 59.7 11 0.00027 16.4 3.5 25 447-471 43-67 (106) 57 TIGR02894 DNA_bind_RsfA transc 59.6 11 0.00027 16.3 10.3 105 368-521 54-159 (163) 58 pfam01939 DUF91 Protein of unk 58.9 10 0.00026 16.6 3.0 32 678-709 120-153 (228) 59 PHA00728 hypothetical protein 58.6 11 0.00028 16.2 3.6 66 467-545 4-69 (153) 60 PRK13378 protocatechuate 4,5-d 58.3 11 0.00028 16.2 3.5 25 447-471 54-78 (117) 61 COG1618 Predicted nucleotide k 58.1 8 0.0002 17.5 2.3 47 264-311 6-56 (179) 62 pfam07914 DUF1679 Protein of u 57.9 5.4 0.00014 19.0 1.4 64 182-246 161-227 (413) 63 COG0172 SerS Seryl-tRNA synthe 57.8 11 0.00029 16.1 8.3 80 400-514 3-86 (429) 64 cd07921 PCA_45_Doxase_A_like S 57.7 11 0.00029 16.1 3.5 25 447-471 43-67 (106) 65 KOG3985 consensus 57.7 11 0.00029 16.1 3.9 84 158-249 95-194 (283) 66 TIGR01051 topA_bact DNA topois 57.6 3.1 8E-05 21.1 0.2 22 493-514 347-369 (688) 67 KOG0291 consensus 57.2 12 0.00029 16.0 14.0 152 532-716 400-555 (893) 68 PRK04247 hypothetical protein; 57.0 11 0.00027 16.4 2.8 35 678-712 144-180 (250) 69 pfam01401 Peptidase_M2 Angiote 56.6 9.7 0.00025 16.7 2.5 40 467-515 195-234 (595) 70 KOG1507 consensus 56.4 7.8 0.0002 17.6 2.0 74 453-526 48-127 (358) 71 pfam08082 PRO8NT PRO8NT (NUC06 55.4 10 0.00026 16.5 2.5 56 49-111 4-61 (152) 72 KOG0315 consensus 55.2 12 0.00032 15.8 10.8 107 587-712 43-155 (311) 73 TIGR00373 TIGR00373 conserved 53.6 7.1 0.00018 18.0 1.4 12 54-65 48-59 (168) 74 PRK13379 protocatechuate 4,5-d 53.4 13 0.00033 15.6 3.4 25 447-471 55-79 (119) 75 PRK07773 replicative DNA helic 52.6 13 0.00034 15.5 12.1 41 851-894 776-821 (868) 76 pfam06572 DUF1131 Protein of u 52.3 14 0.00034 15.4 4.9 31 839-869 79-112 (192) 77 pfam01208 URO-D Uroporphyrinog 52.3 14 0.00034 15.4 4.9 29 328-356 182-210 (337) 78 pfam03444 DUF293 Domain of unk 51.0 12 0.00031 15.8 2.3 33 49-83 2-34 (79) 79 TIGR02687 TIGR02687 conserved 50.5 14 0.00036 15.2 2.6 11 649-659 676-687 (911) 80 COG1426 Predicted transcriptio 50.4 14 0.00037 15.2 3.3 51 447-497 15-67 (284) 81 TIGR00034 aroFGH phospho-2-deh 50.4 11 0.00028 16.3 2.0 30 685-714 217-247 (348) 82 KOG1359 consensus 50.3 12 0.00031 15.9 2.2 12 170-181 56-67 (417) 83 pfam07746 LigA Aromatic-ring-o 49.6 15 0.00037 15.1 3.4 25 447-471 28-52 (88) 84 PRK06904 replicative DNA helic 49.6 15 0.00038 15.1 2.9 23 493-515 354-376 (472) 85 cd07923 Gallate_dioxygenase_C 49.3 15 0.00038 15.1 3.4 25 447-471 35-59 (94) 86 KOG3584 consensus 49.3 15 0.00038 15.1 5.2 19 496-514 326-344 (348) 87 PRK10718 hypothetical protein; 49.1 15 0.00038 15.0 5.0 59 800-869 38-111 (191) 88 PRK13695 putative NTPase; Prov 48.4 14 0.00035 15.3 2.3 46 265-311 5-54 (174) 89 PRK10727 DNA-binding transcrip 48.1 14 0.00035 15.4 2.2 61 37-102 17-82 (342) 90 TIGR02707 butyr_kinase butyrat 47.4 16 0.0004 14.8 4.9 30 868-898 296-326 (353) 91 TIGR02386 rpoC_TIGR DNA-direct 47.1 16 0.0004 14.8 3.8 92 649-745 1111-1209(1552) 92 COG3879 Uncharacterized protei 47.0 16 0.00041 14.8 5.8 64 469-548 58-125 (247) 93 PRK04778 septation ring format 46.2 16 0.00042 14.7 13.9 28 105-139 151-178 (569) 94 pfam06160 EzrA Septation ring 46.2 16 0.00042 14.7 14.2 20 348-367 301-320 (559) 95 pfam07798 DUF1640 Protein of u 46.1 16 0.00042 14.7 6.0 38 448-491 99-136 (177) 96 cd04618 CBS_pair_5 The CBS dom 46.0 13 0.00033 15.7 1.8 69 46-116 6-85 (98) 97 COG2949 SanA Uncharacterized m 45.2 14 0.00036 15.2 1.9 151 52-208 35-207 (235) 98 pfam05400 FliT Flagellar prote 45.2 17 0.00043 14.6 3.4 42 479-520 60-101 (109) 99 pfam01255 Prenyltransf Putativ 45.0 17 0.00043 14.6 3.4 64 445-517 50-113 (222) 100 pfam02650 HTH_WhiA Sporulation 44.7 17 0.00044 14.5 4.3 38 277-320 41-78 (191) 101 PRK05595 replicative DNA helic 43.9 18 0.00045 14.4 3.3 23 493-515 331-353 (444) 102 KOG4248 consensus 43.8 18 0.00045 14.4 3.8 34 128-161 268-302 (1143) 103 COG2312 Erythromycin esterase 43.7 7.2 0.00018 17.9 0.2 48 73-130 43-92 (405) 104 PRK06266 transcription initiat 42.5 18 0.00045 14.4 2.1 14 317-330 47-60 (178) 105 PRK05431 seryl-tRNA synthetase 42.4 18 0.00047 14.2 11.0 82 401-512 4-89 (422) 106 cd02639 R3H_RRM R3H domain of 42.2 18 0.00047 14.2 2.5 21 48-68 25-46 (60) 107 PRK05729 valS valyl-tRNA synth 42.2 18 0.00047 14.2 5.0 53 54-116 155-211 (877) 108 cd04585 CBS_pair_ACT_assoc2 Th 42.1 18 0.00047 14.2 3.1 75 41-117 26-110 (122) 109 pfam04849 HAP1_N HAP1 N-termin 42.0 19 0.00047 14.2 5.4 45 470-514 244-288 (307) 110 pfam10168 Nup88 Nuclear pore c 41.9 19 0.00047 14.2 11.1 11 380-390 563-573 (717) 111 COG0305 DnaB Replicative DNA h 41.6 19 0.00048 14.2 3.2 54 189-243 1-54 (435) 112 cd04600 CBS_pair_HPP_assoc Thi 41.6 19 0.00048 14.2 2.5 28 90-117 10-37 (124) 113 COG4939 Major membrane immunog 41.2 19 0.00048 14.1 3.2 47 106-152 62-113 (147) 114 PRK08082 consensus 41.1 19 0.00049 14.1 3.1 22 494-515 335-356 (453) 115 cd04469 S1_Hex1 S1_Hex1: Hex1, 40.4 17 0.00044 14.5 1.7 16 236-251 39-54 (75) 116 COG2524 Predicted transcriptio 40.1 20 0.0005 14.0 2.2 23 721-743 200-222 (294) 117 pfam04637 Herpes_pp85 Herpesvi 39.8 20 0.00051 13.9 4.6 180 163-371 66-255 (502) 118 KOG1684 consensus 39.8 12 0.0003 16.0 0.8 15 89-103 66-80 (401) 119 KOG0428 consensus 39.5 20 0.00051 13.9 3.2 10 112-121 123-132 (314) 120 PRK05617 enoyl-CoA hydratase; 39.4 19 0.00048 14.1 1.8 30 176-205 175-205 (356) 121 pfam03131 bZIP_Maf bZIP Maf tr 39.3 20 0.00051 13.9 5.6 37 470-513 55-91 (95) 122 cd03677 MM_CoA_mutase_beta Coe 39.3 20 0.00051 13.9 2.0 23 264-286 181-203 (424) 123 cd03823 GT1_ExpE7_like This fa 39.0 20 0.00052 13.8 2.4 12 231-242 148-159 (359) 124 COG3253 ywfI Predicted heme pe 38.7 9.2 0.00024 16.9 0.1 11 263-273 178-188 (230) 125 KOG2941 consensus 38.5 21 0.00053 13.8 3.4 30 68-98 152-181 (444) 126 PRK08840 replicative DNA helic 38.2 21 0.00053 13.7 3.2 23 493-515 349-371 (464) 127 TIGR01465 cobM_cbiF precorrin- 38.1 13 0.00033 15.6 0.8 14 89-102 80-93 (252) 128 pfam10458 Val_tRNA-synt_C Valy 38.0 21 0.00053 13.7 4.5 34 468-501 4-37 (66) 129 cd04603 CBS_pair_KefB_assoc Th 38.0 15 0.00039 14.9 1.2 86 30-120 12-103 (111) 130 cd04597 CBS_pair_DRTGG_assoc2 37.8 21 0.00054 13.7 3.7 69 49-117 31-101 (113) 131 pfam00465 Fe-ADH Iron-containi 37.7 21 0.00054 13.7 2.2 26 182-207 51-76 (312) 132 pfam03266 DUF265 Protein of un 37.6 21 0.00054 13.7 2.6 45 266-311 2-50 (168) 133 PRK11147 ABC transporter ATPas 37.6 21 0.00054 13.7 6.2 11 201-211 167-177 (632) 134 cd04629 CBS_pair_16 The CBS do 37.2 14 0.00036 15.3 0.9 32 89-120 8-40 (114) 135 cd04617 CBS_pair_4 The CBS dom 37.2 14 0.00036 15.3 0.9 38 78-116 60-102 (118) 136 pfam11802 CENP-K Centromere-as 37.2 22 0.00055 13.6 8.5 62 447-510 52-129 (273) 137 COG1791 Uncharacterized conser 37.1 22 0.00055 13.6 7.3 117 471-636 17-152 (181) 138 PRK10240 undecaprenyl pyrophos 37.0 22 0.00055 13.6 3.2 58 446-512 50-107 (229) 139 pfam12552 DUF3741 Protein of u 37.0 22 0.00055 13.6 2.2 39 183-225 8-46 (46) 140 pfam06838 Alum_res Aluminium r 36.7 22 0.00056 13.6 3.6 14 52-65 26-39 (405) 141 TIGR00683 nanA N-acetylneurami 36.0 22 0.00057 13.5 3.1 51 233-296 111-161 (294) 142 KOG0650 consensus 35.9 22 0.00057 13.5 7.7 50 501-555 347-410 (733) 143 cd04639 CBS_pair_26 The CBS do 35.6 23 0.00058 13.4 2.8 40 78-117 58-99 (111) 144 cd07642 BAR_ASAP2 The Bin/Amph 35.5 23 0.00058 13.4 3.3 68 451-518 83-160 (215) 145 TIGR01341 aconitase_1 aconitat 35.5 15 0.00039 14.9 0.8 74 810-898 795-874 (896) 146 TIGR03268 methan_mark_3 putati 35.5 23 0.00058 13.4 4.5 170 702-890 269-466 (503) 147 KOG3029 consensus 35.4 23 0.00058 13.4 3.3 45 170-225 136-180 (370) 148 TIGR01750 fabZ beta-hydroxyacy 35.4 12 0.00031 15.8 0.3 28 620-647 21-49 (142) 149 pfam08672 APC2 Anaphase promot 35.3 23 0.00058 13.4 3.6 36 184-219 3-41 (60) 150 KOG0787 consensus 35.3 23 0.00058 13.4 8.6 44 477-520 129-173 (414) 151 pfam11892 DUF3412 Domain of un 35.3 22 0.00055 13.6 1.6 57 45-105 28-103 (123) 152 TIGR03449 mycothiol_MshA UDP-N 35.2 23 0.00058 13.4 2.5 18 190-207 229-246 (405) 153 cd07321 Extradiol_Dioxygenase_ 34.9 23 0.00059 13.3 4.0 26 447-472 33-58 (77) 154 PRK09458 pspB phage shock prot 34.8 23 0.00059 13.3 2.3 25 471-495 45-69 (75) 155 KOG4649 consensus 34.8 23 0.00059 13.3 9.2 28 798-825 250-280 (354) 156 TIGR01090 apt adenine phosphor 34.2 15 0.00038 15.1 0.6 51 192-251 28-80 (175) 157 PTZ00233 variable surface prot 34.2 18 0.00046 14.3 1.0 39 477-515 31-74 (509) 158 KOG0596 consensus 34.2 24 0.0006 13.3 2.3 10 219-228 215-224 (677) 159 PTZ00156 60S ribosomal protein 33.8 24 0.00061 13.2 1.7 61 47-118 40-102 (172) 160 pfam00356 LacI Bacterial regul 33.7 24 0.00061 13.2 2.3 35 32-68 11-46 (46) 161 COG0216 PrfA Protein chain rel 33.7 24 0.00061 13.2 6.0 45 470-514 48-94 (363) 162 PRK12806 flagellin; Provisiona 33.6 24 0.00061 13.2 6.9 62 386-488 57-127 (475) 163 KOG1302 consensus 33.4 24 0.00062 13.2 3.5 16 47-62 15-30 (600) 164 cd00225 API3 Ascaris pepsin in 33.3 24 0.00062 13.1 3.6 41 460-500 26-66 (159) 165 TIGR02171 Fb_sc_TIGR02171 Fibr 33.3 24 0.00062 13.1 5.0 166 503-679 222-410 (982) 166 TIGR03300 assembly_YfgL outer 33.1 25 0.00063 13.1 11.1 59 535-603 64-122 (377) 167 COG0493 GltD NADPH-dependent g 33.0 19 0.00049 14.1 1.0 130 219-378 112-250 (457) 168 pfam07569 Hira TUP1-like enhan 32.9 25 0.00063 13.1 5.0 27 579-609 16-42 (219) 169 KOG3091 consensus 32.9 25 0.00063 13.1 12.4 95 374-518 354-453 (508) 170 cd07603 BAR_ACAPs The Bin/Amph 32.6 25 0.00063 13.1 3.8 30 453-482 83-112 (200) 171 PRK07004 replicative DNA helic 32.4 25 0.00064 13.0 3.7 23 493-515 344-366 (460) 172 cd07924 PCA_45_Doxase_A The A 32.2 25 0.00064 13.0 6.9 25 447-471 51-75 (121) 173 KOG3957 consensus 32.1 23 0.00058 13.4 1.2 27 223-249 152-181 (387) 174 PHA02126 hypothetical protein 31.9 23 0.00057 13.5 1.2 50 224-273 50-107 (153) 175 TIGR01052 top6b DNA topoisomer 31.6 22 0.00056 13.5 1.1 15 303-317 172-186 (662) 176 cd04637 CBS_pair_24 The CBS do 31.4 26 0.00066 12.9 2.3 41 76-117 67-110 (122) 177 pfam02624 YcaO YcaO-like famil 31.4 22 0.00057 13.5 1.1 78 123-208 47-136 (332) 178 cd04605 CBS_pair_MET2_assoc Th 31.4 24 0.00062 13.2 1.3 27 91-117 11-37 (110) 179 KOG0319 consensus 31.4 26 0.00066 12.9 16.5 183 531-739 331-523 (775) 180 PRK00969 hypothetical protein; 31.4 26 0.00066 12.9 4.5 171 702-890 272-469 (508) 181 pfam08657 DASH_Spc34 DASH comp 31.3 26 0.00066 12.9 5.5 26 202-227 36-61 (212) 182 COG1293 Predicted RNA-binding 31.1 26 0.00067 12.9 5.5 42 457-498 364-407 (564) 183 PRK07778 consensus 31.1 26 0.00067 12.9 2.2 13 91-103 46-58 (386) 184 pfam06447 consensus 31.1 26 0.00067 12.9 7.8 64 447-510 46-111 (407) 185 pfam04967 HTH_10 HTH DNA bindi 31.0 26 0.00067 12.8 3.4 34 49-83 1-34 (53) 186 COG3394 Uncharacterized protei 30.8 26 0.00067 12.8 4.9 140 48-210 13-176 (257) 187 KOG3314 consensus 30.8 26 0.00067 12.8 2.7 38 51-88 38-75 (194) 188 pfam05565 Sipho_Gp157 Siphovir 30.8 26 0.00067 12.8 5.4 65 474-538 53-125 (162) 189 PRK08760 replicative DNA helic 30.7 27 0.00068 12.8 3.0 19 497-515 363-381 (476) 190 pfam03853 YjeF_N YjeF-related 30.7 25 0.00064 13.1 1.3 116 91-228 14-143 (170) 191 cd04962 GT1_like_5 This family 30.6 27 0.00068 12.8 1.9 35 481-515 324-358 (371) 192 PRK11303 DNA-binding transcrip 30.5 27 0.00068 12.8 2.7 181 37-242 16-206 (330) 193 COG3959 Transketolase, N-termi 30.5 27 0.00068 12.8 3.1 16 86-101 32-47 (243) 194 KOG0275 consensus 30.3 27 0.00068 12.8 12.3 28 840-867 439-466 (508) 195 PRK04028 glutamyl-tRNA(Gln) am 30.2 27 0.00069 12.8 8.4 70 398-511 443-514 (631) 196 pfam11629 Mst1_SARAH C termina 30.2 27 0.00069 12.7 1.9 32 486-520 12-43 (49) 197 COG1637 Predicted nuclease of 30.1 27 0.00069 12.7 3.1 14 730-743 202-215 (253) 198 PRK13377 protocatechuate 4,5-d 29.9 27 0.00069 12.7 6.9 25 447-471 54-78 (129) 199 pfam06952 PsiA PsiA protein. T 29.8 27 0.0007 12.7 2.6 16 177-192 49-64 (238) 200 cd04626 CBS_pair_13 The CBS do 29.8 22 0.00057 13.5 0.9 27 91-117 10-36 (111) 201 TIGR02483 PFK_mixed phosphofru 29.8 27 0.0007 12.7 2.9 31 260-292 197-227 (339) 202 pfam01768 Birna_VP4 Birnavirus 29.8 13 0.00033 15.6 -0.3 24 108-131 14-38 (264) 203 KOG4288 consensus 29.5 28 0.0007 12.7 3.6 35 189-240 243-277 (283) 204 KOG3686 consensus 29.4 28 0.00071 12.6 2.0 22 691-712 532-553 (740) 205 PRK13670 hypothetical protein; 29.2 27 0.0007 12.7 1.3 120 77-226 3-138 (390) 206 cd04613 CBS_pair_SpoIVFB_EriC_ 29.1 24 0.00061 13.2 0.9 28 90-117 9-36 (114) 207 cd04593 CBS_pair_EriC_assoc_ba 29.0 24 0.0006 13.3 0.9 26 91-116 10-35 (115) 208 smart00116 CBS Domain in cysta 29.0 26 0.00067 12.9 1.1 30 88-117 6-35 (49) 209 COG3546 Mn-containing catalase 28.6 28 0.00073 12.5 1.3 33 117-149 29-64 (277) 210 KOG3809 consensus 28.5 29 0.00073 12.5 7.7 42 461-502 532-581 (583) 211 TIGR01122 ilvE_I branched-chai 28.4 22 0.00056 13.5 0.7 22 652-673 196-219 (302) 212 KOG4318 consensus 28.4 29 0.00073 12.5 6.7 178 25-243 194-392 (1088) 213 PRK08694 consensus 28.3 29 0.00073 12.5 3.2 23 493-515 350-372 (468) 214 pfam12529 Xylo_C Xylosyltransf 28.3 29 0.00073 12.5 1.3 41 647-687 85-125 (180) 215 KOG2052 consensus 28.2 27 0.00069 12.7 1.1 16 696-711 354-369 (513) 216 PRK11387 S-methylmethionine tr 27.8 29 0.00075 12.4 2.1 40 175-214 201-240 (465) 217 TIGR01951 nusB transcription a 27.8 29 0.00075 12.4 5.5 54 461-523 78-133 (140) 218 KOG3441 consensus 27.7 13 0.00034 15.5 -0.6 16 848-863 102-117 (149) 219 pfam05110 AF-4 AF-4 proto-onco 27.6 29 0.00075 12.4 9.3 35 372-406 909-947 (1154) 220 PRK10803 hypothetical protein; 27.5 30 0.00075 12.4 6.3 41 471-511 64-104 (262) 221 TIGR00630 uvra excinuclease AB 27.5 30 0.00075 12.4 1.4 136 128-289 49-227 (956) 222 PRK11622 putative ABC transpor 27.5 30 0.00075 12.4 1.5 38 189-240 168-205 (401) 223 PRK10423 transcriptional repre 27.5 30 0.00076 12.4 2.1 176 37-243 14-202 (327) 224 KOG2911 consensus 27.4 30 0.00076 12.4 9.6 89 387-509 289-383 (439) 225 PRK02304 adenine phosphoribosy 27.2 24 0.00061 13.2 0.7 11 731-741 139-149 (174) 226 KOG0533 consensus 27.2 30 0.00076 12.3 3.3 25 264-288 84-108 (243) 227 TIGR01037 pyrD_sub1_fam dihydr 27.2 30 0.00076 12.3 2.5 85 221-315 11-101 (308) 228 pfam09517 RE_Eco29kI Eco29kI r 27.1 24 0.00061 13.2 0.7 20 94-116 102-122 (170) 229 cd04621 CBS_pair_8 The CBS dom 27.0 30 0.00077 12.3 1.5 26 91-116 10-35 (135) 230 TIGR02303 HpaG-C-term 4-hydrox 26.9 30 0.00077 12.3 1.8 16 586-601 35-50 (249) 231 cd04635 CBS_pair_22 The CBS do 26.9 26 0.00067 12.8 0.9 28 89-116 82-109 (122) 232 KOG0005 consensus 26.9 23 0.00059 13.4 0.5 20 46-65 33-52 (70) 233 PRK08227 aldolase; Validated 26.7 30 0.00078 12.3 3.7 23 293-315 153-175 (291) 234 pfam11853 DUF3373 Protein of u 26.5 31 0.00078 12.3 2.9 20 469-488 32-51 (485) 235 TIGR01194 cyc_pep_trnsptr cycl 26.5 31 0.00078 12.3 3.2 41 303-344 104-144 (555) 236 PRK05748 replicative DNA helic 26.5 31 0.00078 12.2 3.7 22 494-515 336-357 (448) 237 KOG0216 consensus 26.4 31 0.00078 12.2 4.4 113 222-343 65-196 (1111) 238 COG4746 Uncharacterized protei 26.3 31 0.00079 12.2 2.2 28 214-245 10-37 (80) 239 PRK00202 nusB transcription an 26.3 31 0.00079 12.2 7.4 28 496-523 96-123 (132) 240 KOG0977 consensus 26.2 31 0.00079 12.2 13.4 46 473-518 294-339 (546) 241 PRK06835 DNA replication prote 26.1 31 0.00079 12.2 1.1 20 20-39 40-59 (330) 242 PRK02753 DNA-directed RNA poly 25.8 31 0.0008 12.2 1.2 14 371-384 13-26 (74) 243 KOG1446 consensus 25.8 31 0.0008 12.1 12.7 72 789-869 191-263 (311) 244 pfam05636 DUF795 Protein of un 25.7 31 0.0008 12.1 1.3 122 77-227 3-140 (389) 245 TIGR03531 selenium_SpcS O-phos 25.7 32 0.0008 12.1 4.0 98 24-145 12-113 (444) 246 pfam10985 DUF2805 Protein of u 25.7 32 0.0008 12.1 3.7 38 397-463 1-38 (73) 247 KOG4437 consensus 25.7 32 0.0008 12.1 5.1 15 319-333 149-163 (482) 248 TIGR01363 strep_his_triad stre 25.7 32 0.00081 12.1 1.5 163 526-725 61-253 (376) 249 COG1363 FrvX Cellulase M and r 25.5 32 0.00081 12.1 7.6 101 476-599 3-110 (355) 250 cd04801 CBS_pair_M50_like This 25.3 31 0.00079 12.2 1.0 23 92-114 77-99 (114) 251 pfam11552 DUF3230 Protein of u 25.3 32 0.00082 12.1 1.3 21 184-208 13-33 (105) 252 PRK08026 flagellin; Validated 25.3 32 0.00082 12.1 6.9 62 386-488 57-127 (566) 253 pfam05718 Pox_int_trans Poxvir 25.3 32 0.00082 12.1 2.4 35 451-491 348-382 (383) 254 CHL00144 odpB pyruvate dehydro 25.2 26 0.00067 12.8 0.6 44 311-363 232-277 (326) 255 pfam10480 ICAP-1_inte_bdg Beta 25.2 32 0.00082 12.1 3.9 39 786-825 97-135 (200) 256 PRK00464 nrdR transcriptional 25.2 32 0.00082 12.1 5.0 25 447-471 98-122 (149) 257 TIGR01219 Pmev_kin_ERG8 phosph 25.1 32 0.00082 12.1 3.7 141 455-617 346-497 (499) 258 PRK09492 treR trehalose repres 25.1 32 0.00082 12.0 2.5 71 31-103 15-90 (315) 259 PRK10401 DNA-binding transcrip 25.0 32 0.00082 12.0 2.5 52 32-85 13-69 (346) 260 cd04777 HTH_MerR-like_sg1 Heli 25.0 32 0.00083 12.0 6.0 47 446-492 53-105 (107) 261 cd04803 CBS_pair_15 The CBS do 24.9 31 0.0008 12.2 0.9 32 89-120 8-40 (122) 262 TIGR01055 parE_Gneg DNA topois 24.7 22 0.00055 13.6 0.1 61 44-117 10-84 (647) 263 pfam05889 SLA_LP_auto_ag Solub 24.7 33 0.00084 12.0 3.2 32 482-513 268-299 (389) 264 pfam05904 DUF863 Plant protein 24.6 27 0.0007 12.7 0.6 12 449-460 522-533 (730) 265 KOG0240 consensus 24.6 33 0.00084 12.0 10.6 56 455-510 416-477 (607) 266 TIGR03643 conserved hypothetic 24.5 33 0.00084 12.0 4.0 39 396-463 1-39 (72) 267 TIGR02817 adh_fam_1 zinc-bindi 24.4 20 0.0005 14.0 -0.2 12 113-125 241-252 (338) 268 TIGR01967 DEAH_box_HrpA ATP-de 24.2 33 0.00085 11.9 1.3 27 360-386 1139-1168(1320) 269 PRK09413 insertion sequence 2 24.2 33 0.00085 11.9 5.1 38 474-511 70-107 (121) 270 cd04612 CBS_pair_SpoIVFB_EriC_ 24.2 30 0.00076 12.4 0.7 10 92-101 74-83 (111) 271 TIGR00345 arsA arsenite-activa 24.2 33 0.00085 11.9 2.2 29 468-496 199-227 (330) 272 cd04619 CBS_pair_6 The CBS dom 24.1 33 0.00085 11.9 1.6 25 90-114 75-99 (114) 273 TIGR02742 TrbC_Ftype type-F co 24.1 28 0.00071 12.6 0.5 14 89-102 107-120 (139) 274 PRK04885 ppnK inorganic polyph 24.1 33 0.00085 11.9 1.5 46 490-550 5-50 (265) 275 TIGR01334 modD modD protein; I 24.1 33 0.00085 11.9 4.3 75 345-460 146-228 (277) 276 TIGR02030 BchI-ChlI magnesium 24.0 18 0.00046 14.3 -0.5 143 188-377 60-226 (340) 277 KOG3011 consensus 23.9 34 0.00086 11.9 2.7 37 129-166 105-142 (293) 278 COG0241 HisB Histidinol phosph 23.7 21 0.00054 13.7 -0.1 50 174-229 51-100 (181) 279 PRK08006 replicative DNA helic 23.7 34 0.00087 11.8 3.0 12 214-225 49-60 (471) 280 pfam06530 Phage_antitermQ Phag 23.6 34 0.00087 11.8 1.2 37 180-216 25-70 (126) 281 COG4800 Predicted transcriptio 23.6 34 0.00087 11.8 2.5 78 208-290 38-123 (170) 282 PRK06819 flagellin; Validated 23.6 34 0.00087 11.8 7.3 22 466-487 104-125 (371) 283 PRK07263 consensus 23.5 34 0.00087 11.8 3.3 23 493-515 334-356 (453) 284 PRK08411 flagellin; Reviewed 23.4 34 0.00088 11.8 6.8 62 386-488 57-127 (573) 285 TIGR00501 met_pdase_II methion 23.4 16 0.00042 14.7 -0.8 38 676-716 205-244 (327) 286 PHA02094 hypothetical protein 23.2 35 0.00088 11.8 1.0 20 71-90 43-62 (81) 287 TIGR00444 mazG MazG family pro 23.1 20 0.00052 13.8 -0.3 15 471-485 163-177 (253) 288 PRK13588 flagellin B; Provisio 23.1 35 0.00089 11.8 6.8 63 386-489 57-128 (514) 289 pfam12226 Astro_capsid_p Turke 23.0 35 0.00089 11.7 2.8 17 676-692 120-136 (230) 290 PRK11462 putative transporter; 23.0 35 0.00089 11.7 1.7 28 456-483 421-448 (460) 291 cd04631 CBS_pair_18 The CBS do 23.0 34 0.00085 11.9 0.8 28 90-117 9-37 (125) 292 KOG4777 consensus 22.9 35 0.00089 11.7 1.2 111 84-213 25-154 (361) 293 PRK13729 conjugal transfer pil 22.7 35 0.0009 11.7 7.6 59 446-509 59-117 (474) 294 PRK04184 DNA topoisomerase VI 22.7 21 0.00054 13.7 -0.3 36 301-337 165-203 (533) 295 pfam04762 IKI3 IKI3 family. Me 22.6 35 0.0009 11.7 9.6 28 680-707 526-553 (918) 296 TIGR02938 nifL_nitrog nitrogen 22.5 36 0.00091 11.7 0.9 10 598-607 371-380 (496) 297 COG1110 Reverse gyrase [DNA re 22.5 36 0.00091 11.7 5.6 70 70-140 67-150 (1187) 298 PRK12756 phospho-2-dehydro-3-d 22.5 36 0.00091 11.7 2.0 22 119-142 62-83 (349) 299 PRK11747 dinG ATP-dependent DN 22.5 36 0.00091 11.7 7.5 21 42-62 17-39 (697) 300 KOG3347 consensus 22.5 36 0.00091 11.7 2.9 37 264-302 8-44 (176) 301 TIGR01916 F420_puta_dedox F420 22.4 32 0.00081 12.1 0.6 120 595-734 51-191 (260) 302 cd00475 CIS_IPPS Cis (Z)-Isopr 22.3 36 0.00092 11.6 2.6 20 385-404 21-40 (221) 303 TIGR02768 TraA_Ti Ti-type conj 22.2 36 0.00092 11.6 2.8 43 644-686 500-543 (888) 304 PRK10977 hypothetical protein; 22.2 36 0.00092 11.6 3.7 59 140-212 48-107 (510) 305 PRK13355 bifunctional HTH-doma 22.2 36 0.00092 11.6 2.6 90 193-297 215-319 (518) 306 COG4026 Uncharacterized protei 22.2 36 0.00092 11.6 5.1 43 471-513 159-201 (290) 307 CHL00191 ycf61 DNA-directed RN 22.2 36 0.00092 11.6 1.2 17 369-385 11-27 (74) 308 PRK10869 recombination and rep 22.1 36 0.00092 11.6 10.9 12 459-470 302-313 (553) 309 pfam00534 Glycos_transf_1 Glyc 22.1 36 0.00092 11.6 1.5 21 190-210 140-160 (172) 310 pfam00768 Peptidase_S11 D-alan 22.1 36 0.00092 11.6 3.2 84 45-145 84-168 (241) 311 pfam07426 Dynactin_p22 Dynacti 22.0 36 0.00093 11.6 7.9 19 477-495 97-115 (172) 312 COG0576 GrpE Molecular chapero 21.9 36 0.00093 11.6 7.1 50 499-548 121-176 (193) 313 TIGR03604 docking_ocin bacteri 21.9 36 0.00093 11.6 2.7 54 149-208 72-136 (377) 314 KOG2896 consensus 21.9 37 0.00093 11.6 12.5 111 358-492 54-169 (377) 315 TIGR01034 metK S-adenosylmethi 21.8 30 0.00077 12.3 0.4 16 176-191 120-135 (393) 316 PRK00927 tryptophanyl-tRNA syn 21.8 37 0.00093 11.6 9.2 115 318-513 208-324 (325) 317 COG2039 Pcp Pyrrolidone-carbox 21.7 37 0.00094 11.5 1.1 19 190-208 40-58 (207) 318 KOG4577 consensus 21.6 37 0.00094 11.5 1.3 54 461-520 199-252 (383) 319 pfam06609 TRI12 Fungal trichot 21.6 31 0.00079 12.2 0.4 32 28-59 53-84 (598) 320 cd04588 CBS_pair_CAP-ED_DUF294 21.6 36 0.00092 11.6 0.7 68 40-117 25-98 (110) 321 PRK10548 flagellar biosynthesi 21.6 37 0.00094 11.5 3.4 52 485-536 66-118 (121) 322 pfam05615 THOC7 Tho complex su 21.5 37 0.00094 11.5 10.7 70 446-516 53-127 (135) 323 TIGR02404 trehalos_R_Bsub treh 21.5 30 0.00077 12.3 0.3 147 214-376 7-163 (236) 324 KOG0998 consensus 21.4 37 0.00095 11.5 4.6 52 468-519 505-556 (847) 325 PRK11779 sbcB exonuclease I; P 21.4 37 0.00095 11.5 12.4 48 308-356 256-313 (477) 326 pfam02827 PKI cAMP-dependent p 21.4 33 0.00083 12.0 0.4 23 26-48 4-28 (74) 327 KOG2303 consensus 21.3 37 0.00095 11.5 4.1 40 281-328 373-413 (706) 328 cd04768 HTH_BmrR-like Helix-Tu 21.3 37 0.00095 11.5 4.5 40 447-490 56-95 (96) 329 PRK10580 proY putative proline 21.3 37 0.00095 11.5 2.0 39 176-214 195-233 (457) 330 pfam09220 LA-virus_coat L-A vi 21.1 28 0.00071 12.6 0.1 67 297-364 201-282 (436) 331 PRK12808 flagellin; Provisiona 21.1 38 0.00096 11.5 6.9 62 386-488 55-125 (460) 332 KOG0306 consensus 21.1 38 0.00096 11.4 12.3 93 643-736 464-565 (888) 333 pfam08961 DUF1875 Domain of un 21.0 38 0.00096 11.4 5.5 40 449-488 123-163 (243) 334 cd04775 HTH_Cfa-like Helix-Tur 21.0 38 0.00096 11.4 5.7 45 447-491 56-101 (102) 335 PRK09109 motC flagellar motor 21.0 38 0.00097 11.4 1.2 26 276-301 73-98 (246) 336 COG4168 SapB ABC-type antimicr 21.0 38 0.00097 11.4 1.0 105 52-207 5-118 (321) 337 cd04642 CBS_pair_29 The CBS do 20.9 38 0.00097 11.4 1.0 25 91-115 10-34 (126) 338 COG1675 TFA1 Transcription ini 20.8 38 0.00097 11.4 1.9 14 205-218 27-40 (176) 339 COG0082 AroC Chorismate syntha 20.8 31 0.00079 12.2 0.2 64 325-390 6-70 (369) 340 TIGR01296 asd_B aspartate-semi 20.7 30 0.00075 12.4 0.1 58 840-900 240-314 (350) 341 pfam09417 consensus 20.7 38 0.00098 11.4 3.3 13 448-460 108-120 (121) 342 KOG0207 consensus 20.6 38 0.00098 11.4 3.1 26 379-404 233-258 (951) 343 TIGR00058 Hemerythrin hemeryth 20.6 37 0.00093 11.6 0.6 42 352-395 40-83 (116) 344 PRK06321 replicative DNA helic 20.6 39 0.00098 11.4 3.6 22 494-515 360-381 (472) 345 TIGR02976 phageshock_pspB phag 20.5 39 0.00098 11.4 3.0 25 471-495 45-69 (75) 346 pfam09942 DUF2174 Uncharacteri 20.5 31 0.00078 12.2 0.2 13 105-117 25-37 (83) 347 pfam02502 LacAB_rpiB Ribose/Ga 20.5 35 0.00089 11.8 0.4 40 338-379 99-138 (140) 348 PRK05469 peptidase T; Provisio 20.5 39 0.00098 11.4 4.6 59 153-211 94-161 (405) 349 TIGR01992 PTS-IIBC-Tre PTS sys 20.3 39 0.00099 11.3 2.6 51 193-244 15-74 (489) 350 PRK10703 DNA-binding transcrip 20.3 39 0.00099 11.3 2.6 46 37-83 17-67 (335) 351 COG5184 ATS1 Alpha-tubulin sup 20.3 39 0.00099 11.3 11.8 18 689-706 236-253 (476) 352 PRK00574 gltX glutamyl-tRNA sy 20.3 39 0.00099 11.3 4.4 17 53-69 56-72 (489) 353 PRK10334 mechanosensitive chan 20.3 25 0.00064 13.0 -0.3 35 172-209 95-129 (285) 354 KOG2230 consensus 20.2 39 0.001 11.3 0.8 39 189-231 161-201 (867) 355 PRK06223 malate dehydrogenase; 20.2 39 0.001 11.3 3.0 35 454-491 277-311 (312) 356 KOG1891 consensus 20.1 38 0.00097 11.4 0.6 25 497-521 233-257 (271) 357 PRK12584 flagellin A; Reviewed 20.1 39 0.001 11.3 6.7 62 386-488 57-127 (510) 358 PRK11706 TDP-4-oxo-6-deoxy-D-g 20.1 39 0.001 11.3 4.5 21 281-301 135-155 (375) 359 pfam08820 DUF1803 Domain of un 20.0 39 0.001 11.3 3.4 11 505-515 31-41 (94) 360 PRK09848 glucuronide transport 20.0 39 0.001 11.3 3.4 31 458-488 422-452 (457) No 1 >TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743 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 II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively. This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=100.00 E-value=0 Score=2802.17 Aligned_cols=854 Identities=51% Similarity=0.842 Sum_probs=810.7 Q ss_pred EEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHH Q ss_conf 66600999998767877799886313754000897367899999998789999981134042556643668870478999 Q gi|254780182|r 16 ITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYD 95 (910) Q Consensus 16 i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~ 95 (910) |.|++|++||++|||+|||||||||||||||||||||||||||||+++||+||+|||||||||||||||||||||+|||| T Consensus 1 i~pv~ie~E~k~SYLdYAMSVIVsRALPDvRDGLKPVHRRiLYaM~~~Gl~~d~~~kKsARIVGDV~GkYHPHGD~aiYD 80 (864) T TIGR01063 1 IVPVNIEEEMKRSYLDYAMSVIVSRALPDVRDGLKPVHRRILYAMYELGLTPDKPYKKSARIVGDVLGKYHPHGDSAIYD 80 (864) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEECCEEEEEECCCCCCCCCCHHHH T ss_conf 94565788999998644111322211541003688504577667766278998866002428741047824898734676 Q ss_pred HHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCH Q ss_conf 99971220111561314788708877697201357899978999999863076840533068988548503432273211 Q gi|254780182|r 96 ALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVL 175 (910) Q Consensus 96 a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL 175 (910) ||||||||||||||||||||||||||||||||||||||||+|+|++||+|||||||||+||||||++||+||||+||||| T Consensus 81 ~LVRMAQDFSlRYpLvDGQGNFGSiDGD~pAAMRYTEaRl~k~a~~ll~DIdKeTVdF~~NYDg~~~EP~VLPs~fPnLL 160 (864) T TIGR01063 81 ALVRMAQDFSLRYPLVDGQGNFGSIDGDPPAAMRYTEARLTKIAEELLRDIDKETVDFVPNYDGSEKEPTVLPSRFPNLL 160 (864) T ss_pred HHHHHCCCHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH T ss_conf 77650587100354416888647888882676521788888999999862043631654488886258820751241456 Q ss_pred HCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEE Q ss_conf 01676101013317898547899999988761877688888863458668874434475889999870120389999886 Q gi|254780182|r 176 VNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSH 255 (910) Q Consensus 176 ~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ 255 (910) ||||||||||||||||||||+||||||+++|+||+||++|||++||||||||||+|+|++||++||+||||||+||||+| T Consensus 161 vNGSsGIAVGMATNIPPHNL~Eiida~~~~i~Np~~~i~eLl~~i~GPDFPTgg~I~G~~GI~~AY~TGRG~i~~Rar~~ 240 (864) T TIGR01063 161 VNGSSGIAVGMATNIPPHNLGEIIDAILAYIDNPDISIEELLEVIKGPDFPTGGIILGRSGIREAYETGRGSIVIRARAE 240 (864) T ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCHHHHHCCCCCHHHHHHCCCCEEEEEEEEE T ss_conf 13247600022257887336899999999871899886799560771137105643050013777335881389999899 Q ss_pred EEECCC--CCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHC-CCCCEEEEEEECCCCCHHHHHHHHHHHCC Q ss_conf 543367--845999924644352899999999998716650144587303-74655799994798877899999997610 Q gi|254780182|r 256 IEKTSG--DREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDES-DRQGYRVVIELKRGASADVILNQLYRYTS 332 (910) Q Consensus 256 ie~~~~--~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeS-dr~giRivielKr~~~~~~vln~Lyk~T~ 332 (910) ||+.++ ||.+||||||||||||++|||||||||++|||+||||||||| ||+|||||||+|||+.|++|||+|||+|+ T Consensus 241 iE~~~~~~gR~~IIvTE~PYqVNKa~LiekIAeLv~ek~ieGIsdiRDESSDr~GiRiVIE~KRD~~a~VvLN~LYk~T~ 320 (864) T TIGR01063 241 IEEDSKKGGREAIIVTEIPYQVNKARLIEKIAELVREKKIEGISDIRDESSDREGIRIVIELKRDAVAEVVLNNLYKQTQ 320 (864) T ss_pred EEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHCCCC T ss_conf 98648899862488862888520268889999874000000321244256687743799997428983015421211264 Q ss_pred HHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH Q ss_conf 11000000245541663000299999999999999999999999999988877899999987406999999861899789 Q gi|254780182|r 333 LQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPET 412 (910) Q Consensus 333 Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~e 412 (910) ||++||+|||||++|.|++|+||++|.+|++||++||+|||.|+|+||++|+||||||++|++||||||+|||+|++++. T Consensus 321 lQ~~Fg~NmLALv~G~Pk~lnLk~~l~~f~~HR~~Vi~RRT~feLrKA~eRaHiL~GL~~AL~niDevI~lIr~S~~~~~ 400 (864) T TIGR01063 321 LQVSFGINMLALVDGLPKVLNLKELLEAFVEHRKDVITRRTIFELRKAEERAHILEGLLIALDNIDEVIALIRASQNTEE 400 (864) T ss_pred CCEECCEEEEEEECCCCCEECHHHHHHHHHHCCEEEEEEEHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHH T ss_conf 50014812321107897501788999999842313355210001022655789999999999721289999742789889 Q ss_pred HHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 87877631269788999997402211122234452369999999998789999888799999989999999998875304 Q gi|254780182|r 413 ARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILS 492 (910) Q Consensus 413 Ak~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~ 492 (910) ||..|+++.|....+..++... ........+.|.|||.||+|||||||||||+||.+||++||++|.++|++|++||+ T Consensus 401 Ak~~L~e~~W~l~di~~ll~~~--~~~~l~~~g~F~l~E~QA~AILdMrL~rLTgLE~~Kl~~E~~~L~~~I~~l~~iL~ 478 (864) T TIGR01063 401 AKTRLVERQWELLDILPLLKLV--LEVELGERGTFSLSEIQAQAILDMRLQRLTGLEREKLEEEYKELLELIADLEDILA 478 (864) T ss_pred HHHHHHCCCCCHHHHHHHHHHH--HHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 9988421686078999999887--67532888865448899999999887677888899999999999999999997503 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCCCEEECC-CCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 9899999999989999984056883310013-434530101456781899907970523310000023345652110001 Q gi|254780182|r 493 SRSRLLGIIKQELLSVKDELDTPRRTRIVEG-LLDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVM 571 (910) Q Consensus 493 s~~~l~~iI~~EL~eik~kygd~RRT~I~~~-~~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ 571 (910) |+.+++++|++||.+|+++|||||||+|+.+ ...++.||||.+|+||||||++|||||+|+++|++|+|||||++|+++ T Consensus 479 ~~~r~~~iireEL~~i~~~Fgd~RRT~I~~~~~~~~D~EDLI~~E~vVvt~s~~GYvKR~p~~~Y~~Q~RGGkG~~g~~~ 558 (864) T TIGR01063 479 SEERVLEIIREELEEIKEQFGDPRRTEIVAEESEDIDIEDLIARENVVVTLSHKGYVKRVPVSAYRSQKRGGKGVSGADL 558 (864) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCHHHHCCCCEEEEEECCCEEEECCHHHHHCCCCCCCCCCCCCC T ss_conf 77689999999999999973885321222024322450344147878999716864786030133257666646432531 Q ss_pred CC-CCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEE-CCCCCCEEEEEEECCCCCCCCCCEEE Q ss_conf 46-41010113323777399995489399982000432244456554124545-36556200256630125666871799 Q gi|254780182|r 572 RD-EDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILS-LNQGERITTIMPFPEDESSWNNLYVV 649 (910) Q Consensus 572 ke-~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~-l~~~E~I~ail~~~~~~~~~~~~~Lv 649 (910) ++ +||+.++|+|+|||+||||||+|||||+|||+||+++|++||.||.|||+ +.++|+|++++|+++|+....+.||| T Consensus 559 ~~G~D~i~~~lvasTHD~~Lfftn~G~vY~lK~Y~iP~~~R~akG~pIvNLL~G~~~dE~I~ai~~v~~f~d~~~~~yl~ 638 (864) T TIGR01063 559 KDGDDFIEQLLVASTHDYLLFFTNRGKVYRLKVYQIPEASRTAKGKPIVNLLEGLQKDERITAILSVKEFEDEAYDLYLF 638 (864) T ss_pred CCCCCEEEEEEEEECCCEEEEEECCCCEEEEEEEECCCCCCCCCCCHHHHHCCCCCCCCEEEEEECCCCCCCCCCCEEEE T ss_conf 23685056778830776078881888268645441787775678712888605787676688873566668552661799 Q ss_pred EEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCE-EEEEECCCEEEEEEHH--HCCCCCCCCCCCEEE Q ss_conf 9947991898423686204777227866158985788896189826-9999369859997587--623547866553576 Q gi|254780182|r 650 FATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQEND-ILLTTKLGQCVRFPIS--AIRVFAGRNSVGVRG 726 (910) Q Consensus 650 l~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~-Iil~T~~G~~lrF~~~--evr~~~GR~a~GVkg 726 (910) |+|++|.|||++|++|.++|++|++||+|+|||+|++|.+|.++++ |+|+|++|+++||+.+ +||+| ||+|+||+| T Consensus 639 ~aTk~G~vKk~~L~~F~~~rs~GiiAi~L~e~D~L~~v~~~~~~~~~v~l~s~~G~~~RF~~~~~~vR~m-gR~~~GV~G 717 (864) T TIGR01063 639 LATKNGVVKKTSLTEFSNIRSNGIIAIKLDEGDELISVRLVDGDDEKVMLGSKNGKAVRFPEEDEEVREM-GRATRGVRG 717 (864) T ss_pred EECCCCEEEEEECHHHHHHHHCCEEEEEEECCCEEEEEEEEECCCCEEEEEECCCCEEECCCCCCCHHCC-CCCCCCEEE T ss_conf 9726743887400144354527869999708968999999607886588651488479836885311002-455676013 Q ss_pred EECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC-EEEEEEC Q ss_conf 752899869998973366654200000122233333334555444444443332222232001110125686-7999975 Q gi|254780182|r 727 ISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQ-FILTVSE 805 (910) Q Consensus 727 IkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~-~IL~vTe 805 (910) |+|+.+|.|+++.++..-.+--+++ +..+...+...-.......++. +||+||+ T Consensus 718 i~L~~~~~v~~~~~~~~i~~~~~D~-------------------------~~~~L~~NlD~vv~~~~~~e~~~~lL~vt~ 772 (864) T TIGR01063 718 IKLKNEDSVISMTVLKGINSIKEDR-------------------------NLEELGVNLDFVVSLEVVSEESQKLLIVTE 772 (864) T ss_pred EEECCCCCCCHHHHHHHHHHHHHHH-------------------------HHHHCCCCEEEEEEEEEECCCCCEEEEEEE T ss_conf 5406777400013443212002222-------------------------465437424344777862499837899830 Q ss_pred CCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEE Q ss_conf 99345301788486675774148876067777686899997289964999945998999990105544515687388980 Q gi|254780182|r 806 KGFGKRTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFST 885 (910) Q Consensus 806 ~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L 885 (910) |||||||++++||.|+|||+||++++++++ +|.||++.+|.++|+||++|+.|++||+.+.+||++||+||||||++| T Consensus 773 nGyGKRt~~~~yr~~~RGg~Gv~~~~~~~r--~G~vVga~~V~~~d~lm~iT~~G~~iR~~~~~vs~~GR~t~GVrL~~l 850 (864) T TIGR01063 773 NGYGKRTSIEEYRLQSRGGKGVKSIKITDR--NGQVVGAIAVDDDDELMLITSSGKLIRTSVQDVSIQGRNTQGVRLIRL 850 (864) T ss_pred CCCCEECCHHHCCCCCCCCCEEEEEEEECC--CCCEEEEEEECCCCHHHHEECCCCEEEEEEEHHCCCCCCCCCEEEEEE T ss_conf 684200426257632656623788998646--896878987458740001010883799761032115653565589851 Q ss_pred CCCCEEEEEEEECC Q ss_conf 89987999998356 Q gi|254780182|r 886 AKDERVVSVERIRE 899 (910) Q Consensus 886 ~~~D~Vv~va~i~~ 899 (910) +++|+|++|+++++ T Consensus 851 ~e~d~vv~v~~~~~ 864 (864) T TIGR01063 851 DEDDKVVSVSLVAK 864 (864) T ss_pred CCCCCEEEEEECCC T ss_conf 78763564220279 No 2 >PRK05560 DNA gyrase subunit A; Validated Probab=100.00 E-value=0 Score=2463.11 Aligned_cols=814 Identities=55% Similarity=0.922 Sum_probs=798.2 Q ss_pred CCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCH Q ss_conf 43235666009999987678777998863137540008973678999999987899999811340425566436688704 Q gi|254780182|r 11 EEEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGN 90 (910) Q Consensus 11 ~~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd 90 (910) ...++|++++|++||++|||+||||||++||||||||||||||||||||||+|||+|++||+|||||||||||||||||| T Consensus 4 ~~~~~i~~~~~~~~~~~~yl~Ya~svi~~RAlPdvrDGlKPv~RRily~M~~l~l~~~~~~~K~ArivG~v~gkyHPHGd 83 (822) T PRK05560 4 ELADRIIPVNIEEEMKRSYLDYAMSVIVGRALPDVRDGLKPVHRRILYAMYELGLTPDKPYKKSARIVGDVMGKYHPHGD 83 (822) T ss_pred HHHCCEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCCCCCC T ss_conf 03344445348999998899888999985128864468850899999999872899999974420664100547789882 Q ss_pred HHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCC Q ss_conf 78999999712201115613147887088776972013578999789999998630768405330689885485034322 Q gi|254780182|r 91 AAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCAR 170 (910) Q Consensus 91 ~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~ 170 (910) +|||||||||||+|+||||||||||||||+||||||||||||||||++|++||+||+++||||+||||||++||+||||+ T Consensus 84 ~siY~alvrmaQ~~~~r~plidg~GNfGsidgd~~AAmRYTE~rl~~~~~~ll~di~~~tV~f~~NfD~s~~EP~vLPa~ 163 (822) T PRK05560 84 SAVYDALVRMAQDFSLRYPLVDGQGNFGSIDGDPAAAMRYTEARLAKIAHELLRDIDKETVDFVPNYDGSEQEPTVLPAR 163 (822) T ss_pred HHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 17999999970022304732715788889999800666678888799999998511306525504889876586525656 Q ss_pred CCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEE Q ss_conf 73211016761010133178985478999999887618776888888634586688744344758899998701203899 Q gi|254780182|r 171 YPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVI 250 (910) Q Consensus 171 ~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~i 250 (910) |||||||||+|||||||||||||||+||||||++||+||++++++||+|||||||||||+|+|.+||++||+||||||++ T Consensus 164 ~PnlLvNGs~GIAVGmATniPpHNL~Evi~a~~~~i~np~~t~~~L~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~i 243 (822) T PRK05560 164 FPNLLVNGSSGIAVGMATNIPPHNLGEVIDACLALIDNPDITIEELMEIIPGPDFPTGGIILGRSGIREAYRTGRGSIIM 243 (822) T ss_pred CCHHHCCCCCCCHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCEEEECCHHHHHHHHHCCCEEEE T ss_conf 64532057751002110588996889999999986359999999994669899799982897848799999837670999 Q ss_pred EEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHH Q ss_conf 99886543367845999924644352899999999998716650144587303746557999947988778999999976 Q gi|254780182|r 251 RGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRY 330 (910) Q Consensus 251 R~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~ 330 (910) ||||++|+.++||++||||||||||||++|||+||+||++|||+||+||||||||+||||||||||+++|++|||+|||| T Consensus 244 R~k~~iE~~~~~r~~IvItEIPY~vnk~~liekIa~lv~~kki~gI~dirDESdr~GiRIVIelKr~~~~~~vln~Lyk~ 323 (822) T PRK05560 244 RAKAEIEEIRKGREAIIVTEIPYQVNKARLIEKIAELVKEKKIEGISDIRDESDRDGMRIVIELKRDAVPEVVLNNLYKH 323 (822) T ss_pred EEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHH T ss_conf 88999998579953899996898577999999999998557544510300356877627999967989979999999860 Q ss_pred CCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH Q ss_conf 10110000002455416630002999999999999999999999999999888778999999874069999998618997 Q gi|254780182|r 331 TSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNP 410 (910) Q Consensus 331 T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~ 410 (910) |+||+||++||+||++|+|++|||+++|++|++||++||+||++|+|+||++|+||||||++|++|||+||+|||+|+|+ T Consensus 324 T~Lq~sf~~N~~al~~g~P~~l~Lk~~L~~fi~hR~~vi~rr~~~~L~ka~~RlhIleGl~~a~~~iDeVI~iIR~S~~~ 403 (822) T PRK05560 324 TQLQTSFGINMLALVDGQPKLLNLKQILEAFVDHRKEVITRRTRFELRKARERAHILEGLLIALDNIDEVIALIRASPTP 403 (822) T ss_pred CCHHHCCCCEEEEEECCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCH T ss_conf 84132036117998799877864999999999999999999999999999988999988999995879999999718987 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89878776312697889999974022111222344523699999999987899998887999999899999999988753 Q gi|254780182|r 411 ETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDI 490 (910) Q Consensus 411 ~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~I 490 (910) ++||.+||++ |+|||.||+|||+|||||||+||+++|++|+++|.++|++|++| T Consensus 404 ~~Ak~~L~~~--------------------------f~lse~QA~AIL~mrL~rLt~Le~~kl~~E~~eL~~~I~~l~~I 457 (822) T PRK05560 404 AEAREGLMER--------------------------YGLSEIQAQAILDMRLQRLTGLEREKIEDEYKELLAEIADLLDI 457 (822) T ss_pred HHHHHHHHHH--------------------------HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 8999989887--------------------------58899999999998999987678999999999999999999988 Q ss_pred HCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCC Q ss_conf 04989999999998999998405688331001343453010145678189990797052331000002334565211000 Q gi|254780182|r 491 LSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLLDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVV 570 (910) Q Consensus 491 L~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~ 570 (910) |+|+++++++|++||.+++++|||||||+|.++.++++.||+|++|+++|++|+.|||||+|+++|++|+|||||+++++ T Consensus 458 L~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~ei~~EDLI~~E~vvVtlS~~GYIKR~~~~~yr~Q~RGGkG~~g~~ 537 (822) T PRK05560 458 LASPERLMEIIREELEEIKEKFGDPRRTEIEAGEGDIDDEDLIANEDVVVTLTHGGYIKRVPLDEYRAQRRGGKGKSGAG 537 (822) T ss_pred HCCHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCHHHCCCCCCEEEEEECCCEEEEECHHHHHHHCCCCCCCCCCC T ss_conf 65999999999999999999829988604415656562544177764699994682688613266553126777743430 Q ss_pred CCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEE Q ss_conf 14641010113323777399995489399982000432244456554124545365562002566301256668717999 Q gi|254780182|r 571 MRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVF 650 (910) Q Consensus 571 ~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl 650 (910) +|++|++.++|.|+|||+||||||.|||||++||+||+++|+++|+||.||+++.++|+|++++++++++ ++.||+| T Consensus 538 ~ke~D~v~~~~~~~Thd~LLfFTn~Grvy~lkv~eIPe~sr~skG~~i~nll~l~~~EkI~ail~v~~~~---~~~~Lv~ 614 (822) T PRK05560 538 TKEDDFVEHLFVANTHDTLLFFTNRGRVYRLKVYELPEGSRTAKGRPIVNLLPLEPGEKITAILPVREFD---DDLYLFF 614 (822) T ss_pred CCCCCHHHHEEEECCCCEEEEEECCCCEEEEEEEECCCCCCCCCCCCHHHHCCCCCCCEEEEEEECCCCC---CCCEEEE T ss_conf 4556534432682478879999369949998916745668777884899716899997367877125678---8856999 Q ss_pred EECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECC Q ss_conf 94799189842368620477722786615898578889618982699993698599975876235478665535767528 Q gi|254780182|r 651 ATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLA 730 (910) Q Consensus 651 ~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~ 730 (910) +|++|+|||+++++|.+++++|++||+|++||+|++|.+++++++|+++|++|++|||++++||+| ||+|+||+||+|+ T Consensus 615 ~Tk~G~IKRt~L~df~~~r~~G~~AikLke~DeLv~v~l~~~~~dIil~T~~G~alRF~~~eVR~~-GR~a~GVkgIkL~ 693 (822) T PRK05560 615 ATKNGTVKKTALSEFSNIRSNGLIAINLDEGDELIGVRLTDGDDDVLLFSANGKAIRFPEEDVRPM-GRTARGVRGIKLR 693 (822) T ss_pred EECCCCEEEECHHHCCCCCCCCEEEEECCCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCC-CCCCCCCCCEECC T ss_conf 957972797136872255525519998589977999998489987999978973999506657777-8877684315519 Q ss_pred CCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEECCCCEE Q ss_conf 99869998973366654200000122233333334555444444443332222232001110125686799997599345 Q gi|254780182|r 731 KGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVSEKGFGK 810 (910) Q Consensus 731 ~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GK 810 (910) ++|+||||.++.+ +++||+||++|||| T Consensus 694 ~gD~VV~~~vv~~-----------------------------------------------------~~~iL~vTe~G~GK 720 (822) T PRK05560 694 EGDEVVSMSVLRD-----------------------------------------------------EQFVLTVTENGYGK 720 (822) T ss_pred CCCEEEEEEEECC-----------------------------------------------------CCEEEEEECCCEEE T ss_conf 9998999998579-----------------------------------------------------98799991898053 Q ss_pred EEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEECCCCE Q ss_conf 30178848667577414887606777768689999728996499994599899999010554451568738898089987 Q gi|254780182|r 811 RTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFSTAKDER 890 (910) Q Consensus 811 Rt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L~~~D~ 890 (910) ||++++||.|+|||+||++|+++++ +|.||+++.|+++||||++|++|++||+++++||++||+||||++|+|+++|+ T Consensus 721 Rt~~~eyr~~~RGgkGv~~ik~~~k--~G~lv~~~~V~~~deI~liT~~G~~iRi~v~~I~~~gR~t~GVrl~~L~~~d~ 798 (822) T PRK05560 721 RTPAEEYRLQGRGGKGVIAIKITER--NGKLVGAVPVDDDDEIMLITDAGKLIRTRVSEIRITGRNTQGVTLIRLDEGEK 798 (822) T ss_pred ECCHHHCCCCCCCCCCEEEEEECCC--CCCEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCEEEEECCCCCE T ss_conf 0528883755778777588996488--88489999917998699992798799987100475675788708998599998 Q ss_pred EEEEEEECCCCCCCCCCCC Q ss_conf 9999983566555665557 Q gi|254780182|r 891 VVSVERIRESEIVDEAEST 909 (910) Q Consensus 891 Vv~va~i~~~e~~de~e~~ 909 (910) |++|++|++++++++.+.+ T Consensus 799 v~~va~v~~~~~~~~e~~~ 817 (822) T PRK05560 799 VVSVARVAEEEEEEEEEGE 817 (822) T ss_pred EEEEEEECCCCCCCCCCCC T ss_conf 9999980787665445544 No 3 >PRK13979 DNA topoisomerase IV subunit A; Provisional,Validated Probab=100.00 E-value=0 Score=2378.21 Aligned_cols=855 Identities=36% Similarity=0.551 Sum_probs=779.8 Q ss_pred CCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCC Q ss_conf 76432356660099999876787779988631375400089736789999999878999998113404255664366887 Q gi|254780182|r 9 DEEEEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPH 88 (910) Q Consensus 9 ~~~~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPH 88 (910) +=|.+++|++++|++||++|||+||||||++||||||||||||||||||||||+||++|++||+|||||||||||||||| T Consensus 7 ~~p~~~~i~~~~i~~em~~syl~YamsVI~~RAlPDvRDGLKPVhRRiLy~M~~lg~~~~~~~~KsArivGdv~GkyHPH 86 (959) T PRK13979 7 VIPKDNNIIKFPLEEAMPENYLPYAVEVAKDRALPDVRDGLKPVHRRILYGAYMLKAFPDKPYYKSARIVGDILGKYHPH 86 (959) T ss_pred CCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCCCCC T ss_conf 78986875561489999988998889987750077644688518999999998738999999841235511026477898 Q ss_pred CHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECC Q ss_conf 04789999997122011156131478870887769720135789997899999986307684053306898854850343 Q gi|254780182|r 89 GNAAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLC 168 (910) Q Consensus 89 Gd~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP 168 (910) ||+|||||||||||+||||||||||||||||+||||||||||||||||++|++||.|||++||||+||||||++||+||| T Consensus 87 GD~avYdalVrmaQ~fs~r~pLidgqGNfGSidgD~~AAmRYTEarl~~~a~~ll~di~k~tVdf~~NyD~s~~EP~VLP 166 (959) T PRK13979 87 GDSSVYDAMVILAQNFTTRMPLIDGHGNWGSIDGDSAAAMRYTEARLTPIAMEMLRDIDKDVVDMVDNYSDSEKEPKVLP 166 (959) T ss_pred CCHHHHHHHHHHHCCHHHCCCCEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC T ss_conf 70479999999700013127606067867899998103430688888999999983304277476148898876865135 Q ss_pred CCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEE Q ss_conf 22732110167610101331789854789999998876187768888886345866887443447588999987012038 Q gi|254780182|r 169 ARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSI 248 (910) Q Consensus 169 ~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i 248 (910) |+|||||||||+|||||||||||||||+||||||++||+||++++++||+|||||||||||+|+|.+||++||+||||+| T Consensus 167 a~~PnLLvNGs~GIAVGMATnIPpHNL~Evida~~a~i~np~~t~~eLm~~i~GPDFPTGGiI~g~~gi~~aY~TGrG~i 246 (959) T PRK13979 167 ARYPNLLVNGAFGIAVGLATNIPPHNLKEVIDGTLAYIDNNEITTKELMNYIKGPDLPTGGILIGKKSLLSAYETGEGKV 246 (959) T ss_pred CCCCHHHHCCCCCCHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCEEECCHHHHHHHHHCCCEE T ss_conf 77743221377401141225879978899999999997089988999982187998899848988787999998489839 Q ss_pred EEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCC----CCHHHHHHHHCCCCCEEEEEEECCCCCHH--- Q ss_conf 99998865433678459999246443528999999999987166----50144587303746557999947988778--- Q gi|254780182|r 249 VIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKR----IVDIADLRDESDRQGYRVVIELKRGASAD--- 321 (910) Q Consensus 249 ~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~k----i~gI~dirDeSdr~giRivielKr~~~~~--- 321 (910) ++||||++|+.++||++||||||||||||++|+|+||+||++|| |+||+|+||||||+||||||||||+++|+ T Consensus 247 ~iRak~~iE~~~~gr~~IiItEiPY~vnka~lie~Iaelv~~kk~~k~i~gIsdiRDESDr~GiRIVIelKr~a~~~v~e 326 (959) T PRK13979 247 TLRAKTTIEKLENGRLGIVITEFPYRRNKAKLLQTISEMTADKKHSKALENISDIRDESDRNGIRAVIEFKKSADEDVAE 326 (959) T ss_pred EEEEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHH T ss_conf 99988899961788448999966875778999999999997131336688600420136778638999976889757699 Q ss_pred HHHHHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999997610110000002455416630002999999999999999999999999999888778999999874069999 Q gi|254780182|r 322 VILNQLYRYTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVV 401 (910) Q Consensus 322 ~vln~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI 401 (910) +|||+|||||+||+||++||+||++|+|++|||+++|++|++||++||+|||+|+|+||++|+||||||++|++|||+|| T Consensus 327 ~vLn~Lyk~T~LQ~sf~vNmlaL~~g~P~~l~Lk~iL~~fl~hR~eVI~RRt~~~L~ka~~R~HILeGL~iAl~nIDevI 406 (959) T PRK13979 327 KVLKYLYKKTDLQCNISFNMVALADGKPETMGLKAIIKHYVEHQKEVVTRRTKKELEIAEKRFHIVEGFIKAIGIMDEII 406 (959) T ss_pred HHHHHHHHHCCCCEEEEEEEEEECCCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH T ss_conf 99999997498836774589973399134977899999999999999999999999889989999998999997899999 Q ss_pred HHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99861899789878776312697889999974022111222344523699999999987899998887999999899999 Q gi|254780182|r 402 RIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLG 481 (910) Q Consensus 402 ~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~ 481 (910) +|||+|+++++||.+||++ |+|||.||+|||+|||||||+||++||++|+++|. T Consensus 407 ~iIR~S~~~~~Ak~~L~~~--------------------------f~lse~QA~AILdmrL~rLT~LE~~ki~~E~~eL~ 460 (959) T PRK13979 407 KTIRASKSKKDASENLIEK--------------------------FGFTDEQAEAILELMLYRLTGLEIKVFEKEYKELE 460 (959) T ss_pred HHHHCCCCHHHHHHHHHHH--------------------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9998189837999989876--------------------------19999999999998999987889999999999999 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCC--CCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCC Q ss_conf 9999887530498999999999899999840568833100134--34530101456781899907970523310000023 Q gi|254780182|r 482 IEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGL--LDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQ 559 (910) Q Consensus 482 ~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~--~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q 559 (910) ++|++|++||+|+++++++|++||.+++++|||||||+|+++. .+++.||||++|+++||+|+.|||||+|+++| T Consensus 461 ~~I~~l~~IL~s~~~l~~iIk~EL~eik~kygd~RRT~Ii~~~~~~~~~~EDLI~~EdvVVtlS~~GYIKR~pl~~Y--- 537 (959) T PRK13979 461 KLIKKLEKILSSEKELLKVIKKELKEVKEKYGDERRTSIIEDDEKAKIDIEELIVVEDVVITLSNEGFIKRIPLKSY--- 537 (959) T ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHCCCCCEEEEEECCCEEEECCHHHH--- T ss_conf 99999999967999999999999999999839987426665632033657673456655999806964750458881--- Q ss_pred CCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEEC--CCCCCEEEEEEEC Q ss_conf 34565211000146410101133237773999954893999820004322444565541245453--6556200256630 Q gi|254780182|r 560 RRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSL--NQGERITTIMPFP 637 (910) Q Consensus 560 ~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l--~~~E~I~ail~~~ 637 (910) +|||+|..|+.++|+|++.++|.|+|||+||||||.|+|||+++|+||+++|++||+||.|++++ .++|+|+++++++ T Consensus 538 ~RgGkG~~g~~~ke~D~v~~l~~a~THd~lLfFTn~GkvY~lKvyeIPe~sr~aKG~~i~Nll~~l~l~~E~I~~il~v~ 617 (959) T PRK13979 538 NRSNSNVEDIEYREGDFNKFLIQSNTKDTLLIFTDKGNMYQIKGINIPEFKWKEKGERLDEIIKTIDLEEEKIIEAYSIE 617 (959) T ss_pred CCCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEECCCEEEEEEEEECCCCCCCCCCCCHHHHCCCCCCCCCEEEEEEECC T ss_conf 36789977875556651026899528963999957985999870566777700389573441055788984589977412 Q ss_pred CCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCE---EEEEECCCEEEEEEHHHCC Q ss_conf 1256668717999947991898423686204777227866158985788896189826---9999369859997587623 Q gi|254780182|r 638 EDESSWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQEND---ILLTTKLGQCVRFPISAIR 714 (910) Q Consensus 638 ~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~---Iil~T~~G~~lrF~~~evr 714 (910) +|. ++.||+|+|++|+||||++++| +.+++|++||+|++||+|++|.+++++++ |++.|++|+++||+++++| T Consensus 618 ~f~---~~~~lvfaTk~G~VKKt~L~~f-~~~~sgiiAIkL~egDeLI~V~l~~~~~~~~~i~l~T~~G~~irf~e~~vR 693 (959) T PRK13979 618 DFT---PQKDFIFITDSGGIKKTSLDKF-NTNYSKLMALKLKKGEELIKVKLVDRTREEKFLKIKTKKGLSFTVEEPELE 693 (959) T ss_pred CCC---CCCEEEEEECCCEEECCCHHHC-CCCCCCCEEEECCCCCEEEEEEEECCCCCCEEEEEECCCCEEEECCCHHCC T ss_conf 267---7754999928986883738982-855678366666999879878973588875079996589659971420224 Q ss_pred CCCCCCCCCEEEEECCCCCEEEEEEEECCCCCCCCCC-------CCCCC--C---------CCC---CCCCCCCCCCCCC Q ss_conf 5478665535767528998699989733666542000-------00122--2---------333---3333455544444 Q gi|254780182|r 715 VFAGRNSVGVRGISLAKGDQVISMAIVLHADADYDER-------ICYMK--H---------MSA---QRRLISGDTEEIT 773 (910) Q Consensus 715 ~~~GR~a~GVkgIkL~~~D~Vv~~~vi~~~~~~~~~~-------~~~~~--~---------~~~---~~~~~~~~~~~~~ 773 (910) +| ||+|+||+||+|+++|+||+|.++.+.+...... ..... . .+. ......+.+...+ T Consensus 694 ~m-GR~a~GVrgi~L~~~D~Vvsm~i~~~~e~~~~~~~i~~~g~i~~~~~~~~~~~~~~~~~~~~~ili~~~~G~~~~~~ 772 (959) T PRK13979 694 PV-DRNILGYQLFNLSPNDSIKKVDFCDNYEYKEFYININKKGIIKISDLKKNKSHISLKTNSSKNLLLFSDKGKVYKIP 772 (959) T ss_pred CC-CCCCCCEEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEECCCCCEEECC T ss_conf 57-87666752143399998986102244420000023342002332210011111111356631135432577233032 Q ss_pred -----CCCCC----------CCCCCCCCCHHHHCCCCCCCEEEEEECCCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCC Q ss_conf -----44433----------322222320011101256867999975993453017884866757741488760677776 Q gi|254780182|r 774 -----SLKND----------SSVEGNISEERCQELKLKEQFILTVSEKGFGKRTSSYDFRISNRSGKGIRATDVSKINEI 838 (910) Q Consensus 774 -----~~~~~----------~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~ 838 (910) ...+. .................++.++|++|++||||||+++|||.++|||+|++.. +++ T Consensus 773 ~~~~~~~~~~g~~i~~~~~~~~~~e~vi~~~~~~~~~e~~~il~vTe~G~GKRT~~~eyr~~g~~~~~~k~~-----~~~ 847 (959) T PRK13979 773 AFMLQNIEESGINISALTGDFEKKESIINAISIFEFEEDLSIYFFSKKGLVKKTLLSEFKGEGNSTQVYKFK-----HKE 847 (959) T ss_pred HHHCCCCCCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEEEE-----ECC T ss_conf 432023355564502222121022302466520357776159999358974666567733467864899988-----448 Q ss_pred CCEEEE-EECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEECCCCEEEEEEEECCCCC Q ss_conf 868999-9728996499994599899999010554451568738898089987999998356655 Q gi|254780182|r 839 GALVAV-FPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFSTAKDERVVSVERIRESEI 902 (910) Q Consensus 839 g~lv~~-~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L~~~D~Vv~va~i~~~e~ 902 (910) |.+|++ +.++++|+||++|++|++||+++++|+++||+||||++++|+++|+|++++++.+++. T Consensus 848 ~~~v~~~~~~~~~d~imliT~~G~~IR~~v~~I~~~GR~tqGV~li~L~~~dkVV~~~~i~~~~~ 912 (959) T PRK13979 848 DELVSVDINEHEQKNILIITKKGMAIRFKSEAVNPMGKIASGVTGISLKDEDKVIFGSIIDENDT 912 (959) T ss_pred CCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCEEEEECCCCCEEEEEEEECCCCC T ss_conf 97899997048996389990798799987243470260368806897389987999999747777 No 4 >PRK05561 DNA topoisomerase IV subunit A; Validated Probab=100.00 E-value=0 Score=2157.71 Aligned_cols=734 Identities=41% Similarity=0.654 Sum_probs=698.8 Q ss_pred CCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCC Q ss_conf 87643235666009999987678777998863137540008973678999999987899999811340425566436688 Q gi|254780182|r 8 SDEEEEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHP 87 (910) Q Consensus 8 ~~~~~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHP 87 (910) .-++..++|++++|++||++|||+||||||++||||||||||||||||||||||+||++|++||+||||||||||||||| T Consensus 3 ~~~~~~e~i~~~~~~~~~~~~yl~Ya~svi~~RalPd~rDGlKPv~RRily~m~~~~l~~~~~~~KsarivG~v~GkyHP 82 (745) T PRK05561 3 MPDPMSEGIEDLPLEEFLEERYLRYSMYVIMDRALPDVRDGLKPVQRRILYAMSELGLTPDAKFKKSARTVGDVLGKYHP 82 (745) T ss_pred CCCCHHCCCEEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEEHHHCCCCCC T ss_conf 99832058157238999998899989999985127764458860999999999972899999973631664100557789 Q ss_pred CCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEEC Q ss_conf 70478999999712201115613147887088776972013578999789999998630768405330689885485034 Q gi|254780182|r 88 HGNAAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVL 167 (910) Q Consensus 88 HGd~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vl 167 (910) |||+|||||||||||+|+||||||||||||||+||||||||||||||||++|++||+|||++||||+||||||++||+|| T Consensus 83 HGD~siY~a~vrmaQ~f~~r~plidg~GNfGsidgd~~AAmRYTE~rls~~~~~~l~di~~~tv~f~~n~D~~~~EP~vL 162 (745) T PRK05561 83 HGDSAIYDAMVRMAQDFSYRYPLVDGQGNFGSIDGDPAAAMRYTEARLSKIAELLLEEIDEGTVDFVPNFDGTLEEPTVL 162 (745) T ss_pred CCHHHHHHHHHHHCCHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEE T ss_conf 87047999999973301315751427887789999843767889887699999999630647513205879997675543 Q ss_pred CCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCC-CCCHHHHHHHHHHCCC Q ss_conf 322732110167610101331789854789999998876187768888886345866887443-4475889999870120 Q gi|254780182|r 168 CARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAV-ILGRTGIKNAYATGRG 246 (910) Q Consensus 168 P~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~-I~~~~~i~~~y~tGrG 246 (910) ||+|||||||||+|||||||||||||||+||||||++||+||++++++||+|||||||||||+ |.|++||++||+|||| T Consensus 163 Pa~~PnlL~NG~~GIAvGmaTnIPpHNl~Ev~~a~i~~i~np~~t~~eL~~~i~GPDFPTGg~Ii~g~~~i~~ay~tGrG 242 (745) T PRK05561 163 PARFPNLLLNGATGIAVGMATDIPPHNLREVIDAAIHLIDNPDATLEELMEFVPGPDFPTGGEIITGRDGIRKAYETGRG 242 (745) T ss_pred CCCCCHHHCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCEEEECHHHHHHHHHHCCC T ss_conf 04687411048862487664487997669999999987449999999998318899799883897288999999984767 Q ss_pred EEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCC-EEEEEEECCC-CCHHHHH Q ss_conf 3899998865433678459999246443528999999999987166501445873037465-5799994798-8778999 Q gi|254780182|r 247 SIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQG-YRVVIELKRG-ASADVIL 324 (910) Q Consensus 247 ~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~g-iRivielKr~-~~~~~vl 324 (910) ||+|||||++|+.++|+++||||||||||||++|||+||+||++|||+||+||||||||+| +|||||||++ +||++|| T Consensus 243 ~i~iRak~~iE~~~~g~~~IvItEIPY~vnk~~liekIa~lv~~kki~gI~dvrDESdr~g~iRIVIelK~~~~d~~~vl 322 (745) T PRK05561 243 SIRVRARWEIEDLARGQWQIVITELPYQVSKAKLIEQIAEQMQAKKLPGIADVRDESDRENPVRIVIEPKSNRVDPEALM 322 (745) T ss_pred EEEEEEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCCEEEEEEECCCCCCHHHHH T ss_conf 09998899999637984179999678768489999999999970866410241036678787799999788887999999 Q ss_pred HHHHHHCCHHCCCCCEEEEEE-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999976101100000024554-1663000299999999999999999999999999988877899999987406999999 Q gi|254780182|r 325 NQLYRYTSLQSLFSVNMVALN-GYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRI 403 (910) Q Consensus 325 n~Lyk~T~Lq~sf~~N~~aL~-~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~i 403 (910) |+|||||+||+||++||+||+ ||+|++|||+++|++|++||++||+||++|+|+||++|+||||||++|++|||+||+| T Consensus 323 n~Lyk~T~Lq~sf~~N~~al~~dg~P~~l~Lk~iL~~~l~hR~~vi~rrt~~~L~Ka~~RlhIleGLliA~~~iD~VI~i 402 (745) T PRK05561 323 NHLFATTDLESSYRVNMNVIGLDGRPRVKGLKEILSEWLDHRREVVTRRSQFRLDKVEKRLHILEGLLIAFLNIDEVIEI 402 (745) T ss_pred HHHHHHCCCHHHCCCEEEEEECCCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHH T ss_conf 99998576242137148999379975582799999999999999999999999999999999998899999676899999 Q ss_pred HHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 86189978987877631269788999997402211122234452369999999998789999888799999989999999 Q gi|254780182|r 404 IRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIE 483 (910) Q Consensus 404 IR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~ 483 (910) ||+|+ +||.+||++ |+|||.||+|||+|||||||+||+++|++|+++|.++ T Consensus 403 IR~S~---dak~~L~~~--------------------------f~lse~QA~AIL~mrL~rLt~LE~~kl~~E~~eL~~~ 453 (745) T PRK05561 403 IRESD---EPKANLMAR--------------------------FGLTEIQAEAILELRLRRLAKLEEIEIRKEQDELRKE 453 (745) T ss_pred HHCCC---HHHHHHHHH--------------------------HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 97063---266777555--------------------------0879999999999999998766799999999999999 Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCC--CCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCC Q ss_conf 998875304989999999998999998405688331001343--453010145678189990797052331000002334 Q gi|254780182|r 484 IKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLL--DMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRR 561 (910) Q Consensus 484 I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~--~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~R 561 (910) |++|++||+|+++++++|++||.+++++|||||||+|.++.. +++.||+|++|+|+|++|+.|||||++...+. T Consensus 454 I~~l~~IL~s~~~~~~iI~~EL~eik~kfgd~RRT~I~~~~~~~~i~~edlI~~E~v~V~lS~~GyIKr~k~~~~~---- 529 (745) T PRK05561 454 IAELEAILASERKLWKLIKKELKADAKKFGDPRRTPIEEREEAKAIDEEALVPDEPVTVVLSKKGWVRRAKGHDID---- 529 (745) T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHCCCCCCEEEECCCEEEEEECCCCCC---- T ss_conf 9999999638999999999999999986389986302267420237877717676618998178049984488867---- Q ss_pred CCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCC Q ss_conf 56521100014641010113323777399995489399982000432244456554124545365562002566301256 Q gi|254780182|r 562 GGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQGERITTIMPFPEDES 641 (910) Q Consensus 562 ggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~ 641 (910) .+++++|++|++.++++|+|||+||||||.||+||+++|+|| +++++|+||.|+++++++|+|++++++++ T Consensus 530 ----~~~~~~Ke~D~v~~~~~~~T~d~LLfFTn~Grvy~lkv~~IP--~~r~~G~pi~nll~L~~~EkIv~vl~~~~--- 600 (745) T PRK05561 530 ----PAGLGYKEGDSLLFAFEARTTDKLLFFTSTGRVYSLPVHELP--SARGQGEPLTGLIDLEPGEEIVHVLVGDP--- 600 (745) T ss_pred ----CCCCCCCCCCCEEEEEEEECCCEEEEEECCCEEEEEEHHHCC--CCCCCCCCHHHCCCCCCCCEEEEEEEECC--- T ss_conf ----544567778532589998069769999579759998922087--86678808988068999996999998589--- Q ss_pred CCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCC-CCEEEEEECCCEEEEEEHHHCCCCCCCC Q ss_conf 668717999947991898423686204777227866158985788896189-8269999369859997587623547866 Q gi|254780182|r 642 SWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQ-ENDILLTTKLGQCVRFPISAIRVFAGRN 720 (910) Q Consensus 642 ~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~-~~~Iil~T~~G~~lrF~~~evr~~~GR~ 720 (910) +.+|+|+|++|++||+++++|.+.+++|++||+|++||++++|..+++ +++|+++|++|+++||+++++|+| || T Consensus 601 ---~~~lllaTk~G~~kr~~l~e~~~~~k~G~~ai~L~~gDelv~~~~i~~~~d~I~lvT~~Gk~lrF~~~evr~~-gR- 675 (745) T PRK05561 601 ---DQKLLLASSAGYGFVVSEEDLVGRNRAGKAVINLKDGDKVLAPVPVEGDEDSLAAITQRGRLLVFPLSELPEL-SR- 675 (745) T ss_pred ---CCEEEEEECCCEEEEEEHHHHCCCCCCCEEEEEECCCCEEEEEEEECCCCCEEEEEECCCCEEEEEHHHCCCC-CC- T ss_conf ---8769999789329997869800446267188861899889888994699988999958982899798887775-75- Q ss_pred CCCEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEE Q ss_conf 55357675289986999897336665420000012223333333455544444444333222223200111012568679 Q gi|254780182|r 721 SVGVRGISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFI 800 (910) Q Consensus 721 a~GVkgIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~I 800 (910) ++||+||+|+++|.|+++.+++..+. -.+ T Consensus 676 gkGVkgikLk~~D~Vv~~~vv~~~~~---------------------------------------------------l~v 704 (745) T PRK05561 676 GKGVKLIELKKEEGLADLAVLPPGDG---------------------------------------------------LTL 704 (745) T ss_pred CCCCCEEEECCCCEEEEEEEECCCCC---------------------------------------------------EEE T ss_conf 46801476689998999999858883---------------------------------------------------499 Q ss_pred EEEECCCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCCCCEE Q ss_conf 999759934530178848667577414887606777768689 Q gi|254780182|r 801 LTVSEKGFGKRTSSYDFRISNRSGKGIRATDVSKINEIGALV 842 (910) Q Consensus 801 L~vTe~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv 842 (910) ++.+++|+||+|++++|+. +|||+|++..+..++ +|++. T Consensus 705 ~s~~~~g~~k~t~l~~y~~-~Rgg~G~~~~k~~~k--~gk~~ 743 (745) T PRK05561 705 HAGKRKLTLKPKDLEEYRG-KRARRGSLLPRGLQR--VDRLS 743 (745) T ss_pred EECCCCCCCCCCCHHHHCC-CCCCCCCCCCCCCCC--CCCCC T ss_conf 9867876345551677462-247788678888887--89717 No 5 >COG0188 GyrA Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair] Probab=100.00 E-value=0 Score=2119.48 Aligned_cols=794 Identities=55% Similarity=0.893 Sum_probs=775.5 Q ss_pred EEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHH Q ss_conf 66600999998767877799886313754000897367899999998789999981134042556643668870478999 Q gi|254780182|r 16 ITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYD 95 (910) Q Consensus 16 i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~ 95 (910) |.+++|+++|++|||+||||||++||||||||||||||||||||||++|++||+||+||||+|||||||||||||+|||| T Consensus 8 i~~v~i~~e~~~syl~YAmsVIv~RALPdVRDGLKPVqRRILYaM~e~gl~~d~~~kKsAriVGdvmGkyHPHGDssiYd 87 (804) T COG0188 8 IEPIDIEDEMKRSYLDYAMSVIVGRALPDVRDGLKPVQRRILYAMFELGLTPDKKYKKSARIVGDVMGKYHPHGDSSIYD 87 (804) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHH T ss_conf 51265999999999988799886401775234786089998899997499989970003066775335678887168999 Q ss_pred HHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCH Q ss_conf 99971220111561314788708877697201357899978999999863076840533068988548503432273211 Q gi|254780182|r 96 ALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVL 175 (910) Q Consensus 96 a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL 175 (910) ||||||||||||||||||||||||+||||||||||||||||++|++||.||+++||||+|||||+++||+||||+||||| T Consensus 88 alVRMAQdfs~RypLVdgqGNFGSiDgD~aAAMRYTEaRLs~ia~elL~di~kdtVdf~~NyDg~~~EP~VLPa~~PnLL 167 (804) T COG0188 88 ALVRMAQDFSLRYPLVDGQGNFGSIDGDPAAAMRYTEARLSKIAEELLEDIDKDTVDFVPNYDGSEKEPEVLPARFPNLL 167 (804) T ss_pred HHHHHHHHHHHCCCCEECCCCCCCCCCCHHHHHHHHHHHCHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCCCCCCCEEE T ss_conf 99997104341576231687788999973787778886231989998744465705144079998558740346687067 Q ss_pred HCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEE Q ss_conf 01676101013317898547899999988761877688888863458668874434475889999870120389999886 Q gi|254780182|r 176 VNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSH 255 (910) Q Consensus 176 ~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ 255 (910) +|||+|||||||||||||||+||||||+++|+||++++++||++||||||||||+|+|.+||++||+||||+|++||+|+ T Consensus 168 vNGssGIAVGmATnIPPHNl~Ev~da~~~li~np~~~~~~lm~~i~GPDFPTgg~I~g~~~I~~aY~tGrG~i~vRa~~~ 247 (804) T COG0188 168 VNGSSGIAVGMATNIPPHNLGEVIDALIALIDNPDATIDELMEIIKGPDFPTGGIIIGRSGIREAYETGRGSIRVRAKAE 247 (804) T ss_pred ECCCCCEECCEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCEEECCHHHHHHHCCCCCEEEEEEEEE T ss_conf 60687410123057799898999999999970999746777310699989986668541456787700784599998999 Q ss_pred EEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHC Q ss_conf 54336784599992464435289999999999871665014458730374655799994798877899999997610110 Q gi|254780182|r 256 IEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQS 335 (910) Q Consensus 256 ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~ 335 (910) +|+.++||++||||||||||||++|||+||+++++||+.||+++||||||+|+|||||+||++.+++|||+|||+|+||+ T Consensus 248 iE~~~~gr~~IvItEiPyqvnka~lie~Iaelv~~kki~gis~vrDEsdr~giRivIelk~~~~~~~vln~Lfk~T~LQ~ 327 (804) T COG0188 248 IEDTKNGREQIVITEIPYQVNKAKLIEKIAELVKEKKIEGISDIRDESDREGIRIVIELKRDAVAEVVLNNLFKLTDLQT 327 (804) T ss_pred EEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHCHHHH T ss_conf 99537883389999669701589999999999854873573000010268870799997776417899999987441877 Q ss_pred CCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH Q ss_conf 00000245541663000299999999999999999999999999988877899999987406999999861899789878 Q gi|254780182|r 336 LFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARR 415 (910) Q Consensus 336 sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~ 415 (910) +|++||+||++|+|++|+|++||++|++||++|++||++|+|+||++|+||||||++|++|||+||+|||+|+++.+||. T Consensus 328 ~f~~nm~ai~~~~P~~~~L~~iL~~~~~hr~~vi~rR~~~~L~Ka~~R~hileGl~~a~~~iDevI~iIr~s~~~~~a~~ 407 (804) T COG0188 328 SFNVNMLALVNGRPKVLNLKEILSEFLEHRLEVVTRRTEYELNKAEERLHILEGLLIALLNIDEVIEIIRESKDKPEAKE 407 (804) T ss_pred HHCCEEEEECCCCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHH T ss_conf 50710687317803153799999999999999988999999999999998998899999714788988870898167899 Q ss_pred HHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH Q ss_conf 77631269788999997402211122234452369999999998789999888799999989999999998875304989 Q gi|254780182|r 416 ELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRS 495 (910) Q Consensus 416 ~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~ 495 (910) .||++ |.||+.||+|||+|||||||+||++++++|+++|.++|++|++||+|++ T Consensus 408 ~L~~~--------------------------f~lse~Qa~aIl~mrL~rLt~le~~~i~~E~~~L~~~i~~l~~iL~s~~ 461 (804) T COG0188 408 ELMAR--------------------------FGLSEKQAEAILDLRLRRLTGLEEEKIEKELKELEKEIADLEKILASEE 461 (804) T ss_pred HHHHH--------------------------CCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCHH T ss_conf 99987--------------------------3896788999986267776404087888899999999999998753889 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCEEECCCC-CCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 999999998999998405688331001343-4530101456781899907970523310000023345652110001464 Q gi|254780182|r 496 RLLGIIKQELLSVKDELDTPRRTRIVEGLL-DMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDE 574 (910) Q Consensus 496 ~l~~iI~~EL~eik~kygd~RRT~I~~~~~-~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~ 574 (910) ++++++++||.+++++||++|||+|..... +++.||+|++|+++|++|+.||+||++++.|++|+ +.++.+|++ T Consensus 462 ~~~~~i~~eL~~~~~k~gd~Rrt~i~~~~~~~~~~edli~~e~vvv~ls~~gyikr~~~~~~~~q~-----~~~~~~ke~ 536 (804) T COG0188 462 RLLDIIKKELLEIKKKFGDERRTEIVEEEEDEIEDEDLIAEEDVVVTLSHKGYIKRVPLKGYEAQR-----VSGLGLKEG 536 (804) T ss_pred HHHHHHHHHHHHHHHHHCCCCEEHHCCCCCCCCCHHHHCCCCCEEEEECCCCEEEECCHHHHHHHH-----HHHCCCCCC T ss_conf 999999999999998718532000115653223213313355449998165327863456643302-----211132434 Q ss_pred CHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECC Q ss_conf 10101133237773999954893999820004322444565541245453655620025663012566687179999479 Q gi|254780182|r 575 DFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKH 654 (910) Q Consensus 575 D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~ 654 (910) |++...++|+|||++|||||.|++|++++|++|+++|+++|+|+.|+++++++|+|+++++++ ++.|++|+|++ T Consensus 537 d~~~~~~~~~t~d~ll~ft~~G~~y~~~~~~lp~~~~~~~G~~i~~ll~~~~~E~i~~v~~~~------~~~~l~~~T~~ 610 (804) T COG0188 537 DFLERLFEANTHDTLLFFTSKGRVYKLKVYELPEGSRRSRGEPIVNLLSLEKGEKITAVLPVN------DDQYLFLATKK 610 (804) T ss_pred CHHHHEEEECCCCEEEEECCCCCEEEECCEECCCCCCCCCCHHHHHHCCCCCCCEEEEEEECC------CCEEEEEEECC T ss_conf 033430550466469998278848973130335556666781035424578885479999707------86059999169 Q ss_pred CCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECC-CCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCC Q ss_conf 9189842368620477722786615898578889618-982699993698599975876235478665535767528998 Q gi|254780182|r 655 GNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCT-QENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGD 733 (910) Q Consensus 655 G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~-~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D 733 (910) |++||+++++|.+.+++|+++|+|+++|+++++..+. ++++++++|++|+++||+.+++|+| ||+|+||+||+|+++| T Consensus 611 G~vK~~~l~~f~~~~~~g~~ai~L~~~d~l~~~~~~~~~~~~i~~~t~~G~~~~F~~~~v~~~-gr~a~Gv~~i~l~~~d 689 (804) T COG0188 611 GYVKKTSLSEFKNIRSKGKIAIKLKEGDELVSVSLTSDGDDDILLVTSNGKALRFPESEVREM-GRGAKGVKGIKLKEGD 689 (804) T ss_pred CCEEEEEHHHHHCCCCCCEEEEECCCCCCEEEEEECCCCCCEEEEEECCCEEEEEEHHHCCCC-CCCCCCCCEEECCCCC T ss_conf 947982035531235677068971777630124521578760899914873787403442211-5413686406437657 Q ss_pred EEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEECCCCEEEEE Q ss_conf 69998973366654200000122233333334555444444443332222232001110125686799997599345301 Q gi|254780182|r 734 QVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVSEKGFGKRTS 813 (910) Q Consensus 734 ~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GKRt~ 813 (910) .++++.++.+.. .++|++|++|||||++ T Consensus 690 ~~~~~~~~~~~~----------------------------------------------------~~~l~~t~~g~~kr~~ 717 (804) T COG0188 690 KVVSLSVVEDDE----------------------------------------------------AKLLTVTERGYGKRTK 717 (804) T ss_pred EEEEEEECCCCC----------------------------------------------------EEEEEEECCCCEEECC T ss_conf 566532014786----------------------------------------------------0589984367200041 Q ss_pred HHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEECCCCEEEE Q ss_conf 78848667577414887606777768689999728996499994599899999010554451568738898089987999 Q gi|254780182|r 814 SYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFSTAKDERVVS 893 (910) Q Consensus 814 ~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L~~~D~Vv~ 893 (910) +.+|+.++||++|++.++.++++ +|.++++..+.++|++|++|+.|+++|+++++|+.+||+|+||+++++.++++|++ T Consensus 718 ~~~~~~~~Rg~~G~~~~~~~~~~-~~~~~~~~~v~~~~~~~~~t~~g~~ir~~~~~i~~~~r~t~gv~~~~~~~~~~v~~ 796 (804) T COG0188 718 ISEYPVTKRGGKGVILIKGTKRN-RGKVVAAITVDEDDEIMLITSRGKLIRTAVSEISITGRNTQGVKLINLDEDEKVVS 796 (804) T ss_pred HHHCCCCCCCCCCEECCCCCCCC-CCEEEEEECCCCCCEEEEECCCCEEEEEECCCCCCCCCCCCCEEEEECCCCCEEEE T ss_conf 42134246676641245455565-53377641368875389982696389853143231244456627653179973788 Q ss_pred EEEECCC Q ss_conf 9983566 Q gi|254780182|r 894 VERIRES 900 (910) Q Consensus 894 va~i~~~ 900 (910) ++++.++ T Consensus 797 ~~~~~~~ 803 (804) T COG0188 797 VARVKEE 803 (804) T ss_pred EEECCCC T ss_conf 7740578 No 6 >TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit; InterPro: IPR005741 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 II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit A (parC) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=100.00 E-value=0 Score=1906.90 Aligned_cols=729 Identities=38% Similarity=0.635 Sum_probs=706.1 Q ss_pred EEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHH Q ss_conf 66600999998767877799886313754000897367899999998789999981134042556643668870478999 Q gi|254780182|r 16 ITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYD 95 (910) Q Consensus 16 i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~ 95 (910) +.+.+|++.|..||-.||.|+|++|||||+|||||||||||||||+++|++||+|||||||.||+||||||||||||||| T Consensus 1 ~~~~~Le~v~g~~F~kYaKYIIQDRALPD~RDGLKPVQRRILYaM~~~G~~fdk~YkKSAr~VGev~GkYHPHGDSSiYd 80 (745) T TIGR01061 1 IINLPLEEVVGESFGKYAKYIIQDRALPDIRDGLKPVQRRILYAMSEDGNTFDKPYKKSARTVGEVIGKYHPHGDSSIYD 80 (745) T ss_pred CCCCCHHHHHHCCCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCCCCCCCCCCHHHH T ss_conf 97875035440000000251340456665111577035778766532378668870012011102226712898644778 Q ss_pred HHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCH Q ss_conf 99971220111561314788708877697201357899978999999863076840533068988548503432273211 Q gi|254780182|r 96 ALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVL 175 (910) Q Consensus 96 a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL 175 (910) |||||+|+|.+|..||+.|||-||+||||||||||||||||++|.+||+||||+||.|+||||+|++||+||||.||||| T Consensus 81 AmvRMSQ~WKn~~~lv~mHGNnGSiDGDnaAAMRYTEaRLS~iA~~LL~di~K~~V~F~~NFDDseKEP~vLP~lfPNLL 160 (745) T TIGR01061 81 AMVRMSQDWKNNLVLVEMHGNNGSIDGDNAAAMRYTEARLSKIASELLKDIDKKTVKFIPNFDDSEKEPTVLPALFPNLL 160 (745) T ss_pred HHHHCCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCHHHHHHHHHH T ss_conf 86414746334318998506667889985155432476677999999740477831033687788877742344213456 Q ss_pred HCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEE Q ss_conf 01676101013317898547899999988761877688888863458668874434475889999870120389999886 Q gi|254780182|r 176 VNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSH 255 (910) Q Consensus 176 ~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ 255 (910) ||||||||.||||||||||++||+||+|+.||+|+|++++||+++|||||||||+|++.+||++||+||+|+|.|||+++ T Consensus 161 iNGatGIaAGYATnIpPHn~~Ev~Da~i~rId~P~c~v~~L~e~~kgPDFPTGG~i~~~~~~~~aY~tGkGk~iirak~~ 240 (745) T TIGR01061 161 INGATGIAAGYATNIPPHNLNEVIDALIYRIDHPDCSVDKLMEIVKGPDFPTGGIIQGEDGIKKAYETGKGKFIIRAKIE 240 (745) T ss_pred HHHHHHHHCCHHCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCEEECHHHHHHHHHCCCCEEEEEEEEE T ss_conf 52013320000047788876689999986138988417889854484115887246141547889854981399986425 Q ss_pred EEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHC Q ss_conf 54336784599992464435289999999999871665014458730374655799994798877899999997610110 Q gi|254780182|r 256 IEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQS 335 (910) Q Consensus 256 ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~ 335 (910) +|..++|++|||||||||.||||.||.+|.|..-++|+.||+.|||||||+|+||+||+|++++++.|||+|||+|+||. T Consensus 241 ~e~~~ng~~QI~It~IPYE~nKAnlvK~iedi~~d~kv~gi~eVrDeSDr~GlriiI~~Kk~~~~e~v~nyLyK~T~Lqi 320 (745) T TIGR01061 241 IEVNKNGLNQIVITEIPYETNKANLVKKIEDIIVDKKVAGIEEVRDESDRKGLRIIIELKKDANAEKVLNYLYKKTDLQI 320 (745) T ss_pred EEEECCCCCEEEECCCCHHHHHHHHEEEEEEEEECCEEHHHHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHCCCCCCEE T ss_conf 53205882048974574677667640000026764500000100344575755465605452475567875413435438 Q ss_pred CCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH Q ss_conf 00000245541663000299999999999999999999999999988877899999987406999999861899789878 Q gi|254780182|r 336 LFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARR 415 (910) Q Consensus 336 sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~ 415 (910) ||++||+||++..|.++||..+|++|+.|++|||.+|..|+|+||+.|+||+|||++|++-|||||++||+|.|+.|||+ T Consensus 321 ~YN~n~vaI~nr~P~lv~L~~yLd~yi~h~~evi~~~~~Ydl~ka~~R~~IveGLik~isilDeiI~~IRas~~k~DAk~ 400 (745) T TIGR01061 321 NYNFNMVAIANRTPILVGLLSYLDAYIKHSKEVIINRSLYDLEKAKKRLEIVEGLIKAISILDEIIKLIRASEDKSDAKE 400 (745) T ss_pred EECCCCEEECCCCCEEECHHHHHHHHHHHHHHHEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHH T ss_conf 64324178404763364401688888723023200246423888987889888899999998789887730245336034 Q ss_pred HHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH Q ss_conf 77631269788999997402211122234452369999999998789999888799999989999999998875304989 Q gi|254780182|r 416 ELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRS 495 (910) Q Consensus 416 ~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~ 495 (910) +|+.. |.||+.|||||..|||||||+.++-.|++|.+||.++|+.|+.+|+|++ T Consensus 401 ~Li~~--------------------------f~FT~~QAEAIv~LrLY~LTnTDi~~L~~E~~eL~~~~~~l~~~i~~~k 454 (745) T TIGR01061 401 NLIDK--------------------------FEFTENQAEAIVSLRLYRLTNTDIFELKEEEEELEKKIKSLEEIIASEK 454 (745) T ss_pred HHCCC--------------------------CCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 31011--------------------------3777257999999886037320377778789999999999999876578 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCEEECCCC--CCCCCCCCCCCCEEEEEECCC-EECCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 999999998999998405688331001343--453010145678189990797-05233100000233456521100014 Q gi|254780182|r 496 RLLGIIKQELLSVKDELDTPRRTRIVEGLL--DMEDEDCIVREDMVVTVSHLG-YVKRVPLSVYRAQRRGGKGRSGVVMR 572 (910) Q Consensus 496 ~l~~iI~~EL~eik~kygd~RRT~I~~~~~--~i~~EdlI~~E~vvV~lS~~G-yIKr~~~~~yr~Q~RggkG~~~~~~k 572 (910) .+.++|+++|.++||+|+++|||.|.+... +++.+.||+++++-|++|+.| |+||++..+|.+.+ ...++.+ T Consensus 455 ~~~~~lk~~l~~~KK~F~~~R~s~l~~~~~~~~i~~~~li~~~~~~v~itk~GnY~K~~S~~sf~ss~-----~~d~g~~ 529 (745) T TIGR01061 455 ARKKLLKKKLKELKKKFAQERRSKLEDEIEKIKINEDELIEKEDLYVVITKDGNYIKRTSKRSFASSK-----YDDFGLK 529 (745) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHEECCHHHHHHHCCCEEEEEECCCEEHHHHHHHHHHCC-----CCCCCCC T ss_conf 99999899999872310575045675116530104678532146407998447630001266762047-----3115775 Q ss_pred CCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEE-CCCCCCEEEEEEECCCCCCCCCCEEEEE Q ss_conf 641010113323777399995489399982000432244456554124545-3655620025663012566687179999 Q gi|254780182|r 573 DEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILS-LNQGERITTIMPFPEDESSWNNLYVVFA 651 (910) Q Consensus 573 e~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~-l~~~E~I~ail~~~~~~~~~~~~~Lvl~ 651 (910) ++|-+.+...++|||.||+|||.|++..++||+||..+|+.-|.|++|.+. +..+|+|+.+.++++|+ .+..+|||+ T Consensus 530 ~~d~l~~~~~~nttd~lL~~Ts~g~~In~pvh~La~~rwkd~g~hls~~~~n~~~~E~iv~v~~~~~fd--v~~~~L~l~ 607 (745) T TIGR01061 530 DDDILFYQTIANTTDKLLIFTSKGNLINLPVHKLADIRWKDLGEHLSNKITNFDENETIVAVEILNEFD--VDEAILVLA 607 (745) T ss_pred CCHHHHHHHHHHCCCEEEEEECCCCEEEEEEEECCCCCHHHHHHHHCCHHHHHHCCCCEEEEEEECCCC--CCHHHHHHH T ss_conf 533453546521225378876166664213031456656689987200011021068489998613225--746898998 Q ss_pred ECCCCEEEECHHHHHHCC---CCCEEEEEECCCCEEEEEEECCC--CCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEE Q ss_conf 479918984236862047---77227866158985788896189--8269999369859997587623547866553576 Q gi|254780182|r 652 TKHGNVRRNKLSDFIQIN---RSGKIAMKLDSRDEILSVETCTQ--ENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRG 726 (910) Q Consensus 652 Tk~G~VKkt~l~ef~~~r---~~G~~aikLkegD~Li~v~~~~~--~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkg 726 (910) |+.|+|||+.+++|.-.+ +..+.+++|+++|.||+|++..+ ++.|+++|+.|++|+|.++||+.+ |+.|+|||| T Consensus 608 sklg~vKriel~~l~~~~~y~sK~~~~~~L~D~d~li~a~~~~~Gh~~~i~lvS~~gy~l~F~~~Ei~~~-~~~A~GvK~ 686 (745) T TIGR01061 608 SKLGMVKRIELTELDIKRNYRSKAILILKLKDEDELISAFLQKKGHDKLIILVSKLGYALLFLVEEINVV-GAKAAGVKG 686 (745) T ss_pred HHCCCEEEEECCCCCCCCCCHHHHHHHHHCCCCCCEEEEEEECCCCCCEEEEEEECCCEEEECCEEECCC-CCCCCCEEE T ss_conf 7558747876032477865101223321117895438999841888441899973683577302033231-446673113 Q ss_pred EECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEECC Q ss_conf 75289986999897336665420000012223333333455544444444333222223200111012568679999759 Q gi|254780182|r 727 ISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVSEK 806 (910) Q Consensus 727 IkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~ 806 (910) |+|+++|.|.+..+....+ ++..+|.. T Consensus 687 mkLK~~D~v~~~~i~~~~~-----------------------------------------------------~~vll~~~ 713 (745) T TIGR01061 687 MKLKEDDEVKSGLILEANE-----------------------------------------------------SLVLLTQR 713 (745) T ss_pred EECCCCCEEEEEEEECCCC-----------------------------------------------------CEEEEEEC T ss_conf 3057676389999982799-----------------------------------------------------55899736 Q ss_pred CCEEEEEHHHCCCCCCCCCCEEEEE Q ss_conf 9345301788486675774148876 Q gi|254780182|r 807 GFGKRTSSYDFRISNRSGKGIRATD 831 (910) Q Consensus 807 G~GKRt~~~eyr~q~RGgkGv~~ik 831 (910) |-.||.+++|+..++|+..|+..++ T Consensus 714 Gs~k~~~~~El~~~sRa~~~~~llR 738 (745) T TIGR01061 714 GSVKRLSISELKVTSRAATGVKLLR 738 (745) T ss_pred CCEEEEEHHHHHHHHHHCCCCHHHC T ss_conf 8256510365555343116511110 No 7 >TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit; InterPro: IPR005742 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 II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit A (parC) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=100.00 E-value=0 Score=1568.00 Aligned_cols=683 Identities=36% Similarity=0.598 Sum_probs=641.7 Q ss_pred EEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHH Q ss_conf 66600999998767877799886313754000897367899999998789999981134042556643668870478999 Q gi|254780182|r 16 ITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYD 95 (910) Q Consensus 16 i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~ 95 (910) |..+++.+..+++||.||||||++|||||||||||||||||+|||.+|||.++..||||||+||||+||||||||+|||| T Consensus 1 iE~~~l~~~~~~~YL~Y~~~~IM~RaLP~i~DGLKPV~RR~~YAM~~L~L~a~a~yKKsAR~VGDVlGKyHPHGD~A~Y~ 80 (747) T TIGR01062 1 IENLDLRNFTEEAYLNYSLYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNANAKYKKSARTVGDVLGKYHPHGDSAVYE 80 (747) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEECCEECCCCCCCCCCCCHHHHH T ss_conf 97651578988888888888887423772025775146899888887164767775200102102124605896248999 Q ss_pred HHHHHCCCHHCCCCCCCCCCCCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCC Q ss_conf 999712201115613147887088776-9720135789997899999986307684053306898854850343227321 Q gi|254780182|r 96 ALARMAQDWSLRLLLIEGQGNFGSVDG-DPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNV 174 (910) Q Consensus 96 a~v~maq~~~~r~plidg~GnfGs~dg-d~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~l 174 (910) |||+|||+||+|||||||||||||+|+ |++|||||||+|||++++-||.||+++||||+||||||..||.+|||+|||| T Consensus 81 ~~V~~AQ~FS~RYPLvDGQGN~Ga~DdP~~~AAMRYTESRl~~~s~lLl~~l~~~TvD~~~~fD~~~~EP~~lPA~lP~~ 160 (747) T TIGR01062 81 ALVLLAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKISELLLEELGQGTVDFRPNFDGTLLEPKILPARLPNI 160 (747) T ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHH T ss_conf 99986211123476201677868898742123433246678999999998618872133457887424644253112055 Q ss_pred HHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCC-CHHHHHHHHHHCCCEEEEEEE Q ss_conf 1016761010133178985478999999887618776888888634586688744344-758899998701203899998 Q gi|254780182|r 175 LVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVIL-GRTGIKNAYATGRGSIVIRGV 253 (910) Q Consensus 175 L~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~-~~~~i~~~y~tGrG~i~iR~k 253 (910) |+||++|||||||||||||||.|||||+++|||||.++++++|++|+||||||+|+|+ ..+.|+.+|++|||||++||. T Consensus 161 L~NG~~GIAVGMAT~IPPHNl~E~adA~~~LiD~P~agl~d~l~~v~GPDfPT~a~II~~~~~I~~~Y~~GRGS~r~Ra~ 240 (747) T TIGR01062 161 LLNGTTGIAVGMATDIPPHNLRELADAALYLIDNPKAGLDDILNIVQGPDFPTEAEIIDKKEEIRKIYETGRGSVRMRAR 240 (747) T ss_pred HCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHCCCCEEEEEEE T ss_conf 60688724752217888623799999999985288321689999734857898765747189999998569833897226 Q ss_pred EEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCC-CCEEEEEEEC-CCCCHHHHHHHHHHHC Q ss_conf 8654336784599992464435289999999999871665014458730374-6557999947-9887789999999761 Q gi|254780182|r 254 SHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDR-QGYRVVIELK-RGASADVILNQLYRYT 331 (910) Q Consensus 254 ~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr-~giRivielK-r~~~~~~vln~Lyk~T 331 (910) |+-|+...|-++||||+||||++++++|++||.+.++||||-|+|+|||||. +-+||||+++ +..|++.||++||+.| T Consensus 241 W~KE~~syGty~ivi~~lP~Q~~~sk~i~QIA~~~~~KKlP~~~~iRDEsDH~~~iR~Vi~PR~~~~D~~~vM~~LF~~T 320 (747) T TIGR01062 241 WKKEDGSYGTYQIVISALPHQISKSKVIEQIAIQLKDKKLPLISDIRDESDHENPIRVVIVPRSNRVDPDIVMEHLFATT 320 (747) T ss_pred EEECCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH T ss_conf 53014666502676522775354015889999999717887024203423677856899843887768799999986542 Q ss_pred CHHCCCCCEEEEE-ECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH Q ss_conf 0110000002455-416630002999999999999999999999999999888778999999874069999998618997 Q gi|254780182|r 332 SLQSLFSVNMVAL-NGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNP 410 (910) Q Consensus 332 ~Lq~sf~~N~~aL-~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~ 410 (910) +||.+|.+||++| .|++|.++||.|||++|+.||+++|+||++|+|+|...|+|||+||.+|+.||||||+|||+-++| T Consensus 321 ~LE~~~~~N~N~IG~~~~P~V~nlLEIL~E~L~fR~~~v~RR~~Y~L~Kv~~RL~IL~~L~i~fLN~DEvIEIIR~EDeP 400 (747) T TIGR01062 321 DLEKSYRLNMNMIGLDNKPAVKNLLEILQEWLVFRRNTVIRRLTYRLNKVLKRLHILEGLLIAFLNIDEVIEIIREEDEP 400 (747) T ss_pred CHHHHEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC T ss_conf 20011233224640698960454899999999855888787888779999989988764755202100101222379984 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89878776312697889999974022111222344523699999999987899998887999999899999999988753 Q gi|254780182|r 411 ETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDI 490 (910) Q Consensus 411 ~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~I 490 (910) |..||+| |+||+.||+|||++|||.|.+||+.+|..|+.+|.++...|++| T Consensus 401 ---K~~lM~R--------------------------F~ls~~Q~e~IL~~rLR~L~KLEE~~i~~E~~~L~K~~~~L~~I 451 (747) T TIGR01062 401 ---KTILMER--------------------------FKLSEIQAEAILNLRLRHLAKLEEHKIKDEQSELEKERAILEKI 451 (747) T ss_pred ---HHHHHHH--------------------------HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf ---2899855--------------------------06358999999865555654577888876566778999999999 Q ss_pred HCCHHHHHHHHHHHHHHHHHHCCC-----CCCCEEECCCC--CCCCC-CCCCCCCEEEEEECCCEECCCCCCCCCCCCCC Q ss_conf 049899999999989999984056-----88331001343--45301-01456781899907970523310000023345 Q gi|254780182|r 491 LSSRSRLLGIIKQELLSVKDELDT-----PRRTRIVEGLL--DMEDE-DCIVREDMVVTVSHLGYVKRVPLSVYRAQRRG 562 (910) Q Consensus 491 L~s~~~l~~iI~~EL~eik~kygd-----~RRT~I~~~~~--~i~~E-dlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~Rg 562 (910) |+|++++|+++|+|+++..++||+ +|||.+.+-+. .+.+. |+++.|||+|++|+.|||+..+-++- T Consensus 452 L~~~~~l~~l~KKEi~~~~~~yg~ntiiG~R~~~l~E~~~~~~~~~~t~~~~~EPvTii~S~MGWVRs~KGH~~------ 525 (747) T TIGR01062 452 LKSERKLNQLVKKEIQADAKKYGLNTIIGARRSSLEEREEAKQVSEITDMIPKEPVTIILSKMGWVRSAKGHDI------ 525 (747) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEECCCCCC------ T ss_conf 87568999999899999998740242203554513567888888766530367881799827773550466566------ Q ss_pred CCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCC-CCEEEEEEECCCCC Q ss_conf 65211000146410101133237773999954893999820004322444565541245453655-62002566301256 Q gi|254780182|r 563 GKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQG-ERITTIMPFPEDES 641 (910) Q Consensus 563 gkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~-E~I~ail~~~~~~~ 641 (910) ...++++|+||.....+.+.|+|.++|++|+||.|.+.+..||.+ ++.|.|+.-=|.++.| ..|..++-.+ T Consensus 526 --D~~~l~YK~GD~~~~~~~~~~~~~v~~i~S~GR~y~l~~~~l~~a--~g~G~Pl~~KL~l~~Gn~~i~~~l~~~---- 597 (747) T TIGR01062 526 --DLSTLKYKAGDSEKAIIEGKSNQKVVFIDSTGRSYALDPLNLPSA--RGQGEPLTGKLLLPIGNATIENILMES---- 597 (747) T ss_pred --CCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEEECCCCCCCC--CCCCCCEEEEEECCCCCCCEEEEEEEC---- T ss_conf --714354136861233455127751799972885266311204345--677872268873268862310777635---- Q ss_pred CCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCC-EEEEEECCCEEEEEEHHHCCCCCCCC Q ss_conf 66871799994799189842368620477722786615898578889618982-69999369859997587623547866 Q gi|254780182|r 642 SWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQEN-DILLTTKLGQCVRFPISAIRVFAGRN 720 (910) Q Consensus 642 ~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~-~Iil~T~~G~~lrF~~~evr~~~GR~ 720 (910) +++.|+|++.-|+.+-...+++...++.|+..|+|-|+-+++.+..+.+++ -|+++|..|++|.|++++++.|+ + T Consensus 598 --~~Q~LL~AS~~G~GF~~~~~~liA~~k~GK~l~~lPE~~~~~~p~~~~~~s~~~~aI~~a~R~L~F~~~~lP~l~--K 673 (747) T TIGR01062 598 --ENQKLLLASDAGYGFLVKFNDLIARNKAGKALINLPENASVLAPLVVNDDSDLIVAITEAGRLLVFPIDDLPELS--K 673 (747) T ss_pred --CCCCEEEECCCCCCEEEECHHHHHHCHHCHHHCCCCCCCEEECCEEECCCCCEEEEECCCCEEEEECHHHCCCCC--C T ss_conf --885321000168624740043333110040200178886110443423761024441136706874211177634--7 Q ss_pred CCCEEEEECCC------CCEEEEEEEECCCC Q ss_conf 55357675289------98699989733666 Q gi|254780182|r 721 SVGVRGISLAK------GDQVISMAIVLHAD 745 (910) Q Consensus 721 a~GVkgIkL~~------~D~Vv~~~vi~~~~ 745 (910) ++|++.++++. .|-+....++++.+ T Consensus 674 G~G~~~~~~~~a~A~~~~~~L~~l~~~~~Q~ 704 (747) T TIGR01062 674 GKGNKLIRIPAANAKDREELLLDLKILNKQD 704 (747) T ss_pred CCCCEEEEECCHHHCCCCCCCEEEEEECCCC T ss_conf 8730577505410012000101234535777 No 8 >PRK09631 DNA topoisomerase IV subunit A; Provisional Probab=100.00 E-value=0 Score=1402.78 Aligned_cols=609 Identities=25% Similarity=0.421 Sum_probs=511.4 Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHH Q ss_conf 09999987678777998863137540008973678999999987899999811340425566436688704789999997 Q gi|254780182|r 20 SITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALAR 99 (910) Q Consensus 20 ~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~ 99 (910) +|+++|++|||+||||||++|||||||||||||||||||||++++ +++|+|||||||+|| |||||||+|||||||| T Consensus 2 ~i~~~~~~~~l~Ya~~VI~~RAlPdv~DGLKPvqRRiL~~m~~~~---~~~~~K~A~ivG~~m-kyHPHGd~siy~alV~ 77 (626) T PRK09631 2 DIKTLLKDNFLQYSSYVIKDRAIASVIDGFKPVQRRIIHSLFEMH---DGNFHKVANVVGNTM-KYHPHGDTSIYEALVN 77 (626) T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCC---CCCCCEEEEEECCCC-CCCCCCCHHHHHHHHH T ss_conf 868999999998889998850277521488659999999998648---999857628850511-2689982479999999 Q ss_pred HCCCHHCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCC Q ss_conf 122011156131478870887-7697201357899978999999863076840533068988548503432273211016 Q gi|254780182|r 100 MAQDWSLRLLLIEGQGNFGSV-DGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNG 178 (910) Q Consensus 100 maq~~~~r~plidg~GnfGs~-dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG 178 (910) ||| |||||||||||||+ ||||||||||||||||++|++|| ++++||||+|||||+++||+||||+|||||+|| T Consensus 78 maq----~~~lid~qGNfGsi~~gD~aAA~RYtEaRls~~a~e~l--~~~~tv~~~~nyDg~~~EP~vLP~~~PnLL~nG 151 (626) T PRK09631 78 IAN----KDLFIEKQGNFGNLFTGDPASASRYIECRLTPLAFEVL--YSKEITSYEPSYDGRNNEPLIFPAKIPVILIQG 151 (626) T ss_pred HHC----CCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH--CCCCCCEECCCCCCCCCCCEEEECCCCHHHHCC T ss_conf 856----57605278888899998834566689897799999983--787851201278987446405553573777526 Q ss_pred CCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEEE Q ss_conf 76101013317898547899999988761877688888863458668874434475889999870120389999886543 Q gi|254780182|r 179 GGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSHIEK 258 (910) Q Consensus 179 ~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ie~ 258 (910) |+|||||||||||||||+|||||++++|+||++++ +|||||||+|.. +.|+||||+|++|||+++++ T Consensus 152 ~~GIAVGmaT~IpPHNl~Evida~i~~l~~~~~~~--------~PDFPTGG~i~~-----~~Y~tG~G~i~vRak~e~~~ 218 (626) T PRK09631 152 SEGIAVGMAAKILPHNFNEILEAVKSELLGESYDL--------YPDFPTGGIVDV-----NEYADGNGKVLVRAKIETTD 218 (626) T ss_pred CCCHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCC--------CCCCCCCCCCCH-----HHHHCCCEEEEEEEEEEECC T ss_conf 74221222106899888999999998533898766--------999998751033-----25634862799999999817 Q ss_pred CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCCC Q ss_conf 36784599992464435289999999999871665014458730374655799994798877899999997610110000 Q gi|254780182|r 259 TSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQSLFS 338 (910) Q Consensus 259 ~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf~ 338 (910) +.+||||||||||||++|||+|++++++|||+ |+||||||+ +++||||+||||++|+++||+||++|+||+||| T Consensus 219 ----~~~ivItEiPy~v~k~~lie~I~~~~~~~ki~-I~~i~D~s~-~~vrIvi~lk~~~~~~~vln~Ly~~T~lq~sf~ 292 (626) T PRK09631 219 ----EKTIVIRELPFGETTESLIASIEKAIRKNYIK-VSSINDFTA-ENVEIELKLPRGVYASEVIEKLYHYTNCQVSIS 292 (626) T ss_pred ----CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCC-CCCCCCCCC-CCEEEEEEECCCCCHHHHHHHHHHHCCHHHEEC T ss_conf ----83599995687777899999999999725676-211414689-827999998999998999999875097132176 Q ss_pred CEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH Q ss_conf 00245541663000299999999999999999999999999988877899999987406999999861899789878776 Q gi|254780182|r 339 VNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELM 418 (910) Q Consensus 339 ~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~ 418 (910) +||+||+||+|++|||+++|++|++||++|++||++|+|+++++|+|...+..+++++ +|++.|+.+++.+++...+. T Consensus 293 ~n~~ai~~~~P~~l~l~eiL~~~~~h~~~vl~r~le~~l~k~~er~H~~sLe~IfIe~--rIy~~Ie~~~~~e~v~~~i~ 370 (626) T PRK09631 293 VNLLLLSDRYPVIYTVTDIIKFHAEHLQKILKMELELERSKILEKIFSKTLEQIFIEK--KIYKILETISKEEDVVSIVL 370 (626) T ss_pred CEEEEEECCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHCCCHHHHHHHHH T ss_conf 2689998998279879999999999999999999998899899868999999998666--68999884201688999999 Q ss_pred HHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH Q ss_conf 31269788999997402211122234452369999999998789999888799999989999999998875304989999 Q gi|254780182|r 419 QRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLL 498 (910) Q Consensus 419 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~ 498 (910) +...... ..-...+|+.|++|||+|||+|||++|++|.++|+++|.++|+++++.|++ +. T Consensus 371 ~~l~pf~-----------------~~l~r~ite~d~~aLleirL~RIT~~didK~~eei~~L~~eI~eI~~~L~~---l~ 430 (626) T PRK09631 371 SELLPFK-----------------SSLSRDVTEDDVENLLKIPIRKISLFDIDKNNKDIRILNKELKSIESNIKS---IK 430 (626) T ss_pred HHHHHHH-----------------HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HH T ss_conf 8777678-----------------876301579999999998998853430887999999999999999863776---89 Q ss_pred HHHHHHHHHHHHHCCCC--CCCEEECCCCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCH Q ss_conf 99999899999840568--8331001343453010145678189990797052331000002334565211000146410 Q gi|254780182|r 499 GIIKQELLSVKDELDTP--RRTRIVEGLLDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDF 576 (910) Q Consensus 499 ~iI~~EL~eik~kygd~--RRT~I~~~~~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~ 576 (910) .++++|+.+++++||+. |||+| ++++.+|+||+++++|+.|.|+|+|+.|+++|++|| T Consensus 431 ~~~I~~l~~Lk~kYG~~~~RKTEI--------------------~lfd~i~aKrVa~~n~Kly~nr~~GFiGtslKkdDf 490 (626) T PRK09631 431 GYAINFIDKLLAKYSKEYKRKTEI--------------------SLIKSKNVREIATKNMKVYLNLETGFVGTSLIDGEF 490 (626) T ss_pred HHHHHHHHHHHHHHCCCCCCEEEE--------------------EEECCEEEEEEECCCCEEEECCCCCEEEECCCCCCE T ss_conf 999999999998735477725799--------------------976444369957023325665888556103567845 Q ss_pred HEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCC-CEEEEEEECCCCCCCCCCEEEEEECCC Q ss_conf 1011332377739999548939998200043224445655412454536556-200256630125666871799994799 Q gi|254780182|r 577 VTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQGE-RITTIMPFPEDESSWNNLYVVFATKHG 655 (910) Q Consensus 577 v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~E-~I~ail~~~~~~~~~~~~~Lvl~Tk~G 655 (910) + +.|++||+|||||| |+ .++..+|+....+|+.-..+++...++. .|-.++- ++-+ +... T Consensus 491 V---~~CSd~DdILvF~d-G~---ykV~kV~~K~Fvgk~i~~v~v~~k~d~~~tiyn~IY-rDgk-----------~g~~ 551 (626) T PRK09631 491 I---GNASYYDKILIFKD-GS---YVLKNIEDKTFIDKKNVCVLVYDINNSKEQVFSIIY-RDKL-----------DNFY 551 (626) T ss_pred E---EECCCCCEEEEEEC-CE---EEEEECCCCCEECCCCEEEEEEECCCCCCEEEEEEE-ECCC-----------CCCE T ss_conf 6---73356653999989-85---999985776054688379999852787650799999-8699-----------8836 Q ss_pred CEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEE-ECCCEEEEEEHHHCCCCCCCCCCCEEE Q ss_conf 18984236862047772278661589857888961898269999-369859997587623547866553576 Q gi|254780182|r 656 NVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLT-TKLGQCVRFPISAIRVFAGRNSVGVRG 726 (910) Q Consensus 656 ~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~-T~~G~~lrF~~~evr~~~GR~a~GVkg 726 (910) ++||.....+..-+ .-.. ..+|.+++....-. + +.-. .....-.-|+-+++. ..||+|+|... T Consensus 552 yiKRF~V~~~trdK--~Y~l--~~~~s~~l~fs~n~-n--l~~~~~~k~~~~~~df~~~~-iKgr~skGn~v 615 (626) T PRK09631 552 YVKRFKIDKFILDK--VYEF--LPENDEFLDFSLNP-E--FVPFSRSKDIVKMIEIDNFM-VKSRSSKGKRI 615 (626) T ss_pred EEEEEEECCEEECC--CCCC--CCCCCEEEEEEECC-C--CCCCCCCCCEEEEECHHHEE-EECCCCCCEEE T ss_conf 89998832388425--2245--79998799999777-6--57454424514773211403-41444555176 No 9 >PRK09630 DNA topoisomerase IV subunit A; Provisional Probab=100.00 E-value=0 Score=1299.61 Aligned_cols=468 Identities=28% Similarity=0.438 Sum_probs=426.7 Q ss_pred ECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHH Q ss_conf 00999998767877799886313754000897367899999998789999981134042556643668870478999999 Q gi|254780182|r 19 VSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALA 98 (910) Q Consensus 19 ~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v 98 (910) .+|+++|++|||+||||||++|||||||||||||||||||||++++ +++|+|||||||+||| ||||||+||||||| T Consensus 2 ~~i~~~~~~~yl~Ya~~vI~~RAlPdvrDGLKPVqRRiLy~m~~~~---~~~~~K~ArvvG~v~g-yHPHGd~siy~alv 77 (479) T PRK09630 2 SDVSDLFKTHFMHYASYVILERAIPHILDGLKPVQRRLLWTLFRMD---DGKMHKVANIAGRTMA-LHPHGDAPIVEALV 77 (479) T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCC---CCCCCEEEEEECCEEC-CCCCCHHHHHHHHH T ss_conf 6279999999998889999851177532588609999999983068---9987134244213511-48887278999999 Q ss_pred HHCCCHHCCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHC Q ss_conf 712201115613147887088-7769720135789997899999986307684053306898854850343227321101 Q gi|254780182|r 99 RMAQDWSLRLLLIEGQGNFGS-VDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVN 177 (910) Q Consensus 99 ~maq~~~~r~plidg~GnfGs-~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~n 177 (910) |||| ||||||||||||| +||||||||||||||||++|.+|| ++++||||+||||||++||+||||+|||||+| T Consensus 78 rmaq----r~~LvdgqGNfGs~~dgd~~AAmRYtE~rls~~a~~~l--~~~dtv~f~~NyDgs~~EP~vLPa~~PnLLvN 151 (479) T PRK09630 78 VLAN----KGYLIDTQGNFGNPLTGDPHAAARYIEARLSPLAKEVL--FNTDLMTFHDSYDGREKEPDILPAKLPLLLLH 151 (479) T ss_pred HHHC----CCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH--CCCCCCCCCCCCCCCCCCCCEEECCCCHHHHC T ss_conf 9856----76156467888999899804677899987589999983--55685467789899855771211457187754 Q ss_pred CCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEE Q ss_conf 67610101331789854789999998876187768888886345866887443447588999987012038999988654 Q gi|254780182|r 178 GGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSHIE 257 (910) Q Consensus 178 G~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ie 257 (910) ||+|||||||||||||||+|||||++++|+||++++ ||||||||+|.+.+ |+||||+|++||+|+++ T Consensus 152 Gs~GIAVGmAT~IpPHNl~EvidA~i~~i~~~~~~~--------~PDFPTGGii~~~~-----Y~tGrG~i~vRak~~~~ 218 (479) T PRK09630 152 GVDGIAVGMTTKIFPHNFCELLEAQIAILNDQPFTL--------LPDFPSGGLMDASE-----YQDGLGSITLRASIDII 218 (479) T ss_pred CCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCC--------CCCCCCCCEECHHH-----HCCCCCEEEEEEEEEEE T ss_conf 775222345525899898999999999762898775--------89999977305466-----55789818999999997 Q ss_pred ECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCC Q ss_conf 33678459999246443528999999999987166501445873037465579999479887789999999761011000 Q gi|254780182|r 258 KTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQSLF 337 (910) Q Consensus 258 ~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf 337 (910) +. ++||||||||||||++|+++|+++++++++ +|+|+||||+ +++||||+|||+++|+.|||+|||||+||+|| T Consensus 219 ~~----k~ivItEiPy~v~k~~lie~I~~~~~~~~~-~I~~i~D~s~-~~~rivI~lkr~~~~~~vl~~Lyk~T~Lq~sf 292 (479) T PRK09630 219 ND----KTLLIKEICPSTTTETLIRSIENAAKRGII-KIDSIQDFST-DLPHIEIKLPKGIYAKDLLPPLFEHTECQVIL 292 (479) T ss_pred EC----CEEEEEECCCCCCHHHHHHHHHHHHHCCCC-CCCCEEECCC-CCCEEEEECCCCCCHHHHHHHHHHCCCHHHEE T ss_conf 14----438997068656699999999999864876-6885113357-98559984799999999999998369624122 Q ss_pred CCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHH---HHHHHHHHHHHHHHHCCCHH Q ss_conf 000245541663000299999999999999999999999999988877---899999---98740699999986189978 Q gi|254780182|r 338 SVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAH---VLVGLA---IAVANLDEVVRIIRFSPNPE 411 (910) Q Consensus 338 ~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~H---ILeGL~---~Al~nIDeVI~iIR~S~d~~ 411 (910) |+||+||++|+|++|+|+++|++|++||.++++||+.+ +.++..|.| +||++. .++++||+||++||+|++.+ T Consensus 293 ~~N~~aI~~g~P~~l~l~eiL~~~~~~~~~~lrr~l~~-~~~~~~r~~~~k~Le~l~I~~~~~d~I~eiI~~i~~~~~~e 371 (479) T PRK09630 293 TSKPTAIYQNKPVETSISEILKLHTEALQGYLKKELLI-LQDSLTREHYHKTLEYIFIKHKLYDTVREMLSKRKTKPSAS 371 (479) T ss_pred CCCEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHH T ss_conf 33237888890866668999999999875543466899-98999999999888899998778999999999885389899 Q ss_pred HHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 98787763126978899999740221112223445236999999999-87899998887999999899999999988753 Q gi|254780182|r 412 TARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAIL-ELRLARLTGLGRDDIRNELNSLGIEIKECLDI 490 (910) Q Consensus 412 eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AIL-dMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~I 490 (910) +|+..+++..+... .......+.|+.++| +|+|+|||+||++++++|+++|.++++.++++ T Consensus 372 d~~~~l~~~~~~~~------------------~~~~~~i~~q~~~~L~~l~l~kL~~Le~~k~~~El~~l~~~i~~l~~~ 433 (479) T PRK09630 372 DLHNAVLHALEPFL------------------HTLPTAPDKQATSQLASLTIKKILCFNENAYTKELAAIEKKQAAVQKD 433 (479) T ss_pred HHHHHHHHHHHHHH------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999998765667------------------877543389999999998999875133999999999999999999999 Q ss_pred HCCHHHHHHHHHHHHHHHHHHCCC--CCCCEEECCCCCCCCCCCCCCCCEE Q ss_conf 049899999999989999984056--8833100134345301014567818 Q gi|254780182|r 491 LSSRSRLLGIIKQELLSVKDELDT--PRRTRIVEGLLDMEDEDCIVREDMV 539 (910) Q Consensus 491 L~s~~~l~~iI~~EL~eik~kygd--~RRT~I~~~~~~i~~EdlI~~E~vv 539 (910) |+ ++++++++||++++++||| +|||+|.+.+. ..+++|+.|+++ T Consensus 434 l~---~l~kiii~eL~~ikekYGd~~eRRTeI~~~~~--~~~~~~~~e~~v 479 (479) T PRK09630 434 LS---QLKKYTVKYLKGLLERYGHLGHRKTQITKFKA--KKTSILKQQTLI 479 (479) T ss_pred HH---HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC--HHHHCCCHHCCC T ss_conf 99---99999999999999985899877675602432--343024200259 No 10 >smart00434 TOP4c DNA Topoisomerase IV. Bacterial DNA topoisomerase IV, GyrA, ParC Probab=100.00 E-value=0 Score=1187.07 Aligned_cols=439 Identities=55% Similarity=0.851 Sum_probs=426.8 Q ss_pred ECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHH Q ss_conf 00999998767877799886313754000897367899999998789999981134042556643668870478999999 Q gi|254780182|r 19 VSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALA 98 (910) Q Consensus 19 ~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v 98 (910) ++|+++|.++|++||||||.+|||||+|||||||||||||||++++++++++|+|||++||+|||+||||||+|+|+||| T Consensus 1 i~i~d~~~~~~~~ys~~vi~~RaiP~~~DGLKPvqRriLy~~~~~~l~~~~~~~k~a~~~g~~~~~YHpHGd~s~~~aiv 80 (445) T smart00434 1 IDIEDFINKEYLDYSMSVINGRAIPDVRDGLKPVQRRILYAMFKRGLTPDEPKVKSARGVGDVMGKYHPHGDSSLYDAIV 80 (445) T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEHHCCCCCCCHHHHHHHHH T ss_conf 97799998999998899876034884002787899999999997389889862788888861001788886889999999 Q ss_pred HHCCCHHCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHC Q ss_conf 7122011156131478870887-769720135789997899999986307684053306898854850343227321101 Q gi|254780182|r 99 RMAQDWSLRLLLIEGQGNFGSV-DGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVN 177 (910) Q Consensus 99 ~maq~~~~r~plidg~GnfGs~-dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~n 177 (910) ||||+|||||||+||||||||+ |||+||||||||||||++|..||.++|++||+|+|||||+..||+|||+.||||||| T Consensus 81 ~mAQ~fs~n~~Ll~~~GnFGs~~~G~~aAa~RYie~rLs~~~~~~~~~~d~~~~~~~~n~Dg~~~EP~~~~p~iP~lLvN 160 (445) T smart00434 81 RMAQDFSNNYPLLDGQGNFGSRLDGDDAAAMRYTETRLSPLARELLPDIDKDTVDFVPNYDGQEIEPTVLPPIIPNLLVN 160 (445) T ss_pred HHHHHHHCCCCCEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCHHCCCCCCHHEEE T ss_conf 98474340554230588867889998203367888637799999876438780755438898726751027766730030 Q ss_pred CCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEE Q ss_conf 67610101331789854789999998876187768888886345866887443447588999987012038999988654 Q gi|254780182|r 178 GGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSHIE 257 (910) Q Consensus 178 G~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ie 257 (910) ||+|||||||||||||||+||++||+++|++|+++.++||.+++||||||||+|. |+|+|++||+|++| T Consensus 161 Gs~GIavG~sT~IPphN~~evi~a~~~~l~~~~~~~~~l~~~p~~pdF~gg~~~~-----------g~g~~~~rg~~~~~ 229 (445) T smart00434 161 GSSGIAVGMATNIPPHNLREVIDAVRRLIDNPEASIDELMMIPWGPDFPTGGEII-----------GPGSYVVRGKIEIE 229 (445) T ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCEEEE-----------CCCEEEEEEEEEEE T ss_conf 7874254230477887889999988766518878889996388428999816993-----------39869999999998 Q ss_pred ECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHC-CCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCC Q ss_conf 3367845999924644352899999999998716650144587303-746557999947988778999999976101100 Q gi|254780182|r 258 KTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDES-DRQGYRVVIELKRGASADVILNQLYRYTSLQSL 336 (910) Q Consensus 258 ~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeS-dr~giRivielKr~~~~~~vln~Lyk~T~Lq~s 336 (910) + ++++|+||||||++++++++|+|+++++++|++||.|++||| +++|+||||++|++++++.++++|||+|+||+| T Consensus 230 ~---~~~~i~ItELP~g~~t~~~~e~i~~lv~~~ki~~i~~~~des~~~~~vrivI~lk~~~~~~~~~~~L~k~tkL~~s 306 (445) T smart00434 230 D---GRNTIVITELPYQVNKAKLIEKIAELVKDKKIEGIIDVRDESHDRTGVRIVIELKRGAMAEVVLNGLYKLTKLQST 306 (445) T ss_pred C---CCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHEE T ss_conf 7---9627999946876748999999999851356665010354328877526999988998989999999987201434 Q ss_pred CCCEEEEEE-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCH-HHH Q ss_conf 000024554-166300029999999999999999999999999998-88778999999874069999998618997-898 Q gi|254780182|r 337 FSVNMVALN-GYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKAR-DRAHVLVGLAIAVANLDEVVRIIRFSPNP-ETA 413 (910) Q Consensus 337 f~~N~~aL~-~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~-~R~HILeGL~~Al~nIDeVI~iIR~S~d~-~eA 413 (910) |++||++|+ +|+|+++++++||++|++||.++++||++|+|+|++ +|+|+++|+.++..++|+||.+||+|++. ++| T Consensus 307 ~s~N~~~l~~~g~p~~~~~~eIL~~f~~~R~~~~~kR~~~~L~kl~~~r~~i~~~~fi~~~~~d~ii~~~r~~~~~~~~l 386 (445) T smart00434 307 FSINMLALFDNGKPKKYNLKEILKEFLDHRLEVYTRRKEYLLGKLEAERLHILEGLFIALSIIDEIIVLIRSSKDLAKEA 386 (445) T ss_pred CCEEEEEEECCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCHHHHH T ss_conf 15179999769935785259999999999999999999999999999999998869999973465776553687269999 Q ss_pred HHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 78776312697889999974022111222344523699999999987899998887999999899999999988753049 Q gi|254780182|r 414 RRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSS 493 (910) Q Consensus 414 k~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s 493 (910) +..++++ |.+|+.||+|||+|||+|||++|+++|++|+++|.++|++|+++|++ T Consensus 387 k~~l~~~--------------------------~~~s~~q~~yLL~M~L~~LT~~e~~kL~~E~~~l~~ei~~l~~~l~~ 440 (445) T smart00434 387 KELLMER--------------------------FELSEEQADAILDMRLRRLTKLEVEKLEKELKELEKEIEDLEKILAS 440 (445) T ss_pred HHHCCCC--------------------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH T ss_conf 9818866--------------------------79999999999966899872889999999999999999999846869 Q ss_pred HHHH Q ss_conf 8999 Q gi|254780182|r 494 RSRL 497 (910) Q Consensus 494 ~~~l 497 (910) +..+ T Consensus 441 ~~wl 444 (445) T smart00434 441 ELWL 444 (445) T ss_pred HHCC T ss_conf 6544 No 11 >cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth. Probab=100.00 E-value=0 Score=1148.96 Aligned_cols=443 Identities=53% Similarity=0.847 Sum_probs=432.3 Q ss_pred HHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCC Q ss_conf 31375400089736789999999878999998113404255664366887047899999971220111561314788708 Q gi|254780182|r 39 GRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFG 118 (910) Q Consensus 39 ~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~GnfG 118 (910) +|||||+|||||||||||||||++++++++++|+|||++||+|||+||||||+|+|+|||||||+||+|+||++|||||| T Consensus 2 ~RaiP~~~DGlKP~qRkiL~~~~~~~l~~~~~~~Kva~l~G~v~~~~~~HGe~sl~~aiv~mAQ~fsnn~~Ll~~~GnFG 81 (445) T cd00187 2 GRALPDVRDGLKPVQRRILYAMFKRGLTPDKPEKKVARLVGDVAGKYHPHGDSSLYDTIVRMAQDFSNNIPLLDPQGNFG 81 (445) T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCEECCCCCC T ss_conf 87788611488789999999999707988998515510046565046898688999999998676550575331689889 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHH Q ss_conf 87769720135789997899999986307684053306898854850343227321101676101013317898547899 Q gi|254780182|r 119 SVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEV 198 (910) Q Consensus 119 s~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev 198 (910) |++||+||||||||||||+++..||.++|+++|+|+|||||+..||+|||+.+|++|||||+|||||||||||||||.|| T Consensus 82 sr~g~~aAa~RYi~trLs~~~~~lf~~~d~~~l~y~~nyDg~~~EP~~~~p~iP~iLvNGa~GIgtG~sT~IP~hNp~ei 161 (445) T cd00187 82 SRDGDDAAAMRYTETRLSPIARLLLPDIDDPTVDFVPNYDGQEVEPEVLPPIFPNLLVNGSSGIAVGMATNIPPHNLREV 161 (445) T ss_pred CCCCCCCCCHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHCCCCHHHHHCCCEEEEEEECCCCCCCCHHHH T ss_conf 99998321034565320076999864026450335358899736742205433077634661334200056788788999 Q ss_pred HHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHH Q ss_conf 99998876187768888886345866887443447588999987012038999988654336784599992464435289 Q gi|254780182|r 199 VDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKA 278 (910) Q Consensus 199 ~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~ 278 (910) ++|++++|++|+++.++||++++||||||||.|.+.+|+.++|+||+|++++||+|++++.+ ++++|+|||||||++++ T Consensus 162 i~~~~~~i~~~~~~~~~l~~~~~~P~f~~~g~I~~~~~~~~~~~tG~g~~~~rg~~~~~~~~-~~~~I~ITELP~g~~t~ 240 (445) T cd00187 162 IDALRALIDNPEASIDELMEIIKGPDFPTGGIIEGRAGIREAYETGRGRYIIRGKYEIEDDE-GRNTIEITELPYQVNKA 240 (445) T ss_pred HHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCEEECCCCCHHHEECCCCEEEEEEEEEEEECC-CCCEEEEEECCCCCCHH T ss_conf 99998776077765788736788998999946855654012123279738997899998048-86279999558878899 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCCCCEEEEEE-CCCCCCCCHHHH Q ss_conf 9999999998716650144587303746557999947988778999999976101100000024554-166300029999 Q gi|254780182|r 279 AMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQSLFSVNMVALN-GYKPERFTLIGI 357 (910) Q Consensus 279 ~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf~~N~~aL~-~g~P~~l~Lk~i 357 (910) +++|+|++++++||++||+|++|+|+++|+||||++|++++++.++++|||+|+||+||++||+|++ +|+|+.+++.+| T Consensus 241 ~~~e~i~~lv~~kk~~~I~d~~D~st~~~v~~vI~lk~~~~~~~~~~~L~k~tkL~~s~s~Nm~~~~~~g~p~~~~~~eI 320 (445) T cd00187 241 KLKEKIAELVKDKKIEGISDVRDESDREGIRFVIELKRGAMAEVVLNGLYKVTKLQTTFGINMVAFDPNGRPKKLNLKEI 320 (445) T ss_pred HHHHHHHHHHHCCCCCCEEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCHHEEECCEEEEEECCCCEEECCHHHH T ss_conf 99999999862477874665222688772479999779866688999999871501030333899937997755069999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCC Q ss_conf 99999999999999999999999888778999999874069999998618997898787763126978899999740221 Q gi|254780182|r 358 LKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDS 437 (910) Q Consensus 358 L~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~ 437 (910) |++|++||.++++||.+|+|+++++|+|||+|+++++.+||+||++||.|+++.++..+++++ T Consensus 321 L~~f~~~R~~~y~kR~~~~L~kl~~rl~il~~~~~fi~~id~ii~~ir~~~~~k~~l~~~l~~----------------- 383 (445) T cd00187 321 LQEFLDHRLEVYTRRKEYELGKAEARLHILEGLLKAILNIDEVINLIRSSDEAKKALIEELEK----------------- 383 (445) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----------------- T ss_conf 999999999999999999999999999998649999997999999998535179999999876----------------- Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH Q ss_conf 11222344523699999999987899998887999999899999999988753049899999999989999 Q gi|254780182|r 438 SYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSV 508 (910) Q Consensus 438 ~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~ei 508 (910) |+|++.|++|||+|||++||++|+++|++|+++|++++++|+++|+|++++++++++||.|. T Consensus 384 ---------~~~~~~q~dyLL~M~L~~LT~~e~~kL~~e~~~l~~ei~~L~~~l~~~~~~~~~~~~EL~ef 445 (445) T cd00187 384 ---------LGFSEIQADAILDMRLRRLTKLEREKLLKELKELEAEIEDLEKILASEERPKDLWKEELDEF 445 (445) T ss_pred ---------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCC T ss_conf ---------79999999999976699875899999999999999999999998679688999999998509 No 12 >pfam00521 DNA_topoisoIV DNA gyrase/topoisomerase IV, subunit A. Probab=100.00 E-value=0 Score=1083.97 Aligned_cols=423 Identities=54% Similarity=0.849 Sum_probs=411.5 Q ss_pred HCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCC Q ss_conf 13754000897367899999998789999981134042556643668870478999999712201115613147887088 Q gi|254780182|r 40 RAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFGS 119 (910) Q Consensus 40 RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~GnfGs 119 (910) |||||++||||||||||||||++++++++++|+|||++||+|||+||||||+|+|+|||+|||+|++|+||++||||||| T Consensus 1 RaiP~~~DGLKP~qRkil~~~~~~~l~~~~~~~Kva~l~G~v~~~YHpHGe~sl~~tiv~mAQ~f~~n~~Ll~~~GnFGs 80 (428) T pfam00521 1 RAIPDVRDGLKPVQRRILYAMFELGLNLDKKYKKVARLVGDVMGKYHPHGDASIYDALVRMAQDFVGNIPLLDGQGNFGS 80 (428) T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC T ss_conf 99985234787899999999997278889986056433365663568885899999999986763156553216888888 Q ss_pred C-CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHH Q ss_conf 7-769720135789997899999986307684053306898854850343227321101676101013317898547899 Q gi|254780182|r 120 V-DGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEV 198 (910) Q Consensus 120 ~-dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev 198 (910) + +||+||||||||||||+++..||.++|.++|+|+|||||+..||+++|+.+|++|||||+||||||||||||||+.|| T Consensus 81 r~~g~~~AA~RYi~trLs~~~~~if~~~d~~~l~~~~~yDg~~~EP~~y~piiP~iLvNG~~GIgtG~sT~IP~hNp~ei 160 (428) T pfam00521 81 RLDGDKAAAMRYTEARLSKIARELFKDIDKDTVDFVPNYDGSEKEPTVLPPIIPNLLVNGASGIAVGMATNIPPHNLGEV 160 (428) T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHCCCCCCHHHHCCCCCCEEHEECCCCCCCHHHH T ss_conf 88898327788999757499999976426350155057898706751106655676623787301000027788888999 Q ss_pred HHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHH Q ss_conf 99998876187768888886345866887443447588999987012038999988654336784599992464435289 Q gi|254780182|r 199 VDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKA 278 (910) Q Consensus 199 ~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~ 278 (910) ++||+++|++|++++ +..++||||||||.+++.+++.++|+||+|+|++||+|++++ +++|+||||||+++++ T Consensus 161 i~~~~~~l~~~~~~~---~~~~~~P~f~~f~g~i~~~~~~~~y~tG~G~~~~rg~~~i~~----~~~i~ITELP~g~~t~ 233 (428) T pfam00521 161 IDALIALLDGPEITL---LLKIPGPDFPTGGGIIGSGGIREAYKTGRGKITVRAKIEIEE----RKTIVITELPYGVWTE 233 (428) T ss_pred HHHHHHHHCCCCCCC---CCCCCCCCCCCCCEEECCCCHHHHHHCCCCEEEEEEEEEEEC----CCEEEEEECCCCCCHH T ss_conf 999999853997223---575789979998624566116777643883599987999940----5269999447777899 Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHH Q ss_conf 99999999987166501445873037465579999479887789999999761011000000245541663000299999 Q gi|254780182|r 279 AMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQSLFSVNMVALNGYKPERFTLIGIL 358 (910) Q Consensus 279 ~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL 358 (910) +++|+|+++++++|+++ +|+||+||+ |+||||++|++++++.++++|||+|+||+||++||++|.|++|+.+++++|| T Consensus 234 ~~~e~l~~l~~~~ki~~-~di~D~Sd~-~vr~vI~lk~~~~~~~~~~~L~k~~kL~~s~s~nnm~l~d~~pk~~s~~eIL 311 (428) T pfam00521 234 KLIESIEELVKNGKIKG-SDIRDESDR-GVRIVIELKRGADPEVVLNKLYKKTKLQSSFSTNNLVLFDGGPKYLNLKEIL 311 (428) T ss_pred HHHHHHHHHHHCCCCCC-CCCCCCCCC-CEEEEEEECCCCCHHHHHHHHHHHHHHHEECCCEEEEEECCCCCHHHHHHHH T ss_conf 99999999984588787-731016788-5679998578765678999999863001004637999967987374299999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCC Q ss_conf 99999999999999999999998887789999998740699999986189978987877631269788999997402211 Q gi|254780182|r 359 KAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSS 438 (910) Q Consensus 359 ~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~ 438 (910) ++|++||.++++||++|+|+++++|+|||+||++|++++|+||++||+|.+...||..|+++ T Consensus 312 ~~f~~~R~~~y~kR~~~~l~kl~~~l~iL~gl~~~~~~idfIi~iI~~s~~~~~~k~~L~~~------------------ 373 (428) T pfam00521 312 KEFLEHRLEVYKRRKEYLLEKLEERLHILEGLLKALNKIDFVIEVIRGSIDLNKAKKELIEE------------------ 373 (428) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH------------------ T ss_conf 99999999999999999999999999999889999984999999997689616899999997------------------ Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH Q ss_conf 1222344523699999999987899998887999999899999999988753049899999 Q gi|254780182|r 439 YTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLG 499 (910) Q Consensus 439 ~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~ 499 (910) |++.|++|||+|||++||++|.++|++|+++|.+++++|+++|+|++.+|. T Consensus 374 ----------L~~~q~dyLL~m~L~~LT~~e~~kL~~e~~~l~~ei~~l~~~l~s~~~lw~ 424 (428) T pfam00521 374 ----------LSEIQADYLLDMRLRRLTKEEIEKLEKEIEELEKEIAELEKILASEKKLWI 424 (428) T ss_pred ----------CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH T ss_conf ----------489989999976899872889999999999999999999977389999988 No 13 >PRK12758 DNA topoisomerase IV subunit A; Provisional Probab=100.00 E-value=0 Score=887.31 Aligned_cols=695 Identities=25% Similarity=0.372 Sum_probs=525.5 Q ss_pred CCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCC Q ss_conf 87643235666009999987678777998863137540008973678999999987899999811340425566436688 Q gi|254780182|r 8 SDEEEEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHP 87 (910) Q Consensus 8 ~~~~~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHP 87 (910) ++++....+.+ +..--+.+||+||+|||.+||+|+++||||||||||||+|++|. |..|.|+|+|||++| +||| T Consensus 14 ~~~~~~~~~~~--~~gmy~~wfldYasyvil~RAvp~i~DGlKPvqRril~sm~~~~---dgr~~KvAnivG~tm-~yhP 87 (879) T PRK12758 14 PENEPIHDTTH--VGGMYQNWFLDYASYVILERAVPHIEDGLKPVQRRILHSMKRLD---DGRYNKVANIVGHTM-QYHP 87 (879) T ss_pred CCCCCCHHEEE--CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHH---CCCCCEEEEECCCCC-CCCC T ss_conf 76664010245--01347888887768653352056400278538999999998610---776302320102320-2488 Q ss_pred CCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEE Q ss_conf 704789999997122011156131478870887-7697201357899978999999863076840533068988548503 Q gi|254780182|r 88 HGNAAIYDALARMAQDWSLRLLLIEGQGNFGSV-DGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVV 166 (910) Q Consensus 88 HGd~siy~a~v~maq~~~~r~plidg~GnfGs~-dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~v 166 (910) |||+|||||||.|+| +..|||+|||||++ +||+|||+||+|||||++|.+++ .+++|++|.++|||+.+||++ T Consensus 88 HGdasi~dalv~~~q----k~~lid~qGN~Gni~tgd~aaA~RYiE~rls~fa~ev~--fn~~~t~~~~sYDgr~kEP~~ 161 (879) T PRK12758 88 HGDASIGDALVQLGQ----KDLLIDCQGNWGNILTGDGAAAPRYIEARLSKFALEVL--FNPKTTEWQLSYDGRKKEPVT 161 (879) T ss_pred CCCCHHHHHHHHHHC----CCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHE--ECCCCCEEEECCCCCCCCCCC T ss_conf 874238999998624----33368647776676878722314467564207779870--387755345456876578642 Q ss_pred CCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCC- Q ss_conf 4322732110167610101331789854789999998876187768888886345866887443447588999987012- Q gi|254780182|r 167 LCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGR- 245 (910) Q Consensus 167 lP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGr- 245 (910) ||++||+||++|+.||||||||+|+|||+.|+|+|+++++++..+++- |||||||++- ..-|..|+ T Consensus 162 lP~kfPllL~~g~eGIAVGlstkilphNf~El~~a~i~~l~~~~~~l~--------PDF~tgG~~d-----~s~YndG~r 228 (879) T PRK12758 162 LPVKFPLLLAQGVEGIAVGLSSKILPHNFNELIDASIAYLRGEEFKLY--------PDFQTGGSID-----VSNYNDGER 228 (879) T ss_pred CCCCCHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEC--------CCCCCCCEEC-----HHHHHCCCC T ss_conf 552116777616762685001464887889999999999759985488--------7898875405-----645104445 Q ss_pred -CEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHH Q ss_conf -0389999886543367845999924644352899999999998716650144587303746557999947988778999 Q gi|254780182|r 246 -GSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVIL 324 (910) Q Consensus 246 -G~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vl 324 (910) |++++|||++..+ ++.|||+||||++++++||++|..+.+.+||. |..|.|.+..+ +-|.|.|.+|.+|+..+ T Consensus 229 gG~v~vRaki~~~d----~~tl~I~eiP~g~tt~sLi~SI~kAn~kGKIK-Ikki~DnTa~~-VEI~i~L~~Gvs~dkti 302 (879) T PRK12758 229 GGRVKVRAKINKLD----NKTLVITEIPYGTTTSSLIDSILKANDKGKIK-IKKVDDNTAAD-VEILVHLAPGVSSDKTI 302 (879) T ss_pred CCEEEEEEEEEEEC----CCEEEEEECCCCCCHHHHHHHHHHHHHCCCCC-EEEECCCCCCC-EEEEEECCCCCCHHHHH T ss_conf 85489999999805----96699985499875799999999998759711-46632467774-06999838999878989 Q ss_pred HHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHH Q ss_conf 9999761011000000245541663000299999999999999999999999999988877899999987406---9999 Q gi|254780182|r 325 NQLYRYTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANL---DEVV 401 (910) Q Consensus 325 n~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nI---DeVI 401 (910) ..||++|+||+|.|.|.++|.|++|..+++.++|+.-.+|-.+.+++..+.+|.+.++++|-- .|+.| .+|. T Consensus 303 daLYAFTdCEvSISPn~cVI~dnkP~fl~VseiLk~std~t~~LLk~ELei~l~eLeekwH~~-----SLErIFIEnRIY 377 (879) T PRK12758 303 DALYAFTDCEVSISPNCCVIDDDKPHFLGVSEVLRISTDRTLDLLKQELEIQLEELLEQLHFA-----SLEKIFIEERIY 377 (879) T ss_pred HHHHHHCCCEECCCCCEEEEECCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHH T ss_conf 987630356220587649998994438428999999999999999999998899999999999-----899999775651 Q ss_pred H--HHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9--98618997898787763126978899999740221112223445236999999999878999988879999998999 Q gi|254780182|r 402 R--IIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNS 479 (910) Q Consensus 402 ~--iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~e 479 (910) + -|..+++-+++-..+-+. +.+...... -..++.-..-.+++|.+|.++.+.+|-+++++. T Consensus 378 rd~~IEe~~t~E~Vi~~I~~g---------L~Pf~~~L~--------ReVt~eDI~rLtEIkIkRISkFDidKa~e~I~~ 440 (879) T PRK12758 378 KDKEFEESETWEDALLHIDDR---------LEPFKKQFI--------REVTEDDILRLTEIKMKRILKFNSDKAEELIAR 440 (879) T ss_pred CCCHHCCCCCHHHHHHHHHHH---------HHHHHHHHC--------CCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHH T ss_conf 440003556899999999999---------999888633--------788889999986313777554187889999999 Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCC--CCCCEEECCCCCCCC-CCCCCCCCEEEEEECCCEECCCCCCCC Q ss_conf 99999988753049899999999989999984056--883310013434530-101456781899907970523310000 Q gi|254780182|r 480 LGIEIKECLDILSSRSRLLGIIKQELLSVKDELDT--PRRTRIVEGLLDMED-EDCIVREDMVVTVSHLGYVKRVPLSVY 556 (910) Q Consensus 480 L~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd--~RRT~I~~~~~~i~~-EdlI~~E~vvV~lS~~GyIKr~~~~~y 556 (910) |.++|++.+.-|++ +...-++-++.|+++||. ||||+|...+. ++. .-.+.++ .=|+-|- T Consensus 441 le~~I~eVk~nL~n---lt~YaI~yf~~LkkKYGkg~~RKTEI~~Fd~-I~A~kVa~~N~--------KLYvNRe----- 503 (879) T PRK12758 441 LEEDIAEVEHHLEH---IIDYTIAWFTMLKEKYGKGFPRRTELRNFDT-IEATKVVEANE--------KLYINRE----- 503 (879) T ss_pred HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHCCCCCCCCEEEECCC-EEHHHHHHHHC--------EEEEECC----- T ss_conf 99999999988887---8999999999999986699976403410031-52777735317--------7998245----- Q ss_pred CCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEE--EECCCCCCEEEEE Q ss_conf 02334565211000146410101133237773999954893999820004322444565541245--4536556200256 Q gi|254780182|r 557 RAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINI--LSLNQGERITTIM 634 (910) Q Consensus 557 r~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nl--l~l~~~E~I~ail 634 (910) -|..|+++|.+. +++.|+.-|.+++|+..|++-..++-+ ..--|+.|... ++-.+...|-.|+ T Consensus 504 -------eGFiGt~lKkdE---fv~dCSdiDDIIvF~kDG~~~VtKV~d-----K~FVGKdIihv~vfkK~D~rtiYN~I 568 (879) T PRK12758 504 -------EGFIGTGLKKDE---FVADCSDIDDVIVFYRDGKYMVTKVAD-----KKFVGKDIIYVAVFKKNDKRTIYNVI 568 (879) T ss_pred -------CCEECCCCCCCC---EEEECCCCCEEEEEECCCCEEEEECCC-----CEEECCCCEEEEEEECCCCCEEEEEE T ss_conf -------661101324774---443035712289992388589998167-----44533675799975058873288999 Q ss_pred EECCCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEE-EECCCCEEEEEEE-CCCCCEEEEEE----CCCEEEEE Q ss_conf 630125666871799994799189842368620477722786-6158985788896-18982699993----69859997 Q gi|254780182|r 635 PFPEDESSWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAM-KLDSRDEILSVET-CTQENDILLTT----KLGQCVRF 708 (910) Q Consensus 635 ~~~~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~ai-kLkegD~Li~v~~-~~~~~~Iil~T----~~G~~lrF 708 (910) +++-+ +..-++||.....+.. ....-+ +=.+|-++..... -+|+.+++-+. ..-+-+.| T Consensus 569 -YrDGk-----------~g~syiKRF~VtgvtR---Dk~Y~lt~g~~gSkvlYfsaNpNGEAE~V~v~Lr~~~~~kkl~~ 633 (879) T PRK12758 569 -YRDGK-----------SGPSYIKRFNVTGVTR---DKEYDLTQGTPGSRVLYFSANPNGEAEVVTVTLKPNPRIRKLVF 633 (879) T ss_pred -EECCC-----------CCCEEEEEEECCCEEE---CCCCCCCCCCCCCEEEEEECCCCCCEEEEEEEECCCCCCCCEEE T ss_conf -97388-----------8856557631241431---34024667999988999951899862689999645855341564 Q ss_pred E--HHHCCCCCCCCCCCEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf 5--87623547866553576752899869998973366654200000122233333334555444444443332222232 Q gi|254780182|r 709 P--ISAIRVFAGRNSVGVRGISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNIS 786 (910) Q Consensus 709 ~--~~evr~~~GR~a~GVkgIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 786 (910) + -+++. ..||.|+|...-|-.= -+| . ......+.......|.++.......+. T Consensus 634 d~DFsdi~-IKGR~skGNivTK~~V-~kI-~----------------------lKe~G~STL~~RKIWFD~~V~RLN~d~ 688 (879) T PRK12758 634 EKDFSEIA-IKGRQSQGNILTKYPV-HKI-E----------------------LKQKGGSTLGGRKVWFDRDVLRLNYDG 688 (879) T ss_pred ECCHHHHH-CCCCCCCCEEEECCCE-EEE-E----------------------EECCCCCCCCCEEEEECCCCCCCCCCC T ss_conf 13677710-0144556516750320-267-4----------------------101475555771576346423015466 Q ss_pred CHHHHCCCCCCCEEEEEECCCCEEEEEHHHCCCCCCCCCCEEEE Q ss_conf 00111012568679999759934530178848667577414887 Q gi|254780182|r 787 EERCQELKLKEQFILTVSEKGFGKRTSSYDFRISNRSGKGIRAT 830 (910) Q Consensus 787 ~e~~~~~~~~~~~IL~vTe~G~GKRt~~~eyr~q~RGgkGv~~i 830 (910) ...+......+..||+++.+|--+.+. |-+.+|-.-.+..+ T Consensus 689 RG~lLGeF~~dD~iLvi~~~G~~~~~~---~dls~hfd~d~i~l 729 (879) T PRK12758 689 RGEYLGEFQSDDRILVILQNGEFYTTN---FELTNHYDPNMIVI 729 (879) T ss_pred CCCEEEECCCCCEEEEEECCCEEEECC---CCHHCCCCCCCEEE T ss_conf 653650027886699995488189815---30312588773699 No 14 >PTZ00108 DNA topoisomerase II; Provisional Probab=100.00 E-value=2.8e-45 Score=423.59 Aligned_cols=468 Identities=21% Similarity=0.333 Sum_probs=349.1 Q ss_pred CCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHH--CCCCCCC Q ss_conf 32356660099999876787779988631375400089736789999999878999998113404255664--3668870 Q gi|254780182|r 12 EEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVM--GKYHPHG 89 (910) Q Consensus 12 ~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~--gkyHPHG 89 (910) .+.....+++.+-+.+..+-|||+= ..|++|.+.|||||.||.|||+++.-++ +.-.|+|..+|.|- ..|| || T Consensus 721 ld~~~~~i~~~dFinkELi~FS~~D-~~RSIPs~~DGlKp~QRKvl~~~fkrn~---~~eiKVaQlaGyVse~saYH-HG 795 (1506) T PTZ00108 721 VDHKEKDLSYYDFVNKELIYYSRYD-TERSIPNIMDGWKPGQRKVLYGCFKRNL---KNECKVAQLVGYIAEHSAYH-HG 795 (1506) T ss_pred CCCCCCCCCHHHHHHHHHHHCCHHH-HHHHCCHHHCCCCHHHHHHHHHHHHHCC---CCCEEHHHHHHHHHHHCCCC-CC T ss_conf 3566785438774437888642887-6512411330577124424498786347---76223215088987630467-63 Q ss_pred HHHHHHHHHHHCCCH--HCCCCCCCCCCCCCCC--CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCE Q ss_conf 478999999712201--1156131478870887--769720135789997899999986307684053306898854850 Q gi|254780182|r 90 NAAIYDALARMAQDW--SLRLLLIEGQGNFGSV--DGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPV 165 (910) Q Consensus 90 d~siy~a~v~maq~~--~~r~plidg~GnfGs~--dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~ 165 (910) ++|...|+|.|||+| |++.+|+.+-|+|||. .|.-+||+||+.++|++++..++..-|.....|. +=||...||+ T Consensus 796 E~SL~~tIv~mAQ~fvGsNNinlL~P~GqFGtR~~GGkDaas~RYIfT~l~~~~r~iF~~~Dd~lL~y~-~ddg~~iEP~ 874 (1506) T PTZ00108 796 ESSLQQTIINMAQTFVGSNNINFLEPCGQFGSRKEGGKDASAARYIFTKLASSTRSIFNEYDDPILKYL-NEEGQKIEPQ 874 (1506) T ss_pred HHHHHHHHHHHHHHCCCCCCHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHHCCCCCHHHHHCC-CCCCCCCCCC T ss_conf 899999999998753565663104557875254558875556025766315888853893302255020-3689631543 Q ss_pred -ECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHC Q ss_conf -3432273211016761010133178985478999999887618776888888634586688744344758899998701 Q gi|254780182|r 166 -VLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATG 244 (910) Q Consensus 166 -vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tG 244 (910) ++|. +|.+||||+.||++||+|+|||||+.||++.+..+|+..+.. .+.-+-+| | +|-+ .++| T Consensus 875 ~Y~Pi-iPmvLvNG~~GIGTGwSt~ip~ynp~dii~ni~r~l~ge~~~--~m~Pwy~g--f-~G~i----------~~~~ 938 (1506) T PTZ00108 875 YYIPV-IPTILVNGCEGIGTGYSSFIPNYNYKDIIDNIKRYINKEPLI--PMIPWYKD--F-KGRI----------ESNG 938 (1506) T ss_pred EECCC-CCEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCC--CCCCCCCC--C-CCEE----------EECC T ss_conf 02055-667873377620266347789999999999999985699886--27755379--6-2169----------9868 Q ss_pred CCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHH Q ss_conf 20389999886543367845999924644352899999999998716650144587303746557999947988778999 Q gi|254780182|r 245 RGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVIL 324 (910) Q Consensus 245 rG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vl 324 (910) .+++++.|.++.. +.+.|.|||||-.+-....-|.+..++.+++-+-|.|.+++++-..++++|.+....-.+..- T Consensus 939 ~~~y~~~G~~~~~----~~~t~~ItELPi~~WT~~yKe~le~~~~~~~~~~i~d~~e~~t~~~V~F~i~~~~~~~~~~~~ 1014 (1506) T PTZ00108 939 KTGYETIGIIHKI----DDDTLEINELPIKKWTQDYKEFLEELLTDEKHQLILDYIDNSSHEDICFTIKMDPAKLKKAEE 1014 (1506) T ss_pred CCEEEEEEEEEEE----CCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHCCCCCEEEEEEEECHHHHHHHHH T ss_conf 9718998799995----798799985898762699999999875046777400004317997589999958899899876 Q ss_pred HHHHHHCCHHCCCCC-EEEEEE-CCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHH Q ss_conf 999976101100000-024554-166-300029999999999999999999999999998887789999998740-6999 Q gi|254780182|r 325 NQLYRYTSLQSLFSV-NMVALN-GYK-PERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVAN-LDEV 400 (910) Q Consensus 325 n~Lyk~T~Lq~sf~~-N~~aL~-~g~-P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~n-IDeV 400 (910) .-|.+.-.|+++++. ||++.. .|+ -+--+..+||++|...|.+...+|-.|.|.+.+..+.+|+--..-+.. ||. T Consensus 1015 ~gl~k~fKL~~~i~t~Nm~~Fd~~g~i~kY~~~~~Il~eF~~~Rl~~Y~kRK~~l~~~l~~~~~~l~nqaRFI~~vi~~- 1093 (1506) T PTZ00108 1015 EGLEKVFKLKSTLTTTNMTLFDPNLKLQRYSTELDILKDFCFHRLKAYENRKSYLISKLEKEKKIISNKSKFILAIVNN- 1093 (1506) T ss_pred HCHHHHHCCCCEEEECCEEEECCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC- T ss_conf 0666651123134205268988999966459999999999999999999999999999999999864255656640067- Q ss_pred HHHHHHCCCHHHHHHHHHHHCCCHHH-HHHHH-HHC-------CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99986189978987877631269788-99999-740-------2211122234452369999999998789999888799 Q gi|254780182|r 401 VRIIRFSPNPETARRELMQRSWNASD-IKDLI-DLI-------DDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRD 471 (910) Q Consensus 401 I~iIR~S~d~~eAk~~L~~~~~~~~~-~~~~~-~~~-------~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~ 471 (910) +++=+-+.+++--..|.++.|..-. ..... ... .....+......-+++..--+++|.|+|..||.--.+ T Consensus 1094 -~l~v~nkkk~~li~eL~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ydYLL~M~iwsLT~Er~~ 1172 (1506) T PTZ00108 1094 -ELIVNKKKKKVLVEELYRKGYDPYKDINKIKKEEIFEQELLDAADNPEDNEEIIAGISVKDYDYLLSMPIFSLTLEKVE 1172 (1506) T ss_pred -EEEEECCCHHHHHHHHHHCCCCCCCCHHHHHHHCCCHHHHHCCCCCCCCCHHHCCCCCCCCCHHHHCCCHHHCCHHHHH T ss_conf -5899357689999999974999774112433301000221012235544201014677678436638812320099999 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC Q ss_conf 99998999999999887530498999999999899999840 Q gi|254780182|r 472 DIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDEL 512 (910) Q Consensus 472 kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~ky 512 (910) +|..+.++..++.+.|... +++.+|.- +|.++-+.| T Consensus 1173 ~L~~~~~~k~~El~~L~~~--s~~dlW~~---DLd~fee~~ 1208 (1506) T PTZ00108 1173 DLLAQHKEKEKELEILKNI--TVETMWLK---DIEKVEEAI 1208 (1506) T ss_pred HHHHHHHHHHHHHHHHHCC--CHHHHHHH---HHHHHHHHH T ss_conf 9999999999999999768--98999999---999999999 No 15 >KOG0355 consensus Probab=100.00 E-value=2.6e-42 Score=397.72 Aligned_cols=752 Identities=11% Similarity=-0.035 Sum_probs=579.7 Q ss_pred CCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCH Q ss_conf 43235666009999987678777998863137540008973678999999987899999811340425566436688704 Q gi|254780182|r 11 EEEKGITSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGN 90 (910) Q Consensus 11 ~~~~~i~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd 90 (910) ..+-+++++.|..|-...++-|+-++|-.|+.|+.+++++|+++++|++|+..+-...|++.+|++.++.+.+.+|||++ T Consensus 71 d~~m~~i~v~i~~e~~~isv~nnGkGIPv~~H~~ek~yvpelifg~Lltssny~d~ekK~tggrngygakLcniFs~~f~ 150 (842) T KOG0355 71 DPKMNTIKVTIDKEKNEISVYNNGKGIPVTIHKVEKVYVPELIFGNLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFT 150 (842) T ss_pred CCCCCEEEEEECCCCCEEEEEECCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCCCCE T ss_conf 87765268887167767999957972131223422245347887664411567887543236777502034321145403 Q ss_pred HHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH-HHHHHCCCCCCCCEECCCCCCCCCEECCC Q ss_conf 78999999712201115613147887088776972013578999789999-99863076840533068988548503432 Q gi|254780182|r 91 AAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAH-FLLDDLGKDTVDFRPNYDGSFQEPVVLCA 169 (910) Q Consensus 91 ~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~-~~l~~i~~~tv~~~~n~D~~~~EP~vlP~ 169 (910) ..+||..++|||-++.+-++.-+|++|++.+.|++ ||+||++|-.+ ..+.++|.|||+++.+++-...+|. +|+ T Consensus 151 ~Et~d~~~~~~~kQ~w~~nm~~~~~~~i~~~~~~~----yTkitF~PDl~~F~m~eLD~Div~l~~rr~~d~a~~~-~~v 225 (842) T KOG0355 151 VETADREYKMAFKQTWINNMTRDEEPKIVPSTDED----YTKITFSPDLEKFKMKELDDDIVALMARRAYDLAGSV-KSV 225 (842) T ss_pred EEEEEHHHHHHHHHHHHCCCCCCCCCEEECCCCCC----CCEEEECCCHHHCCCHHHCCHHHHHHHHHHHHHCCCC-CCE T ss_conf 65300677778777652687656786552258999----5369968476752722322318876776666523442-121 Q ss_pred CCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEE Q ss_conf 27321101676101013317898547899999988761877688888863458668874434475889999870120389 Q gi|254780182|r 170 RYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIV 249 (910) Q Consensus 170 ~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~ 249 (910) ++|..+-|++++++++||+++|| |+ -.+..+.+|.++...--|+.-...-++|++ +..........+-|+.+-++ T Consensus 226 kv~ln~~~~~~~~f~~yv~~~~~-~~--~~~~~~~~ihe~~~~RwEv~~a~s~~~fqq--isfvNsI~T~kGGThVd~V~ 300 (842) T KOG0355 226 KVELNGKNIPVKGFYDYVKMYLE-VL--WLNDDLKPLHEVLNFRWEVALALSDVGFQQ--VSFVNSIATTKGGTHVDYVV 300 (842) T ss_pred EEEECCCCCCCHHHHHHHHHCCC-CC--CCCCCCHHHHCCCCHHHHHHHHHCCCCCCE--EEEECCCEECCCCCCCCHHH T ss_conf 56516887752017788762353-22--246752222004324888865504466533--54200101047986544166 Q ss_pred EEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHH Q ss_conf 99988654336784599992464435289999999999871665014458730374655799994798877899999997 Q gi|254780182|r 250 IRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASADVILNQLYR 329 (910) Q Consensus 250 iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk 329 (910) -+.+..+++.-..++.-.++++||+.+|+.|.-.|..++.+...++.++.++.++..+.+.+.+|+....+...++. +- T Consensus 301 D~iv~~l~~vvkKk~~~~~~svk~f~vkn~L~vfVN~lIENPtFesQTke~lt~~~~~fgs~~elsek~~k~~~~~~-i~ 379 (842) T KOG0355 301 DQIVAKLIDVVKKKKVKKDISVKPFQVKNHLWVFVNCLIENPTFESQTKERLTLRPKRFGSDCELSEKFTKAIELKG-VV 379 (842) T ss_pred HHHHHHHHHHHCCCCCCCCCCCCHHHHHCCEEEEEEEEECCCCCCCCCHHHCCCCCCCCCCEEEEHHHHHHHHHHCC-HH T ss_conf 55777888874211346654446453303569999887427663443310126663454326763167799998676-49 Q ss_pred HCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 61011000000245541663000299999999999999999999999999988877899999987406999999861899 Q gi|254780182|r 330 YTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPN 409 (910) Q Consensus 330 ~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d 409 (910) .+-+|.++++++..|.+++|+.++..+-+..+.+.+....+ +..+-..-+.++-|..++-+-.+...++.+--|=- T Consensus 380 esils~s~~~~~~dL~kk~~~~~s~~e~I~KleDa~~ag~k-~s~kctlIltEgdsaksLavsGl~vvgRd~~gVfp--- 455 (842) T KOG0355 380 ESILSKSLNKYKDDLAKKRGKLTSRSKGIPKLEDANDAGTK-TSEKCTLILTEGDSAKSLAVSGLSVVGRDYYGVFP--- 455 (842) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCC-CCCCEEEEEECCCCCHHHEECCCCCCCEEEEEECC--- T ss_conf 99999888889876544434443320130676523324434-55431688861552033201355546604675501--- Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 78987877631269788999997402211122234452369999999998789999888799999989999999998875 Q gi|254780182|r 410 PETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLD 489 (910) Q Consensus 410 ~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~ 489 (910) ++..|.+ .........+...|++||+..=..++++.+.. .|--.+-+.|-.... T Consensus 456 ---lrgklLN--------------------v~e~s~kqilkn~EI~aIikIlgl~~~~~y~~---~eslryg~~mimtDQ 509 (842) T KOG0355 456 ---LRGKLLN--------------------VREASHKQILKNAEINAIIKILGLQYKKKYFD---VESLRYGKLMIMTDQ 509 (842) T ss_pred ---CCCCHHH--------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC---CCCCCHHHEEEEECC T ss_conf ---1231344--------------------57777988877999999999998877533133---122242224665123 Q ss_pred HHCCHHHHHHHHHHH-HHHHHHHCCCCCCCEEECCCC-CCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCC Q ss_conf 304989999999998-999998405688331001343-453010145678189990797052331000002334565211 Q gi|254780182|r 490 ILSSRSRLLGIIKQE-LLSVKDELDTPRRTRIVEGLL-DMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRS 567 (910) Q Consensus 490 IL~s~~~l~~iI~~E-L~eik~kygd~RRT~I~~~~~-~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~ 567 (910) .-|-+.+..+|++- ..+....|..| -|++... .+..++-++++. ..|-.+|.|+....++ .|+++-|+.+ T Consensus 510 -d~dgshikgllInf~~~~~psl~~~~---fleefitpi~k~~~~~~~~~---fys~pey~kw~~~~~~-~~~~~ikyyk 581 (842) T KOG0355 510 -DHDGSHIKGLLINFIHHFWPSLLQIP---FLEEFITPIVKATKGKQEVS---FYSLPEYEKWKKNTDN-WKSWKIKYYK 581 (842) T ss_pred -CCCCCHHHHHHHHHHHHHHHHHHCCC---CHHHCCCCCEEECCCCCCEE---EECCHHHHHHHHCCCC-CCCCCEEEEE T ss_conf -45643477788988987658863587---42104776457404774314---5445657888754844-2442237751 Q ss_pred CCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCE Q ss_conf 00014641010113323777399995489399982000432244456554124545365562002566301256668717 Q gi|254780182|r 568 GVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGKALINILSLNQGERITTIMPFPEDESSWNNLY 647 (910) Q Consensus 568 ~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~ 647 (910) |..+...|.....|.|..|+.++||.+.|..+....+.+|..++.+++++|.++.+...+ +.+..+++++|- +.+ T Consensus 582 glgts~~~e~keyf~~~~~h~~~F~~~~~~d~~~i~~af~k~k~~~rk~wL~~~~~~~~~-~~~~~v~~sdf~----~el 656 (842) T KOG0355 582 GLGTSTSKEAKEYFSDLDRHRILFKYDGGIDDEAIDMAFSKKKIDARKEWLRKYMPEYLY-KTTKFVTISDFV----KEL 656 (842) T ss_pred CCCCCCHHHHHHHHHCHHHHEEEEECCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHCC-CCCCEEEHHHHH----HHH T ss_conf 477454789999861600123787525750477886422310066677689986566413-665255789999----999 Q ss_pred EEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEE Q ss_conf 99994799189842368620477722786615898578889618982699993698599975876235478665535767 Q gi|254780182|r 648 VVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGI 727 (910) Q Consensus 648 Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgI 727 (910) ++|.+.+ -|+.+...-+..+|+.+..++++.+++|+-.|+++.-.+.+.....+++.+.-.+-.++. ...| T Consensus 657 ilf~~~~-sIp~~~dglkpgqRkv~~~~~k~n~~~E~Kv~ql~g~v~~~s~yhhge~sl~~ti~~l~q----~~~g---- 727 (842) T KOG0355 657 ILFSNAD-SIPSLVDGLKPGQRKVLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQSLMSTIVNLAQ----DFVG---- 727 (842) T ss_pred HHHHHCC-CCHHHHHCCCCCCHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHCCCHHHHHHHHHHHH----HHCC---- T ss_conf 9987215-207677235866223346767644766255433024788888774342769999998887----5058---- Q ss_pred ECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEECCC Q ss_conf 52899869998973366654200000122233333334555444444443332222232001110125686799997599 Q gi|254780182|r 728 SLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVSEKG 807 (910) Q Consensus 728 kL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G 807 (910) .| + +.+. |. . + .....-.......++.|+.-++| T Consensus 728 ----kd----a-----a~~r------yi-----~--------------------t--~l~~~tr~~f~~~dd~ll~~~~~ 761 (842) T KOG0355 728 ----KD----A-----ASAR------YI-----F--------------------T--KLSPLTRLLFPPADDLLLKYLNE 761 (842) T ss_pred ----CC----C-----HHHH------HH-----H--------------------H--HCCHHHHHCCCCCCHHHHHHHCC T ss_conf ----84----0-----2367------89-----8--------------------8--52736540278883267665225 Q ss_pred CEEEEEHHHCCCCCC-----CCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEE Q ss_conf 345301788486675-----774148876067777686899997289964999945998999990105544515687388 Q gi|254780182|r 808 FGKRTSSYDFRISNR-----SGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVI 882 (910) Q Consensus 808 ~GKRt~~~eyr~q~R-----GgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i 882 (910) +|+|++.+ |+.--- |+.|+= +|- ..-.++-+..||+.....+..-+ ++.+++++.|...|..- T Consensus 762 ~~~~vep~-y~pi~p~vlvngaegiG---------tGw-s~~i~n~n~~~iv~~~r~~~~~~-~~~~~~p~yr~frg~i~ 829 (842) T KOG0355 762 DGQRVEPE-YCPIIPMVLVNGAEGIG---------TGW-STFIPNYNPREIVKNIRRLINGE-PPKAMAPWYRNFRGTIE 829 (842) T ss_pred CCCCCCCC-CCCCEEEEEEECCCCCC---------CCC-CCCCCCCCHHHHHHHHHHHHCCC-CCCCCCCHHHHCCEEEE T ss_conf 78671752-24414688850565455---------676-56688889899999998863699-85217803520442799 Q ss_pred E Q ss_conf 9 Q gi|254780182|r 883 F 883 (910) Q Consensus 883 ~ 883 (910) . T Consensus 830 ~ 830 (842) T KOG0355 830 V 830 (842) T ss_pred E T ss_conf 9 No 16 >PRK13979 DNA topoisomerase IV subunit A; Provisional,Validated Probab=99.94 E-value=4.9e-24 Score=234.12 Aligned_cols=240 Identities=21% Similarity=0.286 Sum_probs=162.0 Q ss_pred CCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCE---EEEEECCCCEEEEECCCCCCCCCC Q ss_conf 78189990797052331000002334565211000146410101133237773---999954893999820004322444 Q gi|254780182|r 536 EDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTS---VLFFSSLGFVYKEKVWRLPIGSPQ 612 (910) Q Consensus 536 E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~---LLfFTs~Gkvy~l~v~~IP~~sr~ 612 (910) ...++..|+.|+|||++++.|+. +|+| ..+++++++|.+..+..|...+. +++.|..|.++...--++...+|+ T Consensus 622 ~~~lvfaTk~G~VKKt~L~~f~~-~~sg--iiAIkL~egDeLI~V~l~~~~~~~~~i~l~T~~G~~irf~e~~vR~mGR~ 698 (959) T PRK13979 622 QKDFIFITDSGGIKKTSLDKFNT-NYSK--LMALKLKKGEELIKVKLVDRTREEKFLKIKTKKGLSFTVEEPELEPVDRN 698 (959) T ss_pred CCEEEEEECCCEEECCCHHHCCC-CCCC--CEEEECCCCCEEEEEEEECCCCCCEEEEEECCCCEEEECCCHHCCCCCCC T ss_conf 75499992898688373898285-5678--36666699987987897358887507999658965997142022457876 Q ss_pred CCCCC--------------------------------------------------------------------------- Q ss_conf 56554--------------------------------------------------------------------------- Q gi|254780182|r 613 ARGKA--------------------------------------------------------------------------- 617 (910) Q Consensus 613 skG~p--------------------------------------------------------------------------- 617 (910) +.|.- T Consensus 699 a~GVrgi~L~~~D~Vvsm~i~~~~e~~~~~~~i~~~g~i~~~~~~~~~~~~~~~~~~~~~ili~~~~G~~~~~~~~~~~~ 778 (959) T PRK13979 699 ILGYQLFNLSPNDSIKKVDFCDNYEYKEFYININKKGIIKISDLKKNKSHISLKTNSSKNLLLFSDKGKVYKIPAFMLQN 778 (959) T ss_pred CCCEEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEECCCCCEEECCHHHCCC T ss_conf 66752143399998986102244420000023342002332210011111111356631135432577233032432023 Q ss_pred -------CEEEEE-CCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEE Q ss_conf -------124545-365562002566301256668717999947991898423686204777227866158985788896 Q gi|254780182|r 618 -------LINILS-LNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVET 689 (910) Q Consensus 618 -------i~nll~-l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~ 689 (910) +..+.. +..+|.|++++++..+ .++.+++.+|++|++|||++.+|....+.|+....-.+.|.++++.. T Consensus 779 ~~~~g~~i~~~~~~~~~~e~vi~~~~~~~~---~e~~~il~vTe~G~GKRT~~~eyr~~g~~~~~~k~~~~~~~~v~~~~ 855 (959) T PRK13979 779 IEESGINISALTGDFEKKESIINAISIFEF---EEDLSIYFFSKKGLVKKTLLSEFKGEGNSTQVYKFKHKEDELVSVDI 855 (959) T ss_pred CCCCCCCCHHHHHHHCCCCCEEEEEECCCC---CCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEEEEECCCCEEEEEE T ss_conf 355564502222121022302466520357---77615999935897466656773346786489998844897899997 Q ss_pred -CCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCC Q ss_conf -1898269999369859997587623547866553576752899869998973366654200000122233333334555 Q gi|254780182|r 690 -CTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGD 768 (910) Q Consensus 690 -~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~ 768 (910) ..++++|+++|++|+++||+.+++|.+ ||+|+||++|+|+++|+||++.++.+.+. T Consensus 856 ~~~~~d~imliT~~G~~IR~~v~~I~~~-GR~tqGV~li~L~~~dkVV~~~~i~~~~~---------------------- 912 (959) T PRK13979 856 NEHEQKNILIITKKGMAIRFKSEAVNPM-GKIASGVTGISLKDEDKVIFGSIIDENDT---------------------- 912 (959) T ss_pred ECCCCCEEEEEECCCEEEEEEHHHCCCC-CCCCCCEEEEECCCCCEEEEEEEECCCCC---------------------- T ss_conf 0489963899907987999872434702-60368806897389987999999747777---------------------- Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEECCCCEEEEEHHHCCCCCCCCCCEEEEECC Q ss_conf 44444444333222223200111012568679999759934530178848667577414887606 Q gi|254780182|r 769 TEEITSLKNDSSVEGNISEERCQELKLKEQFILTVSEKGFGKRTSSYDFRISNRSGKGIRATDVS 833 (910) Q Consensus 769 ~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GKRt~~~eyr~q~RGgkGv~~ik~~ 833 (910) ..|.+.|.+|.+|-+.+.+...|||+|+|...|-+. T Consensus 913 -----------------------------~~~~~~~k~~~~~~~~~~~~~~q~~~g~g~~~~~~~ 948 (959) T PRK13979 913 -----------------------------RKIKLKSKAKDKGEIEIEDIKLQNRAGRGNSLMPLL 948 (959) T ss_pred -----------------------------CEEEEEECCCCCCEEEHHHHHHCCCCCCCCEEEEEE T ss_conf -----------------------------459999738866278711311000267872478862 No 17 >PRK05560 DNA gyrase subunit A; Validated Probab=99.92 E-value=7.2e-23 Score=223.69 Aligned_cols=199 Identities=24% Similarity=0.390 Sum_probs=145.4 Q ss_pred CCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCC Q ss_conf 67818999079705233100000233456521100014641010113323777399995489399982000432244456 Q gi|254780182|r 535 REDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQAR 614 (910) Q Consensus 535 ~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~sk 614 (910) ++..++.+|++|+|||++++.|...++ .|+.+++++++|.+..+..|+..+.++++|+.|++...+..++|..+|+++ T Consensus 608 ~~~~Lv~~Tk~G~IKRt~L~df~~~r~--~G~~AikLke~DeLv~v~l~~~~~dIil~T~~G~alRF~~~eVR~~GR~a~ 685 (822) T PRK05560 608 DDLYLFFATKNGTVKKTALSEFSNIRS--NGLIAINLDEGDELIGVRLTDGDDDVLLFSANGKAIRFPEEDVRPMGRTAR 685 (822) T ss_pred CCCEEEEEECCCCEEEECHHHCCCCCC--CCEEEEECCCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCC T ss_conf 885699995797279713687225552--551999858997799999848998799997897399950665777788776 Q ss_pred CCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCC--CEEEEEEC-CCCEEEEEEECC Q ss_conf 554124545365562002566301256668717999947991898423686204777--22786615-898578889618 Q gi|254780182|r 615 GKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRNKLSDFIQINRS--GKIAMKLD-SRDEILSVETCT 691 (910) Q Consensus 615 G~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~--G~~aikLk-egD~Li~v~~~~ 691 (910) |.-- +.|.++++|+++..+++ +.+|+++|++|++|||++++|...++. |.++|++. .++.|+++..+. T Consensus 686 GVkg---IkL~~gD~VV~~~vv~~------~~~iL~vTe~G~GKRt~~~eyr~~~RGgkGv~~ik~~~k~G~lv~~~~V~ 756 (822) T PRK05560 686 GVRG---IKLREGDEVVSMSVLRD------EQFVLTVTENGYGKRTPAEEYRLQGRGGKGVIAIKITERNGKLVGAVPVD 756 (822) T ss_pred CCCC---EECCCCCEEEEEEEECC------CCEEEEEECCCEEEECCHHHCCCCCCCCCCEEEEEECCCCCCEEEEEECC T ss_conf 8431---55199998999998579------98799991898053052888375577877758899648888489999917 Q ss_pred CCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCCEEEEEEEECCCC Q ss_conf 982699993698599975876235478665535767528998699989733666 Q gi|254780182|r 692 QENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGDQVISMAIVLHAD 745 (910) Q Consensus 692 ~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D~Vv~~~vi~~~~ 745 (910) ++++|+++|+.|+++|++.+++|. +||+|+||+.|+|+++|+|++.+.+...+ T Consensus 757 ~~deI~liT~~G~~iRi~v~~I~~-~gR~t~GVrl~~L~~~d~v~~va~v~~~~ 809 (822) T PRK05560 757 DDDEIMLITDAGKLIRTRVSEIRI-TGRNTQGVTLIRLDEGEKVVSVARVAEEE 809 (822) T ss_pred CCCEEEEEECCCEEEEEEHHHCCC-CCCCCCCEEEEECCCCCEEEEEEEECCCC T ss_conf 998699992798799987100475-67578870899859999899999807876 No 18 >TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743 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 II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively. This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=99.91 E-value=3.9e-22 Score=217.13 Aligned_cols=192 Identities=19% Similarity=0.337 Sum_probs=98.6 Q ss_pred EEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCE-EEEEECCCCEEEEECC--CCCCCCCCCC Q ss_conf 189990797052331000002334565211000146410101133237773-9999548939998200--0432244456 Q gi|254780182|r 538 MVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTS-VLFFSSLGFVYKEKVW--RLPIGSPQAR 614 (910) Q Consensus 538 vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~-LLfFTs~Gkvy~l~v~--~IP~~sr~sk 614 (910) .++..|++|+|||+.+++|..-+ ..|+.++++.|+|.+..+..|...|. +++||.+|++...+.- ++-..+|++. T Consensus 636 yl~~aTk~G~vKk~~L~~F~~~r--s~GiiAi~L~e~D~L~~v~~~~~~~~~v~l~s~~G~~~RF~~~~~~vR~mgR~~~ 713 (864) T TIGR01063 636 YLFLATKNGVVKKTSLTEFSNIR--SNGIIAIKLDEGDELISVRLVDGDDEKVMLGSKNGKAVRFPEEDEEVREMGRATR 713 (864) T ss_pred EEEEECCCCEEEEEECHHHHHHH--HCCEEEEEEECCCEEEEEEEEECCCCEEEEEECCCCEEECCCCCCCHHCCCCCCC T ss_conf 79997267438874001443545--2786999970896899999960788658865148847983688531100245567 Q ss_pred CCCCEEEEECCCC----------------------------CCEEEEEEECCCCCCCCCC-EEEEEECCCCEEEECHHHH Q ss_conf 5541245453655----------------------------6200256630125666871-7999947991898423686 Q gi|254780182|r 615 GKALINILSLNQG----------------------------ERITTIMPFPEDESSWNNL-YVVFATKHGNVRRNKLSDF 665 (910) Q Consensus 615 G~pi~nll~l~~~----------------------------E~I~ail~~~~~~~~~~~~-~Lvl~Tk~G~VKkt~l~ef 665 (910) |.-= ++|..+ +.++++..++ ++. +|+.+|.||+.|||++++| T Consensus 714 GV~G---i~L~~~~~v~~~~~~~~i~~~~~D~~~~~L~~NlD~vv~~~~~~------e~~~~lL~vt~nGyGKRt~~~~y 784 (864) T TIGR01063 714 GVRG---IKLKNEDSVISMTVLKGINSIKEDRNLEELGVNLDFVVSLEVVS------EESQKLLIVTENGYGKRTSIEEY 784 (864) T ss_pred CEEE---EEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEC------CCCCEEEEEEECCCCEECCHHHC T ss_conf 6013---54067774000134432120022224654374243447778624------99837899830684200426257 Q ss_pred HHCCCCC--EEEEEEC-CCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCCEEEEEEEE Q ss_conf 2047772--2786615-89857888961898269999369859997587623547866553576752899869998973 Q gi|254780182|r 666 IQINRSG--KIAMKLD-SRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGDQVISMAIV 741 (910) Q Consensus 666 ~~~r~~G--~~aikLk-egD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D~Vv~~~vi 741 (910) ....++| .+.++.. .+..||+|..++++|+|+++|+.|+++|.+.++||. +||+|+|||.|+|+++|.|+++..+ T Consensus 785 r~~~RGg~Gv~~~~~~~r~G~vVga~~V~~~d~lm~iT~~G~~iR~~~~~vs~-~GR~t~GVrL~~l~e~d~vv~v~~~ 862 (864) T TIGR01063 785 RLQSRGGKGVKSIKITDRNGQVVGAIAVDDDDELMLITSSGKLIRTSVQDVSI-QGRNTQGVRLIRLDEDDKVVSVSLV 862 (864) T ss_pred CCCCCCCCEEEEEEEECCCCCEEEEEEECCCCHHHHEECCCCEEEEEEEHHCC-CCCCCCCEEEEEECCCCCEEEEEEC T ss_conf 63265662378899864689687898745874000101088379976103211-5653565589851787635642202 No 19 >KOG0355 consensus Probab=99.86 E-value=1.5e-21 Score=211.99 Aligned_cols=185 Identities=31% Similarity=0.477 Sum_probs=154.5 Q ss_pred EEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHH--HCCCCCCCHHHHH Q ss_conf 66009999987678777998863137540008973678999999987899999811340425566--4366887047899 Q gi|254780182|r 17 TSVSITDEMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEV--MGKYHPHGNAAIY 94 (910) Q Consensus 17 ~~~~~~~~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v--~gkyHPHGd~siy 94 (910) ..+++.+-. +.|+-++|.= .+|.+.|||||-||.+||...+.+. +.-.|.|+.+|-| +.-|| ||.+|.- T Consensus 645 ~~v~~sdf~-~elilf~~~~----sIp~~~dglkpgqRkv~~~~~k~n~---~~E~Kv~ql~g~v~~~s~yh-hge~sl~ 715 (842) T KOG0355 645 KFVTISDFV-KELILFSNAD----SIPSLVDGLKPGQRKVLFTCFKRND---KREVKVAQLAGSVAEMSAYH-HGEQSLM 715 (842) T ss_pred CEEEHHHHH-HHHHHHHHCC----CCHHHHHCCCCCCHHHHHHHHHHCC---CCCEEEEEECCHHHHHHHHH-CCCHHHH T ss_conf 255789999-9999987215----2076772358662233467676447---66255433024788888774-3427699 Q ss_pred HHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCC Q ss_conf 99997122011156131478870887769720135789997899999986307684053306898854850343227321 Q gi|254780182|r 95 DALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNV 174 (910) Q Consensus 95 ~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~l 174 (910) .|.|+|||+|.. .+||+.||.+..|++.+.-++.--|.....|. |=||...||+++|. +|++ T Consensus 716 ~ti~~l~q~~~g----------------kdaa~~ryi~t~l~~~tr~~f~~~dd~ll~~~-~~~~~~vep~y~pi-~p~v 777 (842) T KOG0355 716 STIVNLAQDFVG----------------KDAASARYIFTKLSPLTRLLFPPADDLLLKYL-NEDGQRVEPEYCPI-IPMV 777 (842) T ss_pred HHHHHHHHHHCC----------------CCCHHHHHHHHHCCHHHHHCCCCCCHHHHHHH-CCCCCCCCCCCCCC-EEEE T ss_conf 999988875058----------------84023678988527365402788832676652-25786717522441-4688 Q ss_pred HHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEE Q ss_conf 10167610101331789854789999998876187768888886345866887443447588999987012038999 Q gi|254780182|r 175 LVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIR 251 (910) Q Consensus 175 L~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR 251 (910) |+||+.||+.||+|.||++|..||+.-+..++++.+. . .|...|+.-||++.+- T Consensus 778 lvngaegiGtGws~~i~n~n~~~iv~~~r~~~~~~~~--~---------------------~~~p~yr~frg~i~~~ 831 (842) T KOG0355 778 LVNGAEGIGTGWSTFIPNYNPREIVKNIRRLINGEPP--K---------------------AMAPWYRNFRGTIEVI 831 (842) T ss_pred EEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCC--C---------------------CCCCHHHHCCEEEEEE T ss_conf 8505654556765668888989999999886369985--2---------------------1780352044279995 No 20 >PRK05561 DNA topoisomerase IV subunit A; Validated Probab=99.85 E-value=9.9e-19 Score=186.69 Aligned_cols=188 Identities=23% Similarity=0.373 Sum_probs=156.6 Q ss_pred CEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEE Q ss_conf 17999947991898423686204777227866158985788896189826999936985999758762354786655357 Q gi|254780182|r 646 LYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVR 725 (910) Q Consensus 646 ~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVk 725 (910) ...|.+|++|+|||++...+ +...++++++|.+...+.++..+.++++|+.|++...+..+++ .|| ++|.- T Consensus 509 ~v~V~lS~~GyIKr~k~~~~------~~~~~~~Ke~D~v~~~~~~~T~d~LLfFTn~Grvy~lkv~~IP--~~r-~~G~p 579 (745) T PRK05561 509 PVTVVLSKKGWVRRAKGHDI------DPAGLGYKEGDSLLFAFEARTTDKLLFFTSTGRVYSLPVHELP--SAR-GQGEP 579 (745) T ss_pred CCEEEECCCEEEEEECCCCC------CCCCCCCCCCCCEEEEEEEECCCEEEEEECCCEEEEEEHHHCC--CCC-CCCCC T ss_conf 61899817804998448886------7544567778532589998069769999579759998922087--866-78808 Q ss_pred ---EEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEE Q ss_conf ---67528998699989733666542000001222333333345554444444433322222320011101256867999 Q gi|254780182|r 726 ---GISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILT 802 (910) Q Consensus 726 ---gIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~ 802 (910) .+.|.++++|+++..+. +++++++ T Consensus 580 i~nll~L~~~EkIv~vl~~~-----------------------------------------------------~~~~lll 606 (745) T PRK05561 580 LTGLIDLEPGEEIVHVLVGD-----------------------------------------------------PDQKLLL 606 (745) T ss_pred HHHCCCCCCCCEEEEEEEEC-----------------------------------------------------CCCEEEE T ss_conf 98806899999699999858-----------------------------------------------------9876999 Q ss_pred EECCCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCC-CCEEEEEECCCEEEEEECCCCCCCCCCCCCCE Q ss_conf 97599345301788486675774148876067777686899997289-96499994599899999010554451568738 Q gi|254780182|r 803 VSEKGFGKRTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVND-NDQIILVSDKGTLIRVPVNEIRIASRATKGVV 881 (910) Q Consensus 803 vTe~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~-~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~ 881 (910) +|.+|+||++++++|...++ .|.++|++.+. +.++++..+.. +|+|+++|++|+++|++.+++|.+|| ++||+ T Consensus 607 aTk~G~~kr~~l~e~~~~~k--~G~~ai~L~~g---Delv~~~~i~~~~d~I~lvT~~Gk~lrF~~~evr~~gR-gkGVk 680 (745) T PRK05561 607 ASSAGYGFVVSEEDLVGRNR--AGKAVINLKDG---DKVLAPVPVEGDEDSLAAITQRGRLLVFPLSELPELSR-GKGVK 680 (745) T ss_pred EECCCEEEEEEHHHHCCCCC--CCEEEEEECCC---CEEEEEEEECCCCCEEEEEECCCCEEEEEHHHCCCCCC-CCCCC T ss_conf 97893299978698004462--67188861899---88988899469998899995898289979888777575-46801 Q ss_pred EEEECCCCEEEEEEEECCCC Q ss_conf 89808998799999835665 Q gi|254780182|r 882 IFSTAKDERVVSVERIRESE 901 (910) Q Consensus 882 i~~L~~~D~Vv~va~i~~~e 901 (910) .|+|.++|.|+++..++.++ T Consensus 681 gikLk~~D~Vv~~~vv~~~~ 700 (745) T PRK05561 681 LIELKKEEGLADLAVLPPGD 700 (745) T ss_pred EEEECCCCEEEEEEEECCCC T ss_conf 47668999899999985888 No 21 >COG0188 GyrA Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair] Probab=99.72 E-value=1.5e-15 Score=158.12 Aligned_cols=81 Identities=25% Similarity=0.322 Sum_probs=34.3 Q ss_pred EEEEECCCCEEEECHHHHHHC--CCCCEEEEEECCCCEEEEEEECCCCC-EEEEEECCCEEEEEEHHHCCCCCCCCCCCE Q ss_conf 999947991898423686204--77722786615898578889618982-699993698599975876235478665535 Q gi|254780182|r 648 VVFATKHGNVRRNKLSDFIQI--NRSGKIAMKLDSRDEILSVETCTQEN-DILLTTKLGQCVRFPISAIRVFAGRNSVGV 724 (910) Q Consensus 648 Lvl~Tk~G~VKkt~l~ef~~~--r~~G~~aikLkegD~Li~v~~~~~~~-~Iil~T~~G~~lrF~~~evr~~~GR~a~GV 724 (910) ++++|.+|+.-+.+.+++... ...|...|+|+++|.++++..+..++ .++.+|.+|...|.+.++.+. ++|+++|+ T Consensus 653 i~~~t~~G~~~~F~~~~v~~~gr~a~Gv~~i~l~~~d~~~~~~~~~~~~~~~l~~t~~g~~kr~~~~~~~~-~~Rg~~G~ 731 (804) T COG0188 653 ILLVTSNGKALRFPESEVREMGRGAKGVKGIKLKEGDKVVSLSVVEDDEAKLLTVTERGYGKRTKISEYPV-TKRGGKGV 731 (804) T ss_pred EEEEECCCEEEEEEHHHCCCCCCCCCCCCEEECCCCCEEEEEEECCCCCEEEEEEECCCCEEECCHHHCCC-CCCCCCCE T ss_conf 89991487378740344221154136864064376575665320147860589984367200041421342-46676641 Q ss_pred EEEEC Q ss_conf 76752 Q gi|254780182|r 725 RGISL 729 (910) Q Consensus 725 kgIkL 729 (910) ..++. T Consensus 732 ~~~~~ 736 (804) T COG0188 732 ILIKG 736 (804) T ss_pred ECCCC T ss_conf 24545 No 22 >TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit; InterPro: IPR005741 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 II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit A (parC) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=99.52 E-value=4.9e-14 Score=144.68 Aligned_cols=199 Identities=21% Similarity=0.311 Sum_probs=167.7 Q ss_pred EEEEEECCC-CEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCE- Q ss_conf 799994799-189842368620477722786615898578889618982699993698599975876235478665535- Q gi|254780182|r 647 YVVFATKHG-NVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGV- 724 (910) Q Consensus 647 ~Lvl~Tk~G-~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GV- 724 (910) +-|.+||.| ++|+++-..|... -..=++++++|.|+.....+..|+|+++|+.|.+|-.|.-++.-+ -.+-.|- T Consensus 499 ~~v~itk~GnY~K~~S~~sf~ss---~~~d~g~~~~d~l~~~~~~nttd~lL~~Ts~g~~In~pvh~La~~-rwkd~g~h 574 (745) T TIGR01061 499 LYVVITKDGNYIKRTSKRSFASS---KYDDFGLKDDDILFYQTIANTTDKLLIFTSKGNLINLPVHKLADI-RWKDLGEH 574 (745) T ss_pred CEEEEEECCCEEHHHHHHHHHHC---CCCCCCCCCCHHHHHHHHHHCCCEEEEEECCCCEEEEEEEECCCC-CHHHHHHH T ss_conf 40799844763000126676204---731157755334535465212253788761666642130314566-56689987 Q ss_pred --EEEE-CCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEE Q ss_conf --7675-2899869998973366654200000122233333334555444444443332222232001110125686799 Q gi|254780182|r 725 --RGIS-LAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFIL 801 (910) Q Consensus 725 --kgIk-L~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL 801 (910) +-+. +..++.||.+.+++..+. ++..++ T Consensus 575 ls~~~~n~~~~E~iv~v~~~~~fdv-------------------------------------------------~~~~L~ 605 (745) T TIGR01061 575 LSNKITNFDENETIVAVEILNEFDV-------------------------------------------------DEAILV 605 (745) T ss_pred HCCHHHHHHCCCCEEEEEEECCCCC-------------------------------------------------CHHHHH T ss_conf 2000110210684899986132257-------------------------------------------------468989 Q ss_pred EEECCCCEEEEEHHHCCCCCC-CCCCEEEEECCCCCCCCCEEEEEECCC--CCEEEEEECCCEEEEEECCCCCCCCCCCC Q ss_conf 997599345301788486675-774148876067777686899997289--96499994599899999010554451568 Q gi|254780182|r 802 TVSEKGFGKRTSSYDFRISNR-SGKGIRATDVSKINEIGALVAVFPVND--NDQIILVSDKGTLIRVPVNEIRIASRATK 878 (910) Q Consensus 802 ~vTe~G~GKRt~~~eyr~q~R-GgkGv~~ik~~~~n~~g~lv~~~~V~~--~DeIlliT~~G~iiR~~v~~I~~~gR~a~ 878 (910) +.|.+|..||+.+.+|..+.- --|-+.+|++... +.||.|+.... ++.|+++|+.|-..+|.++|||..|+-|+ T Consensus 606 l~sklg~vKriel~~l~~~~~y~sK~~~~~~L~D~---d~li~a~~~~~Gh~~~i~lvS~~gy~l~F~~~Ei~~~~~~A~ 682 (745) T TIGR01061 606 LASKLGMVKRIELTELDIKRNYRSKAILILKLKDE---DELISAFLQKKGHDKLIILVSKLGYALLFLVEEINVVGAKAA 682 (745) T ss_pred HHHHCCCEEEEECCCCCCCCCCHHHHHHHHHCCCC---CCEEEEEEECCCCCCEEEEEEECCCEEEECCEEECCCCCCCC T ss_conf 98755874787603247786510122332111789---543899984188844189997368357730203323144667 Q ss_pred CCEEEEECCCCEEEEEEEECCCC Q ss_conf 73889808998799999835665 Q gi|254780182|r 879 GVVIFSTAKDERVVSVERIRESE 901 (910) Q Consensus 879 GV~i~~L~~~D~Vv~va~i~~~e 901 (910) ||+.|+|+++|.|.++...+..+ T Consensus 683 GvK~mkLK~~D~v~~~~i~~~~~ 705 (745) T TIGR01061 683 GVKGMKLKEDDEVKSGLILEANE 705 (745) T ss_pred CEEEEECCCCCEEEEEEEECCCC T ss_conf 31133057676389999982799 No 23 >TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit; InterPro: IPR005742 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 II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit A (parC) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=98.71 E-value=1.1e-06 Score=78.88 Aligned_cols=186 Identities=19% Similarity=0.307 Sum_probs=140.1 Q ss_pred EEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEE Q ss_conf 99994799189842368620477722786615898578889618982699993698599975876235478665535767 Q gi|254780182|r 648 VVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGI 727 (910) Q Consensus 648 Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgI 727 (910) -+.+++.|-|.-....+.. ...++-|+||.-........++.|+++++.|+.--.....++ +||+..|--.+ T Consensus 508 Tii~S~MGWVRs~KGH~~D------~~~l~YK~GD~~~~~~~~~~~~~v~~i~S~GR~y~l~~~~l~--~a~g~G~Pl~~ 579 (747) T TIGR01062 508 TIILSKMGWVRSAKGHDID------LSTLKYKAGDSEKAIIEGKSNQKVVFIDSTGRSYALDPLNLP--SARGQGEPLTG 579 (747) T ss_pred EEEECCCCCEEECCCCCCC------CCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEEEECCCCCC--CCCCCCCCEEE T ss_conf 7998277735504665667------143541368612334551277517999728852663112043--45677872268 Q ss_pred EC--CCC-CEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEE Q ss_conf 52--899-869998973366654200000122233333334555444444443332222232001110125686799997 Q gi|254780182|r 728 SL--AKG-DQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVS 804 (910) Q Consensus 728 kL--~~~-D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vT 804 (910) || ..| ..|-.+. + ..+++.+|+.| T Consensus 580 KL~l~~Gn~~i~~~l-~----------------------------------------------------~~~~Q~LL~AS 606 (747) T TIGR01062 580 KLLLPIGNATIENIL-M----------------------------------------------------ESENQKLLLAS 606 (747) T ss_pred EEECCCCCCCEEEEE-E----------------------------------------------------ECCCCCEEEEC T ss_conf 873268862310777-6----------------------------------------------------35885321000 Q ss_pred CCCCEEEEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCC-CEEEEEECCCEEEEEECCCCCCCCCCCCCCEEE Q ss_conf 5993453017884866757741488760677776868999972899-649999459989999901055445156873889 Q gi|254780182|r 805 EKGFGKRTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDN-DQIILVSDKGTLIRVPVNEIRIASRATKGVVIF 883 (910) Q Consensus 805 e~G~GKRt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~-DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~ 883 (910) +-|||-.+..++.=-++|+||-+.++. + | ..++.+.+|+++ +-|+.||+.|+++-+++++||.+++. +|++++ T Consensus 607 ~~G~GF~~~~~~liA~~k~GK~l~~lP--E-~--~~~~~p~~~~~~s~~~~aI~~a~R~L~F~~~~lP~l~KG-~G~~~~ 680 (747) T TIGR01062 607 DAGYGFLVKFNDLIARNKAGKALINLP--E-N--ASVLAPLVVNDDSDLIVAITEAGRLLVFPIDDLPELSKG-KGNKLI 680 (747) T ss_pred CCCCCEEEECHHHHHHCHHCHHHCCCC--C-C--CEEECCEEECCCCCEEEEECCCCEEEEECHHHCCCCCCC-CCCEEE T ss_conf 168624740043333110040200178--8-8--611044342376102444113670687421117763478-730577 Q ss_pred EECC------CCEEEEEEEECCC Q ss_conf 8089------9879999983566 Q gi|254780182|r 884 STAK------DERVVSVERIRES 900 (910) Q Consensus 884 ~L~~------~D~Vv~va~i~~~ 900 (910) +... .|.+..+..++.. T Consensus 681 ~~~~a~A~~~~~~L~~l~~~~~Q 703 (747) T TIGR01062 681 RIPAANAKDREELLLDLKILNKQ 703 (747) T ss_pred EECCHHHCCCCCCCEEEEEECCC T ss_conf 50541001200010123453577 No 24 >PRK09631 DNA topoisomerase IV subunit A; Provisional Probab=98.06 E-value=0.0034 Score=47.68 Aligned_cols=68 Identities=22% Similarity=0.173 Sum_probs=39.6 Q ss_pred CCCCEEEECHHHHHH--CCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEE Q ss_conf 799189842368620--4777227866158985788896189826999936985999758762354786655357 Q gi|254780182|r 653 KHGNVRRNKLSDFIQ--INRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGVR 725 (910) Q Consensus 653 k~G~VKkt~l~ef~~--~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVk 725 (910) .++.+||++++.|.. .+..|.+.+.|++||.+.. |+.-|+|++.| +|........+- ...|++-.-|. T Consensus 458 d~i~aKrVa~~n~Kly~nr~~GFiGtslKkdDfV~~---CSd~DdILvF~-dG~ykV~kV~~K-~Fvgk~i~~v~ 527 (626) T PRK09631 458 KSKNVREIATKNMKVYLNLETGFVGTSLIDGEFIGN---ASYYDKILIFK-DGSYVLKNIEDK-TFIDKKNVCVL 527 (626) T ss_pred CCEEEEEEECCCCEEEECCCCCEEEECCCCCCEEEE---CCCCCEEEEEE-CCEEEEEECCCC-CEECCCCEEEE T ss_conf 444369957023325665888556103567845673---35665399998-985999985776-05468837999 No 25 >pfam03989 DNA_gyraseA_C DNA gyrase C-terminal domain, beta-propeller. This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a beta-propeller structure. This region has been shown to bind DNA non-specifically and may stabilize the DNA-topoisomerase complex. Probab=97.96 E-value=3.3e-05 Score=65.71 Aligned_cols=47 Identities=32% Similarity=0.555 Sum_probs=21.2 Q ss_pred CEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEECCCCEEEEEEEE Q ss_conf 64999945998999990105544515687388980899879999983 Q gi|254780182|r 851 DQIILVSDKGTLIRVPVNEIRIASRATKGVVIFSTAKDERVVSVERI 897 (910) Q Consensus 851 DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L~~~D~Vv~va~i 897 (910) |+++++|+.|.++|++++++|.++|.++||++|+|.++|+|+++..+ T Consensus 2 ~~lll~T~~G~~~r~~~~~~~~~~r~~~Gv~~~~l~~~d~v~~~~~~ 48 (50) T pfam03989 2 DDLLLITSKGYVKRTPLSEFPEQGRGAKGVKAINLKEGDKVVSVLVV 48 (50) T ss_pred CEEEEEECCCEEEEEECHHCCCCCCCCCCEEEEECCCCCEEEEEEEC T ss_conf 78999908998999893154546876878797887999999999991 No 26 >pfam03989 DNA_gyraseA_C DNA gyrase C-terminal domain, beta-propeller. This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a beta-propeller structure. This region has been shown to bind DNA non-specifically and may stabilize the DNA-topoisomerase complex. Probab=97.86 E-value=6.2e-05 Score=63.21 Aligned_cols=48 Identities=42% Similarity=0.694 Sum_probs=34.8 Q ss_pred CCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCCEEEEEEEE Q ss_conf 8269999369859997587623547866553576752899869998973 Q gi|254780182|r 693 ENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGDQVISMAIV 741 (910) Q Consensus 693 ~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D~Vv~~~vi 741 (910) +++++++|+.|++.||+.+++++ +||+++||++|+|+++|+|+++.++ T Consensus 1 ~~~lll~T~~G~~~r~~~~~~~~-~~r~~~Gv~~~~l~~~d~v~~~~~~ 48 (50) T pfam03989 1 EDDLLLITSKGYVKRTPLSEFPE-QGRGAKGVKAINLKEGDKVVSVLVV 48 (50) T ss_pred CCEEEEEECCCEEEEEECHHCCC-CCCCCCCEEEEECCCCCEEEEEEEC T ss_conf 97899990899899989315454-6876878797887999999999991 No 27 >PRK09630 DNA topoisomerase IV subunit A; Provisional Probab=97.56 E-value=0.0059 Score=45.50 Aligned_cols=112 Identities=12% Similarity=-0.028 Sum_probs=77.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHH Q ss_conf 999999999999999999999999888778999999874-------0699999986189978987877631269788999 Q gi|254780182|r 357 ILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVA-------NLDEVVRIIRFSPNPETARRELMQRSWNASDIKD 429 (910) Q Consensus 357 iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~-------nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~ 429 (910) -|.+|++|+.+.+++..++++...++|+.- +-+...++ .+|.|+++|+..++...++...... T Consensus 308 ~l~eiL~~~~~~~~~~lrr~l~~~~~~~~r-~~~~k~Le~l~I~~~~~d~I~eiI~~i~~~~~~ed~~~~l--------- 377 (479) T PRK09630 308 SISEILKLHTEALQGYLKKELLILQDSLTR-EHYHKTLEYIFIKHKLYDTVREMLSKRKTKPSASDLHNAV--------- 377 (479) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH--------- T ss_conf 689999999998755434668999899999-9999888899998778999999999885389899999999--------- Q ss_pred HHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH Q ss_conf 99740221112223445236999999999878999988879999-998999999999887530 Q gi|254780182|r 430 LIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDI-RNELNSLGIEIKECLDIL 491 (910) Q Consensus 430 ~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl-~~E~~eL~~~I~~l~~IL 491 (910) ......|+..|+++|++|++++|+.|+..+| .-|..++.++++++++-+ T Consensus 378 -------------~~~~~~~~~~~~~~i~~q~~~~L~~l~l~kL~~Le~~k~~~El~~l~~~i 427 (479) T PRK09630 378 -------------LHALEPFLHTLPTAPDKQATSQLASLTIKKILCFNENAYTKELAAIEKKQ 427 (479) T ss_pred -------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf -------------98765667877543389999999998999875133999999999999999 No 28 >KOG1240 consensus Probab=96.68 E-value=0.095 Score=34.72 Aligned_cols=153 Identities=18% Similarity=0.242 Sum_probs=102.9 Q ss_pred CEEEEEECCCCEEEECHHHHHHCCCCCEEEEEEC-CCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCE Q ss_conf 1799994799189842368620477722786615-898578889618982699993698599975876235478665535 Q gi|254780182|r 646 LYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLD-SRDEILSVETCTQENDILLTTKLGQCVRFPISAIRVFAGRNSVGV 724 (910) Q Consensus 646 ~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLk-egD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GV 724 (910) .|++-++.+|.||-..+.+...-...-.--.+.. ++-..-.+..|...+.+++.|++|.+..+.++.... .-+.+.-+ T Consensus 1062 s~FvsgS~DGtVKvW~~~k~~~~~~s~rS~ltys~~~sr~~~vt~~~~~~~~Av~t~DG~v~~~~id~~~~-~~~~~~~~ 1140 (1431) T KOG1240 1062 SLFVSGSDDGTVKVWNLRKLEGEGGSARSELTYSPEGSRVEKVTMCGNGDQFAVSTKDGSVRVLRIDHYNV-SKRVATQV 1140 (1431) T ss_pred CEEEEECCCCEEEEEEEHHHHCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEECCCCEEEEEECCCCCC-CCCEEEEE T ss_conf 65797058865898651112167640355688712688468998516887688972787289997254343-31002333 Q ss_pred EEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCEEEEEE Q ss_conf 76752899869998973366654200000122233333334555444444443332222232001110125686799997 Q gi|254780182|r 725 RGISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDTEEITSLKNDSSVEGNISEERCQELKLKEQFILTVS 804 (910) Q Consensus 725 kgIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~IL~vT 804 (910) +-.++++.+.||+|-....... ...++.+| T Consensus 1141 ri~n~~~~g~vv~m~a~~~~~~--------------------------------------------------S~~lvy~T 1170 (1431) T KOG1240 1141 RIPNLKKDGVVVSMHAFTAIVQ--------------------------------------------------SHVLVYAT 1170 (1431) T ss_pred ECCCCCCCCCEEEEECCCCCCC--------------------------------------------------CEEEEEEE T ss_conf 1356657883688633420036--------------------------------------------------52699997 Q ss_pred CCCCEE----EEEHHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCC-CEEEEEECCCEEE Q ss_conf 599345----3017884866757741488760677776868999972899-6499994599899 Q gi|254780182|r 805 EKGFGK----RTSSYDFRISNRSGKGIRATDVSKINEIGALVAVFPVNDN-DQIILVSDKGTLI 863 (910) Q Consensus 805 e~G~GK----Rt~~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~-DeIlliT~~G~ii 863 (910) .+|-+- |+..+-.+.|+ .. +.| +|...++++. ..+++-|++|+++ T Consensus 1171 ~~~~iv~~D~r~~~~~w~lk~-----------~~--~hG-~vTSi~idp~~~WlviGts~G~l~ 1220 (1431) T KOG1240 1171 DLSRIVSWDTRMRHDAWRLKN-----------QL--RHG-LVTSIVIDPWCNWLVIGTSRGQLV 1220 (1431) T ss_pred ECCCEEEECCHHHHHHHHHHC-----------CC--CCC-CEEEEEECCCCEEEEEECCCCEEE T ss_conf 126268841312566776405-----------74--556-046798558761899965785599 No 29 >KOG3863 consensus Probab=87.30 E-value=2.4 Score=22.21 Aligned_cols=64 Identities=22% Similarity=0.270 Sum_probs=42.7 Q ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH---------- Q ss_conf 7406999999861899789878776312697889999974022111222344523699999999987899---------- Q gi|254780182|r 394 VANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLA---------- 463 (910) Q Consensus 394 l~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~---------- 463 (910) --.-|+||.+.+.+ =..++++ |+||+.|-.-|=|.|=| T Consensus 458 PF~vd~IinLp~~d------Fne~ls~--------------------------~~lte~QLslIrDIRRRgKNkvAAQnC 505 (604) T KOG3863 458 PFSVDEIINLPVDD------FNEMLSK--------------------------YKLTEEQLSLIRDIRRRGKNKVAAQNC 505 (604) T ss_pred CCCHHHHCCCCHHH------HHHHHHH--------------------------CCCCHHHHHHHHCCCCCCCCCHHCCCH T ss_conf 87667653786889------9999985--------------------------026898877765021045651001320 Q ss_pred HHHHHHH-HHHHHHHHHHHHHHHHHHH Q ss_conf 9988879-9999989999999998875 Q gi|254780182|r 464 RLTGLGR-DDIRNELNSLGIEIKECLD 489 (910) Q Consensus 464 rLt~LE~-~kl~~E~~eL~~~I~~l~~ 489 (910) |=.+|+. ..|+.|...|.++.+.|.+ T Consensus 506 RKRKLd~I~nLE~ev~~l~~eKeqLl~ 532 (604) T KOG3863 506 RKRKLDCILNLEDEVEKLQKEKEQLLR 532 (604) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 356778999888999988888898899 No 30 >KOG1920 consensus Probab=86.96 E-value=2.5 Score=22.06 Aligned_cols=16 Identities=31% Similarity=0.503 Sum_probs=8.2 Q ss_pred CEEEEEEECCCCCHHHHH Q ss_conf 557999947988778999 Q gi|254780182|r 307 GYRVVIELKRGASADVIL 324 (910) Q Consensus 307 giRivielKr~~~~~~vl 324 (910) |-+||=-++.+ +.+|| T Consensus 649 GsklVa~~~~k--a~VvL 664 (1265) T KOG1920 649 GSKLVAVVPQK--AAVVL 664 (1265) T ss_pred CCEEEEECCCH--HHHHH T ss_conf 05578862412--56867 No 31 >TIGR02895 spore_sigI RNA polymerase sigma-I factor; InterPro: IPR014244 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the transcription factor Sigma-I. This protein is found in endospore-forming species in the Firmicutes lineage of bacteria, such as Bacillus subtilis, but is not universally present among such species. Sigma-I was shown to be induced by heat shock in B. subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. Probab=85.67 E-value=2.5 Score=21.93 Aligned_cols=100 Identities=25% Similarity=0.300 Sum_probs=81.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCC Q ss_conf 99999999999999999999988877899999987406999999861899789878776312697889999974022111 Q gi|254780182|r 360 AFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSY 439 (910) Q Consensus 360 ~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~ 439 (910) .|+.|-.-||+|| ||+-||.-....++ T Consensus 64 sFL~FA~l~IkRr---------------------------~IDy~R~n~k~~~~-------------------------- 90 (225) T TIGR02895 64 SFLSFAKLIIKRR---------------------------VIDYIRKNQKYKNL-------------------------- 90 (225) T ss_pred HHHHHHHHHHHHH---------------------------HHHHHHHHHHHHHC-------------------------- T ss_conf 1699999988999---------------------------88888741112211-------------------------- Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCE Q ss_conf 22234452369999999998789999888799999989999999998875304989999999998999998405688331 Q gi|254780182|r 440 TIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTR 519 (910) Q Consensus 440 ~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~ 519 (910) ....+.|.=||.|++--|+|.+. +|.-+=+-|...-+.+|-+|++.|. +|++=-.||-+.-=||-|-|.+. T Consensus 91 -~~l~e~y~n~E~~~~~~~~~~~~----~e~y~~~i~~~~RrlEILey~~~L~----~f~I~f~eLv~~SPKH~d~R~~~ 161 (225) T TIGR02895 91 -VYLDEDYDNSEENDENSLEIKVS----LEEYKNEIENENRRLEILEYKKLLK----QFGIEFVELVKVSPKHRDARKKA 161 (225) T ss_pred -CCCCCCCCCHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHH----HHCCCHHHHHCCCCCHHHHHHHH T ss_conf -67677656403577548999999----9999987588866899999999998----73870768741077768899999 Q ss_pred EE Q ss_conf 00 Q gi|254780182|r 520 IV 521 (910) Q Consensus 520 I~ 521 (910) |. T Consensus 162 ~~ 163 (225) T TIGR02895 162 IK 163 (225) T ss_pred HH T ss_conf 99 No 32 >pfam11197 DUF2835 Protein of unknown function (DUF2835). This is a bacterial family of uncharacterized proteins. One member of this family is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV). Probab=84.82 E-value=2.9 Score=21.37 Aligned_cols=45 Identities=18% Similarity=0.522 Sum_probs=35.2 Q ss_pred CCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCEEE---EECCCCCEEEEE Q ss_conf 98269999369859997587623547866553576---752899869998 Q gi|254780182|r 692 QENDILLTTKLGQCVRFPISAIRVFAGRNSVGVRG---ISLAKGDQVISM 738 (910) Q Consensus 692 ~~~~Iil~T~~G~~lrF~~~evr~~~GR~a~GVkg---IkL~~~D~Vv~~ 738 (910) ..+.|.+.|.+|+-++||.+.+||.- +..||+| |.+.++-+.++. T Consensus 19 ~a~~V~v~~~~Gr~l~lPa~~lrpFv--t~~GI~G~F~l~~d~~~kf~sL 66 (68) T pfam11197 19 AASKVVVRSRDGRRLQLPARRLRPFL--THDGIRGRFRLEFDDNGKFVSL 66 (68) T ss_pred CCCEEEEEECCCCEEEEEHHHCCCCC--CCCCCEEEEEEEECCCCCEEEE T ss_conf 46589999079949997679875305--6788459999999899989872 No 33 >KOG4212 consensus Probab=82.44 E-value=1.9 Score=22.97 Aligned_cols=63 Identities=30% Similarity=0.472 Sum_probs=45.6 Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHCCC--CCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHC Q ss_conf 9999246443528999999999987166--501445873037465579999479887789999999761 Q gi|254780182|r 265 QIVVTEIPYQVNKAAMLEKIAELVREKR--IVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYT 331 (910) Q Consensus 265 ~ivItEiPY~vnk~~lie~Ia~lv~~~k--i~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T 331 (910) ...||.|||.+. | ..+.+||++|- ++-+.=+-|+|.|--=.-|+|.|-..+.++-+..|-||. T Consensus 46 ~vfItNIpyd~r---W-qdLKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~~E~~qKa~E~lnk~~ 110 (608) T KOG4212 46 SVFITNIPYDYR---W-QDLKDLVREKVGEVEYVELLFDESGKARGCAVVEFKDPENVQKALEKLNKYE 110 (608) T ss_pred EEEEECCCCHHH---H-HHHHHHHHHHCCCEEEEEEECCCCCCCCCCEEEEEECHHHHHHHHHHHHHCC T ss_conf 478865753211---3-7699999974473586652013478857734798507778999999864434 No 34 >pfam04201 TPD52 Tumour protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other. Probab=81.25 E-value=3.1 Score=21.12 Aligned_cols=49 Identities=22% Similarity=0.407 Sum_probs=37.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 98887999999899999999988753049899999999989999984056883310 Q gi|254780182|r 465 LTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRI 520 (910) Q Consensus 465 Lt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I 520 (910) |+--|++.++.|+..+.++|..|+..|+.+.+... +||.+.|.-.-.+| T Consensus 26 lseee~eel~~EL~kvEeEI~tLrqvLaaKer~~~-------elKrkLGit~~~eL 74 (162) T pfam04201 26 LSEAEKEELRTELAKLEEEISTLRQVLAAKEKHLA-------ELKRKLGLTPLSEL 74 (162) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHCCCHHHHH T ss_conf 78999999999999999999999999999999999-------99998687569999 No 35 >pfam05133 Phage_prot_Gp6 Phage portal protein, SPP1 Gp6-like. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, Gp6 participates in the procapsid assembly reaction. This family also includes family Phage_min_cap, pfam05126. Probab=79.96 E-value=4.3 Score=19.84 Aligned_cols=12 Identities=42% Similarity=0.495 Sum_probs=7.4 Q ss_pred CCCCCCHHHHHH Q ss_conf 769720135789 Q gi|254780182|r 121 DGDPPAAERYTE 132 (910) Q Consensus 121 dgd~~AA~RYte 132 (910) ++.++|+.||.. T Consensus 140 ~~~~~~~vr~~~ 151 (435) T pfam05133 140 DRELAAAVRYYT 151 (435) T ss_pred CCCEEEEEEEEE T ss_conf 876359999999 No 36 >COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones] Probab=77.10 E-value=0.67 Score=27.14 Aligned_cols=14 Identities=14% Similarity=-0.028 Sum_probs=6.0 Q ss_pred CHHHHHHHHHHHCC Q ss_conf 04789999997122 Q gi|254780182|r 89 GNAAIYDALARMAQ 102 (910) Q Consensus 89 Gd~siy~a~v~maq 102 (910) |..|+|.+-+..+| T Consensus 162 ~~~s~~~~ni~~~~ 175 (749) T COG5207 162 GPSSIEMGNIGGLK 175 (749) T ss_pred CCCCCCCCCCCCCE T ss_conf 99863013557732 No 37 >KOG4010 consensus Probab=76.56 E-value=5.3 Score=19.07 Aligned_cols=43 Identities=23% Similarity=0.386 Sum_probs=35.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH Q ss_conf 9998887999999899999999988753049899999999989 Q gi|254780182|r 463 ARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQEL 505 (910) Q Consensus 463 ~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL 505 (910) --|+--|.+.|+.|+..+.++|..|+..|+.+++-..-||.-| T Consensus 39 ~~LSe~Ekeelr~EL~kvEeEI~TLrqVLaAKerH~~ELKRKL 81 (208) T KOG4010 39 EALSEEEKEELRTELAKVEEEIVTLRQVLAAKERHAAELKRKL 81 (208) T ss_pred HHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 6506888999999999999999999999999888899999986 No 38 >pfam12395 DUF3658 Protein of unknown function. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam08874. There are two completely conserved residues (D and R) that may be functionally important. Probab=75.61 E-value=1.5 Score=24.08 Aligned_cols=53 Identities=26% Similarity=0.354 Sum_probs=31.3 Q ss_pred CCCCEEEEHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHH Q ss_conf 99981134042556643668-8704789999997122011156131478870887769720135789 Q gi|254780182|r 67 WNKKYVKCARISGEVMGKYH-PHGNAAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTE 132 (910) Q Consensus 67 ~~~~~~K~a~ivg~v~gkyH-PHGd~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte 132 (910) ....|.|+||+||+|||++. +-||.=+.=-+=-|+ -||-|=-. |++ .+||+-+ T Consensus 57 ~~~~~~~a~rvIg~v~g~~~~~v~D~fl~~Rir~Li-----------~~G~le~~-G~~-~~m~~~~ 110 (111) T pfam12395 57 ATDEFQKAARVVGEVMGHLEQLVGDTFLEYRIRELI-----------KQGVLELK-GDL-KSMRDYS 110 (111) T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH-----------HCCCEEEE-CCC-CHHHCCC T ss_conf 835445999999999986677777899999999999-----------88988996-584-3523021 No 39 >PRK03992 proteasome-activating nucleotidase; Provisional Probab=72.01 E-value=6.6 Score=18.20 Aligned_cols=130 Identities=17% Similarity=0.041 Sum_probs=62.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEE-ECCCCCCCCCCCCCCCCEEEEEECCC-EE Q ss_conf 99999899999999988753049899999999989999984056883310-01343453010145678189990797-05 Q gi|254780182|r 471 DDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRI-VEGLLDMEDEDCIVREDMVVTVSHLG-YV 548 (910) Q Consensus 471 ~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I-~~~~~~i~~EdlI~~E~vvV~lS~~G-yI 548 (910) +++.+++.+|..++.+|+.-+..-+..+.-+++|+..+++.-..=|..-. +.. ..+.+.+..++|-.|... |+ T Consensus 5 ~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~l~~~~~~l~~e~~~l~~~p~~vg~-----~~~~~~~~~~iv~~~~g~~~~ 79 (390) T PRK03992 5 EKLDDREEQLESRNEELEEQLRDLEAENERLERELERLKSELEKLRTPPLIVAT-----VLEVLDDGRVVVKSSTGPQFV 79 (390) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE-----EEEEECCCEEEEEECCCCEEE T ss_conf 999999999999999999999999999999999999999999985489948999-----999837974999978998799 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCCCCCCCC Q ss_conf 23310000023345652110001464101011332377739999548939998200043224445655 Q gi|254780182|r 549 KRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGSPQARGK 616 (910) Q Consensus 549 Kr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~sr~skG~ 616 (910) =++... +.--.++.++.|.---.+.+--.+|=-....+|+.+.+-+-|..+|..-|- T Consensus 80 v~~~~~-----------~~~~~l~pg~~V~l~~~~~~i~~~l~~~~d~~v~~m~v~e~P~v~~~dIGG 136 (390) T PRK03992 80 VTVSSF-----------VDRDKLKPGARVALNQQTLAIVEVLPSEKDPRVRAMEVIESPDVTYEDIGG 136 (390) T ss_pred EECCCC-----------CCHHHCCCCCEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCCCCHHHHCC T ss_conf 965787-----------688887999989985353030564688878621104214799998466149 No 40 >pfam10977 DUF2797 Protein of unknown function (DUF2797). This family of proteins has no known function. Probab=71.60 E-value=4.4 Score=19.81 Aligned_cols=25 Identities=24% Similarity=-0.064 Sum_probs=11.1 Q ss_pred EEECCCCEEEEECCCCCCCCCCCCCC Q ss_conf 99548939998200043224445655 Q gi|254780182|r 591 FFSSLGFVYKEKVWRLPIGSPQARGK 616 (910) Q Consensus 591 fFTs~Gkvy~l~v~~IP~~sr~skG~ 616 (910) .-||.=||=..+..++| ..|-..|- T Consensus 76 A~ss~~KVGITR~~q~p-tRWiDQGA 100 (233) T pfam10977 76 ANSSGVKVGITRKTQLP-TRWIDQGA 100 (233) T ss_pred ECCCCCEEEEECCCCCC-CCHHHCCC T ss_conf 84898478787789986-45566181 No 41 >pfam03982 DAGAT Diacylglycerol acyltransferase. The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT). Probab=71.54 E-value=1 Score=25.53 Aligned_cols=67 Identities=22% Similarity=0.433 Sum_probs=37.1 Q ss_pred HHHHHHHHHHHCCCCCCCCCCHHHHHHHH-------HHH----------HCCCCCCCCEEEEHHHHHHHHCCCCCCCHHH Q ss_conf 87779988631375400089736789999-------999----------8789999981134042556643668870478 Q gi|254780182|r 30 LTYAINVILGRAIPDLRDGLKPVHRRILF-------GMM----------QMGVEWNKKYVKCARISGEVMGKYHPHGNAA 92 (910) Q Consensus 30 l~Ya~svI~~RAlPd~rDGlKpv~Rrily-------~m~----------~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~s 92 (910) +-|+.....+|.-|.- .| ||.-| --+ .-.|.|++.| +.| |||||=.+ T Consensus 13 ~~Y~~w~~~d~~tp~~-gg-----r~~~w~R~~~iwk~~~~YFPi~Lvkt~~L~p~~nY---------ifg-~hPHGil~ 76 (297) T pfam03982 13 VLYALWLFYDWNSPKR-GG-----YRSNWARNWRIWKWFANYFPVKLHKTAELPPNRNY---------LFG-YHPHGILS 76 (297) T ss_pred HHHHHHHHEECCCCCC-CC-----CCCHHEECCHHHHHHHHHCCCEEEECCCCCCCCCE---------EEE-ECCCCEEC T ss_conf 9999774046788889-99-----71511013777887875188147875668998454---------888-76851032 Q ss_pred HHHHHHHHCCC---HHCCCCCCCC Q ss_conf 99999971220---1115613147 Q gi|254780182|r 93 IYDALARMAQD---WSLRLLLIEG 113 (910) Q Consensus 93 iy~a~v~maq~---~~~r~plidg 113 (910) + .|.+.+|.+ |+--+|-+.. T Consensus 77 ~-Ga~~~f~t~~~~f~~lfPgi~~ 99 (297) T pfam03982 77 V-GAFSNFSTNATGFMDKFPGIRP 99 (297) T ss_pred C-CHHEEECCCCCCCHHHCCCCCC T ss_conf 4-2110323455585756799987 No 42 >TIGR02515 IV_pilus_PilQ type IV pilus secretin PilQ; InterPro: IPR013355 A number of proteins homologous to PilQ are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also referred to as the main terminal branch of the general secretion pathway). Members of this family include PilQ itself, which is a component of the type IV pilus structure, from a number of species. In Haemophilus influenzae, the member of this family is associated with the uptake of exogenous DNA, rather than with formation of a type IV pilus - the surface structure required for this may be considered an unusual, incomplete type IV pilus structure.; GO: 0009297 pilus biogenesis, 0009306 protein secretion. Probab=70.30 E-value=5.5 Score=18.95 Aligned_cols=36 Identities=17% Similarity=0.408 Sum_probs=23.5 Q ss_pred CCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEE Q ss_conf 6757741488760677776868999972899649999459989999 Q gi|254780182|r 820 SNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRV 865 (910) Q Consensus 820 q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~ 865 (910) ..-|+.|+.+|+.. .+-.-..|++++-+.| |-++.. T Consensus 385 ~~~a~~~~~~I~k~------ei~T~VlV~nGeTvVi----GGIY~~ 420 (464) T TIGR02515 385 VSQAGGGVPAIDKR------EINTQVLVKNGETVVI----GGIYEQ 420 (464) T ss_pred CCCCCCCCCCEEEE------EEEEEEEEECCCEEEE----EEEEEE T ss_conf 34678701504402------6778999725888998----128985 No 43 >TIGR00909 2A0306 amino acid transporter; InterPro: IPR004758 Amino acid permeases are integral membrane proteins involved in the transport of amino acids into the cell. A number of such proteins have been found to be evolutionary related , , . These proteins seem to contain up to 12 transmembrane segments. The best conserved region in this family is located in the second transmembrane segment. Some proteins in this group are involved in the transport of the cationic amino acids (arginine,lysine and ornithine).. Probab=69.38 E-value=4.1 Score=20.07 Aligned_cols=35 Identities=26% Similarity=0.354 Sum_probs=27.0 Q ss_pred HHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHH Q ss_conf 67899999998789999981134042556643668870478999999 Q gi|254780182|r 52 VHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALA 98 (910) Q Consensus 52 v~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v 98 (910) -|=|+||||.+-|+-|. .+.|-||.=|+.-|.+++ T Consensus 316 g~~RvlFAmSRDGllP~------------slSkvH~k~~tP~~~~~~ 350 (451) T TIGR00909 316 GTSRVLFAMSRDGLLPK------------SLSKVHPKTKTPHVSILI 350 (451) T ss_pred HHHHHHHHHHHCCCCCC------------HHHHHCCCCCCCCHHHHH T ss_conf 89999999986177530------------376323446875048999 No 44 >cd04793 LanC LanC is the cyclase enzyme of the lanthionine synthetase. Lanthinoine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as precursor peptides and then post-translationally modified to contain thioether cross-links called lanthionines (Lans) or methyllanthionines (MeLans) in addition to 2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine (Dhb). These unusual amino acids are introduced by the dehydration of serine and threonine residues, followed by thioether formation via addition of cysteine thiols, catalysed by LanB and LanC or LanM. LanC, the cyclase component, is a zinc metalloprotein, whose bound metal has been proposed to activate the thiol substrate for nucleophilic addition. Probab=68.40 E-value=7.7 Score=17.61 Aligned_cols=70 Identities=21% Similarity=0.281 Sum_probs=35.0 Q ss_pred HHCCCCCEEEHHHHCCCC--CCHHHHHHHHHHHHHCCCCCH------HHHHHHCCCCCCCCC----CCCCCHHHHH---- Q ss_conf 101676101013317898--547899999988761877688------888863458668874----4344758899---- Q gi|254780182|r 175 LVNGGGGIAVGMATNIPT--HNLGEVVDGCVAVIDNPDIDL------DALMEIIRGPDFPTG----AVILGRTGIK---- 238 (910) Q Consensus 175 L~nG~~GIAvGmaTnipp--HNl~Ev~~a~~~~i~~p~~~~------~eL~~~i~GPDFPTG----G~I~~~~~i~---- 238 (910) +++|.+||+.-+-....+ +-+..+.+.+..+.+.-.... +....-..-+.||.| |.-+|-.|+. T Consensus 103 ~i~G~sGi~~yLL~~~~~~~~~~~~i~~~L~~l~~~~~~~~~~~~~~~~~~~~~~~~~~p~G~~nlG~AHGiaGil~~La 182 (382) T cd04793 103 VISGLSGIGRYLLLRHEPDSELLREILDYLVYLTEPLNQDITLYIWSENQPSETESKEFPEGHINLGLAHGIAGPLALLA 182 (382) T ss_pred CCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCHHHHHHHHHHHH T ss_conf 12778999999985046781689999999999998773268777782013671011117777756761054899999999 Q ss_pred HHHHHC Q ss_conf 998701 Q gi|254780182|r 239 NAYATG 244 (910) Q Consensus 239 ~~y~tG 244 (910) .+|+.| T Consensus 183 la~~~g 188 (382) T cd04793 183 LAKERG 188 (382) T ss_pred HHHHHC T ss_conf 999846 No 45 >TIGR00019 prfA peptide chain release factor 1; InterPro: IPR004373 This family describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognise and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cut-off for this model. RF-1 does not have a translational frameshift.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm. Probab=67.27 E-value=8.1 Score=17.43 Aligned_cols=46 Identities=22% Similarity=0.304 Sum_probs=41.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHCCC Q ss_conf 799999989999999998875304---9899999999989999984056 Q gi|254780182|r 469 GRDDIRNELNSLGIEIKECLDILS---SRSRLLGIIKQELLSVKDELDT 514 (910) Q Consensus 469 E~~kl~~E~~eL~~~I~~l~~IL~---s~~~l~~iI~~EL~eik~kygd 514 (910) ++.....+|+.+.+.|++-+.||. ++..+.+.+++||.+++++-.+ T Consensus 48 ~i~~~~~~~~~~~~~~~~A~~~l~E~~~D~El~elak~El~~l~~~~~~ 96 (373) T TIGR00019 48 EIVDKYEEYKKAQEDLKEAKELLEEKGDDKELRELAKEELEELEKEIEE 96 (373) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 8999999999999999999999974258865899999999999988888 No 46 >cd06461 M2_ACE Peptidase family M2 Angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor ocatapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ACE and the sperm-specific germinal ACE, both encoded by the same gene through transcription from alternative promoters. Somatic ACE has two tandem active sites with distinct catalytic properties, whereas germinal ACE, the function of which is largely unknown, has just a single active site. Recently, an ACE homolog, ACE2, has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function. ACE homologs (also known as members of the M2 gluzincin family) have been found in a wide variety of species, including those that neither h Probab=63.90 E-value=6.8 Score=18.10 Aligned_cols=55 Identities=27% Similarity=0.300 Sum_probs=43.6 Q ss_pred HHCCCHHCCCCCCCCCCCCCCCCCCCCCHHH---HHHHHHHHHHHHHHHHCCCCCCCCEECC Q ss_conf 7122011156131478870887769720135---7899978999999863076840533068 Q gi|254780182|r 99 RMAQDWSLRLLLIEGQGNFGSVDGDPPAAER---YTECRLQKAAHFLLDDLGKDTVDFRPNY 157 (910) Q Consensus 99 ~maq~~~~r~plidg~GnfGs~dgd~~AA~R---Yte~rl~~~~~~~l~~i~~~tv~~~~n~ 157 (910) .-||+|++-|+++.+..+-+++|- ..+|. ||..+|-+.|++.+..|.-.-+ -++| T Consensus 149 mWaQ~W~ni~dl~~P~p~~~~~Dv--t~~m~~q~~t~~~mf~~ae~FF~SLGl~~m--p~~F 206 (477) T cd06461 149 MWAQSWSNIYDLVKPYPGKPLLDV--TDAMVEQGYTAKRMFKEAEEFFTSLGLPPM--PPSF 206 (477) T ss_pred HHHHHHHHHHHCCCCCCCCCCCCC--CHHHHHCCCCHHHHHHHHHHHHHHCCCCCC--CHHH T ss_conf 665436654201357999888881--599998599899999999999996799769--9778 No 47 >KOG2264 consensus Probab=62.87 E-value=9.5 Score=16.79 Aligned_cols=46 Identities=20% Similarity=0.350 Sum_probs=21.1 Q ss_pred HHHHHHCCCCCCCCCCC---CCC--HH----HHHHHHHHCCCEEEEEEEEEEEECC Q ss_conf 88886345866887443---447--58----8999987012038999988654336 Q gi|254780182|r 214 DALMEIIRGPDFPTGAV---ILG--RT----GIKNAYATGRGSIVIRGVSHIEKTS 260 (910) Q Consensus 214 ~eL~~~i~GPDFPTGG~---I~~--~~----~i~~~y~tGrG~i~iR~k~~ie~~~ 260 (910) .||-+.--=|-+-|.|. +.+ +. .+.--+.||| +|.+.+...-++.. T Consensus 256 ~eleklyslp~w~~dg~Nhvl~Nl~r~s~~~n~lyn~~t~r-aivvQssf~~~q~R 310 (907) T KOG2264 256 AELEKLYSLPHWRTDGFNHVLFNLGRPSDTQNLLYNFQTGR-AIVVQSSFYTVQIR 310 (907) T ss_pred HHHHHHHCCCCCCCCCCCEEEEECCCCCCCCCCEEEECCCC-EEEEEECCEEEEEC T ss_conf 76666405765567876338997368655666306721572-68985121145312 No 48 >pfam04799 Fzo_mitofusin fzo-like conserved region. Family of putative transmembrane GTPase. The fzo protein is a mediator of mitochondrial fusion. This conserved region is also found in the human mitofusin protein. Probab=62.43 E-value=9.7 Score=16.73 Aligned_cols=54 Identities=24% Similarity=0.307 Sum_probs=42.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH---HHHHHHHHHHHHHCCC Q ss_conf 89999888799999989999999998875304989999---9999989999984056 Q gi|254780182|r 461 RLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLL---GIIKQELLSVKDELDT 514 (910) Q Consensus 461 rL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~---~iI~~EL~eik~kygd 514 (910) ||-+...--...++.|.++|.++|..|+.+-+.-+.++ ..+-.||...-+.|=. T Consensus 113 rLc~qVd~~~~~le~ei~~L~~ei~~LE~iq~~~K~LRnKA~~l~~eL~~F~~~yL~ 169 (171) T pfam04799 113 RLCQQVDVTSKDLEEEIAELTKEIQRLETIQSRSKLLRNKANLLENELEDFTKTFLT 169 (171) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 999998689999999999999999999999999899986898999999999997458 No 49 >PRK03298 hypothetical protein; Provisional Probab=61.79 E-value=8.4 Score=17.27 Aligned_cols=34 Identities=21% Similarity=0.170 Sum_probs=18.7 Q ss_pred ECCCCEEEEEEEC--CCCCEEEEEECCCEEEEEEHH Q ss_conf 1589857888961--898269999369859997587 Q gi|254780182|r 678 LDSRDEILSVETC--TQENDILLTTKLGQCVRFPIS 711 (910) Q Consensus 678 LkegD~Li~v~~~--~~~~~Iil~T~~G~~lrF~~~ 711 (910) +.+|=+++.--.- .|--||+..-++|........ T Consensus 119 ie~Gf~~v~rE~~T~~G~VDll~~D~~G~~V~VEiK 154 (224) T PRK03298 119 LGEGYTLVRREYMTAIGPVDLLCRDADGATVAVEIK 154 (224) T ss_pred HCCCCEEEEEEECCCCCCEEEEEECCCCCEEEEEEE T ss_conf 158989877873179883538998799999999998 No 50 >KOG0640 consensus Probab=61.53 E-value=10 Score=16.61 Aligned_cols=24 Identities=17% Similarity=0.220 Sum_probs=12.8 Q ss_pred CCCCCCCEEEEECCCCEEEEEEEE Q ss_conf 515687388980899879999983 Q gi|254780182|r 874 SRATKGVVIFSTAKDERVVSVERI 897 (910) Q Consensus 874 gR~a~GV~i~~L~~~D~Vv~va~i 897 (910) .|++--+++..|....-+.++.-- T Consensus 382 aRtadr~~l~slgHn~a~R~i~HS 405 (430) T KOG0640 382 ARTADRVALLSLGHNGAVRWIVHS 405 (430) T ss_pred CCCHHHHHHCCCCCCCCCEEEEEC T ss_conf 654345431025788873489857 No 51 >PRK10834 hypothetical protein; Provisional Probab=61.44 E-value=3.6 Score=20.53 Aligned_cols=125 Identities=22% Similarity=0.251 Sum_probs=61.0 Q ss_pred HHHHHC--CCCCCCH-HHHH----HHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHH-HHHHHHHHHHHHHHH-CCC Q ss_conf 556643--6688704-7899----999971220111561314788708877697201357-899978999999863-076 Q gi|254780182|r 78 SGEVMG--KYHPHGN-AAIY----DALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERY-TECRLQKAAHFLLDD-LGK 148 (910) Q Consensus 78 vg~v~g--kyHPHGd-~siy----~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RY-te~rl~~~~~~~l~~-i~~ 148 (910) ||-|+| ||++.|. +..| ||.+.+=+.=..++.|+.|. -|+.+.|.|.+||- --.+=- -++.++.| -.- T Consensus 47 valVLGtak~~~~G~pn~~~~~RldaA~~LY~~GKv~~iLvSGD--n~~~~YnEp~~Mk~~Li~~GV-P~e~I~~D~AGf 123 (239) T PRK10834 47 VGVVLGTAKYYRTGVINQYYRYRIQGAINAYNSGKVNYLLLSGD--NALQSYNEPMTMRKDLIAAGV-DPADIVLDYAGF 123 (239) T ss_pred EEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCC--CCCCCCCCHHHHHHHHHHCCC-CHHHEECCCCCC T ss_conf 69994576467899819899999999999998699748986689--998889828999999998599-899950566765 Q ss_pred CCCC----CEECCCCCCCCCEECCCCCCC---CHHCCCCCE-EEHHHHCCCC----CCHHHHHHHHHHHHH Q ss_conf 8405----330689885485034322732---110167610-1013317898----547899999988761 Q gi|254780182|r 149 DTVD----FRPNYDGSFQEPVVLCARYPN---VLVNGGGGI-AVGMATNIPT----HNLGEVVDGCVAVID 207 (910) Q Consensus 149 ~tv~----~~~n~D~~~~EP~vlP~~~P~---lL~nG~~GI-AvGmaTnipp----HNl~Ev~~a~~~~i~ 207 (910) .|-| -..-|+- ..-++.--+|-+ |.+--.-|| |+|++..-|- -.++|+..-+.+++| T Consensus 124 rT~DS~vRAk~VF~~--~~~iIVTQ~FH~~RAlfiAr~~GidA~g~~a~~~~~~~k~r~RE~~AR~ka~~D 192 (239) T PRK10834 124 RTLDSIVRTRKVFDT--NDFIIITQRFHCERALFIALHMGIQAQCYAVPSPKNMLSVRVREFAARFGALAD 192 (239) T ss_pred CHHHHHHHHHHHHCC--CCEEEEECCHHHHHHHHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 489999999998099--828999460138999999997498369971688654411059999999988856 No 52 >KOG1764 consensus Probab=60.45 E-value=8.5 Score=17.25 Aligned_cols=17 Identities=18% Similarity=0.173 Sum_probs=7.2 Q ss_pred HHHHHHHHHCCCEEEEEE Q ss_conf 889999870120389999 Q gi|254780182|r 235 TGIKNAYATGRGSIVIRG 252 (910) Q Consensus 235 ~~i~~~y~tGrG~i~iR~ 252 (910) -.+.+|+... +..-+|+ T Consensus 85 ~~v~~a~~~l-~~~~~~~ 101 (381) T KOG1764 85 LSVKKAFNAL-VQNGVRA 101 (381) T ss_pred CCHHHHHHHH-HHHEEEE T ss_conf 8499999988-8623763 No 53 >COG3953 SLT domain proteins [General function prediction only] Probab=60.29 E-value=3.6 Score=20.54 Aligned_cols=23 Identities=43% Similarity=0.670 Sum_probs=16.7 Q ss_pred CCCCCCC-CCCCCCCHHHHHHHHHH Q ss_conf 7887088-77697201357899978 Q gi|254780182|r 113 GQGNFGS-VDGDPPAAERYTECRLQ 136 (910) Q Consensus 113 g~GnfGs-~dgd~~AA~RYte~rl~ 136 (910) |||||=. +| -.+|||||++.|+- T Consensus 66 g~~ni~Npid-na~AAi~yi~~rYG 89 (235) T COG3953 66 GQGNILNPID-NAAAAIRYIKTRYG 89 (235) T ss_pred CCCCHHCHHH-HHHHHHHHHHHHCC T ss_conf 7400003266-89999998862225 No 54 >KOG0243 consensus Probab=60.07 E-value=11 Score=16.41 Aligned_cols=25 Identities=28% Similarity=0.363 Sum_probs=12.6 Q ss_pred CCCCCEEEHHHHCCCCCCHHHHHHH Q ss_conf 1676101013317898547899999 Q gi|254780182|r 177 NGGGGIAVGMATNIPTHNLGEVVDG 201 (910) Q Consensus 177 nG~~GIAvGmaTnippHNl~Ev~~a 201 (910) +|-.|+-|-=.--||-||-.|+..- T Consensus 220 ~~kggV~vkGlEEi~V~~A~ei~kl 244 (1041) T KOG0243 220 DGKGGVIVKGLEEIIVTNADEIYKL 244 (1041) T ss_pred CCCCCEEEECCEEEEECCHHHHHHH T ss_conf 7868679743526653465689999 No 55 >COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only] Probab=60.00 E-value=11 Score=16.40 Aligned_cols=63 Identities=17% Similarity=0.223 Sum_probs=30.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 999987899998887999999899999999988753049899999999989999984056883 Q gi|254780182|r 455 RAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRR 517 (910) Q Consensus 455 ~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RR 517 (910) .++=+++=++==.-|...++.....|..++.++.+.+..-+.........+..+.+.+++.|. T Consensus 83 ~~v~~~~e~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~~~i~~l~~~~~~~e~~~~e~~~ 145 (239) T COG1579 83 SAVKDERELRALNIEIQIAKERINSLEDELAELMEEIEKLEKEIEDLKERLERLEKNLAEAEA 145 (239) T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 612569999987889999999999999999999999998898899889999999988999999 No 56 >cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. Probab=59.67 E-value=11 Score=16.36 Aligned_cols=25 Identities=20% Similarity=0.259 Sum_probs=21.9 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2369999999998789999888799 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRD 471 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~ 471 (910) |+||++|-+||++....+|-.+.-+ T Consensus 43 ~~Lt~eqk~aV~~RD~~~ll~~Ggn 67 (106) T cd07925 43 FGLTPEQKQAVRNRDVLRMLEAGGN 67 (106) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCH T ss_conf 6999999999997369999990663 No 57 >TIGR02894 DNA_bind_RsfA transcription factor, RsfA family; InterPro: IPR014243 This entry represents a set of transcription factors found in some endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria). In some species these proteins are encoded multiple times. The best characterised protein in this entry is the prespore-specific transcription factor RsfA from Bacillus subtilis, previously known as YwfN. Expression of RsfA is controlled by sigma factor F, and it seems to improve the efficiency of sporulation by fine-tuning the expression of genes in the sigma F regulon, particularly the timing of their expression . It also negatively regulates spoIIR and its own synthesis. A paralog in B. subtilis is designated YlbO, though its function is not known. A highly variable linker region separates two very strongly conserved sequence regions within the protein. . Probab=59.55 E-value=11 Score=16.34 Aligned_cols=105 Identities=17% Similarity=0.218 Sum_probs=62.8 Q ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 999999999999988-8778999999874069999998618997898787763126978899999740221112223445 Q gi|254780182|r 368 VVVRRTKYLLNKARD-RAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGT 446 (910) Q Consensus 368 vi~rRt~~~L~ka~~-R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 446 (910) +|+++++-.++.|++ |.|---.--..-.-|..||....+-++...+-.. T Consensus 54 ~VRk~Y~~aI~lAKK~RK~~KRak~~~~lTl~~VI~FLq~~~~~~~~~~~------------------------------ 103 (163) T TIGR02894 54 VVRKRYEEAIELAKKQRKERKRAKKAESLTLQDVISFLQNLKTTNPSDQA------------------------------ 103 (163) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH------------------------------ T ss_conf 87585899999998861478864378626878899999998887799999------------------------------ Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEE Q ss_conf 236999999999878999988879999998999999999887530498999999999899999840568833100 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIV 521 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~ 521 (910) ...|.++|.+|...|.+++++|++=|..=.....+|-++-..+.+--.-.|+=.+. T Consensus 104 -------------------l~~E~~~L~~~~~~Lq~~ne~L~~el~~L~~~~~~~eEDY~~L~~IMdRARkl~~~ 159 (163) T TIGR02894 104 -------------------LQKENERLKKELESLQKRNEELEKELEKLEKRQSTIEEDYETLIDIMDRARKLAVV 159 (163) T ss_pred -------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf -------------------99899999999999999999999999999998467899999999999887375440 No 58 >pfam01939 DUF91 Protein of unknown function DUF91. The function of this prokaryotic protein is unknown. Probab=58.87 E-value=10 Score=16.56 Aligned_cols=32 Identities=19% Similarity=0.060 Sum_probs=15.6 Q ss_pred ECCCCEEEEEEECC--CCCEEEEEECCCEEEEEE Q ss_conf 15898578889618--982699993698599975 Q gi|254780182|r 678 LDSRDEILSVETCT--QENDILLTTKLGQCVRFP 709 (910) Q Consensus 678 LkegD~Li~v~~~~--~~~~Iil~T~~G~~lrF~ 709 (910) +.+|=+++.--.-. |--||+..-++|...... T Consensus 120 ie~G~~~v~rE~~T~~G~VDil~~D~~G~~VvVE 153 (228) T pfam01939 120 IEEGFKPVRREYQIAHGIVDILGKDEDGNIVILE 153 (228) T ss_pred HCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEE T ss_conf 2489899988852588736689987999999999 No 59 >PHA00728 hypothetical protein Probab=58.64 E-value=11 Score=16.22 Aligned_cols=66 Identities=14% Similarity=0.181 Sum_probs=42.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCEEEEEECC Q ss_conf 8879999998999999999887530498999999999899999840568833100134345301014567818999079 Q gi|254780182|r 467 GLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLLDMEDEDCIVREDMVVTVSHL 545 (910) Q Consensus 467 ~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~~i~~EdlI~~E~vvV~lS~~ 545 (910) +.|.+.|+.|-++|.++.++|+.+++++..-. -+++.+|-+-|-..-|+ +.+|+...+.+..||.+ T Consensus 4 ~teveql~keneelkkkla~leal~nne~~~~---~e~~~eiEnPYTVTNRa----------IsElV~PkDTMfYLsgn 69 (153) T PHA00728 4 KTEVEQLKKENEELKKKLAKLEALLNNESAEE---EEELQEIENPYTVTNRA----------ITELVEPKDTMFYLSGN 69 (153) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH---HHHHHHHCCCCEEHHHH----------HHHHCCCCCCEEEECCC T ss_conf 46899999866999999999999974788503---56687723871220578----------88755976415886377 No 60 >PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional Probab=58.34 E-value=11 Score=16.18 Aligned_cols=25 Identities=28% Similarity=0.270 Sum_probs=21.9 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2369999999998789999888799 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRD 471 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~ 471 (910) |+||++|-+||++....+|-.+.-+ T Consensus 54 ~~Lteeqr~aV~~RD~~~ll~lGgn 78 (117) T PRK13378 54 YGLNEEQKEAIRNRDVLQLLAAGGN 78 (117) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCH T ss_conf 6999999999997379999994674 No 61 >COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism] Probab=58.07 E-value=8 Score=17.47 Aligned_cols=47 Identities=34% Similarity=0.615 Sum_probs=36.4 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHCC--CCCHH--HHHHHHCCCCCEEEE Q ss_conf 5999924644352899999999998716--65014--458730374655799 Q gi|254780182|r 264 EQIVVTEIPYQVNKAAMLEKIAELVREK--RIVDI--ADLRDESDRQGYRVV 311 (910) Q Consensus 264 ~~ivItEiPY~vnk~~lie~Ia~lv~~~--ki~gI--~dirDeSdr~giRiv 311 (910) -+|.||--| +|.|+.++.+|++..+++ ++-|+ ..||+.--|.|.+|| T Consensus 6 mki~ITG~P-GvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR~gGkR~GF~Iv 56 (179) T COG1618 6 MKIFITGRP-GVGKTTLVLKIAEKLREKGYKVGGFITPEVREGGKRIGFKIV 56 (179) T ss_pred EEEEEECCC-CCCHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCEEEEEEEE T ss_conf 599986799-845899999999999855966513983114208827515999 No 62 >pfam07914 DUF1679 Protein of unknown function (DUF1679). The region featured in this family is found in a number of C. elegans proteins, in one case as a repeat. In many of the family members, this region is associated with the CHK region described by SMART as being found in ZnF_C4 and HLH domain-containing kinases. In fact, one member of this family is annotated as being a member of the nuclear hormone receptor family, and contains regions typical of such proteins (Interpro:IPR000536, Interpro:IPR008946, and Interpro:IPR001628). Probab=57.93 E-value=5.4 Score=18.97 Aligned_cols=64 Identities=19% Similarity=0.243 Sum_probs=46.8 Q ss_pred EEEHHHHCCCCCCHHHHHHHHHHHHHC-CCCCHHHHHHHCCCCCCCC--CCCCCCHHHHHHHHHHCCC Q ss_conf 010133178985478999999887618-7768888886345866887--4434475889999870120 Q gi|254780182|r 182 IAVGMATNIPTHNLGEVVDGCVAVIDN-PDIDLDALMEIIRGPDFPT--GAVILGRTGIKNAYATGRG 246 (910) Q Consensus 182 IAvGmaTnippHNl~Ev~~a~~~~i~~-p~~~~~eL~~~i~GPDFPT--GG~I~~~~~i~~~y~tGrG 246 (910) ..++|-.|+||..|-.|++|+..+-.. -..+.+|. +.+.||||.- =+..++.+++...|..=|. T Consensus 161 ~~~~~y~ni~~deL~~vv~~iA~fqA~~~~LseEE~-k~i~g~df~~~~~~~~~~~~~~~~~f~~lr~ 227 (413) T pfam07914 161 HTRHMYENIPADELIPVLRAIATFQALGESLSEEEK-KSANGADFLEQMFETFMSEEGLKGIFDQLRN 227 (413) T ss_pred EEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHH-HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 687254898989999999999999986434998997-5356757999999987236779999999975 No 63 >COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis] Probab=57.76 E-value=11 Score=16.11 Aligned_cols=80 Identities=24% Similarity=0.296 Sum_probs=40.2 Q ss_pred HHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99998618997898787763126978899999740221112223445236999999999878999988879999998999 Q gi|254780182|r 400 VVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNELNS 479 (910) Q Consensus 400 VI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~e 479 (910) .++.||+ +++.-+++|.++ +-+....+.|++|-- ++.++..+.++ T Consensus 3 d~k~ir~--n~d~v~~~l~~r---------------------------~~~~~~~~~~~~ld~------~~r~~~~~~e~ 47 (429) T COG0172 3 DLKLIRE--NPDAVREKLKKR---------------------------GGDALDVDKLLELDE------ERRKLLRELEE 47 (429) T ss_pred HHHHHHH--CHHHHHHHHHHC---------------------------CCCHHHHHHHHHHHH------HHHHHHHHHHH T ss_conf 4877650--999999987634---------------------------883767899999999------99999999999 Q ss_pred HHHHHHHHHHHHCC----HHHHHHHHHHHHHHHHHHCCC Q ss_conf 99999988753049----899999999989999984056 Q gi|254780182|r 480 LGIEIKECLDILSS----RSRLLGIIKQELLSVKDELDT 514 (910) Q Consensus 480 L~~~I~~l~~IL~s----~~~l~~iI~~EL~eik~kygd 514 (910) |+.+.+.+.+.++. ...-..-++.|..+++++..+ T Consensus 48 l~~~rn~~sk~ig~~~~~~~~~~~~l~~e~~~l~~~l~~ 86 (429) T COG0172 48 LQAERNELSKEIGRALKRGEDDAEELIAEVKELKEKLKE 86 (429) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf 999988999999987632621489999988988899872 No 64 >cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. Probab=57.72 E-value=11 Score=16.10 Aligned_cols=25 Identities=36% Similarity=0.472 Sum_probs=21.9 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2369999999998789999888799 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRD 471 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~ 471 (910) |+||++|-+||++....+|-.+.-+ T Consensus 43 ~~Lt~eqk~aV~~RD~~~ll~~Ggn 67 (106) T cd07921 43 FGLTEEQKQAVLDRDWLRLLELGGN 67 (106) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCH T ss_conf 6999999999997369999990663 No 65 >KOG3985 consensus Probab=57.70 E-value=11 Score=16.10 Aligned_cols=84 Identities=29% Similarity=0.414 Sum_probs=47.5 Q ss_pred CCCCCC---CE--ECCCCC-------CCCHHCCCCCEEEH--HHHCCCCCC--HHHHHHHHHHHHHCCCCCHHHHHHHCC Q ss_conf 988548---50--343227-------32110167610101--331789854--789999998876187768888886345 Q gi|254780182|r 158 DGSFQE---PV--VLCARY-------PNVLVNGGGGIAVG--MATNIPTHN--LGEVVDGCVAVIDNPDIDLDALMEIIR 221 (910) Q Consensus 158 D~~~~E---P~--vlP~~~-------P~lL~nG~~GIAvG--maTnippHN--l~Ev~~a~~~~i~~p~~~~~eL~~~i~ 221 (910) =||++| |. |||-.| |+-.-+|+---|-| --.--||++ ++|++-.+-.-+.+|.-+ +--+-.|. T Consensus 95 cGSLre~I~Pgd~v~p~q~IDrTt~R~~tffdg~~~~a~gVcHv~~~~pf~~k~reil~~~a~~l~~~~hd-~~tvVciE 173 (283) T KOG3985 95 CGSLREEIKPGDFVLPDQIIDRTTGRPSTFFDGSYDQAGGVCHVPFGPPFSQKLREILISTAKELTNPHHD-DGTVVCIE 173 (283) T ss_pred CCCCCCCCCCCCEECCHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHHHHHHHHCCCCCC-CEEEEEEE T ss_conf 24443458986675634554443367531115754578826761678872789999999998872687678-53699851 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHCCCEEE Q ss_conf 8668874434475889999870120389 Q gi|254780182|r 222 GPDFPTGAVILGRTGIKNAYATGRGSIV 249 (910) Q Consensus 222 GPDFPTGG~I~~~~~i~~~y~tGrG~i~ 249 (910) ||-|.|-+. -..|++--|++. T Consensus 174 GPrFStRAE-------S~mfR~wGa~vI 194 (283) T KOG3985 174 GPRFSTRAE-------SKMFRSWGASVI 194 (283) T ss_pred CCCCCHHHH-------HHHHHHHCCCEE T ss_conf 786541788-------889987451533 No 66 >TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand . Topoisomerase I require Mg2+ as a cofactor for catalysis to take place. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=57.61 E-value=3.1 Score=21.11 Aligned_cols=22 Identities=14% Similarity=0.163 Sum_probs=10.1 Q ss_pred CHHHHHHHHHHHHHH-HHHHCCC Q ss_conf 989999999998999-9984056 Q gi|254780182|r 493 SRSRLLGIIKQELLS-VKDELDT 514 (910) Q Consensus 493 s~~~l~~iI~~EL~e-ik~kygd 514 (910) |--++-+--++|.+. |.+.||+ T Consensus 347 DS~~lS~~A~~eaR~~I~~~yG~ 369 (688) T TIGR01051 347 DSTRLSNEAVNEARNLIDKNYGK 369 (688) T ss_pred CCHHHHHHHHHHHHHHHHHHCCH T ss_conf 30578999999999888862112 No 67 >KOG0291 consensus Probab=57.24 E-value=12 Score=16.04 Aligned_cols=152 Identities=19% Similarity=0.231 Sum_probs=73.5 Q ss_pred CCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCC--EEEEEECCCCEEEEECCCCCCC Q ss_conf 14567818999079705233100000233456521100014641010113323777--3999954893999820004322 Q gi|254780182|r 532 CIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHT--SVLFFSSLGFVYKEKVWRLPIG 609 (910) Q Consensus 532 lI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d--~LLfFTs~Gkvy~l~v~~IP~~ 609 (910) +-..-.+++..|-+|-++...+.-||--+ .. ..... ..|.|-+-| -.+.+--.=-+|-+.+|.+..| T Consensus 400 f~~~g~~llssSLDGtVRAwDlkRYrNfR-------Tf---t~P~p-~QfscvavD~sGelV~AG~~d~F~IfvWS~qTG 468 (893) T KOG0291 400 FTARGNVLLSSSLDGTVRAWDLKRYRNFR-------TF---TSPEP-IQFSCVAVDPSGELVCAGAQDSFEIFVWSVQTG 468 (893) T ss_pred EEECCCEEEEEECCCEEEEEEECCCCEEE-------EE---CCCCC-EEEEEEEECCCCCEEEEECCCEEEEEEEEEECC T ss_conf 99628789996238717843410332024-------31---27886-036688875888789960466178999980057 Q ss_pred CCCCCCCCCEEEEE-CCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCCC-EEEEEECCCCEEEEE Q ss_conf 44456554124545-3655620025663012566687179999479918984236862047772-278661589857888 Q gi|254780182|r 610 SPQARGKALINILS-LNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRNKLSDFIQINRSG-KIAMKLDSRDEILSV 687 (910) Q Consensus 610 sr~skG~pi~nll~-l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G-~~aikLkegD~Li~v 687 (910) ++++ |...|--+.-++++. ....|.-.+=+-.|+.... |. ++| .--+.+. -.+..+ T Consensus 469 ----------qllDiLsGHEgPVs~l~f~~-----~~~~LaS~SWDkTVRiW~i--f~---s~~~vEtl~i~--sdvl~v 526 (893) T KOG0291 469 ----------QLLDILSGHEGPVSGLSFSP-----DGSLLASGSWDKTVRIWDI--FS---SSGTVETLEIR--SDVLAV 526 (893) T ss_pred ----------EEEEHHCCCCCCCEEEEECC-----CCCEEEECCCCCEEEEEEE--EC---CCCEEEEEEEC--CCEEEE T ss_conf ----------14301327777610257756-----6686775135542788886--32---67603567602--211378 Q ss_pred EECCCCCEEEEEECCCEEEEEEHHHCCCC Q ss_conf 96189826999936985999758762354 Q gi|254780182|r 688 ETCTQENDILLTTKLGQCVRFPISAIRVF 716 (910) Q Consensus 688 ~~~~~~~~Iil~T~~G~~lrF~~~evr~~ 716 (910) ..-..+.+++++|-+|.+-.|+..+--.+ T Consensus 527 sfrPdG~elaVaTldgqItf~d~~~~~q~ 555 (893) T KOG0291 527 SFRPDGKELAVATLDGQITFFDIKEAVQV 555 (893) T ss_pred EECCCCCEEEEEEECCEEEEEEHHHCEEE T ss_conf 87479976889981564899882354241 No 68 >PRK04247 hypothetical protein; Provisional Probab=57.01 E-value=11 Score=16.40 Aligned_cols=35 Identities=23% Similarity=0.127 Sum_probs=20.3 Q ss_pred ECCCCEEEEEEECC--CCCEEEEEECCCEEEEEEHHH Q ss_conf 15898578889618--982699993698599975876 Q gi|254780182|r 678 LDSRDEILSVETCT--QENDILLTTKLGQCVRFPISA 712 (910) Q Consensus 678 LkegD~Li~v~~~~--~~~~Iil~T~~G~~lrF~~~e 712 (910) +.+|=+++.--.-. |--||+..-+.|........- T Consensus 144 ie~G~~~v~rE~~T~~G~VDil~~D~~G~~V~VEvKR 180 (250) T PRK04247 144 IEEGFRPVAREYETPAGIIDILGRDKEGNLVVLELKR 180 (250) T ss_pred HCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEEE T ss_conf 2589889988873598846489987998999999971 No 69 >pfam01401 Peptidase_M2 Angiotensin-converting enzyme. Members of this family are dipeptidyl carboxydipeptidases (cleave carboxyl dipeptides) and most notably convert angiotensin I to angiotensin II. Many members of this family contain a tandem duplication of the 600 amino acid peptidase domain, both of these are catalytically active. Most members are secreted membrane bound ectoenzymes. Probab=56.55 E-value=9.7 Score=16.70 Aligned_cols=40 Identities=10% Similarity=0.122 Sum_probs=24.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 8879999998999999999887530498999999999899999840568 Q gi|254780182|r 467 GLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 467 ~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~ 515 (910) ..|-..++++.+.|-.+++=|=+- |-..+..+ +.++||++ T Consensus 195 ~Ye~~~f~~~~e~lw~qvkPLY~~------LHayVR~k---L~~~YG~~ 234 (595) T pfam01401 195 WYESPTLEQDLERLYQELQPLYLN------LHAYVRRA---LHRHYGDQ 234 (595) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHH---HHHHCCCC T ss_conf 631143999999999998899999------99999999---99866621 No 70 >KOG1507 consensus Probab=56.44 E-value=7.8 Score=17.57 Aligned_cols=74 Identities=18% Similarity=0.244 Sum_probs=56.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC------CCCEEECCCCC Q ss_conf 999999878999988879999998999999999887530498999999999899999840568------83310013434 Q gi|254780182|r 453 QTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTP------RRTRIVEGLLD 526 (910) Q Consensus 453 QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~------RRT~I~~~~~~ 526 (910) +.-+-+.+||..|..+...-+++=-...+++|..|+.|-..-..+-.-..+|.-+|-.||... ||.+|+....+ T Consensus 48 ~~~~~~~~r~~~l~~~~s~~v~~Lp~~Vk~Rv~aLk~lQ~~~~~ie~~F~~e~~~LE~ky~~~yqplfdkR~eIi~g~~E 127 (358) T KOG1507 48 KLLSALDGRLASLAGLLSDMVENLPPAVKNRVLALKNLQLECDEIEAKFQEEVHELERKYAKLYQPLFDKRREIINGEVE 127 (358) T ss_pred HHHCCCCHHHHCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCC T ss_conf 55413411331346778046665699999999999998999999999999999999999998756499999999707766 No 71 >pfam08082 PRO8NT PRO8NT (NUC069), PrP8 N-terminal domain. The PRO8NT domain is found at the N-terminus of pre-mRNA splicing factors of PRO8 family. The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly variable proline-rich region. Probab=55.44 E-value=10 Score=16.50 Aligned_cols=56 Identities=30% Similarity=0.543 Sum_probs=39.6 Q ss_pred CCHHH-HHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH-HCCCCCC Q ss_conf 97367-899999998789999981134042556643668870478999999712201-1156131 Q gi|254780182|r 49 LKPVH-RRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMAQDW-SLRLLLI 111 (910) Q Consensus 49 lKpv~-Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~-~~r~pli 111 (910) +-|-| |+|+ .+-|-.+++.|+.--|+.=.-| ||-|| |||--|-+|-|+| ..||.=| T Consensus 4 mPPEhlRKIi---~dhgDmsskkf~~dkr~~lgaL-kY~Ph---Av~KLLEnmPmPWE~~r~V~V 61 (152) T pfam08082 4 MPPEHLRKII---KDHGDMSSKKFASDKRSYLGAL-KYMPH---ALLKLLENMPMPWEQVRYVKV 61 (152) T ss_pred CCHHHHHHHH---HHCCCCCHHHCCHHHHHHHHHH-HHHHH---HHHHHHHCCCCCHHHHCCEEE T ss_conf 9879999999---7445744011011358887677-54268---999998718985777403247 No 72 >KOG0315 consensus Probab=55.18 E-value=12 Score=15.78 Aligned_cols=107 Identities=8% Similarity=0.136 Sum_probs=57.7 Q ss_pred CEEEEEECCCCEE------EEECCCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEE Q ss_conf 7399995489399------9820004322444565541245453655620025663012566687179999479918984 Q gi|254780182|r 587 TSVLFFSSLGFVY------KEKVWRLPIGSPQARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRN 660 (910) Q Consensus 587 d~LLfFTs~Gkvy------~l~v~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt 660 (910) =.-|-+|+.++.. .++.|+|-.++ -.|+.+|-.-..+ |+ .+.|. .+...+.-.+.+|.+|-- T Consensus 43 VNrLeiTpdk~~LAaa~~qhvRlyD~~S~n----p~Pv~t~e~h~kN--Vt-aVgF~-----~dgrWMyTgseDgt~kIW 110 (311) T KOG0315 43 VNRLEITPDKKDLAAAGNQHVRLYDLNSNN----PNPVATFEGHTKN--VT-AVGFQ-----CDGRWMYTGSEDGTVKIW 110 (311) T ss_pred EEEEEECCCCCHHHHCCCCEEEEEECCCCC----CCCEEEEECCCCC--EE-EEEEE-----ECCEEEEECCCCCEEEEE T ss_conf 206997687124543248706999746899----9953687636786--68-99972-----357698854888348998 Q ss_pred CHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHH Q ss_conf 2368620477722786615898578889618982699993698599975876 Q gi|254780182|r 661 KLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISA 712 (910) Q Consensus 661 ~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~e 712 (910) .+....-.|- ++-.--+-.+.+-....+++..+.+|.+=..+..+ T Consensus 111 dlR~~~~qR~-------~~~~spVn~vvlhpnQteLis~dqsg~irvWDl~~ 155 (311) T KOG0315 111 DLRSLSCQRN-------YQHNSPVNTVVLHPNQTELISGDQSGNIRVWDLGE 155 (311) T ss_pred ECCCCCCCCC-------CCCCCCCCEEEECCCCCEEEEECCCCCEEEEECCC T ss_conf 6247021100-------15789743587469861488605878789987167 No 73 >TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241 This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. . Probab=53.61 E-value=7.1 Score=17.95 Aligned_cols=12 Identities=25% Similarity=0.816 Sum_probs=4.5 Q ss_pred HHHHHHHHHCCC Q ss_conf 899999998789 Q gi|254780182|r 54 RRILFGMMQMGV 65 (910) Q Consensus 54 Rrily~m~~~~~ 65 (910) ||+||++|+.|| T Consensus 48 Rk~Ly~LYdagl 59 (168) T TIGR00373 48 RKLLYKLYDAGL 59 (168) T ss_pred HHHHHHHHCCEE T ss_conf 899998730301 No 74 >PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional Probab=53.42 E-value=13 Score=15.56 Aligned_cols=25 Identities=20% Similarity=0.171 Sum_probs=22.0 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2369999999998789999888799 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRD 471 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~ 471 (910) |+||++|-+||++-....|..+.-+ T Consensus 55 ~~LTeEqk~aV~~RDw~~li~~Ggn 79 (119) T PRK13379 55 ADLTEQEKELIRARDWLGLVQYGAN 79 (119) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCH T ss_conf 5999999999996159999984763 No 75 >PRK07773 replicative DNA helicase; Validated Probab=52.63 E-value=13 Score=15.47 Aligned_cols=41 Identities=15% Similarity=0.261 Sum_probs=20.2 Q ss_pred CEEEEEECCCEEEEEECCCC--CCC-CCCCCCCEEEEECCC--CEEEEE Q ss_conf 64999945998999990105--544-515687388980899--879999 Q gi|254780182|r 851 DQIILVSDKGTLIRVPVNEI--RIA-SRATKGVVIFSTAKD--ERVVSV 894 (910) Q Consensus 851 DeIlliT~~G~iiR~~v~~I--~~~-gR~a~GV~i~~L~~~--D~Vv~v 894 (910) |+|.-|+.-|.- .|.++ |-+ .=.|+|..+-|--+- |-|+.+ T Consensus 776 DeIvsIe~~Gee---eVyDLTVpgtHNFVAndIivHNSIEQDAD~vi~l 821 (868) T PRK07773 776 DEIVEITSIGEE---EVFDGTVPGTHNFVANGISVHNSIEQDADLVILL 821 (868) T ss_pred EEEEEEEECCCE---EEEEEECCCCCCCEECCEEECCCCCCCCCEEEEE T ss_conf 458999887850---2577635676530056752116613247789997 No 76 >pfam06572 DUF1131 Protein of unknown function (DUF1131). This family consists of several hypothetical bacterial proteins of unknown function. Probab=52.35 E-value=14 Score=15.43 Aligned_cols=31 Identities=39% Similarity=0.601 Sum_probs=17.9 Q ss_pred CCEEEEEECCCCCEEEEE-E--CCCEEEEEECCC Q ss_conf 868999972899649999-4--599899999010 Q gi|254780182|r 839 GALVAVFPVNDNDQIILV-S--DKGTLIRVPVNE 869 (910) Q Consensus 839 g~lv~~~~V~~~DeIlli-T--~~G~iiR~~v~~ 869 (910) |.+|..+..-.+|++-|+ + .+|++-|+.|.+ T Consensus 79 G~iv~~fqAmk~d~V~lvI~G~~kGtV~RI~V~D 112 (192) T pfam06572 79 GQIVRYFQAMKGDQVKLVINGQPKGTVSRIDVMD 112 (192) T ss_pred CEEEEEEEEECCCCEEEEEECCCCCEEEEEEEEC T ss_conf 8199998760688179999668886499999855 No 77 >pfam01208 URO-D Uroporphyrinogen decarboxylase (URO-D). Probab=52.32 E-value=14 Score=15.43 Aligned_cols=29 Identities=7% Similarity=-0.042 Sum_probs=17.7 Q ss_pred HHHCCHHCCCCCEEEEEECCCCCCCCHHH Q ss_conf 97610110000002455416630002999 Q gi|254780182|r 328 YRYTSLQSLFSVNMVALNGYKPERFTLIG 356 (910) Q Consensus 328 yk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~ 356 (910) -.+...|..-++..+.+.|.-.-.|+-.. T Consensus 182 ~~~~~~qi~aGad~i~i~Ds~~~~ls~~~ 210 (337) T pfam01208 182 IEYLKAQIEAGADAIQIFDSWAGLLSPED 210 (337) T ss_pred HHHHHHHHHHCCCEEEEECCCCCCCCHHH T ss_conf 99999999829967998347888789899 No 78 >pfam03444 DUF293 Domain of unknown function. This domain is always found with a pair of CBS domains pfam00571. this region may be distantly related to the HrcA proteins of prokaryotes (Bateman A pers. obs.). Probab=51.04 E-value=12 Score=15.85 Aligned_cols=33 Identities=27% Similarity=0.541 Sum_probs=21.8 Q ss_pred CCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHC Q ss_conf 97367899999998789999981134042556643 Q gi|254780182|r 49 LKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMG 83 (910) Q Consensus 49 lKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~g 83 (910) |-|+||.||.+.-++-...+.| .||..|. +.++ T Consensus 2 LT~~Qr~IL~aLI~lY~~~~~p-Vks~~IA-e~l~ 34 (79) T pfam03444 2 LTPVQKEILQALINLYRKKGRA-VKGEEIA-DIIG 34 (79) T ss_pred CCHHHHHHHHHHHHHHHHCCCC-CCHHHHH-HHHC T ss_conf 7789999999999999972998-6679999-9987 No 79 >TIGR02687 TIGR02687 conserved hypothetical protein TIGR02687; InterPro: IPR014060 Members of this family are uncharacterised proteins sporadically distributed in bacteria and archaea, about 880 amino acids in length. Proteins in this entry are encoded by genes that are repeatedly found upstream of another uncharacterised gene which encodes proteins of about 470 amino acids in length (see IPR014061 from INTERPRO).. Probab=50.49 E-value=14 Score=15.22 Aligned_cols=11 Identities=27% Similarity=0.555 Sum_probs=5.6 Q ss_pred EEEEC-CCCEEE Q ss_conf 99947-991898 Q gi|254780182|r 649 VFATK-HGNVRR 659 (910) Q Consensus 649 vl~Tk-~G~VKk 659 (910) |+||. +|++-+ T Consensus 676 ilVTADHGFlYq 687 (911) T TIGR02687 676 ILVTADHGFLYQ 687 (911) T ss_pred EEEECCCCHHHH T ss_conf 588415561445 No 80 >COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown] Probab=50.40 E-value=14 Score=15.20 Aligned_cols=51 Identities=16% Similarity=0.034 Sum_probs=39.0 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHCCHHHH Q ss_conf 23699999999987899998887999999899999--9999887530498999 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRDDIRNELNSLG--IEIKECLDILSSRSRL 497 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~--~~I~~l~~IL~s~~~l 497 (910) -+||-.|+.+.+.+|++-|..||..++..=-.+.- --|+.|-+.|+-+... T Consensus 15 ~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~ 67 (284) T COG1426 15 KGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDE 67 (284) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCHHH T ss_conf 49999999988577599999986677010641576789999999996899899 No 81 >TIGR00034 aroFGH phospho-2-dehydro-3-deoxyheptonate aldolase; InterPro: IPR006219 Members of this group catalyze the first enzymatic reaction of the shikimate pathway. The common (shikimate) pathway links metabolism of carbohydrates to biosynthesis of aromatic amino acids phenylalanine, tyrosine, tryptophan, and derivatives in microorganisms and in plants. In a sequence of seven enzymatic reactions, D-erythrose 4-phosphate (E4P), an intermediate of the pentose phosphate pathway, and phosphoenol pyruvate (PEP), a glycolytic intermediate, are converted to chorismate. The pathway begins with the stereospecific condensation of E4P and PEP to yield 7-phospho 2-dehydro 3-deoxy-D-arabino-heptulosonate (DAHP), catalyzed by 3-deoxy-7-phosphoheptulonate synthase (DAHPS) (EC 2.5.1.54, formerly EC 4.1.2.15). The divalent metal cation requirement of this enzyme can be satisfied by a broad range of metals . A Cys residue in a Cys-X-X-His motif has been identified as part of a metal binding site . In Escherichia coli, the enzyme exists in three isoforms, each specifically inhibited by one of the three aromatic amino acids. DAHP synthetases fall into two classes, class I (represented by this entry) and class II (represented by PIRSF015573 from PIRSF). Class I was believed to be limited to microorganisms and class II to plants. However, a more recent study showed that class II also contains enzymes from a microbial eukaryote and several bacteria . Brick and Woodard proposed that the difference between the two classes lies in their metal ion requirement for activity. Whereas class I requires no metal cation, class II is dependent on a metal cation for activity. However, recently a class I DAHP synthase from Thermotoga maritima has been purified, characterised, and shown to be a metalloenzyme . The three-dimentional structures of DAHP synthases have been determined , , , , . The DAHPS(Phe) monomer is a (beta/alpha)8 barrel with an additional N-terminal beta strand and helices and an extra beta sheet near the C terminus . The active site is located in a cleft at the carboxyl end of the barrel . The allosteric feedback inhibition binding site of DAHPS(Phe) is composed of residues from two adjacent subunits of a tight dimer and is at least 20 angstroms away from the closest active site . The absence of the shikimate pathway in animals makes it an attractive target for nontoxic herbicidal, antimicrobial, and antifungal agents. The nontoxic herbicide glyphosphate competitively inhibits 3-phosphoshikimate 1-carboxyvinyltransferase, the sixth enzymatic reaction of the pathway.; GO: 0003849 3-deoxy-7-phosphoheptulonate synthase activity, 0009073 aromatic amino acid family biosynthetic process. Probab=50.39 E-value=11 Score=16.28 Aligned_cols=30 Identities=7% Similarity=0.150 Sum_probs=14.5 Q ss_pred EEEEECCCCCEEEEEECCCEE-EEEEHHHCC Q ss_conf 888961898269999369859-997587623 Q gi|254780182|r 685 LSVETCTQENDILLTTKLGQC-VRFPISAIR 714 (910) Q Consensus 685 i~v~~~~~~~~Iil~T~~G~~-lrF~~~evr 714 (910) ..+.-|.|+.+-.++=+.|+. =-|+..+|. T Consensus 217 ~ai~~T~GN~~~HiILRGG~~GPNY~a~~V~ 247 (348) T TIGR00034 217 MAIVQTSGNPDGHIILRGGKKGPNYDAADVA 247 (348) T ss_pred EEEEECCCCCCCEEEECCCCCCCCCCHHHHH T ss_conf 6787526798524886168767688988899 No 82 >KOG1359 consensus Probab=50.30 E-value=12 Score=15.86 Aligned_cols=12 Identities=25% Similarity=0.482 Sum_probs=4.5 Q ss_pred CCCCCHHCCCCC Q ss_conf 273211016761 Q gi|254780182|r 170 RYPNVLVNGGGG 181 (910) Q Consensus 170 ~~P~lL~nG~~G 181 (910) +.|.+-+.|+++ T Consensus 56 q~p~i~v~G~~k 67 (417) T KOG1359 56 QGPTIQVKGSDK 67 (417) T ss_pred CCCEEEEECCCC T ss_conf 564499812665 No 83 >pfam07746 LigA Aromatic-ring-opening dioxygenase LigAB, LigA subunit. This is a family of aromatic ring opening dioxygenases which catalyse the ring-opening reaction of protocatechuate and related compounds. Probab=49.64 E-value=15 Score=15.11 Aligned_cols=25 Identities=28% Similarity=0.264 Sum_probs=22.2 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2369999999998789999888799 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRD 471 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~ 471 (910) |+||+.|-+||++-...+|..+.-+ T Consensus 28 ~~Lt~eqr~av~~rD~~~L~~~G~n 52 (88) T pfam07746 28 YGLTEEQKAAVRARDWNGLIALGGN 52 (88) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCH T ss_conf 7999999999982669999994585 No 84 >PRK06904 replicative DNA helicase; Validated Probab=49.60 E-value=15 Score=15.10 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=14.3 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 98999999999899999840568 Q gi|254780182|r 493 SRSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 493 s~~~l~~iI~~EL~eik~kygd~ 515 (910) ++......|-..|+.+.+.++-| T Consensus 354 ~r~~ei~~isr~LK~lAkel~ip 376 (472) T PRK06904 354 NRTLEIAEISRSLKALAKELKVP 376 (472) T ss_pred CHHHHHHHHHHHHHHHHHHHCCC T ss_conf 78899999999999999997998 No 85 >cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi Probab=49.28 E-value=15 Score=15.06 Aligned_cols=25 Identities=16% Similarity=0.033 Sum_probs=21.8 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2369999999998789999888799 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRD 471 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~ 471 (910) |+||++|-+||++....+|..+.-+ T Consensus 35 ~~Lt~eqk~av~~RDw~~mi~~Ggn 59 (94) T cd07923 35 AGLTEEERTLIRNRDWIGMIRYGVI 59 (94) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCH T ss_conf 6999999999996169999983764 No 86 >KOG3584 consensus Probab=49.26 E-value=15 Score=15.06 Aligned_cols=19 Identities=16% Similarity=0.083 Sum_probs=14.9 Q ss_pred HHHHHHHHHHHHHHHHCCC Q ss_conf 9999999989999984056 Q gi|254780182|r 496 RLLGIIKQELLSVKDELDT 514 (910) Q Consensus 496 ~l~~iI~~EL~eik~kygd 514 (910) .+++-+++||+.+|+.|-. T Consensus 326 NQNKaLIEELKtLKeLYc~ 344 (348) T KOG3584 326 NQNKALIEELKTLKELYCH 344 (348) T ss_pred CCCHHHHHHHHHHHHHHHC T ss_conf 1458999999989998623 No 87 >PRK10718 hypothetical protein; Provisional Probab=49.05 E-value=15 Score=15.04 Aligned_cols=59 Identities=36% Similarity=0.602 Sum_probs=31.6 Q ss_pred EEEEECCCCEEEEEHHH-------------CCCCCCCCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEE--ECCCEEEE Q ss_conf 99997599345301788-------------4866757741488760677776868999972899649999--45998999 Q gi|254780182|r 800 ILTVSEKGFGKRTSSYD-------------FRISNRSGKGIRATDVSKINEIGALVAVFPVNDNDQIILV--SDKGTLIR 864 (910) Q Consensus 800 IL~vTe~G~GKRt~~~e-------------yr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlli--T~~G~iiR 864 (910) =|.||+.|-|..|...- ||+ |. |..+ ..|.+|..+..-.+|++-++ -++|++-| T Consensus 38 ~l~vs~~GVG~Ita~Tpm~e~aI~~aL~g~Y~l--Rs--GM~t-------~~G~iv~~fqA~k~d~V~lvi~G~kgtV~r 106 (191) T PRK10718 38 STKVSEQGVGEITASTPLQEQAIADALDGDYRL--RS--GMKT-------ANGNVVRFFEAMKGDQVAMVINGQQGTVSR 106 (191) T ss_pred CEEEECCCCCCCCCCCCCCHHHHHHHHCCCCEE--CC--CCEE-------CCCEEEEEEEECCCCEEEEEEECCCCEEEE T ss_conf 338842653431358836789999874897366--36--5521-------498499988541788189999668863999 Q ss_pred EECCC Q ss_conf 99010 Q gi|254780182|r 865 VPVNE 869 (910) Q Consensus 865 ~~v~~ 869 (910) +.|.+ T Consensus 107 I~V~D 111 (191) T PRK10718 107 IDVLD 111 (191) T ss_pred EEEEC T ss_conf 99855 No 88 >PRK13695 putative NTPase; Provisional Probab=48.37 E-value=14 Score=15.32 Aligned_cols=46 Identities=28% Similarity=0.617 Sum_probs=32.9 Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHCC--CCCHH--HHHHHHCCCCCEEEE Q ss_conf 999924644352899999999998716--65014--458730374655799 Q gi|254780182|r 265 QIVVTEIPYQVNKAAMLEKIAELVREK--RIVDI--ADLRDESDRQGYRVV 311 (910) Q Consensus 265 ~ivItEiPY~vnk~~lie~Ia~lv~~~--ki~gI--~dirDeSdr~giRiv 311 (910) .|.||=-| ++.|+.|+.||.+...+. ++.|. ..+|+...|-|..++ T Consensus 5 kI~iTG~P-GvGKTTli~Kv~~~L~~~g~~v~GF~T~Evre~G~R~GF~vv 54 (174) T PRK13695 5 RIGITGMP-GVGKTTLVLKIAELLAREGYKVGGFITEEVREGGKRIGFKII 54 (174) T ss_pred EEEEECCC-CCCHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCEEEEEEEE T ss_conf 99987899-988999999999998636961746995256038828505999 No 89 >PRK10727 DNA-binding transcriptional regulator GalR; Provisional Probab=48.09 E-value=14 Score=15.42 Aligned_cols=61 Identities=13% Similarity=0.181 Sum_probs=38.2 Q ss_pred HHHHCCCCCCCCCCH-HHHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHCCCCCCCHHHHHHHHHHHCC Q ss_conf 863137540008973-678999999987899999811----340425566436688704789999997122 Q gi|254780182|r 37 ILGRAIPDLRDGLKP-VHRRILFGMMQMGVEWNKKYV----KCARISGEVMGKYHPHGNAAIYDALARMAQ 102 (910) Q Consensus 37 I~~RAlPd~rDGlKp-v~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~gkyHPHGd~siy~a~v~maq 102 (910) -|||+|=+- .+..| ..+||+=++.+||..||..-+ +..+++|-+++.+. ...|..+++-.+ T Consensus 17 TVSrvLN~~-~~Vs~~Tr~rV~~aa~eLgY~Pn~~Ar~L~~~~s~~Igviv~~~~----~~f~~~~~~~i~ 82 (342) T PRK10727 17 TVSRVINNS-PKASEASRLAVHSAMESLSYHPNANARALAQQSTETVGLVVGDVS----DPFFGAMVKAVE 82 (342) T ss_pred HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCEEEEEECCCC----CCHHHHHHHHHH T ss_conf 999997797-999999999999999993998588888650177887999958775----421467788999 No 90 >TIGR02707 butyr_kinase butyrate kinase; InterPro: IPR011245 This group represents bacterial butyrate kinase, an enzyme that facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate . The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-CoA:acetate CoA-transferase, the latter providing the dominant route for butyrate formation in human colonic bacteria .; GO: 0005524 ATP binding, 0047761 butyrate kinase activity, 0016310 phosphorylation, 0005737 cytoplasm. Probab=47.36 E-value=16 Score=14.83 Aligned_cols=30 Identities=13% Similarity=0.171 Sum_probs=11.3 Q ss_pred CCCCCCCCCCCCCE-EEEECCCCEEEEEEEEC Q ss_conf 10554451568738-89808998799999835 Q gi|254780182|r 868 NEIRIASRATKGVV-IFSTAKDERVVSVERIR 898 (910) Q Consensus 868 ~~I~~~gR~a~GV~-i~~L~~~D~Vv~va~i~ 898 (910) +-|=.||=-|..-. ++.--. ++|.|+|.|. T Consensus 296 DAI~LTGGlAys~~f~v~~I~-~~v~fIAPv~ 326 (353) T TIGR02707 296 DAIILTGGLAYSKYFFVSEIR-KRVSFIAPVL 326 (353) T ss_pred EEEEECCCHHCCCCHHHHHHH-HCCCEECCEE T ss_conf 689854601306204558776-1332103668 No 91 >TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=47.13 E-value=16 Score=14.81 Aligned_cols=92 Identities=12% Similarity=0.229 Sum_probs=42.2 Q ss_pred EEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEE--EEECCCCCEEEEEECCCEEEE-----EEHHHCCCCCCCCC Q ss_conf 99947991898423686204777227866158985788--896189826999936985999-----75876235478665 Q gi|254780182|r 649 VFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILS--VETCTQENDILLTTKLGQCVR-----FPISAIRVFAGRNS 721 (910) Q Consensus 649 vl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~--v~~~~~~~~Iil~T~~G~~lr-----F~~~evr~~~GR~a 721 (910) .+.|++|.++-..+ |...+-.-..-++..++-++.. ...++.....++++..|+... |..++.... -.- T Consensus 1111 ~~F~R~G~~~i~~~--~~~~k~~~~~~~~V~~~Q~V~KG~~l~~~~~Ge~~v~~~~G~~~~~~~~f~i~~ee~~~--~V~ 1186 (1552) T TIGR02386 1111 ILFSRKGSLKILRY--FQELKTVEISELKVLDSQKVIKGENLVVDKKGEEIVVSEEGRIKIEDKKFLIVEEEEVV--PVK 1186 (1552) T ss_pred EEEEECCEEEEEEE--ECHHHEEECCEEEEECCCEEECCCEEEECCCCCEEEECCCCEEEEECCCEEEECCCEEE--ECC T ss_conf 57863260788762--00100110012564057355337136765888767707888788505857764032156--426 Q ss_pred CCEEEEECCCCCEEEEEEEECCCC Q ss_conf 535767528998699989733666 Q gi|254780182|r 722 VGVRGISLAKGDQVISMAIVLHAD 745 (910) Q Consensus 722 ~GVkgIkL~~~D~Vv~~~vi~~~~ 745 (910) .|+ -|....||.|-...++...| T Consensus 1187 ~G~-~i~V~~g~~V~~G~~~aefD 1209 (1552) T TIGR02386 1187 LGT-KILVEDGDAVKEGQRIAEFD 1209 (1552) T ss_pred CCC-EEEEECCCCCCCCCEEEEEC T ss_conf 566-88861586205887578844 No 92 >COG3879 Uncharacterized protein conserved in bacteria [Function unknown] Probab=47.00 E-value=16 Score=14.79 Aligned_cols=64 Identities=16% Similarity=0.242 Sum_probs=44.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHH----HHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCEEEEEEC Q ss_conf 799999989999999998875304989----9999999989999984056883310013434530101456781899907 Q gi|254780182|r 469 GRDDIRNELNSLGIEIKECLDILSSRS----RLLGIIKQELLSVKDELDTPRRTRIVEGLLDMEDEDCIVREDMVVTVSH 544 (910) Q Consensus 469 E~~kl~~E~~eL~~~I~~l~~IL~s~~----~l~~iI~~EL~eik~kygd~RRT~I~~~~~~i~~EdlI~~E~vvV~lS~ 544 (910) |...+++...+|..+++.|++-++|-. .....|-++|..++.--|.- -+.-+-++||++. T Consensus 58 e~~s~Q~~~~~L~~ev~~~~~~~~s~~~~~~t~~~~ie~~l~~l~~~aG~v----------------~V~G~Gl~ITi~d 121 (247) T COG3879 58 ELRSLQKKVNTLAAEVEDLENKLDSVRRSVLTDDAALEDRLEKLRMLAGSV----------------PVTGPGLVITIDD 121 (247) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----------------CCCCCCEEEEECC T ss_conf 989999999999999999999998877767769999999999998885557----------------7747857999658 Q ss_pred CCEE Q ss_conf 9705 Q gi|254780182|r 545 LGYV 548 (910) Q Consensus 545 ~GyI 548 (910) .||. T Consensus 122 ~~~~ 125 (247) T COG3879 122 PGYS 125 (247) T ss_pred CCCC T ss_conf 9878 No 93 >PRK04778 septation ring formation regulator EzrA; Provisional Probab=46.18 E-value=16 Score=14.69 Aligned_cols=28 Identities=29% Similarity=0.296 Sum_probs=13.8 Q ss_pred HCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH Q ss_conf 11561314788708877697201357899978999 Q gi|254780182|r 105 SLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAA 139 (910) Q Consensus 105 ~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~ 139 (910) .+|--|...-..||. |....|.+|+.+. T Consensus 151 ~lrk~ll~~~~~yG~-------a~~~LE~~L~~le 178 (569) T PRK04778 151 ELRKSLLANSFSFGP-------ALDELEKQLENLE 178 (569) T ss_pred HHHHHHHHHCCCCCH-------HHHHHHHHHHHHH T ss_conf 999999985221033-------6999999999999 No 94 >pfam06160 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. Probab=46.17 E-value=16 Score=14.69 Aligned_cols=20 Identities=25% Similarity=0.132 Sum_probs=9.2 Q ss_pred CCCCCCHHHHHHHHHHHHHH Q ss_conf 63000299999999999999 Q gi|254780182|r 348 KPERFTLIGILKAFVAFREE 367 (910) Q Consensus 348 ~P~~l~Lk~iL~~fi~hR~e 367 (910) +|.+......+..|+.|-.+ T Consensus 301 k~~V~~~~~~i~~~l~~~~~ 320 (559) T pfam06160 301 KKFVEKNIDKLTDFLEHARE 320 (559) T ss_pred HHHHHHHHHHHHHHHHHHHH T ss_conf 99999857889999999999 No 95 >pfam07798 DUF1640 Protein of unknown function (DUF1640). This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured. Probab=46.11 E-value=16 Score=14.69 Aligned_cols=38 Identities=29% Similarity=0.395 Sum_probs=19.5 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 36999999999878999988879999998999999999887530 Q gi|254780182|r 448 YLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDIL 491 (910) Q Consensus 448 ~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL 491 (910) .++..+|+.=|||- ||+-.+++|......+|.++..=+ T Consensus 99 ei~k~~a~~klDlN------leK~riree~~~~e~ki~e~~~kI 136 (177) T pfam07798 99 EIDKVTAGVRLDLN------LEKGRIREELAEQELKIKETDTKI 136 (177) T ss_pred HHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99986152576545------552077899987999999999899 No 96 >cd04618 CBS_pair_5 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera Probab=45.98 E-value=13 Score=15.65 Aligned_cols=69 Identities=17% Similarity=0.286 Sum_probs=45.6 Q ss_pred CCCCCHHHHHHHHHHHHCCCCCCCCE--EEEHHHHH--------HHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCC- Q ss_conf 00897367899999998789999981--13404255--------66436688704789999997122011156131478- Q gi|254780182|r 46 RDGLKPVHRRILFGMMQMGVEWNKKY--VKCARISG--------EVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQ- 114 (910) Q Consensus 46 rDGlKpv~Rrily~m~~~~~~~~~~~--~K~a~ivg--------~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~- 114 (910) -|+--|| ++-+++|.+.|...- |- .+..+.|| +++--.|-|-+.|+|||.-.|-|.=.-|.|++|.. T Consensus 6 ~D~~l~v-k~Af~al~~ngi~~a-plWds~~~~fvGmLt~~DfI~il~lv~i~P~~sL~da~~~l~~~~ihrlPvid~~~ 83 (98) T cd04618 6 FDTKLPV-KKAFNALVENGIRSA-PLWDSRKQQFVGMLTITDFILILRLVSIHPERSLFDAALLLLKNKIHRLPVIDPST 83 (98) T ss_pred EECCCCH-HHHHHHHHHCCCEEE-EEECCCCCEEEEEEEHHHHHHHHHHEECCCCCHHHHHHHHHHHCCCCCCCCCCCCC T ss_conf 9489758-999999998692699-98728876788886479999887624448761299999999867875052164799 Q ss_pred CC Q ss_conf 87 Q gi|254780182|r 115 GN 116 (910) Q Consensus 115 Gn 116 (910) || T Consensus 84 ~~ 85 (98) T cd04618 84 GT 85 (98) T ss_pred CC T ss_conf 96 No 97 >COG2949 SanA Uncharacterized membrane protein [Function unknown] Probab=45.21 E-value=14 Score=15.24 Aligned_cols=151 Identities=25% Similarity=0.311 Sum_probs=70.9 Q ss_pred HHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHC--CCCCCCHHHHH-----HHHHHHCCCHHCCCCCCCCCCCCCCCCCCC Q ss_conf 67899999998789999981134042556643--66887047899-----999971220111561314788708877697 Q gi|254780182|r 52 VHRRILFGMMQMGVEWNKKYVKCARISGEVMG--KYHPHGNAAIY-----DALARMAQDWSLRLLLIEGQGNFGSVDGDP 124 (910) Q Consensus 52 v~Rrily~m~~~~~~~~~~~~K~a~ivg~v~g--kyHPHGd~siy-----~a~v~maq~~~~r~plidg~GnfGs~dgd~ 124 (910) .+|-|-|+ --++.++.+-.--+|-||-|+| ||-+.|---.| +|.+.+=+-=..+|.|+.|. .++..-+. T Consensus 35 ~dr~i~~~--t~~~i~~~~~~lP~r~vgvVLGtsky~~~g~~N~yy~~Ri~aA~~ly~~gKV~~LLlSGD--N~~~sYnE 110 (235) T COG2949 35 ADRWISWA--TAGLIYDDIQDLPARQVGVVLGTSKYLAKGPPNRYYTYRIDAAIALYKAGKVNYLLLSGD--NATVSYNE 110 (235) T ss_pred HHHHHHHH--HCCCCCCCHHHCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEEEECC--CCCCCCCC T ss_conf 87887765--347621685458862048997223002479955768999999999986477049998168--77534654 Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-CCCCCC----CEECCCCCCCCCEECCCCCCC---CHHCCCCCE-EEHHHHCCC---- Q ss_conf 2013578999789999998630-768405----330689885485034322732---110167610-101331789---- Q gi|254780182|r 125 PAAERYTECRLQKAAHFLLDDL-GKDTVD----FRPNYDGSFQEPVVLCARYPN---VLVNGGGGI-AVGMATNIP---- 191 (910) Q Consensus 125 ~AA~RYte~rl~~~~~~~l~~i-~~~tv~----~~~n~D~~~~EP~vlP~~~P~---lL~nG~~GI-AvGmaTnip---- 191 (910) |-+|+=---++---++.|+-|- .--|.| -..-||-.. =++.--+|-+ |.+--.-|| |+|+++-=| T Consensus 111 p~tM~kdL~~~GVp~~~i~lDyAGFrTLDSvvRA~kVF~~~~--ftIItQ~FHceRAlfiA~~~gIdAic~~ap~p~~~~ 188 (235) T COG2949 111 PRTMRKDLIAAGVPAKNIFLDYAGFRTLDSVVRARKVFGTND--FTIITQRFHCERALFIARQMGIDAICFAAPDPEGRS 188 (235) T ss_pred HHHHHHHHHHCCCCHHHEEECCCCCCHHHHHHHHHHHCCCCC--EEEEECCCCCHHHHHHHHHHCCCEEEECCCCCCCCC T ss_conf 589999999839988890320037417898998998707672--799820123488999999829754786589944467 Q ss_pred --CCCHHHHHHHHHHHHHC Q ss_conf --85478999999887618 Q gi|254780182|r 192 --THNLGEVVDGCVAVIDN 208 (910) Q Consensus 192 --pHNl~Ev~~a~~~~i~~ 208 (910) +--++|+..-+.|++|- T Consensus 189 ~~~vrlRE~~ARv~Av~D~ 207 (235) T COG2949 189 GLSVRLREFLARVKAVLDL 207 (235) T ss_pred CCEEHHHHHHHHHHHHHHH T ss_conf 7020799999888787410 No 98 >pfam05400 FliT Flagellar protein FliT. This family contains several bacterial flagellar FliT proteins. The flagellar proteins FlgN and FliT have been proposed to act as substrate specific export chaperones, facilitating incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum. In Salmonella typhimurium flgN and fliT mutants, the export of target HAPs is reduced, concomitant with loss of unincorporated flagellin into the surrounding medium. Probab=45.18 E-value=17 Score=14.58 Aligned_cols=42 Identities=12% Similarity=0.181 Sum_probs=34.3 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 999999988753049899999999989999984056883310 Q gi|254780182|r 479 SLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRI 520 (910) Q Consensus 479 eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I 520 (910) +......-++.||.++.+++.++...|.++.+.++.-||..- T Consensus 60 ~~~~~~~lL~~IL~nda~IR~Ll~prl~~Ls~li~q~~~q~~ 101 (109) T pfam05400 60 EQEQKRELLQKILDNEAEIKDLLQPRLDELSQLIGQSRRQQS 101 (109) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999987999999889999999999988788889 No 99 >pfam01255 Prenyltransf Putative undecaprenyl diphosphate synthase. Previously known as uncharacterized protein family UPF0015, a single member of this family has been identified as an undecaprenyl diphosphate synthase. Probab=45.00 E-value=17 Score=14.55 Aligned_cols=64 Identities=11% Similarity=0.084 Sum_probs=32.1 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 4523699999999987899998887999999899999999988753049899999999989999984056883 Q gi|254780182|r 445 GTMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRR 517 (910) Q Consensus 445 ~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RR 517 (910) ++|+=+....+++.++=.+.|. .+..++.+ -.---.++++.+.+-.-+++.+.++.+.-...++ T Consensus 50 EN~~R~~~Ev~~L~~l~~~~l~--------~~~~~~~~-~~iki~~iG~~~~Lp~~l~~~i~~~e~~T~~n~~ 113 (222) T pfam01255 50 ENWKRPKEEVDFLMELLEEKLR--------RLLEDLHK-NGVRVRVIGDLSLLPEDLRKAIEDAEEATKNNTG 113 (222) T ss_pred HHCCCCHHHHHHHHHHHHHHHH--------HHHHHHHH-CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCC T ss_conf 7549998999999999999999--------99999998-6938999526556898999999999997157885 No 100 >pfam02650 HTH_WhiA Sporulation Regulator WhiA C terminal domain. This domain is found at the C terminal of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure. WhiA is a distant homologue of LAGLIDADG homing endonucleases. Probab=44.68 E-value=17 Score=14.52 Aligned_cols=38 Identities=18% Similarity=0.323 Sum_probs=18.2 Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEECCCCCH Q ss_conf 89999999999871665014458730374655799994798877 Q gi|254780182|r 277 KAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVIELKRGASA 320 (910) Q Consensus 277 k~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivielKr~~~~ 320 (910) ...+.+.+.++.+.-.++. -+ ..|. =+.++.+|+..+. T Consensus 41 ~~~~a~~l~~~l~~~~~~~--k~---~~r~-~~~ivYlK~~e~I 78 (191) T pfam02650 41 DEEFAEQLQKLLNEFGLNA--KI---IERR-NKYVVYLKDAEQI 78 (191) T ss_pred CHHHHHHHHHHHHHCCCCC--EE---EEEC-CCEEEEECCHHHH T ss_conf 8999999999999779984--69---8876-9569998579999 No 101 >PRK05595 replicative DNA helicase; Provisional Probab=43.86 E-value=18 Score=14.42 Aligned_cols=23 Identities=22% Similarity=0.450 Sum_probs=16.4 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 98999999999899999840568 Q gi|254780182|r 493 SRSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 493 s~~~l~~iI~~EL~eik~kygd~ 515 (910) ++......|-..|+.+.+.++-| T Consensus 331 ~r~~ev~~isr~LK~lAkel~ip 353 (444) T PRK05595 331 SRQQEVSEISRSIKALAKEMECP 353 (444) T ss_pred CHHHHHHHHHHHHHHHHHHHCCC T ss_conf 89999999999999999996997 No 102 >KOG4248 consensus Probab=43.84 E-value=18 Score=14.42 Aligned_cols=34 Identities=29% Similarity=0.294 Sum_probs=11.8 Q ss_pred HHHHHHHHHHHHHHHHHHCCCC-CCCCEECCCCCC Q ss_conf 3578999789999998630768-405330689885 Q gi|254780182|r 128 ERYTECRLQKAAHFLLDDLGKD-TVDFRPNYDGSF 161 (910) Q Consensus 128 ~RYte~rl~~~~~~~l~~i~~~-tv~~~~n~D~~~ 161 (910) ||--|+||.+|-+.++.++... |++|..|-+|++ T Consensus 268 ~r~~~~r~~~fl~~~~e~ln~~~t~~~n~nh~g~e 302 (1143) T KOG4248 268 LRRLESRLQPFLQRYYEVLNAAATTDYNNNHEGRE 302 (1143) T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCCHH T ss_conf 99999988899999999861352022114654304 No 103 >COG2312 Erythromycin esterase homolog [General function prediction only] Probab=43.69 E-value=7.2 Score=17.86 Aligned_cols=48 Identities=33% Similarity=0.515 Sum_probs=36.2 Q ss_pred EEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCC--CCCCCCHHHH Q ss_conf 340425566436688704789999997122011156131478870887--7697201357 Q gi|254780182|r 73 KCARISGEVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFGSV--DGDPPAAERY 130 (910) Q Consensus 73 K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~GnfGs~--dgd~~AA~RY 130 (910) +-+|||+ +|.=- ||+..+|.+=+||-+. ||+-+| |+++ .-|.|.+++- T Consensus 43 ~~~RiV~--LGE~s-HGt~e~~~~k~rm~r~------Lvee~G-f~~iA~EA~~~d~~av 92 (405) T COG2312 43 TDARIVL--LGEPS-HGTGEFFAFKARMFRA------LVEELG-FRAIAFEADFPDAQAV 92 (405) T ss_pred CCCEEEE--ECCCC-CCCCHHHHHHHHHHHH------HHHHHC-CCEEEECCCCHHHHHH T ss_conf 6773898--43777-7740789999999999------999838-6268741683778889 No 104 >PRK06266 transcription initiation factor E subunit alpha; Validated Probab=42.46 E-value=18 Score=14.37 Aligned_cols=14 Identities=21% Similarity=0.506 Sum_probs=6.5 Q ss_pred CCCHHHHHHHHHHH Q ss_conf 88778999999976 Q gi|254780182|r 317 GASADVILNQLYRY 330 (910) Q Consensus 317 ~~~~~~vln~Lyk~ 330 (910) +...+.|-+-||+. T Consensus 47 gi~lN~VRk~LY~L 60 (178) T PRK06266 47 GIKLNTVRKILYKL 60 (178) T ss_pred CCCHHHHHHHHHHH T ss_conf 99789999999999 No 105 >PRK05431 seryl-tRNA synthetase; Provisional Probab=42.39 E-value=18 Score=14.25 Aligned_cols=82 Identities=23% Similarity=0.355 Sum_probs=41.7 Q ss_pred HHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH Q ss_conf 999861899789878776312697889999974022111222344523699999999987-8999988879999998999 Q gi|254780182|r 401 VRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILEL-RLARLTGLGRDDIRNELNS 479 (910) Q Consensus 401 I~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdM-rL~rLt~LE~~kl~~E~~e 479 (910) |+.||. |++..+.+|-.|. + ..-.+.|+++ .-+|-...+.+.|+.|... T Consensus 4 ik~IRe--Npe~v~~~lkkR~-------------------------~---~~~id~il~lD~~rr~l~~e~e~Lr~erN~ 53 (422) T PRK05431 4 IKLIRE--NPDAVKEKLAKRG-------------------------D---PLDVDELLELDEERRELQTETEELQAERNA 53 (422) T ss_pred HHHHHH--CHHHHHHHHHHCC-------------------------C---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 789874--9999999998659-------------------------8---451999999999999999999999999999 Q ss_pred HHHHHHHHHHHHCCHHH---HHHHHHHHHHHHHHHC Q ss_conf 99999988753049899---9999999899999840 Q gi|254780182|r 480 LGIEIKECLDILSSRSR---LLGIIKQELLSVKDEL 512 (910) Q Consensus 480 L~~~I~~l~~IL~s~~~---l~~iI~~EL~eik~ky 512 (910) +.++|..+.+-=.+.+. ..+-+++++.++.++. T Consensus 54 iSK~Ig~~kk~g~~~~~l~~~~~~lk~~i~~le~~~ 89 (422) T PRK05431 54 LSKEIGQAKAKGEDAEELIAEVKELKEEIKALEAEL 89 (422) T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999987489779999999999999999999999 No 106 >cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. Probab=42.22 E-value=18 Score=14.23 Aligned_cols=21 Identities=29% Similarity=0.561 Sum_probs=17.7 Q ss_pred CCCHHHHHHHHHH-HHCCCCCC Q ss_conf 8973678999999-98789999 Q gi|254780182|r 48 GLKPVHRRILFGM-MQMGVEWN 68 (910) Q Consensus 48 GlKpv~Rrily~m-~~~~~~~~ 68 (910) +|-|.||||+... +.|||.+. T Consensus 25 ~lsp~qRrivh~La~~lGL~h~ 46 (60) T cd02639 25 SLSPAERRIVHLLASRLGLNHV 46 (60) T ss_pred CCCHHHHHHHHHHHHHCCCCEE T ss_conf 9999999999999988199204 No 107 >PRK05729 valS valyl-tRNA synthetase; Reviewed Probab=42.17 E-value=18 Score=14.22 Aligned_cols=53 Identities=19% Similarity=0.450 Sum_probs=31.2 Q ss_pred HHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCC----CHHCCCCCCCCCCC Q ss_conf 8999999987899999811340425566436688704789999997122----01115613147887 Q gi|254780182|r 54 RRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMAQ----DWSLRLLLIEGQGN 116 (910) Q Consensus 54 Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq----~~~~r~plidg~Gn 116 (910) ..+.--||+-|+-+ +.-++| .|-|+-.+++-++=|-... -|..+|||.|+.+- T Consensus 155 ~~~F~~L~~kGliy-----r~~~~V-----~wcp~~~Tals~~EV~~~~~~~~~~~ikf~l~~~~~~ 211 (877) T PRK05729 155 REVFVRLYEKGLIY-----RGKRLV-----NWDPKLQTALSDLEVEYKEVKGKLWHIRYPLADGSDY 211 (877) T ss_pred HHHHHHHHHCCCEE-----ECCEEC-----CCCCCCCCHHHHHHHHCCCCCCCEEEEECCCCCCCCE T ss_conf 99999999889978-----413123-----6688778843567873245667338984132478874 No 108 >cd04585 CBS_pair_ACT_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms. They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these CBS domains are associated with a downstream ACT domain, which is linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The i Probab=42.14 E-value=18 Score=14.22 Aligned_cols=75 Identities=19% Similarity=0.269 Sum_probs=35.1 Q ss_pred CCCCCCCCCCHH----HHHHHHHHHHCCCCCC---CCEEEEHHHHHHHHCCCCC---CCHHHHHHHHHHHCCCHHCCCCC Q ss_conf 375400089736----7899999998789999---9811340425566436688---70478999999712201115613 Q gi|254780182|r 41 AIPDLRDGLKPV----HRRILFGMMQMGVEWN---KKYVKCARISGEVMGKYHP---HGNAAIYDALARMAQDWSLRLLL 110 (910) Q Consensus 41 AlPd~rDGlKpv----~Rrily~m~~~~~~~~---~~~~K~a~ivg~v~gkyHP---HGd~siy~a~v~maq~~~~r~pl 110 (910) ++|=+-+| |++ +|-|+.+|...+...+ ..+.....-|+++|- -+| +.|.++++|+-.|.+.---+.|. T Consensus 26 ~lpVvd~~-~lvGiit~~Di~~~~~~~~~~~~~~~~~~~~~~~~v~~im~-~~~~tv~~~~~l~~a~~~m~~~~i~~lpV 103 (122) T cd04585 26 RLPVVDRG-KLVGIVTDRDLKLASPSKATTLDIWELYYLLSKIKVSDIMT-RDPITVSPDASVEEAAELMLERKISGLPV 103 (122) T ss_pred EEEEEECC-EEEEEEEHHHHHHHHHCCCCCCCHHHHHCCCCCCCHHHHCC-CCCEEEECCCCHHHHHHHHHHCCCCEEEE T ss_conf 89999899-99999988999987750465533355421203889999577-89889938866999999998759878999 Q ss_pred CCCCCCC Q ss_conf 1478870 Q gi|254780182|r 111 IEGQGNF 117 (910) Q Consensus 111 idg~Gnf 117 (910) +|.+|.+ T Consensus 104 vd~~g~l 110 (122) T cd04585 104 VDDQGRL 110 (122) T ss_pred EECCCEE T ss_conf 9589989 No 109 >pfam04849 HAP1_N HAP1 N-terminal conserved region. This family represents an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntington's disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34. Probab=42.02 E-value=19 Score=14.20 Aligned_cols=45 Identities=18% Similarity=0.228 Sum_probs=38.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCC Q ss_conf 999999899999999988753049899999999989999984056 Q gi|254780182|r 470 RDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDT 514 (910) Q Consensus 470 ~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd 514 (910) ...++...+.+..+-+++...|...+..-..+..||.+++++|.. T Consensus 244 i~dLq~r~k~l~~EnEEL~~~L~~~ke~Q~~L~~El~el~~rY~E 288 (307) T pfam04849 244 IVDLQKKCKSYALENEELQQHLAAAKDAQRQLQAELQELQDKYAE 288 (307) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999988548999999999899899999999999999999 No 110 >pfam10168 Nup88 Nuclear pore component. Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells. Probab=41.93 E-value=19 Score=14.19 Aligned_cols=11 Identities=18% Similarity=0.081 Sum_probs=4.2 Q ss_pred HHHHHHHHHHH Q ss_conf 98887789999 Q gi|254780182|r 380 ARDRAHVLVGL 390 (910) Q Consensus 380 a~~R~HILeGL 390 (910) .++|.++|... T Consensus 563 i~kRV~~L~~q 573 (717) T pfam10168 563 FQRRVKLLQLQ 573 (717) T ss_pred HHHHHHHHHHH T ss_conf 99999999999 No 111 >COG0305 DnaB Replicative DNA helicase [DNA replication, recombination, and repair] Probab=41.64 E-value=19 Score=14.16 Aligned_cols=54 Identities=20% Similarity=0.289 Sum_probs=36.2 Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 7898547899999988761877688888863458668874434475889999870 Q gi|254780182|r 189 NIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYAT 243 (910) Q Consensus 189 nippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~t 243 (910) ..||||+.--.-.+=+++-+|+. .+....++..-||+...+=.=-..+.+.|+. T Consensus 1 ~~~p~~~eAE~~vLG~il~~~~~-~~~i~~~l~~~dFy~~~H~~IF~a~~~l~~~ 54 (435) T COG0305 1 RLPPQDIEAEQAVLGGILLDPDA-IERVSERLRPEDFYRPAHRLIYQAILDLYGQ 54 (435) T ss_pred CCCCCCHHHHHHHHHHHHCCHHH-HHHHHHHCCHHHCCCHHHHHHHHHHHHHHHC T ss_conf 98997779999986654048888-9999972685320767899999999999866 No 112 >cd04600 CBS_pair_HPP_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is uncertain, but they are thought to be transporters. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Probab=41.63 E-value=19 Score=14.16 Aligned_cols=28 Identities=14% Similarity=0.296 Sum_probs=15.2 Q ss_pred HHHHHHHHHHHCCCHHCCCCCCCCCCCC Q ss_conf 4789999997122011156131478870 Q gi|254780182|r 90 NAAIYDALARMAQDWSLRLLLIEGQGNF 117 (910) Q Consensus 90 d~siy~a~v~maq~~~~r~plidg~Gnf 117 (910) |+++.+|+-.|.+.--.++|.+|.+|.+ T Consensus 10 ~~tl~~a~~~m~~~~~~~lpVvd~~g~l 37 (124) T cd04600 10 DTSLEEAWALLRRHRIKALPVVDGDRRL 37 (124) T ss_pred CCCHHHHHHHHHHCCCCEEEEEECCCCE T ss_conf 3979999999997299789999569808 No 113 >COG4939 Major membrane immunogen, membrane-anchored lipoprotein [Function unknown] Probab=41.23 E-value=19 Score=14.11 Aligned_cols=47 Identities=21% Similarity=0.208 Sum_probs=35.9 Q ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHH-----HHHHHHHHHHHHHHCCCCCCC Q ss_conf 15613147887088776972013578-----999789999998630768405 Q gi|254780182|r 106 LRLLLIEGQGNFGSVDGDPPAAERYT-----ECRLQKAAHFLLDDLGKDTVD 152 (910) Q Consensus 106 ~r~plidg~GnfGs~dgd~~AA~RYt-----e~rl~~~~~~~l~~i~~~tv~ 152 (910) -.|-.-++.|||-|-|.|-+-+|.|- +--++.+|..|++--+.+-|| T Consensus 62 ~~ydy~~k~G~~Ks~DAdy~~~mk~~~g~gp~~~f~~laD~Lve~q~p~~Vd 113 (147) T COG4939 62 CTYDYRDKKGNIKSDDADYAGEMKYMKGQGPVQGFSTLADKLVEVQDPNEVD 113 (147) T ss_pred EEEEEECCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCEE T ss_conf 8855064778736653336777777416377899999999987248945055 No 114 >PRK08082 consensus Probab=41.12 E-value=19 Score=14.09 Aligned_cols=22 Identities=27% Similarity=0.465 Sum_probs=13.0 Q ss_pred HHHHHHHHHHHHHHHHHHCCCC Q ss_conf 8999999999899999840568 Q gi|254780182|r 494 RSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 494 ~~~l~~iI~~EL~eik~kygd~ 515 (910) +......|-..|+.+.+.++-| T Consensus 335 r~~ev~~isr~LK~lAkel~ip 356 (453) T PRK08082 335 RQQEVSEISRTLKALARELEVP 356 (453) T ss_pred HHHHHHHHHHHHHHHHHHHCCC T ss_conf 9999999999999999996997 No 115 >cd04469 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome. Probab=40.38 E-value=17 Score=14.51 Aligned_cols=16 Identities=38% Similarity=0.762 Sum_probs=7.4 Q ss_pred HHHHHHHHCCCEEEEE Q ss_conf 8999987012038999 Q gi|254780182|r 236 GIKNAYATGRGSIVIR 251 (910) Q Consensus 236 ~i~~~y~tGrG~i~iR 251 (910) -|.+||+.||||+++- T Consensus 39 Rl~~Afe~grgsVR~L 54 (75) T cd04469 39 RLKTAFESGRGSVRVL 54 (75) T ss_pred HHHHHHHCCCCCEEEE T ss_conf 9999976489839999 No 116 >COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription] Probab=40.13 E-value=20 Score=13.98 Aligned_cols=23 Identities=17% Similarity=0.517 Sum_probs=12.9 Q ss_pred CCCEEEEECCCCCEEEEEEEECC Q ss_conf 55357675289986999897336 Q gi|254780182|r 721 SVGVRGISLAKGDQVISMAIVLH 743 (910) Q Consensus 721 a~GVkgIkL~~~D~Vv~~~vi~~ 743 (910) ..|++|.-.-++|++||.....+ T Consensus 200 ~~~i~GaPVvd~dk~vGiit~~d 222 (294) T COG2524 200 EKGIRGAPVVDDDKIVGIITLSD 222 (294) T ss_pred HCCCCCCCEECCCCEEEEEEHHH T ss_conf 72866785102894589998899 No 117 >pfam04637 Herpes_pp85 Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25). This family includes UL25 proteins from HCMV, as well as U14 proteins from HHV 6 and HHV7. These 85 kD phosphoproteins appear to act as structural antigens, but their precise function is otherwise unknown. Probab=39.82 E-value=20 Score=13.94 Aligned_cols=180 Identities=21% Similarity=0.284 Sum_probs=98.9 Q ss_pred CCEECCCCCCCCHHCCCCCEEEHHHHCC-----CCCCHHHHHHHHHHH--HHCCCCCHHHHHHHCCCCCCCCCCCCCCHH Q ss_conf 8503432273211016761010133178-----985478999999887--618776888888634586688744344758 Q gi|254780182|r 163 EPVVLCARYPNVLVNGGGGIAVGMATNI-----PTHNLGEVVDGCVAV--IDNPDIDLDALMEIIRGPDFPTGAVILGRT 235 (910) Q Consensus 163 EP~vlP~~~P~lL~nG~~GIAvGmaTni-----ppHNl~Ev~~a~~~~--i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~ 235 (910) ||++-=+-+=|-+.|| .|+++-|-|.+ ||+ ..-+-.++.-+ -.+.+..-..|+..+--=|.|.|-. .. T Consensus 66 ~~VIrl~V~iN~y~ng-~~~L~~m~~~~~~l~~~~~-~~rl~~gL~~L~~a~~~~~~p~~l~~~l~~~~ltdg~~---~~ 140 (502) T pfam04637 66 RPVIRLAVLINHYYNG-KGILRHMRAALKSLMNPPT-MRRLDRGLRRLCRALQDSDNPPDLSESLGDLDLTDGQY---KA 140 (502) T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCCHH-HHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHH---HH T ss_conf 9999999999999988-9999999999998629547-89999999887540137987589998726689866899---99 Q ss_pred HHHHHHHHCCCEEEEEEEEEEEEC---CCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEE Q ss_conf 899998701203899998865433---67845999924644352899999999998716650144587303746557999 Q gi|254780182|r 236 GIKNAYATGRGSIVIRGVSHIEKT---SGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDESDRQGYRVVI 312 (910) Q Consensus 236 ~i~~~y~tGrG~i~iR~k~~ie~~---~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDeSdr~giRivi 312 (910) .++.+|...+ ++-.|-..+.+.. =+. ++.- ...|-=++++.+--. -+.++|+.+-..+ .+|.+. T Consensus 141 ~L~~l~~l~~-s~~~~~~~~~~~~y~~Lr~-yN~L-f~~P~ft~~eAv~lY---------~~NL~dLt~~~~~-~l~Llt 207 (502) T pfam04637 141 ALRTLYRLLK-SLGLRESPELESCYETLRA-YNLL-FKPPRFTTREAVDLY---------AENLADLTQRINR-PLRLLT 207 (502) T ss_pred HHHHHHHHHH-HCCCCCCHHHHHHHHHHHH-CCCC-CCCCCCCHHHHHHHH---------HHHHHHHHHHCCC-CCEEEE T ss_conf 9999999998-6078864567888999865-0001-268764218999999---------9999997652268-860676 Q ss_pred EECCCCCHHHHHHHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 94798877899999997610110000002455416630002999999999999999999 Q gi|254780182|r 313 ELKRGASADVILNQLYRYTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVR 371 (910) Q Consensus 313 elKr~~~~~~vln~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~r 371 (910) ..|+.-+++-|+|.++-...+. ||+.-... .| ..|..||-++.+.+.- T Consensus 208 ~~~~~~~~e~vlND~lFLls~~-----nmi~~~~~-----~l-r~LR~wI~~qln~l~e 255 (502) T pfam04637 208 TIKRSKTPEDVLNDLLFLLSLG-----NMIYRHRR-----EL-RALRKWIVLQLNSLCE 255 (502) T ss_pred EECCCCCHHHHHHHHHHHHHHH-----HHHHHHHH-----HH-HHHHHHHHHHHHHHHH T ss_conf 3068897488898999999888-----89999999-----99-9999999999999999 No 118 >KOG1684 consensus Probab=39.78 E-value=12 Score=15.99 Aligned_cols=15 Identities=20% Similarity=0.233 Sum_probs=7.3 Q ss_pred CHHHHHHHHHHHCCC Q ss_conf 047899999971220 Q gi|254780182|r 89 GNAAIYDALARMAQD 103 (910) Q Consensus 89 Gd~siy~a~v~maq~ 103 (910) =+-++|-.|+-..++ T Consensus 66 Mv~~~~~~L~~we~s 80 (401) T KOG1684 66 MVLSIYPKLVEWEKS 80 (401) T ss_pred HHHHHHHHHHHHCCC T ss_conf 899889988754027 No 119 >KOG0428 consensus Probab=39.48 E-value=20 Score=13.90 Aligned_cols=10 Identities=40% Similarity=0.830 Sum_probs=4.5 Q ss_pred CCCCCCCCCC Q ss_conf 4788708877 Q gi|254780182|r 112 EGQGNFGSVD 121 (910) Q Consensus 112 dg~GnfGs~d 121 (910) -+.|-.||+| T Consensus 123 ~p~GAlGSlD 132 (314) T KOG0428 123 KPEGALGSLD 132 (314) T ss_pred CCCCCCCCCC T ss_conf 9887534676 No 120 >PRK05617 enoyl-CoA hydratase; Provisional Probab=39.39 E-value=19 Score=14.11 Aligned_cols=30 Identities=17% Similarity=0.318 Sum_probs=18.5 Q ss_pred HCCCCCEEEHHHHCCCC-CCHHHHHHHHHHH Q ss_conf 01676101013317898-5478999999887 Q gi|254780182|r 176 VNGGGGIAVGMATNIPT-HNLGEVVDGCVAV 205 (910) Q Consensus 176 ~nG~~GIAvGmaTnipp-HNl~Ev~~a~~~~ 205 (910) +||+.-+..|+||..-| .++.++.+++..+ T Consensus 175 l~~~Da~~~GlA~~~v~s~~~~~l~~~L~~~ 205 (356) T PRK05617 175 ISAADALYAGLADHFVPSADLPAFLDALEAT 205 (356) T ss_pred CCHHHHHHCCCCCEECCHHHHHHHHHHHHHC T ss_conf 6999998749442235874699999999826 No 121 >pfam03131 bZIP_Maf bZIP Maf transcription factor. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Thus, this family is probably related to pfam00170. Probab=39.28 E-value=20 Score=13.88 Aligned_cols=37 Identities=14% Similarity=0.245 Sum_probs=25.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 99999989999999998875304989999999998999998405 Q gi|254780182|r 470 RDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELD 513 (910) Q Consensus 470 ~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kyg 513 (910) ...|+.|..+|..++..|+.= ..-+..|...++.||- T Consensus 55 ~~~LE~e~~~L~~e~e~Lk~E-------~~~~~~E~d~~k~K~e 91 (95) T pfam03131 55 RHELEKEKSQLQQQVEQLKQE-------NARLRRERDALKAKYE 91 (95) T ss_pred HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHH T ss_conf 999999999999999999999-------9999999999999998 No 122 >cd03677 MM_CoA_mutase_beta Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta heterodimers. For P. shermanni MCM, it is known that only the alpha subunit binds coenzyme B12 and substrates. The role of the beta subunit is unclear. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. Methylobacterium extorquens MCM participates in the glyoxylate regeneration pathway. In M. extorquens, MCM forms a complex with MeaB; MeaB may protect MCM from irreversib Probab=39.25 E-value=20 Score=13.87 Aligned_cols=23 Identities=26% Similarity=0.439 Sum_probs=13.9 Q ss_pred EEEEEECCCCCCCHHHHHHHHHH Q ss_conf 59999246443528999999999 Q gi|254780182|r 264 EQIVVTEIPYQVNKAAMLEKIAE 286 (910) Q Consensus 264 ~~ivItEiPY~vnk~~lie~Ia~ 286 (910) ..|.|.--+|+-.-+..++.+|- T Consensus 181 ~~i~idg~~~~~AGAt~vQELA~ 203 (424) T cd03677 181 RAITVDAVPYHNAGATAAQELAY 203 (424) T ss_pred EEEEEECHHHHHCCCCHHHHHHH T ss_conf 07998526687679999999999 No 123 >cd03823 GT1_ExpE7_like This family is most closely related to the GT1 family of glycosyltransferases. ExpE7 in Sinorhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucans (exopolysaccharide II). Probab=39.01 E-value=20 Score=13.84 Aligned_cols=12 Identities=17% Similarity=0.163 Sum_probs=4.5 Q ss_pred CCCHHHHHHHHH Q ss_conf 447588999987 Q gi|254780182|r 231 ILGRTGIKNAYA 242 (910) Q Consensus 231 I~~~~~i~~~y~ 242 (910) |.-.+.+++.|. T Consensus 148 i~~S~~~~~~~~ 159 (359) T cd03823 148 IAPSRFLLDRYV 159 (359) T ss_pred EECCHHHHHHHH T ss_conf 999999999999 No 124 >COG3253 ywfI Predicted heme peroxidase involved in anaerobic stress response [General function prediction only] Probab=38.72 E-value=9.2 Score=16.91 Aligned_cols=11 Identities=27% Similarity=0.093 Sum_probs=5.5 Q ss_pred CEEEEEECCCC Q ss_conf 45999924644 Q gi|254780182|r 263 REQIVVTEIPY 273 (910) Q Consensus 263 k~~ivItEiPY 273 (910) ..-.|.-|+|+ T Consensus 178 yEwvV~~e~dd 188 (230) T COG3253 178 YEWVVTYEADD 188 (230) T ss_pred EEEEEEEECCC T ss_conf 58999984676 No 125 >KOG2941 consensus Probab=38.46 E-value=21 Score=13.78 Aligned_cols=30 Identities=20% Similarity=0.245 Sum_probs=10.7 Q ss_pred CCCEEEEHHHHHHHHCCCCCCCHHHHHHHHH Q ss_conf 9981134042556643668870478999999 Q gi|254780182|r 68 NKKYVKCARISGEVMGKYHPHGNAAIYDALA 98 (910) Q Consensus 68 ~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v 98 (910) +.|+.+++|.+---+||.- |+.-.|..||- T Consensus 152 ~h~lV~l~~~~E~~fgk~a-~~nLcVT~AMr 181 (444) T KOG2941 152 QHPLVRLVRWLEKYFGKLA-DYNLCVTKAMR 181 (444) T ss_pred CCCHHHHHHHHHHHHHCCC-CCCHHHHHHHH T ss_conf 8705889999999861334-32224588899 No 126 >PRK08840 replicative DNA helicase; Provisional Probab=38.18 E-value=21 Score=13.74 Aligned_cols=23 Identities=26% Similarity=0.447 Sum_probs=15.8 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 98999999999899999840568 Q gi|254780182|r 493 SRSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 493 s~~~l~~iI~~EL~eik~kygd~ 515 (910) ++......|-..|+.+.+.++-| T Consensus 349 ~r~~~i~~isr~lK~lAkel~vp 371 (464) T PRK08840 349 NRTLEIAEISRSLKALAKELNVP 371 (464) T ss_pred HHHHHHHHHHHHHHHHHHHHCCC T ss_conf 36789999999999999996998 No 127 >TIGR01465 cobM_cbiF precorrin-4 C11-methyltransferase; InterPro: IPR006362 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase . There are at least two distinct cobalamin biosynthetic pathways in bacteria : Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobM and CibF precorrin-4 C11-methyltransferase (2.1.1.133 from EC), both as stand-alone enzymes and when CobJ forms part of a bifunctional enzyme. In the aerobic pathway, CobM catalyses the methylation of precorrin-4 at C-11 to yield precorrin-5. The extruded acyl group is then removed in the subsequent step catalysed by CobF. In the anaerobic pathway, CibF catalyses the methylation of cobalt-precorrin-4 to cobalt-precoriin-5 . Nomenclature note: occasionally precorrin-4 C11-methyltransferase is one of two methyltransferases often referred to as precorrin-3 methylase (the other is precorrin-3 methylase (the other is precorrin-4 C11-methyltransferase, 2.1.1.131 from EC). ; GO: 0046026 precorrin-4 C11-methyltransferase activity, 0009236 cobalamin biosynthetic process. Probab=38.11 E-value=13 Score=15.57 Aligned_cols=14 Identities=43% Similarity=0.741 Sum_probs=5.7 Q ss_pred CHHHHHHHHHHHCC Q ss_conf 04789999997122 Q gi|254780182|r 89 GNAAIYDALARMAQ 102 (910) Q Consensus 89 Gd~siy~a~v~maq 102 (910) ||-|||.|+.=+-| T Consensus 80 GDPsIYGA~~EQ~~ 93 (252) T TIGR01465 80 GDPSIYGAIAEQMQ 93 (252) T ss_pred CCHHHHHHHHHHHH T ss_conf 87557766999999 No 128 >pfam10458 Val_tRNA-synt_C Valyl tRNA synthetase tRNA binding arm. This domain is found at the C-terminus of Valyl tRNA synthetases. Probab=38.02 E-value=21 Score=13.72 Aligned_cols=34 Identities=24% Similarity=0.174 Sum_probs=26.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH Q ss_conf 8799999989999999998875304989999999 Q gi|254780182|r 468 LGRDDIRNELNSLGIEIKECLDILSSRSRLLGII 501 (910) Q Consensus 468 LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI 501 (910) -|..+|..|++.+.++|..++.-|+++.-+.+.= T Consensus 4 ~E~~RL~Kel~kl~~~i~~~~~kL~N~~Fv~kAP 37 (66) T pfam10458 4 KERARLEKELAKLQKEIERLQKKLSNPGFVAKAP 37 (66) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCC T ss_conf 8999899999999999999998778767777098 No 129 >cd04603 CBS_pair_KefB_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the KefB (Kef-type K+ transport systems) domain which is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Probab=38.01 E-value=15 Score=14.94 Aligned_cols=86 Identities=17% Similarity=0.133 Sum_probs=52.8 Q ss_pred HHHHHHHHHH---HCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCC--CCCHHHHHHHHHHHCCCH Q ss_conf 8777998863---13754000897367899999998789999981134042556643668--870478999999712201 Q gi|254780182|r 30 LTYAINVILG---RAIPDLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYH--PHGNAAIYDALARMAQDW 104 (910) Q Consensus 30 l~Ya~svI~~---RAlPd~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyH--PHGd~siy~a~v~maq~~ 104 (910) |.-|+..+.+ ||+|=|-++.||+-==-+-.|.+ +.++ .-+---|+|+|=+=- -|-|++++|||-.|.|.- T Consensus 12 L~~a~~~~~e~~~~~i~VVD~~~k~vG~it~~Dll~--~~~~---~~~~~~V~d~m~~~v~~i~~~~~v~dalr~~~~~~ 86 (111) T cd04603 12 LREAIKMINELGARAVVVVDEENKVLGQVTLSDLLE--IGPN---DYETLKVCEVYIVPVPIVYCDSKVTDLLRIFRETE 86 (111) T ss_pred HHHHHHHHHHCCCCEEEEECCCCCEEEEEEHHHHHH--HCHH---HHHCCCHHHHHCCCCCCCCCCCCHHHHHHHHHHCC T ss_conf 999999998769976899889996889988999864--3844---55324387751567746389976899999987449 Q ss_pred HCCCCCCCCCCCC-CCC Q ss_conf 1156131478870-887 Q gi|254780182|r 105 SLRLLLIEGQGNF-GSV 120 (910) Q Consensus 105 ~~r~plidg~Gnf-Gs~ 120 (910) .-+.|.+|+-|.| |.| T Consensus 87 ~~~l~VVD~~grlvGiI 103 (111) T cd04603 87 PPVVAVVDKEGKLVGTI 103 (111) T ss_pred CCEEEEECCCCCEEEEE T ss_conf 98899993899799999 No 130 >cd04597 CBS_pair_DRTGG_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Probab=37.82 E-value=21 Score=13.70 Aligned_cols=69 Identities=14% Similarity=0.159 Sum_probs=52.0 Q ss_pred CCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCC--CCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCC Q ss_conf 9736789999999878999998113404255664366--88704789999997122011156131478870 Q gi|254780182|r 49 LKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKY--HPHGNAAIYDALARMAQDWSLRLLLIEGQGNF 117 (910) Q Consensus 49 lKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gky--HPHGd~siy~a~v~maq~~~~r~plidg~Gnf 117 (910) +-++.+..-|.+...|+.+-.=-....--|+|+|-+- --+.|.|+.+|+-.|.+.---+.|.+|.+|.+ T Consensus 31 ~G~~n~et~~vL~~f~~~~P~li~~v~~qV~DIm~~~~vti~~~~sl~eA~~lM~e~~i~~LPVVD~~g~l 101 (113) T cd04597 31 LGEPNPQTRYVLEYLGIEPPILLADVHPRVRDVINRKPVTARPNDPLREALNLMHEHNIRTLPVVDDDGTP 101 (113) T ss_pred CCCCCHHHHHHHHHCCCCCCEECCCCCCHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCCCEE T ss_conf 68999899999998499998002156505666313788341999829999999998499878698899939 No 131 >pfam00465 Fe-ADH Iron-containing alcohol dehydrogenase. Probab=37.75 E-value=21 Score=13.69 Aligned_cols=26 Identities=23% Similarity=0.157 Sum_probs=11.1 Q ss_pred EEEHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 01013317898547899999988761 Q gi|254780182|r 182 IAVGMATNIPTHNLGEVVDGCVAVID 207 (910) Q Consensus 182 IAvGmaTnippHNl~Ev~~a~~~~i~ 207 (910) +-+..-+.+.||---|-++.++..++ T Consensus 51 ~~~~~~~~v~~~p~~~~v~~~~~~~~ 76 (312) T pfam00465 51 IEVVVFDGVEPNPTLEEVDEAAAAAR 76 (312) T ss_pred CEEEEECCCCCCCCHHHHHHHHHHHH T ss_conf 94999858279999999999999999 No 132 >pfam03266 DUF265 Protein of unknown function, DUF265. Probab=37.60 E-value=21 Score=13.67 Aligned_cols=45 Identities=27% Similarity=0.602 Sum_probs=27.8 Q ss_pred EEEECCCCCCCHHHHHHHHHHHHHCC--CCCHH--HHHHHHCCCCCEEEE Q ss_conf 99924644352899999999998716--65014--458730374655799 Q gi|254780182|r 266 IVVTEIPYQVNKAAMLEKIAELVREK--RIVDI--ADLRDESDRQGYRVV 311 (910) Q Consensus 266 ivItEiPY~vnk~~lie~Ia~lv~~~--ki~gI--~dirDeSdr~giRiv 311 (910) |.||= |.++.|++|+.++++..++. ++.|. ..+|+..-|-|..++ T Consensus 2 i~ITG-~pGvGKTTli~kv~~~l~~~~~~v~GF~T~evre~g~R~GF~iv 50 (168) T pfam03266 2 IFITG-PPGVGKTTLVKKVIELLKSEGVKVGGFYTPEVREGGRRIGFDIV 50 (168) T ss_pred EEEEC-CCCCCHHHHHHHHHHHHHHCCCEEEEEEECCEECCCCEEEEEEE T ss_conf 89978-99988999999999999867970748993021258937899999 No 133 >PRK11147 ABC transporter ATPase component; Reviewed Probab=37.56 E-value=21 Score=13.67 Aligned_cols=11 Identities=36% Similarity=0.640 Sum_probs=5.2 Q ss_pred HHHHHHHCCCC Q ss_conf 99887618776 Q gi|254780182|r 201 GCVAVIDNPDI 211 (910) Q Consensus 201 a~~~~i~~p~~ 211 (910) -+.+++.+|++ T Consensus 167 LA~aL~~~Pdl 177 (632) T PRK11147 167 LARALVSNPDV 177 (632) T ss_pred HHHHHCCCCCE T ss_conf 99985689999 No 134 >cd04629 CBS_pair_16 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener Probab=37.23 E-value=14 Score=15.28 Aligned_cols=32 Identities=13% Similarity=0.280 Sum_probs=20.2 Q ss_pred CHHHHHHHHHHHCCCHHCCCCCCCCCCCC-CCC Q ss_conf 04789999997122011156131478870-887 Q gi|254780182|r 89 GNAAIYDALARMAQDWSLRLLLIEGQGNF-GSV 120 (910) Q Consensus 89 Gd~siy~a~v~maq~~~~r~plidg~Gnf-Gs~ 120 (910) -|+++++|+-.|++.--...|.+|.+|.+ |-+ T Consensus 8 ~~~tl~~a~~~m~~~~~~~~pVvd~~~~lvGii 40 (114) T cd04629 8 PDMSVTEAVEKLLKSKISGGPVVDDNGNLVGFL 40 (114) T ss_pred CCCCHHHHHHHHHHHCCCEEEEECCCCEEEEEE T ss_conf 929999999999971997899994899299999 No 135 >cd04617 CBS_pair_4 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera Probab=37.22 E-value=14 Score=15.30 Aligned_cols=38 Identities=16% Similarity=0.293 Sum_probs=21.4 Q ss_pred HHHHHCCCCC-----CCHHHHHHHHHHHCCCHHCCCCCCCCCCC Q ss_conf 5566436688-----70478999999712201115613147887 Q gi|254780182|r 78 SGEVMGKYHP-----HGNAAIYDALARMAQDWSLRLLLIEGQGN 116 (910) Q Consensus 78 vg~v~gkyHP-----HGd~siy~a~v~maq~~~~r~plidg~Gn 116 (910) |+++|-+ +| +-|.++++|+-.|.+.---+.|.+|..|+ T Consensus 60 V~~iMT~-~P~vvt~~pd~~v~~A~~~M~~~~i~~LPVVd~~~~ 102 (118) T cd04617 60 VGVIMTR-MPNITTTTPEESVLEAAKKLIEHQVDSLPVVEKVDE 102 (118) T ss_pred HHHHHCC-CCCEEEECCCCCHHHHHHHHHHCCCCEECEEECCCC T ss_conf 9998577-997199789993999999999829998567943997 No 136 >pfam11802 CENP-K Centromere-associated protein K. CENP-K is one of seven new CENP-A-nucleosome distal (CAD) centromere components (the others being CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S) that are identified as assembling on the CENP-A nucleosome associated complex, NAC. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling. CENP-K is centromere-associated through its interaction with one or more components of the CENP-A NAC. Probab=37.22 E-value=22 Score=13.63 Aligned_cols=62 Identities=18% Similarity=0.149 Sum_probs=35.1 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHH----------------HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH Q ss_conf 23699999999987899998887999999----------------89999999998875304989999999998999998 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRDDIRN----------------ELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKD 510 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~kl~~----------------E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~ 510 (910) +-.|+.|- ++|-||.+.||+ |.++.+. =.++|.+.+.+|+..|+.-+...+.++++|.-.+. T Consensus 52 l~~sd~q~-~ll~~~~k~Lta-E~~qwqk~~peii~~n~~vL~~lgKeelqk~~~dLe~vLs~vqsk~~~LkedLerEqq 129 (273) T pfam11802 52 LPESDAQL-SLLIMQMKALTA-EYEQWQKRTPEIISLNEDVLLTLGKEELQKLRQDLEMVLSSVQSKNEKLKEDLEREQQ 129 (273) T ss_pred CCCCCCCH-HHHHHHHHHHHH-HHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 89764008-999999999999-9999997099567898899999879999999999999999999989999999999999 No 137 >COG1791 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown] Probab=37.12 E-value=22 Score=13.62 Aligned_cols=117 Identities=15% Similarity=0.224 Sum_probs=65.7 Q ss_pred HHHHHHHHHHHHHHHHHH-----HHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCC---------CCCCCCCCCC Q ss_conf 999998999999999887-----53049899999999989999984056883310013434---------5301014567 Q gi|254780182|r 471 DDIRNELNSLGIEIKECL-----DILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLLD---------MEDEDCIVRE 536 (910) Q Consensus 471 ~kl~~E~~eL~~~I~~l~-----~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~~---------i~~EdlI~~E 536 (910) +.+..|+..+.-.-++++ +.++++..+......|+..|..++|-.-+-.+.-.... +-.|-+-.++ T Consensus 17 deia~~l~~i~v~~e~we~~~~~~~~~~~~~i~~a~~~eid~l~~e~Gyk~~Dvvsv~~~~pk~del~akF~~EH~H~d~ 96 (181) T COG1791 17 DEIAPELSKIEVSFERWEATALIKHGAEKEHIIDAYETEIDRLIRERGYKNRDVVSVSPSNPKLDELRAKFLQEHLHTDD 96 (181) T ss_pred HHHHHHCCCCEEEHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCC T ss_conf 67400014534676563302555457524424766898999999861972133798579993289999999998536781 Q ss_pred CEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCC-----CCCCCC Q ss_conf 818999079705233100000233456521100014641010113323777399995489399982000-----432244 Q gi|254780182|r 537 DMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWR-----LPIGSP 611 (910) Q Consensus 537 ~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~-----IP~~sr 611 (910) ++-..+.-.|| .-+-+..|++|++.+-. +|.| T Consensus 97 EvRy~vaG~Gi-----------------------------------------F~v~~~d~~~~~i~c~~gDLI~vP~g-- 133 (181) T COG1791 97 EVRYFVAGEGI-----------------------------------------FDVHSPDGKVYQIRCEKGDLISVPPG-- 133 (181) T ss_pred EEEEEEECCEE-----------------------------------------EEEECCCCCEEEEEECCCCEEECCCC-- T ss_conf 17999936558-----------------------------------------99987999689999835987952898-- Q ss_pred CCCCCCCEEEEECCCCCCEEEEEEE Q ss_conf 4565541245453655620025663 Q gi|254780182|r 612 QARGKALINILSLNQGERITTIMPF 636 (910) Q Consensus 612 ~skG~pi~nll~l~~~E~I~ail~~ 636 (910) +...+.|..+-.+.|+--+ T Consensus 134 ------i~HwFtlt~~~~f~AvRlF 152 (181) T COG1791 134 ------IYHWFTLTESPNFKAVRLF 152 (181) T ss_pred ------CEEEEECCCCCCEEEEEEE T ss_conf ------4388773679867899976 No 138 >PRK10240 undecaprenyl pyrophosphate synthase; Provisional Probab=37.03 E-value=22 Score=13.61 Aligned_cols=58 Identities=17% Similarity=0.160 Sum_probs=24.8 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC Q ss_conf 5236999999999878999988879999998999999999887530498999999999899999840 Q gi|254780182|r 446 TMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDEL 512 (910) Q Consensus 446 ~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~ky 512 (910) +|+=+....+++.++= ...++.+.+++.+.--. -.++++...+-+-+.+.+.++.+.= T Consensus 50 Nw~R~~~EV~~Lm~L~--------~~~l~~~~~~l~~~~ir-i~~iGd~~~Lp~~l~~~i~~~e~~T 107 (229) T PRK10240 50 NWNRPAQEVSALMELF--------VWALDSEVKSLHRHNVR-LRIIGDTSRFNSRLQERIRKSEALT 107 (229) T ss_pred HCCCCHHHHHHHHHHH--------HHHHHHHHHHHHHCCEE-EEEEECCCCCCHHHHHHHHHHHHHH T ss_conf 6499979999999999--------99999999999987948-9996441006758999999999974 No 139 >pfam12552 DUF3741 Protein of unknown function (DUF3741). This domain family is found in eukaryotes, and is approximately 50 amino acids in length. Probab=36.97 E-value=22 Score=13.60 Aligned_cols=39 Identities=21% Similarity=0.336 Sum_probs=30.3 Q ss_pred EEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCC Q ss_conf 1013317898547899999988761877688888863458668 Q gi|254780182|r 183 AVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDF 225 (910) Q Consensus 183 AvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDF 225 (910) |-+++|+.-+|+-.|..||+-.+=-|.+ =++++++.|+. T Consensus 8 ~K~ls~d~~~~~SKEf~DAleiL~snkd----lflk~LQdP~s 46 (46) T pfam12552 8 AKRLSTDEKLHQSKEFLDALEVLNSNKD----LFLKFLQDPNS 46 (46) T ss_pred HCCCCCCCCCCCHHHHHHHHHHHHHCHH----HHHHHHCCCCC T ss_conf 0014555641210999999999971789----99999708998 No 140 >pfam06838 Alum_res Aluminium resistance protein. This family represents the aluminium resistance protein, which confers resistance to aluminium in bacteria. Probab=36.71 E-value=22 Score=13.57 Aligned_cols=14 Identities=14% Similarity=0.178 Sum_probs=10.0 Q ss_pred HHHHHHHHHHHCCC Q ss_conf 67899999998789 Q gi|254780182|r 52 VHRRILFGMMQMGV 65 (910) Q Consensus 52 v~Rrily~m~~~~~ 65 (910) -|.|+|-||++.++ T Consensus 26 Nq~KVL~Af~~~~v 39 (405) T pfam06838 26 NQLKVLNAFQEHRV 39 (405) T ss_pred HHHHHHHHHHHCCC T ss_conf 99999999998097 No 141 >TIGR00683 nanA N-acetylneuraminate lyase; InterPro: IPR005264 N-acetylneuraminate lyase catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetyl-D-mannosamine. The enzyme plays an important role in the regulation of sialic acid metabolism in bacteria.. Probab=35.98 E-value=22 Score=13.48 Aligned_cols=51 Identities=27% Similarity=0.388 Sum_probs=37.1 Q ss_pred CHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHH Q ss_conf 7588999987012038999988654336784599992464435289999999999871665014 Q gi|254780182|r 233 GRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDI 296 (910) Q Consensus 233 ~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI 296 (910) +-+++.+.|+| |-... |....||..||+-+.-.-=|++|.+|+...++-++ T Consensus 111 SF~E~~~~Y~~------------II~~~-~G~~M~VY~IP~L~GV~l~~~Q~~~L~~~P~V~~~ 161 (294) T TIGR00683 111 SFEEIKDYYDA------------IIDEA-DGLNMVVYSIPALSGVKLTLDQINELVKLPKVLAL 161 (294) T ss_pred CCHHHHHHHHH------------HHHHC-CCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCEEE T ss_conf 73677778999------------98524-89823787453201212218888887517872145 No 142 >KOG0650 consensus Probab=35.94 E-value=22 Score=13.47 Aligned_cols=50 Identities=22% Similarity=0.370 Sum_probs=25.6 Q ss_pred HHHHHHHHHHHCCCC--CCCEEECCCCCCCCCCCCCC------------CCEEEEEECCCEECCCCCCC Q ss_conf 999899999840568--83310013434530101456------------78189990797052331000 Q gi|254780182|r 501 IKQELLSVKDELDTP--RRTRIVEGLLDMEDEDCIVR------------EDMVVTVSHLGYVKRVPLSV 555 (910) Q Consensus 501 I~~EL~eik~kygd~--RRT~I~~~~~~i~~EdlI~~------------E~vvV~lS~~GyIKr~~~~~ 555 (910) |++-+.---+-|=-| ||..+. ++.|+|||+ .--.|.--+.|-++.++++- T Consensus 347 irErFeRcLDLYL~PR~rK~rln-----iDpe~LiPkLPsp~dLrPFPt~~~lvyrGHtg~Vr~iSvdp 410 (733) T KOG0650 347 IRERFERCLDLYLAPRVRKMRLN-----IDPESLIPKLPSPKDLRPFPTRCALVYRGHTGLVRSISVDP 410 (733) T ss_pred HHHHHHHHHHHHHCCCCCCCEEC-----CCHHHHCCCCCCHHHCCCCCCEEEEEEECCCCEEEEEEECC T ss_conf 99999986776507201231104-----79778552489833257775000246733577378977657 No 143 >cd04639 CBS_pair_26 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener Probab=35.59 E-value=23 Score=13.43 Aligned_cols=40 Identities=20% Similarity=0.238 Sum_probs=19.8 Q ss_pred HHHHHCC--CCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCC Q ss_conf 5566436--688704789999997122011156131478870 Q gi|254780182|r 78 SGEVMGK--YHPHGNAAIYDALARMAQDWSLRLLLIEGQGNF 117 (910) Q Consensus 78 vg~v~gk--yHPHGd~siy~a~v~maq~~~~r~plidg~Gnf 117 (910) |.++|-+ ..=+-|.++++++-+|.+.-.-+.|.+|.+|.+ T Consensus 58 V~~vM~~~v~tv~~~~~l~~~~~~m~~~~~~~lpVVd~~g~l 99 (111) T cd04639 58 VRGVMRRDFPTVSPSATLDAVLRLMQQGGAPAVPVVDGSGRL 99 (111) T ss_pred HHHHCCCCCEEECCCCCHHHHHHHHHHCCCCEEEEECCCCEE T ss_conf 576354698799899949999999995899889899579929 No 144 >cd07642 BAR_ASAP2 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP2 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2) is also known as DDEF2 (Development and Differentiation Enhancing Factor 2), AMAP2, centaurin beta-3, or PAG3. ASAP2 mediates the functions of Arf GTPases vial dual mechanisms: it exhibits GTPase activating protein (GAP) activity towards class I (Arf1) and II (Arf5) Arfs; and binds class III Arfs (GTP-Arf6) stably without GAP activity. It binds paxillin and is implicated in Fcgamma receptor-mediated phagocytosis in macrophages and in cell migration. ASAP2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, i Probab=35.51 E-value=23 Score=13.42 Aligned_cols=68 Identities=16% Similarity=0.323 Sum_probs=33.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHH-------CCHHHHHHHHHHHHH--HHHHHCCCCCCC Q ss_conf 9999999987899998887999999899-9999999887530-------498999999999899--999840568833 Q gi|254780182|r 451 EVQTRAILELRLARLTGLGRDDIRNELN-SLGIEIKECLDIL-------SSRSRLLGIIKQELL--SVKDELDTPRRT 518 (910) Q Consensus 451 e~QA~AILdMrL~rLt~LE~~kl~~E~~-eL~~~I~~l~~IL-------~s~~~l~~iI~~EL~--eik~kygd~RRT 518 (910) -.|.+.|+..||.+|.+-+..+++.|++ ...+..++|+.-+ ....++.+++..|.. |+.+.+-.+||. T Consensus 83 ~~n~~~~v~~pL~~f~k~DLk~~K~dlKK~FdKaskdyeak~~K~ek~k~~~aK~~g~~r~E~~~~E~a~~l~~eRr~ 160 (215) T cd07642 83 VQNMNNIITFPLDSLLKGDLKGVKGDLKKPFDKAWKDYETKVTKIEKEKKEHAKMHGMIRTEISGAEIAEEMEKERRF 160 (215) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHCCCHHHHHHHHHHHHHH T ss_conf 999999998799999998888736888726789889999999999888787433024511022167788999999999 No 145 >TIGR01341 aconitase_1 aconitate hydratase 1; InterPro: IPR006249 Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop , . Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) . Below is a description of some of the multi-functional activities associated with different aconitases. Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway . The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA. Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) , . As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated . IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis . Although IRP2 is homologous to IRP1, IPR2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes . In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system. Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica , . In S.enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress. This entry represents bacterial aconitase A (AcnA), eukaryotic cytosolic aconitase (cAcn/IRP1), iron regulatory protein 2 (IRP2), and a few mitochondrial aconitases (certain mAcn proteins, but not the majority of these enzymes). More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0051539 4 iron 4 sulfur cluster binding, 0008152 metabolic process. Probab=35.48 E-value=15 Score=14.93 Aligned_cols=74 Identities=20% Similarity=0.260 Sum_probs=34.5 Q ss_pred EEEEHHHCCCCCC---CCCCEEEEECCCCCCCCCEEEEEECCCCCEEEEEECCCEEEEEECCCCCCC-CCCCCCCEEEEE Q ss_conf 5301788486675---774148876067777686899997289964999945998999990105544-515687388980 Q gi|254780182|r 810 KRTSSYDFRISNR---SGKGIRATDVSKINEIGALVAVFPVNDNDQIILVSDKGTLIRVPVNEIRIA-SRATKGVVIFST 885 (910) Q Consensus 810 KRt~~~eyr~q~R---GgkGv~~ik~~~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v~~I~~~-gR~a~GV~i~~L 885 (910) |-+=+.+|-.-+| =|+||.=+.+...+.. +- |-=++-.++.+++++|... -|..-=|+..+- T Consensus 795 kaVIAeSFERIHRSNLVgMGviPl~f~~g~~a------------~T--LGl~G~E~~~id~~~i~~~~Pg~~vtv~~~~~ 860 (896) T TIGR01341 795 KAVIAESFERIHRSNLVGMGVIPLEFKQGEDA------------ET--LGLTGEELITIDVDDIKEIKPGKEVTVTLTNK 860 (896) T ss_pred EEEEECCCCHHHHHHHHHHCCCCCCCCCCCCC------------CC--CCCCCCEEEEEECCCCCCCCCCCCEEEEEECC T ss_conf 79983253303323324304122105888871------------12--57875369998658866348897025899836 Q ss_pred CCCCEEE--EEEEEC Q ss_conf 8998799--999835 Q gi|254780182|r 886 AKDERVV--SVERIR 898 (910) Q Consensus 886 ~~~D~Vv--~va~i~ 898 (910) + |++.+ .+.|+. T Consensus 861 ~-G~~~t~~~~~R~D 874 (896) T TIGR01341 861 D-GEKETFECVLRID 874 (896) T ss_pred C-CCEEEEEEEEEEC T ss_conf 8-9788997888725 No 146 >TIGR03268 methan_mark_3 putative methanogenesis marker protein 3. A single member of this protein family is found in each of the first ten complete genome sequences of archaeal methanogens, and nowhere else. This protein family was detected by the method of partial phylogenetic profiling (see Haft, et al., 2006). The functions of proteins in this family are unknown, but their role is likely one essential to methanogenesis. Probab=35.47 E-value=23 Score=13.41 Aligned_cols=170 Identities=16% Similarity=0.163 Sum_probs=72.4 Q ss_pred CCEEEEEEHHHCCC----CCCCCCCCEEEEECCC-CCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCC Q ss_conf 98599975876235----4786655357675289-98699989733666542000001222333333345554--44444 Q gi|254780182|r 702 LGQCVRFPISAIRV----FAGRNSVGVRGISLAK-GDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDT--EEITS 774 (910) Q Consensus 702 ~G~~lrF~~~evr~----~~GR~a~GVkgIkL~~-~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~ 774 (910) .|++-.+.++-... .-||...|...+++.+ ||++ +....+.--. ...+....+........+ ..... T Consensus 269 ~G~vYIYredr~ss~sHtvVG~V~~GiELid~a~~G~~l-tv~t~Peri~-----llGlt~~eA~~~~~~~gIe~~~dG~ 342 (503) T TIGR03268 269 EGRVYIYREDRPSSLSHNVVGHVTRGIELIDIAQEGDRL-SVETEPPRID-----LVGLTQEEAEELLEELGIELEKEGV 342 (503) T ss_pred CEEEEEECCCCCCCCCCCEEEEEECCEEEEEHHCCCCEE-EEEECCHHHE-----ECCCCHHHHHHHHHHCCCEEEECCC T ss_conf 446999867878876630467880351321031479779-9984745704-----2388899999999866968984477 Q ss_pred CCCCCCCCCCCCCHHHHCCCCCCCEEEEEECCCCEEEEE--------HHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEE Q ss_conf 443332222232001110125686799997599345301--------788486675774148876067777686899997 Q gi|254780182|r 775 LKNDSSVEGNISEERCQELKLKEQFILTVSEKGFGKRTS--------SYDFRISNRSGKGIRATDVSKINEIGALVAVFP 846 (910) Q Consensus 775 ~~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GKRt~--------~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~ 846 (910) ...++.+....+...+.-++...-.+..|.........- +.=||. ..|++. .+.|.|---|. T Consensus 343 ~~~daVVV~Q~P~~TleIL~~~kV~~~~v~~~~vi~IeLydd~AP~s~~yFR~----~tGL~~------~~VG~L~v~F~ 412 (503) T TIGR03268 343 DGDDAVVVKQEPPYTLDVLKEGKVKVEGVPKDKVIEIELYDDNAPRSVWYFRK----FTGLKT------KPVGRLPVHFA 412 (503) T ss_pred CCCCCEEEECCCCHHHHHHHCCCEEEEEECHHHEEEEEECCCCCCHHHHHHHH----HCCCCC------CCCCEEEEEEE T ss_conf 78984899658942787752581799961868779999746578357899988----518752------43660577886 Q ss_pred CCCCCEEEEE-ECCCEE----------EEEECCCCCCC--CCCCCCCEEEEECCCCE Q ss_conf 2899649999-459989----------99990105544--51568738898089987 Q gi|254780182|r 847 VNDNDQIILV-SDKGTL----------IRVPVNEIRIA--SRATKGVVIFSTAKDER 890 (910) Q Consensus 847 V~~~DeIlli-T~~G~i----------iR~~v~~I~~~--gR~a~GV~i~~L~~~D~ 890 (910) .++ ++|+ .+.... -++++..|-++ .|-..|.--++|.++|+ T Consensus 413 ~~d---~~lFk~~~~~~k~liPEN~P~~~V~ag~IgvTN~a~k~~G~iGVRl~d~de 466 (503) T TIGR03268 413 FKE---MIMFKGNKELAKGLIPENTPEDKVEAGVIGVTNQACKHVGMIGVRLEDSDE 466 (503) T ss_pred ECC---EEEECCCCHHCCCCCCCCCCCCCCCCCEEEEECHHHHCCCEEEEEECCCCC T ss_conf 387---799637811035568888887753234676660145418657898057754 No 147 >KOG3029 consensus Probab=35.42 E-value=23 Score=13.41 Aligned_cols=45 Identities=16% Similarity=0.390 Sum_probs=37.4 Q ss_pred CCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCC Q ss_conf 27321101676101013317898547899999988761877688888863458668 Q gi|254780182|r 170 RYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDF 225 (910) Q Consensus 170 ~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDF 225 (910) ++|.|++.|-. |--+ .-||+++.-|+..|.-+++|+.++-|.-+| T Consensus 136 KVPil~~~Geq-----m~dS------svIIs~laTyLq~~~q~l~eiiq~yPa~~~ 180 (370) T KOG3029 136 KVPILLIRGEQ-----MVDS------SVIISLLATYLQDKRQDLGEIIQMYPATSF 180 (370) T ss_pred CCCEEEECCCE-----ECHH------HHHHHHHHHHHCCCCCCHHHHHHHCCCCCC T ss_conf 33079963614-----0205------899999999854678888999986664000 No 148 >TIGR01750 fabZ beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabZ; InterPro: IPR010084 Fatty acids biosynthesis occurs by two distinct pathways: in fungi, mammals and mycobacteria, type I or associative fatty-acid biosynthesis (type I FAS) is accomplished by multifunctional proteins in which distinct domains catalyse specific reactions; in plants and most bacteria, type II or dissociative fatty-acid biosynthesis (type II FAS) is accomplished by distinct enzymes . FabZ is the primary dehydratase involved in fatty-acid elongation in type II FAS. Both FabZ and FabA catalyse the dehydration of beta-hydroxyacyl acyl carrier protein (ACP) to trans 2-enoyl ACP. However, FabZ and FabA display subtle differences in substrate specificities, whereby FabA is most effective on acyl ACPs of 9-11 carbon atoms in length, while FabZ is less specific. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains. ; GO: 0016836 hydro-lyase activity, 0006633 fatty acid biosynthetic process, 0005737 cytoplasm. Probab=35.37 E-value=12 Score=15.84 Aligned_cols=28 Identities=29% Similarity=0.487 Sum_probs=14.5 Q ss_pred EEEECCC-CCCEEEEEEECCCCCCCCCCE Q ss_conf 4545365-562002566301256668717 Q gi|254780182|r 620 NILSLNQ-GERITTIMPFPEDESSWNNLY 647 (910) Q Consensus 620 nll~l~~-~E~I~ail~~~~~~~~~~~~~ 647 (910) ..++++. +.+|+|+=+++-.|-.-..|| T Consensus 21 Ri~e~~~~~~~ivA~KNVTINEPfF~GHF 49 (142) T TIGR01750 21 RILELEPEGKRIVAIKNVTINEPFFQGHF 49 (142) T ss_pred EEEEEECCCCEEEEEEEEEECCCCCCCCC T ss_conf 68887249978999711677489888988 No 149 >pfam08672 APC2 Anaphase promoting complex (APC) subunit 2. The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate protein. Probab=35.35 E-value=23 Score=13.40 Aligned_cols=36 Identities=28% Similarity=0.345 Sum_probs=22.9 Q ss_pred EHHHHCCCCCCHHHHHHHHHHHHHCC---CCCHHHHHHH Q ss_conf 01331789854789999998876187---7688888863 Q gi|254780182|r 184 VGMATNIPTHNLGEVVDGCVAVIDNP---DIDLDALMEI 219 (910) Q Consensus 184 vGmaTnippHNl~Ev~~a~~~~i~~p---~~~~~eL~~~ 219 (910) |||-||.++-.|.-+..-+....-.| ++|.++|-.| T Consensus 3 ~gMLtN~~slpl~RIh~mLkmfv~~~~~~~~t~~eL~~f 41 (60) T pfam08672 3 VGMLTNLGSLPLERIHSMLKMFPKDPGGYTISQEELEEF 41 (60) T ss_pred CHHHHCCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHH T ss_conf 208445787889999999997476999987699999999 No 150 >KOG0787 consensus Probab=35.35 E-value=23 Score=13.40 Aligned_cols=44 Identities=14% Similarity=0.166 Sum_probs=32.2 Q ss_pred HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCC-CCEE Q ss_conf 9999999998875304989999999998999998405688-3310 Q gi|254780182|r 477 LNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPR-RTRI 520 (910) Q Consensus 477 ~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~R-RT~I 520 (910) .+.+.+--..+..|++.-.-..-.+.+-+.|.+++|+||- +..| T Consensus 129 ~~~~~qf~d~l~~l~~rH~dvv~~lA~Gl~E~~~~~~dp~~~~~i 173 (414) T KOG0787 129 LEDLSQFNDLLNTLRNRHNDVVPTLAQGLIEYREKDGDPVTEKNI 173 (414) T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCCHHHHH T ss_conf 330999999999997302105899998899999852884067789 No 151 >pfam11892 DUF3412 Domain of unknown function (DUF3412). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain is found associated with pfam03641. Probab=35.27 E-value=22 Score=13.61 Aligned_cols=57 Identities=16% Similarity=0.458 Sum_probs=37.9 Q ss_pred CCCCCCHHHHHHHHHHHHCCCCCCCCEEE---------EHHHHHHH----------HCCCCCCCHHHHHHHHHHHCCCHH Q ss_conf 00089736789999999878999998113---------40425566----------436688704789999997122011 Q gi|254780182|r 45 LRDGLKPVHRRILFGMMQMGVEWNKKYVK---------CARISGEV----------MGKYHPHGNAAIYDALARMAQDWS 105 (910) Q Consensus 45 ~rDGlKpv~Rrily~m~~~~~~~~~~~~K---------~a~ivg~v----------~gkyHPHGd~siy~a~v~maq~~~ 105 (910) ..--+-|.|- .|..|.|+.+.|--. |.=|.|.| -|-|.-|||..|.++|=.+-|.|. T Consensus 28 fQ~PF~PTHe----nMa~L~L~~~qp~~~LAanLRrAFSGIVAGNVK~~gi~~Ie~~GPf~i~GD~~im~~lD~LL~~FV 103 (123) T pfam11892 28 FQQPFEPTHE----NMANLNLHRDQPPHELAANLRRAFSGIVAGNVKEEGIRAIEKHGPFEIHGDPELMKKMDKLLQAFV 103 (123) T ss_pred HCCCCCCCHH----HHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCEEECCHHHHHHHHHHHHHHH T ss_conf 6489888477----786464787799899999999986364205546799999997699155088999999999999999 No 152 >TIGR03449 mycothiol_MshA UDP-N-acetylglucosamine: 1L-myo-inositol-1-phosphate 1-alpha-D-N-acetylglucosaminyltransferase. Members of this protein family, found exclusively in the Actinobacteria, are MshA, the glycosyltransferase of mycothiol biosynthesis. Mycothiol replaces glutathione in these species. Probab=35.20 E-value=23 Score=13.38 Aligned_cols=18 Identities=11% Similarity=0.257 Sum_probs=9.2 Q ss_pred CCCCCHHHHHHHHHHHHH Q ss_conf 898547899999988761 Q gi|254780182|r 190 IPTHNLGEVVDGCVAVID 207 (910) Q Consensus 190 ippHNl~Ev~~a~~~~i~ 207 (910) .|-.|+..+++|+-.+++ T Consensus 229 ~~~Kg~~~li~A~~~l~~ 246 (405) T TIGR03449 229 QPLKAPDVLLRAVAELLD 246 (405) T ss_pred CHHHHHHHHHHHHHHHHH T ss_conf 501148999999999998 No 153 >cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c Probab=34.90 E-value=23 Score=13.34 Aligned_cols=26 Identities=23% Similarity=0.225 Sum_probs=22.7 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 23699999999987899998887999 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRDD 472 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~k 472 (910) |+||+.|-+||++--...|..+..+- T Consensus 33 ~~Lt~ee~~al~~~D~~~L~~lGvn~ 58 (77) T cd07321 33 YGLTPEEKAALLARDVGALYVLGVNP 58 (77) T ss_pred CCCCHHHHHHHHCCCHHHHHHCCCCH T ss_conf 69999999998856899999979969 No 154 >PRK09458 pspB phage shock protein B; Provisional Probab=34.83 E-value=23 Score=13.34 Aligned_cols=25 Identities=12% Similarity=0.205 Sum_probs=19.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCHH Q ss_conf 9999989999999998875304989 Q gi|254780182|r 471 DDIRNELNSLGIEIKECLDILSSRS 495 (910) Q Consensus 471 ~kl~~E~~eL~~~I~~l~~IL~s~~ 495 (910) +.|-+..+.+.++|..|+.||+.+. T Consensus 45 ~~L~~~A~~m~eRI~tLE~ILDae~ 69 (75) T PRK09458 45 AQLTEKAEKMRERIQTLEAILDAEH 69 (75) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 9999999999999999999972669 No 155 >KOG4649 consensus Probab=34.79 E-value=23 Score=13.33 Aligned_cols=28 Identities=11% Similarity=0.075 Sum_probs=21.1 Q ss_pred CEEEEEECCCCEEEEEHHH---CCCCCCCCC Q ss_conf 6799997599345301788---486675774 Q gi|254780182|r 798 QFILTVSEKGFGKRTSSYD---FRISNRSGK 825 (910) Q Consensus 798 ~~IL~vTe~G~GKRt~~~e---yr~q~RGgk 825 (910) .+++..++-|---+..+++ |...+-++. T Consensus 250 ghL~w~~~~g~t~~vy~~p~l~F~~h~~~~S 280 (354) T KOG4649 250 GHLLWATQSGTTLHVYLSPKLRFDLHSPGIS 280 (354) T ss_pred CEEEEEECCCCEEEEEECCCCCEECCCCCCC T ss_conf 4189983477089999576421003687886 No 156 >TIGR01090 apt adenine phosphoribosyltransferase; InterPro: IPR005764 Adenine phosphoribosyltransferase (APRTase, 2.4.2.7 from EC) is a widely distributed enzyme, and its deficiency in humans causes the accumulation of 2,8-dihydroxyadenine. It is the sole catalyst for adenine recycling in most eukaryotes.AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate ; GO: 0003999 adenine phosphoribosyltransferase activity, 0006168 adenine salvage. Probab=34.23 E-value=15 Score=15.09 Aligned_cols=51 Identities=27% Similarity=0.393 Sum_probs=32.4 Q ss_pred CCCHHHHHHHHHHHHHCCC--CCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEE Q ss_conf 8547899999988761877--68888886345866887443447588999987012038999 Q gi|254780182|r 192 THNLGEVVDGCVAVIDNPD--IDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIVIR 251 (910) Q Consensus 192 pHNl~Ev~~a~~~~i~~p~--~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~iR 251 (910) |--++.++|.++..+++-+ ++.| +|=|||= =|.|.| -.=||++|-|=|-|| T Consensus 28 ~~~f~~~id~l~~~~~~~~~~id~d----~iVG~Ea--RGFifG---~~LA~~LgvGFVPVR 80 (175) T TIGR01090 28 PELFRFLIDLLVERYKDANGEIDAD----LIVGLEA--RGFIFG---AALAYKLGVGFVPVR 80 (175) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCEE----EEECCCC--CHHHHH---HHHHHHHCCCEEEEE T ss_conf 7789999999999998607951513----6876766--725778---899997089806754 No 157 >PTZ00233 variable surface protein Vir18; Provisional Probab=34.22 E-value=18 Score=14.31 Aligned_cols=39 Identities=13% Similarity=0.080 Sum_probs=21.3 Q ss_pred HHHHHHHHHHHHHH-----HCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 99999999988753-----0498999999999899999840568 Q gi|254780182|r 477 LNSLGIEIKECLDI-----LSSRSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 477 ~~eL~~~I~~l~~I-----L~s~~~l~~iI~~EL~eik~kygd~ 515 (910) ..|..++|..|.++ -..=..|++.|++-=.|||.=|... T Consensus 31 K~eIEqkId~f~~~~~~nfyk~w~~L~k~I~~KN~ElK~Cy~~~ 74 (509) T PTZ00233 31 KSDIEQKIDDFNKATHTNIYTQWDQLNKYIITKDAELKHCYDNG 74 (509) T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 99999999998612630367889999999876025776653078 No 158 >KOG0596 consensus Probab=34.22 E-value=24 Score=13.26 Aligned_cols=10 Identities=20% Similarity=0.770 Sum_probs=3.9 Q ss_pred HCCCCCCCCC Q ss_conf 3458668874 Q gi|254780182|r 219 IIRGPDFPTG 228 (910) Q Consensus 219 ~i~GPDFPTG 228 (910) ++.+||.||- T Consensus 215 ~~~k~nlp~~ 224 (677) T KOG0596 215 LLNKPNLPVK 224 (677) T ss_pred CCCCCCCCCC T ss_conf 0258998866 No 159 >PTZ00156 60S ribosomal protein L11; Provisional Probab=33.82 E-value=24 Score=13.21 Aligned_cols=61 Identities=26% Similarity=0.464 Sum_probs=27.0 Q ss_pred CCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHC--CCHHCCCCCCCCCCCCC Q ss_conf 0897367899999998789999981134042556643668870478999999712--20111561314788708 Q gi|254780182|r 47 DGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMA--QDWSLRLLLIEGQGNFG 118 (910) Q Consensus 47 DGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~ma--q~~~~r~plidg~GnfG 118 (910) -|-|||.++-=++....|+..+-|- .++| ++ .|+.+ |+-|-|+- .+|..+--=.|.+|||+ T Consensus 40 TGQkPv~tkAkkti~~F~iRkg~pI--G~kV---TL-----Rg~ka-~efL~r~l~v~d~~L~~~~Fd~~GNfs 102 (172) T PTZ00156 40 TGQKPVFSKARLTVRSFGIRRNEKI--AVHC---TV-----RGKKA-EEILERGLKVKEFELKKRNFSDTGNFG 102 (172) T ss_pred HCCCCEEEEECCCHHCCCCCCCCEE--EEEE---EE-----CHHHH-HHHHHHHHHHCCCCCCCCCCCCCCCEE T ss_conf 3997136531100110476789857--8999---97-----66889-999999884314673623528998514 No 160 >pfam00356 LacI Bacterial regulatory proteins, lacI family. Probab=33.75 E-value=24 Score=13.20 Aligned_cols=35 Identities=11% Similarity=0.195 Sum_probs=24.2 Q ss_pred HHHHHHHHHCCCCCCCCCCH-HHHHHHHHHHHCCCCCC Q ss_conf 77998863137540008973-67899999998789999 Q gi|254780182|r 32 YAINVILGRAIPDLRDGLKP-VHRRILFGMMQMGVEWN 68 (910) Q Consensus 32 Ya~svI~~RAlPd~rDGlKp-v~Rrily~m~~~~~~~~ 68 (910) .+.+ -++|||-+- ++.+| ...||+-++.+||..|| T Consensus 11 VS~~-TVSr~ln~~-~~vs~~tr~rI~~~a~~lgY~pN 46 (46) T pfam00356 11 VSKA-TVSRVLNNP-ERVSEETREKVEAAMEELGYVPN 46 (46) T ss_pred CCHH-HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCC T ss_conf 7999-999998797-98999999999999999789999 No 161 >COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis] Probab=33.75 E-value=24 Score=13.20 Aligned_cols=45 Identities=7% Similarity=0.227 Sum_probs=38.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHCCC Q ss_conf 999999899999999988753049--899999999989999984056 Q gi|254780182|r 470 RDDIRNELNSLGIEIKECLDILSS--RSRLLGIIKQELLSVKDELDT 514 (910) Q Consensus 470 ~~kl~~E~~eL~~~I~~l~~IL~s--~~~l~~iI~~EL~eik~kygd 514 (910) ......||+.+.+.+++.+.+|++ +..+.....+|+.+++++... T Consensus 48 iv~~~~~~~~~~~~l~~a~~~l~~~~D~em~ema~~Ei~~~~~~~~~ 94 (363) T COG0216 48 IVEKYREYKKAQEDLEDAKEMLAEEKDPEMREMAEEEIKELEAKIEE 94 (363) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999983568878999999999999998999 No 162 >PRK12806 flagellin; Provisional Probab=33.61 E-value=24 Score=13.18 Aligned_cols=62 Identities=21% Similarity=0.380 Sum_probs=36.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 89999998740699999986189978987877631269788999997402211122234452369999999998789999 Q gi|254780182|r 386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL 465 (910) Q Consensus 386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL 465 (910) -+.||-.|..|.-.-|.++.-++ ..|-+ . ..||. |+|.| T Consensus 57 qi~gl~qa~~N~~dgiSl~qtAe------gAL~e--------------------------------v--~~iLq-RmReL 95 (475) T PRK12806 57 QIRGMNQAVRNANDGISLAQVAE------GAMQE--------------------------------T--TNILQ-RMREL 95 (475) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHHHH--------------------------------H--HHHHH-HHHHH T ss_conf 99889999998998999999999------99999--------------------------------9--99999-99999 Q ss_pred ---------HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---------88879999998999999999887 Q gi|254780182|r 466 ---------TGLGRDDIRNELNSLGIEIKECL 488 (910) Q Consensus 466 ---------t~LE~~kl~~E~~eL~~~I~~l~ 488 (910) +.-++..|++|+++|..+|..+- T Consensus 96 AvQAaNgTn~~~DR~aiq~Ei~qL~~eIdrIa 127 (475) T PRK12806 96 SVQAANSTNNSSDRASIQSEISQLKSELERIA 127 (475) T ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99861688877889999999999999998786 No 163 >KOG1302 consensus Probab=33.42 E-value=24 Score=13.16 Aligned_cols=16 Identities=38% Similarity=0.702 Sum_probs=8.6 Q ss_pred CCCCHHHHHHHHHHHH Q ss_conf 0897367899999998 Q gi|254780182|r 47 DGLKPVHRRILFGMMQ 62 (910) Q Consensus 47 DGlKpv~Rrily~m~~ 62 (910) -|++++-||-|...-+ T Consensus 15 ~~lq~~a~~eL~~lLd 30 (600) T KOG1302 15 QGLQEVARRELISLLD 30 (600) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 8879999999999996 No 164 >cd00225 API3 Ascaris pepsin inhibitor-3 (API3); protein inhibitor that reversibly inhibits aspartic proteinase cathepsin E, and gastric enzymes pepsin and gastricsin. Probab=33.31 E-value=24 Score=13.15 Aligned_cols=41 Identities=17% Similarity=0.172 Sum_probs=25.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH Q ss_conf 78999988879999998999999999887530498999999 Q gi|254780182|r 460 LRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGI 500 (910) Q Consensus 460 MrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~i 500 (910) .+||.||.-|..+|.+-.++..+-.++++.+|+-+.+-|+. T Consensus 26 ~~lReLt~~Eq~Ela~y~~e~~~yK~~~k~~l~er~~~~~~ 66 (159) T cd00225 26 FPLRELTPDEQQELAQYVEDVADYKEEVKQALKERQEGLKL 66 (159) T ss_pred CCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 22221888899999999999999999999999999988887 No 165 >TIGR02171 Fb_sc_TIGR02171 Fibrobacter succinogenes paralogous family TIGR02171. Probab=33.30 E-value=24 Score=13.14 Aligned_cols=166 Identities=19% Similarity=0.196 Sum_probs=79.4 Q ss_pred HHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEE Q ss_conf 98999998405688331001343453010145678189990797052331000002334565211000146410101133 Q gi|254780182|r 503 QELLSVKDELDTPRRTRIVEGLLDMEDEDCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFI 582 (910) Q Consensus 503 ~EL~eik~kygd~RRT~I~~~~~~i~~EdlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~ 582 (910) +=|+=+-+-||+=++|.+..-.+..+...| .+.| =+.|=-+.- +.+-..-.||-.-...++++ .|+|=+=++ T Consensus 222 N~lEwVNDW~~~F~dtTltNyvGs~d~~~l--g~~V----VKGGsY~~~-ps~~~ly~RGDVYPv~~St~-~DY~GFRLv 293 (982) T TIGR02171 222 NVLEWVNDWYASFKDTTLTNYVGSSDEGSL--GERV----VKGGSYRNS-PSAINLYTRGDVYPVTSSTK-GDYVGFRLV 293 (982) T ss_pred CHHHHHCCCCCCCCCCCEEEEECCCCCCCC--CCCE----EECCCCCCC-CCCEECCCCCCCCCEECCCC-CCCCEEEEE T ss_conf 122200560003125620103056775443--6634----535754567-23200147886312003787-762034441 Q ss_pred ECCCCEEEEEECCCCEEEEECCCCC--CCCCCCCCC--CCEE------------EEECCCCC-CEEEEE----EECCCCC Q ss_conf 2377739999548939998200043--224445655--4124------------54536556-200256----6301256 Q gi|254780182|r 583 VSTHTSVLFFSSLGFVYKEKVWRLP--IGSPQARGK--ALIN------------ILSLNQGE-RITTIM----PFPEDES 641 (910) Q Consensus 583 ~~t~d~LLfFTs~Gkvy~l~v~~IP--~~sr~skG~--pi~n------------ll~l~~~E-~I~ail----~~~~~~~ 641 (910) |=+-+.=+-|+++|.+-.-++.-+= ..=|.--|+ .=.. |++...+- +|+-|. .++.+- T Consensus 294 ~G~IPdA~wLd~~G~v~t~~~~~~~~~~~~r~~~gtkky~~KLaFRND~TgnL~yIDy~~~~~~~~EI~D~~~vyHPDI- 372 (982) T TIGR02171 294 LGAIPDATWLDESGKVATSKVKSLISSSEIRELTGTKKYKAKLAFRNDVTGNLAYIDYAKGASKVVEIEDTIKVYHPDI- 372 (982) T ss_pred CCCCCCCCCCCCCCCEEEEEEEEEEEHHHHHHHHCCEEEEEEEEEECCCCCCEEEEEECCCCCEEEEEECCCCEECCCC- T ss_conf 1488875541888967688878752058888530770367777870476433268870588336998303741202740- Q ss_pred CCCCCEEEEEEC-CCCEEEECHHHHH-HCCCCCEEEEEEC Q ss_conf 668717999947-9918984236862-0477722786615 Q gi|254780182|r 642 SWNNLYVVFATK-HGNVRRNKLSDFI-QINRSGKIAMKLD 679 (910) Q Consensus 642 ~~~~~~Lvl~Tk-~G~VKkt~l~ef~-~~r~~G~~aikLk 679 (910) ..+..++-|||. -|.-++.++ |. ++..+|--..||. T Consensus 373 SPDG~~VAFCT~~EG~~GkS~v--YVR~Ln~~G~~LVKL~ 410 (982) T TIGR02171 373 SPDGKKVAFCTGIEGVDGKSEV--YVRDLNASGSGLVKLD 410 (982) T ss_pred CCCCCEEEEECCCCCCCCCCEE--EEECCCCCCCCCEEEC T ss_conf 7986874576341144787438--9844555789812206 No 166 >TIGR03300 assembly_YfgL outer membrane assembly lipoprotein YfgL. Members of this protein family are YfgL, a lipoprotein component of a complex that acts protein insertion into the bacterial outer membrane. Other members of this complex are NlpB, YfiO, and YaeT. This protein contains multiple copies of a repeat that, in other contexts, are associated with binding of the coenzyme PQQ. Probab=33.05 E-value=25 Score=13.11 Aligned_cols=59 Identities=10% Similarity=-0.071 Sum_probs=28.6 Q ss_pred CCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEEC Q ss_conf 678189990797052331000002334565211000146410101133237773999954893999820 Q gi|254780182|r 535 REDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKV 603 (910) Q Consensus 535 ~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v 603 (910) ..+.+.+.+.+|.|..+...+=+..= +.+-++.+. .-.+-..+.+++-|..|.+|.+.+ T Consensus 64 ~~~~vy~~~~~G~v~Ald~~tG~~~W---------~~~~~~~i~-~g~~v~~~~v~vgt~~G~l~Ald~ 122 (377) T TIGR03300 64 AGGKVYAADADGTVVALDAETGKRLW---------RVDLDERLS-GGVGADGGLVFVGTEKGEVIALDA 122 (377) T ss_pred ECCEEEEECCCCEEEEEECCCCCEEE---------EEECCCCEE-EEEEEECCEEEEEECCCEEEEEEC T ss_conf 89999998499759999965894887---------888699815-603882999999909975999997 No 167 >COG0493 GltD NADPH-dependent glutamate synthase beta chain and related oxidoreductases [Amino acid transport and metabolism / General function prediction only] Probab=33.02 E-value=19 Score=14.07 Aligned_cols=130 Identities=23% Similarity=0.284 Sum_probs=60.6 Q ss_pred HCCCC--CCCCCC---CCC-CHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 34586--688744---344-758899998701203899998865433678459999246443528999999999987166 Q gi|254780182|r 219 IIRGP--DFPTGA---VIL-GRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVREKR 292 (910) Q Consensus 219 ~i~GP--DFPTGG---~I~-~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~k 292 (910) ++|++ -=+||- +|- |..|+..++.--+=...|-. ++-+...+| ++-+-||= -++-..| T Consensus 112 ~i~~~~~~~~tg~~VaviGaGPAGl~~a~~L~~~G~~Vtv-~e~~~~~GG---ll~yGIP~----~kl~k~i-------- 175 (457) T COG0493 112 WIPGELPGSRTGKKVAVIGAGPAGLAAADDLSRAGHDVTV-FERVALDGG---LLLYGIPD----FKLPKDI-------- 175 (457) T ss_pred CCCCCCCCCCCCCEEEEECCCCHHHHCHHHHHHCCCEEEE-CCCCCCCCE---EEEECCCH----HHCCCHH-------- T ss_conf 9788788887676799988895155588999868987998-266677744---79814844----6464206-------- Q ss_pred CCHHHHHHHHC-CCCCEEEEEEECC--CCCHHHHHHHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 50144587303-7465579999479--88778999999976101100000024554166300029999999999999999 Q gi|254780182|r 293 IVDIADLRDES-DRQGYRVVIELKR--GASADVILNQLYRYTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVV 369 (910) Q Consensus 293 i~gI~dirDeS-dr~giRivielKr--~~~~~~vln~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi 369 (910) .|-+=++ -+.|+.+++-.++ ++..+.++.. |-.-+++.-.++|+.+++...=..-+.+..+-+ T Consensus 176 ----~d~~i~~l~~~Gv~~~~~~~vG~~it~~~L~~e----------~Dav~l~~G~~~~~~l~i~g~d~~gv~~A~dfL 241 (457) T COG0493 176 ----LDRRLELLERSGVEFKLNVRVGRDITLEELLKE----------YDAVFLATGAGKPRPLDIPGEDAKGVAFALDFL 241 (457) T ss_pred ----HHHHHHHHHHCCCEEEECCEECCCCCHHHHHHH----------HCEEEEECCCCCCCCCCCCCCCCCCCCHHHHHH T ss_conf ----899999998749099986677996789998653----------287999326678876898886777761687999 Q ss_pred HHHHHHHHH Q ss_conf 999999999 Q gi|254780182|r 370 VRRTKYLLN 378 (910) Q Consensus 370 ~rRt~~~L~ 378 (910) ++-++..|. T Consensus 242 ~~~~~~~~~ 250 (457) T COG0493 242 TRLNKEVLG 250 (457) T ss_pred HHHHHHHCC T ss_conf 999998603 No 168 >pfam07569 Hira TUP1-like enhancer of split. The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain pfam00400. Probab=32.91 E-value=25 Score=13.10 Aligned_cols=27 Identities=19% Similarity=0.511 Sum_probs=20.2 Q ss_pred EEEEECCCCEEEEEECCCCEEEEECCCCCCC Q ss_conf 1133237773999954893999820004322 Q gi|254780182|r 579 DLFIVSTHTSVLFFSSLGFVYKEKVWRLPIG 609 (910) Q Consensus 579 ~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~ 609 (910) .++.|+. .+|+++|+.|-+|. |++... T Consensus 16 ~~Le~~~-~~Ll~iT~~G~l~v---Wnv~~~ 42 (219) T pfam07569 16 SFLESNG-SYLLCVTSVGLLYV---WNVKTK 42 (219) T ss_pred EEEEECC-CEEEEEECCCEEEE---EECCCC T ss_conf 6998179-78999925887999---976598 No 169 >KOG3091 consensus Probab=32.89 E-value=25 Score=13.09 Aligned_cols=95 Identities=17% Similarity=0.188 Sum_probs=49.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHH Q ss_conf 99999998887789999998740699999986189978987877631269788999997402211122234452369999 Q gi|254780182|r 374 KYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQ 453 (910) Q Consensus 374 ~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~Q 453 (910) .-+|+...+++.-|. -...|.+++| ++||.++++- |.+ T Consensus 354 r~ri~~i~e~v~eLq-----k~~ad~~~KI-------~~~k~r~~~L-----------------------------s~R- 391 (508) T KOG3091 354 RIRINAIGERVTELQ-----KHHADAVAKI-------EEAKNRHVEL-----------------------------SHR- 391 (508) T ss_pred HHHHHHHHHHHHHHH-----HHHHHHHHHH-------HHHHHHHHHH-----------------------------HHH- T ss_conf 999999998999987-----6301578899-------9999877779-----------------------------999- Q ss_pred HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 999998789999888799-----99998999999999887530498999999999899999840568833 Q gi|254780182|r 454 TRAILELRLARLTGLGRD-----DIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRT 518 (910) Q Consensus 454 A~AILdMrL~rLt~LE~~-----kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT 518 (910) -||=++++|.. -|..+.++|+++...|..-|+.+.++|..+ .+|.++.+--.+.++. T Consensus 392 -------iLRv~ikqeilr~~G~~L~~~EE~Lr~Kldtll~~ln~Pnq~k~Rl-~~L~e~~r~q~~~~~~ 453 (508) T KOG3091 392 -------ILRVMIKQEILRKRGYALTPDEEELRAKLDTLLAQLNAPNQLKARL-DELYEILRMQNSQLKL 453 (508) T ss_pred -------HHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHH-HHHHHHHHHHCCHHCC T ss_conf -------9999999999860487689658999999999998752829899999-9999999754001204 No 170 >cd07603 BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. Vertebrates contain at least three members, ACAP1, ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific GAPs, involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration, by mediating Arf6 signaling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. Probab=32.60 E-value=25 Score=13.06 Aligned_cols=30 Identities=7% Similarity=0.127 Sum_probs=10.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999878999988879999998999999 Q gi|254780182|r 453 QTRAILELRLARLTGLGRDDIRNELNSLGI 482 (910) Q Consensus 453 QA~AILdMrL~rLt~LE~~kl~~E~~eL~~ 482 (910) |++.++--||.++.+-+....++..+...+ T Consensus 83 q~~~~v~~pL~~f~k~dl~~vKe~KK~FdK 112 (200) T cd07603 83 QAQRTVSTQLQNFVKEDIKKVKESKKHFEK 112 (200) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999736899998889998 No 171 >PRK07004 replicative DNA helicase; Provisional Probab=32.38 E-value=25 Score=13.03 Aligned_cols=23 Identities=35% Similarity=0.521 Sum_probs=12.8 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 98999999999899999840568 Q gi|254780182|r 493 SRSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 493 s~~~l~~iI~~EL~eik~kygd~ 515 (910) ++......|-..|+.+.+.++-| T Consensus 344 ~r~~ei~~isr~lK~lAkel~ip 366 (460) T PRK07004 344 NRATEISEISRSLKSLAKELDVP 366 (460) T ss_pred CHHHHHHHHHHHHHHHHHHHCCC T ss_conf 89999999999999999996997 No 172 >cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Probab=32.16 E-value=25 Score=13.00 Aligned_cols=25 Identities=28% Similarity=0.420 Sum_probs=21.8 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2369999999998789999888799 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRD 471 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~ 471 (910) |+||+.|-+||++....+|-.+.-+ T Consensus 51 ~~Lteeqk~aV~~RD~~~li~lGgn 75 (121) T cd07924 51 WPMTEEQKQAVLARDYNRMLALGGN 75 (121) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCC T ss_conf 6999999999997479999992682 No 173 >KOG3957 consensus Probab=32.12 E-value=23 Score=13.44 Aligned_cols=27 Identities=26% Similarity=0.578 Sum_probs=19.9 Q ss_pred CCCCCCCCCC--C-HHHHHHHHHHCCCEEE Q ss_conf 6688744344--7-5889999870120389 Q gi|254780182|r 223 PDFPTGAVIL--G-RTGIKNAYATGRGSIV 249 (910) Q Consensus 223 PDFPTGG~I~--~-~~~i~~~y~tGrG~i~ 249 (910) -||.|||.-- + -.+|.+-|+||||-+. T Consensus 152 aDfAgGgL~aa~gI~~AL~~RtrtgkGqvi 181 (387) T KOG3957 152 ADFAGGGLYAAGGILAALYQRTRTGKGQVI 181 (387) T ss_pred HHHCCCHHHHHHHHHHHHHHHHCCCCCEEE T ss_conf 442365068999999999998416885488 No 174 >PHA02126 hypothetical protein Probab=31.90 E-value=23 Score=13.45 Aligned_cols=50 Identities=26% Similarity=0.302 Sum_probs=32.3 Q ss_pred CCCCCCCCC-CHHHHHHHHHHCCCEEE-------EEEEEEEEECCCCCEEEEEECCCC Q ss_conf 688744344-75889999870120389-------999886543367845999924644 Q gi|254780182|r 224 DFPTGAVIL-GRTGIKNAYATGRGSIV-------IRGVSHIEKTSGDREQIVVTEIPY 273 (910) Q Consensus 224 DFPTGG~I~-~~~~i~~~y~tGrG~i~-------iR~k~~ie~~~~~k~~ivItEiPY 273 (910) -.|.|+.|+ +++-|.++-.-|..+-+ -|-|.|+|-+.+----|.+||+|. T Consensus 50 qlpggalivadrd~i~~~r~~~~nk~rmldtlsfcrdkmhfell~rppviif~t~~~~ 107 (153) T PHA02126 50 QLPGGALIVADRDIITSIRRAGGNKPRMLDTLSFCRDKMHFELLGRPPVIIFNTQTPL 107 (153) T ss_pred CCCCCEEEEECHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCH T ss_conf 4898438995478899886236897425677887654466876189988999536756 No 175 >TIGR01052 top6b DNA topoisomerase VI, B subunit; InterPro: IPR005734 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 II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit B of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea, but also in a few eukayotes, such as the plant Arabidopsis thaliana . This enzyme assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein that mediates double-strand DNA breaks during meiotic recombination in eukaryotes . Therefore, though related to type IIA topoisomerases, topoisomerase VI may have a distinctive mechanism of action. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome. Probab=31.63 E-value=22 Score=13.55 Aligned_cols=15 Identities=27% Similarity=0.428 Sum_probs=7.9 Q ss_pred CCCCCEEEEEEECCC Q ss_conf 374655799994798 Q gi|254780182|r 303 SDRQGYRVVIELKRG 317 (910) Q Consensus 303 Sdr~giRivielKr~ 317 (910) +...|+||.+|+|-+ T Consensus 172 ~~W~GTriEle~~~v 186 (662) T TIGR01052 172 GSWRGTRIELEVKDV 186 (662) T ss_pred CCCEEEEEEEEEECC T ss_conf 981368999998222 No 176 >cd04637 CBS_pair_24 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener Probab=31.45 E-value=26 Score=12.91 Aligned_cols=41 Identities=15% Similarity=0.305 Sum_probs=20.4 Q ss_pred HHHHHHHCCCCC---CCHHHHHHHHHHHCCCHHCCCCCCCCCCCC Q ss_conf 425566436688---704789999997122011156131478870 Q gi|254780182|r 76 RISGEVMGKYHP---HGNAAIYDALARMAQDWSLRLLLIEGQGNF 117 (910) Q Consensus 76 ~ivg~v~gkyHP---HGd~siy~a~v~maq~~~~r~plidg~Gnf 117 (910) +-|+++|-+ +| +.++.+++|+-.|.+.---+.|.+|.+|.. T Consensus 67 ~~v~~iM~~-~~itv~~~~~l~~a~~~m~~~~i~~lPVvd~~~~l 110 (122) T cd04637 67 RRAHQIMTR-DPITVSPDTPVDEASKLLLENSISCLPVVDENGQL 110 (122) T ss_pred CCHHHHCCC-CCEEECCCCCHHHHHHHHHHCCCEEEEEECCCCEE T ss_conf 899994638-98399999849999999997493089999689989 No 177 >pfam02624 YcaO YcaO-like family. Probab=31.45 E-value=22 Score=13.48 Aligned_cols=78 Identities=21% Similarity=0.312 Sum_probs=41.6 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCC-CCCCCCEECCCCCCCCCEECCCCCCCCHH-----------CCCCCEEEHHHHCC Q ss_conf 9720135789997899999986307-68405330689885485034322732110-----------16761010133178 Q gi|254780182|r 123 DPPAAERYTECRLQKAAHFLLDDLG-KDTVDFRPNYDGSFQEPVVLCARYPNVLV-----------NGGGGIAVGMATNI 190 (910) Q Consensus 123 d~~AA~RYte~rl~~~~~~~l~~i~-~~tv~~~~n~D~~~~EP~vlP~~~P~lL~-----------nG~~GIAvGmaTni 190 (910) ||..-.+|......... .....+ ...+.|++-+|=...+|+.+|+.+=.+-. -.|+|.|.|-... T Consensus 47 ~p~~~~~~~~~q~~~~~--~~~~~~~d~~i~Wv~~~~l~~g~~v~vP~~~v~~~~~~~~~~~~~~~~~SnGlAaG~t~~- 123 (332) T pfam02624 47 DPEDLVLYSDEQYAKPG--FPNPYDPDLPLEWVPGWDLLSGEEVYVPANLVYVSNPYPGGEDRFFPSTSNGLAAGNTLE- 123 (332) T ss_pred CHHHHCCCCHHHHCCCC--CCCCCCCCCEEEEEEEEECCCCCEEEEEHHHHHCCCCCCCCCCCEECCCCCEECCCCCHH- T ss_conf 99997268766641335--677789898051068588489968997379973478888766732124787236889999- Q ss_pred CCCCHHHHHHHHHHHHHC Q ss_conf 985478999999887618 Q gi|254780182|r 191 PTHNLGEVVDGCVAVIDN 208 (910) Q Consensus 191 ppHNl~Ev~~a~~~~i~~ 208 (910) .=++.|+.-+|+. T Consensus 124 -----eA~~~gl~EvIER 136 (332) T pfam02624 124 -----EAILHGLLEVIER 136 (332) T ss_pred -----HHHHHHHHHHHHH T ss_conf -----9999999999999 No 178 >cd04605 CBS_pair_MET2_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the MET2 domain. Met2 is a key enzyme in the biosynthesis of methionine. It encodes a homoserine transacetylase involved in converting homoserine to O-acetyl homoserine. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Probab=31.44 E-value=24 Score=13.15 Aligned_cols=27 Identities=22% Similarity=0.311 Sum_probs=10.0 Q ss_pred HHHHHHHHHHCCCHHCCCCCCCCCCCC Q ss_conf 789999997122011156131478870 Q gi|254780182|r 91 AAIYDALARMAQDWSLRLLLIEGQGNF 117 (910) Q Consensus 91 ~siy~a~v~maq~~~~r~plidg~Gnf 117 (910) +++++|+-.|.+.-....|.+|.+|.+ T Consensus 11 ~tv~~a~~~m~~~~~~~lpVvd~~~~~ 37 (110) T cd04605 11 ASIKEAAKLMIEENINHLPVVDEDGRL 37 (110) T ss_pred CCHHHHHHHHHHCCCCEEEEECCCCCE T ss_conf 999999999997299889999799919 No 179 >KOG0319 consensus Probab=31.42 E-value=26 Score=12.91 Aligned_cols=183 Identities=12% Similarity=0.133 Sum_probs=90.4 Q ss_pred CCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEECCCCCCCC Q ss_conf 01456781899907970523310000023345652110001464101011332377739999548939998200043224 Q gi|254780182|r 531 DCIVREDMVVTVSHLGYVKRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKVWRLPIGS 610 (910) Q Consensus 531 dlI~~E~vvV~lS~~GyIKr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v~~IP~~s 610 (910) =+=|+|..+.+-|+.+-+|-.....-..|-- ---.|.|..+-+..+. .+|-+-+|=-+...|.+-... T Consensus 331 ~lG~e~~~laVATNs~~lr~y~~~~~~c~ii---------~GH~e~vlSL~~~~~g---~llat~sKD~svilWr~~~~~ 398 (775) T KOG0319 331 FLGPEESHLAVATNSPELRLYTLPTSYCQII---------PGHTEAVLSLDVWSSG---DLLATGSKDKSVILWRLNNNC 398 (775) T ss_pred ECCCCCCEEEEEECCCCEEEEECCCCCEEEE---------ECCHHHEEEEEECCCC---CEEEEECCCCEEEEEEECCCC T ss_conf 1177545599970797169896499753787---------0754550454321367---389983588669999945896 Q ss_pred CCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEE----CCCCEEEE Q ss_conf 44565541245453655620025663012566687179999479918984236862047772278661----58985788 Q gi|254780182|r 611 PQARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKL----DSRDEILS 686 (910) Q Consensus 611 r~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikL----kegD~Li~ 686 (910) ++-.++...-.. .-.|.+ +... .....|++.++.++.+|...+.. +..... -+.++. .--|+=|. T Consensus 399 --~~~~~~a~~~gH--~~svga-va~~----~~~asffvsvS~D~tlK~W~l~~-s~~~~~-~~~~~~~~t~~aHdKdIN 467 (775) T KOG0319 399 --SKSLCVAQANGH--TNSVGA-VAGS----KLGASFFVSVSQDCTLKLWDLPK-SKETAF-PIVLTCRYTERAHDKDIN 467 (775) T ss_pred --CHHHHHHHHCCC--CCCCCE-EEEC----CCCCCEEEEECCCCEEEEECCCC-CCCCCC-CCEEHHHHHHHHHCCCCC T ss_conf --055436664266--654212-5641----46753899914870699853788-634356-603125677786456565 Q ss_pred EEECCCCCEEE-EEEC--CCEEEEEEHHHCC---CCCCCCCCCEEEEECCCCCEEEEEE Q ss_conf 89618982699-9936--9859997587623---5478665535767528998699989 Q gi|254780182|r 687 VETCTQENDIL-LTTK--LGQCVRFPISAIR---VFAGRNSVGVRGISLAKGDQVISMA 739 (910) Q Consensus 687 v~~~~~~~~Ii-l~T~--~G~~lrF~~~evr---~~~GR~a~GVkgIkL~~~D~Vv~~~ 739 (910) +.-+.+++.++ -.|. ..++..|+ +.+ ++.| -.+||-..+..+.|++++-+ T Consensus 468 ~Vaia~ndkLiAT~SqDktaKiW~le--~~~l~~vLsG-H~RGvw~V~Fs~~dq~laT~ 523 (775) T KOG0319 468 CVAIAPNDKLIATGSQDKTAKIWDLE--QLRLLGVLSG-HTRGVWCVSFSKNDQLLATC 523 (775) T ss_pred CEEECCCCCEEEECCCCCCEEEECCC--CCEEEEEEEC-CCCCEEEEEECCCCCEEEEC T ss_conf 36856877357851666523100146--7638999607-75515888963534045761 No 180 >PRK00969 hypothetical protein; Provisional Probab=31.41 E-value=26 Score=12.91 Aligned_cols=171 Identities=15% Similarity=0.152 Sum_probs=76.4 Q ss_pred CCEEEEEEHHHCCC----CCCCCCCCEEEEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCCCC Q ss_conf 98599975876235----478665535767528998699989733666542000001222333333345554--444444 Q gi|254780182|r 702 LGQCVRFPISAIRV----FAGRNSVGVRGISLAKGDQVISMAIVLHADADYDERICYMKHMSAQRRLISGDT--EEITSL 775 (910) Q Consensus 702 ~G~~lrF~~~evr~----~~GR~a~GVkgIkL~~~D~Vv~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~ 775 (910) .|++-.+.++-... .-||...|...+++.+.-..++....+.--. ...+....+....+...+ ...... T Consensus 272 ~G~vYIYredr~ss~sHtvVG~V~~GiELid~a~~G~~itv~t~Peri~-----llG~t~~eA~~~~~~~gIe~~~dg~~ 346 (508) T PRK00969 272 VGKVYIYREDRPSSLSHTVVGRVTHGIELVDFAEEGDRLTVKTVPERLD-----LLGLTLKEAEELLEKLGIELEKDGYT 346 (508) T ss_pred CEEEEEECCCCCCCCCCCEEEEEECCEEEEECCCCCCEEEEEECCHHHE-----ECCCCHHHHHHHHHHCCCEEEECCCC T ss_conf 4469998678788766204678803523320305787799995746714-----22898999999998669689844777 Q ss_pred CCCCCCCCCCCCHHHHCCCCCCCEEEEEECCCCEEEEE--------HHHCCCCCCCCCCEEEEECCCCCCCCCEEEEEEC Q ss_conf 43332222232001110125686799997599345301--------7884866757741488760677776868999972 Q gi|254780182|r 776 KNDSSVEGNISEERCQELKLKEQFILTVSEKGFGKRTS--------SYDFRISNRSGKGIRATDVSKINEIGALVAVFPV 847 (910) Q Consensus 776 ~~~~~~~~~~~~e~~~~~~~~~~~IL~vTe~G~GKRt~--------~~eyr~q~RGgkGv~~ik~~~~n~~g~lv~~~~V 847 (910) ..++.+....+...+.-++...-.+..|.........- +.=||. ..|++. .+.|.|---|.. T Consensus 347 ~~daVVV~Q~P~~TldIL~~~kV~~~~i~~~~li~IeLydd~AP~s~~yFR~----~tGL~~------~~VG~L~v~F~~ 416 (508) T PRK00969 347 GEDAVVVEQDPPTTLDILKEGKVTTKGIPPDKLIEIELYDDKAPRSVWYFRK----VTGLKT------KPVGKLPVHFKY 416 (508) T ss_pred CCCCEEEECCCCHHHHHHHCCCEEEEEECHHHEEEEEECCCCCCHHHHHHHH----HCCCCC------CCCCEEEEEEEE T ss_conf 8983899658951787751581799961868779999746578357899988----508752------436615889985 Q ss_pred CCCCEEEEE-ECCCEE----------EEEECCCCCCC--CCCCCCCEEEEECCCCE Q ss_conf 899649999-459989----------99990105544--51568738898089987 Q gi|254780182|r 848 NDNDQIILV-SDKGTL----------IRVPVNEIRIA--SRATKGVVIFSTAKDER 890 (910) Q Consensus 848 ~~~DeIlli-T~~G~i----------iR~~v~~I~~~--gR~a~GV~i~~L~~~D~ 890 (910) + +++|+ .+.... -++++.+|-++ .|-..|.--++|.++|+ T Consensus 417 ~---d~~lFk~~~~~~k~liPEN~P~~~V~ag~IgvTN~a~k~~G~iGVRl~d~de 469 (508) T PRK00969 417 D---DIVLFKGNIEYSKGLIPENTPEDKVEAGEIGVTNMAAKYVGMIGVRLEDNDE 469 (508) T ss_pred C---CEEEECCCCHHCCCCCCCCCCCCCCCCCEEEEEEHHHHCCCEEEEEECCCCC T ss_conf 8---7799747803224568888887753045676660145428657998057754 No 181 >pfam08657 DASH_Spc34 DASH complex subunit Spc34. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules. Probab=31.33 E-value=26 Score=12.89 Aligned_cols=26 Identities=23% Similarity=0.231 Sum_probs=19.1 Q ss_pred HHHHHHCCCCCHHHHHHHCCCCCCCC Q ss_conf 98876187768888886345866887 Q gi|254780182|r 202 CVAVIDNPDIDLDALMEIIRGPDFPT 227 (910) Q Consensus 202 ~~~~i~~p~~~~~eL~~~i~GPDFPT 227 (910) +..||++++..-.-|.++-|.+-.|+ T Consensus 36 IT~LIRDte~~EraLf~i~~~~~~~~ 61 (212) T pfam08657 36 ITALIRDTEPHERALFKIDPPKKSPR 61 (212) T ss_pred HHHHHCCCCHHHHHHHCCCCCCCCCC T ss_conf 57886289754565514689888766 No 182 >COG1293 Predicted RNA-binding protein homologous to eukaryotic snRNP [Transcription] Probab=31.11 E-value=26 Score=12.87 Aligned_cols=42 Identities=10% Similarity=0.052 Sum_probs=17.2 Q ss_pred HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHCCHHHHH Q ss_conf 9987899998887--99999989999999998875304989999 Q gi|254780182|r 457 ILELRLARLTGLG--RDDIRNELNSLGIEIKECLDILSSRSRLL 498 (910) Q Consensus 457 ILdMrL~rLt~LE--~~kl~~E~~eL~~~I~~l~~IL~s~~~l~ 498 (910) +.++--.+-.+|+ ...+....+++...+.+|+......++.. T Consensus 364 ~~~~~~~~~~klk~~~~~~~~~~~~~~~~~~y~e~~~~~lek~~ 407 (564) T COG1293 364 NAQRYFKKYKKLKGAKVNLDRQLSELKEAIAYYESAKTALEKAE 407 (564) T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 57888888866246400276666657789999999999998551 No 183 >PRK07778 consensus Probab=31.09 E-value=26 Score=12.86 Aligned_cols=13 Identities=15% Similarity=0.087 Sum_probs=6.8 Q ss_pred HHHHHHHHHHCCC Q ss_conf 7899999971220 Q gi|254780182|r 91 AAIYDALARMAQD 103 (910) Q Consensus 91 ~siy~a~v~maq~ 103 (910) ..|-+|+....++ T Consensus 46 ~~i~~a~~~a~~~ 58 (386) T PRK07778 46 EPVRAAAAAALHR 58 (386) T ss_pred HHHHHHHHHHHCC T ss_conf 9999999998634 No 184 >pfam06447 consensus Probab=31.07 E-value=26 Score=12.86 Aligned_cols=64 Identities=8% Similarity=0.105 Sum_probs=37.1 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH Q ss_conf 236999999999878999988879--9999989999999998875304989999999998999998 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGR--DDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKD 510 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~--~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~ 510 (910) =.|++.=.++-|.-+.+.|..|+. .+++.|.+...+.+++.++-|+.-...+..+++++.++.. T Consensus 46 ~~ft~~v~~~ala~qq~~~~~l~kql~~l~~e~~~~~~~~~~~q~~l~~l~qe~~~L~~q~~~~~~ 111 (407) T pfam06447 46 DDFVNKVNQSAIAEQQKTLSEMQKQIRRLRAEREEKERDLDQNQERIASLEQENQQLREQLAAGQA 111 (407) T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 765003257799999999999999999999999999887888899999999999999999998872 No 185 >pfam04967 HTH_10 HTH DNA binding domain. Probab=30.96 E-value=26 Score=12.85 Aligned_cols=34 Identities=21% Similarity=0.202 Sum_probs=26.6 Q ss_pred CCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHC Q ss_conf 97367899999998789999981134042556643 Q gi|254780182|r 49 LKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMG 83 (910) Q Consensus 49 lKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~g 83 (910) |-|-||++|...+++|. +|-|-+-+..-+.+-|| T Consensus 1 LT~rQ~evl~~A~~~GY-fd~PR~~~l~elA~~lg 34 (53) T pfam04967 1 LTDRQREILRLAYKMGY-FDYPRRVTLKDLAKELG 34 (53) T ss_pred CCHHHHHHHHHHHHCCC-CCCCCCCCHHHHHHHHC T ss_conf 98899999999998689-77887688999999969 No 186 >COG3394 Uncharacterized protein conserved in bacteria [Function unknown] Probab=30.78 E-value=26 Score=12.82 Aligned_cols=140 Identities=19% Similarity=0.180 Sum_probs=58.7 Q ss_pred CCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHH----------HCCCHHCCC------CCC Q ss_conf 8973678999999987899999811340425566436688704789999997----------122011156------131 Q gi|254780182|r 48 GLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALAR----------MAQDWSLRL------LLI 111 (910) Q Consensus 48 GlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~----------maq~~~~r~------pli 111 (910) ||-|-|-+-+-..|+.|...+.- +| -++.++-.|.-+ |-=.++.-. +|+ T Consensus 13 GLs~G~nyGIiea~~~GvvtsTt----------~M-----~n~pa~~hAv~l~k~~p~l~IGlHl~LT~g~Plt~~~~l~ 77 (257) T COG3394 13 GLSKGVNYGIIEAHRTGVVTSTT----------LM-----VNMPAIDHAVALSKKLPALKIGLHLNLTLGKPLTNMPELT 77 (257) T ss_pred CCCCCCCHHHHHHHHCCCEECEE----------EC-----CCCCCCHHHHHHHHHCCCCCEEEEEEECCCCCCCCCCCCC T ss_conf 75655205588898679431202----------30-----5886537799987658887511147860367767886656 Q ss_pred CCCCCCC-C-C-CCCCCCHHHHHHHHHHHHHH--HHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHH Q ss_conf 4788708-8-7-76972013578999789999--9986307684053306898854850343227321101676101013 Q gi|254780182|r 112 EGQGNFG-S-V-DGDPPAAERYTECRLQKAAH--FLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGM 186 (910) Q Consensus 112 dg~GnfG-s-~-dgd~~AA~RYte~rl~~~~~--~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGm 186 (910) |-+|-|+ + . .--+-.+.-+-|..-.-.|+ ..++-... .|.|=+|.+--..+|.-+|-+ .-=+.+.++ T Consensus 78 ~e~G~~~~~~~~~~~~~~~~~~eeV~~El~aQ~erF~~~~G~-----~PshlDsHhh~h~~P~I~p~v-~rlA~e~~i-- 149 (257) T COG3394 78 DENGEFGLKWYWLRALEGALDLEEVTAELIAQYERFVELFGR-----TPSHLDSHHHVHMFPQIAPIV-ARLAEEYGI-- 149 (257) T ss_pred CCCCCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCC-----CCCCCCCCCCCCCCCHHHHHH-HHHHHCCCC-- T ss_conf 899854613454225234999899999999999999998589-----974113543334341478999-999751496-- Q ss_pred HHCCCCC---CHHHHHHHHHHHHHCCC Q ss_conf 3178985---47899999988761877 Q gi|254780182|r 187 ATNIPTH---NLGEVVDGCVAVIDNPD 210 (910) Q Consensus 187 aTnippH---Nl~Ev~~a~~~~i~~p~ 210 (910) +--++++ |.+|...++..+.+..+ T Consensus 150 ~lR~~~~~~~~~~~~~~~ir~~~~~f~ 176 (257) T COG3394 150 PLRIDRTWVSNAGELPAGIRSLLEGFL 176 (257) T ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHH T ss_conf 201575334566656410578876400 No 187 >KOG3314 consensus Probab=30.76 E-value=26 Score=12.82 Aligned_cols=38 Identities=24% Similarity=0.573 Sum_probs=26.8 Q ss_pred HHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCC Q ss_conf 36789999999878999998113404255664366887 Q gi|254780182|r 51 PVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPH 88 (910) Q Consensus 51 pv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPH 88 (910) |+-+-.+-||-.+|-..+-.+.+|----|.|-|-|||- T Consensus 38 P~Vkfl~~am~k~~c~~~d~~isc~~C~~~~~GGy~~~ 75 (194) T KOG3314 38 PIVKFLMEAMEKSGCRVGDNFISCVVCTGPVAGGYTPG 75 (194) T ss_pred CHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCCCCC T ss_conf 38999999999738876677457766899756774688 No 188 >pfam05565 Sipho_Gp157 Siphovirus Gp157. This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophages. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage. Probab=30.75 E-value=26 Score=12.82 Aligned_cols=65 Identities=18% Similarity=0.236 Sum_probs=32.3 Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCC-CCEEE-----CC--CCCCCCCCCCCCCCE Q ss_conf 9989999999998875304989999999998999998405688-33100-----13--434530101456781 Q gi|254780182|r 474 RNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPR-RTRIV-----EG--LLDMEDEDCIVREDM 538 (910) Q Consensus 474 ~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~R-RT~I~-----~~--~~~i~~EdlI~~E~v 538 (910) +.+.+.+.++++.|.+.-.+-+...+-+++.|......-|..+ +|.+. .. ...+.+|++||++-+ T Consensus 53 ea~~~~~k~e~krl~erkk~~enk~~~LK~yl~~~m~~~g~~kikt~~~tis~rk~~~sv~I~de~~iP~ey~ 125 (162) T pfam05565 53 EADIEAIKAEIKRLAERKKSIENKVKRLKDYLEEAMEATGIKKIKTPLFTVSIRKSKPSVEIEDEAKIPAEYF 125 (162) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCEEEEEECCCCCEECCCHHHCCHHHH T ss_conf 9789999999999999999999899999999999999809867763767999737899132489566889985 No 189 >PRK08760 replicative DNA helicase; Provisional Probab=30.68 E-value=27 Score=12.81 Aligned_cols=19 Identities=26% Similarity=0.441 Sum_probs=10.0 Q ss_pred HHHHHHHHHHHHHHHCCCC Q ss_conf 9999999899999840568 Q gi|254780182|r 497 LLGIIKQELLSVKDELDTP 515 (910) Q Consensus 497 l~~iI~~EL~eik~kygd~ 515 (910) ....|-.+|+.+.+.++-| T Consensus 363 ~v~~isr~lK~lAkel~vp 381 (476) T PRK08760 363 EISEISRSLKGLAKELNVP 381 (476) T ss_pred HHHHHHHHHHHHHHHHCCC T ss_conf 9999999999999997997 No 190 >pfam03853 YjeF_N YjeF-related protein N-terminus. Probab=30.67 E-value=25 Score=13.05 Aligned_cols=116 Identities=20% Similarity=0.237 Sum_probs=54.1 Q ss_pred HHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHH--------------HHHHHHHHHHHHCCCCCCCCEEC Q ss_conf 7899999971220111561314788708877697201357899--------------97899999986307684053306 Q gi|254780182|r 91 AAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTEC--------------RLQKAAHFLLDDLGKDTVDFRPN 156 (910) Q Consensus 91 ~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~--------------rl~~~~~~~l~~i~~~tv~~~~n 156 (910) .++++.+.++-.+-..+...+-|.||.| ||+=++.||--. .+++-+...++-..+--+.+.+. T Consensus 14 ~~~a~~i~~~~~~~~~~v~il~G~GNNG---GDGlv~Ar~L~~~g~~V~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 90 (170) T pfam03853 14 RAVARVIRKLLSPAGKRVLVLCGPGNNG---GDGLAAARHLAQRGYKVTVLLLNPDEKLSEDARRALEIAKKLGGKIVSL 90 (170) T ss_pred HHHHHHHHHHCCCCCCEEEEEECCCCCH---HHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCEEEC T ss_conf 9999999986187788699998799872---8899999999987990799996785559999999999999869967615 Q ss_pred CCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCC Q ss_conf 898854850343227321101676101013317898547899999988761877688888863458668874 Q gi|254780182|r 157 YDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTG 228 (910) Q Consensus 157 ~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTG 228 (910) +....+ +..=+-+.|-|--|| |+... +++-+..++.+|+..+.. +=.=|-|+| T Consensus 91 -~~~~~~----~~~~~d~iVDal~G~--Gl~~~-----l~~~~~~~i~~iN~~~~~-------visiDiPSG 143 (170) T pfam03853 91 -NPDEDL----SKALADLIIDALFGT--GLSRP-----LRGEYAELIEWINASKAP-------VLAVDIPSG 143 (170) T ss_pred -CCCCCC----CCCCCCEEEEEEEEC--CCCCC-----CCHHHHHHHHHHHCCCCC-------EEEEECCCC T ss_conf -863201----256662899743523--67988-----988999999999738996-------799737887 No 191 >cd04962 GT1_like_5 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog Probab=30.58 E-value=27 Score=12.80 Aligned_cols=35 Identities=9% Similarity=0.079 Sum_probs=18.5 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 99999887530498999999999899999840568 Q gi|254780182|r 481 GIEIKECLDILSSRSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 481 ~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~ 515 (910) .+-.+.+..+|.+++...+.-.+=...+.++|.-+ T Consensus 324 ~~la~~i~~ll~~~~~~~~~~~~a~~~~~~~fs~~ 358 (371) T cd04962 324 EAMAEYALSLLEDDELWQEFSRAARNRAAERFDSE 358 (371) T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCHH T ss_conf 99999999997699999999999999999868999 No 192 >PRK11303 DNA-binding transcriptional regulator FruR; Provisional Probab=30.55 E-value=27 Score=12.79 Aligned_cols=181 Identities=11% Similarity=0.093 Sum_probs=76.6 Q ss_pred HHHHCCCCCCC--CCC-HHHHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHCCC Q ss_conf 86313754000--897-3678999999987899999811----3404255664366-88704789999997122011156 Q gi|254780182|r 37 ILGRAIPDLRD--GLK-PVHRRILFGMMQMGVEWNKKYV----KCARISGEVMGKY-HPHGNAAIYDALARMAQDWSLRL 108 (910) Q Consensus 37 I~~RAlPd~rD--GlK-pv~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~gky-HPHGd~siy~a~v~maq~~~~r~ 108 (910) -|||+|=.--+ ... -..+||+=+|.+||..||..-+ +..+.+|-++-.+ +|+ -+.+...+-+-++.. .| T Consensus 16 TVSrvLNg~~~~~~Vs~~Tr~rV~~aa~eLgY~Pn~~Ar~L~~~~t~~Igvvvp~~~n~~-~~~l~~~i~~~~~~~--gy 92 (330) T PRK11303 16 TASYVINGKAKQYRISDKTVEKVMAVVREHNYHPNAVAAGLRAGRTRSIGLIIPDLENTS-YARIAKLLEQQARQR--GY 92 (330) T ss_pred HHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCEEEEECCCCCCCH-HHHHHHHHHHHHHHC--CC T ss_conf 998883899988876999999999999996899488898863087776777545444315-678889999999966--98 Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCC-CCCEECCCCCCCCHHCCCCCEEEHHH Q ss_conf 13147887088776972013578999789999998630768405330689885-48503432273211016761010133 Q gi|254780182|r 109 LLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSF-QEPVVLCARYPNVLVNGGGGIAVGMA 187 (910) Q Consensus 109 plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~-~EP~vlP~~~P~lL~nG~~GIAvGma 187 (910) -++- + +-+.|+.--.++. . +|..-.-+-+=..+...... .-....-..+|.++++....- .-. T Consensus 93 ~~li----~-~s~~~~~~e~~~~--------~-~l~~~~vdgiIv~~~~~~~~~~~~~l~~~~iPvV~i~~~~~~--~~~ 156 (330) T PRK11303 93 QLLI----A-CSDDQPDNEMQCA--------E-HLLQRQVDALIVATSLPPEHPFYQRLQNDGFPIIALDRALDR--EHF 156 (330) T ss_pred EEEE----E-ECCCCHHHHHHHH--------H-HHHHCCCCEEEEECCCCCCCHHHHHHHHCCCCEEEECCCCCC--CCC T ss_conf 7999----9-4799989999999--------9-999748998999468888629999998469978997256788--889 Q ss_pred HCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCC-CCCCCCCCCCCHHHHHHHHH Q ss_conf 17898547899999988761877688888863458-66887443447588999987 Q gi|254780182|r 188 TNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRG-PDFPTGAVILGRTGIKNAYA 242 (910) Q Consensus 188 TnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~G-PDFPTGG~I~~~~~i~~~y~ 242 (910) ..+-+-|-.-...|+.++++...-.+ -||-| |++++.- .-..|.+++.+ T Consensus 157 ~~V~~d~~~~~~~a~~~L~~~GhrrI----~~i~~~~~~~~~~--~R~~Gf~~al~ 206 (330) T PRK11303 157 TSVVSDDQDAAEMLAESLLKFPAESI----LLLGALPELSVSF--LREQGFRQALK 206 (330) T ss_pred CEEEECCHHHHHHHHHHHHHCCCCEE----EEEECCCCCHHHH--HHHHHHHHHHH T ss_conf 98997219999999999998699979----9996897563799--99999999999 No 193 >COG3959 Transketolase, N-terminal subunit [Carbohydrate transport and metabolism] Probab=30.54 E-value=27 Score=12.79 Aligned_cols=16 Identities=25% Similarity=0.399 Sum_probs=12.7 Q ss_pred CCCCHHHHHHHHHHHC Q ss_conf 8870478999999712 Q gi|254780182|r 86 HPHGNAAIYDALARMA 101 (910) Q Consensus 86 HPHGd~siy~a~v~ma 101 (910) ||||.-|+-|-|.-+= T Consensus 32 H~G~SLS~~eILa~LY 47 (243) T COG3959 32 HVGGSLSVVEILAVLY 47 (243) T ss_pred CCCCCCHHHHHHHHHH T ss_conf 7576210999999999 No 194 >KOG0275 consensus Probab=30.34 E-value=27 Score=12.77 Aligned_cols=28 Identities=14% Similarity=0.268 Sum_probs=11.3 Q ss_pred CEEEEEECCCCCEEEEEECCCEEEEEEC Q ss_conf 6899997289964999945998999990 Q gi|254780182|r 840 ALVAVFPVNDNDQIILVSDKGTLIRVPV 867 (910) Q Consensus 840 ~lv~~~~V~~~DeIlliT~~G~iiR~~v 867 (910) ..+++..-.-++.++.+-..|.+.-+.+ T Consensus 439 dFi~~~lSpkGewiYcigED~vlYCF~~ 466 (508) T KOG0275 439 DFINAILSPKGEWIYCIGEDGVLYCFSV 466 (508) T ss_pred CEEEEEECCCCCEEEEECCCCEEEEEEE T ss_conf 5578884488748999736857999996 No 195 >PRK04028 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated Probab=30.25 E-value=27 Score=12.76 Aligned_cols=70 Identities=17% Similarity=0.165 Sum_probs=44.8 Q ss_pred HHHHHHHHHC--CCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999998618--99789878776312697889999974022111222344523699999999987899998887999999 Q gi|254780182|r 398 DEVVRIIRFS--PNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRN 475 (910) Q Consensus 398 DeVI~iIR~S--~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~ 475 (910) ++.|+=||.+ +-|++-+.+|++. |+||+.+|+.+++=+. + + T Consensus 443 ~e~Ie~Ik~~LPELP~~kr~Rl~~e--------------------------ygLs~~dA~~L~~~~~----------l-~ 485 (631) T PRK04028 443 EELLEKIKKNLPELPEEKLERLVKE--------------------------YGLSEELAEQLANSER----------L-D 485 (631) T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHH--------------------------CCCCHHHHHHHHCCCH----------H-H T ss_conf 9999999971899999999999997--------------------------0989999999974738----------9-9 Q ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH Q ss_conf 899999999988753049899999999989999984 Q gi|254780182|r 476 ELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDE 511 (910) Q Consensus 476 E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~k 511 (910) .++++.+ .-.+++..-+.+...|.+++++ T Consensus 486 ~FE~~v~-------~~~~pk~~An~l~~~l~~L~~~ 514 (631) T PRK04028 486 LFEELVK-------KGVKPTLIARTLVNTLKELKRE 514 (631) T ss_pred HHHHHHH-------CCCCHHHHHHHHHHHHHHHHHC T ss_conf 9999997-------1699999999999999999976 No 196 >pfam11629 Mst1_SARAH C terminal SARAH domain of Mst1. This family of proteins represents the C terminal SARAH domain of Mst1. SARAH controls apoptosis and cell cycle arrest via the Ras, RASSF, MST pathway. The Mst1 SARAH domain interacts with Rassf1 and Rassf5 by forming a heterodimer which mediates the apoptosis process. Probab=30.15 E-value=27 Score=12.74 Aligned_cols=32 Identities=19% Similarity=0.228 Sum_probs=21.3 Q ss_pred HHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 88753049899999999989999984056883310 Q gi|254780182|r 486 ECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRI 520 (910) Q Consensus 486 ~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I 520 (910) +|+.-|+| +..-+-.|+.+++.+|..+|.-.+ T Consensus 12 eL~~rl~s---LD~~ME~Eieelr~RYq~KRqPIL 43 (49) T pfam11629 12 ELEQRLAS---LDPEMETEIEELRQRYQAKRQPIL 43 (49) T ss_pred HHHHHHHH---CCHHHHHHHHHHHHHHHHHHCCHH T ss_conf 99999986---678899999999999887424399 No 197 >COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair] Probab=30.05 E-value=27 Score=12.73 Aligned_cols=14 Identities=21% Similarity=0.382 Sum_probs=7.2 Q ss_pred CCCCEEEEEEEECC Q ss_conf 89986999897336 Q gi|254780182|r 730 AKGDQVISMAIVLH 743 (910) Q Consensus 730 ~~~D~Vv~~~vi~~ 743 (910) ..+++|.|+.+.+. T Consensus 202 ~~~~~VRGiLvAp~ 215 (253) T COG1637 202 DTGDKVRGILVAPS 215 (253) T ss_pred CCCCEEEEEEECCC T ss_conf 46860789998664 No 198 >PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional Probab=29.91 E-value=27 Score=12.71 Aligned_cols=25 Identities=32% Similarity=0.425 Sum_probs=21.9 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2369999999998789999888799 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRD 471 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~ 471 (910) |+||+.|-+||++....+|-.+.-+ T Consensus 54 ~~Lteeqk~aV~~RD~~~li~lGgn 78 (129) T PRK13377 54 WPMTEEQKQAVLARDLNRCIALGGN 78 (129) T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCH T ss_conf 6999999999997379999992673 No 199 >pfam06952 PsiA PsiA protein. This family consists of several Enterobacterial PsiA proteins. The function of PsiA is unknown although it is thought that it may affect the generation of an SOS signal in Escherichia coli. Probab=29.83 E-value=27 Score=12.70 Aligned_cols=16 Identities=44% Similarity=0.607 Sum_probs=7.4 Q ss_pred CCCCCEEEHHHHCCCC Q ss_conf 1676101013317898 Q gi|254780182|r 177 NGGGGIAVGMATNIPT 192 (910) Q Consensus 177 nG~~GIAvGmaTnipp 192 (910) ||+.+|-+--+-.||| T Consensus 49 nGs~rI~~~d~r~i~~ 64 (238) T pfam06952 49 NGSGRINATDARRIPG 64 (238) T ss_pred CCCCCCCHHHHHHCCC T ss_conf 5866442766522587 No 200 >cd04626 CBS_pair_13 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener Probab=29.81 E-value=22 Score=13.46 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=10.4 Q ss_pred HHHHHHHHHHCCCHHCCCCCCCCCCCC Q ss_conf 789999997122011156131478870 Q gi|254780182|r 91 AAIYDALARMAQDWSLRLLLIEGQGNF 117 (910) Q Consensus 91 ~siy~a~v~maq~~~~r~plidg~Gnf 117 (910) +++.+|+-.|.+......|.+|.+|.+ T Consensus 10 ~tl~eA~~~m~~~~~~~~~Vvd~~~~l 36 (111) T cd04626 10 ASIREALHEMLKYNTNEIIVKDNEEKL 36 (111) T ss_pred CCHHHHHHHHHHHCCCEEEEECCCCEE T ss_conf 939999999998499889999699979 No 201 >TIGR02483 PFK_mixed phosphofructokinase; InterPro: IPR012829 Members of this family that are characterised, save one, are phosphofructokinases dependent on pyrophosphate (2.7.1.90 from EC) rather than ATP (2.7.1.11 from EC). The exception is one of three phosphofructokinases from Streptomyces coelicolor. Family members are both bacterial and archaeal.; GO: 0005524 ATP binding, 0008443 phosphofructokinase activity, 0006002 fructose 6-phosphate metabolic process, 0006096 glycolysis. Probab=29.78 E-value=27 Score=12.69 Aligned_cols=31 Identities=26% Similarity=0.617 Sum_probs=23.0 Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCC Q ss_conf 678459999246443528999999999987166 Q gi|254780182|r 260 SGDREQIVVTEIPYQVNKAAMLEKIAELVREKR 292 (910) Q Consensus 260 ~~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~k 292 (910) .+|=+-|.|=|+||.++ ++++||.+.-+.+| T Consensus 197 aGGAd~ILIPE~P~d~~--~v~~~v~~r~~~G~ 227 (339) T TIGR02483 197 AGGADVILIPEIPFDID--SVCEKVRERFARGK 227 (339) T ss_pred HCCCCEEEECCCCCCHH--HHHHHHHHHHHCCC T ss_conf 20876789786048889--99999999987266 No 202 >pfam01768 Birna_VP4 Birnavirus VP4 protein. VP4 is a viral protease. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C). Probab=29.77 E-value=13 Score=15.62 Aligned_cols=24 Identities=33% Similarity=0.566 Sum_probs=9.0 Q ss_pred CCCCCCCCCC-CCCCCCCCCHHHHH Q ss_conf 6131478870-88776972013578 Q gi|254780182|r 108 LLLIEGQGNF-GSVDGDPPAAERYT 131 (910) Q Consensus 108 ~plidg~Gnf-Gs~dgd~~AA~RYt 131 (910) -||++--+.| |.+-||.||+-||+ T Consensus 14 APLigaad~~i~~l~~~~Aa~gr~~ 38 (264) T pfam01768 14 APLIGAADQFIGDLLGDNASGGRYV 38 (264) T ss_pred CCHHHHHHHHHHHHCCCCCCCCCCC T ss_conf 2012246666665316633367624 No 203 >KOG4288 consensus Probab=29.52 E-value=28 Score=12.66 Aligned_cols=35 Identities=31% Similarity=0.440 Sum_probs=20.4 Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHH Q ss_conf 7898547899999988761877688888863458668874434475889999 Q gi|254780182|r 189 NIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNA 240 (910) Q Consensus 189 nippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~ 240 (910) -+||-|..+|.-|.+.-+. -|||+ |+ +..++|.++ T Consensus 243 ~~ppvnve~VA~aal~ai~--------------dp~f~--Gv-v~i~eI~~~ 277 (283) T KOG4288 243 LAPPVNVESVALAALKAIE--------------DPDFK--GV-VTIEEIKKA 277 (283) T ss_pred CCCCCCHHHHHHHHHHHCC--------------CCCCC--CE-EEHHHHHHH T ss_conf 4798678999999997424--------------87757--60-559999998 No 204 >KOG3686 consensus Probab=29.38 E-value=28 Score=12.64 Aligned_cols=22 Identities=14% Similarity=0.039 Sum_probs=15.1 Q ss_pred CCCCEEEEEECCCEEEEEEHHH Q ss_conf 8982699993698599975876 Q gi|254780182|r 691 TQENDILLTTKLGQCVRFPISA 712 (910) Q Consensus 691 ~~~~~Iil~T~~G~~lrF~~~e 712 (910) ...+.+++++...+...|++.. T Consensus 532 ~~~~~~~~~s~~~~~v~fn~~~ 553 (740) T KOG3686 532 ISPHLDVLSSREVHKVAFNEDR 553 (740) T ss_pred CCCCCEEEECCCCCCEEEECCC T ss_conf 7854124304356625885244 No 205 >PRK13670 hypothetical protein; Provisional Probab=29.22 E-value=27 Score=12.69 Aligned_cols=120 Identities=17% Similarity=0.407 Sum_probs=57.7 Q ss_pred HHHHHHCCCCCCCHHHHHH--HHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCE Q ss_conf 2556643668870478999--99971220111561314788708877697201357899978999999863076840533 Q gi|254780182|r 77 ISGEVMGKYHPHGNAAIYD--ALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFR 154 (910) Q Consensus 77 ivg~v~gkyHPHGd~siy~--a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~ 154 (910) +||= +--|.|.-..-.|- ..-... .--+..+-.-|||=-. |.||=...|+-|+++ +..+ ||.| T Consensus 3 ~~GI-IaEYNPFHnGH~Yhi~~ar~~t---~ad~iIaVMSGnFvQR-GEPAi~dKw~Ra~~A-----L~~G-----aDLV 67 (390) T PRK13670 3 ATGI-IVEYNPFHNGHLYHLNQAKKLT---KADVTIAVMSGNFVQR-GEPAIVDKWTRAKMA-----LANG-----ADLV 67 (390) T ss_pred EEEE-EEEECCCCCHHHHHHHHHHHHC---CCCEEEEEECCCCCCC-CCCHHCCHHHHHHHH-----HHCC-----CCEE T ss_conf 3689-9610797410899999999753---9987999943885108-872007878999999-----9859-----9889 Q ss_pred ECCCCCCCCCEECCCCCC----CCHHC---------CCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHC- Q ss_conf 068988548503432273----21101---------6761010133178985478999999887618776888888634- Q gi|254780182|r 155 PNYDGSFQEPVVLCARYP----NVLVN---------GGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEII- 220 (910) Q Consensus 155 ~n~D~~~~EP~vlP~~~P----~lL~n---------G~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i- 220 (910) = =||.-+- -.... |.+-|+-|+-+. ++.....+.-.+.++|+.- +++++++ T Consensus 68 i----------ELP~~ya~qsAe~FA~gaV~lL~~lgvd~l~FGsE~~----d~~~l~~~a~~l~~~~~~~-~~~~~~L~ 132 (390) T PRK13670 68 V----------ELPFVFAVQSADYFAEGAVSILDALGVDDLVFGSESG----DIEDFQKLAKIINEKPEEF-EAFLKKLK 132 (390) T ss_pred E----------ECCHHHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCC----CHHHHHHHHHHHHHCHHHH-HHHHHHHH T ss_conf 9----------8865988625999999999999986999899668889----8999999999998680889-99999866 Q ss_pred CCCCCC Q ss_conf 586688 Q gi|254780182|r 221 RGPDFP 226 (910) Q Consensus 221 ~GPDFP 226 (910) +|=-|| T Consensus 133 ~G~Syp 138 (390) T PRK13670 133 KGLSYP 138 (390) T ss_pred CCCCHH T ss_conf 789999 No 206 >cd04613 CBS_pair_SpoIVFB_EriC_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase a Probab=29.06 E-value=24 Score=13.22 Aligned_cols=28 Identities=11% Similarity=0.287 Sum_probs=15.5 Q ss_pred HHHHHHHHHHHCCCHHCCCCCCCCCCCC Q ss_conf 4789999997122011156131478870 Q gi|254780182|r 90 NAAIYDALARMAQDWSLRLLLIEGQGNF 117 (910) Q Consensus 90 d~siy~a~v~maq~~~~r~plidg~Gnf 117 (910) |+++.+|+-.|.+.--..+|.+|.+|+| T Consensus 9 ~~tl~ea~~~m~~~~~~~~pVvd~~~~l 36 (114) T cd04613 9 DTPLNELLDVIAHSPENNFPVVDDDGRL 36 (114) T ss_pred CCCHHHHHHHHHHCCCCEEEEECCCCEE T ss_conf 0989999999986199789999289949 No 207 >cd04593 CBS_pair_EriC_assoc_bac_arch This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in bacteria and archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS d Probab=29.03 E-value=24 Score=13.27 Aligned_cols=26 Identities=12% Similarity=0.265 Sum_probs=8.9 Q ss_pred HHHHHHHHHHCCCHHCCCCCCCCCCC Q ss_conf 78999999712201115613147887 Q gi|254780182|r 91 AAIYDALARMAQDWSLRLLLIEGQGN 116 (910) Q Consensus 91 ~siy~a~v~maq~~~~r~plidg~Gn 116 (910) ++++||+-.|.+.-....|.+|.+|. T Consensus 10 ~tv~ea~~~m~~~~~~~~pVvD~~g~ 35 (115) T cd04593 10 TPLREAAEQLIESKHGSALVVDRDGG 35 (115) T ss_pred CCHHHHHHHHHHCCCCEEEEECCCCC T ss_conf 99999999998749989999949998 No 208 >smart00116 CBS Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease. Probab=28.96 E-value=26 Score=12.85 Aligned_cols=30 Identities=17% Similarity=0.320 Sum_probs=22.8 Q ss_pred CCHHHHHHHHHHHCCCHHCCCCCCCCCCCC Q ss_conf 704789999997122011156131478870 Q gi|254780182|r 88 HGNAAIYDALARMAQDWSLRLLLIEGQGNF 117 (910) Q Consensus 88 HGd~siy~a~v~maq~~~~r~plidg~Gnf 117 (910) +-++++.+|+-.|.+.---+.|.+|.+|+. T Consensus 6 ~~~~~v~~a~~~m~~~~i~~lPVVd~~~~l 35 (49) T smart00116 6 SPDTTLEEALELLREHGIRRLPVVDEEGRL 35 (49) T ss_pred CCCCCHHHHHHHHHHHCCCEEEEECCCCCE T ss_conf 987929999999998099857699899919 No 209 >COG3546 Mn-containing catalase [Inorganic ion transport and metabolism] Probab=28.59 E-value=28 Score=12.54 Aligned_cols=33 Identities=27% Similarity=0.322 Sum_probs=21.1 Q ss_pred CCCCCCCCCCHHHHHHHHHHHH---HHHHHHHCCCC Q ss_conf 0887769720135789997899---99998630768 Q gi|254780182|r 117 FGSVDGDPPAAERYTECRLQKA---AHFLLDDLGKD 149 (910) Q Consensus 117 fGs~dgd~~AA~RYte~rl~~~---~~~~l~~i~~~ 149 (910) ||-.+|.-+|||||.--+++-- ..+||.||.-+ T Consensus 29 lGG~~GElsaamqYl~Q~fn~r~~~~~dll~DI~TE 64 (277) T COG3546 29 LGGAFGELSAAMQYLFQGFNVRDAKYKDLLMDIGTE 64 (277) T ss_pred HCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH T ss_conf 679624799999998753466753799999986478 No 210 >KOG3809 consensus Probab=28.55 E-value=29 Score=12.53 Aligned_cols=42 Identities=24% Similarity=0.237 Sum_probs=28.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHCCHHHHHHHHH Q ss_conf 89999888799999989999999998875--------3049899999999 Q gi|254780182|r 461 RLARLTGLGRDDIRNELNSLGIEIKECLD--------ILSSRSRLLGIIK 502 (910) Q Consensus 461 rL~rLt~LE~~kl~~E~~eL~~~I~~l~~--------IL~s~~~l~~iI~ 502 (910) +=+++|.-..+-|.+++++|++.|+++++ ||+++.++.+.|- T Consensus 532 ~eq~~t~~a~epL~~~la~lq~~I~d~~e~i~~~r~~IL~Ne~rIqk~i~ 581 (583) T KOG3809 532 NEQAATFGASEPLYNILANLQKEINDTKEEISKARGRILNNEKRIQKFIS 581 (583) T ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 66531334421799999999999999999999999888504899999974 No 211 >TIGR01122 ilvE_I branched-chain amino acid aminotransferase; InterPro: IPR005785 Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped into subfamilies. One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C-terminus side of the PlP-lysine. Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE) (2.6.1.42 from EC). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family more strongly similar to the DAAT family. ; GO: 0004084 branched-chain-amino-acid transaminase activity, 0009081 branched chain family amino acid metabolic process. Probab=28.35 E-value=22 Score=13.52 Aligned_cols=22 Identities=23% Similarity=0.244 Sum_probs=11.3 Q ss_pred ECCCCEEEECHHH--HHHCCCCCE Q ss_conf 4799189842368--620477722 Q gi|254780182|r 652 TKHGNVRRNKLSD--FIQINRSGK 673 (910) Q Consensus 652 Tk~G~VKkt~l~e--f~~~r~~G~ 673 (910) =|+|.++-=|+++ +.-++++-+ T Consensus 196 VK~G~l~TPp~~~s~L~GITRd~V 219 (302) T TIGR01122 196 VKDGVLITPPVSSSILKGITRDTV 219 (302) T ss_pred EECCEEECCCCHHHHCCCCCHHHH T ss_conf 708678789870422488888899 No 212 >KOG4318 consensus Probab=28.35 E-value=29 Score=12.50 Aligned_cols=178 Identities=14% Similarity=0.174 Sum_probs=93.8 Q ss_pred HHHHHHH----HHHHHHHHHCCC-CCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHH Q ss_conf 9876787----779988631375-40008973678999999987899999811340425566436688704789999997 Q gi|254780182|r 25 MQNSYLT----YAINVILGRAIP-DLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALAR 99 (910) Q Consensus 25 m~~syl~----Ya~svI~~RAlP-d~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~ 99 (910) |-+||-. .+.-..+.||+- -.-||-|| +||.|.+-|+ |=++|.=-+=++| -++.++.+-..| T Consensus 194 ~cksl~e~~~s~~l~a~l~~alaag~~d~Ak~----ll~emke~gf-pir~HyFwpLl~g--------~~~~q~~e~vlr 260 (1088) T KOG4318 194 MCKSLVEAPTSETLHAVLKRALAAGDVDGAKN----LLYEMKEKGF-PIRAHYFWPLLLG--------INAAQVFEFVLR 260 (1088) T ss_pred HHHHHHCCCCHHHHHHHHHHHHHCCCHHHHHH----HHHHHHHCCC-CCCCCCCHHHHHC--------CCCCHHHHHHHH T ss_conf 99985137881799999999885276144799----9999997688-7651000356616--------764167999999 Q ss_pred HCCCHHC----------CCCCCCCCCCCCCC--CCCCCCHHHHHHHHHHHHHHH--HHHHCCCCCCCCEECCCCCCCCCE Q ss_conf 1220111----------56131478870887--769720135789997899999--986307684053306898854850 Q gi|254780182|r 100 MAQDWSL----------RLLLIEGQGNFGSV--DGDPPAAERYTECRLQKAAHF--LLDDLGKDTVDFRPNYDGSFQEPV 165 (910) Q Consensus 100 maq~~~~----------r~plidg~GnfGs~--dgd~~AA~RYte~rl~~~~~~--~l~~i~~~tv~~~~n~D~~~~EP~ 165 (910) |-|.++. -.|..+ |+-.- +--.+-+|-.|-+-.+..+.. -..++++++.. T Consensus 261 gmqe~gv~p~seT~adyvip~l~---N~~t~~~~e~sq~~hg~tAavrsaa~rg~~a~k~l~~nl~~------------- 324 (1088) T KOG4318 261 GMQEKGVQPGSETQADYVIPQLS---NGQTKYGEEGSQLAHGFTAAVRSAACRGLLANKRLRQNLRK------------- 324 (1088) T ss_pred HHHHHCCCCCCCHHHHHHHHHHC---CHHHHHCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHH------------- T ss_conf 99994678986225778876411---24555222246243323489999996252767789887899------------- Q ss_pred ECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCH--HHHHHHHHH Q ss_conf 343227321101676101013317898547899999988761877688888863458668874434475--889999870 Q gi|254780182|r 166 VLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGR--TGIKNAYAT 243 (910) Q Consensus 166 vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~--~~i~~~y~t 243 (910) .+|-.+|-+|+-| |.+|| |..-.|.-.++ ..|.-.++.|...++.|-|---|.-++- +.++++|.- T Consensus 325 ~v~~s~k~~fLlg---------~d~~~-aiws~c~~l~h--Qgk~e~veqlvg~l~npt~r~s~~~V~a~~~~lrqyFrr 392 (1088) T KOG4318 325 SVIGSTKKLFLLG---------TDILE-AIWSMCEKLRH--QGKGEEVEQLVGQLLNPTLRDSGQNVDAFGALLRQYFRR 392 (1088) T ss_pred HHHHHHHHHHHHC---------CCCCH-HHHHHHHHHHH--CCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 8787746878860---------45536-89999999997--079851999975652771204751377999999999999 No 213 >PRK08694 consensus Probab=28.28 E-value=29 Score=12.49 Aligned_cols=23 Identities=35% Similarity=0.557 Sum_probs=14.1 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 98999999999899999840568 Q gi|254780182|r 493 SRSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 493 s~~~l~~iI~~EL~eik~kygd~ 515 (910) ++......|-..|+.+.+.++-| T Consensus 350 ~r~~~i~~isr~LK~lAkel~ip 372 (468) T PRK08694 350 NRASELGEISRSLKALAKELQVP 372 (468) T ss_pred CHHHHHHHHHHHHHHHHHHHCCC T ss_conf 59999999999999999997998 No 214 >pfam12529 Xylo_C Xylosyltransferase C terminal. This domain family is found in eukaryotes, and is typically between 169 and 183 amino acids in length. The family is found in association with pfam02485. There is a single completely conserved residue G that may be functionally important. Xylosyltransferases are enzymes involved in the biosynthesis of the glycosaminoglycan linker region in proteoglycans. Probab=28.27 E-value=29 Score=12.49 Aligned_cols=41 Identities=17% Similarity=0.203 Sum_probs=14.8 Q ss_pred EEEEEECCCCEEEECHHHHHHCCCCCEEEEEECCCCEEEEE Q ss_conf 79999479918984236862047772278661589857888 Q gi|254780182|r 647 YVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDSRDEILSV 687 (910) Q Consensus 647 ~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLkegD~Li~v 687 (910) |||-....+.-++..++-+..++.+++.+=.....-+|..+ T Consensus 85 fLV~~~a~~~~~~~~lE~w~~P~~~~~~~~~~~~~~RL~~~ 125 (180) T pfam12529 85 FLVRFEAQATGQRETLETWVSPQVSLKLARALVLSKRLRNL 125 (180) T ss_pred EEEEEEEECCCCCEEEEEEEEECCCEEEECCCCHHCEEEEE T ss_conf 99999996699722367777400201540585400200466 No 215 >KOG2052 consensus Probab=28.16 E-value=27 Score=12.73 Aligned_cols=16 Identities=25% Similarity=0.260 Sum_probs=8.1 Q ss_pred EEEEECCCEEEEEEHH Q ss_conf 9999369859997587 Q gi|254780182|r 696 ILLTTKLGQCVRFPIS 711 (910) Q Consensus 696 Iil~T~~G~~lrF~~~ 711 (910) ...+...|.++|++.. T Consensus 354 ~C~IADLGLAv~h~~~ 369 (513) T KOG2052 354 TCCIADLGLAVRHDSD 369 (513) T ss_pred CEEEEECEEEEEECCC T ss_conf 3798603014772366 No 216 >PRK11387 S-methylmethionine transporter; Provisional Probab=27.76 E-value=29 Score=12.42 Aligned_cols=40 Identities=15% Similarity=0.085 Sum_probs=18.6 Q ss_pred HHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHH Q ss_conf 1016761010133178985478999999887618776888 Q gi|254780182|r 175 LVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLD 214 (910) Q Consensus 175 L~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~ 214 (910) +-||..|+..+|+.-.=.+.=-|.+-..-.-.+||.-++. T Consensus 201 ~~~g~~~i~~~~~~~~faf~G~e~i~~~A~E~knP~r~iP 240 (465) T PRK11387 201 FPHGTLPILMTMVAVNFAFSGTELIGIAAGETENPAKVIP 240 (465) T ss_pred CCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHH T ss_conf 6555899999999999997166999999999718676899 No 217 >TIGR01951 nusB transcription antitermination factor NusB; InterPro: IPR011605 The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. The antitermination proteins of Escherichia coli are recruited in the replication cycle of Bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle. The solution structure indicates that the protein folds into an alpha/alpha-helical topology consisting of six helices; the arginine-rich N-terminus appears to be disordered .; GO: 0003715 transcription termination factor activity, 0006353 transcription termination. Probab=27.75 E-value=29 Score=12.42 Aligned_cols=54 Identities=13% Similarity=0.273 Sum_probs=35.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH--HHHHHHHHHHHCCCCCCCEEECC Q ss_conf 8999988879999998999999999887530498999999--99989999984056883310013 Q gi|254780182|r 461 RLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGI--IKQELLSVKDELDTPRRTRIVEG 523 (910) Q Consensus 461 rL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~i--I~~EL~eik~kygd~RRT~I~~~ 523 (910) +|.||+..|+.=|+= .-|+-+-...+-=.++ +++|--||.|+||++==.+.+.+ T Consensus 78 ~l~RL~~VdraILRl---------~~yEl~~~~~D~P~~VA~~InEAielAK~ys~~~s~kFiNG 133 (140) T TIGR01951 78 TLERLSKVDRAILRL---------AAYELLYLKKDVPVKVAVVINEAIELAKKYSDDKSSKFING 133 (140) T ss_pred CHHHHHHHHHHHHHH---------HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHH T ss_conf 723512878999999---------99999863689894054325789999998426876413787 No 218 >KOG3441 consensus Probab=27.68 E-value=13 Score=15.52 Aligned_cols=16 Identities=31% Similarity=0.692 Sum_probs=6.9 Q ss_pred CCCCEEEEEECCCEEE Q ss_conf 8996499994599899 Q gi|254780182|r 848 NDNDQIILVSDKGTLI 863 (910) Q Consensus 848 ~~~DeIlliT~~G~ii 863 (910) .+...+.|+.++|.-+ T Consensus 102 fDsNniVLiddnGnPl 117 (149) T KOG3441 102 FDSNNIVLIDDNGNPL 117 (149) T ss_pred CCCCCEEEECCCCCCC T ss_conf 1787689987899825 No 219 >pfam05110 AF-4 AF-4 proto-oncoprotein. This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homologue Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila. Probab=27.59 E-value=29 Score=12.40 Aligned_cols=35 Identities=26% Similarity=0.428 Sum_probs=22.9 Q ss_pred HHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999988877----899999987406999999861 Q gi|254780182|r 372 RTKYLLNKARDRAH----VLVGLAIAVANLDEVVRIIRF 406 (910) Q Consensus 372 Rt~~~L~ka~~R~H----ILeGL~~Al~nIDeVI~iIR~ 406 (910) ...|-|..|++-.| +.+-|-+|+.-+|.|...|.- T Consensus 909 ~ad~ym~EAKrlKh~Ad~~~dk~gkA~~YldA~lsFiec 947 (1154) T pfam05110 909 SADYYMQEAKKLKHKADALVDKFGKAVNYLDAVLSFIEC 947 (1154) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 267899999886656778888888999999999999986 No 220 >PRK10803 hypothetical protein; Provisional Probab=27.51 E-value=30 Score=12.39 Aligned_cols=41 Identities=20% Similarity=0.134 Sum_probs=16.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH Q ss_conf 99999899999999988753049899999999989999984 Q gi|254780182|r 471 DDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDE 511 (910) Q Consensus 471 ~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~k 511 (910) +.++.|..+|+-.|+++..-|..-.+.-+-+-.+|..+... T Consensus 64 ~~LQ~EV~~LRGqiEe~~~~l~ql~~rQrd~Y~dLD~~~~~ 104 (262) T PRK10803 64 SDNQSDIDSLRGQIQENQYQLNQVVERQKQIYLQIDSLSSG 104 (262) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999999998799999999999999999999999988734 No 221 >TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602 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). During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex. Probab=27.48 E-value=30 Score=12.39 Aligned_cols=136 Identities=21% Similarity=0.368 Sum_probs=69.2 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHH----- Q ss_conf 357899978999999863076840533068988548503432273211016761010133178985478999999----- Q gi|254780182|r 128 ERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGC----- 202 (910) Q Consensus 128 ~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~----- 202 (910) =||-|. ||.+|-..|..+||=-||++. | .=|| ||+= =+--.||++..+-.+ T Consensus 49 RRYvES-LSaYARQFLg~~~KPdVD~IE---G------LSPA------------IsId--QKtt~~NPRSTVGTvTEIyD 104 (956) T TIGR00630 49 RRYVES-LSAYARQFLGVMDKPDVDSIE---G------LSPA------------ISID--QKTTSHNPRSTVGTVTEIYD 104 (956) T ss_pred CHHHHH-HHHHHHHHCCCCCCCCCCCCC---C------CCCC------------EEEC--CCCCCCCCCCCCCCEEEHHH T ss_conf 002100-158999864787477835014---8------8761------------7851--25247888554443210367 Q ss_pred -----HHHHHC---CC-------CCHHHHHHHCCCCCCCCCC-------CCCCH-----HHHHHHHHHCCCEEEEEEEEE Q ss_conf -----887618---77-------6888888634586688744-------34475-----889999870120389999886 Q gi|254780182|r 203 -----VAVIDN---PD-------IDLDALMEIIRGPDFPTGA-------VILGR-----TGIKNAYATGRGSIVIRGVSH 255 (910) Q Consensus 203 -----~~~i~~---p~-------~~~~eL~~~i~GPDFPTGG-------~I~~~-----~~i~~~y~tGrG~i~iR~k~~ 255 (910) -|.+-. |+ .|.+++..-| =+.|-|- ++-++ +-+.++-+.|==+++|-|... T Consensus 105 YLRLLfArvG~p~CP~~~~~i~~qt~~~Ivd~i--~~~~~g~r~~lLAP~Vr~~KG~f~~~l~~l~~~Gf~RV~vDG~~~ 182 (956) T TIGR00630 105 YLRLLFARVGTPYCPECGRPIEEQTVSQIVDQI--LALPEGTRVILLAPIVRGRKGEFRKLLEKLRKQGFARVRVDGEVY 182 (956) T ss_pred HHHHHHHHCCCCCCCCCCCHHHHCCHHHHHHHH--HHCCCCCEEEEECCCCCCCCCCHHHHHHHHHHCCCEEEEECCEEE T ss_conf 789999836887888777326433878999998--624899658996573247775289999999866961899867788 Q ss_pred E-EEC------CCCCE--EEEEECCCC--CCCHHHHHHHHHHHHH Q ss_conf 5-433------67845--999924644--3528999999999987 Q gi|254780182|r 256 I-EKT------SGDRE--QIVVTEIPY--QVNKAAMLEKIAELVR 289 (910) Q Consensus 256 i-e~~------~~~k~--~ivItEiPY--~vnk~~lie~Ia~lv~ 289 (910) - ++. ++.|. .+||--|-- .-++.+|.|.|....+ T Consensus 183 ~L~~~~~l~L~k~~KH~I~~ViDR~~v~~~~~~~RL~eSvEtaL~ 227 (956) T TIGR00630 183 RLEDEPTLKLEKNKKHTIDVVIDRLVVKDNENRSRLAESVETALR 227 (956) T ss_pred EECCCCCCCCCCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHHHH T ss_conf 622132577765555218999824787674332116899999985 No 222 >PRK11622 putative ABC transporter solute-binding protein; Provisional Probab=27.48 E-value=30 Score=12.39 Aligned_cols=38 Identities=29% Similarity=0.432 Sum_probs=16.9 Q ss_pred CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHH Q ss_conf 7898547899999988761877688888863458668874434475889999 Q gi|254780182|r 189 NIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNA 240 (910) Q Consensus 189 nippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~ 240 (910) .-||.++.|+.+-+. .||-- +-|-+-||| | |..=++++ T Consensus 168 ~~pP~s~~eLl~wak---~nPGr-----fTYP~PPdF-~-----GstFlkq~ 205 (401) T PRK11622 168 PQPPQSPAELLEWAK---ANPGR-----FTYPRPPDF-T-----GTAFLKQL 205 (401) T ss_pred CCCCCCHHHHHHHHH---HCCCC-----CCCCCCCCC-C-----CHHHHHHH T ss_conf 999989999999999---78997-----148999987-5-----37999999 No 223 >PRK10423 transcriptional repressor RbsR; Provisional Probab=27.45 E-value=30 Score=12.38 Aligned_cols=176 Identities=15% Similarity=0.119 Sum_probs=77.9 Q ss_pred HHHHCCCCCCCCCCHH-HHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHCCCCC Q ss_conf 8631375400089736-78999999987899999811----3404255664366-8870478999999712201115613 Q gi|254780182|r 37 ILGRAIPDLRDGLKPV-HRRILFGMMQMGVEWNKKYV----KCARISGEVMGKY-HPHGNAAIYDALARMAQDWSLRLLL 110 (910) Q Consensus 37 I~~RAlPd~rDGlKpv-~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~gky-HPHGd~siy~a~v~maq~~~~r~pl 110 (910) -|||+|=+- .+.+|- ..||+=++.+||..||..-+ +..+++|-++... +|. =+.+..++-+.++. ..|-+ T Consensus 14 TVSrvLn~~-~~Vs~~tr~rV~~aa~elgY~pn~~Ar~L~~~~s~~Igviv~~~~~~f-~~~i~~~i~~~~~~--~gy~~ 89 (327) T PRK10423 14 TVSHVINKD-RFVSEAITAKVEAAIKELNYAPSALARSLKLNQTRTIGMLITASTNPF-YSELVRGVERSCFE--RGYSL 89 (327) T ss_pred HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEECCCCCCH-HHHHHHHHHHHHHH--CCCEE T ss_conf 999997895-999999999999999982998688888775378767999973665512-67889999999998--59989 Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC---CEECCCCCCCCCEE---CCCCCCCCHHCCCCCEEE Q ss_conf 147887088776972013578999789999998630768405---33068988548503---432273211016761010 Q gi|254780182|r 111 IEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVD---FRPNYDGSFQEPVV---LCARYPNVLVNGGGGIAV 184 (910) Q Consensus 111 idg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~---~~~n~D~~~~EP~v---lP~~~P~lL~nG~~GIAv 184 (910) +- .+.++|+.-..++.+. |+. .-|| +.+.. .....+.. +| .+|.++++...- - T Consensus 90 ~l-----~~~~~~~~~~~~~l~~--------l~~----~~vdGiIi~~~~-~~~~~~~~~~~~~-~iP~V~~d~~~~--~ 148 (327) T PRK10423 90 VL-----CNTEGDEQRMNRNLET--------LMQ----KRVDGLLLLCTE-THQPSREIMQRYP-SVPTVMMDWAPF--D 148 (327) T ss_pred EE-----EECCCCHHHHHHHHHH--------HHH----CCCCEEEEECCC-CCCHHHHHHHHCC-CCCEEEECCCCC--C T ss_conf 99-----8268987999999999--------995----598769997477-7762899997279-986899637777--7 Q ss_pred HHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCC-CCCCCCCCCHHHHHHHHHH Q ss_conf 1331789854789999998876187768888886345866-8874434475889999870 Q gi|254780182|r 185 GMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPD-FPTGAVILGRTGIKNAYAT 243 (910) Q Consensus 185 GmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPD-FPTGG~I~~~~~i~~~y~t 243 (910) +...-+...|..-.-.|+-++++...-.+ -|+-||. ..+. -.-.+|.+++.+. T Consensus 149 ~~~~~v~~d~~~~~~~a~~~L~~~Ghr~I----~~i~~~~~~~~~--~~R~~gf~~al~~ 202 (327) T PRK10423 149 GDSDLIQDNSLLGGDLATQYLIDKGHTRI----ACITGPLDKTPA--RLRLEGYRAAMKR 202 (327) T ss_pred CCCCEEEECHHHHHHHHHHHHHHCCCCEE----EEECCCCCCCHH--HHHHHHHHHHHHH T ss_conf 88888987789999999999997599749----996688766179--9999999999998 No 224 >KOG2911 consensus Probab=27.41 E-value=30 Score=12.38 Aligned_cols=89 Identities=21% Similarity=0.142 Sum_probs=51.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 99999987406999999861899789878776312697889999974022111222344523699999999987899998 Q gi|254780182|r 387 LVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLT 466 (910) Q Consensus 387 LeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt 466 (910) +|-+..++.|++.|+.-|-+|.+.+. -|.+ |+-.-.--+|||. +-- T Consensus 289 ~er~~~~l~~l~~vl~~Id~s~~nkv---vl~A---------------------------yksGs~alK~il~----~~~ 334 (439) T KOG2911 289 LERKVSSLNNLETVLSQIDNSQTNKV---VLQA---------------------------YKSGSEALKAILA----QGG 334 (439) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHH---HHHH---------------------------HHHHHHHHHHHHH----CCC T ss_conf 99999999999999998876211089---9999---------------------------9976999999985----268 Q ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHHCCHHHH-----HHHHHHHHHHHH Q ss_conf 887-9999998999999999887530498999-----999999899999 Q gi|254780182|r 467 GLG-RDDIRNELNSLGIEIKECLDILSSRSRL-----LGIIKQELLSVK 509 (910) Q Consensus 467 ~LE-~~kl~~E~~eL~~~I~~l~~IL~s~~~l-----~~iI~~EL~eik 509 (910) +-| .+.+-+|..+...+-++.+++|++.-.- ..-|-+||.++. T Consensus 335 s~ekVed~Ldev~et~d~~~EV~~~la~~~~~~~d~~de~lEkEL~~L~ 383 (439) T KOG2911 335 STEKVEDVLDEVNETLDRQEEVEDALASYNVNNIDFEDEDLEKELEDLE 383 (439) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH T ss_conf 7045999999999988659999999845898887624699999999997 No 225 >PRK02304 adenine phosphoribosyltransferase; Provisional Probab=27.19 E-value=24 Score=13.22 Aligned_cols=11 Identities=36% Similarity=0.573 Sum_probs=4.8 Q ss_pred CCCEEEEEEEE Q ss_conf 99869998973 Q gi|254780182|r 731 KGDQVISMAIV 741 (910) Q Consensus 731 ~~D~Vv~~~vi 741 (910) .|-+|+++.++ T Consensus 139 ~ga~v~~~~~l 149 (174) T PRK02304 139 LGAEVVGAAFV 149 (174) T ss_pred CCCEEEEEEEE T ss_conf 79989999999 No 226 >KOG0533 consensus Probab=27.17 E-value=30 Score=12.34 Aligned_cols=25 Identities=32% Similarity=0.486 Sum_probs=13.5 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHH Q ss_conf 5999924644352899999999998 Q gi|254780182|r 264 EQIVVTEIPYQVNKAAMLEKIAELV 288 (910) Q Consensus 264 ~~ivItEiPY~vnk~~lie~Ia~lv 288 (910) ..+.|..+||+|.-+.|-|-.++.+ T Consensus 84 ~~v~v~NL~~~V~~~Dl~eLF~~~~ 108 (243) T KOG0533 84 TKVNVSNLPYGVIDADLKELFAEFG 108 (243) T ss_pred CEEEEECCCCCCCHHHHHHHHHHHC T ss_conf 2024415886733588999998731 No 227 >TIGR01037 pyrD_sub1_fam dihydroorotate dehydrogenase family protein; InterPro: IPR005720 Dihydroorotate dehydrogenase (1.3.3.1 from EC) (DHOdehase) catalyzes the fourth step in the de novo biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. DHOdehase is a ubiquitous FAD flavoprotein. In bacteria (gene pyrD), DHOdease is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1, subfamily 2), it is a cytosolic protein while in other eukaryotes it is found in the mitochondria . This describes dihydroorotate dehydrogenases subfamily 1 that includes a number of uncharacterised proteins and a domain of dihydropyrimidine dehydrogenase.; GO: 0004158 dihydroorotate oxidase activity, 0006207 'de novo' pyrimidine base biosynthetic process, 0005737 cytoplasm. Probab=27.15 E-value=30 Score=12.34 Aligned_cols=85 Identities=16% Similarity=0.386 Sum_probs=49.1 Q ss_pred CCCCCCCCCCC-CCHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCC-CHHHH----HHHHHHHHHCCCCC Q ss_conf 58668874434-47588999987012038999988654336784599992464435-28999----99999998716650 Q gi|254780182|r 221 RGPDFPTGAVI-LGRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQV-NKAAM----LEKIAELVREKRIV 294 (910) Q Consensus 221 ~GPDFPTGG~I-~~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~v-nk~~l----ie~Ia~lv~~~ki~ 294 (910) |=|=|+--|+. ...+-++=+++.|=|-|+..+----+...+. +=-|-|.||+. |-=-| +|+- ++ T Consensus 11 kNP~~lASG~~G~~~~~l~~~~~~gaGAVvTKs~g~~pr~Gy~--nPtiVE~~~G~lNAiGL~NPG~e~f--------l~ 80 (308) T TIGR01037 11 KNPVILASGVMGSGVEALRRIDRSGAGAVVTKSIGLEPRPGYR--NPTIVEVPCGLLNAIGLQNPGVEAF--------LE 80 (308) T ss_pred CCCCEEECCCCCCCHHHHHHHHCCCCCEEEECCEECCCCCCCC--CCEEEECCCCEEEECCCCCHHHHHH--------HH T ss_conf 0661022110366288999875058863786213315888544--3807981785575235898217999--------98 Q ss_pred HHHHHHHHCCCCCEEEEEEEC Q ss_conf 144587303746557999947 Q gi|254780182|r 295 DIADLRDESDRQGYRVVIELK 315 (910) Q Consensus 295 gI~dirDeSdr~giRivielK 315 (910) .+.+.++|-|+..+||.+-+= T Consensus 81 E~~~~~~e~~t~dvr~I~svy 101 (308) T TIGR01037 81 ELKDVREEVPTHDVRLIASVY 101 (308) T ss_pred HHHHHHHCCCCCCEEEEEEEC T ss_conf 632566438987528999831 No 228 >pfam09517 RE_Eco29kI Eco29kI restriction endonuclease. This family includes the Eco29kI (recognizes and cleaves CCGC^GG ) restriction endonuclease. Probab=27.14 E-value=24 Score=13.19 Aligned_cols=20 Identities=30% Similarity=0.707 Sum_probs=9.2 Q ss_pred HHHHHHHCCC-HHCCCCCCCCCCC Q ss_conf 9999971220-1115613147887 Q gi|254780182|r 94 YDALARMAQD-WSLRLLLIEGQGN 116 (910) Q Consensus 94 y~a~v~maq~-~~~r~plidg~Gn 116 (910) ..+|.+|-|+ |+ -+|||-|| T Consensus 102 Ea~LI~~~~P~WN---~~idGFGN 122 (170) T pfam09517 102 EAALIKLFKPLWN---TVVDGFGN 122 (170) T ss_pred HHHHHHHHHHHHH---HHCCCCCC T ss_conf 9999998527776---30454557 No 229 >cd04621 CBS_pair_8 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera Probab=27.02 E-value=30 Score=12.32 Aligned_cols=26 Identities=12% Similarity=0.376 Sum_probs=10.3 Q ss_pred HHHHHHHHHHCCCHHCCCCCCCCCCC Q ss_conf 78999999712201115613147887 Q gi|254780182|r 91 AAIYDALARMAQDWSLRLLLIEGQGN 116 (910) Q Consensus 91 ~siy~a~v~maq~~~~r~plidg~Gn 116 (910) +++.+|+-.|.+.--.+.|.+|..|. T Consensus 10 ~tl~ea~~~m~~~~i~~lpVvd~~g~ 35 (135) T cd04621 10 HSLLHVVDEMEKNGVGRVIVVDDNGK 35 (135) T ss_pred CCHHHHHHHHHHCCCCEEEEECCCCE T ss_conf 97999999998749977999959993 No 230 >TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; InterPro: IPR012684 This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species, this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (IPR012686 from INTERPRO). In other species such as Pasteurella multocida, these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity. Probab=26.92 E-value=30 Score=12.31 Aligned_cols=16 Identities=13% Similarity=0.017 Sum_probs=7.7 Q ss_pred CCEEEEEECCCCEEEE Q ss_conf 7739999548939998 Q gi|254780182|r 586 HTSVLFFSSLGFVYKE 601 (910) Q Consensus 586 ~d~LLfFTs~Gkvy~l 601 (910) -.||.=|++-|++|.+ T Consensus 35 vTWL~P~~pPG~ifal 50 (249) T TIGR02303 35 VTWLPPVEPPGTIFAL 50 (249) T ss_pred CEECCCCCCCCCEEEE T ss_conf 1226868888605662 No 231 >cd04635 CBS_pair_22 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener Probab=26.89 E-value=26 Score=12.83 Aligned_cols=28 Identities=18% Similarity=0.153 Sum_probs=10.4 Q ss_pred CHHHHHHHHHHHCCCHHCCCCCCCCCCC Q ss_conf 0478999999712201115613147887 Q gi|254780182|r 89 GNAAIYDALARMAQDWSLRLLLIEGQGN 116 (910) Q Consensus 89 Gd~siy~a~v~maq~~~~r~plidg~Gn 116 (910) -|.++.+|+-.|.+.--.+.|.+|.+|+ T Consensus 82 ~~~~l~~a~~~m~~~~i~~lpVvd~~g~ 109 (122) T cd04635 82 PDDSIATAVELMLEHDIGRLPVVNEKDQ 109 (122) T ss_pred CCCCHHHHHHHHHHHCCCEEEEECCCCE T ss_conf 9693999999889809988989937998 No 232 >KOG0005 consensus Probab=26.87 E-value=23 Score=13.36 Aligned_cols=20 Identities=25% Similarity=0.642 Sum_probs=16.0 Q ss_pred CCCCCHHHHHHHHHHHHCCC Q ss_conf 00897367899999998789 Q gi|254780182|r 46 RDGLKPVHRRILFGMMQMGV 65 (910) Q Consensus 46 rDGlKpv~Rrily~m~~~~~ 65 (910) ..|.-|+|.|++|+-.+++- T Consensus 33 keGIPp~qqrli~~gkqm~D 52 (70) T KOG0005 33 KEGIPPQQQRLIYAGKQMND 52 (70) T ss_pred HCCCCCHHHHHHHCCCCCCC T ss_conf 21899166632102300255 No 233 >PRK08227 aldolase; Validated Probab=26.70 E-value=30 Score=12.28 Aligned_cols=23 Identities=26% Similarity=0.254 Sum_probs=14.4 Q ss_pred CCHHHHHHHHCCCCCEEEEEEEC Q ss_conf 50144587303746557999947 Q gi|254780182|r 293 IVDIADLRDESDRQGYRVVIELK 315 (910) Q Consensus 293 i~gI~dirDeSdr~giRivielK 315 (910) |+.+..|.+|.++-||-++...- T Consensus 153 l~~lg~v~~e~~~~GmPlla~~~ 175 (291) T PRK08227 153 IKNIIQLVDAGLRYGMPTMAVTA 175 (291) T ss_pred HHHHHHHHHHHHHCCCCEEEEEC T ss_conf 99999999999982998799834 No 234 >pfam11853 DUF3373 Protein of unknown function (DUF3373). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length. Probab=26.55 E-value=31 Score=12.26 Aligned_cols=20 Identities=20% Similarity=0.346 Sum_probs=12.6 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 79999998999999999887 Q gi|254780182|r 469 GRDDIRNELNSLGIEIKECL 488 (910) Q Consensus 469 E~~kl~~E~~eL~~~I~~l~ 488 (910) ++++|++|+++|+++.++++ T Consensus 32 kI~~L~~ql~eLk~~~~~~~ 51 (485) T pfam11853 32 KIEALKKELAELKAQLKDLN 51 (485) T ss_pred HHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999877 No 235 >TIGR01194 cyc_pep_trnsptr cyclic peptide transporter; InterPro: IPR005898 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). Bacteria have elaborate pathways for the production of toxins and secondary metabolites. Many such compounds, including syringomycin and pyoverdine are synthesized on non-ribosomal templates consisting of a multienzyme complex. On several occasions the proteins of the complex and transporter protein are present on the same operon. Often times these compounds cross the biological membrane by specific transporters. This model describes a family of cyclic peptide transporters in bacteria. Syringomycin is an amphipathic, cyclic lipodepsipeptide when inserted into host causes formation of channels, permeable to a variety of cations. On the other hand, pyoverdine is a cyclic octa-peptidyl dihydroxyquinoline, which is efficient in sequestering iron for uptake.; GO: 0005524 ATP binding, 0015197 peptide transporter activity, 0015833 peptide transport, 0016021 integral to membrane. Probab=26.52 E-value=31 Score=12.25 Aligned_cols=41 Identities=22% Similarity=0.298 Sum_probs=22.1 Q ss_pred CCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCCCCEEEEE Q ss_conf 374655799994798877899999997610110000002455 Q gi|254780182|r 303 SDRQGYRVVIELKRGASADVILNQLYRYTSLQSLFSVNMVAL 344 (910) Q Consensus 303 Sdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf~~N~~aL 344 (910) =||-|..=||.+= -.|.+.+=..+|-.|++-....+-+-|| T Consensus 104 ~~R~~~~~~~~~L-T~DI~~~~~~~l~~~~~~~~~~~~l~~~ 144 (555) T TIGR01194 104 VDRRRAHRLLTLL-TSDIDTLSDFLLIFTTLLVELAVFLFGL 144 (555) T ss_pred HHCCCCCCEEEHH-HCCHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 3105775310002-0454478889987889999999999999 No 236 >PRK05748 replicative DNA helicase; Provisional Probab=26.45 E-value=31 Score=12.24 Aligned_cols=22 Identities=27% Similarity=0.448 Sum_probs=15.4 Q ss_pred HHHHHHHHHHHHHHHHHHCCCC Q ss_conf 8999999999899999840568 Q gi|254780182|r 494 RSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 494 ~~~l~~iI~~EL~eik~kygd~ 515 (910) +......|-..|+.+.+.++-| T Consensus 336 r~~ev~~isr~lK~lAkel~ip 357 (448) T PRK05748 336 RQQEVSEISRSLKALAKELKVP 357 (448) T ss_pred HHHHHHHHHHHHHHHHHHHCCC T ss_conf 9999999999999999996998 No 237 >KOG0216 consensus Probab=26.40 E-value=31 Score=12.24 Aligned_cols=113 Identities=18% Similarity=0.170 Sum_probs=58.7 Q ss_pred CCCCCCCCCCC-----CHHHHHHHHHHCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHH----HHHHHHHHCCC Q ss_conf 86688744344-----7588999987012038999988654336784599992464435289999----99999987166 Q gi|254780182|r 222 GPDFPTGAVIL-----GRTGIKNAYATGRGSIVIRGVSHIEKTSGDREQIVVTEIPYQVNKAAML----EKIAELVREKR 292 (910) Q Consensus 222 GPDFPTGG~I~-----~~~~i~~~y~tGrG~i~iR~k~~ie~~~~~k~~ivItEiPY~vnk~~li----e~Ia~lv~~~k 292 (910) -|-.|++..+. ...+.++.-.|=+|+.++|=.|++-....+......-++|-++- ++++ -.=.+||.-|. T Consensus 65 kP~l~~~~~ss~~r~lyPaEcRqR~~TY~Gkl~v~v~wsVNg~~~~~e~~dlG~vPIMlr-SklChL~g~sp~eLV~hkE 143 (1111) T KOG0216 65 KPMLSDKVHSSDTRKLYPAECRQRGLTYKGKLVVRVSWSVNGGHVVIEKRDLGHVPIMLR-SKLCHLNGASPKELVKHKE 143 (1111) T ss_pred CCCCCCCCCCCCCCCCCCHHHHHCCCEECCEEEEEEEEEECCEEEEEEEEECCCCCEEEE-CCCCCCCCCCHHHHHHCCC T ss_conf 887786641101220055667645660300499999999888553235543476656876-1535668989589863567 Q ss_pred ----------CCHHHHHHHHCCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCCCCCEEEE Q ss_conf ----------501445873037465579999479887789999999761011000000245 Q gi|254780182|r 293 ----------IVDIADLRDESDRQGYRVVIELKRGASADVILNQLYRYTSLQSLFSVNMVA 343 (910) Q Consensus 293 ----------i~gI~dirDeSdr~giRivielKr~~~~~~vln~Lyk~T~Lq~sf~~N~~a 343 (910) +.||..+ +|.+|-.|||.-...+-+..-..++.-+.|++-|-| T Consensus 144 e~~EmGGYFIvNGIEKv--------IRmLIm~RRNHPiAiIR~Sfk~RG~~yS~yGVsmRc 196 (1111) T KOG0216 144 ESSEMGGYFIVNGIEKV--------IRMLIMPRRNHPIAIIRPSFKDRGSSYSDYGVSMRC 196 (1111) T ss_pred CHHHCCCEEEECCHHHH--------HHHHEECCCCCCEEEECHHHHHCCCCCCCCCEEEEE T ss_conf 65441858998174773--------632010357896578424255357772102369988 No 238 >COG4746 Uncharacterized protein conserved in archaea [Function unknown] Probab=26.35 E-value=31 Score=12.23 Aligned_cols=28 Identities=29% Similarity=0.616 Sum_probs=17.2 Q ss_pred HHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCC Q ss_conf 88886345866887443447588999987012 Q gi|254780182|r 214 DALMEIIRGPDFPTGAVILGRTGIKNAYATGR 245 (910) Q Consensus 214 ~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGr 245 (910) ++|..+.+|-||| |.+..++..|.-.|- T Consensus 10 ~qiv~~~k~a~fP----Inn~~eL~~ALP~G~ 37 (80) T COG4746 10 EQIVEALKGADFP----INNPEELVAALPSGP 37 (80) T ss_pred HHHHHHHCCCCCC----CCCHHHHHHHCCCCC T ss_conf 9999997247877----799899997666899 No 239 >PRK00202 nusB transcription antitermination protein NusB; Reviewed Probab=26.26 E-value=31 Score=12.22 Aligned_cols=28 Identities=11% Similarity=0.279 Sum_probs=21.2 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCEEECC Q ss_conf 9999999989999984056883310013 Q gi|254780182|r 496 RLLGIIKQELLSVKDELDTPRRTRIVEG 523 (910) Q Consensus 496 ~l~~iI~~EL~eik~kygd~RRT~I~~~ 523 (910) .=..++++|--++.++|+++.-..++.. T Consensus 96 ~p~~v~InE~v~lak~~~~~~~~~fVNg 123 (132) T PRK00202 96 VPYKVVINEAIELAKKFGDEDSHKFVNG 123 (132) T ss_pred CCHHHHHHHHHHHHHHHCCCCCCHHHHH T ss_conf 7547799999999999778972133699 No 240 >KOG0977 consensus Probab=26.22 E-value=31 Score=12.21 Aligned_cols=46 Identities=20% Similarity=0.238 Sum_probs=21.9 Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 9998999999999887530498999999999899999840568833 Q gi|254780182|r 473 IRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRT 518 (910) Q Consensus 473 l~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT 518 (910) .++|...+...|..|..=|++-+.....+-+.+..++..-.+++|. T Consensus 294 ~rEEl~~~R~~i~~Lr~klselE~~n~~L~~~I~dL~~ql~e~~r~ 339 (546) T KOG0977 294 AREELRRIRSRISGLRAKLSELESRNSALEKRIEDLEYQLDEDQRS 339 (546) T ss_pred HHHHHHHHHHCCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 7899999971021011001130125735898988988654312123 No 241 >PRK06835 DNA replication protein DnaC; Validated Probab=26.08 E-value=31 Score=12.22 Aligned_cols=20 Identities=15% Similarity=0.235 Sum_probs=11.1 Q ss_pred CHHHHHHHHHHHHHHHHHHH Q ss_conf 09999987678777998863 Q gi|254780182|r 20 SITDEMQNSYLTYAINVILG 39 (910) Q Consensus 20 ~~~~~m~~syl~Ya~svI~~ 39 (910) +|.+++...=+.+|...+.+ T Consensus 40 eid~ei~~~~~~~a~~~l~~ 59 (330) T PRK06835 40 EIDREIAKLGIKLSQLILKG 59 (330) T ss_pred HHHHHHHHHHHHHHHHHHCC T ss_conf 99999999999999998659 No 242 >PRK02753 DNA-directed RNA polymerase subunit omega; Provisional Probab=25.83 E-value=31 Score=12.16 Aligned_cols=14 Identities=21% Similarity=0.468 Sum_probs=4.7 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99999999998887 Q gi|254780182|r 371 RRTKYLLNKARDRA 384 (910) Q Consensus 371 rRt~~~L~ka~~R~ 384 (910) +|++..++.+..|- T Consensus 13 ~raE~Li~aasNRY 26 (74) T PRK02753 13 KRAESLIRASSNRY 26 (74) T ss_pred HHHHHHHHHHCCCE T ss_conf 99999998504544 No 243 >KOG1446 consensus Probab=25.78 E-value=31 Score=12.15 Aligned_cols=72 Identities=17% Similarity=0.047 Sum_probs=39.4 Q ss_pred HHHCCCCCCCEEEEEECCCCEEEEEHHHCCCCCCCCCCEEEEECC-CCCCCCCEEEEEECCCCCEEEEEECCCEEEEEEC Q ss_conf 111012568679999759934530178848667577414887606-7777686899997289964999945998999990 Q gi|254780182|r 789 RCQELKLKEQFILTVSEKGFGKRTSSYDFRISNRSGKGIRATDVS-KINEIGALVAVFPVNDNDQIILVSDKGTLIRVPV 867 (910) Q Consensus 789 ~~~~~~~~~~~IL~vTe~G~GKRt~~~eyr~q~RGgkGv~~ik~~-~~n~~g~lv~~~~V~~~DeIlliT~~G~iiR~~v 867 (910) ...+.++++.+||+-|.+|+-... +.|+-+ .--.++ +.+...-=..+.-..+..-||.-+..|.+.--++ T Consensus 191 ~~l~FS~dGK~iLlsT~~s~~~~l--DAf~G~-------~~~tfs~~~~~~~~~~~a~ftPds~Fvl~gs~dg~i~vw~~ 261 (311) T KOG1446 191 TDLEFSPDGKSILLSTNASFIYLL--DAFDGT-------VKSTFSGYPNAGNLPLSATFTPDSKFVLSGSDDGTIHVWNL 261 (311) T ss_pred EEEEECCCCCEEEEEECCCCEEEE--ECCCCC-------EEEEEEECCCCCCCCEEEEECCCCCEEEEECCCCCEEEEEC T ss_conf 443875998789998089728999--714870-------74557624678886411798789748998658980899976 Q ss_pred CC Q ss_conf 10 Q gi|254780182|r 868 NE 869 (910) Q Consensus 868 ~~ 869 (910) +. T Consensus 262 ~t 263 (311) T KOG1446 262 ET 263 (311) T ss_pred CC T ss_conf 78 No 244 >pfam05636 DUF795 Protein of unknown function (DUF795). This family consists of several bacterial proteins of unknown function. Probab=25.74 E-value=31 Score=12.14 Aligned_cols=122 Identities=17% Similarity=0.342 Sum_probs=57.9 Q ss_pred HHHHHHCCCCCCCHHHHH--HHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCE Q ss_conf 255664366887047899--999971220111561314788708877697201357899978999999863076840533 Q gi|254780182|r 77 ISGEVMGKYHPHGNAAIY--DALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYTECRLQKAAHFLLDDLGKDTVDFR 154 (910) Q Consensus 77 ivg~v~gkyHPHGd~siy--~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYte~rl~~~~~~~l~~i~~~tv~~~ 154 (910) +||= +--|.|.-..-.| ...-... .-.+..+-.-|||=-. |.||=...|+-|+++ +..+ ||.| T Consensus 3 ~~GI-IaEYNPFHnGH~Yhi~~ar~~~---~~d~iIavMSGnFvQR-GEPAi~dKw~Ra~~A-----L~~G-----aDLV 67 (389) T pfam05636 3 ATGI-IVEYNPFHNGHLYHLNEAKKLT---KADVKIAVMSGNFVQR-GEPAIIDKWERAKMA-----LSSG-----ADLV 67 (389) T ss_pred EEEE-EEEECCCCCHHHHHHHHHHHHC---CCCEEEEEECCCCCCC-CCCHHCCHHHHHHHH-----HHCC-----CCEE T ss_conf 3689-9610797401899999999864---9985999944885218-862007888999999-----9849-----9989 Q ss_pred ECCCCCCCCCEECCCCCC-------------CCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHC- Q ss_conf 068988548503432273-------------211016761010133178985478999999887618776888888634- Q gi|254780182|r 155 PNYDGSFQEPVVLCARYP-------------NVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEII- 220 (910) Q Consensus 155 ~n~D~~~~EP~vlP~~~P-------------~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i- 220 (910) = =||..+- .|=--|.+-+.-|+-|. |+..+.++.-.+.++|+---+.|-+++ T Consensus 68 i----------ELP~~ya~qsAe~FA~gaV~lL~~lgvd~l~FGsE~~----d~~~l~~~a~~l~~~~~~~~~~lk~~l~ 133 (389) T pfam05636 68 I----------ELPVTYSTQSADIFAEGAVSILDSLGIDTLAFGSEEG----DIEDLKKIAKIYLEKEAEMESSLKELLK 133 (389) T ss_pred E----------ECCHHHHHCCHHHHHHHHHHHHHHCCCCEEEECCCCC----CHHHHHHHHHHHHHCHHHHHHHHHHHHH T ss_conf 9----------8865988615999999999999986999899658889----8999999999998681889999999987 Q ss_pred CCCCCCC Q ss_conf 5866887 Q gi|254780182|r 221 RGPDFPT 227 (910) Q Consensus 221 ~GPDFPT 227 (910) +|=-||. T Consensus 134 ~G~Syp~ 140 (389) T pfam05636 134 KGLSYPR 140 (389) T ss_pred CCCCHHH T ss_conf 7999999 No 245 >TIGR03531 selenium_SpcS O-phosphoseryl-tRNA(Sec) selenium transferase. In the archaea and eukaryotes, the conversion of the mischarged serine to selenocysteine (Sec) on its tRNA is accomplished in two steps. This enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase, acts second, after a phosphophorylation step catalyzed by a homolog of the bacterial SelA protein. Probab=25.72 E-value=32 Score=12.14 Aligned_cols=98 Identities=19% Similarity=0.277 Sum_probs=56.4 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHH---HHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHH Q ss_conf 99876787779988631375400089736789999---999878999998113404255664366887047899999971 Q gi|254780182|r 24 EMQNSYLTYAINVILGRAIPDLRDGLKPVHRRILF---GMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARM 100 (910) Q Consensus 24 ~m~~syl~Ya~svI~~RAlPd~rDGlKpv~Rrily---~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~m 100 (910) +..++....--...-.|.+|+ +|+--.+=-.|. |+++.++.++ . || .| --++-||-.||+- T Consensus 12 ~a~~~~~~~i~~LL~qrklPe--~Gw~d~~Ie~lL~~Ls~mDsNNf~~-----~---vg--vG----EREgRv~s~LV~r 75 (444) T TIGR03531 12 LVLNAHEKLIERLLEQRKIPE--EGWDDETIELFLSELSVMDTNNFPN-----N---VG--VG----EREGRVFSKLVER 75 (444) T ss_pred HHHHHHHHHHHHHHHCCCCCC--CCCCHHHHHHHHHHHHHHCCCCCCC-----C---CC--CC----CCHHHHHHHHHHH T ss_conf 999999999999997487986--7899899999999997413268844-----4---77--55----2057787799997 Q ss_pred CCCHHCCCCCCCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 22011156131478870887-7697201357899978999999863 Q gi|254780182|r 101 AQDWSLRLLLIEGQGNFGSV-DGDPPAAERYTECRLQKAAHFLLDD 145 (910) Q Consensus 101 aq~~~~r~plidg~GnfGs~-dgd~~AA~RYte~rl~~~~~~~l~~ 145 (910) - .|-+-.|=|-=|.+ +--|-||---.=++|+ ..|+.| T Consensus 76 r-----hy~f~HGIGRSGdl~~~QPKAaGSSll~kLT---n~l~ld 113 (444) T TIGR03531 76 R-----HYGFCHGIGRSGDLVAPQPKAAGSSLLYKLT---NKLVKD 113 (444) T ss_pred H-----HCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH---HHHHHH T ss_conf 6-----0376667787555465687762328999999---999999 No 246 >pfam10985 DUF2805 Protein of unknown function (DUF2805). This is a bacterial family of proteins with unknown function. Probab=25.69 E-value=32 Score=12.14 Aligned_cols=38 Identities=16% Similarity=0.193 Sum_probs=24.3 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH Q ss_conf 6999999861899789878776312697889999974022111222344523699999999987899 Q gi|254780182|r 397 LDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLA 463 (910) Q Consensus 397 IDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~ 463 (910) ||+||++-=.-..+=||.... |+|+|.|+..|.--.|. T Consensus 1 i~riIeMAweDrt~FeaI~~~-----------------------------~gl~E~eVi~lMR~~Lk 38 (73) T pfam10985 1 ISRIIEMAWEDRTPFEAIERQ-----------------------------FGLSEKEVIKLMRRELK 38 (73) T ss_pred CHHHHHHHHCCCCCHHHHHHH-----------------------------HCCCHHHHHHHHHHHCC T ss_conf 939999998269989999999-----------------------------89599999999996537 No 247 >KOG4437 consensus Probab=25.67 E-value=32 Score=12.13 Aligned_cols=15 Identities=13% Similarity=0.250 Sum_probs=6.4 Q ss_pred CHHHHHHHHHHHCCH Q ss_conf 778999999976101 Q gi|254780182|r 319 SADVILNQLYRYTSL 333 (910) Q Consensus 319 ~~~~vln~Lyk~T~L 333 (910) +++.-.|..|+.-.+ T Consensus 149 ~~~SkFN~F~ef~ki 163 (482) T KOG4437 149 DPRSKFNLFREFRKL 163 (482) T ss_pred CCHHHHHHHHHHHHH T ss_conf 841022789999999 No 248 >TIGR01363 strep_his_triad streptococcal histidine triad protein; InterPro: IPR006270 The sequences represented in this group are identified by a domain which consists of the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Additional copies of the repeats are found in more poorly conserved regions. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice . . Probab=25.67 E-value=32 Score=12.13 Aligned_cols=163 Identities=20% Similarity=0.295 Sum_probs=78.9 Q ss_pred CCCCCCCCCCCCEEEEEECCCEEC-----------CCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEEC Q ss_conf 453010145678189990797052-----------331000002334565211000146410101133237773999954 Q gi|254780182|r 526 DMEDEDCIVREDMVVTVSHLGYVK-----------RVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSS 594 (910) Q Consensus 526 ~i~~EdlI~~E~vvV~lS~~GyIK-----------r~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs 594 (910) +++.++=|.-|.+||=+|.+|||- ++|-+.-=+.--==+ -=--+||+.|.|..+.-+ .++-= T Consensus 61 ~vS~~EGI~AEQIViKITDQGYVTSHGDHYHyYNGKVPYDAIISEELLM~-DPNY~lK~~DivNEi~~G------YVIKV 133 (376) T TIGR01363 61 EVSKREGINAEQIVIKITDQGYVTSHGDHYHYYNGKVPYDAIISEELLMK-DPNYRLKDSDIVNEIKGG------YVIKV 133 (376) T ss_pred HHHHHHCCCCCEEEEEEECCCEECCCCCEEEEECCCCCCHHHHHHHHHCC-CCCCCCCCCCCEEEECCC------EEEEE T ss_conf 67676288712378997057603136860143278556313221366437-887344643200220386------68988 Q ss_pred CCCEEE----------EEC-----CCCCCCCCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEE Q ss_conf 893999----------820-----00432244456554124545365562002566301256668717999947991898 Q gi|254780182|r 595 LGFVYK----------EKV-----WRLPIGSPQARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRR 659 (910) Q Consensus 595 ~Gkvy~----------l~v-----~~IP~~sr~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKk 659 (910) .|+.|. ++. -+..+.+...++.-+.++..|...+ +.|+- . ...+..| .|.+|+| T Consensus 134 ~G~YYVYLK~aa~~~NiRTK~~I~~Q~~~~~~~~~~~Glaqvahl~~~~-~~AV~-~----A~~QGRY---TTDDGYI-- 202 (376) T TIGR01363 134 NGKYYVYLKDAAHADNIRTKEEIARQKQERSKEAKEKGLAQVAHLSKRE-DAAVA-E----ARRQGRY---TTDDGYI-- 202 (376) T ss_pred CCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEHHHHCHHH-HHHHH-H----HHHCCCC---CCCCCCE-- T ss_conf 5818896172122101301789999987433433225401011203246-78999-9----9847881---0457622-- Q ss_pred ECHHHHHHCCCCCEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCC----CCCCCCCCEE Q ss_conf 42368620477722786615898578889618982699993698599975876235----4786655357 Q gi|254780182|r 660 NKLSDFIQINRSGKIAMKLDSRDEILSVETCTQENDILLTTKLGQCVRFPISAIRV----FAGRNSVGVR 725 (910) Q Consensus 660 t~l~ef~~~r~~G~~aikLkegD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~----~~GR~a~GVk 725 (910) ++.++... +-| .|-++..++|.=-+-++- .+.+|+-+ ..||..+|.+ T Consensus 203 F~a~DII~-----------D~G----DAY~VPHG~HYHYIPK~~----LSaSELAAA~Ay~s~k~~~~~~ 253 (376) T TIGR01363 203 FNASDIIE-----------DTG----DAYIVPHGDHYHYIPKNE----LSASELAAAEAYWSGKQGRGAR 253 (376) T ss_pred ECCHHHHH-----------CCC----CEEECCCCCCCCCCCCCC----CCHHHHHHHHHHHHHCCCCCCC T ss_conf 27122442-----------178----724604787433367545----7876899999987410466677 No 249 >COG1363 FrvX Cellulase M and related proteins [Carbohydrate transport and metabolism] Probab=25.55 E-value=32 Score=12.12 Aligned_cols=101 Identities=18% Similarity=0.184 Sum_probs=60.2 Q ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCC------CCCCCCCCCCCE-EEEEECCCEE Q ss_conf 899999999988753049899999999989999984056883310013434------530101456781-8999079705 Q gi|254780182|r 476 ELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLLD------MEDEDCIVREDM-VVTVSHLGYV 548 (910) Q Consensus 476 E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~~------i~~EdlI~~E~v-vV~lS~~GyI 548 (910) +..++.+++-++..+=..+.+...++++||+.....+-..|.=-|+..... +-.-.-..+=-. |=-+..+|++ T Consensus 3 ~~~~~LkeL~~~~gpsG~E~eVr~~~~~el~~~~~ev~~D~lGnlia~~~g~~g~~~imi~AHmDEiG~mV~~I~~~G~L 82 (355) T COG1363 3 ELLELLKELLEAPGPSGYEEEVRDVLKEELEPLGDEVEVDRLGNLIAKKGGKNGPPKVMIAAHMDEIGFMVKEIEDDGFL 82 (355) T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCEEECCCCCEEEEECCCCCCCCEEEEEECCEEEEEEEEECCCCEE T ss_conf 79999999973989998479999999999987087448867873899916889983278986045110378898789659 Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEE Q ss_conf 233100000233456521100014641010113323777399995489399 Q gi|254780182|r 549 KRVPLSVYRAQRRGGKGRSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVY 599 (910) Q Consensus 549 Kr~~~~~yr~Q~RggkG~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy 599 (910) +-.++--+..|- ---+++-++|.+|+-| T Consensus 83 r~~~iGG~~~~~-----------------------~~gq~v~i~t~~g~~i 110 (355) T COG1363 83 RFVPIGGWDPQV-----------------------LEGQRVTIHTDKGKKI 110 (355) T ss_pred EEEECCCCCHHH-----------------------CCCCEEEEEECCCCEE T ss_conf 999717967434-----------------------0576799994898687 No 250 >cd04801 CBS_pair_M50_like This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the metalloprotease peptidase M50. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Probab=25.29 E-value=31 Score=12.21 Aligned_cols=23 Identities=13% Similarity=0.193 Sum_probs=7.9 Q ss_pred HHHHHHHHHCCCHHCCCCCCCCC Q ss_conf 89999997122011156131478 Q gi|254780182|r 92 AIYDALARMAQDWSLRLLLIEGQ 114 (910) Q Consensus 92 siy~a~v~maq~~~~r~plidg~ 114 (910) ++.+|+-+|.+.---+.|.+|.+ T Consensus 77 ~l~~al~~m~~~~~~~LpVVd~~ 99 (114) T cd04801 77 SLAEVLKLLEEQGLDELAVVEDS 99 (114) T ss_pred CHHHHHHHHHHCCCCEEEEECCC T ss_conf 79999999997698678899479 No 251 >pfam11552 DUF3230 Protein of unknown function (DUF3230). This family of proteins with unknown function appears to be restricted to Streptococcus. Probab=25.29 E-value=32 Score=12.08 Aligned_cols=21 Identities=38% Similarity=0.711 Sum_probs=15.1 Q ss_pred EHHHHCCCCCCHHHHHHHHHHHHHC Q ss_conf 0133178985478999999887618 Q gi|254780182|r 184 VGMATNIPTHNLGEVVDGCVAVIDN 208 (910) Q Consensus 184 vGmaTnippHNl~Ev~~a~~~~i~~ 208 (910) -|.+|++|+ |+||++-..||+ T Consensus 13 fGvvtSLP~----E~IDs~W~IID~ 33 (105) T pfam11552 13 FGVVTSLPD----EVIDSFWYIIDH 33 (105) T ss_pred EEEECCCCH----HHHHHHHHHHHH T ss_conf 305113988----999999999876 No 252 >PRK08026 flagellin; Validated Probab=25.27 E-value=32 Score=12.08 Aligned_cols=62 Identities=23% Similarity=0.308 Sum_probs=39.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 89999998740699999986189978987877631269788999997402211122234452369999999998789999 Q gi|254780182|r 386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL 465 (910) Q Consensus 386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL 465 (910) -+.||-.|..|.-.-|.+|..+ --.|-+ . ..||. |+|-| T Consensus 57 Qi~GL~qA~rNa~DgiSliQTA------EGAL~e--------------------------------v--~~iLq-RmREL 95 (566) T PRK08026 57 NIKGLTQAARNANDGISVAQTT------EGALSE--------------------------------I--NNNLQ-RIREL 95 (566) T ss_pred HHHHHHHHHHHHHHHHHHHHHH------HHHHHH--------------------------------H--HHHHH-HHHHH T ss_conf 9988999998698899999999------999999--------------------------------9--99999-99999 Q ss_pred ---------HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---------88879999998999999999887 Q gi|254780182|r 466 ---------TGLGRDDIRNELNSLGIEIKECL 488 (910) Q Consensus 466 ---------t~LE~~kl~~E~~eL~~~I~~l~ 488 (910) +.-+|..|++|.++|.++|.++- T Consensus 96 AVQAANgTns~~dR~aiQ~Ei~qL~~EIdRIa 127 (566) T PRK08026 96 TVQAATGTNSDSDLDSIQDEIKSRLDEIDRVS 127 (566) T ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99860478999999999999999999999888 No 253 >pfam05718 Pox_int_trans Poxvirus intermediate transcription factor. This family consists of several highly related Poxvirus sequences which are thought to be intermediate transcription factors. Probab=25.25 E-value=32 Score=12.08 Aligned_cols=35 Identities=23% Similarity=0.253 Sum_probs=24.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999878999988879999998999999999887530 Q gi|254780182|r 451 EVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDIL 491 (910) Q Consensus 451 e~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL 491 (910) -.||++||.|-..|=..|+...++. ..+.+|++|| T Consensus 348 V~~a~~il~~M~~rS~~L~~~die~------~sVd~LK~lL 382 (383) T pfam05718 348 VELAESILKMMAERSAILNALDIET------ASVDELKELL 382 (383) T ss_pred HHHHHHHHHHHHHHHHHHHHCCCEE------ECHHHHHHHH T ss_conf 9999999999999987766436300------0499998653 No 254 >CHL00144 odpB pyruvate dehydrogenase E1 component beta subunit; Validated Probab=25.22 E-value=26 Score=12.83 Aligned_cols=44 Identities=18% Similarity=0.071 Sum_probs=24.3 Q ss_pred EEEEC--CCCCHHHHHHHHHHHCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHH Q ss_conf 99947--988778999999976101100000024554166300029999999999 Q gi|254780182|r 311 VIELK--RGASADVILNQLYRYTSLQSLFSVNMVALNGYKPERFTLIGILKAFVA 363 (910) Q Consensus 311 vielK--r~~~~~~vln~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~ 363 (910) ||.++ +-.|.+.|++. -++|. -+..++.-+...|+-.-+.+.+. T Consensus 232 VIDlrtl~PlD~e~I~~s-v~kT~--------rlv~veE~~~~gG~Gsei~a~i~ 277 (326) T CHL00144 232 VIDLISLKPLDMTTISTS-IKKTH--------KVLIVEECMKTGGIGAELLALIN 277 (326) T ss_pred EEECCCCCCCCHHHHHHH-HHHCC--------CEEEEECCCCCCCHHHHHHHHHH T ss_conf 986045799999999999-98549--------89999769988978999999999 No 255 >pfam10480 ICAP-1_inte_bdg Beta-1 integrin binding protein. ICAP-1 is a serine/threonine-rich protein that binds to the cytoplasmic domains of beta-1 integrins in a highly specific manner, binding to a NPXY sequence motif on the beta-1 integrin. The cytoplasmic domains of integrins are essential for cell adhesion, and the fact that phosphorylation of ICAP-1 by interaction with the cell-matrix implies an important role of ICAP-1 during integrin-dependent cell adhesion. Overexpression of ICAP-1 strongly reduces the integrin-mediated cell spreading on extracellular matrix and inhibits both Cdc42 and Rac1. In addition, ICAP-1 induces release of Cdc42 from cellular membranes and prevents the dissociation of GDP from this GTPase. An additional function of ICAP-1 is to promote differentiation of osteoprogenitors by supporting their condensation through modulating the integrin high affinity state, Probab=25.16 E-value=32 Score=12.06 Aligned_cols=39 Identities=26% Similarity=0.275 Sum_probs=23.2 Q ss_pred CCHHHHCCCCCCCEEEEEECCCCEEEEEHHHCCCCCCCCC Q ss_conf 2001110125686799997599345301788486675774 Q gi|254780182|r 786 SEERCQELKLKEQFILTVSEKGFGKRTSSYDFRISNRSGK 825 (910) Q Consensus 786 ~~e~~~~~~~~~~~IL~vTe~G~GKRt~~~eyr~q~RGgk 825 (910) .++.++....+++++|-|+.+|+ |.+..++|.+..|-+. T Consensus 97 qDgKlpFv~~deefil~vSkyGi-KV~~~Dq~dVL~RHpL 135 (200) T pfam10480 97 QDGKLPFVPGDEEFILGVSKYGI-KVASLDQCDVLHRHAL 135 (200) T ss_pred HCCCCCCCCCCCCEEEEECCCCE-EECCCHHHHHHHHCCH T ss_conf 65887755788404787501354-7514335657774334 No 256 >PRK00464 nrdR transcriptional regulator NrdR; Validated Probab=25.16 E-value=32 Score=12.06 Aligned_cols=25 Identities=28% Similarity=0.210 Sum_probs=20.5 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2369999999998789999888799 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRD 471 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~ 471 (910) .+-.|+-+..|-+|=|..|..|+.. T Consensus 98 ~~~~EI~S~~IGe~Vm~~Lk~lD~V 122 (149) T PRK00464 98 SGEREVPSKEIGELVMEELKKLDEV 122 (149) T ss_pred CCCCCCCHHHHHHHHHHHHHHCCCE T ss_conf 3888755999999999988620931 No 257 >TIGR01219 Pmev_kin_ERG8 phosphomevalonate kinase; InterPro: IPR016005 Phosphomevalonate kinase (2.7.4.2 from EC) catalyzes the phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate, an essential step in isoprenoid biosynthesis via the mevalonate pathway. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the higher eukaryotic form and the ERG8 type . This model represents plant and fungal forms of the ERG8 type of phosphomevalonate kinase.. Probab=25.09 E-value=32 Score=12.05 Aligned_cols=141 Identities=19% Similarity=0.142 Sum_probs=69.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCE--EECCCC Q ss_conf 999987899998887999999899999999988-------75304989999999998999998405688331--001343 Q gi|254780182|r 455 RAILELRLARLTGLGRDDIRNELNSLGIEIKEC-------LDILSSRSRLLGIIKQELLSVKDELDTPRRTR--IVEGLL 525 (910) Q Consensus 455 ~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l-------~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~--I~~~~~ 525 (910) +.=|+-.|..|.+ |.+.+.+...+|-+- +-.|.+..-+++.|++|+.|+++.+..=||.- |. .+. T Consensus 346 N~~l~~~L~~L~~-----L~~~H~D~~~~~~~sCsvL~~~~c~l~~~~Pineaiike~~E~r~a~~~IRr~~r~it-~ea 419 (499) T TIGR01219 346 NLRLEDKLSDLDK-----LAKDHDDVYLRVIKSCSVLESEDCVLSAEEPINEAIIKELLEVREAVLSIRRLLRKIT-KEA 419 (499) T ss_pred HHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHH T ss_conf 6788731347777-----6520013678887652012123503315774578999999999999999999999844-550 Q ss_pred CCCCCCCCCCCCEEEEEECCCEECC-CCCCCCCCCCCCCCC-CCCCCCCCCCHHEEEEEECCCCEEEEEECCCCEEEEEC Q ss_conf 4530101456781899907970523-310000023345652-11000146410101133237773999954893999820 Q gi|254780182|r 526 DMEDEDCIVREDMVVTVSHLGYVKR-VPLSVYRAQRRGGKG-RSGVVMRDEDFVTDLFIVSTHTSVLFFSSLGFVYKEKV 603 (910) Q Consensus 526 ~i~~EdlI~~E~vvV~lS~~GyIKr-~~~~~yr~Q~RggkG-~~~~~~ke~D~v~~~~~~~t~d~LLfFTs~Gkvy~l~v 603 (910) .+++|-...-.=.==+.+-.|=|-. +|- =||-. ...+...+-|....+..+.. .-+|.++.| T Consensus 420 ~vdIEP~~QT~lLD~~~~l~GVl~~gvPG-------AGGfDAif~it~~~~d~~~~~~~~w~---------~~~V~~ldV 483 (499) T TIGR01219 420 KVDIEPEKQTSLLDDIESLEGVLLVGVPG-------AGGFDAIFVITLNDVDLREKVIKAWK---------SDKVLALDV 483 (499) T ss_pred CCCCCCHHHHHHHCCCCCCCCEEEEECCC-------CCHHHHHHHHHHCCHHHHHHHHHHHH---------HCCCEEEEE T ss_conf 78888734433430200258636885289-------85478999887402126889987564---------268347760 Q ss_pred CCCCCCCCCCCCCC Q ss_conf 00432244456554 Q gi|254780182|r 604 WRLPIGSPQARGKA 617 (910) Q Consensus 604 ~~IP~~sr~skG~p 617 (910) .+=|.|-+..+|.| T Consensus 484 ~~a~~Gv~~E~GDP 497 (499) T TIGR01219 484 SEADDGVALEKGDP 497 (499) T ss_pred CCCCCCCEECCCCC T ss_conf 45877403168988 No 258 >PRK09492 treR trehalose repressor; Provisional Probab=25.06 E-value=32 Score=12.05 Aligned_cols=71 Identities=10% Similarity=0.135 Sum_probs=44.9 Q ss_pred HHHHHHHHHHCCCCCCCCCCHH-HHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHCCCCCCCHHHHHHHHHHHCCC Q ss_conf 7779988631375400089736-78999999987899999811----3404255664366887047899999971220 Q gi|254780182|r 31 TYAINVILGRAIPDLRDGLKPV-HRRILFGMMQMGVEWNKKYV----KCARISGEVMGKYHPHGNAAIYDALARMAQD 103 (910) Q Consensus 31 ~Ya~svI~~RAlPd~rDGlKpv-~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~gkyHPHGd~siy~a~v~maq~ 103 (910) ..|.+ -|||||=.- .+..|- .+||+=++.+||..|+..-+ +..+++|-|+...+-+.-+.+..++...++. T Consensus 15 GVS~a-TVSrvLn~~-~~vs~eTr~rV~~~a~elgY~Pn~~Ar~L~~~~t~~Ig~i~~~~~~~~~~~~~~~i~~~~~~ 90 (315) T PRK09492 15 GVGKS-TVSRVLNNE-PKVSPRTRERVEAVINQHGFSPSKSARAMRGQSDKVVGIIVSRLDSPSENLAVQTMLPAFYQ 90 (315) T ss_pred CCCHH-HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHH T ss_conf 97999-999997898-99999999999999999699807788975048886466622677883678999999999997 No 259 >PRK10401 DNA-binding transcriptional regulator GalS; Provisional Probab=25.04 E-value=32 Score=12.04 Aligned_cols=52 Identities=12% Similarity=0.183 Sum_probs=33.6 Q ss_pred HHHHHHHHHCCCCCCCCCCHH-HHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHCCC Q ss_conf 779988631375400089736-78999999987899999811----3404255664366 Q gi|254780182|r 32 YAINVILGRAIPDLRDGLKPV-HRRILFGMMQMGVEWNKKYV----KCARISGEVMGKY 85 (910) Q Consensus 32 Ya~svI~~RAlPd~rDGlKpv-~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~gky 85 (910) .|.+ -|||||=+- .+..|- .+||+=++.+||..||..-+ +..+++|-++..+ T Consensus 13 VS~a-TVSrvLn~~-~~Vs~eTr~rV~~aa~eLgY~Pn~~Ar~L~~~~s~~Igvv~~~~ 69 (346) T PRK10401 13 VSVA-TVSRVLNNS-ALVSPDTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMDV 69 (346) T ss_pred CCHH-HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCEEEEEECCC T ss_conf 7999-999997794-99999999999999999499848888865007788799994788 No 260 >cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. Probab=24.96 E-value=32 Score=12.03 Aligned_cols=47 Identities=13% Similarity=0.172 Sum_probs=29.0 Q ss_pred CCCCCHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 52369999999998789------999888799999989999999998875304 Q gi|254780182|r 446 TMYLSEVQTRAILELRL------ARLTGLGRDDIRNELNSLGIEIKECLDILS 492 (910) Q Consensus 446 ~f~lSe~QA~AILdMrL------~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~ 492 (910) .++||-.+...||+++= ......=..-+.+...++.++|++|+..+. T Consensus 53 ~lgfsL~eIk~ll~l~~~~~~~~~~~~~~v~~~l~~k~~eie~ki~eLq~~~~ 105 (107) T cd04777 53 GLGFSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKKDELEKEIEDLKKAIQ 105 (107) T ss_pred HCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 88998999999996243557674888999999999999999999999999996 No 261 >cd04803 CBS_pair_15 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener Probab=24.94 E-value=31 Score=12.16 Aligned_cols=32 Identities=19% Similarity=0.304 Sum_probs=19.9 Q ss_pred CHHHHHHHHHHHCCCHHCCCCCCCCCCCC-CCC Q ss_conf 04789999997122011156131478870-887 Q gi|254780182|r 89 GNAAIYDALARMAQDWSLRLLLIEGQGNF-GSV 120 (910) Q Consensus 89 Gd~siy~a~v~maq~~~~r~plidg~Gnf-Gs~ 120 (910) -|++++||+-.|.+.--.+.|.+|..|.+ |-+ T Consensus 8 ~~~tl~~a~~~m~~~~i~~lpVvd~~~~lvGii 40 (122) T cd04803 8 EDDSLADAEELMREHRIRHLPVVNEDGKLVGLL 40 (122) T ss_pred CCCCHHHHHHHHHHCCCCEEEEECCCCCEEEEE T ss_conf 969999999999974997899990898688896 No 262 >TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit; InterPro: IPR005737 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 II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils . This entry represents subunit B (parE) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome. Probab=24.69 E-value=22 Score=13.61 Aligned_cols=61 Identities=30% Similarity=0.443 Sum_probs=39.7 Q ss_pred CCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHC--------CCHHCC------CC Q ss_conf 4000897367899999998789999981134042556643668870478999999712--------201115------61 Q gi|254780182|r 44 DLRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMA--------QDWSLR------LL 109 (910) Q Consensus 44 d~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~ma--------q~~~~r------~p 109 (910) .|-+||-||+|| =+||-.|-..++|+ ..+-||+ |-|+=||+.--| ||-|.. =. T Consensus 10 ~VL~gLEPVr~R--PGMY~GGtD~~~~~----HL~~EV~-------DN~~DEA~AGfA~~i~v~lH~D~Si~v~D~GRG~ 76 (647) T TIGR01055 10 EVLDGLEPVRKR--PGMYTGGTDTTRPN----HLVQEVI-------DNSVDEALAGFASKIEVILHQDQSIEVIDNGRGM 76 (647) T ss_pred HHHCCCCCCCCC--CCCEECCCCCCCCH----HHHHHHH-------HHHHHHHHCCCCEEEEEEECCCCEEEEEECCCCC T ss_conf 220168773428--87201786565301----3455544-------3335555406530788998289617998888303 Q ss_pred CCCCCCCC Q ss_conf 31478870 Q gi|254780182|r 110 LIEGQGNF 117 (910) Q Consensus 110 lidg~Gnf 117 (910) =||-|-.| T Consensus 77 PvD~HP~~ 84 (647) T TIGR01055 77 PVDIHPKE 84 (647) T ss_pred CCCCCCCC T ss_conf 44278888 No 263 >pfam05889 SLA_LP_auto_ag Soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). This family consists of several eukaryotic and archaeal proteins which are related to the human soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis. The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway. Some archaeal members are annotated as being pyridoxal phosphate-dependent enzymes. Probab=24.67 E-value=33 Score=11.99 Aligned_cols=32 Identities=13% Similarity=0.393 Sum_probs=27.4 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 99998875304989999999998999998405 Q gi|254780182|r 482 IEIKECLDILSSRSRLLGIIKQELLSVKDELD 513 (910) Q Consensus 482 ~~I~~l~~IL~s~~~l~~iI~~EL~eik~kyg 513 (910) -=.+.|+++|..+++....+.++|.++.++|| T Consensus 268 lG~~gy~~Ll~eRke~~~~l~e~L~~~a~~~g 299 (389) T pfam05889 268 LGCKAYLALMKEQKEMFPLLRELLKDLAEEVG 299 (389) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 74888999999999999999999999999829 No 264 >pfam05904 DUF863 Plant protein of unknown function (DUF863). This family consists of a number of hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. Probab=24.60 E-value=27 Score=12.67 Aligned_cols=12 Identities=17% Similarity=0.473 Sum_probs=4.3 Q ss_pred CCHHHHHHHHHH Q ss_conf 699999999987 Q gi|254780182|r 449 LSEVQTRAILEL 460 (910) Q Consensus 449 lSe~QA~AILdM 460 (910) |-.+-|+||..| T Consensus 522 l~~iAAEaIVaI 533 (730) T pfam05904 522 LIKIAAESIVAI 533 (730) T ss_pred HHHHHHHHHHHH T ss_conf 999999999998 No 265 >KOG0240 consensus Probab=24.57 E-value=33 Score=11.98 Aligned_cols=56 Identities=25% Similarity=0.284 Sum_probs=31.3 Q ss_pred HHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH Q ss_conf 9999878999988------8799999989999999998875304989999999998999998 Q gi|254780182|r 455 RAILELRLARLTG------LGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKD 510 (910) Q Consensus 455 ~AILdMrL~rLt~------LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~ 510 (910) ..++.=++.+|-. .+.++..+...+|..+..+=+.++++..++...+..|+.++.+ T Consensus 416 ~~~~~e~~~~L~qqlD~kd~~~n~~sqL~~~lk~q~~~qee~~s~~~~~~e~~q~e~~~~Q~ 477 (607) T KOG0240 416 EDILTERIESLYQQLDQKDDQINKQSQLMEKLKEQLLDQEELLSSTRRLYEDIQQELSEIQE 477 (607) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999998877778888999999999999987776655568879999999999999 No 266 >TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies. Probab=24.48 E-value=33 Score=11.96 Aligned_cols=39 Identities=18% Similarity=0.258 Sum_probs=26.1 Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH Q ss_conf 06999999861899789878776312697889999974022111222344523699999999987899 Q gi|254780182|r 396 NLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLA 463 (910) Q Consensus 396 nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~ 463 (910) .|++||++-=....+=||.... |+|||.|+..|.--.|. T Consensus 1 di~riIemAweDrt~Fe~I~~~-----------------------------~gl~E~evi~lMr~~Lk 39 (72) T TIGR03643 1 DIDRIIEMAWEDRTPFEAIEQQ-----------------------------FGLSEKEVIKLMRQNLK 39 (72) T ss_pred CHHHHHHHHHCCCCCHHHHHHH-----------------------------HCCCHHHHHHHHHHHCC T ss_conf 9889999998379989999999-----------------------------89499999999996338 No 267 >TIGR02817 adh_fam_1 zinc-binding alcohol dehydrogenase family protein; InterPro: IPR014182 Members of this entry form a distinct subset of the larger family of oxidoreductases that includes zinc-binding alcohol dehydrogenases and NADPH:quinone reductases. Some current members of this entry carry designations as putative alginate lyase, however none have been characterised as such.. Probab=24.43 E-value=20 Score=13.95 Aligned_cols=12 Identities=42% Similarity=0.800 Sum_probs=6.6 Q ss_pred CCCCCCCCCCCCC Q ss_conf 7887088776972 Q gi|254780182|r 113 GQGNFGSVDGDPP 125 (910) Q Consensus 113 g~GnfGs~dgd~~ 125 (910) +||-||=|| ||+ T Consensus 241 PQGrlaLID-DP~ 252 (338) T TIGR02817 241 PQGRLALID-DPA 252 (338) T ss_pred CCCCEECCC-CCC T ss_conf 787400002-870 No 268 >TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA; InterPro: IPR010222 This entry represents HrpA, one of two related but uncharacterised DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterised, is about 800 amino acids long. Related characterised eukaryotic proteins are RNA helicases associated with pre-mRNA processing.; GO: 0005524 ATP binding, 0008026 ATP-dependent helicase activity. Probab=24.24 E-value=33 Score=11.93 Aligned_cols=27 Identities=15% Similarity=0.091 Sum_probs=13.1 Q ss_pred HHHHHHH---HHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999---99999999999999888778 Q gi|254780182|r 360 AFVAFRE---EVVVRRTKYLLNKARDRAHV 386 (910) Q Consensus 360 ~fi~hR~---evi~rRt~~~L~ka~~R~HI 386 (910) .+.++.- |-++....|+--+++.|.|+ T Consensus 1139 l~~e~~g~lPe~VR~~a~F~al~~~vR~~l 1168 (1320) T TIGR01967 1139 LIFENGGVLPEQVRTEAEFAALLEKVRAEL 1168 (1320) T ss_pred HHHHCCCCCCCCCCCHHHHHHHHHHHCHHH T ss_conf 987268869877889899999997407324 No 269 >PRK09413 insertion sequence 2 OrfA protein; Reviewed Probab=24.23 E-value=33 Score=11.93 Aligned_cols=38 Identities=18% Similarity=0.196 Sum_probs=29.7 Q ss_pred HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH Q ss_conf 99899999999988753049899999999989999984 Q gi|254780182|r 474 RNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDE 511 (910) Q Consensus 474 ~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~k 511 (910) ..|.+.++++|.+|+.+|+....-.+++++-+.--+.| T Consensus 70 ase~~~~~k~ireLqR~LGkktle~EILkeAve~~r~k 107 (121) T PRK09413 70 ASELAAAMKQIKELQRLLGKKTMENELLKEAVEYGRAK 107 (121) T ss_pred HHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH T ss_conf 79999999889999999665489999999999987665 No 270 >cd04612 CBS_pair_SpoIVFB_EriC_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase an Probab=24.21 E-value=30 Score=12.36 Aligned_cols=10 Identities=60% Similarity=0.790 Sum_probs=3.2 Q ss_pred HHHHHHHHHC Q ss_conf 8999999712 Q gi|254780182|r 92 AIYDALARMA 101 (910) Q Consensus 92 siy~a~v~ma 101 (910) ++++++-.|. T Consensus 74 ~l~~a~~~m~ 83 (111) T cd04612 74 TLRDALKRMA 83 (111) T ss_pred CHHHHHHHHH T ss_conf 7999999999 No 271 >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=24.18 E-value=33 Score=11.92 Aligned_cols=29 Identities=28% Similarity=0.420 Sum_probs=23.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCHHH Q ss_conf 87999999899999999988753049899 Q gi|254780182|r 468 LGRDDIRNELNSLGIEIKECLDILSSRSR 496 (910) Q Consensus 468 LE~~kl~~E~~eL~~~I~~l~~IL~s~~~ 496 (910) |+.+++-++.+++.++|+.+.++|.|+++ T Consensus 199 l~~~~~l~~~~e~Ke~~~~~~~~l~DP~~ 227 (330) T TIGR00345 199 LEDDEALEKLEELKEQIEAAREVLSDPER 227 (330) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 87789999899999999999997249985 No 272 >cd04619 CBS_pair_6 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera Probab=24.13 E-value=33 Score=11.91 Aligned_cols=25 Identities=12% Similarity=0.106 Sum_probs=10.0 Q ss_pred HHHHHHHHHHHCCCHHCCCCCCCCC Q ss_conf 4789999997122011156131478 Q gi|254780182|r 90 NAAIYDALARMAQDWSLRLLLIEGQ 114 (910) Q Consensus 90 d~siy~a~v~maq~~~~r~plidg~ 114 (910) |.++++|+-.|.+.---+.|.+|.. T Consensus 75 ~~~i~~a~~~M~~~~i~~lPVVD~~ 99 (114) T cd04619 75 GDLLHDVWQVMKQRGLKNIPVVDEN 99 (114) T ss_pred CCCHHHHHHHHHHCCCCEEEEEECC T ss_conf 8909999998887698588999079 No 273 >TIGR02742 TrbC_Ftype type-F conjugative transfer system pilin assembly protein TrbC; InterPro: IPR014113 This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA , . The N-terminal portion of these proteins is heterogeneous. . Probab=24.12 E-value=28 Score=12.63 Aligned_cols=14 Identities=50% Similarity=0.736 Sum_probs=5.3 Q ss_pred CHHHHHHHHHHHCC Q ss_conf 04789999997122 Q gi|254780182|r 89 GNAAIYDALARMAQ 102 (910) Q Consensus 89 Gd~siy~a~v~maq 102 (910) ||-|||.||=.|+| T Consensus 107 Gn~Sl~~ALe~~~~ 120 (139) T TIGR02742 107 GNVSLKGALEKMAQ 120 (139) T ss_pred EEEEHHHHHHHHHH T ss_conf 30015778999874 No 274 >PRK04885 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional Probab=24.11 E-value=33 Score=11.91 Aligned_cols=46 Identities=15% Similarity=0.180 Sum_probs=27.5 Q ss_pred HHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCCCCEEEEEECCCEECC Q ss_conf 3049899999999989999984056883310013434530101456781899907970523 Q gi|254780182|r 490 ILSSRSRLLGIIKQELLSVKDELDTPRRTRIVEGLLDMEDEDCIVREDMVVTVSHLGYVKR 550 (910) Q Consensus 490 IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~~~~~~i~~EdlI~~E~vvV~lS~~GyIKr 550 (910) |.+++...-..+++.+++.-+++|-.. +. ++-+++|++=-+|.+=+ T Consensus 5 iv~~~~~~s~~~~~~~~~~l~~~~~~~-----------~~----~~~Dlvi~iGGDGT~L~ 50 (265) T PRK04885 5 IISNGDEKSKRVASKLKKYLKDFGFIL-----------DE----KNPDIVISVGGDGTLLS 50 (265) T ss_pred EEECCCHHHHHHHHHHHHHHHHCCCCC-----------CC----CCCCEEEEECCCHHHHH T ss_conf 996969899999999999998769855-----------87----78999999887399999 No 275 >TIGR01334 modD modD protein; InterPro: IPR006242 The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). Their function is unknown. ; GO: 0016763 transferase activity transferring pentosyl groups. Probab=24.09 E-value=33 Score=11.91 Aligned_cols=75 Identities=20% Similarity=0.202 Sum_probs=54.6 Q ss_pred ECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHH Q ss_conf 41663000299999999999999999999999999988877--------8999999874069999998618997898787 Q gi|254780182|r 345 NGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAH--------VLVGLAIAVANLDEVVRIIRFSPNPETARRE 416 (910) Q Consensus 345 ~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~H--------ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~ 416 (910) -+|.=...||-|-|=-|-+||.=.- -.+|..++=.|+. .|| .+++.+.+.+.|.+.|.= . T Consensus 146 aGG~iHR~glsETlLvFanHr~fl~---D~~Dw~gai~rLkq~APE~KItvE-----adt~~qa~~~l~a~PDil----Q 213 (277) T TIGR01334 146 AGGLIHRAGLSETLLVFANHRTFLS---DNEDWSGAITRLKQQAPEKKITVE-----ADTLKQALAVLRADPDIL----Q 213 (277) T ss_pred HCCHHHHHHHHHHHHHHHHHHHHCC---CCCHHHHHHHHHHHHCCCCCEEEE-----ECCHHHHHHHHHCCCCEE----E T ss_conf 1605654115899999998786417---800278999887743787726874-----059899999974489766----3 Q ss_pred HHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 76312697889999974022111222344523699999999987 Q gi|254780182|r 417 LMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILEL 460 (910) Q Consensus 417 L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdM 460 (910) .-+||..|+..|+++ T Consensus 214 -----------------------------LdKFtpqQ~~~~~~~ 228 (277) T TIGR01334 214 -----------------------------LDKFTPQQVKELLEL 228 (277) T ss_pred -----------------------------CCCCCHHHHHHHHHH T ss_conf -----------------------------236888899999999 No 276 >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=24.02 E-value=18 Score=14.35 Aligned_cols=143 Identities=23% Similarity=0.333 Sum_probs=79.8 Q ss_pred HCCCCCCHHHHHHHHHHHHHCC-CCCHHHHH-HHCCCCCCCCCCC---CCCHHHHHHHHHHCCCEEE--EEEEEEEEECC Q ss_conf 1789854789999998876187-76888888-6345866887443---4475889999870120389--99988654336 Q gi|254780182|r 188 TNIPTHNLGEVVDGCVAVIDNP-DIDLDALM-EIIRGPDFPTGAV---ILGRTGIKNAYATGRGSIV--IRGVSHIEKTS 260 (910) Q Consensus 188 TnippHNl~Ev~~a~~~~i~~p-~~~~~eL~-~~i~GPDFPTGG~---I~~~~~i~~~y~tGrG~i~--iR~k~~ie~~~ 260 (910) -|-.|-.-.+.|+-+.++-+.. +..--.++ +-+|==|.|-|.. +.|.=.|..|...|--.|- +-||+ T Consensus 60 ~n~~Ps~~~~~c~e~r~~~~~~Gkt~~~~~i~~pvpvVDLPLGaTEDRVcGtlDIerALt~GvkAFePGLLArA------ 133 (340) T TIGR02030 60 FNSAPSDREELCEEVRILEDSSGKTKKLAVIEKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARA------ 133 (340) T ss_pred CCCCCCCCCCCCHHHHHHHHCCCCCCCCEEEECCCCEEECCCCCCCCCEECHHHHHHHHHCCCCCCCCCCHHHH------ T ss_conf 78888886135767777531268656751551576536479886213134402476775047210366304666------ Q ss_pred CCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHH----CCCCCEEEEEEECCCCCHHHHHHHHHHHCCHHCC Q ss_conf 784599992464435289999999999871665014458730----3746557999947988778999999976101100 Q gi|254780182|r 261 GDREQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDE----SDRQGYRVVIELKRGASADVILNQLYRYTSLQSL 336 (910) Q Consensus 261 ~~k~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDe----Sdr~giRivielKr~~~~~~vln~Lyk~T~Lq~s 336 (910) +|=-+.|-|. +|+| +.-++-+-|+.-- =-|+|+.|= T Consensus 134 -NRG~LYiDEV-------NLLe-------DHlVDvLLDvAasG~NvVEREG~SiR------------------------- 173 (340) T TIGR02030 134 -NRGYLYIDEV-------NLLE-------DHLVDVLLDVAASGVNVVEREGVSIR------------------------- 173 (340) T ss_pred -CCCCEEEEEE-------HHHH-------HHHHHHHHHHCCCCCEEEEECCEEEE------------------------- T ss_conf -1784255210-------0012-------45665665220478305863560230------------------------- Q ss_pred CCCEEEEEE-CCCCCCCCHH-HHHHHH-----------HHHHHHHHHHHHHHHH Q ss_conf 000024554-1663000299-999999-----------9999999999999999 Q gi|254780182|r 337 FSVNMVALN-GYKPERFTLI-GILKAF-----------VAFREEVVVRRTKYLL 377 (910) Q Consensus 337 f~~N~~aL~-~g~P~~l~Lk-~iL~~f-----------i~hR~evi~rRt~~~L 377 (910) -+.=|+ || -|-|.-=.|+ |+|+.| ++.|.+||+||++||- T Consensus 174 HPARFV-LVGSGNPEEGeLRPQLLDRFGlhaeirt~rdve~RVeiv~rR~eyDa 226 (340) T TIGR02030 174 HPARFV-LVGSGNPEEGELRPQLLDRFGLHAEIRTVRDVEERVEIVKRRDEYDA 226 (340) T ss_pred CCCCEE-EECCCCCCCCCCCCHHHHHCCCEEEEECCCCHHHHHHHEEEHHHHCC T ss_conf 376358-71578887666674015244652787226772220122010033177 No 277 >KOG3011 consensus Probab=23.93 E-value=34 Score=11.88 Aligned_cols=37 Identities=32% Similarity=0.497 Sum_probs=27.8 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCC-EECCCCCCCCCEE Q ss_conf 5789997899999986307684053-3068988548503 Q gi|254780182|r 129 RYTECRLQKAAHFLLDDLGKDTVDF-RPNYDGSFQEPVV 166 (910) Q Consensus 129 RYte~rl~~~~~~~l~~i~~~tv~~-~~n~D~~~~EP~v 166 (910) +.-+.-|+-+|..|++|+....|-| .+|| |+..-|.| T Consensus 105 ~~~~~~La~~aG~i~AD~~SGl~HWaaD~~-Gsv~tP~v 142 (293) T KOG3011 105 LWLEPALAAYAGYITADLGSGVYHWAADNY-GSVSTPWV 142 (293) T ss_pred HHHHHHHHHHHHHHHHHHHCCEEEEECCCC-CCCCCCHH T ss_conf 637999999877998865145067521556-76544046 No 278 >COG0241 HisB Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism] Probab=23.73 E-value=21 Score=13.66 Aligned_cols=50 Identities=20% Similarity=0.444 Sum_probs=18.8 Q ss_pred CHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCC Q ss_conf 11016761010133178985478999999887618776888888634586688744 Q gi|254780182|r 174 VLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLDALMEIIRGPDFPTGA 229 (910) Q Consensus 174 lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~eL~~~i~GPDFPTGG 229 (910) +++---+|||.|+-|. +++...-+.....+..-...++ .+.=+|.+|.++ T Consensus 51 VvvTNQsGi~rgyf~~---~~f~~~~~~m~~~l~~~gv~id---~i~~Cph~p~~~ 100 (181) T COG0241 51 VVVTNQSGIGRGYFTE---ADFDKLHNKMLKILASQGVKID---GILYCPHHPEDN 100 (181) T ss_pred EEEECCCCCCCCCCCH---HHHHHHHHHHHHHHHHCCCCCC---EEEECCCCCCCC T ss_conf 9998777755667668---9999899999999997497036---499878898777 No 279 >PRK08006 replicative DNA helicase; Provisional Probab=23.69 E-value=34 Score=11.85 Aligned_cols=12 Identities=33% Similarity=0.537 Sum_probs=5.1 Q ss_pred HHHHHHCCCCCC Q ss_conf 888863458668 Q gi|254780182|r 214 DALMEIIRGPDF 225 (910) Q Consensus 214 ~eL~~~i~GPDF 225 (910) +++..++..-|| T Consensus 49 ~~v~~~L~~edF 60 (471) T PRK08006 49 DDVAERVVADDF 60 (471) T ss_pred HHHHHHCCHHHC T ss_conf 999963698767 No 280 >pfam06530 Phage_antitermQ Phage antitermination protein Q. This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream. Probab=23.62 E-value=34 Score=11.84 Aligned_cols=37 Identities=27% Similarity=0.376 Sum_probs=19.6 Q ss_pred CCEEEHHHHCCCCCC---------HHHHHHHHHHHHHCCCCCHHHH Q ss_conf 610101331789854---------7899999988761877688888 Q gi|254780182|r 180 GGIAVGMATNIPTHN---------LGEVVDGCVAVIDNPDIDLDAL 216 (910) Q Consensus 180 ~GIAvGmaTnippHN---------l~Ev~~a~~~~i~~p~~~~~eL 216 (910) +-||.|+...+|..+ -+-+||+|++.+...+...-+| T Consensus 25 s~iaAgFk~lip~~~ksR~~CsDdDGliId~~va~L~~~~~~~~~l 70 (126) T pfam06530 25 SPIAAGFKSLLPGRVKTRPMCSDDDGMIISQCVDSLMYIDPKLFGL 70 (126) T ss_pred HHHHHHHHCCCCCCCCCCCCEECCCCCHHHHHHHHHHHCCHHHHHH T ss_conf 7899987135898899877330886332999999998739899999 No 281 >COG4800 Predicted transcriptional regulator with an HTH domain [Transcription] Probab=23.58 E-value=34 Score=11.83 Aligned_cols=78 Identities=19% Similarity=0.238 Sum_probs=37.2 Q ss_pred CCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEE--EEEEEEEEECCC------CCEEEEEECCCCCCCHHH Q ss_conf 877688888863458668874434475889999870120389--999886543367------845999924644352899 Q gi|254780182|r 208 NPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIV--IRGVSHIEKTSG------DREQIVVTEIPYQVNKAA 279 (910) Q Consensus 208 ~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~--iR~k~~ie~~~~------~k~~ivItEiPY~vnk~~ 279 (910) ..++....|.++++|-||----++.=-..|+++-+.-.|-+. +-|++-.++.+- || ...|.|-|- ++ T Consensus 38 ~anIP~StLYKil~G~dpr~~tl~~I~ktir~~ek~en~~fiA~IAAR~vL~~i~~~kk~i~gk-~~~ireYpa----~s 112 (170) T COG4800 38 RANIPLSTLYKILKGSDPRYDTLTRIFKTIRSYEKKENIGFIALIAARYVLEEIKFGKKGINGK-SYLIREYPA----SS 112 (170) T ss_pred HCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEHHHHHHHHHHHHCCCCCC-EEEEEECCC----CC T ss_conf 7099899999998179965778999999999887504778466534488998887601033673-368874364----52 Q ss_pred HHHHHHHHHHC Q ss_conf 99999999871 Q gi|254780182|r 280 MLEKIAELVRE 290 (910) Q Consensus 280 lie~Ia~lv~~ 290 (910) |-|-|...|+. T Consensus 113 lEeaIvAaVrA 123 (170) T COG4800 113 LEEAIVAAVRA 123 (170) T ss_pred HHHHHHHHHHH T ss_conf 89999999986 No 282 >PRK06819 flagellin; Validated Probab=23.57 E-value=34 Score=11.83 Aligned_cols=22 Identities=27% Similarity=0.338 Sum_probs=14.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8887999999899999999988 Q gi|254780182|r 466 TGLGRDDIRNELNSLGIEIKEC 487 (910) Q Consensus 466 t~LE~~kl~~E~~eL~~~I~~l 487 (910) +.-||..|..|+++|..+|..+ T Consensus 104 s~~DR~~i~~Ei~ql~~ei~~i 125 (371) T PRK06819 104 SASDLDSIQDEINQRLAEIDRV 125 (371) T ss_pred CHHHHHHHHHHHHHHHHHHHHH T ss_conf 7678999999999999999999 No 283 >PRK07263 consensus Probab=23.53 E-value=34 Score=11.82 Aligned_cols=23 Identities=26% Similarity=0.406 Sum_probs=16.4 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 98999999999899999840568 Q gi|254780182|r 493 SRSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 493 s~~~l~~iI~~EL~eik~kygd~ 515 (910) ++......|-..|+.+.+.++-| T Consensus 334 ~r~~ev~~isr~lK~lAkel~ip 356 (453) T PRK07263 334 NRQQEVSDISRQLKILAKELKVP 356 (453) T ss_pred CHHHHHHHHHHHHHHHHHHHCCC T ss_conf 59999999999999999987997 No 284 >PRK08411 flagellin; Reviewed Probab=23.44 E-value=34 Score=11.81 Aligned_cols=62 Identities=16% Similarity=0.212 Sum_probs=38.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 89999998740699999986189978987877631269788999997402211122234452369999999998789999 Q gi|254780182|r 386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL 465 (910) Q Consensus 386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL 465 (910) -+.||-.|..|.-.-|.+|..++ -.|-+ ...||. |+|.| T Consensus 57 QI~GL~qA~rNanDgISl~QTAE------GAL~E----------------------------------v~~iLq-RmREL 95 (573) T PRK08411 57 QANTLGQAISNGNDALGILQTAD------KAMDE----------------------------------QLKILD-TIKTK 95 (573) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHHHH----------------------------------HHHHHH-HHHHH T ss_conf 98889999986988999999999------99999----------------------------------999999-99999 Q ss_pred ---------HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---------88879999998999999999887 Q gi|254780182|r 466 ---------TGLGRDDIRNELNSLGIEIKECL 488 (910) Q Consensus 466 ---------t~LE~~kl~~E~~eL~~~I~~l~ 488 (910) +.-+|..|++|+++|.++|.++- T Consensus 96 AVQAAN~tns~~DR~alQ~Ei~qL~~EIdRIa 127 (573) T PRK08411 96 ATQAAQDGQSLKTRTMLQADINRLMEELDNIA 127 (573) T ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99961468998999999999999999997661 No 285 >TIGR00501 met_pdase_II methionine aminopeptidase, type II; InterPro: IPR002468 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of metallopeptidases belong to MEROPS peptidase family M24 (clan MG), subfamily M24A. Methionine aminopeptidase (3.4.11.18 from EC) (MAP) is responsible for the removal of the amino-terminal (initiator) methionine from nascent eukaryotic cytosolic and cytoplasmic prokaryotic proteins if the penultimate amino acid is small and uncharged. All MAP studied to date are monomeric proteins that require cobalt ions for activity. Two subfamilies of MAP enzymes are known to exist , . While being evolutionary related, they only share a limited amount of sequence similarity mostly clustered around the residues shown, in the Escherichia coli MAP , to be involved in cobalt-binding. The first family consists of enzymes from prokaryotes as well as eukaryotic MAP-1, while the second group (IPR002467 from INTERPRO) is made up of archaeal MAP and eukaryotic MAP-2 and includes proteins which do not seem to be MAP, but that are clearly evolutionary related such as mouse proliferation-associated protein 1 and fission yeast curved DNA-binding protein. ; GO: 0004239 methionyl aminopeptidase activity, 0006508 proteolysis. Probab=23.42 E-value=16 Score=14.70 Aligned_cols=38 Identities=21% Similarity=0.225 Sum_probs=25.8 Q ss_pred EEECCCCEE-EEEEECCCCCEEEEEECCCEEEEEEHHHC-CCC Q ss_conf 661589857-88896189826999936985999758762-354 Q gi|254780182|r 676 MKLDSRDEI-LSVETCTQENDILLTTKLGQCVRFPISAI-RVF 716 (910) Q Consensus 676 ikLkegD~L-i~v~~~~~~~~Iil~T~~G~~lrF~~~ev-r~~ 716 (910) -+|.+||-+ |-.|-+ +=+-+||..|.+-.|....- ||+ T Consensus 205 ~~leeG~~~AIEpFAt---~G~G~V~~~~~~~iY~~l~~Drpv 244 (327) T TIGR00501 205 TKLEEGDVVAIEPFAT---DGVGLVTDGGEVEIYKFLAEDRPV 244 (327) T ss_pred CEEECCCEEEECCCCC---CCEEEEECCCCCHHHHHHCCCCCC T ss_conf 4510257888436676---874565128861012210568896 No 286 >PHA02094 hypothetical protein Probab=23.17 E-value=35 Score=11.77 Aligned_cols=20 Identities=30% Similarity=0.620 Sum_probs=14.2 Q ss_pred EEEEHHHHHHHHCCCCCCCH Q ss_conf 11340425566436688704 Q gi|254780182|r 71 YVKCARISGEVMGKYHPHGN 90 (910) Q Consensus 71 ~~K~a~ivg~v~gkyHPHGd 90 (910) |---|+-||+.+|..||..- T Consensus 43 ye~~~ksig~m~g~~hptak 62 (81) T PHA02094 43 YEFFAKSVGAMIGELHPTAK 62 (81) T ss_pred HHHHHHHHHHHHCCCCCCCC T ss_conf 99999999999623586301 No 287 >TIGR00444 mazG MazG family protein; InterPro: IPR011551 This group of prokaryotic proteins has no known function. It includes the uncharacterised protein MazG in Escherichia coli.. Probab=23.07 E-value=20 Score=13.84 Aligned_cols=15 Identities=27% Similarity=0.521 Sum_probs=6.7 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 999998999999999 Q gi|254780182|r 471 DDIRNELNSLGIEIK 485 (910) Q Consensus 471 ~kl~~E~~eL~~~I~ 485 (910) +|+.+|++|...++. T Consensus 163 ~Kv~EEl~E~~~e~~ 177 (253) T TIGR00444 163 DKVSEELEEVKSEVS 177 (253) T ss_pred HHHHHHHHHHHHHHH T ss_conf 877888899999985 No 288 >PRK13588 flagellin B; Provisional Probab=23.06 E-value=35 Score=11.75 Aligned_cols=63 Identities=16% Similarity=0.255 Sum_probs=36.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 89999998740699999986189978987877631269788999997402211122234452369999999998789999 Q gi|254780182|r 386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL 465 (910) Q Consensus 386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL 465 (910) -+.||-.|..|.-.=|.+++-++ -.|-+ . ..||. |+|.| T Consensus 57 Qi~gl~qA~rNa~dgiSliQTAE------GAL~E--------------------------------v--~~iLq-RmREL 95 (514) T PRK13588 57 QAANLGQAIRNANDAIGIVQTAD------KAMDE--------------------------------Q--IKILD-TIKTK 95 (514) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHHHH--------------------------------H--HHHHH-HHHHH T ss_conf 99889999986888999999999------99999--------------------------------9--99999-99999 Q ss_pred ---------HHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---------888799999989999999998875 Q gi|254780182|r 466 ---------TGLGRDDIRNELNSLGIEIKECLD 489 (910) Q Consensus 466 ---------t~LE~~kl~~E~~eL~~~I~~l~~ 489 (910) +.-++..|++|+++|..+|.++-. T Consensus 96 AVQAAN~t~s~~dR~alQ~Ei~qL~~EIdrIa~ 128 (514) T PRK13588 96 AVQAAQDGQTLESRRALQSDIQRLLEELDNIAN 128 (514) T ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 998703789888999999999999999987765 No 289 >pfam12226 Astro_capsid_p Turkey astrovirus capsid protein. This family of proteins is found in viruses. Proteins in this family are typically between 241 and 261 amino acids in length. These proteins are capsid proteins from various astrovirus strains. Probab=23.04 E-value=35 Score=11.75 Aligned_cols=17 Identities=24% Similarity=0.405 Sum_probs=8.4 Q ss_pred EEECCCCEEEEEEECCC Q ss_conf 66158985788896189 Q gi|254780182|r 676 MKLDSRDEILSVETCTQ 692 (910) Q Consensus 676 ikLkegD~Li~v~~~~~ 692 (910) |+|.+||-+++.--+++ T Consensus 120 mnL~EgDPViSmGDt~G 136 (230) T pfam12226 120 LNLAEGDPVISMGDTTG 136 (230) T ss_pred HCCCCCCCEEEECCCCC T ss_conf 33336996565136778 No 290 >PRK11462 putative transporter; Provisional Probab=23.02 E-value=35 Score=11.75 Aligned_cols=28 Identities=21% Similarity=0.145 Sum_probs=18.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9998789999888799999989999999 Q gi|254780182|r 456 AILELRLARLTGLGRDDIRNELNSLGIE 483 (910) Q Consensus 456 AILdMrL~rLt~LE~~kl~~E~~eL~~~ 483 (910) +++-||-|+||+-...+|++|+++-+++ T Consensus 421 ~ii~~~~Y~L~~~~~~eI~~eL~~~~~~ 448 (460) T PRK11462 421 AIIAKRYYSLTTHNLKTVMEQLAQGKRR 448 (460) T ss_pred HHHHHHEECCCHHHHHHHHHHHHHHHHH T ss_conf 9999952359899999999999999884 No 291 >cd04631 CBS_pair_18 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener Probab=22.96 E-value=34 Score=11.90 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=14.3 Q ss_pred HHHHHHHHHHHCCCHHCCCCCCCC-CCCC Q ss_conf 478999999712201115613147-8870 Q gi|254780182|r 90 NAAIYDALARMAQDWSLRLLLIEG-QGNF 117 (910) Q Consensus 90 d~siy~a~v~maq~~~~r~plidg-~Gnf 117 (910) |+++++|+-.|.+.--.+.|.+|- +|.+ T Consensus 9 ~~tl~ea~~~m~~~~v~~~PVvd~~~~~l 37 (125) T cd04631 9 TTPIMEAAKIMVRNGFRRLPVVDEGTGKL 37 (125) T ss_pred CCCHHHHHHHHHHCCCCEEEEEECCCCCE T ss_conf 09499999999983998899997999959 No 292 >KOG4777 consensus Probab=22.89 E-value=35 Score=11.73 Aligned_cols=111 Identities=28% Similarity=0.331 Sum_probs=51.0 Q ss_pred CCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCCCCHHHHH--HHHHHHHH--------------H---HHHH Q ss_conf 668870478999999712201115613147887088776972013578--99978999--------------9---9986 Q gi|254780182|r 84 KYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDPPAAERYT--ECRLQKAA--------------H---FLLD 144 (910) Q Consensus 84 kyHPHGd~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~~AA~RYt--e~rl~~~~--------------~---~~l~ 144 (910) .-|||-.-.+-.|--|-|- .||.. -|||---|--|-.|--|| ||.-..|. . .++. T Consensus 25 sdhP~f~ikvLgAS~RSAG---K~ya~---a~~wkqt~~lp~~~~e~~V~ec~~~~F~ecDIvfsgldad~ageiek~f~ 98 (361) T KOG4777 25 SDHPYFSIKVLGASKRSAG---KRYAF---AGNWKQTDLLPESAHEYTVEECTADSFNECDIVFSGLDADIAGEIEKLFA 98 (361) T ss_pred CCCCCCEEEEECCCCCCCC---CCEEE---CCCCHHCCCCCCHHHHHHHHHCCHHHCCCCCEEEECCCCHHHHHHHHHHH T ss_conf 1698513423013331469---81576---04411202465034341375558402366558985278236656547788 Q ss_pred HCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCH Q ss_conf 307684053306898854850343227321101676101013317898547899999988761877688 Q gi|254780182|r 145 DLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDL 213 (910) Q Consensus 145 ~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~ 213 (910) +-.--.|+-.-||--...-|.|.|.-=|-- -.||++|.-|+-|-.- ++|-|++|++ T Consensus 99 eag~iiVsNaknyRre~~VPLvvP~VNpeh----ld~ik~~~~~~k~~~G---------~iI~nsNCST 154 (361) T KOG4777 99 EAGTIIVSNAKNYRREDGVPLVVPEVNPEH----LDGIKVGLDTGKMGKG---------AIIANSNCST 154 (361) T ss_pred HCCEEEEECCHHCCCCCCCCEEECCCCHHH----HHHHEECCCCCCCCCC---------EEEECCCCCE T ss_conf 668699867143025799745733458778----4253022225888995---------2896698870 No 293 >PRK13729 conjugal transfer pilus assembly protein TraB; Provisional Probab=22.72 E-value=35 Score=11.70 Aligned_cols=59 Identities=5% Similarity=0.004 Sum_probs=31.2 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH Q ss_conf 5236999999999878999988879999998999999999887530498999999999899999 Q gi|254780182|r 446 TMYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVK 509 (910) Q Consensus 446 ~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik 509 (910) .-.|++.-+++-|.-+=..+..|| +.+++|.++++.+..=..+.++.++.+..+..++. T Consensus 59 ~~~Ft~k~~qsAlt~qQ~~~~~le-----k~l~~l~~~l~~~~~~~~~~q~~l~~l~~~~~~l~ 117 (474) T PRK13729 59 DTTFDDKVRQHATTEMQVTAAQMQ-----KQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALA 117 (474) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 753436778879999999999999-----99999999999998765628999999999999999 No 294 >PRK04184 DNA topoisomerase VI subunit B; Validated Probab=22.72 E-value=21 Score=13.72 Aligned_cols=36 Identities=25% Similarity=0.272 Sum_probs=20.4 Q ss_pred HHCC-CCCEEEEEEECCCC-C-HHHHHHHHHHHCCHHCCC Q ss_conf 3037-46557999947988-7-789999999761011000 Q gi|254780182|r 301 DESD-RQGYRVVIELKRGA-S-ADVILNQLYRYTSLQSLF 337 (910) Q Consensus 301 DeSd-r~giRivielKr~~-~-~~~vln~Lyk~T~Lq~sf 337 (910) |..+ ..|+||-++++-+. . -+.|..+| ++|.+-+-+ T Consensus 165 ~~~~~~hGt~Ve~~ieg~~~~~r~~v~eYl-r~TaIvnPh 203 (533) T PRK04184 165 DNWKRWHGTRVELELEGNWYRAKQGIYEYL-KRTAIVNPH 203 (533) T ss_pred CCCCCCCCEEEEEEEEEEHHHHHCCHHHHH-HHHHCCCCC T ss_conf 477788843999999764154423699999-765103784 No 295 >pfam04762 IKI3 IKI3 family. Members of this family are components of the elongator multi-subunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. This region contains WD40 like repeats. Probab=22.59 E-value=35 Score=11.68 Aligned_cols=28 Identities=14% Similarity=0.281 Sum_probs=10.7 Q ss_pred CCCEEEEEEECCCCCEEEEEECCCEEEE Q ss_conf 8985788896189826999936985999 Q gi|254780182|r 680 SRDEILSVETCTQENDILLTTKLGQCVR 707 (910) Q Consensus 680 egD~Li~v~~~~~~~~Iil~T~~G~~lr 707 (910) +.+.++.+....+.+.+++-+.+|+.+. T Consensus 526 ~~~~~v~~~~~~~~~~~~~q~~~G~v~~ 553 (918) T pfam04762 526 ELDGIVLILSSNDYKHVFVQTRDGKVFS 553 (918) T ss_pred CCCCEEEEEEECCCCEEEEEECCCEEEE T ss_conf 1686289994089856999957984999 No 296 >TIGR02938 nifL_nitrog nitrogen fixation negative regulator NifL; InterPro: IPR014285 NifL modulates the activity of the nitrogen fixation positive regulator protein NifA, acting as a negative regulator by binding NifA. NifA and NifL are encoded by adjacent genes.. Probab=22.54 E-value=36 Score=11.67 Aligned_cols=10 Identities=30% Similarity=0.146 Sum_probs=4.4 Q ss_pred EEEEECCCCC Q ss_conf 9998200043 Q gi|254780182|r 598 VYKEKVWRLP 607 (910) Q Consensus 598 vy~l~v~~IP 607 (910) |=|.++..|| T Consensus 371 VdW~Pa~~LP 380 (496) T TIGR02938 371 VDWQPAAVLP 380 (496) T ss_pred ECCCCCCCCC T ss_conf 5165610162 No 297 >COG1110 Reverse gyrase [DNA replication, recombination, and repair] Probab=22.52 E-value=36 Score=11.67 Aligned_cols=70 Identities=17% Similarity=0.257 Sum_probs=48.6 Q ss_pred CEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCC-------CC-------CCCHHHHHHHHH Q ss_conf 8113404255664366887047899999971220111561314788708877-------69-------720135789997 Q gi|254780182|r 70 KYVKCARISGEVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFGSVD-------GD-------PPAAERYTECRL 135 (910) Q Consensus 70 ~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~GnfGs~d-------gd-------~~AA~RYte~rl 135 (910) .|+...+....-.| +-|-|-|-..--=+-+.|.|++--|-=-|.--||.+. |. --.-++-|..|| T Consensus 67 e~e~~~~fF~k~~G-~~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~~a~kgkr~yii~PT~~Lv~Q~~~kl 145 (1187) T COG1110 67 EYEEFEEFFKKATG-FRPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLYLAKKGKRVYIIVPTTTLVRQVYERL 145 (1187) T ss_pred HHHHHHHHHHHHHC-CCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHH T ss_conf 99999999998638-98607889999998737844898278876547999999998755874999966789999999999 Q ss_pred HHHHH Q ss_conf 89999 Q gi|254780182|r 136 QKAAH 140 (910) Q Consensus 136 ~~~~~ 140 (910) .++++ T Consensus 146 ~~~~e 150 (1187) T COG1110 146 KKFAE 150 (1187) T ss_pred HHHHH T ss_conf 99886 No 298 >PRK12756 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional Probab=22.50 E-value=36 Score=11.67 Aligned_cols=22 Identities=36% Similarity=0.407 Sum_probs=9.8 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 877697201357899978999999 Q gi|254780182|r 119 SVDGDPPAAERYTECRLQKAAHFL 142 (910) Q Consensus 119 s~dgd~~AA~RYte~rl~~~~~~~ 142 (910) ||+ ||.||+-|-+ ||.++++++ T Consensus 62 SIH-D~~aaleYA~-rL~~l~~~~ 83 (349) T PRK12756 62 SIH-DTDAALDYAT-RLQALREQY 83 (349) T ss_pred CCC-CHHHHHHHHH-HHHHHHHHH T ss_conf 778-9799999999-999999972 No 299 >PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional Probab=22.50 E-value=36 Score=11.67 Aligned_cols=21 Identities=10% Similarity=0.260 Sum_probs=9.4 Q ss_pred CCCCCCCCC--HHHHHHHHHHHH Q ss_conf 754000897--367899999998 Q gi|254780182|r 42 IPDLRDGLK--PVHRRILFGMMQ 62 (910) Q Consensus 42 lPd~rDGlK--pv~Rrily~m~~ 62 (910) |...-.|+. |-|+...-+.++ T Consensus 17 l~~~~~gfe~R~~Q~~Ma~~V~~ 39 (697) T PRK11747 17 LQEQLPGFIPRAGQRQMIAEVAK 39 (697) T ss_pred HHHHCCCCCCCHHHHHHHHHHHH T ss_conf 99868899718789999999999 No 300 >KOG3347 consensus Probab=22.46 E-value=36 Score=11.66 Aligned_cols=37 Identities=35% Similarity=0.457 Sum_probs=16.1 Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHH Q ss_conf 599992464435289999999999871665014458730 Q gi|254780182|r 264 EQIVVTEIPYQVNKAAMLEKIAELVREKRIVDIADLRDE 302 (910) Q Consensus 264 ~~ivItEiPY~vnk~~lie~Ia~lv~~~ki~gI~dirDe 302 (910) ..|+||--| ++.|+.+-++||+...=+-|. |+|+.-| T Consensus 8 PNILvtGTP-G~GKstl~~~lae~~~~~~i~-isd~vkE 44 (176) T KOG3347 8 PNILVTGTP-GTGKSTLAERLAEKTGLEYIE-ISDLVKE 44 (176) T ss_pred CCEEEECCC-CCCCHHHHHHHHHHHCCCEEE-HHHHHHH T ss_conf 887986799-988025999999973985674-5567766 No 301 >TIGR01916 F420_puta_dedox F420-dependent oxidoreductase, putative; InterPro: IPR008225 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.. Probab=22.43 E-value=32 Score=12.13 Aligned_cols=120 Identities=16% Similarity=0.289 Sum_probs=56.3 Q ss_pred CCCEEEE-------ECCCCCCCCC------CCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCCEEEEEECCCCEEEEC Q ss_conf 8939998-------2000432244------45655412454536556200256630125666871799994799189842 Q gi|254780182|r 595 LGFVYKE-------KVWRLPIGSP------QARGKALINILSLNQGERITTIMPFPEDESSWNNLYVVFATKHGNVRRNK 661 (910) Q Consensus 595 ~Gkvy~l-------~v~~IP~~sr------~skG~pi~nll~l~~~E~I~ail~~~~~~~~~~~~~Lvl~Tk~G~VKkt~ 661 (910) -|++..+ .|.+| ..| +.|--.+.+.+ +.+-++|+.. ...||+-=|+.|+|-=.. T Consensus 51 EG~~~~l~ei~Ps~~A~ei--A~RladvtGtGKDp~~~~ai-l~Ea~ev~~~----------~~~F~itetr~G~VcaNA 117 (260) T TIGR01916 51 EGRIISLEEITPSPEAKEI--AARLADVTGTGKDPRFVQAI-LEEAEEVVRV----------GKPFLITETRHGLVCANA 117 (260) T ss_pred CCCCCCCCCCCCCHHHHHH--HHHHHHCCCCCCCHHHHHHH-HHHCCEEEEE----------CCCEEEEEECCCCEEEEE T ss_conf 6762324678788789999--99875305689868988987-7624066632----------797369832666367750 Q ss_pred HHHHHHCCCCCEEEEEECCCCEEEEEEEC-------CCCCE-EEEEECCCEEEEEEHHHCCCCCCCCCCCEEEEECCCCC Q ss_conf 36862047772278661589857888961-------89826-99993698599975876235478665535767528998 Q gi|254780182|r 662 LSDFIQINRSGKIAMKLDSRDEILSVETC-------TQEND-ILLTTKLGQCVRFPISAIRVFAGRNSVGVRGISLAKGD 733 (910) Q Consensus 662 l~ef~~~r~~G~~aikLkegD~Li~v~~~-------~~~~~-Iil~T~~G~~lrF~~~evr~~~GR~a~GVkgIkL~~~D 733 (910) -=+=+|.-..-+..+-.+.+- +|... .+.+- |++.=.+|++.|--.-.+ +. | +.||+.++=..|+ T Consensus 118 GvD~SN~~~G~~llLP~dPD~---SA~~ir~~L~el~G~~VgVIITDT~GRpFR~G~vGv-Ai-G--~aG~~~l~D~~G~ 190 (260) T TIGR01916 118 GVDESNVEEGELLLLPEDPDA---SAEKIRRGLRELLGKDVGVIITDTNGRPFREGQVGV-AI-G--AAGVKALKDWRGE 190 (260) T ss_pred CCCCCCCCCCEEECCCCCHHH---HHHHHHHHHHHHHCCEEEEEEECCCCCCCCCCCCEE-EE-E--ECCCHHHHHCCCC T ss_conf 557112478567358988378---999999999986398478999718888401687437-88-1--0040478732789 Q ss_pred E Q ss_conf 6 Q gi|254780182|r 734 Q 734 (910) Q Consensus 734 ~ 734 (910) + T Consensus 191 ~ 191 (260) T TIGR01916 191 K 191 (260) T ss_pred C T ss_conf 5 No 302 >cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity. Probab=22.28 E-value=36 Score=11.63 Aligned_cols=20 Identities=15% Similarity=0.290 Sum_probs=10.3 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 78999999874069999998 Q gi|254780182|r 385 HVLVGLAIAVANLDEVVRII 404 (910) Q Consensus 385 HILeGL~~Al~nIDeVI~iI 404 (910) ...+|...-.+++.++++-. T Consensus 21 ~~~~Gh~~G~~~~~~i~~~~ 40 (221) T cd00475 21 DRIEGHKAGAEKLRDILRWC 40 (221) T ss_pred CHHHHHHHHHHHHHHHHHHH T ss_conf 87899999999999999999 No 303 >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=22.24 E-value=36 Score=11.63 Aligned_cols=43 Identities=9% Similarity=0.258 Sum_probs=21.9 Q ss_pred CCCEEEEEECCCCEEEECHHHHHH-CCCCCEEEEEECCCCEEEE Q ss_conf 871799994799189842368620-4777227866158985788 Q gi|254780182|r 644 NNLYVVFATKHGNVRRNKLSDFIQ-INRSGKIAMKLDSRDEILS 686 (910) Q Consensus 644 ~~~~Lvl~Tk~G~VKkt~l~ef~~-~r~~G~~aikLkegD~Li~ 686 (910) .+..+|.+=.-|||---.+.-|.. ..+.|-++.-+-|.+.|-. T Consensus 500 ~~~dvLviDEAGMV~S~Qm~r~l~~A~~AGaKvVLvGD~~QLqa 543 (888) T TIGR02768 500 EDKDVLVIDEAGMVGSRQMARVLKEAEEAGAKVVLVGDPEQLQA 543 (888) T ss_pred CCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCEEEECCHHHHCH T ss_conf 47766898515441467788999999872760598488578244 No 304 >PRK10977 hypothetical protein; Provisional Probab=22.21 E-value=36 Score=11.62 Aligned_cols=59 Identities=22% Similarity=0.364 Sum_probs=47.3 Q ss_pred HHHHHHCCCCCCCCEECCCCCCCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHH-HCCCCC Q ss_conf 9998630768405330689885485034322732110167610101331789854789999998876-187768 Q gi|254780182|r 140 HFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYPNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVI-DNPDID 212 (910) Q Consensus 140 ~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i-~~p~~~ 212 (910) +.++-|+-+...+|+|-| |||- +.-.|-|||.= --==||-+|-|.++++.-+- .=|.+| T Consensus 48 ~g~iCDmfEGhAPyrPRY--------ilPD-Y~kfl~~Gs~f-----LeL~pp~dldeAln~L~IlYhHVPSvT 107 (510) T PRK10977 48 EGVICDMFEGHAPYKPRY--------VLPD-YAKFLANGSEF-----LELEPAKDLDEALNLLTILYHHVPSVT 107 (510) T ss_pred CCCEECCCCCCCCCCCCC--------CCCC-HHHHHHCCCHH-----HCCCCCCCHHHHHHHHHHHHHCCCCCC T ss_conf 292420457888898750--------0866-99999734354-----277982459999988999985188557 No 305 >PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional Probab=22.20 E-value=36 Score=11.62 Aligned_cols=90 Identities=20% Similarity=0.402 Sum_probs=45.0 Q ss_pred CCHHHHHHHH-HHHHHCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEE-EEE----EEE--EEEC---CC Q ss_conf 5478999999-88761877688888863458668874434475889999870120389-999----886--5433---67 Q gi|254780182|r 193 HNLGEVVDGC-VAVIDNPDIDLDALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIV-IRG----VSH--IEKT---SG 261 (910) Q Consensus 193 HNl~Ev~~a~-~~~i~~p~~~~~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~-iR~----k~~--ie~~---~~ 261 (910) +-..|.|+-+ -|++++.|- . .||.||||+-.-.+...| |.-+ .+. .|. +|+. =. T Consensus 215 nGvSE~i~~am~Alln~GDe----V--LiP~P~YPlyta~v~L~G---------g~pV~y~~dEe~~w~PDiedLe~kIT 279 (518) T PRK13355 215 NGVSELINLSMSALLDDGDE----V--LVPSPDYPLWTACVNLAG---------GTAVHYRCDEESEWYPDIDDIRSKIT 279 (518) T ss_pred CCHHHHHHHHHHHHCCCCCE----E--EECCCCCCCHHHHHHHCC---------CEEEEEEECCCCCCCCCHHHHHHHCC T ss_conf 77679999999983689998----9--825999977899988609---------87889874522177889999985357 Q ss_pred CCEEEEEECCCC---C-CCHHHHHHHHHHHHHCCCCCHHH Q ss_conf 845999924644---3-52899999999998716650144 Q gi|254780182|r 262 DREQIVVTEIPY---Q-VNKAAMLEKIAELVREKRIVDIA 297 (910) Q Consensus 262 ~k~~ivItEiPY---~-vnk~~lie~Ia~lv~~~ki~gI~ 297 (910) .|++.+|--=|= + |=....+++|+++.++..|--|+ T Consensus 280 ~kTKAIVInNPNNPTGAVyS~E~LeeIaeiArehdLiIIS 319 (518) T PRK13355 280 SKTKAIVIINPNNPTGALYPKEVLQQIVDIAREHQLIIFS 319 (518) T ss_pred CCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHCCEEEEE T ss_conf 1557999968989888788999999999999985969996 No 306 >COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only] Probab=22.20 E-value=36 Score=11.62 Aligned_cols=43 Identities=16% Similarity=0.203 Sum_probs=26.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 9999989999999998875304989999999998999998405 Q gi|254780182|r 471 DDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELD 513 (910) Q Consensus 471 ~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kyg 513 (910) ..++.|+.+++.+++.|+.=++--....+.+-.|...++++|. T Consensus 159 eele~e~ee~~erlk~le~E~s~LeE~~~~l~~ev~~L~~r~~ 201 (290) T COG4026 159 EELEAEYEEVQERLKRLEVENSRLEEMLKKLPGEVYDLKKRWD 201 (290) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH T ss_conf 9999899999999999987898899999866218999999999 No 307 >CHL00191 ycf61 DNA-directed RNA polymerase subunit omega; Provisional Probab=22.18 E-value=36 Score=11.62 Aligned_cols=17 Identities=35% Similarity=0.524 Sum_probs=7.4 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 99999999999988877 Q gi|254780182|r 369 VVRRTKYLLNKARDRAH 385 (910) Q Consensus 369 i~rRt~~~L~ka~~R~H 385 (910) |.+|++..++.+..|-. T Consensus 11 i~~r~E~Li~aasNRY~ 27 (74) T CHL00191 11 ILYRSEELLNAASNRYK 27 (74) T ss_pred HHHHHHHHHHHHCCCEE T ss_conf 99999999985135446 No 308 >PRK10869 recombination and repair protein; Provisional Probab=22.15 E-value=36 Score=11.61 Aligned_cols=12 Identities=42% Similarity=0.609 Sum_probs=5.7 Q ss_pred HHHHHHHHHHHH Q ss_conf 878999988879 Q gi|254780182|r 459 ELRLARLTGLGR 470 (910) Q Consensus 459 dMrL~rLt~LE~ 470 (910) +-||..|.+|.+ T Consensus 302 e~RL~~i~~L~R 313 (553) T PRK10869 302 EQRLSKQISLAR 313 (553) T ss_pred HHHHHHHHHHHH T ss_conf 999999999998 No 309 >pfam00534 Glycos_transf_1 Glycosyl transferases group 1. Mutations in this domain of subunit A of phosphatidylinositol N-acetylglucosaminyltransferase lead to disease (Paroxysmal Nocturnal haemoglobinuria). Members of this family transfer activated sugars to a variety of substrates, including glycogen, Fructose-6-phosphate and lipopolysaccharides. Members of this family transfer UDP, ADP, GDP or CMP linked sugars. The eukaryotic glycogen synthases may be distant members of this family. Probab=22.14 E-value=36 Score=11.61 Aligned_cols=21 Identities=0% Similarity=0.200 Sum_probs=11.5 Q ss_pred CCCCCHHHHHHHHHHHHHCCC Q ss_conf 898547899999988761877 Q gi|254780182|r 190 IPTHNLGEVVDGCVAVIDNPD 210 (910) Q Consensus 190 ippHNl~Ev~~a~~~~i~~p~ 210 (910) ++|-|..++++++..+++||+ T Consensus 140 ~~~~~~~~l~~~i~~li~n~~ 160 (172) T pfam00534 140 VDPGDAEALAEAIEKLLKDEE 160 (172) T ss_pred ECCCCHHHHHHHHHHHHCCHH T ss_conf 789999999999999987999 No 310 >pfam00768 Peptidase_S11 D-alanyl-D-alanine carboxypeptidase. Probab=22.11 E-value=36 Score=11.61 Aligned_cols=84 Identities=19% Similarity=0.246 Sum_probs=49.3 Q ss_pred CCCCCCHHHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHCCCCCCCCCCCCCCCCCCC Q ss_conf 00089736789999999878999998113404255664366887047899999971220111561314788708877697 Q gi|254780182|r 45 LRDGLKPVHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGNAAIYDALARMAQDWSLRLLLIEGQGNFGSVDGDP 124 (910) Q Consensus 45 ~rDGlKpv~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd~siy~a~v~maq~~~~r~plidg~GnfGs~dgd~ 124 (910) ++.|-+.--|-.||+|.- .||.=...+++.+...+...--+.|=.-|+.|.|.. =+|-+..|-+ T Consensus 84 l~~G~~~tv~dLl~~lll----------~S~NdAA~aLA~~v~Gs~~~Fv~~MN~~A~~LGm~~------T~F~np~GL~ 147 (241) T pfam00768 84 LKPGDKVTVRDLLRGLLV----------SSGNDAAVALAEKIAGSEKAFVKMMNAKAKQLGLKN------TRFVNPTGLD 147 (241) T ss_pred ECCCCEEEHHHHHHHHHH----------HCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCC------CEEECCCCCC T ss_conf 348999889999999987----------564599999999845829999999999999819999------8666687777 Q ss_pred CCHHHHHHH-HHHHHHHHHHHH Q ss_conf 201357899-978999999863 Q gi|254780182|r 125 PAAERYTEC-RLQKAAHFLLDD 145 (910) Q Consensus 125 ~AA~RYte~-rl~~~~~~~l~~ 145 (910) ... -||-| -|+.++.+.+++ T Consensus 148 ~~~-~~sTA~Dla~l~~~~~~~ 168 (241) T pfam00768 148 NHG-QYSSARDLAILARALIKD 168 (241) T ss_pred CCC-CEECHHHHHHHHHHHHHH T ss_conf 888-666799999999999874 No 311 >pfam07426 Dynactin_p22 Dynactin subunit p22. This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localizes to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis. Family members are approximately 170 residues long and seem to be restricted to mammals. Probab=21.98 E-value=36 Score=11.59 Aligned_cols=19 Identities=16% Similarity=0.118 Sum_probs=7.9 Q ss_pred HHHHHHHHHHHHHHHCCHH Q ss_conf 9999999998875304989 Q gi|254780182|r 477 LNSLGIEIKECLDILSSRS 495 (910) Q Consensus 477 ~~eL~~~I~~l~~IL~s~~ 495 (910) ..++.++|+.|+.+|+|+. T Consensus 97 ~~~~Le~i~~L~~vLds~~ 115 (172) T pfam07426 97 QAALLEQVHSLQPLLDSAH 115 (172) T ss_pred HHHHHHHHHHHHHHCCCHH T ss_conf 9999999997451038298 No 312 >COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones] Probab=21.90 E-value=36 Score=11.58 Aligned_cols=50 Identities=20% Similarity=0.159 Sum_probs=25.8 Q ss_pred HHHHHHHHHHHHHCCCCCCCEEECC-CCC----CCCC-CCCCCCCEEEEEECCCEE Q ss_conf 9999989999984056883310013-434----5301-014567818999079705 Q gi|254780182|r 499 GIIKQELLSVKDELDTPRRTRIVEG-LLD----MEDE-DCIVREDMVVTVSHLGYV 548 (910) Q Consensus 499 ~iI~~EL~eik~kygd~RRT~I~~~-~~~----i~~E-dlI~~E~vvV~lS~~GyI 548 (910) ..+.++|..+-++||-..=....+. +.. +..+ +-=.....+|.+-+.||. T Consensus 121 em~~~~l~~~L~k~Gv~~i~~~Ge~FDP~~HeAv~~~~~~~~~~~tVv~v~qkGY~ 176 (193) T COG0576 121 EMTLDQLLDALEKLGVEEIGPEGEKFDPNLHEAVQRVESEDVEPNTVVEVLQKGYK 176 (193) T ss_pred HHHHHHHHHHHHHCCCEEECCCCCCCCHHHHHHEEEECCCCCCCCEEEEEEECCEE T ss_conf 99999999999987987807889988978855103436789999948898505706 No 313 >TIGR03604 docking_ocin bacteriocin biosynthesis docking scaffold, SagD family. prokaryotic systems for making a general class of heterocycle-containing bacteriocins. Probab=21.88 E-value=36 Score=11.57 Aligned_cols=54 Identities=19% Similarity=0.317 Sum_probs=33.2 Q ss_pred CCCCCEECCCCCCCCCEECCCCCCCCHHC-----------CCCCEEEHHHHCCCCCCHHHHHHHHHHHHHC Q ss_conf 84053306898854850343227321101-----------6761010133178985478999999887618 Q gi|254780182|r 149 DTVDFRPNYDGSFQEPVVLCARYPNVLVN-----------GGGGIAVGMATNIPTHNLGEVVDGCVAVIDN 208 (910) Q Consensus 149 ~tv~~~~n~D~~~~EP~vlP~~~P~lL~n-----------G~~GIAvGmaTnippHNl~Ev~~a~~~~i~~ 208 (910) ..++|++-+|=...+|+.+|+.+=.+... .|+|.|.|-... .-++.|++-+|+. T Consensus 72 ~~i~W~~g~~L~~g~~v~VPa~~v~~~~~~~~~~~~~~~~~SnGlAaG~t~~------eA~~~gL~EviER 136 (377) T TIGR03604 72 TPIGWVPGKSLTTGRPVLVPAQLVYYSYPEERGEDYIVPSTSTGLAAGETLE------EAILNGLLEVIER 136 (377) T ss_pred CEEECEECCCCCCCCEEEEEHHHHHCCCCCCCCCCCEECCCCCCCCCCCCHH------HHHHHHHHHHHHH T ss_conf 8140548424578966785479964679877777714246787168889999------9999999999999 No 314 >KOG2896 consensus Probab=21.86 E-value=37 Score=11.57 Aligned_cols=111 Identities=14% Similarity=0.092 Sum_probs=48.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCC Q ss_conf 99999999999999999999999888778999999874069999998618997898787763126978899999740221 Q gi|254780182|r 358 LKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDS 437 (910) Q Consensus 358 L~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~ 437 (910) |+--+---.++...|..++-.- ++++..+-...-.+..+-+.-+...++|.+|.-+... ...+..+ T Consensus 54 lqk~i~~~k~~~c~r~~~r~~~-------~~~~~~~q~~~~q~~~~~~~~~~v~~ek~rl~~~~i~------~~iL~~~- 119 (377) T KOG2896 54 LQKSIRLKKDVECKRTELRVKI-------LERLHVEQCLSAQVQSMRVEMKEVSEEKLRLQIECIQ------LKILVLE- 119 (377) T ss_pred HHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHH- T ss_conf 9999999998865588899886-------5678899999999999999888888999998999988------8899888- Q ss_pred CCCCCCCCCCCCCHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 11222344523699999999-----98789999888799999989999999998875304 Q gi|254780182|r 438 SYTIGSDGTMYLSEVQTRAI-----LELRLARLTGLGRDDIRNELNSLGIEIKECLDILS 492 (910) Q Consensus 438 ~~~~~~~~~f~lSe~QA~AI-----LdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~ 492 (910) ..=..|-+|| ..+++++...--+..+.++..+|.++++.|.++.+ T Consensus 120 ----------~~l~~~~Ealsk~~~~~~k~~~kL~~kr~q~~~~q~~l~k~~k~l~e~~~ 169 (377) T KOG2896 120 ----------SNLQRQIEALSKKRAHLEKTKQKLEDKRQQFNASQVKLQKQLKSLIELRN 169 (377) T ss_pred ----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf ----------89999999888899899999999999999987778888776999999999 No 315 >TIGR01034 metK S-adenosylmethionine synthetase; InterPro: IPR002133 S-adenosylmethionine synthetase (MAT, 2.5.1.6 from EC) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP . AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis. In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family. The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex, and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance .; GO: 0004478 methionine adenosyltransferase activity, 0005524 ATP binding, 0006730 one-carbon compound metabolic process. Probab=21.77 E-value=30 Score=12.30 Aligned_cols=16 Identities=44% Similarity=0.513 Sum_probs=9.2 Q ss_pred HCCCCCEEEHHHHCCC Q ss_conf 0167610101331789 Q gi|254780182|r 176 VNGGGGIAVGMATNIP 191 (910) Q Consensus 176 ~nG~~GIAvGmaTnip 191 (910) ==|=.||-+|||||=- T Consensus 120 GAGDQGimFGYAt~ET 135 (393) T TIGR01034 120 GAGDQGIMFGYATNET 135 (393) T ss_pred CCCCEEEEEEEECCCH T ss_conf 8984057854422400 No 316 >PRK00927 tryptophanyl-tRNA synthetase; Reviewed Probab=21.76 E-value=37 Score=11.55 Aligned_cols=115 Identities=16% Similarity=0.170 Sum_probs=66.5 Q ss_pred CCHHHHHHHHHH-HCCHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 877899999997-6101100000024554166300029999999999999999999999999998887789999998740 Q gi|254780182|r 318 ASADVILNQLYR-YTSLQSLFSVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGLAIAVAN 396 (910) Q Consensus 318 ~~~~~vln~Lyk-~T~Lq~sf~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL~~Al~n 396 (910) .+++.|.+++-+ .|+-+...... ..++|...||-.|...|-+- . T Consensus 208 d~~~~i~kKi~~a~TDs~~~i~~d----~~~rPev~NL~~I~s~fs~~-------------------------------~ 252 (325) T PRK00927 208 DDPKTIAKKIKKAVTDSERPIRYD----DPGKPEVSNLLTIYSAFTGK-------------------------------S 252 (325) T ss_pred CCHHHHHHHHHHCCCCCCCCCCCC----CCCCCCCCHHHHHHHHHCCC-------------------------------C T ss_conf 899999999885757998775556----89998636499999984899-------------------------------8 Q ss_pred HHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 69999998618997898787763126978899999740221112223445236999999999878999988879999998 Q gi|254780182|r 397 LDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARLTGLGRDDIRNE 476 (910) Q Consensus 397 IDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rLt~LE~~kl~~E 476 (910) ++++.+-.+ ...-.++|+.|.+ +| .-+..-++++ T Consensus 253 ~eei~~~y~-g~g~g~~Kk~Lae------------------------------------~I---------i~~L~PIrek 286 (325) T PRK00927 253 IEELEAEYE-GKGYGDFKKDLAE------------------------------------AV---------VEFLAPIQER 286 (325) T ss_pred HHHHHHHHC-CCCHHHHHHHHHH------------------------------------HH---------HHHHHHHHHH T ss_conf 999999968-9988999999999------------------------------------99---------9996899999 Q ss_pred HHHHHHHHHHHHHHHCCHHHHHHH-HHHHHHHHHHHCC Q ss_conf 999999999887530498999999-9998999998405 Q gi|254780182|r 477 LNSLGIEIKECLDILSSRSRLLGI-IKQELLSVKDELD 513 (910) Q Consensus 477 ~~eL~~~I~~l~~IL~s~~~l~~i-I~~EL~eik~kyg 513 (910) +++|.+...++.+||.+-.+.-.. -.+=|.++++..| T Consensus 287 ~~~L~~d~~~l~~IL~~Ga~KAr~iA~~tl~~Vr~~~G 324 (325) T PRK00927 287 YEELLADPAYLDEILAEGAEKARAVASKTLKKVREAMG 324 (325) T ss_pred HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 99998399999999999999999999999999998629 No 317 >COG2039 Pcp Pyrrolidone-carboxylate peptidase (N-terminal pyroglutamyl peptidase) [Posttranslational modification, protein turnover, chaperones] Probab=21.71 E-value=37 Score=11.55 Aligned_cols=19 Identities=21% Similarity=0.237 Sum_probs=11.7 Q ss_pred CCCCCHHHHHHHHHHHHHC Q ss_conf 8985478999999887618 Q gi|254780182|r 190 IPTHNLGEVVDGCVAVIDN 208 (910) Q Consensus 190 ippHNl~Ev~~a~~~~i~~ 208 (910) +-|--+++..+++...|+. T Consensus 40 ~lP~~f~~s~~~l~~~i~~ 58 (207) T COG2039 40 ILPVVFKKSIDALVQAIAE 58 (207) T ss_pred ECCCCHHHHHHHHHHHHHH T ss_conf 8574188899999999985 No 318 >KOG4577 consensus Probab=21.61 E-value=37 Score=11.53 Aligned_cols=54 Identities=19% Similarity=0.119 Sum_probs=21.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEE Q ss_conf 899998887999999899999999988753049899999999989999984056883310 Q gi|254780182|r 461 RLARLTGLGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRI 520 (910) Q Consensus 461 rL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I 520 (910) +|.+=|+|+--.++-=++.-+++-+.|++=-+- ..|. +.++.+|.. |.+|--+- T Consensus 199 QLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR--~RWg---qyfrsmK~s-gs~r~ekd 252 (383) T KOG4577 199 QLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR--TRWG---QYFRSMKRS-GSSRAEKD 252 (383) T ss_pred HHHHCCCCCEEEHHHHHHHHHHHHHHHHHHCCH--HHHH---HHHHHHHCC-CCCCCCCC T ss_conf 850113866133146654116777765430033--5789---998874126-88632123 No 319 >pfam06609 TRI12 Fungal trichothecene efflux pump (TRI12). This family consists of several fungal specific trichothecene efflux pump proteins. Many of the genes involved in trichothecene toxin biosynthesis in Fusarium sporotrichioides are present within a gene cluster.It has been suggested that TRI12 may play a role in F. sporotrichioides self-protection against trichothecenes. Probab=21.60 E-value=31 Score=12.23 Aligned_cols=32 Identities=19% Similarity=0.288 Sum_probs=24.6 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHH Q ss_conf 67877799886313754000897367899999 Q gi|254780182|r 28 SYLTYAINVILGRAIPDLRDGLKPVHRRILFG 59 (910) Q Consensus 28 syl~Ya~svI~~RAlPd~rDGlKpv~Rrily~ 59 (910) .|+.|-=.+|++-|||.+-+-|....+---|+ T Consensus 53 ~~~~~ld~tivatAlP~I~~dl~~~~~~~W~~ 84 (598) T pfam06609 53 VCATYFVLQASASALPNILQDIGQSENQGLFS 84 (598) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCEEHHH T ss_conf 99999500276634716998708987735499 No 320 >cd04588 CBS_pair_CAP-ED_DUF294_assoc_arch This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the archaeal CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. Probab=21.60 E-value=36 Score=11.60 Aligned_cols=68 Identities=24% Similarity=0.266 Sum_probs=36.2 Q ss_pred HCCCCCCCCCCHH----HHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCC--CCCCCHHHHHHHHHHHCCCHHCCCCCCCC Q ss_conf 1375400089736----78999999987899999811340425566436--68870478999999712201115613147 Q gi|254780182|r 40 RAIPDLRDGLKPV----HRRILFGMMQMGVEWNKKYVKCARISGEVMGK--YHPHGNAAIYDALARMAQDWSLRLLLIEG 113 (910) Q Consensus 40 RAlPd~rDGlKpv----~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gk--yHPHGd~siy~a~v~maq~~~~r~plidg 113 (910) +++|=+.|| |++ .|.|+.+..+... + .-|+++|.+ +.=|-|.++++|+-.|.+.---+.|.+|. T Consensus 25 ~~~pVvd~~-~lvGiit~~Di~~~~~~~~~--~-------~~V~~~M~~~~~tv~~d~~l~~~~~~m~~~~v~~l~Vvd~ 94 (110) T cd04588 25 HGAPVVDDG-KLVGIVTLSDIAHAIARGLE--L-------AKVKDVMTKDVITIDEDEQLYDAIRLMNKHNVGRLIVTDD 94 (110) T ss_pred CEEEEEECC-EEEEEEEHHHHHHHHHCCCC--C-------CHHHHHCCCCCCEECCCCCHHHHHHHHHHCCCCEEEEEEC T ss_conf 889999899-99999966898999873797--7-------8034520489729858996999999998779978999966 Q ss_pred CCCC Q ss_conf 8870 Q gi|254780182|r 114 QGNF 117 (910) Q Consensus 114 ~Gnf 117 (910) +|.. T Consensus 95 ~~~l 98 (110) T cd04588 95 EGRP 98 (110) T ss_pred CCEE T ss_conf 9999 No 321 >PRK10548 flagellar biosynthesis protein FliT; Provisional Probab=21.59 E-value=37 Score=11.53 Aligned_cols=52 Identities=13% Similarity=0.150 Sum_probs=34.4 Q ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCCCCCCC Q ss_conf 9887530498999999999899999840568833100-134345301014567 Q gi|254780182|r 485 KECLDILSSRSRLLGIIKQELLSVKDELDTPRRTRIV-EGLLDMEDEDCIVRE 536 (910) Q Consensus 485 ~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~I~-~~~~~i~~EdlI~~E 536 (910) .-|+.||+++.+++.++..-+.++..--|..||..=. ..-+.++.--+.|++ T Consensus 66 ~lL~~IL~ne~~ir~Llq~RmdeL~~Li~qs~rQ~~ln~aYg~~sg~~l~p~~ 118 (121) T PRK10548 66 PMLRQILDNESELKQLLQQRMDELSKLIGQSTRQKSVNSAYGQLSGFLLLPDD 118 (121) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEECCCC T ss_conf 99999998789999999999999999999889999999999705887208998 No 322 >pfam05615 THOC7 Tho complex subunit 7. The Tho complex is involved in transcription elongation and mRNA export from the nucleus. Probab=21.53 E-value=37 Score=11.52 Aligned_cols=70 Identities=17% Similarity=0.172 Sum_probs=48.6 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH---HCCCCC Q ss_conf 5236999999999878999988879--9999989999999998875304989999999998999998---405688 Q gi|254780182|r 446 TMYLSEVQTRAILELRLARLTGLGR--DDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKD---ELDTPR 516 (910) Q Consensus 446 ~f~lSe~QA~AILdMrL~rLt~LE~--~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~---kygd~R 516 (910) .|.|+-.-++++++|-.+..-+-+. ..|+.....+.++|++|+.=|..-+..++.-+ |..++.+ .++.+| T Consensus 53 ~~e~s~~k~q~v~~~n~~E~e~Y~~~~~~I~~~i~~~k~~i~~lk~~L~~Ak~~r~~r~-eyD~La~~I~~~P~~R 127 (135) T pfam05615 53 ALELSMLKLQFVIEMNERERENYEQEKEEIETTIENAKEEIEELKKELEEAKRERKNRK-EYDELAKKITSQPVTR 127 (135) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHCCCCC T ss_conf 88999999999999999999999999999999999999999999999999999999799-9999999998389981 No 323 >TIGR02404 trehalos_R_Bsub trehalose operon repressor; InterPro: IPR012770 This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from Escherichia coli.. Probab=21.52 E-value=30 Score=12.29 Aligned_cols=147 Identities=13% Similarity=0.162 Sum_probs=85.0 Q ss_pred HHHHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCEEE----EEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHH Q ss_conf 888863458668874434475889999870120389----9998865433678459999246443528999999999987 Q gi|254780182|r 214 DALMEIIRGPDFPTGAVILGRTGIKNAYATGRGSIV----IRGVSHIEKTSGDREQIVVTEIPYQVNKAAMLEKIAELVR 289 (910) Q Consensus 214 ~eL~~~i~GPDFPTGG~I~~~~~i~~~y~tGrG~i~----iR~k~~ie~~~~~k~~ivItEiPY~vnk~~lie~Ia~lv~ 289 (910) .||.+-|.+-++|-|-.+=.-..+.+.|..-||.|+ +-...-.-...+||=.||+.-=+|+.+-+.|+- =.||.+ T Consensus 7 ~dL~~~I~~~~yk~G~~LPSE~~L~~~Y~~SReTvRKAL~~L~~~GyIQKi~GKGsiVl~~~~~~fP~SGivS-y~EL~~ 85 (236) T TIGR02404 7 KDLEQKIDAGQYKEGDLLPSEHELMEQYGASRETVRKALNLLTEAGYIQKIRGKGSIVLNREKYEFPISGIVS-YKELAE 85 (236) T ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEEEECCCCCCCCCCCCHH-HHHHHH T ss_conf 9999860057478877388878999860687458899999998578716761523487667631048630011-278776 Q ss_pred CCCCCHHHHHHHHCCCCCEEEEEEECCCCCHH-HHHHHHHHHCCHHCCCCCEEEEE-----ECCCCCCCCHHHHHHHHHH Q ss_conf 16650144587303746557999947988778-99999997610110000002455-----4166300029999999999 Q gi|254780182|r 290 EKRIVDIADLRDESDRQGYRVVIELKRGASAD-VILNQLYRYTSLQSLFSVNMVAL-----NGYKPERFTLIGILKAFVA 363 (910) Q Consensus 290 ~~ki~gI~dirDeSdr~giRivielKr~~~~~-~vln~Lyk~T~Lq~sf~~N~~aL-----~~g~P~~l~Lk~iL~~fi~ 363 (910) .-.+ +-.=.|+++-++.-.+ .|=..+...|.|+. .+..+| +||++.+|..-=+++.++- T Consensus 86 ~l~~------------~~~T~V~~~~~e~~~~~~~a~~~~~~tel~~---~~i~~i~R~R~IdGe~~ILD~DYl~~~~vP 150 (236) T TIGR02404 86 TLGL------------EAKTEVVELQKELPLEESLAKLTGLETELEG---SLIWRIKRVRVIDGEAVILDIDYLLKKLVP 150 (236) T ss_pred HCCC------------CEEEEEEECCCCCCCHHHHHHHCCCCCCCCC---CCCEEEEEEEEECCEEEEECCHHHHHHCCC T ss_conf 4298------------2357787327898870678977056565278---862178998776787566301112101178 Q ss_pred HHHHHHHHHHHHH Q ss_conf 9999999999999 Q gi|254780182|r 364 FREEVVVRRTKYL 376 (910) Q Consensus 364 hR~evi~rRt~~~ 376 (910) +=-.-|-=.+-|+ T Consensus 151 ~l~keiAE~SIY~ 163 (236) T TIGR02404 151 GLTKEIAEDSIYD 163 (236) T ss_pred CCHHHHHHHHHHH T ss_conf 6337898877998 No 324 >KOG0998 consensus Probab=21.44 E-value=37 Score=11.50 Aligned_cols=52 Identities=17% Similarity=0.204 Sum_probs=43.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCE Q ss_conf 8799999989999999998875304989999999998999998405688331 Q gi|254780182|r 468 LGRDDIRNELNSLGIEIKECLDILSSRSRLLGIIKQELLSVKDELDTPRRTR 519 (910) Q Consensus 468 LE~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~RRT~ 519 (910) -|+..+..++.++.++-..|...+.+.....+-+.++|..+..+.++.|.+. T Consensus 505 ~ei~~~~~~ln~~~qq~~~l~~~v~~~~~~ve~l~~~L~~~~~~~~~~~s~~ 556 (847) T KOG0998 505 REISSLEKELNELQQQLSVLEGSVKAIESQVENLQKELLDLIYEMADTRSKS 556 (847) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH T ss_conf 6688777776656667767764320234424566777999999987640410 No 325 >PRK11779 sbcB exonuclease I; Provisional Probab=21.39 E-value=37 Score=11.50 Aligned_cols=48 Identities=21% Similarity=0.223 Sum_probs=25.5 Q ss_pred EEEEEEECCCC------CHHHHHHHHHHHC-CHH---CCCCCEEEEEECCCCCCCCHHH Q ss_conf 57999947988------7789999999761-011---0000002455416630002999 Q gi|254780182|r 308 YRVVIELKRGA------SADVILNQLYRYT-SLQ---SLFSVNMVALNGYKPERFTLIG 356 (910) Q Consensus 308 iRivielKr~~------~~~~vln~Lyk~T-~Lq---~sf~~N~~aL~~g~P~~l~Lk~ 356 (910) -.||+.|+.|- +.+.+...||+.. .|. ...++-.+.+ +..|.++..+- T Consensus 256 ~~i~fDL~~DP~~ll~ls~~eL~~~l~t~~~~l~~~~~~~plk~I~i-NK~Pil~p~~~ 313 (477) T PRK11779 256 AVIVCDLAGDPSPLLELDADTLRERLYTRRADLAEGELPVPLKLVHL-NKCPVLAPAKT 313 (477) T ss_pred CEEEEECCCCHHHHHCCCHHHHHHHHCCCHHHHHCCCCCCCEEEEEE-CCCCEECCHHH T ss_conf 65888735797998669999999997154322103467765067530-78880176575 No 326 >pfam02827 PKI cAMP-dependent protein kinase inhibitor. Members of this family are extremely potent competitive inhibitors of camp-dependent protein kinase activity. These proteins interact with the catalytic subunit of the enzyme after the cAMP-induced dissociation of its regulatory chains. Probab=21.37 E-value=33 Score=12.02 Aligned_cols=23 Identities=26% Similarity=0.541 Sum_probs=11.0 Q ss_pred HHHHHHHHHHHHHHH--CCCCCCCC Q ss_conf 876787779988631--37540008 Q gi|254780182|r 26 QNSYLTYAINVILGR--AIPDLRDG 48 (910) Q Consensus 26 ~~syl~Ya~svI~~R--AlPd~rDG 48 (910) +.+|.+|+.+==.+| ||||+--. T Consensus 4 E~~~sdFis~~RtGRRNAvpDI~gs 28 (74) T pfam02827 4 ESVYSDFISSGRTGRRNALPDIQGS 28 (74) T ss_pred HHHHHHHHHCCCCCCCCCCCCCCCC T ss_conf 1568888870543443445200257 No 327 >KOG2303 consensus Probab=21.33 E-value=37 Score=11.49 Aligned_cols=40 Identities=15% Similarity=0.267 Sum_probs=16.2 Q ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCCCEEEEEEEC-CCCCHHHHHHHHH Q ss_conf 99999998716650144587303746557999947-9887789999999 Q gi|254780182|r 281 LEKIAELVREKRIVDIADLRDESDRQGYRVVIELK-RGASADVILNQLY 328 (910) Q Consensus 281 ie~Ia~lv~~~ki~gI~dirDeSdr~giRivielK-r~~~~~~vln~Ly 328 (910) .+++.+.++.+.-.-+.|+|- |+-..+ -..||..+.|++| T Consensus 373 C~~V~~av~~g~eqv~~Dvr~--------i~~~~~~~p~dp~~l~nri~ 413 (706) T KOG2303 373 CRQVCKAVQSGDEQVLADVRR--------IVNDISYTPTDPADLCNRIL 413 (706) T ss_pred HHHHHHHHHCCCHHHHHHHHH--------HHCCCCCCCCCHHHHHHHHH T ss_conf 999999997473654320687--------71488868889899987666 No 328 >cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Probab=21.27 E-value=37 Score=11.48 Aligned_cols=40 Identities=13% Similarity=0.236 Sum_probs=21.6 Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 23699999999987899998887999999899999999988753 Q gi|254780182|r 447 MYLSEVQTRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDI 490 (910) Q Consensus 447 f~lSe~QA~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~I 490 (910) ++||-.+...+|+.....+. .-+++..+++.++|++|+.| T Consensus 56 ~G~~L~eIk~~l~~~~~~~~----~~l~~~~~~i~~~I~~L~~l 95 (96) T cd04768 56 LGFSLAEIKELLDTEMEELT----AMLLEKKQAIQQKIDRLQQL 95 (96) T ss_pred CCCCHHHHHHHHCCCCHHHH----HHHHHHHHHHHHHHHHHHHC T ss_conf 79999999999939969999----99999999999999999821 No 329 >PRK10580 proY putative proline-specific permease; Provisional Probab=21.27 E-value=37 Score=11.48 Aligned_cols=39 Identities=13% Similarity=0.146 Sum_probs=17.5 Q ss_pred HCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCCCCCHH Q ss_conf 016761010133178985478999999887618776888 Q gi|254780182|r 176 VNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNPDIDLD 214 (910) Q Consensus 176 ~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p~~~~~ 214 (910) -+|-.|+..+++.-+-.+-=-|.+--+-.=.+||.-++. T Consensus 195 ~~g~~g~~~a~~~~~faf~G~e~i~~~a~E~knP~r~iP 233 (457) T PRK10580 195 SNGWLGMVMSLQMVMFAYGGIEIIGITAGEAKDPEKSIP 233 (457) T ss_pred CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHH T ss_conf 644789999999999998289999999886208666799 No 330 >pfam09220 LA-virus_coat L-A virus, major coat protein. Members of this family form the major coat protein of the Saccharomyces cerevisiae L-A virus. Probab=21.14 E-value=28 Score=12.63 Aligned_cols=67 Identities=13% Similarity=0.109 Sum_probs=26.8 Q ss_pred HHHHHHCCCCCEEEEEEE----CCC------C-CHHHHHHHHHHHCCHHCCCCCEE----EEEECCCCCCCCHHHHHHHH Q ss_conf 458730374655799994----798------8-77899999997610110000002----45541663000299999999 Q gi|254780182|r 297 ADLRDESDRQGYRVVIEL----KRG------A-SADVILNQLYRYTSLQSLFSVNM----VALNGYKPERFTLIGILKAF 361 (910) Q Consensus 297 ~dirDeSdr~giRiviel----Kr~------~-~~~~vln~Lyk~T~Lq~sf~~N~----~aL~~g~P~~l~Lk~iL~~f 361 (910) -|+|-.+-.+ .+||+-. |+. . .|+.--.-.|++..--.++.-=. ++=.-+-|.--=....|+-| T Consensus 201 iDlR~Lt~~E-a~~VLmM~~eWk~qTn~klDf~~p~La~ki~YR~~~~i~~~~~Wl~~~~~~~~~~~P~s~v~~SALrKY 279 (436) T pfam09220 201 LDVRPLTVTE-VNFVLMMMSKWHRRTNLAIDYEAPQLADKFAYRHALTVQDADEWIEGDRTDDQFRPPSSKVMLSALRKY 279 (436) T ss_pred EECCCCCHHH-HEEEEEECCCCCCCCCEEECCCCHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHH T ss_conf 3347798546-215565214545554324413677788999887418813455442565557667899417899999999 Q ss_pred HHH Q ss_conf 999 Q gi|254780182|r 362 VAF 364 (910) Q Consensus 362 i~h 364 (910) +.| T Consensus 280 V~~ 282 (436) T pfam09220 280 VNH 282 (436) T ss_pred HHC T ss_conf 841 No 331 >PRK12808 flagellin; Provisional Probab=21.11 E-value=38 Score=11.45 Aligned_cols=62 Identities=24% Similarity=0.306 Sum_probs=37.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 89999998740699999986189978987877631269788999997402211122234452369999999998789999 Q gi|254780182|r 386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL 465 (910) Q Consensus 386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL 465 (910) -+.||-.|..|...-|.++.- |-..|-+ ...||. |+|.| T Consensus 55 qi~gl~qa~~Na~dgiS~~qt------AEgal~e----------------------------------v~~iLq-RmReL 93 (460) T PRK12808 55 RESGLGVAANNTQDGMSLIRT------ADSAMNS----------------------------------VSNILL-RMRDL 93 (460) T ss_pred HHHHHHHHHHHHHHHHHHHHH------HHHHHHH----------------------------------HHHHHH-HHHHH T ss_conf 998899999989989999999------9999999----------------------------------999999-99999 Q ss_pred ---------HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---------88879999998999999999887 Q gi|254780182|r 466 ---------TGLGRDDIRNELNSLGIEIKECL 488 (910) Q Consensus 466 ---------t~LE~~kl~~E~~eL~~~I~~l~ 488 (910) +.-++..|+.|+.+|..+|..+- T Consensus 94 AVQAANgTns~~DR~aiQ~Ei~qL~~EIdrIa 125 (460) T PRK12808 94 ANQSANGTNTDKNQAALQKEFAELQKQIDYIA 125 (460) T ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99861566887889999999999999999998 No 332 >KOG0306 consensus Probab=21.08 E-value=38 Score=11.44 Aligned_cols=93 Identities=12% Similarity=0.193 Sum_probs=46.0 Q ss_pred CCCCEEEEEECCCCEEEECHHHHHHCCCCCEEEEEECC------CCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCC- Q ss_conf 68717999947991898423686204777227866158------98578889618982699993698599975876235- Q gi|254780182|r 643 WNNLYVVFATKHGNVRRNKLSDFIQINRSGKIAMKLDS------RDEILSVETCTQENDILLTTKLGQCVRFPISAIRV- 715 (910) Q Consensus 643 ~~~~~Lvl~Tk~G~VKkt~l~ef~~~r~~G~~aikLke------gD~Li~v~~~~~~~~Iil~T~~G~~lrF~~~evr~- 715 (910) .++.+++.++++-.||-..+.-......+..+.++|+. .|.+..+..+.++..+++.=-+..+-.|-.+.+.- T Consensus 464 pD~~g~vT~saDktVkfWdf~l~~~~~gt~~k~lsl~~~rtLel~ddvL~v~~Spdgk~LaVsLLdnTVkVyflDtlKFf 543 (888) T KOG0306 464 PDNKGFVTGSADKTVKFWDFKLVVSVPGTQKKVLSLKHTRTLELEDDVLCVSVSPDGKLLAVSLLDNTVKVYFLDTLKFF 543 (888) T ss_pred CCCCCEEEECCCCEEEEEEEEEEECCCCCCCEEEEECCCEEEECCCCEEEEEECCCCCEEEEEECCCEEEEEEECCEEEE T ss_conf 88886087328737999767999426764210454011207843662789997699848988732675799996251446 Q ss_pred --CCCCCCCCEEEEECCCCCEEE Q ss_conf --478665535767528998699 Q gi|254780182|r 716 --FAGRNSVGVRGISLAKGDQVI 736 (910) Q Consensus 716 --~~GR~a~GVkgIkL~~~D~Vv 736 (910) +-| -+--|..|.+..+.+.+ T Consensus 544 lsLYG-HkLPV~smDIS~DSkli 565 (888) T KOG0306 544 LSLYG-HKLPVLSMDISPDSKLI 565 (888) T ss_pred EEECC-CCCCEEEEECCCCCCEE T ss_conf 54315-65643688506886737 No 333 >pfam08961 DUF1875 Domain of unknown function (DUF1875). The MIT domain, found in Nuclear receptor-binding factor 2, has no known function. Probab=21.04 E-value=38 Score=11.44 Aligned_cols=40 Identities=23% Similarity=0.244 Sum_probs=23.1 Q ss_pred CCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 699999999987899-9988879999998999999999887 Q gi|254780182|r 449 LSEVQTRAILELRLA-RLTGLGRDDIRNELNSLGIEIKECL 488 (910) Q Consensus 449 lSe~QA~AILdMrL~-rLt~LE~~kl~~E~~eL~~~I~~l~ 488 (910) .-|.||..|.|++-. -.---|-+.|+.|-+.|.++.+.|. T Consensus 123 ~iEEQaT~IadLkr~Ve~LvaeNerLrkENkqL~AekaRL~ 163 (243) T pfam08961 123 IIEEQATKIADLKRHVEFLVAENERLRKENKQLKAEKARLL 163 (243) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 89998877999999999998600999998888868998875 No 334 >cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil Probab=20.99 E-value=38 Score=11.43 Aligned_cols=45 Identities=13% Similarity=0.023 Sum_probs=18.8 Q ss_pred CCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 2369999999998789-99988879999998999999999887530 Q gi|254780182|r 447 MYLSEVQTRAILELRL-ARLTGLGRDDIRNELNSLGIEIKECLDIL 491 (910) Q Consensus 447 f~lSe~QA~AILdMrL-~rLt~LE~~kl~~E~~eL~~~I~~l~~IL 491 (910) ++||-.+...+|+.+- +.+..-....|+++.++|.+..+.|+.+| T Consensus 56 ~G~sL~eIk~lL~~~~~~~~l~~~~~~i~~~I~~L~~~r~~L~~ll 101 (102) T cd04775 56 GGLPLEEIAGCLAQPHVQAILEERLQSLNREIQRLRQQQQVLAAIL 101 (102) T ss_pred CCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 6999999999985995799999999999999999999999999873 No 335 >PRK09109 motC flagellar motor protein; Reviewed Probab=20.97 E-value=38 Score=11.43 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=17.4 Q ss_pred CHHHHHHHHHHHHHCCCCCHHHHHHH Q ss_conf 28999999999987166501445873 Q gi|254780182|r 276 NKAAMLEKIAELVREKRIVDIADLRD 301 (910) Q Consensus 276 nk~~lie~Ia~lv~~~ki~gI~dirD 301 (910) +...+++.+.++.+.-+-+|+..+-+ T Consensus 73 ~~~~~i~~l~~la~~aR~~GllaLE~ 98 (246) T PRK09109 73 DLEGGIDRIVEWSMTARKEGLLGLED 98 (246) T ss_pred CHHHHHHHHHHHHHHHHHCCHHHHHH T ss_conf 99999999999999997645311566 No 336 >COG4168 SapB ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms] Probab=20.95 E-value=38 Score=11.42 Aligned_cols=105 Identities=24% Similarity=0.376 Sum_probs=56.9 Q ss_pred HHHHHHHHHHHCCCCCCCCEEEEHHHHHHHHCCCCCCCH---HHHHHHHHHHCCCHHCCCCCCCCCCCCC--CCCCCCCC Q ss_conf 678999999987899999811340425566436688704---7899999971220111561314788708--87769720 Q gi|254780182|r 52 VHRRILFGMMQMGVEWNKKYVKCARISGEVMGKYHPHGN---AAIYDALARMAQDWSLRLLLIEGQGNFG--SVDGDPPA 126 (910) Q Consensus 52 v~Rrily~m~~~~~~~~~~~~K~a~ivg~v~gkyHPHGd---~siy~a~v~maq~~~~r~plidg~GnfG--s~dgd~~A 126 (910) +-|||++-.--+=+ -..||-++.-+.||.. +++|++-+-- .. -| -||+|| |+.|+|-+ T Consensus 5 tlR~ill~~ltLli---------Lslvgfsl~~fdP~apl~~~~l~~g~~~y-----~~-~L--lq~dFGis~~nG~pi~ 67 (321) T COG4168 5 TLRRILLLILTLLI---------LTLVGFSLSYFDPHAPLQGASLWQGWVFY-----FN-GL--LQWDFGISSINGQPIA 67 (321) T ss_pred HHHHHHHHHHHHHH---------HHHHHHHHHHCCCCCCHHHHHHHHHHHHH-----HH-HH--HCCCCCCCCCCCCHHH T ss_conf 99999999999999---------99998885213899730130699999999-----98-88--5203252156980089 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCEECCCCCC----CCHHCCCCCEEEHHHHCCCCCCHHHHHHHH Q ss_conf 1357899978999999863076840533068988548503432273----211016761010133178985478999999 Q gi|254780182|r 127 AERYTECRLQKAAHFLLDDLGKDTVDFRPNYDGSFQEPVVLCARYP----NVLVNGGGGIAVGMATNIPTHNLGEVVDGC 202 (910) Q Consensus 127 A~RYte~rl~~~~~~~l~~i~~~tv~~~~n~D~~~~EP~vlP~~~P----~lL~nG~~GIAvGmaTnippHNl~Ev~~a~ 202 (910) + .++. |+|+..- .+..-=--||-+||-.-+-.|-.-+..=.+ T Consensus 68 ~-------------~l~~---------------------vfPaT~ELC~~af~lal~~GiPlG~iagv~~~kw~d~~i~~ 113 (321) T COG4168 68 E-------------QLLE---------------------VFPATMELCFLAFGLALIVGIPLGMIAGVTRHKWLDKLISA 113 (321) T ss_pred H-------------HHHH---------------------HCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHCHHHHHHHHH T ss_conf 9-------------9998---------------------66618999999999999984647988775423078899999 Q ss_pred HHHHH Q ss_conf 88761 Q gi|254780182|r 203 VAVID 207 (910) Q Consensus 203 ~~~i~ 207 (910) ++++- T Consensus 114 is~~G 118 (321) T COG4168 114 ISLLG 118 (321) T ss_pred HHHHC T ss_conf 99854 No 337 >cd04642 CBS_pair_29 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener Probab=20.91 E-value=38 Score=11.42 Aligned_cols=25 Identities=20% Similarity=0.328 Sum_probs=9.4 Q ss_pred HHHHHHHHHHCCCHHCCCCCCCCCC Q ss_conf 7899999971220111561314788 Q gi|254780182|r 91 AAIYDALARMAQDWSLRLLLIEGQG 115 (910) Q Consensus 91 ~siy~a~v~maq~~~~r~plidg~G 115 (910) +++.+|+-.|++.---..|.+|.+| T Consensus 10 ~~l~eA~~lm~~~~i~~lPVvd~~g 34 (126) T cd04642 10 ERVLDAFKLMRKNNISGLPVVDEKG 34 (126) T ss_pred CCHHHHHHHHHHCCCCEEEEEECCC T ss_conf 9999999999980987899992899 No 338 >COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription] Probab=20.79 E-value=38 Score=11.40 Aligned_cols=14 Identities=14% Similarity=0.420 Sum_probs=6.6 Q ss_pred HHHCCCCCHHHHHH Q ss_conf 76187768888886 Q gi|254780182|r 205 VIDNPDIDLDALME 218 (910) Q Consensus 205 ~i~~p~~~~~eL~~ 218 (910) +++..+++.++|-+ T Consensus 27 l~~kge~tDeela~ 40 (176) T COG1675 27 LLEKGELTDEELAE 40 (176) T ss_pred HHHCCCCCHHHHHH T ss_conf 87527767489988 No 339 >COG0082 AroC Chorismate synthase [Amino acid transport and metabolism] Probab=20.77 E-value=31 Score=12.19 Aligned_cols=64 Identities=20% Similarity=0.250 Sum_probs=38.3 Q ss_pred HHHHHHCCHHCCCCCEEEEEECCCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999761011000000245541663000299-99999999999999999999999998887789999 Q gi|254780182|r 325 NQLYRYTSLQSLFSVNMVALNGYKPERFTLI-GILKAFVAFREEVVVRRTKYLLNKARDRAHVLVGL 390 (910) Q Consensus 325 n~Lyk~T~Lq~sf~~N~~aL~~g~P~~l~Lk-~iL~~fi~hR~evi~rRt~~~L~ka~~R~HILeGL 390 (910) -+||+.|-.=.|-+.-+-|++||.|--|.|. +.++.+++-|+--.-|-+ .-++-.++.+||-|. T Consensus 6 G~~fr~tT~GESHG~alg~VIdG~PaGl~l~~edIq~eL~RRrpG~~r~~--t~R~E~D~veIlSGv 70 (369) T COG0082 6 GRLFRVTTFGESHGPALGAVIDGCPAGLELSEEDIQKELDRRRPGYSRGT--TMRKEKDEVEILSGV 70 (369) T ss_pred CCEEEEEEECCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCC--CCCCCCCCEEEEEEE T ss_conf 54179875005678735899935599970699999999974479988875--545678614880015 No 340 >TIGR01296 asd_B aspartate-semialdehyde dehydrogenase; InterPro: IPR005986 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see . Aspartate-semialdehyde dehydrogenase, the second enzyme in the aspartate pathway, converts aspartyl phosphate to aspartate-semialdehyde, the branch point intermediate between the lysine and threonine/methionine pathways. Based on sequence alignments, the aspartate-semialdehyde dehydrogenase family appears to have two distinct subgroups, one found in most bacteria (Gram-positve and Gram-negative), while the other is found primarily in organisms lacking peptidoglycan (archaea,fungi and some bacteria). Most studies have been performed on enzymes isolated from Gram-negative bacteria , , , . The N-terminal domain forms the active site and NADP-binding pocket, while C-terminal domain is primarily involved in hydrophobic intersubunit contacts. The catalytic mechanism involves the formation of a covalent thioester acyl-enzyme intermediate mediated through nucleophilic attack by an active site cysteine residue on the substrate aspartyl phosphate. Release of inorganic phosphate is followed by hydride transfer from NADPH to yield the product. The recently described archaeal structure suggests that the two subgroups of aspartate semi-aldehyde dehydrogenase share similar structures and have an identical catalytic mechanism, despite their relatively low sequence identity . Unlike the bacterial enzymes, the archaeal enzyme utilised both NAD and NADP as cofactor. This entry represents the subgroup of aspartate-semialdehyde dehydrogenase most commonly found in bacteria. Note that some bacteria, such as Chlamydia, contain the enzyme from the other subgroup (IPR005676 from INTERPRO) instead.; GO: 0004073 aspartate-semialdehyde dehydrogenase activity, 0009086 methionine biosynthetic process, 0009088 threonine biosynthetic process. Probab=20.71 E-value=30 Score=12.39 Aligned_cols=58 Identities=22% Similarity=0.335 Sum_probs=29.8 Q ss_pred CEEEEEEC------CCCCEEEEEECCCEEEEEECCCCCCCCCCCCCCEEEEECCC-----------CEEEEEEEECCC Q ss_conf 68999972------89964999945998999990105544515687388980899-----------879999983566 Q gi|254780182|r 840 ALVAVFPV------NDNDQIILVSDKGTLIRVPVNEIRIASRATKGVVIFSTAKD-----------ERVVSVERIRES 900 (910) Q Consensus 840 ~lv~~~~V------~~~DeIlliT~~G~iiR~~v~~I~~~gR~a~GV~i~~L~~~-----------D~Vv~va~i~~~ 900 (910) -.|++++| ....-|-+-+++.. +.+.++++.=++|.||.+++-..+ .-=++|.||..+ T Consensus 240 ~~vSaTCVRvPVf~GHS~S~~iEf~~d~---~~~e~~~E~Lk~ApGV~~~D~P~~~~Yp~P~~A~G~D~VfVGRIRkD 314 (350) T TIGR01296 240 LKVSATCVRVPVFTGHSESVNIEFEKDE---ISPEDVREVLKNAPGVVVIDDPSQNLYPTPLEAVGEDEVFVGRIRKD 314 (350) T ss_pred CCEEEEEEECCCHHCCHHHHHHHHCCCC---CCHHHHHHHHCCCCEEEEEECCCCCCCCCCHHEECCCCEEEEEEECC T ss_conf 4451578874111111232100111688---78889999734798679987688877888310102571567544447 No 341 >pfam09417 consensus Probab=20.70 E-value=38 Score=11.38 Aligned_cols=13 Identities=46% Similarity=0.552 Sum_probs=11.3 Q ss_pred CCCHHHHHHHHHH Q ss_conf 3699999999987 Q gi|254780182|r 448 YLSEVQTRAILEL 460 (910) Q Consensus 448 ~lSe~QA~AILdM 460 (910) .|||.|.++||++ T Consensus 108 R~tEe~~e~il~~ 120 (121) T pfam09417 108 RFTEEQIEEILEL 120 (121) T ss_pred CCCHHHHHHHHHH T ss_conf 5998999999975 No 342 >KOG0207 consensus Probab=20.65 E-value=38 Score=11.38 Aligned_cols=26 Identities=12% Similarity=0.123 Sum_probs=11.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99888778999999874069999998 Q gi|254780182|r 379 KARDRAHVLVGLAIAVANLDEVVRII 404 (910) Q Consensus 379 ka~~R~HILeGL~~Al~nIDeVI~iI 404 (910) +-..+.-+..|+.+++--+--+...+ T Consensus 233 ~w~~~fl~s~~~~~~v~~~~~~~~~~ 258 (951) T KOG0207 233 KWKRPFLISLGFSLPVSFAMIICPPL 258 (951) T ss_pred HCCHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 61168899999999999999986543 No 343 >TIGR00058 Hemerythrin hemerythrin family non-heme iron proteins; InterPro: IPR002063 The hemerythrin family is composed of hemerythrin proteins found in invertebrates, and a broader collection of bacterial and archaeal homologues. Hemerythrin is an oxygen-binding protein found in the vascular system and coelemic fluid, or in muscles (myohemerythrin) in invertebrates . Many of the lhomologous proteins found in prokaryotes are multi-domain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (IPR000160 from INTERPRO) and methyl-accepting chemotaxis protein (MCP) signalling domain (IPR004089 from INTERPRO). Most hemerythrins are oxygen-carriers with a bound non-haem iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. The prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium. Hemerythrins and myohemerythrins , are small proteins of about 110 to 129 amino acid residues that bind two iron atoms. They are left-twisted 4-alpha-helical bundles, which provide a hydrophobic pocket where dioxygen binds as a peroxo species, interacting with adjacent aliphatic side chains via van der Waals forces . In both hemerythrins and myohemerythrins, the active centre is a binuclear iron complex, bound directly to the protein via 7 amino acid side chains , 5 His, 1 Glu and 1 Asp . Ovohemerythrin , a yolk protein from the leech Theromyzon tessulatum seems to belong to this family of proteins, it may play a role in the detoxification of free iron after a blood meal . This entry represents the hemerythrin family of proteins.; GO: 0005344 oxygen transporter activity, 0005506 iron ion binding, 0006810 transport. Probab=20.63 E-value=37 Score=11.57 Aligned_cols=42 Identities=17% Similarity=0.230 Sum_probs=20.6 Q ss_pred CCHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 0299999999999--9999999999999999888778999999874 Q gi|254780182|r 352 FTLIGILKAFVAF--REEVVVRRTKYLLNKARDRAHVLVGLAIAVA 395 (910) Q Consensus 352 l~Lk~iL~~fi~h--R~evi~rRt~~~L~ka~~R~HILeGL~~Al~ 395 (910) -+|++++++...| -.|..=.+++|.=-..=+..| +||+-++. T Consensus 40 ~~Lk~l~~v~~~HF~~EE~~M~~a~Y~~~~~HK~~H--~~F~~~~~ 83 (116) T TIGR00058 40 TALKELIDVTVKHFLDEEAMMEAANYSDYDEHKKAH--DDFLAKLR 83 (116) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH--HHHHHHHC T ss_conf 678899999998668899999887227875358999--99999723 No 344 >PRK06321 replicative DNA helicase; Provisional Probab=20.56 E-value=39 Score=11.36 Aligned_cols=22 Identities=27% Similarity=0.406 Sum_probs=12.9 Q ss_pred HHHHHHHHHHHHHHHHHHCCCC Q ss_conf 8999999999899999840568 Q gi|254780182|r 494 RSRLLGIIKQELLSVKDELDTP 515 (910) Q Consensus 494 ~~~l~~iI~~EL~eik~kygd~ 515 (910) +......|-..|+.+.+.++-| T Consensus 360 r~~~i~~isr~lK~lAkel~vp 381 (472) T PRK06321 360 RQTEISEISRMLKNLARELNIP 381 (472) T ss_pred HHHHHHHHHHHHHHHHHHHCCC T ss_conf 9999999999999999997997 No 345 >TIGR02976 phageshock_pspB phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages . Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one .. Probab=20.53 E-value=39 Score=11.36 Aligned_cols=25 Identities=16% Similarity=0.226 Sum_probs=21.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCHH Q ss_conf 9999989999999998875304989 Q gi|254780182|r 471 DDIRNELNSLGIEIKECLDILSSRS 495 (910) Q Consensus 471 ~kl~~E~~eL~~~I~~l~~IL~s~~ 495 (910) ..|.+..+.|.++|+.||.||.++. T Consensus 45 ~~L~~~A~Rl~~Ri~tLE~iLd~e~ 69 (75) T TIGR02976 45 QELYAKADRLEERIDTLERILDAEH 69 (75) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 9999999899999999999872048 No 346 >pfam09942 DUF2174 Uncharacterized conserved protein (DUF2174). This domain, found in various hypothetical bacterial proteins, has no known function. Probab=20.52 E-value=31 Score=12.24 Aligned_cols=13 Identities=23% Similarity=0.818 Sum_probs=10.5 Q ss_pred HCCCCCCCCCCCC Q ss_conf 1156131478870 Q gi|254780182|r 105 SLRLLLIEGQGNF 117 (910) Q Consensus 105 ~~r~plidg~Gnf 117 (910) .|+|..||||||= T Consensus 25 ~~~fl~idG~GdP 37 (83) T pfam09942 25 AMNFLMVDGKGDP 37 (83) T ss_pred CCCEEEEEEECCC T ss_conf 9537987403599 No 347 >pfam02502 LacAB_rpiB Ribose/Galactose Isomerase. This family of proteins contains the sugar isomerase enzymes ribose 5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB). Probab=20.52 E-value=35 Score=11.76 Aligned_cols=40 Identities=23% Similarity=0.145 Sum_probs=19.7 Q ss_pred CCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 000245541663000299999999999999999999999999 Q gi|254780182|r 338 SVNMVALNGYKPERFTLIGILKAFVAFREEVVVRRTKYLLNK 379 (910) Q Consensus 338 ~~N~~aL~~g~P~~l~Lk~iL~~fi~hR~evi~rRt~~~L~k 379 (910) ++|.+||=...-..--.++|++.|++..++ --|-+-+++| T Consensus 99 naNVl~lG~r~~~~~~a~~iv~~fl~t~F~--ggRh~~Rv~k 138 (140) T pfam02502 99 NANVLCLGARVIGPELAKEIVDAFLATEFE--GGRHARRVDK 138 (140) T ss_pred CCCEEEECCCCCCHHHHHHHHHHHHCCCCC--CCCHHHHHHH T ss_conf 985899765324999999999999769988--8637999986 No 348 >PRK05469 peptidase T; Provisional Probab=20.51 E-value=39 Score=11.35 Aligned_cols=59 Identities=22% Similarity=0.353 Sum_probs=22.7 Q ss_pred CEECCCCC-----CCCCEECCCCCCCCHHCCCCCEEEHHHHCCCCC----CHHHHHHHHHHHHHCCCC Q ss_conf 33068988-----548503432273211016761010133178985----478999999887618776 Q gi|254780182|r 153 FRPNYDGS-----FQEPVVLCARYPNVLVNGGGGIAVGMATNIPTH----NLGEVVDGCVAVIDNPDI 211 (910) Q Consensus 153 ~~~n~D~~-----~~EP~vlP~~~P~lL~nG~~GIAvGmaTnippH----Nl~Ev~~a~~~~i~~p~~ 211 (910) .+.||||. ..+-+.=|+.||.|.---...|=+.=-|.+--- -+-++++++..+.++|++ T Consensus 94 v~~nYdG~di~l~~~~~~l~~~~~P~L~~~~G~~iI~sdGtTlLGADDKAGIA~Ime~~~~L~e~~~i 161 (405) T PRK05469 94 IIENYDGGDIALGIGNEVLSPAEFPELKNYIGQTLITTDGTTLLGADDKAGIAEIMTALEYLIAHPEI 161 (405) T ss_pred EEECCCCCCEEECCCCCEECHHHCCHHHHHCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHCCCC T ss_conf 97367887234068870765564813676159857967997112343388999999999999868999 No 349 >TIGR01992 PTS-IIBC-Tre PTS system, trehalose-specific IIBC component; InterPro: IPR011296 This entry represents the fused enzyme II B and C components of the trehalose-specific PTS sugar transporter system . Trehalose is converted to trehalose-6-phosphate in the process of translocation into the cell. These transporters lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr) . The exceptions to this rule are Staphylococci and Streptococci which contain their own A domain as a C-terminal fusion. This family is closely related to the sucrose transporting PTS IIBC enzymes described by the IIB component and the IIC component (IPR004719 from INTERPRO), respectively. In Escherichia coli, Bacillus subtilis and Pseudomonas fluorescens the presence of this gene is associated with the presence of trehalase which degrades T6P to glucose and glucose-6-P. Trehalose may also be transported (in Salmonella) via the mannose PTS or galactose permease systems , or (in Sinorhizobium, Thermococcus and Sulfolobus, for instance) by ABC transporters , , .; GO: 0015574 trehalose transmembrane transporter activity, 0015771 trehalose transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=20.32 E-value=39 Score=11.32 Aligned_cols=51 Identities=24% Similarity=0.517 Sum_probs=37.2 Q ss_pred CCHHHHHHHH----HHHHHCCCCCHHHHHH--HCCCCCCCCCC---CCCCHHHHHHHHHHC Q ss_conf 5478999999----8876187768888886--34586688744---344758899998701 Q gi|254780182|r 193 HNLGEVVDGC----VAVIDNPDIDLDALME--IIRGPDFPTGA---VILGRTGIKNAYATG 244 (910) Q Consensus 193 HNl~Ev~~a~----~~~i~~p~~~~~eL~~--~i~GPDFPTGG---~I~~~~~i~~~y~tG 244 (910) -|+..+..|+ .+|.|+.++..++|=+ .+|| -|-|+| +|+|.....+.|+.= T Consensus 15 eNi~~atHCvTRLRfvL~D~~~v~~~~l~~~~~VKG-~F~~~GQFQVvIGpg~V~~~Y~~l 74 (489) T TIGR01992 15 ENIEAATHCVTRLRFVLKDPSKVDVEALEQIDLVKG-SFTTAGQFQVVIGPGDVEKVYAEL 74 (489) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCC-EEECCCEEEEEECCCCHHHHHHHH T ss_conf 016687568888888616813378567636882244-142485279986379879999999 No 350 >PRK10703 DNA-binding transcriptional repressor PurR; Provisional Probab=20.31 E-value=39 Score=11.32 Aligned_cols=46 Identities=4% Similarity=-0.021 Sum_probs=30.9 Q ss_pred HHHHCCCCCCCCCCH-HHHHHHHHHHHCCCCCCCCEE----EEHHHHHHHHC Q ss_conf 863137540008973-678999999987899999811----34042556643 Q gi|254780182|r 37 ILGRAIPDLRDGLKP-VHRRILFGMMQMGVEWNKKYV----KCARISGEVMG 83 (910) Q Consensus 37 I~~RAlPd~rDGlKp-v~Rrily~m~~~~~~~~~~~~----K~a~ivg~v~g 83 (910) -|||+|=+- .+..| ...||+=++.+||..|+..-+ +..+.+|-++. T Consensus 17 TVSrvLn~~-~~Vs~~Tr~rV~~aa~eLgY~pn~~Ar~L~~~~s~~Igviv~ 67 (335) T PRK10703 17 TVSHVINKT-RFVAEETRNAVWAAIKELHYSPSAVARSLKVNHTKSIGLLAT 67 (335) T ss_pred HHHHHHCCC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCCEEEEEEC T ss_conf 999996896-998999999999999982999787787541177745999954 No 351 >COG5184 ATS1 Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell division and chromosome partitioning / Cytoskeleton] Probab=20.29 E-value=39 Score=11.32 Aligned_cols=18 Identities=11% Similarity=0.224 Sum_probs=8.0 Q ss_pred ECCCCCEEEEEECCCEEE Q ss_conf 618982699993698599 Q gi|254780182|r 689 TCTQENDILLTTKLGQCV 706 (910) Q Consensus 689 ~~~~~~~Iil~T~~G~~l 706 (910) ++.+.++++++|+.|++- T Consensus 236 la~G~dh~i~lt~~G~vy 253 (476) T COG5184 236 LAAGADHLIALTNEGKVY 253 (476) T ss_pred ECCCCCEEEEEECCCCEE T ss_conf 205885399993598288 No 352 >PRK00574 gltX glutamyl-tRNA synthetase; Reviewed Probab=20.27 E-value=39 Score=11.31 Aligned_cols=17 Identities=18% Similarity=0.602 Sum_probs=12.3 Q ss_pred HHHHHHHHHHCCCCCCC Q ss_conf 78999999987899999 Q gi|254780182|r 53 HRRILFGMMQMGVEWNK 69 (910) Q Consensus 53 ~Rrily~m~~~~~~~~~ 69 (910) -..|+=+|..+|+.+|- T Consensus 56 ~~~I~~~L~wlgl~~DE 72 (489) T PRK00574 56 EESQLENLKWLGIDWDE 72 (489) T ss_pred HHHHHHHHHHCCCCCCC T ss_conf 99999999987988877 No 353 >PRK10334 mechanosensitive channel MscS; Provisional Probab=20.26 E-value=25 Score=13.05 Aligned_cols=35 Identities=31% Similarity=0.547 Sum_probs=28.1 Q ss_pred CCCHHCCCCCEEEHHHHCCCCCCHHHHHHHHHHHHHCC Q ss_conf 32110167610101331789854789999998876187 Q gi|254780182|r 172 PNVLVNGGGGIAVGMATNIPTHNLGEVVDGCVAVIDNP 209 (910) Q Consensus 172 P~lL~nG~~GIAvGmaTnippHNl~Ev~~a~~~~i~~p 209 (910) |.+-.=|+-|+|+|+|-. -.|+.++.++.-++++| T Consensus 95 sl~A~~G~~GlaIGlAlQ---~~lsN~~sGi~Il~~rp 129 (285) T PRK10334 95 SVIAVLGAAGLAVGLALQ---GSLSNLAAGVLLVMFRP 129 (285) T ss_pred HHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHCCCC T ss_conf 999999999999999999---99999998758640388 No 354 >KOG2230 consensus Probab=20.22 E-value=39 Score=11.31 Aligned_cols=39 Identities=21% Similarity=0.375 Sum_probs=18.9 Q ss_pred CCCCCCHHHHHHHHH--HHHHCCCCCHHHHHHHCCCCCCCCCCCC Q ss_conf 789854789999998--8761877688888863458668874434 Q gi|254780182|r 189 NIPTHNLGEVVDGCV--AVIDNPDIDLDALMEIIRGPDFPTGAVI 231 (910) Q Consensus 189 nippHNl~Ev~~a~~--~~i~~p~~~~~eL~~~i~GPDFPTGG~I 231 (910) +.||--..++-.+-| .+|+...++- ..==||-|||-||= T Consensus 161 svPPdC~p~iyhGECH~NfiRK~Q~SF----sWDWGPsfPt~GI~ 201 (867) T KOG2230 161 SLPPDCNPDIYHGECHQNFIRKAQYSF----AWDWGPSFPTVGIP 201 (867) T ss_pred CCCCCCCCHHHCCCHHHHHHHHHHCCE----ECCCCCCCCCCCCC T ss_conf 799898950011604788998754004----11347788667887 No 355 >PRK06223 malate dehydrogenase; Reviewed Probab=20.19 E-value=39 Score=11.30 Aligned_cols=35 Identities=14% Similarity=0.240 Sum_probs=26.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999878999988879999998999999999887530 Q gi|254780182|r 454 TRAILELRLARLTGLGRDDIRNELNSLGIEIKECLDIL 491 (910) Q Consensus 454 A~AILdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL 491 (910) .+.|+++ .|+..|++++++=.+.|++.++.++++| T Consensus 277 i~~i~~l---~L~~~E~~~l~~sa~~i~~~~~~vk~ll 311 (312) T PRK06223 277 VEKVIEI---ELTEDEKEAFDKSVEAVKKLCEALKSIL 311 (312) T ss_pred EEEECCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf 5998389---9999999999999999999999998458 No 356 >KOG1891 consensus Probab=20.12 E-value=38 Score=11.39 Aligned_cols=25 Identities=32% Similarity=0.555 Sum_probs=13.7 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCEEE Q ss_conf 9999999899999840568833100 Q gi|254780182|r 497 LLGIIKQELLSVKDELDTPRRTRIV 521 (910) Q Consensus 497 l~~iI~~EL~eik~kygd~RRT~I~ 521 (910) +.++.++||..|.++|-.=||..|. T Consensus 233 l~~LfkqEl~~IVk~YErYRrALil 257 (271) T KOG1891 233 LMKLFKQELFDIVKKYERYRRALIL 257 (271) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999999999998 No 357 >PRK12584 flagellin A; Reviewed Probab=20.09 E-value=39 Score=11.29 Aligned_cols=62 Identities=19% Similarity=0.210 Sum_probs=37.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 89999998740699999986189978987877631269788999997402211122234452369999999998789999 Q gi|254780182|r 386 VLVGLAIAVANLDEVVRIIRFSPNPETARRELMQRSWNASDIKDLIDLIDDSSYTIGSDGTMYLSEVQTRAILELRLARL 465 (910) Q Consensus 386 ILeGL~~Al~nIDeVI~iIR~S~d~~eAk~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~lSe~QA~AILdMrL~rL 465 (910) -+.||-.|..|.-.-|.+++.++ -.|-+ . ..||. |+|.| T Consensus 57 QI~gL~qA~rNa~DgiSliQTAE------GAL~e--------------------------------v--~~iLq-RmREL 95 (510) T PRK12584 57 QASSLGQAIANTNDGMGIIQVAD------KAMDE--------------------------------Q--LKILD-TVKVK 95 (510) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHHHH--------------------------------H--HHHHH-HHHHH T ss_conf 99889999884887999999999------99999--------------------------------9--99999-99999 Q ss_pred ---------HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf ---------88879999998999999999887 Q gi|254780182|r 466 ---------TGLGRDDIRNELNSLGIEIKECL 488 (910) Q Consensus 466 ---------t~LE~~kl~~E~~eL~~~I~~l~ 488 (910) +.-+|.-|++|+++|..+|.++- T Consensus 96 AVQAAN~tns~~dR~aiQ~Ei~qL~~EIdRIa 127 (510) T PRK12584 96 ATQAAQDGQTTESRKAIQSDIVRLIQGLDNIG 127 (510) T ss_pred HHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99860388988899999999999999985662 No 358 >PRK11706 TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional Probab=20.06 E-value=39 Score=11.28 Aligned_cols=21 Identities=14% Similarity=0.393 Sum_probs=14.1 Q ss_pred HHHHHHHHHCCCCCHHHHHHH Q ss_conf 999999987166501445873 Q gi|254780182|r 281 LEKIAELVREKRIVDIADLRD 301 (910) Q Consensus 281 ie~Ia~lv~~~ki~gI~dirD 301 (910) +++|.++.++..|.-|.|-.. T Consensus 135 ~~~I~~iak~~~i~vIEDaA~ 155 (375) T PRK11706 135 MDTIMALAKKHNLFVVEDAAQ 155 (375) T ss_pred HHHHHHHHHHCCCEEEECCCC T ss_conf 899999885379089834400 No 359 >pfam08820 DUF1803 Domain of unknown function (DUF1803). This small domain is found in one or two copies in proteins from bacteria. The function of this domain is unknown. Probab=20.02 E-value=39 Score=11.27 Aligned_cols=11 Identities=18% Similarity=0.395 Sum_probs=4.9 Q ss_pred HHHHHHHCCCC Q ss_conf 99999840568 Q gi|254780182|r 505 LLSVKDELDTP 515 (910) Q Consensus 505 L~eik~kygd~ 515 (910) |+++|+.|.+. T Consensus 31 LR~iKk~f~~q 41 (94) T pfam08820 31 LRQIKKDFADQ 41 (94) T ss_pred HHHHHHHCCCC T ss_conf 99999876540 No 360 >PRK09848 glucuronide transporter; Provisional Probab=20.01 E-value=39 Score=11.27 Aligned_cols=31 Identities=13% Similarity=0.080 Sum_probs=18.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9878999988879999998999999999887 Q gi|254780182|r 458 LELRLARLTGLGRDDIRNELNSLGIEIKECL 488 (910) Q Consensus 458 LdMrL~rLt~LE~~kl~~E~~eL~~~I~~l~ 488 (910) +=|..++||+=...++++|+++-++.-+++. T Consensus 422 ~~~~~Y~Lt~~~~~eI~~eL~~rr~~~~~~~ 452 (457) T PRK09848 422 VIIWFYPLTDKKFKEIVVEIDNRKKVQQQLI 452 (457) T ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9998615889999999999999999876533 Done!