Query gi|254780683|ref|YP_003065096.1| lipoprotein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 84 No_of_seqs 112 out of 5508 Neff 6.5 Searched_HMMs 39220 Date Tue May 31 15:06:25 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780683.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK11637 hypothetical protein; 100.0 3.5E-33 9E-38 195.7 8.8 80 1-81 325-404 (404) 2 PRK10871 nlpD lipoprotein NlpD 100.0 3.8E-31 9.7E-36 185.0 9.3 81 1-82 294-374 (374) 3 PRK11649 hypothetical protein; 100.0 6.9E-29 1.8E-33 173.1 8.3 77 1-78 312-388 (418) 4 COG4942 Membrane-bound metallo 99.9 2.5E-27 6.4E-32 164.8 3.8 80 1-81 341-420 (420) 5 COG0739 NlpD Membrane proteins 99.9 1.7E-25 4.4E-30 155.1 8.8 82 1-82 183-267 (277) 6 pfam01551 Peptidase_M23 Peptid 99.9 6.1E-23 1.5E-27 141.7 7.9 74 1-75 23-96 (96) 7 PRK06148 hypothetical protein; 98.8 1.7E-08 4.3E-13 65.3 6.3 59 10-68 474-541 (1015) 8 PRK06149 hypothetical protein; 96.4 0.0046 1.2E-07 36.6 4.0 54 10-70 455-508 (972) 9 TIGR01843 type_I_hlyD type I s 90.6 0.21 5.5E-06 27.8 2.7 39 12-55 40-78 (434) 10 pfam00529 HlyD HlyD family sec 88.8 0.2 5.1E-06 28.0 1.4 26 29-54 11-36 (304) 11 TIGR02971 heterocyst_DevB ABC 87.3 0.26 6.7E-06 27.3 1.2 42 13-54 11-53 (363) 12 cd00210 PTS_IIA_glc PTS_IIA, P 86.9 0.83 2.1E-05 24.7 3.6 42 12-54 52-104 (124) 13 TIGR01349 PDHac_trf_mito pyruv 86.8 0.6 1.5E-05 25.4 2.8 38 29-70 14-51 (584) 14 pfam00358 PTS_EIIA_1 phosphoen 86.6 0.92 2.4E-05 24.5 3.7 42 12-54 57-109 (133) 15 PRK09578 periplasmic multidrug 84.6 0.48 1.2E-05 25.9 1.5 26 29-54 72-97 (385) 16 PRK03598 hypothetical protein; 84.5 0.45 1.2E-05 26.1 1.3 24 31-54 54-77 (331) 17 PRK09439 glucose-specific PTS 84.4 1.5 3.7E-05 23.4 3.8 42 12-54 74-126 (169) 18 PRK11556 multidrug efflux syst 84.2 0.5 1.3E-05 25.9 1.4 26 29-54 96-121 (415) 19 PRK11578 macrolide transporter 82.5 0.66 1.7E-05 25.2 1.5 23 31-53 49-71 (347) 20 COG0511 AccB Biotin carboxyl c 82.1 1 2.6E-05 24.2 2.3 44 33-76 83-132 (140) 21 PRK09859 multidrug efflux syst 81.7 0.71 1.8E-05 25.1 1.4 23 31-53 72-94 (385) 22 PRK06302 acetyl-CoA carboxylas 81.7 0.87 2.2E-05 24.6 1.8 23 32-54 98-120 (155) 23 cd06850 biotinyl_domain The bi 81.7 0.74 1.9E-05 25.0 1.5 25 31-55 10-34 (67) 24 PRK10476 multidrug resistance 80.7 0.78 2E-05 24.8 1.3 26 29-54 59-84 (348) 25 PRK07051 hypothetical protein; 78.2 1.3 3.4E-05 23.6 1.9 45 32-76 22-72 (80) 26 TIGR01945 rnfC electron transp 76.5 1 2.6E-05 24.2 0.9 21 33-53 44-64 (444) 27 TIGR01995 PTS-II-ABC-beta PTS 76.1 1.1 2.7E-05 24.1 0.9 42 12-54 563-615 (660) 28 cd06252 M14_ASTE_ASPA_like_2 A 75.5 4.4 0.00011 20.9 3.9 40 15-54 235-277 (316) 29 cd06254 M14_ASTE_ASPA_like_4 A 74.4 2.1 5.4E-05 22.6 2.0 25 30-54 232-256 (288) 30 PRK11892 pyruvate dehydrogenas 74.0 1.7 4.4E-05 23.0 1.5 27 29-55 17-43 (464) 31 PRK05352 Na(+)-translocating N 73.7 1.7 4.3E-05 23.0 1.4 22 33-54 43-64 (448) 32 PRK08225 acetyl-CoA carboxylas 73.2 1.8 4.6E-05 22.9 1.4 24 31-54 12-35 (70) 33 TIGR03309 matur_yqeB selenium- 73.1 5.8 0.00015 20.2 4.0 29 27-55 167-198 (256) 34 PRK10255 N-acetyl glucosamine 72.7 5.8 0.00015 20.2 3.9 42 12-54 552-604 (648) 35 PRK05889 putative acetyl-CoA c 72.6 1.9 4.8E-05 22.8 1.4 21 33-53 15-35 (71) 36 TIGR00830 PTBA PTS system, glu 72.5 1.9 4.9E-05 22.8 1.5 21 34-54 92-112 (129) 37 cd06663 Biotinyl_lipoyl_domain 72.5 2 5E-05 22.7 1.5 27 29-55 14-40 (73) 38 cd06255 M14_ASTE_ASPA_like_5 A 72.2 2.3 5.9E-05 22.3 1.8 27 28-54 238-264 (293) 39 PRK09824 beta-glucoside-specif 71.0 7 0.00018 19.8 4.0 42 12-54 530-582 (625) 40 PRK10559 p-hydroxybenzoic acid 69.8 2.5 6.3E-05 22.2 1.5 19 33-51 60-78 (310) 41 cd06253 M14_ASTE_ASPA_like_3 A 69.7 5.7 0.00015 20.3 3.4 33 22-54 227-262 (298) 42 PRK05305 phosphatidylserine de 67.5 6.7 0.00017 19.9 3.3 40 14-53 133-179 (214) 43 TIGR01043 ATP_syn_A_arch ATP s 67.3 3.2 8.2E-05 21.6 1.7 23 34-56 121-143 (584) 44 pfam06898 YqfD Putative stage 67.0 7.2 0.00018 19.7 3.4 41 17-57 192-235 (383) 45 cd06849 lipoyl_domain Lipoyl d 66.1 3.6 9.2E-05 21.3 1.7 27 29-55 15-41 (74) 46 COG2190 NagE Phosphotransferas 64.7 11 0.00028 18.8 4.0 40 13-53 60-110 (156) 47 cd06251 M14_ASTE_ASPA_like_1 A 64.7 5.3 0.00014 20.4 2.4 30 25-54 220-252 (287) 48 PRK09282 pyruvate carboxylase 64.3 3.4 8.6E-05 21.5 1.3 22 32-53 523-544 (580) 49 pfam00364 Biotin_lipoyl Biotin 63.8 4 0.0001 21.1 1.6 23 33-55 18-40 (73) 50 TIGR01348 PDHac_trf_long pyruv 63.4 3.7 9.5E-05 21.3 1.4 24 31-54 54-77 (655) 51 pfam01333 Apocytochr_F_C Apocy 61.6 9.9 0.00025 19.0 3.3 40 13-53 23-65 (118) 52 pfam05896 NQRA Na(+)-transloca 61.3 3.3 8.5E-05 21.5 0.8 22 33-54 42-63 (257) 53 PRK05035 electron transport co 61.2 4.2 0.00011 21.0 1.4 21 33-53 56-76 (725) 54 PRK05641 putative acetyl-CoA c 60.9 4.5 0.00012 20.8 1.5 23 32-54 91-113 (148) 55 PTZ00144 dihydrolipoamide succ 60.0 5.4 0.00014 20.4 1.7 27 29-55 72-98 (430) 56 TIGR01394 TypA_BipA GTP-bindin 59.7 4.8 0.00012 20.6 1.4 41 14-54 495-540 (609) 57 COG0845 AcrA Membrane-fusion p 57.7 5.5 0.00014 20.4 1.4 25 30-54 76-100 (372) 58 TIGR02644 Y_phosphoryl pyrimid 57.1 8 0.0002 19.5 2.2 21 34-54 386-406 (425) 59 COG1726 NqrA Na+-transporting 56.9 15 0.00039 18.0 3.6 27 28-54 36-63 (447) 60 TIGR02013 rpoB DNA-directed RN 56.1 5.5 0.00014 20.4 1.2 22 33-54 851-872 (1449) 61 TIGR01347 sucB 2-oxoglutarate 56.0 6.3 0.00016 20.1 1.5 40 14-53 33-76 (435) 62 PRK12999 pyruvate carboxylase; 55.3 6.1 0.00015 20.1 1.3 21 33-53 1090-1110(1147) 63 pfam07831 PYNP_C Pyrimidine nu 54.6 7 0.00018 19.8 1.5 21 34-54 36-56 (75) 64 PRK06549 acetyl-CoA carboxylas 54.2 6.8 0.00017 19.9 1.4 24 31-54 74-97 (132) 65 cd06250 M14_PaAOTO_like An unc 49.8 9.5 0.00024 19.1 1.6 32 23-54 288-322 (359) 66 COG0508 AceF Pyruvate/2-oxoglu 49.5 11 0.00028 18.8 1.8 26 30-55 55-80 (404) 67 cd01134 V_A-ATPase_A V/A-type 49.0 11 0.00028 18.8 1.8 22 34-55 53-74 (369) 68 COG4656 RnfC Predicted NADH:ub 48.6 7.5 0.00019 19.6 0.9 21 33-53 46-66 (529) 69 COG1155 NtpA Archaeal/vacuolar 48.6 11 0.00028 18.8 1.8 21 35-55 121-141 (588) 70 PRK03934 phosphatidylserine de 48.2 9.6 0.00025 19.1 1.4 15 39-53 220-234 (267) 71 pfam02666 PS_Dcarbxylase Phosp 45.8 12 0.0003 18.6 1.6 39 15-53 124-169 (201) 72 PRK11856 branched-chain alpha- 45.7 12 0.00031 18.5 1.6 21 31-51 55-75 (324) 73 PRK05704 dihydrolipoamide succ 45.0 17 0.00042 17.8 2.2 26 30-55 55-80 (406) 74 COG3608 Predicted deacylase [G 44.3 11 0.00028 18.8 1.2 26 30-55 265-290 (331) 75 KOG0557 consensus 44.3 17 0.00045 17.7 2.3 35 32-70 56-90 (470) 76 cd05830 Sortase_D_5 Sortase D 42.8 20 0.0005 17.4 2.3 36 5-42 36-72 (137) 77 TIGR01846 type_I_sec_HlyB type 39.8 18 0.00045 17.7 1.7 18 40-57 486-503 (703) 78 TIGR02876 spore_yqfD sporulati 38.7 30 0.00077 16.5 2.7 42 12-55 191-240 (406) 79 PRK11855 dihydrolipoamide acet 38.6 23 0.00059 17.1 2.2 22 31-52 171-192 (549) 80 COG1038 PycA Pyruvate carboxyl 35.4 15 0.00038 18.1 0.8 21 33-53 1092-1112(1149) 81 TIGR02211 LolD_lipo_ex lipopro 35.4 9 0.00023 19.2 -0.4 24 40-63 26-49 (221) 82 COG1566 EmrA Multidrug resista 35.1 20 0.0005 17.4 1.3 30 15-50 209-238 (352) 83 PRK06748 hypothetical protein; 34.3 41 0.001 15.7 3.7 45 10-54 28-77 (84) 84 COG4770 Acetyl/propionyl-CoA c 33.1 23 0.00058 17.1 1.4 21 33-53 588-608 (645) 85 TIGR02712 urea_carbox urea car 32.7 43 0.0011 15.6 2.8 36 19-54 1152-1191(1226) 86 PRK09783 copper/silver efflux 32.4 24 0.00061 17.0 1.4 31 24-54 207-241 (407) 87 PRK04350 thymidine phosphoryla 31.7 26 0.00065 16.8 1.5 21 34-54 455-475 (502) 88 PRK05820 deoA thymidine phosph 31.4 26 0.00067 16.8 1.5 22 34-55 385-406 (440) 89 PRK12784 hypothetical protein; 30.9 47 0.0012 15.4 3.7 45 10-54 28-77 (84) 90 TIGR02645 ARCH_P_rylase putati 30.8 22 0.00057 17.1 1.0 37 17-53 422-476 (499) 91 TIGR01235 pyruv_carbox pyruvat 30.7 19 0.00048 17.6 0.6 45 33-79 1113-1165(1169) 92 TIGR00078 nadC nicotinate-nucl 30.4 30 0.00077 16.5 1.6 21 34-54 64-84 (276) 93 PRK02693 apocytochrome f; Revi 30.3 48 0.0012 15.4 2.9 40 13-53 217-259 (312) 94 PRK06078 pyrimidine-nucleoside 30.2 29 0.00073 16.6 1.5 21 34-54 380-400 (434) 95 TIGR00653 GlnA glutamine synth 30.1 39 0.00099 15.9 2.2 61 10-73 209-294 (486) 96 PRK10218 GTP-binding protein; 29.7 37 0.00094 16.0 2.0 41 14-54 485-530 (607) 97 TIGR02386 rpoC_TIGR DNA-direct 29.6 29 0.00074 16.5 1.5 18 34-51 1191-1208(1552) 98 PRK04192 V-type ATP synthase s 29.5 30 0.00076 16.5 1.5 22 35-56 123-144 (585) 99 TIGR02770 nickel_nikD nickel i 28.9 37 0.00095 16.0 1.9 36 41-76 8-57 (239) 100 PRK11854 aceF dihydrolipoamide 28.7 35 0.00089 16.1 1.7 23 31-53 157-179 (630) 101 cd06165 Sortase_A_1 Sortase A 28.6 52 0.0013 15.2 2.6 59 5-77 34-93 (127) 102 KOG0559 consensus 28.4 26 0.00067 16.8 1.1 23 31-53 126-148 (457) 103 TIGR01936 nqrA NADH:ubiquinone 27.2 19 0.00048 17.5 0.2 43 28-72 36-85 (466) 104 TIGR01448 recD_rel helicase, R 26.1 4.1 0.0001 21.0 -3.4 52 1-57 367-418 (769) 105 TIGR03327 AMP_phos AMP phospho 25.6 38 0.00098 15.9 1.5 21 34-54 452-472 (500) 106 pfam02749 QRPTase_N Quinolinat 25.2 39 0.00099 15.9 1.5 20 34-53 49-68 (88) 107 TIGR01108 oadA oxaloacetate de 25.2 26 0.00067 16.8 0.6 46 31-78 562-615 (616) 108 TIGR02203 MsbA_lipidA lipid A 24.5 46 0.0012 15.5 1.7 30 24-57 366-400 (603) 109 COG0444 DppD ABC-type dipeptid 24.5 50 0.0013 15.3 1.9 17 40-56 26-42 (316) 110 cd03237 ABC_RNaseL_inhibitor_d 24.1 45 0.0012 15.5 1.6 28 27-56 9-36 (246) 111 TIGR00998 8a0101 efflux pump m 22.7 30 0.00076 16.5 0.5 30 16-51 246-275 (379) 112 cd04493 BRCA2DBD_OB1 BRCA2DBD_ 22.6 68 0.0017 14.6 5.6 59 13-72 20-90 (100) 113 PRK00044 psd phosphatidylserin 22.6 45 0.0011 15.5 1.4 14 41-54 239-254 (291) 114 COG1217 TypA Predicted membran 22.4 62 0.0016 14.8 2.0 45 10-54 480-529 (603) 115 COG0213 DeoA Thymidine phospho 22.3 59 0.0015 14.9 1.9 20 34-53 381-400 (435) 116 PRK03140 phosphatidylserine de 21.9 44 0.0011 15.6 1.2 18 36-53 207-224 (259) 117 KOG0369 consensus 21.9 34 0.00088 16.2 0.6 20 33-52 1119-1138(1176) 118 KOG2419 consensus 21.5 61 0.0016 14.8 1.9 21 34-54 898-918 (975) 119 CHL00117 rpoC2 RNA polymerase 21.2 55 0.0014 15.1 1.6 21 33-53 408-428 (1350) 120 PRK00624 glycine cleavage syst 20.7 58 0.0015 14.9 1.6 22 36-57 39-60 (113) No 1 >PRK11637 hypothetical protein; Provisional Probab=100.00 E-value=3.5e-33 Score=195.73 Aligned_cols=80 Identities=28% Similarity=0.497 Sum_probs=77.4 Q ss_pred CEEEECCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEEECCEECCHHHHHH Q ss_conf 59996069865511999998998899841156344112002203124899805788888569999978689805269875 Q gi|254780683|r 1 MVIYVGNDLVELGNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNAIAMDPIKFLE 80 (84) Q Consensus 1 VVv~~g~~~~~~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg~~~g~hLhfei~~~g~~vdP~~~l~ 80 (84) .|+|++| +++||++|||+||+||+|+|+||+++.|++||.|++||+||+||+||.+++||||||||++|+++||++||. T Consensus 325 ~Vv~a~~-~~gyG~~ViIdHG~g~~TlYah~s~l~v~~Gq~V~~Gq~Ig~vG~tG~s~g~~LhFEir~~g~~vnP~~wL~ 403 (404) T PRK11637 325 RVILADW-LQGYGLVVVVEHGKGDMSLYGYNQSALVSVGAQVRAGQPIALVGSSGGQGRPSLYFEIRRQGQAVNPQPWLG 403 (404) T ss_pred EEEEEEE-CCCCCCEEEEECCCCCEEECCCCCCCCCCCCCEECCCCEEEEEECCCCCCCCEEEEEEEECCEEECHHHHHC T ss_conf 9999114-088885799986994657152889588899799899996987326899999658999998999847588628 Q ss_pred C Q ss_conf 0 Q gi|254780683|r 81 E 81 (84) Q Consensus 81 ~ 81 (84) . T Consensus 404 r 404 (404) T PRK11637 404 R 404 (404) T ss_pred C T ss_conf 2 No 2 >PRK10871 nlpD lipoprotein NlpD; Provisional Probab=99.97 E-value=3.8e-31 Score=184.99 Aligned_cols=81 Identities=35% Similarity=0.714 Sum_probs=78.0 Q ss_pred CEEEECCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEEECCEECCHHHHHH Q ss_conf 59996069865511999998998899841156344112002203124899805788888569999978689805269875 Q gi|254780683|r 1 MVIYVGNDLVELGNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNAIAMDPIKFLE 80 (84) Q Consensus 1 VVv~~g~~~~~~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg~~~g~hLhfei~~~g~~vdP~~~l~ 80 (84) .|+|+|+.+++|||+|||+|+++|.|.|+|++++.|++||.|++||.||++|++|.+. +|||||||++|+++||+.||+ T Consensus 294 ~VvyaG~~l~gyGnliiIkH~~~~lsaYahn~~~lVkeg~~V~~Gq~Ia~~G~tg~~~-~~LHFEiR~~g~pvdP~~yLP 372 (374) T PRK10871 294 RVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVKAGQKIATMGSTGTSS-TRLHFEIRYKGKSVNPLRYLP 372 (374) T ss_pred EEEEECCCCCCCCEEEEEECCCCCEEEEECCCCCCCCCCCEECCCCEEEEECCCCCCC-CEEEEEEEECCEECCHHHHCC T ss_conf 8999247878776289998499867861676626678889988999898643789998-308999977998669489764 Q ss_pred CC Q ss_conf 03 Q gi|254780683|r 81 EK 82 (84) Q Consensus 81 ~k 82 (84) +| T Consensus 373 kR 374 (374) T PRK10871 373 QR 374 (374) T ss_pred CC T ss_conf 99 No 3 >PRK11649 hypothetical protein; Provisional Probab=99.96 E-value=6.9e-29 Score=173.07 Aligned_cols=77 Identities=35% Similarity=0.580 Sum_probs=74.4 Q ss_pred CEEEECCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEEECCEECCHHHH Q ss_conf 599960698655119999989988998411563441120022031248998057888885699999786898052698 Q gi|254780683|r 1 MVIYVGNDLVELGNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNAIAMDPIKF 78 (84) Q Consensus 1 VVv~~g~~~~~~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg~~~g~hLhfei~~~g~~vdP~~~ 78 (84) +|+++|+. .+|||+|+|+|+++|.|.|+||+++.|+.||.|++||+||++|+||.++|||||||+|.+|+++||+.. T Consensus 312 ~V~~ag~~-~~yG~~V~I~H~~~~~T~Y~HLs~~~V~~Gq~V~~Gq~Ig~vGsTG~sTGPHLHyEv~~ng~~vnPl~v 388 (418) T PRK11649 312 EVVVAKRS-GAAGNYVAIRHGRQYTTRYMHLRKLLVKPGQKVKRGDRIALSGNTGRSTGPHLHYEVWINQQAVNPLTA 388 (418) T ss_pred EEEEEEEC-CCCCCEEEEECCCCEEEEEECCCCCCCCCCCEECCCCEEEEECCCCCCCCCEEEEEEEECCEECCCCCC T ss_conf 99997881-899977999819930999617684777994999989989802688378897338999999979599534 No 4 >COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning] Probab=99.93 E-value=2.5e-27 Score=164.81 Aligned_cols=80 Identities=28% Similarity=0.502 Sum_probs=76.9 Q ss_pred CEEEECCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEEECCEECCHHHHHH Q ss_conf 59996069865511999998998899841156344112002203124899805788888569999978689805269875 Q gi|254780683|r 1 MVIYVGNDLVELGNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNAIAMDPIKFLE 80 (84) Q Consensus 1 VVv~~g~~~~~~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg~~~g~hLhfei~~~g~~vdP~~~l~ 80 (84) .|+||+| +.+||.+|||+||+||.++|++|++|.|++|+.|.+||+||.||++|....|-||||||++|+|+||.+||. T Consensus 341 ~VvyA~~-l~GYG~vvIldhG~gy~slyg~~~~i~v~~G~~V~AGepIa~~G~sgg~~~p~LYfEiR~~G~pvnP~pW~~ 419 (420) T COG4942 341 RVVYADW-LRGYGLVVILDHGGGYHSLYGGNQSILVNPGQFVKAGEPIALVGSSGGQGRPALYFEIRRQGQPVNPQPWLR 419 (420) T ss_pred EEEECHH-HCCCCEEEEEECCCCCEEEECCCCEEEECCCCEEECCCCHHHCCCCCCCCCCCHHHHHHHCCCCCCCHHHHC T ss_conf 6995433-256756999974885378861664221068977556971532267789998410021460597479512220 Q ss_pred C Q ss_conf 0 Q gi|254780683|r 81 E 81 (84) Q Consensus 81 ~ 81 (84) . T Consensus 420 ~ 420 (420) T COG4942 420 R 420 (420) T ss_pred C T ss_conf 9 No 5 >COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane] Probab=99.92 E-value=1.7e-25 Score=155.12 Aligned_cols=82 Identities=39% Similarity=0.771 Sum_probs=77.1 Q ss_pred CEEEECCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEEECCE---ECCHHH Q ss_conf 59996069865511999998998899841156344112002203124899805788888569999978689---805269 Q gi|254780683|r 1 MVIYVGNDLVELGNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNAI---AMDPIK 77 (84) Q Consensus 1 VVv~~g~~~~~~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg~~~g~hLhfei~~~g~---~vdP~~ 77 (84) +|+++++...+|||+|+|+|++|+.|+|+||+++.|+.||.|++||.||++|+||.+++||||||++++++ ++||.. T Consensus 183 ~V~~~~~~~~~yGn~v~i~H~~g~~t~Y~Hl~~~~V~~G~~V~~G~~Ig~~G~tG~stgphLHfev~~~g~~~~~~~p~~ 262 (277) T COG0739 183 VVVFAGNGGWGYGNLVIIKHGDGYVTVYAHLSSILVKEGQKVKAGQVIGYVGSTGRSTGPHLHFEVRKNGKLVPPVNPAR 262 (277) T ss_pred EEEEECCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCCEEECCCEEEECCCCCCCCCCEEEEEEEECCCCCCCCCHHH T ss_conf 89997047666770899974896588996065013158978846978997257677579758898875870367578556 Q ss_pred HHHCC Q ss_conf 87503 Q gi|254780683|r 78 FLEEK 82 (84) Q Consensus 78 ~l~~k 82 (84) ||..+ T Consensus 263 ~l~~~ 267 (277) T COG0739 263 YLPKG 267 (277) T ss_pred HCCCC T ss_conf 22444 No 6 >pfam01551 Peptidase_M23 Peptidase family M23. Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins, for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown. Probab=99.88 E-value=6.1e-23 Score=141.66 Aligned_cols=74 Identities=36% Similarity=0.714 Sum_probs=70.5 Q ss_pred CEEEECCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEEECCEECCH Q ss_conf 599960698655119999989988998411563441120022031248998057888885699999786898052 Q gi|254780683|r 1 MVIYVGNDLVELGNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNAIAMDP 75 (84) Q Consensus 1 VVv~~g~~~~~~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg~~~g~hLhfei~~~g~~vdP 75 (84) .|+++++. .++|++|+|+|++++.++|+||+++.|++||.|++||.||++|+++.+++||||||||++++++|| T Consensus 23 ~V~~~~~~-~~~G~~v~i~h~~g~~~~Y~hl~~~~V~~G~~V~~G~~IG~~G~sg~~~~~hLHfei~~~~~~vdP 96 (96) T pfam01551 23 VVVFAGYL-GGYGNLVIIDHGNGYETLYAHLSKILVKVGQRVKAGQVIGTVGSTGRSTGPHLHFEIRKNGKPVDP 96 (96) T ss_pred EEEEEEEC-CCCCEEEEEEECCCCEEEECCCEEEEECCCCCHHHCCEEEEECCCCCCCCEEEEEEEEECCEECCC T ss_conf 99998983-998859999938987699836446779589890139999986789998980899999999999877 No 7 >PRK06148 hypothetical protein; Provisional Probab=98.77 E-value=1.7e-08 Score=65.33 Aligned_cols=59 Identities=20% Similarity=0.546 Sum_probs=49.3 Q ss_pred CCCCEEEEEECC----CCEEEEEECCCCC---CCCCCEEEECCEEEEEECCCCCCC--CCEEEEEEEE Q ss_conf 655119999989----9889984115634---411200220312489980578888--8569999978 Q gi|254780683|r 10 VELGNTILIRHD----DSIVTVYSHIDTP---YVQKGQKVSRGHTIGLSGKSGNAQ--HPQVHFELRK 68 (84) Q Consensus 10 ~~~G~~V~I~h~----~g~~t~Y~hl~~i---~v~~G~~V~~G~~IG~vg~tg~~~--g~hLhfei~~ 68 (84) .+||-+|+++|. +-++|+|+||+.. .++.||.|++||.||.+|+....- .|||||++.. T Consensus 474 l~yGg~iiL~h~~~~~~~F~tLyGhl~~~~~~~l~~G~~i~~G~~ig~~G~~~~nggw~phlh~Ql~~ 541 (1015) T PRK06148 474 LGYGGLIALEHEPPGCPPFYTLWGHLAHEAVSRLKPGDRLAAGELVGHMGDAHENGGWAPHLHFQIST 541 (1015) T ss_pred CCCCCEEEEEECCCCCCCEEEEECCCCHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCEEEEEEE T ss_conf 56775489984258887505652357725531268888504677123426654468877615898851 No 8 >PRK06149 hypothetical protein; Provisional Probab=96.35 E-value=0.0046 Score=36.62 Aligned_cols=54 Identities=19% Similarity=0.225 Sum_probs=41.1 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEEECC Q ss_conf 6551199999899889984115634411200220312489980578888856999997868 Q gi|254780683|r 10 VELGNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNA 70 (84) Q Consensus 10 ~~~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg~~~g~hLhfei~~~g 70 (84) ..+|..++++|..-..|+|+...+ ++.|+.|++||.||..++.| +|||++.... T Consensus 455 ~~~~g~~~l~~~~~~~~L~g~~~~--~~~g~~i~~G~~ig~~~~~g-----~l~~ql~~~~ 508 (972) T PRK06149 455 RDGDGRLTLRGDAWELHLTGVEPA--VADGAAVEAGQPLGSASALG-----FLRVQLCPVA 508 (972) T ss_pred ECCCCEEEEECCCEEEEEECCCCC--CCCCCEEECCCCCCCCCCCC-----CEEEEEECCC T ss_conf 716964898517548998256776--67767520677003366688-----4799972167 No 9 >TIGR01843 type_I_hlyD type I secretion membrane fusion protein, HlyD family; InterPro: IPR010129 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). Type I secretion is an ABC transporter that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C terminus of the transported protein. This entry represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This entry selects a group of sequences closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins.; GO: 0015031 protein transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=90.65 E-value=0.21 Score=27.80 Aligned_cols=39 Identities=18% Similarity=0.337 Sum_probs=28.9 Q ss_pred CCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEECCCC Q ss_conf 51199999899889984115634411200220312489980578 Q gi|254780683|r 12 LGNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 12 ~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg 55 (84) -|+.-.|+|-.| +=+.+|.|++||.|++||++..+..+. T Consensus 40 ~g~~k~vQhleg-----Gi~~~I~V~EG~~V~~Gq~L~~Ld~t~ 78 (434) T TIGR01843 40 SGNVKVVQHLEG-----GIVREILVREGDRVKAGQVLVELDATS 78 (434) T ss_pred CCCEEEEECCCC-----CEEEEEEECCCCEECCCCCCEEECHHH T ss_conf 074779966865-----344135522586420377013541357 No 10 >pfam00529 HlyD HlyD family secretion protein. Probab=88.78 E-value=0.2 Score=27.98 Aligned_cols=26 Identities=15% Similarity=0.221 Sum_probs=21.4 Q ss_pred ECCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 11563441120022031248998057 Q gi|254780683|r 29 SHIDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 29 ~hl~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +-+.++.|+.||.|++||+|..+..+ T Consensus 11 G~V~~i~V~~Gd~VkkGq~L~~lD~~ 36 (304) T pfam00529 11 GIVIRILVKEGDRVKAGDVLVRLDPT 36 (304) T ss_pred EEEEEEECCCCCEECCCCEEEEECCH T ss_conf 79999986890998899989999868 No 11 >TIGR02971 heterocyst_DevB ABC exporter membrane fusion protein, DevB family; InterPro: IPR014315 Members of this protein are found mostly in the Cyanobacteria, but also in the Planctomycetes. DevB from Anabaena sp. (strain PCC 7120) is partially characterised as a membrane fusion protein of the DevBCA ABC exporter, probably a glycolipid exporter required for heterocyst formation. Most Cyanobacteria have one member only, but Nostoc sp. which has seven members.. Probab=87.25 E-value=0.26 Score=27.34 Aligned_cols=42 Identities=17% Similarity=0.249 Sum_probs=28.3 Q ss_pred CEEEEEECCCCEEEEEECCCCCC-CCCCEEEECCEEEEEECCC Q ss_conf 11999998998899841156344-1120022031248998057 Q gi|254780683|r 13 GNTILIRHDDSIVTVYSHIDTPY-VQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 13 G~~V~I~h~~g~~t~Y~hl~~i~-v~~G~~V~~G~~IG~vg~t 54 (84) |.++-+--+.+-+.-=--++++. |++||.|.+||+|+...+- T Consensus 11 G~v~~v~aP~~Gf~g~~Ri~~LlPV~eGD~V~~Gq~lA~Ld~~ 53 (363) T TIGR02971 11 GEVVAVAAPSSGFAGTDRIKKLLPVAEGDRVKAGQVLAELDSR 53 (363) T ss_pred CCEEEEECCCCCCCCCCHHHHHCCCCCCCCCCCCCEEEEECCC T ss_conf 8668841478888775315550677888701157536764570 No 12 >cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. Probab=86.90 E-value=0.83 Score=24.69 Aligned_cols=42 Identities=29% Similarity=0.355 Sum_probs=29.8 Q ss_pred CCEEEEEECCCCEEEEEECC--C---------CCCCCCCEEEECCEEEEEECCC Q ss_conf 51199999899889984115--6---------3441120022031248998057 Q gi|254780683|r 12 LGNTILIRHDDSIVTVYSHI--D---------TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 12 ~G~~V~I~h~~g~~t~Y~hl--~---------~i~v~~G~~V~~G~~IG~vg~t 54 (84) .+..+.|+..+|... .-|+ + +..|++||+|++||+|.++... T Consensus 52 T~HAigi~t~~G~ev-LiHiGiDTV~L~G~gF~~~v~~Gd~V~~G~~L~~~D~~ 104 (124) T cd00210 52 TKHAIGIESDSGVEI-LIHIGIDTVKLNGEGFTSHVEEGQRVKQGDKLLEFDLP 104 (124) T ss_pred CCCEEEEEECCCCEE-EEEEEECCCCCCCCCEEEEECCCCEECCCCEEEEECHH T ss_conf 896999996899899-99973042014895318997488999899999998599 No 13 >TIGR01349 PDHac_trf_mito pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006257 This group of sequences represent one of several closely related clades of the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex. It includes sequences from mitochondria and from alpha and beta branches of the proteobacteria, as well as from some other bacteria, but not the Gram-positive bacteria.; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006090 pyruvate metabolic process, 0045254 pyruvate dehydrogenase complex. Probab=86.79 E-value=0.6 Score=25.43 Aligned_cols=38 Identities=21% Similarity=0.326 Sum_probs=25.1 Q ss_pred ECCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEEECC Q ss_conf 115634411200220312489980578888856999997868 Q gi|254780683|r 29 SHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNA 70 (84) Q Consensus 29 ~hl~~i~v~~G~~V~~G~~IG~vg~tg~~~g~hLhfei~~~g 70 (84) |+|-+-..|+||+|+.||+|+++..+. + -+-||-..+| T Consensus 14 Gnla~W~KKeGDkv~~GDViaEIETDK-A---tm~~e~~~eG 51 (584) T TIGR01349 14 GNLAKWLKKEGDKVKPGDVIAEIETDK-A---TMEFEAQEEG 51 (584) T ss_pred CCCEEEEECCCCEECCCCEEEEEECCC-C---EEEEEECCCC T ss_conf 621024411377716887698874584-2---6745762685 No 14 >pfam00358 PTS_EIIA_1 phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1. Probab=86.58 E-value=0.92 Score=24.46 Aligned_cols=42 Identities=21% Similarity=0.340 Sum_probs=29.7 Q ss_pred CCEEEEEECCCCEEEEEECC--C---------CCCCCCCEEEECCEEEEEECCC Q ss_conf 51199999899889984115--6---------3441120022031248998057 Q gi|254780683|r 12 LGNTILIRHDDSIVTVYSHI--D---------TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 12 ~G~~V~I~h~~g~~t~Y~hl--~---------~i~v~~G~~V~~G~~IG~vg~t 54 (84) .+..+.|+..+|.. +.-|+ + +..|++||+|++||+|.++... T Consensus 57 T~HAigi~~~~G~e-iLiHiGiDTV~L~G~gF~~~v~~Gd~V~~G~~L~~~D~~ 109 (133) T pfam00358 57 TKHAIGIESDGGVE-ILIHVGIDTVKLNGEGFESHVEEGDRVKQGDKLLEFDLP 109 (133) T ss_pred CCCEEEEEECCCCE-EEEEECCCCEECCCCCEEEEECCCCEECCCCEEEEECHH T ss_conf 99799999689989-999986452233896318997589999899999998599 No 15 >PRK09578 periplasmic multidrug efflux lipoprotein precursor; Reviewed Probab=84.58 E-value=0.48 Score=25.93 Aligned_cols=26 Identities=15% Similarity=0.212 Sum_probs=19.5 Q ss_pred ECCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 11563441120022031248998057 Q gi|254780683|r 29 SHIDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 29 ~hl~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +.+.++.|++||.|++||+|+++..+ T Consensus 72 G~v~~v~v~~Gd~V~kGq~La~lD~~ 97 (385) T PRK09578 72 GIVTARTYEEGQEVKQGAVLFRIDPA 97 (385) T ss_pred EEEEEEEECCCCEECCCCEEEEECCH T ss_conf 69999980799987389889998534 No 16 >PRK03598 hypothetical protein; Provisional Probab=84.51 E-value=0.45 Score=26.09 Aligned_cols=24 Identities=21% Similarity=0.405 Sum_probs=15.4 Q ss_pred CCCCCCCCCEEEECCEEEEEECCC Q ss_conf 563441120022031248998057 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +.++.|++||.|++||+|.....+ T Consensus 54 V~~v~V~eGd~Vk~Gq~La~LD~~ 77 (331) T PRK03598 54 LASLAVDEGDAVKAGQVLGELDHA 77 (331) T ss_pred EEEEECCCCCEECCCCEEEEECCH T ss_conf 999986897987799889998808 No 17 >PRK09439 glucose-specific PTS system component; Provisional Probab=84.40 E-value=1.5 Score=23.41 Aligned_cols=42 Identities=21% Similarity=0.315 Sum_probs=29.9 Q ss_pred CCEEEEEECCCCEEEEEECC--C---------CCCCCCCEEEECCEEEEEECCC Q ss_conf 51199999899889984115--6---------3441120022031248998057 Q gi|254780683|r 12 LGNTILIRHDDSIVTVYSHI--D---------TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 12 ~G~~V~I~h~~g~~t~Y~hl--~---------~i~v~~G~~V~~G~~IG~vg~t 54 (84) .+.-+-|+..+|... .-|+ + +..|++||.|++||+|.++... T Consensus 74 T~HAigi~~~~G~ei-LIHiGiDTV~L~G~gF~~~v~~Gd~Vk~G~~L~~~D~~ 126 (169) T PRK09439 74 TNHAFSIESDSGVEL-FVHFGIDTVELKGEGFKRIAEEGQRVKVGDPIIEFDLE 126 (169) T ss_pred CCCEEEEECCCCCEE-EEEECCCCEECCCCCEEEEEECCCEECCCCEEEEECHH T ss_conf 893899992899899-99976240233896726999276998899999998699 No 18 >PRK11556 multidrug efflux system subunit MdtA; Provisional Probab=84.23 E-value=0.5 Score=25.85 Aligned_cols=26 Identities=23% Similarity=0.275 Sum_probs=20.6 Q ss_pred ECCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 11563441120022031248998057 Q gi|254780683|r 29 SHIDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 29 ~hl~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +-+.++.|++||.|++||+|+++..+ T Consensus 96 G~I~~i~v~~Gd~VkkGqvLa~iD~~ 121 (415) T PRK11556 96 GQLMALHFQEGQQVKAGDLLAEIDPS 121 (415) T ss_pred EEEEEEECCCCCEECCCCEEEEECCH T ss_conf 29999985898997899999998835 No 19 >PRK11578 macrolide transporter subunit MacA; Provisional Probab=82.49 E-value=0.66 Score=25.22 Aligned_cols=23 Identities=26% Similarity=0.414 Sum_probs=15.0 Q ss_pred CCCCCCCCCEEEECCEEEEEECC Q ss_conf 56344112002203124899805 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg~ 53 (84) +.++.|++||.|++||+|..... T Consensus 49 I~~i~v~~Gd~V~kGqvL~~ld~ 71 (347) T PRK11578 49 LKTLSVAIGDKVKKDQLLGVIDP 71 (347) T ss_pred EEEEECCCCCEECCCCEEEEECH T ss_conf 99999899398889999999874 No 20 >COG0511 AccB Biotin carboxyl carrier protein [Lipid metabolism] Probab=82.14 E-value=1 Score=24.23 Aligned_cols=44 Identities=25% Similarity=0.314 Sum_probs=28.1 Q ss_pred CCCCCCCEEEECCEEEEEECCCC-----CCCCCEEEEEEE-ECCEECCHH Q ss_conf 34411200220312489980578-----888856999997-868980526 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGKSG-----NAQHPQVHFELR-KNAIAMDPI 76 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~tg-----~~~g~hLhfei~-~~g~~vdP~ 76 (84) +++|++||.|++||.+..+-.-. .+...-.==+|. ++|.++++- T Consensus 83 ~~~V~vGd~V~~Gq~l~IiEAMKmeneI~A~~~G~V~~Ilv~~G~~Ve~G 132 (140) T COG0511 83 KPFVEVGDTVKAGQTLAIIEAMKMENEIEAPADGVVKEILVKNGDPVEYG 132 (140) T ss_pred EEEECCCCEECCCCEEEEEEEEECCCEECCCCCCEEEEEEECCCCCCCCC T ss_conf 98765799975899999998200155322899968999994489852689 No 21 >PRK09859 multidrug efflux system protein MdtE; Provisional Probab=81.73 E-value=0.71 Score=25.07 Aligned_cols=23 Identities=22% Similarity=0.253 Sum_probs=16.0 Q ss_pred CCCCCCCCCEEEECCEEEEEECC Q ss_conf 56344112002203124899805 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg~ 53 (84) +.++.|++||.|++||+|++... T Consensus 72 v~~~~v~~Gd~VkkGq~La~LD~ 94 (385) T PRK09859 72 IIKRNFIEGDKVNQGDSLYQIDP 94 (385) T ss_pred EEEEECCCCCEEECCCEEEEECC T ss_conf 99998389998848988998284 No 22 >PRK06302 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated Probab=81.72 E-value=0.87 Score=24.59 Aligned_cols=23 Identities=26% Similarity=0.536 Sum_probs=19.6 Q ss_pred CCCCCCCCEEEECCEEEEEECCC Q ss_conf 63441120022031248998057 Q gi|254780683|r 32 DTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 32 ~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +.-+|+.||.|++||+|+.+-.- T Consensus 98 ~~pFV~vGd~V~~Gq~v~iIEaM 120 (155) T PRK06302 98 APPFVEVGDTVKEGQTLCIIEAM 120 (155) T ss_pred CCCCCCCCCEECCCCEEEEEEEC T ss_conf 99742468672489889999842 No 23 >cd06850 biotinyl_domain The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine. Probab=81.66 E-value=0.74 Score=24.95 Aligned_cols=25 Identities=20% Similarity=0.341 Sum_probs=20.7 Q ss_pred CCCCCCCCCEEEECCEEEEEECCCC Q ss_conf 5634411200220312489980578 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg~tg 55 (84) +.++.|+.||.|++||.|+.+.... T Consensus 10 v~~~~V~~Gd~V~~G~~l~~iE~mK 34 (67) T cd06850 10 VVKVLVKEGDKVEAGQPLAVLEAMK 34 (67) T ss_pred EEEEEECCCCEECCCCEEEEEEECC T ss_conf 9999957999997899999999366 No 24 >PRK10476 multidrug resistance protein MdtN; Provisional Probab=80.72 E-value=0.78 Score=24.84 Aligned_cols=26 Identities=19% Similarity=0.125 Sum_probs=17.9 Q ss_pred ECCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 11563441120022031248998057 Q gi|254780683|r 29 SHIDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 29 ~hl~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +.+.++.|+.||.|++||+|.++..+ T Consensus 59 G~V~~V~V~egq~VkkGq~L~~LD~~ 84 (348) T PRK10476 59 GRIVELAVTENQAVKKGDLLFRIDPR 84 (348) T ss_pred EEEEEEEECCCCEECCCCEEEEECCH T ss_conf 59999994699986489789997768 No 25 >PRK07051 hypothetical protein; Validated Probab=78.21 E-value=1.3 Score=23.59 Aligned_cols=45 Identities=22% Similarity=0.343 Sum_probs=27.4 Q ss_pred CCCCCCCCEEEECCEEEEEECCCCC-----CCCCEEEEEEE-ECCEECCHH Q ss_conf 6344112002203124899805788-----88856999997-868980526 Q gi|254780683|r 32 DTPYVQKGQKVSRGHTIGLSGKSGN-----AQHPQVHFELR-KNAIAMDPI 76 (84) Q Consensus 32 ~~i~v~~G~~V~~G~~IG~vg~tg~-----~~g~hLhfei~-~~g~~vdP~ 76 (84) ...+|++||.|++||.|+.+-...- +.-.-.=-++. .+|.++++- T Consensus 22 ~~pfV~~Gd~V~~G~~v~iiEaMKm~~~V~A~~~G~V~~ilv~~G~~V~~G 72 (80) T PRK07051 22 APPYVEVGDTVAAGDVVGLVEVMKQFSEVEAEVAGRVVRFLVDDGEPVDAG 72 (80) T ss_pred CCCCCCCCCEECCCCEEEEEEECCCCCEEECCCCCEEEEEEECCCCEECCC T ss_conf 998136799988999999997002774672699829999995698986799 No 26 >TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit; InterPro: IPR010208 The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation . A closely related complex in Escherichia coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized . This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase (IPR003667 from INTERPRO), but is distinct. This entry describes the C subunit.; GO: 0051539 4 iron 4 sulfur cluster binding, 0006118 electron transport, 0016020 membrane. Probab=76.49 E-value=1 Score=24.19 Aligned_cols=21 Identities=33% Similarity=0.536 Sum_probs=18.1 Q ss_pred CCCCCCCEEEECCEEEEEECC Q ss_conf 344112002203124899805 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~ 53 (84) +..|++||+|.+||.||.-.. T Consensus 44 ~p~V~~GD~VLkGq~Ia~~~G 64 (444) T TIGR01945 44 EPIVKVGDKVLKGQLIAKADG 64 (444) T ss_pred CCEECCCCEEECCCEECCCCC T ss_conf 730027865206611006774 No 27 >TIGR01995 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component; InterPro: IPR011297 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) , is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , . This entry represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (hydroquinone-O-beta-D-glucopyranoside) . These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters.; GO: 0008982 protein-N(PI)-phosphohistidine-sugar phosphotransferase activity, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system. Probab=76.06 E-value=1.1 Score=24.12 Aligned_cols=42 Identities=29% Similarity=0.332 Sum_probs=30.1 Q ss_pred CCEEEEEECCCCEEEEEEC--CC---------CCCCCCCEEEECCEEEEEECCC Q ss_conf 5119999989988998411--56---------3441120022031248998057 Q gi|254780683|r 12 LGNTILIRHDDSIVTVYSH--ID---------TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 12 ~G~~V~I~h~~g~~t~Y~h--l~---------~i~v~~G~~V~~G~~IG~vg~t 54 (84) .+.-+=|+..||..- .=| +| ++.|++||+|++||.++++.-+ T Consensus 563 T~HAiGi~~~nG~E~-LIHvGIDTV~L~G~~Fe~~V~~Gd~v~~Gq~L~~~D~d 615 (660) T TIGR01995 563 TKHAIGIRSDNGVEI-LIHVGIDTVELKGEYFEILVKVGDKVKAGQLLLTFDLD 615 (660) T ss_pred CCCEEEECCCCCEEE-EEEEEEEEEEECCEEEEEEEEECCEEEECCCCCEEEHH T ss_conf 862274126897289-99841234565450122214566787506631221068 No 28 >cd06252 M14_ASTE_ASPA_like_2 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=75.45 E-value=4.4 Score=20.90 Aligned_cols=40 Identities=25% Similarity=0.289 Sum_probs=25.5 Q ss_pred EEEEECCCCEEEEEECCC---CCCCCCCEEEECCEEEEEECCC Q ss_conf 999998998899841156---3441120022031248998057 Q gi|254780683|r 15 TILIRHDDSIVTVYSHID---TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 15 ~V~I~h~~g~~t~Y~hl~---~i~v~~G~~V~~G~~IG~vg~t 54 (84) ...+.-.+....+++.-+ ...++.||.|++||+||++-+. T Consensus 235 ~~~~~~~~~~~~v~Ap~~Gif~~~v~lG~~V~kGq~lg~I~dp 277 (316) T cd06252 235 TRALDVPDARCYVFAPHPGLFEPLVDLGDEVSAGQVAGRIHFP 277 (316) T ss_pred EEEEEECCCCEEEECCCCEEEEEECCCCCEECCCCEEEEEECC T ss_conf 2788706897799769986999917889997799999999688 No 29 >cd06254 M14_ASTE_ASPA_like_4 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=74.37 E-value=2.1 Score=22.56 Aligned_cols=25 Identities=24% Similarity=0.478 Sum_probs=20.0 Q ss_pred CCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 1563441120022031248998057 Q gi|254780683|r 30 HIDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 30 hl~~i~v~~G~~V~~G~~IG~vg~t 54 (84) .+=...++.||.|++||+||++-+. T Consensus 232 Gl~~~~v~~G~~V~~Gq~lg~I~dp 256 (288) T cd06254 232 GLWYPFVKAGDTVQKGALLGYVTDY 256 (288) T ss_pred EEEEEECCCCCEECCCCEEEEEECC T ss_conf 4999936889997689999999689 No 30 >PRK11892 pyruvate dehydrogenase subunit beta; Provisional Probab=74.02 E-value=1.7 Score=23.00 Aligned_cols=27 Identities=19% Similarity=0.228 Sum_probs=22.3 Q ss_pred ECCCCCCCCCCEEEECCEEEEEECCCC Q ss_conf 115634411200220312489980578 Q gi|254780683|r 29 SHIDTPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 29 ~hl~~i~v~~G~~V~~G~~IG~vg~tg 55 (84) +.|.+-.+|+||.|++||+|+.+..+. T Consensus 17 g~l~kw~~~~gd~v~~gd~~aeietdk 43 (464) T PRK11892 17 GTLAKWLKKEGDKVKSGDVIAEIETDK 43 (464) T ss_pred CCCEEEECCCCCCCCCCCEEEEEEECC T ss_conf 712146446897525786689975065 No 31 >PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional Probab=73.74 E-value=1.7 Score=23.05 Aligned_cols=22 Identities=32% Similarity=0.413 Sum_probs=18.8 Q ss_pred CCCCCCCEEEECCEEEEEECCC Q ss_conf 3441120022031248998057 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~t 54 (84) +..||+||.|++||+|.....+ T Consensus 43 kl~VkeGD~V~~Gq~Lf~dK~~ 64 (448) T PRK05352 43 TMKVKEGDKVKKGQPLFEDKKN 64 (448) T ss_pred CEEECCCCEECCCCEEEECCCC T ss_conf 5685579997479855653898 No 32 >PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated Probab=73.21 E-value=1.8 Score=22.93 Aligned_cols=24 Identities=17% Similarity=0.215 Sum_probs=18.5 Q ss_pred CCCCCCCCCEEEECCEEEEEECCC Q ss_conf 563441120022031248998057 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +-++.|+.||.|++||.|..+-.- T Consensus 12 V~~v~V~~Gd~V~~G~~l~vlEAM 35 (70) T PRK08225 12 VWKIVVKVGDTVEEGQDVVILESM 35 (70) T ss_pred EEEEEECCCCEECCCCEEEEEEEC T ss_conf 999992898998999999999711 No 33 >TIGR03309 matur_yqeB selenium-dependent molybdenum hydroxylase system protein, YqeB family. Members of this protein family are probable accessory proteins for the biosynthesis of enzymes with labile selenium-containing centers, different from selenocysteine-containing proteins. Probab=73.11 E-value=5.8 Score=20.22 Aligned_cols=29 Identities=28% Similarity=0.410 Sum_probs=21.3 Q ss_pred EEECCC---CCCCCCCEEEECCEEEEEECCCC Q ss_conf 841156---34411200220312489980578 Q gi|254780683|r 27 VYSHID---TPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 27 ~Y~hl~---~i~v~~G~~V~~G~~IG~vg~tg 55 (84) +|+..+ ...++-|+.|++||+||.++... T Consensus 167 i~Ap~~G~~~~~~~IGd~V~kG~vig~v~~~p 198 (256) T TIGR03309 167 LRAPADGIVTPTKAIGDSVKKGDVIATVGDVP 198 (256) T ss_pred EECCCCCCEECHHHCCCEEECCCEEEEECCEE T ss_conf 97587853854144189686796899989988 No 34 >PRK10255 N-acetyl glucosamine specific PTS system components IIABC; Provisional Probab=72.69 E-value=5.8 Score=20.23 Aligned_cols=42 Identities=21% Similarity=0.290 Sum_probs=28.9 Q ss_pred CCEEEEEECCCCEEEEEEC--CC---------CCCCCCCEEEECCEEEEEECCC Q ss_conf 5119999989988998411--56---------3441120022031248998057 Q gi|254780683|r 12 LGNTILIRHDDSIVTVYSH--ID---------TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 12 ~G~~V~I~h~~g~~t~Y~h--l~---------~i~v~~G~~V~~G~~IG~vg~t 54 (84) ++.-+-|+..+|... .-| +| +..|++||+|++||.|.+..-+ T Consensus 552 T~HA~gi~~~~G~Ei-LiHiGiDTV~L~G~gF~~~v~~Gd~Vk~G~~l~~~D~~ 604 (648) T PRK10255 552 TNHAFCLETEKGAEI-VVHMGIDTVALEGKGFKRLVEEGAQVSAGQPILEMDLD 604 (648) T ss_pred CCCEEEEECCCCCEE-EEEEEECCEEECCCCCEEEECCCCEECCCCEEEEECHH T ss_conf 885799984898189-99954452421780534883485996799988997499 No 35 >PRK05889 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Provisional Probab=72.61 E-value=1.9 Score=22.81 Aligned_cols=21 Identities=24% Similarity=0.404 Sum_probs=12.0 Q ss_pred CCCCCCCEEEECCEEEEEECC Q ss_conf 344112002203124899805 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~ 53 (84) ++.|++||.|++||.|..+.. T Consensus 15 ~v~V~~Gd~V~~Gd~l~vlEA 35 (71) T PRK05889 15 EVVVNEGDQIGEGDTLVLLES 35 (71) T ss_pred EEEECCCCEECCCCEEEEEEH T ss_conf 999799999889999999982 No 36 >TIGR00830 PTBA PTS system, glucose subfamily, IIA component; InterPro: IPR001127 The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) , is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars. The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII). The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site. An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , . ; GO: 0005351 sugar:hydrogen ion symporter activity, 0006810 transport, 0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system, 0016020 membrane. Probab=72.54 E-value=1.9 Score=22.77 Aligned_cols=21 Identities=24% Similarity=0.314 Sum_probs=17.9 Q ss_pred CCCCCCEEEECCEEEEEECCC Q ss_conf 441120022031248998057 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~t 54 (84) ..|++||+|++||.|.++... T Consensus 92 ~~v~~G~~V~~Gd~l~efD~~ 112 (129) T TIGR00830 92 SHVEEGDKVKKGDPLLEFDLP 112 (129) T ss_pred EEEEECCEECCCCEEEEECHH T ss_conf 876438787179779995669 No 37 >cd06663 Biotinyl_lipoyl_domains Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue. Probab=72.48 E-value=2 Score=22.74 Aligned_cols=27 Identities=15% Similarity=0.155 Sum_probs=20.9 Q ss_pred ECCCCCCCCCCEEEECCEEEEEECCCC Q ss_conf 115634411200220312489980578 Q gi|254780683|r 29 SHIDTPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 29 ~hl~~i~v~~G~~V~~G~~IG~vg~tg 55 (84) +-+.++.+++||.|++||.|..+-... T Consensus 14 g~I~~~~v~~Gd~V~~Gd~l~~iEa~K 40 (73) T cd06663 14 GTVVKWLKKVGDKVKKGDVLAEIEAMK 40 (73) T ss_pred EEEEEEEECCCCEECCCCEEEEEEEEE T ss_conf 999999926999997999999999500 No 38 >cd06255 M14_ASTE_ASPA_like_5 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=72.20 E-value=2.3 Score=22.34 Aligned_cols=27 Identities=19% Similarity=0.288 Sum_probs=21.2 Q ss_pred EECCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 411563441120022031248998057 Q gi|254780683|r 28 YSHIDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 28 Y~hl~~i~v~~G~~V~~G~~IG~vg~t 54 (84) .+.+=...++.||.|++||+||++-+. T Consensus 238 ~~Gl~~~~v~~G~~V~kGq~lg~I~dp 264 (293) T cd06255 238 HGGLFEPSVPAGDTIPAGQPLGRVVDL 264 (293) T ss_pred CCEEEEEECCCCCEECCCCEEEEEECC T ss_conf 985999837889997799999999899 No 39 >PRK09824 beta-glucoside-specific PTS system components IIABC; Provisional Probab=70.98 E-value=7 Score=19.81 Aligned_cols=42 Identities=26% Similarity=0.301 Sum_probs=29.3 Q ss_pred CCEEEEEECCCCEEEEEECC--C---------CCCCCCCEEEECCEEEEEECCC Q ss_conf 51199999899889984115--6---------3441120022031248998057 Q gi|254780683|r 12 LGNTILIRHDDSIVTVYSHI--D---------TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 12 ~G~~V~I~h~~g~~t~Y~hl--~---------~i~v~~G~~V~~G~~IG~vg~t 54 (84) .+.-+-|+..+|... .-|+ | +..|++||+|++||.+.+..-. T Consensus 530 t~HAig~~~~~G~e~-liHiGidTV~l~G~~F~~~v~~g~~V~~g~~l~~~d~~ 582 (625) T PRK09824 530 TLHAIGIESDDGVEI-LIHVGIDTVKLDGKFFSAHVNVGDKVNTGDRLISFDIP 582 (625) T ss_pred CCCEEEEECCCCCEE-EEEECCCCCCCCCCCCEEEECCCCEECCCCEEEEECHH T ss_conf 896789972898189-99966165010891541674678996799989997499 No 40 >PRK10559 p-hydroxybenzoic acid efflux subunit AaeA; Provisional Probab=69.82 E-value=2.5 Score=22.19 Aligned_cols=19 Identities=21% Similarity=0.202 Sum_probs=7.5 Q ss_pred CCCCCCCEEEECCEEEEEE Q ss_conf 3441120022031248998 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLS 51 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~v 51 (84) ++.|+.||.|++||+|..+ T Consensus 60 eV~V~dnq~VkkGdvL~~I 78 (310) T PRK10559 60 QVNVHDNQLVKKGQVLFTI 78 (310) T ss_pred EEECCCCCEECCCCEEEEE T ss_conf 9991794987699889998 No 41 >cd06253 M14_ASTE_ASPA_like_3 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=69.71 E-value=5.7 Score=20.27 Aligned_cols=33 Identities=27% Similarity=0.357 Sum_probs=23.6 Q ss_pred CCEEEEEECCC---CCCCCCCEEEECCEEEEEECCC Q ss_conf 98899841156---3441120022031248998057 Q gi|254780683|r 22 DSIVTVYSHID---TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 22 ~g~~t~Y~hl~---~i~v~~G~~V~~G~~IG~vg~t 54 (84) .+...+|+--+ ...++.||.|++||+||++-+. T Consensus 227 ~~~~~i~Ap~~Gl~~~~~~lG~~V~~G~~lg~I~dp 262 (298) T cd06253 227 RDVVYVNAETSGIFVPAKHLGDIVKRGDVIGEIVDP 262 (298) T ss_pred CCEEEEECCCCEEEEEECCCCCEECCCCEEEEEECC T ss_conf 870899659998999946889988789999999688 No 42 >PRK05305 phosphatidylserine decarboxylase; Provisional Probab=67.46 E-value=6.7 Score=19.92 Aligned_cols=40 Identities=28% Similarity=0.411 Sum_probs=25.9 Q ss_pred EEEEEECCCCEEEEEECCC-----C--CCCCCCEEEECCEEEEEECC Q ss_conf 1999998998899841156-----3--44112002203124899805 Q gi|254780683|r 14 NTILIRHDDSIVTVYSHID-----T--PYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 14 ~~V~I~h~~g~~t~Y~hl~-----~--i~v~~G~~V~~G~~IG~vg~ 53 (84) ..+.|++.+|......... + ..+++||.+++||.+|.+.- T Consensus 133 ~~i~i~~~~g~~i~~~qIaG~~ARrIv~~~~~g~~l~~G~r~G~I~f 179 (214) T PRK05305 133 NAVVIETADGGEIGVVQIAGLVARRIVCYVEEGDELERGERFGLIRF 179 (214) T ss_pred EEEEEECCCCCEEEEEECCCHHHHHEEECCCCCCEEECCCEEEEEEC T ss_conf 79999848998899999253213224622678978853777737960 No 43 >TIGR01043 ATP_syn_A_arch ATP synthase archaeal, A subunit; InterPro: IPR005726 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , . F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. A-ATPases (or A1A0-ATPase) (3.6.3.14 from EC) are found exclusively in Archaea and display a close resemblance in structure and subunit composition with V-ATPases, although their function in both ATP synthesis and ATP hydrolysis is closer to that of F-ATPases . A-ATPases are composed of two linked complexes: the A1 complex consisting of seven subunits contains the catalytic core that synthesizes/hydrolyses ATP, while the A0 complex consisting of at least two subunits forms the membrane-spanning pore . The rotary motor in A-ATPases is composed of only two subunits, the stator subunit I and the rotor subunit C . A-ATPases may have arisen as an adaptation to the different cellular needs and the more extreme environmental conditions faced by Archaeal species. This entry represents the alpha subunit from the A1 complex of A-ATPases. The A1 complex contains three copies each of subunits alpha (or A) and beta (or B) (IPR005724 from INTERPRO), both of which form the headpiece that participates in nucleotide binding. However, only the alpha subunit is catalytic, the beta subunit being regulatory in function . More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0016820 hydrolase activity acting on acid anhydrides catalyzing transmembrane movement of substances, 0015986 ATP synthesis coupled proton transport, 0016021 integral to membrane, 0016469 proton-transporting two-sector ATPase complex. Probab=67.28 E-value=3.2 Score=21.60 Aligned_cols=23 Identities=35% Similarity=0.609 Sum_probs=20.0 Q ss_pred CCCCCCEEEECCEEEEEECCCCC Q ss_conf 44112002203124899805788 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKSGN 56 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~tg~ 56 (84) -.|+.||.|..|++||.|..|.. T Consensus 121 P~v~~Gd~V~~Gd~~G~V~ET~~ 143 (584) T TIGR01043 121 PTVKEGDKVEGGDIIGVVQETSL 143 (584) T ss_pred CEECCCCEECCCCEEEEECCCCC T ss_conf 21226864347615877637650 No 44 >pfam06898 YqfD Putative stage IV sporulation protein YqfD. This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis is known to be essential for efficient sporulation although its exact function is unknown. Probab=66.97 E-value=7.2 Score=19.75 Aligned_cols=41 Identities=32% Similarity=0.579 Sum_probs=28.2 Q ss_pred EEECCCC-EEEEEECCCCCCCCCCEEEECCEEE--EEECCCCCC Q ss_conf 9998998-8998411563441120022031248--998057888 Q gi|254780683|r 17 LIRHDDS-IVTVYSHIDTPYVQKGQKVSRGHTI--GLSGKSGNA 57 (84) Q Consensus 17 ~I~h~~g-~~t~Y~hl~~i~v~~G~~V~~G~~I--G~vg~tg~~ 57 (84) ++.-.+| ...++..-....|++||.|++||++ |.++..+.. T Consensus 192 iVA~k~GvI~~i~v~~G~p~Vk~GD~VkkGqiLVsG~i~~e~~~ 235 (383) T pfam06898 192 IVAKKDGIITRMYVTKGTAVVKVGDVVKKGDILVSGQIGKEGNE 235 (383) T ss_pred EEECCCCEEEEEEECCCEEEECCCCEECCCCEEEEEEECCCCCC T ss_conf 58999979999996477177658998778989996356578981 No 45 >cd06849 lipoyl_domain Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid dehydrogenase (BCDH), contain at least three different enzymes, 2-oxo acid dehydrogenase (E1), dihydrolipoyl acyltransferase (E2) and dihydrolipoamide dehydrogenase (E3) and play a key role in redox regulation. E2, the central component of the complex, catalyzes the transfer of the acyl group of CoA from E1 to E3 via reductive acetylation of a lipoyl group covalently attached to a lysine residue. Probab=66.10 E-value=3.6 Score=21.33 Aligned_cols=27 Identities=19% Similarity=0.236 Sum_probs=20.7 Q ss_pred ECCCCCCCCCCEEEECCEEEEEECCCC Q ss_conf 115634411200220312489980578 Q gi|254780683|r 29 SHIDTPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 29 ~hl~~i~v~~G~~V~~G~~IG~vg~tg 55 (84) +-+.+..++.||.|++||.|..+-.+. T Consensus 15 g~i~~w~v~~Gd~V~~gd~l~~vEt~K 41 (74) T cd06849 15 GTIVEWLVKEGDSVEEGDVLAEVETDK 41 (74) T ss_pred EEEEEEEECCCCEECCCCEEEEEECCC T ss_conf 999999927989997899999998585 No 46 >COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism] Probab=64.73 E-value=11 Score=18.78 Aligned_cols=40 Identities=28% Similarity=0.365 Sum_probs=26.5 Q ss_pred CEEEEEECCCCEEEEEEC--CC---------CCCCCCCEEEECCEEEEEECC Q ss_conf 119999989988998411--56---------344112002203124899805 Q gi|254780683|r 13 GNTILIRHDDSIVTVYSH--ID---------TPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 13 G~~V~I~h~~g~~t~Y~h--l~---------~i~v~~G~~V~~G~~IG~vg~ 53 (84) +.-+-|+..+|... .-| ++ +..|++||.|++||.|-+..- T Consensus 60 kHAigi~t~~GvEi-LiHiGiDTV~L~GegF~~~v~~Gd~Vk~Gd~Li~fDl 110 (156) T COG2190 60 KHAIGIETDEGVEI-LIHIGIDTVKLNGEGFESLVKEGDKVKAGDPLLEFDL 110 (156) T ss_pred CCEEEEECCCCCEE-EEEECEEEEEECCCCEEEEEECCCEECCCCEEEEECH T ss_conf 84799983899599-9995640586889324787507998815989899979 No 47 >cd06251 M14_ASTE_ASPA_like_1 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. Probab=64.66 E-value=5.3 Score=20.44 Aligned_cols=30 Identities=23% Similarity=0.292 Sum_probs=21.6 Q ss_pred EEEEECCC---CCCCCCCEEEECCEEEEEECCC Q ss_conf 99841156---3441120022031248998057 Q gi|254780683|r 25 VTVYSHID---TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 25 ~t~Y~hl~---~i~v~~G~~V~~G~~IG~vg~t 54 (84) ..+++.-+ ...++.|+.|++||+||++-+. T Consensus 220 ~~v~A~~~Gl~~~~~~~G~~V~~Gq~lg~I~dp 252 (287) T cd06251 220 VWVRAPQGGLLRSLVKLGDKVKKGQLLATITDP 252 (287) T ss_pred EEEECCCCCEEEECCCCCCEECCCCEEEEEECC T ss_conf 799769998798858988994799989999789 No 48 >PRK09282 pyruvate carboxylase subunit B; Validated Probab=64.31 E-value=3.4 Score=21.47 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=18.8 Q ss_pred CCCCCCCCEEEECCEEEEEECC Q ss_conf 6344112002203124899805 Q gi|254780683|r 32 DTPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 32 ~~i~v~~G~~V~~G~~IG~vg~ 53 (84) -++.|++||.|++||.|..+.. T Consensus 523 ~~V~Vk~Gd~V~~Gd~L~vlEA 544 (580) T PRK09282 523 VKVLVKEGDKVKEGDVLLILEA 544 (580) T ss_pred EEEEECCCCEECCCCEEEEEEH T ss_conf 9999789998789998999851 No 49 >pfam00364 Biotin_lipoyl Biotin-requiring enzyme. This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the model may not recognize the Glycine cleavage system H proteins. Probab=63.78 E-value=4 Score=21.12 Aligned_cols=23 Identities=22% Similarity=0.188 Sum_probs=19.8 Q ss_pred CCCCCCCEEEECCEEEEEECCCC Q ss_conf 34411200220312489980578 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~tg 55 (84) +..+++||.|++||.|..+.... T Consensus 18 ~w~v~~Gd~V~~g~~l~~iEt~K 40 (73) T pfam00364 18 EWLVKVGDKVKAGQVLCEVEAMK 40 (73) T ss_pred EEEECCCCEECCCCEEEEEEECC T ss_conf 48658989992899899999665 No 50 >TIGR01348 PDHac_trf_long pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006256 This group of sequences are a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and percent identity (UPGMA) trees. Members contain two or three copies of the lipoyl-binding domain. Escherichia coli AceF is included in this set while mitochondrial and some other bacterial forms are excluded. dihydrolipoyllysine-residue acetyltransferase E2 component of pyruvate dehydrogenase complex; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006096 glycolysis, 0045254 pyruvate dehydrogenase complex. Probab=63.37 E-value=3.7 Score=21.25 Aligned_cols=24 Identities=29% Similarity=0.361 Sum_probs=16.8 Q ss_pred CCCCCCCCCEEEECCEEEEEECCC Q ss_conf 563441120022031248998057 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg~t 54 (84) .++|+||+||+++.|++|...+.. T Consensus 54 ik~ikvkVGDt~~~G~~i~~l~~~ 77 (655) T TIGR01348 54 IKEIKVKVGDTLKEGDVIALLEVS 77 (655) T ss_pred EEEEEEEECCCCCCCCEEEEECCC T ss_conf 788975446654778789997166 No 51 >pfam01333 Apocytochr_F_C Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034. Probab=61.56 E-value=9.9 Score=19.01 Aligned_cols=40 Identities=20% Similarity=0.208 Sum_probs=28.2 Q ss_pred CEEEEEECCCCEEEE---EECCCCCCCCCCEEEECCEEEEEECC Q ss_conf 119999989988998---41156344112002203124899805 Q gi|254780683|r 13 GNTILIRHDDSIVTV---YSHIDTPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 13 G~~V~I~h~~g~~t~---Y~hl~~i~v~~G~~V~~G~~IG~vg~ 53 (84) |..|.|+..||-... =..+ ++.|++||.|++||.+-.-.| T Consensus 23 ~~~vtI~t~dG~~v~~~IP~Gp-eliV~~G~~V~~dqpLT~nPN 65 (118) T pfam01333 23 GYEVTIETADGETVVETIPAGP-ELIVSEGQTVKADQPLTNNPN 65 (118) T ss_pred CEEEEEECCCCCEEEEECCCCC-EEEECCCCEEECCCCCCCCCC T ss_conf 5799998699989988539997-489738988866984445998 No 52 >pfam05896 NQRA Na(+)-translocating NADH-quinone reductase subunit A (NQRA). This family consists of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration. Probab=61.34 E-value=3.3 Score=21.51 Aligned_cols=22 Identities=27% Similarity=0.359 Sum_probs=18.6 Q ss_pred CCCCCCCEEEECCEEEEEECCC Q ss_conf 3441120022031248998057 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~t 54 (84) +..|++||.|++||+|=.--++ T Consensus 42 kl~VkeGD~Vk~G~pLF~dK~n 63 (257) T pfam05896 42 KMLVKEGDKVKAGQPLFEDKKN 63 (257) T ss_pred EEEEECCCEEECCCEEEEEECC T ss_conf 6998349998558757997369 No 53 >PRK05035 electron transport complex protein RnfC; Provisional Probab=61.24 E-value=4.2 Score=20.96 Aligned_cols=21 Identities=19% Similarity=0.336 Sum_probs=18.2 Q ss_pred CCCCCCCEEEECCEEEEEECC Q ss_conf 344112002203124899805 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~ 53 (84) ...|++||.|.+||.||.... T Consensus 56 ~p~VkvGD~VlkGQ~I~~~~g 76 (725) T PRK05035 56 ELLVSVGDRVLKGQPLTQGDG 76 (725) T ss_pred CCCCCCCCEECCCCEEEECCC T ss_conf 141478999768887454698 No 54 >PRK05641 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated Probab=60.91 E-value=4.5 Score=20.80 Aligned_cols=23 Identities=17% Similarity=0.221 Sum_probs=18.9 Q ss_pred CCCCCCCCEEEECCEEEEEECCC Q ss_conf 63441120022031248998057 Q gi|254780683|r 32 DTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 32 ~~i~v~~G~~V~~G~~IG~vg~t 54 (84) -++.|++||.|++||.+..+-.. T Consensus 91 ~~v~v~~Gd~V~~g~~l~vlEaM 113 (148) T PRK05641 91 LKILVKEGDQVKTGQGLLILEAM 113 (148) T ss_pred EEEEECCCCEECCCCEEEEEEHH T ss_conf 99996899998799999999943 No 55 >PTZ00144 dihydrolipoamide succinyltransferase; Provisional Probab=60.03 E-value=5.4 Score=20.41 Aligned_cols=27 Identities=15% Similarity=0.116 Sum_probs=17.3 Q ss_pred ECCCCCCCCCCEEEECCEEEEEECCCC Q ss_conf 115634411200220312489980578 Q gi|254780683|r 29 SHIDTPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 29 ~hl~~i~v~~G~~V~~G~~IG~vg~tg 55 (84) +-+.+-.|++||.|++||.|..+.++. T Consensus 72 G~Iv~WlvkeGD~V~~gd~L~EVETDK 98 (430) T PTZ00144 72 GTLSEWKKKVGDYVKVDETIAIVETDK 98 (430) T ss_pred EEEEEEECCCCCEECCCCCEEEEECCC T ss_conf 999799818999868999089998588 No 56 >TIGR01394 TypA_BipA GTP-binding protein TypA; InterPro: IPR006298 This bacterial (and Arabidopsis) protein, termed TypA or BipA, is a GTP-binding protein. It is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.; GO: 0005525 GTP binding, 0005622 intracellular. Probab=59.66 E-value=4.8 Score=20.65 Aligned_cols=41 Identities=27% Similarity=0.498 Sum_probs=31.1 Q ss_pred EEEEEECCCCEEEEEE--CCC---CCCCCCCEEEECCEEEEEECCC Q ss_conf 1999998998899841--156---3441120022031248998057 Q gi|254780683|r 14 NTILIRHDDSIVTVYS--HID---TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 14 ~~V~I~h~~g~~t~Y~--hl~---~i~v~~G~~V~~G~~IG~vg~t 54 (84) |=++|...+|..+.|| +|+ .++|.+|+.|-+|++||.=... T Consensus 495 ~GsLVs~~~G~a~~YaL~nLqeRG~~Fv~pG~~VY~GMIiGEhsR~ 540 (609) T TIGR01394 495 NGSLVSMEDGTATAYALWNLQERGRLFVSPGTEVYEGMIIGEHSRE 540 (609) T ss_pred CCEEEEECCCCHHHHHHHHHHHCCCEEECCCCCEECCEEEEECCCC T ss_conf 4158992688106676873875384330788626334788723886 No 57 >COG0845 AcrA Membrane-fusion protein [Cell envelope biogenesis, outer membrane] Probab=57.68 E-value=5.5 Score=20.37 Aligned_cols=25 Identities=20% Similarity=0.369 Sum_probs=21.4 Q ss_pred CCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 1563441120022031248998057 Q gi|254780683|r 30 HIDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 30 hl~~i~v~~G~~V~~G~~IG~vg~t 54 (84) -+.++.|++||.|++||.+....++ T Consensus 76 ~v~~i~v~~G~~Vk~Gq~L~~ld~~ 100 (372) T COG0845 76 IVAEILVKEGDRVKKGQLLARLDPS 100 (372) T ss_pred EEEEEEECCCCEEECCCEEEEECCH T ss_conf 7989983689888359748995532 No 58 >TIGR02644 Y_phosphoryl pyrimidine-nucleoside phosphorylase; InterPro: IPR000053 Two highly similar activities are represented in this group: thymidine phosphorylase (TP, gene deoA, 2.4.2.4 from EC) and pyrimidine-nucleoside phosphorylase (PyNP, gene pdp, 2.4.2.2 from EC). Both are dimeric enzymes that function in the salvage pathway to catalyse the reversible phosphorolysis of pyrimidine nucleosides to the free base and sugar moieties. In the case of thymidine phosphorylase, thymidine (and to a lesser extent, 2'-deoxyuridine) is lysed to produce thymine (or uracil) and 2'-deoxyribose-1-phosphate. Pyrimidine-nucleoside phosphorylase performs the analogous reaction on thymidine (to produce the same products) and uridine (to produce uracil and ribose-1-phosphate). PyNP is typically the only pyrimidine nucleoside phosphorylase encoded by Gram positive bacteria, while eukaryotes and proteobacteria encode two: TP, and the unrelated uridine phosphorylase. In humans, TP was originally characterised as platelet-derived endothelial cell growth factor and gliostatin . Structurally, the enzymes are homodimers, each composed of a rigid all alpha-helix lobe and a mixed alpha-helix/beta-sheet lobe, which are connected by a flexible hinge , . Prior to substrate binding, the lobes are separated by a large cleft. A functional active site and subsequent catalysis occurs upon closing of the cleft. The active site, composed of a phosphate binding site and a (deoxy)ribonucleotide binding site within the cleft region, is highly conserved between the two enzymes of this group. Active site residues (Escherichia coli DeoA numbering) include the phosphate binding Lys84 and Ser86 (close to a glycine-rich loop), Ser113, and Thr123, and the pyrimidine nucleoside-binding Arg171, Ser186, and Lys190. Sequence comparison between the active site residues for both enzymes reveals only one difference , which has been proposed to partially mediate substrate specificity. In TP, position 111 is a methionine, while the analogous position in PyNP is lysine. It should be noted that the uncharacterised archaeal members of this family differ in a number of respects from either of the characterised activities. The residue at position 108 is lysine, indicating the activity might be PyNP-like (though the determinants of substrate specificity have not been fully elucidated). Position 171 is glutamate (negative charge side chain) rather than arginine (positive charge side chain). In addition, a large loop that may "lock in" the substrates within the active site is much smaller than in the characterised members. It is not clear what effect these and other differences have on activity and specificity.; GO: 0006206 pyrimidine base metabolic process. Probab=57.14 E-value=8 Score=19.51 Aligned_cols=21 Identities=29% Similarity=0.271 Sum_probs=18.0 Q ss_pred CCCCCCEEEECCEEEEEECCC Q ss_conf 441120022031248998057 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~t 54 (84) +..+.||.|++||+|.++=.+ T Consensus 386 l~~k~Gd~V~~Gd~~~tlY~~ 406 (425) T TIGR02644 386 LHKKVGDKVKKGDPIATLYSS 406 (425) T ss_pred EECCCCCEEECCCEEEEEECC T ss_conf 765668753237579998628 No 59 >COG1726 NqrA Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion] Probab=56.90 E-value=15 Score=18.01 Aligned_cols=27 Identities=22% Similarity=0.373 Sum_probs=21.2 Q ss_pred EECCC-CCCCCCCEEEECCEEEEEECCC Q ss_conf 41156-3441120022031248998057 Q gi|254780683|r 28 YSHID-TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 28 Y~hl~-~i~v~~G~~V~~G~~IG~vg~t 54 (84) |..|. +..|++||.|++||++.+-... T Consensus 36 y~gmrp~mkV~~gD~VkkGq~LfEdKkn 63 (447) T COG1726 36 YVGMRPSMKVREGDAVKKGQVLFEDKKN 63 (447) T ss_pred CCCCCCCCEECCCCEEECCCEEEECCCC T ss_conf 4688874153347722026531121568 No 60 >TIGR02013 rpoB DNA-directed RNA polymerase, beta subunit; InterPro: IPR010243 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 describes orthologues of the beta subunit of bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription. Probab=56.09 E-value=5.5 Score=20.38 Aligned_cols=22 Identities=23% Similarity=0.433 Sum_probs=18.0 Q ss_pred CCCCCCCEEEECCEEEEEECCC Q ss_conf 3441120022031248998057 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~t 54 (84) ...|++||+|.+||+||=-.+| T Consensus 851 ~PiV~~GDrV~~GdvlADGPsT 872 (1449) T TIGR02013 851 RPIVSVGDRVEAGDVLADGPST 872 (1449) T ss_pred EEECCCCCEECCCCEEECCCCC T ss_conf 3550148681021277347666 No 61 >TIGR01347 sucB 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase; InterPro: IPR006255 These sequences describe the TCA cycle 2-oxoglutarate system E2 component, dihydrolipoamide succinyltransferase. It is closely related to the pyruvate dehydrogenase E2 component, dihydrolipoamide acetyltransferase. Members include the mitochondrial and Gram-negative bacterial forms. Mycobacterial candidates are highly derived, differ in having and extra copy of the lipoyl-binding domain at the N-terminus and are generally excluded from this group of sequences as are all examples of dihydrolipoamide acetyltransferase. ; GO: 0004149 dihydrolipoyllysine-residue succinyltransferase activity, 0006099 tricarboxylic acid cycle, 0045252 oxoglutarate dehydrogenase complex. Probab=55.97 E-value=6.3 Score=20.07 Aligned_cols=40 Identities=15% Similarity=0.283 Sum_probs=27.9 Q ss_pred EEEEEECCCCEEEEE----ECCCCCCCCCCEEEECCEEEEEECC Q ss_conf 199999899889984----1156344112002203124899805 Q gi|254780683|r 14 NTILIRHDDSIVTVY----SHIDTPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 14 ~~V~I~h~~g~~t~Y----~hl~~i~v~~G~~V~~G~~IG~vg~ 53 (84) +.|.|..+.=-.=+- |=|++|..++|++|..||.||.+.. T Consensus 33 ~iveiETDKV~lEV~Sp~dGvl~~~~~~eG~TV~~g~~La~~~E 76 (435) T TIGR01347 33 LIVEIETDKVVLEVPSPADGVLQEILEKEGDTVTSGQVLAVLEE 76 (435) T ss_pred EEEEEECCCEEEEEECCCCCHHHHHHCCCCCEECCCEEEEEEEC T ss_conf 68975207446788288530217430689888505507788823 No 62 >PRK12999 pyruvate carboxylase; Reviewed Probab=55.28 E-value=6.1 Score=20.13 Aligned_cols=21 Identities=24% Similarity=0.327 Sum_probs=18.4 Q ss_pred CCCCCCCEEEECCEEEEEECC Q ss_conf 344112002203124899805 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~ 53 (84) ++.|++||.|++||.|-.+.. T Consensus 1090 kV~Vk~GD~VkkGd~LlvlEA 1110 (1147) T PRK12999 1090 TVAVKEGDEVKAGDPLLVIEA 1110 (1147) T ss_pred EEEECCCCEECCCCEEEEEEH T ss_conf 999689998789998999851 No 63 >pfam07831 PYNP_C Pyrimidine nucleoside phosphorylase C-terminal domain. This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP). The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer. Probab=54.61 E-value=7 Score=19.82 Aligned_cols=21 Identities=19% Similarity=0.229 Sum_probs=17.6 Q ss_pred CCCCCCEEEECCEEEEEECCC Q ss_conf 441120022031248998057 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~t 54 (84) +..+.||.|++||+|.++=.+ T Consensus 36 l~~k~Gd~V~~g~pl~~i~~~ 56 (75) T pfam07831 36 LHKKVGDKVKKGDPLATIYAN 56 (75) T ss_pred EECCCCCEECCCCEEEEEECC T ss_conf 024689996699939999779 No 64 >PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated Probab=54.15 E-value=6.8 Score=19.86 Aligned_cols=24 Identities=17% Similarity=0.173 Sum_probs=19.2 Q ss_pred CCCCCCCCCEEEECCEEEEEECCC Q ss_conf 563441120022031248998057 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +-++.|+.||.|++||.|..+-.. T Consensus 74 v~~i~v~~Gd~V~~g~~l~vlEAM 97 (132) T PRK06549 74 ILKVLVAVGDQVTENQPLLILEAM 97 (132) T ss_pred EEEEEECCCCEECCCCEEEEEEEH T ss_conf 999993899998799989999801 No 65 >cd06250 M14_PaAOTO_like An uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the the M14 family of metallocarboxypeptidases. This subgroup includes Pseudomonas aeruginosa AotO and related proteins. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. The gene encoding Probab=49.75 E-value=9.5 Score=19.11 Aligned_cols=32 Identities=13% Similarity=0.146 Sum_probs=22.8 Q ss_pred CEEEEEEC---CCCCCCCCCEEEECCEEEEEECCC Q ss_conf 88998411---563441120022031248998057 Q gi|254780683|r 23 SIVTVYSH---IDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 23 g~~t~Y~h---l~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +...+++- +=...++.|+.|++||+||++-+. T Consensus 288 ~~~~v~Ap~~Gi~~~~~~~G~~V~~G~~la~I~dP 322 (359) T cd06250 288 GVEMLYAPAGGMVVYRAAPGDWVEAGDVLAEILDP 322 (359) T ss_pred CCEEEECCCCEEEEECCCCCCEECCCCEEEEEECC T ss_conf 66799569986898727999997799989999489 No 66 >COG0508 AceF Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component, and related enzymes [Energy production and conversion] Probab=49.49 E-value=11 Score=18.81 Aligned_cols=26 Identities=23% Similarity=0.350 Sum_probs=19.1 Q ss_pred CCCCCCCCCCEEEECCEEEEEECCCC Q ss_conf 15634411200220312489980578 Q gi|254780683|r 30 HIDTPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 30 hl~~i~v~~G~~V~~G~~IG~vg~tg 55 (84) -|.+|.+++|+.|.-|++|++++..+ T Consensus 55 ~l~~i~~~~G~~V~Vg~~I~~i~~~~ 80 (404) T COG0508 55 VLAKILVEEGDTVPVGAVIARIEEEG 80 (404) T ss_pred EEEEEECCCCCEECCCCEEEEEECCC T ss_conf 99676205898875898589993377 No 67 >cd01134 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. The Vacuolar (V-type) ATPase is found in the membranes of vacuoles, the golgi apparatus and in other coated vesicles in eukaryotes. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. Probab=49.02 E-value=11 Score=18.78 Aligned_cols=22 Identities=27% Similarity=0.564 Sum_probs=18.8 Q ss_pred CCCCCCEEEECCEEEEEECCCC Q ss_conf 4411200220312489980578 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~tg 55 (84) ..+++||.|+.||++|++-.+. T Consensus 53 p~v~~Gd~V~~GDi~G~V~E~~ 74 (369) T cd01134 53 PLVKVGDHVTGGDILGTVPENS 74 (369) T ss_pred CCCCCCCEECCCCEEEEEECCC T ss_conf 0267799962786799985578 No 68 >COG4656 RnfC Predicted NADH:ubiquinone oxidoreductase, subunit RnfC [Energy production and conversion] Probab=48.62 E-value=7.5 Score=19.64 Aligned_cols=21 Identities=24% Similarity=0.333 Sum_probs=17.8 Q ss_pred CCCCCCCEEEECCEEEEEECC Q ss_conf 344112002203124899805 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~ 53 (84) .+.|++||+|.+||+|+.-.. T Consensus 46 ~~~Vkvgd~V~~GQ~l~~~~g 66 (529) T COG4656 46 ILLVKVGDKVLKGQPLTRGEG 66 (529) T ss_pred CEEEEECCEEECCCEEECCCC T ss_conf 448830888850864203678 No 69 >COG1155 NtpA Archaeal/vacuolar-type H+-ATPase subunit A [Energy production and conversion] Probab=48.57 E-value=11 Score=18.77 Aligned_cols=21 Identities=29% Similarity=0.482 Sum_probs=18.1 Q ss_pred CCCCCEEEECCEEEEEECCCC Q ss_conf 411200220312489980578 Q gi|254780683|r 35 YVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 35 ~v~~G~~V~~G~~IG~vg~tg 55 (84) .+++||.|..||+||+|-.+. T Consensus 121 ~~~~Gd~V~~GdvlGtV~Et~ 141 (588) T COG1155 121 AVKKGDTVYPGDVLGTVQETS 141 (588) T ss_pred CCCCCCEECCCCEEEEECCCC T ss_conf 666698752685489860677 No 70 >PRK03934 phosphatidylserine decarboxylase; Provisional Probab=48.25 E-value=9.6 Score=19.08 Aligned_cols=15 Identities=20% Similarity=0.333 Sum_probs=9.9 Q ss_pred CEEEECCEEEEEECC Q ss_conf 002203124899805 Q gi|254780683|r 39 GQKVSRGHTIGLSGK 53 (84) Q Consensus 39 G~~V~~G~~IG~vg~ 53 (84) ...+++||.+|.--- T Consensus 220 ~~~~~KGdElG~F~~ 234 (267) T PRK03934 220 NLKLKKGEELGNFEM 234 (267) T ss_pred CCEECCCCEEEEECC T ss_conf 864732138223067 No 71 >pfam02666 PS_Dcarbxylase Phosphatidylserine decarboxylase. This is a family of phosphatidylserine decarboxylases, EC:4.1.1.65. These enzymes catalyse the reaction: Phosphatidyl-L-serine <= phosphatidylethanolamine + CO2. Phosphatidylserine decarboxylase plays a central role in the biosynthesis of aminophospholipids by converting phosphatidylserine to phosphatidylethanolamine. Probab=45.80 E-value=12 Score=18.60 Aligned_cols=39 Identities=23% Similarity=0.420 Sum_probs=22.2 Q ss_pred EEEEECCCCEEEEE--E--CCCCC--CC-CCCEEEECCEEEEEECC Q ss_conf 99999899889984--1--15634--41-12002203124899805 Q gi|254780683|r 15 TILIRHDDSIVTVY--S--HIDTP--YV-QKGQKVSRGHTIGLSGK 53 (84) Q Consensus 15 ~V~I~h~~g~~t~Y--~--hl~~i--~v-~~G~~V~~G~~IG~vg~ 53 (84) ++.|+...|...+- + ...+| .. ++|+.+++||.+|..-- T Consensus 124 ~~~i~~~~G~v~~v~Vga~~v~~I~~~~~~~g~~v~kG~e~G~f~f 169 (201) T pfam02666 124 VIVIETKFGKVAVVQVGALNVGSIVLYFKEEGDEVKKGDELGYFKF 169 (201) T ss_pred EEEEECCCCCEEEEEECCCCCCEEEEEECCCCCEEECCCEEEEEEC T ss_conf 9999948970999995530136789997158979845748807962 No 72 >PRK11856 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed Probab=45.69 E-value=12 Score=18.53 Aligned_cols=21 Identities=24% Similarity=0.387 Sum_probs=11.0 Q ss_pred CCCCCCCCCEEEECCEEEEEE Q ss_conf 563441120022031248998 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLS 51 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~v 51 (84) |.++.+++|+.|.-|++|+.+ T Consensus 55 l~~i~~~~G~~v~VG~~ia~i 75 (324) T PRK11856 55 LRKILVEEGDVVPVGAPIAVI 75 (324) T ss_pred EEEEECCCCCEECCCCEEEEE T ss_conf 989960897995799989994 No 73 >PRK05704 dihydrolipoamide succinyltransferase; Validated Probab=45.05 E-value=17 Score=17.82 Aligned_cols=26 Identities=15% Similarity=0.354 Sum_probs=18.1 Q ss_pred CCCCCCCCCCEEEECCEEEEEECCCC Q ss_conf 15634411200220312489980578 Q gi|254780683|r 30 HIDTPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 30 hl~~i~v~~G~~V~~G~~IG~vg~tg 55 (84) -|.++.+++|+.|.-|++|+.++..+ T Consensus 55 ~l~ki~~~eGd~v~VG~~ia~I~~~~ 80 (406) T PRK05704 55 VLSEILAEEGDTVTVGQVLGRIDEGA 80 (406) T ss_pred EEEEEEECCCCEECCCCEEEEEECCC T ss_conf 99998308989966899899982688 No 74 >COG3608 Predicted deacylase [General function prediction only] Probab=44.33 E-value=11 Score=18.75 Aligned_cols=26 Identities=19% Similarity=0.202 Sum_probs=21.1 Q ss_pred CCCCCCCCCCEEEECCEEEEEECCCC Q ss_conf 15634411200220312489980578 Q gi|254780683|r 30 HIDTPYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 30 hl~~i~v~~G~~V~~G~~IG~vg~tg 55 (84) .+=+..|+.||+|.+||+++++-..+ T Consensus 265 G~v~~~v~lGd~VeaG~~la~i~~~~ 290 (331) T COG3608 265 GLVEFLVDLGDKVEAGDVLATIHDPP 290 (331) T ss_pred CEEEEEECCCCCCCCCCEEEEEECCC T ss_conf 54877416788021787679973688 No 75 >KOG0557 consensus Probab=44.29 E-value=17 Score=17.71 Aligned_cols=35 Identities=14% Similarity=0.153 Sum_probs=23.3 Q ss_pred CCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEEECC Q ss_conf 634411200220312489980578888856999997868 Q gi|254780683|r 32 DTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNA 70 (84) Q Consensus 32 ~~i~v~~G~~V~~G~~IG~vg~tg~~~g~hLhfei~~~g 70 (84) -+-.-|+||.+.+||+|..+..+.. .+-||...+| T Consensus 56 vsW~kKeGdkls~GDvl~EVETDKA----tmd~E~~ddG 90 (470) T KOG0557 56 VSWKKKEGDKLSAGDVLLEVETDKA----TMDVEAQDDG 90 (470) T ss_pred EEEEECCCCCCCCCCEEEEEECCCC----EEEEEECCCC T ss_conf 6675225775688865899960451----2334403677 No 76 >cd05830 Sortase_D_5 Sortase D (SrtD) is a membrane transpeptidase found in gram-positive bacteria that anchors surface proteins to peptidoglycans of the bacterial cell wall envelope. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. Class D sortases are further classified into subfamilies 4 and 5. This group contains a subset of Class D sortases belonging to subfamily-5 represented by Streptomyces avermitilis SAV4337. Subfamily-5 sortases recognize a nonstandard sorting signal (LAXTG) and have replaced Sortase A in some gram-postive bacteria. They may play a housekeeping role in the cell. Probab=42.80 E-value=20 Score=17.44 Aligned_cols=36 Identities=17% Similarity=0.329 Sum_probs=22.8 Q ss_pred ECCCCCC-CCEEEEEECCCCEEEEEECCCCCCCCCCEEE Q ss_conf 6069865-5119999989988998411563441120022 Q gi|254780683|r 5 VGNDLVE-LGNTILIRHDDSIVTVYSHIDTPYVQKGQKV 42 (84) Q Consensus 5 ~g~~~~~-~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V 42 (84) .++.++| -||+++--|.+.+-..+.+|+++ ++||.| T Consensus 36 ~~t~~PG~~Gn~viaGHr~~~~~~F~~L~~l--~~GD~I 72 (137) T cd05830 36 PETAMPGEVGNFAVAGHRTTYGAPFNDLDKL--RPGDKI 72 (137) T ss_pred CCCCCCCCCCEEEEEECCCCCCCCCCCHHCC--CCCCEE T ss_conf 5888899997199997228977556013538--999999 No 77 >TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132 Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane. Probab=39.83 E-value=18 Score=17.70 Aligned_cols=18 Identities=33% Similarity=0.682 Sum_probs=14.5 Q ss_pred EEEECCEEEEEECCCCCC Q ss_conf 022031248998057888 Q gi|254780683|r 40 QKVSRGHTIGLSGKSGNA 57 (84) Q Consensus 40 ~~V~~G~~IG~vg~tg~~ 57 (84) =.+++||.||-+|.||.. T Consensus 486 L~I~~Ge~IGIvGpSGSG 503 (703) T TIGR01846 486 LDIKPGEVIGIVGPSGSG 503 (703) T ss_pred CCCCCCEEEEEECCCCCC T ss_conf 765786579987278986 No 78 >TIGR02876 spore_yqfD sporulation protein YqfD; InterPro: IPR010690 This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis (P54469 from SWISSPROT) is known to be essential for efficient sporulation although its exact function is unknown .. Probab=38.68 E-value=30 Score=16.47 Aligned_cols=42 Identities=33% Similarity=0.552 Sum_probs=28.2 Q ss_pred CCEEEEEECCCC-EEEEEECCCCCCCCCCEEEECCEEE--EEE-----CCCC Q ss_conf 511999998998-8998411563441120022031248--998-----0578 Q gi|254780683|r 12 LGNTILIRHDDS-IVTVYSHIDTPYVQKGQKVSRGHTI--GLS-----GKSG 55 (84) Q Consensus 12 ~G~~V~I~h~~g-~~t~Y~hl~~i~v~~G~~V~~G~~I--G~v-----g~tg 55 (84) ..|.|.=+ +| ..-+|---.+.-|+.||.|++||++ |.. |..+ T Consensus 191 p~niVAkk--~G~i~~~~v~~G~~~Vk~GD~VkkGd~Li~G~~rYWaGG~e~ 240 (406) T TIGR02876 191 PRNIVAKK--DGVIKRVYVTSGEAVVKKGDVVKKGDLLISGILRYWAGGKEG 240 (406) T ss_pred CCCEEEEC--CEEEEEEEEECCEEEECCCCEECCCCEEEEECCCCCCCCCCC T ss_conf 72326633--408888655111648548887657717871110010588898 No 79 >PRK11855 dihydrolipoamide acetyltransferase; Reviewed Probab=38.62 E-value=23 Score=17.07 Aligned_cols=22 Identities=27% Similarity=0.219 Sum_probs=9.6 Q ss_pred CCCCCCCCCEEEECCEEEEEEC Q ss_conf 5634411200220312489980 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSG 52 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg 52 (84) +.++.+++|+.|..|++|+.++ T Consensus 171 l~ki~v~eGd~v~VG~~ia~i~ 192 (549) T PRK11855 171 VKEIKVKVGDKVSVGSLLFKIE 192 (549) T ss_pred EEEEEECCCCCCCCCCEEEEEE T ss_conf 4476505898045798789972 No 80 >COG1038 PycA Pyruvate carboxylase [Energy production and conversion] Probab=35.40 E-value=15 Score=18.06 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=18.1 Q ss_pred CCCCCCCEEEECCEEEEEECC Q ss_conf 344112002203124899805 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~ 53 (84) ++.|++||.|++||.+..+.. T Consensus 1092 ~v~V~~G~~Vk~Gd~l~~ieA 1112 (1149) T COG1038 1092 EVKVKKGDKVKKGDVLAVIEA 1112 (1149) T ss_pred EEEECCCCCCCCCCEEEEEHH T ss_conf 999745873047986533022 No 81 >TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein; InterPro: IPR011924 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This entry represents LolD, a member of the ABC transporter family. LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on the residue immediately following the modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. Excluded from this entry are homologs from the archaeal genus Methanosarcina .; GO: 0005524 ATP binding, 0006810 transport, 0016020 membrane. Probab=35.39 E-value=9 Score=19.23 Aligned_cols=24 Identities=21% Similarity=0.570 Sum_probs=16.6 Q ss_pred EEEECCEEEEEECCCCCCCCCEEE Q ss_conf 022031248998057888885699 Q gi|254780683|r 40 QKVSRGHTIGLSGKSGNAQHPQVH 63 (84) Q Consensus 40 ~~V~~G~~IG~vg~tg~~~g~hLh 63 (84) =.|.+||.+|.||+||...-+=|| T Consensus 26 l~i~~GE~~~IvG~SGSGKSTLLH 49 (221) T TIGR02211 26 LSIGKGEIVAIVGSSGSGKSTLLH 49 (221) T ss_pred CEEECCCEEEEECCCCCCHHHHHH T ss_conf 123066337987367871689999 No 82 >COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms] Probab=35.15 E-value=20 Score=17.43 Aligned_cols=30 Identities=33% Similarity=0.311 Sum_probs=13.9 Q ss_pred EEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEE Q ss_conf 999998998899841156344112002203124899 Q gi|254780683|r 15 TILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGL 50 (84) Q Consensus 15 ~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~ 50 (84) +.+.---+|+.+ +..++.||.|.+|..+-. T Consensus 209 T~IrAP~dG~V~------~~~v~~G~~V~~G~~l~a 238 (352) T COG1566 209 TVIRAPVDGYVT------NLSVRVGQYVSAGTPLMA 238 (352) T ss_pred CEEECCCCCEEE------EECCCCCCEECCCCCEEE T ss_conf 899877896697------003557875048973499 No 83 >PRK06748 hypothetical protein; Validated Probab=34.35 E-value=41 Score=15.75 Aligned_cols=45 Identities=18% Similarity=0.135 Sum_probs=32.5 Q ss_pred CCCCEEEEEECCCCEEE-----EEECCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 65511999998998899-----8411563441120022031248998057 Q gi|254780683|r 10 VELGNTILIRHDDSIVT-----VYSHIDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 10 ~~~G~~V~I~h~~g~~t-----~Y~hl~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +.|-+...|+..||-.- +=++...+.|.+||.|..+..+.++-.+ T Consensus 28 yEWEkL~~I~~~dg~le~v~vGisG~I~~v~Ve~Gq~i~~~~lL~~vedD 77 (84) T PRK06748 28 YEWEKLALIETIDKQKVEIKVGISGYIESLEVVEGQAIADQKLLITVRDD 77 (84) T ss_pred EEEEEEEEEEECCCCEEEEEEEEEEEEEEEEEECCCEECCCCEEEEEECC T ss_conf 86423457750698289999821427889886228465377389998714 No 84 >COG4770 Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid metabolism] Probab=33.08 E-value=23 Score=17.12 Aligned_cols=21 Identities=29% Similarity=0.363 Sum_probs=18.0 Q ss_pred CCCCCCCEEEECCEEEEEECC Q ss_conf 344112002203124899805 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~ 53 (84) ++.|++||.|.+||.+-.+.. T Consensus 588 ~v~V~~G~~V~~G~~lvvlEA 608 (645) T COG4770 588 SVAVKEGQEVSAGDLLVVLEA 608 (645) T ss_pred EEEECCCCEECCCCEEEEEEE T ss_conf 999368977547986788671 No 85 >TIGR02712 urea_carbox urea carboxylase; InterPro: IPR014084 Members of this family are ATP-dependent urea carboxylases, including characterised members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae (Baker's yeast). The allophanate hydrolase domain of the yeast enzyme is not included in this entry and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from O. sagaranensis was shown to be highly active on acetamide and formamide as well as urea.. Probab=32.67 E-value=43 Score=15.62 Aligned_cols=36 Identities=19% Similarity=0.276 Sum_probs=28.3 Q ss_pred ECCCCEEEEEECCC----CCCCCCCEEEECCEEEEEECCC Q ss_conf 98998899841156----3441120022031248998057 Q gi|254780683|r 19 RHDDSIVTVYSHID----TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 19 ~h~~g~~t~Y~hl~----~i~v~~G~~V~~G~~IG~vg~t 54 (84) +-.+|-..+++++. ++.|..||.|++||.|-.+... T Consensus 1152 ~~~~g~~~V~s~~~G~~WK~~V~~G~~V~~G~~l~i~EaM 1191 (1226) T TIGR02712 1152 DLPEGAVQVESEVAGNVWKVLVEVGDRVEAGQPLVIIEAM 1191 (1226) T ss_pred CCCCCCEEEEEECEEEEEEEEECCCCEEECCCEEEEEEEC T ss_conf 3657714898502014656652126632048738999435 No 86 >PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional Probab=32.38 E-value=24 Score=16.99 Aligned_cols=31 Identities=13% Similarity=0.177 Sum_probs=17.1 Q ss_pred EEEEEECCC----CCCCCCCEEEECCEEEEEECCC Q ss_conf 899841156----3441120022031248998057 Q gi|254780683|r 24 IVTVYSHID----TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 24 ~~t~Y~hl~----~i~v~~G~~V~~G~~IG~vg~t 54 (84) ..++|+-.+ +..+.+|+.|.+|+.|-++.+- T Consensus 207 ~~ti~AP~sGvV~~~~v~~G~~V~~G~~Lf~IaDL 241 (407) T PRK09783 207 RFTLKAPIDGVITAFDLRAGMNIAKDNVVAKIQGM 241 (407) T ss_pred EEEEECCCCCEEEEEECCCCCEECCCCEEEEEECC T ss_conf 38997688807999744789566799806999647 No 87 >PRK04350 thymidine phosphorylase; Provisional Probab=31.66 E-value=26 Score=16.82 Aligned_cols=21 Identities=19% Similarity=0.140 Sum_probs=16.0 Q ss_pred CCCCCCEEEECCEEEEEECCC Q ss_conf 441120022031248998057 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~t 54 (84) +.+|.||.|++||+|.++=.+ T Consensus 455 l~~KvGd~V~kGdpL~tIhA~ 475 (502) T PRK04350 455 LHKKIGDKVKKGDPLYTIYAE 475 (502) T ss_pred EEECCCCEECCCCEEEEEECC T ss_conf 960487996799849999669 No 88 >PRK05820 deoA thymidine phosphorylase; Reviewed Probab=31.36 E-value=26 Score=16.76 Aligned_cols=22 Identities=14% Similarity=0.218 Sum_probs=18.6 Q ss_pred CCCCCCEEEECCEEEEEECCCC Q ss_conf 4411200220312489980578 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKSG 55 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~tg 55 (84) +.++.||.|++||+|.++-.+. T Consensus 385 l~~k~Gd~V~kGdpl~~iya~~ 406 (440) T PRK05820 385 LHARLGDRVDAGEPLATLHADD 406 (440) T ss_pred EECCCCCEECCCCEEEEEECCC T ss_conf 8515889967999499997499 No 89 >PRK12784 hypothetical protein; Provisional Probab=30.91 E-value=47 Score=15.43 Aligned_cols=45 Identities=16% Similarity=0.213 Sum_probs=32.3 Q ss_pred CCCCEEEEEECCCCEEE-----EEECCCCCCCCCCEEEECCEEEEEECCC Q ss_conf 65511999998998899-----8411563441120022031248998057 Q gi|254780683|r 10 VELGNTILIRHDDSIVT-----VYSHIDTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 10 ~~~G~~V~I~h~~g~~t-----~Y~hl~~i~v~~G~~V~~G~~IG~vg~t 54 (84) +.|-+...|+..||-.- +=++...+.|.+||.|..+..+.++-.+ T Consensus 28 YEWEkL~~I~~~dg~le~v~vGiSG~I~~v~Ve~Gq~i~~~tlL~~~edD 77 (84) T PRK12784 28 YEWEKLMMIRKNNGELEKVAVGISGNIRLVNVVVGQQIHTDTLLVRLEDD 77 (84) T ss_pred EEEEEEEEEEECCCCEEEEEEEEEEEEEEEEEECCCEECCCCEEEEEECC T ss_conf 86423457750698289999820116899986228543477189998603 No 90 >TIGR02645 ARCH_P_rylase putative thymidine phosphorylase; InterPro: IPR013466 Proteins in this entry are closely related to characterised examples of thymidine phosphorylase (2.4.2.4 from EC) and pyrimidine nucleoside phosphorylase (2.4.2.2 from EC). Most examples are found in the archaea, but other examples are found in bacteria such as Legionella pneumophila (strain Paris) and Rhodopseudomonas palustris CGA009.; GO: 0009032 thymidine phosphorylase activity. Probab=30.80 E-value=22 Score=17.15 Aligned_cols=37 Identities=22% Similarity=0.194 Sum_probs=27.6 Q ss_pred EEECCCCEEEEEECCC------------------CCCCCCCEEEECCEEEEEECC Q ss_conf 9998998899841156------------------344112002203124899805 Q gi|254780683|r 17 LIRHDDSIVTVYSHID------------------TPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 17 ~I~h~~g~~t~Y~hl~------------------~i~v~~G~~V~~G~~IG~vg~ 53 (84) |.-.-|||.|..-+.. ++.||.|++|++|++|=++=. T Consensus 422 I~A~~DG~Vt~IDN~~i~~IAr~AGAP~DKgAGv~lhvK~G~~Vk~GdPL~TIyA 476 (499) T TIGR02645 422 IHAETDGYVTEIDNKRITRIARLAGAPNDKGAGVELHVKVGDKVKKGDPLYTIYA 476 (499) T ss_pred EEECCCCEEHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCEEECCCCCEEEEC T ss_conf 8736886150423889999998718887676843888654677203870158850 No 91 >TIGR01235 pyruv_carbox pyruvate carboxylase; InterPro: IPR005930 In the postabsorptive state, blood glucose concentration is kept constant by a combination of glycogenolysis and gluconeogenesis. During prolonged fasting, when hepatic glycogen is exhausted, gluconeogenesis becomes the only source of plasma glucose. Gluconeogenesis (the production of new glucose molecules) occurs mainly in liver and, to a small extent, in kidneys. Pyruvate carboxylase (6.4.1.1 from EC), a member of the biotin-dependent enzyme family, catalyses the ATP-dependent carboxylation of pyruvate to oxaloacetate, thus playing a crucial role in gluconeogenesis.ATP + pyruvate + HCO3- = ADP + phosphate + oxaloacetate Most well characterised forms of active enzyme consist of four identical subunits arranged in a tetrahedron-like structure. Each subunit contains three functional domains: the biotin carboxylation domain, the transcarboxylation domain and the biotin carboxyl carrier domain.; GO: 0004736 pyruvate carboxylase activity, 0006094 gluconeogenesis, 0005737 cytoplasm. Probab=30.66 E-value=19 Score=17.55 Aligned_cols=45 Identities=22% Similarity=0.251 Sum_probs=27.7 Q ss_pred CCCCCCCEEEECCEEEEEECCCC-------CCCCCEEEEEEE-ECCEECCHHHHH Q ss_conf 34411200220312489980578-------888856999997-868980526987 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGKSG-------NAQHPQVHFELR-KNAIAMDPIKFL 79 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~tg-------~~~g~hLhfei~-~~g~~vdP~~~l 79 (84) +|.|+.|+.|++||++.....-. -..| .==|+. ++|..||-.+.| T Consensus 1113 ~v~v~~G~~v~kGd~l~~~~AMKME~~v~ap~~G--~vk~v~v~~G~~i~~~DLL 1165 (1169) T TIGR01235 1113 EVKVEAGQKVNKGDPLVVLEAMKMETVVQAPKDG--TVKEVLVKDGEKIDAKDLL 1165 (1169) T ss_pred EEEEECCCEECCCCEEEEEECCCCCCEEECCCCC--EEEEEEECCCCCCCCCCEE T ss_conf 9994138730167848996037632046678997--2468883588703512113 No 92 >TIGR00078 nadC nicotinate-nucleotide pyrophosphorylase; InterPro: IPR004393 Nicotinate-nucleotide pyrophosphorylase (2.4.2.19 from EC), also known as quinolinate phosphoribosyltransferase (decarboxylating), catalyses the conversion of nicotinate D-ribonucleotide, pyrophosphate and carbon dioxide into pyridine-2,3-dicarboxylate and 5-phospho-alpha-D-ribose 1-diphosphate. This enzyme is a type II phosphoribosyltransferase which provides the de novo source of nicotinate mononucleotide (NAMN) for NAD biosynthesis in both prokaryotes and eukaryotes , . Structural studies have shown that the active form of this enzyme is a homodimer with an unsual fold , , . The N-terminal forms a mixed alpha/beta domain, while the C-terminal region forms a multi-stranded, open alpha/beta barrel. The active site is found at the C-terminal ends of the beta strands of the alpha/beta barrel, and is bordered by the N-terminal domain of the second subunit of the dimer. It contains several conserved charged residues thought to be important determinants of substrate binding and catalysis. ; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0019363 pyridine nucleotide biosynthetic process. Probab=30.36 E-value=30 Score=16.45 Aligned_cols=21 Identities=19% Similarity=0.278 Sum_probs=17.5 Q ss_pred CCCCCCEEEECCEEEEEECCC Q ss_conf 441120022031248998057 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~t 54 (84) ..++.|+.|++||.|+++--+ T Consensus 64 ~~~~DG~~~~~G~~v~~~~G~ 84 (276) T TIGR00078 64 WLVKDGDEVEAGEVVAEVEGP 84 (276) T ss_pred EECCCCCEECCCCEEEEEECC T ss_conf 103788774477389999746 No 93 >PRK02693 apocytochrome f; Reviewed Probab=30.31 E-value=48 Score=15.37 Aligned_cols=40 Identities=18% Similarity=0.229 Sum_probs=27.2 Q ss_pred CEEEEEECCCCEEE---EEECCCCCCCCCCEEEECCEEEEEECC Q ss_conf 11999998998899---841156344112002203124899805 Q gi|254780683|r 13 GNTILIRHDDSIVT---VYSHIDTPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 13 G~~V~I~h~~g~~t---~Y~hl~~i~v~~G~~V~~G~~IG~vg~ 53 (84) |..|.|...+|-.. +-... ++.|++||.|++||.+-.-.| T Consensus 217 ~~~v~I~t~~G~~v~~~iP~Gp-~liV~~G~~v~~~qpLT~nPN 259 (312) T PRK02693 217 SYVVTITTEDGEVVTETIPAGP-ELIVKEGDAVEAGAPLTNDPN 259 (312) T ss_pred CEEEEEECCCCCEEEEECCCCC-EEEECCCCEEECCCCCCCCCC T ss_conf 6799998899999988529998-589727988856986667998 No 94 >PRK06078 pyrimidine-nucleoside phosphorylase; Reviewed Probab=30.16 E-value=29 Score=16.56 Aligned_cols=21 Identities=14% Similarity=0.148 Sum_probs=18.0 Q ss_pred CCCCCCEEEECCEEEEEECCC Q ss_conf 441120022031248998057 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~t 54 (84) +.++.||.|++||+|.++-.+ T Consensus 380 l~~k~Gd~V~kGdpL~tiya~ 400 (434) T PRK06078 380 LRKKVGDSVKKGESLVTIYAN 400 (434) T ss_pred EECCCCCEECCCCEEEEEECC T ss_conf 725695995799949999748 No 95 >TIGR00653 GlnA glutamine synthetase, type I; InterPro: IPR004809 Glutamine synthetase type I (or glutamate-ammonia ligase) has a dodecameric form, which can be subdivided into 1-alpha and 1-beta forms. The phylogeny of the 1-alpha and 1-beta forms appears polyphyletic. Escherichia coli, Synechocystis sp. (strain PCC 6803) , Aquifex aeolicus, and the crenarcheon Sulfolobus acidocaldarius have form 1-beta, while Bacillus subtilis, Thermotoga maritima, and various euryarchaea has form 1-alpha. The 1-beta dodecamer from the crenarcheon S. acidocaldarius differs from that in E. coli in that it is not regulated by adenylation. ; GO: 0004356 glutamate-ammonia ligase activity, 0009399 nitrogen fixation, 0005737 cytoplasm. Probab=30.11 E-value=39 Score=15.87 Aligned_cols=61 Identities=13% Similarity=0.078 Sum_probs=37.8 Q ss_pred CCCCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEECC------------------C---CCCCCCEEEEEEEE Q ss_conf 65511999998998899841156344112002203124899805------------------7---88888569999978 Q gi|254780683|r 10 VELGNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGK------------------S---GNAQHPQVHFELRK 68 (84) Q Consensus 10 ~~~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~------------------t---g~~~g~hLhfei~~ 68 (84) ..+|-.|..-| ..-.=+.-.+|.+|-.+-|+++|-|=+.-- . -+.+|=|.|++||+ T Consensus 209 ~~~G~~~E~~H---HEVA~aGQ~Eid~kf~~l~~~AD~~~~yKyvvK~vA~~~Gk~ATFMPKPlfGdNGSGMH~H~SLWK 285 (486) T TIGR00653 209 EQLGLDVEVHH---HEVATAGQHEIDFKFDTLLKTADDIQTYKYVVKNVAKKHGKTATFMPKPLFGDNGSGMHCHQSLWK 285 (486) T ss_pred HHCCCEEEEEE---CCCCCCCCEEEECCHHHHHHHHCCEEEHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEEEEEEE T ss_conf 86598288860---101478742530464789874050451478998999983887974587887726685548355632 Q ss_pred ----CCEEC Q ss_conf ----68980 Q gi|254780683|r 69 ----NAIAM 73 (84) Q Consensus 69 ----~g~~v 73 (84) +|+++ T Consensus 286 ~ePf~Genl 294 (486) T TIGR00653 286 GEPFDGENL 294 (486) T ss_pred CCCCCCCEE T ss_conf 778888400 No 96 >PRK10218 GTP-binding protein; Provisional Probab=29.66 E-value=37 Score=16.00 Aligned_cols=41 Identities=22% Similarity=0.507 Sum_probs=28.1 Q ss_pred EEEEEECCCCEEEEEE--CCC---CCCCCCCEEEECCEEEEEECCC Q ss_conf 1999998998899841--156---3441120022031248998057 Q gi|254780683|r 14 NTILIRHDDSIVTVYS--HID---TPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 14 ~~V~I~h~~g~~t~Y~--hl~---~i~v~~G~~V~~G~~IG~vg~t 54 (84) +-++|....|-.|.|+ +|+ .++|.+|+.|-.|++||.-..+ T Consensus 485 ~G~lis~~~g~~t~yal~~lq~rg~lfv~pg~~vy~GmivGe~~r~ 530 (607) T PRK10218 485 NGVLISNGQGKAVAFALFGLQDRGKLFLGHGAEVYEGQIIGIHSRS 530 (607) T ss_pred CEEEEECCCCEEHHHHHHHHHHCCCEEECCCCCEECCEEEEEECCC T ss_conf 5137975776178987753875453673699966887586760786 No 97 >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=29.62 E-value=29 Score=16.55 Aligned_cols=18 Identities=28% Similarity=0.381 Sum_probs=8.4 Q ss_pred CCCCCCEEEECCEEEEEE Q ss_conf 441120022031248998 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLS 51 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~v 51 (84) |.|+.|+.|++|+.||+. T Consensus 1191 i~V~~g~~V~~G~~~aef 1208 (1552) T TIGR02386 1191 ILVEDGDAVKEGQRIAEF 1208 (1552) T ss_pred EEEECCCCCCCCCEEEEE T ss_conf 886158620588757884 No 98 >PRK04192 V-type ATP synthase subunit A; Provisional Probab=29.46 E-value=30 Score=16.49 Aligned_cols=22 Identities=32% Similarity=0.563 Sum_probs=18.4 Q ss_pred CCCCCEEEECCEEEEEECCCCC Q ss_conf 4112002203124899805788 Q gi|254780683|r 35 YVQKGQKVSRGHTIGLSGKSGN 56 (84) Q Consensus 35 ~v~~G~~V~~G~~IG~vg~tg~ 56 (84) .++.||.|..|+.||++-.++. T Consensus 123 ~~~~Gd~v~~Gdilg~V~Et~~ 144 (585) T PRK04192 123 TVKVGDKVVAGDVLGTVQETGS 144 (585) T ss_pred CCCCCCCCCCCCEEEEEECCCC T ss_conf 1355874157865788504665 No 99 >TIGR02770 nickel_nikD nickel import ATP-binding protein NikD; InterPro: IPR014138 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are related families.. Probab=28.91 E-value=37 Score=15.96 Aligned_cols=36 Identities=22% Similarity=0.345 Sum_probs=25.6 Q ss_pred EEECCEEEEEECCCCCC--------------CCCEEEEEEEECCEECCHH Q ss_conf 22031248998057888--------------8856999997868980526 Q gi|254780683|r 41 KVSRGHTIGLSGKSGNA--------------QHPQVHFELRKNAIAMDPI 76 (84) Q Consensus 41 ~V~~G~~IG~vg~tg~~--------------~g~hLhfei~~~g~~vdP~ 76 (84) .++.|+++|.+|.||.. .-..--=||+-+|++++|. T Consensus 8 ~lk~G~~~aLvG~SGSGKS~tc~A~Lg~L~~~~~~~~G~i~l~G~~~~~~ 57 (239) T TIGR02770 8 SLKRGEVLALVGESGSGKSLTCLAILGLLPPGLTQTSGEILLDGRPLLAL 57 (239) T ss_pred EEECCEEEEEECCCCCCHHHHHHHHHCCCCCCCEEEEEEEEECCCCCCCC T ss_conf 03324378887487875899999985035865223102667717231458 No 100 >PRK11854 aceF dihydrolipoamide acetyltransferase; Validated Probab=28.69 E-value=35 Score=16.13 Aligned_cols=23 Identities=30% Similarity=0.283 Sum_probs=11.6 Q ss_pred CCCCCCCCCEEEECCEEEEEECC Q ss_conf 56344112002203124899805 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg~ 53 (84) +.+|.+++|+.|..|+.|+.++. T Consensus 157 ~~~i~~~~g~~v~~g~~i~~i~~ 179 (630) T PRK11854 157 VKEIKVNVGDKVSTGSLIMVFEV 179 (630) T ss_pred EEEECCCCCCEECCCCEEEEECC T ss_conf 88712689988447976788536 No 101 >cd06165 Sortase_A_1 Sortase A (SrtA) or subfamily-1 sortases are cysteine transpeptidases found in gram-positive bacteria that anchor surface proteins to peptidoglycans of the bacterial cell wall envelope. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal (usually a pentapeptide motif), and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes and subfamilies based on sequence, membrane topology, genomic positioning, and cleavage site preference. This group contains a subset of Class A (subfamily-1) sortases, excluding SrtA from Staphylococcus aureus. Sortase A cleaves between threonine and glycine of the LPXTG motif in a wide range of protein substrates. It affects the ability of a pathogen to establish successful infection. Sortase A contains an N-terminal region that functions as both a signal peptide for secretion and a stop-tra Probab=28.56 E-value=52 Score=15.22 Aligned_cols=59 Identities=19% Similarity=0.264 Sum_probs=30.4 Q ss_pred ECCCCCCCCEEEEEECCCCE-EEEEECCCCCCCCCCEEEECCEEEEEECCCCCCCCCEEEEEEEECCEECCHHH Q ss_conf 60698655119999989988-99841156344112002203124899805788888569999978689805269 Q gi|254780683|r 5 VGNDLVELGNTILIRHDDSI-VTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNAQHPQVHFELRKNAIAMDPIK 77 (84) Q Consensus 5 ~g~~~~~~G~~V~I~h~~g~-~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg~~~g~hLhfei~~~g~~vdP~~ 77 (84) .++...+-||+++--|..++ -+.+.+|+++. +||.| =..... ....|++... +.++|.+ T Consensus 34 ~~~~~~G~gN~viaGH~~~~~~~~F~~L~~l~--~GD~I------~v~~~~-----~~~~Y~V~~~-~iV~p~d 93 (127) T cd06165 34 KEDQKMGKGNYALAGHNMRNKGVLFSPLYKVK--VGDKI------YLTDKD-----NVYEYKVTSK-KIVDPTR 93 (127) T ss_pred CCCCCCCCCCEEEEECCCCCCCCCCCCHHHCC--CCCEE------EEEECC-----CEEEEEEEEE-EEECCCC T ss_conf 58766998869999365886765466765689--99999------999899-----3999999489-9999887 No 102 >KOG0559 consensus Probab=28.42 E-value=26 Score=16.76 Aligned_cols=23 Identities=22% Similarity=0.374 Sum_probs=15.3 Q ss_pred CCCCCCCCCEEEECCEEEEEECC Q ss_conf 56344112002203124899805 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg~ 53 (84) +.++.|+.||+|+.||.++.+.. T Consensus 126 i~e~lvk~gdtV~~g~~la~i~~ 148 (457) T KOG0559 126 ITELLVKDGDTVTPGQKLAKISP 148 (457) T ss_pred EEEEECCCCCCCCCCCEEEEECC T ss_conf 45774078975047864577358 No 103 >TIGR01936 nqrA NADH:ubiquinone oxidoreductase, Na(+)-translocating, A subunit; InterPro: IPR008703 This family consists of several bacterial Na^+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na^+-translocating NADH: ubiquinone oxidoreductase (Na^+-NQR) generates an electrochemical Na^+ potential driven by aerobic respiration .; GO: 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0006814 sodium ion transport. Probab=27.24 E-value=19 Score=17.54 Aligned_cols=43 Identities=16% Similarity=0.202 Sum_probs=27.4 Q ss_pred EECCC-CCCCCCCEEEECCEEEEEECCCCC------CCCCEEEEEEEECCEE Q ss_conf 41156-344112002203124899805788------8885699999786898 Q gi|254780683|r 28 YSHID-TPYVQKGQKVSRGHTIGLSGKSGN------AQHPQVHFELRKNAIA 72 (84) Q Consensus 28 Y~hl~-~i~v~~G~~V~~G~~IG~vg~tg~------~~g~hLhfei~~~g~~ 72 (84) |..|. ++.|++||.|++||+|..--.-.. .+| -=.+|+++.|. T Consensus 36 f~g~~p~~~v~~GD~V~~G~~L~~~K~~P~v~fTsPvsG--~V~ai~RG~KR 85 (466) T TIGR01936 36 FEGLRPKMKVRPGDKVKAGQVLFEDKKNPGVKFTSPVSG--EVVAINRGAKR 85 (466) T ss_pred CCCCCCEEEEEECCEEEECCHHHHHCCCCCCEEECCCCC--EEEEEECCCCC T ss_conf 878665067700770100222333026898568617775--69997418972 No 104 >TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345 These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. . Probab=26.14 E-value=4.1 Score=21.02 Aligned_cols=52 Identities=23% Similarity=0.383 Sum_probs=43.5 Q ss_pred CEEEECCCCCCCCEEEEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEECCCCCC Q ss_conf 599960698655119999989988998411563441120022031248998057888 Q gi|254780683|r 1 MVIYVGNDLVELGNTILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLSGKSGNA 57 (84) Q Consensus 1 VVv~~g~~~~~~G~~V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg~~ 57 (84) |++.+| .+|+|++-+|+ +...+|.-++......-+.|.-.+.|....=||++ T Consensus 367 v~iLTG--GPGTGKtT~t~---~i~~~~~~~~gl~l~~~~~vndd~~v~LaAPTGrA 418 (769) T TIGR01448 367 VVILTG--GPGTGKTTITK---AIIELYEELKGLDLDKDDYVNDDLPVVLAAPTGRA 418 (769) T ss_pred EEEEEC--CCCCCHHHHHH---HHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCHHH T ss_conf 899857--78886168999---99999987168775531245677648873774378 No 105 >TIGR03327 AMP_phos AMP phosphorylase. This enzyme family is found, so far, strictly in the Archaea, and only in those with a type III Rubisco enzyme. Most of the members previously were annotated as thymidine phosphorylase, or DeoA. The AMP metabolized by this enzyme may be produced by ADP-dependent sugar kinases. Probab=25.62 E-value=38 Score=15.91 Aligned_cols=21 Identities=24% Similarity=0.240 Sum_probs=15.0 Q ss_pred CCCCCCEEEECCEEEEEECCC Q ss_conf 441120022031248998057 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~t 54 (84) +.+|.||.|++||+|.++=.+ T Consensus 452 l~~k~Gd~V~~GdpL~tiha~ 472 (500) T TIGR03327 452 LHVKVGEKVKKGDPLYTIYAE 472 (500) T ss_pred EECCCCCEECCCCEEEEEECC T ss_conf 843687987799939999779 No 106 >pfam02749 QRPTase_N Quinolinate phosphoribosyl transferase, N-terminal domain. Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase EC:2.4.2.19 is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other. The N-terminal domain has an alpha/beta hammerhead fold. Probab=25.20 E-value=39 Score=15.87 Aligned_cols=20 Identities=25% Similarity=0.243 Sum_probs=16.6 Q ss_pred CCCCCCEEEECCEEEEEECC Q ss_conf 44112002203124899805 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~ 53 (84) ..++.|+.|++||+|.++-. T Consensus 49 ~~~~dG~~v~~g~~i~~i~G 68 (88) T pfam02749 49 WLVKDGERVEAGDVILEIEG 68 (88) T ss_pred EECCCCCEECCCCEEEEEEE T ss_conf 99688999179999999998 No 107 >TIGR01108 oadA oxaloacetate decarboxylase alpha subunit; InterPro: IPR005776 This family describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea . The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.; GO: 0008948 oxaloacetate decarboxylase activity, 0006814 sodium ion transport. Probab=25.15 E-value=26 Score=16.77 Aligned_cols=46 Identities=20% Similarity=0.199 Sum_probs=26.1 Q ss_pred CCCCCCCCCEEEECCEEEEEECCCC-----CC--CCCEEE-EEEEECCEECCHHHH Q ss_conf 5634411200220312489980578-----88--885699-999786898052698 Q gi|254780683|r 31 IDTPYVQKGQKVSRGHTIGLSGKSG-----NA--QHPQVH-FELRKNAIAMDPIKF 78 (84) Q Consensus 31 l~~i~v~~G~~V~~G~~IG~vg~tg-----~~--~g~hLh-fei~~~g~~vdP~~~ 78 (84) .=++.|+.||.|++||++=-+..-. .+ .| -++ |-+ +.|..|+|-+. T Consensus 562 i~~~~V~~G~~V~~G~vlL~~EAMKME~Ei~A~~aG-~V~~i~v-~~Gd~V~~gqV 615 (616) T TIGR01108 562 IVKITVSEGDEVKEGEVLLVVEAMKMETEIKAAAAG-IVEEILV-KKGDKVSPGQV 615 (616) T ss_pred EEEEEECCCCEECCCCEEEEEECCCCCHHHCCCCCC-CEEEEEE-CCCCEECCCCC T ss_conf 699983578743157758853100111220054357-0112344-57875088667 No 108 >TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA; InterPro: IPR011917 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes .; GO: 0005524 ATP binding, 0006869 lipid transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane. Probab=24.54 E-value=46 Score=15.48 Aligned_cols=30 Identities=30% Similarity=0.503 Sum_probs=20.3 Q ss_pred EEEEEEC-----CCCCCCCCCEEEECCEEEEEECCCCCC Q ss_conf 8998411-----563441120022031248998057888 Q gi|254780683|r 24 IVTVYSH-----IDTPYVQKGQKVSRGHTIGLSGKSGNA 57 (84) Q Consensus 24 ~~t~Y~h-----l~~i~v~~G~~V~~G~~IG~vg~tg~~ 57 (84) ....|.. |++|+ =.|++|+.+|.||.||.. T Consensus 366 v~~~Yp~~~~~aL~~i~----l~~~~G~~vALVGRSGSG 400 (603) T TIGR02203 366 VTFRYPGRDRPALDSIS----LVVEPGETVALVGRSGSG 400 (603) T ss_pred EEEEECCCCHHHHCCCC----CEECCCCEEEEECCCCCH T ss_conf 66653788724123666----511587359987068853 No 109 >COG0444 DppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism] Probab=24.48 E-value=50 Score=15.30 Aligned_cols=17 Identities=29% Similarity=0.751 Sum_probs=14.2 Q ss_pred EEEECCEEEEEECCCCC Q ss_conf 02203124899805788 Q gi|254780683|r 40 QKVSRGHTIGLSGKSGN 56 (84) Q Consensus 40 ~~V~~G~~IG~vg~tg~ 56 (84) =.|++|+.+|.+|.||. T Consensus 26 ~~i~~GE~lgiVGESGs 42 (316) T COG0444 26 FELKKGEILGIVGESGS 42 (316) T ss_pred EEECCCCEEEEECCCCC T ss_conf 88758968999838978 No 110 >cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor. The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology. Probab=24.11 E-value=45 Score=15.52 Aligned_cols=28 Identities=25% Similarity=0.430 Sum_probs=20.0 Q ss_pred EEECCCCCCCCCCEEEECCEEEEEECCCCC Q ss_conf 841156344112002203124899805788 Q gi|254780683|r 27 VYSHIDTPYVQKGQKVSRGHTIGLSGKSGN 56 (84) Q Consensus 27 ~Y~hl~~i~v~~G~~V~~G~~IG~vg~tg~ 56 (84) ++.+++ +.++.| .+++|+.+|.+|.+|. T Consensus 9 ~l~~~s-L~i~~G-ti~~GEiv~liGpNGa 36 (246) T cd03237 9 TLGEFT-LEVEGG-SISESEVIGILGPNGI 36 (246) T ss_pred ECCEEE-EEECCC-CCCCCCEEEEECCCCC T ss_conf 615068-985688-4657989999979997 No 111 >TIGR00998 8a0101 efflux pump membrane protein; InterPro: IPR005694 emrA and emrB confer resistance to carbonylcyanide m-chlorophenylhydrazone, nalidixic acid, and a number of other toxic compounds. EmrB encodes a highly hydrophobic 56.2-kDa peptide, with 14 potential alpha-helices to span the inner membrane. EmrA encodes a putative 42.7-kDa peptide containing a single hydrophobic domain and a large C-terminal hydrophilic domain.; GO: 0015238 drug transporter activity, 0006855 multidrug transport, 0009276 1-2nm peptidoglycan-based cell wall. Probab=22.73 E-value=30 Score=16.47 Aligned_cols=30 Identities=30% Similarity=0.206 Sum_probs=17.3 Q ss_pred EEEECCCCEEEEEECCCCCCCCCCEEEECCEEEEEE Q ss_conf 999989988998411563441120022031248998 Q gi|254780683|r 16 ILIRHDDSIVTVYSHIDTPYVQKGQKVSRGHTIGLS 51 (84) Q Consensus 16 V~I~h~~g~~t~Y~hl~~i~v~~G~~V~~G~~IG~v 51 (84) .++.-=+|+.+ +..|++||.|++|++|=.+ T Consensus 246 ~iraP~dG~Va------~r~vqvG~~vS~g~p~ma~ 275 (379) T TIGR00998 246 EIRAPFDGYVA------RRKVQVGQVVSPGQPLMAV 275 (379) T ss_pred EEECCCCCEEE------EEECCCCCEECCCCCEEEE T ss_conf 64367220587------7630788611589725777 No 112 >cd04493 BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). BRCA2DBD OB1 binds DNA weakly. Probab=22.62 E-value=68 Score=14.59 Aligned_cols=59 Identities=22% Similarity=0.457 Sum_probs=39.7 Q ss_pred CEEEEEECCCCEEEEEECCCCCC---CCCCEEEECCEEEEEECCC--CCC-------CCCEEEEEEEECCEE Q ss_conf 11999998998899841156344---1120022031248998057--888-------885699999786898 Q gi|254780683|r 13 GNTILIRHDDSIVTVYSHIDTPY---VQKGQKVSRGHTIGLSGKS--GNA-------QHPQVHFELRKNAIA 72 (84) Q Consensus 13 G~~V~I~h~~g~~t~Y~hl~~i~---v~~G~~V~~G~~IG~vg~t--g~~-------~g~hLhfei~~~g~~ 72 (84) ..+-+|.-.|||+++.+.||... +++|. +.-||.|...|.. +.. ....+.+.+..|+.. T Consensus 20 ~~~~~ieltDGWY~i~a~lD~~L~~~l~~Gk-l~vGqKL~i~GA~L~g~~~~~sple~~~~~~L~i~~Nstr 90 (100) T cd04493 20 PHMPIIELTDGWYSIRAQLDPPLTNLVRKGK-LRVGQKLRICGAELLGSANPCSPLEAPDSVRLKINANSTR 90 (100) T ss_pred CCCCEEEEECCCEEEEEECCHHHHHHHHCCC-CCCCCEEEEECCEEECCCCCCCCCCCCCCEEEEEECCCCC T ss_conf 8536799954818986872998999998597-2147589998878645889858415624439999647630 No 113 >PRK00044 psd phosphatidylserine decarboxylase; Reviewed Probab=22.61 E-value=45 Score=15.55 Aligned_cols=14 Identities=21% Similarity=0.596 Sum_probs=9.5 Q ss_pred EEECCEEEEE--ECCC Q ss_conf 2203124899--8057 Q gi|254780683|r 41 KVSRGHTIGL--SGKS 54 (84) Q Consensus 41 ~V~~G~~IG~--vg~t 54 (84) .+++||.+|. .|+| T Consensus 239 ~l~KGeElG~F~~GST 254 (291) T PRK00044 239 ALEKGQEMGRFKLGST 254 (291) T ss_pred CCCCCCEEEEECCCCE T ss_conf 3134327327547881 No 114 >COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms] Probab=22.35 E-value=62 Score=14.82 Aligned_cols=45 Identities=22% Similarity=0.380 Sum_probs=31.4 Q ss_pred CCCCEEEEEECCCCEEEEEECC-----CCCCCCCCEEEECCEEEEEECCC Q ss_conf 6551199999899889984115-----63441120022031248998057 Q gi|254780683|r 10 VELGNTILIRHDDSIVTVYSHI-----DTPYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 10 ~~~G~~V~I~h~~g~~t~Y~hl-----~~i~v~~G~~V~~G~~IG~vg~t 54 (84) .+--|-+.|...+|-.+.|+-. ..+++.+|+.|-.|.+||.-..+ T Consensus 480 ~~R~nGvLiS~~~G~a~~yal~~lqdRG~~Fi~pG~~vYeGmiiG~hsR~ 529 (603) T COG1217 480 GGRHNGVLISNETGKAVAYALFNLQDRGKLFIEPGTKVYEGMIIGEHSRD 529 (603) T ss_pred CCCCCCEEEECCCCCCHHHHHHHHHHCCCEEECCCCCEEEEEEEEEECCC T ss_conf 55545159976898434765535875375664599726501698530675 No 115 >COG0213 DeoA Thymidine phosphorylase [Nucleotide transport and metabolism] Probab=22.34 E-value=59 Score=14.90 Aligned_cols=20 Identities=20% Similarity=0.232 Sum_probs=17.0 Q ss_pred CCCCCCEEEECCEEEEEECC Q ss_conf 44112002203124899805 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~ 53 (84) +..|.|+.|++|++|.++-. T Consensus 381 l~kk~ge~Vk~Gd~l~tiya 400 (435) T COG0213 381 LHKKLGEKVKKGDPLATIYA 400 (435) T ss_pred EEECCCCEECCCCEEEEEEC T ss_conf 98317983026974799862 No 116 >PRK03140 phosphatidylserine decarboxylase; Provisional Probab=21.93 E-value=44 Score=15.60 Aligned_cols=18 Identities=11% Similarity=0.241 Sum_probs=14.1 Q ss_pred CCCCEEEECCEEEEEECC Q ss_conf 112002203124899805 Q gi|254780683|r 36 VQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 36 v~~G~~V~~G~~IG~vg~ 53 (84) ...++.|++||.+|.--- T Consensus 207 t~~~~~v~KGdE~G~F~~ 224 (259) T PRK03140 207 THERDTVQKGEEMAYFSF 224 (259) T ss_pred ECCCCEECCCCEEEEECC T ss_conf 579971711428423257 No 117 >KOG0369 consensus Probab=21.86 E-value=34 Score=16.16 Aligned_cols=20 Identities=25% Similarity=0.474 Sum_probs=17.0 Q ss_pred CCCCCCCEEEECCEEEEEEC Q ss_conf 34411200220312489980 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSG 52 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg 52 (84) +|.|++|++|++||+|.-.. T Consensus 1119 eikvk~G~kV~Kgqpl~VLS 1138 (1176) T KOG0369 1119 EIKVKEGAKVKKGQPLAVLS 1138 (1176) T ss_pred EEEEECCCEECCCCCEEEEE T ss_conf 99983075103798357612 No 118 >KOG2419 consensus Probab=21.55 E-value=61 Score=14.82 Aligned_cols=21 Identities=19% Similarity=0.324 Sum_probs=17.4 Q ss_pred CCCCCCEEEECCEEEEEECCC Q ss_conf 441120022031248998057 Q gi|254780683|r 34 PYVQKGQKVSRGHTIGLSGKS 54 (84) Q Consensus 34 i~v~~G~~V~~G~~IG~vg~t 54 (84) +.+++|+.|++||.+|+-.-- T Consensus 898 lt~kEgd~V~~gdELGYFkFG 918 (975) T KOG2419 898 LTRKEGDHVKKGDELGYFKFG 918 (975) T ss_pred EEEECCCCCCCCCCCCEEEEC T ss_conf 996057601246600047507 No 119 >CHL00117 rpoC2 RNA polymerase beta'' subunit; Reviewed Probab=21.20 E-value=55 Score=15.08 Aligned_cols=21 Identities=24% Similarity=0.102 Sum_probs=17.9 Q ss_pred CCCCCCCEEEECCEEEEEECC Q ss_conf 344112002203124899805 Q gi|254780683|r 33 TPYVQKGQKVSRGHTIGLSGK 53 (84) Q Consensus 33 ~i~v~~G~~V~~G~~IG~vg~ 53 (84) -+.|+.||.|+++|+||.+-. T Consensus 408 lL~V~n~q~V~s~QvIAEi~~ 428 (1350) T CHL00117 408 LLLVQNDQYVESEQVIAEIRA 428 (1350) T ss_pred EEEEECCCEEECCCEEEEEEC T ss_conf 899989958751618999705 No 120 >PRK00624 glycine cleavage system protein H; Provisional Probab=20.69 E-value=58 Score=14.94 Aligned_cols=22 Identities=18% Similarity=0.178 Sum_probs=18.5 Q ss_pred CCCCEEEECCEEEEEECCCCCC Q ss_conf 1120022031248998057888 Q gi|254780683|r 36 VQKGQKVSRGHTIGLSGKSGNA 57 (84) Q Consensus 36 v~~G~~V~~G~~IG~vg~tg~~ 57 (84) -+.|+.|++|+.+|.+.+.... T Consensus 39 p~~G~~v~~g~~~~~iEs~K~~ 60 (113) T PRK00624 39 PSVGSFCKEGEVLVILESSKSA 60 (113) T ss_pred CCCCCEEECCCEEEEEEECCEE T ss_conf 9999988479859999965244 Done!