Query gi|254781206|ref|YP_003065619.1| hypothetical protein CLIBASIA_05565 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 1246 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Tue May 31 16:24:06 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254781206.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam03469 XH XH domain. The XH 85.1 0.65 1.7E-05 25.0 2.3 86 903-989 19-118 (135) 2 KOG2007 consensus 82.8 3.1 8E-05 20.0 10.8 16 944-959 541-556 (586) 3 PHA00661 hypothetical protein 80.5 0.44 1.1E-05 26.2 0.0 83 1153-1235 641-730 (734) 4 COG0275 Predicted S-adenosylme 77.2 4.2 0.00011 19.1 4.1 217 684-935 6-229 (314) 5 KOG3088 consensus 68.5 3.9 0.0001 19.3 2.3 68 561-628 60-139 (313) 6 TIGR02401 trehalose_TreY malto 53.2 13 0.00033 15.5 3.2 37 845-881 869-906 (971) 7 KOG0760 consensus 47.9 7.4 0.00019 17.3 0.8 22 801-822 111-132 (302) 8 TIGR01793 cit_synth_euk citrat 44.7 8 0.0002 17.1 0.6 17 519-535 128-144 (430) 9 TIGR02858 spore_III_AA stage I 44.7 14 0.00036 15.3 1.8 27 799-825 8-36 (282) 10 TIGR03549 conserved hypothetic 44.6 18 0.00045 14.6 2.8 60 679-738 335-406 (718) 11 pfam08355 EF_assoc_1 EF hand a 41.9 6.8 0.00017 17.6 -0.1 26 645-670 9-34 (75) 12 TIGR00441 gmhA phosphoheptose 38.0 4.3 0.00011 19.0 -1.7 56 641-715 80-135 (186) 13 PRK06770 hypothetical protein; 37.2 22 0.00057 13.8 5.3 61 133-194 77-137 (185) 14 pfam07886 BA14K BA14K-like pro 37.1 15 0.00037 15.2 1.0 21 618-638 4-24 (31) 15 KOG1302 consensus 36.0 23 0.00059 13.7 1.8 23 736-758 195-217 (600) 16 KOG1831 consensus 35.1 24 0.00062 13.6 4.1 58 214-271 382-443 (1591) 17 pfam07159 DUF1394 Protein of u 33.5 10 0.00026 16.3 -0.3 17 642-658 131-147 (304) 18 pfam01582 TIR TIR domain. The 32.9 26 0.00067 13.3 2.2 99 953-1061 10-123 (139) 19 COG0279 GmhA Phosphoheptose is 32.4 12 0.00031 15.8 -0.1 66 632-716 72-138 (176) 20 pfam06265 DUF1027 Protein of u 32.1 11 0.00027 16.1 -0.4 11 54-64 31-41 (86) 21 TIGR02622 CDP_4_6_dhtase CDP-g 31.8 15 0.00038 15.1 0.3 31 984-1014 94-124 (361) 22 TIGR03354 VI_FHA type VI secre 30.7 28 0.00072 13.1 1.7 31 677-707 299-329 (396) 23 COG3102 Uncharacterized protei 30.5 20 0.0005 14.2 0.7 64 1032-1097 111-174 (185) 24 KOG1029 consensus 30.4 29 0.00073 13.1 4.3 39 389-427 325-363 (1118) 25 PRK11700 hypothetical protein; 28.1 29 0.00074 13.0 1.3 52 1032-1085 110-161 (186) 26 TIGR01330 bisphos_HAL2 3'(2'), 27.8 32 0.0008 12.8 4.3 59 1133-1196 134-192 (382) 27 KOG2874 consensus 26.8 33 0.00084 12.6 2.8 90 921-1020 127-223 (356) 28 pfam01591 6PF2K 6-phosphofruct 25.7 34 0.00087 12.5 1.8 24 608-631 157-180 (223) 29 pfam07852 DUF1642 Protein of u 23.5 18 0.00047 14.5 -0.5 16 844-859 114-131 (136) 30 TIGR01026 fliI_yscN ATPase Fli 23.4 38 0.00096 12.2 3.3 45 632-691 409-455 (455) 31 KOG2830 consensus 23.4 38 0.00096 12.2 2.7 26 449-479 249-274 (324) 32 KOG4003 consensus 23.3 5.8 0.00015 18.1 -3.1 39 659-698 60-101 (223) 33 pfam02572 CobA_CobO_BtuR ATP:c 23.1 30 0.00076 12.9 0.5 45 72-116 94-138 (172) 34 TIGR02924 ICDH_alpha isocitrat 23.0 21 0.00052 14.1 -0.3 233 642-926 78-333 (481) 35 KOG0616 consensus 22.9 32 0.00082 12.7 0.7 34 764-806 90-123 (355) 36 pfam06593 RBDV_coat Raspberry 22.9 37 0.00095 12.2 1.0 23 1134-1156 225-247 (274) 37 pfam05565 Sipho_Gp157 Siphovir 22.5 23 0.00058 13.8 -0.2 31 20-50 22-52 (162) 38 pfam03846 SulA Cell division i 21.9 38 0.00097 12.2 0.9 18 701-718 96-113 (119) 39 KOG4682 consensus 21.9 40 0.001 12.0 4.9 79 665-756 126-215 (488) 40 pfam04227 Indigoidine_A Indigo 21.5 16 0.0004 15.0 -1.2 34 85-118 145-178 (293) 41 PHA00652 hypothetical protein 21.5 41 0.001 11.9 5.5 11 71-81 16-26 (128) 42 TIGR02790 nickel_nikC nickel A 21.2 34 0.00088 12.5 0.5 11 986-996 38-48 (258) 43 pfam09568 RE_MjaI MjaI restric 21.2 6.6 0.00017 17.7 -3.2 53 918-974 2-59 (201) 44 COG4710 Predicted DNA-binding 20.8 42 0.0011 11.8 2.4 55 64-118 16-73 (80) 45 cd01820 PAF_acetylesterase_lik 20.7 42 0.0011 11.8 1.4 19 674-692 190-208 (214) No 1 >pfam03469 XH XH domain. The XH (rice gene X Homology) domain is found in a family of plant proteins including gene X. The molecular function of these proteins is unknown. However these proteins usually contain an XS domain that is also found in the PTGS protein SGS3. This domain contains a conserved glutamate residue that may be functionally important. Probab=85.11 E-value=0.65 Score=24.95 Aligned_cols=86 Identities=31% Similarity=0.468 Sum_probs=61.4 Q ss_pred HHHHHHCCHHHHHHHHHHHHHHHHHHHH----HHHHCCCCCCCCCCHHHHHHHHHHHHH----HHHHHHHHHHCCCCCCC Q ss_conf 6633211388999999998899999999----986200013878870178999999999----99999766642664200 Q gi|254781206|r 903 AKKYKESNDERIVSFIRSEFEREIKELK----SVIEADAKENPNPNKNQKKLQKTREKL----VAQLSSRLKELNIDNAY 974 (1246) Q Consensus 903 akkykesnderivsfirsefereikelk----svieadakenpnpnknqkklqktrekl----vaqlssrlkelnidnay 974 (1246) -+||-+..-+--.+.+.|..+.+|+... -||..+.++-.--|.+..+||.-++.+ ..-...-|.|+|--|+- T Consensus 19 k~k~~~~~~~~~a~~l~S~Wq~~ikdp~whPFkvv~~~g~~~evi~edDekL~~Lk~e~Geevy~aV~~AL~E~nEyN~s 98 (135) T pfam03469 19 KRKYVEEDAEVRAAELCSLWEENIKDPDWHPFKVVETGEIEKEVVDEDDEKLKKLKEEWGEEVYNAVKKALLEMNEYNPS 98 (135) T ss_pred HHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 86678116889999999999998348887861686219857774058709999999998599999999999999850878 Q ss_pred C------HHHHHHHHHHHHCC Q ss_conf 0------03667765653015 Q gi|254781206|r 975 G------LWNEYKEDFKASFE 989 (1246) Q Consensus 975 g------lwneykedfkasfe 989 (1246) | ||| |||+-||+.. T Consensus 99 Gry~v~ELWN-fke~RKATlk 118 (135) T pfam03469 99 GRYPTPELWN-FKEGRKATLK 118 (135) T ss_pred CCCCCCCCCC-CCCCCCCCHH T ss_conf 8877521345-5345645599 No 2 >KOG2007 consensus Probab=82.77 E-value=3.1 Score=20.01 Aligned_cols=16 Identities=44% Similarity=0.667 Sum_probs=8.6 Q ss_pred CHHHHHHHHHHHHHHH Q ss_conf 7017899999999999 Q gi|254781206|r 944 NKNQKKLQKTREKLVA 959 (1246) Q Consensus 944 nknqkklqktreklva 959 (1246) +|.++|.+..|+++.+ T Consensus 541 ~K~~~k~d~~~~~~~~ 556 (586) T KOG2007 541 NKDKEKSDRIREELAA 556 (586) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 7777778999999987 No 3 >PHA00661 hypothetical protein Probab=80.54 E-value=0.44 Score=26.16 Aligned_cols=83 Identities=19% Similarity=0.190 Sum_probs=62.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHH----HHCCC---CCCCCEEEEECCCCCCCHHEEEEECCCCEE Q ss_conf 23443211357998887874000010211034432088----85599---866715888217787772018886488547 Q gi|254781206|r 1153 SFNSTMGKKRRIFKVVVRVINTADLEVGILGFPIVPVE----ELRGK---PKTGEFEVLVPSDASLNPEIIIRQKTGGYF 1225 (1246) Q Consensus 1153 sfnstmgkkrrifkvvvrvintadlevgilgfpivpve----elrgk---pktgefevlvpsdaslnpeiiirqktggyf 1225 (1246) .-.+.+|++|||-.|++|+-+|-.+.||--+-.+.++. +--+. +.||..++.+++.-+-.+.|.|+|-.-=-+ T Consensus 641 ~~G~~~G~~krI~~v~~rl~~T~g~~vg~~~~~l~~~~~r~~~~~~~p~~~~tg~~~v~~~~g~~~~g~i~i~Q~~PLPl 720 (734) T PHA00661 641 DGSFGQGKVKNINKLWLRVHRSSGIFAGPHADALTEVKQRESEPYGSPPALKSEEVPLVLSSKWGDSGQLFVRQADPLPL 720 (734) T ss_pred CCCCCCCEEEEEEEEEEEEEECCCEEECCCCCCCEECCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCEEEEECCCCCE T ss_conf 87744662489999999998013579789867425656556322368986566746756378978786189994799876 Q ss_pred EEEEECCCCC Q ss_conf 7652011222 Q gi|254781206|r 1226 CLTSITAHTQ 1235 (1246) Q Consensus 1226 cltsitahtq 1235 (1246) -+-+|...-. T Consensus 721 tvLai~~~v~ 730 (734) T PHA00661 721 MILSMSPELA 730 (734) T ss_pred EEEEEEEEEE T ss_conf 9998899998 No 4 >COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane] Probab=77.17 E-value=4.2 Score=19.12 Aligned_cols=217 Identities=23% Similarity=0.294 Sum_probs=118.0 Q ss_pred HHHHHHHHHHHHHHHCCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 999999999986521261378--88898876216656665588764200020-233778999999988886663612242 Q gi|254781206|r 684 QKLDVLFRHCIENLRANKNAV--DAMSKAVEAGESSVRKHSFEVLSSKHQKS-VIAVNNFIKEITHHTRRLVKEDPKRGK 760 (1246) Q Consensus 684 qkldvlfrhcienlranknav--damskaveagessvrkhsfevlsskhqks-viavnnfikeithhtrrlvkedpkrgk 760 (1246) ...-||...||++|..+.+++ |+. -..--||-..|+.--... +|+..-=-.-|..-..+|..-++.-.- T Consensus 6 ~HipVLl~E~i~~L~~~~~giyiD~T--------lG~GGHS~~iL~~l~~~~~li~~DrD~~Ai~~a~~~l~~~~~r~~~ 77 (314) T COG0275 6 RHIPVLLNEVVELLAPKPDGIYIDGT--------LGAGGHSRAILEKLPDLGRLIGIDRDPQAIAIAKERLKEFDGRVTL 77 (314) T ss_pred CCCCHHHHHHHHHCCCCCCCEEEEEC--------CCCCHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHCCCCCEEE T ss_conf 76211799999852648994799823--------7774768999985898870899768989999999985303784899 Q ss_pred HHHHHHHHHHHHHHHHHHEEEEEEEEEEEEHHHHCCCCCCCEEEEECCCCHHCCCCCCCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 14578999999998531100026655522013317532798268831851010376357986434102320035888998 Q gi|254781206|r 761 SESYLSDIRSELQKVNKTVMDIRIKLRLYGIFQDIPQEQPPLYTIISGSEKILQGDYTFPPLSSLDVQSKFDSSYSKLFE 840 (1246) Q Consensus 761 sesylsdirselqkvnktvmdiriklrlygifqdipqeqpplytiisgsekilqgdytfpplssldvqskfdssysklfe 840 (1246) -.+-.+++...|...+.+ ..-||.-|+----|-|-.- .-.+.|---..||..-.-++..| T Consensus 78 v~~~F~~l~~~l~~~~i~--------~vDGiL~DLGVSS~QLD~~--------eRGFSf~~d~pLDMRMd~~~~ls---- 137 (314) T COG0275 78 VHGNFANLAEALKELGIG--------KVDGILLDLGVSSPQLDDA--------ERGFSFRKDGPLDMRMDQTQGLS---- 137 (314) T ss_pred EECCHHHHHHHHHHCCCC--------CEEEEEEECCCCCCCCCCC--------CCCCCCCCCCCCCCCCCCCCCCC---- T ss_conf 957687899888763887--------2227999536783202887--------67860278898656748888978---- Q ss_pred HHHCCCCCCCCCCCCEEEEEEE--EHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH-HHH-HCCHHHHHH Q ss_conf 8831123221000120231110--033200111235688752033087743011899999887666-332-113889999 Q gi|254781206|r 841 IFYGDWTNNAIKEERYWTIYAF--ERSLKNQAHLNAEVERLSGLAQQPSDSTADLKELQTQLSRAK-KYK-ESNDERIVS 916 (1246) Q Consensus 841 ifygdwtnnaikeerywtiyaf--erslknqahlnaeverlsglaqqpsdstadlkelqtqlsrak-kyk-esnderivs 916 (1246) --||-|+.-.++-.|-+|-| ||--+--| .+-|++-. .+|-.+|.+|.|+-.+...++ +++ -.--.|+.- T Consensus 138 --A~evvN~~~e~~L~~I~~~yGEEr~arrIA--~aIv~~R~---~~pi~tT~eLaeiI~~~~p~~~~~k~~hPAtr~FQ 210 (314) T COG0275 138 --AAEVVNTYSEEDLARIFKEYGEERFAKRIA--RAIVERRK---KKPIETTKELAEIIKSAIPAKEKRKKIHPATRTFQ 210 (314) T ss_pred --HHHHHHCCCHHHHHHHHHHHCCHHHHHHHH--HHHHHHHC---CCCCCCHHHHHHHHHHHCCCHHCCCCCCCCHHHHH T ss_conf --999985599999999999845176689999--99999862---69876699999999986770111367895066563 Q ss_pred HHHHHHHHHHHHHHHHHHC Q ss_conf 9999889999999998620 Q gi|254781206|r 917 FIRSEFEREIKELKSVIEA 935 (1246) Q Consensus 917 firsefereikelksviea 935 (1246) -||-+..+|..+|+..+++ T Consensus 211 AiRI~VNdEL~~L~~~L~~ 229 (314) T COG0275 211 AIRIYVNDELEELEEALEA 229 (314) T ss_pred HHEEEEHHHHHHHHHHHHH T ss_conf 4100005679999999999 No 5 >KOG3088 consensus Probab=68.46 E-value=3.9 Score=19.30 Aligned_cols=68 Identities=28% Similarity=0.445 Sum_probs=40.9 Q ss_pred CEECHHHHHHHHHHHCCHHHH--HHHH-HHCCH--HHHHHHHHHHHHHHCCCCH-------HHHHHHHHHHHHHHHHCCC Q ss_conf 011012688787784330999--9876-31124--5666753221564405897-------8999999999988751357 Q gi|254781206|r 561 IKLTKKEKELQEQEENLRVAE--IIQQ-SRMQS--EDLQEKAWDSYKEWKSLSP-------DEIKQRFQKYAKVFYRSYS 628 (1246) Q Consensus 561 ikltkkekelqeqeenlrvae--iiqq-srmqs--edlqekawdsykewkslsp-------deikqrfqkyakvfyrsys 628 (1246) -.+.+|++|||.++|.||--| +-.. ..||. --.+++-|-..-.|-..-| .||-..|||-.|+.|..+- T Consensus 60 ~~~~~kq~eL~~rqeEL~Rke~ELdRREr~~a~~g~~~~~nNWPPLP~~~pv~PcfyqD~s~EIPv~~Qk~vk~~yylwm 139 (313) T KOG3088 60 KDLAKKQAELLKKQEELRRKEQELDRRERALARAGIVIRENNWPPLPSFIPVFPCFYQDISNEIPVEFQKLVKRAYYLWM 139 (313) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 68999999999999999878988737899986246766546899997778755500113322268999999999999999 No 6 >TIGR02401 trehalose_TreY malto-oligosyltrehalose synthase; InterPro: IPR012767 This enzyme, formally named (1->4)-alpha-D-glucan 1-alpha-D-glucosylmutase, is the TreY enzyme of the TreYZ pathway of trehalose biosynthesis, an alternative to the OtsAB pathway. Trehalose may be incorporated into more complex compounds but is best known as compatible solute. It is one of the most effective osmoprotectants, and unlike the various betaines does not require nitrogen for its synthesis.. Probab=53.23 E-value=13 Score=15.52 Aligned_cols=37 Identities=27% Similarity=0.175 Sum_probs=16.0 Q ss_pred CCCCCCCCCCCEEEEEEEEHHHCCHHH-HHHHHHHHHH Q ss_conf 123221000120231110033200111-2356887520 Q gi|254781206|r 845 DWTNNAIKEERYWTIYAFERSLKNQAH-LNAEVERLSG 881 (1246) Q Consensus 845 dwtnnaikeerywtiyaferslknqah-lnaeverlsg 881 (1246) |+----+.-.+-=-+-||.|+..+|+- +-.-|.||+- T Consensus 869 dY~Pl~~~G~~a~HviAF~R~~~~~~~s~iv~v~Rl~~ 906 (971) T TIGR02401 869 DYRPLEASGPGAAHVIAFARGTDRQALSAIVVVTRLSL 906 (971) T ss_pred CCEEEECCCCCCCEEEEEEECCCCCCEEEEEEEECCCH T ss_conf 81256445766325888710688854577887502103 No 7 >KOG0760 consensus Probab=47.86 E-value=7.4 Score=17.31 Aligned_cols=22 Identities=36% Similarity=0.484 Sum_probs=9.3 Q ss_pred CEEEEECCCCHHCCCCCCCCCC Q ss_conf 8268831851010376357986 Q gi|254781206|r 801 PLYTIISGSEKILQGDYTFPPL 822 (1246) Q Consensus 801 plytiisgsekilqgdytfppl 822 (1246) ||-+-|||.--.+-.|.-+-|+ T Consensus 111 ~la~aisG~~At~~sDAvm~P~ 132 (302) T KOG0760 111 PLAYAISGACATLISDAVMNPF 132 (302) T ss_pred HHHHHHHHHHHHHHHHHHCCHH T ss_conf 7898987889999988756989 No 8 >TIGR01793 cit_synth_euk citrate (Si)-synthase, eukaryotic; InterPro: IPR010109 Citrate synthase 2.3.3.1 from EC is a member of a small family of enzymes that can directly form a carbon-carbon bond without the presence of metal ion cofactors. It catalyses the first reaction in the Krebs' cycle, namely the conversion of oxaloacetate and acetyl-coenzyme A into citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The reaction proceeds via a non-covalently bound citryl-coenzyme A intermediate in a 2-step process (aldol-Claisen condensation followed by the hydrolysis of citryl-CoA). Citrate synthase enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and archaea) form homodimers and have shorter sequences than type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. In both types, the monomer is composed of two domains: a large alpha-helical domain consisting of two structural repeats, where the second repeat is interrupted by a small alpha-helical domain. The cleft between these domains forms the active site, where both citrate and acetyl-coenzyme A bind. The enzyme undergoes a conformational change upon binding of the oxaloacetate ligand, whereby the active site cleft closes over in order to form the acetyl-CoA binding site . The energy required for domain closure comes from the interaction of the enzyme with the substrate. Type II enzymes possess an extra N-terminal beta-sheet domain, and some type II enzymes are allosterically inhibited by NADH . This entry includes both mitochondrial and peroxisomal forms of citrate synthase. Peroxisomal forms of the enzyme, recognized by the C-terminal targeting motif SKL, act in the glyoxylate cycle. Eukaryotic homologs include a Tetrahymena thermophila citrate synthase that doubles as a filament protein, a putative citrate synthase from Plasmodium falciparum (no TCA cycle), and a methylcitrate synthase from Aspergillus nidulans (Emericella nidulans).; GO: 0004108 citrate (Si)-synthase activity, 0044262 cellular carbohydrate metabolic process. Probab=44.74 E-value=8 Score=17.06 Aligned_cols=17 Identities=29% Similarity=0.403 Sum_probs=7.6 Q ss_pred CCCCCCCCCHHHHCCCC Q ss_conf 67766788046530430 Q gi|254781206|r 519 AIPTAKAPPAQAHKGIQ 535 (1246) Q Consensus 519 aiptakappaqahkgiq 535 (1246) ++|..--|-||---+|. T Consensus 128 ~~P~tlHPMaQF~~av~ 144 (430) T TIGR01793 128 ALPSTLHPMAQFALAVA 144 (430) T ss_pred HCCCCCCHHHHHHHHHH T ss_conf 05743572789999999 No 9 >TIGR02858 spore_III_AA stage III sporulation protein AA; InterPro: IPR014217 Proteins in this entry include the stage III sporulation protein AA that is encoded by one of several genes in the spoIIIA locus. This protein is only found in species that are capable of endospore formation.. Probab=44.68 E-value=14 Score=15.27 Aligned_cols=27 Identities=26% Similarity=0.370 Sum_probs=20.5 Q ss_pred CCCEEEEECCCCHHCC--CCCCCCCCCCC Q ss_conf 7982688318510103--76357986434 Q gi|254781206|r 799 QPPLYTIISGSEKILQ--GDYTFPPLSSL 825 (1246) Q Consensus 799 qpplytiisgsekilq--gdytfpplssl 825 (1246) +-||--|..|.+.++. |.|||-|-++. T Consensus 8 grPl~l~~~~~~~~~~~~Gelt~~~~~~y 36 (282) T TIGR02858 8 GRPLELVFDGEEVFVTTDGELTAESDSDY 36 (282) T ss_pred CCCEEEEECCCCEEECCCCEEEECCCCCC T ss_conf 88579986795278758820320588771 No 10 >TIGR03549 conserved hypothetical protein TIGR03549. This family consists of remarkably well-conserved proteins from gamma and beta Proteobacteria, heavily skewed towards organisms of marine environments. This family has an OsmC-like N-terminal domain. It shares a central domain, modeled by pfam02624 and TIGR00702, with other families of smaller proteins. The function is unknown. Fifteen of the first sixteen members of this family are from selenouridine-positive genomes, but this correlation may be fortuitous. Probab=44.61 E-value=18 Score=14.60 Aligned_cols=60 Identities=25% Similarity=0.257 Sum_probs=31.6 Q ss_pred HHHHHHHHHHHHHHHHHHH--------HCCHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHCCCHHHHHH Q ss_conf 9999999999999998652--------126137888898876216656665588764----20002023377 Q gi|254781206|r 679 VEAVYQKLDVLFRHCIENL--------RANKNAVDAMSKAVEAGESSVRKHSFEVLS----SKHQKSVIAVN 738 (1246) Q Consensus 679 veavyqkldvlfrhcienl--------ranknavdamskaveagessvrkhsfevls----skhqksviavn 738 (1246) .||-.|-|.-.|...+.|- -.--..|-+--..+.+|-...+.+.|.|+. ---|-.|++|. T Consensus 335 ~EArVQ~LSEIFER~VK~~II~e~isLP~IP~eVlaryP~I~~~I~~Le~~Gfpv~v~DASLGG~fPVmcVt 406 (718) T TIGR03549 335 AEAQVQCLSEIFERAVKKEIIEEEIVLPDVPQEVLAKYPGILAGIKALEEQGFPVLVKDASLGGQFPVMCVT 406 (718) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCHHHHHHHHHHCCCCEEEEECCCCCCCCEEEEE T ss_conf 999999999999999999998614788887699998573099999999867982799854568977558999 No 11 >pfam08355 EF_assoc_1 EF hand associated. This region typically appears on the C-terminus of EF hands in GTP-binding proteins such as Arht/Rhot (may be involved in mitochondrial homeostasis and apoptosis). The EF hand associated region is found in yeast, vertebrates and plants. Probab=41.89 E-value=6.8 Score=17.56 Aligned_cols=26 Identities=31% Similarity=0.668 Sum_probs=19.8 Q ss_pred HHHHHCCCHHHHHHHHHHHCCCCCEE Q ss_conf 87652663068898786304744113 Q gi|254781206|r 645 NHFLDNDFGYYRIHNFLSQWSPLGLM 670 (1246) Q Consensus 645 nhfldndfgyyrihnflsqwsplglm 670 (1246) +...-|+-|+--.+.||+||+-.-++ T Consensus 9 ~s~~~n~~G~lTl~G~LaqW~l~T~l 34 (75) T pfam08355 9 DSTVTNEDGYLTLQGWLAQWSLTTLL 34 (75) T ss_pred CCEEECCCCCEEHHHHHHHHHHHHHH T ss_conf 72477377877156699987999984 No 12 >TIGR00441 gmhA phosphoheptose isomerase; InterPro: IPR004515 Phosphoheptose isomerase is involved in lipopolysaccharide biosynthesis, and more specifically in the synthesis of glyceromannoheptose 7-phosphate. It may also have a role in virulence in Haemophilus ducreyi.; GO: 0008968 phosphoheptose isomerase activity, 0009244 lipopolysaccharide core region biosynthetic process, 0005737 cytoplasm. Probab=37.97 E-value=4.3 Score=19.04 Aligned_cols=56 Identities=34% Similarity=0.462 Sum_probs=39.8 Q ss_pred HHHHHHHHHCCCHHHHHHHHHHHCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH Q ss_conf 678887652663068898786304744113202232459999999999999998652126137888898876216 Q gi|254781206|r 641 DKAINHFLDNDFGYYRIHNFLSQWSPLGLMYEKDELHGVEAVYQKLDVLFRHCIENLRANKNAVDAMSKAVEAGE 715 (1246) Q Consensus 641 dkainhfldndfgyyrihnflsqwsplglmyekdelhgveavyqkldvlfrhcienlranknavdamskaveage 715 (1246) |-.+=--.-|||||-+|.. .-|||+=|+=|||+- |-.----+|-+.|..+|++-|- T Consensus 80 D~S~Ltai~NDygyd~vF~-----------------RqVEAlG~~GDVL~G--iSTSGNS~NvlkA~~~Ak~~gm 135 (186) T TIGR00441 80 DISILTAIANDYGYDEVFS-----------------RQVEALGQEGDVLLG--ISTSGNSKNVLKAIEAAKDKGM 135 (186) T ss_pred HHHHHHHCCCHHHHHHHHH-----------------HHHHHCCCCCCEEEE--EECCCCCHHHHHHHHHHHHCCC T ss_conf 2353232001102567877-----------------776632889868887--4247670889999998845796 No 13 >PRK06770 hypothetical protein; Provisional Probab=37.21 E-value=22 Score=13.82 Aligned_cols=61 Identities=31% Similarity=0.389 Sum_probs=46.3 Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 57759999888754886024588899988876135378899999988654310234456654 Q gi|254781206|r 133 HKINKQVRDALESAGFDLESTQENIRKVESALINNNMKDAFRFLELAQKSKETADSHIIEAI 194 (1246) Q Consensus 133 hkinkqvrdalesagfdlestqenirkvesalinnnmkdafrflelaqksketadshiieai 194 (1246) |+...|---|-+--|| .+-||+||.++-+++-++|++.--.+|....+-+.--=|+++|.- T Consensus 77 H~MtHQKV~A~~KwG~-i~mt~e~ie~l~~ii~~sn~~~k~~~l~Il~RW~~gDFS~~vedH 137 (185) T PRK06770 77 HKMTHQKVKADEKWGF-IEMTQENIEKLKDIINSSNFVQKEELLAILERWEKGDFSKIVEDH 137 (185) T ss_pred HHHHHHHHHHHCCCCC-EECCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHHHHHH T ss_conf 9987788775113254-545799999999998623546499999999988516724788998 No 14 >pfam07886 BA14K BA14K-like protein. The sequences found in this family are similar to the BA14K proteins expressed by Brucella abortus and by Brucella suis. BA14K was found to be strongly immunoreactive; it induces both humoral and cellular responses in hosts throughout the infective process. Probab=37.11 E-value=15 Score=15.16 Aligned_cols=21 Identities=48% Similarity=0.953 Sum_probs=16.3 Q ss_pred HHHHHHHHCCCCCCCCCCCCH Q ss_conf 999887513576776544530 Q gi|254781206|r 618 KYAKVFYRSYSPVDGSYKGTQ 638 (1246) Q Consensus 618 kyakvfyrsyspvdgsykgtq 638 (1246) .|-.--||||-|.||+|.|-. T Consensus 4 ~~C~~rYrSy~p~~~Ty~~~~ 24 (31) T pfam07886 4 AYCSRRYRSYDPSDGTYQGYD 24 (31) T ss_pred HHHHHHHCCCCCCCCCCCCCC T ss_conf 899988635788998562888 No 15 >KOG1302 consensus Probab=36.02 E-value=23 Score=13.71 Aligned_cols=23 Identities=13% Similarity=0.237 Sum_probs=10.8 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 37789999999888866636122 Q gi|254781206|r 736 AVNNFIKEITHHTRRLVKEDPKR 758 (1246) Q Consensus 736 avnnfikeithhtrrlvkedpkr 758 (1246) ...++-|..-++-+++-.|.+-. T Consensus 195 g~G~~ak~~~~l~~~l~~e~~t~ 217 (600) T KOG1302 195 GKGECAKRVWELLKKLEREEATE 217 (600) T ss_pred ECCHHHHHHHHHHHHHHHCCCCC T ss_conf 14488999999999975321445 No 16 >KOG1831 consensus Probab=35.07 E-value=24 Score=13.59 Aligned_cols=58 Identities=19% Similarity=0.287 Sum_probs=26.3 Q ss_pred HHHHHCCCHHHHHHHHHHHHH----HHHCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH Q ss_conf 888613660477999999999----9741025324443100000034546799999998755 Q gi|254781206|r 214 KVLLKSNNMQDVVFTKIKEVV----KKHVNAELGHRKLRGLAFDHTYFNDKLNQFLKEIKNH 271 (1246) Q Consensus 214 kvllksnnmqdvvftkikevv----kkhvnaelghrklrglafdhtyfndklnqflkeiknh 271 (1246) |++.--||.--.-|++-.+-| +.++-..+.|+-..+-+--.--|.+-.++|+-+|+|- T Consensus 382 kilF~lNNlsq~N~~qKvdevk~~ltp~y~~Wfs~YiV~qR~S~E~Nf~~LY~kFi~ai~n~ 443 (1591) T KOG1831 382 KILFPLNNLSQLNFNQKVDEVKEILTPEYYPWFSQYIVTQRVSKEINFHELYSKFISAIKNS 443 (1591) T ss_pred HHEEEECHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCC T ss_conf 12002222766416788999999747655899998874423202445699999999997475 No 17 >pfam07159 DUF1394 Protein of unknown function (DUF1394). This family consists of several hypothetical eukaryotic proteins of around 320 residues in length. The function of this family is unknown. Probab=33.50 E-value=10 Score=16.27 Aligned_cols=17 Identities=47% Similarity=0.774 Sum_probs=13.2 Q ss_pred HHHHHHHHCCCHHHHHH Q ss_conf 78887652663068898 Q gi|254781206|r 642 KAINHFLDNDFGYYRIH 658 (1246) Q Consensus 642 kainhfldndfgyyrih 658 (1246) |.-|-++.|||.|||-. T Consensus 131 Km~nPaIQNDFSYYRRt 147 (304) T pfam07159 131 KMTNPAIQNDFSYYRRT 147 (304) T ss_pred CCCCCCCCCHHHHHHHH T ss_conf 15781002206899988 No 18 >pfam01582 TIR TIR domain. The Toll/interleukin-1 receptor (TIR) homology domain is an intracellular signalling domain found in MyD88, interleukin 1 receptor and the Toll receptor. It contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins thought to be involved in resistance to disease. When activated, TIR domains recruit cytoplasmic adaptor proteins MyD88 and TOLLIP (Toll interacting protein). In turn, these associate with various kinases to set off signalling cascades. Probab=32.89 E-value=26 Score=13.35 Aligned_cols=99 Identities=25% Similarity=0.387 Sum_probs=58.0 Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCH----HHHHH--------HHH Q ss_conf 999999999976664266420000366776565301577654535788777545430305----56889--------988 Q gi|254781206|r 953 TREKLVAQLSSRLKELNIDNAYGLWNEYKEDFKASFEYPLGTYEPAILGAMKDMDRLHPI----YSVSK--------TIQ 1020 (1246) Q Consensus 953 treklvaqlssrlkelnidnayglwneykedfkasfeyplgtyepailgamkdmdrlhpi----ysvsk--------tiq 1020 (1246) +++..+..|...|.+- ..|-++-. ..|+. |-+..-+.|+.++..-.+.-.| |..|. ..+ T Consensus 10 ~~~~f~~~L~~~L~~~---~g~~~~~~-~rd~~-----~G~~i~~~i~~aI~~Sr~~ivVlS~~y~~S~wcl~El~~~~~ 80 (139) T pfam01582 10 DRDTFVSHLLKELEEK---QGIKLCID-DRDEL-----PGESILENLFEAIEKSRRAIVIFSSNYASSEWCLDELVEAMK 80 (139) T ss_pred CHHHHHHHHHHHHHHC---CCEEEEEE-CCCCC-----CCCCHHHHHHHHHHHHCCHHEEEECCCCCCHHHHHHHHHHHH T ss_conf 3777999999999718---99068853-77777-----998459999999997080450433411257024999999999 Q ss_pred ---HCCCCHHEECCHHHCCHHHHHCCCCHHHHHHHHHHHCCCCC Q ss_conf ---60898110401322687675305726799999987231420 Q gi|254781206|r 1021 ---KAGGDPSLMMDYEKVEPSDVMAGLPDDLAKRFKALLSWKGW 1061 (1246) Q Consensus 1021 ---kaggdpslmmdyekvepsdvmaglpddlakrfkallswkgw 1061 (1246) .-|++.-.+.-+++|+|+||+ -.-...++.|...+-|.|- T Consensus 81 ~~~~~~~~~~Ilpvfy~V~p~~v~-~q~g~~~~~f~~~~~~~~~ 123 (139) T pfam01582 81 CALEQGNKKVILPIFYKVDPSDVR-KQSGKFGKAFLKTLKWSGD 123 (139) T ss_pred HHHHCCCCEEEEEEECCCCHHHHH-HHHHHHHHHHHHHHCCCCC T ss_conf 998569980899985277855402-1307999999999604365 No 19 >COG0279 GmhA Phosphoheptose isomerase [Carbohydrate transport and metabolism] Probab=32.38 E-value=12 Score=15.76 Aligned_cols=66 Identities=32% Similarity=0.377 Sum_probs=41.0 Q ss_pred CCCCCCHHH-HHHHHHHHHCCCHHHHHHHHHHHCCCCCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH Q ss_conf 654453013-6788876526630688987863047441132022324599999999999999986521261378888988 Q gi|254781206|r 632 GSYKGTQES-DKAINHFLDNDFGYYRIHNFLSQWSPLGLMYEKDELHGVEAVYQKLDVLFRHCIENLRANKNAVDAMSKA 710 (1246) Q Consensus 632 gsykgtqes-dkainhfldndfgyyrihnflsqwsplglmyekdelhgveavyqkldvlfrhcienlranknavdamska 710 (1246) -+|..---+ |-++..-+-|||||-.+. -+.|||+-|.=|||+- |-..--.+|-+.|+.+| T Consensus 72 ~~lpaIaLt~dsS~lTai~NDy~yd~vF-----------------sRqveA~g~~GDvLig--ISTSGNS~nVi~Ai~~A 132 (176) T COG0279 72 PSLPAIALSTDSSVLTAIANDYGYDEVF-----------------SRQVEALGQPGDVLIG--ISTSGNSKNVLKAIEAA 132 (176) T ss_pred CCCCEEEEECCCHHHHHHHCCCCHHHHH-----------------HHHHHHCCCCCCEEEE--EECCCCCHHHHHHHHHH T ss_conf 8987368642637776565045588999-----------------9999952788878999--81799977899999999 Q ss_pred HHHHHH Q ss_conf 762166 Q gi|254781206|r 711 VEAGES 716 (1246) Q Consensus 711 veages 716 (1246) ++-|-. T Consensus 133 k~~gm~ 138 (176) T COG0279 133 KEKGMT 138 (176) T ss_pred HHCCCE T ss_conf 876987 No 20 >pfam06265 DUF1027 Protein of unknown function (DUF1027). This family consists of several hypothetical bacterial proteins of unknown function. Probab=32.05 E-value=11 Score=16.13 Aligned_cols=11 Identities=64% Similarity=1.123 Sum_probs=6.2 Q ss_pred CCCHHHHHCCH Q ss_conf 11000001108 Q gi|254781206|r 54 KDRYDYIVGPI 64 (1246) Q Consensus 54 kdrydyivgpi 64 (1246) -++||||||-+ T Consensus 31 L~kYDYIVGDw 41 (86) T pfam06265 31 LDKYDYIVGDW 41 (86) T ss_pred HHHCCEEEECC T ss_conf 87389587645 No 21 >TIGR02622 CDP_4_6_dhtase CDP-glucose 4,6-dehydratase; InterPro: IPR013445 This entry contains CDP-glucose 4,6-dehydratases from a variety of Gram-negative and Gram-positive bacteria. Members are typically encoded next to a gene that encodes a glucose-1-phosphate cytidylyltransferase, which produces the substrate CDP-D-glucose. This is used by the proteins in this entry to produce CDP-4-keto-6-deoxyglucose.. Probab=31.77 E-value=15 Score=15.09 Aligned_cols=31 Identities=26% Similarity=0.569 Sum_probs=23.6 Q ss_pred HHHHCCCCCCCCCHHHHHHHHHHHHHCCHHH Q ss_conf 6530157765453578877754543030556 Q gi|254781206|r 984 FKASFEYPLGTYEPAILGAMKDMDRLHPIYS 1014 (1246) Q Consensus 984 fkasfeyplgtyepailgamkdmdrlhpiys 1014 (1246) .+.|++.|++||+--++|.+.=++-+.-+-+ T Consensus 94 Vr~SY~~P~~Tf~TNVmGT~~lLea~r~~~~ 124 (361) T TIGR02622 94 VRKSYADPLETFETNVMGTVNLLEAIRAIKS 124 (361) T ss_pred HHHHHHCHHHHEEEHHHHHHHHHHHHHHCCC T ss_conf 8986732020222003222577889974699 No 22 >TIGR03354 VI_FHA type VI secretion system FHA domain protein. Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc. Probab=30.74 E-value=28 Score=13.10 Aligned_cols=31 Identities=23% Similarity=0.204 Sum_probs=11.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH Q ss_conf 4599999999999999986521261378888 Q gi|254781206|r 677 HGVEAVYQKLDVLFRHCIENLRANKNAVDAM 707 (1246) Q Consensus 677 hgveavyqkldvlfrhcienlranknavdam 707 (1246) .+..||-+-+.-+-.|-+-.+.|-.-|++.| T Consensus 299 s~~~Ai~eaf~Di~~Hq~a~~~a~~~Al~~~ 329 (396) T TIGR03354 299 SAEAAIEEAFRDLRAHQVALLAAVRAALRRM 329 (396) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9899999999879999999999999999999 No 23 >COG3102 Uncharacterized protein conserved in bacteria [Function unknown] Probab=30.49 E-value=20 Score=14.22 Aligned_cols=64 Identities=31% Similarity=0.385 Sum_probs=46.4 Q ss_pred HHHCCHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEHHHCCCHHHHCCCCCCCHHHH Q ss_conf 322687675305726799999987231420015778756786300120168877035433210199 Q gi|254781206|r 1032 YEKVEPSDVMAGLPDDLAKRFKALLSWKGWHQLTPAPKISTPSFEVSSYVNPKRMHADTESDIYFE 1097 (1246) Q Consensus 1032 yekvepsdvmaglpddlakrfkallswkgwhqltpapkistpsfevssyvnpkrmhadtesdiyfe 1097 (1246) +|.+| -||.|+|..|..|.-+|++--+--++.-.-|.|.|.-|--...||.-.-.|...-|-|. T Consensus 111 WEHIE--iVlP~~p~el~~~~~~l~~~~~l~~~gi~vk~ssp~ge~erl~nptlav~~~~~~ik~h 174 (185) T COG3102 111 WEHIE--IVLPGDPEELNARALALLNDEFLWELGISVKLSSPQGEHERLPNPTLAVTDGKTTIKFH 174 (185) T ss_pred CEEEE--EECCCCHHHHHHHHHHHCCHHHCCCCCEEEEECCCCCCCCCCCCCCEEEECCCCEEEEC T ss_conf 34689--97579928888788865225432557607872598776652799827873188469962 No 24 >KOG1029 consensus Probab=30.41 E-value=29 Score=13.06 Aligned_cols=39 Identities=38% Similarity=0.559 Sum_probs=26.5 Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 543555303216899988888887664776456888765 Q gi|254781206|r 389 KQATVLARANAQEEKQRREQEAKEKADREKADKEAKEKA 427 (1246) Q Consensus 389 kqatvlaranaqeekqrreqeakekadrekadkeakeka 427 (1246) -|+-.--|-.+-+|.||||+|-+++-.||..+|.-+|.- T Consensus 325 GqaELerRRq~leeqqqreree~eqkEreE~ekkererq 363 (1118) T KOG1029 325 GQAELERRRQALEEQQQREREEVEQKEREEEEKKERERQ 363 (1118) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 247799999999988899999998877778888788888 No 25 >PRK11700 hypothetical protein; Provisional Probab=28.14 E-value=29 Score=13.01 Aligned_cols=52 Identities=35% Similarity=0.357 Sum_probs=36.6 Q ss_pred HHHCCHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEHHHCCCHHH Q ss_conf 322687675305726799999987231420015778756786300120168877 Q gi|254781206|r 1032 YEKVEPSDVMAGLPDDLAKRFKALLSWKGWHQLTPAPKISTPSFEVSSYVNPKR 1085 (1246) Q Consensus 1032 yekvepsdvmaglpddlakrfkallswkgwhqltpapkistpsfevssyvnpkr 1085 (1246) +|.|| -|+.+.|..+..+-.+|++|-++-+..-.-|+|.|.-|---..||.- T Consensus 110 WEHIE--~Vlp~~~~t~~~~~~~ll~~~~~~~~~ikvK~SsPkge~ErL~NPTi 161 (186) T PRK11700 110 WEHIE--IVLPGDPETLEARALALLSDEGLSLPGIKVKTSSPKGEGERLPNPTI 161 (186) T ss_pred CEEEE--EEECCCCCCHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCCEE T ss_conf 45899--99538976899999997567650588964770387666764799807 No 26 >TIGR01330 bisphos_HAL2 3'(2'),5'-bisphosphate nucleotidase; InterPro: IPR006239 Sulphate is incorporated into 3-phosphoadenylylsulphate, PAPS, for utilization in pathways such as methionine biosynthesis. Transfer of sulphate from PAPS to an acceptor leaves adenosine 3'-5'-bisphosphate, APS. In plants these sequences represent a form of the enzyme, 3'(2'),5'-bisphosphate nucleotidase, which removes the 3'-phosphate from APS to regenerate AMP and help drive the cycle. Sensitivity of this essential enzyme to sodium and other metal ions results is responsible for characterization of this enzyme as a salt tolerance protein . Some members of this family are active also as inositol 1-monophosphatase. ; GO: 0008441 3'(2')5'-bisphosphate nucleotidase activity, 0006790 sulfur metabolic process. Probab=27.79 E-value=32 Score=12.75 Aligned_cols=59 Identities=24% Similarity=0.531 Sum_probs=50.3 Q ss_pred HHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHCCCC Q ss_conf 1027777405860346530123443211357998887874000010211034432088855998 Q gi|254781206|r 1133 EYEGGANERYVCIPSMDTSESFNSTMGKKRRIFKVVVRVINTADLEVGILGFPIVPVEELRGKP 1196 (1246) Q Consensus 1133 eyegganeryvcipsmdtsesfnstmgkkrrifkvvvrvintadlevgilgfpivpveelrgkp 1196 (1246) .|+||.|-|+-|+-..|-..-|- .---|-|..-.|.-.-.-+|.||.|=.|+...-+.| T Consensus 134 ~y~GGr~GR~W~LDPiDGTkGFl-----RG~QYAvaLALie~Gkv~lg~lGCPNlp~~~~~~~~ 192 (382) T TIGR01330 134 NYEGGRKGRHWVLDPIDGTKGFL-----RGDQYAVALALIENGKVVLGVLGCPNLPLKSEAAQN 192 (382) T ss_pred CCCCCCCCCEEEECCCCCCCCCC-----CHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHCCCC T ss_conf 88988898757716756765562-----256899998765279079998606885101102683 No 27 >KOG2874 consensus Probab=26.77 E-value=33 Score=12.63 Aligned_cols=90 Identities=26% Similarity=0.457 Sum_probs=59.4 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCCCHHHHHHHHHHHHCCCCCCCCC--- Q ss_conf 88999999999862000138788701789999999999999976664266-42000036677656530157765453--- Q gi|254781206|r 921 EFEREIKELKSVIEADAKENPNPNKNQKKLQKTREKLVAQLSSRLKELNI-DNAYGLWNEYKEDFKASFEYPLGTYE--- 996 (1246) Q Consensus 921 efereikelksvieadakenpnpnknqkklqktreklvaqlssrlkelni-dnayglwneykedfkasfeyplgtye--- 996 (1246) -|+..++-|..-+-.|.-.--|--.|....-|.|..||..-++.||.|.| .+.|-|-.. .---.+|.|. T Consensus 127 p~eqAvkiLqDev~CdiIkIgn~V~nkerFvKRRqRLiGpng~TLKAlelLT~CYilVqG-------~TVsaiGpfkGlk 199 (356) T KOG2874 127 PFEQAVKILQDEVACDIIKIGNLVRNKERFVKRRQRLIGPNGSTLKALELLTNCYILVQG-------NTVSAIGPFKGLK 199 (356) T ss_pred CHHHHHHHHHHCCCEEEEEHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHCEEEEEC-------CEEEEECCCCHHH T ss_conf 889999997203020246452353117999998887318882057999997521798607-------6777634730089 Q ss_pred ---HHHHHHHHHHHHHCCHHHHHHHHH Q ss_conf ---578877754543030556889988 Q gi|254781206|r 997 ---PAILGAMKDMDRLHPIYSVSKTIQ 1020 (1246) Q Consensus 997 ---pailgamkdmdrlhpiysvsktiq 1020 (1246) -.++.. |...||||.+-.-.- T Consensus 200 evr~IV~Dc---M~NiHPiY~IK~Lmi 223 (356) T KOG2874 200 EVRKIVEDC---MKNIHPIYNIKTLMI 223 (356) T ss_pred HHHHHHHHH---HHCCCHHHHHHHHHH T ss_conf 999999999---852550788999999 No 28 >pfam01591 6PF2K 6-phosphofructo-2-kinase. This enzyme occurs as a bifunctional enzyme with fructose-2,6-bisphosphatase. The bifunctional enzyme catalyses both the synthesis and degradation of fructose-2,6-bisphosphate, a potent regulator of glycolysis. This enzyme contains a P-loop motif. Probab=25.67 E-value=34 Score=12.49 Aligned_cols=24 Identities=29% Similarity=0.650 Sum_probs=10.9 Q ss_pred CHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf 978999999999988751357677 Q gi|254781206|r 608 SPDEIKQRFQKYAKVFYRSYSPVD 631 (1246) Q Consensus 608 spdeikqrfqkyakvfyrsyspvd 631 (1246) +|++....|.+-...+...|.|++ T Consensus 157 ~~e~A~~DF~~Ri~~ye~~Yepl~ 180 (223) T pfam01591 157 PPEEAIDDFMKRLECYEKQYEPLD 180 (223) T ss_pred CHHHHHHHHHHHHHHHHCCEECCC T ss_conf 999999999999997534242388 No 29 >pfam07852 DUF1642 Protein of unknown function (DUF1642). The sequences making up this family are derived from various hypothetical phage and prophage proteins. The region in question is approximately 140 amino acids long. Probab=23.48 E-value=18 Score=14.47 Aligned_cols=16 Identities=38% Similarity=0.632 Sum_probs=11.4 Q ss_pred CCCCCCCCCC--CCEEEE Q ss_conf 1123221000--120231 Q gi|254781206|r 844 GDWTNNAIKE--ERYWTI 859 (1246) Q Consensus 844 gdwtnnaike--erywti 859 (1246) .-.|-..||. +|||-. T Consensus 114 ~k~TE~EIk~ide~yW~F 131 (136) T pfam07852 114 LKLTEQEIKSIDEFYWQF 131 (136) T ss_pred HHHCHHHHHCCCHHHCCC T ss_conf 230599885375312663 No 30 >TIGR01026 fliI_yscN ATPase FliI/YscN family; InterPro: IPR005714 Proteins in this entry show extensive homology to the ATP synthase F1 beta subunit, and are involved in type III protein secretion. They fall into the two separate functional groups outlined below. The first group, exemplified by the Salmonella typhimurium FliI protein (P26465 from SWISSPROT), is needed for flagellar assembly. Most structural components of the bacterial flagellum are translocated through the central channel of the growing flagellar structure by the type III flagellar protein-export apparatus in an ATPase-driven manner, to be assembled at the growing end. FliI is the ATPase that couples ATP hydrolysis to the translocation reaction , . The second group couples ATP hydrolysis to protein translocation in non-flagellar type III secretion systems. Often these systems are involved in virulence and pathogenicity. YscN (P40290 from SWISSPROT) from pathogenic Yersinia species, for example, energises the injection of antihost factors directly into eukaryotic cells, thus overcoming host defences .; GO: 0016887 ATPase activity, 0009058 biosynthetic process, 0015031 protein transport, 0005737 cytoplasm. Probab=23.41 E-value=38 Score=12.20 Aligned_cols=45 Identities=36% Similarity=0.535 Sum_probs=27.7 Q ss_pred CCCCC--CHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCEEEEHHHHHHHHHHHHHHHHHHH Q ss_conf 65445--3013678887652663068898786304744113202232459999999999999 Q gi|254781206|r 632 GSYKG--TQESDKAINHFLDNDFGYYRIHNFLSQWSPLGLMYEKDELHGVEAVYQKLDVLFR 691 (1246) Q Consensus 632 gsykg--tqesdkainhfldndfgyyrihnflsqwsplglmyekdelhgveavyqkldvlfr 691 (1246) |.|+. -.|-|+||++ |-.+-+||.|= .+|..--|.-.|.|+-+|+ T Consensus 409 G~Y~~GSd~e~D~AI~~-------~~~le~FL~Qg--------~~E~~~fE~s~~~L~~I~~ 455 (455) T TIGR01026 409 GAYKKGSDKELDKAIAK-------YPKLERFLKQG--------INEKVNFEESLQQLEEILS 455 (455) T ss_pred CCCCCCCCHHHHHHHHH-------HHHHHHHHCCC--------CCCCCHHHHHHHHHHHHCC T ss_conf 02558788668999857-------99988875479--------4346308999999987349 No 31 >KOG2830 consensus Probab=23.38 E-value=38 Score=12.20 Aligned_cols=26 Identities=46% Similarity=0.816 Sum_probs=19.2 Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHC Q ss_conf 3315776775531278856788998740001 Q gi|254781206|r 449 FGLGLPSVPTHSVKLPPKEEELEEVKDEGKK 479 (1246) Q Consensus 449 fglglpsvpthsvklppkeeeleevkdegkk 479 (1246) ||+|-|+.||-|| +|-+.++-.+|.- T Consensus 249 fG~Gyp~lPtMsv-----dE~~~~~~~~g~a 274 (324) T KOG2830 249 FGLGYPGLPTMTV-----DEFLDQEFEEGIA 274 (324) T ss_pred HHCCCCCCCCCCH-----HHHHHHHHHHHHC T ss_conf 4067889862009-----9999999984010 No 32 >KOG4003 consensus Probab=23.28 E-value=5.8 Score=18.08 Aligned_cols=39 Identities=18% Similarity=0.310 Sum_probs=20.3 Q ss_pred HHHHHCCCCCEEEEHHHHHHHHHH--HHHHHHHH-HHHHHHHH Q ss_conf 786304744113202232459999--99999999-99986521 Q gi|254781206|r 659 NFLSQWSPLGLMYEKDELHGVEAV--YQKLDVLF-RHCIENLR 698 (1246) Q Consensus 659 nflsqwsplglmyekdelhgveav--yqkldvlf-rhcienlr 698 (1246) .|++|-+- ..||++++.|..++- -|++.+|+ -|||+|-- T Consensus 60 SF~~~h~~-~~p~~~~t~~~~~~~d~V~~~~vl~p~HCv~ntw 101 (223) T KOG4003 60 SFAKNHKD-KEPYSTYTYHSPRPGDDVTQEGILWPVHCVKNTW 101 (223) T ss_pred EHHHHCCC-CCCCCCCCCCCCCCCCCEEEEEECCHHHHHCCCC T ss_conf 04443367-8788777553677677414675315114200588 No 33 >pfam02572 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin adenosyltransferase, EC:2.5.1.17, involved in cobalamin (vitamin B12) biosynthesis. These enzymes catalyse the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin. Probab=23.13 E-value=30 Score=12.94 Aligned_cols=45 Identities=31% Similarity=0.472 Sum_probs=35.3 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEECCCC Q ss_conf 999998763003666542477799998999987622546652663 Q gi|254781206|r 72 SERYERVVSRDLTLVIEAGLKDLKEVGDTLKRLAETGEVILSDKS 116 (1246) Q Consensus 72 seryervvsrdltlvieaglkdlkevgdtlkrlaetgevilsdks 116 (1246) +..|.-||--.+...+..||-+..+|-+.|+.-.+.-||||+-.. T Consensus 94 ~~~~dlvVLDEi~~ai~~gli~~~~v~~~l~~rp~~~evVlTGr~ 138 (172) T pfam02572 94 SGSYDLVVLDELNYALKYGYLDLEEVLELLRNRPEGQHVVLTGRG 138 (172) T ss_pred CCCCCEEEEHHHHHHHHCCCCCHHHHHHHHHHCCCCCEEEEECCC T ss_conf 889899973557999755996899999999828998779998999 No 34 >TIGR02924 ICDH_alpha isocitrate dehydrogenase; InterPro: IPR014273 This entry represents a group of isocitrate dehydrogenases found mainly in the alphaproteobacteria. Many of the species containing these proteins appear to have a TCA cycle lacking only a determined isocitrate dehydrogenase. The precise identity of the cofactor (NADH -- 1.1.1.41 from EC vs. NADPH -- 1.1.1.42 from EC) is unclear.. Probab=22.95 E-value=21 Score=14.10 Aligned_cols=233 Identities=28% Similarity=0.441 Sum_probs=134.8 Q ss_pred HHHHHHHHCCCHHHH-------HHHHHHHCCC-CCEE----EEHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH Q ss_conf 788876526630688-------9878630474-4113----202232459999999999999998652126137888898 Q gi|254781206|r 642 KAINHFLDNDFGYYR-------IHNFLSQWSP-LGLM----YEKDELHGVEAVYQKLDVLFRHCIENLRANKNAVDAMSK 709 (1246) Q Consensus 642 kainhfldndfgyyr-------ihnflsqwsp-lglm----yekdelhgveavyqkldvlfrhcienlranknavdamsk 709 (1246) |-.|--|-...|.|- -|-|+..-+| |-+. -|-|---|+|- |-..|+-.+.-- T Consensus 78 KSLNVtlRK~LGLyANiRPCvsyhP~i~t~~p~ldiVivRENEEDlYtGiEY----------------R~T~d~Y~c~K~ 141 (481) T TIGR02924 78 KSLNVTLRKTLGLYANIRPCVSYHPVIETKYPNLDIVIVRENEEDLYTGIEY----------------RQTQDTYECTKV 141 (481) T ss_pred EEHHHHHHHHCCCEEECCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCEEE----------------EECCCCEEEEEE T ss_conf 4124464322475041266530035241677983469998356423255114----------------305781025553 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHH--HHHHH---HHHHHHH-HHHHHCCCCCCHHHHHHHHHHHHHHHHHHEEEEE Q ss_conf 8762166566655887642000202337--78999---9999888-8666361224214578999999998531100026 Q gi|254781206|r 710 AVEAGESSVRKHSFEVLSSKHQKSVIAV--NNFIK---EITHHTR-RLVKEDPKRGKSESYLSDIRSELQKVNKTVMDIR 783 (1246) Q Consensus 710 aveagessvrkhsfevlsskhqksviav--nnfik---eithhtr-rlvkedpkrgksesylsdirselqkvnktvmdir 783 (1246) --+.|---.-.-.||---..|.|-|-.. .|-.| -|-|..= ..-+|=|. =++|-|.-||-.-----+-+-.|+= T Consensus 142 ITrsgsEkIcrYAF~YA~~~nRKkVTCl~KDNIMK~TDGiFHk~F~~IA~eYPd-I~~EhyIvDIG~Ar~A~~PE~FDVI 220 (481) T TIGR02924 142 ITRSGSEKICRYAFEYARKHNRKKVTCLIKDNIMKLTDGIFHKIFDKIAKEYPD-IESEHYIVDIGMARIATNPENFDVI 220 (481) T ss_pred EECCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHCCCC-CCCCCEEEECCHHHHCCCCCCCCEE T ss_conf 406862578999989877649868999620371301223678778997431788-5416406810334113679865458 Q ss_pred EEEEEEE-HHHHCCCCCCCEEEEECCCCHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEE Q ss_conf 6555220-133175327982688318510103763579864341023200358889988831123221000120231110 Q gi|254781206|r 784 IKLRLYG-IFQDIPQEQPPLYTIISGSEKILQGDYTFPPLSSLDVQSKFDSSYSKLFEIFYGDWTNNAIKEERYWTIYAF 862 (1246) Q Consensus 784 iklrlyg-ifqdipqeqpplytiisgsekilqgdytfpplssldvqskfdssysklfeifygdwtnnaikeerywtiyaf 862 (1246) +-.-||| |.-||--| ||||--. -| -+-..++|. .||-.-|-=.+-|=| T Consensus 221 VT~NLYGDIlSDvaA~-------~SGSvGL-aG------------SaNIG~~YA-MFEAVHGSAPdIAGk---------- 269 (481) T TIGR02924 221 VTPNLYGDILSDVAAE-------ISGSVGL-AG------------SANIGEEYA-MFEAVHGSAPDIAGK---------- 269 (481) T ss_pred ECCCCCCCHHHHHHHH-------HHCCHHH-HH------------HHHHCCCCC-EEEEECCCCCCCCCC---------- T ss_conf 7477676547778887-------6142222-23------------441246886-045432778541566---------- Q ss_pred EHHHCCH-HHHHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH Q ss_conf 0332001-11235688752033087743---0118999998876663321138899999999889999 Q gi|254781206|r 863 ERSLKNQ-AHLNAEVERLSGLAQQPSDS---TADLKELQTQLSRAKKYKESNDERIVSFIRSEFEREI 926 (1246) Q Consensus 863 erslknq-ahlnaeverlsglaqqpsds---tadlkelqtqlsrakkykesnderivsfirseferei 926 (1246) .+-|- .-|||-|.-|.-+.|.---+ -|=||-|.--..-|-=|+|-+-..-|+- .||-.++ T Consensus 270 --nIANPSGLLNAAi~MLvyigQ~d~A~liynAwLKTLEdGvHTADIy~~k~Sk~KVgT--keFA~aV 333 (481) T TIGR02924 270 --NIANPSGLLNAAIQMLVYIGQKDIAQLIYNAWLKTLEDGVHTADIYNEKTSKKKVGT--KEFAEAV 333 (481) T ss_pred --CCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCHHHHCCCCCCCCCCCC--HHHHHHH T ss_conf --766700579999998640045468999987764442137431332123366666652--5799999 No 35 >KOG0616 consensus Probab=22.92 E-value=32 Score=12.70 Aligned_cols=34 Identities=26% Similarity=0.524 Sum_probs=15.0 Q ss_pred HHHHHHHHHHHHHHHEEEEEEEEEEEEHHHHCCCCCCCEEEEE Q ss_conf 7899999999853110002665552201331753279826883 Q gi|254781206|r 764 YLSDIRSELQKVNKTVMDIRIKLRLYGIFQDIPQEQPPLYTII 806 (1246) Q Consensus 764 ylsdirselqkvnktvmdiriklrlygifqdipqeqpplytii 806 (1246) -..+-++-|+.+.- -.-.+||+-|+|-- -||-|. T Consensus 90 H~~nEk~vL~~v~~-----PFlv~l~~t~kd~~----~lymvm 123 (355) T KOG0616 90 HTHNEKRVLKAVSH-----PFLVKLYGTFKDNS----NLYMVM 123 (355) T ss_pred HHHHHHHHHHHCCC-----CEEEEEEEEECCCC----EEEEEE T ss_conf 77618989754048-----73778878641377----789998 No 36 >pfam06593 RBDV_coat Raspberry bushy dwarf virus coat protein. This family consists of several Raspberry bushy dwarf virus coat proteins. Probab=22.88 E-value=37 Score=12.23 Aligned_cols=23 Identities=39% Similarity=0.420 Sum_probs=17.6 Q ss_pred HCCCCCCEEEEECCCCCCHHHHH Q ss_conf 02777740586034653012344 Q gi|254781206|r 1134 YEGGANERYVCIPSMDTSESFNS 1156 (1246) Q Consensus 1134 yegganeryvcipsmdtsesfns 1156 (1246) ...-.|||-|||-.-|++.||-- T Consensus 225 i~sllnerkvci~~~d~~ssfyi 247 (274) T pfam06593 225 IPSLLNERKVCVFQNDDSSSFYI 247 (274) T ss_pred HHHHHCCCEEEEEECCCCCCHHH T ss_conf 78774433379995288751049 No 37 >pfam05565 Sipho_Gp157 Siphovirus Gp157. This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophages. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage. Probab=22.49 E-value=23 Score=13.79 Aligned_cols=31 Identities=29% Similarity=0.347 Sum_probs=15.0 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 7847899888877876999999887750478 Q gi|254781206|r 20 IPSEDVAKTLTSIQDNIKHLREFIIAWSSDL 50 (1246) Q Consensus 20 ipsedvaktltsiqdnikhlrefiiawssdl 50 (1246) +..|.++.||-+|++.+.---+-|+.|--++ T Consensus 22 ~D~e~~~DTLe~i~~~~~~K~~~i~~~iknl 52 (162) T pfam05565 22 LDPEALADTLESIEEEFEDKVENIAKVIKNL 52 (162) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9989999999999999999999999999832 No 38 >pfam03846 SulA Cell division inhibitor SulA. Probab=21.92 E-value=38 Score=12.18 Aligned_cols=18 Identities=33% Similarity=0.565 Sum_probs=14.2 Q ss_pred HHHHHHHHHHHHHHHHHH Q ss_conf 137888898876216656 Q gi|254781206|r 701 KNAVDAMSKAVEAGESSV 718 (1246) Q Consensus 701 knavdamskaveagessv 718 (1246) -..||||-||...|..|| T Consensus 96 ~~tv~aMeKAL~tGNySv 113 (119) T pfam03846 96 LHTVESMERALRTGNYSV 113 (119) T ss_pred HHHHHHHHHHHHCCCCEE T ss_conf 638999999997099448 No 39 >KOG4682 consensus Probab=21.90 E-value=40 Score=12.00 Aligned_cols=79 Identities=30% Similarity=0.415 Sum_probs=53.0 Q ss_pred CCCCEEEEH------HHHHHHH--HHHHHHHHHHHHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH Q ss_conf 744113202------2324599--99999999999998652126---137888898876216656665588764200020 Q gi|254781206|r 665 SPLGLMYEK------DELHGVE--AVYQKLDVLFRHCIENLRAN---KNAVDAMSKAVEAGESSVRKHSFEVLSSKHQKS 733 (1246) Q Consensus 665 splglmyek------delhgve--avyqkldvlfrhcienlran---knavdamskaveagessvrkhsfevlsskhqks 733 (1246) +.+|-||-. +.+-||- |.|-.||-||..|.|-.-++ |+|+.-..-+..-|+-+|++.++|+|- T Consensus 126 ~a~gsLY~dEveI~l~dv~gvlAaA~~lqldgl~qrC~evMie~lspkta~~yYea~ckYgle~vk~kc~ewl~------ 199 (488) T KOG4682 126 VAFGSLYRDEVEIKLSDVVGVLAAACLLQLDGLIQRCGEVMIETLSPKTACGYYEAACKYGLESVKKKCLEWLL------ 199 (488) T ss_pred HHHHHHHHHHEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH------ T ss_conf 99876532012214999999998768886604999999999975380546778788877416888787999999------ Q ss_pred HHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 23377899999998888666361 Q gi|254781206|r 734 VIAVNNFIKEITHHTRRLVKEDP 756 (1246) Q Consensus 734 viavnnfikeithhtrrlvkedp 756 (1246) +||.+ +.+.++.+|-| T Consensus 200 ----~nl~~---i~~~q~l~ei~ 215 (488) T KOG4682 200 ----NNLMT---IQNVQLLKEIS 215 (488) T ss_pred ----HHHHH---HHHHHHHHHCC T ss_conf ----86675---41077786648 No 40 >pfam04227 Indigoidine_A Indigoidine synthase A like protein. Indigoidine is a blue pigment synthesized by Erwinia chrysanthemi implicated in pathogenicity and protection from oxidative stress. IdgA is involved in indigoidine biosynthesis, but its specific function is unknown. Probab=21.47 E-value=16 Score=14.98 Aligned_cols=34 Identities=26% Similarity=0.402 Sum_probs=17.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCEEECCCCHH Q ss_conf 6654247779999899998762254665266315 Q gi|254781206|r 85 LVIEAGLKDLKEVGDTLKRLAETGEVILSDKSDR 118 (1246) Q Consensus 85 lvieaglkdlkevgdtlkrlaetgevilsdksdr 118 (1246) .|+-+|.|..-.++-||..|-.-|--++.-++|. T Consensus 145 ~VVcaG~KsILDi~~TlE~LET~GV~V~gy~td~ 178 (293) T pfam04227 145 AVVCAGAKSILDIPKTLEYLETQGVPVIGYGTDE 178 (293) T ss_pred EEEECCCHHHHCCHHHHHHHHHCCCEEEEECCCC T ss_conf 9994260765054468999997594389745876 No 41 >PHA00652 hypothetical protein Probab=21.45 E-value=41 Score=11.93 Aligned_cols=11 Identities=64% Similarity=1.011 Sum_probs=7.9 Q ss_pred HHHHHHHHHHH Q ss_conf 99999987630 Q gi|254781206|r 71 VSERYERVVSR 81 (1246) Q Consensus 71 vseryervvsr 81 (1246) .-|+||||+|- T Consensus 16 mvEkYERVi~Y 26 (128) T PHA00652 16 IVERYERVISY 26 (128) T ss_pred HHHHHHHHHHH T ss_conf 99999999999 No 42 >TIGR02790 nickel_nikC nickel ABC transporter, permease subunit NikC; InterPro: IPR014157 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 the NikC family of nickel ABC transporter permeases. Operons that contain this protein also contain a homologous permease subunit NikB. Nickel is used in cells as part of urease or certain hydrogenases or superoxide dismutases.. Probab=21.20 E-value=34 Score=12.47 Aligned_cols=11 Identities=64% Similarity=1.023 Sum_probs=6.3 Q ss_pred HHCCCCCCCCC Q ss_conf 30157765453 Q gi|254781206|r 986 ASFEYPLGTYE 996 (1246) Q Consensus 986 asfeyplgtye 996 (1246) -|.||||||-+ T Consensus 38 pS~~YpLGTD~ 48 (258) T TIGR02790 38 PSMEYPLGTDH 48 (258) T ss_pred CCCCCCCCCCC T ss_conf 96547898875 No 43 >pfam09568 RE_MjaI MjaI restriction endonuclease. This family includes the MjaI (recognizes CTAG but cleavage site unknown) restriction endonuclease. Probab=21.17 E-value=6.6 Score=17.69 Aligned_cols=53 Identities=34% Similarity=0.290 Sum_probs=31.4 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCC-----CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 9998899999999986200013878-----87017899999999999999766642664200 Q gi|254781206|r 918 IRSEFEREIKELKSVIEADAKENPN-----PNKNQKKLQKTREKLVAQLSSRLKELNIDNAY 974 (1246) Q Consensus 918 irsefereikelksvieadakenpn-----pnknqkklqktreklvaqlssrlkelnidnay 974 (1246) ||-+++|||+|+.+-- -+-|. -|-...--|-||-|.|.|+|--.+|.+-...+ T Consensus 2 i~~~~~~~~~~~~~~~----~efPKY~tQiINLAN~~a~gTrPkvVGQmSelIkef~~~~g~ 59 (201) T pfam09568 2 IRFDEEDEIKEIPGKE----VEFPKYASQIINLANIFAQGTRPKVVGQMSDLIHEFRKCGDK 59 (201) T ss_pred CCCHHHHHHHHCCCCC----CCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCCC T ss_conf 5403778997467888----785245888987740145677875021389999998733885 No 44 >COG4710 Predicted DNA-binding protein with an HTH domain [General function prediction only] Probab=20.85 E-value=42 Score=11.85 Aligned_cols=55 Identities=24% Similarity=0.331 Sum_probs=34.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHCCCEEECCCCHH Q ss_conf 899999999999987630036665424777999---9899998762254665266315 Q gi|254781206|r 64 IEQRLKKVSERYERVVSRDLTLVIEAGLKDLKE---VGDTLKRLAETGEVILSDKSDR 118 (1246) Q Consensus 64 ieqrlkkvseryervvsrdltlvieaglkdlke---vgdtlkrlaetgevilsdksdr 118 (1246) .++||+..|++-.|.-+--+.-.||+++.+... .-+.|.|+-...+-+.|.+-++ T Consensus 16 ~~eRL~~Ls~~tgrtkayyvrEaIE~~ieemED~ylA~~aler~k~G~~q~~Sa~~~~ 73 (80) T COG4710 16 LKERLDNLSKNTGRTKAYYVREAIEAYIEEMEDFYLAVNALERLKDGDYQKASAKIDK 73 (80) T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH T ss_conf 9999999987048854699999999999999999999999999873278887799999 No 45 >cd01820 PAF_acetylesterase_like PAF_acetylhydrolase (PAF-AH)_like subfamily of SGNH-hydrolases. Platelet-activating factor (PAF) and PAF-AH are key players in inflammation and in atherosclerosis. PAF-AH is a calcium independent phospholipase A2 which exhibits strong substrate specificity towards PAF, hydrolyzing an acetyl ester at the sn-2 position. PAF-AH also degrades a family of oxidized PAF-like phospholipids with short sn-2 residues. In addition, PAF and PAF-AH are associated with neural migration and mammalian reproduction. Probab=20.69 E-value=42 Score=11.83 Aligned_cols=19 Identities=32% Similarity=0.275 Sum_probs=8.6 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 2324599999999999999 Q gi|254781206|r 674 DELHGVEAVYQKLDVLFRH 692 (1246) Q Consensus 674 delhgveavyqkldvlfrh 692 (1246) |-||--++-|+...-..+- T Consensus 190 DgLHln~~GY~~w~~~i~p 208 (214) T cd01820 190 DYLHLTAAGYRKWADALHP 208 (214) T ss_pred CCCCCCHHHHHHHHHHHHH T ss_conf 8889999999999999999 Done!