Query gi|255764487|ref|YP_003065115.2| heat shock protein [Candidatus Liberibacter asiaticus str. psy62] Match_columns 219 No_of_seqs 122 out of 2077 Neff 7.2 Searched_HMMs 39220 Date Sun May 29 21:22:56 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 255764487.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK10325 heat shock protein Gr 100.0 0 0 336.0 18.4 147 36-190 51-197 (197) 2 COG0576 GrpE Molecular chapero 100.0 0 0 323.1 17.4 151 31-189 43-193 (193) 3 pfam01025 GrpE GrpE. 100.0 4.2E-45 0 309.3 16.6 155 24-187 8-162 (162) 4 cd00446 GrpE GrpE is the adeni 100.0 2.8E-42 0 290.8 14.0 137 40-185 1-137 (137) 5 KOG3003 consensus 100.0 2.4E-40 5.6E-45 278.4 16.4 155 35-191 81-235 (236) 6 pfam11500 Cut12 Spindle-body f 66.7 8.2 0.00021 19.4 3.7 31 48-80 69-99 (151) 7 pfam08780 NTase_sub_bind Nucle 65.4 12 0.00029 18.4 4.3 25 109-133 28-56 (123) 8 KOG1962 consensus 56.4 9.8 0.00025 18.9 2.6 12 109-120 184-195 (216) 9 pfam05470 eIF-3c_N Eukaryotic 38.6 31 0.0008 15.7 9.8 104 31-134 27-135 (593) 10 TIGR00060 L18_bact ribosomal p 37.0 6.9 0.00018 19.9 -0.7 14 79-92 47-60 (118) 11 KOG0250 consensus 34.0 37 0.00094 15.2 10.1 21 132-152 493-516 (1074) 12 pfam04108 APG17 Autophagy prot 32.1 40 0.001 15.0 6.0 40 33-72 124-163 (410) 13 TIGR02943 Sig70_famx1 RNA poly 30.8 42 0.0011 14.9 4.5 70 39-133 7-76 (194) 14 PTZ00156 60S ribosomal protein 30.8 25 0.00063 16.3 1.3 49 129-186 102-150 (172) 15 KOG3895 consensus 28.1 46 0.0012 14.6 3.0 36 119-155 204-239 (488) 16 TIGR01364 serC_1 phosphoserine 25.9 34 0.00086 15.4 1.3 41 47-88 16-65 (391) 17 KOG2700 consensus 25.8 51 0.0013 14.3 5.3 75 74-148 170-246 (481) 18 pfam02963 EcoRI Restriction en 25.8 36 0.00092 15.3 1.4 53 133-190 48-100 (257) 19 TIGR01661 ELAV_HUD_SF ELAV/HuD 25.3 33 0.00084 15.5 1.1 27 145-183 404-430 (436) 20 TIGR02168 SMC_prok_B chromosom 24.7 53 0.0014 14.2 10.0 20 74-93 527-546 (1191) 21 KOG0493 consensus 23.1 57 0.0015 14.0 3.5 27 43-69 254-280 (342) 22 pfam11062 DUF2863 Protein of u 21.5 46 0.0012 14.6 1.2 30 119-148 339-368 (398) 23 TIGR00273 TIGR00273 iron-sulfu 21.3 45 0.0011 14.7 1.1 34 123-164 105-139 (450) 24 pfam04914 DltD_C DltD C-termin 21.0 63 0.0016 13.7 4.6 72 82-153 33-111 (130) 25 CHL00139 rpl18 ribosomal prote 20.2 21 0.00053 16.8 -0.7 10 168-177 86-95 (109) 26 PRK05593 rplR 50S ribosomal pr 20.1 21 0.00054 16.7 -0.7 10 168-177 92-101 (115) No 1 >PRK10325 heat shock protein GrpE; Provisional Probab=100.00 E-value=0 Score=335.97 Aligned_cols=147 Identities=36% Similarity=0.635 Sum_probs=136.8 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH Q ss_conf 99999999999999998899999999999999999642433432031578999999721222332101112789987644 Q gi|255764487|r 36 SLNQSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLKSLIEG 115 (219) Q Consensus 36 ~~~e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~~G 115 (219) +.+....++|+|+|++|||+|||||+++++.++++||+++|+++||||+|||+||+.+.. ..+..+.+|++| T Consensus 51 l~e~~~~~kD~~lR~~Ae~eN~rkR~~ke~~~~~~~a~~~~~~~lLpv~DnlerAl~~~~--------~~~~~~~~~~eG 122 (197) T PRK10325 51 LAEAQTRERDGILRVKAEMENLRRRTELDIEKAHKFALEKFINELLPVIDSLDRALEVAD--------KANPDMSAMVEG 122 (197) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------CCCHHHHHHHHH T ss_conf 999999889999999998999999999999999999999999997007768999998563--------117258999999 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEEECCCC Q ss_conf 799999999998641100013688875700577752243458977459999708817756782000248604888 Q gi|255764487|r 116 IEMTRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSISKGKT 190 (219) Q Consensus 116 i~mi~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~Vsk~~~ 190 (219) |.||+++|.++|.++||++|+++|++|||++||||++++++++++|||++|+|+||+|+|||||||+|+|||+|+ T Consensus 123 v~mi~k~l~~~l~~~gv~~i~~~G~~FDP~~HeAv~~~~~~~~~~~~Iv~v~qkGY~l~~rvlRpA~V~VsK~k~ 197 (197) T PRK10325 123 IELTLKSMLDVVRKFGVEVIAETNVPLDPNVHQAIAMVESDDVAPGNVLGIMQKGYTLNGRTIRAAMVTVAKAKA 197 (197) T ss_pred HHHHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHHEEECCCCCCCCEEEEEEECCEEECCEEECCCEEEEECCCC T ss_conf 999999999999988935757889999806654010107899993907899657838899971064489817999 No 2 >COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones] Probab=100.00 E-value=0 Score=323.14 Aligned_cols=151 Identities=46% Similarity=0.780 Sum_probs=140.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHH Q ss_conf 03999999999999999999988999999999999999996424334320315789999997212223321011127899 Q gi|255764487|r 31 NIPEESLNQSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLK 110 (219) Q Consensus 31 ~~~e~~~~e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~ 110 (219) ..+..+..++++++++|+|++|||+|||||++++++++++|+.++|+.+||||+|||+|||.+.... .... + T Consensus 43 ~~i~~Le~q~~e~~~~~lr~~Ae~eN~rkR~~re~e~~~k~a~e~~~~dlLpviDnlerAl~~~~~~-------~d~~-~ 114 (193) T COG0576 43 QEIAELEAQLEELKDKYLRAQAEFENLRKRTEREREEAKKYAIEKFAKDLLPVIDNLERALEAAEDD-------KDPE-K 114 (193) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-------CCHH-H T ss_conf 8999999999999999999999999999999999999999999999999888887999999712345-------4157-7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEEECCC Q ss_conf 8764479999999999864110001368887570057775224345897745999970881775678200024860488 Q gi|255764487|r 111 SLIEGIEMTRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSISKGK 189 (219) Q Consensus 111 ~~~~Gi~mi~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~Vsk~~ 189 (219) +|++||.||+++|.++|.++||+.|.+.|+.|||++|+||++++++++++|||++|+|+||+|+|||||||||+||+++ T Consensus 115 ~l~~Gvem~~~~l~~~L~k~Gv~~i~~~Ge~FDP~~HeAv~~~~~~~~~~~tVv~v~qkGY~l~dRVLRpA~V~Vak~~ 193 (193) T COG0576 115 ALLEGVEMTLDQLLDALEKLGVEEIGPEGEKFDPNLHEAVQRVESEDVEPNTVVEVLQKGYKLNDRVLRPAMVKVAKKE 193 (193) T ss_pred HHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCHHHHHHEEEECCCCCCCCEEEEEEECCEEECCEECCCEEEEEECCC T ss_conf 8999999999999999998798780788998897885510343678999994889850570648985211279972589 No 3 >pfam01025 GrpE GrpE. Probab=100.00 E-value=4.2e-45 Score=309.30 Aligned_cols=155 Identities=45% Similarity=0.763 Sum_probs=142.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCC Q ss_conf 22232310399999999999999999998899999999999999999642433432031578999999721222332101 Q gi|255764487|r 24 AEEKSEINIPEESLNQSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEK 103 (219) Q Consensus 24 ~~~~~~~~~~e~~~~e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~ 103 (219) .........+..+..++++++++|+|++|||+|||||+++++.+++.|+.++|+.+||||+|+|+||+.+.+. T Consensus 8 ~~~~~l~~~l~~l~~e~~~~~~~~~r~~Ae~eN~rkr~~ke~~~~~~~a~~~~~~~lL~v~D~leral~~~~~------- 80 (162) T pfam01025 8 DEEEALEEELEELEEEIEELKDRLLRLLAEFENYRKRTEREREEAKKYAIEKFAKDLLPVLDNLERALAAAKE------- 80 (162) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC------- T ss_conf 4799999999999999999999999999999999999999999999999999999860165269999972613------- Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEE Q ss_conf 11278998764479999999999864110001368887570057775224345897745999970881775678200024 Q gi|255764487|r 104 KSESVLKSLIEGIEMTRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALV 183 (219) Q Consensus 104 ~~~~~~~~~~~Gi~mi~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V 183 (219) .....+|++||.||+++|.++|+++||++|+|+|++|||++||||++++++++++|||++|+|+||+|+|||||||+| T Consensus 81 --~~~~~~~~~G~~~i~~~l~~~l~~~gv~~i~~~G~~FDP~~HeAv~~~~~~~~~~~~I~~v~q~GY~l~~rvlRpA~V 158 (162) T pfam01025 81 --NEDVKSLVEGVEMILKQLLKVLEKHGVEKIEPEGEPFDPNLHEAVSQVPSDEKPPGTVVEVLQKGYKLHDRVLRPAMV 158 (162) T ss_pred --CCHHHHHHHHHHHHHHHHHHHHHHCCEEEECCCCCCCCHHHHCEEEEECCCCCCCCEEEEEEECCCEECCEEECCCEE T ss_conf --101789999999999999999986552331677885785783011453689999298999854593879997206368 Q ss_pred EEEC Q ss_conf 8604 Q gi|255764487|r 184 SISK 187 (219) Q Consensus 184 ~Vsk 187 (219) +||| T Consensus 159 ~Vsk 162 (162) T pfam01025 159 VVSK 162 (162) T ss_pred EECC T ss_conf 8679 No 4 >cd00446 GrpE GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding. In eukaryotes, only the mitochondrial Hsp70, not the cytosolic form, is GrpE dependent. Probab=100.00 E-value=2.8e-42 Score=290.80 Aligned_cols=137 Identities=47% Similarity=0.852 Sum_probs=131.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 99999999999988999999999999999996424334320315789999997212223321011127899876447999 Q gi|255764487|r 40 SEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLKSLIEGIEMT 119 (219) Q Consensus 40 ~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~~Gi~mi 119 (219) +++++++|+|++|||+|||||+.+++++++.|+.++|+++||||+|+|+||+++... +...++|++||.|| T Consensus 1 ~~~~~d~~~r~~Ae~~N~rkr~~~e~~~~~~~~~~~~~~~lL~v~D~l~~al~~~~~---------~~~~~~~~~Gi~~i 71 (137) T cd00446 1 LEELKDKLLRALAEFENYRKRTEREREEARKYAIEKFAKDLLPVLDNLERALEAAKK---------EEELKNLVEGVEMT 71 (137) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC---------CHHHHHHHHHHHHH T ss_conf 967899999999869999999999999999999999999615645259999982633---------13588899999999 Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEE Q ss_conf 999999986411000136888757005777522434589774599997088177567820002486 Q gi|255764487|r 120 RREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSI 185 (219) Q Consensus 120 ~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~V 185 (219) +++|.++|+++||++|+++|++|||++||||++++++++++|+|++|+|+||+|+|||||||+|+| T Consensus 72 ~~~l~~~L~~~gi~~i~~~g~~FDP~~HeAv~~~~~~~~~~~~I~~v~~~GY~l~~rvlRpA~V~V 137 (137) T cd00446 72 LKQLLDVLEKHGVEKIEPEGEPFDPNLHEAVMQVPSPDVEPGTVVEVLQKGYKLGDRVLRPAMVVV 137 (137) T ss_pred HHHHHHHHHHCCCEEECCCCCCCCHHHHHEEEEECCCCCCCCEEEEEEECCCEECCEEEECCEEEC T ss_conf 999999999869952245699689467104356368999939899996569386999710637469 No 5 >KOG3003 consensus Probab=100.00 E-value=2.4e-40 Score=278.41 Aligned_cols=155 Identities=37% Similarity=0.660 Sum_probs=145.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH Q ss_conf 99999999999999999889999999999999999964243343203157899999972122233210111278998764 Q gi|255764487|r 35 ESLNQSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLKSLIE 114 (219) Q Consensus 35 ~~~~e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~~ 114 (219) .+.++..+|+|+|+|..||++|.|+|+.|..++++.||+++|+++||.|.|+|++|.+..+.+.. ....+..++.+++ T Consensus 81 k~~~e~~eLkdk~~rs~Ad~eNlr~R~~r~~edak~FaiQ~f~kdLleVaD~Le~a~~~v~ee~~--~~d~~~~L~~l~e 158 (236) T KOG3003 81 KLEKEEQELKDKYLRSLAECENLRDRTIRDVEDAKKFAIQSFCKDLLEVADNLEKATECVKEESE--KEDQKKDLKDLFE 158 (236) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHC--CCCCCHHHHHHHH T ss_conf 88889999999999988888889999888788888899999999999988788899874342106--3200257999974 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEEECCCCC Q ss_conf 47999999999986411000136888757005777522434589774599997088177567820002486048888 Q gi|255764487|r 115 GIEMTRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSISKGKTQ 191 (219) Q Consensus 115 Gi~mi~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~Vsk~~~~ 191 (219) |+.|++++|.++|.+||++..+|+|++|||+.|||++++|...+++|||..|.+.||+||||+||||+|+|++++.. T Consensus 159 Gl~mte~ql~~vf~KhGLekldPigekFDPn~HEAvfq~p~~~k~pgtV~~v~k~Gy~L~~R~IRPA~VgV~~~~~~ 235 (236) T KOG3003 159 GLSMTEAQLKEVFAKHGLEKLDPIGEKFDPNEHEAVFQVPDAAKEPGTVALVTKKGYKLNGRVIRPAMVGVVKGGEN 235 (236) T ss_pred HHHHHHHHHHHHHHHCCCEECCCCCCCCCCCHHHEEEECCCCCCCCCEEEEEECCCCCCCCEEECHHHEEEECCCCC T ss_conf 89999999999999749544178788889550222575445677997589880467401773500344145227789 No 6 >pfam11500 Cut12 Spindle-body formation-associated protein. This is the central coiled-coil region of cut12 also found in other fungi, barring S. cerevisiae. The full protein has two predicted coiled-coil regions, and one consensus phosphorylation site for p34cdc2 and two for MAP kinase. During fission yeast mitosis, the duplicated spindle pole bodies (SPBs) nucleate microtubule arrays that interdigitate to form the mitotic spindle. Cut12 is localized to the SPB throughout the cell cycle, predominantly around the inner face of the interphase SPB, adjacent to the nucleus. Cut12 associates with Fin1 and is important in this context for the activity of Plo1. Probab=66.72 E-value=8.2 Score=19.38 Aligned_cols=31 Identities=26% Similarity=0.374 Sum_probs=23.5 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999988999999999999999996424334320 Q gi|255764487|r 48 LRVIAEMENLRRRTDREKKDAQSYSIAKFARDM 80 (219) Q Consensus 48 lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~l 80 (219) .+-.++|++||-++.+|+..+++|- ++++.+ T Consensus 69 kYWK~efesY~~~~~~Ei~kLi~yr--~~aKsy 99 (151) T pfam11500 69 KYWKAEFDSYHSKTEREIKKLIQYK--QLAKSY 99 (151) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHH T ss_conf 0489999999998899999999999--999999 No 7 >pfam08780 NTase_sub_bind Nucleotidyltransferase substrate binding protein like. Nucleotidyltransferases (EC 2.7.7) comprise a large enzyme family with diverse roles in polynucleotide synthesis and modification. This domain is structurally related to kanamycin nucleotidyltransferase (KNTase) and forms a complex with HI0073, a sequence homolog of the nucleotide-binding domain of this nucleotidyltransferase superfamily. Probab=65.39 E-value=12 Score=18.42 Aligned_cols=25 Identities=24% Similarity=0.323 Sum_probs=11.2 Q ss_pred HHHHHHHHHHHH----HHHHHHHHHHHHC Q ss_conf 998764479999----9999998641100 Q gi|255764487|r 109 LKSLIEGIEMTR----REMMSTLERYGVK 133 (219) Q Consensus 109 ~~~~~~Gi~mi~----k~l~~~L~~~GV~ 133 (219) ...+++.|+.++ |-|...|+..|+. T Consensus 28 rdg~IqrFE~t~ElaWK~lK~~L~~~g~~ 56 (123) T pfam08780 28 RDGVIQRFEFTYELAWKLLKDYLEYQGIV 56 (123) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 99689999999999999999999980876 No 8 >KOG1962 consensus Probab=56.45 E-value=9.8 Score=18.87 Aligned_cols=12 Identities=33% Similarity=0.382 Sum_probs=4.0 Q ss_pred HHHHHHHHHHHH Q ss_conf 998764479999 Q gi|255764487|r 109 LKSLIEGIEMTR 120 (219) Q Consensus 109 ~~~~~~Gi~mi~ 120 (219) +.+..+|+..-+ T Consensus 184 l~Kq~e~~~~Ey 195 (216) T KOG1962 184 LKKQSEGLQDEY 195 (216) T ss_pred HHHHHHHCCCHH T ss_conf 999998711089 No 9 >pfam05470 eIF-3c_N Eukaryotic translation initiation factor 3 subunit 8 N-terminus. The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA. Probab=38.57 E-value=31 Score=15.65 Aligned_cols=104 Identities=13% Similarity=0.252 Sum_probs=60.4 Q ss_pred HHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCC Q ss_conf 03999999999999-----9999999889999999999999999964243343203157899999972122233210111 Q gi|255764487|r 31 NIPEESLNQSEEFR-----DKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKS 105 (219) Q Consensus 31 ~~~e~~~~e~~elk-----dk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~ 105 (219) ..++++..-++.++ +.|..+..+|+++.|.++|-+.-.-..++=+|....|--+++|-.....-+...-.-.+.+ T Consensus 27 Kr~eel~~~i~~i~na~ki~Dw~~i~~eFd~L~k~~~K~~~v~~~~~~P~fyIk~L~~LEd~v~e~~~dke~~Kkmsk~n 106 (593) T pfam05470 27 KRFEEMTSTIKTIKNAMKINDWVSLLEEFDKLNKAYQKAKRVSENVKTPRFYIKTLVMLEDFLNELWADKEAKKKMSKNN 106 (593) T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHCCHHH T ss_conf 67999999999999887622399999999999999999885553489985999999999999999885757776508877 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCC Q ss_conf 27899876447999999999986411000 Q gi|255764487|r 106 ESVLKSLIEGIEMTRREMMSTLERYGVKK 134 (219) Q Consensus 106 ~~~~~~~~~Gi~mi~k~l~~~L~~~GV~~ 134 (219) +.++..+.+-|+=..+.+...+.++--.+ T Consensus 107 akalntlkQklkK~~k~ye~~i~~yrenP 135 (593) T pfam05470 107 AKALNTLKQKVKKNNKQFEDDITRYREDP 135 (593) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 77789999999985077899999987296 No 10 >TIGR00060 L18_bact ribosomal protein L18; InterPro: IPR004389 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This is the ribosomal protein L18 family. The archaebacterial and eukaryotic type rpL18 is not included in this family.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=36.98 E-value=6.9 Score=19.86 Aligned_cols=14 Identities=21% Similarity=0.328 Sum_probs=8.4 Q ss_pred HHCCHHHHHHHHHH Q ss_conf 20315789999997 Q gi|255764487|r 79 DMLSVSDNLSRALD 92 (219) Q Consensus 79 ~lL~v~D~lerAl~ 92 (219) ..|--++.|++.|. T Consensus 47 ~tlas~Stl~~~l~ 60 (118) T TIGR00060 47 VTLASASTLEKKLK 60 (118) T ss_pred EEEEEHHHHHHHHH T ss_conf 47873155668877 No 11 >KOG0250 consensus Probab=34.01 E-value=37 Score=15.19 Aligned_cols=21 Identities=10% Similarity=-0.021 Sum_probs=8.4 Q ss_pred HCCCCCCCC---CCCCCHHHHHHC Q ss_conf 000136888---757005777522 Q gi|255764487|r 132 VKKIDAKDQ---KFNPNMHQAMFE 152 (219) Q Consensus 132 V~~i~~~G~---~FDP~~HeAi~~ 152 (219) -.+++|+|. .-+|.||-||.. T Consensus 493 ~~P~GPlG~~Vtl~~~KWa~aIE~ 516 (1074) T KOG0250 493 TPPKGPLGKYVTLKEPKWALAIER 516 (1074) T ss_pred CCCCCCCCCEEEECCCHHHHHHHH T ss_conf 999887654367258088999999 No 12 >pfam04108 APG17 Autophagy protein Apg17. Apg17 is required for activating Apg1 protein kinases. Probab=32.05 E-value=40 Score=14.99 Aligned_cols=40 Identities=15% Similarity=0.143 Sum_probs=22.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999889999999999999999964 Q gi|255764487|r 33 PEESLNQSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYS 72 (219) Q Consensus 33 ~e~~~~e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a 72 (219) .+.+...++...+..--+++.++|...++..+.....+.. T Consensus 124 ve~L~~~lk~~i~e~~~~~~~~d~~~~~fd~~l~~l~~~l 163 (410) T pfam04108 124 VELLRDNLKIYIDEVPAIRAQLDNILNQFDSDLDSLQEQL 163 (410) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999898758999988627899999999999998 No 13 >TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family; InterPro: IPR014289 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are part of the larger sigma-70 family. From homology, tree building, bidirectional best hits and their one-to-a-genome distribution, they appear to represent a conserved family.. Probab=30.78 E-value=42 Score=14.86 Aligned_cols=70 Identities=21% Similarity=0.359 Sum_probs=42.7 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHH Q ss_conf 99999999999998899999999999999999642433432031578999999721222332101112789987644799 Q gi|255764487|r 39 QSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLKSLIEGIEM 118 (219) Q Consensus 39 e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~~Gi~m 118 (219) .+.+++-.+|| .|.++ -|+..++-+-+++.-+..-+.-.|+| .+...++.|+-|| T Consensus 7 ~l~~~Rr~LLr-FA~lQ------LRdh~d~AEDaVQEtLl~Al~~~~~F----------------~G~s~lkTWl~~I-- 61 (194) T TIGR02943 7 ELEDLRRDLLR-FARLQ------LRDHEDLAEDAVQETLLAALEHADSF----------------AGRSALKTWLFAI-- 61 (194) T ss_pred HHHHHHHHHHH-HHHHC------CCCCHHHHHHHHHHHHHHHHHCCCCC----------------HHHHHHHHHHHHH-- T ss_conf 99998799999-98623------88826788899999999987357760----------------1489999999999-- Q ss_pred HHHHHHHHHHHHHHC Q ss_conf 999999998641100 Q gi|255764487|r 119 TRREMMSTLERYGVK 133 (219) Q Consensus 119 i~k~l~~~L~~~GV~ 133 (219) ...+|+++|..-|=+ T Consensus 62 LknKiID~LR~~~R~ 76 (194) T TIGR02943 62 LKNKIIDVLRAKGRE 76 (194) T ss_pred HHHHHHHHHHCCCCE T ss_conf 999999998346754 No 14 >PTZ00156 60S ribosomal protein L11; Provisional Probab=30.77 E-value=25 Score=16.31 Aligned_cols=49 Identities=16% Similarity=0.234 Sum_probs=35.8 Q ss_pred HHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEEE Q ss_conf 4110001368887570057775224345897745999970881775678200024860 Q gi|255764487|r 129 RYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSIS 186 (219) Q Consensus 129 ~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~Vs 186 (219) .+||.+--..|.+|||..-- +-=+..|..-++||....|=++.+.|.-. T Consensus 102 sFGI~EhId~G~kYDP~iGI---------~Gmdv~V~l~RpG~Rv~~Rk~~~~~i~~~ 150 (172) T PTZ00156 102 GFGIQEHIDLGIKYDPSTGI---------YGMDFYVVLSRPGERVAHRKRRNSRVGKS 150 (172) T ss_pred EECCHHHEECCCEECCCCCE---------EEEEEEEEEECCCCEEEEHHHHCCCCCCC T ss_conf 41522223577421686777---------65368999715874311011322558867 No 15 >KOG3895 consensus Probab=28.06 E-value=46 Score=14.56 Aligned_cols=36 Identities=25% Similarity=0.493 Sum_probs=31.5 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCC Q ss_conf 9999999986411000136888757005777522434 Q gi|255764487|r 119 TRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPH 155 (219) Q Consensus 119 i~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~ 155 (219) +++||..++.+.|-+.|.-+-+.|=|+ |.-+.+.++ T Consensus 204 vf~Qlvki~~slG~e~fPli~qt~yPn-HK~m~s~~t 239 (488) T KOG3895 204 VFAQLVKITKSLGPEKFPLIEQTFYPN-HKEMLSQPT 239 (488) T ss_pred HHHHHHHHHHHCCCCCCCCCCEEECCC-CHHHCCCCC T ss_conf 999999998751854455440010687-442214887 No 16 >TIGR01364 serC_1 phosphoserine aminotransferase; InterPro: IPR003248 Phosphoserine aminotransferases (2.6.1.52 from EC) catalyse the conversion of O-phospho-L-serine and oxoglutarate to 3-phosphonooxypyruvate and L-glutamate in the major phosphorylated serine biosynthesis pathway. In bacteria it is also equired for the biosynthesis of pyridoxine. The enzyme requires pyridoxal phosphate as a cofactor, and is part of the aminotransferase class-V family.; GO: 0006564 L-serine biosynthetic process. Probab=25.91 E-value=34 Score=15.44 Aligned_cols=41 Identities=20% Similarity=0.235 Sum_probs=29.9 Q ss_pred HHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHCCHHHHHH Q ss_conf 99999889999999---------9999999999642433432031578999 Q gi|255764487|r 47 YLRVIAEMENLRRR---------TDREKKDAQSYSIAKFARDMLSVSDNLS 88 (219) Q Consensus 47 ~lR~~AE~eN~rkR---------~~ke~~~~~~~a~~~~~~~lL~v~D~le 88 (219) +.++++|+-||+.. -.++-. ..-...++.+|+||.|=||++ T Consensus 16 L~~aq~Ellnf~~~G~SVmEiSHRsk~F~-~v~~~Ae~dlR~LL~iPd~Y~ 65 (391) T TIGR01364 16 LEQAQKELLNFNGLGMSVMEISHRSKEFE-AVASEAESDLRELLNIPDNYE 65 (391) T ss_pred HHHHHHHHHHHHHCCCCEEEEECCCHHHH-HHHHHHHHHHHHHHCCCCCCE T ss_conf 99999998657517976699853868999-999999999998824799826 No 17 >KOG2700 consensus Probab=25.81 E-value=51 Score=14.30 Aligned_cols=75 Identities=12% Similarity=0.152 Sum_probs=46.4 Q ss_pred HHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCC-CCCCCCCCHHH Q ss_conf 433432031578999999721222332101112789987644799999999998-6411000136-88875700577 Q gi|255764487|r 74 AKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLKSLIEGIEMTRREMMSTL-ERYGVKKIDA-KDQKFNPNMHQ 148 (219) Q Consensus 74 ~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~~Gi~mi~k~l~~~L-~~~GV~~i~~-~G~~FDP~~He 148 (219) .-++-+|+-.+-+|.||+....--....--+.-..+.++..|..-=..++++.. +.+|..+.-+ .|+.+.|..+- T Consensus 170 ~~~~qel~~~l~~f~~~~~~~~~~~~kga~gtqasf~~l~~~~~~kv~~ld~Lv~k~~gf~~~~~~TGQt~sr~~~~ 246 (481) T KOG2700 170 CLWIQELLRDLERFHRARTDVRFRGLKGATGTQASFLSLFLGDMDKVEKLDSLVTKELGFVPMYIVTGQTYSRKTDA 246 (481) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHH T ss_conf 99899999999999986312001566521301888888633518889989999999818886554458867831578 No 18 >pfam02963 EcoRI Restriction endonuclease EcoRI. Probab=25.79 E-value=36 Score=15.27 Aligned_cols=53 Identities=28% Similarity=0.406 Sum_probs=39.1 Q ss_pred CCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEEECCCC Q ss_conf 0013688875700577752243458977459999708817756782000248604888 Q gi|255764487|r 133 KKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSISKGKT 190 (219) Q Consensus 133 ~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~Vsk~~~ 190 (219) .+|+..=..+||.+-+.+....+.=+|+|-|++|--. +--.||-+|.-||.-+ T Consensus 48 ~eIN~~L~~idp~LGqTlFv~~ssikPDGGIievKd~-----~g~wr~iLv~EaK~QG 100 (257) T pfam02963 48 KEINEALKKIDPDLGQTLFVENASIKPDGGIVEVKDD-----YGNWRVVLVAEAKHQG 100 (257) T ss_pred HHHHHHHHCCCCCCCCCEEECCCCCCCCCCEEEEEEC-----CCCEEEEEEEEHHHCC T ss_conf 9998988415834484033057752688876999806-----8988999987354247 No 19 >TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor; InterPro: IPR006548 These sequences represent the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human . ELAV stands for the Drosophila Embryonic lethal abnormalvisual protein . ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (IPR006546 from INTERPRO). ; GO: 0003723 RNA binding. Probab=25.27 E-value=33 Score=15.52 Aligned_cols=27 Identities=26% Similarity=0.442 Sum_probs=16.1 Q ss_pred CHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEE Q ss_conf 057775224345897745999970881775678200024 Q gi|255764487|r 145 NMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALV 183 (219) Q Consensus 145 ~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V 183 (219) |+.||++-+-+= -||.|++|||-.+-+ T Consensus 404 NY~EA~~Ai~SL------------NGy~Lg~rvLQv~fk 430 (436) T TIGR01661 404 NYDEAAMAIRSL------------NGYTLGNRVLQVSFK 430 (436) T ss_pred CHHHHHHHHHHH------------CCCCCCCCEEEEEEE T ss_conf 089999999871------------474102717999985 No 20 >TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890 The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases . All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome. Probab=24.74 E-value=53 Score=14.18 Aligned_cols=20 Identities=10% Similarity=0.365 Sum_probs=7.0 Q ss_pred HHHHHHHCCHHHHHHHHHHH Q ss_conf 43343203157899999972 Q gi|255764487|r 74 AKFARDMLSVSDNLSRALDS 93 (219) Q Consensus 74 ~~~~~~lL~v~D~lerAl~~ 93 (219) ..++.++|.|--.++.|+.. T Consensus 527 ~g~l~~~i~v~~~ye~A~e~ 546 (1191) T TIGR02168 527 VGVLSELIEVDEGYEAAIEA 546 (1191) T ss_pred CHHHHHHHCCCHHHHHHHHH T ss_conf 00357652154889999999 No 21 >KOG0493 consensus Probab=23.08 E-value=57 Score=13.97 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=19.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999889999999999999999 Q gi|255764487|r 43 FRDKYLRVIAEMENLRRRTDREKKDAQ 69 (219) Q Consensus 43 lkdk~lR~~AE~eN~rkR~~ke~~~~~ 69 (219) --+|+.|++|||.--|--+++.+..+- T Consensus 254 taeQL~RLK~EF~enRYlTEqRRQ~La 280 (342) T KOG0493 254 TAEQLQRLKAEFQENRYLTEQRRQELA 280 (342) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 499999999998660357899999999 No 22 >pfam11062 DUF2863 Protein of unknown function (DUF2863). This bacterial family of proteins have no known function. Probab=21.49 E-value=46 Score=14.59 Aligned_cols=30 Identities=20% Similarity=0.389 Sum_probs=20.4 Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCHHH Q ss_conf 999999998641100013688875700577 Q gi|255764487|r 119 TRREMMSTLERYGVKKIDAKDQKFNPNMHQ 148 (219) Q Consensus 119 i~k~l~~~L~~~GV~~i~~~G~~FDP~~He 148 (219) ...++..+|+..||+.|....+.|.|++.+ T Consensus 339 ~~~~I~~~Lre~GV~~v~~~~~~f~~EyCd 368 (398) T pfam11062 339 PIEQIEALLRECGVTDIRRLAERFPPEYCE 368 (398) T ss_pred HHHHHHHHHHHCCHHHHHHHHHCCCCHHHC T ss_conf 599999999981819999765118943331 No 23 >TIGR00273 TIGR00273 iron-sulfur cluster binding protein; InterPro: IPR004452 Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulphur clusters.. Probab=21.30 E-value=45 Score=14.67 Aligned_cols=34 Identities=12% Similarity=0.414 Sum_probs=26.3 Q ss_pred HHHHHHHHHHCCCCC-CCCCCCCCHHHHHHCCCCCCCCCCEEE Q ss_conf 999986411000136-888757005777522434589774599 Q gi|255764487|r 123 MMSTLERYGVKKIDA-KDQKFNPNMHQAMFEEPHDTVPANTII 164 (219) Q Consensus 123 l~~~L~~~GV~~i~~-~G~~FDP~~HeAi~~~~~~~~~~~tVi 164 (219) |-.+|++.|++.+++ +|+ -|.++.+.+.|...|| T Consensus 105 Ln~~L~~~G~~v~ETDLGE--------lI~Q~~d~d~P~H~Vv 139 (450) T TIGR00273 105 LNEVLEKKGIEVVETDLGE--------LILQLDDNDPPSHIVV 139 (450) T ss_pred HHHHHHHCCCEEEEECCCE--------EEEEEECCCCCEEEEE T ss_conf 1488876597799800430--------7887745888427885 No 24 >pfam04914 DltD_C DltD C-terminal region. DltD is and integral membrane protein involved in the biosynthesis of D-alanyl-lipoteichoic acid. This is important in controlling the net ionic charge in lipoteichoic acid (LTA). This family is found in bacteria of the Bacillus/Clostridium group. DltD binds Dcp and ligates it with D-alanine. DltD does not ligate acyl carrier protein (ACP) with D-alanine. It also has thioesterase activity for mischarged D-alanyl-acyl carrier protein (ACP). DltD is thought to be responsible for discriminating between Dcp involved in the D-alanylation of LTA, and ACP involved in fatty acid biosynthesis. This family consists of the C-terminal region of DltD. Probab=20.96 E-value=63 Score=13.70 Aligned_cols=72 Identities=17% Similarity=0.103 Sum_probs=42.6 Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHH-------HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCC Q ss_conf 15789999997212223321011127899876-------4479999999999864110001368887570057775224 Q gi|255764487|r 82 SVSDNLSRALDSAPLDLANSEKKSESVLKSLI-------EGIEMTRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEE 153 (219) Q Consensus 82 ~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~-------~Gi~mi~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~ 153 (219) |=..+|.+.|.........+.----+....|+ +..+-.++++..+++++|+..++-....++|.+++=.+|+ T Consensus 33 pEy~Dlql~L~~~~~~~~~vlfVi~PvNgkWydytGl~k~~r~~~y~KI~~~~~~~Gf~i~Dls~~~y~pYfm~DtiHl 111 (130) T pfam04914 33 PEYNDLQLVLDQFAKAGADVLFVIPPVNGKWYDYTGLSKEMRQQYYKKIKYQLKSQGFNIADLSDDGYEPYFMQDTIHL 111 (130) T ss_pred CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCEEEECCCC T ss_conf 4406899999999984994189854777058887089999999999999999998798387244578987635423325 No 25 >CHL00139 rpl18 ribosomal protein L18; Validated Probab=20.18 E-value=21 Score=16.78 Aligned_cols=10 Identities=20% Similarity=0.415 Sum_probs=7.3 Q ss_pred CCCEEECCEE Q ss_conf 0881775678 Q gi|255764487|r 168 QDGYAINERV 177 (219) Q Consensus 168 q~GY~l~~rv 177 (219) +.||+||||| T Consensus 86 Rggy~YHGrV 95 (109) T CHL00139 86 RGGKLYHGRI 95 (109) T ss_pred CCCCCCHHHH T ss_conf 8998422199 No 26 >PRK05593 rplR 50S ribosomal protein L18; Reviewed Probab=20.12 E-value=21 Score=16.72 Aligned_cols=10 Identities=40% Similarity=0.780 Sum_probs=7.9 Q ss_pred CCCEEECCEE Q ss_conf 0881775678 Q gi|255764487|r 168 QDGYAINERV 177 (219) Q Consensus 168 q~GY~l~~rv 177 (219) +.||+||||| T Consensus 92 R~g~~YHGrv 101 (115) T PRK05593 92 RGGYKYHGRV 101 (115) T ss_pred CCCCCCCHHH T ss_conf 8998422399 Done!