RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780545|ref|YP_003064958.1| metalloprotease [Candidatus Liberibacter asiaticus str. psy62] (647 letters) >gnl|CDD|162266 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. Length = 495 Score = 788 bits (2038), Expect = 0.0 Identities = 306/497 (61%), Positives = 384/497 (77%), Gaps = 4/497 (0%) Query: 95 LLSYLGSWFPLVLV-VLVWMFLMRQIQGGGARGAMGFGKSKAKLLSGNVGSVTFKDVAGV 153 LL +L S P +L+ V VW F RQ+QGGG A FGKSKAKLL+ VTFKDVAG+ Sbjct: 2 LLGFLFSLLPPILLLVGVWFFFRRQMQGGG-GRAFSFGKSKAKLLNEEKPKVTFKDVAGI 60 Query: 154 DEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEANVPFFTIS 213 DEAKE+L EIVDFL +P KF +LG +IP GVLLVGPPGTGKTLLA+AVAGEA VPFF+IS Sbjct: 61 DEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSIS 120 Query: 214 GSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQ 273 GSDFVE+FVGVGASRVRD+FEQAK N+PCI+F+DEIDAVGR RG GLGGGNDEREQTLNQ Sbjct: 121 GSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQ 180 Query: 274 LLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVGREHILMVHSRN 333 LLVEMDGF ++ GVI+IAATNRPDVLD ALLRPGRFDRQ+ V PDI GRE IL VH++N Sbjct: 181 LLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKN 240 Query: 334 VPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFEDAKDKILMGAE 393 LAP+V LK +AR TPGFSGADL NL+NEAAL+AAR+N+ +TM + E+A D+++ G E Sbjct: 241 KKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTEITMNDIEEAIDRVIAGPE 300 Query: 394 RRSTAMTEEEKKITAYHEAGHAVVACHVPKADPLHKATIIPRGRALGMVMQLPEADRHST 453 ++S ++E+EKK+ AYHEAGHA+V + ADP+HK TIIPRG+ALG LPE D++ Sbjct: 301 KKSRVISEKEKKLVAYHEAGHALVGLLLKDADPVHKVTIIPRGQALGYTQFLPEEDKYLY 360 Query: 454 TYVWMTSRLTILMGGRVAEEFTFGEDNVTSGAMSDIEYATKLARVMVTQFGFSNLLGKVS 513 T + +++ +L+GGR AEE FGE VT+GA +DI+ AT +AR MVT++G S+ LG V+ Sbjct: 361 TKSQLLAQIAVLLGGRAAEEIIFGE--VTTGASNDIKQATNIARAMVTEWGMSDKLGPVA 418 Query: 514 YEEGQQEALLSHPVSRPRSISEETAQKIDKEVFRLIEEAYQKAKSIIQEKNDNFVAIAEA 573 Y + L ++ + SEETA++ID+EV R+IEEAY++AK I+ E D +A+A Sbjct: 419 YGSDGGDVFLGRGFAKAKEYSEETAREIDEEVKRIIEEAYKRAKQILTENRDELELLAKA 478 Query: 574 LLEYETLSGKEIASLIR 590 LLE ET++ +EI L+ Sbjct: 479 LLEKETITREEIKELLA 495 >gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed. Length = 644 Score = 679 bits (1753), Expect = 0.0 Identities = 333/598 (55%), Positives = 443/598 (74%), Gaps = 5/598 (0%) Query: 1 MIALCLIASFSIFQAPSAGQDGVQDISYSQFIKDVDAGRVRKISVIGTHITGFYVNGESS 60 +IA+ L+ S+FQ+ + + + YS F+++V+ +VR+ + G I + Sbjct: 10 VIAVVLM---SVFQSFGPSESNGRKVDYSTFLQEVNQDQVREARINGREIN-VTKKDSNR 65 Query: 61 FQTYMPLVGSKLLDKLQSKDIEISSRPVNDGSPGLLSYLGSWFPLVLVVLVWMFLMRQIQ 120 + TY+P+ KLLD L +K++++ P + S L S SWFP++L++ VW+F MRQ+Q Sbjct: 66 YTTYIPVNDPKLLDNLLTKNVKVVGEPPEEPSL-LASIFISWFPMLLLIGVWIFFMRQMQ 124 Query: 121 GGGARGAMGFGKSKAKLLSGNVGSVTFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRI 180 GGG +GAM FGKSKA++L+ + TF DVAG DEAKE++ E+V++L +P +F++LGG+I Sbjct: 125 GGGGKGAMSFGKSKARMLTEDQIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKI 184 Query: 181 PHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNS 240 P GVL+VGPPGTGKTLLA+A+AGEA VPFFTISGSDFVE+FVGVGASRVRDMFEQAK + Sbjct: 185 PKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAA 244 Query: 241 PCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLD 300 PCI+F+DEIDAVGR RG GLGGG+DEREQTLNQ+LVEMDGFE +EG+I+IAATNRPDVLD Sbjct: 245 PCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLD 304 Query: 301 AALLRPGRFDRQITVPNPDIVGREHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNL 360 ALLRPGRFDRQ+ V PD+ GRE IL VH R VPLAP++ IARGTPGFSGADL NL Sbjct: 305 PALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANL 364 Query: 361 VNEAALMAARRNRRLVTMQEFEDAKDKILMGAERRSTAMTEEEKKITAYHEAGHAVVACH 420 VNEAAL AAR N+R+V+M EFE AKDKI+MGAERRS MTE +K+ TAYHEAGHA++ Sbjct: 365 VNEAALFAARGNKRVVSMVEFEKAKDKIMMGAERRSMVMTEAQKESTAYHEAGHAIIGRL 424 Query: 421 VPKADPLHKATIIPRGRALGMVMQLPEADRHSTTYVWMTSRLTILMGGRVAEEFTFGEDN 480 VP+ DP+HK TIIPRGRALG+ LPE D S + + S+++ L GGR+AEE +G ++ Sbjct: 425 VPEHDPVHKVTIIPRGRALGVTFFLPEGDAISASRQKLESQISTLYGGRLAEEIIYGPEH 484 Query: 481 VTSGAMSDIEYATKLARVMVTQFGFSNLLGKVSYEEGQQEALLSHPVSRPRSISEETAQK 540 V++GA +DI+ AT LAR MVTQ+GFS LG + Y E + E L V++ + +S+ETA+ Sbjct: 485 VSTGASNDIKVATNLARNMVTQWGFSEKLGPLLYAEEEGEVFLGRSVAKAKHMSDETARI 544 Query: 541 IDKEVFRLIEEAYQKAKSIIQEKNDNFVAIAEALLEYETLSGKEIASLIRGEKISRPS 598 ID+EV LIE Y +A+ ++ + D A+ +AL++YET+ +I L+ + P+ Sbjct: 545 IDQEVKALIERNYNRARQLLTDNMDILHAMKDALMKYETIDAPQIDDLMARRDVRPPA 602 >gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional. Length = 389 Score = 307 bits (790), Expect = 5e-84 Identities = 121/260 (46%), Positives = 169/260 (65%), Gaps = 1/260 (0%) Query: 144 SVTFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202 +VT++D+ G++E +++E V+ L P+ F+ +G P GVLL GPPGTGKTLLA+AVA Sbjct: 127 NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVA 186 Query: 203 GEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGG 262 E N F + GS+ V+ F+G GA VR++FE A+ +P I+F+DEIDA+ R Sbjct: 187 HETNATFIRVVGSELVQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTS 246 Query: 263 GNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVG 322 G+ E ++TL QLL EMDGF+ V +IAATNR D+LD A+LRPGRFDR I VP PD G Sbjct: 247 GDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEG 306 Query: 323 REHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFE 382 R IL +H+R + LA +V L+ +A T G SGADL+ + EA + A R +R VTM++F Sbjct: 307 RLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICTEAGMFAIRDDRTEVTMEDFL 366 Query: 383 DAKDKILMGAERRSTAMTEE 402 A +K++ E+ S Sbjct: 367 KAIEKVMGKEEKDSMEEPGV 386 >gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal. Length = 364 Score = 264 bits (677), Expect = 4e-71 Identities = 121/246 (49%), Positives = 164/246 (66%), Gaps = 1/246 (0%) Query: 145 VTFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAG 203 V+++D+ G++E +++E V+ L P+ F+ +G P GVLL GPPGTGKTLLA+AVA Sbjct: 119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAH 178 Query: 204 EANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGG 263 E N F + GS+ V ++G GA VR++FE AK +P I+F+DEIDA+ R G Sbjct: 179 ETNATFIRVVGSELVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSG 238 Query: 264 NDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVGR 323 + E ++TL QLL E+DGF+ V +IAATNRPD+LD ALLRPGRFDR I VP PD GR Sbjct: 239 DREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGR 298 Query: 324 EHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFED 383 IL +H+R + LA +V L+ IA+ T G SGADL+ + EA + A R R VTM +F Sbjct: 299 LEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIK 358 Query: 384 AKDKIL 389 A +K+L Sbjct: 359 AVEKVL 364 >gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733 Score = 231 bits (591), Expect = 4e-61 Identities = 111/266 (41%), Positives = 166/266 (62%), Gaps = 3/266 (1%) Query: 142 VGSVTFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARA 200 V +V + D+ G++E K++L+E V++ L P+ F+++G R P GVLL GPPGTGKTLLA+A Sbjct: 447 VPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKA 506 Query: 201 VAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGL 260 VA E+ F + G + + +VG +R++F +A+ +P I+F DEIDA+ RG Sbjct: 507 VATESGANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARF 566 Query: 261 GGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDI 320 +R +NQLL EMDG + V++IAATNRPD+LD ALLRPGRFDR I VP PD Sbjct: 567 DTSVTDR--IVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRFDRLILVPPPDE 624 Query: 321 VGREHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQE 380 R+ I +H+R++PLA +V L+ +A T G++GAD+ + EAA+ A R + ++ Sbjct: 625 EARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGSPAKEK 684 Query: 381 FEDAKDKILMGAERRSTAMTEEEKKI 406 E +++ L + E KK+ Sbjct: 685 LEVGEEEFLKDLKVEMRHFLEALKKV 710 Score = 215 bits (548), Expect = 4e-56 Identities = 111/231 (48%), Positives = 152/231 (65%), Gaps = 4/231 (1%) Query: 142 VGSVTFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARA 200 V VT++D+ G+ EAKE ++E+V+ + P+ F+ LG P GVLL GPPGTGKTLLA+A Sbjct: 172 VPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKA 231 Query: 201 VAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGL 260 VA EA F +I+G + + + G R+R++F++A+ N+P I+F+DEIDA+ R Sbjct: 232 VANEAGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVT 291 Query: 261 GGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDI 320 G + ++ + QLL MDG + VI+I ATNRPD LD AL RPGRFDR+I + PD Sbjct: 292 G---EVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDK 348 Query: 321 VGREHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARR 371 R+ IL VH+RN+PLA +V L +A T GF GADL L EAA+ A RR Sbjct: 349 RARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRR 399 >gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like protein; Provisional. Length = 438 Score = 208 bits (531), Expect = 4e-54 Identities = 101/245 (41%), Positives = 155/245 (63%), Gaps = 1/245 (0%) Query: 146 TFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGE 204 ++ D+ G+++ ++++E V+ L P+ + +G + P GV+L GPPGTGKTLLA+AVA E Sbjct: 181 SYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANE 240 Query: 205 ANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGN 264 + F + GS+ ++ ++G G VR++F A+ N+P IVF+DEIDA+G R GG Sbjct: 241 TSATFLRVVGSELIQKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGE 300 Query: 265 DEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVGRE 324 E ++T+ +LL ++DGF+S V +I ATNR + LD AL+RPGR DR+I PNPD + Sbjct: 301 KEIQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKR 360 Query: 325 HILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFEDA 384 I +H+ + LA +V L+ SGAD++ + EA L+A R R VT +F A Sbjct: 361 RIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRERRMKVTQADFRKA 420 Query: 385 KDKIL 389 K+K+L Sbjct: 421 KEKVL 425 >gnl|CDD|185633 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like protein; Provisional. Length = 398 Score = 204 bits (521), Expect = 6e-53 Identities = 95/242 (39%), Positives = 145/242 (59%), Gaps = 1/242 (0%) Query: 144 SVTFKDVAGVDEAKEDLQEIVDF-LCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202 VT+ D+ G+D K++++E V+ L P+ ++++G P GVLL GPPGTGKT+LA+AVA Sbjct: 141 DVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVA 200 Query: 203 GEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGG 262 F + GS+FV+ ++G G VRD+F A+ N+P I+F+DE+D++ R G Sbjct: 201 HHTTATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTG 260 Query: 263 GNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVG 322 + E ++ L +LL +MDGF+ + V +I ATNR D LD ALLRPGR DR+I P PD Sbjct: 261 ADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQ 320 Query: 323 REHILMVHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFE 382 + I + + L+ V L+ S AD+ + EA + A R+NR ++ ++FE Sbjct: 321 KRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRKNRYVILPKDFE 380 Query: 383 DA 384 Sbjct: 381 KG 382 >gnl|CDD|163401 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity. Length = 512 Score = 139 bits (352), Expect = 2e-33 Identities = 89/277 (32%), Positives = 139/277 (50%), Gaps = 25/277 (9%) Query: 142 VGSVTFKDVAGVDEAKEDLQEIVD--FLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLAR 199 V VT+ D+ G+D E +++ V+ FL P+ ++ + P GVLL GPPG GKTL+A+ Sbjct: 176 VPDVTYADIGGLDSQIEQIRDAVELPFL-HPELYREYDLKPPKGVLLYGPPGCGKTLIAK 234 Query: 200 AVA------GEANVP----FFTISGSDFVELFVGVGASRVRDMFEQAK----NNSPCIVF 245 AVA A F I G + + +VG ++R +F++A+ + P IVF Sbjct: 235 AVANSLAQRIGAETGDKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVF 294 Query: 246 VDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLR 305 DE+D++ R RG G+ +D + QLL E+DG ES + VI+I A+NR D++D A+LR Sbjct: 295 FDEMDSIFRTRGSGVS--SDVETTVVPQLLSELDGVESLDNVIVIGASNREDMIDPAILR 352 Query: 306 PGRFDRQITVPNPDIVGREHILMVH-SRNVPLAPNVILKTIARGTPGFSGADLRNLVNEA 364 PGR D +I + PD I + + ++PL ++ R A L + Sbjct: 353 PGRLDVKIRIERPDAEAAADIFSKYLTDSLPLDADLAEFDGDREAT---AAALIQRAVD- 408 Query: 365 ALMAARRNRRLVTMQEFEDAKDKILMGAERRSTAMTE 401 L A R V + + ++L + S AM Sbjct: 409 HLYATSEENRYVEVTY-ANGSTEVLYFKDFVSGAMIA 444 >gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148 Score = 85.1 bits (210), Expect = 5e-17 Identities = 46/156 (29%), Positives = 66/156 (42%), Gaps = 26/156 (16%) Query: 181 PHGVLLVGPPGTGKTLLARAVAGEANVP---FFTISGSDFVE--------------LFVG 223 +L+VGPPG+GKT LARA+A E P I G D +E G Sbjct: 2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61 Query: 224 VGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFES 283 G R+R A+ P ++ +DEI ++ E L + L + +S Sbjct: 62 SGELRLRLALALARKLKPDVLILDEITSLLDAEQ--------EALLLLLEELRLLLLLKS 113 Query: 284 SEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPD 319 + + +I TN L ALLR RFDR+I + Sbjct: 114 EKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148 >gnl|CDD|183986 PRK13342, PRK13342, recombination factor protein RarA; Reviewed. Length = 413 Score = 66.3 bits (163), Expect = 2e-11 Identities = 30/84 (35%), Positives = 43/84 (51%), Gaps = 17/84 (20%) Query: 177 GGRIPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQA 236 GR+ ++L GPPGTGKT LAR +AG + PF +S G +R++ E+A Sbjct: 33 AGRLSS-MILWGPPGTGKTTLARIIAGATDAPFEALSAVTS-------GVKDLREVIEEA 84 Query: 237 KNNS----PCIVFVDEIDAVGRHR 256 + I+F+DEI HR Sbjct: 85 RQRRSAGRRTILFIDEI-----HR 103 Score = 27.7 bits (63), Expect = 9.3 Identities = 25/102 (24%), Positives = 38/102 (37%), Gaps = 40/102 (39%) Query: 301 AALLRPGRFDRQITVPNPDIVGREHIL--------MVHSRNVPLAPNVIL-------KT- 344 A +RP D ++VG+EH+L M+ + + ++IL KT Sbjct: 3 AERMRPKTLD--------EVVGQEHLLGPGKPLRRMIEAGRL---SSMILWGPPGTGKTT 51 Query: 345 ----IARGT--------PGFSG-ADLRNLVNEAALMAARRNR 373 IA T SG DLR ++ EA + R Sbjct: 52 LARIIAGATDAPFEALSAVTSGVKDLREVIEEARQRRSAGRR 93 >gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit; Provisional. Length = 482 Score = 58.0 bits (141), Expect = 8e-09 Identities = 33/110 (30%), Positives = 52/110 (47%), Gaps = 18/110 (16%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 T DV G ++AKE L+E ++ L G+ +LL GPPG GKT LA A+A + Sbjct: 12 TLSDVVGNEKAKEQLREWIE--------SWLKGKPKKALLLYGPPGVGKTSLAHALANDY 63 Query: 206 NVPFFTISGSDF-----VELFVGVGASRVRDMFEQAKNNSPCIVFVDEID 250 ++ SD +E G A+ +F + ++ +DE+D Sbjct: 64 GWEVIELNASDQRTADVIERVAG-EAATSGSLFGARRK----LILLDEVD 108 >gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K. Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group. Length = 261 Score = 54.7 bits (132), Expect = 7e-08 Identities = 65/249 (26%), Positives = 107/249 (42%), Gaps = 36/249 (14%) Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVL---LVGPPGTGKTLLARAVAG 203 + G+DE K ++EI ++ +K K G + VL G PGTGKT +AR + Sbjct: 5 LSRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGK 64 Query: 204 ---EANV----PFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHR 256 E NV + +D V ++G A + R++ ++A ++F+DE ++ R Sbjct: 65 LFKEMNVLSKGHLIEVERADLVGEYIGHTAQKTREVIKKALGG---VLFIDEAYSLAR-- 119 Query: 257 GIGLGGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAAL-LRPG---RFDRQ 312 GG D ++ ++ L+ M+ ++ +LI A D +D L L PG RF Sbjct: 120 ----GGEKDFGKEAIDTLVKGME--DNRNEFVLILA-GYSDEMDYFLSLNPGLRSRFPIS 172 Query: 313 ITVPNPDIVGREHIL--MVHSRNVPLAPNV------ILKTIARGTPG-FSGADL-RNLVN 362 I P+ + I MV R L L + + + FS A RN++ Sbjct: 173 IDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLREHLYKVDQLSSREFSNARYVRNIIE 232 Query: 363 EAALMAARR 371 +A A R Sbjct: 233 KAIRRQAVR 241 >gnl|CDD|162028 TIGR00763, lon, ATP-dependent protease La. This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock. Length = 775 Score = 53.8 bits (130), Expect = 1e-07 Identities = 38/120 (31%), Positives = 60/120 (50%), Gaps = 17/120 (14%) Query: 148 KDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEANV 207 +D G+ + KE I+++L + ++ G I + LVGPPG GKT L +++A N Sbjct: 320 EDHYGLKKVKE---RILEYLAVQKLRGKMKGPI---LCLVGPPGVGKTSLGKSIAKALNR 373 Query: 208 PFFTIS-G--SDFVEL------FVGVGASRVRDMFEQAKNNSPCIVFVDEIDAVGR-HRG 257 F S G D E+ +VG R+ ++AK +P + +DEID +G RG Sbjct: 374 KFVRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKNPLFL-LDEIDKIGSSFRG 432 >gnl|CDD|148219 pfam06480, FtsH_ext, FtsH Extracellular. This domain is found in the FtsH family of proteins. FtsH is the only membrane-bound ATP-dependent protease universally conserved in prokaryotes. It only efficiently degrades proteins that have a low thermodynamic stability - e.g. it lacks robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni FtsH is involved in protection against environmental stress. and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded (personal obs: Yeats C). The precise function of this N-terminal region is unclear. Length = 104 Score = 52.2 bits (125), Expect = 4e-07 Identities = 27/99 (27%), Positives = 51/99 (51%), Gaps = 15/99 (15%) Query: 2 IALCLIASFSIFQAPSAGQDGVQDISYSQFIKDVDAGRVRKISVIGTHIT-------GFY 54 I L L+ F +F S+ ++ISYS+F++ ++AG+V+K+ + IT G Sbjct: 7 ILLVLLLLFLLFLLSSSSS--TKEISYSEFLELLEAGKVKKVVIDDDEITKPTGDVAGKL 64 Query: 55 VNGESSFQTYMPLVGS------KLLDKLQSKDIEISSRP 87 +G ++P + S KL + L K +++S++P Sbjct: 65 KDGSKFTTYFIPTLPSVDSFLEKLEEALVEKGVKVSAKP 103 >gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases. Length = 395 Score = 51.2 bits (123), Expect = 9e-07 Identities = 31/81 (38%), Positives = 42/81 (51%), Gaps = 18/81 (22%) Query: 139 SGNVGSVTFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLA 198 G VG ++ AGV IV+ + K ++ GR VL+ GPPGTGKT LA Sbjct: 24 EGLVGQEKAREAAGV---------IVEMI----KEGKIAGR---AVLIAGPPGTGKTALA 67 Query: 199 RAVAGE--ANVPFFTISGSDF 217 A++ E + PF ISGS+ Sbjct: 68 IAISKELGEDTPFCPISGSEV 88 >gnl|CDD|149019 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 139 Score = 49.2 bits (118), Expect = 3e-06 Identities = 40/144 (27%), Positives = 53/144 (36%), Gaps = 22/144 (15%) Query: 183 GVLLVGPPGTGKTLLARAVAGE-ANVPFFTISGSDFVE--------LFVGVGASRVRDMF 233 GVLLVGPPGTGK+ LA +A +N P F + + S V Sbjct: 1 GVLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTSWVDGPL 60 Query: 234 EQAKNNSPCIVFVDEIDAVGRH-RGIGLGGGNDEREQTLN---QLLVEMDGFESSEGVIL 289 +A I +DEI+ L ++ R + V D F ++ L Sbjct: 61 VRAA-REGEIAVLDEINRANPDVLNSLLSLLDERRLLLPEGGELVKVAPDDF--AKRFRL 117 Query: 290 IAATNRPD----VLDAALLRPGRF 309 IA N D L AL RF Sbjct: 118 IATMNPLDRGLNELSPALRS--RF 139 >gnl|CDD|177379 PHA02544, 44, clamp loader, small subunit; Provisional. Length = 316 Score = 48.1 bits (115), Expect = 8e-06 Identities = 17/39 (43%), Positives = 24/39 (61%) Query: 178 GRIPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSD 216 GRIP+ +L PGTGKT +A+A+ E ++GSD Sbjct: 40 GRIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSD 78 >gnl|CDD|161849 TIGR00382, clpX, endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction. Length = 413 Score = 45.9 bits (109), Expect = 3e-05 Identities = 27/77 (35%), Positives = 40/77 (51%), Gaps = 6/77 (7%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVEL-FVGVGASRVRDMFEQA-----K 237 +LL+GP G+GKTLLA+ +A NVPF + E +VG + QA + Sbjct: 119 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYDVE 178 Query: 238 NNSPCIVFVDEIDAVGR 254 I+++DEID + R Sbjct: 179 KAQKGIIYIDEIDKISR 195 >gnl|CDD|178847 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed. Length = 328 Score = 45.1 bits (108), Expect = 5e-05 Identities = 25/79 (31%), Positives = 31/79 (39%), Gaps = 25/79 (31%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISG------SDFVELFVGVGASRVRDMFEQAK 237 VLL GPPG GKT LA +A E V SG D + + D Sbjct: 54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKPGDLAAILTNLEE---GD------ 104 Query: 238 NNSPCIVFVDEIDAVGRHR 256 ++F+DEI HR Sbjct: 105 -----VLFIDEI-----HR 113 >gnl|CDD|180029 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX; Provisional. Length = 412 Score = 44.0 bits (105), Expect = 1e-04 Identities = 15/26 (57%), Positives = 21/26 (80%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPF 209 +LL+GP G+GKTLLA+ +A +VPF Sbjct: 111 ILLIGPTGSGKTLLAQTLARILDVPF 136 >gnl|CDD|161852 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit. This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment. Length = 441 Score = 42.9 bits (101), Expect = 3e-04 Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 2/61 (3%) Query: 180 IPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVEL-FVGVGA-SRVRDMFEQAK 237 P +L++GP G GKT +AR +A AN PF + + F E+ +VG S VRD+ + A Sbjct: 46 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRDVESMVRDLTDAAV 105 Query: 238 N 238 Sbjct: 106 K 106 >gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. Length = 305 Score = 41.9 bits (99), Expect = 6e-04 Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 20/77 (25%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISG------SDFVELFVGVGASRVRDMFEQAK 237 +LL GPPG GKT LA +A E V SG D + + + Sbjct: 33 LLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLAAILTNL----------EEG 82 Query: 238 NNSPCIVFVDEIDAVGR 254 + ++F+DEI + Sbjct: 83 D----VLFIDEIHRLSP 95 >gnl|CDD|179026 PRK00440, rfc, replication factor C small subunit; Reviewed. Length = 319 Score = 41.8 bits (99), Expect = 6e-04 Identities = 34/119 (28%), Positives = 53/119 (44%), Gaps = 33/119 (27%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 T ++ G +E E L+ V +PH +L GPPGTGKT A A+A E Sbjct: 15 TLDEIVGQEEIVERLKSYVK-----------EKNMPH-LLFAGPPGTGKTTAALALARE- 61 Query: 206 NVPFFTISGSDFVELFVGVGAS----------RVRDMFEQAK--NNSPC-IVFVDEIDA 251 + G D+ E F+ + AS ++++ F + +P I+F+DE D Sbjct: 62 ------LYGEDWRENFLELNASDERGIDVIRNKIKE-FARTAPVGGAPFKIIFLDEADN 113 >gnl|CDD|161993 TIGR00678, holB, DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau. Length = 188 Score = 41.5 bits (98), Expect = 6e-04 Identities = 14/26 (53%), Positives = 16/26 (61%) Query: 177 GGRIPHGVLLVGPPGTGKTLLARAVA 202 GR+ H L GP G GK LLA A+A Sbjct: 10 KGRLAHAYLFAGPEGVGKELLALALA 35 >gnl|CDD|116338 pfam07724, AAA_2, AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 168 Score = 41.0 bits (97), Expect = 0.001 Identities = 25/88 (28%), Positives = 37/88 (42%), Gaps = 15/88 (17%) Query: 184 VLLVGPPGTGKTLLARAVAGEANV---PFFTISGSDFVE-----LFVG-----VGASRVR 230 L +GP G GKT LA+A+A I S+++E +G VG Sbjct: 6 FLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGG 65 Query: 231 DMFEQAKNNSPCIVFVDEIDAVGRHRGI 258 + E + IV +DEI+ H G+ Sbjct: 66 QLTEAVRRKPYSIVLIDEIEKA--HPGV 91 >gnl|CDD|183503 PRK12402, PRK12402, replication factor C small subunit 2; Reviewed. Length = 337 Score = 40.7 bits (96), Expect = 0.001 Identities = 29/92 (31%), Positives = 40/92 (43%), Gaps = 22/92 (23%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 +D+ G DE E L VD +PH +L+ GPPG+GKT RA+A E Sbjct: 13 LLEDILGQDEVVERLSRAVD-----------SPNLPH-LLVQGPPGSGKTAAVRALAREL 60 Query: 206 NVPFFTISGSDFVELFVGVGASRVRDMFEQAK 237 + ++F E V D F+Q K Sbjct: 61 ---YGDPWENNFTEF-------NVADFFDQGK 82 >gnl|CDD|162839 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis. Length = 355 Score = 39.5 bits (93), Expect = 0.002 Identities = 21/57 (36%), Positives = 27/57 (47%), Gaps = 11/57 (19%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202 TF+DV G + + L+ + GRI H L GP GTGKT +AR A Sbjct: 12 TFEDVIGQEHIVQTLKNAIKN-----------GRIAHAYLFSGPRGTGKTSIARIFA 57 >gnl|CDD|183985 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed. Length = 725 Score = 39.7 bits (93), Expect = 0.003 Identities = 24/77 (31%), Positives = 35/77 (45%), Gaps = 17/77 (22%) Query: 185 LLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKN-----N 239 +L GPPG GKT LAR +A F +++ V G +R ++AK Sbjct: 56 ILYGPPGVGKTTLARIIANHTRAHFSSLNA-------VLAGVKDLRAEVDRAKERLERHG 108 Query: 240 SPCIVFVDEIDAVGRHR 256 I+F+DE+ HR Sbjct: 109 KRTILFIDEV-----HR 120 >gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain. Length = 499 Score = 37.9 bits (88), Expect = 0.008 Identities = 23/57 (40%), Positives = 28/57 (49%), Gaps = 14/57 (24%) Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAG 203 KD+ G AK L EI GG H +LL GPPG+GKT+LA + G Sbjct: 191 LKDIKGQQHAKRAL-EIA----------AAGG---HNLLLFGPPGSGKTMLASRLQG 233 >gnl|CDD|182120 PRK09862, PRK09862, putative ATP-dependent protease; Provisional. Length = 506 Score = 36.9 bits (85), Expect = 0.015 Identities = 14/22 (63%), Positives = 18/22 (81%) Query: 182 HGVLLVGPPGTGKTLLARAVAG 203 H +LL+GPPGTGKT+LA + G Sbjct: 211 HNLLLIGPPGTGKTMLASRING 232 >gnl|CDD|148381 pfam06745, KaiC, KaiC. This family represents a conserved region within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria. Length = 231 Score = 36.1 bits (84), Expect = 0.030 Identities = 14/25 (56%), Positives = 16/25 (64%), Gaps = 2/25 (8%) Query: 176 LGGRIPHG--VLLVGPPGTGKTLLA 198 L G IP G VL+ G PGTGKT+ Sbjct: 12 LKGGIPEGRVVLITGGPGTGKTIFG 36 >gnl|CDD|180989 PRK07471, PRK07471, DNA polymerase III subunit delta'; Validated. Length = 365 Score = 35.8 bits (83), Expect = 0.035 Identities = 12/26 (46%), Positives = 15/26 (57%) Query: 177 GGRIPHGVLLVGPPGTGKTLLARAVA 202 GR+ H L+ GP G GK LA +A Sbjct: 37 SGRLHHAWLIGGPQGIGKATLAYRMA 62 >gnl|CDD|181233 PRK08116, PRK08116, hypothetical protein; Validated. Length = 268 Score = 35.8 bits (83), Expect = 0.040 Identities = 13/22 (59%), Positives = 15/22 (68%) Query: 183 GVLLVGPPGTGKTLLARAVAGE 204 G+LL G GTGKT LA +A E Sbjct: 116 GLLLWGSVGTGKTYLAACIANE 137 >gnl|CDD|163076 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other. Length = 365 Score = 35.3 bits (82), Expect = 0.044 Identities = 11/26 (42%), Positives = 14/26 (53%) Query: 176 LGGRIPHGVLLVGPPGTGKTLLARAV 201 L G P V + G GTGKT + + V Sbjct: 35 LRGSRPSNVFIYGKTGTGKTAVTKYV 60 >gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis. Length = 531 Score = 35.1 bits (81), Expect = 0.051 Identities = 27/79 (34%), Positives = 37/79 (46%), Gaps = 18/79 (22%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 +F ++ G +E + L+ LC P P V++ GPPG GKT AR V EA Sbjct: 63 SFDEIIGQEEGIKALKAA---LCGPN---------PQHVIIYGPPGVGKTAAARLVLEEA 110 Query: 206 N----VPFFTISGSDFVEL 220 PF G+ FVE+ Sbjct: 111 KKNPASPF--KEGAAFVEI 127 >gnl|CDD|162400 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide adenylyltransferase, NadR type. E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this model share that activity. Length = 325 Score = 35.2 bits (81), Expect = 0.051 Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 3/54 (5%) Query: 170 PQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVG 223 P++ + + V ++G TGK+ L +A N ++VE +G Sbjct: 154 PREVRPFFVKT---VAILGGESTGKSTLVNKLAAVFNTTSAWEYAREYVEEKLG 204 >gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN. Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728). Length = 262 Score = 35.2 bits (81), Expect = 0.054 Identities = 23/56 (41%), Positives = 28/56 (50%), Gaps = 6/56 (10%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISG------SDFVELFVGVGASRVRDMF 233 V L GP GTGKT LA VA + + P I+G SD V + G +V D F Sbjct: 24 VHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQF 79 >gnl|CDD|116340 pfam07726, AAA_3, ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 131 Score = 35.2 bits (82), Expect = 0.055 Identities = 13/19 (68%), Positives = 14/19 (73%) Query: 184 VLLVGPPGTGKTLLARAVA 202 VLL G PG KTLLAR +A Sbjct: 2 VLLEGVPGLAKTLLARTLA 20 >gnl|CDD|184914 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau; Provisional. Length = 585 Score = 35.2 bits (81), Expect = 0.058 Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 4/35 (11%) Query: 178 GRIPHGVLLVGPPGTGKT----LLARAVAGEANVP 208 GR+ H L GP G GKT +LA+AV N P Sbjct: 35 GRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP 69 >gnl|CDD|182842 PRK10923, glnG, nitrogen regulation protein NR(I); Provisional. Length = 469 Score = 34.8 bits (80), Expect = 0.076 Identities = 32/97 (32%), Positives = 47/97 (48%), Gaps = 21/97 (21%) Query: 171 QKFKRLGGRIPHG---VLLVGPPGTGKTLLARAV---AGEANVPFFTISGS----DFV-- 218 Q R+ GR+ VL+ G GTGK L+A A+ + A PF ++ + D + Sbjct: 148 QDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDLIES 207 Query: 219 ELF-----VGVGASRVRD-MFEQAKNNSPCIVFVDEI 249 ELF GA+ +R FEQA + +F+DEI Sbjct: 208 ELFGHEKGAFTGANTIRQGRFEQADGGT---LFLDEI 241 >gnl|CDD|184312 PRK13765, PRK13765, ATP-dependent protease Lon; Provisional. Length = 637 Score = 34.6 bits (80), Expect = 0.076 Identities = 11/19 (57%), Positives = 18/19 (94%) Query: 184 VLLVGPPGTGKTLLARAVA 202 V+++G PGTGK++LA+A+A Sbjct: 53 VMMIGSPGTGKSMLAKAMA 71 >gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit clpA. Length = 731 Score = 34.6 bits (80), Expect = 0.078 Identities = 24/78 (30%), Positives = 34/78 (43%), Gaps = 14/78 (17%) Query: 185 LLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVE-----LFVGVGASRVRDMFEQ---- 235 L GP G GKT LA+ +A V S+++E +G V FEQ Sbjct: 488 LFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHTVSRLIGAPPGYVG--FEQGGLL 545 Query: 236 --AKNNSP-CIVFVDEID 250 A P C++ +DEI+ Sbjct: 546 TEAVRKHPHCVLLLDEIE 563 >gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional. Length = 319 Score = 34.7 bits (80), Expect = 0.083 Identities = 36/116 (31%), Positives = 52/116 (44%), Gaps = 32/116 (27%) Query: 149 DVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEANVP 208 D+ G ++A LQ I G +P+ ++L GPPGTGKT A+A E Sbjct: 14 DIVGNEDAVSRLQVIAR-----------DGNMPN-LILSGPPGTGKTTSILALAHE---- 57 Query: 209 FFTISGSDFVELFVGVGASR------VRD---MFEQAKNNSPC----IVFVDEIDA 251 + G ++ E + + AS VR+ MF Q K P IV +DE D+ Sbjct: 58 ---LLGPNYKEAVLELNASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADS 110 >gnl|CDD|179962 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU; Provisional. Length = 443 Score = 34.7 bits (81), Expect = 0.084 Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 6/61 (9%) Query: 180 IPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVG-VG---ASRVRDMFEQ 235 P +L++GP G GKT +AR +A AN PF + + F E VG VG S +RD+ E Sbjct: 49 TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTE--VGYVGRDVESIIRDLVEI 106 Query: 236 A 236 A Sbjct: 107 A 107 >gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau; Provisional. Length = 504 Score = 34.4 bits (79), Expect = 0.088 Identities = 21/62 (33%), Positives = 27/62 (43%), Gaps = 11/62 (17%) Query: 145 VTFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGE 204 +TF +V G + KE L + GR+ H L GP G GKT AR +A Sbjct: 11 ITFDEVVGQEHVKEVLLAALR-----------QGRLGHAYLFSGPRGVGKTTTARLIAMA 59 Query: 205 AN 206 N Sbjct: 60 VN 61 >gnl|CDD|180779 PRK06964, PRK06964, DNA polymerase III subunit delta'; Validated. Length = 342 Score = 34.3 bits (79), Expect = 0.091 Identities = 13/34 (38%), Positives = 19/34 (55%) Query: 169 DPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202 D + + L R+PH +LL G G GK A+ +A Sbjct: 9 DWNRLQALRARLPHALLLHGQAGIGKLDFAQHLA 42 >gnl|CDD|180856 PRK07133, PRK07133, DNA polymerase III subunits gamma and tau; Validated. Length = 725 Score = 34.4 bits (79), Expect = 0.100 Identities = 20/61 (32%), Positives = 27/61 (44%), Gaps = 11/61 (18%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 TF D+ G D + L+ I+ +I H L GP GTGKT +A+ A Sbjct: 16 TFDDIVGQDHIVQTLKNIIKS-----------NKISHAYLFSGPRGTGKTSVAKIFANAL 64 Query: 206 N 206 N Sbjct: 65 N 65 >gnl|CDD|184925 PRK14961, PRK14961, DNA polymerase III subunits gamma and tau; Provisional. Length = 363 Score = 34.4 bits (79), Expect = 0.10 Identities = 33/123 (26%), Positives = 43/123 (34%), Gaps = 37/123 (30%) Query: 170 PQKFKR---------------LGGRIPHGVLLVGPPGTGKTLLARAVAGEANVPF----- 209 PQ F+ GRI H LL G G GKT +AR +A N Sbjct: 12 PQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSN 71 Query: 210 --------FTISGSDFVELFVGVGASR--VRDMFEQAKN--NSPC-----IVFVDEIDAV 252 I ++L ASR V +M E N SP + +DE+ + Sbjct: 72 PCRKCIICKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHML 131 Query: 253 GRH 255 RH Sbjct: 132 SRH 134 >gnl|CDD|183088 PRK11331, PRK11331, 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional. Length = 459 Score = 34.3 bits (78), Expect = 0.11 Identities = 49/167 (29%), Positives = 73/167 (43%), Gaps = 32/167 (19%) Query: 173 FKRLGGRIPHGVLLVGPPGTGKTLLARAVA----GE-----ANVPFF--TISGSDFVELF 221 KRL I ++L GPPG GKT +AR +A GE N+ F + S DF++ + Sbjct: 188 LKRL--TIKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGY 245 Query: 222 V--GVGASRVRDMF----EQAKNN--SPCIVFVDEIDAVGRHRGIG---LGGGNDEREQT 270 GVG R +F +QAK + +DEI+ + G + +D+R + Sbjct: 246 RPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGEN 305 Query: 271 LNQLLV----EMDGFESSEGVILIAATNRPD----VLDAALLRPGRF 309 + L + + F E V +I N D V+D AL R F Sbjct: 306 WSVPLTYSENDEERFYVPENVYIIGLMNTADRSLAVVDYALRRRFSF 352 >gnl|CDD|180215 PRK05707, PRK05707, DNA polymerase III subunit delta'; Validated. Length = 328 Score = 34.3 bits (79), Expect = 0.11 Identities = 14/25 (56%), Positives = 15/25 (60%) Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202 GR PH LL GP G GK LA +A Sbjct: 19 GRHPHAYLLHGPAGIGKRALAERLA 43 >gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit; Provisional. Length = 351 Score = 33.9 bits (78), Expect = 0.12 Identities = 38/120 (31%), Positives = 53/120 (44%), Gaps = 35/120 (29%) Query: 180 IPHG--VLLVGPPGTGKTLLARAVAGEANVP----FFTISGSDFVELFVGVGASRVRDMF 233 I G V L+GP G GKT + R VAG P F I G D V + + RD+ Sbjct: 29 IKQGTMVTLLGPSGCGKTTVLRLVAGLEK-PTEGQIF-IDGED-----VTHRSIQQRDI- 80 Query: 234 EQAKNNSPCIVFVDEIDAVGRHRGIG---------LGGGNDEREQTLNQLL--VEMDGFE 282 C+VF + A+ H +G LG +ER+Q + + L V++ GFE Sbjct: 81 --------CMVF--QSYALFPHMSLGENVGYGLKMLGVPKEERKQRVKEALELVDLAGFE 130 >gnl|CDD|184926 PRK14962, PRK14962, DNA polymerase III subunits gamma and tau; Provisional. Length = 472 Score = 34.0 bits (78), Expect = 0.12 Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 11/61 (18%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 TF +V G D K+ + + I H + GP GTGKT +AR +A Sbjct: 12 TFSEVVGQDHVKKLIINAL-----------KKNSISHAYIFAGPRGTGKTTVARILAKSL 60 Query: 206 N 206 N Sbjct: 61 N 61 >gnl|CDD|163222 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system. Length = 852 Score = 33.8 bits (78), Expect = 0.15 Identities = 27/59 (45%), Positives = 32/59 (54%), Gaps = 16/59 (27%) Query: 167 LCDPQKFKRLGGRIPHGV-LLVGPPGTGKTLLARAVA-----GEANVPFFTISGSDFVE 219 L DP+K P GV LLVGP G GKT A A+A GE N+ TI+ S+F E Sbjct: 589 LEDPRK--------PLGVFLLVGPSGVGKTETALALAELLYGGEQNL--ITINMSEFQE 637 >gnl|CDD|179010 PRK00411, cdc6, cell division control protein 6; Reviewed. Length = 394 Score = 33.7 bits (78), Expect = 0.15 Identities = 14/28 (50%), Positives = 16/28 (57%) Query: 178 GRIPHGVLLVGPPGTGKTLLARAVAGEA 205 G P VL+ GPPGTGKT + V E Sbjct: 52 GSRPLNVLIYGPPGTGKTTTVKKVFEEL 79 Score = 29.4 bits (67), Expect = 2.8 Identities = 20/77 (25%), Positives = 29/77 (37%), Gaps = 9/77 (11%) Query: 336 LAPNVI----LKTIARGTPGFSGADLR---NLVNEAALMAARRNRRLVTMQEFEDAKDKI 388 P V+ L IA T D R +L+ A L+A R R VT ++ A +K Sbjct: 224 FYPGVVDDEVLDLIADLT-AREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 Query: 389 LMGAERRS-TAMTEEEK 404 + + EK Sbjct: 283 EIVHLSEVLRTLPLHEK 299 >gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional. Length = 602 Score = 33.3 bits (77), Expect = 0.19 Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 1/29 (3%) Query: 174 KRLGGRIPHGVLLVGPPGTGKTLLARAVA 202 +RL R G+L+ G PG GK+ A+A+A Sbjct: 251 ERLEER-AEGILIAGAPGAGKSTFAQALA 278 >gnl|CDD|184917 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau; Provisional. Length = 486 Score = 33.3 bits (76), Expect = 0.22 Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 11/61 (18%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 FK+V G + L+ V R+ H + GP GTGKT +AR +A Sbjct: 14 FFKEVIGQEIVVRILKNAVKL-----------QRVSHAYIFAGPRGTGKTTIARILAKVL 62 Query: 206 N 206 N Sbjct: 63 N 63 >gnl|CDD|150034 pfam09217, EcoRII-N, Restriction endonuclease EcoRII, N-terminal. The N-terminal effector-binding domain of the Restriction Endonuclease EcoRII has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not. Length = 156 Score = 32.9 bits (75), Expect = 0.25 Identities = 33/174 (18%), Positives = 55/174 (31%), Gaps = 32/174 (18%) Query: 27 SYSQFIKDVDAGRVRKISVIGTHITGFYVNGESSFQTYMPLVGSKLLDKLQSKDIEISSR 86 +Y+ FIK + A G H GFY+ + + + +K + + S Sbjct: 6 NYAVFIKRLSANDTGAT---GGHQAGFYIPKGFAEDLFPDINHTKEENPSVMLKAKWQSH 62 Query: 87 PVNDGSPGLLSYLGSWFPLVLVVLVWMFLMRQIQGGGARGA---MGFGKSKAKLLSGNVG 143 V D + Y GG R FG N G Sbjct: 63 SVTDSEARAIYYNQRLR------------------GGTRNEARITRFGGGFPLQDPDNTG 104 Query: 144 SVTFKDVAGVDEAKEDLQEIVDFLCDPQK-----FKRLGGRIPHGVLLVGPPGT 192 ++ +A + D + ++C + +G +P G L+VGP G Sbjct: 105 ALAV--LAFLPHQGGDCLLVHAWVCSTDEEEDLFEAEIGEVLP-GSLVVGPAGE 155 >gnl|CDD|183099 PRK11361, PRK11361, acetoacetate metabolism regulatory protein AtoC; Provisional. Length = 457 Score = 32.9 bits (75), Expect = 0.28 Identities = 41/149 (27%), Positives = 61/149 (40%), Gaps = 42/149 (28%) Query: 184 VLLVGPPGTGKTLLARAV---AGEANVPFFTISGSDFVE-------------LFVGVGAS 227 VL+ G GTGK L+ARA+ + A PF ++ + E F G Sbjct: 169 VLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLLESELFGHEKGAFTGAQTL 228 Query: 228 RVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEG- 286 R + +FE+A + + +DEI + L ERE FE G Sbjct: 229 R-QGLFERANEGT---LLLDEIGEMPLVLQAKLLRILQERE------------FERIGGH 272 Query: 287 ------VILIAATNRPDVLDAALLRPGRF 309 + +IAATNR D+ A+++ G F Sbjct: 273 QTIKVDIRIIAATNR-DL--QAMVKEGTF 298 >gnl|CDD|184929 PRK14965, PRK14965, DNA polymerase III subunits gamma and tau; Provisional. Length = 576 Score = 32.8 bits (75), Expect = 0.28 Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 11/57 (19%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202 TF D+ G + LQ +D GR+ H L G G GKT AR +A Sbjct: 14 TFSDLTGQEHVSRTLQNAID-----------TGRVAHAFLFTGARGVGKTSTARILA 59 >gnl|CDD|163066 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC. Length = 615 Score = 32.9 bits (75), Expect = 0.29 Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 4/33 (12%) Query: 181 PHGVLLVGPPGTGKTLLARAVAGEA----NVPF 209 P ++L GPPG GKT AR EA + PF Sbjct: 175 PQHIILYGPPGVGKTTAARLALEEAKKLKHTPF 207 >gnl|CDD|182730 PRK10787, PRK10787, DNA-binding ATP-dependent protease La; Provisional. Length = 784 Score = 32.6 bits (74), Expect = 0.36 Identities = 18/55 (32%), Positives = 31/55 (56%), Gaps = 6/55 (10%) Query: 148 KDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202 D G++ K+ I+++L + ++ G I + LVGPPG GKT L +++A Sbjct: 322 TDHYGLERVKD---RILEYLAVQSRVNKIKGPI---LCLVGPPGVGKTSLGQSIA 370 >gnl|CDD|180523 PRK06305, PRK06305, DNA polymerase III subunits gamma and tau; Validated. Length = 451 Score = 32.4 bits (74), Expect = 0.36 Identities = 21/63 (33%), Positives = 26/63 (41%), Gaps = 11/63 (17%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 TF ++ G D +V L + +F R H L G GTGKT LAR A Sbjct: 15 TFSEILGQDA-------VVAVLKNALRFNRAA----HAYLFSGIRGTGKTTLARIFAKAL 63 Query: 206 NVP 208 N Sbjct: 64 NCQ 66 >gnl|CDD|162029 TIGR00764, lon_rel, lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein. Length = 608 Score = 32.1 bits (73), Expect = 0.51 Identities = 12/19 (63%), Positives = 17/19 (89%) Query: 184 VLLVGPPGTGKTLLARAVA 202 VLL+G PG GK++LA+A+A Sbjct: 40 VLLIGEPGVGKSMLAKAMA 58 >gnl|CDD|162545 TIGR01818, ntrC, nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc. Length = 463 Score = 31.6 bits (72), Expect = 0.60 Identities = 34/97 (35%), Positives = 47/97 (48%), Gaps = 21/97 (21%) Query: 171 QKFKRLGGRIPHG---VLLVGPPGTGKTLLARAVAGE---ANVPFFTISGS----DFV-- 218 Q+ R GR+ VL+ G GTGK L+ARA+ AN PF ++ + D + Sbjct: 144 QEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIES 203 Query: 219 ELF-----VGVGASRVRD-MFEQAKNNSPCIVFVDEI 249 ELF GA+ R FEQA + +F+DEI Sbjct: 204 ELFGHEKGAFTGANTRRQGRFEQADGGT---LFLDEI 237 >gnl|CDD|148176 pfam06414, Zeta_toxin, Zeta toxin. This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid. Length = 191 Score = 31.9 bits (73), Expect = 0.62 Identities = 16/42 (38%), Positives = 18/42 (42%), Gaps = 1/42 (2%) Query: 181 PHGVLLVGPPGTGKTLLARAVAGE-ANVPFFTISGSDFVELF 221 P VLL G PG GKT LARA+ E I + Sbjct: 12 PVAVLLGGQPGAGKTELARALLEELGGGNVVRIDPDELRTYH 53 >gnl|CDD|184916 PRK14952, PRK14952, DNA polymerase III subunits gamma and tau; Provisional. Length = 584 Score = 31.8 bits (72), Expect = 0.64 Identities = 22/61 (36%), Positives = 26/61 (42%), Gaps = 11/61 (18%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 TF +V G + E L +D GRI H L GP G GKT AR +A Sbjct: 11 TFAEVVGQEHVTEPLSSALD-----------AGRINHAYLFSGPRGCGKTSSARILARSL 59 Query: 206 N 206 N Sbjct: 60 N 60 >gnl|CDD|152572 pfam12137, RapA_C, RNA polymerase recycling family C-terminal. This domain is found in bacteria. This domain is about 360 amino acids in length. This domain is found associated with pfam00271, pfam00176. The function of this domain is not known, but structurally it forms an alpha-beta fold in nature with a central beta-sheet flanked by helices and loops, the beta-sheet being mainly antiparallel and flanked by four alpha helices, among which the two longer helices exhibit a coiled-coil arrangement. Length = 362 Score = 31.7 bits (73), Expect = 0.64 Identities = 29/109 (26%), Positives = 53/109 (48%), Gaps = 21/109 (19%) Query: 497 RVMVTQFGFSNLLGKVSYEEGQQEALLSHPVSRPRSISEETAQKIDKEVFRLIEEAYQKA 556 R+++ + G +NL +VS+E ++ PV+R TA+K+ K + IE+ QKA Sbjct: 238 RLLLDKNG-NNLSAQVSFESLNKQL---SPVNR------HTARKLVKALRPQIEQLLQKA 287 Query: 557 KSIIQEKNDNFVAIAEALLEYETLSGKEIASL---------IRGEKISR 596 + + +E+ + I +A + + E+A L IR E+I Sbjct: 288 EKLAEEQLEEI--IEQAKQQMQQQLSAELARLKALKAVNPNIRDEEIEA 334 >gnl|CDD|181656 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau; Validated. Length = 598 Score = 31.4 bits (72), Expect = 0.66 Identities = 13/27 (48%), Positives = 15/27 (55%), Gaps = 4/27 (14%) Query: 178 GRIPHGVLLVGPPGTGKT----LLARA 200 GRI +L G G GKT +LARA Sbjct: 43 GRIAQAFMLTGVRGVGKTTTARILARA 69 >gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional. Length = 173 Score = 31.3 bits (71), Expect = 0.72 Identities = 11/29 (37%), Positives = 16/29 (55%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTI 212 + L G P GKT +A+A ++PFF Sbjct: 3 IFLCGLPTVGKTSFGKALAKFLSLPFFDT 31 >gnl|CDD|184928 PRK14964, PRK14964, DNA polymerase III subunits gamma and tau; Provisional. Length = 491 Score = 31.3 bits (71), Expect = 0.72 Identities = 12/25 (48%), Positives = 16/25 (64%) Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202 +IP +LLVG G GKT AR ++ Sbjct: 32 NKIPQSILLVGASGVGKTTCARIIS 56 >gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau; Provisional. Length = 484 Score = 31.5 bits (71), Expect = 0.74 Identities = 21/60 (35%), Positives = 26/60 (43%), Gaps = 11/60 (18%) Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEAN 206 F+DV D A LQ K G+I H + GP G GKT +AR +A N Sbjct: 17 FRDVIHQDLAIGALQ---------NALK--SGKIGHAYIFFGPRGVGKTTIARILAKRLN 65 >gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional. Length = 237 Score = 31.5 bits (72), Expect = 0.76 Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 11/71 (15%) Query: 175 RLGGRIPHG--VLLVGPPGTGKTLLARAVAGEA-----NVPFFTI--SGSDFVELF--VG 223 L ++ G VLL PG GKTLL +A EA FFT+ + D + +G Sbjct: 56 ELFSQLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTLEYTEQDVRDRLRALG 115 Query: 224 VGASRVRDMFE 234 ++ D+FE Sbjct: 116 ADRAQFADLFE 126 >gnl|CDD|130041 TIGR00968, 3a0106s01, sulfate ABC transporter, ATP-binding protein. Length = 237 Score = 31.3 bits (71), Expect = 0.81 Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 2/37 (5%) Query: 169 DPQKFKRLGGRIPHG--VLLVGPPGTGKTLLARAVAG 203 Q + +P G V L+GP G+GK+ L R +AG Sbjct: 12 SFQALDDVNLEVPTGSLVALLGPSGSGKSTLLRIIAG 48 >gnl|CDD|169554 PRK08691, PRK08691, DNA polymerase III subunits gamma and tau; Validated. Length = 709 Score = 31.2 bits (70), Expect = 0.82 Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 11/61 (18%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 TF D+ G + + LQ +D GR+ H LL G G GKT +AR +A Sbjct: 14 TFADLVGQEHVVKALQNALD-----------EGRLHHAYLLTGTRGVGKTTIARILAKSL 62 Query: 206 N 206 N Sbjct: 63 N 63 >gnl|CDD|163293 TIGR03498, FliI_clade3, flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively. Length = 418 Score = 31.1 bits (71), Expect = 0.89 Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 10/57 (17%) Query: 341 ILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFEDAKDKILMGAERRST 397 +L +++R P + R LV RR R L + +E+ +D I +GA R+ + Sbjct: 333 VLASVSRLAPRVWSPEERKLV--------RRLRAL--LARYEETEDLIRLGAYRKGS 379 >gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit; Provisional. Length = 353 Score = 31.2 bits (71), Expect = 0.92 Identities = 15/26 (57%), Positives = 18/26 (69%), Gaps = 2/26 (7%) Query: 180 IPHG--VLLVGPPGTGKTLLARAVAG 203 IP G V L+GP G+GKT L R +AG Sbjct: 25 IPSGQMVALLGPSGSGKTTLLRIIAG 50 >gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed. Length = 230 Score = 31.2 bits (71), Expect = 0.98 Identities = 15/31 (48%), Positives = 22/31 (70%), Gaps = 2/31 (6%) Query: 174 KRLGGRIPHG--VLLVGPPGTGKTLLARAVA 202 KRLGG IP G +L+ G TGK++L++ +A Sbjct: 15 KRLGGGIPAGSLILIEGDESTGKSILSQRLA 45 >gnl|CDD|182917 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional. Length = 758 Score = 31.0 bits (70), Expect = 0.99 Identities = 28/89 (31%), Positives = 40/89 (44%), Gaps = 17/89 (19%) Query: 185 LLVGPPGTGKTLLARAVAG---EANVPFF----TISGSDFVELFVGVG-----ASRVRDM 232 LLVG G GKT +A +A + +VP TI D L G R + + Sbjct: 211 LLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKAL 270 Query: 233 FEQAKNNSPCIVFVDEIDAVGRHRGIGLG 261 +Q + ++ I+F+DEI H IG G Sbjct: 271 LKQLEQDTNSILFIDEI-----HTIIGAG 294 >gnl|CDD|180959 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated. Length = 314 Score = 31.0 bits (71), Expect = 1.0 Identities = 14/54 (25%), Positives = 18/54 (33%), Gaps = 11/54 (20%) Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARA 200 F ++ G A E L + RI L GP G G+ L A Sbjct: 3 FANLIGQPLAIELLTAAIK-----------QNRIAPAYLFAGPEGVGRKLAALC 45 >gnl|CDD|178887 PRK00131, aroK, shikimate kinase; Reviewed. Length = 175 Score = 30.9 bits (71), Expect = 1.0 Identities = 8/27 (29%), Positives = 14/27 (51%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFF 210 ++L+G G GK+ + R +A F Sbjct: 7 IVLIGFMGAGKSTIGRLLAKRLGYDFI 33 >gnl|CDD|184934 PRK14970, PRK14970, DNA polymerase III subunits gamma and tau; Provisional. Length = 367 Score = 31.0 bits (70), Expect = 1.1 Identities = 29/104 (27%), Positives = 42/104 (40%), Gaps = 25/104 (24%) Query: 146 TFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 TF DV G I + L + + L +L GP G GKT AR +A + Sbjct: 15 TFDDVVG-------QSHITNTLLNAIENNHLA----QALLFCGPRGVGKTTCARILARKI 63 Query: 206 NVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEI 249 N P + DF + + ++ + A NNS VD+I Sbjct: 64 NQPGYDDPNEDF--------SFNIFEL-DAASNNS-----VDDI 93 >gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional. Length = 259 Score = 30.8 bits (70), Expect = 1.2 Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 5/70 (7%) Query: 184 VLLVGPPGTGKTLLARAV---AGEANVPFFTISGSDFV-ELFVGVGASRVRDMFEQAKNN 239 ++L+GP G GKT LA A+ A A + + +D + +L R + ++ Sbjct: 105 IVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMA 164 Query: 240 SPCIVFVDEI 249 P ++ +DEI Sbjct: 165 -PRLLIIDEI 173 >gnl|CDD|162744 TIGR02173, cyt_kin_arch, cytidylate kinase, putative. Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017. Length = 171 Score = 30.9 bits (70), Expect = 1.2 Identities = 16/54 (29%), Positives = 28/54 (51%), Gaps = 5/54 (9%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAK 237 + + GPPG+GKT +A+ +A + ++ IS D +F + A D+ E Sbjct: 3 ITISGPPGSGKTTVAKILAEKLSLKL--ISAGD---IFRELAAKMGLDLIEFLN 51 >gnl|CDD|128474 smart00177, ARF, ARF-like small GTPases; ARF, ADP-ribosylation factor. Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop). Length = 175 Score = 30.7 bits (69), Expect = 1.3 Identities = 40/142 (28%), Positives = 63/142 (44%), Gaps = 25/142 (17%) Query: 173 FKRLGGRIPHGVLLVGPPGTGK-TLLARAVAGEA---------NVPFFTISGSDFVELFV 222 F +L G +L+VG GK T+L + GE+ NV T F V Sbjct: 5 FSKLFGNKEMRILMVGLDAAGKTTILYKLKLGESVTTIPTIGFNVETVTYKNISFTVWDV 64 Query: 223 GVGASRVRDMFEQAKNNSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFE 282 G G ++R ++ N+ ++FV +D+ R R DE + L+++L E E Sbjct: 65 G-GQDKIRPLWRHYYTNTQGLIFV--VDSNDRDR-------IDEAREELHRMLNED---E 111 Query: 283 SSEGVILIAATNR--PDVLDAA 302 + VIL+ A + PD + AA Sbjct: 112 LRDAVILVFANKQDLPDAMKAA 133 >gnl|CDD|181551 PRK08769, PRK08769, DNA polymerase III subunit delta'; Validated. Length = 319 Score = 30.3 bits (68), Expect = 1.4 Identities = 13/25 (52%), Positives = 18/25 (72%) Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202 GR+ HG+L+ GP G GK +A A+A Sbjct: 23 GRLGHGLLICGPEGLGKRAVALALA 47 >gnl|CDD|129002 smart00763, AAA_PrkA, PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain. Length = 361 Score = 30.3 bits (69), Expect = 1.5 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 10/56 (17%) Query: 148 KDVAGVDEAKEDLQEIVDFLCDPQKFKRLG--GRIPHGVLLVGPPGTGKTLLARAV 201 D G++EA ++ V++ + L +I + L+GP G GK+ L + Sbjct: 51 HDFFGMEEA---IERFVNYFKSAAQ--GLEERKQI---LYLLGPVGGGKSSLVECL 98 >gnl|CDD|183530 PRK12444, PRK12444, threonyl-tRNA synthetase; Reviewed. Length = 639 Score = 30.5 bits (69), Expect = 1.6 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 13/75 (17%) Query: 530 PRSISEETAQKIDKEVFRLIEE---------AYQKAKSIIQEKNDNF-VAIAEALLEYET 579 P S++ E +KI+KE+ ++I E + ++A + QE ND + + EA+ E+ Sbjct: 113 PSSVNVEDLRKIEKEMKKIINENIKIERVEVSREEAAKLFQEMNDRLKLELLEAIPSGES 172 Query: 580 LS---GKEIASLIRG 591 ++ E L RG Sbjct: 173 ITLYKQGEFVDLCRG 187 >gnl|CDD|180131 PRK05563, PRK05563, DNA polymerase III subunits gamma and tau; Validated. Length = 559 Score = 30.2 bits (69), Expect = 1.6 Identities = 14/28 (50%), Positives = 17/28 (60%), Gaps = 4/28 (14%) Query: 178 GRIPHGVLLVGPPGTGKT----LLARAV 201 G+I H L GP GTGKT + A+AV Sbjct: 35 GKISHAYLFSGPRGTGKTSAAKIFAKAV 62 >gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated. Length = 233 Score = 30.2 bits (68), Expect = 1.6 Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 7/73 (9%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCI 243 + L GP GTGKT LA A+ A +G L + A R+RD E + S + Sbjct: 44 LYLSGPAGTGKTHLALALCAAAEQ-----AGRSSAYLPLQAAAGRLRDALEALEGRS--L 96 Query: 244 VFVDEIDAVGRHR 256 V +D ++++ R Sbjct: 97 VALDGLESIAGQR 109 >gnl|CDD|178685 PLN03140, PLN03140, ABC transporter G family member; Provisional. Length = 1470 Score = 30.2 bits (68), Expect = 1.6 Identities = 15/30 (50%), Positives = 21/30 (70%), Gaps = 1/30 (3%) Query: 185 LLVGPPGTGKTLLARAVAGEANVPFFTISG 214 LL+GPP +GKT L A+AG+ + P +SG Sbjct: 195 LLLGPPSSGKTTLLLALAGKLD-PSLKVSG 223 >gnl|CDD|116881 pfam08298, AAA_PrkA, PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain. Length = 358 Score = 30.1 bits (68), Expect = 1.8 Identities = 24/92 (26%), Positives = 40/92 (43%), Gaps = 10/92 (10%) Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVL-LVGPPGTGKTLLARAV-AGE 204 F D G++E ++ IV++ + G +L L+GP G GK+ LA + Sbjct: 57 FADFFGMEET---IERIVNYF----RHAAQGLEERKQILYLLGPVGGGKSSLAERLKKLL 109 Query: 205 ANVPFFTISGSDFVELFVG-VGASRVRDMFEQ 235 VP + + GS E + +RD+ E Sbjct: 110 ELVPIYALKGSPVFESPLHLFNPHHLRDILED 141 >gnl|CDD|179771 PRK04182, PRK04182, cytidylate kinase; Provisional. Length = 180 Score = 30.2 bits (69), Expect = 1.9 Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 2/30 (6%) Query: 188 GPPGTGKTLLARAVAGEANVPFFTISGSDF 217 GPPG+GKT +AR +A + + +S + Sbjct: 7 GPPGSGKTTVARLLAEKLGLKH--VSAGEI 34 >gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family. Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain. Length = 229 Score = 30.1 bits (68), Expect = 2.1 Identities = 14/26 (53%), Positives = 16/26 (61%), Gaps = 2/26 (7%) Query: 174 KRLGGRIPHG--VLLVGPPGTGKTLL 197 K L G IP G V + G PGTGKT+ Sbjct: 11 KLLEGGIPRGFFVAVTGEPGTGKTIF 36 >gnl|CDD|182930 PRK11054, helD, DNA helicase IV; Provisional. Length = 684 Score = 29.9 bits (68), Expect = 2.1 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%) Query: 268 EQTLNQLLVEMDGFESSEGVILIAATN---RPDVLDAALLR 305 E L LL ++ G+ + IL+ A RP +LD A R Sbjct: 543 EDQLEALLDKLSGYAKPDERILLLARYHHLRPALLDKAATR 583 >gnl|CDD|131585 TIGR02533, type_II_gspE, general secretory pathway protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis. Length = 486 Score = 29.7 bits (67), Expect = 2.3 Identities = 18/39 (46%), Positives = 23/39 (58%), Gaps = 2/39 (5%) Query: 171 QKFKRLGGRIPHGVLLV-GPPGTGKTLLARAVAGEANVP 208 +F+RL R PHG++LV GP G+GKT A N P Sbjct: 232 SRFERLIRR-PHGIILVTGPTGSGKTTTLYAALSRLNTP 269 >gnl|CDD|150789 pfam10156, Med17, Subunit 17 of Mediator complex. This Mediator complex subunit was formerly known as Srb4 in yeasts or Trap80 in Drosophila and human. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of cerevisiae lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures. Length = 454 Score = 29.6 bits (67), Expect = 2.4 Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 4/34 (11%) Query: 378 MQEFEDAKDKILMGAERRSTAMTEEEKKITAYHE 411 ++ +A D +L AER + +E T Y Sbjct: 176 LKSLNEAADLLLKAAERLEKEVAKE----TKYWS 205 >gnl|CDD|181256 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional regulator; Reviewed. Length = 309 Score = 29.5 bits (67), Expect = 2.4 Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 14/78 (17%) Query: 150 VAGVDEAKEDLQEIVDFL-----CDPQKFKRLGGRIP---------HGVLLVGPPGTGKT 195 + VD + D I + L + + + + L+G G GK+ Sbjct: 88 LGDVDTSSPDWLLIRELLEQASPAQLARVRDALSGMLGAGRRAARRRRIALIGLRGAGKS 147 Query: 196 LLARAVAGEANVPFFTIS 213 L R +A VPF ++ Sbjct: 148 TLGRMLAARLGVPFVELN 165 >gnl|CDD|181175 PRK07940, PRK07940, DNA polymerase III subunit delta'; Validated. Length = 394 Score = 29.5 bits (67), Expect = 2.5 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 2/56 (3%) Query: 147 FKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202 + D+ G + +L+ G + H L GPPG+G+++ ARA A Sbjct: 4 WDDLVGQEAVVAELRAAA--RAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFA 57 >gnl|CDD|181538 PRK08699, PRK08699, DNA polymerase III subunit delta'; Validated. Length = 325 Score = 29.8 bits (67), Expect = 2.5 Identities = 11/24 (45%), Positives = 12/24 (50%) Query: 179 RIPHGVLLVGPPGTGKTLLARAVA 202 R P+ L G G GKT AR A Sbjct: 19 RRPNAWLFAGKKGIGKTAFARFAA 42 >gnl|CDD|180644 PRK06647, PRK06647, DNA polymerase III subunits gamma and tau; Validated. Length = 563 Score = 29.7 bits (67), Expect = 2.6 Identities = 11/25 (44%), Positives = 14/25 (56%) Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202 +I + + GP G GKT ARA A Sbjct: 35 NKIANAYIFSGPRGVGKTSSARAFA 59 >gnl|CDD|180719 PRK06835, PRK06835, DNA replication protein DnaC; Validated. Length = 329 Score = 29.5 bits (67), Expect = 2.8 Identities = 10/20 (50%), Positives = 12/20 (60%) Query: 185 LLVGPPGTGKTLLARAVAGE 204 L G GTGKT L+ +A E Sbjct: 187 LFYGNTGTGKTFLSNCIAKE 206 >gnl|CDD|180132 PRK05564, PRK05564, DNA polymerase III subunit delta'; Validated. Length = 313 Score = 29.6 bits (67), Expect = 2.8 Identities = 11/25 (44%), Positives = 16/25 (64%) Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202 R H ++VG G GK+LLA+ +A Sbjct: 23 NRFSHAHIIVGEDGIGKSLLAKEIA 47 >gnl|CDD|180790 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau; Validated. Length = 830 Score = 29.4 bits (66), Expect = 2.9 Identities = 14/30 (46%), Positives = 16/30 (53%) Query: 177 GGRIPHGVLLVGPPGTGKTLLARAVAGEAN 206 GGR+ H L G G GKT L+R A N Sbjct: 34 GGRLHHAYLFTGTRGVGKTTLSRIFAKALN 63 >gnl|CDD|140006 PRK13949, PRK13949, shikimate kinase; Provisional. Length = 169 Score = 29.3 bits (66), Expect = 3.0 Identities = 12/26 (46%), Positives = 16/26 (61%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPF 209 + LVG G GKT L +A+A E + F Sbjct: 4 IFLVGYMGAGKTTLGKALARELGLSF 29 >gnl|CDD|163585 TIGR03873, F420-0_ABC_ATP, proposed F420-0 ABC transporter, ATP-binding protein. This small clade of ABC-type transporter ATP-binding protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and a permease (TIGR03869). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this ATP-binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter. Length = 256 Score = 29.4 bits (66), Expect = 3.0 Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 11/40 (27%) Query: 175 RLGGRI---------PHGVL--LVGPPGTGKTLLARAVAG 203 GGR+ P G L L+GP G+GK+ L R +AG Sbjct: 10 SAGGRLIVDGVDVTAPPGSLTGLLGPNGSGKSTLLRLLAG 49 >gnl|CDD|182758 PRK10820, PRK10820, DNA-binding transcriptional regulator TyrR; Provisional. Length = 520 Score = 29.3 bits (66), Expect = 3.3 Identities = 28/81 (34%), Positives = 33/81 (40%), Gaps = 20/81 (24%) Query: 185 LLVGPPGTGKTLLARAV---AGEANVPFFTI---SGSDFV---ELFVGVGASRV------ 229 L+ G GTGK LLA A + PF + S D V ELF G Sbjct: 231 LITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIPDDVVESELF-GHAPGAYPNALEG 289 Query: 230 -RDMFEQAKNNSPCIVFVDEI 249 + FEQA S V +DEI Sbjct: 290 KKGFFEQANGGS---VLLDEI 307 >gnl|CDD|162808 TIGR02329, propionate_PrpR, propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR. Length = 526 Score = 29.1 bits (65), Expect = 3.3 Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 3/48 (6%) Query: 175 RLGGRIPHGVLLVGPPGTGKTLLARA---VAGEANVPFFTISGSDFVE 219 RL R VL++G GTGK L+A+A ++G + PF I+ E Sbjct: 229 RLYARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIAE 276 >gnl|CDD|169667 PRK09112, PRK09112, DNA polymerase III subunit delta'; Validated. Length = 351 Score = 29.2 bits (66), Expect = 3.3 Identities = 10/21 (47%), Positives = 13/21 (61%) Query: 178 GRIPHGVLLVGPPGTGKTLLA 198 G++ H +L GP G GK LA Sbjct: 42 GKLHHALLFEGPEGIGKATLA 62 >gnl|CDD|163196 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein. This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely. Length = 353 Score = 29.2 bits (66), Expect = 3.3 Identities = 12/20 (60%), Positives = 14/20 (70%) Query: 184 VLLVGPPGTGKTLLARAVAG 203 V L+GP G GKT L R +AG Sbjct: 33 VCLLGPSGCGKTTLLRIIAG 52 >gnl|CDD|181743 PRK09270, PRK09270, nucleoside triphosphate hydrolase domain-containing protein; Reviewed. Length = 229 Score = 29.1 bits (66), Expect = 3.4 Identities = 10/30 (33%), Positives = 13/30 (43%), Gaps = 2/30 (6%) Query: 173 FKRLGGRIPHGVLLVGPPGTGKTLLARAVA 202 R V + GPPG GK+ LA + Sbjct: 27 QAEPQRRTI--VGIAGPPGAGKSTLAEFLE 54 >gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional. Length = 254 Score = 29.1 bits (65), Expect = 3.4 Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 5/36 (13%) Query: 184 VLLVGPPGTGKTLLA-----RAVAGEANVPFFTISG 214 V+ +GPPGTGKT LA RA V F T + Sbjct: 101 VVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQ 136 >gnl|CDD|163508 TIGR03796, NHPM_micro_ABC1, NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes an multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHPM, Nitrile Hydratase Propeptide Microcin. Length = 710 Score = 29.1 bits (66), Expect = 3.7 Identities = 12/26 (46%), Positives = 17/26 (65%), Gaps = 2/26 (7%) Query: 180 IPHG--VLLVGPPGTGKTLLARAVAG 203 + G V LVG G+GK+ +A+ VAG Sbjct: 502 LQPGQRVALVGGSGSGKSTIAKLVAG 527 >gnl|CDD|182852 PRK10938, PRK10938, putative molybdenum transport ATP-binding protein ModF; Provisional. Length = 490 Score = 29.2 bits (66), Expect = 3.8 Identities = 12/18 (66%), Positives = 15/18 (83%) Query: 187 VGPPGTGKTLLARAVAGE 204 VG G+GK+ LARA+AGE Sbjct: 35 VGANGSGKSALARALAGE 52 >gnl|CDD|149505 pfam08477, Miro, Miro-like protein. Mitochondrial Rho proteins (Miro-1 and Miro-2), are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (pfam00036), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis. Length = 118 Score = 28.9 bits (65), Expect = 3.8 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 6/75 (8%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFFTIS------GSDFVELFVGVGASRVRDMFEQAK 237 V+++G G+GK+ L + G P D +E+ + D + + Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEIPEEIQGDTLAVDTLEVDGDTELLHIWDFGGREE 61 Query: 238 NNSPCIVFVDEIDAV 252 I+F+ DA+ Sbjct: 62 LKFEHIIFMKTADAI 76 >gnl|CDD|130283 TIGR01216, ATP_synt_epsi, ATP synthase, F1 epsilon subunit (delta in mitochondria). This model describes one of the five types of subunits in the F1 part of F1/F0 ATP synthases. Members of this family are designated epsilon in bacterial and chloroplast systems but designated delta in mitochondria, where the counterpart of the bacterial delta subunit is designated OSCP. In a few cases (Propionigenium modestum, Acetobacterium woodii) scoring above the trusted cutoff and designated here as exceptions, Na+ replaces H+ for translocation. Length = 130 Score = 28.8 bits (65), Expect = 4.1 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 4/43 (9%) Query: 536 ETAQKIDKEVFRLIEEAYQKAKSIIQEKNDNFVAIAEALLEYE 578 A ID+ E+A + A+ +++ D+ +AEALL+ + Sbjct: 82 VFADDIDEAE---AEKALEAAEKLLESAEDDK-DLAEALLKLK 120 >gnl|CDD|179826 PRK04328, PRK04328, hypothetical protein; Provisional. Length = 249 Score = 28.9 bits (65), Expect = 4.1 Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 2/26 (7%) Query: 176 LGGRIP--HGVLLVGPPGTGKTLLAR 199 L G IP + VLL G PGTGK++ ++ Sbjct: 16 LYGGIPERNVVLLSGGPGTGKSIFSQ 41 >gnl|CDD|184126 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA; Provisional. Length = 207 Score = 28.7 bits (65), Expect = 4.3 Identities = 11/20 (55%), Positives = 15/20 (75%) Query: 184 VLLVGPPGTGKTLLARAVAG 203 ++L GP G+GKT L R +AG Sbjct: 31 LVLTGPNGSGKTTLLRLIAG 50 >gnl|CDD|184118 PRK13531, PRK13531, regulatory ATPase RavA; Provisional. Length = 498 Score = 28.8 bits (65), Expect = 4.3 Identities = 10/16 (62%), Positives = 13/16 (81%) Query: 184 VLLVGPPGTGKTLLAR 199 V L+GPPG K+L+AR Sbjct: 42 VFLLGPPGIAKSLIAR 57 >gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional. Length = 172 Score = 28.9 bits (65), Expect = 4.3 Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 1/30 (3%) Query: 176 LGGRIPHGVLLVGPPGTGKTLLARAVAGEA 205 GG + VL+ G G+GKT LA A+A Sbjct: 11 CGGGMIT-VLIDGRSGSGKTTLAGALAART 39 >gnl|CDD|181214 PRK08058, PRK08058, DNA polymerase III subunit delta'; Validated. Length = 329 Score = 28.7 bits (65), Expect = 4.4 Identities = 10/25 (40%), Positives = 12/25 (48%) Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202 R+ H L G GTGK A +A Sbjct: 25 NRLSHAYLFEGAKGTGKKATALWLA 49 >gnl|CDD|183258 PRK11650, ugpC, glycerol-3-phosphate transporter ATP-binding subunit; Provisional. Length = 356 Score = 28.7 bits (65), Expect = 4.4 Identities = 12/20 (60%), Positives = 15/20 (75%) Query: 184 VLLVGPPGTGKTLLARAVAG 203 ++LVGP G GK+ L R VAG Sbjct: 33 IVLVGPSGCGKSTLLRMVAG 52 >gnl|CDD|177743 PLN00134, PLN00134, fumarate hydratase; Provisional. Length = 458 Score = 28.9 bits (65), Expect = 4.4 Identities = 13/46 (28%), Positives = 25/46 (54%) Query: 553 YQKAKSIIQEKNDNFVAIAEALLEYETLSGKEIASLIRGEKISRPS 598 Y KA ++ ++ + + EA L+ L+ +E L+ EK++ PS Sbjct: 410 YDKAAAVAKKAHKEGTTLKEAALKLGVLTAEEFDELVVPEKMTGPS 455 >gnl|CDD|172992 PRK14526, PRK14526, adenylate kinase; Provisional. Length = 211 Score = 28.7 bits (64), Expect = 4.5 Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 2/35 (5%) Query: 183 GVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDF 217 ++ +GPPG+GK +A+ ++ E N ++ IS D Sbjct: 2 KLVFLGPPGSGKGTIAKILSNELN--YYHISTGDL 34 >gnl|CDD|179891 PRK04914, PRK04914, ATP-dependent helicase HepA; Validated. Length = 956 Score = 28.7 bits (65), Expect = 4.6 Identities = 22/99 (22%), Positives = 40/99 (40%), Gaps = 20/99 (20%) Query: 507 NLLGKVSYEEGQQEALLSHPVSRPRSISEETAQKIDKEVFRLIEEAYQKAKSIIQEKNDN 566 +L +V +E + V+R TA K+ K V + I + QKA++ + + Sbjct: 841 DLSAQVEFESLNR---QLSAVNRH------TASKLVKAVQQDIHKLLQKAEAQAEAQARE 891 Query: 567 FVAIAEALLEYETLSGKEIASL---------IRGEKISR 596 I +A E + E++ L IR ++I Sbjct: 892 L--IEQAKQEADEKLSAELSRLEALKAVNPNIRDDEIEA 928 >gnl|CDD|162095 TIGR00895, 2A0115, benzoate transport. Length = 398 Score = 28.9 bits (65), Expect = 4.6 Identities = 8/18 (44%), Positives = 13/18 (72%) Query: 98 YLGSWFPLVLVVLVWMFL 115 Y+G PL+L++L+ FL Sbjct: 175 YVGGIAPLLLLLLLMRFL 192 >gnl|CDD|180308 PRK05896, PRK05896, DNA polymerase III subunits gamma and tau; Validated. Length = 605 Score = 28.7 bits (64), Expect = 4.7 Identities = 10/28 (35%), Positives = 15/28 (53%) Query: 179 RIPHGVLLVGPPGTGKTLLARAVAGEAN 206 ++ H + GP G GKT +A+ A N Sbjct: 36 KLTHAYIFSGPRGIGKTSIAKIFAKAIN 63 >gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein; Provisional. Length = 445 Score = 28.6 bits (64), Expect = 4.8 Identities = 40/140 (28%), Positives = 59/140 (42%), Gaps = 23/140 (16%) Query: 184 VLLVGPPGTGKTLLARAVAG---EANVPFFTISGSDFVELFVGVGASRVRDM--FEQAKN 238 + L GP G+GKT L +A E+ + F E V A R +M F Q Sbjct: 144 IYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHL--VSAIRSGEMQRFRQFYR 201 Query: 239 NSPCIVFVDEIDAVGRHRGIGLGGGNDEREQTLNQLLVEMDGFESSEG-VILIAATNRPD 297 N +F+++I+ G G +E T N L +EG +I+I++T P Sbjct: 202 NVD-ALFIEDIEVFS-----GKGATQEEFFHTFNSL--------HTEGKLIVISSTCAPQ 247 Query: 298 VLDAALLR-PGRFDRQITVP 316 L A R RF+ I +P Sbjct: 248 DLKAMEERLISRFEWGIAIP 267 >gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family. Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga. Length = 237 Score = 28.6 bits (64), Expect = 5.0 Identities = 13/26 (50%), Positives = 18/26 (69%), Gaps = 2/26 (7%) Query: 176 LGGRIP--HGVLLVGPPGTGKTLLAR 199 L G IP + VLL G PGTGK++ ++ Sbjct: 14 LHGGIPERNVVLLSGGPGTGKSIFSQ 39 >gnl|CDD|179011 PRK00413, thrS, threonyl-tRNA synthetase; Reviewed. Length = 638 Score = 28.5 bits (65), Expect = 5.2 Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 10/65 (15%) Query: 527 VSRPRSISEETAQKIDKEVFRLIEEAY---------QKAKSIIQEKNDNF-VAIAEALLE 576 R R + E + I+KE+ +I+E Y ++A + +++ + + V + E + E Sbjct: 106 FDRERPFTPEDLEAIEKEMKEIIKENYPIEREVVSREEAIELFKDRGEPYKVELIEEIPE 165 Query: 577 YETLS 581 E +S Sbjct: 166 DEEIS 170 >gnl|CDD|162612 TIGR01932, hflC, HflC protein. HflK and HflC are paralogs encoded by tandem genes in Proteobacteria, spirochetes, and some other bacterial lineages. The HflKC complex is anchored in the membrane and exposed to the periplasm. The complex is not active as a protease, but rather binds to and appears to modulate the ATP-dependent protease FtsH. The overall function of HflKC is not fully described.//Regulation of FtsH protease appears to be negative (PubMed:8947034, PubMed:96367). Length = 317 Score = 28.6 bits (64), Expect = 5.3 Identities = 24/89 (26%), Positives = 40/89 (44%), Gaps = 17/89 (19%) Query: 508 LLGKVSYEEGQQEALLSHPVS-------RPRSISEETAQKI----DKEVFRLIEEAYQKA 556 + K++Y + E++ + S RS EE A++I + EV +++ EAY+ A Sbjct: 199 RIKKINYSDELSESIYNRMRSEREQIARMHRSQGEEKAEEILGKAEYEVRKILSEAYRTA 258 Query: 557 KSIIQEKNDNFVAIAEALLEYETLSGKEI 585 + I E AEA Y GK+ Sbjct: 259 RIIKGE------GDAEAAKIYSDAYGKDP 281 >gnl|CDD|179408 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional. Length = 188 Score = 28.4 bits (64), Expect = 5.4 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 10/60 (16%) Query: 528 SRPRSISEETAQKIDKEVFRLIEEAYQKAKSIIQEKNDNFVAIAEALLEYETLSGKEIAS 587 +R I E D+E +I EA A+ I+++ AEA E E L +E++S Sbjct: 16 ARASEIRAEA----DEEAEEIIAEAEADAEEILED------REAEAEREIEQLREQELSS 65 >gnl|CDD|181800 PRK09362, PRK09362, phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed. Length = 238 Score = 28.5 bits (65), Expect = 5.9 Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 4/34 (11%) Query: 536 ETAQKIDKEVFRL----IEEAYQKAKSIIQEKND 565 ET +K+DK+ FR + EAY++ + E + Sbjct: 205 ETNEKLDKDRFRRDLGGVIEAYEEVLKRLGELLE 238 >gnl|CDD|130214 TIGR01144, ATP_synt_b, ATP synthase, F0 subunit b. This model describes the F1/F0 ATP synthase b subunit in bacteria only. Scoring just below the trusted cutoff are the N-terminal domains of Mycobacterial b/delta fusion proteins and a subunit from an archaeon, Methanosarcina barkeri, in which the ATP synthase homolog differs in architecture and is not experimentally confirmed. This model helps resolve b from the related b' subunit. Within the family is an example from a sodium-translocating rather than proton-translocating ATP synthase. Length = 147 Score = 28.5 bits (64), Expect = 6.1 Identities = 14/56 (25%), Positives = 24/56 (42%), Gaps = 1/56 (1%) Query: 533 ISEETAQKIDKEVFRLIEEAYQKAKSIIQEKNDNFVAI-AEALLEYETLSGKEIAS 587 +++ A K+ +++EA +A+ II+ N I EA E K A Sbjct: 40 RAKKEAALAQKKAQVILKEAKDEAQEIIENANKRGSEILEEAKAEAREEREKIKAQ 95 >gnl|CDD|163225 TIGR03348, VI_IcmF, type VI secretion protein IcmF. Members of this protein family are IcmF homologs and tend to be associated with type VI secretion systems. Length = 1169 Score = 28.5 bits (64), Expect = 6.1 Identities = 10/17 (58%), Positives = 14/17 (82%), Gaps = 1/17 (5%) Query: 185 LLVGPPGTGKT-LLARA 200 L++GPPG+GKT LL + Sbjct: 115 LVIGPPGSGKTTLLQNS 131 >gnl|CDD|132302 TIGR03258, PhnT, 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT. This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate. Length = 362 Score = 28.4 bits (63), Expect = 6.4 Identities = 11/18 (61%), Positives = 13/18 (72%) Query: 186 LVGPPGTGKTLLARAVAG 203 L+G G GKT L RA+AG Sbjct: 36 LIGKSGCGKTTLLRAIAG 53 >gnl|CDD|149899 pfam08975, 2H-phosphodiest, Domain of unknown function (DUF1868). This group of 2H-phosphodiesterases comprises a single family typified by the protein mlr3352 from M.loti. Members are also present in various alpha-proteobacteria, Synechocystis, Streptococcus and Chilo iridescent virus. The presence of a member of this predominantly bacterial group in a large eukaryotic DNA virus represents a potential case of horizontal transfer from a bacterial source into a virus. Several proteins of bacterial origin have been noticed in the insect viruses (L.M.Iyer, E.V.Koonin and L.Aravind, unpublished observations and these appear to have been acquired from endo-symbiotic or parasitic bacteria that share the same host cells with the viruses. Presence of 2H proteins in the proteomes of large DNA viruses (e.g. T4 57B protein and the Fowl-pox virus FPV025) may point to some role for these proteins in regulating the viral tRNA metabolism. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. Length = 112 Score = 28.1 bits (63), Expect = 6.8 Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 5/41 (12%) Query: 410 HEAGHAVVACHVPKADPLHKATIIPRGRALGMVMQLPEADR 450 G+ VV CH+ + P + A + R R + P AD+ Sbjct: 10 PFPGNTVV-CHLDQQSPGYAAVLDIRRRLKAL----PFADK 45 >gnl|CDD|185327 PRK15429, PRK15429, formate hydrogenlyase transcriptional activator FhlA; Provisional. Length = 686 Score = 28.3 bits (63), Expect = 6.8 Identities = 11/18 (61%), Positives = 15/18 (83%) Query: 184 VLLVGPPGTGKTLLARAV 201 VL++G GTGK L+ARA+ Sbjct: 402 VLILGETGTGKELIARAI 419 >gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional. Length = 590 Score = 28.2 bits (64), Expect = 7.0 Identities = 15/30 (50%), Positives = 19/30 (63%), Gaps = 2/30 (6%) Query: 177 GGRIPHG-VL-LVGPPGTGKTLLARAVAGE 204 GG I G V+ +VGP G GKT A+ +AG Sbjct: 359 GGEIYEGEVIGIVGPNGIGKTTFAKLLAGV 388 >gnl|CDD|162243 TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA. This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c. Length = 198 Score = 28.1 bits (63), Expect = 7.1 Identities = 10/22 (45%), Positives = 13/22 (59%) Query: 182 HGVLLVGPPGTGKTLLARAVAG 203 + + GP G GKT L R +AG Sbjct: 27 EALQVTGPNGIGKTTLLRILAG 48 >gnl|CDD|162129 TIGR00954, 3a01203, Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protei. Length = 659 Score = 28.2 bits (63), Expect = 7.2 Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 2/31 (6%) Query: 175 RLGGRIPHG--VLLVGPPGTGKTLLARAVAG 203 L +P G +L+ GP G GK+ L R + Sbjct: 470 SLSFEVPSGNHLLICGPNGCGKSSLFRILGE 500 >gnl|CDD|162298 TIGR01313, therm_gnt_kin, carbohydrate kinase, thermoresistant glucokinase family. This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases. Length = 163 Score = 28.1 bits (63), Expect = 7.7 Identities = 12/32 (37%), Positives = 17/32 (53%), Gaps = 2/32 (6%) Query: 186 LVGPPGTGKTLLARAVAGEANVPFFTISGSDF 217 L+G G+GK+ +A A+A F I G D Sbjct: 3 LMGVAGSGKSTIASALAHRLGAKF--IEGDDL 32 >gnl|CDD|184924 PRK14960, PRK14960, DNA polymerase III subunits gamma and tau; Provisional. Length = 702 Score = 28.1 bits (62), Expect = 7.8 Identities = 12/25 (48%), Positives = 15/25 (60%) Query: 178 GRIPHGVLLVGPPGTGKTLLARAVA 202 GR+ H L G G GKT +AR +A Sbjct: 34 GRLHHAYLFTGTRGVGKTTIARILA 58 >gnl|CDD|162555 TIGR01842, type_I_sec_PrtD, type I secretion system ABC transporter, PrtD family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. Length = 544 Score = 28.1 bits (63), Expect = 8.1 Identities = 16/47 (34%), Positives = 24/47 (51%), Gaps = 5/47 (10%) Query: 162 EIVDFLCDPQKFKRLGG---RIPHG--VLLVGPPGTGKTLLARAVAG 203 E V + K L G R+ G + ++GP G+GK+ LAR + G Sbjct: 320 ENVTIVPPGGKKPTLRGISFRLQAGEALAIIGPSGSGKSTLARLIVG 366 >gnl|CDD|180213 PRK05703, flhF, flagellar biosynthesis regulator FlhF; Validated. Length = 424 Score = 27.9 bits (63), Expect = 8.1 Identities = 12/26 (46%), Positives = 12/26 (46%), Gaps = 5/26 (19%) Query: 184 VLLVGPPGTGKT-----LLARAVAGE 204 V LVGP G GKT L AR Sbjct: 224 VALVGPTGVGKTTTLAKLAARYALLY 249 >gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family protein. Length = 1394 Score = 27.8 bits (62), Expect = 8.2 Identities = 6/21 (28%), Positives = 13/21 (61%) Query: 184 VLLVGPPGTGKTLLARAVAGE 204 +++G PG+G + L + +A Sbjct: 90 TVVLGRPGSGCSTLLKTIASN 110 >gnl|CDD|131926 TIGR02880, cbbX_cfxQ, probable Rubsico expression protein CbbX. Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis. Length = 284 Score = 27.9 bits (62), Expect = 8.5 Identities = 54/228 (23%), Positives = 93/228 (40%), Gaps = 38/228 (16%) Query: 188 GPPGTGKTLLARAVAGEANVPFF-------TISGSDFVELFVGVGASRVRDMFEQAKNNS 240 G PGTGKT +A +A + + +++ D V ++G A + +++ ++A Sbjct: 65 GNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEILKRAMGG- 123 Query: 241 PCIVFVDEIDAVGRHRGIGLGGGNDERE---QTLNQLLVEMDGFESSEGVILIAATNRPD 297 ++F+DE A +R ++ER+ + + LL M+ VIL +R D Sbjct: 124 --VLFIDE--AYYLYR------PDNERDYGQEAIEILLQVMENQRDDLVVILAGYKDRMD 173 Query: 298 VLDAALLRPGRFDRQIT--VPNPDIVGREHI----LMVHSRNVPLAPN---VILKTIA-- 346 + PG F ++ V PD E + LM+ + + IA Sbjct: 174 SFFES--NPG-FSSRVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAEAEEAFADYIALR 230 Query: 347 RGTPGFSGA-DLRNLVNEAALMAARRNRRLVTMQEFEDAKDKILMGAE 393 R P F+ A +RN ++ A L A NR + D D + E Sbjct: 231 RTQPHFANARSIRNAIDRARLRQA--NRLFCDLDRVLDKSDLETIDPE 276 >gnl|CDD|151168 pfam10662, PduV-EutP, Ethanolamine utilisation - propanediol utilisation. Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood. Length = 143 Score = 28.0 bits (63), Expect = 8.6 Identities = 10/21 (47%), Positives = 15/21 (71%) Query: 184 VLLVGPPGTGKTLLARAVAGE 204 ++L+G G GKT L +A+ GE Sbjct: 4 IMLIGRSGCGKTTLTQALNGE 24 >gnl|CDD|182441 PRK10416, PRK10416, signal recognition particle-docking protein FtsY; Provisional. Length = 318 Score = 27.8 bits (63), Expect = 8.6 Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 1/52 (1%) Query: 145 VTFKDVAGVDEAKEDL-QEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKT 195 V K++ +E KE L +E+ + L +K + + P +L+VG G GKT Sbjct: 77 VKRKNLKDPEELKELLKEELAEILEPVEKPLNIEEKKPFVILVVGVNGVGKT 128 >gnl|CDD|184919 PRK14955, PRK14955, DNA polymerase III subunits gamma and tau; Provisional. Length = 397 Score = 27.9 bits (62), Expect = 8.7 Identities = 13/29 (44%), Positives = 15/29 (51%) Query: 178 GRIPHGVLLVGPPGTGKTLLARAVAGEAN 206 GR+ HG + G G GKT AR A N Sbjct: 35 GRVGHGYIFSGLRGVGKTTAARVFAKAVN 63 >gnl|CDD|169949 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed. Length = 402 Score = 27.9 bits (62), Expect = 8.8 Identities = 13/22 (59%), Positives = 14/22 (63%) Query: 182 HGVLLVGPPGTGKTLLARAVAG 203 V LVGP G GKT L RA+ G Sbjct: 30 SLVGLVGPNGAGKTTLLRAING 51 >gnl|CDD|181587 PRK08939, PRK08939, primosomal protein DnaI; Reviewed. Length = 306 Score = 27.9 bits (63), Expect = 8.9 Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 10/63 (15%) Query: 145 VTFKDVAGVDEAKED-LQEIVDFLCD--PQKFKRLGGRIPHGVLLVGPPGTGKTLLARAV 201 + D+ D + D L +DFL P + + G+ L G G GK+ L A+ Sbjct: 124 ASLADIDLDDRDRLDALMAALDFLEAYPPGEKVK-------GLYLYGDFGVGKSYLLAAI 176 Query: 202 AGE 204 A E Sbjct: 177 ANE 179 >gnl|CDD|185081 PRK15127, PRK15127, multidrug efflux system protein AcrB; Provisional. Length = 1049 Score = 27.9 bits (62), Expect = 8.9 Identities = 47/197 (23%), Positives = 70/197 (35%), Gaps = 49/197 (24%) Query: 35 VDAGRVRKISVIGT--------HITGFYVNGE-------SSFQTYMPLVGSKLLDKLQS- 78 +D GRV+K+ V+ I +YV S+F + GS L++ Sbjct: 763 IDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGL 822 Query: 79 KDIEISSRPVNDGSPGLLSYLGSWFPLVLVVLVWMFLMRQIQGGGARGAMGF---GKSKA 135 +EI + S G M LM ++ G +G+ G S Sbjct: 823 PSMEILGQAAPGKSTGEA----------------MELMEELASKLPTG-VGYDWTGMSYQ 865 Query: 136 KLLSGNVGSVTFKDVAGVDEAKEDLQEIVDFLCDPQKFKRLGGRIPHGVLLVGPPGTGKT 195 + LSGN + + IV FLC ++ IP V+LV P G Sbjct: 866 ERLSGNQAPALYA-----------ISLIVVFLCLAALYESWS--IPFSVMLVVPLGVIGA 912 Query: 196 LLARAVAGEANVPFFTI 212 LLA G N +F + Sbjct: 913 LLAATFRGLTNDVYFQV 929 >gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. Length = 201 Score = 27.8 bits (62), Expect = 9.0 Identities = 9/17 (52%), Positives = 11/17 (64%) Query: 182 HGVLLVGPPGTGKTLLA 198 V+L P G+GKTL A Sbjct: 25 RDVILAAPTGSGKTLAA 41 >gnl|CDD|163070 TIGR02915, PEP_resp_reg, putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158). Length = 445 Score = 27.8 bits (62), Expect = 9.1 Identities = 12/18 (66%), Positives = 15/18 (83%) Query: 184 VLLVGPPGTGKTLLARAV 201 VLL+G GTGK +LARA+ Sbjct: 165 VLLLGESGTGKEVLARAL 182 >gnl|CDD|177488 PHA02774, PHA02774, E1; Provisional. Length = 613 Score = 27.9 bits (63), Expect = 9.2 Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 5/39 (12%) Query: 162 EIVDFLCDPQKFKRLGGRIP--HGVLLVGPPGTGKTLLA 198 E + FL K IP + +++ GPP TGK++ Sbjct: 416 EFISFLT---ALKDFLKGIPKKNCLVIYGPPDTGKSMFC 451 >gnl|CDD|179921 PRK05057, aroK, shikimate kinase I; Reviewed. Length = 172 Score = 27.8 bits (62), Expect = 9.2 Identities = 11/27 (40%), Positives = 18/27 (66%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFF 210 + LVGP G GK+ + R +A + N+ F+ Sbjct: 7 IFLVGPMGAGKSTIGRQLAQQLNMEFY 33 >gnl|CDD|182710 PRK10765, PRK10765, nitroreductase A; Provisional. Length = 240 Score = 27.6 bits (62), Expect = 9.5 Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 5/39 (12%) Query: 520 EALLSHPVSRPRSISEETAQKIDKEVFRLIEEAYQKAKS 558 E +LSH RSI T + I + I A + A S Sbjct: 6 ELILSH-----RSIRHFTDEPISEAQREAIINAARAASS 39 >gnl|CDD|181235 PRK08118, PRK08118, topology modulation protein; Reviewed. Length = 167 Score = 27.7 bits (62), Expect = 9.6 Identities = 10/27 (37%), Positives = 18/27 (66%) Query: 184 VLLVGPPGTGKTLLARAVAGEANVPFF 210 ++L+G G+GK+ LAR + + N+P Sbjct: 4 IILIGSGGSGKSTLARQLGEKLNIPVH 30 >gnl|CDD|182893 PRK11000, PRK11000, maltose/maltodextrin transporter ATP-binding protein; Provisional. Length = 369 Score = 27.7 bits (62), Expect = 9.8 Identities = 11/20 (55%), Positives = 14/20 (70%) Query: 184 VLLVGPPGTGKTLLARAVAG 203 V+ VGP G GK+ L R +AG Sbjct: 32 VVFVGPSGCGKSTLLRMIAG 51 >gnl|CDD|183622 PRK12608, PRK12608, transcription termination factor Rho; Provisional. Length = 380 Score = 27.7 bits (62), Expect = 9.9 Identities = 15/28 (53%), Positives = 17/28 (60%), Gaps = 6/28 (21%) Query: 185 LLVGPPGTGKTLL----ARAVAGEANVP 208 L+V PP GKT+L A AVA AN P Sbjct: 137 LIVAPPRAGKTVLLQQIAAAVA--ANHP 162 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.317 0.135 0.380 Gapped Lambda K H 0.267 0.0669 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 10,736,177 Number of extensions: 739306 Number of successful extensions: 2285 Number of sequences better than 10.0: 1 Number of HSP's gapped: 2259 Number of HSP's successfully gapped: 229 Length of query: 647 Length of database: 5,994,473 Length adjustment: 100 Effective length of query: 547 Effective length of database: 3,833,673 Effective search space: 2097019131 Effective search space used: 2097019131 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 60 (27.0 bits)