RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780809|ref|YP_003065222.1| tRNA modification GTPase TrmE [Candidatus Liberibacter asiaticus str. psy62] (440 letters) >gnl|CDD|179996 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed. Length = 449 Score = 514 bits (1326), Expect = e-146 Identities = 184/450 (40%), Positives = 269/450 (59%), Gaps = 16/450 (3%) Query: 4 EKETIFAVSTGALPSAISIIRLSGPSCFQVCEFICKKKKPFPRKASLRYFFGLDGRILDK 63 +TI A++T I IIR+SGP ++ + + KK P PR A + G ++D+ Sbjct: 3 MNDTIAAIATPPGRGGIGIIRISGPDALEIAQKLFGKKLPKPRTAHYGHIRD-PGEVIDE 61 Query: 64 GLLIVFPSPESFTGEDSAEFHVHGGIAVVNGILEELAKMPNLRLANPGEFSRRAFENGKI 123 L++ FP+P SFTGED E HGG AV+N ILE L + RLA PGEF++RAF NGK+ Sbjct: 62 VLVLYFPAPNSFTGEDVVEIQCHGGPAVLNLILELLLALG-ARLAEPGEFTKRAFLNGKL 120 Query: 124 DLLEAESLADLISSETEMQRRLSMEGMSGELSSLYGQWIDKLTHIRSFIEADLDFSEEED 183 DL +AE++ADLI ++TE RL++ + G LS L + ++L + + +EA +DF EE D Sbjct: 121 DLTQAEAIADLIDAKTEAAARLALRQLQGALSKLINELREELLELLALVEAAIDFPEE-D 179 Query: 184 VQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKD 243 ++ S +++L + L ++ + ++ + GEI+R G K+VI G N GKSSL NAL ++ Sbjct: 180 IEFLSDEKILEKLEELIAELEALLASARQGEILREGLKVVIAGRPNVGKSSLLNALLGEE 239 Query: 244 VAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVENADLIL 303 AIVTDI GTTRDV+ ++L+G +++ DTAGIRETDD VEK GI+R+ +E ADL+L Sbjct: 240 RAIVTDIAGTTRDVIEEHINLDGIPLRLIDTAGIRETDDEVEKIGIERSREAIEEADLVL 299 Query: 304 LL------KEINSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDH-----LISSFTGEGLE 352 L+ + + K+ I + K+DL E ++ IS+ TGEG++ Sbjct: 300 LVLDASEPLTEEDDEILEELKDKPVIVVLNKADLTGEIDLEEENGKPVIRISAKTGEGID 359 Query: 353 ELINKIKSILSNKFKKLPFS-IPSHKRHLYHLSQTVRYLEMASLN-EKDCGLDIIAENLR 410 EL IK + F ++ RHL L + + +LE A E L+++AE+LR Sbjct: 360 ELREAIKELAFGGFGGNQEGVFLTNARHLEALERALEHLERALEGLESGLPLELLAEDLR 419 Query: 411 LASVSLGKITGCVDVEQLLDIIFSKFCIGK 440 LA +LG+ITG V E LLD IFS FCIGK Sbjct: 420 LALEALGEITGEVTSEDLLDRIFSSFCIGK 449 >gnl|CDD|161885 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE, also called MnmE and previously designated ThdF (thiophene and furan oxidation protein), is a GTPase involved in tRNA modification to create 5-methylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and GidA form an alpha2/beta2 heterotetramer. Length = 442 Score = 260 bits (667), Expect = 3e-70 Identities = 147/448 (32%), Positives = 232/448 (51%), Gaps = 25/448 (5%) Query: 12 STGALPSAISIIRLSGPSCFQVCEFI-CKKKKPFPRKASLRYFFGLDGRILDKGLLIVFP 70 +T SAI IIRLSGP + + I K + + + + D LL F Sbjct: 1 ATPPFNSAIHIIRLSGPDSLSILKKITNKLNTASGMRIQYGHIIDSNNKCKDDELLFKFV 60 Query: 71 SPESFTGEDSAEFHVHGGIAVVNGILEELAKMPNLRLANPGEFSRRAFENGKIDLLEAES 130 +P S+TGED E HG + +V IL+ K RLA PGEF++RAF NGK+DL +AE+ Sbjct: 61 APNSYTGEDVIEIQCHGSMLIVQEILQLCLKS-GARLAQPGEFTQRAFLNGKMDLTQAEA 119 Query: 131 LADLISSETEMQRRLSMEGMSGELSSLYGQWIDKLTHIRSFIEADLDFSEEEDVQNFSSK 190 + +LI + + +++ ++GEL L + + +E ++D+ E++D Q+ ++ Sbjct: 120 INELILAPNNKVKDIALNKLAGELDQKIEAIRKSLLQLLAQVEVNIDYEEDDDEQDSLNQ 179 Query: 191 EVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDI 250 +L+ I LK+ I E + +G+K+ I+G N GKSSL NAL K+D AIV+DI Sbjct: 180 LLLSIIAELKD-----ILNSYKLEKLDDGFKLAIVGSPNVGKSSLLNALLKQDRAIVSDI 234 Query: 251 PGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEINS 310 GTTRDV+ D +L G L+K+ DTAGIRE D VE+ GI+++F ++ ADL++ + + + Sbjct: 235 KGTTRDVVEGDFELNGILIKLLDTAGIREHADFVERLGIEKSFKAIKQADLVIYVLDASQ 294 Query: 311 KKE-----ISFPK--NIDFIFIGTKSDLYSTYTEEYDHLISSFTG----------EGLEE 353 I FI + K DL E + + ++ Sbjct: 295 PLTKDDFLIIDLNKSKKPFILVLNKIDLKINSLEFFVSSKVLNSSNLSAKQLKIKALVDL 354 Query: 354 LINKIKSILSNKFKKLPFSIPSHKRHLYHLSQTVRYLE-MASLNEKDCGLDIIAENLRLA 412 L KI + S + +L + S + + L + + L+ S ++ LD++ +LR A Sbjct: 355 LTQKINAFYSKERVELDDYLISSWQAMILLEKAIAQLQQFLSKLDRQLFLDMLVFHLREA 414 Query: 413 SVSLGKITGCVDVEQLLDIIFSKFCIGK 440 LG++TG V E +LD IFS FC+GK Sbjct: 415 INCLGQVTGEVVTEDVLDEIFSNFCLGK 442 >gnl|CDD|150979 pfam10396, TrmE_N, GTP-binding protein TrmE N-terminus. This family represents the shorter, B, chain of the homo-dimeric structure which is a guanine nucleotide-binding protein that binds and hydrolyses GTP. TrmE is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. This B chain is the N-terminal portion of the protein consisting of five beta-strands and three alpha helices and is necessary for mediating dimer formation within the protein. Length = 114 Score = 168 bits (428), Expect = 3e-42 Identities = 54/116 (46%), Positives = 72/116 (62%), Gaps = 2/116 (1%) Query: 7 TIFAVSTGALPSAISIIRLSGPSCFQVCEFICKKKKPFPRKASLRYFFGLDGRILDKGLL 66 TI A++T I+IIR+SGP ++ + + K P PR A +G ++D+ L+ Sbjct: 1 TIAAIATPPGRGGIAIIRISGPDALEIAKKLFGKL-PKPRTAHYGTIRDPNGEVIDEVLV 59 Query: 67 IVFPSPESFTGEDSAEFHVHGGIAVVNGILEELAKMPNLRLANPGEFSRRAFENGK 122 + FP+P SFTGED E H HGG AVV IL+ L K+ RLA PGEF+RRAF NGK Sbjct: 60 LYFPAPNSFTGEDVVEIHCHGGPAVVQAILQALLKLG-ARLAEPGEFTRRAFLNGK 114 >gnl|CDD|163343 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability. Length = 429 Score = 97.9 bits (245), Expect = 4e-21 Identities = 52/180 (28%), Positives = 87/180 (48%), Gaps = 32/180 (17%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR-- 278 KI I+G N GKS+L NAL ++ IV+DI GTTRD + I + G + DTAGIR Sbjct: 174 KIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTRDSIDIPFERNGKKYLLIDTAGIRRK 233 Query: 279 -ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS----------FPKNIDFIFIGT 327 + + VEK + RT +E AD++LL+ +++ + I+ + + Sbjct: 234 GKVTEGVEKYSVLRTLKAIERADVVLLV--LDATEGITEQDLRIAGLILEAGKALVIVVN 291 Query: 328 KSDL------YSTYTEEYD-----------HLISSFTGEGLEELINKIKSILSNKFKKLP 370 K DL + +E IS+ TG+G+++L++ I + N +++ Sbjct: 292 KWDLVKDEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVDKLLDAIDEVYENANRRIS 351 Score = 81.3 bits (202), Expect = 5e-16 Identities = 45/164 (27%), Positives = 75/164 (45%), Gaps = 21/164 (12%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRET 280 + I+G N GKS+LFN L K AIV+D PG TRD D + G + DT GI E Sbjct: 1 VVAIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIEED 60 Query: 281 DDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS----------FPKNIDFIFIGTKSD 330 DD ++K+ ++ + +E AD+IL + ++ ++ ++ I + K D Sbjct: 61 DDGLDKQIREQAEIAIEEADVILFV--VDGREGLTPEDEEIAKWLRKSGKPVILVANKID 118 Query: 331 LYSTYTEEYD---------HLISSFTGEGLEELINKIKSILSNK 365 + IS+ G G+ +L++ I +L + Sbjct: 119 GKKEDAVAAEFYSLGFGEPIPISAEHGRGIGDLLDAILELLPEE 162 >gnl|CDD|178858 PRK00093, PRK00093, GTP-binding protein Der; Reviewed. Length = 435 Score = 94.4 bits (236), Expect = 5e-20 Identities = 56/179 (31%), Positives = 87/179 (48%), Gaps = 31/179 (17%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR-- 278 KI I+G N GKSSL NAL ++ IV+DI GTTRD + + +G + DTAGIR Sbjct: 175 KIAIIGRPNVGKSSLINALLGEERVIVSDIAGTTRDSIDTPFERDGQKYTLIDTAGIRRK 234 Query: 279 -ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS-FPKNI-DF--------IFIGT 327 + + VEK + RT +E AD++LL+ I++ + I+ I + + Sbjct: 235 GKVTEGVEKYSVIRTLKAIERADVVLLV--IDATEGITEQDLRIAGLALEAGRALVIVVN 292 Query: 328 KSDLYSTYT-EEYD---------------HLISSFTGEGLEELINKIKSILSNKFKKLP 370 K DL T EE+ IS+ TG+G+++L+ I N +++ Sbjct: 293 KWDLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLLEAIDEAYENANRRIS 351 Score = 83.2 bits (207), Expect = 1e-16 Identities = 47/162 (29%), Positives = 76/162 (46%), Gaps = 23/162 (14%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRET 280 + I+G N GKS+LFN L K AIV D PG TRD + + + G + DT GI Sbjct: 3 VVAIVGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILIDTGGIEPD 62 Query: 281 DDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDF-----------IFIGTKS 329 DD EK+ ++ L +E AD+IL + ++ + ++ P + + I + K Sbjct: 63 DDGFEKQIREQAELAIEEADVILFV--VDGRAGLT-PADEEIAKILRKSNKPVILVVNKV 119 Query: 330 DLYSTYTEEYD---------HLISSFTGEGLEELINKIKSIL 362 D + Y+ + IS+ G G+ +L++ I L Sbjct: 120 DGPDEEADAYEFYSLGLGEPYPISAEHGRGIGDLLDAILEEL 161 >gnl|CDD|161778 TIGR00231, small_GTP, small GTP-binding protein domain. This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. Length = 161 Score = 63.2 bits (154), Expect = 1e-10 Identities = 38/121 (31%), Positives = 58/121 (47%), Gaps = 11/121 (9%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLT--IDLDLEGYLVKISDTAGI 277 KIVI+G N GKS+L N L I PGTTR+ +T I+ D + Y + DTAG Sbjct: 2 IKIVIVGDPNVGKSTLLNRLLGNK-FITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAG- 59 Query: 278 RETDDIVEKEGIKRTFLEVENADLILLLKEINS-----KKEI--SFPKNIDFIFIGTKSD 330 +E + + + + D+++L+ ++ KEI N+ I +G K D Sbjct: 60 QEDYRAIRRLYYRAVESSLRVFDIVILVLDVEEILEKQTKEIIHHAESNVPIILVGNKID 119 Query: 331 L 331 L Sbjct: 120 L 120 >gnl|CDD|161878 TIGR00437, feoB, ferrous iron transporter FeoB. FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum. Length = 591 Score = 55.9 bits (135), Expect = 2e-08 Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 1/78 (1%) Query: 226 GHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVE 285 G+ N GKS+LFNAL + V + PG T + L +G ++I D GI Sbjct: 1 GNPNVGKSTLFNALTGAN-QTVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSL 59 Query: 286 KEGIKRTFLEVENADLIL 303 +E + R +L E DL++ Sbjct: 60 EEEVARDYLLNEKPDLVV 77 >gnl|CDD|178854 PRK00089, era, GTPase Era; Reviewed. Length = 292 Score = 54.7 bits (133), Expect = 5e-08 Identities = 38/165 (23%), Positives = 71/165 (43%), Gaps = 26/165 (15%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281 + I+G N GKS+L NAL + ++IV+ P TTR + + + + DT GI + Sbjct: 8 VAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDAQIIFVDTPGIHKPK 67 Query: 282 DIVEKEGIKRTFLEVENADLILLLKEINSKKEISF----------PKNIDFIFIGTKSDL 331 + + K + +++ DL+L + +++ ++I I + K DL Sbjct: 68 RALNRAMNKAAWSSLKDVDLVLFV--VDADEKIGPGDEFILEKLKKVKTPVILVLNKIDL 125 Query: 332 ----------YSTYTEEYDHL----ISSFTGEGLEELINKIKSIL 362 +E D IS+ G+ ++EL++ I L Sbjct: 126 VKDKEELLPLLEELSELMDFAEIVPISALKGDNVDELLDVIAKYL 170 >gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed. Length = 472 Score = 54.6 bits (132), Expect = 6e-08 Identities = 23/58 (39%), Positives = 37/58 (63%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR 278 ++ ++G N GKSSL N LA ++ ++V D+ GTT D + ++L G + DTAG+R Sbjct: 213 RVALVGKPNVGKSSLLNKLAGEERSVVDDVAGTTVDPVDSLIELGGKTWRFVDTAGLR 270 Score = 42.6 bits (101), Expect = 2e-04 Identities = 27/86 (31%), Positives = 44/86 (51%), Gaps = 10/86 (11%) Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDI 283 ++G N GKS+L N + + A+V D+PG TRD ++ D + G + DT G E D Sbjct: 43 VVGRPNVGKSTLVNRILGRREAVVEDVPGVTRDRVSYDAEWNGRRFTVVDTGGW-EPD-- 99 Query: 284 VEKEGIKRTFLE-----VENADLILL 304 +G++ + E + AD +L Sbjct: 100 --AKGLQASVAEQAEVAMRTADAVLF 123 >gnl|CDD|163162 TIGR03156, GTP_HflX, GTP-binding protein HflX. This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like). Length = 351 Score = 54.4 bits (132), Expect = 6e-08 Identities = 54/176 (30%), Positives = 77/176 (43%), Gaps = 40/176 (22%) Query: 217 RNGYKIVIL-GHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDL-EGYLVKISDT 274 R V L G++NAGKS+LFNAL DV D T D T LDL +G V ++DT Sbjct: 186 RADVPTVALVGYTNAGKSTLFNALTGADV-YAADQLFATLDPTTRRLDLPDGGEVLLTDT 244 Query: 275 AG-IRE-TDDIVEKEGIKRTFLEVENADLIL-------------------LLKEINSKKE 313 G IR+ ++V + T EV ADL+L +L+E+ + Sbjct: 245 VGFIRDLPHELV--AAFRATLEEVREADLLLHVVDASDPDREEQIEAVEKVLEELGA--- 299 Query: 314 ISFPKNIDFIFIGTKSDLYSTYTEEYDH-------LISSFTGEGLEELINKIKSIL 362 ++I + + K DL E +S+ TGEGL+ L+ I L Sbjct: 300 ----EDIPQLLVYNKIDLLDEPRIERLEEGYPEAVFVSAKTGEGLDLLLEAIAERL 351 >gnl|CDD|181925 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der; Reviewed. Length = 712 Score = 52.5 bits (126), Expect = 2e-07 Identities = 23/58 (39%), Positives = 37/58 (63%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR 278 ++ ++G N GKSSL N L ++ A+V D+ GTTRD + ++++G DTAGI+ Sbjct: 452 RVALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDPVDEIVEIDGEDWLFIDTAGIK 509 Score = 49.4 bits (118), Expect = 2e-06 Identities = 50/238 (21%), Positives = 90/238 (37%), Gaps = 33/238 (13%) Query: 174 ADLDFSE---------EEDVQNF-SSKEVLNDILFLKNDISSHI------SQGKLGEIIR 217 +DLDF E E+ ++ + N + ++ + G + Sbjct: 214 SDLDFDETLDLLIGLVEDAIEEQEYDQYAANLEGYELDEGDEDLLEGSGFVAGDEKAGPK 273 Query: 218 NGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI 277 + I+G N GKS+L N + + A+V D PG TRD ++ D + G K+ DT G Sbjct: 274 AVGVVAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGTDFKLVDTGGW 333 Query: 278 RETDDIVEKEGIKRTFLEVENADLILLLKE----INSKKEISFPK----NIDFIFIGTKS 329 + ++ + + V AD ++ + + + S E + K Sbjct: 334 EADVEGIDSAIASQAQIAVSLADAVVFVVDGQVGLTSTDERIVRMLRRAGKPVVLAVNKI 393 Query: 330 DLYSTY--TEEYDHL-------ISSFTGEGLEELINKIKSILSNKFKKLPFSIPSHKR 378 D ++ E+ L IS+ G G+ +L+++ L K F PS R Sbjct: 394 DDQASEYDAAEFWKLGLGEPYPISAMHGRGVGDLLDEALDSLKVAEKTSGFLTPSGLR 451 >gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional. Length = 339 Score = 52.0 bits (124), Expect = 3e-07 Identities = 49/159 (30%), Positives = 82/159 (51%), Gaps = 20/159 (12%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281 + I+G N+GKS+L N + + ++IVT TTR ++T + L+ V + DT GI E Sbjct: 55 VCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTPGIFEPK 114 Query: 282 DIVEKEGIKRTFLEVENADLILL-LKEINSKKEISF-------PKNIDFIFIGTKSDLYS 333 +EK ++ + + +ADL+LL + + S +I+ NI IF+ K D+ S Sbjct: 115 GSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDITHNILDKLRSLNIVPIFLLNKIDIES 174 Query: 334 TY--------TEEY-DHL---ISSFTGEGLEELINKIKS 360 Y TE + D L IS+ +G+ ++ L+ I S Sbjct: 175 KYLNDIKAFLTENHPDSLLFPISALSGKNIDGLLEYITS 213 >gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed. Length = 298 Score = 51.4 bits (124), Expect = 5e-07 Identities = 26/81 (32%), Positives = 33/81 (40%), Gaps = 11/81 (13%) Query: 223 VILGHSNAGKSSLFNALAKKDVAIVTDIPG-------TTRDVLTIDLDLEGYLVKISDTA 275 V+ G S GKS+L NALA +I TT V DL G L+ DT Sbjct: 168 VLAGQSGVGKSTLLNALAPDLELKTGEISEALGRGKHTTTHVELYDLPGGGLLI---DTP 224 Query: 276 GIRETD-DIVEKEGIKRTFLE 295 G +E E ++ F E Sbjct: 225 GFSSFGLHDLEAEELEHYFPE 245 >gnl|CDD|132636 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli. Length = 360 Score = 50.7 bits (122), Expect = 7e-07 Identities = 36/111 (32%), Positives = 48/111 (43%), Gaps = 29/111 (26%) Query: 214 EIIRNGYKIVILGHSNAGKSSLFNALAK-----KDVAIVTDIPGTTRDVLTIDLDLEGYL 268 + RN + ++G +N GKSSL N L K KDV + PGTT D++ I LD L Sbjct: 149 KKARNKKDVYVVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSL 208 Query: 269 VKISDTAGI----RETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS 315 DT GI + + +K+ LK I KKEI Sbjct: 209 Y---DTPGIINSHQMAHYLDKKD-----------------LKYITPKKEIK 239 >gnl|CDD|163345 TIGR03596, GTPase_YlqF, ribosome biogenesis GTP-binding protein YlqF. Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other GTPases. This model is built for bacterial members. Length = 276 Score = 44.8 bits (107), Expect = 5e-05 Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 3/57 (5%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI 277 + +I+G N GKS+L N LA K VA V + PG T+ I L +++ DT GI Sbjct: 120 RAMIVGIPNVGKSTLINRLAGKKVAKVGNRPGVTKGQQWIKLSDG---LELLDTPGI 173 >gnl|CDD|179346 PRK01889, PRK01889, GTPase RsgA; Reviewed. Length = 356 Score = 43.0 bits (102), Expect = 2e-04 Identities = 30/109 (27%), Positives = 50/109 (45%), Gaps = 22/109 (20%) Query: 203 ISSHISQG--KLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPG-------- 252 +S+ +G L + G + +LG S GKS+L NAL ++V + Sbjct: 177 VSALDGEGLDVLAAWLSGGKTVALLGSSGVGKSTLVNALLGEEVQKTGAVREDDSKGRHT 236 Query: 253 -TTRDVLTIDLDLEGYLVKISDTAGIRE---TDDIVEKEGIKRTFLEVE 297 T R++ L G L+ DT G+RE D ++G++ TF ++E Sbjct: 237 TTHRELHP--LPSGGLLI---DTPGMRELQLWD---AEDGVEETFSDIE 277 >gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional. Length = 201 Score = 43.0 bits (102), Expect = 2e-04 Identities = 30/92 (32%), Positives = 42/92 (45%), Gaps = 17/92 (18%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR--------DVLTIDLDLEGYLVKIS 272 +IV +G SN GKS+L L K V V PG TR D + DL G++ + Sbjct: 11 EIVFVGRSNVGKSTLVRELTGKKVR-VGKRPGVTRKPNHYDWGDFILTDLPGFGFMSGVP 69 Query: 273 DTAGIRETDDIVEKEGIKRTFLEVENADLILL 304 + D+IV ++E +NAD IL Sbjct: 70 KEVQEKIKDEIVR-------YIE-DNADRILA 93 >gnl|CDD|184332 PRK13796, PRK13796, GTPase YqeH; Provisional. Length = 365 Score = 42.9 bits (102), Expect = 2e-04 Identities = 36/107 (33%), Positives = 49/107 (45%), Gaps = 29/107 (27%) Query: 217 RNGYKIVILGHSNAGKSSLFNALAK-----KDVAIVTDIPGTTRDVLTIDLDLEGYLVKI 271 R G + ++G +N GKS+L N + K KDV + PGTT D + I LD +L Sbjct: 158 REGRDVYVVGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLDKIEIPLDDGSFLY-- 215 Query: 272 SDTAGIRETDDIVEKEGIKR----TFLEVENADLILLLKEINSKKEI 314 DT GI I R +L ++ LK I+ KKEI Sbjct: 216 -DTPGI-----------IHRHQMAHYLSAKD------LKIISPKKEI 244 >gnl|CDD|129528 TIGR00436, era, GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein. Length = 270 Score = 42.0 bits (99), Expect = 3e-04 Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 2/60 (3%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD-VLTIDLDLEGYLVKISDTAGIRE 279 + ILG N GKS+L N L + ++I + TTR+ + I ++ I DT G E Sbjct: 2 FVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFI-DTPGFHE 60 >gnl|CDD|181957 PRK09563, rbgA, GTPase YlqF; Reviewed. Length = 287 Score = 41.7 bits (99), Expect = 4e-04 Identities = 21/57 (36%), Positives = 31/57 (54%), Gaps = 3/57 (5%) Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI 277 + +I+G N GKS+L N LA K +A + PG T+ I L +++ DT GI Sbjct: 123 RAMIIGIPNVGKSTLINRLAGKKIAKTGNRPGVTKAQQWIKLGKG---LELLDTPGI 176 >gnl|CDD|161735 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option). Length = 245 Score = 41.2 bits (97), Expect = 6e-04 Identities = 36/135 (26%), Positives = 51/135 (37%), Gaps = 22/135 (16%) Query: 177 DFSEEEDVQNFSSKEVLN---DILFLKNDISSHISQG--KLGEIIRNGYKIVILGHSNAG 231 D ++ED++ N +L SS G +L E ++N + G S G Sbjct: 78 DLLDDEDMEKEQLDIYRNIGYQVLM----TSSKNQDGLKELIEALQNRISVFA-GQSGVG 132 Query: 232 KSSLFNALAKKDVAIVTDIPG-------TTRDVLTIDLDLEGYLVKISDTAGIRETD-DI 283 KSSL NAL V DI TT V G + DT G E Sbjct: 133 KSSLINALDPSVKQQVNDISSKLGLGKHTTTHVELFHFH-GGLIA---DTPGFNEFGLWH 188 Query: 284 VEKEGIKRTFLEVEN 298 +E E + + F+E + Sbjct: 189 LEPEQLTQGFVEFRD 203 >gnl|CDD|179035 PRK00454, engB, GTP-binding protein YsxC; Reviewed. Length = 196 Score = 40.5 bits (96), Expect = 0.001 Identities = 44/183 (24%), Positives = 74/183 (40%), Gaps = 44/183 (24%) Query: 218 NGYKIVILGHSNAGKSSLFNALA-KKDVAIVTDIPGTTRDVLTI---DLDLEGYLV---- 269 +G +I G SN GKSSL NAL +K++A + PG T+ I +++ + LV Sbjct: 23 DGPEIAFAGRSNVGKSSLINALTNRKNLARTSKTPGRTQ---LINFFEVNDKLRLVDLPG 79 Query: 270 ----KISDTAGIRE------TDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISF--P 317 K+S +E + + +E +K L + D LKE++ + I + Sbjct: 80 YGYAKVSKE--EKEKWQKLIEEYLRTRENLKGVVLLI---DSRHPLKELD-LQMIEWLKE 133 Query: 318 KNIDFIFIGTKSD---------LYSTYTEEYD------HLISSFTGEGLEELINKIKSIL 362 I + + TK+D + L SS +G++EL I L Sbjct: 134 YGIPVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGIDELRAAIAKWL 193 Query: 363 SNK 365 + Sbjct: 194 AEA 196 >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 = 39.3 bits (92), Expect = 0.002 Identities = 35/128 (27%), Positives = 52/128 (40%), Gaps = 28/128 (21%) Query: 221 KIVILGHSNAGKSSLFNALAK--KDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR 278 K+V++G +GKSSL + L I +I G T V T+++D + L+ I D G R Sbjct: 1 KVVVIGDKGSGKSSLLSQLVGGEFPPEIPEEIQGDTLAVDTLEVDGDTELLHIWDFGG-R 59 Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISF----------------PKNIDF 322 E E + ++ AD ILL+ + S K I Sbjct: 60 E-------ELKFEHIIFMKTADAILLV--YDLTDRESLNRVSRLIAWLPHLRKLGKKIPV 110 Query: 323 IFIGTKSD 330 I +G K D Sbjct: 111 ILVGNKFD 118 >gnl|CDD|128472 smart00175, RAB, Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking. Length = 164 Score = 37.5 bits (88), Expect = 0.007 Identities = 34/131 (25%), Positives = 51/131 (38%), Gaps = 33/131 (25%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVK--ISDTAG- 276 +KI+++G S GKSSL + D T ++++G VK I DTAG Sbjct: 1 FKIILIGDSGVGKSSLLSRFT-DGKFSEQYKSTIGVDFKTKTIEVDGKRVKLQIWDTAGQ 59 Query: 277 ----------IRETD------DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNI 320 R DI +E +F ++N LKE+ N+ Sbjct: 60 ERFRSITSSYYRGAVGALLVYDITNRE----SFENLKN-----WLKELREYA----DPNV 106 Query: 321 DFIFIGTKSDL 331 + +G KSDL Sbjct: 107 VIMLVGNKSDL 117 >gnl|CDD|163346 TIGR03598, GTPase_YsxC, ribosome biogenesis GTP-binding protein YsxC/EngB. Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes. Length = 179 Score = 37.1 bits (87), Expect = 0.008 Identities = 18/39 (46%), Positives = 23/39 (58%), Gaps = 1/39 (2%) Query: 218 NGYKIVILGHSNAGKSSLFNALAK-KDVAIVTDIPGTTR 255 +G +I G SN GKSSL NAL K +A + PG T+ Sbjct: 17 DGPEIAFAGRSNVGKSSLINALTNRKKLARTSKTPGRTQ 55 >gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional. Length = 426 Score = 36.2 bits (84), Expect = 0.016 Identities = 29/85 (34%), Positives = 43/85 (50%), Gaps = 6/85 (7%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVL-TIDLDLEGYLVKISDTAG-IRE 279 + ++G++NAGKS+LFN + + V + T L ID+ G V ++DT G IR Sbjct: 200 VSLVGYTNAGKSTLFNRITEARVYAADQLFATLDPTLRRIDVADVGETV-LADTVGFIRH 258 Query: 280 -TDDIVEKEGIKRTFLEVENADLIL 303 D+V K T E A L+L Sbjct: 259 LPHDLV--AAFKATLQETRQATLLL 281 >gnl|CDD|183014 PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed. Length = 588 Score = 36.0 bits (84), Expect = 0.018 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 11/78 (14%) Query: 168 IRSFIEADLDFSEEEDVQNFSSKEVLNDILFLKN-DISSHISQGK--LGEI---IRNGYK 221 + +F+E L ++ + + +S + + + ++ +I S GK G + + G + Sbjct: 324 LVTFLETPLAHPQQGE-KELASNDPVT--IEAEDLEILSP--DGKTLAGPLNFTLPAGQR 378 Query: 222 IVILGHSNAGKSSLFNAL 239 I ++G S AGK+SL NAL Sbjct: 379 IALVGPSGAGKTSLLNAL 396 >gnl|CDD|181982 PRK09602, PRK09602, translation-associated GTPase; Reviewed. Length = 396 Score = 34.4 bits (80), Expect = 0.055 Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 1/37 (2%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD 256 I ++G N GKS+ FNA DV I + P TT D Sbjct: 2 ITIGLVGKPNVGKSTFFNAATLADVEI-ANYPFTTID 37 >gnl|CDD|178387 PLN02790, PLN02790, transketolase. Length = 654 Score = 34.6 bits (80), Expect = 0.056 Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 9/45 (20%) Query: 147 MEGMSGELSSLYGQW-IDKLT------HIRSFIEADLDFSEEEDV 184 MEG+S E +SL G W + KL HI I+ D + + EDV Sbjct: 150 MEGISNEAASLAGHWGLGKLIVLYDDNHIS--IDGDTEIAFTEDV 192 >gnl|CDD|181981 PRK09601, PRK09601, GTP-binding protein YchF; Reviewed. Length = 364 Score = 33.5 bits (78), Expect = 0.10 Identities = 14/28 (50%), Positives = 16/28 (57%) Query: 219 GYKIVILGHSNAGKSSLFNALAKKDVAI 246 G K I+G N GKS+LFNAL K Sbjct: 2 GLKCGIVGLPNVGKSTLFNALTKAGAEA 29 >gnl|CDD|163042 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD. Length = 529 Score = 33.4 bits (77), Expect = 0.12 Identities = 10/25 (40%), Positives = 16/25 (64%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 + G ++ ++G S AGKS+L N L Sbjct: 345 VPPGERVALVGPSGAGKSTLLNLLL 369 >gnl|CDD|162989 TIGR02729, Obg_CgtA, Obg family GTPase CgtA. This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal. Length = 329 Score = 32.4 bits (75), Expect = 0.24 Identities = 44/208 (21%), Positives = 80/208 (38%), Gaps = 74/208 (35%) Query: 210 GKLGEI--IRNGYKIV----ILGHSNAGKSSLFNAL--AKKDVA---------------- 245 G+ GE +R K++ ++G NAGKS+L +A+ AK +A Sbjct: 142 GEPGEERWLRLELKLLADVGLVGLPNAGKSTLISAVSAAKPKIADYPFTTLVPNLGVVRV 201 Query: 246 ------IVTDIPGTTRDVLTIDLDLEG-------------------YLVKISDTAGIRET 280 ++ DIPG +EG L+ + D + + + Sbjct: 202 DDGRSFVIADIPGL----------IEGASEGAGLGHRFLKHIERTRVLLHLIDISPL-DG 250 Query: 281 DDIVEKEGIKRTFLEVENADL-----ILLLKEINSKKEISFPKNIDFIFIGTKSDLYSTY 335 D +E I R L+ + +L I++L +I+ E + + + ++ Sbjct: 251 RDPIEDYEIIRNELKKYSPELAEKPRIVVLNKIDLLDEEELAELLKELKKALGKPVF--- 307 Query: 336 TEEYDHLISSFTGEGLEELINKIKSILS 363 IS+ TGEGL+EL+ + +L Sbjct: 308 ------PISALTGEGLDELLYALAELLE 329 >gnl|CDD|162130 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP) Family protein. Length = 617 Score = 32.3 bits (74), Expect = 0.24 Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 9/42 (21%) Query: 199 LKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA 240 L ++S G+L + ++G S AGK++L NALA Sbjct: 40 LLKNVSGVAKPGEL---------LAVMGSSGAGKTTLMNALA 72 >gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit; Provisional. Length = 232 Score = 32.2 bits (74), Expect = 0.25 Identities = 12/25 (48%), Positives = 17/25 (68%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 + G ++ ILG S AGKS+L N +A Sbjct: 22 VERGERVAILGPSGAGKSTLLNLIA 46 >gnl|CDD|185530 PTZ00258, PTZ00258, GTP-binding protein; Provisional. Length = 390 Score = 31.5 bits (72), Expect = 0.42 Identities = 14/27 (51%), Positives = 18/27 (66%) Query: 218 NGYKIVILGHSNAGKSSLFNALAKKDV 244 N K+ I+G N GKS+ FNAL K+ V Sbjct: 20 NNLKMGIVGLPNVGKSTTFNALCKQQV 46 >gnl|CDD|183417 PRK12299, obgE, GTPase CgtA; Reviewed. Length = 335 Score = 30.8 bits (71), Expect = 0.67 Identities = 11/22 (50%), Positives = 16/22 (72%) Query: 342 LISSFTGEGLEELINKIKSILS 363 LIS+ TGEGL+EL+ + +L Sbjct: 307 LISAVTGEGLDELLRALWELLE 328 Score = 27.7 bits (63), Expect = 6.0 Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 5/33 (15%) Query: 224 ILGHSNAGKSSLFNAL--AKKDVAIVTDIPGTT 254 ++G NAGKS+L +A+ AK +A D P TT Sbjct: 163 LVGLPNAGKSTLISAVSAAKPKIA---DYPFTT 192 >gnl|CDD|178676 PLN03130, PLN03130, ABC transporter C family member; Provisional. Length = 1622 Score = 30.5 bits (69), Expect = 0.80 Identities = 12/24 (50%), Positives = 16/24 (66%) Query: 216 IRNGYKIVILGHSNAGKSSLFNAL 239 I K+ I+G + AGKSS+ NAL Sbjct: 1262 ISPSEKVGIVGRTGAGKSSMLNAL 1285 >gnl|CDD|173562 PTZ00369, PTZ00369, Ras-like protein; Provisional. Length = 189 Score = 30.2 bits (68), Expect = 0.96 Identities = 42/144 (29%), Positives = 60/144 (41%), Gaps = 21/144 (14%) Query: 218 NGYKIVILGHSNAGKSSLFNALAKKDVAIVTD--IPGTTRDVLTIDLDLEGYLVKISDTA 275 YK+V++G GKS+L + D I + R ID + L+ I DTA Sbjct: 4 TEYKLVVVGGGGVGKSALTIQFIQNHFIDEYDPTIEDSYRKQCVIDEET--CLLDILDTA 61 Query: 276 GIRETDDIVEKEGIKRT---FLEVENADLILLLKEINS-KKEISFPKNID---FIFIGTK 328 G E + ++ RT FL V + +EI S +++I K+ D I +G K Sbjct: 62 GQEEYSAM--RDQYMRTGQGFLCVYSITSRSSFEEIASFREQILRVKDKDRVPMILVGNK 119 Query: 329 SDLYSTYTEEYDHLISSFTGEGLE 352 DL D TGEG E Sbjct: 120 CDL--------DSERQVSTGEGQE 135 >gnl|CDD|130252 TIGR01184, ntrCD, nitrate transport ATP-binding subunits C and D. This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase. Length = 230 Score = 29.7 bits (67), Expect = 1.4 Identities = 11/25 (44%), Positives = 17/25 (68%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 I+ G I ++GHS GKS+L N ++ Sbjct: 8 IQQGEFISLIGHSGCGKSTLLNLIS 32 >gnl|CDD|161805 TIGR00287, cas1, CRISPR-associated endonuclease Cas1. This model identifies CRISPR-associated protein Cas1, the most universal CRISPR system protein. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, a system for heritable host defense by prokaryotic cells against phage and other foreign DNA. Cas1 is a metal-dependent DNA-specific endonuclease. Length = 323 Score = 29.6 bits (67), Expect = 1.6 Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 4/63 (6%) Query: 283 IVEKEGIKRTFLEVENADLILLLKEIN-SKKEISF--PKNIDFIFIGTKSD-LYSTYTEE 338 +VEKEG K+ + V N D I+L ++ S I + ID +F+G + L +E Sbjct: 19 VVEKEGKKKWNIPVANVDCIVLFGGVSISSAAIRELAKRGIDIVFLGGDGNYLGRLSPQE 78 Query: 339 YDH 341 Sbjct: 79 SGS 81 >gnl|CDD|180911 PRK07261, PRK07261, topology modulation protein; Provisional. Length = 171 Score = 29.7 bits (67), Expect = 1.7 Identities = 10/22 (45%), Positives = 16/22 (72%) Query: 221 KIVILGHSNAGKSSLFNALAKK 242 KI I+G+S +GKS+L L++ Sbjct: 2 KIAIIGYSGSGKSTLARKLSQH 23 >gnl|CDD|168499 PRK06274, PRK06274, indolepyruvate oxidoreductase subunit B; Reviewed. Length = 197 Score = 29.2 bits (66), Expect = 2.0 Identities = 24/112 (21%), Positives = 47/112 (41%), Gaps = 13/112 (11%) Query: 265 EGYLVKISDTAGIRETDDIVEK-----EGIKRTFLEVENADLILLLKEINSKKEISFPKN 319 EG+ V+ ++T G+ + + V + I + ADL+L L+ + + F K Sbjct: 29 EGFHVRTAETLGMSQREGSVISHLRFGDEISSPLIPEGQADLLLALEPAEVARNLHFLKK 88 Query: 320 IDFIFIGTKSDLYST--YTEEYDHLISSFTGEGLEELINKIKSILSNKFKKL 369 I + + +T +E+YD + ++ KI ++ F KL Sbjct: 89 GGKIIVNAYAIHPATTVGSEKYDPE------KEIKFAKEKICDVICIDFTKL 134 >gnl|CDD|128471 smart00174, RHO, Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms. Length = 174 Score = 29.5 bits (67), Expect = 2.0 Identities = 40/158 (25%), Positives = 67/158 (42%), Gaps = 29/158 (18%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTD-IPGTTRDVLTIDLDLEGYLVKIS--DTAGIR 278 +V++G GK+ L + A D +P T + + D++++G V++ DTAG Sbjct: 1 LVVVGDGAVGKTCLLISYTTN--AFPEDYVP-TVFENYSADVEVDGKPVELGLWDTAGQE 57 Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINS--------KK---EIS-FPKNIDFIFIG 326 + D + R L + D+ L+ ++S +K E+ F N I +G Sbjct: 58 DYDRL-------RP-LSYPDTDVFLICFSVDSPASFENVKEKWYPEVKHFCPNTPIILVG 109 Query: 327 TKSDLY---STYTEEYDHLISSFTGEGLEELINKIKSI 361 TK DL ST E T E E L +I ++ Sbjct: 110 TKLDLREDKSTLRELSKQKQEPVTYEQGEALAKRIGAV 147 >gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family protein. Length = 1394 Score = 29.3 bits (66), Expect = 2.1 Identities = 22/82 (26%), Positives = 36/82 (43%), Gaps = 10/82 (12%) Query: 178 FSEEEDVQN--FSSKEVLNDILFLKN-DISSHISQGK---LGEI---IRNGYKIVILGHS 228 E +DV + KE DI +N I + K L + ++ G ++G S Sbjct: 739 TDESDDVNDEKDMEKESGEDIFHWRNLTYEVKIKKEKRVILNNVDGWVKPGTLTALMGAS 798 Query: 229 NAGKSSLFNALA-KKDVAIVTD 249 AGK++L N LA + ++T Sbjct: 799 GAGKTTLLNVLAERVTTGVITG 820 >gnl|CDD|183003 PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed. Length = 574 Score = 29.0 bits (66), Expect = 2.2 Identities = 15/77 (19%), Positives = 28/77 (36%), Gaps = 17/77 (22%) Query: 173 EADLDFSEEEDVQNFSSKEVLNDILF--------LKNDISSHISQGKLGEIIRNGYKIVI 224 + ++ F LN++ F + +S I G+ K+ + Sbjct: 321 KPEVTFPTTSTAAADQVSLTLNNVSFTYPDQPQPVLKGLSLQIKAGE---------KVAL 371 Query: 225 LGHSNAGKSSLFNALAK 241 LG + GKS+L L + Sbjct: 372 LGRTGCGKSTLLQLLTR 388 >gnl|CDD|151679 pfam11237, DUF3038, Protein of unknown function (DUF3038). This family of proteins with unknown function appear to be restricted to Cyanobacteria. Length = 171 Score = 29.2 bits (66), Expect = 2.3 Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 11/78 (14%) Query: 105 LRLANPGEFSRRAFENGKIDLLEAESLADLISS----ETEMQRRL--SMEGMSG-ELSSL 157 LR NP RR+ G + + EA +L +I + R+L +E MS E L Sbjct: 49 LRCTNP---LRRSTRRGPLTVEEARALVLIICYLAKRLYPLIRQLLLLLEQMSSQEPPPL 105 Query: 158 YGQ-WIDKLTHIRSFIEA 174 Q + L RS I+ Sbjct: 106 QTQLLSEYLDRFRSLIQE 123 >gnl|CDD|183407 PRK12289, PRK12289, GTPase RsgA; Reviewed. Length = 352 Score = 28.8 bits (65), Expect = 2.6 Identities = 35/116 (30%), Positives = 45/116 (38%), Gaps = 27/116 (23%) Query: 203 ISSHISQG--KLGEIIRNGYKIVIL-GHSNAGKSSLFNAL---AKKDVAIVTDIPG---- 252 IS G L E +RN KI ++ G S GKSSL N L + V V+ G Sbjct: 155 ISVETGIGLEALLEQLRN--KITVVAGPSGVGKSSLINRLIPDVELRVGKVSGKLGRGRH 212 Query: 253 TTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEI 308 TTR V +L G L +DT G + D L+ +L E Sbjct: 213 TTRHVELFELPNGGLL---ADTPGFNQPD------------LDCSPRELAHYFPEA 253 >gnl|CDD|161762 TIGR00201, comF, comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis. Length = 190 Score = 29.0 bits (65), Expect = 2.8 Identities = 17/55 (30%), Positives = 22/55 (40%), Gaps = 8/55 (14%) Query: 334 TYTEEYDHLISSFTGEGLEELINKIKSILSNKFKKLPFSIP--------SHKRHL 380 TY E LIS F G E+I + S+LS K +P S +R Sbjct: 40 TYNEPLKELISRFKFRGQAEIIRALASLLSLTVSKAYRDLPDVIVPVPLSKEREW 94 >gnl|CDD|129567 TIGR00475, selB, selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes. Length = 581 Score = 28.7 bits (64), Expect = 2.9 Identities = 38/186 (20%), Positives = 63/186 (33%), Gaps = 41/186 (22%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDL-----DLEGYLVKISDT-- 274 I GH + GK++L AL +P + +TIDL L Y + D Sbjct: 3 IATAGHVDHGKTTLLKALTGIAAD---RLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVPG 59 Query: 275 ---------AGIRETDD---IVE-KEGIKRTFLEVENADLILLLKEINSKKEISFPKNID 321 AG D +V+ EG+ + + + +L + I D Sbjct: 60 HEKFISNAIAGGGGIDAALLVVDADEGVM-----TQTGEHLAVLDLLGIPHTIVVITKAD 114 Query: 322 FI---FIGTKSDLYSTYTEEYDHL-------ISSFTGEGLEELINKIKSIL---SNKFKK 368 + I Y L S+ TG+G+ EL ++K++L K + Sbjct: 115 RVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKELKNLLESLDIKRIQ 174 Query: 369 LPFSIP 374 P + Sbjct: 175 KPLRMA 180 >gnl|CDD|132307 TIGR03263, guanyl_kin, guanylate kinase. Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP. Length = 180 Score = 28.6 bits (65), Expect = 3.0 Identities = 16/35 (45%), Positives = 20/35 (57%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD 256 IVI G S GKS+L AL ++D + I TTR Sbjct: 4 IVISGPSGVGKSTLVKALLEEDPNLKFSISATTRK 38 >gnl|CDD|182600 PRK10631, PRK10631, p-hydroxybenzoic acid efflux subunit AaeB; Provisional. Length = 652 Score = 28.5 bits (64), Expect = 3.3 Identities = 11/26 (42%), Positives = 15/26 (57%) Query: 12 STGALPSAISIIRLSGPSCFQVCEFI 37 S GAL S I+I+ L P F +F+ Sbjct: 456 SLGALASTINILVLDNPMTFHFSQFL 481 >gnl|CDD|184206 PRK13647, cbiO, cobalt transporter ATP-binding subunit; Provisional. Length = 274 Score = 28.6 bits (64), Expect = 3.3 Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 3/27 (11%) Query: 216 IRNGYKIVILGHSNAGKSSL---FNAL 239 I G K +LG + AGKS+L N + Sbjct: 28 IPEGSKTALLGPNGAGKSTLLLHLNGI 54 >gnl|CDD|178968 PRK00300, gmk, guanylate kinase; Provisional. Length = 205 Score = 28.5 bits (65), Expect = 3.3 Identities = 15/34 (44%), Positives = 21/34 (61%) Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR 255 IV+ G S AGKS+L AL ++D + + TTR Sbjct: 8 IVLSGPSGAGKSTLVKALLERDPNLQLSVSATTR 41 >gnl|CDD|183415 PRK12297, obgE, GTPase CgtA; Reviewed. Length = 424 Score = 28.5 bits (65), Expect = 3.4 Identities = 9/22 (40%), Positives = 15/22 (68%) Query: 343 ISSFTGEGLEELINKIKSILSN 364 IS+ TG+GL+EL+ + +L Sbjct: 307 ISALTGQGLDELLYAVAELLEE 328 >gnl|CDD|184193 PRK13633, PRK13633, cobalt transporter ATP-binding subunit; Provisional. Length = 280 Score = 28.5 bits (64), Expect = 3.7 Identities = 11/27 (40%), Positives = 18/27 (66%), Gaps = 3/27 (11%) Query: 216 IRNGYKIVILGHSNAGKSSL---FNAL 239 ++ G +VILG + +GKS++ NAL Sbjct: 33 VKKGEFLVILGRNGSGKSTIAKHMNAL 59 >gnl|CDD|163017 TIGR02782, TrbB_P, P-type conjugative transfer ATPase TrbB. The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA. Length = 299 Score = 28.6 bits (64), Expect = 3.7 Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 3/56 (5%) Query: 198 FLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGT 253 +++ I + + L E + I+++G + +GK++L NAL + I + P Sbjct: 111 YVEAGIMTAAQRDVLREAVLARKNILVVGGTGSGKTTLANALLAE---IAKNDPTD 163 >gnl|CDD|133958 PHA01753, PHA01753, Holliday junction resolvase. Length = 121 Score = 28.3 bits (63), Expect = 3.8 Identities = 15/46 (32%), Positives = 28/46 (60%), Gaps = 1/46 (2%) Query: 217 RNGYKIVILGHSNAGKSSLFNALAKKDVAIVT-DIPGTTRDVLTID 261 NG+K + + S GK +L + +A K+ I ++ T++DV+T+D Sbjct: 20 SNGFKALRIPVSGTGKQALPDIIATKNNTIYPIEVKSTSKDVVTVD 65 >gnl|CDD|183416 PRK12298, obgE, GTPase CgtA; Reviewed. Length = 390 Score = 28.3 bits (64), Expect = 4.0 Identities = 16/33 (48%), Positives = 18/33 (54%), Gaps = 5/33 (15%) Query: 225 LGHSNAGKSSLFNAL--AKKDVAIVTDIPGTTR 255 LG NAGKS+ A+ AK VA D P TT Sbjct: 165 LGLPNAGKSTFIRAVSAAKPKVA---DYPFTTL 194 >gnl|CDD|152975 pfam12541, DUF3737, Protein of unknown function (DUF3737). This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 281 and 297 amino acids in length. Length = 278 Score = 28.4 bits (64), Expect = 4.3 Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 6/62 (9%) Query: 162 IDKLTHIR-SFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGY 220 ID L I DL F E +V ++ I +KN +S I +GEII + Sbjct: 212 IDNLVLENCILINTDLAF-EYSNVD----ADIKGWIDSVKNPLSGKIRADSIGEIILDET 266 Query: 221 KI 222 KI Sbjct: 267 KI 268 >gnl|CDD|183001 PRK11153, metN, DL-methionine transporter ATP-binding subunit; Provisional. Length = 343 Score = 28.2 bits (64), Expect = 4.3 Identities = 13/35 (37%), Positives = 19/35 (54%), Gaps = 9/35 (25%) Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSL 235 N++S HI G++ +I G S AGKS+L Sbjct: 22 NNVSLHIPAGEIFGVI---------GASGAGKSTL 47 >gnl|CDD|150775 pfam10139, Virul_Fac, Putative bacterial virulence factor. Members of this family of prokaryotic proteins include various putative virulence factor effector proteins. Their exact function is, as yet, unknown. Length = 852 Score = 28.2 bits (63), Expect = 4.5 Identities = 12/30 (40%), Positives = 15/30 (50%) Query: 211 KLGEIIRNGYKIVILGHSNAGKSSLFNALA 240 +LG + G S AGKS L +ALA Sbjct: 35 RLGAAADTPMSVGFFGPSQAGKSYLISALA 64 >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 = 28.1 bits (62), Expect = 4.8 Identities = 16/90 (17%), Positives = 35/90 (38%), Gaps = 11/90 (12%) Query: 219 GYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLD----LEGYLVKISDT 274 G I+I+G +GK++L ALA++ + V+ ID + + + Sbjct: 2 GEVILIVGPPGSGKTTLARALARE-------LGPPGGGVIYIDGEDILEEVLDQLLLIIV 54 Query: 275 AGIRETDDIVEKEGIKRTFLEVENADLILL 304 G + + + + D+++L Sbjct: 55 GGKKASGSGELRLRLALALARKLKPDVLIL 84 >gnl|CDD|131721 TIGR02673, FtsE, cell division ATP-binding protein FtsE. This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein. Length = 214 Score = 28.0 bits (63), Expect = 4.9 Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 10/51 (19%) Query: 189 SKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNAL 239 SK + L D+S HI +G+ + + G S AGK++L L Sbjct: 8 SKAYPGGVAALH-DVSLHIRKGEF---------LFLTGPSGAGKTTLLKLL 48 >gnl|CDD|182993 PRK11144, modC, molybdate transporter ATP-binding protein; Provisional. Length = 352 Score = 27.9 bits (63), Expect = 5.1 Identities = 10/17 (58%), Positives = 13/17 (76%) Query: 224 ILGHSNAGKSSLFNALA 240 I G S AGK+SL NA++ Sbjct: 29 IFGRSGAGKTSLINAIS 45 >gnl|CDD|130064 TIGR00991, 3a0901s02IAP34, GTP-binding protein (Chloroplast Envelope Protein Translocase). Length = 313 Score = 27.9 bits (62), Expect = 5.6 Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 1/95 (1%) Query: 210 GKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLV 269 GKL E + I+++G GKSS N++ + +A V+ + + G+ + Sbjct: 29 GKLKEEDVSSLTILVMGKGGVGKSSTVNSIIGERIATVSAFQSEGLRPMMVSRTRAGFTL 88 Query: 270 KISDTAGIRETDDIVEKE-GIKRTFLEVENADLIL 303 I DT G+ E I ++ I + FL + D++L Sbjct: 89 NIIDTPGLIEGGYINDQAVNIIKRFLLGKTIDVLL 123 >gnl|CDD|128470 smart00173, RAS, Ras subfamily of RAS small GTPases. Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades. Length = 164 Score = 27.9 bits (63), Expect = 6.0 Identities = 23/62 (37%), Positives = 30/62 (48%), Gaps = 4/62 (6%) Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLT--IDLDLEGYLVKISDTAGI 277 YK+V+LG GKS+L + V D T D I++D E L+ I DTAG Sbjct: 1 YKLVVLGSGGVGKSALTIQFVQG--HFVDDYDPTIEDSYRKQIEIDGEVCLLDILDTAGQ 58 Query: 278 RE 279 E Sbjct: 59 EE 60 >gnl|CDD|183414 PRK12296, obgE, GTPase CgtA; Reviewed. Length = 500 Score = 27.5 bits (62), Expect = 6.5 Identities = 16/32 (50%), Positives = 20/32 (62%), Gaps = 5/32 (15%) Query: 225 LGHSNAGKSSLFNAL--AKKDVAIVTDIPGTT 254 +G +AGKSSL +AL AK +A D P TT Sbjct: 165 VGFPSAGKSSLISALSAAKPKIA---DYPFTT 193 >gnl|CDD|130344 TIGR01277, thiQ, thiamine ABC transporter, ATP-binding protein. This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found. Length = 213 Score = 27.5 bits (61), Expect = 6.8 Identities = 11/25 (44%), Positives = 17/25 (68%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 + +G + I+G S AGKS+L N +A Sbjct: 21 VADGEIVAIMGPSGAGKSTLLNLIA 45 >gnl|CDD|131259 TIGR02204, MsbA_rel, ABC transporter, permease/ATP-binding protein. This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins. Length = 576 Score = 27.7 bits (62), Expect = 6.8 Identities = 11/24 (45%), Positives = 16/24 (66%) Query: 216 IRNGYKIVILGHSNAGKSSLFNAL 239 +R G + ++G S AGKS+LF L Sbjct: 363 VRPGETVALVGPSGAGKSTLFQLL 386 >gnl|CDD|161779 TIGR00232, tktlase_bact, transketolase, bacterial and yeast. This model is designed to capture orthologs of bacterial transketolases. The group includes two from the yeast Saccharomyces cerevisiae but excludes dihydroxyactetone synthases (formaldehyde transketolases) from various yeasts and the even more distant mammalian transketolases. Among the family of thiamine diphosphate-dependent enzymes that includes transketolases, dihydroxyacetone synthases, pyruvate dehydrogenase E1-beta subunits, and deoxyxylulose-5-phosphate synthases, mammalian and bacterial transketolases seem not to be orthologous. Length = 653 Score = 27.4 bits (61), Expect = 7.1 Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 5/44 (11%) Query: 147 MEGMSGELSSLYGQW-IDKLTHI----RSFIEADLDFSEEEDVQ 185 EG+S E++SL G + KL + R I+ +D S EDV Sbjct: 155 QEGISYEVASLAGHLKLGKLIVLYDSNRISIDGAVDGSFTEDVA 198 >gnl|CDD|163239 TIGR03375, type_I_sec_LssB, type I secretion system ATPase, LssB 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. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export. Length = 694 Score = 27.5 bits (62), Expect = 7.5 Identities = 11/25 (44%), Positives = 15/25 (60%) Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240 IR G K+ I+G +GKS+L L Sbjct: 488 IRPGEKVAIIGRIGSGKSTLLKLLL 512 >gnl|CDD|180635 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed. Length = 284 Score = 27.4 bits (62), Expect = 8.1 Identities = 25/99 (25%), Positives = 39/99 (39%), Gaps = 16/99 (16%) Query: 121 GKIDLL---EAESLA-DL-ISSE--TEMQRRLSMEGMSGELSSL-----YGQWIDKLTHI 168 ++ L E E +A +L +S E EM+ RLS + S + G D L Sbjct: 144 KRLGWLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDK 203 Query: 169 RSFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHI 207 S L+ ED + + +L D L ++ S I Sbjct: 204 SSDPADVLEEDNWEDQR----RALLADALEGLDERSRDI 238 >gnl|CDD|178750 PLN03211, PLN03211, ABC transporter G-25; Provisional. Length = 659 Score = 27.2 bits (60), Expect = 8.9 Identities = 12/22 (54%), Positives = 16/22 (72%) Query: 219 GYKIVILGHSNAGKSSLFNALA 240 G + +LG S +GKS+L NALA Sbjct: 94 GEILAVLGPSGSGKSTLLNALA 115 >gnl|CDD|149336 pfam08217, DUF1712, Fungal domain of unknown function (DUF1712). The function of this family of proteins is unknown. Length = 468 Score = 27.0 bits (60), Expect = 9.1 Identities = 12/52 (23%), Positives = 24/52 (46%), Gaps = 4/52 (7%) Query: 171 FIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKI 222 F A +E++ ++ ++ + + L DI H+S+ GE N Y + Sbjct: 313 FDPAFSKINEQDYLKELDAQ-LYPQLSLLYLDIEEHLSKEANGE---NAYDV 360 >gnl|CDD|177350 PHA02109, PHA02109, hypothetical protein. Length = 233 Score = 26.9 bits (59), Expect = 9.8 Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 12/74 (16%) Query: 317 PKNIDFIFIGTKSDLYSTYTEEYDHLISSFTGEGLEELINKIKSI--LSNKFKKLPFSIP 374 PK ++ ++++ TE D + S TGE LE L +K+K I L+ K + L Sbjct: 161 PKAVE---------IHAS-TERIDQVERSHTGENLEGLTDKLKQISELTIKLEALSDEAC 210 Query: 375 SHKRHLYHLSQTVR 388 K + +L V+ Sbjct: 211 QVKHKILNLRAEVK 224 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 0.318 0.138 0.385 Gapped Lambda K H 0.267 0.0771 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 7,178,138 Number of extensions: 483488 Number of successful extensions: 1376 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1348 Number of HSP's successfully gapped: 113 Length of query: 440 Length of database: 5,994,473 Length adjustment: 96 Effective length of query: 344 Effective length of database: 3,920,105 Effective search space: 1348516120 Effective search space used: 1348516120 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 59 (26.4 bits)