RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780941|ref|YP_003065354.1| GTP-binding protein Era [Candidatus Liberibacter asiaticus str. psy62] (311 letters) >gnl|CDD|178854 PRK00089, era, GTPase Era; Reviewed. Length = 292 Score = 364 bits (937), Expect = e-101 Identities = 126/284 (44%), Positives = 179/284 (63%), Gaps = 3/284 (1%) Query: 21 RSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI 80 +SG VA+VG N GKSTL+N VG K+SIV+ K QTTR +RGIV+E ++QI+F+DTPGI Sbjct: 4 KSGFVAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRHRIRGIVTEDDAQIIFVDTPGI 63 Query: 81 FNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKI 140 K + ++ M + +WS++K D+V VVD+ ++ +L+++ K + +IL+LNKI Sbjct: 64 HKPKRALNRAMNKAAWSSLKDVDLVLFVVDADEKIGPGDEFILEKLKKVKTPVILVLNKI 123 Query: 141 DCVKP-ERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCSTLPLAPWVYSADQIS 199 D VK E LL E ++L+ + +SA KG D++L+ + LP P Y DQI+ Sbjct: 124 DLVKDKEELLPLLEELSELMDFAEIVPISALKGDNVDELLDVIAKYLPEGPPYYPEDQIT 183 Query: 200 DLPMFHFTAEITREKLFLHLHKEIPYSSCVVTEKWEEKKDGSILIRQVIYVERPSQKKIM 259 D P AEI REKL L E+PYS V EK+EE+ G + I IYVER SQK I+ Sbjct: 184 DRPERFLAAEIIREKLLRLLGDELPYSVAVEIEKFEER--GLVRIEATIYVERDSQKGII 241 Query: 260 LGKNGQNIKTISLEAKKEIAEILEQPVHLILFVKVQKDWGHDPK 303 +GK G +K I EA+K+I ++L + V L L+VKV+K W D K Sbjct: 242 IGKGGAMLKKIGTEARKDIEKLLGKKVFLELWVKVKKGWRDDEK 285 >gnl|CDD|185391 PRK15494, era, GTPase Era; Provisional. Length = 339 Score = 236 bits (604), Expect = 4e-63 Identities = 125/286 (43%), Positives = 180/286 (62%), Gaps = 13/286 (4%) Query: 19 NSRSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTP 78 N ++ V ++G N+GKSTL+NR +G K+SIVT KVQTTRSI+ GI++ K++Q++ DTP Sbjct: 49 NQKTVSVCIIGRPNSGKSTLLNRIIGEKLSIVTPKVQTTRSIITGIITLKDTQVILYDTP 108 Query: 79 GIFNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILN 138 GIF K S K M+R +WS++ AD+V L++DS + H++L ++ + I +LN Sbjct: 109 GIFEPKGSLEKAMVRCAWSSLHSADLVLLIIDSLKSFDDITHNILDKLRSLNIVPIFLLN 168 Query: 139 KIDCVKPERLLEQAEIANKLVFIEKT------FMVSATKGHGCDDVLNYLCSTLPLAPWV 192 KID +E + + F+ + F +SA G D +L Y+ S ++PW+ Sbjct: 169 KID-------IESKYLNDIKAFLTENHPDSLLFPISALSGKNIDGLLEYITSKAKISPWL 221 Query: 193 YSADQISDLPMFHFTAEITREKLFLHLHKEIPYSSCVVTEKWEEKKDGSILIRQVIYVER 252 Y+ D I+DLPM AEITRE+LFL+L KE+PY V TEKWE+ KD S+ I QVI V R Sbjct: 222 YAEDDITDLPMRFIAAEITREQLFLNLQKELPYKLTVQTEKWEDLKDKSVKINQVIVVSR 281 Query: 253 PSQKKIMLGKNGQNIKTISLEAKKEIAEILEQPVHLILFVKVQKDW 298 S K I+LGKNG IK I +++ ++ PVHL LFVKV++ W Sbjct: 282 ESYKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLFLFVKVRELW 327 >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 = 192 bits (491), Expect = 7e-50 Identities = 98/272 (36%), Positives = 150/272 (55%), Gaps = 3/272 (1%) Query: 23 GCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFN 82 G VA++G N GKSTL+N+ G K+SI + K QTTR+ + GI + SQI+F+DTPG Sbjct: 1 GFVAILGRPNVGKSTLLNQLHGQKISITSPKAQTTRNRISGIHTTGASQIIFIDTPGFHE 60 Query: 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSR-LILILNKID 141 K S ++LM++ + S I D++ VVDS + + + + R ++L NK+D Sbjct: 61 KKHSLNRLMMKEARSAIGGVDLILFVVDSDQWNG--DGEFVLTKLQNLKRPVVLTRNKLD 118 Query: 142 CVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCSTLPLAPWVYSADQISDL 201 ++LL + L + +SA G + ++ LP P+ Y D ++D Sbjct: 119 NKFKDKLLPLIDKYAILEDFKDIVPISALTGDNTSFLAAFIEVHLPEGPFRYPEDYVTDQ 178 Query: 202 PMFHFTAEITREKLFLHLHKEIPYSSCVVTEKWEEKKDGSILIRQVIYVERPSQKKIMLG 261 P +EI REK+ + +EIP+S V E+ + G + I +I VER SQKKI++G Sbjct: 179 PDRFKISEIIREKIIRYTKEEIPHSVRVEIERKSFNEKGLLKIHALISVERESQKKIIIG 238 Query: 262 KNGQNIKTISLEAKKEIAEILEQPVHLILFVK 293 KNG IK I + A+K+I E+ + V L LFVK Sbjct: 239 KNGSMIKAIGIAARKDILELFDCDVFLELFVK 270 >gnl|CDD|179996 PRK05291, trmE, tRNA modification GTPase TrmE; Reviewed. Length = 449 Score = 96.7 bits (242), Expect = 6e-21 Identities = 45/158 (28%), Positives = 76/158 (48%), Gaps = 10/158 (6%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84 V + G N GKS+L+N +G + +IVT TTR ++ ++ + +DT GI Sbjct: 218 VVIAGRPNVGKSSLLNALLGEERAIVTDIAGTTRDVIEEHINLDGIPLRLIDTAGIRETD 277 Query: 85 DSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCVK 144 D K+ I S I+ AD+V LV+D+ L ++L+E+ + +I++LNK D Sbjct: 278 DEVEKIGIERSREAIEEADLVLLVLDASEPLTEEDDEILEELKDK--PVIVVLNKADLTG 335 Query: 145 PERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYL 182 L E+ + +SA G G D++ + Sbjct: 336 EIDLEEEN--------GKPVIRISAKTGEGIDELREAI 365 >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 = 92.9 bits (232), Expect = 1e-19 Identities = 52/163 (31%), Positives = 75/163 (46%), Gaps = 4/163 (2%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84 VA+VG N GKSTL NR G + +IV+ TR G + + +DT GI Sbjct: 2 VAIVGRPNVGKSTLFNRLTGKRDAIVSDTPGVTRDRKYGDAEWGGREFILIDTGGIEEDD 61 Query: 85 DSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCVK 144 D K + + I+ AD++ VVD L ++ K + K +IL+ NKID K Sbjct: 62 DGLDKQIREQAEIAIEEADVILFVVDGREGLTPEDEEIAKWLRKSGKPVILVANKIDGKK 121 Query: 145 PERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCSTLP 187 + AE L F + +SA G G D+L+ + LP Sbjct: 122 ED--AVAAEFY-SLGF-GEPIPISAEHGRGIGDLLDAILELLP 160 Score = 84.4 bits (210), Expect = 4e-17 Identities = 50/184 (27%), Positives = 86/184 (46%), Gaps = 11/184 (5%) Query: 6 ITFFNEHKDFVQDNSRSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIV 65 + E ++ ++ +A++G N GKSTLVN +G + IV+ TTR + Sbjct: 156 LELLPEEEEEEEEEDGPIKIAIIGRPNVGKSTLVNALLGEERVIVSDIAGTTRDSIDIPF 215 Query: 66 SEKESQIVFLDTPGI---FNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDL 122 + + +DT GI + K + + I+ AD+V LV+D+ + DL Sbjct: 216 ERNGKKYLLIDTAGIRRKGKVTEGVEKYSVLRTLKAIERADVVLLVLDATEG--ITEQDL 273 Query: 123 --LKEIAKRSSRLILILNKIDCVKPERLLEQ--AEIANKLVFIE--KTFMVSATKGHGCD 176 I + L++++NK D VK E+ E+ E+ KL F++ +SA G G D Sbjct: 274 RIAGLILEAGKALVIVVNKWDLVKDEKTREEFKKELRRKLPFLDFAPIVFISALTGQGVD 333 Query: 177 DVLN 180 +L+ Sbjct: 334 KLLD 337 >gnl|CDD|178858 PRK00093, PRK00093, GTP-binding protein Der; Reviewed. Length = 435 Score = 82.8 bits (206), Expect = 1e-16 Identities = 51/169 (30%), Positives = 80/169 (47%), Gaps = 16/169 (9%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVS--EKESQIVFLDTPGIFN 82 VA+VG N GKSTL NR G + +IV TR + G +E ++ DT GI Sbjct: 4 VAIVGRPNVGKSTLFNRLTGKRDAIVADTPGVTRDRIYGEAEWLGREFILI--DTGGIEP 61 Query: 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIA----KRSSRLILILN 138 D + K + + I+ AD++ VVD + + +EIA K + +IL++N Sbjct: 62 DDDGFEKQIREQAELAIEEADVILFVVDG----RAGLTPADEEIAKILRKSNKPVILVVN 117 Query: 139 KIDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCSTLP 187 K+D P+ + E L + + +SA G G D+L+ + LP Sbjct: 118 KVD--GPDEEADAYE-FYSLGL-GEPYPISAEHGRGIGDLLDAILEELP 162 Score = 72.4 bits (179), Expect = 2e-13 Identities = 46/164 (28%), Positives = 80/164 (48%), Gaps = 12/164 (7%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI---F 81 +A++G N GKS+L+N +G + IV+ TTR + + +DT GI Sbjct: 176 IAIIGRPNVGKSSLINALLGEERVIVSDIAGTTRDSIDTPFERDGQKYTLIDTAGIRRKG 235 Query: 82 NAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELK---VNIHDLLKEIAKRSSRLILILN 138 + K + + I+ AD+V LV+D+ + + I L E A R+ L++++N Sbjct: 236 KVTEGVEKYSVIRTLKAIERADVVLLVIDATEGITEQDLRIAGLALE-AGRA--LVIVVN 292 Query: 139 KIDCVKPERLLE-QAEIANKLVFIE--KTFMVSATKGHGCDDVL 179 K D V + + E + E+ +L F++ +SA G G D +L Sbjct: 293 KWDLVDEKTMEEFKKELRRRLPFLDYAPIVFISALTGQGVDKLL 336 >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 = 75.2 bits (185), Expect = 2e-14 Identities = 43/138 (31%), Positives = 65/138 (47%), Gaps = 1/138 (0%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84 +A+VG+ N GKS+L+N + +IV+ TTR +V G I LDT GI Sbjct: 206 LAIVGSPNVGKSSLLNALLKQDRAIVSDIKGTTRDVVEGDFELNGILIKLLDTAGIREHA 265 Query: 85 DSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCVK 144 D +L I S+ IK AD+V V+D+ + L + L+ ++ K IL+LNKID Sbjct: 266 DFVERLGIEKSFKAIKQADLVIYVLDASQPLTKD-DFLIIDLNKSKKPFILVLNKIDLKI 324 Query: 145 PERLLEQAEIANKLVFIE 162 + + Sbjct: 325 NSLEFFVSSKVLNSSNLS 342 >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 = 64.8 bits (159), Expect = 3e-11 Identities = 53/168 (31%), Positives = 77/168 (45%), Gaps = 28/168 (16%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ---TTRSIVRGIVSEKESQIVFLDTPG-I 80 VALVG TNAGKSTL N GA V Q T R + +++ DT G I Sbjct: 192 VALVGYTNAGKSTLFNALTGADVYA---ADQLFATLDPTTRRLDLPDGGEVLLTDTVGFI 248 Query: 81 FNAKDSYHKLM--IRLSWSTI---KHADIVCLVVD-SHRELKVNI---HDLLKEIAKRSS 131 +D H+L+ R +T+ + AD++ VVD S + + I +L+E+ Sbjct: 249 ---RDLPHELVAAFR---ATLEEVREADLLLHVVDASDPDREEQIEAVEKVLEELGAEDI 302 Query: 132 RLILILNKIDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVL 179 +L+ NKID + R+ E + VF+ SA G G D +L Sbjct: 303 PQLLVYNKIDLLDEPRIERLEEGYPEAVFV------SAKTGEGLDLLL 344 >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 = 62.8 bits (153), Expect = 1e-10 Identities = 50/163 (30%), Positives = 75/163 (46%), Gaps = 12/163 (7%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVF--LDTPGIFN 82 + +VG N GKSTL+NR +G K I +K TTR+ V ++ E F LDT G Sbjct: 4 IVIVGDPNVGKSTLLNRLLGNK-FITEYKPGTTRNYVTTVIEEDGKTYKFNLLDTAGQ-E 61 Query: 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEI---AKRSSRLILILNK 139 + +L R S+++ DIV LV+D ++ + KEI A+ + +IL+ NK Sbjct: 62 DYRAIRRLYYRAVESSLRVFDIVILVLD----VEEILEKQTKEIIHHAESNVPIILVGNK 117 Query: 140 IDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYL 182 ID + A + KL +SA G D + Sbjct: 118 IDLRDAKLKTHVAFLFAKLNGEPI-IPLSAETGKNIDSAFKIV 159 >gnl|CDD|181925 PRK09518, PRK09518, bifunctional cytidylate kinase/GTPase Der; Reviewed. Length = 712 Score = 59.4 bits (144), Expect = 1e-09 Identities = 45/186 (24%), Positives = 75/186 (40%), Gaps = 21/186 (11%) Query: 14 DFVQDNSRSGC-VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQI 72 + ++ VA+VG N GKSTLVNR +G + ++V TR V + Sbjct: 266 GDEKAGPKAVGVVAIVGRPNVGKSTLVNRILGRREAVVEDTPGVTRDRVSYDAEWAGTDF 325 Query: 73 VFLDTPGIFNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSR 132 +DT G + + + + AD V VVD +V + + I + R Sbjct: 326 KLVDTGGWEADVEGIDSAIASQAQIAVSLADAVVFVVDG----QVGLTSTDERIVRMLRR 381 Query: 133 ----LILILNKIDCVKPERLLEQAEIANKLVF----IEKTFMVSATKGHGCDDVLNYLCS 184 ++L +NKID E + F + + + +SA G G D+L+ Sbjct: 382 AGKPVVLAVNKIDDQASEYDAAE--------FWKLGLGEPYPISAMHGRGVGDLLDEALD 433 Query: 185 TLPLAP 190 +L +A Sbjct: 434 SLKVAE 439 Score = 52.9 bits (127), Expect = 1e-07 Identities = 42/148 (28%), Positives = 66/148 (44%), Gaps = 24/148 (16%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84 VALVG N GKS+L+N+ + ++V TTR V IV +F+DT GI K Sbjct: 453 VALVGRPNVGKSSLLNQLTHEERAVVNDLAGTTRDPVDEIVEIDGEDWLFIDTAGI---K 509 Query: 85 DSYHKLM-------IRLSWSTIKHADIVCLVVD-----SHRELKVNIHDLLKEIAKRSSR 132 HKL +R + + I+ +++ + D S ++LKV + Sbjct: 510 RRQHKLTGAEYYSSLR-TQAAIERSELALFLFDASQPISEQDLKV-----MSMAVDAGRA 563 Query: 133 LILILNKIDCVKPER--LLEQAEIANKL 158 L+L+ NK D + R LE+ + Sbjct: 564 LVLVFNKWDLMDEFRRQRLER-LWKTEF 590 >gnl|CDD|179525 PRK03003, PRK03003, GTP-binding protein Der; Reviewed. Length = 472 Score = 58.4 bits (142), Expect = 2e-09 Identities = 56/178 (31%), Positives = 81/178 (45%), Gaps = 18/178 (10%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPG-IFNA 83 VA+VG N GKSTLVNR +G + ++V TR V + +DT G +A Sbjct: 41 VAVVGRPNVGKSTLVNRILGRREAVVEDVPGVTRDRVSYDAEWNGRRFTVVDTGGWEPDA 100 Query: 84 KDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAK---RSSR-LILILNK 139 K + + ++ AD V VVD+ V + +A+ RS + +IL NK Sbjct: 101 KG-LQASVAEQAEVAMRTADAVLFVVDA----TVGATATDEAVARVLRRSGKPVILAANK 155 Query: 140 IDCVKPERLLEQAEIAN--KLVFIEKTFMVSATKGHGCDDVLNYLCSTLPLAPWVYSA 195 +D + E A+ A L E VSA G G D+L+ + + LP P V SA Sbjct: 156 VDDERGE-----ADAAALWSLGLGEP-HPVSALHGRGVGDLLDAVLAALPEVPRVGSA 207 Score = 49.2 bits (118), Expect = 1e-06 Identities = 40/143 (27%), Positives = 66/143 (46%), Gaps = 12/143 (8%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI---- 80 VALVG N GKS+L+N+ G + S+V TT V ++ F+DT G+ Sbjct: 214 VALVGKPNVGKSSLLNKLAGEERSVVDDVAGTTVDPVDSLIELGGKTWRFVDTAGLRRRV 273 Query: 81 FNAK--DSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILN 138 A + Y L + I+ A++ +++D+ + +L + + L+L N Sbjct: 274 KQASGHEYYASLRTH---AAIEAAEVAVVLIDASEPISEQDQRVLSMVIEAGRALVLAFN 330 Query: 139 KIDCVKPER--LLEQAEIANKLV 159 K D V +R LE+ EI +L Sbjct: 331 KWDLVDEDRRYYLER-EIDRELA 352 >gnl|CDD|179035 PRK00454, engB, GTP-binding protein YsxC; Reviewed. Length = 196 Score = 54.0 bits (131), Expect = 5e-08 Identities = 43/183 (23%), Positives = 78/183 (42%), Gaps = 37/183 (20%) Query: 25 VALVGATNAGKSTLVNRFVG----AKVSIVTHKVQT---TRSIVRGIVSEKESQIVFLDT 77 +A G +N GKS+L+N A+ S +T T+ I E ++ +D Sbjct: 27 IAFAGRSNVGKSSLINALTNRKNLARTS------KTPGRTQLI---NFFEVNDKLRLVDL 77 Query: 78 PGIF-------NAKDSYHKLMIR--LSWSTIKHADIVCLVVDSHRELK---VNIHDLLKE 125 PG + K+ + KL+ + +K V L++DS LK + + + LKE Sbjct: 78 PG-YGYAKVSKEEKEKWQKLIEEYLRTRENLK---GVVLLIDSRHPLKELDLQMIEWLKE 133 Query: 126 IAKRSSRLILILNKIDCVKP-ERLLEQAEIANKLVFIEKT-FMVSATKGHGCDDVLNYLC 183 ++++L K D +K ER + ++ L F + + S+ K G D++ + Sbjct: 134 YGI---PVLIVLTKADKLKKGERKKQLKKVRKALKFGDDEVILFSSLKKQGIDELRAAIA 190 Query: 184 STL 186 L Sbjct: 191 KWL 193 >gnl|CDD|183417 PRK12299, obgE, GTPase CgtA; Reviewed. Length = 335 Score = 51.6 bits (125), Expect = 2e-07 Identities = 52/180 (28%), Positives = 73/180 (40%), Gaps = 31/180 (17%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ----TTRSIVRGIVS-EKESQIVFLDTPG 79 V LVG NAGKSTL++ AK K+ TT G+V + V D PG Sbjct: 161 VGLVGLPNAGKSTLISAVSAAKP-----KIADYPFTTLHPNLGVVRVDDYKSFVIADIPG 215 Query: 80 IF-NAKDSYHK---LMIRLSWSTIKH---ADIVCLVVDSHRELKV-NIHDLLKEIAKRSS 131 + A + L R +KH ++ +VD V + + E+ K S Sbjct: 216 LIEGA----SEGAGLGHRF----LKHIERTRLLLHLVDIEAVDPVEDYKTIRNELEKYSP 267 Query: 132 RL-----ILILNKIDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCSTL 186 L IL+LNKID + E E+ F++SA G G D++L L L Sbjct: 268 ELADKPRILVLNKIDLLDEEEEREKRAALELAALGGPVFLISAVTGEGLDELLRALWELL 327 >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 = 50.9 bits (123), Expect = 5e-07 Identities = 55/184 (29%), Positives = 80/184 (43%), Gaps = 45/184 (24%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ----TTRSIVRGIVSEKESQ-IVFLDTPG 79 V LVG NAGKSTL++ AK K+ TT G+V + + V D PG Sbjct: 160 VGLVGLPNAGKSTLISAVSAAKP-----KIADYPFTTLVPNLGVVRVDDGRSFVIADIPG 214 Query: 80 -IFNAKDSYHK---LMIRLSWSTIKH---ADIVCLVVDSHRELKVN-IHD---LLKEIAK 128 I A + L R +KH ++ ++D + I D + E+ K Sbjct: 215 LIEGA----SEGAGLGHRF----LKHIERTRVLLHLIDISPLDGRDPIEDYEIIRNELKK 266 Query: 129 RSSRL-----ILILNKIDCVKPERLLEQAEIANKLVFIEK-----TFMVSATKGHGCDDV 178 S L I++LNKID LL++ E+A L ++K F +SA G G D++ Sbjct: 267 YSPELAEKPRIVVLNKID------LLDEEELAELLKELKKALGKPVFPISALTGEGLDEL 320 Query: 179 LNYL 182 L L Sbjct: 321 LYAL 324 >gnl|CDD|182934 PRK11058, PRK11058, GTPase HflX; Provisional. Length = 426 Score = 48.2 bits (115), Expect = 3e-06 Identities = 39/125 (31%), Positives = 60/125 (48%), Gaps = 8/125 (6%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84 V+LVG TNAGKSTL NR A+V T +R I + V DT G + Sbjct: 200 VSLVGYTNAGKSTLFNRITEARVYAADQLFATLDPTLRRIDVADVGETVLADTVGFI--R 257 Query: 85 DSYHKLM--IRLSWSTIKHADIVCLVVD-SHRELKVNI---HDLLKEIAKRSSRLILILN 138 H L+ + + + A ++ VVD + ++ NI + +L+EI +L++N Sbjct: 258 HLPHDLVAAFKATLQETRQATLLLHVVDAADVRVQENIEAVNTVLEEIDAHEIPTLLVMN 317 Query: 139 KIDCV 143 KID + Sbjct: 318 KIDML 322 >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 = 47.9 bits (115), Expect = 4e-06 Identities = 40/174 (22%), Positives = 69/174 (39%), Gaps = 37/174 (21%) Query: 25 VALVGATNAGKSTLVNRFVG----AKVSIVTHKVQT---TRSIVRGIVSEKESQIVFLDT 77 +A G +N GKS+L+N A+ S +T T+ I V++ +D Sbjct: 21 IAFAGRSNVGKSSLINALTNRKKLARTS------KTPGRTQLINFFEVND---GFRLVDL 71 Query: 78 PGIFNAK------DSYHKLMIR--LSWSTIKHADIVCLVVDSHRELK---VNIHDLLKEI 126 PG AK + + KL+ +K V L++D LK + + + L+E Sbjct: 72 PGYGYAKVSKEEKEKWQKLIEEYLEKRENLKG---VVLLMDIRHPLKELDLEMLEWLRE- 127 Query: 127 AKRSSRLILILNKIDCVKP-ERLLEQAEIANKLVFIE---KTFMVSATKGHGCD 176 ++++L K D +K E + +I L + S+ K G D Sbjct: 128 RGIP--VLIVLTKADKLKKSELNKQLKKIKKALKKDADDPSVQLFSSLKKTGID 179 >gnl|CDD|183416 PRK12298, obgE, GTPase CgtA; Reviewed. Length = 390 Score = 46.0 bits (110), Expect = 1e-05 Identities = 48/177 (27%), Positives = 72/177 (40%), Gaps = 29/177 (16%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ----TTRSIVRGIVSEKESQ-IVFLDTPG 79 V L+G NAGKST + AK KV TT G+V + + V D PG Sbjct: 162 VGLLGLPNAGKSTFIRAVSAAK-----PKVADYPFTTLVPNLGVVRVDDERSFVVADIPG 216 Query: 80 IFNAKDSYHKLMIRLSWSTIKHAD--------IVCLVVDSHRELKVNIHDLLKEIAKRSS 131 + L IR +KH + I +D ++ N ++ E+ K S Sbjct: 217 LIEGASEGAGLGIRF----LKHLERCRVLLHLIDIAPIDGSDPVE-NARIIINELEKYSP 271 Query: 132 RL-----ILILNKIDCVKPERLLEQA-EIANKLVFIEKTFMVSATKGHGCDDVLNYL 182 +L L+ NKID + E E+A I L + +++SA G G ++ L Sbjct: 272 KLAEKPRWLVFNKIDLLDEEEAEERAKAIVEALGWEGPVYLISAASGLGVKELCWDL 328 >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 = 44.4 bits (106), Expect = 4e-05 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 3/57 (5%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIF 81 +VG N GKSTL+NR G KV+ V ++ T+ +S+ + LDTPGI Sbjct: 121 AMIVGIPNVGKSTLINRLAGKKVAKVGNRPGVTKGQQWIKLSD---GLELLDTPGIL 174 >gnl|CDD|116265 pfam07650, KH_2, KH domain. Length = 55 Score = 42.8 bits (102), Expect = 1e-04 Identities = 15/33 (45%), Positives = 19/33 (57%) Query: 246 QVIYVERPSQKKIMLGKNGQNIKTISLEAKKEI 278 VI V R SQ I++GK G NIK + E +K Sbjct: 1 AVIVVIRTSQPGIVIGKGGSNIKKLGKELRKRF 33 >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 = 42.6 bits (101), Expect = 1e-04 Identities = 43/165 (26%), Positives = 62/165 (37%), Gaps = 34/165 (20%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIF-NA 83 + L+G + GK+TL G + K Q I DTPG + Sbjct: 4 IMLIGRSGCGKTTLTQALNGE--ELKYKKTQAIEFSDNMI-----------DTPGEYLEN 50 Query: 84 KDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKV------NIHDLLKEIAKRSSRLILIL 137 + Y L++ T AD++ LV D+ V ++ K + I I+ Sbjct: 51 RRFYSALIV-----TAADADVIALVQDATEPWSVFPPGFASM--FNKPV-------IGII 96 Query: 138 NKIDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYL 182 KID K E +E E EK F VSA G D++ YL Sbjct: 97 TKIDLAKDEANIEMVEEWLNNAGAEKIFEVSAVTNEGIDELFAYL 141 >gnl|CDD|181957 PRK09563, rbgA, GTPase YlqF; Reviewed. Length = 287 Score = 41.3 bits (98), Expect = 3e-04 Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 3/54 (5%) Query: 28 VGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIF 81 +G N GKSTL+NR G K++ ++ T++ + + + LDTPGI Sbjct: 127 IGIPNVGKSTLINRLAGKKIAKTGNRPGVTKAQQWIKLGK---GLELLDTPGIL 177 Score = 28.2 bits (64), Expect = 3.0 Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 14/55 (25%) Query: 99 IKHADIVCLVVD------SHRELKVNIHDLLKEIAKRSSRLILILNKIDCVKPER 147 +K D+V V+D S + ++ +I R +LILNK D PE Sbjct: 22 LKLVDVVIEVLDARIPLSSE-------NPMIDKIIGNKPR-LLILNKSDLADPEV 68 >gnl|CDD|131580 TIGR02528, EutP, ethanolamine utilization protein, EutP. This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site. Length = 142 Score = 40.1 bits (94), Expect = 7e-04 Identities = 33/161 (20%), Positives = 65/161 (40%), Gaps = 22/161 (13%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPG-IFNA 83 + +G+ GK+TL G ++ + T+++ E + DTPG Sbjct: 3 IMFIGSVGCGKTTLTQALQGEEI-----LYKKTQAV------EYNDGAI--DTPGEYVEN 49 Query: 84 KDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCV 143 + Y L++ T AD++ LV + K +I ++ KID Sbjct: 50 RRLYSALIV-----TAADADVIALVQSATDPESRFPPGFASIFVK---PVIGLVTKIDLA 101 Query: 144 KPERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYLCS 184 + + +E+A+ + E F +S+ G + +++YL S Sbjct: 102 EADVDIERAKELLETAGAEPIFEISSVDEQGLEALVDYLNS 142 >gnl|CDD|184214 PRK13657, PRK13657, cyclic beta-1,2-glucan ABC transporter; Provisional. Length = 588 Score = 39.9 bits (94), Expect = 0.001 Identities = 20/49 (40%), Positives = 24/49 (48%), Gaps = 14/49 (28%) Query: 4 GEITFFNEHKDFVQDNSRSG------------CVALVGATNAGKSTLVN 40 G + F + F DNSR G VA+VG T AGKSTL+N Sbjct: 333 GAVEF--DDVSFSYDNSRQGVEDVSFEAKPGQTVAIVGPTGAGKSTLIN 379 >gnl|CDD|179346 PRK01889, PRK01889, GTPase RsgA; Reviewed. Length = 356 Score = 38.0 bits (89), Expect = 0.003 Identities = 22/70 (31%), Positives = 33/70 (47%), Gaps = 24/70 (34%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ----------TTRSIVR----GIVSEKES 70 VAL+G++ GKSTLVN +G +V T V+ T R + G++ Sbjct: 198 VALLGSSGVGKSTLVNALLGEEV-QKTGAVREDDSKGRHTTTHRELHPLPSGGLL----- 251 Query: 71 QIVFLDTPGI 80 +DTPG+ Sbjct: 252 ----IDTPGM 257 >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 = 37.4 bits (87), Expect = 0.004 Identities = 37/149 (24%), Positives = 65/149 (43%), Gaps = 4/149 (2%) Query: 29 GATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAKDSYH 88 G N GKSTL N GA V + T G + + I +D PGI++ Sbjct: 1 GNPNVGKSTLFNALTGANQ-TVGNWPGVTVEKKEGKLGFQGEDIEIVDLPGIYSLTTFSL 59 Query: 89 KLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNKIDCVKPERL 148 + + + + D+V VVD+ L+ N++ L ++ + +IL LN +D + + + Sbjct: 60 EEEVARDYLLNEKPDLVVNVVDA-SNLERNLY-LTLQLLELGIPMILALNLVDEAEKKGI 117 Query: 149 LEQAEIANKLVFIEKTFMVSATKGHGCDD 177 E + + + SAT+G G + Sbjct: 118 RIDEEKLEERLGV-PVVPTSATEGRGIER 145 >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 = 37.4 bits (87), Expect = 0.005 Identities = 25/125 (20%), Positives = 51/125 (40%), Gaps = 16/125 (12%) Query: 25 VALVGATNAGKSTLVNRFVGA-KVSIVTHKVQTTRSIVRGIVSEKESQIV-FLDTPGIFN 82 V ++G +GKS+L+++ VG + ++Q V + + +++++ D G Sbjct: 2 VVVIGDKGSGKSSLLSQLVGGEFPPEIPEEIQGDTLAVDTLEVDGDTELLHIWDFGG--- 58 Query: 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHR----ELKVNIHDLLKEIAKRSSR--LILI 136 + + +K AD + LV D + L + K + +IL+ Sbjct: 59 -----REELKFEHIIFMKTADAILLVYDLTDRESLNRVSRLIAWLPHLRKLGKKIPVILV 113 Query: 137 LNKID 141 NK D Sbjct: 114 GNKFD 118 >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 = 36.1 bits (84), Expect = 0.014 Identities = 22/62 (35%), Positives = 29/62 (46%), Gaps = 6/62 (9%) Query: 25 VALVGATNAGKSTLVNR----FVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI 80 V +VG TN GKS+L+N+ G K I T T + I + + DTPGI Sbjct: 157 VYVVGVTNVGKSSLINKLLKQNNGDKDVITTSPFPGTTLDLIEIPLDDGHSLY--DTPGI 214 Query: 81 FN 82 N Sbjct: 215 IN 216 Score = 33.0 bits (76), Expect = 0.11 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 7/66 (10%) Query: 123 LKEIAKRSSRLILILNKIDC----VKPERLLE--QAEIANKLVFIEKTFMVSATKGHGCD 176 LK + ++L+ NKID V ++ E + + +VSA KG+G D Sbjct: 84 LKRFVGGN-PVLLVGNKIDLLPKSVNLSKIKEWMKKRAKELGLKPVDIILVSAKKGNGID 142 Query: 177 DVLNYL 182 ++L+ + Sbjct: 143 ELLDKI 148 >gnl|CDD|184332 PRK13796, PRK13796, GTPase YqeH; Provisional. Length = 365 Score = 35.2 bits (82), Expect = 0.023 Identities = 25/64 (39%), Positives = 31/64 (48%), Gaps = 8/64 (12%) Query: 25 VALVGATNAGKSTLVNR----FVGAKVSIVT-HKVQTTRSIVRGIVSEKESQIVFLDTPG 79 V +VG TN GKSTL+NR G K I T TT + I + S + DTPG Sbjct: 163 VYVVGVTNVGKSTLINRIIKEITGEKDVITTSRFPGTTLDKIE-IPLDDGSFLY--DTPG 219 Query: 80 IFNA 83 I + Sbjct: 220 IIHR 223 Score = 30.6 bits (70), Expect = 0.56 Identities = 17/56 (30%), Positives = 29/56 (51%), Gaps = 8/56 (14%) Query: 134 ILILNKIDC----VKPERLLE--QAEIANKL-VFIEKTFMVSATKGHGCDDVLNYL 182 +L+ NK D VK ++ + E A +L + ++SA KGHG D++L + Sbjct: 100 LLVGNKADLLPKSVKKNKVKNWLRQE-AKELGLRPVDVVLISAQKGHGIDELLEAI 154 >gnl|CDD|129582 TIGR00491, aIF-2, translation initiation factor aIF-2/yIF-2. This model describes archaeal and eukaryotic orthologs of bacterial IF-2. Like IF-2, it helps convey the initiator tRNA to the ribosome, although the initiator is N-formyl-Met in bacteria and Met here. This protein is not closely related to the subunits of eIF-2 of eukaryotes, which is also involved in the initiation of translation. The aIF-2 of Methanococcus jannaschii contains a large intein interrupting a region of very strongly conserved sequence very near the amino end; this model does not correctly align the sequences from Methanococcus jannaschii and Pyrococcus horikoshii in this region. Length = 590 Score = 34.8 bits (80), Expect = 0.029 Identities = 33/140 (23%), Positives = 60/140 (42%), Gaps = 25/140 (17%) Query: 19 NSRSGCVALVGATNAGKSTLVNRFVGAKVSI-----VTHKVQTTR---SIVRGI------ 64 RS V+++G + GK+TL+++ G+ V+ +T + T ++ GI Sbjct: 1 KLRSPIVSVLGHVDHGKTTLLDKIRGSAVAKREAGGITQHIGATEIPMDVIEGICGDLLK 60 Query: 65 ---VSEKESQIVFLDTPGIFNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHD 121 + K ++F+DTPG H+ L AD+ L+VD + K + Sbjct: 61 KFKIRLKIPGLLFIDTPG--------HEAFTNLRKRGGALADLAILIVDINEGFKPQTQE 112 Query: 122 LLKEIAKRSSRLILILNKID 141 L + + ++ NKID Sbjct: 113 ALNILRMYKTPFVVAANKID 132 >gnl|CDD|131816 TIGR02769, nickel_nikE, nickel import ATP-binding protein NikE. This family represents the NikE subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. Length = 265 Score = 34.8 bits (80), Expect = 0.032 Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 9/70 (12%) Query: 24 CVALVGATNAGKSTLVNRFVG------AKVSIVTHKV-QTTRSIVRGIVSEKESQIVFLD 76 V L+G + GKSTL +G VS + Q R R ++ Q+VF D Sbjct: 39 TVGLLGRSGCGKSTLARLLLGLEKPAQGTVSFRGQDLYQLDRKQRRAF--RRDVQLVFQD 96 Query: 77 TPGIFNAKDS 86 +P N + + Sbjct: 97 SPSAVNPRMT 106 >gnl|CDD|162115 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase, VirB4 family. Type IV secretion systems are found in Gram-negative pathogens. They export proteins, DNA, or complexes in different systems and are related to plasmid conjugation systems. This model represents related ATPases that include VirB4 in Agrobacterium tumefaciens (DNA export) CagE in Helicobacter pylori (protein export) and plasmid TraB (conjugation). Length = 785 Score = 34.6 bits (80), Expect = 0.033 Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%) Query: 8 FFNEHKDFVQDNSRSGCVALVGATNAGKSTLVN 40 +FN H V+D G + G T +GK+TL+N Sbjct: 423 YFNFH---VRDAKVLGHTLIFGPTGSGKTTLLN 452 >gnl|CDD|183415 PRK12297, obgE, GTPase CgtA; Reviewed. Length = 424 Score = 34.3 bits (80), Expect = 0.038 Identities = 53/221 (23%), Positives = 87/221 (39%), Gaps = 54/221 (24%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQ----TTRSIVRGIV-SEKESQIVFLDTPG 79 V LVG N GKSTL++ AK K+ TT G+V ++ V D PG Sbjct: 161 VGLVGFPNVGKSTLLSVVSNAKP-----KIANYHFTTLVPNLGVVETDDGRSFVMADIPG 215 Query: 80 -IFNAKDSYHK---LMIRLSWSTIKHAD---IVCLVVD----SHRELKVNIHDLLKEIAK 128 I A + L + ++H + ++ V+D R+ + + KE+ Sbjct: 216 LIEGA----SEGVGLGHQF----LRHIERTRVIVHVIDMSGSEGRDPIEDYEKINKELKL 267 Query: 129 RSSRL-----ILILNKIDCVKPERLLEQAEIANKL--VFIEKTFMVSATKGHGCDDVLNY 181 + RL I++ NK+D L E E + K F +SA G G D++L Sbjct: 268 YNPRLLERPQIVVANKMD------LPEAEENLEEFKEKLGPKVFPISALTGQGLDELLYA 321 Query: 182 LCSTLPLAPWVYSADQISDLPMFHFTAEITREKLFLHLHKE 222 + A+ + + P F E E+++ +E Sbjct: 322 V------------AELLEETPEFPLEEEEVEEEVYYKFEEE 350 >gnl|CDD|161900 TIGR00487, IF-2, translation initiation factor IF-2. This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam model GTP_EFTU. Length = 587 Score = 34.0 bits (78), Expect = 0.054 Identities = 41/170 (24%), Positives = 71/170 (41%), Gaps = 24/170 (14%) Query: 21 RSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSI-VRGIVSEKESQIVFLDTPG 79 R V ++G + GK++L++ KV+ T+ I + +E I FLDTPG Sbjct: 86 RPPVVTIMGHVDHGKTSLLDSIRKTKVA-QGEAGGITQHIGAYHVENEDGKMITFLDTPG 144 Query: 80 IFNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRLILILNK 139 H+ + K DIV LVV + + + + + +I+ +NK Sbjct: 145 --------HEAFTSMRARGAKVTDIVVLVVAADDGVMPQTIEAISHAKAANVPIIVAINK 196 Query: 140 ID--CVKPERLLEQ--------AEIANKLVFIEKTFMVSATKGHGCDDVL 179 ID P+R+ ++ + +F+ VSA G G D++L Sbjct: 197 IDKPEANPDRVKQELSEYGLVPEDWGGDTIFV----PVSALTGDGIDELL 242 >gnl|CDD|185557 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2 gamma subunit; Provisional. Length = 460 Score = 33.4 bits (77), Expect = 0.075 Identities = 24/72 (33%), Positives = 37/72 (51%), Gaps = 12/72 (16%) Query: 125 EIAKRSSRLILILNKIDCVKPERLLEQ-AEIANKLVFIEKTFM-------VSATKGHGCD 176 EI K +I++ NKID VK + +Q EI N F++ T +SA + D Sbjct: 167 EIMKLK-HIIILQNKIDLVKEAQAQDQYEEIRN---FVKGTIADNAPIIPISAQLKYNID 222 Query: 177 DVLNYLCSTLPL 188 VL Y+C+ +P+ Sbjct: 223 VVLEYICTQIPI 234 >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 = 33.3 bits (76), Expect = 0.088 Identities = 36/168 (21%), Positives = 66/168 (39%), Gaps = 19/168 (11%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVS--EKESQIVFLDTPGIFN 82 +A G + GK+TL+ G + + + +I G + ++ F+D PG Sbjct: 3 IATAGHVDHGKTTLLKALTGIAADRLPEEKKRGMTIDLGFAYFPLPDYRLGFIDVPG--- 59 Query: 83 AKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSS--RLILILNKI 140 H+ I + + D LVVD+ + + L + I+++ K Sbjct: 60 -----HEKFISNAIAGGGGIDAALLVVDADEGVMTQTGEHLA-VLDLLGIPHTIVVITKA 113 Query: 141 DCVKPERL----LEQAEIANKLVFIE--KTFMVSATKGHGCDDVLNYL 182 D V E + + +I N +F++ K F SA G G ++ L Sbjct: 114 DRVNEEEIKRTEMFMKQILNSYIFLKNAKIFKTSAKTGQGIGELKKEL 161 >gnl|CDD|184050 PRK13430, PRK13430, F0F1 ATP synthase subunit delta; Provisional. Length = 271 Score = 31.8 bits (73), Expect = 0.20 Identities = 17/56 (30%), Positives = 21/56 (37%), Gaps = 8/56 (14%) Query: 18 DNSRSGCVALV--GATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQ 71 D RS AL K LV R G KVS T +V V ++ S+ Sbjct: 42 DRERSLRRALTDPARPPEAKVELVKRLFGGKVS------PATLEVVSDAVRQRWSR 91 >gnl|CDD|178972 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed. Length = 232 Score = 32.0 bits (74), Expect = 0.20 Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 8/51 (15%) Query: 244 IRQVIYVERPSQKKIMLGKNGQNIKTISLEAKKEIAEILEQPVHL-ILFVK 293 +R I+ RP I++GK G I+ + +KE+ ++ +PV + I+ VK Sbjct: 64 VRVTIHTARPG---IVIGKKGAEIEKL----RKELEKLTGKPVQINIVEVK 107 >gnl|CDD|182733 PRK10790, PRK10790, putative multidrug transporter membrane\ATP-binding components; Provisional. Length = 592 Score = 32.0 bits (73), Expect = 0.20 Identities = 13/22 (59%), Positives = 16/22 (72%) Query: 23 GCVALVGATNAGKSTLVNRFVG 44 G VALVG T +GKSTL + +G Sbjct: 368 GFVALVGHTGSGKSTLASLLMG 389 >gnl|CDD|183014 PRK11174, PRK11174, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed. Length = 588 Score = 31.7 bits (73), Expect = 0.24 Identities = 10/20 (50%), Positives = 16/20 (80%) Query: 25 VALVGATNAGKSTLVNRFVG 44 +ALVG + AGK++L+N +G Sbjct: 379 IALVGPSGAGKTSLLNALLG 398 >gnl|CDD|183414 PRK12296, obgE, GTPase CgtA; Reviewed. Length = 500 Score = 31.8 bits (73), Expect = 0.25 Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 1/56 (1%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI 80 V LVG +AGKS+L++ AK I + TT G+V +++ D PG+ Sbjct: 162 VGLVGFPSAGKSSLISALSAAKPKIADYPF-TTLVPNLGVVQAGDTRFTVADVPGL 216 >gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed. Length = 298 Score = 31.3 bits (72), Expect = 0.32 Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 10/61 (16%) Query: 27 LVGATNAGKSTLVNRFVG---AKVSIVTHKVQ----TTRSIVRGIVSEKESQIVFLDTPG 79 L G + GKSTL+N K ++ + TT V ++ DTPG Sbjct: 169 LAGQSGVGKSTLLNALAPDLELKTGEISEALGRGKHTTTH-VELYDLPGGGLLI--DTPG 225 Query: 80 I 80 Sbjct: 226 F 226 Score = 27.9 bits (63), Expect = 3.6 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 9/53 (16%) Query: 134 ILILNKIDCVKPERLLEQAEIANKLVFIEK----TFMVSATKGHGCDDVLNYL 182 I++LNKID + + L E E+ +SA +G G D++ L Sbjct: 115 IIVLNKIDLL--DDLEEARELLA---LYRAIGYDVLELSAKEGEGLDELKPLL 162 >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 = 31.1 bits (71), Expect = 0.35 Identities = 12/16 (75%), Positives = 14/16 (87%) Query: 25 VALVGATNAGKSTLVN 40 VALVG + AGKSTL+N Sbjct: 351 VALVGPSGAGKSTLLN 366 >gnl|CDD|179790 PRK04213, PRK04213, GTP-binding protein; Provisional. Length = 201 Score = 31.0 bits (71), Expect = 0.44 Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 5/55 (9%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPG 79 + VG +N GKSTLV G KV V + TR + + D PG Sbjct: 12 IVFVGRSNVGKSTLVRELTGKKVR-VGKRPGVTRKPNHYDWGDF----ILTDLPG 61 >gnl|CDD|131258 TIGR02203, MsbA_lipidA, lipid A export permease/ATP-binding protein MsbA. This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes. Length = 571 Score = 30.8 bits (70), Expect = 0.48 Identities = 14/22 (63%), Positives = 16/22 (72%), Gaps = 3/22 (13%) Query: 25 VALVGATNAGKSTLVN---RFV 43 VALVG + +GKSTLVN RF Sbjct: 361 VALVGRSGSGKSTLVNLIPRFY 382 >gnl|CDD|181948 PRK09554, feoB, ferrous iron transport protein B; Reviewed. Length = 772 Score = 30.5 bits (69), Expect = 0.58 Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 11/62 (17%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSI-----VTHKVQTTRSIVRGIVSEKESQIVFLDTPG 79 + L+G N+GK+TL N+ GA+ + VT + + G S + Q+ +D PG Sbjct: 6 IGLIGNPNSGKTTLFNQLTGARQRVGNWAGVTVERKE------GQFSTTDHQVTLVDLPG 59 Query: 80 IF 81 + Sbjct: 60 TY 61 >gnl|CDD|181413 PRK08406, PRK08406, transcription elongation factor NusA-like protein; Validated. Length = 140 Score = 30.6 bits (70), Expect = 0.58 Identities = 19/48 (39%), Positives = 26/48 (54%), Gaps = 5/48 (10%) Query: 230 VTEKWEEKKDGSILIRQVIYVE-RPSQKKIMLGKNGQNIKTISLEAKK 276 V +KK+G +V YVE P K I +GKNG+NI+ AK+ Sbjct: 87 VRSVTIKKKNG----DKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKR 130 >gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional. Length = 741 Score = 30.6 bits (69), Expect = 0.59 Identities = 12/23 (52%), Positives = 16/23 (69%) Query: 25 VALVGATNAGKSTLVNRFVGAKV 47 +A+VG AGKST +N VG +V Sbjct: 72 LAIVGTMKAGKSTTINAIVGTEV 94 >gnl|CDD|183713 PRK12740, PRK12740, elongation factor G; Reviewed. Length = 668 Score = 30.1 bits (69), Expect = 0.80 Identities = 13/53 (24%), Positives = 22/53 (41%), Gaps = 11/53 (20%) Query: 146 ERLLEQAEIANKLVF--IEK---------TFMVSATKGHGCDDVLNYLCSTLP 187 E+ LE E++ + + + K F SA K G +L+ + LP Sbjct: 210 EKYLEGEELSEEEIKAGLRKATLAGEIVPVFCGSALKNKGVQRLLDAVVDYLP 262 >gnl|CDD|130260 TIGR01192, chvA, glucan exporter ATP-binding protein. This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related. Length = 585 Score = 29.9 bits (67), Expect = 0.83 Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 14/49 (28%) Query: 4 GEITFFNEHKDFVQDNSRSGC------------VALVGATNAGKSTLVN 40 G + F + +F NS G VA+VG T AGK+TL+N Sbjct: 333 GAVEFRHITFEFA--NSSQGVFDVSFEAKAGQTVAIVGPTGAGKTTLIN 379 >gnl|CDD|131633 TIGR02584, cas_NE0113, CRISPR-associated protein, NE0113 family. Members of this minor CRISPR-associated (Cas) protein family are found in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum. Length = 209 Score = 29.8 bits (67), Expect = 0.84 Identities = 10/38 (26%), Positives = 16/38 (42%) Query: 244 IRQVIYVERPSQKKIMLGKNGQNIKTISLEAKKEIAEI 281 IR Y R + ++G + EA E+AE+ Sbjct: 162 IRGFYYPPRKGPILEIRTRDGPPAPADTSEAVVELAEL 199 >gnl|CDD|183705 PRK12727, PRK12727, flagellar biosynthesis regulator FlhF; Provisional. Length = 559 Score = 30.0 bits (67), Expect = 0.88 Identities = 19/46 (41%), Positives = 23/46 (50%), Gaps = 10/46 (21%) Query: 21 RSGCVALVGATNAGKST----LVNRFVGAK----VSIVTHKVQTTR 58 R G +ALVG T AGK+T L RF V++VT T R Sbjct: 349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVT--TDTQR 392 >gnl|CDD|164820 PHA00520, PHA00520, packaging NTPase P4. Length = 330 Score = 29.8 bits (67), Expect = 0.95 Identities = 9/19 (47%), Positives = 13/19 (68%) Query: 22 SGCVALVGATNAGKSTLVN 40 SG +VG T +GK+ L+N Sbjct: 124 SGVEVVVGGTGSGKTPLLN 142 >gnl|CDD|162685 TIGR02073, PBP_1c, penicillin-binding protein 1C. This subfamily of the penicillin binding proteins includes the member from E. coli designated penicillin-binding protein 1C. Members have both transglycosylase and transpeptidase domains and are involved in forming cross-links in the late stages of peptidoglycan biosynthesis. All members of this subfamily are presumed to have the same basic function. Length = 727 Score = 29.7 bits (67), Expect = 0.97 Identities = 16/44 (36%), Positives = 22/44 (50%) Query: 240 GSILIRQVIYVERPSQKKIMLGKNGQNIKTISLEAKKEIAEILE 283 GS L Q+ + P + + GK Q + I LEA+ EILE Sbjct: 85 GSTLTMQLARLLDPELSRTLTGKLRQMWRAIQLEARYSKREILE 128 >gnl|CDD|180787 PRK06995, flhF, flagellar biosynthesis regulator FlhF; Validated. Length = 484 Score = 29.6 bits (67), Expect = 1.0 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 8/39 (20%) Query: 21 RSGCVALVGATNAGKST----LVNRFV---GA-KVSIVT 51 R G AL+G T GK+T L R V GA KV+++T Sbjct: 255 RGGVFALMGPTGVGKTTTTAKLAARCVMRHGASKVALLT 293 >gnl|CDD|182918 PRK11036, PRK11036, putative S-adenosyl-L-methionine-dependent methyltransferase; Provisional. Length = 255 Score = 29.5 bits (67), Expect = 1.1 Identities = 16/30 (53%), Positives = 20/30 (66%), Gaps = 1/30 (3%) Query: 274 AKKEIAEILEQPVHLILFVKVQKDWGHDPK 303 A ++IA+ LE PV LILF V +W DPK Sbjct: 101 AAQDIAQHLETPVDLILFHAVL-EWVADPK 129 >gnl|CDD|182528 PRK10535, PRK10535, macrolide transporter ATP-binding /permease protein; Provisional. Length = 648 Score = 29.7 bits (67), Expect = 1.1 Identities = 11/16 (68%), Positives = 15/16 (93%) Query: 25 VALVGATNAGKSTLVN 40 VA+VGA+ +GKSTL+N Sbjct: 37 VAIVGASGSGKSTLMN 52 >gnl|CDD|184132 PRK13547, hmuV, hemin importer ATP-binding subunit; Provisional. Length = 272 Score = 29.4 bits (66), Expect = 1.2 Identities = 15/43 (34%), Positives = 21/43 (48%), Gaps = 4/43 (9%) Query: 6 ITFFNEHKDFVQDNS---RSGCV-ALVGATNAGKSTLVNRFVG 44 + H+ ++D S G V AL+G AGKSTL+ G Sbjct: 7 LHVARRHRAILRDLSLRIEPGRVTALLGRNGAGKSTLLKALAG 49 >gnl|CDD|148992 pfam07693, KAP_NTPase, KAP family P-loop domain. The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side. Length = 301 Score = 29.3 bits (66), Expect = 1.2 Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 4/73 (5%) Query: 102 ADIVCLVVDSHRELKVNIHDLLKEIAKR----SSRLILILNKIDCVKPERLLEQAEIANK 157 + L ++ ++L+ I +L +IA R+++I++ +D +PE +E E Sbjct: 127 KSLKLLSIEPLKKLQTEIEELRTDIASTLDDLQKRIVVIIDDLDRCEPEEAVELLEAVRL 186 Query: 158 LVFIEKTFMVSAT 170 L + A Sbjct: 187 LFDFPNVVFILAY 199 >gnl|CDD|182479 PRK10463, PRK10463, hydrogenase nickel incorporation protein HypB; Provisional. Length = 290 Score = 29.4 bits (66), Expect = 1.3 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 10/55 (18%) Query: 134 ILILNKIDCVKP------ERLLEQAEIANKLVFIEKTFMVSATKGHGCDDVLNYL 182 +++LNK+D + P E+ + A N + I ++SAT G G D LN+L Sbjct: 234 LMLLNKVDLL-PYLNFDVEKCIACAREVNPEIEI---ILISATSGEGMDQWLNWL 284 >gnl|CDD|162997 TIGR02746, TraC-F-type, type-IV secretion system protein TraC. The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase. Length = 797 Score = 29.2 bits (66), Expect = 1.4 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 10/53 (18%) Query: 4 GEITFFNEHKDFVQDNSRSGCVALVGATNAGKSTLVN------RFVGAKVSIV 50 G+++ F D +S + +A+VG + AGKS + G KV ++ Sbjct: 416 GQLSAF----DPFDSDSTNYNIAVVGGSGAGKSFFMQELIVDNLSRGGKVWVI 464 >gnl|CDD|152038 pfam11602, NTPase_P4, ATPase P4 of dsRNA bacteriophage phi-12. P4 is a packaging motor which is involved in the packaging of phi-12 genome into preformed capsids using ATP. P4 is located at the vertices of the icosahedral capsid. ATP drives RNA translocation through cooperative conformational changes. Length = 320 Score = 28.8 bits (64), Expect = 1.7 Identities = 9/22 (40%), Positives = 12/22 (54%) Query: 19 NSRSGCVALVGATNAGKSTLVN 40 SG V + G T +GKS +N Sbjct: 108 GIYSGMVIVTGKTGSGKSEALN 129 >gnl|CDD|172889 PRK14413, PRK14413, membrane protein; Provisional. Length = 197 Score = 29.0 bits (65), Expect = 1.8 Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%) Query: 29 GATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIV 61 G+ N G ST V R VG K+SI+T + + I+ Sbjct: 35 GSGNIG-STNVKRIVGTKISIITQIIDVLKGII 66 >gnl|CDD|179775 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed. Length = 207 Score = 28.7 bits (65), Expect = 1.9 Identities = 15/39 (38%), Positives = 22/39 (56%), Gaps = 11/39 (28%) Query: 245 RQVIYVERPSQKKIMLGKNGQNIKTISLEAKKEIAEILE 283 R IY ERP +++G+ G+NI +E+ EILE Sbjct: 43 RITIYAERPG---MVIGRGGKNI--------RELTEILE 70 >gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Length = 529 Score = 28.9 bits (65), Expect = 2.0 Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 6/48 (12%) Query: 25 VALVGATNAGKSTLVNRFVGA------KVSIVTHKVQTTRSIVRGIVS 66 VA++G + +GKSTL+ G +V++ V + + +R +S Sbjct: 364 VAILGPSGSGKSTLLMLLTGLLDPLQGEVTLDGVSVSSLQDELRRRIS 411 >gnl|CDD|177488 PHA02774, PHA02774, E1; Provisional. Length = 613 Score = 28.7 bits (65), Expect = 2.0 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 4/54 (7%) Query: 6 ITFFNEHKDFVQDNSRSGCVALVGATNAGKSTLVN---RFVGAKV-SIVTHKVQ 55 I+F KDF++ + C+ + G + GKS +F+ KV S V K Sbjct: 418 ISFLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKSH 471 >gnl|CDD|183016 PRK11176, PRK11176, lipid transporter ATP-binding/permease protein; Provisional. Length = 582 Score = 28.8 bits (65), Expect = 2.0 Identities = 12/21 (57%), Positives = 15/21 (71%), Gaps = 3/21 (14%) Query: 25 VALVGATNAGKSTLVN---RF 42 VALVG + +GKST+ N RF Sbjct: 372 VALVGRSGSGKSTIANLLTRF 392 >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 = 28.5 bits (63), Expect = 2.2 Identities = 21/126 (16%), Positives = 38/126 (30%), Gaps = 14/126 (11%) Query: 21 RSGCVALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGI 80 + +VG +GK+TL A+ + G +E L Sbjct: 1 PGEVILIVGPPGSGKTTLARAL--ARELGPPGGGV---IYIDGEDILEEVLDQLLLIIVG 55 Query: 81 FNAKDSYHKLMIRLSWSTIKHADIVCLVVD---------SHRELKVNIHDLLKEIAKRSS 131 +L +RL+ + + L++D L + L + K Sbjct: 56 GKKASGSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKSEK 115 Query: 132 RLILIL 137 L +IL Sbjct: 116 NLTVIL 121 >gnl|CDD|181982 PRK09602, PRK09602, translation-associated GTPase; Reviewed. Length = 396 Score = 28.6 bits (65), Expect = 2.2 Identities = 9/16 (56%), Positives = 10/16 (62%) Query: 25 VALVGATNAGKSTLVN 40 + LVG N GKST N Sbjct: 4 IGLVGKPNVGKSTFFN 19 >gnl|CDD|185364 PRK15467, PRK15467, ethanolamine utilization protein EutP; Provisional. Length = 158 Score = 28.4 bits (63), Expect = 2.3 Identities = 33/121 (27%), Positives = 50/121 (41%), Gaps = 26/121 (21%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPG-IFNA 83 +A VGA AGK+TL N G + K Q +G + DTPG F+ Sbjct: 4 IAFVGAVGAGKTTLFNALQGNYT--LARKTQAVEFNDKGDI----------DTPGEYFSH 51 Query: 84 KDSYHKLMIRLSWSTIKHADIVCLV---VDSHRELKVNIHDLLKEIAKRSSRLILILNKI 140 YH L+ +T++ D++ V D L + D+ S R I +++K Sbjct: 52 PRWYHALI-----TTLQDVDMLIYVHGANDPESRLPAGLLDI-----GVSKRQIAVISKT 101 Query: 141 D 141 D Sbjct: 102 D 102 >gnl|CDD|181256 PRK08154, PRK08154, anaerobic benzoate catabolism transcriptional regulator; Reviewed. Length = 309 Score = 28.4 bits (64), Expect = 2.4 Identities = 10/22 (45%), Positives = 14/22 (63%) Query: 17 QDNSRSGCVALVGATNAGKSTL 38 + +R +AL+G AGKSTL Sbjct: 128 RRAARRRRIALIGLRGAGKSTL 149 >gnl|CDD|131377 TIGR02324, CP_lyasePhnL, phosphonate C-P lyase system protein PhnL. Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se. Length = 224 Score = 28.5 bits (64), Expect = 2.5 Identities = 11/15 (73%), Positives = 12/15 (80%) Query: 24 CVALVGATNAGKSTL 38 CVAL G + AGKSTL Sbjct: 36 CVALSGPSGAGKSTL 50 >gnl|CDD|184205 PRK13646, cbiO, cobalt transporter ATP-binding subunit; Provisional. Length = 286 Score = 28.2 bits (63), Expect = 2.8 Identities = 27/100 (27%), Positives = 43/100 (43%), Gaps = 29/100 (29%) Query: 26 ALVGATNAGKSTLVNRFVG------AKVSI----VTHK-----VQTTRSIVRGIVSEKES 70 A+VG T +GKSTL+ V++ +THK ++ R + + ES Sbjct: 37 AIVGQTGSGKSTLIQNINALLKPTTGTVTVDDITITHKTKDKYIRPVRKRIGMVFQFPES 96 Query: 71 QIVFLDT--------PGIFN-----AKDSYHKLMIRLSWS 97 Q+ F DT P F K+ H+L++ L +S Sbjct: 97 QL-FEDTVEREIIFGPKNFKMNLDEVKNYAHRLLMDLGFS 135 >gnl|CDD|130082 TIGR01009, rpsC_bact, ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea. Length = 211 Score = 28.1 bits (63), Expect = 2.9 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 8/51 (15%) Query: 244 IRQVIYVERPSQKKIMLGKNGQNIKTISLEAKKEIAEILEQPVHL-ILFVK 293 IR I+ RP I++GK G I+ + +K++ ++ + V + I VK Sbjct: 64 IRVTIHTARPG---IVIGKKGSEIEKL----RKDLQKLTGKEVQINIAEVK 107 >gnl|CDD|162700 TIGR02095, glgA, glycogen/starch synthases, ADP-glucose type. This family consists of glycogen (or starch) synthases that use ADP-glucose (EC 2.4.1.21), rather than UDP-glucose (EC 2.4.1.11) as in animals, as the glucose donor. This enzyme is found in bacteria and plants. Whether the name given is glycogen synthase or starch synthase depends on context, and therefore on substrate. Length = 473 Score = 28.0 bits (63), Expect = 2.9 Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 9/50 (18%) Query: 99 IKHADIVCLVVDSH-RELK-----VNIHDLLKEIAKRSSRLILILNKIDC 142 I +AD V V ++ RE+ + +LK RS +L ILN ID Sbjct: 203 IVYADRVTTVSPTYAREILTPEFGYGLDGVLKA---RSGKLRGILNGIDT 249 >gnl|CDD|182996 PRK11147, PRK11147, ABC transporter ATPase component; Reviewed. Length = 635 Score = 28.0 bits (63), Expect = 3.3 Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 4/29 (13%) Query: 11 EHKDF-VQDNSRSGCVALVGATNAGKSTL 38 ++ + ++DN R V LVG AGKSTL Sbjct: 20 DNAELHIEDNER---VCLVGRNGAGKSTL 45 >gnl|CDD|178665 PLN03118, PLN03118, Rab family protein; Provisional. Length = 211 Score = 28.1 bits (62), Expect = 3.3 Identities = 38/157 (24%), Positives = 68/157 (43%), Gaps = 27/157 (17%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNAK 84 + L+G + GKS+L+ F+ + V + + I + V K ++ DT G Sbjct: 17 ILLIGDSGVGKSSLLVSFISSSVEDLAPTIGVDFKIKQLTVGGKRLKLTIWDTAG----- 71 Query: 85 DSYHKLMIRLSWSTIKHADIVCLVVD-SHRELKVNIHDLL-KEIAKRSSRL----ILILN 138 + L+ S ++A + LV D + RE N+ D+ KE+ S+ +L+ N Sbjct: 72 ---QERFRTLTSSYYRNAQGIILVYDVTRRETFTNLSDVWGKEVELYSTNQDCVKMLVGN 128 Query: 139 KIDCVKPERLLEQAEIANKLVFIEKTFMVSATKGHGC 175 K+D + ER + + E ++ K HGC Sbjct: 129 KVD-RESERDVSREE------------GMALAKEHGC 152 >gnl|CDD|183990 PRK13351, PRK13351, elongation factor G; Reviewed. Length = 687 Score = 28.0 bits (63), Expect = 3.5 Identities = 17/72 (23%), Positives = 27/72 (37%), Gaps = 17/72 (23%) Query: 25 VALVGATNAGKSTLVNR--FVGAKVSIV--THKVQTT-----RSIVRGI--------VSE 67 + ++ +AGK+TL R F K+ + T + RGI Sbjct: 11 IGILAHIDAGKTTLTERILFYTGKIHKMGEVEDGTTVTDWMPQEQERGITIESAATSCDW 70 Query: 68 KESQIVFLDTPG 79 +I +DTPG Sbjct: 71 DNHRINLIDTPG 82 >gnl|CDD|116538 pfam07928, Vps54, Vps54-like protein. This family contains various proteins that are homologs of the yeast Vps54 protein, such as the rat homolog , the human homolog, and the mouse homolog. In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments. All Vps54 homologs contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs. Length = 133 Score = 28.0 bits (63), Expect = 3.6 Identities = 13/41 (31%), Positives = 22/41 (53%) Query: 121 DLLKEIAKRSSRLILILNKIDCVKPERLLEQAEIANKLVFI 161 ++ +R+ + +LN+ D V+ + Q EI NKLV I Sbjct: 88 PYIRRHLRRAPKQSSLLNEFDKVRRDYQEHQNEIHNKLVSI 128 >gnl|CDD|130234 TIGR01166, cbiO, cobalt transport protein ATP-binding subunit. This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux. Length = 190 Score = 27.8 bits (62), Expect = 3.6 Identities = 12/25 (48%), Positives = 15/25 (60%) Query: 20 SRSGCVALVGATNAGKSTLVNRFVG 44 R +AL+GA AGKSTL+ G Sbjct: 16 ERGEVLALLGANGAGKSTLLLHLNG 40 >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 = 27.9 bits (62), Expect = 3.7 Identities = 11/20 (55%), Positives = 15/20 (75%) Query: 25 VALVGATNAGKSTLVNRFVG 44 VA++G + AGKSTL+N G Sbjct: 27 VAIMGPSGAGKSTLLNLIAG 46 >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 = 27.6 bits (62), Expect = 3.8 Identities = 9/14 (64%), Positives = 12/14 (85%) Query: 25 VALVGATNAGKSTL 38 VALVG + +GKST+ Sbjct: 508 VALVGGSGSGKSTI 521 >gnl|CDD|184133 PRK13548, hmuV, hemin importer ATP-binding subunit; Provisional. Length = 258 Score = 27.8 bits (63), Expect = 4.0 Identities = 9/14 (64%), Positives = 11/14 (78%) Query: 25 VALVGATNAGKSTL 38 VA++G AGKSTL Sbjct: 31 VAILGPNGAGKSTL 44 >gnl|CDD|150474 pfam09810, Morph_protein1, Defects in morphology protein 1, mitochondrial precursor. Members of this family of proteins are thought to be involved in cellular morphology, though little else is known about them. Length = 329 Score = 27.8 bits (62), Expect = 4.0 Identities = 13/42 (30%), Positives = 22/42 (52%) Query: 255 QKKIMLGKNGQNIKTISLEAKKEIAEILEQPVHLILFVKVQK 296 Q + L K G+ +T +++ +I E LE VH + V+V Sbjct: 28 QYEYTLTKFGRKERTPAMKRGIKIHEKLELEVHTTVPVEVTT 69 >gnl|CDD|184201 PRK13641, cbiO, cobalt transporter ATP-binding subunit; Provisional. Length = 287 Score = 27.9 bits (62), Expect = 4.0 Identities = 12/18 (66%), Positives = 14/18 (77%) Query: 25 VALVGATNAGKSTLVNRF 42 VALVG T +GKSTL+ F Sbjct: 36 VALVGHTGSGKSTLMQHF 53 >gnl|CDD|163393 TIGR03680, eif2g_arch, translation initiation factor 2 subunit gamma. eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. Length = 406 Score = 27.7 bits (62), Expect = 4.1 Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 11/64 (17%) Query: 133 LILILNKIDCVKPERLLEQ-AEIANKLVFIEKTFM-------VSATKGHGCDDVLNYLCS 184 ++++ NKID V E+ LE EI F++ T VSA D +L + Sbjct: 137 IVIVQNKIDLVSKEKALENYEEIKE---FVKGTVAENAPIIPVSALHNANIDALLEAIEK 193 Query: 185 TLPL 188 +P Sbjct: 194 FIPT 197 >gnl|CDD|163509 TIGR03797, NHPM_micro_ABC2, NHPM bacteriocin system ABC transporter, ATP-binding protein. Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif. Length = 686 Score = 27.6 bits (62), Expect = 4.1 Identities = 9/14 (64%), Positives = 12/14 (85%) Query: 25 VALVGATNAGKSTL 38 VA+VG + +GKSTL Sbjct: 482 VAIVGPSGSGKSTL 495 >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 = 4.4 Identities = 11/14 (78%), Positives = 12/14 (85%) Query: 25 VALVGATNAGKSTL 38 VALVG + AGKSTL Sbjct: 369 VALVGPSGAGKSTL 382 >gnl|CDD|178771 PLN03232, PLN03232, ABC transporter C family member; Provisional. Length = 1495 Score = 27.6 bits (61), Expect = 4.5 Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 11/59 (18%) Query: 25 VALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNA 83 VA+VG T GK++L++ +G ++H +T+ ++RG V+ IFNA Sbjct: 646 VAIVGGTGEGKTSLISAMLGE----LSH-AETSSVVIRGSVAYVPQ------VSWIFNA 693 >gnl|CDD|183321 PRK11809, putA, trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed. Length = 1318 Score = 27.6 bits (62), Expect = 4.6 Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 5/27 (18%) Query: 83 AKDSYHKLMIRLS----W-STIKHADI 104 A+ S +LMIRL W S IK A + Sbjct: 421 ARRSRRRLMIRLVKGAYWDSEIKRAQV 447 >gnl|CDD|183003 PRK11160, PRK11160, cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed. Length = 574 Score = 27.5 bits (62), Expect = 4.6 Identities = 10/14 (71%), Positives = 11/14 (78%) Query: 25 VALVGATNAGKSTL 38 VAL+G T GKSTL Sbjct: 369 VALLGRTGCGKSTL 382 >gnl|CDD|162130 TIGR00955, 3a01204, The Eye Pigment Precursor Transporter (EPP) Family protein. Length = 617 Score = 27.3 bits (61), Expect = 4.9 Identities = 8/16 (50%), Positives = 15/16 (93%) Query: 25 VALVGATNAGKSTLVN 40 +A++G++ AGK+TL+N Sbjct: 54 LAVMGSSGAGKTTLMN 69 >gnl|CDD|151508 pfam11062, DUF2863, Protein of unknown function (DUF2863). This bacterial family of proteins have no known function. Length = 398 Score = 27.3 bits (61), Expect = 4.9 Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 4/29 (13%) Query: 186 LPLAPWVYSADQISDLPM-FHFTAEITRE 213 L LAP+++S DQ LP TAE+ R+ Sbjct: 140 LALAPFLFSIDQ---LPRSHCETAELARK 165 >gnl|CDD|130815 TIGR01754, flav_RNR, ribonucleotide reductase-associated flavodoxin, putative. This model represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulfate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation. Length = 140 Score = 27.5 bits (61), Expect = 5.0 Identities = 11/32 (34%), Positives = 17/32 (53%) Query: 273 EAKKEIAEILEQPVHLILFVKVQKDWGHDPKC 304 E K IAE+ +P ++ +F + WG D C Sbjct: 69 EMKDFIAELGYKPSNVAIFGTGETQWGDDLYC 100 >gnl|CDD|129594 TIGR00503, prfC, peptide chain release factor 3. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus. Length = 527 Score = 27.2 bits (60), Expect = 5.5 Identities = 19/82 (23%), Positives = 37/82 (45%), Gaps = 10/82 (12%) Query: 74 FLDTPGIFNAKDSYHKLMIRLSWSTIKHADIVCLVVDSHRELKVNIHDLLKEIAKRSSRL 133 LDTPG H+ ++ T+ D +V+D+ + ++ L++ R + + Sbjct: 84 LLDTPG--------HEDFSEDTYRTLTAVDNCLMVIDAAKGVETRTRKLMEVTRLRDTPI 135 Query: 134 ILILNKID--CVKPERLLEQAE 153 +NK+D P LL++ E Sbjct: 136 FTFMNKLDRDIRDPLELLDEVE 157 >gnl|CDD|182707 PRK10762, PRK10762, D-ribose transporter ATP binding protein; Provisional. Length = 501 Score = 27.3 bits (61), Expect = 5.8 Identities = 20/62 (32%), Positives = 25/62 (40%), Gaps = 20/62 (32%) Query: 26 ALVGATNAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKESQIVFLDTPGIFNA-K 84 ALVG AGKST++ KV T GI + I++L FN K Sbjct: 34 ALVGENGAGKSTMM-------------KVLT------GIYTRDAGSILYLGKEVTFNGPK 74 Query: 85 DS 86 S Sbjct: 75 SS 76 >gnl|CDD|182182 PRK09984, PRK09984, phosphonate/organophosphate ester transporter subunit; Provisional. Length = 262 Score = 27.3 bits (60), Expect = 6.0 Identities = 20/68 (29%), Positives = 33/68 (48%), Gaps = 12/68 (17%) Query: 9 FNEHKDF--VQDNSRSG-CVALVGATNAGKSTLV---------NRFVGAKVSIVTHKVQT 56 FN+H+ V N G VAL+G + +GKSTL+ ++ G+ + ++ VQ Sbjct: 14 FNQHQALHAVDLNIHHGEMVALLGPSGSGKSTLLRHLSGLITGDKSAGSHIELLGRTVQR 73 Query: 57 TRSIVRGI 64 + R I Sbjct: 74 EGRLARDI 81 >gnl|CDD|183231 PRK11614, livF, leucine/isoleucine/valine transporter ATP-binding subunit; Provisional. Length = 237 Score = 27.2 bits (60), Expect = 6.4 Identities = 21/87 (24%), Positives = 33/87 (37%), Gaps = 17/87 (19%) Query: 25 VALVGATNAGKSTLVNRFVG----AKVSIV-----THKVQTTRSIVRGIVSEKESQIVF- 74 V L+GA AGK+TL+ G IV QT + + + E + VF Sbjct: 34 VTLIGANGAGKTTLLGTLCGDPRATSGRIVFDGKDITDWQTAKIMREAVAIVPEGRRVFS 93 Query: 75 -------LDTPGIFNAKDSYHKLMIRL 94 L G F +D + + + + Sbjct: 94 RMTVEENLAMGGFFAERDQFQERIKWV 120 >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 = 26.9 bits (60), Expect = 6.8 Identities = 9/21 (42%), Positives = 14/21 (66%) Query: 25 VALVGATNAGKSTLVNRFVGA 45 +A++G + +GKSTL VG Sbjct: 347 LAIIGPSGSGKSTLARLIVGI 367 >gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family protein. Length = 1394 Score = 27.0 bits (60), Expect = 7.2 Identities = 10/15 (66%), Positives = 14/15 (93%) Query: 26 ALVGATNAGKSTLVN 40 AL+GA+ AGK+TL+N Sbjct: 793 ALMGASGAGKTTLLN 807 >gnl|CDD|184048 PRK13428, PRK13428, F0F1 ATP synthase subunit delta; Provisional. Length = 445 Score = 26.6 bits (59), Expect = 8.1 Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 6/39 (15%) Query: 32 NAGKSTLVNRFVGAKVSIVTHKVQTTRSIVRGIVSEKES 70 A K LV R KV T ++R VS++ S Sbjct: 230 AAPKIRLVERLFSGKVG------APTLEVLRTAVSQRWS 262 >gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. Length = 282 Score = 26.5 bits (59), Expect = 8.7 Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 31/91 (34%) Query: 20 SRSGCVALVGATNAGKST----LVNRFV----GAKVSIVT-------------------- 51 + G +ALVG T GK+T L RFV KV+++T Sbjct: 192 EQGGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTYRIGAVEQLKTYAKILG 251 Query: 52 ---HKVQTTRSIVRGIVSEKESQIVFLDTPG 79 + + + + + ++ ++ +DT G Sbjct: 252 VPVKVARDPKELRKALDRLRDKDLILIDTAG 282 >gnl|CDD|184134 PRK13549, PRK13549, xylose transporter ATP-binding subunit; Provisional. Length = 506 Score = 26.4 bits (59), Expect = 10.0 Identities = 9/15 (60%), Positives = 10/15 (66%) Query: 24 CVALVGATNAGKSTL 38 V+L G AGKSTL Sbjct: 33 IVSLCGENGAGKSTL 47 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 0.321 0.136 0.401 Gapped Lambda K H 0.267 0.0756 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 4,858,433 Number of extensions: 299911 Number of successful extensions: 974 Number of sequences better than 10.0: 1 Number of HSP's gapped: 940 Number of HSP's successfully gapped: 140 Length of query: 311 Length of database: 5,994,473 Length adjustment: 93 Effective length of query: 218 Effective length of database: 3,984,929 Effective search space: 868714522 Effective search space used: 868714522 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 (21.9 bits) S2: 57 (25.7 bits)