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)