RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780226|ref|YP_003064639.1| translation-associated GTPase
[Candidatus Liberibacter asiaticus str. psy62]
         (367 letters)



>gnl|CDD|30362 COG0012, COG0012, Predicted GTPase, probable translation factor
           [Translation, ribosomal structure and biogenesis].
          Length = 372

 Score =  481 bits (1239), Expect = e-136
 Identities = 214/373 (57%), Positives = 267/373 (71%), Gaps = 7/373 (1%)

Query: 1   MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAE 60
           M  K GI+GLPNVGKSTLFNALT+ A A+ ANYPFCTIEPN G V VPD R+ +LAEI +
Sbjct: 1   MSLKIGIVGLPNVGKSTLFNALTK-AGAEIANYPFCTIEPNVGVVYVPDCRLDELAEIVK 59

Query: 61  -SKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGR 119
               + P  + FVDIAGLV+GASKGEGLGN+FL +IREVDAIIHV+RCF D +I HVEG+
Sbjct: 60  CPPKIRPAPVEFVDIAGLVKGASKGEGLGNKFLDNIREVDAIIHVVRCFGDTDIEHVEGK 119

Query: 120 IDPINDIETIETELMLSDLERLERLFEK-NKKYRNHKSEEIVLLQ--SIISSSLRLIEEG 176
           +DP+ DIE I TEL+L DLE LE+ +E+  K+ +  K  +  L +  S++      +EEG
Sbjct: 120 VDPVEDIEIINTELILWDLESLEKRWERLEKRAKAGKKLDKELKEELSLLGKLEEHLEEG 179

Query: 177 KPVRSL-LESLDSDAIPIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNA 235
           KP R L L     + +    SLNLLTAKP+LY+ NVSE D    N Y + ++ LA+++NA
Sbjct: 180 KPARGLDLSKWSEEDLEALASLNLLTAKPMLYVANVSEDDLANLNEYVKRLKELAAKENA 239

Query: 236 EMIIISAAIEAEISQLPE-EERALFMEELDISISGLELLIRSGYRLLDLITYFTVGPKET 294
           E++ +SAAIE E+ +L + EE+  F+ EL    SGL  LIR+GY LL L TYFT G KE 
Sbjct: 240 EVVPVSAAIELELRELADAEEKGEFLIELGQKESGLNELIRAGYGLLGLQTYFTAGVKEV 299

Query: 295 RAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYI 354
           RAWTI  G+ A  AAGVIH DFEKGFIRA  ISY D +  GGE AAKEAGK R EGK+YI
Sbjct: 300 RAWTIKDGSKAPDAAGVIHPDFEKGFIRAEVISYADLIHYGGEAAAKEAGKRRLEGKDYI 359

Query: 355 VKDGDILHFRFNV 367
           V+DGD++HF+FNV
Sbjct: 360 VQDGDVIHFKFNV 372


>gnl|CDD|133300 cd01900, YchF, YchF subfamily.  YchF is a member of the Obg family,
           which includes four other subfamilies of GTPases: Obg,
           DRG, Ygr210, and NOG1.  Obg is an essential gene that is
           involved in DNA replication in C. crescentus and
           Streptomyces griseus and is associated with the
           ribosome.  Several members of the family, including
           YchF, possess the TGS domain related to the RNA-binding
           proteins.  Experimental data and genomic analysis
           suggest that YchF may be part of a nucleoprotein complex
           and may function as a GTP-dependent translational
           factor.
          Length = 274

 Score =  412 bits (1061), Expect = e-115
 Identities = 165/281 (58%), Positives = 207/281 (73%), Gaps = 11/281 (3%)

Query: 5   CGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDL 64
            GI+GLPNVGKSTLFNALT+ A A+AANYPFCTIEPN G V VPD R+ KLAEI + K +
Sbjct: 1   IGIVGLPNVGKSTLFNALTK-AGAEAANYPFCTIEPNVGIVPVPDERLDKLAEIVKPKKI 59

Query: 65  VPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIN 124
           VP  + FVDIAGLV+GASKGEGLGN+FL+HIREVDAI HV+RCF+D++I HVEG +DP+ 
Sbjct: 60  VPATIEFVDIAGLVKGASKGEGLGNKFLSHIREVDAIAHVVRCFEDDDITHVEGSVDPVR 119

Query: 125 DIETIETELMLSDLERLERLFEK-NKKYRNHKSE---EIVLLQSIISSSLRLIEEGKPVR 180
           DIE I TEL+L+DLE +E+  E+  KK ++   E   E+ LL+ I       +EEGKP R
Sbjct: 120 DIEIINTELILADLETVEKRLERLEKKAKSGDKEAKAELELLEKIKE----HLEEGKPAR 175

Query: 181 SLLESLDSDAIPIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNAEMIII 240
           SL   L  + I I  SL LLTAKP+LY+ NVSE D   GN     V+ +A+++ AE+I I
Sbjct: 176 SL--ELTEEEIEILNSLQLLTAKPVLYVANVSEDDLANGNNKVLKVREIAAKEGAEVIPI 233

Query: 241 SAAIEAEISQLPEEERALFMEELDISISGLELLIRSGYRLL 281
           SA IEAE+++L EEE A F+EEL +  SGL+ LIR+GY LL
Sbjct: 234 SAKIEAELAELDEEEAAEFLEELGLEESGLDRLIRAGYELL 274


>gnl|CDD|36704 KOG1491, KOG1491, KOG1491, Predicted GTP-binding protein (ODN
           superfamily) [General function prediction only].
          Length = 391

 Score =  378 bits (971), Expect = e-105
 Identities = 182/376 (48%), Positives = 238/376 (63%), Gaps = 12/376 (3%)

Query: 1   MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAE 60
              K GI+GLPNVGKST FNALT+ + A AAN+PFCTI+PN   V VPD R   L  I  
Sbjct: 19  NNLKIGIVGLPNVGKSTFFNALTK-SKAGAANFPFCTIDPNEARVEVPDSRFDLLCPIYG 77

Query: 61  SKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRI 120
            K  VP  ++  DIAGLV+GAS GEGLGN+FL+HIR VDAI HV+R F+D +IIHVEG +
Sbjct: 78  PKSKVPAFLTVYDIAGLVKGASAGEGLGNKFLSHIRHVDAIFHVVRAFEDTDIIHVEGGV 137

Query: 121 DPINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSL------RLIE 174
           DP+ DIE I+ EL L DLE LE+  EK +K        +   Q      L      +L++
Sbjct: 138 DPVRDIEIIQEELRLKDLEFLEKRLEKLEKKHKRTKSNLETKQLKFEYGLLEKVKEKLLD 197

Query: 175 EGKPVRSLLESLDSDAIPIFKSLNLLTAKPILYICNVSEHD-CKKGNIYTEAVQRLASQQ 233
             KPVR   E  + + I I   L LLTAKP +Y+ N+SEHD  +K N     ++    + 
Sbjct: 198 GKKPVRP-KEKWNDEEIEILNKLFLLTAKPTVYLLNLSEHDYARKKNKKLPKIKEWVDEV 256

Query: 234 N--AEMIIISAAIEAEISQLPEEERALFMEELDISISGLELLIRSGYRLLDLITYFTVGP 291
           +    +I+ SAA E+++ +L EEE    +E+L  S S L  +I++GY  L+LI +FT G 
Sbjct: 257 SPGDVVIVFSAAFESQLFELYEEEAVKELEDLGDS-SALPKIIKTGYSALNLIVFFTCGE 315

Query: 292 KETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGK 351
            E RAWTI +GT A +AAGVIH+DFEKGFI A  + ++D+     E+A K AGK R  GK
Sbjct: 316 DEVRAWTIRKGTKAPQAAGVIHSDFEKGFIMAEVMKFEDFKEYKSESACKAAGKYRQVGK 375

Query: 352 EYIVKDGDILHFRFNV 367
           EYIV+DGDI+ F+FN 
Sbjct: 376 EYIVEDGDIIFFKFNP 391


>gnl|CDD|133281 cd01881, Obg_like, The Obg-like subfamily consists of five
           well-delimited, ancient subfamilies, namely Obg, DRG,
           YyaF/YchF, Ygr210, and NOG1.  Four of these groups (Obg,
           DRG, YyaF/YchF, and Ygr210) are characterized by a
           distinct glycine-rich motif immediately following the
           Walker B motif (G3 box).  Obg/CgtA is an essential gene
           that is involved in the initiation of sporulation and
           DNA replication in the bacteria Caulobacter and
           Bacillus, but its exact molecular role is unknown.
           Furthermore, several OBG family members possess a
           C-terminal RNA-binding domain, the TGS domain, which is
           also present in threonyl-tRNA synthetase and in
           bacterial guanosine polyphosphatase SpoT.  Nog1 is a
           nucleolar protein that might function in ribosome
           assembly.  The DRG and Nog1 subfamilies are ubiquitous
           in archaea and eukaryotes, the Ygr210 subfamily is
           present in archaea and fungi, and the Obg and YyaF/YchF
           subfamilies are ubiquitous in bacteria and eukaryotes.
           The Obg/Nog1 and DRG subfamilies appear to form one
           major branch of the Obg family and the Ygr210 and YchF
           subfamilies form another branch. No GEFs, GAPs, or GDIs
           for Obg have been identified.
          Length = 176

 Score =  180 bits (460), Expect = 5e-46
 Identities = 92/275 (33%), Positives = 119/275 (43%), Gaps = 99/275 (36%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
           ++GLPNVGKSTL NALT  A  + ANYPF T+EPN G V VPD                 
Sbjct: 1   LVGLPNVGKSTLLNALTN-AKPKVANYPFTTLEPNLGVVEVPDG---------------- 43

Query: 67  TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPINDI 126
            R+   DI GL+ GAS+G GLGNQFLAHIR  DAI+HV+   +D++I    G +DP+ D 
Sbjct: 44  ARIQVADIPGLIEGASEGRGLGNQFLAHIRRADAILHVVDASEDDDI----GGVDPLEDY 99

Query: 127 ETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLESL 186
           E +  EL L DLE +  L                                KPV       
Sbjct: 100 EILNAELKLYDLETILGLLTA-----------------------------KPV------- 123

Query: 187 DSDAIPIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNAEMIIISAAIEA 246
                              +Y+ N  + D  +     E V+ LA ++ AE++ ISA  E 
Sbjct: 124 -------------------IYVLNKIDLDDAEELEE-ELVRELALEEGAEVVPISAKTEE 163

Query: 247 EISQLPEEERALFMEELDISISGLELLIRSGYRLL 281
                                 GL+ LIR+ Y LL
Sbjct: 164 ----------------------GLDELIRAIYELL 176


>gnl|CDD|133440 cd04867, TGS_YchF_C, TGS_YchF_C: This subfamily represents TGS
           domain-containing YchF GTP-binding protein, a
           universally conserved GTPase whose function is unknown.
           The N-terminal domain of the YchF protein belongs to the
           Obg-like family of GTPases, and some members of the
           family contain a C-terminal TGS domain. TGS is a small
           domain of about 50 amino acid residues with a
           predominantly beta-sheet structure. There is no direct
           information on the function of the TGS domain, but its
           presence in two types of regulatory proteins (the
           GTPases and guanosine polyphosphate
           phosphohydrolases/synthetases) suggests a ligand (most
           likely nucleotide)-binding, regulatory role.
          Length = 83

 Score =  160 bits (406), Expect = 8e-40
 Identities = 55/83 (66%), Positives = 67/83 (80%)

Query: 283 LITYFTVGPKETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKE 342
           LI++FT GP E RAWTI +GT A +AAGVIHTDFEKGFIRA  + Y+D V +G E AAKE
Sbjct: 1   LISFFTAGPDEVRAWTIRKGTKAPQAAGVIHTDFEKGFIRAEVMKYEDLVELGSEAAAKE 60

Query: 343 AGKARDEGKEYIVKDGDILHFRF 365
           AGK R EGK+Y+V+DGDI+ F+F
Sbjct: 61  AGKYRQEGKDYVVQDGDIIFFKF 83


>gnl|CDD|133299 cd01899, Ygr210, Ygr210 subfamily.  Ygr210 is a member of Obg-like
           family and present in archaea and fungi.  They are
           characterized by a distinct glycine-rich motif
           immediately following the Walker B motif.  The Ygr210
           and YyaF/YchF subfamilies appear to form one major
           branch of the Obg-like family.  Among eukaryotes, the
           Ygr210 subfamily is represented only in fungi.  These
           fungal proteins form a tight cluster with their archaeal
           orthologs, which suggests the possibility of horizontal
           transfer from archaea to fungi.
          Length = 318

 Score =  123 bits (312), Expect = 5e-29
 Identities = 79/266 (29%), Positives = 122/266 (45%), Gaps = 40/266 (15%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGE----VAVPDPRMHKLAEIAES 61
           G++G PN GKST FNA T  A  + ANYPF TI+PN G     V  P   +         
Sbjct: 2   GLVGKPNAGKSTFFNAATL-ADVEIANYPFTTIDPNVGVGYVRVECPCKELGVSCNPRYG 60

Query: 62  KD-----LVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKD------ 110
           K       VP  +  +D+AGLV GA +G+GLGN+FL  +R+ DA+IHV+    D      
Sbjct: 61  KCIDGKRYVPVEL--IDVAGLVPGAHEGKGLGNKFLDDLRDADALIHVV----DASGGTD 114

Query: 111 -ENIIHVEGRIDPINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIIS-S 168
            E      G  DP+ DIE +E E+ +     LE+ +EK    R   +E+  +++++    
Sbjct: 115 AEGNGVETGGHDPLEDIEFLENEIDMWIYGILEKNWEKIV--RKADAEKTDIVEALSEQL 172

Query: 169 SLRLIEEGKPVRSLLESLDSDAIP-------IFKSLNLLT--AKPILYICNVSEHDCKKG 219
           S   + E   V   LE L+            + +    L   +KP++   N ++    + 
Sbjct: 173 SGFGVNEKD-VIEALEELELPEDLSKWTDEDLLRLARALRKRSKPMVIAANKADIPDAEN 231

Query: 220 NIYTEAVQRLASQQNAEMIIISAAIE 245
           NI    ++      +  ++  SA  E
Sbjct: 232 NISKLRLKYP----DEIVVPTSAEAE 253


>gnl|CDD|133298 cd01898, Obg, Obg subfamily.  The Obg nucleotide binding protein
           subfamily has been implicated in stress response,
           chromosome partitioning, replication initiation,
           mycelium development, and sporulation.  Obg proteins are
           among a large group of GTP binding proteins conserved
           from bacteria to humans.  The E. coli homolog, ObgE is
           believed to function in ribosomal biogenesis.  Members
           of the subfamily contain two equally and highly
           conserved domains, a C-terminal GTP binding domain and
           an N-terminal glycine-rich domain.
          Length = 170

 Score = 95.9 bits (240), Expect = 1e-20
 Identities = 53/138 (38%), Positives = 74/138 (53%), Gaps = 26/138 (18%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
           G++GLPN GKSTL +A++  A  + A+YPF T+ PN G V V D R              
Sbjct: 4   GLVGLPNAGKSTLLSAISN-AKPKIADYPFTTLVPNLGVVRVDDGR-------------- 48

Query: 66  PTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIND 125
                  DI GL+ GAS+G+GLG++FL HI     ++HV+    D+         DP+ D
Sbjct: 49  --SFVVADIPGLIEGASEGKGLGHRFLRHIERTRLLLHVIDLSGDD---------DPVED 97

Query: 126 IETIETELMLSDLERLER 143
            +TI  EL L + E LE+
Sbjct: 98  YKTIRNELELYNPELLEK 115


>gnl|CDD|30882 COG0536, Obg, Predicted GTPase [General function prediction only].
          Length = 369

 Score = 96.0 bits (239), Expect = 2e-20
 Identities = 50/130 (38%), Positives = 66/130 (50%), Gaps = 28/130 (21%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
           G++GLPN GKSTL +A++  A  + A+YPF T+ PN G V V                  
Sbjct: 163 GLVGLPNAGKSTLLSAVSA-AKPKIADYPFTTLVPNLGVVRVDGGE-------------- 207

Query: 66  PTRMSFV--DIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPI 123
               SFV  DI GL+ GAS+G GLG +FL HI     ++HV+     +         DPI
Sbjct: 208 ----SFVVADIPGLIEGASEGVGLGLRFLRHIERTRVLLHVIDLSPIDG-------RDPI 256

Query: 124 NDIETIETEL 133
            D +TI  EL
Sbjct: 257 EDYQTIRNEL 266


>gnl|CDD|145217 pfam01926, MMR_HSR1, GTPase of unknown function. 
          Length = 106

 Score = 86.6 bits (215), Expect = 9e-18
 Identities = 38/105 (36%), Positives = 51/105 (48%), Gaps = 18/105 (17%)

Query: 14  GKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVPTRMSFVD 73
           GKSTL NALT    A  ++YP  T +PN G V +   ++                   VD
Sbjct: 1   GKSTLINALTGKKRAIVSDYPGTTRDPNEGRVELDGKQII-----------------LVD 43

Query: 74  IAGLVRGASKGEG-LGNQFLAHIREVDAIIHVLRCFKDENIIHVE 117
             G++ GASKGEG LGN+ L  I E D I+HV+   +      +E
Sbjct: 44  TPGIIEGASKGEGELGNRTLEAIEEADLILHVVDASEGLTEEDLE 88


>gnl|CDD|133296 cd01896, DRG, The developmentally regulated GTP-binding protein
           (DRG) subfamily is an uncharacterized member of the Obg
           family, an evolutionary branch of GTPase superfamily
           proteins.  GTPases act as molecular switches regulating
           diverse cellular processes.  DRG2 and DRG1 comprise the
           DRG subfamily in eukaryotes.  In view of their
           widespread expression in various tissues and high
           conservation among distantly related species in
           eukaryotes and archaea, DRG proteins may regulate
           fundamental cellular processes.  It is proposed that the
           DRG subfamily proteins play their physiological roles
           through RNA binding.
          Length = 233

 Score = 82.6 bits (205), Expect = 2e-16
 Identities = 41/129 (31%), Positives = 57/129 (44%), Gaps = 30/129 (23%)

Query: 5   CGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDL 64
             ++G P+VGKSTL + LT T S   A Y F T+        VP    +K A+I      
Sbjct: 3   VALVGFPSVGKSTLLSKLTNTKSE-VAAYEFTTLTC------VPGVLEYKGAKI------ 49

Query: 65  VPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIN 124
                  +D+ G++ GA+ G+G G Q +A  R  D I+ VL   K E             
Sbjct: 50  -----QLLDLPGIIEGAADGKGRGRQVIAVARTADLILMVLDATKPE------------G 92

Query: 125 DIETIETEL 133
             E +E EL
Sbjct: 93  HREILEREL 101


>gnl|CDD|31357 COG1163, DRG, Predicted GTPase [General function prediction only].
          Length = 365

 Score = 76.8 bits (189), Expect = 1e-14
 Identities = 81/364 (22%), Positives = 139/364 (38%), Gaps = 78/364 (21%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
            ++G P+VGKSTL N LT T S + A+YPF T+EP  G +       +K A+I       
Sbjct: 67  ALVGFPSVGKSTLLNKLTNTKS-EVADYPFTTLEPVPGMLE------YKGAQI------- 112

Query: 66  PTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPIND 125
                 +D+ G++ GAS G G G Q L+  R  D II VL  F+D               
Sbjct: 113 ----QLLDLPGIIEGASSGRGRGRQVLSVARNADLIIIVLDVFEDP-------------- 154

Query: 126 IETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLES 185
                        + +ER  E      N +  ++ + +         I         L  
Sbjct: 155 ----------HHRDIIERELEDVGIRLNKRPPDVTIKKKESGG----IRINGTGP--LTH 198

Query: 186 LDSDAI-PIFKSLNLLTAKPILYICNVSEHDCKKGNIYTEAVQRLASQQNAEMII--ISA 242
           LD D +  I +   +  A  +L   +V+  D        +A++     + A  ++  I  
Sbjct: 199 LDEDTVRAILREYRIHNAD-VLIREDVTLDD------LIDALEGNRVYKPALYVVNKIDL 251

Query: 243 AIEAEISQLPEEERALFME-ELDISISGLELLIRSGYRLLDLITYFT----VGPKETRAW 297
               E+ +L  +  ++ +  +  I    L+ L    + +L LI  +T      P      
Sbjct: 252 PGLEELERLARKPNSVPISAKKGI---NLDELKERIWDVLGLIRVYTKPPGEEPDFDEPL 308

Query: 298 TIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYIVKD 357
            + RG+        IH D  + F          Y  + G++      +    G +++++D
Sbjct: 309 ILRRGSTVGDVCRKIHRDLVENF---------RYARVWGKSVKHPGQRV---GLDHVLED 356

Query: 358 GDIL 361
            DI+
Sbjct: 357 EDIV 360


>gnl|CDD|36702 KOG1489, KOG1489, KOG1489, Predicted GTP-binding protein (ODN
           superfamily) [General function prediction only].
          Length = 366

 Score = 73.4 bits (180), Expect = 9e-14
 Identities = 36/102 (35%), Positives = 51/102 (50%), Gaps = 17/102 (16%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
           G++G PN GKSTL NAL+R A  + A+Y F T+ P+ G V   D        +A      
Sbjct: 200 GLVGFPNAGKSTLLNALSR-AKPKVAHYAFTTLRPHIGTVNYDD---FSQITVA------ 249

Query: 66  PTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRC 107
                  DI G++ GA   +GLG +FL HI     ++ V+  
Sbjct: 250 -------DIPGIIEGAHMNKGLGYKFLRHIERCKGLLFVVDL 284


>gnl|CDD|133256 cd00880, Era_like, Era (E. coli Ras-like protein)-like.  This
           family includes several distinct subfamilies (TrmE/ThdF,
           FeoB, YihA (EngG), Era, and EngA/YfgK) that generally
           show sequence conservation in the region between the
           Walker A and B motifs (G1 and G3 box motifs), to the
           exclusion of other GTPases. TrmE is ubiquitous in
           bacteria and is a widespread mitochondrial protein in
           eukaryotes, but is absent from archaea. The yeast member
           of TrmE family, MSS1, is involved in mitochondrial
           translation; bacterial members are often present in
           translation-related operons.  FeoB represents an unusual
           adaptation of GTPases for high-affinity iron (II)
           transport. YihA (EngB) family of GTPases is typified by
           the E. coli YihA, which is an essential protein involved
           in cell division control.  Era is characterized by a
           distinct derivative of the KH domain (the pseudo-KH
           domain) which is located C-terminal to the GTPase
           domain.  EngA and its orthologs are composed of two
           GTPase domains and, since the sequences of the two
           domains are more similar to each other than to other
           GTPases, it is likely that an ancient gene duplication,
           rather than a fusion of evolutionarily distinct GTPases,
           gave rise to this family.
          Length = 163

 Score = 69.7 bits (171), Expect = 1e-12
 Identities = 19/101 (18%), Positives = 30/101 (29%), Gaps = 16/101 (15%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
           + G  N GKS+L NAL     A  +  P  T +P      +                   
Sbjct: 1   LFGRTNAGKSSLLNALLGQEVAIVSPVPGTTTDPVEYVWELGPLG--------------- 45

Query: 67  TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRC 107
             +  +D  G+      G          +   D I+ V+  
Sbjct: 46  -PVVLIDTPGIDEAGGLGREREELARRVLERADLILFVVDA 85


>gnl|CDD|133441 cd04938, TGS_Obg-like, TGS_Obg-like: The C-terminal TGS domain of
           Obg-like GTPases such as those present in DRG
           (developmentally regulated GTP-binding protein), and
           GTP-binding proteins Ygr210 and YchF. The TGS domain
           (named after the ThrRS, GTPase, and SpoT proteins where
           it occurs) is a small domain of about 50 amino acid
           residues with a predominantly beta-sheet structure.
           There is no direct information on the function of the
           TGS domain, but its presence in two types of regulatory
           proteins (the GTPases and guanosine polyphosphate
           phosphohydrolases/synthetases) suggests a ligand (most
           likely nucleotide)-binding, regulatory role.
          Length = 76

 Score = 61.7 bits (150), Expect = 4e-10
 Identities = 26/94 (27%), Positives = 34/94 (36%), Gaps = 29/94 (30%)

Query: 283 LITYFTV-----------GPKETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDY 331
           LI  + V           G        + +GT     A  IH D EKGFI A+       
Sbjct: 1   LIPVYPVKNIHTFTNGSGGNVFRDCVLVKKGTTVGDVARKIHGDLEKGFIEAVG------ 54

Query: 332 VAMGGENAAKEAGKARDEGKEYIVKDGDILHFRF 365
                       G+ R EGK+ I+   DIL F+ 
Sbjct: 55  ------------GRRRLEGKDVILGKNDILKFKT 76


>gnl|CDD|36699 KOG1486, KOG1486, KOG1486, GTP-binding protein DRG2 (ODN
           superfamily) [Signal transduction mechanisms].
          Length = 364

 Score = 60.3 bits (146), Expect = 8e-10
 Identities = 35/105 (33%), Positives = 52/105 (49%), Gaps = 18/105 (17%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
           +IG P+VGKSTL + +T T S +AA+Y F T+    G +                     
Sbjct: 67  LIGFPSVGKSTLLSKITSTHS-EAASYEFTTLTCIPGVIHYNG----------------- 108

Query: 67  TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDE 111
             +  +D+ G++ GAS+G+G G Q +A  R  D I+ VL   K E
Sbjct: 109 ANIQLLDLPGIIEGASQGKGRGRQVIAVARTADLILMVLDATKSE 153


>gnl|CDD|36700 KOG1487, KOG1487, KOG1487, GTP-binding protein DRG1 (ODN
           superfamily) [Signal transduction mechanisms].
          Length = 358

 Score = 51.9 bits (124), Expect = 3e-07
 Identities = 41/130 (31%), Positives = 59/130 (45%), Gaps = 30/130 (23%)

Query: 4   KCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKD 63
           + G +G P+VGKSTL + LT T S + A Y F T+        VP    +K A+I     
Sbjct: 61  RVGFVGFPSVGKSTLLSKLTGTFS-EVAAYEFTTL------TTVPGVIRYKGAKIQ---- 109

Query: 64  LVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPI 123
                   +D+ G++ GA  G+G G Q +A  R  + I  VL   K            P+
Sbjct: 110 -------LLDLPGIIEGAKDGKGRGKQVIAVARTCNLIFIVLDVLK------------PL 150

Query: 124 NDIETIETEL 133
           +  + IE EL
Sbjct: 151 SHKKIIEKEL 160


>gnl|CDD|133435 cd01616, TGS, The TGS domain, named after the ThrRS, GTPase, and
           SpoT/RelA proteins where it occurs, is structurally
           similar to ubiquitin. TGS is a small domain of about 50
           amino acid residues with a predominantly beta-sheet
           structure. There is no direct information on the
           function of the TGS domain, but its presence in two
           types of regulatory proteins (the GTPases and guanosine
           polyphosphate phosphohydrolases/synthetases) suggests a
           ligand (most likely nucleotide)-binding, regulatory
           role.
          Length = 60

 Score = 50.0 bits (120), Expect = 1e-06
 Identities = 21/82 (25%), Positives = 28/82 (34%), Gaps = 22/82 (26%)

Query: 284 ITYFTVGPKETRAWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEA 343
           +  FT       A  +P+G  A   A  IHTD  KGFI AL                   
Sbjct: 1   MIIFTPD---GSAVELPKGATAMDFALKIHTDLGKGFIGALVN----------------- 40

Query: 344 GKARDEGKEYIVKDGDILHFRF 365
              +     Y ++DGD +    
Sbjct: 41  --GQLVDLSYTLQDGDTVSIVT 60


>gnl|CDD|31354 COG1160, COG1160, Predicted GTPases [General function prediction
           only].
          Length = 444

 Score = 49.0 bits (117), Expect = 2e-06
 Identities = 30/101 (29%), Positives = 41/101 (40%), Gaps = 19/101 (18%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
           I+G PNVGKSTLFN LT    A  ++ P  T +   G+                  + + 
Sbjct: 8   IVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDA-----------------EWLG 50

Query: 67  TRMSFVDIAGLVRGASK--GEGLGNQFLAHIREVDAIIHVL 105
                +D  GL  G      E +  Q L  I E D I+ V+
Sbjct: 51  REFILIDTGGLDDGDEDELQELIREQALIAIEEADVILFVV 91



 Score = 35.5 bits (82), Expect = 0.025
 Identities = 22/103 (21%), Positives = 35/103 (33%), Gaps = 19/103 (18%)

Query: 2   GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAES 61
             K  IIG PNVGKS+L NA+        ++    T +       +         +    
Sbjct: 178 PIKIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDS------IDIEFERDGRKY--- 228

Query: 62  KDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHV 104
                     +D AG+ R     E +  +  +  R + AI   
Sbjct: 229 --------VLIDTAGIRRKGKITESV--EKYSVARTLKAIERA 261


>gnl|CDD|133280 cd01879, FeoB, Ferrous iron transport protein B (FeoB) subfamily.
           E. coli has an iron(II) transport system, known as
          feo, which may make an important contribution to the
          iron supply of the cell under anaerobic conditions.
          FeoB has been identified as part of this transport
          system.  FeoB is a large 700-800 amino acid integral
          membrane protein. The N terminus contains a P-loop
          motif suggesting that iron transport may be ATP
          dependent.
          Length = 158

 Score = 47.4 bits (114), Expect = 6e-06
 Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 7  IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPD 49
          ++G PNVGK+TLFNALT  A  +  N+P  T+E   G   +  
Sbjct: 1  LVGNPNVGKTTLFNALTG-ARQKVGNWPGVTVEKKEGRFKLGG 42


>gnl|CDD|133294 cd01894, EngA1, EngA1 subfamily.  This CD represents the first
          GTPase domain of EngA and its orthologs, which are
          composed of two adjacent GTPase domains.  Since the
          sequences of the two domains are more similar to each
          other than to other GTPases, it is likely that an
          ancient gene duplication, rather than a fusion of
          evolutionarily distinct GTPases, gave rise to this
          family. Although the exact function of these proteins
          has not been elucidated, studies have revealed that the
          E. coli EngA homolog, Der, and Neisseria gonorrhoeae
          EngA are essential for cell viability.  A recent report
          suggests that E. coli Der functions in ribosome
          assembly and stability.
          Length = 157

 Score = 47.4 bits (114), Expect = 7e-06
 Identities = 16/28 (57%), Positives = 18/28 (64%)

Query: 7  IIGLPNVGKSTLFNALTRTASAQAANYP 34
          I+G PNVGKSTLFN LT    A   + P
Sbjct: 2  IVGRPNVGKSTLFNRLTGRRDAIVEDTP 29


>gnl|CDD|57927 cd01856, YlqF, YlqF.  Proteins of the YlqF family contain all
           sequence motifs typical of the vast class of
           P-loop-containing GTPases, but show a circular
           permutation, with a G4-G1-G3 pattern of motifs as
           opposed to the regular G1-G3-G4 pattern seen in most
           GTPases. The YlqF subfamily is represented in a
           phylogenetically diverse array of bacteria (including
           gram-positive bacteria, proteobacteria, Synechocystis,
           Borrelia, and Thermotoga) and in all eukaryotes..
          Length = 171

 Score = 46.0 bits (109), Expect = 2e-05
 Identities = 15/33 (45%), Positives = 20/33 (60%)

Query: 2   GFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
           G +  ++G+PNVGKSTL N L     A+  N P
Sbjct: 115 GIRAMVVGIPNVGKSTLINRLRGKKVAKVGNKP 147


>gnl|CDD|30719 COG0370, FeoB, Fe2+ transport system protein B [Inorganic ion
           transport and metabolism].
          Length = 653

 Score = 46.0 bits (109), Expect = 2e-05
 Identities = 29/102 (28%), Positives = 47/102 (46%), Gaps = 21/102 (20%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
            ++G PNVGK+TLFNALT  A+ +  N+P  T+E   G++      +             
Sbjct: 7   ALVGNPNVGKTTLFNALTG-ANQKVGNWPGVTVEKKEGKLKYKGHEIE------------ 53

Query: 66  PTRMSFVDIAGL--VRGASKGEGLGNQFLAHIREVDAIIHVL 105
                 VD+ G   +   S+ E +   FL    + D I++V+
Sbjct: 54  -----IVDLPGTYSLTAYSEDEKVARDFLLE-GKPDLIVNVV 89


>gnl|CDD|145523 pfam02421, FeoB_N, Ferrous iron transport protein B.  Escherichia
          coli has an iron(II) transport system (feo) which may
          make an important contribution to the iron supply of
          the cell under anaerobic conditions. FeoB has been
          identified as part of this transport system. FeoB is a
          large 700-800 amino acid integral membrane protein. The
          N terminus contains a P-loop motif suggesting that iron
          transport may be ATP dependent.
          Length = 188

 Score = 44.4 bits (106), Expect = 5e-05
 Identities = 19/40 (47%), Positives = 24/40 (60%), Gaps = 1/40 (2%)

Query: 4  KCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSG 43
             ++G PNVGK+TLFNALT  A     N+P  T+E   G
Sbjct: 1  TIALVGNPNVGKTTLFNALTG-ARQHVGNWPGVTVEKKEG 39


>gnl|CDD|32443 COG2262, HflX, GTPases [General function prediction only].
          Length = 411

 Score = 44.1 bits (104), Expect = 6e-05
 Identities = 36/136 (26%), Positives = 58/136 (42%), Gaps = 18/136 (13%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
            ++G  N GKSTLFNALT  A    A+  F T++P +  + + D R   L +       +
Sbjct: 196 ALVGYTNAGKSTLFNALT-GADVYVADQLFATLDPTTRRIELGDGRKVLLTDTVGFIRDL 254

Query: 66  PTRM--SF---------VDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENII 114
           P  +  +F          D+   V  AS  E      L  +  V+ ++  +    +  II
Sbjct: 255 PHPLVEAFKSTLEEVKEADLLLHVVDASDPE-----ILEKLEAVEDVLAEIGA-DEIPII 308

Query: 115 HVEGRIDPINDIETIE 130
            V  +ID + D E + 
Sbjct: 309 LVLNKIDLLEDEEILA 324


>gnl|CDD|133297 cd01897, NOG, NOG1 is a nucleolar GTP-binding protein present in
          eukaryotes ranging from trypanosomes to humans.  NOG1
          is functionally linked to ribosome biogenesis and found
          in association with the nuclear pore complexes and
          identified in many preribosomal complexes.  Thus,
          defects in NOG1 can lead to defects in 60S biogenesis. 
          The S. cerevisiae NOG1 gene is essential for cell
          viability, and mutations in the predicted G motifs
          abrogate function.  It is a member of the ODN family of
          GTP-binding proteins that also includes the bacterial
          Obg and DRG proteins.
          Length = 168

 Score = 44.1 bits (105), Expect = 6e-05
 Identities = 19/31 (61%), Positives = 21/31 (67%), Gaps = 1/31 (3%)

Query: 7  IIGLPNVGKSTLFNALTRTASAQAANYPFCT 37
          I G PNVGKS+L N LTR A  + A YPF T
Sbjct: 5  IAGYPNVGKSSLVNKLTR-AKPEVAPYPFTT 34


>gnl|CDD|133363 cd04163, Era, Era subfamily.  Era (E. coli Ras-like protein) is a
          multifunctional GTPase found in all bacteria except
          some eubacteria.  It binds to the 16S ribosomal RNA
          (rRNA) of the 30S subunit and appears to play a role in
          the assembly of the 30S subunit, possibly by
          chaperoning the 16S rRNA.  It also contacts several
          assembly elements of the 30S subunit.  Era couples cell
          growth with cytokinesis and plays a role in cell
          division and energy metabolism.  Homologs have also
          been found in eukaryotes. Era contains two domains: the
          N-terminal GTPase domain and a C-terminal domain KH
          domain that is critical for RNA binding.  Both domains
          are important for Era function.  Era is functionally
          able to compensate for deletion of RbfA, a cold-shock
          adaptation protein that is required for efficient
          processing of the 16S rRNA.
          Length = 168

 Score = 43.2 bits (103), Expect = 1e-04
 Identities = 16/23 (69%), Positives = 17/23 (73%), Gaps = 3/23 (13%)

Query: 3  FKCG---IIGLPNVGKSTLFNAL 22
          FK G   I+G PNVGKSTL NAL
Sbjct: 1  FKSGFVAIVGRPNVGKSTLLNAL 23


>gnl|CDD|133364 cd04164, trmE, TrmE (MnmE, ThdF, MSS1) is a 3-domain protein
          found in bacteria and eukaryotes.  It controls
          modification of the uridine at the wobble position
          (U34) of tRNAs that read codons ending with A or G in
          the mixed codon family boxes.  TrmE contains a GTPase
          domain that forms a canonical Ras-like fold.  It
          functions a molecular switch GTPase, and apparently
          uses a conformational change associated with GTP
          hydrolysis to promote the tRNA modification reaction,
          in which the conserved cysteine in the C-terminal
          domain is thought to function as a catalytic residue.
          In bacteria that are able to survive in extremely low
          pH conditions, TrmE regulates glutamate-dependent acid
          resistance.
          Length = 157

 Score = 41.3 bits (98), Expect = 4e-04
 Identities = 14/23 (60%), Positives = 16/23 (69%)

Query: 2  GFKCGIIGLPNVGKSTLFNALTR 24
          G K  I+G PNVGKS+L NAL  
Sbjct: 1  GIKVVIVGKPNVGKSSLLNALAG 23


>gnl|CDD|31355 COG1161, COG1161, Predicted GTPases [General function prediction
           only].
          Length = 322

 Score = 41.2 bits (96), Expect = 4e-04
 Identities = 15/34 (44%), Positives = 20/34 (58%)

Query: 1   MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
              + G++G PNVGKSTL N L     A+ +N P
Sbjct: 131 RKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRP 164


>gnl|CDD|31353 COG1159, Era, GTPase [General function prediction only].
          Length = 298

 Score = 40.5 bits (95), Expect = 6e-04
 Identities = 31/110 (28%), Positives = 49/110 (44%), Gaps = 21/110 (19%)

Query: 1   MGFKCG---IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAE 57
           M FK G   IIG PNVGKSTL NAL     +  +  P  T               +++  
Sbjct: 2   MKFKSGFVAIIGRPNVGKSTLLNALVGQKISIVSPKPQTT--------------RNRIRG 47

Query: 58  IAESKDLVPTRMSFVDIAGLVRGASK-GEGLGNQFLAHIREVDAIIHVLR 106
           I  + +    ++ FVD  G+ +     GE +     + +++VD I+ V+ 
Sbjct: 48  IVTTDN---AQIIFVDTPGIHKPKHALGELMNKAARSALKDVDLILFVVD 94


>gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only].
          Length = 454

 Score = 39.8 bits (93), Expect = 0.001
 Identities = 16/33 (48%), Positives = 18/33 (54%)

Query: 2   GFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
           G K  IIG PNVGKS+L NAL     A   +  
Sbjct: 217 GLKVVIIGRPNVGKSSLLNALLGRDRAIVTDIA 249


>gnl|CDD|133279 cd01878, HflX, HflX subfamily.  A distinct conserved domain with a
           glycine-rich segment N-terminal of the GTPase domain
           characterizes the HflX subfamily.  The E. coli HflX has
           been implicated in the control of the lambda cII
           repressor proteolysis, but the actual biological
           functions of these GTPases remain unclear.  HflX is
           widespread, but not universally represented in all three
           superkingdoms.
          Length = 204

 Score = 39.3 bits (93), Expect = 0.002
 Identities = 29/110 (26%), Positives = 41/110 (37%), Gaps = 38/110 (34%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
            ++G  N GKSTLFNALT  A   A +  F T+          DP   +L         +
Sbjct: 45  ALVGYTNAGKSTLFNALTG-ADVYAEDQLFATL----------DPTTRRL--------RL 85

Query: 66  PTRMSFV--DIAGLVRG------ASKGEGLGNQF---LAHIREVDAIIHV 104
           P     +  D  G +R        +        F   L  + E D ++HV
Sbjct: 86  PDGREVLLTDTVGFIRDLPHQLVEA--------FRSTLEEVAEADLLLHV 127


>gnl|CDD|31281 COG1084, COG1084, Predicted GTPase [General function prediction
           only].
          Length = 346

 Score = 39.1 bits (91), Expect = 0.002
 Identities = 17/31 (54%), Positives = 20/31 (64%), Gaps = 1/31 (3%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYPFCT 37
           + G PNVGKS+L   LT TA  + A YPF T
Sbjct: 173 VAGYPNVGKSSLVRKLT-TAKPEVAPYPFTT 202


>gnl|CDD|57924 cd01849, YlqF_related_GTPase, YlqF-related GTPases.  These proteins
           are found in bacteria, eukaryotes, and archaea.  They
           all exhibit a circular permutation of the GTPase
           signature motifs so that the order of the conserved G
           box motifs is G4-G5-G1-G2-G3, with G4 and G5 being
           permuted from the C-terminal region of proteins in the
           Ras superfamily to the N-terminus of YlqF-related
           GTPases..
          Length = 155

 Score = 38.8 bits (90), Expect = 0.002
 Identities = 14/29 (48%), Positives = 18/29 (62%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYP 34
           G+IG PNVGKS++ NAL      +  N P
Sbjct: 104 GVIGYPNVGKSSVINALLNKLKLKVGNVP 132


>gnl|CDD|57931 cd04178, Nucleostemin_like, Nucleostemin-like.  Nucleostemin (NS)
           is a nucleolar protein that functions as a regulator of
           cell growth and proliferation in stem cells and in
           several types of cancer cells, but is not expressed in
           the differentiated cells of most mammalian adult
           tissues.  NS shuttles between the nucleolus and
           nucleoplasm bidirectionally at a rate that is fast and
           independent of cell type.  Lowering GTP levels decreases
           the nucleolar retention of NS, and expression of NS is
           abruptly down-regulated during differentiation prior to
           terminal cell division.  Found only in eukaryotes, NS
           consists of an N-terminal basic domain, a coiled-coil
           domain, a GTP-binding domain, an intermediate domain,
           and a C-terminal acidic domain.  Experimental evidence
           indicates that NS uses its GTP-binding property as a
           molecular switch to control the transition between the
           nucleolus and nucleoplasm, and this process involves
           interaction between the basic, GTP-binding, and
           intermediate domains of the protein..
          Length = 172

 Score = 37.9 bits (88), Expect = 0.004
 Identities = 13/31 (41%), Positives = 19/31 (61%)

Query: 4   KCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
             G++G PNVGKS+L N+L R+ +      P
Sbjct: 119 TVGVVGFPNVGKSSLINSLKRSRACNVGATP 149


>gnl|CDD|133295 cd01895, EngA2, EngA2 subfamily.  This CD represents the second
          GTPase domain of EngA and its orthologs, which are
          composed of two adjacent GTPase domains.  Since the
          sequences of the two domains are more similar to each
          other than to other GTPases, it is likely that an
          ancient gene duplication, rather than a fusion of
          evolutionarily distinct GTPases, gave rise to this
          family.  Although the exact function of these proteins
          has not been elucidated, studies have revealed that the
          E. coli EngA homolog, Der, and Neisseria gonorrhoeae
          EngA are essential for cell viability. A recent report
          suggests that E. coli Der functions in ribosome
          assembly and stability.
          Length = 174

 Score = 37.4 bits (88), Expect = 0.007
 Identities = 13/22 (59%), Positives = 15/22 (68%)

Query: 2  GFKCGIIGLPNVGKSTLFNALT 23
            +  IIG PNVGKS+L NAL 
Sbjct: 2  PIRIAIIGRPNVGKSSLVNALL 23


>gnl|CDD|37695 KOG2484, KOG2484, KOG2484, GTPase [General function prediction
           only].
          Length = 435

 Score = 36.9 bits (85), Expect = 0.008
 Identities = 15/29 (51%), Positives = 19/29 (65%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYP 34
           GIIG PNVGKS++ N+L R  +    N P
Sbjct: 256 GIIGYPNVGKSSVINSLKRRKACNVGNVP 284


>gnl|CDD|57930 cd01859, MJ1464, MJ1464.  This family represents archaeal GTPase
           typified by the protein MJ1464 from Methanococcus
           jannaschii. The members of this family show a circular
           permutation of the GTPase signature motifs so that
           C-terminal strands 5, 6, and 7 (strands 6 contain the
           NKxD motif) are relocated to the N terminus..
          Length = 156

 Score = 36.8 bits (85), Expect = 0.009
 Identities = 15/32 (46%), Positives = 20/32 (62%)

Query: 3   FKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
            K G++G PNVGKS++ NAL    SA  +  P
Sbjct: 102 GKVGVVGYPNVGKSSIINALKGRHSASTSPSP 133


>gnl|CDD|36637 KOG1423, KOG1423, KOG1423, Ras-like GTPase ERA [Cell cycle control,
           cell division, chromosome partitioning, Signal
           transduction mechanisms].
          Length = 379

 Score = 35.8 bits (82), Expect = 0.022
 Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 17/73 (23%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLV 65
            +IG PNVGKSTL N +     +  +     T     G +   +                
Sbjct: 76  AVIGAPNVGKSTLTNQMIGQKVSAVSRKVHTTRHRILGIITSGE---------------- 119

Query: 66  PTRMSFVDIAGLV 78
            T++ F D  GLV
Sbjct: 120 -TQLVFYDTPGLV 131


>gnl|CDD|35631 KOG0410, KOG0410, KOG0410, Predicted GTP binding protein [General
           function prediction only].
          Length = 410

 Score = 35.4 bits (81), Expect = 0.028
 Identities = 29/144 (20%), Positives = 53/144 (36%), Gaps = 23/144 (15%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
           ++G  N GKSTL  ALT+ A+    +  F T++P      +P      L +       +P
Sbjct: 183 VVGYTNAGKSTLIKALTK-AALYPNDRLFATLDPTLHSAHLPSGNFVLLTDTVGFISDLP 241

Query: 67  TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRIDPINDI 126
                     LV             L  + E D ++HV+      +I H          +
Sbjct: 242 I--------QLVAAFQAT-------LEEVAEADLLLHVV------DISHPNAEEQ-RETV 279

Query: 127 ETIETELMLSDLERLERLFEKNKK 150
             +  ++ +    +L+ + E + K
Sbjct: 280 LHVLNQIGVPSEPKLQNMIEVDNK 303


>gnl|CDD|133278 cd01876, YihA_EngB, The YihA (EngB) subfamily.  This subfamily of
          GTPases is typified by the E. coli YihA, an essential
          protein involved in cell division control.  YihA and
          its orthologs are small proteins that typically contain
          less than 200 amino acid residues and consists of the
          GTPase domain only (some of the eukaryotic homologs
          contain an N-terminal extension of about 120 residues
          that might be involved in organellar targeting).
          Homologs of yihA are found in most Gram-positive and
          Gram-negative pathogenic bacteria, with the exception
          of Mycobacterium tuberculosis.  The broad-spectrum
          nature of YihA and its essentiality for cell viability
          in bacteria make it an attractive antibacterial target.
          Length = 170

 Score = 34.4 bits (80), Expect = 0.050
 Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 1/36 (2%)

Query: 7  IIGLPNVGKSTLFNALTRTAS-AQAANYPFCTIEPN 41
            G  NVGKS+L NALT     A+ +  P  T   N
Sbjct: 4  FAGRSNVGKSSLINALTNRKKLARTSKTPGKTQLIN 39


>gnl|CDD|173737 cd07834, STKc_MAPK, Catalytic domain of the Serine/Threonine
           Kinase, Mitogen-Activated Protein Kinase.
           Serine/Threonine Kinases (STKs), Mitogen-Activated
           Protein Kinase (MAPK) subfamily, catalytic (c) domain.
           STKs catalyze the transfer of the gamma-phosphoryl group
           from ATP to serine/threonine residues on protein
           substrates. The MAPK subfamily is part of a larger
           superfamily that includes the catalytic domains of other
           protein STKs, protein tyrosine kinases, RIO kinases,
           aminoglycoside phosphotransferase, choline kinase, and
           phosphoinositide 3-kinase. MAPKs serve as important
           mediators of cellular responses to extracellular
           signals. They control critical cellular functions
           including differentiation, proliferation, migration, and
           apoptosis. They are also implicated in the pathogenesis
           of many diseases including multiple types of cancer,
           stroke, diabetes, and chronic inflammation. Typical MAPK
           pathways involve a triple kinase core cascade comprising
           of the MAPK, which is phosphorylated and activated by a
           MAPK kinase (MAP2K or MKK), which itself is
           phosphorylated and activated by a MAPK kinase kinase
           (MAP3K or MKKK). Each cascade is activated either by a
           small GTP-binding protein or by an adaptor protein,
           which transmits the signal either directly to a MAP3K to
           start the triple kinase core cascade or indirectly
           through a mediator kinase, a MAP4K. There are three main
           typical MAPK subfamilies: Extracellular signal-Regulated
           Kinase (ERK), c-Jun N-terminal Kinase (JNK), and p38.
           Some MAPKs are atypical in that they are not regulated
           by MAP2Ks. These include MAPK4, MAPK6, NLK, and ERK7.
          Length = 330

 Score = 34.4 bits (80), Expect = 0.053
 Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 10/51 (19%)

Query: 96  REVDAIIHVLRCFKDENIIHVEGRIDPINDIET-----IETELMLSDLERL 141
           RE    I +LR  + ENII +   I      E      I TELM +DL ++
Sbjct: 48  RE----IKLLRHLRHENIIGLL-DILRPPSPEDFNDVYIVTELMETDLHKV 93


>gnl|CDD|57926 cd01855, YqeH, YqeH.  YqeH is an essential GTP-binding protein.
           Depletion of YqeH induces an excess initiation of DNA
           replication, suggesting that it negatively controls
           initiation of chromosome replication. The YqeH subfamily
           is common in eukaryotes and sporadically present in
           bacteria with probable acquisition by plants from
           chloroplasts.  Proteins of the YqeH family contain all
           sequence motifs typical of the vast class of
           P-loop-containing GTPases, but show a circular
           permutation, with a G4-G1-G3 pattern of motifs as
           opposed to the regular G1-G3-G4 pattern seen in most
           GTPases..
          Length = 190

 Score = 34.1 bits (78), Expect = 0.060
 Identities = 11/19 (57%), Positives = 14/19 (73%)

Query: 7   IIGLPNVGKSTLFNALTRT 25
           ++G  NVGKSTL NAL + 
Sbjct: 132 VVGATNVGKSTLINALLKK 150


>gnl|CDD|31297 COG1100, COG1100, GTPase SAR1 and related small G proteins [General
           function prediction only].
          Length = 219

 Score = 34.2 bits (77), Expect = 0.065
 Identities = 38/211 (18%), Positives = 63/211 (29%), Gaps = 15/211 (7%)

Query: 3   FKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKL-----AE 57
           FK  ++G   VGK+TL N L          YP      +  +   P  R  KL     A 
Sbjct: 6   FKIVVLGDGGVGKTTLLNRLVG--DEFPEGYPPTIGNLDPAKTIEPYRRNIKLQLWDTAG 63

Query: 58  IAESKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVE 117
             E + L P      +   +V  ++  E           E    +  L    D  I+ V 
Sbjct: 64  QEEYRSLRPEYYRGANGILIVYDSTLRESSDE----LTEEWLEELREL-APDDVPILLVG 118

Query: 118 GRIDPINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGK 177
            +ID  ++  + E    + +    E +                 L    + SL      +
Sbjct: 119 NKIDLFDEQSSSE---EILNQLNREVVLLVLAPKAVLPEVANPALLETSAKSLTGPNVNE 175

Query: 178 PVRSLLESLDSDAIPIFKSLNLLTAKPILYI 208
             + LL  L  +   +     L     +   
Sbjct: 176 LFKELLRKLLEEIEKLVLKNELRQLDRLNNP 206


>gnl|CDD|57928 cd01857, HSR1_MMR1, HSR1/MMR1.  Human HSR1, is localized to the
           human MHC class I region and is highly homologous to a
           putative GTP-binding protein, MMR1 from mouse. These
           proteins represent a new subfamily of GTP-binding
           proteins that has only eukaryote members. This subfamily
           shows a circular permutation of the GTPase signature
           motifs so that the C-terminal strands 5, 6, and 7
           (strand 6 contains the G4 box with sequence NKXD) are
           relocated to the N terminus..
          Length = 141

 Score = 33.6 bits (77), Expect = 0.081
 Identities = 12/17 (70%), Positives = 15/17 (88%)

Query: 6   GIIGLPNVGKSTLFNAL 22
           G++G PNVGKS+L NAL
Sbjct: 87  GLVGYPNVGKSSLINAL 103


>gnl|CDD|36405 KOG1191, KOG1191, KOG1191, Mitochondrial GTPase [Translation,
           ribosomal structure and biogenesis].
          Length = 531

 Score = 33.4 bits (76), Expect = 0.088
 Identities = 14/23 (60%), Positives = 18/23 (78%)

Query: 2   GFKCGIIGLPNVGKSTLFNALTR 24
           G +  I+G PNVGKS+L NAL+R
Sbjct: 268 GLQIAIVGRPNVGKSSLLNALSR 290


>gnl|CDD|72973 cd03214, ABC_Iron-Siderophores_B12_Hemin, ABC transporters,
          involved in the uptake of siderophores, heme, and
          vitamin B12, are widely conserved in bacteria and
          archaea.  Only very few species lack representatives of
          the siderophore family transporters.  The E. coli BtuCD
          protein is an ABC transporter mediating vitamin B12
          uptake.  The two ATP-binding cassettes (BtuD) are in
          close contact with each other, as are the two
          membrane-spanning subunits (BtuC); this arrangement is
          distinct from that observed for the E. coli lipid
          flippase MsbA.  The BtuC subunits provide 20
          transmembrane helices grouped around a translocation
          pathway that is closed to the cytoplasm by a gate
          region, whereas the dimer arrangement of the BtuD
          subunits resembles the ATP-bound form of the Rad50 DNA
          repair enzyme.  A prominent cytoplasmic loop of BtuC
          forms the contact region with the ATP-binding cassette
          and represent a conserved motif among the ABC
          transporters..
          Length = 180

 Score = 33.1 bits (76), Expect = 0.11
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 16/76 (21%)

Query: 5  CGIIGLPN-VGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKL--AEIAES 61
           GI+G PN  GKSTL   L               ++P+SGE+ +    +  L   E+A  
Sbjct: 28 VGILG-PNGAGKSTLLKTLAG------------LLKPSSGEILLDGKDLASLSPKELARK 74

Query: 62 KDLVPTRMSFVDIAGL 77
             VP  +  + +A L
Sbjct: 75 IAYVPQALELLGLAHL 90


>gnl|CDD|57929 cd01858, NGP_1, NGP-1.  Autoantigen NGP-1 (Nucleolar G-protein gene
           1) has been shown to localize in the nucleolus and
           nucleolar organizers in all cell types analyzed, which
           is indicative of a function in ribosomal assembly. NGP-1
           and its homologs show a circular permutation of the
           GTPase signature motifs so that the C-terminal strands
           5, 6, and 7 (strand 6 contains the G4 box with NKXD
           motif) are relocated to the N terminus..
          Length = 157

 Score = 32.9 bits (75), Expect = 0.13
 Identities = 13/29 (44%), Positives = 16/29 (55%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYP 34
           G IG PNVGKS++ N L      + A  P
Sbjct: 106 GFIGYPNVGKSSIINTLRSKKVCKVAPIP 134


>gnl|CDD|133439 cd01669, TGS_Ygr210_C, TGS_Ygr210_C: The C-terminal TGS domain of
           Ygr210 GTP-binding protein which is a member of Obg-like
           family of GTPases, and present in archaea. Several
           Obg-like family members possess a C-terminal RNA-binding
           domain, the TGS domain, which is also present in
           threonyl-tRNA synthetase and in bacterial guanosine
           polyphosphatase SpoT. TGS is a small domain of about 50
           amino acid residues with a predominantly beta-sheet
           structure. There is no direct information on the
           function of the TGS domain, but its presence in two
           types of regulatory proteins (the GTPases and guanosine
           polyphosphate phosphohydrolases/synthetases) suggests a
           ligand (most likely nucleotide)-binding, regulatory
           role.
          Length = 76

 Score = 32.6 bits (75), Expect = 0.16
 Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 17/67 (25%)

Query: 296 AWTIPRGTNAQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYIV 355
           A+ +P+G+ A+  A  IHTD   GF+ A+                 +A   R  G++Y +
Sbjct: 24  AFLLPKGSTARDLAYAIHTDIGDGFLHAI-----------------DARTGRRVGEDYEL 66

Query: 356 KDGDILH 362
           K  D++ 
Sbjct: 67  KHRDVIK 73


>gnl|CDD|37696 KOG2485, KOG2485, KOG2485, Conserved ATP/GTP binding protein
           [General function prediction only].
          Length = 335

 Score = 32.6 bits (74), Expect = 0.18
 Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 5/37 (13%)

Query: 7   IIGLPNVGKSTLFNALTR-----TASAQAANYPFCTI 38
           ++G+PNVGKS+L NAL         +A+    P  T 
Sbjct: 148 VVGVPNVGKSSLINALRNVHLRKKKAARVGAEPGVTR 184


>gnl|CDD|37634 KOG2423, KOG2423, KOG2423, Nucleolar GTPase [General function
           prediction only].
          Length = 572

 Score = 31.5 bits (71), Expect = 0.36
 Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 8/42 (19%)

Query: 6   GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAV 47
           G IG PNVGKS++ N L             C + P  GE  V
Sbjct: 311 GFIGYPNVGKSSIINTLR--------KKKVCKVAPIPGETKV 344


>gnl|CDD|36638 KOG1424, KOG1424, KOG1424, Predicted GTP-binding protein MMR1
           [General function prediction only].
          Length = 562

 Score = 31.1 bits (70), Expect = 0.43
 Identities = 11/17 (64%), Positives = 13/17 (76%)

Query: 6   GIIGLPNVGKSTLFNAL 22
           G +G PNVGKS+  NAL
Sbjct: 318 GFVGYPNVGKSSTINAL 334


>gnl|CDD|30567 COG0218, COG0218, Predicted GTPase [General function prediction
          only].
          Length = 200

 Score = 31.0 bits (70), Expect = 0.48
 Identities = 17/40 (42%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 8  IGLPNVGKSTLFNALT-RTASAQAANYPFCTIEPNSGEVA 46
           G  NVGKS+L NALT +   A+ +  P  T   N  EV 
Sbjct: 30 AGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVD 69


>gnl|CDD|48378 cd03114, ArgK-like, The function of this protein family is
          unkown. The protein sequences are similar to the ArgK
          protein in E. coli. ArgK protein is a membrane ATPase
          which is required for transporting arginine, ornithine
          and lysine into the cells by the arginine and ornithine
          (AO system) and lysine, arginine and ornithine (LAO)
          transport systems..
          Length = 148

 Score = 30.2 bits (68), Expect = 0.84
 Identities = 15/37 (40%), Positives = 20/37 (54%)

Query: 6  GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNS 42
          GI G+P  GKSTL +AL     A+        I+P+S
Sbjct: 3  GITGVPGAGKSTLIDALITALRARGKRVAVLAIDPSS 39


>gnl|CDD|31317 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
           systems, ATPase components [Inorganic ion transport and
           metabolism / Coenzyme metabolism].
          Length = 258

 Score = 30.1 bits (68), Expect = 0.86
 Identities = 26/111 (23%), Positives = 40/111 (36%), Gaps = 23/111 (20%)

Query: 5   CGIIGLPN-VGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKD 63
            GI+G PN  GKSTL   L               ++P SGEV +    +  L+    +K 
Sbjct: 31  TGILG-PNGSGKSTLLKCLAG------------LLKPKSGEVLLDGKDIASLSPKELAKK 77

Query: 64  L--------VPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLR 106
           L         P  ++  ++  L R    G   G         V+  + +L 
Sbjct: 78  LAYVPQSPSAPFGLTVYELVLLGRYPHLG-LFGRPSKEDEEIVEEALELLG 127


>gnl|CDD|73015 cd03256, ABC_PhnC_transporter, ABC-type phosphate/phosphonate
          transport system.  Phosphonates are a class of
          organophosphorus compounds characterized by a
          chemically stable carbon-to-phosphorus (C-P) bond.
          Phosphonates are widespread among naturally occurring
          compounds in all kingdoms of wildlife, but only
          procaryotic microorganisms are able to cleave this
          bond.  Certain bacteria such as E. coli can use
          alkylphosphonates as a phosphorus source.  ABC
          transporters are a subset of nucleotide hydrolases that
          contain a signature motif, Q-loop, and H-loop/switch
          region, in addition to, the Walker A motif/P-loop and
          Walker B motif commonly found in a number of ATP- and
          GTP-binding and hydrolyzing proteins..
          Length = 241

 Score = 30.1 bits (68), Expect = 0.91
 Identities = 16/54 (29%), Positives = 21/54 (38%), Gaps = 12/54 (22%)

Query: 2  GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKL 55
          G    +IG    GKSTL   L               +EP SG V +    ++KL
Sbjct: 27 GEFVALIGPSGAGKSTLLRCLNG------------LVEPTSGSVLIDGTDINKL 68


>gnl|CDD|36703 KOG1490, KOG1490, KOG1490, GTP-binding protein CRFG/NOG1 (ODN
           superfamily) [General function prediction only].
          Length = 620

 Score = 30.0 bits (67), Expect = 0.97
 Identities = 14/31 (45%), Positives = 18/31 (58%), Gaps = 1/31 (3%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYPFCT 37
           + G PNVGKS+  N +TR A  +   Y F T
Sbjct: 173 VCGYPNVGKSSFNNKVTR-ADDEVQPYAFTT 202


>gnl|CDD|143354 cd07849, STKc_ERK1_2_like, Catalytic domain of Extracellular
           signal-Regulated Kinase 1 and 2-like Serine/Threonine
           Kinases.  Serine/Threonine Kinases (STKs), Extracellular
           signal-regulated kinases 1 and 2 (ERK1/2) and Fus3
           subfamily, catalytic (c) domain. STKs catalyze the
           transfer of the gamma-phosphoryl group from ATP to
           serine/threonine residues on protein substrates. This
           ERK1/2-like subfamily is part of a larger superfamily
           that includes the catalytic domains of other protein
           STKs, protein tyrosine kinases, RIO kinases,
           aminoglycoside phosphotransferase, choline kinase, and
           phosphoinositide 3-kinase. This subfamily is composed of
           the mitogen-activated protein kinases (MAPKs) ERK1,
           ERK2, baker's yeast Fus3, and similar proteins. MAPK
           pathways are important mediators of cellular responses
           to extracellular signals. ERK1/2 activation is
           preferentially by mitogenic factors, differentiation
           stimuli, and cytokines, through a kinase cascade
           involving the MAPK kinases MEK1/2 and a MAPK kinase
           kinase from the Raf family. ERK1/2 have numerous
           substrates, many of which are nuclear and participate in
           transcriptional regulation of many cellular processes.
           They regulate cell growth, cell proliferation, and cell
           cycle progression from G1 to S phase. Although the
           distinct roles of ERK1 and ERK2 have not been fully
           determined, it is known that ERK2 can maintain most
           functions in the absence of ERK1, and that the deletion
           of ERK2 is embryonically lethal. The MAPK, Fus3,
           regulates yeast mating processes including
           mating-specific gene expression, G1 arrest, mating
           projection, and cell fusion.
          Length = 336

 Score = 29.6 bits (67), Expect = 1.5
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 10/54 (18%)

Query: 95  IREVDAIIHVLRCFKDENIIHV-----EGRIDPINDIETIETELMLSDLERLER 143
           +RE    I +LR FK ENII +         +  ND+  ++ ELM +DL +L +
Sbjct: 51  LRE----IKILRRFKHENIIGILDIIRPPSFESFNDVYIVQ-ELMETDLYKLIK 99


>gnl|CDD|39443 KOG4242, KOG4242, KOG4242, Predicted myosin-I-binding protein [Cell
           motility].
          Length = 553

 Score = 29.3 bits (65), Expect = 1.7
 Identities = 15/71 (21%), Positives = 25/71 (35%)

Query: 248 ISQLPEEERALFMEELDISISGLELLIRSGYRLLDLITYFTVGPKETRAWTIPRGTNAQK 307
           IS+L  +   L++ ELD+S +G +  I                 + T    +   T+   
Sbjct: 204 ISKLLIQSGRLWLTELDLSTNGGKDDIPRTLNKKAGTLVLFKLDRSTTGIRLDLLTSPLA 263

Query: 308 AAGVIHTDFEK 318
           A       F K
Sbjct: 264 AGRTTKLTFGK 274


>gnl|CDD|73053 cd03294, ABC_Pro_Gly_Bertaine, This family comprises the glycine
           betaine/L-proline ATP binding subunit in bacteria and
           its equivalents in archaea.  This transport system
           belong to the larger ATP-Binding Cassette (ABC)
           transporter superfamily.  The characteristic feature of
           these transporters is the obligatory coupling of ATP
           hydrolysis to substrate translocation.  ABC transporters
           are a subset of nucleotide hydrolases that contain a
           signature motif, Q-loop, and H-loop/switch region, in
           addition to, the Walker A motif/P-loop and Walker B
           motif commonly found in a number of ATP- and GTP-binding
           and hydrolyzing proteins..
          Length = 269

 Score = 29.4 bits (66), Expect = 1.9
 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 13/66 (19%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
           I+GL   GKSTL   + R             IEP SG+V +    +  ++   E ++L  
Sbjct: 55  IMGLSGSGKSTLLRCINR------------LIEPTSGKVLIDGQDIAAMSR-KELRELRR 101

Query: 67  TRMSFV 72
            ++S V
Sbjct: 102 KKISMV 107


>gnl|CDD|72980 cd03221, ABCF_EF-3, ABCF_EF-3  Elongation factor 3 (EF-3) is a
          cytosolic protein required by fungal ribosomes for in
          vitro protein synthesis and for in vivo growth.  EF-3
          stimulates the binding of the EF-1: GTP: aa-tRNA
          ternary complex to the ribosomal A site by facilitated
          release of the deacylated tRNA from the E site.  The
          reaction requires ATP hydrolysis.  EF-3 contains two
          ATP nucleotide binding sequence (NBS) motifs.  NBSI is
          sufficient for the intrinsic ATPase activity. NBSII is
          essential for the ribosome-stimulated functions..
          Length = 144

 Score = 29.3 bits (66), Expect = 1.9
 Identities = 12/49 (24%), Positives = 18/49 (36%), Gaps = 12/49 (24%)

Query: 1  MGFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPD 49
           G + G++G    GKSTL   +               +EP+ G V    
Sbjct: 25 PGDRIGLVGRNGAGKSTLLKLIA------------GELEPDEGIVTWGS 61


>gnl|CDD|133258 cd00882, Ras_like_GTPase, Ras-like GTPase superfamily. The Ras-like
           superfamily of small GTPases consists of several
           families with an extremely high degree of structural and
           functional similarity. The Ras superfamily is divided
           into at least four families in eukaryotes: the Ras, Rho,
           Rab, and Sar1/Arf families.  This superfamily also
           includes proteins like the GTP translation factors,
           Era-like GTPases, and G-alpha chain of the
           heterotrimeric G proteins.  Members of the Ras
           superfamily regulate a wide variety of cellular
           functions: the Ras family regulates gene expression, the
           Rho family regulates cytoskeletal reorganization and
           gene expression, the Rab and Sar1/Arf families regulate
           vesicle trafficking, and the Ran family regulates
           nucleocytoplasmic transport and microtubule
           organization. The GTP translation factor family regulate
           initiation, elongation, termination, and release in
           translation, and the Era-like GTPase family regulates
           cell division, sporulation, and DNA replication. Members
           of the Ras superfamily are identified by the GTP binding
           site, which is made up of five characteristic sequence
           motifs, and the switch I and switch II regions.
          Length = 157

 Score = 29.0 bits (65), Expect = 2.0
 Identities = 19/98 (19%), Positives = 27/98 (27%), Gaps = 23/98 (23%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAESKDLVP 66
           ++G   VGK++L N                  E    E        +         D   
Sbjct: 1   VVGDSGVGKTSLLNR-------------LLGGEFVPEEYETTIIDFYS---KTIEVDGKK 44

Query: 67  TRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHV 104
            ++   D AG  R  S           + R  D II V
Sbjct: 45  VKLQIWDTAGQERFRSLRR-------LYYRGADGIILV 75


>gnl|CDD|37772 KOG2561, KOG2561, KOG2561, Adaptor protein NUB1, contains UBA
           domain [Posttranslational modification, protein
           turnover, chaperones, Signal transduction mechanisms].
          Length = 568

 Score = 29.2 bits (65), Expect = 2.0
 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 4/60 (6%)

Query: 142 ERLFEKNKKYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLESLDSDAIPIFKSLNLLT 201
           ER   + KKY N   ++ V  +S+     RL+  G       E+L  +   I K+L+LL 
Sbjct: 356 EREILERKKYGNTPMKKWVNPRSLE----RLVSMGYERELAAEALRRNENDIQKALDLLQ 411


>gnl|CDD|72978 cd03219, ABC_Mj1267_LivG_branched, The Mj1267/LivG ABC
          transporter subfamily is involved in the transport of
          the hydrophobic amino acids leucine, isoleucine and
          valine.  MJ1267 is a branched-chain amino acid
          transporter with 29% similarity to both the LivF and
          LivG components of the E. coli  branched-chain amino
          acid transporter.  MJ1267 contains an insertion from
          residues 114 to 123 characteristic of LivG
          (Leucine-Isoleucine-Valine) homologs.  The
          branched-chain amino acid transporter from E. coli
          comprises a heterodimer of ABCs (LivF and LivG), a
          heterodimer of six-helix TM domains (LivM and LivH),
          and one of two alternative soluble periplasmic
          substrate binding proteins (LivK or LivJ)..
          Length = 236

 Score = 28.9 bits (65), Expect = 2.2
 Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 14/42 (33%)

Query: 5  CGIIGLPN-VGKSTLFNALTRTASAQAANYPFCTIEPNSGEV 45
           G+IG PN  GK+TLFN ++              + P SG V
Sbjct: 29 HGLIG-PNGAGKTTLFNLISG------------FLRPTSGSV 57


>gnl|CDD|36138 KOG0920, KOG0920, KOG0920, ATP-dependent RNA helicase A [RNA
           processing and modification].
          Length = 924

 Score = 28.7 bits (64), Expect = 2.5
 Identities = 18/91 (19%), Positives = 33/91 (36%), Gaps = 13/91 (14%)

Query: 108 FKDENIIHVEGRIDPINDIETIETELMLSD-LERLERLFEKNKKYRNHKSEEIVLLQSII 166
           F    +I + GR  P+        E  L D L +   + E +      +  ++ L +  +
Sbjct: 338 FGGCPVITIPGRTFPV-------KEYFLEDILSKTGYVSEDDSARSGPERSQLRLARLKL 390

Query: 167 SSS---LRLIEEGKPVRSLLESLDSDAIPIF 194
                   LIE+   +  + E     AI +F
Sbjct: 391 WEPEIDYDLIED--LIEYIDEREFEGAILVF 419


>gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system,
           ATPase component [Amino acid transport and metabolism].
          Length = 386

 Score = 28.8 bits (64), Expect = 2.8
 Identities = 28/94 (29%), Positives = 40/94 (42%), Gaps = 27/94 (28%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEV-------------AVPDPRMH 53
           I+GL   GKSTL   L R             IEP  GE+              + + R  
Sbjct: 59  IMGLSGSGKSTLVRLLNR------------LIEPTRGEILVDGKDIAKLSAAELRELRRK 106

Query: 54  KLAEIAESKDLVPTRMSFVDIA-GL-VRGASKGE 85
           K++ + +S  L+P R    ++A GL V+G  K E
Sbjct: 107 KISMVFQSFALLPHRTVLENVAFGLEVQGVPKAE 140


>gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and
          related GTPases of G3E family [Amino acid transport and
          metabolism].
          Length = 323

 Score = 28.4 bits (63), Expect = 3.1
 Identities = 14/37 (37%), Positives = 19/37 (51%)

Query: 6  GIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNS 42
          GI G+P  GKSTL  AL R    +        ++P+S
Sbjct: 55 GITGVPGAGKSTLIEALGRELRERGHRVAVLAVDPSS 91


>gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide
          transport and metabolism].
          Length = 178

 Score = 28.3 bits (63), Expect = 3.3
 Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 10/63 (15%)

Query: 7  IIGLPNVGKSTLFNALTRTASAQAANYPFC---TIEPNSGEVAVPDPRMHKLAEIAESKD 63
          I+G P  GKSTL       A   A         T +     +A       ++ +  +  +
Sbjct: 5  ILGPPGAGKSTL-------AKKLAKKLGLPHLDTGDILRAAIAERTELGEEIKKYIDKGE 57

Query: 64 LVP 66
          LVP
Sbjct: 58 LVP 60


>gnl|CDD|133292 cd01892, Miro2, Miro2 subfamily.  Miro (mitochondrial Rho)
          proteins have tandem GTP-binding domains separated by a
          linker region containing putative calcium-binding EF
          hand motifs.  Genes encoding Miro-like proteins were
          found in several eukaryotic organisms.  This CD
          represents the putative GTPase domain in the C terminus
          of Miro proteins.  These atypical Rho GTPases have
          roles in mitochondrial homeostasis and apoptosis.  Most
          Rho proteins contain a lipid modification site at the
          C-terminus; however, Miro is one of few Rho subfamilies
          that lack this feature.
          Length = 169

 Score = 28.3 bits (64), Expect = 3.3
 Identities = 8/20 (40%), Positives = 10/20 (50%)

Query: 3  FKCGIIGLPNVGKSTLFNAL 22
          F C ++G    GKS L  A 
Sbjct: 5  FLCFVLGAKGSGKSALLRAF 24


>gnl|CDD|73006 cd03247, ABCC_cytochrome_bd, The CYD subfamily implicated in
           cytochrome bd biogenesis.  The CydC and CydD proteins
           are important for the formation of cytochrome bd
           terminal oxidase of E. coli and it has been proposed
           that they were necessary for biosynthesis of the
           cytochrome bd quinol oxidase and for periplasmic c-type
           cytochromes.  CydCD were proposed to determine a
           heterooligomeric complex important for heme export into
           the periplasm or to be involved in the maintenance of
           the proper redox state of the periplasmic space.  In
           Bacillus subtilius, the absence of CydCD does not affect
           the presence of halo-cytochrome c in the membrane and
           this observation suggests that CydCD proteins are not
           involved in the export of heme in this organism..
          Length = 178

 Score = 28.2 bits (63), Expect = 3.6
 Identities = 26/134 (19%), Positives = 54/134 (40%), Gaps = 25/134 (18%)

Query: 2   GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAES 61
           G K  ++G    GKSTL   LT              ++P  GE+ +          +++ 
Sbjct: 28  GEKIALLGRSGSGKSTLLQLLTG------------DLKPQQGEITLDG------VPVSDL 69

Query: 62  KDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHV----E 117
           +  + + +S ++    +   +    LG +F    R+  A+  +L   +D  I+ +     
Sbjct: 70  EKALSSLISVLNQRPYLFDTTLRNNLGRRFSGGERQRLALARIL--LQDAPIVLLDEPTV 127

Query: 118 GRIDPINDIETIET 131
           G +DPI + + +  
Sbjct: 128 G-LDPITERQLLSL 140


>gnl|CDD|33698 COG3911, COG3911, Predicted ATPase [General function prediction
          only].
          Length = 183

 Score = 28.0 bits (62), Expect = 3.7
 Identities = 20/64 (31%), Positives = 25/64 (39%), Gaps = 2/64 (3%)

Query: 7  IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNS--GEVAVPDPRMHKLAEIAESKDL 64
          + G P  GK+TL  AL R   A         I   S  G  A+P       AE+   + L
Sbjct: 14 LTGGPGAGKTTLLAALARAGFATVEEAGRDIIALESAQGGTALPWTDPGAFAELVGLQRL 73

Query: 65 VPTR 68
            TR
Sbjct: 74 RQTR 77


>gnl|CDD|146421 pfam03770, IPK, Inositol polyphosphate kinase.  ArgRIII has has
           been demonstrated to be an inositol polyphosphate
           kinase.
          Length = 184

 Score = 28.3 bits (64), Expect = 3.8
 Identities = 15/81 (18%), Positives = 22/81 (27%), Gaps = 19/81 (23%)

Query: 103 HVLRCFKDENIIH-----VEGRIDPINDIETIETELMLSDLERLERLFEKNKKYRNHKSE 157
           +  R    E +                  + I     L  L+ L    E  + YR     
Sbjct: 73  YYGRSLSAEEVKEALKRFFSNGKSLRRSKKLIPR--FLERLQELRNWLESQESYR----- 125

Query: 158 EIVLLQSIISSSLRLIEEGKP 178
                    SSSL  + +G P
Sbjct: 126 -------FYSSSLLFVYDGDP 139


>gnl|CDD|36463 KOG1249, KOG1249, KOG1249, Predicted GTPases [General function
           prediction only].
          Length = 572

 Score = 28.0 bits (62), Expect = 4.0
 Identities = 28/115 (24%), Positives = 40/115 (34%), Gaps = 17/115 (14%)

Query: 8   IGLPNVGKSTLFNALTR-----------TASAQAANYPFCTIEPNSGEVAVPDP-RMHKL 55
           +G  NVGKSTLFNAL                A  +++P  T+      V VP P R+   
Sbjct: 219 VGATNVGKSTLFNALLESDLCSVNAPKLVDRATISDWPGTTLSLLKFPVLVPHPYRLGGR 278

Query: 56  -----AEIAESKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVL 105
                     +K  +  R       G    A     +G  F      ++A+   L
Sbjct: 279 RKRLGVHSVSAKKDMGERDLLALETGDAGKAGPVAAVGRTFAGSEELINAMAKEL 333


>gnl|CDD|132953 cd06622, PKc_MAPKK_PBS2_like, Catalytic domain of fungal PBS2-like
           dual-specificity MAP kinase kinases.  Protein kinases
           (PKs), MAP kinase kinase (MAPKK) subfamily, fungal
           PBS2-like proteins, catalytic (c) domain. PKs catalyze
           the transfer of the gamma-phosphoryl group from ATP to
           serine/threonine or tyrosine residues on protein
           substrates. The MAPKK subfamily is part of a larger
           superfamily that includes the catalytic domains of other
           protein serine/threonine kinases, protein tyrosine
           kinases, RIO kinases, aminoglycoside phosphotransferase,
           choline kinase, and phosphoinositide 3-kinase. The
           mitogen-activated protein (MAP) kinase signaling
           pathways are important mediators of cellular responses
           to extracellular signals. The pathways involve a triple
           kinase core cascade comprising of the MAP kinase (MAPK),
           which is phosphorylated and activated by a MAPK kinase
           (MAPKK or MKK), which itself is phosphorylated and
           activated by a MAPK kinase kinase (MAPKKK or MKKK).
           Members of this group include the MAPKKs Polymyxin B
           resistance protein 2 (PBS2) from Saccharomyces
           cerevisiae, Wis1 from Schizosaccharomyces pombe, and
           related proteins. PBS2 and Wis1 are components of
           stress-activated MAPK cascades in budding and fission
           yeast, respectively. PBS2 is the specific activator of
           the MAPK Hog1, which plays a central role in the
           response of budding yeast to stress including exposure
           to arsenite and hyperosmotic environments. Wis1
           phosphorylates and activates the MAPK Sty1 (also called
           Spc1 or Phh1), which stimulates a transcriptional
           response to a wide range of cellular insults through the
           bZip transcription factors Atf1, Pcr1, and Pap1.
          Length = 286

 Score = 27.9 bits (62), Expect = 4.2
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 6/51 (11%)

Query: 69  MSFVD---IAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDE-NIIH 115
           M ++D   +  L  G    EG+    L  I    A++  L+  K+E NIIH
Sbjct: 78  MEYMDAGSLDKLYAGGVATEGIPEDVLRRI--TYAVVKGLKFLKEEHNIIH 126


>gnl|CDD|35277 KOG0054, KOG0054, KOG0054, Multidrug resistance-associated
            protein/mitoxantrone resistance protein, ABC superfamily
            [Secondary metabolites biosynthesis, transport and
            catabolism].
          Length = 1381

 Score = 27.9 bits (62), Expect = 4.3
 Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 12/46 (26%)

Query: 2    GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAV 47
            G K GI+G    GKS+L  AL R             +EP  GE+ +
Sbjct: 1166 GEKVGIVGRTGAGKSSLILALFR------------LVEPAEGEILI 1199


>gnl|CDD|143363 cd07858, STKc_TEY_MAPK_plant, Catalytic domain of the
           Serine/Threonine Kinases, TEY Mitogen-Activated Protein
           Kinases from Plants.  Serine/Threonine Kinases (STKs),
           Plant TEY Mitogen-Activated Protein Kinase (MAPK)
           subfamily, catalytic (c) domain. STKs catalyze the
           transfer of the gamma-phosphoryl group from ATP to
           serine/threonine residues on protein substrates. The TEY
           MAPK subfamily is part of a larger superfamily that
           includes the catalytic domains of other protein STKs,
           protein tyrosine kinases, RIO kinases, aminoglycoside
           phosphotransferase, choline kinase, and phosphoinositide
           3-kinase. MAPKs are important mediators of cellular
           responses to extracellular signals. In plants, MAPKs are
           associated with physiological, developmental, hormonal,
           and stress responses. Some plants show numerous gene
           duplications of MAPKs. Arabidopsis thaliana harbors at
           least 20 MAPKs, named AtMPK1-20. There are two subtypes
           of plant MAPKs based on the conserved phosphorylation
           motif present in the activation loop, TEY and TDY. This
           subfamily represents the TEY subtype and is further
           subdivided into three groups (A, B, and C). Group A is
           represented by AtMPK3, AtMPK6, Nicotiana tabacum BTF4
           (NtNTF4), among others. They are mostly involved in
           environmental and hormonal responses. AtMPK3 and  AtMPK6
           are also key regulators for stomatal development and
           patterning. Group B is represented by AtMPK4, AtMPK13,
           and NtNTF6, among others. They may be involved in both
           cell division and environmental stress response. AtMPK4
           also participates in regulating innate immunity. Group C
           is represented by AtMPK1, AtMPK2, NtNTF3, Oryza sativa
           MAPK4 (OsMAPK4), among others. They may also be involved
           in stress responses. AtMPK1 and AtMPK2 are activated
           following mechanical injury and in the presence of
           stress chemicals such as jasmonic acid, hydrogen
           peroxide and abscisic acid. OsMAPK4 is also called
           OsMSRMK3 for Multiple Stress-Responsive MAPK3.
          Length = 337

 Score = 28.1 bits (63), Expect = 4.4
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 6/47 (12%)

Query: 102 IHVLRCFKDENIIHVEGRIDPI-----NDIETIETELMLSDLERLER 143
           I +LR    EN+I ++  + P      ND+  I  ELM +DL ++ R
Sbjct: 55  IKLLRHLDHENVIAIKDIMPPPHREAFNDV-YIVYELMDTDLHQIIR 100


>gnl|CDD|37292 KOG2081, KOG2081, KOG2081, Nuclear transport regulator
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 559

 Score = 28.0 bits (62), Expect = 4.8
 Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 2/71 (2%)

Query: 195 KSLNLLTAKPILYICNVSEHD--CKKGNIYTEAVQRLASQQNAEMIIISAAIEAEISQLP 252
           K L    A     IC+       C   ++        ++Q N E   +   I   IS LP
Sbjct: 480 KRLASAAALAFHRICSACRVQMTCLIPSLLELIRSLDSTQINEEAACLLQGISLIISNLP 539

Query: 253 EEERALFMEEL 263
             +  + +EEL
Sbjct: 540 AHKAKIALEEL 550


>gnl|CDD|147781 pfam05816, TelA, Toxic anion resistance protein (TelA).  This
           family consists of several prokaryotic TelA like
           proteins. TelA and KlA are associated with tellurite
           resistance and plasmid fertility inhibition.
          Length = 333

 Score = 27.9 bits (63), Expect = 5.0
 Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 2/37 (5%)

Query: 116 VEGRIDPI-NDIETIETELMLSDLERLERLFEKNKKY 151
           V G+ID I  ++E  + EL+  D   L++L++KN +Y
Sbjct: 96  VGGQIDKILVELEKGKDELL-KDNAMLDQLYDKNLEY 131


>gnl|CDD|110135 pfam01112, Asparaginase_2, Asparaginase. 
          Length = 296

 Score = 27.8 bits (62), Expect = 5.2
 Identities = 9/56 (16%), Positives = 19/56 (33%)

Query: 305 AQKAAGVIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGKEYIVKDGDI 360
           A+ AA  I     +G    + +++K  +             A ++G      +  I
Sbjct: 238 AEAAAKRITKALPRGSGGLIALNHKGEIGAPCNTTGMFRATATEDGTTLEYSEIGI 293


>gnl|CDD|112137 pfam03308, ArgK, ArgK protein.  The ArgK protein acts as an
          ATPase enzyme and as a kinase, and phosphorylates
          periplasmic binding proteins involved in the LAO
          (lysine, arginine, ornithine)/AO transport systems.
          Length = 267

 Score = 27.7 bits (62), Expect = 5.6
 Identities = 11/18 (61%), Positives = 12/18 (66%)

Query: 6  GIIGLPNVGKSTLFNALT 23
          GI G+P  GKSTL  AL 
Sbjct: 33 GITGVPGAGKSTLIEALG 50


>gnl|CDD|30834 COG0488, Uup, ATPase components of ABC transporters with duplicated
           ATPase domains [General function prediction only].
          Length = 530

 Score = 27.5 bits (61), Expect = 5.6
 Identities = 27/145 (18%), Positives = 50/145 (34%), Gaps = 30/145 (20%)

Query: 2   GFKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGEVAVPDPRMHKLAEIAES 61
           G + G++G    GKSTL   L               +EP+SGEV  P     ++  +++ 
Sbjct: 29  GERIGLVGRNGAGKSTLLKILAG------------ELEPDSGEVTRPKG--LRVGYLSQE 74

Query: 62  KDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDAIIHVLRCFKDENIIHVEGRID 121
             L P +     +                    + E++    +L    DE +  +E  ++
Sbjct: 75  PPLDPEKTVLDYVIEGFGELR----------ELLAELEEAYALLADPDDELLAELEALLE 124

Query: 122 PIN------DIETIETELMLSDLER 140
            ++        E     L   D +R
Sbjct: 125 ELDGWTLEARAEEALLGLGFPDEDR 149


>gnl|CDD|38920 KOG3716, KOG3716, KOG3716, Carnitine O-acyltransferase CPTI [Lipid
           transport and metabolism].
          Length = 764

 Score = 27.6 bits (61), Expect = 5.6
 Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 5/41 (12%)

Query: 311 VIHTDFEKGFIRALTISYKDYVAMGGENAAKEAGKARDEGK 351
           ++ TDF KGFI+   +S   ++ M     A +    RD+GK
Sbjct: 540 LVFTDFGKGFIKKCGVSPDAFIQM-----ALQLAYYRDQGK 575


>gnl|CDD|133359 cd04159, Arl10_like, Arl10-like subfamily.  Arl9/Arl10 was
          identified from a human cancer-derived EST dataset.  No
          functional information about the subfamily is available
          at the current time, but crystal structures of human
          Arl10b and Arl10c have been solved.
          Length = 159

 Score = 27.3 bits (61), Expect = 6.5
 Identities = 8/18 (44%), Positives = 12/18 (66%)

Query: 6  GIIGLPNVGKSTLFNALT 23
           ++GL N GK+TL N + 
Sbjct: 3  TLVGLQNSGKTTLVNVIA 20


>gnl|CDD|39796 KOG4596, KOG4596, KOG4596, Uncharacterized conserved protein
            [Function unknown].
          Length = 1936

 Score = 27.3 bits (60), Expect = 7.1
 Identities = 46/222 (20%), Positives = 80/222 (36%), Gaps = 58/222 (26%)

Query: 53   HKLAEIAESKDLVPTRMSFVDIAGLVRGASKGEGLGNQFLAHIREVDA-IIHVLRCFKDE 111
            H++    E +D   T + F                GNQ +AHI EV A II +   +K  
Sbjct: 1072 HEIYNWTELQDTSLTCIEF----------------GNQKIAHINEVHAAIILLTSKYKGI 1115

Query: 112  NIIHVEGRID----------PINDIETIETELMLSDLERLERLFEKNKKYRNHKSEEIVL 161
            +    EG +D               ET E+  +L D  +LE +          +S     
Sbjct: 1116 SDPEFEGLLDLWFPPNKPIPNAFLRETGESNQLLPDWLKLEMI----------RSVV--- 1162

Query: 162  LQSIISSSLRLIEE----------GKPVRS---LLESLDSDAIPIFKSL--NLLTAKPIL 206
             Q ++ ++L  +            G PV S   LL+ LD+  +P    +   +L+   + 
Sbjct: 1163 -QRLVDAALIDLSPHQAQLFVQVFGMPVESMSKLLKMLDNAVMPDLDRIDHQILSKMYLA 1221

Query: 207  YICNVSEHDCKKGNIYTEAVQRLASQQNAEMIIISAAIEAEI 248
            ++         +       + R+ SQ +  +  I+     EI
Sbjct: 1222 HLIEGQRMRGAQSGETL--INRIHSQMDNLLPFIAKEEPMEI 1261


>gnl|CDD|143799 pfam00006, ATP-synt_ab, ATP synthase alpha/beta family,
          nucleotide-binding domain.  This family includes the
          ATP synthase alpha and beta subunits, the ATP synthase
          associated with flagella and the termination factor
          Rho.
          Length = 213

 Score = 27.0 bits (61), Expect = 7.9
 Identities = 10/33 (30%), Positives = 13/33 (39%), Gaps = 3/33 (9%)

Query: 2  GFKCGIIGLPNVGKSTLFNALTRTASAQAANYP 34
          G + GI G    GK+ L   L   A    A+  
Sbjct: 15 GQRIGIFGGSGTGKTVL---LGMIARNAKADVV 44


>gnl|CDD|33396 COG3596, COG3596, Predicted GTPase [General function prediction
          only].
          Length = 296

 Score = 27.2 bits (60), Expect = 8.1
 Identities = 9/35 (25%), Positives = 15/35 (42%)

Query: 7  IIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPN 41
          ++G    GKS+L NAL +    + +     T    
Sbjct: 44 LMGATGAGKSSLINALFQGEVKEVSKVGVGTDITT 78


>gnl|CDD|34791 COG5192, BMS1, GTP-binding protein required for 40S ribosome
           biogenesis [Translation, ribosomal structure and
           biogenesis].
          Length = 1077

 Score = 27.1 bits (59), Expect = 8.3
 Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 7/69 (10%)

Query: 3   FKCGIIGLPNVGKSTLFNALTRTASAQAANYPFCTIEPNSGE------VAVPDPRMHKLA 56
           F   ++G P  GKSTL  +L R  + Q  +     I   SG+      +  P   +H++ 
Sbjct: 70  FIVAVVGPPGTGKSTLIRSLVRRFTKQTIDEIRGPITVVSGKTRRITFLECPSD-LHQMI 128

Query: 57  EIAESKDLV 65
           ++A+  DLV
Sbjct: 129 DVAKIADLV 137


>gnl|CDD|133282 cd01882, BMS1, Bms1.  Bms1 is an essential, evolutionarily
          conserved, nucleolar protein.  Its depletion interferes
          with processing of the 35S pre-rRNA at sites A0, A1,
          and A2, and the formation of 40S subunits.  Bms1, the
          putative endonuclease Rc11, and the essential U3 small
          nucleolar RNA form a stable subcomplex that is believed
          to control an early step in the formation of the 40S
          subumit.  The C-terminal domain of Bms1 contains a
          GTPase-activating protein (GAP) that functions
          intramolecularly.  It is believed that Rc11 activates
          Bms1 by acting as a guanine-nucleotide exchange factor
          (GEF) to promote GDP/GTP exchange, and that activated
          (GTP-bound) Bms1 delivers Rc11 to the preribosomes.
          Length = 225

 Score = 26.9 bits (60), Expect = 8.3
 Identities = 9/23 (39%), Positives = 15/23 (65%)

Query: 7  IIGLPNVGKSTLFNALTRTASAQ 29
          ++G P VGK+TL  +L +  + Q
Sbjct: 44 VVGPPGVGKTTLIKSLVKNYTKQ 66


>gnl|CDD|88298 cd05027, S-100B, S-100B: S-100B domain found in proteins similar to
           S100B. S100B is a calcium-binding protein belonging to a
           large S100 vertebrate-specific protein family within the
           EF-hand superfamily of calcium-binding proteins. Note
           that the S-100 hierarchy, to which this S-100B group
           belongs, contains only S-100 EF-hand domains, other
           EF-hands have been modeled separately. S100B is most
           abundant in glial cells of the central nervous system,
           predominately in astrocytes. S100B is involved in signal
           transduction via the inhibition of protein
           phoshorylation, regulation of enzyme activity and by
           affecting the calcium homeostasis. Upon calcium binding
           the S100B homodimer changes conformation to expose a
           hydrophobic cleft, which represents the interaction site
           of S100B with its more than 20 known target  proteins.
           These target proteins include several cellular
           architecture proteins such as tubulin and GFAP; S100B
           can inhibit polymerization of these oligomeric
           molecules. Furthermore, S100B inhibits the
           phosphorylation of multiple kinase substrates including
           the Alzheimer protein tau and neuromodulin (GAP-43)
           through a calcium-sensitive interaction with the protein
           substrates..
          Length = 88

 Score = 26.9 bits (59), Expect = 8.3
 Identities = 15/40 (37%), Positives = 25/40 (62%)

Query: 150 KYRNHKSEEIVLLQSIISSSLRLIEEGKPVRSLLESLDSD 189
           K++  KSE   L+ + +S  L  I+E + V  ++E+LDSD
Sbjct: 24  KHKLKKSELKELINNELSHFLEEIKEQEVVDKVMETLDSD 63


>gnl|CDD|36919 KOG1707, KOG1707, KOG1707, Predicted Ras related/Rac-GTP binding
           protein [Defense mechanisms].
          Length = 625

 Score = 26.9 bits (59), Expect = 9.0
 Identities = 8/20 (40%), Positives = 12/20 (60%)

Query: 3   FKCGIIGLPNVGKSTLFNAL 22
           F+C ++G  N GKS L  + 
Sbjct: 426 FQCFVVGPKNCGKSALLQSF 445


>gnl|CDD|99995 cd04299, GT1_Glycogen_Phosphorylase_like, This family is most
           closely related to the oligosaccharide phosphorylase
           domain family and other unidentified sequences.
           Oligosaccharide phosphorylase catalyzes the breakdown of
           oligosaccharides into glucose-1-phosphate units. They
           are important allosteric enzymes in carbohydrate
           metabolism. The members of this family are found in
           bacteria and Archaea..
          Length = 778

 Score = 26.7 bits (60), Expect = 9.1
 Identities = 8/12 (66%), Positives = 10/12 (83%)

Query: 133 LMLSDLERLERL 144
           L+L D ERL+RL
Sbjct: 495 LLLRDPERLKRL 506


>gnl|CDD|146089 pfam03280, Lipase_chap, Proteobacterial lipase chaperone protein. 
          Length = 195

 Score = 26.8 bits (60), Expect = 9.1
 Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 2/35 (5%)

Query: 225 AVQRLASQQNAEMIIIS--AAIEAEISQLPEEERA 257
           A++RL  +Q+  +        + A I+QLPE+ R 
Sbjct: 65  ALERLRIKQDPSLSDEQKARRLAALIAQLPEDLRE 99


>gnl|CDD|33644 COG3854, SpoIIIAA, ncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 308

 Score = 26.9 bits (59), Expect = 9.6
 Identities = 11/28 (39%), Positives = 14/28 (50%)

Query: 7   IIGLPNVGKSTLFNALTRTASAQAANYP 34
           IIG P VGK+TL   + R  S     + 
Sbjct: 142 IIGPPQVGKTTLLRDIARLLSDGINQFL 169


>gnl|CDD|30807 COG0459, GroL, Chaperonin GroEL (HSP60 family) [Posttranslational
           modification, protein turnover, chaperones].
          Length = 524

 Score = 26.7 bits (59), Expect = 9.6
 Identities = 21/94 (22%), Positives = 37/94 (39%), Gaps = 12/94 (12%)

Query: 159 IVLLQSIISSSLRLIEEG-----------KPVRSLLESLDSDAIPIFKSLNLLTAKPILY 207
           +VL  +++  + +LI  G             V   +E L   A P+  S   L       
Sbjct: 89  VVLAGALLKEAEKLIAAGIHPTVIKRGYRLAVEKAVEELKEIAKPVSDSEEELKIAITSV 148

Query: 208 ICNVSEHDCKKGNIYTEAVQRLA-SQQNAEMIII 240
               +  D + G +  EAV+++   Q + + III
Sbjct: 149 ASKSANSDEEIGELVVEAVEKVGKEQSDLDGIII 182


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.318    0.136    0.383 

Gapped
Lambda     K      H
   0.267   0.0790    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,297,598
Number of extensions: 229035
Number of successful extensions: 1029
Number of sequences better than 10.0: 1
Number of HSP's gapped: 989
Number of HSP's successfully gapped: 139
Length of query: 367
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 272
Effective length of database: 4,210,882
Effective search space: 1145359904
Effective search space used: 1145359904
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 58 (26.0 bits)