RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780809|ref|YP_003065222.1| tRNA modification GTPase TrmE
[Candidatus Liberibacter asiaticus str. psy62]
         (440 letters)



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

 Score =  441 bits (1135), Expect = e-124
 Identities = 186/454 (40%), Positives = 261/454 (57%), Gaps = 19/454 (4%)

Query: 4   EKETIFAVSTGALPSAISIIRLSGPSCFQVCEFICKKKK-PFPRKASLRYFFGLDGRILD 62
             +TI A++T     AI I+R+SGP   ++ + +    K P PR A   +    +G I+D
Sbjct: 3   MFDTIAAIATAPGEGAIGIVRISGPDALEIAQKLFGGLKLPKPRTAHYGHIKDENGEIID 62

Query: 63  KGLLIVFPSPESFTGEDSAEFHVHGGIAVVNGILEELAKMPNLRLANPGEFSRRAFENGK 122
           + L++ F +P SFTGED  E   HGG  VVN ILE L K+   RLA PGEFS+RAF NGK
Sbjct: 63  EVLVLYFKAPNSFTGEDVVEIQCHGGPVVVNLILELLLKLG-ARLAEPGEFSKRAFLNGK 121

Query: 123 IDLLEAESLADLISSETEMQRRLSMEGMSGELSSLYGQWIDKLTHIRSFIEADLDFSEEE 182
           +DL +AE++ADLI ++TE   R+++  + G LS L  +  + L  + + +EA++DF EE+
Sbjct: 122 LDLTQAEAIADLIDAKTEQAARIALRQLQGALSQLINELREALLELLAQVEANIDFPEED 181

Query: 183 DVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKK 242
             +    K +   +  L  ++   ++  K G+I+R G K+VI+G  N GKSSL NAL  +
Sbjct: 182 IEELVLEK-IREKLEELIAELDELLATAKQGKILREGLKVVIIGRPNVGKSSLLNALLGR 240

Query: 243 DVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVENADLI 302
           D AIVTDI GTTRDV+  D++L G  V++ DTAGIRETDD+VE+ GI+R    +E ADL+
Sbjct: 241 DRAIVTDIAGTTRDVIEEDINLNGIPVRLVDTAGIRETDDVVERIGIERAKKAIEEADLV 300

Query: 303 LLL-------KEINSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDHL--------ISSFT 347
           L +        + +       PK    I +  K+DL S    E + L        IS+ T
Sbjct: 301 LFVLDASQPLDKEDLALIELLPKKKPIIVVLNKADLVSKIELESEKLANGDAIISISAKT 360

Query: 348 GEGLEELINKIKSILSNKFKKLPFSIPSHKRHLYHLSQTVRYLEMA-SLNEKDCGLDIIA 406
           GEGL+ L   IK +             S+ RH+  L Q   +LE A    E    LD++A
Sbjct: 361 GEGLDALREAIKQLFGKGLGNQEGLFLSNLRHIQLLEQAAEHLEDALQQLELGQPLDLLA 420

Query: 407 ENLRLASVSLGKITGCVDVEQLLDIIFSKFCIGK 440
           E+LRLA  +LG+ITG    E LLD IFS FCIGK
Sbjct: 421 EDLRLAQEALGEITGEFVSEDLLDEIFSNFCIGK 454


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

 Score =  296 bits (758), Expect = 1e-80
 Identities = 175/490 (35%), Positives = 249/490 (50%), Gaps = 57/490 (11%)

Query: 7   TIFAVSTGA-LPSAISIIRLSGP-SCFQVCEFICKKKKPFPRKASLR---------YFFG 55
           TIFA+STG  L SAI+I R+SGP +       +     P  R A LR         Y   
Sbjct: 43  TIFALSTGIGLTSAIAIFRISGPDATKVARRLLRSVMVPKRRNAGLRALYNPEVRVYVVD 102

Query: 56  LDGRILDKGLLIVFPSPESFTGEDSAEFHVHGGIAVVNGILEELAK--MPNLRLANPGEF 113
            DG   D+ L + F  P+SFTGED  E   HG  AVV G+L  L    +P +RLA PGEF
Sbjct: 103 EDGVTRDRALGLYFLGPQSFTGEDVVELQTHGSSAVVVGVLTALGASGIPGIRLAEPGEF 162

Query: 114 SRRAFENGKIDLLEAESLADLISSETEMQRRLSMEGMSGELSSLYGQWIDKLTHIRSFIE 173
           +RRAF NGK+DL +AE + DLI +ETE QRR +++ ++GE  +L   W   L    + +E
Sbjct: 163 TRRAFLNGKLDLTQAEGIIDLIVAETESQRRAALDEVAGEALALCFGWRKILIEALAGLE 222

Query: 174 ADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKS 233
           A +DF EE  ++   + E+  + L L +D+ SH+++    E +++G +I I+G  N GKS
Sbjct: 223 ARIDFEEERPLEEIETVEIFIESLSLLDDVLSHLNKADEIERLQSGLQIAIVGRPNVGKS 282

Query: 234 SLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRE-TDDIVEKEGIKRT 292
           SL NAL+++D +IV+ +PGTTRD +   + + G  V++SDTAGIRE ++D +E  GI+R 
Sbjct: 283 SLLNALSREDRSIVSPVPGTTRDAIEAQVTVNGVPVRLSDTAGIREESNDGIEALGIERA 342

Query: 293 FLEVENADLILLLKEINS----------------KKEISFPKNIDF----IFIGTKSDLY 332
              +E AD+ILL+ +                      +    N       I +  KSDL 
Sbjct: 343 RKRIERADVILLVVDAEESDTESDLKIARILETEGVGLVVIVNKMEKQRIILVANKSDLV 402

Query: 333 STYTE-----------------EYDHLISSFTGEGLEELINKIKSIL---SNKFKKLPFS 372
           S   E                      +S  T EG E L   + +I+          P +
Sbjct: 403 SKIPEMTKIPVVYPSAEGRSVFPIVVEVSCTTKEGCERLSTALLNIVERLVVSPHSAPPT 462

Query: 373 IPSHKRHLYHLSQTVRY-LEMASL-NEKDCGLDIIAENLRLASVSLGKITGCVDVEQLLD 430
           + S KR    L       LE   L  +    +D+  E LRLA  S+ +ITG    E++L 
Sbjct: 463 L-SQKRIKELLRTCAAPELERRFLAKQLKEDIDLAGEPLRLAQRSIARITGGGGTEEVLS 521

Query: 431 IIFSKFCIGK 440
            IF KFCIGK
Sbjct: 522 SIFQKFCIGK 531


>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 =  181 bits (463), Expect = 2e-46
 Identities = 64/156 (41%), Positives = 90/156 (57%), Gaps = 12/156 (7%)

Query: 219 GYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR 278
           G K+VI+G  N GKSSL NALA +D AIV+DI GTTRDV+   +D+ G  V++ DTAGIR
Sbjct: 1   GIKVVIVGKPNVGKSSLLNALAGRDRAIVSDIAGTTRDVIEESIDIGGIPVRLIDTAGIR 60

Query: 279 ETDDIVEKEGIKRTFLEVENADLILLL----KEINS--KKEISFPKNIDFIFIGTKSDLY 332
           ET+D +EK GI+R    +E ADL+L +    + ++    + +  P +   I +  KSDL 
Sbjct: 61  ETEDEIEKIGIERAREAIEEADLVLFVIDASRGLDEEDLEILELPADKPIIVVLNKSDLL 120

Query: 333 STYTEEYD------HLISSFTGEGLEELINKIKSIL 362
                           IS+ TGEGL+EL   +  + 
Sbjct: 121 PDSELLSLLAGKPIIAISAKTGEGLDELKEALLELA 156


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

 Score = 93.9 bits (234), Expect = 8e-20
 Identities = 35/75 (46%), Positives = 44/75 (58%)

Query: 231 GKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIK 290
           GKS+L NAL  K  AIV+D PGTTRD     ++L+G  + + DT GI E     E E   
Sbjct: 1   GKSTLINALTGKKRAIVSDYPGTTRDPNEGRVELDGKQIILVDTPGIIEGASKGEGELGN 60

Query: 291 RTFLEVENADLILLL 305
           RT   +E ADLIL +
Sbjct: 61  RTLEAIEEADLILHV 75


>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 = 89.8 bits (224), Expect = 1e-18
 Identities = 37/88 (42%), Positives = 55/88 (62%), Gaps = 3/88 (3%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRE- 279
           +I I+G  N GKSSL NAL  ++  IV+DI GTTRD + +  + +G    + DTAGIR  
Sbjct: 4   RIAIIGRPNVGKSSLVNALLGEERVIVSDIAGTTRDSIDVPFEYDGKKYTLIDTAGIRRK 63

Query: 280 --TDDIVEKEGIKRTFLEVENADLILLL 305
              ++ +EK  + RT   +E AD++LL+
Sbjct: 64  GKVEEGIEKYSVLRTLKAIERADVVLLV 91


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

 Score = 85.2 bits (211), Expect = 3e-17
 Identities = 57/183 (31%), Positives = 87/183 (47%), Gaps = 33/183 (18%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR-- 278
           KI I+G  N GKSSL NA+  ++  IV+DI GTTRD + I+ + +G    + DTAGIR  
Sbjct: 180 KIAIIGRPNVGKSSLINAILGEERVIVSDIAGTTRDSIDIEFERDGRKYVLIDTAGIRRK 239

Query: 279 -ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS--FPKNIDFI--------FIGT 327
            +  + VEK  + RT   +E AD++LL+  I++ + IS    +    I         +  
Sbjct: 240 GKITESVEKYSVARTLKAIERADVVLLV--IDATEGISEQDLRIAGLIEEAGRGIVIVVN 297

Query: 328 KSDLYSTYTEEYDHL------------------ISSFTGEGLEELINKIKSILSNKFKKL 369
           K DL        +                    IS+ TG+GL++L   IK I     +++
Sbjct: 298 KWDLVEEDEATMEEFKKKLRRKLPFLDFAPIVFISALTGQGLDKLFEAIKEIYECATRRI 357

Query: 370 PFS 372
             S
Sbjct: 358 STS 360



 Score = 81.4 bits (201), Expect = 5e-16
 Identities = 43/166 (25%), Positives = 77/166 (46%), Gaps = 24/166 (14%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRE- 279
            + I+G  N GKS+LFN L  + +AIV+D PG TRD +  D +  G    + DT G+ + 
Sbjct: 5   VVAIVGRPNVGKSTLFNRLTGRRIAIVSDTPGVTRDRIYGDAEWLGREFILIDTGGLDDG 64

Query: 280 TDDIVEKEGIKRTFLEVENADLILLLKEINSKKEIS----------FPKNIDFIFIGTKS 329
            +D +++   ++  + +E AD+IL +  ++ ++ I+                 I +  K 
Sbjct: 65  DEDELQELIREQALIAIEEADVILFV--VDGREGITPADEEIAKILRRSKKPVILVVNKI 122

Query: 330 D----------LYSTYTEEYDHLISSFTGEGLEELINKIKSILSNK 365
           D           YS    E    IS+  G G+ +L++ +  +L   
Sbjct: 123 DNLKAEELAYEFYSLGFGEP-VPISAEHGRGIGDLLDAVLELLPPD 167


>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 = 83.1 bits (206), Expect = 1e-16
 Identities = 48/164 (29%), Positives = 73/164 (44%), Gaps = 26/164 (15%)

Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGY-LVKISDTAGIRETDD 282
           + G +NAGKSSL NAL  ++VAIV+ +PGTT D +    +L     V + DT GI E   
Sbjct: 1   LFGRTNAGKSSLLNALLGQEVAIVSPVPGTTTDPVEYVWELGPLGPVVLIDTPGIDEAGG 60

Query: 283 IVEKEGIKRTFLEVENADLILLLKEINSKKEISFPK--------NIDFIFIGTKSDLYST 334
           +  +E  +     +E ADLIL + + + + +    K            + +  K DL   
Sbjct: 61  L-GREREELARRVLERADLILFVVDADLRADEEEEKLLELLRERGKPVLLVLNKIDLLPE 119

Query: 335 YTEEYD----------------HLISSFTGEGLEELINKIKSIL 362
             EE                    +S+ TGEG++EL   +   L
Sbjct: 120 EEEEELLELRLLILLLLLGLPVIAVSALTGEGIDELREALIEAL 163


>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 = 82.5 bits (205), Expect = 2e-16
 Identities = 45/157 (28%), Positives = 70/157 (44%), Gaps = 17/157 (10%)

Query: 223 VILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDD 282
            I+G  N GKS+LFN L  +  AIV D PG TRD +  + +  G    + DT GI   D+
Sbjct: 1   AIVGRPNVGKSTLFNRLTGRRDAIVEDTPGVTRDRIYGEAEWGGREFILIDTGGIEPDDE 60

Query: 283 IVEKEGIKRTFLEVENADLILLL---KEINSKKEISF-----PKNIDFIFIGTKSDLYST 334
            + KE  ++  L +E AD+IL +   +E  +  +              I +  K D    
Sbjct: 61  GISKEIREQAELAIEEADVILFVVDGREGLTPADEEIAKYLRKSKKPVILVVNKVDNIKE 120

Query: 335 YTEEYD---------HLISSFTGEGLEELINKIKSIL 362
             E  +           IS+  G G+ +L++ I  +L
Sbjct: 121 EDEAAEFYSLGFGEPIPISAEHGRGIGDLLDAILELL 157


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

 Score = 56.8 bits (137), Expect = 1e-08
 Identities = 49/238 (20%), Positives = 88/238 (36%), Gaps = 27/238 (11%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRE 279
             + ++G+ N GK++LFNAL   +   V + PG T +     L  +G+ ++I D  G   
Sbjct: 4   LTVALVGNPNVGKTTLFNALTGANQK-VGNWPGVTVEKKEGKLKYKGHEIEIVDLPGTYS 62

Query: 280 TDDIVEKEGIKRTFLEVENADLIL-LLKEINSKKEISFPK-----NIDFIFIGTKSDLYS 333
                E E + R FL     DLI+ ++   N ++ +          I  I      D   
Sbjct: 63  LTAYSEDEKVARDFLLEGKPDLIVNVVDATNLERNLYLTLQLLELGIPMILALNMIDEAK 122

Query: 334 TYTEEYDH------------LISSFTGEGLEELINKIKSILSNKFKKL----PFSIPSHK 377
                 D                +  GEGLEEL   I  +  +K           I    
Sbjct: 123 KRGIRIDIEKLSKLLGVPVVPTVAKRGEGLEELKRAIIELAESKTTPREVDYGEEIEEEI 182

Query: 378 RHLYHLSQTVRYLEMASLNEKDCGLDIIAENLRLASVSLGKITGCVDVEQLLDIIFSK 435
           + L  LS+  R+L +  L       +++   L+     + ++   +  E+   ++ + 
Sbjct: 183 KELEALSEDPRWLAIKLLE----DDELVEAVLKEPEKRVEELLEELSEEEGHLLLIAD 236


>gnl|CDD|57925 cd01854, YjeQ_engC, YjeQ/EngC.  YjeQ (YloQ in Bacillus subtilis)
           represents a protein family whose members are broadly
           conserved in bacteria and have been shown to be
           essential to the growth of E. coli and B. subtilis.
           Proteins of the YjeQ 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. All YjeQ family proteins display a
           unique domain architecture, which includes an N-terminal
           OB-fold RNA-binding domain, the central permuted GTPase
           domain, and a zinc knuckle-like C-terminal cysteine
           domain. This domain architecture suggests a role for
           YjeQ as a regulator of translation..
          Length = 287

 Score = 56.3 bits (136), Expect = 1e-08
 Identities = 35/136 (25%), Positives = 56/136 (41%), Gaps = 18/136 (13%)

Query: 174 ADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQG--KLGEIIRNGYKIVILGHSNAG 231
           ADL   EEE+++   +  +   +L     +S+   +G  +L E ++     V++G S  G
Sbjct: 119 ADLLDDEEEELELVEALALGYPVLA----VSAKTGEGLDELREYLKGK-TSVLVGQSGVG 173

Query: 232 KSSLFNALAKKDVAIVTDIPG-------TTRDVLTIDLDLEGYLVKISDTAGIRETDDI- 283
           KS+L NAL         +I         TT       L   G L+   DT G RE   + 
Sbjct: 174 KSTLINALLPDLDLATGEISEKLGRGRHTTTHRELFPLPGGGLLI---DTPGFREFGLLH 230

Query: 284 VEKEGIKRTFLEVENA 299
           ++ E +   F E    
Sbjct: 231 IDPEELAHYFPEFREL 246


>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 = 55.9 bits (136), Expect = 2e-08
 Identities = 40/170 (23%), Positives = 69/170 (40%), Gaps = 34/170 (20%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR-DVLTIDLDLEGYLVKISDTAGIRE 279
            + I+G  N GKS+L NAL  + ++IV+  P TTR  +  I  D +  ++ + DT GI  
Sbjct: 5   FVAIVGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIYTDDDAQIIFV-DTPGI-- 61

Query: 280 TDDIVEKEGIKRTFLEV-----ENADLILLLKEINSKK--------EISFPKNIDFIFIG 326
                 K+ +    ++      ++ DL+L + + +           E+        I + 
Sbjct: 62  ---HKPKKKLGERMVKAAWSALKDVDLVLFVVDASEPIGEGDEFILELLKKSKTPVILVL 118

Query: 327 TKSDL----------YSTYTEEYD----HLISSFTGEGLEELINKIKSIL 362
            K DL               E         IS+  GE ++EL+ +I   L
Sbjct: 119 NKIDLVKDKEDLLPLLEKLKELGPFAEIFPISALKGENVDELLEEIVKYL 168


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

 Score = 55.2 bits (133), Expect = 3e-08
 Identities = 38/165 (23%), Positives = 66/165 (40%), Gaps = 24/165 (14%)

Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD-VLTIDLDLEGYLVKISDTAGIRET 280
           + I+G  N GKS+L NAL  + ++IV+  P TTR+ +  I       ++ + DT GI + 
Sbjct: 9   VAIIGRPNVGKSTLLNALVGQKISIVSPKPQTTRNRIRGIVTTDNAQIIFV-DTPGIHKP 67

Query: 281 DDIVEKEGIKRTFLEVENADLILLLKEINSKK--------EISFPKNIDFIFIGTKSDLY 332
              + +   K     +++ DLIL + + +           E         I +  K D  
Sbjct: 68  KHALGELMNKAARSALKDVDLILFVVDADEGWGPGDEFILEQLKKTKTPVILVVNKIDKV 127

Query: 333 STYTEEYDHL--------------ISSFTGEGLEELINKIKSILS 363
              T     +              IS+  G+ ++ L+  IK  L 
Sbjct: 128 KPKTVLLKLIAFLKKLLPFKEIVPISALKGDNVDTLLEIIKEYLP 172


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

 Score = 55.3 bits (133), Expect = 3e-08
 Identities = 57/184 (30%), Positives = 81/184 (44%), Gaps = 29/184 (15%)

Query: 217 RNGYKIV-ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLE-GYLVKISDT 274
           R+G  +V ++G++NAGKS+LFNAL   DV  V D    T D  T  ++L  G  V ++DT
Sbjct: 189 RSGIPLVALVGYTNAGKSTLFNALTGADVY-VADQLFATLDPTTRRIELGDGRKVLLTDT 247

Query: 275 AG-IRETD-DIVEKEGIKRTFLEVENADLILL-------------------LKEIN--SK 311
            G IR+    +VE    K T  EV+ ADL+L                    L EI     
Sbjct: 248 VGFIRDLPHPLVE--AFKSTLEEVKEADLLLHVVDASDPEILEKLEAVEDVLAEIGADEI 305

Query: 312 KEISFPKNIDFIFIGTKSDLYSTYTEEYDHLISSFTGEGLEELINKIKSILSNKFKKLPF 371
             I     ID +            +      IS+ TGEGL+ L  +I  +LS    ++  
Sbjct: 306 PIILVLNKIDLLEDEEILAELERGSPNP-VFISAKTGEGLDLLRERIIELLSGLRTEVTL 364

Query: 372 SIPS 375
            +P 
Sbjct: 365 ELPY 368


>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 = 54.0 bits (130), Expect = 8e-08
 Identities = 33/156 (21%), Positives = 57/156 (36%), Gaps = 22/156 (14%)

Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKIS--DTAGIRETD 281
           ++G S  GK+SL N L   +         T  D  +  ++++G  VK+   DTAG     
Sbjct: 1   VVGDSGVGKTSLLNRLLGGEFVPEEYET-TIIDFYSKTIEVDGKKVKLQIWDTAGQERFR 59

Query: 282 DIVEK-----EGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFIGTKSDLYSTYT 336
            +        +GI   +   +      + + +         +NI  I +G K DL     
Sbjct: 60  SLRRLYYRGADGIILVYDVTDRESFENVKEWLLLILINKEGENIPIILVGNKIDLPEERV 119

Query: 337 EEYD--------------HLISSFTGEGLEELINKI 358
              +                 S+ TGE +EEL  ++
Sbjct: 120 VSEEELAEQLAKELGVPYFETSAKTGENVEELFEEL 155


>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 = 53.7 bits (129), Expect = 9e-08
 Identities = 26/69 (37%), Positives = 36/69 (52%), Gaps = 11/69 (15%)

Query: 217 RNGYKIVILGHSNAGKSSLFNALAKKD--------VAIVTDIPGTTRDVLTIDLDLEGYL 268
           + G  + ++G +N GKS+L NAL KKD        +   + IPGTT D++ I L     L
Sbjct: 125 KKGGDVYVVGATNVGKSTLINALLKKDNGKKKLKDLLTTSPIPGTTLDLIKIPLGNGKKL 184

Query: 269 VKISDTAGI 277
               DT GI
Sbjct: 185 Y---DTPGI 190



 Score = 32.9 bits (75), Expect = 0.19
 Identities = 18/62 (29%), Positives = 21/62 (33%), Gaps = 20/62 (32%)

Query: 318 KNIDFIFIGTKSDLYSTYTEEYD--------------------HLISSFTGEGLEELINK 357
            N   I +G K DL                              LIS+  G G+EELIN 
Sbjct: 60  GNNPVILVGNKIDLLPKDKNLVRIKNWLRAKAAAGLGLKPKDVILISAKKGWGVEELINA 119

Query: 358 IK 359
           IK
Sbjct: 120 IK 121


>gnl|CDD|146027 pfam03193, DUF258, Protein of unknown function, DUF258. 
          Length = 161

 Score = 53.7 bits (130), Expect = 1e-07
 Identities = 25/86 (29%), Positives = 33/86 (38%), Gaps = 11/86 (12%)

Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPG-------TTRDVLTIDLDLEGYLVKISDT 274
            V+ G S  GKS+L NAL  +      +I         TT  V    L   G L+   DT
Sbjct: 38  SVLAGQSGVGKSTLLNALLPELDLRTGEISEKLGRGRHTTTHVELFPLPGGGLLI---DT 94

Query: 275 AGIRETD-DIVEKEGIKRTFLEVENA 299
            G RE     ++ E +   F E    
Sbjct: 95  PGFRELGLWHLDPEELAEYFPEFREL 120


>gnl|CDD|31356 COG1162, COG1162, Predicted GTPases [General function prediction
           only].
          Length = 301

 Score = 53.4 bits (128), Expect = 1e-07
 Identities = 32/133 (24%), Positives = 49/133 (36%), Gaps = 14/133 (10%)

Query: 177 DFSEEEDVQNFSSKEVLNDIL--FLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSS 234
           D  ++E+           DI    L     +     +L E++      V+LG S  GKS+
Sbjct: 121 DLLDDEEAAVKELLREYEDIGYPVLFVSAKNGDGLEELAELLAGKI-TVLLGQSGVGKST 179

Query: 235 LFNALAKKDVAIVTDIPG-------TTRDVLTIDLDLEGYLVKISDTAGIRETD-DIVEK 286
           L NAL  +      +I         TT  V    L   G+++   DT G R      +E 
Sbjct: 180 LINALLPELNQKTGEISEKLGRGRHTTTHVELFPLPGGGWII---DTPGFRSLGLAHLEP 236

Query: 287 EGIKRTFLEVENA 299
           E + + F E    
Sbjct: 237 EDLVQAFPEFAEL 249


>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 = 52.1 bits (125), Expect = 3e-07
 Identities = 29/88 (32%), Positives = 43/88 (48%), Gaps = 7/88 (7%)

Query: 190 KEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTD 249
           K++L     L  DI    ++G L   IR     +++G  N GKS+L N L  K VA V +
Sbjct: 90  KKLLKAAKKLLKDIEKLKAKGLLPRGIR----AMVVGIPNVGKSTLINRLRGKKVAKVGN 145

Query: 250 IPGTTRDVLTIDLDLEGYLVKISDTAGI 277
            PG T+ +  I +      + + DT GI
Sbjct: 146 KPGVTKGIQWIKI---SPGIYLLDTPGI 170


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

 Score = 51.2 bits (122), Expect = 5e-07
 Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 3/85 (3%)

Query: 207 ISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEG 266
           I + K   +++   ++ ++G+ N GKS+L N L  K VA  ++ PGTT+ +  I LD   
Sbjct: 120 IKRLKKKGLLKRKIRVGVVGYPNVGKSTLINRLLGKKVAKTSNRPGTTKGIQWIKLDDGI 179

Query: 267 YLVKISDTAGIRETDDIVEKEGIKR 291
           YL+   DT GI       ++  + +
Sbjct: 180 YLL---DTPGIIPPKFDDDELVLLK 201


>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 = 50.5 bits (122), Expect = 8e-07
 Identities = 58/180 (32%), Positives = 81/180 (45%), Gaps = 47/180 (26%)

Query: 217 RNGYKIV-ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLT--IDLDLEGYLVKISD 273
           R+G   V ++G++NAGKS+LFNAL   DV    D    T D  T  + L  +G  V ++D
Sbjct: 38  RSGIPTVALVGYTNAGKSTLFNALTGADVY-AEDQLFATLDPTTRRLRLP-DGREVLLTD 95

Query: 274 TAG-IRETD---DIVEKEGIKRTFLEVENADLILL-------------------LKEINS 310
           T G IR  D    +V  E  + T  EV  ADL+L                    LKE+ +
Sbjct: 96  TVGFIR--DLPHQLV--EAFRSTLEEVAEADLLLHVVDASDPDYEEQIETVEKVLKELGA 151

Query: 311 KKEISFPKNIDFIFIGTKSDLYSTYTEEYD--------HLISSFTGEGLEELINKIKSIL 362
                  ++I  I +  K DL      E            IS+ TGEGL+EL+  I+ +L
Sbjct: 152 -------EDIPMILVLNKIDLLDDEELEERLEAGRPDAVFISAKTGEGLDELLEAIEELL 204


>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 = 50.2 bits (121), Expect = 1e-06
 Identities = 46/181 (25%), Positives = 70/181 (38%), Gaps = 52/181 (28%)

Query: 222 IVILGHSNAGKSSLFNALA-KKDVAIVTDIPGTTRDVLTI---DLDLEGYLV-------- 269
           I   G SN GKSSL NAL  +K +A  +  PG T+    I   +++ +  LV        
Sbjct: 2   IAFAGRSNVGKSSLINALTNRKKLARTSKTPGKTQ---LINFFNVNDKFRLVDLPGYGYA 58

Query: 270 KISDTAGIRETDDIVEKEGIKRTFLEV-ENADLILLLKEINSKKEIS----------FPK 318
           K+S     +    I E       +LE  EN   ++LL  I+S+   +             
Sbjct: 59  KVSKEVKEKWGKLIEE-------YLENRENLKGVVLL--IDSRHGPTEIDLEMLDWLEEL 109

Query: 319 NIDFIFIGTKSD-------------LYSTYTEEYDH----LISSFTGEGLEELINKIKSI 361
            I F+ + TK+D             +              L SS  G+G++EL   I+  
Sbjct: 110 GIPFLVVLTKADKLKKSELAKALKEIKKELKLFEIDPPIILFSSLKGQGIDELRALIEKW 169

Query: 362 L 362
           L
Sbjct: 170 L 170


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

 Score = 48.8 bits (116), Expect = 3e-06
 Identities = 30/123 (24%), Positives = 60/123 (48%), Gaps = 5/123 (4%)

Query: 192 VLNDILFLKNDISSHIS-QGKLGEIIRNGY-KIVILGHSNAGKSSLFNALAKKDVAIVTD 249
           VL  +L L + +S  I  Q ++ ++       ++++G + AGKSSL NAL + +V  V+ 
Sbjct: 10  VLKGLLGLPSLLSERILEQLRMLQLTEKEPVNVLLMGATGAGKSSLINALFQGEVKEVSK 69

Query: 250 IPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVEN-ADLILLLKEI 308
           +   T     + L  +G  + + DT G+   D   +    ++ + +     DL+L L + 
Sbjct: 70  VGVGTDITTRLRLSYDGENLVLWDTPGLG--DGKDKDAEHRQLYRDYLPKLDLVLWLIKA 127

Query: 309 NSK 311
           + +
Sbjct: 128 DDR 130


>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 = 47.9 bits (115), Expect = 6e-06
 Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 1/83 (1%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRET 280
            I ++G+ N GK++LFNAL       V + PG T +        +GY ++I D  G    
Sbjct: 1   TIALVGNPNVGKTTLFNALTGARQ-HVGNWPGVTVEKKEGTFKYKGYEIEIVDLPGTYSL 59

Query: 281 DDIVEKEGIKRTFLEVENADLIL 303
               E+E + R +L  E  D+I+
Sbjct: 60  SPYSEEEKVARDYLLEEKPDVII 82


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

 Score = 47.3 bits (112), Expect = 9e-06
 Identities = 48/181 (26%), Positives = 73/181 (40%), Gaps = 35/181 (19%)

Query: 209 QGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYL 268
           Q ++G    +   I ++G++NAGKS+L  AL K  +           D L   LD   + 
Sbjct: 168 QRRVGREGESSPVIAVVGYTNAGKSTLIKALTKAAL--------YPNDRLFATLDPTLHS 219

Query: 269 VKI--------SDTAGIRETDDIVEKEGIKRTFLEVENADLIL----------------L 304
             +        +DT G      I      + T  EV  ADL+L                +
Sbjct: 220 AHLPSGNFVLLTDTVGFISDLPIQLVAAFQATLEEVAEADLLLHVVDISHPNAEEQRETV 279

Query: 305 LKEINSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDHL---ISSFTGEGLEELINKIKSI 361
           L  +N     S PK  + I +  K D      EE  +L   IS+ TG+GLEEL+   ++ 
Sbjct: 280 LHVLNQIGVPSEPKLQNMIEVDNKIDYEEDEVEEEKNLDVGISALTGDGLEELLKAEETK 339

Query: 362 L 362
           +
Sbjct: 340 V 340


>gnl|CDD|133250 cd00154, Rab, Rab family.  Rab GTPases form the largest family
           within the Ras superfamily.  There are at least 60 Rab
           genes in the human genome, and a number of Rab GTPases
           are conserved from yeast to humans. Rab GTPases are
           small, monomeric proteins that function as molecular
           switches to regulate vesicle trafficking pathways.  The
           different Rab GTPases are localized to the cytosolic
           face of specific intracellular membranes, where they
           regulate distinct steps in membrane traffic pathways. In
           the GTP-bound form, Rab GTPases recruit specific sets of
           effector proteins onto membranes. Through their
           effectors, Rab GTPases regulate vesicle formation,
           actin- and tubulin-dependent vesicle movement, and
           membrane fusion.  GTPase activating proteins (GAPs)
           interact with GTP-bound Rab and accelerate the
           hydrolysis of GTP to GDP. Guanine nucleotide exchange
           factors (GEFs) interact with GDP-bound Rabs to promote
           the formation of the GTP-bound state.  Rabs are further
           regulated by guanine nucleotide dissociation inhibitors
           (GDIs), which mask C-terminal lipid binding and promote
           cytosolic localization.  While most unicellular
           organisms possess 5-20 Rab members, several have been
           found to possess 60 or more Rabs; for many of these Rab
           isoforms, homologous proteins are not found in other
           organisms.  Most Rab GTPases contain a lipid
           modification site at the C-terminus, with sequence
           motifs CC, CXC, or CCX. Lipid binding is essential for
           membrane attachment, a key feature of most Rab proteins.
            Since crystal structures often lack C-terminal
           residues, the lipid modification site is not available
           for annotation in many of the CDs in the hierarchy, but
           is included where possible.
          Length = 159

 Score = 46.7 bits (112), Expect = 1e-05
 Identities = 42/173 (24%), Positives = 66/173 (38%), Gaps = 50/173 (28%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTT--RDVLTIDLDLEGYLVKIS--DTA 275
           +KIV++G S  GK+SL             +   +T   D  +  ++++G  VK+   DTA
Sbjct: 1   FKIVLIGDSGVGKTSLLLRFVDG---KFDENYKSTIGVDFKSKTIEIDGKTVKLQIWDTA 57

Query: 276 G-----------IRETD------DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPK 318
           G            R         DI  +E    +F  ++       LKE+        P+
Sbjct: 58  GQERFRSITPSYYRGAHGAILVYDITNRE----SFENLDK-----WLKELKEY----APE 104

Query: 319 NIDFIFIGTKSDLYST----------YTEEYD---HLISSFTGEGLEELINKI 358
           NI  I +G K DL             + +E        S+ TGE +EEL   +
Sbjct: 105 NIPIILVGNKIDLEDQRQVSTEEAQQFAKENGLLFFETSAKTGENVEELFQSL 157


>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 = 46.3 bits (111), Expect = 2e-05
 Identities = 41/182 (22%), Positives = 72/182 (39%), Gaps = 49/182 (26%)

Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD----VLTIDLDLEGYLVKISDTAGIRE 279
           ++G  N GKS+L NAL      +  + P TT +    V+ +        ++++D  G+  
Sbjct: 1   LVGLPNVGKSTLLNALTNAKPKV-ANYPFTTLEPNLGVVEVPDGAR---IQVADIPGL-- 54

Query: 280 TDDIVEKEGIKRTFL-EVENADLILLL------------------KEINSKKEISFPKNI 320
            +   E  G+   FL  +  AD IL +                  + +N++ ++   + I
Sbjct: 55  IEGASEGRGLGNQFLAHIRRADAILHVVDASEDDDIGGVDPLEDYEILNAELKLYDLETI 114

Query: 321 DF-------IFIGTKSDLYSTYTEEYDHL-------------ISSFTGEGLEELINKIKS 360
                    I++  K DL      E + +             IS+ T EGL+ELI  I  
Sbjct: 115 LGLLTAKPVIYVLNKIDLDDAEELEEELVRELALEEGAEVVPISAKTEEGLDELIRAIYE 174

Query: 361 IL 362
           +L
Sbjct: 175 LL 176


>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 = 46.3 bits (111), Expect = 2e-05
 Identities = 27/80 (33%), Positives = 38/80 (47%), Gaps = 1/80 (1%)

Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDI 283
           ++G+ N GK++LFNAL       V + PG T +       L G  ++I D  G       
Sbjct: 1   LVGNPNVGKTTLFNALTGAR-QKVGNWPGVTVEKKEGRFKLGGKEIEIVDLPGTYSLSPY 59

Query: 284 VEKEGIKRTFLEVENADLIL 303
            E E + R FL  E  DLI+
Sbjct: 60  SEDEKVARDFLLGEKPDLIV 79


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

 Score = 45.0 bits (105), Expect = 4e-05
 Identities = 32/154 (20%), Positives = 53/154 (34%), Gaps = 16/154 (10%)

Query: 218 NGYKIVILGHSNAGKSSLFNALAK------KDVAIVTDIPGTTRDVLTIDLDLEGYLVKI 271
             +KIV+LG    GK++L N L            I    P  T +    ++ L+     +
Sbjct: 4   KEFKIVVLGDGGVGKTTLLNRLVGDEFPEGYPPTIGNLDPAKTIEPYRRNIKLQ-----L 58

Query: 272 SDTAGIRETDDIVEK-----EGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFIG 326
            DTAG  E   +  +      GI   +          L +E   +     P ++  + +G
Sbjct: 59  WDTAGQEEYRSLRPEYYRGANGILIVYDSTLRESSDELTEEWLEELRELAPDDVPILLVG 118

Query: 327 TKSDLYSTYTEEYDHLISSFTGEGLEELINKIKS 360
            K DL+   +   + L        L  L  K   
Sbjct: 119 NKIDLFDEQSSSEEILNQLNREVVLLVLAPKAVL 152


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

 Score = 44.9 bits (106), Expect = 4e-05
 Identities = 43/184 (23%), Positives = 78/184 (42%), Gaps = 23/184 (12%)

Query: 190 KEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTD 249
           K++ +D+ FL      H+   KL  I  +   IV+ G+ N GKSSL   L      +   
Sbjct: 142 KKIDDDLEFL-RKARDHLK--KLPAIDPDLPTIVVAGYPNVGKSSLVRKLTTAKPEV-AP 197

Query: 250 IPGTTRDVLTIDLDLEGYLVKISDTAGI--RETDDIVEKEGIKRTFLEVEN-ADLILLL- 305
            P TT+ +     +     +++ DT G+  R  ++  E E  ++  L + + A +IL L 
Sbjct: 198 YPFTTKGIHVGHFERGYLRIQVIDTPGLLDRPLEERNEIE--RQAILALRHLAGVILFLF 255

Query: 306 -----------KEINSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDHLISSFTGEGLEEL 354
                      ++I+  +EI        + +  K D+     E+ + + +S   EG EE 
Sbjct: 256 DPSETCGYSLEEQISLLEEIKELFKAPIVVVINKIDI--ADEEKLEEIEASVLEEGGEEP 313

Query: 355 INKI 358
           +   
Sbjct: 314 LKIS 317


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

 Score = 44.9 bits (106), Expect = 4e-05
 Identities = 42/179 (23%), Positives = 68/179 (37%), Gaps = 37/179 (20%)

Query: 221 KIVILGHSNAGKSSLFNALA-KKDVAIVTDIPGTTRDVLTIDLDLEGYLV--------KI 271
           +I   G SN GKSSL NAL  +K++A  +  PG T+ +   ++D E  LV        K+
Sbjct: 26  EIAFAGRSNVGKSSLINALTNQKNLARTSKTPGRTQLINFFEVDDELRLVDLPGYGYAKV 85

Query: 272 SDTAGIRETDDIVE----KEGIKRTFLEVENADLILLLKEINSKKEISFPK--NIDFIFI 325
                 +    I E    +  +K   L ++         +   ++ I F     I  I +
Sbjct: 86  PKEVKEKWKKLIEEYLEKRANLKGVVLLIDARHPP----KDLDREMIEFLLELGIPVIVV 141

Query: 326 GTKSD------------------LYSTYTEEYDHLISSFTGEGLEELINKIKSILSNKF 366
            TK+D                        +++  L SS   +G++EL  KI   L    
Sbjct: 142 LTKADKLKKSERNKQLNKVAEELKKPPPDDQWVVLFSSLKKKGIDELKAKILEWLKEAK 200


>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 = 44.2 bits (104), Expect = 7e-05
 Identities = 28/118 (23%), Positives = 44/118 (37%), Gaps = 11/118 (9%)

Query: 160 QWIDKLTHIRSFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNG 219
           +W+  L H  S+       S          +              +   + K        
Sbjct: 49  KWLAYLRH--SYPTIPFKISATNGQGIEKKESAFTKQTNSNLKSYAKDGKLK------KS 100

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI 277
             + ++G+ N GKSS+ NAL  K    V ++PGTT     + LD +  L+   DT GI
Sbjct: 101 ITVGVIGYPNVGKSSVINALLNKLKLKVGNVPGTTTSQQEVKLDNKIKLL---DTPGI 155


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

 Score = 42.3 bits (99), Expect = 3e-04
 Identities = 22/105 (20%), Positives = 45/105 (42%), Gaps = 17/105 (16%)

Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281
           + ++G  N GKS+L N +  + V+ V+    TTR  +   +      +   DT G     
Sbjct: 75  VAVIGAPNVGKSTLTNQMIGQKVSAVSRKVHTTRHRILGIITSGETQLVFYDTPG----- 129

Query: 282 DIVEKEGIKRTFLE----------VENADLILLLKEI-NSKKEIS 315
            +V K+  +R  L            +NAD ++++ +   ++  + 
Sbjct: 130 -LVSKKMHRRHHLMMSVLQNPRDAAQNADCVVVVVDASATRTPLH 173


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

 Score = 42.2 bits (99), Expect = 3e-04
 Identities = 29/81 (35%), Positives = 36/81 (44%), Gaps = 6/81 (7%)

Query: 219 GYKIVILGHSNAGKSSLFNA-----LAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISD 273
            Y ++++G  N GKSSL NA     L KK  A V   PG TR V           V + D
Sbjct: 143 EYNVMVVGVPNVGKSSLINALRNVHLRKKKAARVGAEPGVTRRVSERIRISHRPPVYLID 202

Query: 274 TAGIRETDDIVEKEGIKRTFL 294
           T GI     IV+ E   +  L
Sbjct: 203 TPGIL-VPSIVDVEDGLKLAL 222


>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 = 39.9 bits (94), Expect = 0.002
 Identities = 50/175 (28%), Positives = 75/175 (42%), Gaps = 44/175 (25%)

Query: 222 IVILGHSNAGKSSLFNAL--AKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI-- 277
           +VI G+ N GKSSL N L  AK +VA     P TT+ +     D +    ++ DT G+  
Sbjct: 3   LVIAGYPNVGKSSLVNKLTRAKPEVA---PYPFTTKSLFVGHFDYKYLRWQVIDTPGLLD 59

Query: 278 RETDD--IVEKEGIKRTFLE-VENADL----------------ILLLKEINSKKEISFPK 318
           R  ++   +E + I  T L  +  A L                + L +EI   K +   K
Sbjct: 60  RPLEERNTIEMQAI--TALAHLRAAVLFLFDPSETCGYSLEEQLSLFEEI---KPLFKNK 114

Query: 319 NIDFIFIGTKSDL-----YSTYTEEYD------HLISSFTGEGLEELINKIKSIL 362
            +  I +  K DL      S   EE +        IS+ T EG++E+ NK   +L
Sbjct: 115 PV--IVVLNKIDLLTFEDLSEIEEEEELEGEEVLKISTLTEEGVDEVKNKACELL 167


>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 = 39.5 bits (92), Expect = 0.002
 Identities = 21/62 (33%), Positives = 33/62 (53%), Gaps = 3/62 (4%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTA 275
           I+    + ++G  N GKSSL N+L +     V   PG T+ +  + LD +   VK+ D+ 
Sbjct: 114 IKTSITVGVVGFPNVGKSSLINSLKRSRACNVGATPGVTKSMQEVHLDKK---VKLLDSP 170

Query: 276 GI 277
           GI
Sbjct: 171 GI 172


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

 Score = 38.5 bits (89), Expect = 0.003
 Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 3/74 (4%)

Query: 225 LGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIV 284
           +G+ N GKSS+ N L KK V  V  IPG T+    I L    +L+   D  G+       
Sbjct: 313 IGYPNVGKSSIINTLRKKKVCKVAPIPGETKVWQYITLMKRIFLI---DCPGVVYPSSDS 369

Query: 285 EKEGIKRTFLEVEN 298
           E + + +  + VEN
Sbjct: 370 ETDIVLKGVVRVEN 383


>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 = 38.2 bits (89), Expect = 0.004
 Identities = 20/52 (38%), Positives = 26/52 (50%), Gaps = 3/52 (5%)

Query: 226 GHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGI 277
           G+ N GKSSL NAL  K    V+  PG T+   TI L      + + D  G+
Sbjct: 90  GYPNVGKSSLINALVGKKKVSVSATPGKTKHFQTIFLTPT---ITLCDCPGL 138


>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 = 37.9 bits (88), Expect = 0.005
 Identities = 15/32 (46%), Positives = 19/32 (59%)

Query: 224 ILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR 255
            +G+ N GKSS+ N L  K V  V  IPG T+
Sbjct: 107 FIGYPNVGKSSIINTLRSKKVCKVAPIPGETK 138


>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 = 37.6 bits (87), Expect = 0.006
 Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 3/67 (4%)

Query: 211 KLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVK 270
           +L +I     K+ ++G+ N GKSS+ NAL  +  A  +  PG T+    + +  + YL+ 
Sbjct: 93  ELAKIDGKEGKVGVVGYPNVGKSSIINALKGRHSASTSPSPGYTKGEQLVKITSKIYLL- 151

Query: 271 ISDTAGI 277
             DT G+
Sbjct: 152 --DTPGV 156


>gnl|CDD|133251 cd00157, Rho, Rho (Ras homology) family.  Members of the Rho family
           include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop.
           There are 22 human Rho family members identified
           currently.  These proteins are all involved in the
           reorganization of the actin cytoskeleton in response to
           external stimuli.  They also have roles in cell
           transformation by Ras in cytokinesis, in focal adhesion
           formation and in the stimulation of stress-activated
           kinase.  These various functions are controlled through
           distinct effector proteins and mediated through a
           GTP-binding/GTPase cycle involving three classes of
           regulating proteins: GAPs (GTPase-activating proteins),
           GEFs (guanine nucleotide exchange factors), and GDIs
           (guanine nucleotide dissociation inhibitors).  Most Rho
           proteins contain a lipid modification site at the
           C-terminus, with a typical sequence motif CaaX, where a
           = an aliphatic amino acid and X = any amino acid.  Lipid
           binding is essential for membrane attachment, a key
           feature of most Rho proteins.  Since crystal structures
           often lack C-terminal residues, this feature is not
           available for annotation in many of the CDs in the
           hierarchy.
          Length = 171

 Score = 37.5 bits (88), Expect = 0.008
 Identities = 32/130 (24%), Positives = 48/130 (36%), Gaps = 34/130 (26%)

Query: 221 KIVILGHSNAGKSSLFNALAK-----KDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTA 275
           KIV++G    GK+ L  +        + V  V D         T+ +D +   + + DTA
Sbjct: 2   KIVVVGDGAVGKTCLLISYTTGKFPTEYVPTVFDN-----YSATVTVDGKQVNLGLWDTA 56

Query: 276 GIRETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNID-------------- 321
           G  E D +       R  L   N D+ L+   ++S    SF                   
Sbjct: 57  GQEEYDRL-------RP-LSYPNTDVFLICFSVDSPS--SFENVKTKWIPEIRHYCPNVP 106

Query: 322 FIFIGTKSDL 331
            I +GTK DL
Sbjct: 107 IILVGTKIDL 116


>gnl|CDD|144080 pfam00350, Dynamin_N, Dynamin family. 
          Length = 168

 Score = 37.2 bits (87), Expect = 0.008
 Identities = 26/102 (25%), Positives = 38/102 (37%), Gaps = 15/102 (14%)

Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281
           I ++G  +AGKSS+ NAL  +D+      P TTR  L + L   G        A   E  
Sbjct: 1   IAVVGDQSAGKSSVLNALLGRDILPRGPGP-TTRRPLVLRL---GEEPGAIPGAVKVEYK 56

Query: 282 DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFI 323
           D ++K             D   L +EI  + +          
Sbjct: 57  DGLKKF-----------EDFSELREEIEDETDKISGTGKGIS 87


>gnl|CDD|35317 KOG0094, KOG0094, KOG0094, GTPase Rab6/YPT6/Ryh1, small G protein
           superfamily [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 221

 Score = 36.8 bits (85), Expect = 0.012
 Identities = 39/188 (20%), Positives = 63/188 (33%), Gaps = 37/188 (19%)

Query: 203 ISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDL 262
           +                YK+V LG  + GK+SL       D    T       D L+  +
Sbjct: 6   VCLACQTMATFGAPLKKYKLVFLGDQSVGKTSLITRF-MYDKFDNTYQATIGIDFLSKTM 64

Query: 263 DLEGYLVKIS--DTAG-----------IRETDDIVEKEGI--KRTFLEVENADLILLLKE 307
            LE   V++   DTAG           IR++   V    I  + +F            K 
Sbjct: 65  YLEDRTVRLQLWDTAGQERFRSLIPSYIRDSSVAVIVYDITDRNSFENTS--------KW 116

Query: 308 INSKKEISFPKNIDFIFIGTKSDLYS---TYTEEYDHL----------ISSFTGEGLEEL 354
           I   +      ++    +G K+DL        EE +             S+  GE +++L
Sbjct: 117 IEDVRRERGSDDVIIFLVGNKTDLSDKRQVSIEEGERKAKELNAEFIETSAKAGENVKQL 176

Query: 355 INKIKSIL 362
             +I + L
Sbjct: 177 FRRIAAAL 184


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

 Score = 36.3 bits (84), Expect = 0.016
 Identities = 15/29 (51%), Positives = 17/29 (58%)

Query: 218 NGYKIVILGHSNAGKSSLFNALAKKDVAI 246
              KI I+G  N GKS+LFNAL K    I
Sbjct: 1   MSLKIGIVGLPNVGKSTLFNALTKAGAEI 29


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

 Score = 35.8 bits (82), Expect = 0.023
 Identities = 16/39 (41%), Positives = 21/39 (53%)

Query: 225 LGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLD 263
           +G+ N GKSS  NAL  +    V+  PG T+   TI L 
Sbjct: 320 VGYPNVGKSSTINALVGRKKVSVSSTPGKTKHFQTIFLS 358


>gnl|CDD|143853 pfam00071, Ras, Ras family.  Includes sub-families Ras, Rab, Rac,
           Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
           GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
           pfam00063. As regards Rab GTPases, these are important
           regulators of vesicle formation, motility and fusion.
           They share a fold in common with all Ras GTPases: this
           is a six-stranded beta-sheet surrounded by five
           alpha-helices.
          Length = 162

 Score = 35.9 bits (84), Expect = 0.023
 Identities = 33/131 (25%), Positives = 50/131 (38%), Gaps = 35/131 (26%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTD-IPGTTRDVLTIDLDLEGYLVK--ISDTAG- 276
           K+V++G    GKSSL     +       + IP    D  T  ++++G  VK  I DTAG 
Sbjct: 1   KLVLVGDGGVGKSSLLIRFTQNK--FPEEYIPTIGVDFYTKTIEVDGKTVKLQIWDTAGQ 58

Query: 277 ----------IRETD------DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNI 320
                      R         DI  ++    +F  V+       L+EI          N+
Sbjct: 59  ERFRALRPLYYRGAQGFLLVYDITSRD----SFENVKK-----WLEEILRHA----DDNV 105

Query: 321 DFIFIGTKSDL 331
             + +G K DL
Sbjct: 106 PIVLVGNKCDL 116


>gnl|CDD|133293 cd01893, Miro1, Miro1 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
           N-terminal GTPase domain 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 = 166

 Score = 35.4 bits (82), Expect = 0.028
 Identities = 26/130 (20%), Positives = 53/130 (40%), Gaps = 23/130 (17%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDV-LTIDLDLEGYLVKISDTAGIRE 279
           +IV++G    GKSSL  +L  ++     ++P    ++ +  D+  E     I DT+   +
Sbjct: 2   RIVLIGDEGVGKSSLIMSLVSEE--FPENVPRVLPEITIPADVTPERVPTTIVDTSSRPQ 59

Query: 280 TDDIVEKEGIKRTFLEVENADLILLLKEINSKKEI------------SFPKNIDFIFIGT 327
               +  E I++       A++I L+  ++    +                 +  I +G 
Sbjct: 60  DRANLAAE-IRK-------ANVICLVYSVDRPSTLERIRTKWLPLIRRLGVKVPIILVGN 111

Query: 328 KSDLYSTYTE 337
           KSDL    ++
Sbjct: 112 KSDLRDGSSQ 121


>gnl|CDD|35314 KOG0091, KOG0091, KOG0091, GTPase Rab39, small G protein
           superfamily [General function prediction only].
          Length = 213

 Score = 35.3 bits (81), Expect = 0.032
 Identities = 35/131 (26%), Positives = 57/131 (43%), Gaps = 24/131 (18%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLE-GYLVKIS--DTAG 276
           ++++++G S  GKSSL     +   A ++D P    D     ++L  GY +K+   DTAG
Sbjct: 9   FRLIVIGDSTVGKSSLLRYFTEGKFAELSD-PTVGVDFFARLIELRPGYRIKLQLWDTAG 67

Query: 277 IRETDDIVEKE-----GI--------KRTFLEVENADLILLLKEINSKKEISFPKNIDFI 323
                 I +       G+        + +F  VEN      +KE  +      P  + F+
Sbjct: 68  QERFRSITKSYYRNSVGVLLVYDITNRESFEHVEN-----WVKE--AAMATQGPDKVVFL 120

Query: 324 FIGTKSDLYST 334
            +G KSDL S 
Sbjct: 121 LVGHKSDLQSQ 131


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

 Score = 34.6 bits (79), Expect = 0.060
 Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 3/62 (4%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTA 275
           ++   ++ I+G+ N GKSS+ N+L ++    V ++PG TR +  + LD +   +++ D+ 
Sbjct: 249 LKTSIRVGIIGYPNVGKSSVINSLKRRKACNVGNVPGVTRSMQEVKLDKK---IRLLDSP 305

Query: 276 GI 277
           GI
Sbjct: 306 GI 307


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

 Score = 34.0 bits (78), Expect = 0.073
 Identities = 41/177 (23%), Positives = 71/177 (40%), Gaps = 42/177 (23%)

Query: 224 ILGHSNAGKSSLFNAL--AKKDVAIVTDIPGTTR--DVLTIDLDLEGYLVKISDTAGIRE 279
           ++G  NAGKS+L +A+  AK  +A   D P TT   ++  + +D     V ++D  G+ E
Sbjct: 164 LVGLPNAGKSTLLSAVSAAKPKIA---DYPFTTLVPNLGVVRVDGGESFV-VADIPGLIE 219

Query: 280 TDDIVEKEGIKRTFLE-VENADLILLLKEINSKKEISFPKNI-----------------D 321
                E  G+   FL  +E   ++L + +++        ++                   
Sbjct: 220 --GASEGVGLGLRFLRHIERTRVLLHVIDLSPIDGRDPIEDYQTIRNELEKYSPKLAEKP 277

Query: 322 FIFIGTKSD--------------LYSTYTEEYDHLISSFTGEGLEELINKIKSILSN 364
            I +  K D              L      E  +LIS+ T EGL+EL+  +  +L  
Sbjct: 278 RIVVLNKIDLPLDEEELEELKKALAEALGWEVFYLISALTREGLDELLRALAELLEE 334


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

 Score = 34.0 bits (78), Expect = 0.074
 Identities = 23/84 (27%), Positives = 41/84 (48%), Gaps = 2/84 (2%)

Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281
           + ++G  + GKS+L N L       V D P TT + +   L+ +G  +++ D  GI E  
Sbjct: 66  VALVGFPSVGKSTLLNKLTNTKSE-VADYPFTTLEPVPGMLEYKGAQIQLLDLPGIIE-G 123

Query: 282 DIVEKEGIKRTFLEVENADLILLL 305
               +   ++      NADLI+++
Sbjct: 124 ASSGRGRGRQVLSVARNADLIIIV 147


>gnl|CDD|35315 KOG0092, KOG0092, KOG0092, GTPase Rab5/YPT51 and related small G
           protein superfamily GTPases [Intracellular trafficking,
           secretion, and vesicular transport].
          Length = 200

 Score = 34.1 bits (78), Expect = 0.076
 Identities = 47/196 (23%), Positives = 75/196 (38%), Gaps = 47/196 (23%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVK--ISDTAGIR 278
           K+V+LG S  GKSSL     K         P      LT  + ++   +K  I DTAG +
Sbjct: 7   KVVLLGDSGVGKSSLVLRFVKDQFH-ENIEPTIGAAFLTKTVTVDDNTIKFEIWDTAG-Q 64

Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISF--------------PKNIDFIF 324
           E    +         +    A+  +++ +I  ++  SF                NI    
Sbjct: 65  ERYHSLAP-------MYYRGANAAIVVYDITDEE--SFEKAKNWVKELQRQASPNIVIAL 115

Query: 325 IGTKSDLYSTYTEEYD---------HLI----SSFTGEGLEELINKIKSILSNKFKKLPF 371
           +G K+DL      E++          L+    S+ TGE + E+   I        +KLP 
Sbjct: 116 VGNKADLLERREVEFEEAQAYAESQGLLFFETSAKTGENVNEIFQAI-------AEKLPC 168

Query: 372 SIPSHKRHLYHLSQTV 387
           S P  ++ L +  Q V
Sbjct: 169 SDPQERQGLPNRRQGV 184


>gnl|CDD|133265 cd01862, Rab7, Rab7 subfamily.  Rab7 is a small Rab GTPase that
           regulates vesicular traffic from early to late endosomal
           stages of the endocytic pathway.  The yeast Ypt7 and
           mammalian Rab7 are both involved in transport to the
           vacuole/lysosome, whereas Ypt7 is also required for
           homotypic vacuole fusion.  Mammalian Rab7 is an
           essential participant in the autophagic pathway for
           sequestration and targeting of cytoplasmic components to
           the lytic compartment. Mammalian Rab7 is also proposed
           to function as a tumor suppressor. GTPase activating
           proteins (GAPs) interact with GTP-bound Rab and
           accelerate the hydrolysis of GTP to GDP. Guanine
           nucleotide exchange factors (GEFs) interact with
           GDP-bound Rabs to promote the formation of the GTP-bound
           state.  Rabs are further regulated by guanine nucleotide
           dissociation inhibitors (GDIs), which facilitate Rab
           recycling by masking C-terminal lipid binding and
           promoting cytosolic localization.  Most Rab GTPases
           contain a lipid modification site at the C-terminus,
           with sequence motifs CC, CXC, or CCX. Lipid binding is
           essential for membrane attachment, a key feature of most
           Rab proteins. Due to the presence of truncated sequences
           in this CD, the lipid modification site is not available
           for annotation.
          Length = 172

 Score = 34.2 bits (79), Expect = 0.085
 Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 5/60 (8%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTT-RDVLTIDLDLEGYLV--KISDTAG 276
            K++ILG S  GK+SL N    K  +       T   D LT ++ ++  LV  +I DTAG
Sbjct: 1   LKVIILGDSGVGKTSLMNQYVNKKFS--NQYKATIGADFLTKEVTVDDKLVTLQIWDTAG 58


>gnl|CDD|133335 cd04135, Tc10, TC10 subfamily.  TC10 is a Rho family protein that
           has been shown to induce microspike formation and
           neurite outgrowth in vitro.  Its expression changes
           dramatically after peripheral nerve injury, suggesting
           an important role in promoting axonal outgrowth and
           regeneration.  TC10 regulates translocation of
           insulin-stimulated GLUT4 in adipocytes and has also been
           shown to bind directly to Golgi COPI coat proteins.
           GTP-bound TC10 in vitro can bind numerous potential
           effectors.  Depending on its subcellular localization
           and distinct functional domains, TC10 can differentially
           regulate two types of filamentous actin in adipocytes.
           TC10 mRNAs are highly expressed in three types of mouse
           muscle tissues:  leg skeletal muscle, cardiac muscle,
           and uterus; they were also present in brain, with higher
           levels in adults than in newborns.  TC10 has also been
           shown to play a role in regulating the expression of
           cystic fibrosis transmembrane conductance regulator
           (CFTR) through interactions with CFTR-associated ligand
           (CAL).  The GTP-bound form of TC10 directs the
           trafficking of CFTR from the juxtanuclear region to the
           secretory pathway toward the plasma membrane, away from
           CAL-mediated DFTR degradation in the lysosome.  Most Rho
           proteins contain a lipid modification site at the
           C-terminus, with a typical sequence motif CaaX, where a
           = an aliphatic amino acid and X = any amino acid.  Lipid
           binding is essential for membrane attachment, a key
           feature of most Rho proteins.  Due to the presence of
           truncated sequences in this CD, the lipid modification
           site is not available for annotation.
          Length = 174

 Score = 33.7 bits (77), Expect = 0.098
 Identities = 28/125 (22%), Positives = 51/125 (40%), Gaps = 24/125 (19%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD--VLTIDLDLEGYLVKISDTAGIR 278
           K V++G    GK+ L  + A    A   +   T  D   +++ +  + YL+ + DTAG  
Sbjct: 2   KCVVVGDGAVGKTCLLMSYAND--AFPEEYVPTVFDHYAVSVTVGGKQYLLGLYDTAGQE 59

Query: 279 ETDDIVEKEGIKRTFLEVENADLILLL------KEINSKKEISFPK------NIDFIFIG 326
           + D +          L     D+ L+           + KE   P+      N+ ++ +G
Sbjct: 60  DYDRLRP--------LSYPMTDVFLICFSVVNPASFQNVKEEWVPELKEYAPNVPYLLVG 111

Query: 327 TKSDL 331
           T+ DL
Sbjct: 112 TQIDL 116


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

 Score = 33.4 bits (76), Expect = 0.11
 Identities = 27/140 (19%), Positives = 52/140 (37%), Gaps = 26/140 (18%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDV-LTIDLDLEGYLVKISDTAGIRE 279
           +IV++G    GK+SL  +L +++   V  +P     + +  D+  E     I DT+   +
Sbjct: 11  RIVLIGDEGVGKTSLIMSLLEEE--FVDAVPRRLPRILIPADVTPENVPTSIVDTSSDSD 68

Query: 280 TDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISF---------------PKNIDFIF 324
               + KE I++       AD+I L+  ++ +  +                       I 
Sbjct: 69  DRLCLRKE-IRK-------ADVICLVYAVDDESTVDRISTKWLPLIRQLFGDYHETPVIL 120

Query: 325 IGTKSDLYSTYTEEYDHLIS 344
           +G KSD         +    
Sbjct: 121 VGNKSDNGDNENNSDEVNTL 140


>gnl|CDD|133252 cd00876, Ras, Ras family.  The Ras family of the Ras superfamily
           includes classical N-Ras, H-Ras, and K-Ras, as well as
           R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1,
           RRP22, Ras2, Ras-dva, and RGK proteins.  Ras proteins
           regulate cell growth, proliferation and differentiation.
            Ras is activated by guanine nucleotide exchange factors
           (GEFs) that release GDP and allow GTP binding.  Many
           RasGEFs have been identified.  These are sequestered in
           the cytosol until activation by growth factors triggers
           recruitment to the plasma membrane or Golgi, where the
           GEF colocalizes with Ras.  Active GTP-bound Ras
           interacts with several effector proteins: among the best
           characterized are the Raf kinases, phosphatidylinositol
           3-kinase (PI3K), RalGEFs and NORE/MST1.  Most Ras
           proteins contain a lipid modification site at the
           C-terminus, with a typical sequence motif CaaX, where a
           = an aliphatic amino acid and X = any amino acid.  Lipid
           binding is essential for membrane attachment, a key
           feature of most Ras proteins.  Due to the presence of
           truncated sequences in this CD, the lipid modification
           site is not available for annotation.
          Length = 160

 Score = 33.7 bits (78), Expect = 0.12
 Identities = 34/130 (26%), Positives = 54/130 (41%), Gaps = 33/130 (25%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRD--VLTIDLDLEGYLVKISDTAG-- 276
           K+V+LG    GKS++     K     V +   T  D    TI +D E Y + I DTAG  
Sbjct: 1   KVVVLGAGGVGKSAITIQFVKGT--FVEEYDPTIEDSYRKTIVVDGETYTLDILDTAGQE 58

Query: 277 ---------IRETD------DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNID 321
                    IR+ D       I ++E    +F E++        ++I     +   ++I 
Sbjct: 59  EFSAMRDLYIRQGDGFILVYSITDRE----SFEEIKG-----YREQI---LRVKDDEDIP 106

Query: 322 FIFIGTKSDL 331
            + +G K DL
Sbjct: 107 IVLVGNKCDL 116


>gnl|CDD|34593 COG4988, CydD, ABC-type transport system involved in cytochrome bd
           biosynthesis, ATPase and permease components [Energy
           production and conversion / Posttranslational
           modification, protein turnover, chaperones].
          Length = 559

 Score = 33.3 bits (76), Expect = 0.13
 Identities = 11/26 (42%), Positives = 15/26 (57%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALAK 241
           I+ G    ++G S AGKS+L N L  
Sbjct: 344 IKAGQLTALVGASGAGKSTLLNLLLG 369


>gnl|CDD|35616 KOG0395, KOG0395, KOG0395, Ras-related GTPase [General function
           prediction only].
          Length = 196

 Score = 33.0 bits (75), Expect = 0.17
 Identities = 34/134 (25%), Positives = 50/134 (37%), Gaps = 29/134 (21%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLT--IDLDLEGYLVKISDTAGI 277
           YK+V+LG    GKS+L           V D   T  D     + +D E  +++I DTAG 
Sbjct: 4   YKVVVLGAGGVGKSALTIQFLTGRF--VEDYDPTIEDSYRKELTVDGEVCMLEILDTAGQ 61

Query: 278 RETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISF---------------PKNIDF 322
            E   + +        L + N D  LL+  I  +   SF                 ++  
Sbjct: 62  EEFSAMRD--------LYIRNGDGFLLVYSITDRS--SFEEAKQLREQILRVKGRDDVPI 111

Query: 323 IFIGTKSDLYSTYT 336
           I +G K DL     
Sbjct: 112 ILVGNKCDLERERQ 125


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

 Score = 32.7 bits (74), Expect = 0.23
 Identities = 28/91 (30%), Positives = 45/91 (49%), Gaps = 7/91 (7%)

Query: 203 ISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDL 262
           +  H+S  +L  I  N   +++ G+ N GKSS  N + + D   V     TT+ +L   L
Sbjct: 154 VRQHLS--RLPAIDPNTRTLLVCGYPNVGKSSFNNKVTRADDE-VQPYAFTTKLLLVGHL 210

Query: 263 DLEGYLVKISDTAGI--RETDD--IVEKEGI 289
           D +    ++ DT GI  R  +D  I+E + I
Sbjct: 211 DYKYLRWQVIDTPGILDRPEEDRNIIEMQII 241


>gnl|CDD|133355 cd04155, Arl3, Arl3 subfamily.  Arl3 (Arf-like 3) is an Arf family
           protein that differs from most Arf family members in the
           N-terminal extension.  In is inactive, GDP-bound form,
           the N-terminal extension forms an elongated loop that is
           hydrophobically anchored into the membrane surface;
           however, it has been proposed that this region might
           form a helix in the GTP-bound form.  The delta subunit
           of the rod-specific cyclic GMP phosphodiesterase type 6
           (PDEdelta) is an Arl3 effector.  Arl3 binds microtubules
           in a regulated manner to alter specific aspects of
           cytokinesis via interactions with retinitis pigmentosa 2
           (RP2).  It has been proposed that RP2 functions in
           concert with Arl3 to link the cell membrane and the
           cytoskeleton in photoreceptors as part of the cell
           signaling or vesicular transport machinery.  In mice,
           the absence of Arl3 is associated with abnormal
           epithelial cell proliferation and cyst formation.
          Length = 173

 Score = 32.7 bits (75), Expect = 0.23
 Identities = 12/28 (42%), Positives = 21/28 (75%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVT 248
           +I+ILG  NAGK+++   LA +D++ +T
Sbjct: 16  RILILGLDNAGKTTILKQLASEDISHIT 43


>gnl|CDD|35669 KOG0448, KOG0448, KOG0448, Mitofusin 1 GTPase, involved in
           mitochondrila biogenesis [Posttranslational
           modification, protein turnover, chaperones].
          Length = 749

 Score = 32.3 bits (73), Expect = 0.28
 Identities = 20/80 (25%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 166 THIRSFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEII-RNGYKIVI 224
           +  R+F+E      E  D   F+ +E L +   +       +    + E++ R   K+ I
Sbjct: 60  SEPRTFLEGTYKNPELND---FALEERLLEDEVMSGGYEDKLDA--IDEVLARRHMKVAI 114

Query: 225 LGHSNAGKSSLFNALAKKDV 244
            G ++AGKS++ NA+  K +
Sbjct: 115 FGRTSAGKSTVINAMLHKKL 134


>gnl|CDD|33918 COG4178, COG4178, ABC-type uncharacterized transport system,
           permease and ATPase components [General function
           prediction only].
          Length = 604

 Score = 32.2 bits (73), Expect = 0.31
 Identities = 13/25 (52%), Positives = 18/25 (72%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
           +R G +++I G S AGK+SL  ALA
Sbjct: 416 VRPGERLLITGESGAGKTSLLRALA 440


>gnl|CDD|133377 cd04177, RSR1, RSR1 subgroup.  RSR1/Bud1p is a member of the Rap
           subfamily of the Ras family that is found in fungi.  In
           budding yeasts, RSR1 is involved in selecting a site for
           bud growth on the cell cortex, which directs the
           establishment of cell polarization.  The Rho family
           GTPase cdc42 and its GEF, cdc24, then establish an axis
           of polarized growth by organizing the actin cytoskeleton
           and secretory apparatus at the bud site.  It is believed
           that cdc42 interacts directly with RSR1 in vivo.  In
           filamentous fungi, polar growth occurs at the tips of
           hypha and at novel growth sites along the extending
           hypha.  In Ashbya gossypii, RSR1 is a key regulator of
           hyphal growth, localizing at the tip region and
           regulating in apical polarization of the actin
           cytoskeleton.  Most Ras proteins contain a lipid
           modification site at the C-terminus, with a typical
           sequence motif CaaX, where a = an aliphatic amino acid
           and X = any amino acid.  Lipid binding is essential for
           membrane attachment, a key feature of most Ras proteins.
          Length = 168

 Score = 32.1 bits (73), Expect = 0.31
 Identities = 35/121 (28%), Positives = 56/121 (46%), Gaps = 13/121 (10%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVL--TIDLDLEGYLVKISDTAGI 277
           YKIV+LG    GKS+L      ++V I +  P T  D     +++D     ++I DTAG 
Sbjct: 2   YKIVVLGAGGVGKSAL-TVQFVQNVFIESYDP-TIEDSYRKQVEIDGRQCDLEILDTAGT 59

Query: 278 RE---TDDIVEKEGIKRTFLEVENADLILLLKEINSKKE----ISFPKNIDFIFIGTKSD 330
            +     ++  K G  + FL V +      L E+   +E    I    N+  + +G K+D
Sbjct: 60  EQFTAMRELYIKSG--QGFLLVYSVTSEASLNELGELREQVLRIKDSDNVPMVLVGNKAD 117

Query: 331 L 331
           L
Sbjct: 118 L 118


>gnl|CDD|133262 cd01853, Toc34_like, Toc34-like (Translocon at the Outer-envelope
           membrane of Chloroplasts).  This family contains several
           Toc proteins, including Toc34, Toc33, Toc120, Toc159,
           Toc86, Toc125, and Toc90.  The Toc complex at the outer
           envelope membrane of chloroplasts is a molecular machine
           of ~500 kDa that contains a single Toc159 protein, four
           Toc75 molecules, and four or five copies of Toc34. Toc64
           and Toc12 are associated with the translocon, but do not
           appear to be part of the core complex.  The Toc
           translocon initiates the import of nuclear-encoded
           preproteins from the cytosol into the organelle.  Toc34
           and Toc159 are both GTPases, while Toc75 is a
           beta-barrel integral membrane protein.  Toc159 is
           equally distributed between a soluble cytoplasmic form
           and a membrane-inserted form, suggesting that assembly
           of the Toc complex is dynamic.  Toc34 and Toc75 act
           sequentially to mediate docking and insertion of Toc159
           resulting in assembly of the functional translocon.
          Length = 249

 Score = 31.9 bits (73), Expect = 0.38
 Identities = 21/79 (26%), Positives = 37/79 (46%), Gaps = 7/79 (8%)

Query: 209 QGKLGEIIRNGYK-------IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTID 261
           Q K  E+   G +       I++LG +  GKSS  N++  +  A  +     T  V  + 
Sbjct: 14  QTKALELEAKGKEELDFSLTILVLGKTGVGKSSTINSIFGERKAATSAFQSETLRVREVS 73

Query: 262 LDLEGYLVKISDTAGIRET 280
             ++G+ + I DT G+ E+
Sbjct: 74  GTVDGFKLNIIDTPGLLES 92


>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 = 31.8 bits (73), Expect = 0.43
 Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTT 254
           I ++G  NAGKS+ FNA    DV I  + P TT
Sbjct: 1   IGLVGKPNAGKSTFFNAATLADVEI-ANYPFTT 32


>gnl|CDD|72984 cd03225, ABC_cobalt_CbiO_domain1, Domain I of the ABC component of
           a cobalt transport family found in bacteria, archaea,
           and eukaryota.  The transition metal cobalt is an
           essential component of many enzymes and must be
           transported into cells in appropriate amounts when
           needed.  This ABC transport system of the CbiMNQO family
           is involved in cobalt transport in association with the
           cobalamin (vitamin B12) biosynthetic pathways.  Most of
           cobalt (Cbi) transport systems possess a separate CbiN
           component, the cobalt-binding periplasmic protein, and
           they are encoded by the conserved gene cluster cbiMNQO. 
           Both the CbiM and CbiQ proteins are integral cytoplasmic
           membrane proteins, and the CbiO protein has the linker
           peptide and the Walker A and B motifs commonly found in
           the ATPase components of the ABC-type transport
           systems..
          Length = 211

 Score = 31.6 bits (72), Expect = 0.46
 Identities = 9/25 (36%), Positives = 16/25 (64%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
           I+ G  ++I+G + +GKS+L   L 
Sbjct: 24  IKKGEFVLIVGPNGSGKSTLLRLLN 48


>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
           Translocation is mediated by EF-G (also called
           translocase).  The structure of EF-G closely resembles
           that of the complex between EF-Tu and tRNA.  This is an
           example of molecular mimicry; a protein domain evolved
           so that it mimics the shape of a tRNA molecule.  EF-G in
           the GTP form binds to the ribosome, primarily through
           the interaction of its EF-Tu-like domain with the 50S
           subunit.  The binding of EF-G to the ribosome in this
           manner stimulates the GTPase activity of EF-G.  On GTP
           hydrolysis, EF-G undergoes a conformational change that
           forces its arm deeper into the A site on the 30S
           subunit.  To accommodate this domain, the peptidyl-tRNA
           in the A site moves to the P site, carrying the mRNA and
           the deacylated tRNA with it.  The ribosome may be
           prepared for these rearrangements by the initial binding
           of EF-G as well.  The dissociation of EF-G leaves the
           ribosome ready to accept the next aminoacyl-tRNA into
           the A site.  This group contains only bacterial members.
          Length = 268

 Score = 31.4 bits (72), Expect = 0.46
 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 7/38 (18%)

Query: 222 IVILGHSNAGKSSLFNALAKKDVAI-----VTDIPGTT 254
           I ++GHS +GK++L  AL     AI     V D  GTT
Sbjct: 2   IALVGHSGSGKTTLAEALLYATGAIDRLGSVED--GTT 37


>gnl|CDD|37697 KOG2486, KOG2486, KOG2486, Predicted GTPase [General function
           prediction only].
          Length = 320

 Score = 31.2 bits (70), Expect = 0.59
 Identities = 35/168 (20%), Positives = 56/168 (33%), Gaps = 23/168 (13%)

Query: 169 RSFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHS 228
           +S+ +  L  S   DV  F +++ +     +  D S         +       +   G S
Sbjct: 91  KSYRKRVLSGSNI-DVSPFLARKQVKSEKRVHGDGSVTAEDCPKDKRPE----LAFYGRS 145

Query: 229 NAGKSSLFNALAKKDVAIVTDIPGTTRDVLTID----------LDLEGYLVKISDTAGIR 278
           N GKSSL N L +      T           I+          +DL GY           
Sbjct: 146 NVGKSSLLNDLVRVKNIADTSKS-KNGKTQAINHFHVGKSWYEVDLPGYGRAGYGFELPA 204

Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFIG 326
           + D        K   LE EN   + LL  +++   I    N +  ++G
Sbjct: 205 DWDKFT-----KSYLLERENLVRVFLL--VDASVPIQPTDNPEIAWLG 245


>gnl|CDD|30753 COG0404, GcvT, Glycine cleavage system T protein
           (aminomethyltransferase) [Amino acid transport and
           metabolism].
          Length = 379

 Score = 31.0 bits (70), Expect = 0.60
 Identities = 20/102 (19%), Positives = 39/102 (38%), Gaps = 8/102 (7%)

Query: 3   HEKETIFAVSTGALPSAISIIRLSGPSCFQVCEFICKKKKPFPRKASLRYFFGLDGRILD 62
           H+      V+  ++   ++++ L GP   +V      K        +L +F   +  I  
Sbjct: 131 HQAGPDLDVTLTSVTEDLAVLALQGPKAREVLA----KLVDGDLVEALPFFAFKEVTIGG 186

Query: 63  KGLLIVFPSPESFTGEDSAEFHVHG--GIAVVNGILEELAKM 102
              + +  +   +TGE   E +V      AV + +LE   K 
Sbjct: 187 GVPVRISRT--GYTGELGFEIYVPAEDAAAVWDALLEAGEKF 226


>gnl|CDD|72972 cd03213, ABCG_EPDR, ABCG transporters are involved in eye pigment
           (EP) precursor transport, regulation of
           lipid-trafficking mechanisms, and pleiotropic drug
           resistance (DR).  DR is a well-described phenomenon
           occurring in fungi and shares several similarities with
           processes in bacteria and higher eukaryotes.  Compared
           to other members of the ABC transporter subfamilies, the
           ABCG transporter family is composed of proteins that
           have an ATP-binding cassette domain at the N-terminus
           and a TM (transmembrane) domain at the C-terminus..
          Length = 194

 Score = 31.3 bits (71), Expect = 0.63
 Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 9/61 (14%)

Query: 182 EDVQNFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAK 241
            ++              L  ++S     G+L           I+G S AGKS+L NALA 
Sbjct: 7   RNLTVTVKSSPSKSGKQLLKNVSGKAKPGEL---------TAIMGPSGAGKSTLLNALAG 57

Query: 242 K 242
           +
Sbjct: 58  R 58


>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 = 30.9 bits (71), Expect = 0.73
 Identities = 12/22 (54%), Positives = 14/22 (63%)

Query: 224 ILGHSNAGKSSLFNALAKKDVA 245
           I+G  N GKS+LFNAL K    
Sbjct: 3   IVGLPNVGKSTLFNALTKAGAE 24


>gnl|CDD|133263 cd01860, Rab5_related, Rab5-related subfamily.  This subfamily
           includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of
           yeast, and RabF of plants. The members of this subfamily
           are involved in endocytosis and endocytic-sorting
           pathways.  In mammals, Rab5 GTPases localize to early
           endosomes and regulate fusion of clathrin-coated
           vesicles to early endosomes and fusion between early
           endosomes. In yeast, Ypt51p family members similarly
           regulate membrane trafficking through prevacuolar
           compartments. GTPase activating proteins (GAPs) interact
           with GTP-bound Rab and accelerate the hydrolysis of GTP
           to GDP. Guanine nucleotide exchange factors (GEFs)
           interact with GDP-bound Rabs to promote the formation of
           the GTP-bound state.  Rabs are further regulated by
           guanine nucleotide dissociation inhibitors (GDIs), which
           facilitate Rab recycling by masking C-terminal lipid
           binding and promoting cytosolic localization.  Most Rab
           GTPases contain a lipid modification site at the
           C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
           binding is essential for membrane attachment, a key
           feature of most Rab proteins. Due to the presence of
           truncated sequences in this CD, the lipid modification
           site is not available for annotation.
          Length = 163

 Score = 30.9 bits (71), Expect = 0.74
 Identities = 22/61 (36%), Positives = 33/61 (54%), Gaps = 7/61 (11%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTT--RDVLTIDLDLEGYLVK--ISDTA 275
           +K+V+LG S+ GKSSL     K +    ++   +T     LT  ++L+   VK  I DTA
Sbjct: 2   FKLVLLGDSSVGKSSLVLRFVKNE---FSENQESTIGAAFLTQTVNLDDTTVKFEIWDTA 58

Query: 276 G 276
           G
Sbjct: 59  G 59


>gnl|CDD|133334 cd04134, Rho3, Rho3 subfamily.  Rho3 is a member of the Rho family
           found only in fungi.  Rho3 is believed to regulate cell
           polarity by interacting with the diaphanous/formin
           family protein For3 to control both the actin
           cytoskeleton and microtubules.  Rho3 is also believed to
           have a direct role in exocytosis that is independent of
           its role in regulating actin polarity.  The function in
           exocytosis may be two-pronged: first, in the transport
           of post-Golgi vesicles from the mother cell to the bud,
           mediated by myosin (Myo2); second, in the docking and
           fusion of vesicles to the plasma membrane, mediated by
           an exocyst (Exo70) protein.  Most Rho proteins contain a
           lipid modification site at the C-terminus, with a
           typical sequence motif CaaX, where a = an aliphatic
           amino acid and X = any amino acid.  Lipid binding is
           essential for membrane attachment, a key feature of most
           Rho proteins.
          Length = 189

 Score = 31.0 bits (70), Expect = 0.75
 Identities = 27/93 (29%), Positives = 46/93 (49%), Gaps = 12/93 (12%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKIS--DTAGIR 278
           K+V+LG    GK+SL N   +     V + P T  +    D+ ++G  +++S  DTAG  
Sbjct: 2   KVVVLGDGACGKTSLLNVFTRGYFPQVYE-P-TVFENYVHDIFVDGLHIELSLWDTAGQE 59

Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINSK 311
           E D +       R+ L   + D+I+L   ++S 
Sbjct: 60  EFDRL-------RS-LSYADTDVIMLCFSVDSP 84


>gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter
           nucleotide-binding domain; ABC transporters are a large
           family of proteins involved in the transport of a wide
           variety of different compounds, like sugars, ions,
           peptides, and more complex organic molecules.  The
           nucleotide-binding domain shows the highest similarity
           between all members of the family.  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 = 157

 Score = 30.7 bits (69), Expect = 0.80
 Identities = 8/25 (32%), Positives = 17/25 (68%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
           ++ G  + ++G + +GKS+L  A+A
Sbjct: 22  LKAGEIVALVGPNGSGKSTLLRAIA 46


>gnl|CDD|35280 KOG0057, KOG0057, KOG0057, Mitochondrial Fe/S cluster exporter, ABC
           superfamily [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 591

 Score = 30.6 bits (69), Expect = 0.83
 Identities = 23/91 (25%), Positives = 37/91 (40%), Gaps = 6/91 (6%)

Query: 153 ELSSLYGQWIDKLTHIR-SFIEADLDFSEEEDVQNFSSKEVLNDILFLKNDISSHISQGK 211
            L S+Y +    LT +R  FI  ++D   +E             I F     S    +  
Sbjct: 310 FLGSVYRELRQALTDMRTLFILLEVDEDIQEAALPIELFG--GSIEFDDVHFSYGPKRKV 367

Query: 212 LGEI---IRNGYKIVILGHSNAGKSSLFNAL 239
           L  +   I  G K+ I+G + +GKS++   L
Sbjct: 368 LKGVSFTIPKGEKVAIVGSNGSGKSTILRLL 398


>gnl|CDD|35615 KOG0394, KOG0394, KOG0394, Ras-related GTPase [General function
           prediction only].
          Length = 210

 Score = 30.7 bits (69), Expect = 0.86
 Identities = 34/131 (25%), Positives = 51/131 (38%), Gaps = 31/131 (23%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDV-----AIVTDIPGTTRDVLTIDLDLEGYLV--KISD 273
           K++ILG S  GK+SL N    K       A +        D LT ++ ++   V  +I D
Sbjct: 11  KVIILGDSGVGKTSLMNQYVNKKFSQQYKATI------GADFLTKEVQVDDRSVTLQIWD 64

Query: 274 TAG-----------IRETDDIVEKE--GIKRTFLEVENADLILLLKEINSKKEISFPKNI 320
           TAG            R  D  V        ++F  +EN       KE   +     P+  
Sbjct: 65  TAGQERFQSLGVAFYRGADCCVLVYDVNNPKSFENLENWR-----KEFLIQASPQDPETF 119

Query: 321 DFIFIGTKSDL 331
            F+ +G K D+
Sbjct: 120 PFVILGNKIDV 130


>gnl|CDD|133332 cd04132, Rho4_like, Rho4-like subfamily.  Rho4 is a GTPase that
           controls septum degradation by regulating secretion of
           Eng1 or Agn1 during cytokinesis.  Rho4 also plays a role
           in cell morphogenesis.  Rho4 regulates septation and
           cell morphology by controlling the actin cytoskeleton
           and cytoplasmic microtubules.  The localization of Rho4
           is modulated by Rdi1, which may function as a GDI, and
           by Rga9, which is believed to function as a GAP.  In S.
           pombe, both Rho4 deletion and Rho4 overexpression result
           in a defective cell wall, suggesting a role for Rho4 in
           maintaining cell wall integrity.  Most Rho proteins
           contain a lipid modification site at the C-terminus,
           with a typical sequence motif CaaX, where a = an
           aliphatic amino acid and X = any amino acid.  Lipid
           binding is essential for membrane attachment, a key
           feature of most Rho proteins.
          Length = 187

 Score = 30.7 bits (70), Expect = 0.87
 Identities = 30/136 (22%), Positives = 50/136 (36%), Gaps = 39/136 (28%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVA----------IVTDIPGTTRDVLTIDLDLEGYLVK 270
           KIV++G    GK+ L    ++               VT+I G       I+L L      
Sbjct: 2   KIVVVGDGGCGKTCLLIVYSQGKFPEEYVPTVFENYVTNIQGPNGK--IIELAL------ 53

Query: 271 ISDTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEINSK------KEISFP------K 318
             DTAG  E D +       R  L   + D++L+   +++       ++  FP       
Sbjct: 54  -WDTAGQEEYDRL-------RP-LSYPDVDVLLICYAVDNPTSLDNVEDKWFPEVNHFCP 104

Query: 319 NIDFIFIGTKSDLYST 334
               + +G K+DL   
Sbjct: 105 GTPIMLVGLKTDLRKD 120


>gnl|CDD|72982 cd03223, ABCD_peroxisomal_ALDP, Peroxisomal ATP-binding cassette
           transporter (Pat) is involved in the import of very
           long-chain fatty acids (VLCFA) into the peroxisome.  The
           peroxisomal membrane forms a permeability barrier for a
           wide variety of metabolites required for and formed
           during fatty acid beta-oxidation.  To communicate with
           the cytoplasm and mitochondria, peroxisomes need
           dedicated proteins to transport such hydrophilic
           molecules across their membranes.  X-linked
           adrenoleukodystrophy (X-ALD) is caused by mutations in
           the ALD gene, which encodes ALDP (adrenoleukodystrophy
           protein ), a peroxisomal integral membrane protein that
           is a member of the ATP-binding cassette (ABC)
           transporter protein family.  The disease is
           characterized by a striking and unpredictable variation
           in phenotypic expression.  Phenotypes include the
           rapidly progressive childhood cerebral form (CCALD), the
           milder adult form, adrenomyeloneuropathy (AMN), and
           variants without neurologic involvement (i.e.
           asymptomatic)..
          Length = 166

 Score = 30.5 bits (69), Expect = 0.99
 Identities = 14/25 (56%), Positives = 18/25 (72%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
           I+ G +++I G S  GKSSLF ALA
Sbjct: 24  IKPGDRLLITGPSGTGKSSLFRALA 48


>gnl|CDD|133311 cd04111, Rab39, Rab39 subfamily.  Found in eukaryotes, Rab39 is
           mainly found in epithelial cell lines, but is
           distributed widely in various human tissues and cell
           lines.  It is believed to be a novel Rab protein
           involved in regulating Golgi-associated vesicular
           transport during cellular endocytosis. GTPase activating
           proteins (GAPs) interact with GTP-bound Rab and
           accelerate the hydrolysis of GTP to GDP. Guanine
           nucleotide exchange factors (GEFs) interact with
           GDP-bound Rabs to promote the formation of the GTP-bound
           state.  Rabs are further regulated by guanine nucleotide
           dissociation inhibitors (GDIs), which facilitate Rab
           recycling by masking C-terminal lipid binding and
           promoting cytosolic localization.   Most Rab GTPases
           contain a lipid modification site at the C-terminus,
           with sequence motifs CC, CXC, or CCX. Lipid binding is
           essential for membrane attachment, a key feature of most
           Rab proteins.
          Length = 211

 Score = 30.5 bits (69), Expect = 1.0
 Identities = 35/131 (26%), Positives = 60/131 (45%), Gaps = 31/131 (23%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLE-GYLVKIS--DTAG 276
           ++++++G S  GKSSL     +   A V+D P    D  +  +++E G  +K+   DTAG
Sbjct: 3   FRLIVIGDSTVGKSSLLKRFTEGRFAEVSD-PTVGVDFFSRLIEIEPGVRIKLQLWDTAG 61

Query: 277 IRETDDIVEK-EGIKRTFLEVENADLILLLKEINSKKEISF---------------PKNI 320
                   E+   I R++    N+  +LL+ +I +++  SF               P   
Sbjct: 62  -------QERFRSITRSYY--RNSVGVLLVFDITNRE--SFEHVHDWLEEARSHIQPHRP 110

Query: 321 DFIFIGTKSDL 331
            FI +G K DL
Sbjct: 111 VFILVGHKCDL 121


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

 Score = 30.4 bits (68), Expect = 1.1
 Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%)

Query: 217 RNGYKIVIL-GHSNAGKSSLFNALAKKDVAIVTDIP 251
            N +K  IL G   AGK++L  ALA+   A V +  
Sbjct: 6   FNRHKRFILTGGPGAGKTTLLAALARAGFATVEEAG 41


>gnl|CDD|35307 KOG0084, KOG0084, KOG0084, GTPase Rab1/YPT1, small G protein
           superfamily, and related GTP-binding proteins [Signal
           transduction mechanisms, Intracellular trafficking,
           secretion, and vesicular transport].
          Length = 205

 Score = 30.2 bits (68), Expect = 1.1
 Identities = 30/128 (23%), Positives = 53/128 (41%), Gaps = 27/128 (21%)

Query: 220 YKIVILGHSNAGKSSL---FNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAG 276
           +KI+++G S  GK+ L   F      +  I T   G    + T++LD +   ++I DTAG
Sbjct: 10  FKIILIGDSGVGKTCLLLRFKDDTFTESYISTI--GVDFKIRTVELDGKTIKLQIWDTAG 67

Query: 277 IRETDDIVEKEGIKRTFLEV-ENADLILLLKEINSK----------KEISF--PKNIDFI 323
                    +E  +         A  I+ + +I  +          +EI     +N+  +
Sbjct: 68  ---------QERFRTITSSYYRGAHGIIFVYDITKQESFNNVKRWIQEIDRYASENVPKL 118

Query: 324 FIGTKSDL 331
            +G K DL
Sbjct: 119 LVGNKCDL 126


>gnl|CDD|133271 cd01868, Rab11_like, Rab11-like.  Rab11a, Rab11b, and Rab25 are
           closely related, evolutionary conserved Rab proteins
           that are differentially expressed. Rab11a is
           ubiquitously synthesized, Rab11b is enriched in brain
           and heart and Rab25 is only found in epithelia. Rab11/25
           proteins seem to regulate recycling pathways from
           endosomes to the plasma membrane and to the trans-Golgi
           network. Furthermore, Rab11a is thought to function in
           the histamine-induced fusion of tubulovesicles
           containing H+, K+ ATPase with the plasma membrane in
           gastric parietal cells and in insulin-stimulated
           insertion of GLUT4 in the plasma membrane of
           cardiomyocytes. Overexpression of Rab25 has recently
           been observed in ovarian cancer and breast cancer, and
           has been correlated with worsened outcomes in both
           diseases. In addition, Rab25 overexpression has also
           been observed in prostate cancer, transitional cell
           carcinoma of the bladder, and invasive breast tumor
           cells. GTPase activating proteins (GAPs) interact with
           GTP-bound Rab and accelerate the hydrolysis of GTP to
           GDP. Guanine nucleotide exchange factors (GEFs) interact
           with GDP-bound Rabs to promote the formation of the
           GTP-bound state.  Rabs are further regulated by guanine
           nucleotide dissociation inhibitors (GDIs), which
           facilitate Rab recycling by masking C-terminal lipid
           binding and promoting cytosolic localization.   Most Rab
           GTPases contain a lipid modification site at the
           C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
           binding is essential for membrane attachment, a key
           feature of most Rab proteins.  Due to the presence of
           truncated sequences in this CD, the lipid modification
           site is not available for annotation.
          Length = 165

 Score = 30.2 bits (69), Expect = 1.1
 Identities = 38/134 (28%), Positives = 61/134 (45%), Gaps = 39/134 (29%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDV--LTIDLDLEGYLVK--ISDTA 275
           +KIV++G S  GKS+L +   + +  + +    +T  V   T  + ++G  +K  I DTA
Sbjct: 4   FKIVLIGDSGVGKSNLLSRFTRNEFNLDSK---STIGVEFATRSIQIDGKTIKAQIWDTA 60

Query: 276 GIRE-----TD-------------DIVEKEGIKRTFLEVENADLILLLKEINSKKEISFP 317
           G +E     T              DI +    K+TF  VE       LKE+   ++ +  
Sbjct: 61  G-QERYRAITSAYYRGAVGALLVYDITK----KQTFENVE-----RWLKEL---RDHA-D 106

Query: 318 KNIDFIFIGTKSDL 331
            NI  + +G KSDL
Sbjct: 107 SNIVIMLVGNKSDL 120


>gnl|CDD|72987 cd03228, ABCC_MRP_Like, The MRP (Mutidrug Resistance Protein)-like
           transporters are involved in drug, peptide, and lipid
           export.  They belong to the subfamily C of the
           ATP-binding cassette (ABC) superfamily of transport
           proteins.  The ABCC subfamily contains transporters with
           a diverse functional spectrum that includes ion
           transport, cell surface receptor, and toxin secretion
           activities.  The MRP-like family, simlar to all ABC
           proteins, have a common four-domain core structure
           constituted by two membrane-spanning domains, each
           composed of six transmembrane (TM) helices, and two
           nucleotide-binding domains (NBD).  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 = 171

 Score = 30.4 bits (69), Expect = 1.1
 Identities = 11/26 (42%), Positives = 17/26 (65%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALAK 241
           I+ G K+ I+G S +GKS+L   L +
Sbjct: 25  IKPGEKVAIVGPSGSGKSTLLKLLLR 50


>gnl|CDD|73003 cd03244, ABCC_MRP_domain2, Domain 2 of the ABC subfamily C.  This
           family is also known as MRP (mulrtidrug
           resisitance-associated protein).  Some of the MRP
           members have five additional transmembrane segments in
           their N-terminus, but the function of these additional
           membrane-spanning domains is not clear.  The MRP was
           found in the multidrug-resistance lung cancer cell in
           which p-glycoprotein was not overexpressed.  MRP exports
           glutathione by drug stimulation, as well as, certain
           substrates in conjugated forms with anions, such as
           glutathione, glucuronate, and sulfate..
          Length = 221

 Score = 30.1 bits (68), Expect = 1.1
 Identities = 12/24 (50%), Positives = 17/24 (70%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNAL 239
           I+ G K+ I+G + +GKSSL  AL
Sbjct: 27  IKPGEKVGIVGRTGSGKSSLLLAL 50


>gnl|CDD|35310 KOG0087, KOG0087, KOG0087, GTPase Rab11/YPT3, small G protein
           superfamily [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 222

 Score = 30.3 bits (68), Expect = 1.2
 Identities = 35/137 (25%), Positives = 57/137 (41%), Gaps = 26/137 (18%)

Query: 219 GYKIVILGHSNAGKSSLFNALAKKDVAIVTDIP-GTTRDVLTIDLDLEGYLVKISDTAGI 277
            +KIV++G S  GKS+L +   + + ++ +    G      T+++D +    +I DTAG 
Sbjct: 14  LFKIVLIGDSAVGKSNLLSRFTRNEFSLESKSTIGVEFATRTVNVDGKTVKAQIWDTAGQ 73

Query: 278 RETDDI-------------VEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIF 324
                I             V     ++TF  VE       LKE+          NI  + 
Sbjct: 74  ERYRAITSAYYRGAVGALLVYDITRRQTFENVE-----RWLKELRD----HADSNIVIML 124

Query: 325 IGTKSDLY---STYTEE 338
           +G KSDL    +  TE+
Sbjct: 125 VGNKSDLNHLRAVPTED 141


>gnl|CDD|31298 COG1101, PhnK, ABC-type uncharacterized transport system, ATPase
           component [General function prediction only].
          Length = 263

 Score = 30.2 bits (68), Expect = 1.2
 Identities = 9/19 (47%), Positives = 15/19 (78%)

Query: 222 IVILGHSNAGKSSLFNALA 240
           + ++G + AGKS+L NA+A
Sbjct: 35  VTVIGSNGAGKSTLLNAIA 53


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

 Score = 30.2 bits (68), Expect = 1.2
 Identities = 13/24 (54%), Positives = 17/24 (70%)

Query: 216  IRNGYKIVILGHSNAGKSSLFNAL 239
            I+ G K+ I+G + AGKSSL  AL
Sbjct: 1163 IKPGEKVGIVGRTGAGKSSLILAL 1186


>gnl|CDD|133305 cd04105, SR_beta, Signal recognition particle receptor, beta
           subunit (SR-beta).  SR-beta and SR-alpha form the
           heterodimeric signal recognition particle (SRP or SR)
           receptor that binds SRP to regulate protein
           translocation across the ER membrane.  Nascent
           polypeptide chains are synthesized with an N-terminal
           hydrophobic signal sequence that binds SRP54, a
           component of the SRP.  SRP directs targeting of the
           ribosome-nascent chain complex (RNC) to the ER membrane
           via interaction with the SR, which is localized to the
           ER membrane.  The RNC is then transferred to the
           protein-conducting channel, or translocon, which
           facilitates polypeptide translation across the ER
           membrane or integration into the ER membrane.  SR-beta
           is found only in eukaryotes; it is believed to control
           the release of the signal sequence from SRP54 upon
           binding of the ribosome to the translocon.  High
           expression of SR-beta has been observed in human colon
           cancer, suggesting it may play a role in the development
           of this type of cancer.
          Length = 203

 Score = 30.0 bits (68), Expect = 1.3
 Identities = 32/130 (24%), Positives = 54/130 (41%), Gaps = 17/130 (13%)

Query: 222 IVILGHSNAGKSSLFNAL-AKKDVAIVTDIPGTTRDVLTIDLDLE--GYLVKISDTAG-- 276
           +++LG S++GK++LF  L   K  + VT I     +V T  L+ E  G   ++ D  G  
Sbjct: 3   VLLLGPSDSGKTALFTKLTTGKYRSTVTSI---EPNVATFILNSEGKGKKFRLVDVPGHP 59

Query: 277 -IRETDDIVEKEGIKRTFLEVENADLI-------LLLKEINSKKEISFPKNIDFIFIGTK 328
            +R+      K   K     V++A            L +I +  E    K I  +    K
Sbjct: 60  KLRDKLLETLKNSAKGIVFVVDSATFQKNLKDVAEFLYDILTDLEKVKNK-IPVLIACNK 118

Query: 329 SDLYSTYTEE 338
            DL++    +
Sbjct: 119 QDLFTAKPAK 128


>gnl|CDD|34590 COG4985, COG4985, ABC-type phosphate transport system, auxiliary
           component [Inorganic ion transport and metabolism].
          Length = 289

 Score = 30.0 bits (67), Expect = 1.4
 Identities = 22/121 (18%), Positives = 47/121 (38%), Gaps = 20/121 (16%)

Query: 53  FFGLDGRILDKGLLIVFPSPESFTGEDSAEFHVHGGIAVVNGILEELAKMP--NLRLANP 110
            +G   R    G  +           D  E  +   +  V  + +++ KM    +R+ N 
Sbjct: 143 LYGKLLRFDSNGQELD---------GDPLERELQKRLLEVETLRDQVDKMVEQQVRVINS 193

Query: 111 GEFSRRAFENGKIDL---LEAESLADLISSETEMQRRLS-----MEGMSGELSSLYGQWI 162
               R   E  ++ L   L+ E     ++ ++E+Q+RL+     ++ +  EL   +   +
Sbjct: 194 Q-LERLRLEKRRLQLNGQLDDEFQQHYVAEKSELQKRLAQLQTELDALRAELERQFLYLV 252

Query: 163 D 163
           D
Sbjct: 253 D 253


>gnl|CDD|143815 pfam00025, Arf, ADP-ribosylation factor family.  Pfam combines a
           number of different Prosite families together.
          Length = 174

 Score = 29.9 bits (68), Expect = 1.4
 Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 2/32 (6%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDIP 251
            +I+ILG  NAGK+++   L   +  IVT IP
Sbjct: 15  MRILILGLDNAGKTTILYKLKLGE--IVTTIP 44


>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 = 30.0 bits (68), Expect = 1.4
 Identities = 10/36 (27%), Positives = 18/36 (50%)

Query: 215 IIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDI 250
            I  G +I ++G + AGKS+L   +A +       +
Sbjct: 22  TINPGDRIGLVGRNGAGKSTLLKLIAGELEPDEGIV 57


>gnl|CDD|31313 COG1116, TauB, ABC-type nitrate/sulfonate/bicarbonate transport
           system, ATPase component [Inorganic ion transport and
           metabolism].
          Length = 248

 Score = 29.8 bits (67), Expect = 1.4
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
           +  G  + ILG S  GKS+L   +A
Sbjct: 26  VEKGEFVAILGPSGCGKSTLLRLIA 50


>gnl|CDD|34592 COG4987, CydC, ABC-type transport system involved in cytochrome bd
           biosynthesis, fused ATPase and permease components
           [Energy production and conversion / Posttranslational
           modification, protein turnover, chaperones].
          Length = 573

 Score = 29.8 bits (67), Expect = 1.4
 Identities = 12/26 (46%), Positives = 16/26 (61%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALAK 241
           +  G K+ ILG S +GKS+L   LA 
Sbjct: 361 LAQGEKVAILGRSGSGKSTLLQLLAG 386


>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 = 29.7 bits (68), Expect = 1.6
 Identities = 47/180 (26%), Positives = 68/180 (37%), Gaps = 55/180 (30%)

Query: 224 ILGHSNAGKSSLFNAL--AKKDVAIVTDIPGTTRDVLTIDLDLEGYL--VKISDTAGIRE 279
           ++G  NAGKS+L +A+  AK  +A   D P TT         L   L  V++ D      
Sbjct: 5   LVGLPNAGKSTLLSAISNAKPKIA---DYPFTT---------LVPNLGVVRVDDGRSFVV 52

Query: 280 TD--DIVE--KEG----------IKRTFL--------EVEN--ADLILLLKEINSKKEIS 315
            D   ++E   EG          I+RT L          ++   D   +  E+       
Sbjct: 53  ADIPGLIEGASEGKGLGHRFLRHIERTRLLLHVIDLSGDDDPVEDYKTIRNELELYNPEL 112

Query: 316 FPKNIDFIFIGTKSDLYSTYT------EEYDHL-------ISSFTGEGLEELINKIKSIL 362
             K    I +  K DL           E    L       IS+ TGEGL+EL+ K+  +L
Sbjct: 113 LEKPR--IVVLNKIDLLDEEELFELLKELLKELWGKPVFPISALTGEGLDELLRKLAELL 170


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

 Score = 29.8 bits (67), Expect = 1.6
 Identities = 12/29 (41%), Positives = 17/29 (58%)

Query: 215 IIRNGYKIVILGHSNAGKSSLFNALAKKD 243
            I  G +I I+G + AGKS+L   LA + 
Sbjct: 344 RIDRGDRIAIVGPNGAGKSTLLKLLAGEL 372



 Score = 27.1 bits (60), Expect = 9.5
 Identities = 10/31 (32%), Positives = 17/31 (54%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALAKKDVAI 246
           +  G +I ++G + AGKS+L   LA +    
Sbjct: 26  LNPGERIGLVGRNGAGKSTLLKILAGELEPD 56


>gnl|CDD|73051 cd03292, ABC_FtsE_transporter, FtsE is a hydrophilic
           nucleotide-binding protein that binds FtsX to form a
           heterodimeric ATP-binding cassette (ABC)-type
           transporter that associates with the bacterial inner
           membrane.  The FtsE/X transporter is thought to be
           involved in cell division and is important for assembly
           or stability of the septal ring..
          Length = 214

 Score = 29.5 bits (66), Expect = 1.8
 Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 10/55 (18%)

Query: 189 SKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKD 243
           +K   N    L + I+  IS G+          + ++G S AGKS+L   + K++
Sbjct: 7   TKTYPNGTAAL-DGINISISAGEF---------VFLVGPSGAGKSTLLKLIYKEE 51


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

 Score = 29.8 bits (67), Expect = 1.8
 Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 9/40 (22%)

Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA 240
           +D+S  I +G++           ILG + +GKS+L   LA
Sbjct: 19  DDLSFSIPKGEI---------TGILGPNGSGKSTLLKCLA 49


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

 Score = 29.5 bits (66), Expect = 1.9
 Identities = 14/24 (58%), Positives = 16/24 (66%)

Query: 218 NGYKIVILGHSNAGKSSLFNALAK 241
           N  KI I+G  N GKS+ FNAL K
Sbjct: 19  NNLKIGIVGLPNVGKSTFFNALTK 42


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

 Score = 29.6 bits (66), Expect = 1.9
 Identities = 17/40 (42%), Positives = 22/40 (55%), Gaps = 11/40 (27%)

Query: 226 GHSNAGKSSLFNALAKKD-----------VAIVTDIPGTT 254
           G +N GKS+LFNAL + D            A ++D PGTT
Sbjct: 220 GATNVGKSTLFNALLESDLCSVNAPKLVDRATISDWPGTT 259


>gnl|CDD|133316 cd04116, Rab9, Rab9 subfamily.  Rab9 is found in late endosomes,
           together with mannose 6-phosphate receptors (MPRs) and
           the tail-interacting protein of 47 kD (TIP47).  Rab9 is
           a key mediator of vesicular transport from late
           endosomes to the trans-Golgi network (TGN) by
           redirecting the MPRs.  Rab9 has been identified as a key
           component for the replication of several viruses,
           including HIV1, Ebola, Marburg, and measles, making it a
           potential target for inhibiting a variety of viruses.
           GTPase activating proteins (GAPs) interact with
           GTP-bound Rab and accelerate the hydrolysis of GTP to
           GDP. Guanine nucleotide exchange factors (GEFs) interact
           with GDP-bound Rabs to promote the formation of the
           GTP-bound state.  Rabs are further regulated by guanine
           nucleotide dissociation inhibitors (GDIs), which
           facilitate Rab recycling by masking C-terminal lipid
           binding and promoting cytosolic localization.  Most Rab
           GTPases contain a lipid modification site at the
           C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
           binding is essential for membrane attachment, a key
           feature of most Rab proteins.  Due to the presence of
           truncated sequences in this CD, the lipid modification
           site is not available for annotation.
          Length = 170

 Score = 29.4 bits (66), Expect = 2.0
 Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 15/64 (23%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR------DVLTIDLDLEGYLV--KIS 272
           K+++LG    GKSSL N         VT+   T        + L  DL+++G+ V  +I 
Sbjct: 7   KVILLGDGGVGKSSLMNRY-------VTNKFDTQLFHTIGVEFLNKDLEVDGHFVTLQIW 59

Query: 273 DTAG 276
           DTAG
Sbjct: 60  DTAG 63


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

 Score = 29.5 bits (66), Expect = 2.0
 Identities = 44/176 (25%), Positives = 75/176 (42%), Gaps = 47/176 (26%)

Query: 224 ILGHSNAGKSSLFNAL--AKKDVAIVTDIPGTT--RDVLTIDLDLEGYLVKISDTAGIRE 279
           ++G  NAGKS+L NAL  AK  VA       TT    + T++ D +   + ++D  GI E
Sbjct: 201 LVGFPNAGKSTLLNALSRAKPKVA---HYAFTTLRPHIGTVNYD-DFSQITVADIPGIIE 256

Query: 280 TDDIVEKEGIKRTFLE-VENADLILLLKEINSKKEISFPKNIDF---------------- 322
                  +G+   FL  +E    +L + +++ K+  +  + +                  
Sbjct: 257 --GAHMNKGLGYKFLRHIERCKGLLFVVDLSGKQLRNPWQQLQLLIEELELYEKGLADRP 314

Query: 323 -IFIGTKSDLYSTYTEEYDHLISSF---------------TGEGLEELINKIKSIL 362
            + +  K DL     E   +L+SS                +GEGLEEL+N ++ +L
Sbjct: 315 ALIVANKIDL----PEAEKNLLSSLAKRLQNPHVVPVSAKSGEGLEELLNGLRELL 366


>gnl|CDD|133372 cd04172, Rnd3_RhoE_Rho8, Rnd3/RhoE/Rho8 subfamily.  Rnd3/RhoE/Rho8
           is a member of the novel Rho subfamily Rnd, together
           with Rnd1/Rho6 and Rnd2/Rho7.  Rnd3/RhoE is known to
           bind the serine-threonine kinase ROCK I.
           Unphosphorylated Rnd3/RhoE associates primarily with
           membranes, but ROCK I-phosphorylated Rnd3/RhoE localizes
           in the cytosol.  Phosphorylation of Rnd3/RhoE correlates
           with its activity in disrupting RhoA-induced stress
           fibers and inhibiting Ras-induced fibroblast
           transformation.  In cells that lack stress fibers, such
           as macrophages and monocytes, Rnd3/RhoE induces a
           redistribution of actin, causing morphological changes
           in the cell.  In addition, Rnd3/RhoE has been shown to
           inhibit cell cycle progression in G1 phase at a point
           upstream of the pRb family pocket protein checkpoint.
           Rnd3/RhoE has also been shown to inhibit Ras- and
           Raf-induced fibroblast transformation.  In mammary
           epithelial tumor cells, Rnd3/RhoE regulates the assembly
           of the apical junction complex and tight junction
           formation.  Rnd3/RhoE is underexpressed in prostate
           cancer cells both in vitro and in vivo; re-expression of
           Rnd3/RhoE suppresses cell cycle progression and
           increases apoptosis, suggesting it may play a role in
           tumor suppression.  Most Rho proteins contain a lipid
           modification site at the C-terminus, with a typical
           sequence motif CaaX, where a = an aliphatic amino acid
           and X = any amino acid.  Lipid binding is essential for
           membrane attachment, a key feature of most Rho proteins.
            Due to the presence of truncated sequences in this CD,
           the lipid modification site is not available for
           annotation.
          Length = 182

 Score = 29.3 bits (65), Expect = 2.1
 Identities = 36/138 (26%), Positives = 62/138 (44%), Gaps = 27/138 (19%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKIS--DTAGIR 278
           KIV++G S  GK++L +  A KD      +P T  +  T   +++   +++S  DT+G  
Sbjct: 7   KIVVVGDSQCGKTALLHVFA-KDCFPENYVP-TVFENYTASFEIDTQRIELSLWDTSGSP 64

Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINS-----------KKEIS-FPKNIDFIFIG 326
             D++          L   ++D +L+  +I+            K EI  F  N   + +G
Sbjct: 65  YYDNVRP--------LSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVG 116

Query: 327 TKSDL---YSTYTEEYDH 341
            KSDL    +T  E  +H
Sbjct: 117 CKSDLRTDLTTLVELSNH 134


>gnl|CDD|143431 cd07113, ALDH_PADH_NahF, Escherichia coli NAD+-dependent
           phenylacetaldehyde dehydrogenase PadA-like.
           NAD+-dependent, homodimeric, phenylacetaldehyde
           dehydrogenase (PADH, EC=1.2.1.39) PadA of Escherichia
           coli involved in the catabolism of 2-phenylethylamine,
           and other related sequences, are present in this CD.
           Also included is the Pseudomonas fluorescens ST StyD
           PADH involved in styrene catabolism, the Sphingomonas
           sp. LB126 FldD protein involved in fluorene degradation,
           and the Novosphingobium aromaticivorans NahF
           salicylaldehyde dehydrogenase involved in the
           NAD+-dependent conversion of salicylaldehyde to
           salicylate.
          Length = 477

 Score = 29.3 bits (66), Expect = 2.2
 Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 3/47 (6%)

Query: 50  LRYFFGLDGRILDKGLLIVFPSPESFTGEDSAEFHVHGGIAVVNGIL 96
           LRYF G   +I  + L    PS +   GE    F     + VV GI+
Sbjct: 107 LRYFAGWATKINGETLAPSIPSMQ---GERYTAFTRREPVGVVAGIV 150


>gnl|CDD|35309 KOG0086, KOG0086, KOG0086, GTPase Rab4, small G protein superfamily
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 214

 Score = 29.2 bits (65), Expect = 2.2
 Identities = 35/167 (20%), Positives = 62/167 (37%), Gaps = 24/167 (14%)

Query: 220 YKIVILGHSNAGKSSLFNALAKK----DVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTA 275
           +K +++G +  GKS L +   +     D +    +   +R    +++  +   ++I DTA
Sbjct: 10  FKFLVIGSAGTGKSCLLHQFIENKFKDDSSHTIGVEFGSR---IVNVGGKTVKLQIWDTA 66

Query: 276 GIRETDDIVEK--EGIKRTFL--EVENADLILLLKEINSKKEISFPKNIDFIFIGTKSDL 331
           G      +      G     L  ++ + D    L    +        NI  I  G K DL
Sbjct: 67  GQERFRSVTRSYYRGAAGALLVYDITSRDSFNALTNWLTDARTLASPNIVVILCGNKKDL 126

Query: 332 ----------YSTYTEEYD---HLISSFTGEGLEELINKIKSILSNK 365
                      S + +E +      S+ TGE +EE   K    + NK
Sbjct: 127 DPEREVTFLEASRFAQENELMFLETSALTGENVEEAFLKCARTILNK 173


>gnl|CDD|31319 COG1122, CbiO, ABC-type cobalt transport system, ATPase component
           [Inorganic ion transport and metabolism].
          Length = 235

 Score = 29.1 bits (65), Expect = 2.2
 Identities = 16/77 (20%), Positives = 33/77 (42%), Gaps = 14/77 (18%)

Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTI 260
            D+S  I +G+          ++++G + +GKS+L   L      ++    G    V  +
Sbjct: 21  KDVSLEIEKGER---------VLLIGPNGSGKSTLLKLLN----GLLKPTSGEVL-VDGL 66

Query: 261 DLDLEGYLVKISDTAGI 277
           D   E  L+++    G+
Sbjct: 67  DTSSEKSLLELRQKVGL 83


>gnl|CDD|113806 pfam05049, IIGP, Interferon-inducible GTPase (IIGP).
           Interferon-inducible GTPase (IIGP) is thought to play a
           role in in intracellular defence. IIGP is predominantly
           associated with the Golgi apparatus and also localizes
           to the endoplasmic reticulum and exerts a distinct role
           in IFN-induced intracellular membrane trafficking or
           processing.
          Length = 375

 Score = 29.4 bits (66), Expect = 2.3
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 4/55 (7%)

Query: 189 SKEVLNDIL--FLKNDISSHISQGK--LGEIIRNGYKIVILGHSNAGKSSLFNAL 239
           S EV+  I     + ++   +S  K  + EI     KI + G S  GKSS  NAL
Sbjct: 1   SPEVITLIETALREGNLQKVVSIIKKAIQEISSAPLKIAVTGDSGNGKSSFINAL 55


>gnl|CDD|133374 cd04174, Rnd1_Rho6, Rnd1/Rho6 subfamily.  Rnd1/Rho6 is a member of
           the novel Rho subfamily Rnd, together with Rnd2/Rho7 and
           Rnd3/RhoE/Rho8.  Rnd1/Rho6 binds GTP but does not
           hydrolyze it to GDP, indicating that it is
           constitutively active.  In rat, Rnd1/Rho6 is highly
           expressed in the cerebral cortex and hippocampus during
           synapse formation, and plays a role in spine formation. 
           Rnd1/Rho6 is also expressed in the liver and in
           endothelial cells, and is upregulated in uterine
           myometrial cells during pregnancy.  Like Rnd3/RhoE/Rho8,
           Rnd1/Rho6 is believed to function as an antagonist to
           RhoA.  Most Rho proteins contain a lipid modification
           site at the C-terminus, with a typical sequence motif
           CaaX, where a = an aliphatic amino acid and X = any
           amino acid.  Lipid binding is essential for membrane
           attachment, a key feature of most Rho proteins.  Due to
           the presence of truncated sequences in this CD, the
           lipid modification site is not available for annotation.
          Length = 232

 Score = 29.3 bits (65), Expect = 2.3
 Identities = 34/125 (27%), Positives = 57/125 (45%), Gaps = 24/125 (19%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKIS--DTAGIR 278
           K+V++G    GK+++   LA KD    T +P T  +  T  L+ E   V++S  DT+G  
Sbjct: 15  KLVLVGDVQCGKTAMLQVLA-KDCYPETYVP-TVFENYTAGLETEEQRVELSLWDTSGSP 72

Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINS-----------KKEI-SFPKNIDFIFIG 326
             D++          L   ++D +LL  +I+            K EI  +  +   + IG
Sbjct: 73  YYDNVRP--------LCYSDSDAVLLCFDISRPETVDSALKKWKAEIMDYCPSTRILLIG 124

Query: 327 TKSDL 331
            K+DL
Sbjct: 125 CKTDL 129


>gnl|CDD|133254 cd00878, Arf_Arl, Arf (ADP-ribosylation factor)/Arl (Arf-like)
           small GTPases.  Arf proteins are activators of
           phospholipase D isoforms.  Unlike Ras proteins they lack
           cysteine residues at their C-termini and therefore are
           unlikely to be prenylated.  Arfs are N-terminally
           myristoylated.  Members of the Arf family are regulators
           of vesicle formation in intracellular traffic that
           interact reversibly with membranes of the secretory and
           endocytic compartments in a GTP-dependent manner.  They
           depart from other small GTP-binding proteins by a unique
           structural device, interswitch toggle, that implements
           front-back communication from N-terminus to the
           nucleotide binding site.  Arf-like (Arl) proteins are
           close relatives of the Arf, but only Arl1 has been shown
           to function in membrane traffic like the Arf proteins.
           Arl2 has an unrelated function in the folding of native
           tubulin, and Arl4 may function in the nucleus.  Most
           other Arf family proteins are so far relatively poorly
           characterized.  Thus, despite their significant sequence
           homologies, Arf family proteins may regulate unrelated
           functions.
          Length = 158

 Score = 29.1 bits (66), Expect = 2.4
 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 2/31 (6%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIP 251
           +I+ILG   AGK+++   L   +V  VT IP
Sbjct: 1   RILILGLDGAGKTTILYKLKLGEV--VTTIP 29


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

 Score = 29.1 bits (65), Expect = 2.7
 Identities = 13/22 (59%), Positives = 16/22 (72%)

Query: 221 KIVILGHSNAGKSSLFNALAKK 242
           +I+ILG   AGKS+L   LAKK
Sbjct: 2   RILILGPPGAGKSTLAKKLAKK 23


>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 = 29.0 bits (65), Expect = 2.7
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 192 VLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA 240
            +N++ F   +    + +  L   ++ G KI +LG S +GKS+L   L 
Sbjct: 2   SINNVSFSYPEQEQQVLKN-LSLELKQGEKIALLGRSGSGKSTLLQLLT 49


>gnl|CDD|133353 cd04153, Arl5_Arl8, Arl5/Arl8 subfamily.  Arl5 (Arf-like 5) and
           Arl8, like Arl4 and Arl7, are localized to the nucleus
           and nucleolus.  Arl5 is developmentally regulated during
           embryogenesis in mice.  Human Arl5 interacts with the
           heterochromatin protein 1-alpha (HP1alpha), a nonhistone
           chromosomal protein that is associated with
           heterochromatin and telomeres, and prevents telomere
           fusion.  Arl5 may also play a role in embryonic nuclear
           dynamics and/or signaling cascades. Arl8 was identified
           from a fetal cartilage cDNA library.  It is found in
           brain, heart, lung, cartilage, and kidney.  No function
           has been assigned for Arl8 to date.
          Length = 174

 Score = 28.9 bits (65), Expect = 2.7
 Identities = 9/25 (36%), Positives = 16/25 (64%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDV 244
           YK++I+G  NAGK+++       +V
Sbjct: 16  YKVIIVGLDNAGKTTILYQFLLGEV 40


>gnl|CDD|73009 cd03250, ABCC_MRP_domain1, Domain 1 of the ABC subfamily C.  This
           family is also known as MRP (mulrtidrug
           resisitance-associated protein).  Some of the MRP
           members have five additional transmembrane segments in
           their N-terminas, but the function of these additional
           membrane-spanning domains is not clear.  The MRP was
           found in the multidrug-resisting lung cancer cell in
           which p-glycoprotein was not overexpressed. MRP exports
           glutathione by drug stimulation, as well as, certain
           substrates in conjugated forms with anions, such as
           glutathione, glucuronate, and sulfate..
          Length = 204

 Score = 28.9 bits (65), Expect = 2.9
 Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 9/54 (16%)

Query: 186 NFSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNAL 239
           +F+      +  F   DI+  + +G+L         + I+G   +GKSSL +AL
Sbjct: 7   SFTWDSGEQETSFTLKDINLEVPKGEL---------VAIVGPVGSGKSSLLSAL 51


>gnl|CDD|35300 KOG0077, KOG0077, KOG0077, Vesicle coat complex COPII, GTPase
           subunit SAR1 [Intracellular trafficking, secretion, and
           vesicular transport].
          Length = 193

 Score = 28.8 bits (64), Expect = 2.9
 Identities = 31/133 (23%), Positives = 53/133 (39%), Gaps = 29/133 (21%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPG--TTRDVLTID------LDLEGYLVK-- 270
           K++ LG  NAGK++L + L  KD  +   +P    T + L+I        DL G+L    
Sbjct: 22  KLLFLGLDNAGKTTLLHML--KDDRLGQHVPTLHPTSEELSIGGMTFTTFDLGGHLQARR 79

Query: 271 -----ISDTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFI 325
                      I    D  ++E     F E +        KE+++         + F+ +
Sbjct: 80  VWKDYFPQVDAIVYLVDAYDQE----RFAESK--------KELDALLSDESLATVPFLIL 127

Query: 326 GTKSDLYSTYTEE 338
           G K D+    +E+
Sbjct: 128 GNKIDIPYAASED 140


>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 = 28.6 bits (65), Expect = 3.0
 Identities = 23/85 (27%), Positives = 40/85 (47%), Gaps = 4/85 (4%)

Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETD 281
           + ++G  + GKS+L + L       V     TT   +   L+ +G  +++ D  GI E  
Sbjct: 3   VALVGFPSVGKSTLLSKLTNTKSE-VAAYEFTTLTCVPGVLEYKGAKIQLLDLPGIIE-- 59

Query: 282 DIVEKEGIKRTFLEV-ENADLILLL 305
              + +G  R  + V   ADLIL++
Sbjct: 60  GAADGKGRGRQVIAVARTADLILMV 84


>gnl|CDD|73022 cd03263, ABC_subfamily_A, The ABCA subfamily mediates the transport
           of a variety of lipid compounds.  Mutations of members
           of ABCA subfamily are associated with human genetic
           diseases, such as, familial high-density lipoprotein
           (HDL) deficiency, neonatal surfactant deficiency,
           degenerative retinopathies, and congenital
           keratinization disorders.  The ABCA1 protein is involved
           in disorders of cholesterol transport and high-density
           lipoprotein (HDL) biosynthesis.  The ABCA4 (ABCR)
           protein transports vitamin A derivatives in the outer
           segments of photoreceptor cells, and therefore, performs
           a crucial step in the visual cycle.  The ABCA genes are
           not present in yeast.  However, evolutionary studies of
           ABCA genes indicate that they arose as transporters that
           subsequently duplicated and that certain sets of ABCA
           genes were lost in different eukaryotic lineages..
          Length = 220

 Score = 28.6 bits (64), Expect = 3.3
 Identities = 8/25 (32%), Positives = 13/25 (52%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
           +  G    +LGH+ AGK++    L 
Sbjct: 25  VYKGEIFGLLGHNGAGKTTTLKMLT 49


>gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
           an N-terminal double-glycine peptidase domain [Defense
           mechanisms].
          Length = 709

 Score = 28.6 bits (64), Expect = 3.4
 Identities = 11/25 (44%), Positives = 15/25 (60%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
           I  G K+ I+G S +GKS+L   L 
Sbjct: 496 IPPGEKVAIVGRSGSGKSTLLKLLL 520


>gnl|CDD|133336 cd04136, Rap_like, Rap-like subfamily.  The Rap subfamily consists
           of the Rap1, Rap2, and RSR1.  Rap subfamily proteins
           perform different cellular functions, depending on the
           isoform and its subcellular localization. For example,
           in rat salivary gland, neutrophils, and platelets, Rap1
           localizes to secretory granules and is believed to
           regulate exocytosis or the formation of secretory
           granules.  Rap1 has also been shown to localize in the
           Golgi of rat fibroblasts, zymogen granules, plasma
           membrane, and microsomal membrane of the pancreatic
           acini, as well as in the endocytic compartment of
           skeletal muscle cells and fibroblasts.   Rap1 localizes
           in the nucleus of human oropharyngeal squamous cell
           carcinomas (SCCs) and cell lines.  Rap1 plays a role in
           phagocytosis by controlling the binding of adhesion
           receptors (typically integrins) to their ligands.  In
           yeast, Rap1 has been implicated in multiple functions,
           including activation and silencing of transcription and
           maintenance of telomeres.  Rap2 is involved in multiple
           functions, including activation of c-Jun N-terminal
           kinase (JNK) to regulate the actin cytoskeleton and
           activation of the Wnt/beta-catenin signaling pathway in
           embryonic Xenopus.  A number of effector proteins for
           Rap2 have been identified, including isoform 3 of the
           human mitogen-activated protein kinase kinase kinase
           kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase
           (TNIK), and the RalGEFs RalGDS, RGL, and Rlf, which also
           interact with Rap1 and Ras. RSR1 is the fungal homolog
           of Rap1 and Rap2.  In budding yeasts, it is involved in
           selecting a site for bud growth, which directs the
           establishment of cell polarization.  The Rho family
           GTPase Cdc42 and its GEF, Cdc24, then establish an axis
           of polarized growth.  It is believed that Cdc42
           interacts directly with RSR1 in vivo.  In filamentous
           fungi such as Ashbya gossypii, RSR1 is a key regulator
           of polar growth in the hypha.  Most Ras proteins contain
           a lipid modification site at the C-terminus, with a
           typical sequence motif CaaX, where a = an aliphatic
           amino acid and X = any amino acid.  Lipid binding is
           essential for membrane attachment, a key feature of most
           Ras proteins.  Due to the presence of truncated
           sequences in this CD, the lipid modification site is not
           available for annotation.
          Length = 163

 Score = 28.4 bits (64), Expect = 3.5
 Identities = 22/66 (33%), Positives = 31/66 (46%), Gaps = 16/66 (24%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVAIVTDI------PGTTRDVL--TIDLDLEGYLVKI 271
           YK+V+LG    GKS+L        V  V  I      P T  D     I++D +  +++I
Sbjct: 2   YKVVVLGSGGVGKSAL-------TVQFVQGIFVEKYDP-TIEDSYRKQIEVDGQQCMLEI 53

Query: 272 SDTAGI 277
            DTAG 
Sbjct: 54  LDTAGT 59


>gnl|CDD|73018 cd03259, ABC_Carb_Solutes_like, ABC Carbohydrate and Solute
           Transporters-like subgroup.  This family is comprised of
           proteins involved in the transport of apparently
           unrelated solutes and proteins specific for di- and
           oligosaccharides and polyols.  ABC transporters are a
           large family of proteins involved in the transport of a
           wide variety of different compounds, like sugars, ions,
           peptides and more complex organic molecules.  The
           nucleotide-binding domain shows the highest similarity
           between all members of the family.   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 = 213

 Score = 28.6 bits (64), Expect = 3.6
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 19/67 (28%)

Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA------KKDVAI----VTDI 250
           +D+S  +  G+          + +LG S  GK++L   +A        ++ I    VT +
Sbjct: 17  DDLSLTVEPGEF---------LALLGPSGCGKTTLLRLIAGLERPDSGEILIDGRDVTGV 67

Query: 251 PGTTRDV 257
           P   R++
Sbjct: 68  PPERRNI 74


>gnl|CDD|133310 cd04110, Rab35, Rab35 subfamily.  Rab35 is one of several Rab
           proteins to be found to participate in the regulation of
           osteoclast cells in rats. In addition, Rab35 has been
           identified as a protein that interacts with
           nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in
           human cells.  Overexpression of NPM-ALK is a key
           oncogenic event in some anaplastic large-cell lymphomas;
           since Rab35 interacts with N|PM-ALK, it may provide a
           target for cancer treatments. GTPase activating proteins
           (GAPs) interact with GTP-bound Rab and accelerate the
           hydrolysis of GTP to GDP. Guanine nucleotide exchange
           factors (GEFs) interact with GDP-bound Rabs to promote
           the formation of the GTP-bound state.  Rabs are further
           regulated by guanine nucleotide dissociation inhibitors
           (GDIs), which facilitate Rab recycling by masking
           C-terminal lipid binding and promoting cytosolic
           localization.  Most Rab GTPases contain a lipid
           modification site at the C-terminus, with sequence
           motifs CC, CXC, or CCX. Lipid binding is essential for
           membrane attachment, a key feature of most Rab proteins.
          Length = 199

 Score = 28.7 bits (64), Expect = 3.8
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 220 YKIVILGHSNAGKSSLFNALAKKDVA--IVTDIPGTTRDVLTIDLDLEGYLVKISDTAG 276
           +K++I+G S  GKSSL    A    +   +T I G    + T++++ E   ++I DTAG
Sbjct: 7   FKLLIIGDSGVGKSSLLLRFADNTFSGSYITTI-GVDFKIRTVEINGERVKLQIWDTAG 64


>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 = 28.5 bits (64), Expect = 4.0
 Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 9/41 (21%)

Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAK 241
           +D+S  I  G++         + ILG + AGKS+L   LA 
Sbjct: 16  DDLSLSIEAGEI---------VGILGPNGAGKSTLLKTLAG 47


>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 = 4.0
 Identities = 27/131 (20%), Positives = 51/131 (38%), Gaps = 28/131 (21%)

Query: 217 RNGYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTID-LDLEG---YLVKIS 272
           RN +   +LG   +GKS+L  A   +  + +     T +    ++ +++ G   YL+   
Sbjct: 2   RNVFLCFVLGAKGSGKSALLRAFLGRSFS-LNAYSPTIKPRYAVNTVEVYGQEKYLI--- 57

Query: 273 DTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFP------------KNI 320
               +RE     ++  I     E+   D+  L+   +S    SF               I
Sbjct: 58  ----LREVG--EDEVAILLNDAELAACDVACLV--YDSSDPKSFSYCAEVYKKYFMLGEI 109

Query: 321 DFIFIGTKSDL 331
             +F+  K+DL
Sbjct: 110 PCLFVAAKADL 120


>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 = 28.2 bits (63), Expect = 4.5
 Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 9/39 (23%)

Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNAL 239
            D+S  I+ G+          + ++G S AGKS+L   L
Sbjct: 18  KDVSLSINPGEF---------VALIGPSGAGKSTLLRCL 47


>gnl|CDD|176731 cd08316, Death_FAS_TNFRSF6, Death domain of FAS or TNF receptor
           superfamily member 6.  Death Domain (DD) found in the
           FS7-associated cell surface antigen (FAS). FAS, also
           known as TNFRSF6 (TNF receptor superfamily member 6),
           APT1, CD95, FAS1, or APO-1, together with FADD
           (Fas-associating via Death Domain) and caspase 8, is an
           integral part of the death inducing signalling complex
           (DISC), which plays an important role in the induction
           of apoptosis and is activated by binding of the ligand
           FasL to FAS. FAS also plays a critical role in
           self-tolerance by eliminating cell types (autoreactive T
           and B cells) that contribute to autoimmunity. DDs are
           protein-protein interaction domains found in a variety
           of domain architectures. Their common feature is that
           they form homodimers by self-association or heterodimers
           by associating with other members of the DD superfamily
           including CARD (Caspase activation and recruitment
           domain), DED (Death Effector Domain), and PYRIN. They
           serve as adaptors in signaling pathways and can recruit
           other proteins into signaling complexes.
          Length = 97

 Score = 28.1 bits (63), Expect = 4.7
 Identities = 8/36 (22%), Positives = 18/36 (50%)

Query: 260 IDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLE 295
            D+DL  ++  I+D   +++    V K G+    ++
Sbjct: 3   SDVDLSKHIPDIADVMTLKDVKKFVRKSGLSEPKID 38


>gnl|CDD|73052 cd03293, ABC_NrtD_SsuB_transporters, NrtD and SsuB are the
           ATP-binding subunits of the bacterial ABC-type nitrate
           and sulfonate transport systems, respectively.  ABC
           transporters are a large family of proteins involved in
           the transport of a wide variety of different compounds,
           like sugars, ions, peptides, and more complex organic
           molecules.  The nucleotide binding domain shows the
           highest similarity between all members of the family.
           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 = 220

 Score = 28.1 bits (63), Expect = 4.7
 Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 9/40 (22%)

Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA 240
            DIS  + +G+          + ++G S  GKS+L   +A
Sbjct: 21  EDISLSVEEGEF---------VALVGPSGCGKSTLLRIIA 51


>gnl|CDD|133304 cd04104, p47_IIGP_like, p47 (47-kDa) family.  The p47 GTPase family
           consists of several highly homologous proteins,
           including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and
           IIGP1.  They are found in higher eukaryotes where they
           play a role in immune resistance against intracellular
           pathogens.  p47 proteins exist at low resting levels in
           mouse cells, but are strongly induced by Type II
           interferon (IFN-gamma).  ITGP is critical for resistance
           to Toxoplasma gondii infection and in involved in
           inhibition of Coxsackievirus-B3-induced apoptosis.  TGTP
           was shown to limit vesicular stomatitis virus (VSV)
           infection of fibroblasts in vitro.  IRG-47 is involved
           in resistance to T. gondii infection.  LRG-47 has been
           implicated in resistance to T. gondii, Listeria
           monocytogenes, Leishmania, and mycobacterial infections.
            IIGP1 has been shown to localize to the ER and to the
           Golgi membranes in IFN-induced cells and inflamed
           tissues.  In macrophages, IIGP1 interacts with hook3, a
           microtubule binding protein that participates in the
           organization of the cis-Golgi compartment.
          Length = 197

 Score = 28.1 bits (63), Expect = 4.7
 Identities = 11/19 (57%), Positives = 12/19 (63%)

Query: 221 KIVILGHSNAGKSSLFNAL 239
            I + G S AGKSS  NAL
Sbjct: 3   NIAVTGESGAGKSSFINAL 21


>gnl|CDD|110369 pfam01364, Peptidase_C25, Peptidase family C25. 
          Length = 349

 Score = 28.1 bits (62), Expect = 5.1
 Identities = 21/98 (21%), Positives = 38/98 (38%), Gaps = 12/98 (12%)

Query: 269 VKISDTAGIRETDDIVEKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFIGTK 328
           VK+++      T + + ++ +K+ + +  N    +LL  +   K+I           G K
Sbjct: 40  VKVAEDIASPVTANAI-QQFVKQEYEKEGNDLTYVLL--VGDHKDIPAKITP-----GIK 91

Query: 329 SDLYSTYTEEYDHLISSFTG----EGLEELINKIKSIL 362
           SD         DH    F G    E  E+L  +I   +
Sbjct: 92  SDQVYGQIVGNDHYNEVFIGRFSCESKEDLKTQIDRTI 129


>gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase components
           [Carbohydrate transport and metabolism].
          Length = 338

 Score = 27.9 bits (62), Expect = 5.1
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 10/52 (19%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA------KKDVAI----VTDIPGTTRDV 257
           I +G  +V+LG S  GKS+L   +A        ++ I    VTD+P   R +
Sbjct: 26  IEDGEFVVLLGPSGCGKSTLLRMIAGLEEPTSGEILIDGRDVTDLPPEKRGI 77


>gnl|CDD|133255 cd00879, Sar1, Sar1 subfamily.  Sar1 is an essential component of
           COPII vesicle coats involved in export of cargo from the
           ER.  The GTPase activity of Sar1 functions as a
           molecular switch to control protein-protein and
           protein-lipid interactions that direct vesicle budding
           from the ER.  Activation of the GDP to the GTP-bound
           form of Sar1 involves the membrane-associated guanine
           nucleotide exchange factor (GEF) Sec12.  Sar1 is unlike
           all Ras superfamily GTPases that use either myristoyl or
           prenyl groups to direct membrane association and
           function, in that Sar1 lacks such modification.
           Instead, Sar1 contains a unique nine-amino-acid
           N-terminal extension.  This extension contains an
           evolutionarily conserved cluster of bulky hydrophobic
           amino acids, referred to as the Sar1-N-terminal
           activation recruitment (STAR) motif.  The STAR motif
           mediates the recruitment of Sar1 to ER membranes and
           facilitates its interaction with mammalian Sec12 GEF
           leading to activation.
          Length = 190

 Score = 28.0 bits (63), Expect = 5.1
 Identities = 13/31 (41%), Positives = 19/31 (61%), Gaps = 2/31 (6%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIP 251
           KI+ LG  NAGK++L + L  KD  +   +P
Sbjct: 21  KILFLGLDNAGKTTLLHML--KDDRLAQHVP 49


>gnl|CDD|33632 COG3840, ThiQ, ABC-type thiamine transport system, ATPase component
           [Coenzyme metabolism].
          Length = 231

 Score = 28.0 bits (62), Expect = 5.2
 Identities = 12/25 (48%), Positives = 16/25 (64%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
           +  G  + ILG S AGKS+L N +A
Sbjct: 22  VPAGEIVAILGPSGAGKSTLLNLIA 46


>gnl|CDD|133315 cd04115, Rab33B_Rab33A, Rab33B/Rab33A subfamily.  Rab33B is
           ubiquitously expressed in mouse tissues and cells, where
           it is localized to the medial Golgi cisternae. It
           colocalizes with alpha-mannose II.  Together with the
           other cisternal Rabs, Rab6A and Rab6A', it is believed
           to regulate the Golgi response to stress and is likely a
           molecular target in stress-activated signaling pathways.
           Rab33A (previously known as S10) is expressed primarily
           in the brain and immune system cells.  In humans, it is
           located on the X chromosome at Xq26 and its expression
           is down-regulated in tuberculosis patients. Experimental
           evidence suggests that Rab33A is a novel CD8+ T cell
           factor that likely plays a role in tuberculosis disease
           processes.  GTPase activating proteins (GAPs) interact
           with GTP-bound Rab and accelerate the hydrolysis of GTP
           to GDP. Guanine nucleotide exchange factors (GEFs)
           interact with GDP-bound Rabs to promote the formation of
           the GTP-bound state.  Rabs are further regulated by
           guanine nucleotide dissociation inhibitors (GDIs), which
           facilitate Rab recycling by masking C-terminal lipid
           binding and promoting cytosolic localization. Most Rab
           GTPases contain a lipid modification site at the
           C-terminus, with sequence motifs CC, CXC, or CCX. Lipid
           binding is essential for membrane attachment, a key
           feature of most Rab proteins.  Due to the presence of
           truncated sequences in this CD, the lipid modification
           site is not available for annotation.
          Length = 170

 Score = 28.2 bits (63), Expect = 5.3
 Identities = 18/65 (27%), Positives = 33/65 (50%), Gaps = 15/65 (23%)

Query: 220 YKIVILGHSNAGKSSL-FNALAKKDVAIVTDIPGTTRDVLTID-----LDLEGYLVKIS- 272
           +KI+++G SN GK+ L +   A +        P  T   + +D     ++++G  +K+  
Sbjct: 3   FKIIVIGDSNVGKTCLTYRFCAGR-------FPERTEATIGVDFRERTVEIDGERIKVQL 55

Query: 273 -DTAG 276
            DTAG
Sbjct: 56  WDTAG 60


>gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC
           transporters homologous to the Drosophila white gene,
           which acts as a dimeric importer for eye pigment
           precursors.  The eye pigmentation of Drosophila is
           developed from the synthesis and deposition in the cells
           of red pigments, which are synthesized from guanine, and
           brown pigments, which are synthesized from tryptophan.
           The pigment precursors are encoded by the white, brown,
           and scarlet genes, respectively.  Evidence from genetic
           and biochemical studies suggest that the White and Brown
           proteins function as heterodimers to import guanine,
           while the White and Scarlet proteins function to import
           tryptophan.  However, a recent study also suggests that
           White may be involved in the transport of a metabolite,
           such as 3-hydroxykynurenine, across intracellular
           membranes.  Mammalian ABC transporters belonging to the
           White subfamily (ABCG1, ABCG5, and ABCG8) have been
           shown to be involved in the regulation of
           lipid-trafficking mechanisms in macrophages,
           hepatocytes, and intestinal mucosa cells.  ABCG1 (ABC8),
           the human homolog of the Drosophila white gene is
           induced in monocyte-derived macrophages during
           cholesterol influx mediated by acetylated low-density
           lipoprotein.  It is possible that human ABCG1 forms
           heterodimers with several heterologous partners..
          Length = 226

 Score = 27.9 bits (62), Expect = 5.4
 Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 9/43 (20%)

Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAKKD 243
           ND+S H+  G++         + ILG S +GK++L +A++ + 
Sbjct: 24  NDVSLHVESGQV---------MAILGSSGSGKTTLLDAISGRV 57


>gnl|CDD|31445 COG1253, TlyC, Hemolysins and related proteins containing CBS
           domains [General function prediction only].
          Length = 429

 Score = 28.0 bits (62), Expect = 5.6
 Identities = 19/87 (21%), Positives = 39/87 (44%), Gaps = 6/87 (6%)

Query: 240 AKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRETDDIVEKEGIKRTFLEVENA 299
            +  +AIV D  G    ++T++  +E  + +I D     E +DI++++     +L     
Sbjct: 300 ERTHMAIVVDEYGGVEGLVTLEDIIEEIVGEIPDEHDEDEEEDIIQRDD--DGWL----V 353

Query: 300 DLILLLKEINSKKEISFPKNIDFIFIG 326
           D  + L+E+     I   +  D+  I 
Sbjct: 354 DGRVPLEELEELLGIDLDEEEDYDTIA 380


>gnl|CDD|30002 cd01136, ATPase_flagellum-secretory_path_III, Flagellum-specific
           ATPase/type III secretory pathway virulence-related
           protein. This group of ATPases are responsible for the
           export of flagellum and virulence-related proteins. The
           bacterial flagellar motor is similar to the F0F1-ATPase,
           in that they both are proton driven rotary molecular
           devices. However, the main function of the bacterial
           flagellar motor is to rotate the flagellar filament for
           cell motility. Intracellular pathogens such as
           Salmonella and Chlamydia also have proteins which are
           similar to the flagellar-specific ATPase, but function
           in the secretion of virulence-related proteins via the
           type III secretory pathway..
          Length = 326

 Score = 27.9 bits (62), Expect = 5.8
 Identities = 28/92 (30%), Positives = 41/92 (44%), Gaps = 24/92 (26%)

Query: 219 GYKIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIR 278
           G ++ I   S  GKS+L   +A+          GTT DV  I L        I +    R
Sbjct: 69  GQRLGIFAGSGVGKSTLLGMIAR----------GTTADVNVIAL--------IGERG--R 108

Query: 279 ETDDIVEK----EGIKRTFLEVENADLILLLK 306
           E  + +EK    EG+KR+ + V  +D   LL+
Sbjct: 109 EVREFIEKDLGEEGLKRSVVVVATSDESPLLR 140


>gnl|CDD|33436 COG3638, COG3638, ABC-type phosphate/phosphonate transport system,
           ATPase component [Inorganic ion transport and
           metabolism].
          Length = 258

 Score = 27.9 bits (62), Expect = 6.2
 Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 9/40 (22%)

Query: 201 NDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALA 240
            D++  I+QG++         + I+G S AGKS+L  +L 
Sbjct: 21  KDVNLEINQGEM---------VAIIGPSGAGKSTLLRSLN 51


>gnl|CDD|72991 cd03232, ABC_PDR_domain2, The pleiotropic drug resistance-like
           (PDR) family of ATP-binding cassette (ABC) transporters.
           PDR is a well-described phenomenon occurring in fungi
           and shares several similarities with processes in
           bacteria and higher eukaryotes.  This PDR subfamily
           represents domain I of its (ABC-IM)2 organization.  ABC
           transporters are a large family of proteins involved in
           the transport of a wide variety of different compounds
           including sugars, ions, peptides, and more complex
           organic molecules.  The nucleotide binding domain shows
           the highest similarity between all members of the
           family.  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 = 192

 Score = 27.8 bits (62), Expect = 6.3
 Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 10/51 (19%)

Query: 199 LKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSLFNALAK-KDVAIVT 248
           L N+IS ++  G L           ++G S AGK++L + LA  K   ++T
Sbjct: 22  LLNNISGYVKPGTL---------TALMGESGAGKTTLLDVLAGRKTAGVIT 63


>gnl|CDD|35296 KOG0073, KOG0073, KOG0073, GTP-binding ADP-ribosylation factor-like
           protein ARL2 [Intracellular trafficking, secretion, and
           vesicular transport, Cytoskeleton].
          Length = 185

 Score = 27.9 bits (62), Expect = 6.4
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAGIRE 279
           +I+ILG  N+GK+++   L  +D    TD    T       L+ +GY + I D  G + 
Sbjct: 18  RILILGLDNSGKTTIVKKLLGED----TDTISPTLGFQIKTLEYKGYTLNIWDVGGQKT 72


>gnl|CDD|30543 COG0194, Gmk, Guanylate kinase [Nucleotide transport and
           metabolism].
          Length = 191

 Score = 27.8 bits (62), Expect = 6.6
 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 222 IVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTR 255
           IV+ G S  GKS+L  AL + D  +   +  TTR
Sbjct: 7   IVLSGPSGVGKSTLVKALLEDD-KLRFSVSATTR 39


>gnl|CDD|147764 pfam05789, Baculo_VP1054, Baculovirus VP1054 protein.  This family
           consists of several VP1054 proteins from the
           Baculoviruses. VP1054 is a virus structural protein
           required for nucleocapsid assembly.
          Length = 314

 Score = 27.6 bits (62), Expect = 6.6
 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 5/43 (11%)

Query: 277 IRETDDIVEKEGIKRTFLEVENADLILLLKEIN----SKKEIS 315
           + E D+ V  + I +TFL V N  L ++LK+ N    + K IS
Sbjct: 178 VPEYDEAVASQDIYKTFL-VYNTVLTMMLKQKNPFNDANKSIS 219


>gnl|CDD|39086 KOG3883, KOG3883, KOG3883, Ras family small GTPase [Signal
           transduction mechanisms].
          Length = 198

 Score = 27.7 bits (61), Expect = 6.6
 Identities = 24/128 (18%), Positives = 55/128 (42%), Gaps = 25/128 (19%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEG---YLVKISDTAGI 277
           K+V+ G  + GK+++   L   +    T++  T  D+    ++ +      +++ DTAG+
Sbjct: 11  KVVVCGMKSVGKTAILEQLLYGNHVPGTELHPTIEDIYVASVETDRGAREQLRLYDTAGL 70

Query: 278 RETDDIVEKEGIKRTFLEVENADLI--------------LLLKEINSKKEISFPKNIDFI 323
           +       ++ + R + +  +A ++              LL KEI+  K+    K +  +
Sbjct: 71  QG-----GQQELPRHYFQFADAFVLVYSPMDPESFQRVELLKKEIDKHKD---KKEVPIV 122

Query: 324 FIGTKSDL 331
            +  K D 
Sbjct: 123 VLANKRDR 130


>gnl|CDD|35301 KOG0078, KOG0078, KOG0078, GTP-binding protein SEC4, small G
           protein superfamily, and related Ras family GTP-binding
           proteins [Signal transduction mechanisms, Intracellular
           trafficking, secretion, and vesicular transport].
          Length = 207

 Score = 27.5 bits (61), Expect = 6.7
 Identities = 17/59 (28%), Positives = 33/59 (55%), Gaps = 3/59 (5%)

Query: 220 YKIVILGHSNAGKSSLFNALAKK--DVAIVTDIPGTTRDVLTIDLDLEGYLVKISDTAG 276
           +K++++G S  GK+ L    +    + + ++ I G    + TI+LD +   ++I DTAG
Sbjct: 13  FKLLLIGDSGVGKTCLLLRFSDDSFNTSFISTI-GIDFKIKTIELDGKKIKLQIWDTAG 70


>gnl|CDD|73021 cd03262, ABC_HisP_GlnQ_permeases, HisP and GlnQ are the ATP-binding
           components of the bacterial periplasmic histidine and
           glutamine permeases, repectively.  Histidine permease is
           a multisubunit complex containing the HisQ and HisM
           integral membrane subunits and two copies of HisP.  HisP
           has properties intermediate between those of integral
           and peripheral membrane proteins and is accessible from
           both sides of the membrane, presumably by its
           interaction with HisQ and HisM.  The two HisP subunits
           form a homodimer within the complex.  The domain
           structure of the amino acid uptake systems is typical
           for prokaryote extracellular solute binding
           protein-dependent uptake systems.  All of the amino acid
           uptake systems also have at least one, and in a few
           cases, two extracellular solute binding proteins located
           in the periplasm of Gram-negative bacteria, or attached
           to the cell membrane of Gram-positive bacteria.  The
           best-studied member of the PAAT (polar amino acid
           transport) family is the HisJQMP system of S.
           typhimurium, where HisJ is the extracellular solute
           binding proteins and HisP is the ABC protein..
          Length = 213

 Score = 27.4 bits (61), Expect = 7.1
 Identities = 16/81 (19%), Positives = 29/81 (35%), Gaps = 23/81 (28%)

Query: 187 FSSKEVLNDILFLKNDISSHISQGKLGEIIRNGYKIVILGHSNAGKSSL---FNALAKKD 243
           F    VL  I                   ++ G  +VI+G S +GKS+L    N L + D
Sbjct: 10  FGDFHVLKGIDL----------------TVKKGEVVVIIGPSGSGKSTLLRCINLLEEPD 53

Query: 244 VAIVT----DIPGTTRDVLTI 260
              +      +    +++  +
Sbjct: 54  SGTIIIDGLKLTDDKKNINEL 74


>gnl|CDD|133331 cd04131, Rnd, Rnd subfamily.  The Rnd subfamily contains Rnd1/Rho6,
           Rnd2/Rho7, and Rnd3/RhoE/Rho8.  These novel Rho family
           proteins have substantial structural differences
           compared to other Rho members, including N- and
           C-terminal extensions relative to other Rhos.  Rnd3/RhoE
           is farnesylated at the C-terminal prenylation site,
           unlike most other Rho proteins that are
           geranylgeranylated.  In addition, Rnd members are unable
           to hydrolyze GTP and are resistant to GAP activity.
           They are believed to exist only in the GTP-bound
           conformation, and are antagonists of RhoA activity.
           Most Rho proteins contain a lipid modification site at
           the C-terminus, with a typical sequence motif CaaX,
           where a = an aliphatic amino acid and X = any amino
           acid.  Lipid binding is essential for membrane
           attachment, a key feature of most Rho proteins.  Due to
           the presence of truncated sequences in this CD, the
           lipid modification site is not available for annotation.
          Length = 178

 Score = 27.6 bits (61), Expect = 7.3
 Identities = 31/125 (24%), Positives = 56/125 (44%), Gaps = 24/125 (19%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLDLEGYLVKIS--DTAGIR 278
           KIV++G    GK++L    A KD    T +P T  +  T   +++   +++S  DT+G  
Sbjct: 3   KIVVVGDVQCGKTALLQVFA-KDCYPETYVP-TVFENYTASFEIDEQRIELSLWDTSGSP 60

Query: 279 ETDDIVEKEGIKRTFLEVENADLILLLKEINS-----------KKEI-SFPKNIDFIFIG 326
             D++          L   ++D +L+  +I+            + EI  F  N   + +G
Sbjct: 61  YYDNVRP--------LCYPDSDAVLICFDISRPETLDSVLKKWRGEIQEFCPNTKVLLVG 112

Query: 327 TKSDL 331
            K+DL
Sbjct: 113 CKTDL 117


>gnl|CDD|73004 cd03245, ABCC_bacteriocin_exporters, ABC-type bacteriocin
           exporters. Many non-lantibiotic bacteriocins of lactic
           acid bacteria are produced as precursors which have
           N-terminal leader peptides that share similarities in
           amino acid sequence and contain a conserved processing
           site of two glycine residues in positions -1 and -2.  A
           dedicated ATP-binding cassette (ABC) transporter is
           responsible for the proteolytic cleavage of the leader
           peptides and subsequent translocation of the
           bacteriocins across the cytoplasmic membrane..
          Length = 220

 Score = 27.4 bits (61), Expect = 7.5
 Identities = 12/25 (48%), Positives = 16/25 (64%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
           IR G K+ I+G   +GKS+L   LA
Sbjct: 27  IRAGEKVAIIGRVGSGKSTLLKLLA 51


>gnl|CDD|133356 cd04156, ARLTS1, ARLTS1 subfamily.  ARLTS1 (Arf-like tumor
           suppressor gene 1), also known as Arl11, is a member of
           the Arf family of small GTPases that is believed to play
           a major role in apoptotic signaling.  ARLTS1 is widely
           expressed and functions as a tumor suppressor gene in
           several human cancers.  ARLTS1 is a low-penetrance
           suppressor that accounts for a small percentage of
           familial melanoma or familial chronic lymphocytic
           leukemia (CLL).  ARLTS1 inactivation seems to occur most
           frequently through biallelic down-regulation by
           hypermethylation of the promoter.  In breast cancer,
           ARLTS1 alterations were typically a combination of a
           hypomorphic polymorphism plus loss of heterozygosity.
           In a case of thyroid adenoma, ARLTS1 alterations were
           polymorphism plus promoter hypermethylation.  The
           nonsense polymorphism Trp149Stop occurs with
           significantly greater frequency in familial cancer cases
           than in sporadic cancer cases, and the Cys148Arg
           polymorphism is associated with an increase in high-risk
           familial breast cancer.
          Length = 160

 Score = 27.4 bits (61), Expect = 8.2
 Identities = 44/176 (25%), Positives = 71/176 (40%), Gaps = 51/176 (28%)

Query: 221 KIVILGHSNAGKSSLFNALAKKDVAIVTDIPGTTRDVLTIDLD----------------- 263
           ++++LG  +AGKS+L   L  K   +VT IP    +V  + L+                 
Sbjct: 1   QVLLLGLDSAGKSTLLYKL--KHAELVTTIPTVGFNVEMLQLEKHLSLTVWDVGGQEKMR 58

Query: 264 ------LEG-----YLVKISDTAGI----RETDDIVEKEGIKRTFLEVENADLILLLKEI 308
                 LE      Y+V  SD A +    +E   I++ E IK          ++LL    
Sbjct: 59  TVWKCYLENTDGLVYVVDSSDEARLDESQKELKHILKNEHIK-------GVPVVLLA--- 108

Query: 309 NSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDHLI---SSFTGEGLEELINKIKSI 361
            +K+++  P  +    I  +  L   Y  + D  +   S+ TGEGL E   K+ S 
Sbjct: 109 -NKQDL--PGALTAEEITRRFKL-KKYCSDRDWYVQPCSAVTGEGLAEAFRKLASF 160


>gnl|CDD|36358 KOG1143, KOG1143, KOG1143, Predicted translation elongation factor
           [Translation, ribosomal structure and biogenesis].
          Length = 591

 Score = 27.3 bits (60), Expect = 8.4
 Identities = 40/199 (20%), Positives = 77/199 (38%), Gaps = 28/199 (14%)

Query: 178 FSEEEDVQNFSSKEVLNDILFLKN--DISSHISQGKLGEIIRNGYKIVIL----GHSNAG 231
           F    ++Q+  +  + N++L   N   + ++       EI+    K+V      GH+   
Sbjct: 204 FRHPHEIQSGRTSSISNEVLGFDNRGKVVNYAQNMTAEEIVEKSSKLVTFIDLAGHAKYQ 263

Query: 232 KSSLFNA------LAKKDVAIVTDIPGTTRDVLTIDLDLE-GYLVKISDTAGIRETDDIV 284
           K+++          A   V+    I  TTR+ L +   L   + V ++         D+V
Sbjct: 264 KTTIHGLTGYTPHFACLVVSADRGITWTTREHLGLIAALNIPFFVLVTKM-------DLV 316

Query: 285 EKEGIKRTFLEVENADLILLLKEINSKKEISFPKNIDFIFIGTKSDLYSTYTEEYDHLIS 344
           +++G+K+T  ++ N     LL +    K        D      +          +   +S
Sbjct: 317 DRQGLKKTVKDLSN-----LLAKAGCTKVPKRVTTKDDAVKAAQELCSGNIVPIF--AVS 369

Query: 345 SFTGEGLEELINKIKSILS 363
           S +GEGL  L+    + LS
Sbjct: 370 SVSGEGL-RLLRTFLNCLS 387


>gnl|CDD|39877 KOG4679, KOG4679, KOG4679, Uncharacterized protein PSP1 (suppressor
           of DNA polymerase alpha mutations in yeast) [General
           function prediction only].
          Length = 572

 Score = 27.4 bits (60), Expect = 8.5
 Identities = 22/63 (34%), Positives = 29/63 (46%), Gaps = 12/63 (19%)

Query: 105 LRLANPGEFSRRAFENGKIDLLEAESLADLISSETEMQRRLSMEGMSGELSSLYGQW-ID 163
           LR A P E      +    D LEA +LA     E  + R+L+ME ++ E      QW   
Sbjct: 470 LRKATPWELDTLKQK----DELEALALA--QCRERVLNRKLNMEILNCEY-----QWDRK 518

Query: 164 KLT 166
           KLT
Sbjct: 519 KLT 521


>gnl|CDD|39539 KOG4338, KOG4338, KOG4338, Predicted lipoprotein [Lipid transport and
            metabolism].
          Length = 1680

 Score = 27.3 bits (60), Expect = 8.7
 Identities = 25/124 (20%), Positives = 45/124 (36%), Gaps = 11/124 (8%)

Query: 284  VEKEGIKRTFLEVENADLIL----LLKEINSKKEISFPKNIDFIFIG-----TKSDLYST 334
             E E       + +N          L E NS++ + +  N+   +         +DL   
Sbjct: 1528 EECEKELERESKEKNYRDKSDRLEELSEYNSEQTMDYEGNLMEKYPERTIHFGFNDLTGK 1587

Query: 335  YTE-EYDHLISSFTGEGLEELINKIKSILSNKFKKLPFSIPSHKRHLYHLSQTVRYLEMA 393
                E+ H I  F+ E + E    ++S  S+ +KK    +P H      L + +R  +  
Sbjct: 1588 TAIKEFSHRIC-FSIEPVSECRRGLESEESHNWKKRFTCLPRHSSRARRLLKEIRSQKNL 1646

Query: 394  SLNE 397
             L  
Sbjct: 1647 DLVN 1650


>gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast
           cancer resistance protein) [Secondary metabolites
           biosynthesis, transport and catabolism].
          Length = 613

 Score = 27.3 bits (60), Expect = 9.2
 Identities = 11/26 (42%), Positives = 17/26 (65%)

Query: 215 IIRNGYKIVILGHSNAGKSSLFNALA 240
             + G  + I+G S +GK++L NALA
Sbjct: 52  TAKPGELLAIMGPSGSGKTTLLNALA 77


>gnl|CDD|133346 cd04146, RERG_RasL11_like, RERG/RasL11-like subfamily.  RERG
           (Ras-related and Estrogen- Regulated Growth inhibitor)
           and Ras-like 11 are members of a novel subfamily of Ras
           that were identified based on their behavior in breast
           and prostate tumors, respectively.  RERG expression was
           decreased or lost in a significant fraction of primary
           human breast tumors that lack estrogen receptor and are
           correlated with poor clinical prognosis.  Elevated RERG
           expression correlated with favorable patient outcome in
           a breast tumor subtype that is positive for estrogen
           receptor expression.  In contrast to most Ras proteins,
           RERG overexpression inhibited the growth of breast tumor
           cells in vitro and in vivo.  RasL11 was found to be
           ubiquitously expressed in human tissue, but
           down-regulated in prostate tumors.  Both RERG and RasL11
           lack the C-terminal CaaX prenylation motif, where a = an
           aliphatic amino acid and X = any amino acid, and are
           localized primarily in the cytoplasm.  Both are believed
           to have tumor suppressor activity.
          Length = 165

 Score = 27.2 bits (61), Expect = 9.2
 Identities = 9/15 (60%), Positives = 11/15 (73%)

Query: 221 KIVILGHSNAGKSSL 235
           KI +LG S  GKS+L
Sbjct: 1   KIAVLGASGVGKSAL 15


>gnl|CDD|29996 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
           VirB11, and related ATPases. The homohexamer, VirB11 is
           one of eleven Vir proteins, which are required for
           T-pilus biogenesis and virulence in the transfer of
           T-DNA from the Ti (tumor-inducing) plasmid of bacterial
           to plant cells. The pilus is a fibrous cell surface
           organelle, which mediates adhesion between bacteria
           during conjugative transfer or between bacteria and host
           eukaryotic cells during infection. VirB11- related
           ATPases include the archaeal flagella biosynthesis
           protein and the pilus assembly proteins CpaF/TadA and
           TrbB.  This alignment contains the C-terminal domain,
           which is the ATPase..
          Length = 186

 Score = 27.1 bits (60), Expect = 9.8
 Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 3/40 (7%)

Query: 212 LGEIIRNGYKIVILGHSNAGKSSLFNALAK---KDVAIVT 248
           L   +     I+I G + +GK++L NAL      D  I+T
Sbjct: 18  LWLAVEARKNILISGGTGSGKTTLLNALLAFIPPDERIIT 57


>gnl|CDD|72979 cd03220, ABC_KpsT_Wzt, ABC_KpsT_Wzt   The KpsT/Wzt ABC transporter
           subfamily is involved in extracellular polysaccharide
           export.  Among the variety of membrane-linked or
           extracellular polysaccharides excreted by bacteria, only
           capsular polysaccharides, lipopolysaccharides, and
           teichoic acids have been shown to be exported by ABC
           transporters.  A typical system is made of a conserved
           integral membrane and an ABC.  In addition to these
           proteins, capsular polysaccharide exporter systems
           require two 'accessory' proteins to perform their
           function: a periplasmic (E.coli) or a lipid-anchored
           outer membrane protein called OMA (Neisseria
           meningitidis and Haemophilus influenzae) and a
           cytoplasmic membrane protein MPA2..
          Length = 224

 Score = 27.0 bits (60), Expect = 9.9
 Identities = 10/25 (40%), Positives = 16/25 (64%)

Query: 216 IRNGYKIVILGHSNAGKSSLFNALA 240
           +  G +I ++G + AGKS+L   LA
Sbjct: 45  VPRGERIGLIGRNGAGKSTLLRLLA 69


  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    0.138    0.385 

Gapped
Lambda     K      H
   0.267   0.0762    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,222,913
Number of extensions: 285839
Number of successful extensions: 1254
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1211
Number of HSP's successfully gapped: 217
Length of query: 440
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 343
Effective length of database: 4,167,664
Effective search space: 1429508752
Effective search space used: 1429508752
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (26.4 bits)