RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|255764460|ref|YP_003064605.2| recombinase A [Candidatus
Liberibacter asiaticus str. psy62]
         (363 letters)



>gnl|CDD|181793 PRK09354, recA, recombinase A; Provisional.
          Length = 349

 Score =  648 bits (1674), Expect = 0.0
 Identities = 233/346 (67%), Positives = 293/346 (84%), Gaps = 2/346 (0%)

Query: 11  DKSKALEAALSQIQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRIV 70
           +K KALEAAL QI++ +GKG+IM+LG   +    +EV+S+GSL LDIALGIGG P+GRIV
Sbjct: 6   EKQKALEAALKQIEKQFGKGSIMRLGDDAA--MDVEVISTGSLALDIALGIGGLPRGRIV 63

Query: 71  EIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKNLLISQPDTG 130
           EIYGPESSGKTTLALH IA++QK GGT AF+DAEHALD +YA+KLGVD+ NLL+SQPDTG
Sbjct: 64  EIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTG 123

Query: 131 EQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSI 190
           EQALEI D LVRSGAVD+IV+DSVAAL P+AEIEG+MG+S  G+QARLMSQALRKLT +I
Sbjct: 124 EQALEIADTLVRSGAVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGNI 183

Query: 191 SRSKCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRRVGSIKDKDSITGNQT 250
           S+S   ++FINQ+R KIGVMFG+PETTTGGNALKFY+SVRLDIRR+G+IKD D + GN+T
Sbjct: 184 SKSNTTVIFINQIREKIGVMFGNPETTTGGNALKFYASVRLDIRRIGTIKDGDEVIGNRT 243

Query: 251 RVKVVKNKMASPFKQVEFDIMYGEGISFFGELIDLGVKASIVDKSGAWFSFKGQRLGQGR 310
           +VKVVKNK+A PFKQ EFDIMYGEGIS  GELIDLGV+  I++KSGAW+S+ G+++GQGR
Sbjct: 244 KVKVVKNKVAPPFKQAEFDIMYGEGISREGELIDLGVELGIIEKSGAWYSYNGEKIGQGR 303

Query: 311 ENSKIFLRENIEIAENIESLLRQNAGLVADSLLQEPAINTKDDADK 356
           EN+K +L+EN E+A+ IE  +R+  GL A +  +E   + +++ ++
Sbjct: 304 ENAKQYLKENPELADEIEKKIREKLGLSAAAAEEEEEEDEEEEEEE 349


>gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA.  This model describes
           orthologs of the recA protein. RecA promotes
           hybridization of homolgous regions of DNA. A segment of
           ssDNA can be hybridized to another ssDNA region, or to a
           dsDNA region. ATP is hydrolyzed in the process. Part of
           the SOS respones, it is regulated by LexA via
           autocatalytic cleavage.
          Length = 321

 Score =  555 bits (1431), Expect = e-159
 Identities = 215/323 (66%), Positives = 274/323 (84%), Gaps = 2/323 (0%)

Query: 11  DKSKALEAALSQIQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRIV 70
           +K KALEAAL+QI++ +GKG+IM+LG +      +E +S+GSL LD+ALG+GG P+GRI+
Sbjct: 1   EKQKALEAALAQIEKQFGKGSIMRLGEKSV--MDVETISTGSLSLDLALGVGGLPRGRII 58

Query: 71  EIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKNLLISQPDTG 130
           EIYGPESSGKTTLALH IA++QK GGT AF+DAEHALD +YARKLGVD+ NLL+SQPDTG
Sbjct: 59  EIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTG 118

Query: 131 EQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSI 190
           EQALEI + LVRSGAVDIIV+DSVAAL P+AEIEG+MG+S  G+QARLMSQALRKLT ++
Sbjct: 119 EQALEIAETLVRSGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGAL 178

Query: 191 SRSKCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRRVGSIKDKDSITGNQT 250
           S+S    +FINQ+R KIGVMFG+PETTTGG ALKFY+SVRLDIRR+G +K  + + GN+T
Sbjct: 179 SKSNTTAIFINQIREKIGVMFGNPETTTGGRALKFYASVRLDIRRIGQVKQGEEVVGNRT 238

Query: 251 RVKVVKNKMASPFKQVEFDIMYGEGISFFGELIDLGVKASIVDKSGAWFSFKGQRLGQGR 310
           +VKVVKNK+A PFK+ EFDI+YGEGIS  GE+IDL V+  I+ K+G+W+S+  ++LGQGR
Sbjct: 239 KVKVVKNKVAPPFKEAEFDILYGEGISKLGEIIDLAVELDIIKKAGSWYSYGDEKLGQGR 298

Query: 311 ENSKIFLRENIEIAENIESLLRQ 333
           EN+K +L+EN E+A+ IE  +R+
Sbjct: 299 ENAKAYLKENPELAQEIEKKVRE 321


>gnl|CDD|77219 PRK09519, recA, DNA recombination protein RecA; Reviewed.
          Length = 790

 Score =  335 bits (861), Expect = 8e-93
 Identities = 164/248 (66%), Positives = 208/248 (83%), Gaps = 2/248 (0%)

Query: 11  DKSKALEAALSQIQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRIV 70
           D+ KALE A++QI++ YGKG++M+LG +    + I V+ +GS+ LD+ALGIGG P+GR++
Sbjct: 6   DREKALELAVAQIEKSYGKGSVMRLGDEAR--QPISVIPTGSIALDVALGIGGLPRGRVI 63

Query: 71  EIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKNLLISQPDTG 130
           EIYGPESSGKTT+ALH +A +Q  GG  AF+DAEHALD  YA+KLGVD  +LL+SQPDTG
Sbjct: 64  EIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTG 123

Query: 131 EQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSI 190
           EQALEI DML+RSGA+DI+VIDSVAAL PRAE+EG+MG+S  G+QARLMSQALRK+T ++
Sbjct: 124 EQALEIADMLIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGAL 183

Query: 191 SRSKCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRRVGSIKDKDSITGNQT 250
           + S    +FINQ+R KIGVMFGSPETTTGG ALKFY+SVR+D+RRV ++KD  +  GN+T
Sbjct: 184 NNSGTTAIFINQLRDKIGVMFGSPETTTGGKALKFYASVRMDVRRVETLKDGTNAVGNRT 243

Query: 251 RVKVVKNK 258
           RVKVVKNK
Sbjct: 244 RVKVVKNK 251



 Score = 94.8 bits (235), Expect = 3e-20
 Identities = 43/86 (50%), Positives = 65/86 (75%)

Query: 254 VVKNKMASPFKQVEFDIMYGEGISFFGELIDLGVKASIVDKSGAWFSFKGQRLGQGRENS 313
           VV +  + PFKQ EFDI+YG+GIS  G LID+GV   ++ KSGAWF+++G++LGQG+EN+
Sbjct: 687 VVVHNCSPPFKQAEFDILYGKGISREGSLIDMGVDQGLIRKSGAWFTYEGEQLGQGKENA 746

Query: 314 KIFLRENIEIAENIESLLRQNAGLVA 339
           + FL EN ++A+ IE  +++  G+ A
Sbjct: 747 RNFLVENADVADEIEKKIKEKLGIGA 772


>gnl|CDD|181799 PRK09361, radB, DNA repair and recombination protein RadB;
           Provisional.
          Length = 225

 Score = 63.3 bits (155), Expect = 9e-11
 Identities = 60/205 (29%), Positives = 90/205 (43%), Gaps = 22/205 (10%)

Query: 44  GIEVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDA 103
             E + +G   LD  LG GGF +G I +IYGP  SGKT + L    ++ K G    ++D 
Sbjct: 1   MDERLPTGCKMLDELLG-GGFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDT 59

Query: 104 E----HALDSIYARKLGVDLKNLLISQP-DTGEQALEITDM--LVRSGAVDIIVIDSVAA 156
           E         I        L N++I +P    EQ+  I     L +   V +IV+DS  +
Sbjct: 60  EGLSPERFKQIAGEDFEELLSNIIIFEPSSFEEQSEAIRKAEKLAKEN-VGLIVLDSATS 118

Query: 157 LTPRAEIEGDM-GESLPGMQARLMSQALRKLTSSISRSKCILVFI-NQMRMKIGVMFGSP 214
           L  R E+E +     L     R ++  L      ++R   + V I NQ+   I      P
Sbjct: 119 LY-RLELEDEEDNSKLNRELGRQLTHLL-----KLARKHDLAVVITNQVYSDIDSDGLRP 172

Query: 215 ETTTGGNALKFYSS--VRLDIRRVG 237
               GG+ L+ +S   +RL+  R G
Sbjct: 173 ---LGGHTLEHWSKTILRLEKFRNG 194


>gnl|CDD|162777 TIGR02237, recomb_radB, DNA repair and recombination protein RadB. 
           This family consists exclusively of archaeal RadB
           protein, a homolog of bacterial RecA (TIGR02012),
           eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
           archaeal RadA (TIGR02236).
          Length = 209

 Score = 60.5 bits (147), Expect = 7e-10
 Identities = 48/189 (25%), Positives = 81/189 (42%), Gaps = 19/189 (10%)

Query: 55  LDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAE----HALDSI 110
           +D  LG GG  +G I +IYGP  SGKT + +     + + G    ++D E         I
Sbjct: 1   IDELLG-GGVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEGLSPERFKQI 59

Query: 111 YARKLGVDLKNLLISQP---DTGEQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDM 167
              +    L N ++ +    D    A++ T   +   +  ++V+DS  AL  R E+  D 
Sbjct: 60  AEDRPERALSNFIVFEVFDFDEQGVAIQKTSKFIDRDSASLVVVDSFTALY-RLELSDDR 118

Query: 168 GESLPGMQARLMSQALRKLTSSISRSKCILVFI-NQMRMKIGVMFGSPETTTGGNALKFY 226
                 +  +L       L  S++R K + V I NQ+   +      P    GG+ L+ +
Sbjct: 119 ISRNRELARQL------TLLLSLARKKNLAVVITNQVYTDVNNGTLRP---LGGHLLEHW 169

Query: 227 SSVRLDIRR 235
           S V L + +
Sbjct: 170 SKVILRLEK 178


>gnl|CDD|178729 PLN03187, PLN03187, meiotic recombination protein DMC1 homolog;
           Provisional.
          Length = 344

 Score = 58.6 bits (142), Expect = 2e-09
 Identities = 61/211 (28%), Positives = 97/211 (45%), Gaps = 32/211 (15%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQS----QKTGGTC---AF 100
           +++GS  LD  LG GG     I E +G   SGKT LA HT+  +     + GG     A+
Sbjct: 108 ITTGSQALDELLG-GGIETRCITEAFGEFRSGKTQLA-HTLCVTTQLPTEMGGGNGKVAY 165

Query: 101 VDAEHAL--DSI--YARKLGVD----LKNLLISQPDTGEQALEITDMLVRSGA------V 146
           +D E     D I   A + G+D    L N++ ++  T E      ++L+   A       
Sbjct: 166 IDTEGTFRPDRIVPIAERFGMDADAVLDNIIYARAYTYEH---QYNLLLGLAAKMAEEPF 222

Query: 147 DIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFINQMRMK 206
            ++++DSV AL  R +  G  GE L   Q +L +Q L +LT         +   NQ+   
Sbjct: 223 RLLIVDSVIALF-RVDFTG-RGE-LAERQQKL-AQMLSRLTKIAEEFNVAVYMTNQVIAD 278

Query: 207 IG--VMFGSPETTTGGNALKFYSSVRLDIRR 235
            G  +    P+   GG+ L   +++RL +R+
Sbjct: 279 PGGGMFISDPKKPAGGHVLAHAATIRLMLRK 309


>gnl|CDD|148381 pfam06745, KaiC, KaiC.  This family represents a conserved region
           within bacterial and archaeal proteins, most of which
           are hypothetical. More than one copy is sometimes found
           in each protein. This family includes KaiC, which is one
           of the Kai proteins among which direct protein-protein
           association may be a critical process in the generation
           of circadian rhythms in cyanobacteria.
          Length = 231

 Score = 57.2 bits (139), Expect = 6e-09
 Identities = 48/216 (22%), Positives = 79/216 (36%), Gaps = 47/216 (21%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQS-QKTGGTCAFVDAEHA 106
           V +G  GLD  +  GG P+GR+V I G   +GKT   L  +     + G    +V  E  
Sbjct: 1   VKTGIPGLD-EILKGGIPEGRVVLITGGPGTGKTIFGLQFLYNGALEYGEPGVYVTLEEP 59

Query: 107 LDSIY--ARKLGVDL-----KNLLI----SQPDTGEQALEITDML----------VRSGA 145
            + +   A+  G DL     +  L     S    G   ++    L          +R   
Sbjct: 60  PEDLRENAKSFGWDLEKLEEEGKLAIIDASTSGIGIAEVKGRFDLEELIERLREAIREIG 119

Query: 146 VDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFINQMRM 205
              +VIDS+  L             L    AR   + LR+L   + +     +F ++   
Sbjct: 120 AKRVVIDSITTLF----------YLLKPAMAR---EILRRLKRVLKKLGVTAIFTSEKP- 165

Query: 206 KIGVMFGSPETTTGGNALKFYSS---VRLDIRRVGS 238
                  S E   GG  ++ +     +RLD++ +  
Sbjct: 166 -------SGEGGIGGYGVEEFVVDGVIRLDLKEIEG 194


>gnl|CDD|179814 PRK04301, radA, DNA repair and recombination protein RadA;
           Validated.
          Length = 317

 Score = 54.5 bits (132), Expect = 4e-08
 Identities = 58/217 (26%), Positives = 89/217 (41%), Gaps = 45/217 (20%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQS-QKT------GGTCAF 100
           +++GS  LD  LG GG     I E YG   SGKT +  H +A + Q         G   +
Sbjct: 84  ITTGSKELDELLG-GGIETQSITEFYGEFGSGKTQIC-HQLAVNVQLPEEKGGLEGKAVY 141

Query: 101 VDAE--------------------HALDSI-YARKLGVDLKNLLISQPDTGEQALEITDM 139
           +D E                      LD+I  AR    D + LL       E+A E    
Sbjct: 142 IDTEGTFRPERIEQMAEALGLDPDEVLDNIHVARAYNSDHQMLLA------EKAEE---- 191

Query: 140 LVRSG-AVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILV 198
           L++ G  + ++++DS+ A   RAE  G    +L   Q +L  + L  L          +V
Sbjct: 192 LIKEGENIKLVIVDSLTAHF-RAEYVGR--GNLAERQQKLN-KHLHDLLRLADLYNAAVV 247

Query: 199 FINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRR 235
             NQ+  +    FG P    GG+ L   ++ R+ +R+
Sbjct: 248 VTNQVMARPDAFFGDPTQPIGGHILGHTATFRIYLRK 284


>gnl|CDD|128665 smart00382, AAA, ATPases associated with a variety of cellular
           activities.  AAA - ATPases associated with a variety of
           cellular activities. This profile/alignment only detects
           a fraction of this vast family. The poorly conserved
           N-terminal helix is missing from the alignment.
          Length = 148

 Score = 53.2 bits (127), Expect = 1e-07
 Identities = 35/171 (20%), Positives = 62/171 (36%), Gaps = 24/171 (14%)

Query: 66  KGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLKNLLIS 125
            G ++ I GP  SGKTTLA     +    GG   ++D E  L+ +  + L + +     S
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60

Query: 126 QPDTGEQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRK 185
              +GE  L +   L R    D++++D + +L    +               L+ + LR 
Sbjct: 61  --GSGELRLRLALALARKLKPDVLILDEITSLLDAEQ-----------EALLLLLEELRL 107

Query: 186 LTSSISRSKCILVFINQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRRV 236
           L    S     ++                E   G   L+     R+ +  +
Sbjct: 108 LLLLKSEKNLTVILTTN-----------DEKDLGPALLRRRFDRRIVLLLI 147


>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family.  This
           model represents a rather narrowly distributed archaeal
           protein family in which members have a single copy of
           the KaiC domain. This stands in contrast to the
           circadian clock protein KaiC itself, with two copies of
           the domain. Members are expected to have weak ATPase
           activity, by homology to the
           autokinase/autophosphorylase KaiC itself.
          Length = 224

 Score = 51.2 bits (123), Expect = 4e-07
 Identities = 35/117 (29%), Positives = 56/117 (47%), Gaps = 14/117 (11%)

Query: 54  GLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSI--Y 111
           GLD  LG GGFP+G ++ + G   +GKTT +L  + Q  K G    ++  E   + I  Y
Sbjct: 4   GLDEMLG-GGFPEGHVIVVIGEYGTGKTTFSLQFLYQGLKNGEKAMYISLEEREERILGY 62

Query: 112 ARKLGVDL-----KNLLISQPDTGEQALEITDM------LVRSGAVDIIVIDSVAAL 157
           A+  G DL     K+L I + D  +    +  +      L++      +VID ++ L
Sbjct: 63  AKSKGWDLEDYIDKSLYIVRLDPSDFKTSLNRIKNELPILIKELGASRVVIDPISLL 119


>gnl|CDD|131292 TIGR02238, recomb_DMC1, meiotic recombinase Dmc1.  This model
           describes DMC1, a subfamily of a larger family of DNA
           repair and recombination proteins. It is eukaryotic only
           and most closely related to eukaryotic RAD51. It also
           resembles archaeal RadA (TIGR02236) and RadB (TIGR02237)
           and bacterial RecA (TIGR02012). It has been
           characterized for human as a recombinase active only in
           meiosis.
          Length = 313

 Score = 50.9 bits (122), Expect = 5e-07
 Identities = 64/211 (30%), Positives = 104/211 (49%), Gaps = 29/211 (13%)

Query: 47  VVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQK-------TGGTCA 99
            +++GS  LD  LG GG     I E++G    GKT L+ HT+  + +         G  A
Sbjct: 77  KITTGSQALDGILG-GGIESMSITEVFGEFRCGKTQLS-HTLCVTAQLPREMGGGNGKVA 134

Query: 100 FVDAEHAL--DSI--YARKLGVD----LKNLLISQPDTGEQALEITDMLVRSGAVD---I 148
           ++D E     D I   A + GVD    L N+L ++  T E  +E+ D L    + +   +
Sbjct: 135 YIDTEGTFRPDRIRAIAERFGVDPDAVLDNILYARAYTSEHQMELLDYLAAKFSEEPFRL 194

Query: 149 IVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFI-NQMRMKI 207
           +++DS+ AL  R +  G  GE L   Q +L +Q L +L   IS    + VF+ NQ++   
Sbjct: 195 LIVDSIMALF-RVDFSG-RGE-LSERQQKL-AQMLSRLN-KISEEFNVAVFVTNQVQADP 249

Query: 208 G--VMFGS-PETTTGGNALKFYSSVRLDIRR 235
           G  + F + P+   GG+ L   S+ R+ +R+
Sbjct: 250 GATMTFIADPKKPIGGHVLAHASTTRILLRK 280


>gnl|CDD|117002 pfam08423, Rad51, Rad51.  Rad51 is a DNA repair and recombination
           protein and is a homologue of the bacterial ATPase RecA
           protein.
          Length = 261

 Score = 50.0 bits (120), Expect = 1e-06
 Identities = 55/211 (26%), Positives = 97/211 (45%), Gaps = 31/211 (14%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQK-------TGGTCAF 100
           +++GS  LD  LG GG   G I E++G   +GKT L  HT+  + +         G   +
Sbjct: 25  ITTGSKELDKLLG-GGIETGSITEVFGEFRTGKTQLC-HTLCVTCQLPLEMGGGEGKALY 82

Query: 101 VDAE-----HALDSIYARKLGVD----LKNLLISQPDTGEQALEITDM---LVRSGAVDI 148
           +D E       + +I A + G+D    L N+  ++    E  +++      ++      +
Sbjct: 83  IDTEGTFRPERIVAI-AERFGLDPEEVLDNIAYARAYNTEHQMQLLLQAAAMMSESRFAL 141

Query: 149 IVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFI-NQMRMKI 207
           +++DS  AL  R +  G  GE L   Q  L ++ LR L   ++    + V I NQ+  ++
Sbjct: 142 LIVDSATALY-RTDFSG-RGE-LAERQQHL-AKFLRSL-QRLADEFGVAVVITNQVVAQV 196

Query: 208 G--VMF-GSPETTTGGNALKFYSSVRLDIRR 235
               MF   P+   GG+ +   S+ RL +R+
Sbjct: 197 DGAAMFAADPKKPIGGHIMAHASTTRLYLRK 227


>gnl|CDD|185407 PTZ00035, PTZ00035, Rad51 protein; Provisional.
          Length = 337

 Score = 48.8 bits (117), Expect = 2e-06
 Identities = 60/230 (26%), Positives = 98/230 (42%), Gaps = 40/230 (17%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIA------QSQKTG-GTCAF 100
           +++GS  LD  LG GG   G I E++G   +GKT L  HT+         Q  G G   +
Sbjct: 100 ITTGSTQLDKLLG-GGIETGSITELFGEFRTGKTQLC-HTLCVTCQLPIEQGGGEGKVLY 157

Query: 101 VDAEHA-----LDSIYARKLGVD----LKNLLISQPDTGEQALEITDMLVRSGAVD---I 148
           +D E       +  I A + G+D    L N+  ++    E  +++        A +   +
Sbjct: 158 IDTEGTFRPERIVQI-AERFGLDPEDVLDNIAYARAYNHEHQMQLLSQAAAKMAEERFAL 216

Query: 149 IVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVFI-NQMRMKI 207
           +++DS  AL  R +  G  GE L   Q  L  + LR L   ++    + V I NQ+   +
Sbjct: 217 LIVDSATALF-RVDYSG-RGE-LAERQQHL-GKFLRAL-QKLADEFNVAVVITNQVMADV 271

Query: 208 G---VMFGSPETTTGGNALKFYSSVRLDIRRVGSIKDKDSITGNQTRVKV 254
               +    P+   GG+ +   S+ RL +R     K +    G Q   K+
Sbjct: 272 DGASMFVADPKKPIGGHIIAHASTTRLSLR-----KGR----GEQRICKI 312


>gnl|CDD|162778 TIGR02239, recomb_RAD51, DNA repair protein RAD51.  This eukaryotic
           sequence family consists of RAD51, a protein involved in
           DNA homologous recombination and repair. It is similar
           in sequence the exclusively meiotic recombinase DMC1
           (TIGR02238), to archaeal families RadA (TIGR02236) and
           RadB (TIGR02237), and to bacterial RecA (TIGR02012).
          Length = 316

 Score = 47.4 bits (113), Expect = 6e-06
 Identities = 65/222 (29%), Positives = 93/222 (41%), Gaps = 52/222 (23%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIA------QSQKTG-GTCAF 100
           +++GS  LD  LG GG   G I EI+G   +GKT L  HT+A        Q  G G   +
Sbjct: 78  LTTGSKELDKLLG-GGIETGSITEIFGEFRTGKTQLC-HTLAVTCQLPIDQGGGEGKALY 135

Query: 101 VDAE--------------------HALDSI-YARKLGVDLKNLLISQPDTGEQALEITDM 139
           +D E                      LD++ YAR    D +  L+ Q            M
Sbjct: 136 IDTEGTFRPERLLAIAERYGLNPEDVLDNVAYARAYNTDHQLQLLQQA---------AAM 186

Query: 140 LVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQA--LRKLTSSISRSKCIL 197
           +  S    ++++DS  AL  R +  G  GE    + AR M  A  LR L          +
Sbjct: 187 MSES-RFALLIVDSATALY-RTDFSG-RGE----LSARQMHLARFLRSLQRLADEFGVAV 239

Query: 198 VFINQMRMKI---GVMF-GSPETTTGGNALKFYSSVRLDIRR 235
           V  NQ+  ++   G MF G P+   GGN +   S+ RL +R+
Sbjct: 240 VITNQVVAQVDGAGSMFAGDPKKPIGGNIMAHASTTRLSLRK 281


>gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family.
           Members of this protein family are archaeal
           single-domain KaiC_related proteins, homologous to the
           Cyanobacterial circadian clock cycle protein KaiC, an
           autokinase/autophosphorylase that has two copies of the
           domain.
          Length = 229

 Score = 46.3 bits (110), Expect = 1e-05
 Identities = 35/124 (28%), Positives = 53/124 (42%), Gaps = 26/124 (20%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHAL 107
           +S+G  GLD  L  GG P+G  V + G   +GKT   LH   +  + G    +V  E + 
Sbjct: 2   LSTGVEGLDKLLE-GGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTTEESR 60

Query: 108 DSIY--ARKLGVDLKNLLISQPDTGEQALEITDMLVRSGAVDIIVIDSVAALTPRAEIEG 165
           +SI   A + G+D            E+A+E   +         ++ID   AL    E E 
Sbjct: 61  ESIIRQAAQFGMDF-----------EKAIEEGKL---------VIID---ALMKEKEDEW 97

Query: 166 DMGE 169
            + E
Sbjct: 98  SLRE 101


>gnl|CDD|178728 PLN03186, PLN03186, DNA repair protein RAD51 homolog; Provisional.
          Length = 342

 Score = 45.9 bits (109), Expect = 1e-05
 Identities = 57/213 (26%), Positives = 93/213 (43%), Gaps = 35/213 (16%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQS-----QKTGGT--CAF 100
           +++GS  LD  L  GG   G I EIYG   +GKT L  HT+  +      + GG     +
Sbjct: 105 ITTGSRELDKILE-GGIETGSITEIYGEFRTGKTQLC-HTLCVTCQLPLDQGGGEGKAMY 162

Query: 101 VDAE-----HALDSIYARKLGVD----LKNLLISQPDTGEQALEI----TDMLVRSGAVD 147
           +D E       L  I A + G++    L+N+  ++    +   E+      M+  +    
Sbjct: 163 IDTEGTFRPQRLIQI-AERFGLNGADVLENVAYARAYNTDHQSELLLEAASMMAET-RFA 220

Query: 148 IIVIDSVAALTPRAEIEGDMGESLPGMQAR--LMSQALRKLTSSISRSKCILVFINQMRM 205
           ++++DS  AL  R E  G  GE    + AR   + + LR L          +V  NQ+  
Sbjct: 221 LMIVDSATALY-RTEFSG-RGE----LSARQMHLGKFLRSLQRLADEFGVAVVITNQVVA 274

Query: 206 KI--GVMFGSPETT-TGGNALKFYSSVRLDIRR 235
           ++     F  P+    GGN +   S+ RL +R+
Sbjct: 275 QVDGSAFFAGPQLKPIGGNIMAHASTTRLALRK 307


>gnl|CDD|131290 TIGR02236, recomb_radA, DNA repair and recombination protein RadA. 
           This family consists exclusively of archaeal RadA
           protein, a homolog of bacterial RecA (TIGR02012),
           eukaryotic RAD51 (TIGR02239), and archaeal RadB
           (TIGR02237). This protein is involved in DNA repair and
           recombination. The member from Pyrococcus horikoshii
           contains an intein.
          Length = 310

 Score = 44.7 bits (106), Expect = 4e-05
 Identities = 54/216 (25%), Positives = 92/216 (42%), Gaps = 42/216 (19%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIA-------QSQKTGGTCAF 100
           +++GS  LD  LG GG     I E++G   SGKT +  H +A       +    GG   +
Sbjct: 77  ITTGSKELDELLG-GGIETQAITEVFGEFGSGKTQIC-HQLAVNVQLPEEKGGLGGKAVY 134

Query: 101 VDAEH--------------------ALDSIY-ARKLGVDLKNLLISQPDTGEQALEITDM 139
           +D E+                     L +IY AR    + + LL+      E+A ++   
Sbjct: 135 IDTENTFRPERIMQMAEARGLDPDEVLKNIYVARAYNSNHQMLLV------EKAEDLIKE 188

Query: 140 LVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSISRSKCILVF 199
           L  +  V ++++DS+ +   RAE  G    +L   Q +L ++ L  L          +V 
Sbjct: 189 L--NNPVKLLIVDSLTS-HFRAEYVGR--GALAERQQKL-NKHLHDLLRLADLYNAAVVV 242

Query: 200 INQMRMKIGVMFGSPETTTGGNALKFYSSVRLDIRR 235
            NQ+  +    FG P    GG+ L   ++ R+ +R+
Sbjct: 243 TNQVMARPDAFFGDPTRPIGGHILGHAATFRVYLRK 278


>gnl|CDD|161868 TIGR00416, sms, DNA repair protein RadA.  The gene protuct codes
           for a probable ATP-dependent protease involved in both
           DNA repair and degradation of proteins, peptides,
           glycopeptides. Also known as sms. Residues 11-28 of the
           SEED alignment contain a putative Zn binding domain.
           Residues 110-117 of the seed contain a putative ATP
           binding site both documented in Haemophilus and in
           Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
           178:5045-5048(1996)).
          Length = 454

 Score = 40.6 bits (95), Expect = 6e-04
 Identities = 35/112 (31%), Positives = 45/112 (40%), Gaps = 7/112 (6%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHAL 107
            SSG   LD  LG GG   G ++ I G    GK+TL L    Q  K      +V  E +L
Sbjct: 76  FSSGFGELDRVLG-GGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESL 134

Query: 108 DSIYAR--KLGVDLKNLLISQPDTGEQALEITDMLVRSGAVDIIVIDSVAAL 157
             I  R  +LG+   NL +      E   E     +        VIDS+  L
Sbjct: 135 QQIKMRAIRLGLPEPNLYV----LSETNWEQICANIEEENPQACVIDSIQTL 182


>gnl|CDD|181771 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
          Length = 509

 Score = 40.6 bits (96), Expect = 6e-04
 Identities = 38/125 (30%), Positives = 52/125 (41%), Gaps = 13/125 (10%)

Query: 46  EVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEH 105
           E +SSG   LD  LG GGF +G I+ + G   +GKT LA      + + G  C     E 
Sbjct: 253 ERISSGVPDLDEMLG-GGFFRGSIILVSGATGTGKTLLASKFAEAACRRGERCLLFAFEE 311

Query: 106 ALDSIY--ARKLGVDL-----KNLLISQPD----TG-EQALEITDMLVRSGAVDIIVIDS 153
           +   +   AR  G+DL     K LL          G E  L I    +       + ID 
Sbjct: 312 SRAQLIRNARSWGIDLEKMEEKGLLKIICARPESYGLEDHLIIIKREIEEFKPSRVAIDP 371

Query: 154 VAALT 158
           ++AL 
Sbjct: 372 LSALA 376



 Score = 34.1 bits (79), Expect = 0.051
 Identities = 43/144 (29%), Positives = 61/144 (42%), Gaps = 26/144 (18%)

Query: 37  SQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALH-TIAQSQKTG 95
           +Q S   GIE + +G  G D     GG PKGR   + G   +GKT  AL   +   ++  
Sbjct: 2   NQPSASPGIEKLPTGIEGFDDITH-GGLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFD 60

Query: 96  GTCAFVDAEHALDSIY--ARKLGVDLKNLL---------IS-----QPDTGEQALEITDM 139
               FV  E + + I       G DL+ L+          S     Q + GE  LE   +
Sbjct: 61  EPGVFVTFEESPEDIIRNVASFGWDLQKLIDEGKLFILDASPDPSEQEEAGEYDLE--AL 118

Query: 140 LVRSG-AVDII-----VIDSVAAL 157
            +R   A+D I     V+DS+ AL
Sbjct: 119 FIRIEYAIDKIGAKRVVLDSIEAL 142


>gnl|CDD|183326 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
          Length = 446

 Score = 39.7 bits (94), Expect = 0.001
 Identities = 36/110 (32%), Positives = 51/110 (46%), Gaps = 9/110 (8%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHAL 107
           +S+G   LD  LG GG   G +V I G    GK+TL L   A+    GG   +V  E + 
Sbjct: 62  ISTGIGELDRVLG-GGLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEESA 120

Query: 108 DSIY--ARKLGVDLKNLLISQPDTG-EQALEITDMLVRSGAVDIIVIDSV 154
             I   A +LG+   NL +   +T  E  L      +     D++VIDS+
Sbjct: 121 SQIKLRAERLGLPSDNLYLL-AETNLEAILAT----IEEEKPDLVVIDSI 165


>gnl|CDD|182778 PRK10851, PRK10851, sulfate/thiosulfate transporter subunit;
           Provisional.
          Length = 353

 Score = 34.7 bits (80), Expect = 0.038
 Identities = 28/66 (42%), Positives = 34/66 (51%), Gaps = 13/66 (19%)

Query: 56  DIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQ-SQKTGGTCAF----VDAEHALDSI 110
           DI+L I   P G++V + GP  SGKTTL L  IA    +T G   F    V   HA D  
Sbjct: 20  DISLDI---PSGQMVALLGPSGSGKTTL-LRIIAGLEHQTSGHIRFHGTDVSRLHARD-- 73

Query: 111 YARKLG 116
             RK+G
Sbjct: 74  --RKVG 77


>gnl|CDD|161968 TIGR00630, uvra, excinuclease ABC, A subunit.  This family is
          based on the phylogenomic analysis of JA Eisen (1999,
          Ph.D. Thesis, Stanford University).
          Length = 924

 Score = 32.7 bits (75), Expect = 0.17
 Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTI-AQSQK 93
           P+ ++V I G   SGK++LA  TI A+ Q+
Sbjct: 19 IPRDKLVVITGLSGSGKSSLAFDTIYAEGQR 49


>gnl|CDD|184206 PRK13647, cbiO, cobalt transporter ATP-binding subunit;
          Provisional.
          Length = 274

 Score = 32.4 bits (74), Expect = 0.18
 Identities = 10/24 (41%), Positives = 14/24 (58%)

Query: 63 GFPKGRIVEIYGPESSGKTTLALH 86
            P+G    + GP  +GK+TL LH
Sbjct: 27 SIPEGSKTALLGPNGAGKSTLLLH 50


>gnl|CDD|168322 PRK05973, PRK05973, replicative DNA helicase; Provisional.
          Length = 237

 Score = 31.9 bits (73), Expect = 0.28
 Identities = 36/131 (27%), Positives = 52/131 (39%), Gaps = 22/131 (16%)

Query: 79  GKTTLALHTIAQSQKTGGTCAFVDAEH----ALDSIYARKLGVDLKNLL-ISQPDTGEQ- 132
           GKT L L    ++ K+G T  F   E+      D +  R LG D      + + DT +  
Sbjct: 76  GKTLLGLELAVEAMKSGRTGVFFTLEYTEQDVRDRL--RALGADRAQFADLFEFDTSDAI 133

Query: 133 -ALEITDMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALRKLTSSIS 191
            A  I   L  +    ++VID +  L  R E            +  L  Q +R L S   
Sbjct: 134 CADYIIARLASAPRGTLVVIDYLQLLDQRRE------------KPDLSVQ-VRALKSFAR 180

Query: 192 RSKCILVFINQ 202
               I+VFI+Q
Sbjct: 181 ERGLIIVFISQ 191


>gnl|CDD|162400 TIGR01526, nadR_NMN_Atrans, nicotinamide-nucleotide
           adenylyltransferase, NadR type.  E. coli NadR has also
           been found to regulate the import of its substrate,
           nicotinamide ribonucleotide, but it is not known if the
           other members of this model share that activity.
          Length = 325

 Score = 31.4 bits (71), Expect = 0.37
 Identities = 9/17 (52%), Positives = 12/17 (70%)

Query: 68  RIVEIYGPESSGKTTLA 84
           + V I G ES+GK+TL 
Sbjct: 163 KTVAILGGESTGKSTLV 179


>gnl|CDD|162115 TIGR00929, VirB4_CagE, type IV secretion/conjugal transfer ATPase,
           VirB4 family.  Type IV secretion systems are found in
           Gram-negative pathogens. They export proteins, DNA, or
           complexes in different systems and are related to
           plasmid conjugation systems. This model represents
           related ATPases that include VirB4 in Agrobacterium
           tumefaciens (DNA export) CagE in Helicobacter pylori
           (protein export) and plasmid TraB (conjugation).
          Length = 785

 Score = 31.5 bits (72), Expect = 0.39
 Identities = 19/48 (39%), Positives = 21/48 (43%), Gaps = 8/48 (16%)

Query: 72  IYGPESSGKTTLALHTIAQSQKTGGTCAFV-----DAEH---ALDSIY 111
           I+GP  SGKTTL    +AQ QK GG   F        E    A    Y
Sbjct: 439 IFGPTGSGKTTLLNFLLAQMQKYGGMTIFAFDKDRGMEIFIRAFGGAY 486


>gnl|CDD|163051 TIGR02868, CydC, thiol reductant ABC exporter, CydC subunit.  The
           gene pair cydCD encodes an ABC-family transporter in
           which each gene contains an N-terminal membrane-spanning
           domain (pfam00664) and a C-terminal ATP-binding domain
           (pfam00005). In E. coli these genes were discovered as
           mutants which caused the terminal heme-copper oxidase
           complex cytochrome bd to fail to assemble. Recent work
           has shown that the transporter is involved in export of
           redox-active thiol compounds such as cysteine and
           glutathione. The linkage to assembly of the cytochrome
           bd complex is further supported by the conserved operon
           structure found outside the gammaproteobacteria
           (cydABCD) containing both the transporter and oxidase
           genes components. The genes used as the seed members for
           this model are all either found in the
           gammproteobacterial context or the CydABCD context. All
           members of this family scoring above trusted at the time
           of its creation were from genomes which encode a
           cytochrome bd complex.
          Length = 529

 Score = 30.8 bits (70), Expect = 0.54
 Identities = 34/145 (23%), Positives = 53/145 (36%), Gaps = 41/145 (28%)

Query: 65  PKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDSIYARKLGVDLK---- 120
           P G  V I GP  SGK+TL L  +       G    +  E  LD +    L  +L+    
Sbjct: 359 PPGERVAILGPSGSGKSTL-LMLLT------GLLDPLQGEVTLDGVSVSSLQDELRRRIS 411

Query: 121 ---------------NLLISQPDTGEQALEITDMLVRSGAVDIIVIDSVAALTPRAEIE- 164
                          NL + +PD  ++  E+   L R G  D +      +L    +   
Sbjct: 412 VFAQDAHLFDTTVRDNLRLGRPDATDE--ELWAALERVGLADWL-----RSLPDGLDTVL 464

Query: 165 GDMGESLPGMQAR-------LMSQA 182
           G+ G  L G + +       L++ A
Sbjct: 465 GEGGARLSGGERQRLALARALLADA 489


>gnl|CDD|183515 PRK12415, PRK12415, fructose 1,6-bisphosphatase II; Reviewed.
          Length = 322

 Score = 30.9 bits (70), Expect = 0.59
 Identities = 19/47 (40%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 23  IQRVYGKGAIMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRI 69
           I RV  KGA ++L   G +   I     G+ G+D+ +GIGG P+G I
Sbjct: 171 IDRVRAKGARVKLFGDGDVGASIATALPGT-GIDLFVGIGGAPEGVI 216


>gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated.
          Length = 234

 Score = 30.3 bits (69), Expect = 0.74
 Identities = 30/137 (21%), Positives = 56/137 (40%), Gaps = 18/137 (13%)

Query: 45  IEVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAE 104
            E++S+G+  LD  LG GG P   ++ I G   +GK+ L+   +  + K G     +  E
Sbjct: 4   KEIISTGNEELDRKLG-GGIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITTE 62

Query: 105 HALDSIYA--RKLGVDLKNLLIS---------------QPDTGEQALEITDMLVRSGAVD 147
           +   S       + +D+ +  +                      + LE+    ++S   D
Sbjct: 63  NTSKSYLKQMESVKIDISDFFLWGYLRIFPLNTEGFEWNSTLANKLLELIIEFIKSKRED 122

Query: 148 IIVIDSVAALTPRAEIE 164
           +I+IDS+      AE +
Sbjct: 123 VIIIDSLTIFATYAEED 139


>gnl|CDD|163294 TIGR03499, FlhF, flagellar biosynthetic protein FlhF. 
          Length = 282

 Score = 30.0 bits (68), Expect = 0.94
 Identities = 25/106 (23%), Positives = 39/106 (36%), Gaps = 30/106 (28%)

Query: 64  FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHA-----LDS--------- 109
             +G ++ + GP   GKTT    T+A   K                   D+         
Sbjct: 191 LEQGGVIALVGPTGVGKTT----TLA---KLAARFVLEHGNKKVALITTDTYRIGAVEQL 243

Query: 110 -IYARKLGVDLKNLLISQPDTGEQALEITDMLVRSGAVDIIVIDSV 154
             YA+ LGV +K  +   P    +AL+      R    D+I+ID+ 
Sbjct: 244 KTYAKILGVPVK--VARDPKELRKALD------RLRDKDLILIDTA 281


>gnl|CDD|162636 TIGR01978, sufC, FeS assembly ATPase SufC.  SufC is part of the SUF
           system, shown in E. coli to consist of six proteins and
           believed to act in Fe-S cluster formation during
           oxidative stress. SufC forms a complex with SufB and
           SufD. SufC belongs to the ATP-binding cassette
           transporter family (pfam00005) but is no longer thought
           to be part of a transporter. The complex is reported as
           cytosolic (PubMed:12554644) or associated with the
           membrane (PubMed:11943156). The SUF system also includes
           a cysteine desulfurase (SufS, enhanced by SufE) and a
           probable iron-sulfur cluster assembly scaffold protein,
           SufA.
          Length = 243

 Score = 29.9 bits (68), Expect = 1.0
 Identities = 18/39 (46%), Positives = 20/39 (51%), Gaps = 4/39 (10%)

Query: 65  PKGRIVEIYGPESSGKTTLALHTIAQSQK---TGGTCAF 100
            KG I  I GP  SGK+TL+  TIA       T GT  F
Sbjct: 24  KKGEIHAIMGPNGSGKSTLS-KTIAGHPSYEVTSGTILF 61


>gnl|CDD|132302 TIGR03258, PhnT, 2-aminoethylphosphonate ABC transport system,
           ATP-binding component PhnT.  This ATP-binding component
           of an ABC transport system is found in Salmonella and
           Burkholderia lineages in the vicinity of enzymes for the
           breakdown of 2-aminoethylphosphonate.
          Length = 362

 Score = 29.6 bits (66), Expect = 1.2
 Identities = 20/89 (22%), Positives = 35/89 (39%), Gaps = 6/89 (6%)

Query: 36  GSQGSIFEGIEVVSSGSLGLD-IALGIGGFPKGRIVEIYGPESSGKTTL--ALHTIAQSQ 92
              G   + + V    +  LD ++L I     G ++ + G    GKTTL  A+    ++ 
Sbjct: 2   ACGGIRIDHLRVAYGANTVLDDLSLEIEA---GELLALIGKSGCGKTTLLRAIAGFVKAA 58

Query: 93  KTGGTCAFVDAEHALDSIYARKLGVDLKN 121
              G  A  D +      + R L +  +N
Sbjct: 59  GLTGRIAIADRDLTHAPPHKRGLALLFQN 87


>gnl|CDD|181229 PRK08099, PRK08099, bifunctional DNA-binding transcriptional
           repressor/ NMN adenylyltransferase; Provisional.
          Length = 399

 Score = 29.6 bits (67), Expect = 1.3
 Identities = 11/16 (68%), Positives = 12/16 (75%)

Query: 68  RIVEIYGPESSGKTTL 83
           R V I G ESSGK+TL
Sbjct: 220 RTVAILGGESSGKSTL 235


>gnl|CDD|183331 PRK11831, PRK11831, putative ABC transporter ATP-binding protein
          YrbF; Provisional.
          Length = 269

 Score = 29.3 bits (66), Expect = 1.4
 Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 3/28 (10%)

Query: 56 DIALGIGGFPKGRIVEIYGPESSGKTTL 83
          +I+L +   P+G+I  I GP   GKTTL
Sbjct: 25 NISLTV---PRGKITAIMGPSGIGKTTL 49


>gnl|CDD|163431 TIGR03719, ABC_ABC_ChvD, ATP-binding cassette protein, ChvD family.
            Members of this protein family have two copies of the
           ABC transporter ATP-binding cassette, but are found
           outside the common ABC transporter operon structure that
           features integral membrane permease proteins and
           substrate-binding proteins encoded next to the
           ATP-binding cassette (ABC domain) protein. The member
           protein ChvD from Agrobacterium tumefaciens was
           identified as both a candidate to interact with VirB8,
           based on yeast two-hybrid analysis, and as an apparent
           regulator of VirG. The general function of this protein
           family is unknown.
          Length = 552

 Score = 29.5 bits (67), Expect = 1.5
 Identities = 10/19 (52%), Positives = 13/19 (68%)

Query: 65  PKGRIVEIYGPESSGKTTL 83
           P G IV + GP  +GK+TL
Sbjct: 346 PPGGIVGVIGPNGAGKSTL 364


>gnl|CDD|183324 PRK11819, PRK11819, putative ABC transporter ATP-binding protein;
           Reviewed.
          Length = 556

 Score = 28.9 bits (66), Expect = 1.8
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 65  PKGRIVEIYGPESSGKTTL 83
           P G IV I GP  +GK+TL
Sbjct: 348 PPGGIVGIIGPNGAGKSTL 366


>gnl|CDD|177441 PHA02624, PHA02624, large T antigen; Provisional.
          Length = 647

 Score = 29.2 bits (66), Expect = 1.9
 Identities = 12/20 (60%), Positives = 13/20 (65%)

Query: 65  PKGRIVEIYGPESSGKTTLA 84
           PK R     GP +SGKTTLA
Sbjct: 429 PKRRYWLFKGPVNSGKTTLA 448


>gnl|CDD|131688 TIGR02640, gas_vesic_GvpN, gas vesicle protein GvpN.  Members of
          this family are the GvpN protein associated with the
          production of gas vesicles produced in some prokaryotes
          to give cells buoyancy. This family belongs to a larger
          family of ATPases (pfam07728).
          Length = 262

 Score = 29.0 bits (65), Expect = 2.0
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 67 GRIVEIYGPESSGKTTLALHTIAQ 90
          G  V + GP  +GKTTLA+H   +
Sbjct: 21 GYPVHLRGPAGTGKTTLAMHVARK 44


>gnl|CDD|183521 PRK12422, PRK12422, chromosomal replication initiation protein;
           Provisional.
          Length = 445

 Score = 29.0 bits (65), Expect = 2.0
 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 61  IGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAE 104
             GFP   I  ++GPE SGKT L    +   +++GG   +V +E
Sbjct: 136 GKGFPFNPIY-LFGPEGSGKTHLMQAAVHALRESGGKILYVRSE 178


>gnl|CDD|130234 TIGR01166, cbiO, cobalt transport protein ATP-binding subunit.
          This model describes the ATP binding subunit of the
          multisubunit cobalt transporter in bacteria and its
          equivalents in archaea. The model is restricted to ATP
          subunit that is a part of the cobalt transporter, which
          belongs to the ABC transporter superfamily (ATP Binding
          Cassette). The model excludes ATP binding subunit that
          are associated with other transporters belonging to ABC
          transporter superfamily. This superfamily includes two
          groups, one which catalyze the uptake of small
          molecules, including ions from the external milieu and
          the other group which is engaged in the efflux of small
          molecular weight compounds and ions from within the
          cell. Energy derived from the hydrolysis of ATP drive
          the both the process of uptake and efflux.
          Length = 190

 Score = 28.9 bits (65), Expect = 2.3
 Identities = 9/34 (26%), Positives = 16/34 (47%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGT 97
            +G ++ + G   +GK+TL LH     +   G 
Sbjct: 15 AERGEVLALLGANGAGKSTLLLHLNGLLRPQSGA 48


>gnl|CDD|130041 TIGR00968, 3a0106s01, sulfate ABC transporter, ATP-binding
          protein. 
          Length = 237

 Score = 28.6 bits (64), Expect = 2.7
 Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 4/34 (11%)

Query: 56 DIALGIGGFPKGRIVEIYGPESSGKTTLALHTIA 89
          D+ L +   P G +V + GP  SGK+TL L  IA
Sbjct: 18 DVNLEV---PTGSLVALLGPSGSGKSTL-LRIIA 47


>gnl|CDD|184797 PRK14703, PRK14703, glutaminyl-tRNA synthetase/YqeY domain fusion
           protein; Provisional.
          Length = 771

 Score = 28.5 bits (64), Expect = 3.1
 Identities = 18/75 (24%), Positives = 29/75 (38%), Gaps = 20/75 (26%)

Query: 65  PKGRIVEI---YGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDS---IYARKLGVD 118
             G + E+   Y PES+             +K  G   +V A+HAL +   +Y R   V 
Sbjct: 434 ADGAVTELRCTYDPESAKGE-------DTGRKAAGVIHWVSAKHALPAEVRLYDRLFKVP 486

Query: 119 LKNLLISQPDTGEQA 133
                  QP+  ++ 
Sbjct: 487 -------QPEAADED 494


>gnl|CDD|184199 PRK13639, cbiO, cobalt transporter ATP-binding subunit;
          Provisional.
          Length = 275

 Score = 28.5 bits (64), Expect = 3.1
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 66 KGRIVEIYGPESSGKTTLALH 86
          KG +V + GP  +GK+TL LH
Sbjct: 27 KGEMVALLGPNGAGKSTLFLH 47


>gnl|CDD|163352 TIGR03608, L_ocin_972_ABC, putative bacteriocin export ABC
          transporter, lactococcin 972 group.  A gene pair with a
          fairly wide distribution consists of a polypeptide
          related to the lactococcin 972 (see TIGR01653) and
          multiple-membrane-spanning putative immunity protein
          (see TIGR01654). This model represents a small clade
          within the ABC transporters that regularly are found
          adjacent to these bacteriocin system gene pairs and are
          likely serve as export proteins.
          Length = 206

 Score = 28.0 bits (63), Expect = 3.6
 Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIA 89
            KG++  I G   SGK+TL L+ I 
Sbjct: 21 IEKGKMYAIIGESGSGKSTL-LNIIG 45


>gnl|CDD|180615 PRK06547, PRK06547, hypothetical protein; Provisional.
          Length = 172

 Score = 28.2 bits (63), Expect = 3.6
 Identities = 10/17 (58%), Positives = 10/17 (58%)

Query: 68 RIVEIYGPESSGKTTLA 84
            V I G   SGKTTLA
Sbjct: 16 ITVLIDGRSGSGKTTLA 32


>gnl|CDD|132639 TIGR03600, phage_DnaB, phage replicative helicase, DnaB family,
           HK022 subfamily.  Members of this family are phage (or
           prophage-region) homologs of the bacterial homohexameric
           replicative helicase DnaB. Some phage may rely on host
           DnaB, while others encode their own verions. This model
           describes the largest phage-specific clade among the
           close homologs of DnaB, but there are, or course, other
           DnaB homologs from phage that fall outside the scope of
           this model.
          Length = 421

 Score = 28.1 bits (63), Expect = 3.7
 Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 48  VSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQ--SQKTGGTCAFVDAEH 105
           +S+G   LD      G  KG ++ I    S GKTTLAL  IA+  + + G    F   E 
Sbjct: 177 LSTGLPKLDRL--TNGLVKGDLIVIGARPSMGKTTLAL-NIAENVALREGKPVLFFSLEM 233

Query: 106 ALDSIYARKLG 116
           + + +  R L 
Sbjct: 234 SAEQLGERLLA 244


>gnl|CDD|172753 PRK14265, PRK14265, phosphate ABC transporter ATP-binding
          protein; Provisional.
          Length = 274

 Score = 28.1 bits (62), Expect = 3.8
 Identities = 19/47 (40%), Positives = 26/47 (55%), Gaps = 6/47 (12%)

Query: 40 SIF--EGIEVVSSGSLGL-DIALGIGGFPKGRIVEIYGPESSGKTTL 83
          S+F  EG++V   G L L D+ L I   P  +I+   GP   GK+TL
Sbjct: 19 SVFEVEGVKVFYGGFLALVDVHLKI---PAKKIIAFIGPSGCGKSTL 62


>gnl|CDD|162243 TIGR01189, ccmA, heme ABC exporter, ATP-binding protein CcmA.  This
           model describes the cyt c biogenesis protein encoded by
           ccmA in bacteria. An exception is, an arabidopsis
           protein. Quite likely this is encoded by an organelle.
           Bacterial c-type cytocromes are located on the
           periplasmic side of the cytoplasmic membrane. Several
           gene products encoded in a locus designated as 'ccm' are
           implicated in the transport and assembly of the
           functional cytochrome C. This cluster includes genes:
           ccmA;B;C;D;E;F;G and H. The posttranslational pathway
           includes the transport of heme moiety, the secretion of
           the apoprotein and the covalent attachment of the heme
           with the apoprotein. The proteins ccmA and B represent
           an ABC transporter; ccmC and D participate in heme
           transfer to ccmE, which function as a periplasmic heme
           chaperone. The presence of ccmF, G and H is suggested to
           be obligatory for the final functional assembly of
           cytochrome c.
          Length = 198

 Score = 28.1 bits (63), Expect = 3.9
 Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 67  GRIVEIYGPESSGKTTLALHTIAQ-SQKTGGTCAFVDAEHA 106
           G  +++ GP   GKTTL L  +A   +   G   +     A
Sbjct: 26  GEALQVTGPNGIGKTTL-LRILAGLLRPDSGEVRWNGTALA 65


>gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated.
          Length = 233

 Score = 27.9 bits (62), Expect = 3.9
 Identities = 32/120 (26%), Positives = 57/120 (47%), Gaps = 20/120 (16%)

Query: 74  GPESSGKTTLALHTIAQSQKTGGTCAFVDAE-------HALDSIYARKLGVDLKNLLISQ 126
           GP  +GKT LAL   A +++ G + A++  +        AL+++  R L V L  L   +
Sbjct: 48  GPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAAGRLRDALEALEGRSL-VALDGL---E 103

Query: 127 PDTGEQALEIT--DMLVRSGAVDIIVIDSVAALTPRAEIEGDMGESLPGMQARLMSQALR 184
              G++  E+   D   R+ A  I ++      T R  +   +   LP +++RL +Q +R
Sbjct: 104 SIAGQREDEVALFDFHNRARAAGITLL-----YTARQ-MPDGLALVLPDLRSRL-AQCIR 156


>gnl|CDD|163196 TIGR03265, PhnT2, putative 2-aminoethylphosphonate ABC
          transporter, ATP-binding protein.  This ABC transporter
          ATP-binding protein is found in a number of genomes in
          operon-like contexts strongly suggesting a substrate
          specificity for 2-aminoethylphosphonate (2-AEP). The
          characterized PhnSTUV system is absent in the genomes
          in which this system is found. These genomes encode
          systems for the catabolism of 2-AEP, making the need
          for a 2-AEP-specific transporter likely.
          Length = 353

 Score = 28.1 bits (63), Expect = 4.1
 Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 4/34 (11%)

Query: 56 DIALGIGGFPKGRIVEIYGPESSGKTTLALHTIA 89
          DI+L +    KG  V + GP   GKTTL L  IA
Sbjct: 22 DISLSVK---KGEFVCLLGPSGCGKTTL-LRIIA 51


>gnl|CDD|180863 PRK07165, PRK07165, F0F1 ATP synthase subunit alpha; Validated.
          Length = 507

 Score = 28.0 bits (63), Expect = 4.1
 Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 46  EVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFV 101
           E + +G + +D+ + IG   KG+   I G   +GKT +AL+TI   + T   C +V
Sbjct: 125 EQLYTGIIAIDLLIPIG---KGQRELIIGDRQTGKTHIALNTIINQKNTNVKCIYV 177


>gnl|CDD|116561 pfam07951, Toxin_R_bind_C, Clostridium neurotoxin, C-terminal
           receptor binding.  The Clostridium neurotoxin family is
           composed of tetanus neurotoxins and seven serotypes of
           botulinum neurotoxin. The structure of the botulinum
           neurotoxin reveals a four domain protein. The N-terminal
           catalytic domain (pfam01742), the central translocation
           domains and two receptor binding domains. This domains
           is the C-terminal receptor binding domain, which adopts
           a modified beta-trefoil fold with a six stranded
           beta-barrel and a beta-hairpin triplet capping the
           domain. The first step in the intoxication process is a
           binding event between this domains and the pre-synaptic
           nerve ending.
          Length = 209

 Score = 27.8 bits (62), Expect = 4.8
 Identities = 15/89 (16%), Positives = 31/89 (34%), Gaps = 8/89 (8%)

Query: 212 GSPETTTGGNALKFYSSVRLDIRRVGSIKDKDSITGNQTRVK---VVKNK-----MASPF 263
           G+       N    Y  ++  I+RV    + D+       +    V+ NK       +  
Sbjct: 49  GTIVFNIYLNYRDLYEGLKFIIKRVSDNSNNDNRVRKGDYIYLNVVINNKEYRLYAYATS 108

Query: 264 KQVEFDIMYGEGISFFGELIDLGVKASIV 292
           K  +  ++Y   +S   + I+  +   I 
Sbjct: 109 KSEKEKLIYALRLSSSNDNINQYIVMQIK 137


>gnl|CDD|179763 PRK04171, PRK04171, ribosome biogenesis protein; Provisional.
          Length = 222

 Score = 27.6 bits (62), Expect = 5.0
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 51  GSLGLDIALGIGGFPKG 67
           G    +IA+GIGGFP G
Sbjct: 165 GKENENIAVGIGGFPHG 181


>gnl|CDD|162555 TIGR01842, type_I_sec_PrtD, type I secretion system ABC
           transporter, PrtD family.  Type I protein secretion is a
           system in some Gram-negative bacteria to export proteins
           (often proteases) across both inner and outer membranes
           to the extracellular medium. This is one of three
           proteins of the type I secretion apparatus. Targeted
           proteins are not cleaved at the N-terminus, but rather
           carry signals located toward the extreme C-terminus to
           direct type I secretion.
          Length = 544

 Score = 27.7 bits (62), Expect = 5.5
 Identities = 10/20 (50%), Positives = 12/20 (60%)

Query: 65  PKGRIVEIYGPESSGKTTLA 84
             G  + I GP  SGK+TLA
Sbjct: 342 QAGEALAIIGPSGSGKSTLA 361


>gnl|CDD|181459 PRK08533, PRK08533, flagellar accessory protein FlaH; Reviewed.
          Length = 230

 Score = 27.3 bits (61), Expect = 5.6
 Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)

Query: 55 LDIALGIGGFPKGRIVEIYGPESSGKTTLAL 85
          L   LG GG P G ++ I G ES+GK+ L+ 
Sbjct: 13 LHKRLG-GGIPAGSLILIEGDESTGKSILSQ 42


>gnl|CDD|183063 PRK11264, PRK11264, putative amino-acid ABC transporter
          ATP-binding protein YecC; Provisional.
          Length = 250

 Score = 27.4 bits (61), Expect = 5.7
 Identities = 11/18 (61%), Positives = 12/18 (66%)

Query: 66 KGRIVEIYGPESSGKTTL 83
           G +V I GP  SGKTTL
Sbjct: 28 PGEVVAIIGPSGSGKTTL 45


>gnl|CDD|128807 smart00534, MUTSac, ATPase domain of DNA mismatch repair MUTS
           family. 
          Length = 185

 Score = 27.5 bits (62), Expect = 5.8
 Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 11/54 (20%)

Query: 72  IYGPESSGKTTLALHTIAQSQ---KTGGTCAFVDAEHA----LDSIYARKLGVD 118
           I GP   GK+T  L  +       + G   +FV AE A     D I+ R    D
Sbjct: 4   ITGPNMGGKSTY-LRQVGLIVIMAQIG---SFVPAESAELPVFDRIFTRIGASD 53


>gnl|CDD|181906 PRK09493, glnQ, glutamine ABC transporter ATP-binding protein;
           Reviewed.
          Length = 240

 Score = 27.4 bits (61), Expect = 6.3
 Identities = 20/58 (34%), Positives = 24/58 (41%), Gaps = 14/58 (24%)

Query: 56  DIALGIGGFPKGRIVEIYGPESSGKTTL-----ALHTIAQSQKTGGTCAFVDAEHALD 108
           +I L I    +G +V I GP  SGK+TL      L  I     T G    VD     D
Sbjct: 19  NIDLNID---QGEVVVIIGPSGSGKSTLLRCINKLEEI-----TSGDL-IVDGLKVND 67


>gnl|CDD|131197 TIGR02142, modC_ABC, molybdenum ABC transporter, ATP-binding
          protein.  This model represents the ATP-binding
          cassette (ABC) protein of the three subunit molybdate
          ABC transporter. The three proteins of this complex are
          homologous to proteins of the sulfate ABC transporter.
          Molybdenum may be used in nitrogenases of
          nitrogen-fixing bacteria and in molybdopterin
          cofactors. In some cases, molybdate may be transported
          by a sulfate transporter rather than by a specific
          molybdate transporter.
          Length = 354

 Score = 27.4 bits (61), Expect = 6.7
 Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 4/39 (10%)

Query: 51 GSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIA 89
          G   LD    +   P   +  I+G   SGKTTL +  IA
Sbjct: 10 GDFSLDADFTL---PGQGVTAIFGRSGSGKTTL-IRLIA 44


>gnl|CDD|150847 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
          3.  This is a family of conserved proteins which were
          originally described as death-associated-protein-3
          (DAP-3). The proteins carry a P-loop DNA-binding motif,
          and induce apoptosis. DAP3 has been shown to be a
          pro-apoptotic factor in the mitochondrial matrix and to
          be crucial for mitochondrial biogenesis and so has also
          been designated as MRP-S29 (mitochondrial ribosomal
          protein subunit 29).
          Length = 274

 Score = 27.2 bits (61), Expect = 7.1
 Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 1/25 (4%)

Query: 65 PKGRIVEIYGPESSGKTTLALHTIA 89
             R V + G   SGK+ L    +A
Sbjct: 22 KVVRFV-LTGERGSGKSVLLAQAMA 45


>gnl|CDD|106587 PRK13644, cbiO, cobalt transporter ATP-binding subunit;
          Provisional.
          Length = 274

 Score = 26.9 bits (59), Expect = 7.5
 Identities = 12/24 (50%), Positives = 14/24 (58%)

Query: 63 GFPKGRIVEIYGPESSGKTTLALH 86
             KG  + I G   SGK+TLALH
Sbjct: 24 VIKKGEYIGIIGKNGSGKSTLALH 47


>gnl|CDD|183044 PRK11231, fecE, iron-dicitrate transporter ATP-binding subunit;
          Provisional.
          Length = 255

 Score = 26.9 bits (60), Expect = 7.6
 Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 1/26 (3%)

Query: 64 FPKGRIVEIYGPESSGKTTLALHTIA 89
           P G+I  + GP   GK+TL L   A
Sbjct: 25 LPTGKITALIGPNGCGKSTL-LKCFA 49


>gnl|CDD|130045 TIGR00972, 3a0107s01c2, phosphate ABC transporter, ATP-binding
          protein.  This model represents the ATP-binding protein
          of a family of ABC transporters for inorganic
          phosphate. In the model species Escherichia coli, a
          constitutive transporter for inorganic phosphate, with
          low affinity, is also present. The high affinity
          transporter that includes this polypeptide is induced
          when extracellular phosphate concentrations are low.
          The proteins most similar to the members of this family
          but not included appear to be amino acid transporters.
          Length = 247

 Score = 26.9 bits (60), Expect = 7.9
 Identities = 8/21 (38%), Positives = 12/21 (57%)

Query: 63 GFPKGRIVEIYGPESSGKTTL 83
            PK ++  + GP   GK+TL
Sbjct: 23 DIPKNQVTALIGPSGCGKSTL 43


>gnl|CDD|178685 PLN03140, PLN03140, ABC transporter G family member; Provisional.
          Length = 1470

 Score = 27.1 bits (60), Expect = 7.9
 Identities = 11/19 (57%), Positives = 13/19 (68%)

Query: 67  GRIVEIYGPESSGKTTLAL 85
            R+  + GP SSGKTTL L
Sbjct: 191 SRMTLLLGPPSSGKTTLLL 209


>gnl|CDD|181207 PRK08043, PRK08043, bifunctional acyl-[acyl carrier protein]
           synthetase/2-acylglycerophosphoethanolamine
           acyltransferase; Validated.
          Length = 718

 Score = 27.0 bits (60), Expect = 8.7
 Identities = 13/27 (48%), Positives = 16/27 (59%)

Query: 154 VAALTPRAEIEGDMGESLPGMQARLMS 180
           V+   P A   G +G  LPGM ARL+S
Sbjct: 520 VSINVPMAAKPGTVGRILPGMDARLLS 546


>gnl|CDD|183133 PRK11432, fbpC, ferric transporter ATP-binding subunit;
           Provisional.
          Length = 351

 Score = 27.0 bits (60), Expect = 9.0
 Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 1/45 (2%)

Query: 65  PKGRIVEIYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEHALDS 109
            +G +V + GP   GKTT+ L  +A  +K      F+D E     
Sbjct: 30  KQGTMVTLLGPSGCGKTTV-LRLVAGLEKPTEGQIFIDGEDVTHR 73


>gnl|CDD|172418 PRK13898, PRK13898, type IV secretion system ATPase VirB4;
           Provisional.
          Length = 800

 Score = 26.7 bits (59), Expect = 9.0
 Identities = 15/47 (31%), Positives = 20/47 (42%), Gaps = 7/47 (14%)

Query: 72  IYGPESSGKTTLALHTIAQSQKTGGTCAFVDAEH-------ALDSIY 111
           I GP  +GKT L     AQ+ K      F D +        AL+ +Y
Sbjct: 451 IIGPTGAGKTVLMNFLCAQAMKFSPRMFFFDKDRGAEIFIRALNGVY 497


>gnl|CDD|181111 PRK07773, PRK07773, replicative DNA helicase; Validated.
          Length = 886

 Score = 26.6 bits (59), Expect = 9.0
 Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 6/60 (10%)

Query: 32  IMQLGSQGSIFEGIEVVSSGSLGLDIALGIGGFPKGRIVEIYGPESSGKTTLALHTIAQS 91
           I  + S G +  G   V +G   LD A+   G   G+++ +    S GKTT  L   A++
Sbjct: 187 IDAIASSGGLARG---VPTGFTELD-AM-TNGLHPGQLIIVAARPSMGKTTFGL-DFARN 240


>gnl|CDD|179813 PRK04296, PRK04296, thymidine kinase; Provisional.
          Length = 190

 Score = 26.6 bits (60), Expect = 9.1
 Identities = 8/19 (42%), Positives = 12/19 (63%)

Query: 67 GRIVEIYGPESSGKTTLAL 85
           ++  IYG  +SGK+T  L
Sbjct: 2  AKLEFIYGAMNSGKSTELL 20


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.316    0.134    0.365 

Gapped
Lambda     K      H
   0.267   0.0669    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,801,923
Number of extensions: 381683
Number of successful extensions: 1109
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1093
Number of HSP's successfully gapped: 115
Length of query: 363
Length of database: 5,994,473
Length adjustment: 95
Effective length of query: 268
Effective length of database: 3,941,713
Effective search space: 1056379084
Effective search space used: 1056379084
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.2 bits)