RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780766|ref|YP_003065179.1| recombination protein F
[Candidatus Liberibacter asiaticus str. psy62]
         (375 letters)



>gnl|CDD|178835 PRK00064, recF, recombination protein F; Reviewed.
          Length = 361

 Score =  344 bits (886), Expect = 2e-95
 Identities = 124/365 (33%), Positives = 191/365 (52%), Gaps = 13/365 (3%)

Query: 7   IKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTR 66
           +  L++++FRNY  L L       + VG+NG GKTN+LEAI  L+PGR  R A   ++ R
Sbjct: 3   LTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAIYLLAPGRSHRTARDKELIR 62

Query: 67  IGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLV 126
            G+ +      RVE       + ++++ +  R VR   IN    R + EL   L +    
Sbjct: 63  FGAEAAV-IHGRVEKGGRELPLGLEIDKKGGRKVR---INGEPQRKLAELAGLLNVVLFT 118

Query: 127 PSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDSSWCSSI 186
           P   R+  G   ERRRFLDR++F I+P +   +  +ER ++ RN LL +   D +W    
Sbjct: 119 PEDLRLVKGGPSERRRFLDRLLFQIEPVYASALSQYERALKQRNALLKQA--DYAWLDVW 176

Query: 187 EAQMAELGVKINIARVEMINALSSLIMEYVQKEN--FPHIKLSLTGFLDGKFDQSFCALK 244
           + Q+AELG  I  AR+E +  L+ L  +  Q+ +  F    LS    +    +     ++
Sbjct: 177 DEQLAELGAAIAAARLEYLERLAPLAAKTHQEISPEFELASLSYQSSV----EDDAEKIE 232

Query: 245 EEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHA 304
           E+  + L   R+ D    RTL+GPHR DL     +       GSTG+QK++L+ + LA A
Sbjct: 233 EDLLEALAKNRERDRARGRTLVGPHRDDLRF-RINGLPAADFGSTGQQKLLLLALKLAEA 291

Query: 305 RLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVFDSLNETAKF 364
            L+   TG APILLLD++++ LD+ +R AL   +  +G+Q+F+T TD      L E AK 
Sbjct: 292 ELLKEETGEAPILLLDDVASELDDGRRAALLERLKGLGAQVFITTTDLEDLADLLENAKI 351

Query: 365 MRISN 369
             +  
Sbjct: 352 FHVEQ 356


>gnl|CDD|161957 TIGR00611, recf, recF protein.  All proteins in this family for
           which functions are known are DNA binding proteins that
           assist the filamentation of RecA onto DNA for the
           initiation of recombination or recombinational repair.
           This family is based on the phylogenomic analysis of JA
           Eisen (1999, Ph.D. Thesis, Stanford University).
          Length = 365

 Score =  151 bits (384), Expect = 2e-37
 Identities = 97/350 (27%), Positives = 165/350 (47%), Gaps = 13/350 (3%)

Query: 6   KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVT 65
            +  L +++FRNY ++ L       + VG NG GKTN+LEAI +L+ GR  R +    + 
Sbjct: 2   YLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAIYYLALGRSHRTSRDKPLI 61

Query: 66  RIGSPSFFSTFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWL 125
           R G+ +F     RV   +   +++I LE    +  +  ++N      + +L   L +   
Sbjct: 62  RFGAEAFV-IEGRVSKGDR--EVTIPLEGLLKKKGKKAKVNIDGQDKLSDLAGLLPMQLF 118

Query: 126 VPSMDRIFSGLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEG---YFDSSW 182
            P    +  G    RRRFLD  +F ++P +     D++R+++ RN  L +    Y D + 
Sbjct: 119 APEDLTLVKGSPKYRRRFLDWGLFQVEPVYLSAWSDYQRVLKQRNAALKQAQRQYGDRTT 178

Query: 183 CSSIEAQMAELGVKINIARVEMINALSSLIMEYVQKENFPHIKLSLTGFLDGKFDQSFCA 242
               ++Q+AELG K++  R E I  L     +  Q         SL+ F  G+       
Sbjct: 179 LEVWDSQLAELGAKVSAWRAEFIEKLEPEAQKAHQ--LLLPELESLSLFYRGELW----D 232

Query: 243 LKEEYAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLA 302
            + +YA+ L    + D     TL+GPHR DL     +        S G+ + + + + LA
Sbjct: 233 KETDYAEALARNFERDLERGYTLVGPHRDDLRF-RLNGLPVEDFASQGQLRSLALALRLA 291

Query: 303 HARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDK 352
              L+    G  PILLLD++++ LD+ +R  L  ++  +G Q+F+T    
Sbjct: 292 EGELLREEGGEYPILLLDDVASELDDQRRRLLAELLQSLGVQVFVTAISL 341


>gnl|CDD|184491 PRK14079, recF, recombination protein F; Provisional.
          Length = 349

 Score =  107 bits (268), Expect = 6e-24
 Identities = 94/339 (27%), Positives = 152/339 (44%), Gaps = 24/339 (7%)

Query: 15  FRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFS 74
           +RN A   L F    T  VG+N  GKTN+LEAI +L+          AD+ R G    + 
Sbjct: 11  YRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAI-YLALTGELPNGRLADLVRFGEGEAW- 68

Query: 75  TFARVEGMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDRIFS 134
             A VE   GL+    +LE       R L+++ V + +  EL +      + P    +  
Sbjct: 69  VHAEVETGGGLS----RLEVGLGPGRRELKLDGVRVSL-RELARLPGAVLIRPEDLELVL 123

Query: 135 GLSMERRRFLDRMVFAIDPRHRRRMIDFERLMRGRNRLLTEGYFDSSWCSSI-EAQMAEL 193
           G    RR +LDR++  +  R+   +  +ER ++ RN  L  G     W   + + ++ +L
Sbjct: 124 GPPEGRRAYLDRLLSRLSARYAALLSAYERAVQQRNAALKSG---GGWGLHVWDDELVKL 180

Query: 194 GVKINIARVEMINALSSLIME-YVQKENFPHIKLSLTGFLDGKFDQSFCALKEEYAKKLF 252
           G +I   R   +  LS L  E Y +  +   ++L L+               E Y   L 
Sbjct: 181 GDEIMALRRRALTRLSELAREAYAELGSRKPLRLELSESTAP----------EGYLAALE 230

Query: 253 DGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHARLISNTTG 312
             R  +     T++GPHR DL++    +     + S GE + V + + LA  RL+    G
Sbjct: 231 ARRAEELARGATVVGPHRDDLVLTLEGRPAH-RYASRGEARTVALALRLAEHRLLWEHFG 289

Query: 313 FAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTD 351
            AP+LL+D+ +A LD  +R AL  +   +  Q  + GT+
Sbjct: 290 EAPVLLVDDFTAELDPRRRGALLALAASL-PQAIVAGTE 327


>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
          Length = 880

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 25/68 (36%), Positives = 36/68 (52%), Gaps = 3/68 (4%)

Query: 5  IKIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAIS---FLSPGRGFRRASY 61
          +KI+ L I  FR++ S  + FD    + +G NG GK++ILEAI    +   G   +    
Sbjct: 1  MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILVGLYWGHGSKPKGLKK 60

Query: 62 ADVTRIGS 69
           D TRIG 
Sbjct: 61 DDFTRIGG 68


>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 = 35.8 bits (82), Expect = 0.018
 Identities = 24/142 (16%), Positives = 42/142 (29%), Gaps = 7/142 (4%)

Query: 28  QHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFARVEGMEGLAD 87
           +  + VG  G GKT +  A++      G     Y D   I           + G +  + 
Sbjct: 3   EVILIVGPPGSGKTTLARALARELGPPG-GGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61

Query: 88  ISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDRIFSGLSMERRRFLDRM 147
                  R   ++      DV+I  +DE+   L        +      L +  +   +  
Sbjct: 62  SGELRL-RLALALARKLKPDVLI--LDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLT 118

Query: 148 VFAIDPRHRRRMIDFERLMRGR 169
           V                L+R R
Sbjct: 119 VILT---TNDEKDLGPALLRRR 137


>gnl|CDD|177394 PHA02562, 46, endonuclease subunit; Provisional.
          Length = 562

 Score = 34.6 bits (80), Expect = 0.039
 Identities = 13/32 (40%), Positives = 20/32 (62%)

Query: 26 DAQHTIFVGDNGVGKTNILEAISFLSPGRGFR 57
            + T+  G NG GK+ +LEA++F   G+ FR
Sbjct: 26 KVKKTLITGKNGAGKSTMLEALTFALFGKPFR 57


>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
          Length = 895

 Score = 34.5 bits (79), Expect = 0.044
 Identities = 15/43 (34%), Positives = 24/43 (55%)

Query: 7  IKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISF 49
          IK + +  F ++    + FD    I  G NG GK++I++AI F
Sbjct: 3  IKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAIRF 45



 Score = 32.6 bits (74), Expect = 0.20
 Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 3/51 (5%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338
           S GE+  V   + +A A+ ++N       L++DE +A LDED+R  L  I+
Sbjct: 803 SGGEKTAVAFALRVAVAQFLNNDKSL---LIMDEPTAFLDEDRRTNLKDII 850


>gnl|CDD|169949 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed.
          Length = 402

 Score = 34.4 bits (79), Expect = 0.046
 Identities = 29/95 (30%), Positives = 40/95 (42%), Gaps = 34/95 (35%)

Query: 252 FDGRKMDSMSRRTLIGPHRS---------DLIVD----------YCDKAITIAHGSTGEQ 292
           FD R++  M R     PHRS            V+          + D+ +T   G  GE+
Sbjct: 92  FDVRQVVEMGRT----PHRSRFDTWTETDRAAVERAMERTGVAQFADRPVTSLSG--GER 145

Query: 293 KVVLVGIFLAHARLISNTTGFAPILLLDEISAHLD 327
           + VL+   LA A          P+LLLDE +A LD
Sbjct: 146 QRVLLARALAQA---------TPVLLLDEPTASLD 171



 Score = 28.3 bits (63), Expect = 3.3
 Identities = 13/24 (54%), Positives = 16/24 (66%), Gaps = 1/24 (4%)

Query: 33 VGDNGVGKTNILEAIS-FLSPGRG 55
          VG NG GKT +L AI+  L+P  G
Sbjct: 35 VGPNGAGKTTLLRAINGTLTPTAG 58


>gnl|CDD|161971 TIGR00634, recN, DNA repair protein RecN.  All proteins in this
           family for which functions are known are ATP binding
           proteins involved in the initiation of recombination and
           recombinational repair.
          Length = 563

 Score = 34.3 bits (79), Expect = 0.047
 Identities = 23/98 (23%), Positives = 36/98 (36%), Gaps = 11/98 (11%)

Query: 10  LNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGS 69
           L I+ F     L + F+   T+  G+ G GK+ I++A+S L   R       A   R G 
Sbjct: 5   LRINNFALIRVLTVEFERGLTVLTGETGAGKSMIIDALSLLGGQRA-----GASRVRSGE 59

Query: 70  PS------FFSTFARVEGMEGLADISIKLETRDDRSVR 101
                   F +          L  I ++ E  D   + 
Sbjct: 60  NRAVVEGRFTTESLDDADYPALQAIELEEEDEDGEVIL 97


>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
          Length = 880

 Score = 33.9 bits (78), Expect = 0.066
 Identities = 14/44 (31%), Positives = 23/44 (52%)

Query: 6  KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISF 49
          +   + +  F+ YA   L  +   T+  G NG GK+++LEA  F
Sbjct: 2  RFDRVRLENFKCYADADLRLEDGVTVIHGVNGSGKSSLLEACFF 45


>gnl|CDD|162740 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
           primarily archaeal type.  SMC (structural maintenance of
           chromosomes) proteins bind DNA and act in organizing and
           segregating chromosomes for partition. SMC proteins are
           found in bacteria, archaea, and eukaryotes. It is found
           in a single copy and is homodimeric in prokaryotes, but
           six paralogs (excluded from this family) are found in
           eukarotes, where SMC proteins are heterodimeric. This
           family represents the SMC protein of archaea and a few
           bacteria (Aquifex, Synechocystis, etc); the SMC of other
           bacteria is described by TIGR02168. The N- and
           C-terminal domains of this protein are well conserved,
           but the central hinge region is skewed in composition
           and highly divergent.
          Length = 1164

 Score = 33.9 bits (78), Expect = 0.076
 Identities = 29/128 (22%), Positives = 45/128 (35%), Gaps = 16/128 (12%)

Query: 6   KIKFLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISF---LSPGRGFRRASYA 62
           +I+  N   F       + F    T+  G NG GK+NI +AI F   LS  +  R    +
Sbjct: 4   RIELENFKSFGKKK--VIPFSKGFTVISGPNGSGKSNIGDAILFALGLSSSKAMRAERLS 61

Query: 63  DVTRIGSPSFFSTFARVE--------GMEGLADISIKLETRDDRSVRCLQINDVVIR--- 111
           D+   G        A V               ++  +L+  DD       +N   +R   
Sbjct: 62  DLISNGKNGQSGNEAYVTVTFKNDDGKFPDELEVVRRLKVTDDGKYSYYYLNGQRVRLSE 121

Query: 112 VVDELNKH 119
           + D L   
Sbjct: 122 IHDFLAAA 129


>gnl|CDD|162972 TIGR02680, TIGR02680, conserved hypothetical protein TIGR02680.
            Members of this protein family belong to a conserved gene
            four-gene neighborhood found sporadically in a
            phylogenetically broad range of bacteria: Nocardia
            farcinica, Symbiobacterium thermophilum, and Streptomyces
            avermitilis (Actinobacteria), Geobacillus kaustophilus
            (Firmicutes), Azoarcus sp. EbN1 and Ralstonia
            solanacearum (Betaproteobacteria). Proteins in this
            family average over 1400 amino acids in length.
          Length = 1353

 Score = 32.9 bits (75), Expect = 0.16
 Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 3/64 (4%)

Query: 288  STGEQKVVL-VGIFLA-HARLISNTTGFAP-ILLLDEISAHLDEDKRNALFRIVTDIGSQ 344
            S GE+ + L V +F A  +         AP ++LLDE  A +D++ R  LF ++  +   
Sbjct: 1249 SGGERALALYVPLFAAASSHYTQEAYPHAPRLILLDEAFAGVDDNARAHLFGLLRALDLD 1308

Query: 345  IFMT 348
              MT
Sbjct: 1309 FVMT 1312


>gnl|CDD|179632 PRK03695, PRK03695, vitamin B12-transporter ATPase; Provisional.
          Length = 248

 Score = 31.8 bits (73), Expect = 0.27
 Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 27/87 (31%)

Query: 288 STGE-QKVVLVGIFL-------AHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVT 339
           S GE Q+V L  + L          +L          LLLDE    LD  ++ AL R+++
Sbjct: 128 SGGEWQRVRLAAVVLQVWPDINPAGQL----------LLLDEPMNSLDVAQQAALDRLLS 177

Query: 340 DIGSQ---IFMTGTDKSVFDSLNETAK 363
           ++  Q   + M+  D      LN T +
Sbjct: 178 ELCQQGIAVVMSSHD------LNHTLR 198



 Score = 28.0 bits (63), Expect = 3.8
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 32 FVGDNGVGKTNILEAISFLSPGRG 55
           VG NG GK+ +L  ++ L PG G
Sbjct: 27 LVGPNGAGKSTLLARMAGLLPGSG 50


>gnl|CDD|162739 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
          bacterial type.  SMC (structural maintenance of
          chromosomes) proteins bind DNA and act in organizing
          and segregating chromosomes for partition. SMC proteins
          are found in bacteria, archaea, and eukaryotes. This
          family represents the SMC protein of most bacteria. The
          smc gene is often associated with scpB (TIGR00281) and
          scpA genes, where scp stands for segregation and
          condensation protein. SMC was shown (in Caulobacter
          crescentus) to be induced early in S phase but present
          and bound to DNA throughout the cell cycle.
          Length = 1179

 Score = 32.0 bits (73), Expect = 0.28
 Identities = 17/43 (39%), Positives = 28/43 (65%), Gaps = 1/43 (2%)

Query: 6  KIKFLNISEFRNYA-SLRLVFDAQHTIFVGDNGVGKTNILEAI 47
          ++K L ++ F+++A    + FD   T  VG NG GK+NI++AI
Sbjct: 1  RLKKLELAGFKSFADPTTINFDKGITGIVGPNGCGKSNIVDAI 43


>gnl|CDD|182331 PRK10247, PRK10247, putative ABC transporter ATP-binding protein
           YbbL; Provisional.
          Length = 225

 Score = 31.6 bits (72), Expect = 0.33
 Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 4/36 (11%)

Query: 306 LISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDI 341
           LI N      +LLLDEI++ LDE  +      V +I
Sbjct: 148 LIRNLQFMPKVLLLDEITSALDESNK----HNVNEI 179


>gnl|CDD|129694 TIGR00606, rad50, rad50.  This family is based on the
          phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
          Stanford University).
          Length = 1311

 Score = 31.6 bits (71), Expect = 0.36
 Identities = 12/24 (50%), Positives = 16/24 (66%)

Query: 30 TIFVGDNGVGKTNILEAISFLSPG 53
          TI VG NG GKT I+E + ++  G
Sbjct: 31 TILVGPNGAGKTTIIECLKYICTG 54


>gnl|CDD|163042 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit.
           Unfortunately, the gene symbol nomenclature adopted
           based on this operon in B. subtilis assigns cydC to the
           third gene in the operon where this gene is actually
           homologous to the E. coli cydD gene. We have chosen to
           name all homologs in this family in accordance with the
           precedence of publication of the E. coli name, CydD.
          Length = 529

 Score = 31.1 bits (71), Expect = 0.44
 Identities = 11/25 (44%), Positives = 16/25 (64%)

Query: 314 APILLLDEISAHLDEDKRNALFRIV 338
           AP+LLLDE +AHLD +    +   +
Sbjct: 477 APLLLLDEPTAHLDAETEALVTEAL 501


>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 = 0.53
 Identities = 17/37 (45%), Positives = 22/37 (59%), Gaps = 5/37 (13%)

Query: 301 LAHAR-LISNTTGFAPILLLDEISAHLDEDKRNALFR 336
           LA AR L+++    APILLLDE + HLD    + L  
Sbjct: 479 LALARALLAD----APILLLDEPTEHLDAGTESELLE 511


>gnl|CDD|129705 TIGR00618, sbcc, exonuclease SbcC.  This family is based on the
            phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
            Stanford University).
          Length = 1042

 Score = 29.6 bits (66), Expect = 1.4
 Identities = 29/101 (28%), Positives = 38/101 (37%), Gaps = 5/101 (4%)

Query: 252  FDGRKMDSMSRRTLIGPHRSDLIVD--YCDKAITIAHGSTGEQKVVLVGIFLAHARLISN 309
            F GR  DS             L+V   Y       A  S GE  +  + + LA A L+S 
Sbjct: 916  FHGRYADSHVNAR--KYQGLALLVADAYTGSVRPSATLSGGETFLASLSLALALADLLST 973

Query: 310  TTGFA-PILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTG 349
            + G     L +DE    LDED  +    I+  I     M G
Sbjct: 974  SGGTVLDSLFIDEGFGSLDEDSLDRAIGILDAIREGSKMIG 1014



 Score = 28.0 bits (62), Expect = 4.2
 Identities = 22/85 (25%), Positives = 34/85 (40%), Gaps = 13/85 (15%)

Query: 25  FDAQHTIFV--GDNGVGKTNILEAISFLSPGRGFRRASYADVTRIGSPSFFSTFARVEGM 82
           F A   IF+  G  G GKT +L+AI++   G+   R S    +                 
Sbjct: 22  FTALGPIFLICGKTGAGKTTLLDAITYALYGK-LPRRSEVIRSLNS-------LYAAPSE 73

Query: 83  EGLADISIKLET---RDDRSVRCLQ 104
              A++   L T   R  R++RC +
Sbjct: 74  AAFAELEFSLGTKIYRVHRTLRCTR 98


>gnl|CDD|184128 PRK13541, PRK13541, cytochrome c biogenesis protein CcmA;
           Provisional.
          Length = 195

 Score = 29.1 bits (65), Expect = 1.8
 Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 9/51 (17%)

Query: 288 STGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIV 338
           S+G QK+V      A ARLI+     + + LLDE+  +L ++ R+ L  ++
Sbjct: 125 SSGMQKIV------AIARLIA---CQSDLWLLDEVETNLSKENRDLLNNLI 166


>gnl|CDD|151518 pfam11073, NSs, Rift valley fever virus non structural protein
           (NSs) like.  This family contains several Phlebovirus
           non structural proteins which act as a major determinant
           of virulence by antagonising interferon beta gene
           expression.
          Length = 238

 Score = 29.2 bits (66), Expect = 2.0
 Identities = 30/142 (21%), Positives = 47/142 (33%), Gaps = 34/142 (23%)

Query: 155 HRRRMIDFERLMRGRNRLLTEGYFDSSW---CSSIEAQMAELGVKINIARVEMINALSSL 211
            R  + DF           + G F + W   CSS+     +            I  LS  
Sbjct: 48  SRPTLSDF----------YSVGEFPARWGPGCSSVTKPSTKF-------FDGTIEDLSRF 90

Query: 212 IMEYVQKENFPHIKLSL---TGFLDGKF-DQSFCALKEEYAKKLFDGRKMDSMSRRTLIG 267
            +E   +   P+IK +L    G+   +F + S     + Y        K D  ++   +G
Sbjct: 91  DIESFLRSCLPNIKKALSWPLGYPSLEFFELSNI---DSY--LFLWETKCDFATQILRMG 145

Query: 268 PHRSDLIVDYCDKAITIAHGST 289
              S L     D +I  AH   
Sbjct: 146 LQGSGL-----DDSIVEAHKKI 162


>gnl|CDD|182605 PRK10636, PRK10636, putative ABC transporter ATP-binding protein;
           Provisional.
          Length = 638

 Score = 28.6 bits (64), Expect = 3.0
 Identities = 12/19 (63%), Positives = 14/19 (73%)

Query: 316 ILLLDEISAHLDEDKRNAL 334
           +LLLDE + HLD D R AL
Sbjct: 451 LLLLDEPTNHLDLDMRQAL 469


>gnl|CDD|162958 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
           clpA. 
          Length = 731

 Score = 28.1 bits (63), Expect = 3.4
 Identities = 9/15 (60%), Positives = 11/15 (73%)

Query: 31  IFVGDNGVGKTNILE 45
           + VG+ GVGKT I E
Sbjct: 207 LLVGEPGVGKTAIAE 221


>gnl|CDD|181161 PRK07899, rpsA, 30S ribosomal protein S1; Reviewed.
          Length = 486

 Score = 28.1 bits (63), Expect = 3.5
 Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 21/71 (29%)

Query: 73  FSTFARVE-GMEGLADISIKLETRDDRSVRCLQINDVVIRVVDELNKHLRISWLVPSMDR 131
           F  F RVE G+EGL  IS       + + R +++ + V++V DE+         V  +D 
Sbjct: 307 FGAFVRVEEGIEGLVHIS-------ELAERHVEVPEQVVQVGDEV--------FVKVID- 350

Query: 132 IFSGLSMERRR 142
               + +ERRR
Sbjct: 351 ----IDLERRR 357


>gnl|CDD|130324 TIGR01257, rim_protein, retinal-specific rim ABC transporter.  This
           model describes the photoreceptor protein (rim protein)
           in eukaryotes. It is the member of ABC transporter
           superfamily. Rim protein is a membrane glycoprotein
           which is localized in the photoreceptor outer segment
           discs. Mutation/s in its genetic loci is implicated in
           the recessive Stargardt's disease.
          Length = 2272

 Score = 28.1 bits (62), Expect = 3.8
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 25  FDAQHTIFVGDNGVGKTNILEAISFLSP 52
           ++ Q T F+G NG GKT  L  ++ L P
Sbjct: 954 YENQITAFLGHNGAGKTTTLSILTGLLP 981


>gnl|CDD|161735 TIGR00157, TIGR00157, ribosome small subunit-dependent GTPase A.
           The Aquifex aeolicus ortholog is split into consecutive
           open reading frames. Consequently, this model was build
           in fragment mode (-f option).
          Length = 245

 Score = 28.1 bits (63), Expect = 3.9
 Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 4/49 (8%)

Query: 300 FLAHARLISNTTGFAPILLLDEISAHLDEDKRNALFRIVTDIGSQIFMT 348
           FL  A          PI++L++I    DED       I  +IG Q+ MT
Sbjct: 59  FLVVA----EAQNIEPIIVLNKIDLLDDEDMEKEQLDIYRNIGYQVLMT 103


>gnl|CDD|179591 PRK03545, PRK03545, putative arabinose transporter; Provisional.
          Length = 390

 Score = 27.9 bits (63), Expect = 4.6
 Identities = 12/29 (41%), Positives = 16/29 (55%)

Query: 299 IFLAHARLISNTTGFAPILLLDEISAHLD 327
           + LA A  I NTT F P+ LL +I+    
Sbjct: 12  VTLALAAFIFNTTEFVPVGLLSDIAQSFH 40


>gnl|CDD|128472 smart00175, RAB, Rab subfamily of small GTPases.  Rab GTPases are
          implicated in vesicle trafficking.
          Length = 164

 Score = 27.9 bits (63), Expect = 5.0
 Identities = 8/15 (53%), Positives = 13/15 (86%)

Query: 31 IFVGDNGVGKTNILE 45
          I +GD+GVGK+++L 
Sbjct: 4  ILIGDSGVGKSSLLS 18


>gnl|CDD|162147 TIGR00990, 3a0801s09, mitochondrial precursor proteins import
           receptor (72 kDa mitochondrial outermembrane protein)
           (mitochondrial import receptor for the ADP/ATP carrier)
           (translocase of outermembrane tom70). 
          Length = 615

 Score = 27.6 bits (61), Expect = 5.1
 Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 2/33 (6%)

Query: 221 FPHIKLSLTGFLDGKFDQSFCALKEEYAKKLFD 253
           F HI+L +T + +G    S    +    KK F 
Sbjct: 434 FSHIQLGVTQYKEGSIASSMATFRR--CKKNFP 464


>gnl|CDD|150993 pfam10412, TrwB_AAD_bind, Type IV secretion-system coupling
          protein DNA-binding domain.  The plasmid conjugative
          coupling protein TrwB forms hexamers from six
          structurally very similar protomers. This hexamer
          contains a central channel running from the cytosolic
          pole (made up by the AADs) to the membrane pole ending
          at the transmembrane pore shaped by 12 transmembrane
          helices, rendering an overall mushroom-like structure.
          The TrwB_AAD (all-alpha domain) domain appears to be
          the DNA-binding domain of the structure. TrwB, a basic
          integral inner-membrane nucleoside-triphosphate-binding
          protein, is the structural prototype for the type IV
          secretion system coupling proteins, a family of
          proteins essential for macromolecular transport between
          cells and export.
          Length = 386

 Score = 27.6 bits (62), Expect = 5.2
 Identities = 9/23 (39%), Positives = 12/23 (52%)

Query: 25 FDAQHTIFVGDNGVGKTNILEAI 47
           + QH + VG  G GKT  L  +
Sbjct: 13 SETQHILIVGTTGTGKTQALREL 35


>gnl|CDD|178861 PRK00098, PRK00098, GTPase RsgA; Reviewed.
          Length = 298

 Score = 27.5 bits (62), Expect = 5.7
 Identities = 11/39 (28%), Positives = 20/39 (51%)

Query: 9   FLNISEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAI 47
            L+  E      L+ +   + T+  G +GVGK+ +L A+
Sbjct: 146 ELSAKEGEGLDELKPLLAGKVTVLAGQSGVGKSTLLNAL 184


>gnl|CDD|149065 pfam07793, DUF1631, Protein of unknown function (DUF1631).  The
           members of this family are sequences derived from a
           group of hypothetical proteins expressed by certain
           bacterial species. The region concerned is approximately
           440 amino acid residues in length.
          Length = 729

 Score = 27.6 bits (62), Expect = 5.8
 Identities = 22/95 (23%), Positives = 38/95 (40%), Gaps = 26/95 (27%)

Query: 85  LADISIKLETRDDRSVRCL--QINDVVIRVVDELNKHLRISWLVPSMDRIFSGLSMERRR 142
           +A+  I     DD     L  +I ++V R+++E +              +F+ L  E + 
Sbjct: 407 IAEAGIGWGGDDDGLRDSLYAKIEEIVQRILNEFDDDP----------SLFAELLEEFQA 456

Query: 143 FLDRMVFAIDPRHR-----RRMIDFERLMRGRNRL 172
           FL++       R R     +R  + E    GR RL
Sbjct: 457 FLEQE------RRRSELVEQRTREAE---EGRARL 482


>gnl|CDD|180838 PRK07102, PRK07102, short chain dehydrogenase; Provisional.
          Length = 243

 Score = 27.6 bits (62), Expect = 6.3
 Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 2/51 (3%)

Query: 284 IAHGSTGEQKVVLVGIFLAHARLISNTTGFAPILLLDEISAHLDEDKRNAL 334
           IA G+ G+Q         A A     T    PI LL  ++   +      +
Sbjct: 82  IAVGTLGDQAACEAD--PALALREFRTNFEGPIALLTLLANRFEARGSGTI 130


>gnl|CDD|178142 PLN02527, PLN02527, aspartate carbamoyltransferase.
          Length = 306

 Score = 27.4 bits (61), Expect = 6.5
 Identities = 11/22 (50%), Positives = 14/22 (63%)

Query: 315 PILLLDEISAHLDEDKRNALFR 336
           P+  LDEI+  +D D R A FR
Sbjct: 265 PLPRLDEITTDVDSDPRAAYFR 286


>gnl|CDD|163250 TIGR03410, urea_trans_UrtE, urea ABC transporter, ATP-binding
          protein UrtE.  Members of this protein family are ABC
          transporter ATP-binding subunits associated with urea
          transport and metabolism. This protein is found in a
          conserved five-gene transport operon typically found
          adjacent to urease genes. It was shown in Cyanobacteria
          that disruption leads to the loss of high-affinity urea
          transport activity.
          Length = 230

 Score = 27.5 bits (62), Expect = 6.6
 Identities = 10/22 (45%), Positives = 14/22 (63%)

Query: 34 GDNGVGKTNILEAISFLSPGRG 55
          G NGVGKT +L+ +  L P + 
Sbjct: 33 GRNGVGKTTLLKTLMGLLPVKS 54


>gnl|CDD|183835 PRK12999, PRK12999, pyruvate carboxylase; Reviewed.
          Length = 1146

 Score = 27.4 bits (62), Expect = 7.1
 Identities = 10/37 (27%), Positives = 19/37 (51%), Gaps = 6/37 (16%)

Query: 57   RRASYADVTRIGSPSFFSTFARVEGMEGLADISIKLE 93
             R  Y DV+ + +P+FF       G+    +I +++E
Sbjct: 990  HREEYGDVSVLPTPTFF------YGLRPGEEIEVEIE 1020


>gnl|CDD|184037 PRK13409, PRK13409, putative ATPase RIL; Provisional.
          Length = 590

 Score = 27.1 bits (61), Expect = 7.3
 Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 5/42 (11%)

Query: 314 APILLLDEISAHLDEDKRNALFRIVTDIGSQIFMTGTDKSVF 355
           A + LLDE SAHLD ++R A+ + +     +      + +  
Sbjct: 472 ADLYLLDEPSAHLDVEQRLAVAKAI-----RRIAEEREATAL 508


>gnl|CDD|183531 PRK12447, PRK12447, histidinol dehydrogenase; Reviewed.
          Length = 426

 Score = 27.2 bits (61), Expect = 7.4
 Identities = 23/81 (28%), Positives = 34/81 (41%), Gaps = 13/81 (16%)

Query: 16  RNYASLRLVFDAQHT-IFVGDNGVGKTNIL---EAISF---LSPGRGFRRASYADVTRIG 68
            NY +L   F  + T +  GD  +G  ++L    A  +   L  G+  +  +Y  VT   
Sbjct: 336 TNYGAL---FLGERTNVAYGDKVIGTNHVLPTSGAARYTGGLWVGKFLKTVTYQRVTDEA 392

Query: 69  SPSF---FSTFARVEGMEGLA 86
           S       S   R+EG EG A
Sbjct: 393 SAEIGEYCSRLCRLEGFEGHA 413


>gnl|CDD|178337 PLN02736, PLN02736, long-chain acyl-CoA synthetase.
          Length = 651

 Score = 27.0 bits (60), Expect = 7.8
 Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 14/68 (20%)

Query: 247 YAKKLFDGRKMDSMSRRTLIGPHRSDLIVDYCDKAITIAHGSTGEQKVVLVGIFLAHARL 306
           Y+K L  GR     S +    P   D+        I    G+TG  K    G+ L H  L
Sbjct: 201 YSKLLAQGR----SSPQPFRPPKPEDV------ATICYTSGTTGTPK----GVVLTHGNL 246

Query: 307 ISNTTGFA 314
           I+N  G +
Sbjct: 247 IANVAGSS 254


>gnl|CDD|178657 PLN03110, PLN03110, Rab GTPase; Provisional.
          Length = 216

 Score = 27.2 bits (60), Expect = 7.9
 Identities = 9/14 (64%), Positives = 13/14 (92%)

Query: 31 IFVGDNGVGKTNIL 44
          + +GD+GVGK+NIL
Sbjct: 16 VLIGDSGVGKSNIL 29


>gnl|CDD|131499 TIGR02446, FadI, fatty oxidation complex, beta subunit FadI.  This
           subunit of the FadJI complex has acetyl-CoA
           C-acyltransferase (EC 2.3.1.16) activity, and is also
           known as beta-ketothiolase and fatty oxidation complex,
           beta subunit, and YfcY. This protein is almost always
           located adjacent to FadJ (TIGR02440). The FadJI complex
           is needed for anaerobic beta-oxidation of short-chain
           fatty acids in E. coli.
          Length = 430

 Score = 26.9 bits (59), Expect = 8.6
 Identities = 13/42 (30%), Positives = 17/42 (40%)

Query: 13  SEFRNYASLRLVFDAQHTIFVGDNGVGKTNILEAISFLSPGR 54
           S    YA LR  FD +H      N    T+   A+  +  GR
Sbjct: 242 STLAGYAKLRPAFDRKHGSVTAANSTPLTDGAAAVILMREGR 283


>gnl|CDD|184587 PRK14241, PRK14241, phosphate transporter ATP-binding protein;
          Provisional.
          Length = 258

 Score = 27.0 bits (60), Expect = 8.6
 Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 11/51 (21%)

Query: 1  MTNRIKIKFLNISEFRNYASLRLVFDAQHTI-------FVGDNGVGKTNIL 44
          M  RI +K LNI     Y S   V D    I       F+G +G GK+ +L
Sbjct: 1  MAKRIDVKDLNIY----YGSFHAVEDVNLNIEPRSVTAFIGPSGCGKSTVL 47


>gnl|CDD|162277 TIGR01271, CFTR_protein, cystic fibrosis transmembrane conductor
            regulator (CFTR).  The model describes the cystis
            fibrosis transmembrane conductor regulator (CFTR) in
            eukaryotes. The principal role of this protein is
            chloride ion conductance. The protein is predicted to
            consist of 12 transmembrane domains. Mutations or lesions
            in the genetic loci have been linked to the aetiology of
            asthma, bronchiectasis, chronic obstructive pulmonary
            disease etc. Disease-causing mutations have been studied
            by 36Cl efflux assays in vitro cell cultures and
            electrophysiology, all of which point to the impairment
            of chloride channel stability and not the biosynthetic
            processing per se.
          Length = 1490

 Score = 26.8 bits (59), Expect = 8.6
 Identities = 12/14 (85%), Positives = 12/14 (85%)

Query: 314  APILLLDEISAHLD 327
            A ILLLDE SAHLD
Sbjct: 1372 AKILLLDEPSAHLD 1385


>gnl|CDD|178622 PLN03073, PLN03073, ABC transporter F family; Provisional.
          Length = 718

 Score = 26.7 bits (59), Expect = 8.9
 Identities = 13/19 (68%), Positives = 13/19 (68%)

Query: 316 ILLLDEISAHLDEDKRNAL 334
           ILLLDE S HLD D   AL
Sbjct: 648 ILLLDEPSNHLDLDAVEAL 666


>gnl|CDD|182716 PRK10771, thiQ, thiamine transporter ATP-binding subunit;
           Provisional.
          Length = 232

 Score = 26.9 bits (60), Expect = 9.5
 Identities = 11/27 (40%), Positives = 16/27 (59%)

Query: 315 PILLLDEISAHLDEDKRNALFRIVTDI 341
           PILLLDE  + LD   R  +  +V+ +
Sbjct: 149 PILLLDEPFSALDPALRQEMLTLVSQV 175


>gnl|CDD|163455 TIGR03743, SXT_TraD, conjugative coupling factor TraD, SXT/TOL
           subfamily.  Members of this protein family are the
           putative conjugative coupling factor, TraD (or TraG),
           rather distantly related to the well-characterized TraD
           of the F plasmid. Members are associated with
           conjugative-transposon-like mobile genetic elements of
           the class that includes SXT, an antibiotic resistance
           transfer element in some Vibrio cholerae strains.
          Length = 634

 Score = 26.9 bits (60), Expect = 9.5
 Identities = 9/21 (42%), Positives = 13/21 (61%)

Query: 29  HTIFVGDNGVGKTNILEAISF 49
           HT+ +G  GVGKT + E +  
Sbjct: 178 HTLVLGTTGVGKTRLAELLIT 198


  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
   0.326    0.139    0.402 

Gapped
Lambda     K      H
   0.267   0.0746    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 6,245,335
Number of extensions: 421075
Number of successful extensions: 1383
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1369
Number of HSP's successfully gapped: 75
Length of query: 375
Length of database: 5,994,473
Length adjustment: 95
Effective length of query: 280
Effective length of database: 3,941,713
Effective search space: 1103679640
Effective search space used: 1103679640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.1 bits)