RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780171|ref|YP_003064584.1| ABC transporter membrane
spanning protein (amino acid) [Candidatus Liberibacter asiaticus str.
psy62]
         (398 letters)



>gnl|CDD|185062 PRK15107, PRK15107, glutamate/aspartate transport system permease
           GltK; Provisional.
          Length = 224

 Score = 86.8 bits (215), Expect = 8e-18
 Identities = 44/125 (35%), Positives = 80/125 (64%)

Query: 267 MSLYIALSCYTAAFIAEIVRSGLIAVPRGQMEAAIALGLTHRKATRLVLLPQAMRSIIPP 326
           +S  +A S + AA+ +EI+R+G+ ++ RGQ  AA+ALG+TH ++ +L++LPQA R+++P 
Sbjct: 98  ISAMVAFSMFEAAYYSEIIRAGIQSISRGQSSAALALGMTHWQSMKLIILPQAFRAMVPL 157

Query: 327 LTSQYLNLLKNSSLAVAVGFADLVSVGGTIINQTGQAIEIILIWMFIYLSLSIMIALFMN 386
           L +Q + L +++SL   +  AD      TI  + G  +E+IL   F+Y  +S+  +L ++
Sbjct: 158 LLTQGIVLFQDTSLVYVLSLADFFRTASTIGERDGTQVEMILFAGFVYFVISLSASLLVS 217

Query: 387 RLNAK 391
            L  +
Sbjct: 218 YLKKR 222



 Score = 42.9 bits (101), Expect = 1e-04
 Identities = 24/68 (35%), Positives = 39/68 (57%)

Query: 89  ILVGFVNTFWLAFSGMIPATIIGTLVGAGRLSANKLVAWICRVYVEVFRNIPPLVVIFFL 148
           +L G V T  +  + ++   + GT++   RLS+ K VAW  + YV VFR+IP ++V+ + 
Sbjct: 16  LLDGLVITLKITVTAVVIGILWGTILAVMRLSSFKPVAWFAKAYVNVFRSIPLVMVLLWF 75

Query: 149 YKSVLSVL 156
           Y  V   L
Sbjct: 76  YLIVPGFL 83


>gnl|CDD|132048 TIGR03003, ectoine_ehuD, ectoine/hydroxyectoine ABC transporter,
           permease protein EhuD.  Members of this family are
           presumed to act as permease subunits of ectoine ABC
           transporters. Operons containing this gene also contain
           the other genes of the ABC transporter and typically are
           found next to either ectoine utilization or ectoine
           biosynthesis operons.
          Length = 212

 Score = 82.6 bits (204), Expect = 2e-16
 Identities = 67/213 (31%), Positives = 108/213 (50%), Gaps = 18/213 (8%)

Query: 180 TLTMDTNAKIFVFSFVLGIVLSLFATRLSRHFHEKTGKALPLLYISTFLIFGLPTLVLIA 239
            +T+   A  F  + VLG+V ++   R S      T  + P  ++  F I G P LV   
Sbjct: 18  KITILATALGFAIAAVLGLVFAIL--RRSA----PTPISWPTSFVVEF-IRGTPLLV--- 67

Query: 240 LKYQLHFDKPVLGQFNFIGGSTVSPEFMSLYIALSCYTAAFIAEIVRSGLIAVPRGQMEA 299
              QL+F   VL            P  ++  + L  + A + AE+ R+G+ AVPRGQ EA
Sbjct: 68  ---QLYFLYYVLPDI-----GIRLPALVAGVLGLGLHYATYAAEVYRAGIEAVPRGQWEA 119

Query: 300 AIALGLTHRKATRLVLLPQAMRSIIPPLTSQYLNLLKNSSLAVAVGFADLVSVGGTIINQ 359
           A AL LT R+  R ++LPQA+  IIP L +  + + K + +  A+   +L++   +I N 
Sbjct: 120 ATALNLTARQTYRHIILPQAIPPIIPALGNYLVAMFKETPVLSAITVLELMNQAKSIGNS 179

Query: 360 TGQAIEIILIWMFIYLSLSIMIALFMNRLNAKI 392
           T + +E + +    +L LSI+   F+ RL A++
Sbjct: 180 TFRYLEPMTLVGVFFLILSIISVFFLRRLEARL 212



 Score = 44.1 bits (104), Expect = 6e-05
 Identities = 23/78 (29%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 89  ILVGFVNTFWLAFSGMIPATIIGTLVGAGRLSANKLVAWICRVYVEVFRNIPPLVVIFFL 148
           ++ G   T      G   A ++G +    R SA   ++W     VE  R  P LV ++FL
Sbjct: 13  LIEGLKITILATALGFAIAAVLGLVFAILRRSAPTPISWPTSFVVEFIRGTPLLVQLYFL 72

Query: 149 YKSVLSVLPIPDHSIVLP 166
           Y        +PD  I LP
Sbjct: 73  Y------YVLPDIGIRLP 84


>gnl|CDD|181907 PRK09494, glnP, glutamine ABC transporter permease protein;
           Reviewed.
          Length = 219

 Score = 82.4 bits (204), Expect = 2e-16
 Identities = 59/205 (28%), Positives = 107/205 (52%), Gaps = 12/205 (5%)

Query: 188 KIFVFSFVLGIVLSLFATRLSRHFHEKTGKALPLLYISTFLIFGLPTLVLIALKYQLHFD 247
            I V     G+V+ L A   +R +       + L++I   LI G P +V +   Y   F 
Sbjct: 24  WISVLGLAGGLVIGLLAG-FARAYGGWIANHIALVFIE--LIRGTPIVVQVMFIY---FA 77

Query: 248 KPVLGQFNFIGGSTVSPEFMSLYIALSCYTAAFIAEIVRSGLIAVPRGQMEAAIALGLTH 307
            P+           + P F +  + +   + A+IAEI R  ++++ +G  EA +ALGL+ 
Sbjct: 78  LPMA-----FNDLRIDP-FTAAVVTIMINSGAYIAEITRGAVLSIHKGFREAGLALGLSR 131

Query: 308 RKATRLVLLPQAMRSIIPPLTSQYLNLLKNSSLAVAVGFADLVSVGGTIINQTGQAIEII 367
           R+  R V+ P A+R ++PPL +Q++  +K++SL + +G A+L   G  II    +A+EI 
Sbjct: 132 RETLRYVIGPLALRRMLPPLGNQWIISIKDTSLFIVIGVAELTRQGQEIIAGNFRALEIW 191

Query: 368 LIWMFIYLSLSIMIALFMNRLNAKI 392
                IYL ++++++  + RL  ++
Sbjct: 192 SAVAVIYLIITLVLSFILRRLERRM 216



 Score = 39.7 bits (93), Expect = 0.001
 Identities = 18/62 (29%), Positives = 30/62 (48%)

Query: 88  AILVGFVNTFWLAFSGMIPATIIGTLVGAGRLSANKLVAWICRVYVEVFRNIPPLVVIFF 147
            +L G   T W++  G+    +IG L G  R     +   I  V++E+ R  P +V + F
Sbjct: 14  LLLEGAKMTLWISVLGLAGGLVIGLLAGFARAYGGWIANHIALVFIELIRGTPIVVQVMF 73

Query: 148 LY 149
           +Y
Sbjct: 74  IY 75


>gnl|CDD|185055 PRK15100, PRK15100, amino acid ABC transporter permease;
           Provisional.
          Length = 220

 Score = 82.1 bits (203), Expect = 2e-16
 Identities = 56/206 (27%), Positives = 103/206 (50%), Gaps = 18/206 (8%)

Query: 192 FSFVLGIVLSLFATRLSRHFHEKTGKALPLLYISTFLIFGLPTLVLIALKYQLHFDKPVL 251
           F  +LG +L+L   RLS        + L   Y+S F   G P +  + + Y   +  P  
Sbjct: 32  FGLLLGFILALM--RLSPI---WPVRWLARFYVSIFR--GTPLIAQLFMIY---YGLPQF 81

Query: 252 GQFNFIGGSTVSPEFMSLYIALSCYTAAFIAEIVRSGLIAVPRGQMEAAIALGLTHRKAT 311
           G               +  I LS  TAA+ AE +R+ + ++ +GQ EAA ++G+T  +  
Sbjct: 82  G--------IELDPIPAAMIGLSLNTAAYAAETLRAAISSIDKGQWEAAASIGMTRWQTL 133

Query: 312 RLVLLPQAMRSIIPPLTSQYLNLLKNSSLAVAVGFADLVSVGGTIINQTGQAIEIILIWM 371
           R  +LPQA R+ +PPL++ +++L+K++SLA  +   +L      I ++T +   + L   
Sbjct: 134 RRAILPQAARTALPPLSNSFISLVKDTSLAATIQVPELFRQAQLITSRTLEVFTMYLAAS 193

Query: 372 FIYLSLSIMIALFMNRLNAKIALKEK 397
            IY  ++ +++   NR   ++  +E+
Sbjct: 194 LIYWIMATVLSALQNRFENQLNRQER 219



 Score = 44.7 bits (106), Expect = 4e-05
 Identities = 21/64 (32%), Positives = 32/64 (50%)

Query: 86  ATAILVGFVNTFWLAFSGMIPATIIGTLVGAGRLSANKLVAWICRVYVEVFRNIPPLVVI 145
           A  +L G   T  L+  GM    ++G ++   RLS    V W+ R YV +FR  P +  +
Sbjct: 12  APFLLKGAGYTLQLSIGGMFFGLLLGFILALMRLSPIWPVRWLARFYVSIFRGTPLIAQL 71

Query: 146 FFLY 149
           F +Y
Sbjct: 72  FMIY 75


>gnl|CDD|132049 TIGR03004, ectoine_ehuC, ectoine/hydroxyectoine ABC transporter,
           permease protein EhuC.  Members of this family are
           presumed to act as permease subunits of ectoine ABC
           transporters. Operons containing this gene also contain
           the other genes of the ABC transporter and typically are
           found next to either ectoine utilization or ectoine
           biosynthesis operons. Permease subunits EhuC and EhuD
           are homologous.
          Length = 214

 Score = 72.2 bits (177), Expect = 2e-13
 Identities = 39/123 (31%), Positives = 61/123 (49%)

Query: 271 IALSCYTAAFIAEIVRSGLIAVPRGQMEAAIALGLTHRKATRLVLLPQAMRSIIPPLTSQ 330
           + L  +  A+ AEIVR  L +V   Q+EA  AL  T  +  R + LPQA+  ++P   + 
Sbjct: 85  MVLGLHAGAYGAEIVRGALSSVSVQQLEACRALNFTRFQTLRRISLPQALVEMMPAFGNL 144

Query: 331 YLNLLKNSSLAVAVGFADLVSVGGTIINQTGQAIEIILIWMFIYLSLSIMIALFMNRLNA 390
            + LLK +SL   +  ADL     +I N T   + I  I +  Y  ++++I L M  L  
Sbjct: 145 AIELLKLTSLVSLISLADLTFAAQSIRNLTLDTLSIFAITLLCYFVMALIIMLIMRVLER 204

Query: 391 KIA 393
            + 
Sbjct: 205 VVR 207



 Score = 44.8 bits (106), Expect = 4e-05
 Identities = 20/67 (29%), Positives = 35/67 (52%)

Query: 83  SSYATAILVGFVNTFWLAFSGMIPATIIGTLVGAGRLSANKLVAWICRVYVEVFRNIPPL 142
           ++Y   +L G   T  +  +G + AT++    G GR+S   ++  +   Y+EVFR    L
Sbjct: 1   TAYLPLLLQGAWVTMQITLAGSVLATVLAFFAGLGRVSGGPILRTVALCYIEVFRGTSLL 60

Query: 143 VVIFFLY 149
           V +F+ Y
Sbjct: 61  VQLFWFY 67


>gnl|CDD|182979 PRK11123, PRK11123, arginine transporter permease subunit ArtQ;
           Provisional.
          Length = 238

 Score = 67.8 bits (166), Expect = 5e-12
 Identities = 54/180 (30%), Positives = 90/180 (50%), Gaps = 6/180 (3%)

Query: 217 KALPLLYISTFLIFGLPTLVL-IALKYQLHFDKPVLGQFNFIGGSTVSPEFMSLYIALSC 275
           + LP + +  F+ FG   L+L ++  + L+     +     I    VSP F+   IALS 
Sbjct: 55  RGLPEILVVLFIYFGSSQLLLTLSDGFTLNLGFVQIPVQMDIENFEVSP-FLCGVIALSL 113

Query: 276 YTAAFIAEIVRSGLIAVPRGQMEAAIALGLTHRKATRLVLLPQAMRSIIPPLTSQYLNLL 335
             AA+ ++ +R  L AVP GQ E+  ALGL+       +++PQ  R  +P L +Q+L LL
Sbjct: 114 LYAAYASQTLRGALKAVPVGQWESGQALGLSKSAIFFRLVMPQMWRHALPGLGNQWLVLL 173

Query: 336 KNSSLAVAVGFADLVSVGGTIINQTGQAIEIILIWMFIYLSLSIMIALFMNRLNAKIALK 395
           K+++L   +   DL+    +I  +T +     +I   IYL    +I L    +  +I L+
Sbjct: 174 KDTALVSLISVNDLMLQTKSIATRTQEPFTWYIIAAAIYL----VITLISQYILKRIELR 229



 Score = 31.6 bits (72), Expect = 0.42
 Identities = 14/54 (25%), Positives = 24/54 (44%)

Query: 96  TFWLAFSGMIPATIIGTLVGAGRLSANKLVAWICRVYVEVFRNIPPLVVIFFLY 149
           T  LA   +I    +  L      +  + VAW     V + R +P ++V+ F+Y
Sbjct: 14  TVGLAVCALIVGLALAMLFAVWESAKWRPVAWPGTALVTLLRGLPEILVVLFIY 67


>gnl|CDD|130787 TIGR01726, HEQRo_perm_3TM, amine acid ABC transporter, permease
           protein, 3-TM region, His/Glu/Gln/Arg/opine family.
           This model represents one of several classes of multiple
           membrane spanning regions found immediately N-terminal
           to the domain described by pfam00528,
           binding-protein-dependent transport systems inner
           membrane component. The region covered by this model
           generally is predicted to contain three transmembrane
           helices. Substrate specificities attributed to members
           of this family include histidine, arginine, glutamine,
           glutamate, and (in Agrobacterium) the opines octopine
           and nopaline.
          Length = 99

 Score = 64.1 bits (157), Expect = 6e-11
 Identities = 24/62 (38%), Positives = 37/62 (59%)

Query: 88  AILVGFVNTFWLAFSGMIPATIIGTLVGAGRLSANKLVAWICRVYVEVFRNIPPLVVIFF 147
            +L G + T  L+   ++   ++G L+   RLS N+ + WI  VYVE+FR  P LV +FF
Sbjct: 4   FLLKGLLLTLLLSVLSILLGLVLGLLLALLRLSGNRPLRWIATVYVELFRGTPLLVQLFF 63

Query: 148 LY 149
           +Y
Sbjct: 64  IY 65



 Score = 33.7 bits (78), Expect = 0.079
 Identities = 26/99 (26%), Positives = 45/99 (45%), Gaps = 14/99 (14%)

Query: 189 IFVFSFVLGIVLSLFATRLSRHFHEKTGKALPLLYISTFLIFGLPTLVLIALKYQLHFDK 248
           + V S +LG+VL L    L R    +  + +  +Y+  F   G P LV +   + ++F  
Sbjct: 15  LSVLSILLGLVLGLLLA-LLRLSGNRPLRWIATVYVELFR--GTPLLVQL---FFIYFGL 68

Query: 249 PVLGQFNFIGGSTVSPEFMSLYIALSCYTAAFIAEIVRS 287
           P++G               +  IAL+ +  A++AEI R 
Sbjct: 69  PLIG--------IRLSPLTAAVIALTLFYGAYLAEIFRG 99


>gnl|CDD|185089 PRK15135, PRK15135, histidine/lysine/arginine/ornithine ABC
           transporter permease HisQ; Provisional.
          Length = 228

 Score = 54.0 bits (130), Expect = 7e-08
 Identities = 46/166 (27%), Positives = 77/166 (46%), Gaps = 5/166 (3%)

Query: 226 TFLIFGLPTLVLIALK-YQLHFDKPVLGQFNFIGGSTVSPEFMSLYIALSCYTAAFIAEI 284
           T LI G+P LVL+ L  Y L      + +   +G   + P    + I L     A+  E 
Sbjct: 53  TTLIRGVPDLVLMLLIFYGLQIALNSVTEALGVGQIDIDPMVAGI-ITLGFIYGAYFTET 111

Query: 285 VRSGLIAVPRGQMEAAIALGLTHRKATRLVLLPQAMRSIIPPLTSQYLNLLKNSSLAVAV 344
            R   +AVP+G +EAA A G T  +  R ++ P  MR  +P + + +  +LK ++L   +
Sbjct: 112 FRGAFMAVPKGHIEAATAFGFTRGQVFRRIMFPAMMRYALPGIGNNWQVILKATALVSLL 171

Query: 345 GFADLVSVGGTIINQTGQAIEIILIWMFIYL---SLSIMIALFMNR 387
           G  D+V         T +     ++   IYL   ++S  + L++ R
Sbjct: 172 GLEDVVKATQLAGKSTWEPFYFAIVCGVIYLVFTTVSNGVLLWLER 217



 Score = 39.0 bits (91), Expect = 0.002
 Identities = 22/65 (33%), Positives = 37/65 (56%)

Query: 85  YATAILVGFVNTFWLAFSGMIPATIIGTLVGAGRLSANKLVAWICRVYVEVFRNIPPLVV 144
           ++  IL G + T  LA S ++ A IIG +   G+LS N+L+  I   Y  + R +P LV+
Sbjct: 5   FSGVILQGALVTLELALSSVVLAVIIGLIGAGGKLSQNRLLGLIFEGYTTLIRGVPDLVL 64

Query: 145 IFFLY 149
           +  ++
Sbjct: 65  MLLIF 69


>gnl|CDD|185029 PRK15069, PRK15069, histidine/lysine/arginine/ornithine ABC
           transporter permease HisM; Provisional.
          Length = 234

 Score = 47.4 bits (113), Expect = 6e-06
 Identities = 34/115 (29%), Positives = 64/115 (55%), Gaps = 1/115 (0%)

Query: 271 IALSCYTAAFIAEIVRSGLIAVPRGQMEAAIALGLTHRKATRLVLLPQAMRSIIPPLTSQ 330
           +A +  T A+  EI    + +VP G++EAA A G++  K  R ++LP A+R  +P  +++
Sbjct: 107 LAFTLNTCAYTTEIFAGAIRSVPHGEIEAARAYGMSTFKLYRRIILPSALRRALPAYSNE 166

Query: 331 YLNLLKNSSLAVAVGFADLVSVGGTIINQTGQAIEIILIWMFIYLSLS-IMIALF 384
            + +L  ++LA      D++ +   I + T Q  +   I   +YL +S ++I+LF
Sbjct: 167 VILMLHATTLAFTATVPDILKIARDINSATYQPFQAFGIAAVLYLIISFVLISLF 221



 Score = 30.8 bits (70), Expect = 0.62
 Identities = 17/78 (21%), Positives = 34/78 (43%)

Query: 90  LVGFVNTFWLAFSGMIPATIIGTLVGAGRLSANKLVAWICRVYVEVFRNIPPLVVIFFLY 149
             G   T WL  + ++   ++   +   R+S+NK + +   +Y  VFR  P  V +   Y
Sbjct: 20  FTGLAITLWLLVASVVIGFVLAVPLAIARVSSNKWIRFPVWLYTYVFRGTPLYVQLLVFY 79

Query: 150 KSVLSVLPIPDHSIVLPF 167
             + S+  +    ++  F
Sbjct: 80  TGMYSLEIVRGTDLLDAF 97


>gnl|CDD|182726 PRK10782, PRK10782, DL-methionine transporter permease subunit;
           Provisional.
          Length = 217

 Score = 44.7 bits (106), Expect = 4e-05
 Identities = 28/83 (33%), Positives = 47/83 (56%)

Query: 271 IALSCYTAAFIAEIVRSGLIAVPRGQMEAAIALGLTHRKATRLVLLPQAMRSIIPPLTSQ 330
           + L+   A FIA +V + L+ +P G +EA+ A+G T  +  R VLLP+A+  ++   T  
Sbjct: 94  VPLTVGAAPFIARMVENALLEIPTGLIEASRAMGATPMQIVRKVLLPEALPGLVNAATIT 153

Query: 331 YLNLLKNSSLAVAVGFADLVSVG 353
            + L+  S++  AVG   L  +G
Sbjct: 154 LITLVGYSAMGGAVGAGGLGQIG 176


>gnl|CDD|182978 PRK11122, artM, arginine transporter permease subunit ArtM;
           Provisional.
          Length = 222

 Score = 43.0 bits (102), Expect = 1e-04
 Identities = 51/207 (24%), Positives = 95/207 (45%), Gaps = 16/207 (7%)

Query: 191 VFSFVLGIVLSLFATRLSRHFHEKTGKALPLLYISTFLIFGLPTLVLIALKYQLHFDKPV 250
           V S ++ +VL+L  T +           L   YI+ F   G P LV I L Y      P 
Sbjct: 20  VASLLVALVLALIFT-IILTLKTPVLVWLVRGYITLFT--GTPLLVQIFLIYY----GP- 71

Query: 251 LGQFNFIGGSTVSPEFMS-----LYIALSCYTAAFIAEIVRSGLIAVPRGQMEAAIALGL 305
            GQF ++         +S       +AL+  +AA+  ++    + A+P GQ ++  ALG+
Sbjct: 72  -GQFPWLQEYPWLWHLLSQPWLCAMLALALNSAAYSTQLFYGAVRAIPEGQWQSCAALGM 130

Query: 306 THRKATRLVLLPQAMRSIIPPLTSQYLNLLKNSSLAVAVGFADLVSVGGTIINQTGQAIE 365
           + +K T  +LLP A +  +   +++ + + K++SLA  +   D++     +  +T   + 
Sbjct: 131 S-KKQTLRILLPYAFKRALSSYSNEVVLVFKSTSLAYTITLMDVMGYSQLLYGRTYDVM- 188

Query: 366 IILIWMFIYLSLSIMIALFMNRLNAKI 392
           +      IYL ++ ++ L M  +  K 
Sbjct: 189 VFGAAGIIYLVVNGLLTLLMRLIERKA 215



 Score = 27.6 bits (62), Expect = 6.0
 Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 17/79 (21%)

Query: 71  EIDQGIVPYTSDSSYATAILVGFVNTFWLAFSGMIPATIIGTLVGAGRLSANKLVAWICR 130
           E+ +G+   TS +    ++LV  V             TII TL          ++ W+ R
Sbjct: 7   ELLKGLH--TSLTLTVASLLVALVLALIF--------TIILTL-------KTPVLVWLVR 49

Query: 131 VYVEVFRNIPPLVVIFFLY 149
            Y+ +F   P LV IF +Y
Sbjct: 50  GYITLFTGTPLLVQIFLIY 68


>gnl|CDD|162724 TIGR02138, phosphate_pstC, phosphate ABC transporter, permease
           protein PstC.  The typical operon for the high affinity
           inorganic phosphate ABC transporter encodes an
           ATP-binding protein, a phosphate-binding protein, and
           two permease proteins. This family consists of one of
           the two permease proteins, PstC, which is homologous to
           PstA (TIGR00974). In the model bacterium Escherichia
           coli, this transport system is induced when the
           concentration of extrallular inorganic phosphate is low.
           A constitutive, lower affinity transporter operates
           otherwise.
          Length = 295

 Score = 41.1 bits (97), Expect = 6e-04
 Identities = 29/96 (30%), Positives = 41/96 (42%), Gaps = 2/96 (2%)

Query: 229 IFGLPTLVLIALKYQLHFDKPVLGQFNFIGGSTVSPEFMSLYIALSCYTAAFIAEIVRSG 288
           ++G   L ++    + HF   +      I      P   +  I L+      IA I R  
Sbjct: 116 VYGFWGLFVLVPFLKPHFQPFLGSNLGLIPL-FGGPILTAG-IVLAIMILPTIASISRDA 173

Query: 289 LIAVPRGQMEAAIALGLTHRKATRLVLLPQAMRSII 324
           L AVPR   EA+ ALG T  +  R V+LP A   I+
Sbjct: 174 LRAVPRSYKEASYALGATKWETIRRVILPAARSGIV 209


>gnl|CDD|162141 TIGR00974, 3a0107s02c, phosphate ABC transporter, permease protein
           PstA.  This model describes PtsA, one of a pair of
           permease proteins in the ABC (high affinity) phosphate
           transporter. In a number of species, this permease is
           fused with the PtsC protein (TIGR02138). In the model
           bacterium Escherichia coli, this transport system is
           induced when the concentration of extrallular inorganic
           phosphate is low. A constitutive, lower affinity
           transporter operates otherwise.
          Length = 271

 Score = 36.1 bits (84), Expect = 0.019
 Identities = 29/134 (21%), Positives = 56/134 (41%), Gaps = 15/134 (11%)

Query: 191 VFSFVLGIVLSLFATRLSRHFHEKTGKALPLLYISTFLIFGLPTLVLIALKYQLHFDKPV 250
           V +  LGI  +++    +        +   ++  +  ++ G+P++V+    Y       +
Sbjct: 68  VIAVPLGIGAAIYLAEYANE-----SRFTKVIRFAVDILAGVPSIVVGLFGYGFFVLTML 122

Query: 251 LGQFNFIGGSTVSPEFMSLYIALSCYTAAFIAEIVRSGLIAVPRGQMEAAIALGLTHRKA 310
            G F+ + G+          +AL+      I       L AVP+   EA+ ALG T  + 
Sbjct: 123 GGGFSLLAGA----------LALALLILPVIIRTTEEALKAVPKDLREASYALGATKWQT 172

Query: 311 TRLVLLPQAMRSII 324
              V+LP A+  I+
Sbjct: 173 IFKVVLPAALPGIL 186


>gnl|CDD|163466 TIGR03754, conj_TOL_TraD, conjugative coupling factor TraD, TOL
           family.  Members of this protein are assigned by
           homology to the TraD family of conjugative coupling
           factor. This particular clade serves as a marker for an
           extended gene region that occurs occasionally on
           plasmids, including the toluene catabolism TOL plasmid.
           More commonly, the gene region is chromosomal, flanked
           by various markers of conjugative transfer and
           insertion.
          Length = 643

 Score = 32.3 bits (74), Expect = 0.20
 Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 3/28 (10%)

Query: 332 LNLLKNSSLAVAVG---FADLVSVGGTI 356
           L+ L ++ +A AVG   FADLVSV G I
Sbjct: 446 LDALSDAEVAAAVGNSMFADLVSVAGHI 473


>gnl|CDD|162201 TIGR01097, PhnE, phosphonate ABC transporter, permease protein
           PhnE.  Phosphonates are a class of compound analogous to
           organic phosphates, but in which the C-O-P linkage is
           replaced by a direct, stable C-P bond. Some bacteria can
           utilize phosphonates as a source of phosphorus. This
           family consists of permease proteins of known or
           predicted phosphonate ABC transporters. Often this
           protein is found as a duplicated pair, occasionally as a
           fused pair. Certain "second" copies score in between the
           trusted and noise cutoff and should be considered true
           hits (by context).
          Length = 250

 Score = 31.0 bits (71), Expect = 0.54
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 3/66 (4%)

Query: 82  DSSYATAILVGFVNTFWLAFSGMIPATIIGTLVG---AGRLSANKLVAWICRVYVEVFRN 138
           D SY   IL   + T  +A  G + A I+   +    A  ++ +  ++ + R+ +   R 
Sbjct: 49  DWSYLPKILKALLETLAMAILGTVLAAILALPLALLAARNITPSPWLSGLARLLLNFLRA 108

Query: 139 IPPLVV 144
           IP LV 
Sbjct: 109 IPELVW 114


>gnl|CDD|132457 TIGR03416, ABC_choXWV_perm, choline ABC transporter, permease
           protein. 
          Length = 267

 Score = 30.0 bits (68), Expect = 1.1
 Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 6/67 (8%)

Query: 288 GLIAVPRGQMEAAIALGLTHRKATRLVLLPQAMRSIIPPLTSQYLNLLKNSSLAVAVGFA 347
           G+ +VP+  +EA  A G T  +    V LP AM  I+  LT Q + L    SL++ V  A
Sbjct: 172 GISSVPQELVEAGEAFGATPSQLLWKVELPYAMPQIMAGLT-QTIML----SLSMVV-IA 225

Query: 348 DLVSVGG 354
            LV   G
Sbjct: 226 ALVGADG 232


>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 = 29.6 bits (67), Expect = 1.4
 Identities = 15/30 (50%), Positives = 20/30 (66%), Gaps = 3/30 (10%)

Query: 332 LNLLKNSSLAVAVG---FADLVSVGGTIIN 358
           L+ L + ++A AVG    ADLVSV G+I N
Sbjct: 446 LDSLSDPTVASAVGNSMLADLVSVAGSIYN 475


>gnl|CDD|131015 TIGR01960, ndhF3_CO2, NAD(P)H dehydrogenase, subunit NdhF3 family. 
           This family represents a subfamily of NAD(P)H
           dehydrogenase subunit 5, or ndhF. It is restricted to
           two paralogs in each completed cyanobacterial genome, in
           which several subtypes of ndhF are found. Included in
           this family is NdhF3, shown to play a role in
           high-affinity CO2 uptake in Synechococcus sp. PCC7002.
           In all cases, neighboring genes include a paralog of
           ndhD but do include other NAD(P)H dehydrogenase
           subunits. Instead, genes related to C02 uptake tend to
           be found nearby.
          Length = 606

 Score = 28.2 bits (63), Expect = 3.9
 Identities = 35/110 (31%), Positives = 52/110 (47%), Gaps = 13/110 (11%)

Query: 250 VLGQFNFIGGSTVSPEFMSLYIALSCYTAAFIAEIVRSGLIAVPRGQMEAAIALGLTHRK 309
            +G    IGGS ++   + +  ALS   +A++  +     IAV  GQ + A+ L LTH  
Sbjct: 289 AIGSVTAIGGSLIAIAQIDIKRALSYSVSAYMGLV----FIAVGLGQGDLALLLLLTH-- 342

Query: 310 ATRLVLLPQAMRSIIPPLTSQYLNLLKN-------SSLAVAVGFADLVSV 352
           A    LL  ++ SII    +Q L  L         S L+  VG A L++V
Sbjct: 343 AIAKALLFMSIGSIIWNTVTQDLTELGGLWSRRPISGLSFVVGSAGLIAV 392


>gnl|CDD|150959 pfam10369, ALS_ss_C, Small subunit of acetolactate synthase.
           ALS_ss_C is the C-terminal half of a family of proteins
           which are the small subunits of acetolactate synthase.
           Acetolactate synthase is a tetrameric enzyme, containing
           probably two large and two small subunits, which
           catalyses the first step in branched-chain amino acid
           biosynthesis. This reaction is sensitive to certain
           herbicides.
          Length = 75

 Score = 28.2 bits (64), Expect = 4.1
 Identities = 8/15 (53%), Positives = 13/15 (86%)

Query: 281 IAEIVRSGLIAVPRG 295
           I E+VR+G++A+ RG
Sbjct: 61  ILEVVRTGVVAIARG 75


>gnl|CDD|179437 PRK02509, PRK02509, hypothetical protein; Provisional.
          Length = 973

 Score = 28.1 bits (63), Expect = 4.2
 Identities = 28/119 (23%), Positives = 41/119 (34%), Gaps = 6/119 (5%)

Query: 124 LVAWICRVYVEVFRNIPPLVVIFFLYKSVLSVLPIPDHSIVLPFGMFLNNRGLSFPTLTM 183
           L  W       +    PPL   F L      +  I      L   + L    L  P   +
Sbjct: 131 LQYWTPDF--TLPNVSPPLPSPFRLEWLWNLLTQILSQLWKLGLILLLAILILIRPKFLL 188

Query: 184 DTNAKIFVFSFVLGIVLSLFATRLSRHFH-EKTGKALPLLYIS-TFLIFGLPTLVLIAL 240
              A   + S   G++LS    R+ ++FH     +  PL     +F IF LP   L+  
Sbjct: 189 RGIA--IILSLAFGLILSGNWARVLQYFHSTPFNETDPLFGRDISFYIFQLPLWELLEF 245


>gnl|CDD|180206 PRK05692, PRK05692, hydroxymethylglutaryl-CoA lyase; Provisional.
          Length = 287

 Score = 27.9 bits (63), Expect = 4.3
 Identities = 16/32 (50%), Positives = 21/32 (65%), Gaps = 1/32 (3%)

Query: 195 VLGIVLSLF-ATRLSRHFHEKTGKALPLLYIS 225
           VL  VL+ F A RL+ HFH+  G+AL  +Y S
Sbjct: 189 VLEAVLAEFPAERLAGHFHDTYGQALANIYAS 220


>gnl|CDD|139879 PRK13817, PRK13817, ribosome-binding factor A; Provisional.
          Length = 119

 Score = 27.8 bits (61), Expect = 5.0
 Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 3/34 (8%)

Query: 5   ARKTVTRYFSRMKFLYD---MRVHNISVQIILAL 35
           A+ TV RY  +++F+YD    R H IS+ I  AL
Sbjct: 77  AQATVLRYVPKLEFVYDESIERAHRISLLIERAL 110


>gnl|CDD|183329 PRK11829, PRK11829, biofilm formation regulator HmsP; Provisional.
          Length = 660

 Score = 27.2 bits (60), Expect = 8.2
 Identities = 9/20 (45%), Positives = 15/20 (75%)

Query: 27  ISVQIILALLLTVIFLWCVN 46
           +S  ++LAL+L+V   WC+N
Sbjct: 150 LSTYLLLALVLSVSIAWCIN 169


>gnl|CDD|183989 PRK13348, PRK13348, chromosome replication initiation inhibitor
           protein; Provisional.
          Length = 294

 Score = 27.2 bits (61), Expect = 8.4
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 12/61 (19%)

Query: 62  GFLSERAGFEID---QGIVPYTSDSSYATAILVGFVNTFWLAFSGMIPATIIGTLVGAGR 118
            FL +  G  +    +  VP  S  ++  AI  G      L + GM+P  +IG L+ AGR
Sbjct: 202 SFLEQLFGLPVGAYPRHYVP--STHAHLAAIRHG------LGY-GMVPELLIGPLLAAGR 252

Query: 119 L 119
           L
Sbjct: 253 L 253


>gnl|CDD|162501 TIGR01716, RGG_Cterm, transcriptional activator, Rgg/GadR/MutR
           family, C-terminal domain.  This model describes the
           whole, except for a 60 residue N-terminal
           helix-turn-helix DNA-binding domain (PFAM pfam01381) of
           the family of proteins related to the transcriptional
           regulator Rgg, also called RopB. Rgg is required for
           secretion of several proteins, including a cysteine
           proteinase associated with virulence. GadR is a positive
           regulator of a glutamate-dependent acid resistance
           mechanism. MutR is a transcriptional activator for
           mutacin biosynthesis genes in Streptococcus mutans. This
           family appears restricted to the low-GC Gram-positive
           bacteria, including at least eight members in
           Lactococcus lactis.
          Length = 220

 Score = 27.2 bits (61), Expect = 8.5
 Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 5/54 (9%)

Query: 199 VLSLFATRLSRHFHEKTGKALPLL--YISTFLIFGLPTLVLIALKYQLHFDKPV 250
           +L  F   +  +   +       +   I  F   G PT   +A  YQ   +K V
Sbjct: 168 ILFNFLKGIILYKEGQKESGEEKIEQAIEIFDELGYPT---LAAYYQKLLEKFV 218


>gnl|CDD|180799 PRK07028, PRK07028, bifunctional hexulose-6-phosphate
           synthase/ribonuclease regulator; Validated.
          Length = 430

 Score = 26.9 bits (60), Expect = 10.0
 Identities = 15/32 (46%), Positives = 20/32 (62%), Gaps = 4/32 (12%)

Query: 338 SSLAVAVGFADLVSVGGTII---NQTGQAIEI 366
           ++ AVA G AD+V VGG II   + T  A +I
Sbjct: 176 AAKAVAAG-ADIVIVGGNIIKSADVTEAARKI 206


  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
   0.329    0.142    0.417 

Gapped
Lambda     K      H
   0.267   0.0702    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 6,548,253
Number of extensions: 442783
Number of successful extensions: 1522
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1511
Number of HSP's successfully gapped: 105
Length of query: 398
Length of database: 5,994,473
Length adjustment: 95
Effective length of query: 303
Effective length of database: 3,941,713
Effective search space: 1194339039
Effective search space used: 1194339039
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 58 (26.2 bits)