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)