Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate PP_0075 PP_0075 putative choline sulfate transporter
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__Putida:PP_0075 Length = 521 Score = 195 bits (496), Expect = 3e-54 Identities = 148/505 (29%), Positives = 243/505 (48%), Gaps = 40/505 (7%) Query: 20 WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79 W + + +DL+ G++ I+A+P ++A A+ +G+ +YGLY A V ++ L G S Sbjct: 13 WLPRQSGRSLRQDLLVGLSGAILALPQSIAYALIAGLPAEYGLYAAIVPVLIACLWGSSW 72 Query: 80 FSVSGPTAAFVVILYPVSQQFGLAG-------LLVATLLSGIFLILMGLARFGRLIEYIP 132 + + GPTAA ++LY +AG +L+ T L GIF +L+GL RFG L+ ++ Sbjct: 73 YLICGPTAAISIVLYASISPLAVAGSADYITLVLLLTFLGGIFQLLLGLLRFGALVNFVS 132 Query: 133 VSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVT 192 SV LGFT G I I Q+ + LG+ + L V L +++ +G+ T Sbjct: 133 HSVVLGFTLGAAIVIALGQLPNLLGMALPSQATA-LMTVQDLASHAGEVDLPSLLLGLAT 191 Query: 193 LGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQ 252 + I + R P L +L+ + ++ GHV + + Q Sbjct: 192 VVIGAAFKLWRPRWPSLLISLILVSLLAWLLPGFFGHVPRVAAF-------------TGQ 238 Query: 253 LLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANS 312 L P LP L + + LLP+A ++ MLG + SL A L + + Sbjct: 239 LPPFSPLP--------LLDMELMLRLLPSAVAVGMLGLVTSLSIARSLSARSEQLIDPDQ 290 Query: 313 ELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLS 372 E+ QGL NI FF G + + RS + AGA SP++ V ++ V L + A L++ Sbjct: 291 EIRAQGLSNIAGAFFSGYLSAGSFTRSGLSYEAGARSPMAGVFSALWVALFAVTGAGLIA 350 Query: 373 WLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIV 432 LP+ AMA +L++ W + + H+ + L + + +VM L + T+L ++ AI G++ Sbjct: 351 HLPIPAMAGSILLICWGLVD-HRGIRALFRVSRSEFLVMALTAAATLLLELQTAIYAGVL 409 Query: 433 LASLLFMRRIARMTRLAPVVVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVIL 492 + +++R +R + D VLRV G +FF AA L L+ R +G +VI Sbjct: 410 ASLFFYLKRTSR----PRIQQSREGDADVLRVGGSIFFGAAHYLQVRLQ-RCQGPHVVI- 463 Query: 493 KWDA--VPVLDAGGLDAFQRFVKRL 515 DA V +D G+D R +RL Sbjct: 464 --DARQVNFIDYSGVDMLHREARRL 486 Lambda K H 0.328 0.142 0.425 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 658 Number of extensions: 40 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 559 Length of database: 521 Length adjustment: 35 Effective length of query: 524 Effective length of database: 486 Effective search space: 254664 Effective search space used: 254664 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 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory