Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate SMc00476 SMc00476 transport transmembrane protein
Query= SwissProt::P0AFR2 (559 letters) >FitnessBrowser__Smeli:SMc00476 Length = 551 Score = 327 bits (838), Expect = 7e-94 Identities = 204/538 (37%), Positives = 298/538 (55%), Gaps = 41/538 (7%) Query: 22 EKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFS 81 E Y AAR D AG+TV I+A+PL+MA+AI SGV P GLYTA V G +++L GGSR Sbjct: 15 EGYGAARLKADAFAGLTVAIVALPLSMAIAIASGVTPDRGLYTAIVGGFLVSLLGGSRVQ 74 Query: 82 VSGPTAAFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTS 141 + GP AF+V++ + G+ GLL+ATL+SG LI G R GR I++IP VT+GFT+ Sbjct: 75 IGGPAGAFIVLVAATVARHGVDGLLLATLMSGFMLIAAGYLRLGRYIKFIPYPVTVGFTA 134 Query: 142 GIGITIGTMQIKDFLGLQMAHV-PEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWP 200 GI + I Q++D GL +A P + KV AL A T++ +T+GI++ Sbjct: 135 GIAVIIFASQLRDLFGLTLAGAEPGPIVDKVAALAQAAGTVSWAAVLTAALTVGIILALR 194 Query: 201 RLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVLP 260 R+ PG L A+ A + ++ L TIGS+F GIP+ LP LP Sbjct: 195 RVRPHWPGMLIAVAAASTFVALLQL---PTETIGSRF----------GGIPRGLPLPALP 241 Query: 261 WDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLG 320 L+ + + P A S A+LGAIESLL AVV DGMTG +H+++ ELV QG Sbjct: 242 --------PLSLEKAAAVFPDALSFALLGAIESLLSAVVADGMTGRRHRSSVELVAQGAA 293 Query: 321 NIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMA 380 NI + FGGI T IAR+A NVRAGATSP+S ++HS ++L +L+ APL S++PL+++A Sbjct: 294 NICSALFGGICVTGTIARTATNVRAGATSPVSGILHSAFLLLFMLLAAPLASYIPLASLA 353 Query: 381 ALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMR 440 +L +VAWNM E + LLR + D +V+L + V ++ I VG L ++LF+ Sbjct: 354 GVLAIVAWNMIEKPAFMALLR-SSYGDAVVLLATFLIVVFRELTEGIVVGFALGAVLFID 412 Query: 441 RIARMTRL----------------APVVVDVPDDVLVLRVIGPLFFAAAEGLFTDLESRL 484 R+AR + PV+ D PD V + R+ G FF +A + T L+ Sbjct: 413 RMARSISVQEARPLSAQRQENGDERPVIADDPDTV-IYRLSGIFFFGSAATVGTVLDRIA 471 Query: 485 EGKRIVILKWDAVPVLDAGGLDAFQRFVKRLPE-GCELRVCNVEFQPLRTMARAGIQP 541 + +R IL VP +D+ + + +++ G + Q R + + ++P Sbjct: 472 DQRRNFILDCSDVPFMDSTAANVIEGTLRKAERTGVRFIITGARSQVRRALYQHHVRP 529 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: 610 Number of extensions: 25 Number of successful extensions: 4 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: 551 Length adjustment: 36 Effective length of query: 523 Effective length of database: 515 Effective search space: 269345 Effective search space used: 269345 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: 53 (25.0 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