Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_011372369.1 SUDEN_RS03855 SulP family inorganic anion transporter
Query= SwissProt::P0AFR2 (559 letters) >NCBI__GCF_000012965.1:WP_011372369.1 Length = 545 Score = 340 bits (873), Expect = 6e-98 Identities = 194/525 (36%), Positives = 313/525 (59%), Gaps = 31/525 (5%) Query: 28 RFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSRFSVSGPTA 87 R + D+ AGI VGI+A+PL++A A+ SGV+P+ GL TA VAG +I++ GGSR + GPT Sbjct: 21 RLSSDIFAGIVVGIVALPLSIAFAVASGVSPEKGLITAIVAGFIISILGGSRVQIGGPTG 80 Query: 88 AFVVILYPVSQQFGLAGLLVATLLSGIFLILMGLARFGRLIEYIPVSVTLGFTSGIGITI 147 AF+VILY + +++G+ GL+++T+++G+FL++ G R G L++Y P + +GFTSGI + I Sbjct: 81 AFIVILYAIVEEYGIDGLMISTIMAGVFLVIFGFLRLGNLLKYFPHPLIVGFTSGIAVVI 140 Query: 148 GTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVTLGILVFWPRLGIRLP 207 + QIKD LGL + +P + K F + N+ + IVT+ I ++ ++ ++P Sbjct: 141 FSTQIKDALGLNIEKLPSEFFHKWLTYFSNIGDTNLYALLLSIVTILITIYSKKVTTKVP 200 Query: 208 GHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQLLPQLVLPWDLPNSE 267 G A++ AV V + V TI + F G N P + L Sbjct: 201 GSFIAII---AVTLFVQIASIPVTTIETFF------GEIPNSFALQFPNIEL-------- 243 Query: 268 FTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANSELVGQGLGNIIAPFF 327 ++ L A ++A+LG +ESLL AVV DGM G H++N+EL+ QG+ NI+ PFF Sbjct: 244 -----SNLYMYLAPALTIALLGGVESLLSAVVADGMIGGNHRSNTELIAQGVANIVTPFF 298 Query: 328 GGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLSWLPLSAMAALLLMVA 387 GGI AT AIAR+A NV+ G +PI+ ++HS+ ++L +L+ A +P+SA+A +L++V+ Sbjct: 299 GGIAATGAIARTATNVKNGGRTPIAGIVHSLTLLLIMLIFASYAKLIPMSALAGILIVVS 358 Query: 388 WNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIVLASLLFMRRIARM-- 445 +NMSE V +LR DIIV+L LTV D+ IAI +G+VL+SLLFM+R+A + Sbjct: 359 YNMSEWRSFVSILR-GSNFDIIVLLSTFLLTVFVDLTIAIQIGVVLSSLLFMKRMADIGI 417 Query: 446 -TRLAPVVV----DVPDDVLVLRVIGPLFFAAAEGLFTDLESRLEGKRIVILKWDAVPVL 500 T++ V+ +VP + + + GP FFA+A+ +++ +I+I++ VP + Sbjct: 418 KTQVDSDVLEDYSEVPKGISIYEISGPFFFASAKQYTEVIKNVGIKSKILIIRMRHVPFV 477 Query: 501 DAGGLDAFQRFVKRLPE-GCELRVCNVEFQPLRTMARAGIQPIPG 544 D+ L FQ +K L + ++ + V+ L + + GI + G Sbjct: 478 DSTALHNFQETIKTLQQLDVKIVLSGVQNSVLEDLKKDGITSLIG 522 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: 588 Number of extensions: 18 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: 545 Length adjustment: 36 Effective length of query: 523 Effective length of database: 509 Effective search space: 266207 Effective search space used: 266207 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 Apr 09 2024. 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