Align C4-dicarboxylic acid transporter DauA; Dicarboxylic acid uptake system A (characterized)
to candidate WP_086511761.1 BZY95_RS20600 SulP family inorganic anion transporter
Query= SwissProt::P0AFR2 (559 letters) >NCBI__GCF_002151265.1:WP_086511761.1 Length = 550 Score = 228 bits (581), Expect = 5e-64 Identities = 160/537 (29%), Positives = 261/537 (48%), Gaps = 43/537 (8%) Query: 20 WKEKYTAARFTRDLIAGITVGIIAIPLAMALAIGSGVAPQYGLYTAAVAGIVIALTGGSR 79 W + T+ D +AG+T ++ +P +A A+ +G+ P+YGLYTA V ++ AL G SR Sbjct: 23 WLPQQTSRSLRADAVAGLTGAVLVVPQGVAYALLAGLPPEYGLYTAIVPTVLAALFGSSR 82 Query: 80 FSVSGPTAAFVVILYPVSQQFGLAG-------LLVATLLSGIFLILMGLARFGRLIEYIP 132 VSGPTAA + L+ Q F AG +L TLL+G+F +L+GLAR G L++ + Sbjct: 83 QMVSGPTAALSIALFATLQPFAEAGSGEFIALVLTLTLLAGVFQLLLGLARLGVLVDLVS 142 Query: 133 VSVTLGFTSGIGITIGTMQIKDFLGLQMAHVPEHYLQKVGALFMALPTINVGDAAIGIVT 192 SV GFT+G + I T Q+ LGL ++ LF + I I T Sbjct: 143 HSVVTGFTAGAALIIATSQLPHALGLPPL-ASGGFIDLWPQLFARVGDIRPDAVLIAATT 201 Query: 193 LGILVFWPRLGIRLPGHLPALLAGCAVMGIVNLLGGHVATIGSQFHYVLADGSQGNGIPQ 252 L + + + R R PG L +L+A + ++ + I +P Sbjct: 202 LTLCLAFQRWLPRWPGMLLSLVAASLLAAWLDPTHSEILRIAE--------------VPA 247 Query: 253 LLPQLVLPWDLPNSEFTLTWDSIRTLLPAAFSMAMLGAIESLLCAVVLDGMTGTKHKANS 312 LP L LP ++ D++R L P A ++ +LG +E+ A +G + +N Sbjct: 248 GLPPLALP--------DVSTDTLRLLTPGAIALGLLGLVEAAAIARAFAARSGERLNSNQ 299 Query: 313 ELVGQGLGNIIAPFFGGITATAAIARSAANVRAGATSPISAVIHSILVILALLVLAPLLS 372 E +GQGL NI F ++ + RS N AGA SP++AV+ + +I LLV APLL Sbjct: 300 EFIGQGLSNIGGACFSAYVSSGSFTRSGLNASAGARSPLAAVLSAAFLIPILLVAAPLLH 359 Query: 373 WLPLSAMAALLLMVAWNMSEAHKVVDLLRHAPKDDIIVMLLCMSLTVLFDMVIAISVGIV 432 +P+SAMA LLL+VA + + + + + L+ + + ++L+ T+L + AI G++ Sbjct: 360 HVPMSAMAGLLLLVAAKLVDRNSIRETLK-ISRSETAILLITFFSTLLLALEFAIYFGVL 418 Query: 433 LASLLFMRRIARMTRLAPVVVDVPDDV---------LVLRVIGPLFFAAAEGLFTDLESR 483 + ++++RR R + + P ++ V+R+ G LFF A E + LES Sbjct: 419 ASLVVYLRRTTRPPVVVCALSQAPAELQQTLTEPGCSVVRIDGSLFFGACESVARQLESH 478 Query: 484 LEGKRIVILKWDAVPVLDAGGLDAFQRFVKRL-PEGCELRVCNVEFQPLRTMARAGI 539 +V+ + +D G+ Q +R G L + + L + RAG+ Sbjct: 479 DRPNLVVLAA--GINFIDLSGIHLLQHQARRCRARGGRLYLAGTKPDVLACLQRAGL 533 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: 603 Number of extensions: 26 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: 550 Length adjustment: 36 Effective length of query: 523 Effective length of database: 514 Effective search space: 268822 Effective search space used: 268822 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