Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_011383335.1 AMB_RS04550 C4-dicarboxylate ABC transporter permease
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_000009985.1:WP_011383335.1 Length = 427 Score = 392 bits (1006), Expect = e-113 Identities = 210/459 (45%), Positives = 297/459 (64%), Gaps = 35/459 (7%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M+ ++F ++I L+L G+PI+++LGL+ FL +++ + SVA LF E F ++AI Sbjct: 1 MNSAVIFGLLIVLMLTGMPISISLGLTVLSFLFLFTQVPIESVALKLFTGIE-KFEIMAI 59 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 PFFILA +F+T GGVARR+I F+ A VGH GGL +AGV AC LFAA+SGSSPATVVAIG Sbjct: 60 PFFILAGNFLTHGGVARRMINFATAMVGHWYGGLGLAGVMACALFAAVSGSSPATVVAIG 119 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 SI++ M + G+ +F AGVI +G LGILIPPS+VMV+YA A SVG +F+AGVIPGL Sbjct: 120 SIILPAMVKQGFPNKFGAGVITTSGALGILIPPSLVMVMYAVATNTSVGALFMAGVIPGL 179 Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTE 240 + +L + +A + P+ W + + A GL LI I++GGIY G+FTPTE Sbjct: 180 VLATVLGAVTWYIAWKNDYPRLPPATWAQRFRAFREAIWGLALIVIVIGGIYTGVFTPTE 239 Query: 241 AAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTR 300 AAA+++VYAF +A FVY+DM PLK K Sbjct: 240 AAAMSAVYAFLIAVFVYKDM-PLKGVGK-------------------------------- 266 Query: 301 HALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLI 360 L + ++ LL++I NA++ VL +E +P IA ++ G + FL+VVNV+LL+ Sbjct: 267 -ILLSSASMSAMLLYIITNAVLFSFVLANENIPHAIADWIVGKELGVIAFLLVVNVLLLV 325 Query: 361 GGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVA 420 G FMEPS +++I+AP++FP+A++LGIDPIH GI++VVNME+GM PPVGLNL+V SG+ Sbjct: 326 AGNFMEPSSIVLIMAPILFPVAMKLGIDPIHFGILIVVNMEVGMCHPPVGLNLYVASGIT 385 Query: 421 GMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAV 459 M + + A P+L + FL+++TY P +S LP A+ Sbjct: 386 KMGITELTVAVWPWLLAMLGFLMVVTYWPPLSIWLPRAL 424 Lambda K H 0.329 0.144 0.421 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: 602 Number of extensions: 28 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: 467 Length of database: 427 Length adjustment: 33 Effective length of query: 434 Effective length of database: 394 Effective search space: 170996 Effective search space used: 170996 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: 51 (24.3 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