Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate HSERO_RS04250 HSERO_RS04250 C4-dicarboxylate ABC transporter permease
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__HerbieS:HSERO_RS04250 Length = 426 Score = 415 bits (1067), Expect = e-120 Identities = 211/459 (45%), Positives = 307/459 (66%), Gaps = 35/459 (7%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M+ +++F ++ L+L G+PI+++LGL+ FL ++ + SVA LF E F ++AI Sbjct: 1 MNALIIFVLLFALMLTGMPISISLGLTVLTFLFTMTEVPIQSVALKLFTGIE-KFEIMAI 59 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 PFFILA +F+T GGVARR+I F+ + VGH GGLA+AGV AC LFAA+SGSSPATVVAIG Sbjct: 60 PFFILAGNFLTHGGVARRMINFATSMVGHWHGGLALAGVLACALFAAVSGSSPATVVAIG 119 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 SI++ M + G+ F AGVI +G LGILIPPSIVMV+Y+ + SVG++F+AGV+PGL Sbjct: 120 SIILPAMVKQGFPNRFGAGVITTSGALGILIPPSIVMVMYSVSTNTSVGKLFMAGVVPGL 179 Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTE 240 + +L VT + +A+ N P+ + W E AA+ + GL LI I++GGIY G+FTPTE Sbjct: 180 LLAFLLGVTTWFLARKNNYPRLKKATWAERAAAFRKSGWGLFLIVIVMGGIYTGVFTPTE 239 Query: 241 AAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTR 300 AAA+A+VYAFF+A FVY+D+ LK PK Sbjct: 240 AAAMAAVYAFFIAVFVYKDL-TLKQVPK-------------------------------- 266 Query: 301 HALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLI 360 L ++ ++ LL++I NA++ ++T E +PQ +A + +G GP+ FL+VVN++LL+ Sbjct: 267 -VLLDSASMSAMLLYIITNAVLFSFLVTSENIPQAMAAWITDSGLGPITFLLVVNILLLL 325 Query: 361 GGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVA 420 G MEPS +++I+AP++FP+A++LGIDP+H GI++VVNME+GM PPVGLNL+V SG+ Sbjct: 326 AGNVMEPSSIVLILAPILFPVAMKLGIDPVHFGILIVVNMEVGMCHPPVGLNLYVASGIT 385 Query: 421 GMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAV 459 M + + A +P+L + FL ++TY P +S LPN + Sbjct: 386 KMGITELTIAVMPWLLTMLGFLALVTYWPALSLWLPNLI 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: 589 Number of extensions: 27 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 467 Length of database: 426 Length adjustment: 32 Effective length of query: 435 Effective length of database: 394 Effective search space: 171390 Effective search space used: 171390 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