Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate 3609368 Dshi_2753 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__Dino:3609368 Length = 429 Score = 282 bits (722), Expect = 1e-80 Identities = 162/456 (35%), Positives = 256/456 (56%), Gaps = 37/456 (8%) Query: 4 VLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEG--HFTLLAIP 61 +L++ + + LL + + + V GL + LL++ + + + G F L+AIP Sbjct: 1 MLIWFLPLFLLFLMIGLPVFFGLLAAPGLLLWLNGQERDITLLYRNVYNGMDSFPLMAIP 60 Query: 62 FFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGS 121 FF+LA M GG+ R++ F+ A +GH GGLA + + MLFA LSGS+ A A+GS Sbjct: 61 FFMLAGELMNRGGITLRLVEFAQALMGHFRGGLAHVNILSSMLFAGLSGSAVADTSALGS 120 Query: 122 IVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLM 181 ++I M + GY++ FAA + + +G +IPPS +M++YA + SV +FLAG++PG++ Sbjct: 121 MLIPAMEKQGYTRRFAAAITAASSVIGPIIPPSGIMIIYAYVMGESVAALFLAGIVPGIL 180 Query: 182 AGLMLMVTIYVMAKVKNLP-KGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTE 240 G+ LM + +MA + P WG+ ++ A L+ IILGGI G+FTPTE Sbjct: 181 VGVGLMGVVKLMADKYDFPVASAKTTWGQRGQASLKAFFPLMTPVIILGGILAGVFTPTE 240 Query: 241 AAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTR 300 AAAVA YA + FV R + K D LP +LG+ Sbjct: 241 AAAVAVAYALIIGFFVMRTL-------KVSD-------LPDILGR--------------- 271 Query: 301 HALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLI 360 AG + +L ++ A+ K V++ PQ +A MLS P++ L+++N++L + Sbjct: 272 -----AGITSAVVLLLVGAAMAFKTVVSLSYAPQIMADFMLSLSENPLILLLLINLLLFV 326 Query: 361 GGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVA 420 G F++ ++I+ P++ PI ++LG+DPIH IIM VN+ +G+ TPP+GL LFV S V+ Sbjct: 327 VGMFLDAGPAIIILGPILGPIFVDLGVDPIHFAIIMSVNLTVGLATPPMGLVLFVASSVS 386 Query: 421 GMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456 G + + +A LPFLAV + + +ITY P IS +P Sbjct: 387 GERVERIAKAILPFLAVEILVIFLITYFPAISMTIP 422 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: 614 Number of extensions: 27 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: 429 Length adjustment: 33 Effective length of query: 434 Effective length of database: 396 Effective search space: 171864 Effective search space used: 171864 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