Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate 3607387 Dshi_0801 TRAP C4-dicarboxylate transport system permease DctM subunit (RefSeq)
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__Dino:3607387 Length = 452 Score = 236 bits (601), Expect = 2e-66 Identities = 153/471 (32%), Positives = 251/471 (53%), Gaps = 42/471 (8%) Query: 3 VVLLFSMVIGLLLIGVPI--AVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 V L+ V L ++GVP+ +A + F+L +L ++ + F F LLA+ Sbjct: 7 VTLISVGVTFLFMLGVPVFLVIAYWVIGCSFVL---GLTLDNMGAEILNVFNKGFALLAM 63 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 P FIL + G+ARR+ F+ AC+G L GGLA+A + AC LFAA+SGS+ AT IG Sbjct: 64 PLFILTGDLINKSGIARRLSDFAYACLGWLRGGLAMASLGACGLFAAISGSNSATTATIG 123 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 S++ M + GY + F+A GT+GI+IPPSI+ +VY + + + +F+AG+IPG Sbjct: 124 SMLHPEMVKGGYDERFSAATAAAGGTVGIIIPPSIIFIVYGFLMNLPISDLFVAGIIPGA 183 Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWG--------EVAASAANASVGLLLIGIILGGIY 232 + + + + +++ ++ GWG V +A A +G IG++L GIY Sbjct: 184 LMVIGMQLACWIICRIN--------GWGFIIPLQLNRVLKTAFGAWLGFFAIGLVLWGIY 235 Query: 233 GGIFTPTEAAAVASVYAFF--VATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYF 290 G F+PTEAA V + + ++V + L+S T K G+ +V Sbjct: 236 TGKFSPTEAAGVTVGFCVIAGLVSWVLTRVLRLRSDK---------TWEEKSYGEMLV-- 284 Query: 291 IPSFFHADTRHALFEAGKLTVTLLFVIANALILKHVLT---DEQVPQQIATAMLSAGFGP 347 + F + ++T L +IA +++++ +L+ +QV T+M G+ Sbjct: 285 VEGFTLRQIPGITMRSAEITGILAPLIAISVVMQQILSLLGAQQVIGDFVTSM--GGYHA 342 Query: 348 VMFLIVVNVILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITP 407 V+F + VI+ G +E + +I+AP++ PIA +G+DPIH +I +V IG ITP Sbjct: 343 VLFTAM--VIVFFSGMVLESLPVTIILAPILAPIAASVGVDPIHFAVIFLVGASIGFITP 400 Query: 408 PVGLNLFVTSGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWIST-VLPN 457 P GLNL+V SGV G+P ++R +P+L L I+++ P ++ +LPN Sbjct: 401 PYGLNLYVASGVTGVPYFRLLRYTVPYLVALISVWILVSLTPELALFLLPN 451 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: 582 Number of extensions: 28 Number of successful extensions: 2 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: 452 Length adjustment: 33 Effective length of query: 434 Effective length of database: 419 Effective search space: 181846 Effective search space used: 181846 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