Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate 206131 DVU0705 TRAP dicarboxylate transporter, putative
Query= uniprot:I7DRS6 (467 letters) >MicrobesOnline__882:206131 Length = 427 Score = 240 bits (613), Expect = 6e-68 Identities = 146/455 (32%), Positives = 237/455 (52%), Gaps = 38/455 (8%) Query: 4 VLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFF 63 +LLF + ++ IGVP+A A+GLS+T+ + + L SV +++ + LLAIP F Sbjct: 3 ILLFGLFAVMMFIGVPLATAMGLSATVAIAA-AKLGLLSVPISVYTGV-AKYPLLAIPMF 60 Query: 64 ILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIV 123 I A GVA R++ F++A VG L GGLAIA + CM+ +SGS PA A+ ++ Sbjct: 61 IFAGMVFERSGVALRLVNFTVALVGPLRGGLAIASIMVCMVLGGISGSGPADAAAVAMVM 120 Query: 124 IAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAV-EVSVGRMFLAGVIPGLMA 182 I GM GY K F+AG+I AG+ ILIPPSI ++Y+ V + SV +F AG+IPG +A Sbjct: 121 IPGMAAAGYPKAFSAGLIAAAGSTAILIPPSIAFILYSVLVPQASVPALFAAGLIPGFLA 180 Query: 183 GLMLMVTIYVMAKVKNLP-KGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEA 241 G+ L++ + ++ G+ G + + A GLL IILGGI G FTPTEA Sbjct: 181 GIALIIPAWALSVRHGFGLVGDDASCGSILIAFKEAIWGLLAPVIILGGIRSGYFTPTEA 240 Query: 242 AAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRH 301 A A Y FV FVYR LT+ Sbjct: 241 AVAAVFYGLFVGFFVYRT----------------LTL------------------RGIYE 266 Query: 302 ALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIG 361 L E+ +++ ++ +IA + + + + + A++ M L+ V ++L+I Sbjct: 267 LLVESAEVSAVVMMIIALSSVFAWAGSTLGAFEAMGNALIGISTSETMTLLAVVLVLIIA 326 Query: 362 GQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAG 421 G F++ +L I P++ P+ G + + G+IM + + IG TPP+ LNL VT+ +A Sbjct: 327 GMFLDGVSILFIFIPILLPVMTHFGWNAVWFGVIMTMCLAIGQFTPPLALNLMVTTRIAD 386 Query: 422 MPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456 + + V L F+ + + ++++ ++P ++T++P Sbjct: 387 IGIEETVPWVLWFVLAMTIAMLLVVFVPQLATLVP 421 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: 646 Number of extensions: 43 Number of successful extensions: 5 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: 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