Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate 208936 DVU0009 DedA family protein
Query= uniprot:I7DRS6 (467 letters) >MicrobesOnline__882:208936 Length = 426 Score = 281 bits (719), Expect = 3e-80 Identities = 169/465 (36%), Positives = 253/465 (54%), Gaps = 42/465 (9%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M ++LF M+ L PI +A+G S+ LLI L+ + F LLA+ Sbjct: 1 MTALVLFGMLGLLFACNAPIMLAVGASAFAALLIKGGMDPMVAVQRLYAGADS-FPLLAV 59 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 P F+ A M+ GG+++RI+R + VGHLPGGLA+ V + M FA +SGS+ A A+G Sbjct: 60 PLFMTAGQLMSAGGISQRIVRLADTLVGHLPGGLAVVSVVSSMFFAGVSGSAAADTAAVG 119 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 SI+I M GYS FA V AG++G++IPPSI M+V+ A S+G++F GV+PGL Sbjct: 120 SILIPSMVARGYSPAFAGAVQAAAGSIGVVIPPSIPMIVFGALTGASIGKLFAGGVMPGL 179 Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAA---SAANASVGLLLIGIILGGIYGGIFT 237 + G +T+ + L G E AA + A L IILGGI G+ T Sbjct: 180 LMG----ITLSAWCVHEGLRSGRETRRFEPAAVWPALLRAGWSLGAPAIILGGIISGVCT 235 Query: 238 PTEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHA 297 TEAAAVA VYAF V F +R++ L LP + Sbjct: 236 ATEAAAVAVVYAFLVGLFAHRELD--------------LRRLPAL--------------- 266 Query: 298 DTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVI 357 L +A + ++ +IA A + V+ E++P +A A+L+ G M L+ VN++ Sbjct: 267 -----LLDAAVTSGVVMSIIAAASLFGWVMAIERIPAALADAILAVGGEGWMLLLAVNIL 321 Query: 358 LLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTS 417 LL+ G +E + L+++ P++ + +GID IHLG+I+V+N+ IGM+TPP+G+ L V+ Sbjct: 322 LLLAGTMLETTAALILLVPVLVQLLPRMGIDLIHLGVIVVMNLSIGMLTPPLGVCLMVSC 381 Query: 418 GVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAVMGP 462 G+A +P+ + RA LP LAVL V L+++TYIPW ++ P Sbjct: 382 GIARVPLATLARAVLPLLAVLVVDLMLVTYIPWFVAAFSTDIIAP 426 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: 571 Number of extensions: 33 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 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