Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_029132222.1 A3GO_RS0103480 TRAP transporter large permease
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_000428045.1:WP_029132222.1 Length = 452 Score = 673 bits (1737), Expect = 0.0 Identities = 346/467 (74%), Positives = 400/467 (85%), Gaps = 15/467 (3%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 MD+++LF MVIGL+LIGVPIAV+LGLSS +FL ++S++SLASVA TLF AF GH+TLLAI Sbjct: 1 MDILILFGMVIGLMLIGVPIAVSLGLSSIIFLFMHSEASLASVAQTLFSAFAGHYTLLAI 60 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 PFFILASSFM+TGGVARRIIRF++A VG PGGLA+A VFACM+FAALSGSSPATVVAIG Sbjct: 61 PFFILASSFMSTGGVARRIIRFAVAVVGWFPGGLAMASVFACMMFAALSGSSPATVVAIG 120 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 SIVIAGM + GY+KEFAAGVICNAGTLGILIPPSIVMVVYAAA +VSVGRMFLAGVIPG Sbjct: 121 SIVIAGMVKAGYTKEFAAGVICNAGTLGILIPPSIVMVVYAAATDVSVGRMFLAGVIPGS 180 Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTE 240 +AG+MLM+ IY+ A+VK LP + GWGEV SA +A GL+LI IILGGIYGGIFTPTE Sbjct: 181 LAGVMLMIGIYIAARVKGLPSQPFAGWGEVFESARDAGWGLMLIVIILGGIYGGIFTPTE 240 Query: 241 AAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTR 300 AAAVA+VYAF +A F+Y+DMGPL + K G F T L I F+H DT+ Sbjct: 241 AAAVAAVYAFLIANFIYKDMGPLAT----KTRGNFFTAL-----------ITVFWHKDTK 285 Query: 301 HALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLI 360 H LFEAGKLT+ LLF+IANALILKHVLT+E++PQ I AMLSAGFGP+MFLIVVNV+LLI Sbjct: 286 HTLFEAGKLTIMLLFIIANALILKHVLTEERIPQMITEAMLSAGFGPIMFLIVVNVLLLI 345 Query: 361 GGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVA 420 GGQFMEPSGLL+IVAPLVFPIA+ LGIDPIHLGIIMVVNMEIGMITPPVGLNLFVT+GV+ Sbjct: 346 GGQFMEPSGLLIIVAPLVFPIAMTLGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTAGVS 405 Query: 421 GMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAVMGPEIITK 467 M MM VV+AA P+L ++F+FLI++TY+PWIST LP +MGPEIITK Sbjct: 406 HMSMMRVVKAAAPWLGIMFLFLIIVTYVPWISTWLPTIMMGPEIITK 452 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: 802 Number of extensions: 25 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 24 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