Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate WP_045582020.1 AL072_RS00100 TRAP transporter large permease subunit
Query= uniprot:I7DRS6 (467 letters) >NCBI__GCF_001305595.1:WP_045582020.1 Length = 432 Score = 389 bits (1000), Expect = e-113 Identities = 207/461 (44%), Positives = 295/461 (63%), Gaps = 40/461 (8%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M+ ++F +++ L+L G+PI+++LGL+ FL + + +VA LF E F ++AI Sbjct: 1 MNAAIIFGLLLALMLTGMPISISLGLTVLSFLFFMTTVPIDAVALKLFTGIE-KFEIMAI 59 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 PFFILA +F+T GGVARR+I F+ A VGH GGL +AGV AC LFAA+SGSSPATVVAIG Sbjct: 60 PFFILAGNFLTHGGVARRMINFATAMVGHWHGGLGLAGVMACALFAAVSGSSPATVVAIG 119 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVE-----VSVGRMFLAG 175 SI++ M G+ K F AG++ +G LGILIPPSIVMV+Y A S+G+MF+AG Sbjct: 120 SIILPAMVAQGFPKHFGAGIVTTSGALGILIPPSIVMVMYCVATTGHPQAPSIGQMFIAG 179 Query: 176 VIPGLMAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGI 235 V+PGLM L L T + A+ P+ + + + + GLLLI +++GGIY GI Sbjct: 180 VVPGLMLALFLGFTTWNRARRFGYPRLPKASFAQRLHALRESFWGLLLIVVVMGGIYSGI 239 Query: 236 FTPTEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFF 295 FTPTEAAA+A+VYAF VA FVY+DM PL PK Sbjct: 240 FTPTEAAAMAAVYAFVVAVFVYKDM-PLSRVPK--------------------------- 271 Query: 296 HADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVN 355 L ++ ++ LL++I NA++ ++T EQ+PQ +A +L G +FL+VVN Sbjct: 272 ------VLLDSASMSAMLLYIITNAVLFSFLMTSEQIPQNMAAWILDQNMGVWVFLLVVN 325 Query: 356 VILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFV 415 +ILL G FMEPS +++I+AP++FP+A++LGIDP+H GI+++VNME+GM PPVGLNL+V Sbjct: 326 IILLAAGNFMEPSSIVLIMAPILFPVAMKLGIDPVHFGILIIVNMEVGMCHPPVGLNLYV 385 Query: 416 TSGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456 SG+ M + + A P+L + +FL ++TY+P I+ P Sbjct: 386 ASGITKMGITELTVAVWPWLLTMLIFLGLVTYVPAITLWFP 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: 630 Number of extensions: 30 Number of successful extensions: 5 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: 432 Length adjustment: 33 Effective length of query: 434 Effective length of database: 399 Effective search space: 173166 Effective search space used: 173166 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