Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate SM_b20297 SM_b20297 permease
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__Smeli:SM_b20297 Length = 426 Score = 284 bits (726), Expect = 5e-81 Identities = 160/456 (35%), Positives = 255/456 (55%), Gaps = 36/456 (7%) Query: 6 LFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFFIL 65 LF LL+ G+P+ L +++ ++L + + L + AG A F LLA+PFFIL Sbjct: 4 LFGGWFALLIAGMPVGFTLIVAALAYML-WQGTGL-NFAGQRMIAGLNSFPLLAVPFFIL 61 Query: 66 ASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGSIVIA 125 + M GV RI F+ A VGH+ GGL + A +LF+ +SGS+ A +G + I Sbjct: 62 TAQLMNLSGVTERIFDFAKALVGHIRGGLGHVNIMASVLFSGMSGSAVADAAGLGQLEIK 121 Query: 126 GMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLMAGLM 185 MR GY ++F+ + + +G LIPPSI +VVY S+G +FL G++PGL+ Sbjct: 122 AMRDAGYDEQFSGSITAASAIIGPLIPPSIPLVVYGVIANTSIGGLFLGGIVPGLLCAAS 181 Query: 186 LMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTEAAAVA 245 LM+ +YV+A +N + G+ V ++ +A + L+ II+GGI+ G+F+PTEAA VA Sbjct: 182 LMIMVYVIAWRRNYATAQRAGFRRVWSTFWHALLPLITPFIIIGGIFAGVFSPTEAAVVA 241 Query: 246 SVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTRHALFE 305 + YA F+ VYR++ K L +L +TV + Sbjct: 242 ASYALFLGVVVYREITFAK--------------LVTVLRETVSH---------------- 271 Query: 306 AGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLIGGQFM 365 T + +I + +V+ EQVPQ +AT L+ P+ FLI+VN++LL G F+ Sbjct: 272 ----TAAVGLLIMGVSLFGYVIAREQVPQHVATFFLTYAEDPLTFLILVNLMLLALGTFI 327 Query: 366 EPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVAGMPMM 425 E +L+++ P++ P A++ G+DP+H G+++V N+ IG++TPP+G+ LFV S VA +P Sbjct: 328 EALAILLLIVPVLVPTALQFGVDPVHFGVMVVFNLMIGILTPPMGVALFVVSKVADIPFG 387 Query: 426 AVVRAALPFLAVLFVFLIMITYIPWISTVLPNAVMG 461 + R LP L L V L++IT P + T +P+ ++G Sbjct: 388 VLARGILPLLIPLVVVLVLITIFPALVTFIPDQMLG 423 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: 592 Number of extensions: 40 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 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