Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate SM_b20297 SM_b20297 permease
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__Smeli:SM_b20297 Length = 426 Score = 293 bits (749), Expect = 9e-84 Identities = 155/421 (36%), Positives = 246/421 (58%), Gaps = 2/421 (0%) Query: 6 LLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPFFVLAG 65 L G + L++ GMPV + L ++AL W L ++ +G+N F LLA+PFF+L Sbjct: 4 LFGGWFALLIAGMPVGFTLIVAALAYMLWQGTGLNFAGQRMIAGLNSFPLLAVPFFILTA 63 Query: 66 AIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSVLIPEM 125 +M G++ R+ FA LVG +RGGL VNIMAS F +SGS+VAD A +G + I M Sbjct: 64 QLMNLSGVTERIFDFAKALVGHIRGGLGHVNIMASVLFSGMSGSAVADAAGLGQLEIKAM 123 Query: 126 ERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGLLLSAV 185 GY +FS ++T + ++ L PPS V+Y + A SI LF+ GI+PGLL +A Sbjct: 124 RDAGYDEQFSGSITAASAIIGPLIPPSIPLVVYGVIAN--TSIGGLFLGGIVPGLLCAAS 181 Query: 186 MMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATESAAVA 245 +M + + A +RNY + R AL L+ II+GGI +GVF+ TE+A VA Sbjct: 182 LMIMVYVIAWRRNYATAQRAGFRRVWSTFWHALLPLITPFIIIGGIFAGVFSPTEAAVVA 241 Query: 246 VVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPSKITTA 305 ++ F+ + +YR+ + L ++ TV + V +LI + FGYV+ Q+P + T Sbjct: 242 ASYALFLGVVVYREITFAKLVTVLRETVSHTAAVGLLIMGVSLFGYVIAREQVPQHVATF 301 Query: 306 FLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGMIMLVN 365 FLT +++ L+ +N ML+ LGT ++ ++L++ P+L+P GVDPVHFG++++ N Sbjct: 302 FLTYAEDPLTFLILVNLMLLALGTFIEALAILLLIVPVLVPTALQFGVDPVHFGVMVVFN 361 Query: 366 LGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLWLPSVV 425 L IG++TPP+G LFV S + + + ++P + L +VL+ +T PA+ ++P + Sbjct: 362 LMIGILTPPMGVALFVVSKVADIPFGVLARGILPLLIPLVVVLVLITIFPALVTFIPDQM 421 Query: 426 L 426 L Sbjct: 422 L 422 Lambda K H 0.329 0.142 0.418 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: 583 Number of extensions: 27 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: 426 Length of database: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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