Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized, see rationale)
to candidate 3607544 Dshi_0956 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q9KQS1 (453 letters) >FitnessBrowser__Dino:3607544 Length = 428 Score = 272 bits (695), Expect = 2e-77 Identities = 145/444 (32%), Positives = 252/444 (56%), Gaps = 25/444 (5%) Query: 5 LLFILVIGMMIVGVPIAISLGLSSILFLLWHSDASLASVAQTLFNAFAGHYTLLAIPFFI 64 ++ IL++ ++I G+PIA LG+++ + +L A + + + A +Y L+A F+ Sbjct: 8 IILILLVVLLIAGLPIAFVLGVTAAVMILL-DPAVVPQIIGLIPFGGANNYLLVAALLFM 66 Query: 65 LASTFMSTGGVAKRIIRFAIAMVGWFRGGLAIASVVACMMFAALSGSSPATVVAIGSIVI 124 +A M+ G +A+++I FA ++VG RGGLA +++ + F+ +SG++ + AIGS++I Sbjct: 67 IAGEIMNQGKIAEKLIAFASSLVGHIRGGLAHVNILTSLFFSEISGTATSDAAAIGSVMI 126 Query: 125 AGMVKNGYSKEFAAGVICNAGTLGILIPPSIVMVVYSAATNVSVGRMFLGGVVPGLLAGL 184 M K GY FAA V + T+ I++PPS+ +++Y+ N S+ +F G+VPG L Sbjct: 127 PQMRKRGYPAAFAAAVTSTSATMAIIVPPSLNLILYAYVANASIAELFAAGIVPGFLVCG 186 Query: 185 MLIIAIYITARIKNLPKQPFVGWKEALKAAKEASWGLLLVVIILGGIYGGIFTPTEAAAV 244 +L+ YI + + P + W + K+A+ L L +++L GI GGIFT TEA A+ Sbjct: 187 LLMGTAYIISVKRGYPTEGAFSWGRVAETGKDAAIPLTLPILVLAGILGGIFTATEAGAI 246 Query: 245 AAVYSFFIANFIYR--DMGPFADKTNTKPVLVKVVETFVHKDTKATLYDAGKLTIMLMFI 302 AA +S +A FIYR +G D TL AGK + MLMFI Sbjct: 247 AAFWSIVLAAFIYRTVKLGTLID----------------------TLRIAGKRSAMLMFI 284 Query: 303 IANALILKHVLTEERIPQMITESMLSAGLGPITFLIVVNLILLVGGQFMEPSGLLVIVAP 362 +A + +L LT +RIPQ I E +L L+ +N+ L+ G + + ++++ P Sbjct: 285 VATSTLLGWYLTNQRIPQDIAEGILGLSDNYWVILLAINVFFLLAGTIIHGTPAILMLVP 344 Query: 363 LVFPIAIALGIDPIHLGIMMVVNMEIGMITPPVGLNLFVTSGVAKMSMMNVVKAALPWVG 422 + P+A LGID +H G+++ +N+ IG TPPV + +T +AK+S+ ++ + L ++G Sbjct: 345 IFLPLADQLGIDRVHFGLILTINLGIGQQTPPVASVVLITCAIAKISIAKIIPSMLMFIG 404 Query: 423 VMFLFLIIVTYVPWVSTWLPTLLM 446 M + L+++ P +S WLP++++ Sbjct: 405 AMLVALLLINLFPALSLWLPSVIL 428 Lambda K H 0.329 0.142 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: 469 Number of extensions: 21 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: 453 Length of database: 428 Length adjustment: 32 Effective length of query: 421 Effective length of database: 396 Effective search space: 166716 Effective search space used: 166716 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