Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized, see rationale)
to candidate GFF3083 HP15_3026 TRAP dicarboxylate transporter, DctM subunit
Query= uniprot:Q9KQS1 (453 letters) >FitnessBrowser__Marino:GFF3083 Length = 499 Score = 191 bits (484), Expect = 6e-53 Identities = 126/463 (27%), Positives = 228/463 (49%), Gaps = 41/463 (8%) Query: 5 LLFILVIGMMIVGVPIAISLGLSSILFLLWHSDASLASVAQTLFNAFAGHYTLLAIPFFI 64 L+F + +++G+P+A G ++F+ DA + ++ + + AIP FI Sbjct: 58 LMFGSLAVALMMGLPLAFVTGGLGVMFIYLVGDAMMLNIVPGRIFPLMANPDIAAIPLFI 117 Query: 65 LASTFMSTGGVAKRIIRFAIAMVGWFRGGLAIASVVACMMFAALSGSSPATVVAIGSIVI 124 ++ + G+ + + +G GGLA A++VA + AA+ G A VV +G I + Sbjct: 118 FMASMLERAGLIEEMFSVVYKWMGGISGGLAAATIVASTILAAMVGVIGAAVVTMGIIAL 177 Query: 125 AGMVKNGYSKEFAAGVICNAGTLGILIPPSIVMVVYSAATNVSVGRMFLGGVVPGL-LAG 183 M+K Y + A G I GTLGILIPPSI+ ++Y+ SVG ++LG ++PGL L+G Sbjct: 178 PAMLKRHYDHKIAIGSIMAGGTLGILIPPSILAILYAVVAQQSVGELYLGSLLPGLMLSG 237 Query: 184 LML---IIAIYITARI-KNLPKQPFVGWKEALKAAKEASWGLLLVVIILGGIYGGIFTPT 239 L L ++ ++ ++ +P + + KE LK L LV ++LG ++GGI TP Sbjct: 238 LYLTYVLVRSWLNPKLGPPIPVEDRISLKEKLKLLGNLIAPLALVGLVLGLLFGGIATPV 297 Query: 240 EAAAVAAVYSFFIANFIYRDMGPFADKTNTKPVLVKVVETFVHKDTKATLYDAGKLTIML 299 EAA + + + +A + + F + K + M+ Sbjct: 298 EAAGIGSFGAIIVA---------------------MMHKKFSIAGLREASVTTAKASAMV 336 Query: 300 MFIIANALILKHVLTEERIPQMITESMLSAGLGPITFLIVVNLILLVGGQFMEPSGLLVI 359 ++I+ A + + Q +T+++L G+ L ++ ++L+V G F++ G+L++ Sbjct: 337 LWIMFGASVFVGFYILQGGQQFVTDAILGTGMSAYGILFLLMVLLVVLGMFLDWVGILLL 396 Query: 360 VAPLVFPIAIAL------GIDPI-------HLGIMMVVNMEIGMITPPVGLNLFVTSGVA 406 P+ PI AL G P+ G++ +VNM++ ++PP G LF GV Sbjct: 397 AVPIFIPIVKALEFPGLFGFPPVAGDDVVLWFGVLYLVNMQMSFLSPPFGYALFYIRGVC 456 Query: 407 --KMSMMNVVKAALPWVGVMFLFLIIVTYVPWVSTWLPTLLMG 447 ++SM + K++L ++ + L + +P + TWLP L+ G Sbjct: 457 PPEISMGTIFKSSLVFLAIQAFGLFMCVLIPGIVTWLPGLVYG 499 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: 641 Number of extensions: 29 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 453 Length of database: 499 Length adjustment: 33 Effective length of query: 420 Effective length of database: 466 Effective search space: 195720 Effective search space used: 195720 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