Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_041097902.1 SUTH_RS06085 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_000828635.1:WP_041097902.1 Length = 441 Score = 257 bits (657), Expect = 4e-73 Identities = 149/428 (34%), Positives = 245/428 (57%), Gaps = 14/428 (3%) Query: 6 LFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSV---RSLAIKLFETSEHYTLLAIPFF 62 +F +L L+ + +PI +++ + GA + D++ SL + +Y L+ IP F Sbjct: 10 MFGILMALLVVRIPIGIAMFMVGAGGYVYLVGDTLPLLNSLKNLAYARLSNYDLVVIPLF 69 Query: 63 LLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGSIA 122 LL G F T GG+++ L F +A +GH +GG+AIAA+ AC F A+ GSS AT A +G + Sbjct: 70 LLMGQFATHGGLSKALFRFVSAFLGHFKGGVAIAAIGACAGFGAICGSSLATAATMGQVT 129 Query: 123 IAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLLLG 182 + + R GY + G + GTLGI+IPPS+ +V+YA T+ S+GKLF+A V+PG++ Sbjct: 130 LPELKRFGYSGSLSTGALAAGGTLGIMIPPSVPLVIYAILTQESIGKLFMAAVLPGIIAM 189 Query: 183 LILMVVIYIVARVKKL--PAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTEA 240 L M+VI I+ + PA P S E L S L LL+ VI++ GIY G PTEA Sbjct: 190 LGYMIVIRIIVTLDPAAGPAGPATSWAEKLKSFVAVLPVLLVFVIVIVGIYGGWANPTEA 249 Query: 241 AAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQS 300 AAV A+ +A+ V MR + ++ + + T M+ ++ A + L Q+P Sbjct: 250 AAVGAMACGILAV-VTGGMRFEGLMESIVGTAQTTAMIFLVLLGADMLNTALAVSQMPTE 308 Query: 301 IASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGI-------D 353 +A+WV + GLSP + +L++ ++ ++ G M+ A+IL+ PIF+P+ M L Sbjct: 309 LAAWVKDSGLSPMLVMLMILLIYVLLGCVMDSLAMILLTIPIFYPMVMGLDYWGMSQVDK 368 Query: 354 PIHLGIIMVVNMEIGLITPPVGLNLFVTSAVT-GMPLGATIRAALPWLMILLVFLIIVTY 412 + GI+ ++ +EIGL+ PPVG+N+++ + + +PL T + +P+L + + ++ Y Sbjct: 369 SVWFGILALMVVEIGLVHPPVGMNVYIINRLAKDVPLVETFKGVMPFLASDFIRIALLLY 428 Query: 413 IPAVSLAL 420 P +SL L Sbjct: 429 FPVISLYL 436 Lambda K H 0.330 0.144 0.425 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: 465 Number of extensions: 29 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: 427 Length of database: 441 Length adjustment: 32 Effective length of query: 395 Effective length of database: 409 Effective search space: 161555 Effective search space used: 161555 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 (21.9 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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