Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate WP_028584552.1 G494_RS0110760 TRAP transporter large permease
Query= SwissProt::Q9HU16 (427 letters) >NCBI__GCF_000429965.1:WP_028584552.1 Length = 426 Score = 291 bits (746), Expect = 2e-83 Identities = 155/422 (36%), Positives = 243/422 (57%), Gaps = 3/422 (0%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLGLSGALTILLFSPDSVRSLAIKLFETSEHYTLLAIP 60 +T+ FL L FLL+ VPI V++GLS + + L K+ + + + L+A+P Sbjct: 5 ITLTFLSLATFLLL--SVPIGVAIGLSVVVGMTASDMLPYEFLIQKMVTSLDVFPLMAVP 62 Query: 61 FFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVGS 120 FF+++G M G +A RL+ + A VGH+ GG+A +VL M + +LSGS+PATVAAVG Sbjct: 63 FFIMAGEIMQKGSMAHRLLAISRALVGHLTGGMAHISVLTSMFYGSLSGSAPATVAAVGG 122 Query: 121 IAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGVVPGLL 180 I I M + GY +F + AG LG++IPPS+ +++Y SVG LFIAG++PGL Sbjct: 123 IMIPAMKKEGYSTSFSTAVNTAAGCLGVIIPPSVPLIIYGTTAGVSVGDLFIAGIIPGLF 182 Query: 181 LGLILMVVIYIVARVKKLPAM-PRVSLREWLASARKALWGLLLMVIILGGIYSGAFTPTE 239 +GL LM+ YI+AR R +E L + R AL L++ +I+LGGIY G TPTE Sbjct: 183 VGLALMICSYILARKYGFTGSGSRAPFKEILVAFRDALPALMVPIIVLGGIYGGLTTPTE 242 Query: 240 AAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTEQIPQ 299 A +A VYS R + + V + T + ++A A +L +P Sbjct: 243 AGVIAVVYSLIAEGIFLRTLSWQKVIDVFKGTALTTASIFLVVATATALGQILLFYNLPN 302 Query: 300 SIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPIHLGI 359 + + + + ++ L ++ + L++ G FM+ A ILIL P+ P+ LGIDPI GI Sbjct: 303 MLVEILVGISDNKYILLPIILLFLIVMGTFMDALANILILTPLLLPVVRHLGIDPIQFGI 362 Query: 360 IMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPAVSLA 419 +M+V +G +TPPVG+NLFV ++ + + A +P+L+ +++ L+ +T+IP ++L Sbjct: 363 VMIVTSSMGFLTPPVGVNLFVGCSIANISIERLSLAVMPFLLTMVLALLALTFIPQIALW 422 Query: 420 LP 421 LP Sbjct: 423 LP 424 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: 467 Number of extensions: 31 Number of successful extensions: 3 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: 427 Length of database: 426 Length adjustment: 32 Effective length of query: 395 Effective length of database: 394 Effective search space: 155630 Effective search space used: 155630 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 Sep 24 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