Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate GFF2912 PS417_14900 C4-dicarboxylate ABC transporter permease
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__WCS417:GFF2912 Length = 426 Score = 499 bits (1284), Expect = e-146 Identities = 259/457 (56%), Positives = 336/457 (73%), Gaps = 35/457 (7%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAI 60 M V+ LF ++ + +GVPIA++LGLS + +L++S S++S+A LFE + +T LAI Sbjct: 1 MAVLCLFLLLFVFMFLGVPIAISLGLSGAVSILMFSQDSVSSLAIKLFETSDA-YTFLAI 59 Query: 61 PFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIG 120 PFF+L+ +FMTTGGVA+R+I F+ ACVGH+ GGLAIA V ACMLFAALSGSSPATV A+G Sbjct: 60 PFFLLSGAFMTTGGVAQRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVG 119 Query: 121 SIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGL 180 SI +AGM + GY K F AG+ICNAGTLGILIPPSIVMVVY+AA E SVG++F+AGVIPGL Sbjct: 120 SIAVAGMVRSGYPKAFGAGIICNAGTLGILIPPSIVMVVYSAATETSVGKLFMAGVIPGL 179 Query: 181 MAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGIFTPTE 240 + GLMLM+ IY++A++K LP + E SA A GLLL+ IILGGIY G+FTPTE Sbjct: 180 LLGLMLMIAIYIVARIKKLPAQPRATFREWLTSARRAFWGLLLLVIILGGIYSGMFTPTE 239 Query: 241 AAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHADTR 300 AAAVA+VY+ FVA F+Y+DM L+ PK Sbjct: 240 AAAVAAVYSAFVALFIYKDM-QLRDCPK-------------------------------- 266 Query: 301 HALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVILLI 360 L E+G+L + L+F+IANA++ HVLT EQ+PQ+I +LS G P+ FLI+VNV+LLI Sbjct: 267 -VLLESGRLAIMLMFIIANAMLFAHVLTTEQIPQEITAWVLSEGLTPIGFLIMVNVVLLI 325 Query: 361 GGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSGVA 420 G FMEPS +++I+AP+ FPIA++LGIDPIHLGI+MVVNMEIG++ PPVGLNLFVTS V Sbjct: 326 AGSFMEPSAIVLILAPIFFPIAMKLGIDPIHLGIVMVVNMEIGLVHPPVGLNLFVTSAVT 385 Query: 421 GMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPN 457 G+ + +RAALP+L +L VFLIM+TY+P+IS LP+ Sbjct: 386 GLTLGQTIRAALPWLMILLVFLIMVTYLPFISLALPH 422 Lambda K H 0.329 0.144 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: 667 Number of extensions: 22 Number of successful extensions: 4 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: 467 Length of database: 426 Length adjustment: 32 Effective length of query: 435 Effective length of database: 394 Effective search space: 171390 Effective search space used: 171390 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