Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate BPHYT_RS24185 BPHYT_RS24185 C4-dicarboxylate ABC transporter permease
Query= SwissProt::O07838 (440 letters) >FitnessBrowser__BFirm:BPHYT_RS24185 Length = 450 Score = 298 bits (762), Expect = 3e-85 Identities = 158/447 (35%), Positives = 258/447 (57%), Gaps = 12/447 (2%) Query: 1 MSALIIFGLLIALMLTGMPISISLGLT-VLTFLFTMTQVPIDTVALKLFTGIEKFEIMAI 59 M I+ + +L G+P+S LGL VLT+L+ +P T + +GI F +A+ Sbjct: 1 MELAILSVSFLVFLLLGVPVSFGLGLACVLTYLYE--GLPAATAMQSMISGINGFSFLAV 58 Query: 60 PFFILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIG 119 PFFIL+G + HGG+A R++ FA A VGH+ GGLG+A V+AC LF VSGS A A+G Sbjct: 59 PFFILSGELMLHGGIADRILRFAQATVGHFRGGLGMANVVACTLFGGVSGSPSADTSAMG 118 Query: 120 SVILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSA 179 V++P M +G+ + V T S G L+P S M++YA A G+ T +G P+S Sbjct: 119 GVVIPLMKREGYSAAYAVNVTTHSSLAGALMPTSTNMIIYAFAAQGITGT-LNGHPMSGV 177 Query: 180 SVGELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQR----WTA----FREAA 231 S+G+L +G++P L + GF+ + +A K+GYPR S + W A F A Sbjct: 178 SIGDLLFSGLLPVLWVMGFVLIAAYWQAVKYGYPRRADGSTELQKFPGWYAVARTFLGAL 237 Query: 232 WGLMLIVVVIGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAM 291 GLM+I +++ + GI T TEAAA++ Y+ +++ VY+ +T++ + L +A + + Sbjct: 238 PGLMVIAIILVCVAKGIATATEAAAIAVFYSLVLTIVVYRSMTMKKLFHALSKAAKTTGV 297 Query: 292 LLYIITNAVLFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVL 351 +L +I + + + MA+ IP A+ + A W+ L+ +N++ + G F++ ++ +L Sbjct: 298 VLLLIGVSNMLRYQMAYLEIPDAIEHMLDGATSLPWLMLLYINLIQIFLGTFVDMAAHIL 357 Query: 352 IMAPILFPVAVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVW 411 I P+ P+A+ G+ PV FGIMI++N +G+ HPP+G ++ I + I E T W Sbjct: 358 ITTPLFLPMAMHAGVGPVQFGIMILLNCALGLVHPPIGSVQFIGCAIGNVSIGETTKVAW 417 Query: 412 PWLLTMLAFLVLVTYVPAISLALPNLL 438 P+ L + + + +VTYVP S LP+L+ Sbjct: 418 PYYLAIFSAINIVTYVPMFSTWLPSLI 444 Lambda K H 0.329 0.142 0.431 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: 607 Number of extensions: 43 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: 440 Length of database: 450 Length adjustment: 32 Effective length of query: 408 Effective length of database: 418 Effective search space: 170544 Effective search space used: 170544 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