Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate H281DRAFT_05326 H281DRAFT_05326 TRAP transporter, DctM subunit
Query= SwissProt::O07838 (440 letters) >FitnessBrowser__Burk376:H281DRAFT_05326 Length = 450 Score = 294 bits (753), Expect = 3e-84 Identities = 158/445 (35%), Positives = 261/445 (58%), Gaps = 13/445 (2%) Query: 3 ALIIFGLLIALMLTGMPISISLGLT-VLTFLFTMTQVPIDTVALKLFTGIEKFEIMAIPF 61 AL+ ++ L+L G+P+S +LGL+ VLT+L+ +P T + +G+ F +A+PF Sbjct: 4 ALLSISFIVFLVL-GVPVSFALGLSCVLTYLYE--GLPAATAMQSMISGMNAFSFLAVPF 60 Query: 62 FILAGNFLTHGGVAKRMINFATAMVGHWHGGLGLAGVIACALFAAVSGSSPATVVAIGSV 121 FI +G + HGG+A R++ FA A VGH+ GGLG+A V+AC LF VSGS A A+G V Sbjct: 61 FIFSGELMLHGGIADRILRFAQATVGHFRGGLGMANVVACTLFGGVSGSPTADTSAMGGV 120 Query: 122 ILPAMVNQGFPKQFGAGVITTSGALGILIPPSIVMVMYAVATSGMVVTGPDGQPVSSASV 181 ++P M +G+ + V T S G L+P S M++YA A G+ T +G P+S S+ Sbjct: 121 VIPLMKREGYSAAYAVNVTTHSSLAGALMPTSTNMIIYAFAAQGITGT-LNGVPMSGVSI 179 Query: 182 GELFMAGVVPGLMLAGFLAFTTWNRARKFGYPRLEKASLRQR----WTA----FREAAWG 233 G+L +G++P L + GF+ + +A ++GYPR S + W A F A G Sbjct: 180 GDLLFSGLLPVLWVMGFVLIAAYWQAVRYGYPRRPDGSTALQRFPGWMAVARTFLGALPG 239 Query: 234 LMLIVVVIGGIYAGIFTPTEAAAMSAVYAFFISVFVYKDLTLRDVPRVLLSSANMSAMLL 293 LM+I +++ + GI T TEAAA++ Y+ ++V VY+ +TL+ + L +A + ++L Sbjct: 240 LMVIAIILVCVAKGIATATEAAAIAVAYSLVLTVVVYRSMTLKKLSFALSKAAKTTGVVL 299 Query: 294 YIITNAVLFSFLMAHEGIPQALGEWMVNAGLSWWMFLIIVNILLLAAGNFMEPSSIVLIM 353 +I + + + MA+ IP A+ + A W+ L+ +NI+ + G F++ ++ +LI Sbjct: 300 LLIGVSNMLRYQMAYLEIPDAIEHMLDGATSIPWLMLLYINIIQVFLGTFVDMAAHILIT 359 Query: 354 APILFPVAVRLGIDPVHFGIMIVVNMEVGMCHPPVGLNLYVASGITKMGITELTVAVWPW 413 P+ P+A+ G+ PV FGIMI++N +G+ HPP+G ++ I + I E T WP+ Sbjct: 360 TPLFLPMAMHSGVGPVQFGIMILLNCALGLVHPPIGSVQFIGCAIGNVSIGETTKVAWPY 419 Query: 414 LLTMLAFLVLVTYVPAISLALPNLL 438 L + + + +VTYVP S LP+++ Sbjct: 420 YLAIFSAINIVTYVPMFSTWLPSVI 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: 596 Number of extensions: 40 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