Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__Miya:8501407 Length = 427 Score = 270 bits (691), Expect = 5e-77 Identities = 166/457 (36%), Positives = 254/457 (55%), Gaps = 44/457 (9%) Query: 6 LFISLFLCMLLGMPIAIALG---FSSMLTILLFSDDSLASV-ALKLYESTSEHYTLLAIP 61 LF + L L P+A+ALG F+++L L L + A++ + ++ + LLA+P Sbjct: 6 LFGGMVLLFALNAPVAVALGGAAFAAVLAKGLTMPVGLEPMLAVQRLYAGADSFPLLAVP 65 Query: 62 FFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGS 121 F+L+ +S GG++RRI+ A VGH+ GGLA SV++ M FA VSGS+ A AA+GS Sbjct: 66 LFMLAGELMSAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAADTAAVGS 125 Query: 122 IVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLM 181 I+I M+R GYP A V G +G++IPPSI M+V+ A T S R+F G++PGL+ Sbjct: 126 ILIPAMIRRGYPAPLAGAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAGGVLPGLL 185 Query: 182 MGL-LLMLAIYIVARIKKLPSRPFP--GFRPLAISSAKAMGGLALIVIVLGSIYGGIASP 238 MG L+ L + R ++P R F P S A A+G A I+LG+I GG+A+ Sbjct: 186 MGASLVALCVVEARRTGRVPERRFDARALWPAIRSGAWALGAPA---IILGTIIGGVATA 242 Query: 239 TEAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKE 298 TE+AA+A YA + ++ +R++ WRD Sbjct: 243 TESAAMAVAYALPVGLYAHREL------RWRD---------------------------- 268 Query: 299 IRHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLL 358 + + S +++ IIA A LF V+ ER+P IA ++ + L++VNLLL Sbjct: 269 LPRLALCAGVTSAVVMLIIAAASLFGWVMALERLPQAIAAWMLSLSGDRIVLLLLVNLLL 328 Query: 359 LAAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAG 418 L G F+E +A +L+ P+L P+ LGID +HLG+I+VVN+ IGMLTPP+G+ L V+ Sbjct: 329 LVVGAFLETTAAILLFVPVLVPLLPALGIDLVHLGVIVVVNLAIGMLTPPLGVCLVVSCS 388 Query: 419 ITGRSMGWVIHSCIPWLALLLFFLALITYIPQISLFL 455 I + + + +P L +L+ L L+T+ P + L+L Sbjct: 389 IARIPLSAISRAIVPMLVVLIVDLLLVTFFPPLVLWL 425 Lambda K H 0.330 0.144 0.424 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: 610 Number of extensions: 44 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 465 Length of database: 427 Length adjustment: 32 Effective length of query: 433 Effective length of database: 395 Effective search space: 171035 Effective search space used: 171035 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