Align C4-dicarboxylate TRAP transporter large permease protein DctM (characterized)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= SwissProt::Q9HU16 (427 letters) >FitnessBrowser__Miya:8501407 Length = 427 Score = 317 bits (813), Expect = 3e-91 Identities = 171/430 (39%), Positives = 264/430 (61%), Gaps = 9/430 (2%) Query: 1 MTILFLFLLLFLLMFIGVPIAVSLGLSGALTIL---LFSPDSVRSLAI--KLFETSEHYT 55 M L LF + LL + P+AV+LG + +L L P + + +L+ ++ + Sbjct: 1 MVGLILFGGMVLLFALNAPVAVALGGAAFAAVLAKGLTMPVGLEPMLAVQRLYAGADSFP 60 Query: 56 LLAIPFFLLSGAFMTTGGVARRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATV 115 LLA+P F+L+G M+ GG++RR++ A+A VGH+ GGLA +V++ M FA +SGS+ A Sbjct: 61 LLAVPLFMLAGELMSAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAADT 120 Query: 116 AAVGSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVYAAATETSVGKLFIAGV 175 AAVGSI I M+R GYP + G +G++IPPSI M+V+ A T S+G+LF GV Sbjct: 121 AAVGSILIPAMIRRGYPAPLAGAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAGGV 180 Query: 176 VPGLLLGLILMVVIYIVARVKKLPAMPRVSLREWLASARKALWGLLLMVIILGGIYSGAF 235 +PGLL+G L+ + + AR R R + R W L IILG I G Sbjct: 181 LPGLLMGASLVALCVVEARRTGRVPERRFDARALWPAIRSGAWALGAPAIILGTIIGGVA 240 Query: 236 TPTEAAAVAAVYSAFVALFVYRDMRLSECPKVLLESGKLTIMLMFIIANAMLFAHVLTTE 295 T TE+AA+A Y+ V L+ +R++R + P++ L +G + ++M IIA A LF V+ E Sbjct: 241 TATESAAMAVAYALPVGLYAHRELRWRDLPRLALCAGVTSAVVMLIIAAASLFGWVMALE 300 Query: 296 QIPQSIASWVTELGLSPWMFLLVVNIVLLIAGNFMEPSAIILILAPIFFPIAMELGIDPI 355 ++PQ+IA+W+ L + LL+VN++LL+ G F+E +A IL+ P+ P+ LGID + Sbjct: 301 RLPQAIAAWMLSLSGDRIVLLLLVNLLLLVVGAFLETTAAILLFVPVLVPLLPALGIDLV 360 Query: 356 HLGIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLGATIRAALPWLMILLVFLIIVTYIPA 415 HLG+I+VVN+ IG++TPP+G+ L V+ ++ +PL A RA +P L++L+V L++VT+ P Sbjct: 361 HLGVIVVVNLAIGMLTPPLGVCLVVSCSIARIPLSAISRAIVPMLVVLIVDLLLVTFFPP 420 Query: 416 VSLALPNWLG 425 + L WLG Sbjct: 421 LVL----WLG 426 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: 531 Number of extensions: 31 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: 427 Length of database: 427 Length adjustment: 32 Effective length of query: 395 Effective length of database: 395 Effective search space: 156025 Effective search space used: 156025 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 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