Align TRAP-type large permease component (characterized, see rationale)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__Miya:8501407 Length = 427 Score = 319 bits (818), Expect = 9e-92 Identities = 173/409 (42%), Positives = 249/409 (60%), Gaps = 5/409 (1%) Query: 15 AIGVPVAFSLMFCGVVLMWYMGM-----FNTQIIAQNMIAGADTFTLLAIPFFILAGELM 69 A+ PVA +L + G+ + Q + AGAD+F LLA+P F+LAGELM Sbjct: 15 ALNAPVAVALGGAAFAAVLAKGLTMPVGLEPMLAVQRLYAGADSFPLLAVPLFMLAGELM 74 Query: 70 NAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILIPMMAKA 129 +AGG+SRRI+ A A VGH+ GGL V++++A+ A +SGSAAADTAA+ +ILIP M + Sbjct: 75 SAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAADTAAVGSILIPAMIRR 134 Query: 130 GYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMGIALVATW 189 GY P + + AAGG I +IPPS+ IVFG SI +LF G++PGL+MG +LVA Sbjct: 135 GYPAPLAGAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAGGVLPGLLMGASLVALC 194 Query: 190 LLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEAAVVAAVYAL 249 ++ R+ P R + A WALG P IILG I GV T TE+A +A YAL Sbjct: 195 VVEARRTGRVPERRFDARALWPAIRSGAWALGAPAIILGTIIGGVATATESAAMAVAYAL 254 Query: 250 FVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGFISPLI 309 VG+ +REL+ RDLP + L A T+AV+M ++ AA + W++ +P I ++ L Sbjct: 255 PVGLYAHRELRWRDLPRLALCAGVTSAVVMLIIAAASLFGWVMALERLPQAIAAWMLSLS 314 Query: 310 DRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIMNTCIGL 369 +L+ ++ L++LVVG L+ T IL+ PVL+P++ GID V+ GV+ ++N IG+ Sbjct: 315 GDRIVLLLLVNLLLLVVGAFLETTAAILLFVPVLVPLLPALGIDLVHLGVIVVVNLAIGM 374 Query: 370 LTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDIVI 418 LTPP+GV L V + R+PL + + P LV I+ L L+ FP +V+ Sbjct: 375 LTPPLGVCLVVSCSIARIPLSAISRAIVPMLVVLIVDLLLVTFFPPLVL 423 Lambda K H 0.331 0.145 0.430 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: 526 Number of extensions: 20 Number of successful extensions: 1 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: 425 Length of database: 427 Length adjustment: 32 Effective length of query: 393 Effective length of database: 395 Effective search space: 155235 Effective search space used: 155235 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 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