Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Dsui_2060 Dsui_2060 branched-chain amino acid ABC-type transport system, permease component
Query= TCDB::P74318 (286 letters) >FitnessBrowser__PS:Dsui_2060 Length = 293 Score = 147 bits (370), Expect = 4e-40 Identities = 92/285 (32%), Positives = 156/285 (54%), Gaps = 6/285 (2%) Query: 3 LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTSGIN--LW 60 L Q + N + +GS+ AL A+G TL +G+L + N +HG + +Y A S +N LW Sbjct: 2 LEQQLLNALTLGSVYALFALGFTLVFGVLAVINLSHGAVFMVGSYAAL-AMVSHLNAPLW 60 Query: 61 LSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGGNNQN 120 ++M V + + + L+ KP+RAR A +I +IG+ + L + ++G Sbjct: 61 VAMLGAMVVSGTIGLLVDVLVLKPLRARNAPHLIPMIATIGVGIMLTSAAQGLFGAEVLR 120 Query: 121 YRVPIVPAQDFM--GIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVDLAK 178 + ++PA +FM + + ++A+A M VL IL+RT++G+A+RA+A++ A Sbjct: 121 FPEDVMPAGEFMVGDVHVRALEIAIVAIAFLLMAVLFTILKRTQLGRALRAIAESPKAAY 180 Query: 179 VSGINVEWVVMWTWVMTAVLTALGGSMYGL-MTTLKPNMGWFLILPMFASVILGGIGNPY 237 + GINVE + T + A L + G + GL + P MG ++ A +ILGG+G+ Sbjct: 181 LLGINVEGLFHITSFVAAALGGIAGVLIGLNFNAITPFMGQPMLHKGIAVIILGGMGDIR 240 Query: 238 GAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLF 282 GA+ GG+ +G A+ +S + + VA L+ +IL +RP GLF Sbjct: 241 GALIGGLFLGFAEVISKAYLSSQMGDAVAFGLLFLILLVRPSGLF 285 Lambda K H 0.329 0.143 0.450 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: 210 Number of extensions: 13 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: 286 Length of database: 293 Length adjustment: 26 Effective length of query: 260 Effective length of database: 267 Effective search space: 69420 Effective search space used: 69420 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: 48 (23.1 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