Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate BWI76_RS26345 BWI76_RS26345 branched-chain amino acid ABC transporter permease LivH
Query= TCDB::P74318 (286 letters) >FitnessBrowser__Koxy:BWI76_RS26345 Length = 308 Score = 148 bits (374), Expect = 1e-40 Identities = 92/298 (30%), Positives = 166/298 (55%), Gaps = 29/298 (9%) Query: 5 QLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGD---------FMTLAAYLTWWANTS 55 Q +FNG+ +GS AL A+G T+ YGI+ + NFAHG+ FM +AA + +TS Sbjct: 10 QQMFNGVTLGSTYALIAIGYTMVYGIIGMINFAHGEVYMIGSYVSFMIIAALMMMGIDTS 69 Query: 56 GINLWLSMALGCVGTIIAMFIGEWLL----WKPMRARRATATTLIIISIGLALFLRNGIL 111 WL +A G VG I+ W + ++P+R+ + +I +IG+++FL+N + Sbjct: 70 ----WLLVAAGFVGAIVIASAYGWSIERVAYRPVRSSKRLIA--LISAIGMSIFLQNYVS 123 Query: 112 LIWGGNNQNYRVP-------IVPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVG 164 L G +++ +P V + D +L++ + AM+ L L ++ +++G Sbjct: 124 LTEG--SRDVALPSLFNGQWTVGSSDNFSATITTMQLVIWVVTFIAMLALTLFIRYSRMG 181 Query: 165 KAMRAVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYG-LMTTLKPNMGWFLILP 223 +A RA A+++ +A + GIN + V+ T+V+ A + A+ G + G + P +G+ + Sbjct: 182 RACRACAEDLKMASLLGINTDRVIALTFVIGAAMAAVAGVLLGQFYGVINPYIGFMAGMK 241 Query: 224 MFASVILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281 F + +LGGIG+ GA+ GG+I+G+A+ +S + T YK V+ L+I++L + P G+ Sbjct: 242 AFTAAVLGGIGSIPGAMIGGLILGIAEALSSAYLSTEYKDVVSFALLILVLLVMPTGI 299 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: 217 Number of extensions: 12 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: 308 Length adjustment: 26 Effective length of query: 260 Effective length of database: 282 Effective search space: 73320 Effective search space used: 73320 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