Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Ac3H11_3210 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)
Query= TCDB::P74318 (286 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3210 Length = 292 Score = 151 bits (382), Expect = 1e-41 Identities = 88/284 (30%), Positives = 157/284 (55%), Gaps = 6/284 (2%) Query: 4 SQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANT-SGINLWLS 62 ++L+ +G+ G I AL A+GL L YG++R+ N +HG+F+ L A+LTWWA+T +GI+ L Sbjct: 7 AELVASGLITGGIYALVAMGLNLQYGLMRIMNISHGEFLMLGAFLTWWAHTATGISPLLL 66 Query: 63 MALGCVGTIIAMFIGEWLLWKPMRARRATATTL----IIISIGLALFLRNGILLIWGGNN 118 M L + + + L +K + AR +++ GL ++N LLIWGG+ Sbjct: 67 MPLAFISLFVLGVVVHALCFKRLAARAPNVDVFEARSLMVGFGLMFLVQNTALLIWGGDL 126 Query: 119 QNYRVPIVPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVDLAK 178 + Y P Q G++F +L++ +A+A L +L+ T +GKA+RA+ + A+ Sbjct: 127 RGYEYLADPVQ-IAGMRFTENKLVLFGVALALSAGLIALLRLTLLGKAVRALMQSPTGAQ 185 Query: 179 VSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGGIGNPYG 238 + GIN + + + L+ + G++ + + P+MG + + LGG G+ G Sbjct: 186 LVGINTRRLHPMMFGIGLGLSGVAGALLSMTYEISPSMGEPYTVTALIVITLGGFGSLAG 245 Query: 239 AIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLF 282 ++AGG+++GV + + + + S KM ++ + I +L RP GLF Sbjct: 246 SLAGGLLLGVVEALGMHFSSPSLKMLLSYAVFIGVLIWRPNGLF 289 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: 221 Number of extensions: 10 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: 292 Length adjustment: 26 Effective length of query: 260 Effective length of database: 266 Effective search space: 69160 Effective search space used: 69160 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