Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate Ac3H11_1695 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_1695 Length = 309 Score = 145 bits (367), Expect = 8e-40 Identities = 93/300 (31%), Positives = 160/300 (53%), Gaps = 24/300 (8%) Query: 3 LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWW----------A 52 L Q I NG+ +GS+ AL A+G T+ YGI++L NFAHG+ + + A +W Sbjct: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63 Query: 53 NTSGINLWLSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILL 112 + L L+ + CV F+ E + ++P+R+ A +I +IG+++ L+ ++ Sbjct: 64 APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAP--LITAIGMSILLQTLAMI 121 Query: 113 IWGGNNQNYRVPIVPAQDFM--GIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAV 170 IW N + Y ++P+ F G ++L++ + A+ L ++ T +G+AMRA Sbjct: 122 IWKPNYKPYPT-MLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 Query: 171 ADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGL-MTTLKPNMGWFLILPMFASVI 229 A+N +A + G+ + V+ T+++ AVL A+ G MY T + MG+ L F + + Sbjct: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240 Query: 230 LGGIGNPYGAIAGGIIIGVAQEVSVPWFGT--------SYKMGVALLLMIIILFIRPQGL 281 GGIGN GA+ GGI++G+ + + + GT Y A +++IIIL +RP GL Sbjct: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 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: 227 Number of extensions: 14 Number of successful extensions: 5 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: 309 Length adjustment: 26 Effective length of query: 260 Effective length of database: 283 Effective search space: 73580 Effective search space used: 73580 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