Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_061533630.1 CAter10_RS12285 branched-chain amino acid ABC transporter permease
Query= TCDB::P74318 (286 letters) >NCBI__GCF_001584165.1:WP_061533630.1 Length = 296 Score = 131 bits (330), Expect = 2e-35 Identities = 88/290 (30%), Positives = 155/290 (53%), Gaps = 9/290 (3%) Query: 3 LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAY--LTWWANTSG---I 57 L QL+F+GIA+G I A+ A G LT+ NF G+ + L A L+ N G + Sbjct: 4 LLQLVFSGIALGMIYAVIAFGYQLTFATSGTLNFGQGEALMLGALVGLSLVGNIHGGPYL 63 Query: 58 NLWLSMALGCVGTIIAMFIGEWLLWKPMRARRATATTLIIISIGLALFLRNGILLIWGGN 117 N WL + + V + + EW+ +P + + I+ +I LA+ +N IWG + Sbjct: 64 NYWLMIPVVIVFGALQGVVVEWIGVRPA-LKIKSEFGWIMSTIALAIIFKNVAENIWGKD 122 Query: 118 NQNYRVPI--VPAQDFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVD 175 + + P+ P Q +G + +++V+ A+A M+ + + +++ GKA+ A +++ D Sbjct: 123 DLTFPTPLSATPFQ-VLGANVQPMQVVVVLGALAMMLAVEIFNRKSIYGKAVVATSNDRD 181 Query: 176 LAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGGIGN 235 A + GIN V+ +++ +++ A G + +T MG L L FA I+GG+ + Sbjct: 182 AAGLMGINTSMVITFSYALSSATAAFAGVLVAPLTLTGATMGTALGLKAFAVAIIGGLTS 241 Query: 236 PYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGLFKGT 285 GAI GG+I+G+A+ ++ + T YK LLL++++L I+P GLF T Sbjct: 242 GMGAIVGGLILGIAETLTGFYISTGYKEVPGLLLLLLVLAIKPAGLFGKT 291 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: 203 Number of extensions: 9 Number of successful extensions: 2 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: 296 Length adjustment: 26 Effective length of query: 260 Effective length of database: 270 Effective search space: 70200 Effective search space used: 70200 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 24 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