Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_108402619.1 B9Z44_RS12860 branched-chain amino acid ABC transporter permease
Query= TCDB::P74318 (286 letters) >NCBI__GCF_003063475.1:WP_108402619.1 Length = 291 Score = 140 bits (352), Expect = 4e-38 Identities = 89/285 (31%), Positives = 152/285 (53%), Gaps = 10/285 (3%) Query: 2 DLSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTSGINLWL 61 D QL F+G+A GSI AL A+G TL + NFA G+F+ L A++ +G L L Sbjct: 3 DFLQLFFSGLATGSIYALAALGFTLLWQASGTINFAQGEFVMLPAFMMLGFLAAGFPLVL 62 Query: 62 SMALGCVGTIIAMFIGEWLLWKPM--RARRATATTLIIISIGLALFLRNGILLIWGGNNQ 119 S A CV +++F+ WL + + + +++ +IGL++ +RN + G + + Sbjct: 63 SFAASCV---VSVFVLGWLFKRGVVDPLFKFGMMPIVVATIGLSIAMRNAVRA--GYSAE 117 Query: 120 NYRVP-IVPAQ--DFMGIKFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMRAVADNVDL 176 + P + P + + G+ + AIA ++V L +T G+AM+AVA N + Sbjct: 118 PHPFPNLFPDEVYNIAGVTISATDIGTFVFAIALVLVTQAFLAKTVTGRAMQAVAQNTES 177 Query: 177 AKVSGINVEWVVMWTWVMTAVLTALGGSMYGLMTTLKPNMGWFLILPMFASVILGGIGNP 236 A V GINV ++ +T+ + A+L A + K +MG L F + I+GG N Sbjct: 178 ASVLGINVPRMIFYTFAINALLAAAAAILVTPTYLAKFDMGASLGNKAFFAAIIGGFNNS 237 Query: 237 YGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281 GA+ GG+I+GV + ++ + +YK VAL++ ++++ +PQGL Sbjct: 238 RGALLGGVIVGVCENLAAAYISPAYKDAVALVIFMVVILFKPQGL 282 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: 176 Number of extensions: 12 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: 291 Length adjustment: 26 Effective length of query: 260 Effective length of database: 265 Effective search space: 68900 Effective search space used: 68900 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