Align NatD aka LivH aka SLR0949, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_028321170.1 H567_RS0109125 branched-chain amino acid ABC transporter permease
Query= TCDB::P74318 (286 letters) >NCBI__GCF_000422285.1:WP_028321170.1 Length = 308 Score = 147 bits (371), Expect = 3e-40 Identities = 93/294 (31%), Positives = 162/294 (55%), Gaps = 19/294 (6%) Query: 3 LSQLIFNGIAVGSIIALGAVGLTLTYGILRLSNFAHGDFMTLAAYLTWWANTSGINLWLS 62 L + NG+ +G I AL A+G TL YGIL + NFAHG+ ++ + A T + + Sbjct: 10 LCDQLINGLTIGGIYALIALGYTLVYGILFMINFAHGEIFMFGSFAGYAALTFLLQYGFT 69 Query: 63 --------MALGCVGTIIAMFIG---EWLLWKPMRARRATATTLIIISIGLALFLRNGIL 111 +A +++ +G E + ++P+R RA+ +I +IG ++FL+N +L Sbjct: 70 EQRPLASILAAFLAAMVVSALLGTILERIAYRPLR--RASRLAPLISAIGASIFLQNVML 127 Query: 112 LIWGGNNQNYRVPIVPAQDFMGI---KFEYYRLLVIAMAIAAMVVLHLILQRTKVGKAMR 168 +I G Q Y P + + F I +++++I + M L++ +QRT+ G+AMR Sbjct: 128 IIIKGRMQVY--PDLLHETFFEIGWFNISNFQIMIILGSFFLMAGLYIFIQRTRTGRAMR 185 Query: 169 AVADNVDLAKVSGINVEWVVMWTWVMTAVLTALGGSMYGLM-TTLKPNMGWFLILPMFAS 227 AVA++ A + GI+V ++M T+V+ + L A G M G+ T + MG+ + F + Sbjct: 186 AVAEDRSAAALMGIDVNRIIMITFVIGSALAAAAGVMVGMYYTQINHMMGFIPGIKAFTA 245 Query: 228 VILGGIGNPYGAIAGGIIIGVAQEVSVPWFGTSYKMGVALLLMIIILFIRPQGL 281 +LGGIGN GA+ GG+ +G+A+ V + YK +A L++++L RP+G+ Sbjct: 246 AVLGGIGNVPGAMLGGLFLGLAEAFGVLFMPAQYKDVIAFALLVLVLIFRPRGI 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: 194 Number of extensions: 11 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 Apr 09 2024. 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