Align NatD, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_041099055.1 SUTH_RS10315 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >NCBI__GCF_000828635.1:WP_041099055.1 Length = 294 Score = 132 bits (331), Expect = 1e-35 Identities = 88/276 (31%), Positives = 143/276 (51%), Gaps = 7/276 (2%) Query: 12 GIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTF-FVNTFGVNIWLSMIVAVV 70 GI G + ALA + L + ++ N A G+ L +GAY F +T G IWL ++VAV+ Sbjct: 15 GIGSGGLYALAGLAFVLIFKATKVVNLAIGEMLMMGAYFFFAMASTLGWPIWLGVLVAVL 74 Query: 71 GTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWGGRNQNYN--LPIT 128 G+ + L E+LL M + + ++ +I+IGL+ L + LIWG +P Sbjct: 75 GSGALGALVERLLIRPM--LGESPISVFMITIGLSSILVGAVELIWGADQMRLPDFMPSD 132 Query: 129 PALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDLDLAKVSGIDVEQ 188 P L I VP +A I + + + + G A+RA A D A GI+V + Sbjct: 133 PVL-IGEAMVPPKIFYGFLVATSLIAIVLVVFRFWRGGIALRATASDQAAAYSMGINVPR 191 Query: 189 VIFWTWLIAGTVTSLGGSMYGLITAVRPNMGWFLILPLFASVILGGIGNPYGAIAAAFII 248 V W++ V ++ G + G I+++ P MG F L + VI+GG+ + GA+ ++ Sbjct: 192 VFSMAWVVGAMVAAIAGIIVGSISSLSPTMGVFG-LSVLVVVIVGGLDSVAGALIGGILV 250 Query: 249 GIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGLF 284 G+V+ S +LG +YK +++LVL++RP GLF Sbjct: 251 GLVEAWSGTYLGGEYKMLATFSLLVLVLMVRPYGLF 286 Lambda K H 0.328 0.144 0.426 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: 271 Number of extensions: 19 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: 288 Length of database: 294 Length adjustment: 26 Effective length of query: 262 Effective length of database: 268 Effective search space: 70216 Effective search space used: 70216 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 (21.7 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