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_028321170.1 H567_RS0109125 branched-chain amino acid ABC transporter permease
Query= TCDB::Q8YXD0 (288 letters) >NCBI__GCF_000422285.1:WP_028321170.1 Length = 308 Score = 152 bits (383), Expect = 1e-41 Identities = 89/288 (30%), Positives = 160/288 (55%), Gaps = 15/288 (5%) Query: 9 IVNGIAVGSIIALAAVGLTLTYGILRLSNFAHGDFLTLGAYLTFFVNTFGV--------- 59 ++NG+ +G I AL A+G TL YGIL + NFAHG+ G++ + TF + Sbjct: 14 LINGLTIGGIYALIALGYTLVYGILFMINFAHGEIFMFGSFAGYAALTFLLQYGFTEQRP 73 Query: 60 --NIWLSMIVAVVGTVGVMLLSEKLLWSRMRSIRANSTTLIIISIGLALFLRNGIILIWG 117 +I + + A+V + + + E++ + +R RA+ +I +IG ++FL+N +++I Sbjct: 74 LASILAAFLAAMVVSALLGTILERIAYRPLR--RASRLAPLISAIGASIFLQNVMLIIIK 131 Query: 118 GRNQNY-NLPITPALDIFGVKVPQNQLLVLALAVLSIGALHYLLQNTKIGKAMRAVADDL 176 GR Q Y +L +I + Q++++ + + L+ +Q T+ G+AMRAVA+D Sbjct: 132 GRMQVYPDLLHETFFEIGWFNISNFQIMIILGSFFLMAGLYIFIQRTRTGRAMRAVAEDR 191 Query: 177 DLAKVSGIDVEQVIFWTWLIAGTVTSLGGSMYGLI-TAVRPNMGWFLILPLFASVILGGI 235 A + GIDV ++I T++I + + G M G+ T + MG+ + F + +LGGI Sbjct: 192 SAAALMGIDVNRIIMITFVIGSALAAAAGVMVGMYYTQINHMMGFIPGIKAFTAAVLGGI 251 Query: 236 GNPYGAIAAAFIIGIVQEVSTPFLGSQYKQGVALLIMILVLLIRPKGL 283 GN GA+ +G+ + F+ +QYK +A +++LVL+ RP+G+ Sbjct: 252 GNVPGAMLGGLFLGLAEAFGVLFMPAQYKDVIAFALLVLVLIFRPRGI 299 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: 221 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: 288 Length of database: 308 Length adjustment: 26 Effective length of query: 262 Effective length of database: 282 Effective search space: 73884 Effective search space used: 73884 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