Align NatB aka SLR0559, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_089303492.1 CHB84_RS21595 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::Q55387 (454 letters) >NCBI__GCF_900188115.1:WP_089303492.1 Length = 413 Score = 160 bits (404), Expect = 9e-44 Identities = 132/427 (30%), Positives = 193/427 (45%), Gaps = 30/427 (7%) Query: 30 ALAGTTAGLMFACAEPEPTPGDGASQPSTGGEGGALKLGALLPATGDLSSIGQNMPLAVQ 89 AL TA ++ ACA+ GDGA E L+LG +LP TGDL+ +G A+ Sbjct: 3 ALVAATALVVTACADDN---GDGADTGEDSAE--PLELGYVLPETGDLAFLGPPQIEALG 57 Query: 90 LAVDTINACGGVNGQDVTVVIEDDQTDPTAGVSAMTKLAEADQVAGVVGSFASSVSSAAV 149 A+ TIN GGV Q++ V+ D++D + S + V ++G+ +S+ S A V Sbjct: 58 FAMQTINDAGGVLDQELPAVVGRDESDQESVASQSADEVLREGVDALIGAASSAKSLAFV 117 Query: 150 PIAVRNNIMMISPGSTSPVFTDQAKKGEFKGFWARTAPPDTYQAQALAALAKKQGFTDAA 209 + ++ S +T+P FTD E F+ RTAP D Q LA G + A Sbjct: 118 DRVMDAGVVQCSGSNTAPTFTDL----ENGDFYFRTAPSDVMQGPVLADTIVGDGHSRVA 173 Query: 210 TVVINNDYGVGFEKVFVESFTADGGNVTNKDNPVRYDPKAATLDTEAAQGFANSPDAVAA 269 +DYG G + S G V N YDP++ D + PDAV Sbjct: 174 LAARADDYGRGLLQATENSLEEAGAEVV---NTTTYDPRSTNFDPVVSDLTNGDPDAVVI 230 Query: 270 ILYADTGSVLVQSAYRQGLMDG------VTLLLTDGVYSPDFVEKVGKDANGVSLLSGAL 323 + + + VL QGL++G + + DG+ + E V + GV L G Sbjct: 231 VSFEEGVQVL------QGLIEGGFGPDEIGIYGADGLKEENLGELVSSEDPGV--LEGMK 282 Query: 324 GTVPGADGKSLEAFTAQWKDATGGKDVTAFVPHTYDATVLMMLAAEAAKSNTGAGIQSKI 383 GT P A E F ++ + F P YD + + LAAEAA S A IQ ++ Sbjct: 283 GTAPAAPED--EQFQEDLQEYAPDLEGFQFSPQVYDCVITIALAAEAAGSTDPADIQQEM 340 Query: 384 RDVSNGPGEEVTDACEAIAMVREGKDINYQGASGNVDIDENGD-VVGTYDVWTVKGDGTL 442 V+ G E T E ++ +G DI+Y G SG +D ENG+ T ++ V DGT Sbjct: 341 VGVTR-DGTECTTFEECKGLLSDGDDIDYNGVSGPLDFTENGEPSQSTIGIYEVDEDGTT 399 Query: 443 EVIDKVT 449 +D+ T Sbjct: 400 ADVDEET 406 Lambda K H 0.313 0.131 0.374 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: 507 Number of extensions: 27 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: 454 Length of database: 413 Length adjustment: 32 Effective length of query: 422 Effective length of database: 381 Effective search space: 160782 Effective search space used: 160782 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 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