Align NatB aka SLR0559, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_086510703.1 BZY95_RS14935 amino acid ABC transporter substrate-binding protein
Query= TCDB::Q55387 (454 letters) >NCBI__GCF_002151265.1:WP_086510703.1 Length = 401 Score = 164 bits (414), Expect = 6e-45 Identities = 114/386 (29%), Positives = 179/386 (46%), Gaps = 20/386 (5%) Query: 59 GGEGGALKLGALLPATGDLSSIGQNMPLAVQLAVDTINACGGVNGQDVTVVIEDDQT--D 116 G +K+G + TG + S+ + +LAV IN GG+ G V+ D T D Sbjct: 19 GAAQAEVKIGFIGGFTGPIESLTPPIYDGARLAVQQINEQGGILGGQTLVMPSADTTCSD 78 Query: 117 PTAGVSAMTKLAEADQVAGVVGSFASSVSSAAV-PIAVRNNIMMISPGSTSPVFTDQAKK 175 +A +A ++ + V +VG+ + + AA A+ ++M+SP ST+P T+ Sbjct: 79 ASAASNAADRMVNTENVTAIVGALCTGATVAAANSAAIPGGVVMVSPASTAPAVTEL--- 135 Query: 176 GEFKGFWARTAPPDTYQAQALAALAKKQGFTDAATVVINNDYGVGFEKVFVESFTADGGN 235 + RT P D YQ + LA L +GF + A +NNDYG G F +F A GG Sbjct: 136 -DDNDLVFRTVPSDAYQGEILAKLMLDKGFDEVAVTYVNNDYGRGLADAFTAAFEAGGGM 194 Query: 236 VTNKDNPVRYDPKAATLDTEAAQGFANSPDAVAAILYAD-TGSVLVQSAYRQGLMDGVTL 294 V + ++ A +E A+ + + + YAD +G +++ AY G Sbjct: 195 VAEN---LAHEDGRADYRSELGSLSASGAETLVVLAYADGSGQTILRQAYESGAF--TQF 249 Query: 295 LLTDGVYSPDFVEKVGKDANGVSLLSGALGTVPGADGKSLEAFTAQWKDATGGKDVTAFV 354 DG+ +E VG D +L G + T PG+ A+ +A F Sbjct: 250 AGADGMVGSSLIEAVGAD-----VLEGMIATRPGSPELPGTEIFAEAAEAADLDPTAVFA 304 Query: 355 PHTYDATVLMMLAAEAAKSNTGAGIQSKIRDVSNGPGEEVT--DACEAIAMVREGKDINY 412 YDA L+ LA E S G+ +R VS+ PGE + + +A+ ++ G++INY Sbjct: 305 AQAYDAAFLLALAIEQNGSAEREGLSQALRSVSSAPGEVILPGEWEKAVELIAAGEEINY 364 Query: 413 QGASGNVDIDENGDVVGTYDVWTVKG 438 +GASG+ + DENGDV G V+G Sbjct: 365 EGASGSHEFDENGDVPGVVVEMVVEG 390 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: 456 Number of extensions: 28 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: 401 Length adjustment: 32 Effective length of query: 422 Effective length of database: 369 Effective search space: 155718 Effective search space used: 155718 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