Align ABC transporter permease (characterized, see rationale)
to candidate WP_049991587.1 LT39_RS16410 sugar ABC transporter permease
Query= uniprot:A0A165KPZ4 (293 letters) >NCBI__GCF_000784335.1:WP_049991587.1 Length = 319 Score = 178 bits (452), Expect = 1e-49 Identities = 104/282 (36%), Positives = 151/282 (53%), Gaps = 20/282 (7%) Query: 17 PAFVLGFAFIYGLMVWNGVLSLTVSRML--PNYEWAGLAQYERLWEMDRWWVALKNLGIF 74 P +L F+YG + WN V+SLT L P Y L Y +L + AL+N Sbjct: 49 PPTLLVLLFVYGAIGWNVVISLTGWSGLGQPEYTNFSLEMYRQLPADQNFRAALRNTVAL 108 Query: 75 GVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKW------LLNP 128 VG+ G SLL+G+ LA+L+D+KIR E RTIYL PMALSFVVT W W L+N Sbjct: 109 LVGFTGVSLLVGLGLALLVDRKIRFENTFRTIYLLPMALSFVVTAIFWSWMYASNGLINA 168 Query: 129 GLGIEKMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSIIK 188 L I WL + + + V+ A +WQ +G+ M ++LAGLR I D + Sbjct: 169 VLPISP------------DWLGNPRLKLAAVIFALVWQFSGYCMIVYLAGLRSIPDDHYE 216 Query: 189 AAQVDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGPGFATDVPAT 248 AA++DGAS ++YWR+++P LR +VL A+K+FD + + PG + D+ A Sbjct: 217 AARIDGASTLKLYWRVIIPQLRSSTVGATVVLMVFALKAFDFIYVMFGTNPGRSVDILAV 276 Query: 249 FMYTMSFSRGQIGLGAASATMMLATVAALVIPYLYSELRTKA 290 MY +FS + GAA A ++ ++ PY Y++ + A Sbjct: 277 MMYREAFSAAEWAYGAAVAVVLFLLALTIIGPYAYTQYKRGA 318 Lambda K H 0.327 0.141 0.451 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: 301 Number of extensions: 13 Number of successful extensions: 3 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: 293 Length of database: 319 Length adjustment: 27 Effective length of query: 266 Effective length of database: 292 Effective search space: 77672 Effective search space used: 77672 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 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