Align ABC transporter permease (characterized, see rationale)
to candidate WP_085638900.1 MGEO_RS13915 sugar ABC transporter permease
Query= uniprot:A0A165KPZ4 (293 letters) >NCBI__GCF_002115805.1:WP_085638900.1 Length = 339 Score = 110 bits (274), Expect = 6e-29 Identities = 88/288 (30%), Positives = 140/288 (48%), Gaps = 19/288 (6%) Query: 11 PKLVVAPAFVLGFAFIYGLMVWNGV-LSLTVSRMLPN----YEWAGLAQYERLWEMDRWW 65 P L + PA +L V+ + LSLT + L + Y + GLA Y ++ E ++W Sbjct: 53 PWLFLLPA-ILALGLYLAYPVFETIRLSLTERQTLSDGTTVYNFVGLANYAQMSEDPKFW 111 Query: 66 VALKNLGIFGVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKWL 125 AL N + + S G++ A L D +I +++ PMA+SFV WK + Sbjct: 112 EALVNNMFWLIVVPAASTAFGLLAAQLTD-RISWGNLAKSLIFMPMAISFVGAAVIWKLV 170 Query: 126 LN---PG---LGIEKMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGL 179 + PG +G+ + W N WL + ++I IW GFAM + A L Sbjct: 171 YDARPPGTEQIGVLNAIYVWLTGNDPQQWLTTPFWNSFLLMIVLIWIQTGFAMVILSAAL 230 Query: 180 RGIDDSIIKAAQVDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGP 239 RGI + I+AA VDGA+ +I+++I +P + ++ + +K FD+V A+T G Sbjct: 231 RGIPEETIEAAIVDGANPFQIFFKIKMPQIAGTIVVVWTTITLVVLKVFDIVFAMTNGQW 290 Query: 240 GFATDVPATFMYTMSFSRGQIGLGAASATMMLATVAALVIPYLYSELR 287 G T V A +M+ F G+G+ASA +++ LV P LY +R Sbjct: 291 G--TQVLANYMFNQLFVARDWGVGSASAMIIM----LLVTPILYWNVR 332 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: 327 Number of extensions: 27 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: 293 Length of database: 339 Length adjustment: 27 Effective length of query: 266 Effective length of database: 312 Effective search space: 82992 Effective search space used: 82992 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