Align ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized)
to candidate BPHYT_RS29185 BPHYT_RS29185 sugar ABC transporter permease
Query= reanno::Smeli:SMc04258 (302 letters) >FitnessBrowser__BFirm:BPHYT_RS29185 Length = 314 Score = 283 bits (725), Expect = 3e-81 Identities = 130/273 (47%), Positives = 188/273 (68%) Query: 20 AKIASIPMILTAMVIFVGGTAWTVVYSFTNSKLLPRLAFVGFDQYERLWAAPRWLVSIQN 79 A +A +PM++T + ++G WT S +NS+ P F GF QY RL+ RWL+S+QN Sbjct: 31 AWLALLPMVMTVVFAYLGTMVWTARVSLSNSRTFPSGDFAGFTQYARLFNNDRWLLSLQN 90 Query: 80 LAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLYPFALSFIVTGLVWQWLLNPQY 139 + ++G +V +VIG +LA +DQ++ E RT+ LYP+A+SF+ TGLVWQW+LNP+ Sbjct: 91 IVIYGACFIVACMVIGLLLAIFIDQRVVAEGALRTVFLYPYAMSFVATGLVWQWILNPEL 150 Query: 140 GIQSIVRSLGWTSFSFDPLYNSNIVIYGILIAALWQGTGLVMCLMLAGLRGIDEDIWKAA 199 G Q+++ LG+ FD + + + VIY I+IA +WQ +GLVM L+LAGLRGID+++WKAA Sbjct: 151 GAQAVLHKLGFAHARFDWIVDQDWVIYTIVIATVWQASGLVMALLLAGLRGIDDELWKAA 210 Query: 200 RVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKVYDLVVAQTSGGPGIASEVPAKYV 259 R+DGIP W+ YV I++PM+ T V++ +VK+YD VVA T GGPG ASEVPAK++ Sbjct: 211 RIDGIPRWRVYVSIVVPMLGPSISTAFVLLFVMVVKLYDAVVAMTQGGPGTASEVPAKFI 270 Query: 260 YDYMFQAQNLGQGFAASTMMLVTVAIIIVPWAY 292 DY+F N+G AAS ++L TV I+ P+ Y Sbjct: 271 MDYLFGRANIGLASAASIVLLATVLAILAPFFY 303 Lambda K H 0.329 0.142 0.449 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: 355 Number of extensions: 13 Number of successful extensions: 1 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: 302 Length of database: 314 Length adjustment: 27 Effective length of query: 275 Effective length of database: 287 Effective search space: 78925 Effective search space used: 78925 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 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