Align ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized)
to candidate H281DRAFT_05891 H281DRAFT_05891 carbohydrate ABC transporter membrane protein 1, CUT1 family
Query= reanno::Smeli:SMc04258 (302 letters) >FitnessBrowser__Burk376:H281DRAFT_05891 Length = 318 Score = 108 bits (271), Expect = 1e-28 Identities = 86/287 (29%), Positives = 137/287 (47%), Gaps = 12/287 (4%) Query: 2 TGLTRGSARPNQWLRNLNAKIASIPMILTAMVIFVGGTAWTVVYSFTNSKL-LPRLA--F 58 T LT S R WL L P IL + I + W + SFTN K +P + F Sbjct: 22 TRLTGLSDRTIAWLFIL-------PTILLLLAINIFPLIWALRLSFTNFKSNMPSVPARF 74 Query: 59 VGFDQYERLWAAPRWLVSIQNLAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLY 118 VG D Y + ++Q A F S+ +++GF LA L++++ R + + T++L Sbjct: 75 VGIDNYVDILTDEDIWYAMQVTARFVFWSVGLEVLLGFGLALLINRQFRGHSFWTTLILL 134 Query: 119 PFALSFIVTGLVWQWLLNPQYGIQSIVRSL--GWTSFSFDPLYNSNIVIYGILIAALWQG 176 P LS V G W +LL PQ G+ + + G SF + + ++ + I++ W Sbjct: 135 PMMLSPAVVGNFWTFLLQPQTGLFNDIVGFFTGIAPGSFQMIGDVSLAPWTIVMVDTWMW 194 Query: 177 TGLVMCLMLAGLRGIDEDIWKAARVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKV 236 T VM + LAGLR I + I++AA VD W+ + I +PM + ++ K+ Sbjct: 195 TPYVMLICLAGLRSIPDYIYEAAEVDRATPWRQFWSITLPMTLPFLMLAVLFRGIENFKM 254 Query: 237 YDLVVAQTSGGPGIASEVPAKYVYDYMFQAQNLGQGFAASTMMLVTV 283 +D+V TSGGPG +E + + F+ G A + ++ VTV Sbjct: 255 FDMVNLLTSGGPGSVTETVSITLKRAAFEKWQTGYSSALAIILFVTV 301 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: 308 Number of extensions: 18 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: 302 Length of database: 318 Length adjustment: 27 Effective length of query: 275 Effective length of database: 291 Effective search space: 80025 Effective search space used: 80025 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