Align ABC transporter for D-Cellobiose and D-Salicin, permease component 2 (characterized)
to candidate GFF3853 PGA1_78p00170 putative sn-glycerol-3-phosphate transport system permease protein UgpA
Query= reanno::Smeli:SMc04258 (302 letters) >FitnessBrowser__Phaeo:GFF3853 Length = 310 Score = 454 bits (1167), Expect = e-132 Identities = 216/293 (73%), Positives = 258/293 (88%), Gaps = 1/293 (0%) Query: 10 RPNQWLRNLNAKIASIPMILTAMVIFVGGTAWTVVYSFTNSKLLPRLAFVGFDQYERLWA 69 RP + LRNLNAKIAS+PMILTA+V+F+GGTAWTV +SFT S+LLP+ FVGFDQYERLW+ Sbjct: 19 RPPRVLRNLNAKIASVPMILTALVVFMGGTAWTVAHSFTKSRLLPKWKFVGFDQYERLWS 78 Query: 70 APRWLVSIQNLAVFGCLSLVFSLVIGFVLAALMDQKIRFENTFRTIMLYPFALSFIVTGL 129 + RWL+S++NL ++G SLV ++ IGF LAAL+D+KIRFE FRTI LYPFALSF+VTGL Sbjct: 79 SNRWLISVENLLIYGLCSLVLTMAIGFTLAALLDRKIRFEGAFRTIFLYPFALSFVVTGL 138 Query: 130 VWQWLLNPQYGIQSIVRSLGWTSFSFDPLYNSNIVIYGILIAALWQGTGLVMCLMLAGLR 189 WQW+LNP +GIQ++VRS GW SF+FDPL N VI+G+LIA LWQG+G VM +MLAGLR Sbjct: 139 AWQWILNPDFGIQNVVRSWGWESFAFDPLNNPETVIFGVLIAGLWQGSGFVMVIMLAGLR 198 Query: 190 GIDEDIWKAARVDGIPMWKTYVLIIIPMMRGVFITTLVIIASGIVKVYDLVVAQTSGGPG 249 GIDEDIWKAARVDGI + KTYV +IIPMMR VF+T LVIIASGI+K+YDLVVAQT+GGPG Sbjct: 199 GIDEDIWKAARVDGIGVTKTYVRVIIPMMRPVFVTALVIIASGIIKLYDLVVAQTNGGPG 258 Query: 250 IASEVPAKYVYDYMFQAQNLGQGFAASTMMLVTVAIIIVPWAYLEFGGGRKRG 302 I+SEVPAKYV +YMF+AQNLGQGFAASTMML++V II+VPWAYLEF GG+KRG Sbjct: 259 ISSEVPAKYVINYMFEAQNLGQGFAASTMMLLSVIIILVPWAYLEF-GGKKRG 310 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: 446 Number of extensions: 20 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: 310 Length adjustment: 27 Effective length of query: 275 Effective length of database: 283 Effective search space: 77825 Effective search space used: 77825 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