Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__WCS417:GFF2365 Length = 325 Score = 236 bits (602), Expect = 6e-67 Identities = 123/303 (40%), Positives = 203/303 (66%), Gaps = 9/303 (2%) Query: 44 LLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVM 103 +L+ + +F+S FM N + IL+ T++NG+LA+ TYVI+T GIDLSVG+++ F + Sbjct: 32 ILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFAGLC 91 Query: 104 AGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVIS 163 + +V T G L ++A +F GA+ G ++G ++A L +PPF+ATLGM+ + +G++ +++ Sbjct: 92 SAMVATQ-GYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTFILN 150 Query: 164 GTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFA 223 PI + + + A+ IG + P + +P ++I +VA+ ++L T +GRY +A Sbjct: 151 DGSPIT-DLPDAYLALG----IGKIGP-IGVP--IIIFAVVALIFWMVLRYTTYGRYVYA 202 Query: 224 LGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAV 283 +G NE++ R SG+ V +VY SG + G+AG+++++R SA P G YELDAIAAV Sbjct: 203 VGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAV 262 Query: 284 VIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRR 343 VIGGTSLSGGTG+I+GT+ GA ++ V+ NGL ++ V+ +Q V G+II+ AV +D+ R+ Sbjct: 263 VIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVLIDVWRK 322 Query: 344 RRR 346 ++R Sbjct: 323 KKR 325 Lambda K H 0.326 0.139 0.398 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: 272 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: 347 Length of database: 325 Length adjustment: 28 Effective length of query: 319 Effective length of database: 297 Effective search space: 94743 Effective search space used: 94743 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: 49 (23.5 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