Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1841 Length = 892 Score = 201 bits (510), Expect = 7e-56 Identities = 124/329 (37%), Positives = 186/329 (56%), Gaps = 7/329 (2%) Query: 1 MNAKTITAPVTAAPRNRL--RLSLDRFGLPLVFILLCVVMAFSS--EYFMTWRNWMDILR 56 MNA T A A P + R L + L L+ +L +V FSS EYF + ++ I Sbjct: 563 MNAPTAPAAPAATPSSASVWRSQLGTY-LGLLAVLAGMVALFSSLSEYFWSAETFITIAN 621 Query: 57 QTSINGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQ-GYGLLAAVSAGMFAGAM 115 + ++AVGMT+V++ GIDLSVGS++A A SA Q G+ + AA + + G + Sbjct: 622 EIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAAAILQWGWTVPAAAALALATGLV 681 Query: 116 LGVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGV 175 G + G + +P F+ +LGML RG +++ D S + DA L G I Sbjct: 682 CGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTD-SRTQYVGDAISWLSAPFFGGISF 740 Query: 176 PIIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLA 235 ++ V+ ++ +VL T +GR V +G NE++ R +G+ R + V+ ++GLLAGLA Sbjct: 741 AFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGVDPRPIRVIVFAMTGLLAGLA 800 Query: 236 GVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNL 295 G++ SAR +A P AG EL IAAVVIGGTSL GG GS+V T FG L+I V+ GL Sbjct: 801 GLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGSVVNTAFGVLIIAVLEAGLAQ 860 Query: 296 LGVSSYYQQVAKGLIIVFAVLIDVWRKKK 324 +G S +++ G +IV AV++D R+++ Sbjct: 861 VGASEPSKRIITGFVIVAAVIVDTLRQRR 889 Lambda K H 0.326 0.141 0.412 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: 523 Number of extensions: 26 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: 325 Length of database: 892 Length adjustment: 35 Effective length of query: 290 Effective length of database: 857 Effective search space: 248530 Effective search space used: 248530 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 (21.6 bits) S2: 52 (24.6 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