Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate PP_2761 PP_2761 putative Ribose ABC transporter, permease protein
Query= uniprot:A0A1N7UKA9 (325 letters) >FitnessBrowser__Putida:PP_2761 Length = 328 Score = 171 bits (432), Expect = 3e-47 Identities = 104/315 (33%), Positives = 174/315 (55%), Gaps = 4/315 (1%) Query: 5 TITAPVTAAPRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSIN-GI 63 +++AP A +L R +P +F + + A + F+T N +L + I Sbjct: 4 SLSAPQPAGLTGLSGRALLRLVMPTLFAAVLLFFALKAPGFLTVGNLSSLLLNNFVLLAI 63 Query: 64 LAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFM 123 +A+GMTY I GIDLSVG+ L F+ L ++ G+GL A+ G+ AG++ G+ N + Sbjct: 64 VAIGMTYAIAAGGIDLSVGTALDFSALTFVLLLNAGFGLYVAIPGGLLAGSLAGLFNAGL 123 Query: 124 VANLSIPPFVATLGMLSIARGMTFILNDGSPITDLPDAYLALGIGKIGPIGVPI--IIFA 181 +A L I PF+ATLG L I + +L++G L +A + G+ +GVP+ ++ A Sbjct: 124 IAGLRISPFLATLGTLFIGSSVQKLLSEGGQPIYL-EAQVRSGLATERMLGVPLPLLLVA 182 Query: 182 VVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSA 241 ++AL++ +VL GR + +G AR SG+ R++ V++ S + LAG++L A Sbjct: 183 LLALVYGVVLARGRLGREIIVLGSQPLVARYSGLAQRRIAALVFIASAFASALAGILLPA 242 Query: 242 RTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSY 301 + P +G ++ ++AI AV IG T ++ GTL G L + V NGL L+G + + Sbjct: 243 TVNAYAPMSGNAFLMNAIGAVFIGATLSLHNRVNVPGTLLGVLFLNVTANGLLLIGWNFF 302 Query: 302 YQQVAKGLIIVFAVL 316 +QQVA G++I+ +L Sbjct: 303 WQQVATGVLILSVLL 317 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: 261 Number of extensions: 22 Number of successful extensions: 2 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: 328 Length adjustment: 28 Effective length of query: 297 Effective length of database: 300 Effective search space: 89100 Effective search space used: 89100 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: 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