Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate PP_2761 PP_2761 putative Ribose ABC transporter, permease protein
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Putida:PP_2761 Length = 328 Score = 147 bits (370), Expect = 5e-40 Identities = 103/337 (30%), Positives = 170/337 (50%), Gaps = 16/337 (4%) Query: 10 SASTTMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQS 69 S S + A GL R A +L+ ++LFF+ +P F+ V NL S+L + Sbjct: 2 SDSLSAPQPAGLTGLSGR-----ALLRLVMPTLFAAVLLFFALKAPGFLTVGNLSSLLLN 56 Query: 70 TAVN-GVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGMPLPLGIAAAIFFGAL 128 V ++AI TY I GIDLSVGT + F A + V+L N G L + I + G+L Sbjct: 57 NFVLLAIVAIGMTYAIAAGGIDLSVGTALDFSA-LTFVLLLNAGFGLYVAIPGGLLAGSL 115 Query: 129 SGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVIS-GTRPIYFNDTEGFSAIAQDSLIGD 187 +G + +IA L++ PF+ATLG + + + ++S G +PIY + + S +A + ++G Sbjct: 116 AGLFNAGLIAGLRISPFLATLGTLFIGSSVQKLLSEGGQPIYL-EAQVRSGLATERMLG- 173 Query: 188 LIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYT 247 +P +L++ L+A+ ++L + GR LGS R SG+ V+ Sbjct: 174 ------VPLPLLLVALLALVYGVVLARGRLGREIIVLGSQPLVARYSGLAQRRIAALVFI 227 Query: 248 FSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIM 307 S +AG+++ + +N+ P G + ++AI AV IG T + GT++G + Sbjct: 228 ASAFASALAGILLPATVNAYAPMSGNAFLMNAIGAVFIGATLSLHNRVNVPGTLLGVLFL 287 Query: 308 SVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRR 344 +V NGL ++ WQ V TGV+I+ + RR Sbjct: 288 NVTANGLLLIGWNFFWQQVATGVLILSVLLFSFASRR 324 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: 262 Number of extensions: 15 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: 347 Length of database: 328 Length adjustment: 28 Effective length of query: 319 Effective length of database: 300 Effective search space: 95700 Effective search space used: 95700 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