Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate AZOBR_RS25585 AZOBR_RS25585 ABC transporter permease
Query= reanno::BFirm:BPHYT_RS16110 (311 letters) >FitnessBrowser__azobra:AZOBR_RS25585 Length = 301 Score = 126 bits (316), Expect = 7e-34 Identities = 86/286 (30%), Positives = 144/286 (50%), Gaps = 12/286 (4%) Query: 22 RKANSARWL-ATPSVAVLVLWMAIPLAMTIWFSFSRYNLLNPDLKGF--AGFDNYKYLAS 78 R+ A WL P + VL PL T++FSF+ L L+GF G DNY +L Sbjct: 12 RQRRRAAWLFLLPMLIVLAGVAGWPLFRTVFFSFTDATLAT--LEGFQGVGLDNYLWLMR 69 Query: 79 DPSFGPSIGHTLELIISVLVITVVGGVLMAILFDRKFYGQGIARLLAIAPFFVMPTVSAL 138 DP + ++ +TL + + I G+ +A++ + G+G+ R + P+ + VSA Sbjct: 70 DPVWWRAVWNTLVFTVVSVGIETALGLGIALILNAHLPGRGLLRAAVLIPWAIPTVVSAQ 129 Query: 139 IWKNMILHPVYGLIAQGMRAMGM--QPIDWFAE--YPLTAVIMIVAWQWLPFAFLILFTA 194 +W + H +YG++ + +G+ +P W A+ L VI + W+ PF L++ A Sbjct: 130 MW-GWMFHDLYGVVNAILMGLGLIAEPRAWTADPDLALPVVIAVDVWKSTPFMALLILAA 188 Query: 195 IQSLDQEQKEAARIDGAGPFSMFFYITLPHLKRAIAVVVMMETIFLLSIFAEIYTTTGGG 254 +Q L ++ EAAR+DG P +F ITLP ++ A+ V V+ T+ L +F +Y TG Sbjct: 189 LQMLPRDLYEAARVDGVHPVKVFVRITLPLIRPALMVAVLFRTLDALRVFDLMYVLTGNS 248 Query: 255 PGTATTNLSYLIYSLGLQQFDVGLASAGGILAVVLANIVSFFLVRM 300 T + ++ Y + Q DVG SA L V++ + + V + Sbjct: 249 RSTMSMSVYARQYLIDFQ--DVGYGSAAATLLVLVLAVATVLAVTL 292 Lambda K H 0.328 0.141 0.431 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: 290 Number of extensions: 16 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: 311 Length of database: 301 Length adjustment: 27 Effective length of query: 284 Effective length of database: 274 Effective search space: 77816 Effective search space used: 77816 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: 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