Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Burk376:H281DRAFT_02703 Length = 333 Score = 219 bits (559), Expect = 6e-62 Identities = 131/339 (38%), Positives = 196/339 (57%), Gaps = 12/339 (3%) Query: 12 STTMANTASAQGLRARLFNPAARQKLLAFASLLLMILFFSFASPNFMEVDNLVSILQSTA 71 ++T AN A + L R+ FA+L+++ + S ASP F+ L +I+ + Sbjct: 2 TSTAANRADTEALSRRVIRQLRSGIGPLFAALVIICIALSIASPEFLTTSTLTNIMVQVS 61 Query: 72 VNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLTNWGM-PLPLGIA---AAIFFGA 127 V G+ A+ T+VIITSGIDLSVG+++ ++A V+ + LGIA AA+ GA Sbjct: 62 VVGIAAVGGTFVIITSGIDLSVGSLVALTGMVAATVMAGSSPGAIGLGIAGLCAALAVGA 121 Query: 128 LSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSAIAQDSLIGD 187 +G ++G+ +A L++ PFI TL MM + +GL+L IS R F+ F+A ++ G Sbjct: 122 AAGALNGLAVAWLRLVPFIVTLAMMAMARGLTLAISDGRT-KFDFPNAFTAFGAKTVAG- 179 Query: 188 LIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYT 247 LP+P V+++ V ++L KT FG FA+G N+EA RL+G+ V Y Sbjct: 180 ----LPMPMIVMLVIFVI--GHVLLRKTTFGHQVFAVGGNQEAARLAGIPVHRVVFLTYM 233 Query: 248 FSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIM 307 +G IAG+++A RLNSA P+ G EL IAAVVIGGTSL+GG G+I+GT IG ++ Sbjct: 234 LAGVTAAIAGIVLAGRLNSALPSAANGLELQVIAAVVIGGTSLAGGRGSIVGTFIGVVLI 293 Query: 308 SVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRRRR 346 V+ GL ++ V W + G +I AV LD L +RR+ Sbjct: 294 GVINVGLSLLGVNPFWTQFIQGGVIFAAVLLDALSQRRK 332 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: 277 Number of extensions: 21 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: 347 Length of database: 333 Length adjustment: 28 Effective length of query: 319 Effective length of database: 305 Effective search space: 97295 Effective search space used: 97295 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