Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate H281DRAFT_04148 H281DRAFT_04148 monosaccharide ABC transporter membrane protein, CUT2 family
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Burk376:H281DRAFT_04148 Length = 335 Score = 210 bits (535), Expect = 4e-59 Identities = 126/346 (36%), Positives = 201/346 (58%), Gaps = 17/346 (4%) Query: 4 NIHSATSASTTMANTASAQGLRARLFNPAARQKLL--AFASLLLMILFFSFASPNFMEVD 61 N + +S+ T ++ G R A ++ L F LL++ + FAS +F+ Sbjct: 2 NTPNPSSSPKTSTVSSDTPGAPVRFTWAALKRSTLFYPFIGLLVVCIVMVFASDSFLSGA 61 Query: 62 NLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAVMAGVVLT---NWGMPLPLG 118 N+ ++L+ ++N ++A+ T VI+T GIDLSVG++M +A ++ N L +G Sbjct: 62 NIENVLRQVSINAIIAVGMTCVILTGGIDLSVGSVMALAGTLAAGLMVAGMNALAALAVG 121 Query: 119 IAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVISGTRPIYFNDTEGFSA 178 +A + FGA +G+ +A +PP I TL M + +GL+L+ +G PI + S Sbjct: 122 VAVGLGFGAANGFF----VAFAGMPPIIVTLATMGIARGLALIYTGGYPID-GLPDWVSF 176 Query: 179 IAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTFALGSNEEALRLSGVKV 238 ++G P V+I+ ++ + A ++L + FGRY +A+G NE+A RLSGV+V Sbjct: 177 FGSGKILGIQAP-------VVIMAVIYVIAWVLLERMPFGRYVYAIGGNEQATRLSGVRV 229 Query: 239 DFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAAVVIGGTSLSGGTGTIL 298 K+ VYT +G A +++ +RL S QP G G+ELDAIAAVV+GGTS+SGG G+I+ Sbjct: 230 ARVKLIVYTIAGLTSSFAAIVLTARLMSGQPNAGVGFELDAIAAVVMGGTSISGGRGSII 289 Query: 299 GTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILRRR 344 GT+IGA ++ VL NGL ++ V Q V+ G II+LA+Y+ RR+ Sbjct: 290 GTLIGALLLGVLNNGLNMVGVNPYVQNVIKGGIILLAIYISRDRRK 335 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: 263 Number of extensions: 14 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: 335 Length adjustment: 29 Effective length of query: 318 Effective length of database: 306 Effective search space: 97308 Effective search space used: 97308 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