Align Sugar ABC transporter, periplasmic sugar-binding protein (characterized, see rationale)
to candidate H281DRAFT_02713 H281DRAFT_02713 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= uniprot:Q9WXW9 (335 letters) >FitnessBrowser__Burk376:H281DRAFT_02713 Length = 313 Score = 187 bits (474), Expect = 4e-52 Identities = 121/297 (40%), Positives = 171/297 (57%), Gaps = 18/297 (6%) Query: 32 LTIGVIGKSVHPYWSQVEQGVKAAGKALGVDTKFFVPQKEDINAQLQMLESFIAEGVNGI 91 +++ VI K P++ +G K A GV ++ VPQ + Q+Q++E I+ V+GI Sbjct: 31 ISVAVIPKVAVPFFDDCNKGAKTAAGKAGVKYQWVVPQNTQGSTQVQIIEDLISRHVDGI 90 Query: 92 AIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVYIGTDNYQAGYTAGLIMKELLG 151 AI+ ++P +V +K+A + GI V+T D+DSP SGR +YIGT+N QAG T M + L Sbjct: 91 AISVNEPKSVESVMKRAEQSGIKVLTYDSDSPRSGRSMYIGTNNEQAGATMAETMGKALN 150 Query: 152 GKGKVVIGTGSLTAMNSLQRIQGFKDAI-KDSEIEIVDILNDEEDGARAVSLAEAALNAH 210 G+G+V I TG L A+N +RI G K + K I+IV+ ++D AR VS+ E L AH Sbjct: 151 GQGEVAIITGQLGAVNLNERIAGIKKGLAKYPGIKIVETQGTDDDLARGVSVVETTLRAH 210 Query: 211 PDLDAFFGVYAYNGPAQALVV--KNAGKV-GKVKIVCFDTTPDILQYVKEGVIQATMGQR 267 P L FGV GPA A V+ K G + GK++++ FD PD L+ +KEG IQ M QR Sbjct: 211 PQLKGIFGVSQVGGPAVAKVLNTKEFGTMKGKLEVLAFDDLPDTLKGLKEGYIQGIMVQR 270 Query: 268 PYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLDEYLK 324 P MG S+ V +L+ +I Q PK IDTGV VVT +N+ Y K Sbjct: 271 PVTMG--SLAVEHLVAQIQGQEA---QPK---------DIDTGVTVVTKDNMTSYTK 313 Lambda K H 0.318 0.137 0.388 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: 252 Number of extensions: 20 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: 335 Length of database: 313 Length adjustment: 28 Effective length of query: 307 Effective length of database: 285 Effective search space: 87495 Effective search space used: 87495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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