Align Sugar ABC transporter, periplasmic sugar-binding protein (characterized, see rationale)
to candidate H281DRAFT_03378 H281DRAFT_03378 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= uniprot:Q9WXW9 (335 letters) >FitnessBrowser__Burk376:H281DRAFT_03378 Length = 315 Score = 133 bits (334), Expect = 7e-36 Identities = 96/294 (32%), Positives = 148/294 (50%), Gaps = 22/294 (7%) Query: 34 IGVIGKSVHP-YWSQVEQGVKAA-GKALGVDTKFFVPQKEDINA-QLQMLESFIAEGVNG 90 I VI K+ + YW V++G AA A G F P E A ++ M+E+ + V G Sbjct: 28 IAVIVKTANSNYWQNVQKGATAAMADAKGYTMTFQGPAAESAIADEVNMVENAVNRHVAG 87 Query: 91 IAIAPSDPTAVIPTIKKALEMGIPVVTLDTDSPDSGRYVY---IGTDNYQAGYTAGLIMK 147 I +APSDP A++P +KKA E IPVV +D+ D+G+ Y + TDN +AG M Sbjct: 88 IVLAPSDPDALVPAMKKAWEAHIPVVLIDSTVSDAGKQYYQSFLSTDNVKAGELCAKAMI 147 Query: 148 ELLGGKGKVVIGTGSLTAMNSLQRIQGFKDAIK-DSEIEIVDILNDEEDGARAVSLAEAA 206 + +G GKV + + A + + R+ GF+ I S++++V + A A++ Sbjct: 148 DRVGQTGKVAVMSYVPGAGSEVGRVGGFRKYIAAHSKLQLVGPFYSQSQMANALNQTTDV 207 Query: 207 LNAHPDLDAFFGVYAYNGPAQALVVKNAGKVGKVKIVCFDTTPDILQYVKEGVIQATMGQ 266 L+A+PDL FG ++ +GK GKV + FD D+ +V++G IQA Q Sbjct: 208 LSANPDLKGIFGANEPTAVGMGRALQQSGKGGKVIAIGFDGNQDLQGFVRDGTIQAIAVQ 267 Query: 267 RPYMMGYLSVTVLYLMNKIGVQNTLMMLPKVKVDGKVDYVIDTGVDVVTPENLD 320 Y MGY G+Q + ++ + V +V DTGV +V +NLD Sbjct: 268 SSYQMGYK-----------GIQTLVNVIERKPVSKQV----DTGVMMVEKQNLD 306 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: 238 Number of extensions: 16 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: 315 Length adjustment: 28 Effective length of query: 307 Effective length of database: 287 Effective search space: 88109 Effective search space used: 88109 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