Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3036 Length = 319 Score = 206 bits (524), Expect = 7e-58 Identities = 123/290 (42%), Positives = 177/290 (61%), Gaps = 12/290 (4%) Query: 57 TSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAP 116 + F SA+N IL+QV + V+A G T VILTAGIDLS G V+A+ ++ + A Sbjct: 31 SERFLSAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVMALGGIV--MTKMAADY 88 Query: 117 GWAIPMFIFSGLVM----GMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNN 172 G + P+ I G+ + G++NG +V + + F+VTLGT+ A L + T+ Sbjct: 89 GLSAPVAIACGMAVTMLFGLINGLLVTKIKLPPFIVTLGTLNIAFAATQLYSGAQTI--T 146 Query: 173 DIPS-FEWIGNGDFLHVPWLIWVAV---AVVLLSWVILRKTVLGMHIYAIGGNLQAARLT 228 DIP+ +GN L ++W AV A+ L++W LR+T G H+YA+G + +A RLT Sbjct: 147 DIPAGMTALGNTFQLGQTAIVWGAVLMLALYLVTWFALRETAPGRHVYAVGNSPEATRLT 206 Query: 229 GIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGV 288 GI VLL VY ++GLF G+A +S +R + N G LDAI+AVVLGGTSL GG Sbjct: 207 GIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQTENLDAISAVVLGGTSLFGGR 266 Query: 289 GSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQK 338 G I GT+VGALI+GV NGLT++G+SS +Q + G +++LAV D+ +K Sbjct: 267 GVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVILAVATDQLSRK 316 Lambda K H 0.324 0.138 0.417 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: 296 Number of extensions: 19 Number of successful extensions: 5 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: 344 Length of database: 319 Length adjustment: 28 Effective length of query: 316 Effective length of database: 291 Effective search space: 91956 Effective search space used: 91956 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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