Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3036 Length = 319 Score = 185 bits (470), Expect = 1e-51 Identities = 108/305 (35%), Positives = 175/305 (57%), Gaps = 6/305 (1%) Query: 13 LGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPG 72 LGP +AL+ F A + RFL+A N + +Q+ + ++AIG+T VI++ G IDLS G Sbjct: 14 LGPFIALILACAFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLVILTAG--IDLSCG 71 Query: 73 SMVALTG-VMVAWLMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTI 131 ++AL G VM +G+ +++ + ++ G +GL VTK+++P FI+TLGTL I Sbjct: 72 MVMALGGIVMTKMAADYGLSAPVAIACGMAVTMLFGLINGLLVTKIKLPPFIVTLGTLNI 131 Query: 132 ARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVW---ILLAVALVADFFLRKTVYGK 188 A + + I +P+ +G L VW ++LA+ LV F LR+T G+ Sbjct: 132 AFAATQLYSGAQTITDIPAGMTALGNTFQLGQTAIVWGAVLMLALYLVTWFALRETAPGR 191 Query: 189 HLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYA 248 H+ A G + A R +G+ D+V + ++++G G+ ++ AR G P G L A Sbjct: 192 HVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQTENLDA 251 Query: 249 IASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLD 308 I++ V+GGTSL GG G +LG +VGA I+ + N L L+ VS+ + +V GI++++AV D Sbjct: 252 ISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVILAVATD 311 Query: 309 ILRRR 313 L R+ Sbjct: 312 QLSRK 316 Lambda K H 0.328 0.143 0.424 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: 261 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: 317 Length of database: 319 Length adjustment: 27 Effective length of query: 290 Effective length of database: 292 Effective search space: 84680 Effective search space used: 84680 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: 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