Align Monosaccharide-transporting ATPase, component of Xylose transporter, XylFGH (XylF (R), 359 aas; XylG (C), 525 aas; XylH (M), 389 aas (characterized)
to candidate BPHYT_RS32810 BPHYT_RS32810 xylose ABC transporter permease
Query= TCDB::A6LW12 (389 letters) >FitnessBrowser__BFirm:BPHYT_RS32810 Length = 399 Score = 391 bits (1005), Expect = e-113 Identities = 194/366 (53%), Positives = 267/366 (72%) Query: 24 KMAAILIATAAIWVLFTFLTDGNFLTTRNLSNLFRQMSITGVLAIGMVFVIILGEIDLSA 83 K+ A+LIA AAIW+ F+ LT G F+T RNLSNL RQMSITG+LA GMVFVII GEIDLS Sbjct: 33 KILALLIAVAAIWIFFSALTHGAFVTPRNLSNLLRQMSITGMLACGMVFVIIAGEIDLSV 92 Query: 84 GSTLGLLGGIAAILNVWFGFSAIPTVVITLILGVIMGAWNGYWIAFRNVPSFIVTLASML 143 GS LGLLGG+AAIL+V + T+ + ++LGV++G +NG+W +R VPSFIV L ML Sbjct: 93 GSLLGLLGGVAAILDVNRHWPIGVTLPVVMLLGVLVGMFNGWWSTYRRVPSFIVGLGGML 152 Query: 144 VFRGVLIGITGGNTVAPLTADFKAIGQAYLPTVVGYILVVLAIVGSAYLILGNRKNKIKY 203 +RG+L+G+TGG+T+AP++ F +GQ YLP + G L V+ + A+L + R+N+ +Y Sbjct: 153 AYRGILLGVTGGSTIAPVSDSFVFVGQGYLPRLAGDTLAVVLFLLLAFLTIRQRRNRERY 212 Query: 204 NIEVRPMALDVLTIVGIGVISLVLVLILNDYQGFPIPVFIMLLLALILAFVGTKTIFGRR 263 + V P+ DV+ +VG GVI V L+ Y G P+PV ++L L I ++ T+T+FGRR Sbjct: 213 QLRVVPVWQDVVKVVGAGVILAGFVATLDRYGGIPVPVLLLLALLGIFTWIATQTVFGRR 272 Query: 264 IYGIGGNRDAARLSGINVKKHIIVIYSVLGLLCAVAGILLTSRLNAGSVSAGQNAEMDAI 323 IY +G N +A RLSG+N + + I++++GL+CA GI+ T+RL AGS SAG E+DAI Sbjct: 273 IYAVGSNLEATRLSGVNTNRVKLAIFALMGLMCAFGGIVNTARLAAGSPSAGSMGELDAI 332 Query: 324 ASCVIGGASLAGGSGTVAGALVGALVMASIDNGMSMMNTPTFWQYIVKGLILLIAVWMDI 383 A+C IGG S+ GGSGTV GAL+GALVMAS+DNGMSM++ +WQ IVKG IL++AVW+D+ Sbjct: 333 AACFIGGTSMRGGSGTVYGALIGALVMASLDNGMSMLDVDAYWQMIVKGSILVLAVWIDV 392 Query: 384 SSKNKK 389 S + + Sbjct: 393 VSGSNR 398 Lambda K H 0.326 0.142 0.410 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: 449 Number of extensions: 21 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: 389 Length of database: 399 Length adjustment: 31 Effective length of query: 358 Effective length of database: 368 Effective search space: 131744 Effective search space used: 131744 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 (21.6 bits) S2: 50 (23.9 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