Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate SM_b20352 SM_b20352 sugar ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Smeli:SM_b20352 Length = 354 Score = 246 bits (628), Expect = 6e-70 Identities = 134/323 (41%), Positives = 204/323 (63%), Gaps = 19/323 (5%) Query: 9 TFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAID 68 T +L +AL ++ F +I P FL+ NL + + +A+ LA+G TFVII+GG ID Sbjct: 21 TLMKLRTFIALFAVVAFFSIFAPNFLSTANLILMSKHVALNAFLAMGMTFVIITGG--ID 78 Query: 69 LSPGSMVALTGVMVAWLMTHGVP------VWISVILILLFSIGAG----AWHGLFVTKLR 118 LS GS+V L G++ L+ +G+ V+ +V+ + L ++ G A +GL +TKL Sbjct: 79 LSVGSIVGLCGMVAGGLILNGIDLQFGYTVYFNVVEVCLITLAVGIVIGAVNGLLITKLN 138 Query: 119 VPAFIITLGTLTIARGMAAVITKGWP---IIGLP----SSFLKIGQGEFLKIPIPVWILL 171 V FI TLGTL +ARG A + + G ++G P + F +G G L +P+ +W+L+ Sbjct: 139 VAPFIATLGTLYVARGFALLSSGGQTFPNLVGKPELATTGFAFLGSGRLLGLPVSIWVLI 198 Query: 172 AVALVADFFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAA 231 VAL A + R T G+H+ A GGNE AAR SG+ VDRV+M +M SGF A +VG++I++ Sbjct: 199 VVALAAAYVARYTPIGRHIFAVGGNERAARMSGIRVDRVKMFVYMFSGFCAAIVGLVISS 258 Query: 232 RLSQGQPGVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTY 291 L P G+ +EL AIA+ V+GGTS++GG G++ G I+GA +I +L + LV++ +S++ Sbjct: 259 ELMASHPATGNSFELNAIAAAVLGGTSMSGGRGTIGGTIIGAFVIGILSDGLVMMGISSF 318 Query: 292 WHNVVIGIVIVVAVTLDILRRRL 314 W V+ GIVI+VAV +D +RRL Sbjct: 319 WQMVIKGIVIIVAVVVDQAQRRL 341 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: 346 Number of extensions: 24 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: 354 Length adjustment: 28 Effective length of query: 289 Effective length of database: 326 Effective search space: 94214 Effective search space used: 94214 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: 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