Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate 7024901 Shewana3_2075 inner-membrane translocator (RefSeq)
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__ANA3:7024901 Length = 405 Score = 135 bits (340), Expect = 2e-36 Identities = 101/320 (31%), Positives = 168/320 (52%), Gaps = 18/320 (5%) Query: 11 RELGPLVALVSLAVFTAILNPRF---------LTAFNLQALGRQIAIFGLLAIGETFVII 61 R L PL+AL L + ++ F L + L R + LL+IG + VI Sbjct: 61 RYLWPLLALSILLLANLFIDSSFFNISYQDDRLYGSLIDILNRSAPV-ALLSIGMSLVIA 119 Query: 62 SGGGAIDLSPGSMVALTGVMVAWLMTHGVPVWISVILI-LLFSIGAGAWHGLFVTKLRVP 120 +GG IDLS G+++A+ G + A L+ ++VI L+ + AG +G V+ L + Sbjct: 120 TGG--IDLSVGAVMAIAGAVCANLLLVPDISLVTVIAAGLIVGLLAGCINGGLVSFLGIQ 177 Query: 121 AFIITLGTLTIARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFF 180 + TL + RG+A +I +G I F IG G+FL +P+PVWI++ + + Sbjct: 178 PIVATLLLMVAGRGVAQLINQGQIITFQHPGFAAIGVGQFLGLPMPVWIVIGMLTFSQLL 237 Query: 181 LRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQP-- 238 LRKT G + A G N A+R+ G+N +++ A+ ++G A + G+I A + QG Sbjct: 238 LRKTALGLFIEAVGCNAKASRYLGINDKSIKLFAYGIAGLCAALAGMISTADI-QGSDAN 296 Query: 239 GVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIG 298 G EL A+ + VIGG +LTGG S++ ++VGA II L +++ + ++ ++ Sbjct: 297 NAGLWLELDAVLAVVIGGAALTGGRFSLILSVVGALIIQTLATTIIVSGLPAKFNLLIKA 356 Query: 299 IVIVVAVTLDI--LRRRLAS 316 IVI+ + L RR+L++ Sbjct: 357 IVILTVLLLQSAKFRRQLSA 376 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: 308 Number of extensions: 19 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: 317 Length of database: 405 Length adjustment: 29 Effective length of query: 288 Effective length of database: 376 Effective search space: 108288 Effective search space used: 108288 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