Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate SMc02031 SMc02031 permease
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__Smeli:SMc02031 Length = 349 Score = 226 bits (575), Expect = 8e-64 Identities = 130/327 (39%), Positives = 191/327 (58%), Gaps = 19/327 (5%) Query: 3 SKFKKRTFRELGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIIS 62 +K K F + GPL+ALV L + A FLT NL + RQ A +LA+G+TFVI++ Sbjct: 21 TKLKAVVF-QAGPLIALVLLMAYLAFATSNFLTLDNLSNVARQSAFVAILAVGQTFVILT 79 Query: 63 GGGAIDLSPGSMVALTGVMVAWLMTHG----------VPVWISVILILLFSIGAGAWHGL 112 GG IDLS ++ AL+ + A L+T VP +++++ +L + AGA +G Sbjct: 80 GG--IDLSVAAIAALSASITAVLLTQPLVLFGIDFGFVPPPVAILIGILIGMAAGALNGW 137 Query: 113 FVTKLRVPAFIITLGTLTIARGMAAVITKGWPIIG------LPSSFLKIGQGEFLKIPIP 166 ++K ++P FI TLGT+T RG A ++T G P+ LP S + +G G+ +P+ Sbjct: 138 LISKFKIPDFIATLGTMTAFRGAALLVTDGLPVPSFNAGRQLPESLIWVGGGQLFGVPVS 197 Query: 167 VWILLAVALVADFFLRKTVYGKHLRASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVG 226 I L A + LR T G+ + A GGN AA SG+++ R +++ + +SG LA + G Sbjct: 198 ALIALLCAAAGWYVLRYTALGRAIYAVGGNRAAAHSSGISISRTKIMTYAISGLLAAIAG 257 Query: 227 IIIAARLSQGQPGVGSMYELYAIASTVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLL 286 II+ RL+ + EL +IAS VIGGT+L GGEG V G+I+GA+II +L N L LL Sbjct: 258 IILVGRLNSANALMADGEELRSIASVVIGGTNLFGGEGGVWGSIIGAAIIGVLGNGLNLL 317 Query: 287 NVSTYWHNVVIGIVIVVAVTLDILRRR 313 +VS +W + G+VIVV V D RRR Sbjct: 318 DVSPFWQRIAQGVVIVVVVIFDQWRRR 344 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: 372 Number of extensions: 22 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: 349 Length adjustment: 28 Effective length of query: 289 Effective length of database: 321 Effective search space: 92769 Effective search space used: 92769 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