Align ABC-type transporter, integral membrane subunit, component of Xylose porter (Nanavati et al. 2006). Regulated by xylose-responsive regulator XylR (characterized)
to candidate AO353_20825 AO353_20825 ABC transporter permease
Query= TCDB::Q9WXW7 (317 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20825 Length = 325 Score = 162 bits (411), Expect = 8e-45 Identities = 110/306 (35%), Positives = 162/306 (52%), Gaps = 4/306 (1%) Query: 13 LGPLVALVSLAVFTAILNPRFLTAFNLQALGRQIAIFGLLAIGETFVIISGGGAIDLSPG 72 LG AL+++ ++L+ FL+ L QI +LA+G TFV+I GG IDLS G Sbjct: 21 LGLAGALLAMIALFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGG--IDLSVG 78 Query: 73 SMVALTGVMVAW-LMTHGVPVWISVILILLFSIGAGAWHGLFVTKLRVPAFIITLGTLTI 131 S++AL G V+ ++ G V + +L + + AG G R+P+FI++LG L + Sbjct: 79 SVLALAGSTVSVAILGWGWSVLPAALLGMAAAAVAGTITGSITVAWRIPSFIVSLGVLEM 138 Query: 132 ARGMAAVITKGWPIIGLPSSFLKIGQGEFLKIPIPVWILLAVALVADFFLRKTVYGKHLR 191 ARG+A +T G + +F + I I L V +A L +TV+G++L Sbjct: 139 ARGVAYQMT-GSRTAYIGDAFAWLSNPITFGISPSFIIALLVIFIAQAVLTRTVFGRYLI 197 Query: 192 ASGGNEVAARFSGVNVDRVRMIAFMVSGFLAGVVGIIIAARLSQGQPGVGSMYELYAIAS 251 G NE A R +G+N +++ F + G LAG+ + +RL P GS EL IA+ Sbjct: 198 GIGTNEEAVRLAGINPKPYKILVFSLMGLLAGIAALFQISRLEAADPNAGSGLELQVIAA 257 Query: 252 TVIGGTSLTGGEGSVLGAIVGASIISLLWNALVLLNVSTYWHNVVIGIVIVVAVTLDILR 311 VIGGTSL GG GSV+ G IIS+L L + + ++ G VIVVAV LD R Sbjct: 258 VVIGGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTYR 317 Query: 312 RRLASK 317 + AS+ Sbjct: 318 SQRASR 323 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: 306 Number of extensions: 20 Number of successful extensions: 6 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: 325 Length adjustment: 28 Effective length of query: 289 Effective length of database: 297 Effective search space: 85833 Effective search space used: 85833 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