Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= uniprot:Q4J711 (356 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 123 bits (309), Expect = 6e-33 Identities = 90/303 (29%), Positives = 145/303 (47%), Gaps = 12/303 (3%) Query: 11 EFQLFLVNVIIALFFYFENSAYFSSNNITTIFQYLAEIGIIAIGEAMLMLCGEIDLSPPA 70 E L +V I+ L F + S NN + + A IGI A ++++ GEID+S Sbjct: 26 EIGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAMTLIIISGEIDVSVGP 85 Query: 71 LANFVPLITLTIYNSIYQAISPTPAIVVSILLSLGLASLIGLMNGLITTKAKVNSLITTV 130 + FV + + + + V+ LL L L +L+G + G++ V S + T+ Sbjct: 86 MVAFVSVCLAFL-------LQFEVPLAVACLLVLLLGALMGTLAGVLRGVFNVPSFVATL 138 Query: 131 GTLFLFNGIALIYSGGYP---ESFPYFRFLGGTVSILPVPFIWSLGALVFLILLLHYTKI 187 G G+ L + P + +LGG +PV + + + + T Sbjct: 139 GLWSALRGMGLFMTNALPVPIDENEVLDWLGGQFLGVPVSALIMIVLFALFVFISRKTAF 198 Query: 188 GVWTIAAGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTIGATNFTADVV 247 G A G N T A G+ V RV+I+ F + + A+ GI+ +R L G + Sbjct: 199 GRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAAR-LGSGNAGAANGLE 257 Query: 248 LEGIAAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYEFDAILGGAIVVVM 307 + IAA V+GGT+L GG+GSL G LG + I+ + NG +LGIN++ F ++ G I+VV Sbjct: 258 FDVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSF-FQQVVRGVIIVVA 316 Query: 308 VLS 310 VL+ Sbjct: 317 VLA 319 Lambda K H 0.325 0.143 0.404 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: 323 Number of extensions: 16 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: 356 Length of database: 332 Length adjustment: 29 Effective length of query: 327 Effective length of database: 303 Effective search space: 99081 Effective search space used: 99081 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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