Align Xylose/arabinose import permease protein XylH (characterized, see rationale)
to candidate GFF2333 PS417_11895 ABC transporter
Query= uniprot:Q4J711 (356 letters) >FitnessBrowser__WCS417:GFF2333 Length = 340 Score = 132 bits (332), Expect = 1e-35 Identities = 94/321 (29%), Positives = 156/321 (48%), Gaps = 16/321 (4%) Query: 11 EFQLFLVNVIIALFFYF------ENSAYFSSNNITTIFQYLAEIGIIAIGEAMLMLCGEI 64 E +FLV + I L F + S +S + + ++ IG++AIG +++ I Sbjct: 23 ELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGI 82 Query: 65 DLSPPALANFVPLITLTIYNS------IYQAISPTPAIVVSILLSLGLASLIGLMNGLIT 118 DLS ++ +I ++ + ++ +++ P + + + + LG+ L G +NG I Sbjct: 83 DLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLP-VWIPVAMGLGVGLLAGAINGSII 141 Query: 119 TKAKVNSLITTVGTLFLFNGIALIYSGGYPESFPYFRFLGGTVSILPVPFIWSLGALVFL 178 + I T+G + G+A Y+ G P S + +PV I+ + A++F Sbjct: 142 AVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAMPV-IIFLVVAVIFH 200 Query: 179 ILLLHYTKIGVWTIAAGSNPTGASEVGVPVDRVKIINFIIMANIGALVGIIQGSRVLTIG 238 I L YTK G +T A G N A G+ V R II + I + L G++ +R T G Sbjct: 201 IAL-RYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAAT-G 258 Query: 239 ATNFTADVVLEGIAAAVIGGTSLVGGKGSLVGAFLGSVFISELLNGFNILGINAYEFDAI 298 L+ IAAAVIGGTSL GG G + G +G++ + + +GF +G++AY D I Sbjct: 259 QAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDII 318 Query: 299 LGGAIVVVMVLSYYAKRASYK 319 G IVV +V+ Y + K Sbjct: 319 KGLIIVVAVVIDQYRNKRKLK 339 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: 289 Number of extensions: 23 Number of successful extensions: 3 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: 340 Length adjustment: 29 Effective length of query: 327 Effective length of database: 311 Effective search space: 101697 Effective search space used: 101697 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