Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF717 PGA1_c07320 sugar ABC transporter, ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Phaeo:GFF717 Length = 261 Score = 187 bits (474), Expect = 2e-52 Identities = 103/242 (42%), Positives = 153/242 (63%), Gaps = 12/242 (4%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 L+ ++ + K FG+V AL GVS+++ GE LLGDNGAGKST IK +SG HKP +GD++F Sbjct: 7 LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF 66 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNK--------K 115 EG+ + F P DA + GI T++Q LA+IP + + N F+ E KI K + Sbjct: 67 EGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANR 126 Query: 116 KMMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVV 175 MEE +K+ + +R PD V LSGG+RQ VA+ARAV+F AK++++DEPT+AL V Sbjct: 127 ITMEEMRKM--GINLRGPD--QAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVR 182 Query: 176 EARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITE 235 + VL ++K+G+ V+ ITHN+ V DR VL+RGK + ++ + + EE+ + Sbjct: 183 QTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQD 242 Query: 236 VM 237 +M Sbjct: 243 MM 244 Lambda K H 0.318 0.137 0.371 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: 144 Number of extensions: 3 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: 251 Length of database: 261 Length adjustment: 24 Effective length of query: 227 Effective length of database: 237 Effective search space: 53799 Effective search space used: 53799 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 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