Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 3607868 Dshi_1276 ABC transporter related (RefSeq)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Dino:3607868 Length = 264 Score = 192 bits (489), Expect = 4e-54 Identities = 104/242 (42%), Positives = 156/242 (64%), Gaps = 12/242 (4%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +++++++ K FGAV AL GVS++I GE LLGDNGAGKST IK +SG HKP +G+++F Sbjct: 10 IIQMKNIEKHFGAVIALAGVSIDIFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGEIIF 69 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI----FLNK----K 115 EG+ + F P DA GI T++Q LA+IP + + N F+ E KI FL++ + Sbjct: 70 EGRPMHFEDPRDAMEAGIATVHQHLAMIPLMSVSRNFFMGNEPVKKIAGINFLDREFADR 129 Query: 116 KMMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVV 175 MEE +K+ + +R PD V LSGG+RQ VA++RAVYF AK++++DEPT+AL V Sbjct: 130 VTMEEMRKM--GINLRGPD--QAVGTLSGGERQTVAISRAVYFGAKVLILDEPTSALGVR 185 Query: 176 EARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITE 235 + VL ++K+G+ V+ ITHN+ V DR VL+RG+ + ++ E EE+ + Sbjct: 186 QTSNVLATIDKVRKQGVAVVFITHNVRHAMAVGDRFTVLNRGQTLGTAERGEITPEELQD 245 Query: 236 VM 237 +M Sbjct: 246 MM 247 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: 156 Number of extensions: 5 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: 264 Length adjustment: 24 Effective length of query: 227 Effective length of database: 240 Effective search space: 54480 Effective search space used: 54480 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