Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Synpcc7942_0249 Synpcc7942_0249 ATPase
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__SynE:Synpcc7942_0249 Length = 261 Score = 110 bits (275), Expect = 3e-29 Identities = 68/217 (31%), Positives = 124/217 (57%), Gaps = 13/217 (5%) Query: 10 VHKSFG-AVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKV 68 V K +G +AL GVS+ + +GEVV ++G +G+GKST ++ ++ RG++ EG ++ Sbjct: 27 VEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRL 86 Query: 69 IFNSPNDARSLG-----IETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123 +D R + + ++Q L P L + N+ LA + + + + +++ Sbjct: 87 ----SHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEAT--ARQ 140 Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183 LL+ ++I + LSGGQ+Q VA+ARA+ +++L DEPT+AL R+VL++ Sbjct: 141 LLERVRIA-EQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDV 199 Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220 R+L +G+ +L+ TH + EVADR+ ++ G+I+ Sbjct: 200 MRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIV 236 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: 102 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