Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate SMa0216 SMa0216 ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Smeli:SMa0216 Length = 246 Score = 202 bits (513), Expect = 7e-57 Identities = 106/237 (44%), Positives = 157/237 (66%), Gaps = 5/237 (2%) Query: 3 DLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLV 62 +LLE+ ++ KSFGA+ AL +S I +GEVV LLGDNGAGKST + +ISG HKP G L Sbjct: 6 NLLELHNISKSFGALTALRNLSFHIGEGEVVGLLGDNGAGKSTTVNLISGIHKPTDGYLS 65 Query: 63 FEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMMEES 121 +GKK F+ +D+ GIETIYQ AL+ L I NIF+ RE+T++ FL +++M + + Sbjct: 66 VDGKKTTFSCRSDSADAGIETIYQHTALVDSLSITRNIFMGRELTDRFGFLRQREMRDIA 125 Query: 122 KKLLDSLQIRIPDINMK---VENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178 ++L + + I I+ V NLSGGQ+QAVA+ARAVYF +++L+DEPT+ALSV E Sbjct: 126 MEVLQN-AVHISGIDSPDTLVGNLSGGQKQAVAIARAVYFKKRVLLLDEPTSALSVRETE 184 Query: 179 KVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITE 235 +L LK + + +++THN+ Y+V DR ++ G +F +K +T + ++TE Sbjct: 185 ALLNQVLKLKAENVSSVLVTHNLYHAYQVCDRFVIMSHGTKVFDVQKADTTISQLTE 241 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: 164 Number of extensions: 9 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: 251 Length of database: 246 Length adjustment: 24 Effective length of query: 227 Effective length of database: 222 Effective search space: 50394 Effective search space used: 50394 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: 46 (22.3 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