Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate H281DRAFT_04460 H281DRAFT_04460 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Burk376:H281DRAFT_04460 Length = 279 Score = 199 bits (506), Expect = 5e-56 Identities = 101/251 (40%), Positives = 159/251 (63%), Gaps = 5/251 (1%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +L + +V+K FG V AL GV++ + +GEV LLGDNGAGKSTLIK ++G H+P G + Sbjct: 23 ILALENVNKYFGKVIALSGVTLRLKRGEVHCLLGDNGAGKSTLIKTLAGVHQPSSGQYLV 82 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIF-----LNKKKMM 118 +GK V+F SP DA LGI T+YQDLAL+P L + N F+ RE K+F ++ + Sbjct: 83 DGKPVLFESPKDALDLGIATVYQDLALVPLLSVARNFFMGREPQRKLFGFLNVMDLETSA 142 Query: 119 EESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178 ++ L + I + D + + +SGG++Q +A+ARA++F A+++++DEPTAAL V ++ Sbjct: 143 TTARDKLAEMGINVRDPHQPIGTMSGGEKQCLAIARAIHFGARVLILDEPTAALGVKQSF 202 Query: 179 KVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMT 238 VL+L + KG+ V+ ITHN+ Y + D +L+RGK + KE + +E+ ++M Sbjct: 203 NVLKLIHKARAKGISVIFITHNVHHAYPIGDSFTLLNRGKSLGTFTKETISKDEVLDMMA 262 Query: 239 SFALGKVNLGE 249 A + +GE Sbjct: 263 GGAEMQKMIGE 273 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: 174 Number of extensions: 9 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: 279 Length adjustment: 25 Effective length of query: 226 Effective length of database: 254 Effective search space: 57404 Effective search space used: 57404 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