Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate Ga0059261_2703 Ga0059261_2703 ABC-type multidrug transport system, ATPase component
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Korea:Ga0059261_2703 Length = 313 Score = 113 bits (283), Expect = 4e-30 Identities = 75/230 (32%), Positives = 129/230 (56%), Gaps = 13/230 (5%) Query: 1 MSDLLEIRDVHKSFGAV-KALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRG 59 M +L +R V K++ + KAL V ++INKGE+ ALLG NGAGK+TLI II G P G Sbjct: 1 MQPILSVRGVSKTYASGHKALGSVDLDINKGEIFALLGPNGAGKTTLISIICGIVTPSSG 60 Query: 60 DLVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKK--M 117 +V +G I + P AR + I + Q+L++ ++ + + ++F Sbjct: 61 TIVVDGHDAI-SEPRAAR-MKIGLVPQELSV----DMFETVQATTRYSRRLFGRPANDAY 114 Query: 118 MEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEA 177 +++ K L R N KV LSGG ++ V +A+A+ ++ +DEPTA + V Sbjct: 115 IDQVLKDLSLYDKR----NSKVMELSGGMKRRVLIAKALAHEPDILFLDEPTAGVDVSLR 170 Query: 178 RKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEE 227 R + +L +L+++G +++ TH I + E+ADR+ V+++G+++ + K E Sbjct: 171 RDMWKLIGSLRERGTTIILTTHYIEEAEEMADRVGVINKGELLLVEGKAE 220 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: 162 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: 313 Length adjustment: 26 Effective length of query: 225 Effective length of database: 287 Effective search space: 64575 Effective search space used: 64575 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