Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate CA265_RS04345 CA265_RS04345 lipoprotein-releasing system ATP-binding protein LolD
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__Pedo557:CA265_RS04345 Length = 216 Score = 95.5 bits (236), Expect = 8e-25 Identities = 68/221 (30%), Positives = 118/221 (53%), Gaps = 9/221 (4%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +L+ + KS+G ++ L GV+ E+ KGE+V+++G +GAGKSTL+ I+ KPD G + Sbjct: 1 MLKATGIRKSYGNLQILKGVNFEVQKGEIVSIIGPSGAGKSTLLHILGTLDKPDDGSVQL 60 Query: 64 EG---KKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEE 120 +G K+ + + R+ I ++Q L+P+ NI + + NKK+ Sbjct: 61 KGTVINKLNGDLLSTFRNQNIGFVFQFHHLLPEFSAIENICIPAFIAK---TNKKQAETR 117 Query: 121 SKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV 180 + +LLD ++ K LSGG++Q VA+ARA+ + +IL DEP+ L A + Sbjct: 118 AFELLDLFGLK-DRAQHKPNQLSGGEQQRVAIARALINNPSIILADEPSGNLDSENAAGL 176 Query: 181 LELARNLKKK-GLGVLIITHNIIQGYEVADRIYVLDRGKII 220 +L +L+ +I+THN + +DR+ + G I+ Sbjct: 177 HQLFVSLRDNFHQTFVIVTHNEHLA-KTSDRVVSMKDGLIV 216 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: 108 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: 216 Length adjustment: 23 Effective length of query: 228 Effective length of database: 193 Effective search space: 44004 Effective search space used: 44004 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