Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_025329853.1 SALWKB2_RS01070 sulfate ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_000600005.1:WP_025329853.1 Length = 360 Score = 107 bits (267), Expect = 3e-28 Identities = 71/220 (32%), Positives = 127/220 (57%), Gaps = 12/220 (5%) Query: 5 LEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFE 64 + I+ ++K +G +AL +++++ G + ALLG +G GK+TL++II+G + D G+L F Sbjct: 3 IRIKQLNKYYGDYQALQNINLQVPTGSLTALLGPSGCGKTTLLRIIAGLERADSGELFFA 62 Query: 65 GKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNK-IFLNKKKMMEESKK 123 +V S R + ++Q AL + ++ N+ +V K I NK ++ + + Sbjct: 63 DDEV---SNLHVRERRVGFMFQHYALFRHMTVFDNVAFGLQVLPKRIRPNKAEIADRVHE 119 Query: 124 LLDSLQIRIPDINMKV--ENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVL 181 LL +Q+ D KV + LSGGQRQ +A+ARA+ K++L+DEP AL + RK L Sbjct: 120 LLQLVQL---DWLAKVYPQQLSGGQRQRIALARALATRPKLLLLDEPFGALD-AKVRKEL 175 Query: 182 E--LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKI 219 L + G+ +++TH+ + E+A++I V+++GK+ Sbjct: 176 RQWLLEIHHQLGITSVLVTHDQEEALEMAEQIVVMNQGKV 215 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: 144 Number of extensions: 5 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: 360 Length adjustment: 27 Effective length of query: 224 Effective length of database: 333 Effective search space: 74592 Effective search space used: 74592 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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