Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085544777.1 B9Y55_RS07660 ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_900177735.1:WP_085544777.1 Length = 351 Score = 239 bits (610), Expect = 9e-68 Identities = 122/266 (45%), Positives = 178/266 (66%), Gaps = 9/266 (3%) Query: 3 QIQLTDLTKRF----GDTV--AVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPT 56 ++++++++K F G V AVD ++L + D E + L+GPSGCGK+T LRM+AG E P+ Sbjct: 2 ELRISEVSKVFPSHDGGAVVRAVDSVNLTVADGELVTLLGPSGCGKTTLLRMIAGFEDPS 61 Query: 57 SGDIYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVV 116 GD+Y G +N P R+ +VFQ YA++PH+ V +NI FGL + G + ++ Sbjct: 62 EGDLYFGDRRVNNVAPNRRNATLVFQSYAIFPHLNVFENIAFGLRLK-GLKEGDIRSKME 120 Query: 117 EVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTE 176 +V +G+ + R+P +LSGGQQQRVAL RA+V +PE+ L DEPLSNLDAKLR +MR + Sbjct: 121 KVVHMVGLGGMETRRPSQLSGGQQQRVALARAVVMEPELLLFDEPLSNLDAKLREQMRID 180 Query: 177 LQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIG 236 ++ LQ L +T+VYVTH+Q EAM+++DR+ VM DG ++Q SP + Y P N FVA+FIG Sbjct: 181 IRRLQKALGITSVYVTHDQAEAMSISDRVVVMKDGRIEQSGSPVDLYARPRNRFVADFIG 240 Query: 237 EPMINLVRGTRSESTFVGEHFSYPLD 262 + N + GT SE + SYP+D Sbjct: 241 K--ANFLDGTASEGGVILGGKSYPMD 264 Lambda K H 0.317 0.135 0.386 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: 324 Number of extensions: 14 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: 383 Length of database: 351 Length adjustment: 30 Effective length of query: 353 Effective length of database: 321 Effective search space: 113313 Effective search space used: 113313 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 (21.6 bits) S2: 49 (23.5 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