Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 8500851 DvMF_1589 ABC transporter related (RefSeq)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Miya:8500851 Length = 354 Score = 213 bits (543), Expect = 5e-60 Identities = 111/242 (45%), Positives = 159/242 (65%), Gaps = 7/242 (2%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M ++L ++TKRFG AVD L+L+I E ++GPSGCGK+TTLRM+AG E G+I Sbjct: 1 MSYVRLVNVTKRFGGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEI 60 Query: 61 YIGGDHMN------YRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDER 114 ++G ++ Y P+ RD MVFQ +A++PH++V +N+ F L ++AE D R Sbjct: 61 HVGDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRR-LSAAEIDRR 119 Query: 115 VVEVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMR 174 E +AD+ + PD+LSGG +QRVAL RA+ +P+V L+DEPLS+LD LR EMR Sbjct: 120 TREALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMR 179 Query: 175 TELQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEF 234 E+++LQ + +YVTH+Q+EAM ++DRI VM +G +QQV +P + Y P N FV F Sbjct: 180 FEIKDLQRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGF 239 Query: 235 IG 236 IG Sbjct: 240 IG 241 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: 333 Number of extensions: 13 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: 383 Length of database: 354 Length adjustment: 30 Effective length of query: 353 Effective length of database: 324 Effective search space: 114372 Effective search space used: 114372 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 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