Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 351279 BT1751 Glycine betaine transport ATP-binding protein (NCBI ptt file)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Btheta:351279 Length = 408 Score = 177 bits (448), Expect = 6e-49 Identities = 96/235 (40%), Positives = 144/235 (61%), Gaps = 7/235 (2%) Query: 7 TDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDH 66 +++ K G TVAV D +L I++ E V++G SG GKST LR + L PTSG++ I G Sbjct: 31 SEILKATGCTVAVKDANLSINEGEIFVIMGLSGSGKSTLLRCINRLIRPTSGEVIINGTD 90 Query: 67 M------NYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 + + +++AMVFQ++ L PH +V NI FGLE + G ER+++ +E + Sbjct: 91 IAKVSDKELLQIRRKELAMVFQNFGLLPHRSVLHNIAFGLELQ-GVKKGEREQKAMESMQ 149 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 +G+ ++ ELSGG QQRV L RA+ +PEV LMDE S LD +R +M+ EL L Sbjct: 150 LVGLKGYENQMVSELSGGMQQRVGLARALANNPEVLLMDEAFSALDPLIRVQMQDELLTL 209 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFI 235 Q ++ T V++TH+ +EA+ + DRIA+M DGE+ Q+ + E EP N +V F+ Sbjct: 210 QSKMKKTIVFITHDLSEAIKLGDRIAIMKDGEIVQIGTSEEILTEPANAYVERFV 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: 271 Number of extensions: 11 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: 408 Length adjustment: 31 Effective length of query: 352 Effective length of database: 377 Effective search space: 132704 Effective search space used: 132704 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: 50 (23.9 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