Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 207786 DVU2299 glycine/betaine/L-proline ABC transporter, ATP binding protein
Query= uniprot:D4GP38 (383 letters) >MicrobesOnline__882:207786 Length = 397 Score = 174 bits (440), Expect = 5e-48 Identities = 96/242 (39%), Positives = 143/242 (59%), Gaps = 7/242 (2%) Query: 8 DLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHM 67 ++ +R V VD S D+++ E +V++G SG GKST +R L L PT+G + + G + Sbjct: 32 EIHRRTSHAVGVDRASFDVEEGEIVVVMGLSGSGKSTLVRCLNRLIEPTAGTVTVDGRDV 91 Query: 68 N------YRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAET 121 R + R MVFQ++AL+PH TV QN FGLE G AER+ + + E Sbjct: 92 TSMPVDELRRLRQRSFGMVFQNFALFPHRTVLQNAAFGLEAM-GVPRAERERQAMVSLER 150 Query: 122 LGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQ 181 +G+A+ +P +LSGG QQRV L RA+ DP++ LMDE S LD +R +M+ EL LQ Sbjct: 151 VGLAEWAASRPAQLSGGMQQRVGLARALSLDPDILLMDEAFSALDPLIRRDMQDELLRLQ 210 Query: 182 DQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMIN 241 D L T V+++H+ EA+ + DRI +M DG + Q+ +P + P + +VA F+GE + Sbjct: 211 DDLQKTIVFISHDLDEALKLGDRIVLMRDGAVVQIGTPEDILTNPADDYVARFVGEADVT 270 Query: 242 LV 243 V Sbjct: 271 KV 272 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: 374 Number of extensions: 26 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: 397 Length adjustment: 30 Effective length of query: 353 Effective length of database: 367 Effective search space: 129551 Effective search space used: 129551 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