Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 209027 DVU0098 polyamine ABC transporter, ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >MicrobesOnline__882:209027 Length = 368 Score = 237 bits (604), Expect = 4e-67 Identities = 131/301 (43%), Positives = 192/301 (63%), Gaps = 17/301 (5%) Query: 4 IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63 I+L +TK F DT A+D++ L+I + EFL L+GPSGCGK+T LR+++G E P +G I + Sbjct: 8 IELRGVTKNFEDTCALDNIDLEIRNGEFLTLLGPSGCGKTTILRLISGFEKPDAGVITLK 67 Query: 64 GDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLG 123 G M+ P+ R + VFQ+YAL+PHM+VR+N+ FGL + +DE V + L Sbjct: 68 GQRMDDAPPEARQVNTVFQNYALFPHMSVRENVGFGLRMQR----RPKDEIARRVHDALR 123 Query: 124 IADL---LDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 + L DR+P +LSGGQQQRVA+ RA+V +P V L+DEP S LD KLR +M+ E+++L Sbjct: 124 MVHLEAHADRRPRQLSGGQQQRVAIARAVVNNPLVLLLDEPFSALDYKLRKQMQLEIKHL 183 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 Q QL +T V+VTH+Q EA M+DR+ VM+DG+++Q+ SP E Y EP NL+VA F+GE I Sbjct: 184 QRQLGITFVFVTHDQEEAFAMSDRVVVMNDGKIEQIGSPQEIYEEPANLYVARFVGE--I 241 Query: 241 NLVRGTRSESTFVG------EHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDA 294 N++ + + G E ++P+ + D+ + +L RPED+ V D Sbjct: 242 NILNAVIAANHGDGLYDAVIEGVTFPIRSQRTFAPGDKVNVLL--RPEDLRVYTLTEDRP 299 Query: 295 A 295 A Sbjct: 300 A 300 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: 360 Number of extensions: 12 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: 368 Length adjustment: 30 Effective length of query: 353 Effective length of database: 338 Effective search space: 119314 Effective search space used: 119314 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