Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >MicrobesOnline__882:208681 Length = 349 Score = 278 bits (710), Expect = 2e-79 Identities = 166/366 (45%), Positives = 213/366 (58%), Gaps = 25/366 (6%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M I L +++ +GD AVDD+S +++ + LVL+GPSGCGKSTTLR++AGLE+ TSG I Sbjct: 1 MSTIVLDKVSRHWGDVRAVDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRI 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 IGG + P R +AMVFQ YAL+PH+TVR NI FGL + +AER +R+ E Sbjct: 61 LIGGRDVTNLPPAQRQLAMVFQSYALFPHLTVRDNILFGLVVRK-VPAAERQKRLDRAVE 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 LG+ LL+RKP ELSGGQQQRVALGRA+V + V LMDEPLSNLDAKLR EMR E++ L Sbjct: 120 ILGLGKLLERKPGELSGGQQQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRAL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 Q L +T VYVTH+QTEAM+MADRI +M G + Q A+P E Y P F FIG P + Sbjct: 180 QQTLGMTMVYVTHDQTEAMSMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPPM 239 Query: 241 NLVR--GTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDD 298 NLVR G G + D +LG+RPE I + D Sbjct: 240 NLVRLQGNDDGIRVAGSRSG-------RVTCHAGADCMLGIRPEHIRIV----------D 282 Query: 299 HDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHL 358 + V VE G +VL + L V G+ G + + P + +H+ Sbjct: 283 DGWRAVVESVEYLGSNSVLSCR-----VGSEELSVVVHGVTDTVVGAEIYLHCPEEHVHI 337 Query: 359 FDAETG 364 FDA TG Sbjct: 338 FDAATG 343 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: 319 Number of extensions: 10 Number of successful extensions: 4 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: 349 Length adjustment: 30 Effective length of query: 353 Effective length of database: 319 Effective search space: 112607 Effective search space used: 112607 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