Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 246 bits (628), Expect = 7e-70 Identities = 145/362 (40%), Positives = 203/362 (56%), Gaps = 25/362 (6%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M +QL + K FG+ A+ + L I EF+V VGPSGCGKST LR++AGLE G + Sbjct: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 + G + + RD+AMVFQ YALYPHM+V +N+ F L+ + DE+V A Sbjct: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAK-VDKQVIDEKVQNAAR 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 L + L R P ELSGGQ+QRVA+GRAIVR P+VFL DEPLSNLDA LR + R E+ L Sbjct: 120 ILNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 L TT+YVTH+Q EAMT+ADR+ V+ DG ++QV +P E Y +P N FVA+FIG P + Sbjct: 180 HRDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQM 239 Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEV--ADAAPDDAALDD 298 N+V + P+ + + +G+RPE+I V A P +D Sbjct: 240 NVV---------PVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQVD- 289 Query: 299 HDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHL 358 ++E G + +++++ P T+ + GD V++ I + H Sbjct: 290 --------LIEALGAETLIYVTTPGGAQFVSRQNDRTD----LRVGDAVSLDIDASQAHW 337 Query: 359 FD 360 FD Sbjct: 338 FD 339 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: 320 Number of extensions: 14 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: 350 Length adjustment: 30 Effective length of query: 353 Effective length of database: 320 Effective search space: 112960 Effective search space used: 112960 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