Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Keio:18063 Length = 371 Score = 296 bits (757), Expect = 8e-85 Identities = 172/373 (46%), Positives = 229/373 (61%), Gaps = 19/373 (5%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M +QL ++TK +G+ V D++LDI + EF+V VGPSGCGKST LRM+AGLET TSGD+ Sbjct: 1 MASVQLQNVTKAWGEVVVSKDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDL 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 +IG MN P R + MVFQ YALYPH++V +N+ FGL+ G ++RV +VAE Sbjct: 61 FIGEKRMNDTPPAERGVGMVFQSYALYPHLSVAENMSFGLKLA-GAKKEVINQRVNQVAE 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 L +A LLDRKP LSGGQ+QRVA+GR +V +P VFL+DEPLSNLDA LR +MR E+ L Sbjct: 120 VLQLAHLLDRKPKALSGGQRQRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 +L T +YVTH+Q EAMT+AD+I V+D G + QV P E YH P + FVA FIG P + Sbjct: 180 HKRLGRTMIYVTHDQVEAMTLADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKM 239 Query: 241 NL--VRGTRSESTFVGEHFSYPLDEDVMESVDDRD-----DFVLGVRPEDIEVADAAPDD 293 N V+ T + V P + V V+ RD + LG+RPE + +D A Sbjct: 240 NFLPVKVTATAIDQVQVELPMPNRQQVWLPVESRDVQVGANMSLGIRPEHLLPSDIA--- 296 Query: 294 AALDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPP 353 D L+ +V VVE G++ +H+ PS L + LV G + +PP Sbjct: 297 ----DVILEGEVQVVEQLGNETQIHI---QIPSIRQNLVYRQNDVVLVEEGATFAIGLPP 349 Query: 354 DKIHLFDAETGTA 366 ++ HLF E GTA Sbjct: 350 ERCHLF-REDGTA 361 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: 21 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: 371 Length adjustment: 30 Effective length of query: 353 Effective length of database: 341 Effective search space: 120373 Effective search space used: 120373 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