Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate 3608008 Dshi_1416 ABC transporter related (RefSeq)
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Dino:3608008 Length = 347 Score = 294 bits (752), Expect = 3e-84 Identities = 168/365 (46%), Positives = 223/365 (61%), Gaps = 22/365 (6%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M +I+L + KR+G V V+D L I D EFLVL+GPSGCGK+TT+RM+AGLE P+SG+I Sbjct: 1 MAEIRLNHVQKRWGSFVGVEDFHLTIPDREFLVLLGPSGCGKTTTMRMIAGLEEPSSGEI 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 +IG +N P++RD+AMVFQ Y LYP+M V +NIRF L+ + E + RV+ + Sbjct: 61 WIGDRMVNALDPKDRDVAMVFQSYGLYPNMNVYENIRFPLKVRK-VPEVEHEARVMRASA 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 + + D L RKP LSGGQ+QRVAL RAIVR+P VFLMDEPLSNLDAKLR R +++NL Sbjct: 120 MVELDDFLHRKPAALSGGQRQRVALARAIVREPNVFLMDEPLSNLDAKLRVSTRAQIKNL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 +L VTT+YVTH+Q EAMT+ADR+ VM G +QQV +P E Y P N FVA FIG P + Sbjct: 180 SHELQVTTIYVTHDQIEAMTLADRVVVMSAGVVQQVGTPMEIYDRPANTFVASFIGSPAM 239 Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAA-LDDH 299 NL+ G ++ TF G+ + V LG R ED +V D+ AA + Sbjct: 240 NLMEGAVTDGTFHGDRVAIAGLSGAAGRV------TLGFRAEDAQVVDSDGQIAAPVYSM 293 Query: 300 DLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHLF 359 +L D T+V ++ + P + A+ G V + IP HLF Sbjct: 294 ELLGDATMVTVKAGGTLVAVKAPKEFRAE--------------IGAPVQIRIPTGICHLF 339 Query: 360 DAETG 364 DA+TG Sbjct: 340 DAQTG 344 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: 387 Number of extensions: 14 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: 347 Length adjustment: 29 Effective length of query: 354 Effective length of database: 318 Effective search space: 112572 Effective search space used: 112572 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