Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__HerbieS:HSERO_RS02210 Length = 372 Score = 275 bits (702), Expect = 2e-78 Identities = 163/367 (44%), Positives = 214/367 (58%), Gaps = 17/367 (4%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M + + +L KR+ D + D++L+I+D EF+V VGPSGCGKST LRM+AGLE + GD+ Sbjct: 1 MAAVSIRNLAKRYDDNEVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDGDL 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 IG MN R +AMVFQ YALYPHM++ N+ FGL+ G + AE D V A+ Sbjct: 61 DIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIA-GKSKAEIDAAVQHAAK 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 L I LLDRKP LSGGQ+QRVA+GRAI R P VFL DEPLSNLDA LR +MR E L Sbjct: 120 ILHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAKL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 D L T +YVTH+Q EAMT+AD+I V+ +G ++QV SP + YH P N FVA FIG P + Sbjct: 180 HDDLKTTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPKM 239 Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVDDR-----DDFVLGVRPEDIEVADAAPDDAA 295 N + GT + G P +VD LGVRPE + +A AA Sbjct: 240 NFIDGTVAAIQADGVQVQLPGGGLQWAAVDGSTLQVGQKVTLGVRPEHLNIAQG---QAA 296 Query: 296 LDDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDK 355 LQ T +E GD + L+ ++ + S D + V + + G + + P + Sbjct: 297 -----LQARCTALELLGDFSYLYAAY--EGSEDALILRVPDSLD-APHGSVLPLAADPAR 348 Query: 356 IHLFDAE 362 HLF A+ Sbjct: 349 CHLFGAD 355 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: 18 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: 372 Length adjustment: 30 Effective length of query: 353 Effective length of database: 342 Effective search space: 120726 Effective search space used: 120726 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