Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 289 bits (740), Expect = 7e-83 Identities = 171/369 (46%), Positives = 234/369 (63%), Gaps = 29/369 (7%) Query: 1 MGQIQLTDLTKRFGDTV-AVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 M Q+ L + K + + V AV S I+D EF+VLVGPSGCGKST LRM+AGLE T G Sbjct: 1 MAQVTLNSVRKVYPNGVEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEGT 60 Query: 60 IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119 + IG +N P +RDIAMVFQ+YALYPHMTVR+NI +GL+ + AE ++V E A Sbjct: 61 LEIGDRVVNNVDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKT-PEAEIKQKVAEAA 119 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 + L + + LDRKP +LSGGQ+QRVA+GRAIVRDP +FL DEPLSNLDAKLR +MR E++ Sbjct: 120 KMLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMRIEIKA 179 Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239 LQ +L VT++YVTH+Q EAMTMADRI V++ G ++Q+ +P E YH P ++FVA F+G P Sbjct: 180 LQRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASFMGAPP 239 Query: 240 INLVRGTRSESTFVGEHFSYPLDEDVMESVDD--RDDFVLGVRPEDIEVADAAPDDAALD 297 +NL+ ++T + P D M ++D + LG+RPED+++ + Sbjct: 240 MNLL-----DATIANGQVTLP-DGVSMGALDTSAQGAVKLGIRPEDVQL---------VA 284 Query: 298 DHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQ--AVTEGMHLVTRGDRVTVTIPPDK 355 + L +DV ++E G +LH QP L+ V G H +++ P Sbjct: 285 EGGLAIDVELIEELGAHRLLHGKLGGQPFTIHVLKDIPVDPGTH--------QISVDPAA 336 Query: 356 IHLFDAETG 364 I LFDAE+G Sbjct: 337 ICLFDAESG 345 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: 371 Number of extensions: 12 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: 348 Length adjustment: 30 Effective length of query: 353 Effective length of database: 318 Effective search space: 112254 Effective search space used: 112254 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