Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_022947842.1 H035_RS0104685 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000421465.1:WP_022947842.1 Length = 381 Score = 280 bits (717), Expect = 4e-80 Identities = 167/379 (44%), Positives = 230/379 (60%), Gaps = 20/379 (5%) Query: 1 MGQIQLTDLTKRFGD-TVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 M +IQL +TKRF D T AV ++S I D EF +LVGPSGCGKST L M+ GLE + G Sbjct: 1 MAEIQLEGITKRFADGTEAVKNVSFTIRDGEFFILVGPSGCGKSTLLNMIVGLERISEGR 60 Query: 60 IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119 + + G +N P++R++AMVFQ YA+YPHMTVR+N+ F L+ + + AE + RV EVA Sbjct: 61 LLLNGRCINDLDPKDRNMAMVFQSYAIYPHMTVRRNMAFPLKMAKR-SKAEIERRVEEVA 119 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 L + +LL+RKP LSGGQ+QRVA+GRA+VRDPE FL+DEPLSNLDA+LR +MRTE+ Sbjct: 120 RILELTELLERKPANLSGGQRQRVAMGRAMVRDPEAFLLDEPLSNLDARLRVQMRTEIAR 179 Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239 LQ QL T VYVTH+QTEAMT+ +RIAV++ GE+QQ+ +P + Y P N FVA FIG P Sbjct: 180 LQKQLGTTMVYVTHDQTEAMTLGERIAVLERGEVQQIGTPRDLYERPANRFVAGFIGSPT 239 Query: 240 INLVRGTRSESTFVGEHFSYPLDEDVMESVDD-RDDFVLGVRPEDIEVADAAPDDAALDD 298 +N + T L + + + + G+RPE + P D + Sbjct: 240 MNFLPATIENGRLQLPMVELELPDCFRKHRPPIQGPVIAGIRPE--HLLSTPPRDKS--S 295 Query: 299 HDLQMDVTVVEPHGDQNVLH--LSHPDQPSADDALQAVTEG--MHLVTRGDR-------- 346 ++ V +VE G +H LS +P + L + + +L+ R D Sbjct: 296 PSFRLPVELVEWLGADLFVHLPLSVDRRPPHETRLPEIGQSFKFYLIARLDASIQVNKSQ 355 Query: 347 -VTVTIPPDKIHLFDAETG 364 + + + PDK+HLFD TG Sbjct: 356 PIELWLAPDKLHLFDVHTG 374 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: 361 Number of extensions: 13 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: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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 24 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