Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_164924745.1 NGR_RS30975 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000018545.1:WP_164924745.1 Length = 355 Score = 296 bits (757), Expect = 8e-85 Identities = 167/371 (45%), Positives = 229/371 (61%), Gaps = 22/371 (5%) Query: 1 MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60 M + + ++TKR+G + LS I+D EF+VLVGPSGCGKST LRMLAGLE + GD+ Sbjct: 1 MTDVTIRNVTKRYGALTVIPQLSFRIEDGEFVVLVGPSGCGKSTLLRMLAGLEEISGGDL 60 Query: 61 YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120 +G D +N R + RD+A+VFQ+YALYPHMTV +N+ F L+ + AE DERV + A Sbjct: 61 LMGADVINDRPAKERDMAIVFQNYALYPHMTVAENMGFALKLRKR-PRAEIDERVDKAAA 119 Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180 LG+ LLDR P LSGGQ+QRVA+GRAIVRDP+VFL DEPLSNLDAKLR +MR E++ L Sbjct: 120 ILGLGKLLDRYPRALSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKAL 179 Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240 +L +TTVYVTH+Q EAMTMAD+I VM++G ++Q+ +P E Y P N+FVA FIG P + Sbjct: 180 HQRLKITTVYVTHDQIEAMTMADKIVVMNEGRVEQMGTPLELYDRPANIFVAGFIGSPSM 239 Query: 241 NL----VRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAAL 296 N V T E + P+D ++ R + G+RPE +++ + Sbjct: 240 NFLPATVAATNGPLLKTPEGVALPIDGG--PTLTGRSEVTYGIRPEHLQLGETG------ 291 Query: 297 DDHDLQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKI 356 + +V VVEP G + L+++ + AV V G+++ +T Sbjct: 292 ----IPAEVVVVEPTGSETQLYVT-----VGGREVVAVLRDRVDVRPGEKIWLTPRKGCA 342 Query: 357 HLFDAETGTAV 367 HLFD TG + Sbjct: 343 HLFDPNTGARI 353 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: 370 Number of extensions: 16 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: 355 Length adjustment: 30 Effective length of query: 353 Effective length of database: 325 Effective search space: 114725 Effective search space used: 114725 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 Apr 09 2024. 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