Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= uniprot:D4GP38 (383 letters) >NCBI__GCF_000759345.1:WP_043527041.1 Length = 354 Score = 268 bits (686), Expect = 1e-76 Identities = 160/367 (43%), Positives = 225/367 (61%), Gaps = 24/367 (6%) Query: 1 MGQIQLTDLTKRF-GDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59 M IQLT L K + G+ AV + L+I D EF+VLVGPSGCGKST LRM+AGLET T G Sbjct: 1 MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60 Query: 60 IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119 + I +N P RDIAMVFQ+YALYPHMTV N+ +GL+ G E + RV + A Sbjct: 61 LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNR-GVKREEIERRVHDAA 119 Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179 L I L+RKP +LSGGQ+QRVA+GRA+VR+P FL DEPLSNLDAKLR +MR E++ Sbjct: 120 AMLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQ 179 Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239 LQ +L T++YVTH+Q EA+T+ DR+ V++ G ++QV +P E Y +P ++FVA FIG P Sbjct: 180 LQRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPA 239 Query: 240 INLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDH 299 +N++ ++ E + L + + D V+G+RP+D+ + APD+ D Sbjct: 240 MNML-----PVAYLRERGANGLLDHLAADTD-----VIGIRPDDLRI--EAPDE---DHL 284 Query: 300 DLQMDVTVVEPHGDQNVLHLS--HPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIH 357 + V + E G ++ L++S DQP+ T V G+ + + P +H Sbjct: 285 VVTGTVELFEAAGAESHLYVSLEGSDQPTV-----IRTSARPPVAEGETMRFHVLPSALH 339 Query: 358 LFDAETG 364 F+ +G Sbjct: 340 PFNQASG 346 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: 342 Number of extensions: 14 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: 354 Length adjustment: 30 Effective length of query: 353 Effective length of database: 324 Effective search space: 114372 Effective search space used: 114372 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 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