Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components
Query= uniprot:D4GP38 (383 letters) >FitnessBrowser__Cola:Echvi_1022 Length = 345 Score = 159 bits (403), Expect = 9e-44 Identities = 99/325 (30%), Positives = 172/325 (52%), Gaps = 23/325 (7%) Query: 1 MGQIQLTDLTKRFGDT--VAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSG 58 M +QL ++K+F T AV D+ ++I++ +VG +G GK+T L+++AGLE P G Sbjct: 1 MSLLQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKG 60 Query: 59 DIYIGGDHM---NYRVPQN-RDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDER 114 +I G + +P N R++ ++FQ+YAL+P MT+ +N+R L +E S + Sbjct: 61 EIVFSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQE----SRNARQI 116 Query: 115 VVEVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMR 174 ++ G+ D P +LS GQ+QR AL RA+ P++ L+D+P +LD + + E+ Sbjct: 117 AMDSLALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEIS 176 Query: 175 TELQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEF 234 +++++ +T + +H+ +A+++AD IA++ G LQQV +P E Y +P N +VA F Sbjct: 177 EDIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANF 236 Query: 235 IGEPMINLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDA 294 G+ N + T +E F P +S D + R ED ++ + Sbjct: 237 FGKR--NELLATPTEDGFYAGFGFIPHP----DSASYTDKVKILFRSEDAKIKKST---- 286 Query: 295 ALDDHDLQMDVTVVEPHGDQNVLHL 319 + L VT V +GD ++ L Sbjct: 287 ---EQPLSGIVTRVLFYGDHQIVKL 308 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: 260 Number of extensions: 17 Number of successful extensions: 3 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: 345 Length adjustment: 29 Effective length of query: 354 Effective length of database: 316 Effective search space: 111864 Effective search space used: 111864 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