Align L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) (characterized)
to candidate 3609057 Dshi_2446 dihydrodipicolinate synthetase (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_603 (294 letters) >FitnessBrowser__Dino:3609057 Length = 303 Score = 335 bits (858), Expect = 1e-96 Identities = 173/293 (59%), Positives = 209/293 (71%), Gaps = 1/293 (0%) Query: 2 PTTFHEDGTLDLDSQKRCLDFMIDAGVDGVCILANFSEQFSLSDAEREVLTRTSLEHVAG 61 PT F+EDGTLDLD KR LD +ID G DG+C+LAN+SEQF +SDAEREVL R S+EHVAG Sbjct: 12 PTPFNEDGTLDLDGMKRVLDCLIDQGADGICVLANYSEQFLISDAEREVLARLSVEHVAG 71 Query: 62 RVPVIVTTTHYGTRVCAERSRAAQDMGAAMVMVMPPYHGATFRVPEAQIYEFYARVSDAI 121 RVPVIVT +H+ T++ ER+R A+D+GA +VM+MPPYHGA + Q +E +A V + + Sbjct: 72 RVPVIVTISHFATQIAVERARFAKDLGADIVMMMPPYHGALLKGTPEQSFEQFAAVGE-V 130 Query: 122 RIPIMVQDAPASGTVLSAPFLARMAQEIENLAYFKIEVPGAASKLRELIRLGGDAIEGPW 181 IPIMVQDAP SG L L RMA+EIE + FKIE P AA+K+R LI GG AIEGP+ Sbjct: 131 GIPIMVQDAPLSGVDLPVDLLVRMAREIEAVKLFKIECPRAANKIRALIAQGGAAIEGPF 190 Query: 182 DGEEAITLLADLDAGATGAMTGGAFPDGIRPIIEAHRQGDMDQAFALYQRWLPLINHENR 241 DGEEAITLLADLDAGATG MT G D I+P++ + GD+ A Y R I HENR Sbjct: 191 DGEEAITLLADLDAGATGTMTSGMIVDQIKPVLTRYHAGDVSGATEAYGRVAMAIIHENR 250 Query: 242 QGGILTAKALMKEGGVIACEAGRHPFPAMHPEVRRGLVDIARRLDPLVLRWAR 294 Q G + KA M EGGVIA E RHP +HP +R L+D+ R LDPLVLRW R Sbjct: 251 QCGWQSCKAAMVEGGVIASEFCRHPIAPLHPAIRARLIDLLRPLDPLVLRWGR 303 Lambda K H 0.322 0.138 0.415 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: 293 Number of extensions: 8 Number of successful extensions: 2 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: 294 Length of database: 303 Length adjustment: 27 Effective length of query: 267 Effective length of database: 276 Effective search space: 73692 Effective search space used: 73692 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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