Align L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) (characterized)
to candidate PP_2036 PP_2036 putative 4-hydroxy-tetrahydrodipicolinate synthase
Query= reanno::acidovorax_3H11:Ac3H11_603 (294 letters) >FitnessBrowser__Putida:PP_2036 Length = 295 Score = 114 bits (286), Expect = 2e-30 Identities = 90/254 (35%), Positives = 131/254 (51%), Gaps = 9/254 (3%) Query: 3 TTFHEDGTLDLDSQKRCLDFMIDAGVDGVCILANFSEQFSLSDAEREVLTRTSLEHVAGR 62 T F DGTLDLD+ +D +I GV + L + E LSD+E E + R S +AGR Sbjct: 15 TPFTADGTLDLDALGTSIDSLIAGGVHAIAPLGSTGEGAYLSDSEWETVVRFSQARIAGR 74 Query: 63 VPVIVTTTHYGTRVCAERSRAAQDMGAAMVMVMPPYHGATFRVPEAQIYEFYARVSDAIR 122 VP +V+ + T +R+R AQ GA VMV+P + +++ EA++ Y V AI Sbjct: 75 VPSVVSVSDLTTARTVQRARLAQACGATAVMVLPISY---WKLTEAEVVAHYKAVGAAID 131 Query: 123 IPIMVQDAP-ASGTVLSAPFLARMAQEIENLAYFKIEVPGAASKLRELIRLGGDAIEGPW 181 IPIM+ + P SGT LS + R+ E+ N+ K E G ++ L D + Sbjct: 132 IPIMLYNNPGTSGTDLSVELILRILGEVPNVTMVK-ESTGDIQRMHRLF-TATDGQVAFY 189 Query: 182 DGEEAITLLADLDAGATGAMTG--GAFPDGIRPIIEAHRQGDMDQAFALYQRWLPLINHE 239 +G +TL A L AGATG T P + +A +QGD+ +A AL+ R L+ + Sbjct: 190 NGCNPLTLEA-LVAGATGWCTAAPNLIPALNLALWDAVQQGDLAEARALFYRQYELLEYI 248 Query: 240 NRQGGILTAKALMK 253 R+G T KA +K Sbjct: 249 TRRGLPTTIKAGLK 262 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: 209 Number of extensions: 8 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: 294 Length of database: 295 Length adjustment: 26 Effective length of query: 268 Effective length of database: 269 Effective search space: 72092 Effective search space used: 72092 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