Align L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) (characterized)
to candidate GFF1354 PS417_06885 dihydrodipicolinate synthase
Query= reanno::acidovorax_3H11:Ac3H11_603 (294 letters) >FitnessBrowser__WCS417:GFF1354 Length = 290 Score = 101 bits (252), Expect = 2e-26 Identities = 85/270 (31%), Positives = 137/270 (50%), Gaps = 12/270 (4%) Query: 3 TTFHEDGT-LDLDSQKRCLDFMIDAGVDGVCILANFSEQFSLSDAEREVLTRTSLEHVAG 61 T F DG +DL++ R +D +I+ GV + L + E LSDAE + ++ SL +A Sbjct: 15 TPFSTDGQRIDLNTLGRSIDRLIEGGVHAIAPLGSTGEGAYLSDAEWDEVSAYSLAKIAR 74 Query: 62 RVPVIVTTTHYGTRVCAERSRAAQDMGAAMVMVMPPYHGATFRVPEAQIYEFYARVSDAI 121 RVP IV+ + T R+R A+ GA +VMV+P + +++ EA+I YA + D+I Sbjct: 75 RVPTIVSVSDLTTAKAVRRARYAEANGADVVMVLPTSY---WKLSEAEILAHYAAIGDSI 131 Query: 122 RIPIMVQDAPA-SGTVLSAPFLARMAQEIENLAYFKIEVPGAASKLRELIRLGGDAIEGP 180 +PIM+ + PA SGT +S + R+ +++ N+ K E G ++ L R Sbjct: 132 GVPIMLYNNPATSGTDMSVDLILRIIKQVPNVTMVK-ESTGDIQRMHHLHRQSDVPF--- 187 Query: 181 WDGEEAITLLADLDAGATGAMTG--GAFPDGIRPIIEAHRQGDMDQAFALYQRWLPLINH 238 ++G + L A AGA G T P+ + EA D+ QA ++ R LPL++ Sbjct: 188 YNGCNPLALEA-FAAGAKGWCTAAPNLIPELNLALYEAVLANDLTQAREVFYRQLPLLDF 246 Query: 239 ENRQGGILTAKALMKEGGVIACEAGRHPFP 268 + G T KA ++ G+ A + FP Sbjct: 247 ILKGGLPATIKAGLRLTGLEAGDPRLPVFP 276 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: 204 Number of extensions: 9 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: 290 Length adjustment: 26 Effective length of query: 268 Effective length of database: 264 Effective search space: 70752 Effective search space used: 70752 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