Align L-2-keto-3-deoxyarabonate dehydratase (EC 4.2.1.43) (characterized)
to candidate PfGW456L13_4553 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
Query= reanno::acidovorax_3H11:Ac3H11_603 (294 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4553 Length = 295 Score = 110 bits (274), Expect = 5e-29 Identities = 85/259 (32%), Positives = 136/259 (52%), Gaps = 10/259 (3%) Query: 2 PTTFHEDGTLDLDSQKRCLDFMIDAGVDGVCILANFSEQFSLSDAEREVLTRTSLEHVAG 61 P T H +G +DLD+ R +D +I+ GV + L + E LSDAE + ++ S+ HVA Sbjct: 16 PFTPHGEG-VDLDALGRSIDRLIEGGVHAIAPLGSTGEGAYLSDAEWDQVSEFSIRHVAR 74 Query: 62 RVPVIVTTTHYGTRVCAERSRAAQDMGAAMVMVMPPYHGATFRVPEAQIYEFYARVSDAI 121 RVP +V+ + T R+R A+ GA +VMV+P + +++ EA+I Y + D+I Sbjct: 75 RVPTVVSVSDLTTAKAVRRARFAEAHGADVVMVLPTSY---WKLSEAEILAHYRAIGDSI 131 Query: 122 RIPIMVQDAPA-SGTVLSAPFLARMAQEIENLAYFKIEVPGAASKLRELIRLGGDAIEGP 180 +PIM+ + PA SGT +S + R+ +EN+ K E G ++ +L RLG + Sbjct: 132 GVPIMLYNNPATSGTDMSVDLILRIVNAVENVTMVK-ESTGDIQRMHQLQRLGEGQVPF- 189 Query: 181 WDGEEAITLLADLDAGATGAMTG--GAFPDGIRPIIEAHRQGDMDQAFALYQRWLPLINH 238 ++G + L A AGA G T P + EA D+ +A L+ R LPL++ Sbjct: 190 YNGCNPLALEA-FAAGAKGWCTAAPNLIPQLNLDLYEAVLANDLRKARELFYRQLPLLDF 248 Query: 239 ENRQGGILTAKALMKEGGV 257 + G T KA ++ G+ Sbjct: 249 ILKGGLPATIKAGLRATGL 267 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: 208 Number of extensions: 7 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 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