Align 2-dehydro-3-deoxy-D-arabinonate dehydratase (EC 4.2.1.141) (characterized)
to candidate Pf6N2E2_1662 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase.
Query= BRENDA::Q97UA0 (298 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1662 Length = 282 Score = 60.8 bits (146), Expect = 3e-14 Identities = 51/169 (30%), Positives = 81/169 (47%), Gaps = 17/169 (10%) Query: 118 PEIFFKATPNRCVGHGEAIAVRSDSEWTLPEPELAVVLDSNGK----------ILGYTIM 167 P IF K T C G + I + S T E EL VV+ G+ + GY ++ Sbjct: 95 PIIFNKWTSAIC-GPNDDIQIPRGSLKTDWEVELGVVIGKGGRYIDEANAMEHVAGYCVI 153 Query: 168 DDVSARDLEAENPLYLPQSKIYAGCCAFGPVIVTSDEIKNPYSLDITLKIVREGRVFFEG 227 +DVS R+ + E + K + GP +VT DEI +P++LD+ L++ +G + G Sbjct: 154 NDVSEREWQLERGGTWDKGKGFDTFGPLGPWLVTRDEIADPHTLDLWLEV--DGHRYQNG 211 Query: 228 SVNTNKMRRKIEEQIQYLIRDNPIPDGTILTTGTAIVPGRDKGLKDEDI 276 NT + + + I YL R + G +++TGT PG G+K + Sbjct: 212 --NTRTLIFSVPQLIAYLSRCMSLQPGDVISTGTP--PGVGLGIKPNPV 256 Lambda K H 0.319 0.139 0.400 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: 191 Number of extensions: 11 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: 298 Length of database: 282 Length adjustment: 26 Effective length of query: 272 Effective length of database: 256 Effective search space: 69632 Effective search space used: 69632 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 (21.7 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