Align 4-carboxy-4-hydroxy-2-oxoadipate aldolase; CHA aldolase; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.3.17; EC 4.1.1.112 (characterized)
to candidate AZOBR_RS26905 AZOBR_RS26905 hypothetical protein
Query= SwissProt::G2IQQ8 (228 letters) >FitnessBrowser__azobra:AZOBR_RS26905 Length = 223 Score = 310 bits (795), Expect = 1e-89 Identities = 161/223 (72%), Positives = 181/223 (81%) Query: 6 MGVVVQNIERAPLEVIDGLAACGVATVHEAQGRTGLLASYMRPIYRGARVAGSALTISAP 65 M VVVQ IERA VI GLA CGVATVHEAQGR GLLAS +RPIY GA+ A SA+TI AP Sbjct: 1 MNVVVQTIERADPAVIAGLAECGVATVHEAQGRKGLLASALRPIYPGAQFAASAVTILAP 60 Query: 66 PGDNWMVHVAIEQLKAGDILLLAPTSPCEDGYFGDLLATSAQARGCRGLVIDAGVRDVRD 125 P DNWM+HVAIEQ+K GD+L+LA TSP + GYFGDLLATSA+ARGC GLVIDAGVRDVR Sbjct: 61 PADNWMLHVAIEQVKPGDVLVLATTSPSDAGYFGDLLATSAKARGCAGLVIDAGVRDVRT 120 Query: 126 LTEMNFPVWSKAIYAQGTVKNTLGSVNVPVVCANALVNPGDVIVADDDGVCVVPLANAEK 185 LT+M+FPVWS+A+ AQGTVK TLGSVNVPVVCA ALVNPGDVIVADDDGVCVV A + Sbjct: 121 LTDMSFPVWSRAVCAQGTVKETLGSVNVPVVCAGALVNPGDVIVADDDGVCVVRREEAAE 180 Query: 186 VLEAARAREANEGDKREKMANGVLGLDLYKMRERLEKEGLKYV 228 VL A+ R A E +KR ++A G LGLDLY MR L +GL+YV Sbjct: 181 VLAKAQDRLAKEEEKRARLAAGELGLDLYGMRGPLAAKGLRYV 223 Lambda K H 0.318 0.136 0.397 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: 229 Number of extensions: 8 Number of successful extensions: 1 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: 228 Length of database: 223 Length adjustment: 22 Effective length of query: 206 Effective length of database: 201 Effective search space: 41406 Effective search space used: 41406 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: 46 (22.3 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