Align Putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase; HMG aldolase; EC 4.1.3.17; Oxaloacetate decarboxylase; OAA decarboxylase; EC 4.1.1.112; Regulator of ribonuclease activity homolog; RraA-like protein (uncharacterized)
to candidate WP_086509644.1 BZY95_RS09195 ribonuclease E inhibitor RraA
Query= curated2:Q9S4U0 (163 letters) >NCBI__GCF_002151265.1:WP_086509644.1 Length = 162 Score = 211 bits (537), Expect = 5e-60 Identities = 98/157 (62%), Positives = 127/157 (80%), Gaps = 1/157 (0%) Query: 5 VTPDLCDAYPELVQVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQADQPGAGKVLVV 64 +TPD+CDA+PE VQV++P+F ++GGR++F G I T+KCFEDNSLVK+ +PG G VLVV Sbjct: 5 ITPDICDAHPE-VQVLDPIFVSYGGREAFCGPIRTVKCFEDNSLVKQAVSEPGEGAVLVV 63 Query: 65 DGGGSLRRALLGDMIAEKAAKNGWEGLVIYGCVRDVDVLAQTDLGVQALAPHPMKTDKRG 124 D GGS R A+LGDM+AE+A NGW G+V+YGCVRDVDVLA+TDLGV AL HP K++KRG Sbjct: 64 DAGGSHRCAMLGDMLAEQAVDNGWSGVVMYGCVRDVDVLAETDLGVHALGAHPRKSEKRG 123 Query: 125 IGDLNVVVTFASVTFRPGEYVYADNNGVIVSPSPLKM 161 G +V VTFA VT RPG+++YADNNG++V+ L + Sbjct: 124 EGSRDVAVTFAGVTLRPGQWLYADNNGIVVAEERLPL 160 Lambda K H 0.319 0.140 0.418 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: 136 Number of extensions: 5 Number of successful extensions: 2 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: 163 Length of database: 162 Length adjustment: 18 Effective length of query: 145 Effective length of database: 144 Effective search space: 20880 Effective search space used: 20880 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: 43 (21.2 bits)
This GapMind analysis is from Sep 24 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