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 GFF2278 HP15_2228 ribonuclease activity regulator protein RraA
Query= curated2:Q9S4U0 (163 letters) >FitnessBrowser__Marino:GFF2278 Length = 159 Score = 234 bits (596), Expect = 7e-67 Identities = 111/159 (69%), Positives = 129/159 (81%), Gaps = 1/159 (0%) Query: 1 MIHYVTPDLCDAYPELVQVVEPMFSNFGGRDSFGGEIVTIKCFEDNSLVKEQADQPGAGK 60 M +TPDLCD +PE++ VVEP F+N+GG +FGGEIVT+KCFEDNS+VKEQ QPG G+ Sbjct: 1 MTTIITPDLCDEFPEVL-VVEPGFNNYGGNKAFGGEIVTVKCFEDNSVVKEQVGQPGNGR 59 Query: 61 VLVVDGGGSLRRALLGDMIAEKAAKNGWEGLVIYGCVRDVDVLAQTDLGVQALAPHPMKT 120 V+VVDGG S R ALLGDM+AEKAA NGW GL+IYGCVRDVD + T LGVQAL HP K+ Sbjct: 60 VMVVDGGASKRHALLGDMLAEKAASNGWAGLIIYGCVRDVDEIGNTALGVQALGTHPRKS 119 Query: 121 DKRGIGDLNVVVTFASVTFRPGEYVYADNNGVIVSPSPL 159 +KRG+GDLNV VTF VTF PG YVYADNNG+IVS PL Sbjct: 120 EKRGLGDLNVPVTFHGVTFHPGHYVYADNNGIIVSEKPL 158 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: 158 Number of extensions: 3 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: 159 Length adjustment: 17 Effective length of query: 146 Effective length of database: 142 Effective search space: 20732 Effective search space used: 20732 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 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