Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate AZOBR_RS26375 AZOBR_RS26375 hypothetical protein
Query= BRENDA::A0A076VF18 (308 letters) >FitnessBrowser__azobra:AZOBR_RS26375 Length = 293 Score = 119 bits (299), Expect = 7e-32 Identities = 71/194 (36%), Positives = 102/194 (52%), Gaps = 9/194 (4%) Query: 96 DKPPVACLFF-KASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSF 154 D P A +FF K + + GD I P D DYE EL VV+GK + + + +A Sbjct: 105 DAIPEAPIFFTKPPETVIANGDPIRYPHGVSDSL-DYEAELGVVIGKGGRGITKAEAYDH 163 Query: 155 VGGYCVVNDVSSRGLCAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGK 214 V GY ++ND+++R ++ QW +GKS+DT+CP GP L + + D L + VN + Sbjct: 164 VFGYVIINDMTARDWQSRHKQWFLGKSFDTFCPMGPWLATTDEV--DAANLALRCWVNDE 221 Query: 215 LAQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSPFMKDGD 274 L Q NT DL+ IP +I LS G TL G +I TG+P + G F+K GD Sbjct: 222 LRQNANTRDLIFDIPTMIETLSAGITLYPGDIIATGTPAGV-----GIGFNPPKFLKPGD 276 Query: 275 EIRCFVEGCGTLIN 288 + ++G G L N Sbjct: 277 RVTIEIDGLGRLSN 290 Lambda K H 0.316 0.135 0.411 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: 240 Number of extensions: 15 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: 308 Length of database: 293 Length adjustment: 27 Effective length of query: 281 Effective length of database: 266 Effective search space: 74746 Effective search space used: 74746 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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