Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_011606903.1 FRAAL_RS25420 FAA hydrolase family protein
Query= BRENDA::A0A076VF18 (308 letters) >NCBI__GCF_000058485.1:WP_011606903.1 Length = 259 Score = 123 bits (309), Expect = 4e-33 Identities = 90/253 (35%), Positives = 127/253 (50%), Gaps = 34/253 (13%) Query: 46 VAAPWTSSPAS-TSSPRVLTVQTLLSPLAPTDVPAIRGMGLQYS-------GDPANPQDK 97 V AP P S T + R L LL+P+ P+ V + G Y+ GD P ++ Sbjct: 30 VIAPHPFGPFSFTGARRPLGDVRLLAPVLPSKVLCV---GKNYADHVREMGGD--TPPER 84 Query: 98 PPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGG 157 P LF K S +++GPGD I LP ++ D+E EL VV+G+ +DV + A V G Sbjct: 85 P---ILFLKPSTSVSGPGDPITLP--PDSDRVDFEGELAVVIGRLCRDVPAERAFDVVLG 139 Query: 158 YCVVNDVSSRGLCAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKLAQ 217 Y NDV++R GQW K +D++CP GP + + DP L+I T ++G+L Q Sbjct: 140 YTCANDVTARDQQQTDGQWTRAKGHDSFCPIGPWIETE----LDPTDLSIRTTLDGELRQ 195 Query: 218 KGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSPFMKDGDEIR 277 T L+ +P LIA +S TL G ++LTG+P +G PG V + Sbjct: 196 NSRTKLLLRDVPALIAAMSAAMTLLPGDVLLTGTPAGVGPMRPGQTVAVT---------- 245 Query: 278 CFVEGCGTLINSV 290 VEG GTL N V Sbjct: 246 --VEGIGTLTNPV 256 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: 275 Number of extensions: 16 Number of successful extensions: 4 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: 259 Length adjustment: 26 Effective length of query: 282 Effective length of database: 233 Effective search space: 65706 Effective search space used: 65706 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: 47 (22.7 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