Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_050656959.1 C1M55_RS12530 fumarylacetoacetate hydrolase family protein
Query= BRENDA::A0A076VF18 (308 letters) >NCBI__GCF_002893965.1:WP_050656959.1 Length = 257 Score = 120 bits (301), Expect = 3e-32 Identities = 85/253 (33%), Positives = 124/253 (49%), Gaps = 22/253 (8%) Query: 39 ERITARVVAAPWTSSPASTSSPRVLTVQTLLSPLAPTDVPAIRGMGLQYSGDPANPQDKP 98 + + A+ +A +P T L LL+P+ + V I G Y+ A + Sbjct: 22 DALVAKEIAEHPFGNPTFTGRSWPLADVRLLAPILASKVICI---GKNYADHIAEMGGEA 78 Query: 99 PV-ACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVGG 157 P +F K + ++ GPG IVLP + + +E EL VV+G+ KDV A+S V G Sbjct: 79 PADPVIFLKPNTSIVGPGAPIVLPPTSNEVH--FEGELAVVIGQPCKDVPAAKALSVVLG 136 Query: 158 YCVVNDVSSRGLCAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKLAQ 217 Y + NDVS+R GQW K +DT+CP GP + + D + I T VNG++ Q Sbjct: 137 YTIANDVSARDHQRHDGQWTRAKGHDTFCPLGPWIET----SLDASDVDIRTEVNGQVKQ 192 Query: 218 KGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSPFMKDGDEIR 277 +TA L+ IP++I +S TL G +ILTG+P +G + DGD + Sbjct: 193 DSSTAFLLHDIPKIIEWISAVMTLLPGDVILTGTPAGVGP------------IVDGDSVS 240 Query: 278 CFVEGCGTLINSV 290 V G GTL N V Sbjct: 241 VTVSGIGTLTNPV 253 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: 251 Number of extensions: 18 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: 257 Length adjustment: 26 Effective length of query: 282 Effective length of database: 231 Effective search space: 65142 Effective search space used: 65142 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