Align fumarylacetoacetase (EC 3.7.1.2) (characterized)
to candidate WP_012334628.1 M446_RS23630 FAA hydrolase family protein
Query= BRENDA::A0A076VF18 (308 letters) >NCBI__GCF_000019365.1:WP_012334628.1 Length = 286 Score = 133 bits (334), Expect = 6e-36 Identities = 93/250 (37%), Positives = 132/250 (52%), Gaps = 24/250 (9%) Query: 49 PWTSSPASTSS---------PRVLTVQTLLSPLAPTDVPAIRGMGLQYSGDPAN---PQD 96 P T SPA ++ PRV L PLA V +GL Y+ A P Sbjct: 35 PDTLSPAGLAALAKLDPAGLPRVEGSPRLGVPLA--GVGKFIAIGLNYADHAAESNLPIP 92 Query: 97 KPPVACLFFKASQALAGPGDDIVLPRLARDEKNDYEVELCVVLGKDAKDVDEKDAMSFVG 156 K PV +F KA +L+GP D ++LPR K+D+EVEL +V+G+ A V++ +A+ +V Sbjct: 93 KEPV--VFTKAISSLSGPNDPVMLPR--DSVKSDWEVELGIVIGRRAAYVEQAEALDYVA 148 Query: 157 GYCVVNDVSSRGL-CAKGGQWGMGKSYDTWCPFGPCLVSPSALGADPHKLTITTHVNGKL 215 GYCVVNDVS R +GG W GK DT+ P GP LV+ +G DP L + +NG+ Sbjct: 149 GYCVVNDVSEREYQIERGGTWDKGKGCDTFGPVGPWLVTADEVG-DPQSLDMWLDLNGRR 207 Query: 216 AQKGNTADLVLKIPELIARLSHGTTLQAGSLILTGSPIALGRKAPGDAVEQSPFMKDGDE 275 Q GNT ++ E+++ +S TL G +I TG+P +G + V F+K GD Sbjct: 208 MQTGNTRTMIFPCAEIVSYVSRFLTLMPGDIITTGTPPGVGMGIKPEPV----FLKPGDV 263 Query: 276 IRCFVEGCGT 285 + +E GT Sbjct: 264 MTLGIEKLGT 273 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: 286 Number of extensions: 15 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: 286 Length adjustment: 26 Effective length of query: 282 Effective length of database: 260 Effective search space: 73320 Effective search space used: 73320 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 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