Align Fumarylacetoacetase; FAA; Beta-diketonase; Fumarylacetoacetate hydrolase; EC 3.7.1.2 (characterized)
to candidate WP_049755528.1 AFER_RS04140 hypothetical protein
Query= SwissProt::P16930 (419 letters) >NCBI__GCF_000023265.1:WP_049755528.1 Length = 400 Score = 248 bits (634), Expect = 2e-70 Identities = 159/418 (38%), Positives = 220/418 (52%), Gaps = 27/418 (6%) Query: 2 SFIPVAEDSDFPIHNLPYGVFSTRGDPRPRIGVAIGDQILDLSIIKHLFTGPVLSKHQDV 61 S+I + + + +LP GV + + V IGD L L+ + + G + S + Sbjct: 3 SWIDTDLEHGYGLDHLPLGVDAEG------VVVRIGDVALRLAPL--VDDGLLRSVSHGL 54 Query: 62 FNQPTLNSFMGLGQAAWKEARVFLQNLLSVSQARLRDDTELRKCAFISQASATMHLPATI 121 TL G A R ++ ++ R DD R+ +S + + +P Sbjct: 55 VAARTLGPLFAAGSATMARLR---DEIVVLASGR-PDDAVARR--LVSIDALELSVPIRP 108 Query: 122 GDYTDFYSSRQHATNVGIMFRDKENALMPNWLHLPVGYHGRASSVVVSGTPIRRPMGQMK 181 Y DFY+S HATN G +FR + L W LP+GYHGRAS+VVVSGTPI RP G + Sbjct: 109 RTYVDFYASEAHATNAGRIFRPDGDPLPAAWRRLPIGYHGRASTVVVSGTPIVRPWGLRR 168 Query: 182 PDDSKPPVYGACKLLDMELEMAFFVGPGNRLGEPIPISKAHEHIFGMVLMNDWSARDIQK 241 + + V G +LD+E E+ F VG + G P+ E + G+VL NDWSARDIQ Sbjct: 169 --EGEGVVLGPSAMLDLEAEVGFVVGRASERGRPVSAGAFAEMVGGVVLANDWSARDIQA 226 Query: 242 WEYVPLGPFLGKSFGTTVSPWVVPMDALMPFAVPNPKQDPRPLPYLCHDEPYTFDINLSV 301 E PLGPF GKSF T++S WV P+ AL V P QDP P L +P+ D+ L + Sbjct: 227 LESFPLGPFAGKSFATSISAWVTPLSALDAARVTPPVQDPAPSANLVDPDPWCLDLRLEL 286 Query: 302 NLKGEGMSQ--AATICKSNFKYMYWTMLQQLTHHSVNGCNLRPGDLLASGTISGPEPENF 359 L G +++ AAT YWT Q L H + NG + P DL SGT+SG P+ Sbjct: 287 RLNGTVLTRPPAAT--------TYWTPGQLLAHLTDNGAPVEPEDLFCSGTVSGAAPDEV 338 Query: 360 GSMLELSWKGTKPIDLGNGQTRKFLLDGDEVIITGYCQG-DGYRIGFGQCAGKVLPAL 416 GS+LEL+W GT+P+ L +G R +L+DGDEV IT DG I G+ G+V+ A+ Sbjct: 339 GSLLELTWGGTRPVRLDDGHMRTWLVDGDEVTITATAPALDGGFIRLGEVTGRVVSAI 396 Lambda K H 0.321 0.139 0.440 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: 511 Number of extensions: 31 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: 419 Length of database: 400 Length adjustment: 31 Effective length of query: 388 Effective length of database: 369 Effective search space: 143172 Effective search space used: 143172 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 (21.8 bits) S2: 50 (23.9 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