Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate WP_012567672.1 RC1_RS12035 FAA hydrolase family protein
Query= reanno::psRCH2:GFF3447 (327 letters) >NCBI__GCF_000016185.1:WP_012567672.1 Length = 346 Score = 439 bits (1128), Expect = e-128 Identities = 225/335 (67%), Positives = 257/335 (76%), Gaps = 13/335 (3%) Query: 1 MKLATLNQG-RDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLN-DG 58 MKLA+L G RDG LVVVSRDL++ VP +A TLQ ALD W +P+LE + L DG Sbjct: 1 MKLASLKAGGRDGTLVVVSRDLSRCAPVPAVARTLQEALDRWAEVRPRLEGIAAGLETDG 60 Query: 59 LEEGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGAD 118 EG FD ACHSPLPRA+ WADGSAYVNHV LVRKARGAEMP+SFW DPLMYQGG+D Sbjct: 61 GVEGVMPFDPDACHSPLPRAFQWADGSAYVNHVALVRKARGAEMPDSFWTDPLMYQGGSD 120 Query: 119 AFIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIP 178 +F+ P PI ADE WGIDLE E+AV+T DVPMG PA A I L+MLVNDVSLR LIP Sbjct: 121 SFLGPRDPILAADEGWGIDLEAEVAVVTTDVPMGIDPAAALDRIALVMLVNDVSLRGLIP 180 Query: 179 GELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMT 238 GELAKGFGF+QSKPSS+FSPVAVTPDELG WR+GK+HRPL+S ING+ FG+PDAGTDMT Sbjct: 181 GELAKGFGFFQSKPSSAFSPVAVTPDELGGAWREGKLHRPLLSWINGQPFGRPDAGTDMT 240 Query: 239 FNFPTLVAHAARTRPLGAGTIIGSGTVSNYDRSAGS-----------SCLAEKRMLEVVE 287 F+F LVAHAA+TRPL AG+IIGSGTVSN D G SCLAE R +E++ Sbjct: 241 FDFGRLVAHAAKTRPLCAGSIIGSGTVSNRDPDGGPGRPIAEGGCGYSCLAEIRTVEMLR 300 Query: 288 HGEAKTPFLKFGDRVRIEMFDAAGQSIFGAIDQQV 322 G +TPFL+FGDRVRIEM DA G+SIFGAI+Q V Sbjct: 301 EGRPRTPFLRFGDRVRIEMLDADGRSIFGAIEQTV 335 Lambda K H 0.318 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: 449 Number of extensions: 13 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: 327 Length of database: 346 Length adjustment: 28 Effective length of query: 299 Effective length of database: 318 Effective search space: 95082 Effective search space used: 95082 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 (21.7 bits) S2: 49 (23.5 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