Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate WP_004299449.1 C665_RS02585 FAA hydrolase family protein
Query= reanno::psRCH2:GFF3447 (327 letters) >NCBI__GCF_000310185.1:WP_004299449.1 Length = 336 Score = 427 bits (1099), Expect = e-124 Identities = 221/333 (66%), Positives = 254/333 (76%), Gaps = 13/333 (3%) Query: 1 MKLATLNQG-RDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGL 59 MKLATL QG RDG LVVVSRDL + VP IA +LQAALDDW C+P L VY+ LN G Sbjct: 1 MKLATLKQGGRDGTLVVVSRDLTRCRAVPAIARSLQAALDDWQACEPPLRQVYEALNSGA 60 Query: 60 EEGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGADA 119 + A FDQTAC SPLPRAY WADGSAY+NHVELVRKAR AEMP SF+ DPLMYQGG+D+ Sbjct: 61 VD-AQPFDQTACASPLPRAYQWADGSAYINHVELVRKARNAEMPPSFYTDPLMYQGGSDS 119 Query: 120 FIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIPG 179 FI P + +ADEAWGID E E+ V+T DVPMGATPAEAA I+L+MLVNDVSLRNLIP Sbjct: 120 FIGPRDAV-VADEAWGIDFEAEVTVVTGDVPMGATPAEAAQAIRLVMLVNDVSLRNLIPN 178 Query: 180 ELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMTF 239 ELAKGFGF+QSKP+S+FSPVAVTPDELGE WRD KVH PLV H+NG+LFG+P+AG DMTF Sbjct: 179 ELAKGFGFFQSKPASAFSPVAVTPDELGEAWRDAKVHLPLVVHLNGKLFGKPEAGVDMTF 238 Query: 240 NFPTLVAHAARTRPLGAGTIIGSGTVSNYD----------RSAGSSCLAEKRMLEVVEHG 289 +F LVAH ARTR L AG+IIGSGTVSN G CLAE R E +E G Sbjct: 239 DFGQLVAHVARTRELEAGSIIGSGTVSNKQGDLWGSSIDHGGVGYCCLAEVRTYETIEQG 298 Query: 290 EAKTPFLKFGDRVRIEMFDAAGQSIFGAIDQQV 322 + T F++ GD VRIEMFD G+++FG I+ +V Sbjct: 299 KPATSFMRDGDVVRIEMFDRQGRNVFGTIENRV 331 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: 413 Number of extensions: 13 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: 327 Length of database: 336 Length adjustment: 28 Effective length of query: 299 Effective length of database: 308 Effective search space: 92092 Effective search space used: 92092 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