Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate PP_3205 PP_3205 Fumarylacetoacetate hydrolase family protein
Query= reanno::psRCH2:GFF3447 (327 letters) >FitnessBrowser__Putida:PP_3205 Length = 330 Score = 342 bits (878), Expect = 6e-99 Identities = 176/327 (53%), Positives = 226/327 (69%), Gaps = 2/327 (0%) Query: 1 MKLATLNQG-RDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGL 59 MKLAT + G RDG L+VV+RDL AV IA +LQ AL++W + +L+A+YQ+LND Sbjct: 1 MKLATFDDGSRDGRLLVVARDLGHAVDASDIATSLQVALENWPQVEARLQALYQQLNDDA 60 Query: 60 EEGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGADA 119 GAFA D +PLPRA W DGS +++H L++KA + E H PL+YQG +D Sbjct: 61 VAGAFALDLARLAAPLPRASQWLDGSCFLSHGALMQKAFNLDPIEGVEHTPLIYQGASDD 120 Query: 120 FIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIPG 179 F+ P + I L EA GID EGE AV+ DDVPMG +A H++L++ +NDVSLR L P Sbjct: 121 FLGPLADIPLPSEAHGIDFEGEFAVLLDDVPMGCPAEQALQHVRLILQLNDVSLRALAPR 180 Query: 180 ELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMTF 239 E+ GFGF Q+KP+SSF+PVAVTPDELGE WRDG+VH PL H NGE FG P G M F Sbjct: 181 EMKTGFGFLQAKPASSFAPVAVTPDELGEAWRDGRVHLPLHVHWNGEWFGHPHGGA-MHF 239 Query: 240 NFPTLVAHAARTRPLGAGTIIGSGTVSNYDRSAGSSCLAEKRMLEVVEHGEAKTPFLKFG 299 F L+AHAA TR L AGT++GSGTVSN +RS GS+C+AE+R +E + G +T F++FG Sbjct: 240 GFHQLIAHAALTRRLSAGTLLGSGTVSNAERSVGSACIAERRAIETIACGAPRTAFMRFG 299 Query: 300 DRVRIEMFDAAGQSIFGAIDQQVERYG 326 DRVR+E G+ +FGAIDQ+V R G Sbjct: 300 DRVRMEARGPEGEVLFGAIDQRVVRGG 326 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: 383 Number of extensions: 13 Number of successful extensions: 2 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: 330 Length adjustment: 28 Effective length of query: 299 Effective length of database: 302 Effective search space: 90298 Effective search space used: 90298 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 17 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