Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate YP_002827492.1 NGR_c29960 aromatic amino acid degradation protein
Query= reanno::psRCH2:GFF3447 (327 letters) >NCBI__GCF_000018545.1:YP_002827492.1 Length = 338 Score = 423 bits (1087), Expect = e-123 Identities = 220/336 (65%), Positives = 252/336 (75%), Gaps = 12/336 (3%) Query: 1 MKLATLNQG-RDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGL 59 MKLATL RDG LVVVSRDL + +V IA TLQ ALDDW + P+L V + + G Sbjct: 1 MKLATLKDSTRDGKLVVVSRDLTRCSEVGHIARTLQTALDDWAHAGPRLARVAEGIETG- 59 Query: 60 EEGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGADA 119 + F + SPLPRA+HWADGSAYVNHVELVRKAR AEMP SFW DPL+YQGG+D+ Sbjct: 60 SQPTMRFHEHDAASPLPRAFHWADGSAYVNHVELVRKARDAEMPASFWTDPLIYQGGSDS 119 Query: 120 FIPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIPG 179 F+ P PI++ADEAWGIDLEGE+AVI DDVPMGAT EA I+L+MLVNDVSLR LIPG Sbjct: 120 FVGPRDPIQVADEAWGIDLEGEVAVIVDDVPMGATVDEAREAIRLVMLVNDVSLRGLIPG 179 Query: 180 ELAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMTF 239 ELAKGFGFYQSKPSS+FSPV VTPDELG+ W GK+H PL +NG+ FG+ +AG DMTF Sbjct: 180 ELAKGFGFYQSKPSSAFSPVGVTPDELGDAWDGGKMHLPLRVDLNGKPFGRANAGIDMTF 239 Query: 240 NFPTLVAHAARTRPLGAGTIIGSGTVSN----------YDRSAGSSCLAEKRMLEVVEHG 289 +FP L+ HAARTRPL AGTIIGSGTVSN D G SC+AE RM+E +E G Sbjct: 240 DFPQLIVHAARTRPLSAGTIIGSGTVSNKLDGGPGKPVSDGGVGYSCIAELRMIETIETG 299 Query: 290 EAKTPFLKFGDRVRIEMFDAAGQSIFGAIDQQVERY 325 AKT FLKFGD VRIEM D G SIFGAI+Q+VERY Sbjct: 300 AAKTSFLKFGDVVRIEMKDKTGHSIFGAIEQKVERY 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: 412 Number of extensions: 19 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: 338 Length adjustment: 28 Effective length of query: 299 Effective length of database: 310 Effective search space: 92690 Effective search space used: 92690 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