Align fumarylacetoacetate (FAA) hydrolase (EC 3.7.1.2) (characterized)
to candidate WP_011444733.1 SARO_RS05360 FAA hydrolase family protein
Query= reanno::psRCH2:GFF3447 (327 letters) >NCBI__GCF_000013325.1:WP_011444733.1 Length = 335 Score = 355 bits (912), Expect = e-103 Identities = 187/335 (55%), Positives = 232/335 (69%), Gaps = 12/335 (3%) Query: 1 MKLATLNQGRDGVLVVVSRDLAQAVKVPQIAATLQAALDDWNYCKPKLEAVYQRLNDGLE 60 MKLA+L QGRDG L+VVS DLA I T+Q LDDW+ P +EA+ L Sbjct: 1 MKLASLPQGRDGRLIVVSDDLAWYADADHIVPTMQGLLDDWDRHFPLIEALAIELAHEAI 60 Query: 61 EGAFAFDQTACHSPLPRAYHWADGSAYVNHVELVRKARGAEMPESFWHDPLMYQGGADAF 120 ++ AC +PLPRA+ WADGSAYVNHVELVRKARGAE+PESFW DPLMYQGG+D Sbjct: 61 PLKRFHEREAC-APLPRAFQWADGSAYVNHVELVRKARGAELPESFWTDPLMYQGGSDDM 119 Query: 121 IPPHSPIRLADEAWGIDLEGELAVITDDVPMGATPAEAASHIQLLMLVNDVSLRNLIPGE 180 P+ LADEAWG D E E+ V+T DVP G +P EA HI+L+ LVNDVSLRNLIPGE Sbjct: 120 RGGRDPLVLADEAWGGDFEAEIVVVTGDVPQGVSPEEALKHIRLVGLVNDVSLRNLIPGE 179 Query: 181 LAKGFGFYQSKPSSSFSPVAVTPDELGETWRDGKVHRPLVSHINGELFGQPDAGTDMTFN 240 L+KGFGF QSKP+S FSPV VTP+ LG+ W G++ + L+ +NGE FG+ +A + TF+ Sbjct: 180 LSKGFGFVQSKPASHFSPVFVTPETLGDAWAGGRLSQTLMVDLNGEPFGRIEAAEECTFD 239 Query: 241 FPTLVAHAARTRPLGAGTIIGSGTVSNYDRSA-----------GSSCLAEKRMLEVVEHG 289 F L+AH A+TR +GAG+IIGSGTVSN D G +C+AE+RM+E + G Sbjct: 240 FGVLIAHLAKTRSIGAGSIIGSGTVSNRDPDGSPGRPVAQGGRGYACIAEQRMVETIASG 299 Query: 290 EAKTPFLKFGDRVRIEMFDAAGQSIFGAIDQQVER 324 + T FL++GD VRIEM D G+SIFGAI+Q V R Sbjct: 300 QPSTAFLRWGDTVRIEMRDDKGKSIFGAIEQTVVR 334 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: 387 Number of extensions: 9 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: 335 Length adjustment: 28 Effective length of query: 299 Effective length of database: 307 Effective search space: 91793 Effective search space used: 91793 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