Align fumarylacetoacetate hydrolase (EC 3.7.1.2) (characterized)
to candidate H281DRAFT_02070 H281DRAFT_02070 fumarylacetoacetate (FAA) hydrolase
Query= reanno::MR1:200835 (328 letters) >FitnessBrowser__Burk376:H281DRAFT_02070 Length = 327 Score = 428 bits (1100), Expect = e-124 Identities = 203/323 (62%), Positives = 252/323 (78%) Query: 1 MKLASYNNGRRDGQLMLVSRDLTQTVAVPAIAHTMQQLLDGWELLKPQLQELYDALNEGK 60 MKLA+ +G RDGQL++VSRDL AIA T+Q++LD W PQL +LYDALN+G+ Sbjct: 1 MKLATLKDGTRDGQLIVVSRDLHTAAVADAIAPTLQRVLDDWTFYAPQLHDLYDALNQGR 60 Query: 61 LPNTQTFDETKCLSPLPRAYQWADGSAYVNHVELVRKARGAEMPETFWTDPLFYQGGSDS 120 NT +FD + C++PLPRA+QWADGS+YVNHVELVR+ARGAEMP FWTDPL YQGGSD Sbjct: 61 ARNTFSFDASDCMAPLPRAFQWADGSSYVNHVELVRRARGAEMPPEFWTDPLMYQGGSDD 120 Query: 121 FIAPKADIPLASEDWGIDFESEIAVITDDVPMGVSAENAAKHIKLLMLVNDVSLRNLIPA 180 FI P+ D+ ASE +GIDFE+E+AVIT DVPMG + E + K ++L+ LVNDVSLRNLIPA Sbjct: 121 FIGPEDDVVCASEAFGIDFEAEVAVITTDVPMGATPEQSLKSVRLITLVNDVSLRNLIPA 180 Query: 181 ELAKGFGFFQSKPSSSFSPVAITPDELGHRWEDSKVHLPLITYLNGELFGRPNAGVDMTF 240 ELAKGFGFFQSKP+SSF+PVA+TPDELG W + +VH P+I + NG+ G+P+AG DM F Sbjct: 181 ELAKGFGFFQSKPASSFAPVAVTPDELGEHWREGRVHRPMIVHWNGKKVGQPDAGTDMVF 240 Query: 241 NFSQLVSHVAKTRPLGAGAIIGSGTISNYDRSAGSSCLAEKRMLEVIADGKASTPFMRFG 300 +F QL++H AKTR L AGAI+GSGT+SN D G C+AEKR LE I G T FM++G Sbjct: 241 HFGQLIAHAAKTRNLRAGAIVGSGTVSNKDAKRGYCCIAEKRCLETIEHGAPQTEFMKYG 300 Query: 301 DTVRIEMLDDNGVSIFGSIDQKV 323 DTV+IEM D+ G SIFGSI+Q + Sbjct: 301 DTVKIEMFDEAGKSIFGSIEQSI 323 Lambda K H 0.317 0.134 0.397 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: 333 Number of extensions: 6 Number of successful extensions: 1 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: 328 Length of database: 327 Length adjustment: 28 Effective length of query: 300 Effective length of database: 299 Effective search space: 89700 Effective search space used: 89700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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