Align fumarylacetoacetate hydrolase (EC 3.7.1.2) (characterized)
to candidate Ac3H11_4507 Fumarylacetoacetate hydrolase family protein
Query= reanno::MR1:200835 (328 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4507 Length = 337 Score = 390 bits (1001), Expect = e-113 Identities = 195/332 (58%), Positives = 246/332 (74%), Gaps = 9/332 (2%) Query: 1 MKLASYNNGRRDGQLMLVSRDLTQTVAVPAIAHTMQQLLDGWELLKPQLQELYDALNEGK 60 MKLA+Y +G RDGQL++VSRDL IA +QQ+LD W L PQLQ+LYD LN G+ Sbjct: 1 MKLATYKDGSRDGQLVVVSRDLGTAHYATGIASKLQQVLDDWGFLSPQLQDLYDQLNSGR 60 Query: 61 LPNTQTFDETKCLSPLPRAYQWADGSAYVNHVELVRKARGAEMPETFWTDPLFYQGGSDS 120 + FD +C++PLPRAYQWADGSAY+NHVELVRKAR +E+PE+F+TDPL YQGGSD Sbjct: 61 ARHAFPFDPAQCMAPLPRAYQWADGSAYINHVELVRKARNSEVPESFYTDPLMYQGGSDD 120 Query: 121 FIAPKADIPLASEDWGIDFESEIAVITDDVPMGVSAENAAKHIKLLMLVNDVSLRNLIPA 180 FI P D+ + SE GIDFE+EIAV+T DV MG +A+ A I+L+M+ NDVSLRNLIPA Sbjct: 121 FIGPCDDVVVPSEAMGIDFEAEIAVVTGDVKMGTNADQALDGIRLVMIANDVSLRNLIPA 180 Query: 181 ELAKGFGFFQSKPSSSFSPVAITPDELGHRWEDSKVHLPLITYLNGELFGRPNAGVDMTF 240 ELAKGFGFFQSKP+++F PVA+T DELG W+ +V+L + + NG G +AG +MTF Sbjct: 181 ELAKGFGFFQSKPATAFGPVAVTLDELGDAWDHGRVNLTVQSTWNGRKVGMCDAGPEMTF 240 Query: 241 NFSQLVSHVAKTRPLGAGAIIGSGTISN---------YDRSAGSSCLAEKRMLEVIADGK 291 +F QL++HVAKTR L AG+IIGSGT+SN + G SC+AEKR +E I DGK Sbjct: 241 HFGQLIAHVAKTRNLRAGSIIGSGTVSNKGITDANGRTEWPKGYSCIAEKRCIETIQDGK 300 Query: 292 ASTPFMRFGDTVRIEMLDDNGVSIFGSIDQKV 323 ST FM+FGDT+RIE+ +G SIFG+IDQ + Sbjct: 301 PSTDFMKFGDTIRIEVKGKDGASIFGAIDQAI 332 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: 332 Number of extensions: 10 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: 328 Length of database: 337 Length adjustment: 28 Effective length of query: 300 Effective length of database: 309 Effective search space: 92700 Effective search space used: 92700 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: 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