Align FAA hydrolase family protein (characterized, see rationale)
to candidate Ac3H11_2308 Fumarylacetoacetate hydrolase family protein
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2308 Length = 231 Score = 120 bits (300), Expect = 4e-32 Identities = 72/210 (34%), Positives = 103/210 (49%), Gaps = 16/210 (7%) Query: 70 IGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVV----GPNDDVKIPRGSKKTDWEV 125 + + C+G NY +HA E P F K A+V G + P + E+ Sbjct: 24 VHRIYCVGRNYEEHAKEMGFTGREPPFFFMKPADAIVVVNTGETGQLPYPSLTANLHHEI 83 Query: 126 ELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIE---RGGTWDKGKGCDTFGPIG 182 EL V IGKGG I DA +H+ GY V D++ R+ Q + +G W GKG D PIG Sbjct: 84 ELVVAIGKGGKNIKAADAFAHIYGYAVGLDMTRRDLQNDMKKQGRPWCIGKGFDASAPIG 143 Query: 183 PWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTG 242 P + + D +WL+V+G Q + +I+ +A + +LS LQPGD+I TG Sbjct: 144 P-ITPAAQAGDVANAAIWLQVNGADRQRSTVAQLIWNIAETIEHLSAAWELQPGDLIYTG 202 Query: 243 TPPGVGMGVKPEAVYLRAGQTMRLGIDGLG 272 TP GVG V+ G + G++GLG Sbjct: 203 TPEGVGAVVR--------GDVLEGGVEGLG 224 Lambda K H 0.316 0.138 0.419 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: 201 Number of extensions: 11 Number of successful extensions: 4 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: 281 Length of database: 231 Length adjustment: 24 Effective length of query: 257 Effective length of database: 207 Effective search space: 53199 Effective search space used: 53199 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: 42 (22.0 bits) S2: 47 (22.7 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