Align FAA hydrolase family protein (characterized, see rationale)
to candidate 3607555 Dshi_0967 fumarylacetoacetate (FAA) hydrolase (RefSeq)
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Dino:3607555 Length = 294 Score = 152 bits (385), Expect = 6e-42 Identities = 81/216 (37%), Positives = 124/216 (57%), Gaps = 4/216 (1%) Query: 67 VGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVE 126 + + G IC+GLNY +H E IP P +F + ++++ + P S+ D+E E Sbjct: 70 IAHPGTIICLGLNYVEHIREGGYEIPGYPALFMRGRNSIMPSGAPMVRPACSETLDYEAE 129 Query: 127 LGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLV 186 L +++G+GG +I E A+ HV GY ND S REYQ + W GK D G +GP +V Sbjct: 130 LMLIVGEGGRHIPEDAALEHVFGYTTFNDGSVREYQ-RKTHQWTPGKNFDATGAVGPIVV 188 Query: 187 TRDEVADPQKLGMWLE--VDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTP 244 T DE+ + K G+ +E V + Q+ NT MI+G A +S +S + +L+PGD+I+ GTP Sbjct: 189 TPDELPEGAK-GLKIESRVGNEILQSSNTENMIWGAAKTLSIISEYTTLEPGDLIALGTP 247 Query: 245 PGVGMGVKPEAVYLRAGQTMRLGIDGLGEQQQKTID 280 PGVG KP +LR G+ + + I+G+G +D Sbjct: 248 PGVGHAKKPGPRWLRPGEVIEVEIEGIGTCANPVVD 283 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: 283 Number of extensions: 15 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: 281 Length of database: 294 Length adjustment: 26 Effective length of query: 255 Effective length of database: 268 Effective search space: 68340 Effective search space used: 68340 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