Align FAA hydrolase family protein (characterized, see rationale)
to candidate 3609154 Dshi_2542 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase (RefSeq)
Query= uniprot:A0A2E7P912 (281 letters) >FitnessBrowser__Dino:3609154 Length = 308 Score = 170 bits (430), Expect = 4e-47 Identities = 93/206 (45%), Positives = 127/206 (61%), Gaps = 8/206 (3%) Query: 75 CIGLNYADHAAE------SNLPIPAEPVVFNKWTSAVVGPNDDVKI-PRGSKKTDWEVEL 127 C+G NYA+H AE + + I PV F K +AVVG DV I P S+K D+EVEL Sbjct: 96 CVGRNYAEHIAEGERAQNAKIGITEHPVYFTKPATAVVGHGGDVLIFPSVSEKIDYEVEL 155 Query: 128 GVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLVT 187 VVIG G I + A +HV GY ++ND++ R+ Q GG + KGK D PIGPW+VT Sbjct: 156 AVVIGTTGRDIPKDRAFAHVFGYTILNDITARDVQRRHGGQYFKGKSLDGSCPIGPWIVT 215 Query: 188 RDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGV 247 DE+ DPQ L + L V+G+ QNG T MIF + +++ LS ++L+PGD+I+TGTP GV Sbjct: 216 ADEITDPQDLSISLSVNGELRQNGWTHDMIFDIPTLIASLSEGLTLEPGDIIATGTPSGV 275 Query: 248 GMGVKPEAVYLRAGQTMRLGIDGLGE 273 G + P YL+ G T+ I +G+ Sbjct: 276 GYAMDPPQ-YLKPGDTVICDIANIGQ 300 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: 266 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: 308 Length adjustment: 26 Effective length of query: 255 Effective length of database: 282 Effective search space: 71910 Effective search space used: 71910 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: 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