Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_028488570.1 Q394_RS0106530 fumarylacetoacetate hydrolase family protein
Query= uniprot:A0A2E7P912 (281 letters) >NCBI__GCF_000621325.1:WP_028488570.1 Length = 294 Score = 159 bits (401), Expect = 9e-44 Identities = 88/206 (42%), Positives = 123/206 (59%), Gaps = 9/206 (4%) Query: 74 ICIGLNYADHAAESNLPI------PAEPVVFNKWTSAVVGPNDDVKI-PRGSKKTDWEVE 126 +C+GLNY +HA E+ I P P+VF K ++V+G + V P + DWE E Sbjct: 81 MCLGLNYLEHAEETANQIGRTGKAPQYPIVFTKCPTSVIGQDAVVPFDPDTCSQLDWEAE 140 Query: 127 LGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLV 186 LGVV+GKGG I +A+ HV GY V+ND+S R+ Q+ + GK D P+GPW+V Sbjct: 141 LGVVLGKGGKKIAAANALDHVFGYTVINDLSARDIQLSHK-QYFLGKSLDGGCPMGPWIV 199 Query: 187 TRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPG 246 T D++ADPQ L + V+G Q NT MIF VA I+ +LSR M+L+ GDVI+TGTP G Sbjct: 200 TADDIADPQNLAIACRVNGVTKQASNTRNMIFNVASIIEWLSRGMTLEAGDVIATGTPSG 259 Query: 247 VGMGVKPEAVYLRAGQTMRLGIDGLG 272 VG V+ +L G + ++ +G Sbjct: 260 VGF-VREPPEFLLPGDVVECEVESVG 284 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: 245 Number of extensions: 16 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 Apr 09 2024. 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