Align Carbon-nitrogen hydrolase family protein; EC 3.5.-.- (characterized, see rationale)
to candidate WP_057687408.1 ABB28_RS16215 acyltransferase
Query= uniprot:Q5NHL7_FRATT (286 letters) >NCBI__GCF_001431535.1:WP_057687408.1 Length = 295 Score = 210 bits (535), Expect = 3e-59 Identities = 117/289 (40%), Positives = 174/289 (60%), Gaps = 8/289 (2%) Query: 4 IKVAVVQLSFNDNEAENLAKLESKIIQAAKNGAKIILTPELPSYLYFCKKQNSKYFDLAK 63 + VA++Q + + A NLA +ES++ +AA GAK+IL EL + YFC+ ++ FDLA+ Sbjct: 7 LTVALIQERNHGDAAANLAVIESRVAEAAAQGAKLILLQELHNGAYFCQHESVDEFDLAE 66 Query: 64 TIDESPIVKLYKLLAHKYNIVLPASFFERDGNACYNSIAMI-DADGSIMGVYRKAHIPDG 122 I P + LA ++ +V+ AS FER Y++ A++ + DGS++G YRK HIPD Sbjct: 67 PIP-GPSTERIGALAKQHGVVIVASLFERRAAGLYHNTAVVFEKDGSLLGKYRKMHIPDD 125 Query: 123 IGYQEKYYFSPGSAGFKVWDTKYAKVGVGICWDQWFPEAARVMALKGAEILLYPTAIGSE 182 G+ EK+YF+PG GF DT ++GV +CWDQW+PEAAR+MAL GAE+LLYPTAIG + Sbjct: 126 PGFYEKFYFTPGDLGFTPIDTSVGRLGVLVCWDQWYPEAARLMALAGAELLLYPTAIGWD 185 Query: 183 PHLPDYD---SKDHWQRVMQGHAAANMLPVLASNRYATEANDDITA--TYYGSSFITDHT 237 P + +D W +GHA AN +PVL+ NR E + + ++G+S + Sbjct: 186 PDDQQDEKNRQRDAWVLSHRGHAVANGVPVLSCNRVGHEPSPMGASGIRFWGNSHVVGPQ 245 Query: 238 GDKIAEADRSGDDILYATFDFAELQQQRFYWGLFRDRRPELYDEIVRKY 286 G+ IAEA + IL D + R W RDRR + Y +++++Y Sbjct: 246 GEFIAEAG-GEETILVCEVDLQRSEHVRRIWPFLRDRRIDAYGDLLKRY 293 Lambda K H 0.320 0.136 0.413 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: 248 Number of extensions: 18 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: 286 Length of database: 295 Length adjustment: 26 Effective length of query: 260 Effective length of database: 269 Effective search space: 69940 Effective search space used: 69940 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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