Align arylformamidase (EC 3.5.1.9) (characterized)
to candidate HSERO_RS18245 HSERO_RS18245 lipase
Query= BRENDA::E1C2H6 (293 letters) >FitnessBrowser__HerbieS:HSERO_RS18245 Length = 282 Score = 99.8 bits (247), Expect = 6e-26 Identities = 64/179 (35%), Positives = 95/179 (53%), Gaps = 14/179 (7%) Query: 43 QKARAAAHTLL---HVPYGDGEGEKLDIYFPADSSETFPVFVYIHGGYWQCLSKDASGFA 99 Q A A TLL + YGD ++ D Y + P+ V+IHGGYWQ K GF Sbjct: 37 QATAAIADTLLTESDISYGDAPLQRFDFYRAEGAQR--PLLVFIHGGYWQGGDKRDIGFI 94 Query: 100 APALLSQGVAVVALGYDIAPRGHMDAMVLQVRRSLAFLVKQYHR----IRGIYLCGHSAG 155 A + G++V + Y +AP+ ++ MV +V+ L+ + +Q R + I L GHSAG Sbjct: 95 AAPYVKAGISVAVINYSLAPQARIEDMVKEVQACLSTIAQQAERLGIDVDRISLMGHSAG 154 Query: 156 AHLAAMVLSTDWTEFGVVPDIRGAVLVSGVYDLEPLLHTYVNDALNMSLEVAQRNSPIL 214 HLAA V + + G +P ++ +SGV+DL PL+ T +N AL + A SP+L Sbjct: 155 GHLAAFVAA----QPGRMP-VQAVFAISGVFDLAPLIPTSLNKALTLDQVRADALSPVL 208 Lambda K H 0.321 0.133 0.398 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: 204 Number of extensions: 11 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: 293 Length of database: 282 Length adjustment: 26 Effective length of query: 267 Effective length of database: 256 Effective search space: 68352 Effective search space used: 68352 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 (21.9 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