Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate AZOBR_RS12550 AZOBR_RS12550 N-formylglutamate amidohydrolase
Query= reanno::Korea:Ga0059261_3962 (264 letters) >FitnessBrowser__azobra:AZOBR_RS12550 Length = 288 Score = 95.5 bits (236), Expect = 1e-24 Identities = 76/234 (32%), Positives = 106/234 (45%), Gaps = 17/234 (7%) Query: 10 PLIVSVPHAGTVIPADIQGLVSPELARYDADLYVDHLYAFARGLDATIVRTTVSRTVIDV 69 P+ PH+GTV P D + R D +VD L+A A AT++ RT ID Sbjct: 20 PVFFDSPHSGTVYPRDFAFVCPLSTLRQAEDTHVDELFAHAPEHGATLLCALFPRTYIDA 79 Query: 70 NR--DPSGQTLYPGQFTTGLCP----------IQTF--DGTPLYEPGALPDAHEIERRRA 115 NR D L G++ L P I+T G PLY+ G L A E+ R Sbjct: 80 NRAIDDIDPALLDGRWPEPLRPTEKSAAGMGLIRTLCRPGMPLYD-GRLSVA-EVAERID 137 Query: 116 EWFDPYHTALAIQIERLRAIHPAIVVYDAHSIRSVVPKLFDGELP-NFNIGTNDGTSCAP 174 ++ PYH +A ++ L A+ D HS+ S V +L +F +G DGTSC P Sbjct: 138 RYYRPYHFQVASVMDDLADRFGAVWHVDCHSMPSAVGPGAAHKLGMDFVLGDRDGTSCEP 197 Query: 175 ALTQAVEAICDASPYSRVTNGRFKGGWITRHYARPAGGVHSIQMELAMRTYLVE 228 T VE + Y N FKG + ++ P G HS+Q+E+ R Y+ E Sbjct: 198 GFTALVERVLTGLGYKVTRNHPFKGVELVSRHSNPTRGRHSLQLEINRRLYMNE 251 Lambda K H 0.321 0.136 0.426 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: 250 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: 264 Length of database: 288 Length adjustment: 25 Effective length of query: 239 Effective length of database: 263 Effective search space: 62857 Effective search space used: 62857 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: 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