Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate WP_011840147.1 RSPH17029_RS00345 N-formylglutamate amidohydrolase
Query= reanno::pseudo6_N2E2:Pf6N2E2_3797 (267 letters) >NCBI__GCF_000015985.1:WP_011840147.1 Length = 286 Score = 96.3 bits (238), Expect = 7e-25 Identities = 75/237 (31%), Positives = 114/237 (48%), Gaps = 22/237 (9%) Query: 14 LLISMPHAGLRLTPAVQAG--LIPEAQSLPDTDWHIPRLYEFAAELGASTLAAEYSRFVV 71 ++ S PH+G R PA G ++ E D + L+ A LGA L A R V Sbjct: 18 VIFSSPHSG-RDYPASLVGRTILDERMLRSSEDAFVDELFSCAPRLGAPLLMARVPRAYV 76 Query: 72 DLNRPSDDKPMY-------------VGATTGLYPATLFDGVPLFRQGLEPSAEERARYLQ 118 D+NR +D+ V + G+ P + +G P++R G P AE AR + Sbjct: 77 DMNRSADEMDPALIEGISRAPHNPRVSSGLGVIPRVVANGRPIYR-GKMPLAEAEAR-IA 134 Query: 119 QIWMPYHQALQQELARLKAEFGYALLFDAHSI--RSVIPHLFDGK-LPDFNLGTFNGASC 175 + W PYHQAL+ + +A F A+L D HS+ ++ H G+ P+ LG GA+ Sbjct: 135 RYWTPYHQALRTLIDESQALFDEAVLVDCHSMPHEAIETHARPGQPTPEVVLGDRFGAAA 194 Query: 176 DPTLASQLEAICARHGQFTHVLNGRFKGGHITRHYGNPAEDIHAVQLELCQSTYMEE 232 + ++EA G V N F G +I + YG P+ + H VQ+E+ +S YM+E Sbjct: 195 SRAVVDRIEAAFVSAG-LRVVRNAPFAGAYIAQAYGRPSRNQHVVQVEVDRSLYMDE 250 Lambda K H 0.322 0.138 0.425 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: 220 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: 267 Length of database: 286 Length adjustment: 25 Effective length of query: 242 Effective length of database: 261 Effective search space: 63162 Effective search space used: 63162 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 Apr 10 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