Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate Ga0059261_1570 Ga0059261_1570 N-formylglutamate amidohydrolase
Query= reanno::pseudo6_N2E2:Pf6N2E2_3797 (267 letters) >FitnessBrowser__Korea:Ga0059261_1570 Length = 279 Score = 87.0 bits (214), Expect = 4e-22 Identities = 80/266 (30%), Positives = 126/266 (47%), Gaps = 37/266 (13%) Query: 13 PLLISMPHAGLRLTPAVQAGL-IPEAQSLPDTDWHIPRLYEFAAELGASTLAAEYSRFVV 71 P+++S+PHAG ++A L +P A LP D H RL AA + L A +R + Sbjct: 18 PVVLSVPHAGRDYPLPLRAALRVPLASLLPLEDRHADRL-TLAARGAETLLVANRARAWI 76 Query: 72 DLNRPSDDK---------PMYVGATT-------GLYPATLFDGVPLFRQGLEPSAEERAR 115 DLNR ++ P+ GA + GL P G L+R+ + EE + Sbjct: 77 DLNRAEHERDPRIDEGATPIPEGAMSLKLRSGLGLVPRRA-GGADLWRRRF--ADEEVRQ 133 Query: 116 YLQQIWMPYHQALQQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASC 175 +++ PYH A++ ELA + FG A+L D HS+ P L G +G G S Sbjct: 134 RIERDHRPYHAAIEAELAAARDRFGVAVLLDIHSM----PPLASGGAR-IVIGDRFGRSA 188 Query: 176 DPTLASQLEAICARHGQFTHVLNGRFKGGHITRHYGNPAEDIHAVQLELCQSTYMEEYEP 235 ++E G T V N + GGH+ + +PA +IHA+Q+E+ +S Y++ Sbjct: 189 AARFVGRIEGAVHAAGIRTAV-NTPYAGGHVLDRHADPAANIHAIQIEIDRSLYLDR--- 244 Query: 236 FNYRADLA----EPTQVVLRQLLEGL 257 R DL EP +LR++++ + Sbjct: 245 ---RRDLPGPGFEPAAALLRRIIDAV 267 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: 210 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: 279 Length adjustment: 25 Effective length of query: 242 Effective length of database: 254 Effective search space: 61468 Effective search space used: 61468 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