Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate GFF3195 PGA1_c32480 N-formylglutamate amidohydrolase
Query= reanno::BFirm:BPHYT_RS07585 (271 letters) >FitnessBrowser__Phaeo:GFF3195 Length = 286 Score = 89.7 bits (221), Expect = 6e-23 Identities = 72/238 (30%), Positives = 111/238 (46%), Gaps = 22/238 (9%) Query: 19 LLISIPHLGTQIPAD-IAATMTPAAQRTDDCDWHLDRLYAFAKRMGASILAPTYARYVID 77 ++ + PH G+ A +A T+ Q D +D L+A A R G +L R +D Sbjct: 18 VVFASPHSGSDYSAAFLAQTILDPLQLRSSEDAFVDELFAAAPRFGMPLLTARAPRAYVD 77 Query: 78 LNRPPDGAN-------LYPGQDTT-----GLLPVDTFDKEPLYLDGQLPDEAETTRRRDA 125 LNR + + + GQ+ G++P +Y G+L + E RR ++ Sbjct: 78 LNRSTEELDPALIEGVIKRGQNPRVASGLGVVPRVVAHGRAIY-HGKL-SQCEARRRIES 135 Query: 126 YWKPYHEALQGELAALKAKHGKVLLWEAHSIRSHVPRFFEGR----LPDFNFGTSNGASA 181 YW+PYH ALQ L + G+ +L + HS+ H GR LPD G GA+A Sbjct: 136 YWRPYHAALQQLLDQARIGFGQAVLIDCHSM-PHEAISAAGRRGAGLPDVVLGDRFGAAA 194 Query: 182 VAGLAEEMAATVEQYDGGYTAVANGRFKGGYITREYGQPSQGVHALQLELSQITYMEE 239 + + + + A G N F G YIT+ YG+PS+ HA+Q+E+ + YM E Sbjct: 195 SSEVMDRVEAAF--VGAGLRVARNTPFAGAYITQTYGRPSRAQHAVQVEIDRSLYMNE 250 Lambda K H 0.317 0.134 0.403 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: 189 Number of extensions: 5 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: 271 Length of database: 286 Length adjustment: 25 Effective length of query: 246 Effective length of database: 261 Effective search space: 64206 Effective search space used: 64206 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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