Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate CCNA_00780 CCNA_00780 N-formylglutamate deformylase
Query= reanno::acidovorax_3H11:Ac3H11_2548 (270 letters) >FitnessBrowser__Caulo:CCNA_00780 Length = 308 Score = 101 bits (252), Expect = 2e-26 Identities = 86/269 (31%), Positives = 123/269 (45%), Gaps = 33/269 (12%) Query: 5 PPPFTFHQGTAPLLVSMPHAGTYVPP--VLAARFTDEARQVPDTDWHMERLYAFAKDMGA 62 PPP L+ + PH+G P V A R E + + D ++R+ A +GA Sbjct: 36 PPP-------TALVFASPHSGDLYPEDMVAAVRLPLETLRASE-DAFVDRIIGGAPALGA 87 Query: 63 SILVATHSRYVVDLNRPP--------DGASLYPGQSVT-------GLCPVDTFDDTPIYA 107 +++ A +R VDLNR P DG Q T G P + PIY Sbjct: 88 AVVRARFARAYVDLNREPWELDPAMFDGDLPDYAQGRTARVAAGLGTIPRVAGEGRPIYG 147 Query: 108 QGDVPDDAEVAARRDAVWAPYHAQLRAELSRIRAQHGVAVLWDAHSIRSVLPRFFE---G 164 + D+A R + PYH L +L+ RA HG A+L D HS+ + R G Sbjct: 148 RKLSFDEART--RVELAHRPYHDALDRQLAAARAAHGAAILIDWHSMPAAAARGQRTKGG 205 Query: 165 KLPDLNLGTADGASCDPALAQALLAIAQSAPGYTGVLNGRFKGGHITRHYGQPAQNIHAV 224 + D+ LG GA+C P L AL+ A GY N + GG+ T HYG+PA+ HA+ Sbjct: 206 GVCDIVLGDRFGAACSPKLT-ALVERELEALGYNVARNAPYAGGYTTEHYGRPAKRTHAL 264 Query: 225 QLEMTQCSYMQEA--LPFDYLPEVAAEVQ 251 Q+E+ + YM E P D L + A+ + Sbjct: 265 QIEINRALYMDETTRAPTDGLARLIADAE 293 Lambda K H 0.321 0.135 0.416 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: 212 Number of extensions: 18 Number of successful extensions: 4 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: 270 Length of database: 308 Length adjustment: 26 Effective length of query: 244 Effective length of database: 282 Effective search space: 68808 Effective search space used: 68808 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: 48 (23.1 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