Align Formimidoylglutamase; Formiminoglutamase; Formiminoglutamate hydrolase; N-formimino-L-glutamate formiminohydrolase; EC 3.5.3.8 (characterized)
to candidate WP_011777371.1 MVAN_RS00255 agmatinase
Query= SwissProt::P42068 (319 letters) >NCBI__GCF_000015305.1:WP_011777371.1 Length = 321 Score = 115 bits (288), Expect = 1e-30 Identities = 88/276 (31%), Positives = 145/276 (52%), Gaps = 18/276 (6%) Query: 38 ALIGVPLSKSSISHSGASFAPGTIRQALKHSSAY--SAELGEHVVSELLYDLGDIDIHVT 95 A+IGVP GA F P IRQA + Y + E+ ++++ D GDI + Sbjct: 46 AVIGVPFDSGVTYRPGARFGPAAIRQASRLLKPYHPALEVSPFATAQVV-DAGDIAANPF 104 Query: 96 DIVKSHHHIFQTMHALLSDHPDWVPLILGGDNSISYSTIKAIAQTKGTTAVIQFDAHHDV 155 DI + I + L++ P+ ++LGGD++I+ ++A+ + G A++ FDAH D Sbjct: 105 DITTAVEQIKDGILGLVTS-PEQRFVLLGGDHTIALPALQAVNELHGPVALVHFDAHLDT 163 Query: 156 RNTEDGGP-TNGTPFRRLLDEEIIEGQHLIQLGIREFSNSQAYEAY-----AKKHNVNIH 209 +T G P T+GTPFRR ++ +I H +GIR Y+A A+ +H Sbjct: 164 WDTYFGAPCTHGTPFRRASEQGLIVKGHSAHVGIR----GSLYDAADLLDDAELGFTAVH 219 Query: 210 TMDMIREKGLIPTIKEILPVVQDKTDFIFISVDMDVLDQSHAPGCPAIGPGGLYTDELLE 269 D+ R G+ I+ +L V + +++S+D+DVLD + APG GG+ + EL+ Sbjct: 220 CRDIDR-IGVDGVIERVLERVGEHP--VYVSIDVDVLDPAFAPGTGTPEIGGMTSRELV- 275 Query: 270 AVKYIAQQPNVAGIEIVEVDPTLDFRDMTSRAAAHV 305 AV + N+ G ++VEV P D ++T+ AAA++ Sbjct: 276 AVLRAMRALNIVGADVVEVAPAYDHAEVTAVAAANL 311 Lambda K H 0.318 0.136 0.396 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: 301 Number of extensions: 15 Number of successful extensions: 5 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: 319 Length of database: 321 Length adjustment: 28 Effective length of query: 291 Effective length of database: 293 Effective search space: 85263 Effective search space used: 85263 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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