Align Formimidoylglutamase; EC 3.5.3.8; Formiminoglutamase; Formiminoglutamate hydrolase (uncharacterized)
to candidate HSERO_RS08555 HSERO_RS08555 agmatinase
Query= curated2:Q9KBE3 (319 letters) >FitnessBrowser__HerbieS:HSERO_RS08555 Length = 317 Score = 112 bits (279), Expect = 2e-29 Identities = 83/277 (29%), Positives = 132/277 (47%), Gaps = 11/277 (3%) Query: 38 GLIGAPLSKSSISHSGASFAPTVIRKCLHAFSTYSVE-EDLDLAQLKLTDLGDITMHVTD 96 G +G PL + + SG F P IR Y++ LK+ DLGD+ ++ Sbjct: 38 GFVGVPLDIGTSNRSGTRFGPRQIRTESVLLRPYNMATRAAPFDSLKVADLGDVALNPYS 97 Query: 97 IVGSQARIEETMTKLLENEQNWQPIVLGGDHSISFPSIKAFASAKGTIGVIQFDAHHDLR 156 ++ S IEE ++ + I LGGDH+++ P ++A A +G +G+I DAH D+ Sbjct: 98 LLDSVRMIEEAYDRIYAT--GCKTISLGGDHTLTLPILRALARYRGPVGLIHVDAHADVN 155 Query: 157 NLEDGGP-CNGTPFRSLLETGSLVGEHLVQIGIRDFSNSYPYRKYAEKHGVKVYTMKDVN 215 + +G +GTPFR E G L + +VQIG+R + G +V ++ Sbjct: 156 DTMNGEKIAHGTPFRRAFEEGLLDPQRVVQIGLRGTGYHADDFDWCRAQGFRVVQAEECW 215 Query: 216 ARGLLTILDEAVAKLKRSVDVIYVSVDMDVLDQAHAPGCPAIGPGGMDSTTLLQG--IFH 273 R L +++E A++ +Y++ D+D LD A APG GG+ T+ QG I Sbjct: 216 HRSLAPLMEEVRAQM--GDGPVYLTFDIDGLDPAFAPGTGTPEIGGL---TVQQGLEIIR 270 Query: 274 LGKDSLVQGMDIVEVDPTLDFREMTSRAAAHVILNYL 310 K + D+VEV P D T+ AA++ L Sbjct: 271 GCKGLDIVSADVVEVSPPYDQAGTTALVAANLAYEML 307 Lambda K H 0.319 0.138 0.408 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: 275 Number of extensions: 19 Number of successful extensions: 6 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: 317 Length adjustment: 27 Effective length of query: 292 Effective length of database: 290 Effective search space: 84680 Effective search space used: 84680 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 (21.8 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