Align Formimidoylglutamase; EC 3.5.3.8; Formiminoglutamase; Formiminoglutamate hydrolase (uncharacterized)
to candidate Echvi_3131 Echvi_3131 Arginase/agmatinase/formimionoglutamate hydrolase, arginase family
Query= curated2:Q9KBE3 (319 letters) >FitnessBrowser__Cola:Echvi_3131 Length = 356 Score = 72.4 bits (176), Expect = 2e-17 Identities = 59/194 (30%), Positives = 89/194 (45%), Gaps = 17/194 (8%) Query: 122 VLGGDHSISFPSIKAFASAKGTIGVIQFDAHHDLRNLEDG-GPCNGTPFRSLLETGSLVG 180 ++GGDHS IKA + + G++Q DAH DLR+ +G + + + L + Sbjct: 154 LVGGDHSTPLGHIKALSERYSSFGILQIDAHADLRDQYEGFNYSHASISHNFLNIPQV-- 211 Query: 181 EHLVQIGIRDFSNSYPYRKYAE-------KHGVKVYTMKDVNARGLLTILDEAVAKLKRS 233 E LVQ+G+RD+ R + H +K + V R TI D+ +A L R Sbjct: 212 EKLVQVGVRDYCEEESDRIDGDDRITTFFDHHIKEQLYEGVTWR---TICDQVIASLPRE 268 Query: 234 VDVIYVSVDMDVLDQAHAPGCPAIGPGGMDSTTLLQGIFHLGKDS-LVQGMDIVEVDPTL 292 IY+++D+D LD P PGG D LL + + K + G D+VEV P Sbjct: 269 ---IYITIDIDGLDPKLCPHTGTPVPGGFDLNQLLYLMKLIVKSGRKIIGFDLVEVAPGE 325 Query: 293 DFREMTSRAAAHVI 306 D E A ++ Sbjct: 326 DDSEWDGNVGARLL 339 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: 271 Number of extensions: 22 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: 319 Length of database: 356 Length adjustment: 28 Effective length of query: 291 Effective length of database: 328 Effective search space: 95448 Effective search space used: 95448 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: 49 (23.5 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