Align Formimidoylglutamase; EC 3.5.3.8; Formiminoglutamase; Formiminoglutamate hydrolase (uncharacterized)
to candidate HSERO_RS00305 HSERO_RS00305 arginase
Query= curated2:Q7WJ55 (317 letters) >FitnessBrowser__HerbieS:HSERO_RS00305 Length = 302 Score = 88.6 bits (218), Expect = 2e-22 Identities = 86/310 (27%), Positives = 131/310 (42%), Gaps = 58/310 (18%) Query: 43 VLGFACDAGVARNQGRRGAALAPRAIR--RMMAGLPAHNLRRLVDAGDVVCED------- 93 ++G D G +R RGA++AP A+R + GL H L ++D GD+ Sbjct: 6 MMGAPTDVGASR----RGASMAPAALRVAELQRGLQQHGLD-VIDGGDLAGPANPQQPPV 60 Query: 94 ------DQLEAAQDALAGRVAALLQAGAHPVVLGGGHEIAWGSFQGLRRWLDARGDREPV 147 +Q+ + VA L G P+++GG H +A GS + ++G + + Sbjct: 61 QGLRHLEQVVQWNQTVHEAVAQCLADGELPLLMGGDHALAVGSIAAVAAHCRSQG--KEL 118 Query: 148 LVLNLDAHFDLRTGRPGSSGTPFDQIAEYCAARGHALQYACL-GVSPL------GNTPAL 200 VL LDAH D T S TP I H + ACL GV P G TPAL Sbjct: 119 RVLWLDAHADANT----SQSTPTGNI--------HGMPVACLLGVGPAALTAIGGQTPAL 166 Query: 201 YARAA-----------------EVGAVWVEDRHMQEAHLGERLAQLDALLAAAGHVYLTI 243 + E+G + RH+ E + + + + A + H++++ Sbjct: 167 QPQQICQVGIRSVDREEKRHLRELGVRVFDMRHIDEYGMRQTMEEALAGVGPQTHLHVSF 226 Query: 244 DLDVLPAATAPGVSAPAPYGVPLAVVEEVAMHVRASGKLRLADLAECNPAYDIDHRTARV 303 D+D L AA APGV P G + + +G L D+ E NPA D+ ++TA + Sbjct: 227 DVDFLDAALAPGVGTAVPGGPTYREAQLCMEMIADTGALASLDVMELNPACDVRNQTAEL 286 Query: 304 AARLAWRLLG 313 L L G Sbjct: 287 VVDLVESLFG 296 Lambda K H 0.321 0.135 0.412 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: 251 Number of extensions: 18 Number of successful extensions: 2 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: 317 Length of database: 302 Length adjustment: 27 Effective length of query: 290 Effective length of database: 275 Effective search space: 79750 Effective search space used: 79750 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