Align Formiminoglutamase (EC 3.5.3.8) (characterized)
to candidate Dsui_0671 Dsui_0671 arginase family hydrolase, arginase/agmainase/formiminoglutamate hydrolase
Query= reanno::Koxy:BWI76_RS08725 (318 letters) >FitnessBrowser__PS:Dsui_0671 Length = 292 Score = 76.6 bits (187), Expect = 7e-19 Identities = 71/220 (32%), Positives = 96/220 (43%), Gaps = 22/220 (10%) Query: 107 QALREAVTACQRAGKRTLVLGGGHETAFGHGAGVLDAFPGEEVGIINLDAHLDLRIADRA 166 Q L EAV + G+ +VLGG H A G +GV A P VG++ LDAHLD + Sbjct: 67 QRLAEAVRQARERGETPVVLGGDHSCAIGTWSGVRAASPAP-VGLLWLDAHLDSHTPEST 125 Query: 167 SSGTPFRQLALAC---EAQRRAF------------HYACIGV-SRAANTQALLDEAARRG 210 SG + LAC + RR H A IGV S + LD R Sbjct: 126 HSGA-LHGMPLACLLGQGDRRLVTVGGPGPKLLPGHVALIGVRSYEPEEREFLDRLGVRV 184 Query: 211 VTIIEDLDV-LNAFEARAIPELARNIARYDRLYLTIDLDVLPAREMPAVSAPAALGIPLA 269 TI E L A A+ + + Y +++DLDV RE P V +P G+ Sbjct: 185 FTIDEVRQRGLPAVFGEALARVRQAPGGYG---VSLDLDVFDPREAPGVGSPEPAGLSQT 241 Query: 270 TLLRIVEPLCRSGKLQAVDLVEFNPQYDIDSQGARAAARL 309 L+ + L L A++++EFNP D + A ARL Sbjct: 242 ELMPALAGLAGDPALLALEVMEFNPDRDAGGRTAALLARL 281 Lambda K H 0.322 0.135 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: 267 Number of extensions: 20 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: 318 Length of database: 292 Length adjustment: 27 Effective length of query: 291 Effective length of database: 265 Effective search space: 77115 Effective search space used: 77115 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