Align Arginase; EC 3.5.3.1 (uncharacterized)
to candidate RR42_RS14625 RR42_RS14625 formimidoylglutamase
Query= curated2:Q7M0Z3 (298 letters) >FitnessBrowser__Cup4G11:RR42_RS14625 Length = 312 Score = 68.2 bits (165), Expect = 2e-16 Identities = 86/296 (29%), Positives = 113/296 (38%), Gaps = 55/296 (18%) Query: 9 GVPMDLGADRRGVDMGPSAIRYAGVVARLEKMGFN-IEDRGDIFVTLPHHFTETENHKYL 67 GV +LG R G GP IR A +A + G D GD+ H + E Sbjct: 50 GVLRNLG--RPGAAGGPREIRRA--LAGIPAHGLAAFHDAGDVVC----HDGDLET---- 97 Query: 68 DEVVEANEKLANVVSDIMTAGRFPLVLGGDHSIALGTIAGVAKHVKNLG------VICLD 121 A + LA V+ + G FPLVLGG H IA GT G+ H+ G VI LD Sbjct: 98 -----AQQALATAVAAELAQGAFPLVLGGGHEIAWGTWQGLRAHLDARGDHGRVLVINLD 152 Query: 122 AHGDLNTGATSPSGNIHGMPLAASLGYGH---------ERLTNIGGYTPKVKAENVVIIG 172 AH DL TG SG A G RL N +A V + Sbjct: 153 AHFDLRTGRPGSSGTPFDQIAQACHERGQRFEYACLGVSRLGNTAALFAHAQALGVHYV- 211 Query: 173 ARDLDQGERELIKRIGMKVFTMHEIDKLGMARVMDEAIAHVSKNTDGVHLSLDLDGLDPH 232 D+ ER L R+ + +MD D V+L++DLD L Sbjct: 212 -EDVQMQERHLDARLA------------ELQGLMDA--------VDHVYLTIDLDVLPAA 250 Query: 233 DAPGVGTPVIGGISYREGHVSLEMLADADILCSAEFVEVNPILDRENMTARVAVAL 288 P V P G+ + ++ + L A+ E NP+ DR+ AR A L Sbjct: 251 VMPAVSAPAPYGVPLPVVEEVVALVRASGKLRVADLAEFNPLYDRDACGARAAARL 306 Lambda K H 0.319 0.138 0.398 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: 264 Number of extensions: 27 Number of successful extensions: 4 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: 298 Length of database: 312 Length adjustment: 27 Effective length of query: 271 Effective length of database: 285 Effective search space: 77235 Effective search space used: 77235 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 (21.7 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