Align Guanidinobutyrase; EC 3.5.3.7 (characterized)
to candidate AZOBR_RS30430 AZOBR_RS30430 arginase
Query= SwissProt::Q9I3S3 (319 letters) >FitnessBrowser__azobra:AZOBR_RS30430 Length = 319 Score = 114 bits (284), Expect = 4e-30 Identities = 72/227 (31%), Positives = 117/227 (51%), Gaps = 8/227 (3%) Query: 86 LNVADIGDVAINTFNLLEAVRIIEQEYDRILGHGILPLTLGGDHTITLPILRAIKKKHGK 145 + V D GDV N +L R E +L G+LP+ +GGDH I +P+LRA + G Sbjct: 87 IKVVDCGDVKANPRDLDLHYRNAEAVVRAMLAKGMLPIIIGGDHGIPIPVLRAYDDQ-GP 145 Query: 146 VGLVHVDAHADVNDHMFGEKIAHGTTFRRAVEEDLLDCDRVVQIGLRAQGYT-AEDFNWS 204 + LVH+DAH D DH+ G + + + RRA E D ++ QIGLR+ G E+ + Sbjct: 146 ITLVHIDAHLDWRDHVNGARGGYSSPIRRAAEMD--HVGQIFQIGLRSAGSARPEEVEAA 203 Query: 205 RKQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDIDGIDPAWAPGTGTPEIGGLT 264 + G ++ E ++ ++ + + GG YL+ D DG+DP P P GG+T Sbjct: 204 QAYGAVLIPDVELQDVGMKAVLDRIPD---GGRYYLTIDADGMDPTIMPAVNGPAPGGVT 260 Query: 265 TIQAMEIIRG-CQGLDLIGCDLVEVSPPYDTTGNTSLLGANLLYEML 310 Q +I G + ++G D+VE++P D G T++ ++ ++ Sbjct: 261 YPQIRTLIHGLVKKGRVVGMDIVEITPKKDVNGITAITAGRIICNLI 307 Lambda K H 0.321 0.141 0.428 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: 291 Number of extensions: 19 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: 319 Length of database: 319 Length adjustment: 28 Effective length of query: 291 Effective length of database: 291 Effective search space: 84681 Effective search space used: 84681 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