Align guanidinobutyrase subunit (EC 3.5.3.7) (characterized)
to candidate AZOBR_RS30775 AZOBR_RS30775 agmatinase
Query= metacyc::MONOMER-11557 (320 letters) >FitnessBrowser__azobra:AZOBR_RS30775 Length = 351 Score = 249 bits (635), Expect = 9e-71 Identities = 134/307 (43%), Positives = 194/307 (63%), Gaps = 11/307 (3%) Query: 14 GGNEMPRFGGIATMLRLPHLQSAK------GLDAAFIGVPLDIGTSLRSGTRFGPRQIRA 67 GG + F G++T+L P+ A GLD A IGVP+D+G + R+G R GPR +R Sbjct: 37 GGKRVQPFAGVSTLLDAPYRPDAADAADFGGLDIALIGVPMDLGVTNRAGARLGPRAVRG 96 Query: 68 ESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVR-IIEEAYDEIVEHNVIPMTL 126 I PY A P S +AD+GDV +++ L+A I Y+ +++ V+P+++ Sbjct: 97 ME-RIGPYEHALRMVPAASCKLADVGDVPLSSRFSLEACHGDILAFYNRVMDAGVVPLSV 155 Query: 127 GGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLLDCDR 186 GGDH+IT IL+AL ++ +G++H DAH D G K HG FR+AV +G+LD +R Sbjct: 156 GGDHSITYSILKALGRER-PVGMIHFDAHCDTGGPYEGAKFHHGGPFRQAVLDGVLDPER 214 Query: 187 VVQIGLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDID 246 VQIG+R G T + +S G V+ AE+ + + ++ R+ VG GPVY+SFD+D Sbjct: 215 TVQIGIR--GSTEYLWEFSYDSGMTVIHAEDIPERGIASVIETARKVVGDGPVYVSFDVD 272 Query: 247 GIDPAWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTSLLGANL 306 +DP +APGTGTPE+GGLTT +A+ I+RG GLD+IG D+VEV+P YD T NT+ GA + Sbjct: 273 CLDPVFAPGTGTPEVGGLTTREALAILRGLDGLDIIGGDVVEVAPQYDATTNTAHAGAQM 332 Query: 307 LFEMLCV 313 LFE+LC+ Sbjct: 333 LFEILCL 339 Lambda K H 0.322 0.141 0.431 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: 401 Number of extensions: 28 Number of successful extensions: 7 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: 320 Length of database: 351 Length adjustment: 28 Effective length of query: 292 Effective length of database: 323 Effective search space: 94316 Effective search space used: 94316 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: 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