Align guanidinobutyrase subunit (EC 3.5.3.7) (characterized)
to candidate RR42_RS02455 RR42_RS02455 agmatinase
Query= metacyc::MONOMER-11557 (320 letters) >FitnessBrowser__Cup4G11:RR42_RS02455 Length = 328 Score = 470 bits (1210), Expect = e-137 Identities = 225/318 (70%), Positives = 261/318 (82%) Query: 3 PTVDKTLHQPLGGNEMPRFGGIATMLRLPHLQSAKGLDAAFIGVPLDIGTSLRSGTRFGP 62 P + L QP+ GN MPRFGGIATM+RLP S GLDA F+GVP D+GTS R+G R GP Sbjct: 9 PADEAGLFQPMSGNAMPRFGGIATMMRLPAAASTAGLDACFVGVPFDLGTSNRNGARLGP 68 Query: 63 RQIRAESVMIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHNVI 122 RQIRAESV++RPYNMAT AAPFDSL VADIGDVA N +NL DA+ IE AY +I+ Sbjct: 69 RQIRAESVLLRPYNMATRAAPFDSLRVADIGDVATNPYNLHDAIARIEAAYRDIIATGCR 128 Query: 123 PMTLGGDHTITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLL 182 P+ LGGDHT+TLPILRA+H +HG++GL+H+DAHADVND MFGEKIAHGT FRRAVEEGLL Sbjct: 129 PIGLGGDHTVTLPILRAMHARHGRLGLIHVDAHADVNDTMFGEKIAHGTPFRRAVEEGLL 188 Query: 183 DCDRVVQIGLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLS 242 DC RVVQIGLR GY A+DF+W R+QGFRV+ AE CW++SL PLM E+ ++ GGPVY+S Sbjct: 189 DCGRVVQIGLRGTGYAAEDFDWCRQQGFRVITAEACWYRSLAPLMEEIGMRLQGGPVYIS 248 Query: 243 FDIDGIDPAWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTSLL 302 FDIDGIDPA+APGTGTPEIGGLT QA+EIIRG GLD++G DLVEVSPPYD G T+LL Sbjct: 249 FDIDGIDPAYAPGTGTPEIGGLTVPQALEIIRGARGLDIVGADLVEVSPPYDPFGTTALL 308 Query: 303 GANLLFEMLCVLPGVVRR 320 GANL FE+LCVLPGVV R Sbjct: 309 GANLAFELLCVLPGVVYR 326 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: 467 Number of extensions: 26 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: 320 Length of database: 328 Length adjustment: 28 Effective length of query: 292 Effective length of database: 300 Effective search space: 87600 Effective search space used: 87600 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