Align guanidinobutyrase subunit (EC 3.5.3.7) (characterized)
to candidate H281DRAFT_00178 H281DRAFT_00178 agmatinase
Query= metacyc::MONOMER-11557 (320 letters) >FitnessBrowser__Burk376:H281DRAFT_00178 Length = 329 Score = 478 bits (1230), Expect = e-140 Identities = 226/310 (72%), Positives = 266/310 (85%) Query: 11 QPLGGNEMPRFGGIATMLRLPHLQSAKGLDAAFIGVPLDIGTSLRSGTRFGPRQIRAESV 70 QPL GN MPR GGIATM+RLP++ SA+G DA F+GVP D+GTS R+G RFGPRQIR+ESV Sbjct: 16 QPLSGNAMPRSGGIATMMRLPNVGSAEGFDACFVGVPFDLGTSNRTGARFGPRQIRSESV 75 Query: 71 MIRPYNMATGAAPFDSLSVADIGDVAINTFNLLDAVRIIEEAYDEIVEHNVIPMTLGGDH 130 ++RPYNMAT AAPFDSL VAD+GDVAIN +NL D++ IE AYDEI++H+ P+TLGGDH Sbjct: 76 LLRPYNMATRAAPFDSLRVADLGDVAINPYNLHDSIARIETAYDEILQHDCKPVTLGGDH 135 Query: 131 TITLPILRALHKKHGKIGLVHIDAHADVNDHMFGEKIAHGTTFRRAVEEGLLDCDRVVQI 190 TI LPILRA+H+KHGK+GL+H+DAHADVND M GEKIAHGT FRRAVEEGLLDC+RVVQI Sbjct: 136 TIALPILRAIHRKHGKVGLIHVDAHADVNDTMMGEKIAHGTPFRRAVEEGLLDCERVVQI 195 Query: 191 GLRAQGYTADDFNWSRRQGFRVVQAEECWHKSLEPLMAEVREKVGGGPVYLSFDIDGIDP 250 GLR GY A+DF+W R QGF VVQAE CW++SL PLMA VRE++G GPVY++FDIDGIDP Sbjct: 196 GLRGTGYAAEDFDWCRDQGFDVVQAEACWNQSLAPLMARVRERMGDGPVYITFDIDGIDP 255 Query: 251 AWAPGTGTPEIGGLTTIQAMEIIRGCHGLDLIGCDLVEVSPPYDTTGNTSLLGANLLFEM 310 A+APGTGTPEI GLT QA+EIIRG GL+++GCDLVEV+PPYD G T+LL ANL FE+ Sbjct: 256 AFAPGTGTPEIAGLTVPQALEIIRGARGLNIVGCDLVEVAPPYDPFGTTALLAANLAFEL 315 Query: 311 LCVLPGVVRR 320 LCVLPGV R Sbjct: 316 LCVLPGVEYR 325 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: 437 Number of extensions: 16 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 320 Length of database: 329 Length adjustment: 28 Effective length of query: 292 Effective length of database: 301 Effective search space: 87892 Effective search space used: 87892 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