Align 4-guanidinobutyramide hydrolase; SubName: Full=Carbon-nitrogen hydrolase (characterized, see rationale)
to candidate WP_109969118.1 DK846_RS11600 carbon-nitrogen hydrolase family protein
Query= uniprot:A0A291T0X0 (265 letters) >NCBI__GCF_003173355.1:WP_109969118.1 Length = 261 Score = 97.8 bits (242), Expect = 2e-25 Identities = 77/253 (30%), Positives = 114/253 (45%), Gaps = 11/253 (4%) Query: 17 DPAGNLKVLDEAAARAAADGAGLLVTAEMFLTGYAIGGGVRDLAEPADGPSGRAVADIAA 76 +P L + A A A + E +TG+ G ++ + + + A Sbjct: 14 NPECTLTSIKTRIAEAVEYDASFISFPEQVITGWDPLDG-KNFVQTESDEIVSVLCEYAC 72 Query: 77 AHGLAILYGYPERHAGAVHNSARLVGADGTELANYRKTHLYGC-FERASFTPGETPVVQA 135 + IL Y E++ N+A + DG L Y K HL+ E ++ PGE + + Sbjct: 73 DFSIGILGSYREKYQPHPRNTAIAIAPDGRILGRYSKMHLFSPGHEDQAYCPGEEIALFS 132 Query: 136 TVGELTVGILVCYDVEFPENVRAHALAGTDLLLVPTA----QMHPFEFVAESLIPVRAFE 191 G GI +CYD+ F + R + A DL++VP+A +M FE A + RA E Sbjct: 133 YDG-CRCGIAICYDLRFADLFRLYRDADVDLVMVPSAWPASRMRYFELFATA----RAAE 187 Query: 192 SQMYIAYVNRSGPEGEFDFVGLSCLAGPDGATCLRAGRGEELLLGDVDPKLLTTSRRINP 251 QMY+A +N G + G S +AGPDGA R EELL D+ P L+ R P Sbjct: 188 FQMYVAGINTVGRTPVDLYSGGSLIAGPDGAVICRGSEVEELLFSDICPDLVAGIRESFP 247 Query: 252 YLRDRRPGLYTSL 264 DRR +Y +L Sbjct: 248 VHSDRRSEVYQNL 260 Lambda K H 0.319 0.138 0.414 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: 177 Number of extensions: 6 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: 265 Length of database: 261 Length adjustment: 25 Effective length of query: 240 Effective length of database: 236 Effective search space: 56640 Effective search space used: 56640 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: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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