Align 4-guanidinobutyramide hydrolase; SubName: Full=Carbon-nitrogen hydrolase (characterized, see rationale)
to candidate AO353_28330 AO353_28330 carbon-nitrogen hydrolase
Query= uniprot:A0A291T0X0 (265 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28330 Length = 287 Score = 142 bits (359), Expect = 6e-39 Identities = 97/255 (38%), Positives = 136/255 (53%), Gaps = 5/255 (1%) Query: 4 LRTALLQNSGHPGDPAGNLKVLDEAAARAAADGAGLLVTAEMFLTGYAIGGGVRDLAEPA 63 ++ L+Q +G GD A NL+ +A A AAD LL+ E L G+A + ++AEP Sbjct: 1 MKIELVQLTGRDGDTAYNLERTLQAIATCAAD-TDLLIFPETQLMGFASAQQLAEVAEPL 59 Query: 64 DGPSGRAVADIAAAHGLAILYGYPERHAGAVHNSARLVGADGTELANYRKTHLYGCFERA 123 +GPS +AV A ++++ G E +G +N++ LV G L+ YRKTHL+ ER Sbjct: 60 NGPSVQAVQRAARERNVSVVVGMAENDSGTFYNTSLLVTPQGIALS-YRKTHLWPS-ERG 117 Query: 124 SFTPGETPVVQATVGELTVGILVCYDVEFPENVRAHALAGTDLLLVPTAQMHPFEFVAES 183 F PG+ G + VGIL+CYD+E PE+ RA G +L+LV M P+ V + Sbjct: 118 LFQPGDRYATAIWKG-VRVGILICYDIELPESARALGQLGAELILVTNGNMDPYGPVHRT 176 Query: 184 LIPVRAFESQMYIAYVNRSGPEGE-FDFVGLSCLAGPDGATCLRAGRGEELLLGDVDPKL 242 I RA E+Q + VNR G E F G S P G T AGR E + ++D L Sbjct: 177 AIMARAQENQAFTVMVNRVGDGDEGLVFAGGSAAIDPFGRTLFEAGRAECRQVVELDLDL 236 Query: 243 LTTSRRINPYLRDRR 257 L ++RR YL DRR Sbjct: 237 LRSARRDYDYLNDRR 251 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: 202 Number of extensions: 10 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: 265 Length of database: 287 Length adjustment: 25 Effective length of query: 240 Effective length of database: 262 Effective search space: 62880 Effective search space used: 62880 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 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