Align 4-guanidinobutyramide hydrolase; SubName: Full=Carbon-nitrogen hydrolase (characterized, see rationale)
to candidate AZOBR_RS30770 AZOBR_RS30770 carbon-nitrogen hydrolase
Query= uniprot:A0A291T0X0 (265 letters) >FitnessBrowser__azobra:AZOBR_RS30770 Length = 268 Score = 261 bits (668), Expect = 8e-75 Identities = 143/260 (55%), Positives = 170/260 (65%), Gaps = 6/260 (2%) Query: 4 LRTALLQNSGHPGDPAGNLKVLDEAAARAAADGAGLLVTAEMFLTGYAIGGG-VRDLAEP 62 +R L Q PG P NL L+ AAA AA G LLV EM LT Y IG VR LAEP Sbjct: 1 MRLTLFQTDAEPGAPHRNLDRLERAAAEAAERGPALLVGPEMGLTSYDIGAETVRALAEP 60 Query: 63 ADGPSGRAVADIAAAHGLAILYGYPERHA-GAVHNSARLVGADGTELANYRKTHLYGCFE 121 DGP VA+IA HG+AILYGYPER A GAV+N+A+L+G+DG L N RKTHLYG + Sbjct: 61 VDGPMAARVAEIARRHGIAILYGYPERGADGAVYNAAQLIGSDGQSLLNQRKTHLYGDLD 120 Query: 122 RASFTPGETPVVQATVGELTVGILVCYDVEFPENVRAHALAGTDLLLVPTAQMHPFEFVA 181 R SF PG A V + VG+ +CYDVEFPE VR HALAG D+LLVPTA M P+E VA Sbjct: 121 RGSFAPGGDAFPTAEVDGMRVGVAICYDVEFPELVRRHALAGVDVLLVPTALMTPYEIVA 180 Query: 182 ESLIPVRAFESQMYIAYVNRSGPEGEFDFVGLSCLAGPDGATCLRAGRGEELLLGDVDPK 241 ++IP RAFE+ +++AY NR G EG + GLS +A PDG+ RAG GE LL D+D Sbjct: 181 TTVIPARAFENGIFVAYANRCGREGTLRYCGLSSVAAPDGSVLARAGDGEALLTVDLDAA 240 Query: 242 LLTTSRRINPYLRDRRPGLY 261 L RR+ +L DRRP LY Sbjct: 241 L----RRVGTHLADRRPDLY 256 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: 258 Number of extensions: 14 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: 268 Length adjustment: 25 Effective length of query: 240 Effective length of database: 243 Effective search space: 58320 Effective search space used: 58320 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