Align Putative 4-guanidinobutyryl amide hydrolase (characterized, see rationale)
to candidate Synpcc7942_2145 Synpcc7942_2145 hypothetical protein
Query= uniprot:A0A291T3M3 (267 letters) >FitnessBrowser__SynE:Synpcc7942_2145 Length = 295 Score = 88.2 bits (217), Expect = 2e-22 Identities = 84/271 (30%), Positives = 124/271 (45%), Gaps = 32/271 (11%) Query: 24 AACRRARAEGAELLVTTELFITGYDIGDTVRDLARTD----LLTPARQ----MAASHGIA 75 AA R A A GAEL+V E+ GY T D A+ D + P+ +A + Sbjct: 27 AAIREAAAAGAELIVLPEIH-GGYYFCQT-EDPAQFDRAESIPGPSTDYYSAIARELSVV 84 Query: 76 LVLGAPEYDS-GAYYNSAFFIDPAGTVLGRHRKNHLFGE---LDRRYFTPGDRTAPVIDY 131 L+L E + G Y+N+A I+ GT+ GR+RK H+ + ++ YFTPGD I Sbjct: 85 LILSLFERRAAGLYHNTAVVIERDGTIAGRYRKMHIPDDPAYYEKFYFTPGDLGFEPIQT 144 Query: 132 GGVRIAMLICYDVEFPENVRAAALAGADLVAVPTA-QMRPYEFIAEHLLRVRAWE----- 185 ++ +L+C+D +PE R ALAGA+L+ PTA P + E ++ AW+ Sbjct: 145 SVGKLGVLVCWDQWYPEAARLMALAGAELLIYPTAIGWDPQDVPEEQQRQLEAWQTVQRG 204 Query: 186 ----NQIYIAYVNHDGDEGS-------QRYVGRSSIVSPSATVLDSV-EHGNRLLFATVD 233 N I + VN G E S ++ G S I P L + LL A +D Sbjct: 205 HAIANGIPVLSVNRVGFEPSPDPAAAGSQFWGSSFIAGPQGEWLAKAGDREPELLIADLD 264 Query: 234 PYTVREARKANPYLADLRPDLFTPSARATKD 264 + R+ P+L D R D + R +D Sbjct: 265 RDRSEQVRRIWPFLRDRRIDAYGDLVRRYRD 295 Lambda K H 0.320 0.137 0.407 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: 214 Number of extensions: 14 Number of successful extensions: 2 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: 267 Length of database: 295 Length adjustment: 26 Effective length of query: 241 Effective length of database: 269 Effective search space: 64829 Effective search space used: 64829 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 (21.8 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