Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate Synpcc7942_2145 Synpcc7942_2145 hypothetical protein
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__SynE:Synpcc7942_2145 Length = 295 Score = 97.8 bits (242), Expect = 2e-25 Identities = 82/253 (32%), Positives = 121/253 (47%), Gaps = 27/253 (10%) Query: 29 AAERGAQLLVCPEMFLTGYNI----GLAQVERLAEAADGPAAMTVVEIAQAHRIAIVYGY 84 AA GA+L+V PE+ GY AQ +R AE+ GP+ IA+ + ++ Sbjct: 32 AAAAGAELIVLPEIH-GGYYFCQTEDPAQFDR-AESIPGPSTDYYSAIARELSVVLILSL 89 Query: 85 PERGDDGAIYNSVQLIDAHGRSLSNYRKTHLFGE---LDRSMFSPGADHFPVVELEGWKV 141 ER G +N+ +I+ G YRK H+ + ++ F+PG F ++ K+ Sbjct: 90 FERRAAGLYHNTAVVIERDGTIAGRYRKMHIPDDPAYYEKFYFTPGDLGFEPIQTSVGKL 149 Query: 142 GLLICYDIEFPENARRLALDGAELILVPTA-NMTPYDF---------TCQVTVRARAQEN 191 G+L+C+D +PE AR +AL GAEL++ PTA P D Q R A N Sbjct: 150 GVLVCWDQWYPEAARLMALAGAELLIYPTAIGWDPQDVPEEQQRQLEAWQTVQRGHAIAN 209 Query: 192 QCYLVYANYCGAEDE-------IEYCGQSSIIGPDGSLLAMAGRDECQLL-AELEHERVV 243 ++ N G E ++ G S I GP G LA AG E +LL A+L+ +R Sbjct: 210 GIPVLSVNRVGFEPSPDPAAAGSQFWGSSFIAGPQGEWLAKAGDREPELLIADLDRDRSE 269 Query: 244 QGRTAFPYLTDLR 256 Q R +P+L D R Sbjct: 270 QVRRIWPFLRDRR 282 Lambda K H 0.322 0.139 0.416 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: 190 Number of extensions: 16 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: 264 Length of database: 295 Length adjustment: 26 Effective length of query: 238 Effective length of database: 269 Effective search space: 64022 Effective search space used: 64022 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: 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