Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate Ga0059261_3603 Ga0059261_3603 Predicted amidohydrolase
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__Korea:Ga0059261_3603 Length = 275 Score = 71.6 bits (174), Expect = 2e-17 Identities = 86/274 (31%), Positives = 113/274 (41%), Gaps = 26/274 (9%) Query: 1 MRIALYQGAPKPLDVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQVERLAEA 60 MR A+ Q +D N L A+ GA +L PEM GL +R A Sbjct: 1 MRAAILQ-MTSGIDALANAATLADGVAKASAGGAAMLFTPEMS------GLLDRQRERAA 53 Query: 61 A------DGPAAMTVVEIAQAHRIAIVYG-YPERGD-DGAIYNSVQLIDAHGRSLSNYRK 112 A + V E A H + + G +G+ DG N +ID G + Y K Sbjct: 54 ANIVLESEDRVLAAVREAAAKHGVWVHLGSLALKGEADGRFVNRGFVIDGSGEIRARYDK 113 Query: 113 THLF------GELDRSM--FSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAE 164 HLF GE R ++PGA VV K+GL ICYD+ FP+ R L GA Sbjct: 114 LHLFDVDLPTGERWRESDAYAPGASA-AVVGTPLGKLGLAICYDLRFPDLFRALTDAGAT 172 Query: 165 LILVPTANMTPY-DFTCQVTVRARAQENQCYLVYANYCGA-EDEIEYCGQSSIIGPDGSL 222 L+ VP A P V +RARA E +++ A G ED G S I P G + Sbjct: 173 LLAVPAAFTRPTGQAHWHVLLRARAIEAGVHVIAAAQTGEHEDGRATYGHSVAIDPWGEV 232 Query: 223 LAMAGRDECQLLAELEHERVVQGRTAFPYLTDLR 256 L G AE++ RV R+ P + R Sbjct: 233 LLDMGEGAGLGFAEIDPARVADVRSRVPAIAHRR 266 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: 166 Number of extensions: 10 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: 275 Length adjustment: 25 Effective length of query: 239 Effective length of database: 250 Effective search space: 59750 Effective search space used: 59750 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