Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_011842335.1 RSPH17029_RS17110 carbon-nitrogen hydrolase family protein
Query= BRENDA::B3IVI7 (264 letters) >NCBI__GCF_000015985.1:WP_011842335.1 Length = 280 Score = 100 bits (250), Expect = 3e-26 Identities = 78/235 (33%), Positives = 113/235 (48%), Gaps = 10/235 (4%) Query: 1 MRIALYQGAPKPLDVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNI----GLAQVER 56 M+IA Q +P D P + + A+ AA GA+L+V PE FLTG + L Q Sbjct: 1 MKIAFAQLSPVHGDTPATVALVAEAARAAAADGARLIVFPECFLTGGSFDDRAALLQAAV 60 Query: 57 LAEAADGPAAMTVVEIAQAHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHL- 115 E D + A H +V G+ ++ A+ N+ LI G + + K HL Sbjct: 61 DIERGDLEPLLLAAREADIH---VVVGFYQKSGPQAL-NTAALIGPEG-IIGLHHKMHLP 115 Query: 116 FGELDRSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTANMTP 175 F DR P + V + ++GL ICY+I FPE R LAL+GAEL+++P A Sbjct: 116 FMIGDRFADIPQIEGPSVFDTAIGRIGLAICYEIRFPEVIRTLALEGAELVVLPAAWPEA 175 Query: 176 YDFTCQVTVRARAQENQCYLVYANYCGAEDEIEYCGQSSIIGPDGSLLAMAGRDE 230 + R RA EN Y + +N +D + + G S +IGPDG+ + AG E Sbjct: 176 ARILPDLFSRVRAAENFVYFLSSNRIDVDDGMAFMGSSHVIGPDGNEIFNAGMQE 230 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: 197 Number of extensions: 13 Number of successful extensions: 3 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: 280 Length adjustment: 25 Effective length of query: 239 Effective length of database: 255 Effective search space: 60945 Effective search space used: 60945 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 Apr 10 2024. 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