Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_109969118.1 DK846_RS11600 carbon-nitrogen hydrolase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_2504 (264 letters) >NCBI__GCF_003173355.1:WP_109969118.1 Length = 261 Score = 81.3 bits (199), Expect = 2e-20 Identities = 69/232 (29%), Positives = 104/232 (44%), Gaps = 5/232 (2%) Query: 32 ADLLVLPEMFLTGYNIGIDAVSVLAEVHNGESAQQIARIAKTTGIAILYGYPERTEDGQI 91 A + PE +TG++ +D + + + + E + A I IL Y E+ + Sbjct: 34 ASFISFPEQVITGWD-PLDGKNFV-QTESDEIVSVLCEYACDFSIGILGSYREKYQPHPR 91 Query: 92 YNAVQLIDANGERLCNYRKTHLFGD-LDHSMFSPGPDEFPLVELNGWKLGFLICYDLEFP 150 A+ I +G L Y K HLF + + PG +E L +G + G ICYDL F Sbjct: 92 NTAIA-IAPDGRILGRYSKMHLFSPGHEDQAYCPG-EEIALFSYDGCRCGIAICYDLRFA 149 Query: 151 ENARRLALAGAELILVPTANMIPYDFIADVTVRARAFENQCYVAYANYCGHEGEIQYCGQ 210 + R A +L++VP+A ++ ARA E Q YVA N G Y G Sbjct: 150 DLFRLYRDADVDLVMVPSAWPASRMRYFELFATARAAEFQMYVAGINTVGRTPVDLYSGG 209 Query: 211 SSIAAPDGSRIAQAGLDEALIVGELDRQLMIDSRAANRYFLDRRPELYGELN 262 S IA PDG+ I + E L+ ++ L+ R + DRR E+Y L+ Sbjct: 210 SLIAGPDGAVICRGSEVEELLFSDICPDLVAGIRESFPVHSDRRSEVYQNLS 261 Lambda K H 0.322 0.140 0.420 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: 203 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: 264 Length of database: 261 Length adjustment: 25 Effective length of query: 239 Effective length of database: 236 Effective search space: 56404 Effective search space used: 56404 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 24 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