Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_092482045.1 BM299_RS03315 carbon-nitrogen hydrolase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1170 (264 letters) >NCBI__GCF_900115975.1:WP_092482045.1 Length = 277 Score = 122 bits (307), Expect = 6e-33 Identities = 95/262 (36%), Positives = 141/262 (53%), Gaps = 18/262 (6%) Query: 16 AGNLQRLQQLALEAKG--ADLLVLPEMFLTGYNIGVDAVSVLAEVY-NGESAQQVARIAK 72 A N++R + + EA G A ++VLPEMF Y + AE Y +GE+ + ++R+A Sbjct: 19 AENIRRAEDMIREAAGMGARVVVLPEMFNCPYETRL--FPDYAEPYPDGETVRMLSRVAA 76 Query: 73 AAGIAILYGYPERTEDGQIYNAVQLIDSDGERVCNYRKTHLFG-DL------DHSMFSAG 125 AGI ++ G + +YN GE + +RK HLF DL + S G Sbjct: 77 DAGIVLVGGSIPEKDGDIVYNTCFTFGPRGELLGRHRKVHLFDVDLPNLRVRESSTLGPG 136 Query: 126 SDEFPIVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTA-NMIPFDFVADVTVRA 184 +D +++ KLG +IC+D+ FPE AR LAL G ++++VP A N I D+ +RA Sbjct: 137 ND-VAVMDAGFVKLGVMICFDVRFPELARLLALGGIDVLVVPAAFNTITGPAHWDLNMRA 195 Query: 185 RAFENQCYVAYANYCGHE--GDIHYCGQSSIAAPDGSRIAQAGLDESLIVGELDRQLMVD 242 RA +NQ YVA A+ E G + Y G S + P G +A+AG E +I+GE+D + + + Sbjct: 196 RAVDNQVYVAAASPARDENAGYVVY-GHSMVVDPWGDTVARAGTGEEIIIGEIDPERIKE 254 Query: 243 SRAANRYLLDRRPELYGELNKS 264 RA L R +LY EL KS Sbjct: 255 VRARLPLLAQMRTDLY-ELRKS 275 Lambda K H 0.321 0.139 0.411 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: 215 Number of extensions: 15 Number of successful extensions: 5 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: 277 Length adjustment: 25 Effective length of query: 239 Effective length of database: 252 Effective search space: 60228 Effective search space used: 60228 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 Apr 09 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