Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_110207698.1 DNK54_RS14440 carbon-nitrogen hydrolase family protein
Query= reanno::pseudo3_N2E3:AO353_07425 (264 letters) >NCBI__GCF_003194585.1:WP_110207698.1 Length = 272 Score = 107 bits (266), Expect = 3e-28 Identities = 90/267 (33%), Positives = 126/267 (47%), Gaps = 22/267 (8%) Query: 1 MRVALYQCPPLPLDVAGNLQRLQKLATE--AKGADLLVFPEMFLTGYNIGAEAVGALAEA 58 +RVAL Q LD A N + LA E A ADL+V PE + + + AE+ Sbjct: 11 LRVALAQLAS-GLDPAENRAAIAGLAEEPSAMTADLVVLPEAIARDFGSPRDDLAPYAES 69 Query: 59 QDGTCAQYIASIAKASGIAIVYGYPERAEDGQIYNAVQLIDSRGQRLANYRKTHL---FG 115 G AQ I ++A S +V G E G +N + + RG R A+YRK HL FG Sbjct: 70 TSGPFAQAITALA-GSDRTVVAGMFEAYPGGHPFNTLVM---RGARSADYRKIHLYDSFG 125 Query: 116 ELDHSMFSVGPDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVP---TANMI 172 + + GP E V+L G++LG + CYDL FPE AR L GA++++VP A Sbjct: 126 YRESERLTAGPWEPVTVDLAGFRLGLMTCYDLRFPELARDLVDRGADVLVVPAAWVAGRT 185 Query: 173 PYDFIADV-----TVRSRAFENQCYVAYANYCGHEGEIHYCGQSSIAAPDGSRIAQAGLD 227 P + V VR+RA EN YV + Y G S + P G + +AG Sbjct: 186 PEEHALKVEHWRTLVRARAIENVAYVVAVG----QPSPRYTGHSMVVDPTGRVLVEAGDA 241 Query: 228 EALIVGTLDRQLMVDSRAANRYFLDRR 254 ++ TL+ + +R AN +RR Sbjct: 242 TEVLCATLEASTLRAAREANPSLDNRR 268 Lambda K H 0.322 0.139 0.414 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: 198 Number of extensions: 12 Number of successful extensions: 4 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: 272 Length adjustment: 25 Effective length of query: 239 Effective length of database: 247 Effective search space: 59033 Effective search space used: 59033 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