Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate PfGW456L13_2704 N-carbamoylputrescine amidase (3.5.1.53)
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2704 Length = 302 Score = 100 bits (248), Expect = 5e-26 Identities = 86/272 (31%), Positives = 128/272 (47%), Gaps = 22/272 (8%) Query: 10 PKPLDVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQVERLA---EAADGPAA 66 P D+ NL + + AA +GAQ+++ E+F T Y + LA E + Sbjct: 12 PCTWDLKHNLDQAEQLVREAAAKGAQVILLQELFATPYFCIEQHHKHLALAEEYRESHVL 71 Query: 67 MTVVEIAQAHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHL---FGELDRSM 123 +A+ + + + E+ + A +NS+ + DA GR L YRKTH+ G ++ Sbjct: 72 QRFAALAKELGVVLPLSWYEKAGN-AYFNSLSVADADGRLLGVYRKTHIPNAIGYQEKEY 130 Query: 124 FSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTA-NMTPYDFTC-- 180 FSPG F V + ++GL IC+D FPE AR LAL GAE++L PTA P T Sbjct: 131 FSPGDSGFRVWDTAFGRIGLGICWDQWFPETARCLALMGAEVLLFPTAIGSEPGCATLDS 190 Query: 181 ----QVTVRARAQENQCYLVYANYCGAED-------EIEYCGQSSIIGPDGSLLAMAGRD 229 Q+T+R A N +V AN G E ++ + G S I G LLA A RD Sbjct: 191 RDHWQMTMRGHAAANLLPVVAANRVGREAATTDPTLQMSFYGSSFICNHKGKLLAEADRD 250 Query: 230 ECQLLA-ELEHERVVQGRTAFPYLTDLRQELH 260 +L L+ + + R + D R E++ Sbjct: 251 STGVLVHSLDLAAMREDRLTWGIYRDRRPEMY 282 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: 181 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: 302 Length adjustment: 26 Effective length of query: 238 Effective length of database: 276 Effective search space: 65688 Effective search space used: 65688 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