Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate 8499888 DvMF_0653 N-carbamoylputrescine amidase (RefSeq)
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__Miya:8499888 Length = 313 Score = 99.4 bits (246), Expect = 8e-26 Identities = 82/261 (31%), Positives = 123/261 (47%), Gaps = 19/261 (7%) Query: 18 NLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQVERLAEAA---DGPAAMTVVEIAQ 74 N+ R+ + AA GA +++ E+F Y E A A + PA + +A Sbjct: 20 NIDRVCELVREAAAMGAHIVLPQELFSGPYFCKDELPEHFALARPLDESPAVRRMSALAA 79 Query: 75 AHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHLF---GELDRSMFSPGADHF 131 + I + ER + YNS+ +IDA GR + YRK+H+ G ++ FSPG F Sbjct: 80 ELGVVIPVSFFERSNQ-VYYNSLAMIDADGRVMGLYRKSHIPQGPGYEEKFYFSPGDTGF 138 Query: 132 PVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTA-NMTPYDFTCQV------TV 184 V VG+ +C+D FPE AR +AL GA+++L PTA P + C T+ Sbjct: 139 RVWRTRYGTVGVGVCWDQWFPECARSMALLGADVLLYPTAIGSEPAEPACDSSGHWTRTM 198 Query: 185 RARAQENQCYLVYANYCGAE----DEIEYCGQSSIIGPDGSLLAMAGR-DECQLLAELEH 239 + A N LV +N G E + + G S I GP G ++ AGR +EC L A + Sbjct: 199 QGHAAANMMPLVASNRVGEEFGKGFSMTFYGSSFIAGPQGEIVQQAGRSEECVLTAAFDF 258 Query: 240 ERVVQGRTAFPYLTDLRQELH 260 E + R + D R +L+ Sbjct: 259 EAIRAERAGWGLFRDRRPDLY 279 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: 233 Number of extensions: 10 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: 313 Length adjustment: 26 Effective length of query: 238 Effective length of database: 287 Effective search space: 68306 Effective search space used: 68306 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