Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate 6936284 Sama_0473 carbon-nitrogen family hydrolase (RefSeq)
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__SB2B:6936284 Length = 280 Score = 95.1 bits (235), Expect = 1e-24 Identities = 85/272 (31%), Positives = 129/272 (47%), Gaps = 21/272 (7%) Query: 1 MRIALYQGAPKPLDVPGNLQRLRHQAQ-LAAERGA-QLLVCPEMFLTGYNIGLAQVERLA 58 M+++L Q DV NL + Q + L G QL+V PE L G + E+LA Sbjct: 1 MQVSLLQ-CQSSRDVEANLAFIESQLERLPRVPGEPQLVVLPECCLL---FGGHESEQLA 56 Query: 59 -EAADGPAAMTVVEIAQAHRIAIVYG-YPERGDDGAIYNSVQLIDAHGRSLSNYRKTHLF 116 D P + +A + +V G P R DG +Y+ + D G L +Y K HLF Sbjct: 57 WSGEDEPLKHALAALAARFGVFLVAGTIPARSGDGRVYSRCYVFDDAGNVLGHYEKIHLF 116 Query: 117 GE---------LDRSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELIL 167 + F PG ++ VV+ K+GL ICYD+ FP+ R L L GAE+I Sbjct: 117 DVDVADGTKTYRESDTFCPG-ENLVVVDTPFGKLGLAICYDVRFPDMFRALRLAGAEIIA 175 Query: 168 VPTA-NMTPYDFTCQVTVRARAQENQCYLVYANYCGAED--EIEYCGQSSIIGPDGSLLA 224 +P A + ++ ++ARA E+QC+++ A GA + E GQS +I P G LA Sbjct: 176 LPAAFTRVTGEAHWEILLKARAIESQCFVLGAAQWGAHNTGSRETWGQSMLIDPWGRTLA 235 Query: 225 MAGRDECQLLAELEHERVVQGRTAFPYLTDLR 256 + + A L+ + + + R A P ++ R Sbjct: 236 ELVQGTGWVQARLDRDELTRVRAAMPVVSHNR 267 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: 218 Number of extensions: 13 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: 280 Length adjustment: 25 Effective length of query: 239 Effective length of database: 255 Effective search space: 60945 Effective search space used: 60945 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