Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate H281DRAFT_03146 H281DRAFT_03146 Predicted amidohydrolase
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__Burk376:H281DRAFT_03146 Length = 295 Score = 108 bits (271), Expect = 1e-28 Identities = 77/241 (31%), Positives = 127/241 (52%), Gaps = 8/241 (3%) Query: 1 MRIALYQGAPKPLDVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQVERLAEA 60 ++IA Q P DV N+ + AA+RGA+L+V PE FL+GY GL + +E Sbjct: 13 LQIAAAQAQPVCGDVTANIAKTVELTGRAADRGARLVVFPEKFLSGYEPGLIAGDP-SEY 71 Query: 61 ADGPAAMTVVEIAQA---HRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHLFG 117 A G + + I +A H IA + G R D G ++ S + D G + Y K +L+ Sbjct: 72 AFGQSDSRLDPIREACRRHAIAAIVGAATR-DAGELHISSLVFDRRGEDVEPYHKQYLY- 129 Query: 118 ELDRSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTANMTPYD 177 + + ++ G ++EL+GW++ L +CYD FPE+AR A++GA LV Sbjct: 130 KSEAEIYRAGMRGC-MLELDGWRLALGVCYDSGFPEHARHAAVNGAHAYLVSGLFSVKSG 188 Query: 178 F-TCQVTVRARAQENQCYLVYANYCGAEDEIEYCGQSSIIGPDGSLLAMAGRDECQLLAE 236 + ++ ARA +N Y++ +N+ G + CG S+I P G ++A AGR+ ++++ Sbjct: 189 YHQSRIWFPARAFDNTMYVLLSNHIGTTGGWDTCGASAIWSPYGDVIAEAGREREEVISA 248 Query: 237 L 237 L Sbjct: 249 L 249 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: 208 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: 295 Length adjustment: 26 Effective length of query: 238 Effective length of database: 269 Effective search space: 64022 Effective search space used: 64022 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