Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate RR42_RS26020 RR42_RS26020 hydrolase
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__Cup4G11:RR42_RS26020 Length = 282 Score = 75.5 bits (184), Expect = 1e-18 Identities = 60/192 (31%), Positives = 94/192 (48%), Gaps = 10/192 (5%) Query: 58 AEAADGPAAMTVVEIAQAHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHLFG 117 AE G A + E+A + + ++ G DGAIYN+ +ID G ++ +RK F Sbjct: 55 AEEMPGAAEARLCEMAAKYGLWLIPGSLFERRDGAIYNTAPVIDPAGNVVARFRKLFPFR 114 Query: 118 ELDRSMFSPGADHFPVVEL-EGWKVGLLICYDIEFPENARRLALDGAELILVPTANMT-P 175 ++ + + F V ++ + + G+ ICYD+ FPE R L GAE+IL PT T Sbjct: 115 PYEQGIAA--GSEFVVFDVPDAGRFGISICYDMWFPETTRTLVAMGAEVILHPTMTDTID 172 Query: 176 YDFTCQVTVRARAQENQCYLVYANYCGAEDEIEYCGQSSIIGPDGSLLAMAGRDECQLL- 234 D + VRA A NQ Y N G G+S ++ P G +L AG +++ Sbjct: 173 RDIELSI-VRASAATNQVYFFDINGVGDGG----VGRSIVVDPAGYVLHEAGPGTAEIIP 227 Query: 235 AELEHERVVQGR 246 E++ E+V + R Sbjct: 228 VEIDFEKVRRER 239 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: 198 Number of extensions: 12 Number of successful extensions: 2 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: 282 Length adjustment: 25 Effective length of query: 239 Effective length of database: 257 Effective search space: 61423 Effective search space used: 61423 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