Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate H281DRAFT_05434 H281DRAFT_05434 Predicted amidohydrolase
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__Burk376:H281DRAFT_05434 Length = 298 Score = 95.9 bits (237), Expect = 9e-25 Identities = 89/271 (32%), Positives = 121/271 (44%), Gaps = 16/271 (5%) Query: 3 IALYQGAPKPLDVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIG-LAQVERLAE-A 60 +A Q P + N+ R + AAE GA L+V PE+ TGY + LAE Sbjct: 18 VACVQMEPHVGEKQANVARSIKLIEEAAEHGASLVVLPELANTGYVFSDRDEAFTLAEDV 77 Query: 61 ADGPAAMTVVEIAQAHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHLFGELD 120 G A+ + AQ + +V G ER D +YNS L+ G + YRK HL+ + Sbjct: 78 PSGETALAWADAAQRLGVHVVAGIAER-DRVRLYNSALLVGPSG-IVGTYRKLHLWNN-E 134 Query: 121 RSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPT----ANMTPY 176 F PG PV ++ + ICYD FPE R A GA+L+ VPT P Sbjct: 135 NLFFEPGNKGVPVFHTPLGRIAIAICYDGWFPEVYRLAATQGADLVCVPTNWVPMQGQPA 194 Query: 177 DFTCQVT--VRARAQENQCYLVYANYCGAEDEIEYCGQSSIIGPDGSLLA--MAGRDECQ 232 D T A A N + AN G E + GQS I+G DG LA ++ E Sbjct: 195 DQPAMATTLTMAAAHSNGLMVACANRIGTERGQLFVGQSLIVGGDGWPLAGPVSSDHEEI 254 Query: 233 LLAELEHERVVQGRTAFPY---LTDLRQELH 260 L AE++ R GR P+ L D R +++ Sbjct: 255 LYAEIDLNRTRAGRNLNPFNHVLRDRRTDVY 285 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: 199 Number of extensions: 13 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: 298 Length adjustment: 26 Effective length of query: 238 Effective length of database: 272 Effective search space: 64736 Effective search space used: 64736 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