Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate 203176 SO4092 hydrolase, carbon-nitrogen family (NCBI ptt file)
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__MR1:203176 Length = 282 Score = 101 bits (252), Expect = 2e-26 Identities = 86/275 (31%), Positives = 131/275 (47%), Gaps = 28/275 (10%) Query: 1 MRIALYQGAPKPLDVPGNL-------QRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQ 53 MRI+L Q DV NL + L + Q + L+V PE L G + Sbjct: 1 MRISLLQ-CQSSRDVSANLLFIESQLEELTQERQQWGDNSPHLVVLPECSLL---FGGHE 56 Query: 54 VERLAEAADGPAAM---TVVEIAQAHRIAIVYG-YPERGDDGAIYNSVQLIDAHGRSLSN 109 ++LA A D + + +A +R+ +V G P + G +Y+ L D G +L + Sbjct: 57 SQQLAYAGDSHHSQLKSALSALATRYRVFMVAGTIPALAEGGRVYSRCYLFDDKGDTLGH 116 Query: 110 YRKTHLFGE---------LDRSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLAL 160 Y K HLF + F PG DH V++ K+GL ICYD+ FP+ R + L Sbjct: 117 YDKLHLFDVDVADGTKQYRESETFCPG-DHISVIDTPFGKIGLSICYDLRFPDLFRAMRL 175 Query: 161 DGAELILVPTA-NMTPYDFTCQVTVRARAQENQCYLVYANYCGAEDE--IEYCGQSSIIG 217 GAE+I VP+A + QV ++ARA E QC++V A GA ++ E GQS +IG Sbjct: 176 AGAEIITVPSAFTKVTGEAHWQVLLQARAIETQCFIVAAAQWGAHNQGSRETWGQSMVIG 235 Query: 218 PDGSLLAMAGRDECQLLAELEHERVVQGRTAFPYL 252 P G+++A + A+++ V R+ P + Sbjct: 236 PWGNIIAERKTGTGWVHADIDLTEVNSIRSKMPVM 270 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: 187 Number of extensions: 8 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: 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