Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate PfGW456L13_4783 Aliphatic amidase AmiE (EC 3.5.1.4)
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4783 Length = 273 Score = 155 bits (391), Expect = 1e-42 Identities = 102/260 (39%), Positives = 142/260 (54%), Gaps = 7/260 (2%) Query: 1 MRIALYQGAPKPLDVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQVERLAEA 60 M++ L Q A + D NL+R A A +QL++ PE L G+ V +AE Sbjct: 1 MKVELAQLAGRDNDTAYNLERTL-AAMAACAADSQLILFPEGHLMGFP-SAESVAEVAEP 58 Query: 61 ADGPAAMTVVEIAQAHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHLFGELD 120 DGP+ V+ A+ H I++ G E D+G YN+ LI G +L YRKTHL+ D Sbjct: 59 LDGPSVSAVIAAARQHNISVAIGMAEN-DNGRFYNTTLLITPEGIALK-YRKTHLWAS-D 115 Query: 121 RSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTANMTPYDFTC 180 R ++ G D + G +VGLLICYDIEFPE+AR LA GAEL++V NM PY T Sbjct: 116 RGVYEAG-DRYATCLWNGVRVGLLICYDIEFPESARALAQLGAELLIVTNGNMDPYGPTH 174 Query: 181 QVTVRARAQENQCYLVYANYCGAED-EIEYCGQSSIIGPDGSLLAMAGRDECQLLAELEH 239 + + ARAQENQ + + N D + + G S+++ P G+LL AGR+E Q EL+ Sbjct: 175 RTAIMARAQENQAFALMVNRVEEGDGGLLFAGGSALVDPLGTLLFEAGREEGQFAVELDL 234 Query: 240 ERVVQGRTAFPYLTDLRQEL 259 ++ R + YL D R L Sbjct: 235 NQLTVARQDYRYLDDQRLRL 254 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: 221 Number of extensions: 16 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: 273 Length adjustment: 25 Effective length of query: 239 Effective length of database: 248 Effective search space: 59272 Effective search space used: 59272 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