Align aryl-acylamidase (EC 3.5.1.13); amidase (EC 3.5.1.4) (characterized)
to candidate CCNA_00871 CCNA_00871 carbon-nitrogen hydrolase family protein
Query= BRENDA::A0A088BHP3 (267 letters) >FitnessBrowser__Caulo:CCNA_00871 Length = 283 Score = 84.3 bits (207), Expect = 3e-21 Identities = 86/271 (31%), Positives = 125/271 (46%), Gaps = 26/271 (9%) Query: 5 GLQTAGTPGDVAANLRELDAACRRARAEGAELLITTELF-ITGYD---IGDAVRDLARTD 60 GL TP AA L + R A A GA++++T E + D + A++ L Sbjct: 10 GLIQTRTPATHAAALGHVAPLVREAIAGGAKVVLTPECTNVVQKDRSLLLPALKTLDEDP 69 Query: 61 LLSPAQEIAAAHGIALVLGAP----EHDDGACYNSAFFIDPAGAILGRHRKNHLFG-DLD 115 ++ +EIAA G + +G+ E D A N IDP GAI+ + K H+F DL Sbjct: 70 VVLGLREIAAQTGTWIAIGSALVRRETGDKAA-NRQVVIDPTGAIVATYDKLHMFDVDLP 128 Query: 116 RR------------YFTPGDRTAPVIDYAGVRIAMLICYDVEFPENVRAAALAGADLVAV 163 R + PGD A V+D ++ + ICYD+ FP RA ALAGA ++ V Sbjct: 129 PRDGKAGETARESSAYEPGD-AAVVVDTPWAKLGLTICYDMRFPALHRALALAGATVLTV 187 Query: 164 PTAQMQPY-EFIAEHLLRVRAWENQIYIAYVNHDG-DEGSLRYVGRSSIVSPSATVLDSV 221 P A +P E E LLR RA E ++ G E GRS +V P ++ ++ Sbjct: 188 PAAFTRPTGEAHWEILLRARAIETGSFVLAAAQGGFHEDGRGTWGRSIVVGPWGEIIATL 247 Query: 222 EHGN-RLLFATVEPHTVRTARKANPYLADLR 251 +H +L A ++ AR A P L + R Sbjct: 248 DHDEPGVLLADLDLPAADKARAAIPALKNAR 278 Lambda K H 0.321 0.137 0.407 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: 163 Number of extensions: 9 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: 267 Length of database: 283 Length adjustment: 25 Effective length of query: 242 Effective length of database: 258 Effective search space: 62436 Effective search space used: 62436 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