Align 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (EC 4.1.1.45) (characterized)
to candidate Ac3H11_2743 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (EC 4.1.1.45)
Query= metacyc::MONOMER-15635 (336 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2743 Length = 362 Score = 114 bits (284), Expect = 5e-30 Identities = 86/288 (29%), Positives = 134/288 (46%), Gaps = 15/288 (5%) Query: 56 PQKRIQDMEREKVDMQVISPIPVTFSYWAPVEEALAMARIQNDFIAEVVKQYPDRFIGLG 115 P+ R+ M+ + QV+S + YWA E ++ A ND +A+ PDR + Sbjct: 71 PKNRLNGMDAAGQNAQVLSVPSHCYMYWADPEFSVRFATKVNDILADYCSAAPDRLMFWA 130 Query: 116 TVPLQDVEIAIREMDRCVHELGLKGLEI-GTNVNGANLDDPALLPFFEMCEQWNVPLFVH 174 PL A +E+ R ELG KGL G N G D P L ++ ++P+F+H Sbjct: 131 HAPLNAPHDAAKEIRRACTELGAKGLVAGGANFGGLEADSPQLDVVWKTMCDLDLPIFIH 190 Query: 175 PWETLGRERMPLHNLMY----TVGMPSETALAAASLILGGVMAKFPRLKICFAHGGGSFP 230 + M + Y VGM + LI GGV+ +FP LK+ HGGG P Sbjct: 191 GYNQSVTWGMQADHDQYETTAIVGMNYDETRFFWYLINGGVLDRFPNLKVYITHGGGYIP 250 Query: 231 YILARLDQGWRVWPHLRLLDQPPSYYAKNFYFDSLVYEPVNIQYLIERFGHERIMMGSDY 290 Y L RL Q R + +P Y KNF+FD ++E Q LI+ G +R++ GS++ Sbjct: 251 YQLGRLAQTNRNL-DVAFNKKPVEEYLKNFWFDVELHEVPMRQALIDIIGADRVLYGSNF 309 Query: 291 ---PFLLREIPPGEAVDRTLELTEEQHRAIFGENALRFLNMSPVKVSE 335 + ++ G L L+++ + I +NA L++ P K+ + Sbjct: 310 GGSDAVRHDLTDG------LRLSDDDLQKIRWKNACELLHLDPAKLGK 351 Lambda K H 0.324 0.141 0.446 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: 333 Number of extensions: 21 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: 336 Length of database: 362 Length adjustment: 29 Effective length of query: 307 Effective length of database: 333 Effective search space: 102231 Effective search space used: 102231 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 49 (23.5 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