Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate Ac3H11_517 NAD synthetase (EC 6.3.1.5) / Glutamine amidotransferase chain of NAD synthetase
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_517 Length = 552 Score = 90.9 bits (224), Expect = 5e-23 Identities = 78/239 (32%), Positives = 116/239 (48%), Gaps = 16/239 (6%) Query: 14 DVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQVERLAEAADGPAAMTVV-EI 72 D+PGN Q++ A+ A +GA+LL+ PE+ + GY + AA A TV E Sbjct: 16 DMPGNAQKIIAAAREAYAQGARLLLTPELAICGYAAEDLFLRPAFIAACDDAVKTVARET 75 Query: 73 AQAHRIAIVYGYPER-GDDG----AIYNSVQLIDAHGRSLSNYRKTHL--FGELDRSMFS 125 A +AIV G+P+ D A +N+ ++ GR Y K L + D + Sbjct: 76 AGLKGLAIVLGHPQALAPDAPAFSACHNAASVL-RDGRIEQTYAKRELPNYQVFDERRYF 134 Query: 126 PGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTANMTPYDF----TCQ 181 V E+EG +VGLL+C D F E AR A GA+L+ V N +P+ + Sbjct: 135 VAGTAPCVFEVEGVRVGLLVCEDAWFAEPARSTAAAGAQLLAV--INASPFHLGKSAERE 192 Query: 182 VTVRARAQENQCYLVYANYCGAEDEIEYCGQSSIIGPDGSLLAMA-GRDECQLLAELEH 239 T+R R E LVYA+ G +DE+ + G+S + DGS+ A G +E + A + H Sbjct: 193 ATMRERVAETGLPLVYAHLVGGQDEVVFEGRSFALNADGSVAGRAPGFEEKLVFARVHH 251 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: 318 Number of extensions: 15 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: 552 Length adjustment: 30 Effective length of query: 234 Effective length of database: 522 Effective search space: 122148 Effective search space used: 122148 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: 50 (23.9 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