Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate AZOBR_RS04215 AZOBR_RS04215 NAD synthetase
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__azobra:AZOBR_RS04215 Length = 554 Score = 83.6 bits (205), Expect = 9e-21 Identities = 77/245 (31%), Positives = 115/245 (46%), Gaps = 36/245 (14%) Query: 1 MRIALYQGAPKPLDVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYN------------ 48 + IAL Q P + N+ R+R AA RGA L+VCPE+ +TGY Sbjct: 5 LSIALAQINPTVGAITTNIDRIRDARAEAAARGADLMVCPELAVTGYPPEDLVLKPFFLD 64 Query: 49 -IGLAQVERLAEAADGPAAMTVVEIAQAHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSL 107 + A E AE ADG A+ V G P R D +N+ L+D GR Sbjct: 65 VVEQAVRELAAETADGGPALLV-------------GAPWRDGDKR-HNAALLLDG-GRIA 109 Query: 108 SNYRKTHL--FGELD-RSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAE 164 + K L +G D + +F+PG P + + G ++G+ IC D+ + LA GAE Sbjct: 110 ATRFKVDLPNYGVFDEKRVFTPGPLPGP-INVRGVRLGVPICEDMWSADVIETLAESGAE 168 Query: 165 LILVPTAN---MTPYDFTCQVTVRARAQENQCYLVYANYCGAEDEIEYCGQSSIIGPDGS 221 +++VP + + +D Q+ V R E+ L+Y N G +DE+ + G S +G D Sbjct: 169 ILVVPNGSPFELGKHDQRVQLAV-GRVTESSLPLLYVNQVGGQDELVFDGASFALGADCR 227 Query: 222 LLAMA 226 L+A A Sbjct: 228 LVAQA 232 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: 383 Number of extensions: 18 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: 554 Length adjustment: 30 Effective length of query: 234 Effective length of database: 524 Effective search space: 122616 Effective search space used: 122616 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