Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate AO356_07100 AO356_07100 carbon-nitrogen hydrolase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4777 (264 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07100 Length = 287 Score = 84.7 bits (208), Expect = 2e-21 Identities = 91/268 (33%), Positives = 119/268 (44%), Gaps = 38/268 (14%) Query: 14 DPAGNLHRLHQVALE---ARGADVLVLPEMFMTGYNIGVDAVNVLAEVYNGE---WAQQI 67 D NL R +V LE A GA + VLPE F + + G W +Q+ Sbjct: 13 DVLANLARA-RVLLEQAAAGGARLAVLPENFAAMGRRDIADIGRAEAFGQGPILPWLKQV 71 Query: 68 ARIAKAAGLAIVYGY----PERGEDGQIYNAVQLIDAQGERLANYRKSHLFGDLDHA--- 120 AR K L IV G P + + + L+D QG+ +A Y K HLF D+D A Sbjct: 72 ARDLK---LWIVAGTLPLPPVDQPEARSHACSLLVDDQGQIVARYDKLHLF-DVDVADNR 127 Query: 121 -MFSAGD-----AALPIVELNGWKLGLLICYDLEFPENARRLALAGAELILVPTANMQPY 174 + D A + + + ++GL +CYDL FPE L AGAELI P+A Sbjct: 128 GRYRESDDYAYGANVVVADTPVGRVGLTVCYDLRFPELYSELRAAGAELITAPSA----- 182 Query: 175 EFIA-------DVTVRARAIENQCFVAYANYCG-HEGELQYCGQSSIAAPNGSRPALAGL 226 F A DV +RARAIE QC+V A G H G + G ++I P G A Sbjct: 183 -FTAVTGAAHWDVLIRARAIETQCYVLAAAQGGVHPGPRETFGHAAIVDPWGRVLAQQDQ 241 Query: 227 DEALIVAELDRQLMDDSRAAYNYLHDRR 254 EA++VAE D RA RR Sbjct: 242 GEAVLVAERDSSEQASIRARMPVASHRR 269 Lambda K H 0.321 0.139 0.419 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: 206 Number of extensions: 11 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: 264 Length of database: 287 Length adjustment: 25 Effective length of query: 239 Effective length of database: 262 Effective search space: 62618 Effective search space used: 62618 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