Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_011384016.1 AMB_RS08115 carbon-nitrogen hydrolase family protein
Query= reanno::pseudo5_N2C3_1:AO356_14225 (264 letters) >NCBI__GCF_000009985.1:WP_011384016.1 Length = 275 Score = 80.9 bits (198), Expect = 3e-20 Identities = 82/261 (31%), Positives = 119/261 (45%), Gaps = 26/261 (9%) Query: 14 DPAGNLHRLHQVALEAR--GADVLVLPE----MFMTGYNIGVDAV---NVLAEVYNGEWA 64 D N +A+EAR GAD++++PE M NI + A LA + + A Sbjct: 16 DLTANCEAAAALAVEARAAGADLILMPENVAMMEWGRSNIVLKAQPEEEHLALKFFRDLA 75 Query: 65 QQIGRIAKAANLAIVYGYPERGEDGQIYNAVQLIDAQGERLANYRKSHLFG-DL------ 117 ++IG +L ++ E G + N +I G A Y K H+F DL Sbjct: 76 REIGAWLHIGSLHVLL------EGGMVANRTYVISPDGGIAARYSKIHMFDVDLGLGEVY 129 Query: 118 -DHAMFSAGDSALPIVELNGWKLGLLICYDLEFPENARRLALAGAELILVPTA-NMQPYE 175 + A F GD A+ V+L +LGL ICYDL FP R LA +G+ + VP A + Sbjct: 130 KESATFQPGDEAV-CVDLPWGRLGLSICYDLRFPHLYRALAHSGSSFLAVPAAFTRTTGK 188 Query: 176 FIADVTVRARAIENQCFVAYANYCG-HEAELQYCGQSSIAAPNGSRPALAGLDEALIVGE 234 V +RARAIE C+V CG H + Q G + I +P G A A ++ + Sbjct: 189 AHWHVLLRARAIETGCYVFAPAQCGEHVNDRQTYGHALIVSPWGEVLADALERPGWVMAD 248 Query: 235 LDRQLLDDSRAAYNYLHDRRP 255 +D + + D+R L RP Sbjct: 249 IDPEKVKDARRKIPCLDHDRP 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: 193 Number of extensions: 14 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: 275 Length adjustment: 25 Effective length of query: 239 Effective length of database: 250 Effective search space: 59750 Effective search space used: 59750 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 (21.8 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