Align N-carbamoylputrescine amidase; EC 3.5.1.53 (characterized)
to candidate Pf1N1B4_2504 5-aminopentanamidase (EC 3.5.1.30)
Query= SwissProt::Q9XGI9 (300 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2504 Length = 264 Score = 95.9 bits (237), Expect = 9e-25 Identities = 83/269 (30%), Positives = 128/269 (47%), Gaps = 25/269 (9%) Query: 20 DVSTNVATAERLVRAAHQKGANIILIQELFEGYYFCQAQKEEFFHRAKPYPGHPTIVRMQ 79 DV+ N+ +L A KGA+++++ E+F Y A+ + G + ++ Sbjct: 14 DVAGNLQRLHQL--ALEAKGADLLVLPEMFLTGYNIGIDAVSVL--AEVHNGE-SAQQIA 68 Query: 80 NLAKELGVVIPVSFFEEANNAH-YNSVAIIDADGTDLGLYRKSHIPDGPGYQEKYYFNPG 138 +AK G+ I + E + YN+V +IDA+G L YRK+H+ G + F+PG Sbjct: 69 RIAKTTGIAILYGYPERTEDGQIYNAVQLIDANGERLCNYRKTHLF---GDLDHSMFSPG 125 Query: 139 DTGFKVFQTKYAKIGVAICWDQWFPEAARAMALQGAEVLFYPTAIGSEPQDDGLDSRDHW 198 F + + K+G IC+D FPE AR +AL GAE++ PTA P D D Sbjct: 126 PDEFPLVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTA-NMIPYDFIADV---- 180 Query: 199 RRVMQGHAGANVVPLVASNRIGKEIIETEHGNSEITFYGYSFIAGPTGELVAAAGDKEEA 258 ++ A N + +N G E EI + G S IA P G +A AG +EA Sbjct: 181 --TVRARAFENQCYVAYANYCGHE--------GEIQYCGQSSIAAPDGSRIAQAG-LDEA 229 Query: 259 VLVAQFDLDKIKSKRHGWGVYRDRRPDLY 287 ++V + D + R + DRRP+LY Sbjct: 230 LIVGELDRQLMIDSRAANRYFLDRRPELY 258 Lambda K H 0.319 0.137 0.414 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: 220 Number of extensions: 12 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: 300 Length of database: 264 Length adjustment: 26 Effective length of query: 274 Effective length of database: 238 Effective search space: 65212 Effective search space used: 65212 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