Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate BPHYT_RS22155 BPHYT_RS22155 carbon-nitrogen hydrolase
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__BFirm:BPHYT_RS22155 Length = 291 Score = 115 bits (289), Expect = 8e-31 Identities = 80/241 (33%), Positives = 123/241 (51%), Gaps = 8/241 (3%) Query: 1 MRIALYQGAPKPLDVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQVERLAEA 60 +RIA Q P DV GN+ R LAA+ GA+L+V PE FLTGY L + A Sbjct: 13 LRIAAAQAQPISGDVTGNIARTVELTALAADAGAKLVVFPEKFLTGYEPDLIAGDPAKYA 72 Query: 61 ADGPAAM--TVVEIAQAHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHLFGE 118 D A + +I + IA++ G RG+ G ++ S + G L +Y K +L+ Sbjct: 73 FDAHDARLEPIRDICRQREIAVIVGAATRGERG-LHISSLVFSRSGAQLDSYHKQYLYSS 131 Query: 119 LDRSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPT--ANMTPY 176 R ++ PG ++EL+GW++ L +CYD F E+AR A++GA LV + T Y Sbjct: 132 ETR-IYQPGTQG-RMLELDGWRLALGVCYDSGFAEHARHAAVNGAHAYLVSALFSVQTGY 189 Query: 177 DFTCQVTVRARAQENQCYLVYANYCGAEDEIEYCGQSSIIGPDGSLLAMAGRDECQLLAE 236 ++ ARA +N Y + +N+ G CG S+I P G ++A A R+ +++ Sbjct: 190 -HQSRIWFPARAFDNTMYALLSNHVGTTGGWATCGASAIWSPSGDVIAQASREREEVITA 248 Query: 237 L 237 L Sbjct: 249 L 249 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: 180 Number of extensions: 10 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: 291 Length adjustment: 25 Effective length of query: 239 Effective length of database: 266 Effective search space: 63574 Effective search space used: 63574 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