Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate GFF843 PS417_04280 carbon-nitrogen hydrolase
Query= BRENDA::B3IVI7 (264 letters) >FitnessBrowser__WCS417:GFF843 Length = 282 Score = 95.9 bits (237), Expect = 8e-25 Identities = 83/263 (31%), Positives = 113/263 (42%), Gaps = 26/263 (9%) Query: 14 DVPGNLQRLRHQAQLAAERGAQLLVCPEMFLTGYNIGLAQVERLAEAADGPAAMTVVEIA 73 DV NL + R + AA GA+L V PE F +A + R +GP + + A Sbjct: 13 DVLANLAQARRLLEHAAAGGAKLAVLPENFAAMGRRDVADIGRAEALGEGPILPWLKQTA 72 Query: 74 QAHRIAIVYG---YPERGDDGAIYNSVQL-IDAHGRSLSNYRKTHLF--------GELDR 121 + + IV G P + A N+ L +D G ++ Y K HLF G Sbjct: 73 RDLTLWIVAGTLPLPPKDRPNAKSNACSLLVDDQGEIVARYDKLHLFDVDVADARGRYRE 132 Query: 122 SMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTANMTPYDFTC- 180 S DH V + ++GL +CYD+ FPE L GAELI P+A FT Sbjct: 133 SDDYAFGDHVVVADTPVGRLGLTVCYDLRFPELYSELRAAGAELITAPSA------FTAV 186 Query: 181 ------QVTVRARAQENQCYLVYANYCGAE-DEIEYCGQSSIIGPDGSLLAMAGRDECQL 233 V +RARA E QCYL+ A G E G ++I+ P G +LA + E L Sbjct: 187 TGAAHWDVLIRARAIETQCYLLAAAQGGVHPGPRETYGHAAIVDPWGRVLAQQDKGEAVL 246 Query: 234 LAELEHERVVQGRTAFPYLTDLR 256 LAE + R P + R Sbjct: 247 LAERDSSEQASIRARMPVVNHRR 269 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: 182 Number of extensions: 9 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: 282 Length adjustment: 25 Effective length of query: 239 Effective length of database: 257 Effective search space: 61423 Effective search space used: 61423 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