Align 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase; Picolinate carboxylase; EC 4.1.1.45 (characterized)
to candidate N515DRAFT_3778 N515DRAFT_3778 aminocarboxymuconate-semialdehyde decarboxylase
Query= SwissProt::Q8TDX5 (336 letters) >FitnessBrowser__Dyella79:N515DRAFT_3778 Length = 337 Score = 358 bits (920), Expect = e-104 Identities = 169/335 (50%), Positives = 234/335 (69%), Gaps = 2/335 (0%) Query: 1 MKIDIHSHILPKEWPDLKKRFGYGGWVQLQHHSKGEAKLLKDGKVFRVVRENCWDPEVRI 60 +KID H+H+LP++WP+L +F + + HH G+ ++ KDGK FR V E+ +DP+ RI Sbjct: 2 LKIDTHAHVLPRDWPNLAAKFDDLRFPVMTHHD-GKHRIYKDGKFFREVWESAFDPQHRI 60 Query: 61 REMDQKGVTVQALSTVPVMFSYWAKPEDTLNLCQLLNNDLASTVVSYPRRFVGLGTLPMQ 120 + + GV VQ +STVPV+FSYWA L L + LN+ +A YPR + G+ T+P+Q Sbjct: 61 DDYARFGVAVQVVSTVPVLFSYWAPGYQALELHRHLNDHVAGLCRDYPRHYAGIATVPLQ 120 Query: 121 APELAVKEMERCVKELGFPGVQIGTHVNEWDLNAQELFPVYAAAERLKCSLFVHPWDMQM 180 +P+LA++E+ERC+ ELG GVQ+G+H N+W+L+A ELFP + AA L ++ VHPWDM Sbjct: 121 SPDLAIRELERCIDELGLHGVQVGSHCNDWNLDAPELFPFFEAAADLGAAVMVHPWDMMG 180 Query: 181 DGRMAKYWLPWLVGMPAETTIAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTVGRISHGF 240 M KYWLPWLVGMPAE + A C ++ GGV E+ P+L+V AHGGG+FP+++GRI HGF Sbjct: 181 AASMPKYWLPWLVGMPAEQSRAGCCLVFGGVLERLPRLRVMLAHGGGSFPWSIGRIEHGF 240 Query: 241 SMRPDLCAQDNPMNPKKYLGSFYTDALVHDPLSLKLLTDVIGKDKVILGTDYPFPLGELE 300 MRPDL A DNP NP++YL Y D+ VHDP +L+ L DV G ++V+LGTDYPFPLGE Sbjct: 241 RMRPDLVATDNPRNPREYLKRLYFDSCVHDPQALRYLLDVTGVERVMLGTDYPFPLGEQH 300 Query: 301 PGKLIESMEEFDEETKNKLKAGNALAFLGLERKQF 335 PG IE++ +E + +L G AL +LGL +F Sbjct: 301 PGSGIEAL-GLEEAARARLFHGTALEWLGLPLYRF 334 Lambda K H 0.322 0.139 0.442 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: 434 Number of extensions: 15 Number of successful extensions: 2 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: 336 Length of database: 337 Length adjustment: 28 Effective length of query: 308 Effective length of database: 309 Effective search space: 95172 Effective search space used: 95172 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: 49 (23.5 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