Align aminocarboxymuconate-semialdehyde decarboxylase (EC 4.1.1.45) (characterized)
to candidate WP_007510589.1 R2APBS1_RS05970 amidohydrolase
Query= BRENDA::Q8R519 (336 letters) >NCBI__GCF_000230695.2:WP_007510589.1 Length = 344 Score = 363 bits (931), Expect = e-105 Identities = 173/335 (51%), Positives = 226/335 (67%), Gaps = 2/335 (0%) Query: 1 MKIDIHTHILPKEWPDLEKRFGYGGWVQLQQQGKGEAKMIKDGKLFRVIQQNCWDPEVRI 60 +KID H HILP++WP+L R+G + + G ++ KD + FR + + +DP+ RI Sbjct: 2 LKIDTHAHILPRDWPNLAARYGDDRF-PVMTHTDGRHRIYKDSRFFREVWDSAFDPQTRI 60 Query: 61 REMNQKGVTVQALSTVPVMFSYWAKPKDTLELCQFLNNDLAATVARYPRRFVGLGTLPMQ 120 + + GV VQ +STVPV+FSYWA LEL + LN +A +PR + G+GT+P+Q Sbjct: 61 DDYARFGVDVQVISTVPVLFSYWAPGHQALELHRHLNEHMAGICRDHPRHYAGIGTVPLQ 120 Query: 121 APELAVEEMERCVKALGFPGIQIGSHINTWDLNDPELFPIYAAAERLNCSLFVHPWDMQM 180 AP+LAV E+ERC+ LG G+QIGSH W+L+ PELFP + AA L ++ VHPWDM Sbjct: 121 APQLAVRELERCIDELGLQGVQIGSHCGDWNLDAPELFPFFEAAADLGAAVLVHPWDMMG 180 Query: 181 DGRMAKYWLPWLVGMPSETTMAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTIGRIAHGF 240 M KYW+PWLVGMP+E + A C ++ GGV E+ PKL+V AHGGG+FP+TIGRI HGF Sbjct: 181 MASMPKYWMPWLVGMPAEQSRAACCLVFGGVLERLPKLRVMLAHGGGSFPYTIGRIEHGF 240 Query: 241 NMRPDLCAQDNPSDPRKYLGSFYTDSLVHDPLSLKLLTDVIGKDKVMLGTDYPFPLGEQE 300 MRPDL A DNP +PR+YL FY DS VHD +L+ L DV G +VMLGTDYPFPLGEQ Sbjct: 241 RMRPDLVATDNPRNPREYLKRFYFDSCVHDDQALRYLLDVTGARQVMLGTDYPFPLGEQA 300 Query: 301 PGKLIESMAEFDEETKDKLTAGNALAFLGLERKLF 335 PG IE++ DE + +L G AL +LGL R F Sbjct: 301 PGSGIEALG-LDEADRARLFHGTALEWLGLPRHRF 334 Lambda K H 0.322 0.140 0.446 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: 463 Number of extensions: 16 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: 336 Length of database: 344 Length adjustment: 28 Effective length of query: 308 Effective length of database: 316 Effective search space: 97328 Effective search space used: 97328 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 24 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