Align 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase (EC 4.1.1.45) (characterized)
to candidate BPHYT_RS07270 BPHYT_RS07270 aminocarboxymuconate-semialdehyde decarboxylase
Query= metacyc::MONOMER-13360 (334 letters) >FitnessBrowser__BFirm:BPHYT_RS07270 Length = 340 Score = 486 bits (1250), Expect = e-142 Identities = 234/331 (70%), Positives = 264/331 (79%), Gaps = 1/331 (0%) Query: 5 RIDMHSHFFPRISEQEAAKFDANHAPWLQVSAKGDTGSIMMGKNNFRPVYQALWDPAFRI 64 RIDMHSHFFP I+ +EAA+ DA HAPWLQ+ A G+ G IM G+ FRPVY+ALWDPA RI Sbjct: 4 RIDMHSHFFPPIAREEAARLDAQHAPWLQIDADGERGMIMTGEKRFRPVYRALWDPAARI 63 Query: 65 EEMDAQGVDVQVTCATPVMFGYTWEANKAAQWAERMNDFALEFAAHNPQRIKVLAQVPLQ 124 EMDA GVD+Q+ CATPVMFGY + A A WA RMND ALE AH PQR+ LAQVPLQ Sbjct: 64 AEMDALGVDIQLMCATPVMFGYGYGAAAAHDWAARMNDHALELCAHAPQRLMALAQVPLQ 123 Query: 125 DLDLACKEASRAVAAGHLGIQIGNHLGDKDLDDATLEAFLTHCANEDIPILVHPWDMMGG 184 D++LAC+EA+RA AGH G+QIGNHLG +DLDD L FLTHCANE IP+LVHPWDMM Sbjct: 124 DVELACREATRAHRAGHRGVQIGNHLGPRDLDDEHLVTFLTHCANEGIPVLVHPWDMMTD 183 Query: 185 QRMKKWMLPWLVAMPAETQLAILSLILSGAFERIPKSLKICFGHGGGSFAFLLGRVDNAW 244 RMKKWMLPWLVAMPAETQL+++SLILSGAFERIPKSLK+CF HGGGSFAFLLGRV NAW Sbjct: 184 GRMKKWMLPWLVAMPAETQLSMVSLILSGAFERIPKSLKLCFAHGGGSFAFLLGRVQNAW 243 Query: 245 RHRDIVREDCPRPPSEYVDRFFVDSAVFNPGALELLVSVMGEDRVMLGSDYPFPLGEQKI 304 RDIVREDCP PP Y++RF VDSAVF+ GAL LLV MGED V+LGSDYPFPLGE KI Sbjct: 244 EQRDIVREDCPNPPVSYLERFHVDSAVFDEGALRLLVETMGEDHVLLGSDYPFPLGELKI 303 Query: 305 GGLVL-SSNLGESAKDKIISGNASKFFNINV 334 G LV L E+AK KI+ NA +FF + V Sbjct: 304 GDLVAHHPQLSETAKAKILGANAQRFFGLPV 334 Lambda K H 0.322 0.137 0.430 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: 421 Number of extensions: 6 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: 334 Length of database: 340 Length adjustment: 28 Effective length of query: 306 Effective length of database: 312 Effective search space: 95472 Effective search space used: 95472 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