Align 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase (EC 4.1.1.45) (characterized)
to candidate RR42_RS05075 RR42_RS05075 aminocarboxymuconate-semialdehyde decarboxylase
Query= metacyc::MONOMER-13360 (334 letters) >FitnessBrowser__Cup4G11:RR42_RS05075 Length = 337 Score = 488 bits (1257), Expect = e-143 Identities = 229/327 (70%), Positives = 268/327 (81%), Gaps = 1/327 (0%) Query: 6 IDMHSHFFPRISEQEAAKFDANHAPWLQVSAKGDTGSIMMGKNNFRPVYQALWDPAFRIE 65 +D+HSHFFP IS +EAA D APWLQ + DT IM G FRPVY ALWDPA RIE Sbjct: 7 VDIHSHFFPPISRREAAALDPVAAPWLQANGT-DTAMIMTGDQPFRPVYSALWDPARRIE 65 Query: 66 EMDAQGVDVQVTCATPVMFGYTWEANKAAQWAERMNDFALEFAAHNPQRIKVLAQVPLQD 125 EMD GVD+Q+ CATPVMFGY + A+ A W++RMND+ALE AH P R+K LAQVPLQD Sbjct: 66 EMDRCGVDIQLMCATPVMFGYRYPAHVAVPWSQRMNDYALELCAHRPARLKALAQVPLQD 125 Query: 126 LDLACKEASRAVAAGHLGIQIGNHLGDKDLDDATLEAFLTHCANEDIPILVHPWDMMGGQ 185 +D AC+EASRA A GH+G+QIGNHLG++DLDD L FL HCANE I +LVHPWDMMG Sbjct: 126 IDAACREASRAKAGGHVGVQIGNHLGERDLDDEGLITFLIHCANEGIAVLVHPWDMMGAP 185 Query: 186 RMKKWMLPWLVAMPAETQLAILSLILSGAFERIPKSLKICFGHGGGSFAFLLGRVDNAWR 245 RMKKWMLPWLV+MPAETQL ILSLILSGAFERIP SLK+CF HGGGSFAFLLGR+DNAWR Sbjct: 186 RMKKWMLPWLVSMPAETQLGILSLILSGAFERIPASLKLCFAHGGGSFAFLLGRIDNAWR 245 Query: 246 HRDIVREDCPRPPSEYVDRFFVDSAVFNPGALELLVSVMGEDRVMLGSDYPFPLGEQKIG 305 HRDIVREDCP PPS YV+RFFVDSAVF+P AL+LLV VMGEDRVMLGSDYP+PLGEQ++G Sbjct: 246 HRDIVREDCPHPPSSYVNRFFVDSAVFDPRALKLLVDVMGEDRVMLGSDYPYPLGEQQVG 305 Query: 306 GLVLSSNLGESAKDKIISGNASKFFNI 332 L+ +++L ++A+ K++ NA+ FF + Sbjct: 306 ALIRATDLADAARRKLLGANAAAFFGL 332 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: 468 Number of extensions: 12 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: 337 Length adjustment: 28 Effective length of query: 306 Effective length of database: 309 Effective search space: 94554 Effective search space used: 94554 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