Align 4-oxalocrotonate decarboxylase; EC 4.1.1.77 (characterized)
to candidate H281DRAFT_01664 H281DRAFT_01664 2-oxo-3-hexenedioate decarboxylase
Query= SwissProt::Q9KWS3 (256 letters) >FitnessBrowser__Burk376:H281DRAFT_01664 Length = 255 Score = 275 bits (704), Expect = 5e-79 Identities = 137/247 (55%), Positives = 189/247 (76%) Query: 4 SRIAQRLDEAAVSGKATPQLTGDDAVTVREAAEIQRLLIAHRIERGARQVGLKMGFTSRA 63 + +A+ LD+AA++ + + +++ EA IQ I R++RG R+VG+KMGFTSRA Sbjct: 5 AELAKLLDDAALNATEVTRFDREGRLSLDEAYRIQAESIRRRLDRGERRVGVKMGFTSRA 64 Query: 64 KMAQMGVSDLIWGRLTSDMWVEEGGEIDLAHYVHPRVEPEICYLLGKRLEGNVTPLEALA 123 KM QMG+SD+IWGRLT M +EEG IDL+ ++H R EPEI ++L + LEGNVT +ALA Sbjct: 65 KMVQMGLSDVIWGRLTDAMQIEEGTAIDLSRFIHARCEPEIAFILKRPLEGNVTGPQALA 124 Query: 124 AVEAVAPAMEIIDSRYRDFKFSLPDVIADNASSSGFVVGAWHKPETDVSNLGMVMSFDGR 183 AVEA+APA+EIIDSRY+DFKFSLP+VIADNASSSGFV+GAW P+ D SNLG+ +S DGR Sbjct: 125 AVEAIAPAIEIIDSRYKDFKFSLPEVIADNASSSGFVIGAWCDPKIDFSNLGLTVSIDGR 184 Query: 184 AVELGTSAAILGSPIRALVAAARLAAQQGEALEAGSLILAGAATAAVALRPGISVRCEVQ 243 V++G++AA+LG P+R+LVAAARL+A+ GE L+AG +++AG AT A ++ G +++ Sbjct: 185 VVQVGSTAALLGHPLRSLVAAARLSAEAGEPLQAGWIVMAGGATPAEWIKLGQYTSVDME 244 Query: 244 NLGSLSF 250 LGS+ F Sbjct: 245 QLGSVGF 251 Lambda K H 0.318 0.132 0.372 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: 200 Number of extensions: 6 Number of successful extensions: 1 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: 256 Length of database: 255 Length adjustment: 24 Effective length of query: 232 Effective length of database: 231 Effective search space: 53592 Effective search space used: 53592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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