Align (4E)-oxalomesaconate Delta-isomerase; OMA isomerase; 1,3-allylic isomerase LigU; EC 5.3.3.- (characterized)
to candidate Ga0059261_0523 Ga0059261_0523 Uncharacterized protein conserved in bacteria
Query= SwissProt::Q0KJL4 (357 letters) >FitnessBrowser__Korea:Ga0059261_0523 Length = 351 Score = 548 bits (1413), Expect = e-161 Identities = 275/348 (79%), Positives = 298/348 (85%) Query: 9 DSAPCMWMRGGTSKGGYFLRADLPADTAARDAFLLAVMGSPDPRQIDGMGGADPLTSKVA 68 D CMWMRGGTSKGGYFL+ DLPADTAARDA LL VMGSPDPRQIDGMGGADPLTSKVA Sbjct: 3 DGIRCMWMRGGTSKGGYFLKEDLPADTAARDALLLRVMGSPDPRQIDGMGGADPLTSKVA 62 Query: 69 VVSKSERPGIDVDYLFLQVFVDQAIVTDAQNCGNILAGVGPFAIERGLVAASGDETRVAI 128 VVSKS R GIDVDYLFLQVFVDQAIVTDAQNCGNILAG+GPFAIERGLV A ETRVAI Sbjct: 63 VVSKSARDGIDVDYLFLQVFVDQAIVTDAQNCGNILAGIGPFAIERGLVEAQDGETRVAI 122 Query: 129 FMENTGQVAVATVRTPGGSVTYAGDAAIDGVPGTHAPIPTEFRDTAGSSCGALLPSGNAV 188 FMENT QVAVATV+TPGG V YAGDAAI GVPGT APIP FRDTAG+SCGALLP+GN V Sbjct: 123 FMENTAQVAVATVQTPGGRVRYAGDAAISGVPGTAAPIPLAFRDTAGASCGALLPTGNGV 182 Query: 189 DVVNGLPVTLIDNGMPCVVMKAADVGITGYEDRDSLDANAELKAKIEAIRLAVGELMNLG 248 D ++G+ VTLIDNGMPCVV+ A+D+GITGYEDRD+LDA+ +KA++EAIRL G LMNLG Sbjct: 183 DEIDGIKVTLIDNGMPCVVIAASDMGITGYEDRDTLDADTAMKARVEAIRLKAGPLMNLG 242 Query: 249 DVTEKSVPKMMLVAPPRDGGAVCVRSFIPHRAHATIGVLGAVSVATACLIPGSPAAEVAV 308 DV EKSVPKMMLVAPPRDGGA+ VRS IPHR HA+IGVLGAVSVATACLI GSPAA +A Sbjct: 243 DVIEKSVPKMMLVAPPRDGGAIAVRSLIPHRVHASIGVLGAVSVATACLIEGSPAAALAQ 302 Query: 309 VPEGARKTLSIEHPTGEMSCVLEVDDAGNVVSAALLRTARKLMDGVVF 356 VP G +TL +EHPTG CV+ VD G V A +LRTARKLMDG VF Sbjct: 303 VPAGGTRTLGVEHPTGVTECVVTVDANGAPVEAGMLRTARKLMDGKVF 350 Lambda K H 0.318 0.135 0.396 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: 557 Number of extensions: 29 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: 357 Length of database: 351 Length adjustment: 29 Effective length of query: 328 Effective length of database: 322 Effective search space: 105616 Effective search space used: 105616 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: 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