Align (4E)-oxalomesaconate Delta-isomerase; OMA isomerase; 1,3-allylic isomerase LigU; EC 5.3.3.- (characterized)
to candidate SMc00497 SMc00497 tramsmembrane protein
Query= SwissProt::Q0KJL4 (357 letters) >FitnessBrowser__Smeli:SMc00497 Length = 352 Score = 465 bits (1197), Expect = e-136 Identities = 231/348 (66%), Positives = 272/348 (78%) Query: 9 DSAPCMWMRGGTSKGGYFLRADLPADTAARDAFLLAVMGSPDPRQIDGMGGADPLTSKVA 68 D CM MRGGTSKG YFL DLPAD RD LL +MGSPDPRQIDG+GGADPLTSKVA Sbjct: 4 DGIACMMMRGGTSKGAYFLADDLPADAGERDRLLLRIMGSPDPRQIDGIGGADPLTSKVA 63 Query: 69 VVSKSERPGIDVDYLFLQVFVDQAIVTDAQNCGNILAGVGPFAIERGLVAASGDETRVAI 128 VV S RP DVD+LFLQVFVDQA+V+D+QNCGNILAGVG FA+ERGLV A+ ET + I Sbjct: 64 VVRASARPDFDVDFLFLQVFVDQALVSDSQNCGNILAGVGAFAVERGLVEAAEGETAIRI 123 Query: 129 FMENTGQVAVATVRTPGGSVTYAGDAAIDGVPGTHAPIPTEFRDTAGSSCGALLPSGNAV 188 +MENT Q AVA +RT G YAGDA+IDGVP AP+ F D AGSSCGALLP+G+A Sbjct: 124 YMENTSQSAVARIRTANGRPVYAGDASIDGVPTPAAPVYLTFTDAAGSSCGALLPTGSAA 183 Query: 189 DVVNGLPVTLIDNGMPCVVMKAADVGITGYEDRDSLDANAELKAKIEAIRLAVGELMNLG 248 + + G+ TLIDNGMP VVM+AAD G+TGYE R+ L+AN +KA+IE IRLA G LMNLG Sbjct: 184 NEIEGVACTLIDNGMPVVVMRAADFGLTGYESREELEANESVKARIERIRLAAGPLMNLG 243 Query: 249 DVTEKSVPKMMLVAPPRDGGAVCVRSFIPHRAHATIGVLGAVSVATACLIPGSPAAEVAV 308 DV +KSVPKM LVA P +GGA+ RSFIPHR HA+IGV GA+SVATACL+P SPAA +A+ Sbjct: 244 DVMKKSVPKMTLVALPVNGGAIMTRSFIPHRVHASIGVFGALSVATACLLPNSPAASLAI 303 Query: 309 VPEGARKTLSIEHPTGEMSCVLEVDDAGNVVSAALLRTARKLMDGVVF 356 +PEG KT+++EHPTG M +L +D+AG+V + LRTARKL DG VF Sbjct: 304 LPEGEEKTVAVEHPTGRMEILLRLDNAGSVEECSFLRTARKLFDGRVF 351 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: 432 Number of extensions: 12 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: 352 Length adjustment: 29 Effective length of query: 328 Effective length of database: 323 Effective search space: 105944 Effective search space used: 105944 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