Align (4E)-oxalomesaconate Delta-isomerase; OMA isomerase; 1,3-allylic isomerase LigU; EC 5.3.3.- (characterized)
to candidate AZOBR_RS26900 AZOBR_RS26900 hypothetical protein
Query= SwissProt::Q0KJL4 (357 letters) >FitnessBrowser__azobra:AZOBR_RS26900 Length = 352 Score = 520 bits (1338), Expect = e-152 Identities = 260/348 (74%), Positives = 293/348 (84%) Query: 9 DSAPCMWMRGGTSKGGYFLRADLPADTAARDAFLLAVMGSPDPRQIDGMGGADPLTSKVA 68 D C+WMRGGTSKGGYFL DLP TAARDAFLL VMGSPD RQIDGMGGADPLTSKVA Sbjct: 3 DGVRCLWMRGGTSKGGYFLADDLPPGTAARDAFLLRVMGSPDSRQIDGMGGADPLTSKVA 62 Query: 69 VVSKSERPGIDVDYLFLQVFVDQAIVTDAQNCGNILAGVGPFAIERGLVAASGDETRVAI 128 VV +SERPG+DVDYLFLQVFVD+AIVTDAQNCGNILAGVGPFAIERGLV A T V I Sbjct: 63 VVRRSERPGVDVDYLFLQVFVDKAIVTDAQNCGNILAGVGPFAIERGLVPARDGVTPVTI 122 Query: 129 FMENTGQVAVATVRTPGGSVTYAGDAAIDGVPGTHAPIPTEFRDTAGSSCGALLPSGNAV 188 MENTGQVAVA V TPGG+VTY G+A IDGVPGT A IP EFRDTAGSSCGALLP+GN V Sbjct: 123 HMENTGQVAVAAVPTPGGTVTYRGEARIDGVPGTAAAIPIEFRDTAGSSCGALLPTGNVV 182 Query: 189 DVVNGLPVTLIDNGMPCVVMKAADVGITGYEDRDSLDANAELKAKIEAIRLAVGELMNLG 248 DV++G+PVT IDNGMP VV++AAD+G+ G E R+ LD +A LKA++E+IRL G M LG Sbjct: 183 DVIDGVPVTCIDNGMPVVVLRAADLGVRGDETREELDGDAALKARLESIRLQAGPRMKLG 242 Query: 249 DVTEKSVPKMMLVAPPRDGGAVCVRSFIPHRAHATIGVLGAVSVATACLIPGSPAAEVAV 308 DVT+KSVPKM LV+ P +GGAV R+FIPHR HA+IGVLGAVSVATAC + GSPAA +AV Sbjct: 243 DVTDKSVPKMTLVSAPANGGAVSTRTFIPHRCHASIGVLGAVSVATACALEGSPAASLAV 302 Query: 309 VPEGARKTLSIEHPTGEMSCVLEVDDAGNVVSAALLRTARKLMDGVVF 356 VP+GA KTLS+EHPTGEM+ VL++D+AG V AALLRTARKL DG V+ Sbjct: 303 VPDGAAKTLSVEHPTGEMTVVLDLDEAGTVTRAALLRTARKLFDGTVY 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: 517 Number of extensions: 25 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