Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate AZOBR_RS31945 AZOBR_RS31945 oxalyl-CoA decarboxylase
Query= BRENDA::P9WG39 (547 letters) >FitnessBrowser__azobra:AZOBR_RS31945 Length = 585 Score = 228 bits (582), Expect = 4e-64 Identities = 181/560 (32%), Positives = 290/560 (51%), Gaps = 35/560 (6%) Query: 2 STDTAPAQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAA 61 +TD PA T +L+ LK +GI+ ++ + G + + + EG+R+I RHEQ A Sbjct: 14 ATDAEPALT-DGFQLVIDALKLNGIENLYVVPGIPISDLLRMAQGEGLRVISFRHEQNAG 72 Query: 62 FAAEGWSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPA--LRWGMGSL 119 AA +T+ PGV + PG NG++A+A A N P++++ G + + G Sbjct: 73 NAAAIAGFLTKKPGVCMTVSAPGFLNGLTALANATTNCFPMILISGSSEREIVDLQQGDY 132 Query: 120 QEIDHVPFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFS--MSS 177 +E+D + P+ + A A++ G+ V +A++AAVS G ++D P FS M + Sbjct: 133 EEMDQLAIAKPLCKAAFRVLHAQDIGIAVARAIRAAVSGRPGGVYLDLPAK-LFSQVMDA 191 Query: 178 DNGRPGALTELPAGPT--PAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEE 235 G + + A P P+ D++ RA +L A+RP+I+ G + A+ A+ LVE+ Sbjct: 192 AEGARSLVKVVDAAPAQLPSPDSVARALEVLKGAKRPLIILGKGAAYAQADEAVRELVEK 251 Query: 236 RHIPVLMNGMARGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRLGFG-----GVFG 290 IP L MA+G++P H + ARS L +ADV ++VG +++ L G G G Sbjct: 252 SGIPFLPMSMAKGLLPDTHPQSAGAARSMVLKDADVVVLVGARLNWLLSHGKGKTWGEPG 311 Query: 291 STTQLIVADRVEPAREHPRPVA--AGLYGDLTATLSALAGSGGTDHQGWI---EELATAE 345 S T + +EP RE VA A L GD+ + +SAL +GW E A Sbjct: 312 SKT--FIQIDIEP-REMDSNVAIVAPLVGDIGSCVSALTAGMA---KGWTPPPAEWTGAV 365 Query: 346 TMARDLEKAELVDDRIP-LHPMRVYAELAAL----LER-DALVVIDAGDFGSYAGRMIDS 399 + ++ A++ + PM + L AL ER +AL+V + + A +ID Sbjct: 366 SARKEANIAKMAPKLMSNASPMNFHGALGALRRVVQERPEALLVNEGANTLDLARGIIDM 425 Query: 400 YLPGCWLDSGPFGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAV 459 + P LD G +G +G G G+A+AA + + V+ ++GD AFGFSGME +T+ R+N+ V Sbjct: 426 HQPRKRLDVGTWGVMGIGMGFAVAAAV-ESGKPVLAVEGDSAFGFSGMEVETICRYNLPV 484 Query: 460 -VSVIGNNGIW-GLEKHPMEALYGYSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPA 517 + V NNGI+ G + +P +V P +RYD+++ A GG G V+ P EL A Sbjct: 485 CIVVFNNNGIYKGTDVNPTGGSDPSPMV--FVPDSRYDKMMEAFGGAGVNVTTPDELYRA 542 Query: 518 LERAFASGLPAVVNVLTDPS 537 + A SG P ++N + DP+ Sbjct: 543 VSAAMDSGRPTLINAVIDPN 562 Lambda K H 0.319 0.135 0.405 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: 759 Number of extensions: 50 Number of successful extensions: 6 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: 547 Length of database: 585 Length adjustment: 36 Effective length of query: 511 Effective length of database: 549 Effective search space: 280539 Effective search space used: 280539 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 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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