Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate YP_002824752.1 NGR_c01990 hypothetical protein
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000018545.1:YP_002824752.1 Length = 537 Score = 162 bits (411), Expect = 2e-44 Identities = 160/498 (32%), Positives = 233/498 (46%), Gaps = 54/498 (10%) Query: 9 QTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGWS 68 +T G ++ L+A+G++ VF + G H +Y G IR + RHEQ A F A+G++ Sbjct: 4 ETKTVGEVLVDLLEANGVEVVFGIPGVHTVELYRGLAASKIRHVTPRHEQGAGFMADGYA 63 Query: 69 KVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGG--RAPALRWGMGSLQEI-DHV 125 +V+ PGVA + GPG+TN ++AMA A+Q+ P++V+ G R +L G G L E+ D Sbjct: 64 RVSGKPGVALVITGPGLTNTITAMAQARQDSIPMLVISGVNRRDSLGHGRGLLHELPDQQ 123 Query: 126 PFVAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMD-HAFSMSSDNGRPGA 184 + +A ++ T + + L+VD+A +S G ++ P D A + S +P A Sbjct: 124 GMMKTLALYSHTLINPADLPLVVDRAFAVLLSGRPGPVHIEIPTDVMAERIESRGTKPAA 183 Query: 185 LTELPAGPTPAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNG 244 T P G+ L RAA L + A RPVI+ G AEA + L E+ PV+ Sbjct: 184 ATR----PRSDGETLQRAAILCAEASRPVILCGGGAL--TAEAEVRGLAEQIGAPVVTTV 237 Query: 245 MARGV-------VPADHRLAFSRARSKALGEADVALIVGVPM---DFRLGFGGVFGSTTQ 294 ARG+ VPA L RA L +AD+ L +G M D+ L G F Sbjct: 238 NARGMLAGHPLRVPASPSLKAVRA---LLRDADLVLALGTEMGQTDYDLYADGGFPMLRN 294 Query: 295 LIVADRVEPAREHPRPVAAGLYGDLTATLSALAGSGGTDHQGWIEELATAETMARD---- 350 LI D ++ A+ P AA LS L+G+ I T ARD Sbjct: 295 LIRTD-IDAAQLARGPQAA---------LSVLSGARAA--TAGILGFLPGHTAARDGASR 342 Query: 351 ---LEKAELVDDRIPLHP-MRVYAELAALLER---DALVVIDAGDFGSYAGRM-IDSYLP 402 KA L + L P MR + L+ + D +V D+ YAG + D+ Sbjct: 343 ADATRKAALKE----LTPKMRAEVGIIDLIYKALPDCTIVGDSTQ-AVYAGNLYCDAPRQ 397 Query: 403 GCWLDSGP-FGCLGSGPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVS 461 W +S +G LG P A+ A +A R VV L GDG F FS E + V V+ Sbjct: 398 RAWFNSATGYGSLGYAPPAAVGAAVADRARPVVCLVGDGGFQFSLAEIGSAVDAGARVIF 457 Query: 462 VIGNN-GIWGLEKHPMEA 478 ++ NN G +E H +EA Sbjct: 458 LVWNNDGYREIESHMVEA 475 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: 750 Number of extensions: 44 Number of successful extensions: 3 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: 537 Length adjustment: 35 Effective length of query: 512 Effective length of database: 502 Effective search space: 257024 Effective search space used: 257024 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: 52 (24.6 bits)
This GapMind analysis is from Apr 10 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