Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_089303187.1 CHB84_RS19910 acetolactate synthase
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_900188115.1:WP_089303187.1 Length = 550 Score = 509 bits (1312), Expect = e-149 Identities = 274/546 (50%), Positives = 344/546 (63%), Gaps = 18/546 (3%) Query: 10 TMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCR--EEGIRLIDTRHEQTAAFAAEGW 67 T H GRL + GI T+FTLSGGH+F +YDG E +RL+D RHEQTA FAAEG Sbjct: 5 TGHGGRLATDVARTHGIRTMFTLSGGHVFPLYDGALQGEPPLRLVDVRHEQTAVFAAEGT 64 Query: 68 SKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPALRWGMGSLQEIDHVPF 127 +++TR PG+A LTAGPGITNG+S + A N SPL+ +GGRAP RWG GSLQE+DH P Sbjct: 65 ARLTRTPGLAVLTAGPGITNGVSGVTTAHFNGSPLLTIGGRAPQARWGSGSLQELDHPPL 124 Query: 128 VAPVARFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFSMSSDNGRPGALTE 187 +APV + +AT + E V ALQ A + G F+D P++ F ++ P A + Sbjct: 125 LAPVTKLSATIERTEKVPYAVHDALQVACTPHRGPVFLDIPIEQVFGEATSTAAPPAERQ 184 Query: 188 LPAGPTPAGDA-LDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNGMA 246 P P LD A L++TAQRPV++ G++VW AE A R E +P + NG A Sbjct: 185 ----PVPPDQGRLDEIARLMATAQRPVLVLGSDVWTDGAEDAARRAAETIGLPTITNGTA 240 Query: 247 RGVVPADHRLAFSRARSKALGEADVALIVGVPMDFRLG---FGGVFGSTTQLI--VADRV 301 RGV+PA H L +RARS+A G AD+ ++VG P+DFRLG FGG GS + +AD Sbjct: 241 RGVLPAGHPLLVTRARSRAFGAADLVVVVGTPLDFRLGYGSFGGKDGSPAAQVCHIADSP 300 Query: 302 EPAREHPRPVAAGLYGDLTATLSALAG-----SGGTDHQGWIEELATAETMARDLEKAEL 356 E H +A GDLT L L S T H W EL A + A+L Sbjct: 301 EQLAGHV-DLAGSASGDLTLALDGLTSAWQRQSAHTTHADWAAELRRTADAAIASDAADL 359 Query: 357 VDDRIPLHPMRVYAELAALLERDALVVIDAGDFGSYAGRMIDSYLPGCWLDSGPFGCLGS 416 D +P+HP R+Y EL + D +V+ D GDF SYAGR ++ PGCWLD GP+GCLG+ Sbjct: 360 DSDAVPIHPARIYRELLRHTDDDTVVIGDGGDFVSYAGRYVEPRRPGCWLDPGPYGCLGT 419 Query: 417 GPGYALAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNGIWGLEKHPM 476 G GYA+AA+LARP VVLL GDGA GFS M+ DTLVRH + VV ++GNN WGLEKHPM Sbjct: 420 GLGYAMAARLARPSSPVVLLLGDGAAGFSLMDVDTLVRHRLPVVMIMGNNSGWGLEKHPM 479 Query: 477 EALYGYSVVAELRPGTRYDEVVRALGGHGELVSVPAELRPALERAFASGLPAVVNVLTDP 536 + LYGY AEL GTRYDEVVRALGG GE+V+ P E+ PAL RA + +P +VNV+TDP Sbjct: 480 QFLYGYHAAAELGSGTRYDEVVRALGGGGEMVTEPGEIGPALRRALDADVPYLVNVITDP 539 Query: 537 SVAYPR 542 AYPR Sbjct: 540 DNAYPR 545 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: 943 Number of extensions: 40 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: 550 Length adjustment: 36 Effective length of query: 511 Effective length of database: 514 Effective search space: 262654 Effective search space used: 262654 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 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