Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate Ga0059261_0603 Ga0059261_0603 Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase]
Query= curated2:Q02137 (575 letters) >FitnessBrowser__Korea:Ga0059261_0603 Length = 607 Score = 240 bits (613), Expect = 1e-67 Identities = 176/579 (30%), Positives = 267/579 (46%), Gaps = 37/579 (6%) Query: 13 SQLVLQTLKELGVEIIFGYPGGAMLPLYDAIHNFEGIQHILARHEQGATHEAEGYAKSSG 72 S V TL + G+ +F GG + L ++ ++ HEQ AE Y + + Sbjct: 7 SDWVADTLAQRGIRDVFMLTGGGAMHLNHSLGTHPALKTTFTHHEQALAMAAEAYYRLTN 66 Query: 73 KVGVVVVTSGPGATNAVTGIADAYLDSVPLLVFTGQVGP--------LSIGKDAFQEADT 124 ++ VV VTSGPG TNA+TG+ AY+DS+ +LV +GQV L + + QE D Sbjct: 67 RLAVVNVTSGPGGTNAITGVYGAYVDSIGMLVISGQVKTETTVRHTGLPLRQFGDQELDI 126 Query: 125 VGITAPITKYNYQIRETADIPRIVTEAYYLARTGRPGPVEIDLPKDVSTLEVTEINDPSL 184 + PITKY + + I + +A +LA +GRPGPV +D+P DV ++ DP Sbjct: 127 EELVRPITKYATMVLDPRSIRYHLEKAIHLATSGRPGPVWLDIPLDVQAAKI----DPDD 182 Query: 185 NLPHYHESE-------KATDEQLQELLTELSVSKKPVIIAGGGINYSGSVDIFRAFVEKY 237 LP + +E D +L +L+ +++PV+ AGGG+ SG+ D F +E+ Sbjct: 183 LLPGFDPAELDQPWQAADLDATADAILAKLAAAQRPVVFAGGGVRLSGAHDAFLKLIERL 242 Query: 238 QIPVVSTLLGLGTLPISHELQLGMAGMHGSYAANMALVEADYIINLGSRFDDRVVS-NPA 296 IPVV+ L H L G G G NM AD ++ LGSR + R VS N Sbjct: 243 GIPVVTGWNAHDVLWNDHPLYCGRPGTVGDRGGNMVTQSADLLLVLGSRLNIRQVSYNWK 302 Query: 297 KVAKNAVVAHIDIDAAELGK-IVKTDIPILSDLKAALSRLLQL-----NKVRTDFNDWIK 350 A+ A +DID EL K V D+P+++DL + LL ++ DW + Sbjct: 303 SFAREAYKIWVDIDPVELAKPTVTPDMPVVADLADLIPALLDRPYAGPTPAHDEWLDWSR 362 Query: 351 TVTKNKEKAPFTYEPQNHDIRPQETIKLIGEYTQGDAIIVTDVGQHQMWVAQYYPYKNAR 410 N Y I P + + D ++VT G + Q K + Sbjct: 363 ERVFNFPAVLPEYRHHGPSIHPYVAMDELFVQLGEDDVVVTGNGSACVVSFQTANLKQGQ 422 Query: 411 QLITSGGMGTMGFGIPAAIGAKLA-QPNKNVIVFVGDGGFQMTNQELALLNGYGIAIKVV 469 +L T+ G TMG+ +PAAIG A K +I GDG M QEL + GY + +KV Sbjct: 423 RLWTNSGCATMGYDLPAAIGVWAATNGEKRIIAIAGDGSIMMNIQELQTIAGYDMPVKVF 482 Query: 470 LINNHSLGMVRQWQESFYE------ERRSQSVFDVEPNFQLLAEAYGIKHVKLDNPKTLA 523 L+NN + Q +F+ +S F P+F +A A+G + + ++ L Sbjct: 483 LVNNSGYVSIFQTHRNFFNGVEVGGGPKSNVTF---PDFGKVATAFGFAYFRAESHNDLP 539 Query: 524 DDL-KIITEDEPMLIEVLISKSEHVLPMIPAGLHSDEMI 561 + + D P+L E++I + P + A H D I Sbjct: 540 GTIAAALAADGPVLCELIIDEHVGFAPKLGAKAHPDGRI 578 Lambda K H 0.316 0.135 0.385 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: 878 Number of extensions: 41 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: 575 Length of database: 607 Length adjustment: 37 Effective length of query: 538 Effective length of database: 570 Effective search space: 306660 Effective search space used: 306660 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 (21.6 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