Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate AZOBR_RS29985 AZOBR_RS29985 pyruvate oxidase
Query= curated2:P37251 (574 letters) >FitnessBrowser__azobra:AZOBR_RS29985 Length = 584 Score = 221 bits (563), Expect = 6e-62 Identities = 174/552 (31%), Positives = 256/552 (46%), Gaps = 29/552 (5%) Query: 23 MLIESLKKEKVEMIFGYPGGAVLPIYDKLYN--SGLVHILPRHEQGAIHAAEGYARVSGK 80 +L++ L V+ IFG PG + I + L + I RHE+ A AA GYA+ +G+ Sbjct: 8 ILVDVLVDWGVDTIFGMPGDGINGIVEALRRRQDEIRFIQVRHEEAAAFAACGYAKFTGR 67 Query: 81 PGVVIATSGPGATNLVTGLADAMIDSLPLVVFTGQVATSVIGSDAFQEADILGITMPVTK 140 GV IATSGPG +L+ GL DA +D P++ TG ++G+ Q+ ++ + V Sbjct: 68 LGVCIATSGPGGLHLLNGLYDAKLDHQPVLAITGLQYHDLVGTYTQQDVELDKVFQDVAL 127 Query: 141 HSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEFSYDHEMNLPGYQPTT 200 ++ +V + I A A R G I IP D+ N+ G+ Sbjct: 128 YNQRVMGAAHVRNIANLACRTALAHR-GVSHITIPVDLQEQGIGADMRAPRNVKGHNTAL 186 Query: 201 ------EPNYLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQQQIPVAHTLLG 254 P+ Q R+ VE + + K+ VILAG G L KA+++L+ A++ + LLG Sbjct: 187 FAPQLPVPSEAQTRRAVEILDAGKRVVILAGQGAL--KATDQLERLADKLGAVIVKALLG 244 Query: 255 LGGFPADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTGNLKHFAR--NAKIA 312 P D P G G+ GT + AL CD L+ G+ F ++++ + A+ Sbjct: 245 KAAVPDDSPFTTGQVGLLGTAPSQEALETCDTLLIAGSTFP-----YIEYYPKPGQARAI 299 Query: 313 HIDIDPAEIGKIMKTQIPVVGDSKIVLQELIKQDGKQSDSSEWKKQLAEWKEEYPLWYVD 372 IDID A IG + +VGD + L L ++ + D S K A E W Sbjct: 300 QIDIDAARIGLRYPVEAGLVGDCGLALDILTERVRRHEDRSFLKTAQAGKAE----WMKL 355 Query: 373 NEEEG------FKPQKLIEYIHQFTKGEAIVATDVGQHQMWSAQFYPFQKADKWVTSGGL 426 EE G KPQ + + + AIVA D G W A+ P ++ SG L Sbjct: 356 MEERGTRPDLPMKPQVVAWELGKRLSDTAIVACDSGTIATWWARQIPARRGQMHSLSGNL 415 Query: 427 GTMGFGLPAAIGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELNLPVKVVILNNACLGM 486 TM G+P AI AQLA VVA VGDGGF M + + + LP+KV+I NN LG Sbjct: 416 ATMAPGVPYAIAAQLAHPGRQVVAYVGDGGFSMLMADFATAVKYKLPIKVIISNNNSLGQ 475 Query: 487 VRQWQEIFYEERYSESKFASQPDFVKLSEAYGIKGIRISSEAEAKEKLEEALTSREPVVI 546 ++ W++I DF K++EA G +G I+ + L+ AL PVV+ Sbjct: 476 IK-WEQIAMLGNPEYVCDLQPIDFAKVAEACGGRGFTITDPKDCGATLDAALAHPGPVVV 534 Query: 547 DVRVASEEKVFP 558 D V + E P Sbjct: 535 DCLVDTNEPPMP 546 Lambda K H 0.317 0.135 0.391 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: 810 Number of extensions: 46 Number of successful extensions: 7 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: 574 Length of database: 584 Length adjustment: 36 Effective length of query: 538 Effective length of database: 548 Effective search space: 294824 Effective search space used: 294824 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