Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS; Vegetative protein 105; VEG105 (uncharacterized)
to candidate WP_004305660.1 C665_RS08765 thiamine pyrophosphate-binding protein
Query= curated2:P37251 (574 letters) >NCBI__GCF_000310185.1:WP_004305660.1 Length = 607 Score = 270 bits (690), Expect = 1e-76 Identities = 194/573 (33%), Positives = 280/573 (48%), Gaps = 40/573 (6%) Query: 17 TMSGALMLIESLKKEKVEMIFGYPGGAVLPIYDKLYNSGLVHILP-RHEQGAIHAAEGYA 75 T+ A L+ L E + IF PGG + + D L V+ +P HEQ A AAE Sbjct: 2 TIRVADWLLARLADEGIHHIFMLPGGGAMYLNDALACEPRVNAVPCHHEQAAAIAAEAAG 61 Query: 76 RV--SGKPG--VVIATSGPGATNLVTGLADAMIDSLPLVVFTGQ------VATSVIGSDA 125 R +G PG V + T+GPGATN +T +A A IDS+P++V +GQ + I Sbjct: 62 RTGNAGNPGFGVAMVTTGPGATNAITPVAGAWIDSVPMLVLSGQAKRPDRLGGRPIRQGG 121 Query: 126 FQEADILGITMPVTKHSYQVRQPEDLPRIIKEAFHIATTGRPGPVLIDIPKDVATIEGEF 185 QE DI+ I P+TK++ + P+ + +++A H+ TGRPGPV ID+P DV + Sbjct: 122 VQEVDIVPIVSPITKYAVTLDDPQSVRVHLEKALHLMKTGRPGPVWIDVPLDVQAAPID- 180 Query: 186 SYDHEMNLPGYQPTTEPN--YLQIRKLVEAVSSAKKPVILAGAGVLHGKASEELKNYAEQ 243 LPG+ P + + ++ ++ AK+P+ILAG GV A++ + + Sbjct: 181 ----PATLPGWTPPADATAPMPDLTPVLTMLAEAKRPLILAGHGVRLAGAADAFRQLVDH 236 Query: 244 QQIPVAHTLLGLGGFPADHPLFLGMAGMHGTYTANMALHECDLLISIGARFDDRVTG-NL 302 Q+P T L P DHPL +G G+ AN A+ CDLLISIGAR D VT N Sbjct: 237 LQVPAVLTWNALDLLPYDHPLNIGRPGVVAARAANFAVQNCDLLISIGARLDMIVTAYNP 296 Query: 303 KHFARNAKIAHIDIDPAEIG--KIMKTQIPVVGDSKIVLQELIKQDGKQSDSSEWKKQLA 360 K FAR A +D+D E+ M P+ D+ +Q L+ D+++W+ + Sbjct: 297 KGFARAALKVVVDVDANELADKTAMAIDQPLAMDAGDFIQTLLAA-AIPGDTTDWRARCT 355 Query: 361 EWKEEYPLWYVDNEEEGFKPQ------KLIEYIHQFTKGEAIVATDVGQHQMWSAQFYP- 413 WK Y NE F P +E + + ++AT G + FY Sbjct: 356 RWKAR----YTQNEGRVFPPSGPIGHAHFVEALSDAAPADTLIAT--GSSGLAVEFFYAG 409 Query: 414 --FQKADKWVTSGGLGTMGFGLPAAIGAQLAEKDATVVAVVGDGGFQMTLQELDVIRELN 471 ++ + + GLG MG+GLPAAIGA L ++AV DG Q+ LQEL + L Sbjct: 410 FRNKRGQRTFLTSGLGAMGYGLPAAIGACLGNDRKPMLAVESDGSLQLNLQELATLTGLQ 469 Query: 472 LPVKVVILNNACLGMVRQWQEIFYEERYSESKFAS---QPDFVKLSEAYGIKGIRISSEA 528 LP+ + I+NN +R Q ++ RY S AS PD KL+ YG+ +RI A Sbjct: 470 LPICLFIMNNGGYASIRNTQRNYFNGRYVGSGPASGLFMPDLEKLAAVYGLPYLRIDDCA 529 Query: 529 EAKEKLEEALTSREPVVIDVRVASEEKVFPMVA 561 E L A P +IDVR+ EE + P A Sbjct: 530 ELAAALARAQALPRPCLIDVRLIPEESLQPKCA 562 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: 862 Number of extensions: 45 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: 607 Length adjustment: 37 Effective length of query: 537 Effective length of database: 570 Effective search space: 306090 Effective search space used: 306090 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 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