Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_012850832.1 TCUR_RS02195 acetolactate synthase
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000024385.1:WP_012850832.1 Length = 534 Score = 241 bits (614), Expect = 8e-68 Identities = 194/551 (35%), Positives = 265/551 (48%), Gaps = 38/551 (6%) Query: 20 TISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAAD 79 T++G AL+ AL HGVDTIFG PG L Y A+ ++HI RHEQ +AAD Sbjct: 3 TMTGGEALIAALAAHGVDTIFGIPGTHNLSAYAAM----KRHGIRHISPRHEQGAGYAAD 58 Query: 80 AYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVP--RPAIGTDAFQET- 136 YAR++G+ GVC T+GP N + A DSVP++ ++ +P P G E Sbjct: 59 GYARSSGRPGVCLTTTGPAILNAASAALQAYSDSVPVLFVSPGMPLRHPGRGNGLLHEVK 118 Query: 137 DIFGITLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVPVE 196 D G I+ S V A++ VAQA+ GRP PV ++IP D+ +E+ V+ Sbjct: 119 DQSGAMAAILGRSHRVTSVAEIPLAVAQAWTDLTGGRPRPVHLEIPLDLLEERAEVTVVD 178 Query: 197 PGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQLP 256 P +P P P A AAA A+RP+L VGGGA A A + LAE P Sbjct: 179 P---VPATTCTPAPESVTAGAAAC---AGARRPVLVVGGGARRAGAE--VIALAEAVGAP 230 Query: 257 VTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARF--DDRVTGKLDTF 314 + T GKG E+ L VG H + + DL+IAVG F D G D Sbjct: 231 ILATSNGKGIVPEDHPLFVGAGLQHRCVLD--LMDDSDLVIAVGTEFAPSDWWIGLPDL- 287 Query: 315 APRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERINTW 374 +V+ ++DPA I N V V+GD ++L R + L R P A +R W Sbjct: 288 --SGKVLRIDVDPAGIVTNVVPAVPVVGDAAVAL-RALRAELDR---PAPAGAAQRAAQW 341 Query: 375 KDRYPLTIPPAEGAIYPQEVLLAVRDLAPDAIVTTDVGQHQMWAAQHLRN----GPRGWI 430 +DR+ AEG + V L DAIV D + A L N P ++ Sbjct: 342 RDRHRQAAR-AEGEPWLPIVSAIAEALPRDAIVAADSAMACYYGA--LSNLPLHRPGAFL 398 Query: 431 SSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNN 490 G GT+GFG+PA +GA++A PD V+ + GD + + EL A G+ + VV+V+N Sbjct: 399 YPTGAGTLGFGLPAGIGAKIADPDAAVLVLQGDGGTMFTVAELAAAAELGIALPVVVVDN 458 Query: 491 HWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAALQS 550 G +R D + G PDF ALARS G GV+ D L + AAL++ Sbjct: 459 GGYGEIR---NEMADRGEPVHAVALGRPDFPALARSLGCHGVRAADPAELTGAVKAALEA 515 Query: 551 PTPTMIDVHVR 561 PT+I HVR Sbjct: 516 DRPTLI--HVR 524 Lambda K H 0.320 0.136 0.414 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: 1001 Number of extensions: 66 Number of successful extensions: 8 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: 617 Length of database: 534 Length adjustment: 36 Effective length of query: 581 Effective length of database: 498 Effective search space: 289338 Effective search space used: 289338 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