Align Probable acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_092998117.1 BLP65_RS13155 acetolactate synthase large subunit
Query= curated2:O08353 (599 letters) >NCBI__GCF_900102855.1:WP_092998117.1 Length = 545 Score = 321 bits (823), Expect = 4e-92 Identities = 200/555 (36%), Positives = 305/555 (54%), Gaps = 31/555 (5%) Query: 1 MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60 M AE K LE E +E +FG PG L DAL S + + RHEQ AA AD Y R Sbjct: 1 MKTAEFFAKCLENEGIEYIFGIPGEENLDLMDALLDSPIRFITVRHEQGAAFMADVYGRL 60 Query: 61 SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120 +G GVC+ T GPGATNL+TGVA A+ D +P+VA+ GQ T + ++ Q +D +F P Sbjct: 61 TGHAGVCLSTLGPGATNLITGVADANMDHAPVVAIAGQADTTRLHKESHQVLDLEAMFAP 120 Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180 K++ ++ E+ R AF++AQT + G I+ P+++ +E++ D+ P VK Sbjct: 121 FTKYSTRLVSPEITSEVVRKAFKLAQTDKTGATFIEFPENIARMEVEDDR---PLMVK-- 175 Query: 181 GYNPTTIGHPR--QIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTL 238 NP ++ P ++++A +LI+ A++PIILAG GV+ + A ++L L E LNIPV T Sbjct: 176 --NP-SLPEPAVDRVERASQLISDARQPIILAGNGVVRAKAWKQLADLSERLNIPVANTF 232 Query: 239 MGKGCIS-ENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKI 297 M KG + +PLALG VG+ + ++DV+I IG + + + + I Sbjct: 233 MAKGVVPFARNPLALGSVGLQSRDYVSCGFDQADVIICIGYDLVE-YHPHLWHPSRDRTI 291 Query: 298 IHIDIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVN 357 IH+D PAE+ + V+V +VGD K L + + + D +E ++ Sbjct: 292 IHVDTTPAEVDAHYPVEVGVVGDIKHSLLRIAALATPHQGRSLRALRD-----ALVEEMD 346 Query: 358 SLKKSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQT 417 + K D D+ P+KPQKI+ +L +D I DVG ++MWMA F+ + Sbjct: 347 ACK-------DDDEFPVKPQKIIWDLRTAMD-----LKDIAICDVGAHKMWMARMFRCEV 394 Query: 418 PRSFLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVI 477 P + L S G MG P AI AK+A PD K++ +TGD G +MN QEL T +P+V+ Sbjct: 395 PNTCLISNGFAAMGIALPGAIAAKLAFPDRKIVAVTGDAGILMNIQELETAVRLKLPLVV 454 Query: 478 CIFDNRTLGMVYQWQNLFYGKRQCSVNFGGAPDFIKLAESYGIKARRIESPNEINEALKE 537 I+++ G++ +W+ L R V+F PDFIKLAES+G K RIE +++ L++ Sbjct: 455 LIWNDDGYGLI-KWKQLNQFGRPSHVDFTN-PDFIKLAESFGAKGYRIERVSDLLPTLEK 512 Query: 538 AINCDEPYLLDFAID 552 A+ D ++D +D Sbjct: 513 ALADDAVTIIDCPVD 527 Lambda K H 0.319 0.137 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: 705 Number of extensions: 32 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: 599 Length of database: 545 Length adjustment: 36 Effective length of query: 563 Effective length of database: 509 Effective search space: 286567 Effective search space used: 286567 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 (21.7 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