Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate WP_092057383.1 BQ4888_RS11415 thiamine pyrophosphate-binding protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_900111775.1:WP_092057383.1 Length = 603 Score = 221 bits (562), Expect = 8e-62 Identities = 174/565 (30%), Positives = 269/565 (47%), Gaps = 56/565 (9%) Query: 7 VVHALRAQGVNTVFGYPGGAIMPVYDALYD----GGVEHLLCRHEQGAAMAAIGYARATG 62 +V L ++ VFG PGGAI P Y+AL GG+ ++ RHE GAA A GYAR TG Sbjct: 27 IVSYLEELHIDYVFGVPGGAIEPFYNALARSARRGGIRPVVARHESGAAFMADGYARETG 86 Query: 63 KTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQE-----VDVLGL 117 K GVC AT+GPGATNLITG+A A +DS+P++ IT Q S P G A Q+ VD +G+ Sbjct: 87 KLGVCCATTGPGATNLITGVASAFMDSVPLLVITAQTSLPQFGKRALQDSSCTAVDTVGM 146 Query: 118 SLACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDI-----QLASGDLEPWF 172 CT+++ L+ +L + A A G GP + IP DI ++ +G P Sbjct: 147 FRHCTRYNTLISHRGQLEGKLVAAIMAAHRG-SGPAHISIPSDILREPRRIRNGADRPVA 205 Query: 173 ---TTVENEVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATC 229 T + VE+ RQ L KA+K ++ +GG G A+ E LA T+ Sbjct: 206 GDETLRQKFSLIDPTAVEKLRQALEKAKKMVIVIGGACG-----EAMDEILAFTENTGAL 260 Query: 230 TL---KGLGAVEADYPYYLGMLGMHGTKAANFAV--QECDLLIAVGARFDDR-VTGKLNT 283 + +G G ++ +P Y G+ G G ++A A+ +E DL++AV R + + G Sbjct: 261 LISGPEGKGWIDPWHPQYRGVYGFAGHESARQALFDEEVDLVLAVNTRLGEMLLCGGEEK 320 Query: 284 FAPHASVIHMDIDPAEMNKLRQAHVALQGDLNALLPALQQPLNQYDWQQHCA-------- 335 + ++H+D + A + + G A+ +L + L Q Sbjct: 321 RLLNDKLVHIDGVAEHFTRSPMARLHVCGQPRAVFESLNRSLRQVRRAAESTTSLKSGPT 380 Query: 336 --------QLRDEHSW-RYDHPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHI 386 + D +W D P + ++ +L+ R P + D G WA ++ Sbjct: 381 IAGIPPHLTIEDGSTWLAADGP---LKPQRVMVELAVRFPENSRFLVDAGNSWAWATHYL 437 Query: 387 AHTRPENFITSSGLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQL 446 + + G G+M + + AA+G + P + VVC++GDGSF+M+ QEL ++L Sbjct: 438 HPKSAGRYRIAMGFGSMTWAIGAAIGTALGCPGNPVVCLTGDGSFLMSGQELSVAVTEKL 497 Query: 447 PLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTDNP--DFLMLASAFGIHGQHITRKDQV 504 P+ VLL+++ LGMV+ Q+L E + P DF +A A G I D + Sbjct: 498 PVIFVLLNDRALGMVKHGQRL----GGGEAIAFELPPVDFCGIARAMGARACRIASLDDL 553 Query: 505 EAA-LDTMLNSDGPYLLHVSIDELE 528 + + + GP LL + ID E Sbjct: 554 NRLDVAEICAAPGPTLLEIHIDPEE 578 Lambda K H 0.320 0.135 0.410 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: 814 Number of extensions: 32 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 548 Length of database: 603 Length adjustment: 36 Effective length of query: 512 Effective length of database: 567 Effective search space: 290304 Effective search space used: 290304 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