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_011913261.1 PST_RS10765 thiamine pyrophosphate-requiring protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000013785.1:WP_011913261.1 Length = 600 Score = 183 bits (465), Expect = 1e-50 Identities = 167/565 (29%), Positives = 253/565 (44%), Gaps = 43/565 (7%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGG--VEHLLCRHEQGAAMAAIGYA 58 M ++V L GV ++GYPG I V AL G + + RHE+ AA A A Sbjct: 4 MTVGDYLVERLYQWGVRRIYGYPGDGINGVLGALNRAGGKIRFIQARHEEMAAFMASADA 63 Query: 59 RATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLS 118 + G GVC++TSGPGA++L+TGL DA LD +PV+AI GQ + +G QE+D+ + Sbjct: 64 KFGGGLGVCLSTSGPGASHLLTGLYDARLDHVPVLAIAGQQARTALGAHYQQEIDLPAMF 123 Query: 119 LACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLA--------SGDLEP 170 S R + + + G + +P D+Q A G + Sbjct: 124 KDVAGAFVQQASAPAQVRHLVDRAIRSAIGERKVAAIILPNDLQEAPYSEPPRTHGAVLS 183 Query: 171 WFTTVENEVTFPHAEVEQARQMLAKAQKPMLYVGGGVGMA-QAVPALREFLAATKMPATC 229 ++ A++++A ++L K + VG G A V A+ E L A A Sbjct: 184 GIGYSRPKIVPYDADLQRAAEVLNAGSKVAILVGAGALQATDEVIAVAETLGAGVAKA-- 241 Query: 230 TLKGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTFAP--- 286 L G AV D P+ G +G+ GT+ + + ECD L+ +G+ F + F P Sbjct: 242 -LLGKAAVPDDLPWVTGAIGLLGTEPSYKLMNECDTLLMIGSGF------PYSEFLPEEG 294 Query: 287 HASVIHMDIDPAEMNKLRQAHVALQGD----LNALLPALQQPLNQYDWQQHCAQLRDEHS 342 A + +D+ P ++ V L G+ L ALLP L++ ++ WQQ R + Sbjct: 295 QARGVQIDLKPDMLSIRYPMEVNLHGEAGETLRALLPLLEKKSDR-SWQQQVEAWRADWD 353 Query: 343 WRYDHPGDAIYAPL----LLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSS 398 + A P+ + +LS R P ++T+D G W A+ I R S Sbjct: 354 RTLEERAMAAADPINPQRVAWELSPRLPERAIITSDSGSCANWYARDIRMRRGMMGSLSG 413 Query: 399 GLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMM-NVQELGTVKR-----KQLPLKIVL 452 GL +MG +P A+ A+ A P+ VV + GDG+ M N+ EL TV + + + Sbjct: 414 GLASMGAAVPYAIAAKFAHPDRPVVALVGDGAMQMNNMAELITVAKYWSQWQNHQWICCV 473 Query: 453 LDNQRLGMVRQWQQLFFQERYSETTLTDNPD--FLMLASAFGIHGQHITRKDQVEAALDT 510 +NQ L V W+Q + + PD + A G+ G R+DQV AA + Sbjct: 474 FNNQDLNQV-TWEQRVMEGDPKFEASQNLPDVPYHRFAELIGLQGIFCDREDQVAAAWEQ 532 Query: 511 MLNSDGPYLLHVSIDELENVWPLVP 535 L +D P LL D NV PL P Sbjct: 533 ALAADRPVLLEFRTD--PNVPPLPP 555 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: 777 Number of extensions: 36 Number of successful extensions: 5 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: 548 Length of database: 600 Length adjustment: 36 Effective length of query: 512 Effective length of database: 564 Effective search space: 288768 Effective search space used: 288768 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