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_085635546.1 MGEO_RS04765 thiamine pyrophosphate-binding protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_002115805.1:WP_085635546.1 Length = 550 Score = 264 bits (675), Expect = 6e-75 Identities = 164/535 (30%), Positives = 262/535 (48%), Gaps = 13/535 (2%) Query: 1 MNGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALY--DGGVEHLLCRHEQGAAMAAIGYA 58 + A +V L AQG FG PG + +PV DA Y + + + CR E GAAM A Y Sbjct: 8 IRAADLLVDQLVAQGTTAAFGVPGESYLPVLDAFYGRESDIRFVTCRQEGGAAMMADAYG 67 Query: 59 RATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLS 118 + TG+ G+C AT GPGATN G+ A DS P++ GQV+ + +AFQE+D + Sbjct: 68 KLTGRPGICFATRGPGATNASAGVHVAFQDSTPMILFLGQVARDMLDREAFQEIDYRRMF 127 Query: 119 LACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENE 178 K + L ++ AF A SGRPGPV++ +P+D+ VE Sbjct: 128 GQMAKWVAQIDDASRLQEYVSRAFRTAMSGRPGPVVLALPEDMLYDEIPRPKPPARVETP 187 Query: 179 VTFP-HAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAV 237 P HA + R +A+A+ P++ GGG ++ + AL+ F +P + +L+ G + Sbjct: 188 RFGPGHAALNAIRDRIAQAKSPLVMAGGGGWTSKGIAALQTFAETQGLPVSVSLRCQGLM 247 Query: 238 EADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVT---GKLNTFAPHASVIHMD 294 + +P Y+G G+ + E DL IA+G R + T L+ P+ S+IH+ Sbjct: 248 DNRHPNYIGHYGVGTPPYLKDIMAETDLFIAIGPRLGEMTTAGYSLLSPPVPNLSLIHVF 307 Query: 295 IDPAEMNKLRQAHVALQGDLNALLPALQ--QPLNQYDWQQHCAQLRDEHSWRYDHPGDAI 352 +P E+ ++ + +A+ D + A+ +P+ + +LR ++ + P Sbjct: 308 PEPEELGRVFEPEIAVAADTESFCEAVADWEPITPGTFTDRTTELRKQYE-TFSDPASVS 366 Query: 353 YAPL--LLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGLGTMGFGLPAA 410 PL L L+ P + +V G + W + + P + + + G+MG+GLPAA Sbjct: 367 GDPLAPLFAHLAGVLPENAIVCNGAGNYAAWLHRFYCYRAPGSQLAPTS-GSMGYGLPAA 425 Query: 411 VGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQ 470 +GA + P+ + I+GDG FMM QE+ T L L +++++N R G +R Q+ + Sbjct: 426 IGAAICEPDREIFAIAGDGCFMMTCQEMATAAHHGLNLTVIIINNARYGTIRAHQEREYP 485 Query: 471 ERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525 +R S T LT NPDF A +FG H + D+ A L G L+ V D Sbjct: 486 DRVSGTALT-NPDFCDFARSFGAHAERAGDIDRFAAVLAAARERGGLNLIEVPAD 539 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: 736 Number of extensions: 34 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: 548 Length of database: 550 Length adjustment: 36 Effective length of query: 512 Effective length of database: 514 Effective search space: 263168 Effective search space used: 263168 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 Jul 26 2024. The underlying query database was built on Jul 25 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