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_041377194.1 PNAP_RS11090 thiamine pyrophosphate-binding protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000015505.1:WP_041377194.1 Length = 564 Score = 235 bits (599), Expect = 4e-66 Identities = 162/537 (30%), Positives = 254/537 (47%), Gaps = 22/537 (4%) Query: 7 VVHALRAQGVNTVFGYPGGAIMPVYDALYD--GGVEHLLCRHEQGAAMAAIGYARATGKT 64 +V L AQGV FG PG + + V D L+ + + CR E GAA A + + TG+ Sbjct: 10 LVDCLLAQGVTHAFGVPGESYLAVLDGLHARRDQIRFITCRQEGGAAFMAEAHGKLTGRP 69 Query: 65 GVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGL----SLA 120 GVC+ T GPGATN G+ A DS P+V + G V++ +AFQEVD + Sbjct: 70 GVCMVTRGPGATNASIGVHTAFQDSTPMVLLVGDVASDCRDREAFQEVDYSSFFGPSTKG 129 Query: 121 CTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVT 180 K + + +P +A AF A +GRPGPV++ +P+D+ P + Sbjct: 130 FAKRVERIDDADRIPEYVARAFATAMNGRPGPVVLVLPEDMLTRMTAARPLPRVEAVQAW 189 Query: 181 FPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEAD 240 + R+ML +++P++ GGG Q+ AL+ F K+P + + Sbjct: 190 SDPGALRTLREMLLASKQPLIIAGGGGWTPQSAQALQRFAENWKLPVGNAFRFQDTFDNH 249 Query: 241 YPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGK---LNTFAPHASVIHMDIDP 297 +P Y G +G+ + V+ DL+IA+G R + TG + P ++H+ Sbjct: 250 HPLYAGDVGIGLSPKLAARVKASDLIIAIGPRLGEMTTGNYTLIEAPRPKQKLVHIHASA 309 Query: 298 AEMNKLRQAHVALQGDLNAL---LPALQQPLNQYDWQQHCAQLRDEHSWR---YDHPGDA 351 E+N++ QA +A+ +NA L L P++ W+ A +++ PGD Sbjct: 310 EELNRVFQADLAINATMNAAARSLEVLSAPVS-VPWEAWTASANEDYLANLVPQALPGD- 367 Query: 352 IYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAH---TRPENFITSSGLGTMGFGLP 408 + P ++ L PAD V+T G W + H + + +G MG+G+P Sbjct: 368 VDMPAIVGLLQRYLPADAVLTNGAGNFASWIHRFFKHHGLAKGHKTQLAPTVGAMGYGVP 427 Query: 409 AAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLF 468 A + A + I+GDG F+MN QEL T + IVLL+N G +R Q+ Sbjct: 428 AGIAAAIT-TGRVAFTIAGDGDFLMNGQELATAVQHGAKSIIVLLNNGMYGTIRMHQEKQ 486 Query: 469 FQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525 + + S + L +NPDF LA A+G G ITR D+ EA L L+ L+ V++D Sbjct: 487 YPQHESGSRL-NNPDFAALARAYGYAGVRITRTDEFEAELLAALDRSEGTLIEVTLD 542 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: 746 Number of extensions: 49 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: 548 Length of database: 564 Length adjustment: 36 Effective length of query: 512 Effective length of database: 528 Effective search space: 270336 Effective search space used: 270336 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