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_013417759.1 RVAN_RS00315 thiamine pyrophosphate TPP-binding domain-containing protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000166055.1:WP_013417759.1 Length = 558 Score = 248 bits (632), Expect = 6e-70 Identities = 167/538 (31%), Positives = 258/538 (47%), Gaps = 21/538 (3%) Query: 2 NGAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDG--GVEHLLCRHEQGAAMAAIGYAR 59 +G Q + LR G +FG PG + + V DALYD + +++CR E GAAM A Y + Sbjct: 7 SGGQILADQLRLHGARMIFGVPGESYLAVLDALYDHERDMPYIVCRQEGGAAMMAEAYGK 66 Query: 60 ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSL 119 TG+ G+C+ T GPGATN GL A DS P++ I GQV +AFQE+D + Sbjct: 67 LTGEPGICMVTRGPGATNASAGLHVARQDSTPLILIVGQVGRSMRDREAFQEIDFRRMFG 126 Query: 120 ACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEV 179 +K ++ +P +A AF A SGRPGPV++ +P+D+ + E Sbjct: 127 EVSKWVAEIEEAARIPEYVARAFATATSGRPGPVVLAVPEDVLRERATVADAVPYSRVEA 186 Query: 180 TFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEA 239 A + + R+ LA A++P++ VGGG ++ F + +P + + + Sbjct: 187 APARARMAEFRKRLAAAERPLMIVGGGGWDKDVALKVKAFAEHSGLPVAASFRRQSYFDN 246 Query: 240 DYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNTF---APHASVIHMDID 296 P Y+G LG+ A + E DL+IA G R + + F P IH+ Sbjct: 247 TSPCYVGDLGISLNPALKRRIDESDLIIAFGPRLGEMPSQGYTLFDIPKPKQPFIHIHAG 306 Query: 297 PAEMNKLRQAHVALQGDLNALLPALQ--QPLNQYDWQQHCAQLR-DEHSWRYDH--PGDA 351 E+ ++ QA +A+ +A AL+ +PL+ W R D +W PG A Sbjct: 307 AEELGRVYQADLAINAGPHAFADALEDMKPLDGSAWGAWRESARGDYEAWIAPEKTPG-A 365 Query: 352 IYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSSGL----GTMGFGL 407 + ++ L + P + ++ G W H +T E +GL G+MG+G+ Sbjct: 366 LQLAEVVAYLRETLPGNAIIANGAGNFAAWV--HRFYTYRE---CGTGLAPISGSMGYGV 420 Query: 408 PAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQL 467 PA V A++ P TVV +GDG F+M QE T + P+ ++++N G +R Q+ Sbjct: 421 PAGVAAKLVHPGRTVVTFAGDGDFLMTGQEFATAVQHGAPVIFIVVNNGMYGTIRMHQER 480 Query: 468 FFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525 + R S T+L NPDF A AFG HG + R + AA + S P +L + ID Sbjct: 481 HYPGRVSGTSLR-NPDFAAYARAFGGHGALVERTEDFPAAFEEARASGLPSILELRID 537 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: 733 Number of extensions: 35 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: 558 Length adjustment: 36 Effective length of query: 512 Effective length of database: 522 Effective search space: 267264 Effective search space used: 267264 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