Align Acetolactate synthase isozyme 1 large subunit; AHAS-I; EC 2.2.1.6; Acetohydroxy-acid synthase I large subunit; ALS-I (uncharacterized)
to candidate PfGW456L13_3207 Acetolactate synthase large subunit (EC 2.2.1.6)
Query= curated2:P08142 (562 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3207 Length = 535 Score = 244 bits (622), Expect = 8e-69 Identities = 169/538 (31%), Positives = 263/538 (48%), Gaps = 20/538 (3%) Query: 11 KRFTGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQGM 70 K TG + +V L G+ V GIPG L +Y L S IRH+L RHEQGA F+A G Sbjct: 4 KTLTGGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGASFMADGY 62 Query: 71 ARTDGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGT---DAFQEVDT 127 AR GKP VC +GPG TN T I A DSIP++ I+ ++ +G + D Sbjct: 63 ARVSGKPGVCFVITGPGVTNAATGIGQAYADSIPMLVISSVNHSASLGKGWGSLHECQDQ 122 Query: 128 YGISIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFEIETQPAM 187 ++ PIT + + E+LP++++ A+ + S RP PV I +P DV +A + + Sbjct: 123 RAMTAPITAFSAVALTAEDLPELIARAYAVFDSERPRPVHISVPLDVLSAPIARDWSNEV 182 Query: 188 AEKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPTTMTLMAL 247 + S +I A A +NAAKRP++ GGG +NA + ++E++ + P ++ Sbjct: 183 VRRPGRGPASTTAIDQAVAKLNAAKRPMIIAGGGALNATSELQEVSTRLAAPLFTSVAGK 242 Query: 248 GMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPNAKIIHVD 307 G+LP PL+ G V ++ EAD+++ +G D + E+ N +++ VD Sbjct: 243 GLLPPDAPLNAG--SSLCVEPGWNLIAEADVVLAVGTEMADTDFWR-ERLPLNGELLRVD 299 Query: 308 IDRAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRAEWHQL--VADLQREFPCPIPKAC 365 ID + VA+ D L+ L+ + R + VA L++ + + Sbjct: 300 IDPRKFNDFYPCAVALHGDAQQTLSGLLERLPTDVREASAAIASVAALRK----AVKASH 355 Query: 366 DPLS--HYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMGFGL 423 PL H +++ +AA + DNA I+TD+ Q A+ R WL G GT+G+GL Sbjct: 356 GPLQSIHQSILDRIAAELPDNAFISTDMTQLAYTGNYAFDSLAIRSWLHPTGYGTLGYGL 415 Query: 424 PAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLD--VKIILMNNEALGLVHQQQ 481 PA IGA P R L GDG + QE+AT+ E +LD + ++L NN+ALG + Sbjct: 416 PAGIGAKFGAPQRPGLVLVGDGGFLYTAQELATSVE-ELDSPLVVLLWNNDALGQIRDDM 474 Query: 482 SLFYEQGVFAATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVR 539 + + P +F +A FG + A+ Q L+ R G LI ++ Sbjct: 475 LGLDIEPI--GVLPRNPDFAALARAFGCTVTQPQSLAELQTDLRHGFKRNGVTLIELK 530 Lambda K H 0.320 0.135 0.400 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: 793 Number of extensions: 38 Number of successful extensions: 4 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: 562 Length of database: 535 Length adjustment: 36 Effective length of query: 526 Effective length of database: 499 Effective search space: 262474 Effective search space used: 262474 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 09 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