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 AO353_24845 AO353_24845 decarboxylase
Query= curated2:P08142 (562 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24845 Length = 535 Score = 238 bits (608), Expect = 3e-67 Identities = 166/535 (31%), Positives = 255/535 (47%), Gaps = 20/535 (3%) Query: 14 TGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQGMART 73 TG + +V L G+ V GIPG L +Y L S IRH+L RHEQGA F+A G AR Sbjct: 7 TGGQALVRLLANYGVDTVFGIPGVHTLELYRGLPGSG-IRHVLTRHEQGASFMADGYARV 65 Query: 74 DGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTD---AFQEVDTYGI 130 GKP VC +GPG TN T I A DSIP++ I+ + +G + D + Sbjct: 66 SGKPGVCFIITGPGVTNAATGIGQAYADSIPMLVISSVNHTASLGKGWGCLHETQDQRAM 125 Query: 131 SIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFEIETQPAMAEK 190 + PIT + + E+LP++++ A+ + S RP PV I +P DV +A + + + Sbjct: 126 TAPITAFSAVALSTEDLPELIARAYAVFDSERPRPVHISVPLDVLSAQVTRDWSHEVVRR 185 Query: 191 AAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPTTMTLMALGML 250 + ++ A A + AKRP++ GGG +NA ++ L+ + +P ++ G+L Sbjct: 186 PGRGVPAATALEQAVAKLQTAKRPMIIAGGGALNAAQELQSLSTRLAVPFFTSVAGKGLL 245 Query: 251 PKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPNAKIIHVDIDR 310 P PL+ G V ++ EAD+++ +G D + E+ A+++ VDID Sbjct: 246 PPDAPLNAG--STLCVEPGWQLIAEADVVLAVGTEMADTDFWR-ERLPLKAELLRVDIDP 302 Query: 311 AELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRAEWHQL--VADLQREFPCPIPKACDPL 368 + VA+ D LA L+ + R + VA L+ + PL Sbjct: 303 RKFNDFYPCAVALHGDAQQTLAALLERLSPATRDASAPIAAVAALRE----AVKAGHGPL 358 Query: 369 S--HYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMGFGLPAA 426 H ++ +AA + DNA I+TD+ Q A+ PR WL G GT+G+GLPA Sbjct: 359 QSIHQAILERIAAELPDNAFISTDMTQLAYTGNYAFNSLAPRSWLHPTGYGTLGYGLPAG 418 Query: 427 IGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLD--VKIILMNNEALGLVHQQQSLF 484 IGA P R L GDG + QE+ATA E +LD + ++L NN+ALG + Sbjct: 419 IGAKFGAPQRPGLVLVGDGGFLYTAQELATAVE-ELDSPLVVLLWNNDALGQIRDDMLGL 477 Query: 485 YEQGVFAATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVR 539 + + P +F + FG + A+ Q L+ R G LI ++ Sbjct: 478 DIEPI--GVLPRNPDFAALGRAFGCSVSQPQSLAELQTDLRHGFKRNGVTLIELK 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: 803 Number of extensions: 40 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: 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