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 YP_001325873.1 Smed_0179 hypothetical protein
Query= curated2:P08142 (562 letters) >NCBI__GCF_000017145.1:YP_001325873.1 Length = 537 Score = 248 bits (634), Expect = 3e-70 Identities = 174/535 (32%), Positives = 272/535 (50%), Gaps = 24/535 (4%) Query: 14 TGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQGMART 73 T E +V LE G+++V GIPG + +Y LS S +IRH+ RHEQGAGF+A G AR Sbjct: 7 TVGETLVDLLEANGVEVVFGIPGVHTVELYRGLSAS-KIRHVTPRHEQGAGFMADGYARV 65 Query: 74 DGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTD---AFQEVDTYGI 130 GKP V + +GPG TN +TA+A AR DSIP++ I+G +G + D +G+ Sbjct: 66 SGKPGVALVITGPGLTNTITAMAQARQDSIPMLVISGVNRRDSLGHGQGLLHELPDQHGM 125 Query: 131 SIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFEIETQPAMAEK 190 + +++ + + +LP V+ AF + SGRPGPV I+IP DV IE +P+ Sbjct: 126 IKTLALYSHTLLNPADLPLVVDRAFAVLLSGRPGPVHIEIPTDVM--ALRIEDRPSAPAT 183 Query: 191 AAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPTTMTLMALGML 250 A P E+++ AA + A RPV+ GGG + A A VRELAE+ P T+ A G+L Sbjct: 184 ATRPRSDSETLQRAAILCAEAARPVIVCGGGALTAEAEVRELAERIGAPVVTTVNARGIL 243 Query: 251 PKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARF--DDRAIGKTEQFCPNAKIIHVDI 308 HPL + +++ +L+EADL++ LG D + F P ++ DI Sbjct: 244 -AGHPLRVP--ASPSLKAVRALLREADLVLALGTEMGQTDYDLYADGGFPPLKNLVRTDI 300 Query: 309 DRAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRAEWHQLVADLQREFPCP--IPKACD 366 D A+L + Q ++I + A ++ + A L A+ R+ PK Sbjct: 301 DAAQLARGPQAALSILSGARAATAGILGFLPDHAAARDGILRAEATRKAALRELTPKM-- 358 Query: 367 PLSHYGLINAVAACVDDNAIITTDVGQHQMWTAQAY-PLNRPRQWLTSG-GLGTMGFGLP 424 L+ G++ A+ + D II D Q ++ Y R R W S G G++G+ P Sbjct: 359 -LAEVGVVEAIYRTLPD-CIIVGDSTQ-AVYAGNLYCDAPRQRAWFNSATGYGSLGYAPP 415 Query: 425 AAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLVHQQQSLF 484 AA+GAA+A+ +R V+C GDG ++ E+ +A + V ++ NN+ + +S Sbjct: 416 AAVGAAVADRERPVICLVGDGGFQFSLAEIGSAVDAAAQVVFLVWNNDG---YREIESYM 472 Query: 485 YEQGVF-AATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHV 538 E G+ P +F+ A +G+ L D +L + ++R GP+LI + Sbjct: 473 VENGITPEGVKPSAPDFLLAAKAYGVPAERLATVKDLPRALADAVSRSGPSLIEI 527 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: 736 Number of extensions: 45 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: 537 Length adjustment: 36 Effective length of query: 526 Effective length of database: 501 Effective search space: 263526 Effective search space used: 263526 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