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 WP_012050478.1 SWIT_RS21745 hypothetical protein
Query= curated2:P08142 (562 letters) >NCBI__GCF_000016765.1:WP_012050478.1 Length = 569 Score = 245 bits (625), Expect = 4e-69 Identities = 170/554 (30%), Positives = 283/554 (51%), Gaps = 24/554 (4%) Query: 11 KRFTGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALS-QSTQIRHILARHEQGAGFIAQG 69 K TG E V L ++G+ V GIPG + + L + +I ++ RHEQ A ++A G Sbjct: 17 KEMTGGEAFVAQLIEEGVVDVFGIPGVQLDWAVEPLRVAANRINFVVTRHEQAASYMADG 76 Query: 70 MARTDGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTD--AFQEV-D 126 ART G+ VCM GPG N + ++ A S ++ + GQ+P+ IG E+ D Sbjct: 77 YARTTGREGVCMVVPGPGMLNALAGLSTAYACSSRVLFVAGQIPSPTIGKGFGMLHEIPD 136 Query: 127 TYGISIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTAVFEIETQPA 186 GI +TK + + R +E++P ++ AF +SG P PV I++P D+ E+ P Sbjct: 137 QSGILKSLTKWHGIARRVEDVPAIVHQAFVELRSGHPRPVAIELPPDILQGRAEVAILPR 196 Query: 187 MAEKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPA--RVRELAEKAQLPTTMTL 244 AP ++++ +AA ++ A+ PV+Y GGG A A V+ LAE Q P MT Sbjct: 197 AEAAPLAPP--QDAVTEAAKLLAEARFPVIYAGGGAAAAGAGDAVKALAEALQAPVVMTE 254 Query: 245 MALGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQFCPNAKII 304 G L AHPL+L LG V L AD+++V G+RF D A+ K + I Sbjct: 255 GGRGTLSDAHPLALVSLGGRAV------LPHADVVLVAGSRFVD-AVAKPTHSAEGTRFI 307 Query: 305 HVDIDRAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRAEWHQLVADLQREFPCPIPKA 364 ++++ + +QP +AIQ DV + ++ + A+ R + VA +++ I A Sbjct: 308 YLNVAADHMAAPRQPGLAIQGDVHLGVEGILAALPARDRPSRAEQVASVKQWCDGQI-SA 366 Query: 365 CDPLSHYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSGGLGTMGFGLP 424 P +G + A+ A + D+ I+ +++ Q ++ A+P+ PR ++T G G++G+G Sbjct: 367 IQP--QHGFMRALRASMADDDILVSELTQLGYYSNIAFPILAPRSFVTPGYQGSLGYGFN 424 Query: 425 AAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLVHQQQSLF 484 A+GAA N R+ + SGDG IQE++T + +QLD+ I++ + G V + Q Sbjct: 425 TALGAAHGNRGRRTVSISGDGGFGWGIQELSTVARDQLDISIVVFVDGKFGNVQRIQKRT 484 Query: 485 YEQGVFAATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGPALIHVRIDAEE 544 + GV AT ++ +AA +G+ + +++ + L + GP LI VR+ Sbjct: 485 F--GVEFATDLVNPDYATLAAAYGIPSAEVDTPEALEERLVAAKAKGGPMLIAVRVGEMP 542 Query: 545 K----VYPMVPPGA 554 ++P VPP + Sbjct: 543 SPWALIHPFVPPAS 556 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: 813 Number of extensions: 50 Number of successful extensions: 9 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: 569 Length adjustment: 36 Effective length of query: 526 Effective length of database: 533 Effective search space: 280358 Effective search space used: 280358 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