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 PP_1394 PP_1394 putative Acetolactate synthase, large subunit
Query= curated2:P08142 (562 letters) >FitnessBrowser__Putida:PP_1394 Length = 545 Score = 239 bits (611), Expect = 2e-67 Identities = 173/545 (31%), Positives = 278/545 (51%), Gaps = 33/545 (6%) Query: 14 TGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQGMART 73 T E +V LE G+ V GIPG + +Y L+ S+ IRHI RHEQGAGF+A G ART Sbjct: 3 TCGEVLVKLLEGYGVDHVFGIPGVHTVELYRGLAGSS-IRHITPRHEQGAGFMADGYART 61 Query: 74 DGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMI--GTDAFQEVDTYGIS 131 GKP VC +GPG TN+ TA+ A DSIP++ I+ + G E+ Sbjct: 62 RGKPGVCFIITGPGMTNITTAMGQAYADSIPMLVISSVQSRDQLGGGRGKLHELPNQAAL 121 Query: 132 IP-ITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKD--VQTAVFEIETQPAMA 188 + + ++ + +LPQV++ AF + S RP PV I+IP D V+ A F + +P Sbjct: 122 VSGVAAFSHTLMSAADLPQVLARAFAVFDSARPRPVHIEIPLDVLVEPADFLLPGRPVRG 181 Query: 189 EKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPTTMTLMALG 248 +A A + +++ A + +A+RP++ GGG + A A + LAE Q P +T+ A G Sbjct: 182 SRAGA---APQAVAQMAERLASARRPLILAGGGALAAGAALARLAEHLQAPVALTINAKG 238 Query: 249 MLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARFDDRAIGKTEQ--FCPNAKIIHV 306 +LP +HPL +G + +T ++ EAD+++ +G + T + F +++ + Sbjct: 239 LLPASHPLQIG--STQSLPATRALVAEADVVLAIGTELAETDYDVTFKGGFEIPGRLLRI 296 Query: 307 DIDRAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPR----AEWH-QLVADLQREFPCPI 361 DID + + P +A+ AD + L+ V+AQP+ + W VADL++ Sbjct: 297 DIDPDQTVRNYLPELALVADAELAAEALLGAVQAQPQPVHESTWGVARVADLRKVLAADW 356 Query: 362 PKACDPLSHYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWL-TSGGLGTMG 420 + LS L++A+ + D AI+ D Q + +PR+W S G GT+G Sbjct: 357 DQ--PTLSQTRLLSAILERLPD-AILVGDSTQPVYTGNLTLDMQQPRRWFNASTGYGTLG 413 Query: 421 FGLPAAIGAALANPDRKV-----LCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALG 475 + LPAA+GA L + ++ V +C GDG L + E+A+A E Q+ + ++L NN+ Sbjct: 414 YALPAAMGAWLGSAEQAVERAPAVCLIGDGGLQFTLPELASAVEAQVPLIVLLWNNQGYE 473 Query: 476 LV--HQQQSLFYEQGVFAATYPGKINFMQIAAGFGLETCDLNNEADPQASLQEIINRPGP 533 + + GV T +F+ +A G ++ + A QA+L + + R GP Sbjct: 474 EIKKYMVNRAIEPVGVDIHT----PDFIGVARALGAAAENVADIAQLQAALGQAVERKGP 529 Query: 534 ALIHV 538 LI V Sbjct: 530 TLIQV 534 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: 777 Number of extensions: 49 Number of successful extensions: 6 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: 545 Length adjustment: 36 Effective length of query: 526 Effective length of database: 509 Effective search space: 267734 Effective search space used: 267734 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