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_090448242.1 BLS63_RS23590 5-guanidino-2-oxopentanoate decarboxylase
Query= curated2:P08142 (562 letters) >NCBI__GCF_900100495.1:WP_090448242.1 Length = 533 Score = 246 bits (627), Expect = 2e-69 Identities = 171/507 (33%), Positives = 258/507 (50%), Gaps = 25/507 (4%) Query: 14 TGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQGMART 73 T EF+V LE G+ V GIPG + +Y L ST IRHI RHEQGAGF+A G AR Sbjct: 3 TCGEFLVKQLEAWGVDTVFGIPGVHTVELYRGLPHST-IRHITPRHEQGAGFMADGYARV 61 Query: 74 DGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIGTD---AFQEVDTYGI 130 GKP VC +GPG TN++TA+A A DSIP++ I+ +G + + + Sbjct: 62 SGKPGVCFIITGPGMTNILTAMAQAYADSIPMLVISSVNERERLGLGKGYLHELPNQRAL 121 Query: 131 SIPITKHNYLVRHIEELPQVMSDAFRIAQSGRPGPVWIDIPKDVQTA-VFEIETQPAMAE 189 + +T ++ + +EELP V++ AF + + RP PV I++P D+ TA + Q + Sbjct: 122 TAGVTAFSHTLMSVEELPAVLARAFAVFEGQRPRPVHIELPLDIITAPAGHLRVQARSSV 181 Query: 190 KAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPTTMTLMALGM 249 APA ++ +R+AAA + AAKRP+L LGGG + A R LA PT +T+ A G+ Sbjct: 182 SRPAPALAQ--LREAAAKLRAAKRPLLLLGGGCVAAQVEARALAMALDAPTALTINAKGL 239 Query: 250 LPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGARF--DDRAIGKTEQFCPNAKIIHVD 307 LP HPL LG + + +AD+++ +G D + F ++I +D Sbjct: 240 LPPGHPLLLG--SNQSLVPVRQLALQADVVLAIGTELGETDYDVVFDGNFKLGGELIRID 297 Query: 308 IDRAELGKIKQPHVAIQADVDDVLAQL---IPLVEAQPRAEWHQLVADLQREFPCPIPKA 364 ID +L + P +AIQ+D + L +P E + + + A +Q + + + Sbjct: 298 IDAQQLLRNFAPSLAIQSDARLAMRMLLADLPAGELRADSPGARRTAAVQAQ----LAED 353 Query: 365 CDPLSHYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSG-GLGTMGFGL 423 +HY + A D Q L+ R+W S G GT+G+GL Sbjct: 354 LSGWAHYRQLFDTLLGALPQARFVGDSTQTVYSGNHLVELDGARRWFNSSTGYGTLGYGL 413 Query: 424 PAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEALGLV--HQQQ 481 PAAIGA LA P R V+C GDG L ++ E+A+A E ++ + ++L NN G + + Q+ Sbjct: 414 PAAIGARLAEPGRPVICLIGDGGLQFSLAELASAVEARVGIIVLLWNNCGYGEIKRYMQR 473 Query: 482 SLFYEQGVFAATYPGKINFMQIAAGFG 508 GV T +F+ +A GFG Sbjct: 474 RDITPLGVDIYT----PDFIALAHGFG 496 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: 753 Number of extensions: 42 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: 533 Length adjustment: 36 Effective length of query: 526 Effective length of database: 497 Effective search space: 261422 Effective search space used: 261422 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