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 GFF3828 PGA1_262p02320 putative acetolactate synthase isozyme 1 large subunit
Query= curated2:P08142 (562 letters) >FitnessBrowser__Phaeo:GFF3828 Length = 551 Score = 187 bits (474), Expect = 1e-51 Identities = 159/549 (28%), Positives = 256/549 (46%), Gaps = 44/549 (8%) Query: 14 TGAEFIVHFLEQQGIKIVTGIPGGSILPVYDALSQSTQIRHILARHEQGAGFIAQGMART 73 T E +V L +G++ V GIPG + +Y L +S +RHI RHEQGAGF+A G AR Sbjct: 10 TVGEALVEELAARGVQHVFGIPGVHTVELYRGLGRS-DLRHITPRHEQGAGFMADGYARV 68 Query: 74 DGKPAVCMACSGPGATNLVTAIADARLDSIPLICITGQVPASMIG---TDAFQEVDTYGI 130 G+P V +GPG TN +T +A AR DS+P++ ++G + +G + D + + Sbjct: 69 SGRPGVAFVITGPGLTNTLTPMAQARADSVPMLVVSGVNESGSLGHGMGHLHELPDQHAL 128 Query: 131 SIPITKHNYLVRHIEELPQVMSDAFRI---AQSGRPGPVWIDIPKDVQ-TAVFEIETQPA 186 + + + V E+L + AF A RPGP + IP DV +A + + Q + Sbjct: 129 AKMVALKSEHVAAPEQLTPALDQAFAPIAGAALSRPGPTHVQIPLDVAGSAARDGDGQES 188 Query: 187 MAEKAAAPAFSEESIRDAAAMINAAKRPVLYLGGGVINAPARVRELAEKAQLPTTMTLMA 246 S + + AA+RPV+ GGG ++R+LAE P T+ A Sbjct: 189 APTGEQDRTVSPADLAALMQRLTAAERPVILAGGGARFCADQLRQLAEYLGAPVVQTVNA 248 Query: 247 LGMLPKAHPLSLGMLGMHGVRSTNYILQEADLLIVLGAR-----FDDRAIGKTEQFCPNA 301 G++ HPLS+ G S +++ AD+++ LG +D A G Q Sbjct: 249 RGVM-FDHPLSVPASPSLG--SVRELIEAADMVLALGTELGPTDYDMYATGTMPQM---P 302 Query: 302 KIIHVDIDRAELGKIKQPHVAIQADVDDVLAQLIPLVEAQPRA--EWHQLVADLQREFPC 359 +I +D+ +L + + + +Q DV VL+ + + R+ +W +A+ R Sbjct: 303 GLIRIDLCADQLAR-HRAELTVQGDVAAVLSAALAEWKPDVRSTTDWGIGLAEQTR---- 357 Query: 360 PIPKACDPL-----SHYGLINAVAACVDDNAIITTDVGQHQMWTAQAYPLNRPRQWLTSG 414 A D + + ++NA+ A V AI+ D Q Y +RP W + Sbjct: 358 --TAAWDEIGESYRAQVMVLNALRAAV-PGAIVVGDSAQPIYAGNLYYDHDRPGGWFNAA 414 Query: 415 -GLGTMGFGLPAAIGAALANPDRKVLCFSGDGSLMMNIQEMATASENQLDVKIILMNNEA 473 G G +G+G+PAAIGAA+A P+ V+C +GDG ++ E+ TA + L + I+ NN Sbjct: 415 TGYGALGYGIPAAIGAAVAAPETPVICITGDGGAQFSLPEIMTAVDEALSITFIVWNNHG 474 Query: 474 LGLVHQQQSLFYEQGV-FAATYPGKINFMQIAAGFGLETCDLNNEADPQ---ASLQEIIN 529 + + + GV P +F A FG+ ++ ADPQ +L Sbjct: 475 YQEIARSMQ---DVGVPVVGCDPTPPDFAATARSFGISHRAVS--ADPQEVAVALHSAAT 529 Query: 530 RPGPALIHV 538 GP +I + Sbjct: 530 ETGPRMIEI 538 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: 42 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: 551 Length adjustment: 36 Effective length of query: 526 Effective length of database: 515 Effective search space: 270890 Effective search space used: 270890 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