Align acetolactate synthase isozyme 2 large subunit; EC 2.2.1.6 (characterized)
to candidate 202370 SO3262 acetolactate synthase isozyme I, large subunit (NCBI ptt file)
Query= CharProtDB::CH_003896 (548 letters) >FitnessBrowser__MR1:202370 Length = 581 Score = 323 bits (828), Expect = 1e-92 Identities = 202/562 (35%), Positives = 294/562 (52%), Gaps = 28/562 (4%) Query: 4 AQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATGK 63 A ++ L QG+ YPGG I P+ DA GV R+EQGA AA+ + T Sbjct: 10 ADAIIEFLAHQGIKAFHNYPGGTIAPLLDACKRFGVTVYTSRNEQGAGYAALAQGKLTQL 69 Query: 64 TGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSA------PFIGTDAFQEVDVLGL 117 G+ TSGPG TN++T +ADA D IP++ TGQV + FQEVD L Sbjct: 70 PGIVAVTSGPGVTNVLTPVADAYFDGIPMLVFTGQVGTGDLTGQKRVRQSGFQEVDTPSL 129 Query: 118 SLACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVEN 177 TK F ++ EEL I+ A+ +A GR GPV +D+P D+Q ++ V Sbjct: 130 MKPITKGQFQPKNSEELYAILPIAWQLALEGRKGPVSIDLPMDVQRSAAIKS---IKVPE 186 Query: 178 EVTFPHAEVE------QARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTL 231 VT+P E + + +QKP++ G G+ V A+R P + +L Sbjct: 187 IVTYPVNRTELGTFIDELINAIDHSQKPVIICGNGMTSPALVDAIRTLRNYWPAPVSHSL 246 Query: 232 KGLGAVEADYPYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGKLNT-FAPHASV 290 G+G ++ D LG G G++ A A+ ECDLL+ +G+R D R TG L T FA +A + Sbjct: 247 LGVGVLDTDDSGSLGFHGHTGSQLAGKAIAECDLLLVLGSRLDVRQTGTLKTAFASNAKI 306 Query: 291 IHMDIDPAEMNKLRQAH-VALQGDLNALLPALQ------QPLNQYDWQQHCAQLRDEHSW 343 +D+D E+ R AH A+Q +L AL P N W +Q + + +W Sbjct: 307 FRVDLDIGELTDSRIAHHKAVQAELEQFFDALHPKFAQLSPPNLSSWHNTISQWKAQLAW 366 Query: 344 RY-DHPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPEN-FITSSGLG 401 Y D+PG I LLL++LS+ P + +VTT VG HQ W A+H P TS+G G Sbjct: 367 PYPDYPG--IAPKLLLEKLSNSLPENTIVTTGVGAHQHWVARHFRFALPHRQLFTSAGHG 424 Query: 402 TMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMV 461 TMG+ LP A+GA + P T++CI+GDGSF MN+QELG +K L +KI++LDN RLG+V Sbjct: 425 TMGYDLPTAIGAAIHSPESTILCIAGDGSFQMNIQELGVIKELGLKIKILVLDNHRLGLV 484 Query: 462 RQWQQLFFQERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLH 521 Q+ QL E + +P+F ++A +GI H + ++E L + +D LLH Sbjct: 485 SQF-QLMNWETDTACGNKQSPNFALIAQGYGIKALHCSDSAKLEQTLAEFIETDESILLH 543 Query: 522 VSIDELENVWPLVPPGASNSEM 543 + I +V P++ G + +M Sbjct: 544 IEIATQHDVLPMLLGGQTTDKM 565 Lambda K H 0.320 0.135 0.410 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: 773 Number of extensions: 28 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: 548 Length of database: 581 Length adjustment: 36 Effective length of query: 512 Effective length of database: 545 Effective search space: 279040 Effective search space used: 279040 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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