Align 3-methylcrotonyl-CoA carboxylase biotin-containig subunit; EC 6.4.1.4 (characterized)
to candidate 200026 SO0840 acetyl-CoA carboxylase multifunctional enzyme accADC, carboxyl transferase subunit alpha/carboxyl transferase subunit beta/biotin carboxylase (NCBI ptt file)
Query= CharProtDB::CH_122249 (723 letters) >FitnessBrowser__MR1:200026 Length = 1517 Score = 294 bits (752), Expect = 3e-83 Identities = 180/502 (35%), Positives = 271/502 (53%), Gaps = 21/502 (4%) Query: 1 MPLSSLLRTSARLGQTVVARRSRRTASTVTSNSSSNFRALDSILIANRGEIALRVGRTAA 60 MP + + T+V V ++ + ++ +L+ RG A+++ R A Sbjct: 901 MPTAKINEVIINALSTLVVEAPAEEEEIVQNDPRKLMKPINKVLVHARGCTAVKLIRKAH 960 Query: 61 QHGIRVTTLYTDPDSQAQHALSTPYAFNL----GSVS--AYLDGDRIIEIAKAQGCQGIH 114 + I V + +DPD A A + L G+ S +YL+ ++++A+ + +H Sbjct: 961 DNNINVVLVASDPDMTAVPADMLKESDKLVCLGGNTSDESYLNAYSVLKVAEYEQVDALH 1020 Query: 115 PGYGFLSENSEFARKCTEAGLVFIGPPWKAIEDMGDKRCSKHIMTAAGVPCVPSYHGENQ 174 PG GFLSE+ +FA C G+ F+GP ++ MG+K + A VP VP HG Sbjct: 1021 PGIGFLSESPQFAALCVNNGVNFVGPSVHSMTTMGNKSNAIKTSQAQNVPVVPGSHGILT 1080 Query: 175 DPNFLEAEADKIKYPVLIKAIKGGGGKGMRIARSKEEFQAQLQSAKSEAMNSFGDDHVLV 234 + A +I YPVL+KA++GGGGKG+++ + E+ Q +EA +FG+ + + Sbjct: 1081 NAEQAVNVASEIGYPVLLKAVQGGGGKGIQVVKRPEDMIGLFQKTATEAAAAFGNGDLYL 1140 Query: 235 EKYITTPRHIEVQVFADKHGNCVALGERDCSIQRRHQKILEESPAPHLPDATRKDIWAKA 294 EKY+T+ RHIEVQ+ DK G+ LG RDCS+QR +QK++EES + LPD +K + A Sbjct: 1141 EKYVTSLRHIEVQLLRDKFGHAKVLGLRDCSVQRNNQKVVEESGSTMLPDELKKQVLAYT 1200 Query: 295 RSAALAVRYEGAGTVEFIFDNDTGEFFFMEMNTRLQVEHPVTEMVTGQDLVHWQLKVAEG 354 R+ A Y GAGTVEFI++ D E +FMEMNTRLQVEHPVTE +G D+V Q +A G Sbjct: 1201 RALGDATDYMGAGTVEFIYNLDANEVYFMEMNTRLQVEHPVTEATSGIDIVSAQFDIAAG 1260 Query: 355 AELP-LTQEEVEANIATHGHAIEARIYAENPAQG------FIPDSGALLHVRTPATTEDV 407 + L +E+ G+A+E R+ AE A IP+ G + P DV Sbjct: 1261 RSIEHLEPKEI-------GYAMEVRVTAEKAALDSHGVLQLIPNPGKITECVFP-DHPDV 1312 Query: 408 RIDAGFVQGDEVSAHYDPMIAKLIVRGADRQEAIRKLACSIGRVEVAGPATNIEFLKSVC 467 I + G EVS +YD +IA++I+RG +R++ I KL + V + G ATNI LK + Sbjct: 1313 EIISIAAPGKEVSPYYDSLIAQVIMRGENREDVIAKLHAYLDSVVLKGIATNIPLLKLIL 1372 Query: 468 KSADFISGKVETGYIEKHHDEL 489 F G +T Y+ + EL Sbjct: 1373 SDGTFKEGVYDTNYLPRFMAEL 1394 Lambda K H 0.318 0.132 0.385 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: 1977 Number of extensions: 89 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 723 Length of database: 1517 Length adjustment: 45 Effective length of query: 678 Effective length of database: 1472 Effective search space: 998016 Effective search space used: 998016 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 58 (26.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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