Align methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate Ga0059261_3982 Ga0059261_3982 Acetyl-CoA carboxylase, carboxyltransferase component (subunits alpha and beta)
Query= BRENDA::Q9LDD8 (587 letters) >FitnessBrowser__Korea:Ga0059261_3982 Length = 508 Score = 252 bits (644), Expect = 2e-71 Identities = 162/523 (30%), Positives = 261/523 (49%), Gaps = 36/523 (6%) Query: 68 MEGILSELRSHIKKVLAGGGEEAVKRNRSRNKLLPRERIDRLLDPGSSFLELSQLAGHE- 126 M + EL GGG++ + ++ KL RER++ LLD GS F EL H Sbjct: 1 MSSTIEELERRRAAARLGGGQKRIDAQHAKGKLTARERVEVLLDEGS-FEELDMYVEHNC 59 Query: 127 ----LYEEPLPSGGIITGIGPIHGRICMFMANDPTVKGGTYYPITIKKHLRAQEIAARCR 182 + ++ +P G++TG G I+GR+ + D TV GG+ +K + ++A + Sbjct: 60 VDFGMPDQVVPGDGVVTGSGTINGRLVFVFSQDFTVFGGSLSERHAQKICKIMDMAMKVG 119 Query: 183 LPCIYLVDSGGAYLPKQAEVFPDKENFGRVFYNESVMSSDGIPQIAIVLGSCTAGGAYIP 242 P I L DSGGA + E + VF +V++S +PQ+++++G C G Y P Sbjct: 120 APVIGLNDSGGARIQ---EGVASLAGYAEVF-QRNVLASGVVPQLSLIMGPCAGGAVYSP 175 Query: 243 AMADESVMVKGNGTIFLAGPPLVKAATGEEVSAEDLGGATVHCTVSGVSDYFAQDELHGL 302 AM D MVK + +F+ GP +VK T E V+ EDLGGA H T SGV+D ++++ L Sbjct: 176 AMTDFIFMVKDSSYMFVTGPDVVKTVTNEIVTQEDLGGAVTHTTKSGVADVAFENDIEAL 235 Query: 303 AIGRNIVKNLHMAAKQGMEGTFGSKNLVYKEPLYDINE-LRSIAPVDHKQQFDVRSIIAR 361 R+ V L + ++ + ++P I + L ++ P Q +D+ +I + Sbjct: 236 LAARDFVDFLPASNREPV------PERPCEDPWDRIEDSLDTLIPPSANQPYDMHELIRK 289 Query: 362 IVDGSEFDEFKKQYGTTLVTGFARIYGQTVGIIGNN-----GILFNESALKGAHFIELCS 416 VD +F E + + ++ GF RI G+TVGI+ N G+L S+ K A F+ C Sbjct: 290 TVDEGDFFEVQPTHAANIIIGFGRIEGRTVGIVANQPMVLAGVLDINSSKKAARFVRFCD 349 Query: 417 QRKIPLVFLQNITGFMVGSRAEANGIAKAGAKMVMAVSCAKVPKITIITGASFGAGNYAM 476 +IP+V ++ GF+ G E +GI K GAK++ A + A VPKIT+IT ++G M Sbjct: 350 AFEIPIVTFVDVPGFLPGVGQEHSGIIKHGAKLLFAYAEATVPKITVITRKAYGGAYDVM 409 Query: 477 CGRAYSPDFMFIWPNARIGIMGGAQAAGVLTQIERATKKRQGIKWTEEEEEAFKKKTVDA 536 + D + WP A I +MG A ++ + + E ++T + Sbjct: 410 ASKHLRGDLNYAWPTAEIAVMGAKGAVEII--------------FRGKTPEEIAERTAEY 455 Query: 537 YEREANPYYSTARLWDDGVIDPCDTRKVLGLCLSAALNRPLED 579 R ANP+ + ++ + D VI P TR+ + L L N+ LE+ Sbjct: 456 EARFANPFVAASKGFVDEVIMPHSTRRRIALGLRKLRNKSLEN 498 Lambda K H 0.320 0.138 0.408 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: 703 Number of extensions: 36 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: 587 Length of database: 508 Length adjustment: 35 Effective length of query: 552 Effective length of database: 473 Effective search space: 261096 Effective search space used: 261096 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: 52 (24.6 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