Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA carboxylase biotin-containing subunit; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate WP_004315433.1 C665_RS13945 acetyl/propionyl/methylcrotonyl-CoA carboxylase subunit alpha
Query= SwissProt::Q99MR8 (717 letters) >NCBI__GCF_000310185.1:WP_004315433.1 Length = 667 Score = 648 bits (1671), Expect = 0.0 Identities = 332/665 (49%), Positives = 445/665 (66%), Gaps = 5/665 (0%) Query: 47 KVLIANRGEIACRVIRTAKKMGVQSVAVYSEADRNSMHVDMADEAYSIGPAPSQQSYLAM 106 K+LIANRGEIACRVI+TA++MG+++VAVYSEAD N+ HV +ADEA IGPA +++SYL + Sbjct: 4 KILIANRGEIACRVIKTARRMGIKTVAVYSEADANARHVRLADEAVLIGPAAARESYLVI 63 Query: 107 EKIIQVAKSSAAQAIHPGYGFLSENMEFAELCKQEGIIFIGPPSSAIRDMGIKSTSKSIM 166 +KII A+ + AQAIHPGYGFLSEN +F C++EGI+FIGPP SAIR MG KS +K +M Sbjct: 64 DKIIAAARQTGAQAIHPGYGFLSENEDFCHACEREGIVFIGPPVSAIRAMGSKSEAKKLM 123 Query: 167 AAAGVPVVEGYHGKDQSDQCLREHAGKIGYPVMIKAVRGGGGKGMRIVRSEREFQEQLES 226 AAGVP+ GYHG DQ L + A IGYPV+IKA GGGGKGMR+V +F + L S Sbjct: 124 EAAGVPLTPGYHGDDQDPAWLHQQADAIGYPVLIKAAAGGGGKGMRLVDRSEDFIDLLAS 183 Query: 227 ARREAKKSFNDDAMLIEKFVDTPRHVEVQVFGDHHGNAVYLFERDCSVQRRHQKIIEEAP 286 +REA SF DD +L+EK++ PRH+E+QVFGD HGN VYLFERDCSVQRRHQK++EEAP Sbjct: 184 CKREAISSFGDDHVLVEKYITKPRHIEIQVFGDTHGNVVYLFERDCSVQRRHQKVLEEAP 243 Query: 287 APGINPEVRRKLGEAAVRAAKAVKYVGAGTVEFIMDSRHNFYFMEMNTRLQVEHPVTEMI 346 APG+ E R +G+AAV AAKAV YVGAGTVEFI + +FYFMEMNTRLQVEHPVTEMI Sbjct: 244 APGMTLERRAAMGKAAVDAAKAVGYVGAGTVEFIANQDGSFYFMEMNTRLQVEHPVTEMI 303 Query: 347 TGTDLVEWQLRIAAGEKIPLSQEEIPLQGHAFEARIYAEDPDNNFMPGAGPLVHLSTPSA 406 TG DLVEWQLR+A+GEK+PL+QE++ ++GHA EARIYAEDP F+P G LVHL+ P+ Sbjct: 304 TGLDLVEWQLRVASGEKLPLAQEQLQIRGHALEARIYAEDPAKGFLPSTGKLVHLAPPAE 363 Query: 407 DMSTRIETGVRQGDEVSVHYDPMIAKLVVWASDRQSALSKLRYCLHQYNIVGLRSNVDFL 466 + R++TGV +GDE+S HYDPMIAKL+VW +R AL+++ L Y +VG+ +N++FL Sbjct: 364 SLHVRVDTGVEEGDEISPHYDPMIAKLIVWDINRDRALARMLQALADYRVVGVANNIEFL 423 Query: 467 LRLSGHPEFEAGNVHTDFIPQHHKDLLPSHSTIAKESVCQAALGLILKEKEMTSAFKLHT 526 RL+ P F ++ T I + L P+ + E + AAL +L++ Sbjct: 424 SRLTACPAFAGADLDTGLIEREKAYLFPADEAVPAEVLQIAALAELLRDAAFADRRAARG 483 Query: 527 QDQFSPFSFSSGRRLNISYTRNMTLRSGKSDIVIAVTYNRDGSYDMQIDNKSFRVLGDLS 586 D SP+ G R+N + R++ R G+S+ + V Y G++ + + + S G+L+ Sbjct: 484 ADPASPWHARDGWRMNATACRSLLFRHGESERAVEVAY-LPGAWRLTVGSSSVVARGELN 542 Query: 587 SEDGCTYLKSSINGVARKSKFILLDNTVHLFSMEGSIEVGIPVPKYLSPVSAEGAQGGTI 646 L+ ++G + I H+F+ + ++ P + GA+GG + Sbjct: 543 PRG---LLRVELDGTRMDATVIAAAGRRHVFARGRAWQLAAVDPLHHGG-EGGGAEGGLM 598 Query: 647 APMTGTIEKVFVKAGDRVKAGDSLMVMIAMKMEHTIKAPKDGRIKKVFFSEGAQANRHAP 706 APM G + + G +V+ G L+++ AMKMEHTI AP G +K F G Q A Sbjct: 599 APMPGKVIALVAAEGAKVEKGAPLLILEAMKMEHTITAPAAGTVKAFRFGVGDQVGDGAE 658 Query: 707 LVEFE 711 LVEFE Sbjct: 659 LVEFE 663 Lambda K H 0.318 0.133 0.382 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: 1184 Number of extensions: 49 Number of successful extensions: 3 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: 717 Length of database: 667 Length adjustment: 39 Effective length of query: 678 Effective length of database: 628 Effective search space: 425784 Effective search space used: 425784 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: 54 (25.4 bits)
This GapMind analysis is from Sep 24 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