Align Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; MCCase subunit alpha; 3-methylcrotonyl-CoA carboxylase 1; 3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; EC 6.4.1.4 (characterized)
to candidate Ga0059261_0292 Ga0059261_0292 acetyl-CoA carboxylase, biotin carboxylase subunit
Query= SwissProt::Q2QMG2 (737 letters) >FitnessBrowser__Korea:Ga0059261_0292 Length = 454 Score = 430 bits (1106), Expect = e-125 Identities = 228/447 (51%), Positives = 298/447 (66%), Gaps = 6/447 (1%) Query: 39 VEKVLVANRGEIACRVMRTARRLGIPTVAVYSDADRGALHVRAADEAVRLGPPPARESYL 98 ++K+L+ANRGEIA R+ R +GI TVAV+S AD A+HVR AD+AV +GPP A +SYL Sbjct: 4 IKKLLIANRGEIALRIHRACHEMGIKTVAVHSTADADAMHVRLADQAVCIGPPAAADSYL 63 Query: 99 NASAIVDAALRTGAKAIHPGYGFLSESADFAQLCKAEGLTFIGPPPSAIRDMGDKSASKR 158 N I+ AA +GA AIHPGYGFLSE+A FA++ + L F+GP P IR MGDK +KR Sbjct: 64 NIPNIISAAEISGADAIHPGYGFLSENAKFAEIVELHNLIFVGPKPEHIRVMGDKVEAKR 123 Query: 159 IMGAAGVPLVPGYHGAEQDIELLKLEANKIGYPVLIKPTHGGGGKGMRIVQRPEDFVDSV 218 GA G+PLVPG GA D+E K A +IGYPV+IK GGGG+GM++ P+ F + Sbjct: 124 TAGALGLPLVPGSDGAISDVEEAKKLAAEIGYPVIIKAASGGGGRGMKVCTDPDQFETLM 183 Query: 219 LSAQREAAASFGINTLLVEKYITQPRHIEVQIFGDQHGNVIHLYERDCSLQRRHQKIIEE 278 A EA A+FG T+ +EKY+ PRHIE+Q+FGD +GN IHL ERDCSLQRRHQK++EE Sbjct: 184 QQAGSEAKAAFGDATVYLEKYLGNPRHIEIQVFGDGNGNAIHLGERDCSLQRRHQKVLEE 243 Query: 279 APAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEHPVT 338 AP+P ++ + R+ IGE A +GY AGT+EF+ + +GEFYF+EMNTRLQVEHPVT Sbjct: 244 APSPVLSTEERNRIGEICAKAMADMGYRGAGTIEFLWE--NGEFYFIEMNTRLQVEHPVT 301 Query: 339 EMIVGQDLVEWQIRIANGECLPLSQEQVPLNGHAFEARIYAENVPRGFLPATGTLHHYRP 398 E I G DLV QIR+A G L L QE V GHA E RI AE+ PR F P+ G + Y Sbjct: 302 EAITGLDLVREQIRVAEGHGLTLRQEDVQFRGHAIECRINAED-PRTFAPSPGRVSQYH- 359 Query: 399 VPSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSNFQIA--GLPT 456 P VRV++G+ G V +YD MIAKL+V+G +R AL +L+ +L F I G+ T Sbjct: 360 APGGMNVRVDSGLYSGYKVPPYYDSMIAKLIVYGTTRQGALRRLRRALEEFVIEGDGMKT 419 Query: 457 NVGFLQELAGHSAFEKGLVDTHFIERY 483 + Q L + F++G ++E + Sbjct: 420 TIPLHQALLDNPQFQQGDYTIKWLEEW 446 Lambda K H 0.317 0.133 0.389 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: 35 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: 737 Length of database: 454 Length adjustment: 36 Effective length of query: 701 Effective length of database: 418 Effective search space: 293018 Effective search space used: 293018 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: 53 (25.0 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