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 AZOBR_RS12015 AZOBR_RS12015 acetyl-CoA carboxylase biotin carboxylase subunit
Query= SwissProt::Q2QMG2 (737 letters) >FitnessBrowser__azobra:AZOBR_RS12015 Length = 447 Score = 420 bits (1079), Expect = e-122 Identities = 214/443 (48%), Positives = 293/443 (66%), Gaps = 4/443 (0%) Query: 40 EKVLVANRGEIACRVMRTARRLGIPTVAVYSDADRGALHVRAADEAVRLGPPPARESYLN 99 EKVL+ANRGEIA R+ R R +GI TVAV+S AD A+HVR ADE+V +GP ARESYLN Sbjct: 3 EKVLIANRGEIALRIHRACREMGIQTVAVHSTADADAMHVRLADESVCIGPASARESYLN 62 Query: 100 ASAIVDAALRTGAKAIHPGYGFLSESADFAQLCKAEGLTFIGPPPSAIRDMGDKSASKRI 159 AI+ AA TGA AIHPG GFLSE+A FA++ + G TFIGP IR MGDK +K+ Sbjct: 63 IPAILSAASITGADAIHPGIGFLSENAQFAEMVEEHGFTFIGPTAEHIRIMGDKVTAKKT 122 Query: 160 MGAAGVPLVPGYHGAEQDIELLKLEANKIGYPVLIKPTHGGGGKGMRIVQRPEDFVDSVL 219 + G+P+VPG G +E + + GYP+LIK GGGGKGM++ + P+ ++ Sbjct: 123 VMEQGLPVVPGSDGPVPTLEEAEKIGRETGYPILIKAAAGGGGKGMKVARNPDQLKEAYQ 182 Query: 220 SAQREAAASFGINTLLVEKYITQPRHIEVQIFGDQHGNVIHLYERDCSLQRRHQKIIEEA 279 A+ EA A+FG + + +EKY+ +PRHIE+Q+ GD+HGN +H ERDCS+QRRHQK+IEEA Sbjct: 183 LARGEARAAFGNDEVYIEKYLGKPRHIEIQLLGDEHGNCVHFGERDCSVQRRHQKVIEEA 242 Query: 280 PAPNVTAQFRSHIGEAAVSAAKAVGYYSAGTVEFIVDTLSGEFYFMEMNTRLQVEHPVTE 339 P+P + A+ R+ IG+ A A A+GY GT+EF+ + G+FYF+EMNTRLQVEH +TE Sbjct: 243 PSPALNAEQRAFIGDLAAKTAAAIGYRGVGTMEFLFE--DGQFYFIEMNTRLQVEHTITE 300 Query: 340 MIVGQDLVEWQIRIANGECLPLSQEQVPLNGHAFEARIYAENVPRGFLPATGTLHHYRPV 399 MI G DLV QIR+A G L Q + GH+ E R+ AE+ P F+P+ G + Y Sbjct: 301 MITGIDLVREQIRVATGAPLGYGQADIRFQGHSIECRVNAEH-PETFIPSPGKIDGYH-A 358 Query: 400 PSTATVRVETGVEEGDTVSMHYDPMIAKLVVWGESRNAALVKLKNSLSNFQIAGLPTNVG 459 P VRV++ + +G + HYD +IAKLVV G +RN L++L+ ++ + I G+ T + Sbjct: 359 PGGLGVRVDSALYDGYRIPPHYDSLIAKLVVHGTTRNECLMRLRRTIEEYVIGGVDTTLP 418 Query: 460 FLQELAGHSAFEKGLVDTHFIER 482 Q + AF G D H++E+ Sbjct: 419 LHQRIIAQQAFIDGNYDIHWLEQ 441 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: 775 Number of extensions: 34 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: 447 Length adjustment: 36 Effective length of query: 701 Effective length of database: 411 Effective search space: 288111 Effective search space used: 288111 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