Align fatty acid oxidation complex subunit alpha; EC 1.1.1.35; EC 4.2.1.17; EC 5.1.2.3 (characterized)
to candidate CCNA_00074 CCNA_00074 multifunctional fatty acid oxidation complex subunit alpha FadJ
Query= CharProtDB::CH_003230 (714 letters) >FitnessBrowser__Caulo:CCNA_00074 Length = 733 Score = 426 bits (1094), Expect = e-123 Identities = 269/724 (37%), Positives = 384/724 (53%), Gaps = 29/724 (4%) Query: 7 FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 F + V D +A++T DVPG MNTL A ++ I+++++ + E++GVV S K F Sbjct: 4 FKIEVDSDGVALVTFDVPGRSMNTLTASVIKEIGEIVERIKSDAEIKGVVITSGKTTGFC 63 Query: 67 AGADINMIGN----CKTAQEAEALARQG-------QQLMAEIHALPIQVIAAIHGACLGG 115 AGAD+ +G A EA + + + V AAI+G +GG Sbjct: 64 AGADLGELGGGGGMAGGAAGGEAALKAAFDAGFALNKAFRGLETCGKPVAAAINGLAMGG 123 Query: 116 GLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLR 175 GLE+ALACH RV D PK L LPE ++GLLPG+GGTQRLPRL+GV A +L GK ++ Sbjct: 124 GLEIALACHYRVVADHPKIQLALPEAKVGLLPGAGGTQRLPRLMGVMAAAPYLLEGKSMK 183 Query: 176 AKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG-----PLGRALLFK 230 +AL +V +VVP ++EAA K + P ++ L G P G +F Sbjct: 184 PAEALANKVVHEVVPVDQVVEAAKTWVKTKGDPVAPWDKKDFKLPGGGPYTPTG-GQVFI 242 Query: 231 MVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQAL-RSIF 289 M +T GNYPA IL+ V G + E R F + M+PQ++ + R++F Sbjct: 243 MGNAMLRKQTYGNYPAQLNILKAVYEGTQVPFDAAIRIETRYFLKTMMSPQAKGMIRTLF 302 Query: 290 FASTDVKKDPG--SDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINH 347 + ++ K G +D PP+ V +LG G+MG GIAYV A AGI + D + + Sbjct: 303 LSLQELGKGSGRPADVPPSEAKKVAVLGAGMMGAGIAYVQAM-AGIETVLIDQSQEAAEK 361 Query: 348 ALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMV 407 Y+ + L+ V R + + D LALI+ TTDY DL+IEAVFE+ E+K + Sbjct: 362 GKGYAENLLKKAVSRGKMTQDKADAVLALITPTTDYAHVKGSDLVIEAVFESREIKADVT 421 Query: 408 AEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSA 467 + E A IF SNTS+LPI +A + RP+ IG+HFFSPV+KM LVEII TS Sbjct: 422 QKAEAQLAEDAIFGSNTSTLPITGLAKASVRPKNFIGIHFFSPVDKMGLVEIIMGEETSD 481 Query: 468 QTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFG 527 + +A ++ K KTPIVV D GFY +R ++ E + ML G ID G Sbjct: 482 EALAKSIDYVLKIKKTPIVVNDSRGFYTSRCFGTFVQEGLEMLADGIAPAIIDNVGRATG 541 Query: 528 FPVGPIQLLDEVGIDTGTKIIPVLEAAYGERFS----APANVVSSILNDDRKGRKNGRGF 583 P GP+++ D+V +D G K+ + G++F AP + ++ R GRKNG+GF Sbjct: 542 MPRGPLEMNDDVALDLGYKVTQQTKKDLGDKFEDRPFAPI-IEKMVVELQRFGRKNGKGF 600 Query: 584 YLYGQKGRKSKKQVDPAIYPL-IGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSV 642 Y Y + G K+ + + P+ I Q I ++ R + EA RC +E VI Sbjct: 601 YDYPETGPKTLWKGLSELAPVTIAEADQALIQ--EIRTRLLYRQAVEAARCFEEGVITDP 658 Query: 643 RDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARG 702 R+ D+GA+ G GF P+ GGP ID +GA V +LA +YG RF P L EM +G Sbjct: 659 READVGAILGWGFAPWTGGPISLIDGVGAKAFVETCDQLAQKYGKRFAPPALLREMAEKG 718 Query: 703 ESFW 706 E+F+ Sbjct: 719 ETFY 722 Lambda K H 0.319 0.137 0.393 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: 1043 Number of extensions: 48 Number of successful extensions: 8 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: 714 Length of database: 733 Length adjustment: 40 Effective length of query: 674 Effective length of database: 693 Effective search space: 467082 Effective search space used: 467082 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: 55 (25.8 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