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 SMc02227 SMc02227 fatty oxidation complex enoyl-COA hydratase/3-hydroxyacyl-COA dehydrogenase/3-hydroxybutyryl-COA epimerase
Query= CharProtDB::CH_003230 (714 letters) >FitnessBrowser__Smeli:SMc02227 Length = 737 Score = 404 bits (1039), Expect = e-117 Identities = 255/723 (35%), Positives = 381/723 (52%), Gaps = 27/723 (3%) Query: 7 FTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFI 66 F + D IA++T D+P + MN E ++ AII Q + ++GVV S K +F Sbjct: 6 FKIETDADGIALVTWDMPDKSMNVFTEEVMKELDAIIDQTTADPAVKGVVITSGK-SSFS 64 Query: 67 AGADINMIGNCKTAQEAEA------LARQGQQLMAEIHALPIQV-------IAAIHGACL 113 GAD++MI + T Q E AR+ L+ + L ++ ++AI+G C+ Sbjct: 65 GGADLSMIKSMFTFQAEERKKDPDNAARKLFDLVGRMTGLFRKLETSGKPWVSAINGTCM 124 Query: 114 GGGLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQ 173 GG E++LACHGRV ++ + LPEV++G+ PG+GGTQR+PRL AL+M+ TG Sbjct: 125 GGAFEMSLACHGRVASNAKSVKIALPEVKVGIFPGAGGTQRVPRLTNTQDALQMMTTGSS 184 Query: 174 LRAKQALKLGLVDDVVPHSILLEAAVELAKKERPSSRPLPVRERILAG----PLGRALLF 229 L +A +GLV +VV L+EAA + K +P + L G A L+ Sbjct: 185 LTPARAKAMGLVHEVVDPDKLIEAAKAMIKNGLKPVQPWDEKGFKLPGGGIWTPASAQLW 244 Query: 230 KMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQS-QALRSI 288 +T GNYP IL+ V GL + E R F E+ T ++ +RS+ Sbjct: 245 PAASGILRRETYGNYPGAIAILKCVYEGLQVPFDTALKIEQRYFTEILQTTEAFSMIRSL 304 Query: 289 FFASTDVKKDPGSDA--PPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGIN 346 F + ++ K A P L VG++G G MG IAYVTA GIPV + D + + Sbjct: 305 FVSMQELGKGARRPAGVPKTELKKVGVVGAGFMGASIAYVTAA-GGIPVTLIDRDMEAAE 363 Query: 347 HALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQM 406 +S ++ + + L E + L+ I+ + DY L+IEAVFE+ ++K+ + Sbjct: 364 KGKTHSEGLVKDAIGKGRLTKEEGEALLSRITPSADYGDLRDAGLVIEAVFEDRQVKKDV 423 Query: 407 VAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTS 466 + +VE A IFASNTS+LPI +A ++ RP++ IG+HFFSPVEKM L E+I T Sbjct: 424 IEKVEAVIAEDAIFASNTSTLPITGLARNSKRPDRFIGIHFFSPVEKMMLTEVILGKETG 483 Query: 467 AQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKF 526 + +A + KTPIVV D GFYVNR + YI+EA ML +G I+ A Sbjct: 484 DRALAAALDYVAAIRKTPIVVNDTRGFYVNRCVFRYIHEAYDMLIEGVPPAMIENAAKMA 543 Query: 527 GFPVGPIQLLDEVGIDTGTKIIPVLEAAYGER---FSAPANVVSSILNDDRKGRKNGRGF 583 G PVGP+ L DEV ID KI+ A G++ A + + DR+GRKNG+GF Sbjct: 544 GMPVGPLSLNDEVAIDLSQKILKAAVADLGDKAVDLRHMALIDKMVDELDRRGRKNGKGF 603 Query: 584 YLYGQKGRKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVR 643 Y Y K ++K + P + L + G I + +R ++ + EA R ++E ++ R Sbjct: 604 YEYPAK--PARKYLWPGLKELYPQKDAGEIEVGVLKQRLLVTIALEAARTIEEGIVTDPR 661 Query: 644 DGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGARGE 703 + D+G++ G GF P+ GG YID +GA V + ++LA +G F P L EM +GE Sbjct: 662 EADVGSILGFGFAPYTGGTLSYIDGMGAKAFVELCEKLAADHGDHFRPTPLLKEMAEKGE 721 Query: 704 SFW 706 +F+ Sbjct: 722 TFY 724 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: 1024 Number of extensions: 40 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: 714 Length of database: 737 Length adjustment: 40 Effective length of query: 674 Effective length of database: 697 Effective search space: 469778 Effective search space used: 469778 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