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 Pf6N2E2_6000 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= CharProtDB::CH_003230 (714 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_6000 Length = 714 Score = 382 bits (981), Expect = e-110 Identities = 268/725 (36%), Positives = 373/725 (51%), Gaps = 33/725 (4%) Query: 3 MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAK 61 MT A D I V+T+D+PG+ NT+ A + + A + +L+ K+ + GV+ SAK Sbjct: 1 MTDAIRYETGQDRIVVLTLDMPGQSANTMNAVYREAMAACVARLQAEKDSIAGVIITSAK 60 Query: 62 PDNFIAGADINMIGNCKTAQ-EAEALARQGQQLMAEIHALPI---QVIAAIHGACLGGGL 117 F AG D+N + K + EA+A L A++ L V+AAI+GA LGGG Sbjct: 61 -HTFFAGGDLNEL--IKVGKPEAKAFYDMVLLLKAQLRTLETLGKPVVAAINGAALGGGW 117 Query: 118 ELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAK 177 E+ LACH RV D P LGLPEV LGLLPG GG R+ RL+G+ AL +L GK++ A+ Sbjct: 118 EICLACHHRVALDLPSVQLGLPEVTLGLLPGGGGVVRMVRLLGLEKALPYLLEGKKVNAQ 177 Query: 178 QALKLGLVDDVVPHSILLEAAVELAKKERPSS-RPLPVRERILAGPLGR----ALLFKMV 232 QAL GL+D++ L A PS +P + L G A + + Sbjct: 178 QALLAGLIDELAKDRNELLAKSRAWILANPSVIQPWDAKGYRLPGGTPSDPKVAQMLAIA 237 Query: 233 GKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAS 292 +KTQG PA E+IL G + + E R F EL ++ L F+ Sbjct: 238 PSILRNKTQGCLPAPEKILCAAVEGAQVDFDTAHLIETRYFTELTTGQVAKNLIGTFWFQ 297 Query: 293 TDVKKDPGS---DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHAL 349 + K GS P VG+LG G+MG GIAYV+A AGI V +KD++ Sbjct: 298 LNEIKAGGSRPQGLAPYLTKKVGVLGAGMMGAGIAYVSAV-AGIAVVLKDVDLAAAEKGK 356 Query: 350 KYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAE 409 S L+ K+ R L A +R+ LA I T A DL+IEAVFE+ +K + A Sbjct: 357 ARSAALLDKKIARGQLTAEQREATLARIHPTDSNADLAGCDLVIEAVFEDRAVKASVSAA 416 Query: 410 VEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQT 469 + + ASNTS+LPI +A P + IGLHFFSPVEKMPLVEII A TS +T Sbjct: 417 AQAVVGDDAVIASNTSTLPITGLAMAVPDPTKFIGLHFFSPVEKMPLVEIIKGARTSDET 476 Query: 470 IATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFP 529 +A + KTPIVV D GF+ +R+ + NE I ML +G I+ K G P Sbjct: 477 LARGFDFVLQINKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVSAPMIETEARKAGMP 536 Query: 530 VGPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPA-NVVSSILND-DRKGRKNGRGF 583 VGP+ + DEV + + I L A PA V+ +LN+ R G+ G GF Sbjct: 537 VGPLAVSDEVSLSLMSHIRAQTAKDLHAEGKMPIEHPAFAVIDLLLNEYKRPGKAAGAGF 596 Query: 584 YLYGQKGRKSKKQVDPAIYPLIGTQGQ---GRISAPQVAERCVMLMLNEAVRCVDEQVIR 640 Y Y G+K ++P + ++ + G+IS + +R + + E VRC++E V+ Sbjct: 597 YEYPANGQK-------YLWPQLKSRFEKTDGQISPQDIRDRLLFIQALETVRCIEEGVLT 649 Query: 641 SVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEMGA 700 S D +IG++FGIGF + GG ++I+ G + V Q LA QYG RF+P L+E A Sbjct: 650 STADANIGSIFGIGFAAWTGGALQFINQYGLQDFVGRAQYLAEQYGERFSPPALLLEKAA 709 Query: 701 RGESF 705 R E F Sbjct: 710 RHELF 714 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: 984 Number of extensions: 39 Number of successful extensions: 7 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: 714 Length adjustment: 39 Effective length of query: 675 Effective length of database: 675 Effective search space: 455625 Effective search space used: 455625 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