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 Pf1N1B4_3796 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__pseudo1_N1B4:Pf1N1B4_3796 Length = 714 Score = 377 bits (969), Expect = e-109 Identities = 270/733 (36%), Positives = 374/733 (51%), Gaps = 49/733 (6%) Query: 3 MTSAFTLNVRLDNIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKE-LRGVVFVSAK 61 MT A D I V+TID+PG+ NT+ A + + + +L K+ + GV+ SAK Sbjct: 1 MTQAIRYEKGQDQIVVLTIDMPGQSANTMNAVYRDAMATCVARLVAEKDAIAGVIITSAK 60 Query: 62 PDNFIAGADINMIGNCKTAQ-EAEA-----LARQGQQLMAEIHALPIQVIAAIHGACLGG 115 F AG D+N + K + EA+A L +GQ E P V+AAI+GA LGG Sbjct: 61 K-TFFAGGDLNEL--IKVGKPEAKAFYDMVLILKGQLRTLETLGKP--VVAAINGAALGG 115 Query: 116 GLELALACHGRVCTDDPKTVLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLR 175 G E+ LACH RV DDP +LGLPEV LGLLPG GG R+ R++G+ AL +L GK++R Sbjct: 116 GWEICLACHHRVVLDDPSVLLGLPEVTLGLLPGGGGVVRMVRMLGIEKALPYLLEGKKIR 175 Query: 176 AKQALKLGLVDDVVPHSILLEAAVELAKKERP--SSRPLPVRERILAG---PLGR----- 225 +QAL+ L+D+ L EL K R P+ V+ + G P G Sbjct: 176 PQQALQARLIDE------LAADRDELMAKARAWIVDHPVAVQRWDVKGYQIPGGTPSDPK 229 Query: 226 -ALLFKMVGKKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQA 284 A + + KTQG PA E+IL G + + E R F EL S+ Sbjct: 230 LAPMLAITPSILRSKTQGCLPAPEKILCAAVEGAQVDFDTAHLIETRYFTELTTGQVSKN 289 Query: 285 LRSIFFASTDVKKDPGS---DAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDIN 341 L F+ + GS P VG+LG G+MG GIA+V+A AGI V +KDIN Sbjct: 290 LIGTFWFQLNEINAGGSRPQGIAPYVTKKVGVLGAGMMGAGIAFVSAL-AGIDVVLKDIN 348 Query: 342 PQGINHALKYSWDQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLE 401 +S L+ KV R L +R++ LA I T + A DL+IEAVFE+ E Sbjct: 349 LAAAEKGKAHSAALLDKKVARGQLTREQREEILARIHATENDADLAGCDLVIEAVFEDRE 408 Query: 402 LKQQMVAEVEQNCAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIP 461 LK ++ + + + ASNTS+LPI +A + IGLHFFSPVEKMPLVEII Sbjct: 409 LKTKVSSAAQAVVGPDAVIASNTSTLPISGLAIAVPDQTKFIGLHFFSPVEKMPLVEIIK 468 Query: 462 HAGTSAQTIATTVKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDA 521 TS +T+A + KTPIVV D GF+ +R+ + NE I ML +G I+ Sbjct: 469 GVHTSDETLARGFDFVLQIKKTPIVVNDSRGFFTSRVFGTFTNEGIAMLGEGVSAPMIET 528 Query: 522 ALVKFGFPVGPIQLLDEVGIDTGTKI----IPVLEAAYGERFSAPANVVSSILNDD--RK 575 K G PVGP+ + DEV + + I L A PA V +L + R Sbjct: 529 EARKAGMPVGPLAISDEVSLSLMSHIREQTAKDLRAEGKTLIEHPAFAVIDLLLKEYKRP 588 Query: 576 GRKNGRGFYLYGQKGRKSKKQVDPAIYPLIGT---QGQGRISAPQVAERCVMLMLNEAVR 632 G+ G GFY Y G+K ++P + + + G+IS + +R + + E VR Sbjct: 589 GKAAGGGFYDYPATGQKH-------LWPELKSRFEKADGQISPQDIRDRLLFVQAIETVR 641 Query: 633 CVDEQVIRSVRDGDIGAVFGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPC 692 C++E V+ S D ++G++FGIGF + GG ++I+ G + VA Q LA QYG RFTP Sbjct: 642 CMEEGVLTSTADANVGSIFGIGFAAWTGGALQFINQYGVKDFVARAQYLAEQYGERFTPP 701 Query: 693 ERLVEMGARGESF 705 L+E A+ F Sbjct: 702 ALLLEKAAKNALF 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: 1011 Number of extensions: 42 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