Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate Pf6N2E2_1850 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= metacyc::MONOMER-17591 (715 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1850 Length = 715 Score = 365 bits (937), Expect = e-105 Identities = 254/715 (35%), Positives = 371/715 (51%), Gaps = 31/715 (4%) Query: 16 GIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTSGKDVFIVGADITEFV 75 GIV + D+ G VN N+L + A V+ ++ + + GV++ S K F G D+ E Sbjct: 12 GIVTVTMDMPGP-VNAMNQLYRETMAATVNRLEQENGLTGVVIASAKSTFFAGGDLNELT 70 Query: 76 DNFQLPDEELMAGNLEANKI-FSDFEDLDVPTVAAINGIALGGGLEMCLAADFRVM--SA 132 D F+ DE +E K E L VP VAAING ALGGG E+ LA ++RV+ S Sbjct: 71 D-FKPGDEADFQAKIELTKNDLRRLERLPVPVVAAINGAALGGGFEIALACNYRVLLNSP 129 Query: 133 TAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDALKVGAVDAVVAPE 192 A VGLPEV LG+ PG GG VRL +G + A+ + GK K +AL +G V+ ++ Sbjct: 130 AAVVGLPEVSLGLLPGGGGIVRLVHHLGLERALPLLLEGKRMKPAEALALGLVNELIEQA 189 Query: 193 QLQAAALDLAKRAVAGE-------LDHKARRQPKLEKLKLNAIEQMMAFETAKGFVAGQA 245 A +A G+ DHK + P + + + QM+A A+ A Sbjct: 190 DALVPAAKAWIKAQVGDDGVSLQPWDHKGHKIPGGTAQQPH-VAQMIA--GAQAMTAKNT 246 Query: 246 GPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIG-LFLNDQELKKKA 304 PAP + +A D AL VE G LA + A+++I +F E+ + Sbjct: 247 RGLLPAPERILAVAVEATLLDFDAALLVETRGLTHLAASVQAKNIINTMFFQMNEVNGGS 306 Query: 305 KKYDEVAKD-VKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAKLLGK 363 + K V ++GAG+MG GIA+ SA G +++ D+ E + G KLL K Sbjct: 307 SRPTGFDKSKVSKLGIIGAGMMGNGIAHVSAKVGIEVMLLDVSLEAAERGKANVEKLLSK 366 Query: 364 RVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAVKEDA 423 V +GRL+ AK E L I+PT+ Y D VD VVEAV E+ +K V + E + E A Sbjct: 367 TVSQGRLSEAKKDEILALIKPTVDYADLQGVDFVVEAVFESVDLKGKVTQQAEAQLPESA 426 Query: 424 IIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTVAYAK 483 + +NTST+ ISLLA A KRP NF G+HFF+PV MPLVE+I GE+T + A+A +A+ Sbjct: 427 VFGTNTSTLPISLLANASKRPANFIGIHFFSPVERMPLVEIICGEQTSDAALAKAFDFAR 486 Query: 484 KMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAYLSDV 543 ++GK+ IVVND GF +R YF KLL GVD + ID + ++ G P+GP + D Sbjct: 487 QIGKTAIVVNDSLGFFTSRTFGSYFDEGCKLLQEGVDPLLIDNLGKQIGMPVGPLTVLDE 546 Query: 544 VGIDTGHHGRDVMAE--GFPDRMAVEGKTAVD--VMYEANRLGQKNGKGFYAYETDKRGK 599 V ++ + E F AV ++ E NR G+ G GFY Y Sbjct: 547 VSLELMRKVNETQKEMGVFATVFDNSHSDAVGNILIKEYNRPGRHYGGGFYDYPEG---- 602 Query: 600 PKKVTDPQAYEV-LKPIVVEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGL 658 +K P YE+ ++P VV + EDI ++ +E V+CL++G++ + A+ ++G Sbjct: 603 GEKTIWPGLYELFVRPEVV----LPVEDIKERLLFRQVIEAVKCLQEGVLRSVADGNVGS 658 Query: 659 IYGIGFPPFRGGALRYIDSIGVAEFVALADKYAE-LGALYHPTAKLREMAKNGQK 712 I GIG P + GG L++++ GV FV A + A+ G + P L E A G++ Sbjct: 659 ILGIGAPTWTGGFLQFVNGYGVERFVQRARELAQTYGERFTPPVLLLEKAAKGEE 713 Lambda K H 0.318 0.137 0.388 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: 1100 Number of extensions: 48 Number of successful extensions: 5 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: 715 Length of database: 715 Length adjustment: 39 Effective length of query: 676 Effective length of database: 676 Effective search space: 456976 Effective search space used: 456976 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: 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