Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate WP_036259721.1 DL86_RS06940 fatty acid oxidation complex subunit alpha FadB
Query= metacyc::MONOMER-17591 (715 letters) >NCBI__GCF_000746085.1:WP_036259721.1 Length = 720 Score = 687 bits (1774), Expect = 0.0 Identities = 358/719 (49%), Positives = 483/719 (67%), Gaps = 6/719 (0%) Query: 1 MIYQGKAITVK----PLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGV 56 M++ G+ + ++ E GI EL F+ E VNK + LT SELR A++ I A ++KGV Sbjct: 1 MLFDGQTVKLEWPGERQEEGIAELRFERGAEPVNKLDALTFSELRRALEIIAATPAIKGV 60 Query: 57 IVTSGKDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALG 116 ++ S KD FIVGADI EF F+ P E+++A + ++I + DL VPTVAAING+ALG Sbjct: 61 LIASAKDAFIVGADIFEFTAIFKRPPEDIVAFVAQNSEIITALADLPVPTVAAINGLALG 120 Query: 117 GGLEMCLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKA 176 GGLE+ LAADFRVMS+ A++G PEV LG++PG+GGTVRLPRLIG + EWIASG + K Sbjct: 121 GGLELALAADFRVMSSAARIGFPEVHLGLFPGYGGTVRLPRLIGLVASAEWIASGAQQKP 180 Query: 177 EDALKVGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFET 236 E AL+ GAVDAVVAPE L+AAAL +RA+ + RR+ + L++ E ++ Sbjct: 181 EAALEEGAVDAVVAPEDLRAAALATLERAIEAPGEWSQRRRDLRKSLRIAPEEASRLLDS 240 Query: 237 AKGFVAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLN 296 AK A + P+ PA A++ ++ A++ RD AL +EA F K AKT A SL+ +F+N Sbjct: 241 AKA-AAAKTLPHLPAAHIALELLEAASDLDRDSALTLEAQAFAKAAKTQAAASLVTIFIN 299 Query: 297 DQELKKKAKKYDEVAKDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNE 356 +Q LKK ++ Y + A V+ AAV+GAG+MGGGIAYQSA +G PI+MKDI E+ + +G++E Sbjct: 300 EQALKKISRGYAKKAAPVRKAAVVGAGVMGGGIAYQSAARGVPIIMKDIAEQALDLGMSE 359 Query: 357 AAKLLGKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVE 416 A KLL ++VE+GRL AK L I P ++Y F VD+V+EAVVEN VK+AVL+E+E Sbjct: 360 ARKLLARQVEQGRLDQAKADAILGAIAPGLTYEGFDGVDVVIEAVVENIAVKKAVLSELE 419 Query: 417 GAVKEDAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIA 476 E AI+ASNTS++ I L + L+RP+ F GMHFFNPV M LVEV+RG KT E IA Sbjct: 420 RVTGEAAILASNTSSLRIGDLTEGLRRPDKFIGMHFFNPVPRMALVEVVRGPKTSEETIA 479 Query: 477 TTVAYAKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMG 536 T V YA MGK+PIV+ DCPGF+VNR L PY F +L+ G DF +DKVME FGWPMG Sbjct: 480 TIVGYADAMGKTPIVMQDCPGFVVNRALTPYLIAFLRLVHDGADFAHVDKVMETFGWPMG 539 Query: 537 PAYLSDVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDK 596 PAYL DV+G+D HH ++++ GFP+RM +A+D++ RLGQKNG GFY Y D Sbjct: 540 PAYLIDVIGMDISHHVVEIVSAGFPERMQTSFASAIDILLREKRLGQKNGHGFYKYAKDA 599 Query: 597 RGKPKKVTDPQAYEVLKPIVVEQR-EVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEAD 655 +G+P+K DP+ +L + + +++IV MM+PL E RC+EDG+V + EAD Sbjct: 600 KGRPRKELDPETDRLLAEARPNGKIAIGEDEIVERMMLPLIFEAARCVEDGVVGSRGEAD 659 Query: 656 MGLIYGIGFPPFRGGALRYIDSIGVAEFVALADKYAELGALYHPTAKLREMAKNGQKFF 714 M LI G+G P + GGAL+Y D +GVA VA A K+ LGA+Y P+ MA G F+ Sbjct: 660 MSLILGLGLPRYLGGALKYADHLGVANVVASAAKWESLGAIYRPSEGFSAMAAAGDVFY 718 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: 1190 Number of extensions: 50 Number of successful extensions: 3 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: 720 Length adjustment: 40 Effective length of query: 675 Effective length of database: 680 Effective search space: 459000 Effective search space used: 459000 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 Apr 09 2024. 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