Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate WP_086510728.1 BZY95_RS15080 fatty acid oxidation complex subunit alpha FadB
Query= metacyc::MONOMER-17591 (715 letters) >NCBI__GCF_002151265.1:WP_086510728.1 Length = 725 Score = 953 bits (2463), Expect = 0.0 Identities = 488/719 (67%), Positives = 578/719 (80%), Gaps = 5/719 (0%) Query: 1 MIYQGKAITVK--PLEGG--IVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGV 56 MIYQG AITV GG + L FDLK ES+NK + ++EL AV AI+A++ +KG+ Sbjct: 1 MIYQGNAITVARGTKNGGDDVAMLTFDLKDESINKLSSAVIAELDEAVQAIRAESGLKGL 60 Query: 57 IVTSGKDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALG 116 ++ S K+ FIVGADITEF F E L + ++ + IF+ EDL PTV AING+ALG Sbjct: 61 VIGSAKESFIVGADITEFQTMFGKGAEFLESMLMKVHDIFNAIEDLPFPTVTAINGLALG 120 Query: 117 GGLEMCLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKA 176 GG E+ L DFRVM AK+GLPE KLGI PG+GG VRLPR+IG DNAVEWIA G EN+A Sbjct: 121 GGCEVTLTTDFRVMGDKAKIGLPETKLGILPGWGGCVRLPRMIGSDNAVEWIAGGTENRA 180 Query: 177 EDALKVGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFET 236 + ALKVGAVDAVV +QL+AAALD+ RA AGELD++ARR K LKLNAIEQMMAFET Sbjct: 181 DAALKVGAVDAVVPNDQLEAAALDILARANAGELDYQARRAEKTGPLKLNAIEQMMAFET 240 Query: 237 AKGFVAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLN 296 AKG+VAG+AGP+YPAP+EAIK+IQK A R +A +EA F KLA T VA +L+GLF+N Sbjct: 241 AKGYVAGKAGPHYPAPIEAIKAIQKGAGEERARAQAIEAKAFAKLAMTDVAFNLVGLFMN 300 Query: 297 DQELKKKAKKYDEVAKDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNE 356 DQ +KKKA K+++ AK V AVLGAGIMGGGIAYQSA KGTPILMKDI+EE +++GL E Sbjct: 301 DQVVKKKAGKFEKQAKAVNQTAVLGAGIMGGGIAYQSASKGTPILMKDIKEEAVELGLKE 360 Query: 357 AAKLLGKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVE 416 + KL K+VE+G+LT +MAE L IRPT+SYGDFG+VD+VVEAVVENPKVK AVL EVE Sbjct: 361 SRKLFAKQVERGKLTTEQMAEKLTLIRPTLSYGDFGHVDLVVEAVVENPKVKDAVLTEVE 420 Query: 417 GAVKEDAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIA 476 G V ED I+ SNTSTISI+ LAQ LKRPENFCGMHFFNPVH MPLVEVIRGEKTG+ A+A Sbjct: 421 GLVSEDTILTSNTSTISITRLAQNLKRPENFCGMHFFNPVHRMPLVEVIRGEKTGDAAVA 480 Query: 477 TTVAYAKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMG 536 TVAYA+ MGK+PIVVNDCPGFLVNRVLFPYFGGF+ L+ G DF R+DKVMEKFGWPMG Sbjct: 481 ATVAYARAMGKTPIVVNDCPGFLVNRVLFPYFGGFSLLVEQGADFQRVDKVMEKFGWPMG 540 Query: 537 PAYLSDVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDK 596 PAYL DVVG+DT H +VMAEGFP+RMA +GKTA+ VMYE RLGQKN KGFYAYE DK Sbjct: 541 PAYLLDVVGMDTAVHANEVMAEGFPERMARDGKTAIQVMYENERLGQKNDKGFYAYEEDK 600 Query: 597 RGKPKKVTDPQAYEVLKPIVVEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADM 656 +GKPKKV+D +AYE++K +VV ++E +DE+I+ MM+PLCLETVRCLED IVET AEADM Sbjct: 601 KGKPKKVSDDKAYELVKQVVVSEKEFSDEEIIARMMVPLCLETVRCLEDDIVETPAEADM 660 Query: 657 GLIYGIGFPPFRGGALRYIDSIGVAEFVALADKYA-ELGALYHPTAKLREMAKNGQKFF 714 LIYGIGFPPFRGGALRYID++GVAEFV LAD A ELG LY PT KLR+MA++G++F+ Sbjct: 661 ALIYGIGFPPFRGGALRYIDAMGVAEFVKLADGLAEELGPLYAPTDKLRKMAESGERFY 719 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: 1381 Number of extensions: 42 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: 725 Length adjustment: 40 Effective length of query: 675 Effective length of database: 685 Effective search space: 462375 Effective search space used: 462375 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 24 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