Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate WP_090272540.1 BLU11_RS06160 fatty acid oxidation complex subunit alpha FadB
Query= metacyc::MONOMER-17591 (715 letters) >NCBI__GCF_900105005.1:WP_090272540.1 Length = 715 Score = 1164 bits (3011), Expect = 0.0 Identities = 577/715 (80%), Positives = 647/715 (90%) Query: 1 MIYQGKAITVKPLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTS 60 MIY+GKAITV+ LE GI +L FDL+GESVNKFN+ TL+EL+AAVD I++D+S+KGVIVTS Sbjct: 1 MIYEGKAITVQILEDGIADLRFDLQGESVNKFNQATLAELKAAVDKIQSDSSIKGVIVTS 60 Query: 61 GKDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALGGGLE 120 GKDVFIVGADITEFV F+L +EEL+ NLE N+IF+ FE L+VPTVAAING+ALGGGLE Sbjct: 61 GKDVFIVGADITEFVQAFKLSEEELVTANLETNRIFNAFEGLNVPTVAAINGLALGGGLE 120 Query: 121 MCLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDAL 180 MCLA DFRVM+ + K+GLPE KLGIYPGFGGTVRLPRLIG DNAVEWIA G E +A+ AL Sbjct: 121 MCLACDFRVMAQSTKIGLPETKLGIYPGFGGTVRLPRLIGVDNAVEWIAGGTEQRADSAL 180 Query: 181 KVGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFETAKGF 240 KV AVDAVVA ++L+ AALDL +RA++GELD +A+RQPKLEK+KLN IEQMMAFET KGF Sbjct: 181 KVRAVDAVVADDKLRDAALDLVRRAISGELDFRAKRQPKLEKIKLNTIEQMMAFETTKGF 240 Query: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLNDQEL 300 VAGQAGPNYPAPVEAIK+IQKAAN GRDKALE+EAAGF KLAKT+VA SL+GLFLNDQ L Sbjct: 241 VAGQAGPNYPAPVEAIKTIQKAANHGRDKALEIEAAGFAKLAKTTVAASLVGLFLNDQAL 300 Query: 301 KKKAKKYDEVAKDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAKL 360 K KAKKYD+ A +VKLAAVLGAGIMGGGIAYQSA KGTPILMKDIREEGIQ+GL+EA+KL Sbjct: 301 KSKAKKYDKQAGEVKLAAVLGAGIMGGGIAYQSASKGTPILMKDIREEGIQLGLDEASKL 360 Query: 361 LGKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAVK 420 LGKRV KGR+ P +MA ALN IRPTMSYGDFGNVDIVVEAVVENPKVK AVLAEVE VK Sbjct: 361 LGKRVAKGRMKPEQMAAALNAIRPTMSYGDFGNVDIVVEAVVENPKVKHAVLAEVEQYVK 420 Query: 421 EDAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTVA 480 EDAIIASNTSTISI+ LAQALKRPENF GMHFFNPVHMMPLVEVIRGEK+ E A+ATTVA Sbjct: 421 EDAIIASNTSTISITYLAQALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSEKAVATTVA 480 Query: 481 YAKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAYL 540 YAKKMGK+PIVVNDCPGFLVNRVLFPYFGGFA+L+ G DF R+DK+MEKFGWPMGPAYL Sbjct: 481 YAKKMGKTPIVVNDCPGFLVNRVLFPYFGGFARLIGMGADFQRVDKIMEKFGWPMGPAYL 540 Query: 541 SDVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDKRGKP 600 DVVG+DTGHHGRDVMAEG+PDRMA + KTAVDVMYEANRLGQK GKGFYAYE DK+GK Sbjct: 541 MDVVGMDTGHHGRDVMAEGYPDRMADKTKTAVDVMYEANRLGQKTGKGFYAYELDKKGKT 600 Query: 601 KKVTDPQAYEVLKPIVVEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLIY 660 KKV DPQ+YE+LKP+V+EQRE +DE+I+ MM+PLCLETVRCLEDG+VE+AA+ADMGLIY Sbjct: 601 KKVADPQSYELLKPVVLEQREFSDEEIIEIMMVPLCLETVRCLEDGVVESAADADMGLIY 660 Query: 661 GIGFPPFRGGALRYIDSIGVAEFVALADKYAELGALYHPTAKLREMAKNGQKFFG 715 GIGFPPFRGGALRYID+IGVAEFVA+ADKYAE G +YHPT KLREMA NG+KFFG Sbjct: 661 GIGFPPFRGGALRYIDTIGVAEFVAIADKYAEFGPMYHPTEKLREMAANGKKFFG 715 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: 1484 Number of extensions: 55 Number of successful extensions: 1 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 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