Align fatty acid oxidation complex α subunit (EC 1.1.1.35; EC 4.2.1.17) (characterized)
to candidate WP_090442259.1 BLS63_RS07890 fatty acid oxidation complex subunit alpha FadB
Query= metacyc::MONOMER-17591 (715 letters) >NCBI__GCF_900100495.1:WP_090442259.1 Length = 715 Score = 1289 bits (3336), Expect = 0.0 Identities = 649/715 (90%), Positives = 687/715 (96%) Query: 1 MIYQGKAITVKPLEGGIVELNFDLKGESVNKFNRLTLSELRAAVDAIKADASVKGVIVTS 60 MIY+GKAITVK LE GIVEL FDLKGESVNKFNRLTL+ELR +VDAIKAD S+KGVIVTS Sbjct: 1 MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQSVDAIKADGSIKGVIVTS 60 Query: 61 GKDVFIVGADITEFVDNFQLPDEELMAGNLEANKIFSDFEDLDVPTVAAINGIALGGGLE 120 GKDVFIVGADITEFVDNF+LPDEEL+AGNLEANKIFSDFEDL+VPTVAAINGIALGGG E Sbjct: 61 GKDVFIVGADITEFVDNFKLPDEELVAGNLEANKIFSDFEDLNVPTVAAINGIALGGGFE 120 Query: 121 MCLAADFRVMSATAKVGLPEVKLGIYPGFGGTVRLPRLIGCDNAVEWIASGKENKAEDAL 180 MCLAAD+RVM+ +AKVGLPEVKLGIYPGFGGTVRLPRLIG DNAVEWIA+GKEN+A+DAL Sbjct: 121 MCLAADYRVMADSAKVGLPEVKLGIYPGFGGTVRLPRLIGTDNAVEWIAAGKENRADDAL 180 Query: 181 KVGAVDAVVAPEQLQAAALDLAKRAVAGELDHKARRQPKLEKLKLNAIEQMMAFETAKGF 240 KVGAVDAVVA ++LQAAALDL KRA++GELD+KA+RQPKL+KLKLNAIEQMM FETAKGF Sbjct: 181 KVGAVDAVVAADKLQAAALDLVKRAISGELDYKAKRQPKLDKLKLNAIEQMMCFETAKGF 240 Query: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFVKLAKTSVAQSLIGLFLNDQEL 300 VAGQAGPNYPAPVEAIK+IQKAANFGRDKALEVEA GFVKLAKTSVA+SLIGLFLNDQEL Sbjct: 241 VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEATGFVKLAKTSVAESLIGLFLNDQEL 300 Query: 301 KKKAKKYDEVAKDVKLAAVLGAGIMGGGIAYQSALKGTPILMKDIREEGIQMGLNEAAKL 360 KKKAK +DE+AKDVKLAAVLGAGIMGGGIAYQSA+KGTPILMKDIREEGIQMGLNEA+KL Sbjct: 301 KKKAKHHDEIAKDVKLAAVLGAGIMGGGIAYQSAVKGTPILMKDIREEGIQMGLNEASKL 360 Query: 361 LGKRVEKGRLTPAKMAEALNGIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVEGAVK 420 LG RV KGRLTPAKMAEALN IRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVE AVK Sbjct: 361 LGNRVAKGRLTPAKMAEALNAIRPTMSYGDFGNVDIVVEAVVENPKVKQAVLAEVESAVK 420 Query: 421 EDAIIASNTSTISISLLAQALKRPENFCGMHFFNPVHMMPLVEVIRGEKTGETAIATTVA 480 ED I+ASNTSTISISLLA+ALKRPENF GMHFFNPVHMMPLVEVIRGEK+ E A+ATTVA Sbjct: 421 EDTILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSEVAVATTVA 480 Query: 481 YAKKMGKSPIVVNDCPGFLVNRVLFPYFGGFAKLLSFGVDFVRIDKVMEKFGWPMGPAYL 540 YAKKMGK+P+VVNDCPGFLVNRVLFPYFGGF+KLL FGVDFVRIDKVMEKFGWPMGPAYL Sbjct: 481 YAKKMGKTPVVVNDCPGFLVNRVLFPYFGGFSKLLGFGVDFVRIDKVMEKFGWPMGPAYL 540 Query: 541 SDVVGIDTGHHGRDVMAEGFPDRMAVEGKTAVDVMYEANRLGQKNGKGFYAYETDKRGKP 600 SDVVGIDTGHHGRDVMAEGFPDRMAVEG+TAVDVMYEANRLGQKNGKGFYAYE DKRGKP Sbjct: 541 SDVVGIDTGHHGRDVMAEGFPDRMAVEGRTAVDVMYEANRLGQKNGKGFYAYEMDKRGKP 600 Query: 601 KKVTDPQAYEVLKPIVVEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLIY 660 KKV+DP AYE+LK IV EQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLIY Sbjct: 601 KKVSDPVAYELLKSIVTEQREVTDEDIVNFMMIPLCLETVRCLEDGIVETAAEADMGLIY 660 Query: 661 GIGFPPFRGGALRYIDSIGVAEFVALADKYAELGALYHPTAKLREMAKNGQKFFG 715 GIGFPPFRGGALRYIDS+GVAEFVALADKYA+LGALY PT KLREMAKNGQKFFG Sbjct: 661 GIGFPPFRGGALRYIDSLGVAEFVALADKYADLGALYFPTEKLREMAKNGQKFFG 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: 1599 Number of extensions: 54 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