Align FadB (EC 5.3.3.8; EC 1.1.1.35; EC 5.1.2.3; EC 4.2.1.17; EC 1.1.1.36) (characterized)
to candidate WP_046010920.1 OLEAN_RS07250 fatty acid oxidation complex subunit alpha FadB
Query= metacyc::G1G01-2277-MONOMER (715 letters) >NCBI__GCF_000967895.1:WP_046010920.1 Length = 715 Score = 974 bits (2518), Expect = 0.0 Identities = 491/714 (68%), Positives = 583/714 (81%) Query: 1 MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIRADASVKGVIVRS 60 MIY+G AITVK +E GI EL F+L GESVNKFNR+TL L+ A DAI+ ++ VKGV+V S Sbjct: 1 MIYDGTAITVKMIEDGIAELNFNLDGESVNKFNRVTLENLKAATDAIKGNSDVKGVLVTS 60 Query: 61 GKDVFIVGADITEFVDNFKLPEAELVAGNLEANRIFNAFEDLEVPTVAAINGIALGGGLE 120 GKD FIVGADITEF + FKLPE E+V +E N+IFNA EDL VPT+ AINGIALGGG E Sbjct: 61 GKDCFIVGADITEFGEAFKLPEEEIVEWIVEGNQIFNAIEDLPVPTLTAINGIALGGGFE 120 Query: 121 MCLAADYRVMSTSARIGLPEVKLGIYPGFGGTVRLPRLIGSDNAIEWIAAGKENRAEDAL 180 MCLA D+RVMS A++GLPEVKLG+ PGFGGTVRL R+IG+DNAIEWI G ENRA+ AL Sbjct: 121 MCLATDFRVMSEKAKVGLPEVKLGLMPGFGGTVRLSRVIGADNAIEWICMGAENRADKAL 180 Query: 181 KVGAVDAVVAPELLLAGALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGF 240 K+GAVDAVVAPE + ++ +++ AI+GELD++A+R K K L+++E MM FETAKGF Sbjct: 181 KMGAVDAVVAPEAVREQSIAMLQSAIAGELDFEARRAVKTGKGLLDSMESMMVFETAKGF 240 Query: 241 VAGQAGPNYPAPVEAIKSIQKAANFGRDKALEVEAAGFAKLAKTSVAESLIGLFLNDQEL 300 V GQ +YPAP+EAIK +QK N RDKA VEA GFAKLAKT+ + +LIGLF NDQ L Sbjct: 241 VKGQTKGHYPAPIEAIKVMQKHHNLTRDKAQAVEAKGFAKLAKTTESAALIGLFNNDQLL 300 Query: 301 KRKAKAHDEIAHDVKQAAVLGAGIMGGGIAYQSAVKGTPILMKDIREEAIQLGLNEASKL 360 K+KAK +D IA V +AAVLGAGIMGGGIAY SA+KGTPILMKDI E I+LGLNEA+KL Sbjct: 301 KKKAKEYDAIAKPVNKAAVLGAGIMGGGIAYISALKGTPILMKDIAEAGIELGLNEANKL 360 Query: 361 LGNRVEKGRLTPAKMAEALNAIRPTLSYGDFANVDIVVEAVVENPKVKQAVLAEVEGQVK 420 L RVE+ ++ P M EALN IRPTLSY +F +VDIVVEAVVENPKVK VLAEVE V Sbjct: 361 LSKRVERKKMKPLAMGEALNRIRPTLSYAEFGDVDIVVEAVVENPKVKGIVLAEVEQHVG 420 Query: 421 DDAILASNTSTISINLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDVAVATTVA 480 ++AI+ASNTSTISI+ LAK++KRPENF+GMHFFNPVHMMPLVE+IRGEK+S+ AVATTVA Sbjct: 421 ENAIIASNTSTISIDFLAKSVKRPENFLGMHFFNPVHMMPLVEIIRGEKTSEEAVATTVA 480 Query: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540 YAKKMGK P+VVNDCPGFLVNRVLFPYFGGFA L+ G DF +IDKVMEKFG+PMGPAYL Sbjct: 481 YAKKMGKTPVVVNDCPGFLVNRVLFPYFGGFAGLMKDGADFRQIDKVMEKFGFPMGPAYL 540 Query: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDERRSAVDALYEANRLGQKNGKGFYAYETDKRGKP 600 MDVVGIDTG H DVMAEGFP+RMK + SA+D LYE GQKN KGFY Y DK+GKP Sbjct: 541 MDVVGIDTGKHANDVMAEGFPERMKADFTSAMDVLYENGFYGQKNNKGFYTYVEDKKGKP 600 Query: 601 KKVFDATVLDVLKPIVFEQREVTDEDIINWMMVPLCLETVRCLEDGIVETAAEADMGLVY 660 KKVFD ++L++L P++ E RE + E+II M+P+C E VRCLE+GIV+TAAEADM LV+ Sbjct: 601 KKVFDESILELLAPVLGEAREFSAEEIIARCMIPMCNEVVRCLEEGIVDTAAEADMALVF 660 Query: 661 GIGFPPFRGGALRYIDSIGVAEFVALADQYADLGPLYHPTAKLREMAKNGQRFF 714 G+GFPPFRGGALRYID++G+A FV LAD+Y D+ PLYH T K+REMA NG+ +F Sbjct: 661 GVGFPPFRGGALRYIDTVGLANFVELADKYKDISPLYHVTDKMREMAANGESYF 714 Lambda K H 0.319 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: 1514 Number of extensions: 60 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 ( 7.4 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