Align Fatty acid oxidation complex subunit alpha; EC 4.2.1.17; EC 5.1.2.3; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate AO356_02330 AO356_02330 multifunctional fatty acid oxidation complex subunit alpha
Query= SwissProt::P28793 (715 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_02330 Length = 715 Score = 1316 bits (3407), Expect = 0.0 Identities = 670/715 (93%), Positives = 691/715 (96%) Query: 1 MIYEGKAITVTALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIKADASVKGVIVSS 60 MIYEGKAITV ALESGIVELKFDLKGESVNKFNRLTLNELRQAVD IKADAS+KGVIVSS Sbjct: 1 MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQAVDTIKADASIKGVIVSS 60 Query: 61 GKDVFIVGADITEFVENFKLPDAELIAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLE 120 GKDVFIVGADITEFV+NFKLPDAELIAGNLEAN+IFSDFEDLNVPTVAAINGIALGGGLE Sbjct: 61 GKDVFIVGADITEFVDNFKLPDAELIAGNLEANRIFSDFEDLNVPTVAAINGIALGGGLE 120 Query: 121 MCLAADFRVMADSAKIGLPEVKLGIYPGFGGTVRLPRLIGVDNAVEWIASGKENRAEDAL 180 MCLAAD+RVMA +AKIGLPEVKLGIYPGFGGTVRLPRLIG DNA+EWIA+GKENRAEDAL Sbjct: 121 MCLAADYRVMATTAKIGLPEVKLGIYPGFGGTVRLPRLIGADNAIEWIAAGKENRAEDAL 180 Query: 181 KVSAVDAVVTADKLGAAALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGF 240 KV AVDAVV KL AAL+ IKRAISGE DYKAKRQPKLEKLKLNAIEQMMAFETAKGF Sbjct: 181 KVGAVDAVVEPGKLHEAALETIKRAISGEFDYKAKRQPKLEKLKLNAIEQMMAFETAKGF 240 Query: 241 VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGFAKLAKTSASNCLIGLFLNDQEL 300 VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGF KLAKTSA+ LIGLFLNDQEL Sbjct: 241 VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGFVKLAKTSAAQSLIGLFLNDQEL 300 Query: 301 KKKAKVYDKIAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL 360 KKKAK YD+IA+DVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL Sbjct: 301 KKKAKAYDEIARDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL 360 Query: 361 LVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFGNVDLVVEAVVENPKVKQAVLAEVENHVR 420 LVGRVDKGRMT AKMAEVLNGIRPTLSYGDFG+VDLVVEAVVENPKVKQAVLAEVE+ V+ Sbjct: 361 LVGRVDKGRMTAAKMAEVLNGIRPTLSYGDFGHVDLVVEAVVENPKVKQAVLAEVEDKVK 420 Query: 421 EDAILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDLAVATTVA 480 ED ILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSS+LAVATTVA Sbjct: 421 EDTILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSELAVATTVA 480 Query: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDK+MEKFGWPMGPAYL Sbjct: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKIMEKFGWPMGPAYL 540 Query: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQ 600 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSA+D LYEAKRLGQKNGKGFYAYE DK+GKQ Sbjct: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAVDVLYEAKRLGQKNGKGFYAYETDKRGKQ 600 Query: 601 KKLVDSSVLEVLKPIVYEQRDVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVY 660 KK+ DSSVLEVLKPIVYEQR+VTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVY Sbjct: 601 KKVADSSVLEVLKPIVYEQREVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVY 660 Query: 661 GIGFPLFRGGALRYIDSIGVAEFVALADQYAELGALYHPTAKLREMAKNGQSFFG 715 GIGFP FRGGALRYIDSIGVAEFVALADQYA+LGALYHPTAKLREMAKNGQ FFG Sbjct: 661 GIGFPPFRGGALRYIDSIGVAEFVALADQYADLGALYHPTAKLREMAKNGQRFFG 715 Lambda K H 0.318 0.137 0.386 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: 1705 Number of extensions: 61 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 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