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 GFF1489 PS417_07575 multifunctional fatty acid oxidation complex subunit alpha
Query= SwissProt::P28793 (715 letters) >FitnessBrowser__WCS417:GFF1489 Length = 715 Score = 1308 bits (3385), Expect = 0.0 Identities = 667/715 (93%), Positives = 689/715 (96%) Query: 1 MIYEGKAITVTALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIKADASVKGVIVSS 60 MIYEGKAITV ALESGIVELKFDLKGESVNKFNRLTLNELRQAVD IKADASVKGVIVSS Sbjct: 1 MIYEGKAITVKALESGIVELKFDLKGESVNKFNRLTLNELRQAVDTIKADASVKGVIVSS 60 Query: 61 GKDVFIVGADITEFVENFKLPDAELIAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLE 120 GKDVFIVGADITEFV+NFKLPDAEL+AGNLEANKIFSDFEDLNVPTVAAINGIALGGGLE Sbjct: 61 GKDVFIVGADITEFVDNFKLPDAELVAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLE 120 Query: 121 MCLAADFRVMADSAKIGLPEVKLGIYPGFGGTVRLPRLIGVDNAVEWIASGKENRAEDAL 180 MCLAADFRVM+ +AKIGLPEVKLGIYPGFGGTVRLPRLIG DNA+EWIA+GKEN+AEDAL Sbjct: 121 MCLAADFRVMSATAKIGLPEVKLGIYPGFGGTVRLPRLIGADNAIEWIAAGKENKAEDAL 180 Query: 181 KVSAVDAVVTADKLGAAALDLIKRAISGELDYKAKRQPKLEKLKLNAIEQMMAFETAKGF 240 KV AVDAVV DKL AAL+LIK AISGE DYKAKRQPKLEKLKLNAIEQMM+FETAKGF Sbjct: 181 KVGAVDAVVAPDKLAEAALNLIKGAISGEFDYKAKRQPKLEKLKLNAIEQMMSFETAKGF 240 Query: 241 VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGFAKLAKTSASNCLIGLFLNDQEL 300 VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGF KLAKTSA+ LIGLFLNDQEL Sbjct: 241 VAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGFVKLAKTSAAQSLIGLFLNDQEL 300 Query: 301 KKKAKVYDKIAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL 360 KKKAK YD+IAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL Sbjct: 301 KKKAKAYDEIAKDVKQAAVLGAGIMGGGIAYQSASKGTPILMKDINEHGIEQGLAEAAKL 360 Query: 361 LVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFGNVDLVVEAVVENPKVKQAVLAEVENHVR 420 LVGRVDKGRMT AKMAEVLNGIRPTLSYGDFG+VDLVVEAVVENPKVKQAVLAEVE V+ Sbjct: 361 LVGRVDKGRMTAAKMAEVLNGIRPTLSYGDFGHVDLVVEAVVENPKVKQAVLAEVEAQVK 420 Query: 421 EDAILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSDLAVATTVA 480 +D ILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSS+LAVATTVA Sbjct: 421 DDTILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVEVIRGEKSSELAVATTVA 480 Query: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL Sbjct: 481 YAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVRIDKVMEKFGWPMGPAYL 540 Query: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQ 600 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQ Sbjct: 541 MDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALYEAKRLGQKNGKGFYAYEADKKGKQ 600 Query: 601 KKLVDSSVLEVLKPIVYEQRDVTDEDIINWMMIPLCLETVRCLEDGIVETAAEADMGLVY 660 KK+ D SV EVL P++YEQR+V+DEDIINWMMI LCLETVRCLEDGIVETAAEADMGLVY Sbjct: 601 KKVADPSVHEVLAPVIYEQREVSDEDIINWMMIALCLETVRCLEDGIVETAAEADMGLVY 660 Query: 661 GIGFPLFRGGALRYIDSIGVAEFVALADQYAELGALYHPTAKLREMAKNGQSFFG 715 GIGFP FRGGALRYIDSIGVAEFVALAD+YA+LG LYHPTAKLREMAKNGQSFFG Sbjct: 661 GIGFPPFRGGALRYIDSIGVAEFVALADKYADLGPLYHPTAKLREMAKNGQSFFG 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: 1704 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 Sep 17 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