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 WP_012543218.1 KVAR_RS24485 fatty acid oxidation complex subunit alpha FadB
Query= SwissProt::P21177 (729 letters) >NCBI__GCF_000025465.1:WP_012543218.1 Length = 729 Score = 1371 bits (3549), Expect = 0.0 Identities = 686/729 (94%), Positives = 710/729 (97%) Query: 1 MLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGEAIGVLEQQSDLKGLLLRSN 60 MLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLG A+ VLE+Q+DLKGLLLRS Sbjct: 1 MLYKGDTLYLDWLEDGIAELVFDAPGSVNKLDTATVASLGHALDVLEKQNDLKGLLLRSE 60 Query: 61 KAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTIAAVNGYALGGGCEC 120 KAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTI+AVNGYALGGGCEC Sbjct: 61 KAAFIVGADITEFLSLFLVPEEQLSQWLHFANSVFNRLEDLPVPTISAVNGYALGGGCEC 120 Query: 121 VLATDYRLATPDLRIGLPETKLGIMPGFGGSVRMPRMLGADSALEIIAAGKDVGADQALK 180 VLATDYRLATPDLRIGLPETKLGIMPGFGGSVR+PR+LGADSALEIIAAGKDVGADQALK Sbjct: 121 VLATDYRLATPDLRIGLPETKLGIMPGFGGSVRLPRLLGADSALEIIAAGKDVGADQALK 180 Query: 181 IGLVDGVVKAEKLVEGAKAVLRQAINGDLDWKAKRQPKLEPLKLSKIEATMSFTIAKGMV 240 IGLVDGVV AEKL +GA A+LRQAINGDLDWKAKRQPKLEPLKLSKIEATMSFTIAKGMV Sbjct: 181 IGLVDGVVAAEKLRDGALAILRQAINGDLDWKAKRQPKLEPLKLSKIEATMSFTIAKGMV 240 Query: 241 AQTAGKHYPAPITAVKTIEAAARFGREEALNLENKSFVPLAHTNEARALVGIFLNDQYVK 300 AQTAGKHYPAPITAVKTIEAAAR GREEAL LENKSFVPLAHTNEARALVGIFLNDQYVK Sbjct: 241 AQTAGKHYPAPITAVKTIEAAARLGREEALVLENKSFVPLAHTNEARALVGIFLNDQYVK 300 Query: 301 GKAKKLTKDVETPKQAAVLGAGIMGGGIAYQSAWKGVPVVMKDINDKSLTLGMTEAAKLL 360 KAKKLTKDVETPK AAVLGAGIMGGGIAYQSAWKGVPVVMKDI+DKSLTLGMTEAAKLL Sbjct: 301 AKAKKLTKDVETPKHAAVLGAGIMGGGIAYQSAWKGVPVVMKDISDKSLTLGMTEAAKLL 360 Query: 361 NKQLERGKIDGLKLAGVISTIHPTLDYAGFDRVDIVVEAVVENPKVKKAVLAETEQKVRQ 420 NKQLERGKIDGLKLAGVISTI PTL+Y+GFDRVD+VVEAVVENPKVKKAVLAETE KVR Sbjct: 361 NKQLERGKIDGLKLAGVISTIQPTLEYSGFDRVDVVVEAVVENPKVKKAVLAETEAKVRP 420 Query: 421 DTVLASNTSTIPISELANALERPENFCGMHFFNPVHRMPLVEIIRGEKSSDETIAKVVAW 480 DTVLASNTSTIPISELA+ L+RPENFCGMHFFNPVHRMPLVE+IRGEK+SD+TIAKVVAW Sbjct: 421 DTVLASNTSTIPISELASVLQRPENFCGMHFFNPVHRMPLVEVIRGEKTSDKTIAKVVAW 480 Query: 481 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKIDKVMEKQFGWPMGPAYL 540 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRK+DKVMEKQFGWPMGPAYL Sbjct: 481 ASKMGKTPIVVNDCPGFFVNRVLFPYFAGFSQLLRDGADFRKVDKVMEKQFGWPMGPAYL 540 Query: 541 LDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP 600 LDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP Sbjct: 541 LDVVGIDTAHHAQAVMAAGFPQRMQKDYRDAIDALFDANRFGQKNGLGFWRYKEDSKGKP 600 Query: 601 KKEEDAAVEDLLAEVSQPKRDFSEEEIIARMMIPMVNEVVRCLEEGIIATPAEADMALVY 660 KKEEDAAV+ LLA+VSQPKRDFS+EEIIARMMIPMVNEVVRCLEEGIIA+PAEADMALVY Sbjct: 601 KKEEDAAVDSLLADVSQPKRDFSDEEIIARMMIPMVNEVVRCLEEGIIASPAEADMALVY 660 Query: 661 GLGFPPFHGGAFRWLDTLGSAKYLDMAQQYQHLGPLYEVPEGLRNKARHNEPYYPPVEPA 720 GLGFPPFHGGAFRWLDT+GSAKYLDMAQQYQHLGPLYEVP GLR+KARHNE YYP VEPA Sbjct: 661 GLGFPPFHGGAFRWLDTIGSAKYLDMAQQYQHLGPLYEVPAGLRDKARHNEAYYPQVEPA 720 Query: 721 RPVGDLKTA 729 RPVG LKTA Sbjct: 721 RPVGALKTA 729 Lambda K H 0.318 0.136 0.399 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: 1700 Number of extensions: 51 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: 729 Length of database: 729 Length adjustment: 40 Effective length of query: 689 Effective length of database: 689 Effective search space: 474721 Effective search space used: 474721 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