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 Ac3H11_1931 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= SwissProt::P28793 (715 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1931 Length = 727 Score = 335 bits (859), Expect = 5e-96 Identities = 247/739 (33%), Positives = 363/739 (49%), Gaps = 52/739 (7%) Query: 8 ITVTALESGIVELKFDLKGESVNKFNRLTLNELRQAVDAIKAD-----ASVKGVIVSSGK 62 I + + + FD VN R EL + + AD A++KG++++S K Sbjct: 9 IPAQGTDGEVAVITFDETNSPVNTMCRQWQQELGEVTARVAADRERLGAALKGIVLASAK 68 Query: 63 DVFIVGADITEFVENFKLPDAELIAGNLEA-NKIFSDFEDLNVPTVAAINGIALGGGLEM 121 F GAD+ + DA G +E K F E L +P VA +NG ALGGG E+ Sbjct: 69 TSFFAGADLKATMR-LTPADAPNAFGEIERMKKHFRTLETLGIPVVACLNGAALGGGWEV 127 Query: 122 CLAADFRVMADSAKI--GLPEVKLGIYPGFGGTVRLPRLIGVDNAVEWIASGKENRAEDA 179 L A +R+ KI GLPEV LG+ PG G ++ RL+G+ A +I GK +A Sbjct: 128 ALVAHYRIAVADPKIQFGLPEVTLGLMPGATGVTKMTRLLGLMGAQPYILEGKLFNPAEA 187 Query: 180 LKVSAV-DAVVTADKLGAAALDLIK---RAIS--GELDYK----AKRQPKLEKLKLNAIE 229 L++ V + V T ++L AAL I A+ + +YK PK+ + Sbjct: 188 LELQLVHELVATREQLLPAALAHISTHPHAVQPWDDKNYKMPGGTPANPKIAGAL--TVA 245 Query: 230 QMMAFETAKGFVAGQAGPNYPAPVEAIKTIQKAANFGRDKALEVEAAGFAKLAKTSASNC 289 M +T +G YPAP A+ + + A D AL +E+ A+L + Sbjct: 246 PAMLKKTTRG--------RYPAPEAALAAMVEGAMVDYDTALRIESRYLARLMTGPVARN 297 Query: 290 LIGLFLNDQELKKKAK----VYDKIAKDVK--QAAVLGAGIMGGGIAYQSASKGTPILMK 343 +I F D K K V +A K + +LGAG+MG GIA+ AS+G ++K Sbjct: 298 MINTFFFDMNAIKSGKSRPAVNGAVAPRYKPQKVGILGAGMMGAGIAWAQASRGIATVLK 357 Query: 344 DINEHGIEQGLAEAAKLLVGRVDKGRMTPAKMAEVLNGIRPTLSYGDFGNVDLVVEAVVE 403 D++ E G A +AKL RVDKGRMT +L+ I PT S D DL++EAV E Sbjct: 358 DVSAEKAEAGKAYSAKLTQARVDKGRMTAEAQQALLSRITPTASAADLAGCDLIIEAVFE 417 Query: 404 NPKVKQAVLAEVENHVREDAILASNTSTISISLLAKALKRPENFVGMHFFNPVHMMPLVE 463 + +K V E E + ASNTST+ IS LA A RPE FVG+HFF+PV M LVE Sbjct: 418 SRDLKAKVTQEAEPQLAPGGFFASNTSTLPISGLATASSRPEKFVGIHFFSPVDKMKLVE 477 Query: 464 VIRGEKSSDLAVATTVAYAKKMGKNPIVVNDCPGFLVNRVLFPYFGGFAKLVSAGVDFVR 523 +IRG ++ D VA Y + +GK PIVVND GF +R + A ++ G+ Sbjct: 478 IIRGNQTDDETVARAFDYVQALGKVPIVVNDSRGFYTSRTFGTFVMEGAAMLGEGIPAAA 537 Query: 524 IDKVMEKFGWPMGPAYLMDVVGIDTGHHGRDVMAEGFPDRMKDDRRSAIDALY-----EA 578 I+ + G P+GP +MD + H D + K + + L E Sbjct: 538 IENAAMQAGLPVGPLAVMDETALTLSVHVLDQTRADYATEGKTYTATPGELLVERMVKEL 597 Query: 579 KRLGQKNGKGFYAYEADKKGKQKKLVDSSVLEVLKPIVYEQRDV--TDEDIINWMMIPLC 636 KR G+ G GFY Y A G +K L LKP+ +E+ V + ++I + ++ Sbjct: 598 KRPGRAGGGGFYDYPA---GAKKHLWPE-----LKPL-FEKPGVEWSVQEIQDRLLYRQA 648 Query: 637 LETVRCLEDGIVETAAEADMGLVYGIGFPLFRGGALRYIDSIGVAEFVALADQY-AELGA 695 +ET RCL +G++ + +A++G ++GIGFP + GGA+++I GV F+ AD+ A+ G Sbjct: 649 IETARCLAEGVLTSVHDANIGSIFGIGFPAWTGGAMQFIYGTGVEAFLKRADELAAKYGT 708 Query: 696 LYHPTAKLREMAKNGQSFF 714 + TA+ R N Q + Sbjct: 709 GFALTARARATVANFQPVY 727 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: 1082 Number of extensions: 47 Number of successful extensions: 5 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: 727 Length adjustment: 40 Effective length of query: 675 Effective length of database: 687 Effective search space: 463725 Effective search space used: 463725 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