Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate BWI76_RS20455 BWI76_RS20455 multifunctional fatty acid oxidation complex subunit alpha
Query= BRENDA::Q64428 (763 letters) >FitnessBrowser__Koxy:BWI76_RS20455 Length = 714 Score = 520 bits (1339), Expect = e-151 Identities = 300/717 (41%), Positives = 437/717 (60%), Gaps = 33/717 (4%) Query: 48 DVAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINML 107 ++AVI I++P K+NTL E SE ++ +I N ++R AV IS+KP F+AGADINM+ Sbjct: 15 NIAVITIDAPGEKMNTLKAEFASEVRGIIRQIRDNKELRGAVFISAKPDNFIAGADINMI 74 Query: 108 ASCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKT 167 A C + QEA ++++GQ++ ++ PV+AAI G+CLGGGLELA+AC R+ + D KT Sbjct: 75 ARCHSAQEAEALARQGQQIMAEIHGLSIPVIAAIHGACLGGGLELALACHGRVCSDDDKT 134 Query: 168 VLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGP 227 LG+PEV LG+LPG+GGTQRLP+++GV A +M+LTG+ +R +A K GLVD++V Sbjct: 135 RLGLPEVQLGLLPGSGGTQRLPRLIGVSGALEMILTGKQLRPRQALKAGLVDEVV----- 189 Query: 228 GIKSPEERTIEYLEEVAVNFA-KGL-ADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKT 285 +TI L + AV A KG A R V A++ + P R +++ Sbjct: 190 ------AQTI--LLQTAVELALKGRPASRAVPARER----------ILAGPLGRSLLFRL 231 Query: 286 VEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNG 345 V +K +T+G YPA +I+ ++TGL QG +GY E+ FGELA+T +S+AL ++ Sbjct: 232 VAKKTHHKTQGNYPATERILQVMETGLAQGCSSGYAEEARAFGELAMTPQSQALRSIFFA 291 Query: 346 QVLCKKNKFGAPQKTV--QQLAILGAGLMGAGIAQVSVDKG-LKTLLKDTTVTGLGRGQQ 402 KK++ GA + V + + ILG GLMG GIA V+ KG L +KD G+ + Sbjct: 292 STDLKKDR-GADAEPVALRSVGILGGGLMGGGIAYVTACKGGLPVRIKDIQPRGINHALK 350 Query: 403 QVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEV 462 + L+ +V+++ L + ERD + G LDY+GF D+VIEAVFEDLA+K K++ EV Sbjct: 351 YSWDLLDKQVRRRYLRASERDRQIGLISGSLDYQGFAHRDVVIEAVFEDLALKQKMVSEV 410 Query: 463 ESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTT 522 E IFASNTS+LPI +IAA + RP++VIG+H+FSPVDKM L+E+I T + T Sbjct: 411 EQHCRPETIFASNTSSLPIGEIAAQASRPQRVIGLHFFSPVDKMPLVEVIPHIGTDRQTI 470 Query: 523 ASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPV 582 A+AV + QGK IVV D GFY R LAP ++E +R+L EG + +D FGFPV Sbjct: 471 ATAVKLAKLQGKTPIVVADKAGFYVNRILAPYINEAMRLLMEGEPVEHIDNALVKFGFPV 530 Query: 583 GAATLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSG 642 G L DEVGID + L A+GERF ++ +++ GRK+ +GFY+Y Sbjct: 531 GPIQLLDEVGIDTGTKIIPVLEAAWGERF-SPPANIISSILNDDRKGRKNNRGFYLY--A 587 Query: 643 SKNKNLNSEIDNILVNLRLPAKPEVS-SDEDIQYRVITRFVNEAVLCLQEGILATPEEGD 701 +K + D + +L + P+ S++ + R + +NEA C E ++ + +GD Sbjct: 588 AKGRKSKKRPDPAIYSLLGISSPQARLSEQQVAERCVMMMLNEAARCFDERVVRSARDGD 647 Query: 702 IGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANNSS 758 IGAVFG+GFPP LGGPFR++D GA +V L++ + YG +FTPC L +A + Sbjct: 648 IGAVFGIGFPPFLGGPFRYMDTLGAGEVAAILQRLAAQYGPRFTPCDTLLHMAEQGA 704 Lambda K H 0.317 0.135 0.380 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: 1070 Number of extensions: 45 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 763 Length of database: 714 Length adjustment: 40 Effective length of query: 723 Effective length of database: 674 Effective search space: 487302 Effective search space used: 487302 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