Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_110804971.1 C8J30_RS06890 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::Q64428 (763 letters) >NCBI__GCF_003217355.1:WP_110804971.1 Length = 728 Score = 328 bits (840), Expect = 8e-94 Identities = 225/728 (30%), Positives = 363/728 (49%), Gaps = 53/728 (7%) Query: 49 VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLA 108 VAVI + + +N ++ E ++ +++ A+ + VL S K F G D+N++A Sbjct: 13 VAVITWDVADKSMNVMSLEGFAQLSALVDGCLADPACKGIVLTSGKKD-FAGGMDLNVIA 71 Query: 109 SCTTPQEAA-------------RISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIA 155 A +I + G M K K KP+ + G+ LG GLEL ++ Sbjct: 72 KMRAGGAEAIFAGVMQMHAVLRKIERAG--MDPKTLKGAKPIACVLPGTALGIGLELPLS 129 Query: 156 CQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKM 215 C A ++ K +G+PE+++GI PGAGGT RL + +G A +L G+ AK Sbjct: 130 CHRIFAAENPKAKIGLPEIMVGIFPGAGGTTRLVRKMGAMMAAPFLLEGKLSDPKAAKAA 189 Query: 216 GLVDQL-VDPLGPG----IKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTS 270 G++D++ DP+ +K+ + ++ + AKG + G M + + Sbjct: 190 GIIDEVCADPMAAARDWVLKATDADLVKPWD------AKGYKMPGGAPYHPAGFMTYVGA 243 Query: 271 YAMTIPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGEL 330 AM V +T G+YPA ++ AV G D E+ F ++ Sbjct: 244 SAM----------------VHGKTMGVYPAAKALLSAVYEGALVPFDQALRIEARWFTKV 287 Query: 331 ALTKESKALMG--LYNGQVLCK-KNKFGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKT 387 + S A++ N + L K N+ ++V +L +LGAG+MGAGIA V+ + G++ Sbjct: 288 LMNPSSGAMIRSLFINKEALEKGANRPKVADQSVTKLGVLGAGMMGAGIAYVAANAGIEV 347 Query: 388 LLKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEA 447 +L D + RG+ L+ ++++ +T ++ + + DY D+V+EA Sbjct: 348 VLIDASQEAADRGKSYSTGILDKGIQRRKVTEAKKAEVLDRITATTDYAALAGCDLVVEA 407 Query: 448 VFEDLAVKHKVLKEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQ 507 VFED VK +V + E+V IFA+NTS LPI+ +A SQRP IG+H+FSPVDKM Sbjct: 408 VFEDPKVKAEVTAKAEAVIGAGAIFATNTSTLPISGLAKASQRPANFIGIHFFSPVDKMN 467 Query: 508 LLEIITTDKTSKDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVD 567 L+EII T + A A+ K IVV D FY RC+ P ++E IR++ EGV+ Sbjct: 468 LVEIIRGKDTGEVAVAKALDFVRAIRKTPIVVNDARFFYANRCIIPYINEGIRMVAEGVN 527 Query: 568 PKKLDALTTGFGFPVGAATLADEVGIDVAQHVAEDLGKAFGERFGGGSV-ELLKLMVSKG 626 P ++ G P+G L DE ID+ +A+ A G+ + G+V E++ M +G Sbjct: 528 PVLVENAAKLVGMPLGPLQLVDETSIDLGVKIAKATKAAMGDAYPDGAVDEVVFWMAEQG 587 Query: 627 FLGRKSGKGFYIYQSGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAV 686 LG+K+ GFY Y +G + + ++ + P + +Q+R++ V EAV Sbjct: 588 RLGKKADAGFYTYDAGKRGGMWDG------LSAQYPRAADQPDLTHVQHRLLMVQVLEAV 641 Query: 687 LCLQEGILATPEEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTP 746 ++G+L EGD+GA+ G GF P GGPF ++D+ GA + V+ + YG +F P Sbjct: 642 RAFEQGVLTDIREGDVGAILGWGFAPWSGGPFAWLDILGAARAVEICDGLAAQYGARFEP 701 Query: 747 CQLLRDLA 754 LLRD+A Sbjct: 702 PALLRDIA 709 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: 1111 Number of extensions: 63 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 763 Length of database: 728 Length adjustment: 40 Effective length of query: 723 Effective length of database: 688 Effective search space: 497424 Effective search space used: 497424 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