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_028583934.1 G494_RS0106850 hypothetical protein
Query= BRENDA::Q64428 (763 letters) >NCBI__GCF_000429965.1:WP_028583934.1 Length = 680 Score = 325 bits (833), Expect = 5e-93 Identities = 216/700 (30%), Positives = 360/700 (51%), Gaps = 57/700 (8%) Query: 52 IRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINMLASCT 111 + I+ N L++EV E ++ DQ + ++ S+K F+AGADI+ + Sbjct: 23 LTIDVAGRSTNVLSREVLEELGSLVQRC-RRDQATALLISSAKQNGFIAGADIHSFTRLS 81 Query: 112 TPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKTVLGV 171 + +EA + ++GQ++F +LE+ P + I G CLGGGLELA+AC YR+A T +G+ Sbjct: 82 SREEALELIRQGQEIFSQLEELPMTTICQIHGFCLGGGLELALACDYRLAADTPATRIGL 141 Query: 172 PEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGPGIKS 231 PEV LGI PG GGT RL +++G A +ML+GR + A +A + G++ V P Sbjct: 142 PEVKLGIHPGFGGTVRLSRLLGGDRALPLMLSGRTLSARQAARAGVITHAVAP------R 195 Query: 232 PEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTVEEKVK 291 + +++L + + R V++ + P V + + +KV+ Sbjct: 196 LLQTAVQHLIQTPPSALPNWRCRLVNSSPVR-------------PLVAAMARRKLRQKVR 242 Query: 292 KQTKGLYPAPLKIIDAVKTGLEQGNDAGYLA--ESEKFGELALTKESKALMGLYNGQVLC 349 ++ YPAP ++ K E GN + E+ EL + ++ L+ + Q Sbjct: 243 EEH---YPAPFALL---KLWEEYGNKPARMMTQEAASVAELIRSPTARNLIRAFLLQERL 296 Query: 350 KK---NKFGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLGRGQQQVFK 406 K ++ APQ + ++GAG+MG IA KGL+ L+DT+V L R ++ Sbjct: 297 KSLPADRSFAPQ----HIHVIGAGVMGGDIAAWCALKGLRVTLQDTSVEVLARAVKRSHD 352 Query: 407 GLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESVT 466 K+K L D + G G +A++VIEA+FED+ K ++L+ +E Sbjct: 353 LFRRKLKTPHLVKAALDRFTPDREGH----GLTRAEVVIEAIFEDVTAKQELLRSLEPRL 408 Query: 467 PEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASAV 526 + A+NTS++PI +AA + P +++G+H+F+PV KM L+E+++T T+++ A+ Sbjct: 409 KPSTLLATNTSSIPIETLAAALEDPGRLLGLHFFNPVAKMLLVEVVSTSYTTEEQQHKAI 468 Query: 527 AVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAAT 586 + GK+ + V+ GPGF R L P + E + EG+ P+ +D + FG PVG Sbjct: 469 QLTKTIGKLPLPVQSGPGFLVNRILMPYLHEAALMEAEGIAPQLIDQVAEEFGMPVGPIE 528 Query: 587 LADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKNK 646 L D VG+D+ Q VA + A GE + L ++ G LG+KSG G+Y Y + +K Sbjct: 529 LIDLVGLDICQSVARFMA-AEGEEY---MPRRLTELIEAGRLGKKSGAGYYEYHA---HK 581 Query: 647 NLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAVLCLQEGILATPEEGDIGAVF 706 L D P+ + ++++ R++ R +NE V CL+EG++ + D G +F Sbjct: 582 ALKPTPD-----------PKHAPPKELEERLLLRLLNEGVTCLREGVVDDGDLLDAGMIF 630 Query: 707 GLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTP 746 GF P GG ++ GA ++ RLR+ E +G +FTP Sbjct: 631 ATGFAPFRGGLIHYLHDQGAGMLLTRLRRLEQQFGPRFTP 670 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: 1053 Number of extensions: 43 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 763 Length of database: 680 Length adjustment: 40 Effective length of query: 723 Effective length of database: 640 Effective search space: 462720 Effective search space used: 462720 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