Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_101447209.1 BD749_RS18290 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= SwissProt::O32178 (789 letters) >NCBI__GCF_002846395.1:WP_101447209.1 Length = 800 Score = 758 bits (1958), Expect = 0.0 Identities = 396/801 (49%), Positives = 539/801 (67%), Gaps = 13/801 (1%) Query: 1 MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60 M + I+K AVLGSGVMGS IA H ANIG+ VLLLDIVP +LT +EEKKGLT +S VR+R Sbjct: 1 MKRIIKKVAVLGSGVMGSRIACHFANIGVQVLLLDIVPRELTPDEEKKGLTLESKHVRNR 60 Query: 61 LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120 + A++ + P+PL + I GN ED+ +++ ADW IEVVVENL++KK +F Sbjct: 61 IVNSALQAAINSNPSPLYRKSDARLIQTGNFEDNMKEIATADWTIEVVVENLKIKKTVFD 120 Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180 V++HRK G++++SNTSGI + M EGRSDDFK HF GTHFFNP RYLKLLEIIP +TD Sbjct: 121 QVEQHRKPGTLITSNTSGIPIHMMLEGRSDDFKKHFCGTHFFNPPRYLKLLEIIPTPDTD 180 Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240 D++ F+ +G+ LGK V AKDTP FIANR+G Y ++ +Q M K G V EVD I+G Sbjct: 181 QDVVDFLMHYGDLYLGKTTVLAKDTPAFIANRVGIYAIMQGLQVMNKLGLNVDEVDRISG 240 Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSK 299 P+IGRPKSATFRTLDVVGLDT A+VA +Y + DE +E+F++P ++ M+E W+G K Sbjct: 241 PMIGRPKSATFRTLDVVGLDTLANVANGLYQTGEQDESRELFKLPDYLQKMVENKWLGDK 300 Query: 300 AGQGFYKK----EGKT-IYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDD 354 GQGFYKK +GKT I LD T+ YG + + K +LE K + K ++KA +D Sbjct: 301 TGQGFYKKTKDAKGKTEILTLDLNTMEYGPKQRAKFQSLEVLKPIEDLKKRIKAFSKQED 360 Query: 355 RAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEK 414 +A + Y + + EI+D+++ ID AM+ GFGWELGPFE WDAIG ++ ++ Sbjct: 361 KAAKFFNESLYGLFQYVSNRIPEISDELYRIDDAMRAGFGWELGPFEYWDAIGAREGVQR 420 Query: 415 LEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETK 472 + + G W++EML+ G E+FY+ ENG YYD EY+A+ + I L+ L+ K Sbjct: 421 MIENGYQPARWVEEMLEHGKESFYVVENGNRRYYDINSKEYKAIPGAENFIILENLRGNK 480 Query: 473 GVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKN 532 +I KNSGAS+IDLGD + +EFH+K N +G D+I ++KG+E E++++G+V+GNQG N Sbjct: 481 -LIWKNSGASIIDLGDGILNVEFHTKMNTMGGDVIMALNKGIELAEKDFRGMVVGNQGTN 539 Query: 533 FCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACL 592 F GAN+ +I M D ++ E++ +IR+FQ TMM+++YSA PVV AP G+TLGGG E L Sbjct: 540 FSAGANVGLIYMYALDQDYDELNMIIRQFQNTMMRMRYSAIPVVGAPHGLTLGGGCELNL 599 Query: 593 PAARIQAASEAYMGLVESGVGLIPGGGGNKELYI---NHLRRGHDPMNAAMKTFETIAMA 649 IQAA+E YMGLVE GVGLIPGGGG KE+ + + G +N F I MA Sbjct: 600 HCDHIQAAAETYMGLVEFGVGLIPGGGGTKEMTLRAADMYADGDIELNDLKNVFLNIGMA 659 Query: 650 KVSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPV-KEKVKVPGETG 708 KVS SA+EA ++ ++++D ISVN + + DAK A L + G+ P+ + +KV G Sbjct: 660 KVSTSAKEAIDLGYIRKSDGISVNSNRQIADAKAQAIRLAEAGYTKPIQRTNIKVQGRGA 719 Query: 709 YAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLS 768 L GA M Y+SEHD KI++KLAYV+ GG + TEV E+YLL++EREAFLSL+ Sbjct: 720 LGMFLTGANAMFTGRYMSEHDLKISQKLAYVMCGGDLSAPTEVSEQYLLDLEREAFLSLT 779 Query: 769 GEAKSQARMQHMLVKGKPLRN 789 GE K+ R+Q +L GKPLRN Sbjct: 780 GERKTLERIQSILTTGKPLRN 800 Lambda K H 0.316 0.134 0.382 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: 1474 Number of extensions: 69 Number of successful extensions: 7 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: 789 Length of database: 800 Length adjustment: 41 Effective length of query: 748 Effective length of database: 759 Effective search space: 567732 Effective search space used: 567732 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 (21.6 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