Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_066324596.1 BLR17_RS15685 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= SwissProt::O32178 (789 letters) >NCBI__GCF_900100165.1:WP_066324596.1 Length = 796 Score = 718 bits (1853), Expect = 0.0 Identities = 384/797 (48%), Positives = 516/797 (64%), Gaps = 9/797 (1%) Query: 1 MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60 M + I+K AV+GSG+MGSGIA H ANIG+ VLLLDI+P +LT+ E KKGLT +S VR+R Sbjct: 1 MKRTIKKVAVIGSGIMGSGIACHFANIGVEVLLLDIIPKELTETESKKGLTLESKVVRNR 60 Query: 61 LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120 + + + LK KP+P+ SAK S I+ N DD K+ DWIIEVVVE L+VKK +F Sbjct: 61 IVNEHLANSLKSKPSPIYSAKFASRISTRNTTDDMAKIAAVDWIIEVVVERLDVKKLVFE 120 Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180 +D++R G++V+SNTSGI + M+EGRS+DF+ HF GTHFFNPARYLKL EIIP +T Sbjct: 121 QIDKYRTPGTLVTSNTSGIPIHFMSEGRSEDFQKHFCGTHFFNPARYLKLFEIIPGPKTS 180 Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240 ++L F+ +GE LGK V AKDTP FI NRIG +G+ + + G + +VD +TG Sbjct: 181 SEVLDFLKNYGEQFLGKTSVVAKDTPAFIGNRIGVFGIQSLFHLVKEMGLTIEQVDKLTG 240 Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSK 299 P+IGRPKSATFRT+DVVGLDT HVA +Y+ DE E+F++P F+ M+E W GSK Sbjct: 241 PVIGRPKSATFRTVDVVGLDTLVHVANGIYENCPEDEAHELFQLPEFIKKMVENKWFGSK 300 Query: 300 AGQGFYKKEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDRAGRL 359 GQGFYKK K I LD TL Y K LE K + + K LI D+AG Sbjct: 301 TGQGFYKKVDKDILSLDLDTLEYRPAKKTSFATLELTKTIEKPIDRFKVLIKGQDKAGEF 360 Query: 360 LWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKLEQLG 419 + Y + + EI+D+++ ID AMK GFGWE GPFE+WDAIG+++ E ++ G Sbjct: 361 YRKSFAALFAYVSNRIPEISDELYKIDNAMKAGFGWENGPFEIWDAIGVEKGIEMIKAEG 420 Query: 420 ADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETKGVIAK 477 W+ EML G+ +FY + G ++YD + V I L ++E+K V + Sbjct: 421 YTPAPWVNEMLASGSSSFYTIKEGATYFYDISKKSQEKVPGQDAFIILNNIRESKKVWS- 479 Query: 478 NSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFCVGA 537 NSGA + DLGD + +EF SK N IG D++Q I+KG++ E+ Y GLVIGNQ NF VGA Sbjct: 480 NSGAIIEDLGDGILNIEFKSKMNTIGGDVLQAINKGIDLAEKEYSGLVIGNQAANFSVGA 539 Query: 538 NLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPAARI 597 N+ MI M + + E++ I+ FQ+TMM+++YS+ PVV AP GMT GGG E L A ++ Sbjct: 540 NIGMIFMMAVEQEYDELNMAIKLFQDTMMRVRYSSIPVVVAPHGMTFGGGCEMSLHADKV 599 Query: 598 QAASEAYMGLVESGVGLIPGGGGNKELYI---NHLRRGHDPMNAAMKTFETIAMAKVSAS 654 AA+E YMGLVE GVG+IPGGGG+KE+ + + R+ +N + F TIAMAKVS S Sbjct: 600 VAAAETYMGLVEFGVGVIPGGGGSKEMTLRAADLFRKNDVELNTLQEYFLTIAMAKVSTS 659 Query: 655 AQEAREMNILKE-TDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEK-VKVPGETGYAAL 712 EA + +L+ D I VN+D + +AK+ A + + G+ P++ +KV G+ Sbjct: 660 GYEAFDTGLLQHGKDIIVVNKDRQIAEAKKHALLMAEAGYTQPIRRNDIKVLGKQALGMF 719 Query: 713 LLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEAK 772 L+G +QM YISEHD KIA KLAYV+AGG + T V E+YLL++EREAFLSL E K Sbjct: 720 LVGTDQMVAGSYISEHDKKIANKLAYVMAGGDLSEPTLVSEQYLLDLEREAFLSLCTERK 779 Query: 773 SQARMQHMLVKGKPLRN 789 + R+Q+ML GKPLRN Sbjct: 780 TLERIQYMLKAGKPLRN 796 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: 1467 Number of extensions: 62 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: 796 Length adjustment: 41 Effective length of query: 748 Effective length of database: 755 Effective search space: 564740 Effective search space used: 564740 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