Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_111391465.1 CLV31_RS03385 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= SwissProt::O32178 (789 letters) >NCBI__GCF_003253485.1:WP_111391465.1 Length = 801 Score = 718 bits (1854), Expect = 0.0 Identities = 384/801 (47%), Positives = 524/801 (65%), Gaps = 12/801 (1%) Query: 1 MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60 M++ I+K AVLGSGVMGS IA H ANIG+ VLLLDIVP +LT+EE+KKGLTKD VR+R Sbjct: 1 MNRTIKKVAVLGSGVMGSRIACHFANIGVQVLLLDIVPFELTEEEQKKGLTKDHPAVRNR 60 Query: 61 LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120 + A++ LK P+ + S I+ GN +DD K+K+ DW+IEVVVE L++K++++ Sbjct: 61 IVTTALQNTLKSNPSAIYDKAFASLISTGNFDDDLPKIKDYDWVIEVVVERLDIKQQLYE 120 Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180 V+++RK G++++SNTSGI + M EGRS+DF+ HF GTHFFNP RYL+LLEIIP +T Sbjct: 121 KVEKYRKPGTLITSNTSGIPMHLMCEGRSEDFQTHFAGTHFFNPPRYLRLLEIIPGPKTK 180 Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240 P+I+ F+ +G+ LGK V KDTP FIANRIG Y ++ + + K G+ V EVD +TG Sbjct: 181 PEIIDFLMDYGDRYLGKETVLCKDTPAFIANRIGVYAIISGMHAIEKAGFGVSEVDKLTG 240 Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE-KEVFRIPSFMNDMLEKGWIGSK 299 P+IGR KSATFRT+DVVGLDT +VA N++ DE ++ F++P + + W G K Sbjct: 241 PVIGRAKSATFRTMDVVGLDTTVNVANNLHKALPHDESRDKFKLPKIVEVLYNNKWFGDK 300 Query: 300 AGQGFYK----KEG-KTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDD 354 GQG++K K+G K + ELD T Y + K K ALEA+K+ K ++K L+ DD Sbjct: 301 TGQGYFKMIRHKDGSKELKELDLKTFEYKDVEKPKFKALEASKEIDDLKKRIKFLVNFDD 360 Query: 355 RAGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEK 414 RAG Y + + EI+D+++ IDQA+ GFGWELGPFE WD +G+K++ EK Sbjct: 361 RAGEFYRASFYDLFKYCSHRIPEISDELYRIDQAVCAGFGWELGPFETWDVLGVKETVEK 420 Query: 415 LEQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD--RGEYRAVKENKKRIHLQALKETK 472 +E G W+ EML G+++FY ENG YYD Y + + I L LK Sbjct: 421 MEAAGEKAAPWVHEMLGAGHDSFYKVENGKRKYYDIPSKSYVEIPGIEDFIILDTLKSAG 480 Query: 473 GVIAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKN 532 + N+G+++ D+GD+V LEFH+K N++G ++I+ I+ + E++YKGLVIGN+G N Sbjct: 481 KKVWGNAGSTIYDMGDEVIGLEFHTKMNSMGAEVIEGINTAIGMAEKSYKGLVIGNEGGN 540 Query: 533 FCVGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACL 592 F GANLAM+ M D F E++ +I +FQ TMM+ +YS+ PVV AP M LGGG E L Sbjct: 541 FSAGANLAMLFMFAGDQEFDEINLMIAQFQNTMMRARYSSVPVVVAPHNMALGGGCELSL 600 Query: 593 PAARIQAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIAMA 649 A IQA +E YMGLVE GVGLIP GGG KE+ + N + G +N + F IA A Sbjct: 601 HADHIQAHAELYMGLVEVGVGLIPAGGGTKEMTRRFANGVIAGDVELNQLQEYFMNIATA 660 Query: 650 KVSASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKE-KVKVPGETG 708 KVS SA+EAR + L+ D IS+N+ L DAK SL D G+ P ++ +KV G+T Sbjct: 661 KVSTSAEEARGLGYLRTQDGISLNRKRQLADAKAKVLSLSDLGYTQPAQQTNIKVLGKTS 720 Query: 709 YAALLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLS 768 A G M YISEHD KIA+KLA+V++GG + TEV E+YLL++EREAFLSL+ Sbjct: 721 LALFEAGITGMIYGNYISEHDAKIARKLAWVMSGGDLSSPTEVSEQYLLDLEREAFLSLT 780 Query: 769 GEAKSQARMQHMLVKGKPLRN 789 GE K+ R+ +L KGKPLRN Sbjct: 781 GEQKTLERIHSILFKGKPLRN 801 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: 1523 Number of extensions: 73 Number of successful extensions: 8 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: 801 Length adjustment: 41 Effective length of query: 748 Effective length of database: 760 Effective search space: 568480 Effective search space used: 568480 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