Align Probable 3-hydroxyacyl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_059153517.1 V474_RS22775 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein
Query= SwissProt::O32178 (789 letters) >NCBI__GCF_001046635.1:WP_059153517.1 Length = 774 Score = 513 bits (1322), Expect = e-149 Identities = 306/798 (38%), Positives = 445/798 (55%), Gaps = 33/798 (4%) Query: 1 MHKHIRKAAVLGSGVMGSGIAAHLANIGIPVLLLDIVPNDLTKEEEKKGLTKDSSEVRSR 60 M IRK V+G+G MG+GIAA +AN G+PVLLLDIVP D R+ Sbjct: 1 MSDTIRKVCVIGAGTMGAGIAAQVANAGVPVLLLDIVPKDAGN--------------RNA 46 Query: 61 LSRQAMKKLLKQKPAPLTSAKNTSYITPGNLEDDAEKLKEADWIIEVVVENLEVKKKIFA 120 ++ A+ K+LK +PAP S + GN+ED EK+ E DW+IE V+E L++K+ ++A Sbjct: 47 IAEGAVAKMLKTEPAPFMSKSAAKLVETGNIEDHLEKIAECDWVIEAVIERLDIKQGLYA 106 Query: 121 LVDEHRKTGSIVSSNTSGISVQEMAEGRSDDFKAHFLGTHFFNPARYLKLLEIIPIKETD 180 ++ ++ G+ VSSNTS I + ++ EGRS F+ FL THFFNP RY++LLEI+ TD Sbjct: 107 RIEAVKRDGTAVSSNTSTIPLAQLVEGRSAAFQRDFLITHFFNPPRYMRLLEIVTGPATD 166 Query: 181 PDILKFMTAFGENVLGKGVVTAKDTPNFIANRIGTYGLLVTVQEMLKGGYQVGEVDSITG 240 I + F + LGK VV A DTP FIANRIGTY + + + G V D+I G Sbjct: 167 TAIAAKVERFSDAALGKTVVRANDTPGFIANRIGTYWIQLGLNAAFDMGLTVELADAIAG 226 Query: 241 PLIGRPKSATFRTLDVVGLDTFAHVARNVYDKADGDE--KEVFRIPSFMNDMLEKGWIGS 298 +G PK+ F +D+VG+D H+ ++ D+ + R + M+ +G+ G Sbjct: 227 KPMGVPKTGIFGLVDLVGIDLMPHLQASLTSTLPKDDPYHAIARTMPLIEKMIGEGYTGR 286 Query: 299 KAGQGFY---KKEGKTIYELDPVTLTYGERTKMKSPALEAAKQAKGTKAKMKALIYSDDR 355 K GFY K+ G+ +D + Y E + P+ A K ++AL+ + + Sbjct: 287 KGKGGFYRLNKEMGRRKETIDLASGEYRETIRAFGPSGAAG------KGDLRALVETKGK 340 Query: 356 AGRLLWNITSQTLLYSAELLGEIADDIHAIDQAMKWGFGWELGPFEMWDAIGLKQSAEKL 415 G W + TL Y+A L+ A D+ AID AMK G+ W+ GPFEM D +G A++L Sbjct: 341 IGDYAWAVLGGTLAYAAALVPSAAGDVVAIDDAMKLGYNWKAGPFEMIDKLGAAWLAQRL 400 Query: 416 EQLGADMPGWIKEMLDKGNETFYIKENGTVFYYD-RGEYRAVKENKKRIHLQALKETKGV 474 E G +P +K G+ TFY E+G Y D G YR +K + + L +K Sbjct: 401 ESEGKPVPEILK---IAGDRTFYRVEDGKRQYLDLDGTYRDIKRPEGVLKLSDIKLASKP 457 Query: 475 IAKNSGASLIDLGDDVALLEFHSKSNAIGLDIIQMIHKGLEETERNYKGLVIGNQGKNFC 534 + +N A+L D+GD V LEF K NA+ D++++I + + + YK LV+ N +F Sbjct: 458 LLRNGSAALWDVGDGVVALEFTGKMNALDGDVMKLIVEAIPLVKAKYKALVVYNDADSFS 517 Query: 535 VGANLAMILMEVQDDNFLEVDFVIRRFQETMMKIKYSAKPVVAAPFGMTLGGGTEACLPA 594 GANL + L V + E++ +I Q +KY+ PVV AP G+ +GGG E L Sbjct: 518 AGANLGLALFAVNIAAWGEIEKLIAGGQMAYKGLKYAPFPVVGAPAGLAVGGGCEILLHC 577 Query: 595 ARIQAASEAYMGLVESGVGLIPGGGGNKEL---YINHLRRGHDPMNAAMKTFETIAMAKV 651 +QA +E YMGLVE GVGLIPG GGN E+ + + PM A K FET++ A V Sbjct: 578 DAVQAHAELYMGLVECGVGLIPGWGGNGEMLDRWQKNKGMPKGPMPAVAKVFETVSTASV 637 Query: 652 SASAQEAREMNILKETDQISVNQDHLLYDAKQLAASLYDTGWRPPVKEKVKVPGETGYAA 711 S SA +A+E+ L+ D +++N+D LLYDAKQ A SL + G+ P ++PGE+G A Sbjct: 638 SRSAAQAKELLFLRADDGVTMNRDRLLYDAKQKALSLVE-GYAAPEAPTFRLPGESGRTA 696 Query: 712 LLLGAEQMKLSGYISEHDFKIAKKLAYVIAGGKVPFGTEVDEEYLLEIEREAFLSLSGEA 771 L + AE G +++D ++ LA V++GG+ V E LL++ERE F+ L E Sbjct: 697 LGMAAEGFHKQGKATDYDMVVSAALAGVLSGGEADLVDTVSEAELLKLERETFMRLVREP 756 Query: 772 KSQARMQHMLVKGKPLRN 789 +S R++HML GKPLRN Sbjct: 757 RSIVRVEHMLETGKPLRN 774 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: 1434 Number of extensions: 71 Number of successful extensions: 6 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: 774 Length adjustment: 41 Effective length of query: 748 Effective length of database: 733 Effective search space: 548284 Effective search space used: 548284 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