Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate WP_110207373.1 DNK54_RS12945 3-hydroxyacyl-CoA dehydrogenase
Query= BRENDA::A4YDS4 (651 letters) >NCBI__GCF_003194585.1:WP_110207373.1 Length = 731 Score = 157 bits (398), Expect = 1e-42 Identities = 121/407 (29%), Positives = 193/407 (47%), Gaps = 37/407 (9%) Query: 2 KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESG-SLKEGV 60 KV V+G+G+MG GIA + A AG EV + D+ ++ + L K G S +E Sbjct: 327 KVGVLGAGMMGAGIAYVCAQAGMEVVLKDVEVANAEKGKAYSEGILDKAIAKGRSTEEKK 386 Query: 61 EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120 +L RI D A L G D VIEAV ED+ LK+ +F H +P A+L +NTS+LPI Sbjct: 387 AALLGRITATADPAD-LAGCDLVIEAVFEDVALKQKVFAEVIDHVNPDALLCSNTSTLPI 445 Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180 +E+AS + P +G+HFF+P MPLVEI+RGK+TSDE + ++ + + K IVV D Sbjct: 446 TELASGVARPADFIGLHFFSPVDKMPLVEIIRGKETSDEALAKAYDVVQQIRKTPIVVND 505 Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGI--ASIQEVDSSAIEELGFPMGVFLLADYTGLDIGY 238 GF+ +RV+ + G ++ +G+ SI+ ++A GFP+G ++D +++ Sbjct: 506 SRGFYTSRVIGTQINEGLAMLAEGVHPMSIERAATTA----GFPVGPLQISDELNMELMA 561 Query: 239 SVWKA---VTAR-GFKAFPCSS---TEKLVSQGKLGVKSGSGYYQYPSPGKF-----VRP 286 + KA AR G P + K++ G+ G+G+Y Y + + Sbjct: 562 KIRKATADAAARDGIDLGPDPAGDVVNKMIEVGRPSRLKGAGFYNYVEGRRTNLWEGIGE 621 Query: 287 TLPSTSKKL------GRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLP-------- 332 PS ++ R + A+ + A G ++G+G P Sbjct: 622 AFPSAEVQIPIQDMRDRMMFIEALETAKCFEENVVTSSVAANIGSIMGIGFPANTGGAAQ 681 Query: 333 --KGILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377 G EIG+ V +E+ + G + + P L G+ Sbjct: 682 FMTGYEGADGEIGLTAFVKRADELAEAYG-ERFRPTQWLRDRAASGE 727 Score = 84.0 bits (206), Expect = 2e-20 Identities = 56/173 (32%), Positives = 90/173 (52%), Gaps = 9/173 (5%) Query: 410 IVLNRPTRY-NAINGDMIREINQALDSL-EEREDVRVIAITGQGRVFSAGADVTEFGSLT 467 + L+ PT N +N +N A+D L E +DV + I + F AG ++ T Sbjct: 20 LTLDDPTASANTMNELYQSSMNAAVDRLYAEADDVTGVVIASAKKTFFAGGNLKNMVQST 79 Query: 468 PVKAMIASRKFHEV---FMKIQFLTKPVIAVINGLALGGGMELALSADFRVA--SKTAEM 522 A V +++ +PV+A ING ALGGG E+ L+ + R+A + ++ Sbjct: 80 KDDAQAVFEMAESVKAGLRRLELFPRPVVAAINGAALGGGFEICLATNHRIAWDDNSVQI 139 Query: 523 GQPEINLGLIPGGGGTQRLSRLSGRKG--LELVLTGRRVKAEEAYRLGIVEFL 573 G PE +LGL+PGGGG R++RL G + ++++L G R K A G+++ L Sbjct: 140 GLPEASLGLLPGGGGVTRVTRLLGIQSALMDVLLQGPRFKPAAAKAKGLIDEL 192 Lambda K H 0.316 0.134 0.377 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: 1009 Number of extensions: 49 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 651 Length of database: 731 Length adjustment: 39 Effective length of query: 612 Effective length of database: 692 Effective search space: 423504 Effective search space used: 423504 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: 54 (25.4 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