GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Nocardioides daejeonensis MJ31

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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