GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Duganella sacchari Sac-22

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate WP_072787138.1 BUA36_RS20265 AMP-binding protein

Query= BRENDA::A4YDT1
         (564 letters)



>NCBI__GCF_900143065.1:WP_072787138.1
          Length = 538

 Score =  204 bits (518), Expect = 9e-57
 Identities = 158/498 (31%), Positives = 238/498 (47%), Gaps = 22/498 (4%)

Query: 54  GSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKH-GLKKGDVVYLMTKVHPMHWAV 112
           G +TAL       G +   +Y +L    +R+   LR    L+ G+ V L     PM  A 
Sbjct: 55  GGRTALC------GAQGDWTYAQLRERVDRIAHVLRGPLQLEAGNRVLLRGANTPMMAAC 108

Query: 113 FLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAII-SDSLRASVMEEALGSLKVEKFLI 171
            LAV+K G + VP+   L   E+       + +A++ +DSLRA +    L      + L 
Sbjct: 109 ILAVMKAGLIAVPTMPLLRARELGKIADKAQINAVLCADSLRAELEAATLPEAARARTLF 168

Query: 172 ---DGKRETWNSLEDESSNAEPEDTRGEDVIINYFTSGTTGMPKRVIHTAVSYPV-GSIT 227
              DG+      +  +    E  DT  +DV +  FTSGTTG+PK  +H      V     
Sbjct: 169 FGTDGEDALEALMATQPPAFEAVDTAADDVCLISFTSGTTGIPKGTMHFHRDVMVICDCF 228

Query: 228 TASIVGVRESDLHLNLSATGWAKFAWSSFFSPLLVGATVVGINYEGKLDTRRYLGEVENL 287
             SI+  R  D+ +      +          PL VG T V +    KL     L  +E  
Sbjct: 229 PRSILQSRPGDIFIGTPPLAFTFGLGGLLLFPLRVGGTAVLLE---KLTPETLLKAIETY 285

Query: 288 GVTSFCAPPTAWRQFITLDLDQFRFERLRSVVSAGEPLNPEVIKIWKDKFNLTIRDFYGQ 347
             T     PT +RQ   L   QF    L+  VSAGE L     + W+    L + D  G 
Sbjct: 286 RATVCFTAPTFYRQMAVL-APQFDLASLQKSVSAGEALPLATRESWRQATGLRMIDGIGA 344

Query: 348 TETTAMVGNFPFLKVKPGSMGKPHPLYDIRLLDDEGKEITKPYEVGHITVKLNPRPIGLF 407
           TE   +  +    +++PG+ GKP P Y   +LD +G  +  P  +G + VK    P G  
Sbjct: 345 TELLHIFISASGEQIRPGATGKPVPGYQACILDFDGNPVG-PGVIGRLAVK---GPTGC- 399

Query: 408 LGYSDEKKNMESFREGYYYTGDKAYFDEEGYFYFVGRGDDVIKTSDYRVGPFEVESALLE 467
             Y  + +  +    G+  TGD    D +GYFY+  R DD+I ++ Y +   EVE  LL 
Sbjct: 400 -RYLADDRQRDYVLNGWNLTGDAYEMDADGYFYYRSRTDDMIISAGYNIAGPEVEDVLLR 458

Query: 468 HPAVAEAAVVGVPDTVRWQLVKAYIVLKKGYMPSKELAEEIREKMKTLLSPYKVPRIIEF 527
           HPAVAE  V+G PD  R Q+V+A++VL+ G+  S EL  ++++ +K  ++PYK PR ++F
Sbjct: 459 HPAVAECGVIGRPDEERGQIVEAHVVLRAGFAASPELVVQLQDFVKEQIAPYKYPRAVKF 518

Query: 528 VDELPKTISGKIRRVELR 545
           +  LP+T +GK++R +LR
Sbjct: 519 LKALPRTETGKLQRFKLR 536


Lambda     K      H
   0.318    0.137    0.402 

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: 548
Number of extensions: 30
Number of successful extensions: 5
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: 564
Length of database: 538
Length adjustment: 36
Effective length of query: 528
Effective length of database: 502
Effective search space:   265056
Effective search space used:   265056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 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