GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hcl in Dechlorosoma suillum PS

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate Dsui_3212 Dsui_3212 acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II

Query= SwissProt::Q8GQN9
         (527 letters)



>lcl|FitnessBrowser__PS:Dsui_3212 Dsui_3212 acyl-CoA synthetase
           (AMP-forming)/AMP-acid ligase II
          Length = 555

 Score =  191 bits (486), Expect = 5e-53
 Identities = 151/524 (28%), Positives = 234/524 (44%), Gaps = 44/524 (8%)

Query: 40  KTVYIDDAGSYTYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGG 99
           +  YI+     TY EL        + L+  L L    RV + + + + +P    GA++ G
Sbjct: 39  RVAYINMGVGITYGELDRLSRDFAAYLQDVLKLPQGARVALMMPNLLQYPVCMFGALRAG 98

Query: 100 VVPIAINTLLTESDYEYMLTDSAARVAVVSQELLPLFAPMLGKVPTLEHLVVAGGAGEDS 159
            V +  N L T  + E+ L DS A   V+ +         L  VP L+H++V      D 
Sbjct: 99  YVVVNCNPLYTHRELEHQLKDSGAEAIVIVENFAHTLEQALPLVPGLKHVIVTSLG--DM 156

Query: 160 LAALLATGSE-------------------QFEAAPTRP------------DDHCFWLYSS 188
           L AL  T                      +F+AA  R             +D  +  Y+ 
Sbjct: 157 LGALKGTVVNLVVRHVKKMVPAWKLPRHVKFKAAMARGKGATLRPVQVGHEDIAYLQYTG 216

Query: 189 GSTGAPKGTVHIHSDLI---HTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLA 245
           G+TG  KG + +H ++I     A  +  P L  ++  ++ +A  L+  + L    +  L 
Sbjct: 217 GTTGVAKGAMLLHRNIIANLQQAHAWIEPFLH-KDQQLIITALPLYHIFSLTANCLTFLK 275

Query: 246 VGATAVLMAERPTPAAVFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRACTSAG 305
           +GAT VL+          + L +++  +  GV TL+ ++L NPD  K     LRA    G
Sbjct: 276 IGATNVLITNPRDIPGFVKELAQYKFTVITGVNTLFNALLNNPDFAKLDFSALRAALGGG 335

Query: 306 EALPEDVGRRWQARFGVDILDGIGSTEMLHIFLSNRAGDVHY-GTSGKPVPGYRLRLIDE 364
            A+ + V ++W+   G  +++  G TE       N      + G  G P+    + + D+
Sbjct: 336 MAVQKSVAQKWRQVTGKPLIEAYGLTETSPAATINPLDLGEFNGAIGLPISSTEIVIRDD 395

Query: 365 DGAEITTAGVAGELQISGPSSAVMYWNNPEKTAATFMGE-WTRSGDKYLVNDEGYYVYAG 423
            G ++   G AGE+ I GP     YW  P++TA  F  + + R+GD  +++++G+     
Sbjct: 396 LGNDLPV-GQAGEICIRGPQVMKGYWLRPDETATVFYADGFLRTGDVGVMDEKGFVRIVD 454

Query: 424 RSDDMLKVSGIYVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEA 483
           R  DM+ VSG  V P EVE+ +  H AV+E A VG   E      K F+VLK        
Sbjct: 455 RKKDMILVSGFNVYPNEVEAVVAMHPAVMEVAAVGVPSEHSGEAVKIFVVLKD----KSV 510

Query: 484 LRTDLKAHVKNLLAPYKYPRWIEFVDDLPKTATGKIQRFKLRSA 527
            +  L AH K  L  YK P  +EF DDLPKT  GKI R  L+ A
Sbjct: 511 TKEQLIAHCKENLTGYKVPHLVEFRDDLPKTNVGKILRRALKEA 554


Lambda     K      H
   0.319    0.138    0.412 

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: 656
Number of extensions: 35
Number of successful extensions: 7
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: 527
Length of database: 555
Length adjustment: 35
Effective length of query: 492
Effective length of database: 520
Effective search space:   255840
Effective search space used:   255840
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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