GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Pseudomonas simiae WCS417

Align Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized)
to candidate GFF3565 PS417_18255 AMP-binding protein

Query= SwissProt::Q3UNX5
         (580 letters)



>FitnessBrowser__WCS417:GFF3565
          Length = 546

 Score =  248 bits (632), Expect = 6e-70
 Identities = 169/500 (33%), Positives = 261/500 (52%), Gaps = 20/500 (4%)

Query: 83  NGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLI 142
           +G     +F EL   + +F N L E   ++ G+RV  ++P+  E  +A +   R G V  
Sbjct: 52  DGRATHHTFSELQAHAARFGNFLREQ-GVKPGERVAGLMPRTVELLIAILGTWRIGAVYQ 110

Query: 143 PGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGWGNL 202
           P  T    K I  RL  S+A+ I+TD    P +D V   C     ++IV+        + 
Sbjct: 111 PLFTAFGPKAIEQRLGCSEARWIVTDAHNRPKLDDVI-DCP----RIIVTGAGPRNPDDY 165

Query: 203 KEMMKYASDSHTCVDTKHDEM--MAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDL 260
                       CV    D      +  TSGTTGP K +    S+  L      R  +DL
Sbjct: 166 DFWTVLDRQQADCVPELLDASAPFLLMCTSGTTGPAKPLEVPLSAI-LAFKGYMRDSIDL 224

Query: 261 IASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSA 320
              D  WN +D GWA   + +V  P   G     +  P F   S  + ++K+ IT    +
Sbjct: 225 REDDHFWNLADPGWAYGLYYAVTGPLACGRATLFYDGP-FAVDSTCRIIAKYAITNLAGS 283

Query: 321 PTAYRMLVQND--MSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLI 378
           PTAYR+L+      +      L+   SAGEP+NP+V+  +  + G+ I++ YGQTE  ++
Sbjct: 284 PTAYRLLIAAGAAFADTVRGRLRVISSAGEPLNPQVIRWFADELGVVIHDHYGQTEIGMV 343

Query: 379 CGNFKGMK--IKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYV 436
             N  G++  ++ GS G   P + + +LD+    LPPG+ G +A+      P   F  Y 
Sbjct: 344 LCNHHGLRHPVREGSAGYAVPGYRIVVLDDAHRELPPGRPGVLAVD-RERSPLCWFEGYF 402

Query: 437 DNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPS 496
             P++        +Y++GD   +++DG   FV R+DD+I +SGYR+GPF+VESALIEHP+
Sbjct: 403 GMPTQA---FVDRYYLSGDIVELNDDGSISFVGRNDDVITTSGYRVGPFDVESALIEHPA 459

Query: 497 IAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFI 556
           + E+AV+  PDP R E++KAF+VLN   +S    +L + ++ HV++  A + YPR++EF+
Sbjct: 460 VVEAAVIGKPDPQRTELIKAFVVLNS--QSLPSTELAEVLRLHVRQRLAAHAYPREIEFV 517

Query: 557 EELPKTVSGKVKRNELRKKE 576
           E LPKT SGK++R  LR +E
Sbjct: 518 EHLPKTPSGKLQRFILRNQE 537


Lambda     K      H
   0.319    0.134    0.416 

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: 774
Number of extensions: 40
Number of successful extensions: 8
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: 580
Length of database: 546
Length adjustment: 36
Effective length of query: 544
Effective length of database: 510
Effective search space:   277440
Effective search space used:   277440
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 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 (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