GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaK in Phyllobacterium brassicacearum STM 196

Align medium-chain acyl-CoA ligase (EC 6.2.1.2); phenylacetate-CoA ligase (EC 6.2.1.30) (characterized)
to candidate WP_106709349.1 CU102_RS02485 acyl--CoA ligase

Query= BRENDA::O74725
         (578 letters)



>NCBI__GCF_003010955.1:WP_106709349.1
          Length = 512

 Score =  148 bits (374), Expect = 5e-40
 Identities = 144/533 (27%), Positives = 250/533 (46%), Gaps = 58/533 (10%)

Query: 48  GKSYSSKEVANRVDSLARSLSKEFGWAPNEGSEWDKTLAVFALNTIDSLPLFWAVHRLGG 107
           G+  +  E+ +  D LA +L     W+  +G      + VF  N  ++    +A+ + G 
Sbjct: 24  GERLTYAELDDLSDRLAAAL-----WS--QGVTRGDRVLVFMNNCWEATVAIYAILKAGA 76

Query: 108 VLTPANASYSAAELTHQLLDSKAKALVTCVPLLSISLEAAAKAGLPKNRIYLLDVPEQLL 167
           V +P NAS  A +L + + + +A+A++    L  +++EA    G   +   ++    + L
Sbjct: 77  VFSPINASTKADKLAYIIENCRARAIIAQEKLAPVAVEAM---GDRTSCDLIVTTKNETL 133

Query: 168 GGVKPPAGYKSVSELTQAGKSLPPVDELRWSAGEGARRTAFVCYSSGTSGLPKGVMISHR 227
                       +   ++  SL  V+ +    G      A + Y+SG++G PKGVM++HR
Sbjct: 134 A-----------APYARSFDSLLQVEPMPVPHGGIDVDLAMLIYTSGSTGRPKGVMMNHR 182

Query: 228 NVIANTLQIKAFEQNYRDGGGTKPASTEVALGLLPQSHIYALVVIGHAGAYRGDQTIVLP 287
           N+ A    I  + QN  D         ++ L +LP +  Y L  +      R   T+VL 
Sbjct: 183 NIEAAATSITTYVQNVED---------DIILNVLPLAFDYGLYQLFMT--IRTGATLVLE 231

Query: 288 -KFEL-KSYLNAIQQYKISALFLVPPIIIHMLGTQDVCSKY--DLSSVTSLFTGAAPLGM 343
             F   ++  + +++  ++   LVP +   +L  +D+   +  DL  +T+    AA L  
Sbjct: 232 TSFSFPQAIFDVMRREHVTGFPLVPTMAALILQMRDIEPGFLPDLRYITNT---AAALPP 288

Query: 344 ETAADFLKLYPNILIRQGYGLTET--CTVVSSTHPHDIWLGSSGALLPGVEARIVTPENK 401
              A   +L+P + +   YGLTE   CT +      D   GS G  +P  E  +V  E K
Sbjct: 289 AHIARLRELFPGVRLYSMYGLTECKRCTYLPPQQL-DHRPGSVGIAIPNTETFVVDDEGK 347

Query: 402 EITTYDSPGELVVRSPSVVLGYLNNEKATAETFVDG---WMR---TGDEAVIRRSPKGIE 455
            +      GELV+R P V+ GY  N++ATA     G   W +   TGD      S  G  
Sbjct: 348 AVAP-GVVGELVIRGPHVMQGYWENDEATARMLRPGLNPWEKVLYTGDLF----SMDGDG 402

Query: 456 HVFIVDRIKELIKVKGLQVAPAELEAHILAHPDVSDCAVIAIPDDRAGEVPKAIVVKSAS 515
           +++ V R  ++IK +G +VAP E+E  + +HP +++  VI IPD   G+  +AIVV S  
Sbjct: 403 YLYFVGRKDDIIKTRGEKVAPKEVETVLHSHPGIAEAVVIGIPDPVLGQAIRAIVVLSDP 462

Query: 516 AGSDESVSQALVKYVEDHKARHKWLKGGIRFVDAIPKSPSGKILRRLIRDQEK 568
           + +D  + +   K +ED       +   + F  ++PK+ +GK+ RRL  + ++
Sbjct: 463 SLTDREIIRHCSKNLEDF-----MVPKSVEFRTSLPKTDTGKVSRRLAAEPQE 510


Lambda     K      H
   0.316    0.134    0.392 

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: 641
Number of extensions: 28
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: 578
Length of database: 512
Length adjustment: 35
Effective length of query: 543
Effective length of database: 477
Effective search space:   259011
Effective search space used:   259011
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: 52 (24.6 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