GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Rhodanobacter denitrificans 2APBS1

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate WP_015448186.1 R2APBS1_RS12475 acetyl-CoA C-acyltransferase

Query= SwissProt::Q8VPF1
         (401 letters)



>NCBI__GCF_000230695.2:WP_015448186.1
          Length = 394

 Score =  239 bits (610), Expect = 1e-67
 Identities = 155/399 (38%), Positives = 225/399 (56%), Gaps = 17/399 (4%)

Query: 5   VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64
           V I  A RT IG F G    V    L A  ++A +E++  V  + + EV +GC   A   
Sbjct: 6   VVIVGAKRTAIGSFLGQFTGVPTPKLGATAIRAALEQSG-VAPADVGEVIMGCVLPANL- 63

Query: 65  NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124
            +  AR A L A LP      T+N++C SGM A+      I +G A +V+AGG+ESM+ A
Sbjct: 64  GQAPARQASLGADLPAGTGCTTINKVCGSGMKAIMLGHDLIKAGSAAIVVAGGMESMTNA 123

Query: 125 PY-VMGKADSAFGRGQKIEDTTIGWRFI-NPLMKAQYGVDAMPETADNVADDYKVSRADQ 182
           P+ V  +    +G GQ ++   + W  + NP     Y   AM    +  AD Y  +R  Q
Sbjct: 124 PHMVQARTGIRYGDGQLVDH--MAWDGLTNP-----YDGKAMGVFGELCADKYHFTREAQ 176

Query: 183 DAFALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHL-RPDTTLEALAKLKPV 241
           DAFA+ S   A  AQ  G FA EIVPV + G+KG+ VVD DE   R D     +  LKP 
Sbjct: 177 DAFAIESVNRAKAAQQNGAFAGEIVPVTVSGRKGDVVVDTDEQPGRSDVA--KIPSLKPA 234

Query: 242 NGPDK-TVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPV 300
              +  T+TA ++S ++DG+ A++L SA+   K GLK  A+++  A+    P      PV
Sbjct: 235 FRKENGTITAASSSSISDGAAAVVLLSADDANKRGLKPLARIVAHATHSQEPEWFTTAPV 294

Query: 301 PAVRKLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLG 360
            A++K+L++    V + D+ E+NEAFA   +   +ELGI    A++N NGGA ALGHP+G
Sbjct: 295 GAIQKVLDKAGWKVDEVDLFEINEAFAVVAMTPMKELGI--QHAKLNVNGGACALGHPIG 352

Query: 361 ASGARLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVE 399
           ASGARLV+T ++ L+  G +RG+ ++C+G G+  A+AVE
Sbjct: 353 ASGARLVVTLLNALKVRGLKRGVASLCIGGGEATAIAVE 391


Lambda     K      H
   0.317    0.134    0.379 

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: 394
Number of extensions: 24
Number of successful extensions: 4
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: 401
Length of database: 394
Length adjustment: 31
Effective length of query: 370
Effective length of database: 363
Effective search space:   134310
Effective search space used:   134310
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: 50 (23.9 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