GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Phaeobacter inhibens BS107

Align Beta-ketoadipyl-CoA thiolase; 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized)
to candidate GFF329 PGA1_c03400 acetyl-CoA acetyltransferase PhaA

Query= SwissProt::Q8VPF1
         (401 letters)



>FitnessBrowser__Phaeo:GFF329
          Length = 391

 Score =  298 bits (762), Expect = 2e-85
 Identities = 168/396 (42%), Positives = 246/396 (62%), Gaps = 9/396 (2%)

Query: 5   VYICDAVRTPIGRFGGSLAAVRADDLAAVPVKALVERNPQVDWSQLDEVYLGCANQAGED 64
           V I  A RT +G FGG+ A   A DL A  ++A+VER   +D S++ E  LG    A + 
Sbjct: 4   VVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVER-AGIDKSEVSETILGQVLTAAQ- 61

Query: 65  NRNVARMALLLAGLPDSVPGVTLNRLCASGMDAVGTAFRAIASGEAELVIAGGVESMSRA 124
            +N AR A + AGLP      +LN++C SG+ AV  A + I  G+A +V AGG E+M+ +
Sbjct: 62  GQNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTLS 121

Query: 125 PYVMGKADSAFGRGQKIEDTTIGWRFINPLMKAQYGVDAMPETADNVADDYKVSRADQDA 184
           P+           G K+ D +     I   +   +    M +TA+NVA+ +++SR  QD 
Sbjct: 122 PHAAN-----LRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDE 176

Query: 185 FALRSQQLAGRAQAAGYFAEEIVPVVIKGKKGETVVDADEHLRPDTTLEALAKLKPVNGP 244
           FA+ SQ  A  AQ AG FA+EI    +K +KG+ +VD DE++R   T+EA+ KL+P    
Sbjct: 177 FAVASQNKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAK 236

Query: 245 DKTVTAGNASGVNDGSVALILASAEAVKKHGLKARAKVLGMASAGVAPRVMGIGPVPAVR 304
           D +VTA NASG+NDG+ A +L SA+  +K G++  A++   A+AG+ P +MG+GP+ A R
Sbjct: 237 DGSVTAANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASR 296

Query: 305 KLLERLNLSVADFDVIELNEAFAAQGLAVTRELGIADDDARVNPNGGAIALGHPLGASGA 364
           K LE+   SV D D++E NEAFAAQ  AV +++G   D A VN NGGAIA+GHP+GASG 
Sbjct: 297 KALEKAGWSVDDLDLVEANEAFAAQACAVNKDMGW--DPAIVNVNGGAIAIGHPIGASGC 354

Query: 365 RLVLTAVHQLEKSGGQRGLCTMCVGVGQGVALAVER 400
           R++ T + ++++   ++GL T+C+G G GVA+ VER
Sbjct: 355 RVLNTLLFEMKRRDAKKGLATLCIGGGMGVAMCVER 390


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: 381
Number of extensions: 18
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: 391
Length adjustment: 31
Effective length of query: 370
Effective length of database: 360
Effective search space:   133200
Effective search space used:   133200
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 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