GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Neptunomonas antarctica S3-22

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_054342029.1 Nant_RS12665 acetyl-CoA C-acyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>NCBI__GCF_001305295.1:WP_054342029.1
          Length = 393

 Score =  246 bits (628), Expect = 8e-70
 Identities = 142/397 (35%), Positives = 224/397 (56%), Gaps = 9/397 (2%)

Query: 4   VFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGED 63
           V I  A RTP+G   GAL+ VRA DL A  +KA +E    ++   +DEV  GC   AG  
Sbjct: 6   VVIVSAARTPMGGMMGALSEVRAPDLCATAIKAAVE-RAGIKGADIDEVIMGCVLPAGL- 63

Query: 64  NRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRA 123
            +  AR A   AG+P++    T+N++C SGM A+  A   I +G++ + +AGG+E+MS +
Sbjct: 64  GQAPARQASRGAGIPDAAGATTVNKMCGSGMKAVMLAHDQIMAGQVNIMVAGGMENMSLS 123

Query: 124 PFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQDA 183
           P+++ KA +G    M++    +        ++  Y    M   A   AD + V+R   D 
Sbjct: 124 PYLLPKARAG----MRMGHAQVLDHMFCDGLEDAYEGGLMGAFAQQSADAFNVTREAMDD 179

Query: 184 FALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPVNGP 243
           FA+ S  KA  A   G F +EI  V +  +KG+ +V+ DE       ++ +  L P    
Sbjct: 180 FAIGSLNKALKAIETGAFKDEIAAVTVKSRKGDVVVDTDEQ-PGNARIDKIRSLNPAFKK 238

Query: 244 DKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPAVR 303
           D TVTA N+S ++DG +AL+L         GL P AR++  ++    P    I P+ A++
Sbjct: 239 DGTVTAANSSSISDGGSALVLMKESDANARGLKPLARIVAHSTHAQLPAEFSIAPIGAIQ 298

Query: 304 KLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMSGA 363
           K+ ++ G +  D D+ E+NEAFA   +  + ELG+  DA +VN  GGA ALGHP+G SG+
Sbjct: 299 KVLKKAGWSKDDVDLYEINEAFAVVSMLAISELGL--DADKVNVKGGACALGHPIGSSGS 356

Query: 364 RLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           R+++T L+ L+ +G  KG+A++C+G G+  A+A+E +
Sbjct: 357 RILVTLLYALKHAGKSKGVASLCIGGGEATAVAVEMI 393


Lambda     K      H
   0.318    0.134    0.383 

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: 391
Number of extensions: 18
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: 400
Length of database: 393
Length adjustment: 31
Effective length of query: 369
Effective length of database: 362
Effective search space:   133578
Effective search space used:   133578
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 (21.7 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