GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Phaeobacter inhibens BS107

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate GFF3267 PGA1_c33180 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Phaeo:GFF3267
          Length = 390

 Score =  283 bits (725), Expect = 5e-81
 Identities = 169/400 (42%), Positives = 236/400 (59%), Gaps = 10/400 (2%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M+ V I  A RTP+G F G   GV A +L    ++A +    A     VDE+  GC   A
Sbjct: 1   MKTVVIAGAARTPMGGFQGMYDGVAAAELGGSAIRAALAGAGATT---VDEILMGCVLPA 57

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
           G+  +  AR A   AGL E +P  TLN++C SGM A   A+  IA G+ +  IAGG+ESM
Sbjct: 58  GQ-GQAPARQAGFAAGLGEEVPATTLNKMCGSGMKAAMMAYDQIALGQADTMIAGGMESM 116

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           + AP+++ K  +G           +   F++ L  +      M   A++ A+ YQ +R  
Sbjct: 117 TNAPYLLPKMRNGARLG---HGQVVDHMFLDGLEDAYDKGRLMGTFAEDCAETYQFTREA 173

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240
           QD +AL S   A AAQ +G F  EI PV +  +KGET+   DE  +     + +  LKP 
Sbjct: 174 QDEYALTSLSNALAAQESGAFDAEIAPVTVKTRKGETVTNADEQPKSARP-DKIPTLKPA 232

Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300
              D TVTA NAS ++DGAAAL+LAS +A +  GLT RAR++G AS   AP +    PVP
Sbjct: 233 FRKDGTVTAANASSISDGAAALVLASEDAAEAQGLTVRARIMGHASHAQAPGLFTTAPVP 292

Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360
           A +KL  +LG  VSD D+ E+NEAFA   +A + E+G+  D  +VN NGGA ALGHP+G 
Sbjct: 293 AAKKLMAQLGWTVSDVDLWEVNEAFAVVPMAFMHEMGLPRD--KVNVNGGACALGHPIGA 350

Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           SGAR+++T L+ LEK   ++G+A +C+G G+G A+AIER+
Sbjct: 351 SGARIMVTLLNALEKRNLKRGIAAICIGGGEGTAIAIERM 390


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: 15
Number of successful extensions: 6
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: 390
Length adjustment: 31
Effective length of query: 369
Effective length of database: 359
Effective search space:   132471
Effective search space used:   132471
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 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