GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pad-dh in Phaeobacter inhibens BS107

Align phenylacetaldehyde dehydrogenase monomer (EC 1.2.1.39) (characterized)
to candidate GFF2074 PGA1_c21070 betaine aldehyde dehydrogenase BetB

Query= metacyc::MONOMER-15732
         (497 letters)



>FitnessBrowser__Phaeo:GFF2074
          Length = 488

 Score =  325 bits (832), Expect = 3e-93
 Identities = 187/483 (38%), Positives = 270/483 (55%), Gaps = 12/483 (2%)

Query: 17  RKLKMRIGADWQDAASGRTLSFRNPATGEVLGEVPAADAEDVDRAVRAARQAFDDSPWSR 76
           ++ +  IG  + D ++      R+PA+GEV   +P A A DV+ AV AAR AF    W+ 
Sbjct: 2   QQFQQYIGGVFSDGSA--RFESRDPASGEVWAMMPEARASDVEAAVAAARAAFHAPDWAG 59

Query: 77  LRPRERQNLLWRLADLMERDARQLAELECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATK 136
           +    R  LL+RLADL+  +A  LA+LE  + GK           +A D+ RY AG A K
Sbjct: 60  MTATGRGKLLYRLADLIAENAETLAQLETRDTGKIIRETSAQIAYVA-DYYRYYAGLADK 118

Query: 137 IEGSTVEASMPLMPNDQFHGFVRREAIGVVGAIVAWNFPLLLACWKLGPALATGCTIVLK 196
           IEG+ +    P M       ++RRE +GVV A+V WN  L LA  K+GPALA GCT+VLK
Sbjct: 119 IEGAHLPIDKPDM-----EVWLRREPLGVVAAVVPWNSQLFLAAVKIGPALAAGCTVVLK 173

Query: 197 PADETPLSVLKLAELVDEAGYPAGVFNVVTGTGLNAGAALSRHPGVDKLTFTGSTEVGKL 256
            ++E P  +L+ A + D+AG+P GV NV+TG G + GA L+ HPG+D + FTG  +  + 
Sbjct: 174 ASEEAPAPLLEFARIFDQAGFPRGVLNVITGFGADCGAVLTAHPGIDHIAFTGGPDTARH 233

Query: 257 IGKAAMDNMTRVTLELGGKSPTIVMPDANLQEAAAGAATAIFFNQGQVCCAGSRLYVHRK 316
           + + + +N+   +LELGGKSP IV  D ++  A     +AIF   GQ C AGSRL +  +
Sbjct: 234 VVRNSAENLASTSLELGGKSPFIVFEDVDIDSAVNAQVSAIFAATGQSCVAGSRLIISNQ 293

Query: 317 HFDNVVADIAGIANGMKLGNGLDPAVQMGPLISAKQQDRVTGYIELGRELGATVACGGEG 376
                +  +   A  +++G    P  ++GPL +  Q  R    +      GA +  GG+ 
Sbjct: 294 IKAQFLHRLKEKAENIRIGAPELPETEVGPLCTDAQMRRAVELVAASLAAGARIVTGGQP 353

Query: 377 F-GPGYFVKPTVIVDVDQRHR--LVQEEIFGPVLVAMPFDDLDEVIGMANDNPYGLGASI 433
             G G F  PT I+D  +      ++EE FGPVL    FD   E + +AND  +GL + +
Sbjct: 354 LEGEGNFFPPT-ILDCSEAPEAPCLREEFFGPVLSVCGFDTEAEALALANDTAHGLASGV 412

Query: 434 WSNDLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREVGAAAIEHYTELKSV 493
           ++ DL   HRMI  I++G VWVN + A+ P  PFGG  +SG GRE G  A   YT +K+V
Sbjct: 413 FTRDLTRAHRMIRGIRAGIVWVNTYRAVSPIAPFGGQGLSGHGREGGLQAALDYTRVKTV 472

Query: 494 LIK 496
            ++
Sbjct: 473 WLR 475


Lambda     K      H
   0.320    0.137    0.413 

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: 579
Number of extensions: 24
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: 497
Length of database: 488
Length adjustment: 34
Effective length of query: 463
Effective length of database: 454
Effective search space:   210202
Effective search space used:   210202
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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