GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Burkholderia phytofirmans PsJN

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate BPHYT_RS25160 BPHYT_RS25160 NAD/NADP-dependent betaine aldehyde dehydrogenase

Query= metacyc::MONOMER-16244
         (495 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS25160 BPHYT_RS25160
           NAD/NADP-dependent betaine aldehyde dehydrogenase
          Length = 489

 Score =  366 bits (940), Expect = e-106
 Identities = 193/476 (40%), Positives = 286/476 (60%), Gaps = 7/476 (1%)

Query: 23  LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQV 82
           L+I   +V + S +TF T+ P+T E +  V +A + D+D AV +A       W+      
Sbjct: 9   LYIGGGYVDATSGETFDTLDPATGETLASVQQASAADVDRAVRSAKQG-QREWAALTAMQ 67

Query: 83  RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSV 141
           R ++L +  DL+ E  D LA +E  D GK +  +   D+   A      AG    I+G  
Sbjct: 68  RSRILRRAVDLLRERNDELAALETRDTGKPIAETLAVDIVTGADVIEYYAGLATAIEGQQ 127

Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201
           I    T F YTRREP+GVC  I  WN+P+ +A WK  P L  G   + K +E TPLSAL 
Sbjct: 128 IPLRPTSFVYTRREPLGVCAGIGAWNYPIQIACWKSAPALAAGNAMIFKPSEITPLSALK 187

Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261
           LA +  EAG P GV NVV G G   GA +++HP I+K++FTG   TG+ +M  A  S+LK
Sbjct: 188 LAEIFTEAGVPAGVFNVVQGDG-RVGAMLAAHPDIEKISFTGGVETGKKVMSMAGASSLK 246

Query: 262 KVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321
           +VT+ELGGKSP +VFDDA+++       +  F+++G+VC  G+R++VQ G+ D+  +   
Sbjct: 247 EVTMELGGKSPLLVFDDANLERAADIATSANFFSSGQVCTNGTRVFVQRGVLDRFEALVL 306

Query: 322 NAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN----KGY 377
              + +++G P    T  G   S  QL K+L YI+ GK+EGA ++ GG+R        G 
Sbjct: 307 ERVKRIRVGKPTDAATNFGPLVSAAQLHKVLGYIESGKQEGARLVAGGKRLTEGHFAGGQ 366

Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437
           +++PT+F D ++D +IVR+EIFGPV++I  F   +E IA AN + YGLAAGV T NL+ A
Sbjct: 367 YVEPTVFADCRDDMRIVREEIFGPVMSILVFDDEDEAIARANHTAYGLAAGVVTENLARA 426

Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493
             V +++ +G  W+NT+ +    +P GGY QSG+GRE G   L++YT++K+V++ L
Sbjct: 427 HRVIHRLEAGICWINTWGESPAEMPVGGYKQSGVGRENGITTLEHYTRIKSVQVEL 482


Lambda     K      H
   0.316    0.133    0.389 

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: 590
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: 495
Length of database: 489
Length adjustment: 34
Effective length of query: 461
Effective length of database: 455
Effective search space:   209755
Effective search space used:   209755
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: 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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