GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS25160
          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:

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