GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pseudomonas simiae WCS417

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF5142 PS417_26340 betaine-aldehyde dehydrogenase

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



>FitnessBrowser__WCS417:GFF5142
          Length = 490

 Score =  353 bits (905), Expect = e-101
 Identities = 185/476 (38%), Positives = 287/476 (60%), Gaps = 6/476 (1%)

Query: 23  LFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQV 82
           L+I+  +  + S  TF  ++P+  E + QV  A  ED++ AV +A       W+      
Sbjct: 9   LYIDGGYTDAGSDATFEAINPANGEVLAQVQRATKEDVERAVVSAEKG-QKIWAAMTAME 67

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

Query: 142 IETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201
           I   DT F YTRREP+GV   I  WN+P+ +A WK  P L  G   + K +E T L+ L 
Sbjct: 128 IPLRDTSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLK 187

Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261
           LA +  EAG P GV NV++G G   G  ++ HP+I+KV+FTG T TG+ +M +A+ S+LK
Sbjct: 188 LAEIYTEAGVPAGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTDTGKKVMASASSSSLK 247

Query: 262 KVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321
           +VT+ELGGKSP IVF+DAD+       +   FY++G+VC  G+R++V + +     ++  
Sbjct: 248 EVTMELGGKSPLIVFEDADLDRAADIAMMANFYSSGQVCTNGTRVFVPKHLQAAFEAKIV 307

Query: 322 NAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN----KGY 377
                +++G+P  ++T  G   S   ++ +L YI  GK+EGA V+ GG+R  +    KG 
Sbjct: 308 ERVARIRVGNPQDDNTNFGPLVSFAHMESVLGYIAKGKEEGARVLCGGDRLTDGEFAKGA 367

Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437
           F+ PT+F D  ++  IVR+EIFGPV++I  ++T EEVI  AND+++GLAAG+ T +L+ A
Sbjct: 368 FVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTDFGLAAGLVTKDLNRA 427

Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493
             V +++ +G  W+N + +    +P GGY QSG+GRE G  +L+N+T++K+V++ L
Sbjct: 428 HRVIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVEL 483


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: 611
Number of extensions: 35
Number of successful extensions: 4
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: 490
Length adjustment: 34
Effective length of query: 461
Effective length of database: 456
Effective search space:   210216
Effective search space used:   210216
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