GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Pseudomonas fluorescens FW300-N2C3

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate AO356_28685 AO356_28685 betaine-aldehyde dehydrogenase

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28685 AO356_28685
           betaine-aldehyde dehydrogenase
          Length = 496

 Score =  427 bits (1097), Expect = e-124
 Identities = 215/482 (44%), Positives = 307/482 (63%), Gaps = 7/482 (1%)

Query: 19  QPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTS 78
           QP  LFI   +  + + + F   +P+TE  + +V E    D+D AV AA AAF  +W+  
Sbjct: 16  QPGRLFIGGTWQDAANGRRFAVENPATEHTLAEVAEGGERDVDAAVAAARAAFTGTWAQQ 75

Query: 79  DPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIK 138
            P  R  +L++LA+L+D+H + LA +  L+NGK +  ++G+ A  A   R  AGW  KI+
Sbjct: 76  SPAQRGLLLFRLAELLDQHREELAQLITLENGKPIGAARGEAASAANIIRYFAGWPTKIE 135

Query: 139 GSVI----ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194
           GS +     +G    NYT REP+GVC  I+PWNFPL M  WKLGPVL TGC  VLK AE 
Sbjct: 136 GSTLPVSPSSGAPMLNYTLREPVGVCALIVPWNFPLTMCVWKLGPVLATGCVAVLKPAEQ 195

Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKA 254
           TPL A+ L  LI+ AG P GVVN+++G G   GAP++ HP + K+AFTGST  GR I +A
Sbjct: 196 TPLVAIRLVQLIEAAGFPAGVVNLLTGLGAQTGAPLAQHPDVDKIAFTGSTQVGRLIAQA 255

Query: 255 AAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYD 314
           A   N+KKV+LELGGKSPNI+  DAD+    +    GIFYN G+VC AGSR+YV   + D
Sbjct: 256 AT-GNMKKVSLELGGKSPNIILPDADIVRAAKGAADGIFYNQGQVCTAGSRLYVHASVLD 314

Query: 315 KIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN 374
           +++ E +  A +  +G      + MG   S  QL  +  Y+  G++EGA +I GG+R  +
Sbjct: 315 QVLEELQRHAAAHVLGPGLDPASSMGPLVSARQLGTVRGYLQRGQEEGAELICGGDRPAH 374

Query: 375 --KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTT 432
             +G+FI+P++F D  E   + R+EIFGPV+T+  +  ++E++  ANDS YGLAAG+ T 
Sbjct: 375 LERGHFIRPSVFLDRAERACVAREEIFGPVLTVMSWTEIDELVLRANDSPYGLAAGLWTR 434

Query: 433 NLSTAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492
           +L +A  V+ ++ +G++W+N +N   P  PFGGY QSG GREMG+  +D YT+ K+V + 
Sbjct: 435 DLRSAHRVAAQLKAGSVWINCWNVVDPASPFGGYKQSGWGREMGKNVIDAYTETKSVYVD 494

Query: 493 LS 494
           L+
Sbjct: 495 LA 496


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: 632
Number of extensions: 25
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: 496
Length adjustment: 34
Effective length of query: 461
Effective length of database: 462
Effective search space:   212982
Effective search space used:   212982
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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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