GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28685
          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.

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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