GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Acidovorax sp. GW101-3H11

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate Ac3H11_1486 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1486
          Length = 485

 Score =  325 bits (834), Expect = 2e-93
 Identities = 188/468 (40%), Positives = 264/468 (56%), Gaps = 12/468 (2%)

Query: 33  KSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLAD 92
           +S++ F TV+P+T+E + +V    + ++  AV AA  AF  +W+      R K++ KL D
Sbjct: 13  ESREYFETVNPATQEVLAEVASGGAAEVHAAVAAAKDAF-PAWAGLPAPERAKLVRKLGD 71

Query: 93  LIDEHADTLAHIEALDNGKSL-MCSKGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNY 151
           LI     TLA  E  D G+ +    K  +   A  F   A    ++ G    T  TH NY
Sbjct: 72  LIAAEVPTLALTETKDTGQVIGQTGKALIPRAADNFYYFAEMCTRVDGHTYPT-PTHLNY 130

Query: 152 TRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGA 211
           T   P+GVC  I PWN P + ++WK+ P L  G T VLK +E +PL+A  L  L  EAG 
Sbjct: 131 TLFHPVGVCALISPWNVPFMTSTWKVAPALAFGNTAVLKMSELSPLTAARLGELALEAGI 190

Query: 212 PPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKKVTLELGGKS 271
           P GV+NVV G+G  AG P+ +HP ++ ++FTGSTATG  I++AA    LKK ++ELGGKS
Sbjct: 191 PAGVLNVVHGYGKDAGEPLCTHPDVRAISFTGSTATGNRIVQAA---GLKKFSMELGGKS 247

Query: 272 PNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKNAAESLKIGD 331
           P +VF DAD+   +   +  IF N GE C AGSRI VQ+ IY     +F   A  + +GD
Sbjct: 248 PFVVFADADLDRALDAALFMIFSNNGERCTAGSRILVQKSIYADFAEKFAARARRIVVGD 307

Query: 332 PFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGG------ERFGNKGYFIKPTIFG 385
           P  E T +G   SQ  L K+  YI++G KEGAT++ GG           KG F+ PT+F 
Sbjct: 308 PLDEKTIVGPMISQAHLAKVRSYIELGPKEGATLLCGGLGTPDLPAHLQKGNFVLPTVFA 367

Query: 386 DVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSNKIN 445
           DV    +I ++EIFGPV  +  F+   E I LAND +YGL++ V T N+  A  V+  I 
Sbjct: 368 DVDNRMKIAQEEIFGPVACLIPFEDEAEAIRLANDIQYGLSSYVWTENIGRAHRVAAGIE 427

Query: 446 SGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGL 493
           +G  +VN+ N      PFGG   SG GRE G  + + + + K + + +
Sbjct: 428 AGMCFVNSQNVRDLRQPFGGTKGSGTGREGGTWSYEVFLEPKNIAVSM 475


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: 618
Number of extensions: 30
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: 485
Length adjustment: 34
Effective length of query: 461
Effective length of database: 451
Effective search space:   207911
Effective search space used:   207911
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 (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