GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Sinorhizobium meliloti 1021

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate SMa0796 SMa0796 hypothetical protein

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



>FitnessBrowser__Smeli:SMa0796
          Length = 487

 Score =  359 bits (922), Expect = e-103
 Identities = 194/468 (41%), Positives = 278/468 (59%), Gaps = 5/468 (1%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSS-WSTSDPQV 82
           +IN EF   +++  F ++ P+T     ++ EA   D++ AVEAA  A H   WST     
Sbjct: 7   YINGEFADGEAR--FESIDPTTGRAWAEMPEAREADVNRAVEAARIALHDQPWSTLTATQ 64

Query: 83  RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVI 142
           R K+LYKLADL+ E+A  LA +E  D GK +  +   +A  A Y+R  AG  DKI+GS +
Sbjct: 65  RGKLLYKLADLVAENAGRLAELETRDTGKIIRETSSQIAYVADYYRYYAGIADKIEGSYL 124

Query: 143 ETGDTHFN-YTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALY 201
                  + + RREPIGV   ++PWN  L +++ K+GP L  GCT V+K +E  P   L 
Sbjct: 125 PIDKPDMDVWLRREPIGVVAMVVPWNSQLFLSAVKIGPALAAGCTMVVKASEDGPAPLLE 184

Query: 202 LASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLK 261
            A L+  AG P GVVN+V+GFGP+ GA +S HP++  +AFTG   T RHI++ +AE NL 
Sbjct: 185 FARLVHAAGFPAGVVNIVTGFGPSCGAALSRHPQVDHIAFTGGPETARHIVRNSAE-NLA 243

Query: 262 KVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFK 321
             +LELGGKSP IVF DAD++S     + GIF  TG+ C AGSR+ V++ + D+ +   K
Sbjct: 244 STSLELGGKSPFIVFADADLESAANAQIAGIFAATGQSCVAGSRLIVEKSVKDRFLQILK 303

Query: 322 NAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKP 381
             AE+++IG P +  T +G   ++ Q + +   +      GA ++TGG      G++ +P
Sbjct: 304 AKAETIRIGSPLEMSTEVGPLATERQSNHVKTLVARSLAAGAKLVTGGTAPEGAGFYYRP 363

Query: 382 TIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVS 441
           TI          + +E FGPV+++  F+T  E + LANDS +GLAAGV T NL+ A  + 
Sbjct: 364 TILDCDGSASPSLENEFFGPVLSVLSFETEAEALHLANDSRFGLAAGVFTQNLTRAHRLM 423

Query: 442 NKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAV 489
             I +G +WVNTY    P+ PFGG+  SG GRE G EA  +YT+ K V
Sbjct: 424 KGIRAGIVWVNTYRAVSPVAPFGGFGLSGHGREGGLEAALDYTRSKTV 471


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: 566
Number of extensions: 28
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: 487
Length adjustment: 34
Effective length of query: 461
Effective length of database: 453
Effective search space:   208833
Effective search space used:   208833
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