GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMa0796 SMa0796 hypothetical protein
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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