GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Herbaspirillum seropedicae SmR1

Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate HSERO_RS19755 HSERO_RS19755 betaine-aldehyde dehydrogenase

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



>lcl|FitnessBrowser__HerbieS:HSERO_RS19755 HSERO_RS19755
           betaine-aldehyde dehydrogenase
          Length = 484

 Score =  362 bits (929), Expect = e-104
 Identities = 201/477 (42%), Positives = 278/477 (58%), Gaps = 7/477 (1%)

Query: 24  FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHS-SWSTSDPQV 82
           FI  E  ++   +    V+P  EE      +  + D+  AV AA A     +WS      
Sbjct: 8   FIAGEATEASDGQRMNLVNPINEEIYASAAQGTAADVARAVAAAKAQLEGGAWSKLSGLQ 67

Query: 83  RMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSV 141
           R ++L+KLA L++   D LA ++A   G+S M  +  DV    ++ R+ AGW ++++G  
Sbjct: 68  RGQLLHKLAALVERDTDLLADMDARAIGRSPMEPRMMDVPNAISHLRAAAGWANQMEGRT 127

Query: 142 IET----GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPL 197
           I T    G    +YT REPIGV G I+PWN PL++ SWK+  +L  GCT V+K AE TP 
Sbjct: 128 IPTAGYMGKPTLSYTVREPIGVVGAILPWNAPLMITSWKVAALLAAGCTVVIKPAEETPQ 187

Query: 198 SALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAE 257
           SAL+LA L +EAG P GV+NVV+G+G + G  +  HP + K++FTGS   GR I + A E
Sbjct: 188 SALHLARLAQEAGFPDGVINVVTGYGNSVGRALCEHPDVAKISFTGSPEAGRAIQRIAGE 247

Query: 258 SNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIV 317
              K+VTLELGGKSP IVFDDA  +  +     G+F N G+VC AGSRI VQ  +  +  
Sbjct: 248 Q-FKRVTLELGGKSPQIVFDDAPFEDALFGCTLGLFVNQGQVCAAGSRILVQRSLAQRFA 306

Query: 318 SEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGY 377
                AA  + +GDP +    MG    + Q +++ +YI  G  EGAT++ GG    +KG+
Sbjct: 307 KALAEAAAGITVGDPSQPGVRMGPVAKKAQFERVNRYIQQGLDEGATLLAGGVSRPDKGW 366

Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437
           F++PTIF D      I R+EIFGPV TI  F T EE IALANDS+YGLAA V TTNL+ A
Sbjct: 367 FVQPTIFADANNGMSIAREEIFGPVGTIISFDTEEEAIALANDSKYGLAATVWTTNLARA 426

Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIGLS 494
             V+  +  G + VN ++     +P+GG   SG+GRE G      YT+ K V + L+
Sbjct: 427 HRVAAGVKVGAVGVNCWSPLDANLPWGGIKDSGMGREGGLAGALAYTEEKTVTVLLA 483


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: 569
Number of extensions: 23
Number of successful extensions: 3
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: 484
Length adjustment: 34
Effective length of query: 461
Effective length of database: 450
Effective search space:   207450
Effective search space used:   207450
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 preprint 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