GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Sinorhizobium meliloti 1021

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate SM_b20891 SM_b20891 dehydrogenase

Query= BRENDA::Q97UA1
         (478 letters)



>lcl|FitnessBrowser__Smeli:SM_b20891 SM_b20891 dehydrogenase
          Length = 477

 Score =  361 bits (926), Expect = e-104
 Identities = 195/475 (41%), Positives = 283/475 (59%), Gaps = 14/475 (2%)

Query: 7   LADKWIKGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGS 66
           +A +W+ G G    +INP++ D V+ +    + +D K AI  A A F  WSR+   +R +
Sbjct: 8   IAGEWVGGDG--VANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHA 65

Query: 67  ILLKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSA 126
           IL K  + +     E   L++ EEGKTL + + E  R+  + +F+     +++G+ +PS 
Sbjct: 66  ILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPSV 125

Query: 127 DPNTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVE 186
            P   +   +EP GVV +ITPWNFP++IP WKLAPAL  GNT V KPA   P     +V+
Sbjct: 126 RPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVD 185

Query: 187 VLSKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRI 246
           +L +AGLP+GV+NLV+GKGS VG  ++   ++ A++FTGST  GKR+       NR  + 
Sbjct: 186 ILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNR--KY 243

Query: 247 QLELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLER 306
           QLE+GGKN   V   ADL++A E AV   F  TGQ CTA+SR+I+ + ++ +F   + ER
Sbjct: 244 QLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGER 303

Query: 307 VKKWRVG----PGTEDVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII--PGKGYF 360
           +K   V     PGT    +GPVVD+ Q  +D +YI  GK  GAKL +GG +I     G++
Sbjct: 304 IKGLVVDDALKPGTH---IGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFY 360

Query: 361 LEPTIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAIN 420
           L+P +F   T++MR+ +EEIFGPV +V   KD DEA+ + N   +G ++GI  + +K   
Sbjct: 361 LQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHAT 420

Query: 421 EFVSRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475
            F    EAG++ VN PT G++   PFGG K S     +E G+ A EFY   KT Y
Sbjct: 421 HFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGP-REQGKYAAEFYTNVKTAY 474


Lambda     K      H
   0.316    0.135    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: 642
Number of extensions: 29
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: 478
Length of database: 477
Length adjustment: 34
Effective length of query: 444
Effective length of database: 443
Effective search space:   196692
Effective search space used:   196692
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: 51 (24.3 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