GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Epibacterium ulvae U95

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_090218033.1 CV091_RS10640 aldehyde dehydrogenase family protein

Query= BRENDA::Q97UA1
         (478 letters)



>NCBI__GCF_002796795.1:WP_090218033.1
          Length = 483

 Score =  314 bits (805), Expect = 4e-90
 Identities = 171/472 (36%), Positives = 262/472 (55%), Gaps = 7/472 (1%)

Query: 7   LADKWIKGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGS 66
           +A  W  G  +E  + NP+D   ++      + D +   +++A     EW+     ++ +
Sbjct: 9   IAGSWTVGV-DEIENRNPSDLSDLVGMFAQASSDQLDATLDQAKIAQAEWAAYGIERKYN 67

Query: 67  ILLKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSA 126
           +L+  G  M   A+E   L++ EEGK L +   EV R+     +Y A   +  G+   S 
Sbjct: 68  VLMAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAETLRQIGENADSV 127

Query: 127 DPNTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVE 186
                I   +E +G VA+I+PWNFP +   WK+APAL  GN  V KPA  TP     L E
Sbjct: 128 REGIEIDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANATPASAVALTE 187

Query: 187 VLSKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRI 246
           ++ +  +P+G+ +LV+G G E+G  +V    + A+SFTGS  VGK I         +T++
Sbjct: 188 IIERQDIPKGLFSLVMGAGREIGQRLVESSKVDAISFTGSVPVGKGIASAA--IQNLTKV 245

Query: 247 QLELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLER 306
           Q+E+G KNAL V   AD+ LA  LA+ G FG TGQ CTA+SRL+++  V+ +F  +L+  
Sbjct: 246 QMEMGSKNALAVMDDADIDLAVSLALGGAFGGTGQKCTASSRLVVHSAVHDEFVSKLVAG 305

Query: 307 VKKWRVGPGTE-DVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII--PGKGYFLEP 363
            K  +VG   E    +GPVV E Q  ++L Y++ GK+ GA+L+ GG  +  P +GY++ P
Sbjct: 306 AKAMKVGHALEAGTQIGPVVTEQQLNENLAYVDLGKSEGAELLCGGQRLEMPHQGYYMNP 365

Query: 364 TIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFV 423
            IF G T+DMR+ +EE+F P+ +V +    DEA+ +VN  ++G T+GIV   +   N F 
Sbjct: 366 GIFIGTTNDMRINREEMFAPLAAVIKVSGYDEALSVVNDTNFGLTSGIVTKSLARANHFR 425

Query: 424 SRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVY 475
              + G + VN PT G +   PFGG +   +   +E G+ A EFY   KT Y
Sbjct: 426 RNAQTGCVMVNLPTAGTDYHVPFGG-RGDSSYGPREQGKAAAEFYTTVKTAY 476


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: 591
Number of extensions: 41
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: 483
Length adjustment: 34
Effective length of query: 444
Effective length of database: 449
Effective search space:   199356
Effective search space used:   199356
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 24 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