Alignments for a candidate for davD in Desulfobacter vibrioformis DSM 8776

GapMind for catabolism of small carbon sources

Alignments for a candidate for davD in Desulfobacter vibrioformis DSM 8776

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_211251871.1 Q366_RS07005 gamma-aminobutyraldehyde dehydrogenase

Query= BRENDA::Q88RC0
         (480 letters)



>NCBI__GCF_000745975.1:WP_211251871.1
          Length = 469

 Score =  286 bits (731), Expect = 1e-81
 Identities = 163/469 (34%), Positives = 253/469 (53%), Gaps = 12/469 (2%)

Query: 15  INGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSA 74
           ING  +D +  +T  + +P   E I  VP   TA+   A++AA+ A PAW+  +  +R+ 
Sbjct: 10  INGNIVDGEAEKT-SLFSPENNEFIVDVPCATTAQVDLAVDAANAAFPAWKRKSFADRAT 68

Query: 75  KLRRWFELMIENQDDLARLMTTEQGKPLAEA-KGEIAYAASFIEWFAEEAKRIYGDTIPG 133
            L ++ + + E    LA+L +   GKP     + E+   +    +FA   + + G     
Sbjct: 69  VLYKFADRIDEKAQLLAKLESLNCGKPFQRMLEDEMPAISDHFRFFAGACRCMSGSAAGE 128

Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALV 193
           +      ++ + P+GV   I PWN+P  M   K  PALAAG T+V KP+  TP + L LV
Sbjct: 129 YLEGFTSMIRRDPVGVVGQIAPWNYPLMMAAWKIAPALAAGNTVVFKPSECTPLTMLGLV 188

Query: 194 ELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVS 253
           E       PAGVL++VTG    +G  + G+  ++ +S TGS   G+Q++     ++K+  
Sbjct: 189 EDIKEL-FPAGVLNIVTGKGSVIGKHIAGHEKIQMVSVTGSVNTGKQVLASATSNVKRTH 247

Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAV 313
           LELGG AP I FDD D+D  VE   +  Y N GQ C  A R+YVQD +Y    EKL AAV
Sbjct: 248 LELGGKAPVIAFDDCDIDDLVENMTLWGYYNAGQDCTAACRLYVQDKIYPEVVEKLTAAV 307

Query: 314 AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVS-KGAKVLSGG-KLIEGNFFEPTIL 371
             + + +        GPLI  +    V   +E A      K+++GG K+  G F+EPT++
Sbjct: 308 KSIDVND-------IGPLISAEQREIVSSFVERAKKVPHLKIVAGGNKIDRGYFYEPTLI 360

Query: 372 VDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEAL 431
           +D  +   V +EE FGP+  + RF D  + I  +ND ++GLAS  + RD+ +  RV+  L
Sbjct: 361 IDARQDDEVVQEEIFGPVVSVTRFNDADQAIEWANDCKYGLASSIWTRDIEKAHRVSSML 420

Query: 432 EYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCISV 480
           ++G+  INT  +     P GG K SG G++ S YG+EDY  ++++ + +
Sbjct: 421 QFGVTWINTYFMYASEMPHGGFKMSGYGKDLSMYGLEDYTVVRHIMVKM 469


Lambda     K      H
   0.317    0.134    0.384 

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: 511
Number of extensions: 19
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: 480
Length of database: 469
Length adjustment: 33
Effective length of query: 447
Effective length of database: 436
Effective search space:   194892
Effective search space used:   194892
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources