GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Desulfovibrio vulgaris Hildenborough

Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate 208821 DVU3294 aldehyde dehydrogenase (NADP) family protein

Query= BRENDA::P80668
         (499 letters)



>lcl|MicrobesOnline__882:208821 DVU3294 aldehyde dehydrogenase
           (NADP) family protein
          Length = 464

 Score =  189 bits (481), Expect = 1e-52
 Identities = 133/405 (32%), Positives = 203/405 (50%), Gaps = 8/405 (1%)

Query: 76  AGRLPA-ERERILLRFADLVEQHSEELAQLETLEQGKSIAISRAFEVGCTLNWMRYTAGL 134
           A R+PA ER  IL R A L+  H+E L +    E GK  A S   EV   ++ +R+ A  
Sbjct: 41  AHRIPAHERLAILERLATLMRTHAEALVRDAVREGGKPWADS-VVEVERAIDGVRWAARE 99

Query: 135 TTKIAGKTLDLSIPLPQGARYQAWTRKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSI 194
             ++ G+ + + +  P  A   A+T +EP GVV  I  +N P+ + + + +PA AAGC +
Sbjct: 100 LAQLGGREVPMGLT-PASAGRLAFTVREPRGVVLAISAFNHPVNLIVHQAVPAFAAGCPV 158

Query: 195 VIKPSETTPLTMLRVAELASEAGIPDGVFNVVTGSGAVCGAALTSHPHVAKISFTGSTAT 254
           ++KP+  TPL+   V  L  EAG+P+  +  +    A     L + P VA +SF GS+  
Sbjct: 159 LVKPASATPLSCRNVLRLMHEAGVPE-AWATMLPCAAATAEKLVADPRVAFLSFIGSSRV 217

Query: 255 GKGIARTAADHLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIYI 314
           G  +    A   T   LE GG  P ++   AD    +  L+ G F + GQVC +  R++ 
Sbjct: 218 GWHLRSKLAPGAT-CALEHGGAAPVVLDASADLDAALPLLLKGGFYHAGQVCVSVQRVFA 276

Query: 315 EAPLFDTLVSGFEQAVKSLQVGPGMSPVAQINPLVSRAHCDKVCSFLDDAQAQQAELIRG 374
                 T       A   L  G  M     + PL+      +V  ++++A+A    ++ G
Sbjct: 277 PHETARTFAERLAAAAAQLPTGDPMRHDTAVGPLIDPREVSRVHEWVEEARAGGGTVLCG 336

Query: 375 SNGPAGEGYYVAPTLVVNPDAKLRLTREEVFGPVVNLVRVADGEEALQLANDTEYGLTAS 434
              P  E  Y +PT+V +P    RL R EVFGPVV +    D +EA+  AND  +   A+
Sbjct: 337 -GAPLSETLY-SPTVVYDPPQGCRLARNEVFGPVVAVFSTRDRDEAIARANDVPFIFQAA 394

Query: 435 VWTQNLSQALEYSDRLQAGTVWVNSHTLIDAN-LPFGGMKQSGTG 478
           V+ +++  AL+ + RL A  V VN HT    + +PFGG  +SG G
Sbjct: 395 VFARDVDVALDTARRLNATGVMVNDHTAFRVDWMPFGGRGESGMG 439


Lambda     K      H
   0.318    0.133    0.402 

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: 588
Number of extensions: 34
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: 499
Length of database: 464
Length adjustment: 34
Effective length of query: 465
Effective length of database: 430
Effective search space:   199950
Effective search space used:   199950
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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