GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Desulfobacter vibrioformis DSM 8776

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P76217
         (492 letters)



>NCBI__GCF_000745975.1:WP_035239838.1
          Length = 484

 Score =  209 bits (533), Expect = 1e-58
 Identities = 152/468 (32%), Positives = 231/468 (49%), Gaps = 22/468 (4%)

Query: 4   WINGDWITGQGASRVK-RNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERH 62
           +I  +W+       V   NP +G++L       A + ++A  AA  +   W   +  ER 
Sbjct: 15  FIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANESLDAWRSKTAGERS 74

Query: 63  AVVERFAALLESNKAELTAIIARETGKPRWEAATEVT---AMINKIAISIKAYHVRTGEQ 119
           A++ ++  LL  N+ +L  I+  E GKP  E+  E+    A     A   K  +      
Sbjct: 75  AILRKWYDLLMENQEDLAVIMTAEQGKPLAESRGEIAYAAAFFEWFAEEAKRVY------ 128

Query: 120 RSEMPDGAASLR----HRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPW 175
              +P   AS R     +P GV+A   P+NFP  +       AL AG T++ KP+  TP+
Sbjct: 129 GDVIPQTVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLKPATATPF 188

Query: 176 SGEAVMRLWQQAGLPPGVLNLVQGGRET-GQALSALEDLDGLLFTGSANTGYQLHRQLSG 234
           S  A+ +L QQAG+P GV N+V G     G  L+A   +  L FTGS   G +L R  +G
Sbjct: 189 SALAIAKLGQQAGVPKGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKKLMRDCAG 248

Query: 235 QPEKILALEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAF 294
             ++ L++E+GGN P I+ + ADIDAAV   +   +  +GQ C CA R+ +++G   D F
Sbjct: 249 TMKR-LSMELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAGVY-DEF 306

Query: 295 LARLVAVSQRLTPGN-WDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQA 353
             +L A  Q L  GN +DD  Q   G LI   A + V +  +     GG+ L        
Sbjct: 307 CRKLTAAVQELKVGNGFDDGVQQ--GPLIDMAAVETVESHIKDAVDKGGKVLAGGTRHAL 364

Query: 354 GTSLLTPGII-EMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPER 412
           G +   P II ++T    V  EE FGPL  V+++DT +E +R AN+T FGL+    + + 
Sbjct: 365 GRTFFAPTIIADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYTRDM 424

Query: 413 EKFDQLLLEARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAAD 460
            +  ++  +   G+V  N  +  +   APFGG+  SGN R  + Y  D
Sbjct: 425 ARSWRIGEKLEYGLVGINSGII-SNPVAPFGGVKESGNGREGSKYGLD 471


Lambda     K      H
   0.318    0.134    0.412 

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: 562
Number of extensions: 23
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: 492
Length of database: 484
Length adjustment: 34
Effective length of query: 458
Effective length of database: 450
Effective search space:   206100
Effective search space used:   206100
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Apr 09 2024. 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