GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Desulfobacter vibrioformis DSM 8776

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25526
         (482 letters)



>NCBI__GCF_000745975.1:WP_035239838.1
          Length = 484

 Score =  660 bits (1703), Expect = 0.0
 Identities = 314/480 (65%), Positives = 395/480 (82%)

Query: 1   MKLNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRA 60
           +K+ ++ LF +   I  EW+ A++G+ +DVTNPA G  LG+VP  GADET+ AI+AAN +
Sbjct: 2   LKIKNTALFCRHCFIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANES 61

Query: 61  LPAWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFA 120
           L AWR+ TA ER+ ILR W++L+ME+Q+DLA +MT EQGKPLAE++GEI+YAA+F EWFA
Sbjct: 62  LDAWRSKTAGERSAILRKWYDLLMENQEDLAVIMTAEQGKPLAESRGEIAYAAAFFEWFA 121

Query: 121 EEGKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLK 180
           EE KR+YGD IP   A +RL+VIKQP+GV AAITPWNFP+AMITRKAG ALAAGCTMVLK
Sbjct: 122 EEAKRVYGDVIPQTVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLK 181

Query: 181 PASQTPFSALALAELAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQ 240
           PA+ TPFSALA+A+L  +AGVP GVFNVVTGS+ A+G ELT+NP+VRKL+FTGST++G++
Sbjct: 182 PATATPFSALAIAKLGQQAGVPKGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKK 241

Query: 241 LMEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDG 300
           LM  CA  +K++S+ELGGNAPFIVFDDAD+D AVEGA+A K+RN+GQTCVCANR+YVQ G
Sbjct: 242 LMRDCAGTMKRLSMELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAG 301

Query: 301 VYDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKA 360
           VYD F  KL  AV +L +G+G D+GV  GPLID  AV  VE HI DA++KG +V+ GG  
Sbjct: 302 VYDEFCRKLTAAVQELKVGNGFDDGVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTR 361

Query: 361 HERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYA 420
           H  G  FF PTI+ DV  + +V++EETFGPLAP+F+F  E +V+ +ANDTEFGLAAYFY 
Sbjct: 362 HALGRTFFAPTIIADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYT 421

Query: 421 RDLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCI 480
           RD++R +R+GE LEYG+VGIN+GIISN VAPFGG+K SG GREGSKYG++DYLEIKYMC+
Sbjct: 422 RDMARSWRIGEKLEYGLVGINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLEIKYMCM 481


Lambda     K      H
   0.318    0.135    0.395 

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: 708
Number of extensions: 17
Number of successful extensions: 1
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: 482
Length of database: 484
Length adjustment: 34
Effective length of query: 448
Effective length of database: 450
Effective search space:   201600
Effective search space used:   201600
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: 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