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.- (characterized)
to candidate WP_035239838.1 Q366_RS13505 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>NCBI__GCF_000745975.1:WP_035239838.1
          Length = 484

 Score =  673 bits (1737), Expect = 0.0
 Identities = 319/483 (66%), Positives = 402/483 (83%)

Query: 1   MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60
           +++K+  LF +  ++   WV AD+G+T+ V NPATG+I+G+VP  GA ET+RAI AA+++
Sbjct: 2   LKIKNTALFCRHCFIQDEWVAADSGKTVDVTNPATGQILGTVPFCGADETQRAINAANES 61

Query: 61  LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120
           L AWR+ TA ER+  LR+W+DL++ENQ+DLA +MT EQGKPLAE++GEIAYAA+F EWF 
Sbjct: 62  LDAWRSKTAGERSAILRKWYDLLMENQEDLAVIMTAEQGKPLAESRGEIAYAAAFFEWFA 121

Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180
           EEAKR+YGD IP     +R++VIKQP+GV AAITPWNFPSAMITRKAG ALAAGCTMVLK
Sbjct: 122 EEAKRVYGDVIPQTVASQRLVVIKQPVGVVAAITPWNFPSAMITRKAGAALAAGCTMVLK 181

Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQ 240
           PA+ TP+SALA+A+L ++AG+PKGVF+VVTGS+  +GGELT+NPIVRKLTFTGST++G++
Sbjct: 182 PATATPFSALAIAKLGQQAGVPKGVFNVVTGSSSAIGGELTANPIVRKLTFTGSTQVGKK 241

Query: 241 LMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDG 300
           LM +CA  +K++S+ELGGNAPFIVFDDAD+DAAVEGA+  KYRN+GQTCVCANR+YVQ G
Sbjct: 242 LMRDCAGTMKRLSMELGGNAPFIVFDDADIDAAVEGAMACKYRNSGQTCVCANRMYVQAG 301

Query: 301 VYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP 360
           VYD F  KL AAV +L +GNG + GV  GPLID  AV  VE HI DAV KG KV++GG  
Sbjct: 302 VYDEFCRKLTAAVQELKVGNGFDDGVQQGPLIDMAAVETVESHIKDAVDKGGKVLAGGTR 361

Query: 361 HALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYA 420
           HALG TFF PTI+ DV  +  V+++ETFGPLAPVF+F  E EV+  +NDTEFGLA+YFY 
Sbjct: 362 HALGRTFFAPTIIADVTDDMRVAREETFGPLAPVFKFDTEEEVVRKANDTEFGLAAYFYT 421

Query: 421 RDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCL 480
           RD+AR +R+ E+LEYG+VGIN+G+ISN VAPFGG+K SG GREGSKYG++DYLEIKY+C+
Sbjct: 422 RDMARSWRIGEKLEYGLVGINSGIISNPVAPFGGVKESGNGREGSKYGLDDYLEIKYMCM 481

Query: 481 GGI 483
            GI
Sbjct: 482 AGI 484


Lambda     K      H
   0.317    0.135    0.391 

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: 702
Number of extensions: 12
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: 483
Length of database: 484
Length adjustment: 34
Effective length of query: 449
Effective length of database: 450
Effective search space:   202050
Effective search space used:   202050
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