GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Caulobacter crescentus NA1000

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate CCNA_03242 CCNA_03242 succinic semialdehyde dehydrogenase

Query= BRENDA::P25526
         (482 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03242 CCNA_03242 succinic
           semialdehyde dehydrogenase
          Length = 485

 Score =  578 bits (1491), Expect = e-169
 Identities = 292/477 (61%), Positives = 360/477 (75%), Gaps = 5/477 (1%)

Query: 7   NLFRQQALINGEWLDANNGEA-IDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWR 65
           NL    ALI+G+W+    GEA  DV NPA+G  + +V  +GA ET  AIDAA+RALPAW 
Sbjct: 8   NLVETAALIDGQWV---RGEASFDVLNPADGTLIAAVADLGAAETTLAIDAAHRALPAWA 64

Query: 66  ALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKR 125
           A TAKER  ILR W +L++ H DDLARLMT EQGKPLAEAKGE+ Y ASFI+WFAEE KR
Sbjct: 65  ARTAKERGAILRRWSDLILAHADDLARLMTDEQGKPLAEAKGEVVYGASFIDWFAEEAKR 124

Query: 126 IYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQT 185
            YG TIP     KRL  IKQP+GV AAI PWNFP AMITRK GPALAAGCT+V+KPA++T
Sbjct: 125 AYGHTIPTPMPGKRLASIKQPVGVCAAIAPWNFPIAMITRKVGPALAAGCTVVVKPAAET 184

Query: 186 PFSALALAELAIRAGVPAGVFNVVTGSAGA-VGNELTSNPLVRKLSFTGSTEIGRQLMEQ 244
           P SALA+A LA  AGVPAGV N+VT +  + VG  L  +  VRKLSFTGST IG+ L +Q
Sbjct: 185 PLSALAIARLATEAGVPAGVLNIVTTTRSSEVGKVLCDDSRVRKLSFTGSTPIGKVLYQQ 244

Query: 245 CAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVYDR 304
           CA  +KK+SLELGGNAPFIVFDDADL+ AV+GA+ASK+RNAGQTCVCANRL VQ G++D 
Sbjct: 245 CAGTMKKLSLELGGNAPFIVFDDADLEAAVDGAIASKYRNAGQTCVCANRLIVQSGIHDA 304

Query: 305 FAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAHERG 364
           FA +L + V+ L +G G   GV IGPLI+EKA+ KV   ++ A++ GA V+ GG  H  G
Sbjct: 305 FAARLAEKVAALKVGPGTGEGVQIGPLINEKALTKVVGLVSGAVQAGAEVLTGGDVHGLG 364

Query: 365 GNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLS 424
           G+F+QPT+LV      ++ +EE FGP+AP+ +F+ EA+ +  AN T FGLAAYFY+RD+ 
Sbjct: 365 GHFYQPTVLVGATPEMRIFQEEIFGPVAPIVKFETEAEAVELANATPFGLAAYFYSRDVG 424

Query: 425 RVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481
           R +RV E +E G+VGIN G+IS EVAPFGG+K SGLGREG+  G+++YLE KY+C G
Sbjct: 425 RCWRVAEQIEAGMVGINEGLISTEVAPFGGVKESGLGREGASEGLDEYLETKYLCFG 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: 664
Number of extensions: 19
Number of successful extensions: 2
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: 485
Length adjustment: 34
Effective length of query: 448
Effective length of database: 451
Effective search space:   202048
Effective search space used:   202048
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 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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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