GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Dinoroseobacter shibae DFL-12

Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 3607155 Dshi_0577 aldehyde dehydrogenase (RefSeq)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_495
         (480 letters)



>lcl|FitnessBrowser__Dino:3607155 Dshi_0577 aldehyde dehydrogenase
           (RefSeq)
          Length = 483

 Score =  301 bits (772), Expect = 2e-86
 Identities = 174/472 (36%), Positives = 251/472 (53%), Gaps = 9/472 (1%)

Query: 10  RQQAFIDGAWVDADNGQTIKVNNPA-TGEILGTVPKMGAAETRRAIEAADKALPAWRALT 68
           R Q +IDGAW +      I+  NP+ T +++G   +  A +   A+ AA +A PAW A  
Sbjct: 4   RTQLYIDGAWTEGT--AQIENRNPSDTTDLIGMYAQADAGQLDTALAAARRAQPAWWAAG 61

Query: 69  AKERATKLRRWYELIIENQDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYG 128
            ++R   L      ++   D++ RL++ E+GKPLAE KGE+  A  F  +FA EA R +G
Sbjct: 62  IQKRHDVLMAIGTELMARSDEIGRLLSREEGKPLAEGKGEVYRAGQFFTYFAAEALRQHG 121

Query: 129 DVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFS 188
           D+    +P   + V ++ +GV A I+PWNFP A    K  PALA G  +V KPA+ TP S
Sbjct: 122 DLAESVRPGIEIDVRREAVGVVAIISPWNFPVATPAWKIAPALAFGNAVVWKPANVTPAS 181

Query: 189 AFALAELAQRAGIPAGVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKD 248
           A AL E+  R  IP G+F++V+G   D+G  L  +  V  +SFTGS  +GR + +   ++
Sbjct: 182 AIALTEIIARQDIPKGLFNLVAGPGRDVGQRLVESAEVDAISFTGSVPVGRGIAAAAVQN 241

Query: 249 IKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEK 308
           + KV +E+G   P IV DD DLD AV  A  S +   GQ C  A+RL +   V+DAF EK
Sbjct: 242 MTKVQMEMGSKNPLIVMDDCDLDLAVAHAASSAFGGTGQKCTAASRLIVHSAVHDAFVEK 301

Query: 309 LKVAVAKLKIGNGLEAGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPME----GN 364
           L  A   +K+G+ LE GT  GP++ E  + +  E+I     +GA +L GG  +E    G 
Sbjct: 302 LVAAARAMKVGHALEDGTQLGPVVSESQLNQNMEYIGVGKDEGAELLCGGDRLEMATDGY 361

Query: 365 FFEPTILTNVPNNAAVAKEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRV 424
           F  P +     N+  + +EE F P+  + R     + +A +NDT+FGL +      L R 
Sbjct: 362 FMAPAVFAGTANDMRINREEMFAPITAVQRVDSYDEALARANDTQFGLTAGIMTTSLARA 421

Query: 425 FRVAEALEYGMVGVNTGLISNEV-APFGGIKASGLG-REGSKYGIEDYLEIK 474
                 +  G V VN      +   PFGG  AS  G RE   Y  E Y  +K
Sbjct: 422 SHFRAHMRAGCVMVNLPTAGTDYHVPFGGRGASSFGPREQGSYAAEFYTTVK 473


Lambda     K      H
   0.317    0.135    0.390 

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: 551
Number of extensions: 22
Number of successful extensions: 3
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: 480
Length of database: 483
Length adjustment: 34
Effective length of query: 446
Effective length of database: 449
Effective search space:   200254
Effective search space used:   200254
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