GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Dinoroseobacter shibae DFL-12

Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate 3607155 Dshi_0577 aldehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-15736
         (480 letters)



>FitnessBrowser__Dino:3607155
          Length = 483

 Score =  310 bits (793), Expect = 9e-89
 Identities = 180/472 (38%), Positives = 254/472 (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  AKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYG 128
            ++R   L      L+   D++GRL++ E+GKPLAE KGE+  A  F  +FA EA R +G
Sbjct: 62  IQKRHDVLMAIGTELMARSDEIGRLLSREEGKPLAEGKGEVYRAGQFFTYFAAEALRQHG 121

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

Query: 189 ALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQLMAECAKD 248
           A+AL E+  R  IPKG+ ++V G   D+G  L  +  V  +SFTGS  +GR + A   ++
Sbjct: 182 AIALTEIIARQDIPKGLFNLVAGPGRDVGQRLVESAEVDAISFTGSVPVGRGIAAAAVQN 241

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

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

Query: 365 FFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRV 424
           F  P +      D  + +EE F P+  + R     E +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: 548
Number of extensions: 18
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:

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