GapMind for catabolism of small carbon sources

 

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

Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate 3607284 Dshi_0699 TRAP C4-dicarboxylate transport system permease DctM subunit (RefSeq)

Query= TCDB::Q8YSQ7
         (445 letters)



>FitnessBrowser__Dino:3607284
          Length = 437

 Score =  239 bits (611), Expect = 1e-67
 Identities = 149/436 (34%), Positives = 230/436 (52%), Gaps = 11/436 (2%)

Query: 12  MFAGALV-LLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLA 70
           +  GA+V L++ G PVA +     +   +LG  + +     +  +     G +  Y L+ 
Sbjct: 9   LLLGAIVALMALGMPVALAF----LAANILGAWVFMGGERGIVQLLNNGLGALTTYALVP 64

Query: 71  IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130
           IP F+ MG +   +G+  R+   +  LLGRL G L+   VL G   +  +G    +   +
Sbjct: 65  IPLFLLMGEIFFHTGLGGRMFTAIDRLLGRLPGRLSYVTVLGGTGFSTLSGSSMGSTALL 124

Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPG 190
           G + +P M   GY   ++ G I  +G L  IIPPS + V+L     I VG L I  VIPG
Sbjct: 125 GSLMVPEMNARGYKSHMSIGPILGTGGLAIIIPPSALAVLLATLAQIDVGALLIAGVIPG 184

Query: 191 LMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSIF 250
           LM+A  +   + I     P  APA       +G K LG  +++ ++P + ++++++  + 
Sbjct: 185 LMLAGFYIATIWIQTRRDPSAAPAYEVAEVSLGAK-LGL-LLRDVVPMVGVMVVIVSLMI 242

Query: 251 FGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFS--L 308
           FG  TP+EA A G  G I LAAA    T+E+LR+     L++T M   I+ GS  FS  L
Sbjct: 243 FGIVTPSEAAAFGALGVIILAAAFRCLTVEALRRSVVGALKVTLMAYMIVFGSATFSQLL 302

Query: 309 VFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKL 368
            F G +G    +    +L    I  L      + +LG F++   I  + +P+F P+AQ L
Sbjct: 303 AFSGASGGLIGWATGFDLD--PIWMLLAMFGVLLVLGMFMEQISIMLLTVPIFFPLAQSL 360

Query: 369 GIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLL 428
           G DL+W+ +I+   L+ SF TPPFG  LF ++GVAPP  T  +IY   IPFI   LL++ 
Sbjct: 361 GFDLIWFALIMLLALEISFTTPPFGLLLFVMKGVAPPSTTMREIYLAAIPFIACSLLLVA 420

Query: 429 LIIIFPGIVSFLPSLG 444
           L+I+FP + ++LP LG
Sbjct: 421 LLILFPPLATWLPGLG 436


Lambda     K      H
   0.331    0.149    0.437 

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: 536
Number of extensions: 32
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: 445
Length of database: 437
Length adjustment: 32
Effective length of query: 413
Effective length of database: 405
Effective search space:   167265
Effective search space used:   167265
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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