GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_3627 Echvi_3627 TRAP transporter, DctM subunit

Query= TCDB::Q8YSQ7
         (445 letters)



>FitnessBrowser__Cola:Echvi_3627
          Length = 431

 Score =  199 bits (505), Expect = 2e-55
 Identities = 140/435 (32%), Positives = 212/435 (48%), Gaps = 16/435 (3%)

Query: 11  VMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLA 70
           ++    + L+  G PVA+SLG       LL + + V     +T + QR+   + +++LLA
Sbjct: 8   ILVLSFITLMGLGVPVAWSLG----FSSLLTLMVTVAAVPSMTTIAQRMGAGLNSFSLLA 63

Query: 71  IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130
           IP+FI  G ++ K GIA RL+     L G+L GGL    V+   L  A  G   A   A+
Sbjct: 64  IPFFILAGEIMNKGGIANRLINLAKALTGKLPGGLLYVNVIAAMLFGAIAGSAVAAASAL 123

Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLG-DQLGISVGDLFIGSVIP 189
           G I    M   GY KEL   V   S T G +IPPS VL+V      G+S+  LF+   IP
Sbjct: 124 GGILGKRMEDEGYPKELGVAVNVTSSTTGLVIPPSNVLIVYSLASGGVSIAALFVAGYIP 183

Query: 190 GLMMASAFALHVLIVAFIRPDVAPA-LPAQVREIGGKALGKRVIQVMIPPLILILLVLGS 248
           GL M     L +    FI+    PA  P   +E+G      +V     P L L+++V+G 
Sbjct: 184 GLFMG--LLLMLTAAYFIKKKKLPAGEPTSFKELG------KVFFSAAPSLTLLVIVIGG 235

Query: 249 IFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFSL 308
           I  G  T TEA A+     + L+   G+     L  +   +   T++V  ++  S A S 
Sbjct: 236 IVMGVFTATEASAIAVLYCLGLSFFYGELKPRDLPAILLKSSATTAVVAMLIATSMAMSW 295

Query: 309 VFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKL 368
           V    +  Q +  VL +L   K   L +    +  +G F+D      I  P+F+PV  +L
Sbjct: 296 VMSSEDIPQSISAVLLSLSDNKFVILIIINLILLFVGIFMDMTPAVLIFTPIFLPVVTEL 355

Query: 369 GIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLL 428
           GID V +G+I+  NL     TPP G  LF   GV   + + S++ + ++PF +  ++ L 
Sbjct: 356 GIDPVHFGIIMVLNLCIGLCTPPVGSVLFI--GVGVAKTSISNVVKPLLPFFIAMIIGLA 413

Query: 429 LIIIFPGIVSFLPSL 443
           +I I+P +  +LPSL
Sbjct: 414 VITIWPQLTLWLPSL 428


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: 475
Number of extensions: 27
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: 431
Length adjustment: 32
Effective length of query: 413
Effective length of database: 399
Effective search space:   164787
Effective search space used:   164787
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