GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctM in Pseudomonas simiae WCS417

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 GFF2912 PS417_14900 C4-dicarboxylate ABC transporter permease

Query= TCDB::Q8YSQ7
         (445 letters)



>FitnessBrowser__WCS417:GFF2912
          Length = 426

 Score =  206 bits (524), Expect = 1e-57
 Identities = 144/434 (33%), Positives = 225/434 (51%), Gaps = 22/434 (5%)

Query: 12  MFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLAI 71
           +F    V +  G P+A SLG    L G + I +  F    ++++  ++F     YT LAI
Sbjct: 6   LFLLLFVFMFLGVPIAISLG----LSGAVSILM--FSQDSVSSLAIKLFETSDAYTFLAI 59

Query: 72  PYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAMG 131
           P+F+  GA +   G+A+RL++     +G +RGGLA+A VL   L AA +G   ATV A+G
Sbjct: 60  PFFLLSGAFMTTGGVAQRLIDFANACVGHIRGGLAIAAVLACMLFAALSGSSPATVAAVG 119

Query: 132 LISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPGL 191
            I++  M+R GY K    G+I  +GTLG +IPPS+V+VV       SVG LF+  VIPGL
Sbjct: 120 SIAVAGMVRSGYPKAFGAGIICNAGTLGILIPPSIVMVVYSAATETSVGKLFMAGVIPGL 179

Query: 192 MMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSIFF 251
           ++     + + IVA I+      LPAQ R    + L     +     L+L++++LG I+ 
Sbjct: 180 LLGLMLMIAIYIVARIK-----KLPAQPRATFREWLTS--ARRAFWGLLLLVIILGGIYS 232

Query: 252 GFATPTEAGAVGCA-GAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFSLVF 310
           G  TPTEA AV     A           L    +V   + R+  M++FI+  +  F+ V 
Sbjct: 233 GMFTPTEAAAVAAVYSAFVALFIYKDMQLRDCPKVLLESGRLAIMLMFIIANAMLFAHV- 291

Query: 311 RGLNGDQFMFDVLA-NLPGG--KIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQK 367
             L  +Q   ++ A  L  G   IGFL +    + + G F++   I  I+ P+F P+A K
Sbjct: 292 --LTTEQIPQEITAWVLSEGLTPIGFLIMVNVVLLIAGSFMEPSAIVLILAPIFFPIAMK 349

Query: 368 LGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVL 427
           LGID +  G+++  N++   + PP G  LF    V    +T     R  +P++++ L+ L
Sbjct: 350 LGIDPIHLGIVMVVNMEIGLVHPPVGLNLFVTSAVT--GLTLGQTIRAALPWLMILLVFL 407

Query: 428 LLIIIFPGIVSFLP 441
           +++   P I   LP
Sbjct: 408 IMVTYLPFISLALP 421


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: 432
Number of extensions: 19
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: 426
Length adjustment: 32
Effective length of query: 413
Effective length of database: 394
Effective search space:   162722
Effective search space used:   162722
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