GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Shewanella oneidensis MR-1

Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate 200106 SO0922 proton/glutamate symporter (NCBI ptt file)

Query= TCDB::P96603
         (421 letters)



>FitnessBrowser__MR1:200106
          Length = 424

 Score =  273 bits (698), Expect = 7e-78
 Identities = 136/399 (34%), Positives = 240/399 (60%), Gaps = 9/399 (2%)

Query: 7   LTVQVITAVIIGVIVGLVWPDVGKEMKPLGDTFINAVKMVIAPIIFFTIVLGIAKMGDMK 66
           L +Q+   +++G++VG+   +    +KP+G  F+N +KM+I P++F ++++G+  M D  
Sbjct: 5   LWLQIFVGMVLGILVGVTLGEQASYLKPIGTLFVNTIKMLIVPLVFCSLIVGVTSMEDTA 64

Query: 67  KVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQYTQNGGQGIDW 126
           K+G++G K+F ++   T +A+ +GL V  +++PGAG+   + E  + ++   +       
Sbjct: 65  KMGRIGFKSFSFYLCTTAIAISLGLVVGYVIQPGAGVPLLQHEAVNTAKEVPSV------ 118

Query: 127 IEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKSVIDFFDKVSHVFFKII 186
           ++ +  IVP+N V A A G ILQV+ F++  G+ L  +G+ GK  I  F+ ++   +K+ 
Sbjct: 119 MQTLIDIVPTNPVAALASGQILQVIVFAVALGIALVLIGDHGKPAIKVFESLAEAMYKLT 178

Query: 187 GYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFLFVFVALNIICKLYG-FS 245
             +M+ AP G FG MA+  G +G+D + PL  ++++VYI   + V    +I+ +L+   +
Sbjct: 179 DMVMKLAPYGVFGLMAWVAGEYGIDMLWPLIKVIIAVYIGCIIHVLGFYSIVLRLFAKLN 238

Query: 246 LWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERY-GCSKSVVGLVIPTGYSFNLDGTSI 304
             ++ + I + + +   TSSS   LP  M     Y G +K +   V+P G + N+DGT++
Sbjct: 239 PLHFFKGISNAMAVAFTTSSSAGTLPASMKCASEYLGVNKKISSFVLPLGTTINMDGTAL 298

Query: 305 YLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFIVLASTLSALQVIPLE 364
           Y  +  +F+AQ FG+DL+    +TIIL   L S G AGV G+G ++L   LS +  +PLE
Sbjct: 299 YQGVTALFVAQAFGIDLTWVDYLTIILTATLASIGTAGVPGAGLVMLTLVLSTVG-LPLE 357

Query: 365 GLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFD 403
           G+AL+ G+DR +   R +VN+ G+ +AT ++AKSENE D
Sbjct: 358 GVALIAGIDRILDMARTVVNVSGDLVATTVIAKSENELD 396


Lambda     K      H
   0.326    0.143    0.408 

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: 444
Number of extensions: 30
Number of successful extensions: 5
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: 421
Length of database: 424
Length adjustment: 32
Effective length of query: 389
Effective length of database: 392
Effective search space:   152488
Effective search space used:   152488
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 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