GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Escherichia coli BW25113

Align The dicarboxylate (succinate, fumarate, malate and oxaloacetate):H+ symporter, DctA (probably 3H+ are transported per succinate taken up (characterized)
to candidate 18105 b4077 glutamate/aspartate:proton symporter (NCBI)

Query= TCDB::P96603
         (421 letters)



>FitnessBrowser__Keio:18105
          Length = 437

 Score =  364 bits (935), Expect = e-105
 Identities = 179/419 (42%), Positives = 285/419 (68%), Gaps = 20/419 (4%)

Query: 6   NLTVQVITAVIIGVIVGLV---------WPDVGKEMKPLGDTFINAVKMVIAPIIFFTIV 56
           +L  Q++ A+++G+++G           W  V   + P GD FI+ +KM++ PI+  T+V
Sbjct: 7   SLAWQILFAMVLGILLGSYLHYHSDSRDWLVVNL-LSPAGDIFIHLIKMIVVPIVISTLV 65

Query: 57  LGIAKMGDMKKVGKVGGKAFIYFEVVTTLALIIGLFVVNIMKPGAGLDYSKLEKGDVSQY 116
           +GIA +GD K++G++G K  IYFEV+TT+A+I+G+ + N+ +PGAG+D S+L   D+S+Y
Sbjct: 66  VGIAGVGDAKQLGRIGAKTIIYFEVITTVAIILGITLANVFQPGAGVDMSQLATVDISKY 125

Query: 117 ------TQNGGQGIDWIEFITHIVPSNMVDAFAKGDILQVLFFSILFGVGLAALGEKGKS 170
                  Q+   GI  +  I  +VP+N+V + AKG++L ++FFS+LFG+GL++L    + 
Sbjct: 126 QSTTEAVQSSSHGI--MGTILSLVPTNIVASMAKGEMLPIIFFSVLFGLGLSSLPATHRE 183

Query: 171 -VIDFFDKVSHVFFKIIGYIMRAAPIGAFGAMAYTIGHFGLDSIKPLASLMMSVYITMFL 229
            ++  F  +S   FK+   +MR AP+G F  +A T+ +FG  S+ PLA L++ V+  +  
Sbjct: 184 PLVTVFRSISETMFKVTHMVMRYAPVGVFALIAVTVANFGFSSLWPLAKLVLLVHFAILF 243

Query: 230 FVFVALNIICKLYGFSLWNYLRFIKDELLIVLGTSSSESVLPRMMDKMERYGCSKSVVGL 289
           F  V L I+ +L G S+W  +R +KDEL++   T+SSESVLPR+++KME YG   S+   
Sbjct: 244 FALVVLGIVARLCGLSVWILIRILKDELILAYSTASSESVLPRIIEKMEAYGAPVSITSF 303

Query: 290 VIPTGYSFNLDGTSIYLSMATVFLAQVFGVDLSIGQQITIILVLMLTSKGAAGVTGSGFI 349
           V+PTGYSFNLDG+++Y S+A +F+AQ++G+DLSI Q+I ++L LM+TSKG AGV G  F+
Sbjct: 304 VVPTGYSFNLDGSTLYQSIAAIFIAQLYGIDLSIWQEIILVLTLMVTSKGIAGVPGVSFV 363

Query: 350 VLASTLSALQVIPLEGLALLLGVDRFMSEGRAIVNLIGNGIATIIVAKSENEFDEAKSI 408
           VL +TL ++  IPLEGLA + GVDR +   R  +N++GN +A +++AK E++FD  K++
Sbjct: 364 VLLATLGSVG-IPLEGLAFIAGVDRILDMARTALNVVGNALAVLVIAKWEHKFDRKKAL 421


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: 509
Number of extensions: 17
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: 437
Length adjustment: 32
Effective length of query: 389
Effective length of database: 405
Effective search space:   157545
Effective search space used:   157545
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: 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