GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC13A5 in Marinobacter adhaerens HP15

Align tonoplast dicarboxylate transporter (characterized)
to candidate GFF2170 HP15_2124 sodium: dicarboxylate cotransporter

Query= CharProtDB::CH_091173
         (540 letters)



>FitnessBrowser__Marino:GFF2170
          Length = 493

 Score =  270 bits (689), Expect = 1e-76
 Identities = 155/466 (33%), Positives = 250/466 (53%), Gaps = 27/466 (5%)

Query: 72  ARNMLGVLVWMFAWWLTEAVPMPITSMTPLFLFPLFGISAADDVANSYMDDVISLVLGSF 131
           A + LG+++ M  WW TEA+P+P T++ P+ L P  G+    +    Y + +I L LG F
Sbjct: 50  AWSALGLMLLMATWWSTEAIPIPATALLPIVLVPALGLGTVGEATEPYANPIIFLFLGGF 109

Query: 132 ILALAVEHYNIHRRLALNITLVFCVEPLNAPLLLLGICATTAFVSMWMHNVAAAVMMMPV 191
            L LA++ +N+HRR+AL        +P      + G    TAF+SMW+ N A A+MM+P+
Sbjct: 110 TLGLAMQRWNLHRRIALMTLKAVGSKPRRQ---IAGFMLATAFLSMWVSNTATAIMMLPI 166

Query: 192 ATGILQRLPSSSSTTEVVHPAVGKFSRAVVLGVIYSAAVGGMSTLTGTGVNLILVGMWKS 251
              ++  + ++ +        V +++ A++L + YSA++GG++TL GT  N +L     +
Sbjct: 167 GLSVVAMMDTNDNPE-----GVRRYATALLLAIAYSASIGGIATLIGTPPNALLA----A 217

Query: 252 YFPEADPIS--FSQWFFFGFPLALCIFVVLWCVLCVMYCPKGAGQALSPYLHKSHLRREL 309
           Y  E   +S  F+QW   G P+ + + V+ W  L      +  G   S    K+ +R+EL
Sbjct: 218 YLSENQGVSVGFAQWMLLGVPVTIVMLVLAWWWLT----RRDFGLGNSGDGGKA-IRQEL 272

Query: 310 DLLGPMNFAEKMVLAVFGGLVVLWMTRNITDD-IPGWGRIFAGRAGDGTVSVMMATLLFI 368
           + LG +   EK+V  VF      W+ R +  D +  W         D  +++  A  +F+
Sbjct: 273 EALGTLGKGEKLVALVFLVTASAWIFRPLLSDRLMPW-------LSDTGIAIAAAIAMFL 325

Query: 369 IPSNIKKGEKLMDWNKCKKLPWNIVLLLGAGFAIADGVRTSGLAEVLSKGLVFLETAPYW 428
           IP N +  E L+DW   K +PW ++LL G G A+A  + +SGLAE +++ L      P  
Sbjct: 326 IPVNTRNREFLLDWETAKGIPWGVLLLFGGGLAMAGVISSSGLAEWIAQSLGVAGALPML 385

Query: 429 AIAPTVCLIAATITEFTSNNATTTLLVPLLIEIAKNMGIHPLLLMVPGAIGAQFAFLLPT 488
            +   V  +   +TE TSN AT    +PLL  +A + G+ PLLL VP AI A  AF++P 
Sbjct: 386 VMILLVVGVIIFLTEVTSNTATAAAFLPLLGALALSQGVSPLLLTVPAAIAASCAFMMPV 445

Query: 489 GTPSNVVGFTTGHIEIKDMIKTGLPLKIAGTIFLSILMPTLGAYVF 534
            TP N + F++GH++I DMI+ G  L + G + +++L   L   VF
Sbjct: 446 ATPPNAIVFSSGHMQIGDMIRAGFALNLLGIVVVTVLSYLLLGVVF 491


Lambda     K      H
   0.326    0.140    0.441 

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: 825
Number of extensions: 46
Number of successful extensions: 6
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: 540
Length of database: 493
Length adjustment: 35
Effective length of query: 505
Effective length of database: 458
Effective search space:   231290
Effective search space used:   231290
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: 52 (24.6 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