GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SLC13A5 in Echinicola vietnamensis KMM 6221, DSM 17526

Align tonoplast dicarboxylate transporter (characterized)
to candidate Echvi_4197 Echvi_4197 anion transporter

Query= CharProtDB::CH_091173
         (540 letters)



>FitnessBrowser__Cola:Echvi_4197
          Length = 491

 Score =  271 bits (693), Expect = 4e-77
 Identities = 166/492 (33%), Positives = 261/492 (53%), Gaps = 30/492 (6%)

Query: 44  KNCYIALGPLLCAVVCLCVDLGGDETTTARNMLGVLVWMFAWWLTEAVPMPITSMTPLFL 103
           K   + LGP++   + L +D     +  A  +L V +WM  WW+ EAVP+ +T++ P+ L
Sbjct: 7   KKWSLILGPMVFIGLIL-LDPPSGMSEEALKVLAVTLWMAIWWIAEAVPIAVTALLPIVL 65

Query: 104 FPLFGISAADDVANSYMDDVISLVLGSFILALAVEHYNIHRRLALNITLVFCVEPLNAPL 163
           FP+ G         +Y    I L +G FILALA+E + +H+R+AL   ++  +   N   
Sbjct: 66  FPITGAVEIGITTEAYGHKYIFLYMGGFILALAIERWGLHQRIAL---IIISLIGSNMNS 122

Query: 164 LLLGICATTAFVSMWMHNVAAAVMMMPVATGILQRLPSSSST-TEVVHPAVGKFSRAVVL 222
           ++LG    TAF+SMW+ N A AVMM+P+   I+ +    S    +     VGK   A++L
Sbjct: 123 IMLGFMLATAFLSMWISNTATAVMMLPIGMAIVNQFAKVSDIYPDNREKEVGK---ALML 179

Query: 223 GVIYSAAVGGMSTLTGTGVNLILVGMWKSYFPEADPISFSQWFFFGFPLALCIFVVLWCV 282
            + YSA++GG +TL GT  NL+L G+ +  +     +SF  W  FGFPL++ + ++ W  
Sbjct: 180 AIAYSASIGGFATLIGTPPNLVLAGIIEELYDVK--LSFLDWMKFGFPLSMLLLIICWKY 237

Query: 283 LCVMY--CPKGAGQALSPYLHKSHLRRELDLLGPMNFAEKMVLAVFGGLVVLWMTRNITD 340
           L      C K           K  + + L  LG ++F EK VL +F      W+ R+   
Sbjct: 238 LTTYAFDCKKVDFPG-----GKQEINKMLKALGKISFEEKWVLIIFALTAAAWILRSFIQ 292

Query: 341 DIPGWGRIFAGRAGDGTVSVMMATLLFIIPSNIKKGEKLMDWNKCKKLPWNIVLLLGAGF 400
                 R+  G   D  +++M A  LF++PS   K  KL++W +  KLPW I+LL G G 
Sbjct: 293 ------RLLPG-IDDAVIALMAAITLFVLPSKSGK-RKLINWEEAVKLPWGIILLFGGGM 344

Query: 401 AIADGVRTSGLAEVLSKGLVFLETAPYWAIAPTVCLIAATITEFTSNNATTTLLVPLLIE 460
           A+A G   +GLAE ++  +  +       +   +  +   +TE TSN ATT +++P+L  
Sbjct: 345 ALAKGFGITGLAEWIAGKMGQMNGMSMILMILILVAMVNFLTEITSNLATTAMILPVLAP 404

Query: 461 IAKNMGIHPLLLMVPGAIGAQFAFLLPTGTPSNVVGFTTGHIEIKDMIKTGLPLKIAGTI 520
           +A +   HP +LMVP  + A  AF+LP  TP N V F +G+++I DM+K G  + I    
Sbjct: 405 LAMSFNAHPFMLMVPVTVAASCAFMLPVATPPNAVVFGSGYLKIPDMVKAGFWMNI---- 460

Query: 521 FLSILMPTLGAY 532
             SIL+ T+ +Y
Sbjct: 461 -FSILLVTIVSY 471


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: 774
Number of extensions: 40
Number of successful extensions: 7
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: 491
Length adjustment: 35
Effective length of query: 505
Effective length of database: 456
Effective search space:   230280
Effective search space used:   230280
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