GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deh in Dyella japonica UNC79MFTsu3.2

Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate N515DRAFT_0011 N515DRAFT_0011 MFS transporter, MHS family, alpha-ketoglutarate permease

Query= TCDB::M1Q159
         (468 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0011
          Length = 435

 Score =  207 bits (528), Expect = 4e-58
 Identities = 129/430 (30%), Positives = 218/430 (50%), Gaps = 26/430 (6%)

Query: 17  IFASSAGTVIEWYDFYIFGALATTLASKFYNTGTPIGDIIAWLGTFAVGFLVRPFGAIVF 76
           IF+ S G ++EWYD+Y++ A +   A  F+        ++   G FAVGFL+RP G  + 
Sbjct: 24  IFSGSIGNLVEWYDWYVYSAFSLYFAQVFFPASDQTTQLLNTSGIFAVGFLMRPLGGWLL 83

Query: 77  GRIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQYG 136
           G   D  GRK   L+++ +M   + +IGL P    +G  A I+L+  R+LQGL++GG+YG
Sbjct: 84  GTFADRRGRKAALLLSVFMMSLGSLIIGLSPGYAQIGVAAPILLVLARLLQGLSIGGEYG 143

Query: 137 GAATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITR-ISLGEADFNEWGWRLPFM 195
            +AT+++E AP+  RGF++S    T   G LI+L ++++ +   L     ++WGWR+PF+
Sbjct: 144 TSATYLSEMAPRESRGFWSSIQYVTLVAGQLIALALLVVLQHFVLSTQQLHDWGWRIPFL 203

Query: 196 ASILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATMGQ 255
              LL ++++ IRR + E+  F++ +      ++PL+    +P      ++ + G TMG 
Sbjct: 204 IGALLAVIAVIIRRNMDETASFKKARQL----ESPLRTLMRHPRE----VLTVIGLTMGG 255

Query: 256 GVVWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLSMPFFVFFGSLSDRIGRKKVMLSG 315
            + +YT   Y   +L         D+  I  AAL +       FG+LSDRIGR+ +++  
Sbjct: 256 TLAFYTFTTYMQKFLVNSAGMSKADATSISTAALFVYALLQPAFGALSDRIGRRPLLIGF 315

Query: 316 MLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYGPIAAF 375
            +L  L  YPI   +          H  +   G        L+   +I V+      A  
Sbjct: 316 GVLGALLTYPILSTLKE-------AHDWWQAFG--------LIMAALIIVSGYTSINAVV 360

Query: 376 LVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAIAGICLVV 435
             ELFPT+IR   + LPY +   VFGG    + L        D+   +W +     C ++
Sbjct: 361 KAELFPTEIRAIGVGLPYALALSVFGGTAEYVALWFKKIGHEDY--FYWYVTACIACSLL 418

Query: 436 GFLLIKETNK 445
            ++ +++T +
Sbjct: 419 VYIGMRDTRR 428


Lambda     K      H
   0.328    0.144    0.450 

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: 602
Number of extensions: 36
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: 468
Length of database: 435
Length adjustment: 33
Effective length of query: 435
Effective length of database: 402
Effective search space:   174870
Effective search space used:   174870
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 (21.7 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