GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kgtP in Endozoicomonas montiporae CL-33

Align Alpha-ketoglutarate permease (characterized)
to candidate WP_051790058.1 EZMO1_RS17450 MFS transporter

Query= SwissProt::P0AEX3
         (432 letters)



>NCBI__GCF_001583435.1:WP_051790058.1
          Length = 434

 Score =  201 bits (511), Expect = 4e-56
 Identities = 126/398 (31%), Positives = 203/398 (51%), Gaps = 10/398 (2%)

Query: 28  SSGNLVEWFDFYVYSFCSLYFAHIFFPSGNTTTQLLQTAGVFAAGFLMRPIGGWLFGRIA 87
           S G ++E +DF VY+  + Y A  FFPS +  T LL T   FA G+L RP+GG+ FG + 
Sbjct: 24  SLGGMLEMYDFMVYAMMASYIAESFFPSSDPMTSLLGTFATFAVGYLSRPLGGFFFGHLG 83

Query: 88  DKHGRKKSMLLSVCMMCFGSLVIACLPGYETIGTWAPALLLLARLFQGLSVGGEYGTSAT 147
           D++GRK +  L++ +M   + +I C+P Y++IG  APALL+L RLFQG S+GGE   + T
Sbjct: 84  DRYGRKSTFTLTISIMALTTALIGCMPTYDSIGILAPALLVLLRLFQGFSLGGELPGAMT 143

Query: 148 YMSEVAVEGRKGFYASFQYVTLIGGQLLALLVVVVLQHTMEDAALREWGWRIPFALGAVL 207
           Y+SE    GR G      +++   G  LA  V  +L   +   A+  WGWR+PF +G +L
Sbjct: 144 YVSE-TTPGRSGLVIGILFMSFTLGFSLATFVHGLLTLILSPEAMSGWGWRVPFWVGGLL 202

Query: 208 AVVALWLRRQLDET----SQQETRALKEAGSLKGLWRNRRAFIMVLGFTAAGSLCFYTFT 263
             ++ ++R + DE+    +    R  +    L+ + ++RR F    G  A          
Sbjct: 203 GGLSYYIRLRFDESGLFMALNLVRQRQMIPMLELVRKHRRGFFCGFGIAAVCGSAVTLLG 262

Query: 264 TYMQKYLVNTAGMHANVASGIMTAALFVFMLIQPLIGALSDKIGRRTSMLCFGSLAAIFT 323
            YM  YL    G      +   + A  +F  +  L+G ++D+   +  + C   L A   
Sbjct: 263 AYMPGYLTTLHGFSRAEVAWHSSLAYIMFAPLCLLMGLVTDRCSHKKLLFCSIVLIAGVC 322

Query: 324 VPILSALQNVSSPYAAFG-LVMCALLIVSFYTSISGILKAEMFPAQVRALGVGLSYAVAN 382
           +P     Q VSS  A    ++M A ++ SF       +   +FP++VR  GV  SY +  
Sbjct: 323 LPY---YQYVSSHEAELSRIMMVAAILSSFVIGTLPPMLVRLFPSEVRYTGVATSYNLGM 379

Query: 383 AIFGGSAEY-VALSLKSIGMETAFFWYVTLMAVVAFLV 419
           A+FGG A   +   +K+ G+      Y+ ++++V  L+
Sbjct: 380 ALFGGLAPVSITPLIKAYGLALGPALYLIIISLVTLLI 417


Lambda     K      H
   0.328    0.138    0.419 

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: 454
Number of extensions: 33
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 432
Length of database: 434
Length adjustment: 32
Effective length of query: 400
Effective length of database: 402
Effective search space:   160800
Effective search space used:   160800
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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