GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deh in Burkholderia phytofirmans PsJN

Align Acetate/monochloroacetate permease, Deh4p, of 468 aas and 12 TMSs (characterized)
to candidate BPHYT_RS07110 BPHYT_RS07110 LysR family transcriptional regulator

Query= TCDB::M1Q159
         (468 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS07110 BPHYT_RS07110 LysR family
           transcriptional regulator
          Length = 437

 Score =  252 bits (643), Expect = 2e-71
 Identities = 147/425 (34%), Positives = 235/425 (55%), Gaps = 36/425 (8%)

Query: 19  ASSAGTVIEWYDFYIFGALATTLASKFYNTGT-PIGDIIAWLGTFAVGFLVRPFGAIVFG 77
           A+  GT IEWYDFYI+   +  +  K +  G+ P    +A  GTFAVGF  RPFG +VFG
Sbjct: 20  AAFVGTTIEWYDFYIYATASALIFGKLFFPGSDPFFATLASFGTFAVGFFARPFGGLVFG 79

Query: 78  RIGDLVGRKFTYLITITIMGSCTFLIGLLPTQDVLGAWAGIILITMRILQGLALGGQYGG 137
            +GD +GRK   + T+ IMG  T  IG LPT    G WA ++L+ +R+ QG+A+GG++GG
Sbjct: 80  HLGDRIGRKKALVATLAIMGVGTVGIGFLPTYASAGVWAPVLLVLLRVAQGIAIGGEWGG 139

Query: 138 AATFVAEHAPQGKRGFYTSWIQTTATFGLLISLGVILITRISLGEADFNEWGWRLPFMAS 197
           A    +EHAPQG+R F+ S+ Q  +  GL++SL +      S+ +  F  WGWRLPF+AS
Sbjct: 140 AVLMASEHAPQGRRTFFASFAQLGSPAGLILSL-LAFRAVASMDKDAFLGWGWRLPFLAS 198

Query: 198 ILLVILSLWIRRALKESPLFQQLKDTKAVSKNPLKESFANPYNLRWVLIALFGATMGQGV 257
            +L+++ L IR  + ESP F+ LK  + V+  P+ E   + +  R +L+ L    +G   
Sbjct: 199 AVLLVVGLLIRAGVDESPEFKALKAQRRVAALPVAEVVRDAW--RTLLLCLGANVIGVAG 256

Query: 258 VWYTGQFYALFYLQKIFNTPLIDSNLIVGAALLLS-MPFFVFFGS--LSDRIGRKKVMLS 314
            W+   F   +  Q    T  +D +LI+    +++ +  F   GS   + RIG  + +  
Sbjct: 257 AWFVNTFMLNYTTQ----TLGLDRSLILDCLFVVAFIQLFTQLGSGWFAQRIGTGRFLKG 312

Query: 315 GMLLAVLTYYPIYGLMAAFAPTDPGQHFLFAYIGYNPVILGLLVFIQVIYVTMVYGPIAA 374
              LA+L+ YP++ L++   P                +++G  + + V+ ++  Y  +A 
Sbjct: 313 AAALAMLSPYPMFALVSTGRPV--------------AIVIG--IALAVMCMSSSYAVMAG 356

Query: 375 FLVELFPTKIRYTSMSLPYHIGNGVFGGLVPMIGLILINATGNDFAGLWWPMAI-----A 429
           F+   FP ++RY+++SL Y +   + GGL P+IG +L     + + G WWP+A+     A
Sbjct: 357 FMSTAFPVRVRYSAISLSYQVCAALAGGLTPLIGTLL----AHRYPGAWWPLAVFYSVLA 412

Query: 430 GICLV 434
           G+ LV
Sbjct: 413 GVSLV 417


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: 639
Number of extensions: 38
Number of successful extensions: 8
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: 437
Length adjustment: 33
Effective length of query: 435
Effective length of database: 404
Effective search space:   175740
Effective search space used:   175740
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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