GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Burkholderia phytofirmans PsJN

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate BPHYT_RS23175 BPHYT_RS23175 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= SwissProt::O50174
         (487 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS23175 BPHYT_RS23175
           gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
          Length = 497

 Score =  202 bits (515), Expect = 2e-56
 Identities = 157/470 (33%), Positives = 235/470 (50%), Gaps = 21/470 (4%)

Query: 5   YIAGQWLAGQG-ETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPA--WARRPLEQ 61
           +I G++   +G  T + L P+   ++     + A  VDAAV AAR AF +  W+     Q
Sbjct: 23  FIDGEYRDAEGGRTFDCLSPIDGKLLAKVADSGAADVDAAVAAARRAFDSGVWSGLNPRQ 82

Query: 62  RIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSM-VNKVAISVQAFRERTGEK 120
           R  +L R+AA+++   DELA +   + GKP+     + TS+ V   A  V+ F E   + 
Sbjct: 83  RKAVLLRWAASIREHMDELALLETLDAGKPI----ADTTSVDVPGAAYCVEWFAEAIDKI 138

Query: 121 SGPLADAT----AVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPK 176
            G +A A      ++  +P GVVA   P+NFP  + +    PAL AGN VV KPSE +P 
Sbjct: 139 GGEVAPADHHLLGLVTREPIGVVAAVVPWNFPILMASWKFGPALAAGNSVVLKPSEKSPL 198

Query: 177 VAELTLKAWIQAGLPAGVLNLVQGGRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQ 236
            A    +  + AG+PAGV N+V G  E G  LA H+ +D L FTGS+  G L+    G  
Sbjct: 199 TAIRLAQLALDAGIPAGVFNVVPGAGEPGKLLALHQDVDCLAFTGSTNVGKLIMQYAGQS 258

Query: 237 PQKILALEMGGNNP-LVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDAL 295
             K + LE+GG +P +V+ +  D+D A      + F + G+ CT   RLLV +    D  
Sbjct: 259 NLKRVWLELGGKSPNIVMPDCPDMDRAANAAAGAIFYNMGEMCTAGSRLLVHRDI-KDVF 317

Query: 296 LARLVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLL---AMTQP 352
           + +L+A + +   G     P   MGA++     E +L   E   G+    LL   A  + 
Sbjct: 318 IDKLIAAARSYTPGN-PLDPDTSMGAIVDKVQLERVLGYIE--AGRAEAKLLLGGARVKE 374

Query: 353 IDGAALLTPGILDV-SAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSD 411
             G   + P I ++  + A+   EE FGP+L VI +     AIR AN ++YGLAA + + 
Sbjct: 375 DTGGFYIEPTIFEIPGSGAKVAREEIFGPVLSVITFDTVEEAIRIANDSEYGLAAAVWTS 434

Query: 412 SRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYAAD 461
           +     +   + RAG V  N    G   + PFGG   SGN R  + +A +
Sbjct: 435 NLTTAHEVSRKLRAGTVWVNCYDEGGDMNFPFGGYKQSGNGRDKSLHALE 484


Lambda     K      H
   0.318    0.134    0.396 

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: 581
Number of extensions: 30
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: 487
Length of database: 497
Length adjustment: 34
Effective length of query: 453
Effective length of database: 463
Effective search space:   209739
Effective search space used:   209739
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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