GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__BFirm:BPHYT_RS23175
          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.

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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