GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Paraburkholderia bryophila 376MFSha3.1

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate H281DRAFT_00213 H281DRAFT_00213 aldehyde dehydrogenase (NAD+)

Query= SwissProt::O50174
         (487 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00213 H281DRAFT_00213
           aldehyde dehydrogenase (NAD+)
          Length = 479

 Score =  215 bits (547), Expect = 3e-60
 Identities = 161/466 (34%), Positives = 227/466 (48%), Gaps = 17/466 (3%)

Query: 4   HYIAGQWLAGQG-ETLESLDPV-GQGVVWSGRGADATQVDAAVCAAREAFP-AWARRPLE 60
           H+I G+W A  G ET+  LDP  GQ      RG  A  +DAAV AAR AF  AW      
Sbjct: 6   HFIGGEWSAASGGETIAVLDPSDGQPFTQLARGT-AADIDAAVHAARRAFEGAWGAASAA 64

Query: 61  QRIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEK 120
           +R  +L R +  + +R +ELA++   +TGKPL ++  +  ++V        A  +  GE 
Sbjct: 65  ERGRVLYRLSMLVAARQEELAQLEARDTGKPLKQARADSAALVRYFEFYAGAADKLHGET 124

Query: 121 SGPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSE----LTPK 176
               A  T +   +PHGV     P+N+P  +    +  AL  GN  V KP+E       +
Sbjct: 125 LPYQAGYTVMTIREPHGVTGHIVPWNYPMQIFGRSVGAALAVGNACVVKPAEDACLSVLR 184

Query: 177 VAELTLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGG 235
           VAEL      +AGLPAG LN+V G G E G ALA H G+D + FTGS  TG L+ +Q   
Sbjct: 185 VAELA----AEAGLPAGALNIVTGYGHEAGAALARHSGIDHISFTGSPETGKLV-TQMAA 239

Query: 236 QPQKILALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDAL 295
           +    + LE+GG +P +V   ADLDAA+  ++ +   +AGQ C+   R+L+ +  + + L
Sbjct: 240 ENHVPVTLELGGKSPQLVFADADLDAALPVLVSAIVQNAGQTCSAGSRVLIDRAIY-EPL 298

Query: 296 LARLVAVSATLRVG--RFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPI 353
           L RL +    LRVG    D    P + A       + L  AQ   I   A   +    P 
Sbjct: 299 LDRLSSAFNALRVGPSHADLDCGPLINAKQQRRVWDFLSDAQHDGIAMAAHGEVIPEAPE 358

Query: 354 DGAALLTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSR 413
            G       + DV A      +E FGP+L  + +SD   A+  AN TQYGL AG+ +   
Sbjct: 359 SGFYQAPTLLRDVPASHRLARDEVFGPVLAAMSFSDEDEALALANGTQYGLVAGIWTRDG 418

Query: 414 ERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYA 459
            R  +     R+G V  N    G     PFGG+  SG+ R   + A
Sbjct: 419 ARQMRLARRLRSGQVFINNYGAGGGVELPFGGVKHSGHGREKGFEA 464


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: 575
Number of extensions: 41
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: 487
Length of database: 479
Length adjustment: 34
Effective length of query: 453
Effective length of database: 445
Effective search space:   201585
Effective search space used:   201585
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 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