GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Sphingomonas koreensis DSMZ 15582

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Ga0059261_3374 Ga0059261_3374 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::O50174
         (487 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_3374 Ga0059261_3374
           NAD-dependent aldehyde dehydrogenases
          Length = 474

 Score =  186 bits (471), Expect = 2e-51
 Identities = 152/465 (32%), Positives = 229/465 (49%), Gaps = 33/465 (7%)

Query: 4   HYIAGQWLAGQGETLES-LDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQR 62
           HYI G+W+  +G T    ++P  +  V           D AV AA+ AF +++R  +++R
Sbjct: 7   HYIGGEWVESEGGTRHDVINPATEAPVTEITLGSEADADKAVAAAKAAFDSFSRTSVDER 66

Query: 63  IELLERFAATLKSRADELARVIGEETGKPLWESAT-EVTSMVNKVAISVQAFRERTGEKS 121
           I LLE   A  K+RA +LA  I  E G P+  + T +V S +  +  ++ A +    E S
Sbjct: 67  IALLEAILAEYKNRAGDLADAIAAEMGAPISLAKTAQVGSGIGHLMSTINALK--AFEFS 124

Query: 122 GPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELT 181
             +  +  V  H+P GVVA+  P+N+P +     + PAL AGN +V KPSE  P  A + 
Sbjct: 125 EQIGQSLVV--HEPIGVVALITPWNWPLNQIVAKVAPALAAGNTMVLKPSEEAPGSAAIF 182

Query: 182 LKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKI 240
            +   +AG+PAGV NLVQG G   G AL+ HR +D + FTGS+R G +  ++   +  K 
Sbjct: 183 AEIMDKAGVPAGVFNLVQGDGPIVGTALSRHRDVDMVSFTGSTRAG-IQVAKNAAETVKR 241

Query: 241 LALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDAL----- 295
           +  E+GG +P V+   ADL  AV   + S  +++GQ C    R+LV +    +A      
Sbjct: 242 VHQELGGKSPNVILPGADLSRAVQVGLFSVVMNSGQSCIAPARMLVHESQAAEAAQIASG 301

Query: 296 LARLVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDG 355
           L + V      + GR        +G V++ +  E +       + +GA+         DG
Sbjct: 302 LMKAVETGDPAQEGRH-------IGPVVNKAQWEKIQGLIRKGMEEGAKLETGGPGRPDG 354

Query: 356 AAL-------LTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGL 408
                     L  G+ +   +A    EE FGP++ +I Y D   A+R AN T YGL+A +
Sbjct: 355 IETGYFVKPTLFSGVRNDMTIAR---EEIFGPVITIIPYRDEEEAVRIANDTDYGLSA-V 410

Query: 409 LSDSRERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHR 453
           L  S E  ++     RAG+V  N        S PFGG   SGN R
Sbjct: 411 LFGSPEEVKRVAPRLRAGMVYINGGQPD--PSLPFGGYKQSGNGR 453


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: 558
Number of extensions: 37
Number of successful extensions: 7
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: 487
Length of database: 474
Length adjustment: 34
Effective length of query: 453
Effective length of database: 440
Effective search space:   199320
Effective search space used:   199320
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: 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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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