GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Korea:Ga0059261_3374
          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:

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