GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Sphingobium czechense LL01

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_066609128.1 V473_RS20300 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::O50174
         (487 letters)



>NCBI__GCF_001046645.1:WP_066609128.1
          Length = 487

 Score =  208 bits (530), Expect = 3e-58
 Identities = 154/457 (33%), Positives = 225/457 (49%), Gaps = 8/457 (1%)

Query: 5   YIAGQWL-AGQGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRI 63
           +I G W+ A  G T+   +P    ++ +          AA+ AA  AFPAW  +    R 
Sbjct: 16  FIGGAWVGATSGATVPVDNPATGAIIGTVPDCGEADTLAAIAAAEAAFPAWKAQTAGDRA 75

Query: 64  ELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVA-ISVQAFRERTGEKSG 122
            +LER+ A + +   +L R++  E GKP+ E+  E+    + +   + +  R   G    
Sbjct: 76  AVLERWHALVLANVADLGRIMTAEQGKPIAEAEGEIRYAASFIKWFAEEGRRVDGGIVPA 135

Query: 123 PLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELTL 182
           P A+   ++  +P GV A   P+NFP  +      PAL AG  VV KPSELTP  A    
Sbjct: 136 PEANRRILVMKEPVGVSAAITPWNFPAAMITRKCAPALAAGCPVVVKPSELTPFTALALA 195

Query: 183 KAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKIL 241
           K   +AG+PAGV N+V G     G AL A   +  L FTGS+R G+LL  Q     +++ 
Sbjct: 196 KLAEEAGIPAGVFNIVTGLPTAIGGALTASPVVRKLSFTGSTRVGSLLMRQCADTIKRV- 254

Query: 242 ALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLVA 301
           + E+GGN PL+V + AD+D AV + + S F +AGQ C CA R+LV  G + D    +L  
Sbjct: 255 SFELGGNAPLIVFDDADVDIAVASAMVSKFRNAGQTCVCANRILVQDGVY-DQFAEKLAR 313

Query: 302 VSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGAALLTP 361
             + L+V   D +    +G +I+++A E +    E  +  GA           GA   TP
Sbjct: 314 AVSALKVAPGD-RTGSTIGPLINVAAVEKVQAHVEDALSHGATLFAQAANDATGARFATP 372

Query: 362 GILDVSAVAER-PDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRERFEQFL 420
            IL  +    R   EE FGP+  + R++     I  ANAT YGLAA   +++  R  +  
Sbjct: 373 VILTGATRDMRLAQEETFGPVAPLFRFTHEEEGIELANATSYGLAAYFYTENLHRAFRVA 432

Query: 421 VESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAY 457
               AG+V  N     A   APFGG+  SG  R  A+
Sbjct: 433 ERLEAGMVALNSGAI-AMEVAPFGGVKMSGLGREGAH 468


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: 552
Number of extensions: 29
Number of successful extensions: 7
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: 487
Length adjustment: 34
Effective length of query: 453
Effective length of database: 453
Effective search space:   205209
Effective search space used:   205209
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 24 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