GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Sinorhizobium fredii NGR234

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_012709782.1 NGR_RS27645 aldehyde dehydrogenase family protein

Query= SwissProt::O50174
         (487 letters)



>NCBI__GCF_000018545.1:WP_012709782.1
          Length = 502

 Score =  201 bits (510), Expect = 6e-56
 Identities = 163/469 (34%), Positives = 236/469 (50%), Gaps = 23/469 (4%)

Query: 6   IAGQWLAG-QGETLESLDPVGQGVVWSGRGADATQVDA--AVCAAREAFP--AWARRPLE 60
           I GQW+AG +G T+E + P G GVV S R   AT VDA  A+ AAR AF    W R    
Sbjct: 22  IDGQWMAGAEGRTIERVAP-GHGVVVS-RYQAATMVDAERAIAAARRAFDDGPWPRMTAS 79

Query: 61  QRIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEK 120
           +R  +L R A  + +RADELA +   E+GKP+ ++  E+    +    +    RE +GE 
Sbjct: 80  ERSLILLRAADMIAARADELAYLDAIESGKPISQAKGELAGAADIWRYAAALARELSGES 139

Query: 121 SGPLADAT-AVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAE 179
              L + T  V+  +  GVV++  P+NFP  + +  +  AL AG   V KPSELT     
Sbjct: 140 YNTLGEGTLGVVLREAIGVVSIITPWNFPFLIVSQKLPFALAAGCTTVVKPSELTSASTL 199

Query: 180 LTLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQ 238
           +  +    AG+PAGV+N++ G G E G  LA H  +D + FTGS+  G L  +    Q  
Sbjct: 200 VLGEILEAAGVPAGVVNIIVGTGPEVGAPLATHPDVDMISFTGSTGIGRLTMAN-AAQTL 258

Query: 239 KILALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLAR 298
           K ++LE+GG NP +V   ADLDA +   +  A+ +AG+ C    RL++ +    + + AR
Sbjct: 259 KKVSLELGGKNPQIVYPDADLDAFIDAAVFGAYFNAGECCNAGSRLILHRDI-AEEVTAR 317

Query: 299 LVAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQ-PIDGAA 357
           + ++SA ++VG     P   +GA+I+    E +        G+GA      T   +    
Sbjct: 318 ITSLSAKVKVGD-PLDPETQVGAIITPQHLEKIAGYVTAAAGEGAAVSHGGTALDLGMGQ 376

Query: 358 LLTPGILDVSAVAERPD-----EEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDS 412
            + P IL     A RP+     EE FGP+L V+ +     AIR AN+  YGL+AG+ S  
Sbjct: 377 FMAPTILS----AVRPEMAVAREEVFGPVLSVLTFETTEEAIRIANSIDYGLSAGVWSRD 432

Query: 413 RERFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYAAD 461
            +         RAG V W       A   PFGG   SG  R    +A +
Sbjct: 433 FDTCLTIGRRVRAGTV-WMNTFMDGACELPFGGYRQSGLGRELGRHAVE 480


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: 585
Number of extensions: 39
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: 502
Length adjustment: 34
Effective length of query: 453
Effective length of database: 468
Effective search space:   212004
Effective search space used:   212004
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 Apr 09 2024. 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