GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astD in Streptomyces kebangsaanensis SUK12

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase

Query= SwissProt::O50174
         (487 letters)



>NCBI__GCF_001906585.1:WP_073950325.1
          Length = 511

 Score =  203 bits (517), Expect = 1e-56
 Identities = 158/465 (33%), Positives = 227/465 (48%), Gaps = 17/465 (3%)

Query: 5   YIAGQWLAG-QGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLEQRI 63
           YIAG+   G  G T   +DP     V +   A    VDAAV AAREAFP WA      R 
Sbjct: 24  YIAGRLTKGTSGRTHAVVDPATGEEVHTYELAGPDDVDAAVAAAREAFPGWAGATPGDRS 83

Query: 64  ELLERFAATLKSRADELARVIGEETGKPLWESAT-EVTSMVNKVAISVQAFRERTGEKSG 122
           + L RFA  L  RA++ AR    + GKPL  +   +V   ++  A    A R   G+ +G
Sbjct: 84  DALHRFAEVLADRAEDFARAESLQCGKPLKLTREFDVPGTIDNAAFFAGAARHLQGQSAG 143

Query: 123 PLA-DATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAELT 181
             + D T+ +R +P GVV    P+N+P  +    ++PA+ AGN +V KP+ELTP  + L 
Sbjct: 144 EYSGDHTSYVRREPIGVVGSIAPWNYPLQMAAWKVLPAIAAGNTIVLKPAELTPLTSLLF 203

Query: 182 LKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQKI 240
            +A  +AG+P GV+N+V G G+E G  L  H  +  + FTGS+  G  + ++      K 
Sbjct: 204 AQAATEAGIPDGVINIVTGTGKEAGEHLVGHPDVAMVSFTGSTAVGKRV-AEIATASVKR 262

Query: 241 LALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARLV 300
           L LE+GG  P VV + ADL+AAV   +  A I+ GQ CT A R  V +  + +  +AR  
Sbjct: 263 LHLELGGKAPFVVFDDADLEAAVNGAVAGALINTGQDCTAATRAYVQRPLY-EEFVARTA 321

Query: 301 AVSATLRVGRFDEQPAPFMGAVIS------LSAAEHLLKAQEHLIGKGAQPLLAMTQPID 354
           A+  T+R+G     P   +G +IS      ++      +A   ++  G  P     +  +
Sbjct: 322 ALMETVRLGD-PFAPGTDLGPLISHVHRDRVAGFVDRARAYARVVTGGEAP---QGELKN 377

Query: 355 GAALLTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDSRE 414
           GA      I   +  +E    E FGP+L V+ +      IR AN T YGLAA   S    
Sbjct: 378 GAYYRPTLIAGAAQDSEIVQSEIFGPVLVVLPFDSDDEGIRLANDTAYGLAASAWSRDVY 437

Query: 415 RFEQFLVESRAGIVNWNKQLTGAASSAPFGGIGASGNHRPSAYYA 459
           R  +   E +AG V W        S  P GG   SG  +  + Y+
Sbjct: 438 RANRATREIKAGCV-WVNDHIPIISEMPHGGSKQSGFGKDMSSYS 481


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: 655
Number of extensions: 37
Number of successful extensions: 6
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: 511
Length adjustment: 34
Effective length of query: 453
Effective length of database: 477
Effective search space:   216081
Effective search space used:   216081
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