GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Halomonas desiderata SP1

Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate WP_086509800.1 BZY95_RS10050 NAD-dependent succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9DBF1
         (539 letters)



>NCBI__GCF_002151265.1:WP_086509800.1
          Length = 485

 Score =  226 bits (576), Expect = 2e-63
 Identities = 147/466 (31%), Positives = 228/466 (48%), Gaps = 11/466 (2%)

Query: 56  NGSW--GGRGEVITTYCPANNEPIARVRQASLKDYEETIGKAKKAWNIWADIPAPKRGEI 113
           +GSW     GE I    PA  E    V +    + E  I  A  A   W  + A +R +I
Sbjct: 17  DGSWVAADSGEQIEVVNPATGETFGTVPRLGRAETERAIAAADAALVGWRALTAQERADI 76

Query: 114 VRKIGDAFREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSER 173
           + K  D   E    L  +++ E GK L E  GE+        + A  +R I G T+P+ +
Sbjct: 77  LMKWHDLMMEHQDDLAMIMTHEQGKPLKEAAGEIAYAASFLRWFAEEARRIYGETIPAAK 136

Query: 174 PGHALIEMWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSVAVTKI 233
           P   ++    P+G+VG IT +NFP A+       AL  G   + K A  T   + A    
Sbjct: 137 PNQRIVVTKQPVGVVGAITPWNFPAAMITRKAGAALAAGCTIVIKPASQTPFSATA---- 192

Query: 234 IAQVLEDNLLPGAICSLVCGGA-DIGTTMARDERVNLLSFTGSTQVGKEVALMVQERFGK 292
           +A + E   +P  + ++V G A +I + M     V  ++FTGST+VG+E+         K
Sbjct: 193 LALLAERAGIPRGVFNVVPGRASEIASAMTESPLVRKITFTGSTEVGRELMAQASRHIQK 252

Query: 293 SLLELGGNNAIIAFEDADLSLVVPSVLFAAVGTAGQRCTTVRRLFLHESIHNEVVDRLRS 352
             LELGGN   I FEDADL   V   + A    AGQ C    R  +  S+ N   ++L  
Sbjct: 253 ISLELGGNAPFIVFEDADLDAAVEGAMAAKFRNAGQTCICTNRFLVQSSVINAFCEKLAV 312

Query: 353 AY-SQIRVGNPWDPNILYGPLHTKQAVSMFVRAVEEAKKQGGTVVYGGKVMDHPGNYVEP 411
           A  S+++VG+  +P+I  GPL  ++AV+     V +A  +G  ++ GG      GN+  P
Sbjct: 313 AMNSELKVGDGTEPDINIGPLIDEKAVAKVSEHVHDAVDKGAELLLGGNPHPLGGNFFSP 372

Query: 412 TIVTGLAHDAPIVHQETFAPILYVFKFQDEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWL 471
           T+++    D  + H+ETF P+  VF F+DEE+  +  N+ + GL+S  +++DLGR+  W 
Sbjct: 373 TLISFANADMKVAHEETFGPLAAVFPFEDEEDAVQMANDTQYGLASYFYSRDLGRV--WR 430

Query: 472 GPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM 517
                + G+V +N     +     FGG K +G GRE G    ++++
Sbjct: 431 VADALEYGMVGINTGLI-SNTAAPFGGVKASGLGREGGHQGIEEFL 475


Lambda     K      H
   0.319    0.137    0.421 

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: 641
Number of extensions: 42
Number of successful extensions: 4
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: 539
Length of database: 485
Length adjustment: 35
Effective length of query: 504
Effective length of database: 450
Effective search space:   226800
Effective search space used:   226800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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.

Links

Downloads

Related tools

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