GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Rhizobium etli CFN 42

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_011425015.1 RHE_RS08800 aldehyde dehydrogenase family protein

Query= SwissProt::Q9DBF1
         (539 letters)



>NCBI__GCF_000092045.1:WP_011425015.1
          Length = 506

 Score =  214 bits (544), Expect = 8e-60
 Identities = 147/487 (30%), Positives = 233/487 (47%), Gaps = 24/487 (4%)

Query: 50  DNEGVYNGSW-GGRGEVITTYCPANNEPIARVRQASLKDYEETIGKAKKAWNI--WADIP 106
           D + + +G W  G    I    P++   ++R    S  D E  I  A+KA++   W  + 
Sbjct: 17  DFKMLIDGKWEAGASHPIERIAPSHGVTVSRFPAGSATDAERAIAAARKAFDEGPWPRMT 76

Query: 107 APKRGEIVRKIGDAFREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGG 166
           A +R  I+ K  D    + + L  L ++E GK + +  GE+   VD+  YAA L+R + G
Sbjct: 77  ASERSAILLKAADLIAARAEELAFLDAIEAGKPITQVRGEIAGSVDIWRYAAALARDLHG 136

Query: 167 PTLPSERPGHALIEMWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLV 226
            +  +   G   + +   +G+V IIT +NFP  + G     AL  G   + K +  TS  
Sbjct: 137 ESYNTLGDGTVGVVLREAIGVVSIITPWNFPFLIVGQKLPFALAAGCTTVVKPSELTS-- 194

Query: 227 SVAVTKIIAQVLEDNLLPGAICSLVCG-GADIGTTMARDERVNLLSFTGSTQVGKEVALM 285
               T ++ ++L+   +P  + ++V G G ++G  M     V+++SFTGST VGK     
Sbjct: 195 --GSTLVLGEILQQAGVPDGVVNIVTGTGPEVGAVMTSHPDVDMISFTGSTGVGKLTMKN 252

Query: 286 VQERFGKSLLELGGNNAIIAFEDADLSLVVPSVLFAAVGTAGQRCTTVRRLFLHESIHNE 345
             +   K  LELGG N  I F DADL   + + +F A   AG+ C    RL LH+SI ++
Sbjct: 253 AAQTLKKVSLELGGKNPQIVFPDADLDAFIDAAVFGAYFNAGECCNAGSRLILHKSIASD 312

Query: 346 VVDRLRSAYSQIRVGNPWDPNILYGPLHTKQAVSMFVRAVEEAKKQGGTVVYGGKVMD-H 404
           VV R+      ++VG+P DP    G + T Q +      V  A+  G  V +GG+ +D  
Sbjct: 313 VVRRVAELSKGVKVGDPLDPQTQVGAIITPQHLEKISGYVAGARSNGARVTHGGETLDLG 372

Query: 405 PGNYVEPTIVTGLAHDAPIVHQETFAPILYVFKFQDEEEVFEWNNEVKQGLSSSIFTKD- 463
            G ++ PTI+  +  D  +  +E F P+L V  F+   E     N +  GLS+ ++++D 
Sbjct: 373 MGQFMSPTILEAVTPDMAVAREEVFGPVLSVLTFETTAEAVRIANSIDYGLSAGVWSRDF 432

Query: 464 -----LGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMR 518
                +GR  R         G + +N    GA     FGG K +G GRE G  A + Y  
Sbjct: 433 DTCLTIGRSVR--------AGTIWMNTFMDGAS-ELPFGGYKQSGLGRELGRHAVEDYTE 483

Query: 519 RSTCTIN 525
             T  ++
Sbjct: 484 TKTLNMH 490


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: 640
Number of extensions: 35
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: 506
Length adjustment: 35
Effective length of query: 504
Effective length of database: 471
Effective search space:   237384
Effective search space used:   237384
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.

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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