GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Echinicola vietnamensis KMM 6221, DSM 17526

Align Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 (uncharacterized)
to candidate Echvi_0535 Echvi_0535 NAD-dependent aldehyde dehydrogenases

Query= curated2:O32507
         (477 letters)



>FitnessBrowser__Cola:Echvi_0535
          Length = 514

 Score =  162 bits (409), Expect = 3e-44
 Identities = 123/449 (27%), Positives = 219/449 (48%), Gaps = 15/449 (3%)

Query: 16  ATVNPYTGETVKTFPFLESAEIPALIERADQAYREWGQRPVTERAAIMRRAAELMLERTD 75
           ++ +P  G+ +             ++++A++A++ W + P  +R  ++R+    +  +  
Sbjct: 38  SSYSPVDGKELGKVQMTTRESYEKVLDQAEKAFKAWRKVPAPQRGEVVRQIGIELRNKKS 97

Query: 76  ELASLITLEMGKLLREAKGEVALAASILNY-YGEQGPSFLEPKTIPVPQGEAAVLHAPLG 134
            L  L++ EMGK  +E  GEV     I ++  G     +        P         PLG
Sbjct: 98  LLGKLVSYEMGKSYQEGLGEVQEMIDICDFAVGLSRQLYGLTMHSERPSHRMYEQWHPLG 157

Query: 135 VLLGIEPWNYPLYQVVRFAAPNLVVGNTVLLKHSELCPQSALALE----QLFHDAGVPQG 190
           ++  I  +N+P+           V G+  + K SE  P +++A +     +F+  G P+G
Sbjct: 158 IVGVISAFNFPVAVWSWNTMIAWVCGDVCVWKPSEKTPLTSVACQLIAADVFNRNGFPEG 217

Query: 191 AYTNLFLRIADIEQVIAH-PAVQGVSLTGSERAGASVAELAGRHLKKCVLELGGSDPFIV 249
             T+L +  A++   +   P V  +S TGS + G SV E  G  L K +LELGG++  I+
Sbjct: 218 I-TSLLIGGANVGAFLTQDPRVALISATGSTQMGKSVGETVGGRLGKVLLELGGNNAIII 276

Query: 250 LDAEDLDTTVKAAATGRLSNTGQACIAAKRLMVVDDLYDEFVSRLGQTFSAFVPGDPADP 309
            +  DLD  ++ A  G +   GQ C + +RL++ + +++E   R+   +S    G+P D 
Sbjct: 277 TEHADLDIAIRGALFGAVGTAGQRCTSTRRLIIHESVFEEVKERMVAAYSKLTIGNPLDE 336

Query: 310 STRLGPLSSEQAARD-LQAQVQDAIDKGATVVAGG--QRPEH-PGAFVQPTVLTDVTPDM 365
              +GPL  + A ++ L A  +   + G  VVAGG  +  E+  G +V+P+V  +     
Sbjct: 337 DNIVGPLIDKDAVQNYLTAIERVKAEGGKEVVAGGLLEGEEYVSGCYVRPSVF-EAENHF 395

Query: 366 RAYHEELFGPVAVVYRVRDEDEAVALANASTYGLGGAVFSSDLDRAQRV--AERLDTGMV 423
           +   +E FGP+  + +  + DEA+A+ N    GL  A+ ++++  A+R   +E  D G+ 
Sbjct: 396 QIVQKETFGPILYLMKYSEFDEAIAMQNNVPQGLSSAIMTTNMREAERYLSSEGSDCGIS 455

Query: 424 WINHPTSSA-ADLPFGGVKRSGFGRELSS 451
            +N  TS A     FGG K +G GRE  S
Sbjct: 456 NVNIGTSGAEIGGAFGGEKETGGGRESGS 484


Lambda     K      H
   0.317    0.133    0.384 

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: 566
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: 477
Length of database: 514
Length adjustment: 34
Effective length of query: 443
Effective length of database: 480
Effective search space:   212640
Effective search space used:   212640
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 17 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