GapMind for catabolism of small carbon sources

 

Aligments for a candidate for astD in Marinobacter adhaerens HP15

Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate GFF4005 HP15_3945 aldehyde dehydrogenase family protein

Query= SwissProt::O50174
         (487 letters)



>lcl|FitnessBrowser__Marino:GFF4005 HP15_3945 aldehyde dehydrogenase
           family protein
          Length = 471

 Score =  190 bits (483), Expect = 8e-53
 Identities = 145/460 (31%), Positives = 229/460 (49%), Gaps = 23/460 (5%)

Query: 1   MSTHYIAGQWLAGQGETLESLDPVGQGVVWSGRGADATQVDAAVCAAREAFPAWARRPLE 60
           ++ +YI GQW++  G+ ++  +     V+     A A +++ A+ AA  AF +W+   LE
Sbjct: 4   LNRNYINGQWVSWAGDMIDVHEAGTGDVIARVPAAGADEMEQAIAAADAAFESWSESTLE 63

Query: 61  QRIELLERFAATLKSRADELARVIGEETGKPLWESATEVTSMVNKVAISVQAFRERTGEK 120
           +RI++LE+  A LK RA E+A  +  E G P+ + AT +       A   +++ +   + 
Sbjct: 64  ERIKVLEQLHAGLKERAPEIAETVCREVGMPI-KLATPI--QAGMPAAVTKSYLKLLPDF 120

Query: 121 SGPLADATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNCVVFKPSELTPKVAEL 180
                   + +++ P GVV    P+N+P H     IVPA+ AG  VV KPSE+ P+ A +
Sbjct: 121 PFTEQSGNSEVQYAPVGVVGCITPWNYPLHQVILKIVPAIAAGCTVVLKPSEIAPQTAFI 180

Query: 181 TLKAWIQAGLPAGVLNLVQG-GRETGVALAAHRGLDGLFFTGSSRTGNLLHSQFGGQPQK 239
             +      LP GV N+V G G   G  L  H  +  + FTGS+RTGNL+ +       K
Sbjct: 181 LAEILDGTDLPKGVFNMVCGYGHTVGDTLIKHPDVRMVSFTGSTRTGNLI-AHAAADDFK 239

Query: 240 ILALEMGGNNPLVVEEVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDALLARL 299
             ALEMGG +  V+   ADL AAV   I +  +++GQ CT   R+LVP     +A     
Sbjct: 240 RFALEMGGKSASVILPDADLAAAVKGTINNCLLNSGQTCTALTRMLVPADKHDEACELAA 299

Query: 300 VAVSATLRVGRFDEQPAPFMGAVISLSAAEHLLKAQEHLIGKGAQPLLAMTQPIDGA--- 356
            AV+        +E     +G + S    + ++   +  + +GA+ +    +  +G    
Sbjct: 300 AAVAKMTPGNPLEETTR--LGPLSSAQQRDKVIDYIKLGVQEGAKLIAGGPEAPEGCEKG 357

Query: 357 ----ALLTPGILDVSAVAERPDEEFFGPLLQVIRYSDFAAAIREANATQYGLAAGLLSDS 412
               A +   +   S +A+   EE FGP+L VI Y+D A A++ AN TQYGL+  + S  
Sbjct: 358 YFVKATVFGNVKPDSRIAQ---EEIFGPVLCVIPYNDEAEAVKIANGTQYGLSGAVWSGD 414

Query: 413 RERFEQFLVESRAGIVNWNKQLTGAASS--APFGGIGASG 450
             + ++   + R G V  N    G A +  APFGG G SG
Sbjct: 415 DAKAKKIASKLRTGQVFVN----GGAFNPMAPFGGFGHSG 450


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: 565
Number of extensions: 25
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: 471
Length adjustment: 34
Effective length of query: 453
Effective length of database: 437
Effective search space:   197961
Effective search space used:   197961
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: 51 (24.3 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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