GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Marino:GFF4005
          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:

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