GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Erythrobacter marinus HWDM-33

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_047092826.1 AAV99_RS05570 NAD-dependent succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>NCBI__GCF_001013305.1:WP_047092826.1
          Length = 476

 Score =  244 bits (623), Expect = 5e-69
 Identities = 145/473 (30%), Positives = 244/473 (51%), Gaps = 3/473 (0%)

Query: 4   PVQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEAL 63
           P  H + IDG+  +  G    DV+NPATE V+  +P     D  +A++AA+R   EW   
Sbjct: 5   PTLH-LLIDGEQHSGDGRKTEDVINPATEEVLGTLPHATPADLDRALEAAQRGFHEWRRT 63

Query: 64  PAIERASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYE 123
            A +RAS L K +  IRERA EI   +  E GK       E +++A+ +++ A+  +R  
Sbjct: 64  SADKRASILTKAAGLIRERAKEIGETLCLEQGKPVAEGRGEASYSANLLEFYAQECKRIY 123

Query: 124 GEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPN 183
           G  +     G    +    +G   G  PWNFP   + RK+  AL  G ++++KPSE TP 
Sbjct: 124 GRTLVRGE-GARAEVQYHPVGPIAGFAPWNFPAINVMRKIGGALAAGCSVIVKPSEETPA 182

Query: 184 NAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK 243
           + IA  + + + G+P GV   V G    V ++L G+P +  ++ TGS   G+++   AA 
Sbjct: 183 SGIAVVQALLDSGVPGGVVQCVFGVPSDVSEQLIGSPIIRKITFTGSTPVGKQLAKMAAD 242

Query: 244 NITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVN 303
           ++    +ELGG  P +V +D+DL   +  +V ++  N+GQVC    R  +++ I+D+F +
Sbjct: 243 DLKIATMELGGHGPVLVFNDSDLTKVLDTMVANKFRNAGQVCVSPTRFLIEEDIFDKFRD 302

Query: 304 RLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGY 363
              E  +A+  GN  ++    MGP+ NA  L+ + + +A A ++GA +  GG+ +  +G+
Sbjct: 303 GFVERAKALTVGNGMDKG-TDMGPMANARGLDNIAKLIANAQDKGANLLTGGERIGNQGF 361

Query: 364 YYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVA 423
           ++ PT+L +V  +  IM+ E FGPV  + A       I  AN   YGL +  +T +    
Sbjct: 362 FFQPTVLSEVPLDSDIMNNEPFGPVAILNAMPGEAAMIEEANRLPYGLAAYAWTNDPARR 421

Query: 424 MKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVY 476
            +    ++ G   IN      +     G + SG G  DG+ G+   +  + ++
Sbjct: 422 RRLAAEVEAGMLAINTGGVSTVDAPFGGVKWSGYGSEDGREGVMACMVVKAIH 474


Lambda     K      H
   0.318    0.135    0.392 

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: 568
Number of extensions: 24
Number of successful extensions: 3
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: 479
Length of database: 476
Length adjustment: 34
Effective length of query: 445
Effective length of database: 442
Effective search space:   196690
Effective search space used:   196690
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 24 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