GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pseudomonas putida KT2440

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate PP_1481 PP_1481 medium chain aldehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__Putida:PP_1481
          Length = 474

 Score =  302 bits (774), Expect = 1e-86
 Identities = 172/467 (36%), Positives = 262/467 (56%), Gaps = 5/467 (1%)

Query: 5   VQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALP 64
           +Q  M I+GQ V  +G AW  V+NPA    +++I +        A+ AA++A   W    
Sbjct: 1   MQTQMLINGQLVAGQGPAWT-VLNPALGTALAQINEATEAQVDSAVRAADQAFDSWSQTS 59

Query: 65  AIERASWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYE 123
             ER+  L  ++  I     E++ L  +  GK +      E+   AD   + A  AR   
Sbjct: 60  PKERSQALLALADAIEAHGDELARLESQNCGKPLSAALNDEIPAIADVFRFFAGAARCLG 119

Query: 124 GEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPN 183
           G       PG   ++ +  LGV   I PWN+P  ++A K+APAL  GNT+VIKPSE TP 
Sbjct: 120 GSAAGEYLPGHTSMIRRDPLGVVASIAPWNYPLMMLAWKIAPALAAGNTVVIKPSELTPL 179

Query: 184 NAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK 243
            A+   ++  ++ LP GV N++ GRG+TVG  L  +PKV MVS+TGS+  G  I++  A 
Sbjct: 180 TALRLGELAQDL-LPPGVLNILFGRGQTVGNPLITHPKVRMVSLTGSIPTGAHIISATAD 238

Query: 244 NITKVCLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVN 303
           ++ ++ +ELGGKAP +V DDAD++ A+  I      N+GQ C  A R+YVQ GIY++FV 
Sbjct: 239 SVKRMHMELGGKAPVLVFDDADIDAAIDGIRTFGFYNAGQDCTAACRLYVQDGIYERFVE 298

Query: 304 RLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAV-EEGARVAFGGKAVEGKG 362
           RLG+A+ +++ G   E  +  +GPLI+A   ++V   V RA+ +   R+  GGK + G G
Sbjct: 299 RLGKAVASLKPG-LQESEETELGPLISAQHRDKVAGLVQRAIAQPHIRLVTGGKPIAGDG 357

Query: 363 YYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNV 422
           +++ PT+L D  Q+  I+  E FGPV+ V  F     A+  ANDS+YGL SS++T++   
Sbjct: 358 FFFEPTVLADALQDDEIVRNEVFGPVVSVTRFTDEAQALEWANDSNYGLASSVWTRDTGR 417

Query: 423 AMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEY 469
           A +    L++G T++N       +  H G + SG G     +GL +Y
Sbjct: 418 AHRLAARLQYGCTWVNTHFMLVSEMPHGGQKHSGYGKDMSMYGLEDY 464


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: 528
Number of extensions: 24
Number of successful extensions: 5
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: 474
Length adjustment: 33
Effective length of query: 446
Effective length of database: 441
Effective search space:   196686
Effective search space used:   196686
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