GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Shewanella amazonensis SB2B

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__SB2B:6938545
          Length = 498

 Score =  239 bits (609), Expect = 2e-67
 Identities = 151/476 (31%), Positives = 251/476 (52%), Gaps = 11/476 (2%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPE---WEALPAI 66
           +I+G +    G    D ++P    +++++   Q  DA  A+ A  RA  E   W     +
Sbjct: 24  FINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAV-ANARAVFESGVWSLQSPV 82

Query: 67  ERASWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYEGE 125
           +R   + + +  +   A E++ L   + GK I     V+VA  A  I +  E   +   E
Sbjct: 83  KRKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDVAGAARAIRWSGEAIDKIYDE 142

Query: 126 IIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNA 185
           +  +    E  ++ +  +GV   I+PWNFP  +   K+ PAL TGN++V+KPSE +P  A
Sbjct: 143 LAPTPH-NEIGMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNSVVLKPSEKSPLTA 201

Query: 186 IAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAK-N 244
           I  A++  E GLP GV N++ G G TVGQ LA +  V  +  TGS    +++M  A + N
Sbjct: 202 IRMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTKIAKQLMVYAGQSN 261

Query: 245 ITKVCLELGGKAPAIVMDDA-DLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVN 303
           + +V LE GGK+P IV +DA DL+ A +A   +   N G+VC    R+ V+ G+ D+ + 
Sbjct: 262 MKRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSRLLVESGVKDELIK 321

Query: 304 RLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAV--EGK 361
            + + M+A Q G+P +      G +++   L+ V   +    +EGA++  GG  V  E  
Sbjct: 322 LIVKEMEAWQPGHPLD-PATTCGAVVDKQQLDTVLGYIKAGHDEGAKLMCGGSQVLAETG 380

Query: 362 GYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLN 421
           G Y  PT+   V  +M I  EE FGPV+ V+ FD +++A+++AND+ YGL + ++T +++
Sbjct: 381 GVYVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTIYGLAAGVWTSDIS 440

Query: 422 VAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477
            A K  K L+ G  +IN  +   M     G+++SG G     H   +Y + +  ++
Sbjct: 441 KAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFEKYTEVKATWI 496


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: 532
Number of extensions: 28
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: 498
Length adjustment: 34
Effective length of query: 445
Effective length of database: 464
Effective search space:   206480
Effective search space used:   206480
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