Alignments for a candidate for aldA in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Shewanella loihica PV-4

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P25553
         (479 letters)



>FitnessBrowser__PV4:5208455
          Length = 498

 Score =  251 bits (641), Expect = 4e-71
 Identities = 153/483 (31%), Positives = 260/483 (53%), Gaps = 9/483 (1%)

Query: 2   SVPVQHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERA--QPE 59
           S+ +Q   +I+G++     +   D ++P    V++++      DA +A+  A     + +
Sbjct: 16  SLVIQGQAFINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANAREVFERGD 75

Query: 60  WEALPAIERASWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEW 118
           W  LP ++R   + + +  +     E++ L   + GK I+    V+VA  A  + +  E 
Sbjct: 76  WSQLPPVKRKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARALRWSGEA 135

Query: 119 ARRYEGEIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPS 178
             +   EI  +    E  ++ +  +GV   I+PWNFP  +   K+ PAL TGN++V+KPS
Sbjct: 136 VDKIYDEIAPTAH-NEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSVVLKPS 194

Query: 179 EFTPNNAIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIM 238
           E +P  AI  A++  E G+P+GV N++ G G TVG+ LA +  V  +  TGS    +++M
Sbjct: 195 EKSPLTAIRMAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLM 254

Query: 239 ATAAK-NITKVCLELGGKAPAIVMDDA-DLELAVKAIVDSRVINSGQVCNCAERVYVQKG 296
             A + N+ +V LE GGK+P IV +DA +L+ A  A   +   N G+VC    R+ V+ G
Sbjct: 255 IYAGESNMKRVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRLLVESG 314

Query: 297 IYDQFVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGK 356
           + ++ +N +   MQA Q G+P +      G +++   LE V + +   V EGA++  GG+
Sbjct: 315 VKEELINLIEAEMQAWQPGHPLD-PATTCGAVVDQQQLENVLRYIRAGVAEGAQLRQGGQ 373

Query: 357 AV--EGKGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSS 414
            V  E  G Y  PT+  +V+ EM+I  EE FGPVL V+ FD +E+AI + ND+ YGL + 
Sbjct: 374 QVLAETGGVYVAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYGLAAG 433

Query: 415 IYTQNLNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQV 474
           ++T +++ A K  K L+ G  +IN  +   M     G+++SG G     H   +Y + + 
Sbjct: 434 VWTSDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFDKYTEIKA 493

Query: 475 VYL 477
            ++
Sbjct: 494 TWI 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: 538
Number of extensions: 25
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources