Alignments for a candidate for adh in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Escherichia coli BW25113

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 15646 b1525 putative aldehyde dehydrogenase (VIMSS)

Query= BRENDA::A6T8Z5
         (462 letters)



>FitnessBrowser__Keio:15646
          Length = 462

 Score =  722 bits (1864), Expect = 0.0
 Identities = 352/456 (77%), Positives = 394/456 (86%)

Query: 6   ATHAVSVNPTTGEVVSSLPWASEREVDAAITLAAAGYRQWRQTPLADRADALRRIGAALR 65
           ATHA+S+NP TGE +S LPWA   +++ A+ LAAAG+R WR+T +  RA+ LR IG ALR
Sbjct: 6   ATHAISINPATGEQLSVLPWAGADDIENALQLAAAGFRDWRETNIDYRAEKLRDIGKALR 65

Query: 66  ARGEEVAQMITLEMGKPIAQARGEVAKSANLCDWYAEHGPAMLATEATLVENNQAVIEYR 125
           AR EE+AQMIT EMGKPI QAR EVAKSANLCDWYAEHGPAML  E TLVEN QAVIEYR
Sbjct: 66  ARSEEMAQMITREMGKPINQARAEVAKSANLCDWYAEHGPAMLKAEPTLVENQQAVIEYR 125

Query: 126 PLGAILAVMPWNFPVWQVMRGAVPILLAGNSYLLKHAPNVMGSARLLGEIFAAAGLPDGV 185
           PLG ILA+MPWNFP+WQVMRGAVPI+LAGN YLLKHAPNVMG A+L+ ++F  AG+P GV
Sbjct: 126 PLGTILAIMPWNFPLWQVMRGAVPIILAGNGYLLKHAPNVMGCAQLIAQVFKDAGIPQGV 185

Query: 186 FGWVNATNDGVSQIINDDRIAAVTVTGSVRAGKAIGAQAGAALKKCVLELGGSDPFIVLN 245
           +GW+NA NDGVSQ+I D RIAAVTVTGSVRAG AIGAQAGAALKKCVLELGGSDPFIVLN
Sbjct: 186 YGWLNADNDGVSQMIKDSRIAAVTVTGSVRAGAAIGAQAGAALKKCVLELGGSDPFIVLN 245

Query: 246 DADLDEAVKAAVTGRYQNSGQVCAASKRFILEAGIAEAFTRKFVDAVAALKMGDPRDEQN 305
           DADL+ AVKAAV GRYQN+GQVCAA+KRFI+E GIA AFT +FV A AALKMGDPRDE+N
Sbjct: 246 DADLELAVKAAVAGRYQNTGQVCAAAKRFIIEEGIASAFTERFVAAAAALKMGDPRDEEN 305

Query: 306 YVGPMARFDLRDELHQQVTATLDEGATLLLGAEKIEGAGNYYAPTVLGNVTAGMTGFRQE 365
            +GPMARFDLRDELH QV  TL +GA LLLG EK+ GAGNYY PTVL NVT  MT FR+E
Sbjct: 306 ALGPMARFDLRDELHHQVEKTLAQGARLLLGGEKMAGAGNYYPPTVLANVTPEMTAFREE 365

Query: 366 LFGPVATLTTARDADHALALANDSEFGLSATVYTTDEAQAQRFARELECGGVFLNGYCAS 425
           +FGPVA +T A+DA+HAL LANDSEFGLSAT++TTDE QA++ A  LECGGVF+NGYCAS
Sbjct: 366 MFGPVAAITIAKDAEHALELANDSEFGLSATIFTTDETQARQMAARLECGGVFINGYCAS 425

Query: 426 DARVAFGGVKKSGFGRELSHFGLHEFCNAQTVWKDR 461
           DARVAFGGVKKSGFGRELSHFGLHEFCN QTVWKDR
Sbjct: 426 DARVAFGGVKKSGFGRELSHFGLHEFCNIQTVWKDR 461


Lambda     K      H
   0.319    0.133    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: 642
Number of extensions: 10
Number of successful extensions: 1
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: 462
Length of database: 462
Length adjustment: 33
Effective length of query: 429
Effective length of database: 429
Effective search space:   184041
Effective search space used:   184041
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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, or view the source code.

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