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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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