GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Dechlorosoma suillum PS

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__PS:Dsui_0105
          Length = 476

 Score =  219 bits (558), Expect = 2e-61
 Identities = 153/456 (33%), Positives = 225/456 (49%), Gaps = 17/456 (3%)

Query: 10  YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRA 69
           YI G+WV    + + DV NPAT+ V+ +VP  T  D D AA+ AA AF  W+ ++   R 
Sbjct: 8   YIGGQWVAPDGNAFIDVENPATETVIARVPEGTATDADRAARAAAAAFPAWAALSGAERG 67

Query: 70  RILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS 129
             L      L   ++EL  LI  E G   K A   V  G     FAA A     G +   
Sbjct: 68  AFLQKIADGLKARQDELGRLIASEVGMPVKLAT-RVQAGNPIFTFAACARIAAEGFAEER 126

Query: 130 IATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLV 189
           I    ++   + P G V  I P+NFP+         A+A G T +LKPSE  PL    L 
Sbjct: 127 IG---QSLVLKVPTGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAFLLA 183

Query: 190 ELFEKAGLPKGVFNVVYGAHDVVNGILE-HPEIKAISFVGSKPVGEYVYKKGSENLKRVQ 248
           E+ E AGLP GVFN+V G   VV   L  HP + A+SF GS   G+ V    +  +KRV 
Sbjct: 184 EVIEAAGLPAGVFNLVTGYGPVVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVKRVS 243

Query: 249 SLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKV 308
              G K+ ++VL DA+L   V   V   F ++G+ C A   + V +    E  A   +  
Sbjct: 244 LELGGKSASVVLPDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAVQAA 303

Query: 309 ADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVS--DDGYFVGP 366
           A   +G+ L +G  LGP++    ++R  + IE+ + +GA L+C G         GY+V P
Sbjct: 304 AAYTLGDPLAEGSRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSAAPEGLPTGYYVRP 363

Query: 367 TIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFR 426
           T+F  V  +  + ++E+F PVL+++  ++  EA  IAN +++   A ++++       F 
Sbjct: 364 TVFGRVRPDAALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARALAFA 423

Query: 427 ENIDAGMLGINLGVPAPMAFF----PFSGWKSSFFG 458
             + AG + IN       AFF    PF G+K S +G
Sbjct: 424 RRLRAGQVDIN------GAFFNLLAPFGGFKQSGYG 453


Lambda     K      H
   0.318    0.136    0.396 

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: 518
Number of extensions: 28
Number of successful extensions: 4
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: 487
Length of database: 476
Length adjustment: 34
Effective length of query: 453
Effective length of database: 442
Effective search space:   200226
Effective search space used:   200226
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