GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Dechlorosoma suillum PS

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Dsui_0437 Dsui_0437 succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__PS:Dsui_0437
          Length = 483

 Score =  551 bits (1419), Expect = e-161
 Identities = 276/481 (57%), Positives = 361/481 (75%), Gaps = 7/481 (1%)

Query: 44  ADLLRGDSFVGGRWLPTPATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           ++LLR   ++ G+W+   + FPV++PASGA+L  V   G  E RAA+ AA  A+ +W+  
Sbjct: 6   SNLLRQQCYLNGQWVGGESDFPVHNPASGAELARVPRFGAAETRAAIAAADAAWPAWRSR 65

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           + KER+ +LR+W++LM Q+ D+LA ++T+E GKPL EA+GE+ Y+A F+EWF+EEA+R Y
Sbjct: 66  TAKERTGVLRRWFELMNQHADDLALLMTSEQGKPLAEARGEVAYAASFVEWFAEEAKRAY 125

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           G+ I   A DKR LV+KQP+GV + ITPWNFP+AMITRKV  ALAAGCTVVVKPAE TP 
Sbjct: 126 GETIPAVAADKRMLVIKQPIGVCAAITPWNFPAAMITRKVAPALAAGCTVVVKPAEQTPL 185

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           +ALALA+LA++AG P GV+NVI         +G  L ++P V K+SFTGST  G++L+  
Sbjct: 186 TALALAELAHRAGFPAGVFNVITGDPV---AIGGELTSNPTVRKLSFTGSTEVGRLLMGQ 242

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
            A S+K++S+ELGG APFIVFD A++D AV GAM SK+RN GQTCVC+NR LVQ GI+++
Sbjct: 243 CAPSIKKLSLELGGNAPFIVFDDADLDAAVEGAMISKYRNTGQTCVCANRLLVQDGIYEA 302

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQ- 402
           F  + A A   +L+VG G E G TQGPLI+  A+ KVE H+ DAVA GA V+ GG+RH+ 
Sbjct: 303 FAARLA-AKVATLKVGEGTEAGVTQGPLIDADALAKVEAHIADAVAHGARVLAGGRRHER 361

Query: 403 --SGGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYS 460
              GG FF+PT+L++VT  M    EETFGPVAP+ +F  EEEA+A+ANA + GLA YFYS
Sbjct: 362 YREGGAFFQPTVLADVTPQMRVAREETFGPVAPLFRFQTEEEAIALANATEFGLASYFYS 421

Query: 461 QDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCY 520
           +D  +I+RV E LE GMVGVN GLIS+   PFGG+KQSGLGREGSKYG++EYLEVKY+C 
Sbjct: 422 RDIGRIFRVGEALEYGMVGVNTGLISNEVAPFGGIKQSGLGREGSKYGLEEYLEVKYLCL 481

Query: 521 G 521
           G
Sbjct: 482 G 482


Lambda     K      H
   0.318    0.135    0.400 

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: 636
Number of extensions: 20
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: 523
Length of database: 483
Length adjustment: 34
Effective length of query: 489
Effective length of database: 449
Effective search space:   219561
Effective search space used:   219561
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