GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Shewanella oneidensis MR-1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 200453 SO1275 succinate-semialdehyde dehydrogenase (NCBI ptt file)

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__MR1:200453
          Length = 482

 Score =  530 bits (1365), Expect = e-155
 Identities = 261/476 (54%), Positives = 346/476 (72%), Gaps = 6/476 (1%)

Query: 46  LLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           LLR   ++ G+W    +  T  + +PA+GA +  V   G  E +AA+ AA  A  +W+ +
Sbjct: 8   LLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPAWRAL 67

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           + KER + LR+W++L+ +N D+LA ++T+E GKPL EA+GE+ Y+A F+EWF+EEA+R+Y
Sbjct: 68  TAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEEAKRIY 127

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           GD I     DKR +V+KQPVGV + ITPWNFP+AMITRK   ALAAGCT+VVKPA  TP+
Sbjct: 128 GDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPF 187

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           +ALALA LA +AGIP GV++VI      A  +G  +CT+P+V K+SFTGST  G  L+  
Sbjct: 188 TALALAVLAERAGIPAGVFSVI---TGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLMAQ 244

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
            A ++K++S+ELGG APFIVFD AN+D AV GAM +K+RNAGQTCVC+NR  VQ G++D 
Sbjct: 245 CAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDE 304

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  K + A+ K L+VG G   G T GPLIN  AVEKV+ H+ DA+ KGATV+ GGK H+ 
Sbjct: 305 FAEKLSMAVAK-LKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHEL 363

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
           GGNFFEPT+L+N  + M    EETFGP+AP+ KF+  ++ +  AN  + GLA YFY +D 
Sbjct: 364 GGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRDI 423

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVC 519
           + +W+VAE LE GMVGVN GLIS+   PFGG+K SGLGREGSKYGI+EYLE+KY+C
Sbjct: 424 SLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYIC 479


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: 646
Number of extensions: 30
Number of successful extensions: 3
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: 482
Length adjustment: 34
Effective length of query: 489
Effective length of database: 448
Effective search space:   219072
Effective search space used:   219072
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