GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Pseudomonas stutzeri RCH2

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF4164 Psest_4237 succinate-semialdehyde dehydrogenase

Query= BRENDA::P51650
         (523 letters)



>FitnessBrowser__psRCH2:GFF4164
          Length = 482

 Score =  539 bits (1389), Expect = e-158
 Identities = 265/478 (55%), Positives = 351/478 (73%), Gaps = 6/478 (1%)

Query: 46  LLRGDSFVGGRWLPTPA--TFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103
           L R  +++ G WL   +  T  V +PA+G  LGTV   G  E R A+ AA  A  +W+++
Sbjct: 8   LFRQQAYIDGAWLDADSGQTISVNNPATGETLGTVPKMGAAETRRAIDAAERALPAWRDL 67

Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163
           + KERS  LR+W++L+++N+D+L +++T E GKPL EA+GEI Y+A F+EWF+EEA+R+Y
Sbjct: 68  TAKERSQKLRRWFELLMENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAKRIY 127

Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223
           GD I    KDKR +V+KQP+GV + ITPWNFP+AMITRK G ALAAGCT+V+KPA  TP+
Sbjct: 128 GDTIPGHQKDKRIIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPF 187

Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283
           SALA+ +LA +AGIP GV +V+  S   A ++G  L  +P V KISFTGST  G  L+  
Sbjct: 188 SALAMVELAERAGIPKGVLSVVTGS---AGDIGNELTANPKVRKISFTGSTEVGAKLMEQ 244

Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343
            A  +K+VS+ELGG APFIVFD A++D+AV GA+ SK+RNAGQTCVC NR  VQ G++D+
Sbjct: 245 CAPGIKKVSLELGGNAPFIVFDDADLDEAVKGAVQSKYRNAGQTCVCVNRIYVQDGVYDT 304

Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403
           F  KF  A+ K LRVGNG EEGT  GPLI+++A  KV +H+ DAVA+GA +V GG+ H  
Sbjct: 305 FAEKFQAAVAK-LRVGNGLEEGTDLGPLIDDRAAAKVREHIEDAVAQGARLVAGGQAHAL 363

Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463
           GG++FEPT+L NV        EETFGP+AP+ +F  E +A+A AN  + GLA YFY++D 
Sbjct: 364 GGSYFEPTVLVNVPDSAKVAKEETFGPLAPLFRFKDEADAIAKANDTEFGLASYFYARDL 423

Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYG 521
            +++RVAE LE GMVG+N GLIS+   PFGGVK SGLGREGSKYGI++YLE+KY+C G
Sbjct: 424 GRVFRVAEALEYGMVGINTGLISTEVAPFGGVKSSGLGREGSKYGIEDYLEIKYLCMG 481


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: 620
Number of extensions: 19
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