GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Shewanella loihica PV-4

Align 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 5208453 Shew_0965 methylmalonate-semialdehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-20632
         (478 letters)



>FitnessBrowser__PV4:5208453
          Length = 496

 Score =  269 bits (687), Expect = 2e-76
 Identities = 152/471 (32%), Positives = 246/471 (52%), Gaps = 3/471 (0%)

Query: 5   LRHYIGGERVAADAPAESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEV 64
           + HYI G+     A + ++    T +  A V +    EVDAA++ A+KA   W++ +P  
Sbjct: 4   INHYINGQHTQPSARSAAVFEPATGEHKANVSLASALEVDAAIELAKKAHGPWSEMTPLN 63

Query: 65  RSDLLDKVGSTIIARSADIGRLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRRHGQNL 124
           R+ +L K  + + A   ++  ++ RE GK L +  GE +R   + ++  G      G++ 
Sbjct: 64  RARILFKFKALVEANMDELAAMITREHGKVLDDAKGEIIRGLEVVEFACGIPHLLKGEHT 123

Query: 125 ESTRPGVEIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATANV 184
           E    GV+  T  Q++GV   I P+NFP+ +P W    A+A GNT ++KP+   P +   
Sbjct: 124 EQVGGGVDAWTLNQSLGVVAGIAPFNFPVMVPMWMFPIAIAAGNTFIMKPSEKDPTSVMR 183

Query: 185 LADIMAECGAPAGVFNMLFGRGSMGDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQARV 244
           +A+++ E G P GVFN++ G     D L+ HKD+  VSF GS  +   +   A A   RV
Sbjct: 184 MAELLTEAGLPDGVFNVVNGDKEAVDTLLTHKDIQAVSFVGSTPIAEYIYQTAAAHGKRV 243

Query: 245 QLEMGGKNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLAEK 304
           Q   G KN ++++ DADL++AV+  +  ++ + G+RC A S ++    + D  V  L  +
Sbjct: 244 QALGGAKNHMLLMPDADLDQAVSALMGAAYGSAGERCMAISVVLAVGEVGDALVEKLLPQ 303

Query: 305 VAALRVGDALDPNTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKL--DNPGWYV 362
           + AL+VG+ L+   ++GP +S   ++    Y+D   SEG  ++  G ++ +     G+++
Sbjct: 304 IQALKVGNGLEGEMEMGPLISAQHLDKVRSYVDTGVSEGASLLADGRQLTVADHEQGYFL 363

Query: 363 RPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHARH 422
              L       M I  EE+FGPV + +RVK Y EAL + N  EFG    I T S + ARH
Sbjct: 364 GGCLFDHVTPEMTIYKEEIFGPVLTIVRVKDYAEALTLINEHEFGNGTAIFTQSGEAARH 423

Query: 423 FQRYARAGMTMVNLATAGVDYHVPFGGTKSSSYG-AREQGFAAVEFFTQTK 472
           F  + + GM  VN+          FGG K S +G     G   V F+T+ K
Sbjct: 424 FCHHVQVGMVGVNVPIPVPMAFHSFGGWKRSLFGPLHMHGPDGVRFYTKRK 474


Lambda     K      H
   0.317    0.133    0.384 

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: 559
Number of extensions: 18
Number of successful extensions: 2
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: 478
Length of database: 496
Length adjustment: 34
Effective length of query: 444
Effective length of database: 462
Effective search space:   205128
Effective search space used:   205128
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