GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Duganella sacchari Sac-22

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate WP_072783883.1 BUA36_RS09525 2-hydroxyacid dehydrogenase

Query= BRENDA::Q9I530
         (329 letters)



>NCBI__GCF_900143065.1:WP_072783883.1
          Length = 331

 Score =  349 bits (895), Expect = e-101
 Identities = 178/321 (55%), Positives = 228/321 (71%)

Query: 1   MRILFFSSQAYDSESFQASNHRHGFELHFQQAHLQADTAVLAQGFEVVCAFVNDDLSRPV 60
           M+   FS++ YD      +N   G EL F +  L   +A LA G E VC FVND +   V
Sbjct: 1   MKTAVFSTRRYDKTMLVRANASAGHELRFLEDRLSVASAPLAAGCEAVCVFVNDTVDAEV 60

Query: 61  LERLAAGGTRLVALRSAGYNHVDLAAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRL 120
           L  LA  GTRLVA RS GYN +D AAAE  G+ VV V  YSP++VAE AVGL+L +NR++
Sbjct: 61  LAILAQQGTRLVATRSTGYNQIDAAAAERHGIAVVRVTDYSPYSVAEFAVGLLLAVNRKI 120

Query: 121 HRAYNRTREGDFSLHGLTGFDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYPNPR 180
            RA  RTREG+F L GL GFDLHGK VGVIGTG+IG  FARIM GFGC ++ +D YP+  
Sbjct: 121 ARASVRTREGNFDLDGLMGFDLHGKTVGVIGTGKIGSIFARIMIGFGCTVVGHDRYPSAA 180

Query: 181 IQALGGRYLALDALLAESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNA 240
            +ALGGRY+++  LLA SD+VSLHCPLT +TRH+++A  LA  K G++L+NT RG LV+ 
Sbjct: 181 FEALGGRYVSVQELLACSDVVSLHCPLTDETRHIVNAASLARAKRGSILVNTSRGGLVDT 240

Query: 241 AALIEALKSGQLGYLGLDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLT 300
            A  EALK+GQLG L +DVYE+EA++FF+D S   + DDV+ RL+SFPNV+VT HQAF T
Sbjct: 241 EAATEALKTGQLGGLAIDVYEQEANLFFQDLSSTIICDDVIQRLVSFPNVIVTGHQAFFT 300

Query: 301 REALAAIADTTLDNIAAWQDG 321
            EA+  I  TT+D+I+A++ G
Sbjct: 301 EEAIGQIMQTTIDSISAFERG 321


Lambda     K      H
   0.323    0.137    0.402 

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: 335
Number of extensions: 10
Number of successful extensions: 1
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: 329
Length of database: 331
Length adjustment: 28
Effective length of query: 301
Effective length of database: 303
Effective search space:    91203
Effective search space used:    91203
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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