GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Haloglycomyces albus DSM 45210

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_025272126.1 HALAL_RS0100575 SDR family NAD(P)-dependent oxidoreductase

Query= SwissProt::Q1NEI6
         (249 letters)



>NCBI__GCF_000527155.1:WP_025272126.1
          Length = 290

 Score =  119 bits (298), Expect = 7e-32
 Identities = 88/246 (35%), Positives = 125/246 (50%), Gaps = 18/246 (7%)

Query: 10  GRCAIVTGGAS--GLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVVALDVSDH 67
           G+ A+VTG  +  G+G  +A R+   G  +AL       +     E+DA   VA D++D 
Sbjct: 48  GKTALVTGAGADDGIGMAIATRLRLAGARLALVSTT-KRIHERANELDAVGFVA-DLTDE 105

Query: 68  AAVAAAAKDSAAALGKVDILICSAGITGATVPVWEFPV-----DSFQRVIDINLNGLFYC 122
           A VA         LG+VDI++ +AG+T  T P    PV     D ++  I  NL+  F  
Sbjct: 106 AEVAGLGDAVTEGLGEVDIVVNNAGMTSKTAPAVTKPVAQLGFDDWEAEITRNLHSTFLV 165

Query: 123 NREVVPFMLENGYGRIVNLASVAGKEG-NPNASAYSASKAGVIGFTKSLGKELAGKGVIA 181
           +R  V  M E+G+GRIVN+++ AG     P  +AY+++KAGV G T++L  E+   GV  
Sbjct: 166 SRYFVQSMAESGWGRIVNVSATAGVSSVMPAEAAYASAKAGVAGLTRALATEVVADGVTV 225

Query: 182 NALTPATFE--SPILDQLPQSQVDYMRSKIPMGRLGLVEESAAMVCFMASEECSFTTAST 239
           NA+ P      S  + +L Q  VD      P+GR G  EE AA V F  S   S+ T  T
Sbjct: 226 NAVAPGLIHTGSSTVPEL-QRGVD-----SPLGRPGTPEEVAAAVAFFCSPSASYVTGQT 279

Query: 240 FDTSGG 245
               GG
Sbjct: 280 LVVDGG 285


Lambda     K      H
   0.318    0.132    0.381 

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: 170
Number of extensions: 9
Number of successful extensions: 5
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: 249
Length of database: 290
Length adjustment: 25
Effective length of query: 224
Effective length of database: 265
Effective search space:    59360
Effective search space used:    59360
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: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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