GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Halococcus hamelinensis 100A6

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_007691810.1 C447_RS05850 SDR family oxidoreductase

Query= metacyc::MONOMER-16231
         (254 letters)



>NCBI__GCF_000336675.1:WP_007691810.1
          Length = 259

 Score =  152 bits (383), Expect = 9e-42
 Identities = 95/246 (38%), Positives = 135/246 (54%), Gaps = 5/246 (2%)

Query: 7   KTVLVTGASTGIGRAAAIGAAQHGADVA---INYAHSDGPAQSCVAE-IEALGQRAIAVK 62
           +TV+VTGAS+GIGRA A+   + GA V    +     D  A+    E I   G  +  V+
Sbjct: 11  ETVIVTGASSGIGRAVALAFGEAGATVVNADVRAEPKDHDAERPTHEAIREAGGESEYVE 70

Query: 63  GDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFKVNLHGAYFM 122
            DV+DP   +  V +A   FG VDVM++NAG+     F ++  + +ER  +VN  G +F 
Sbjct: 71  TDVSDPAEIES-VVEAAREFGGVDVMINNAGVHVSRRFREVSPEDLERVHRVNTVGTFFG 129

Query: 123 VQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAIALGKHGIRC 182
            QAAA  M+ +G  G IV  +S +A +      HY  TK  +  + +S A+ L ++ IR 
Sbjct: 130 TQAAANDMIERGEPGCIVNTASSTASMPDWEHAHYAATKGAIRMVTRSAALELAQYDIRV 189

Query: 183 NSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASDMAAYVTGAA 242
           NSV PG + TEI +      E+    + RTP  R G P DLAG  ++LAS+ A YVTG  
Sbjct: 190 NSVAPGPVATEITEGWSERAEESVGGDGRTPPTRAGRPSDLAGAYLYLASEGADYVTGEQ 249

Query: 243 LLVDGG 248
           + VDGG
Sbjct: 250 VWVDGG 255


Lambda     K      H
   0.318    0.133    0.379 

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: 135
Number of extensions: 5
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: 254
Length of database: 259
Length adjustment: 24
Effective length of query: 230
Effective length of database: 235
Effective search space:    54050
Effective search space used:    54050
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 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