GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Rhodococcus qingshengii djl-6-2

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_102999338.1 C1M55_RS10010 glucose 1-dehydrogenase

Query= reanno::Burk376:H281DRAFT_00644
         (263 letters)



>NCBI__GCF_002893965.1:WP_102999338.1
          Length = 256

 Score =  114 bits (286), Expect = 2e-30
 Identities = 79/242 (32%), Positives = 121/242 (50%), Gaps = 4/242 (1%)

Query: 17  VSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGIADVSKQAQVDQII 76
           V+   AGIG AIA AF    A V + D+N  A            A   DV+ + QV  ++
Sbjct: 12  VTGAGAGIGAAIARAFGAEGARVVVSDINGGAAQAVADSIDGAIAVTTDVTDEQQVKDLV 71

Query: 77  DDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKAVPVLKETS 136
             A  + GGL+V+V NAGIA  T  + E     W   +S NLN  F  +R ++P L   S
Sbjct: 72  ARAVEEFGGLNVVVPNAGIATTTPLI-ETSFEDWRKVMSVNLNGVFLTVRHSLPAL-VAS 129

Query: 137 DCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAILPGVVEGER 196
              SI+ +SS++   G P    YA+ K A+  L ++L+AEL    +R NA+LPG ++ + 
Sbjct: 130 GGGSIVNISSISSTTGSPLIGSYAAAKAAVRNLTETLSAELRFHGIRANALLPGFIDTDL 189

Query: 197 MDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSNVTGQAISV 256
           +        +ALG+      +  + K +  R    +++AA A+F AS   S   G ++ +
Sbjct: 190 VKSHQQDFENALGLESGGFDDLMVTKQT--RYGRTEEVAAAAVFFASDQSSWCNGSSLVL 247

Query: 257 DG 258
           DG
Sbjct: 248 DG 249


Lambda     K      H
   0.318    0.134    0.375 

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: 116
Number of extensions: 6
Number of successful extensions: 4
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: 263
Length of database: 256
Length adjustment: 24
Effective length of query: 239
Effective length of database: 232
Effective search space:    55448
Effective search space used:    55448
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