GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Marinobacter guineae M3B

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_099616258.1 CLH62_RS00775 glucose 1-dehydrogenase

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



>NCBI__GCF_002744735.1:WP_099616258.1
          Length = 256

 Score =  108 bits (269), Expect = 1e-28
 Identities = 78/246 (31%), Positives = 115/246 (46%), Gaps = 9/246 (3%)

Query: 17  VSAGAAGIGLAIAEAFIEAQAEVYICDVN----QAAIDEATSRFPKLHAGIADVSKQAQV 72
           V+ G+ GIG A A    E  A V I D      +A   + T R  K      DVSK+ +V
Sbjct: 11  VTGGSVGIGAATATRMAEEGAAVAILDCQDKDGEALASQLTDRGLKAGYWHCDVSKEQEV 70

Query: 73  DQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKAVPVL 132
            Q++D      G L VLVNNAGIAG      EL   +W+   + N+   F+  + A+P +
Sbjct: 71  KQVLDKVAETFGSLTVLVNNAGIAGANKPTHELTEEEWDLVQNVNVKGVFFCTKHAIPHM 130

Query: 133 KETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAILPGVV 192
           K  +   SII +SS+ G +  P   PY ++K A+  + K+ A      N+R N+I PG +
Sbjct: 131 KR-AGVGSIINLSSIYGLVSAPDIPPYHASKGAVRLMSKTDAMLYATENIRANSIHPGFI 189

Query: 193 EGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSNVTGQ 252
                  ++     + G      R+       +  M   DDIA  A++LAS     VTG 
Sbjct: 190 ----WTPLVEGHLKSTGQDPEEARKATAALHPVGHMGEPDDIAWGAVYLASDESKFVTGS 245

Query: 253 AISVDG 258
            + +DG
Sbjct: 246 ELVIDG 251


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: 125
Number of extensions: 6
Number of successful extensions: 3
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