GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Azospirillum brasilense Sp245

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate AZOBR_RS29790 AZOBR_RS29790 3-ketoacyl-ACP reductase

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



>FitnessBrowser__azobra:AZOBR_RS29790
          Length = 250

 Score =  109 bits (272), Expect = 6e-29
 Identities = 78/254 (30%), Positives = 116/254 (45%), Gaps = 9/254 (3%)

Query: 6   LLKPRPGLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGIA- 64
           + K   G    ++  A G+GLA+AE F+     V + D+N  A      R  +   GIA 
Sbjct: 1   MTKRLDGKVALITGAAQGLGLAMAETFVREGGRVAVVDINGDAAKAVAERLGESAIGIAA 60

Query: 65  DVSKQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYF 124
           +V++ A V+  I     K G LD+LVNNAG     G  E +   +++   + N+ S  Y 
Sbjct: 61  NVTRMADVEMTIAATVEKFGRLDILVNNAGSTHANGPFENVTEEEFDRVFALNVKS-IYL 119

Query: 125 LRKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRV 184
             KAV           I+ + S AG    P    Y +TK A+  + KSLA EL P N+RV
Sbjct: 120 YSKAVVATMRAQKSGVILNLGSTAGLRPRPGLVWYNATKGAVHNITKSLALELAPDNIRV 179

Query: 185 NAILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASP 244
            A+ P   E   +       A  +G      R   +  + L R+    D+A  AL+LAS 
Sbjct: 180 CALAPVATETPLL-------ATFMGGDTPEKRARMMGIVPLGRLGQPTDVANAALYLASD 232

Query: 245 AGSNVTGQAISVDG 258
             + +TG  + +DG
Sbjct: 233 EAAFLTGVVLEIDG 246


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: 136
Number of extensions: 10
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: 250
Length adjustment: 24
Effective length of query: 239
Effective length of database: 226
Effective search space:    54014
Effective search space used:    54014
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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