GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Herbaspirillum seropedicae SmR1

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate HSERO_RS17235 HSERO_RS17235 3-ketoacyl-ACP reductase

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



>FitnessBrowser__HerbieS:HSERO_RS17235
          Length = 261

 Score =  245 bits (626), Expect = 6e-70
 Identities = 129/255 (50%), Positives = 184/255 (72%), Gaps = 8/255 (3%)

Query: 14  RVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGIA----DVSKQ 69
           +V V+AGA GIGLAI  AF+EA A V+ICDV++  +  A +RF   HA ++    DVS +
Sbjct: 9   KVIVTAGAQGIGLAITAAFVEAGAHVHICDVSEDFLASARARFG--HAPVSYSRTDVSSE 66

Query: 70  AQVDQIIDD-ARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKA 128
            +VD +  D A+R  G LDVL+NNAGIAGPT  VEE+  + W+ T++ NL   F   R+A
Sbjct: 67  REVDAMFADLAQRWSGRLDVLINNAGIAGPTSPVEEVALSDWDQTLAVNLTGPFLCTRRA 126

Query: 129 VPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAIL 188
           VP+LK+    A I+ +SSVAGRLG+  RTPY+++K+ ++GL ++ A ELGPS++RVNA+L
Sbjct: 127 VPLLKKNGGGA-IVNISSVAGRLGFALRTPYSASKYGVIGLTETWAIELGPSHIRVNAVL 185

Query: 189 PGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSN 248
           PG+VEG R +R+++A+A A GI    MR+  L ++SLR+MVT +DIA   +FL SPAG++
Sbjct: 186 PGIVEGARQERIVAAKAAAYGIGHEEMRQRLLSRVSLRKMVTAEDIANQVIFLCSPAGAS 245

Query: 249 VTGQAISVDGNVEYL 263
           ++GQ++SV GNVE L
Sbjct: 246 ISGQSLSVCGNVEVL 260


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: 169
Number of extensions: 7
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: 261
Length adjustment: 25
Effective length of query: 238
Effective length of database: 236
Effective search space:    56168
Effective search space used:    56168
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.

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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