GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Magnetospirillum magneticum AMB-1

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_011385057.1 AMB_RS13470 3-hydroxybutyrate dehydrogenase

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



>NCBI__GCF_000009985.1:WP_011385057.1
          Length = 260

 Score =  125 bits (315), Expect = 7e-34
 Identities = 85/254 (33%), Positives = 132/254 (51%), Gaps = 9/254 (3%)

Query: 12  GLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGI------AD 65
           G R  V+   +GIGL IA A     A V +      A  EA         G+      AD
Sbjct: 4   GKRALVTGSTSGIGLGIARALAAQGASVMLNGFGDGAEIEALRAGLAKEFGVTVLYNGAD 63

Query: 66  VSKQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFL 125
           +SK      ++ DA  +LGG+D+LVNNAGI      VEE    +W++ ++ NL S F  +
Sbjct: 64  LSKPDGAGVLVRDAEARLGGVDILVNNAGIQH-VSPVEEFPLERWDAVIAINLTSVFQAI 122

Query: 126 RKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVN 185
           R A+P +K       II ++S  G +    ++ Y ++K  ++GL K +  E   ++V  N
Sbjct: 123 RAALPGMKARG-WGRIINVASAHGLVASVNKSAYVASKHGVLGLTKVVGLETAETDVTCN 181

Query: 186 AILPGVVEGERMDRVISARADALGIPF-NAMREEYLKKISLRRMVTVDDIAAMALFLASP 244
           AI PG V    + + I ARA+A G+P   A R+   +K   ++  T + I  +A+FL S 
Sbjct: 182 AICPGWVLTPLVQKQIDARAEAQGVPVEQAGRDLLSEKQPSKKFTTPEQIGDLAVFLCSG 241

Query: 245 AGSNVTGQAISVDG 258
           AG+N+TG ++++DG
Sbjct: 242 AGANMTGTSLTMDG 255


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: 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: 260
Length adjustment: 25
Effective length of query: 238
Effective length of database: 235
Effective search space:    55930
Effective search space used:    55930
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