GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Paraburkholderia bryophila 376MFSha3.1

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate H281DRAFT_06109 H281DRAFT_06109 3-oxoacyl-[acyl-carrier protein] reductase

Query= reanno::BFirm:BPHYT_RS04775
         (263 letters)



>FitnessBrowser__Burk376:H281DRAFT_06109
          Length = 252

 Score =  123 bits (308), Expect = 4e-33
 Identities = 86/243 (35%), Positives = 129/243 (53%), Gaps = 19/243 (7%)

Query: 12  GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAI----DRARTAHPQLHAGVADVS 67
           G R +++GAA+GIGAAIA A+   GA + + D++ A +    D  R    ++   VADV 
Sbjct: 9   GRRAVVTGAASGIGAAIALAYAQAGARLVLADLNEARLAAHADACRANGVEVQTIVADVG 68

Query: 68  DCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYFLRK 127
           D      I+D   +  GG+D+L+NNAG+        DL    W+  +  +L S F   R+
Sbjct: 69  DETGAHGIVDRCIAAYGGIDILVNNAGMLTQARCT-DLTTQMWDDMLRVDLRSVFLCSRR 127

Query: 128 AVPLLKETSANPG-IIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRVNA 186
           A+P +  T+   G II +AS  G  G A  T YAA+K  ++G  KSLA+E  P+NV VNA
Sbjct: 128 ALPSM--TAQRWGRIINVASQLGIKGGAELTHYAAAKAGVIGFTKSLALEAAPDNVLVNA 185

Query: 187 ILPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASPAG 246
           I PG +E   +D + ++  E+             +++ LRR     +VA  A+ LAS  G
Sbjct: 186 IAPGPIETPLVDGISASWKEAKS-----------KELPLRRFGRADEVAPTAVLLASDPG 234

Query: 247 QNI 249
            N+
Sbjct: 235 GNL 237


Lambda     K      H
   0.320    0.136    0.391 

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: 181
Number of extensions: 11
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: 252
Length adjustment: 24
Effective length of query: 239
Effective length of database: 228
Effective search space:    54492
Effective search space used:    54492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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