GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoA in Herbaspirillum seropedicae SmR1

Align Probable 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; 2-oxo-3-deoxygalactonate 6-phosphate aldolase; 6-phospho-2-dehydro-3-deoxygalactonate aldolase; 6-phospho-2-keto-3-deoxygalactonate aldolase; KDPGal; EC 4.1.2.21 (characterized)
to candidate HSERO_RS05155 HSERO_RS05155 2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Query= SwissProt::Q92RN8
         (212 letters)



>FitnessBrowser__HerbieS:HSERO_RS05155
          Length = 212

 Score =  184 bits (468), Expect = 8e-52
 Identities = 100/195 (51%), Positives = 128/195 (65%)

Query: 13  LIAILRGLKPEEAEGVVGALIETGFTAIEIPLNSPDPFRSIETAVKMAPAGCLIGAGTVL 72
           +IAILRG++  EAE +  AL E+GF  IE+PLNSP+P  SI    K  PA C++GAGTVL
Sbjct: 17  MIAILRGVRNAEAEAIGAALYESGFRIIEVPLNSPEPLLSITALRKSLPADCIVGAGTVL 76

Query: 73  TTAQVERLADVGGRLMVSPNVEPAVIRLAATKGMVTMPGVFTPTEALAAAAAGASGLKFF 132
             AQVE++ D GG L+V P+ + AVIR A   G+ + PGV T TEA AA   GA  LK F
Sbjct: 77  KPAQVEQVKDAGGELIVMPHSDGAVIRAARDAGLYSAPGVATVTEAFAALDNGADVLKMF 136

Query: 133 PASVLGPSGITAIRAVLPGDLEIAAVGGVSEVNFADYAAIGIRSFGLGSSLYKPGMSAGD 192
           PA  LGP  + A RAV+  D+ +  VGG++    A + A G   FGLGS+LY PG+SA  
Sbjct: 137 PAEQLGPQVVKAWRAVIARDIALLPVGGITPEGMAVFHAAGASGFGLGSALYTPGLSAEQ 196

Query: 193 VRQRAIATLAAYDAV 207
           VRQRA A +AA+ A+
Sbjct: 197 VRQRAEAFVAAWKAL 211


Lambda     K      H
   0.318    0.136    0.387 

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: 160
Number of extensions: 10
Number of successful extensions: 1
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: 212
Length of database: 212
Length adjustment: 21
Effective length of query: 191
Effective length of database: 191
Effective search space:    36481
Effective search space used:    36481
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: 45 (21.9 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