GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gci in Sphingomonas koreensis DSMZ 15582

Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate Ga0059261_0522 Ga0059261_0522 Predicted metal-dependent hydrolase of the TIM-barrel fold

Query= BRENDA::A9CEQ7
         (292 letters)



>FitnessBrowser__Korea:Ga0059261_0522
          Length = 295

 Score =  112 bits (281), Expect = 8e-30
 Identities = 86/283 (30%), Positives = 123/283 (43%), Gaps = 11/283 (3%)

Query: 8   LSGTAPNPAFPRGAVDTQMHMYLP--GYPALPGGPGLPPGALPGPEDYRRLMQWLGIDRV 65
           L  + P    P GAVD   H++ P   +P  P    LP  A   P+    L + LG  R 
Sbjct: 13  LDPSKPRYTPPPGAVDAHCHVFGPMAQFPFSPKAKYLPQDA--DPDALFALRERLGFARN 70

Query: 66  IITQGNAHQRDNGNTLACVAEMGEAAHAVVIIDATTTEKDMEKLTAAGTVGAR---IMDL 122
           +I Q + H  DN  TL  +A        V ++D   ++  ++ L   G  G R   +  L
Sbjct: 71  VIVQASCHGTDNRATLNGIAASNGTCRGVAVVDPAISDAGLDTLHEGGIRGVRFNFLKRL 130

Query: 123 PGGAVNLSELDAVDERAHAADWMVAVQFDGNGLLDHLPRLQKIRSRWVFDHHGKFFKGIR 182
              A     LD +  R     W V V F+ + L +  P L  I    V DH G+      
Sbjct: 131 VDDAPKDKFLD-IARRIQRLGWHVVVYFEADILEEMKPFLAAIPVPVVIDHMGRPDVRQG 189

Query: 183 TDGPEMAALLKLID-RGNLWFKFAGVYESSRKSWPYADVAAFSRVIAAHAPERIVWGTNW 241
            DG +MAA   L+D R ++W K            PYAD     R +    P+R++WGT+W
Sbjct: 190 PDGADMAAFRALLDSRDDIWTKVTCPDRLDPAGPPYADFVRSVRPLVEAYPDRVLWGTDW 249

Query: 242 PHNSVRETAAYPDDARLAELTLGWLPDEAARHRALVENPEALF 284
           PH ++ E    PDD  L +L     P    +H+ LV+NP  L+
Sbjct: 250 PHPNMEE--VLPDDGALVDLIPAIAPTAELQHKLLVDNPMRLY 290


Lambda     K      H
   0.319    0.136    0.426 

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: 266
Number of extensions: 24
Number of successful extensions: 5
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: 292
Length of database: 295
Length adjustment: 26
Effective length of query: 266
Effective length of database: 269
Effective search space:    71554
Effective search space used:    71554
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: 48 (23.1 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