GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylC in Erythrobacter marinus HWDM-33

Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate WP_047094223.1 AAV99_RS11825 SMP-30/gluconolactonase/LRE family protein

Query= reanno::Korea:Ga0059261_1893
         (295 letters)



>NCBI__GCF_001013305.1:WP_047094223.1
          Length = 294

 Score =  225 bits (573), Expect = 1e-63
 Identities = 122/277 (44%), Positives = 156/277 (56%), Gaps = 3/277 (1%)

Query: 20  EGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGLQTGL 79
           EG +W      +WFVDIK HR+  +DP +G     +AP Q+G+ LPA NG  + GLQ GL
Sbjct: 19  EGVLWDAARGVVWFVDIKQHRLWHYDPDTGSNSFTEAPGQIGWALPADNGMLLCGLQDGL 78

Query: 80  AIFDPADRSFTPLTDPEPALPGNRLNDGTVDPAGRLWFGTMDDGESEATGRIYRLGGDGR 139
            +F P   +F  L         NRLND   DP GR+WFG+MDD ES A+GR Y       
Sbjct: 79  YVFHPELSTFEKLAAVPGEPAANRLNDACTDPWGRVWFGSMDDTESAASGRFYCFDRGEI 138

Query: 140 CVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIGDDGILGDSRVFATIPN--SEG 197
             A  + ++I+NGPAV+  G  +Y  DT    I  A +  DG+ G++R FA       + 
Sbjct: 139 TPAGPSGITITNGPAVNAQGDRIYFTDTTAQKIMVANLTPDGV-GEARPFADTGALFPDA 197

Query: 198 FPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVAFGGPDLRTVYATT 257
           +PDGP VDAE  VW GLY G  V R+SP GEL   +  P   ITK+AFGG D RT Y T+
Sbjct: 198 YPDGPVVDAEDHVWTGLYLGGRVARFSPDGELTATIDMPARDITKLAFGGADFRTGYVTS 257

Query: 258 ASKHLDADGRAEEPHAGDLFAFRVSVPGMPGTEVSVG 294
           A+K++  D  A  P AG LFAF   V G   T V +G
Sbjct: 258 ATKNMTEDDMALYPQAGSLFAFDAPVAGFAQTRVRIG 294


Lambda     K      H
   0.319    0.139    0.439 

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: 414
Number of extensions: 35
Number of successful extensions: 2
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: 295
Length of database: 294
Length adjustment: 26
Effective length of query: 269
Effective length of database: 268
Effective search space:    72092
Effective search space used:    72092
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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