GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylC in Pseudomonas stutzeri RCH2

Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate GFF363 Psest_0364 Gluconolactonase

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



>lcl|FitnessBrowser__psRCH2:GFF363 Psest_0364 Gluconolactonase
          Length = 296

 Score =  131 bits (330), Expect = 2e-35
 Identities = 94/284 (33%), Positives = 135/284 (47%), Gaps = 15/284 (5%)

Query: 14  LGAPLLEGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVA 73
           LG    E PVWV  + AL++VDI +  + R++ A G+   W     +  C+      +VA
Sbjct: 11  LGCATGESPVWVAAEQALYWVDIPNRELLRWNAADGQISRWQGDEMLA-CIARHGDGWVA 69

Query: 74  GLQTGLAIFD--PADRSFTPLTDP-EPALPGNRLNDGTVDPAGRLWFGTM--DDGESEAT 128
           G+++G       P  R  + L    +  LP  R+NDG  D  GR W G+M  D       
Sbjct: 70  GMESGFFSLQTRPDGRLDSHLLATIDHQLPAMRMNDGRCDREGRFWAGSMALDMAAGHPV 129

Query: 129 GRIYRLGG---DGRCVAETAAVSISNGPAVSPDGRTLYHVDTLGGVIHSAAIG---DDGI 182
           G +YRL     D   V +     + NG A SPDGRT+Y  D+   V    A     D G 
Sbjct: 130 GALYRLDSKSIDAPLVPQLDGFIVPNGLAFSPDGRTMYLSDSHPSVQKIWAFDYDIDSGT 189

Query: 183 LGDSRVFATIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITK 242
               R+F  + +  G PDG AVDA+GC WI   +   + R++P G L   +A PV   + 
Sbjct: 190 PSRRRLFVDMLDHPGRPDGAAVDADGCYWICGNDAGFIHRFTPDGRLDRSLAVPVKKPSM 249

Query: 243 VAFGGPDLRTVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGM 286
            AFGG  L T++ T+     D    +++P AG +FA    V G+
Sbjct: 250 CAFGGARLDTLFVTSIRPGGDL---SDQPLAGGVFALNPGVTGL 290


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: 411
Number of extensions: 34
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: 295
Length of database: 296
Length adjustment: 26
Effective length of query: 269
Effective length of database: 270
Effective search space:    72630
Effective search space used:    72630
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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