GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylC in Burkholderia phytofirmans PsJN

Align Xylonolactonase (EC 3.1.1.68) (characterized)
to candidate BPHYT_RS24170 BPHYT_RS24170 gluconolactonase

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



>FitnessBrowser__BFirm:BPHYT_RS24170
          Length = 309

 Score =  129 bits (324), Expect = 8e-35
 Identities = 97/286 (33%), Positives = 130/286 (45%), Gaps = 20/286 (6%)

Query: 20  EGPVWVQRDAALWFVDIKSHRIHRFDPASGERRSWDAPAQVGFCLPAANGKFVAGLQTGL 79
           E PVW   + AL++VDI + +I R    SGER  W  P +V        G  +AG +TGL
Sbjct: 24  ESPVWRAAEQALYWVDIPAQKIVRLRIDSGERSEWLLPEKVACIAFDHRGTVLAGCETGL 83

Query: 80  AIFDPADRSFT---------PLTDPEPALPGNRLNDGTVDPAGRLWFGTM--DDGESEAT 128
                 + +            L  P+ A    R NDG  D  GR W GTM  D   ++  
Sbjct: 84  FALTLTESAANGEAVQVTGRKLAAPDFACDDMRFNDGRCDRQGRFWAGTMVQDMAAAKPA 143

Query: 129 GRIYRLGGDGRCVAETAAVSIS-NGPAVSPDGRTLYHVDTLGGVIHSAAIGDDGILGDSR 187
           G +YR    G   A      I+ NG A SPDG T+Y  D+        A   D   G+ R
Sbjct: 144 GALYRFDERGMLSAPVVEELITQNGLAWSPDGATMYLSDSHPLRRQIWAFDYDIESGEPR 203

Query: 188 ---VFATIPNSEGFPDGPAVDAEGCVWIGLYNGAAVRRYSPAGELLDVVAFPVGAITKVA 244
              VFA +    G PDG AVDA+GC WI   +   + R++P G+L   +A P       A
Sbjct: 204 NRRVFADLNQHAGRPDGAAVDADGCYWICANDAGLLLRFTPEGKLDRQIAVPAIKPAMCA 263

Query: 245 FGGPDLRTVYATTASKHLDADGRAEEPHAGDLFAFRVSVPGMPGTE 290
           FGG +L T++ T+     +A       H G LFA R  + G+P  E
Sbjct: 264 FGGRELDTLFVTSIRPAANA-----SEHDGHLFAVRPGITGLPEPE 304


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: 385
Number of extensions: 29
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: 309
Length adjustment: 27
Effective length of query: 268
Effective length of database: 282
Effective search space:    75576
Effective search space used:    75576
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:

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