GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuL in Burkholderia phytofirmans PsJN

Align SMP-30/Gluconolaconase/LRE domain protein (characterized, see rationale)
to candidate BPHYT_RS24170 BPHYT_RS24170 gluconolactonase

Query= uniprot:B2UIY8
         (300 letters)



>FitnessBrowser__BFirm:BPHYT_RS24170
          Length = 309

 Score =  326 bits (836), Expect = 4e-94
 Identities = 172/307 (56%), Positives = 199/307 (64%), Gaps = 15/307 (4%)

Query: 1   MHLNVEPAVERI---GNMQCGVGESPVWHAGEQALYWTDIPGRTLWRWNFFSGQTNNWPL 57
           M     P VER+   G     VGESPVW A EQALYW DIP + + R    SG+ + W L
Sbjct: 1   MSAAANPRVERVEAAGQAPAAVGESPVWRAAEQALYWVDIPAQKIVRLRIDSGERSEWLL 60

Query: 58  PEMAGCIAMAPNGWAMA-METGIFLAPPPSPGIELGPLQ----RLATVAHARPDMRFNDG 112
           PE   CIA    G  +A  ETG+F             +Q    +LA    A  DMRFNDG
Sbjct: 61  PEKVACIAFDHRGTVLAGCETGLFALTLTESAANGEAVQVTGRKLAAPDFACDDMRFNDG 120

Query: 113 RCDRQGRFWAGTMVLDTSLGLPLGKLYRLDAAAARTGRVDA-VIDDLIVPNGLAFSPEGK 171
           RCDRQGRFWAGTMV D +   P G LYR D      G + A V+++LI  NGLA+SP+G 
Sbjct: 121 RCDRQGRFWAGTMVQDMAAAKPAGALYRFD----ERGMLSAPVVEELITQNGLAWSPDGA 176

Query: 172 TMYLSDSHASRQTVWAFDYDIDTGTPHNRRVFIDMNAYPGRPDGAAVDADGCYWICGNDA 231
           TMYLSDSH  R+ +WAFDYDI++G P NRRVF D+N + GRPDGAAVDADGCYWIC NDA
Sbjct: 177 TMYLSDSHPLRRQIWAFDYDIESGEPRNRRVFADLNQHAGRPDGAAVDADGCYWICANDA 236

Query: 232 GFVHRFTPDGRLDRSIAIPTSKPAMCAFGGPGLDTLFVTSIR--IGDDPLSGATFAVRPG 289
           G + RFTP+G+LDR IA+P  KPAMCAFGG  LDTLFVTSIR         G  FAVRPG
Sbjct: 237 GLLLRFTPEGKLDRQIAVPAIKPAMCAFGGRELDTLFVTSIRPAANASEHDGHLFAVRPG 296

Query: 290 VTGLPEP 296
           +TGLPEP
Sbjct: 297 ITGLPEP 303


Lambda     K      H
   0.322    0.140    0.466 

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: 394
Number of extensions: 9
Number of successful extensions: 4
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: 300
Length of database: 309
Length adjustment: 27
Effective length of query: 273
Effective length of database: 282
Effective search space:    76986
Effective search space used:    76986
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 (21.9 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