GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuL in Paraburkholderia bryophila 376MFSha3.1

Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate H281DRAFT_05978 H281DRAFT_05978 Sugar lactone lactonase YvrE

Query= uniprot:Q888H2
         (294 letters)



>FitnessBrowser__Burk376:H281DRAFT_05978
          Length = 303

 Score =  207 bits (526), Expect = 3e-58
 Identities = 115/296 (38%), Positives = 168/296 (56%), Gaps = 15/296 (5%)

Query: 6   IVDAQNAT----GESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAAD 61
           ++D  ++T    GES +W  + Q L+WVD     +HR D S    +SW   + +  I   
Sbjct: 16  VIDVVDSTPDVLGESIIWDEKTQLLWWVDGIGQSIHRLDISSGAKKSWPMQEEIGSIGLR 75

Query: 62  SRGGWIAGMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMD 121
           ++GG I GM +G Y   P + G L        E  +   RFNDG+CDR GR+W+GT+  +
Sbjct: 76  AKGGLIVGMRSGFYFFSP-ETGELTEVARPDAERPKN--RFNDGKCDRHGRYWSGTV--E 130

Query: 122 MAAGAVVGALYRYSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDYD 181
            AA    G L+R     K  +  ++ +   NGL+FSPD + MY++DS     +I  FDYD
Sbjct: 131 AAAYTPRGRLFRLDPDLKP-KLIMEGITCINGLSFSPDNRLMYMTDSFSC--QIDVFDYD 187

Query: 182 TDSGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVPV 241
           +  G  ++RR F ++    G  DG+ +DADGC+W    D   V R+ P G++D  + +PV
Sbjct: 188 SVDGAIYNRRKFAEVPLGRGICDGSTVDADGCFWSANMDGWCVTRYDPRGRIDMVINLPV 247

Query: 242 KKPAMCAFGGPNLDTLFVTSIR---PGGDLSDQPLAGGVFALRPGVKGLEEPVFQG 294
           ++ +   FGGP+LDTLF+T+ R      +L+ QPLAG V A+RPGVKGL EP F G
Sbjct: 248 RRVSSLCFGGPDLDTLFITTARRRMSEKELAQQPLAGNVLAVRPGVKGLPEPEFLG 303


Lambda     K      H
   0.320    0.138    0.441 

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: 341
Number of extensions: 24
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 294
Length of database: 303
Length adjustment: 27
Effective length of query: 267
Effective length of database: 276
Effective search space:    73692
Effective search space used:    73692
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