GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuL in Dyella japonica UNC79MFTsu3.2

Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate N515DRAFT_1229 N515DRAFT_1229 L-arabinonolactonase (EC 3.1.1.15)

Query= uniprot:Q888H2
         (294 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1229
          Length = 300

 Score =  199 bits (507), Expect = 5e-56
 Identities = 125/301 (41%), Positives = 161/301 (53%), Gaps = 17/301 (5%)

Query: 1   MDAELIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAA 60
           M+A ++    N  GE  +W  REQALYW DI    L R   +   TRSW+ P+ L C+A 
Sbjct: 1   MNARVVHHPANTLGEGILWCEREQALYWTDIQAATLWRHRPADGATRSWEMPERLGCLAL 60

Query: 61  DSRGGWIA-GMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTML 119
               GW+  G+   L   +P DD   +   L SVE      R NDG CDRQGRF  GT L
Sbjct: 61  CEADGWLLLGLATRLAFFRPEDD---LLLPLVSVE-PDLPTRLNDGACDRQGRFVFGT-L 115

Query: 120 MDMAAGAV---VGALYRYSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIW 176
            + AAG     +GA YR +A        L  + + N +AFSPDG+TMY  DS   V  I 
Sbjct: 116 HEPAAGETRQPIGAFYRLNADLTLERLNLPGIGISNSVAFSPDGRTMYFCDSPSRV--IQ 173

Query: 177 AFDYDTDSGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRS 236
             DY    G P   R+F  +++  G PDG+A+DA GC W      G V R+ P+G++DR 
Sbjct: 174 CCDYGDRCGEP---RVFARVDDERGEPDGSAVDAQGCLWNAQWGLGRVVRYAPDGRVDRI 230

Query: 237 LVVPVKKPAMCAFGGPNLDTLFVTSIRPG---GDLSDQPLAGGVFALRPGVKGLEEPVFQ 293
           + VP  +P   AFG   LDTL++TS R G     L+ QPLAG +FA   G  GL EP F+
Sbjct: 231 VEVPATQPTRPAFGDSPLDTLYITSARDGLSSAALATQPLAGALFAADAGASGLPEPRFR 290

Query: 294 G 294
           G
Sbjct: 291 G 291


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: 359
Number of extensions: 25
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: 294
Length of database: 300
Length adjustment: 26
Effective length of query: 268
Effective length of database: 274
Effective search space:    73432
Effective search space used:    73432
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