GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuL in Sinorhizobium meliloti 1021

Align Senescence marker protein-30 family protein (characterized, see rationale)
to candidate SMc04142 SMc04142 hypothetical protein

Query= uniprot:Q888H2
         (294 letters)



>FitnessBrowser__Smeli:SMc04142
          Length = 294

 Score =  156 bits (394), Expect = 6e-43
 Identities = 103/284 (36%), Positives = 148/284 (52%), Gaps = 7/284 (2%)

Query: 4   ELIVDAQNATGESPVWSVREQALYWVDIPNGELHRWDSSQDRTRSWKAPQMLACIAADSR 63
           E ++D++    ESPV+  R   L++VDI    LHR D S      W   +  AC    +R
Sbjct: 8   ECLLDSRCDVAESPVFDERRNCLFFVDIGRSALHRVDLSGAGHVEWTI-EGGACSTGLAR 66

Query: 64  GGWIAGMENGLYHLQPCDDGSLISTLLASVEHAQTGMRFNDGRCDRQGRFWAGTMLMDMA 123
            G +   +     L   D G+ ++  +A++E      R NDG+    G FW GTM  D+ 
Sbjct: 67  SGRLVLAQRDRVVLFDPDAGA-VTREIAAIEPDIADTRLNDGKVGPDGAFWVGTM-HDVP 124

Query: 124 AGAVVGALYRYSAGQKTLEAQLKDLIVPNGLAFSPDGKTMYLSDSHPAVQKIWAFDYDTD 183
               V +LYR S  +  +E +++ ++  NGLA+S DG  ++ SDS  A    W FD  T 
Sbjct: 125 DRRPVASLYRVSP-EGAVERKVEGVVCSNGLAWSGDGSLLFHSDSRGAWIDRWQFDPAT- 182

Query: 184 SGTPHDRRLFVDMNNYLGRPDGAAIDADGCYWICGNDAGLVHRFTPNGKLDRSLVVPVKK 243
            G    RR    ++   GRPDGAA DA+  YW  G  AG+V+RF+P G+L  +   PV  
Sbjct: 183 -GALSGRRRLASLDEASGRPDGAATDAEAHYWSAGVSAGIVNRFSPEGRLVGTHRFPVPA 241

Query: 244 PAMCAFGGPNLDTLFVTSIRPGGDLSDQPLAGGVFALRPGVKGL 287
           P M  F GP+L TL VTS+RP G +  +  +GG+F  R  V G+
Sbjct: 242 PTMPCFAGPDLKTLLVTSLRPAG-IGKENRSGGIFVARSPVAGV 284


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: 384
Number of extensions: 31
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: 294
Length of database: 294
Length adjustment: 26
Effective length of query: 268
Effective length of database: 268
Effective search space:    71824
Effective search space used:    71824
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