GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutC in Pseudomonas stutzeri RCH2

Align Protein containing DUF162 (characterized, see rationale)
to candidate GFF923 Psest_0952 Uncharacterized conserved protein

Query= uniprot:E4PLR7
         (223 letters)



>FitnessBrowser__psRCH2:GFF923
          Length = 223

 Score =  288 bits (736), Expect = 8e-83
 Identities = 142/223 (63%), Positives = 169/223 (75%)

Query: 1   MSARANILGKLRNSLAGTTPRPDEFDERLVTAPWRYAPEDRIERLRSLMEAVHTEVHPCR 60
           MSA+ANIL KL+NSL GTTP  D++D  LVT PW YAPE RI RLR LMEAVHTE+H   
Sbjct: 1   MSAKANILAKLKNSLEGTTPIVDDYDVSLVTQPWSYAPEQRIARLRQLMEAVHTEIHLTT 60

Query: 61  SDNWPELVAELLNKRNLTNLLCAPSKEHGRALQAYFEATEQKVELLAYDQPVEAWKEELF 120
              WP L+ +LL+ R L +LL AP+  +G+   A+    E    L AYD+PVE WK+ELF
Sbjct: 61  DAGWPALLEQLLHDRQLPSLLIAPTTPYGQRFTAHCAGREGLPTLKAYDRPVEDWKDELF 120

Query: 121 WSVEASLTGTLGGIAATGTLVLWPDCHEPRLMSLVPPVHIALLKASEIHDNLYDMMVAQD 180
               ASLTGTLG IA+TG+L++WP   EPRLMSLVPPVH A+LKASEIHDN Y++     
Sbjct: 121 NDTPASLTGTLGAIASTGSLIMWPTREEPRLMSLVPPVHFAILKASEIHDNFYEIQQKFQ 180

Query: 181 WAAGLPTNVLLVSGPSKTADIEQVLAYGAHGPRELIVLVLEDA 223
           WAAG+PTN LLVSGPSKTADIEQVLAYGAHGP++LI+L+LEDA
Sbjct: 181 WAAGMPTNALLVSGPSKTADIEQVLAYGAHGPKDLILLILEDA 223


Lambda     K      H
   0.317    0.133    0.406 

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: 217
Number of extensions: 9
Number of successful extensions: 1
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: 223
Length of database: 223
Length adjustment: 22
Effective length of query: 201
Effective length of database: 201
Effective search space:    40401
Effective search space used:    40401
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 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