GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutC in Marinobacter adhaerens HP15

Align Protein containing DUF162 (characterized, see rationale)
to candidate GFF2944 HP15_2888 protein containing DUF162

Query= uniprot:E4PLR7
         (223 letters)



>FitnessBrowser__Marino:GFF2944
          Length = 217

 Score =  226 bits (577), Expect = 2e-64
 Identities = 116/221 (52%), Positives = 153/221 (69%), Gaps = 4/221 (1%)

Query: 1   MSARANILGKLRNSLAGTTPRPDEFDERLVTAPWRYAPEDRIERLRSLMEAVHTEVHPCR 60
           MS+R  IL +LRN   G    P+     LV   W  + ++RIER   ++E+VH EVH C 
Sbjct: 1   MSSRETILQRLRNRTGGELTVPECDFSVLVRDDW--STKERIERFEKMIESVHGEVHHCT 58

Query: 61  SDNWPELVAELLNKRNLTNLLCAPSKEHGRALQAYFEATEQKVELLAYDQPVEAWKEELF 120
            D W + +AE+LN R   NLL     E G++L++         ELL YD+P+E+W+  LF
Sbjct: 59  EDMWMDRLAEVLNTRGARNLLIPKQHEIGQSLRS--AGRNDLPELLIYDEPIESWQAHLF 116

Query: 121 WSVEASLTGTLGGIAATGTLVLWPDCHEPRLMSLVPPVHIALLKASEIHDNLYDMMVAQD 180
             V+AS+T T GGIA TG+L+LWP+  EPRLMSLVPPVHIA+L+ASE++   ++ M AQ+
Sbjct: 117 NEVDASITSTRGGIAETGSLILWPNEDEPRLMSLVPPVHIAVLRASELYTTFHEAMKAQN 176

Query: 181 WAAGLPTNVLLVSGPSKTADIEQVLAYGAHGPRELIVLVLE 221
           WAAG+PTN LL+SGPSKTADIEQ LAYG HGP+ELIVL++E
Sbjct: 177 WAAGMPTNALLISGPSKTADIEQTLAYGVHGPKELIVLIIE 217


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: 187
Number of extensions: 5
Number of successful extensions: 2
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: 217
Length adjustment: 22
Effective length of query: 201
Effective length of database: 195
Effective search space:    39195
Effective search space used:    39195
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: 45 (21.9 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