GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutC in Dechlorosoma suillum PS

Align LUD_dom domain-containing protein (characterized, see rationale)
to candidate Dsui_0123 Dsui_0123 hypothetical protein

Query= uniprot:A0A0C4YFN9
         (234 letters)



>FitnessBrowser__PS:Dsui_0123
          Length = 218

 Score = 73.6 bits (179), Expect = 3e-18
 Identities = 74/227 (32%), Positives = 99/227 (43%), Gaps = 18/227 (7%)

Query: 4   LSARERMLGRLRAAAPATTADA-SQLDARIDAHYDARREAATPAELAQAMQAALGASHAL 62
           +SAR  +L R+R    A  A+A  Q  A + A    +R+   P E A  +      + AL
Sbjct: 1   MSARNDILNRVRLRLGADEAEARKQRVAAVLAARPGQRQGPRPTERADLLGEFRRRAEAL 60

Query: 63  AWCASA-EAW---PAQLAGKLAAAGVRRLLLDPAAEQGAALMRALPASVAPLSYARPIEA 118
           A        W   PA LA  LAA  + R        QG A         A       I A
Sbjct: 61  ASTVDVVSGWADAPAALARYLAAKDLPR--------QGVAWPALAHLDWAAAGLEIRIGA 112

Query: 119 WKAELFDTVDAGFTVARSGIAATGTLVLAPDAQTPRTVSLVPPLHIALVYAETLHPDLHC 178
            + +  D +  G T     IA TGTL+L  +       SL+P  H+ALV A +L   +  
Sbjct: 113 ARGD--DRL--GLTTCYCAIAETGTLMLLGEVDNHGVTSLLPETHVALVPASSLVWGMEE 168

Query: 179 AARAERWSAGMPTNLV-LVSGPSKTSDIQQTLAYGAHGPRELWVIIV 224
                R   G P   V  VSGPS+T DI+QTL  GAHGP  + +I++
Sbjct: 169 GWARLRAERGAPPRAVNFVSGPSRTGDIEQTLVLGAHGPYRVHLILL 215


Lambda     K      H
   0.317    0.127    0.375 

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: 177
Number of extensions: 13
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: 234
Length of database: 218
Length adjustment: 22
Effective length of query: 212
Effective length of database: 196
Effective search space:    41552
Effective search space used:    41552
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