GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fdh in Cupriavidus basilensis 4G11

Align Short-chain dehydrogenase (characterized, see rationale)
to candidate RR42_RS24995 RR42_RS24995 hypothetical protein

Query= uniprot:A0A2E7P8M8
         (258 letters)



>FitnessBrowser__Cup4G11:RR42_RS24995
          Length = 259

 Score =  115 bits (287), Expect = 1e-30
 Identities = 86/250 (34%), Positives = 126/250 (50%), Gaps = 7/250 (2%)

Query: 5   LQDKVVIVTGGASGIGGAISLQLAAEGAIPVVFARSEPDPQFWARLTGLQPRAALFQLEL 64
           ++ K +IVTGGASGIG A +  LAA GA+  +  R          LT    RA   + ++
Sbjct: 12  IEGKSIIVTGGASGIGEAAARLLAANGALLTIADRGSNGAALAKELTDQGLRAQFVETDI 71

Query: 65  QDEARCGEAVAETVRRFGRLDGLVNNAGVNDSVGL--DAGRNEFVASLERNLIHYYV-MA 121
             EA     V   VR +GRLD   NNAGV ++  L  +    +F    + N+I  ++ M 
Sbjct: 72  SSEADVIAMVEAAVRSYGRLDRAFNNAGVPNAGKLLAELTEEDFRRCHDVNVIGTFLCMK 131

Query: 122 HYCVPHLKATRGAILNVSSKTALTGQGNTSGYCASKGAQLSLTREWAAALRDDGVRVNAL 181
           H  +  LK   GAI+N SS   L      + Y ASK A   +T+  AA      +RVNA+
Sbjct: 132 HEILAMLKTGGGAIVNCSSIHGLIYTARAAEYTASKHAITGMTKAAAADYGLQNIRVNAI 191

Query: 182 IPAEVMTPLYEKWIATFENPQEKLDAITSKIPLGKRFTTSEEMADMAVFLLSGRSSHTTG 241
            P+   TP+Y  ++ T  + +E+++     + L  R +   E A  A++LLS  +S  TG
Sbjct: 192 APSSTRTPMYLHYLKTKPDHEERVNG----LHLLGRASEPIEQAQAAMWLLSDAASFVTG 247

Query: 242 QWVFVDGGYT 251
             + VDGGYT
Sbjct: 248 VTLPVDGGYT 257


Lambda     K      H
   0.318    0.134    0.394 

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: 133
Number of extensions: 5
Number of successful extensions: 3
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: 258
Length of database: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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 (21.7 bits)
S2: 47 (22.7 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