GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Shewanella oneidensis MR-1

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate 202371 SO3263 3-oxoacyl-(acyl-carrier-protein) reductase, putative (NCBI ptt file)

Query= uniprot:B2T9V3
         (247 letters)



>FitnessBrowser__MR1:202371
          Length = 255

 Score =  105 bits (262), Expect = 9e-28
 Identities = 75/249 (30%), Positives = 118/249 (47%), Gaps = 23/249 (9%)

Query: 8   KTALITAAGQGIGLATAELFAREGARVIAT-------DIRIDGLAGKPVEARKLDVRDDA 60
           K  LIT   +GIG   A+ FA  G  V  T        + +  + G  V A  LD     
Sbjct: 14  KLVLITGGSRGIGAGIAKAFAEAGYWVAITYLNHQDKAVSLANILGDKVAAFALDQSKPE 73

Query: 61  AIKALAAEIG-----AVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAFLP 115
           +IK    E+      ++DVL N           + + +D+    + N++  + + +A +P
Sbjct: 74  SIKQCITEVEKYFNRSIDVLINNGAIAQEKPFSDITADDFTTMLNTNLRGPFLLAQACIP 133

Query: 116 AMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAICPG 175
           AM   G G IIN+ S      G  N+  Y+A+KA +I L++S+A  +   G+R N I  G
Sbjct: 134 AMQQHGFGRIINIGSIGGQWGGY-NQVHYAAAKAGLINLSQSIAKIYSRDGIRTNTIAIG 192

Query: 176 TVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSFTT 235
            VA+   E  +  +A  Q A          A  P+GR+GK E+IA++AL+L S +S + +
Sbjct: 193 LVATEMTEHELTTEAGKQKA----------AAIPVGRLGKVEDIASIALFLASQDSDYLS 242

Query: 236 GHAHVIDGG 244
           G     +GG
Sbjct: 243 GQTLNANGG 251


Lambda     K      H
   0.320    0.133    0.381 

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: 120
Number of extensions: 7
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: 247
Length of database: 255
Length adjustment: 24
Effective length of query: 223
Effective length of database: 231
Effective search space:    51513
Effective search space used:    51513
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: 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