GapMind for catabolism of small carbon sources

 

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

Align L-arabinose 1-dehydrogenase / D-galactose 1-dehydrogenase (EC 1.1.1.46; EC 1.1.1.48) (characterized)
to candidate 201911 SO2776 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI ptt file)

Query= reanno::pseudo1_N1B4:Pf1N1B4_412
         (272 letters)



>FitnessBrowser__MR1:201911
          Length = 248

 Score =  112 bits (281), Expect = 6e-30
 Identities = 76/247 (30%), Positives = 122/247 (49%), Gaps = 9/247 (3%)

Query: 19  LKNKVVLLTGAAQGIGEAIVATFASQQARLVISDIQGEKVEKVAAHWREQGADVVAIKAD 78
           L  KV L+TGA++GIG AI  T     A ++ +    +    +  +  ++G  +V    D
Sbjct: 7   LAGKVALVTGASRGIGRAIAETLVEAGAVVIGTATSEKGAAAIQEYLGDKGFGLVLNVTD 66

Query: 79  VSRQQDLHAMARLAIELHGRIDVLVNCAGVNVFRDPLQMTEEDWHRCFAIDLDGAWYGCK 138
                DL    +   E  G +D+LVN AG+      ++M +++W+     +L   +   K
Sbjct: 67  SQSVTDLFDSIK---EKAGDVDILVNNAGITRDNLLMRMKDDEWNDIIDTNLTSLFRLSK 123

Query: 139 AVLPQMIEQGIGSIINIASTHSTHIIPGCFPYPVAKHGLLGLTRALGIEYAPKGIRVNAI 198
            V+  M+++  G IINI S   T    G   Y  AK GL+G T++L  E A + I VNAI
Sbjct: 124 PVMRTMMKKRFGRIINIGSVVGTMGNAGQVNYSAAKAGLIGFTKSLAREVASRQITVNAI 183

Query: 199 APGYIETQLNVDYWNGFADPHAERQRAFDLHPPRRIGQPIEVAMTAVFLASDEAPFINAS 258
           APG+I+T +  +          +++      P  R+GQ  E+A   +FLASD A +I   
Sbjct: 184 APGFIQTDMTDEL------TEDQQKAIMSQVPMERLGQAQEIANAVLFLASDSAAYITGE 237

Query: 259 CITIDGG 265
            + ++GG
Sbjct: 238 TLHVNGG 244


Lambda     K      H
   0.321    0.138    0.424 

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: 124
Number of extensions: 8
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: 272
Length of database: 248
Length adjustment: 24
Effective length of query: 248
Effective length of database: 224
Effective search space:    55552
Effective search space used:    55552
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 (21.9 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