GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Bacteroides thetaiotaomicron VPI-5482

Align sorbitol-6-phosphate dehydrogenase subunit (EC 1.1.1.140) (characterized)
to candidate 353297 BT3771 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file)

Query= metacyc::MONOMER-13092
         (266 letters)



>FitnessBrowser__Btheta:353297
          Length = 248

 Score =  113 bits (283), Expect = 3e-30
 Identities = 86/264 (32%), Positives = 128/264 (48%), Gaps = 34/264 (12%)

Query: 9   GKTVIVTGASSGIGKAIVDELLSLKVKVANFDLT--DNGEKH----ENLLFQKVDVTSRE 62
           GKT IVTGA+ GIGKAI  +  +    +A  DL   +N EK     E +  +     S  
Sbjct: 6   GKTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNA 65

Query: 63  QVEASVAAVVEH----FGTVDAVVNNAGINIPRLLVDPKDPHGQYELDDATFEKITMINQ 118
                 A VVE     FG +D +VNNAGI    L++          + +  ++ +  +N 
Sbjct: 66  ANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMM---------RMSEQQWDMVINVNL 116

Query: 119 KGLYLVSQAVGRLLVAKKKGVIINMASEAGLEGSEGQSAYAGTKAAVYSYTRSWAKELGK 178
           K  +    A   +++ +K G IINMAS  G+ G+ GQ+ YA +KA + +  +S A+ELG 
Sbjct: 117 KSAFNFIHACTPVMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQELGS 176

Query: 179 YGVRVVGIAPGIMEATGLRTLAYEEALGYTRGKTVEEIRAGYASTTTTPLGRSGKLSEVA 238
            G+R   IAPG +       L+             +E+RA +A     PL R G   +VA
Sbjct: 177 RGIRANAIAPGFILTDMTAALS-------------DEVRAEWAK--KIPLRRGGTPEDVA 221

Query: 239 DLVAYYISDRSSYITGITTNVAGG 262
           ++  +  SD SSY++G    V GG
Sbjct: 222 NIATFLASDMSSYVSGQVIQVDGG 245


Lambda     K      H
   0.313    0.131    0.361 

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: 175
Number of extensions: 12
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: 266
Length of database: 248
Length adjustment: 24
Effective length of query: 242
Effective length of database: 224
Effective search space:    54208
Effective search space used:    54208
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (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