GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Billgrantia desiderata SP1

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate WP_086511094.1 BZY95_RS17060 mercury(II) reductase

Query= SwissProt::P14218
         (478 letters)



>NCBI__GCF_002151265.1:WP_086511094.1
          Length = 363

 Score =  158 bits (399), Expect = 3e-43
 Identities = 105/345 (30%), Positives = 169/345 (48%), Gaps = 8/345 (2%)

Query: 115 VTSFEGHGKLLANKQVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAP-LSDDIIVDSTG 173
           +T   G  + +    + V   +G  QV+  +  +I +G+RP  +PP P L+D   + ST 
Sbjct: 7   ITVLHGEARFIDAHSLMVKLNEGGEQVVHFDRALIGTGARPA-VPPIPGLADTPYLTSTS 65

Query: 174 ALEFQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLT 233
           AL    +P++L VIGA V+ LEL   +ARLG+ VTVL A  + L   D  +         
Sbjct: 66  ALALDTLPERLIVIGASVVALELAQAFARLGSRVTVL-ARSRLLSQEDPAVGDAVEAAFR 124

Query: 234 KQGLNIRLGARVTASEVKKKQVTVTFTDANGEQKETFDKLIVAVGRRPVTTDLLAADSGV 293
           ++ + +    + +  +    +  V   D N       D+L+VA GR P T  L  A  GV
Sbjct: 125 RESIEVLKQTQASRVDYTDNEFIV---DTNAGTLRA-DQLLVATGRTPNTEALNLASLGV 180

Query: 294 TLDERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLI 353
               RG I VD+H  T+VPG++A GD        + A+  G   A  + G +A ++   +
Sbjct: 181 ET-ARGAILVDEHLHTTVPGLYAAGDCTDQPEFVYVAAAGGSRAAVNMTGGEATLDLSAM 239

Query: 354 PSVIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDR 413
           P+VI+T P++A VG TE     +G  V+          RA+   DT G +K++A+  + R
Sbjct: 240 PAVIFTDPQVATVGLTEAEAIEQGFSVDTRELDLENVPRALVNFDTGGFIKLVAERDSGR 299

Query: 414 VLGVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEAL 458
           +LGV  +   A EL+Q   + +    +  D+   +F + T+ E L
Sbjct: 300 LLGVQAVAGEAGELIQTAVMALRARMTVHDIANELFPYLTMVEGL 344


Lambda     K      H
   0.316    0.134    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: 359
Number of extensions: 23
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: 478
Length of database: 363
Length adjustment: 31
Effective length of query: 447
Effective length of database: 332
Effective search space:   148404
Effective search space used:   148404
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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