GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Neptunomonas antarctica S3-22

Align alpha-ketoglutarate TRAP transporter, solute receptor component (characterized)
to candidate WP_054340456.1 Nant_RS04530 TRAP transporter substrate-binding protein

Query= reanno::SB2B:6938088
         (339 letters)



>NCBI__GCF_001305295.1:WP_054340456.1
          Length = 327

 Score =  451 bits (1159), Expect = e-131
 Identities = 223/319 (69%), Positives = 267/319 (83%), Gaps = 3/319 (0%)

Query: 23  TVLGFSFGA---VAEPVEIKFSHVVAENTPKGQMALKFKELVESRLPGEYKVSVFPNSQL 79
           T L  +FGA   VA PVEIKFSHVVAENTPKGQMA+KFKELV  RL G  +V VFP+SQL
Sbjct: 9   TTLALAFGAQAAVASPVEIKFSHVVAENTPKGQMAIKFKELVAERLAGRVEVDVFPSSQL 68

Query: 80  FGDNNELAALLLNDVQLVAPSLSKFERYTKKLQVFDLPFLFEDMDAVDRFQQSEAGQQLL 139
           FGDN  L A+LL DVQL APSLSKF++YTK+LQ++DLPFLF+DM+AV+RFQQ   GQ LL
Sbjct: 69  FGDNKVLEAMLLGDVQLAAPSLSKFQQYTKQLQIYDLPFLFKDMEAVERFQQGPDGQGLL 128

Query: 140 NSMSRKGLVGLGYLHNGMKQFSANNALSLPGDAAGKKFRIMPSDVIAAQFEAVGAIPVKK 199
           +S+  KGLVGLGYLHNGMKQ SA+N + +P DAAG+KFRIM SDV+ AQFEAV A+P+KK
Sbjct: 129 SSLESKGLVGLGYLHNGMKQLSASNPIKVPADAAGRKFRIMTSDVLQAQFEAVDAVPLKK 188

Query: 200 PFSEVFTLLQTRAIDGQENTWSNIYSKKFYEVQTHITESNHGVLDYMLVTSETFWKSLPK 259
           PFSEVFTLLQT+AIDGQENTWSNIYSKKF+EVQ  ITESNHGVLDY++VTS  FW SL  
Sbjct: 189 PFSEVFTLLQTKAIDGQENTWSNIYSKKFFEVQPFITESNHGVLDYLVVTSAEFWMSLDD 248

Query: 260 DKREIIKQSMDEAVALGNKLALEKANEDRQLILDSKRVELVTLTPEQRQAWVNAMRPVWS 319
           D R  +K+++D+A+A GN +A EKANED+Q I+DSKR E++TLT  +RQ WV+AM+PVW 
Sbjct: 249 DLRIELKKALDDAIAYGNGIAAEKANEDKQQIVDSKRSEVITLTDAERQQWVDAMKPVWK 308

Query: 320 QFEDKIGKDLIEAAESANK 338
           QFE +IG DLIEAA+++NK
Sbjct: 309 QFEAEIGADLIEAAQASNK 327


Lambda     K      H
   0.316    0.132    0.368 

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: 370
Number of extensions: 5
Number of successful extensions: 1
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: 339
Length of database: 327
Length adjustment: 28
Effective length of query: 311
Effective length of database: 299
Effective search space:    92989
Effective search space used:    92989
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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