GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Pseudovibrio axinellae Ad2

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized, see rationale)
to candidate WP_068003520.1 PsAD2_RS05450 DctP family TRAP transporter solute-binding subunit

Query= uniprot:I7END8
         (333 letters)



>NCBI__GCF_001623255.1:WP_068003520.1
          Length = 337

 Score =  365 bits (937), Expect = e-106
 Identities = 181/327 (55%), Positives = 232/327 (70%), Gaps = 1/327 (0%)

Query: 5   TAAATAVALTMSAGT-AMAACDDGEIVVKFSHVTNTDKHPKGIAASLLEKRINEEMNGTM 63
           TA   A+ +   A   A   C  GE+V+KFSHV     HPKG  A +L +R+N E+NG  
Sbjct: 6   TAVILALGIVFGAPAFAQIDCKPGEVVIKFSHVVPPSGHPKGDFARMLAERVNTELNGKA 65

Query: 64  CLEVYPNSTLYNDNKVLEAMLQGDVQLAAPSLSKFEKFTKQFRLFDLPFMFKNIDAVDAF 123
           C++V+P S LY+D KV+EA++ GDVQLAAPSLSK E +T ++RLFDLPF+F+++DAV  F
Sbjct: 66  CMQVFPFSQLYDDEKVMEALILGDVQLAAPSLSKLEVYTNKYRLFDLPFLFEDMDAVQRF 125

Query: 124 QGSENGQAMLDSMQRRGLQGLSYWHNGMKQMSANKPLINPSDANGLKFRVQSSDVLVAQM 183
             SE GQ +L  M   G+ GL Y  +G+K  SA+KPL+ PSD  GLKFRVQ+SDV VA +
Sbjct: 126 TASEKGQELLGVMSDFGVVGLGYLFDGLKHFSADKPLLVPSDGAGLKFRVQNSDVAVAMI 185

Query: 184 EAIGGSPQKMAFSEVYGALQQGVVDGQENTWSNIYGKKFFEVQDGVTETNHGALDYLVVT 243
           EA+G S QK+AF EVYGALQ GVVDGQEN+WSNI+  +FFEVQDG TETNH  L Y+V T
Sbjct: 186 EAMGASAQKLAFKEVYGALQLGVVDGQENSWSNIFTSRFFEVQDGTTETNHQLLAYVVFT 245

Query: 244 SVDWLDSLDPAVREQFLTILGEVTATRNSESTKVNAEARQSIIDAGGVVRELTPEQRAAW 303
             +WL+SL+P VRE FLTI  E     N ++ K +   RQ I+DAG  VRELTP+QR  W
Sbjct: 246 PQEWLESLEPDVRELFLTIFRETLVKANGQAAKTSEVNRQRIVDAGYTVRELTPKQRQQW 305

Query: 304 VEAMKPVWEQFAGDVGQDMIDAAQAIN 330
           V+ M+PVW  F  ++G+D+IDAA+A N
Sbjct: 306 VDVMRPVWGDFEDEIGKDLIDAAEAAN 332


Lambda     K      H
   0.316    0.130    0.371 

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: 315
Number of extensions: 10
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: 333
Length of database: 337
Length adjustment: 28
Effective length of query: 305
Effective length of database: 309
Effective search space:    94245
Effective search space used:    94245
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