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_068003513.1 PsAD2_RS05435 DctP family TRAP transporter solute-binding subunit

Query= uniprot:I7END8
         (333 letters)



>NCBI__GCF_001623255.1:WP_068003513.1
          Length = 333

 Score =  391 bits (1005), Expect = e-113
 Identities = 193/330 (58%), Positives = 246/330 (74%), Gaps = 1/330 (0%)

Query: 2   KFVTAAATAVALTMSAGTAMA-ACDDGEIVVKFSHVTNTDKHPKGIAASLLEKRINEEMN 60
           K +TAA  A  +  +  T  A ACD GE+V+KFSHV +   HPKG  A+ L +R+N EMN
Sbjct: 3   KIITAATVAAGMFTATQTVAAEACDPGEVVIKFSHVVSATGHPKGDFATALAERVNTEMN 62

Query: 61  GTMCLEVYPNSTLYNDNKVLEAMLQGDVQLAAPSLSKFEKFTKQFRLFDLPFMFKNIDAV 120
           G  C++V+P+S L++D+KV+EA+L GDVQ+AAPSLSKFE +T ++R+FDLPF+F +++AV
Sbjct: 63  GKACMQVFPSSQLFDDDKVMEALLLGDVQIAAPSLSKFEAYTLKYRVFDLPFLFSDMNAV 122

Query: 121 DAFQGSENGQAMLDSMQRRGLQGLSYWHNGMKQMSANKPLINPSDANGLKFRVQSSDVLV 180
           + F     GQ +L +M   G  GL Y +NG+K  SANKPL+ P+DA GLKFRVQ+SDV V
Sbjct: 123 NNFTQGPTGQELLGAMSDIGFVGLGYVYNGIKHFSANKPLLTPADAAGLKFRVQTSDVAV 182

Query: 181 AQMEAIGGSPQKMAFSEVYGALQQGVVDGQENTWSNIYGKKFFEVQDGVTETNHGALDYL 240
           A +EA+  + QK+AF EVYGALQ GVVDGQENTWSNIY KKFFEVQDG+TET+H  L YL
Sbjct: 183 AMIEAMEANAQKLAFKEVYGALQTGVVDGQENTWSNIYTKKFFEVQDGITETSHQLLSYL 242

Query: 241 VVTSVDWLDSLDPAVREQFLTILGEVTATRNSESTKVNAEARQSIIDAGGVVRELTPEQR 300
            VTS +WLDSLDP VR+QF+TI  EVT   N+ S+ +N   +Q II++G  VR LTPEQR
Sbjct: 243 AVTSQEWLDSLDPEVRDQFVTIFTEVTNEANARSSAINEANKQKIIESGVEVRTLTPEQR 302

Query: 301 AAWVEAMKPVWEQFAGDVGQDMIDAAQAIN 330
             WV  MKPVW +FA D+GQD+IDAA A N
Sbjct: 303 EQWVVVMKPVWAKFADDIGQDVIDAAVAAN 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: 339
Number of extensions: 6
Number of successful extensions: 2
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: 333
Length adjustment: 28
Effective length of query: 305
Effective length of database: 305
Effective search space:    93025
Effective search space used:    93025
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