GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Desulfoscipio geothermicus DSM 3669

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized)
to candidate WP_092483299.1 BM299_RS09265 TRAP transporter substrate-binding protein

Query= SwissProt::A3QCW5
         (336 letters)



>NCBI__GCF_900115975.1:WP_092483299.1
          Length = 343

 Score =  142 bits (357), Expect = 2e-38
 Identities = 90/294 (30%), Positives = 144/294 (48%), Gaps = 5/294 (1%)

Query: 36  IKFSHVVAENTPKGQMALKFKQLVEERLPGEYQVNVFPNSQLFGDNNELSALLLNDVQFV 95
           +K  H VAE+ P      KFKQ+VEE+  G+ Q++++ N  +  + + +  L L  +  V
Sbjct: 43  LKAGHAVAESHPYHLGLEKFKQIVEEKTGGQVQIDIYANGTIGSERDMIEGLQLGTIDLV 102

Query: 96  APSLSKFERYTKKLQLFDLPFLFKDMDAVNRFQQSDAGQQLLNSMKRKGVVGLGYLHNGM 155
             S      +  ++ + DLPFLF   +   +    + GQ LL      G+VGL +  NG 
Sbjct: 103 LTSTGPVINFVPEMGVVDLPFLFSSREHAYQVLDGEIGQDLLEQFGDIGIVGLAFWENGF 162

Query: 156 KQFSASS-PLVLPEDAQGKKFRIMASDVLAAQFQAVEAIPVKKPFSEVFTLLQTRAIDGQ 214
           +  + S  P+   ED QG K R M ++V  A F+ + A P    + EV+T LQ + IDGQ
Sbjct: 163 RNLTNSERPINSVEDIQGLKIRTMENEVHQAAFKELGADPTPMAWGEVYTALQQKTIDGQ 222

Query: 215 ENTWSNIYSKKFYEVQSNITESNHGVLDYMVVTSNTFWKSLPADKRKVIKASLDEAIAYG 274
           EN    IY+ K YEVQ  +  + H     +++        L  +++ +IK +  EA  Y 
Sbjct: 223 ENPIPIIYNMKIYEVQKYLALTGHFYSPALLLIGQKSLDKLSPEQQNIIKKAAVEAATYE 282

Query: 275 NEIAAAKVNKDKQAIIDSKRSEVTYLTPEQRAAWVNAMKPVWAQFEDKIGKDLI 328
            E    KV +D+Q     ++  V  +T   + A   A   V+ ++E + GKD I
Sbjct: 283 RE--QIKVQEDEQLAKLEEKGMV--ITRPDKNALREATMAVYEKYEGRFGKDTI 332


Lambda     K      H
   0.317    0.130    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: 248
Number of extensions: 10
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: 336
Length of database: 343
Length adjustment: 28
Effective length of query: 308
Effective length of database: 315
Effective search space:    97020
Effective search space used:    97020
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 (21.7 bits)
S2: 49 (23.5 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