Table 4.
T. pallidum NCBI proteome annotation errors.
| Locus tag | Functional annotation | NCBI Proteome Annotation Error (in Nichols strain NC_021490, July 2021 annotation) |
MS detection |
|---|---|---|---|
| TPANIC_RS02075* | Hypothetical protein | Protein deleted from proteome | Present, Osbak25 |
| TPANIC_0928* | Hypothetical protein |
Protein deleted from proteome Protein replaced by TPANIC_RS05505 (“Pseudo” hypothetical protein, homologous to TPANIC_0928 N-terminus) and TPANIC_RS05510 (hypothetical protein, homologous to TPANIC_0928 C-terminus) TPANIC_0928 peptide (R)ELSFEDAVATGSTK(V) detected in 3 samples (peptide is not present in TPANIC_RS05505 or TPANIC_RS05510) |
Present, Osbak25 |
| TPANIC_RS04705* | Hypothetical protein | Protein deleted from proteome | Present |
| TPANIC_0446 | (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase |
Incorrectly truncated N-terminus (MNQRDERAARQPEEKV peptide truncated at N-terminus of TPANIC_0446 [latest version, WP_010881894]) TPANIC_0446 (former version, WP_014342797) peptide (K)VDSSAGVSPCNSPYGSGLLDVPLK(L) detected in 2 samples (peptide is not present in the latest version of TPANIC_0466) |
Present, Osbak25 |
| TPANIC_0535 | Hypothetical protein |
Incorrectly truncated N-terminus (MSAAWVGNMDKGVMVRLAEVEDAAAVLVEKAQEQAQR peptide truncated at N-terminus of TPANIC_0535 [latest version, WP_010881982]) TPANIC_0535/TP_RS02625 (former version, WP_014342464) peptide (R)LAEVEDAAAVLVEK(A) detected in 5 samples (peptide is not present in the latest version of TPANIC_0535) |
Present |
| TPANIC_0765** | ATP-dependent zinc metalloprotease FtsH |
Incorrectly truncated N-terminus (113 amino acids**** truncated at N-terminus of TPANIC_0765 [latest version, WP_187145723]) TPANIC_0765 (former version, WP_014342822) peptide (K)QSDDSSDPFGFFK(F) detected in 2 samples (peptide is not present in the latest version of TPANIC_0765) |
Present, Osbak25, McGill24 |
| TPANIC_0007 | DUF3798 domain-containing protein | “Pseudo” (non-coding annotation) | Present, Osbak25 |
| TPANIC_RS01255*** | Hypothetical protein |
“Pseudo” (non-coding annotation) (Previously annotated as TP_0248 in the Osbak et al. study) |
Present, Osbak25 |
| TPANIC_0533*** | V-type ATP synthase subunit I | “Pseudo” (non-coding annotation) | Present, Osbak25 |
| TPANIC_0813*** | Hypothetical | “Pseudo” (non-coding annotation) | Present, Osbak25 |
| TPANIC_0897 | MSP porin (TprK) | “Pseudo” (non-coding annotation) | Present |
| TPANIC_0993*** | Septal ring lytic transglycosylase RlpA family protein | “Pseudo” (non-coding annotation) | Present, Osbak25 |
*Proteins have been re-added in the Nichols strain (March 2023 Nichols NC_021490 annotation [TPANIC_RS02075 locus tag corresponds to TPANIC_0425 in the March 2023 annotation; TPANIC_RS04705 locus tag corresponds to TPANIC_RS05630 in the March 2023 annotation which has an incorrectly truncated N-terminus based on the results from the present study]).
**Protein has been re-annotated with the correct N-terminus (March 2023 Nichols NC_021490 annotation).
***Proteins have been re-annotated as coding proteins (March 2023 Nichols NC_021490 annotation).
****Truncated amino acids: MCFFAAPCIPPQRTSLSCAVRLSHSLSTFHLLFVYHGPACPRALQKGALTEMNTRYKQSDDSSDPFGFFKFSPRPQKGPSSSRERPPRRNSRKVLSLVLLALCALLALANHFL.
McGill: Proteins detected in McGill et al. study (2010). Osbak: Proteins detected in Osbak et al. study (2016). Present: Proteins detected in the present study (Present: protein identification based on the detection of one tryptic peptide).
Proteins in bold font: Proteins from in vivo-grown T. pallidum that were identified only in the present study.