Bioinformatics Institute

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| Supplementary materials to:
| More than 1001 problems with protein domain databases: transmembrane regions, signalpeptides and the issue of sequence homology

Wing-Cheong Wong, Sebastian Maurer-Stroh, Frank Eisenhaber

List of problematic Pfam domains (Release 23)

- 1050 problematic TM domains click here
- 135 problematic SP domains click here
- 29 problematic SP&TM domains click here

List of 'clean' alignments and HMM (non-SP/TM segment >= 40 positions)
Below, we provide three individual lists of domain models from Pfam release 23 (with TM region, with SP region and with both). In a tabulated form, the reader can look up the location of the SP&TM regions in the model, the cleaned alignment (in "aln" format and the HMM derived from it (the latter two as individual files). Further down, we have an additional table with Pfam domain models where the remaining globular part would be shorter than 40 residue positions; therefore, no cleanup alignment or HMM are provided.

- TM-containing domains (783 of 1050 entries) click here
- SP-containing domains (127 of 135 entries) click here
- SP&TM-containing domains (25 of 29 entries) click here
- SPTM-containing HMM (935 models) download
  (file "Pfam_rel23_globalHMM_cleanup.rar" compressed by WinRAR)

Supplementary information of Supplementary file Table S3, Figure 4

- PF01537.9 Herpes_glycop_D HMM alignment, validation proof
- PF03381.7 CDC50 HMM alignment, validation proof
- PF00690.18 Cation_ATPase_N HMM alignment, validation proof
- PF00482.15 GSPII_F HMM alignment, validation proof
- PF01569.12 PAP2 HMM alignment, validation proof
- PF01001.11 HCV_NS4b HMM alignment, validation proof

Supplementary information of Supplementary file Table S4, Figure 5

- PF08510.4 PIG-P HMM alignment, validation proof
- PF01569.12 PAP2 HMM alignment, validation proof
- PF01105.15 EMP24_GP25L HMM alignment, validation proof
- PF04387.6 PTPLA HMM alignment, validation proof
- PF01299.9 Lamp HMM alignment, validation proof
- PF02416.8 MttA_Hcf106 HMM alignment, validation proof
- PF0672.17 HAMP HMM alignment, validation proof
- PF07127.3 Nodulin_late HMM alignment, validation proof
- PF07172.3 GRP HMM alignment, validation proof
- PF00822.12 PMP22_Claudin (additional example) HMM alignment, validation proof

Supplementary information of Supplementary file Table S5

- PF08510.4 PIG-P HMM alignment, validation proof
- PF01569.12 PAP2 HMM alignment, validation proof
- PF04387.6 PTPLA HMM alignment, validation proof
- PF0672.17 HAMP HMM alignment, validation proof
- PF00690.18 Cation_ATPase_N HMM alignment, validation proof
- PF01544.10 CorA HMM alignment, validation proof
- PF00558.11 Vpu HMM alignment, validation proof
- PF07365.4 Toxin_8 HMM alignment, validation proof
- PF00482.15 GSPII_F HMM alignment, validation proof
- PF04901.5 RAMP HMM alignment, validation proof

Supplementary information of Table 5

- PF00690.18 Cation_ATPase_N (74 hits) HMM alignment, validation proof
- PF01105.15 EMP24_GP25L (8 hits) HMM alignment, validation proof
- PF01299.9 Lamp (2 hits) HMM alignment, validation proof
- PF01544.10 CorA (15 hits) HMM alignment, validation proof
- PF01569.12 PAP2 (108 hits) HMM alignment, validation proof
- PF02416.8 MttA_Hcf106 (283 hits) HMM alignment, validation proof
- PF04387.6 PTPLA (3 hits) HMM alignment, validation proof
- PF04612.4 GspM (19 hits) HMM alignment, validation proof
- PF07172.3 GRP (12 hits) HMM alignment, validation proof
- PF08294.3 TIM21 (7 hits) HMM alignment, validation proof
- PF08510.4 PIG-P (4 hits) HMM alignment, validation proof