Understanding the 8-state transmembrane topology

Dear LalalaGartija.

Below please find the original label defined by PDBTM:

PDBTM manual
http://pdbtm.enzim.hu/?_=/docs/manual

All protein chains generated using the biomatrix or listed in the pdb file
have a CHAIN record. This record has three attributes:

   - CHAINID: the chain identifier given in the original pdb file or
   generated by the biomatrix transformation;
   - NUM_TM: the number of transmembrane segments;
   - TYPE: the type of transmembrane segments (alpha, beta or coil (i.e.
   non alpha and non beta)) or the type of the chain if it does not cross the
   membrane (non_tm) or if it is not a protein chain (lipid).

Each CHAIN record contains one or more REGION records which locates the
chain segment in the space relative to the membrane. The type of REGION can
be 1, 2, B, H, C, I, L, F and U for Side1, Side2, Beta-strand, alpha-helix,
coil, membrane-inside, membrane-loop, interfacial helix and unknown
localizations, respectively. Side1 and Side2 refers to the two sides of the
membrane (based solely on the information from the PDB file it is not
possible to determine which side is outside or inside). Membrane-inside is
the inside part of a beta barrel. Membrane-loop corresponds to a region of
the polypeptide chain which does not cross the membrane, just dips into the
membrane (for example in aquaporins or potassium-channels). Interfacial
helices are alpha helical regions longer than 4 consecutive residues that
are close to the membrane surface with a tilt angle smaller than a
pre-determined threshold.

The pdb_beg and pdb_end attributes contain the segment localization using
the pdb numbering while theseq_beg and seq_end use the numbering in the
sequence found in the SEQ record. The sequence in SEQrecord is generated by
the alignment

<CHAIN CHAINID="A" NUM_TM="7" TYPE="alpha"> <SEQ> AVRENALLSS SLWVNVALAG
IAILVFVYMG RTIRPGRPRL IWGATLMIPL VSISSYLGLL SGLTVGMIEM PAGHALAGEM
VRSQWGRYLT WALSTPMILL ALGLLADVDL GSLFTVIAAD IGMCVTGLAA AMTTSALLFR
WAFYAISCAF FVVVLSALVT DWAASASSAG TAEIFDTLRV LTVVLWLGYP IVWAVGVEGL
ALVQSVGATS WAYSVLDVFA KYVFAFILLR WVANNERTVA VAGQTLGTMS SDD </SEQ> <REGION
seq_beg="1" pdb_beg="22" seq_end="2" pdb_end="23" type="U"/> <REGION
seq_beg="3" pdb_beg="24" seq_end="9" pdb_end="30" type="1"/> <REGION
seq_beg="10" pdb_beg="31" seq_end="31" pdb_end="52" type="H"/> <REGION
seq_beg="32" pdb_beg="53" seq_end="38" pdb_end="59" type="2"/> <REGION
seq_beg="39" pdb_beg="60" seq_end="59" pdb_end="80" type="H"/> <REGION
seq_beg="60" pdb_beg="81" seq_end="84" pdb_end="105" type="1"/> <REGION
seq_beg="85" pdb_beg="106" seq_end="104" pdb_end="125" type="H"/> <REGION
seq_beg="105" pdb_beg="126" seq_end="109" pdb_end="130" type="2"/> <REGION
seq_beg="110" pdb_beg="131" seq_end="131" pdb_end="152" type="H"/> <REGION
seq_beg="132" pdb_beg="153" seq_end="138" pdb_end="159" type="1"/> <REGION
seq_beg="139" pdb_beg="160" seq_end="160" pdb_end="181" type="H"/> <REGION
seq_beg="161" pdb_beg="182" seq_end="176" pdb_end="197" type="2"/> <REGION
seq_beg="177" pdb_beg="198" seq_end="196" pdb_end="217" type="H"/> <REGION
seq_beg="197" pdb_beg="218" seq_end="208" pdb_end="229" type="1"/> <REGION
seq_beg="209" pdb_beg="230" seq_end="230" pdb_end="251" type="H"/> <REGION
seq_beg="231" pdb_beg="252" seq_end="241" pdb_end="262" type="2"/> <REGION
seq_beg="242" pdb_beg="263" seq_end="253" pdb_end="274" type="U"/> </CHAIN>
++++++++++++++++++++++++++++++++++

*[Description]:*

1  -> Side1
2  -> Side2
B  -> Beta-strand
H  -> alpha-helix
C  -> coil
I  -> membrane-inside
L  -> membrane-loop
F  -> interfacial helix
U  -> unknown localizations

===========================

From the above definition, I transferred the original 9 labels into 8, by the following rules:

1,2 -> _ B -> E H -> H C -> C I -> I L -> L F -> F U -> X

======================================

Hope these information helps.

Best, -Sheng

On Thu, Oct 26, 2023 at 10:21 PM lalalagartija @.***> wrote:

Hi, First of all, thank you for this user-friendly tool that you provided. I like it a lot. Then, could you please give some more help on the tm8 files ? You say : "#TopoPred_TM8: 8-state transmembrane topology prediction results by no_profile mode

probabilities are in the order of H E C I L F X _, the 8 transmembrane

topology types used in PDBTM " But I don't see how the letters correspond to what I find in the PDBTM database which is : Legend: Inside - Membrane - Outside -Re-entrant loop - Beta barrel - inside - Periplasm - Interfacial helix ex : https://pdbtm.unitmp.org/entry/6edq

What are each column ?

Thanks

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realbigws / Predict_Property

Understanding the 8-state transmembrane topology #2

probabilities are in the order of H E C I L F X _, the 8 transmembrane topology types used

probabilities are in the order of H E C I L F X _, the 8 transmembrane