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Update elm.md
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lauraluebbert authored Nov 6, 2023
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Expand Up @@ -36,18 +36,59 @@ Python: Use `json=True` to return output in JSON format.
Command-line only. Prevents progress information from being displayed.
Python: Use `verbose=False` to prevent progress information from being displayed.

### Example
### Examples
Find ELMs in an amino acid sequence:
```bash
gget setup elm # Downloads/updates local ELM database
gget elm -o gget_elm_results LIAQSIGQASFV
```
```python
# Python
gget.setup(“elm”) # Downloads/updates local ELM database
ortholog_df, regex_df = gget.elm("LIAQSIGQASFV")
```

Find ELMs giving a UniProt ID as input:
```bash
gget setup elm # Downloads/updates local ELM database
gget elm -o gget_elm_results --uniprot Q02410
```
```python
# Python
gget.setup(“elm”) # Downloads/updates local ELM database
ortholog_df, regex_df = gget.elm(“LIAQSIGQASFV”)
ortholog_df, regex_df = gget.elm(“Q02410”, uniprot=True)
ortholog_df, regex_df = gget.elm("Q02410", uniprot=True)
```
→ Returns two data frames containing extensive information about linear motifs associated with orthologous proteins and motifs found in the input sequence directly based on their regex expressions.
→ Returns two data frames (or JSON formatted dictionaries for command line) containing extensive information about linear motifs associated with orthologous proteins and motifs found in the input sequence directly based on their regex expressions:

Ortholog data frame:
|Ortholog_UniProt_ID|ProteinName|class_accession|ELMIdentifier |FunctionalSiteName |Description |Regex |Probability |Methods |Organism |query_seq_length|subject_seq_length|alignment_length|identity_percentage|motif_in_query|query_start|query_end|subject_start|subject_end|motif_start_in_subject|motif_end_in_subject|References |InstanceLogic|PDB |#Instances|#Instances_in_PDB|
|-------------------|-----------|---------------|---------------|-------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------|-----------------------------|-----------------|--------------------------------------------------------------------------------------------------------------------|------------|----------------|------------------|----------------|-------------------|--------------|-----------|---------|-------------|-----------|----------------------|--------------------|----------------|-------------|----|----------|-----------------|
|Q02410 |APBA1_HUMAN|ELME000357 |LIG_CaMK_CASK_1|CASK CaMK domain binding ligand motif|Motif that mediates binding to the calmodulin-dependent protein kinase (CaMK) domain of the peripheral plasma membrane protein CASK/Lin2.|[STED].{0,2}[IV]W[IVLM].[RHK]|1.11776693962e-05|comigration in gel electrophoresis; far western blotting; glutathione s tranferase tag; mutation analysis; pull down|Homo sapiens| | | | | | | | | |376 |382 |9952408 21763699|true positive| |7 |3 |
|Q02410 |APBA1_HUMAN|ELME000091 |LIG_PDZ_Class_2|PDZ domain ligands |The C-terminal class 2 PDZ-binding motif is classically represented by a pattern such as (VYF)X(VIL)* |...[VLIFY].[ACVILF]$ |7.88851572129e-05|mutation analysis; nuclear magnetic resonance; two hybrid |Homo sapiens| | | | | | | | | |832 |837 |16007100 |true positive|1U38|13 |8 |


Regex data frame:
|Instance_accession|ELMIdentifier |FunctionalSiteName |ELMType|Description |Regex |Instances (Matched Sequence)|motif_start_in_query|motif_end_in_query|ProteinName |Organism |References |InstanceLogic |#Instances|#Instances_in_PDB|
|------------------|-------------------|-------------------------------------------|-------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------|----------------------------|--------------------|------------------|----------------|-------------------------------------------------------------------|-----------------------------------|--------------|----------|-----------------|
|ELME000321 |CLV_C14_Caspase3-7 |Caspase cleavage motif |CLV |Caspase-3 and Caspase-7 cleavage site. |[DSTE][^P][^DEWHFYC]D[GSAN]|EIGDA |199 |204 |A0A0H3NIK3_SALTS|Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344|20947770 |true positive |41 |0 |
|ELME000321 |CLV_C14_Caspase3-7 |Caspase cleavage motif |CLV |Caspase-3 and Caspase-7 cleavage site. |[DSTE][^P][^DEWHFYC]D[GSAN]|DLIDG |453 |458 |STK4_HUMAN |Homo sapiens |11278283 11278782 |true positive |41 |0 |
|ELME000321 |CLV_C14_Caspase3-7 |Caspase cleavage motif |CLV |Caspase-3 and Caspase-7 cleavage site. |[DSTE][^P][^DEWHFYC]D[GSAN]|DLIDG |453 |458 |VDR_HUMAN |Homo sapiens |18832097 |true positive |41 |0 |
|ELME000102 |CLV_NRD_NRD_1 |NRD cleavage site |CLV |N-Arg dibasic convertase (NRD/Nardilysin) cleavage site (X-|-R-K or R-|-R-X). |(.RK)|(RR[^KR]) |RRA |142 |145 |PDYN_RAT |Rattus norvegicus |8294457 |true positive |2 |0 |
|ELME000102 |CLV_NRD_NRD_1 |NRD cleavage site |CLV |N-Arg dibasic convertase (NRD/Nardilysin) cleavage site (X-|-R-K or R-|-R-X). |(.RK)|(RR[^KR]) |RRA |142 |145 |SMS_RAT |Rattus norvegicus |8294457 |true positive |2 |0 |
|ELME000108 |CLV_PCSK_KEX2_1 |PCSK cleavage site |CLV |Yeast kexin 2 cleavage site (K-R-|-X or R-R-|-X). |[KR]R. |KRQ |581 |584 |CIS3_YEAST |Saccharomyces cerevisiae S288c |10438739 |true positive |1 |0 |
|ELME000146 |CLV_PCSK_SKI1_1 |PCSK cleavage site |CLV |Subtilisin/kexin isozyme-1 (SKI1) cleavage site ([RK]-X-[hydrophobic]-[LTKF]-|-X). |[RK].[AILMFV][LTKF]. |RLLTA |825 |830 |ATF6A_HUMAN |Homo sapiens |11163209 |true positive |2 |0 |
|ELME000146 |CLV_PCSK_SKI1_1 |PCSK cleavage site |CLV |Subtilisin/kexin isozyme-1 (SKI1) cleavage site ([RK]-X-[hydrophobic]-[LTKF]-|-X). |[RK].[AILMFV][LTKF]. |RLLTA |825 |830 |SRBP2_HUMAN |Homo sapiens |9139737 |true positive |2 |0 |
|ELME000231 |DEG_APCC_DBOX_1 |APCC-binding Destruction motifs |DEG |An RxxL-based motif that binds to the Cdh1 and Cdc20 components of APC/C thereby targeting the protein for destruction in a cell cycle dependent manner |.R..L..[LIVM]. |SRVKLNIVR |732 |741 |ACM1_YEAST |Saccharomyces cerevisiae S288c |23707760 18596038 18498748 18519589|true positive |18 |3 |
|ELME000231 |DEG_APCC_DBOX_1 |APCC-binding Destruction motifs |DEG |An RxxL-based motif that binds to the Cdh1 and Cdc20 components of APC/C thereby targeting the protein for destruction in a cell cycle dependent manner |.R..L..[LIVM]. |SRVKLNIVR |732 |741 |AURKB_HUMAN |Homo sapiens |16204042 15923616 |false positive|18 |3 |
|ELME000231 |DEG_APCC_DBOX_1 |APCC-binding Destruction motifs |DEG |An RxxL-based motif that binds to the Cdh1 and Cdc20 components of APC/C thereby targeting the protein for destruction in a cell cycle dependent manner |.R..L..[LIVM]. |SRVKLNIVR |732 |741 |STK6A_XENLA |Xenopus laevis |12208850 11707286 |false positive|18 |3 |
|ELME000231 |DEG_APCC_DBOX_1 |APCC-binding Destruction motifs |DEG |An RxxL-based motif that binds to the Cdh1 and Cdc20 components of APC/C thereby targeting the protein for destruction in a cell cycle dependent manner |.R..L..[LIVM]. |SRVKLNIVR |732 |741 |STK6_HUMAN |Homo sapiens |15536123 |false positive|18 |3 |
|ELME000353 |DEG_Nend_UBRbox_3 |N-degron | |N-terminal motif that initiates protein degradation by binding to the UBR-box of N-recognins. This N-degron variant comprises N-terminal Asn or Gln as destabilizing residue. |^M{0,1}([NQ]). |MNH |0 |3 | | | | |0 |0 |
|ELME000322 |DEG_SCF_SKP2-CKS1_1|SCF ubiquitin ligase binding Phosphodegrons|DEG |Degradation motif recognised by a pre-assembled complex consisting of Skp2 (an F box protein of the SCF E3 ubiquitin ligase) and Cks1, which leads to ubiquitylation and subsequent proteosomal degradation.|..[DE].(T)P.K |LSDKTPSK |471 |479 |CDN1B_HUMAN |Homo sapiens |16209941 |true positive |3 |1 |
|ELME000322 |DEG_SCF_SKP2-CKS1_1|SCF ubiquitin ligase binding Phosphodegrons|DEG |Degradation motif recognised by a pre-assembled complex consisting of Skp2 (an F box protein of the SCF E3 ubiquitin ligase) and Cks1, which leads to ubiquitylation and subsequent proteosomal degradation.|..[DE].(T)P.K |LSDKTPSK |471 |479 |CDN1C_HUMAN |Homo sapiens |12925736 |true positive |3 |1 |
|ELME000388 |DEG_SPOP_SBC_1 |SPOP SBC docking motif |DEG |The S/T rich motif known as the SPOP-binding consensus (SBC) of the MATH-BTB protein, SPOP, is present in substrates that undergo SPOP/Cul3-dependant ubiquitination. |[AVP].[ST][ST][ST] |AESSS |411 |416 |Q9VHV8_DROME |Drosophila melanogaster |19818708 |true positive |8 |6 |
|ELME000485 |DOC_CDC14_PxL_1 |Yeast Cdc14 phosphatase docking site |DOC |The PxL substrate docking motif enhances the Cdc14 phosphatase–substrate interaction and promotes subsequent dephosphorylation. |[FYLIM]..[YVILA]P.L.. |IGDAPELDA |200 |209 |ACE2_YEAST |Saccharomyces cerevisiae S288c |27826861 |unknown |10 |2 |
|… |… |… |… |… |… |… |… |… |… |… |… |… |… |… |

(Motifs that occur in many different species might look repeated, but all rows should be unique.)

#### [More examples](https://github.com/pachterlab/gget_examples)

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