Added minimal alignment (Figure S2)

README.md

@@ -5,16 +5,17 @@ Phylogenetic analyses related with the evolutionary history of SIRanc (FAM118B)
 Bonhomme, Vaysset, Ednacot, Rodrigues, Cury, Hernandez Trejo, Benaroch, Morehouse, Bernheim & Poirier (2024).
 
 ### Directory
-- `dev/initial_mixed_detection` : Initial detection of SIR2 subfamily and SIRim proteins
-- `dev/sirim/1_detection` : Detection of SIRim subfamily proteins 
+- `dev/initial_mixed_detection` : Initial detection of SIR2 subfamily and SIRim proteins (data not shown)
+- `dev/minimal_alignment` : Alignment of a subsample of SIR2 and SIRim subfamily proteins (Figure S2)
+- `dev/sirim/1_detection` : Detection of SIRim subfamily proteins (Used in all phylogenetic analyses)
 - `dev/sirim/2_align` : Alignment of SIRim subfamily proteins
-- `dev/sirim/3_phylo_sirim_domain`: Phylogeny of SIRim subfamily proteins
-- `dev/sirim/3.1_additional_trees`: Phylogeny of SIRim subfamily proteins
+- `dev/sirim/3_phylo_sirim_domain`: Phylogeny of SIRim subfamily proteins (Figure 4a)
+- `dev/sirim/3.1_additional_trees`: Phylogeny of SIRim subfamily proteins (Figure S7)
 - `dev/sirim/3.2_phylo_full_protein`: Phylogeny of SIRim subfamily proteins
-- `dev/sirim/3.3_phylo_euk`: Phylogeny of SIRim subfamily proteins
-- `dev/sirim/4_defense_systems`: Detection of which of the SIR2 and SIRim subfamily proteins are involved in known defense systems (DefenseFinder) / are in genomic contexts enriched in defense systems
+- `dev/sirim/3.3_phylo_euk`: Phylogeny of SIRim subfamily proteins (Figure S6, S8)
+- `dev/sirim/4_defense_systems`: Detection of which of the SIR2 and SIRim subfamily proteins are involved in known defense systems (DefenseFinder) / are in genomic contexts enriched in defense systems (Figure S1)
 - `dev/sirim/5_focus_eukaryotes` : Analyses regaring clades of eukaryotic SIRim (Figure 4, Figures S6-S8)
-- `dev/sirtuins/1_detection` : Detection of SIR2 subfamily proteins
-- `dev/phylo_sir2_sirim` : Joint phylogeny of SIR2 and SIRim subfamily proteins
+- `dev/sirtuins/1_detection` : Detection of SIR2 subfamily proteins (Used in all phylogenetic analyses)
+- `dev/phylo_sir2_sirim` : Joint phylogeny of SIR2 and SIRim subfamily proteins (Figure 1a)
 
 This repository is currently being updated.

dev/minimal_alignment/Multiple_alignment_268-539.afa

+>SIRT1 (H. Sapiens, NP_036370)
+IIVLTGAGVSVSCGIPDFRS-RDGIY--------------------------ARLA------------------------
+-------------------VDFPDLPDPQAMFDIEYF-----------RKDPR-------PFFKFAKEIY-PGQFQPSLC
+H------------------KFIALSD-----KEGKLLRNYTQNIDTLEQVAGIQR-------------------------
+---------------------IIQCHGSFATA
+>SIRT2 (H. sapiens, NP_036369)
+VICLVGAGISTSAGIPDFRSPSTGLY--------------------------DNL-------------------------
+--------------------EKYHLPYPEAIFEISYF-----------KKHPE-------PFFALAKELY-PGQFKPTIC
+H------------------YFMRLLK-----DKGLLLRCYTQNIDTLERIAGLEQE------------------------
+--------------------DLVEAHGTFYTS
+>SIRT3 (H. sapiens, NP_001357239)
+VVVMVGAGISTPSGIPDFRSPGSGLY--------------------------SNL-------------------------
+--------------------QQYDLPYPEAIFELPFF-----------FHNPK-------PFFTLAKELY-PGNYKPNVT
+H------------------YFLRLLH-----DKGLLLRLYTQNIDGLERVSGIPAS------------------------
+--------------------KLVEAHGTFASA
+>SIRT4 (H. sapiens, NP_001372662)
+LLVMTGAGISTESGIPDYRSEKVGLY--------------------------ART-------------------------
+--------------------DRRPIQHGDF------V-----------RSAPIRQ--RYWARNFVGWPQF--SSHQPNPA
+H------------------WALSTWE-----KLGKLYWLVTQNVDALHTKAGSRR-------------------------
+---------------------LTELHGCMDRV
+>SIRT5 (H. sapiens, NP_001363736)
+IVIISGAGVSAESGVPTFRGAG-GYW--------------------------RKW-------------------------
+--------------------QAQDLATPLA------F-----------AHNP--S--RVWEFYHYRREVM--GSKEPNAG
+H------------------RAIAECETRL-GKQGRRVVVITQNIDELHRKAGTKN-------------------------
+---------------------LLEIHGSLFKT
+>SIRT7 (H. sapiens, NP_057622)
+LVVYTGAGISTAASIPDYRGPN-GVW--------------------------TLL-------------------------
+--------------------QKGRSVS-AADL----------------------------------------SEAEPTLT
+H------------------MSITRLH-----EQKLVQHVVSQNCDGLHLRSGLPRT------------------------
+--------------------AISELHGNMYIE
+>SIRT6 (H. sapiens, NP_057623)
+VVFHTGAGISTASGIPDFRGPH-GVW--------------------------TME-------------------------
+--------------------ERGLAPKFDTTF----------------------------------------ESARPTQT
+H------------------MALVQLE-----RVGLLRFLVSQNVDGLHVRSGFPRD------------------------
+--------------------KLAELHGNMFVE
+>SIRanc (H. sapiens, NP_078832.1)
+LVLVIGTGISAAVAP---QVPALKSW--------------------------KGLIQALLDAAI-DFDLLEDEESKKF--
+-QKCLH-------------EDKNLVHVAHDLIQ---------------KLSPRTSNVRSTFFKDCLYEVF-DDLESKMED
+SG----------------KQLLQSVL----HLMENGALVLTTNFDNLLELYAADQGKQLES-------------------
+-LDLTDEKKVLEWAQEKRKLSVLHIHGVYTNP
+>SIRanc2 (H. sapiens, NP_001336845)
+LLLVIGTGVSAAVAP---GIPALCSW--------------------------RSCIEAVIEAAE-QLEVLHPGDVAEF--
+-RRKVT-------------KDRDLLVVAHDLIR---------------KMSPRTGDAKPSFFQDCLMEVF-DDLEQHIRS
+P------------------VVLQSIL----SLMDRGAMVLTTNYDNLLEAFGRRQNKPMES-------------------
+-LDLKDKTKVLEWARGHMKYGVLHIHGLYTDP
+>Dsr2 (B. cereus, WP_235354834)
+VSVMIGAGFSLNAKKVESSFEGMALW--------------------------SDLKTRLIKD------------------
+--LTHHSGI----------EDKGVLEVSQIFVE---------------EYG-RTS------LDEILKEAIPDDNYEPDKI
+H------------------HDLLKL---------PWSDVYTTNYDTLLERAKKRVYERNYQ-------------------
+-V-IYDVNDIPSSVQPR----IVKLHGSFPAH
+>Dsr2 (Mesorhizobium sp., WP_172352521)
+AALLVGAGFSRNATPVQGSGATMPGW--------------------------NDIYETMVDQLY-PAPPAHVTSGPAFVG
+GGLSHREWLL-----TQSGATSAYLRVAEEFEA---------------QFG-RNA------LDQLILRNVPDRQFAPGKL
+H------------------KMLVEL---------PWADIMTTNWDTLLERAAEGAEERVYN-------------------
+-V-LRTVEEIPEARAPR----VIKLHGSFPSH
+>ThsA (Sphingobacterium sp., WP_198386063.1)
+AAIFAGAGLSAALGFVD--------W--------------------------KGLLKDLAEEL-----------------
+-KLDIK-------------KEHDLISIAQYHTN---------------KFN-RGK------INEKIKNEF-TSLSKGSEN
+H------------------FILSRL---------DIDTFWTTNYDQLIEKTLESYGKTVER-------------------
+-K-IRNVD--FGSNIKKKDAILYKMHGDKDSP
+>LmuA (B. cereus, WP_021728720.1)
+AAVFAGAGLSQPAGHVN--------W--------------------------KELMRELADDL-----------------
+-GLNVD-------------LETDLVALAQYHVN---------------EFDGRGK------INQILIEEF-TKGVQTTEN
+H------------------TLLADL---------PISTYWTTNYDSLIETTLKNMGKKVDT-------------------
+-K-IVPEN--LAHTTPKTDAVIYKMHGDSSLP
+>Avs (H. frisingense, WP_234295629.1)
+CIPFIGAGFTAGESARQGEVPSGEEF--------------------------TELMRSALLKS--------PVENKPS--
+---------------DQSLKDYGFQELADEYF--------------------REEIVDVKEIKETLNALF-TKVRISSEA
+K------------------RSFLRW---------QWDYLYTLNIDDAIEHELD---------------------------
+---AIKVLPYKNFARHESRQFVYKLHGDATDA
+>pAgo (P. vulgatus, WP_229508514.1)
+FAFLLGAGASITSGVQS-AEDCIWDW--------------------------KKLIYISNNPTC-ESFL--DIHADYC--
+-RKRIQTWIDEQGGYPKAKSEEEYVFYAENTFP---------------FPGDRTK------Y-------FKDLCSNKSPN
+IG----------------YKLLCLLH-----KYGVLKSVWTTNFDGLVERAAHQANITPIN---------VNLDNPDRIY
+----RSENTQ-------DL-LYIALHGDYKYS
+>pAgo (S. macrogoltabida, WP_054725867.1)
+LMWLLGAGASVSAGIPS-AWDMIWQF--------------------------KQTLFVAQRKASPQSVA--DLGNPAI--
+-RALLDSHIASSERLPSPGSPDEYAALFEATYP---------------VERDRTT------F-------IQGMISGAKLA
+YG----------------HLALASLL-----KAGHTQLVWTTNFDHLIEDACARTYGTTGT------LSVVALDAPELAG
+----QLIGAQ-------KWPIAVKLHGDFRSR
+>Nezha (E. coli, WP_032308110.1)
+VGVLLGAGASVGCG-----GKTMKDV---------WESF-------------KQNYPELLGALI-DKYL-----------
+-------LVSQIDSDNNLVN---VELLIDEA---TKFLSVAKTRR---CEDEEEE------FRKILSSLYK-EVTKAALL
+TGEQFREKNQGKKDAFKYHKELISKLISNRQPGQSAPAIFTTNYDLALEWAAEDLGIQLFNGFSGLHTRQFYPQNFDLAF
+----RNVNAKGEARFGHYHAYLYKLHGSLTWY
+>PD-T7-2 (Hymenobacter sp., WP_044518239.1)
+VLFLLGAGCSANAGIPV-SGEMVANVHRLVEEDPRWQSYRDLYYYLRSSIQFADGIFGNFHA----VFNIEKLLI-----
+-------VMAEIEK--------------KERNPVYPFIGAWSNRLLDLAGPNFQR------VTELRDLITQELVTH----
+------WVKPSAYREAAYYDGFKNLQFGTTGL-GFNVKVFSLNYDLCFEKRVGKDNIEL----------GFDENTSEWSY
+NNFARD---------EDKSYTLYKLHGSLDWF
+>PD-T7-2 (S. mutans, WP_172964888.1)
+IVFLAGAGASVVGGNSN-YGKTVKMI--------------------------ADNVFEELHKSD-DIFTLEDLAQK-C--
+-QYNNGDILEEIKSENSSTSNEKPEYKLKESFNLENFLSTLFHYRPFVSEDDREK------FEETIEKILQ-LIKE----
+------NTNYSYNSKVLKHGALLNLLSSLSGKDGNKFSVITTNYDVLIEQAAAENNFVVFDGFNFTPLPKFDSNMFEWNL
+VKEVQNVNTR-EVEFKDKTFNLVKIHGSLTWE
+>Dsr1 (B. multivorans, WP_206380853.1)
+VVFFCGAGISYPAGLPG----------------------------------FKGLVEAIYKL---NGTALSDIEREAF--
+----------------ERGQFDATLDLLERRLP-------------GQRLAVRRK------LAEALRPNL--RRKGATDT
+Q------------------AALLRLA----RSRKGALRLVTTNFDRIFQAAAKRTGQEFQVY------------------
+------TAPMFPVPKNSRWNGLVYLHGLLPEK