Supplementary Table 1. Functional domain analysis and comparison to protein domains in eight other fungi.
Ashgo, Ashbya gossypii; Canal, Candida albicans; Cangl = Candid glabrata; Debha, Debaryomyces hansenii;Klua, Klyveromyces lactis; Picst, Pichia stipitis; Sacce, Saccharomyces cerevisiae; Schpo, Schizosaccharomyces pombe; Yarli, Yarrowia lipolytica
Total number of distinct pfam domains for different fungi
AshgoCanalCanglDebhaKlulaPicstSacceSchpoYarli
169316731696175417431712182318201749
Number of pfam domains shared by P. stipitis with other fungi
AshgoCanalCanglDebhaKlulaPicstSacceSchpoYarli
155515961551163915901712160215341589
4 pfam domains present in P. stipitis, but absent in other 8 fungi
AshgoCanalCanglDebhaKlulaPicstSacceSchpoYarliDomain
PF02129000001000Peptidase_S15
PF03702000001000UPF0075
PF00331000001000Glyco_hydro_10
PF08129000001000Antimicrobial17
21 Conserved fungal domains absent in P. stipitis
AshgoCanalCanglDebhaKlulaPicstSacceSchpoYarliDomain
PF03159222220222XRN_N
PF04098222220221Rad52_Rad22
PF00536111110143SAM_1
PF08226111110131DUF1720
PF01020111110221Ribosomal_L40e
PF03556111110111DUF298
PF05206111110111DUF715
PF03997111110111VPS28
PF02268111110111TFIIA_gamma_N
PF08228111110111RNase_P_pop3
PF05492111110111NAF1
PF02517111110111Abi
PF02970111110111TBCA
PF07572111110111BCNT
PF00475111110111IGPD
PF07957111110111Ribosomal_MRP8
PF02270111110111TFIIF_beta
PF07541111110111EIF_2_alpha
PF03801111110111Ndc80_HEC
PF05916111110111Sld5
List of top Pfam domains in P. stipitis:
DescriptionOccurrences
PF00069Protein kinase domain89
PF00400WD domain, G-beta repeat82
PF00172Fungal Zn(2)-Cys(6) binuclear cluster domain74
PF07690Major Facilitator Superfamily61
PF00271Helicase conserved C-terminal domain53
PF00083Sugar (and other) transporter45
PF04082Fungal specific transcription factor domain44
PF00076RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)41
PF00270DEAD/DEAH box helicase35
PF00096Zinc finger, C2H2 type34
PF00153Mitochondrial carrier protein34
PF00005ABC transporter30
PF02985HEAT repeat30
PF00004ATPase family associated with various cellular activities (AAA)28
PF00560Leucine Rich Repeat27
PF00324Amino acid permease25
PF00106short chain dehydrogenase24
PF00097Zinc finger, C3HC4 type (RING finger)24
PF00226DnaJ domain23
PF00018SH3 domain21
PF00071Ras family21
PF08240Alcohol dehydrogenase GroES-like domain21
PF00702haloacid dehalogenase-like hydrolase17
PF08242Methyltransferase domain16
PF01370NAD dependent epimerase/dehydratase family16
PF00107Zinc-binding dehydrogenase16
PF00248Aldo/keto reductase family16
PF00176SNF2 family N-terminal domain16
PF00561alpha/beta hydrolase fold16
PF00646F-box domain15
PF08241Methyltransferase domain15
PF07719Tetratricopeptide repeat15
PF00227Proteasome A-type and B-type14
PF00173Cytochrome b5-like Heme/Steroid binding domain14
PF00009Elongation factor Tu GTP binding domain14
PF07728ATPase family associated with various cellular activities (AAA)14
PF00149Calcineurin-like phosphoesterase14
PF07653Variant SH3 domain14
PF00300Phosphoglycerate mutase family13
PF00023Ankyrin repeat13
PF07714Protein tyrosine kinase13
PF00724NADH:flavin oxidoreductase / NADH oxidase family13
PF01926GTPase of unknown function13
PF00179Ubiquitin-conjugating enzyme12
PF00628PHD-finger12
PF01423LSM domain12
PF00125Core histone H2A/H2B/H3/H412
PF00515Tetratricopeptide repeat11
PF00249Myb-like DNA-binding domain11
PF00664ABC transporter transmembrane region11
PF00169PH domain11
PF00155Aminotransferase class I and II11
PF03144Elongation factor Tu domain 211
PF00583Acetyltransferase (GNAT) family11
74 Pfam Domains absent in D. hansenii but present in P. stipitis
AshgoCanalCanglDebhaKlulaPicstSacceSchpoYarliDomain
PF07691012036610PA14
PF07723210052121LRR_2
PF06814112011221Lung_7-TM_R
PF07529102001222HSA
PF01168011011141Ala_racemase_N
PF03835111011121Rad4
PF07544102011211CSE2
PF02811111011112PHP
PF04506111011111Rft-1
PF03986111011111Autophagy_N
PF03850111011111Tfb4
PF04840111011111Vps16_C
PF04190111011111DUF410
PF05176111011111ATP-synt_10
PF06423111011111GWT1
PF03870111011111RNA_pol_Rpb8
PF02469011011112Fasciclin
PF03839111011111Sec62
PF01974111021101tRNA_int_endo
PF02861111011111Clp_N
PF02185101011121HR1
PF03980111011111Nnf1
PF01213111011111CAP
PF07522101011111DRMBL
PF04090111011110RNA_pol_I_TF
PF02330111011110MAM33
PF05285101011111SDA1
PF05620011011111DUF788
PF03051111001102Peptidase_C1_2
PF00658111001111PABP
PF07885011011102Ion_trans_2
PF04841101011111Vps16_N
PF03982101011111DAGAT
PF07962111011101Swi3
PF05843101011111Suf
PF08286101011111Spc24
PF05832101011111DUF846
PF05022111011110SRP40_C
PF04428001011211Choline_kin_N
PF05967011011111DUF887
PF04182101011110B-block_TFIIIC
PF05141111011100DIT1_PvcA
PF06432110001111GPI2
PF01608011001111I_LWEQ
PF00994101011101MoCF_biosynth
PF05132101001111RNA_pol_Rpc4
PF05093100011111DUF689
PF01627011011110Hpt
PF04603001011111Mog1
PF06516020002010NUP
PF07923100011110N1221
PF04547100001111DUF590
PF00576010011011Transthyretin
PF01590010001021GAF
PF07904100011110CT20
PF01480010001011PWI
PF07061100001110DUF1337
PF05345110001100He_PIG
PF06427010001011UDP-g_GGTase
PF02875100011100Mur_ligase_C
PF07928000001011Vps54
PF02453011001000Reticulon
PF04106000001011APG5
PF06831010001001H2TH
PF03069010001010FmdA_AmdA
PF06032100011000DUF917
PF01661010001000A1pp
PF05699000011000hATC
PF06807000001010Clp1
PF02129000001000Peptidase_S15
PF03702000001000UPF0075
PF00331000001000Glyco_hydro_10
PF08129000001000Antimicrobial17
116 Pfam Domains present in D. hansenii but absent in P. stipitis
AshgoCanalCanglDebhaKlulaPicstSacceSchpoYarliDomain
PF00665051400441112rve
PF077270303104200RVT_2
PF03159222220222XRN_N
PF00230204120313MIP
PF04098222220221Rad52_Rad22
PF03595011210171C4dic_mal_tran
PF00536111110143SAM_1
PF00633022310131HHH
PF03731201210221Ku_N
PF05131051110111Pep3_Vps18
PF08226111110131DUF1720
PF04185100110007Phosphoesterase
PF01020111110221Ribosomal_L40e
PF03556111110111DUF298
PF05206111110111DUF715
PF03997111110111VPS28
PF01465111100121GRIP
PF05172102110210MPPN
PF02268111110111TFIIA_gamma_N
PF08228111110111RNase_P_pop3
PF04667011110211Endosulfine
PF05492111110111NAF1
PF02517111110111Abi
PF02970111110111TBCA
PF07572111110111BCNT
PF00475111110111IGPD
PF07957111110111Ribosomal_MRP8
PF02270111110111TFIIF_beta
PF04425102110300Bul1_N
PF00595111210200PDZ
PF07541111110111EIF_2_alpha
PF03801111110111Ndc80_HEC
PF05916111110111Sld5
PF00251100110121Glyco_hydro_32N
PF08058101110111NPCC
PF05365101110111UCR_UQCRX_QCR9
PF06331101110111REX1
PF00041110100112fn3
PF07558101110120Shugoshin_N
PF04032110110111Rpr2
PF07743101110111HSCB_C
PF03657111110101UPF0113
PF03126101110111Plus-3
PF04119011110111HSP9_HSP12
PF04869101110111Uso1_p115_head
PF07574111110110SMC_Nse1
PF04627021110110ATP-synt_Eps
PF04112011110111Mak10
PF00135000110014COesterase
PF05185101110111PRMT5
PF07683011120011CobW_C
PF06127011110110DUF962
PF04147101110110Nop14
PF03215101110110Rad17
PF0209610110011160KD_IMP
PF00444110110110Ribosomal_L36
PF03941101100111INCENP_ARK-bind
PF07106101110110TBPIP
PF03656101110110Pam16
PF04882101110101Peroxin-3
PF05238101110110CHL4
PF00077101110101RVP
PF01997010100022Translin
PF08296101110110SNM1
PF05712000110111MRG
PF02935100110110COX7C
PF02179001100111BAG
PF01027000110111UPF0005
PF08209101110100Sgf11
PF07971110110000Glyco_hydro_92
PF02320101110000UCR_hinge
PF03732100200001Retrotrans_gag
PF01244000110020Peptidase_M19
PF02617101100100ClpS
PF06957110100010COPI_C
PF00116100100110COX2
PF07189100100011SF3b10
PF04420010100110CHD5
PF07297010100011DPM2
PF03879100100110Cgr1
PF08244100100101Glyco_hydro_32C
PF03441000110100FAD_binding_7
PF04057010100010Rep-A_N
PF044190001100104F5
PF00165010100001HTH_AraC
PF08227010100010DUF1721
PF05368000300000NmrA
PF01977010100100UbiD
PF00875000110100DNA_photolyase
PF06172000110100Cupin_5
PF05388000100100Carbpep_Y_N
PF08193000100010DUF1711
PF06244010100000DUF1014
PF01476010100000LysM
PF02464000100001CinA
PF07393000100010Sec10
PF07519000200000Tannase
PF07665000100010MpPF2
PF02065000100010Melibiase
PF06645000100100SPC12
PF07632000100000DUF1593
PF07470000100000Glyco_hydro_88
PF00061000100000Lipocalin
PF01391000100000Collagen
PF08212000100000Lipocalin_2
PF01581000100000FARP
PF04892000100000VanZ
PF03328000100000HpcH_HpaI
PF02123000100000RdRP_4
PF00187000100000Chitin_bind_1
PF04908000100000SH3BGR
PF04324000100000Fer2_BFD
PF06964000100000Alpha-L-AF_C
PF04982000100000HPP
PF00891000100000Methyltransf_2
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