Query psy3604
Match_columns 496
No_of_seqs 363 out of 1748
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 20:51:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3604.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3604hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03078 Putative tRNA pseudou 100.0 6.3E-52 1.4E-56 439.3 19.2 325 80-453 56-492 (513)
2 PRK12434 tRNA pseudouridine sy 100.0 5.4E-48 1.2E-52 382.2 21.8 221 95-374 2-245 (245)
3 COG0101 TruA Pseudouridylate s 100.0 7.3E-48 1.6E-52 384.1 22.8 227 96-383 3-252 (266)
4 PRK14589 tRNA pseudouridine sy 100.0 1.1E-47 2.5E-52 383.5 21.7 249 96-409 2-261 (265)
5 cd02569 PseudoU_synth_ScPus3 P 100.0 3.3E-47 7.2E-52 378.7 21.1 233 100-374 2-256 (256)
6 PRK00021 truA tRNA pseudouridi 100.0 6.5E-47 1.4E-51 374.1 21.9 220 95-374 2-244 (244)
7 cd00497 PseudoU_synth_TruA_lik 100.0 5.2E-47 1.1E-51 370.6 20.1 217 101-374 1-224 (224)
8 PRK14588 tRNA pseudouridine sy 100.0 1.1E-46 2.3E-51 378.0 22.2 227 95-382 2-255 (272)
9 TIGR00071 hisT_truA pseudourid 100.0 2.8E-46 6.1E-51 366.1 20.8 214 96-369 2-227 (227)
10 PRK14586 tRNA pseudouridine sy 100.0 4E-46 8.7E-51 368.8 21.7 220 95-374 2-245 (245)
11 cd02570 PseudoU_synth_EcTruA P 100.0 7.4E-46 1.6E-50 365.3 21.4 215 100-374 2-239 (239)
12 cd02866 PseudoU_synth_TruA_Arc 100.0 6.4E-46 1.4E-50 362.3 19.8 213 100-374 2-221 (221)
13 PRK14587 tRNA pseudouridine sy 100.0 6.7E-45 1.5E-49 361.5 23.1 224 96-398 2-233 (256)
14 cd02568 PseudoU_synth_PUS1_PUS 100.0 1.5E-44 3.2E-49 357.4 20.2 230 100-374 2-245 (245)
15 KOG2554|consensus 100.0 1.6E-44 3.4E-49 363.5 16.4 251 93-385 64-331 (425)
16 KOG2553|consensus 100.0 1.1E-38 2.4E-43 328.1 19.3 273 93-430 35-382 (416)
17 KOG4393|consensus 99.9 4E-27 8.7E-32 229.9 15.4 181 183-375 54-277 (295)
18 KOG4336|consensus 99.9 6E-23 1.3E-27 204.0 7.8 136 10-202 5-149 (323)
19 KOG2389|consensus 99.8 5.3E-19 1.2E-23 179.0 10.0 141 3-201 22-187 (353)
20 smart00576 BTP Bromodomain tra 99.7 1.8E-16 4E-21 130.9 6.8 76 5-137 1-76 (77)
21 PF07524 Bromo_TP: Bromodomain 99.6 2.7E-16 5.9E-21 129.6 7.0 77 5-138 1-77 (77)
22 PF01416 PseudoU_synth_1: tRNA 99.6 1.1E-17 2.3E-22 144.3 -6.5 98 271-375 1-105 (105)
23 PF10406 TAF8_C: Transcription 97.5 3.4E-05 7.4E-10 59.2 1.5 25 176-200 1-25 (51)
24 cd08049 TAF8 TATA Binding Prot 97.5 4.6E-05 1E-09 59.1 1.5 25 176-200 1-25 (54)
25 PF10105 DUF2344: Uncharacteri 96.7 0.02 4.3E-07 55.2 12.0 116 188-314 55-172 (187)
26 cd07979 TAF9 TATA Binding Prot 96.7 0.0019 4.2E-08 57.8 4.3 64 14-134 5-68 (117)
27 cd00076 H4 Histone H4, one of 96.4 0.0054 1.2E-07 52.0 4.9 75 7-138 10-84 (85)
28 PTZ00015 histone H4; Provision 96.2 0.0069 1.5E-07 53.0 4.5 74 8-138 28-101 (102)
29 PLN00035 histone H4; Provision 96.1 0.011 2.3E-07 51.9 5.2 72 11-139 30-101 (103)
30 smart00803 TAF TATA box bindin 95.6 0.016 3.5E-07 46.6 4.1 61 13-130 5-65 (65)
31 COG2036 HHT1 Histones H3 and H 95.1 0.024 5.2E-07 48.7 3.8 69 12-137 21-89 (91)
32 PF02291 TFIID-31kDa: Transcri 95.0 0.035 7.5E-07 50.6 4.7 61 14-131 16-76 (129)
33 PF15630 CENP-S: Kinetochore c 92.5 0.18 4E-06 41.9 4.2 65 9-130 4-71 (76)
34 PF02969 TAF: TATA box binding 92.2 0.26 5.6E-06 40.0 4.6 61 13-130 6-66 (66)
35 smart00417 H4 Histone H4. 89.7 0.2 4.4E-06 41.5 1.8 65 6-127 9-73 (74)
36 cd08050 TAF6 TATA Binding Prot 87.3 0.94 2E-05 47.6 5.4 70 14-142 3-72 (343)
37 cd07981 TAF12 TATA Binding Pro 87.3 1.4 3E-05 36.0 5.3 59 16-131 7-66 (72)
38 KOG3334|consensus 82.7 2.2 4.8E-05 39.5 4.9 61 14-131 17-77 (148)
39 PF00808 CBFD_NFYB_HMF: Histon 72.3 5.7 0.00012 31.3 3.9 30 100-129 36-65 (65)
40 PF00125 Histone: Core histone 67.9 7.2 0.00016 31.3 3.7 31 100-130 43-73 (75)
41 KOG3423|consensus 65.2 10 0.00022 36.1 4.6 67 14-137 90-170 (176)
42 COG5011 Uncharacterized protei 54.8 13 0.00027 36.6 3.3 44 189-241 57-100 (228)
43 PF03540 TFIID_30kDa: Transcri 50.2 17 0.00036 28.2 2.7 29 14-42 6-34 (51)
44 KOG3467|consensus 48.7 36 0.00078 29.2 4.7 40 100-139 62-101 (103)
45 smart00428 H3 Histone H3. 39.3 66 0.0014 28.5 5.1 34 100-133 69-102 (105)
46 COG5094 TAF9 Transcription ini 38.3 36 0.00077 31.1 3.3 60 15-131 19-81 (145)
47 TIGR01213 conserved hypothetic 34.5 2.7E+02 0.0058 30.3 9.7 107 213-320 236-348 (388)
48 KOG2549|consensus 32.7 69 0.0015 36.0 5.1 70 14-142 15-84 (576)
49 KOG0870|consensus 29.8 73 0.0016 30.5 4.0 35 100-134 46-80 (172)
50 PF01416 PseudoU_synth_1: tRNA 26.4 29 0.00062 29.4 0.7 42 183-248 60-105 (105)
51 cd07978 TAF13 The TATA Binding 25.6 1.2E+02 0.0027 26.0 4.5 34 100-134 36-69 (92)
52 KOG2987|consensus 22.9 38 0.00083 34.7 0.9 34 432-465 258-291 (324)
No 1
>PLN03078 Putative tRNA pseudouridine synthase; Provisional
Probab=100.00 E-value=6.3e-52 Score=439.32 Aligned_cols=325 Identities=17% Similarity=0.167 Sum_probs=247.2
Q ss_pred chhhhhhhhhhhhhcceeeeeeeeeccccHHHhhhcC--CCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCC
Q psy3604 80 VEDCYQRNWYKRAVTSVIGLVIKEVGGLSHDFCELAN--RQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPS 157 (496)
Q Consensus 80 ~~~~~~~~~y~r~~~~~i~~yL~~lG~sa~~~ae~ag--RTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~ 157 (496)
..+-+-..+.....++++++.|+|+|+.|+|||.+.+ ...++.+.++.||..+|...+.-.
T Consensus 56 ~~~~~~~~~w~~~~krrvaL~IaYdGt~Y~G~Q~Q~n~~~~~TVEg~LE~AL~k~~~I~e~n~----------------- 118 (513)
T PLN03078 56 NSDQGGGMKWESARKKKVVLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNY----------------- 118 (513)
T ss_pred ccCCCCCCCcccccceEEEEEEEEcCCCcceeeECCCCCCCCCHHHHHHHHHHHHhCcccccc-----------------
Confidence 3333445555566778889999999999999998876 245789999999998764211100
Q ss_pred CCCCCchhccccccCCCCCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEE
Q psy3604 158 TQPKPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWS 237 (496)
Q Consensus 158 ~~p~~~~fL~aG~~~~~p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~ 237 (496)
| .+..|--..++|||+||||++||++|+++.+ ...|..+.+...|...||++||+||||+++.
T Consensus 119 -----------~----~~~ki~~~rAgRTDkGVHA~gQVvsf~l~~p--~~~~~~d~~~~~L~~~LN~~LP~DIRVl~v~ 181 (513)
T PLN03078 119 -----------G----NLHKIGWARSSRTDKGVHSLATMISLKMEIP--ENAWKDDPDGIALAKFINSHLPDNIRVFSIL 181 (513)
T ss_pred -----------c----cccceeEEeeccCCcCccccccEEEEeccCc--chhccccchHHHHHHHHHhcCCCCeEEEEEE
Confidence 0 0001111346789999999999999998542 1111112334578899999999999999999
Q ss_pred ecCCCCCccccCCceeEEEecCCC-------------CccHHHHHHHHHHccccccccccccccccCC------------
Q psy3604 238 PVPEKYSARFDCLFRNYKYWFPQA-------------GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNG------------ 292 (496)
Q Consensus 238 ~V~~~FhARfsa~~R~Y~Y~~~~~-------------~LDie~M~eAak~fvGtHDF~nF~~~~~~~~------------ 292 (496)
+|+++|||||+|++|+|+|+||.. ..|+++|++|+++|+|+|||+|||.......
T Consensus 182 ~V~~~FhAR~sc~sRtY~Y~iP~~~~~~k~~f~~~~~~~dI~kMneAl~~fiGtHDFhNFT~r~~y~~~~~~~~~~~~~~ 261 (513)
T PLN03078 182 PAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFSSEEIDEHISEFNSILNGFEGEHPFHNYTARSKYRKKLPGKHKQRNGA 261 (513)
T ss_pred ECCCCcCCCCCCCceEEEEEEccccccCCCccchhhhHHHHHHHHHHHHhcccccCcccccCCCccCccccccccccccc
Confidence 999999999999999999999751 0279999999999999999999986531100
Q ss_pred -----------------------------------------------------------------------CCCceEEEE
Q psy3604 293 -----------------------------------------------------------------------VVNFKRLVT 301 (496)
Q Consensus 293 -----------------------------------------------------------------------~~stvRtI~ 301 (496)
..+..|.|+
T Consensus 262 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~wl~e~d~~d~i~~s~~R~I~ 341 (513)
T PLN03078 262 VSRRAKSSKEMSSSESEENHGEISEEDEEDLSFSSIPSGSSDENEDILKFQSSQVQIRARWLHEPDETDRISASHFRKIF 341 (513)
T ss_pred cccccccccccccccccccccccccchhhhhccccccccccccccccccccccchhhhhhhccCCccccccchhheEEEE
Confidence 003379999
Q ss_pred EEEEEec-----ceEEEEEEeeCce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCee
Q psy3604 302 HAGVTSA-----WQNVQFNDIKEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNEL 369 (496)
Q Consensus 302 ~i~i~~~-----~~~i~i~I~G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L 369 (496)
+|.+... .+++.|+|.|+|| | ||++++|++|..+++.|..+|....+ + .+|+|| ++||+|
T Consensus 342 ~~~~~~~~~~~g~~fv~i~I~GqSFmlhQIRKMIG~~~aV~rg~~~~~~i~~~L~~~~r--~---~~P~AP---~~GL~L 413 (513)
T PLN03078 342 RCSCGKLEKSLGFDFVELSIWGESFMLHQIRKMVGTAVAVKRELLPRDIIRLSLTKFSR--I---VLPLAP---SEVLIL 413 (513)
T ss_pred EeecCCccccCCceEEEEEEEehhHHHHHHHHHHHHHHHHHhccCCHHHHHHHhccccc--c---ccccCC---CcceEE
Confidence 9988542 2799999999999 8 99999999999999999999986433 2 345776 999999
Q ss_pred eeeccCCCCcccccchHHHH--HHHHHHHhhhhcccccccccchhhhhhhccccchhhcccCcccccccccccCCCCcch
Q psy3604 370 FRRVFLLSFLAWVDQYRIRQ--TAHCNIFTNLCTFYVPTYLPSLGEMIKDTVRESKCTMGDLDINHLIEGEFDSRPGRIL 447 (496)
Q Consensus 370 ~~V~Y~~~~l~f~~~~~~~~--~~~~~i~~~~~~~y~~~~lp~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 447 (496)
++|.|+..+..=......+. -..+.+.+.+.+||..+++|+|+++++.+.++|++|++||| +|++||+.||
T Consensus 414 ~~~~F~~yn~~~~~~~p~~~~~~e~e~~~~~i~eF~~~~i~p~i~~~~~~~~~~w~~w~~nl~-------~~~~~~~~~~ 486 (513)
T PLN03078 414 RGNSFSVRKKPGNIKRPGMETMNESEEILKGVEEFYRAVMLPQVSKFLDPSKPPWKEWVENLD-------RFTSIPDAQL 486 (513)
T ss_pred EeeeccccccccccCCCCccccccHHHHHHHHHHHHHHhhhHHHHHHhccccchHHHHHHHHH-------hhcCCCHHHH
Confidence 99999732111000111121 13334467778888899999999999999999999999999 9999999999
Q ss_pred hhhccc
Q psy3604 448 SETGKL 453 (496)
Q Consensus 448 ~e~~~~ 453 (496)
+|||+-
T Consensus 487 ~~v~~~ 492 (513)
T PLN03078 487 DEVRKA 492 (513)
T ss_pred HHHHHH
Confidence 999974
No 2
>PRK12434 tRNA pseudouridine synthase A; Reviewed
Probab=100.00 E-value=5.4e-48 Score=382.18 Aligned_cols=221 Identities=24% Similarity=0.256 Sum_probs=188.7
Q ss_pred ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCC
Q psy3604 95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPH 174 (496)
Q Consensus 95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~ 174 (496)
.+|++.|+|+|+.++|||.+.+...++.+.++.||..++.. + ..+.
T Consensus 2 ~~~~l~i~YdGt~y~G~Q~Q~~~~~TVq~~le~aL~~~~~~----------~----------------~~~~-------- 47 (245)
T PRK12434 2 RNIKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVLSEMTGE----------E----------------IEII-------- 47 (245)
T ss_pred ceEEEEEEECCCccceEeeCCCCCCCHHHHHHHHHHHHhCC----------C----------------eEEE--------
Confidence 46789999999999999998754456788888888875421 0 0112
Q ss_pred CCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeE
Q psy3604 175 PPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNY 254 (496)
Q Consensus 175 p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y 254 (496)
.++|||+||||++||++|+++..+ ++..+..+||+.||+||+|+++.+||++|||||+|++|+|
T Consensus 48 -------~agRTD~GVHA~~qv~~f~~~~~~---------~~~~l~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y 111 (245)
T PRK12434 48 -------GCGRTDAGVHALNQVANFQTDEKL---------SEDKIKKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTY 111 (245)
T ss_pred -------EeccCCCCcCccCcEEEEEcCCCC---------CHHHHHHHHHccCCCCeEEEEEEECCCCcccccCCCcEEE
Confidence 246799999999999999987643 5778999999999999999999999999999999999999
Q ss_pred EEecCC----------------CCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEee
Q psy3604 255 KYWFPQ----------------AGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIK 318 (496)
Q Consensus 255 ~Y~~~~----------------~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G 318 (496)
+|+|+. .++|+++|++|++.|+|+|||+|||+.+ +..++++|+|+++++.+.++++.|+|+|
T Consensus 112 ~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~~~~--~~~~~~~R~I~~~~v~~~~~~~~i~i~g 189 (245)
T PRK12434 112 LYKIWNEKFHNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFTSFTNAK--SKKKSTVREIYSIDIMEEDGFVQIRVSG 189 (245)
T ss_pred EEEEccCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcCHHhhcCCC--CCCCCCEEEEEEEEEEEeCCEEEEEEEe
Confidence 999852 4689999999999999999999999764 2357999999999999888899999999
Q ss_pred Cce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604 319 EVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF 374 (496)
Q Consensus 319 ~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y 374 (496)
+|| | ||+|++||+|++++++|+++|+.+++ .. ..|+|||+||+|++|.|
T Consensus 190 ~~FL~~mVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r--~~-----~~~~APa~GL~L~~V~Y 245 (245)
T PRK12434 190 NGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDR--NQ-----ANCTAPASGLYLENVEY 245 (245)
T ss_pred cHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCc--cc-----CCCccCCCCCEEeEeEC
Confidence 999 7 99999999999999999999997543 21 12356699999999998
No 3
>COG0101 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.3e-48 Score=384.06 Aligned_cols=227 Identities=23% Similarity=0.266 Sum_probs=194.9
Q ss_pred eeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCC
Q psy3604 96 VIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHP 175 (496)
Q Consensus 96 ~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p 175 (496)
+|++.|+|+|+.++|||.|++- .++.++++.||..++.... .+..+
T Consensus 3 ri~l~iaYdGt~f~G~Q~Qp~~-~TVQ~~le~aL~~i~~~~~--------------------------~i~~A------- 48 (266)
T COG0101 3 RIALKIAYDGTRFHGWQRQPNV-RTVQGELEKALSKIGGESV--------------------------RVIGA------- 48 (266)
T ss_pred eEEEEEEEcCCceeeeccCCCC-CCHHHHHHHHHHHhcCCcc--------------------------eeEEe-------
Confidence 7899999999999999999774 5688889999998775311 12333
Q ss_pred CCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEE
Q psy3604 176 PHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK 255 (496)
Q Consensus 176 ~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~ 255 (496)
.|||+||||.+||+||+++... .+..|..+||+.||+||+|+++++||++|||||+|.+|+|+
T Consensus 49 --------GRTD~GVHA~gqv~hfd~~~~~---------~~~~~~~~lN~~Lp~dI~V~~~~~v~~~FhaRfsa~~R~Y~ 111 (266)
T COG0101 49 --------GRTDAGVHALGQVVHFDTPADR---------PLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYR 111 (266)
T ss_pred --------cCCCcCccccccEEEEEcCCcc---------cHHHHHHHHHhcCCCCcEEEEEEECCCCCCCcccccceEEE
Confidence 4699999999999999987643 37899999999999999999999999999999999999999
Q ss_pred EecCC----------------CCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeC
Q psy3604 256 YWFPQ----------------AGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKE 319 (496)
Q Consensus 256 Y~~~~----------------~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~ 319 (496)
|+|+. .+||+++|++|++.|+|+|||+|||+.+. +..|++|+|++++|.+.++.+.|+|+|+
T Consensus 112 Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~aa~~l~G~HDF~sF~~~~~--~~~s~vRti~~~~v~~~~~~i~i~i~g~ 189 (266)
T COG0101 112 YIIYNAPLRPPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFTSFRKAGC--QSKSPVRTIYRIDVSRDGDLIVIDISGN 189 (266)
T ss_pred EEEcCccCCChhhhcccccccCcCCHHHHHHHHHHccccccchhhccCCC--ccCCCeEEEEEEEEEecCCEEEEEEEeC
Confidence 99863 35799999999999999999999999753 3458999999999999999999999999
Q ss_pred ce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccCCCCccccc
Q psy3604 320 VV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVD 383 (496)
Q Consensus 320 sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~~~~l~f~~ 383 (496)
|| | ||+|++||+|++++++|.++|+.+++. . ..+ +|||+||+|++|.|+ +..++..
T Consensus 190 sFL~~mVR~iVg~l~~vg~g~~~~~~i~~ll~~~~r~--~--~~~---~Apa~GL~L~~v~Y~-~~~~~~~ 252 (266)
T COG0101 190 SFLWHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRK--L--AGP---TAPAEGLYLVRVDYP-EDFELPE 252 (266)
T ss_pred hhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhccCcc--c--CCC---CCCCCccEEEeeccC-Ccccccc
Confidence 99 7 999999999999999999999964432 2 233 556999999999997 3344443
No 4
>PRK14589 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=1.1e-47 Score=383.49 Aligned_cols=249 Identities=21% Similarity=0.260 Sum_probs=203.6
Q ss_pred eeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCC
Q psy3604 96 VIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHP 175 (496)
Q Consensus 96 ~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p 175 (496)
+|++.|+|+|+.++|||.+.+ ..++.+.++.||..++... +.. + ..+
T Consensus 2 ~~~l~i~YdGt~y~G~Q~Q~~-~~TVq~~Le~aL~~~~~~~-~~~-----~----------------~~i---------- 48 (265)
T PRK14589 2 RLAFRISYIGTRFFGSQYQPD-QRTVEGEFIAACRRLGLFS-DWR-----E----------------AGF---------- 48 (265)
T ss_pred cEEEEEEEcCCCeeeeeeCCC-CCCHHHHHHHHHHHhhCcc-CCc-----e----------------eeE----------
Confidence 578899999999999999887 3467888889998877421 000 0 011
Q ss_pred CCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEE
Q psy3604 176 PHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK 255 (496)
Q Consensus 176 ~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~ 255 (496)
..++|||+||||++||++|+++. +..+...||+.||+||+|+++.+|+++|||||+|++|+|+
T Consensus 49 -----~~agRTDaGVHA~gqv~~f~~~~------------~~~~~~~lN~~LP~dI~V~~~~~v~~~FhAR~~a~~R~Y~ 111 (265)
T PRK14589 49 -----ALAGRTDRGVHARGQVLAFSTHK------------PERAVEALNGQLPPDIWCTGWAEVPESFHPRYDAISRTYR 111 (265)
T ss_pred -----EEeccCCcCccccccEEEEEeCC------------hHHHHHHHHhhCCCCeEEEEEEEcCCCCCcccCCceeEEE
Confidence 23567999999999999999752 4578899999999999999999999999999999999999
Q ss_pred EecCCCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce-----e--hhHHHH
Q psy3604 256 YWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-----D--SEPSFK 328 (496)
Q Consensus 256 Y~~~~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-----R--VGtLv~ 328 (496)
|+|+..++|+++|++|++.|+|+|||+|||+.+ .++++|+|+++++.+.++.+.|+|+|+|| | ||+|++
T Consensus 112 Y~i~~~~lD~~~m~~a~~~f~G~HDF~~F~~~~----~~~~vRtI~~i~v~~~~~~~~~~i~G~~FL~~mVR~mVG~ll~ 187 (265)
T PRK14589 112 YYFSRPPSDINAMRDAAGEFIGTHDFSCFARVE----GKSPVRTILRIRVFSDGGFPVFEVTAQSFLWHMVRCMAGALLQ 187 (265)
T ss_pred EEEecCccHHHHHHHHHHHccCCccHHHHhccC----CCCCeEEEEEEEEEEeCCEEEEEEEechhHHHHHHHHHHHHHH
Confidence 999989999999999999999999999999863 46899999999999988899999999999 7 999999
Q ss_pred HhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccCCCCcccccchHHHHH----HHHHHHhhhhcccc
Q psy3604 329 KGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQT----AHCNIFTNLCTFYV 404 (496)
Q Consensus 329 VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~~~~l~f~~~~~~~~~----~~~~i~~~~~~~y~ 404 (496)
||+|++++++|+++|+.+++. ..+ +|||+||+|++|.|+. +|....++... ++.+.+...+.++.
T Consensus 188 vg~G~~~~~~i~~~L~~~~r~-----~~~---~APa~GL~L~~V~Y~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 256 (265)
T PRK14589 188 IGEGEMEPDDIERLLSGPCKR-----KVK---PAPAEGLVLWDVDCGL---TFTPIPADPRSVRRIARQRREAHLMETVY 256 (265)
T ss_pred HhCCCCCHHHHHHHHhCcCCC-----CCC---ccCCCCcEEeeeecCC---ccccccchHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999975432 122 4569999999999962 77766555421 33334444555555
Q ss_pred ccccc
Q psy3604 405 PTYLP 409 (496)
Q Consensus 405 ~~~lp 409 (496)
..+||
T Consensus 257 ~~~~~ 261 (265)
T PRK14589 257 ALLLP 261 (265)
T ss_pred HHhcc
Confidence 56665
No 5
>cd02569 PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like. This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya.
Probab=100.00 E-value=3.3e-47 Score=378.68 Aligned_cols=233 Identities=35% Similarity=0.542 Sum_probs=188.4
Q ss_pred eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCCCCCC
Q psy3604 100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIP 179 (496)
Q Consensus 100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p~hIP 179 (496)
.|+|+|+.|+|||.+.+...++.+.++.||..++.--+. . + ..+.
T Consensus 2 ~i~YdGt~y~G~Q~Q~~~~~TVq~~Le~aL~~~~~i~~~-~-----~----------------~~~~------------- 46 (256)
T cd02569 2 RFAYLGWNYNGFAVQEETTNTVEETLFEALEKTRLIEDR-Q-----T----------------SNYS------------- 46 (256)
T ss_pred EEEEeCCcceeeeECCCCCCCHHHHHHHHHHHhcCCCCC-C-----c----------------eeEE-------------
Confidence 689999999999998763356888889999987631000 0 0 1111
Q ss_pred CCCCCCCCcccccccceEEEeecccCCCCC---C------CCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCC
Q psy3604 180 PYLPLFPDPHAYIRTPVVTLKIRSKLTSPG---E------ESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCL 250 (496)
Q Consensus 180 ~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~---~------~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~ 250 (496)
.++|||+||||++||++|++...++... + ........+..+||++||+||+|+++.+|+++|||||+|+
T Consensus 47 --~agRTD~GVHA~~qv~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~ 124 (256)
T cd02569 47 --RCGRTDKGVSAFGQVISLDVRSNLKPEDGLDPSTDVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSARFSCV 124 (256)
T ss_pred --eecccCccccccCcEEEEEecCCCCccccccccccccccccchHHHHHHHHHhhCCCCcEEEEEEECCCCcCCCccCC
Confidence 3467999999999999999976542210 0 0011224688999999999999999999999999999999
Q ss_pred ceeEEEecCCCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecc------eEEEEEEeeCce---
Q psy3604 251 FRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAW------QNVQFNDIKEVV--- 321 (496)
Q Consensus 251 ~R~Y~Y~~~~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~------~~i~i~I~G~sF--- 321 (496)
+|+|+|+|+...+|+++|++|+++|+|+|||+|||+.+.+++.++++|+|++++|.+.+ +++.|+|+|+||
T Consensus 125 ~R~Y~Y~i~~~~ldi~~m~~a~~~f~G~HDF~~F~~~~~~~~~~~~~RtI~~~~v~~~~~~~~~~~~~~~~i~g~~FL~~ 204 (256)
T cd02569 125 SRTYRYFFPKGDLDIELMRKAAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFLWH 204 (256)
T ss_pred ceEEEEEecCCCCCHHHHHHHHHHhhCCcchHHHhccCcccCCCCCceEEEEEEEEEccCCCCCCcEEEEEEEEcHHHHH
Confidence 99999999999999999999999999999999999864333457999999999998864 789999999999
Q ss_pred --e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604 322 --D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF 374 (496)
Q Consensus 322 --R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y 374 (496)
| ||+|++||+|++++++|+++|+.+.+...+ .++ +|||+||+|++|.|
T Consensus 205 mVR~mvg~ll~vg~G~~~~~~i~~~L~~~~r~~~~--~~~---~Ap~~GL~L~~v~~ 256 (256)
T cd02569 205 QVRCMMAVLFLIGQGLEPPSVISQLLDVEKNPRKP--QYT---MASEVPLVLYDCGF 256 (256)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHhCccccCCC--CcC---cCCCCCcEEEEeeC
Confidence 7 999999999999999999999986543322 112 45699999999987
No 6
>PRK00021 truA tRNA pseudouridine synthase A; Validated
Probab=100.00 E-value=6.5e-47 Score=374.08 Aligned_cols=220 Identities=25% Similarity=0.293 Sum_probs=189.3
Q ss_pred ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCC
Q psy3604 95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPH 174 (496)
Q Consensus 95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~ 174 (496)
.++++.|+|+|+.++|||.+.+ ..++.+.++.||..++.. . ..+..
T Consensus 2 ~~~~l~i~YdGt~y~G~q~q~~-~~TVq~~le~aL~~~~~~--~------------------------~~~~~------- 47 (244)
T PRK00021 2 MRIALTIEYDGTNFHGWQRQPN-GRTVQGELEKALSKLAGE--P------------------------VRVIG------- 47 (244)
T ss_pred eEEEEEEEECCCccceeeeCCC-CCCHHHHHHHHHHHHhCC--C------------------------eEEEE-------
Confidence 4678999999999999999877 347888889999987751 0 11222
Q ss_pred CCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeE
Q psy3604 175 PPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNY 254 (496)
Q Consensus 175 p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y 254 (496)
++|||+||||++||++|+++..+ ++..+...||+.||+||+|+++.+||++|||||+|++|+|
T Consensus 48 --------agRTD~GVHA~~qvv~~~~~~~~---------~~~~~~~~lN~~Lp~dI~V~~~~~v~~~F~aR~~a~~R~Y 110 (244)
T PRK00021 48 --------AGRTDAGVHALGQVAHFDTPAPR---------PPEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRY 110 (244)
T ss_pred --------EccCCCcccccCcEEEEEeCCCC---------CHHHHHHHHHhcCCCCEEEEEeEecCCCcCcCcCCCceEE
Confidence 45799999999999999997643 6778999999999999999999999999999999999999
Q ss_pred EEecCCC----------------CccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEee
Q psy3604 255 KYWFPQA----------------GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIK 318 (496)
Q Consensus 255 ~Y~~~~~----------------~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G 318 (496)
+|+++.. .+|+++|++|++.|+|+|||+|||+.+ .+.++++|+|.+++|.++++++.|+|+|
T Consensus 111 ~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~a~~~~~G~HdF~~F~~~~--~~~~~~~R~I~~~~v~~~~~~~~i~i~g 188 (244)
T PRK00021 111 RYRIYNRPARPPFLRGYVWHYPYPLDVDAMNEAAQYLLGEHDFTSFRASG--CQSKSPVRTIYEADVTREGDFIVFDISA 188 (244)
T ss_pred EEEEecCCCCChhhCCcEEEeCCCCcHHHHHHHHHHhcCceeeeeeeCCC--CCCCCCeEEEEEEEEEEcCCEEEEEEEE
Confidence 9998743 489999999999999999999998653 3467999999999999888899999999
Q ss_pred Cce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604 319 EVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF 374 (496)
Q Consensus 319 ~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y 374 (496)
+|| | ||+|++||+|++++++|+++|+.+.+. . ..+ +|||+||+|++|.|
T Consensus 189 ~sFL~~qVR~mvg~l~~vg~g~~~~~~i~~~L~~~~~~--~--~~~---~APa~GL~L~~v~Y 244 (244)
T PRK00021 189 NGFLHNMVRNIVGTLLEVGKGKRPPEDIKELLEAKDRT--L--AGP---TAPAEGLYLVEVDY 244 (244)
T ss_pred chhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcc--c--CCC---ccCCCCCEEeeeEC
Confidence 999 7 999999999999999999999975432 2 223 45699999999988
No 7
>cd00497 PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudouridine synthase, TruA family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae PUS1 catalyzes the formation of psi34 and psi36 in the intron containing tRNAIle, psi35 in the intron containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44 in U2 snRNA and, psi38 and psi39 in tRNAs are highly ph
Probab=100.00 E-value=5.2e-47 Score=370.64 Aligned_cols=217 Identities=35% Similarity=0.542 Sum_probs=184.7
Q ss_pred eeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCCCCCCC
Q psy3604 101 IKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIPP 180 (496)
Q Consensus 101 L~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p~hIP~ 180 (496)
|+|+|+.++|||.+.+- .++.+.++.||..++.. +++. + ..+
T Consensus 1 i~YdGt~f~G~Q~Q~~~-~TVq~~le~aL~~~~~~-~~~~-----~----------------~~i--------------- 42 (224)
T cd00497 1 IAYDGWKYHGFQRQPDV-PTVEGELFKALLKTGLI-ESPK-----P----------------SNY--------------- 42 (224)
T ss_pred CEEcCCceeeEeeCcCC-CCHHHHHHHHHHHhhCc-CCCc-----c----------------eeE---------------
Confidence 58999999999999773 46888899999887642 1100 0 112
Q ss_pred CCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEEEecCC
Q psy3604 181 YLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQ 260 (496)
Q Consensus 181 ~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~~ 260 (496)
..++|||+||||++||++|+++..+ + .+...||+.||+||+|+++.+|+++|||||+|++|+|+|+++.
T Consensus 43 ~~agRTD~GVHA~~qv~~~~~~~~~---------~--~~~~~lN~~Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~~ 111 (224)
T cd00497 43 SRAGRTDKGVSALGQVVSLETRSKL---------K--PYPDILNGLLPKDIRVLAWAPVPEDFHARFSCVSRTYRYYFPG 111 (224)
T ss_pred EEeccccccccccccEEEEEECCCc---------H--HHHHHHHhhCCCCcEEEEEEEeCCCCCCCcccCeEEEEEEECC
Confidence 2356799999999999999997543 1 7999999999999999999999999999999999999999998
Q ss_pred CCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce-----e--hhHHHHHhCCC
Q psy3604 261 AGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-----D--SEPSFKKGQGN 333 (496)
Q Consensus 261 ~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-----R--VGtLv~VG~G~ 333 (496)
..+|+++|++|++.|+|+|||+|||+.+. ..++++|+|.++++.+.++++.|+|+|+|| | ||+|++||+|+
T Consensus 112 ~~~d~~~m~~a~~~f~G~HDF~~F~~~~~--~~~~~~RtI~~~~v~~~~~~~~i~i~g~sFL~~mVR~mvg~ll~vg~g~ 189 (224)
T cd00497 112 GDLDIEAMREAAKLLLGTHDFRNFCKKDG--RKKNPVRTIISAEVEEVDDFYVFEVKGKSFLWHQVRRIVAALFLVGQGL 189 (224)
T ss_pred CCcCHHHHHHHHHHccCcccHHHhcCCCC--CCCCCeEEEEEEEEEecCCEEEEEEEEcHHHHHHHHHHHHHHHHHhCCC
Confidence 89999999999999999999999998642 347999999999999888899999999999 6 99999999999
Q ss_pred CCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604 334 EKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF 374 (496)
Q Consensus 334 ~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y 374 (496)
+++++|+++|+.+.+...+ .++|||+||+|++|.|
T Consensus 190 ~~~~~i~~~l~~~~~~~~~------~~~APa~GL~L~~V~Y 224 (224)
T cd00497 190 EPPSIISRLLDEEKRPSKP------QYPAPPEPLVLWDCKY 224 (224)
T ss_pred CCHHHHHHHHhcCCcccCC------CCcCCCCCcEEeeeeC
Confidence 9999999999875432211 1246699999999988
No 8
>PRK14588 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=1.1e-46 Score=377.98 Aligned_cols=227 Identities=19% Similarity=0.198 Sum_probs=191.0
Q ss_pred ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCC
Q psy3604 95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPH 174 (496)
Q Consensus 95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~ 174 (496)
++|++.|+|+|+.++|||.+.+- .++.+.++.||..+.-. + ..+.
T Consensus 2 ~~~~l~iaYdGt~f~G~Q~Q~~~-~TVq~~Le~aL~~l~~~----------~----------------i~i~-------- 46 (272)
T PRK14588 2 RTIALLLEYDGTDFAGSQWQTDG-RTVQGALEAAWQALTQE----------R----------------RRIV-------- 46 (272)
T ss_pred ceEEEEEEEcCCceeeeEECCCC-CCHHHHHHHHHHHhhCC----------C----------------ceEE--------
Confidence 46899999999999999998772 35677777888765310 0 0112
Q ss_pred CCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeE
Q psy3604 175 PPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNY 254 (496)
Q Consensus 175 p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y 254 (496)
.++|||+||||++||++|+++..+ ++..+...||+.||+||+|+++.+|+++|||||+|++|+|
T Consensus 47 -------~AgRTDaGVHA~gQv~~f~~~~~~---------~~~~l~~~LN~~LP~dI~V~~v~~v~~~FhaR~~a~~R~Y 110 (272)
T PRK14588 47 -------LAGRTDAGVHARGQVAHVQTDTRH---------SLATIWRGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREY 110 (272)
T ss_pred -------EecCCCcCcCccccEEEEEcCCCC---------CHHHHHHHHHhcCCCCeEEEEEEECCCCcCcccCCCcEEE
Confidence 346799999999999999986543 5778999999999999999999999999999999999999
Q ss_pred EEecCC----------------CCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEec----ceEEEE
Q psy3604 255 KYWFPQ----------------AGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSA----WQNVQF 314 (496)
Q Consensus 255 ~Y~~~~----------------~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~----~~~i~i 314 (496)
+|+|+. ..+|+++|++|++.|+|+|||+|||+.. ..++++|+|+++++.+. ++.+.|
T Consensus 111 ~Y~i~~~~~~~p~~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F~~~~---~~~~~vRtI~~~~~~~~~~~~~~~i~~ 187 (272)
T PRK14588 111 RYVIDCAPAPSPQLRHQVLHYAGTLDVAAMDAALKLLIGTHDFAAFTTAP---QEGSTVRTCYWARCTDTEWFGRPLLAI 187 (272)
T ss_pred EEEEcCCCCCChhhcCceEecCCCCCHHHHHHHHHHccCCcchHhhcCCC---CCCCCeEEEEEEEEEEcccCCCCEEEE
Confidence 999852 4689999999999999999999999862 35789999999999875 368999
Q ss_pred EEeeCce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccCCCCcccc
Q psy3604 315 NDIKEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWV 382 (496)
Q Consensus 315 ~I~G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~~~~l~f~ 382 (496)
+|+|+|| | ||+|++||+|++++++|+++|+.+++ .. ..|+|||+||+|++|.|++..+.|.
T Consensus 188 ~i~g~~FL~~mVR~mVg~ll~vg~g~~~~~~i~~~L~~~~r--~~-----~~~~APa~GL~L~~V~Y~~~~~~~~ 255 (272)
T PRK14588 188 EVAANAFLQHMVRNIVGTLLLVGRGRMTVDQFGAVLASRDR--RL-----AGPTAPAHGLYLTAVRYPPGLIRWV 255 (272)
T ss_pred EEEEchhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCc--cc-----CCCCCCCCCcEEeeEecCchhcccc
Confidence 9999999 7 99999999999999999999987543 22 2235569999999999987777776
No 9
>TIGR00071 hisT_truA pseudouridylate synthase I. universal so far, single copy in all prokaryotes, 3 in yeast. Trusted cutoff for orthology is about 100 based on 1 match only in complete prokaryote with length 200.
Probab=100.00 E-value=2.8e-46 Score=366.11 Aligned_cols=214 Identities=25% Similarity=0.335 Sum_probs=184.7
Q ss_pred eeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCC
Q psy3604 96 VIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHP 175 (496)
Q Consensus 96 ~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p 175 (496)
++++.|+|+|+.++|||.+.+ ..++.+.++.||..++.. + ..+.
T Consensus 2 ~~~l~i~YdGt~f~G~Q~Q~~-~~TVq~~le~aL~~~~~~----------~----------------i~~~--------- 45 (227)
T TIGR00071 2 KIALKIAYDGSNYHGWQRQPN-KRTVQGELEKALEAIGKK----------K----------------ITIM--------- 45 (227)
T ss_pred eEEEEEEEcCCCeeEEeECcC-CCCHHHHHHHHHHHHhCC----------C----------------eeEE---------
Confidence 568899999999999999987 346788888999886641 0 0112
Q ss_pred CCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEE
Q psy3604 176 PHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK 255 (496)
Q Consensus 176 ~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~ 255 (496)
.++|||+||||++||++|+++..+ ++..+..+||++||+||+|+++.+|+++|||||+|++|+|+
T Consensus 46 ------~agRTD~GVHA~~qv~~f~~~~~~---------~~~~~~~~lN~~Lp~dI~V~~~~~v~~~FhaR~~a~~R~Y~ 110 (227)
T TIGR00071 46 ------SAGRTDKGVHAMGQVISFDTPKEI---------PDNKLNAKLNALLPPDIRVKALAPVNDNFHARFSASKRHYR 110 (227)
T ss_pred ------eeccCcCCccccccEEEEEecCCC---------CHHHHHHHHHccCCCCEEEEEEEeCCCCcCCCCCCCcEEEE
Confidence 345799999999999999997643 56789999999999999999999999999999999999999
Q ss_pred EecCCC-----CccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce-----e--h
Q psy3604 256 YWFPQA-----GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-----D--S 323 (496)
Q Consensus 256 Y~~~~~-----~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-----R--V 323 (496)
|+|+.. .+|+++|++|++.|+|+|||+|||+.. .+.++++|+|++++|.+.++++.|+|+|+|| | |
T Consensus 111 Y~i~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~~~~--~~~~~~~R~i~~~~v~~~~~~~~i~i~g~~FL~~mVR~mv 188 (227)
T TIGR00071 111 YILYNHRHYYSPLDLEKMRAAAKQLLGKHDFSNFSKAK--SKSRSPIRTISDIKVSESGEYIIFDIIGNSFLWHMVRKIV 188 (227)
T ss_pred EEEccCcccCCCCCHHHHHHHHHHccCcccHHHhcCCC--CCCCCCeEEEEEEEEEEcCCEEEEEEEecHHHHHHHHHHH
Confidence 999865 699999999999999999999999764 3467999999999999988999999999999 7 9
Q ss_pred hHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCee
Q psy3604 324 EPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNEL 369 (496)
Q Consensus 324 GtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L 369 (496)
|+|++||+|++++++|+++|+.+++... .|+|||+||+|
T Consensus 189 g~l~~vg~g~~~~~~i~~~L~~~~r~~~-------~~~APa~GL~L 227 (227)
T TIGR00071 189 GALVLVGRGKLPPEWVAKLLDAKKRNLA-------PTTAPANGLYL 227 (227)
T ss_pred HHHHHHHCCCCCHHHHHHHHhcCCcccC-------CCCCCCCCCcC
Confidence 9999999999999999999987553221 23456999998
No 10
>PRK14586 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=4e-46 Score=368.83 Aligned_cols=220 Identities=22% Similarity=0.250 Sum_probs=185.1
Q ss_pred ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCC
Q psy3604 95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPH 174 (496)
Q Consensus 95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~ 174 (496)
.+|++.|+|+|+.++|||.+.+ ..++.+.++.||..+.-. + -.+.
T Consensus 2 ~~~~l~i~YdGt~f~G~Q~Q~~-~~TVq~~le~aL~~~~~~----------~----------------i~~~-------- 46 (245)
T PRK14586 2 KRVAAVVSYDGSNFFGYQGQPD-VRTVQGVFEDALERIFKQ----------R----------------IYTQ-------- 46 (245)
T ss_pred eEEEEEEEEcCCceeeEEECCC-CCCHHHHHHHHHHHHhCC----------C----------------eeEE--------
Confidence 4689999999999999999987 236777788888775310 0 0122
Q ss_pred CCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeE
Q psy3604 175 PPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNY 254 (496)
Q Consensus 175 p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y 254 (496)
.++|||+||||++||++|+++.. ..++..+..+||++||+||+|+++.+||++|||||+|++|+|
T Consensus 47 -------~agRTD~GVHA~~qv~~f~~~~~--------~~~~~~l~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y 111 (245)
T PRK14586 47 -------AAGRTDTGVHANGQVIAFNCPND--------RMTEEDIKNAMNANLPDDIYVKKVFEVPKNFHPRFDAKKRIY 111 (245)
T ss_pred -------EecCCccCCCccCcEEEEEecCC--------cCCHHHHHHHHHccCCCCeEEEEEEECCCCcCcccCCCcEEE
Confidence 24579999999999999998754 136789999999999999999999999999999999999999
Q ss_pred EEecCC----------------CCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEe-cceEEEEEEe
Q psy3604 255 KYWFPQ----------------AGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTS-AWQNVQFNDI 317 (496)
Q Consensus 255 ~Y~~~~----------------~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~-~~~~i~i~I~ 317 (496)
+|+|+. .++|+++|++|++.|+|+|||+|| +.. .+.++++|+|+++++.+ .++.+.|+|+
T Consensus 112 ~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~~~l~G~HDF~~F-~~~--~~~~~~vR~I~~~~~~~~~~~~i~~~i~ 188 (245)
T PRK14586 112 HYFILTSKEKNVFLRKYVWWFPYELDLEAMRKAAKYLEGEHDFTSF-KTG--SDERNPVRTIYRIRILRLKKDLILIRVE 188 (245)
T ss_pred EEEEecCCCCChhhCCceEEeCCCCCHHHHHHHHHHccCcchHHhh-cCC--CCCCCCcEEEEEEEEEEccCCEEEEEEE
Confidence 999852 368999999999999999999999 432 34679999999999988 4788999999
Q ss_pred eCce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604 318 KEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF 374 (496)
Q Consensus 318 G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y 374 (496)
|+|| | ||+|++||+|++++++|.++|+.+++. . ..++|||+||+|++|.|
T Consensus 189 g~~FL~~mVR~mvg~l~~vg~g~~~~~~i~~~L~~~~r~--~-----~~~~APa~GL~L~~v~f 245 (245)
T PRK14586 189 GRSFLRRMVRNIVGALVKVGLGQWEPEKIKEVLEARDRS--K-----AAGTAPAHGLYLYKVLF 245 (245)
T ss_pred echhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcc--c-----CCCccCCCCCEEeEeEC
Confidence 9999 7 999999999999999999999976532 1 12356699999999987
No 11
>cd02570 PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA. psi38 and psi39 in tRNAs are highly phylogenetically conserved. P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators.
Probab=100.00 E-value=7.4e-46 Score=365.34 Aligned_cols=215 Identities=23% Similarity=0.304 Sum_probs=185.2
Q ss_pred eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCCCCCC
Q psy3604 100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIP 179 (496)
Q Consensus 100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p~hIP 179 (496)
.|+|+|+.++|||.+.+ ..++.+.++.||..++.. + ..+..
T Consensus 2 ~i~Y~Gt~f~G~q~q~~-~~TVq~~le~aL~~~~~~----------~----------------~~i~~------------ 42 (239)
T cd02570 2 TIEYDGTNFSGWQRQPN-GRTVQGELEKALSKIAGE----------P----------------VRVIG------------ 42 (239)
T ss_pred EEEEeCCccceeeeCCC-CCCHHHHHHHHHHHHhCC----------C----------------eEEEE------------
Confidence 58999999999999987 357888888999887631 0 12222
Q ss_pred CCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEEEecC
Q psy3604 180 PYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFP 259 (496)
Q Consensus 180 ~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~ 259 (496)
++|||+||||++||++|+++..+ ++..+...||+.||+||+|+++.+|+++|||||+|++|+|+|+|+
T Consensus 43 ---agRTD~GVHA~~qvv~~~~~~~~---------~~~~~~~~lN~~Lp~dI~v~~i~~v~~~F~aR~~a~~R~Y~Y~i~ 110 (239)
T cd02570 43 ---AGRTDAGVHALGQVAHFDTPSEI---------PLEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRIL 110 (239)
T ss_pred ---ECcCCCCcCccccEEEEEECCCC---------CHHHHHHHHHccCCCCEEEEEEEECCCCcCcccCCCceEEEEEEc
Confidence 45799999999999999997643 577899999999999999999999999999999999999999997
Q ss_pred CC----------------CccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce--
Q psy3604 260 QA----------------GLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-- 321 (496)
Q Consensus 260 ~~----------------~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-- 321 (496)
.. .+|+++|++|++.|+|+|||+|||+.+. ..++++|+|+++++.+.++++.|+|+|+||
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~d~~~m~~a~~~f~G~HdF~~F~~~~~--~~~~~~R~I~~~~v~~~~~~~~i~i~g~sFL~ 188 (239)
T cd02570 111 NRPVPSPFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFRAAGC--QSKSTVRTIYRADVYREGDLIVFEIRANGFLY 188 (239)
T ss_pred cCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcchhhhCCCCC--CCCCCeEEEEEEEEEEeCCEEEEEEEEcHHHH
Confidence 43 6899999999999999999999998642 357999999999999888899999999999
Q ss_pred ---e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604 322 ---D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF 374 (496)
Q Consensus 322 ---R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y 374 (496)
| ||+|++||+|++++++|+++|+.+.+. . . .|+|||+||+|++|.|
T Consensus 189 ~qVR~mvg~ll~vg~g~~~~~~i~~~l~~~~~~--~--~---~~~APa~GL~L~~v~Y 239 (239)
T cd02570 189 HMVRNIVGTLLEVGRGKLSPEDIKEILEAKDRT--A--A---GPTAPAHGLYLVKVEY 239 (239)
T ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcc--c--C---CCCcCCCCCEEeeeEC
Confidence 7 999999999999999999999865432 1 1 2345699999999988
No 12
>cd02866 PseudoU_synth_TruA_Archea PseudoU_synth_archea: Pseudouridine synthase,. This group consists of archealpseudouridine synthases.Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. This group of proteins make Psedouridine in tRNAs.
Probab=100.00 E-value=6.4e-46 Score=362.26 Aligned_cols=213 Identities=24% Similarity=0.334 Sum_probs=181.2
Q ss_pred eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCCCCCC
Q psy3604 100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIP 179 (496)
Q Consensus 100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p~hIP 179 (496)
.|+|+|+.++|||.+.+ ..++.+.++.||..++... +- .+ ..+
T Consensus 2 ~i~Y~Gt~y~G~q~q~~-~~TVq~~le~aL~~~~~~~-~~-----~~----------------i~~-------------- 44 (221)
T cd02866 2 KVAYDGTPYHGFQRQPD-VRTVEGELIKALRRLGIIE-SP-----KR----------------PRL-------------- 44 (221)
T ss_pred EEEEeCCceeeeeeCCC-CCCHHHHHHHHHHHhhccc-cC-----Cc----------------eEE--------------
Confidence 58999999999999987 3467777888888775321 00 00 112
Q ss_pred CCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEEEecC
Q psy3604 180 PYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFP 259 (496)
Q Consensus 180 ~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~ 259 (496)
..++|||+||||++||++|+++.. . +..+||+.||+||+|+++.+||++|||||+|++|+|+|+++
T Consensus 45 -~~agRTD~GVHA~~qv~~f~~~~~------------~-~~~~lN~~LP~dI~v~~~~~v~~~F~ar~~a~~r~Y~Y~i~ 110 (221)
T cd02866 45 -YSAGRTDAGVSALGNVVAFETEKE------------L-TPPAINNALPKDIRVWAWAKVPEDFHPRRDARRRYYRYYLG 110 (221)
T ss_pred -EEEcCCccccCccccEEEEEeCcH------------H-HHHHHHhhCCCCEEEEEEEEeCCCCCCCccCCeEEEEEEEC
Confidence 235679999999999999998631 1 78999999999999999999999999999999999999999
Q ss_pred CCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce-----e--hhHHHHHhCC
Q psy3604 260 QAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-----D--SEPSFKKGQG 332 (496)
Q Consensus 260 ~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-----R--VGtLv~VG~G 332 (496)
...+|+++|++|++.|+|+|||+|||+.+ ..+++|+|+++++.+.++++.|+|+|+|| | ||+|++||+|
T Consensus 111 ~~~ld~~~m~~a~~~~~G~HDF~~F~~~~----~~~~~R~I~~~~~~~~~~~~~~~i~g~~FL~~mVR~mvg~ll~vg~g 186 (221)
T cd02866 111 AEDYDVEAMAEAAKKLIGTHDFSNFSKRD----GRDPVRTIERIEIRENGEFLVIDVVGESFLWNMVRRIVGALSLVGKG 186 (221)
T ss_pred CCcCCHHHHHHHHHHhcCCcCHHHhhCCC----CCCCcEEEEEEEEEEcCCEEEEEEEEcHHHHHHHHHHHHHHHHHhCC
Confidence 88999999999999999999999999853 13899999999999888999999999999 7 9999999999
Q ss_pred CCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604 333 NEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF 374 (496)
Q Consensus 333 ~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y 374 (496)
++++++|+++|+.+.+... .++|||+||+|++|.|
T Consensus 187 ~~~~~~i~~~l~~~~~~~~-------~~~APa~GL~L~~v~Y 221 (221)
T cd02866 187 KRENEWVDKLLDGEFRKKD-------GVPAPPEGLILVDVKY 221 (221)
T ss_pred CCCHHHHHHHHhCCCcccC-------CCCCCCCCcEEEEeeC
Confidence 9999999999997553221 2246699999999988
No 13
>PRK14587 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=6.7e-45 Score=361.54 Aligned_cols=224 Identities=22% Similarity=0.212 Sum_probs=186.0
Q ss_pred eeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCC
Q psy3604 96 VIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHP 175 (496)
Q Consensus 96 ~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p 175 (496)
+|++.|+|+|+.++|||.+.+ ++.+.+..||..+ +.
T Consensus 2 ~~~l~i~YdGt~f~G~Q~Q~~---TVq~~Le~aL~~i---------------------------------~~-------- 37 (256)
T PRK14587 2 PYLYRIAYDGTLFYGFTGHPN---SLEPALRRVFGEI---------------------------------LG-------- 37 (256)
T ss_pred cEEEEEEECCCcccceecCcc---hHHHHHHHHHHHh---------------------------------cc--------
Confidence 578899999999999999877 3455555555431 00
Q ss_pred CCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEE
Q psy3604 176 PHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYK 255 (496)
Q Consensus 176 ~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~ 255 (496)
.++|||+||||++||++|. ..+ + ..+||+.||+||+|+++.+|+++||||+ |++|+|+
T Consensus 38 ------~agRTDaGVHA~~qv~~~~--~~~---------~----~~~LN~~LP~dI~V~~~~~V~~~FhaR~-a~~R~Y~ 95 (256)
T PRK14587 38 ------RGSRTDPGVSAVGNVVMTS--QKL---------P----LGYVNSKLPRGVWAWAVAEVPEGFNPRR-AKRRRYL 95 (256)
T ss_pred ------CccCCccCCCcccCEEEEC--CcC---------C----HHHHHhcCCCCeEEEEEEECCCCcCcCc-ccceEEE
Confidence 0567999999999999973 222 2 4789999999999999999999999997 9999999
Q ss_pred EecCCCCccHHHHHHHHHHccccccccccccccccCCCCC-ceEEEEEEEEEecceEEEEEEeeCce-----e--hhHHH
Q psy3604 256 YWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVN-FKRLVTHAGVTSAWQNVQFNDIKEVV-----D--SEPSF 327 (496)
Q Consensus 256 Y~~~~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~s-tvRtI~~i~i~~~~~~i~i~I~G~sF-----R--VGtLv 327 (496)
|+++...+|+++|++|++.|+|+|||+|||+.+. ..++ ++|+|++++|.+.++.+.|+|+|+|| | ||+|+
T Consensus 96 Y~i~~~~lDi~~m~~aa~~l~G~HDF~~F~~~~~--~~~~~~vRtI~~i~v~~~~~~i~i~i~g~sFL~~mVR~mVG~Ll 173 (256)
T PRK14587 96 YVAPHWGEDVEAMREAAELLAGTHDYSSFIQRRG--EKATPTVTTVYEIGVELRGDLIYLYFVGRGFRNKMIRKMAWAIL 173 (256)
T ss_pred EEEccCcchHHHHHHHHHHhcCCcChHHhccCCC--CCCCCCEEEEEEEEEEEeCCEEEEEEEechhHHHHHHHHHHHHH
Confidence 9998788999999999999999999999997642 2345 99999999999888899999999999 7 99999
Q ss_pred HHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccCCCCcccccchHHHHHHHHHHHhh
Q psy3604 328 KKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQYRIRQTAHCNIFTN 398 (496)
Q Consensus 328 ~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~~~~l~f~~~~~~~~~~~~~i~~~ 398 (496)
+||+|++++++|+++|+.. + .. ..++ |||+||+|++|.|+ .+|..+++++.++...+++.
T Consensus 174 ~Vg~G~~~~~~i~~~L~~~-r--~~--~~~~---APa~GL~L~~V~Y~---~~~~~~~~~~~~~~~~~~~~ 233 (256)
T PRK14587 174 AAGRGVLSRRDIAELLERP-R--PG--AVPS---APAEGLVLLDIEYD---VKFQVDYTALRKAYVYFLSK 233 (256)
T ss_pred HHhCCCCCHHHHHHHHhcC-c--cc--CCCC---CCCCCCEEeeeccC---ccccCChHHHHHHHHHHHHH
Confidence 9999999999999999843 2 22 2334 55999999999996 28888888887766665544
No 14
>cd02568 PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: Pseudouridine synthase, PUS1/ PUS2 like. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle, psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal. Psi44 in U
Probab=100.00 E-value=1.5e-44 Score=357.43 Aligned_cols=230 Identities=19% Similarity=0.172 Sum_probs=186.8
Q ss_pred eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccCCCCCCCC
Q psy3604 100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQPHPPHIP 179 (496)
Q Consensus 100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~~~p~hIP 179 (496)
.|+|+|+.++|||.+.+--.++.+.++.||..++...+. ..+ .+..|.
T Consensus 2 ~i~Y~Gt~f~G~Q~Q~~~~~TVq~~le~aL~~~~~~~~~---~~~-----------------------------~~~~~~ 49 (245)
T cd02568 2 LFGYCGTGYHGMQYNPGNYKTIEGELERALVKAGAISES---NAG-----------------------------DPKKIG 49 (245)
T ss_pred EEEEeCCCccccccCCCCCCChHHHHHHHHHHcCCcCcc---ccC-----------------------------Chhhcc
Confidence 689999999999999873246788888999987742110 000 001122
Q ss_pred CCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEEEecC
Q psy3604 180 PYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFP 259 (496)
Q Consensus 180 ~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~ 259 (496)
-..++|||+||||++||++|+++..+++. ..++..+..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|+
T Consensus 50 ~~~agRTD~GVHA~~qv~~~~~~~~~~~~----~~~~~~~~~~lN~~Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~ 125 (245)
T cd02568 50 FSRAARTDKGVHAARNVVSLKVIIDDPEG----LGIGEDLVEKLNSHLPEDIRVFGITRVTKSFNARKACDSRTYEYLLP 125 (245)
T ss_pred eeeecccccchhheeeEEEEEEecccccc----ccchHHHHHHHHccCCCceEEEEEEcCCCCCCcchhhhcceeEEECC
Confidence 23467899999999999999997654110 12267899999999999999999999999999999999999999999
Q ss_pred CCC-ccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEec------ceEEEEEEeeCce-----e--hhH
Q psy3604 260 QAG-LDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSA------WQNVQFNDIKEVV-----D--SEP 325 (496)
Q Consensus 260 ~~~-LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~------~~~i~i~I~G~sF-----R--VGt 325 (496)
... +|+++|++|++.|+|+|||+|||+... ...++++|+|.++++.+. ++++.|+|+|+|| | ||+
T Consensus 126 ~~~~~d~~~m~~a~~~~~G~HdF~~F~~~~~-~~~~~~~R~i~~~~~~~~~~~~~~~~~i~i~i~g~~FL~~mVR~mvg~ 204 (245)
T cd02568 126 TFALETLDRFNEILKLYVGTHNFHNFTVRKK-FEDPSANRFIISFYVSEPFVIEEGLEWVSIEIHGQSFMLHQIRKMIGL 204 (245)
T ss_pred cccHhHHHHHHHHHHHhhCccccccCccccc-ccCCCceeEEEEEEEecceeecCCccEEEEEEEechHHHHHHHHHHHH
Confidence 877 699999999999999999999998642 235789999999999874 3789999999999 7 999
Q ss_pred HHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeecc
Q psy3604 326 SFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVF 374 (496)
Q Consensus 326 Lv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y 374 (496)
|++||+|+++++.|+++|+.... . .. |+|||+||+|++|.|
T Consensus 205 l~~vg~g~~~~~~i~~~L~~~~~---~--~~---~~APa~GL~L~~v~y 245 (245)
T cd02568 205 AIAIVRGGAPESLIDLSFNKAKR---I--II---PLAPGLGLLLEYPHF 245 (245)
T ss_pred HHHHHcCCCCHHHHHHHhccccc---c--cc---cCCCCcceeEecccC
Confidence 99999999999999999985322 1 12 345699999999988
No 15
>KOG2554|consensus
Probab=100.00 E-value=1.6e-44 Score=363.49 Aligned_cols=251 Identities=34% Similarity=0.554 Sum_probs=219.5
Q ss_pred hcceeeeeeeeeccccHHHhhhcCCCC-CCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhcccccc
Q psy3604 93 VTSVIGLVIKEVGGLSHDFCELANRQQ-PMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVK 171 (496)
Q Consensus 93 ~~~~i~~yL~~lG~sa~~~ae~agRTq-p~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~ 171 (496)
-++.|++-|.|+|+.|.|++-+...-. ++.+-+..||....+. .+.. +-+|
T Consensus 64 ~kR~IAlkiaY~GW~Y~Gla~Qe~T~~~TIEg~l~eAL~kt~Li-es~~---------------------~~~y------ 115 (425)
T KOG2554|consen 64 SKRHIALKIAYLGWNYQGLAPQEHTNNPTIEGKLFEALKKTRLI-ESRQ---------------------TCNY------ 115 (425)
T ss_pred cceEEEEEEEEeccccCceecCCCCCCcchHHHHHHHHHhhhcc-cCcc---------------------cccc------
Confidence 479999999999999999998844333 6788899999875542 1111 0122
Q ss_pred CCCCCCCCCCCCCCCCcccccccceEEEeecccCCCCC------CCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCc
Q psy3604 172 QPHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPG------EESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSA 245 (496)
Q Consensus 172 ~~~p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~------~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhA 245 (496)
+.+.|||+||+|.+||+++.+++.++..+ .+.+..+..|...||++||+||||.+|++||+.|+|
T Consensus 116 ---------sRCGRTDKGVSAfgQviSl~lRS~~p~~~s~~~~~~~a~~~Ei~Y~~mLN~vLP~dIRi~awapvp~~FsA 186 (425)
T KOG2554|consen 116 ---------SRCGRTDKGVSAFGQVISLVLRSRIPMPDSQRDAVATADSEEIPYVHMLNRVLPPDIRIVAWAPVPPTFSA 186 (425)
T ss_pred ---------cccCCcccchhhhhheeeeeeeccCCCchhhhccccccccccccHHHHHhccCCCcceEEEEecCCCCccc
Confidence 35678999999999999999998876642 223456889999999999999999999999999999
Q ss_pred cccCCceeEEEecCCCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEecce---EEEEEEeeCce-
Q psy3604 246 RFDCLFRNYKYWFPQAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQ---NVQFNDIKEVV- 321 (496)
Q Consensus 246 Rfsa~~R~Y~Y~~~~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~---~i~i~I~G~sF- 321 (496)
||+|..|+|+|+|+..+|||++|++||.+|+|+|||+|||+.+..++..|..|+|.+++|...++ .+.|+|.|++|
T Consensus 187 RFsC~~RtYrY~F~k~dLdI~~M~kAA~l~vGe~DFrNFCK~D~~n~vtny~Rti~s~kV~~~~~~~~my~ldi~g~AFL 266 (425)
T KOG2554|consen 187 RFSCVQRTYRYYFPKKDLDIDRMSKAASLLVGEHDFRNFCKIDVSNGVTNYERTILSAKVEDVGQTPGMYYLDIQGSAFL 266 (425)
T ss_pred eeehhhceeeEeccCCCcCHHHHHHHHHHHhcchhhhhhhhhcchhhhHHHHhhhheeeEEEcCCCCceEEEEeechhhH
Confidence 99999999999999999999999999999999999999999987666788999999999987664 59999999999
Q ss_pred ----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccCCCCcccccch
Q psy3604 322 ----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFLLSFLAWVDQY 385 (496)
Q Consensus 322 ----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~~~~l~f~~~~ 385 (496)
| |++|+.||+|...|+.|.++|+.++.|.+| +|.+|. ..+|+|.+|.|-.++++|....
T Consensus 267 wHqVRcimaiL~liGq~~E~p~lI~dLldIek~P~kP--qY~mA~---~~PL~LydC~f~~e~~ew~~~~ 331 (425)
T KOG2554|consen 267 WHQVRCIMAILFLIGQGLEQPSLISDLLDIEKNPQKP--QYTMAS---DYPLELYDCDFHRENVEWRHDT 331 (425)
T ss_pred HHHHHHHHHHHHHhccccCCchHHHHHHhcccCCCCc--eeeecc---CCceEEEecCCCCccccccccc
Confidence 8 999999999999999999999999999999 999998 9999999999977899997754
No 16
>KOG2553|consensus
Probab=100.00 E-value=1.1e-38 Score=328.14 Aligned_cols=273 Identities=15% Similarity=0.151 Sum_probs=222.6
Q ss_pred hcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccCCCcccCCCCCCCCCCCCchhccccccC
Q psy3604 93 VTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKRPMRTVFPPVAPSTQPKPLSILQAGVKQ 172 (496)
Q Consensus 93 ~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~p~r~~lP~~p~~~~p~~~~fL~aG~~~ 172 (496)
.++++++.+.|+|.+|||+|-+.+ .++|.+|++.||..+|...+.=. .+|
T Consensus 35 ~KrKVail~gY~G~gY~GmQ~N~~-~kTIEgeL~~al~~aGaI~e~n~-----------------~dp------------ 84 (416)
T KOG2553|consen 35 RKRKVAILLGYCGTGYHGMQYNPP-LKTIEGELFEALFKAGAISESNA-----------------GDP------------ 84 (416)
T ss_pred cceEEEEEEEeccCCccceecCCC-CCchHHHHHHHHHHcCCcccccc-----------------cCh------------
Confidence 557789999999999999999999 48999999999999997533211 111
Q ss_pred CCCCCCCCCCCCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCce
Q psy3604 173 PHPPHIPPYLPLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFR 252 (496)
Q Consensus 173 ~~p~hIP~~Lp~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R 252 (496)
.+|---.++|||+||||.+|||++++..+ ...++..||..||++||||++.+|++.||+|..|.+|
T Consensus 85 ---kk~~~~raARTDKGVhA~~nviSlK~~~~-----------~~~lv~~lN~~Lp~~IRv~~v~r~~k~F~pr~~CdsR 150 (416)
T KOG2553|consen 85 ---KKIGFARAARTDKGVHAAGNVISLKLELD-----------DPELVEKLNEILPEQIRVWGVKRVTKSFNPRKQCDSR 150 (416)
T ss_pred ---HHhhhHHhhccccchhhhhheeEEEEeeC-----------cHHHHHHHhhhCCcceEEEEEEecCCCCCccccccce
Confidence 11222357889999999999999998742 3678999999999999999999999999999999999
Q ss_pred eEEEecCC------CC---------------------------------------------ccHHHHHHHHHHccccccc
Q psy3604 253 NYKYWFPQ------AG---------------------------------------------LDIDAMHKAAQYLVGTHDF 281 (496)
Q Consensus 253 ~Y~Y~~~~------~~---------------------------------------------LDie~M~eAak~fvGtHDF 281 (496)
+|.|++|. .+ -.++.++++++.++|+|||
T Consensus 151 ~YeYllPtfal~~p~~~~~~~~~~~~~~e~~~~f~~~~~~~~~~~~s~~~~~~~~~yr~s~~~l~~~~~~ls~Y~GthnF 230 (416)
T KOG2553|consen 151 TYEYLLPTFALAPPKPSSLLEVDIQYDKEFEKEFWNTYPLSAKERLSGQDRKTESGYRLSEEKLEVFNTILSKYVGTHNF 230 (416)
T ss_pred eEEEecceeeecCCCCccHHHhhhhhhhhhhhhhccccchhhhhhhcccccccccceeeCHHHHHHHHHHHHHhhccccc
Confidence 99999872 11 1367889999999999999
Q ss_pred cccccccccCCCCCceEEEEEEEEEe-------cceEEEEEEeeCce-----e--hhHHHHHhCCCCCHHHHHHHHhccC
Q psy3604 282 RNLCKMNVGNGVVNFKRLVTHAGVTS-------AWQNVQFNDIKEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEK 347 (496)
Q Consensus 282 ~nF~~~~~~~~~~stvRtI~~i~i~~-------~~~~i~i~I~G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~ 347 (496)
||||..+. ..+++..|.|.++.+.+ .-+||.+.|+|+|| | ||++++|.|+..+.+.|+..|+...
T Consensus 231 HNfT~~~~-~~dpss~R~I~s~~~~~pfv~~~~~~e~V~i~i~GQSFMLHQIRKMVglav~i~R~~~p~~~i~~af~~~~ 309 (416)
T KOG2553|consen 231 HNFTTGKD-FTDPSSNRFIKSFTVSEPFVINDEGVEFVKIKIHGQSFMLHQIRKMVGLAVLIVRSGAPASTIQRAFNKEH 309 (416)
T ss_pred ceecccCC-CCCccccceeeEEEecCcceeccCCceEEEEEEEcchhHHHHHHHHHHHHHHHHhcCCCHHHHHHhhCCCc
Confidence 99998763 35789999999998872 23799999999999 7 9999999999999999999998433
Q ss_pred CCCCCCCCCCCCCCCCCCCCeeeeeccC----------CCCcccccchHHHHHHHHHHHhhhhcccccccccchhhhhhh
Q psy3604 348 YPRIKSAQFPWSSTGATTPNELFRRVFL----------LSFLAWVDQYRIRQTAHCNIFTNLCTFYVPTYLPSLGEMIKD 417 (496)
Q Consensus 348 ~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~----------~~~l~f~~~~~~~~~~~~~i~~~~~~~y~~~~lp~i~~~~~~ 417 (496)
+. .+|+|| ++||+|.++.|. ++.++|.+.+..++.++.. ++.++|-+. ..
T Consensus 310 ri-----~IP~AP---~~gLlL~~~~F~~yn~~~~~~~~e~i~~~~~e~ei~~fk~~-----------~Iy~~I~~~-E~ 369 (416)
T KOG2553|consen 310 KI-----NIPKAP---GEGLLLEEPHFESYNRKFRPSGHEEIDWDDYEEEIDQFKEK-----------HIYSHIIKT-EE 369 (416)
T ss_pred cc-----cccCCC---cceEEeecccccccccccCCCCcCCcCHHHHHHHHHHHHHH-----------HhchHHhhh-Hh
Confidence 33 455887 999999999996 5778888877777666665 345544433 24
Q ss_pred ccccchhhcccCc
Q psy3604 418 TVRESKCTMGDLD 430 (496)
Q Consensus 418 ~~~~~~~~~~~~~ 430 (496)
.-..|.+|+..||
T Consensus 370 ~~~~f~~wl~~l~ 382 (416)
T KOG2553|consen 370 KEGVFAIWLSSLN 382 (416)
T ss_pred hhhhHHHHHHHHh
Confidence 4567999999999
No 17
>KOG4393|consensus
Probab=99.95 E-value=4e-27 Score=229.91 Aligned_cols=181 Identities=14% Similarity=0.115 Sum_probs=149.8
Q ss_pred CCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcC-CC--CcEEEEEEecCCCCCccccCCceeEEEecC
Q psy3604 183 PLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNL-PR--DIKVVAWSPVPEKYSARFDCLFRNYKYWFP 259 (496)
Q Consensus 183 p~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~L-P~--DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~ 259 (496)
.+|||+||||..+++++.++... .........++|..| ++ ||+|+++..||.+|||||+|.+|+|.|++.
T Consensus 54 ssrtDa~Vha~~naa~~~vpr~s-------g~~~~~~~~a~nt~l~~k~gdirV~dv~~Vps~FhaR~sassRtY~YRla 126 (295)
T KOG4393|consen 54 SSRTDAGVHAYLNAAHYIVPRFS-------GSQQQAKDRAVNTVLQRKDGDIRVIDVRCVPSNFHARYSASSRTYFYRLA 126 (295)
T ss_pred cCCCchhhheeeeeEEEEeeccc-------CCcHHHHHHHHhccccCCCCceEEEEeeecCcchhheecccceeEEEEee
Confidence 35799999999999999997653 124455667777766 44 999999999999999999999999999974
Q ss_pred -----------------CCCccHHHHHHHHHHccccccccccccccccCCCCCceEEEEEEEEEec--------------
Q psy3604 260 -----------------QAGLDIDAMHKAAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSA-------------- 308 (496)
Q Consensus 260 -----------------~~~LDie~M~eAak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~-------------- 308 (496)
+..||..+|++|+++|+|+|||.+|++.. +....+++|+..+.+...
T Consensus 127 ~g~d~l~~fERd~cW~lp~~lna~kmqeaa~lf~G~hdfsaf~~at--s~~y~P~~t~rr~sv~~~g~~~a~~~~~~~e~ 204 (295)
T KOG4393|consen 127 SGSDPLSIFERDRCWHLPEELNARKMQEAAPLFEGSHDFSAFTEAT--STVYFPSITERRLSVLNNGDPLACSNQPETEG 204 (295)
T ss_pred cCCCccChhhhcccccCCcccCHHHHHhhhhhhccchhhhhhhcCC--CCCCCCcccceeeeecccCCccccccCCcccc
Confidence 25789999999999999999999999875 457788888888888532
Q ss_pred --ceEEEEEEeeCce-----e--hhHHHHHhCCCCCHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCeeeeeccC
Q psy3604 309 --WQNVQFNDIKEVV-----D--SEPSFKKGQGNEKPEIIQQLVDIEKYPRIKSAQFPWSSTGATTPNELFRRVFL 375 (496)
Q Consensus 309 --~~~i~i~I~G~sF-----R--VGtLv~VG~G~~~~e~I~~lL~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~ 375 (496)
.+++.+++.++|| | ++.||.+|.+.++...++.+|+.+.....-.-+.+.| ||+||+|..|.|.
T Consensus 205 ~~~~~~nve~e~~gflyrQvRrm~a~LV~~g~~al~~~qv~~iLe~~~~~~l~k~~~~va---pphglfL~sv~Y~ 277 (295)
T KOG4393|consen 205 VTTNVGNVEGETEGFLYRQVRRMRAYLVTAGSRALLYHQVLYILEVRDIVGLLKCVGTVA---PPHGLFLSSVEYV 277 (295)
T ss_pred ceeeeEEEEEEecchHHHHHHhhheeeeeecccccchhhhhhhhhccchhhhhhccCCCC---CCccceeeeEEec
Confidence 2679999999999 3 8999999999999999999999876432222244445 5999999999996
No 18
>KOG4336|consensus
Probab=99.88 E-value=6e-23 Score=204.01 Aligned_cols=136 Identities=42% Similarity=0.707 Sum_probs=118.1
Q ss_pred HHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhh
Q psy3604 10 SLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWY 89 (496)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y 89 (496)
++|..+|.+||+++|||.++++|+|+|++++++
T Consensus 5 ~vl~~VV~~Ll~~~gfd~is~~aletlvell~~----------------------------------------------- 37 (323)
T KOG4336|consen 5 RVLAPVVSNLLKTKGFDSISNAALETLVELLQS----------------------------------------------- 37 (323)
T ss_pred hHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHH-----------------------------------------------
Confidence 489999999999999999999999999999997
Q ss_pred hhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCccccccC-CCc---ccCCCCCCCCC-----C
Q psy3604 90 KRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTYAKR-PMR---TVFPPVAPSTQ-----P 160 (496)
Q Consensus 90 ~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y~k~-p~r---~~lP~~p~~~~-----p 160 (496)
||.++|+++|.||+++|||+|+.+||..+|++|||.++.|..|.+. ++. ..++.+++..+ +
T Consensus 38 ----------yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~v~sL~~~~q~~~~sl~~~~~~aP~~~~q~~ds~~ 107 (323)
T KOG4336|consen 38 ----------YIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIKVSSLYAYFQKQEFSLWSVLIAAPENQEQEEDSEQ 107 (323)
T ss_pred ----------HHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCChhhhHHHHHhccchhhhccccCCCcCCccccccc
Confidence 7899999999999999999999999999999999999999998753 332 33444444443 3
Q ss_pred CCchhccccccCCCCCCCCCCCCCCCCcccccccceEEEeec
Q psy3604 161 KPLSILQAGVKQPHPPHIPPYLPLFPDPHAYIRTPVVTLKIR 202 (496)
Q Consensus 161 ~~~~fL~aG~~~~~p~hIP~~Lp~~~D~~v~a~~qVvsf~l~ 202 (496)
.+...+..|.+.++|.|||+|||+|||+|||..+++...-..
T Consensus 108 ~~~~~l~~gv~~php~yIpshLPpfPdpHTYi~Tpi~~~p~t 149 (323)
T KOG4336|consen 108 QPELLLTLGVSRPHPKYIPSHLPPFPDPHTYIKTPIYKVPDT 149 (323)
T ss_pred cchHhhhcCCCCCCCccccccCCCCCCCcccccCCccCCCCC
Confidence 445667899999999999999999999999999999877543
No 19
>KOG2389|consensus
Probab=99.78 E-value=5.3e-19 Score=179.00 Aligned_cols=141 Identities=29% Similarity=0.512 Sum_probs=120.7
Q ss_pred CchHHHHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchh
Q psy3604 3 TSKDTNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVED 82 (496)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (496)
...+|++++++.+|+|+|+.+||++.+++||++|+++++.
T Consensus 22 ~~~~ya~sla~~avaQIcqslg~~~~~~sale~Ltd~~~q---------------------------------------- 61 (353)
T KOG2389|consen 22 EEAEYAFSLARVAVAQICQSLGYSSTQNSALETLTDVLQQ---------------------------------------- 61 (353)
T ss_pred hHHHHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHH----------------------------------------
Confidence 4679999999999999999999999999999999999996
Q ss_pred hhhhhhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCC---------CCccc-------c----
Q psy3604 83 CYQRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPI---------HGLDT-------Y---- 142 (496)
Q Consensus 83 ~~~~~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v---------~gL~~-------y---- 142 (496)
||+.+|+.+|.|++++||++||++|+++||.++|+++ +.|.+ |
T Consensus 62 -----------------yvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s~~~~~~~~~s~~L~ds~v~rdii~~~g 124 (353)
T KOG2389|consen 62 -----------------YVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSASLGASGSSGESHCLLDSKVLRDIIIFNG 124 (353)
T ss_pred -----------------HHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhhcccccccchhHHHhhhhhHHHHHhhcc
Confidence 8999999999999999999999999999999999988 55555 1
Q ss_pred -c-cCCCcccCCCCCCCCCCCCchhccccc--cCCCCCCCCCCCC-CCCCcccccccceEEEee
Q psy3604 143 -A-KRPMRTVFPPVAPSTQPKPLSILQAGV--KQPHPPHIPPYLP-LFPDPHAYIRTPVVTLKI 201 (496)
Q Consensus 143 -~-k~p~r~~lP~~p~~~~p~~~~fL~aG~--~~~~p~hIP~~Lp-~~~D~~v~a~~qVvsf~l 201 (496)
+ +.||..++|.||++.... .++++.|. ..+++.|||.||| +|||.+.+...+-.+...
T Consensus 125 ~~eevpF~~~lP~Fp~s~s~~-k~~l~~~~~g~~pp~~~Ip~wLP~~fp~~~~~~~s~e~~~~~ 187 (353)
T KOG2389|consen 125 KAEEVPFKDDLPRFPVSKSVN-KPFLKFGSVGAEPPGESIPIWLPPAFPDLEGCSKSPEGNVTV 187 (353)
T ss_pred ccccCCCCCCCCccccccccc-cCCCCccccCCCCCCccccccCCCCCCCcccCCCCccccccc
Confidence 1 358999999999876532 34444443 2489999999999 999999999988555554
No 20
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=99.65 E-value=1.8e-16 Score=130.85 Aligned_cols=76 Identities=42% Similarity=0.680 Sum_probs=73.1
Q ss_pred hHHHHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhh
Q psy3604 5 KDTNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCY 84 (496)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (496)
++|.|++|+.+|+++|++.||+.++++|+|+|+++++.
T Consensus 1 ~~~~~~ll~~~Vaqil~~~Gf~~~~~sale~ltdi~~~------------------------------------------ 38 (77)
T smart00576 1 NELAFALLRIAVAQILESAGFDSFQESALETLTDILQS------------------------------------------ 38 (77)
T ss_pred CHHHHHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHH------------------------------------------
Confidence 57999999999999999999999999999999999997
Q ss_pred hhhhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCC
Q psy3604 85 QRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIH 137 (496)
Q Consensus 85 ~~~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~ 137 (496)
|+..+|+.++.||+++||++|++.||.+||+++|++++
T Consensus 39 ---------------yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~~~ 76 (77)
T smart00576 39 ---------------YIQELGRTAHSYAELAGRTEPNLGDVVLALENLGISVG 76 (77)
T ss_pred ---------------HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcccC
Confidence 78999999999999999999999999999999999865
No 21
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=99.64 E-value=2.7e-16 Score=129.55 Aligned_cols=77 Identities=40% Similarity=0.625 Sum_probs=73.7
Q ss_pred hHHHHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhh
Q psy3604 5 KDTNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCY 84 (496)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (496)
+++.+++|+.+|+++|..+||++++++|||+|++++..
T Consensus 1 ~e~~~~~l~~~va~il~~~GF~~~~~~al~~Ltdi~~~------------------------------------------ 38 (77)
T PF07524_consen 1 DEFARSLLRRSVAQILKHAGFDSASPSALDTLTDILQR------------------------------------------ 38 (77)
T ss_pred CHHHHHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHH------------------------------------------
Confidence 57999999999999999999999999999999999996
Q ss_pred hhhhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCC
Q psy3604 85 QRNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHG 138 (496)
Q Consensus 85 ~~~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~g 138 (496)
||+.+|+.++.|++++||++|++.||.++|.+||+++++
T Consensus 39 ---------------yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~v~e 77 (77)
T PF07524_consen 39 ---------------YLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGISVNE 77 (77)
T ss_pred ---------------HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Confidence 789999999999999999999999999999999998763
No 22
>PF01416 PseudoU_synth_1: tRNA pseudouridine synthase; InterPro: IPR020097 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents pseudouridine synthase I (TruA). TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA [, ]. TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis []. These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1VS3_B 2NR0_B 2NQP_D 1DJ0_A 2NRE_A.
Probab=99.60 E-value=1.1e-17 Score=144.35 Aligned_cols=98 Identities=20% Similarity=0.206 Sum_probs=80.0
Q ss_pred HHHHccccccccccccccccCCCCCceEEEEEEEEEecceEEEEEEeeCce-----e--hhHHHHHhCCCCCHHHHHHHH
Q psy3604 271 AAQYLVGTHDFRNLCKMNVGNGVVNFKRLVTHAGVTSAWQNVQFNDIKEVV-----D--SEPSFKKGQGNEKPEIIQQLV 343 (496)
Q Consensus 271 Aak~fvGtHDF~nF~~~~~~~~~~stvRtI~~i~i~~~~~~i~i~I~G~sF-----R--VGtLv~VG~G~~~~e~I~~lL 343 (496)
|++.|+|+|||++|++.+. ...+++|+|.++.+...++++. +|+|+|| | ||+++.+|+|..+++.|.++|
T Consensus 1 A~~~~~G~HdF~~f~~~~~--~~~~~~r~i~~~~~~~~~~~~~-~i~g~~Fl~~~vR~~vg~~~~~~~G~~~~~~i~~~L 77 (105)
T PF01416_consen 1 AAKLYVGTHDFSGFQKQKT--VEKNTIRTIFSIDIIEEGDVVV-EIHGNSFLRHQVRIMVGTLLRTGRGVHSLEQIAELL 77 (105)
T ss_dssp -CCEETCEEECCGCSSCS---HHHHHCCCEEEEECCCCCCEEE-EEEESS--TTHHHHHHCCCCHHHTTSCEEECCCCCH
T ss_pred CcceeEecCCCcCCEECCc--ccccHHHHHHHHhhhcCCCEEE-EEEecccccccchhhhHHHHHHhcCCCCHHHHHHHH
Confidence 6788999999999998743 2368999999999999889999 9999999 6 999999999999999999999
Q ss_pred hccCCCCCCCCCCCCCCCCCCCCCeeeeeccC
Q psy3604 344 DIEKYPRIKSAQFPWSSTGATTPNELFRRVFL 375 (496)
Q Consensus 344 ~~~~~~~~p~~~~~~Ap~aP~~GL~L~~V~Y~ 375 (496)
+...++..+. .+..| |+.||+|++|.||
T Consensus 78 ~~~~~~~~~~-ri~~a---p~~gL~L~~v~y~ 105 (105)
T PF01416_consen 78 NSKLRPKAPP-RILTA---PAVGLYLFHVRYD 105 (105)
T ss_dssp HHHSCTTS-T-EEEEE---EECCECCEECCTT
T ss_pred hccCccccCC-Cccee---eCCCCCceEeeCc
Confidence 9876442220 12234 5999999999995
No 23
>PF10406 TAF8_C: Transcription factor TFIID complex subunit 8 C-term ; InterPro: IPR019473 This entry represents the C-terminal region of subunit 8 (also known as TAF8) of the transcription factor TFIID []. The adjacent N-terminal region generally contains a histone fold domain (IPR006565 from INTERPRO). This subunit is one of the key subunits of TFIID, being one of several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery [].
Probab=97.54 E-value=3.4e-05 Score=59.16 Aligned_cols=25 Identities=52% Similarity=1.088 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCcccccccceEEEe
Q psy3604 176 PHIPPYLPLFPDPHAYIRTPVVTLK 200 (496)
Q Consensus 176 ~hIP~~Lp~~~D~~v~a~~qVvsf~ 200 (496)
+|||+|||+|||+|||..|++..-.
T Consensus 1 ~~IP~~lP~fP~~HTY~~Tp~~~~~ 25 (51)
T PF10406_consen 1 SHIPDWLPPFPPPHTYKRTPIYNER 25 (51)
T ss_pred CCCcccCCCCCCCcccccCCCCCCC
Confidence 5999999999999999999998654
No 24
>cd08049 TAF8 TATA Binding Protein (TBP) Associated Factor 8. The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promo
Probab=97.49 E-value=4.6e-05 Score=59.06 Aligned_cols=25 Identities=56% Similarity=1.145 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCCcccccccceEEEe
Q psy3604 176 PHIPPYLPLFPDPHAYIRTPVVTLK 200 (496)
Q Consensus 176 ~hIP~~Lp~~~D~~v~a~~qVvsf~ 200 (496)
.|||+|||+|||+|||..+++..-.
T Consensus 1 ~hIP~~LP~FP~~HTY~~Tp~~~~~ 25 (54)
T cd08049 1 AHIPSWLPPFPDPHTYKRTPTYSER 25 (54)
T ss_pred CCCCcCCCCCCCchhhccCCCCCCC
Confidence 5999999999999999999997553
No 25
>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Probab=96.75 E-value=0.02 Score=55.25 Aligned_cols=116 Identities=12% Similarity=0.234 Sum_probs=76.3
Q ss_pred cccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCCCCCccccCCceeEEEecCCCCccHHH
Q psy3604 188 PHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSARFDCLFRNYKYWFPQAGLDIDA 267 (496)
Q Consensus 188 ~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhARfsa~~R~Y~Y~~~~~~LDie~ 267 (496)
-|+.+.+-++.+.+..+ .++..+...||+.||++|+|.++..+|....+ ..+.-..+.|.+.....+.+.
T Consensus 55 vGv~S~~E~~di~l~~~---------~~~~~~~~rLn~~lP~Gl~i~~~~~i~~~~~s-l~~~i~~~~Y~i~~~~~~~~~ 124 (187)
T PF10105_consen 55 VGVESLAEYMDIELEED---------IDPEEVLERLNAVLPEGLRILEAEEIPPKAPS-LMALINAAEYRITLPEIDEEE 124 (187)
T ss_pred CceeeccEEEEEEEecC---------CCHHHHHHHHHHhCCCCCEEEEEEEccCCCcc-hhhhcceEEEEEEecCCCHHH
Confidence 47888999999998754 37889999999999999999999999855443 234446677776555777888
Q ss_pred HHHHHHHccccccccccccc-cccCC-CCCceEEEEEEEEEecceEEEE
Q psy3604 268 MHKAAQYLVGTHDFRNLCKM-NVGNG-VVNFKRLVTHAGVTSAWQNVQF 314 (496)
Q Consensus 268 M~eAak~fvGtHDF~nF~~~-~~~~~-~~stvRtI~~i~i~~~~~~i~i 314 (496)
+++++..|.-..++ ...+. +.+.. ..+-.-.|.++++...++.+.|
T Consensus 125 ~~~~~~~~~~~~~~-~v~k~~Kkg~~~~~dir~~i~~l~~~~~~~~~~l 172 (187)
T PF10105_consen 125 LEEAIEAFLAAEEI-IVEKRTKKGKKKEIDIRPYIKDLELEGSEDNIVL 172 (187)
T ss_pred HHHHHHHHHCCCCE-EEEEeCCCCceEEEEhHHhhheEEEEeCCCeEEE
Confidence 88888777655432 12222 11111 1122234556667665544444
No 26
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=96.70 E-value=0.0019 Score=57.77 Aligned_cols=64 Identities=19% Similarity=0.193 Sum_probs=58.1
Q ss_pred HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604 14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV 93 (496)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~ 93 (496)
.+|.++|++.|=...++.+...|.|.+.+
T Consensus 5 ~~v~~iLk~~Gv~~~~~~v~~~Lle~~~r--------------------------------------------------- 33 (117)
T cd07979 5 RVIAAILKSMGITEYEPRVINQLLEFAYR--------------------------------------------------- 33 (117)
T ss_pred HHHHHHHHHCCCCccCHHHHHHHHHHHHH---------------------------------------------------
Confidence 46889999999999999999999999996
Q ss_pred cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCC
Q psy3604 94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGI 134 (496)
Q Consensus 94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi 134 (496)
|..+++..+..|++|+||..-..+||.+|+...+-
T Consensus 34 ------y~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 34 ------YTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred ------HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 67788999999999999999999999999987553
No 27
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=96.40 E-value=0.0054 Score=52.01 Aligned_cols=75 Identities=17% Similarity=0.251 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhh
Q psy3604 7 TNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQR 86 (496)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (496)
....+-+.+|..|....|=.-+...|.+.+.++++.
T Consensus 10 ~~~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~-------------------------------------------- 45 (85)
T cd00076 10 NIKGITKPAIRRLARRGGVKRISGGVYDEVRNVLKS-------------------------------------------- 45 (85)
T ss_pred hhccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHH--------------------------------------------
Confidence 334455778889999999999999999999999996
Q ss_pred hhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCC
Q psy3604 87 NWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHG 138 (496)
Q Consensus 87 ~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~g 138 (496)
|+.++.+.+-.|++|+||..-+..||..||+.+|-.+-|
T Consensus 46 -------------~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~yg 84 (85)
T cd00076 46 -------------YLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 84 (85)
T ss_pred -------------HHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCccC
Confidence 678889999999999999999999999999999966544
No 28
>PTZ00015 histone H4; Provisional
Probab=96.17 E-value=0.0069 Score=53.01 Aligned_cols=74 Identities=23% Similarity=0.276 Sum_probs=65.6
Q ss_pred HHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhh
Q psy3604 8 NRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRN 87 (496)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (496)
.+.+.+.+|..|+...|=.-+...|.+.+.++++.
T Consensus 28 i~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~--------------------------------------------- 62 (102)
T PTZ00015 28 IRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKA--------------------------------------------- 62 (102)
T ss_pred ccCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHH---------------------------------------------
Confidence 34566889999999999999999999999999986
Q ss_pred hhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCC
Q psy3604 88 WYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHG 138 (496)
Q Consensus 88 ~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~g 138 (496)
|+.++.+.+-.|++|++|..-+..||.+||...|-.+-|
T Consensus 63 ------------~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~yg 101 (102)
T PTZ00015 63 ------------FLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLYG 101 (102)
T ss_pred ------------HHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCCC
Confidence 678889999999999999999999999999999875543
No 29
>PLN00035 histone H4; Provisional
Probab=96.08 E-value=0.011 Score=51.89 Aligned_cols=72 Identities=19% Similarity=0.223 Sum_probs=64.3
Q ss_pred HHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhh
Q psy3604 11 LLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYK 90 (496)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~ 90 (496)
+=+.+|..|+...|=.-+...|.+.|.++++.
T Consensus 30 ipk~~IrRLARr~GvkRIS~~ay~elr~vle~------------------------------------------------ 61 (103)
T PLN00035 30 ITKPAIRRLARRGGVKRISGLIYEETRGVLKI------------------------------------------------ 61 (103)
T ss_pred CCHHHHHHHHHHcCcccchHHHHHHHHHHHHH------------------------------------------------
Confidence 44567888999999999999999999999996
Q ss_pred hhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCc
Q psy3604 91 RAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGL 139 (496)
Q Consensus 91 r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL 139 (496)
|+.++.+.+-.|++|++|..-+..||.+||...|-.+-||
T Consensus 62 ---------~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~lyGf 101 (103)
T PLN00035 62 ---------FLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 101 (103)
T ss_pred ---------HHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCCCC
Confidence 6778889999999999999999999999999999876665
No 30
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=95.61 E-value=0.016 Score=46.62 Aligned_cols=61 Identities=21% Similarity=0.222 Sum_probs=54.9
Q ss_pred HHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhh
Q psy3604 13 KSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRA 92 (496)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~ 92 (496)
+.+|..+.+..|.+.....|.+.|.+.++.
T Consensus 5 ~~~i~ria~~~Gi~ris~~a~~~l~~~~e~-------------------------------------------------- 34 (65)
T smart00803 5 KETIKDVAESLGIGNLSDEAAKLLAEDVEY-------------------------------------------------- 34 (65)
T ss_pred HHHHHHHHHHCCCccccHHHHHHHHHHHHH--------------------------------------------------
Confidence 356778888999999999999999999984
Q ss_pred hcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHH
Q psy3604 93 VTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALI 130 (496)
Q Consensus 93 ~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~ 130 (496)
++.++.+.+-.|++|++|+.-+..||..||.
T Consensus 35 -------rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 35 -------RIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred -------HHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 6788999999999999999999999999873
No 31
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=95.12 E-value=0.024 Score=48.69 Aligned_cols=69 Identities=28% Similarity=0.357 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhh
Q psy3604 12 LKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKR 91 (496)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r 91 (496)
=+.-|..++.+.|=+-++..|.+.|.+.++.
T Consensus 21 p~apv~Ri~r~~~~~Rvs~~A~~~l~~~~e~------------------------------------------------- 51 (91)
T COG2036 21 PKAPVRRILRKAGAERVSSSAIEELQEALEE------------------------------------------------- 51 (91)
T ss_pred CchHHHHHHHHHhHHHhhHHHHHHHHHHHHH-------------------------------------------------
Confidence 3455777888888889999999999999997
Q ss_pred hhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCC
Q psy3604 92 AVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIH 137 (496)
Q Consensus 92 ~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~ 137 (496)
|+.+++..+.-+|.|+||..-...||.+++..+|..+.
T Consensus 52 --------~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~ 89 (91)
T COG2036 52 --------YLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIY 89 (91)
T ss_pred --------HHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccccc
Confidence 78899999999999999999999999999999987643
No 32
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=94.99 E-value=0.035 Score=50.65 Aligned_cols=61 Identities=18% Similarity=0.215 Sum_probs=48.5
Q ss_pred HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604 14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV 93 (496)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~ 93 (496)
.+|.+||++.|-+..++.....|.|.+.+
T Consensus 16 ~~i~~iL~~~Gv~~yeprVv~qLLEfayR--------------------------------------------------- 44 (129)
T PF02291_consen 16 RVIHLILKSMGVTEYEPRVVNQLLEFAYR--------------------------------------------------- 44 (129)
T ss_dssp HHHHHHHHHTT---B-THHHHHHHHHHHH---------------------------------------------------
T ss_pred HHHHHHHHHcCCcccCHHHHHHHHHHHHH---------------------------------------------------
Confidence 57889999999999999999999999985
Q ss_pred cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHh
Q psy3604 94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIE 131 (496)
Q Consensus 94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~ 131 (496)
|..++=..++.|++|+||+.....||-+|..-
T Consensus 45 ------Yt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~ 76 (129)
T PF02291_consen 45 ------YTSDVLEDAQVYADHAGRSTIDADDVRLAIQS 76 (129)
T ss_dssp ------HHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHH
T ss_pred ------HHHHHHHHHHHHHHhcccccCChHHHHHHHHH
Confidence 45556668899999999999999999999983
No 33
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=92.53 E-value=0.18 Score=41.88 Aligned_cols=65 Identities=17% Similarity=0.172 Sum_probs=52.2
Q ss_pred HHHHHHHHHHHHHHhCccc---cChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhh
Q psy3604 9 RSLLKSSVVALLAEVGFDA---ADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQ 85 (496)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (496)
++-|.-+|+.+|++.+=+. +.+.++..|+|++-.
T Consensus 4 Kaal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~------------------------------------------- 40 (76)
T PF15630_consen 4 KAALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYK------------------------------------------- 40 (76)
T ss_dssp HHHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHH-------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHH-------------------------------------------
Confidence 5667889999999996433 788999999999875
Q ss_pred hhhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHH
Q psy3604 86 RNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALI 130 (496)
Q Consensus 86 ~~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~ 130 (496)
++..+|+.-..|+.|+||+.-+.+||.+...
T Consensus 41 --------------q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 41 --------------QLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp --------------HHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred --------------HHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 5678899999999999999999999988654
No 34
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=92.24 E-value=0.26 Score=39.98 Aligned_cols=61 Identities=20% Similarity=0.226 Sum_probs=47.0
Q ss_pred HHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhh
Q psy3604 13 KSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRA 92 (496)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~ 92 (496)
+.+|-.+-+.+|....+..+...|.+-++-
T Consensus 6 ~esvk~iAes~Gi~~l~de~a~~La~dvey-------------------------------------------------- 35 (66)
T PF02969_consen 6 QESVKDIAESLGISNLSDEAAKALAEDVEY-------------------------------------------------- 35 (66)
T ss_dssp HHHHHHHHHHTT---B-HHHHHHHHHHHHH--------------------------------------------------
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHHHHHH--------------------------------------------------
Confidence 456777888999999999999999888872
Q ss_pred hcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHH
Q psy3604 93 VTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALI 130 (496)
Q Consensus 93 ~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~ 130 (496)
-|.++-..+..|+.|+.|+.-+..||..||+
T Consensus 36 -------rlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 36 -------RLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp -------HHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred -------HHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 4677888899999999999999999999984
No 35
>smart00417 H4 Histone H4.
Probab=89.70 E-value=0.2 Score=41.45 Aligned_cols=65 Identities=15% Similarity=0.204 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhh
Q psy3604 6 DTNRSLLKSSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQ 85 (496)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (496)
|....+-+-+|..|+...|=.-....|.+.|.++++.
T Consensus 9 d~i~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~------------------------------------------- 45 (74)
T smart00417 9 DNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKS------------------------------------------- 45 (74)
T ss_pred hhhcCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHH-------------------------------------------
Confidence 4445566788999999999999999999999999986
Q ss_pred hhhhhhhhcceeeeeeeeeccccHHHhhhcCCCCCCHHHHHH
Q psy3604 86 RNWYKRAVTSVIGLVIKEVGGLSHDFCELANRQQPMLADVLL 127 (496)
Q Consensus 86 ~~~y~r~~~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~ 127 (496)
|+.++.+.+-.|++++||..-+..||..
T Consensus 46 --------------~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 46 --------------FLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred --------------HHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 6778899999999999999888999865
No 36
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=87.34 E-value=0.94 Score=47.62 Aligned_cols=70 Identities=19% Similarity=0.223 Sum_probs=60.9
Q ss_pred HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604 14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV 93 (496)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~ 93 (496)
.+|..+.+.+|-+..+..|...|.+.++.
T Consensus 3 ~~i~~ia~~~Gi~~~~~~a~~~La~~~e~--------------------------------------------------- 31 (343)
T cd08050 3 ESIKLIAESLGIDSLSDEVAQLLAEDVEY--------------------------------------------------- 31 (343)
T ss_pred hHHHHHHHHcCCCcCCHHHHHHHHHHHHH---------------------------------------------------
Confidence 46778889999999999999999999884
Q ss_pred cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCcccc
Q psy3604 94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTY 142 (496)
Q Consensus 94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y 142 (496)
++.++.+.|..||++++|+.-+.+||-.||+..++. -|-+|
T Consensus 32 ------~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e--plyG~ 72 (343)
T cd08050 32 ------RLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE--PLYGF 72 (343)
T ss_pred ------HHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC--cccCC
Confidence 678899999999999999999999999999997764 44444
No 37
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=87.33 E-value=1.4 Score=36.01 Aligned_cols=59 Identities=22% Similarity=0.234 Sum_probs=49.7
Q ss_pred HHHHHHHh-CccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhhc
Q psy3604 16 VVALLAEV-GFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAVT 94 (496)
Q Consensus 16 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~~ 94 (496)
+-.++.++ +-...++.|.+.|.++++.
T Consensus 7 l~~lv~~id~~~~~~~da~~~l~~~~e~---------------------------------------------------- 34 (72)
T cd07981 7 LQELLKEIDPREQLDPDVEELLLEIADD---------------------------------------------------- 34 (72)
T ss_pred HHHHHHhhCCCCCcCHHHHHHHHHHHHH----------------------------------------------------
Confidence 33444444 4467999999999999996
Q ss_pred ceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHh
Q psy3604 95 SVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIE 131 (496)
Q Consensus 95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~ 131 (496)
|+..++..+..+|.|+||......||.++|+.
T Consensus 35 -----fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 35 -----FVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred -----HHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 77888899999999999999999999999986
No 38
>KOG3334|consensus
Probab=82.69 E-value=2.2 Score=39.55 Aligned_cols=61 Identities=16% Similarity=0.205 Sum_probs=53.3
Q ss_pred HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604 14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV 93 (496)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~ 93 (496)
.+|+++|.++|-..-++-...-|.|...+
T Consensus 17 ~~i~~iL~s~GI~eyEprVi~qlLefa~r--------------------------------------------------- 45 (148)
T KOG3334|consen 17 RVIASILKSLGIQEYEPRVINQLLEFAYR--------------------------------------------------- 45 (148)
T ss_pred HHHHHHHHHcCccccChHHHHHHHHHHHH---------------------------------------------------
Confidence 46899999999999999999999998885
Q ss_pred cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHh
Q psy3604 94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIE 131 (496)
Q Consensus 94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~ 131 (496)
|.+.+=..+..|++|++++.-..+||-+|..-
T Consensus 46 ------Ytt~vL~DA~vys~HA~ka~i~~eDVrlA~~~ 77 (148)
T KOG3334|consen 46 ------YTTTVLDDAKVYSSHAKKATIDAEDVRLAIQM 77 (148)
T ss_pred ------HHHHHHHHHHHHHHhccCCCCcHHHHHHHHHH
Confidence 44555568899999999999999999999875
No 39
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=72.33 E-value=5.7 Score=31.32 Aligned_cols=30 Identities=17% Similarity=0.222 Sum_probs=26.7
Q ss_pred eeeeeccccHHHhhhcCCCCCCHHHHHHHH
Q psy3604 100 VIKEVGGLSHDFCELANRQQPMLADVLLAL 129 (496)
Q Consensus 100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL 129 (496)
|+.+++..+...++..+|..-...||..|+
T Consensus 36 Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 36 FIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 889999999999999999888999999886
No 40
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=67.91 E-value=7.2 Score=31.34 Aligned_cols=31 Identities=19% Similarity=0.215 Sum_probs=27.1
Q ss_pred eeeeeccccHHHhhhcCCCCCCHHHHHHHHH
Q psy3604 100 VIKEVGGLSHDFCELANRQQPMLADVLLALI 130 (496)
Q Consensus 100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~ 130 (496)
++.++-..+..++.+++|..-.+.|+..|+.
T Consensus 43 ~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 43 LLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp HHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred hhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 5677778888999999999999999999875
No 41
>KOG3423|consensus
Probab=65.16 E-value=10 Score=36.11 Aligned_cols=67 Identities=16% Similarity=0.267 Sum_probs=47.2
Q ss_pred HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604 14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV 93 (496)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~ 93 (496)
.++--.|...||+..|+.-...+.-..|.
T Consensus 90 avt~~yL~~aGf~~~D~rv~RLvsLaAQK--------------------------------------------------- 118 (176)
T KOG3423|consen 90 AVTDHYLKKAGFQTSDPRVKRLVSLAAQK--------------------------------------------------- 118 (176)
T ss_pred HHHHHHHHhcCCCcCcHHHHHHHHHHHHH---------------------------------------------------
Confidence 45667899999999999766655555553
Q ss_pred cceeeeeeeeeccccHHHhhhcCC--------------CCCCHHHHHHHHHhcCCCCC
Q psy3604 94 TSVIGLVIKEVGGLSHDFCELANR--------------QQPMLADVLLALIELGIPIH 137 (496)
Q Consensus 94 ~~~i~~yL~~lG~sa~~~ae~agR--------------Tqp~~~DV~~AL~~~Gi~v~ 137 (496)
|+..|+.++..||...+. .--+..|+.-||.+.||++.
T Consensus 119 ------fvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~EyGinv~ 170 (176)
T KOG3423|consen 119 ------FVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALAEYGINVK 170 (176)
T ss_pred ------HHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHHHhCcccC
Confidence 555666666666654431 12368999999999999864
No 42
>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.77 E-value=13 Score=36.65 Aligned_cols=44 Identities=16% Similarity=0.335 Sum_probs=38.5
Q ss_pred ccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCCCcEEEEEEecCC
Q psy3604 189 HAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPRDIKVVAWSPVPE 241 (496)
Q Consensus 189 ~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~DIrV~~v~~V~~ 241 (496)
|+|.-|-.+-|.+.... +++++...||+.||+|+.+.++..++.
T Consensus 57 G~~ssge~fd~eL~e~v---------~~dk~~etl~~~lp~Dl~~~~v~~iD~ 100 (228)
T COG5011 57 GIYSSGEIFDFELTEEV---------SEDKFKETLNKALPNDLPAYDVEKIDK 100 (228)
T ss_pred ccccCceEEEEEeeeec---------CcHHHHHHHHHhCCCCcchhheeeecC
Confidence 78889999999886543 678999999999999999999999886
No 43
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=50.20 E-value=17 Score=28.16 Aligned_cols=29 Identities=17% Similarity=0.163 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCccccChHHHHHHHHHHHh
Q psy3604 14 SSVVALLAEVGFDAADNAALETLVEICQA 42 (496)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 42 (496)
.++...|+.+||+..|+.-...+.-..|.
T Consensus 6 ~v~~~yL~~~G~~~~D~rv~RLvSLaaQK 34 (51)
T PF03540_consen 6 EVTDYYLERSGFQTSDPRVKRLVSLAAQK 34 (51)
T ss_pred HHHHHHHHHCCCCCCCHhHHHHHHHHHHH
Confidence 46778999999999998877766666663
No 44
>KOG3467|consensus
Probab=48.71 E-value=36 Score=29.21 Aligned_cols=40 Identities=25% Similarity=0.301 Sum_probs=34.4
Q ss_pred eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCc
Q psy3604 100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGL 139 (496)
Q Consensus 100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL 139 (496)
||...-+.+--|++|+.|...+..||+.+|..||+.+-|+
T Consensus 62 fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~~~g~ 101 (103)
T KOG3467|consen 62 FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGF 101 (103)
T ss_pred HHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCceeecc
Confidence 6666667788899999999999999999999999876554
No 45
>smart00428 H3 Histone H3.
Probab=39.33 E-value=66 Score=28.52 Aligned_cols=34 Identities=21% Similarity=0.029 Sum_probs=28.0
Q ss_pred eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcC
Q psy3604 100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELG 133 (496)
Q Consensus 100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~G 133 (496)
|+..+...+...+.|++|..-.+.|+.++..-.|
T Consensus 69 ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir~ 102 (105)
T smart00428 69 YLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIRG 102 (105)
T ss_pred HHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHhc
Confidence 6777778888899999999888999988875444
No 46
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=38.32 E-value=36 Score=31.09 Aligned_cols=60 Identities=18% Similarity=0.205 Sum_probs=45.7
Q ss_pred HHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhhc
Q psy3604 15 SVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAVT 94 (496)
Q Consensus 15 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~~ 94 (496)
.|.-+|++.|-..-++..--.|.+...+
T Consensus 19 lihliL~Slgi~~ye~~VplQLl~FAhR---------------------------------------------------- 46 (145)
T COG5094 19 LIHLILRSLGIEEYEPKVPLQLLEFAHR---------------------------------------------------- 46 (145)
T ss_pred HHHHHHHhcCchhhCccchHHHHHHHHH----------------------------------------------------
Confidence 4566788888888777777777777664
Q ss_pred ceeeeeeeeeccccHHHhhhcCCCCCCH---HHHHHHHHh
Q psy3604 95 SVIGLVIKEVGGLSHDFCELANRQQPML---ADVLLALIE 131 (496)
Q Consensus 95 ~~i~~yL~~lG~sa~~~ae~agRTqp~~---~DV~~AL~~ 131 (496)
|-+.+-.++.-|++++||++-.. +||-+|+.-
T Consensus 47 -----YTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 47 -----YTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred -----HHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 34556678899999999987655 999999874
No 47
>TIGR01213 conserved hypothetical protein TIGR01213. Members of this family show twilight-zone similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.
Probab=34.52 E-value=2.7e+02 Score=30.25 Aligned_cols=107 Identities=9% Similarity=0.026 Sum_probs=68.7
Q ss_pred CCChHHHHHHHHhcCCCCcEEEEEEecCCCCCc--cccCCceeEEEecC-CCCccHHHHHHHHHHccccc--cccccccc
Q psy3604 213 DDNELPYLKMLNNNLPRDIKVVAWSPVPEKYSA--RFDCLFRNYKYWFP-QAGLDIDAMHKAAQYLVGTH--DFRNLCKM 287 (496)
Q Consensus 213 ~~~~~~l~~~LN~~LP~DIrV~~v~~V~~~FhA--Rfsa~~R~Y~Y~~~-~~~LDie~M~eAak~fvGtH--DF~nF~~~ 287 (496)
..+...+...+|+.....|.|.+...++..=-. +.....|+|+=.+. ..+++.+.++++++.|.|.. -.+.-...
T Consensus 236 ~~dl~~le~~IN~~~~g~V~v~~L~~~~~~~v~~ik~~~~~K~Y~alV~~~~~v~~e~L~~~~~~l~g~~I~QrTP~RV~ 315 (388)
T TIGR01213 236 KIDLDPLEEEINTSGKGKVEVEGLKFATREEVEEVKEEKHRKVYRALVEVDGPVSDEDLEELCKELEGATIYQRTPLRVL 315 (388)
T ss_pred CCCHHHHHHHHhhccCCCEEEEEeEEEcHHHHHHHhccCCceEEEEEEEECCCCCHHHHHHHHHhccCCEEEccCCceEE
Confidence 346778899999988889999999876641111 11233688885543 46888999999999988832 11111111
Q ss_pred cccCCCCCceEEEEEEEEEec-ceEEEEEEeeCc
Q psy3604 288 NVGNGVVNFKRLVTHAGVTSA-WQNVQFNDIKEV 320 (496)
Q Consensus 288 ~~~~~~~stvRtI~~i~i~~~-~~~i~i~I~G~s 320 (496)
. ......-.|+|+++++... +..+.+.|.++|
T Consensus 316 h-RRa~~~R~R~I~~i~~~~i~~~~~~l~v~~qa 348 (388)
T TIGR01213 316 H-RRADLVRERRVYQVDLSGLDGNHAELIIEAEG 348 (388)
T ss_pred E-ecCCCceEEEEEEEEEEEEcCCEEEEEEEecC
Confidence 0 0112345699999998764 346667777653
No 48
>KOG2549|consensus
Probab=32.71 E-value=69 Score=36.03 Aligned_cols=70 Identities=26% Similarity=0.292 Sum_probs=55.0
Q ss_pred HHHHHHHHHhCccccChHHHHHHHHHHHhhhccccccchhccccccccccccccCCCCCcccccccchhhhhhhhhhhhh
Q psy3604 14 SSVVALLAEVGFDAADNAALETLVEICQACKYTCLTVTAKVLSSHKEREKEDRIGESEGTCAEVTSVEDCYQRNWYKRAV 93 (496)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~~ 93 (496)
.++--+.+..|-......|+..|.+-+. |
T Consensus 15 Es~k~vAEslGi~nl~deaa~~La~dv~-----------------------------------------------y---- 43 (576)
T KOG2549|consen 15 ESVKVVAESLGITNLNDEAALLLAEDVE-----------------------------------------------Y---- 43 (576)
T ss_pred HHHHHHHHHhCccccCHHHHHHHHHHHH-----------------------------------------------H----
Confidence 4455566778999888888888877666 2
Q ss_pred cceeeeeeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCCCCCCcccc
Q psy3604 94 TSVIGLVIKEVGGLSHDFCELANRQQPMLADVLLALIELGIPIHGLDTY 142 (496)
Q Consensus 94 ~~~i~~yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi~v~gL~~y 142 (496)
-|.++.+.+..|+.++.|+.....||..||.-.++ ..+-+|
T Consensus 44 ------rikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV--ep~yg~ 84 (576)
T KOG2549|consen 44 ------RIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV--EPLYGF 84 (576)
T ss_pred ------HHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc--ccccCc
Confidence 46788899999999999999999999999997654 344444
No 49
>KOG0870|consensus
Probab=29.84 E-value=73 Score=30.50 Aligned_cols=35 Identities=23% Similarity=0.244 Sum_probs=31.0
Q ss_pred eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCC
Q psy3604 100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGI 134 (496)
Q Consensus 100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi 134 (496)
|+.++...+..+|.-..|...+..||+.||..|+.
T Consensus 46 Fv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eief 80 (172)
T KOG0870|consen 46 FVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEF 80 (172)
T ss_pred HHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhch
Confidence 66777778888999999998999999999999886
No 50
>PF01416 PseudoU_synth_1: tRNA pseudouridine synthase; InterPro: IPR020097 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents pseudouridine synthase I (TruA). TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA [, ]. TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis []. These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1VS3_B 2NR0_B 2NQP_D 1DJ0_A 2NRE_A.
Probab=26.36 E-value=29 Score=29.44 Aligned_cols=42 Identities=19% Similarity=0.239 Sum_probs=31.1
Q ss_pred CCCCCcccccccceEEEeecccCCCCCCCCCCChHHHHHHHHhcCCC---CcEEEEEEecC-CCCCcccc
Q psy3604 183 PLFPDPHAYIRTPVVTLKIRSKLTSPGEESDDNELPYLKMLNNNLPR---DIKVVAWSPVP-EKYSARFD 248 (496)
Q Consensus 183 p~~~D~~v~a~~qVvsf~l~~~i~~~~~~~~~~~~~l~~~LN~~LP~---DIrV~~v~~V~-~~FhARfs 248 (496)
-.++|.|+++..++..+ ||..+++ + +|+.+.+++ ..||++|+
T Consensus 60 ~~~~~~G~~~~~~i~~~-----------------------L~~~~~~~~~~-ri~~ap~~gL~L~~v~y~ 105 (105)
T PF01416_consen 60 LLRTGRGVHSLEQIAEL-----------------------LNSKLRPKAPP-RILTAPAVGLYLFHVRYD 105 (105)
T ss_dssp CCHHHTTSCEEECCCCC-----------------------HHHHSCTTS-T-EEEEEEECCECCEECCTT
T ss_pred HHHHhcCCCCHHHHHHH-----------------------HhccCccccCC-CcceeeCCCCCceEeeCc
Confidence 34567777776666433 6777754 5 999999999 99999985
No 51
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=25.56 E-value=1.2e+02 Score=25.97 Aligned_cols=34 Identities=15% Similarity=0.146 Sum_probs=25.8
Q ss_pred eeeeeccccHHHhhhcCCCCCCHHHHHHHHHhcCC
Q psy3604 100 VIKEVGGLSHDFCELANRQQPMLADVLLALIELGI 134 (496)
Q Consensus 100 yL~~lG~sa~~~ae~agRTqp~~~DV~~AL~~~Gi 134 (496)
||.++...+...+. .+|....++|++.+|..--.
T Consensus 36 ~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~ 69 (92)
T cd07978 36 YIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPK 69 (92)
T ss_pred HHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCHH
Confidence 56677777777776 67777899999999976443
No 52
>KOG2987|consensus
Probab=22.86 E-value=38 Score=34.72 Aligned_cols=34 Identities=24% Similarity=0.533 Sum_probs=28.4
Q ss_pred cccccccccCCCCcchhhhccccchhhhccchhh
Q psy3604 432 NHLIEGEFDSRPGRILSETGKLAPRVFQHFSEHS 465 (496)
Q Consensus 432 ~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~ 465 (496)
+|+---.|-.|||+.|-+||++||.-|+++-.|.
T Consensus 258 YH~EHHDFP~Ipg~~Lp~Vr~iApEyYd~lp~~~ 291 (324)
T KOG2987|consen 258 YHVEHHDFPYIPGSRLPKVREIAPEYYDNLPQHK 291 (324)
T ss_pred cccccccCCCCCccccHHHHHhhHHHhcCchhhc
Confidence 3444445999999999999999999999998764
Done!