Query 008562
Match_columns 561
No_of_seqs 192 out of 385
Neff 5.0
Searched_HMMs 46136
Date Thu Mar 28 13:43:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008562.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008562hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01213 conserved hypothetic 100.0 4.2E-99 9E-104 790.8 37.1 381 49-555 2-387 (388)
2 PRK14554 putative pseudouridyl 100.0 5E-98 1E-102 791.8 37.8 392 44-556 3-421 (422)
3 KOG2364 Predicted pseudouridyl 100.0 2E-94 4.4E-99 737.6 11.1 394 99-556 28-426 (433)
4 COG1258 Predicted pseudouridyl 100.0 2.3E-90 4.9E-95 714.2 31.4 385 45-556 4-393 (398)
5 cd02572 PseudoU_synth_hDyskeri 99.5 2.8E-13 6E-18 131.3 14.0 154 385-553 4-163 (182)
6 TIGR00425 CBF5 rRNA pseudourid 99.2 7.9E-11 1.7E-15 123.3 13.4 146 385-553 36-193 (322)
7 PRK04270 H/ACA RNA-protein com 99.2 1.3E-10 2.7E-15 120.7 13.4 152 385-553 24-181 (300)
8 COG0130 TruB Pseudouridine syn 99.1 6.2E-10 1.3E-14 114.0 10.5 153 385-552 17-176 (271)
9 cd00506 PseudoU_synth_TruB_lik 98.9 5E-08 1.1E-12 96.8 14.5 148 387-553 4-196 (210)
10 PRK00020 truB tRNA pseudouridi 98.6 8.8E-07 1.9E-11 89.7 14.7 154 385-553 12-206 (244)
11 PRK02755 truB tRNA pseudouridi 98.6 1.9E-07 4.1E-12 97.0 9.5 149 385-553 5-199 (295)
12 PRK04099 truB tRNA pseudouridi 98.5 1.3E-06 2.8E-11 89.9 14.5 148 386-553 5-195 (273)
13 PRK05033 truB tRNA pseudouridi 98.5 9.4E-07 2E-11 92.5 13.4 149 385-553 12-203 (312)
14 PRK00130 truB tRNA pseudouridi 98.5 8.8E-07 1.9E-11 91.9 13.1 148 386-553 5-196 (290)
15 PRK05389 truB tRNA pseudouridi 98.5 1.1E-06 2.5E-11 91.7 13.5 149 385-553 15-207 (305)
16 cd02573 PseudoU_synth_EcTruB P 98.5 2.3E-06 4.9E-11 88.4 14.9 153 388-553 5-196 (277)
17 TIGR00431 TruB tRNA pseudourid 98.5 2.2E-06 4.8E-11 85.2 14.2 148 386-553 5-195 (209)
18 PRK02193 truB tRNA pseudouridi 98.5 2.1E-06 4.5E-11 88.7 14.0 150 385-553 2-196 (279)
19 PRK14124 tRNA pseudouridine sy 98.5 1.7E-06 3.7E-11 90.4 12.8 148 385-553 5-196 (308)
20 PRK01851 truB tRNA pseudouridi 98.5 1.9E-06 4.1E-11 89.9 13.0 148 385-553 18-209 (303)
21 PRK01550 truB tRNA pseudouridi 98.4 2.9E-06 6.4E-11 88.6 13.9 147 386-553 5-203 (304)
22 PRK04642 truB tRNA pseudouridi 98.4 4.8E-06 1.1E-10 86.8 14.6 149 385-553 12-204 (300)
23 PRK01528 truB tRNA pseudouridi 98.4 3.8E-06 8.3E-11 87.3 13.3 150 385-553 5-198 (292)
24 PRK02484 truB tRNA pseudouridi 98.4 3.8E-06 8.3E-11 87.4 13.0 149 385-553 5-204 (294)
25 PRK03287 truB tRNA pseudouridi 98.4 6.6E-06 1.4E-10 85.8 14.5 151 385-553 11-207 (298)
26 PRK14846 truB tRNA pseudouridi 98.3 7.8E-06 1.7E-10 86.3 14.4 150 385-553 5-198 (345)
27 PRK14122 tRNA pseudouridine sy 98.3 7.8E-06 1.7E-10 85.7 13.3 147 388-553 6-229 (312)
28 KOG2364 Predicted pseudouridyl 98.2 3.4E-08 7.3E-13 103.7 -5.7 121 416-547 294-414 (433)
29 PRK14123 tRNA pseudouridine sy 98.2 1.7E-05 3.7E-10 83.0 14.1 150 385-553 5-204 (305)
30 cd02867 PseudoU_synth_TruB_4 P 98.2 7.8E-06 1.7E-10 85.7 10.1 103 438-553 89-227 (312)
31 PRK00989 truB tRNA pseudouridi 98.1 6.2E-05 1.3E-09 75.9 14.2 152 385-553 11-202 (230)
32 PF01509 TruB_N: TruB family p 97.7 8.7E-05 1.9E-09 70.3 7.7 74 440-520 42-149 (149)
33 cd02868 PseudoU_synth_hTruB2_l 97.7 0.00022 4.7E-09 71.9 10.1 88 451-553 98-203 (226)
34 PRK14586 tRNA pseudouridine sy 96.5 0.09 2E-06 53.5 15.6 164 317-516 10-191 (245)
35 PRK12434 tRNA pseudouridine sy 95.8 0.21 4.5E-06 51.0 13.9 148 344-516 26-191 (245)
36 PRK14588 tRNA pseudouridine sy 95.7 0.3 6.6E-06 50.6 14.8 165 317-516 10-193 (272)
37 TIGR00071 hisT_truA pseudourid 95.6 0.29 6.2E-06 49.3 14.0 163 317-516 9-178 (227)
38 COG0101 TruA Pseudouridylate s 95.6 0.29 6.4E-06 50.7 14.3 151 344-517 25-191 (266)
39 cd02570 PseudoU_synth_EcTruA P 95.2 0.45 9.8E-06 48.0 13.7 148 344-516 20-185 (239)
40 cd00497 PseudoU_synth_TruA_lik 95.0 0.37 8E-06 48.5 12.5 146 344-516 18-169 (224)
41 PRK00021 truA tRNA pseudouridi 95.0 0.6 1.3E-05 47.4 14.0 148 344-516 25-190 (244)
42 cd02568 PseudoU_synth_PUS1_PUS 94.4 0.39 8.3E-06 48.8 11.2 174 317-516 5-192 (245)
43 PRK14589 tRNA pseudouridine sy 93.9 1.3 2.8E-05 45.9 13.8 158 317-516 9-172 (265)
44 cd02866 PseudoU_synth_TruA_Arc 93.0 1.9 4.2E-05 43.3 13.1 157 317-516 5-167 (221)
45 cd02569 PseudoU_synth_ScPus3 P 92.8 2.3 4.9E-05 43.9 13.5 159 344-516 21-200 (256)
46 PRK14587 tRNA pseudouridine sy 84.2 20 0.00043 37.1 13.1 147 317-516 9-159 (256)
47 KOG2529 Pseudouridine synthase 75.7 1.1 2.3E-05 48.9 0.7 96 438-548 128-225 (395)
48 KOG4393 Predicted pseudouridyl 52.0 45 0.00098 35.1 6.9 96 345-446 31-127 (295)
49 KOG2559 Predicted pseudouridin 51.6 11 0.00024 39.1 2.5 58 484-551 186-245 (318)
50 PRK00994 F420-dependent methyl 50.3 6.5 0.00014 40.6 0.6 15 368-382 27-41 (277)
51 PF01993 MTD: methylene-5,6,7, 40.2 7.5 0.00016 40.2 -0.7 15 368-382 26-40 (276)
52 COG1927 Mtd Coenzyme F420-depe 40.2 12 0.00026 38.1 0.7 16 368-383 27-42 (277)
53 COG4994 Uncharacterized protei 35.9 22 0.00048 32.6 1.7 42 514-559 39-80 (120)
54 PF11005 DUF2844: Protein of u 32.9 39 0.00084 31.9 2.8 32 511-542 36-75 (132)
55 PLN03078 Putative tRNA pseudou 31.3 1.4E+02 0.003 34.2 7.2 117 317-448 79-204 (513)
56 TIGR00373 conserved hypothetic 28.2 31 0.00068 33.1 1.4 14 101-114 128-141 (158)
57 PRK06266 transcription initiat 23.7 37 0.0008 33.3 1.0 15 101-115 136-150 (178)
No 1
>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=100.00 E-value=4.2e-99 Score=790.77 Aligned_cols=381 Identities=31% Similarity=0.468 Sum_probs=320.7
Q ss_pred HHHHHhCCCchhhhhhhhcccccccchh----hHHHHHhhhhccccccccccCCCCCcccccccccccccccCCcccccc
Q 008562 49 VKDLLSKEVCLRCIFRLFGMQVPICSSL----SVKSLLCHVLGEQADLHQNISSVEPNICRSCLGILQFTYCGDKERVVE 124 (561)
Q Consensus 49 v~~Lls~G~C~rCi~Rf~~~~~~~~~n~----~lk~~L~~~L~~~~Dl~~~~~~~~~~~C~iClGiLq~~~~d~~~~~~~ 124 (561)
.+.|..|++|++|+||+||.++++.+|. +|+..+.+..+. ...+..++..|++|.|+|+.
T Consensus 2 ~~il~~~plCd~CLGR~Fa~~~~gl~N~eRG~ai~~~~~~e~~~-----~~~~~~~~~~C~iC~g~f~~----------- 65 (388)
T TIGR01213 2 LEILAKYPLCDRCLGRLFAKLGHGTSNRERGEALQLALALELGR-----PVKEFVESEPCDVCGGIFDR----------- 65 (388)
T ss_pred hhhHhcCCCCccccchhhhhhccCCCHHHHHHHHHHHHHhhccc-----cccccCCCCCcccccChHhH-----------
Confidence 4678899999999999999999999999 455556553331 11111244569999999983
Q ss_pred ccchhHHHHHHHHHHHhcCCccceEEEEeecChhHHhhhhHHHHHHHHhccccccccccccccccchhhHHHHhhhhhHH
Q 008562 125 NESACDFAVAIAELVKKEGHQIDSFSLEVSMPPTILENENKLSLYVKRKYRSEAWFKDRSISECSSTKDALKFALTNPLE 204 (561)
Q Consensus 125 ~~~~~d~~~~I~e~vk~~gyef~sF~L~ISLP~~l~lRE~s~~l~l~~~~~~~~~~~~~~~~~~v~~Kea~K~~l~~~l~ 204 (561)
.++|++++.+++ +||||+||.++..+|..+..+|..+|. +||- ...|++|-=+.
T Consensus 66 ---~~~~a~~~~~~l--~~~ef~tf~VGt~~p~~i~e~E~~i~~----~~gl-------------~~~E~iK~E~n---- 119 (388)
T TIGR01213 66 ---FDEAADLVAEKV--GDYDFSTFLVGTRFPPDVIELEEEIRK----EFGS-------------GGGESIKREFN---- 119 (388)
T ss_pred ---HHHHHHHHHHHh--hcCccceEEEeeeCCHHHHHHHHHHHH----HhCC-------------CcchhHHHHHh----
Confidence 278999999999 699999999999999999999999888 7772 12233221111
Q ss_pred hHhccccCCceeEEEEEEecchhhHHHhhhhhhhccccccccccccccccccccccccccccceeeecccccccccccCC
Q 008562 205 TLLDVKCGISTFHIRLTYSRVEASIRIQNFVEKIEGCKRRKVDAKNCLDTVKDKSAITGVENSVVSTTEVIPVDEKSSNG 284 (561)
Q Consensus 205 ~~L~~~~~~s~f~i~v~~~h~~~~~e~~~l~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~i 284 (561)
.|+.+.+....| |...+.+|+ .++..++.
T Consensus 120 ------------------------RevGk~~~~~~g-k~~d~~~Pd-----------------v~i~vd~~--------- 148 (388)
T TIGR01213 120 ------------------------REVGKLFVKRTG-KEVDFERPD-----------------LVIMVEFE--------- 148 (388)
T ss_pred ------------------------HHHHHHHHHHhC-CCccCCCCC-----------------EEEEEEcC---------
Confidence 122223322222 223333343 33333333
Q ss_pred CCCCCCCcccccCCCCCCCCceeeEEEEeccEEEEEEeeecccCCCCcccccCccccCcCcHHHHhhhccccccCCCceE
Q 008562 285 LQDNEPSETHEFPLKKVNEPCRLECLCFRTPIYFGGRYLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCRGDSYK 364 (561)
Q Consensus 285 ~~~~f~~~~~~~Pp~~v~~~~~~~~~~~~~pi~i~GRY~K~sR~lsQTpW~~~g~r~~~~SVeE~I~~~~~~~f~~~~~~ 364 (561)
. -.|.++++||||+|||+|++|+||||||+|++ ++++||||+|+.++.++|+|++++
T Consensus 149 -----------------~----~~v~vq~~pifi~GRY~Kl~R~ipQT~W~~~~--~~~~SVeelI~~~v~~~~~~~~~~ 205 (388)
T TIGR01213 149 -----------------Y----EFVDVQVNSLFIYGRYRKLVRGIPQTRWPCRK--NYPESVEELIASPFLKATGGTDAY 205 (388)
T ss_pred -----------------C----CeEEEEECcEEEEEEEeecccCCCCCccccCC--CcCchHHHHHHHHHHHHhCCceeE
Confidence 0 13588999999999999999999999999976 689999999999999999999999
Q ss_pred EeecCCCCccccccCCCccEEEEEecCccCCcHHHHHHHHHHHhccCCCcEEEEeeEEecchhhhhhhcccccccceEEE
Q 008562 365 FHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAA 444 (561)
Q Consensus 365 F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~a 444 (561)
||+||||||||||||+|||||+||+||+++. .++++|+++||++.+|.|+|+||++++++.+..||+++. .|.|+|
T Consensus 206 Fh~aGREDvDvRMLG~GRPFvlEi~~P~rr~--~dl~~le~~IN~~~~g~V~v~~L~~~~~~~v~~ik~~~~--~K~Y~a 281 (388)
T TIGR01213 206 FHGAGREDVDVRMLGTGRPFVLEVKEPRYRK--IDLDPLEEEINTSGKGKVEVEGLKFATREEVEEVKEEKH--RKVYRA 281 (388)
T ss_pred EeccCccccceeeccCCCceEEEecCCccCC--CCHHHHHHHHhhccCCCEEEEEeEEEcHHHHHHHhccCC--ceEEEE
Confidence 9999999999999999999999999999853 678899999999988999999999999999999997665 699999
Q ss_pred EEEEcCCCCHHHHHH-HHhcccccceeeeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecCCceeeEe
Q 008562 445 LVWISRPLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKEF 523 (561)
Q Consensus 445 lv~~~~~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqaGtYIKEf 523 (561)
+||+++++++++|++ ++.+++ ++|+|+||+||+|||++++|+|+||+|++..+++ ++|+|+|.||||||||||
T Consensus 282 lV~~~~~v~~e~L~~~~~~l~g----~~I~QrTP~RV~hRRa~~~R~R~I~~i~~~~i~~--~~~~l~v~~qaGtYIKEl 355 (388)
T TIGR01213 282 LVEVDGPVSDEDLEELCKELEG----ATIYQRTPLRVLHRRADLVRERRVYQVDLSGLDG--NHAELIIEAEGGLYIKEL 355 (388)
T ss_pred EEEECCCCCHHHHHHHHHhccC----CEEEccCCceEEEecCCCceEEEEEEEEEEEEcC--CEEEEEEEecCCCEEEEE
Confidence 999999999999976 679999 9999999999999999999999999999999975 899999999999999999
Q ss_pred eeCCCCCcCcchhhhcCCccEEEEEEEEEEec
Q 008562 524 VHGDLGRTNPSIGSILGCRAEILQLDVTDVKM 555 (561)
Q Consensus 524 VhGD~GRT~PSl~~iLg~~adileLDV~~V~~ 555 (561)
||||+|||+||||++||++|+|++|||++|+.
T Consensus 356 V~GD~GRT~PSl~~lLg~~a~i~eLDV~~V~~ 387 (388)
T TIGR01213 356 VSGDGGRTRPSVSEVLGVEAVCKELDVLKVCD 387 (388)
T ss_pred EcCCCCCcCCcHHHHhCCCceEEEeEEEEEec
Confidence 99999999999999999999999999999974
No 2
>PRK14554 putative pseudouridylate synthase; Provisional
Probab=100.00 E-value=5e-98 Score=791.82 Aligned_cols=392 Identities=30% Similarity=0.442 Sum_probs=342.6
Q ss_pred CcHHHHHHHHhCCCchhhhhhhhcccccccchh----hHHHHHhhhhcccc---c----------ccc--------ccCC
Q 008562 44 LPTDAVKDLLSKEVCLRCIFRLFGMQVPICSSL----SVKSLLCHVLGEQA---D----------LHQ--------NISS 98 (561)
Q Consensus 44 ~~~~av~~Lls~G~C~rCi~Rf~~~~~~~~~n~----~lk~~L~~~L~~~~---D----------l~~--------~~~~ 98 (561)
+...|.++|..|++|++|+||+||..+++++|. +++..|.+.++... | +++ ....
T Consensus 3 i~e~a~~il~~~plCd~CLGR~Fa~~~~gl~N~eRG~aik~~l~m~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (422)
T PRK14554 3 ILEKARAILEKYPLCDHCLGRLFAKLGYGLTNEERGRAIKTALAMELDEPYKEHKEVDLDEILENLGPIAERLYKLYFIE 82 (422)
T ss_pred hHHHHHHHHhcCCCcccccchHHHHHhcCcCHHHHHHHHHHHHhcccchhhcccchhhhHHHHHhhccchhhhhhhcccc
Confidence 456788899999999999999999999999999 67777777654310 1 111 1222
Q ss_pred CCCcccccccccccccccCCccccccccchhHHHHHHHHHHHhcCCccceEEEEeecChhHHhhhhHHHHHHHHhccccc
Q 008562 99 VEPNICRSCLGILQFTYCGDKERVVENESACDFAVAIAELVKKEGHQIDSFSLEVSMPPTILENENKLSLYVKRKYRSEA 178 (561)
Q Consensus 99 ~~~~~C~iClGiLq~~~~d~~~~~~~~~~~~d~~~~I~e~vk~~gyef~sF~L~ISLP~~l~lRE~s~~l~l~~~~~~~~ 178 (561)
..+..|++|+|+|+. .++|+++|.+++ ++|+|+||+++++||+.+..||..+|. +||-.
T Consensus 83 ~~~~~C~iC~g~f~~--------------~~~~a~~v~~~l--~~~e~~tf~vG~~lp~~~~e~E~~i~~----~~gl~- 141 (422)
T PRK14554 83 EFEERCYICGGIFDE--------------IDEFAEKAAEAL--SGYEFDTFLVGTRLPPEIKEKEEEIWE----EFGLT- 141 (422)
T ss_pred ccCCccccccCCHHH--------------HHHHHHHHHHHh--hcCCcceEEEEEEcCHHHHHHHHHHHH----HcCCC-
Confidence 345569999999983 268999999999 599999999999999999999999995 88731
Q ss_pred cccccccccccchhhHHHHhhhhhHHhHhccccCCceeEEEEEEecchhhHHHhhhhhhhcccccccccccccccccccc
Q 008562 179 WFKDRSISECSSTKDALKFALTNPLETLLDVKCGISTFHIRLTYSRVEASIRIQNFVEKIEGCKRRKVDAKNCLDTVKDK 258 (561)
Q Consensus 179 ~~~~~~~~~~v~~Kea~K~~l~~~l~~~L~~~~~~s~f~i~v~~~h~~~~~e~~~l~~~~~~~k~~~~~~~~~~~~~~~~ 258 (561)
...++|.++|+.++..|++++|++.+...-.|.+.|.+..
T Consensus 142 --------~~e~iK~e~nRevGk~l~~~~gk~~d~~~Pdv~i~~d~~~-------------------------------- 181 (422)
T PRK14554 142 --------YGESIKSEINREVGKRLAARTGKEVDFENPDVVIVVDLET-------------------------------- 181 (422)
T ss_pred --------cchhHHHHHHHHHHHHHHHHhCCCCCCCCCcEEEEEEcCC--------------------------------
Confidence 1368999999999999999999998754324554444331
Q ss_pred ccccccccceeeecccccccccccCCCCCCCCCcccccCCCCCCCCceeeEEEEeccEEEEEEeeecccCCCCcccccC-
Q 008562 259 SAITGVENSVVSTTEVIPVDEKSSNGLQDNEPSETHEFPLKKVNEPCRLECLCFRTPIYFGGRYLKYSRNVSQTRWIID- 337 (561)
Q Consensus 259 ~~~~~~~~~~~i~~~l~~~~~~~~~i~~~~f~~~~~~~Pp~~v~~~~~~~~~~~~~pi~i~GRY~K~sR~lsQTpW~~~- 337 (561)
-.|.++++||||+|||+|++|+||||||+|.
T Consensus 182 ------------------------------------------------~~V~~~~~pi~i~GrY~Kl~R~ipQT~W~~~~ 213 (422)
T PRK14554 182 ------------------------------------------------DKVELQVNPLFIYGRYRKLVRGIPQTRWPCRK 213 (422)
T ss_pred ------------------------------------------------CeEEEEECCEEEEEEEeeccCCCCCCccccCC
Confidence 1358889999999999999999999999996
Q ss_pred ccccCcCcHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCCcHHHHHHHHHHHhccCCCcEEE
Q 008562 338 EERMGEASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRV 417 (561)
Q Consensus 338 g~r~~~~SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~~~V~v 417 (561)
+.++|++||||+|+.++.+.|+|++++||+||||||||||||+|||||+||+||+++. .++++|+..+|. +|.|+|
T Consensus 214 g~~~~~~SVeelI~~~i~~~f~~~~~~fh~aGREDvDVRmLG~GRPFViEi~~p~r~~--~~~~~l~~~~~~--~g~V~v 289 (422)
T PRK14554 214 CKKQYPESVEELIAKPVIEAFGGEDAVFHGAGREDVDARMLGTGRPFVIEVKEPRKRK--VDLEALEEEINA--DGKVEV 289 (422)
T ss_pred CCCCCCCCHHHHHHHHHHHHhCCCceEEecCCCCCcceEecCCCCceEEEecCccccc--CCHHHHHHhhcc--CCCEEE
Confidence 4578999999999999999999999999999999999999999999999999999754 677888866664 678999
Q ss_pred EeeEEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHH-HHhcccccceeeeeecCCeEEEeecCCCceeeEEEEE
Q 008562 418 KNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRSPLEREKIINWM 496 (561)
Q Consensus 418 ~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~ 496 (561)
++|++++++++..||+++.+ |.|+|+||+++++++++|++ ++.+++ ++|+|+||+||+|||++++|+|+||+|
T Consensus 290 ~~l~~~~~~~~~~ik~~~~~--K~YralV~~~~~v~~e~l~~~~~~l~~----~~I~QrTP~RV~hRR~~~~R~R~I~~i 363 (422)
T PRK14554 290 ENLRFATRKEVERIKEEKAS--KTYRALVESDEPVSEEELEKLLDELSG----ATIEQRTPRRVKHRRADLVRVRKVYDI 363 (422)
T ss_pred EEEEEEcHHHHHHHhcCCCc--eEEEEEEEECCCCCHHHHHHHHHhccC----cEeeccCcHhhhhhccccceeeEEEEE
Confidence 99999999999999987754 99999999999999999988 589999 999999999999999999999999999
Q ss_pred EEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEEecc
Q 008562 497 KIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDVKMN 556 (561)
Q Consensus 497 ~~~~i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V~~d 556 (561)
++..+++ ++|+++|.||||||||||||||+|||+||||++||++|+|++|||++|+++
T Consensus 364 ~~~~i~~--~~~~l~i~~eaGtYIKElv~GD~GRT~Psl~~lLg~~a~~~eLDV~~V~~~ 421 (422)
T PRK14554 364 SGELIDD--KHFELRIKCEGGLYIKELISGDEGRTTPSLSELLGTPAIVTELDVLDVEGE 421 (422)
T ss_pred EEEEEcC--cEEEEEEEEecCCEEEEEEeCCCCcccccHHHHhCCCceEEEeeEEEEecC
Confidence 9999975 899999999999999999999999999999999999999999999999875
No 3
>KOG2364 consensus Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-94 Score=737.57 Aligned_cols=394 Identities=30% Similarity=0.402 Sum_probs=352.2
Q ss_pred CCCcccccccccccccccCCccccccccchhHHHHHHHHHHHhcCCccceEEEEeecChhHHhhhhHHHHHHHHhccccc
Q 008562 99 VEPNICRSCLGILQFTYCGDKERVVENESACDFAVAIAELVKKEGHQIDSFSLEVSMPPTILENENKLSLYVKRKYRSEA 178 (561)
Q Consensus 99 ~~~~~C~iClGiLq~~~~d~~~~~~~~~~~~d~~~~I~e~vk~~gyef~sF~L~ISLP~~l~lRE~s~~l~l~~~~~~~~ 178 (561)
.+..+|.+|+|||+..++ +++.++|.+.+.+. |||.+|+|+++||+++.+||+++|+.+++.+|.
T Consensus 28 ~nl~vC~~ClGi~~~~~~------------~e~~~kv~~~~~a~-yd~~s~vla~~lP~~l~lRe~a~w~l~~~~~G~-- 92 (433)
T KOG2364|consen 28 ENLFVCQLCLGIMDQAMI------------DEVGEKVQEELSAL-YDSMSFVLALNLPVGLTLREIAVWRLRPDFNGT-- 92 (433)
T ss_pred cccccHHHHHHHHHHHHH------------HHHHHHHHHHHHhh-hhhhheeeEEeCCcchhHHHHHHHHhhHHhcCC--
Confidence 366789999999996665 78999999999999 999999999999999999999999999999994
Q ss_pred cccccccccccchhhHHHHhhhhhHHhHhccccCCceeEEEEEEecchh-hHHHhhhhhhhccccccccccccccccccc
Q 008562 179 WFKDRSISECSSTKDALKFALTNPLETLLDVKCGISTFHIRLTYSRVEA-SIRIQNFVEKIEGCKRRKVDAKNCLDTVKD 257 (561)
Q Consensus 179 ~~~~~~~~~~v~~Kea~K~~l~~~l~~~L~~~~~~s~f~i~v~~~h~~~-~~e~~~l~~~~~~~k~~~~~~~~~~~~~~~ 257 (561)
.+.|+.|||+||+++|.|++.||+..+.|.++|+++|+|+++ -+++++|....+| +|.+.++
T Consensus 93 -------~~~Vp~Kea~k~i~hp~~~e~lgk~~d~~~L~~~i~f~hee~~~edv~fLv~~~p~----------~F~~~k~ 155 (433)
T KOG2364|consen 93 -------LASVPYKEANKDIYHPKLGEYLGKRPDLSDLQLMITFMHEEQIFEDVKFLVVRHPG----------EFHENKV 155 (433)
T ss_pred -------CcccchHHHhhhhhhhHHHHHhCCCCCccccEEEEEecChhhhhHHHHHHHHhCcc----------ccCcccc
Confidence 346999999999999999999999999999999999999997 5677777755554 4444444
Q ss_pred ccc--ccccccceeeecccccccccccCCCCCCCCCcccccCCCCCCCCc-eeeEEEEeccEEEEEEeeecccCCCCccc
Q 008562 258 KSA--ITGVENSVVSTTEVIPVDEKSSNGLQDNEPSETHEFPLKKVNEPC-RLECLCFRTPIYFGGRYLKYSRNVSQTRW 334 (561)
Q Consensus 258 ~~~--~~~~~~~~~i~~~l~~~~~~~~~i~~~~f~~~~~~~Pp~~v~~~~-~~~~~~~~~pi~i~GRY~K~sR~lsQTpW 334 (561)
.|. .+|+ ++..+++. +++.+.+. ++|++|+..+.+.+ .++|.|++.||||||||+||||+||||||
T Consensus 156 ~q~~~~~tr---~~~~ka~q-------kvk~e~~e-k~f~~~~~~~~~~~~~~eI~~q~~~vyiAGRY~KySR~LpqTPW 224 (433)
T KOG2364|consen 156 YQVSGGGTR---EVDKKALQ-------KVKGEGQE-KWFIPYTEIMVRVQDGVEIVVQNSPVYIAGRYIKYSRNLPQTPW 224 (433)
T ss_pred ceecccccc---HhHHHHHH-------Hhhhcccc-ccccCCcccchhheeeEEEEecCCcEEEeeehhhhhccCCCCCc
Confidence 443 3333 34444444 88889999 99999999998877 57999999999999999999999999999
Q ss_pred ccCccccCcCcHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCCcHHHHHHHHH-HHhccCCC
Q 008562 335 IIDEERMGEASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIES-KINSLENK 413 (561)
Q Consensus 335 ~~~g~r~~~~SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~-~In~~~~~ 413 (561)
+++|.|.++.||||+|..++.++|++++++|++||||||||||||+|||||+||.||||... .++ .+|. .+
T Consensus 225 i~dg~Rl~enSveE~i~dhl~~~F~a~d~~F~sSGREDvDVRmLG~GRPFvlEl~N~rr~~~------~~q~~~n~--~~ 296 (433)
T KOG2364|consen 225 IVDGPRLKENSVEEDIKDHLKEFFSADDVVFISSGREDVDVRMLGTGRPFVLELKNPRRNLG------FEQLRLNL--YG 296 (433)
T ss_pred ccCCcccccccHHHHHHHHHHhhcCccceeeccCCCcceeeEeccCCCceEEEcCCccccch------HHHhhhhc--cC
Confidence 99999999999999999999999999999999999999999999999999999999998542 333 4454 35
Q ss_pred cEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHHHHhcccccceeeeeecCCeEEEeecCCCceeeEE
Q 008562 414 LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQTISSLKETVRCYQILQKTPIRVLHRRSPLEREKII 493 (561)
Q Consensus 414 ~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~l~~~~~~~~~~~I~QkTP~RVlhRR~~~~R~R~I 493 (561)
.+.|.+|+.|+|+....|+.||+.|+|.|.|.+|+-+|+...++.+..+.+. ++|.|+||.||+ .|.|.|
T Consensus 297 ~lqV~~l~~v~re~~~~~~kgee~k~k~y~a~~~s~k~i~~~q~~~~~~~~~----lki~qktp~Rv~------irer~i 366 (433)
T KOG2364|consen 297 GLDVKNLCVVRRECKDMIFKGEEQKSKIYSAFLCCRRPIVLQKNYKVRQRTP----LKILQKTPNRVR------IRERCI 366 (433)
T ss_pred CeeeeeheeehHHhhhhhhhchhHHHHHHHHhhhhhhhHHHHhHHHHhccCc----cchhhhcccchh------hhhhhh
Confidence 7999999999999999999999999999999999999999888888888888 999999999987 899999
Q ss_pred EEEEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEEecc
Q 008562 494 NWMKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDVKMN 556 (561)
Q Consensus 494 y~~~~~~i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V~~d 556 (561)
|.|+..+.+ .|+|.+.+.||||||||||||||||||.||||++++..+ +++|||..|+.+
T Consensus 367 ~~me~~~~d--~hhf~v~leTqagtyIkefvhgdfgrt~psl~sl~nv~~-iLeLDve~vd~~ 426 (433)
T KOG2364|consen 367 LGMEKMEAD--WHHFRVVLETQAGTYIKEFVHGDFGRTAPSLSSLENVCD-ILELDVERVDKR 426 (433)
T ss_pred hhhccCccc--ceEEEEeehhhhhhHHHHHhcCCccccCccccchhhhhh-hhhCcchhhccc
Confidence 999998887 599999999999999999999999999999999999988 999999999876
No 4
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-90 Score=714.25 Aligned_cols=385 Identities=32% Similarity=0.497 Sum_probs=330.6
Q ss_pred cHHHHHHHHhCCCchhhhhhhhcccccccchh----hHHHHHhhhhccccccccccCCCCCcccccccccccccccCCcc
Q 008562 45 PTDAVKDLLSKEVCLRCIFRLFGMQVPICSSL----SVKSLLCHVLGEQADLHQNISSVEPNICRSCLGILQFTYCGDKE 120 (561)
Q Consensus 45 ~~~av~~Lls~G~C~rCi~Rf~~~~~~~~~n~----~lk~~L~~~L~~~~Dl~~~~~~~~~~~C~iClGiLq~~~~d~~~ 120 (561)
...|.+.|..+++|++|++|+|+..+++++|. +++..|.+.++. ...+..++.+|++|.|+|..
T Consensus 4 ie~a~~iL~~~plCd~ClGR~FA~l~~Gl~N~ERGraik~~l~l~~~~-----~~~~~~e~~~C~iC~g~f~~------- 71 (398)
T COG1258 4 IEKALEILAKYPLCDSCLGRCFAKLGTGLENRERGRAIKLSLALELDE-----EYKNEVEPEPCYICGGIFDR------- 71 (398)
T ss_pred HHHHHHHHHhCcchHHHHHHHHHHHccCccchhHHHHHHHHHHhhcCc-----ccccCCCCCCchhHhchHhH-------
Confidence 45688999999999999999999999999998 456666665554 12234577899999999994
Q ss_pred ccccccchhHHHHHHHHHHHhcCCccceEEEEeecChhHHhhhhHHHHHHHHhccccccccccccccccchhhHHHHhhh
Q 008562 121 RVVENESACDFAVAIAELVKKEGHQIDSFSLEVSMPPTILENENKLSLYVKRKYRSEAWFKDRSISECSSTKDALKFALT 200 (561)
Q Consensus 121 ~~~~~~~~~d~~~~I~e~vk~~gyef~sF~L~ISLP~~l~lRE~s~~l~l~~~~~~~~~~~~~~~~~~v~~Kea~K~~l~ 200 (561)
.++|+..+.++| ++|+|.||+++..+|..+..+|..+|. +|| +...|++|
T Consensus 72 -------~~~~~~~v~~~l--~~~ef~tf~VGs~~p~~~~e~E~ei~~----~fg-------------~~~gEsiK---- 121 (398)
T COG1258 72 -------VEEFADLVAKLL--KELEFSTFVVGSRVPEEVKEAESEIWE----EFG-------------IGYGESIK---- 121 (398)
T ss_pred -------HHHHHHHHHHHh--hhcceeEEEeeeecChHHHHHHHHHHH----Hhc-------------cccchhHH----
Confidence 279999999999 899999999999999999999999998 777 22233311
Q ss_pred hhHHhHhccccCCceeEEEEEEecchhhHHHhhhhhhhccccccccccccccccccccccccccccceeeeccccccccc
Q 008562 201 NPLETLLDVKCGISTFHIRLTYSRVEASIRIQNFVEKIEGCKRRKVDAKNCLDTVKDKSAITGVENSVVSTTEVIPVDEK 280 (561)
Q Consensus 201 ~~l~~~L~~~~~~s~f~i~v~~~h~~~~~e~~~l~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~ 280 (561)
+ +...|+.+++....| |...+.+|+ .+|..+++
T Consensus 122 ----------~--------------E~nREvGK~~~~~~G-~~~d~~~Pd-----------------i~i~vd~~----- 154 (398)
T COG1258 122 ----------H--------------EFNREVGKRLASKTG-KEPDFDNPD-----------------IVIVVDLE----- 154 (398)
T ss_pred ----------H--------------HHHHHHHHHHHHhcC-CCCCCCCCC-----------------EEEEEecC-----
Confidence 1 112234444433333 333344444 23333333
Q ss_pred ccCCCCCCCCCcccccCCCCCCCCceeeEEEEeccEEEEEEeeecccCCCCcccccCccccCcCcHHHHhhhccccccCC
Q 008562 281 SSNGLQDNEPSETHEFPLKKVNEPCRLECLCFRTPIYFGGRYLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCRG 360 (561)
Q Consensus 281 ~~~i~~~~f~~~~~~~Pp~~v~~~~~~~~~~~~~pi~i~GRY~K~sR~lsQTpW~~~g~r~~~~SVeE~I~~~~~~~f~~ 360 (561)
...+.++.+||||+|||+|+.||||||+|+|+ .++..||+++|+.++.++|+|
T Consensus 155 -------------------------~~~v~vqvnpi~i~GrY~Kl~R~ipQT~wp~~--~~~~~sve~~i~~~~~~~f~g 207 (398)
T COG1258 155 -------------------------TLKVEVQVNPIYIYGRYRKLVRGIPQTRWPCR--ELYPESVEELIKQPIKEAFGG 207 (398)
T ss_pred -------------------------CcEEEEEEcceEEEEEehhhhcCCCcccCcCc--ccccccHHHHHHHHHHHhccC
Confidence 13568889999999999999999999999997 489999999999999999999
Q ss_pred CceEEeecCCCCccccccCCCccEEEEEecCccCCcHHHHHHHHHHHhccCCCcEEEEeeEEecchhhhhhhcccccccc
Q 008562 361 DSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQK 440 (561)
Q Consensus 361 ~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K 440 (561)
.+++||+||||||||||||+|||||+|+++||++. .+++.|+++||.+. +|+|.+|.+++++++..+|+ ++..+|
T Consensus 208 ~~~~fhgAGREDvDvRMLG~GRPfVlEvk~Pr~R~--~dl~~l~~~in~~~--~vev~~l~f~~~e~v~~ik~-~~~~rK 282 (398)
T COG1258 208 LDAKFHGAGREDVDVRMLGTGRPFVLEVKEPRRRN--VDLDELEEEINRGG--KVEVFDLEFVGREEVEEIKE-TERHRK 282 (398)
T ss_pred ceeEEEccCCCccceeeecCCCceEEEecCccccc--CChHHHHHHhccCC--cEEEEEEEecCHHHHHHHHh-ccccce
Confidence 99999999999999999999999999999998754 78999999999853 79999999999999999999 899999
Q ss_pred eEEEEEEEcCCCCHHHHHH-HHhcccccceeeeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecCCce
Q 008562 441 QYAALVWISRPLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTY 519 (561)
Q Consensus 441 ~Y~alv~~~~~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqaGtY 519 (561)
.|+|+|++++|+++++|.. +.++.+ .+|.|+||.||+||||+++|.|+||.+++..+++ ++|.+.|.|+||||
T Consensus 283 ~YrAlV~~~~~v~~e~l~~~~~~L~g----~~I~QrTP~RV~hrRadlvR~R~V~~l~~~~~~~--~~~~~~i~~egGlY 356 (398)
T COG1258 283 VYRALVYSDRPVSDEKLEEVLGSLEG----KTIRQRTPRRVLHRRADLVRIRRVYELSLDLIDD--RHAELEIEAEGGLY 356 (398)
T ss_pred eEEEEEEECCCcCHHHHHHHHhhccC----cEEeecChHHHhhhhcccceEEEEEEeeeeeccC--ceEEEEEEecccce
Confidence 9999999999999999966 889999 9999999999999999999999999999999964 99999999999999
Q ss_pred eeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEEecc
Q 008562 520 IKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDVKMN 556 (561)
Q Consensus 520 IKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V~~d 556 (561)
||||||||.|||+||+|++||.+|.|.+|||++|.-.
T Consensus 357 IKElIsGD~GRT~PSlse~lg~~a~~~eLDVl~V~~~ 393 (398)
T COG1258 357 IKELISGDGGRTRPSLSEILGVEAVVEELDVLKVEDE 393 (398)
T ss_pred eeeeecCCCCCcCcchHHHhCCcceEEEeeeEEeccC
Confidence 9999999999999999999999999999999999754
No 5
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=99.50 E-value=2.8e-13 Score=131.26 Aligned_cols=154 Identities=20% Similarity=0.293 Sum_probs=112.0
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccCCC-----cEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHH
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLENK-----LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQT 459 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~-----~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~ 459 (561)
++=|..|.-..|..-+..+...+|...-| +-...++-++.-....++-+--....|+|+|.+.+...++.++|++
T Consensus 4 ~l~i~Kp~g~tS~~~v~~~k~~~~~kkvGH~GTLDp~A~GvLiv~~g~~Tk~~~~~~~~~K~Y~a~v~~g~~it~e~l~~ 83 (182)
T cd02572 4 VINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDDVDEEKVRR 83 (182)
T ss_pred EEEEecCCCCCHHHHHHHHHHHhCCCccCcCCCCCCcCeeEEEEEECHHhhhhHHHhCCCCEEEEEEEECCcCCHHHHHH
Confidence 34455676655666666666655542111 0111222222111111121222334499999999999999999977
Q ss_pred -HHhcccccceeeeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhh
Q 008562 460 -ISSLKETVRCYQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSI 538 (561)
Q Consensus 460 -l~~~~~~~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~i 538 (561)
++.|.+ +|.|+||.++.+++. .|+++||++++..++....+|.+++.|++||||++|+|+ ||..
T Consensus 84 ~l~~f~G-----~i~Q~pP~~SA~K~~--~R~v~I~~i~l~~~~~~~~~~~~~v~cs~GTYIRsL~~d--------lg~~ 148 (182)
T cd02572 84 VLEEFTG-----AIFQRPPLISAVKRQ--LRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCVH--------IGLL 148 (182)
T ss_pred HHHHCCC-----cEEeeCCHhheecCC--ceEEEEEEEEEEEEcCCCcEEEEEEEECCCcCHHHHHHH--------HHHH
Confidence 899999 799999999999986 899999999999886433689999999999999999997 9999
Q ss_pred cCCccEEEEEEEEEE
Q 008562 539 LGCRAEILQLDVTDV 553 (561)
Q Consensus 539 Lg~~adileLDV~~V 553 (561)
||+.|.+.+|.=+.+
T Consensus 149 Lg~~a~l~~L~R~~~ 163 (182)
T cd02572 149 LGVGAHMQELRRTRS 163 (182)
T ss_pred HCCCeEEEEEEeEEE
Confidence 999999999987765
No 6
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=99.23 E-value=7.9e-11 Score=123.30 Aligned_cols=146 Identities=22% Similarity=0.330 Sum_probs=111.2
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCCCC
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQ 453 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~ 453 (561)
++=|..|.-..|..-+..+....|... .| |-+--+ ++ ..++-+--....|.|+|.+++..+++
T Consensus 36 ~l~i~KP~g~tS~~~v~~vr~~~~~kkvGH~GTLDP~A~G-vL~v~~---G~--aTkl~~~~~~~~K~Y~~~v~lG~~~~ 109 (322)
T TIGR00425 36 VVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTG-VLPVCI---ER--ATRLVKSLQEAPKEYVCLMRLHRDAK 109 (322)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhcccccCCCCCCCCCCce-EEEEEE---Ch--HhhccHHhccCCCEEEEEEEECCCCC
Confidence 555667776556666667766665321 22 222122 21 12222223345699999999999999
Q ss_pred HHHHHH-HHhcccccceeeeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcC
Q 008562 454 DEDFQT-ISSLKETVRCYQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTN 532 (561)
Q Consensus 454 ~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~ 532 (561)
+++|+. |+.|.| +|.|.+|..+.++|. .|+.+||++++..+++ ..+.+++.|++||||+.|+|.
T Consensus 110 ~~~l~~~l~~f~g-----~i~Q~pP~~SA~k~~--~r~v~I~~~~l~~~~~--~~~~~~v~cskGTYIRsL~~D------ 174 (322)
T TIGR00425 110 EEDILRVLKEFTG-----RIFQRPPLKSAVKRQ--LRVRTIYESELLEKDG--KDVLFRVSCEAGTYIRKLCVD------ 174 (322)
T ss_pred HHHHHHHHHHcCC-----cEEeeCChheEEecc--CeEEEEEEEEEEEecC--CeEEEEEEeCCCcChHHHHHH------
Confidence 999976 999999 799999999999987 8999999999988864 568999999999999999996
Q ss_pred cchhhhcCCccEEEEEEEEEE
Q 008562 533 PSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 533 PSl~~iLg~~adileLDV~~V 553 (561)
||+.||+.+++.+|-=+.+
T Consensus 175 --ig~~Lg~~a~~~~L~R~~~ 193 (322)
T TIGR00425 175 --IGEALGTGAHMQELRRTRS 193 (322)
T ss_pred --HHHHHCCCEEEEEeEeEEE
Confidence 9999999999998865544
No 7
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=99.21 E-value=1.3e-10 Score=120.71 Aligned_cols=152 Identities=21% Similarity=0.315 Sum_probs=111.8
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccCCC-----cEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHH
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLENK-----LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQT 459 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~-----~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~ 459 (561)
++=|..|.-..|..-+..+....+...-| +-...++-++--....++-+--....|+|+|.+++..+++.++++.
T Consensus 24 ~l~i~Kp~g~tS~~~v~~~r~~~~~kkvGH~GTLDp~A~GvL~v~~g~atk~~~~~~~~~K~Y~~~~~~g~~~~~~~~~~ 103 (300)
T PRK04270 24 VVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLESGKEYVCVMHLHGDVPEEDIRK 103 (300)
T ss_pred EEEEECCCCCCHHHHHHHHHHHhccccccCCCCCCCcCeEEEEEEEChHhhhhHHhccCCcEEEEEEEECCCCCHHHHHH
Confidence 45566676555555555665555432111 0111122222111122333334445699999999999999999987
Q ss_pred -HHhcccccceeeeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhh
Q 008562 460 -ISSLKETVRCYQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSI 538 (561)
Q Consensus 460 -l~~~~~~~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~i 538 (561)
|..|.+ +|.|.+|..+.++|+ .|+.+||++++..++. .+|.+++.|+.||||+.|||+ +|..
T Consensus 104 ~l~~~~g-----~i~Q~pP~~SA~k~~--~r~v~I~~i~~~~~~~--~~~~~~v~cs~GtYIRsl~~d--------ig~~ 166 (300)
T PRK04270 104 VFKEFTG-----EIYQKPPLKSAVKRR--LRVRTIYELEILEIDG--RDVLFRVRCESGTYIRKLCHD--------IGLA 166 (300)
T ss_pred HHHHCCC-----cEEeECCHHHhccCC--ceEEEEEEEEEEEecC--CEEEEEEEECCceEHHHHHHH--------HHHH
Confidence 899999 899999999999987 8999999999988864 689999999999999999999 9999
Q ss_pred cCCccEEEEEEEEEE
Q 008562 539 LGCRAEILQLDVTDV 553 (561)
Q Consensus 539 Lg~~adileLDV~~V 553 (561)
||+.|++.+|-=+.+
T Consensus 167 Lg~~a~~~~L~R~~~ 181 (300)
T PRK04270 167 LGTGAHMQELRRTRT 181 (300)
T ss_pred HCCCeEEEEEEeEEE
Confidence 999999998865543
No 8
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=99.07 E-value=6.2e-10 Score=114.04 Aligned_cols=153 Identities=16% Similarity=0.239 Sum_probs=111.1
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccCCCc-----EEEEeeEEecchhhhhhhcccccccceEEEEEEEcCCC-CHHHHH
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLENKL-----VRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPL-QDEDFQ 458 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~~-----V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v-~~e~l~ 458 (561)
++=|-.|+-..|.+-+..+...++...-|. -.+.++=.+--....++-.--.+..|.|+|.++++... +.++++
T Consensus 17 il~ldKP~G~tS~~~v~~vkkil~~~K~GH~GTLDP~atGvLpi~ig~aTKl~~~l~~~~K~Y~a~~~lG~~t~~~e~i~ 96 (271)
T COG0130 17 VINLDKPPGPTSHEVVAWVKRILGVEKAGHGGTLDPLATGVLPICLGEATKLVQYLLDADKEYVATVRLGDQTDSEEEVR 96 (271)
T ss_pred eEEeeCCCCCCHHHHHHHHHHHhCccccccccccCCcccceEEEEechhHhHHHHHhhCCcEEEEEEEeCCcCCCHHHHH
Confidence 344556776556676777777666532210 11111111111111222222234459999999999988 889998
Q ss_pred H-HHhcccccceeeeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhh
Q 008562 459 T-ISSLKETVRCYQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGS 537 (561)
Q Consensus 459 ~-l~~~~~~~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~ 537 (561)
. |..|.| .|.|.+|+.....|. ++.|.||..++..++.....+.+++.|++||||+-++|. ||.
T Consensus 97 ~~l~~F~G-----~I~Q~PP~~SAvK~~--v~~R~V~i~~l~~~~~~~~~~~~~v~CskGTYIRtL~~D--------lG~ 161 (271)
T COG0130 97 AALEAFTG-----EIYQIPPMFSAVKRE--VERRKITIYDLLELDFDRNLVTLRVECSKGTYIRTLARD--------LGE 161 (271)
T ss_pred HHHHhcce-----eeEecCCchhhccce--EeeEEEEEEEeeeccCCCceEEEEEEEecCcCHHHHHHH--------HHH
Confidence 8 899999 999999999999977 555989888888888766799999999999999999999 999
Q ss_pred hcCCccEEEEEEEEE
Q 008562 538 ILGCRAEILQLDVTD 552 (561)
Q Consensus 538 iLg~~adileLDV~~ 552 (561)
.||+.|++.+|-=+.
T Consensus 162 ~LG~gahm~~LrRt~ 176 (271)
T COG0130 162 ALGCGAHMSELRRTR 176 (271)
T ss_pred HHCCccchhhhcccc
Confidence 999999999875443
No 9
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=98.85 E-value=5e-08 Score=96.84 Aligned_cols=148 Identities=19% Similarity=0.265 Sum_probs=106.3
Q ss_pred EEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC-----
Q 008562 387 EIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR----- 450 (561)
Q Consensus 387 Ei~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~----- 450 (561)
=|..|.-..|..-+..+...+|... .| |-+-.+.-.++ ....+. ...|.|.|.+.+..
T Consensus 4 ~i~KP~g~tS~~vv~~ik~~~~~kKvGH~GTLDP~AsG-vLiv~vG~aTk-l~~~~~----~~~K~Y~~~~~lG~~TdT~ 77 (210)
T cd00506 4 AVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATG-VLVVGIGKATK-LLKHLL----AATKDYTAIGRLGQATDTF 77 (210)
T ss_pred EEEcCCCCCHHHHHHHHHHHhCccccCCCCcCCCcCee-EEEEEECHHHh-hhHHHh----cCCceEEEEEEECCcCCCC
Confidence 3455665556666677776665421 22 22222221221 122222 25699999999653
Q ss_pred -------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEee----cC-----------CCceeeEEEEEEEEEE
Q 008562 451 -------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR----RS-----------PLEREKIINWMKIEKI 501 (561)
Q Consensus 451 -------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR----R~-----------~~~R~R~Iy~~~~~~i 501 (561)
.++.+++++ +..|.+ .|.|.+|.-...+ |+ ...|+..||++++...
T Consensus 78 D~~G~v~~~~~~~~it~e~l~~~l~~f~G-----~i~Q~pP~ySAvKv~G~raYelAR~G~~v~~~~r~v~I~~i~ll~~ 152 (210)
T cd00506 78 DATGQVIEETPYDHITHEQLERALETLTG-----DIQQVPPLYSAVKRQGQRAYELARRGLLVPDEARPPTIYELLCIRF 152 (210)
T ss_pred CCCCCEEEEeCCCCCCHHHHHHHHHHCCC-----eEEEeCCchheEEECCHhHHHHHHCCCccccCcEeEEEEEEEEEEE
Confidence 267888988 889999 8999999774444 33 7789999999999887
Q ss_pred cCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 502 AGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 502 ~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
+.....+.+++.|+.||||+.|+|. ||..||+.|.+.+|.-+.+
T Consensus 153 ~~~~~~~~~~v~cs~GTYIRsL~~D--------ig~~Lg~~a~l~~L~R~~~ 196 (210)
T cd00506 153 NPPHFLLEVEVVCETGTYIRTLIHD--------LGLELGVGAHVTELRRTRV 196 (210)
T ss_pred cCCCcEEEEEEEECCCcCHHHHHHH--------HHHHhCCcEEEEEEEEEEE
Confidence 6421489999999999999999997 9999999999999998876
No 10
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=98.60 E-value=8.8e-07 Score=89.75 Aligned_cols=154 Identities=18% Similarity=0.284 Sum_probs=107.9
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccCCCc-----EEEEeeEEecchhhhhhhcccccccceEEEEEEEcC---------
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLENKL-----VRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR--------- 450 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~~-----V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~--------- 450 (561)
++=|..|.-..|..-+..+...++...-|. -...++=++--....++-+--....|.|.|.+++..
T Consensus 12 il~vdKP~G~TS~dvv~~vkr~~~~kKvGH~GTLDP~AtGvLiv~iG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~D~~G 91 (244)
T PRK00020 12 VLLLDKPVGLSSNHALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRATKISGRMLEADKTYQATLQFGEETDSGDLTG 91 (244)
T ss_pred EEEEecCCCCCHHHHHHHHHHHhCCCCCCcCCcCCCcCeeEEEEEECHHhhhhHHhccCCcEEEEEEEeCCcccCCCCCC
Confidence 566777876667677777777665422110 011112111111111222222333499999999764
Q ss_pred -----------CCCHHHHHH-HHhcccccceeeeeecCCeEEEeecC---------------CCceeeEEEEEEEEEEcC
Q 008562 451 -----------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRS---------------PLEREKIINWMKIEKIAG 503 (561)
Q Consensus 451 -----------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~---------------~~~R~R~Iy~~~~~~i~~ 503 (561)
.++.+++++ |..|.| +|.|.+|.-...+.. ...|+-+||++++...+.
T Consensus 92 ~v~~~~~~~~~~it~e~l~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~~~~ 166 (244)
T PRK00020 92 HIVARAPDGFAGVEEAALRDVLSRFVG-----TIEQIPPMYSALKRDGKPLYEYARAGIELDRPPRQVTIRHIELLSFSG 166 (244)
T ss_pred cEEEeccCccCCCCHHHHHHHHHhccC-----eEEEeCChhheEEECCeEHHHHHhCCcccccCCeeEEEEEEEEEEEeC
Confidence 277888888 889999 899999987766544 346888999999988864
Q ss_pred CccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 504 SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 504 ~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
..+.+++.|+.||||+-++|. ||..||+.+.+.+|-=+.+
T Consensus 167 --~~~~~~v~cSkGTYIRSL~~D--------iG~~Lg~~a~l~~LrRt~~ 206 (244)
T PRK00020 167 --MQAQIDVACSKGTYIRTLAQD--------IGRALGCHAHLAALRRTHV 206 (244)
T ss_pred --CEEEEEEEECCCcCHHHHHHH--------HHHHHCCCEEEEEEEeeEE
Confidence 688999999999999999998 9999999999998866554
No 11
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=98.58 E-value=1.9e-07 Score=97.00 Aligned_cols=149 Identities=17% Similarity=0.229 Sum_probs=106.5
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC---
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR--- 450 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~--- 450 (561)
++=|..|.-..|..-+..+...++... .| |-+--+.-.+|- ...+. . .|.|+|.+++..
T Consensus 5 il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtG-vL~i~vG~aTkl-~~~l~----~-~K~Y~a~~~lG~~Td 77 (295)
T PRK02755 5 FLNLDKPAGLTSHDCVARLRRLLRLKRVGHGGTLDPAATG-VLPIALGKATRL-LPYLP----G-EKTYRGTIRFGVRTS 77 (295)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCCccccCCCCCCcCee-EEEEEEChhhhh-HHHhC----C-CcEEEEEEEECCccc
Confidence 344556765556666666666555421 22 323233323321 22332 1 399999999875
Q ss_pred ---------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEee----c-----------CCCceeeEEEEEEEE
Q 008562 451 ---------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR----R-----------SPLEREKIINWMKIE 499 (561)
Q Consensus 451 ---------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR----R-----------~~~~R~R~Iy~~~~~ 499 (561)
+++.+++++ |..|.| +|.|.+|.-...+ | .+..|+-+||++++.
T Consensus 78 T~D~~G~v~~~~~~~~~~~~~l~~~l~~f~G-----~i~Q~PP~ySAvKv~G~r~Y~lAR~G~~ve~~~r~v~I~~~~l~ 152 (295)
T PRK02755 78 TDDLQGEILSSQPWPHLSLAEIETALPQFRG-----KIEQRPPQYSAIQVDGERLYALARRGETMELPARTVTIFRLQLL 152 (295)
T ss_pred CCCCCCCEEEecCCCCCCHHHHHHHHHhccC-----eEEEeCChhheEeeCCHhHHHHHHCCCccccCceEEEEEEEEEE
Confidence 478888888 899999 8999999877665 2 144788899999998
Q ss_pred EEcC-CccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 500 KIAG-SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 500 ~i~~-~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
.++. ....|.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 153 ~~~~~~~~~~~~~v~cskGTYIRsL~~D--------iG~~Lg~~a~m~~LrRt~~ 199 (295)
T PRK02755 153 DWRPGDQPELDLEIHCGAGTYIRSLARD--------LGAVLGTGGTLAALRRTQS 199 (295)
T ss_pred EEcCCCCceEEEEEEECCCcCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 8763 13588999999999999999998 9999999999999865544
No 12
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=98.55 E-value=1.3e-06 Score=89.89 Aligned_cols=148 Identities=14% Similarity=0.210 Sum_probs=104.2
Q ss_pred EEEecCccCCcHHHHHHHHHHHhccCCC----------cEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCC----
Q 008562 386 FEIQNAREVPSELLVKEIESKINSLENK----------LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRP---- 451 (561)
Q Consensus 386 lEi~nPr~~~~~~~~~~l~~~In~~~~~----------~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~---- 451 (561)
+=+..|.-..|..-+..+....+...-| .|-+-.+.-.+| -+..+ ....|+|.|.+|+...
T Consensus 5 l~vdKP~g~tS~~vv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~iG~aTK-l~~~l----~~~~K~Y~a~~~lG~~TdT~ 79 (273)
T PRK04099 5 FVANKPAGMSSNAFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQYTK-LFRFL----KKTPKTYRATLWLGASSPSL 79 (273)
T ss_pred EEEeCCCCCCHHHHHHHHHHHhCCCccccCccCCCCCeeEEEEEEChHhh-hHHHh----ccCCceEEEEEEECCcccCC
Confidence 3355576555666666666655432111 122222222222 12222 2336999999998533
Q ss_pred -------------CCHHHHHH-HHhcccccceeeeeecCCeEEEeecC---------------CCceeeEEEEEEEEEEc
Q 008562 452 -------------LQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRS---------------PLEREKIINWMKIEKIA 502 (561)
Q Consensus 452 -------------v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~---------------~~~R~R~Iy~~~~~~i~ 502 (561)
++.++++. |.+|.| +|.|.+|.=...+.. +..|+.+||++++...+
T Consensus 80 D~e~i~~~~~~~~~~~~~i~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~~~ll~~~ 154 (273)
T PRK04099 80 DIENIESIQIIKPFDKDLIEKILKSLQG-----EISYTPPKFSAKKINGKRAYELARKGEEFELKPITMEIFDCKLLSYN 154 (273)
T ss_pred CCcceEEeccCCCCCHHHHHHHHHhCcc-----eEEEeCChhhEEeeCCHhHHHHHhCCcccccCceeEEEEEEEEEEEe
Confidence 67888888 889999 899999976665532 45699999999988775
Q ss_pred CCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 503 GSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 503 ~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
. .+|.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 155 ~--p~~~f~v~cs~GTYIRSL~~D--------ig~~Lg~~a~m~~LrRt~~ 195 (273)
T PRK04099 155 H--PFLTFEITVSEGAYIRSLGEL--------IAKKLGVNGTLSSLERLSE 195 (273)
T ss_pred C--CEEEEEEEECCCCCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 3 688999999999999999998 9999999999999876554
No 13
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=98.54 E-value=9.4e-07 Score=92.48 Aligned_cols=149 Identities=17% Similarity=0.273 Sum_probs=108.4
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccCCC----------cEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC----
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLENK----------LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR---- 450 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~----------~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~---- 450 (561)
++=|..|.-..|..-+..+...++...-| .|-+-.+.-.+| -...+ ....|.|+|.+.+..
T Consensus 12 il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~aTk-l~~~~----~~~~K~Y~a~~~lG~~TdT 86 (312)
T PRK05033 12 VLLLDKPQGMSSNDALQKVKRLFNANKAGHTGALDPLATGMLPICLGEATK-FSQYL----LDSDKRYRVTARLGQRTDT 86 (312)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCCCCCCCCcCCCcCeeEEEEEECHHhh-hhHHh----cCCCcEEEEEEEECCcccC
Confidence 55566777655666677777666542111 122222222222 12222 234699999999764
Q ss_pred -------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEee---------------cCCCceeeEEEEEEEEEE
Q 008562 451 -------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR---------------RSPLEREKIINWMKIEKI 501 (561)
Q Consensus 451 -------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR---------------R~~~~R~R~Iy~~~~~~i 501 (561)
+++.+++++ |+.|.| .|.|.+|.-...+ .....|+-.||++++..+
T Consensus 87 ~D~~G~v~~~~~~~~t~~~l~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~~ 161 (312)
T PRK05033 87 SDADGEVVEERPVTLSAEQLEAALEKFRG-----DIEQVPSMYSALKYQGQPLYEYARQGIEVEREARPITIYELELIRF 161 (312)
T ss_pred CCCCCCEEEeecCCCCHHHHHHHHHHCcC-----cEEEeCChhHeEeeCCeEHHHHHhCCcccccCceeEEEEEEEEeeE
Confidence 478889998 899999 8999999877765 234588999999999888
Q ss_pred cCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 502 AGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 502 ~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
+. .+|.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 162 ~~--~~~~~~v~cs~GTYIRsL~~D--------ig~~Lg~~a~~~~LrRt~~ 203 (312)
T PRK05033 162 EG--DELELEVHCSKGTYIRTLVDD--------LGEKLGCGAHVIYLRRTQV 203 (312)
T ss_pred eC--CEEEEEEEECCCCCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 64 689999999999999999998 9999999999999865544
No 14
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=98.54 E-value=8.8e-07 Score=91.92 Aligned_cols=148 Identities=22% Similarity=0.235 Sum_probs=105.9
Q ss_pred EEEecCccCCcHHHHHHHHHHHhccCCC----------cEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC-----
Q 008562 386 FEIQNAREVPSELLVKEIESKINSLENK----------LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR----- 450 (561)
Q Consensus 386 lEi~nPr~~~~~~~~~~l~~~In~~~~~----------~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~----- 450 (561)
+=|..|.-..|..-+..+...++...-| .|-+-.+.-.+| ....+. ..-|+|+|.+.+..
T Consensus 5 l~i~KP~G~tS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~aTk-l~~~l~----~~~K~Y~a~~~lG~~TdT~ 79 (290)
T PRK00130 5 LNILKPPGMTSFDVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKATK-IVDYLM----EGKKTYRAEIKLGVETDTY 79 (290)
T ss_pred EEEeCCCCCCHHHHHHHHHHHhCCCccCcCCCCCCCCeeEEEEEEChhhh-hHHHhc----cCCcEEEEEEEECCcccCC
Confidence 3355576555666666776666542211 122222222222 122222 33599999999753
Q ss_pred -------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEee---------------cCCCceeeEEEEEEEEEE
Q 008562 451 -------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR---------------RSPLEREKIINWMKIEKI 501 (561)
Q Consensus 451 -------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR---------------R~~~~R~R~Iy~~~~~~i 501 (561)
+++.+++++ |..|.| +|.|.+|.-...+ .....|+-.||++++..+
T Consensus 80 D~~G~i~~~~~~~~~t~~~l~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~l~~~ 154 (290)
T PRK00130 80 DREGEILKEKEVSHLTEEEIREAILSFQG-----EIDQVPPMYSALKINGKKLYELARQGIEVEREARKITIYDIEILEI 154 (290)
T ss_pred CCCCCEEEecCCCCCCHHHHHHHHHHccC-----eEEEECChHHeEecCCHhHHHHHHCCCccccCceEEEEEEEEEEEE
Confidence 378889988 899999 8999999887776 123489999999999887
Q ss_pred cCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 502 AGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 502 ~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
+. .+|.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 155 ~~--~~~~~~v~cskGTYIRsL~~D--------ig~~Lg~~a~~~~LrRt~~ 196 (290)
T PRK00130 155 DL--PYVIFDVKCSKGTYIRSLCFD--------IGEKLNCGAYMWNLIRTET 196 (290)
T ss_pred eC--CeEEEEEEECCCCCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 64 689999999999999999998 9999999999998865544
No 15
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=98.52 E-value=1.1e-06 Score=91.67 Aligned_cols=149 Identities=17% Similarity=0.233 Sum_probs=107.3
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCC--
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRP-- 451 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~-- 451 (561)
++=|..|.-..|..-+..+...++... .| |-+-.+.-.+| -...+ ....|+|+|.+.+...
T Consensus 15 il~i~KP~G~TS~dvv~~vrk~~~~kKvGH~GTLDP~AtG-vL~v~vG~aTk-l~~~l----~~~~K~Y~a~~~lG~~Td 88 (305)
T PRK05389 15 WLILDKPAGMTSTEAVSKVKWLFDAQKAGHAGTLDPLASG-VLPIALGEATK-TVPYV----MDGTKRYRFTVAWGEERD 88 (305)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhcccccCCcccCCCCCce-EEEEEEChhhh-hhHHh----ccCCcEEEEEEEECCccc
Confidence 566777876556666666666554321 22 22222222221 12222 2245999999997533
Q ss_pred ---------------CCHHHHHH-HHhcccccceeeeeecCCeEEEeecC---------------CCceeeEEEEEEEEE
Q 008562 452 ---------------LQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRS---------------PLEREKIINWMKIEK 500 (561)
Q Consensus 452 ---------------v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~---------------~~~R~R~Iy~~~~~~ 500 (561)
++.+++++ |+.|.| +|.|.+|.-...+.. ...|+-+||++++..
T Consensus 89 T~D~~G~v~~~~~~~~~~~~i~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~ 163 (305)
T PRK05389 89 TDDLEGEVTATSDVRPTDEEIRAALPAFTG-----EIMQVPPQFSAIKIDGERAYDLAREGETVELPARPVEIDRLTLVE 163 (305)
T ss_pred CCCCCCCEEEecCCCCCHHHHHHHHHhccc-----eEEEeCCchheEEECCHhHHHHHHCCCccccCceEEEEEEEEEEE
Confidence 77888888 899999 899999977766643 557888999999988
Q ss_pred EcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 501 IAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 501 i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
.++ ..+|.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 164 ~~~-~~~~~~~v~cskGTYIRsL~~D--------iG~~Lg~~a~~~~LrRt~~ 207 (305)
T PRK05389 164 RPD-ADHAVFEVECGKGTYVRSLARD--------LGRALGCYGHIAALRRTRV 207 (305)
T ss_pred ecC-CCeEEEEEEeCCCCCHHHHHHH--------HHHHHCCCeEEEEEEeEEE
Confidence 743 3588999999999999999998 9999999999998866544
No 16
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=98.50 E-value=2.3e-06 Score=88.38 Aligned_cols=153 Identities=16% Similarity=0.223 Sum_probs=105.0
Q ss_pred EecCccCCcHHHHHHHHHHHhccCCC-----cEEEEeeEEecchhhhhhhcccccccceEEEEEEEc-------------
Q 008562 388 IQNAREVPSELLVKEIESKINSLENK-----LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWIS------------- 449 (561)
Q Consensus 388 i~nPr~~~~~~~~~~l~~~In~~~~~-----~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~------------- 449 (561)
|-.|.-..|..-+..+...++...-| +-...++-++--....++-+--....|+|+|.+.+.
T Consensus 5 i~KP~G~tS~~vv~~vr~~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~~~~~~G~~TdT~D~~G~v~ 84 (277)
T cd02573 5 LDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDADKTYRATVRLGEATDTDDAEGEII 84 (277)
T ss_pred EECCCCCCHHHHHHHHHHHhCcCccCCCCCCCCcCeEEEEEEEChHHhhHHHhcCCCcEEEEEEEECCcccCCCCCCCEE
Confidence 45566555666666666655542111 011122222211111122222223569999999975
Q ss_pred -----CCCCHHHHHH-HHhcccccceeeeeecCCeEEEee---------------cCCCceeeEEEEEEEEEEcCCccEE
Q 008562 450 -----RPLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR---------------RSPLEREKIINWMKIEKIAGSSQYF 508 (561)
Q Consensus 450 -----~~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR---------------R~~~~R~R~Iy~~~~~~i~~~~~~f 508 (561)
..++.+++++ |+.|.+ .|.|.+|.-...+ .....|+-.||++++...+....+|
T Consensus 85 ~~~~~~~~~~~~i~~~l~~f~G-----~i~Q~PP~ySAvkv~G~raYelAR~G~~ve~~~r~v~I~~i~ll~~~~~~~~~ 159 (277)
T cd02573 85 ETSPPPRLTEEEIEAALKAFTG-----EIEQVPPMYSAVKVNGKRLYELARAGEEVERPPRKVTIYSLELLSFDPENPEA 159 (277)
T ss_pred EecCCCCCCHHHHHHHHHHccC-----cEEeeCChhHeEeeCCccHHHHHhCCCccccCCeeEEEEEEEEEEecCCCCeE
Confidence 2378888888 889999 8999999876665 3456899999999998876322589
Q ss_pred EEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 509 LLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 509 ~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
.+++.|+.||||+-++|. ||..||+.|.+.+|-=+.+
T Consensus 160 ~~~v~cs~GTYIRsL~~D--------ig~~Lg~~a~~~~L~Rt~~ 196 (277)
T cd02573 160 DFEVECSKGTYIRSLARD--------LGKALGCGAHLSALRRTRS 196 (277)
T ss_pred EEEEEECCCCcHHHHHHH--------HHHHHCCCeEEEEEEEEEE
Confidence 999999999999999998 9999999999998865544
No 17
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
Probab=98.50 E-value=2.2e-06 Score=85.16 Aligned_cols=148 Identities=18% Similarity=0.231 Sum_probs=105.6
Q ss_pred EEEecCccCCcHHHHHHHHHHHhccCCC----------cEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCC----
Q 008562 386 FEIQNAREVPSELLVKEIESKINSLENK----------LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRP---- 451 (561)
Q Consensus 386 lEi~nPr~~~~~~~~~~l~~~In~~~~~----------~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~---- 451 (561)
+=|..|.-..|..-+..+...++...-| .|-+-.+.-.++ ....+ ...-|.|.+.+.+...
T Consensus 5 l~v~KP~g~tS~~vv~~vkk~~~~kKvGH~GTLDP~AsGvLiv~vG~~Tk-l~~~~----~~~~K~Y~~~~~~G~~TdT~ 79 (209)
T TIGR00431 5 LLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATK-LSPYL----TDLDKEYRAEIRLGVRTDTL 79 (209)
T ss_pred EEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCCCcCceEEEEEEChHhh-hhHHH----cCCCCeEEEEEEECCcCCCC
Confidence 3455676555666677777766542211 122222221121 12222 2456999999997742
Q ss_pred -------------CCHHHHHH-HHhcccccceeeeeecCCeEEEee---------------cCCCceeeEEEEEEEEEEc
Q 008562 452 -------------LQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR---------------RSPLEREKIINWMKIEKIA 502 (561)
Q Consensus 452 -------------v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR---------------R~~~~R~R~Iy~~~~~~i~ 502 (561)
++.+++++ +.+|.+ ++.|.+|.-...+ .+...|+-.||++++...+
T Consensus 80 D~~G~i~~~~~~~~~~~~l~~~l~~f~G-----~~~Q~PP~ySA~Kv~G~raYelAR~g~~v~~~~r~v~I~~i~ll~~~ 154 (209)
T TIGR00431 80 DPDGQIVETRPVNPTTEDVEAALPTFRG-----EIEQIPPMYSALKVNGKRLYEYARQGIEVERKARPVTVYDLQFLKYE 154 (209)
T ss_pred CCCCCEEEecCCCCCHHHHHHHHHHccC-----cEEEECChhhEEeeCCHhHHHHHHCCCccccCcceeEEEEEEEEEEc
Confidence 45678887 889999 8999999877765 2355889999999988876
Q ss_pred CCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 503 GSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 503 ~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
. .+|.+++.|+.||||+-++|. ||..||+.|.+.+|-=+.+
T Consensus 155 ~--~~~~~~v~cs~GTYIRsL~~D--------ig~~L~~~a~l~~L~Rt~~ 195 (209)
T TIGR00431 155 G--PELTLEVHCSKGTYIRTLARD--------LGEKLGCGAYVSHLRRTAV 195 (209)
T ss_pred C--CcEEEEEEECCCCCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 3 589999999999999999998 9999999999999866544
No 18
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=98.48 E-value=2.1e-06 Score=88.70 Aligned_cols=150 Identities=16% Similarity=0.202 Sum_probs=105.5
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC---
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR--- 450 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~--- 450 (561)
++=|..|.-..|..-+..+...++... .| |-+-.+.-.+| ....+ ....|.|+|.+++..
T Consensus 2 il~i~KP~G~tS~dvv~~vrr~~~~kKvGH~GTLDP~AtG-vL~v~vG~aTk-l~~~l----~~~~K~Y~a~~~lG~~Td 75 (279)
T PRK02193 2 IKLLYKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASG-LLLVATDEDTK-LIDYL----DQKDKTYIAKIKFGFIST 75 (279)
T ss_pred EEEEECCCCCCHHHHHHHHHHHcCCCccccCccCCCcCee-EEEEEEChhhh-hhHHh----ccCCcEEEEEEEeCCccc
Confidence 344566765556666666666555321 22 22222222222 12222 344599999999762
Q ss_pred ---------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEee---------------cCCCceeeEEEEEEEE
Q 008562 451 ---------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR---------------RSPLEREKIINWMKIE 499 (561)
Q Consensus 451 ---------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR---------------R~~~~R~R~Iy~~~~~ 499 (561)
+++.++++. |.+|.| +|.|.+|.=...+ .....|+-.||++++.
T Consensus 76 T~D~~G~i~~~~~~~~~~~~~l~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll 150 (279)
T PRK02193 76 TYDSEGQIINVSQNIKVTKENLEEALNNLVG-----SQKQVPPVFSAKKVNGKRAYDLARQGKQIELKPIEIKISKIELL 150 (279)
T ss_pred CCCCCCCEEeecCCCCCCHHHHHHHHHhCcC-----eEEEeCChHHeEeeCCHhHHHHHhCCceeccCCeeEEEEEEEEE
Confidence 367888888 889999 8999999776666 3455677799999998
Q ss_pred EEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 500 KIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 500 ~i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
.++.....+.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 151 ~~~~~~~~~~~~v~cskGTYIRsL~~D--------iG~~Lg~~a~~~~LrRt~~ 196 (279)
T PRK02193 151 NFDEKLQNCVFMWVVSRGTYIRSLIHD--------LGKMLKTGAYMSDLERTKI 196 (279)
T ss_pred EEcCCCceEEEEEEECCCcCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 886422578999999999999999998 9999999999998865544
No 19
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=98.46 E-value=1.7e-06 Score=90.44 Aligned_cols=148 Identities=19% Similarity=0.240 Sum_probs=104.9
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEc----
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWIS---- 449 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~---- 449 (561)
++=|..|.-..|..-+..+...++... .| |-+-.+.-.++ -...+. ...|+|+|.+++.
T Consensus 5 il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtG-vL~v~vG~aTk-l~~~l~----~~~K~Y~a~~~lG~~Td 78 (308)
T PRK14124 5 FLVAYKPKGPTSHDVVDEVRKKLKTRKVGHAGTLDPFATG-VLIVGVNKATR-LLEYLK----NEKKVYYVKMRLGLITE 78 (308)
T ss_pred EEEEECCCCCCHHHHHHHHHHHcCCCccCcCcCCCCCCcE-EEEEEEChHHh-hhHHHh----cCCceEEEEEEeCcccc
Confidence 344666765556666666666555321 22 22222222222 122222 2359999999863
Q ss_pred -------------CCCCHHHHHH-HHhcccccceeeeeecCCeEEEeecC---------------CCceeeEEEEEEEEE
Q 008562 450 -------------RPLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRS---------------PLEREKIINWMKIEK 500 (561)
Q Consensus 450 -------------~~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~---------------~~~R~R~Iy~~~~~~ 500 (561)
.+++.+++++ |..|.| .|.|.+|.-...+.. ...|+-+||++++..
T Consensus 79 T~D~~G~vi~~~~~~~~~~~i~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~ 153 (308)
T PRK14124 79 TFDITGEVVEERECNVTEEEIREAIFSFVG-----EYKQVPPAYSAKKYKGERLYKLAREGKIINLPPKEVKIYEIWDIS 153 (308)
T ss_pred CCCCCCCEEEecCCCCCHHHHHHHHHhCcC-----eEEEeCCchHeEEECChhHHHHHhCCCccccCceeeEEEEEEEEE
Confidence 3478888888 899999 899999987665533 346888999999988
Q ss_pred EcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 501 IAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 501 i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
.+. ..|.+++.|+.||||+-|+|. ||..||+.|.+.+|-=+.+
T Consensus 154 ~~~--~~~~~~v~cskGTYIRsL~~D--------iG~~Lg~~a~m~~LrRt~~ 196 (308)
T PRK14124 154 IEG--PDVSFRVEVSPGTYIRSLCMD--------IGYKLGCGATAVELVRLSV 196 (308)
T ss_pred EeC--CeEEEEEEECCCCCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 764 689999999999999999998 9999999999998865543
No 20
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=98.45 E-value=1.9e-06 Score=89.92 Aligned_cols=148 Identities=15% Similarity=0.215 Sum_probs=106.2
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC---
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR--- 450 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~--- 450 (561)
++=|..|.-..|..-+..+...++... .| |-+-.+.-.+| ....+ ....|.|+|.+.+..
T Consensus 18 il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtG-vL~v~vG~aTk-l~~~l----~~~~K~Y~~~~~lG~~Td 91 (303)
T PRK01851 18 VLLLDKPLGLSSNDALQRAKRLLRAKKAGHTGTLDPLATG-LLPLCFGEATK-FSQDL----LDADKTYEATLRLGVRTS 91 (303)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCcccCCCCCCCCCCCce-EEEEEECHHHh-hhHHh----cccCeEEEEEEEECCccC
Confidence 455667776556666777776665421 22 22222222222 12222 233499999999763
Q ss_pred --------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEeec---------------CCCceeeEEEEEEEEE
Q 008562 451 --------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRR---------------SPLEREKIINWMKIEK 500 (561)
Q Consensus 451 --------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR---------------~~~~R~R~Iy~~~~~~ 500 (561)
+++.+++++ |..|.| .|.|.+|.=...+. ....|+-+||++++..
T Consensus 92 T~D~~G~v~~~~~~~~t~~~i~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~R~v~I~~i~ll~ 166 (303)
T PRK01851 92 TGDAEGEVLATRPVDCDPAALEAALARFTG-----EIRQVPPMYSALKKDGKPLYEYARAGITVEREARDVTIHALDLLA 166 (303)
T ss_pred CCCCCCCEEeecCCCCCHHHHHHHHHhccC-----eeeeeCCchheEeeCCeeHHHHHhCCCccccCCcceEEEEEEEEE
Confidence 278888888 899999 89999997655543 2358888999999988
Q ss_pred EcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 501 IAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 501 i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
++. ..|.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 167 ~~~--~~~~~~v~cskGTYIRsL~~D--------iG~~Lg~~a~~~~LrRt~~ 209 (303)
T PRK01851 167 CDL--PDVTIRVTCSKGTYIRTLAED--------IGEALGCGAHLTALRRTGV 209 (303)
T ss_pred EeC--CEEEEEEEECCCCCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 764 689999999999999999998 9999999999998865544
No 21
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=98.44 E-value=2.9e-06 Score=88.59 Aligned_cols=147 Identities=20% Similarity=0.262 Sum_probs=104.1
Q ss_pred EEEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC----
Q 008562 386 FEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR---- 450 (561)
Q Consensus 386 lEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~---- 450 (561)
+=|..|.-..|..-+..+...++... .| |-+--+.-.+| -...+. ..-|.|+|.+.+..
T Consensus 5 l~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtG-vL~i~vG~aTk-l~~~l~----~~~K~Y~a~~~lG~~TdT 78 (304)
T PRK01550 5 LLLHKPRGMTSHDCVFKLRKILRTKKVGHTGTLDPEVSG-VLPICVGRATK-IAEYLT----DEGKTYEGEVTLGFSTTT 78 (304)
T ss_pred EEEECCCCCCHHHHHHHHHHHcCCCCcccCCCCCCcCee-EEEEEEChhhh-hhHHhc----CCCcEEEEEEEECCcccC
Confidence 34555665556666666666555321 22 22222222222 122222 33599999999741
Q ss_pred ---------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEee-----------------cCCCceeeEEEEEE
Q 008562 451 ---------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR-----------------RSPLEREKIINWMK 497 (561)
Q Consensus 451 ---------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR-----------------R~~~~R~R~Iy~~~ 497 (561)
+++.+++++ |..|.| .|.|.+|.-...+ |+ .|+-.||+++
T Consensus 79 ~D~~G~v~~~~~~~~~~~~~~i~~~l~~f~G-----~i~Q~PP~ySAvKv~Gkr~YelAR~G~~ve~~--~r~v~I~~i~ 151 (304)
T PRK01550 79 EDADGEVVETKPVDRPITREEIEAALASLTG-----TIEQIPPMYSAVKVNGKKLYEYARAGIEVERP--VRQITIHEFV 151 (304)
T ss_pred CCCCCCEEeeccCCCCCCHHHHHHHHHhccc-----eEEEeCChhHeEecCCHhHHHHHHCCCccccC--CcceEEEEEE
Confidence 378899988 899999 8999999888776 55 8888999999
Q ss_pred EEEE----cCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 498 IEKI----AGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 498 ~~~i----~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
+... +.....|.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 152 ll~~~~~~~~~~~~~~~~v~cskGTYIRsL~~D--------ig~~Lg~~a~~~~L~Rt~~ 203 (304)
T PRK01550 152 LLDSREDFEGETQSFRFRVTCSKGTYVRTLAVM--------IGEKLGYPAHMSHLVRTAS 203 (304)
T ss_pred EEeeccccccCCceEEEEEEECCCCCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 8752 2223689999999999999999998 9999999999999866554
No 22
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=98.41 E-value=4.8e-06 Score=86.76 Aligned_cols=149 Identities=18% Similarity=0.236 Sum_probs=105.0
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccCCC----------cEEEEeeEEecchhhhhhhcccccccceEEEEEEEc-----
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLENK----------LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWIS----- 449 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~----------~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~----- 449 (561)
++=|..|.-..|..-+..+...++...-| .|-+--+.-.+ ++-+--...-|.|+|.+.+.
T Consensus 12 il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~~G~aT-----kl~~~l~~~~K~Y~a~~~lG~~TdT 86 (300)
T PRK04642 12 ILLLDKPAGLSSNNALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEAT-----KIAGLLLGSAKAYDAEIVLGVTTDT 86 (300)
T ss_pred EEEEecCCCCCHHHHHHHHHHHhCCCcccCCCccCCcCeeeEEEEEChhh-----hhhHHhcCCCcEEEEEEEECccccC
Confidence 55566777655666666776666542211 12222222122 22222233459999999761
Q ss_pred -----------C--CCCHHHHHH-HHhcccccceeeeeecCCeEEEeecC---------------CCceeeEEEEEEEEE
Q 008562 450 -----------R--PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRS---------------PLEREKIINWMKIEK 500 (561)
Q Consensus 450 -----------~--~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~---------------~~~R~R~Iy~~~~~~ 500 (561)
. +++.+++++ +..|.| +|.|.+|.-...+.. ...|+-.||++++..
T Consensus 87 ~D~~G~v~~~~~~~~~~~~~l~~~l~~f~G-----~i~Q~PP~ySAvKv~GkrlY~lAR~G~~ve~~~R~v~I~~~~ll~ 161 (300)
T PRK04642 87 DDADGQVLRERPVPDLSAAALQAALAPLIG-----RIRQRAPIYSALKQGGEPLYAKARRGEVIEAPVREVEVHAIEVLG 161 (300)
T ss_pred cCCCCCEEEecCCCCCCHHHHHHHHHHCCC-----cEEEeCCchHeEeECCeeHHHHHhCCCccccCcEEEEEEEEEEEE
Confidence 1 368888888 899999 899999976655532 247888999999988
Q ss_pred EcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 501 IAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 501 i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
++. ..+.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 162 ~~~--~~~~~~v~cskGTYIRSL~~D--------ig~~Lg~~a~m~~L~Rt~~ 204 (300)
T PRK04642 162 YAA--PRLRLRVTCGSGTYIRSLARD--------LGEVLGCGAHIAALRRLWV 204 (300)
T ss_pred EeC--CEEEEEEEeCCCcCHHHHHHH--------HHHHhCCCEEEEEeEeeEE
Confidence 764 578999999999999999998 9999999999999876654
No 23
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=98.39 E-value=3.8e-06 Score=87.28 Aligned_cols=150 Identities=17% Similarity=0.140 Sum_probs=103.2
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCC--
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRP-- 451 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~-- 451 (561)
++=|..|.-..|..-+..+...++... .| |-+-.+.-.+| +-+--....|.|+|.+.+...
T Consensus 5 iL~i~KP~G~TS~dvv~~vrk~~~~kKvGH~GTLDP~AtG-vL~v~vG~aTK-----l~~~l~~~~K~Y~~~~~lG~~Td 78 (292)
T PRK01528 5 WLNIYKPRGISSAKLVSIVKKILGKVKIGHAGTLDVEAEG-VLPLAVGEATK-----LVQLLIDAKKTYIFTVKFGKQTD 78 (292)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHcCCCccCcCccCCCcCce-EEEEEEChHhh-----hhHHHhcCCceEEEEEEECCccc
Confidence 445666765556666666666555321 12 22222221221 211222344899999987632
Q ss_pred ---------------CCHHHHHH-HHhcccccceeeeeecCCeEEEeecC---------------CCceeeEEEEEEEEE
Q 008562 452 ---------------LQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRS---------------PLEREKIINWMKIEK 500 (561)
Q Consensus 452 ---------------v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~---------------~~~R~R~Iy~~~~~~ 500 (561)
++.+++++ |..|.| +|.|.+|.-...+.. +..|+-+||++++..
T Consensus 79 T~D~~G~v~~~~~~~~~~e~l~~~l~~f~G-----~i~Q~PP~ySAvKv~G~raYelAR~G~~vel~~r~v~I~~i~ll~ 153 (292)
T PRK01528 79 SGDYAGKVIATKDYIPSKEEAYAVCSKFIG-----NITQIPPAFSALKVNGVRAYKLAREGKEVELKPRNITIYDLKCLN 153 (292)
T ss_pred CCCCCCCEEEecCCCCCHHHHHHHHHhccc-----eEEeeCChhHeEEECCHhHHHHHhCCcccccCceeEEEEEEEEEE
Confidence 46778887 899999 899999976655531 345777999999988
Q ss_pred EcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 501 IAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 501 i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
++.....+.+++.|..||||+-++|. ||..||+.|++..|-=+.+
T Consensus 154 ~~~~~~~~~~~v~cskGTYIRsL~~D--------iG~~Lg~~a~~~~LrRt~~ 198 (292)
T PRK01528 154 FDEKNATATYYTECSKGTYIRTLAED--------LALSLQSLGFVIELRRTQV 198 (292)
T ss_pred EcCCCcEEEEEEEECCCccHHHHHHH--------HHHHHCCceEEeEEEeEEE
Confidence 86423578899999999999999998 9999999999998865543
No 24
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=98.38 E-value=3.8e-06 Score=87.39 Aligned_cols=149 Identities=18% Similarity=0.240 Sum_probs=103.4
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccCCC----------cEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC----
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLENK----------LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR---- 450 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~----------~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~---- 450 (561)
++=|..|.-..|..-+..+...++...-| .|-+-.+.-.+| -...+. ...|+|+|.+++..
T Consensus 5 il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~vG~aTk-l~~~l~----~~~K~Y~a~~~lG~~TdT 79 (294)
T PRK02484 5 IINLKKEAGMTSHDAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKATR-LIEYMT----EAGKVYEGEITLGYSTTT 79 (294)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCCccccCCCCCCCCeeEEEEEEChhhh-hhHHhc----cCCcEEEEEEEECCcccC
Confidence 44456676555666666666666542211 122222222222 122222 23399999999631
Q ss_pred ---------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEee-----------------cCCCceeeEEEEEE
Q 008562 451 ---------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR-----------------RSPLEREKIINWMK 497 (561)
Q Consensus 451 ---------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR-----------------R~~~~R~R~Iy~~~ 497 (561)
+++.+++++ |..|.| +|.|.+|.-...+ |+ .|+-.||+++
T Consensus 80 ~D~~G~vi~~~~~~~~~~~~~l~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~--~r~v~I~~i~ 152 (294)
T PRK02484 80 EDASGEVVAETPLTQPLTEEEVDQAMTSFTG-----KITQIPPMYSAVKVNGKKLYEYARAGEEVERP--KRQVTIYQFE 152 (294)
T ss_pred CCCCCCEEEeccCCCCCCHHHHHHHHHhccC-----eEEEeCChhHeEeeCCHhHHHHHHCCCccccC--ceEEEEEEEE
Confidence 278889988 899999 8999999877766 44 7888999999
Q ss_pred EEE---EcC-CccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 498 IEK---IAG-SSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 498 ~~~---i~~-~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
+.. ++. .+..|.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 153 l~~~~~~~~~~~~~~~~~v~cskGTYIRsL~~D--------iG~~Lg~~a~~~~L~Rt~~ 204 (294)
T PRK02484 153 RTSPLSFDEDGLCRFSFRVACSKGTYVRTLAVD--------LGEKLGYAAHMSFLTRTAS 204 (294)
T ss_pred EeccccccccCCceEEEEEEeCCCCCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 863 321 23589999999999999999998 9999999999998865544
No 25
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=98.37 E-value=6.6e-06 Score=85.77 Aligned_cols=151 Identities=16% Similarity=0.214 Sum_probs=106.3
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccCCC----------cEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC----
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLENK----------LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR---- 450 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~----------~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~---- 450 (561)
++=|..|.-..|..-+..+...++...-| .|-+-.+.-.+| ....+. ..-|.|+|.+.+..
T Consensus 11 il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aTK-l~~~l~----~~~K~Y~a~~~lG~~TdT 85 (298)
T PRK03287 11 LVVVDKPAGMTSHDVVARCRRLFGTRKVGHAGTLDPMATGVLVLGVERATK-LLGHLT----LTDKSYTATIRLGQATTT 85 (298)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCCCCCcCccCCCcceeEEEEEeChhhh-hhHHHh----cCCcEEEEEEEeCccccC
Confidence 45566677655666677777666542211 122222222222 122222 23599999999872
Q ss_pred --------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEeecC---------------CCceeeEEEEEEEEE
Q 008562 451 --------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRS---------------PLEREKIINWMKIEK 500 (561)
Q Consensus 451 --------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~---------------~~~R~R~Iy~~~~~~ 500 (561)
.++.+++++ +.+|.| .|.|.+|.-...+.. +..|+-.||++++..
T Consensus 86 ~D~~G~v~~~~~~~~it~~~i~~~l~~f~G-----~i~Q~PP~ySAvKv~Gkr~YelAR~G~~ve~~~R~v~I~~~~l~~ 160 (298)
T PRK03287 86 DDAEGEVLASADASAVTDEAIAAAVAALTG-----EIMQVPSAVSAIKVDGKRAYARVRAGEEVELPARPVTVSRFEVLA 160 (298)
T ss_pred CCCCCCEEeecCCCCCCHHHHHHHHHhCcC-----eEEEeCChhHeEEECCHHHHHHHhCCCccccCcEEEEeeeeEEEE
Confidence 578999998 889999 899999966555431 235888999999988
Q ss_pred EcCC-c-cEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 501 IAGS-S-QYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 501 i~~~-~-~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
++.. + ..+.+++.|..||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 161 ~~~~~~~~~~~~~v~cskGTYIRSL~~D--------ig~~Lg~~a~~~~LrRt~~ 207 (298)
T PRK03287 161 VRRDGDFIDLDVEVDCSSGTYIRALARD--------LGAALGVGGHLTALRRTRV 207 (298)
T ss_pred EecCCCccEEEEEEEECCCcCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 8642 2 267899999999999999998 9999999999999876554
No 26
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=98.34 E-value=7.8e-06 Score=86.32 Aligned_cols=150 Identities=16% Similarity=0.125 Sum_probs=104.6
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEc----
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWIS---- 449 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~---- 449 (561)
++=|-.|.-..|..-+..+...++... .| |-+-.+.-.+| -+..+ ....|.|+|.+++.
T Consensus 5 iL~idKP~G~TS~dvv~~vrk~l~~kKVGH~GTLDP~AtG-VL~i~vG~aTK-l~~~l----~~~~K~Y~a~~~lG~~TD 78 (345)
T PRK14846 5 WLNIYKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEG-ILPFAVGEATK-LIHLL----IDARKTYIFTVKFGMQTN 78 (345)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCCcCCcCccCCCcCce-EEEEEEChhhh-hhHHH----hcCCceEEEEEEECCccC
Confidence 455666776556666666666555321 12 22222222221 11222 23448899999977
Q ss_pred -------------CCCCHHHHHH-HHhcccccceeeeeecCCeEEEeec----C-----------CCceeeEEEEEEEEE
Q 008562 450 -------------RPLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRR----S-----------PLEREKIINWMKIEK 500 (561)
Q Consensus 450 -------------~~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR----~-----------~~~R~R~Iy~~~~~~ 500 (561)
.+++.++++. |..|.| +|.|.+|.-...+. + ...|+-.||++++..
T Consensus 79 T~D~eG~ii~~~~~~~~~e~l~~~L~~f~G-----~i~Q~PP~ySAvKv~GkraYelARkG~~Vel~~R~V~I~~i~ll~ 153 (345)
T PRK14846 79 SGDCAGKVIATKDCIPSQEEAYAVCSKFIG-----NVTQIPPAFSALKVNGVRAYKLAREGKKVELKPRNITIYDLKCLN 153 (345)
T ss_pred CCCCCCCEEEecCCCCCHHHHHHHHHhCcc-----eEEeeCChhheEeECChhHHHHHhCCCccccCceeEEEEEEEEEE
Confidence 3457778887 899999 89999997665543 1 346777999999988
Q ss_pred EcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 501 IAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 501 i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
++.....+.+++.|+.||||+-++|. ||..||+.|.+.+|-=+.+
T Consensus 154 f~~~~~~~~~~v~CSkGTYIRSLa~D--------IG~~Lg~~A~l~~LrRtr~ 198 (345)
T PRK14846 154 FDEKNATATYYTECSKGTYIRTLAED--------LALSLQSLGFVIELRRTQV 198 (345)
T ss_pred EcCCCcEEEEEEEECCCCcHHHHHHH--------HHHHHCCCEEEeEEEeEEE
Confidence 76433578899999999999999998 9999999999999876654
No 27
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=98.30 E-value=7.8e-06 Score=85.67 Aligned_cols=147 Identities=19% Similarity=0.250 Sum_probs=104.0
Q ss_pred EecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC------
Q 008562 388 IQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR------ 450 (561)
Q Consensus 388 i~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~------ 450 (561)
|..|.-..|..-+..+...++... .| |-+-.+.-.+| -...+ ....|+|.|.+.+..
T Consensus 6 idKP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtG-vL~i~iG~aTK-l~~~l----~~~~K~Y~a~~~lG~~TdT~D 79 (312)
T PRK14122 6 VDKPLGLTSHDVVNRARRALGTRRVGHTGTLDPLATG-VLVLCTDDSTK-LVPFL----SAEDKEYLAWVSFGATTPTLD 79 (312)
T ss_pred EECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcCee-eEEEEEChhhh-hhHHh----cCCCceEEEEEEECCcCCCCC
Confidence 555665556566666666554321 22 33333332333 22233 345599999998764
Q ss_pred ------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEeecC---------------CCceeeEEEEEEEEEEc
Q 008562 451 ------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRS---------------PLEREKIINWMKIEKIA 502 (561)
Q Consensus 451 ------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~---------------~~~R~R~Iy~~~~~~i~ 502 (561)
.++.++|+. |+.|.| .|.|.+|.-...+.. ...|+-.||++++...+
T Consensus 80 ~eG~i~~~~~~~~~~~~~l~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~vel~~R~v~I~~i~ll~~~ 154 (312)
T PRK14122 80 AEGPISEEAPVSPLDEKDLEAALPGFLG-----LTEQVPPQYSAIKVGGVRAYEAARAGGALELPARPVVYHELELLAFE 154 (312)
T ss_pred CCCCEEEecCCCCCCHHHHHHHHHhCcC-----eEEEeCChHHeEEECCeEHHHHHhCCCccccCCeeEEEEEEEEEEec
Confidence 478889988 899999 899999976655532 55788899999988765
Q ss_pred CC--------------------------------ccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEE
Q 008562 503 GS--------------------------------SQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDV 550 (561)
Q Consensus 503 ~~--------------------------------~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV 550 (561)
.. ...+.+++.|+.||||+-++|. ||..||+.|++.+|-=
T Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~cSkGTYIRSLa~D--------iG~~Lg~~a~m~~LrR 226 (312)
T PRK14122 155 PSVAPIPRPIAPSAEGWTPDPRGRPVTLPEPLGEYPTALLRLVVGSGTYVRSFARD--------LGAALGVPAHLSGLVR 226 (312)
T ss_pred ccccccccccccccccccccccccccccccccccCceEEEEEEeCCCcCHHHHHHH--------HHHHHCCCEEEEEEEe
Confidence 31 0368899999999999999998 9999999999999876
Q ss_pred EEE
Q 008562 551 TDV 553 (561)
Q Consensus 551 ~~V 553 (561)
+.+
T Consensus 227 t~~ 229 (312)
T PRK14122 227 TRV 229 (312)
T ss_pred EEE
Confidence 554
No 28
>KOG2364 consensus Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=98.25 E-value=3.4e-08 Score=103.67 Aligned_cols=121 Identities=12% Similarity=0.059 Sum_probs=103.4
Q ss_pred EEEeeEEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHHHHhcccccceeeeeecCCeEEEeecCCCceeeEEEE
Q 008562 416 RVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQTISSLKETVRCYQILQKTPIRVLHRRSPLEREKIINW 495 (561)
Q Consensus 416 ~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~l~~~~~~~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~ 495 (561)
...+|++++...+.+.+.|+..|-+.|++++++.-+.+..-|... +. ....|+||+++.|+++ .|++ ||+
T Consensus 294 ~~~~lqV~~l~~v~re~~~~~~kgee~k~k~y~a~~~s~k~i~~~---q~----~~~~~~~~lki~qktp--~Rv~-ire 363 (433)
T KOG2364|consen 294 LYGGLDVKNLCVVRRECKDMIFKGEEQKSKIYSAFLCCRRPIVLQ---KN----YKVRQRTPLKILQKTP--NRVR-IRE 363 (433)
T ss_pred ccCCeeeeeheeehHHhhhhhhhchhHHHHHHHHhhhhhhhHHHH---hH----HHHhccCccchhhhcc--cchh-hhh
Confidence 345899999999999999999999999999999998886555543 33 4678899999999988 8999 887
Q ss_pred EEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEE
Q 008562 496 MKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQ 547 (561)
Q Consensus 496 ~~~~~i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adile 547 (561)
.-+......+.- ..++++++|||++++|||-+|+|.|+.+..||...++..
T Consensus 364 r~i~~me~~~~d-~hhf~v~leTqagtyIkefvhgdfgrt~psl~sl~nv~~ 414 (433)
T KOG2364|consen 364 RCILGMEKMEAD-WHHFRVVLETQAGTYIKEFVHGDFGRTAPSLSSLENVCD 414 (433)
T ss_pred hhhhhhccCccc-ceEEEEeehhhhhhHHHHHhcCCccccCccccchhhhhh
Confidence 766666654445 899999999999999999999999999999999988875
No 29
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=98.24 E-value=1.7e-05 Score=82.98 Aligned_cols=150 Identities=19% Similarity=0.219 Sum_probs=102.9
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcC---
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR--- 450 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~--- 450 (561)
++=|..|.-..|..-+..+...++... .| |-+--+.-.+| -...+. ...|.|+|.+.+..
T Consensus 5 il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtG-vL~v~vG~aTk-l~~~l~----~~~K~Y~~~~~lG~~Td 78 (305)
T PRK14123 5 ILPVYKERGLTSHDVVFKLRKILKTKKIGHTGTLDPEVAG-VLPVCIGNATR-VSDYVM----DMGKAYEATVSIGRSTT 78 (305)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCCccccCcCCCCcCee-EEEEEEChhhh-hHHHhc----CCCcEEEEEEEECCccc
Confidence 344566765556666666666555421 12 22222222222 122222 24599999998631
Q ss_pred -----------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEee---------------cCCCceeeEEEEEE
Q 008562 451 -----------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR---------------RSPLEREKIINWMK 497 (561)
Q Consensus 451 -----------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR---------------R~~~~R~R~Iy~~~ 497 (561)
.++.++++. |..|.| .|.|.+|.-...+ .....|+=.||+++
T Consensus 79 T~D~~G~vi~~~~~~~~~~~~~~l~~~l~~f~G-----~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ 153 (305)
T PRK14123 79 TEDQTGDTLETKGVHSADFNKDDIDRLLEQFKG-----IIEQIPPMYSSVKVNGKKLYEYARNNETVERPKRKVNIKDIG 153 (305)
T ss_pred CCCCCCCEEEeccCCcCCCCHHHHHHHHHhccC-----ceeecCChhheEeeCCHhHHHHHhCCCcccCCceEEEEEEEE
Confidence 278888988 899999 8999999877765 22335777899988
Q ss_pred EEE---EcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 498 IEK---IAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 498 ~~~---i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
+.. ++.....|.+++.|+.||||+-++|. ||..||+.|++.+|-=+.+
T Consensus 154 ~~~~~~~~~~~~~~~~~v~cskGTYIRsL~~D--------iG~~Lg~~a~~~~LrRt~~ 204 (305)
T PRK14123 154 RISELDFKENECHFKIRVICGKGTYIRTLATD--------IGVKLGFPAHMSKLTRIES 204 (305)
T ss_pred EeecccccCCCceEEEEEEeCCCcCHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 763 33222589999999999999999998 9999999999999876554
No 30
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=98.18 E-value=7.8e-06 Score=85.65 Aligned_cols=103 Identities=17% Similarity=0.239 Sum_probs=85.0
Q ss_pred ccceEEEEEEEc------------------CCCCHHHHHH-HHhcccccceeeeeecCCeEEEeecC-------------
Q 008562 438 KQKQYAALVWIS------------------RPLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRS------------- 485 (561)
Q Consensus 438 k~K~Y~alv~~~------------------~~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~------------- 485 (561)
..|.|.+.+.+. ..++.+++++ |..|.| .|.|.+|+-...+..
T Consensus 89 ~~K~Y~~~~~lG~~TdT~D~eG~Ii~~~~~~~it~e~i~~~l~~F~G-----~i~Q~PP~ySAvKv~GkrlYeyAR~G~~ 163 (312)
T cd02867 89 CSKTYEATGLFGASTTTYDREGKILKKKPYSHITREDIEEVLAKFRG-----DIKQVPPLYSALKMDGKRLYEYAREGKP 163 (312)
T ss_pred CCceEEEEEEeCCcccCCCCCCCEEEecCCCCCCHHHHHHHHHhcce-----eeeeeCcchheeeeCCHHHHHHHhCCcc
Confidence 459999999964 2478999998 889999 899999987776643
Q ss_pred ----CCceeeEEEEEEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 486 ----PLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 486 ----~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
...|+-.||++++...+....+|.+++.|+.||||+-++|. ||..||+.+++.+|-=+.+
T Consensus 164 v~~~~~~R~V~I~~~~l~~~~~~~~~~~~~v~cskGTYIRsL~~D--------ig~~Lg~~a~~~~L~Rt~~ 227 (312)
T cd02867 164 LPRPIERRQVVVSELLVKDWIEPGPLFTRTVEEEGKQYERSVVKM--------LGKELKTFAEVTELTATAE 227 (312)
T ss_pred ccCCCCCceEEEEEEEEEeccCCCCeEEEEEEeCCcCCHHHHHHH--------HHHHhCCCeEEEEEEeeee
Confidence 33677799999987764223589999999999999999998 9999999999998876654
No 31
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=98.10 E-value=6.2e-05 Score=75.95 Aligned_cols=152 Identities=17% Similarity=0.226 Sum_probs=98.6
Q ss_pred EEEEecCccCCcHHHHHHHHHHHhccCCCc-----EEEEeeE--EecchhhhhhhcccccccceEEEEEEEc--------
Q 008562 385 LFEIQNAREVPSELLVKEIESKINSLENKL-----VRVKNLK--IVGSQGWTLMREGEAEKQKQYAALVWIS-------- 449 (561)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~~-----V~v~~L~--~v~r~~~~~ik~~e~~k~K~Y~alv~~~-------- 449 (561)
++=|..|.-..|..-+..+...+|...-|. -...++= .+++...+.+. --...-|.|.+.+.+.
T Consensus 11 ~l~i~KP~g~TS~dvv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~vG~~aTkl~~-~~~~~~K~Y~~~~~~G~~TdT~D~ 89 (230)
T PRK00989 11 ILLVDKPQGRTSFSLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGRKFTRLSD-ILLFEDKEYAAVAHLGTTTDSYDC 89 (230)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCCcCCcCccCCCCCeeEEEEEECCchhhhHH-HhcCCCcEEEEEEEECCcccCCCC
Confidence 445666776556666777777666422110 0111111 22331111111 1122459999999963
Q ss_pred ---------CCCCHHHHHH-HHhcccccceeeeeecCCeEEEeecCC---------------CceeeEEEEEEEEEEcCC
Q 008562 450 ---------RPLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRSP---------------LEREKIINWMKIEKIAGS 504 (561)
Q Consensus 450 ---------~~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~~---------------~~R~R~Iy~~~~~~i~~~ 504 (561)
..++.+++++ |..|.| .+.|.+|.-...+..- ..|.=+|| +++...+.
T Consensus 90 ~G~vi~~~~~~~~~~~i~~~l~~f~G-----~~~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~i~-~~ll~~~~- 162 (230)
T PRK00989 90 DGKIVGRSKKIPTLEEVLSAASYFQG-----EIQQVPPMFSAKKVQGKKLYEYARQGLSIERRPSTVQVH-LQLTKYEY- 162 (230)
T ss_pred CCcEEEecCCCCCHHHHHHHHHhCcc-----eEEeeCChhHeEEECCHhHHHHHhCCCccccCcEEEEEE-EEEEEeeC-
Confidence 3467888888 899999 8999999655544211 12333466 66666543
Q ss_pred ccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 505 SQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 505 ~~~f~l~i~tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
..|.+++.|..||||+-++|. ||..||+.|.+.+|-=+.+
T Consensus 163 -p~~~~~v~cs~GTYIRSL~~D--------iG~~Lg~~a~~~~LrRt~~ 202 (230)
T PRK00989 163 -PLLHFVVQCSKGTYIRSIAHE--------LGNMLGCGAYLEELRRLRS 202 (230)
T ss_pred -CeEEEEEEEcCCCcHHHHHHH--------HHHHHCCCEEEEEEEeEEE
Confidence 689999999999999999998 9999999999998876654
No 32
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 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. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=97.75 E-value=8.7e-05 Score=70.29 Aligned_cols=74 Identities=20% Similarity=0.332 Sum_probs=59.6
Q ss_pred ceEEEEEEEcC------------------CCCHHHHHH-HHhcccccceeeeeecCCeEEEee---------------cC
Q 008562 440 KQYAALVWISR------------------PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR---------------RS 485 (561)
Q Consensus 440 K~Y~alv~~~~------------------~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR---------------R~ 485 (561)
|.|.+.+.+.. .++.++|++ |..|.+ .|.|.+|.-...+ ++
T Consensus 42 K~Y~~~~~lG~~TdT~D~~G~v~~~~~~~~it~e~l~~~l~~f~G-----~~~Q~pP~ySAvki~G~raY~lAR~G~~v~ 116 (149)
T PF01509_consen 42 KEYVATIRLGVETDTYDIEGEVTETKPYDHITEEDLEKVLAKFQG-----EIEQVPPMYSAVKINGKRAYELARKGEEVE 116 (149)
T ss_dssp EEEEEEEEESSEETTSBTTSSEEEE---TT--HHHHHHHHHHTSE-----EEEES-SSSSSSECTTCEHHHHHHTTSSTS
T ss_pred CEEEEEEEEEEEeCCcceeeeEEEeeccccCCHHHHHHHHHhCcC-----CEeeeCchheeEcCCCccHHHHHHCCCccC
Confidence 99999998642 356788888 889999 9999999988766 33
Q ss_pred CCceeeEEEEEEEEEEcCCccEEEEEEEecCCcee
Q 008562 486 PLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYI 520 (561)
Q Consensus 486 ~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqaGtYI 520 (561)
...|+..||++++..++. ..|.+++.|.+||||
T Consensus 117 ~~~r~v~I~~i~l~~~~~--~~~~~~v~cs~GTYi 149 (149)
T PF01509_consen 117 LPPRPVTIYSIELLSFNP--PEFTFEVHCSKGTYI 149 (149)
T ss_dssp SS-EEEEEEEEEEEEEET--TEEEEEEEECTTTTH
T ss_pred CCCeeEEEEEEEEEEEcC--CeEEEEEEEcCcccC
Confidence 457999999999998875 599999999999997
No 33
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=97.69 E-value=0.00022 Score=71.89 Aligned_cols=88 Identities=19% Similarity=0.197 Sum_probs=69.3
Q ss_pred CCCHHHHHH-HHhcccccceeeeeecCCeEEEee---------------cCCCceeeEEEEEEEEEEcCCccEEEEEEEe
Q 008562 451 PLQDEDFQT-ISSLKETVRCYQILQKTPIRVLHR---------------RSPLEREKIINWMKIEKIAGSSQYFLLHMCT 514 (561)
Q Consensus 451 ~v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhR---------------R~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~t 514 (561)
.++.+++++ |..|.+ .+.|.+|.=.+.+ +++..|+=.||++++..++. .+|.+++.|
T Consensus 98 ~it~~~i~~~l~~f~g-----~~~q~~p~~sa~kv~GkraYelAR~G~~ve~~~r~v~I~~i~l~~~~~--p~~~~~v~c 170 (226)
T cd02868 98 HITREKIERLLAVIQS-----GHQQKAFELCSVDDQSQQAAELAARGLIRPADKSPPIIYGIRLLEFRP--PEFTLEVQC 170 (226)
T ss_pred CCCHHHHHHHHHHhhC-----CceEECCceEEEeeCCHHHHHHHHCCCccCCCCcceEEEEEEEEEecC--CeEEEEEEE
Confidence 378888888 889987 4566677433222 33455777899999988753 588999999
Q ss_pred cCCc--eeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008562 515 QAGT--YIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 553 (561)
Q Consensus 515 qaGt--YIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V 553 (561)
..|| ||+-|+|. ||..||+.|.+.+|-=+.+
T Consensus 171 skGT~~YIRsL~~D--------ig~~Lg~~a~~~~L~R~~~ 203 (226)
T cd02868 171 INETQEYLRKLIHE--------IGLELRSSAVCTQVRRTRD 203 (226)
T ss_pred ECCCHHHHHHHHHH--------HHHHhCCcEEEEEEEeeEE
Confidence 9999 99999998 9999999999999866554
No 34
>PRK14586 tRNA pseudouridine synthase ACD; Provisional
Probab=96.52 E-value=0.09 Score=53.55 Aligned_cols=164 Identities=14% Similarity=0.225 Sum_probs=103.6
Q ss_pred EEEEEeeecccCCCCcccccCccccCcCcHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCCc
Q 008562 317 YFGGRYLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPS 396 (561)
Q Consensus 317 ~i~GRY~K~sR~lsQTpW~~~g~r~~~~SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~ 396 (561)
|.+.+|.=+++. | + ..|||+.|...+..+++ ..+.+++|||-|-.|=-+|. ++.+.-|...
T Consensus 10 YdGt~f~G~Q~Q-~-------~----~~TVq~~le~aL~~~~~-~~i~~~~agRTD~GVHA~~q----v~~f~~~~~~-- 70 (245)
T PRK14586 10 YDGSNFFGYQGQ-P-------D----VRTVQGVFEDALERIFK-QRIYTQAAGRTDTGVHANGQ----VIAFNCPNDR-- 70 (245)
T ss_pred EcCCceeeEEEC-C-------C----CCCHHHHHHHHHHHHhC-CCeeEEEecCCccCCCccCc----EEEEEecCCc--
Confidence 556667666653 1 1 24999999988888875 57999999999999999986 3333323220
Q ss_pred HHHHHHHHHHHhccCCCcEEEEeeEEecchhhhhhhcccccccceEEEEEEE---------------cCCCCHHHHHH-H
Q 008562 397 ELLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWI---------------SRPLQDEDFQT-I 460 (561)
Q Consensus 397 ~~~~~~l~~~In~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~---------------~~~v~~e~l~~-l 460 (561)
.+.+.+...+|+.-..+|.|.+...|+..=-. .=.-+.|.|+=+++. ..+++.+.+++ +
T Consensus 71 -~~~~~l~~~lN~~LP~dI~V~~~~~v~~~Fha----R~~a~~R~Y~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~ 145 (245)
T PRK14586 71 -MTEEDIKNAMNANLPDDIYVKKVFEVPKNFHP----RFDAKKRIYHYFILTSKEKNVFLRKYVWWFPYELDLEAMRKAA 145 (245)
T ss_pred -CCHHHHHHHHHccCCCCeEEEEEEECCCCcCc----ccCCCcEEEEEEEecCCCCChhhCCceEEeCCCCCHHHHHHHH
Confidence 12446778899876678999999888754211 123355788877753 34566677776 4
Q ss_pred Hhcccc--cceeeeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecC
Q 008562 461 SSLKET--VRCYQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQA 516 (561)
Q Consensus 461 ~~~~~~--~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqa 516 (561)
+.|.|+ +..+ .+++. ...-.|+||++++....+ ..+.++|..+|
T Consensus 146 ~~l~G~HDF~~F--~~~~~--------~~~~vR~I~~~~~~~~~~--~~i~~~i~g~~ 191 (245)
T PRK14586 146 KYLEGEHDFTSF--KTGSD--------ERNPVRTIYRIRILRLKK--DLILIRVEGRS 191 (245)
T ss_pred HHccCcchHHhh--cCCCC--------CCCCcEEEEEEEEEEccC--CEEEEEEEech
Confidence 445441 1113 12211 123347799988865422 46677777764
No 35
>PRK12434 tRNA pseudouridine synthase A; Reviewed
Probab=95.80 E-value=0.21 Score=50.95 Aligned_cols=148 Identities=15% Similarity=0.208 Sum_probs=94.8
Q ss_pred CcHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCCcHHHHHHHHHHHhccCCCcEEEEeeEEe
Q 008562 344 ASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRVKNLKIV 423 (561)
Q Consensus 344 ~SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~~~V~v~~L~~v 423 (561)
.|||+.|...+.++.+ ..+++++|||-|--|=-+|. -+-+.+ +... +.+.+...+|..-..+|.|.+...|
T Consensus 26 ~TVq~~le~aL~~~~~-~~~~~~~agRTD~GVHA~~q--v~~f~~--~~~~----~~~~l~~~lN~~LP~dI~V~~~~~v 96 (245)
T PRK12434 26 NTIQGKIESVLSEMTG-EEIEIIGCGRTDAGVHALNQ--VANFQT--DEKL----SEDKIKKYLNEYLPNDIVVTNVEEV 96 (245)
T ss_pred CCHHHHHHHHHHHHhC-CCeEEEEeccCCCCcCccCc--EEEEEc--CCCC----CHHHHHHHHHccCCCCeEEEEEEEC
Confidence 5999999988888776 68999999999999999984 233333 2221 2346778899876678999999988
Q ss_pred cchhhhhhhcccccccceEEEEEE---------------EcCCCCHHHHHH-HHhcccc--cceeeeeecCCeEEEeecC
Q 008562 424 GSQGWTLMREGEAEKQKQYAALVW---------------ISRPLQDEDFQT-ISSLKET--VRCYQILQKTPIRVLHRRS 485 (561)
Q Consensus 424 ~r~~~~~ik~~e~~k~K~Y~alv~---------------~~~~v~~e~l~~-l~~~~~~--~~~~~I~QkTP~RVlhRR~ 485 (561)
+.+--.+ =.-+.|.|+=++. ...+++.+.+++ ++.|.|+ +..+. + .+ ..
T Consensus 97 ~~~FhaR----~~a~~R~Y~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~F~---~--~~----~~ 163 (245)
T PRK12434 97 DERFHAR----YNVKSKTYLYKIWNEKFHNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFTSFT---N--AK----SK 163 (245)
T ss_pred CCCcccc----cCCCcEEEEEEEccCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcCHHhhc---C--CC----CC
Confidence 7542111 2335588887763 345567777776 5555552 11121 0 00 01
Q ss_pred CCceeeEEEEEEEEEEcCCccEEEEEEEecC
Q 008562 486 PLEREKIINWMKIEKIAGSSQYFLLHMCTQA 516 (561)
Q Consensus 486 ~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqa 516 (561)
...-.|+|+++++... ...+.+.|..++
T Consensus 164 ~~~~~R~I~~~~v~~~---~~~~~i~i~g~~ 191 (245)
T PRK12434 164 KKSTVREIYSIDIMEE---DGFVQIRVSGNG 191 (245)
T ss_pred CCCCEEEEEEEEEEEe---CCEEEEEEEecH
Confidence 1234567898888653 246777877775
No 36
>PRK14588 tRNA pseudouridine synthase ACD; Provisional
Probab=95.67 E-value=0.3 Score=50.59 Aligned_cols=165 Identities=12% Similarity=0.135 Sum_probs=102.0
Q ss_pred EEEEEeeecccCCCCcccccCccccCcCcHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCCc
Q 008562 317 YFGGRYLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPS 396 (561)
Q Consensus 317 ~i~GRY~K~sR~lsQTpW~~~g~r~~~~SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~ 396 (561)
|.+.+|.=++|. | + ..|||+.|...+..+.+ +.+.+++|||-|--|=-+|.= +-+.+ +..
T Consensus 10 YdGt~f~G~Q~Q-~-------~----~~TVq~~Le~aL~~l~~-~~i~i~~AgRTDaGVHA~gQv--~~f~~--~~~--- 69 (272)
T PRK14588 10 YDGTDFAGSQWQ-T-------D----GRTVQGALEAAWQALTQ-ERRRIVLAGRTDAGVHARGQV--AHVQT--DTR--- 69 (272)
T ss_pred EcCCceeeeEEC-C-------C----CCCHHHHHHHHHHHhhC-CCceEEEecCCCcCcCccccE--EEEEc--CCC---
Confidence 566777666654 1 1 24899999988887764 678999999999999999853 22222 222
Q ss_pred HHHHHHHHHHHhccCCCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEc---------------CCCCHHHHHH-H
Q 008562 397 ELLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWIS---------------RPLQDEDFQT-I 460 (561)
Q Consensus 397 ~~~~~~l~~~In~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~---------------~~v~~e~l~~-l 460 (561)
.+++.+...+|..-..+|.|.+...|+..- ...-.-+.|+|+=+++.. .+++.+.+++ +
T Consensus 70 -~~~~~l~~~LN~~LP~dI~V~~v~~v~~~F----haR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~lDi~~m~~a~ 144 (272)
T PRK14588 70 -HSLATIWRGLNAHLPEDIGVQNAWEAPPDF----HARFSAIQREYRYVIDCAPAPSPQLRHQVLHYAGTLDVAAMDAAL 144 (272)
T ss_pred -CCHHHHHHHHHhcCCCCeEEEEEEECCCCc----CcccCCCcEEEEEEEcCCCCCChhhcCceEecCCCCCHHHHHHHH
Confidence 234567888998766789999999887531 111233568888877542 3466666666 4
Q ss_pred Hhcccc--cceeeeeecCCeEEEeecCCCceeeEEEEEEEEEEcC-CccEEEEEEEecC
Q 008562 461 SSLKET--VRCYQILQKTPIRVLHRRSPLEREKIINWMKIEKIAG-SSQYFLLHMCTQA 516 (561)
Q Consensus 461 ~~~~~~--~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~-~~~~f~l~i~tqa 516 (561)
+.|.|+ +..+. ++ +......|+|+++++..... +.+.+.+.|..++
T Consensus 145 ~~f~G~HDF~~F~---~~-------~~~~~~vRtI~~~~~~~~~~~~~~~i~~~i~g~~ 193 (272)
T PRK14588 145 KLLIGTHDFAAFT---TA-------PQEGSTVRTCYWARCTDTEWFGRPLLAIEVAANA 193 (272)
T ss_pred HHccCCcchHhhc---CC-------CCCCCCeEEEEEEEEEEcccCCCCEEEEEEEEch
Confidence 555552 11121 11 01223456788888765310 1245667777764
No 37
>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=95.62 E-value=0.29 Score=49.34 Aligned_cols=163 Identities=18% Similarity=0.342 Sum_probs=103.8
Q ss_pred EEEEEeeecccCCCCcccccCccccCcCcHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCCc
Q 008562 317 YFGGRYLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPS 396 (561)
Q Consensus 317 ~i~GRY~K~sR~lsQTpW~~~g~r~~~~SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~ 396 (561)
|.+.+|.=+++. .+ ..|||+.|...+..+.+ ..+++++|||-|--|=-+|+ -+-+.+ +...+
T Consensus 9 YdGt~f~G~Q~Q--------~~----~~TVq~~le~aL~~~~~-~~i~~~~agRTD~GVHA~~q--v~~f~~--~~~~~- 70 (227)
T TIGR00071 9 YDGSNYHGWQRQ--------PN----KRTVQGELEKALEAIGK-KKITIMSAGRTDKGVHAMGQ--VISFDT--PKEIP- 70 (227)
T ss_pred EcCCCeeEEeEC--------cC----CCCHHHHHHHHHHHHhC-CCeeEEeeccCcCCcccccc--EEEEEe--cCCCC-
Confidence 566667666653 11 24999999888877654 78999999999999999984 233333 33222
Q ss_pred HHHHHHHHHHHhccCCCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEc----CCCCHHHHHH-HHhcccc--cce
Q 008562 397 ELLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWIS----RPLQDEDFQT-ISSLKET--VRC 469 (561)
Q Consensus 397 ~~~~~~l~~~In~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~----~~v~~e~l~~-l~~~~~~--~~~ 469 (561)
.+.+...+|..-..+|.|.++..|+.+-- .--.-+.|+|+=.+... .+++.+.+++ ++.|.|+ +..
T Consensus 71 ---~~~~~~~lN~~Lp~dI~V~~~~~v~~~Fh----aR~~a~~R~Y~Y~i~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~ 143 (227)
T TIGR00071 71 ---DNKLNAKLNALLPPDIRVKALAPVNDNFH----ARFSASKRHYRYILYNHRHYYSPLDLEKMRAAAKQLLGKHDFSN 143 (227)
T ss_pred ---HHHHHHHHHccCCCCEEEEEEEeCCCCcC----CCCCCCcEEEEEEEccCcccCCCCCHHHHHHHHHHccCcccHHH
Confidence 34677889987667899999998875421 11234568898888654 3677777776 5555552 111
Q ss_pred eeeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecC
Q 008562 470 YQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQA 516 (561)
Q Consensus 470 ~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqa 516 (561)
+.-. + .....-.|+|+++++..- ...+.+.|..++
T Consensus 144 F~~~-~--------~~~~~~~R~i~~~~v~~~---~~~~~i~i~g~~ 178 (227)
T TIGR00071 144 FSKA-K--------SKSRSPIRTISDIKVSES---GEYIIFDIIGNS 178 (227)
T ss_pred hcCC-C--------CCCCCCeEEEEEEEEEEc---CCEEEEEEEecH
Confidence 2210 0 112233467888888652 357777777764
No 38
>COG0101 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=95.62 E-value=0.29 Score=50.75 Aligned_cols=151 Identities=15% Similarity=0.210 Sum_probs=94.4
Q ss_pred CcHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCCcHHHHHHHHHHHhccCCCcEEEEeeEEe
Q 008562 344 ASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRVKNLKIV 423 (561)
Q Consensus 344 ~SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~~~V~v~~L~~v 423 (561)
-|||+.|...+..+.+. ...+++|||-|--|=-+|+ |+.+.-|...+ ...+...+|+.-...|.|.+...|
T Consensus 25 ~TVQ~~le~aL~~i~~~-~~~i~~AGRTD~GVHA~gq----v~hfd~~~~~~----~~~~~~~lN~~Lp~dI~V~~~~~v 95 (266)
T COG0101 25 RTVQGELEKALSKIGGE-SVRVIGAGRTDAGVHALGQ----VVHFDTPADRP----LEKLVRALNALLPPDIRVLDVAEV 95 (266)
T ss_pred CCHHHHHHHHHHHhcCC-cceeEEecCCCcCcccccc----EEEEEcCCccc----HHHHHHHHHhcCCCCcEEEEEEEC
Confidence 59999998777766544 4599999999999999986 44444443322 456778889876668999999998
Q ss_pred cchhhhhhhcccccccceEEEEEEEcCC---------------CCHHHHHH-HHhcccccceeeeeecCCeEEEeecCCC
Q 008562 424 GSQGWTLMREGEAEKQKQYAALVWISRP---------------LQDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRSPL 487 (561)
Q Consensus 424 ~r~~~~~ik~~e~~k~K~Y~alv~~~~~---------------v~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~~~ 487 (561)
+..=-.+ =.-+.|.|+=+++.... ++.+.+++ ++.|.|+ +=-|--+....++.
T Consensus 96 ~~~FhaR----fsa~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~aa~~l~G~------HDF~sF~~~~~~~~- 164 (266)
T COG0101 96 PDDFHAR----FSAKSRTYRYIIYNAPLRPPFLANYVWHVPYPLDLDAMREAAKLLLGT------HDFTSFRKAGCQSK- 164 (266)
T ss_pred CCCCCCc----ccccceEEEEEEcCccCCChhhhcccccccCcCCHHHHHHHHHHcccc------ccchhhccCCCccC-
Confidence 7542111 23355888887776544 45555555 4444441 00011111111111
Q ss_pred ceeeEEEEEEEEEEcCCccEEEEEEEecCC
Q 008562 488 EREKIINWMKIEKIAGSSQYFLLHMCTQAG 517 (561)
Q Consensus 488 ~R~R~Iy~~~~~~i~~~~~~f~l~i~tqaG 517 (561)
.=.|+||++++.... ..+.++|..+|=
T Consensus 165 s~vRti~~~~v~~~~---~~i~i~i~g~sF 191 (266)
T COG0101 165 SPVRTIYRIDVSRDG---DLIVIDISGNSF 191 (266)
T ss_pred CCeEEEEEEEEEecC---CEEEEEEEeChh
Confidence 234678998888753 577778877763
No 39
>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=95.16 E-value=0.45 Score=48.05 Aligned_cols=148 Identities=16% Similarity=0.221 Sum_probs=94.5
Q ss_pred CcHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCCcHHHHHHHHHHHhccCCCcEEEEeeEEe
Q 008562 344 ASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRVKNLKIV 423 (561)
Q Consensus 344 ~SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~~~V~v~~L~~v 423 (561)
.|||+.|...+..+.+ ..+++.+|||-|--|=-+|+ ++.+.=+... +.+.+...+|..-...|.|.++..|
T Consensus 20 ~TVq~~le~aL~~~~~-~~~~i~~agRTD~GVHA~~q----vv~~~~~~~~----~~~~~~~~lN~~Lp~dI~v~~i~~v 90 (239)
T cd02570 20 RTVQGELEKALSKIAG-EPVRVIGAGRTDAGVHALGQ----VAHFDTPSEI----PLEKLIKALNSLLPPDIRVLSAEEV 90 (239)
T ss_pred CCHHHHHHHHHHHHhC-CCeEEEEECcCCCCcCcccc----EEEEEECCCC----CHHHHHHHHHccCCCCEEEEEEEEC
Confidence 5999999888877765 78999999999999999885 3333333322 2457788999876678999999988
Q ss_pred cchhhhhhhcccccccceEEEEEEEc---------------CCCCHHHHHH-HHhcccc--cceeeeeecCCeEEEeecC
Q 008562 424 GSQGWTLMREGEAEKQKQYAALVWIS---------------RPLQDEDFQT-ISSLKET--VRCYQILQKTPIRVLHRRS 485 (561)
Q Consensus 424 ~r~~~~~ik~~e~~k~K~Y~alv~~~---------------~~v~~e~l~~-l~~~~~~--~~~~~I~QkTP~RVlhRR~ 485 (561)
+..-- ..-.-+.|+|+=.+... .+++.+.+++ ++.|.|+ +..+. +. +..
T Consensus 91 ~~~F~----aR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~d~~~m~~a~~~f~G~HdF~~F~-----~~----~~~ 157 (239)
T cd02570 91 PDDFH----ARFSAKSRTYRYRILNRPVPSPFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFR-----AA----GCQ 157 (239)
T ss_pred CCCcC----cccCCCceEEEEEEccCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcchhhhC-----CC----CCC
Confidence 75311 11233567887777554 2455666666 5555552 11121 10 001
Q ss_pred CCceeeEEEEEEEEEEcCCccEEEEEEEecC
Q 008562 486 PLEREKIINWMKIEKIAGSSQYFLLHMCTQA 516 (561)
Q Consensus 486 ~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqa 516 (561)
...=.|+|+++++..-. ..+.+.|..++
T Consensus 158 ~~~~~R~I~~~~v~~~~---~~~~i~i~g~s 185 (239)
T cd02570 158 SKSTVRTIYRADVYREG---DLIVFEIRANG 185 (239)
T ss_pred CCCCeEEEEEEEEEEeC---CEEEEEEEEcH
Confidence 12334678888876532 56777777664
No 40
>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=94.99 E-value=0.37 Score=48.51 Aligned_cols=146 Identities=16% Similarity=0.167 Sum_probs=95.5
Q ss_pred CcHHHHhhhccccccCC---CceEEeecCCCCccccccCCCccEEEEEecCccCCcHHHHHHHHHHHhccCCCcEEEEee
Q 008562 344 ASIEEIIGGNILPMCRG---DSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRVKNL 420 (561)
Q Consensus 344 ~SVeE~I~~~~~~~f~~---~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~~~V~v~~L 420 (561)
.|||+.|...+..+.+. ..+.+.+|||-|--|=-+|+ -+.+++ +...+ .+...+|+.-..+|.|.+.
T Consensus 18 ~TVq~~le~aL~~~~~~~~~~~~~i~~agRTD~GVHA~~q--v~~~~~--~~~~~------~~~~~lN~~Lp~dI~v~~~ 87 (224)
T cd00497 18 PTVEGELFKALLKTGLIESPKPSNYSRAGRTDKGVSALGQ--VVSLET--RSKLK------PYPDILNGLLPKDIRVLAW 87 (224)
T ss_pred CCHHHHHHHHHHHhhCcCCCcceeEEEecccccccccccc--EEEEEE--CCCcH------HHHHHHHhhCCCCcEEEEE
Confidence 58999998888887765 38999999999999999985 333333 22211 5667888776678999999
Q ss_pred EEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHH-HHhcccc--cceeeeeecCCeEEEeecCCCceeeEEEEEE
Q 008562 421 KIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQT-ISSLKET--VRCYQILQKTPIRVLHRRSPLEREKIINWMK 497 (561)
Q Consensus 421 ~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~-l~~~~~~--~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~ 497 (561)
..|+.+ + ..--.-+.|.|+=.++.. +++.+.+++ ++.|.|+ +..+.-.. +....-.|+|++++
T Consensus 88 ~~v~~~-F---~aR~~a~~R~Y~Y~i~~~-~~d~~~m~~a~~~f~G~HDF~~F~~~~---------~~~~~~~RtI~~~~ 153 (224)
T cd00497 88 APVPED-F---HARFSCVSRTYRYYFPGG-DLDIEAMREAAKLLLGTHDFRNFCKKD---------GRKKNPVRTIISAE 153 (224)
T ss_pred EEeCCC-C---CCCcccCeEEEEEEECCC-CcCHHHHHHHHHHccCcccHHHhcCCC---------CCCCCCeEEEEEEE
Confidence 988743 2 222234568898877654 677777776 5555552 11122111 11123456799988
Q ss_pred EEEEcCCccEEEEEEEecC
Q 008562 498 IEKIAGSSQYFLLHMCTQA 516 (561)
Q Consensus 498 ~~~i~~~~~~f~l~i~tqa 516 (561)
+... .+++.+.|..++
T Consensus 154 v~~~---~~~~~i~i~g~s 169 (224)
T cd00497 154 VEEV---DDFYVFEVKGKS 169 (224)
T ss_pred EEec---CCEEEEEEEEcH
Confidence 8763 256777777764
No 41
>PRK00021 truA tRNA pseudouridine synthase A; Validated
Probab=94.95 E-value=0.6 Score=47.40 Aligned_cols=148 Identities=11% Similarity=0.176 Sum_probs=94.4
Q ss_pred CcHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCCcHHHHHHHHHHHhccCCCcEEEEeeEEe
Q 008562 344 ASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRVKNLKIV 423 (561)
Q Consensus 344 ~SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~~~V~v~~L~~v 423 (561)
.|||+.|...+....+ ..+.+.+|||-|-.|=-+|+ ++-+.=+.. .+.+.+...+|..-..+|.|.+...|
T Consensus 25 ~TVq~~le~aL~~~~~-~~~~~~~agRTD~GVHA~~q----vv~~~~~~~----~~~~~~~~~lN~~Lp~dI~V~~~~~v 95 (244)
T PRK00021 25 RTVQGELEKALSKLAG-EPVRVIGAGRTDAGVHALGQ----VAHFDTPAP----RPPEKWRRALNALLPDDIAVLWAEEV 95 (244)
T ss_pred CCHHHHHHHHHHHHhC-CCeEEEEEccCCCcccccCc----EEEEEeCCC----CCHHHHHHHHHhcCCCCEEEEEeEec
Confidence 5999999888777765 68999999999999999885 333332322 23456778889876678999999988
Q ss_pred cchhhhhhhcccccccceEEEEEEEcC---------------CCCHHHHHH-HHhcccc--cceeeeeecCCeEEEeecC
Q 008562 424 GSQGWTLMREGEAEKQKQYAALVWISR---------------PLQDEDFQT-ISSLKET--VRCYQILQKTPIRVLHRRS 485 (561)
Q Consensus 424 ~r~~~~~ik~~e~~k~K~Y~alv~~~~---------------~v~~e~l~~-l~~~~~~--~~~~~I~QkTP~RVlhRR~ 485 (561)
+..=-. .-.-+.|+|+=.+.... +++.+.+++ ++.|.|+ +..+. ++ ++.
T Consensus 96 ~~~F~a----R~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~a~~~~~G~HdF~~F~---~~------~~~ 162 (244)
T PRK00021 96 PDDFHA----RFSAKARRYRYRIYNRPARPPFLRGYVWHYPYPLDVDAMNEAAQYLLGEHDFTSFR---AS------GCQ 162 (244)
T ss_pred CCCcCc----CcCCCceEEEEEEecCCCCChhhCCcEEEeCCCCcHHHHHHHHHHhcCceeeeeee---CC------CCC
Confidence 753111 12335578877765442 356666666 4555551 11121 11 112
Q ss_pred CCceeeEEEEEEEEEEcCCccEEEEEEEecC
Q 008562 486 PLEREKIINWMKIEKIAGSSQYFLLHMCTQA 516 (561)
Q Consensus 486 ~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqa 516 (561)
...-.|+|+++++..- .+.+.+.|..++
T Consensus 163 ~~~~~R~I~~~~v~~~---~~~~~i~i~g~s 190 (244)
T PRK00021 163 SKSPVRTIYEADVTRE---GDFIVFDISANG 190 (244)
T ss_pred CCCCeEEEEEEEEEEc---CCEEEEEEEEch
Confidence 2344578999888652 256777777664
No 42
>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=94.43 E-value=0.39 Score=48.78 Aligned_cols=174 Identities=14% Similarity=0.125 Sum_probs=100.2
Q ss_pred EEEEEeeecccCCCCcccccCccccCcCcHHHHhhhccccccC--------CCceEEeecCCCCccccccCCCccEEEEE
Q 008562 317 YFGGRYLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCR--------GDSYKFHAAGREDIDVRMLGSGRPFLFEI 388 (561)
Q Consensus 317 ~i~GRY~K~sR~lsQTpW~~~g~r~~~~SVeE~I~~~~~~~f~--------~~~~~F~ssGREDvDVRmLG~GRPFvlEi 388 (561)
|.+.+|.=+++. | +. ..|||+.|...+..+.+ ...+++++|||-|-.|=-+|+ -|.+.+
T Consensus 5 Y~Gt~f~G~Q~Q-~-------~~---~~TVq~~le~aL~~~~~~~~~~~~~~~~~~~~~agRTD~GVHA~~q--v~~~~~ 71 (245)
T cd02568 5 YCGTGYHGMQYN-P-------GN---YKTIEGELERALVKAGAISESNAGDPKKIGFSRAARTDKGVHAARN--VVSLKV 71 (245)
T ss_pred EeCCCccccccC-C-------CC---CCChHHHHHHHHHHcCCcCccccCChhhcceeeecccccchhheee--EEEEEE
Confidence 555666665554 1 11 25999999988888775 268999999999999999985 333333
Q ss_pred ecCccCCcHHHHHHHHHHHhccCCCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHH-HHhcccc-
Q 008562 389 QNAREVPSELLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQT-ISSLKET- 466 (561)
Q Consensus 389 ~nPr~~~~~~~~~~l~~~In~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~-l~~~~~~- 466 (561)
..+.. ......+.+...+|..-...|.|.++..|+..- ..--.-+.|.|+=.+....-++.+.+++ ++.|.|.
T Consensus 72 ~~~~~-~~~~~~~~~~~~lN~~Lp~dI~v~~~~~v~~~F----~aR~~a~~R~Y~Y~i~~~~~~d~~~m~~a~~~~~G~H 146 (245)
T cd02568 72 IIDDP-EGLGIGEDLVEKLNSHLPEDIRVFGITRVTKSF----NARKACDSRTYEYLLPTFALETLDRFNEILKLYVGTH 146 (245)
T ss_pred ecccc-ccccchHHHHHHHHccCCCceEEEEEEcCCCCC----CcchhhhcceeEEECCcccHhHHHHHHHHHHHhhCcc
Confidence 22210 001124567788998666689999998886432 1122345688988776543234455554 4444441
Q ss_pred -cceeeeeecCCeEEEeecCCCceeeEEEEEEEEEEc---CCccEEEEEEEecC
Q 008562 467 -VRCYQILQKTPIRVLHRRSPLEREKIINWMKIEKIA---GSSQYFLLHMCTQA 516 (561)
Q Consensus 467 -~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~---~~~~~f~l~i~tqa 516 (561)
+..+.- .+.. ....-.|+|+++++.... .+...+.++|..++
T Consensus 147 dF~~F~~-----~~~~---~~~~~~R~i~~~~~~~~~~~~~~~~~i~i~i~g~~ 192 (245)
T cd02568 147 NFHNFTV-----RKKF---EDPSANRFIISFYVSEPFVIEEGLEWVSIEIHGQS 192 (245)
T ss_pred ccccCcc-----cccc---cCCCceeEEEEEEEecceeecCCccEEEEEEEech
Confidence 111211 0000 012334668888775431 01246666776664
No 43
>PRK14589 tRNA pseudouridine synthase ACD; Provisional
Probab=93.86 E-value=1.3 Score=45.92 Aligned_cols=158 Identities=13% Similarity=0.146 Sum_probs=98.2
Q ss_pred EEEEEeeecccCCCCcccccCccccCcCcHHHHhhhccccccC---CCceEEeecCCCCccccccCCCccEEEEEecCcc
Q 008562 317 YFGGRYLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCR---GDSYKFHAAGREDIDVRMLGSGRPFLFEIQNARE 393 (561)
Q Consensus 317 ~i~GRY~K~sR~lsQTpW~~~g~r~~~~SVeE~I~~~~~~~f~---~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~ 393 (561)
|.+.+|.=+++. .+ ..|||+.|...+..+.. ...+.+++|||-|--|=-+|+ -+-+.+..
T Consensus 9 YdGt~y~G~Q~Q--------~~----~~TVq~~Le~aL~~~~~~~~~~~~~i~~agRTDaGVHA~gq--v~~f~~~~--- 71 (265)
T PRK14589 9 YIGTRFFGSQYQ--------PD----QRTVEGEFIAACRRLGLFSDWREAGFALAGRTDRGVHARGQ--VLAFSTHK--- 71 (265)
T ss_pred EcCCCeeeeeeC--------CC----CCCHHHHHHHHHHHhhCccCCceeeEEEeccCCcCcccccc--EEEEEeCC---
Confidence 566677666553 11 24899999988888753 257899999999999999985 23332221
Q ss_pred CCcHHHHHHHHHHHhccCCCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHH-HHhcccc--ccee
Q 008562 394 VPSELLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQT-ISSLKET--VRCY 470 (561)
Q Consensus 394 ~~~~~~~~~l~~~In~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~-l~~~~~~--~~~~ 470 (561)
.+.+...+|..-..+|.|.+...|+..--.+ -.-+.|+|+=.+. ..+++.+.+++ ++.|.|+ +..+
T Consensus 72 ------~~~~~~~lN~~LP~dI~V~~~~~v~~~FhAR----~~a~~R~Y~Y~i~-~~~lD~~~m~~a~~~f~G~HDF~~F 140 (265)
T PRK14589 72 ------PERAVEALNGQLPPDIWCTGWAEVPESFHPR----YDAISRTYRYYFS-RPPSDINAMRDAAGEFIGTHDFSCF 140 (265)
T ss_pred ------hHHHHHHHHhhCCCCeEEEEEEEcCCCCCcc----cCCceeEEEEEEe-cCccHHHHHHHHHHHccCCccHHHH
Confidence 2345678887666789999999887431111 1234577877663 45677777776 5555552 0002
Q ss_pred eeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecC
Q 008562 471 QILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQA 516 (561)
Q Consensus 471 ~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqa 516 (561)
. +. . ...-.|+|+++++... .+.+.++|..++
T Consensus 141 ~---~~--~------~~~~vRtI~~i~v~~~---~~~~~~~i~G~~ 172 (265)
T PRK14589 141 A---RV--E------GKSPVRTILRIRVFSD---GGFPVFEVTAQS 172 (265)
T ss_pred h---cc--C------CCCCeEEEEEEEEEEe---CCEEEEEEEech
Confidence 1 00 0 1122467888888763 256777777764
No 44
>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=93.01 E-value=1.9 Score=43.34 Aligned_cols=157 Identities=16% Similarity=0.213 Sum_probs=98.5
Q ss_pred EEEEEeeecccCCCCcccccCccccCcCcHHHHhhhccccccC---CCceEEeecCCCCccccccCCCccEEEEEecCcc
Q 008562 317 YFGGRYLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCR---GDSYKFHAAGREDIDVRMLGSGRPFLFEIQNARE 393 (561)
Q Consensus 317 ~i~GRY~K~sR~lsQTpW~~~g~r~~~~SVeE~I~~~~~~~f~---~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~ 393 (561)
|.+.+|.=+++.- + ..|||+.|...+..... ...+.+++|||-|-.|=-+|+= +.+.-|..
T Consensus 5 Y~Gt~y~G~q~q~--------~----~~TVq~~le~aL~~~~~~~~~~~i~~~~agRTD~GVHA~~qv----~~f~~~~~ 68 (221)
T cd02866 5 YDGTPYHGFQRQP--------D----VRTVEGELIKALRRLGIIESPKRPRLYSAGRTDAGVSALGNV----VAFETEKE 68 (221)
T ss_pred EeCCceeeeeeCC--------C----CCCHHHHHHHHHHHhhccccCCceEEEEEcCCccccCccccE----EEEEeCcH
Confidence 5566666655531 1 24899999888887743 2579999999999999999853 33322221
Q ss_pred CCcHHHHHHHHHHHhccCCCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHH-HHhcccc--ccee
Q 008562 394 VPSELLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQT-ISSLKET--VRCY 470 (561)
Q Consensus 394 ~~~~~~~~~l~~~In~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~-l~~~~~~--~~~~ 470 (561)
+ +...+|..-..+|.|.+...|+.+--.+ -.-+.|+|+=.++. .+++.+.+++ ++.|.|+ +..+
T Consensus 69 ------~--~~~~lN~~LP~dI~v~~~~~v~~~F~ar----~~a~~r~Y~Y~i~~-~~ld~~~m~~a~~~~~G~HDF~~F 135 (221)
T cd02866 69 ------L--TPPAINNALPKDIRVWAWAKVPEDFHPR----RDARRRYYRYYLGA-EDYDVEAMAEAAKKLIGTHDFSNF 135 (221)
T ss_pred ------H--HHHHHHhhCCCCEEEEEEEEeCCCCCCC----ccCCeEEEEEEECC-CcCCHHHHHHHHHHhcCCcCHHHh
Confidence 1 4567887666789999999887542222 23466889887765 3677777776 5555552 0012
Q ss_pred eeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecC
Q 008562 471 QILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQA 516 (561)
Q Consensus 471 ~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqa 516 (561)
.-. ++ ..-.|+|+++++... ...+.++|..++
T Consensus 136 ~~~-~~----------~~~~R~I~~~~~~~~---~~~~~~~i~g~~ 167 (221)
T cd02866 136 SKR-DG----------RDPVRTIERIEIREN---GEFLVIDVVGES 167 (221)
T ss_pred hCC-CC----------CCCcEEEEEEEEEEc---CCEEEEEEEEcH
Confidence 110 00 022467888887652 257777777764
No 45
>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=92.82 E-value=2.3 Score=43.86 Aligned_cols=159 Identities=11% Similarity=0.076 Sum_probs=94.3
Q ss_pred CcHHHHhhhccccccC---CCceEEeecCCCCccccccCCCccEEEEEecCccCC------------cHHHHHHHHHHHh
Q 008562 344 ASIEEIIGGNILPMCR---GDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVP------------SELLVKEIESKIN 408 (561)
Q Consensus 344 ~SVeE~I~~~~~~~f~---~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~------------~~~~~~~l~~~In 408 (561)
.|||+.|...+..+.. ...+.+++|||-|--|=-+|+ -+.+.+..+.... ....-..+...+|
T Consensus 21 ~TVq~~Le~aL~~~~~i~~~~~~~~~~agRTD~GVHA~~q--v~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lN 98 (256)
T cd02569 21 NTVEETLFEALEKTRLIEDRQTSNYSRCGRTDKGVSAFGQ--VISLDVRSNLKPEDGLDPSTDVKSTADEEELPYCKILN 98 (256)
T ss_pred CCHHHHHHHHHHHhcCCCCCCceeEEeecccCccccccCc--EEEEEecCCCCccccccccccccccccchHHHHHHHHH
Confidence 4899999988888763 358999999999999999885 3333332111000 0001124667888
Q ss_pred ccCCCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHH-HHhcccc--cceeeeeecCCeEEEeecC
Q 008562 409 SLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQT-ISSLKET--VRCYQILQKTPIRVLHRRS 485 (561)
Q Consensus 409 ~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~-l~~~~~~--~~~~~I~QkTP~RVlhRR~ 485 (561)
..-..+|.|.++..|+..- ...-.-+.|+|+=+++.. +++.+.+++ ++.|.|+ +..+.-. + ....
T Consensus 99 ~~LP~dI~V~~~~~v~~~F----haR~~a~~R~Y~Y~i~~~-~ldi~~m~~a~~~f~G~HDF~~F~~~-----~--~~~~ 166 (256)
T cd02569 99 RVLPPDIRILAWAPVPPDF----SARFSCVSRTYRYFFPKG-DLDIELMRKAAKLLLGEHDFRNFCKM-----D--VANQ 166 (256)
T ss_pred hhCCCCcEEEEEEECCCCc----CCCccCCceEEEEEecCC-CCCHHHHHHHHHHhhCCcchHHHhcc-----C--cccC
Confidence 8766789999999987431 112234668998776654 677777776 5555552 1112110 0 0000
Q ss_pred CCceeeEEEEEEEEEEc---CCccEEEEEEEecC
Q 008562 486 PLEREKIINWMKIEKIA---GSSQYFLLHMCTQA 516 (561)
Q Consensus 486 ~~~R~R~Iy~~~~~~i~---~~~~~f~l~i~tqa 516 (561)
...-.|+|+++++.... +....+.++|..++
T Consensus 167 ~~~~~RtI~~~~v~~~~~~~~~~~~~~~~i~g~~ 200 (256)
T cd02569 167 VTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSA 200 (256)
T ss_pred CCCCceEEEEEEEEEccCCCCCCcEEEEEEEEcH
Confidence 12335678888887632 00246667777664
No 46
>PRK14587 tRNA pseudouridine synthase ACD; Provisional
Probab=84.17 E-value=20 Score=37.14 Aligned_cols=147 Identities=15% Similarity=0.145 Sum_probs=87.7
Q ss_pred EEEEEeeecccCCCCcccccCccccCcCcHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCCc
Q 008562 317 YFGGRYLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPS 396 (561)
Q Consensus 317 ~i~GRY~K~sR~lsQTpW~~~g~r~~~~SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~~ 396 (561)
|.+.+|.=++|. +.|||+.|...+..+++ .|||-|--|=-+|+ ++.+ +...+
T Consensus 9 YdGt~f~G~Q~Q--------------~~TVq~~Le~aL~~i~~-------~agRTDaGVHA~~q----v~~~--~~~~~- 60 (256)
T PRK14587 9 YDGTLFYGFTGH--------------PNSLEPALRRVFGEILG-------RGSRTDPGVSAVGN----VVMT--SQKLP- 60 (256)
T ss_pred ECCCcccceecC--------------cchHHHHHHHHHHHhcc-------CccCCccCCCcccC----EEEE--CCcCC-
Confidence 556666666552 12899999888777643 29999999999987 3333 22222
Q ss_pred HHHHHHHHHHHhccCCCcEEEEeeEEecchhhhhhhcccccccceEEEEEEEcCCCCHHHHHH-HHhcccc--cceeeee
Q 008562 397 ELLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQT-ISSLKET--VRCYQIL 473 (561)
Q Consensus 397 ~~~~~~l~~~In~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~~~~v~~e~l~~-l~~~~~~--~~~~~I~ 473 (561)
+ ..+|..-..+|.|.+...|+..--.+ . -+.|.|+-++ .+.+++.+.+++ ++.|.|+ +..+.
T Consensus 61 ---~----~~LN~~LP~dI~V~~~~~V~~~FhaR-~----a~~R~Y~Y~i-~~~~lDi~~m~~aa~~l~G~HDF~~F~-- 125 (256)
T PRK14587 61 ---L----GYVNSKLPRGVWAWAVAEVPEGFNPR-R----AKRRRYLYVA-PHWGEDVEAMREAAELLAGTHDYSSFI-- 125 (256)
T ss_pred ---H----HHHHhcCCCCeEEEEEEECCCCcCcC-c----ccceEEEEEE-ccCcchHHHHHHHHHHhcCCcChHHhc--
Confidence 1 35676655679999999987542222 1 2668888776 244567677776 5555552 00121
Q ss_pred ecCCeEEEeecCCCc-eeeEEEEEEEEEEcCCccEEEEEEEecC
Q 008562 474 QKTPIRVLHRRSPLE-REKIINWMKIEKIAGSSQYFLLHMCTQA 516 (561)
Q Consensus 474 QkTP~RVlhRR~~~~-R~R~Iy~~~~~~i~~~~~~f~l~i~tqa 516 (561)
+.+ ..... -.|+|+++++..- ...+.+++..++
T Consensus 126 ---~~~----~~~~~~~vRtI~~i~v~~~---~~~i~i~i~g~s 159 (256)
T PRK14587 126 ---QRR----GEKATPTVTTVYEIGVELR---GDLIYLYFVGRG 159 (256)
T ss_pred ---cCC----CCCCCCCEEEEEEEEEEEe---CCEEEEEEEech
Confidence 000 00111 2467888888652 246666776664
No 47
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=75.66 E-value=1.1 Score=48.91 Aligned_cols=96 Identities=18% Similarity=0.303 Sum_probs=70.1
Q ss_pred ccceEEEEEEEcCCC-CHHHHHH-HHhcccccceeeeeecCCeEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEec
Q 008562 438 KQKQYAALVWISRPL-QDEDFQT-ISSLKETVRCYQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQ 515 (561)
Q Consensus 438 k~K~Y~alv~~~~~v-~~e~l~~-l~~~~~~~~~~~I~QkTP~RVlhRR~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tq 515 (561)
--|.|.|.+..+.++ +...+.. +..+-+ ..-|++|+=...+|- .|.|.+|+-....-+-.-++....+.|.
T Consensus 128 ~gk~yvg~~~lt~~v~~~~k~~~~~e~l~g-----~l~~~~pl~~~~kr~--~~v~~~y~s~~ie~d~~~~l~~f~~~~~ 200 (395)
T KOG2529|consen 128 AGKEYVGIGKLTPEVEDALKLHQKLEHLYG-----ALFQRPPLISAVKRV--LRVRTLYESKIIEYDRDYPLLRFGVSCE 200 (395)
T ss_pred cCcEEEEEEecCcchhhhhhhccchhhhhh-----hhccCCchhhhccce--eEeechhhhhcccccccchhcccccccc
Confidence 348899999999988 4444444 445555 688999998877776 8888899888766554446677889999
Q ss_pred CCceeeEeeeCCCCCcCcchhhhcCCccEEEEE
Q 008562 516 AGTYIKEFVHGDLGRTNPSIGSILGCRAEILQL 548 (561)
Q Consensus 516 aGtYIKEfVhGD~GRT~PSl~~iLg~~adileL 548 (561)
+|||+.-.+.- ++.+||+...+.|+
T Consensus 201 ~~t~~rt~~~~--------lg~ll~~g~k~~E~ 225 (395)
T KOG2529|consen 201 AGTYKRTMCVH--------LGLLLGFGGKMQEL 225 (395)
T ss_pred ccchHHHHHHh--------hhhHhhhcchhhhh
Confidence 99999887744 56677765544443
No 48
>KOG4393 consensus Predicted pseudouridylate synthase [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=51.99 E-value=45 Score=35.07 Aligned_cols=96 Identities=11% Similarity=0.047 Sum_probs=65.1
Q ss_pred cHHHHhhhccccccCCCceEEeecCCCCccccccCCCccEEEEEecCccCC-cHHHHHHHHHHHhccCCCcEEEEeeEEe
Q 008562 345 SIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVP-SELLVKEIESKINSLENKLVRVKNLKIV 423 (561)
Q Consensus 345 SVeE~I~~~~~~~f~~~~~~F~ssGREDvDVRmLG~GRPFvlEi~nPr~~~-~~~~~~~l~~~In~~~~~~V~v~~L~~v 423 (561)
.||..|.+...+..+-+..+|.+|+|-|--|--+++ +++..-|+..- ..+.+..-...+-...+|.|+|+|+.-|
T Consensus 31 tIq~~leea~eeqt~l~~l~l~~ssrtDa~Vha~~n----aa~~~vpr~sg~~~~~~~~a~nt~l~~k~gdirV~dv~~V 106 (295)
T KOG4393|consen 31 TIQGFLEEASEEQTGLDRLDLESSSRTDAGVHAYLN----AAHYIVPRFSGSQQQAKDRAVNTVLQRKDGDIRVIDVRCV 106 (295)
T ss_pred ehhhhhhhhHHhhcCCcceeecccCCCchhhheeee----eEEEEeecccCCcHHHHHHHHhccccCCCCceEEEEeeec
Confidence 466666666666677799999999999999999998 66777777632 2234444444444456789999999999
Q ss_pred cchhhhhhhcccccccceEEEEE
Q 008562 424 GSQGWTLMREGEAEKQKQYAALV 446 (561)
Q Consensus 424 ~r~~~~~ik~~e~~k~K~Y~alv 446 (561)
..+--.+-+ ...++=.||-..
T Consensus 107 ps~FhaR~s--assRtY~YRla~ 127 (295)
T KOG4393|consen 107 PSNFHARYS--ASSRTYFYRLAS 127 (295)
T ss_pred Ccchhheec--ccceeEEEEeec
Confidence 876544433 344445555443
No 49
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=51.56 E-value=11 Score=39.10 Aligned_cols=58 Identities=28% Similarity=0.374 Sum_probs=49.3
Q ss_pred cCCCceeeEEEEEEEEEEcCCccEEEEEEEecCCc--eeeEeeeCCCCCcCcchhhhcCCccEEEEEEEE
Q 008562 484 RSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGT--YIKEFVHGDLGRTNPSIGSILGCRAEILQLDVT 551 (561)
Q Consensus 484 R~~~~R~R~Iy~~~~~~i~~~~~~f~l~i~tqaGt--YIKEfVhGD~GRT~PSl~~iLg~~adileLDV~ 551 (561)
||...-.-.||.|++.+.. +-.|.|++.|.+-| |.+.+||- +|.=||+.|.|.+|--.
T Consensus 186 Rp~~~s~~ivygI~l~~F~--~P~F~le~qc~~Etqe~Lr~LVh~--------igl~L~T~a~c~qlrr~ 245 (318)
T KOG2559|consen 186 RPQLPSSQIVYGIDLNWFR--SPKFSLETQCSGETQEMLRQLVHH--------IGLNLGTEATCIQLRRQ 245 (318)
T ss_pred CcCCCCCceEEEEeeeeec--CCccEEEEeeccccHHHHHHHHHH--------Hhhcccceeeeeeeeee
Confidence 4556667789999999986 46788999888877 99999998 99999999999998654
No 50
>PRK00994 F420-dependent methylenetetrahydromethanopterin dehydrogenase; Provisional
Probab=50.34 E-value=6.5 Score=40.61 Aligned_cols=15 Identities=73% Similarity=1.121 Sum_probs=13.5
Q ss_pred cCCCCccccccCCCc
Q 008562 368 AGREDIDVRMLGSGR 382 (561)
Q Consensus 368 sGREDvDVRmLG~GR 382 (561)
+-|||+||||+|+|-
T Consensus 27 AdRedI~vrv~gsGa 41 (277)
T PRK00994 27 ADREDIDVRVVGSGA 41 (277)
T ss_pred hcccCceEEEeccCC
Confidence 569999999999994
No 51
>PF01993 MTD: methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase; InterPro: IPR002844 This archaeal enzyme family is involved in formation of methane from carbon dioxide 1.5.99.9 from EC. The enzyme requires coenzyme F420 [].; GO: 0008901 ferredoxin hydrogenase activity, 0015948 methanogenesis, 0055114 oxidation-reduction process; PDB: 1U6I_D 3IQF_G 1QV9_C 3IQE_F 1U6J_G 3IQZ_D 1U6K_B.
Probab=40.21 E-value=7.5 Score=40.20 Aligned_cols=15 Identities=73% Similarity=1.121 Sum_probs=11.7
Q ss_pred cCCCCccccccCCCc
Q 008562 368 AGREDIDVRMLGSGR 382 (561)
Q Consensus 368 sGREDvDVRmLG~GR 382 (561)
+-|||+||||+|+|-
T Consensus 26 AdRedI~vrv~gsGa 40 (276)
T PF01993_consen 26 ADREDIDVRVVGSGA 40 (276)
T ss_dssp S--SSEEEEEEEEET
T ss_pred hccCCceEEEeccCC
Confidence 569999999999983
No 52
>COG1927 Mtd Coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase [Energy production and conversion]
Probab=40.17 E-value=12 Score=38.13 Aligned_cols=16 Identities=63% Similarity=0.997 Sum_probs=14.2
Q ss_pred cCCCCccccccCCCcc
Q 008562 368 AGREDIDVRMLGSGRP 383 (561)
Q Consensus 368 sGREDvDVRmLG~GRP 383 (561)
+-||||+||++|+|--
T Consensus 27 AdRedi~vrVvgsgaK 42 (277)
T COG1927 27 ADREDIEVRVVGSGAK 42 (277)
T ss_pred cccCCceEEEeccccc
Confidence 6799999999999954
No 53
>COG4994 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.93 E-value=22 Score=32.58 Aligned_cols=42 Identities=24% Similarity=0.416 Sum_probs=26.3
Q ss_pred ecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEEeccccc
Q 008562 514 TQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDVKMNCFL 559 (561)
Q Consensus 514 tqaGtYIKEfVhGD~GRT~PSl~~iLg~~adileLDV~~V~~d~~~ 559 (561)
|++| |++.||||-.--+.-+|++.. -+|..+|+-.++-||.|
T Consensus 39 ~~SG-y~~~yv~g~~~~~~~~lgd~~---wei~d~~ik~l~~d~vL 80 (120)
T COG4994 39 GASG-YSRSYVLGVLDARHGHLGDAF---WEISDLRIKALAPDNVL 80 (120)
T ss_pred ccCc-eeeeeeeeeeccccCchhhhH---HhhhcceeeeecCCcEE
Confidence 7888 999999996655555565542 34444454444444443
No 54
>PF11005 DUF2844: Protein of unknown function (DUF2844); InterPro: IPR021267 This bacterial family of proteins has no known function.
Probab=32.86 E-value=39 Score=31.92 Aligned_cols=32 Identities=31% Similarity=0.547 Sum_probs=27.9
Q ss_pred EEEecCCceeeEeeeCCC--------CCcCcchhhhcCCc
Q 008562 511 HMCTQAGTYIKEFVHGDL--------GRTNPSIGSILGCR 542 (561)
Q Consensus 511 ~i~tqaGtYIKEfVhGD~--------GRT~PSl~~iLg~~ 542 (561)
++.+..||-|+|++..|. |=|.|.|..|||..
T Consensus 36 ~~t~~~Gt~VrEY~~~~G~VFAvaW~GP~~PdL~~LLGsY 75 (132)
T PF11005_consen 36 ETTDASGTTVREYVTPDGIVFAVAWQGPTMPDLQALLGSY 75 (132)
T ss_pred EEEcCCCcEEEEEEcCCCcEEEEEecCCCCccHHHHHHhh
Confidence 456689999999999885 89999999999964
No 55
>PLN03078 Putative tRNA pseudouridine synthase; Provisional
Probab=31.28 E-value=1.4e+02 Score=34.24 Aligned_cols=117 Identities=16% Similarity=0.122 Sum_probs=75.9
Q ss_pred EEEEEeeecccCCCCcccccCccccCcCcHHHHhhhccccccCC--------CceEEeecCCCCccccccCCCccEEEEE
Q 008562 317 YFGGRYLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCRG--------DSYKFHAAGREDIDVRMLGSGRPFLFEI 388 (561)
Q Consensus 317 ~i~GRY~K~sR~lsQTpW~~~g~r~~~~SVeE~I~~~~~~~f~~--------~~~~F~ssGREDvDVRmLG~GRPFvlEi 388 (561)
|.+.+|.=+++. ++.| ...+||+.|...|..+.+- ..+.|+.|||-|--|=-+|.===|-+++
T Consensus 79 YdGt~Y~G~Q~Q-~n~~--------~~~TVEg~LE~AL~k~~~I~e~n~~~~~ki~~~rAgRTDkGVHA~gQVvsf~l~~ 149 (513)
T PLN03078 79 YVGTDYRGLQKQ-RDLS--------SLSTIEGELETAIFKAGGIRESNYGNLHKIGWARSSRTDKGVHSLATMISLKMEI 149 (513)
T ss_pred EcCCCcceeeEC-CCCC--------CCCCHHHHHHHHHHHHhCccccccccccceeEEeeccCCcCccccccEEEEeccC
Confidence 777888777764 1110 1248999998888777652 4789999999999999998633333332
Q ss_pred ecCcc-CCcHHHHHHHHHHHhccCCCcEEEEeeEEecchhhhhhhcccccccceEEEEEEE
Q 008562 389 QNARE-VPSELLVKEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWI 448 (561)
Q Consensus 389 ~nPr~-~~~~~~~~~l~~~In~~~~~~V~v~~L~~v~r~~~~~ik~~e~~k~K~Y~alv~~ 448 (561)
|.. .....+...+...||..-...|.|..+..|+..= ...-.-+.|+|+=++..
T Consensus 150 --p~~~~~~d~~~~~L~~~LN~~LP~DIRVl~v~~V~~~F----hAR~sc~sRtY~Y~iP~ 204 (513)
T PLN03078 150 --PENAWKDDPDGIALAKFINSHLPDNIRVFSILPAQRSF----DPRRECDLRKYSYLLPA 204 (513)
T ss_pred --cchhccccchHHHHHHHHHhcCCCCeEEEEEEECCCCc----CCCCCCCceEEEEEEcc
Confidence 211 0000112256788997766789999999987542 22224466888888866
No 56
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=28.15 E-value=31 Score=33.05 Aligned_cols=14 Identities=21% Similarity=0.586 Sum_probs=11.6
Q ss_pred Cccccccccccccc
Q 008562 101 PNICRSCLGILQFT 114 (561)
Q Consensus 101 ~~~C~iClGiLq~~ 114 (561)
...|..|.|.|.+.
T Consensus 128 ~F~Cp~Cg~~L~~~ 141 (158)
T TIGR00373 128 NFTCPRCGAMLDYL 141 (158)
T ss_pred CCcCCCCCCEeeec
Confidence 46899999999853
No 57
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.70 E-value=37 Score=33.28 Aligned_cols=15 Identities=20% Similarity=0.215 Sum_probs=12.2
Q ss_pred Ccccccccccccccc
Q 008562 101 PNICRSCLGILQFTY 115 (561)
Q Consensus 101 ~~~C~iClGiLq~~~ 115 (561)
...|..|.|.|.+..
T Consensus 136 ~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 136 GFRCPQCGEMLEEYD 150 (178)
T ss_pred CCcCCCCCCCCeecc
Confidence 468999999998543
Done!