Query 009253
Match_columns 539
No_of_seqs 215 out of 1348
Neff 6.0
Searched_HMMs 46136
Date Thu Mar 28 22:18:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009253.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009253hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03078 Putative tRNA pseudou 100.0 7E-117 2E-121 941.2 44.2 511 2-539 1-513 (513)
2 KOG2553 Pseudouridylate syntha 100.0 2.1E-90 4.6E-95 714.4 26.2 331 71-525 30-400 (416)
3 PRK00021 truA tRNA pseudouridi 100.0 6.2E-64 1.3E-68 501.2 26.6 238 77-445 1-244 (244)
4 PRK12434 tRNA pseudouridine sy 100.0 2.7E-63 5.9E-68 496.7 25.9 239 77-445 1-245 (245)
5 COG0101 TruA Pseudouridylate s 100.0 4.9E-63 1.1E-67 497.4 26.5 243 77-450 1-249 (266)
6 cd02570 PseudoU_synth_EcTruA P 100.0 4.7E-63 1E-67 493.4 25.3 233 82-445 1-239 (239)
7 cd02568 PseudoU_synth_PUS1_PUS 100.0 4.7E-63 1E-67 495.2 24.9 244 82-445 1-245 (245)
8 PRK14588 tRNA pseudouridine sy 100.0 2.4E-62 5.1E-67 496.4 26.1 244 77-448 1-250 (272)
9 PRK14589 tRNA pseudouridine sy 100.0 3.1E-62 6.7E-67 493.3 26.7 226 79-447 2-227 (265)
10 TIGR00071 hisT_truA pseudourid 100.0 5.2E-62 1.1E-66 482.5 25.0 226 78-440 1-227 (227)
11 PRK14586 tRNA pseudouridine sy 100.0 6.8E-62 1.5E-66 486.6 25.7 239 77-445 1-245 (245)
12 cd00497 PseudoU_synth_TruA_lik 100.0 6.3E-62 1.4E-66 481.0 24.1 222 84-445 1-224 (224)
13 cd02866 PseudoU_synth_TruA_Arc 100.0 6.8E-62 1.5E-66 479.7 23.7 220 82-445 1-221 (221)
14 cd02569 PseudoU_synth_ScPus3 P 100.0 2.8E-61 6E-66 484.7 26.0 241 82-445 1-256 (256)
15 PRK14587 tRNA pseudouridine sy 100.0 1.9E-56 4.1E-61 448.4 26.7 236 79-481 2-237 (256)
16 KOG2554 Pseudouridylate syntha 100.0 8.9E-47 1.9E-51 381.8 20.6 267 61-451 49-326 (425)
17 KOG4393 Predicted pseudouridyl 100.0 1.3E-35 2.8E-40 290.7 17.6 262 77-448 4-279 (295)
18 PF01416 PseudoU_synth_1: tRNA 99.7 9.8E-20 2.1E-24 158.9 -2.9 79 362-446 23-105 (105)
19 PF01416 PseudoU_synth_1: tRNA 98.0 2.7E-07 5.9E-12 80.4 -3.4 89 83-199 2-105 (105)
20 PF10105 DUF2344: Uncharacteri 94.1 0.44 9.5E-06 46.4 10.3 98 105-210 19-116 (187)
21 COG5011 Uncharacterized protei 54.9 26 0.00057 34.7 5.5 96 108-210 23-119 (228)
22 TIGR01213 conserved hypothetic 24.2 3.5E+02 0.0076 29.6 8.5 115 104-241 185-303 (388)
No 1
>PLN03078 Putative tRNA pseudouridine synthase; Provisional
Probab=100.00 E-value=7.2e-117 Score=941.23 Aligned_cols=511 Identities=65% Similarity=0.978 Sum_probs=421.2
Q ss_pred cccccccccCcccccccCCccccccccCcccccccCCcccccCCCCCC-CCCCCCCcccccCCCCCCCCCCcCccccceE
Q 009253 2 AIYPLRLLHSPWSARSITSTLSTVGFSNKISAVNLLPLSCYRCPASSS-SKSSPSVSHTLTRPTPNSSDDKWEPVRKKKV 80 (539)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~krkv 80 (539)
|++.+|+|++||++.+++++ +.+-+| .+++.++..|.+.++ .++.++....++..+......+|++++|++|
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~---~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~krrv 73 (513)
T PLN03078 1 AVSFLRAPWPLWRFWSSTSL---LRRVNP----RILRTSSSASSSPSSTSLSPPSSDPPLTDNSDQGGGMKWESARKKKV 73 (513)
T ss_pred Ccceecccccccccccchhh---hcccCc----ccccCccceecccccccCCCCCCCcccccccCCCCCCCcccccceEE
Confidence 57899999999999999994 445566 666666644555332 2222222222221122223339999999999
Q ss_pred EEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCCCC
Q 009253 81 ALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDA 160 (539)
Q Consensus 81 al~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~~~ 160 (539)
+|.|+|+||+|+|||+|++.+..+|||++||+||.++|+|.+.|+++++++.|+|||||||||||+||||||++.++...
T Consensus 74 aL~IaYdGt~Y~G~Q~Q~n~~~~~TVEg~LE~AL~k~~~I~e~n~~~~~ki~~~rAgRTDkGVHA~gQVvsf~l~~p~~~ 153 (513)
T PLN03078 74 VLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNYGNLHKIGWARSSRTDKGVHSLATMISLKMEIPENA 153 (513)
T ss_pred EEEEEEcCCCcceeeECCCCCCCCCHHHHHHHHHHHHhCccccccccccceeEEeeccCCcCccccccEEEEeccCcchh
Confidence 99999999999999999875456899999999999999999999999999999999999999999999999999887666
Q ss_pred CCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCcchhhhhhhhHHHHHHHHhhcc
Q 009253 161 WKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFE 240 (539)
Q Consensus 161 ~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~~~~~~i~~~i~~~~~~l~~fe 240 (539)
|..++++..|+..||++||+||||++|.+|+++||||++|++|+|+|+||+++++.+..+....+++++++|++||++|+
T Consensus 154 ~~~d~~~~~L~~~LN~~LP~DIRVl~v~~V~~~FhAR~sc~sRtY~Y~iP~~~~~~k~~f~~~~~~~dI~kMneAl~~fi 233 (513)
T PLN03078 154 WKDDPDGIALAKFINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFSSEEIDEHISEFNSILNGFE 233 (513)
T ss_pred ccccchHHHHHHHHHhcCCCCeEEEEEEECCCCcCCCCCCCceEEEEEEccccccCCCccchhhhHHHHHHHHHHHHhcc
Confidence 76677777799999999999999999999999999999999999999999987776666766666668999999999999
Q ss_pred cccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCchhhhhccccc
Q 009253 241 GEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQNSMV 320 (539)
Q Consensus 241 GtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~ 320 (539)
|+|||||||.+++|++..+ ||+++.++....+.+...+.+..+. +..+++++. .|+|+++..+..
T Consensus 234 GtHDFhNFT~r~~y~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~-------~~~e~~~~~~~~ 298 (513)
T PLN03078 234 GEHPFHNYTARSKYRKKLP--GKHKQRNGAVSRRAKSSKEMSSSES------EENHGEISE-------EDEEDLSFSSIP 298 (513)
T ss_pred cccCcccccCCCccCcccc--ccccccccccccccccccccccccc------ccccccccc-------chhhhhcccccc
Confidence 9999999999999998765 5555555433222111111110000 000111000 011111122222
Q ss_pred cCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeCchhhHHHHH
Q 009253 321 SGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRK 400 (539)
Q Consensus 321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~GqSFLlhQIRk 400 (539)
.+. .+.+.+.++.+++.+.++++|+++++|+||++++|+|+|++|+|+++++..|.+||+|+|.|||||||||||
T Consensus 299 ~~~-----~~~~~~~~~~~~~~~~~~~~wl~e~d~~d~i~~s~~R~I~~~~~~~~~~~~g~~fv~i~I~GqSFmlhQIRK 373 (513)
T PLN03078 299 SGS-----SDENEDILKFQSSQVQIRARWLHEPDETDRISASHFRKIFRCSCGKLEKSLGFDFVELSIWGESFMLHQIRK 373 (513)
T ss_pred ccc-----cccccccccccccchhhhhhhccCCccccccchhheEEEEEeecCCccccCCceEEEEEEEehhHHHHHHHH
Confidence 221 123345556666778889999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHccCCCHHHHHHHHhccCCCCCCCCCCCCeeEeccccCCCCCCC-CCCCccccchhhHHHHHHHHHHHHhhc
Q 009253 401 MVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSVRTRPG-VTRPEMQTMVESEEILKMVDEFYTSVT 479 (539)
Q Consensus 401 MVG~avaV~rG~~p~~~i~~~L~~~~ri~iP~APa~GL~L~~v~f~~~nk~~-~~~~~~~~~~~~~~~~~~~e~Fk~~~i 479 (539)
|||++++|++|.+|++.|+.+|.++.++.+|+||++||||.+|+|+.||+.| ..+|+++.+++++++++.|++|++++|
T Consensus 374 MIG~~~aV~rg~~~~~~i~~~L~~~~r~~~P~AP~~GL~L~~~~F~~yn~~~~~~~p~~~~~~e~e~~~~~i~eF~~~~i 453 (513)
T PLN03078 374 MVGTAVAVKRELLPRDIIRLSLTKFSRIVLPLAPSEVLILRGNSFSVRKKPGNIKRPGMETMNESEEILKGVEEFYRAVM 453 (513)
T ss_pred HHHHHHHHHhccCCHHHHHHHhccccccccccCCCcceEEEeeeccccccccccCCCCccccccHHHHHHHHHHHHHHhh
Confidence 9999999999999999999999998999999999999999999999999876 688999999999999999999999999
Q ss_pred hHhHHhhhhhccCcHHHHHHHhhhcCCCChhhHHHHHHHHHHHHHHHHhhhHHHhhhccC
Q 009253 480 LPEVSKFLDATKSPWTEWIENLEKFTSIPNEQLDEVRNAWQLWKEKRFESKTIVESAISV 539 (539)
Q Consensus 480 ~p~I~~~l~~~~~~~~~W~e~l~~~~~~~~~~~~~~~~~~~~wk~~~~~~~~~~~~~~~~ 539 (539)
||+|+++++.++++|++|++||++|++||++||++||+||++||+++...|+.+.+|+++
T Consensus 454 ~p~i~~~~~~~~~~w~~w~~nl~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~ 513 (513)
T PLN03078 454 LPQVSKFLDPSKPPWKEWVENLDRFTSIPDAQLDEVRKAWKVWKADYDRMKMARKSASSE 513 (513)
T ss_pred hHHHHHHhccccchHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHhhhHHHHhhhcccccC
Confidence 999999999899999999999999999999999999999999999999999999999874
No 2
>KOG2553 consensus Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.1e-90 Score=714.37 Aligned_cols=331 Identities=35% Similarity=0.582 Sum_probs=295.9
Q ss_pred CcCccccceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEE
Q 009253 71 KWEPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMI 150 (539)
Q Consensus 71 ~~~~~~krkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVv 150 (539)
+|++++|+||||+|||||+||||||+|++ .+||||+|++||++||+|+++|++|++++.|+|||||||||||++|||
T Consensus 30 ~~~k~~KrKVail~gY~G~gY~GmQ~N~~---~kTIEgeL~~al~~aGaI~e~n~~dpkk~~~~raARTDKGVhA~~nvi 106 (416)
T KOG2553|consen 30 KAPKPRKRKVAILLGYCGTGYHGMQYNPP---LKTIEGELFEALFKAGAISESNAGDPKKIGFARAARTDKGVHAAGNVI 106 (416)
T ss_pred ccccccceEEEEEEEeccCCccceecCCC---CCchHHHHHHHHHHcCCcccccccChHHhhhHHhhccccchhhhhhee
Confidence 89999999999999999999999999976 499999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCCCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCcchhhh------
Q 009253 151 CLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAE------ 224 (539)
Q Consensus 151 s~kl~i~~~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~~~~~~------ 224 (539)
|++|++++ ..+++.||.+||++||||+|.||+++||||..|++|+|+|+||+++|.+..+.+..+
T Consensus 107 SlK~~~~~---------~~lv~~lN~~Lp~~IRv~~v~r~~k~F~pr~~CdsR~YeYllPtfal~~p~~~~~~~~~~~~~ 177 (416)
T KOG2553|consen 107 SLKLELDD---------PELVEKLNEILPEQIRVWGVKRVTKSFNPRKQCDSRTYEYLLPTFALAPPKPSSLLEVDIQYD 177 (416)
T ss_pred EEEEeeCc---------HHHHHHHhhhCCcceEEEEEEecCCCCCccccccceeEEEecceeeecCCCCccHHHhhhhhh
Confidence 99998653 358999999999999999999999999999999999999999999998765552110
Q ss_pred -----------------------------h---hhhHHHHHHHHhhcccccccccccccccccCCCCCCccccccccchh
Q 009253 225 -----------------------------I---DSHISDFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASK 272 (539)
Q Consensus 225 -----------------------------i---~~~i~~~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~ 272 (539)
. .+.++.++.+|++|+|||||||||.++.+.
T Consensus 178 ~e~~~~f~~~~~~~~~~~~s~~~~~~~~~yr~s~~~l~~~~~~ls~Y~GthnFHNfT~~~~~~----------------- 240 (416)
T KOG2553|consen 178 KEFEKEFWNTYPLSAKERLSGQDRKTESGYRLSEEKLEVFNTILSKYVGTHNFHNFTTGKDFT----------------- 240 (416)
T ss_pred hhhhhhhccccchhhhhhhcccccccccceeeCHHHHHHHHHHHHHhhcccccceecccCCCC-----------------
Confidence 0 136888999999999999999999853210
Q ss_pred hhhhhhcccccCCCCCcccccccCCccccCCCCCccCchhhhhccccccCcccccccccccCCcccCCCcchhhhhhccc
Q 009253 273 DAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYE 352 (539)
Q Consensus 273 ~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (539)
T Consensus 241 -------------------------------------------------------------------------------- 240 (416)
T KOG2553|consen 241 -------------------------------------------------------------------------------- 240 (416)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred ccccccccccceEEEEEeeccccccc--cCccEEEEEEEeCchhhHHHHHHHHHHHHHHccCCCHHHHHHHHhccCCCCC
Q 009253 353 TDEADKLSASHFRKIFSCSCGKLEKS--LGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRIVL 430 (539)
Q Consensus 353 ~~e~dr~~~s~~R~I~s~~~~~~~~~--~g~~~v~i~I~GqSFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~~~~ri~i 430 (539)
.++..|+|.+|.|++|+++ .|.+||.|.|+||||||||||||||+||+|+|+.+|.+.|+.+|.+..+|++
T Consensus 241 -------dpss~R~I~s~~~~~pfv~~~~~~e~V~i~i~GQSFMLHQIRKMVglav~i~R~~~p~~~i~~af~~~~ri~I 313 (416)
T KOG2553|consen 241 -------DPSSNRFIKSFTVSEPFVINDEGVEFVKIKIHGQSFMLHQIRKMVGLAVLIVRSGAPASTIQRAFNKEHKINI 313 (416)
T ss_pred -------CccccceeeEEEecCcceeccCCceEEEEEEEcchhHHHHHHHHHHHHHHHHhcCCCHHHHHHhhCCCccccc
Confidence 1466799999999999987 7999999999999999999999999999999999999999999998899999
Q ss_pred CCCCCCCeeEeccccCCCCCCCCCCCccccchhhHHHHHHHHHHHHhhchHhHHhhhhhccCcHHHHHHHhhhcCCCChh
Q 009253 431 PLAPSEVLFLRANSFSVRTRPGVTRPEMQTMVESEEILKMVDEFYTSVTLPEVSKFLDATKSPWTEWIENLEKFTSIPNE 510 (539)
Q Consensus 431 P~APa~GL~L~~v~f~~~nk~~~~~~~~~~~~~~~~~~~~~e~Fk~~~i~p~I~~~l~~~~~~~~~W~e~l~~~~~~~~~ 510 (539)
|+||++||+|++++|+.||++. ++..+.-++++++++++++||.++|||+|.+. +.++..|..|+..|+++.
T Consensus 314 P~AP~~gLlL~~~~F~~yn~~~--~~~~~e~i~~~~~e~ei~~fk~~~Iy~~I~~~-E~~~~~f~~wl~~l~~~~----- 385 (416)
T KOG2553|consen 314 PKAPGEGLLLEEPHFESYNRKF--RPSGHEEIDWDDYEEEIDQFKEKHIYSHIIKT-EEKEGVFAIWLSSLNQRD----- 385 (416)
T ss_pred cCCCcceEEeeccccccccccc--CCCCcCCcCHHHHHHHHHHHHHHHhchHHhhh-HhhhhhHHHHHHHHhhhc-----
Confidence 9999999999999999999873 33323447788999999999999999999986 667899999999999886
Q ss_pred hHHHHHHHHHHHHHH
Q 009253 511 QLDEVRNAWQLWKEK 525 (539)
Q Consensus 511 ~~~~~~~~~~~wk~~ 525 (539)
....++++|.+|+.+
T Consensus 386 ~~~~~~~~~~~~~~~ 400 (416)
T KOG2553|consen 386 NYPDLRKGSNEFLTD 400 (416)
T ss_pred chhhhhccccccccc
Confidence 345677888888865
No 3
>PRK00021 truA tRNA pseudouridine synthase A; Validated
Probab=100.00 E-value=6.2e-64 Score=501.23 Aligned_cols=238 Identities=26% Similarity=0.385 Sum_probs=204.6
Q ss_pred cceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecC
Q 009253 77 KKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEI 156 (539)
Q Consensus 77 krkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i 156 (539)
|++|+|.|+|+||+|+|||+|++ .+|||++||+||.++++ +++.|.+||||||||||++|||+|++..
T Consensus 1 m~~~~l~i~YdGt~y~G~q~q~~---~~TVq~~le~aL~~~~~---------~~~~~~~agRTD~GVHA~~qvv~~~~~~ 68 (244)
T PRK00021 1 MMRIALTIEYDGTNFHGWQRQPN---GRTVQGELEKALSKLAG---------EPVRVIGAGRTDAGVHALGQVAHFDTPA 68 (244)
T ss_pred CeEEEEEEEECCCccceeeeCCC---CCCHHHHHHHHHHHHhC---------CCeEEEEEccCCCcccccCcEEEEEeCC
Confidence 57999999999999999999976 48999999999999987 5899999999999999999999999864
Q ss_pred CCCCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccC-----CcchhhhhhhhHHH
Q 009253 157 PPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGIN-----SQLTAAEIDSHISD 231 (539)
Q Consensus 157 ~~~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~-----~~~~~~~i~~~i~~ 231 (539)
. .+...+...||++||+||||+++.+|+.+||||++|.+|+|+|+||...+... ..+.... .++++
T Consensus 69 ~-------~~~~~~~~~lN~~Lp~dI~V~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~--ld~~~ 139 (244)
T PRK00021 69 P-------RPPEKWRRALNALLPDDIAVLWAEEVPDDFHARFSAKARRYRYRIYNRPARPPFLRGYVWHYPYP--LDVDA 139 (244)
T ss_pred C-------CCHHHHHHHHHhcCCCCEEEEEeEecCCCcCcCcCCCceEEEEEEecCCCCChhhCCcEEEeCCC--CcHHH
Confidence 2 13456899999999999999999999999999999999999999998754210 0111112 36999
Q ss_pred HHHHHhhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCch
Q 009253 232 FNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDD 311 (539)
Q Consensus 232 ~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~ 311 (539)
|+++++.|+|+||||||+..+. .
T Consensus 140 m~~a~~~~~G~HdF~~F~~~~~-----~---------------------------------------------------- 162 (244)
T PRK00021 140 MNEAAQYLLGEHDFTSFRASGC-----Q---------------------------------------------------- 162 (244)
T ss_pred HHHHHHHhcCceeeeeeeCCCC-----C----------------------------------------------------
Confidence 9999999999999999974210 0
Q ss_pred hhhhccccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeC
Q 009253 312 EKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGE 391 (539)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~Gq 391 (539)
..+++|+|.++++.+ ..+++.|+|+|+
T Consensus 163 ------------------------------------------------~~~~~R~I~~~~v~~-----~~~~~~i~i~g~ 189 (244)
T PRK00021 163 ------------------------------------------------SKSPVRTIYEADVTR-----EGDFIVFDISAN 189 (244)
T ss_pred ------------------------------------------------CCCCeEEEEEEEEEE-----cCCEEEEEEEEc
Confidence 025679999999864 247999999999
Q ss_pred chhhHHHHHHHHHHHHHHccCCCHHHHHHHHhccC-CCCCCCCCCCCeeEecccc
Q 009253 392 SFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHS-RIVLPLAPSEVLFLRANSF 445 (539)
Q Consensus 392 SFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~~~~-ri~iP~APa~GL~L~~v~f 445 (539)
|||+||||+|||++++||+|.++++.|+.+|.... +..+|+|||+||||++|.|
T Consensus 190 sFL~~qVR~mvg~l~~vg~g~~~~~~i~~~L~~~~~~~~~~~APa~GL~L~~v~Y 244 (244)
T PRK00021 190 GFLHNMVRNIVGTLLEVGKGKRPPEDIKELLEAKDRTLAGPTAPAEGLYLVEVDY 244 (244)
T ss_pred hhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccCCCccCCCCCEEeeeEC
Confidence 99999999999999999999999999999997544 4578999999999999987
No 4
>PRK12434 tRNA pseudouridine synthase A; Reviewed
Probab=100.00 E-value=2.7e-63 Score=496.70 Aligned_cols=239 Identities=24% Similarity=0.374 Sum_probs=203.6
Q ss_pred cceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecC
Q 009253 77 KKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEI 156 (539)
Q Consensus 77 krkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i 156 (539)
|++|+|.|+|+||+|+|||+|++. .+|||++||+||.++++ +++.+.+||||||||||++||+||+++.
T Consensus 1 m~~~~l~i~YdGt~y~G~Q~Q~~~--~~TVq~~le~aL~~~~~---------~~~~~~~agRTD~GVHA~~qv~~f~~~~ 69 (245)
T PRK12434 1 MRNIKLTIQYDGSRYKGWQKLGNN--DNTIQGKIESVLSEMTG---------EEIEIIGCGRTDAGVHALNQVANFQTDE 69 (245)
T ss_pred CceEEEEEEECCCccceEeeCCCC--CCCHHHHHHHHHHHHhC---------CCeEEEEeccCCCCcCccCcEEEEEcCC
Confidence 478999999999999999999752 48999999999999876 5799999999999999999999999853
Q ss_pred CCCCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEcccccccc-----CCcchhhhhhhhHHH
Q 009253 157 PPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGI-----NSQLTAAEIDSHISD 231 (539)
Q Consensus 157 ~~~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~-----~~~~~~~~i~~~i~~ 231 (539)
+. +...+...||++||+||||+++.+|+.+||||++|.+|+|.|+|+...... ...+.... .++++
T Consensus 70 ~~-------~~~~l~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~f~~~~~~~~~~~--ld~~~ 140 (245)
T PRK12434 70 KL-------SEDKIKKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNEKFHNVFMRKYSMHVNEK--LDVKA 140 (245)
T ss_pred CC-------CHHHHHHHHHccCCCCeEEEEEEECCCCcccccCCCcEEEEEEEccCCCCChhhCCeEEEeCCC--CCHHH
Confidence 21 234689999999999999999999999999999999999999999764321 01111222 36999
Q ss_pred HHHHHhhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCch
Q 009253 232 FNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDD 311 (539)
Q Consensus 232 ~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~ 311 (539)
|+++++.|+|+|||+||+.... .
T Consensus 141 m~~a~~~~~G~HDF~~F~~~~~-----~---------------------------------------------------- 163 (245)
T PRK12434 141 MKEAAKYLVGSHDFTSFTNAKS-----K---------------------------------------------------- 163 (245)
T ss_pred HHHHHHHccCCcCHHhhcCCCC-----C----------------------------------------------------
Confidence 9999999999999999985210 0
Q ss_pred hhhhccccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeC
Q 009253 312 EKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGE 391 (539)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~Gq 391 (539)
..+++|+|+++++.+ ..+++.|+|+|+
T Consensus 164 ------------------------------------------------~~~~~R~I~~~~v~~-----~~~~~~i~i~g~ 190 (245)
T PRK12434 164 ------------------------------------------------KKSTVREIYSIDIME-----EDGFVQIRVSGN 190 (245)
T ss_pred ------------------------------------------------CCCCEEEEEEEEEEE-----eCCEEEEEEEec
Confidence 025679999998864 346999999999
Q ss_pred chhhHHHHHHHHHHHHHHccCCCHHHHHHHHhccCC-CCCCCCCCCCeeEecccc
Q 009253 392 SFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSR-IVLPLAPSEVLFLRANSF 445 (539)
Q Consensus 392 SFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~~~~r-i~iP~APa~GL~L~~v~f 445 (539)
|||+||||+|||++++||+|.++++.|+.+|+...+ ...|+|||+||||++|.|
T Consensus 191 ~FL~~mVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y 245 (245)
T PRK12434 191 GFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDRNQANCTAPASGLYLENVEY 245 (245)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcccCCCccCCCCCEEeEeEC
Confidence 999999999999999999999999999999975544 468999999999999987
No 5
>COG0101 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-63 Score=497.43 Aligned_cols=243 Identities=27% Similarity=0.425 Sum_probs=210.6
Q ss_pred cceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecC
Q 009253 77 KKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEI 156 (539)
Q Consensus 77 krkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i 156 (539)
|+||+|.|+|+||+|+|||+|++. +||||+||+||.+++++ ++.+.+||||||||||.|||+||++..
T Consensus 1 m~ri~l~iaYdGt~f~G~Q~Qp~~---~TVQ~~le~aL~~i~~~---------~~~i~~AGRTD~GVHA~gqv~hfd~~~ 68 (266)
T COG0101 1 MKRIALKIAYDGTRFHGWQRQPNV---RTVQGELEKALSKIGGE---------SVRVIGAGRTDAGVHALGQVVHFDTPA 68 (266)
T ss_pred CceEEEEEEEcCCceeeeccCCCC---CCHHHHHHHHHHHhcCC---------cceeEEecCCCcCccccccEEEEEcCC
Confidence 459999999999999999999764 89999999999999985 569999999999999999999999864
Q ss_pred CCCCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccC-----CcchhhhhhhhHHH
Q 009253 157 PPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGIN-----SQLTAAEIDSHISD 231 (539)
Q Consensus 157 ~~~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~-----~~~~~~~i~~~i~~ 231 (539)
.. ....+...||++||+||+|+++.+|+++||||++|.+|+|+|+|+...+... ......++ +++.
T Consensus 69 ~~-------~~~~~~~~lN~~Lp~dI~V~~~~~v~~~FhaRfsa~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~l--d~~~ 139 (266)
T COG0101 69 DR-------PLEKLVRALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYRYIIYNAPLRPPFLANYVWHVPYPL--DLDA 139 (266)
T ss_pred cc-------cHHHHHHHHHhcCCCCcEEEEEEECCCCCCCcccccceEEEEEEcCccCCChhhhcccccccCcC--CHHH
Confidence 32 1457899999999999999999999999999999999999999998866211 11112223 5999
Q ss_pred HHHHHhhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCch
Q 009253 232 FNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDD 311 (539)
Q Consensus 232 ~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~ 311 (539)
|+++++.|+|+|||+||+.... +
T Consensus 140 m~~aa~~l~G~HDF~sF~~~~~------------------------------------------------------~--- 162 (266)
T COG0101 140 MREAAKLLLGTHDFTSFRKAGC------------------------------------------------------Q--- 162 (266)
T ss_pred HHHHHHHccccccchhhccCCC------------------------------------------------------c---
Confidence 9999999999999999986321 0
Q ss_pred hhhhccccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeC
Q 009253 312 EKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGE 391 (539)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~Gq 391 (539)
..+.+|+|+++++.+. .+++.|+|+|+
T Consensus 163 ------------------------------------------------~~s~vRti~~~~v~~~-----~~~i~i~i~g~ 189 (266)
T COG0101 163 ------------------------------------------------SKSPVRTIYRIDVSRD-----GDLIVIDISGN 189 (266)
T ss_pred ------------------------------------------------cCCCeEEEEEEEEEec-----CCEEEEEEEeC
Confidence 0256899999998863 68999999999
Q ss_pred chhhHHHHHHHHHHHHHHccCCCHHHHHHHHh-ccCCCCCCCCCCCCeeEeccccCCCCC
Q 009253 392 SFMLHQIRKMVGTAVAVKRKLLPRDILTLSLA-KHSRIVLPLAPSEVLFLRANSFSVRTR 450 (539)
Q Consensus 392 SFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~-~~~ri~iP~APa~GL~L~~v~f~~~nk 450 (539)
|||+||||+|||+++.|++|.++.+.+..+|. ++.+..+|+|||+||||.+|.|+.+++
T Consensus 190 sFL~~mVR~iVg~l~~vg~g~~~~~~i~~ll~~~~r~~~~~~Apa~GL~L~~v~Y~~~~~ 249 (266)
T COG0101 190 SFLWHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRKLAGPTAPAEGLYLVRVDYPEDFE 249 (266)
T ss_pred hhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhccCcccCCCCCCCCccEEEeeccCCccc
Confidence 99999999999999999999999999999997 555688999999999999999987654
No 6
>cd02570 PseudoU_synth_EcTruA PseudoU_synth_EcTruA: Pseudouridine synthase, Escherichia coli TruA like. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA. psi38 and psi39 in tRNAs are highly phylogenetically conserved. P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators.
Probab=100.00 E-value=4.7e-63 Score=493.38 Aligned_cols=233 Identities=26% Similarity=0.374 Sum_probs=199.8
Q ss_pred EEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCCCCC
Q 009253 82 LRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAW 161 (539)
Q Consensus 82 l~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~~~~ 161 (539)
|.|+|+||+|+|||+|++. +|||++||+||.++++ +++.|.+||||||||||++|||||+++...
T Consensus 1 l~i~Y~Gt~f~G~q~q~~~---~TVq~~le~aL~~~~~---------~~~~i~~agRTD~GVHA~~qvv~~~~~~~~--- 65 (239)
T cd02570 1 LTIEYDGTNFSGWQRQPNG---RTVQGELEKALSKIAG---------EPVRVIGAGRTDAGVHALGQVAHFDTPSEI--- 65 (239)
T ss_pred CEEEEeCCccceeeeCCCC---CCHHHHHHHHHHHHhC---------CCeEEEEECcCCCCcCccccEEEEEECCCC---
Confidence 5799999999999999874 8999999999999987 689999999999999999999999996431
Q ss_pred CCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEcccccccc-----CCcchhhhhhhhHHHHHHHH
Q 009253 162 KDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGI-----NSQLTAAEIDSHISDFNAIL 236 (539)
Q Consensus 162 ~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~-----~~~~~~~~i~~~i~~~~~~l 236 (539)
+...++..||++||+||+|+++.+|+++||||++|.+|+|+|+||...... ...+.... .++++|++++
T Consensus 66 ----~~~~~~~~lN~~Lp~dI~v~~i~~v~~~F~aR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~--~d~~~m~~a~ 139 (239)
T cd02570 66 ----PLEKLIKALNSLLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRPVPSPFLRRYVWHVPRP--LDIEAMQEAA 139 (239)
T ss_pred ----CHHHHHHHHHccCCCCEEEEEEEECCCCcCcccCCCceEEEEEEccCCCCChhhCCeEEEeCCC--CCHHHHHHHH
Confidence 245789999999999999999999999999999999999999999874211 01111112 3699999999
Q ss_pred hhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCchhhhhc
Q 009253 237 NEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQ 316 (539)
Q Consensus 237 ~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~ 316 (539)
+.|+|+|||||||..+..
T Consensus 140 ~~f~G~HdF~~F~~~~~~-------------------------------------------------------------- 157 (239)
T cd02570 140 KLLLGTHDFSSFRAAGCQ-------------------------------------------------------------- 157 (239)
T ss_pred HHccCCcchhhhCCCCCC--------------------------------------------------------------
Confidence 999999999999863210
Q ss_pred cccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeCchhhH
Q 009253 317 NSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLH 396 (539)
Q Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~GqSFLlh 396 (539)
+.++.|+|.++++.+ +.+++.|+|+|+|||+|
T Consensus 158 -------------------------------------------~~~~~R~I~~~~v~~-----~~~~~~i~i~g~sFL~~ 189 (239)
T cd02570 158 -------------------------------------------SKSTVRTIYRADVYR-----EGDLIVFEIRANGFLYH 189 (239)
T ss_pred -------------------------------------------CCCCeEEEEEEEEEE-----eCCEEEEEEEEcHHHHH
Confidence 025679999998864 34799999999999999
Q ss_pred HHHHHHHHHHHHHccCCCHHHHHHHHhccCC-CCCCCCCCCCeeEecccc
Q 009253 397 QIRKMVGTAVAVKRKLLPRDILTLSLAKHSR-IVLPLAPSEVLFLRANSF 445 (539)
Q Consensus 397 QIRkMVG~avaV~rG~~p~~~i~~~L~~~~r-i~iP~APa~GL~L~~v~f 445 (539)
|||+|||++++|++|.++++.|+.+|....+ ..+|+|||+||||++|.|
T Consensus 190 qVR~mvg~ll~vg~g~~~~~~i~~~l~~~~~~~~~~~APa~GL~L~~v~Y 239 (239)
T cd02570 190 MVRNIVGTLLEVGRGKLSPEDIKEILEAKDRTAAGPTAPAHGLYLVKVEY 239 (239)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccCCCCcCCCCCEEeeeEC
Confidence 9999999999999999999999999975544 458999999999999987
No 7
>cd02568 PseudoU_synth_PUS1_PUS2 PseudoU_synth_PUS1_PUS2: Pseudouridine synthase, PUS1/ PUS2 like. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle, psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal. Psi44 in U
Probab=100.00 E-value=4.7e-63 Score=495.15 Aligned_cols=244 Identities=44% Similarity=0.711 Sum_probs=210.6
Q ss_pred EEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCCCCC
Q 009253 82 LRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAW 161 (539)
Q Consensus 82 l~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~~~~ 161 (539)
|.|+|+||+|+|||+|++. .+|||++||+||.++++|++.|..+.+++.|.+||||||||||++||+||++..+....
T Consensus 1 l~i~Y~Gt~f~G~Q~Q~~~--~~TVq~~le~aL~~~~~~~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~ 78 (245)
T cd02568 1 LLFGYCGTGYHGMQYNPGN--YKTIEGELERALVKAGAISESNAGDPKKIGFSRAARTDKGVHAARNVVSLKVIIDDPEG 78 (245)
T ss_pred CEEEEeCCCccccccCCCC--CCChHHHHHHHHHHcCCcCccccCChhhcceeeecccccchhheeeEEEEEEecccccc
Confidence 5799999999999999763 37999999999999999998888888999999999999999999999999996432100
Q ss_pred CCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCcchhhhhhhhHHHHHHHHhhccc
Q 009253 162 KDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEG 241 (539)
Q Consensus 162 ~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~~~~~~i~~~i~~~~~~l~~feG 241 (539)
+.+...+...||++||+||+|+++.+|+.+||||++|.+|+|+|+||...+ .++++|+++++.|+|
T Consensus 79 --~~~~~~~~~~lN~~Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~~~------------~d~~~m~~a~~~~~G 144 (245)
T cd02568 79 --LGIGEDLVEKLNSHLPEDIRVFGITRVTKSFNARKACDSRTYEYLLPTFAL------------ETLDRFNEILKLYVG 144 (245)
T ss_pred --ccchHHHHHHHHccCCCceEEEEEEcCCCCCCcchhhhcceeEEECCcccH------------hHHHHHHHHHHHhhC
Confidence 011457899999999999999999999999999999999999999987542 369999999999999
Q ss_pred ccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCchhhhhcccccc
Q 009253 242 EHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQNSMVS 321 (539)
Q Consensus 242 tHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~ 321 (539)
+|||+|||......
T Consensus 145 ~HdF~~F~~~~~~~------------------------------------------------------------------ 158 (245)
T cd02568 145 THNFHNFTVRKKFE------------------------------------------------------------------ 158 (245)
T ss_pred ccccccCccccccc------------------------------------------------------------------
Confidence 99999999632100
Q ss_pred CcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccc-cCccEEEEEEEeCchhhHHHHH
Q 009253 322 GVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKS-LGFGYVEISISGESFMLHQIRK 400 (539)
Q Consensus 322 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~-~g~~~v~i~I~GqSFLlhQIRk 400 (539)
..+++|+|.++.+.+.... .+.+++.|+|+|+|||+||||+
T Consensus 159 --------------------------------------~~~~~R~i~~~~~~~~~~~~~~~~~i~i~i~g~~FL~~mVR~ 200 (245)
T cd02568 159 --------------------------------------DPSANRFIISFYVSEPFVIEEGLEWVSIEIHGQSFMLHQIRK 200 (245)
T ss_pred --------------------------------------CCCceeEEEEEEEecceeecCCccEEEEEEEechHHHHHHHH
Confidence 0256789999988754322 2457999999999999999999
Q ss_pred HHHHHHHHHccCCCHHHHHHHHhccCCCCCCCCCCCCeeEecccc
Q 009253 401 MVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSF 445 (539)
Q Consensus 401 MVG~avaV~rG~~p~~~i~~~L~~~~ri~iP~APa~GL~L~~v~f 445 (539)
|||++++||+|.++++.|+.+|++..+...|+|||+||||++|.|
T Consensus 201 mvg~l~~vg~g~~~~~~i~~~L~~~~~~~~~~APa~GL~L~~v~y 245 (245)
T cd02568 201 MIGLAIAIVRGGAPESLIDLSFNKAKRIIIPLAPGLGLLLEYPHF 245 (245)
T ss_pred HHHHHHHHHcCCCCHHHHHHHhcccccccccCCCCcceeEecccC
Confidence 999999999999999999999987666678999999999999987
No 8
>PRK14588 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=2.4e-62 Score=496.42 Aligned_cols=244 Identities=26% Similarity=0.399 Sum_probs=205.6
Q ss_pred cceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecC
Q 009253 77 KKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEI 156 (539)
Q Consensus 77 krkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i 156 (539)
|++|+|.|+|+||+|+|||+|++. +|||++||+||.+++. +++.|.+||||||||||+|||+||+++.
T Consensus 1 m~~~~l~iaYdGt~f~G~Q~Q~~~---~TVq~~Le~aL~~l~~---------~~i~i~~AgRTDaGVHA~gQv~~f~~~~ 68 (272)
T PRK14588 1 MRTIALLLEYDGTDFAGSQWQTDG---RTVQGALEAAWQALTQ---------ERRRIVLAGRTDAGVHARGQVAHVQTDT 68 (272)
T ss_pred CceEEEEEEEcCCceeeeEECCCC---CCHHHHHHHHHHHhhC---------CCceEEEecCCCcCcCccccEEEEEcCC
Confidence 478999999999999999999764 8999999999999875 5789999999999999999999999853
Q ss_pred CCCCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEcccccccc-----CCcchhhhhhhhHHH
Q 009253 157 PPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGI-----NSQLTAAEIDSHISD 231 (539)
Q Consensus 157 ~~~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~-----~~~~~~~~i~~~i~~ 231 (539)
+. +...|...||++||+||+|+++.+|+.+||||++|.+|+|+|+|+...... ...+.... .|+++
T Consensus 69 ~~-------~~~~l~~~LN~~LP~dI~V~~v~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~--lDi~~ 139 (272)
T PRK14588 69 RH-------SLATIWRGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREYRYVIDCAPAPSPQLRHQVLHYAGT--LDVAA 139 (272)
T ss_pred CC-------CHHHHHHHHHhcCCCCeEEEEEEECCCCcCcccCCCcEEEEEEEcCCCCCChhhcCceEecCCC--CCHHH
Confidence 21 234689999999999999999999999999999999999999998754211 01111122 36999
Q ss_pred HHHHHhhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCch
Q 009253 232 FNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDD 311 (539)
Q Consensus 232 ~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~ 311 (539)
|+++++.|+|+|||+|||... +
T Consensus 140 m~~a~~~f~G~HDF~~F~~~~---~------------------------------------------------------- 161 (272)
T PRK14588 140 MDAALKLLIGTHDFAAFTTAP---Q------------------------------------------------------- 161 (272)
T ss_pred HHHHHHHccCCcchHhhcCCC---C-------------------------------------------------------
Confidence 999999999999999998531 0
Q ss_pred hhhhccccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeC
Q 009253 312 EKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGE 391 (539)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~Gq 391 (539)
..+++|+|+++++.... ..+.+++.|+|+|+
T Consensus 162 ------------------------------------------------~~~~vRtI~~~~~~~~~-~~~~~~i~~~i~g~ 192 (272)
T PRK14588 162 ------------------------------------------------EGSTVRTCYWARCTDTE-WFGRPLLAIEVAAN 192 (272)
T ss_pred ------------------------------------------------CCCCeEEEEEEEEEEcc-cCCCCEEEEEEEEc
Confidence 02567899988886432 12447999999999
Q ss_pred chhhHHHHHHHHHHHHHHccCCCHHHHHHHHhc-cCCCCCCCCCCCCeeEeccccCCC
Q 009253 392 SFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAK-HSRIVLPLAPSEVLFLRANSFSVR 448 (539)
Q Consensus 392 SFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~~-~~ri~iP~APa~GL~L~~v~f~~~ 448 (539)
|||+||||+|||++++||+|.++++.++..|.. +.+...|+|||+||||++|.|+..
T Consensus 193 ~FL~~mVR~mVg~ll~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~V~Y~~~ 250 (272)
T PRK14588 193 AFLQHMVRNIVGTLLLVGRGRMTVDQFGAVLASRDRRLAGPTAPAHGLYLTAVRYPPG 250 (272)
T ss_pred hhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccCCCCCCCCCcEEeeEecCch
Confidence 999999999999999999999999999999964 445688999999999999999753
No 9
>PRK14589 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=3.1e-62 Score=493.26 Aligned_cols=226 Identities=25% Similarity=0.396 Sum_probs=200.8
Q ss_pred eEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCC
Q 009253 79 KVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPP 158 (539)
Q Consensus 79 kval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~ 158 (539)
+|+|.|+|+||+|+|||+|++. +|||++||+||.+++.+. +.+++.|.+||||||||||++||+||++..
T Consensus 2 ~~~l~i~YdGt~y~G~Q~Q~~~---~TVq~~Le~aL~~~~~~~-----~~~~~~i~~agRTDaGVHA~gqv~~f~~~~-- 71 (265)
T PRK14589 2 RLAFRISYIGTRFFGSQYQPDQ---RTVEGEFIAACRRLGLFS-----DWREAGFALAGRTDRGVHARGQVLAFSTHK-- 71 (265)
T ss_pred cEEEEEEEcCCCeeeeeeCCCC---CCHHHHHHHHHHHhhCcc-----CCceeeEEEeccCCcCccccccEEEEEeCC--
Confidence 7999999999999999999764 899999999999998763 235899999999999999999999999843
Q ss_pred CCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCcchhhhhhhhHHHHHHHHhh
Q 009253 159 DAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNE 238 (539)
Q Consensus 159 ~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~~~~~~i~~~i~~~~~~l~~ 238 (539)
+..+...||++||+||+|+++.+|+++||||++|.+|+|+|+|+... .|+++|+++++.
T Consensus 72 --------~~~~~~~lN~~LP~dI~V~~~~~v~~~FhAR~~a~~R~Y~Y~i~~~~-------------lD~~~m~~a~~~ 130 (265)
T PRK14589 72 --------PERAVEALNGQLPPDIWCTGWAEVPESFHPRYDAISRTYRYYFSRPP-------------SDINAMRDAAGE 130 (265)
T ss_pred --------hHHHHHHHHhhCCCCeEEEEEEEcCCCCCcccCCceeEEEEEEecCc-------------cHHHHHHHHHHH
Confidence 23578999999999999999999999999999999999999997532 258999999999
Q ss_pred cccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCchhhhhccc
Q 009253 239 FEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQNS 318 (539)
Q Consensus 239 feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~ 318 (539)
|+|+|||+|||... .
T Consensus 131 f~G~HDF~~F~~~~------~----------------------------------------------------------- 145 (265)
T PRK14589 131 FIGTHDFSCFARVE------G----------------------------------------------------------- 145 (265)
T ss_pred ccCCccHHHHhccC------C-----------------------------------------------------------
Confidence 99999999998521 0
Q ss_pred cccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeCchhhHHH
Q 009253 319 MVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQI 398 (539)
Q Consensus 319 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~GqSFLlhQI 398 (539)
.+++|+|.++++.. ..+++.|+|+|+|||+|||
T Consensus 146 ------------------------------------------~~~vRtI~~i~v~~-----~~~~~~~~i~G~~FL~~mV 178 (265)
T PRK14589 146 ------------------------------------------KSPVRTILRIRVFS-----DGGFPVFEVTAQSFLWHMV 178 (265)
T ss_pred ------------------------------------------CCCeEEEEEEEEEE-----eCCEEEEEEEechhHHHHH
Confidence 24568898888764 3578999999999999999
Q ss_pred HHHHHHHHHHHccCCCHHHHHHHHhccCCCCCCCCCCCCeeEeccccCC
Q 009253 399 RKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSV 447 (539)
Q Consensus 399 RkMVG~avaV~rG~~p~~~i~~~L~~~~ri~iP~APa~GL~L~~v~f~~ 447 (539)
|+|||+++.||+|.++++.|+.+|....+...|+|||+||||++|.|+.
T Consensus 179 R~mVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~APa~GL~L~~V~Y~~ 227 (265)
T PRK14589 179 RCMAGALLQIGEGEMEPDDIERLLSGPCKRKVKPAPAEGLVLWDVDCGL 227 (265)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHhCcCCCCCCccCCCCcEEeeeecCC
Confidence 9999999999999999999999997666667899999999999999974
No 10
>TIGR00071 hisT_truA pseudouridylate synthase I. universal so far, single copy in all prokaryotes, 3 in yeast. Trusted cutoff for orthology is about 100 based on 1 match only in complete prokaryote with length 200.
Probab=100.00 E-value=5.2e-62 Score=482.46 Aligned_cols=226 Identities=31% Similarity=0.510 Sum_probs=197.0
Q ss_pred ceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCC
Q 009253 78 KKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIP 157 (539)
Q Consensus 78 rkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~ 157 (539)
++|+|.|+|+||+|+|||+|++. +|||++||+||.++++ +++.|.+||||||||||++||+||++..+
T Consensus 1 ~~~~l~i~YdGt~f~G~Q~Q~~~---~TVq~~le~aL~~~~~---------~~i~~~~agRTD~GVHA~~qv~~f~~~~~ 68 (227)
T TIGR00071 1 RKIALKIAYDGSNYHGWQRQPNK---RTVQGELEKALEAIGK---------KKITIMSAGRTDKGVHAMGQVISFDTPKE 68 (227)
T ss_pred CeEEEEEEEcCCCeeEEeECcCC---CCHHHHHHHHHHHHhC---------CCeeEEeeccCcCCccccccEEEEEecCC
Confidence 47999999999999999999764 8999999999999987 68999999999999999999999998643
Q ss_pred CCCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCcchhhhhhhhHHHHHHHHh
Q 009253 158 PDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILN 237 (539)
Q Consensus 158 ~~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~~~~~~i~~~i~~~~~~l~ 237 (539)
. +...|...||++||+||+|+++.+|+.+||||++|.+|+|+|+||... ++. .. .++++|+++++
T Consensus 69 ~-------~~~~~~~~lN~~Lp~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~-----~~~-~~--ld~~~m~~a~~ 133 (227)
T TIGR00071 69 I-------PDNKLNAKLNALLPPDIRVKALAPVNDNFHARFSASKRHYRYILYNHR-----HYY-SP--LDLEKMRAAAK 133 (227)
T ss_pred C-------CHHHHHHHHHccCCCCEEEEEEEeCCCCcCCCCCCCcEEEEEEEccCc-----ccC-CC--CCHHHHHHHHH
Confidence 1 234689999999999999999999999999999999999999999753 111 12 36999999999
Q ss_pred hcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCchhhhhcc
Q 009253 238 EFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQN 317 (539)
Q Consensus 238 ~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~ 317 (539)
.|+|+|||+|||.... .
T Consensus 134 ~~~G~HDF~~F~~~~~-----~---------------------------------------------------------- 150 (227)
T TIGR00071 134 QLLGKHDFSNFSKAKS-----K---------------------------------------------------------- 150 (227)
T ss_pred HccCcccHHHhcCCCC-----C----------------------------------------------------------
Confidence 9999999999985310 0
Q ss_pred ccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeCchhhHH
Q 009253 318 SMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQ 397 (539)
Q Consensus 318 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~GqSFLlhQ 397 (539)
..+++|+|+++++.+ +.+++.|+|+|+|||+||
T Consensus 151 ------------------------------------------~~~~~R~i~~~~v~~-----~~~~~~i~i~g~~FL~~m 183 (227)
T TIGR00071 151 ------------------------------------------SRSPIRTISDIKVSE-----SGEYIIFDIIGNSFLWHM 183 (227)
T ss_pred ------------------------------------------CCCCeEEEEEEEEEE-----cCCEEEEEEEecHHHHHH
Confidence 025679999998864 467999999999999999
Q ss_pred HHHHHHHHHHHHccCCCHHHHHHHHhccC-CCCCCCCCCCCeeE
Q 009253 398 IRKMVGTAVAVKRKLLPRDILTLSLAKHS-RIVLPLAPSEVLFL 440 (539)
Q Consensus 398 IRkMVG~avaV~rG~~p~~~i~~~L~~~~-ri~iP~APa~GL~L 440 (539)
||+|||++++||+|.++++.|+.+|.... +...|+|||+||||
T Consensus 184 VR~mvg~l~~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L 227 (227)
T TIGR00071 184 VRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLAPTTAPANGLYL 227 (227)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccCCCCCCCCCCcC
Confidence 99999999999999999999999997544 45678999999998
No 11
>PRK14586 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=6.8e-62 Score=486.63 Aligned_cols=239 Identities=26% Similarity=0.349 Sum_probs=201.2
Q ss_pred cceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecC
Q 009253 77 KKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEI 156 (539)
Q Consensus 77 krkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i 156 (539)
|++|+|.|+|+||+|+|||+|++. +|||++||+||.++++ +++.|.+||||||||||++||+||+++.
T Consensus 1 m~~~~l~i~YdGt~f~G~Q~Q~~~---~TVq~~le~aL~~~~~---------~~i~~~~agRTD~GVHA~~qv~~f~~~~ 68 (245)
T PRK14586 1 MKRVAAVVSYDGSNFFGYQGQPDV---RTVQGVFEDALERIFK---------QRIYTQAAGRTDTGVHANGQVIAFNCPN 68 (245)
T ss_pred CeEEEEEEEEcCCceeeEEECCCC---CCHHHHHHHHHHHHhC---------CCeeEEEecCCccCCCccCcEEEEEecC
Confidence 478999999999999999999763 8999999999999975 5799999999999999999999999854
Q ss_pred CCCCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEcccccccc-----CCcchhhhhhhhHHH
Q 009253 157 PPDAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGI-----NSQLTAAEIDSHISD 231 (539)
Q Consensus 157 ~~~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~-----~~~~~~~~i~~~i~~ 231 (539)
+. .+...|...||++||+||+|+++.+|+.+||||++|.+|+|+|+|+...... ........ .++++
T Consensus 69 ~~------~~~~~l~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~f~~~~~~~~~~~--ld~~~ 140 (245)
T PRK14586 69 DR------MTEEDIKNAMNANLPDDIYVKKVFEVPKNFHPRFDAKKRIYHYFILTSKEKNVFLRKYVWWFPYE--LDLEA 140 (245)
T ss_pred Cc------CCHHHHHHHHHccCCCCeEEEEEEECCCCcCcccCCCcEEEEEEEecCCCCChhhCCceEEeCCC--CCHHH
Confidence 31 1345789999999999999999999999999999999999999998753211 00111122 36999
Q ss_pred HHHHHhhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCch
Q 009253 232 FNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDD 311 (539)
Q Consensus 232 ~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~ 311 (539)
|+++++.|+|+|||+||+.+..
T Consensus 141 m~~a~~~l~G~HDF~~F~~~~~---------------------------------------------------------- 162 (245)
T PRK14586 141 MRKAAKYLEGEHDFTSFKTGSD---------------------------------------------------------- 162 (245)
T ss_pred HHHHHHHccCcchHHhhcCCCC----------------------------------------------------------
Confidence 9999999999999999932110
Q ss_pred hhhhccccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeC
Q 009253 312 EKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGE 391 (539)
Q Consensus 312 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~Gq 391 (539)
..+++|+|+++++.+. ..+++.|+|+|+
T Consensus 163 ------------------------------------------------~~~~vR~I~~~~~~~~----~~~~i~~~i~g~ 190 (245)
T PRK14586 163 ------------------------------------------------ERNPVRTIYRIRILRL----KKDLILIRVEGR 190 (245)
T ss_pred ------------------------------------------------CCCCcEEEEEEEEEEc----cCCEEEEEEEec
Confidence 0245789999887541 246899999999
Q ss_pred chhhHHHHHHHHHHHHHHccCCCHHHHHHHHhccC-CCCCCCCCCCCeeEecccc
Q 009253 392 SFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHS-RIVLPLAPSEVLFLRANSF 445 (539)
Q Consensus 392 SFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~~~~-ri~iP~APa~GL~L~~v~f 445 (539)
|||+||||+|||+|++||+|.++++.|...|.... +...|+|||+||||++|.|
T Consensus 191 ~FL~~mVR~mvg~l~~vg~g~~~~~~i~~~L~~~~r~~~~~~APa~GL~L~~v~f 245 (245)
T PRK14586 191 SFLRRMVRNIVGALVKVGLGQWEPEKIKEVLEARDRSKAAGTAPAHGLYLYKVLF 245 (245)
T ss_pred hhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcccCCCccCCCCCEEeEeEC
Confidence 99999999999999999999999999999996544 4578999999999999987
No 12
>cd00497 PseudoU_synth_TruA_like PseudoU_synth_TruA: Pseudouridine synthase, TruA family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae PUS1 catalyzes the formation of psi34 and psi36 in the intron containing tRNAIle, psi35 in the intron containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44 in U2 snRNA and, psi38 and psi39 in tRNAs are highly ph
Probab=100.00 E-value=6.3e-62 Score=480.95 Aligned_cols=222 Identities=29% Similarity=0.479 Sum_probs=195.9
Q ss_pred EEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCCCCCCC
Q 009253 84 VGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKD 163 (539)
Q Consensus 84 v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~~~~~~ 163 (539)
|+|+||+|+|||+|++. +|||++||+||.+++++.+ ++++.|.+||||||||||++||++|++..+.
T Consensus 1 i~YdGt~f~G~Q~Q~~~---~TVq~~le~aL~~~~~~~~-----~~~~~i~~agRTD~GVHA~~qv~~~~~~~~~----- 67 (224)
T cd00497 1 IAYDGWKYHGFQRQPDV---PTVEGELFKALLKTGLIES-----PKPSNYSRAGRTDKGVSALGQVVSLETRSKL----- 67 (224)
T ss_pred CEEcCCceeeEeeCcCC---CCHHHHHHHHHHHhhCcCC-----CcceeEEEeccccccccccccEEEEEECCCc-----
Confidence 68999999999999764 8999999999999998642 4589999999999999999999999995431
Q ss_pred CCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCcchhhhhhhhHHHHHHHHhhccccc
Q 009253 164 DPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEGEH 243 (539)
Q Consensus 164 dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~~~~~~i~~~i~~~~~~l~~feGtH 243 (539)
+ .+...||++||+||+|+++.+|+.+||||++|.+|+|+|+||... .++++|+++++.|+|+|
T Consensus 68 --~--~~~~~lN~~Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~~-------------~d~~~m~~a~~~f~G~H 130 (224)
T cd00497 68 --K--PYPDILNGLLPKDIRVLAWAPVPEDFHARFSCVSRTYRYYFPGGD-------------LDIEAMREAAKLLLGTH 130 (224)
T ss_pred --H--HHHHHHHhhCCCCcEEEEEEEeCCCCCCCcccCeEEEEEEECCCC-------------cCHHHHHHHHHHccCcc
Confidence 1 588999999999999999999999999999999999999999762 25899999999999999
Q ss_pred ccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCchhhhhccccccCc
Q 009253 244 PFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQNSMVSGV 323 (539)
Q Consensus 244 dFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~ 323 (539)
||+|||...+.
T Consensus 131 DF~~F~~~~~~--------------------------------------------------------------------- 141 (224)
T cd00497 131 DFRNFCKKDGR--------------------------------------------------------------------- 141 (224)
T ss_pred cHHHhcCCCCC---------------------------------------------------------------------
Confidence 99999963210
Q ss_pred ccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeCchhhHHHHHHHH
Q 009253 324 HQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVG 403 (539)
Q Consensus 324 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~GqSFLlhQIRkMVG 403 (539)
..+++|+|.++++.+. .+++.|+|+|+|||+||||+|||
T Consensus 142 ------------------------------------~~~~~RtI~~~~v~~~-----~~~~~i~i~g~sFL~~mVR~mvg 180 (224)
T cd00497 142 ------------------------------------KKNPVRTIISAEVEEV-----DDFYVFEVKGKSFLWHQVRRIVA 180 (224)
T ss_pred ------------------------------------CCCCeEEEEEEEEEec-----CCEEEEEEEEcHHHHHHHHHHHH
Confidence 0256799999998752 47999999999999999999999
Q ss_pred HHHHHHccCCCHHHHHHHHhccCCCCC--CCCCCCCeeEecccc
Q 009253 404 TAVAVKRKLLPRDILTLSLAKHSRIVL--PLAPSEVLFLRANSF 445 (539)
Q Consensus 404 ~avaV~rG~~p~~~i~~~L~~~~ri~i--P~APa~GL~L~~v~f 445 (539)
++++|++|.++++.|+.+|....+... |+|||+||||++|.|
T Consensus 181 ~ll~vg~g~~~~~~i~~~l~~~~~~~~~~~~APa~GL~L~~V~Y 224 (224)
T cd00497 181 ALFLVGQGLEPPSIISRLLDEEKRPSKPQYPAPPEPLVLWDCKY 224 (224)
T ss_pred HHHHHhCCCCCHHHHHHHHhcCCcccCCCCcCCCCCcEEeeeeC
Confidence 999999999999999999986666544 399999999999987
No 13
>cd02866 PseudoU_synth_TruA_Archea PseudoU_synth_archea: Pseudouridine synthase,. This group consists of archealpseudouridine synthases.Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. This group of proteins make Psedouridine in tRNAs.
Probab=100.00 E-value=6.8e-62 Score=479.70 Aligned_cols=220 Identities=29% Similarity=0.439 Sum_probs=194.5
Q ss_pred EEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCCCCC
Q 009253 82 LRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAW 161 (539)
Q Consensus 82 l~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~~~~ 161 (539)
|.|+|+||+|+|||+|++ .+|||++||+||.+++.+.+ .+++.|.+||||||||||++||+||+++.+
T Consensus 1 l~i~Y~Gt~y~G~q~q~~---~~TVq~~le~aL~~~~~~~~-----~~~i~~~~agRTD~GVHA~~qv~~f~~~~~---- 68 (221)
T cd02866 1 LKVAYDGTPYHGFQRQPD---VRTVEGELIKALRRLGIIES-----PKRPRLYSAGRTDAGVSALGNVVAFETEKE---- 68 (221)
T ss_pred CEEEEeCCceeeeeeCCC---CCCHHHHHHHHHHHhhcccc-----CCceEEEEEcCCccccCccccEEEEEeCcH----
Confidence 579999999999999976 48999999999999987642 258999999999999999999999998422
Q ss_pred CCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCcchhhhhhhhHHHHHHHHhhccc
Q 009253 162 KDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEG 241 (539)
Q Consensus 162 ~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~~~~~~i~~~i~~~~~~l~~feG 241 (539)
.+...||++||+||+|+++.+|+.+||||++|.+|+|+|+||... .++++|+++++.|+|
T Consensus 69 -------~~~~~lN~~LP~dI~v~~~~~v~~~F~ar~~a~~r~Y~Y~i~~~~-------------ld~~~m~~a~~~~~G 128 (221)
T cd02866 69 -------LTPPAINNALPKDIRVWAWAKVPEDFHPRRDARRRYYRYYLGAED-------------YDVEAMAEAAKKLIG 128 (221)
T ss_pred -------HHHHHHHhhCCCCEEEEEEEEeCCCCCCCccCCeEEEEEEECCCc-------------CCHHHHHHHHHHhcC
Confidence 168999999999999999999999999999999999999999752 258999999999999
Q ss_pred ccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCchhhhhcccccc
Q 009253 242 EHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQNSMVS 321 (539)
Q Consensus 242 tHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~ 321 (539)
+|||+|||....
T Consensus 129 ~HDF~~F~~~~~-------------------------------------------------------------------- 140 (221)
T cd02866 129 THDFSNFSKRDG-------------------------------------------------------------------- 140 (221)
T ss_pred CcCHHHhhCCCC--------------------------------------------------------------------
Confidence 999999985210
Q ss_pred CcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeCchhhHHHHHH
Q 009253 322 GVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKM 401 (539)
Q Consensus 322 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~GqSFLlhQIRkM 401 (539)
.+++|+|+++++.+ +.+++.|+|+|+|||+||||+|
T Consensus 141 ---------------------------------------~~~~R~I~~~~~~~-----~~~~~~~~i~g~~FL~~mVR~m 176 (221)
T cd02866 141 ---------------------------------------RDPVRTIERIEIRE-----NGEFLVIDVVGESFLWNMVRRI 176 (221)
T ss_pred ---------------------------------------CCCcEEEEEEEEEE-----cCCEEEEEEEEcHHHHHHHHHH
Confidence 13468898888754 3579999999999999999999
Q ss_pred HHHHHHHHccCCCHHHHHHHHhccCCCCC-CCCCCCCeeEecccc
Q 009253 402 VGTAVAVKRKLLPRDILTLSLAKHSRIVL-PLAPSEVLFLRANSF 445 (539)
Q Consensus 402 VG~avaV~rG~~p~~~i~~~L~~~~ri~i-P~APa~GL~L~~v~f 445 (539)
||++++||+|.++++.++.+|....+..+ |+|||+||||++|.|
T Consensus 177 vg~ll~vg~g~~~~~~i~~~l~~~~~~~~~~~APa~GL~L~~v~Y 221 (221)
T cd02866 177 VGALSLVGKGKRENEWVDKLLDGEFRKKDGVPAPPEGLILVDVKY 221 (221)
T ss_pred HHHHHHHhCCCCCHHHHHHHHhCCCcccCCCCCCCCCcEEEEeeC
Confidence 99999999999999999999987666654 599999999999987
No 14
>cd02569 PseudoU_synth_ScPus3 PseudoU_synth_ScPus3-like: Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like. This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya.
Probab=100.00 E-value=2.8e-61 Score=484.74 Aligned_cols=241 Identities=26% Similarity=0.413 Sum_probs=198.9
Q ss_pred EEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCCCCC
Q 009253 82 LRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAW 161 (539)
Q Consensus 82 l~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~~~~ 161 (539)
|.|+|+||+|+|||+|++. .+|||++||+||.++++|.+. +++.|.+||||||||||++||+||++..+...-
T Consensus 1 l~i~YdGt~y~G~Q~Q~~~--~~TVq~~Le~aL~~~~~i~~~-----~~~~~~~agRTD~GVHA~~qv~~f~~~~~~~~~ 73 (256)
T cd02569 1 LRFAYLGWNYNGFAVQEET--TNTVEETLFEALEKTRLIEDR-----QTSNYSRCGRTDKGVSAFGQVISLDVRSNLKPE 73 (256)
T ss_pred CEEEEeCCcceeeeECCCC--CCCHHHHHHHHHHHhcCCCCC-----CceeEEeecccCccccccCcEEEEEecCCCCcc
Confidence 5799999999999999753 379999999999999987431 589999999999999999999999996421100
Q ss_pred ---------C--CCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCcchhhhhhhhHH
Q 009253 162 ---------K--DDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHIS 230 (539)
Q Consensus 162 ---------~--~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~~~~~~i~~~i~ 230 (539)
+ .++....+...||++||+||||+++.+|+++||||++|.+|+|+|+|+... .+++
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~-------------ldi~ 140 (256)
T cd02569 74 DGLDPSTDVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSARFSCVSRTYRYFFPKGD-------------LDIE 140 (256)
T ss_pred ccccccccccccccchHHHHHHHHHhhCCCCcEEEEEEECCCCcCCCccCCceEEEEEecCCC-------------CCHH
Confidence 0 001123588999999999999999999999999999999999999999752 2589
Q ss_pred HHHHHHhhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCc
Q 009253 231 DFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSD 310 (539)
Q Consensus 231 ~~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~ 310 (539)
+|+++++.|+|+|||+|||.......
T Consensus 141 ~m~~a~~~f~G~HDF~~F~~~~~~~~------------------------------------------------------ 166 (256)
T cd02569 141 LMRKAAKLLLGEHDFRNFCKMDVANQ------------------------------------------------------ 166 (256)
T ss_pred HHHHHHHHhhCCcchHHHhccCcccC------------------------------------------------------
Confidence 99999999999999999985320000
Q ss_pred hhhhhccccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeecccccc-ccCccEEEEEEE
Q 009253 311 DEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEK-SLGFGYVEISIS 389 (539)
Q Consensus 311 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~-~~g~~~v~i~I~ 389 (539)
..+++|+|+++++.+... ..+.+++.|+|+
T Consensus 167 -------------------------------------------------~~~~~RtI~~~~v~~~~~~~~~~~~~~~~i~ 197 (256)
T cd02569 167 -------------------------------------------------VTNYVRRVLSAEVEPVDQHPDGDGLYYFEVR 197 (256)
T ss_pred -------------------------------------------------CCCCceEEEEEEEEEccCCCCCCcEEEEEEE
Confidence 025678999998865311 123479999999
Q ss_pred eCchhhHHHHHHHHHHHHHHccCCCHHHHHHHHhccCCC-CCC--CCCCCCeeEecccc
Q 009253 390 GESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRI-VLP--LAPSEVLFLRANSF 445 (539)
Q Consensus 390 GqSFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~~~~ri-~iP--~APa~GL~L~~v~f 445 (539)
|+|||+||||+|||++++||+|.++++.|+.+|..+.+. ..| +|||+||||++|.|
T Consensus 198 g~~FL~~mVR~mvg~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~Ap~~GL~L~~v~~ 256 (256)
T cd02569 198 GSAFLWHQVRCMMAVLFLIGQGLEPPSVISQLLDVEKNPRKPQYTMASEVPLVLYDCGF 256 (256)
T ss_pred EcHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhCccccCCCCcCcCCCCCcEEEEeeC
Confidence 999999999999999999999999999999999866543 445 89999999999987
No 15
>PRK14587 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=1.9e-56 Score=448.44 Aligned_cols=236 Identities=22% Similarity=0.333 Sum_probs=194.7
Q ss_pred eEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCC
Q 009253 79 KVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPP 158 (539)
Q Consensus 79 kval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~ 158 (539)
+|+|.|+|+||+|+|||+|++ |||++||+||.++.+ +|||||+||||++||+++...+
T Consensus 2 ~~~l~i~YdGt~f~G~Q~Q~~-----TVq~~Le~aL~~i~~---------------~agRTDaGVHA~~qv~~~~~~~-- 59 (256)
T PRK14587 2 PYLYRIAYDGTLFYGFTGHPN-----SLEPALRRVFGEILG---------------RGSRTDPGVSAVGNVVMTSQKL-- 59 (256)
T ss_pred cEEEEEEECCCcccceecCcc-----hHHHHHHHHHHHhcc---------------CccCCccCCCcccCEEEECCcC--
Confidence 689999999999999999963 999999999998532 3999999999999999973211
Q ss_pred CCCCCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEccccccccCCcchhhhhhhhHHHHHHHHhh
Q 009253 159 DAWKDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNE 238 (539)
Q Consensus 159 ~~~~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~~l~~~~~~~~~~i~~~i~~~~~~l~~ 238 (539)
+ ...||++||+||+|+++.+|+.+||||+ |.+|+|.|+||.. ..|+++|+++++.
T Consensus 60 -------~----~~~LN~~LP~dI~V~~~~~V~~~FhaR~-a~~R~Y~Y~i~~~-------------~lDi~~m~~aa~~ 114 (256)
T PRK14587 60 -------P----LGYVNSKLPRGVWAWAVAEVPEGFNPRR-AKRRRYLYVAPHW-------------GEDVEAMREAAEL 114 (256)
T ss_pred -------C----HHHHHhcCCCCeEEEEEEECCCCcCcCc-ccceEEEEEEccC-------------cchHHHHHHHHHH
Confidence 1 4689999999999999999999999997 9999999999632 1369999999999
Q ss_pred cccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCccCchhhhhccc
Q 009253 239 FEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEISSDDEKANQNS 318 (539)
Q Consensus 239 feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~ 318 (539)
|+|+|||+||+..+.. .
T Consensus 115 l~G~HDF~~F~~~~~~----~----------------------------------------------------------- 131 (256)
T PRK14587 115 LAGTHDYSSFIQRRGE----K----------------------------------------------------------- 131 (256)
T ss_pred hcCCcChHHhccCCCC----C-----------------------------------------------------------
Confidence 9999999999853200 0
Q ss_pred cccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEEEEeCchhhHHH
Q 009253 319 MVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQI 398 (539)
Q Consensus 319 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~I~GqSFLlhQI 398 (539)
..+++|+|.++++.. ..+++.|+|+|+|||+|||
T Consensus 132 -----------------------------------------~~~~vRtI~~i~v~~-----~~~~i~i~i~g~sFL~~mV 165 (256)
T PRK14587 132 -----------------------------------------ATPTVTTVYEIGVEL-----RGDLIYLYFVGRGFRNKMI 165 (256)
T ss_pred -----------------------------------------CCCCEEEEEEEEEEE-----eCCEEEEEEEechhHHHHH
Confidence 013679999998864 2468999999999999999
Q ss_pred HHHHHHHHHHHccCCCHHHHHHHHhccCCCCCCCCCCCCeeEeccccCCCCCCCCCCCccccchhhHHHHHHHHHHHHhh
Q 009253 399 RKMVGTAVAVKRKLLPRDILTLSLAKHSRIVLPLAPSEVLFLRANSFSVRTRPGVTRPEMQTMVESEEILKMVDEFYTSV 478 (539)
Q Consensus 399 RkMVG~avaV~rG~~p~~~i~~~L~~~~ri~iP~APa~GL~L~~v~f~~~nk~~~~~~~~~~~~~~~~~~~~~e~Fk~~~ 478 (539)
|+|||++++||+|.++++.|+..|..+.....|+|||+||||++|.|+. .+ .. ....+++.+..|.++.
T Consensus 166 R~mVG~Ll~Vg~G~~~~~~i~~~L~~~r~~~~~~APa~GL~L~~V~Y~~---~~-~~-------~~~~~~~~~~~~~~~~ 234 (256)
T PRK14587 166 RKMAWAILAAGRGVLSRRDIAELLERPRPGAVPSAPAEGLVLLDIEYDV---KF-QV-------DYTALRKAYVYFLSKY 234 (256)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHhcCcccCCCCCCCCCCEEeeeccCc---cc-cC-------ChHHHHHHHHHHHHHH
Confidence 9999999999999999999999998665567899999999999999973 11 11 1134566666776665
Q ss_pred chH
Q 009253 479 TLP 481 (539)
Q Consensus 479 i~p 481 (539)
..-
T Consensus 235 ~~~ 237 (256)
T PRK14587 235 RHL 237 (256)
T ss_pred HHH
Confidence 553
No 16
>KOG2554 consensus Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.9e-47 Score=381.75 Aligned_cols=267 Identities=25% Similarity=0.407 Sum_probs=215.4
Q ss_pred cCCCCCCCCCCcCccccceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCC
Q 009253 61 TRPTPNSSDDKWEPVRKKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTD 140 (539)
Q Consensus 61 ~~~~~~~~~~~~~~~~krkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTD 140 (539)
|.+........|....+|.+||.|+|+|-+|+|+..|.+- +.+||||.|++||.+.-.| .++++..++||||||
T Consensus 49 s~~~kk~~~fdfs~~~kR~IAlkiaY~GW~Y~Gla~Qe~T-~~~TIEg~l~eAL~kt~Li-----es~~~~~ysRCGRTD 122 (425)
T KOG2554|consen 49 SRKKKKKKRFDFSAHSKRHIALKIAYLGWNYQGLAPQEHT-NNPTIEGKLFEALKKTRLI-----ESRQTCNYSRCGRTD 122 (425)
T ss_pred ccccccccccchhcccceEEEEEEEEeccccCceecCCCC-CCcchHHHHHHHHHhhhcc-----cCcccccccccCCcc
Confidence 3334444556888999999999999999999999999543 3579999999999999987 345788999999999
Q ss_pred ccccccccEEEEEec--CCC--CCC----CCCCchhHHHHHHHhcCCCCEEEEEEeecCCCCCccCCCCCeEEEEEcccc
Q 009253 141 KGVHSLATMICLKME--IPP--DAW----KDDPYGIDLAKRVNAHLPRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAE 212 (539)
Q Consensus 141 KGVHA~~qVvs~kl~--i~~--~~~----~~dp~~~~l~~~LN~~LP~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~ 212 (539)
|||||.|||+|+.+. +|. +.. +.|-.....+..||.+||+||||+++.+|+.+|+||++|..|+|.|++|-.
T Consensus 123 KGVSAfgQviSl~lRS~~p~~~s~~~~~~~a~~~Ei~Y~~mLN~vLP~dIRi~awapvp~~FsARFsC~~RtYrY~F~k~ 202 (425)
T KOG2554|consen 123 KGVSAFGQVISLVLRSRIPMPDSQRDAVATADSEEIPYVHMLNRVLPPDIRIVAWAPVPPTFSARFSCVQRTYRYYFPKK 202 (425)
T ss_pred cchhhhhheeeeeeeccCCCchhhhccccccccccccHHHHHhccCCCcceEEEEecCCCCccceeehhhceeeEeccCC
Confidence 999999999999985 332 111 111123457889999999999999999999999999999999999999954
Q ss_pred ccccCCcchhhhhhhhHHHHHHHHhhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccc
Q 009253 213 VIGINSQLTAAEIDSHISDFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKV 292 (539)
Q Consensus 213 ~l~~~~~~~~~~i~~~i~~~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~ 292 (539)
- .+|++|++|+.+|+|+|||+||++-+- .+
T Consensus 203 d-------------LdI~~M~kAA~l~vGe~DFrNFCK~D~--------------------------------~n----- 232 (425)
T KOG2554|consen 203 D-------------LDIDRMSKAASLLVGEHDFRNFCKIDV--------------------------------SN----- 232 (425)
T ss_pred C-------------cCHHHHHHHHHHHhcchhhhhhhhhcc--------------------------------hh-----
Confidence 2 359999999999999999999986320 00
Q ss_pred cccCCccccCCCCCccCchhhhhccccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeec
Q 009253 293 EESDGEEDLGIGGEISSDDEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSC 372 (539)
Q Consensus 293 ~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~ 372 (539)
+ + .+..|+|+++.+
T Consensus 233 -----------------------------~----------------------v---------------tny~Rti~s~kV 246 (425)
T KOG2554|consen 233 -----------------------------G----------------------V---------------TNYERTILSAKV 246 (425)
T ss_pred -----------------------------h----------------------h---------------HHHHhhhheeeE
Confidence 0 0 134577888877
Q ss_pred cccccccCccEEEEEEEeCchhhHHHHHHHHHHHHHHccCCCHHHHHHHHh---ccCCCCCCCCCCCCeeEeccccCCCC
Q 009253 373 GKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLA---KHSRIVLPLAPSEVLFLRANSFSVRT 449 (539)
Q Consensus 373 ~~~~~~~g~~~v~i~I~GqSFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~---~~~ri~iP~APa~GL~L~~v~f~~~n 449 (539)
...-.. .+++.++|.|+.||+||||+||+.+..||+|.-++++|..+|+ .+.+...-+|-...|.|.+|.|...+
T Consensus 247 ~~~~~~--~~my~ldi~g~AFLwHqVRcimaiL~liGq~~E~p~lI~dLldIek~P~kPqY~mA~~~PL~LydC~f~~e~ 324 (425)
T KOG2554|consen 247 EDVGQT--PGMYYLDIQGSAFLWHQVRCIMAILFLIGQGLEQPSLISDLLDIEKNPQKPQYTMASDYPLELYDCDFHREN 324 (425)
T ss_pred EEcCCC--CceEEEEeechhhHHHHHHHHHHHHHHhccccCCchHHHHHHhcccCCCCceeeeccCCceEEEecCCCCcc
Confidence 654222 2499999999999999999999999999999999999999886 33344556899999999999996544
Q ss_pred CC
Q 009253 450 RP 451 (539)
Q Consensus 450 k~ 451 (539)
-.
T Consensus 325 ~e 326 (425)
T KOG2554|consen 325 VE 326 (425)
T ss_pred cc
Confidence 43
No 17
>KOG4393 consensus Predicted pseudouridylate synthase [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-35 Score=290.65 Aligned_cols=262 Identities=22% Similarity=0.264 Sum_probs=194.6
Q ss_pred cceEEEEEEEeCCCCccccccCCCCCCCCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecC
Q 009253 77 KKKVALRVGYVGTDYRGLQMQRDEHSLSTIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEI 156 (539)
Q Consensus 77 krkval~v~Y~GT~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i 156 (539)
.+||.++++|+||.|.|||.+..... .|||+-||+|.....+. +++++..|||||+||||.+|++++.+..
T Consensus 4 ~~ryll~i~ydgT~f~e~a~~~s~~~-~tIq~~leea~eeqt~l--------~~l~l~~ssrtDa~Vha~~naa~~~vpr 74 (295)
T KOG4393|consen 4 IMRYLLKIPYDGTAFEESAERLSKVA-RTIQGFLEEASEEQTGL--------DRLDLESSSRTDAGVHAYLNAAHYIVPR 74 (295)
T ss_pred hheeEEEecccccccHHHHhccCCcc-eehhhhhhhhHHhhcCC--------cceeecccCCCchhhheeeeeEEEEeec
Confidence 46899999999999999999976533 59999999999998764 6899999999999999999999999854
Q ss_pred CCCCCCCCCchhHHHHHHHhcC---CCCEEEEEEeecCCCCCccCCCCCeEEEEEcccc--ccccC----Ccchhhhhhh
Q 009253 157 PPDAWKDDPYGIDLAKRVNAHL---PRNIKVFSILPSQRSFDPRRECNLRKYSYLLPAE--VIGIN----SQLTAAEIDS 227 (539)
Q Consensus 157 ~~~~~~~dp~~~~l~~~LN~~L---P~dIRV~~i~rV~~sF~AR~~c~~R~Y~YllP~~--~l~~~----~~~~~~~i~~ 227 (539)
.-. -....+...+|..| |.||||.++..|+.+||||+++.+|+|.|.|.+. .+.+. .+...+++
T Consensus 75 ~sg-----~~~~~~~~a~nt~l~~k~gdirV~dv~~Vps~FhaR~sassRtY~YRla~g~d~l~~fERd~cW~lp~~l-- 147 (295)
T KOG4393|consen 75 FSG-----SQQQAKDRAVNTVLQRKDGDIRVIDVRCVPSNFHARYSASSRTYFYRLASGSDPLSIFERDRCWHLPEEL-- 147 (295)
T ss_pred ccC-----CcHHHHHHHHhccccCCCCceEEEEeeecCcchhheecccceeEEEEeecCCCccChhhhcccccCCccc--
Confidence 311 12345678888888 3499999999999999999999999999999874 11110 11122344
Q ss_pred hHHHHHHHHhhcccccccccccccccccCCCCCCccccccccchhhhhhhhcccccCCCCCcccccccCCccccCCCCCc
Q 009253 228 HISDFNAILNEFEGEHPFHNYTERSKYRRKPHKTGRVSKRAKASKDAVFSRVEESEGEEDGFSKVEESDGEEDLGIGGEI 307 (539)
Q Consensus 228 ~i~~~~~~l~~feGtHdFhnFT~r~~~~~~~~~~~r~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~e~~~~~~~~ 307 (539)
++.+|+++.++|+|+|||.+|++... +.+. .++. +.-++.+.
T Consensus 148 na~kmqeaa~lf~G~hdfsaf~~ats--~~y~------P~~t----------------~rr~sv~~-------------- 189 (295)
T KOG4393|consen 148 NARKMQEAAPLFEGSHDFSAFTEATS--TVYF------PSIT----------------ERRLSVLN-------------- 189 (295)
T ss_pred CHHHHHhhhhhhccchhhhhhhcCCC--CCCC------Cccc----------------ceeeeecc--------------
Confidence 58899999999999999999997431 1100 0000 00000000
Q ss_pred cCchhhhhccccccCcccccccccccCCcccCCCcchhhhhhcccccccccccccceEEEEEeeccccccccCccEEEEE
Q 009253 308 SSDDEKANQNSMVSGVHQEDCCNQHANGLKDQNSSSVIRARWLYETDEADKLSASHFRKIFSCSCGKLEKSLGFGYVEIS 387 (539)
Q Consensus 308 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~dr~~~s~~R~I~s~~~~~~~~~~g~~~v~i~ 387 (539)
++... . |.-..+....-.++..++
T Consensus 190 -------------------------~g~~~--------a-----------------------~~~~~~~e~~~~~~~nve 213 (295)
T KOG4393|consen 190 -------------------------NGDPL--------A-----------------------CSNQPETEGVTTNVGNVE 213 (295)
T ss_pred -------------------------cCCcc--------c-----------------------cccCCccccceeeeEEEE
Confidence 00000 0 000000011124789999
Q ss_pred EEeCchhhHHHHHHHHHHHHHHccCCCHHHHHHHHhccCC-----CCCCCCCCCCeeEeccccCCC
Q 009253 388 ISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSR-----IVLPLAPSEVLFLRANSFSVR 448 (539)
Q Consensus 388 I~GqSFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~~~~r-----i~iP~APa~GL~L~~v~f~~~ 448 (539)
+.++||++.|||+|++.+|+++.+.++...++.+|..+.+ ..++.||++||+|..|.|...
T Consensus 214 ~e~~gflyrQvRrm~a~LV~~g~~al~~~qv~~iLe~~~~~~l~k~~~~vapphglfL~sv~Y~n~ 279 (295)
T KOG4393|consen 214 GETEGFLYRQVRRMRAYLVTAGSRALLYHQVLYILEVRDIVGLLKCVGTVAPPHGLFLSSVEYVNL 279 (295)
T ss_pred EEecchHHHHHHhhheeeeeecccccchhhhhhhhhccchhhhhhccCCCCCCccceeeeEEechh
Confidence 9999999999999999999999999999999999975443 468999999999999999863
No 18
>PF01416 PseudoU_synth_1: tRNA pseudouridine synthase; InterPro: IPR020097 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents pseudouridine synthase I (TruA). TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA [, ]. TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis []. These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1VS3_B 2NR0_B 2NQP_D 1DJ0_A 2NRE_A.
Probab=99.73 E-value=9.8e-20 Score=158.91 Aligned_cols=79 Identities=30% Similarity=0.373 Sum_probs=63.8
Q ss_pred cceEEEEEeeccccccccCccEEEEEEEeCchhhHHHHHHHHHHHHHHccCCCHHHHHHHHhccCCC-CCC---CCCCCC
Q 009253 362 SHFRKIFSCSCGKLEKSLGFGYVEISISGESFMLHQIRKMVGTAVAVKRKLLPRDILTLSLAKHSRI-VLP---LAPSEV 437 (539)
Q Consensus 362 s~~R~I~s~~~~~~~~~~g~~~v~i~I~GqSFLlhQIRkMVG~avaV~rG~~p~~~i~~~L~~~~ri-~iP---~APa~G 437 (539)
+..|+|.++.+.. ..+++. +|+|+|||+||||+|||+++.+++|..+.+.+..+|+...+. ..| +||++|
T Consensus 23 ~~~r~i~~~~~~~-----~~~~~~-~i~g~~Fl~~~vR~~vg~~~~~~~G~~~~~~i~~~L~~~~~~~~~~ri~~ap~~g 96 (105)
T PF01416_consen 23 NTIRTIFSIDIIE-----EGDVVV-EIHGNSFLRHQVRIMVGTLLRTGRGVHSLEQIAELLNSKLRPKAPPRILTAPAVG 96 (105)
T ss_dssp HHCCCEEEEECCC-----CCCEEE-EEEESS--TTHHHHHHCCCCHHHTTSCEEECCCCCHHHHSCTTS-TEEEEEEECC
T ss_pred cHHHHHHHHhhhc-----CCCEEE-EEEecccccccchhhhHHHHHHhcCCCCHHHHHHHHhccCccccCCCcceeeCCC
Confidence 3456777777643 467888 999999999999999999999999999998888888765533 334 999999
Q ss_pred eeEeccccC
Q 009253 438 LFLRANSFS 446 (539)
Q Consensus 438 L~L~~v~f~ 446 (539)
|+|.+|.|+
T Consensus 97 L~L~~v~y~ 105 (105)
T PF01416_consen 97 LYLFHVRYD 105 (105)
T ss_dssp ECCEECCTT
T ss_pred CCceEeeCc
Confidence 999999996
No 19
>PF01416 PseudoU_synth_1: tRNA pseudouridine synthase; InterPro: IPR020097 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents pseudouridine synthase I (TruA). TruA from Escherichia coli modifies positions uracil-38, U-39 and/or U-40 in tRNA [, ]. TruA contains one atom of zinc essential for its native conformation and tRNA recognition and has a strictly conserved aspartic acid that is likely to be involved in catalysis []. These enzymes are dimeric proteins that contain two positively charged, RNA-binding clefts along their surface. Each cleft contains a highly conserved aspartic acid located at its centre. The structural domains have a topological similarity to those of other RNA-binding proteins, though the mode of interaction with tRNA appears to be unique. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1VS3_B 2NR0_B 2NQP_D 1DJ0_A 2NRE_A.
Probab=98.04 E-value=2.7e-07 Score=80.38 Aligned_cols=89 Identities=29% Similarity=0.408 Sum_probs=70.4
Q ss_pred EEEEeCC-CCccccccCCCCCCCCHHHHHHHHHHHhcCCCccc----------CCCcceeeeeecccCCccccccccEEE
Q 009253 83 RVGYVGT-DYRGLQMQRDEHSLSTIEGELETALFKAGGIRESN----------YGNLQKIAWARSSRTDKGVHSLATMIC 151 (539)
Q Consensus 83 ~v~Y~GT-~Y~G~Q~Q~~~~~~~TIE~eLE~AL~kag~I~e~n----------~~~~~ki~~~rSsRTDKGVHA~~qVvs 151 (539)
...|+|+ +|+|||.| +|++...+++|..+..+.+.+ ....-++-+..++|||+||||+.++..
T Consensus 2 ~~~~~G~HdF~~f~~~------~~~~~~~~r~i~~~~~~~~~~~~~~i~g~~Fl~~~vR~~vg~~~~~~~G~~~~~~i~~ 75 (105)
T PF01416_consen 2 AKLYVGTHDFSGFQKQ------KTVEKNTIRTIFSIDIIEEGDVVVEIHGNSFLRHQVRIMVGTLLRTGRGVHSLEQIAE 75 (105)
T ss_dssp CCEETCEEECCGCSSC------S-HHHHHCCCEEEEECCCCCCEEEEEEESS--TTHHHHHHCCCCHHHTTSCEEECCCC
T ss_pred cceeEecCCCcCCEEC------CcccccHHHHHHHHhhhcCCCEEEEEEecccccccchhhhHHHHHHhcCCCCHHHHHH
Confidence 3579999 99999987 589999999999998865544 123345668999999999999988764
Q ss_pred EEecCCCCCCCCCCchhHHHHHHHhcCCC---CEEEEEEeecC-CCCCccCC
Q 009253 152 LKMEIPPDAWKDDPYGIDLAKRVNAHLPR---NIKVFSILPSQ-RSFDPRRE 199 (539)
Q Consensus 152 ~kl~i~~~~~~~dp~~~~l~~~LN~~LP~---dIRV~~i~rV~-~sF~AR~~ 199 (539)
+ ||..+++ + ||+.+.++. -.||+++.
T Consensus 76 ~---------------------L~~~~~~~~~~-ri~~ap~~gL~L~~v~y~ 105 (105)
T PF01416_consen 76 L---------------------LNSKLRPKAPP-RILTAPAVGLYLFHVRYD 105 (105)
T ss_dssp C---------------------HHHHSCTTS-T-EEEEEEECCECCEECCTT
T ss_pred H---------------------HhccCccccCC-CcceeeCCCCCceEeeCc
Confidence 3 7777854 5 999999998 88988863
No 20
>PF10105 DUF2344: Uncharacterized protein conserved in bacteria (DUF2344); InterPro: IPR018768 This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function.
Probab=94.10 E-value=0.44 Score=46.44 Aligned_cols=98 Identities=18% Similarity=0.154 Sum_probs=66.2
Q ss_pred CHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCCCCCCCCCchhHHHHHHHhcCCCCEEE
Q 009253 105 TIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKV 184 (539)
Q Consensus 105 TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~~~~~~dp~~~~l~~~LN~~LP~dIRV 184 (539)
-+...++.||.+||.=..---|-.-...++=+.=.=-||.+.+-++-+.+.-+ .+..++.++||+.||++|+|
T Consensus 19 dl~r~~eRa~rRA~lp~a~SqGFnP~Pkisf~~aLpvGv~S~~E~~di~l~~~-------~~~~~~~~rLn~~lP~Gl~i 91 (187)
T PF10105_consen 19 DLMRVFERALRRAGLPVAYSQGFNPHPKISFAPALPVGVESLAEYMDIELEED-------IDPEEVLERLNAVLPEGLRI 91 (187)
T ss_pred HHHHHHHHHhhhcCCCeeecCCCCCCcceeecccccCceeeccEEEEEEEecC-------CCHHHHHHHHHHhCCCCCEE
Confidence 36678999999998532211232223445555556689999999999998532 24567999999999999999
Q ss_pred EEEeecCCCCCccCCCCCeEEEEEcc
Q 009253 185 FSILPSQRSFDPRRECNLRKYSYLLP 210 (539)
Q Consensus 185 ~~i~rV~~sF~AR~~c~~R~Y~YllP 210 (539)
.++..++....+-. ..-..+.|.+-
T Consensus 92 ~~~~~i~~~~~sl~-~~i~~~~Y~i~ 116 (187)
T PF10105_consen 92 LEAEEIPPKAPSLM-ALINAAEYRIT 116 (187)
T ss_pred EEEEEccCCCcchh-hhcceEEEEEE
Confidence 99999974333221 12234555554
No 21
>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.88 E-value=26 Score=34.65 Aligned_cols=96 Identities=10% Similarity=0.095 Sum_probs=64.5
Q ss_pred HHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecCCCCCCCCCCchhHHHHHHHhcCCCCEEEEEE
Q 009253 108 GELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEIPPDAWKDDPYGIDLAKRVNAHLPRNIKVFSI 187 (539)
Q Consensus 108 ~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i~~~~~~~dp~~~~l~~~LN~~LP~dIRV~~i 187 (539)
.-+++++.+||.--.---|..-+-.++.+.=---|+.+-|-++-|.+.-. ....++++.||+.||.|+-+.++
T Consensus 23 RlidR~iRRAglpiayT~GFhP~prmsia~alpvG~~ssge~fd~eL~e~-------v~~dk~~etl~~~lp~Dl~~~~v 95 (228)
T COG5011 23 RLIDRTIRRAGLPIAYTGGFHPHPRMSIAQALPVGIYSSGEIFDFELTEE-------VSEDKFKETLNKALPNDLPAYDV 95 (228)
T ss_pred HHHHHHHHhcCCceeecCCCCCCCceeeccccccccccCceEEEEEeeee-------cCcHHHHHHHHHhCCCCcchhhe
Confidence 56788899888532222233334556666666778888888888887421 12346899999999999999999
Q ss_pred eecCC-CCCccCCCCCeEEEEEcc
Q 009253 188 LPSQR-SFDPRRECNLRKYSYLLP 210 (539)
Q Consensus 188 ~rV~~-sF~AR~~c~~R~Y~YllP 210 (539)
..+.+ +.++-.--..-+|...+-
T Consensus 96 ~~iD~ksps~nqvl~~arY~i~vi 119 (228)
T COG5011 96 EKIDKKSPSSNQVLEAARYFIKVI 119 (228)
T ss_pred eeecCCCccHHHHHHhhcEEEEEE
Confidence 99974 444444444445665554
No 22
>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=24.22 E-value=3.5e+02 Score=29.60 Aligned_cols=115 Identities=19% Similarity=0.220 Sum_probs=75.1
Q ss_pred CCHHHHHHHHHHHhcCCCcccCCCcceeeeeecccCCccccccccEEEEEecC--CCCCCCCCCchhHHHHHHHhcCCCC
Q 009253 104 STIEGELETALFKAGGIRESNYGNLQKIAWARSSRTDKGVHSLATMICLKMEI--PPDAWKDDPYGIDLAKRVNAHLPRN 181 (539)
Q Consensus 104 ~TIE~eLE~AL~kag~I~e~n~~~~~ki~~~rSsRTDKGVHA~~qVvs~kl~i--~~~~~~~dp~~~~l~~~LN~~LP~d 181 (539)
.+||+.|...+.++.+- ....+..|||-|--|=-+|+===|-+++ |.. ...+...|.+.||+.-...
T Consensus 185 ~SVeelI~~~v~~~~~~--------~~~~Fh~aGREDvDvRMLG~GRPFvlEi~~P~r---r~~dl~~le~~IN~~~~g~ 253 (388)
T TIGR01213 185 ESVEELIASPFLKATGG--------TDAYFHGAGREDVDVRMLGTGRPFVLEVKEPRY---RKIDLDPLEEEINTSGKGK 253 (388)
T ss_pred chHHHHHHHHHHHHhCC--------ceeEEeccCccccceeeccCCCceEEEecCCcc---CCCCHHHHHHHHhhccCCC
Confidence 68999999998888542 4799999999999999997533333332 221 1234557889999998899
Q ss_pred EEEEEEeecCCCCCc--cCCCCCeEEEEEccccccccCCcchhhhhhhhHHHHHHHHhhccc
Q 009253 182 IKVFSILPSQRSFDP--RRECNLRKYSYLLPAEVIGINSQLTAAEIDSHISDFNAILNEFEG 241 (539)
Q Consensus 182 IRV~~i~rV~~sF~A--R~~c~~R~Y~YllP~~~l~~~~~~~~~~i~~~i~~~~~~l~~feG 241 (539)
|.|.+..-+++.=-. +..-..++|.=++-... ..+ -+.+.++++.|.|
T Consensus 254 V~v~~L~~~~~~~v~~ik~~~~~K~Y~alV~~~~-----~v~-------~e~L~~~~~~l~g 303 (388)
T TIGR01213 254 VEVEGLKFATREEVEEVKEEKHRKVYRALVEVDG-----PVS-------DEDLEELCKELEG 303 (388)
T ss_pred EEEEEeEEEcHHHHHHHhccCCceEEEEEEEECC-----CCC-------HHHHHHHHHhccC
Confidence 999998866541100 11112578887765431 111 2345567777766
Done!