Query 043662
Match_columns 330
No_of_seqs 126 out of 1122
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 07:09:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043662.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043662hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK12434 tRNA pseudouridine sy 100.0 5.5E-79 1.2E-83 567.9 29.2 244 48-300 1-245 (245)
2 COG0101 TruA Pseudouridylate s 100.0 4.1E-79 8.9E-84 572.2 28.1 253 48-310 1-253 (266)
3 PRK14588 tRNA pseudouridine sy 100.0 6.2E-78 1.3E-82 568.2 28.8 249 48-306 1-253 (272)
4 PRK14586 tRNA pseudouridine sy 100.0 8.2E-78 1.8E-82 560.0 29.0 244 48-300 1-245 (245)
5 PRK00021 truA tRNA pseudouridi 100.0 3.3E-77 7.1E-82 555.6 29.1 244 48-300 1-244 (244)
6 cd02570 PseudoU_synth_EcTruA P 100.0 1E-75 2.3E-80 543.9 28.4 239 53-300 1-239 (239)
7 TIGR00071 hisT_truA pseudourid 100.0 8.7E-74 1.9E-78 527.5 26.4 227 49-295 1-227 (227)
8 PRK14589 tRNA pseudouridine sy 100.0 2.2E-73 4.8E-78 535.0 26.8 228 49-304 1-229 (265)
9 cd00497 PseudoU_synth_TruA_lik 100.0 1.6E-72 3.4E-77 518.2 24.9 223 55-300 1-224 (224)
10 cd02569 PseudoU_synth_ScPus3 P 100.0 2E-72 4.4E-77 526.6 25.9 231 53-300 1-256 (256)
11 cd02866 PseudoU_synth_TruA_Arc 100.0 1.8E-72 3.8E-77 516.8 24.8 220 53-300 1-221 (221)
12 cd02568 PseudoU_synth_PUS1_PUS 100.0 7.1E-71 1.5E-75 513.3 21.7 228 53-300 1-245 (245)
13 PRK14587 tRNA pseudouridine sy 100.0 2.2E-67 4.8E-72 491.5 23.9 213 49-302 1-214 (256)
14 PLN03078 Putative tRNA pseudou 100.0 4.2E-65 9.2E-70 508.0 27.5 252 44-304 66-422 (513)
15 KOG2553 Pseudouridylate syntha 100.0 2.5E-56 5.5E-61 431.3 20.7 270 39-316 27-345 (416)
16 KOG4393 Predicted pseudouridyl 100.0 4.1E-54 8.9E-59 393.5 17.9 268 47-318 3-294 (295)
17 KOG2554 Pseudouridylate syntha 100.0 1.9E-53 4.1E-58 403.0 19.4 240 45-301 62-321 (425)
18 PF01416 PseudoU_synth_1: tRNA 99.9 3.1E-25 6.6E-30 180.2 -4.5 105 194-301 1-105 (105)
19 PF01416 PseudoU_synth_1: tRNA 98.2 1.8E-07 3.9E-12 75.7 -2.1 82 55-155 3-105 (105)
20 PF10105 DUF2344: Uncharacteri 97.2 0.012 2.5E-07 53.2 13.6 147 73-238 19-173 (187)
21 TIGR01213 conserved hypothetic 95.7 0.51 1.1E-05 47.2 15.9 155 71-243 184-348 (388)
22 PRK14554 putative pseudouridyl 94.2 2.1 4.6E-05 43.4 15.7 153 72-243 220-381 (422)
23 COG1258 Predicted pseudouridyl 92.6 3.1 6.8E-05 41.5 13.5 157 71-246 190-356 (398)
24 cd01291 PseudoU_synth PseudoU_ 91.2 1.6 3.6E-05 33.8 8.1 21 92-113 23-43 (87)
25 COG5011 Uncharacterized protei 65.0 7 0.00015 35.8 3.3 72 77-149 24-101 (228)
26 cd02572 PseudoU_synth_hDyskeri 41.0 2.3E+02 0.0049 25.4 9.0 94 137-250 43-143 (182)
27 PF07683 CobW_C: Cobalamin syn 30.6 2.4E+02 0.0052 21.4 7.4 86 112-198 4-93 (94)
28 TIGR00685 T6PP trehalose-phosp 25.8 94 0.002 28.5 4.1 49 50-100 3-51 (244)
29 PF09153 DUF1938: Domain of un 22.9 34 0.00074 27.0 0.5 28 233-260 25-52 (86)
30 PF05125 Phage_cap_P2: Phage m 21.4 74 0.0016 31.4 2.6 34 71-104 29-78 (333)
No 1
>PRK12434 tRNA pseudouridine synthase A; Reviewed
Probab=100.00 E-value=5.5e-79 Score=567.87 Aligned_cols=244 Identities=38% Similarity=0.652 Sum_probs=229.2
Q ss_pred cceEEEEEEEeCCCceeeeeCCC-CCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHHH
Q 043662 48 GFKWRLVIAYDGTRYAGWQFQTS-PPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESI 126 (330)
Q Consensus 48 ~~r~~l~v~YdGt~y~G~Q~Q~~-~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l 126 (330)
|.+|+|.|+||||+|+|||+|++ .+|||++||+||.+++. +++++.+|||||+||||++||+||+++... +++.+
T Consensus 1 m~~~~l~i~YdGt~y~G~Q~Q~~~~~TVq~~le~aL~~~~~---~~~~~~~agRTD~GVHA~~qv~~f~~~~~~-~~~~l 76 (245)
T PRK12434 1 MRNIKLTIQYDGSRYKGWQKLGNNDNTIQGKIESVLSEMTG---EEIEIIGCGRTDAGVHALNQVANFQTDEKL-SEDKI 76 (245)
T ss_pred CceEEEEEEECCCccceEeeCCCCCCCHHHHHHHHHHHHhC---CCeEEEEeccCCCCcCccCcEEEEEcCCCC-CHHHH
Confidence 46899999999999999999996 89999999999999875 689999999999999999999999998664 57889
Q ss_pred HHHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhccccccccc
Q 043662 127 HAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSA 206 (330)
Q Consensus 127 ~~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~ 206 (330)
..+||+.||+||+|+++.+|+++|||||+|++|+|+|+|++....+||.++|.|++...+|+++|++||+.|+|+|||++
T Consensus 77 ~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~~~~~G~HDF~~ 156 (245)
T PRK12434 77 KKYLNEYLPNDIVVTNVEEVDERFHARYNVKSKTYLYKIWNEKFHNVFMRKYSMHVNEKLDVKAMKEAAKYLVGSHDFTS 156 (245)
T ss_pred HHHHHccCCCCeEEEEEEECCCCcccccCCCcEEEEEEEccCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcCHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCC
Q 043662 207 FVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYAL 286 (330)
Q Consensus 207 F~~~~~~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~ 286 (330)
||+... +.++++|+|++++|.+.++++.|+|+|+||||||||+|||+|++||+|++++++|+++|+.+++... .+
T Consensus 157 F~~~~~--~~~~~~R~I~~~~v~~~~~~~~i~i~g~~FL~~mVR~mvg~ll~vg~g~~~~~~i~~~L~~~~r~~~---~~ 231 (245)
T PRK12434 157 FTNAKS--KKKSTVREIYSIDIMEEDGFVQIRVSGNGFLHNMVRIIVGALIEVGLGQLKAEDIKQILEAKDRNQA---NC 231 (245)
T ss_pred hcCCCC--CCCCCEEEEEEEEEEEeCCEEEEEEEecHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcccC---CC
Confidence 997643 3578999999999998888999999999999999999999999999999999999999999877643 36
Q ss_pred CcCCCCceEeeeec
Q 043662 287 SAPPHGLCLVEVKY 300 (330)
Q Consensus 287 ~APa~GL~L~~V~Y 300 (330)
+|||+||||++|.|
T Consensus 232 ~APa~GL~L~~V~Y 245 (245)
T PRK12434 232 TAPASGLYLENVEY 245 (245)
T ss_pred ccCCCCCEEeEeEC
Confidence 99999999999998
No 2
>COG0101 TruA Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.1e-79 Score=572.23 Aligned_cols=253 Identities=44% Similarity=0.750 Sum_probs=235.6
Q ss_pred cceEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHHHH
Q 043662 48 GFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIH 127 (330)
Q Consensus 48 ~~r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~ 127 (330)
|.||++.|+||||+|+|||+||+.+|||++||+||.+++. .++.+.+|||||+||||.+||+||+++.+. .++++.
T Consensus 1 m~ri~l~iaYdGt~f~G~Q~Qp~~~TVQ~~le~aL~~i~~---~~~~i~~AGRTD~GVHA~gqv~hfd~~~~~-~~~~~~ 76 (266)
T COG0101 1 MKRIALKIAYDGTRFHGWQRQPNVRTVQGELEKALSKIGG---ESVRVIGAGRTDAGVHALGQVVHFDTPADR-PLEKLV 76 (266)
T ss_pred CceEEEEEEEcCCceeeeccCCCCCCHHHHHHHHHHHhcC---CcceeEEecCCCcCccccccEEEEEcCCcc-cHHHHH
Confidence 3599999999999999999999999999999999999987 567999999999999999999999998764 378899
Q ss_pred HHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccccc
Q 043662 128 AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAF 207 (330)
Q Consensus 128 ~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F 207 (330)
.+||++||+||+|+++++||++|||||+|.+|+|+|+|++....+||..+++||+.++||+++|++|++.|+|+|||+||
T Consensus 77 ~~lN~~Lp~dI~V~~~~~v~~~FhaRfsa~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~aa~~l~G~HDF~sF 156 (266)
T COG0101 77 RALNALLPPDIRVLDVAEVPDDFHARFSAKSRTYRYIIYNAPLRPPFLANYVWHVPYPLDLDAMREAAKLLLGTHDFTSF 156 (266)
T ss_pred HHHHhcCCCCcEEEEEEECCCCCCCcccccceEEEEEEcCccCCChhhhcccccccCcCCHHHHHHHHHHccccccchhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccCCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCCC
Q 043662 208 VNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALS 287 (330)
Q Consensus 208 ~~~~~~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~~ 287 (330)
|+..+ +.++++|+|++++|.+.++++.|+|+|+||||||||+|||+|++||+|+++.++|+++|+.+++... .++
T Consensus 157 ~~~~~--~~~s~vRti~~~~v~~~~~~i~i~i~g~sFL~~mVR~iVg~l~~vg~g~~~~~~i~~ll~~~~r~~~---~~~ 231 (266)
T COG0101 157 RKAGC--QSKSPVRTIYRIDVSRDGDLIVIDISGNSFLWHMVRNIVGALLLVGRGKRPVEWIKELLEAKDRKLA---GPT 231 (266)
T ss_pred ccCCC--ccCCCeEEEEEEEEEecCCEEEEEEEeChhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhccCcccC---CCC
Confidence 98865 4458999999999999999999999999999999999999999999999999999999998777632 479
Q ss_pred cCCCCceEeeeecCCCCCCCCCC
Q 043662 288 APPHGLCLVEVKYNEEHLRLPAA 310 (330)
Q Consensus 288 APa~GL~L~~V~Y~~~~~~~~~~ 310 (330)
|||+||||++|.|++.. +++.+
T Consensus 232 Apa~GL~L~~v~Y~~~~-~~~~~ 253 (266)
T COG0101 232 APAEGLYLVRVDYPEDF-ELPED 253 (266)
T ss_pred CCCCccEEEeeccCCcc-ccccc
Confidence 99999999999998765 44433
No 3
>PRK14588 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=6.2e-78 Score=568.24 Aligned_cols=249 Identities=38% Similarity=0.540 Sum_probs=231.1
Q ss_pred cceEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHHHH
Q 043662 48 GFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIH 127 (330)
Q Consensus 48 ~~r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~ 127 (330)
|++|+|.|+||||+|+|||+|++.+|||++||+||.++.. +++.+++||||||||||++||+||+++... +++.+.
T Consensus 1 m~~~~l~iaYdGt~f~G~Q~Q~~~~TVq~~Le~aL~~l~~---~~i~i~~AgRTDaGVHA~gQv~~f~~~~~~-~~~~l~ 76 (272)
T PRK14588 1 MRTIALLLEYDGTDFAGSQWQTDGRTVQGALEAAWQALTQ---ERRRIVLAGRTDAGVHARGQVAHVQTDTRH-SLATIW 76 (272)
T ss_pred CceEEEEEEEcCCceeeeEECCCCCCHHHHHHHHHHHhhC---CCceEEEecCCCcCcCccccEEEEEcCCCC-CHHHHH
Confidence 4689999999999999999999999999999999999875 689999999999999999999999997664 578899
Q ss_pred HHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccccc
Q 043662 128 AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAF 207 (330)
Q Consensus 128 ~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F 207 (330)
.+||+.||+||+|+++++|+++|||||+|++|+|+|+|++....+||.++|.|++...+|+++|++||+.|+|+|||++|
T Consensus 77 ~~LN~~LP~dI~V~~v~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~p~~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F 156 (272)
T PRK14588 77 RGLNAHLPEDIGVQNAWEAPPDFHARFSAIQREYRYVIDCAPAPSPQLRHQVLHYAGTLDVAAMDAALKLLIGTHDFAAF 156 (272)
T ss_pred HHHHhcCCCCeEEEEEEECCCCcCcccCCCcEEEEEEEcCCCCCChhhcCceEecCCCCCHHHHHHHHHHccCCcchHhh
Confidence 99999999999999999999999999999999999999999989999999999999999999999999999999999999
Q ss_pred cccccCCCCCCCeEEEEEEEEEEe----CcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhcc
Q 043662 208 VNVQRNDRLLNPVKSVFRFDVIEM----GALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAK 283 (330)
Q Consensus 208 ~~~~~~~~~~~~~R~I~~~~v~~~----~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~ 283 (330)
|+. . +.++++|+|++++|.+. ++++.|+|+|+||||||||+|||+|++||+|++++++|+++|+++++...
T Consensus 157 ~~~-~--~~~~~vRtI~~~~~~~~~~~~~~~i~~~i~g~~FL~~mVR~mVg~ll~vg~g~~~~~~i~~~L~~~~r~~~-- 231 (272)
T PRK14588 157 TTA-P--QEGSTVRTCYWARCTDTEWFGRPLLAIEVAANAFLQHMVRNIVGTLLLVGRGRMTVDQFGAVLASRDRRLA-- 231 (272)
T ss_pred cCC-C--CCCCCeEEEEEEEEEEcccCCCCEEEEEEEEchhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccC--
Confidence 976 2 34689999999999875 36899999999999999999999999999999999999999998877643
Q ss_pred CCCCcCCCCceEeeeecCCCCCC
Q 043662 284 YALSAPPHGLCLVEVKYNEEHLR 306 (330)
Q Consensus 284 ~~~~APa~GL~L~~V~Y~~~~~~ 306 (330)
.++|||+||||++|.|++..+.
T Consensus 232 -~~~APa~GL~L~~V~Y~~~~~~ 253 (272)
T PRK14588 232 -GPTAPAHGLYLTAVRYPPGLIR 253 (272)
T ss_pred -CCCCCCCCcEEeeEecCchhcc
Confidence 3699999999999999876644
No 4
>PRK14586 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=8.2e-78 Score=559.97 Aligned_cols=244 Identities=38% Similarity=0.619 Sum_probs=227.4
Q ss_pred cceEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHHHH
Q 043662 48 GFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIH 127 (330)
Q Consensus 48 ~~r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~ 127 (330)
|.||+|.|+||||+|+|||+|++.+|||++||+||.++++ +++.+++||||||||||++||+||+++....+++.+.
T Consensus 1 m~~~~l~i~YdGt~f~G~Q~Q~~~~TVq~~le~aL~~~~~---~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~ 77 (245)
T PRK14586 1 MKRVAAVVSYDGSNFFGYQGQPDVRTVQGVFEDALERIFK---QRIYTQAAGRTDTGVHANGQVIAFNCPNDRMTEEDIK 77 (245)
T ss_pred CeEEEEEEEEcCCceeeEEECCCCCCHHHHHHHHHHHHhC---CCeeEEEecCCccCCCccCcEEEEEecCCcCCHHHHH
Confidence 4689999999999999999999999999999999999975 6899999999999999999999999987633578899
Q ss_pred HHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccccc
Q 043662 128 AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAF 207 (330)
Q Consensus 128 ~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F 207 (330)
.+||+.||+||+|+++.+|+++|||||+|++|+|+|+|++....+||.++|.|+....||+++|++||+.|+|+|||++|
T Consensus 78 ~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~~f~~~~~~~~~~~ld~~~m~~a~~~l~G~HDF~~F 157 (245)
T PRK14586 78 NAMNANLPDDIYVKKVFEVPKNFHPRFDAKKRIYHYFILTSKEKNVFLRKYVWWFPYELDLEAMRKAAKYLEGEHDFTSF 157 (245)
T ss_pred HHHHccCCCCeEEEEEEECCCCcCcccCCCcEEEEEEEecCCCCChhhCCceEEeCCCCCHHHHHHHHHHccCcchHHhh
Confidence 99999999999999999999999999999999999999999989999999999999999999999999999999999999
Q ss_pred cccccCCCCCCCeEEEEEEEEEEe-CcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCC
Q 043662 208 VNVQRNDRLLNPVKSVFRFDVIEM-GALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYAL 286 (330)
Q Consensus 208 ~~~~~~~~~~~~~R~I~~~~v~~~-~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~ 286 (330)
+... +.++++|+|++++|.+. +++++|+|+|+||||||||+|||+|++||+|++++++|+++|+.+++... .+
T Consensus 158 -~~~~--~~~~~vR~I~~~~~~~~~~~~i~~~i~g~~FL~~mVR~mvg~l~~vg~g~~~~~~i~~~L~~~~r~~~---~~ 231 (245)
T PRK14586 158 -KTGS--DERNPVRTIYRIRILRLKKDLILIRVEGRSFLRRMVRNIVGALVKVGLGQWEPEKIKEVLEARDRSKA---AG 231 (245)
T ss_pred -cCCC--CCCCCcEEEEEEEEEEccCCEEEEEEEechhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcccC---CC
Confidence 4432 35789999999999884 77899999999999999999999999999999999999999999887643 36
Q ss_pred CcCCCCceEeeeec
Q 043662 287 SAPPHGLCLVEVKY 300 (330)
Q Consensus 287 ~APa~GL~L~~V~Y 300 (330)
+|||+||||++|.|
T Consensus 232 ~APa~GL~L~~v~f 245 (245)
T PRK14586 232 TAPAHGLYLYKVLF 245 (245)
T ss_pred ccCCCCCEEeEeEC
Confidence 99999999999986
No 5
>PRK00021 truA tRNA pseudouridine synthase A; Validated
Probab=100.00 E-value=3.3e-77 Score=555.63 Aligned_cols=244 Identities=43% Similarity=0.714 Sum_probs=229.2
Q ss_pred cceEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHHHH
Q 043662 48 GFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIH 127 (330)
Q Consensus 48 ~~r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~ 127 (330)
|.||+|.++||||+|+|||+|++.+|||++||+||.+++. +++++++||||||||||++||++|+++... +++.+.
T Consensus 1 m~~~~l~i~YdGt~y~G~q~q~~~~TVq~~le~aL~~~~~---~~~~~~~agRTD~GVHA~~qvv~~~~~~~~-~~~~~~ 76 (244)
T PRK00021 1 MMRIALTIEYDGTNFHGWQRQPNGRTVQGELEKALSKLAG---EPVRVIGAGRTDAGVHALGQVAHFDTPAPR-PPEKWR 76 (244)
T ss_pred CeEEEEEEEECCCccceeeeCCCCCCHHHHHHHHHHHHhC---CCeEEEEEccCCCcccccCcEEEEEeCCCC-CHHHHH
Confidence 4689999999999999999999999999999999999986 689999999999999999999999998763 578899
Q ss_pred HHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccccc
Q 043662 128 AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAF 207 (330)
Q Consensus 128 ~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F 207 (330)
..||+.||+||+|+++.+||++||||++|++|+|+|+|+.....+||.+++.|++...+|+++|++|++.|+|+|||+||
T Consensus 77 ~~lN~~Lp~dI~V~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~ld~~~m~~a~~~~~G~HdF~~F 156 (244)
T PRK00021 77 RALNALLPDDIAVLWAEEVPDDFHARFSAKARRYRYRIYNRPARPPFLRGYVWHYPYPLDVDAMNEAAQYLLGEHDFTSF 156 (244)
T ss_pred HHHHhcCCCCEEEEEeEecCCCcCcCcCCCceEEEEEEecCCCCChhhCCcEEEeCCCCcHHHHHHHHHHhcCceeeeee
Confidence 99999999999999999999999999999999999999999989999999999999999999999999999999999999
Q ss_pred cccccCCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCCC
Q 043662 208 VNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALS 287 (330)
Q Consensus 208 ~~~~~~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~~ 287 (330)
|+.+. +.++++|+|.+++|.++++++.|+|+|+||||||||+|||+|++||+|++++++|+++|+++++... .++
T Consensus 157 ~~~~~--~~~~~~R~I~~~~v~~~~~~~~i~i~g~sFL~~qVR~mvg~l~~vg~g~~~~~~i~~~L~~~~~~~~---~~~ 231 (244)
T PRK00021 157 RASGC--QSKSPVRTIYEADVTREGDFIVFDISANGFLHNMVRNIVGTLLEVGKGKRPPEDIKELLEAKDRTLA---GPT 231 (244)
T ss_pred eCCCC--CCCCCeEEEEEEEEEEcCCEEEEEEEEchhHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccC---CCc
Confidence 86543 3578999999999998888999999999999999999999999999999999999999998776532 369
Q ss_pred cCCCCceEeeeec
Q 043662 288 APPHGLCLVEVKY 300 (330)
Q Consensus 288 APa~GL~L~~V~Y 300 (330)
|||+||||++|.|
T Consensus 232 APa~GL~L~~v~Y 244 (244)
T PRK00021 232 APAEGLYLVEVDY 244 (244)
T ss_pred cCCCCCEEeeeEC
Confidence 9999999999998
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=1e-75 Score=543.86 Aligned_cols=239 Identities=46% Similarity=0.774 Sum_probs=225.0
Q ss_pred EEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHHHHHHHHh
Q 043662 53 LVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNG 132 (330)
Q Consensus 53 l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~~~lN~ 132 (330)
++|+||||+|+|||+|++.+|||++||+||.+++. +++++.+|||||+||||++||+||+++... +++.+...||+
T Consensus 1 l~i~Y~Gt~f~G~q~q~~~~TVq~~le~aL~~~~~---~~~~i~~agRTD~GVHA~~qvv~~~~~~~~-~~~~~~~~lN~ 76 (239)
T cd02570 1 LTIEYDGTNFSGWQRQPNGRTVQGELEKALSKIAG---EPVRVIGAGRTDAGVHALGQVAHFDTPSEI-PLEKLIKALNS 76 (239)
T ss_pred CEEEEeCCccceeeeCCCCCCHHHHHHHHHHHHhC---CCeEEEEECcCCCCcCccccEEEEEECCCC-CHHHHHHHHHc
Confidence 57999999999999999999999999999999986 689999999999999999999999998764 57889999999
Q ss_pred cCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhccccccccccccccc
Q 043662 133 LLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQR 212 (330)
Q Consensus 133 ~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F~~~~~ 212 (330)
.||+||+|+++.+|+++||||++|++|+|+|+|+.....+||.+++.|++...+|+++|++|++.|+|+|||+|||+...
T Consensus 77 ~Lp~dI~v~~i~~v~~~F~aR~~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~~d~~~m~~a~~~f~G~HdF~~F~~~~~ 156 (239)
T cd02570 77 LLPPDIRVLSAEEVPDDFHARFSAKSRTYRYRILNRPVPSPFLRRYVWHVPRPLDIEAMQEAAKLLLGTHDFSSFRAAGC 156 (239)
T ss_pred cCCCCEEEEEEEECCCCcCcccCCCceEEEEEEccCCCCChhhCCeEEEeCCCCCHHHHHHHHHHccCCcchhhhCCCCC
Confidence 99999999999999999999999999999999999988899999999999999999999999999999999999997643
Q ss_pred CCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCCCcCCCC
Q 043662 213 NDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHG 292 (330)
Q Consensus 213 ~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~~APa~G 292 (330)
..++++|+|++++|.+.++++.|+|+|+||||||||+|||+|++||+|++++++|+++|+++++... .++|||+|
T Consensus 157 --~~~~~~R~I~~~~v~~~~~~~~i~i~g~sFL~~qVR~mvg~ll~vg~g~~~~~~i~~~l~~~~~~~~---~~~APa~G 231 (239)
T cd02570 157 --QSKSTVRTIYRADVYREGDLIVFEIRANGFLYHMVRNIVGTLLEVGRGKLSPEDIKEILEAKDRTAA---GPTAPAHG 231 (239)
T ss_pred --CCCCCeEEEEEEEEEEeCCEEEEEEEEcHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccC---CCCcCCCC
Confidence 3578999999999999889999999999999999999999999999999999999999998776542 36999999
Q ss_pred ceEeeeec
Q 043662 293 LCLVEVKY 300 (330)
Q Consensus 293 L~L~~V~Y 300 (330)
|||++|.|
T Consensus 232 L~L~~v~Y 239 (239)
T cd02570 232 LYLVKVEY 239 (239)
T ss_pred CEEeeeEC
Confidence 99999998
No 7
>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=8.7e-74 Score=527.49 Aligned_cols=227 Identities=40% Similarity=0.675 Sum_probs=209.7
Q ss_pred ceEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHHHHH
Q 043662 49 FKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHA 128 (330)
Q Consensus 49 ~r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~~ 128 (330)
+||++.|+||||+|+|||+|++.+|||++||+||.+++. +++.+++|||||+||||++||+||+++... +++.+..
T Consensus 1 ~~~~l~i~YdGt~f~G~Q~Q~~~~TVq~~le~aL~~~~~---~~i~~~~agRTD~GVHA~~qv~~f~~~~~~-~~~~~~~ 76 (227)
T TIGR00071 1 RKIALKIAYDGSNYHGWQRQPNKRTVQGELEKALEAIGK---KKITIMSAGRTDKGVHAMGQVISFDTPKEI-PDNKLNA 76 (227)
T ss_pred CeEEEEEEEcCCCeeEEeECcCCCCHHHHHHHHHHHHhC---CCeeEEeeccCcCCccccccEEEEEecCCC-CHHHHHH
Confidence 479999999999999999999999999999999999986 689999999999999999999999998764 5788999
Q ss_pred HHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhccccccccccc
Q 043662 129 ALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFV 208 (330)
Q Consensus 129 ~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F~ 208 (330)
+||+.||+||+|+++++|+++||||++|++|+|+|+|+... +....+|+++|++|++.|+|+|||++||
T Consensus 77 ~lN~~Lp~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~~-----------~~~~~ld~~~m~~a~~~~~G~HDF~~F~ 145 (227)
T TIGR00071 77 KLNALLPPDIRVKALAPVNDNFHARFSASKRHYRYILYNHR-----------HYYSPLDLEKMRAAAKQLLGKHDFSNFS 145 (227)
T ss_pred HHHccCCCCEEEEEEEeCCCCcCCCCCCCcEEEEEEEccCc-----------ccCCCCCHHHHHHHHHHccCcccHHHhc
Confidence 99999999999999999999999999999999999998653 3345799999999999999999999999
Q ss_pred ccccCCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCCCc
Q 043662 209 NVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSA 288 (330)
Q Consensus 209 ~~~~~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~~A 288 (330)
+... +.++++|+|++++|.+.+++++|+|+|+||||||||+|||+|++||+|++++++|+++|+.+++... .++|
T Consensus 146 ~~~~--~~~~~~R~i~~~~v~~~~~~~~i~i~g~~FL~~mVR~mvg~l~~vg~g~~~~~~i~~~L~~~~r~~~---~~~A 220 (227)
T TIGR00071 146 KAKS--KSRSPIRTISDIKVSESGEYIIFDIIGNSFLWHMVRKIVGALVLVGRGKLPPEWVAKLLDAKKRNLA---PTTA 220 (227)
T ss_pred CCCC--CCCCCeEEEEEEEEEEcCCEEEEEEEecHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHhcCCcccC---CCCC
Confidence 7642 4578999999999999889999999999999999999999999999999999999999998877643 3689
Q ss_pred CCCCceE
Q 043662 289 PPHGLCL 295 (330)
Q Consensus 289 Pa~GL~L 295 (330)
||+||||
T Consensus 221 Pa~GL~L 227 (227)
T TIGR00071 221 PANGLYL 227 (227)
T ss_pred CCCCCcC
Confidence 9999998
No 8
>PRK14589 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=2.2e-73 Score=534.98 Aligned_cols=228 Identities=35% Similarity=0.521 Sum_probs=209.6
Q ss_pred ceEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhccc-CcceeeeeccccCccccccccEEEEEeCCCCCCHHHHH
Q 043662 49 FKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLE-REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIH 127 (330)
Q Consensus 49 ~r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~-~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~ 127 (330)
++|+|.|+||||+|+|||+||+.+|||++||+||.+++.+. .+++.+.+|||||+||||++||+||+++. ++.+.
T Consensus 1 ~~~~l~i~YdGt~y~G~Q~Q~~~~TVq~~Le~aL~~~~~~~~~~~~~i~~agRTDaGVHA~gqv~~f~~~~----~~~~~ 76 (265)
T PRK14589 1 MRLAFRISYIGTRFFGSQYQPDQRTVEGEFIAACRRLGLFSDWREAGFALAGRTDRGVHARGQVLAFSTHK----PERAV 76 (265)
T ss_pred CcEEEEEEEcCCCeeeeeeCCCCCCHHHHHHHHHHHhhCccCCceeeEEEeccCCcCccccccEEEEEeCC----hHHHH
Confidence 37999999999999999999999999999999999998643 25799999999999999999999999864 57789
Q ss_pred HHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccccc
Q 043662 128 AALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAF 207 (330)
Q Consensus 128 ~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F 207 (330)
..||+.||+||+|+++.+|+++||||++|++|+|+|+|+. .++|+++|++||+.|+|+|||++|
T Consensus 77 ~~lN~~LP~dI~V~~~~~v~~~FhAR~~a~~R~Y~Y~i~~----------------~~lD~~~m~~a~~~f~G~HDF~~F 140 (265)
T PRK14589 77 EALNGQLPPDIWCTGWAEVPESFHPRYDAISRTYRYYFSR----------------PPSDINAMRDAAGEFIGTHDFSCF 140 (265)
T ss_pred HHHHhhCCCCeEEEEEEEcCCCCCcccCCceeEEEEEEec----------------CccHHHHHHHHHHHccCCccHHHH
Confidence 9999999999999999999999999999999999999842 248999999999999999999999
Q ss_pred cccccCCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCCC
Q 043662 208 VNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALS 287 (330)
Q Consensus 208 ~~~~~~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~~ 287 (330)
|+.. .++++|+|.+++|.+.++.+.|+|+|+||||||||+|||+|++||+|++++++|+++|+++++.. .++
T Consensus 141 ~~~~----~~~~vRtI~~i~v~~~~~~~~~~i~G~~FL~~mVR~mVG~ll~vg~G~~~~~~i~~~L~~~~r~~----~~~ 212 (265)
T PRK14589 141 ARVE----GKSPVRTILRIRVFSDGGFPVFEVTAQSFLWHMVRCMAGALLQIGEGEMEPDDIERLLSGPCKRK----VKP 212 (265)
T ss_pred hccC----CCCCeEEEEEEEEEEeCCEEEEEEEechhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhCcCCCC----CCc
Confidence 9763 36899999999999988999999999999999999999999999999999999999999887753 258
Q ss_pred cCCCCceEeeeecCCCC
Q 043662 288 APPHGLCLVEVKYNEEH 304 (330)
Q Consensus 288 APa~GL~L~~V~Y~~~~ 304 (330)
|||+||||++|.|+...
T Consensus 213 APa~GL~L~~V~Y~~~~ 229 (265)
T PRK14589 213 APAEGLVLWDVDCGLTF 229 (265)
T ss_pred cCCCCcEEeeeecCCcc
Confidence 99999999999998633
No 9
>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=1.6e-72 Score=518.21 Aligned_cols=223 Identities=38% Similarity=0.613 Sum_probs=204.1
Q ss_pred EEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhccc-CcceeeeeccccCccccccccEEEEEeCCCCCCHHHHHHHHHhc
Q 043662 55 IAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLE-REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGL 133 (330)
Q Consensus 55 v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~-~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~~~lN~~ 133 (330)
|+||||+|+|||+|++.+|||++||+||.+++.+. .+++.+++|||||+||||++||+||+++... +.+...||+.
T Consensus 1 i~YdGt~f~G~Q~Q~~~~TVq~~le~aL~~~~~~~~~~~~~i~~agRTD~GVHA~~qv~~~~~~~~~---~~~~~~lN~~ 77 (224)
T cd00497 1 IAYDGWKYHGFQRQPDVPTVEGELFKALLKTGLIESPKPSNYSRAGRTDKGVSALGQVVSLETRSKL---KPYPDILNGL 77 (224)
T ss_pred CEEcCCceeeEeeCcCCCCHHHHHHHHHHHhhCcCCCcceeEEEeccccccccccccEEEEEECCCc---HHHHHHHHhh
Confidence 68999999999999999999999999999998631 2379999999999999999999999998753 2788999999
Q ss_pred CCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccccccccccC
Q 043662 134 LPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRN 213 (330)
Q Consensus 134 LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F~~~~~~ 213 (330)
||+||+|+++++|+++||||++|++|+|+|+|+.. .+|+++|++|++.|+|+|||+|||+...
T Consensus 78 Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~----------------~~d~~~m~~a~~~f~G~HDF~~F~~~~~- 140 (224)
T cd00497 78 LPKDIRVLAWAPVPEDFHARFSCVSRTYRYYFPGG----------------DLDIEAMREAAKLLLGTHDFRNFCKKDG- 140 (224)
T ss_pred CCCCcEEEEEEEeCCCCCCCcccCeEEEEEEECCC----------------CcCHHHHHHHHHHccCcccHHHhcCCCC-
Confidence 99999999999999999999999999999999764 4999999999999999999999997643
Q ss_pred CCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCCCcCCCCc
Q 043662 214 DRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGL 293 (330)
Q Consensus 214 ~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~~APa~GL 293 (330)
..++++|+|++++|.+.++++.|+|+|+||||||||+|||+|++||+|++++++|+++|+.+++.... .++|||+||
T Consensus 141 -~~~~~~RtI~~~~v~~~~~~~~i~i~g~sFL~~mVR~mvg~ll~vg~g~~~~~~i~~~l~~~~~~~~~--~~~APa~GL 217 (224)
T cd00497 141 -RKKNPVRTIISAEVEEVDDFYVFEVKGKSFLWHQVRRIVAALFLVGQGLEPPSIISRLLDEEKRPSKP--QYPAPPEPL 217 (224)
T ss_pred -CCCCCeEEEEEEEEEecCCEEEEEEEEcHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcCCcccCC--CCcCCCCCc
Confidence 34789999999999988889999999999999999999999999999999999999999988776431 238999999
Q ss_pred eEeeeec
Q 043662 294 CLVEVKY 300 (330)
Q Consensus 294 ~L~~V~Y 300 (330)
||++|.|
T Consensus 218 ~L~~V~Y 224 (224)
T cd00497 218 VLWDCKY 224 (224)
T ss_pred EEeeeeC
Confidence 9999998
No 10
>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=2e-72 Score=526.57 Aligned_cols=231 Identities=32% Similarity=0.509 Sum_probs=205.0
Q ss_pred EEEEEeCCCceeeeeCCC-CCcHHHHHHHHHHHhhccc-CcceeeeeccccCccccccccEEEEEeCCCCCCH-------
Q 043662 53 LVIAYDGTRYAGWQFQTS-PPTIQCIVEKALIRVTKLE-REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGL------- 123 (330)
Q Consensus 53 l~v~YdGt~y~G~Q~Q~~-~~TVq~~Le~AL~k~~~i~-~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~------- 123 (330)
|.|+||||+|+|||+|++ .+|||++||+||.+++.+. .+++.+++|||||+||||++||+||+++......
T Consensus 1 l~i~YdGt~y~G~Q~Q~~~~~TVq~~Le~aL~~~~~i~~~~~~~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~~~~~~ 80 (256)
T cd02569 1 LRFAYLGWNYNGFAVQEETTNTVEETLFEALEKTRLIEDRQTSNYSRCGRTDKGVSAFGQVISLDVRSNLKPEDGLDPST 80 (256)
T ss_pred CEEEEeCCcceeeeECCCCCCCHHHHHHHHHHHhcCCCCCCceeEEeecccCccccccCcEEEEEecCCCCccccccccc
Confidence 579999999999999997 5899999999999998653 3689999999999999999999999996543211
Q ss_pred ----------HHHHHHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHH
Q 043662 124 ----------ESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQ 193 (330)
Q Consensus 124 ----------~~l~~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~ 193 (330)
..+..+||+.||+||+|+++.+|+++||||++|++|+|+|+|+.. .+|+++|++
T Consensus 81 ~~~~~~~~~~~~~~~~lN~~LP~dI~V~~~~~v~~~FhaR~~a~~R~Y~Y~i~~~----------------~ldi~~m~~ 144 (256)
T cd02569 81 DVKSTADEEELPYCKILNRVLPPDIRILAWAPVPPDFSARFSCVSRTYRYFFPKG----------------DLDIELMRK 144 (256)
T ss_pred cccccccchHHHHHHHHHhhCCCCcEEEEEEECCCCcCCCccCCceEEEEEecCC----------------CCCHHHHHH
Confidence 257889999999999999999999999999999999999999764 499999999
Q ss_pred HHhhcccccccccccccccCCCCCCCeEEEEEEEEEEeC------cEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcc
Q 043662 194 AAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMG------ALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPD 267 (330)
Q Consensus 194 a~~~f~G~HDF~~F~~~~~~~~~~~~~R~I~~~~v~~~~------~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~ 267 (330)
|+++|+|+|||++||+.....+.++++|+|++++|.+.+ +++.|+|+|+||||||||+|||+|++||+|+++++
T Consensus 145 a~~~f~G~HDF~~F~~~~~~~~~~~~~RtI~~~~v~~~~~~~~~~~~~~~~i~g~~FL~~mVR~mvg~ll~vg~G~~~~~ 224 (256)
T cd02569 145 AAKLLLGEHDFRNFCKMDVANQVTNYVRRVLSAEVEPVDQHPDGDGLYYFEVRGSAFLWHQVRCMMAVLFLIGQGLEPPS 224 (256)
T ss_pred HHHHhhCCcchHHHhccCcccCCCCCceEEEEEEEEEccCCCCCCcEEEEEEEEcHHHHHHHHHHHHHHHHHhCCCCCHH
Confidence 999999999999999764322357899999999998753 78999999999999999999999999999999999
Q ss_pred cHHHHHhcCCcchhccCCCCcCCCCceEeeeec
Q 043662 268 IVPKILATQDRKELAKYALSAPPHGLCLVEVKY 300 (330)
Q Consensus 268 ~i~~~L~~~~r~~~~~~~~~APa~GL~L~~V~Y 300 (330)
+|+++|+++++..... .++|||+||+|++|.|
T Consensus 225 ~i~~~L~~~~r~~~~~-~~~Ap~~GL~L~~v~~ 256 (256)
T cd02569 225 VISQLLDVEKNPRKPQ-YTMASEVPLVLYDCGF 256 (256)
T ss_pred HHHHHHhCccccCCCC-cCcCCCCCcEEEEeeC
Confidence 9999999988765321 1289999999999987
No 11
>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=1.8e-72 Score=516.83 Aligned_cols=220 Identities=38% Similarity=0.577 Sum_probs=202.6
Q ss_pred EEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhccc-CcceeeeeccccCccccccccEEEEEeCCCCCCHHHHHHHHH
Q 043662 53 LVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLE-REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALN 131 (330)
Q Consensus 53 l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~-~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~~~lN 131 (330)
|.|+||||+|+|||+|++.+|||++||+||.+++.+. ++++++++|||||+||||++||+||+++.. .+..+||
T Consensus 1 l~i~Y~Gt~y~G~q~q~~~~TVq~~le~aL~~~~~~~~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~-----~~~~~lN 75 (221)
T cd02866 1 LKVAYDGTPYHGFQRQPDVRTVEGELIKALRRLGIIESPKRPRLYSAGRTDAGVSALGNVVAFETEKE-----LTPPAIN 75 (221)
T ss_pred CEEEEeCCceeeeeeCCCCCCHHHHHHHHHHHhhccccCCceEEEEEcCCccccCccccEEEEEeCcH-----HHHHHHH
Confidence 5799999999999999999999999999999997543 357999999999999999999999999753 1788999
Q ss_pred hcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccccccccc
Q 043662 132 GLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQ 211 (330)
Q Consensus 132 ~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F~~~~ 211 (330)
+.||+||+|+++.+||++||||++|++|+|+|+|+.. .+|+++|++|++.|+|+|||++||+..
T Consensus 76 ~~LP~dI~v~~~~~v~~~F~ar~~a~~r~Y~Y~i~~~----------------~ld~~~m~~a~~~~~G~HDF~~F~~~~ 139 (221)
T cd02866 76 NALPKDIRVWAWAKVPEDFHPRRDARRRYYRYYLGAE----------------DYDVEAMAEAAKKLIGTHDFSNFSKRD 139 (221)
T ss_pred hhCCCCEEEEEEEEeCCCCCCCccCCeEEEEEEECCC----------------cCCHHHHHHHHHHhcCCcCHHHhhCCC
Confidence 9999999999999999999999999999999999753 489999999999999999999999753
Q ss_pred cCCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCCCcCCC
Q 043662 212 RNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPH 291 (330)
Q Consensus 212 ~~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~~APa~ 291 (330)
. .+++|+|+++++.+.++++.|+|+|+||||||||+|||+|++||+|++++++|+++|+.+++... .++|||+
T Consensus 140 ~----~~~~R~I~~~~~~~~~~~~~~~i~g~~FL~~mVR~mvg~ll~vg~g~~~~~~i~~~l~~~~~~~~---~~~APa~ 212 (221)
T cd02866 140 G----RDPVRTIERIEIRENGEFLVIDVVGESFLWNMVRRIVGALSLVGKGKRENEWVDKLLDGEFRKKD---GVPAPPE 212 (221)
T ss_pred C----CCCcEEEEEEEEEEcCCEEEEEEEEcHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhCCCcccC---CCCCCCC
Confidence 2 37899999999998889999999999999999999999999999999999999999999877643 2599999
Q ss_pred CceEeeeec
Q 043662 292 GLCLVEVKY 300 (330)
Q Consensus 292 GL~L~~V~Y 300 (330)
||||++|.|
T Consensus 213 GL~L~~v~Y 221 (221)
T cd02866 213 GLILVDVKY 221 (221)
T ss_pred CcEEEEeeC
Confidence 999999998
No 12
>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=7.1e-71 Score=513.32 Aligned_cols=228 Identities=27% Similarity=0.408 Sum_probs=204.5
Q ss_pred EEEEEeCCCceeeeeCCCC-CcHHHHHHHHHHHhhcccC------cceeeeeccccCccccccccEEEEEeCCCCCC---
Q 043662 53 LVIAYDGTRYAGWQFQTSP-PTIQCIVEKALIRVTKLER------EDLRLVGASRTDTGVHAWGQVAHFITPFSYDG--- 122 (330)
Q Consensus 53 l~v~YdGt~y~G~Q~Q~~~-~TVq~~Le~AL~k~~~i~~------~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~--- 122 (330)
|.|+||||+|+|||+|++. +|||++||+||.+++.+.. +++++++|||||+||||++||+||+++....+
T Consensus 1 l~i~Y~Gt~f~G~Q~Q~~~~~TVq~~le~aL~~~~~~~~~~~~~~~~~~~~~agRTD~GVHA~~qv~~~~~~~~~~~~~~ 80 (245)
T cd02568 1 LLFGYCGTGYHGMQYNPGNYKTIEGELERALVKAGAISESNAGDPKKIGFSRAARTDKGVHAARNVVSLKVIIDDPEGLG 80 (245)
T ss_pred CEEEEeCCCccccccCCCCCCChHHHHHHHHHHcCCcCccccCChhhcceeeecccccchhheeeEEEEEEecccccccc
Confidence 5799999999999999998 9999999999999986532 57999999999999999999999999766432
Q ss_pred -HHHHHHHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccc
Q 043662 123 -LESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGK 201 (330)
Q Consensus 123 -~~~l~~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~ 201 (330)
++++..+||+.||+||+|+++.+|+++||||++|++|+|+|+|+...+ +|+++|++|++.|+|+
T Consensus 81 ~~~~~~~~lN~~Lp~dI~v~~~~~v~~~F~aR~~a~~R~Y~Y~i~~~~~---------------~d~~~m~~a~~~~~G~ 145 (245)
T cd02568 81 IGEDLVEKLNSHLPEDIRVFGITRVTKSFNARKACDSRTYEYLLPTFAL---------------ETLDRFNEILKLYVGT 145 (245)
T ss_pred chHHHHHHHHccCCCceEEEEEEcCCCCCCcchhhhcceeEEECCcccH---------------hHHHHHHHHHHHhhCc
Confidence 678999999999999999999999999999999999999999976431 8999999999999999
Q ss_pred cccccccccccCCCCCCCeEEEEEEEEEEe------CcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhc
Q 043662 202 HDFSAFVNVQRNDRLLNPVKSVFRFDVIEM------GALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILAT 275 (330)
Q Consensus 202 HDF~~F~~~~~~~~~~~~~R~I~~~~v~~~------~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~ 275 (330)
|||++||+... .+.++++|+|.++++.+. .+++.|+|+|+||||||||+|||+|++||+|++++++|+++|+.
T Consensus 146 HdF~~F~~~~~-~~~~~~~R~i~~~~~~~~~~~~~~~~~i~i~i~g~~FL~~mVR~mvg~l~~vg~g~~~~~~i~~~L~~ 224 (245)
T cd02568 146 HNFHNFTVRKK-FEDPSANRFIISFYVSEPFVIEEGLEWVSIEIHGQSFMLHQIRKMIGLAIAIVRGGAPESLIDLSFNK 224 (245)
T ss_pred cccccCccccc-ccCCCceeEEEEEEEecceeecCCccEEEEEEEechHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhcc
Confidence 99999997643 235789999999999864 36899999999999999999999999999999999999999996
Q ss_pred CCcchhccCCCCcCCCCceEeeeec
Q 043662 276 QDRKELAKYALSAPPHGLCLVEVKY 300 (330)
Q Consensus 276 ~~r~~~~~~~~~APa~GL~L~~V~Y 300 (330)
+.+ .. .++|||+||||++|.|
T Consensus 225 ~~~-~~---~~~APa~GL~L~~v~y 245 (245)
T cd02568 225 AKR-II---IPLAPGLGLLLEYPHF 245 (245)
T ss_pred ccc-cc---ccCCCCcceeEecccC
Confidence 443 22 3699999999999988
No 13
>PRK14587 tRNA pseudouridine synthase ACD; Provisional
Probab=100.00 E-value=2.2e-67 Score=491.47 Aligned_cols=213 Identities=27% Similarity=0.428 Sum_probs=189.7
Q ss_pred ceEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCCCCHHHHHH
Q 043662 49 FKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHA 128 (330)
Q Consensus 49 ~r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~~ 128 (330)
++|++.|+||||+|+|||+||+ |||++||+||.++.. .|||||+||||++||+||. .+. + ..
T Consensus 1 ~~~~l~i~YdGt~f~G~Q~Q~~--TVq~~Le~aL~~i~~---------~agRTDaGVHA~~qv~~~~--~~~-~----~~ 62 (256)
T PRK14587 1 MPYLYRIAYDGTLFYGFTGHPN--SLEPALRRVFGEILG---------RGSRTDPGVSAVGNVVMTS--QKL-P----LG 62 (256)
T ss_pred CcEEEEEEECCCcccceecCcc--hHHHHHHHHHHHhcc---------CccCCccCCCcccCEEEEC--CcC-C----HH
Confidence 4799999999999999999998 999999999998643 2999999999999999983 222 1 46
Q ss_pred HHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhccccccccccc
Q 043662 129 ALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFV 208 (330)
Q Consensus 129 ~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F~ 208 (330)
.||+.||+||+|+++.+|+++||||+ |++|+|+|+|+ ...+|+++|++|++.|+|+|||++||
T Consensus 63 ~LN~~LP~dI~V~~~~~V~~~FhaR~-a~~R~Y~Y~i~----------------~~~lDi~~m~~aa~~l~G~HDF~~F~ 125 (256)
T PRK14587 63 YVNSKLPRGVWAWAVAEVPEGFNPRR-AKRRRYLYVAP----------------HWGEDVEAMREAAELLAGTHDYSSFI 125 (256)
T ss_pred HHHhcCCCCeEEEEEEECCCCcCcCc-ccceEEEEEEc----------------cCcchHHHHHHHHHHhcCCcChHHhc
Confidence 89999999999999999999999997 99999999983 12499999999999999999999999
Q ss_pred ccccCCCCCC-CeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCCC
Q 043662 209 NVQRNDRLLN-PVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALS 287 (330)
Q Consensus 209 ~~~~~~~~~~-~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~~ 287 (330)
+.+. +.++ ++|+|++++|...++.+.|+|+|+||||||||+|||+|++||+|++++++|+++|+.+ +... .++
T Consensus 126 ~~~~--~~~~~~vRtI~~i~v~~~~~~i~i~i~g~sFL~~mVR~mVG~Ll~Vg~G~~~~~~i~~~L~~~-r~~~---~~~ 199 (256)
T PRK14587 126 QRRG--EKATPTVTTVYEIGVELRGDLIYLYFVGRGFRNKMIRKMAWAILAAGRGVLSRRDIAELLERP-RPGA---VPS 199 (256)
T ss_pred cCCC--CCCCCCEEEEEEEEEEEeCCEEEEEEEechhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHhcC-cccC---CCC
Confidence 7643 2345 9999999999988889999999999999999999999999999999999999999954 4332 368
Q ss_pred cCCCCceEeeeecCC
Q 043662 288 APPHGLCLVEVKYNE 302 (330)
Q Consensus 288 APa~GL~L~~V~Y~~ 302 (330)
|||+||||++|.|++
T Consensus 200 APa~GL~L~~V~Y~~ 214 (256)
T PRK14587 200 APAEGLVLLDIEYDV 214 (256)
T ss_pred CCCCCCEEeeeccCc
Confidence 999999999999974
No 14
>PLN03078 Putative tRNA pseudouridine synthase; Provisional
Probab=100.00 E-value=4.2e-65 Score=507.98 Aligned_cols=252 Identities=23% Similarity=0.309 Sum_probs=214.4
Q ss_pred CCCCcceEEEEEEEeCCCceeeeeCCC---CCcHHHHHHHHHHHhhccc------CcceeeeeccccCccccccccEEEE
Q 043662 44 DSFPGFKWRLVIAYDGTRYAGWQFQTS---PPTIQCIVEKALIRVTKLE------REDLRLVGASRTDTGVHAWGQVAHF 114 (330)
Q Consensus 44 ~~~~~~r~~l~v~YdGt~y~G~Q~Q~~---~~TVq~~Le~AL~k~~~i~------~~~i~~~~agRTD~GVHA~~qv~~f 114 (330)
...++++|+|.|+|+|++|+|||+|++ .+|||++||+||.+++.+. .+++.+++||||||||||++||+||
T Consensus 66 ~~~~krrvaL~IaYdGt~Y~G~Q~Q~n~~~~~TVEg~LE~AL~k~~~I~e~n~~~~~ki~~~rAgRTDkGVHA~gQVvsf 145 (513)
T PLN03078 66 ESARKKKVVLRVGYVGTDYRGLQKQRDLSSLSTIEGELETAIFKAGGIRESNYGNLHKIGWARSSRTDKGVHSLATMISL 145 (513)
T ss_pred ccccceEEEEEEEEcCCCcceeeECCCCCCCCCHHHHHHHHHHHHhCccccccccccceeEEeeccCCcCccccccEEEE
Confidence 356788999999999999999999987 5799999999999998753 2579999999999999999999999
Q ss_pred EeCCCCC----C--HHHHHHHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEecc--CCCCCcccCCeeeeecCCC
Q 043662 115 ITPFSYD----G--LESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYN--DAVMDPFQRHYAYHSVYKL 186 (330)
Q Consensus 115 ~~~~~~~----~--~~~l~~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~--~~~~~pf~~~~~~~~~~~l 186 (330)
+++.... . ...+...||++||+||+|+++.+|+++||||++|++|+|+|+|++ ....++|.+.+.|+
T Consensus 146 ~l~~p~~~~~~d~~~~~L~~~LN~~LP~DIRVl~v~~V~~~FhAR~sc~sRtY~Y~iP~~~~~~k~~f~~~~~~~----- 220 (513)
T PLN03078 146 KMEIPENAWKDDPDGIALAKFINSHLPDNIRVFSILPAQRSFDPRRECDLRKYSYLLPAEVIGIKSGFSSEEIDE----- 220 (513)
T ss_pred eccCcchhccccchHHHHHHHHHhcCCCCeEEEEEEECCCCcCCCCCCCceEEEEEEccccccCCCccchhhhHH-----
Confidence 9854211 1 235789999999999999999999999999999999999999998 34445566655554
Q ss_pred CHHHHHHHHhhcccccccccccccccCCCC--------------------------------------------------
Q 043662 187 NTTLMRQAAEYFVGKHDFSAFVNVQRNDRL-------------------------------------------------- 216 (330)
Q Consensus 187 Di~~m~~a~~~f~G~HDF~~F~~~~~~~~~-------------------------------------------------- 216 (330)
|+++|++|++.|+|+|||+|||........
T Consensus 221 dI~kMneAl~~fiGtHDFhNFT~r~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~ 300 (513)
T PLN03078 221 HISEFNSILNGFEGEHPFHNYTARSKYRKKLPGKHKQRNGAVSRRAKSSKEMSSSESEENHGEISEEDEEDLSFSSIPSG 300 (513)
T ss_pred HHHHHHHHHHhcccccCcccccCCCccCccccccccccccccccccccccccccccccccccccccchhhhhcccccccc
Confidence 899999999999999999999975421110
Q ss_pred ---------------------------------CCCeEEEEEEEEEE-----eCcEEEEEEEeCcchhHHHHHHHHHHHH
Q 043662 217 ---------------------------------LNPVKSVFRFDVIE-----MGALLQLEVEGSGFLYRQVRNMVALLLQ 258 (330)
Q Consensus 217 ---------------------------------~~~~R~I~~~~v~~-----~~~~v~~~I~G~sFL~~qVR~MVG~ll~ 258 (330)
.+..|.|++|.+.. ..+++.|+|.|+|||+||||+|||++++
T Consensus 301 ~~~~~~~~~~~~~~~~~~~~~wl~e~d~~d~i~~s~~R~I~~~~~~~~~~~~g~~fv~i~I~GqSFmlhQIRKMIG~~~a 380 (513)
T PLN03078 301 SSDENEDILKFQSSQVQIRARWLHEPDETDRISASHFRKIFRCSCGKLEKSLGFDFVELSIWGESFMLHQIRKMVGTAVA 380 (513)
T ss_pred ccccccccccccccchhhhhhhccCCccccccchhheEEEEEeecCCccccCCceEEEEEEEehhHHHHHHHHHHHHHHH
Confidence 02368898888643 2479999999999999999999999999
Q ss_pred HhcCCCCcccHHHHHhcCCcchhccCCCCcCCCCceEeeeecCCCC
Q 043662 259 IGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEH 304 (330)
Q Consensus 259 vg~G~~~~~~i~~~L~~~~r~~~~~~~~~APa~GL~L~~V~Y~~~~ 304 (330)
|++|.++.+.|..+|....+.. .|+||+.||+|+++.|+...
T Consensus 381 V~rg~~~~~~i~~~L~~~~r~~----~P~AP~~GL~L~~~~F~~yn 422 (513)
T PLN03078 381 VKRELLPRDIIRLSLTKFSRIV----LPLAPSEVLILRGNSFSVRK 422 (513)
T ss_pred HHhccCCHHHHHHHhccccccc----cccCCCcceEEEeeeccccc
Confidence 9999999999999998766653 47999999999999999764
No 15
>KOG2553 consensus Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-56 Score=431.28 Aligned_cols=270 Identities=23% Similarity=0.373 Sum_probs=227.7
Q ss_pred CCCCCCCCCcceEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhccc------CcceeeeeccccCccccccccEE
Q 043662 39 KPPTDDSFPGFKWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLE------REDLRLVGASRTDTGVHAWGQVA 112 (330)
Q Consensus 39 ~~~~~~~~~~~r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~------~~~i~~~~agRTD~GVHA~~qv~ 112 (330)
++++..+++++++++.++|.|++|+|+|+|++.+|||++|++||.+++.|. +.++.|.+|+|||+||||.+||+
T Consensus 27 ~e~~~~k~~KrKVail~gY~G~gY~GmQ~N~~~kTIEgeL~~al~~aGaI~e~n~~dpkk~~~~raARTDKGVhA~~nvi 106 (416)
T KOG2553|consen 27 KESKAPKPRKRKVAILLGYCGTGYHGMQYNPPLKTIEGELFEALFKAGAISESNAGDPKKIGFARAARTDKGVHAAGNVI 106 (416)
T ss_pred cccccccccceEEEEEEEeccCCccceecCCCCCchHHHHHHHHHHcCCcccccccChHHhhhHHhhccccchhhhhhee
Confidence 444567789999999999999999999999999999999999999999874 56789999999999999999999
Q ss_pred EEEeCCCCCCHHHHHHHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccC----------------
Q 043662 113 HFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQR---------------- 176 (330)
Q Consensus 113 ~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~---------------- 176 (330)
++++..+. ..+...||..||++|||+++.+|.+.|++|-.|.+|+|+|.||+..+..|-..
T Consensus 107 SlK~~~~~---~~lv~~lN~~Lp~~IRv~~v~r~~k~F~pr~~CdsR~YeYllPtfal~~p~~~~~~~~~~~~~~e~~~~ 183 (416)
T KOG2553|consen 107 SLKLELDD---PELVEKLNEILPEQIRVWGVKRVTKSFNPRKQCDSRTYEYLLPTFALAPPKPSSLLEVDIQYDKEFEKE 183 (416)
T ss_pred EEEEeeCc---HHHHHHHhhhCCcceEEEEEEecCCCCCccccccceeEEEecceeeecCCCCccHHHhhhhhhhhhhhh
Confidence 99997652 56889999999999999999999999999999999999999998765433111
Q ss_pred ---Ce-------------eeeecCCCC---HHHHHHHHhhcccccccccccccccCCCCCCCeEEEEEEEEE-------E
Q 043662 177 ---HY-------------AYHSVYKLN---TTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVI-------E 230 (330)
Q Consensus 177 ---~~-------------~~~~~~~lD---i~~m~~a~~~f~G~HDF~~F~~~~~~~~~~~~~R~I~~~~v~-------~ 230 (330)
.+ .....+.++ ++.++++++.++|+||||||+..+.. ..++..|.|.++.+. .
T Consensus 184 f~~~~~~~~~~~~s~~~~~~~~~yr~s~~~l~~~~~~ls~Y~GthnFHNfT~~~~~-~dpss~R~I~s~~~~~pfv~~~~ 262 (416)
T KOG2553|consen 184 FWNTYPLSAKERLSGQDRKTESGYRLSEEKLEVFNTILSKYVGTHNFHNFTTGKDF-TDPSSNRFIKSFTVSEPFVINDE 262 (416)
T ss_pred hccccchhhhhhhcccccccccceeeCHHHHHHHHHHHHHhhcccccceecccCCC-CCccccceeeEEEecCcceeccC
Confidence 00 011122333 55678999999999999999977542 346778999999887 3
Q ss_pred eCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHHhcCCcchhccCCCCcCCCCceEeeeecCCCCCCCCCC
Q 043662 231 MGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYNEEHLRLPAA 310 (330)
Q Consensus 231 ~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L~~~~r~~~~~~~~~APa~GL~L~~V~Y~~~~~~~~~~ 310 (330)
.-++|.+.|+|+|||.||||+|||.+++|.++.++.+.|+..+++..+.. +|.||+.||+|.++.|+.+..+...+
T Consensus 263 ~~e~V~i~i~GQSFMLHQIRKMVglav~i~R~~~p~~~i~~af~~~~ri~----IP~AP~~gLlL~~~~F~~yn~~~~~~ 338 (416)
T KOG2553|consen 263 GVEFVKIKIHGQSFMLHQIRKMVGLAVLIVRSGAPASTIQRAFNKEHKIN----IPKAPGEGLLLEEPHFESYNRKFRPS 338 (416)
T ss_pred CceEEEEEEEcchhHHHHHHHHHHHHHHHHhcCCCHHHHHHhhCCCcccc----ccCCCcceEEeecccccccccccCCC
Confidence 34799999999999999999999999999999999999999998665543 47999999999999999887665544
Q ss_pred -CCCCCC
Q 043662 311 -CPLSSF 316 (330)
Q Consensus 311 -~~~~~~ 316 (330)
.+.+++
T Consensus 339 ~~e~i~~ 345 (416)
T KOG2553|consen 339 GHEEIDW 345 (416)
T ss_pred CcCCcCH
Confidence 555555
No 16
>KOG4393 consensus Predicted pseudouridylate synthase [RNA processing and modification; Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.1e-54 Score=393.48 Aligned_cols=268 Identities=36% Similarity=0.491 Sum_probs=238.0
Q ss_pred CcceEEEEEEEeCCCceeeeeCCCCC--cHHHHHHHHHHHhhcccCcceeeeeccccCccccccccEEEEEeCCCC-CCH
Q 043662 47 PGFKWRLVIAYDGTRYAGWQFQTSPP--TIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQVAHFITPFSY-DGL 123 (330)
Q Consensus 47 ~~~r~~l~v~YdGt~y~G~Q~Q~~~~--TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~-~~~ 123 (330)
..+||++.++||||.|.|||++.... |||+-||+|..+.+.+ +.+++..+||||+||||+.|++|++++... -+.
T Consensus 3 ~~~ryll~i~ydgT~f~e~a~~~s~~~~tIq~~leea~eeqt~l--~~l~l~~ssrtDa~Vha~~naa~~~vpr~sg~~~ 80 (295)
T KOG4393|consen 3 EIMRYLLKIPYDGTAFEESAERLSKVARTIQGFLEEASEEQTGL--DRLDLESSSRTDAGVHAYLNAAHYIVPRFSGSQQ 80 (295)
T ss_pred chheeEEEecccccccHHHHhccCCcceehhhhhhhhHHhhcCC--cceeecccCCCchhhheeeeeEEEEeecccCCcH
Confidence 35799999999999999999998865 9999999999999875 679999999999999999999999998873 234
Q ss_pred HHHHHHHHhcC-CC--CeEEEEEEecCCCcccccccCceEEEEEecc-CCCCCcccCCeeeeecCCCCHHHHHHHHhhcc
Q 043662 124 ESIHAALNGLL-PP--DIRVREISAAVPEFHARFSAKSKIYHYKIYN-DAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFV 199 (330)
Q Consensus 124 ~~l~~~lN~~L-P~--dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~-~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~ 199 (330)
.....++|..| ++ ||+|.++..||.+||||++|.+|+|.|+|.+ ....++|++.+.|++++.||..+|++|+++|+
T Consensus 81 ~~~~~a~nt~l~~k~gdirV~dv~~Vps~FhaR~sassRtY~YRla~g~d~l~~fERd~cW~lp~~lna~kmqeaa~lf~ 160 (295)
T KOG4393|consen 81 QAKDRAVNTVLQRKDGDIRVIDVRCVPSNFHARYSASSRTYFYRLASGSDPLSIFERDRCWHLPEELNARKMQEAAPLFE 160 (295)
T ss_pred HHHHHHHhccccCCCCceEEEEeeecCcchhheecccceeEEEEeecCCCccChhhhcccccCCcccCHHHHHhhhhhhc
Confidence 45566777666 44 9999999999999999999999999999998 55678899999999999999999999999999
Q ss_pred cccccccccccccCCCCCCCeEEEEEEEEEE----------------eCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCC
Q 043662 200 GKHDFSAFVNVQRNDRLLNPVKSVFRFDVIE----------------MGALLQLEVEGSGFLYRQVRNMVALLLQIGKEA 263 (330)
Q Consensus 200 G~HDF~~F~~~~~~~~~~~~~R~I~~~~v~~----------------~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~ 263 (330)
|+|||.+|++... ....+++++-.+.|.. ..++..++++++|||+.|||+|++.|+.+|.+.
T Consensus 161 G~hdfsaf~~ats--~~y~P~~t~rr~sv~~~g~~~a~~~~~~~e~~~~~~~nve~e~~gflyrQvRrm~a~LV~~g~~a 238 (295)
T KOG4393|consen 161 GSHDFSAFTEATS--TVYFPSITERRLSVLNNGDPLACSNQPETEGVTTNVGNVEGETEGFLYRQVRRMRAYLVTAGSRA 238 (295)
T ss_pred cchhhhhhhcCCC--CCCCCcccceeeeecccCCccccccCCccccceeeeEEEEEEecchHHHHHHhhheeeeeecccc
Confidence 9999999998763 4567778877777631 235789999999999999999999999999999
Q ss_pred CCcccHHHHHhcCCcchhcc-CCCCcCCCCceEeeeecCCCCCCCCCCCCCCCCCC
Q 043662 264 IPPDIVPKILATQDRKELAK-YALSAPPHGLCLVEVKYNEEHLRLPAACPLSSFGR 318 (330)
Q Consensus 264 ~~~~~i~~~L~~~~r~~~~~-~~~~APa~GL~L~~V~Y~~~~~~~~~~~~~~~~~~ 318 (330)
++..+++.+|+.++...+.+ ..+.|||+||+|..|+|++.++..|.++.++++|.
T Consensus 239 l~~~qv~~iLe~~~~~~l~k~~~~vapphglfL~sv~Y~n~l~~~p~~~~vts~g~ 294 (295)
T KOG4393|consen 239 LLYHQVLYILEVRDIVGLLKCVGTVAPPHGLFLSSVEYVNLLHFRPNGRGVTSIGF 294 (295)
T ss_pred cchhhhhhhhhccchhhhhhccCCCCCCccceeeeEEechhhccCCCCCccCCcCC
Confidence 99999999999998865544 35789999999999999999999999999999984
No 17
>KOG2554 consensus Pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-53 Score=402.97 Aligned_cols=240 Identities=29% Similarity=0.460 Sum_probs=207.8
Q ss_pred CCCcceEEEEEEEeCCCceeeeeCC--CCCcHHHHHHHHHHHhhccc-CcceeeeeccccCccccccccEEEEEeCCCCC
Q 043662 45 SFPGFKWRLVIAYDGTRYAGWQFQT--SPPTIQCIVEKALIRVTKLE-REDLRLVGASRTDTGVHAWGQVAHFITPFSYD 121 (330)
Q Consensus 45 ~~~~~r~~l~v~YdGt~y~G~Q~Q~--~~~TVq~~Le~AL~k~~~i~-~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~ 121 (330)
..+++.++|.++|+|.+|.|+..|+ +.+||++.|+.||.+...+. ++...+.+||||||||||.|||+++.+.....
T Consensus 62 ~~~kR~IAlkiaY~GW~Y~Gla~Qe~T~~~TIEg~l~eAL~kt~Lies~~~~~ysRCGRTDKGVSAfgQviSl~lRS~~p 141 (425)
T KOG2554|consen 62 AHSKRHIALKIAYLGWNYQGLAPQEHTNNPTIEGKLFEALKKTRLIESRQTCNYSRCGRTDKGVSAFGQVISLVLRSRIP 141 (425)
T ss_pred cccceEEEEEEEEeccccCceecCCCCCCcchHHHHHHHHHhhhcccCcccccccccCCcccchhhhhheeeeeeeccCC
Confidence 4567889999999999999999995 46799999999999987653 45678999999999999999999998753321
Q ss_pred C--------------HHHHHHHHHhcCCCCeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCC
Q 043662 122 G--------------LESIHAALNGLLPPDIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLN 187 (330)
Q Consensus 122 ~--------------~~~l~~~lN~~LP~dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lD 187 (330)
. .-.....||+.||+||||.+|++||+.|+|||+|.+|+|+|+++. ..||
T Consensus 142 ~~~s~~~~~~~a~~~Ei~Y~~mLN~vLP~dIRi~awapvp~~FsARFsC~~RtYrY~F~k----------------~dLd 205 (425)
T KOG2554|consen 142 MPDSQRDAVATADSEEIPYVHMLNRVLPPDIRIVAWAPVPPTFSARFSCVQRTYRYYFPK----------------KDLD 205 (425)
T ss_pred CchhhhccccccccccccHHHHHhccCCCcceEEEEecCCCCccceeehhhceeeEeccC----------------CCcC
Confidence 1 112467899999999999999999999999999999999999863 3599
Q ss_pred HHHHHHHHhhcccccccccccccccCCCCCCCeEEEEEEEEEEeCc---EEEEEEEeCcchhHHHHHHHHHHHHHhcCCC
Q 043662 188 TTLMRQAAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGA---LLQLEVEGSGFLYRQVRNMVALLLQIGKEAI 264 (330)
Q Consensus 188 i~~m~~a~~~f~G~HDF~~F~~~~~~~~~~~~~R~I~~~~v~~~~~---~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~ 264 (330)
|++|.+||++|+|+|||+|||+-...++..|..|+|.++.|+..++ ++.|+|.|++|||||||+||+.|..||+|..
T Consensus 206 I~~M~kAA~l~vGe~DFrNFCK~D~~n~vtny~Rti~s~kV~~~~~~~~my~ldi~g~AFLwHqVRcimaiL~liGq~~E 285 (425)
T KOG2554|consen 206 IDRMSKAASLLVGEHDFRNFCKIDVSNGVTNYERTILSAKVEDVGQTPGMYYLDIQGSAFLWHQVRCIMAILFLIGQGLE 285 (425)
T ss_pred HHHHHHHHHHHhcchhhhhhhhhcchhhhHHHHhhhheeeEEEcCCCCceEEEEeechhhHHHHHHHHHHHHHHhccccC
Confidence 9999999999999999999998776566788999999999987654 6999999999999999999999999999999
Q ss_pred CcccHHHHHhcCCcchhccCCCCcCCCCceEeeeecC
Q 043662 265 PPDIVPKILATQDRKELAKYALSAPPHGLCLVEVKYN 301 (330)
Q Consensus 265 ~~~~i~~~L~~~~r~~~~~~~~~APa~GL~L~~V~Y~ 301 (330)
.++.|.++|+-+....... -.+|-.-.|.|.+..|.
T Consensus 286 ~p~lI~dLldIek~P~kPq-Y~mA~~~PL~LydC~f~ 321 (425)
T KOG2554|consen 286 QPSLISDLLDIEKNPQKPQ-YTMASDYPLELYDCDFH 321 (425)
T ss_pred CchHHHHHHhcccCCCCce-eeeccCCceEEEecCCC
Confidence 9999999998765443222 34788899999999993
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=99.88 E-value=3.1e-25 Score=180.24 Aligned_cols=105 Identities=35% Similarity=0.618 Sum_probs=87.6
Q ss_pred HHhhcccccccccccccccCCCCCCCeEEEEEEEEEEeCcEEEEEEEeCcchhHHHHHHHHHHHHHhcCCCCcccHHHHH
Q 043662 194 AAEYFVGKHDFSAFVNVQRNDRLLNPVKSVFRFDVIEMGALLQLEVEGSGFLYRQVRNMVALLLQIGKEAIPPDIVPKIL 273 (330)
Q Consensus 194 a~~~f~G~HDF~~F~~~~~~~~~~~~~R~I~~~~v~~~~~~v~~~I~G~sFL~~qVR~MVG~ll~vg~G~~~~~~i~~~L 273 (330)
|++.|+|+|||++|++... ...+++|+|.++++.+.++++. +|+|+|||++|||+|||+++++|+|..+++++.++|
T Consensus 1 A~~~~~G~HdF~~f~~~~~--~~~~~~r~i~~~~~~~~~~~~~-~i~g~~Fl~~~vR~~vg~~~~~~~G~~~~~~i~~~L 77 (105)
T PF01416_consen 1 AAKLYVGTHDFSGFQKQKT--VEKNTIRTIFSIDIIEEGDVVV-EIHGNSFLRHQVRIMVGTLLRTGRGVHSLEQIAELL 77 (105)
T ss_dssp -CCEETCEEECCGCSSCS---HHHHHCCCEEEEECCCCCCEEE-EEEESS--TTHHHHHHCCCCHHHTTSCEEECCCCCH
T ss_pred CcceeEecCCCcCCEECCc--ccccHHHHHHHHhhhcCCCEEE-EEEecccccccchhhhHHHHHHhcCCCCHHHHHHHH
Confidence 5788999999999998743 2367899999999999899999 999999999999999999999999999999999999
Q ss_pred hcCCcchhccCCCCcCCCCceEeeeecC
Q 043662 274 ATQDRKELAKYALSAPPHGLCLVEVKYN 301 (330)
Q Consensus 274 ~~~~r~~~~~~~~~APa~GL~L~~V~Y~ 301 (330)
+...+....+...+|||+||+|++|.||
T Consensus 78 ~~~~~~~~~~ri~~ap~~gL~L~~v~y~ 105 (105)
T PF01416_consen 78 NSKLRPKAPPRILTAPAVGLYLFHVRYD 105 (105)
T ss_dssp HHHSCTTS-TEEEEEEECCECCEECCTT
T ss_pred hccCccccCCCcceeeCCCCCceEeeCc
Confidence 9876543210123899999999999996
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=98.16 E-value=1.8e-07 Score=75.68 Aligned_cols=82 Identities=29% Similarity=0.437 Sum_probs=62.0
Q ss_pred EEEeCC-CceeeeeCCCCCcHHHHHHHHHHHhhcccCc----------------ceeeeeccccCccccccccEEEEEeC
Q 043662 55 IAYDGT-RYAGWQFQTSPPTIQCIVEKALIRVTKLERE----------------DLRLVGASRTDTGVHAWGQVAHFITP 117 (330)
Q Consensus 55 v~YdGt-~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~----------------~i~~~~agRTD~GVHA~~qv~~f~~~ 117 (330)
..|+|+ +|+||++| +|++...+++|..+..+... ..-+..++|||+||||..|+..+
T Consensus 3 ~~~~G~HdF~~f~~~---~~~~~~~~r~i~~~~~~~~~~~~~~i~g~~Fl~~~vR~~vg~~~~~~~G~~~~~~i~~~--- 76 (105)
T PF01416_consen 3 KLYVGTHDFSGFQKQ---KTVEKNTIRTIFSIDIIEEGDVVVEIHGNSFLRHQVRIMVGTLLRTGRGVHSLEQIAEL--- 76 (105)
T ss_dssp CEETCEEECCGCSSC---S-HHHHHCCCEEEEECCCCCCEEEEEEESS--TTHHHHHHCCCCHHHTTSCEEECCCCC---
T ss_pred ceeEecCCCcCCEEC---CcccccHHHHHHHHhhhcCCCEEEEEEecccccccchhhhHHHHHHhcCCCCHHHHHHH---
Confidence 579999 99999999 57776676666665432111 22356799999999999987665
Q ss_pred CCCCCHHHHHHHHHhcCCC---CeEEEEEEecC-CCcccccc
Q 043662 118 FSYDGLESIHAALNGLLPP---DIRVREISAAV-PEFHARFS 155 (330)
Q Consensus 118 ~~~~~~~~l~~~lN~~LP~---dIrV~~i~~v~-~~FhaR~~ 155 (330)
||..+++ + +|..+.+++ -.||++|+
T Consensus 77 ------------L~~~~~~~~~~-ri~~ap~~gL~L~~v~y~ 105 (105)
T PF01416_consen 77 ------------LNSKLRPKAPP-RILTAPAVGLYLFHVRYD 105 (105)
T ss_dssp ------------HHHHSCTTS-T-EEEEEEECCECCEECCTT
T ss_pred ------------HhccCccccCC-CcceeeCCCCCceEeeCc
Confidence 7778855 6 999999999 78999885
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=97.17 E-value=0.012 Score=53.16 Aligned_cols=147 Identities=16% Similarity=0.205 Sum_probs=97.0
Q ss_pred cHHHHHHHHHHHhhc-cc-----CcceeeeeccccCccccccccEEEEEeCCCCCCHHHHHHHHHhcCCCCeEEEEEEec
Q 043662 73 TIQCIVEKALIRVTK-LE-----REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAA 146 (330)
Q Consensus 73 TVq~~Le~AL~k~~~-i~-----~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~i~~v 146 (330)
-+...+|.||.+++. +. ....+++.+.=.=-||.+.+-++.+.+..+. +++.+.+.||+.||++|+|.++..+
T Consensus 19 dl~r~~eRa~rRA~lp~a~SqGFnP~Pkisf~~aLpvGv~S~~E~~di~l~~~~-~~~~~~~rLn~~lP~Gl~i~~~~~i 97 (187)
T PF10105_consen 19 DLMRVFERALRRAGLPVAYSQGFNPHPKISFAPALPVGVESLAEYMDIELEEDI-DPEEVLERLNAVLPEGLRILEAEEI 97 (187)
T ss_pred HHHHHHHHHhhhcCCCeeecCCCCCCcceeecccccCceeeccEEEEEEEecCC-CHHHHHHHHHHhCCCCCEEEEEEEc
Confidence 345689999999874 10 2346778888888999999999999997664 5789999999999999999999999
Q ss_pred CCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccccccccccCCC--CCCCeEEEE
Q 043662 147 VPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQRNDR--LLNPVKSVF 224 (330)
Q Consensus 147 ~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F~~~~~~~~--~~~~~R~I~ 224 (330)
+....+ ..+.-..+.|.|... ..+.+.+.++++.|.-..++. ..+.++..+ ..|-.-.|.
T Consensus 98 ~~~~~s-l~~~i~~~~Y~i~~~----------------~~~~~~~~~~~~~~~~~~~~~-v~k~~Kkg~~~~~dir~~i~ 159 (187)
T PF10105_consen 98 PPKAPS-LMALINAAEYRITLP----------------EIDEEELEEAIEAFLAAEEII-VEKRTKKGKKKEIDIRPYIK 159 (187)
T ss_pred cCCCcc-hhhhcceEEEEEEec----------------CCCHHHHHHHHHHHHCCCCEE-EEEeCCCCceEEEEhHHhhh
Confidence 854432 233445677776432 256777777777776554432 332211111 112222345
Q ss_pred EEEEEEeCcEEEEE
Q 043662 225 RFDVIEMGALLQLE 238 (330)
Q Consensus 225 ~~~v~~~~~~v~~~ 238 (330)
++++...++.+.+.
T Consensus 160 ~l~~~~~~~~~~l~ 173 (187)
T PF10105_consen 160 DLELEGSEDNIVLE 173 (187)
T ss_pred eEEEEeCCCeEEEE
Confidence 66666666554443
No 21
>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=95.73 E-value=0.51 Score=47.23 Aligned_cols=155 Identities=16% Similarity=0.215 Sum_probs=102.9
Q ss_pred CCcHHHHHHHHHHHhhcccCcceeeeeccccCcccccccc----EEEEEeCCC-CCCHHHHHHHHHhcCCCCeEEEEEEe
Q 043662 71 PPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ----VAHFITPFS-YDGLESIHAALNGLLPPDIRVREISA 145 (330)
Q Consensus 71 ~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~q----v~~f~~~~~-~~~~~~l~~~lN~~LP~dIrV~~i~~ 145 (330)
..|||+.|...+.++.. ..+..+.+|||-|--|=-+|. |+-+.-|.. ..+++.+.+.||+.....|.|.+..-
T Consensus 184 ~~SVeelI~~~v~~~~~--~~~~~Fh~aGREDvDvRMLG~GRPFvlEi~~P~rr~~dl~~le~~IN~~~~g~V~v~~L~~ 261 (388)
T TIGR01213 184 PESVEELIASPFLKATG--GTDAYFHGAGREDVDVRMLGTGRPFVLEVKEPRYRKIDLDPLEEEINTSGKGKVEVEGLKF 261 (388)
T ss_pred CchHHHHHHHHHHHHhC--CceeEEeccCccccceeeccCCCceEEEecCCccCCCCHHHHHHHHhhccCCCEEEEEeEE
Confidence 46999999999998876 357999999999999998875 444432322 12467788999999989999999887
Q ss_pred cCCCcc--cccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccccccccc--cCCCCCCCeE
Q 043662 146 AVPEFH--ARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFSAFVNVQ--RNDRLLNPVK 221 (330)
Q Consensus 146 v~~~Fh--aR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~~F~~~~--~~~~~~~~~R 221 (330)
++..=- -+.....|+|.=.+.. ..+++.+.++++++.|.|.. -...+... .......-.|
T Consensus 262 ~~~~~v~~ik~~~~~K~Y~alV~~---------------~~~v~~e~L~~~~~~l~g~~-I~QrTP~RV~hRRa~~~R~R 325 (388)
T TIGR01213 262 ATREEVEEVKEEKHRKVYRALVEV---------------DGPVSDEDLEELCKELEGAT-IYQRTPLRVLHRRADLVRER 325 (388)
T ss_pred EcHHHHHHHhccCCceEEEEEEEE---------------CCCCCHHHHHHHHHhccCCE-EEccCCceEEEecCCCceEE
Confidence 654211 1122235777755533 34688899999999988831 11111100 0001123468
Q ss_pred EEEEEEEEEeC-cEEEEEEEeCc
Q 043662 222 SVFRFDVIEMG-ALLQLEVEGSG 243 (330)
Q Consensus 222 ~I~~~~v~~~~-~~v~~~I~G~s 243 (330)
+|+++++...+ ..+.+.|.+++
T Consensus 326 ~I~~i~~~~i~~~~~~l~v~~qa 348 (388)
T TIGR01213 326 RVYQVDLSGLDGNHAELIIEAEG 348 (388)
T ss_pred EEEEEEEEEEcCCEEEEEEEecC
Confidence 99999987653 46677777765
No 22
>PRK14554 putative pseudouridylate synthase; Provisional
Probab=94.20 E-value=2.1 Score=43.37 Aligned_cols=153 Identities=16% Similarity=0.164 Sum_probs=95.5
Q ss_pred CcHHHHHHHHHHHhhcccCcceeeeeccccCcccccccc----EEEEEeCCCC-CCHHHHHHHHHhcCCCCeEEEEEEec
Q 043662 72 PTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ----VAHFITPFSY-DGLESIHAALNGLLPPDIRVREISAA 146 (330)
Q Consensus 72 ~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~q----v~~f~~~~~~-~~~~~l~~~lN~~LP~dIrV~~i~~v 146 (330)
.|||+.|...+..... ..+..+.+|||-|.-|=-+|. |+-+.-|... .+++.+. +|.+-...|.|.++..+
T Consensus 220 ~SVeelI~~~i~~~f~--~~~~~fh~aGREDvDVRmLG~GRPFViEi~~p~r~~~~~~~l~--~~~~~~g~V~v~~l~~~ 295 (422)
T PRK14554 220 ESVEELIAKPVIEAFG--GEDAVFHGAGREDVDARMLGTGRPFVIEVKEPRKRKVDLEALE--EEINADGKVEVENLRFA 295 (422)
T ss_pred CCHHHHHHHHHHHHhC--CCceEEecCCCCCcceEecCCCCceEEEecCcccccCCHHHHH--HhhccCCCEEEEEEEEE
Confidence 6999999988888765 368999999999999999987 4444433321 2345554 44444678999999977
Q ss_pred CCCccc--ccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhccccccc-ccccccccCCCCCCCeEEE
Q 043662 147 VPEFHA--RFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDF-SAFVNVQRNDRLLNPVKSV 223 (330)
Q Consensus 147 ~~~Fha--R~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF-~~F~~~~~~~~~~~~~R~I 223 (330)
+..--. ......|+|.=.++. ..+++.+.++++++.|.|.-=. +.............-.|+|
T Consensus 296 ~~~~~~~ik~~~~~K~YralV~~---------------~~~v~~e~l~~~~~~l~~~~I~QrTP~RV~hRR~~~~R~R~I 360 (422)
T PRK14554 296 TRKEVERIKEEKASKTYRALVES---------------DEPVSEEELEKLLDELSGATIEQRTPRRVKHRRADLVRVRKV 360 (422)
T ss_pred cHHHHHHHhcCCCceEEEEEEEE---------------CCCCCHHHHHHHHHhccCcEeeccCcHhhhhhccccceeeEE
Confidence 643211 112223777655533 3468888899999988775110 1111111101122456899
Q ss_pred EEEEEEEeC-cEEEEEEEeCc
Q 043662 224 FRFDVIEMG-ALLQLEVEGSG 243 (330)
Q Consensus 224 ~~~~v~~~~-~~v~~~I~G~s 243 (330)
+++++...+ ....+.|.+++
T Consensus 361 ~~i~~~~i~~~~~~l~i~~ea 381 (422)
T PRK14554 361 YDISGELIDDKHFELRIKCEG 381 (422)
T ss_pred EEEEEEEEcCcEEEEEEEEec
Confidence 999887643 44556666654
No 23
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=92.63 E-value=3.1 Score=41.47 Aligned_cols=157 Identities=18% Similarity=0.247 Sum_probs=104.6
Q ss_pred CCcHHHHHHHHHHHhhcccCcceeeeeccccCcccccccc----EEEEEeCCC-CCCHHHHHHHHHhcCCCCeEEEEEEe
Q 043662 71 PPTIQCIVEKALIRVTKLEREDLRLVGASRTDTGVHAWGQ----VAHFITPFS-YDGLESIHAALNGLLPPDIRVREISA 145 (330)
Q Consensus 71 ~~TVq~~Le~AL~k~~~i~~~~i~~~~agRTD~GVHA~~q----v~~f~~~~~-~~~~~~l~~~lN~~LP~dIrV~~i~~ 145 (330)
..||++.|-..+.+++. ..+..+.+|||-|--|--+|. |+-+.-|.. ..+++.+...||.-. .+.|+++.-
T Consensus 190 ~~sve~~i~~~~~~~f~--g~~~~fhgAGREDvDvRMLG~GRPfVlEvk~Pr~R~~dl~~l~~~in~~~--~vev~~l~f 265 (398)
T COG1258 190 PESVEELIKQPIKEAFG--GLDAKFHGAGREDVDVRMLGTGRPFVLEVKEPRRRNVDLDELEEEINRGG--KVEVFDLEF 265 (398)
T ss_pred cccHHHHHHHHHHHhcc--CceeEEEccCCCccceeeecCCCceEEEecCcccccCChHHHHHHhccCC--cEEEEEEEe
Confidence 45899888887777765 358999999999999988884 566555521 135788999999887 899999998
Q ss_pred cCCCcccccc---cCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccc-cccccccccccCCCCCCCeE
Q 043662 146 AVPEFHARFS---AKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGK-HDFSAFVNVQRNDRLLNPVK 221 (330)
Q Consensus 146 v~~~FhaR~~---a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~-HDF~~F~~~~~~~~~~~~~R 221 (330)
+...=-.+.. -..|+|+=.+.. ..+++.+++.+++.-+.|. =.=+.+..........-.+|
T Consensus 266 ~~~e~v~~ik~~~~~rK~YrAlV~~---------------~~~v~~e~l~~~~~~L~g~~I~QrTP~RV~hrRadlvR~R 330 (398)
T COG1258 266 VGREEVEEIKETERHRKVYRALVYS---------------DRPVSDEKLEEVLGSLEGKTIRQRTPRRVLHRRADLVRIR 330 (398)
T ss_pred cCHHHHHHHHhccccceeEEEEEEE---------------CCCcCHHHHHHHHhhccCcEEeecChHHHhhhhcccceEE
Confidence 8643222222 234566555532 3468999999999999994 22222222111001122468
Q ss_pred EEEEEEEEEe-CcEEEEEEEeCcchh
Q 043662 222 SVFRFDVIEM-GALLQLEVEGSGFLY 246 (330)
Q Consensus 222 ~I~~~~v~~~-~~~v~~~I~G~sFL~ 246 (330)
.|+.+++... +....+.|.+.+=||
T Consensus 331 ~V~~l~~~~~~~~~~~~~i~~egGlY 356 (398)
T COG1258 331 RVYELSLDLIDDRHAELEIEAEGGLY 356 (398)
T ss_pred EEEEeeeeeccCceEEEEEEecccce
Confidence 8998888775 456777777776443
No 24
>cd01291 PseudoU_synth PseudoU_synth: Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA).
Probab=91.16 E-value=1.6 Score=33.82 Aligned_cols=21 Identities=24% Similarity=0.120 Sum_probs=18.2
Q ss_pred ceeeeeccccCccccccccEEE
Q 043662 92 DLRLVGASRTDTGVHAWGQVAH 113 (330)
Q Consensus 92 ~i~~~~agRTD~GVHA~~qv~~ 113 (330)
.-++..|||.|+.++.. |+++
T Consensus 23 ~~~i~~aG~kDk~a~t~-q~v~ 43 (87)
T cd01291 23 PKRVGYAGRKDKRAVTT-QLVS 43 (87)
T ss_pred hheEEECccCCCCeeEE-EEEc
Confidence 45788999999999999 7777
No 25
>COG5011 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.97 E-value=7 Score=35.79 Aligned_cols=72 Identities=15% Similarity=0.262 Sum_probs=55.3
Q ss_pred HHHHHHHHhhc-cc-----CcceeeeeccccCccccccccEEEEEeCCCCCCHHHHHHHHHhcCCCCeEEEEEEecCCC
Q 043662 77 IVEKALIRVTK-LE-----REDLRLVGASRTDTGVHAWGQVAHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPE 149 (330)
Q Consensus 77 ~Le~AL~k~~~-i~-----~~~i~~~~agRTD~GVHA~~qv~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~i~~v~~~ 149 (330)
.++.++.+++. +. -...+++.|.=---|+..-|-++-|.+.... ..+++.+.||+.||.|+.+.++..++..
T Consensus 24 lidR~iRRAglpiayT~GFhP~prmsia~alpvG~~ssge~fd~eL~e~v-~~dk~~etl~~~lp~Dl~~~~v~~iD~k 101 (228)
T COG5011 24 LIDRTIRRAGLPIAYTGGFHPHPRMSIAQALPVGIYSSGEIFDFELTEEV-SEDKFKETLNKALPNDLPAYDVEKIDKK 101 (228)
T ss_pred HHHHHHHhcCCceeecCCCCCCCceeeccccccccccCceEEEEEeeeec-CcHHHHHHHHHhCCCCcchhheeeecCC
Confidence 56777777763 10 1235667777777899999999999886553 4689999999999999999999998763
No 26
>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=40.97 E-value=2.3e+02 Score=25.40 Aligned_cols=94 Identities=14% Similarity=0.130 Sum_probs=55.3
Q ss_pred CeEEEEEEecCCCcccccccCceEEEEEeccCCCCCcccCCeeeeecCCCCHHHHHHHHhhcccccccc--cccccccCC
Q 043662 137 DIRVREISAAVPEFHARFSAKSKIYHYKIYNDAVMDPFQRHYAYHSVYKLNTTLMRQAAEYFVGKHDFS--AFVNVQRND 214 (330)
Q Consensus 137 dIrV~~i~~v~~~FhaR~~a~~R~Y~Y~i~~~~~~~pf~~~~~~~~~~~lDi~~m~~a~~~f~G~HDF~--~F~~~~~~~ 214 (330)
++=|..+-+.. .+-..+....|+|+-.+..+. .++.+.++++++.|.|++.=. .|+..+
T Consensus 43 GvLiv~~g~~T-k~~~~~~~~~K~Y~a~v~~g~---------------~it~e~l~~~l~~f~G~i~Q~pP~~SA~K--- 103 (182)
T cd02572 43 GCLPVCIDRAT-RLVKSQQEAGKEYVCVMRLHD---------------DVDEEKVRRVLEEFTGAIFQRPPLISAVK--- 103 (182)
T ss_pred eEEEEEECHHh-hhhHHHhCCCCEEEEEEEECC---------------cCCHHHHHHHHHHCCCcEEeeCCHhheec---
Confidence 34444444422 344445566799988765432 388999999999999985321 233222
Q ss_pred CCCCCeEEEEEEEEEEeC---cEEEEEEEe--CcchhHHHH
Q 043662 215 RLLNPVKSVFRFDVIEMG---ALLQLEVEG--SGFLYRQVR 250 (330)
Q Consensus 215 ~~~~~~R~I~~~~v~~~~---~~v~~~I~G--~sFL~~qVR 250 (330)
.+...++|+++++...+ +.+.|+|+- --..+.-+|
T Consensus 104 -~~~R~v~I~~i~l~~~~~~~~~~~~~v~cs~GTYIRsL~~ 143 (182)
T cd02572 104 -RQLRVRTIYESKLLEYDGERRLVLFRVSCEAGTYIRTLCV 143 (182)
T ss_pred -CCceEEEEEEEEEEEEcCCCcEEEEEEEECCCcCHHHHHH
Confidence 12335688888876643 466666554 334444444
No 27
>PF07683 CobW_C: Cobalamin synthesis protein cobW C-terminal domain; InterPro: IPR011629 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis []. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [].; PDB: 1NIJ_A.
Probab=30.55 E-value=2.4e+02 Score=21.36 Aligned_cols=86 Identities=14% Similarity=0.030 Sum_probs=44.7
Q ss_pred EEEEeCCCCCCHHHHHHHHHhcCCCCeEEEEEEecCCC-cccccccCceEEEEEeccCCCCC---cccCCeeeeecCCCC
Q 043662 112 AHFITPFSYDGLESIHAALNGLLPPDIRVREISAAVPE-FHARFSAKSKIYHYKIYNDAVMD---PFQRHYAYHSVYKLN 187 (330)
Q Consensus 112 ~~f~~~~~~~~~~~l~~~lN~~LP~dIrV~~i~~v~~~-FhaR~~a~~R~Y~Y~i~~~~~~~---pf~~~~~~~~~~~lD 187 (330)
+.|..+... +++++...|+..-++=.|++.+..++.. ----+.+..+.|...-....... .-.......+...+|
T Consensus 4 ~~~~~~~p~-~~~~l~~~l~~~~~~vlR~KG~v~~~~~~~~~~~q~v~~~~~~~~~~~~~~~~~~~~~~~~lV~IG~~ld 82 (94)
T PF07683_consen 4 VTFEFDRPF-DPERLEAWLQELPGDVLRAKGIVWVADGPRRLVFQGVGGRYDIEPAGRWWPPMLGEDRDSRLVFIGKNLD 82 (94)
T ss_dssp EEEEESS-B--HHHHHHHHHHTTTTEEEEEEEE-BTT-SEEEEEEEETTEEEEE-EEEE-TT---S---EEEEEEEES--
T ss_pred EEEEeCCCC-CHHHHHHHHHhCCCCEEEEEEEEEeCCcCeEEEEEeeCCEEEecccccccccccCCCCCeEEEEEECCCC
Confidence 455555543 5788888888844444789999999875 22335556666655421111110 001122334456799
Q ss_pred HHHHHHHHhhc
Q 043662 188 TTLMRQAAEYF 198 (330)
Q Consensus 188 i~~m~~a~~~f 198 (330)
.+.+++++..+
T Consensus 83 ~~~l~~~l~~c 93 (94)
T PF07683_consen 83 KEALREALDAC 93 (94)
T ss_dssp HHHHHHHHHT-
T ss_pred HHHHHHHHHcc
Confidence 99999987653
No 28
>TIGR00685 T6PP trehalose-phosphatase. At least 18 distinct sequences from Arabidopsis have been identified, roughly half of these are of the fungal type, with a fused synthase and half are like the bacterial members having only the phosphatase domain. It has been suggested that trehalose is being used in Arabidopsis as a regulatory molecule in development and possibly other processes.
Probab=25.80 E-value=94 Score=28.52 Aligned_cols=49 Identities=14% Similarity=0.127 Sum_probs=34.6
Q ss_pred eEEEEEEEeCCCceeeeeCCCCCcHHHHHHHHHHHhhcccCcceeeeeccc
Q 043662 50 KWRLVIAYDGTRYAGWQFQTSPPTIQCIVEKALIRVTKLEREDLRLVGASR 100 (330)
Q Consensus 50 r~~l~v~YdGt~y~G~Q~Q~~~~TVq~~Le~AL~k~~~i~~~~i~~~~agR 100 (330)
+.+|.+-||||-- .+...|+...+-..+.++|.++..- ....-++.|||
T Consensus 3 ~~~l~lD~DGTL~-~~~~~p~~~~~~~~~~~~L~~L~~~-~~~~v~ivSGR 51 (244)
T TIGR00685 3 KRAFFFDYDGTLS-EIVPDPDAAVVSDRLLTILQKLAAR-PHNAIWIISGR 51 (244)
T ss_pred cEEEEEecCcccc-CCcCCCcccCCCHHHHHHHHHHHhC-CCCeEEEEECC
Confidence 5678899999974 4666666666777889999988651 11233578999
No 29
>PF09153 DUF1938: Domain of unknown function (DUF1938); InterPro: IPR015236 This domain, which is predominantly found in the archaeal protein O6-alkylguanine-DNA alkyltransferase, adopts a secondary structure consisting of a three stranded antiparallel beta-sheet and three alpha helices. The exact function has not, as yet, been defined, though it has been postulated that this domain may confer thermostability to the protein []. ; GO: 0005737 cytoplasm; PDB: 1MGT_A.
Probab=22.91 E-value=34 Score=27.02 Aligned_cols=28 Identities=18% Similarity=0.485 Sum_probs=23.5
Q ss_pred cEEEEEEEeCcchhHHHHHHHHHHHHHh
Q 043662 233 ALLQLEVEGSGFLYRQVRNMVALLLQIG 260 (330)
Q Consensus 233 ~~v~~~I~G~sFL~~qVR~MVG~ll~vg 260 (330)
+-+.|.+-|.-||.++|+++++.|-.=|
T Consensus 25 qGItfslDg~efl~eri~~L~~~L~kRg 52 (86)
T PF09153_consen 25 QGITFSLDGEEFLRERISRLIEFLKKRG 52 (86)
T ss_dssp EEEEEESSHHHHHH-HHHHHHHHHHHTT
T ss_pred eeEEEEeccHHHHHHHHHHHHHHHHhcC
Confidence 5688999999999999999999997643
No 30
>PF05125 Phage_cap_P2: Phage major capsid protein, P2 family ; InterPro: IPR006441 This entry is represented by Bacteriophage P2, GpN. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family represents the major capsid protein component of the heads (capsids) of bacteriophage P2 and related phage including prophage. These sequences represent one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. ; GO: 0019028 viral capsid
Probab=21.45 E-value=74 Score=31.42 Aligned_cols=34 Identities=35% Similarity=0.492 Sum_probs=23.6
Q ss_pred CCcHHHHHHHHHHHhhc----c--------cCcceeee----eccccCcc
Q 043662 71 PPTIQCIVEKALIRVTK----L--------EREDLRLV----GASRTDTG 104 (330)
Q Consensus 71 ~~TVq~~Le~AL~k~~~----i--------~~~~i~~~----~agRTD~G 104 (330)
.++||..|++++..... | ..+++.+- .|||||++
T Consensus 29 ~P~v~q~L~~~i~ess~FL~~INvv~V~e~~Ge~i~lg~~g~iagrt~t~ 78 (333)
T PF05125_consen 29 EPSVQQKLEDAIQESSEFLKKINVVPVDEQKGEKIGLGVSGPIAGRTDTG 78 (333)
T ss_pred CcHHHHHHHHHHHHHHHHHhcCCccccchhcCcEEeccCCCCccccccCC
Confidence 47999999999865321 1 13455553 49999999
Done!