Query 008711
Match_columns 557
No_of_seqs 194 out of 378
Neff 5.0
Searched_HMMs 29240
Date Mon Mar 25 09:57:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008711.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/008711hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2v9k_A Uncharacterized protein 100.0 8E-122 3E-126 993.2 34.2 469 46-552 10-523 (530)
2 2aus_C Pseudouridine synthase; 99.4 7.4E-13 2.5E-17 137.5 15.0 152 385-549 48-205 (334)
3 2apo_A Probable tRNA pseudouri 99.3 5.4E-12 1.9E-16 132.0 14.1 151 385-549 68-225 (357)
4 1k8w_A TRNA pseudouridine synt 99.0 1.1E-09 3.8E-14 113.2 11.9 165 365-549 11-218 (327)
5 3u28_A H/ACA ribonucleoprotein 99.0 7.5E-10 2.6E-14 117.1 9.5 101 438-549 119-221 (400)
6 1r3e_A TRNA pseudouridine synt 98.8 6.8E-08 2.3E-12 99.3 15.2 149 385-549 5-196 (309)
7 1sgv_A TRNA pseudouridine synt 98.3 4.4E-06 1.5E-10 86.1 13.7 150 385-549 8-204 (316)
8 1dj0_A Pseudouridine synthase 95.3 0.42 1.4E-05 47.9 15.6 146 343-513 26-193 (264)
9 1vs3_A TRNA pseudouridine synt 94.5 0.59 2E-05 46.4 14.2 144 344-512 26-192 (249)
10 1qv9_A F420-dependent methylen 46.2 5.1 0.00017 40.0 0.6 15 368-382 28-42 (283)
No 1
>2v9k_A Uncharacterized protein FLJ32312; pseudouridine synthase, PUS10, RNA modification, thump domai; HET: EPE; 2.0A {Homo sapiens}
Probab=100.00 E-value=8.3e-122 Score=993.22 Aligned_cols=469 Identities=35% Similarity=0.584 Sum_probs=410.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhcccccccchhhHHH---HHhhhhccccc-------------------------ccccC-
Q 008711 46 TDAVKDLLSKEVCLRCIFRLFGMQVPICSSLSVKS---LLCHVLGEQAD-------------------------LHQNI- 96 (557)
Q Consensus 46 ~~av~~Lls~g~C~rCi~Rf~~~~~~~~~n~~l~~---~l~~~L~~~~D-------------------------l~~~~- 96 (557)
.+++++|++.|||.||||||++++++++|..++.. .|+.++.+.++ +.+.+
T Consensus 10 ~~~~~~L~~~g~C~rCilRf~~~~~~~~y~~~~~~l~~~l~~~~~~~~~~~~~~~~~~p~k~~r~~~~~~~~~~~~~~~~ 89 (530)
T 2v9k_A 10 KHVAQLLLNTGTCPRCIFRFCGVDFHAPYKLPYKELLNELQKFLETEKDELILEVMNPPPKKIRLQELEDSIDNLSQNGE 89 (530)
T ss_dssp HHHHHHHHHHTCCHHHHHHHTTCCCSGGGGSCHHHHHHHHHHHHTC----------------------------------
T ss_pred HHHHHHHHHCCCCHHHHhHhhcCccchhhhhhHHHHHHHHHHHhhccccccccccccccchhhccccccccccccccccc
Confidence 58999999999999999999999999999988533 35666553111 11111
Q ss_pred -------------CCCCCcccccccccccccccCCccccccccchhHHHHHHHHHHHhcCCccceEEEEeecChhHHhhh
Q 008711 97 -------------SSVEPNICRSCLGILQFTYCGDKERVVENESACDFAVAIAELVKKEGHQIDSFSLEVSMPPTILENE 163 (557)
Q Consensus 97 -------------~~~~~~~C~iClGiLq~~~~d~~~~~~~~~~~~d~~~~I~e~vk~~gyef~sF~LaISLP~sl~lRE 163 (557)
.....+.|++|+|+||.... ++|+++|+++++++||+|++|+|+++||+++++||
T Consensus 90 ~~~~~~~~~~~~~~~~~~~~C~iClGil~~~~~------------~~~~~~i~~~v~~~~yef~tF~lgvslP~~i~~rE 157 (530)
T 2v9k_A 90 GRISVSHVGSTASKNSNLNVCNVCLGILQEFCE------------KDFIKKVCQKVEASGFEFTSLVFSVSFPPQLSVRE 157 (530)
T ss_dssp ------------------CCCTTTTTTTTGGGS------------HHHHHHHHHHHHHTCCCCSCBEEEEECCTTHHHHH
T ss_pred cccccccccccccccCCCCcCcCccchhhhcch------------HHHHHHHHHHHhhcCCccccEEEEEeCCHHHHHHH
Confidence 11245589999999994321 58999999999999999999999999999999999
Q ss_pred hhHHHHHHHhhcccccccccccccccchhhhhHHhhhhhHHhHhccccCC-ceeEEEEEEecchhhHHHhhhhhhhcccc
Q 008711 164 NKLSLYVKRKYRSEAWFKDRSISECSSTKDALKFALTNPLETLLDVKCGI-STFHIRLTYSRVEASIRIQNFVEKIEGCK 242 (557)
Q Consensus 164 ~s~~l~l~~~~~~~~~~~~~~~~~~v~~Kea~K~~l~~~l~~~L~~~~~~-s~f~i~v~~~h~~~~~e~~~l~~~~~~~k 242 (557)
+++|++++++||+.++..+. ++.+++|++|||.+++.|+++||++++. |+|.|.+.|+|++++.++++|.+..+++
T Consensus 158 ~~l~~~~~~~~~~~~l~~~~--~~~e~iK~e~kr~lgk~l~~~lg~~~~~~sp~~v~v~~~~~~~~~d~~~L~~~~~~~- 234 (530)
T 2v9k_A 158 HAAWLLVKQEMGKQSLSLGR--DDIVQLKEAYKWITHPLFSEELGVPIDGKSLFEVSVVFAHPETVEDCHFLAAICPDC- 234 (530)
T ss_dssp HHHHHHHHHHHHHTTCCCCG--GGSCCHHHHHHHHHHHHHHHHHSSCBCTTCSEEEEEEEECGGGTHHHHHHHTTCTTC-
T ss_pred HHHHHHHHHhccccccccCC--CCceeHHHHHHHHHhHHHHHHhCCCcCCCCCeEEEEEecCccchhhhhhhhhhcccc-
Confidence 99999999999976544433 3579999999999999999999999885 4599999999999989999988655544
Q ss_pred ccccccccccccccccccccccccceeeecccccccccccCCCCCCCCCcccccCCCCCCCCce-eeEEEEeccEEEEEE
Q 008711 243 RRKVDAKNCLDTVKDKSAITGVENSVVSTTEVIPVDEKSSNGLQDNEPSETHEFPLKKVNEPCR-LECLCFRTPIYFGGR 321 (557)
Q Consensus 243 r~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~i~~~~f~~~~~~~Pp~~~~~~~~-~~~~~~~~pi~i~GR 321 (557)
|++.+++++++|+ +.+.++|+ +|++++|. +++++||..+.++|+ ++++|.|+||||+||
T Consensus 235 ---------f~~~k~~~~~~t~---~~v~~~l~-------~i~~~~f~-~~~~~Pp~~~~~~~~~~~i~~~~~pifi~GR 294 (530)
T 2v9k_A 235 ---------FKPAKNKQSVFTR---MAVMKALN-------KIKEEDFL-KQFPCPPNSPKAVCAVLEIECAHGAVFVAGR 294 (530)
T ss_dssp ---------C----------CH---HHHHHHHH-------HSCHHHHH-HHSCSSCCCCSSCCEEEEEEEEECCEEEEEE
T ss_pred ---------cccccccccchhH---HHHHHHHh-------hcChhhHh-hcccCCCCCccccceeEEEEEccCcEEEEEE
Confidence 3444455666654 55666676 89999999 999999999999996 689999999999999
Q ss_pred eeecccCCCCcccccCccccCcCcHHHHhhhccccccCCCceEEeecCCCcccccccCCCccEEEEEccCccCC-cHHHH
Q 008711 322 YLKYSRNVSQTRWIIDEERMGEASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVP-SELLV 400 (557)
Q Consensus 322 Y~K~sR~lsQtpW~~~~~r~~~~SVeE~I~~~~~~~f~~~~~~F~~sGREDvDVRmLG~GRPFvlEi~nPr~~~-~~~~~ 400 (557)
|+|++|+||||||+++|+++|++||||+|+.++.++|+|++++|||||||||||||||+|||||+||+|||++. +..++
T Consensus 295 Y~K~~R~ipQT~W~~~g~r~~~~SVee~I~~~i~~~f~~~~~~Fh~sGREDvDVRmLG~GRPFvlEi~~P~r~~~~~~dl 374 (530)
T 2v9k_A 295 YNKYSRNLPQTPWIIDGERKLESSVEELISDHLLAVFKAESFNFSSSGREDVDVRTLGNGRPFAIELVNPHRVHFTSQEI 374 (530)
T ss_dssp EEECCSSCCSSCCBSSSSBSSSCCHHHHHHTTHHHHHTCSEEEEEESSCCCTTCEEEEEEEEEEEEEESCSCCCCCHHHH
T ss_pred EeeccCCCCCCCcccCCCccCCCCHHHHHHHHHHHhcCCCeEEEeecCCCCCceeecCCCCcEEEEecCccccccchhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998763 56899
Q ss_pred HHHHHHHhccCCCcEEEEeeEEecccchhhhcccccccccEEEEEEEEcCCCCHHHHHHhhcccCceeeccCCcEEEeec
Q 008711 401 KEIESKINSLENKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQTISSLKETQILQKTPIRVLHRR 480 (557)
Q Consensus 401 ~~l~~~In~~~~~~V~v~~L~~v~r~~~~~lk~~e~~k~K~Y~alv~~~~~vt~e~l~~l~~l~~~~I~QrTP~RVlHRR 480 (557)
++|+++||+. .+.|+|++|++++++++..||+|+++|.|.|+|+||+++++++++|+.+..++|++|.||||+||+|||
T Consensus 375 ~~le~~IN~~-~~~V~V~~L~~v~~~~~~~ik~ge~~~~K~Y~alv~~~~~v~~e~l~~~~~l~~l~I~QrtP~RV~hRR 453 (530)
T 2v9k_A 375 KELQQKINNS-SNKIQVRDLQLVTREAIGHMKEGEEEKTKTYSALIWTNKAIQKKDIEFLNDIKDLKIDQKTPLRVLHRR 453 (530)
T ss_dssp HHHHHHHHTT-CSSEEEEEEEEECTHHHHHHHHHHHHCCEEEEEEEEESSCCCHHHHGGGGGCCSEEEEEECCGGGTTTS
T ss_pred HHHHHHHhcc-CCcEEEEeeEEEcHHHHHHHhcccccCCeEEEEEEEEcCCCCHHHHHHHHhcCCceeeccCCeEEEEec
Confidence 9999999974 567999999999999999999999999999999999999999999999888999999999999999999
Q ss_pred CCCceeeEEEEEEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEEecc
Q 008711 481 SPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDVKMN 552 (557)
Q Consensus 481 ~~~~R~R~I~~~~~~~i~~~~~~f~l~l~tqaGtYIKEfVhGD~GRT~Psl~~iLg~~a~ileLDV~~V~~d 552 (557)
++++|+|+||+|++..+++ ++|+|+|.||||||||||||||||||+||||++||++|+|++|||++|+||
T Consensus 454 ~~~~R~R~I~~i~~~~~~~--~~~~l~i~~eaGtYIKelvhGD~GRT~Psl~~lLg~~a~i~eLDV~~V~~d 523 (530)
T 2v9k_A 454 PLAVRARVIHFMETQYVDE--HHFRLHLKTQAGTYIKEFVHGDFGRTKPNIGSLMNVTADILELDVESVDVD 523 (530)
T ss_dssp CCCEEEEEEEEEEEEEEET--TEEEEEEEECTTCCHHHHHHCTTTTEESCHHHHHTSCEEEEEEEEEEECCC
T ss_pred CCCccceEEEEEEEEEecC--CEEEEEEEecCCCEEEEEEcCCCCCcCCcHHHHhCCCcEEEEeEEeEEecc
Confidence 9999999999999999975 999999999999999999999999999999999999999999999999999
No 2
>2aus_C Pseudouridine synthase; isomerase, structural protein, isomerase-structural protein; 2.10A {Pyrococcus abyssi} PDB: 3lwr_A 3lwo_A* 3lwq_A* 3lwp_A 3lwv_A 3hax_A* 2hvy_A* 3hay_A* 2ey4_A 2rfk_A 3mqk_A 3hjw_A* 3hjy_A
Probab=99.45 E-value=7.4e-13 Score=137.52 Aligned_cols=152 Identities=22% Similarity=0.367 Sum_probs=109.3
Q ss_pred EEEEccCccCCcHHHHHHHHHHHhccCCC-----cEEEEeeEEecccchhhhcccccccccEEEEEEEEcCCCCHHHHHH
Q 008711 385 LFEIQNAREVPSELLVKEIESKINSLENK-----LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQT 459 (557)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~-----~V~v~~L~~v~r~~~~~lk~~e~~k~K~Y~alv~~~~~vt~e~l~~ 459 (557)
++-|..|.-..|..-+..+...+|...-| +-...++-++.-....++-+.-....|.|+|.+++..+++++++++
T Consensus 48 il~vdKP~g~tS~~vv~~vr~~~~~~KvGH~GTLDP~atGvL~v~~g~aTk~~~~l~~~~K~Y~~~~~lg~~~~~~~i~~ 127 (334)
T 2aus_C 48 VINLDKPPGPTSHEVVAWIKRILNLEKAGHGGTLDPKVSGVLPVALERATRVVQALLPAGKEYVALMHLHGDVPEDKIRA 127 (334)
T ss_dssp EEEEEECSSSCHHHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGGGGGGGGTTCCEEEEEEEEESSCCCHHHHHH
T ss_pred EEEEECCCCCCHHHHHHHHHHHhCcceeccccccCCccceeEEEEeChhhhhHHHhcccCcEEEEEEEECCCCCHHHHHH
Confidence 78888998777778888888888753110 0012222222222223333333446799999999999999999998
Q ss_pred -hhcccCceeeccCCcEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCc
Q 008711 460 -ISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCR 538 (557)
Q Consensus 460 -l~~l~~~~I~QrTP~RVlHRR~~~~R~R~I~~~~~~~i~~~~~~f~l~l~tqaGtYIKEfVhGD~GRT~Psl~~iLg~~ 538 (557)
+..|.| +|.|.+|.++.++|+ .|+++||++++..++. .+|.+++.|++||||+.|+| | ||..||+.
T Consensus 128 ~l~~f~G-~i~Q~pP~~SA~k~~--~R~v~I~~~~~~~~~~--~~~~~~v~cs~GTYIRsL~~-D-------ig~~Lg~~ 194 (334)
T 2aus_C 128 VMKEFEG-EIIQRPPLRSAVKRR--LRTRKVYYIEILEIDG--RDVLFRVGVEAGTYIRSLIH-H-------IGLALGVG 194 (334)
T ss_dssp HHHHTSE-EEECC--------------EEEEEEEEEEEEET--TEEEEEEEECTTCCHHHHHH-H-------HHHHHSSC
T ss_pred HHHhCcC-eEEEeCCccccCcCC--cCCEEEEEEEEEEeeC--CeEEEEEEECCCcHHHHHHH-H-------HHHHhCCC
Confidence 789999 999999999999987 7999999999998864 79999999999999999999 5 89999999
Q ss_pred cEEEEEEEEEE
Q 008711 539 AEILQLDVTDV 549 (557)
Q Consensus 539 a~ileLDV~~V 549 (557)
|++.+|+.+.+
T Consensus 195 a~~~~LrRt~~ 205 (334)
T 2aus_C 195 AHMAELRRTRS 205 (334)
T ss_dssp EEEEEEEEEEE
T ss_pred EEEeEEEEEEE
Confidence 99999999876
No 3
>2apo_A Probable tRNA pseudouridine synthase B; protein-protein complex, box H/ACA, snoRNP, pseudouridine synthase, RNA modification; 1.95A {Methanocaldococcus jannaschii} SCOP: b.122.1.1 d.265.1.2
Probab=99.35 E-value=5.4e-12 Score=131.98 Aligned_cols=151 Identities=21% Similarity=0.306 Sum_probs=106.6
Q ss_pred EEEEccCccCCcHHHHHHHHHHHhccCCC-----cEEEEeeEEec-ccchhhhcccccccccEEEEEEEEcCCCCHHHHH
Q 008711 385 LFEIQNAREVPSELLVKEIESKINSLENK-----LVRVKNLKIVG-SQGWTLMREGEAEKQKQYAALVWISRPLQDEDFQ 458 (557)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~-----~V~v~~L~~v~-r~~~~~lk~~e~~k~K~Y~alv~~~~~vt~e~l~ 458 (557)
++-|..|.-..+.+-+..+...+|...-| +-...++=++- -++...+ +--....|.|+|.+++..++++++++
T Consensus 68 il~vdKP~G~TS~~vv~~vr~~l~~~KvGH~GTLDP~AtGvL~v~~G~aTk~~-~~l~~~~K~Y~~~~~lG~~~~~~~i~ 146 (357)
T 2apo_A 68 VVVVDKPRGPTSHEVSTWVKKILNLDKAGHGGTLDPKVTGVLPVALERATKTI-PMWHIPPKEYVCLMHLHRDASEEDIL 146 (357)
T ss_dssp EEEEEECSSSCHHHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGGGGG-GGTTSSCEEEEEEEEESSCCCHHHHH
T ss_pred EEEEECCCCCCHHHHHHHHHHHhCccccccccccCCCceeEEEEEeCHHHhHH-HHhccCCcEEEEEEEECCCCCHHHHH
Confidence 77788898766777788888887752100 00111111221 1122222 22223569999999999999999999
Q ss_pred H-hhcccCceeeccCCcEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCC
Q 008711 459 T-ISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGC 537 (557)
Q Consensus 459 ~-l~~l~~~~I~QrTP~RVlHRR~~~~R~R~I~~~~~~~i~~~~~~f~l~l~tqaGtYIKEfVhGD~GRT~Psl~~iLg~ 537 (557)
+ +..|.| +|.|.+|.+..++|+ .|+++||++++..++. ..|.+++.|++||||+.|+| | ||..||+
T Consensus 147 ~~l~~f~G-~i~Q~PP~~SAvK~~--~R~v~I~~~~l~~~~~--~~~~~~v~cs~GTYIRsL~~-D-------iG~~LG~ 213 (357)
T 2apo_A 147 RVFKEFTG-RIYQRPPLKAAVKRR--LRIRKIHELELLDKDG--KDVLFRVKCQSGTYIRKLCE-D-------IGEALGT 213 (357)
T ss_dssp HHHHHHSE-EEECC-------------CEEEEEEEEEEEEET--TEEEEEEEECTTCCHHHHHH-H-------HHHHTTS
T ss_pred HHHHhCcc-cEEEeCCchhhcccc--ccceeEEEEEEEEeeC--CEEEEEEEECCCchHHHHHH-H-------HHHhhCC
Confidence 8 789999 999999999999987 7999999999998864 79999999999999999999 5 8999999
Q ss_pred ccEEEEEEEEEE
Q 008711 538 RAEILQLDVTDV 549 (557)
Q Consensus 538 ~a~ileLDV~~V 549 (557)
.|.+.+|+.+.+
T Consensus 214 ~a~~~~LrRt~~ 225 (357)
T 2apo_A 214 SAHMQELRRTKS 225 (357)
T ss_dssp CEEEEEEEEEEE
T ss_pred CEEEEEEEEEEE
Confidence 999999999876
No 4
>1k8w_A TRNA pseudouridine synthase B; protein-RNA complex, T stem-loop, lyase/RNA complex; HET: FHU; 1.85A {Escherichia coli} SCOP: b.122.1.1 d.265.1.2 PDB: 1zl3_A* 1r3f_A
Probab=99.02 E-value=1.1e-09 Score=113.25 Aligned_cols=165 Identities=15% Similarity=0.248 Sum_probs=117.4
Q ss_pred EeecCCCcccccccCCCccEEEEEccCccCCcHHHHHHHHHHHhccCC----------CcEEEEeeEEecccchhhhccc
Q 008711 365 FHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLEN----------KLVRVKNLKIVGSQGWTLMREG 434 (557)
Q Consensus 365 F~~sGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~----------~~V~v~~L~~v~r~~~~~lk~~ 434 (557)
-|+||----.-|++ +| ++=|..|.-..+..-+..+...++...- ..|-+..+.-.+| .+..|..
T Consensus 11 ~~~~~~~~~~~~~~-~G---il~vdKP~G~TS~dvv~~vr~~l~~kKvGH~GTLDP~AtGvL~i~~G~aTK-l~~~l~~- 84 (327)
T 1k8w_A 11 HHSSGHIEGRHMDI-NG---VLLLDKPQGMSSNDALQKVKRIYNANRAGHTGALDPLATGMLPICLGEATK-FSQYLLD- 84 (327)
T ss_dssp -----------CCC-CE---EEEEEECTTCCHHHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGGG-GTHHHHT-
T ss_pred cccccccccccCCC-Ce---EEEEECCCCCCHHHHHHHHHHhhccceeccCCCCCCCCeeEEEEEECHHHh-HHHHhcc-
Confidence 35666543333333 34 6777788766676767777776664210 0244444444444 4445543
Q ss_pred ccccccEEEEEEEEcC-----------------CCCHHHHHH-hhcccCceeeccCCcEEEee----cC-----------
Q 008711 435 EAEKQKQYAALVWISR-----------------PLQDEDFQT-ISSLKETQILQKTPIRVLHR----RS----------- 481 (557)
Q Consensus 435 e~~k~K~Y~alv~~~~-----------------~vt~e~l~~-l~~l~~~~I~QrTP~RVlHR----R~----------- 481 (557)
..|.|+|.+++.. .++.+++++ |..|.| .|.|.+|....-+ |+
T Consensus 85 ---~~K~Y~a~~~lG~~TdT~D~eG~v~~~~~~~~t~e~i~~~l~~f~G-~i~Q~PP~~SAvKv~GkraYelAR~G~~ve 160 (327)
T 1k8w_A 85 ---SDKRYRVIARLGQRTDTSDADGQIVEERPVTFSAEQLAAALDTFRG-DIEQIPSMYSALKYQGKKLYEYARQGIEVP 160 (327)
T ss_dssp ---SCEEEEEEEEETEEESSSBTTSCEEEECCCCCCHHHHHHHHHTTSE-EEEECCCSSSCCEETTEEHHHHHHTTCCCC
T ss_pred ---CCcEEEEEEEECCcccCCCCCCCEEeecCCCCCHHHHHHHHHhccc-eEEEeCChhheeccCCccHHHHHhCCCccc
Confidence 2599999999876 689999998 889999 9999999986433 33
Q ss_pred CCceeeEEEEEEEEEEcCCccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008711 482 PLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 549 (557)
Q Consensus 482 ~~~R~R~I~~~~~~~i~~~~~~f~l~l~tqaGtYIKEfVhGD~GRT~Psl~~iLg~~a~ileLDV~~V 549 (557)
+..|+.+||++++...+. ..|.+++.|+.||||+.++|. ||..||+.|.+.+|..+.+
T Consensus 161 ~~~R~v~I~~i~ll~~~~--~~~~~~v~CskGTYIRsL~~D--------iG~~Lg~~a~~~~LrRt~~ 218 (327)
T 1k8w_A 161 REARPITVYELLFIRHEG--NELELEIHCSKGTYIRTIIDD--------LGEKLGCGAHVIYLRRLAV 218 (327)
T ss_dssp CCCEEEEEEEEEEEEEET--TEEEEEEEECTTCCHHHHHHH--------HHHHHTSCEEEEEEEEEEE
T ss_pred ccceEEEEEEEEEEEeeC--CEEEEEEEEcCCchHHHHHHH--------HHHHhCCCeEEEEEEEEEE
Confidence 779999999999988763 789999999999999999994 8999999999999999876
No 5
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A
Probab=98.99 E-value=7.5e-10 Score=117.12 Aligned_cols=101 Identities=19% Similarity=0.366 Sum_probs=85.6
Q ss_pred cccEEEEEEEEcCCC-CHHHHHH-hhcccCceeeccCCcEEEeecCCCceeeEEEEEEEEEEcCCccEEEEEEEecCCce
Q 008711 438 KQKQYAALVWISRPL-QDEDFQT-ISSLKETQILQKTPIRVLHRRSPLEREKIINWMKIEKIAGSSQYFLLHMCTQAGTY 515 (557)
Q Consensus 438 k~K~Y~alv~~~~~v-t~e~l~~-l~~l~~~~I~QrTP~RVlHRR~~~~R~R~I~~~~~~~i~~~~~~f~l~l~tqaGtY 515 (557)
..|.|+|.+++.... ++++++. |..|.| .|.|.+|.....+|. .|.++||++++...+....+|.++|.|++|||
T Consensus 119 ~~K~Y~a~~~lG~~~~~~~~i~~~l~~f~G-~i~Q~PP~ySAvK~~--~R~v~I~~i~ll~~~~~~~~~~~~V~CskGTY 195 (400)
T 3u28_A 119 AGKEYVCIVRLHDALKDEKDLGRSLENLTG-ALFQRPPLISAVKRQ--LRVRTIYESNLIEFDNKRNLGVFWASCEAGTY 195 (400)
T ss_dssp SCEEEEEEEEESSCCSSTTHHHHHHHHTCE-EEEECCC-----CCC--CEEEEEEEEEEEEEETTTTEEEEEEEECTTCC
T ss_pred CCcEEEEEEEeCCCCCCHHHHHHHHHhCcC-ceEEECCceecccCC--ceeEEEEEEEEEEEcCCCceEEEEEEECCCCC
Confidence 359999999999766 5788887 889999 799999999999987 69999999999988753368999999999999
Q ss_pred eeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008711 516 IKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 549 (557)
Q Consensus 516 IKEfVhGD~GRT~Psl~~iLg~~a~ileLDV~~V 549 (557)
|+.++|. ||..||+.|+|.+|.-+.+
T Consensus 196 IRsL~~D--------iG~~LG~gahm~~LrRt~~ 221 (400)
T 3u28_A 196 MRTLCVH--------LGMLLGVGGHMQELRRVRS 221 (400)
T ss_dssp HHHHHHH--------HHHHHSSCEEEEEEEEEEE
T ss_pred HHHHHHH--------HHHHHCCCEEEEEEEEEEE
Confidence 9999996 9999999999999998865
No 6
>1r3e_A TRNA pseudouridine synthase B; RNA modification, pseudouridylation, lyase-RNA complex; HET: FHU; 2.10A {Thermotoga maritima} SCOP: b.122.1.1 d.265.1.2 PDB: 1ze2_A* 2ab4_A* 1ze1_A
Probab=98.79 E-value=6.8e-08 Score=99.27 Aligned_cols=149 Identities=19% Similarity=0.213 Sum_probs=110.3
Q ss_pred EEEEccCccCCcHHHHHHHHHHHhccCCC----------cEEEEeeEEecccchhhhcccccccccEEEEEEEEcC----
Q 008711 385 LFEIQNAREVPSELLVKEIESKINSLENK----------LVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWISR---- 450 (557)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~~~----------~V~v~~L~~v~r~~~~~lk~~e~~k~K~Y~alv~~~~---- 450 (557)
++=|..|.-..+..-+..+...+|...-| .|-+-.+.-.+| -+..|. ...|.|+|.+++..
T Consensus 5 il~vdKP~G~TS~~vv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~iG~aTK-l~~~l~----~~~K~Y~a~~~lG~~TdT 79 (309)
T 1r3e_A 5 ILVAYKPKGPTSHDVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQGTR-ILEFYK----DLKKVYWVKMRLGLITET 79 (309)
T ss_dssp EEEEEECSSSCHHHHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGGG-GGGGGT----TSCEEEEEEEEETEEESS
T ss_pred EEEEECCCCCCHHHHHHHHHHHhccceecccccCCCCcceeEEEEECHHHh-HHHHhC----ccCcEEEEEEEECCcccC
Confidence 55566787666777777777777642100 122222211121 222332 33699999999873
Q ss_pred -------------CCCHHHHHH-hhcccCceeeccCCcEEEee----cC-----------CCceeeEEEEEEEEEEcCCc
Q 008711 451 -------------PLQDEDFQT-ISSLKETQILQKTPIRVLHR----RS-----------PLEREKIINWMKIEKIAGSS 501 (557)
Q Consensus 451 -------------~vt~e~l~~-l~~l~~~~I~QrTP~RVlHR----R~-----------~~~R~R~I~~~~~~~i~~~~ 501 (557)
+++.+++++ |..|.| .|.|.+|....-+ |+ ...|+.+||++++...+.
T Consensus 80 ~D~eG~v~~~~~~~~t~~~i~~~l~~f~G-~i~Q~PP~~SAvKv~GkraYelAR~G~~ve~~~R~v~I~~i~ll~~~~-- 156 (309)
T 1r3e_A 80 FDITGEVVEERECNVTEEEIREAIFSFVG-EYDQVPPAYSAKKYKGERLYKLAREGKIINLPPKRVKIFKIWDVNIEG-- 156 (309)
T ss_dssp SBTTSCEEEECCCCCCHHHHHHHHHSSSE-EEEECCCSSSSCEETTEEHHHHHHTTCCCCCCCEEEEEEEEEEEEEET--
T ss_pred CCCCCCEEEEecCCCCHHHHHHHHHhccc-eEEEeCChHHhcccCCccHHHHHhCCCcccccceEEEEEEEEEEEeeC--
Confidence 478999988 899999 9999999876644 32 678999999999988763
Q ss_pred cEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008711 502 QYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 549 (557)
Q Consensus 502 ~~f~l~l~tqaGtYIKEfVhGD~GRT~Psl~~iLg~~a~ileLDV~~V 549 (557)
.+|.+++.|+.||||+.++|. ||..||+.|++.+|.-+.+
T Consensus 157 p~~~~~v~CskGTYIRsL~~D--------iG~~Lg~~a~~~~LrRt~~ 196 (309)
T 1r3e_A 157 RDVSFRVEVSPGTYIRSLCMD--------IGYKLGCGATAVELVRESV 196 (309)
T ss_dssp TEEEEEEEECTTCCHHHHHHH--------HHHHTTSCEEEEEEEEEEE
T ss_pred CEEEEEEEECCCchHHHHHHH--------HHHHhCCCEEEEEEEEEEE
Confidence 689999999999999999995 8999999999999998875
No 7
>1sgv_A TRNA pseudouridine synthase B; hinged motion, tRNA modification, structural genomics, PSI, structure initiative; 1.90A {Mycobacterium tuberculosis} SCOP: b.122.1.1 d.265.1.2
Probab=98.33 E-value=4.4e-06 Score=86.13 Aligned_cols=150 Identities=18% Similarity=0.204 Sum_probs=99.5
Q ss_pred EEEEccCccCCcHHHHHHHHHHHhccC-----------CCcEEEEeeEEecccchhhhcccccccccEEEEEEEEc----
Q 008711 385 LFEIQNAREVPSELLVKEIESKINSLE-----------NKLVRVKNLKIVGSQGWTLMREGEAEKQKQYAALVWIS---- 449 (557)
Q Consensus 385 vlEi~nPr~~~~~~~~~~l~~~In~~~-----------~~~V~v~~L~~v~r~~~~~lk~~e~~k~K~Y~alv~~~---- 449 (557)
++=|..|.-..|..-+..+...++... .| |-+-.+.-.+| -+..| ....|.|.|.+++.
T Consensus 8 il~vdKP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtG-vL~i~iG~aTK-l~~~l----~~~~K~Y~~~~~lG~~Td 81 (316)
T 1sgv_A 8 IVVIDKPAGMTSHDVVGRCRRIFATRRVGHAGTLDPMATG-VLVIGIERATK-ILGLL----TAAPKSYAATIRLGQTTS 81 (316)
T ss_dssp EEEEEECTTCCHHHHHHHHHHHTTCSCEEESSCCCTTCEE-EEEEEEGGGGG-GGGGT----TTSCEEEEEEEEETEEET
T ss_pred EEEEECCCCCCHHHHHHHHHHHhccccccccccCCCCCeE-EEEEEECHHHh-HHHHh----CcCCcEEEEEEEECCccC
Confidence 566677876667777777777776421 11 22222221121 22233 23469999999976
Q ss_pred --------------CCCCHHHHHH-hhcccCceeeccCCcEEEeec---------------CCCceeeEEEEEEEEEEcC
Q 008711 450 --------------RPLQDEDFQT-ISSLKETQILQKTPIRVLHRR---------------SPLEREKIINWMKIEKIAG 499 (557)
Q Consensus 450 --------------~~vt~e~l~~-l~~l~~~~I~QrTP~RVlHRR---------------~~~~R~R~I~~~~~~~i~~ 499 (557)
..++++++++ |..|.| .|.|..|.-..-+. ....|+.+||++++..++.
T Consensus 82 T~D~eG~v~~~~~~~~~t~~~i~~~l~~f~G-~i~Q~PP~ySAvKv~GkrlYelAR~G~~ve~~~R~v~I~~i~ll~~~~ 160 (316)
T 1sgv_A 82 TEDAEGQVLQSVPAKHLTIEAIDAAMERLRG-EIRQVPSSVSAIKVGGRRAYRLARQGRSVQLEARPIRIDRFELLAARR 160 (316)
T ss_dssp TSBTTSCEEEECCCTTCCHHHHHHHHHHTCE-EC----------------------------CCCCCCEEEEEEEEEEEE
T ss_pred CCCCCCCEEEecCCCCCCHHHHHHHHHhccc-cEEEeCCHHHhcccCChhHHHHHhCCCcccccceEEEEEEEEEEEeec
Confidence 3578899988 889999 89999998765442 3457889999999987642
Q ss_pred C--ccEEEEEEEecCCceeeEeeeCCCCCcCcchhhhcCCccEEEEEEEEEE
Q 008711 500 S--SQYFLLHMCTQAGTYIKEFVHGDLGRTNPSIGSILGCRAEILQLDVTDV 549 (557)
Q Consensus 500 ~--~~~f~l~l~tqaGtYIKEfVhGD~GRT~Psl~~iLg~~a~ileLDV~~V 549 (557)
. ...|.+++.|+.||||.-++|. ||..||+.+++.+|-=+.+
T Consensus 161 ~~~~p~~~~~v~CskGTYIRsLa~D--------iG~~Lg~~a~~~~LrRt~~ 204 (316)
T 1sgv_A 161 RDQLIDIDVEIDCSSGTYIRALARD--------LGDALGVGGHVTALRRTRV 204 (316)
T ss_dssp ETTEEEEEEEEEESCCTTHHHHHHH--------HHHHHTSCEEEEEEEEEEE
T ss_pred cCCCceEEEEEEECCCCcHHHHHHH--------HHHHhCCCEEEeeEEEEEE
Confidence 1 2479999999999999999998 9999999999999976654
No 8
>1dj0_A Pseudouridine synthase I; alpha/beta fold, RNA-binding motif, RNA-modifying enzyme, lyase; 1.50A {Escherichia coli} SCOP: d.265.1.1 PDB: 2nqp_A 2nr0_A 2nre_A
Probab=95.29 E-value=0.42 Score=47.88 Aligned_cols=146 Identities=13% Similarity=0.164 Sum_probs=96.5
Q ss_pred cCcHHHHhhhccccccCCCceEEeecCCCcccccccCCCccEEEEEccCccCCcHHHHHHHHHHHhccCCCcEEEEeeEE
Q 008711 343 EASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRVKNLKI 422 (557)
Q Consensus 343 ~~SVeE~I~~~~~~~f~~~~~~F~~sGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~~~V~v~~L~~ 422 (557)
..|||+.|.+.+..++ +..+.+++|||-|--|=-+|. |+.+.-|... +...+...+|..-..+|.|.+...
T Consensus 26 ~~TVq~~Le~AL~~~~-~~~v~~~~agRTDaGVHA~gq----v~~f~~~~~~----~~~~~~~~lN~~LP~dI~V~~~~~ 96 (264)
T 1dj0_A 26 VRSVQEKLEKALSQVA-NEPITVFCAGRTDAGVHGTGQ----VVHFETTALR----KDAAWTLGVNANLPGDIAVRWVKT 96 (264)
T ss_dssp SSCHHHHHHHHHHHHH-TSCCCEEESSCCCTTCEEEEE----EEEEEESCCC----CHHHHHHHHHHTSCTTEEEEEEEE
T ss_pred CCCHHHHHHHHHHHHh-CCCeEEEEeccCCCCCchhhE----EEEEEECCCC----CHHHHHHHHHhhCCcCeEEEEEEe
Confidence 3599999988888887 457999999999999999984 4444334322 244677788987667899999998
Q ss_pred ecccchhhhcccccccccEEEEEEEE---------------cCCCCHHHHHH-hhccc------CceeeccCCcEEEeec
Q 008711 423 VGSQGWTLMREGEAEKQKQYAALVWI---------------SRPLQDEDFQT-ISSLK------ETQILQKTPIRVLHRR 480 (557)
Q Consensus 423 v~r~~~~~lk~~e~~k~K~Y~alv~~---------------~~~vt~e~l~~-l~~l~------~~~I~QrTP~RVlHRR 480 (557)
|+..--.+ -.-+.|.|+=.++. ..+++.+.+++ ++.|. .+.-. ++
T Consensus 97 V~~~FhAR----f~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~lD~~~M~~aa~~l~G~HDF~~F~~~-~~-------- 163 (264)
T 1dj0_A 97 VPDDFHAR----FSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAV-QC-------- 163 (264)
T ss_dssp CCTTCCTT----TTCCEEEEEEEEECSSSCCCTTTTSSEECCSCCCHHHHHHHHGGGCEEEECGGGCCT-TC--------
T ss_pred CCCCCCcc----cccccEEEEEEEccCCCCChhHcCceEeeCCCCCHHHHHHHHHHhcCcccHHHhccC-CC--------
Confidence 87442222 13345888887764 34566666665 33332 32211 00
Q ss_pred CCCceeeEEEEEEEEEEcCCccEEEEEEEecCC
Q 008711 481 SPLEREKIINWMKIEKIAGSSQYFLLHMCTQAG 513 (557)
Q Consensus 481 ~~~~R~R~I~~~~~~~i~~~~~~f~l~l~tqaG 513 (557)
....-.|+|+++++..-. ..+.++|..+|=
T Consensus 164 ~~~s~vR~I~~~~v~~~~---~~i~~~i~g~~F 193 (264)
T 1dj0_A 164 QSRTPWRNVMHINVTRHG---PYVVVDIKANAF 193 (264)
T ss_dssp CCSCCEEEEEEEEEEEET---TEEEEEEEESCC
T ss_pred CCCCcEEEEEEEEEEECC---CEEEEEEEEchH
Confidence 122345788888887642 578888888863
No 9
>1vs3_A TRNA pseudouridine synthase A; TRUA, tRNA modification, structural NPPSFA, national project on protein structural and function analyses; 2.25A {Thermus thermophilus}
Probab=94.52 E-value=0.59 Score=46.37 Aligned_cols=144 Identities=17% Similarity=0.205 Sum_probs=93.0
Q ss_pred CcHHHHhhhccccccCCCceEEeecCCCcccccccCCCccEEEEEccCccCCcHHHHHHHHHHHhccCCCcEEEEeeEEe
Q 008711 344 ASIEEIIGGNILPMCRGDSYKFHAAGREDIDVRMLGSGRPFLFEIQNAREVPSELLVKEIESKINSLENKLVRVKNLKIV 423 (557)
Q Consensus 344 ~SVeE~I~~~~~~~f~~~~~~F~~sGREDvDVRmLG~GRPFvlEi~nPr~~~~~~~~~~l~~~In~~~~~~V~v~~L~~v 423 (557)
.|||+.|.+.|..+ +..+.+++|||-|--|=-+|. |+.+.-|...+ .+.+...+|..-..+|.|.+...|
T Consensus 26 ~TVq~~Le~AL~~~--~~~v~~~~agRTDaGVHA~gq----v~~f~~~~~~~----~~~~~~~lN~~LP~dI~V~~~~~v 95 (249)
T 1vs3_A 26 RTVQGELERALPGI--GALPKAVAAGRTDAGVHALAM----PFHVDVESAIP----VEKVPEALNRLLPEDLKVVGAREV 95 (249)
T ss_dssp CCHHHHHHHHGGGG--TBCSCCEESSCCBTTCEEEEE----EEEEEECSCCC----GGGHHHHHHHHSCTTEEEEEEEEE
T ss_pred CCHHHHHHHHHHHc--CCcceEEEeccCcCCcCcccc----EEEEEECCCCC----HHHHHHHHHhcCCcCEEEEEEEEC
Confidence 59999999888888 678999999999999999985 44443333222 234566788766668999999998
Q ss_pred cccchhhhcccccccccEEEEEEEEc---------------CCCCHHHHHH-hh------cccCceeeccCCcEEEeecC
Q 008711 424 GSQGWTLMREGEAEKQKQYAALVWIS---------------RPLQDEDFQT-IS------SLKETQILQKTPIRVLHRRS 481 (557)
Q Consensus 424 ~r~~~~~lk~~e~~k~K~Y~alv~~~---------------~~vt~e~l~~-l~------~l~~~~I~QrTP~RVlHRR~ 481 (557)
+..--.+ =.-+.|.|+=.++.. .+++.+.+++ ++ +|..+.-.. +
T Consensus 96 ~~~FhAR----f~a~~R~Y~Y~i~~~~~~~~~~~~~~~~~~~~ldi~~m~~aa~~l~G~HDF~~F~~~~-~--------- 161 (249)
T 1vs3_A 96 APDFHAR----KDALWRAYRYRILVRPHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEE-T--------- 161 (249)
T ss_dssp CTTCCTT----TTCSEEEEEEEEEECSSCCTTTTTTSEEECSCCCHHHHHHHHHHHSEEEEGGGGCSSC-C---------
T ss_pred CCCCCcc----cccccEEEEEEEccCCCCChhhCCeeEEeCCCCCHHHHHHHHHHhcCceeHHheecCC-C---------
Confidence 7442222 123458888877653 4677666654 33 333332111 0
Q ss_pred CCceeeEEEEEEEEEEc-CCccEEEEEEEecC
Q 008711 482 PLEREKIINWMKIEKIA-GSSQYFLLHMCTQA 512 (557)
Q Consensus 482 ~~~R~R~I~~~~~~~i~-~~~~~f~l~l~tqa 512 (557)
..-.|+|+++++.... .....+.++|..+|
T Consensus 162 -~~~vR~I~~~~v~~~~~~~~~~i~~~i~g~~ 192 (249)
T 1vs3_A 162 -RPGERELLEARLQVAEGEAGLEVRLYFRGKS 192 (249)
T ss_dssp -SCCEEEEEEEEEEEEECSSSEEEEEEEEESC
T ss_pred -CCCCcEEEEEEEEeccccCCCEEEEEEEECh
Confidence 2345678888876321 11256777888776
No 10
>1qv9_A F420-dependent methylenetetrahydromethanopterin dehydrogenase; monomer: alpha/beta domain, helix bundle, trimer of dimers, oxidoreductase; HET: MSE; 1.54A {Methanopyrus kandleri} SCOP: c.127.1.1 PDB: 1u6i_A 1u6j_A 1u6k_A* 3iqe_A* 3iqf_A* 3iqz_A*
Probab=46.15 E-value=5.1 Score=39.99 Aligned_cols=15 Identities=40% Similarity=0.800 Sum_probs=13.5
Q ss_pred cCCCcccccccCCCc
Q 008711 368 AGREDIDVRMLGSGR 382 (557)
Q Consensus 368 sGREDvDVRmLG~GR 382 (557)
+-|||+||||+|+|-
T Consensus 28 AdRedI~vrv~gsGa 42 (283)
T 1qv9_A 28 ADREDVEFRVVGTSV 42 (283)
T ss_dssp SCCSSEEEEEEECTT
T ss_pred hccCCceEEEeccCC
Confidence 579999999999994
Done!