Query 009530
Match_columns 532
No_of_seqs 226 out of 855
Neff 6.3
Searched_HMMs 46136
Date Thu Mar 28 14:14:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009530hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2339 Uncharacterized conser 100.0 7E-114 1E-118 915.6 32.4 429 10-532 189-619 (624)
2 cd02576 PseudoU_synth_ScPUS7 P 100.0 4.3E-89 9.2E-94 719.2 36.9 333 13-409 8-348 (371)
3 PF01142 TruD: tRNA pseudourid 100.0 1.1E-83 2.4E-88 679.9 20.9 327 12-409 23-353 (378)
4 COG0585 Uncharacterized conser 100.0 2.8E-79 6E-84 643.5 30.2 341 12-409 26-371 (406)
5 cd02577 PSTD1 PSTD1: Pseudouri 100.0 3.4E-78 7.5E-83 621.5 32.0 259 13-277 5-269 (319)
6 TIGR00094 tRNA_TruD_broad tRNA 100.0 1.7E-74 3.7E-79 611.5 33.2 266 12-281 21-290 (387)
7 PRK00984 truD tRNA pseudouridi 100.0 1.2E-71 2.7E-76 578.4 29.0 285 12-407 21-311 (341)
8 cd02552 PseudoU_synth_TruD_lik 100.0 1.1E-60 2.3E-65 471.8 21.4 165 23-276 24-188 (232)
9 cd02575 PseudoU_synth_EcTruD P 100.0 1.3E-58 2.8E-63 460.3 25.5 204 13-283 5-213 (253)
10 cd01291 PseudoU_synth PseudoU_ 99.2 1.5E-11 3.3E-16 103.9 5.4 43 36-78 1-43 (87)
11 cd01291 PseudoU_synth PseudoU_ 97.1 0.00032 6.9E-09 59.1 2.9 24 496-519 64-87 (87)
12 PRK04099 truB tRNA pseudouridi 74.1 38 0.00082 34.9 11.3 101 33-141 4-105 (273)
13 TIGR00094 tRNA_TruD_broad tRNA 56.7 6 0.00013 42.6 1.7 40 242-281 206-245 (387)
14 PRK00020 truB tRNA pseudouridi 55.6 1.6E+02 0.0035 30.0 11.4 104 33-141 12-116 (244)
15 cd02573 PseudoU_synth_EcTruB P 53.2 1.7E+02 0.0038 30.2 11.6 102 33-141 2-104 (277)
16 PRK04642 truB tRNA pseudouridi 51.4 2E+02 0.0043 30.2 11.7 102 33-141 12-114 (300)
17 cd00506 PseudoU_synth_TruB_lik 50.6 2.3E+02 0.0049 28.1 11.5 101 33-141 2-104 (210)
18 TIGR00431 TruB tRNA pseudourid 50.1 2.2E+02 0.0048 28.2 11.3 101 33-141 4-105 (209)
19 PRK00130 truB tRNA pseudouridi 48.6 2.5E+02 0.0053 29.3 11.9 102 33-141 4-106 (290)
20 COG4483 Uncharacterized protei 47.5 7.5 0.00016 31.3 0.5 15 138-152 8-22 (68)
21 PRK00989 truB tRNA pseudouridi 45.6 3.3E+02 0.0072 27.4 11.9 100 33-141 11-113 (230)
22 PRK01851 truB tRNA pseudouridi 45.2 2.3E+02 0.005 29.7 11.0 101 33-141 18-119 (303)
23 PRK01550 truB tRNA pseudouridi 43.6 3E+02 0.0066 28.8 11.7 102 33-141 4-107 (304)
24 PRK05389 truB tRNA pseudouridi 41.4 3.1E+02 0.0067 28.8 11.4 101 33-141 15-116 (305)
25 PRK14122 tRNA pseudouridine sy 41.4 3.3E+02 0.0072 28.7 11.5 102 33-141 3-105 (312)
26 PRK03287 truB tRNA pseudouridi 41.1 3.5E+02 0.0076 28.3 11.6 102 33-141 11-113 (298)
27 PRK05033 truB tRNA pseudouridi 40.0 3.4E+02 0.0074 28.6 11.4 101 33-141 12-113 (312)
28 PRK02755 truB tRNA pseudouridi 39.7 4.4E+02 0.0094 27.6 12.1 101 33-141 5-106 (295)
29 PRK02484 truB tRNA pseudouridi 39.3 4.1E+02 0.009 27.7 11.9 102 33-141 5-108 (294)
30 PRK14124 tRNA pseudouridine sy 37.8 3.8E+02 0.0082 28.2 11.3 101 33-141 5-106 (308)
31 PRK02193 truB tRNA pseudouridi 34.8 4.9E+02 0.011 27.0 11.4 102 33-141 2-104 (279)
32 PF14559 TPR_19: Tetratricopep 34.6 49 0.0011 25.2 3.3 43 169-211 2-47 (68)
33 PRK01528 truB tRNA pseudouridi 34.2 4.2E+02 0.0091 27.7 10.9 101 33-141 5-106 (292)
34 PRK14846 truB tRNA pseudouridi 33.9 4.7E+02 0.01 28.0 11.3 101 33-141 5-106 (345)
35 PRK14123 tRNA pseudouridine sy 32.1 5.8E+02 0.013 26.8 11.6 102 33-141 5-109 (305)
36 cd02572 PseudoU_synth_hDyskeri 29.9 1.2E+02 0.0026 29.3 5.8 46 33-80 4-50 (182)
37 PRK05090 hypothetical protein; 28.4 60 0.0013 28.2 3.0 43 29-71 31-77 (95)
38 PHA01627 DNA binding protein 23.0 1.2E+02 0.0027 26.9 4.0 44 104-153 4-47 (107)
39 smart00668 CTLH C-terminal to 23.0 81 0.0017 23.5 2.6 20 162-181 5-24 (58)
40 PRK01310 hypothetical protein; 22.8 83 0.0018 27.7 2.9 43 30-72 38-84 (104)
41 KOG2310 DNA repair exonuclease 20.5 34 0.00073 38.5 0.0 18 135-152 139-156 (646)
42 PF00772 DnaB: DnaB-like helic 20.5 1.1E+02 0.0023 25.8 3.1 52 212-266 2-53 (103)
43 PRK01530 hypothetical protein; 20.4 92 0.002 27.5 2.7 56 29-88 38-97 (105)
No 1
>KOG2339 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=6.5e-114 Score=915.60 Aligned_cols=429 Identities=50% Similarity=0.841 Sum_probs=400.4
Q ss_pred cCCCCCCCCCCCcCCCCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHH
Q 009530 10 ERGDNPFDSRGSENWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAA 89 (532)
Q Consensus 10 ~~~~~~~~~~~~~~wp~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ 89 (532)
...+.++|.|+.+.|+.+.+.|+||+|+|+|++|++|++.||+.|+++++.|+|+|+|||||||+|+++|+++.++++..
T Consensus 189 ~K~~~~~d~r~~~~~~~~~~~~~~F~l~kenk~t~ea~g~ia~~L~v~p~~~~~~g~Kdkravt~Qrvsv~k~~~~~l~~ 268 (624)
T KOG2339|consen 189 EKPDKPRDARGAEHWSRETADYCHFTLYKENKDTSEALGLIAKLLNVPPSGVRYAGTKDKRAVTTQRVSVRKVTPERLLA 268 (624)
T ss_pred cccCcchhhhcccccccccccEEEEEEecccCCcHHHHHHHHHHhcCCCCCcChhhhhhhhhccceeeeEEEechhHHHH
Confidence 34668999999999998888899999999999999999999999999999999999999999999999999999999999
Q ss_pred HhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHHHHH
Q 009530 90 LNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATL 169 (532)
Q Consensus 90 ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG~~l 169 (532)
+|..++++.+|+|.|.+..|+||+|+||||+|+||++....++.|.+++++++++|||||||+||||+.++.||.||.+|
T Consensus 269 ln~~lk~~~v~n~~~~~~~l~LGdL~GNrF~IvLR~~~~~~~e~i~~~l~sl~e~GFiNYfG~QRFG~~sv~t~~IG~~l 348 (624)
T KOG2339|consen 269 LNRKLKGIIVGNFIYKDDSLKLGDLKGNRFSIVLRGVRDDSEELIHQALESLKEKGFINYFGLQRFGSNSVRTHEIGLAL 348 (624)
T ss_pred HHHhhhheeeeeeecccchhhhccccCceEEEEeccccccHHHHHHHHHHHHHhccchhhhchhhccccccccchhhHHH
Confidence 99999999999999999999999999999999999999878899999999999999999999999999999999999999
Q ss_pred HhhcHHHHHHHhcCCCCCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhC--CCChHHhhhcCChhHHHH
Q 009530 170 LRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKC--PGNYLQALKAIPRTLRMM 247 (532)
Q Consensus 170 L~g~~~~Av~liL~p~~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~--~~~~~~Al~~iPr~lr~m 247 (532)
|+++|+.|+++||.|.....+ +.+|++.|.+++|+++++..+|+.+.+|++||.+|++. ..||.+|+..|||++|+|
T Consensus 349 l~~~~~~A~~lil~p~~~~~~-v~~a~~~~~~t~da~~~l~~~p~~~~~E~~iL~~ls~~~~~~dy~~A~~~IPRnlRmm 427 (624)
T KOG2339|consen 349 LKRDWEKAIKLILTPRDLDYG-VGEARELWVQTRDAEAALSQLPRFKVAEKAILKCLSKGGKEKDYLQALYGIPRNLRML 427 (624)
T ss_pred HHhHHHHHHhhcccccccccc-chHHHHHHHhcchhhhchhhCchHHHHHHHHHHHHHhcCCcccHHHHHHhcchhhhhh
Confidence 999999999999999988888 99999999999999999999999999999999999764 468999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCccccCcEEEecCCCCcccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCccce
Q 009530 248 YVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDGRHNLV 327 (532)
Q Consensus 248 yvhAYQSylwN~~~S~Ri~~~G~~~vv~GDLV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~v 327 (532)
|+|||||||||.+||+||+.||. +||+||||+..+.. | +.+.+. ..+
T Consensus 428 YvHAYQS~iWN~~aS~RIe~yG~-rvV~GDLV~~~e~~---------------d----------------d~~~~~-~~~ 474 (624)
T KOG2339|consen 428 YVHAYQSLIWNEAASRRIEEYGL-RVVEGDLVCVGEDE---------------D----------------DEPFEG-SKI 474 (624)
T ss_pred hhhhhHHHHHHHHHHHHHHHcCc-cccccceeeccCCc---------------c----------------cccccc-cee
Confidence 99999999999999999999998 58999999986321 1 111111 468
Q ss_pred eeehhhhhcCCCccccceeeecCCCCCCCCcchHHHHHHHHHhhcCCChhhhhhhhhhccccccccccccccccccceeE
Q 009530 328 KTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEW 407 (532)
Q Consensus 328 ~~lt~edi~~~~yti~DVvLPLPG~~v~yP~n~~~~~y~eiL~edGl~~~~~~~~~k~~~~~~l~G~YR~li~~P~dl~~ 407 (532)
++||+||++ +|+|+||||||||++++||.|++++||.++|.++|+++..|++..++|+ ++|+||+++++|.|++|
T Consensus 475 k~vt~ee~~--~Ysi~DVVLPLPG~dv~YPkn~~~~~Y~e~l~~d~ld~~nmr~k~r~~s---l~G~YRk~i~rp~nl~w 549 (624)
T KOG2339|consen 475 KVVTEEEIA--KYSIYDVVLPLPGFDVIYPKNEIAQWYVELLKEDGLDEFNMRHKVRDFS---LSGCYRKMIVRPKNLEW 549 (624)
T ss_pred eEeeccccc--cceeeeEeecCCCcCccccCcHHHHHHHHHHHhcCCChhhccchhhhcc---cchhhHhHhcccccceE
Confidence 999999997 9999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred EEEEecCCCCccccchHHHHhhcccchhhhhhhhhcCCCCCCCCccccccccchhhhcccccchhhhhhhhccCCccccc
Q 009530 408 ELLTYIDGNKPLAETDLDKIAKAKLVNIVKEEEAVCGNKEKDPSDCMKQSESLSKDIKLSTENNEAACAKEVKQPHVESV 487 (532)
Q Consensus 408 ~~~~y~d~~~~l~~tDld~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 487 (532)
++++|+||++||+.||+|+|++..++...
T Consensus 550 ~li~Y~d~~~~l~~tD~D~L~~~~~p~~~--------------------------------------------------- 578 (624)
T KOG2339|consen 550 ELIKYDDPEQPLILTDLDRLENRAIPESA--------------------------------------------------- 578 (624)
T ss_pred EEEecCCcccchhhchhhhhcCCCCCccc---------------------------------------------------
Confidence 99999999999999999999875443311
Q ss_pred cCCCCccceeEEEEEEecCCcchhhHHHHHHhccCccHhhhhccC
Q 009530 488 CGADSQGKQMALKLGLTLPSSCYATMAIRELLKTSTSVAFHKTLN 532 (532)
Q Consensus 488 ~~~~~~~~~~al~l~f~Lp~ssYATmalREl~k~~ts~~~q~~l~ 532 (532)
..|+++||.|+|+||+|||||||||||||+|||+.-|+.||
T Consensus 579 ----e~g~~~Al~l~FsLpss~YATmalRE~lk~dts~~~q~~l~ 619 (624)
T KOG2339|consen 579 ----EKGTYLALLLKFSLPSSAYATMALRELLKTDTSSGDQEMLN 619 (624)
T ss_pred ----cccceeEEEEEeccCchHHHHHHHHHHHhhccccccHhhhh
Confidence 23679999999999999999999999999999999999886
No 2
>cd02576 PseudoU_synth_ScPUS7 PseudoU_synth_ScPUS7: Pseudouridine synthase, TruD family. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Saccharomyces cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in yeast U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
Probab=100.00 E-value=4.3e-89 Score=719.19 Aligned_cols=333 Identities=50% Similarity=0.826 Sum_probs=308.3
Q ss_pred CCCCCCCCCcCCCC----CCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHH
Q 009530 13 DNPFDSRGSENWPE----QLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88 (532)
Q Consensus 13 ~~~~~~~~~~~wp~----~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~ 88 (532)
..|.|+...+.+|. ..|+|++|+|+|+|+||++|++.||+.+||++++|+|||+|||||||+|+|||+++.++++.
T Consensus 8 ~~peDF~V~Ei~~~~~~~~~g~y~~~~L~K~~~~T~~ai~~lar~l~i~~~~i~~AG~KDk~AvT~Q~vsi~~~~~~~l~ 87 (371)
T cd02576 8 QRYSDFVVNEIDLDGSVVHLTDYLHFTLYKENKDTMEAINKIAKLLRVKPSDFSYAGTKDKRAVTVQRVSVKKVTASRLK 87 (371)
T ss_pred CCcccceEEEEcCCCCccCCCCEEEEEEEECCCCHHHHHHHHHHHhCCChhheeecccccccceeEEEEEecCCCHHHHH
Confidence 46888888877754 34678999999999999999999999999999999999999999999999999998888888
Q ss_pred HHhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHHHH
Q 009530 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGAT 168 (532)
Q Consensus 89 ~ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG~~ 168 (532)
.+|.+..+++|+++.|++++|++|+|.||+|+|+||+++....+.++++++.|++.|||||||+||||+.+..||.||++
T Consensus 88 ~~~~~~~~i~i~~~~~~~~~l~~G~l~GN~F~I~lR~v~~~~~~~l~~~l~~l~~~GfpNYFG~QRFG~~~~~~~~iG~~ 167 (371)
T cd02576 88 ALNSKLRGIRVGNFEYKDEPLKLGDLKGNEFTIVIRNVKADSEELIKQALESLKEKGFINYYGLQRFGTFSIPTHEIGIA 167 (371)
T ss_pred HHhccCCCeEEEeeEecCCCcCcccCCCCeEEEEEccCCcccHHHHHHHHHHHHhCCcCCCCccccCCCCCCCcHHHHHH
Confidence 88866688999999999999999999999999999999866678899999999999999999999999988999999999
Q ss_pred HHhhcHHHHHHHhcCCC-CCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhh---CCCChHHhhhcCChhH
Q 009530 169 LLRGEWKSAVKMILDPR-EGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKK---CPGNYLQALKAIPRTL 244 (532)
Q Consensus 169 lL~g~~~~Av~liL~p~-~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~---~~~~~~~Al~~iPr~l 244 (532)
||+|+|++|+++||++. +.+.++..+++++|.++||+++|++.+|+++..|+.+|++|.+ .+++|.+|+..+|+++
T Consensus 168 ll~~~~~~Av~~~l~~~~~~~~~~~~~~r~~~~~~~~~~~~l~~~p~~~~~Er~~l~~l~~~~~~~~~~~~a~~~~p~~~ 247 (371)
T cd02576 168 ILKENWKEAVDLILKPRSELEEGDLVEAREIWKETGDAKAALKKLPRKKVAEKALLRGLSKYGNGPNDYLGAIGSIPRNL 247 (371)
T ss_pred HHhhhHHHHHHHHhCCCcccccHHHHHHHHHHHhcCCHHHHHHhchhhhHHHHHHHHHHHhcCCCcchHHHHHHhcCHHH
Confidence 99999999999999865 6778889999999999999999999999999999999999998 6789999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCccccCcEEEecCCCCcccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCc
Q 009530 245 RMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDGRH 324 (532)
Q Consensus 245 r~myvhAYQSylwN~~~S~Ri~~~G~~~vv~GDLV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~ 324 (532)
|+||+|||||||||++||+||+.+|. +|++||+|+.
T Consensus 248 r~l~i~AyqS~lfN~~lS~Ri~~~g~-~~~~GDlv~~------------------------------------------- 283 (371)
T cd02576 248 RSMYVHAYQSYVWNLAVSKRIKLYGL-KVVEGDLVIV------------------------------------------- 283 (371)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHhcCC-CcccCCEEeE-------------------------------------------
Confidence 99999999999999999999999986 6889998754
Q ss_pred cceeeehhhhhcCCCccccceeeecCCCCCCCCcchHHHHHHHHHhhcCCChhhhhhhhhhccccccccccccccccccc
Q 009530 325 NLVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMD 404 (532)
Q Consensus 325 ~~v~~lt~edi~~~~yti~DVvLPLPG~~v~yP~n~~~~~y~eiL~edGl~~~~~~~~~k~~~~~~l~G~YR~li~~P~d 404 (532)
|+||++||||+++.||.+.++++|.++|+++||++++|.....+++ ++|.||+++++|.|
T Consensus 284 -----------------~~dv~lPl~G~~~~~~~~~~~~~~~~iL~~~gi~~~~f~~~~~~~~---~~g~~R~~~~~p~~ 343 (371)
T cd02576 284 -----------------IYDVVLPLPGHDVIYPSNEIGEWYKEVLSKDGLDPDNMRRKEREFS---LSGGYRKILVKPKN 343 (371)
T ss_pred -----------------ecceEEeCCccCCcCCCcchHHHHHHHHHHcCCCHHHhhccccccc---cCCCcceeEEeccC
Confidence 2358999999999999999999999999999999998875555566 99999999999999
Q ss_pred eeEEE
Q 009530 405 FEWEL 409 (532)
Q Consensus 405 l~~~~ 409 (532)
++|++
T Consensus 344 l~~~~ 348 (371)
T cd02576 344 LEYSF 348 (371)
T ss_pred ceEEE
Confidence 99886
No 3
>PF01142 TruD: tRNA pseudouridine synthase D (TruD); InterPro: IPR001656 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. Pseudouridine synthase TruD modifies uracil-13 in tRNA []. TruD belongs to a recently identified and large family of pseudouridine synthases present in all kingdoms of life []. TruD folds into a V-shaped molecule with an RNA-binding cleft formed between its two domains: a catalytic domain and an insertion domain. The catalytic domain differs in sequence but is structurally very similar to the catalytic domain of other pseudouridine synthases. The insertion (or TRUD) domain displays a novel alpha/beta structure that forms a compact fold titled away from the catalytic domain to form a deep cleft in TruD which is lined with basic residues from each domain. The insertion domain is characterised by two conserved sequence motifs that form a part of the hydrophobic core, as well as by large insertions at several specific sites that are seen in many archaeal and eukaryotic homologues. The insertion domain is likely to be involved in substrate recognition and may represent a RNA binding module []. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 1SB7_B 1SI7_A 1SZW_B 1Z2Z_B.
Probab=100.00 E-value=1.1e-83 Score=679.88 Aligned_cols=327 Identities=46% Similarity=0.751 Sum_probs=241.5
Q ss_pred CCCCCCCCCCc---CCCCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHH
Q 009530 12 GDNPFDSRGSE---NWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88 (532)
Q Consensus 12 ~~~~~~~~~~~---~wp~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~ 88 (532)
...|.|+...+ .+|.+.|+|++|+|+|+|+||++|++.||+.|||++++|+|||+|||||||+|+|||+++.+..+.
T Consensus 23 k~~peDF~V~Ei~~~~~~~~g~~~~~~l~K~~~~T~~a~~~ia~~l~i~~~~i~~aG~KDk~avT~Q~vsv~~~~~~~~~ 102 (378)
T PF01142_consen 23 KQTPEDFIVEEIPDFEPSGEGEYLVFTLEKRNIDTMEAIRIIARKLGISPKDISYAGLKDKRAVTTQYVSVPRVSPERLE 102 (378)
T ss_dssp SSSGGGEEEEEEESS--BS-SSEEEEEEEEESS-HHHHHHHHHHHCTS-CCCEEESS---TTSEEEEEEEEET-SCCHHC
T ss_pred ecCCCCEEEEEecCCCCCCCCCEEEEEEEEcCCCHHHHHHHHHHHhCCChhhceeccccccceeEEEEEEEecCCHHHCC
Confidence 34577777654 467889999999999999999999999999999999999999999999999999999998876643
Q ss_pred HHhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCC-CCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHHH
Q 009530 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVV-DSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGA 167 (532)
Q Consensus 89 ~ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~-~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG~ 167 (532)
.+ .+++|+++.|++++|++|+|.||||+|+||+|.. ...+.+.+++++|+++|||||||+||||+.+++||+||+
T Consensus 103 ~~----~~i~l~~~~~~~~~l~~G~l~GNrF~I~lR~~~~~~~~~~~~~~l~~l~~~Gf~NYfG~QRFG~~~~~th~iG~ 178 (378)
T PF01142_consen 103 NL----EGIRLGDFGYVDKPLRLGDLKGNRFRIVLRDVSDEGDREQIEERLESLKKNGFPNYFGYQRFGSKRPNTHLIGK 178 (378)
T ss_dssp CG----TTEEEEEEEEESS---TT-CCEEEEEEEEECES-HHHHHHHHHHHHHHHHHCEE----CCCC-CCSGHHHHHHH
T ss_pred CC----CCeEEEEEEecCCCCcCCcccCceEEEEEeeccccchHHHHHHHHHHhccCCcccccccccccCCCCCcHHHHH
Confidence 33 4899999999999999999999999999999982 245679999999999999999999999999999999999
Q ss_pred HHHhhcHHHHHHHhcCCCCCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhCCCChHHhhhcCChhHHHH
Q 009530 168 TLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMM 247 (532)
Q Consensus 168 ~lL~g~~~~Av~liL~p~~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~~~~~~~Al~~iPr~lr~m 247 (532)
+||+|+|++| +..+.+. .+++.+...++.+.++.. .+++|..|++.||+++|+|
T Consensus 179 ~ll~~~~~~A---~~~~~~~------~~~~~~~~~~~~~~~~~~-----------------~~~~~~~a~~~ip~~~~~~ 232 (378)
T PF01142_consen 179 ALLKGDWEEA---IGEPEKD------RARKAFLRTNDGDWALCL-----------------SPGDYKGALRAIPRNLRSM 232 (378)
T ss_dssp HHHCT-HHHH---HS---TT------HCHHHHHHH--HHHHHHH-----------------STT-HHHHCTTS-CHHHCH
T ss_pred HHHcCCHHHh---hccccch------hhHHHHHhhccHHHHHhh-----------------CCcchHHHHhhCCHHHHHH
Confidence 9999999999 3222222 445555556665544433 5688999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCccccCcEEEecCCCCcccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCccce
Q 009530 248 YVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDGRHNLV 327 (532)
Q Consensus 248 yvhAYQSylwN~~~S~Ri~~~G~~~vv~GDLV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~v 327 (532)
|||||||||||++||+||+.+|++.|++||+|+..+... .|..+ .+
T Consensus 233 yv~AyQS~lwN~~ls~Ri~~~~~~~~~~GDlv~~~~~~~---------~f~~~-------------------------~~ 278 (378)
T PF01142_consen 233 YVHAYQSYLWNRMLSRRIEEFGLNKVVEGDLVQLSGSGS---------VFVVE-------------------------DV 278 (378)
T ss_dssp HHHHHHHHHHHHHHHHHCCTSSTTS--TT-EEEECTCCE---------EEE-T-------------------------CC
T ss_pred HHHHHHHHHHHHHHHHHhhhcccccccccceEEeecccc---------eEeec-------------------------ch
Confidence 999999999999999999999998899999999865321 11000 00
Q ss_pred eeehhhhhcCCCccccceeeecCCCCCCCCcchHHHHHHHHHhhcCCChhhhhhhhhhccccccccccccccccccceeE
Q 009530 328 KTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFEW 407 (532)
Q Consensus 328 ~~lt~edi~~~~yti~DVvLPLPG~~v~yP~n~~~~~y~eiL~edGl~~~~~~~~~k~~~~~~l~G~YR~li~~P~dl~~ 407 (532)
...+++.+. .+.+ +|++||||+++.||.+.++++|+++|+++||++++|. ..++++ +.|+||+++++|.|++|
T Consensus 279 ~~~~~~~~~--~~~~-~v~lPL~G~~~~~p~~~~~ei~~eIL~eegi~~~~f~-~~~~~~---~~g~~R~l~~~P~dl~~ 351 (378)
T PF01142_consen 279 DDEEEERIK--NGDI-DVVLPLPGYDVRYPDNEVGEIYKEILEEEGIDLEDFK-KLKELS---LKGGYRPLLIKPEDLSW 351 (378)
T ss_dssp HHHHHHHHC--TTSE-EEEEEE-SCS--S--CHHHHHHHHHCCCTCH-GGHCC-CHHHCT----B-EEEESEEE-EEEEE
T ss_pred HHHHHHHHH--hccc-cceEEeeCCCCCCCchHHHHHHHHHHhhcccChhhhh-hhhccC---CCcccCCCcccccccee
Confidence 112344443 3444 7999999999999999999999999999999998877 677787 99999999999999999
Q ss_pred EE
Q 009530 408 EL 409 (532)
Q Consensus 408 ~~ 409 (532)
++
T Consensus 352 ~~ 353 (378)
T PF01142_consen 352 EV 353 (378)
T ss_dssp EE
T ss_pred ee
Confidence 96
No 4
>COG0585 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.8e-79 Score=643.54 Aligned_cols=341 Identities=36% Similarity=0.545 Sum_probs=285.3
Q ss_pred CCCCCCCCCCc---CCCCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEec--CChhh
Q 009530 12 GDNPFDSRGSE---NWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFK--QRASK 86 (532)
Q Consensus 12 ~~~~~~~~~~~---~wp~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~--~~~~~ 86 (532)
...|.|+..++ .||.+.|+|++|.|+|+||||++|++.||+.||||.++|+|||||||||||+|||||+. .....
T Consensus 26 k~~pedF~V~Ei~~~~~~~~G~~~~~~l~K~~~dT~~a~~~iak~lgv~~r~v~yAGlKDk~AVT~Q~vsi~~~~~~~~~ 105 (406)
T COG0585 26 KAEPEDFIVEEILGYEPSGDGEYLLFLLRKRGWDTLDAAREIAKRLGVPRRRVGYAGLKDKRAVTTQYVSIPKPGVELAD 105 (406)
T ss_pred eeCCCccEEEeecCcCCCCCCCEEEEEEEEcCCChHHHHHHHHHHhCCChhhcccccccccceeeEEEEEEEcCCCchhh
Confidence 45577777654 57789999999999999999999999999999999999999999999999999999994 44444
Q ss_pred HHHHhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHH
Q 009530 87 LAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVG 166 (532)
Q Consensus 87 l~~ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG 166 (532)
+..+ .+.++.+.++.+++++|++|+|+||+|+|+||++.. ..+.++++++.+++.|||||||+||||+.+++||.||
T Consensus 106 ~~~~--~~~~~~il~~~~~~~~l~lGdL~GN~F~I~vr~~~~-~~~~~~~~~~~~~~~G~PNYFG~QRFGs~r~~tH~vg 182 (406)
T COG0585 106 LSAF--ELEGLEILELGRHGRKLRLGDLKGNRFEIRLRGVTG-PEEKLEERLELLEEGGFPNYFGLQRFGSFRPNTHIVG 182 (406)
T ss_pred hhhc--ccCCcEEEEeeccCCccccccccCCEEEEEEecCCc-hHhHHHHHHHHHHhCCccccccccccCCCCCCcchhh
Confidence 4333 478899999999999999999999999999999986 4677788888899999999999999999999999999
Q ss_pred HHHHhhcHHHHHHHhcCCCCCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhCCCChHHhhhcCChhHHH
Q 009530 167 ATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRM 246 (532)
Q Consensus 167 ~~lL~g~~~~Av~liL~p~~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~~~~~~~Al~~iPr~lr~ 246 (532)
++||+|||++|++++|.+ ....++| +| |+.+|..+..||.+|..|.++ ++|.+||..+|+++|+
T Consensus 183 k~ll~~~~e~A~~~~l~~-----~~~~~~r-~~---------l~~~p~~l~~Er~~l~~~~~~-~~~~~a~~~~p~~lr~ 246 (406)
T COG0585 183 KLLLRGDWEEAARLYLGS-----EESKEAR-LW---------LERLPKALRYERGELNYLARG-GSYKGAFMVLPRNLRS 246 (406)
T ss_pred hhhhcccHHHHHHHHhhh-----hhhhhhH-HH---------HHhhhHhHHHHHHHHHHHhhc-cchhhhhhccCHHHHH
Confidence 999999999999999987 3345666 44 899999999999999999986 8999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCccccCcEEEecCCCCcccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCccc
Q 009530 247 MYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDGRHNL 326 (532)
Q Consensus 247 myvhAYQSylwN~~~S~Ri~~~G~~~vv~GDLV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~ 326 (532)
||+|||||||||+++|+||+.+.++.+++||+....+... .+.. .. .. .
T Consensus 247 ~fv~AyQSylfNr~ls~Rie~g~~~~~~~gD~~~~~~~~~---------~~~~--------------~~-----~~---~ 295 (406)
T COG0585 247 MFVHAYQSYLFNRILSERIEKGSFNRVVEGDILKLKPDGS---------KFKA--------------VT-----SE---E 295 (406)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCcccccccchhhhcccccc---------hhhh--------------hh-----hh---h
Confidence 9999999999999999999998788899999843332111 1000 00 00 0
Q ss_pred eeeehhhhhcCCCccccceeeecCCCCCCCCcchHHHHHHHHHhhcCCChhhhhhhhhhcccccccccccccccccccee
Q 009530 327 VKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDFE 406 (532)
Q Consensus 327 v~~lt~edi~~~~yti~DVvLPLPG~~v~yP~n~~~~~y~eiL~edGl~~~~~~~~~k~~~~~~l~G~YR~li~~P~dl~ 406 (532)
+..++. .-.....+|++|+||+++.++.+..++++.++|+++|+++..|...-..++ ++|+||.++++|.+++
T Consensus 296 ~~~~~~----~~~~~~~~i~~pl~G~~~~~~~~~~~~ie~~il~ee~~~~~~f~~~~~~~~---~~G~rR~l~~k~~~~~ 368 (406)
T COG0585 296 LNELDE----RVEEGELDITAPLPGYDVPPTSGEAGEIEKEILEEEGLSLELFKREKMPLS---LKGSRRALLLKPQGLS 368 (406)
T ss_pred HHHHHH----HHhccccccccccCCccCCCcCCchhHHHHHHHHhcCCChhHhhccCcccc---CCCccceeeeeccccE
Confidence 000000 011223479999999999999999999999999999999887766433345 8999999999999888
Q ss_pred EEE
Q 009530 407 WEL 409 (532)
Q Consensus 407 ~~~ 409 (532)
|..
T Consensus 369 ~~~ 371 (406)
T COG0585 369 VKE 371 (406)
T ss_pred EEE
Confidence 875
No 5
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=100.00 E-value=3.4e-78 Score=621.50 Aligned_cols=259 Identities=36% Similarity=0.559 Sum_probs=230.2
Q ss_pred CCCCCCCCCcCC---CCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHH
Q 009530 13 DNPFDSRGSENW---PEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAA 89 (532)
Q Consensus 13 ~~~~~~~~~~~w---p~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ 89 (532)
..|.|+...+.- +.+.|+|++|+|+|+|+||++|++.||+.|||++++|+|||+|||||||+|+|||+++.++ ..
T Consensus 5 ~~peDF~V~Ei~~~~~~~~g~y~~f~l~K~n~dT~~ai~~lar~l~i~~~~i~~AG~KDk~AvT~Q~vsv~~~~~~--~~ 82 (319)
T cd02577 5 QYPEDFIVEEITPFDIGKKGKYLIYLLEKKNWDTLDAVRRIAKALGISRKRIGYAGTKDKHAVTTQYISIFDPKDE--EK 82 (319)
T ss_pred CCCCceEEEEecCCCCCCCCCEEEEEEEECCCCHHHHHHHHHHHhCCChhheeeccccccccceEEEEEeeccchh--hc
Confidence 457777765533 4778999999999999999999999999999999999999999999999999999988654 22
Q ss_pred HhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHHHHH
Q 009530 90 LNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATL 169 (532)
Q Consensus 90 ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG~~l 169 (532)
+ .+.++++++++|++++|++|||.||+|+|+||+++....+.++++++.+++.|||||||+||||+.+++||+||++|
T Consensus 83 ~--~~~~~~l~~~~~~~~~l~lG~L~GN~F~I~lR~~~~~~~~~~~~~~~~~~~~GfpNYfG~QRFGs~~~~th~iG~~l 160 (319)
T cd02577 83 L--SIKDIELKVLGRSRKPLRLGDLWGNRFEITVRDLGDEEIERIETLVEEVEKGGFPNYFGSQRFGSVRPVTHFVGKLI 160 (319)
T ss_pred c--ccCCeEEEEEEecCCCCCcccccCCEEEEEEecCCchhHHHHHHHHHHHHhcCCCccccccccCCCCCCcHHHHHHH
Confidence 2 46889999999999999999999999999999998766677889999999999999999999999999999999999
Q ss_pred HhhcHHHHHHHhcC-CCC-CCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhCCCChHHhhhcCChhHHHH
Q 009530 170 LRGEWKSAVKMILD-PRE-GERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMM 247 (532)
Q Consensus 170 L~g~~~~Av~liL~-p~~-~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~~~~~~~Al~~iPr~lr~m 247 (532)
|+|||++|+++||+ |.+ .+..+..+++++|.++||+++||++||+++. |+.+++.+ .++++|.+||+.||+++|+|
T Consensus 161 l~gd~~~Av~~il~~~~~~~~~~~~~~ar~~~~~~gd~~~~l~~~p~~~~-e~~l~~l~-~~~~~y~~Al~~iP~~lr~m 238 (319)
T cd02577 161 LEGDYEEAAKTYLTARYPLEETGDKKRALRLFPKWGDWERCLKEYPTNLE-ERRVKHLL-AEPKDYKGAFLALPKNLRRM 238 (319)
T ss_pred HccCHHHHHHHHhcCCcccccchHHHHHHHHHHhcCCHHHHHHHhhHhHH-HHHHHHHh-hCCccHHHHHHhcCHHHHHH
Confidence 99999999999997 434 3456678899999999999999999999998 66555544 46889999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCC-CccccCc
Q 009530 248 YVHSYQSFLWNHAASARVQKHGT-EHVVVGD 277 (532)
Q Consensus 248 yvhAYQSylwN~~~S~Ri~~~G~-~~vv~GD 277 (532)
|||||||||||++||+||+.+|. ..+++||
T Consensus 239 yvhAYQSylfN~~lS~Ri~~~g~~~~~v~GD 269 (319)
T cd02577 239 FVHAYQSYLFNEILSERIEEGGPLNEAVEGD 269 (319)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCccccCC
Confidence 99999999999999999999873 4567776
No 6
>TIGR00094 tRNA_TruD_broad tRNA pseudouridine synthase, TruD family. MJ11364 is a strong partial match from 50 to 230 aa.
Probab=100.00 E-value=1.7e-74 Score=611.52 Aligned_cols=266 Identities=36% Similarity=0.544 Sum_probs=240.0
Q ss_pred CCCCCCCCCCcCC---CCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHH
Q 009530 12 GDNPFDSRGSENW---PEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLA 88 (532)
Q Consensus 12 ~~~~~~~~~~~~w---p~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~ 88 (532)
...|.|+...+.+ |.+.|+|++|+|+|+|+||++|++.|||.+|||+++|+|||+|||||||+|||||+....+++.
T Consensus 21 k~~peDF~V~E~~~~~~~~~g~~~~~~l~K~~~~T~~a~~~iar~l~i~~~~i~yAG~KDk~AvT~Q~~s~~~~~~~~~~ 100 (387)
T TIGR00094 21 KASPEDFIVEEILGFEPSGEGEFIHIRVEKEGCNTLEVARVLAKFLGVSRREIGFAGTKDKRAVTEQWVCLRVKGEEEPD 100 (387)
T ss_pred ccCccceeEEeecCCCCCCCCCEEEEEEEECCcCHHHHHHHHHHHhCCChhheeecccccccceeEEEEEeccCchhhhh
Confidence 4568888876653 4567999999999999999999999999999999999999999999999999999776554433
Q ss_pred HHhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHHHH
Q 009530 89 ALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGAT 168 (532)
Q Consensus 89 ~ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG~~ 168 (532)
..+..+.+++|+++.|++++|++|+|.||+|+|+||++.. ..+.++++++.|+++|||||||+||||+.+++||+||++
T Consensus 101 ~~~~~~~~~~v~~~~~~~~~l~~G~l~GN~F~I~lR~~~~-~~~~~~~~l~~l~~~GfpNYfG~QRFGs~~~~th~iG~~ 179 (387)
T TIGR00094 101 LSNFQLKGVKILEYNRHNRKIRLGDLKGNRFTIRLREVEP-NGDELEERLNELCKKGFPNYFGAQRFGTFRIITHTVGRE 179 (387)
T ss_pred HhhcccCCcEEEEEEecCCCcCcccCCCCEEEEEEecCCC-CHHHHHHHHHHHHhCCccCCCCCcCCcCCCCCchHHHHH
Confidence 3344578999999999999999999999999999999985 456689999999999999999999999999999999999
Q ss_pred HHhhcHHHHHHHhcC-CCCCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhCCCChHHhhhcCChhHHHH
Q 009530 169 LLRGEWKSAVKMILD-PREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMM 247 (532)
Q Consensus 169 lL~g~~~~Av~liL~-p~~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~~~~~~~Al~~iPr~lr~m 247 (532)
||+|||++|+++++. |.+++.+...++++.|..+ |+..||.++|.++.+|+.+|+++.+++.+|..|++.||+++++|
T Consensus 180 ll~~~~~~a~~~~~~~~~~~~~~~~~~~r~~~~~s-~~~s~l~~~~ls~r~e~~~l~~l~~gd~~~~~a~~~ip~~~~~~ 258 (387)
T TIGR00094 180 LLLSNWKGANLQYALRPLQGETKVSDRARRSFWES-DARSALFNMPVAERYERALLNSVLEGDNSYLAAIMSLPKALRTM 258 (387)
T ss_pred HHhhhHHHHHHHHhcCccccCCHHHHHHHHHHHhc-cHHHHHHhhhHHHHHHHHHHHHHhcCchhHHHHHHhcCHHHHHH
Confidence 999999999999875 6667777778898888777 99999999999999999999999987788999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCccccCcEEEe
Q 009530 248 YVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFC 281 (532)
Q Consensus 248 yvhAYQSylwN~~~S~Ri~~~G~~~vv~GDLV~~ 281 (532)
|+||||||||| ++|+|++.++. .+++||+|+.
T Consensus 259 ~v~ayqs~l~N-~ls~r~~~~~~-~pl~Gd~~~~ 290 (387)
T TIGR00094 259 FVHAYQSYLFN-RASERIELMGT-APLPGDGDIA 290 (387)
T ss_pred HHHHHHHHHHH-HHHHHHHhcCC-CCcCCCcccc
Confidence 99999999999 89999998875 5789999875
No 7
>PRK00984 truD tRNA pseudouridine synthase D; Reviewed
Probab=100.00 E-value=1.2e-71 Score=578.39 Aligned_cols=285 Identities=28% Similarity=0.446 Sum_probs=235.0
Q ss_pred CCCCCCCCCCcC--C-CCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEec--CChhh
Q 009530 12 GDNPFDSRGSEN--W-PEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFK--QRASK 86 (532)
Q Consensus 12 ~~~~~~~~~~~~--w-p~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~--~~~~~ 86 (532)
...|.|+...+. + |.+.|+|++|+|+|+|+||++|++.||+.+||++++|+|||+|||||||+|||||+. ..+++
T Consensus 21 k~~peDF~V~E~~~~~~~~~G~~~~~~l~K~~~~T~~~~~~lar~l~i~~~~i~yAG~KDk~AvT~Q~~si~~~~~~~~~ 100 (341)
T PRK00984 21 KANPEDFVVREILGFEPSGEGEHLLVRIRKRGWNTLFVARALAKFLGISLRDVGYAGLKDRHAVTTQWFSIHLPGKEEPD 100 (341)
T ss_pred ecCccceeEEeccCCCCCCCcCEEEEEEEECCCCHHHHHHHHHHHhCCChhheeecccCcCCeeeEEEEEEECCCCChhh
Confidence 556888887653 3 588899999999999999999999999999999999999999999999999999986 34456
Q ss_pred HHHHhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHH
Q 009530 87 LAALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVG 166 (532)
Q Consensus 87 l~~ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG 166 (532)
+..+ .+.+++|+++.|++++|++|+|.||+|+|+||+|.. +.+.++++++.|++.|||||||+||||+.+
T Consensus 101 ~~~~--~~~~~~i~~~~~~~~~l~~G~l~GN~F~I~lR~~~~-~~~~~~~~l~~l~~~GfpNYfG~QRFG~~~------- 170 (341)
T PRK00984 101 LSAF--QLEGLEILELGRHNRKLRLGDLKGNRFTIRLREVSK-DRDKVEQRLEEIAAGGVPNYFGEQRFGSGG------- 170 (341)
T ss_pred Hhhc--ccCCeEEEEEEccCCCCCCCcCCCCEEEEEEecCCC-CHHHHHHHHHHHHhCCCcCCCCCcCCcCCC-------
Confidence 6655 377899999999999999999999999999999986 578899999999999999999999999874
Q ss_pred HHHHhhcHHHHHHHhcCCCCCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhCCCChHHhhhcCChhHHH
Q 009530 167 ATLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRM 246 (532)
Q Consensus 167 ~~lL~g~~~~Av~liL~p~~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~~~~~~~Al~~iPr~lr~ 246 (532)
+||++|. ++.. .+++.||+++|+
T Consensus 171 -----~n~~~a~------------------~~~~----------------------------------~~~~~~p~~lr~ 193 (341)
T PRK00984 171 -----KNLQEAL------------------RWAN----------------------------------GEKKVLDRNLRS 193 (341)
T ss_pred -----CCHHHHH------------------HHHh----------------------------------cccccCChHHHH
Confidence 6666531 1100 124569999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCC-CccccCcEEEecCCCCcccccCCCCcccccCCCCCCCCCCCCCCCCCCCCCCCcc
Q 009530 247 MYVHSYQSFLWNHAASARVQKHGT-EHVVVGDLVFCKGDDTEKELGCVNPEFEYESSNDADDSSHLDEVPETDHPDGRHN 325 (532)
Q Consensus 247 myvhAYQSylwN~~~S~Ri~~~G~-~~vv~GDLV~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~ 325 (532)
||||||||||||++||+||+.+++ +.+++||+|+..++.. .|..+ +..+..
T Consensus 194 m~vsAyQSyLFN~~Ls~Ri~~~~~~~~~~~GD~v~~~~~~~---------~f~~~-----------------~~~~~~-- 245 (341)
T PRK00984 194 FFLSAAQSYLFNRILSERLEKGLPLNQVLEGDALQLAGRGS---------WFVAE-----------------ELEEEL-- 245 (341)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCcccccCCCeEEecCCCc---------eeecc-----------------cchHHH--
Confidence 999999999999999999999987 6799999998765421 11110 000000
Q ss_pred ceeeehhhhhcCCCccccceeeecCCCCCCCCcchHHHHHHHHHhhcCCChhhhhhhhhhccccccccccccccccccce
Q 009530 326 LVKTVTAADINSGKYTIDDVVLPLPGSRVIYPMNDVAEVYHHLAEKDGINLTESLHNVKEFSITSMTGNYRRVFQKPMDF 405 (532)
Q Consensus 326 ~v~~lt~edi~~~~yti~DVvLPLPG~~v~yP~n~~~~~y~eiL~edGl~~~~~~~~~k~~~~~~l~G~YR~li~~P~dl 405 (532)
...++..|+ ++++||||+++.+|.++++++|+++|+++|+.. ...++++ ++|+||+++++|.|+
T Consensus 246 -~~r~~~~~i--------~~~~PL~G~~~~~~~~~~~~~e~~il~e~~i~~----~~~~~~~---~~g~rR~~~~~p~~l 309 (341)
T PRK00984 246 -QRRLKRGDL--------HITAPLPGSGELGTQGEALAIEQEILAEETALF----ALLGREK---VEGARRAILLYPQNL 309 (341)
T ss_pred -HHHHHcCCc--------ccceeccCCCCcCCCcHHHHHHHHHHhhcchhh----hhhhhcC---CCCcceEEEeecccc
Confidence 112344444 499999999999999999999999999999932 4456666 999999999999999
Q ss_pred eE
Q 009530 406 EW 407 (532)
Q Consensus 406 ~~ 407 (532)
+|
T Consensus 310 ~~ 311 (341)
T PRK00984 310 SW 311 (341)
T ss_pred eE
Confidence 98
No 8
>cd02552 PseudoU_synth_TruD_like PseudoU_synth_TruD_like: Pseudouridine synthase, TruD family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruD and Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD and S. cerevisiae Pus7 make psi13 in cytoplasmic tRNAs. In addition S. cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA) and psi35 in pre-tRNATyr. Psi35 in U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35.
Probab=100.00 E-value=1.1e-60 Score=471.81 Aligned_cols=165 Identities=54% Similarity=0.862 Sum_probs=148.3
Q ss_pred CCCCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccE
Q 009530 23 NWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDF 102 (532)
Q Consensus 23 ~wp~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~ 102 (532)
.||.+.|+|++|+|+|+|+||++|++.||+.+||++++|+|||+|||||||+|||||+.+.+.++...+....+++|+++
T Consensus 24 ~~~~~~G~~~~~~l~K~~~~T~~a~~~la~~l~i~~~~i~yAG~KDk~AvT~Q~~sv~~~~~~~~~~~~~~~~~~~v~~~ 103 (232)
T cd02552 24 LWPKGEGEYLHFTLYKENKDTMEALREIAKALGVPPRDIGYAGTKDKRAVTTQRVSVHKPGKERLALLNLELKGIRILEF 103 (232)
T ss_pred cccCCCCCEEEEEEEECCCCHHHHHHHHHHHcCCCHHHEeEcccccCceeeEEEEEEECCcccccchhhcccCCeEEEEE
Confidence 37779999999999999999999999999999999999999999999999999999998876665334445789999999
Q ss_pred EEeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHHHHHHhhcHHHHHHHhc
Q 009530 103 CYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGATLLRGEWKSAVKMIL 182 (532)
Q Consensus 103 ~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG~~lL~g~~~~Av~liL 182 (532)
.|++++|++|+|.||+|+|+||++.......++++++.++++|||||||+||||
T Consensus 104 ~~~~~~L~~G~l~GN~F~I~lR~~~~~~~~~~~~~l~~l~~~GfpNYFG~QRFG-------------------------- 157 (232)
T cd02552 104 GRHDKKLRLGDLKGNRFTITLRGVSPEEDELIERRLESLKEKGFPNYFGLQRFG-------------------------- 157 (232)
T ss_pred EEeCCCCCcCccCCCEEEEEECCCCchHHHHHHHHHHHHHhCCcccccchhcCc--------------------------
Confidence 999999999999999999999999865444446899999999999999999999
Q ss_pred CCCCCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhCCCChHHhhhcCChhHHHHHHHHHHHHHHHHHHH
Q 009530 183 DPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAAS 262 (532)
Q Consensus 183 ~p~~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~~~~~~~Al~~iPr~lr~myvhAYQSylwN~~~S 262 (532)
+||+|||||||||+++|
T Consensus 158 ---------------------------------------------------------------~~~~sA~qS~lfN~~ls 174 (232)
T cd02552 158 ---------------------------------------------------------------SMYLHAYQSYLFNEVLS 174 (232)
T ss_pred ---------------------------------------------------------------ChHHHHHHHHHHHHHHH
Confidence 59999999999999999
Q ss_pred HHHHhcCCCccccC
Q 009530 263 ARVQKHGTEHVVVG 276 (532)
Q Consensus 263 ~Ri~~~G~~~vv~G 276 (532)
+||+.++++.+++|
T Consensus 175 ~Ri~~~~~~~~~~G 188 (232)
T cd02552 175 ERIELYGFNRVVEG 188 (232)
T ss_pred HHHHhcCCCccccC
Confidence 99999886555433
No 9
>cd02575 PseudoU_synth_EcTruD PseudoU_synth_EcTruD: Pseudouridine synthase, TruD family. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs.
Probab=100.00 E-value=1.3e-58 Score=460.35 Aligned_cols=204 Identities=34% Similarity=0.517 Sum_probs=177.9
Q ss_pred CCCCCCCCCc---CCCCCCCCEEEEEEEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecC--ChhhH
Q 009530 13 DNPFDSRGSE---NWPEQLGKFLRFHLYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQ--RASKL 87 (532)
Q Consensus 13 ~~~~~~~~~~---~wp~~~g~y~~f~L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~--~~~~l 87 (532)
..|.|....+ .+|.+.|+|++|+|+|+|+||++|++.||+.+||++++|+|||+|||||||+|||||+.+ ..+.+
T Consensus 5 ~~peDF~V~Ei~~~~~~g~Ge~l~~~l~K~~~~T~~ai~~LAr~lgi~~~~igyAGlKDk~AvT~Q~~sv~~~~~~~~~~ 84 (253)
T cd02575 5 ATPEDFQVEEVLGYEPSGEGEHLLLHIRKTGLNTREVAKELAKALGVKERDVGYAGLKDRHAVTTQWFSVHLPGKEAPDL 84 (253)
T ss_pred CCCcccEEEeecCCCcCCCCCEEEEEEEECCCCHHHHHHHHHHHhCCChhheeecccccCceeeEEEEEEEcCccCchhH
Confidence 4577776654 568999999999999999999999999999999999999999999999999999999873 34455
Q ss_pred HHHhccCCCeEEccEEEeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCCCcCCCCCChHHHHH
Q 009530 88 AALNKRLIGIRLGDFCYVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQRFGSGSVPTHLVGA 167 (532)
Q Consensus 88 ~~ln~~l~~i~vg~~~~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~QRFGs~~~~th~iG~ 167 (532)
..++ +.+++|+++.|++++|++|+|.||+|+|+||++. .+.+.++++++.|++.|||||||+||||+.+ .+|.+|+
T Consensus 85 ~~~~--~~~i~i~~~~~~~~kL~~G~L~GNrF~I~lR~v~-~~~~~l~~~l~~i~~~GfpNYFG~QRFG~~g-~n~~~g~ 160 (253)
T cd02575 85 SALQ--LEGVKILEVTRHNRKLRRGHLKGNRFVIRLRGVS-GNADKLEQRLETIAQKGVPNYFGPQRFGRDG-GNLLQGL 160 (253)
T ss_pred Hhcc--CCCeEEEEEEecCCCcCCCcccCCEEEEEEecCC-CCHHHHHHHHHHHHhCCccCCCcCCCCCCCC-CCHHHHH
Confidence 5554 6789999999999999999999999999999998 3567899999999999999999999999864 5677777
Q ss_pred HHHhhcHHHHHHHhcCCCCCCchhHHHHHHHHHhcCCHHHHHHhCCcchHHHHHHHHHHhhCCCChHHhhhcCChhHHHH
Q 009530 168 TLLRGEWKSAVKMILDPREGERNEISKAREYYKETDDIDGTLRKLPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMM 247 (532)
Q Consensus 168 ~lL~g~~~~Av~liL~p~~~~~~~~~~ar~~~~~~gd~~~al~~~p~~~~~Er~iL~~L~~~~~~~~~Al~~iPr~lr~m 247 (532)
+++.+++. ..|+++|.|
T Consensus 161 ~~~~~~~~---------------------------------------------------------------~~~~~l~~~ 177 (253)
T cd02575 161 RLLAGERK---------------------------------------------------------------VRDRNKRSF 177 (253)
T ss_pred HHhcCCcc---------------------------------------------------------------cCChhHhhh
Confidence 77665421 146789999
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCccccCcEEEecC
Q 009530 248 YVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFCKG 283 (532)
Q Consensus 248 yvhAYQSylwN~~~S~Ri~~~G~~~vv~GDLV~~~~ 283 (532)
|||||||||||++||+||+...++.+++||+|+..+
T Consensus 178 ~lsA~qS~lFN~~Ls~Ri~~~~~~~~~~GD~~~~~~ 213 (253)
T cd02575 178 LLSAARSYLFNRVLSERLEQGSWNRVLDGDVLQLAG 213 (253)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCcccCCCEEEEcC
Confidence 999999999999999999987778899999988753
No 10
>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=99.21 E-value=1.5e-11 Score=103.90 Aligned_cols=43 Identities=53% Similarity=0.812 Sum_probs=42.0
Q ss_pred EEEcccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEE
Q 009530 36 LYKENKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVT 78 (532)
Q Consensus 36 L~K~n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vs 78 (532)
|+|.|++|.+++..+++.++++++.|+|||+|||+|+|+|+||
T Consensus 1 l~K~~~~t~~~~~~~~~~~~~~~~~i~~aG~kDk~a~t~q~v~ 43 (87)
T cd01291 1 LYKPGGDTMEAARQLAKLLGIPPKRVGYAGRKDKRAVTTQLVS 43 (87)
T ss_pred CCCCCCChHHHHHHHHHHhCCChheEEECccCCCCeeEEEEEc
Confidence 5799999999999999999999999999999999999999999
No 11
>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=97.13 E-value=0.00032 Score=59.15 Aligned_cols=24 Identities=54% Similarity=0.703 Sum_probs=22.5
Q ss_pred eeEEEEEEecCCcchhhHHHHHHh
Q 009530 496 QMALKLGLTLPSSCYATMAIRELL 519 (532)
Q Consensus 496 ~~al~l~f~Lp~ssYATmalREl~ 519 (532)
+.+++|+|+||+|+||||+||||+
T Consensus 64 ~~~~~l~f~l~~~~yat~~l~el~ 87 (87)
T cd01291 64 KRALVLEFTLPRGSYATMLLRELG 87 (87)
T ss_pred cceEEEEEEcCCcchHHHHHHHhC
Confidence 579999999999999999999986
No 12
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=74.14 E-value=38 Score=34.93 Aligned_cols=101 Identities=17% Similarity=0.128 Sum_probs=63.6
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.|.+.|- |++..++++.|.|.+++ +.++++||=|..|.-+=-|++-+- .++...-.......++.+.+-... ..
T Consensus 4 il~vdKP~g~tS~~vv~~ikk~~~~--kKvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~~~K~Y~a~~~lG~~T-dT 78 (273)
T PRK04099 4 LFVANKPAGMSSNAFLSRLKRKYGV--KKAGFSGTLDPFAKGVLIVAFGQY--TKLFRFLKKTPKTYRATLWLGASS-PS 78 (273)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCC--CccccCccCCCCCeeEEEEEEChH--hhhHHHhccCCceEEEEEEECCcc-cC
Confidence 5677776 99999999999999976 479999999999988888888543 344333111122222222221111 12
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
.|..| .+...++..-+.+.++++++++
T Consensus 79 ~D~e~---i~~~~~~~~~~~~~i~~~l~~f 105 (273)
T PRK04099 79 LDIEN---IESIQIIKPFDKDLIEKILKSL 105 (273)
T ss_pred CCCcc---eEEeccCCCCCHHHHHHHHHhC
Confidence 36665 3444444333567778777776
No 13
>TIGR00094 tRNA_TruD_broad tRNA pseudouridine synthase, TruD family. MJ11364 is a strong partial match from 50 to 230 aa.
Probab=56.67 E-value=6 Score=42.57 Aligned_cols=40 Identities=23% Similarity=0.316 Sum_probs=32.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhcCCCccccCcEEEe
Q 009530 242 RTLRMMYVHSYQSFLWNHAASARVQKHGTEHVVVGDLVFC 281 (532)
Q Consensus 242 r~lr~myvhAYQSylwN~~~S~Ri~~~G~~~vv~GDLV~~ 281 (532)
+..+.++.++|||+++|..+|.|+++.-++.++.||..+.
T Consensus 206 ~~r~~~~~s~~~s~l~~~~ls~r~e~~~l~~l~~gd~~~~ 245 (387)
T TIGR00094 206 RARRSFWESDARSALFNMPVAERYERALLNSVLEGDNSYL 245 (387)
T ss_pred HHHHHHHhccHHHHHHhhhHHHHHHHHHHHHHhcCchhHH
Confidence 4557789999999999999999999876677778875544
No 14
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=55.63 E-value=1.6e+02 Score=29.95 Aligned_cols=104 Identities=13% Similarity=0.083 Sum_probs=62.1
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++.++++..+.|.++++ .++.+||=|..|--+=-|++-+. .++...-.......+..+.+-. .=--
T Consensus 12 il~vdKP~G~TS~dvv~~vkr~~~~k--KvGH~GTLDP~AtGvLiv~iG~a--TKl~~~l~~~~K~Y~a~~~lG~-~TdT 86 (244)
T PRK00020 12 VLLLDKPVGLSSNHALQRAKRTVDAA--KAGHTGTLDPFATGLLVCCMGRA--TKISGRMLEADKTYQATLQFGE-ETDS 86 (244)
T ss_pred EEEEecCCCCCHHHHHHHHHHHhCCC--CCCcCCcCCCcCeeEEEEEECHH--hhhhHHhccCCcEEEEEEEeCC-cccC
Confidence 5677775 999999999999999874 99999999999988888877432 2333321111122222222211 1134
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+--...--....-+.+.+++.+.++
T Consensus 87 ~D~~G~v~~~~~~~~~~it~e~l~~~l~~f 116 (244)
T PRK00020 87 GDLTGHIVARAPDGFAGVEEAALRDVLSRF 116 (244)
T ss_pred CCCCCcEEEeccCccCCCCHHHHHHHHHhc
Confidence 677886433221111112356677766665
No 15
>cd02573 PseudoU_synth_EcTruB PseudoU_synth_EcTruB: Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine.
Probab=53.19 E-value=1.7e+02 Score=30.16 Aligned_cols=102 Identities=14% Similarity=0.097 Sum_probs=62.5
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++..++++.+.+.++.+ .++.+||=|..|--+=-|+|-+. .++...-.......+..+.+-. .=..
T Consensus 2 il~i~KP~G~tS~~vv~~vr~~~~~k--KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~~~K~Y~~~~~~G~-~TdT 76 (277)
T cd02573 2 ILLLDKPAGLTSHDVVQKVRRLLGTK--KVGHTGTLDPLATGVLPIALGEA--TKLSQYLLDADKTYRATVRLGE-ATDT 76 (277)
T ss_pred EEEEECCCCCCHHHHHHHHHHHhCcC--ccCCCCCCCCcCeEEEEEEEChH--HhhHHHhcCCCcEEEEEEEECC-cccC
Confidence 3566775 999999999999999975 79999999999988888877432 3443331111222222222211 1134
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+-..- .++..-+.+.+++.++++
T Consensus 77 ~D~~G~v~~~--~~~~~~~~~~i~~~l~~f 104 (277)
T cd02573 77 DDAEGEIIET--SPPPRLTEEEIEAALKAF 104 (277)
T ss_pred CCCCCCEEEe--cCCCCCCHHHHHHHHHHc
Confidence 6788864322 122222466777777766
No 16
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=51.39 E-value=2e+02 Score=30.18 Aligned_cols=102 Identities=18% Similarity=0.064 Sum_probs=64.5
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.+.|- |++..++++.+-|.++++ .++.+||=|..|--+=-|++-+ +.++...-.......++.+.+-- .=..
T Consensus 12 il~i~KP~G~TS~dvv~~vrr~~~~k--KvGH~GTLDP~AtGvL~v~~G~--aTkl~~~l~~~~K~Y~a~~~lG~-~TdT 86 (300)
T PRK04642 12 ILLLDKPAGLSSNNALQAARRLLRAE--KGGHTGSLDPLATGLLPLCFGE--ATKIAGLLLGSAKAYDAEIVLGV-TTDT 86 (300)
T ss_pred EEEEecCCCCCHHHHHHHHHHHhCCC--cccCCCccCCcCeeeEEEEECh--hhhhhHHhcCCCcEEEEEEEECc-cccC
Confidence 6677775 999999999999999875 7999999999998888888743 23444332111222222222111 1134
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+-. .-.++..-+.+.+++++.++
T Consensus 87 ~D~~G~v~--~~~~~~~~~~~~l~~~l~~f 114 (300)
T PRK04642 87 DDADGQVL--RERPVPDLSAAALQAALAPL 114 (300)
T ss_pred cCCCCCEE--EecCCCCCCHHHHHHHHHHC
Confidence 78888743 22333222466777777766
No 17
>cd00506 PseudoU_synth_TruB_like PseudoU_synth_TruB: Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dysker
Probab=50.60 E-value=2.3e+02 Score=28.10 Aligned_cols=101 Identities=14% Similarity=0.041 Sum_probs=62.0
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHH-HhccCCCeEEccEEEeecCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAA-LNKRLIGIRLGDFCYVKEGLL 110 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~-ln~~l~~i~vg~~~~~~~~L~ 110 (532)
.+.++|- |++..+++..|.+.+++ +.++.+||=|..|--+=-|.|-+. .++.. +.. .....+..+.+-. .=.
T Consensus 2 il~i~KP~g~tS~~vv~~ik~~~~~--kKvGH~GTLDP~AsGvLiv~vG~a--Tkl~~~~~~-~~K~Y~~~~~lG~-~Td 75 (210)
T cd00506 2 LFAVDKPQGPSSHDVVDTIRRIFLA--EKVGHGGTLDPFATGVLVVGIGKA--TKLLKHLLA-ATKDYTAIGRLGQ-ATD 75 (210)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHhCc--cccCCCCcCCCcCeeEEEEEECHH--HhhhHHHhc-CCceEEEEEEECC-cCC
Confidence 3567775 99999999999999987 489999999999988777777432 23322 221 2222222222211 113
Q ss_pred CCCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 111 LGQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 111 lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
.+|..|+-- .-.+...-+.+.+++.+.++
T Consensus 76 T~D~~G~v~--~~~~~~~it~e~l~~~l~~f 104 (210)
T cd00506 76 TFDATGQVI--EETPYDHITHEQLERALETL 104 (210)
T ss_pred CCCCCCCEE--EEeCCCCCCHHHHHHHHHHC
Confidence 467777632 22233222466777777766
No 18
>TIGR00431 TruB tRNA pseudouridine 55 synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop (not the anticodon loop - beware mis-annotation in Swiss-Prot) of most tRNAs of all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific
Probab=50.13 E-value=2.2e+02 Score=28.22 Aligned_cols=101 Identities=18% Similarity=0.108 Sum_probs=62.5
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++..++++.+.+.++++ .++.+||=|..|--+=-|.+-... ++...-.......+..+.+-. .=.-
T Consensus 4 ~l~v~KP~g~tS~~vv~~vkk~~~~k--KvGH~GTLDP~AsGvLiv~vG~~T--kl~~~~~~~~K~Y~~~~~~G~-~TdT 78 (209)
T TIGR00431 4 VLLLDKPQGMTSFDALAKVRRLLNVK--KVGHTGTLDPFATGVLPILVGKAT--KLSPYLTDLDKEYRAEIRLGV-RTDT 78 (209)
T ss_pred EEEEECCCCCCHHHHHHHHHHHhCCC--cCCCCCCCCCcCceEEEEEEChHh--hhhHHHcCCCCeEEEEEEECC-cCCC
Confidence 5677886 999999999999999875 889999999999888888774322 333321111222222222211 1124
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+-- .-.++.. ..+.+++.+.++
T Consensus 79 ~D~~G~i~--~~~~~~~-~~~~l~~~l~~f 105 (209)
T TIGR00431 79 LDPDGQIV--ETRPVNP-TTEDVEAALPTF 105 (209)
T ss_pred CCCCCCEE--EecCCCC-CHHHHHHHHHHc
Confidence 66777633 2233332 456677777766
No 19
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=48.60 E-value=2.5e+02 Score=29.30 Aligned_cols=102 Identities=16% Similarity=0.069 Sum_probs=62.7
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++..+++..+.|.++.+ .++.+||=|..|--+=-|++-+. .++...-.......+..+.+-. .=.-
T Consensus 4 il~i~KP~G~tS~dvv~~vrr~~~~k--KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~~~K~Y~a~~~lG~-~TdT 78 (290)
T PRK00130 4 ILNILKPPGMTSFDVVRKIRKIAKIK--KVGHTGTLDPLASGVLPVCLGKA--TKIVDYLMEGKKTYRAEIKLGV-ETDT 78 (290)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCC--ccCcCCCCCCCCeeEEEEEEChh--hhhHHHhccCCcEEEEEEEECC-cccC
Confidence 4566665 999999999999999875 89999999999988888887442 3443331111122222221111 1124
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+-.. -.++..-+.+.+++.+.++
T Consensus 79 ~D~~G~i~~--~~~~~~~t~~~l~~~l~~f 106 (290)
T PRK00130 79 YDREGEILK--EKEVSHLTEEEIREAILSF 106 (290)
T ss_pred CCCCCCEEE--ecCCCCCCHHHHHHHHHHc
Confidence 678887432 2233222466777777766
No 20
>COG4483 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.51 E-value=7.5 Score=31.29 Aligned_cols=15 Identities=40% Similarity=0.658 Sum_probs=12.1
Q ss_pred HHhhccccccccccC
Q 009530 138 ANSLGRNGFINYFGL 152 (532)
Q Consensus 138 l~~l~~~GFiNYFG~ 152 (532)
-+-|+..|||+|||-
T Consensus 8 qQlLK~~G~ivyfg~ 22 (68)
T COG4483 8 QQLLKKFGIIVYFGK 22 (68)
T ss_pred HHHHHHCCeeeecCC
Confidence 355789999999974
No 21
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=45.60 E-value=3.3e+02 Score=27.41 Aligned_cols=100 Identities=11% Similarity=0.042 Sum_probs=61.7
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEE--EeecCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFC--YVKEGL 109 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~--~~~~~L 109 (532)
.+.++|- |++.+++++.|.|.++++ .++.+||=|..|--+=-|.|-+. ..++..+-.......+..+. +..
T Consensus 11 ~l~i~KP~g~TS~dvv~~ikk~~~~k--KvGH~GTLDP~AtGvLiv~vG~~-aTkl~~~~~~~~K~Y~~~~~~G~~T--- 84 (230)
T PRK00989 11 ILLVDKPQGRTSFSLIRSLTKLIGVK--KIGHAGTLDPFATGVMVMLIGRK-FTRLSDILLFEDKEYAAVAHLGTTT--- 84 (230)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCC--cCCcCccCCCCCeeEEEEEECCc-hhhhHHHhcCCCcEEEEEEEECCcc---
Confidence 6677775 999999999999999875 89999999999988888877431 23444432112222222222 211
Q ss_pred CCCCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 110 LLGQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 110 ~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
.-.|..|.--.- .+.. .+.+.+++.+.++
T Consensus 85 dT~D~~G~vi~~--~~~~-~~~~~i~~~l~~f 113 (230)
T PRK00989 85 DSYDCDGKIVGR--SKKI-PTLEEVLSAASYF 113 (230)
T ss_pred cCCCCCCcEEEe--cCCC-CCHHHHHHHHHhC
Confidence 235666753221 1221 2456677777665
No 22
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=45.16 E-value=2.3e+02 Score=29.74 Aligned_cols=101 Identities=15% Similarity=0.059 Sum_probs=63.8
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++..+++..+-|.++.+ .++.+||=|..|--+=-|+|-+. .++...-.......+..+.+-. .=.-
T Consensus 18 il~i~KP~G~TS~dvv~~vrr~l~~k--KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~~~K~Y~~~~~lG~-~TdT 92 (303)
T PRK01851 18 VLLLDKPLGLSSNDALQRAKRLLRAK--KAGHTGTLDPLATGLLPLCFGEA--TKFSQDLLDADKTYEATLRLGV-RTST 92 (303)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCcc--cCCCCCCCCCCCceEEEEEECHH--HhhhHHhcccCeEEEEEEEECC-ccCC
Confidence 6777775 999999999999999874 89999999999988888887432 3443331111112222222111 1124
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+-.. -.++. -+.+.+++.+.++
T Consensus 93 ~D~~G~v~~--~~~~~-~t~~~i~~~l~~f 119 (303)
T PRK01851 93 GDAEGEVLA--TRPVD-CDPAALEAALARF 119 (303)
T ss_pred CCCCCCEEe--ecCCC-CCHHHHHHHHHhc
Confidence 677886432 22333 2467778777776
No 23
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=43.57 E-value=3e+02 Score=28.83 Aligned_cols=102 Identities=18% Similarity=0.105 Sum_probs=63.2
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.+.|- |++.++++..+.|.++.+ .++.+||=|..|--+=-|++-+. .++...-.......+..+.+-. .=-.
T Consensus 4 il~i~KP~G~TS~dvv~~vrr~~~~k--KvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~~~K~Y~a~~~lG~-~TdT 78 (304)
T PRK01550 4 VLLLHKPRGMTSHDCVFKLRKILRTK--KVGHTGTLDPEVSGVLPICVGRA--TKIAEYLTDEGKTYEGEVTLGF-STTT 78 (304)
T ss_pred EEEEECCCCCCHHHHHHHHHHHcCCC--CcccCCCCCCcCeeEEEEEEChh--hhhhHHhcCCCcEEEEEEEECC-cccC
Confidence 4566775 999999999999999864 89999999999988888887543 3444332111222222222111 1124
Q ss_pred CCCCCCEEEEEEecCCC-CCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVV-DSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~-~~~~~i~~~l~~l 141 (532)
+|..|+-- .-.++.. -+.+.+++.+.++
T Consensus 79 ~D~~G~v~--~~~~~~~~~~~~~i~~~l~~f 107 (304)
T PRK01550 79 EDADGEVV--ETKPVDRPITREEIEAALASL 107 (304)
T ss_pred CCCCCCEE--eeccCCCCCCHHHHHHHHHhc
Confidence 67778643 2333321 2466777777766
No 24
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=41.44 E-value=3.1e+02 Score=28.80 Aligned_cols=101 Identities=15% Similarity=0.083 Sum_probs=63.4
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++.++++..+.+.++++ .++.+||=|..|--+=-|+|-+. .++...-.......+..+.+-. .=..
T Consensus 15 il~i~KP~G~TS~dvv~~vrk~~~~k--KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~~~K~Y~a~~~lG~-~TdT 89 (305)
T PRK05389 15 WLILDKPAGMTSTEAVSKVKWLFDAQ--KAGHAGTLDPLASGVLPIALGEA--TKTVPYVMDGTKRYRFTVAWGE-ERDT 89 (305)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhccc--ccCCcccCCCCCceEEEEEEChh--hhhhHHhccCCcEEEEEEEECC-cccC
Confidence 6677775 999999999999999874 79999999999988888887542 3443331111122222222211 1134
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+--.- .++. -+.+.+++++.++
T Consensus 90 ~D~~G~v~~~--~~~~-~~~~~i~~~l~~f 116 (305)
T PRK05389 90 DDLEGEVTAT--SDVR-PTDEEIRAALPAF 116 (305)
T ss_pred CCCCCCEEEe--cCCC-CCHHHHHHHHHhc
Confidence 6778874332 2332 2466777777766
No 25
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=41.39 E-value=3.3e+02 Score=28.72 Aligned_cols=102 Identities=14% Similarity=0.037 Sum_probs=61.2
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++.+++++.+-|.++++ .++.+||=|..|--+=-|+|-+.. ++...-.......+..+.+-. .=..
T Consensus 3 il~idKP~G~TS~dvv~~vrr~l~~k--KvGH~GTLDP~AtGvL~i~iG~aT--Kl~~~l~~~~K~Y~a~~~lG~-~TdT 77 (312)
T PRK14122 3 VYAVDKPLGLTSHDVVNRARRALGTR--RVGHTGTLDPLATGVLVLCTDDST--KLVPFLSAEDKEYLAWVSFGA-TTPT 77 (312)
T ss_pred EEEEECCCCCCHHHHHHHHHHHhCCC--CCCCCCCCCCcCeeeEEEEEChhh--hhhHHhcCCCceEEEEEEECC-cCCC
Confidence 4567775 999999999999999874 899999999999888888875432 333321111112222111101 1124
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+-- .-.++..-+.+.+++.+.++
T Consensus 78 ~D~eG~i~--~~~~~~~~~~~~l~~~l~~f 105 (312)
T PRK14122 78 LDAEGPIS--EEAPVSPLDEKDLEAALPGF 105 (312)
T ss_pred CCCCCCEE--EecCCCCCCHHHHHHHHHhC
Confidence 67777532 22233222456667666655
No 26
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=41.08 E-value=3.5e+02 Score=28.31 Aligned_cols=102 Identities=14% Similarity=0.110 Sum_probs=62.3
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++..++++.+.+.++.+ .++.+||=|..|--+=-|++-+. .++...-.......+..+.+-. .=.-
T Consensus 11 il~i~KP~G~TS~dvv~~vrr~~~~k--KvGH~GTLDP~AtGvL~i~vG~a--TKl~~~l~~~~K~Y~a~~~lG~-~TdT 85 (298)
T PRK03287 11 LVVVDKPAGMTSHDVVARCRRLFGTR--KVGHAGTLDPMATGVLVLGVERA--TKLLGHLTLTDKSYTATIRLGQ-ATTT 85 (298)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCC--CCCcCccCCCcceeEEEEEeChh--hhhhHHHhcCCcEEEEEEEeCc-cccC
Confidence 6777775 999999999999999874 89999999999988888887532 2333321111112222111100 1123
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+-.. -.++..-+.+.+++.+.++
T Consensus 86 ~D~~G~v~~--~~~~~~it~~~i~~~l~~f 113 (298)
T PRK03287 86 DDAEGEVLA--SADASAVTDEAIAAAVAAL 113 (298)
T ss_pred CCCCCCEEe--ecCCCCCCHHHHHHHHHhC
Confidence 577775332 1222222466777777766
No 27
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=40.02 E-value=3.4e+02 Score=28.59 Aligned_cols=101 Identities=13% Similarity=0.056 Sum_probs=63.6
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++..+++..+-+.+++ +.++.+||=|..|--+=-|+|-+. .++...-.......+..+.+-. .=..
T Consensus 12 il~i~KP~G~TS~dvv~~vrr~l~~--kKvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~~~~~~K~Y~a~~~lG~-~TdT 86 (312)
T PRK05033 12 VLLLDKPQGMSSNDALQKVKRLFNA--NKAGHTGALDPLATGMLPICLGEA--TKFSQYLLDSDKRYRVTARLGQ-RTDT 86 (312)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCC--CCCCCCCcCCCcCeeEEEEEECHH--hhhhHHhcCCCcEEEEEEEECC-cccC
Confidence 6677775 99999999999999986 489999999999988888887432 3444331111222222222111 1124
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+-.. -.++. -+.+.+++.+.++
T Consensus 87 ~D~~G~v~~--~~~~~-~t~~~l~~~l~~f 113 (312)
T PRK05033 87 SDADGEVVE--ERPVT-LSAEQLEAALEKF 113 (312)
T ss_pred CCCCCCEEE--eecCC-CCHHHHHHHHHHC
Confidence 677886432 23343 2467777777765
No 28
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=39.69 E-value=4.4e+02 Score=27.57 Aligned_cols=101 Identities=14% Similarity=0.126 Sum_probs=62.5
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.+.|- |++.++++..+-|.++++ .++.+||=|..|--+=-|++-+.. ++...-.. ....+..+.+-.. =..
T Consensus 5 il~i~KP~G~TS~dvv~~vrr~~~~k--KvGH~GTLDP~AtGvL~i~vG~aT--kl~~~l~~-~K~Y~a~~~lG~~-TdT 78 (295)
T PRK02755 5 FLNLDKPAGLTSHDCVARLRRLLRLK--RVGHGGTLDPAATGVLPIALGKAT--RLLPYLPG-EKTYRGTIRFGVR-TST 78 (295)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCC--ccccCCCCCCcCeeEEEEEEChhh--hhHHHhCC-CcEEEEEEEECCc-ccC
Confidence 5667775 999999999999999985 799999999999888888885432 44332111 1222222222111 124
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+--.- .++..-+.+.+++.+.++
T Consensus 79 ~D~~G~v~~~--~~~~~~~~~~l~~~l~~f 106 (295)
T PRK02755 79 DDLQGEILSS--QPWPHLSLAEIETALPQF 106 (295)
T ss_pred CCCCCCEEEe--cCCCCCCHHHHHHHHHhc
Confidence 6777764322 222222456677777665
No 29
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=39.35 E-value=4.1e+02 Score=27.71 Aligned_cols=102 Identities=18% Similarity=0.179 Sum_probs=62.0
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.+.|- |++..++++.+-|.+++ +.++.+||=|..|--+=-|+|-+. .++...-.......+..+.+- ..=..
T Consensus 5 il~i~KP~G~TS~dvv~~vrr~l~~--kKvGH~GTLDP~AtGvL~i~vG~a--Tkl~~~l~~~~K~Y~a~~~lG-~~TdT 79 (294)
T PRK02484 5 IINLKKEAGMTSHDAVFKLRKILQT--KKIGHGGTLDPDVVGVLPIAVGKA--TRLIEYMTEAGKVYEGEITLG-YSTTT 79 (294)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCC--CccccCCCCCCCCeeEEEEEEChh--hhhhHHhccCCcEEEEEEEEC-CcccC
Confidence 4566665 99999999999999987 589999999999988888887442 234332111111222211110 01124
Q ss_pred CCCCCCEEEEEEecCCC-CCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVV-DSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~-~~~~~i~~~l~~l 141 (532)
+|..|+-- .-.++.. -+.+.+++.+.++
T Consensus 80 ~D~~G~vi--~~~~~~~~~~~~~l~~~l~~f 108 (294)
T PRK02484 80 EDASGEVV--AETPLTQPLTEEEVDQAMTSF 108 (294)
T ss_pred CCCCCCEE--EeccCCCCCCHHHHHHHHHhc
Confidence 67777632 2223321 2456777777766
No 30
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=37.77 E-value=3.8e+02 Score=28.23 Aligned_cols=101 Identities=19% Similarity=0.108 Sum_probs=61.7
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++..++++.+-|.++++ .++.+||=|..|--+=-|+|-+. .++...-.......+..+.+-. .=..
T Consensus 5 il~i~KP~G~TS~dvv~~vrr~l~~k--KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~~~K~Y~a~~~lG~-~TdT 79 (308)
T PRK14124 5 FLVAYKPKGPTSHDVVDEVRKKLKTR--KVGHAGTLDPFATGVLIVGVNKA--TRLLEYLKNEKKVYYVKMRLGL-ITET 79 (308)
T ss_pred EEEEECCCCCCHHHHHHHHHHHcCCC--ccCcCcCCCCCCcEEEEEEEChH--HhhhHHHhcCCceEEEEEEeCc-cccC
Confidence 4667775 999999999999999875 79999999999988888877432 2333321111112222111100 1134
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+--. -.++. -+.+.+++.+.++
T Consensus 80 ~D~~G~vi~--~~~~~-~~~~~i~~~l~~f 106 (308)
T PRK14124 80 FDITGEVVE--ERECN-VTEEEIREAIFSF 106 (308)
T ss_pred CCCCCCEEE--ecCCC-CCHHHHHHHHHhC
Confidence 677886422 22332 2456677777766
No 31
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=34.84 E-value=4.9e+02 Score=27.02 Aligned_cols=102 Identities=15% Similarity=0.072 Sum_probs=60.6
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.+.|- |++..+++..+.|.++.+ .++.+||=|..|--+=-|+|-+. .++...-.......+..+.+-. .=.-
T Consensus 2 il~i~KP~G~tS~dvv~~vrr~~~~k--KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~~~K~Y~a~~~lG~-~TdT 76 (279)
T PRK02193 2 IKLLYKPKGISSFKFIKNFAKTNNIK--KIGHTGTLDPLASGLLLVATDED--TKLIDYLDQKDKTYIAKIKFGF-ISTT 76 (279)
T ss_pred EEEEECCCCCCHHHHHHHHHHHcCCC--ccccCccCCCcCeeEEEEEEChh--hhhhHHhccCCcEEEEEEEeCC-cccC
Confidence 3556664 999999999999999874 89999999999988888887442 2333321111111222111100 1123
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
+|..|+--.- .+...-+.+.+++.+.++
T Consensus 77 ~D~~G~i~~~--~~~~~~~~~~l~~~l~~f 104 (279)
T PRK02193 77 YDSEGQIINV--SQNIKVTKENLEEALNNL 104 (279)
T ss_pred CCCCCCEEee--cCCCCCCHHHHHHHHHhC
Confidence 5777863321 121112466777777766
No 32
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=34.61 E-value=49 Score=25.22 Aligned_cols=43 Identities=12% Similarity=0.217 Sum_probs=24.4
Q ss_pred HHhhcHHHHHHHhc---CCCCCCchhHHHHHHHHHhcCCHHHHHHh
Q 009530 169 LLRGEWKSAVKMIL---DPREGERNEISKAREYYKETDDIDGTLRK 211 (532)
Q Consensus 169 lL~g~~~~Av~liL---~p~~~~~~~~~~ar~~~~~~gd~~~al~~ 211 (532)
|-.|+|++|+.++= .-.+...+.....-..+...|++++|...
T Consensus 2 l~~~~~~~A~~~~~~~l~~~p~~~~~~~~la~~~~~~g~~~~A~~~ 47 (68)
T PF14559_consen 2 LKQGDYDEAIELLEKALQRNPDNPEARLLLAQCYLKQGQYDEAEEL 47 (68)
T ss_dssp HHTTHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHTT-HHHHHHH
T ss_pred hhccCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHH
Confidence 56789999998772 22232222222333445667888877643
No 33
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=34.16 E-value=4.2e+02 Score=27.67 Aligned_cols=101 Identities=19% Similarity=0.225 Sum_probs=61.1
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++..++++.+.|.++. +.++++||=|..|--+=-|+|-+. .++...-.......+..+.+-. .=.-
T Consensus 5 iL~i~KP~G~TS~dvv~~vrk~~~~--kKvGH~GTLDP~AtGvL~v~vG~a--TKl~~~l~~~~K~Y~~~~~lG~-~TdT 79 (292)
T PRK01528 5 WLNIYKPRGISSAKLVSIVKKILGK--VKIGHAGTLDVEAEGVLPLAVGEA--TKLVQLLIDAKKTYIFTVKFGK-QTDS 79 (292)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHcCC--CccCcCccCCCcCceEEEEEEChH--hhhhHHHhcCCceEEEEEEECC-cccC
Confidence 4566664 99999999999999985 589999999999988888877432 2333221111122222222211 1124
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
.|..|.--. -.++.. +.+.+++.+.++
T Consensus 80 ~D~~G~v~~--~~~~~~-~~e~l~~~l~~f 106 (292)
T PRK01528 80 GDYAGKVIA--TKDYIP-SKEEAYAVCSKF 106 (292)
T ss_pred CCCCCCEEE--ecCCCC-CHHHHHHHHHhc
Confidence 677775322 223332 466777777665
No 34
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=33.94 E-value=4.7e+02 Score=28.00 Aligned_cols=101 Identities=18% Similarity=0.207 Sum_probs=61.6
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.+.|- |++..++++.+.|.+++ +.+|.+||=|..|--+=-|+|-+. .++...-.......+..+.+-. .=.-
T Consensus 5 iL~idKP~G~TS~dvv~~vrk~l~~--kKVGH~GTLDP~AtGVL~i~vG~a--TKl~~~l~~~~K~Y~a~~~lG~-~TDT 79 (345)
T PRK14846 5 WLNIYKPRGISSAQLVSIVKKILGK--TKIGHAGTLDVEAEGILPFAVGEA--TKLIHLLIDARKTYIFTVKFGM-QTNS 79 (345)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCC--CcCCcCccCCCcCceEEEEEEChh--hhhhHHHhcCCceEEEEEEECC-ccCC
Confidence 4566664 99999999999999987 499999999999988888887442 2333221111112222222110 1123
Q ss_pred CCCCCCEEEEEEecCCCCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVVVDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~~~~~~~i~~~l~~l 141 (532)
.|..|.--. -.++.. +.+.+++.+.++
T Consensus 80 ~D~eG~ii~--~~~~~~-~~e~l~~~L~~f 106 (345)
T PRK14846 80 GDCAGKVIA--TKDCIP-SQEEAYAVCSKF 106 (345)
T ss_pred CCCCCCEEE--ecCCCC-CHHHHHHHHHhC
Confidence 577786433 233332 456677777665
No 35
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=32.15 E-value=5.8e+02 Score=26.78 Aligned_cols=102 Identities=15% Similarity=0.158 Sum_probs=61.8
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEecCChhhHHHHhccCCCeEEccEEEeecCCCC
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVFKQRASKLAALNKRLIGIRLGDFCYVKEGLLL 111 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~~~~~~~l~~ln~~l~~i~vg~~~~~~~~L~l 111 (532)
.+.++|- |++.++++..+.|.++++ .++.+||=|..|--+=-|+|-+. .++...-.......+..+.+-. .=..
T Consensus 5 il~i~KP~G~TS~dvv~~vrr~~~~k--KvGH~GTLDP~AtGvL~v~vG~a--Tkl~~~l~~~~K~Y~~~~~lG~-~TdT 79 (305)
T PRK14123 5 ILPVYKERGLTSHDVVFKLRKILKTK--KIGHTGTLDPEVAGVLPVCIGNA--TRVSDYVMDMGKAYEATVSIGR-STTT 79 (305)
T ss_pred EEEEeCCCCCCHHHHHHHHHHHhCCC--ccccCcCCCCcCeeEEEEEEChh--hhhHHHhcCCCcEEEEEEEECC-cccC
Confidence 4566664 999999999999999874 79999999999988888887543 2443331111122222221100 1124
Q ss_pred CCCCCCEEEEEEecCC--CCCHHHHHHHHHhh
Q 009530 112 GQLLGNRFTITLRGVV--VDSEDVIKASANSL 141 (532)
Q Consensus 112 G~L~GN~F~I~LR~v~--~~~~~~i~~~l~~l 141 (532)
.|..|+-- .-.++. .-+.+.+++.+.++
T Consensus 80 ~D~~G~vi--~~~~~~~~~~~~~~l~~~l~~f 109 (305)
T PRK14123 80 EDQTGDTL--ETKGVHSADFNKDDIDRLLEQF 109 (305)
T ss_pred CCCCCCEE--EeccCCcCCCCHHHHHHHHHhc
Confidence 67778632 222331 12456777777766
No 36
>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=29.87 E-value=1.2e+02 Score=29.25 Aligned_cols=46 Identities=24% Similarity=0.362 Sum_probs=39.6
Q ss_pred EEEEEEc-ccCHHHHHHHHHHHhCCCCcceeecccccCCceEEEEEEEe
Q 009530 33 RFHLYKE-NKDTQEALGLISKMLGILPRSFGFAGTKDKRSVSTQRVTVF 80 (532)
Q Consensus 33 ~f~L~K~-n~dT~~ai~~Lar~l~i~~~~~~~AG~KDkrAvT~Q~vsv~ 80 (532)
.+.++|- |++.+++++.+-+.++++ .++.+||=|..|--+=-|.|-
T Consensus 4 ~l~i~Kp~g~tS~~~v~~~k~~~~~k--kvGH~GTLDp~A~GvLiv~~g 50 (182)
T cd02572 4 VINLDKPSGPSSHEVVAWIKRILGVE--KTGHSGTLDPKVTGCLPVCID 50 (182)
T ss_pred EEEEecCCCCCHHHHHHHHHHHhCCC--ccCcCCCCCCcCeeEEEEEEC
Confidence 4667775 999999999999999974 799999999999888777764
No 37
>PRK05090 hypothetical protein; Validated
Probab=28.41 E-value=60 Score=28.18 Aligned_cols=43 Identities=12% Similarity=0.251 Sum_probs=35.6
Q ss_pred CCEEEEEEEE---cccCHHHHHHHHHHHhCCCCcceee-cccccCCc
Q 009530 29 GKFLRFHLYK---ENKDTQEALGLISKMLGILPRSFGF-AGTKDKRS 71 (532)
Q Consensus 29 g~y~~f~L~K---~n~dT~~ai~~Lar~l~i~~~~~~~-AG~KDkrA 71 (532)
|+.+.+.+.- +|.-..+++..||+.|+++.++|.+ .|.+.|+=
T Consensus 31 ~~~lkv~v~ApPveGkAN~ali~~LAk~l~v~ks~I~i~~G~tsr~K 77 (95)
T PRK05090 31 GDELKVAITAPPVDGQANAHLLKFLAKQFRVAKSQVVIEKGELGRHK 77 (95)
T ss_pred CCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCCce
Confidence 4567777764 5888999999999999999999987 88887765
No 38
>PHA01627 DNA binding protein
Probab=22.99 E-value=1.2e+02 Score=26.87 Aligned_cols=44 Identities=16% Similarity=0.371 Sum_probs=33.6
Q ss_pred EeecCCCCCCCCCCEEEEEEecCCCCCHHHHHHHHHhhccccccccccCC
Q 009530 104 YVKEGLLLGQLLGNRFTITLRGVVVDSEDVIKASANSLGRNGFINYFGLQ 153 (532)
Q Consensus 104 ~~~~~L~lG~L~GN~F~I~LR~v~~~~~~~i~~~l~~l~~~GFiNYFG~Q 153 (532)
|--....+..+.|-.+.|.++.++. +++-+.+.+.+|+|+-|.|
T Consensus 4 YllN~fsl~ml~~~~~~v~~~~i~~------~Eak~~v~~~~~vSaIGH~ 47 (107)
T PHA01627 4 YLLNAFSLPMKPGEEYTVVIDKIDI------EEAKELLENEEFVSAIGHD 47 (107)
T ss_pred EEecccccccccCCceEEEEecCCH------HHHHHHhcccCeEEeeccH
Confidence 4555677888888899999999872 3445556688999998876
No 39
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=22.99 E-value=81 Score=23.54 Aligned_cols=20 Identities=20% Similarity=0.665 Sum_probs=16.8
Q ss_pred hHHHHHHHHhhcHHHHHHHh
Q 009530 162 THLVGATLLRGEWKSAVKMI 181 (532)
Q Consensus 162 th~iG~~lL~g~~~~Av~li 181 (532)
...|-.+|+.|+|+.|+..+
T Consensus 5 ~~~i~~~i~~g~~~~a~~~~ 24 (58)
T smart00668 5 RKRIRELILKGDWDEALEWL 24 (58)
T ss_pred HHHHHHHHHcCCHHHHHHHH
Confidence 35678899999999998876
No 40
>PRK01310 hypothetical protein; Validated
Probab=22.78 E-value=83 Score=27.73 Aligned_cols=43 Identities=16% Similarity=0.342 Sum_probs=35.7
Q ss_pred CEEEEEEE---EcccCHHHHHHHHHHHhCCCCcceee-cccccCCce
Q 009530 30 KFLRFHLY---KENKDTQEALGLISKMLGILPRSFGF-AGTKDKRSV 72 (532)
Q Consensus 30 ~y~~f~L~---K~n~dT~~ai~~Lar~l~i~~~~~~~-AG~KDkrAv 72 (532)
.++...|. -+|.-.-+++..||+.|+||.++|.+ .|.+.|+=+
T Consensus 38 ~~lkv~v~apPv~GkAN~ali~~LA~~l~v~ks~I~iv~G~tsR~K~ 84 (104)
T PRK01310 38 AVLKVRVRAVPEGGEANRALIELLAKALGVPKSSVRLLSGATSRLKQ 84 (104)
T ss_pred cEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCCceE
Confidence 36666666 36888999999999999999999997 898888763
No 41
>KOG2310 consensus DNA repair exonuclease MRE11 [Replication, recombination and repair]
Probab=20.52 E-value=34 Score=38.45 Aligned_cols=18 Identities=33% Similarity=0.696 Sum_probs=15.2
Q ss_pred HHHHHhhccccccccccC
Q 009530 135 KASANSLGRNGFINYFGL 152 (532)
Q Consensus 135 ~~~l~~l~~~GFiNYFG~ 152 (532)
-.+|.-|...|++||||-
T Consensus 139 lsalDIL~~~GLVNyFGk 156 (646)
T KOG2310|consen 139 LSALDILSAAGLVNYFGK 156 (646)
T ss_pred cchHHHHHhcchhhhhcc
Confidence 356888899999999994
No 42
>PF00772 DnaB: DnaB-like helicase N terminal domain; InterPro: IPR007693 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity. This domain has a multi-helical structure that forms an orthogonal bundle [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1B79_D 1JWE_A 3GXV_C 3BGW_C 2R6D_B 2R6C_D 2R6E_B 2R6A_A 2VYE_A 2VYF_B ....
Probab=20.52 E-value=1.1e+02 Score=25.76 Aligned_cols=52 Identities=15% Similarity=0.224 Sum_probs=38.6
Q ss_pred CCcchHHHHHHHHHHhhCCCChHHhhhcCChhHHHHHHHHHHHHHHHHHHHHHHH
Q 009530 212 LPRHLVAERAILQCLKKCPGNYLQALKAIPRTLRMMYVHSYQSFLWNHAASARVQ 266 (532)
Q Consensus 212 ~p~~~~~Er~iL~~L~~~~~~~~~Al~~iPr~lr~myvhAYQSylwN~~~S~Ri~ 266 (532)
+|....+|++||..|..++..+......+... +|.+....-||+.+....-+
T Consensus 2 ~p~~~~aE~~lL~~lL~~~~~~~~i~~~L~~e---~F~~~~h~~If~~i~~l~~~ 53 (103)
T PF00772_consen 2 LPYDIEAEKALLGALLNDPEAIDEIIDKLSPE---DFYDPAHRRIFEAILELYRE 53 (103)
T ss_dssp SSHHHHHHHHHHHHHHHSCCHHHHHHTT-SGG---GSSSHHHHHHHHHHHHHHHT
T ss_pred CCCcHHHHHHHHHHHHcChHHHHHHhccCCHH---HhCCHHHHHHHHHHHHHHHc
Confidence 57778899999999988877676666666544 57777777889888776444
No 43
>PRK01530 hypothetical protein; Reviewed
Probab=20.40 E-value=92 Score=27.54 Aligned_cols=56 Identities=11% Similarity=0.205 Sum_probs=43.9
Q ss_pred CCEEEEEEEE---cccCHHHHHHHHHHHhCCCCcceee-cccccCCceEEEEEEEecCChhhHH
Q 009530 29 GKFLRFHLYK---ENKDTQEALGLISKMLGILPRSFGF-AGTKDKRSVSTQRVTVFKQRASKLA 88 (532)
Q Consensus 29 g~y~~f~L~K---~n~dT~~ai~~Lar~l~i~~~~~~~-AG~KDkrAvT~Q~vsv~~~~~~~l~ 88 (532)
+.++...+.- +|.-..+++..||+.|+||.++|.. .|.+-|+= .|.|.++.++.+.
T Consensus 38 ~~~Lki~v~ApPvdGkAN~ali~~LAk~l~v~ks~I~IvsG~tSR~K----~i~I~g~~~~~l~ 97 (105)
T PRK01530 38 IPYLKLSIKAIPEQGKANEEIINYLAKEWKLSRSNIEIIKGHTHSLK----TILIKNINEDYLN 97 (105)
T ss_pred CCEEEEEEecCCCCChHHHHHHHHHHHHhCCChhhEEEEecCCCCce----EEEEeCCCHHHHH
Confidence 4578888875 6899999999999999999999987 78877765 3556666666554
Done!