Query 042463
Match_columns 490
No_of_seqs 308 out of 2814
Neff 6.8
Searched_HMMs 29240
Date Mon Mar 25 10:52:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042463.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/042463hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1v9f_A Ribosomal large subunit 100.0 3.9E-54 1.3E-58 439.3 21.8 299 103-488 14-314 (325)
2 1v9k_A Ribosomal large subunit 100.0 1.7E-47 5.7E-52 371.8 23.9 224 204-487 3-226 (228)
3 2i82_A Ribosomal large subunit 100.0 8.2E-46 2.8E-50 357.3 18.9 202 204-475 13-216 (217)
4 1ksk_A Ribosomal small subunit 100.0 2.5E-41 8.4E-46 329.5 14.7 205 104-398 2-208 (234)
5 1vio_A Ribosomal small subunit 100.0 2.8E-40 9.7E-45 323.9 14.6 203 106-398 3-209 (243)
6 3dh3_A Ribosomal large subunit 100.0 8.6E-37 2.9E-41 305.8 16.0 204 103-397 4-207 (290)
7 2oml_A Ribosomal large subunit 100.0 6.5E-37 2.2E-41 289.1 8.5 165 204-398 5-171 (189)
8 2olw_A Ribosomal large subunit 100.0 8.8E-36 3E-40 287.2 9.6 162 204-398 33-199 (217)
9 2gml_A Ribosomal large subunit 99.9 1.9E-28 6.4E-33 237.9 10.3 141 209-396 13-153 (237)
10 2k6p_A Uncharacterized protein 98.0 1.8E-06 6.1E-11 71.2 1.6 53 106-174 1-53 (92)
11 1dm9_A Hypothetical 15.5 KD pr 97.8 3.3E-05 1.1E-09 68.1 7.4 55 103-173 6-60 (133)
12 1p9k_A ORF, hypothetical prote 97.4 3.2E-05 1.1E-09 61.8 1.0 52 104-171 19-71 (79)
13 1c05_A Ribosomal protein S4 de 97.2 0.00042 1.5E-08 62.9 6.5 52 105-172 50-102 (159)
14 2vqe_D 30S ribosomal protein S 97.1 0.00073 2.5E-08 64.0 6.7 52 105-172 98-150 (209)
15 2cqj_A BRMS2, U3 small nucleol 97.0 0.0004 1.4E-08 54.5 3.7 50 105-170 7-59 (71)
16 3hp7_A Hemolysin, putative; st 97.0 0.00067 2.3E-08 67.5 6.0 54 104-172 5-60 (291)
17 3r8n_D 30S ribosomal protein S 97.0 0.00026 8.9E-09 66.7 2.2 54 105-173 94-147 (205)
18 3bbn_D Ribosomal protein S4; s 96.6 0.00082 2.8E-08 63.2 2.5 54 105-173 88-141 (201)
19 2aus_C Pseudouridine synthase; 96.5 0.002 6.9E-08 65.2 5.2 73 207-308 43-115 (334)
20 1r3e_A TRNA pseudouridine synt 96.5 0.0021 7.1E-08 64.1 5.2 70 210-308 3-72 (309)
21 1sgv_A TRNA pseudouridine synt 96.4 0.0025 8.5E-08 63.7 5.2 71 209-308 5-75 (316)
22 3j20_D 30S ribosomal protein S 96.4 0.0017 5.8E-08 59.9 3.5 51 105-171 102-155 (180)
23 1k8w_A TRNA pseudouridine synt 96.3 0.003 1E-07 63.5 5.1 70 210-308 25-94 (327)
24 2apo_A Probable tRNA pseudouri 96.3 0.003 1E-07 64.4 5.1 73 207-308 63-135 (357)
25 3u28_A H/ACA ribonucleoprotein 96.0 0.0053 1.8E-07 63.2 4.9 76 207-311 56-132 (400)
26 2xzm_D Ribosomal protein S4 co 95.6 0.0057 2E-07 56.5 2.9 50 105-170 106-158 (181)
27 3u5c_J 40S ribosomal protein S 95.0 0.0097 3.3E-07 55.5 2.6 50 105-170 106-158 (197)
28 3j20_E 30S ribosomal protein S 90.2 1.4 4.8E-05 42.2 9.8 55 103-172 40-95 (243)
29 3iz6_C 40S ribosomal protein S 89.7 0.0042 1.5E-07 57.8 -7.9 53 104-172 107-160 (195)
30 3kbg_A 30S ribosomal protein S 83.1 0.91 3.1E-05 42.6 4.0 52 104-170 6-58 (213)
31 2xzm_W 40S ribosomal protein S 69.2 13 0.00044 35.9 7.8 55 102-171 38-95 (260)
32 3u5c_E RP5, S7, YS6, 40S ribos 61.2 14 0.00047 35.7 6.3 54 103-171 39-93 (261)
33 1fm0_D Molybdopterin convertin 47.5 27 0.00093 26.6 5.0 47 106-170 26-74 (81)
34 3iz6_D 40S ribosomal protein S 47.2 11 0.00037 36.5 3.0 53 104-171 40-93 (265)
35 2og0_A Excisionase; protein-DN 43.5 23 0.00079 25.5 3.6 29 106-134 3-31 (52)
36 1h3f_A Tyrosyl-tRNA synthetase 42.6 31 0.0011 35.7 5.9 47 105-166 368-414 (432)
37 2jan_A Tyrosyl-tRNA synthetase 37.6 21 0.00074 36.9 3.7 30 107-136 357-386 (432)
38 1jil_A Tyrrs, tyrosyl-tRNA syn 36.9 7.2 0.00025 40.3 0.0 49 105-168 352-400 (420)
39 1pm6_A Excisionase; antiparall 29.3 46 0.0016 25.6 3.4 29 106-134 3-31 (72)
40 3po0_A Small archaeal modifier 25.0 42 0.0015 26.1 2.7 25 131-171 59-83 (89)
41 2ktl_A Tyrosyl-tRNA synthetase 24.3 66 0.0023 28.7 4.1 32 105-136 49-80 (164)
42 2ts1_A Tyrosyl-tRNA synthetase 23.2 17 0.00059 37.4 0.0 46 106-166 352-397 (419)
43 2hj1_A Hypothetical protein; s 21.3 45 0.0015 27.1 2.1 52 103-172 33-84 (97)
No 1
>1v9f_A Ribosomal large subunit pseudouridine synthase D; RNA binding, lyase; 1.70A {Escherichia coli} SCOP: d.265.1.3 PDB: 2ist_A 1qyu_A 1prz_A
Probab=100.00 E-value=3.9e-54 Score=439.28 Aligned_cols=299 Identities=22% Similarity=0.294 Sum_probs=176.0
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccccccccccc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKR 182 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~~e~~~~~~ 182 (490)
..++||++||++.++.+||+.++++|++|+|+|| |+ ..+++++.|.+||.|.+.....+.
T Consensus 14 ~~g~RLd~~L~~~~~~~SR~~~~~lI~~G~V~VN-----------G~----~v~~~~~~v~~gD~I~v~~~~~~~----- 73 (325)
T 1v9f_A 14 QLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVN-----------GK----VCDKPKEKVLGGEQVAINAEIEEE----- 73 (325)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cCCchHHHHHHhhccccCHHHHHHHHHCCCEEEC-----------CE----EccCCCCEeCCCCEEEEecccccc-----
Confidence 3468999999998878999999999999999999 74 137889999999999996432110
Q ss_pred ccCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCC-CCCHHHHHHHHH-hccCCCCCccccCCCcCCc
Q 042463 183 YDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPV-HNSMDALAAAAL-SYDYNEGPKLVHRLDRESS 260 (490)
Q Consensus 183 ~~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~-~~~~~~ll~~~~-~~~~~~~l~~VHRLDr~TS 260 (490)
....+.. +...|+|||++|+|||||+||+||+.... ..++...+.... ......++++|||||++||
T Consensus 74 ------~~~~~~~-----~~~~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TS 142 (325)
T 1v9f_A 74 ------ARFEPQD-----IPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTT 142 (325)
T ss_dssp --------CCCCC-----CCCCEEEECSSEEEEEECSSCCSSCBTTBSSSSHHHHHHHHCGGGGGSGGGGBCCCCCTTCE
T ss_pred ------ccCCccc-----CCCeEEEECCCEEEEECCCCCeEecCCCCCCccHHHHHHHHHHhcCCCCceeeecCCCCCCe
Confidence 0001111 12349999999999999999999976542 234433332221 1112346899999999999
Q ss_pred eeEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeec
Q 042463 261 GLLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQN 340 (490)
Q Consensus 261 GLLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~ 340 (490)
||||||+|+++++.|+++|.++ .+.|+|+|+|.|.+++ +|.|+.||.+.... . .++.+.
T Consensus 143 Glll~ak~~~~~~~l~~~~~~~---------------~v~K~Y~a~v~G~~~~-~g~i~~~i~~~~~~--~-~~~~v~-- 201 (325)
T 1v9f_A 143 GLMVVAKTVPAQTRLVESLQRR---------------EITREYEAVAIGHMTA-GGTVDEPISRHPTK--R-THMAVH-- 201 (325)
T ss_dssp EEEEEESSHHHHHHHHHHHHTT---------------CSEEEEEEEEESCCCC-CEEEECCEEECSSC--T-TCEEEC--
T ss_pred eEEEEEcCHHHHHHHHHHHHcC---------------CeeEEEEEEEeCCCCC-CCEEeeeeeECCCC--C-EEEEEC--
Confidence 9999999999999999999986 5999999999999987 89999999875322 1 122221
Q ss_pred CCccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCce
Q 042463 341 SGLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPY 420 (490)
Q Consensus 341 ~~~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~ 420 (490)
.+++.|.|+|++++. ..++|+++|+|.||||||||+||+ ++||||+||.+||+.. . .
T Consensus 202 ---~~gk~a~t~~~vl~~-~~~~slv~~~l~TGR~HQIRvhla-~lG~PI~GD~~Yg~~~--~---~------------- 258 (325)
T 1v9f_A 202 ---PMGKPAVTHYRIMEH-FRVHTRLRLRLETGRTHQIRVHMA-HITHPLVGDPVYGGRP--R---P------------- 258 (325)
T ss_dssp ---TTSBCCEEEEEEEEE-CSSEEEEEEEESCCCTTHHHHHHH-HTTCCBTTCTTTTCCC--C---C-------------
T ss_pred ---CCCeeEEEEEEEeEE-cCCeEEEEEEECCCCcHHHHHHHH-hCCCceeCChhhCCcc--c---c-------------
Confidence 357899999999995 457899999999999999999999 8999999999999621 0 0
Q ss_pred eeecCCCcccccccccCCcchhhcccccccccccCCCCCCCCCCCceEEEEecCchhHHHHHHHhhhc
Q 042463 421 KLRRPDGLDVQKGSVLSKVPLLHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSSY 488 (490)
Q Consensus 421 ~~~~p~~~~~~~~~~~~~~~rl~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~~~~~~~~~l~~~ 488 (490)
+.............++|++|||++|.|. ||.+ ++.+.|+||+|++|+.+|+.|+.+
T Consensus 259 ----~~~~~~~~~~~~~~~~r~~LHA~~L~f~--hP~~------~~~~~~~aplp~~~~~~l~~l~~~ 314 (325)
T 1v9f_A 259 ----PKGASEAFISTLRKFDRQALHATMLRLY--HPIS------GIEMEWHAPIPQDMVELIEVMRAD 314 (325)
T ss_dssp ----CTTCCHHHHHHHHHCCSCSEEEEEEEEE--CTTT------CCEEEEECCCCHHHHHHHHHHHHH
T ss_pred ----ccccchhhhhhccCCcChhhheeeeEee--CCCC------CCEEEEEecCcHHHHHHHHHhccc
Confidence 0000000000001135799999999994 6766 557999999999999999988753
No 2
>1v9k_A Ribosomal large subunit pseudouridine synthase C; pseudouridine syntase, RNA binding, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 PDB: 1xpi_A
Probab=100.00 E-value=1.7e-47 Score=371.83 Aligned_cols=224 Identities=29% Similarity=0.380 Sum_probs=175.1
Q ss_pred eeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccc
Q 042463 204 LVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVN 283 (490)
Q Consensus 204 ~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~ 283 (490)
.|+|||++|+|||||+||+||++.....++...+.. .+.....+++|||||++||||||||+|+++++.|+++|.++
T Consensus 3 ~Ilyed~~~lvvnKP~G~~~~~~~~~~~~l~~~l~~--~~~~~~~~~~VhRLD~~TSGlll~ak~~~~~~~l~~~~~~~- 79 (228)
T 1v9k_A 3 VIMYEDDHILVLNKPSGTAVHGGSGLSFGVIEGLRA--LRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREK- 79 (228)
T ss_dssp CEEEECSSEEEEEECTTSCSSCCSSSBCCHHHHHHH--HSTTCSCCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHTT-
T ss_pred CEEEECCCEEEEECCCCCeEecCCChHHHHHHHHHH--HcCCCCccceEecCCCCCeEEEEEEeCHHHHHHHHHHHHhC-
Confidence 499999999999999999999765433333332221 12223468899999999999999999999999999999876
Q ss_pred cccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCc
Q 042463 284 KSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGC 363 (490)
Q Consensus 284 ~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~ 363 (490)
.|+|+|+|+|.|.+++..+.|+.+|.+.....|.. .+.+ .++++.|.|+|++++. ..+.
T Consensus 80 --------------~v~K~Y~a~v~G~~~~~~~~i~~~l~~~~~~~g~~-~~~~-----~~~gk~a~t~~~vl~~-~~~~ 138 (228)
T 1v9k_A 80 --------------GMQKDYLALVRGQWQSHVKSVQAPLLKNILQSGER-IVRV-----SQEGKPSETRFKVEER-YAFA 138 (228)
T ss_dssp --------------CSEEEEEEEEESCCCTTCCEECCCEEEEECTTSCE-EEEE-----CTTSBCCCEEEEEEEE-CSSE
T ss_pred --------------CeeEEEEEEEecccCCCCCEEeCceeccCCCCCce-EEEE-----CCCCcEEEEEEEEEEE-cCCe
Confidence 59999999999999988899999987654434432 1222 1356899999999996 4568
Q ss_pred eEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCceeeecCCCcccccccccCCcchhh
Q 042463 364 SWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPLLH 443 (490)
Q Consensus 364 slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~~~~~p~~~~~~~~~~~~~~~rl~ 443 (490)
|+|+|+|.||||||||+||+ ++||||+||.+||+...+.. +. . .....+|++
T Consensus 139 slv~~~l~TGR~HQIR~hla-~lG~PI~gD~~YG~~~~~~~-----------------~~-------~---~~~~~~r~~ 190 (228)
T 1v9k_A 139 TLVRCSPVTGRTHQIRVHTQ-YAGHPIAFDDRYGDREFDRQ-----------------LT-------E---AGTGLNRLF 190 (228)
T ss_dssp EEEEEEESSCCTTHHHHHHH-HTTCCBTTCTTTSCHHHHHH-----------------HH-------H---TTCCCCSCC
T ss_pred EEEEEEECCCCchHHHHHHH-HCCCcEecCcccCCccccch-----------------hh-------c---ccCCCCChh
Confidence 99999999999999999999 89999999999997321110 00 0 000134799
Q ss_pred cccccccccccCCCCCCCCCCCceEEEEecCchhHHHHHHHhhh
Q 042463 444 LHCRELKSDNLFPTLSSKPDGPDLLRFVASMPSHMKISWNLMSS 487 (490)
Q Consensus 444 LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP~~~~~~~~~l~~ 487 (490)
|||++|.|. ||.+ ++.+.|+||+|++|+.+++.|+.
T Consensus 191 LHa~~l~f~--hP~t------~~~~~~~aplp~~~~~~l~~l~~ 226 (228)
T 1v9k_A 191 LHAAALKFT--HPGT------GEVMRIEAPMDEGLKRCLQKMRN 226 (228)
T ss_dssp EEEEEEEEE--CTTT------CCEEEEECCCCHHHHHHHHHHHH
T ss_pred hccceeEee--CCCC------CCEEEEEeCCcHHHHHHHHHhhh
Confidence 999999994 6766 55799999999999999998864
No 3
>2i82_A Ribosomal large subunit pseudouridine synthase A; lyase/RNA complex; HET: FOU; 2.05A {Escherichia coli}
Probab=100.00 E-value=8.2e-46 Score=357.34 Aligned_cols=202 Identities=30% Similarity=0.427 Sum_probs=161.3
Q ss_pred eeeeeCCeEEEEECCCCccccCCCC--CCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhc
Q 042463 204 LVKYRDSAILVLNKPPKVPLKGHLP--VHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSD 281 (490)
Q Consensus 204 ~IlyeD~~llVvNKP~Gl~v~~~~~--~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~ 281 (490)
.|+|||++|+|||||+||+||++.. ...++...+... + ..+++|||||++||||||||||+++++.|+++|.+
T Consensus 13 ~ilyed~~~lvvnKP~G~~~~~~~~~~~~~tl~~~l~~~--~---~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~f~~ 87 (217)
T 2i82_A 13 VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRD--Y---PQAESVHRLDMATSGVIVVALTKAAERELKRQFRE 87 (217)
T ss_dssp CEEEECSSEEEEEECTTSBSSCCSSGGGCCBHHHHHHHH--C---TTCEESSCCCTTCEEEEEEESSHHHHHHHHHHHHT
T ss_pred eEEEECCCEEEEECCCCCeEeCCCCCCchhHHHHHHHHH--C---CCCceeecCCCCCeEEEEEEeCHHHHHHHHHHHHh
Confidence 3999999999999999999997542 334444433321 1 35789999999999999999999999999999998
Q ss_pred cccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCC
Q 042463 282 VNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMIN 361 (490)
Q Consensus 282 ~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~ 361 (490)
+ .|+|+|+|+|.|.+++.+|.|+.+|...... +. ...+ . .++++.|.|+|++++...+
T Consensus 88 ~---------------~v~K~Y~a~v~G~~~~~~g~i~~~l~~~~~~-~~-~~~v-~----~~~gk~a~t~~~vl~~~~~ 145 (217)
T 2i82_A 88 R---------------EPKKQYVARVWGHPSPAEGLVDLPLICDWPN-RP-KQKV-C----YETGKPAQTEYEVVEYAAD 145 (217)
T ss_dssp T---------------CSEEEEEEEEESCCSSSEEEEECCEEECGGG-TT-CEEE-C----TTTCBCCEEEEEEEEEETT
T ss_pred C---------------CeeEEEEEEEecccCCCCcEEecceeecCCC-Cc-EEEE-e----CCCCcEEEEEEEEEEECCC
Confidence 6 5999999999999998889999999764321 11 1121 1 2456899999999986433
Q ss_pred CceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCchhhhcccCCCccccCCCCCCceeeecCCCcccccccccCCcch
Q 042463 362 GCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGWFVHRRWKQMPRVDIEPTSGKPYKLRRPDGLDVQKGSVLSKVPL 441 (490)
Q Consensus 362 ~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~~~~~~~~~~~~~~~~p~t~~~~~~~~p~~~~~~~~~~~~~~~r 441 (490)
+.|+|+|+|.|||+||||+||+ ++||||+||.+||+..... ..+|
T Consensus 146 ~~slv~~~l~TGR~HQIR~hla-~lG~PIvGD~~Yg~~~~~~----------------------------------~~~r 190 (217)
T 2i82_A 146 NTARVVLKPITGRSHQLRVHML-ALGHPILGDRFYASPEARA----------------------------------MAPR 190 (217)
T ss_dssp TEEEEEEEESSCCTTHHHHHHH-HTTCCBTTCTTTSCHHHHH----------------------------------TCSS
T ss_pred CeEEEEEEECCCCcHHHHHHHH-HCCCcEECccccCCccccC----------------------------------CCCC
Confidence 3799999999999999999999 8999999999999732100 0137
Q ss_pred hhcccccccccccCCCCCCCCCCCceEEEEecCc
Q 042463 442 LHLHCRELKSDNLFPTLSSKPDGPDLLRFVASMP 475 (490)
Q Consensus 442 l~LHa~~L~f~~~hp~~~~~p~~~~~~~~~aplP 475 (490)
++|||++|.| .||.+ ++.+.|+||+|
T Consensus 191 ~~LHa~~l~f--~hP~~------~~~~~~~ap~p 216 (217)
T 2i82_A 191 LLLHAEMLTI--THPAY------GNSMTFKAPAD 216 (217)
T ss_dssp CCEEEEEEEE--ECTTT------CCEEEEECCCC
T ss_pred ceeeeeEeEE--cCCCC------CCEEEEEecCC
Confidence 9999999999 46766 55799999998
No 4
>1ksk_A Ribosomal small subunit pseudouridine synthase A; RSUA, lyase; 2.00A {Escherichia coli} SCOP: d.265.1.3 d.66.1.5 PDB: 1ksl_A 1ksv_A*
Probab=100.00 E-value=2.5e-41 Score=329.50 Aligned_cols=205 Identities=16% Similarity=0.149 Sum_probs=157.4
Q ss_pred CcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecC-CCCcccCCCEEEEcccccccccccc
Q 042463 104 CHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIK-TNEVMEPGARIFLPVSMVEGRISKR 182 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~-~~~~l~~Gd~I~v~~~~~e~~~~~~ 182 (490)
.++||++||+.. +.+||+.++++|++|+|+|| |+ .++ +++.|.+||.|.+..
T Consensus 2 ~~~RLd~~L~~~-~~~SR~~~~~li~~G~V~VN-----------G~-----~v~~~~~~v~~gD~I~v~~---------- 54 (234)
T 1ksk_A 2 SHMRLDKFIAQQ-LGVSRAIAGREIRGNRVTVD-----------GE-----IVRNAAFKLLPEHDVAYDG---------- 54 (234)
T ss_dssp CCEEHHHHHHHH-HTCCHHHHHHHHHTTCEEET-----------TE-----ECCCTTCEECTTCCEEETT----------
T ss_pred CcccHHHHHHHc-CCCCHHHHHHHHHcCeEEEC-----------CE-----EeCCCCCCCCCCCEEEEeC----------
Confidence 468999999986 57999999999999999999 73 454 899999999998821
Q ss_pred ccCCCCCCCCCCcchhhcccceeeee-CCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCce
Q 042463 183 YDTIPSGTLNPNADEIDYLRRLVKYR-DSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSG 261 (490)
Q Consensus 183 ~~~~p~~~~~~~~~~i~~l~~~Ilye-D~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSG 261 (490)
..|+|| |++|+|||||+||+||+..+...++..++. . .....+++|||||++|||
T Consensus 55 --------------------~~i~~e~d~~~lvvnKP~G~~~~~~~~~~~tl~~~l~---~-~~~~~~~~vhRLD~~TsG 110 (234)
T 1ksk_A 55 --------------------NPLAQQHGPRYFMLNKPQGYVCSTDDPDHPTVLYFLD---E-PVAWKLHAAGRLDIDTTG 110 (234)
T ss_dssp --------------------EEECCCCCCCEEEEEECTTCBSSSSCSSSCBGGGGCC---C-TTGGGCEESSCCCTTCEE
T ss_pred --------------------eEeecCCCCEEEEEECCCCCEeCCCCCCCCcHHHHhh---h-hhcCCeeEcCCCCCCCee
Confidence 028999 999999999999999977554444433321 1 111358999999999999
Q ss_pred eEEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecC
Q 042463 262 LLLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNS 341 (490)
Q Consensus 262 LLLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~ 341 (490)
|||||+|+++++.|.+. ++ .+.|+|+|+|.|.+++. .++.+.. |. .. . .
T Consensus 111 lll~ak~~~~~~~l~~~--~~---------------~v~K~Y~a~v~g~~~~~--~i~~~~~------g~----~~-~-~ 159 (234)
T 1ksk_A 111 LVLMTDDGQWSHRITSP--RH---------------HCEKTYLVTLESPVADD--TAEQFAK------GV----QL-H-N 159 (234)
T ss_dssp EEEEESCHHHHHHHHCT--TS---------------CCCEEEEEEESSCCCTT--HHHHHHH------CC----CC-T-T
T ss_pred EEEEEcCHHHHHHHhCC--CC---------------CCCeEEEEEEccCCCHH--HHHHHHC------Ce----EE-C-C
Confidence 99999999999888762 22 49999999999998764 2333221 10 00 0 0
Q ss_pred CccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCc
Q 042463 342 GLEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGW 398 (490)
Q Consensus 342 ~~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~ 398 (490)
....++.|. |++++ .++++|+|.||||||||+||+ ++||||+||..|+.
T Consensus 160 ~~~~~~~a~--~~~~~-----~s~~~~~l~tGR~HQIR~h~~-~lG~pi~gd~ry~~ 208 (234)
T 1ksk_A 160 EKDLTKPAV--LEVIT-----PTQVRLTISEGRYHQVKRMFA-AVGNHVVELHRERI 208 (234)
T ss_dssp CSSCCCCCE--EEEEE-----TTEEEEEESCCCTTHHHHHHH-HTTCCEEEEEEEEE
T ss_pred CCcccceEE--EEEeC-----CeEEEEEEccCCCHHHHHHHH-HcCCeEeeeEEEEE
Confidence 001234444 66765 489999999999999999999 89999999999864
No 5
>1vio_A Ribosomal small subunit pseudouridine synthase A; structural genomics, lyase; 1.59A {Haemophilus influenzae} SCOP: d.265.1.3 d.66.1.5
Probab=100.00 E-value=2.8e-40 Score=323.85 Aligned_cols=203 Identities=18% Similarity=0.187 Sum_probs=154.4
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceec-CCCCcccCCCEEEEcccccccccccccc
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKI-KTNEVMEPGARIFLPVSMVEGRISKRYD 184 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~-~~~~~l~~Gd~I~v~~~~~e~~~~~~~~ 184 (490)
+||++||++. +.+||+.++++|++|+|+|| |+ .+ ++++.|.+||.|.+..
T Consensus 3 ~RLd~~L~~~-~~~SR~~~~~lI~~G~V~VN-----------G~-----~v~~~~~~v~~gD~I~v~~------------ 53 (243)
T 1vio_A 3 LRLDKFIAEN-VGLTRSQATKAIRQSAVKIN-----------GE-----IVKSGSVQISQEDEIYFED------------ 53 (243)
T ss_dssp EEHHHHHHHH-HTCCHHHHHHHHHTTCEEET-----------TE-----ECCCTTCEECTTSCEEETT------------
T ss_pred ccHHHHHHHc-CCCCHHHHHHHHHcCcEEEC-----------CE-----EeCCCCCCcCCCCEEEEec------------
Confidence 6999999996 57999999999999999999 73 55 5899999999888821
Q ss_pred CCCCCCCCCCcchhhcccceeeeeCCe-EEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeE
Q 042463 185 TIPSGTLNPNADEIDYLRRLVKYRDSA-ILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLL 263 (490)
Q Consensus 185 ~~p~~~~~~~~~~i~~l~~~IlyeD~~-llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLL 263 (490)
..|+|||++ |+|+|||+||+|++......++..++.. . ....+++|||||++|||||
T Consensus 54 ------------------~~i~~ed~~~~lvvnKP~G~~~~~~~~~~~tl~~~l~~---~-~~~~~~~vhRLD~~TsGll 111 (243)
T 1vio_A 54 ------------------ELLTWIEEGQYFMLNKPQGCVCSNDDGDYPTIYQFFDY---P-LAGKLHSAGRLDVDTTGLV 111 (243)
T ss_dssp ------------------EECCSSCCCCEEEEEECTTCBSSCCC--CCBGGGGSCT---T-GGGGCEESSCCCTTCEEEE
T ss_pred ------------------cccccCCCCEEEEEECCCCCEeCCCCCCCCcHHHHHhH---H-hcCCEeEccCCCCCCeEEE
Confidence 028999999 9999999999999765444444333321 1 1235899999999999999
Q ss_pred EEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCc
Q 042463 264 LMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGL 343 (490)
Q Consensus 264 LlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~ 343 (490)
|||+|+++++.+..+ ++ .|+|+|+|+|.|.+++. .++.+...... ... .
T Consensus 112 l~ak~~~~a~~l~~~--~~---------------~v~K~Y~a~v~g~~~~~--~i~~~~~g~~~-----------~~~-~ 160 (243)
T 1vio_A 112 LLTDDGQWSHRITSP--KH---------------HCEKTYLVTLADPVEEN--YSAACAEGILL-----------RGE-K 160 (243)
T ss_dssp EEESCHHHHHHHHCT--TS---------------CCCEEEEEEESSCCCTT--HHHHHHHCCCC-----------TTC-S
T ss_pred EEEECHHHHHHHhCC--CC---------------CCCEEEEEEEeCCCCHH--HHHHHhCCeEE-----------CCC-C
Confidence 999999988887652 22 59999999999998764 34333211000 000 0
Q ss_pred cccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCC--CCCc
Q 042463 344 EASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDY--KYGW 398 (490)
Q Consensus 344 ~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~--~YG~ 398 (490)
..++.|. +++++ .++++|+|.||||||||+||+ ++||||+||. .||+
T Consensus 161 ~~~~~a~--~~~l~-----~sl~~~~l~tGR~HQIR~hl~-~lG~pI~gd~r~~~G~ 209 (243)
T 1vio_A 161 EPTKPAK--LEILD-----DYNVNLTISEGRYHQVKRMFA-ALGNKVVGLHRWKIGD 209 (243)
T ss_dssp SCCCCCE--EEECS-----SSEEEEEESCCCTTHHHHHHH-HTTCCEEEEEEEEETT
T ss_pred ccceeEE--EEEeC-----CEEEEEEEccCCcHHHHHHHH-HCCCeEcccEEEEECC
Confidence 1245555 56665 589999999999999999999 8999999999 5665
No 6
>3dh3_A Ribosomal large subunit pseudouridine synthase F; protein-RNA complex, S4 domain, alpha/beta protein, isomerase, RNA-binding, rRNA processing; HET: FHU; 3.00A {Escherichia coli}
Probab=100.00 E-value=8.6e-37 Score=305.77 Aligned_cols=204 Identities=14% Similarity=0.169 Sum_probs=155.1
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccccccccccc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSMVEGRISKR 182 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~~e~~~~~~ 182 (490)
+.++||++||+.. +.+||+.++++|++|+|+|| |+ .+++++.|.+||.|.|....
T Consensus 4 ~~g~RLdk~La~~-g~~SR~~a~~lI~~G~V~VN-----------G~-----~v~~~~~V~~gD~I~v~~~~-------- 58 (290)
T 3dh3_A 4 DSSVRLNKYISES-GICSRREADRYIEQGNVFLN-----------GK-----RATIGDQVKPGDVVKVNGQL-------- 58 (290)
T ss_dssp CCCEEHHHHHHTT-TSSCHHHHHHHHHTTCEEET-----------TE-----ECCTTCEECTTCCEEETTEE--------
T ss_pred ccchHHHHHHHhC-CCCCHHHHHHHHHCCCEEEC-----------CE-----EccCCcCcCCCCEEEecccc--------
Confidence 3579999999995 78999999999999999999 84 56899999999999995421
Q ss_pred ccCCCCCCCCCCcchhhcccceeeeeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCcee
Q 042463 183 YDTIPSGTLNPNADEIDYLRRLVKYRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGL 262 (490)
Q Consensus 183 ~~~~p~~~~~~~~~~i~~l~~~IlyeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGL 262 (490)
+. ...|||++|||+|||+||+||+......++.+++ . ....+++|||||++||||
T Consensus 59 ---------------i~----~~~~ed~~~lvvnKP~G~~~~~~~~~~~tl~~~l---~---~~~~~~~VhRLD~dTSGL 113 (290)
T 3dh3_A 59 ---------------IE----PREAEDLVLIALNKPVGIVSTTEDGERDNIVDFV---N---HSKRVFPIGRLDKDSQGL 113 (290)
T ss_dssp ---------------EC----CCCGGGCCEEEEEECTTCBCCCCSSCTTBHHHHH---T---CSSCCEESSCCCTTCEEE
T ss_pred ---------------cc----ccccccceEEEEECCCccccCCCCCCCCcHHHHh---h---ccCceeeeccCCCCCcce
Confidence 00 0137999999999999999997655444443333 2 145789999999999999
Q ss_pred EEEecCHHHHHHHHhhhhccccccchhhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCC
Q 042463 263 LLMGRTKESVSLLTWLFSDVNKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSG 342 (490)
Q Consensus 263 LLlAk~~~~a~~L~~~f~~~~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~ 342 (490)
||||+|+++++.|.++.. .|+|+|+|+|.|.+++.. +.. + ..|..
T Consensus 114 llla~d~~~~~~L~~~~~-----------------~v~K~Y~a~V~G~~~~~~--i~~-l-----~~Gv~---------- 158 (290)
T 3dh3_A 114 IFLTNHGDLVNKILRAGN-----------------DHEKEYLVTVDKPITEEF--IRG-M-----SAGVP---------- 158 (290)
T ss_dssp EEEESCTTHHHHHHCGGG-----------------CCCEEEEEEESSCCCHHH--HHH-H-----HTCCB----------
T ss_pred EEEcCCHHHHHHHHHhhC-----------------CcCEEEEEEECCCCCHHH--HHH-H-----hcCcc----------
Confidence 999999999999988633 399999999999987532 111 1 11210
Q ss_pred ccccccceeEEEEeeccCCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCC
Q 042463 343 LEASQEAMTEYRVLGPMINGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYG 397 (490)
Q Consensus 343 ~~~~k~a~T~~~vl~~~~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG 397 (490)
.++.....+.++.+ +.++++|+|.|||+||||+||+ ++||||+++..|.
T Consensus 159 l~~~~~~~~~v~~~-----~~~~l~l~l~tGR~HQIR~~~~-~lG~pV~~L~R~~ 207 (290)
T 3dh3_A 159 ILGTVTKKCKVKKE-----APFVFRITLVQGLNRQIRRMCE-HFGYEVKKLERTR 207 (290)
T ss_dssp CSSSBCCCCEEEEC-----SSSEEEEEESCCCTTHHHHHHH-HTTCCEEEEEEEE
T ss_pred cCCcccceEEEEEc-----CCeEEEEEEeCCCChHHHHHHH-HcCCeEEEeEEEE
Confidence 01111222333333 3479999999999999999999 8999999997764
No 7
>2oml_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, thrombin-cleaved, isomerase; 1.20A {Escherichia coli}
Probab=100.00 E-value=6.5e-37 Score=289.07 Aligned_cols=165 Identities=19% Similarity=0.211 Sum_probs=120.2
Q ss_pred eeeeeCCeEEEEECCCCccccCCCCC-CCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhcc
Q 042463 204 LVKYRDSAILVLNKPPKVPLKGHLPV-HNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDV 282 (490)
Q Consensus 204 ~IlyeD~~llVvNKP~Gl~v~~~~~~-~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~ 282 (490)
.|||||++|+|||||+||+||+.... ..++..++. ...+++|||||++||||||||+|+++++.|+++. +
T Consensus 5 ~ilyed~~~lvvnKP~G~~~~~~~~~~~~tl~~~l~-------~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~--~ 75 (189)
T 2oml_A 5 KPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-------VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPG--K 75 (189)
T ss_dssp ---CCCCCEEEEEECTTBCSCSSCCTTCBCGGGTCC-------CSSCEESSCCCTTCEEEEEEESCHHHHHHHHSTT--S
T ss_pred ccccCCCeEEEEECCCCCEecCCCCCCCCCHHHHcC-------CCCceECCCCCCCCeeEEEEEcCHHHHHHHhCcc--C
Confidence 49999999999999999999976542 334433321 2368999999999999999999999999999982 2
Q ss_pred ccccchhhhhhhcccceeeEEEEEEeCCCCCCc-ceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCC
Q 042463 283 NKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQ-GIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMIN 361 (490)
Q Consensus 283 ~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~-g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~ 361 (490)
.++|+|+|+|.|.+++.. +.++.++.. .++......+.. .+ ..+..+.|.|+++.....
T Consensus 76 ---------------~v~K~Y~a~v~G~~~~~~~~~i~~~i~~---~~~~~~~~~~~~-~~-~~~~~~~t~~~v~~~~~~ 135 (189)
T 2oml_A 76 ---------------RTGKIYYVQVEGIPTQDALEALRNGVTL---NDGPTLPAGAEL-VD-EPAWLWPRNPPIRERKSI 135 (189)
T ss_dssp ---------------CCCEEEEEEEESCCCHHHHHHHHHCCEE---TTEECCCCEEEE-EC-CCTTCCCCSSCCC-CTTS
T ss_pred ---------------CCcEEEEEEEcCCCCHHHHHHHHcCcee---CCceeeeeEEEE-ec-ccccccccccccccccCC
Confidence 499999999999987644 345555532 122211110100 01 111234788888875334
Q ss_pred CceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCc
Q 042463 362 GCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGW 398 (490)
Q Consensus 362 ~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~ 398 (490)
++||++|+|.|||+||||+||+ ++||||+||.+||.
T Consensus 136 ~~slv~~~l~TGR~HQIRvhla-~lG~PI~gD~~Y~~ 171 (189)
T 2oml_A 136 PTSWLKITLYEGRNRQVRRMTA-HVGFPTLRLIRYAM 171 (189)
T ss_dssp CEEEEEEEESCCCTTHHHHHHH-HTTCCEEEEEEEEE
T ss_pred CcEEEEEEEeeCCCHHHHHHHH-HcCCcCcceEEEEE
Confidence 6899999999999999999999 89999999999985
No 8
>2olw_A Ribosomal large subunit pseudouridine synthase E; bifurcated beta sheet, isomerase; 1.60A {Escherichia coli}
Probab=100.00 E-value=8.8e-36 Score=287.23 Aligned_cols=162 Identities=20% Similarity=0.250 Sum_probs=112.5
Q ss_pred eeeeeCCeEEEEECCCCccccCCCC-CCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhcc
Q 042463 204 LVKYRDSAILVLNKPPKVPLKGHLP-VHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDV 282 (490)
Q Consensus 204 ~IlyeD~~llVvNKP~Gl~v~~~~~-~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~ 282 (490)
.|||||++|+|||||+||+||+... ...++..++. ...+++|||||++||||||||+|+++++.|++++.
T Consensus 33 ~Ilyed~~~lvvnKP~Gl~~~~~~~~~~~tl~~~l~-------~~~~~~VhRLDr~TSGllllAk~~~~~~~L~~~~~-- 103 (217)
T 2olw_A 33 KPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP-------VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGK-- 103 (217)
T ss_dssp ----CCCCEEEEEECTTBCSCSSCCTTSBCGGGTCC-------CCSCEESSCCCTTCEEEEEEESCHHHHHHHHCTTC--
T ss_pred ceEeeCCcEEEEECCCCCEeccCCCCCCccHHHHhC-------cCCceECCCCCCCCeeEEEEEcCHHHHHHHHcccc--
Confidence 4999999999999999999997643 2334333221 24689999999999999999999999999998832
Q ss_pred ccccchhhhhhhcccceeeEEEEEEeCCCCCCc-ceeecccccccccCCcc--eeEEEeecCCccccccceeEEEEeecc
Q 042463 283 NKSKSLSKAWNDACEAMYQRYWALVIGSPKEKQ-GIIHAPLSKVLLDDGKT--ERIILAQNSGLEASQEAMTEYRVLGPM 359 (490)
Q Consensus 283 ~~~k~~~~~~~~~~~~v~K~Y~AlV~G~~~~~~-g~i~~~l~~~~~~~g~~--~~~~~~~~~~~~~~k~a~T~~~vl~~~ 359 (490)
.|+|+|+|+|.|.+++.. +.++.++.. .+|+. ..+.... . ...+.+.+..+...
T Consensus 104 ---------------~v~K~Y~A~V~G~~~~~~~~~i~~~i~~---~~g~~~~~~~~~~~----~-~~~~~~~~~~v~~~ 160 (217)
T 2olw_A 104 ---------------RTGKIYYVQVEGIPTQDALEALRNGVTL---NDGPTLPAGAELVD----E-PAWLWPRNPPIRER 160 (217)
T ss_dssp ---------------CCCEEEEEEEESCCCHHHHHHHHHCCEE---TTEECCCCEEEEEC----C-CTTCCCCSSCCC-C
T ss_pred ---------------cCCEEEEEEEccCCCHHHHHHHhCCEEe---CCCcccceEEEEec----C-Cccccccccceecc
Confidence 499999999999987654 345555531 12221 1111100 0 00112222112211
Q ss_pred -CCCceEEEEEeccCCCchHHHHhHhhhCCceeeCCCCCc
Q 042463 360 -INGCSWIELRPLTCRKHQLRVHCAEALGTPIVGDYKYGW 398 (490)
Q Consensus 360 -~~~~slvel~l~TGRtHQIR~hla~~lG~PIvGD~~YG~ 398 (490)
..++|||+|+|.|||+||||+||+ ++||||+||.+||.
T Consensus 161 ~~~~~slv~~~l~TGRtHQIRvhla-~lG~PIvgD~rY~~ 199 (217)
T 2olw_A 161 KSIPTSWLKITLYEGRNRQVRRMTA-HVGFPTLRLIRYAM 199 (217)
T ss_dssp CSSCEEEEEEEESCCCTTHHHHHHH-HTTCCEEEEEEEEE
T ss_pred CCCCcEEEEEEECcCCCHHHHHHHH-HCCCcEeCCEEEEE
Confidence 236799999999999999999999 89999999999985
No 9
>2gml_A Ribosomal large subunit pseudouridine synthase F; RLUF, ribosome, RNA modifying enzyme, isomerase; 2.60A {Escherichia coli}
Probab=99.95 E-value=1.9e-28 Score=237.89 Aligned_cols=141 Identities=15% Similarity=0.164 Sum_probs=106.4
Q ss_pred CCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccch
Q 042463 209 DSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSL 288 (490)
Q Consensus 209 D~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~ 288 (490)
+++|||+|||+|++|++......++.+++ . ...++++|||||++||||||||+|++++++|.++..
T Consensus 13 ~~~~lvlnKPaG~vs~~~~~~~~tv~dll----~--~~~rl~~VgRLD~dTSGLLLlT~dg~~a~~L~~p~~-------- 78 (237)
T 2gml_A 13 DLVLIALNKPVGIVSTTEDGERDNIVDFV----N--HSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGN-------- 78 (237)
T ss_dssp CCCEEEEEECTTCBCCSSSSCSSBHHHHS----C--CSSCCEEESCCCTTCEEEEEEESCHHHHHHHHHHHH--------
T ss_pred CCEEEEEECCCCCEeCCCCCCCCCHHHHh----h--ccCCeeEecCCCCCCeeEEEEEcCHHHHHHHhCccC--------
Confidence 34599999999999997655444443332 1 134689999999999999999999999999998633
Q ss_pred hhhhhhcccceeeEEEEEEeCCCCCCcceeecccccccccCCcceeEEEeecCCccccccceeEEEEeeccCCCceEEEE
Q 042463 289 SKAWNDACEAMYQRYWALVIGSPKEKQGIIHAPLSKVLLDDGKTERIILAQNSGLEASQEAMTEYRVLGPMINGCSWIEL 368 (490)
Q Consensus 289 ~~~~~~~~~~v~K~Y~AlV~G~~~~~~g~i~~~l~~~~~~~g~~~~~~~~~~~~~~~~k~a~T~~~vl~~~~~~~slvel 368 (490)
.|+|+|+|+|.|.+++.. ++. + ..|. .+ ++++.+.+.+++++ .++++|
T Consensus 79 ---------~v~K~Y~a~V~G~~~~~~--i~~-l-----~~Gv----~l------~~~~~~~a~~~~l~-----~s~l~i 126 (237)
T 2gml_A 79 ---------DHEKEYLVTVDKPITEEF--IRG-M-----SAGV----PI------LGTVTKKCKVKKEA-----PFVFRI 126 (237)
T ss_dssp ---------HSCEEEEEEESSCCCHHH--HHH-H-----SSCC----EE------TTEECCCCEEEEEE-----TTEEEE
T ss_pred ---------CCCEEEEEEEcccCCHHH--HHH-H-----HcCe----Ee------CCcccccEEEEEeC-----CEEEEE
Confidence 399999999999987532 111 1 1221 11 12344556677664 379999
Q ss_pred EeccCCCchHHHHhHhhhCCceeeCCCC
Q 042463 369 RPLTCRKHQLRVHCAEALGTPIVGDYKY 396 (490)
Q Consensus 369 ~l~TGRtHQIR~hla~~lG~PIvGD~~Y 396 (490)
+|.|||+||||+||+ ++||||+||..|
T Consensus 127 ~L~tGR~HQIRr~~a-~lG~pV~~L~R~ 153 (237)
T 2gml_A 127 TLVQGLNRQIRRMCE-HFGYEVKKLERT 153 (237)
T ss_dssp EECCCSTTHHHHHHH-HTTCCEEEEEEE
T ss_pred EEecCCcHHHHHHHH-HcCCCEeeeEEE
Confidence 999999999999999 899999999665
No 10
>2k6p_A Uncharacterized protein HP_1423; alpha-L motif, RNA-binding, unknown function; NMR {Helicobacter pylori}
Probab=97.97 E-value=1.8e-06 Score=71.19 Aligned_cols=53 Identities=15% Similarity=0.105 Sum_probs=44.5
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcccc
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVSM 174 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~~ 174 (490)
+||++||+......||+.++++|++|.|+|| |+ .+++++.|.+||.|.|....
T Consensus 1 ~RLD~~L~~~~~~~sR~~~~~li~~G~V~VN-----------g~-----~~~~~~~v~~gd~I~v~~~~ 53 (92)
T 2k6p_A 1 MRIDKFLQSVGLVKRRVLATDMCNVGAVWLN-----------GS-----CAKASKEVKAGDTISLHYLK 53 (92)
T ss_dssp CBHHHHSTTTTSCCCCCSSCCHHHHTCCEET-----------TE-----ECCTTCBCCTTCEEEECCSS
T ss_pred ChHHHHHHHCCCCCCHHHHHHHHHCCcEEEC-----------CE-----EcCCCCCcCCCCEEEEEeCC
Confidence 5899999985444599999999999999999 84 56889999999999996543
No 11
>1dm9_A Hypothetical 15.5 KD protein in MRCA-PCKA intergenic region; heat shock proteins, protein-RNA interactions, ribosome, structural genomics; 2.00A {Escherichia coli} SCOP: d.66.1.3 PDB: 3bbu_A
Probab=97.83 E-value=3.3e-05 Score=68.15 Aligned_cols=55 Identities=18% Similarity=0.214 Sum_probs=47.2
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEccc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVS 173 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~ 173 (490)
+.++||++||.......||+.++++|..|.|+|| |+ .+++++.|.+||.|.|...
T Consensus 6 ~~~~RLDk~L~~~~~~~SRs~a~~li~~G~V~VN-----------G~-----~vk~s~~V~~GD~I~I~~~ 60 (133)
T 1dm9_A 6 AVEVRLDKWLWAARFYKTRALAREMIEGGKVHYN-----------GQ-----RSKPSKIVELNATLTLRQG 60 (133)
T ss_dssp TTCCBHHHHHHHTTSSSSHHHHHHHHHTTCEEET-----------TE-----ECCTTCBCCTTCEEEEEET
T ss_pred ccchhHHHHHHHCCCCCCHHHHHHHHHCCcEEEC-----------CE-----EcCCCCEeCCCCEEEEEeC
Confidence 3468999999986445799999999999999999 83 5689999999999999543
No 12
>1p9k_A ORF, hypothetical protein; alfal motif, RNA-binding protein, E.coli, montreal-kingston structural genomics initiative, BSGI; NMR {Escherichia coli} SCOP: d.66.1.6
Probab=97.41 E-value=3.2e-05 Score=61.84 Aligned_cols=52 Identities=13% Similarity=0.212 Sum_probs=43.9
Q ss_pred CcccHHHHHHhcCCcC-CHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 104 CHVTAVSWVKYYFDEV-QDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~-sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
..+||++||+.. +.+ ||+.++++|++|+|+|| |+. ..++++.+.+||.|.+.
T Consensus 19 ~~~RLdk~L~~~-g~~~SR~~a~~lI~~G~V~VN-----------G~~----v~~~~~~v~~gd~I~v~ 71 (79)
T 1p9k_A 19 PHVELCDLLKLE-GWSESGAQAKIAIAEGQVKVD-----------GAV----ETRKRCKIVAGQTVSFA 71 (79)
T ss_dssp SCCCHHHHHHHH-TSCSSSSTTSHHHHHHHHEET-----------TBC----CCCSSCCCCSSEEEEET
T ss_pred CCchHHHHHHHC-CCCCCHHHHHHHHHCCEEEEC-----------CEE----ecCCCCCCCCCCEEEEC
Confidence 348999999995 544 99999999999999999 742 44788999999999884
No 13
>1c05_A Ribosomal protein S4 delta 41; two subdomains, unique topology, possible helix-turn-helix motif, ribosome; NMR {Geobacillus stearothermophilus} SCOP: d.66.1.2 PDB: 1c06_A 1eg0_A 1qd7_C
Probab=97.24 E-value=0.00042 Score=62.85 Aligned_cols=52 Identities=12% Similarity=0.107 Sum_probs=45.4
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceec-CCCCcccCCCEEEEcc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKI-KTNEVMEPGARIFLPV 172 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~-~~~~~l~~Gd~I~v~~ 172 (490)
++||+++|.+.....||+.++++|..|.|+|| |+ ++ ++++.|.+||.|.|..
T Consensus 50 e~RLD~~L~~~g~~~SR~~ar~lI~~G~V~VN-----------G~-----~v~~ps~~V~~gD~I~V~~ 102 (159)
T 1c05_A 50 ESRLDNLVYRLGLARTRRQARQLVTHGHILVD-----------GS-----RVNIPSYRVKPGQTIAVRE 102 (159)
T ss_dssp HHBHHHHHHHTTSCSSHHHHHHHHHTTCEEET-----------TE-----ECCCSSCBCCTTCEEEECG
T ss_pred HHHHHHHHHHcCCcCCHHHHHHHHHCCCEEEC-----------CE-----EeCcCCcEeCCCCEEEEeC
Confidence 58999999986556799999999999999999 84 45 6899999999999954
No 14
>2vqe_D 30S ribosomal protein S4; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: d.66.1.2 PDB: 1hnw_D* 1hnx_D* 1hnz_D* 1ibk_D* 1fka_D* 1ibm_D 1xmo_D* 1ibl_D* 1xnq_D* 1xnr_D* 1yl4_G 2b64_D* 2b9m_D* 2b9o_D* 2hgi_G 2hgp_G 2hgr_G 2hhh_D* 1xmq_D* 2j02_D* ...
Probab=97.09 E-value=0.00073 Score=64.02 Aligned_cols=52 Identities=13% Similarity=0.139 Sum_probs=45.2
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceec-CCCCcccCCCEEEEcc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKI-KTNEVMEPGARIFLPV 172 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~-~~~~~l~~Gd~I~v~~ 172 (490)
++||+++|.+.....||+.++++|..|.|+|| |+ ++ .+++.|.+||.|.|..
T Consensus 98 e~RLD~~L~~~g~~~SR~~arqLI~~G~V~VN-----------G~-----~v~~ps~~V~~gD~I~V~~ 150 (209)
T 2vqe_D 98 ESRLDNVVYRLGFAVSRRQARQLVRHGHITVN-----------GR-----RVDLPSYRVRPGDEIAVAE 150 (209)
T ss_dssp HTBHHHHHHHTTSSSSHHHHHHHHHTTCEEET-----------TE-----ECCCTTCBCCTTCEEEECG
T ss_pred HHHHHHHHHHhcCcCCHHHHHHHHHCCCEEEC-----------CE-----EeCcCCcCcCCCCEEEEcC
Confidence 58999999985545799999999999999999 84 45 5999999999999954
No 15
>2cqj_A BRMS2, U3 small nucleolar ribonucleoprotein protein IMP3 homolog; S4 domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=97.05 E-value=0.0004 Score=54.46 Aligned_cols=50 Identities=4% Similarity=-0.074 Sum_probs=42.7
Q ss_pred cccHHHHHHhcCCcC-CHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccC--CCEEEE
Q 042463 105 HVTAVSWVKYYFDEV-QDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEP--GARIFL 170 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~-sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~--Gd~I~v 170 (490)
..||+.+|.+ .+.+ ||+.++++|..|.|+|| |+ ...++++.+.+ +|.|.+
T Consensus 7 ~~RLD~~l~~-~gla~SR~~A~~lI~~G~V~Vn-----------g~----~v~kps~~V~~~~~d~I~~ 59 (71)
T 2cqj_A 7 GRRLPTVLLK-LRMAQHLQAAVAFVEQGHVRVG-----------PD----VVTDPAFLVTRSMEDFVTW 59 (71)
T ss_dssp EEEHHHHHHH-TTCSSSHHHHHHHHHTTCEEET-----------TB----CCCCTTCEEEHHHHTTEEE
T ss_pred HHHHHHHHHH-hCCcCCHHHHHHHHHCCcEEEC-----------CE----EECCCCCCCCCCCCcEEEE
Confidence 4799999999 5555 99999999999999999 75 26679999988 788876
No 16
>3hp7_A Hemolysin, putative; structural genomics, APC64019, PSI-2, protein STR initiative, midwest center for structural genomics, MCSG; HET: MSE; 1.53A {Streptococcus thermophilus}
Probab=97.01 E-value=0.00067 Score=67.47 Aligned_cols=54 Identities=13% Similarity=-0.135 Sum_probs=46.9
Q ss_pred CcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCC-C-cCcceecCCCCcccCCCEEEEcc
Q 042463 104 CHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQG-Q-MKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~G-k-~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
.++|||+||.......||+.++++|.+|+|+|| | + . ..++++.|.+||.|.|..
T Consensus 5 ~~~RLD~~L~~~g~~~SR~~a~~lI~~G~V~Vn-----------g~~~~----v~kp~~~V~~~d~I~v~g 60 (291)
T 3hp7_A 5 PKERVDVLAYKQGLFETREQAKRGVMAGLVVNV-----------INGER----YDKPGEKIDDGTELKLKG 60 (291)
T ss_dssp CEEEHHHHHHHTTSSSSHHHHHHHHHTTCEEET-----------TTCCB----CCCTTCEEETTCCEEETT
T ss_pred chhhHHHHHHHcCCcccHHHHHHHHHCCeEEEC-----------CeEEE----EccCCCCCCCCCEEEEcc
Confidence 368999999997666799999999999999999 6 5 3 567899999999999954
No 17
>3r8n_D 30S ribosomal protein S4; protein biosynthesis, RNA, tRNA, transfer RNA, 16S ribosomal subunit, RRF; 3.00A {Escherichia coli} PDB: 1p6g_D 1p87_D 2aw7_D 2avy_D 2i2u_D 2i2p_D* 2qan_D* 2qb9_D* 2qbb_D* 2qbd_D 2qbf_D 2qbh_D* 2qbj_D* 2qou_D* 2qow_D* 2qoy_D* 2qp0_D* 2vho_D 2vhp_D 2wwl_D* ...
Probab=96.95 E-value=0.00026 Score=66.72 Aligned_cols=54 Identities=6% Similarity=-0.058 Sum_probs=45.9
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEccc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVS 173 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~ 173 (490)
++|||+||.+.....||+.++++|..|.|+|| |++ +..+++.|.+||.|.|...
T Consensus 94 e~RLD~~L~r~g~~~SR~~ArqLI~~G~V~VN-----------G~~----V~~ps~~Vk~GD~I~V~~~ 147 (205)
T 3r8n_D 94 EGRLDNVVYRMGFGATRAEARQLVSHKAIMVN-----------GRV----VNIASYQVSPNDVVSIREK 147 (205)
T ss_dssp HTBTTHHHHTTSSCSSHHHHHHHHHTTCCBSS-----------SSB----CCCTTCBCCTTBCCBCCSS
T ss_pred HhhHHHHHHHhcchhHHHHHHHHHHCCCEEEC-----------CEE----EccCCcCcCCCCEEEecCc
Confidence 68999999985556799999999999999999 742 4468999999999998544
No 18
>3bbn_D Ribosomal protein S4; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea}
Probab=96.58 E-value=0.00082 Score=63.19 Aligned_cols=54 Identities=7% Similarity=-0.102 Sum_probs=44.8
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEccc
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPVS 173 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~~ 173 (490)
.+|||+||.+..-..||+.++++|..|.|+|| |+ .+..+++.|.+||.|.|...
T Consensus 88 e~RLD~~L~r~g~a~SR~~ArqLI~~G~V~VN-----------G~----~V~~pS~~V~~gD~I~V~~~ 141 (201)
T 3bbn_D 88 EMRLDNILFRLGMAPTIPGARQLVNHRHILVN-----------GR----IVDIPSYRCKPQDTIMARDE 141 (201)
T ss_dssp HSBTTTTTTTTTSSSSSHHHHHHHHTTCEEET-----------TE----ECCCTTCBCCTTEEEEECSS
T ss_pred HHHHHHHHHHcCCcCCHHHHHHHHhCCcEEeC-----------CE----EEeecceecCCCCEEEEccc
Confidence 57889998885444699999999999999999 74 24468999999999999644
No 19
>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=96.53 E-value=0.002 Score=65.21 Aligned_cols=73 Identities=19% Similarity=0.143 Sum_probs=53.6
Q ss_pred eeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhcccccc
Q 042463 207 YRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSK 286 (490)
Q Consensus 207 yeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k 286 (490)
|-.+.+|+||||.|+.+| .++....+.....+.+..+-||-..||||+++-.. + .++...+.+
T Consensus 43 ~~~~Gil~vdKP~g~tS~----------~vv~~vr~~~~~~KvGH~GTLDP~atGvL~v~~g~-a-Tk~~~~l~~----- 105 (334)
T 2aus_C 43 HIQYGVINLDKPPGPTSH----------EVVAWIKRILNLEKAGHGGTLDPKVSGVLPVALER-A-TRVVQALLP----- 105 (334)
T ss_dssp HHHTEEEEEEECSSSCHH----------HHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGG-G-GGGGGGGTT-----
T ss_pred hccCcEEEEECCCCCCHH----------HHHHHHHHHhCcceeccccccCCccceeEEEEeCh-h-hhhHHHhcc-----
Confidence 445679999999999775 33333333345567899999999999999999864 3 355555544
Q ss_pred chhhhhhhcccceeeEEEEEEe
Q 042463 287 SLSKAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 287 ~~~~~~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 106 ------------~~K~Y~~~~~ 115 (334)
T 2aus_C 106 ------------AGKEYVALMH 115 (334)
T ss_dssp ------------CCEEEEEEEE
T ss_pred ------------cCcEEEEEEE
Confidence 5799999875
No 20
>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=96.52 E-value=0.0021 Score=64.15 Aligned_cols=70 Identities=19% Similarity=0.252 Sum_probs=51.8
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||+|+.+| .++....+.....+....+-||-..||||+++-... .++...+..
T Consensus 3 ~Gil~vdKP~G~TS~----------~vv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l~~-------- 62 (309)
T 1r3e_A 3 HGILVAYKPKGPTSH----------DVVDEVRKKLKTRKVGHGGTLDPFACGVLIIGVNQG--TRILEFYKD-------- 62 (309)
T ss_dssp CEEEEEEECSSSCHH----------HHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGG--GGGGGGGTT--------
T ss_pred CeEEEEECCCCCCHH----------HHHHHHHHHhccceecccccCCCCcceeEEEEECHH--HhHHHHhCc--------
Confidence 458999999999875 333333343456678999999999999999998753 244444444
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 63 ---------~~K~Y~a~~~ 72 (309)
T 1r3e_A 63 ---------LKKVYWVKMR 72 (309)
T ss_dssp ---------SCEEEEEEEE
T ss_pred ---------cCcEEEEEEE
Confidence 4799999875
No 21
>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=96.44 E-value=0.0025 Score=63.74 Aligned_cols=71 Identities=17% Similarity=0.240 Sum_probs=52.7
Q ss_pred CCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccch
Q 042463 209 DSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSL 288 (490)
Q Consensus 209 D~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~ 288 (490)
.+.+|+||||.|+.++ .++....+.....+....+-||-..||||+++-... .++...+..
T Consensus 5 ~~Gil~vdKP~G~TS~----------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~iG~a--TKl~~~l~~------- 65 (316)
T 1sgv_A 5 GPGIVVIDKPAGMTSH----------DVVGRCRRIFATRRVGHAGTLDPMATGVLVIGIERA--TKILGLLTA------- 65 (316)
T ss_dssp CSEEEEEEECTTCCHH----------HHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGG--GGGGGGTTT-------
T ss_pred CCeEEEEECCCCCCHH----------HHHHHHHHHhccccccccccCCCCCeEEEEEEECHH--HhHHHHhCc-------
Confidence 3569999999999875 344444444456788999999999999999998753 244444443
Q ss_pred hhhhhhcccceeeEEEEEEe
Q 042463 289 SKAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 289 ~~~~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 66 ----------~~K~Y~~~~~ 75 (316)
T 1sgv_A 66 ----------APKSYAATIR 75 (316)
T ss_dssp ----------SCEEEEEEEE
T ss_pred ----------CCcEEEEEEE
Confidence 5899999875
No 22
>3j20_D 30S ribosomal protein S4P; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=96.41 E-value=0.0017 Score=59.92 Aligned_cols=51 Identities=10% Similarity=0.007 Sum_probs=43.7
Q ss_pred cccHHHHHHhcCCcC-CHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCC--CEEEEc
Q 042463 105 HVTAVSWVKYYFDEV-QDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPG--ARIFLP 171 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~-sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~G--d~I~v~ 171 (490)
.+||+.||.+ .+.+ ||+.++++|..|.|+|| |++ +.++++.|.+| |.|.+.
T Consensus 102 e~RLD~~L~~-~G~a~SR~~Ar~LI~~G~V~VN-----------g~~----V~~Ps~~V~~~~eD~I~v~ 155 (180)
T 3j20_D 102 ERRLQTIVYK-KGLARTMRQARQLIVHGHIEVN-----------GQI----IRSPSYLVLKEEEDTITYA 155 (180)
T ss_dssp HTSHHHHHHH-HTSSSSHHHHHHHHHHTCCEES-----------SSB----CCCSSCCCCTGGGGCEECS
T ss_pred hhhhhheeec-CcccCcHHHHHHHHHcCCeEEC-----------CEE----eCCCCcccCCCCCCEEEEe
Confidence 6899999987 4445 99999999999999999 752 56799999999 889883
No 23
>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=96.34 E-value=0.003 Score=63.53 Aligned_cols=70 Identities=16% Similarity=0.201 Sum_probs=51.1
Q ss_pred CeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhccccccchh
Q 042463 210 SAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSKSLS 289 (490)
Q Consensus 210 ~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k~~~ 289 (490)
+.+|+||||.|+.++ .++....+.....+....+.||-..||||+++-.... ++...+..
T Consensus 25 ~Gil~vdKP~G~TS~----------dvv~~vr~~l~~kKvGH~GTLDP~AtGvL~i~~G~aT--Kl~~~l~~-------- 84 (327)
T 1k8w_A 25 NGVLLLDKPQGMSSN----------DALQKVKRIYNANRAGHTGALDPLATGMLPICLGEAT--KFSQYLLD-------- 84 (327)
T ss_dssp CEEEEEEECTTCCHH----------HHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGGGG--GGTHHHHT--------
T ss_pred CeEEEEECCCCCCHH----------HHHHHHHHhhccceeccCCCCCCCCeeEEEEEECHHH--hHHHHhcc--------
Confidence 459999999999874 3333333444556789999999999999999987532 24444443
Q ss_pred hhhhhcccceeeEEEEEEe
Q 042463 290 KAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 290 ~~~~~~~~~v~K~Y~AlV~ 308 (490)
-.|+|.|.+.
T Consensus 85 ---------~~K~Y~a~~~ 94 (327)
T 1k8w_A 85 ---------SDKRYRVIAR 94 (327)
T ss_dssp ---------SCEEEEEEEE
T ss_pred ---------CCcEEEEEEE
Confidence 4799999875
No 24
>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=96.33 E-value=0.003 Score=64.37 Aligned_cols=73 Identities=12% Similarity=0.099 Sum_probs=53.9
Q ss_pred eeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhcccccc
Q 042463 207 YRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSK 286 (490)
Q Consensus 207 yeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k 286 (490)
|-.+.+|+||||.|+.++ .++....+.....+....+-||-..||||+++-.. + .++...+..
T Consensus 63 ~~~~Gil~vdKP~G~TS~----------~vv~~vr~~l~~~KvGH~GTLDP~AtGvL~v~~G~-a-Tk~~~~l~~----- 125 (357)
T 2apo_A 63 LIKYGVVVVDKPRGPTSH----------EVSTWVKKILNLDKAGHGGTLDPKVTGVLPVALER-A-TKTIPMWHI----- 125 (357)
T ss_dssp HHHTEEEEEEECSSSCHH----------HHHHHHHHHTTCSCEEESSCCCTTCEEEEEEEEGG-G-GGGGGGTTS-----
T ss_pred hccCcEEEEECCCCCCHH----------HHHHHHHHHhCccccccccccCCCceeEEEEEeCH-H-HhHHHHhcc-----
Confidence 445679999999999875 33333334345567899999999999999999864 3 345555544
Q ss_pred chhhhhhhcccceeeEEEEEEe
Q 042463 287 SLSKAWNDACEAMYQRYWALVI 308 (490)
Q Consensus 287 ~~~~~~~~~~~~v~K~Y~AlV~ 308 (490)
..|+|.|.+.
T Consensus 126 ------------~~K~Y~~~~~ 135 (357)
T 2apo_A 126 ------------PPKEYVCLMH 135 (357)
T ss_dssp ------------SCEEEEEEEE
T ss_pred ------------CCcEEEEEEE
Confidence 5799999875
No 25
>3u28_A H/ACA ribonucleoprotein complex subunit 4; pseudouridine synthase, pseudouridylation, H/ACA RNA; 1.90A {Saccharomyces cerevisiae} PDB: 3uai_A
Probab=95.98 E-value=0.0053 Score=63.21 Aligned_cols=76 Identities=18% Similarity=0.161 Sum_probs=54.1
Q ss_pred eeCCeEEEEECCCCccccCCCCCCCCHHHHHHHHHhccCCCCCccccCCCcCCceeEEEecCHHHHHHHHhhhhcccccc
Q 042463 207 YRDSAILVLNKPPKVPLKGHLPVHNSMDALAAAALSYDYNEGPKLVHRLDRESSGLLLMGRTKESVSLLTWLFSDVNKSK 286 (490)
Q Consensus 207 yeD~~llVvNKP~Gl~v~~~~~~~~~~~~ll~~~~~~~~~~~l~~VHRLDr~TSGLLLlAk~~~~a~~L~~~f~~~~~~k 286 (490)
|-.+.+|+||||.|+.+| .++....+.....+....+-||-..||||+++-.. +. ++...+..
T Consensus 56 ~~~~Gil~ldKP~G~TS~----------dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~iG~-aT-Kl~~~l~~----- 118 (400)
T 3u28_A 56 YISSGVINLDKPSNPSSH----------EVVAWIKRILRCEKTGHSGTLDPKVTGCLIVCIDR-AT-RLVKSQQG----- 118 (400)
T ss_dssp HHHTEEEEEEECSSSCHH----------HHHHHHHHHHTCSCEEESSCCCTTCEEEEEEEEGG-GG-GGHHHHHH-----
T ss_pred hccCcEEEEECCCCCCHH----------HHHHHHHHHhCcCcccccCCCCCCCeEEEEEEECh-HH-hHhHHhcC-----
Confidence 455789999999999875 33333333345567899999999999999999864 33 34444443
Q ss_pred chhhhhhhcccceeeEEEEEEe-CCC
Q 042463 287 SLSKAWNDACEAMYQRYWALVI-GSP 311 (490)
Q Consensus 287 ~~~~~~~~~~~~v~K~Y~AlV~-G~~ 311 (490)
-.|+|.|.+. |..
T Consensus 119 ------------~~K~Y~a~~~lG~~ 132 (400)
T 3u28_A 119 ------------AGKEYVCIVRLHDA 132 (400)
T ss_dssp ------------SCEEEEEEEEESSC
T ss_pred ------------CCcEEEEEEEeCCC
Confidence 4799999874 443
No 26
>2xzm_D Ribosomal protein S4 containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_D
Probab=95.56 E-value=0.0057 Score=56.49 Aligned_cols=50 Identities=4% Similarity=-0.092 Sum_probs=42.0
Q ss_pred cccHHHHHHhcCCcC-CHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCC--EEEE
Q 042463 105 HVTAVSWVKYYFDEV-QDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGA--RIFL 170 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~-sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd--~I~v 170 (490)
.+||+.+|.+ .+.+ ||+.++.+|..|.|+|| |+ .+..+++.|.+|| .|.+
T Consensus 106 e~RLD~vL~~-~G~a~SR~~Ar~LI~~G~V~VN-----------g~----~V~~Ps~~V~~~d~~~I~v 158 (181)
T 2xzm_D 106 ERRLQTRVFK-LNLANSIHHSRVLIRQRHIKVG-----------KN----LVNVPSFMVRTDSEKSIDF 158 (181)
T ss_dssp TTBHHHHHHH-TTCSSSTTHHHHHTTTTCCEET-----------TE----ECCCSCCBCCSTTSSCEEC
T ss_pred ccchhHHHHh-ccccCCHHHHHHHHHCCEEEEC-----------CE----EECCCCcCCCCCCceEEEE
Confidence 5899999988 4555 99999999999999999 75 2567999999997 4554
No 27
>3u5c_J 40S ribosomal protein S9-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_C 3o30_E 3o2z_E 3u5g_J 1s1h_D 3jyv_D*
Probab=95.02 E-value=0.0097 Score=55.52 Aligned_cols=50 Identities=6% Similarity=-0.104 Sum_probs=41.9
Q ss_pred cccHHHHHHhcCCcC-CHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCC--EEEE
Q 042463 105 HVTAVSWVKYYFDEV-QDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGA--RIFL 170 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~-sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd--~I~v 170 (490)
.+||+.||.+ .+-+ ||+.++++|..|.|+|| |+ .+..+++.|.+|+ .|.+
T Consensus 106 e~RLD~~L~r-~G~a~Sr~~ArqLI~~GhV~VN-----------G~----~V~~Ps~~V~~g~ed~I~~ 158 (197)
T 3u5c_J 106 ERRLQTQVYK-LGLAKSVHHARVLITQRHIAVG-----------KQ----IVNIPSFMVRLDSEKHIDF 158 (197)
T ss_dssp TTSHHHHHHH-SSTTSSHHHHHHHHHTSCCBSS-----------SC----BCCCTTCCCCSTTGGGCBC
T ss_pred HHHHHHHHHH-ccccCCHHHHHHHHHcCCEEEC-----------CE----EeCCCccccCCCCccEEEE
Confidence 5799999998 5555 99999999999999999 75 3567999999995 5655
No 28
>3j20_E 30S ribosomal protein S4E; archaea, archaeal, KINK-turn, protein synthe ribosome; 6.60A {Pyrococcus furiosus}
Probab=90.21 E-value=1.4 Score=42.20 Aligned_cols=55 Identities=11% Similarity=0.156 Sum_probs=48.0
Q ss_pred CCcccHHHHHHhcCCc-CCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 103 QCHVTAVSWVKYYFDE-VQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~-~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
.+.++|.=||+.+++. .+++++++.+.+|.|+|| |++ +..+.+.+-.+|+|.++.
T Consensus 40 ~~~lPL~i~LRdrLgyA~t~rEar~Iv~~~~I~Vd-----------GKv----r~d~~ypvG~mDVIsI~k 95 (243)
T 3j20_E 40 RTSIPLLYIVRDYLGYAKTAREARKILNEGKFLVD-----------GRV----RKDYKFPVGIMDVVSIPE 95 (243)
T ss_dssp TTCEEHHHHHHTTSCCCSSHHHHHHHHHHCSCEET-----------TEE----CCCSSCEECTTCEEEETT
T ss_pred ccceeehhhhhhhhccccCHHHHHHHHHCCcEEEC-----------CEE----eccccCCcccceEEEecc
Confidence 4458899999999987 778999999999999999 863 677899999999999943
No 29
>3iz6_C 40S ribosomal protein S9 (S4P); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
Probab=89.66 E-value=0.0042 Score=57.84 Aligned_cols=53 Identities=4% Similarity=-0.141 Sum_probs=44.1
Q ss_pred CcccHHHHHHhcCCcC-CHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 104 CHVTAVSWVKYYFDEV-QDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~~-sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
..+||+.||.+ .+-+ ||+.++++|..|.|+|| |+ .+..+++.|.+||.+.|..
T Consensus 107 le~RLD~~L~r-~G~a~SR~~ArqlI~~GhV~VN-----------G~----~V~~Ps~~V~~gde~~I~~ 160 (195)
T 3iz6_C 107 LARRLQTLVFK-AGMAKSIHHARVLIRQRHIRVG-----------RQ----IVNIPSFMVRVESEKHIDF 160 (195)
T ss_dssp TTSCCCSSCCC-CCCHHHHSCTTSHHHHHSTTTS-----------CC----CCCCCCCCCSSSCSSSSCS
T ss_pred HHhhhhHHHHh-ccccCCHHHHHHHHHcCCEEEC-----------CE----EeCCCCcCcCCCCEEEEEe
Confidence 35789999888 5555 99999999999999999 75 2567999999999877743
No 30
>3kbg_A 30S ribosomal protein S4E; RPS4E, RS4E_theac, TAR28, NESG, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.75A {Thermoplasma acidophilum}
Probab=83.14 E-value=0.91 Score=42.64 Aligned_cols=52 Identities=17% Similarity=0.186 Sum_probs=45.3
Q ss_pred CcccHHHHHHhcCCc-CCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEE
Q 042463 104 CHVTAVSWVKYYFDE-VQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFL 170 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~-~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v 170 (490)
+.++|.=||+.+++. .+++++++.+.+|.|+|| |++ +..+.+.+..+|+|.+
T Consensus 6 eslPL~i~LRdrLgyA~t~rEarkIv~~~~I~VD-----------GKv----r~d~~ypvG~mDVIsI 58 (213)
T 3kbg_A 6 QSVTLLSIIRDYLKLSDKEREAARILANGLVKVD-----------GKT----VREKKFAVGFMDVIEI 58 (213)
T ss_dssp SCEEHHHHHHHHHHTTTCGGGHHHHHHTTCEEET-----------TEE----CCCTTCEECTTCEEEE
T ss_pred hceeeHHHHhhhhcccccHHHHHHHHHCCCEEEC-----------CEE----ecccCCCccceeEEEe
Confidence 347888899988876 678999999999999999 863 6778999999999999
No 31
>2xzm_W 40S ribosomal protein S4; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_W
Probab=69.21 E-value=13 Score=35.86 Aligned_cols=55 Identities=7% Similarity=0.009 Sum_probs=43.2
Q ss_pred CCCcccHHHHHHhcCCc-CCHHHHHHHHHc--CcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 102 RQCHVTAVSWVKYYFDE-VQDSVIQSHFNK--GLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 102 ~~~~~rl~~~L~~~~~~-~sr~~i~klI~~--G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
..+.++|.=||+..++. .+.+++++.+.+ |.|+|| |++ +.+..+.+--=|+|.++
T Consensus 38 ~~eslPL~i~LRd~LkyA~t~rEak~Il~q~~~~VkVD-----------Gkv----r~D~~~PvG~MDVIsI~ 95 (260)
T 2xzm_W 38 LRESLPLSVLLKERLNYALNGRDVTLILNDKEQNVFVD-----------GKV----RRDKGYPTGLMDVVRIE 95 (260)
T ss_dssp SSSCEEHHHHHTTTTCSCCSHHHHHHHTTSTTCCEEET-----------TEE----CCCTTCEECTTCEEEEG
T ss_pred cceeehhHhhhhhhhccccchhHHHHHHhccCCeEEEC-----------CEE----eccCCCCCcEEEEEeEc
Confidence 34458899999998876 788899999999 999999 853 44556666556999884
No 32
>3u5c_E RP5, S7, YS6, 40S ribosomal protein S4-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_D 3u5g_E
Probab=61.21 E-value=14 Score=35.65 Aligned_cols=54 Identities=9% Similarity=0.139 Sum_probs=44.0
Q ss_pred CCcccHHHHHHhcCCc-CCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 103 QCHVTAVSWVKYYFDE-VQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~-~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
.+.++|.=||+..++. .+.+++++.+.+|.|+|| |++ +.+..+.+--=|+|.++
T Consensus 39 ~eslPL~i~LRd~LkyA~t~~EakkIl~q~~VkVD-----------Gkv----rtD~~~PvG~MDVIsI~ 93 (261)
T 3u5c_E 39 RESLPLIVFLRNRLKYALNGREVKAILMQRHVKVD-----------GKV----RTDTTYPAGFMDVITLD 93 (261)
T ss_dssp GGEEEHHHHHHHTTCCCSSSHHHHHHHTTTCEEET-----------TBC----CCCTTCEEETTCEEEET
T ss_pred hhheeeHHHhhhhhcccccHHHHHHHHHCCcEEEC-----------CEE----eccCCCCCceEEEEEEc
Confidence 4457899999999987 567999999999999999 864 55666666666999994
No 33
>1fm0_D Molybdopterin convertin factor, subunit 1; molybdenum cofactor biosynthesis, transferase; 1.45A {Escherichia coli} SCOP: d.15.3.1 PDB: 1fma_D 1jw9_D 1jwa_D* 1jwb_D* 3bii_D 1nvi_D
Probab=47.47 E-value=27 Score=26.55 Aligned_cols=47 Identities=9% Similarity=0.093 Sum_probs=29.8
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcC--cEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEE
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKG--LVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFL 170 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G--~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v 170 (490)
.++.+.+.... ... ..+++++..+ .|.|| | +.+..++.|+.||.|.+
T Consensus 26 ~tv~~ll~~L~-~~~-p~~~~~l~~~~~~v~vN-----------~-----~~v~~~~~l~~gD~V~i 74 (81)
T 1fm0_D 26 PTVEALRQHMA-AQS-DRWALALEDGKLLAAVN-----------Q-----TLVSFDHPLTDGDEVAF 74 (81)
T ss_dssp SBHHHHHHHHH-TTC-HHHHHHHCCTTCEEEET-----------T-----EECCTTCBCCTTCEEEE
T ss_pred CCHHHHHHHHH-HHC-hhHHHHhcCCCEEEEEC-----------C-----EECCCCCCCCCCCEEEE
Confidence 45555544421 111 2456666555 48888 7 35677899999999988
No 34
>3iz6_D 40S ribosomal protein S4 (S4E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}
Probab=47.18 E-value=11 Score=36.49 Aligned_cols=53 Identities=9% Similarity=0.062 Sum_probs=39.5
Q ss_pred CcccHHHHHHhcCCc-CCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 104 CHVTAVSWVKYYFDE-VQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 104 ~~~rl~~~L~~~~~~-~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
+.++|.=||+..++. .+.+++++.+.+|.|+|| |++ +.+..+.+--=|+|.++
T Consensus 40 eslPL~i~LRd~LkyA~t~~EakkIl~q~~VkVD-----------Gkv----rtD~~~PvG~MDVIsI~ 93 (265)
T 3iz6_D 40 ECLPLILIIRNRLKYALTYREVISILMQRHVLVD-----------GKV----RTDKTYPAGFMDVISIP 93 (265)
T ss_dssp ---CHHHHHHHHHTTSSCSSSTHHHHHTTCCEET-----------TEE----CCCTTCCCCTTCEEECC
T ss_pred hheeeHHHhhhhhcccccHHHHHHHHHCCcEEEC-----------CEE----eccCCCCCcEEEEEEEc
Confidence 447899999998876 567899999999999999 853 44455555555999884
No 35
>2og0_A Excisionase; protein-DNA complex, DNA architectural protein, 'winged'HELI protein, phage excision; 1.90A {Enterobacteria phage lambda} SCOP: a.6.1.7 PDB: 1lx8_A 1rh6_A 2ief_A
Probab=43.51 E-value=23 Score=25.48 Aligned_cols=29 Identities=7% Similarity=0.051 Sum_probs=25.4
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcCcEE
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKGLVQ 134 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G~V~ 134 (490)
.+|.+|-..+|+..|.+.+.+++++|.|.
T Consensus 3 ltl~EwA~~~~~~~s~~Tl~r~ar~G~I~ 31 (52)
T 2og0_A 3 LTLQEWNARQRRPRSLETVRRWVRESRIF 31 (52)
T ss_dssp EEHHHHHHTSSSCCCHHHHHHHHHTTCEE
T ss_pred eeHHHHHHHhcCCCCHHHHHHHHHCCCCC
Confidence 47899999877668999999999999984
No 36
>1h3f_A Tyrosyl-tRNA synthetase; ligase, aminoacyl-tRNA synthetase; HET: TYE; 2.00A {Thermus thermophilus} SCOP: c.26.1.1 d.66.1.4 PDB: 1h3e_A*
Probab=42.57 E-value=31 Score=35.65 Aligned_cols=47 Identities=2% Similarity=-0.054 Sum_probs=36.4
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCC
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGA 166 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd 166 (490)
+..+.++|...--.-|+++++++|..|-|+|| |+ ++.+.+..+..++
T Consensus 368 ~~~~~~~l~~~~l~~S~~earr~i~~ggv~vn-----------~~----~v~d~~~~~~~~~ 414 (432)
T 1h3f_A 368 RIWVARLFTLAGLTPSNAEARRLIQNRGLRLD-----------GE----VLTDPMLQVDLSR 414 (432)
T ss_dssp EEEHHHHHHHTTSSSSHHHHHHHHHTTCEEET-----------TE----ECCCTTCEEECSS
T ss_pred cCcHHHHHHHhCCcccHHHHHHHHHhCCEEEC-----------CE----EecCccceecCCC
Confidence 46789998874335799999999999999999 64 3556677776655
No 37
>2jan_A Tyrosyl-tRNA synthetase; protein biosynthesis, aminoacyl-tRNA synthetase, tyrrs, ligase, tyrosine, RNA-binding, ATP-binding; 2.9A {Mycobacterium tuberculosis}
Probab=37.65 E-value=21 Score=36.90 Aligned_cols=30 Identities=10% Similarity=0.019 Sum_probs=25.9
Q ss_pred cHHHHHHhcCCcCCHHHHHHHHHcCcEEec
Q 042463 107 TAVSWVKYYFDEVQDSVIQSHFNKGLVQME 136 (490)
Q Consensus 107 rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn 136 (490)
.+.++|...--.-|+++++++|..|-|+||
T Consensus 357 ~~~~ll~~~gl~~S~~earr~i~~ggv~in 386 (432)
T 2jan_A 357 GIVDLLVASGLSASKGAARRTIHEGGVSVN 386 (432)
T ss_dssp SHHHHHHHHTSCSSHHHHHHHHTTTCEEES
T ss_pred hHHHHHHHhCCcccHHHHHHHHHhCCEEEC
Confidence 688888874335699999999999999999
No 38
>1jil_A Tyrrs, tyrosyl-tRNA synthetase; truncation, based inhibitor design, ligase; HET: 485; 2.20A {Staphylococcus aureus} SCOP: c.26.1.1 PDB: 1jij_A* 1jii_A* 1jik_A*
Probab=36.93 E-value=7.2 Score=40.31 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=0.0
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEE
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARI 168 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I 168 (490)
..++.++|...--.-|+++++++|..|.|+|| |+ +....+..+.++|.+
T Consensus 352 ~i~l~~lL~~agl~~SksEARRlI~~GgV~VN-----------ge----kv~d~~~~l~~~dl~ 400 (420)
T 1jil_A 352 TTNIVEVLIETGISPSKRQAREDVNNGAIYIN-----------GE----RQQDVNYALAPEDKI 400 (420)
T ss_dssp ----------------------------------------------------------------
T ss_pred cccHHHHHHHcCCccCHHHHHHHHHhCCEEEC-----------CE----EecccccccCccccc
Confidence 35688888763223599999999999999999 64 344566677666543
No 39
>1pm6_A Excisionase; antiparallel beta-sheet, winged-helix, CIS-trans-trans triproline, gene regulation; NMR {Enterobacteria phage HK022} SCOP: a.6.1.7
Probab=29.31 E-value=46 Score=25.60 Aligned_cols=29 Identities=7% Similarity=0.051 Sum_probs=25.6
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcCcEE
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKGLVQ 134 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G~V~ 134 (490)
.+|.+|-..+|+..|.+.+.+++++|.|.
T Consensus 3 lTl~EwA~~~~~~~s~~Tl~r~ar~G~I~ 31 (72)
T 1pm6_A 3 LTLQEWNARQRRPRSLETVRRWVRESRIF 31 (72)
T ss_dssp EEHHHHHHHSSSCCCHHHHHHHHHHTCEE
T ss_pred eeHHHHHHHhcCCCCHHHHHHHHHCCCCC
Confidence 47899999987668999999999999994
No 40
>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A
Probab=25.01 E-value=42 Score=26.05 Aligned_cols=25 Identities=20% Similarity=0.119 Sum_probs=20.3
Q ss_pred CcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEc
Q 042463 131 GLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLP 171 (490)
Q Consensus 131 G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~ 171 (490)
-.|.|| | +.+..++.|+.||.|.+.
T Consensus 59 ~~v~VN-----------~-----~~v~~~~~l~~gDeV~i~ 83 (89)
T 3po0_A 59 INVLRN-----------G-----EAAALGEATAAGDELALF 83 (89)
T ss_dssp SEEEET-----------T-----EECCTTSBCCTTCEEEEE
T ss_pred EEEEEC-----------C-----EECCCCcccCCCCEEEEE
Confidence 368899 7 466778999999999983
No 41
>2ktl_A Tyrosyl-tRNA synthetase; S4 fold, aminoacyl-tRNA synthetase, ligase; NMR {Aspergillus nidulans fgsc A4}
Probab=24.30 E-value=66 Score=28.73 Aligned_cols=32 Identities=13% Similarity=-0.244 Sum_probs=26.5
Q ss_pred cccHHHHHHhcCCcCCHHHHHHHHHcCcEEec
Q 042463 105 HVTAVSWVKYYFDEVQDSVIQSHFNKGLVQME 136 (490)
Q Consensus 105 ~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn 136 (490)
+..+.++|...--.-|+++++++|..|-|+||
T Consensus 49 g~~ivdlLv~aGLa~SKsEARRlI~qGGv~VN 80 (164)
T 2ktl_A 49 DKTFSKVLWSAGLVASKSEGQRIINNNGAYVG 80 (164)
T ss_dssp SCSHHHHHHHHTSCSTHHHHHHHHHHTCEEEE
T ss_pred CCcHHHHHHHhCcccCHHHHHHHHHhCCEEEC
Confidence 34688988764334699999999999999999
No 42
>2ts1_A Tyrosyl-tRNA synthetase; ligase (synthetase); 2.30A {Geobacillus stearothermophilus} SCOP: c.26.1.1 PDB: 3ts1_A* 1tyd_E* 1tya_E* 1tyc_A 1tyb_E* 4ts1_A* 1jh3_A
Probab=23.23 E-value=17 Score=37.45 Aligned_cols=46 Identities=11% Similarity=0.126 Sum_probs=0.0
Q ss_pred ccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCC
Q 042463 106 VTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGA 166 (490)
Q Consensus 106 ~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd 166 (490)
..+.++|...--.-|+++++++|..|-|+|| |+ ++.+.+..+..+|
T Consensus 352 ~~~~~~l~~~gl~~S~~earr~i~~ggv~in-----------~~----~v~d~~~~~~~~~ 397 (419)
T 2ts1_A 352 VPLVELLVSAGISPSKRQAREDIQNGAIYVN-----------GE----RLQDVGAILTAEH 397 (419)
T ss_dssp -------------------------------------------------------------
T ss_pred ccHHHHHHHhCCCCCHHHHHHHHHhCCEEEC-----------CE----EecCcccccChhh
Confidence 5678887763224699999999999999999 64 3445566665554
No 43
>2hj1_A Hypothetical protein; structural genomics, PSI, protein structure initiative, NEW research center for structural genomics, nysgxrc; 2.10A {Haemophilus influenzae} SCOP: d.15.3.4
Probab=21.25 E-value=45 Score=27.11 Aligned_cols=52 Identities=13% Similarity=0.150 Sum_probs=32.8
Q ss_pred CCcccHHHHHHhcCCcCCHHHHHHHHHcCcEEecccCCCCccccCCCcCcceecCCCCcccCCCEEEEcc
Q 042463 103 QCHVTAVSWVKYYFDEVQDSVIQSHFNKGLVQMECANMGDSFVEQGQMKPIRKIKTNEVMEPGARIFLPV 172 (490)
Q Consensus 103 ~~~~rl~~~L~~~~~~~sr~~i~klI~~G~V~Vn~~~~~~~~~~~Gk~k~~~~~~~~~~l~~Gd~I~v~~ 172 (490)
..+.|+.+.|.. ++.. ...-+=-+....|-|| |+ .++.++.|+.||+|.|+.
T Consensus 33 ~~g~TV~daI~~-~gi~-~~~peIdl~~~~V~Vn-----------g~-----~v~~d~~L~dGDRVEIyr 84 (97)
T 2hj1_A 33 DEGITVQTAITQ-SGIL-SQFPEIDLSTNKIGIF-----------SR-----PIKLTDVLKEGDRIEIYR 84 (97)
T ss_dssp ETTCBHHHHHHH-HTHH-HHCTTCCTTTSEEEEE-----------EC-----SCCTTCBCCTTCEEEECC
T ss_pred CCCCcHHHHHHH-cCCC-ccCCcccccccEEEEc-----------CE-----ECCCCccCCCCCEEEEEe
Confidence 345788888877 4321 1100000124578999 73 577999999999999953
Done!