Query 011455
Match_columns 485
No_of_seqs 135 out of 1273
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 01:33:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011455.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011455hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00431 TruB tRNA pseudourid 100.0 9.4E-57 2E-61 424.5 18.7 166 307-484 1-166 (209)
2 PRK00130 truB tRNA pseudouridi 100.0 1.2E-56 2.6E-61 440.3 18.7 167 307-484 1-167 (290)
3 PRK00020 truB tRNA pseudouridi 100.0 1.7E-56 3.8E-61 431.3 18.1 167 307-484 9-177 (244)
4 cd00506 PseudoU_synth_TruB_lik 100.0 2.1E-56 4.5E-61 421.7 18.1 165 310-484 1-167 (210)
5 PRK02755 truB tRNA pseudouridi 100.0 5.5E-56 1.2E-60 436.9 19.0 166 307-484 2-170 (295)
6 PRK14124 tRNA pseudouridine sy 100.0 7.9E-56 1.7E-60 438.0 18.3 166 307-484 2-167 (308)
7 PRK05033 truB tRNA pseudouridi 100.0 8.2E-56 1.8E-60 438.6 18.2 166 307-484 9-174 (312)
8 PRK02484 truB tRNA pseudouridi 100.0 1E-55 2.2E-60 434.6 18.7 170 307-484 2-175 (294)
9 cd02573 PseudoU_synth_EcTruB P 100.0 1.1E-55 2.4E-60 431.1 18.5 165 310-484 1-167 (277)
10 PRK00989 truB tRNA pseudouridi 100.0 1.5E-55 3.2E-60 421.9 18.8 165 307-484 8-173 (230)
11 PRK01550 truB tRNA pseudouridi 100.0 1.3E-55 2.8E-60 435.7 18.8 173 307-484 1-174 (304)
12 PRK04642 truB tRNA pseudouridi 100.0 1.2E-55 2.7E-60 435.5 18.5 167 307-484 9-175 (300)
13 PRK14123 tRNA pseudouridine sy 100.0 1.7E-55 3.6E-60 435.0 19.0 170 307-484 2-175 (305)
14 PRK01851 truB tRNA pseudouridi 100.0 2.3E-55 5.1E-60 434.0 19.6 166 307-484 15-180 (303)
15 PRK04099 truB tRNA pseudouridi 100.0 2E-55 4.4E-60 429.4 18.4 165 307-483 1-165 (273)
16 PRK05389 truB tRNA pseudouridi 100.0 2.9E-55 6.3E-60 433.4 19.0 166 307-484 12-178 (305)
17 PRK03287 truB tRNA pseudouridi 100.0 3.4E-55 7.4E-60 431.9 18.3 171 307-484 8-178 (298)
18 PRK01528 truB tRNA pseudouridi 100.0 7.7E-55 1.7E-59 428.4 18.2 164 310-484 4-169 (292)
19 PRK02193 truB tRNA pseudouridi 100.0 1.1E-54 2.4E-59 425.0 18.2 165 310-484 1-167 (279)
20 PRK14122 tRNA pseudouridine sy 100.0 2.9E-54 6.2E-59 427.7 18.4 151 311-461 3-153 (312)
21 cd02867 PseudoU_synth_TruB_4 P 100.0 4.1E-54 8.8E-59 426.6 18.1 164 310-483 1-197 (312)
22 PRK14846 truB tRNA pseudouridi 100.0 2.5E-53 5.4E-58 425.2 18.6 164 310-484 4-169 (345)
23 PF01509 TruB_N: TruB family p 100.0 1.2E-51 2.5E-56 371.4 14.4 145 330-484 1-145 (149)
24 cd02868 PseudoU_synth_hTruB2_l 100.0 5.9E-46 1.3E-50 353.9 17.4 165 310-484 1-172 (226)
25 COG0130 TruB Pseudouridine syn 100.0 5.2E-41 1.1E-45 327.9 14.3 140 302-484 6-148 (271)
26 cd02572 PseudoU_synth_hDyskeri 100.0 1.4E-40 3.1E-45 307.6 15.0 130 308-483 2-133 (182)
27 PRK04270 H/ACA RNA-protein com 100.0 7.3E-39 1.6E-43 314.6 15.4 131 307-483 21-151 (300)
28 TIGR00425 CBF5 rRNA pseudourid 100.0 1.6E-38 3.4E-43 315.9 15.7 132 308-484 33-164 (322)
29 KOG2529 Pseudouridine synthase 100.0 5.4E-31 1.2E-35 268.1 -1.5 364 13-389 8-392 (395)
30 KOG2559 Predicted pseudouridin 99.9 3.9E-28 8.5E-33 236.7 10.0 159 303-484 6-216 (318)
31 KOG2529 Pseudouridine synthase 99.6 1.1E-16 2.5E-21 163.9 3.4 165 279-448 38-203 (395)
32 cd01291 PseudoU_synth PseudoU_ 98.3 5.6E-07 1.2E-11 73.5 4.8 50 314-378 1-51 (87)
33 cd02553 PseudoU_synth_RsuA Pse 97.4 0.00019 4.1E-09 65.5 5.0 68 311-378 2-78 (167)
34 PRK10158 23S rRNA/tRNA pseudou 97.3 0.00023 5E-09 67.5 4.7 76 301-381 15-103 (219)
35 TIGR01621 RluA-like pseudourid 97.3 0.00027 5.9E-09 67.1 4.9 70 309-378 9-88 (217)
36 cd02558 PSRA_1 PSRA_1: Pseudou 97.3 0.00038 8.2E-09 67.2 5.2 77 300-378 39-127 (246)
37 cd02557 PseudoU_synth_ScRIB2 P 97.3 0.0004 8.7E-09 65.5 5.3 72 309-381 23-106 (213)
38 cd02566 PseudoU_synth_RluE Pse 97.1 0.00032 7E-09 63.9 3.1 66 311-378 1-75 (168)
39 COG0564 RluA Pseudouridylate s 97.1 0.00083 1.8E-08 67.1 5.8 81 300-383 78-172 (289)
40 cd02563 PseudoU_synth_TruC tRN 96.9 0.0016 3.4E-08 61.7 5.4 71 310-382 9-93 (223)
41 TIGR00005 rluA_subfam pseudour 96.9 0.0011 2.5E-08 64.6 4.6 70 311-381 81-166 (299)
42 cd02550 PseudoU_synth_Rsu_Rlu_ 96.8 0.0012 2.7E-08 58.8 4.0 69 311-381 1-79 (154)
43 PRK11180 rluD 23S rRNA pseudou 96.7 0.0016 3.4E-08 65.2 4.1 69 310-378 92-176 (325)
44 PRK11112 tRNA pseudouridine sy 96.7 0.0023 4.9E-08 62.3 5.0 69 309-378 9-91 (257)
45 PF00849 PseudoU_synth_2: RNA 96.6 0.00045 9.8E-09 60.5 -0.2 75 311-385 2-92 (164)
46 cd02556 PseudoU_synth_RluB Pse 96.6 0.0026 5.7E-08 58.0 4.5 67 311-378 2-78 (167)
47 PRK11025 23S rRNA pseudouridyl 96.5 0.0032 6.8E-08 62.9 5.0 76 301-378 94-181 (317)
48 PF08068 DKCLD: DKCLD (NUC011) 96.5 0.00045 9.7E-09 55.8 -1.2 21 306-326 39-59 (59)
49 PRK11394 23S rRNA pseudouridin 96.4 0.0018 3.9E-08 62.8 2.5 69 310-378 40-114 (217)
50 PRK10475 23S rRNA pseudouridin 96.4 0.0072 1.6E-07 60.7 6.6 66 310-378 68-142 (290)
51 TIGR01213 conserved hypothetic 96.3 0.016 3.5E-07 61.0 8.7 91 351-484 254-348 (388)
52 cd02869 PseudoU_synth_RluCD_li 96.2 0.0049 1.1E-07 54.9 4.0 68 311-378 1-84 (185)
53 PRK10839 16S rRNA pseudouridyl 96.2 0.0022 4.8E-08 60.8 1.6 65 311-376 62-135 (232)
54 cd02555 PSSA_1 PSSA_1: Pseudou 95.9 0.0092 2E-07 55.6 4.3 66 311-378 6-89 (177)
55 PRK10700 23S rRNA pseudouridyl 95.8 0.012 2.5E-07 58.8 4.6 67 311-378 69-145 (289)
56 cd02870 PseudoU_synth_RsuA_lik 95.7 0.0042 9.2E-08 55.1 0.9 65 312-378 2-76 (146)
57 cd02554 PseudoU_synth_RluF Pse 95.3 0.02 4.4E-07 53.1 4.0 67 311-377 2-74 (164)
58 KOG1919 RNA pseudouridylate sy 95.2 0.024 5.2E-07 59.3 4.7 76 307-382 111-199 (371)
59 PRK14554 putative pseudouridyl 94.2 0.21 4.5E-06 53.3 8.8 91 351-484 287-381 (422)
60 COG1187 RsuA 16S rRNA uridine- 87.9 0.34 7.3E-06 48.4 2.3 67 311-378 65-143 (248)
61 TIGR00093 pseudouridine syntha 73.9 3.4 7.4E-05 36.3 3.2 38 341-378 1-40 (128)
62 COG1258 Predicted pseudouridyl 72.0 16 0.00034 39.4 8.0 73 368-483 279-352 (398)
63 cd02577 PSTD1 PSTD1: Pseudouri 60.6 1.1E+02 0.0024 31.8 11.3 69 289-359 7-77 (319)
64 PRK00984 truD tRNA pseudouridi 59.4 92 0.002 32.5 10.6 67 289-357 24-92 (341)
65 COG0585 Uncharacterized conser 52.9 58 0.0013 35.1 8.1 69 287-357 27-97 (406)
66 cd02575 PseudoU_synth_EcTruD P 43.2 39 0.00084 34.2 4.8 46 311-357 28-75 (253)
67 TIGR00094 tRNA_TruD_broad tRNA 40.5 42 0.00092 35.0 4.8 49 309-358 43-93 (387)
68 cd02552 PseudoU_synth_TruD_lik 38.4 1E+02 0.0023 30.5 6.9 54 304-359 28-83 (232)
69 COG0575 CdsA CDP-diglyceride s 34.0 24 0.00052 35.0 1.7 26 322-347 216-247 (265)
70 PF08555 DUF1754: Eukaryotic f 26.0 34 0.00075 29.0 1.1 25 110-134 73-97 (98)
No 1
>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=100.00 E-value=9.4e-57 Score=424.50 Aligned_cols=166 Identities=42% Similarity=0.701 Sum_probs=161.1
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
+|| |++||||.|||||+||++||++++.+||||+|||||+|+|||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 1 ~~G-~l~v~KP~g~tS~~vv~~vkk~~~~kKvGH~GTLDP~AsGvLiv~vG~~Tkl~~~~~~~~K~Y~~~~~~G~~TdT~ 79 (209)
T TIGR00431 1 ING-VLLLDKPQGMTSFDALAKVRRLLNVKKVGHTGTLDPFATGVLPILVGKATKLSPYLTDLDKEYRAEIRLGVRTDTL 79 (209)
T ss_pred CCe-EEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCCCcCceEEEEEEChHhhhhHHHcCCCCeEEEEEEECCcCCCC
Confidence 356 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
|++|+|+++.++. ++.++|++++++|+|+++|+||+|||+||||+|||||||+|+.||+++|+|+||+|++++
T Consensus 80 D~~G~i~~~~~~~-~~~~~l~~~l~~f~G~~~Q~PP~ySA~Kv~G~raYelAR~g~~v~~~~r~v~I~~i~ll~------ 152 (209)
T TIGR00431 80 DPDGQIVETRPVN-PTTEDVEAALPTFRGEIEQIPPMYSALKVNGKRLYEYARQGIEVERKARPVTVYDLQFLK------ 152 (209)
T ss_pred CCCCCEEEecCCC-CCHHHHHHHHHHccCcEEEECChhhEEeeCCHhHHHHHHCCCccccCcceeEEEEEEEEE------
Confidence 9999999999987 478999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCeeEEEEeeec
Q 011455 467 FFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 467 ~~~~F~~P~ftLEV~~~~ 484 (485)
|+.|.|+++|+|-+
T Consensus 153 ----~~~~~~~~~v~cs~ 166 (209)
T TIGR00431 153 ----YEGPELTLEVHCSK 166 (209)
T ss_pred ----EcCCcEEEEEEECC
Confidence 89999999999964
No 2
>PRK00130 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=1.2e-56 Score=440.34 Aligned_cols=167 Identities=44% Similarity=0.751 Sum_probs=163.3
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
++| |++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 1 m~G-il~i~KP~G~tS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~ 79 (290)
T PRK00130 1 MDG-ILNILKPPGMTSFDVVRKIRKIAKIKKVGHTGTLDPLASGVLPVCLGKATKIVDYLMEGKKTYRAEIKLGVETDTY 79 (290)
T ss_pred CCe-EEEEeCCCCCCHHHHHHHHHHHhCCCccCcCCCCCCCCeeEEEEEEChhhhhHHHhccCCcEEEEEEEECCcccCC
Confidence 356 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
|++|+|++++++.|+|.++|+++|++|+|+|+|+||+|||||+||+|||||||+|+.||+++|+|+||+|++++
T Consensus 80 D~~G~i~~~~~~~~~t~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~l~~------ 153 (290)
T PRK00130 80 DREGEILKEKEVSHLTEEEIREAILSFQGEIDQVPPMYSALKINGKKLYELARQGIEVEREARKITIYDIEILE------ 153 (290)
T ss_pred CCCCCEEEecCCCCCCHHHHHHHHHHccCeEEEECChHHeEecCCHhHHHHHHCCCccccCceEEEEEEEEEEE------
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCeeEEEEeeec
Q 011455 467 FFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 467 ~~~~F~~P~ftLEV~~~~ 484 (485)
|+.|.|+++|+|.+
T Consensus 154 ----~~~~~~~~~v~csk 167 (290)
T PRK00130 154 ----IDLPYVIFDVKCSK 167 (290)
T ss_pred ----EeCCeEEEEEEECC
Confidence 88899999999964
No 3
>PRK00020 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=1.7e-56 Score=431.33 Aligned_cols=167 Identities=34% Similarity=0.613 Sum_probs=162.4
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
++| |++||||.|||||+||++||++++.+||||+|||||+||||||||+|++||+++++++.+|+|+++++||.+|||+
T Consensus 9 ~~G-il~vdKP~G~TS~dvv~~vkr~~~~kKvGH~GTLDP~AtGvLiv~iG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~ 87 (244)
T PRK00020 9 LDG-VLLLDKPVGLSSNHALQRAKRTVDAAKAGHTGTLDPFATGLLVCCMGRATKISGRMLEADKTYQATLQFGEETDSG 87 (244)
T ss_pred CCe-EEEEecCCCCCHHHHHHHHHHHhCCCCCCcCCcCCCcCeeEEEEEECHHhhhhHHhccCCcEEEEEEEeCCcccCC
Confidence 577 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeecc--CCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccc
Q 011455 387 DADSPVIQREP--WEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLED 464 (485)
Q Consensus 387 DieGkVIe~sp--~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~d 464 (485)
|++|+|+++.+ +.|+|.++|+++|.+|+|+++|+||+||||||||+|||+|||+|+.||+++|+|+||+|++++
T Consensus 88 D~~G~v~~~~~~~~~~it~e~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~---- 163 (244)
T PRK00020 88 DLTGHIVARAPDGFAGVEEAALRDVLSRFVGTIEQIPPMYSALKRDGKPLYEYARAGIELDRPPRQVTIRHIELLS---- 163 (244)
T ss_pred CCCCcEEEeccCccCCCCHHHHHHHHHhccCeEEEeCChhheEEECCeEHHHHHhCCcccccCCeeEEEEEEEEEE----
Confidence 99999999987 468999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccccCCCCeeEEEEeeec
Q 011455 465 RFFFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 465 r~~~~~F~~P~ftLEV~~~~ 484 (485)
|+.|.++++|+|-+
T Consensus 164 ------~~~~~~~~~v~cSk 177 (244)
T PRK00020 164 ------FSGMQAQIDVACSK 177 (244)
T ss_pred ------EeCCEEEEEEEECC
Confidence 88899999999964
No 4
>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=100.00 E-value=2.1e-56 Score=421.74 Aligned_cols=165 Identities=40% Similarity=0.668 Sum_probs=160.0
Q ss_pred eEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCCCC
Q 011455 310 TMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389 (485)
Q Consensus 310 gIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~Die 389 (485)
||++||||.|||||+||++||++++.+||||+|||||+||||||||+|+|||+++++++.+|+|+++++||.+|||+|++
T Consensus 1 Gil~i~KP~g~tS~~vv~~ik~~~~~kKvGH~GTLDP~AsGvLiv~vG~aTkl~~~~~~~~K~Y~~~~~lG~~TdT~D~~ 80 (210)
T cd00506 1 GLFAVDKPQGPSSHDVVDTIRRIFLAEKVGHGGTLDPFATGVLVVGIGKATKLLKHLLAATKDYTAIGRLGQATDTFDAT 80 (210)
T ss_pred CEEEEEcCCCCCHHHHHHHHHHHhCccccCCCCcCCCcCeeEEEEEECHHHhhhHHHhcCCceEEEEEEECCcCCCCCCC
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccccc
Q 011455 390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFF 469 (485)
Q Consensus 390 GkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~~~ 469 (485)
|+|++++++.|+|.++|++++++|+|+|+|+||+|||||+||+|||||||+|+.||+++|+|+||+|++++
T Consensus 81 G~v~~~~~~~~it~e~l~~~l~~f~G~i~Q~pP~ySAvKv~G~raYelAR~G~~v~~~~r~v~I~~i~ll~--------- 151 (210)
T cd00506 81 GQVIEETPYDHITHEQLERALETLTGDIQQVPPLYSAVKRQGQRAYELARRGLLVPDEARPPTIYELLCIR--------- 151 (210)
T ss_pred CCEEEEeCCCCCCHHHHHHHHHHCCCeEEEeCCchheEEECCHhHHHHHHCCCccccCcEeEEEEEEEEEE---------
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCC--CeeEEEEeeec
Q 011455 470 LFPL--PLKLLDVIHLS 484 (485)
Q Consensus 470 ~F~~--P~ftLEV~~~~ 484 (485)
|+. |.+.++|.|-+
T Consensus 152 -~~~~~~~~~~~v~cs~ 167 (210)
T cd00506 152 -FNPPHFLLEVEVVCET 167 (210)
T ss_pred -EcCCCcEEEEEEEECC
Confidence 766 57888888854
No 5
>PRK02755 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=5.5e-56 Score=436.91 Aligned_cols=166 Identities=42% Similarity=0.738 Sum_probs=161.1
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
++| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++|+.. +|+|+++++||.+|||+
T Consensus 2 m~G-il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aTkl~~~l~~-~K~Y~a~~~lG~~TdT~ 79 (295)
T PRK02755 2 MFG-FLNLDKPAGLTSHDCVARLRRLLRLKRVGHGGTLDPAATGVLPIALGKATRLLPYLPG-EKTYRGTIRFGVRTSTD 79 (295)
T ss_pred cce-EEEEeCCCCCCHHHHHHHHHHHhCCCccccCCCCCCcCeeEEEEEEChhhhhHHHhCC-CcEEEEEEEECCcccCC
Confidence 577 9999999999999999999999999999999999999999999999999999999997 99999999999999999
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
|++|+|+++.++.|++.++|+++|++|+|.|+|+||+|||||+||+|||+|||+|+.||+++|+|+||+|+|++
T Consensus 80 D~~G~v~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~G~r~Y~lAR~G~~ve~~~r~v~I~~~~l~~------ 153 (295)
T PRK02755 80 DLQGEILSSQPWPHLSLAEIETALPQFRGKIEQRPPQYSAIQVDGERLYALARRGETMELPARTVTIFRLQLLD------ 153 (295)
T ss_pred CCCCCEEEecCCCCCCHHHHHHHHHhccCeEEEeCChhheEeeCCHhHHHHHHCCCccccCceEEEEEEEEEEE------
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCC---CCeeEEEEeeec
Q 011455 467 FFFLFP---LPLKLLDVIHLS 484 (485)
Q Consensus 467 ~~~~F~---~P~ftLEV~~~~ 484 (485)
|+ .|.|+++|.|-+
T Consensus 154 ----~~~~~~~~~~~~v~csk 170 (295)
T PRK02755 154 ----WRPGDQPELDLEIHCGA 170 (295)
T ss_pred ----EcCCCCceEEEEEEECC
Confidence 54 489999999964
No 6
>PRK14124 tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=7.9e-56 Score=438.00 Aligned_cols=166 Identities=40% Similarity=0.587 Sum_probs=162.2
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
++| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+
T Consensus 2 m~G-il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~ 80 (308)
T PRK14124 2 KHG-FLVAYKPKGPTSHDVVDEVRKKLKTRKVGHAGTLDPFATGVLIVGVNKATRLLEYLKNEKKVYYVKMRLGLITETF 80 (308)
T ss_pred Cce-EEEEECCCCCCHHHHHHHHHHHcCCCccCcCcCCCCCCcEEEEEEEChHHhhhHHHhcCCceEEEEEEeCccccCC
Confidence 567 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
|++|+|++++++ ++|.++|+++|++|+|.++|+||+|||||+||+|||||||+|+.||+++|+|+||+|++++
T Consensus 81 D~~G~vi~~~~~-~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~------ 153 (308)
T PRK14124 81 DITGEVVEEREC-NVTEEEIREAIFSFVGEYKQVPPAYSAKKYKGERLYKLAREGKIINLPPKEVKIYEIWDIS------ 153 (308)
T ss_pred CCCCCEEEecCC-CCCHHHHHHHHHhCcCeEEEeCCchHeEEECChhHHHHHhCCCccccCceeeEEEEEEEEE------
Confidence 999999999998 7999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCeeEEEEeeec
Q 011455 467 FFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 467 ~~~~F~~P~ftLEV~~~~ 484 (485)
|+.|.|+|+|+|.+
T Consensus 154 ----~~~~~~~~~v~csk 167 (308)
T PRK14124 154 ----IEGPDVSFRVEVSP 167 (308)
T ss_pred ----EeCCeEEEEEEECC
Confidence 88899999999964
No 7
>PRK05033 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=8.2e-56 Score=438.60 Aligned_cols=166 Identities=38% Similarity=0.618 Sum_probs=162.3
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
++| |++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 9 ~~G-il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~~~~~~K~Y~a~~~lG~~TdT~ 87 (312)
T PRK05033 9 ING-VLLLDKPQGMSSNDALQKVKRLFNANKAGHTGALDPLATGMLPICLGEATKFSQYLLDSDKRYRVTARLGQRTDTS 87 (312)
T ss_pred CCe-EEEEeCCCCCCHHHHHHHHHHHhCCCCCCCCCcCCCcCeeEEEEEECHHhhhhHHhcCCCcEEEEEEEECCcccCC
Confidence 577 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
|++|+|++++++ |+|.++|+++|++|+|.|+|+||+|||||+||+|||+|||+|+.||+++|.|+||+|++++
T Consensus 88 D~~G~v~~~~~~-~~t~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~------ 160 (312)
T PRK05033 88 DADGEVVEERPV-TLSAEQLEAALEKFRGDIEQVPSMYSALKYQGQPLYEYARQGIEVEREARPITIYELELIR------ 160 (312)
T ss_pred CCCCCEEEeecC-CCCHHHHHHHHHHCcCcEEEeCChhHeEeeCCeEHHHHHhCCcccccCceeEEEEEEEEee------
Confidence 999999999998 7999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCeeEEEEeeec
Q 011455 467 FFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 467 ~~~~F~~P~ftLEV~~~~ 484 (485)
|+.|.|+++|+|-+
T Consensus 161 ----~~~~~~~~~v~cs~ 174 (312)
T PRK05033 161 ----FEGDELELEVHCSK 174 (312)
T ss_pred ----EeCCEEEEEEEECC
Confidence 88899999999964
No 8
>PRK02484 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=1e-55 Score=434.65 Aligned_cols=170 Identities=39% Similarity=0.624 Sum_probs=162.0
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
++| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 2 m~G-il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~ 80 (294)
T PRK02484 2 ING-IINLKKEAGMTSHDAVFKLRKILQTKKIGHGGTLDPDVVGVLPIAVGKATRLIEYMTEAGKVYEGEITLGYSTTTE 80 (294)
T ss_pred cce-EEEEeCCCCCCHHHHHHHHHHHhCCCccccCCCCCCCCeeEEEEEEChhhhhhHHhccCCcEEEEEEEECCcccCC
Confidence 567 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCC-CCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccc
Q 011455 387 DADSPVIQREPWEH-IKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDR 465 (485)
Q Consensus 387 DieGkVIe~sp~~h-IT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr 465 (485)
|++|+|+++.++.| +|.++|+++|++|+|+|+|+||+|||||+||+|||+|||+|+.|++++|+|+||+|+++..+
T Consensus 81 D~~G~vi~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~l~~~~--- 157 (294)
T PRK02484 81 DASGEVVAETPLTQPLTEEEVDQAMTSFTGKITQIPPMYSAVKVNGKKLYEYARAGEEVERPKRQVTIYQFERTSPL--- 157 (294)
T ss_pred CCCCCEEEeccCCCCCCHHHHHHHHHhccCeEEEeCChhHeEeeCCHhHHHHHHCCCccccCceEEEEEEEEEeccc---
Confidence 99999999999987 99999999999999999999999999999999999999999999999999999999998421
Q ss_pred cccccC---CCCeeEEEEeeec
Q 011455 466 FFFFLF---PLPLKLLDVIHLS 484 (485)
Q Consensus 466 ~~~~~F---~~P~ftLEV~~~~ 484 (485)
.| .+|.|+++|+|-+
T Consensus 158 ----~~~~~~~~~~~~~v~csk 175 (294)
T PRK02484 158 ----SFDEDGLCRFSFRVACSK 175 (294)
T ss_pred ----cccccCCceEEEEEEeCC
Confidence 24 3689999999964
No 9
>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=100.00 E-value=1.1e-55 Score=431.06 Aligned_cols=165 Identities=44% Similarity=0.714 Sum_probs=161.6
Q ss_pred eEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCCCC
Q 011455 310 TMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389 (485)
Q Consensus 310 gIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~Die 389 (485)
||++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+|++
T Consensus 1 Gil~i~KP~G~tS~~vv~~vr~~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~~~~~~G~~TdT~D~~ 80 (277)
T cd02573 1 GILLLDKPAGLTSHDVVQKVRRLLGTKKVGHTGTLDPLATGVLPIALGEATKLSQYLLDADKTYRATVRLGEATDTDDAE 80 (277)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHhCcCccCCCCCCCCcCeEEEEEEEChHHhhHHHhcCCCcEEEEEEEECCcccCCCCC
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccccc
Q 011455 390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFF 469 (485)
Q Consensus 390 GkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~~~ 469 (485)
|+|++++++.|+|.++|+++|++|+|.++|+||+|||||+||+|||+|||+|+.||+++|+|+||+|++++
T Consensus 81 G~v~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvkv~G~raYelAR~G~~ve~~~r~v~I~~i~ll~--------- 151 (277)
T cd02573 81 GEIIETSPPPRLTEEEIEAALKAFTGEIEQVPPMYSAVKVNGKRLYELARAGEEVERPPRKVTIYSLELLS--------- 151 (277)
T ss_pred CCEEEecCCCCCCHHHHHHHHHHccCcEEeeCChhHeEeeCCccHHHHHhCCCccccCCeeEEEEEEEEEE---------
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCC--CeeEEEEeeec
Q 011455 470 LFPL--PLKLLDVIHLS 484 (485)
Q Consensus 470 ~F~~--P~ftLEV~~~~ 484 (485)
|+. |.|+++|+|.+
T Consensus 152 -~~~~~~~~~~~v~cs~ 167 (277)
T cd02573 152 -FDPENPEADFEVECSK 167 (277)
T ss_pred -ecCCCCeEEEEEEECC
Confidence 766 99999999965
No 10
>PRK00989 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=1.5e-55 Score=421.89 Aligned_cols=165 Identities=41% Similarity=0.660 Sum_probs=159.9
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecC-cccccccccCCCcEEEEEEEEcccccC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGK-ATKLVDRYQGMIKGYSGVFRLGEATST 385 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGk-aTKLl~~Ll~~~KeY~at~~LG~~TDT 385 (485)
.|| |++||||.|||||+||++||++++.+||||+|||||+||||||||+|+ +||+++++++.+|+|+++++||.+|||
T Consensus 8 ~~G-~l~i~KP~g~TS~dvv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~vG~~aTkl~~~~~~~~K~Y~~~~~~G~~TdT 86 (230)
T PRK00989 8 KEG-ILLVDKPQGRTSFSLIRSLTKLIGVKKIGHAGTLDPFATGVMVMLIGRKFTRLSDILLFEDKEYAAVAHLGTTTDS 86 (230)
T ss_pred CCE-EEEEeCCCCCCHHHHHHHHHHHhCCCcCCcCccCCCCCeeEEEEEECCchhhhHHHhcCCCcEEEEEEEECCcccC
Confidence 566 999999999999999999999999999999999999999999999998 799999999999999999999999999
Q ss_pred CCCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccc
Q 011455 386 WDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDR 465 (485)
Q Consensus 386 ~DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr 465 (485)
+|++|+|+++.+. +++.++|+++|++|+|.++|+||+|||||+||+|||||||+|+.||+++|.|+|| +++++
T Consensus 87 ~D~~G~vi~~~~~-~~~~~~i~~~l~~f~G~~~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~i~-~~ll~----- 159 (230)
T PRK00989 87 YDCDGKIVGRSKK-IPTLEEVLSAASYFQGEIQQVPPMFSAKKVQGKKLYEYARQGLSIERRPSTVQVH-LQLTK----- 159 (230)
T ss_pred CCCCCcEEEecCC-CCCHHHHHHHHHhCcceEEeeCChhHeEEECCHhHHHHHhCCCccccCcEEEEEE-EEEEE-----
Confidence 9999999999884 7999999999999999999999999999999999999999999999999999999 99998
Q ss_pred cccccCCCCeeEEEEeeec
Q 011455 466 FFFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 466 ~~~~~F~~P~ftLEV~~~~ 484 (485)
|+.|.|+|+|+|.+
T Consensus 160 -----~~~p~~~~~v~cs~ 173 (230)
T PRK00989 160 -----YEYPLLHFVVQCSK 173 (230)
T ss_pred -----eeCCeEEEEEEEcC
Confidence 88899999999975
No 11
>PRK01550 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=1.3e-55 Score=435.66 Aligned_cols=173 Identities=41% Similarity=0.610 Sum_probs=162.0
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
+|| |++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 1 m~G-il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~ 79 (304)
T PRK01550 1 MNG-VLLLHKPRGMTSHDCVFKLRKILRTKKVGHTGTLDPEVSGVLPICVGRATKIAEYLTDEGKTYEGEVTLGFSTTTE 79 (304)
T ss_pred CCe-EEEEECCCCCCHHHHHHHHHHHcCCCCcccCCCCCCcCeeEEEEEEChhhhhhHHhcCCCcEEEEEEEECCcccCC
Confidence 367 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCC-CCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccc
Q 011455 387 DADSPVIQREPWEH-IKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDR 465 (485)
Q Consensus 387 DieGkVIe~sp~~h-IT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr 465 (485)
|++|+|+++.++.| +|.++|+++|++|+|.|+|+||+|||||+||+|||+|||+|+.||+++|+|+||+|+++++..
T Consensus 80 D~~G~v~~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~Gkr~YelAR~G~~ve~~~r~v~I~~i~ll~~~~-- 157 (304)
T PRK01550 80 DADGEVVETKPVDRPITREEIEAALASLTGTIEQIPPMYSAVKVNGKKLYEYARAGIEVERPVRQITIHEFVLLDSRE-- 157 (304)
T ss_pred CCCCCEEeeccCCCCCCHHHHHHHHHhccceEEEeCChhHeEecCCHhHHHHHHCCCccccCCcceEEEEEEEEeecc--
Confidence 99999999999886 999999999999999999999999999999999999999999999999999999999996210
Q ss_pred cccccCCCCeeEEEEeeec
Q 011455 466 FFFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 466 ~~~~~F~~P~ftLEV~~~~ 484 (485)
-+.++.|.|+++|+|-+
T Consensus 158 --~~~~~~~~~~~~v~csk 174 (304)
T PRK01550 158 --DFEGETQSFRFRVTCSK 174 (304)
T ss_pred --ccccCCceEEEEEEECC
Confidence 01134699999999964
No 12
>PRK04642 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=1.2e-55 Score=435.52 Aligned_cols=167 Identities=38% Similarity=0.604 Sum_probs=163.2
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
++| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++|++..+|+|+++++||.+|||+
T Consensus 9 m~G-il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~~G~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~ 87 (300)
T PRK04642 9 LDG-ILLLDKPAGLSSNNALQAARRLLRAEKGGHTGSLDPLATGLLPLCFGEATKIAGLLLGSAKAYDAEIVLGVTTDTD 87 (300)
T ss_pred cCe-EEEEecCCCCCHHHHHHHHHHHhCCCcccCCCccCCcCeeeEEEEEChhhhhhHHhcCCCcEEEEEEEECccccCc
Confidence 577 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
|++|+|+++.++.+++.++|+++|++|.|.|+|+||+|||||+||+|||+|||+|+.||+++|+|+||++++++
T Consensus 88 D~~G~v~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkrlY~lAR~G~~ve~~~R~v~I~~~~ll~------ 161 (300)
T PRK04642 88 DADGQVLRERPVPDLSAAALQAALAPLIGRIRQRAPIYSALKQGGEPLYAKARRGEVIEAPVREVEVHAIEVLG------ 161 (300)
T ss_pred CCCCCEEEecCCCCCCHHHHHHHHHHCCCcEEEeCCchHeEeECCeeHHHHHhCCCccccCcEEEEEEEEEEEE------
Confidence 99999999999988999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCeeEEEEeeec
Q 011455 467 FFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 467 ~~~~F~~P~ftLEV~~~~ 484 (485)
|+.|.++++|.|-+
T Consensus 162 ----~~~~~~~~~v~csk 175 (300)
T PRK04642 162 ----YAAPRLRLRVTCGS 175 (300)
T ss_pred ----EeCCEEEEEEEeCC
Confidence 77899999999964
No 13
>PRK14123 tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=1.7e-55 Score=434.99 Aligned_cols=170 Identities=35% Similarity=0.539 Sum_probs=161.3
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
+|| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||++++++..+|+|+++++||.+|||+
T Consensus 2 m~G-il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~~~~~lG~~TdT~ 80 (305)
T PRK14123 2 YNG-ILPVYKERGLTSHDVVFKLRKILKTKKIGHTGTLDPEVAGVLPVCIGNATRVSDYVMDMGKAYEATVSIGRSTTTE 80 (305)
T ss_pred cce-EEEEeCCCCCCHHHHHHHHHHHhCCCccccCcCCCCcCeeEEEEEEChhhhhHHHhcCCCcEEEEEEEECCcccCC
Confidence 567 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCC--CCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccc
Q 011455 387 DADSPVIQREPWE--HIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLED 464 (485)
Q Consensus 387 DieGkVIe~sp~~--hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~d 464 (485)
|++|+|+++.++. |+|.++|+++|++|+|+|+|+||+|||||+||+|||||||+|+.||+++|+|+||+|+++.
T Consensus 81 D~~G~vi~~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~~~~---- 156 (305)
T PRK14123 81 DQTGDTLETKGVHSADFNKDDIDRLLEQFKGIIEQIPPMYSSVKVNGKKLYEYARNNETVERPKRKVNIKDIGRIS---- 156 (305)
T ss_pred CCCCCEEEeccCCcCCCCHHHHHHHHHhccCceeecCChhheEeeCCHhHHHHHhCCCcccCCceEEEEEEEEEee----
Confidence 9999999999874 7999999999999999999999999999999999999999999999999999999999884
Q ss_pred ccccccCCC--CeeEEEEeeec
Q 011455 465 RFFFFLFPL--PLKLLDVIHLS 484 (485)
Q Consensus 465 r~~~~~F~~--P~ftLEV~~~~ 484 (485)
.+.|+. |.|+|+|+|.+
T Consensus 157 ---~~~~~~~~~~~~~~v~csk 175 (305)
T PRK14123 157 ---ELDFKENECHFKIRVICGK 175 (305)
T ss_pred ---cccccCCCceEEEEEEeCC
Confidence 123544 89999999964
No 14
>PRK01851 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=2.3e-55 Score=433.96 Aligned_cols=166 Identities=39% Similarity=0.617 Sum_probs=162.3
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
++| |++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 15 ~~G-il~i~KP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~~~~~lG~~TdT~ 93 (303)
T PRK01851 15 VDG-VLLLDKPLGLSSNDALQRAKRLLRAKKAGHTGTLDPLATGLLPLCFGEATKFSQDLLDADKTYEATLRLGVRTSTG 93 (303)
T ss_pred CCe-EEEEeCCCCCCHHHHHHHHHHHhCcccCCCCCCCCCCCceEEEEEECHHHhhhHHhcccCeEEEEEEEECCccCCC
Confidence 577 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
|++|+|+++.++. +|.++|+++|++|+|.|+|+||+|||||+||+|||||||+|+.||+++|+|+||+|++++
T Consensus 94 D~~G~v~~~~~~~-~t~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~R~v~I~~i~ll~------ 166 (303)
T PRK01851 94 DAEGEVLATRPVD-CDPAALEAALARFTGEIRQVPPMYSALKKDGKPLYEYARAGITVEREARDVTIHALDLLA------ 166 (303)
T ss_pred CCCCCEEeecCCC-CCHHHHHHHHHhccCeeeeeCCchheEeeCCeeHHHHHhCCCccccCCcceEEEEEEEEE------
Confidence 9999999999987 999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCeeEEEEeeec
Q 011455 467 FFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 467 ~~~~F~~P~ftLEV~~~~ 484 (485)
|+.|.|+++|+|.+
T Consensus 167 ----~~~~~~~~~v~csk 180 (303)
T PRK01851 167 ----CDLPDVTIRVTCSK 180 (303)
T ss_pred ----EeCCEEEEEEEECC
Confidence 88899999999964
No 15
>PRK04099 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=2e-55 Score=429.38 Aligned_cols=165 Identities=33% Similarity=0.529 Sum_probs=161.0
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
+|| |++||||.|||||+||++||++++.+||||+|||||+||||||||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 1 mng-il~vdKP~g~tS~~vv~~ikk~~~~kKvGH~GTLDP~AtGvLiv~iG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~ 79 (273)
T PRK04099 1 MNR-LFVANKPAGMSSNAFLSRLKRKYGVKKAGFSGTLDPFAKGVLIVAFGQYTKLFRFLKKTPKTYRATLWLGASSPSL 79 (273)
T ss_pred CCe-EEEEeCCCCCCHHHHHHHHHHHhCCCccccCccCCCCCeeEEEEEEChHhhhHHHhccCCceEEEEEEECCcccCC
Confidence 367 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
|++| |++..++.++|.++|+++|++|+|+++|+||+|||||+||||||||||+|+.||+++|+|+||++++++
T Consensus 80 D~e~-i~~~~~~~~~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~~~ll~------ 152 (273)
T PRK04099 80 DIEN-IESIQIIKPFDKDLIEKILKSLQGEISYTPPKFSAKKINGKRAYELARKGEEFELKPITMEIFDCKLLS------ 152 (273)
T ss_pred CCcc-eEEeccCCCCCHHHHHHHHHhCcceEEEeCChhhEEeeCCHhHHHHHhCCcccccCceeEEEEEEEEEE------
Confidence 9998 889999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccCCCCeeEEEEeee
Q 011455 467 FFFLFPLPLKLLDVIHL 483 (485)
Q Consensus 467 ~~~~F~~P~ftLEV~~~ 483 (485)
|+.|.|+++|.|-
T Consensus 153 ----~~~p~~~f~v~cs 165 (273)
T PRK04099 153 ----YNHPFLTFEITVS 165 (273)
T ss_pred ----EeCCEEEEEEEEC
Confidence 8889999999994
No 16
>PRK05389 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=2.9e-55 Score=433.41 Aligned_cols=166 Identities=38% Similarity=0.547 Sum_probs=160.8
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
++| |++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 12 ~~G-il~i~KP~G~TS~dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~ 90 (305)
T PRK05389 12 ISG-WLILDKPAGMTSTEAVSKVKWLFDAQKAGHAGTLDPLASGVLPIALGEATKTVPYVMDGTKRYRFTVAWGEERDTD 90 (305)
T ss_pred CCe-EEEEeCCCCCCHHHHHHHHHHHhcccccCCcccCCCCCceEEEEEEChhhhhhHHhccCCcEEEEEEEECCcccCC
Confidence 577 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
|++|+|+++.++. ++.++|+++|++|+|+|+|+||+|||||+||+|||||||+|+.||+++|+|+||+|++++
T Consensus 91 D~~G~v~~~~~~~-~~~~~i~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~------ 163 (305)
T PRK05389 91 DLEGEVTATSDVR-PTDEEIRAALPAFTGEIMQVPPQFSAIKIDGERAYDLAREGETVELPARPVEIDRLTLVE------ 163 (305)
T ss_pred CCCCCEEEecCCC-CCHHHHHHHHHhccceEEEeCCchheEEECCHhHHHHHHCCCccccCceEEEEEEEEEEE------
Confidence 9999999998864 899999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccC-CCCeeEEEEeeec
Q 011455 467 FFFLF-PLPLKLLDVIHLS 484 (485)
Q Consensus 467 ~~~~F-~~P~ftLEV~~~~ 484 (485)
| +.|.|+++|+|-+
T Consensus 164 ----~~~~~~~~~~v~csk 178 (305)
T PRK05389 164 ----RPDADHAVFEVECGK 178 (305)
T ss_pred ----ecCCCeEEEEEEeCC
Confidence 6 4799999999964
No 17
>PRK03287 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=3.4e-55 Score=431.92 Aligned_cols=171 Identities=42% Similarity=0.591 Sum_probs=161.3
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
.+| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+
T Consensus 8 ~~G-il~i~KP~G~TS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~i~vG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~ 86 (298)
T PRK03287 8 GSG-LVVVDKPAGMTSHDVVARCRRLFGTRKVGHAGTLDPMATGVLVLGVERATKLLGHLTLTDKSYTATIRLGQATTTD 86 (298)
T ss_pred cCe-EEEEeCCCCCCHHHHHHHHHHHhCCCCCCcCccCCCcceeEEEEEeChhhhhhHHHhcCCcEEEEEEEeCccccCC
Confidence 566 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
|++|+|+++.++.|+|.++|++++++|+|.|+|+||+|||||+||||||||||+|+.||+++|+|+||+++++.....
T Consensus 87 D~~G~v~~~~~~~~it~~~i~~~l~~f~G~i~Q~PP~ySAvKv~Gkr~YelAR~G~~ve~~~R~v~I~~~~l~~~~~~-- 164 (298)
T PRK03287 87 DAEGEVLASADASAVTDEAIAAAVAALTGEIMQVPSAVSAIKVDGKRAYARVRAGEEVELPARPVTVSRFEVLAVRRD-- 164 (298)
T ss_pred CCCCCEEeecCCCCCCHHHHHHHHHhCcCeEEEeCChhHeEEECCHHHHHHHhCCCccccCcEEEEeeeeEEEEEecC--
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999972110
Q ss_pred ccccCCCCeeEEEEeeec
Q 011455 467 FFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 467 ~~~~F~~P~ftLEV~~~~ 484 (485)
-+.|.++++|+|-+
T Consensus 165 ----~~~~~~~~~v~csk 178 (298)
T PRK03287 165 ----GDFIDLDVEVDCSS 178 (298)
T ss_pred ----CCccEEEEEEEECC
Confidence 12358999999964
No 18
>PRK01528 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=7.7e-55 Score=428.43 Aligned_cols=164 Identities=32% Similarity=0.484 Sum_probs=158.5
Q ss_pred eEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCCCC
Q 011455 310 TMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389 (485)
Q Consensus 310 gIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~Die 389 (485)
||++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+|++
T Consensus 4 GiL~i~KP~G~TS~dvv~~vrk~~~~kKvGH~GTLDP~AtGvL~v~vG~aTKl~~~l~~~~K~Y~~~~~lG~~TdT~D~~ 83 (292)
T PRK01528 4 YWLNIYKPRGISSAKLVSIVKKILGKVKIGHAGTLDVEAEGVLPLAVGEATKLVQLLIDAKKTYIFTVKFGKQTDSGDYA 83 (292)
T ss_pred EEEEEeCCCCCCHHHHHHHHHHHcCCCccCcCccCCCcCceEEEEEEChHhhhhHHHhcCCceEEEEEEECCcccCCCCC
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccccc
Q 011455 390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFF 469 (485)
Q Consensus 390 GkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~~~ 469 (485)
|+|+++.++. ++.++|+++|++|+|+|+|+||+|||+|+||+|||||||+|+.||+++|.|+||+|++++
T Consensus 84 G~v~~~~~~~-~~~e~l~~~l~~f~G~i~Q~PP~ySAvKv~G~raYelAR~G~~vel~~r~v~I~~i~ll~--------- 153 (292)
T PRK01528 84 GKVIATKDYI-PSKEEAYAVCSKFIGNITQIPPAFSALKVNGVRAYKLAREGKEVELKPRNITIYDLKCLN--------- 153 (292)
T ss_pred CCEEEecCCC-CCHHHHHHHHHhccceEEeeCChhHeEEECCHhHHHHHhCCcccccCceeEEEEEEEEEE---------
Confidence 9999999987 599999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCC--CeeEEEEeeec
Q 011455 470 LFPL--PLKLLDVIHLS 484 (485)
Q Consensus 470 ~F~~--P~ftLEV~~~~ 484 (485)
|+. |.+.++|+|.+
T Consensus 154 -~~~~~~~~~~~v~csk 169 (292)
T PRK01528 154 -FDEKNATATYYTECSK 169 (292)
T ss_pred -EcCCCcEEEEEEEECC
Confidence 654 68999999964
No 19
>PRK02193 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=1.1e-54 Score=425.03 Aligned_cols=165 Identities=34% Similarity=0.553 Sum_probs=159.6
Q ss_pred eEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCCCC
Q 011455 310 TMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389 (485)
Q Consensus 310 gIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~Die 389 (485)
+|++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+|++
T Consensus 1 ~il~i~KP~G~tS~dvv~~vrr~~~~kKvGH~GTLDP~AtGvL~v~vG~aTkl~~~l~~~~K~Y~a~~~lG~~TdT~D~~ 80 (279)
T PRK02193 1 MIKLLYKPKGISSFKFIKNFAKTNNIKKIGHTGTLDPLASGLLLVATDEDTKLIDYLDQKDKTYIAKIKFGFISTTYDSE 80 (279)
T ss_pred CEEEEECCCCCCHHHHHHHHHHHcCCCccccCccCCCcCeeEEEEEEChhhhhhHHhccCCcEEEEEEEeCCcccCCCCC
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccccc
Q 011455 390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFF 469 (485)
Q Consensus 390 GkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~~~ 469 (485)
|+|+++.++.++|.++|++++++|+|+|+|+||+|||||+||+|||+|||+|+.||+++|+|+||+|++++
T Consensus 81 G~i~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~ve~~~r~v~I~~i~ll~--------- 151 (279)
T PRK02193 81 GQIINVSQNIKVTKENLEEALNNLVGSQKQVPPVFSAKKVNGKRAYDLARQGKQIELKPIEIKISKIELLN--------- 151 (279)
T ss_pred CCEEeecCCCCCCHHHHHHHHHhCcCeEEEeCChHHeEeeCCHhHHHHHhCCceeccCCeeEEEEEEEEEE---------
Confidence 99999888889999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCCC--eeEEEEeeec
Q 011455 470 LFPLP--LKLLDVIHLS 484 (485)
Q Consensus 470 ~F~~P--~ftLEV~~~~ 484 (485)
|+.| .+.++|.|-+
T Consensus 152 -~~~~~~~~~~~v~csk 167 (279)
T PRK02193 152 -FDEKLQNCVFMWVVSR 167 (279)
T ss_pred -EcCCCceEEEEEEECC
Confidence 7665 7899999854
No 20
>PRK14122 tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=2.9e-54 Score=427.69 Aligned_cols=151 Identities=38% Similarity=0.641 Sum_probs=149.2
Q ss_pred EEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCCCCC
Q 011455 311 MVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADS 390 (485)
Q Consensus 311 IL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~DieG 390 (485)
|++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.+|||+|++|
T Consensus 3 il~idKP~G~TS~dvv~~vrr~l~~kKvGH~GTLDP~AtGvL~i~iG~aTKl~~~l~~~~K~Y~a~~~lG~~TdT~D~eG 82 (312)
T PRK14122 3 VYAVDKPLGLTSHDVVNRARRALGTRRVGHTGTLDPLATGVLVLCTDDSTKLVPFLSAEDKEYLAWVSFGATTPTLDAEG 82 (312)
T ss_pred EEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcCeeeEEEEEChhhhhhHHhcCCCceEEEEEEECCcCCCCCCCC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeee
Q 011455 391 PVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERS 461 (485)
Q Consensus 391 kVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~ 461 (485)
+|++++++.|++.++|+++|++|+|.|+|+||+|||||+||+|||||||+|+.||+++|+|+||+|+|+..
T Consensus 83 ~i~~~~~~~~~~~~~l~~~l~~f~G~i~Q~PP~ySAvKv~GkraYelAR~G~~vel~~R~v~I~~i~ll~~ 153 (312)
T PRK14122 83 PISEEAPVSPLDEKDLEAALPGFLGLTEQVPPQYSAIKVGGVRAYEAARAGGALELPARPVVYHELELLAF 153 (312)
T ss_pred CEEEecCCCCCCHHHHHHHHHhCcCeEEEeCChHHeEEECCeEHHHHHhCCCccccCCeeEEEEEEEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999974
No 21
>cd02867 PseudoU_synth_TruB_4 PseudoU_synth_TruB_4: Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=100.00 E-value=4.1e-54 Score=426.61 Aligned_cols=164 Identities=37% Similarity=0.633 Sum_probs=158.3
Q ss_pred eEEEEeCCCCCCHHHHHHHHHHHhcc-----------------------------cccccccCCCCCCceEEEEEecCcc
Q 011455 310 TMVLVNKPKGWTSFTVCGKLRRLVKV-----------------------------KKVGHAGTLDPMATGLLIVCVGKAT 360 (485)
Q Consensus 310 gIL~VyKP~GiTS~dVV~kIRriLk~-----------------------------kKVGHaGTLDP~ASGVLVVgIGkaT 360 (485)
|||+||||.|||||+||++||++|+. +||||+|||||+||||||||||+||
T Consensus 1 Gil~i~KP~G~TS~~vv~~lk~~l~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~KiGH~GTLDPlAsGVLvvgvG~aT 80 (312)
T cd02867 1 GVFAINKPSGITSAQVLNDLKPLFLNSALFKDKIQRAVAKRGKKARRRKGRKRSKLKIGHGGTLDPLATGVLVVGVGAGT 80 (312)
T ss_pred CeEEEeCCCCCCHHHHHHHHHHHhcccccccchhhhhhhhhhhhhhhhccccccccccccccccCCccceeEEEEECcHH
Confidence 49999999999999999999999975 7999999999999999999999999
Q ss_pred cccccccCCCcEEEEEEEEcccccCCCCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhc
Q 011455 361 KLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARR 440 (485)
Q Consensus 361 KLl~~Ll~~~KeY~at~~LG~~TDT~DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARk 440 (485)
|++++++..+|+|+++++||.+|||+|++|+|+++.++.|||.++|+++|++|+|.|+|+||+|||||+||||||||||+
T Consensus 81 K~l~~~l~~~K~Y~~~~~lG~~TdT~D~eG~Ii~~~~~~~it~e~i~~~l~~F~G~i~Q~PP~ySAvKv~GkrlYeyAR~ 160 (312)
T cd02867 81 KQLQDYLSCSKTYEATGLFGASTTTYDREGKILKKKPYSHITREDIEEVLAKFRGDIKQVPPLYSALKMDGKRLYEYARE 160 (312)
T ss_pred HHHHHHhcCCceEEEEEEeCCcccCCCCCCCEEEecCCCCCCHHHHHHHHHhcceeeeeeCcchheeeeCCHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccC--CceeEEEEEEEeeecccccccccCC--CCeeEEEEeee
Q 011455 441 GESIELS--PRRISIFQFDIERSLEDRFFFFLFP--LPLKLLDVIHL 483 (485)
Q Consensus 441 G~~VEl~--pR~V~IYsIkLi~~l~dr~~~~~F~--~P~ftLEV~~~ 483 (485)
|++||++ +|.|+||+++++. |. .|.|+++|.|-
T Consensus 161 G~~v~~~~~~R~V~I~~~~l~~----------~~~~~~~~~~~v~cs 197 (312)
T cd02867 161 GKPLPRPIERRQVVVSELLVKD----------WIEPGPLFTRTVEEE 197 (312)
T ss_pred CccccCCCCCceEEEEEEEEEe----------ccCCCCeEEEEEEeC
Confidence 9999987 8999999999997 43 59999999994
No 22
>PRK14846 truB tRNA pseudouridine synthase B; Provisional
Probab=100.00 E-value=2.5e-53 Score=425.18 Aligned_cols=164 Identities=31% Similarity=0.472 Sum_probs=157.8
Q ss_pred eEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCCCC
Q 011455 310 TMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389 (485)
Q Consensus 310 gIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~Die 389 (485)
||++||||.|||||+||++||++++.+||||+|||||+||||||||+|+|||+++++++.+|+|+++++||.+|||+|++
T Consensus 4 GiL~idKP~G~TS~dvv~~vrk~l~~kKVGH~GTLDP~AtGVL~i~vG~aTKl~~~l~~~~K~Y~a~~~lG~~TDT~D~e 83 (345)
T PRK14846 4 YWLNIYKPRGISSAQLVSIVKKILGKTKIGHAGTLDVEAEGILPFAVGEATKLIHLLIDARKTYIFTVKFGMQTNSGDCA 83 (345)
T ss_pred eEEEEeCCCCCCHHHHHHHHHHHhCCCcCCcCccCCCcCceEEEEEEChhhhhhHHHhcCCceEEEEEEECCccCCCCCC
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccccc
Q 011455 390 SPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFF 469 (485)
Q Consensus 390 GkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~~~ 469 (485)
|+|+++.++. ++.++|+++|++|+|+|+|+||+|||||+||+|||+|||+|+.||+++|+|+||+|+|++
T Consensus 84 G~ii~~~~~~-~~~e~l~~~L~~f~G~i~Q~PP~ySAvKv~GkraYelARkG~~Vel~~R~V~I~~i~ll~--------- 153 (345)
T PRK14846 84 GKVIATKDCI-PSQEEAYAVCSKFIGNVTQIPPAFSALKVNGVRAYKLAREGKKVELKPRNITIYDLKCLN--------- 153 (345)
T ss_pred CCEEEecCCC-CCHHHHHHHHHhCcceEEeeCChhheEeECChhHHHHHhCCCccccCceeEEEEEEEEEE---------
Confidence 9999998876 789999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCC--CeeEEEEeeec
Q 011455 470 LFPL--PLKLLDVIHLS 484 (485)
Q Consensus 470 ~F~~--P~ftLEV~~~~ 484 (485)
|+. |.+.++|.|-+
T Consensus 154 -f~~~~~~~~~~v~CSk 169 (345)
T PRK14846 154 -FDEKNATATYYTECSK 169 (345)
T ss_pred -EcCCCcEEEEEEEECC
Confidence 654 67899999953
No 23
>PF01509 TruB_N: TruB family pseudouridylate synthase (N terminal domain); InterPro: IPR002501 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. TruB is responsible for the pseudouridine residue present in the T loops of virtually all tRNAs. TruB recognises the preformed 3-D structure of the T loop primarily through shape complementarity. It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA []. This entry represents pseudouridine synthase TruB, as well as Cbf5p that modifies rRNA [].; GO: 0006396 RNA processing; PDB: 1SGV_B 2AUS_C 3UAI_A 3U28_A 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=100.00 E-value=1.2e-51 Score=371.36 Aligned_cols=145 Identities=46% Similarity=0.799 Sum_probs=134.0
Q ss_pred HHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCCCCCCeeeeccCCCCCHHHHHHH
Q 011455 330 RRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKA 409 (485)
Q Consensus 330 RriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~DieGkVIe~sp~~hIT~E~Ieka 409 (485)
|++++.+||||+|||||+||||||||+|+|||+++++++.+|+|+++++||.+|||+|++|+|+++.+++|+|.++|+++
T Consensus 1 r~~~~~~KvGH~GTLDP~AsGvL~v~vg~~Tkl~~~l~~~~K~Y~~~~~lG~~TdT~D~~G~v~~~~~~~~it~e~l~~~ 80 (149)
T PF01509_consen 1 RRILGIKKVGHGGTLDPFASGVLVVGVGKATKLLSYLQNSDKEYVATIRLGVETDTYDIEGEVTETKPYDHITEEDLEKV 80 (149)
T ss_dssp HHHTTBSSEEESS-SSTT-EEEEEEEEGGGGGGHHHHTTSEEEEEEEEEESSEETTSBTTSSEEEE---TT--HHHHHHH
T ss_pred CcccCcceeccccccCCcceEEEEEEECCcchHHHHhhccCCEEEEEEEEEEEeCCcceeeeEEEeeccccCCHHHHHHH
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccccccCCCCeeEEEEeeec
Q 011455 410 AASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 410 LasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~~~~F~~P~ftLEV~~~~ 484 (485)
|++|+|+++|+||+|||||+||||||+|||+|+.||+++|+|+||+|+|++ |..|.|+++|+|-+
T Consensus 81 l~~f~G~~~Q~pP~ySAvki~G~raY~lAR~G~~v~~~~r~v~I~~i~l~~----------~~~~~~~~~v~cs~ 145 (149)
T PF01509_consen 81 LAKFQGEIEQVPPMYSAVKINGKRAYELARKGEEVELPPRPVTIYSIELLS----------FNPPEFTFEVHCSK 145 (149)
T ss_dssp HHHTSEEEEES-SSSSSSECTTCEHHHHHHTTSSTSSS-EEEEEEEEEEEE----------EETTEEEEEEEECT
T ss_pred HHhCcCCEeeeCchheeEcCCCccHHHHHHCCCccCCCCeeEEEEEEEEEE----------EcCCeEEEEEEEcC
Confidence 999999999999999999999999999999999999999999999999999 99999999999975
No 24
>cd02868 PseudoU_synth_hTruB2_like PseudoU_synth_ hTRUB2_Like: Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi).
Probab=100.00 E-value=5.9e-46 Score=353.89 Aligned_cols=165 Identities=21% Similarity=0.243 Sum_probs=157.4
Q ss_pred eEEEEeCCCCCCHHHHHHHHHH----Hhcccccccc-cCCCCCCceEEEEEecCcccccccccCC--CcEEEEEEEEccc
Q 011455 310 TMVLVNKPKGWTSFTVCGKLRR----LVKVKKVGHA-GTLDPMATGLLIVCVGKATKLVDRYQGM--IKGYSGVFRLGEA 382 (485)
Q Consensus 310 gIL~VyKP~GiTS~dVV~kIRr----iLk~kKVGHa-GTLDP~ASGVLVVgIGkaTKLl~~Ll~~--~KeY~at~~LG~~ 382 (485)
||++||||+||+|+++++.+++ .++.+|+||+ |||||+|||||++|+|++||++++++.. .|+|+++++||.+
T Consensus 1 GilvvnKP~Gi~s~~~~~~~~~~l~~~~~~~k~~~~vhrLD~~aSGvl~~a~~~~tkl~~~~~~~~~~K~Y~~~~~lg~~ 80 (226)
T cd02868 1 GLFAVYKPPGVHWKHVRDTIESNLLKYFPEDKVLVGVHRLDAFSSGVLVLGVNHGNKLLSHLYSNHPTRVYTIRGLLGKA 80 (226)
T ss_pred CEEEEEcCCCCChhHHHHHHHHHHHHHccccceeeEccccCCCCceEEEEEeChhHhHHHHHHhcCCCeEEEEEEEEccc
Confidence 3899999999999999998776 3467789999 9999999999999999999999999985 7999999999999
Q ss_pred ccCCCCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeec
Q 011455 383 TSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSL 462 (485)
Q Consensus 383 TDT~DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l 462 (485)
|||+|++|+|++++++.|+|.++|+++|.+|+|.++|.||.|||+|++|+|||+|||+|+.||+++|+|+||+|+|++
T Consensus 81 TdT~D~~G~v~~~~~~~~it~~~i~~~l~~f~g~~~q~~p~~sa~kv~GkraYelAR~G~~ve~~~r~v~I~~i~l~~-- 158 (226)
T cd02868 81 TENFFHTGRVIEKTTYDHITREKIERLLAVIQSGHQQKAFELCSVDDQSQQAAELAARGLIRPADKSPPIIYGIRLLE-- 158 (226)
T ss_pred cCCCCCCCCEEEecCCCCCCHHHHHHHHHHhhCCceEECCceEEEeeCCHHHHHHHHCCCccCCCCcceEEEEEEEEE--
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ccccccccCCCCeeEEEEeeec
Q 011455 463 EDRFFFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 463 ~dr~~~~~F~~P~ftLEV~~~~ 484 (485)
|+.|.|+++|+|-+
T Consensus 159 --------~~~p~~~~~v~csk 172 (226)
T cd02868 159 --------FRPPEFTLEVQCIN 172 (226)
T ss_pred --------ecCCeEEEEEEEEC
Confidence 88999999999964
No 25
>COG0130 TruB Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.2e-41 Score=327.89 Aligned_cols=140 Identities=41% Similarity=0.660 Sum_probs=131.1
Q ss_pred CCcCCCC---ceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEE
Q 011455 302 PTWDGPF---GTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFR 378 (485)
Q Consensus 302 ~~W~~ln---GgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~ 378 (485)
+.+..++ | |+++|||.|||||+|++|+|++|+.+|+||+|||||+|||||+||+|+|||++++++..+|+|+|+++
T Consensus 6 ~~~~~i~~~~G-il~ldKP~G~tS~~~v~~vkkil~~~K~GH~GTLDP~atGvLpi~ig~aTKl~~~l~~~~K~Y~a~~~ 84 (271)
T COG0130 6 PEKRPIEIYIG-VINLDKPPGPTSHEVVAWVKRILGVEKAGHGGTLDPLATGVLPICLGEATKLVQYLLDADKEYVATVR 84 (271)
T ss_pred ccccccccccc-eEEeeCCCCCCHHHHHHHHHHHhCccccccccccCCcccceEEEEechhHhHHHHHhhCCcEEEEEEE
Confidence 3344455 6 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EcccccCCCCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEE
Q 011455 379 LGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDI 458 (485)
Q Consensus 379 LG~~TDT~DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkL 458 (485)
||.+|| +.++|+++|..|+|.|+|+|||||||| +.|++ |.|+||+|.+
T Consensus 85 lG~~t~-----------------~~e~i~~~l~~F~G~I~Q~PP~~SAvK-------------~~v~~--R~V~i~~l~~ 132 (271)
T COG0130 85 LGDQTD-----------------SEEEVRAALEAFTGEIYQIPPMFSAVK-------------REVER--RKITIYDLLE 132 (271)
T ss_pred eCCcCC-----------------CHHHHHHHHHhcceeeEecCCchhhcc-------------ceEee--EEEEEEEeee
Confidence 999998 689999999999999999999999999 66666 9999999999
Q ss_pred eeecccccccccCCCCeeEEEEeeec
Q 011455 459 ERSLEDRFFFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 459 i~~l~dr~~~~~F~~P~ftLEV~~~~ 484 (485)
+. +..|.++++|.|-+
T Consensus 133 ~~----------~~~~~~~~~v~Csk 148 (271)
T COG0130 133 LD----------FDRNLVTLRVECSK 148 (271)
T ss_pred cc----------CCCceEEEEEEEec
Confidence 98 77799999999965
No 26
>cd02572 PseudoU_synth_hDyskerin PseudoU_synth_hDyskerin_Like: Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl r
Probab=100.00 E-value=1.4e-40 Score=307.60 Aligned_cols=130 Identities=36% Similarity=0.610 Sum_probs=123.9
Q ss_pred CceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCC
Q 011455 308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387 (485)
Q Consensus 308 nGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~D 387 (485)
+| |++||||.|||||+||+++|++++.+||||+|||||+|+||||||+|++||++++++..+|+|++++.||..
T Consensus 2 ~g-~l~i~Kp~g~tS~~~v~~~k~~~~~kkvGH~GTLDp~A~GvLiv~~g~~Tk~~~~~~~~~K~Y~a~v~~g~~----- 75 (182)
T cd02572 2 YG-VINLDKPSGPSSHEVVAWIKRILGVEKTGHSGTLDPKVTGCLPVCIDRATRLVKSQQEAGKEYVCVMRLHDD----- 75 (182)
T ss_pred Ce-EEEEecCCCCCHHHHHHHHHHHhCCCccCcCCCCCCcCeeEEEEEECHHhhhhHHHhCCCCEEEEEEEECCc-----
Confidence 45 999999999999999999999999999999999999999999999999999999999999999999999974
Q ss_pred CCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccc
Q 011455 388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFF 467 (485)
Q Consensus 388 ieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~ 467 (485)
+|.++|++++++|+|+++|+||+|||+|+ ++|+++||+++++.
T Consensus 76 -------------it~e~l~~~l~~f~G~i~Q~pP~~SA~K~-----------------~~R~v~I~~i~l~~------- 118 (182)
T cd02572 76 -------------VDEEKVRRVLEEFTGAIFQRPPLISAVKR-----------------QLRVRTIYESKLLE------- 118 (182)
T ss_pred -------------CCHHHHHHHHHHCCCcEEeeCCHhheecC-----------------CceEEEEEEEEEEE-------
Confidence 78999999999999999999999999993 57999999999998
Q ss_pred cccCCC--CeeEEEEeee
Q 011455 468 FFLFPL--PLKLLDVIHL 483 (485)
Q Consensus 468 ~~~F~~--P~ftLEV~~~ 483 (485)
|++ |.|+++|+|-
T Consensus 119 ---~~~~~~~~~~~v~cs 133 (182)
T cd02572 119 ---YDGERRLVLFRVSCE 133 (182)
T ss_pred ---EcCCCcEEEEEEEEC
Confidence 777 9999999994
No 27
>PRK04270 H/ACA RNA-protein complex component Cbf5p; Reviewed
Probab=100.00 E-value=7.3e-39 Score=314.57 Aligned_cols=131 Identities=40% Similarity=0.560 Sum_probs=124.9
Q ss_pred CCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCC
Q 011455 307 PFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTW 386 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~ 386 (485)
.+| |++||||.|||||+||+++|++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|++++.||.
T Consensus 21 ~~g-~l~i~Kp~g~tS~~~v~~~r~~~~~kkvGH~GTLDp~A~GvL~v~~g~atk~~~~~~~~~K~Y~~~~~~g~----- 94 (300)
T PRK04270 21 KFG-VVNLDKPPGPTSHEVAAWVRDILGVEKAGHGGTLDPKVTGVLPVALGKATKVVQALLESGKEYVCVMHLHG----- 94 (300)
T ss_pred CCC-EEEEECCCCCCHHHHHHHHHHHhccccccCCCCCCCcCeEEEEEEEChHhhhhHHhccCCcEEEEEEEECC-----
Confidence 566 99999999999999999999999999999999999999999999999999999999999999999999995
Q ss_pred CCCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeeccccc
Q 011455 387 DADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRF 466 (485)
Q Consensus 387 DieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~ 466 (485)
++|.++|+++|++|+|+|+|+||+|||+| .++|+|+||+|++++
T Consensus 95 -------------~~~~~~~~~~l~~~~g~i~Q~pP~~SA~k-----------------~~~r~v~I~~i~~~~------ 138 (300)
T PRK04270 95 -------------DVPEEDIRKVFKEFTGEIYQKPPLKSAVK-----------------RRLRVRTIYELEILE------ 138 (300)
T ss_pred -------------CCCHHHHHHHHHHCCCcEEeECCHHHhcc-----------------CCceEEEEEEEEEEE------
Confidence 37899999999999999999999999999 358999999999998
Q ss_pred ccccCCCCeeEEEEeee
Q 011455 467 FFFLFPLPLKLLDVIHL 483 (485)
Q Consensus 467 ~~~~F~~P~ftLEV~~~ 483 (485)
|+.|.|+|+|.|-
T Consensus 139 ----~~~~~~~~~v~cs 151 (300)
T PRK04270 139 ----IDGRDVLFRVRCE 151 (300)
T ss_pred ----ecCCEEEEEEEEC
Confidence 7889999999994
No 28
>TIGR00425 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both.
Probab=100.00 E-value=1.6e-38 Score=315.93 Aligned_cols=132 Identities=36% Similarity=0.515 Sum_probs=124.3
Q ss_pred CceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCC
Q 011455 308 FGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWD 387 (485)
Q Consensus 308 nGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~D 387 (485)
.+||++||||.|||||+||++||++++.+||||+|||||+|||||+||+|+|||+++++++.+|+|+++++||.
T Consensus 33 ~~G~l~i~KP~g~tS~~~v~~vr~~~~~kkvGH~GTLDP~A~GvL~v~~G~aTkl~~~~~~~~K~Y~~~v~lG~------ 106 (322)
T TIGR00425 33 SYGVVNLDKPSGPSSHEVVAWVRRILNVEKTGHGGTLDPKVTGVLPVCIERATRLVKSLQEAPKEYVCLMRLHR------ 106 (322)
T ss_pred CCCEEEEeCCCCCCHHHHHHHHHHHhcccccCCCCCCCCCCceEEEEEEChHhhccHHhccCCCEEEEEEEECC------
Confidence 44599999999999999999999999999999999999999999999999999999999999999999999994
Q ss_pred CCCCeeeeccCCCCCHHHHHHHHhhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccc
Q 011455 388 ADSPVIQREPWEHIKDEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFF 467 (485)
Q Consensus 388 ieGkVIe~sp~~hIT~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~ 467 (485)
.++.++|+++|.+|+|.|+|+||+|||+|+ ++|.|+||+++++.
T Consensus 107 ------------~~~~~~l~~~l~~f~g~i~Q~pP~~SA~k~-----------------~~r~v~I~~~~l~~------- 150 (322)
T TIGR00425 107 ------------DAKEEDILRVLKEFTGRIFQRPPLKSAVKR-----------------QLRVRTIYESELLE------- 150 (322)
T ss_pred ------------CCCHHHHHHHHHHcCCcEEeeCChheEEec-----------------cCeEEEEEEEEEEE-------
Confidence 268999999999999999999999999993 48999999999998
Q ss_pred cccCCCCeeEEEEeeec
Q 011455 468 FFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 468 ~~~F~~P~ftLEV~~~~ 484 (485)
|+.|.++++|.|-+
T Consensus 151 ---~~~~~~~~~v~csk 164 (322)
T TIGR00425 151 ---KDGKDVLFRVSCEA 164 (322)
T ss_pred ---ecCCeEEEEEEeCC
Confidence 77889999999953
No 29
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=5.4e-31 Score=268.07 Aligned_cols=364 Identities=21% Similarity=0.183 Sum_probs=299.1
Q ss_pred ccceeecccCCcccccc-cccceEEeeecccccccCCCCccceeeEeeeCCCCCCCCccccCCCCCCCCCCCCCCCCCCC
Q 011455 13 SSRTLSLLLPPPLKDNF-IKKNVYLLSTKAFSSSITSTPYPLQYDMIINNPTQPQQSQTRRRPARVNSTNSDENQNPDGE 91 (485)
Q Consensus 13 ~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 91 (485)
+|+...+.+.|-+...- +-.++.-+--+.|--++++|-||.+ +|++++|.+..-.++++.+.-+. ...+ ...++|
T Consensus 8 ss~~~~~~~kp~~~~a~~~~~~~~~~ll~~~~~~~v~t~~~t~-~~~~~splk~~i~~~~~sgv~~i--~kpa-~pss~e 83 (395)
T KOG2529|consen 8 SSPQFMFMTKPALETAQKFDASIWALLLANMDKLLVRTGHYTP-SAAGVSPLKRGIKEYSRSGVINI--DKPA-NPSSHE 83 (395)
T ss_pred cccccccccCccccccccchhhhhHHHHHHHHhhhhhhcCcCc-hhhhcCHHHHhHHhHhhcCceec--cCCC-CCchHH
Confidence 34444455555544433 4445554445566678899999999 99999999998888888876665 2222 222344
Q ss_pred CCcchhhhhHhHHhhhhcCCCCCchhhhHHHHHHHHHhhccccCCCCCcccCCCCCcceeecceeeecccccccccceec
Q 011455 92 LGFDSWVDKKLEKEAKTRQPGSDNAEMTKSMRKYYNKRRQRMYGTDSEDEYGKNDDGFVELKPEVVEFNRLHKREEELYF 171 (485)
Q Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~ly~ 171 (485)
+.+||+++|. .++++|+|..|++|+++++.++.++++++++++|.++.- .+|++|+|+|.++..+|++.+.||+
T Consensus 84 --~~swvk~iL~-~ek~Gh~gTlDP~vtg~l~v~~~~~tr~~~s~~s~gk~y---vg~~~lt~~v~~~~k~~~~~e~l~g 157 (395)
T KOG2529|consen 84 --VVSWVKNILR-VEKTGHSGTLDPEVTGCLIVCIDRATRLLKSQQSAGKEY---VGIGKLTPEVEDALKLHQKLEHLYG 157 (395)
T ss_pred --HHHHHHHHhh-HHHhCCCCCCCccccceEEEEeecccccccchhccCcEE---EEEEecCcchhhhhhhccchhhhhh
Confidence 9999999999 889999999999999999999999999999999986644 9999999999999999999999999
Q ss_pred cccccCcCccc-chhHHHHHHhhccCCcccccccccCCCCc----hhHHHhhhh------cCCCcccccCC-----ccCC
Q 011455 172 YDTFAYPWEKD-KHYKMVYQLEKKYFPDQCLDKAFLDPSAD----QNVKKMRKK------AGGKSEEKKYN-----KEDD 235 (485)
Q Consensus 172 ~~~~~~p~ek~-~~~~~~~~le~ky~p~~~~d~a~~~~~~~----~~~~~~~~~------~~~~~~~~~~~-----~~~~ 235 (485)
++.+++||+.+ +|+.||++|+..+++++|.|++|+.++.+ ...+.+... -+++..+++-. ++.+
T Consensus 158 ~l~~~~pl~~~~kr~~~v~~~y~s~~ie~d~~~~l~~f~~~~~~~t~~rt~~~~lg~ll~~g~k~~E~~r~r~~~~~E~~ 237 (395)
T KOG2529|consen 158 ALFQRPPLISAVKRVLRVRTLYESKIIEYDRDYPLLRFGVSCEAGTYKRTMCVHLGLLLGFGGKMQELRRVRSGICSEED 237 (395)
T ss_pred hhccCCchhhhccceeEeechhhhhcccccccchhccccccccccchHHHHHHhhhhHhhhcchhhhhhhcccccccccc
Confidence 99999999999 99999999999999999999999999986 222222222 45555555432 3466
Q ss_pred cceeeecccccccccccccccccCcccccchHhHHHHHHHhccCCCCC---CCCCCCcccccCCCCCCCCCcCCCCceEE
Q 011455 236 KRLVFFDDQEKKSEKDSILGEDVNVKGEVSEKKVEEFFKCLKKVPNKE---NEVGSGEPYIVSRSTELPPTWDGPFGTMV 312 (485)
Q Consensus 236 ~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~k~~~~~~---~~~~~~~p~~~~~~~~~p~~W~~lnGgIL 312 (485)
..++++|.++...+.++.. +. --.-.....+|.++...+++.++. +.+-.|.++.++.....++.|+++++.++
T Consensus 238 ~~~t~~d~~~~q~~~d~~~--d~-~~~r~~~~~les~l~~~~~vv~kd~~v~~~cyg~k~~v~~~~r~~~~i~~~~e~v~ 314 (395)
T KOG2529|consen 238 DMLTEHDEQDAQFEYDTER--DE-SYLRRVKKPLESLLTGYKRVVVKDSTVNAPCYGAKLLVPGLLRYSDDIDGPFEVVD 314 (395)
T ss_pred cccccccchhhhhhhcccc--Cc-ceeeeeeeccccccccceeeecccchhcCccccceeeeccccccCccccCceeEEE
Confidence 7899999888777766622 22 234456788999999999999888 55667899999999999999999999999
Q ss_pred EEeCCCCCCHHHHHHHHHHHhcccccccccCCCC-CCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCCCC
Q 011455 313 LVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDP-MATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDAD 389 (485)
Q Consensus 313 ~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP-~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~Die 389 (485)
...|+-++.+.-+....+.......++|++++++ |+.+|.+.|+|.+++.++-.+...+.|.-....|.+|++.|..
T Consensus 315 ~t~k~e~~~~~i~~~~~~~~~s~dh~~~a~~k~~~me~d~~~~~~g~~~~~~~~~e~~~~g~~~~~~~~~~~t~~~~~ 392 (395)
T KOG2529|consen 315 MTTKGEAIASKIAEMSLRQVASCDHGVVAKTKRVIMEADVYERCWGLGPKASPGKEAKAEGKLDKFGKGNETTPKDWI 392 (395)
T ss_pred EeecchhhhhhhhhhhhhhhceeeeeeecccccccccccccceeeccCcccCchHHHHHhhhhhhccCCCCCChhHhc
Confidence 9999999999999999999999999999999999 9999999999999999999888888888888888888876543
No 30
>KOG2559 consensus Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=3.9e-28 Score=236.72 Aligned_cols=159 Identities=22% Similarity=0.334 Sum_probs=148.5
Q ss_pred CcCCCCceEEEEeCCCCCCHHHHHHHHHHHh-c-----------------------------------------------
Q 011455 303 TWDGPFGTMVLVNKPKGWTSFTVCGKLRRLV-K----------------------------------------------- 334 (485)
Q Consensus 303 ~W~~lnGgIL~VyKP~GiTS~dVV~kIRriL-k----------------------------------------------- 334 (485)
.|. ++| |+|||||+||.|..+++.|-+.+ +
T Consensus 6 i~k-l~G-vl~VYKpsGik~khlr~~i~~~i~k~~~~~~~~s~~q~~~~~~g~~eg~e~~~~~~~~~sV~~~~nhPlv~g 83 (318)
T KOG2559|consen 6 IWK-LSG-VLCVYKPSGIKSKHLRKLITRKIAKSVSDIESTSRIQLPLISIGVIEGHEKSLVVVGRNSVADYRNHPLVSG 83 (318)
T ss_pred hhh-hcc-eeEEecCCCccHHHHHHHHHHHHHhhhcccCCCcccccceEeecccccccceeeeecccchhhhccCCcccC
Confidence 577 899 99999999999999999875543 1
Q ss_pred ----ccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEEEcccccCCCCCCCeeeeccCCCCCHHHHHHHH
Q 011455 335 ----VKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAA 410 (485)
Q Consensus 335 ----~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~LG~~TDT~DieGkVIe~sp~~hIT~E~IekaL 410 (485)
..+||-...||-.|+|||++|||.+++++. .+.+|.+|+.+-+||.|++..+++|||.+.|++++
T Consensus 84 ~s~~~~~V~v~h~l~~~~sgvl~~gVghgc~~i~-----------~~mlg~aT~~~r~Dgri~~~~n~dhVs~~ri~~vl 152 (318)
T KOG2559|consen 84 RSIRQEDVQVVHVLPLATSGVLLFGVGHGCESIP-----------ELMLGSATNVYRIDGRIKKSENIDHVSKHRIEKVL 152 (318)
T ss_pred cchhhcceeeEEeecccccceEEEecCcchhhhh-----------hhhhccchhccCccceEeeecccchhhHHHHHHHH
Confidence 246777788999999999999999999998 56799999999999999999999999999999999
Q ss_pred hhCccceEeccccccccccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccccccCCCCeeEEEEeeec
Q 011455 411 ASFRGEIWQVPPMFSAIKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 411 asFqG~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~~~~F~~P~ftLEV~~~~ 484 (485)
+.++|+++...++||+|+++.|+||||||+|.++++.+....||+|+|++ |++|+|+||+||..
T Consensus 153 a~lq~shq~a~f~~~nvDl~tqEAyElA~RGl~Rp~~~s~~ivygI~l~~----------F~~P~F~le~qc~~ 216 (318)
T KOG2559|consen 153 ARLQSSHQSASFRHANVDLETQEAYELARRGLPRPQLPSSQIVYGIDLNW----------FRSPKFSLETQCSG 216 (318)
T ss_pred HHHHHHHHHHHHHhcCCCchhHHHHHHHHccCCCcCCCCCceEEEEeeee----------ecCCccEEEEeecc
Confidence 99999999999999999999999999999999999999999999999999 99999999999964
No 31
>KOG2529 consensus Pseudouridine synthase [Translation, ribosomal structure and biogenesis]
Probab=99.63 E-value=1.1e-16 Score=163.94 Aligned_cols=165 Identities=25% Similarity=0.305 Sum_probs=121.9
Q ss_pred CCCCCCCCCCCcccccCCCCCCCCCcCCCCceEEEEeCCCCCCHHHHHHHHHHHhcccccccccCCCCCCceEEEEEecC
Q 011455 279 VPNKENEVGSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGK 358 (485)
Q Consensus 279 ~~~~~~~~~~~~p~~~~~~~~~p~~W~~lnGgIL~VyKP~GiTS~dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGk 358 (485)
....+.++..++|...-.+.-....-+...-|+++|+||++.+||++++|++++|...|.||.|||||.++|+|++|+++
T Consensus 38 ~~~~~v~t~~~t~~~~~~splk~~i~~~~~sgv~~i~kpa~pss~e~~swvk~iL~~ek~Gh~gTlDP~vtg~l~v~~~~ 117 (395)
T KOG2529|consen 38 MDKLLVRTGHYTPSAAGVSPLKRGIKEYSRSGVINIDKPANPSSHEVVSWVKNILRVEKTGHSGTLDPEVTGCLIVCIDR 117 (395)
T ss_pred HHhhhhhhcCcCchhhhcCHHHHhHHhHhhcCceeccCCCCCchHHHHHHHHHHhhHHHhCCCCCCCccccceEEEEeec
Confidence 33345566667774333332222233333344999999999999999999999999999999999999999999999999
Q ss_pred cccccccccCCCcEEEEEEEEcccccCCCCCCCeeeeccCCCCC-HHHHHHHHhhCccceEeccccccccccCChhhHHH
Q 011455 359 ATKLVDRYQGMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIK-DEDIRKAAASFRGEIWQVPPMFSAIKVGGEKMYDK 437 (485)
Q Consensus 359 aTKLl~~Ll~~~KeY~at~~LG~~TDT~DieGkVIe~sp~~hIT-~E~IekaLasFqG~IqQ~PP~YSAVKIqGKRAYEL 437 (485)
+||++..++...|+|++.+. .|++.+..+++.... .|+. .+-..-=+.++.|.+.|+++.|++..+++.+.|.|
T Consensus 118 ~tr~~~s~~s~gk~yvg~~~---lt~~v~~~~k~~~~~--e~l~g~l~~~~pl~~~~kr~~~v~~~y~s~~ie~d~~~~l 192 (395)
T KOG2529|consen 118 ATRLLKSQQSAGKEYVGIGK---LTPEVEDALKLHQKL--EHLYGALFQRPPLISAVKRVLRVRTLYESKIIEYDRDYPL 192 (395)
T ss_pred ccccccchhccCcEEEEEEe---cCcchhhhhhhccch--hhhhhhhccCCchhhhccceeEeechhhhhcccccccchh
Confidence 99999999999999966555 455555555544332 1222 22223345667788888888888888999999999
Q ss_pred HhcCCccccCC
Q 011455 438 ARRGESIELSP 448 (485)
Q Consensus 438 ARkG~~VEl~p 448 (485)
+|-|...+..+
T Consensus 193 ~~f~~~~~~~t 203 (395)
T KOG2529|consen 193 LRFGVSCEAGT 203 (395)
T ss_pred ccccccccccc
Confidence 99888877544
No 32
>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=98.35 E-value=5.6e-07 Score=73.50 Aligned_cols=50 Identities=26% Similarity=0.240 Sum_probs=45.1
Q ss_pred EeCCCCCCHHHHHHHHH-HHhcccccccccCCCCCCceEEEEEecCcccccccccCCCcEEEEEEE
Q 011455 314 VNKPKGWTSFTVCGKLR-RLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQGMIKGYSGVFR 378 (485)
Q Consensus 314 VyKP~GiTS~dVV~kIR-riLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~~~KeY~at~~ 378 (485)
|+||.+.|++.+....+ ..++.+++||+|++|+.|+|+++|| ++|.++++
T Consensus 1 l~K~~~~t~~~~~~~~~~~~~~~~~i~~aG~kDk~a~t~q~v~---------------n~f~i~~r 51 (87)
T cd01291 1 LYKPGGDTMEAARQLAKLLGIPPKRVGYAGRKDKRAVTTQLVS---------------NRFTITLR 51 (87)
T ss_pred CCCCCCChHHHHHHHHHHhCCChheEEECccCCCCeeEEEEEc---------------ccEEEEEE
Confidence 68999999998888876 4678899999999999999999999 99999998
No 33
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=97.43 E-value=0.00019 Score=65.51 Aligned_cols=68 Identities=25% Similarity=0.315 Sum_probs=50.3
Q ss_pred EEEEeCCCCCCHH-------HHHHHHHHHhcccccccccCCCCCCceEEEEEecCc--ccccccccCCCcEEEEEEE
Q 011455 311 MVLVNKPKGWTSF-------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA--TKLVDRYQGMIKGYSGVFR 378 (485)
Q Consensus 311 IL~VyKP~GiTS~-------dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGka--TKLl~~Ll~~~KeY~at~~ 378 (485)
+++||||+|+.++ .+.+.+...+...+++..|.||..+||||+++-+.. .++...-..-.|+|.|.+.
T Consensus 2 ~ivvnKP~G~~~~~~~~~~~tl~~~l~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~V~ 78 (167)
T cd02553 2 YLMLNKPAGVVCATKDPHHPTVIDLLPEPDRRRDLFPVGRLDKDTTGLLLLTNDGQLAHRLTSPKKHVPKTYEVTLA 78 (167)
T ss_pred EEEEECCCCCEeCCCCCCCCcHHHHhhhhcccCCeEEcccCCCCCEEEEEEEeCHHHHHHhhCCcCCCceEEEEEEc
Confidence 5789999998775 255566655555678899999999999999998762 3333322336799999986
No 34
>PRK10158 23S rRNA/tRNA pseudouridine synthase A; Provisional
Probab=97.35 E-value=0.00023 Score=67.53 Aligned_cols=76 Identities=24% Similarity=0.371 Sum_probs=56.3
Q ss_pred CCCcCCCCceEEEEeCCCCCCHH---------HHHHHHHHHhcccccccccCCCCCCceEEEEEecCccc--ccccccC-
Q 011455 301 PPTWDGPFGTMVLVNKPKGWTSF---------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATK--LVDRYQG- 368 (485)
Q Consensus 301 p~~W~~lnGgIL~VyKP~GiTS~---------dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTK--Ll~~Ll~- 368 (485)
+-.|+ ...+++||||+|+.++ .+.+.++..+ .+++..|.||-..||||++|.++... +.+.+..
T Consensus 15 ~iiye--d~~~lvvnKPaGl~~~~~~~~~~~~sl~~~l~~~~--~~~~~vhRLDr~TSGlll~Akt~~~~~~l~~~f~~~ 90 (219)
T PRK10158 15 VILYQ--DEHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDY--PQAESVHRLDMATSGVIVVALTKAAERELKRQFRER 90 (219)
T ss_pred CEEEe--CCCEEEEECCCCCcEeCCCCCccchhHHHHHHHhC--CCCCEECCCCCCCceEEEEECCHHHHHHHHHHHHhC
Confidence 44554 3347899999998664 2344454433 35889999999999999999988766 7777765
Q ss_pred -CCcEEEEEEEEcc
Q 011455 369 -MIKGYSGVFRLGE 381 (485)
Q Consensus 369 -~~KeY~at~~LG~ 381 (485)
-.|+|.|.+. |.
T Consensus 91 ~v~K~Yla~v~-G~ 103 (219)
T PRK10158 91 EPKKQYVARVW-GH 103 (219)
T ss_pred CccEEEEEEEe-cc
Confidence 4799999887 54
No 35
>TIGR01621 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity.
Probab=97.32 E-value=0.00027 Score=67.05 Aligned_cols=70 Identities=20% Similarity=0.324 Sum_probs=53.3
Q ss_pred ceEEEEeCCCCCCHH------HHHHHHHHHhcccccccccCCCCCCceEEEEEecCc-cc-ccccccC--CCcEEEEEEE
Q 011455 309 GTMVLVNKPKGWTSF------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA-TK-LVDRYQG--MIKGYSGVFR 378 (485)
Q Consensus 309 GgIL~VyKP~GiTS~------dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGka-TK-Ll~~Ll~--~~KeY~at~~ 378 (485)
.-+++||||+|+.++ .+.+.+...++..+++..|.||-.+||||+++-+.. ++ +...+.. -.|+|.|.+.
T Consensus 9 ~~~lvvnKP~Gl~v~~~~~~~~l~~~l~~~~~~~~~~~VhRLDr~TSGlll~Ak~~~~~~~L~~~~~~~~v~K~YlAlV~ 88 (217)
T TIGR01621 9 PDFLLINKHPGISVHKDDGETGLLQEVATQLGVGQVWLVHRLDKMTSGILLLALNAESASELSQGFAKRKIEKTYLALSS 88 (217)
T ss_pred CCEEEEECCCCCeECCCCCcChHHHHHHHhcCCCCccEecCCCCCCceEEEEEcCHHHHHHHHHHHhcCCccEEEEEEEe
Confidence 348999999999875 445556555555679999999999999999998764 33 4443444 4799999987
No 36
>cd02558 PSRA_1 PSRA_1: Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA.
Probab=97.26 E-value=0.00038 Score=67.25 Aligned_cols=77 Identities=19% Similarity=0.218 Sum_probs=58.1
Q ss_pred CCCCcCCCCceEEEEeCCCCCCHH--------HHHHHHHHHhcccccccccCCCCCCceEEEEEecCccc--ccccccC-
Q 011455 300 LPPTWDGPFGTMVLVNKPKGWTSF--------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATK--LVDRYQG- 368 (485)
Q Consensus 300 ~p~~W~~lnGgIL~VyKP~GiTS~--------dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTK--Ll~~Ll~- 368 (485)
+.-.|+ .+-+++||||+|+.++ .+++.++..++...++..+.||-.+||||++|-+.... +...+..
T Consensus 39 ~~Iiye--d~~~lvvnKPaGl~~~~~~~~~~~t~~~~l~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~ 116 (246)
T cd02558 39 ETILHQ--DEHLLVADKPHFLPVTPRGRYVTETLLVRLRRQTGNPDLTPAHRLDRLTAGLVLFSKRPETRGAYQTLFARR 116 (246)
T ss_pred cceEEe--cCCEEEEECCCCCccCCCCcchhhhHHHHHHHHhCCCcccccccCCCCceeEEEEEcCHHHHHHHHHHHHcC
Confidence 344554 3448999999999985 36677776666667888999999999999999987543 4444444
Q ss_pred -CCcEEEEEEE
Q 011455 369 -MIKGYSGVFR 378 (485)
Q Consensus 369 -~~KeY~at~~ 378 (485)
-.|+|.|.+.
T Consensus 117 ~v~K~YlA~v~ 127 (246)
T cd02558 117 EVSKTYEAVAP 127 (246)
T ss_pred CccEEEEEEEe
Confidence 5799999986
No 37
>cd02557 PseudoU_synth_ScRIB2 PseudoU_synth_ScRIB2_like: Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs.
Probab=97.26 E-value=0.0004 Score=65.51 Aligned_cols=72 Identities=24% Similarity=0.420 Sum_probs=55.0
Q ss_pred ceEEEEeCCCCCCHH--------HHHHHHHHHhcccccccccCCCCCCceEEEEEecC-c-ccccccccC--CCcEEEEE
Q 011455 309 GTMVLVNKPKGWTSF--------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGK-A-TKLVDRYQG--MIKGYSGV 376 (485)
Q Consensus 309 GgIL~VyKP~GiTS~--------dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGk-a-TKLl~~Ll~--~~KeY~at 376 (485)
+.+++||||.|+-++ .+.+.+.+.++..++...|.||..+||||+++-+. + .++...+.+ -.|+|.|.
T Consensus 23 ~~~ivvnKP~Gl~~~~~~~~~~~sl~~~l~~~~~~~~~~~vhRLD~~TSGllllak~~~~~~~l~~~f~~~~v~K~Y~a~ 102 (213)
T cd02557 23 DDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGLTELRPCHRLDRLTSGLLLFAKTSQTASRLQQQIRSREVKKEYLAR 102 (213)
T ss_pred CCEEEEECCCCCcCCCCCCCCcChHHHHHHHHcCCCCccCccCCCCCCceEEEEECCHHHHHHHHHHHHcCCccEEEEEE
Confidence 348899999998763 46677777666567889999999999999999876 3 444454444 57999998
Q ss_pred EEEcc
Q 011455 377 FRLGE 381 (485)
Q Consensus 377 ~~LG~ 381 (485)
+. |.
T Consensus 103 v~-G~ 106 (213)
T cd02557 103 VK-GE 106 (213)
T ss_pred Ee-Cc
Confidence 87 54
No 38
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.
Probab=97.13 E-value=0.00032 Score=63.92 Aligned_cols=66 Identities=29% Similarity=0.312 Sum_probs=47.7
Q ss_pred EEEEeCCCCCCHHH-----HHHHHHHHhcccccccccCCCCCCceEEEEEecCcccccccccC----CCcEEEEEEE
Q 011455 311 MVLVNKPKGWTSFT-----VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKATKLVDRYQG----MIKGYSGVFR 378 (485)
Q Consensus 311 IL~VyKP~GiTS~d-----VV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGkaTKLl~~Ll~----~~KeY~at~~ 378 (485)
+++||||.|+-|+. -...+...+...++...|.||-.+||||+++-+. ++...+.. -.|+|.|.+.
T Consensus 1 ~lv~nKP~G~~~~~~~~~~~~~~l~~~l~~~~~~~v~RLD~~TsGlll~a~d~--~~~~~l~~~~~~v~K~Y~a~v~ 75 (168)
T cd02566 1 LILFNKPYGVLSQFTDESEKHKTLKDYIDDPGVYAAGRLDRDSEGLLLLTDDG--RLQHRITDPSFKHPKTYYVQVE 75 (168)
T ss_pred CEEEECCCCCEEecCCCcCCCccHHHHcCcCCeEEccCCCCCCeEEEEEEeCH--HHHHHHHCCCCCCCEEEEEEEC
Confidence 36799999986651 1234555554467889999999999999999765 24444443 5799999884
No 39
>COG0564 RluA Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]
Probab=97.08 E-value=0.00083 Score=67.07 Aligned_cols=81 Identities=28% Similarity=0.459 Sum_probs=63.8
Q ss_pred CCCCcCCCCceEEEEeCCCCCCH--------HHHHHHHHHHhc--ccccccccCCCCCCceEEEEEecC--ccccccccc
Q 011455 300 LPPTWDGPFGTMVLVNKPKGWTS--------FTVCGKLRRLVK--VKKVGHAGTLDPMATGLLIVCVGK--ATKLVDRYQ 367 (485)
Q Consensus 300 ~p~~W~~lnGgIL~VyKP~GiTS--------~dVV~kIRriLk--~kKVGHaGTLDP~ASGVLVVgIGk--aTKLl~~Ll 367 (485)
+.-.|+.- -|++||||+||.+ ..+++.+..-++ ..++|-...||--.||||++|-+. +..|...|.
T Consensus 78 l~IlyED~--~llVvnKP~Gl~vhp~~~~~~~tl~~~l~~~~~~~~~~~~~vHRLDkdTSGlll~AK~~~a~~~l~~~f~ 155 (289)
T COG0564 78 LDILYEDE--DLLVVNKPAGLVVHPGGGHHEGTLVNALLRHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFK 155 (289)
T ss_pred ccEEEecC--CEEEEECCCCCcCcCCCCCccHhHHHHHHHhccccCCceeeeccCCCCCceEEEEECCHHHHHHHHHHHh
Confidence 44455533 3799999999998 577777777655 578999999999999999999998 566667666
Q ss_pred CC--CcEEEEEEEEcccc
Q 011455 368 GM--IKGYSGVFRLGEAT 383 (485)
Q Consensus 368 ~~--~KeY~at~~LG~~T 383 (485)
+. .|+|.|.+. |.-.
T Consensus 156 ~r~v~K~Y~Alv~-G~~~ 172 (289)
T COG0564 156 QRKVKKTYLALVR-GHLP 172 (289)
T ss_pred cCcCcEEEEEEEE-Cccc
Confidence 64 799999998 7544
No 40
>cd02563 PseudoU_synth_TruC tRNA pseudouridine isomerase C: Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved.
Probab=96.88 E-value=0.0016 Score=61.72 Aligned_cols=71 Identities=24% Similarity=0.409 Sum_probs=50.5
Q ss_pred eEEEEeCCCCCCHHH----------HHHHHHHHhcccccccccCCCCCCceEEEEEecCc-cccc-ccccC--CCcEEEE
Q 011455 310 TMVLVNKPKGWTSFT----------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA-TKLV-DRYQG--MIKGYSG 375 (485)
Q Consensus 310 gIL~VyKP~GiTS~d----------VV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGka-TKLl-~~Ll~--~~KeY~a 375 (485)
-+++||||+|+.++- ++..++..++ .+++..+.||..+||||+++-+.. .+.+ ..+.+ -.|+|.|
T Consensus 9 ~~lvvnKP~G~~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~f~~~~v~K~Y~a 87 (223)
T cd02563 9 HLVAINKPSGLLVHRSELDRHETRFALQTLRDQLG-QHVYPVHRLDRPTSGVLLFALSSEVARKLGEQFTEHRVHKTYLA 87 (223)
T ss_pred CEEEEECCCCCeEcCCCCCCCCcHHHHHHHHHHcC-CCcccccCCCCCCeEEEEEEECHHHHHHHHHHHhcCceeEEEEE
Confidence 389999999987652 2334444443 468899999999999999997664 4444 33343 4799999
Q ss_pred EEEEccc
Q 011455 376 VFRLGEA 382 (485)
Q Consensus 376 t~~LG~~ 382 (485)
.+. |.-
T Consensus 88 lv~-G~~ 93 (223)
T cd02563 88 VVR-GYV 93 (223)
T ss_pred EEE-Ccc
Confidence 886 543
No 41
>TIGR00005 rluA_subfam pseudouridine synthase, RluA family. modifies uracil-65 in transfer RNAs to pseudouridine.
Probab=96.87 E-value=0.0011 Score=64.58 Aligned_cols=70 Identities=24% Similarity=0.426 Sum_probs=52.1
Q ss_pred EEEEeCCCCCCHH--------HHHHHHHHHhcc----cccccccCCCCCCceEEEEEecCc-cccc-ccccC--CCcEEE
Q 011455 311 MVLVNKPKGWTSF--------TVCGKLRRLVKV----KKVGHAGTLDPMATGLLIVCVGKA-TKLV-DRYQG--MIKGYS 374 (485)
Q Consensus 311 IL~VyKP~GiTS~--------dVV~kIRriLk~----kKVGHaGTLDP~ASGVLVVgIGka-TKLl-~~Ll~--~~KeY~ 374 (485)
+++||||+|+-++ .+++.+...+.. .++...|.||-.+||||+++-+.. .+.+ ..+.. -.|+|.
T Consensus 81 ~lvvnKP~g~~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~~~v~K~Y~ 160 (299)
T TIGR00005 81 IIVINKPSGLVVHPGGGNPFGTVLNALLAHCPPIAGVERVGIVHRLDRDTSGLMVVAKTPLALRELQRQLKNRTVTKEYV 160 (299)
T ss_pred EEEEECCCCCeEeCCCCCCcccHHHHHHHhcccccCCCcCceECCCCCCCceEEEEEcCHHHHHHHHHHHHhCCcceEEE
Confidence 8999999998765 366667665543 568899999999999999998753 3333 33333 579999
Q ss_pred EEEEEcc
Q 011455 375 GVFRLGE 381 (485)
Q Consensus 375 at~~LG~ 381 (485)
|.+. |.
T Consensus 161 a~v~-g~ 166 (299)
T TIGR00005 161 ALVH-GQ 166 (299)
T ss_pred EEEe-cc
Confidence 9886 44
No 42
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=96.82 E-value=0.0012 Score=58.77 Aligned_cols=69 Identities=30% Similarity=0.485 Sum_probs=47.8
Q ss_pred EEEEeCCCCCCHHH--------HHHHHHHHhcccccccccCCCCCCceEEEEEecCc-c-cccccccCCCcEEEEEEEEc
Q 011455 311 MVLVNKPKGWTSFT--------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA-T-KLVDRYQGMIKGYSGVFRLG 380 (485)
Q Consensus 311 IL~VyKP~GiTS~d--------VV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGka-T-KLl~~Ll~~~KeY~at~~LG 380 (485)
+++||||+|+.++. +...+... ...++...|.||-.+||||+++-+.. . ++...-....|+|.|.+. |
T Consensus 1 ~ivvnKP~G~~~~~~~~~~~~~~~~~l~~~-~~~~~~~vhRLD~~TSGlll~ak~~~~~~~l~~~~~~v~K~Y~a~v~-g 78 (154)
T cd02550 1 ILVLNKPSGLVCHPTDRDRDPTVVVRLDKL-HGPRVHAAGRLDKDTSGLLLLTNDGRLQRRLTEPRREIEKEYLVTVR-G 78 (154)
T ss_pred CEEEECCCCCEEecCCCCCCCcHHHhhhcc-cCCceeEeccCCCCCeeEEEEEcCHHHHHHHhhhhccCcEEEEEEEE-e
Confidence 47799999976552 23333222 23568889999999999999999764 3 444432336899999986 5
Q ss_pred c
Q 011455 381 E 381 (485)
Q Consensus 381 ~ 381 (485)
.
T Consensus 79 ~ 79 (154)
T cd02550 79 E 79 (154)
T ss_pred e
Confidence 4
No 43
>PRK11180 rluD 23S rRNA pseudouridine synthase D; Provisional
Probab=96.70 E-value=0.0016 Score=65.21 Aligned_cols=69 Identities=29% Similarity=0.434 Sum_probs=52.2
Q ss_pred eEEEEeCCCCCCHH--------HHHHHHHHHhc----ccccccccCCCCCCceEEEEEecC--cccccccccC--CCcEE
Q 011455 310 TMVLVNKPKGWTSF--------TVCGKLRRLVK----VKKVGHAGTLDPMATGLLIVCVGK--ATKLVDRYQG--MIKGY 373 (485)
Q Consensus 310 gIL~VyKP~GiTS~--------dVV~kIRriLk----~kKVGHaGTLDP~ASGVLVVgIGk--aTKLl~~Ll~--~~KeY 373 (485)
.+++||||+|+.+| .+++.+...+. ..+++..+.||-.+||||+++-+. +..+.+.+.. -.|+|
T Consensus 92 ~~lvvnKP~gl~~~~~~~~~~~tl~~~l~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~~~~~l~~~~~~~~v~K~Y 171 (325)
T PRK11180 92 DILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQKREITREY 171 (325)
T ss_pred CEEEEECCCCCeEeCCCCCCCCcHHHHHHHHhhhccCCcccceeccCCCCCceeEEEECCHHHHHHHHHHHHhCCcceEE
Confidence 38999999999776 25666665442 246788999999999999999874 3455555554 47999
Q ss_pred EEEEE
Q 011455 374 SGVFR 378 (485)
Q Consensus 374 ~at~~ 378 (485)
.|.+.
T Consensus 172 ~A~v~ 176 (325)
T PRK11180 172 EAVAI 176 (325)
T ss_pred EEEEe
Confidence 99876
No 44
>PRK11112 tRNA pseudouridine synthase C; Provisional
Probab=96.68 E-value=0.0023 Score=62.29 Aligned_cols=69 Identities=28% Similarity=0.490 Sum_probs=49.3
Q ss_pred ceEEEEeCCCCCCHHH----------HHHHHHHHhcccccccccCCCCCCceEEEEEecCc--ccccccccC--CCcEEE
Q 011455 309 GTMVLVNKPKGWTSFT----------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA--TKLVDRYQG--MIKGYS 374 (485)
Q Consensus 309 GgIL~VyKP~GiTS~d----------VV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGka--TKLl~~Ll~--~~KeY~ 374 (485)
..+++||||+|+.++. +...++..++ .++...+.||..+||||++|-+.. .+|...+.. -.|+|.
T Consensus 9 ~~~lvvnKPaGl~~~~~~~~~~~~~~~~~~l~~~~~-~~~~~VHRLDr~TSGlll~Ak~~~~~~~L~~~f~~~~v~K~Y~ 87 (257)
T PRK11112 9 EWLVAVNKPAGWLVHRSWLDRHETVFVMQTVRDQIG-QHVFTAHRLDRPTSGVLLMALSSEVARLLAQQFEQHQIQKTYH 87 (257)
T ss_pred CCEEEEECCCCCeecCCCCCCCchHHHHHHHHHHhC-CCceeeccCCCCCeeEEEEECCHHHHHHHHHHHHhCCcceEEE
Confidence 3489999999997753 2233433333 257789999999999999999764 334444444 479999
Q ss_pred EEEE
Q 011455 375 GVFR 378 (485)
Q Consensus 375 at~~ 378 (485)
|.+.
T Consensus 88 Alv~ 91 (257)
T PRK11112 88 AIVR 91 (257)
T ss_pred EEEE
Confidence 9876
No 45
>PF00849 PseudoU_synth_2: RNA pseudouridylate synthase This Prosite family is a subset of the Pfam family. This Prosite family is a subset of the Pfam family.; InterPro: IPR006145 Pseudouridine synthases catalyse the isomerisation of uridine to pseudouridine (Psi) in a variety of RNA molecules, and may function as RNA chaperones. Pseudouridine is the most abundant modified nucleotide found in all cellular RNAs. There are four distinct families of pseudouridine synthases that share no global sequence similarity, but which do share the same fold of their catalytic domain(s) and uracil-binding site and are descended from a common molecular ancestor. The catalytic domain consists of two subdomains, each of which has an alpha+beta structure that has some similarity to the ferredoxin-like fold (note: some pseudouridine synthases contain additional domains). The active site is the most conserved structural region of the superfamily and is located between the two homologous domains. These families are []: Pseudouridine synthase I, TruA. Pseudouridine synthase II, TruB, which contains and additional C-terminal PUA domain. Pseudouridine synthase RsuA (ribosomal small subunit) and RluC/RluD (ribosomal large subunits), both of which contain an additional N-terminal alpha-L RNA-binding motif. Pseudouridine synthase TruD, which has a natural circular permutation in the catalytic domain, as well as an insertion of a family-specific alpha+beta subdomain. This entry represents several different pseudouridine synthases from family 3, including: RsuA (acts on small ribosomal subunit), RluA, RluB, RluC, RluD, RluE and RluF (act on large ribosomal subunit). RsuA from Escherichia coli catalyses formation of pseudouridine at position 516 in 16S rRNA during assembly of the 30S ribosomal subunit [, ]. RsuA consists of an N-terminal domain connected by an extended linker to the central and C-terminal domains. Uracil and UMP bind in a cleft between the central and C-terminal domains near the catalytic residue Asp 102. The N-terminal domain shows structural similarity to the ribosomal protein S4. Despite only 15% amino acid identity, the other two domains are structurally similar to those of the tRNA-specific psi-synthase TruA, including the position of the catalytic Asp. Our results suggest that all four families of pseudouridine synthases share the same fold of their catalytic domain(s) and uracil-binding site. RluB, RluC, RluD, RluE and RluF are homologous enzymes which each convert specific uridine bases in E. coli ribosomal 23S RNA to pseudouridine: RluB modifies uracil-2605. RluC modifies uracil-955, U-2504, and U-2580. RluD modifies uracil-1911, U-1915, and U-1917. RluE modifies uracil-3457. RluF modifies uracil-2604, and to a lesser extent U-2605. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis [, ]. Both RluC and RluD have an N-terminal S4 RNA binding domain. Despite the conserved topology shared by RluC and RluD, the surface shape and charge distribution are very different. ; GO: 0003723 RNA binding, 0009982 pseudouridine synthase activity, 0001522 pseudouridine synthesis, 0009451 RNA modification; PDB: 2GML_A 3DH3_B 1VIO_A 2I82_B 1XPI_B 1V9K_B 1PRZ_A 1V9F_A 2IST_A 1QYU_A ....
Probab=96.63 E-value=0.00045 Score=60.53 Aligned_cols=75 Identities=24% Similarity=0.320 Sum_probs=48.3
Q ss_pred EEEEeCCCCCCHHHHH-----------HH-HHHHhcccccccccCCCCCCceEEEEEecCc--cccccccc--CCCcEEE
Q 011455 311 MVLVNKPKGWTSFTVC-----------GK-LRRLVKVKKVGHAGTLDPMATGLLIVCVGKA--TKLVDRYQ--GMIKGYS 374 (485)
Q Consensus 311 IL~VyKP~GiTS~dVV-----------~k-IRriLk~kKVGHaGTLDP~ASGVLVVgIGka--TKLl~~Ll--~~~KeY~ 374 (485)
+++||||.|+-++..- .. ........+++-.|.||..+||||+++.... -++...+. ...|+|.
T Consensus 2 ~ivvnKP~G~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~TsGlll~a~~~~~~~~l~~~f~~~~~~K~Y~ 81 (164)
T PF00849_consen 2 LIVVNKPAGVPVHPSDGNESKSVKELPALSLKRGDDPPELYPVHRLDRDTSGLLLFAKDKEAAAKLSKQFPKRKVEKTYL 81 (164)
T ss_dssp EEEEEE-TTSBSSSSSTBSSSSHHCHHHHHHHHCTTSGGGEESS---TT-EEEEEEESSHHHHHHHHHHHHTTCSEEEEE
T ss_pred EEEEECCCCCeEecCCCCCcccccchhhhhhhhccCCCceEECCCCCccccCCeeccCCcccccccccccccCCCcEEEE
Confidence 6889999998665433 11 1222356799999999999999999998653 34455443 3689999
Q ss_pred EEEEEcccccC
Q 011455 375 GVFRLGEATST 385 (485)
Q Consensus 375 at~~LG~~TDT 385 (485)
|.+.-|...+.
T Consensus 82 a~v~~~~~~~~ 92 (164)
T PF00849_consen 82 ALVEGGPVEEE 92 (164)
T ss_dssp EEECSSSSTTC
T ss_pred EeEcccccccc
Confidence 99985555443
No 46
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Probab=96.60 E-value=0.0026 Score=58.01 Aligned_cols=67 Identities=19% Similarity=0.253 Sum_probs=45.7
Q ss_pred EEEEeCCCCCCHHH--------HHHHHHHHhcccccccccCCCCCCceEEEEEecCc-cccccccc-CCCcEEEEEEE
Q 011455 311 MVLVNKPKGWTSFT--------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA-TKLVDRYQ-GMIKGYSGVFR 378 (485)
Q Consensus 311 IL~VyKP~GiTS~d--------VV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGka-TKLl~~Ll-~~~KeY~at~~ 378 (485)
+++||||+|+-|+. +.+.+... ...+++..|.||-.+||||+++-+.. .+.+..-. .-.|+|.|.+.
T Consensus 2 ~lvvnKP~G~~~~~~~~~~~~tl~~~l~~~-~~~~~~~V~RLD~~TsGLll~ak~~~~~~~L~~~~~~i~K~Y~a~V~ 78 (167)
T cd02556 2 VLIYHKPEGLICTRKDPKGRPTVFDLLPKL-GIPRWISVGRLDLNTEGLLLFTNDGELANRLMHPSNEIEREYAVRVF 78 (167)
T ss_pred EEEEECCCCcEECccCCCCCccHHHhhhhh-ccCceEEcCcCCCCCeeEEEEECCHHHHHHHhCCcCCCCeEEEEEEC
Confidence 68899999985542 34444322 13467889999999999999987553 33333211 14799999986
No 47
>PRK11025 23S rRNA pseudouridylate synthase C; Provisional
Probab=96.53 E-value=0.0032 Score=62.94 Aligned_cols=76 Identities=24% Similarity=0.350 Sum_probs=53.0
Q ss_pred CCCcCCCCceEEEEeCCCCCCHH-------HHHHHHHHHhc-ccccccccCCCCCCceEEEEEecCcc--cccccccC--
Q 011455 301 PPTWDGPFGTMVLVNKPKGWTSF-------TVCGKLRRLVK-VKKVGHAGTLDPMATGLLIVCVGKAT--KLVDRYQG-- 368 (485)
Q Consensus 301 p~~W~~lnGgIL~VyKP~GiTS~-------dVV~kIRriLk-~kKVGHaGTLDP~ASGVLVVgIGkaT--KLl~~Ll~-- 368 (485)
.-.|+. .. +++||||+|+.+| .+++.+..... ...++..+.||-..||||++|-+..+ .+...+..
T Consensus 94 ~Ilyed-~~-~lvvnKP~gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~vhRLD~~TSGlll~Ak~~~a~~~l~~~~~~~~ 171 (317)
T PRK11025 94 VILYED-DH-ILVLNKPSGTAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKG 171 (317)
T ss_pred CEEEEC-CC-EEEEECCCCCcCcCCCCCCccHHHHHHHhccCCCcCceeCCCCCCCceEEEEEcCHHHHHHHHHHHHhCC
Confidence 344443 23 8999999999875 34555544322 23467899999999999999998743 34444444
Q ss_pred CCcEEEEEEE
Q 011455 369 MIKGYSGVFR 378 (485)
Q Consensus 369 ~~KeY~at~~ 378 (485)
-.|+|.|.+.
T Consensus 172 v~K~Y~a~v~ 181 (317)
T PRK11025 172 MQKDYLALVR 181 (317)
T ss_pred ccEEEEEEEe
Confidence 5799999876
No 48
>PF08068 DKCLD: DKCLD (NUC011) domain; InterPro: IPR012960 This is an N-terminal domain of dyskerin-like proteins, which is often associated with the TruB N-terminal(IPR002501 from INTERPRO) and PUA(IPR002478 from INTERPRO) domains [].; PDB: 3ZV0_D 3UAI_A 3U28_A 2AUS_C 2RFK_A 3LWV_A 3HJY_A 3HAX_A 3LWO_A 3HAY_A ....
Probab=96.46 E-value=0.00045 Score=55.80 Aligned_cols=21 Identities=29% Similarity=0.178 Sum_probs=15.9
Q ss_pred CCCceEEEEeCCCCCCHHHHH
Q 011455 306 GPFGTMVLVNKPKGWTSFTVC 326 (485)
Q Consensus 306 ~lnGgIL~VyKP~GiTS~dVV 326 (485)
.+.-|||++|||+|+|||+||
T Consensus 39 ~i~~GvinlDKP~gPtSHeVv 59 (59)
T PF08068_consen 39 YIKYGVINLDKPSGPTSHEVV 59 (59)
T ss_dssp HHHTEEEEEEE-SSS-HHHHH
T ss_pred HHhCCcEEeeCCCCCCccccC
Confidence 344559999999999999996
No 49
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=96.43 E-value=0.0018 Score=62.82 Aligned_cols=69 Identities=23% Similarity=0.214 Sum_probs=49.5
Q ss_pred eEEEEeCCCCCCHHHH----HHHHHHHhcccccccccCCCCCCceEEEEEecC-ccccccccc-CCCcEEEEEEE
Q 011455 310 TMVLVNKPKGWTSFTV----CGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGK-ATKLVDRYQ-GMIKGYSGVFR 378 (485)
Q Consensus 310 gIL~VyKP~GiTS~dV----V~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGk-aTKLl~~Ll-~~~KeY~at~~ 378 (485)
.++++|||.|+-|+.- ...|...+...++...|.||..+||||+++-+. +++.+.... .-.|+|.|.+.
T Consensus 40 ~ylllnKP~G~l~~~~d~~~~~tl~d~l~~~~~~~vgRLD~~TsGllLlt~d~~~~~~L~~~~~~i~K~Y~~~v~ 114 (217)
T PRK11394 40 RVILFNKPYDVLPQFTDEAGRKTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYYVQVE 114 (217)
T ss_pred EEEEEECCCCCEEeeCCccCCcchHHhcccCCeEEecCCCCCCeeEEEEECCHHHHHHHhCcccCCCEEEEEEEC
Confidence 3899999999977621 123444444457889999999999999999854 444444433 36899999886
No 50
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=96.40 E-value=0.0072 Score=60.68 Aligned_cols=66 Identities=24% Similarity=0.297 Sum_probs=46.5
Q ss_pred eEEEEeCCCCCCHHH-------HHHHHHHHhcccccccccCCCCCCceEEEEEecCc--ccccccccCCCcEEEEEEE
Q 011455 310 TMVLVNKPKGWTSFT-------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA--TKLVDRYQGMIKGYSGVFR 378 (485)
Q Consensus 310 gIL~VyKP~GiTS~d-------VV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGka--TKLl~~Ll~~~KeY~at~~ 378 (485)
-+++||||.|+.|+. +++.|.. ..++...|.||-.+||||+++-+.. .+|..--....|+|.|++.
T Consensus 68 ~~lvlnKP~G~~~~~~~~~~~tv~~~l~~---~~~l~~VgRLDrdTsGLLLlT~dg~~~~~L~~p~~~i~K~Y~v~V~ 142 (290)
T PRK10475 68 VLIALNKPVGIVSTTEDGERDNIVDFVNH---SKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVD 142 (290)
T ss_pred eEEEEECCCCCCcCCCCCCCCcHHHHhhc---cccccccccCCCCCcceEEEecCHHHHHHhhCcCCCCCeEEEEEEC
Confidence 378999999987762 3333332 2467899999999999999987543 2232222236899999986
No 51
>TIGR01213 conserved hypothetical protein TIGR01213. Members of this family show twilight-zone similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs.
Probab=96.31 E-value=0.016 Score=61.01 Aligned_cols=91 Identities=18% Similarity=0.206 Sum_probs=67.2
Q ss_pred EEEEEecCcccc-cccccC--CCcEEEEEEEEcccccCCCCCCCeeeeccCCCCCHHHHHHHHhhCcc-ceEeccccccc
Q 011455 351 LLIVCVGKATKL-VDRYQG--MIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRG-EIWQVPPMFSA 426 (485)
Q Consensus 351 VLVVgIGkaTKL-l~~Ll~--~~KeY~at~~LG~~TDT~DieGkVIe~sp~~hIT~E~IekaLasFqG-~IqQ~PP~YSA 426 (485)
|-|..+.-+|+- ...+.. ..|+|+|.+.+... |+.+++++++..|+| +|+|.+|.=++
T Consensus 254 V~v~~L~~~~~~~v~~ik~~~~~K~Y~alV~~~~~------------------v~~e~L~~~~~~l~g~~I~QrTP~RV~ 315 (388)
T TIGR01213 254 VEVEGLKFATREEVEEVKEEKHRKVYRALVEVDGP------------------VSDEDLEELCKELEGATIYQRTPLRVL 315 (388)
T ss_pred EEEEEeEEEcHHHHHHHhccCCceEEEEEEEECCC------------------CCHHHHHHHHHhccCCEEEccCCceEE
Confidence 555555543332 122222 57999999998653 788999999999999 89999999888
Q ss_pred cccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccccccCCCCeeEEEEeeec
Q 011455 427 IKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 427 VKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~~~~F~~P~ftLEV~~~~ 484 (485)
.+ +....|.=+||++++.. +..-.|+|+|.|-+
T Consensus 316 hR---------------Ra~~~R~R~I~~i~~~~----------i~~~~~~l~v~~qa 348 (388)
T TIGR01213 316 HR---------------RADLVRERRVYQVDLSG----------LDGNHAELIIEAEG 348 (388)
T ss_pred Ee---------------cCCCceEEEEEEEEEEE----------EcCCEEEEEEEecC
Confidence 64 23446777899999998 66668999999843
No 52
>cd02869 PseudoU_synth_RluCD_like PseudoU_synth_RsuA/RluD: Pseudouridine synthase, RsuA/RluD family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=96.24 E-value=0.0049 Score=54.95 Aligned_cols=68 Identities=29% Similarity=0.432 Sum_probs=47.2
Q ss_pred EEEEeCCCCCCHHH--------HHHHH----HHHhcccccccccCCCCCCceEEEEEecC-c-ccccccccC--CCcEEE
Q 011455 311 MVLVNKPKGWTSFT--------VCGKL----RRLVKVKKVGHAGTLDPMATGLLIVCVGK-A-TKLVDRYQG--MIKGYS 374 (485)
Q Consensus 311 IL~VyKP~GiTS~d--------VV~kI----RriLk~kKVGHaGTLDP~ASGVLVVgIGk-a-TKLl~~Ll~--~~KeY~ 374 (485)
+++||||.|+.++. +...+ ........+...|.||--+||||+++-+. + .++...+.. ..|+|.
T Consensus 1 ~lvvnKP~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~RLD~~tsGlll~ak~~~~~~~l~~~~~~~~~~K~Y~ 80 (185)
T cd02869 1 LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNKKAAAKLSKQFKERKVKKTYL 80 (185)
T ss_pred CEEEECCCCCeeecCCCCCCCCHHHHHHHHHhhcCCCCcCceecccCCCCceEEEEEcCHHHHHHHHHHHhcCceeEEEE
Confidence 47899999985552 23332 11223457889999999999999999855 3 444444333 589999
Q ss_pred EEEE
Q 011455 375 GVFR 378 (485)
Q Consensus 375 at~~ 378 (485)
|...
T Consensus 81 a~v~ 84 (185)
T cd02869 81 ALVD 84 (185)
T ss_pred EEEe
Confidence 9986
No 53
>PRK10839 16S rRNA pseudouridylate synthase A; Provisional
Probab=96.18 E-value=0.0022 Score=60.82 Aligned_cols=65 Identities=25% Similarity=0.264 Sum_probs=42.8
Q ss_pred EEEEeCCCCCCHHHH-------HHHHHHHhcccccccccCCCCCCceEEEEEecCc--ccccccccCCCcEEEEE
Q 011455 311 MVLVNKPKGWTSFTV-------CGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA--TKLVDRYQGMIKGYSGV 376 (485)
Q Consensus 311 IL~VyKP~GiTS~dV-------V~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGka--TKLl~~Ll~~~KeY~at 376 (485)
+++||||+||-+|-- ...+... ...++...|.||-.+||||+++-+.. .++..--..-.|+|.|+
T Consensus 62 ~lvvnKP~G~~~~~~~~~~~tl~~~l~~~-~~~~~~~v~RLD~~TSGlll~ak~~~~~~~l~~~~~~i~K~Y~a~ 135 (232)
T PRK10839 62 YFMLNKPQGYVCSTDDPDHPTVLYFLDEP-VAYKLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVT 135 (232)
T ss_pred EEEEECCCCeEecccCCCCCeEEEecccc-cccCceecCCCCCCceeEEEEecCHHHHHHHhCCCCCCCeEEEEE
Confidence 899999999955521 1111110 11356789999999999999998773 33332112368999995
No 54
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.
Probab=95.91 E-value=0.0092 Score=55.64 Aligned_cols=66 Identities=23% Similarity=0.270 Sum_probs=44.6
Q ss_pred EEEEeCCCCCCHH-H---------------HHHHHHHHhcccccccccCCCCCCceEEEEEecC-ccccccc-ccCCCcE
Q 011455 311 MVLVNKPKGWTSF-T---------------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGK-ATKLVDR-YQGMIKG 372 (485)
Q Consensus 311 IL~VyKP~GiTS~-d---------------VV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGk-aTKLl~~-Ll~~~Ke 372 (485)
.+++|||.|+-|+ . +...+...+ .++...|.||-.+||||+++-.. +++.+.. ...-.|+
T Consensus 6 y~llnKP~G~l~s~~d~~~~~g~~~~~~~~~~~~l~~~~--~~l~~VgRLD~dTsGLLl~t~d~~~~~~L~~~~~~i~K~ 83 (177)
T cd02555 6 TLLLHKPAGMVSEQALALLGPGQRSAADRSGRRPLKGHF--ARLAPIGPLDKDASGLLVFSQDGRVLRKLIGDASRLEQE 83 (177)
T ss_pred EEEEECCCceEecCCCcccccccccccccchhhhhhhcC--CceeEecCCCCCCeeEEEEECCHHHHHHHhChhcCCCEE
Confidence 5789999997542 1 112232222 46889999999999999999743 4443332 2335899
Q ss_pred EEEEEE
Q 011455 373 YSGVFR 378 (485)
Q Consensus 373 Y~at~~ 378 (485)
|.|.+.
T Consensus 84 Y~v~v~ 89 (177)
T cd02555 84 YLVEVR 89 (177)
T ss_pred EEEEEc
Confidence 999986
No 55
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=95.76 E-value=0.012 Score=58.85 Aligned_cols=67 Identities=22% Similarity=0.266 Sum_probs=46.3
Q ss_pred EEEEeCCCCCCHH--------HHHHHHHHHhcccccccccCCCCCCceEEEEEe-cCccccccccc-CCCcEEEEEEE
Q 011455 311 MVLVNKPKGWTSF--------TVCGKLRRLVKVKKVGHAGTLDPMATGLLIVCV-GKATKLVDRYQ-GMIKGYSGVFR 378 (485)
Q Consensus 311 IL~VyKP~GiTS~--------dVV~kIRriLk~kKVGHaGTLDP~ASGVLVVgI-GkaTKLl~~Ll-~~~KeY~at~~ 378 (485)
++++|||.|+-|+ .|++.+... ....+...|.||-.+||||+++- |..+..+..-. .-.|+|.|.+.
T Consensus 69 ylvlnKP~G~~~s~~d~~~~~tv~d~l~~~-~~~~~~~VgRLD~dTsGLLLlTndg~~~~~L~~p~~~i~K~Y~v~V~ 145 (289)
T PRK10700 69 VLAYYKPEGELCTRNDPEGRPTVFDRLPKL-RGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAVRVF 145 (289)
T ss_pred EEEEECCCCCEeecCCCCCCccHHHHhhhh-cCCceeEccCCCCCCceEEEEEcCHHHHHHHhCccCCCCeEEEEEEc
Confidence 7889999998554 244455432 22356789999999999999886 34444443322 25899999985
No 56
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=95.65 E-value=0.0042 Score=55.06 Aligned_cols=65 Identities=29% Similarity=0.366 Sum_probs=43.2
Q ss_pred EEEeCCCCCCHHH--------HHHHHHHHhcccccccccCCCCCCceEEEEEecCc-c-cccccccCCCcEEEEEEE
Q 011455 312 VLVNKPKGWTSFT--------VCGKLRRLVKVKKVGHAGTLDPMATGLLIVCVGKA-T-KLVDRYQGMIKGYSGVFR 378 (485)
Q Consensus 312 L~VyKP~GiTS~d--------VV~kIRriLk~kKVGHaGTLDP~ASGVLVVgIGka-T-KLl~~Ll~~~KeY~at~~ 378 (485)
++||||+|+-++. +.+.+.. ...+++..|.||-.+||||+++-... . ++...-..-.|+|.|.+.
T Consensus 2 ivvnKP~G~~~~~~~~~~~~~l~~~l~~--~~~~~~~vhRLD~~TsGlll~ak~~~~~~~l~~~~~~i~K~Y~a~v~ 76 (146)
T cd02870 2 LLLNKPRGVVSTVRDPEGRPTVLDLLKD--VGERLFPVGRLDYDTEGLLLLTNDGELANRLTHPRYGVEKTYLVKVR 76 (146)
T ss_pred EEEECCCCcEecccCCCCCCEEeeeccc--cCCCEEECCCCCCCCeeEEEEeCCHHHHHHhhCccCCCCeEEEEEEC
Confidence 6789999986542 1112211 13468899999999999999997552 2 232211225799999986
No 57
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=95.27 E-value=0.02 Score=53.14 Aligned_cols=67 Identities=19% Similarity=0.230 Sum_probs=43.2
Q ss_pred EEEEeCCCCCCHHHH---HHHHHHHhc-ccccccccCCCCCCceEEEEEecC-cc-cccccccCCCcEEEEEE
Q 011455 311 MVLVNKPKGWTSFTV---CGKLRRLVK-VKKVGHAGTLDPMATGLLIVCVGK-AT-KLVDRYQGMIKGYSGVF 377 (485)
Q Consensus 311 IL~VyKP~GiTS~dV---V~kIRriLk-~kKVGHaGTLDP~ASGVLVVgIGk-aT-KLl~~Ll~~~KeY~at~ 377 (485)
.+++|||.|+-|+.- ...+...+. ..++-..|.||-.+||||+++-.. .. +|..-.....|+|.+++
T Consensus 2 y~~lnKP~G~l~s~~~~~~~tv~~~l~~~~~~~~vgRLD~~tsGlll~t~dg~~~~~L~~p~~~~~K~Y~V~v 74 (164)
T cd02554 2 YIAYNKPVGIDCTLERADEDNIIDFVNPPPRIFPIGRLDKDSEGLILLTNDGDLVNKILHADNNHEKEYLVTV 74 (164)
T ss_pred EEEEECCCCcEeecCCCCCCcHHHHhcCcCCEEEccCCCCCCeeEEEEEcCHHHHHHHhhhhcCCCeEEEEEE
Confidence 467899998744321 012333332 246888999999999999998743 33 33333334689999994
No 58
>KOG1919 consensus RNA pseudouridylate synthases [RNA processing and modification]
Probab=95.16 E-value=0.024 Score=59.27 Aligned_cols=76 Identities=25% Similarity=0.289 Sum_probs=55.2
Q ss_pred CCceEEEEeCCCCCCHHHH-------HHHH-HHHhcccccccccCCCCCCceEEEEEec--Cccccccccc--CCCcEE-
Q 011455 307 PFGTMVLVNKPKGWTSFTV-------CGKL-RRLVKVKKVGHAGTLDPMATGLLIVCVG--KATKLVDRYQ--GMIKGY- 373 (485)
Q Consensus 307 lnGgIL~VyKP~GiTS~dV-------V~kI-RriLk~kKVGHaGTLDP~ASGVLVVgIG--kaTKLl~~Ll--~~~KeY- 373 (485)
-+..+++||||.|+.+|-+ +..+ ..........-...||+..||||++|-+ .+..+.+.|. ...|.|
T Consensus 111 ed~~~vVvnKP~gipVhp~g~~~~n~i~~~l~~~~~~~~~~~~hRLDr~tSGllvlAkt~~~~~~~~~~~r~~~~~k~Y~ 190 (371)
T KOG1919|consen 111 EDKDYVVVNKPHGIPVHPTGRYRENTITKILAALHKVEGLRPCHRLDRLTSGLLVLAKTKEAADKFHEVLRKRTVKKEYV 190 (371)
T ss_pred ecCCEEEEeCCCCCceeccCccccccchHHHHHhccccccccccccCccccceEEEEechhHhHHHHHHHhcccceeEEE
Confidence 4455899999999999821 1222 2222344566778999999999999999 6788889898 478999
Q ss_pred EEEEEEccc
Q 011455 374 SGVFRLGEA 382 (485)
Q Consensus 374 ~at~~LG~~ 382 (485)
++......-
T Consensus 191 v~~v~g~fp 199 (371)
T KOG1919|consen 191 VARVEGPFP 199 (371)
T ss_pred EEEEeccCC
Confidence 566655444
No 59
>PRK14554 putative pseudouridylate synthase; Provisional
Probab=94.20 E-value=0.21 Score=53.33 Aligned_cols=91 Identities=16% Similarity=0.119 Sum_probs=65.8
Q ss_pred EEEEEecCccccc-ccccC--CCcEEEEEEEEcccccCCCCCCCeeeeccCCCCCHHHHHHHHhhCccc-eEeccccccc
Q 011455 351 LLIVCVGKATKLV-DRYQG--MIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRGE-IWQVPPMFSA 426 (485)
Q Consensus 351 VLVVgIGkaTKLl-~~Ll~--~~KeY~at~~LG~~TDT~DieGkVIe~sp~~hIT~E~IekaLasFqG~-IqQ~PP~YSA 426 (485)
|-|..+.-+++-. ..+.. ..|+|+|.+.+... ++.+++.+++..|+|. |+|.+|.=.+
T Consensus 287 V~v~~l~~~~~~~~~~ik~~~~~K~YralV~~~~~------------------v~~e~l~~~~~~l~~~~I~QrTP~RV~ 348 (422)
T PRK14554 287 VEVENLRFATRKEVERIKEEKASKTYRALVESDEP------------------VSEEELEKLLDELSGATIEQRTPRRVK 348 (422)
T ss_pred EEEEEEEEEcHHHHHHHhcCCCceEEEEEEEECCC------------------CCHHHHHHHHHhccCcEeeccCcHhhh
Confidence 5555555443322 22332 45999999997543 7789999999999997 9999999777
Q ss_pred cccCChhhHHHHhcCCccccCCceeEEEEEEEeeecccccccccCCCCeeEEEEeeec
Q 011455 427 IKVGGEKMYDKARRGESIELSPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHLS 484 (485)
Q Consensus 427 VKIqGKRAYELARkG~~VEl~pR~V~IYsIkLi~~l~dr~~~~~F~~P~ftLEV~~~~ 484 (485)
.+ +....|.=+||++++.. +..-.|+|+|.|-+
T Consensus 349 hR---------------R~~~~R~R~I~~i~~~~----------i~~~~~~l~i~~ea 381 (422)
T PRK14554 349 HR---------------RADLVRVRKVYDISGEL----------IDDKHFELRIKCEG 381 (422)
T ss_pred hh---------------ccccceeeEEEEEEEEE----------EcCcEEEEEEEEec
Confidence 54 22345667799999987 56667999998853
No 60
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=87.93 E-value=0.34 Score=48.45 Aligned_cols=67 Identities=27% Similarity=0.390 Sum_probs=44.5
Q ss_pred EEEEeCCCCCCHHHH----HHHHHHHh-----cccccccccCCCCCCceEEEEEecCc---ccccccccCCCcEEEEEEE
Q 011455 311 MVLVNKPKGWTSFTV----CGKLRRLV-----KVKKVGHAGTLDPMATGLLIVCVGKA---TKLVDRYQGMIKGYSGVFR 378 (485)
Q Consensus 311 IL~VyKP~GiTS~dV----V~kIRriL-----k~kKVGHaGTLDP~ASGVLVVgIGka---TKLl~~Ll~~~KeY~at~~ 378 (485)
.+++|||.|+=|..- ..++-..+ ...++-+.|.||-.++|+|++ +|++ .+|+.==....|+|.+++.
T Consensus 65 y~llnKP~G~v~s~~D~~gr~tv~D~lp~~~~~~~~~~pvGRLD~dTeGLLLL-TnDG~la~rL~~P~~~~~K~Y~v~v~ 143 (248)
T COG1187 65 YLLLNKPRGYVSSTEDDEGRPTVFDLLPERLPRKKRLFPVGRLDKDTEGLLLL-TNDGELAHRLMHPSSEVEKEYLVRVE 143 (248)
T ss_pred EEEEECCCCeEecccCCCCCceeeeecccccccccceeeccccCCCCeeEEEE-eCCHHHHHHhcCCCCCCCEEEEEEEe
Confidence 789999999654432 22222222 233588999999999998876 4554 3333333346899999986
No 61
>TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.
Probab=73.86 E-value=3.4 Score=36.30 Aligned_cols=38 Identities=24% Similarity=0.248 Sum_probs=27.5
Q ss_pred ccCCCCCCceEEEEEecCc-cccccc-ccCCCcEEEEEEE
Q 011455 341 AGTLDPMATGLLIVCVGKA-TKLVDR-YQGMIKGYSGVFR 378 (485)
Q Consensus 341 aGTLDP~ASGVLVVgIGka-TKLl~~-Ll~~~KeY~at~~ 378 (485)
.|.||-.+||||+++-... .+.+.. -..-.|+|.|.+.
T Consensus 1 v~RLD~~TSGlll~akd~~~~~~L~~~~~~i~K~Y~a~v~ 40 (128)
T TIGR00093 1 AGRLDRDSEGLLLLTNDGELVHRLTHPGHHCEKTYLVTVE 40 (128)
T ss_pred CCCCCCCCEEEEEEEeCHHHHHHHhCCCCCCCeEEEEEEC
Confidence 4789999999999988653 333332 2225899999985
No 62
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=72.02 E-value=16 Score=39.40 Aligned_cols=73 Identities=15% Similarity=0.170 Sum_probs=54.7
Q ss_pred CCCcEEEEEEEEcccccCCCCCCCeeeeccCCCCCHHHHHHHHhhCcc-ceEeccccccccccCChhhHHHHhcCCcccc
Q 011455 368 GMIKGYSGVFRLGEATSTWDADSPVIQREPWEHIKDEDIRKAAASFRG-EIWQVPPMFSAIKVGGEKMYDKARRGESIEL 446 (485)
Q Consensus 368 ~~~KeY~at~~LG~~TDT~DieGkVIe~sp~~hIT~E~IekaLasFqG-~IqQ~PP~YSAVKIqGKRAYELARkG~~VEl 446 (485)
...|.|.|.+.+.. .|+.++++.++.++.| .|.|.-|.== ++.. .-
T Consensus 279 ~~rK~YrAlV~~~~------------------~v~~e~l~~~~~~L~g~~I~QrTP~RV--------~hrR-------ad 325 (398)
T COG1258 279 RHRKVYRALVYSDR------------------PVSDEKLEEVLGSLEGKTIRQRTPRRV--------LHRR-------AD 325 (398)
T ss_pred ccceeEEEEEEECC------------------CcCHHHHHHHHhhccCcEEeecChHHH--------hhhh-------cc
Confidence 46899999998654 3889999999999999 8899888621 1111 12
Q ss_pred CCceeEEEEEEEeeecccccccccCCCCeeEEEEeee
Q 011455 447 SPRRISIFQFDIERSLEDRFFFFLFPLPLKLLDVIHL 483 (485)
Q Consensus 447 ~pR~V~IYsIkLi~~l~dr~~~~~F~~P~ftLEV~~~ 483 (485)
..|.-.||.+++.. ...++|.++|.|-
T Consensus 326 lvR~R~V~~l~~~~----------~~~~~~~~~i~~e 352 (398)
T COG1258 326 LVRIRRVYELSLDL----------IDDRHAELEIEAE 352 (398)
T ss_pred cceEEEEEEeeeee----------ccCceEEEEEEec
Confidence 24556688888887 6788888888874
No 63
>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=60.65 E-value=1.1e+02 Score=31.75 Aligned_cols=69 Identities=23% Similarity=0.402 Sum_probs=54.6
Q ss_pred CcccccCCCCCCCCCcCCCCceEEEEeCCCCCCHHHHHHHHHHHhcc--cccccccCCCCCCceEEEEEecCc
Q 011455 289 GEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKV--KKVGHAGTLDPMATGLLIVCVGKA 359 (485)
Q Consensus 289 ~~p~~~~~~~~~p~~W~~lnGgIL~VyKP~GiTS~dVV~kIRriLk~--kKVGHaGTLDP~ASGVLVVgIGka 359 (485)
++=|.|..-...+..+++.+- ++.+.| .|++..++++.|.+.++. +.+|.|||=|-.|-=.=.|+|-..
T Consensus 7 peDF~V~Ei~~~~~~~~g~y~-~f~l~K-~n~dT~~ai~~lar~l~i~~~~i~~AG~KDk~AvT~Q~vsv~~~ 77 (319)
T cd02577 7 PEDFIVEEITPFDIGKKGKYL-IYLLEK-KNWDTLDAVRRIAKALGISRKRIGYAGTKDKHAVTTQYISIFDP 77 (319)
T ss_pred CCceEEEEecCCCCCCCCCEE-EEEEEE-CCCCHHHHHHHHHHHhCCChhheeeccccccccceEEEEEeecc
Confidence 455666666666667776665 777777 799999999999999975 689999999999977777777443
No 64
>PRK00984 truD tRNA pseudouridine synthase D; Reviewed
Probab=59.45 E-value=92 Score=32.51 Aligned_cols=67 Identities=24% Similarity=0.439 Sum_probs=53.0
Q ss_pred CcccccCCCCCCCCCcCCCCceEEEEeCCCCCCHHHHHHHHHHHhcc--cccccccCCCCCCceEEEEEec
Q 011455 289 GEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKV--KKVGHAGTLDPMATGLLIVCVG 357 (485)
Q Consensus 289 ~~p~~~~~~~~~p~~W~~lnGgIL~VyKP~GiTS~dVV~kIRriLk~--kKVGHaGTLDP~ASGVLVVgIG 357 (485)
++=|.|..-...++.+++.+- ++.|.| .|++.++++..|.+.++. +.||.||+=|-.|-=.=-|+|-
T Consensus 24 peDF~V~E~~~~~~~~~G~~~-~~~l~K-~~~~T~~~~~~lar~l~i~~~~i~yAG~KDk~AvT~Q~~si~ 92 (341)
T PRK00984 24 PEDFVVREILGFEPSGEGEHL-LVRIRK-RGWNTLFVARALAKFLGISLRDVGYAGLKDRHAVTTQWFSIH 92 (341)
T ss_pred ccceeEEeccCCCCCCCcCEE-EEEEEE-CCCCHHHHHHHHHHHhCCChhheeecccCcCCeeeEEEEEEE
Confidence 455666666666666776665 777777 799999999999999975 6799999999999777777773
No 65
>COG0585 Uncharacterized conserved protein [Function unknown]
Probab=52.92 E-value=58 Score=35.10 Aligned_cols=69 Identities=26% Similarity=0.474 Sum_probs=53.3
Q ss_pred CCCcccccCCCCCCCCCcCCCCceEEEEeCCCCCCHHHHHHHHHHHhcc--cccccccCCCCCCceEEEEEec
Q 011455 287 GSGEPYIVSRSTELPPTWDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKV--KKVGHAGTLDPMATGLLIVCVG 357 (485)
Q Consensus 287 ~~~~p~~~~~~~~~p~~W~~lnGgIL~VyKP~GiTS~dVV~kIRriLk~--kKVGHaGTLDP~ASGVLVVgIG 357 (485)
..++=|.|-.....++.+++.+= ++.|.| .||+..+++.+|.+.||+ +.||.|||=|-.|-=.=-|||-
T Consensus 27 ~~pedF~V~Ei~~~~~~~~G~~~-~~~l~K-~~~dT~~a~~~iak~lgv~~r~v~yAGlKDk~AVT~Q~vsi~ 97 (406)
T COG0585 27 AEPEDFIVEEILGYEPSGDGEYL-LFLLRK-RGWDTLDAAREIAKRLGVPRRRVGYAGLKDKRAVTTQYVSIP 97 (406)
T ss_pred eCCCccEEEeecCcCCCCCCCEE-EEEEEE-cCCChHHHHHHHHHHhCCChhhcccccccccceeeEEEEEEE
Confidence 34555666666666666555554 666666 799999999999999997 8999999999999776667766
No 66
>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=43.19 E-value=39 Score=34.19 Aligned_cols=46 Identities=26% Similarity=0.327 Sum_probs=39.2
Q ss_pred EEEEeCCCCCCHHHHHHHHHHHhcc--cccccccCCCCCCceEEEEEec
Q 011455 311 MVLVNKPKGWTSFTVCGKLRRLVKV--KKVGHAGTLDPMATGLLIVCVG 357 (485)
Q Consensus 311 IL~VyKP~GiTS~dVV~kIRriLk~--kKVGHaGTLDP~ASGVLVVgIG 357 (485)
++.|.| .|++.++++..|.+.++. +.||+||+=|-.|-=.=-|+|-
T Consensus 28 ~~~l~K-~~~~T~~ai~~LAr~lgi~~~~igyAGlKDk~AvT~Q~~sv~ 75 (253)
T cd02575 28 LLHIRK-TGLNTREVAKELAKALGVKERDVGYAGLKDRHAVTTQWFSVH 75 (253)
T ss_pred EEEEEE-CCCCHHHHHHHHHHHhCCChhheeecccccCceeeEEEEEEE
Confidence 666777 899999999999999875 6899999999999776666663
No 67
>TIGR00094 tRNA_TruD_broad tRNA pseudouridine synthase, TruD family. MJ11364 is a strong partial match from 50 to 230 aa.
Probab=40.49 E-value=42 Score=34.95 Aligned_cols=49 Identities=27% Similarity=0.371 Sum_probs=41.0
Q ss_pred ceEEEEeCCCCCCHHHHHHHHHHHhc--ccccccccCCCCCCceEEEEEecC
Q 011455 309 GTMVLVNKPKGWTSFTVCGKLRRLVK--VKKVGHAGTLDPMATGLLIVCVGK 358 (485)
Q Consensus 309 GgIL~VyKP~GiTS~dVV~kIRriLk--~kKVGHaGTLDP~ASGVLVVgIGk 358 (485)
-.++.|.| .|++..++++.|.+.++ .+.||.||+=|-.|-=.=-|++..
T Consensus 43 ~~~~~l~K-~~~~T~~a~~~iar~l~i~~~~i~yAG~KDk~AvT~Q~~s~~~ 93 (387)
T TIGR00094 43 FIHIRVEK-EGCNTLEVARVLAKFLGVSRREIGFAGTKDKRAVTEQWVCLRV 93 (387)
T ss_pred EEEEEEEE-CCcCHHHHHHHHHHHhCCChhheeecccccccceeEEEEEecc
Confidence 34888999 99999999999999987 478999999999996655556643
No 68
>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=38.41 E-value=1e+02 Score=30.55 Aligned_cols=54 Identities=22% Similarity=0.260 Sum_probs=42.6
Q ss_pred cCCCCceEEEEeCCCCCCHHHHHHHHHHHhcc--cccccccCCCCCCceEEEEEecCc
Q 011455 304 WDGPFGTMVLVNKPKGWTSFTVCGKLRRLVKV--KKVGHAGTLDPMATGLLIVCVGKA 359 (485)
Q Consensus 304 W~~lnGgIL~VyKP~GiTS~dVV~kIRriLk~--kKVGHaGTLDP~ASGVLVVgIGka 359 (485)
..+.+= ++.|.| .|++..+++..|.+.++. +.||++|+-|-.|-=.=-|+|-..
T Consensus 28 ~~G~~~-~~~l~K-~~~~T~~a~~~la~~l~i~~~~i~yAG~KDk~AvT~Q~~sv~~~ 83 (232)
T cd02552 28 GEGEYL-HFTLYK-ENKDTMEALREIAKALGVPPRDIGYAGTKDKRAVTTQRVSVHKP 83 (232)
T ss_pred CCCCEE-EEEEEE-CCCCHHHHHHHHHHHcCCCHHHEeEcccccCceeeEEEEEEECC
Confidence 344444 666777 799999999999999875 589999999999977777776443
No 69
>COG0575 CdsA CDP-diglyceride synthetase [Lipid metabolism]
Probab=34.02 E-value=24 Score=34.95 Aligned_cols=26 Identities=31% Similarity=0.514 Sum_probs=22.1
Q ss_pred HHHHHH-HHHHHhccccc-----ccccCCCCC
Q 011455 322 SFTVCG-KLRRLVKVKKV-----GHAGTLDPM 347 (485)
Q Consensus 322 S~dVV~-kIRriLk~kKV-----GHaGTLDP~ 347 (485)
.+|+++ .+||.++.|.. ||+|-||.+
T Consensus 216 lGDL~eS~iKR~~gvKDsg~liPGHGGilDR~ 247 (265)
T COG0575 216 LGDLFESYIKRLLGIKDSGWLIPGHGGILDRF 247 (265)
T ss_pred HhhHHHHHHHHccCCCCcCCCCCCcCcccccH
Confidence 367788 88999998877 999999976
No 70
>PF08555 DUF1754: Eukaryotic family of unknown function (DUF1754); InterPro: IPR013865 This is a eukaryotic protein of unknown function.
Probab=25.96 E-value=34 Score=29.00 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=21.0
Q ss_pred CCCCCchhhhHHHHHHHHHhhcccc
Q 011455 110 QPGSDNAEMTKSMRKYYNKRRQRMY 134 (485)
Q Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~ 134 (485)
.....++.|+.|.|+|-..||+|++
T Consensus 73 ~~~~~~~~kTeAErrfee~q~KRl~ 97 (98)
T PF08555_consen 73 EDESYDDGKTEAERRFEEAQRKRLM 97 (98)
T ss_pred ccccccCCCCHHHHHHHHHHHHHHc
Confidence 3445678899999999999999985
Done!