Query 024933
Match_columns 260
No_of_seqs 242 out of 1199
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 08:35:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024933.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024933hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0566 SpoU rRNA methylases [ 100.0 2.3E-45 5E-50 331.5 16.5 215 13-236 28-259 (260)
2 PRK11181 23S rRNA (guanosine-2 100.0 1.4E-44 2.9E-49 323.8 17.2 214 13-235 9-243 (244)
3 PRK10864 putative methyltransf 100.0 1.3E-43 2.8E-48 330.3 18.5 213 13-235 115-345 (346)
4 TIGR00186 rRNA_methyl_3 rRNA m 100.0 3.6E-43 7.8E-48 313.2 17.3 213 13-234 8-237 (237)
5 TIGR00185 rRNA_methyl_2 rRNA m 100.0 6.1E-40 1.3E-44 274.7 16.1 150 79-239 2-152 (153)
6 PRK10358 putative rRNA methyla 100.0 1.4E-38 3E-43 267.7 17.7 152 79-242 2-156 (157)
7 PRK11081 tRNA guanosine-2'-O-m 100.0 6.7E-38 1.5E-42 277.9 15.7 167 76-254 17-191 (229)
8 PF00588 SpoU_methylase: SpoU 100.0 2.2E-37 4.7E-42 254.7 12.8 141 78-228 1-142 (142)
9 COG0219 CspR Predicted rRNA me 100.0 6.1E-35 1.3E-39 241.6 15.8 153 78-239 2-154 (155)
10 KOG2506 SpoU rRNA Methylase fa 100.0 7.7E-32 1.7E-36 244.3 8.9 179 46-233 168-370 (371)
11 TIGR00050 rRNA_methyl_1 RNA me 100.0 4.3E-30 9.2E-35 228.8 15.6 141 78-234 3-157 (233)
12 PRK15114 tRNA (cytidine/uridin 100.0 6.8E-30 1.5E-34 229.0 16.0 142 78-233 4-159 (245)
13 PRK10433 putative RNA methyltr 99.9 3.3E-27 7.1E-32 209.5 15.3 140 78-234 2-159 (228)
14 KOG0838 RNA Methylase, SpoU fa 99.9 2.3E-24 5.1E-29 191.4 15.2 201 13-233 49-270 (271)
15 COG0565 LasT rRNA methylase [T 99.9 1.3E-23 2.8E-28 186.4 13.9 140 78-233 4-159 (242)
16 KOG0839 RNA Methylase, SpoU fa 99.8 1.2E-19 2.7E-24 184.5 7.9 148 77-235 1325-1476(1477)
17 PRK03958 tRNA 2'-O-methylase; 98.3 7.2E-06 1.6E-10 70.2 10.2 121 94-232 21-149 (176)
18 COG4080 SpoU rRNA Methylase fa 97.7 0.00044 9.6E-09 56.9 10.3 136 78-232 2-145 (147)
19 PF09936 Methyltrn_RNA_4: SAM- 97.7 4.9E-05 1.1E-09 65.3 4.8 129 92-230 30-182 (185)
20 PF08032 SpoU_sub_bind: RNA 2' 95.9 0.0017 3.8E-08 47.1 -0.5 61 13-74 6-74 (76)
21 PF09895 DUF2122: RecB-family 95.2 0.19 4E-06 39.9 8.8 80 137-230 25-106 (106)
22 COG4752 Uncharacterized protei 95.1 0.085 1.8E-06 44.4 6.9 157 67-233 7-186 (190)
23 COG1303 Uncharacterized protei 95.0 0.34 7.5E-06 41.1 10.1 119 95-233 23-149 (179)
24 PRK12703 tRNA 2'-O-methylase; 93.4 0.74 1.6E-05 43.6 10.1 116 95-232 21-143 (339)
25 PRK02135 hypothetical protein; 89.0 2.3 5E-05 37.4 8.0 84 138-233 114-197 (201)
26 PF01994 Trm56: tRNA ribose 2' 88.3 1.1 2.4E-05 36.2 5.1 84 134-232 7-94 (120)
27 KOG0838 RNA Methylase, SpoU fa 85.3 0.2 4.3E-06 45.6 -0.8 54 173-230 137-190 (271)
28 PF14419 SPOUT_MTase_2: AF2226 80.5 12 0.00025 32.0 8.0 128 91-231 18-170 (173)
29 COG1901 Uncharacterized conser 77.9 21 0.00046 31.2 9.0 86 137-234 111-196 (197)
30 COG1385 Uncharacterized protei 76.9 18 0.00039 32.7 8.8 140 77-228 77-238 (246)
31 PF04452 Methyltrans_RNA: RNA 72.6 49 0.0011 29.0 10.4 111 80-197 63-197 (225)
32 PF04013 Methyltrn_RNA_2: Puta 71.8 16 0.00036 32.1 6.9 84 138-233 113-197 (199)
33 PF04407 DUF531: Protein of un 68.1 77 0.0017 27.1 12.4 47 173-228 119-165 (173)
34 TIGR00046 RNA methyltransferas 64.3 1E+02 0.0023 27.3 13.3 112 80-197 78-207 (240)
35 PF02590 SPOUT_MTase: Predicte 46.5 23 0.0005 29.7 3.3 48 153-207 67-124 (155)
36 PRK00103 rRNA large subunit me 44.9 80 0.0017 26.5 6.3 68 153-233 67-145 (157)
37 COG1576 Uncharacterized conser 44.5 43 0.00093 28.3 4.6 45 152-197 66-119 (155)
38 TIGR00246 tRNA_RlmH_YbeA rRNA 43.1 40 0.00087 28.3 4.2 67 154-233 66-142 (153)
39 COG3426 Butyrate kinase [Energ 39.2 26 0.00056 32.9 2.7 31 85-115 102-134 (358)
40 PRK11713 16S ribosomal RNA met 37.2 2.9E+02 0.0063 24.3 12.1 108 78-197 75-200 (234)
41 COG1772 Uncharacterized protei 30.8 71 0.0015 27.0 3.7 45 173-226 119-163 (178)
42 PF07047 OPA3: Optic atrophy 3 29.4 38 0.00082 27.6 1.9 22 215-236 81-102 (134)
43 PLN03033 2-dehydro-3-deoxyphos 24.0 63 0.0014 30.1 2.5 49 92-149 222-270 (290)
44 TIGR01362 KDO8P_synth 3-deoxy- 22.9 64 0.0014 29.5 2.3 49 92-149 203-251 (258)
45 COG4075 Uncharacterized conser 22.7 1.7E+02 0.0036 23.1 4.2 63 86-160 10-73 (110)
46 PRK12457 2-dehydro-3-deoxyphos 22.5 67 0.0015 29.8 2.4 49 92-149 219-267 (281)
47 PRK01889 GTPase RsgA; Reviewed 21.0 7E+02 0.015 23.4 9.7 35 77-111 113-151 (356)
No 1
>COG0566 SpoU rRNA methylases [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-45 Score=331.54 Aligned_cols=215 Identities=21% Similarity=0.184 Sum_probs=176.9
Q ss_pred hhHHHHhhhcCCcceeeecCccc--cccCCCCcCCC--cccCCC--ccccccCCCCCceEEEEEecCCC----------C
Q 024933 13 VPLHAHFRSRAPNFTQFKNNFSF--SSPLSSFSSFR--FSPICS--LPERENGGFMPRGVGEAVNGLSQ----------N 76 (260)
Q Consensus 13 ~~~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~~~~--~~~~~~--~~~~~~~~~~~qGv~a~~~~~~~----------~ 76 (260)
|++.++|.++.+..+.++..+.. .+++.....++ .+..++ ..+.++++.+||||+|+++++.. .
T Consensus 28 ~~v~~al~~~~~i~~i~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~~~~~~~hqGi~a~~~~~~~~~~~~~~~~~~ 107 (260)
T COG0566 28 HAVLEALASGPKIVRILVTEGRLPRFEELLALAAAKGIPVYVVSEAILDKLSGTENHQGIVAVVKKRRYPLLDDLLDAEA 107 (260)
T ss_pred HHHHHHHhcCCCceEEEEecccchhHHHHHHHHHhcCCeEEEECHHHHHHHhCCCCCCeEEEEEecccccchhhhhhccc
Confidence 89999999999554444443322 11122121122 222222 23447789999999999998752 2
Q ss_pred ccEEEEEeCCCCCCcHHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceEEEEEcC-CHHHHHHHHhhhcCCcE
Q 024933 77 KFLQVVLVSPQIPGNTGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYVVIKVHS-TWAEFRDYFRQQEGEKR 155 (260)
Q Consensus 77 ~~l~vvLd~i~dp~NlGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v~v~~~~-~~~~~l~~lk~~~~g~~ 155 (260)
.+++|+||+|+||+|+|+|+|||+|||++++++..++.++.++++.|+++|+++++++.+.. +..++++.+++. |+|
T Consensus 108 ~~l~lvLd~V~DP~NlGaIiRtA~a~Gv~~Vi~~~~~~~~~~~~v~r~s~Ga~~~vp~~~~~n~~~~~~~~~~~~--G~~ 185 (260)
T COG0566 108 QPLLLVLDGVTDPHNLGAIIRTADAFGVDGVILPKRRADPLNPKVIRASAGAAFHVPVIRVTNLARTLLELLKEA--GFW 185 (260)
T ss_pred CCEEEEEecCcCCcchhhHHhhHHHhCCCEEEECCCccCCccceeEEecCChheeceeEEEeccHHHHHHHHHHc--CeE
Confidence 37999999999999999999999999999999999999999999999999999888866666 577777777655 999
Q ss_pred EEEEEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHHccc
Q 024933 156 LLAFTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAARQLN 235 (260)
Q Consensus 156 iva~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~rq~~ 235 (260)
++|++..+..++++.++++|++||||||+.|||+++++.||. .|+|||.| .++|||||||+||+|||+.||+.
T Consensus 186 v~~t~~~~~~~~~~~~~~~~~aLvlG~Eg~Gls~~~~~~~D~------~v~IPm~G-~v~SLNVsvAagI~Lye~~rq~~ 258 (260)
T COG0566 186 VVATSLDGEVDLYETDLPKKTALVLGNEGEGLSRLLLEHADQ------LVRIPMAG-KVESLNVSVAAGILLYEARRQRR 258 (260)
T ss_pred EEEECCCCCcchhhccccCCEEEEECCCCCCcCHHHHhhCCE------EEEecCCC-CcchhHHHHHHHHHHHHHHHhhc
Confidence 999999998889999999999999999999999999999999 99999999 69999999999999999999985
Q ss_pred c
Q 024933 236 Y 236 (260)
Q Consensus 236 ~ 236 (260)
.
T Consensus 259 ~ 259 (260)
T COG0566 259 A 259 (260)
T ss_pred C
Confidence 3
No 2
>PRK11181 23S rRNA (guanosine-2'-O-)-methyltransferase; Provisional
Probab=100.00 E-value=1.4e-44 Score=323.76 Aligned_cols=214 Identities=18% Similarity=0.164 Sum_probs=179.6
Q ss_pred hhHHHHhhhcCCcceeeecCccccc----cCCCCcC--CCcccCCC--ccccccCCCCCceEEEEEecCC----------
Q 024933 13 VPLHAHFRSRAPNFTQFKNNFSFSS----PLSSFSS--FRFSPICS--LPERENGGFMPRGVGEAVNGLS---------- 74 (260)
Q Consensus 13 ~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~~~~--~~~~~~~~--~~~~~~~~~~~qGv~a~~~~~~---------- 74 (260)
+++.++|++++..+..+++..+... ++..... ...+..++ .++.++++.+||||+|+++.+.
T Consensus 9 ~~v~eal~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~i~~~~v~~~~l~~ls~~~~~qGv~a~~~~~~~~~~~~~~~~ 88 (244)
T PRK11181 9 HAVQALLERAPERFIEVFVLKGREDKRLLPLINELEAQGIVIQLANRQTLDEKAEGAVHQGIIARVKPGRQLQENDLPDL 88 (244)
T ss_pred HHHHHHHhCCCCceeEEEEECCCcchHHHHHHHHHHHcCCcEEEeCHHHHhhhhcCCCCceEEEEEecccccchhhHHHH
Confidence 7899999988778888887542211 1111111 11111222 2456888999999999998632
Q ss_pred ---CCccEEEEEeCCCCCCcHHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhhhc
Q 024933 75 ---QNKFLQVVLVSPQIPGNTGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQQE 151 (260)
Q Consensus 75 ---~~~~l~vvLd~i~dp~NlGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~~~ 151 (260)
...+++++||+|+||+|+|+|+|||++||++.+++.+.+++++++++.|+++|+++++++..+.+++++++.|++.
T Consensus 89 ~~~~~~~~~lvLd~v~dp~NlGai~Rta~a~G~~~vi~~~~~~~~~~~~~~r~s~Ga~~~l~~~~~~~~~~~l~~l~~~- 167 (244)
T PRK11181 89 LASLEQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAETVPLIRVTNLARTMRMLQEK- 167 (244)
T ss_pred HhcCCCCEEEEEcCCCCcchHHHHHHHHHHcCCCEEEECCCCCCCCCCceEEecCCHHHcCeEEEcCCHHHHHHHHHHC-
Confidence 1346899999999999999999999999999999988888899999999999999999998889999999999986
Q ss_pred CCcEEEEEEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHH
Q 024933 152 GEKRLLAFTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAA 231 (260)
Q Consensus 152 ~g~~iva~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~ 231 (260)
|+++++++.++...+.+.+++++++||||||++|||+++++.||. .|+|||.| .++|||||+|+||+|||++
T Consensus 168 -g~~i~~t~~~~~~~~~~~~~~~~~alv~G~E~~Gls~~~~~~~d~------~v~IPm~g-~~~SLNvsvAaaI~lye~~ 239 (244)
T PRK11181 168 -NIWIVGTAGEADHTLYQSKLTGPLALVMGAEGEGMRRLTREHCDE------LISIPMAG-SVSSLNVSVATGICLFEAV 239 (244)
T ss_pred -CCEEEEEeCCCCcchhhcCCCCCEEEEECCCCCCcCHHHHHhCCE------EEEEcCCC-CCceeeHHHHHHHHHHHHH
Confidence 899999998877778888999999999999999999999999999 99999999 6999999999999999999
Q ss_pred Hccc
Q 024933 232 RQLN 235 (260)
Q Consensus 232 rq~~ 235 (260)
||+.
T Consensus 240 rqr~ 243 (244)
T PRK11181 240 RQRS 243 (244)
T ss_pred Hhhc
Confidence 9964
No 3
>PRK10864 putative methyltransferase; Provisional
Probab=100.00 E-value=1.3e-43 Score=330.29 Aligned_cols=213 Identities=19% Similarity=0.131 Sum_probs=177.0
Q ss_pred hhHHHHhhhcCCcceeeecCcccc---ccCCCCcC--CCcccCCC--ccccccCCCCCceEEEEEecCCC----------
Q 024933 13 VPLHAHFRSRAPNFTQFKNNFSFS---SPLSSFSS--FRFSPICS--LPERENGGFMPRGVGEAVNGLSQ---------- 75 (260)
Q Consensus 13 ~~~~~~~~~~~~~~~~l~~~~~~~---~~~~~~~~--~~~~~~~~--~~~~~~~~~~~qGv~a~~~~~~~---------- 75 (260)
|||.++|+++.+.+..|++.+... +++..+.. ...+..++ .++.++++.+||||+|+++.+..
T Consensus 115 ~aV~ealk~~~~~i~~l~~~~~~~~~~~~il~~~~~~~~~v~~V~~~~l~kls~~~~hqGV~A~v~~~~~~~l~~~l~~~ 194 (346)
T PRK10864 115 NACQALFQSRPEAIVRAWFIQSVTPRFKEALRWMAANRKAYHVVDEAELTKASGTEHHGGVCFLIKKRNGTDVQQWLAQA 194 (346)
T ss_pred HHHHHHHhCCCCceeEEEEecCccHHHHHHHHHHHHcCCcEEEeCHHHHHHHhCCCCCCeEEEEEeCCCCCCHHHHhhcc
Confidence 999999999877777777754311 11111111 11233333 24558899999999999987531
Q ss_pred -CccEEEEEeCCCCCCcHHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhhhcCCc
Q 024933 76 -NKFLQVVLVSPQIPGNTGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQQEGEK 154 (260)
Q Consensus 76 -~~~l~vvLd~i~dp~NlGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~~~~g~ 154 (260)
+.+++|+||+|+||+|+|+|+|||++||++.+++.+.+ .+.++++.|+++|.++++++..+.++.++++.|++. ||
T Consensus 195 ~~~~~vlvLd~I~DP~NlGaIiRTA~afGv~~Vil~~~~-~~~~~kvvRaS~Ga~~~v~i~~~~nl~~~L~~lk~~--G~ 271 (346)
T PRK10864 195 GAQDCVLALEDVGNPHNLGGIMRSCAHFGVKGVVVQDAA-LLESGAAIRTAEGGAEHVQPITGDSFVDVLDDFRQA--GY 271 (346)
T ss_pred ccCCeEEEEeCCCCCCcHHHHHHHHHHhCCCEEEECCCC-CCCchhHHHHhcChhhcceEEEeCCHHHHHHHHHHC--CC
Confidence 23689999999999999999999999999999998754 567889999999988888887789999999999976 89
Q ss_pred EEEEEEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHHcc
Q 024933 155 RLLAFTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAARQL 234 (260)
Q Consensus 155 ~iva~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~rq~ 234 (260)
+|++++..+..++.+++++++++||||||+.|||+++++.||. +|+|||.| .++|||||+|+||+|||++||+
T Consensus 272 ~Iv~t~~~~~~~l~~~~~~~k~aLV~GnE~~GLs~~vl~~~D~------~V~IPm~G-~veSLNVSvAaaI~LyE~~Rq~ 344 (346)
T PRK10864 272 TIVTTSSHKGTPLFKASLPAKMVLVLGQEYDGLSDAARQQGDL------SVSIDGTG-NVESLNVSVATGVLLAEWWRQN 344 (346)
T ss_pred EEEEEeCCCCcchhhcccCCCeEEEECCCCCCCCHHHHHhCCE------EEEECCCC-CCCCeEHHHHHHHHHHHHHHhh
Confidence 9999998777889999999999999999999999999999999 99999999 6999999999999999999996
Q ss_pred c
Q 024933 235 N 235 (260)
Q Consensus 235 ~ 235 (260)
.
T Consensus 345 ~ 345 (346)
T PRK10864 345 K 345 (346)
T ss_pred c
Confidence 3
No 4
>TIGR00186 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases
Probab=100.00 E-value=3.6e-43 Score=313.23 Aligned_cols=213 Identities=17% Similarity=0.152 Sum_probs=173.1
Q ss_pred hhHHHHhhhcCCcceeeecCccccccCCCCcCCCccc--CCC--ccccccCCCCCceEEEEEecCC-------------C
Q 024933 13 VPLHAHFRSRAPNFTQFKNNFSFSSPLSSFSSFRFSP--ICS--LPERENGGFMPRGVGEAVNGLS-------------Q 75 (260)
Q Consensus 13 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~--~~~--~~~~~~~~~~~qGv~a~~~~~~-------------~ 75 (260)
+++.++|+++.+.+........-..++.+...++-++ .++ .++.++++.+||||+|+++.+. .
T Consensus 8 ~~v~eal~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~l~~l~~~~~~qGv~a~~~~~~~~~~~~~~~~~~~~ 87 (237)
T TIGR00186 8 NAVLEALLNQQRVFILKGLESKRLKKLIQLAKKQGINIQLVDRQKLDQLTKGGNHQGIAAKVKPILYKDLNDLYKTAKSK 87 (237)
T ss_pred HHHHHHHhCCCEEEEEecCcchHHHHHHHHHHHcCCcEEEeCHHHHHHHhCCCCCCeEEEEEecCCCCCHHHHHHhhhcc
Confidence 7899999988443333221000001111111111111 122 2455888999999999998652 1
Q ss_pred CccEEEEEeCCCCCCcHHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhhhcCCcE
Q 024933 76 NKFLQVVLVSPQIPGNTGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQQEGEKR 155 (260)
Q Consensus 76 ~~~l~vvLd~i~dp~NlGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~~~~g~~ 155 (260)
..+++++||+|+||+|+|+|+|||++||++.+++.+.+++++++++.|+++|+++++++..+.++.++++.++++ |++
T Consensus 88 ~~~~~lvLd~v~dp~NlGaI~Rta~afG~~~vil~~~~~~~~~~~~~r~s~Ga~~~l~~~~~~~~~~~l~~l~~~--g~~ 165 (237)
T TIGR00186 88 KQPFLLILDEITDPHNLGAILRTAEAFGVDGVILPKRRSAPLNSTVVKTSSGAVEYVPLARVTNLSRTITKLKES--GFW 165 (237)
T ss_pred CCCEEEEEcCCCCCccHHHHHHHHHHcCCCEEEECCCCcCCCCCceeeeeccccceeEEEEeCCHHHHHHHHHHC--CCE
Confidence 237899999999999999999999999999999999888999999999999999999998889999999999976 899
Q ss_pred EEEEEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHHcc
Q 024933 156 LLAFTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAARQL 234 (260)
Q Consensus 156 iva~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~rq~ 234 (260)
+++++..+...+.+.++++|++||||||+.|||+++++.||. +|+|||.| .++|||||+|+||+|||++||+
T Consensus 166 i~~~~~~~~~~~~~~~~~~~~~lv~GnE~~Gls~~~l~~~d~------~v~IP~~g-~~~SLNVsvAaaI~lye~~rqr 237 (237)
T TIGR00186 166 TVGTDLDAQDTLYQVKLTKPLALVVGNEGEGVSRLIKENCDF------LIKIPMAG-KVDSLNVSVAAGILLFEIKRQR 237 (237)
T ss_pred EEEEecCCCccccccccCCCEEEEECCCCCCcCHHHHHhCCE------EEEECCCC-CCCcchHHHHHHHHHHHHHhcC
Confidence 999998876667778899999999999999999999999999 99999999 6999999999999999999985
No 5
>TIGR00185 rRNA_methyl_2 rRNA methylase, putative, group 2. this is part of the trmH (spoU) family of rRNA methylases
Probab=100.00 E-value=6.1e-40 Score=274.71 Aligned_cols=150 Identities=56% Similarity=0.945 Sum_probs=137.5
Q ss_pred EEEEEeCCCCCCcHHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhhhcCCcEEEE
Q 024933 79 LQVVLVSPQIPGNTGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQQEGEKRLLA 158 (260)
Q Consensus 79 l~vvLd~i~dp~NlGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~~~~g~~iva 158 (260)
+.||||+++||+|+|+|+|||++||++.+++.+.+.++.++++.|+|++.|+++++..+.++.++++.+++. + +++
T Consensus 2 ~~vvL~~v~dP~NlG~iiRta~afGv~~vi~~~~~~~~~~~~~~ra~~~~~~~~~~~~~~~~~~~l~~l~~~--g--v~~ 77 (153)
T TIGR00185 2 LNIVLYEPEIPPNTGNIARTCAATGTRLHLIEPLGFFLDDKRLKRAGLDYWEFVQLFYHKSWEEFLEAEKPQ--K--LFA 77 (153)
T ss_pred eEEEEcCCCCCChHHHHHHHHHHhCCEEEEECCCCCCCccHHHHhhccchHhcCCeEEeCCHHHHHHhCcCC--C--EEE
Confidence 579999999999999999999999999999987777778888889999999888888889999999999864 4 788
Q ss_pred EEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhhC-cCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHHccccc
Q 024933 159 FTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLDC-TSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAARQLNYE 237 (260)
Q Consensus 159 ~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~c-D~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~rq~~~~ 237 (260)
++.++...+++++++.+.+||||||++|||+++++.| |. .++|||.| .++|||||+|+||+|||++||+..+
T Consensus 78 ~~~~~~~~~~~~~~~~~~alv~GnE~~Gls~~~l~~~~d~------~v~IP~~g-~~~SLNvavA~aI~lye~~rq~~~~ 150 (153)
T TIGR00185 78 LTKKGTPAHSQVTYKLGDYLMFGPETRGLPQSILDNMMEQ------KIRIPMTN-NVRSLNLSNSVAIVVYEAWRQLGYK 150 (153)
T ss_pred EeCCCCCcceeeccCCCCEEEECCCCCCCCHHHHhhCCCC------EEEEcCCC-CCcchHHHHHHHHHHHHHHHccCCc
Confidence 8877777788889999999999999999999999999 99 99999999 6999999999999999999998776
Q ss_pred cC
Q 024933 238 QL 239 (260)
Q Consensus 238 ~~ 239 (260)
++
T Consensus 151 ~~ 152 (153)
T TIGR00185 151 GL 152 (153)
T ss_pred CC
Confidence 64
No 6
>PRK10358 putative rRNA methylase; Provisional
Probab=100.00 E-value=1.4e-38 Score=267.73 Aligned_cols=152 Identities=44% Similarity=0.708 Sum_probs=135.0
Q ss_pred EEEEEeCCCCCCcHHHHHHhhhhcccceEEECCCCCCCChhHHHH-hcCCCcceEEEEEcCCHHHHHHHHhhhcCCcEEE
Q 024933 79 LQVVLVSPQIPGNTGCIARTCAASACGLHLVGPLGFQVDDTKLKR-AGLDYWPYVVIKVHSTWAEFRDYFRQQEGEKRLL 157 (260)
Q Consensus 79 l~vvLd~i~dp~NlGaIiRta~afGv~~viv~~~~~~~~~~k~~r-ag~~~~~~v~v~~~~~~~~~l~~lk~~~~g~~iv 157 (260)
+.|||++|+||+|+|+|+|||+|||++.+++.+. ++++++|+.| +|++++..+++..+.+++++++.++ +++++
T Consensus 2 ~~ivL~~~~dPgNlGti~Rta~a~G~~~viv~~~-~d~~~~k~~raag~~~~~~~~~~~~~~l~~~l~~~~----~~~v~ 76 (157)
T PRK10358 2 LNIVLFEPEIPPNTGNIIRLCANTGFRLHIIEPM-GFAWDDKRLRRAGLDYHEFTAVTRHHDYAAFLEAEN----PQRLF 76 (157)
T ss_pred eEEEEeCCCCcChHHHHHHHHHHhCCEEEEECCC-CCCCChHHHHhcccccccceeeEEcCCHHHHHHhCC----CceEE
Confidence 5799999999999999999999999999999875 4788888776 5788887777777899999988543 58999
Q ss_pred EEEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhh--CcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHHccc
Q 024933 158 AFTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLD--CTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAARQLN 235 (260)
Q Consensus 158 a~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~--cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~rq~~ 235 (260)
+++..++..+.+.+++++.+||||||++|||+++++. ||. .|+|||.| .++|||||+|++|+|||++||++
T Consensus 77 ~~~~~~~~~~~~~~~~~~~~lvfGnE~~GLs~~~~~~~~~d~------~v~IPm~~-~~eSLNvAvA~aI~lyE~~rqr~ 149 (157)
T PRK10358 77 ALTTKGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQ------KIRIPMMP-DSRSMNLSNAVSVVVYEAWRQLG 149 (157)
T ss_pred EEeCCCCCCccccccCCCcEEEECCCCCCCCHHHHhcCCCCe------EEEEcCCC-CCccchHHHHHHHHHHHHHHhhc
Confidence 9999887777777888999999999999999999998 898 99999999 69999999999999999999999
Q ss_pred cccCCCC
Q 024933 236 YEQLKTA 242 (260)
Q Consensus 236 ~~~~~~~ 242 (260)
+.+..++
T Consensus 150 ~~~~~~~ 156 (157)
T PRK10358 150 YPGAVLR 156 (157)
T ss_pred CCccccc
Confidence 8877654
No 7
>PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional
Probab=100.00 E-value=6.7e-38 Score=277.92 Aligned_cols=167 Identities=25% Similarity=0.280 Sum_probs=142.5
Q ss_pred CccEEEEEeCCCCCCcHHHHHHhhhhcccceE-EECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhhhcCCc
Q 024933 76 NKFLQVVLVSPQIPGNTGCIARTCAASACGLH-LVGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQQEGEK 154 (260)
Q Consensus 76 ~~~l~vvLd~i~dp~NlGaIiRta~afGv~~v-iv~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~~~~g~ 154 (260)
+.+++|+||+|+||+|+|+|+|||+|||++.+ ++.+.. ..+...|+++|+...+++..+.+++++++.|+++ |+
T Consensus 17 ~~~l~vvLd~V~~p~NlGAIiRta~AfGv~~V~~v~~~~---~~~~~~~~s~Ga~~wv~i~~~~~~~~~i~~lk~~--g~ 91 (229)
T PRK11081 17 QPDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVWPGS---RMRTMGSTAAGSNSWVQVKTHRTIGDAVAHLKGQ--GM 91 (229)
T ss_pred CCCeEEEEeCCCCcchHHHHHHHHHHhCCCeEEEecCCC---ccchhhhhcCCchheEEEEEeCCHHHHHHHHHhC--CC
Confidence 46799999999999999999999999999854 444321 1234556777776668888899999999999976 89
Q ss_pred EEEEEEcC-CCcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHHc
Q 024933 155 RLLAFTKR-GTSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAARQ 233 (260)
Q Consensus 155 ~iva~~~~-~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~rq 233 (260)
+|+|++.. +..++.++++++|++||||||+.|||+++++.||. .|+|||.| .++|||||||+||+|||+.||
T Consensus 92 ~i~at~~~~~a~~l~~~d~~~p~alV~GnE~~GlS~e~l~~~D~------~v~IPM~G-~v~SLNVSvAaaIiLyE~~Rq 164 (229)
T PRK11081 92 QILATHLSDTAVDFREIDYTRPTCILMGQEKTGISQEALALADQ------DIIIPMIG-MVQSLNVSVASALILYEAQRQ 164 (229)
T ss_pred EEEEEeCCCCCccHhHhcccCCeEEEECCCCCCCCHHHHhcCCC------EEEEeCCC-CCCceeHHHHHHHHHHHHHHh
Confidence 99999965 56789999999999999999999999999999999 99999999 699999999999999999999
Q ss_pred ccc------ccCCCCccccccccCCcc
Q 024933 234 LNY------EQLKTASDTCIDREFPFI 254 (260)
Q Consensus 234 ~~~------~~~~~~~~~~~~~~~~~~ 254 (260)
+.. .+.++++|+..+.-.+|.
T Consensus 165 r~~~g~y~~~~~~l~~~~~~~~~~~~~ 191 (229)
T PRK11081 165 RQNAGMYLRENSMLPEEEQQRLLFEGG 191 (229)
T ss_pred hccCCCcCcCCCCCCHHHHHHHHHhhc
Confidence 874 466678877776666654
No 8
>PF00588 SpoU_methylase: SpoU rRNA Methylase family; InterPro: IPR001537 The spoU gene of Escherichia coli codes for a protein that shows strong similarities to previously characterised 2'-O-methyltransferases [, ]. The Pet56 protein of Saccharomyces cerevisiae has been shown to be required for ribose methylation at a universally conserved nucleotide in the peptidyl transferase centre of the mitochondrial large ribosomal RNA (21S rRNA). Cells reduced in this activity were deficient in formation of functional large subunits of the mitochondrial ribosome. The Pet56 protein catalyzes the site-specific formation of 2'-O-methylguanosine on in vitro transcripts of both mitochondrial 21S rRNA and E. coli 23S rRNA providing evidence for an essential modified nucleotide in rRNA [].; GO: 0003723 RNA binding, 0008173 RNA methyltransferase activity, 0006396 RNA processing; PDB: 3N4J_A 3N4K_A 1IPA_A 3ONP_A 3NK6_A 3NK7_A 3IC6_A 1GZ0_D 1MXI_A 1J85_A ....
Probab=100.00 E-value=2.2e-37 Score=254.65 Aligned_cols=141 Identities=31% Similarity=0.412 Sum_probs=124.6
Q ss_pred cEEEEEeCCCCCCcHHHHHHhhhhcccceEEE-CCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhhhcCCcEE
Q 024933 78 FLQVVLVSPQIPGNTGCIARTCAASACGLHLV-GPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQQEGEKRL 156 (260)
Q Consensus 78 ~l~vvLd~i~dp~NlGaIiRta~afGv~~viv-~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~~~~g~~i 156 (260)
+++|+||+++||+|+|+|+|||++||++.+++ .+.+.+++++++.|++++++.++++..+++++++++++++. |+++
T Consensus 1 ~l~vvl~~~~~p~NlG~i~Rta~afG~~~v~l~~~~~~~~~~~~~~r~s~g~~~~~~~~~~~~~~~~l~~~~~~--g~~i 78 (142)
T PF00588_consen 1 MLIVVLDNVQDPGNLGAIIRTAAAFGVDGVILVGPRCADPYNPKVLRASAGAHEHLPIRRVDDLEEALKDLKEN--GYTI 78 (142)
T ss_dssp SEEEEEES-SSHHHHHHHHHHHHHTTESEEEEESSSSSTTTSHHHHHHTTTGHHCSHEEEESSHHHHHHHHHHT--TEEE
T ss_pred CEEEEEeCCCCcCcHHHHHHHHHHhCCchhheeccccccccccccccccCChhhhhheeeeehhhhhccccccc--cccc
Confidence 57999999999999999999999999975555 66888899999999999998888888899999999999986 8999
Q ss_pred EEEEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHH
Q 024933 157 LAFTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVY 228 (260)
Q Consensus 157 va~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Ly 228 (260)
++++. +.+++.++++++|++||||+|+.|||+++++.||. +|+|||.| .++|||||+|++|+||
T Consensus 79 ~~~~~-~~~~~~~~~~~~~~~lv~G~E~~Gls~~~~~~~d~------~v~IP~~~-~~~SLNva~A~~I~ly 142 (142)
T PF00588_consen 79 VATSP-GATPLYELDFPKKVALVFGNESRGLSEEVLELCDH------RVSIPMYG-GVDSLNVAVAAAIALY 142 (142)
T ss_dssp EEEST-TSCEGGGSHTTSSEEEEEEBTTTBS-HHHHHTSSE------EEE---ST-TSSS--HHHHHHHHHH
T ss_pred ceeee-ccccccccccccceEEEEcCcCCCCCcccccccce------EEEEcCCC-CCCeeEHHHHHHHHHC
Confidence 99999 66678899999999999999999999999999999 99999999 5999999999999998
No 9
>COG0219 CspR Predicted rRNA methylase (SpoU class) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.1e-35 Score=241.61 Aligned_cols=153 Identities=48% Similarity=0.796 Sum_probs=143.7
Q ss_pred cEEEEEeCCCCCCcHHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhhhcCCcEEE
Q 024933 78 FLQVVLVSPQIPGNTGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQQEGEKRLL 157 (260)
Q Consensus 78 ~l~vvLd~i~dp~NlGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~~~~g~~iv 157 (260)
.+.|||.+|+.|+|.|+|+|+|+++|+++++|.|-+++.++++++|||+++|+.+.+++|++|++|++..+. +.+++
T Consensus 2 ~~~IvL~~PeIP~NTGNI~R~ca~tga~LhlI~PlGF~l~dk~lkRAGlDY~~~~~l~~h~s~e~fl~~~~~---~~rl~ 78 (155)
T COG0219 2 MLNIVLYQPEIPPNTGNIIRTCAATGAELHLIEPLGFDLDDKRLKRAGLDYHEKASLTEHDSLEAFLEAEPI---GGRLF 78 (155)
T ss_pred ccEEEEECCCCCCchhHHHHHHHhcCCeEEEEccCCCccchhhhhhcccchHhhcceEEeCCHHHHHhhccC---CceEE
Confidence 467999999999999999999999999999999999999999999999999999999999999999998763 47999
Q ss_pred EEEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHHccccc
Q 024933 158 AFTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAARQLNYE 237 (260)
Q Consensus 158 a~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~rq~~~~ 237 (260)
+++..+...+.+..+.+...|+||.|..||++++++..+. .+++|||.. .++|||+|++++|++||++||.++.
T Consensus 79 ~~tt~~~~~~~~~~f~~~d~llFG~Es~GLP~~i~~~~~~-----~~irIPm~~-~~RSLNLsnsvavv~yEa~RQ~~~~ 152 (155)
T COG0219 79 ALTTKGTTTYTDVSFQKGDYLLFGPESRGLPEEILDAAPD-----RCIRIPMRP-GVRSLNLSNTVAVVLYEALRQLGFA 152 (155)
T ss_pred EEEeccccccccccCCCCCEEEECCCCCCCCHHHHHhCcc-----ceEEeccCC-CCccchHHHHHHHHHHHHHHHhCCc
Confidence 9999999999999999999999999999999999999887 269999998 4999999999999999999999987
Q ss_pred cC
Q 024933 238 QL 239 (260)
Q Consensus 238 ~~ 239 (260)
+.
T Consensus 153 ~~ 154 (155)
T COG0219 153 GL 154 (155)
T ss_pred cC
Confidence 64
No 10
>KOG2506 consensus SpoU rRNA Methylase family protein [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=7.7e-32 Score=244.32 Aligned_cols=179 Identities=25% Similarity=0.210 Sum_probs=140.6
Q ss_pred CcccCCCc-cccccCCCCCceEEEEEecCC----------------CCccEEEEEeCCCCCCcHHHHHHhhhhcccceEE
Q 024933 46 RFSPICSL-PERENGGFMPRGVGEAVNGLS----------------QNKFLQVVLVSPQIPGNTGCIARTCAASACGLHL 108 (260)
Q Consensus 46 ~~~~~~~~-~~~~~~~~~~qGv~a~~~~~~----------------~~~~l~vvLd~i~dp~NlGaIiRta~afGv~~vi 108 (260)
+++...+. ++.+++..+|+|+.|+..+|. ..-++.+|||+|+||+|+|+|+|||+||++++++
T Consensus 168 ~i~kVks~d~K~wSsLvSP~svmaIf~~P~d~hl~k~~a~~q~~~s~~lp~~lvcdnirdpgnlgti~rsaaa~~cs~v~ 247 (371)
T KOG2506|consen 168 RIVKVKSLDMKKWSSLVSPESVMAIFLMPIDLHLDKDIATDQNKWSPSLPRVLVCDNIRDPGNLGTIVRSAAAFNCSGVF 247 (371)
T ss_pred eEEeccHHHHHHHhcccCCcchhhhccCcchhchhhhHHHHHhccCCCCCeEEEeccCCCCcchHHHHHHHhhCCCccee
Confidence 34444443 567999999999999998871 2357999999999999999999999999999999
Q ss_pred ECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhhh-cCCcEEEEEEcCCC-cCcc---cc--cCCCCeEEEEc
Q 024933 109 VGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQQ-EGEKRLLAFTKRGT-STHS---EI--SYRKGDYLIFG 181 (260)
Q Consensus 109 v~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~~-~~g~~iva~~~~~~-~~l~---~~--~~~~~~aLV~G 181 (260)
++++|+|+|++|+.|+|+|+.+.+++.- ++|++.--..... .+.+.++.++.... ++.. |+ ....+.+||+|
T Consensus 248 lt~gccdpwe~kalrag~ga~fr~pi~~-~~w~~l~l~~pp~~ad~c~~~~a~t~qr~~~~~k~~e~ad~~~ap~~liig 326 (371)
T KOG2506|consen 248 LTPGCCDPWEDKALRAGRGASFRLPIVS-GNWNHLKLLEPPFQADLCAGHPATTTQRLKPVSKLVEFADSLAAPLCLIIG 326 (371)
T ss_pred ecCCcCCccchhhhhccCCcceecceec-CchhhhhccCChhHHhhhcCchHhhhhhhccchhhhHHHhhccCceEEEEc
Confidence 9999999999999999999998888754 4887753322210 01344444443221 1111 11 13478999999
Q ss_pred CCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHHc
Q 024933 182 SETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAARQ 233 (260)
Q Consensus 182 nE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~rq 233 (260)
.|++|+|++.++.|. .|.|||.++ +||||||+|++|+|||+.|+
T Consensus 327 ge~~gvseea~~~~~-------lvgip~a~g-~dslnva~a~~illfel~r~ 370 (371)
T KOG2506|consen 327 GEGNGVSEEARKVCV-------LVGIPMAGG-FDSLNVAVAGGILLFELQRL 370 (371)
T ss_pred cCcCCcCHHHHHHHH-------HcCCcccCC-cchhhhHHHHHHHHHHHhhc
Confidence 999999999999998 588999996 99999999999999999886
No 11
>TIGR00050 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1. This is part of the trmH (spoU) family of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and is now characterized, in E. coli, as a tRNA:Cm32/Um32 methyltransferase. It may be named TrMet(Xm32), or TrmJ, according to the nomenclature style chosen
Probab=99.97 E-value=4.3e-30 Score=228.78 Aligned_cols=141 Identities=28% Similarity=0.370 Sum_probs=112.8
Q ss_pred cEEEEEeCCCCCCcHHHHHHhhhhcccc-eEEECCCCCCCChhHHHHhcCCCcceEEE-EEcCCHHHHHHHHhhhcCCcE
Q 024933 78 FLQVVLVSPQIPGNTGCIARTCAASACG-LHLVGPLGFQVDDTKLKRAGLDYWPYVVI-KVHSTWAEFRDYFRQQEGEKR 155 (260)
Q Consensus 78 ~l~vvLd~i~dp~NlGaIiRta~afGv~-~viv~~~~~~~~~~k~~rag~~~~~~v~v-~~~~~~~~~l~~lk~~~~g~~ 155 (260)
.+.|||++|+||+|+|+|+|+|++||++ .+++.+.+ + .++++.++++|+.++++. +.+++++++++.+ .+
T Consensus 3 ~i~vvL~~~~~p~NiGaiaR~~~~fG~~~l~lv~p~~-~-~~~~a~~~a~ga~~~l~~~~v~~~l~eal~~~------~~ 74 (233)
T TIGR00050 3 NIRIVLVEPSHSGNIGSIARAMKNMGLTELCLVNPKS-H-LEEEAYALAAGARDILDNAKVVDDLDEALDDC------DL 74 (233)
T ss_pred CeEEEEECCCCCCCHHHHHHHHHhCCCCEEEEeCCCc-C-CCHHHHHHhCChHHhhccCEEECCHHHHHhcC------CE
Confidence 3789999999999999999999999997 55555544 3 467777776665444432 4578999998742 46
Q ss_pred EEEEEcCCCcCcccc------------cCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHH
Q 024933 156 LLAFTKRGTSTHSEI------------SYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSV 223 (260)
Q Consensus 156 iva~~~~~~~~l~~~------------~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAa 223 (260)
++|++.+.. .+.+. ++.++++||||+|+.||++++++.||. +++|||.+ .++|||||+|+
T Consensus 75 vv~tt~~~~-~~~~~~~~~~~~~~~~~~~~~~~aLvFG~E~~GL~~~~l~~cd~------~v~IP~~~-~~~SLNla~Av 146 (233)
T TIGR00050 75 VVGTSARSR-NLQRPLLTPRELAPKLVAYKGKIAIVFGREDSGLTNEELLKCHV------LVSIPTSE-EYPSLNLSHAV 146 (233)
T ss_pred EEEECCCcC-CCCCCcCCHHHHHHHHHhhcCCEEEEECCCCCCCCHHHHHhCCE------EEEecCCC-CCCeeeHHHHH
Confidence 899886532 22221 245789999999999999999999999 99999999 59999999999
Q ss_pred HHHHHHHHHcc
Q 024933 224 GIAVYEAARQL 234 (260)
Q Consensus 224 aI~Lyel~rq~ 234 (260)
+|+|||+.++.
T Consensus 147 ~I~lye~~~~~ 157 (233)
T TIGR00050 147 AVILYELRMAF 157 (233)
T ss_pred HHHHHHHHHhh
Confidence 99999998875
No 12
>PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional
Probab=99.97 E-value=6.8e-30 Score=229.04 Aligned_cols=142 Identities=19% Similarity=0.186 Sum_probs=111.8
Q ss_pred cEEEEEeCCCCCCcHHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceE-EEEEcCCHHHHHHHHhhhcCCcEE
Q 024933 78 FLQVVLVSPQIPGNTGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYV-VIKVHSTWAEFRDYFRQQEGEKRL 156 (260)
Q Consensus 78 ~l~vvLd~i~dp~NlGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v-~v~~~~~~~~~l~~lk~~~~g~~i 156 (260)
.+.|||++++||+|+|+|+|+|++||++.+++.+.+++++++ +.++++|+.+.+ .+..+++++++++.+ .++
T Consensus 4 ~i~vVLv~~~~pgNiGaiaRa~~~fG~~~l~lv~p~~~~~~~-a~~~a~GA~~~l~~a~i~~~l~eal~~~------~~v 76 (245)
T PRK15114 4 NIRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPDSQ-AIALAAGASDVIGNATIVDTLDEALAGC------SLV 76 (245)
T ss_pred CeEEEEeCCCCCCcHHHHHHHHHhcCCCEEEEeCCCCCCcCH-HHHHcCCchhhcccCeEecCHHHHHhcC------CEE
Confidence 478999999999999999999999999865555444566655 555555544322 223368999988753 479
Q ss_pred EEEEcCCCcCcc-------------cccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHH
Q 024933 157 LAFTKRGTSTHS-------------EISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSV 223 (260)
Q Consensus 157 va~~~~~~~~l~-------------~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAa 223 (260)
||++.++..... ...+.++++||||+|++||+++.++.||. .++|||.+ .++|||||+|+
T Consensus 77 vatt~r~~~~~~~~~~~~~~~~~~~~~~~~~~~alVFG~E~~GLs~e~l~~cd~------~v~IP~~~-~~~SLNla~Av 149 (245)
T PRK15114 77 VGTSARSRTLPWPMLDPRECGLKSVAEAANAPVALVFGRERVGLTNDELQKCHY------HVAIAANP-EYSSLNLAMAV 149 (245)
T ss_pred EEEcCCccCCcccccCHHHHHHHHHhhccCCCEEEEECCCCCCCCHHHHHhCCe------EEEecCCC-CCCcccHHHHH
Confidence 999976532111 11356789999999999999999999999 99999999 59999999999
Q ss_pred HHHHHHHHHc
Q 024933 224 GIAVYEAARQ 233 (260)
Q Consensus 224 aI~Lyel~rq 233 (260)
+|+|||+++.
T Consensus 150 aI~lYE~~~~ 159 (245)
T PRK15114 150 QVIAYEVRMA 159 (245)
T ss_pred HHHHHHHHHH
Confidence 9999998775
No 13
>PRK10433 putative RNA methyltransferase; Provisional
Probab=99.95 E-value=3.3e-27 Score=209.46 Aligned_cols=140 Identities=28% Similarity=0.332 Sum_probs=108.8
Q ss_pred cEEEEEeCCCCCCcHHHHHHhhhhcccc-eEEECCCCCCCChhHHHHh--c-CCCcceEEEEEcCCHHHHHHHHhhhcCC
Q 024933 78 FLQVVLVSPQIPGNTGCIARTCAASACG-LHLVGPLGFQVDDTKLKRA--G-LDYWPYVVIKVHSTWAEFRDYFRQQEGE 153 (260)
Q Consensus 78 ~l~vvLd~i~dp~NlGaIiRta~afGv~-~viv~~~~~~~~~~k~~ra--g-~~~~~~v~v~~~~~~~~~l~~lk~~~~g 153 (260)
.+.|||+++++|+|+|+++|+|++||++ .+++.|.+. + ++...+. | .+.++.+ +++++++++++++
T Consensus 2 ~i~vVLv~p~~p~NiGaiaRam~nfG~~~L~lV~p~~~-~-~~~a~~~A~gA~d~L~~a--~v~~tL~eAl~d~------ 71 (228)
T PRK10433 2 RLTIILVAPARAENVGAAARAMKTMGFSELRIVDSQAH-L-EPAARWVAHGSGDILDNA--KVFDTLAEALHDV------ 71 (228)
T ss_pred ceEEEEEcCCCCccHHHHHHHHHHCCCCEEEEeCCCCC-C-cHHHHHHhccHHHHhcCc--eEECCHHHHHHhC------
Confidence 3789999999999999999999999996 777777653 2 3333332 2 3444443 3468999999874
Q ss_pred cEEEEEEcCCCcCcc-------------cc-cCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccH
Q 024933 154 KRLLAFTKRGTSTHS-------------EI-SYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNL 219 (260)
Q Consensus 154 ~~iva~~~~~~~~l~-------------~~-~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNV 219 (260)
.+++|++.+...... +. ++.++++||||+|+.||++++++.||. .++|||.+ .++||||
T Consensus 72 ~~vigttar~~~~~~~~~~p~~~~~~l~~~~~~~~~~alvfG~E~~Gl~~~~l~~c~~------~~~IP~~~-~~~SLNl 144 (228)
T PRK10433 72 DFTVATTARSRAKFHYYATPAELVPLLEEKSSWMSHAALVFGREDSGLTNEELALADV------LTGVPMAA-DYPSLNL 144 (228)
T ss_pred CeEEEEccCCCCCCCcccCHHHHHHHHHhhhcccCCEEEEECCCCCCCCHHHHHhCCc------EEEecCCC-CCcceeH
Confidence 378888875322111 11 234789999999999999999999999 99999999 5999999
Q ss_pred HHHHHHHHHHHHHcc
Q 024933 220 SVSVGIAVYEAARQL 234 (260)
Q Consensus 220 svAaaI~Lyel~rq~ 234 (260)
|+|++|++||+++..
T Consensus 145 a~A~~i~~ye~~~~~ 159 (228)
T PRK10433 145 GQAVMVYCYQLAGLM 159 (228)
T ss_pred HHHHHHHHHHHHHhh
Confidence 999999999987753
No 14
>KOG0838 consensus RNA Methylase, SpoU family [RNA processing and modification]
Probab=99.92 E-value=2.3e-24 Score=191.42 Aligned_cols=201 Identities=18% Similarity=0.121 Sum_probs=160.0
Q ss_pred hhHHHHhhhcCCcceeeecCccccccCCCCcCCC-------cccCCC--ccccccCCCCCceEEEEEecCCCCccEEEEE
Q 024933 13 VPLHAHFRSRAPNFTQFKNNFSFSSPLSSFSSFR-------FSPICS--LPERENGGFMPRGVGEAVNGLSQNKFLQVVL 83 (260)
Q Consensus 13 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~-------~~~~~~--~~~~~~~~~~~qGv~a~~~~~~~~~~l~vvL 83 (260)
+++.+++...+|.++-+++. +...+.... .+...+ ..++..+...|||++.... +.+.|
T Consensus 49 ~sv~~al~~~kR~~~~~~~~-----~~~~~~~~e~~~v~~~~~~~~s~h~L~~~t~~r~h~g~~leas-------l~vyl 116 (271)
T KOG0838|consen 49 HSVLAALSNGKRDCRGLLLQ-----SATDFRSTEFELVLRRDIEAVSKHDLNSLTDFRPHNGILLEAS-------LCVYL 116 (271)
T ss_pred hhhHHHHhcccccceeeeec-----cccccCcceeeehhhhhhhccChhhHHHHHhhccccceEEeeE-------EEeec
Confidence 78999999999999998873 333333321 122222 1234667778999998664 89999
Q ss_pred eCCCCCCcHHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhhhcCCcEEEEEEcCC
Q 024933 84 VSPQIPGNTGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQQEGEKRLLAFTKRG 163 (260)
Q Consensus 84 d~i~dp~NlGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~~~~g~~iva~~~~~ 163 (260)
|++.||+|+|+|+|+|+++|++.+++......+-.+.+..++++..+++++..+++..++++..+.+ |++++++....
T Consensus 117 de~tDp~n~gaI~rsA~~lg~~~v~lv~~n~s~lS~~vskss~gale~l~I~q~~~~~efl~vsvaa--G~~l~~t~~~~ 194 (271)
T KOG0838|consen 117 DEVTDPQNIGAIIRSAYFLGADGVLLVKGNSSPLSPVVSKSSAGALEVLPIRQVDNPLEFLNVSVAA--GIRLHGTCSWA 194 (271)
T ss_pred cCccCCcchHHHHHhHHHhcCCceEEEeccCCCCchhHHHhhhchhheeeHHHcCCHHHHHHHHHhC--ceEEEEeecCc
Confidence 9999999999999999999999766655433666677777888888888999999999999998876 89999987532
Q ss_pred -------CcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCC----CC-CCccccHHHHHHHHHHHHH
Q 024933 164 -------TSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMV----ET-YVRCLNLSVSVGIAVYEAA 231 (260)
Q Consensus 164 -------~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~----g~-~v~SLNVsvAaaI~Lyel~ 231 (260)
...+...+...|+++|+|||+.|+++.++..||. .++||+. .+ .++|||||+|+++++|++.
T Consensus 195 ~~~~~~~~~~l~~~~~~~Pv~lv~Gneg~Gi~~~vl~~~d~------~~si~~n~~~~d~~~v~SlNvSvaa~ll~~~~~ 268 (271)
T KOG0838|consen 195 PASKTISAVSLKFIDPEEPVALVLGNEGAGIRPGVLELCDL------RVSIPGNGFEKDNGAVDSLNVSVAAGLLLYHFL 268 (271)
T ss_pred CCcccccchhhhhcCCCCCeEEEecccccccChhhhhccce------eEecCCCccccCCcceeeccchHHHHHHHHHHh
Confidence 2345566778999999999999999999999999 9999992 21 3799999999999999987
Q ss_pred Hc
Q 024933 232 RQ 233 (260)
Q Consensus 232 rq 233 (260)
.+
T Consensus 269 ~~ 270 (271)
T KOG0838|consen 269 NE 270 (271)
T ss_pred hc
Confidence 65
No 15
>COG0565 LasT rRNA methylase [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.3e-23 Score=186.45 Aligned_cols=140 Identities=29% Similarity=0.353 Sum_probs=110.6
Q ss_pred cEEEEEeCCCCCCcHHHHHHhhhhcccc-eEEECCCCCCCChhHHHHh-cCCCcceEEEEEcCCHHHHHHHHhhhcCCcE
Q 024933 78 FLQVVLVSPQIPGNTGCIARTCAASACG-LHLVGPLGFQVDDTKLKRA-GLDYWPYVVIKVHSTWAEFRDYFRQQEGEKR 155 (260)
Q Consensus 78 ~l~vvLd~i~dp~NlGaIiRta~afGv~-~viv~~~~~~~~~~k~~ra-g~~~~~~v~v~~~~~~~~~l~~lk~~~~g~~ 155 (260)
.+.|||.+++.|+|+|+++|.++.||++ .++|.|.+. +++.....| |+..+ .-..++++++++++..+ -.
T Consensus 4 ~i~iVLVep~~~gNIG~vARaMKNfGl~eL~LV~Pr~~-~~eeA~a~A~gA~di-le~A~i~~tL~eAl~d~------~~ 75 (242)
T COG0565 4 NIRIVLVEPSHPGNIGSVARAMKNFGLSELRLVNPRAG-LDEEARALAAGARDI-LENAKIVDTLEEALADC------DL 75 (242)
T ss_pred ccEEEEEcCCCCccHHHHHHHHHhCCcceEEEECCCCC-CCHHHHHHhccchhh-hccCeeecCHHHHhcCC------CE
Confidence 4679999999999999999999999996 888888754 555444444 33322 22355679999999864 47
Q ss_pred EEEEEcCCCcCcc--------------cccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHH
Q 024933 156 LLAFTKRGTSTHS--------------EISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSV 221 (260)
Q Consensus 156 iva~~~~~~~~l~--------------~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsv 221 (260)
++||+........ ... ..|++||||+|..||+.|.++.||. .++||+.+ .+.|||+|+
T Consensus 76 v~aTtar~r~~~~~~~~P~e~~~~l~~~~~-~~~vAlvFGRE~~GLtNeEl~~c~~------~v~IP~~p-~Y~sLNLa~ 147 (242)
T COG0565 76 VVATTARSRDLLRPLRTPREAAPELLEKAK-GGKVALVFGRERVGLTNEELALCDV------LVTIPANP-DYPSLNLAQ 147 (242)
T ss_pred EEEeccccCcccccccCHHHHHHHHHHHhc-CCCeEEEECCccCCCCHHHHHhhhE------EEecCCCC-ccccccHHH
Confidence 8888854322111 111 3799999999999999999999999 99999999 599999999
Q ss_pred HHHHHHHHHHHc
Q 024933 222 SVGIAVYEAARQ 233 (260)
Q Consensus 222 AaaI~Lyel~rq 233 (260)
|++|++||+++.
T Consensus 148 AV~ii~YEl~~~ 159 (242)
T COG0565 148 AVQVILYELRKA 159 (242)
T ss_pred HHHHHHHHHHHh
Confidence 999999999874
No 16
>KOG0839 consensus RNA Methylase, SpoU family [RNA processing and modification]
Probab=99.79 E-value=1.2e-19 Score=184.51 Aligned_cols=148 Identities=24% Similarity=0.402 Sum_probs=125.4
Q ss_pred ccEEEEEeCCCCCCcHHHHHHhhhhcccceEEECCCCCCCChh--HHHHhcCCCc-ceEEEEEcCCHHHHHHHHhhhcCC
Q 024933 77 KFLQVVLVSPQIPGNTGCIARTCAASACGLHLVGPLGFQVDDT--KLKRAGLDYW-PYVVIKVHSTWAEFRDYFRQQEGE 153 (260)
Q Consensus 77 ~~l~vvLd~i~dp~NlGaIiRta~afGv~~viv~~~~~~~~~~--k~~rag~~~~-~~v~v~~~~~~~~~l~~lk~~~~g 153 (260)
..++||..=|..|.|+|.|.|||+.||++..+|.+-.+ ..++ +....+++.| |.+.|+ .+++..++++.|++ |
T Consensus 1325 ssLIVVASLVDKppNLgGicRTcEVFgvs~LvVad~~v-i~DkQFk~lSVtAE~W~pieeVk-~~~L~~fLq~kK~E--G 1400 (1477)
T KOG0839|consen 1325 SSLIVVASLVDKPPNLGGICRTCEVFGVSLLVVADIKV-INDKQFKNLSVTAERWMPIEEVK-LDELASFLQEKKKE--G 1400 (1477)
T ss_pred eeEEEEeecccCCCccchhhhhhhhhCcceEEEeeeee-ecchhhhheeeeHHhccchhccC-hHHHHHHHHHhhhc--C
Confidence 46899999999999999999999999999887765332 2233 3344567777 333332 47889999988876 9
Q ss_pred cEEEEEEcCC-CcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHH
Q 024933 154 KRLLAFTKRG-TSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAAR 232 (260)
Q Consensus 154 ~~iva~~~~~-~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~r 232 (260)
|.|+|++..+ +..+.++.||+|.+||+|+|..|+|-..+...|. +|.||+.| .++||||-|++|+++||+.|
T Consensus 1401 yTiIglEQTakSV~Ld~fqFPkKslilLG~EkEGIPvnLl~~LD~------cvEIpQ~G-viRSLNVHVsgAl~iweYTr 1473 (1477)
T KOG0839|consen 1401 YTIIGLEQTAKSVKLDNFQFPKKSLILLGTEKEGIPVNLLSELDL------CVEIPQFG-VIRSLNVHVSGALIIWEYTR 1473 (1477)
T ss_pred cEEEeehhcccccccccccCCcceeEEecccccCCcHHHHHHHhH------heeccccc-eeeeeeeehhHHHHHHHHHH
Confidence 9999999874 5678899999999999999999999999999999 99999999 79999999999999999999
Q ss_pred ccc
Q 024933 233 QLN 235 (260)
Q Consensus 233 q~~ 235 (260)
|+.
T Consensus 1474 Qqr 1476 (1477)
T KOG0839|consen 1474 QQR 1476 (1477)
T ss_pred Hhc
Confidence 975
No 17
>PRK03958 tRNA 2'-O-methylase; Reviewed
Probab=98.28 E-value=7.2e-06 Score=70.21 Aligned_cols=121 Identities=12% Similarity=0.151 Sum_probs=76.8
Q ss_pred HHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCc-ceEEEEEcCCHHHHHHHHhhhcCCcEEEEEEcCCC---cCccc
Q 024933 94 CIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYW-PYVVIKVHSTWAEFRDYFRQQEGEKRLLAFTKRGT---STHSE 169 (260)
Q Consensus 94 aIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~-~~v~v~~~~~~~~~l~~lk~~~~g~~iva~~~~~~---~~l~~ 169 (260)
-++|||-+||++.+++... +..-...++-=.++| -.+.+....+|++++++++ . .| .++-++..|. ..+.+
T Consensus 21 hvartARafGa~~~yiv~~--~~~q~~~v~~I~~~WGg~fnv~~~~s~~~~i~~~k-~-~G-~vvhLtmyga~~~~~~~~ 95 (176)
T PRK03958 21 HVGLTARALGADKIILASN--DEHVKESVEDIVERWGGPFEVEVTKSWKKEIREWK-D-GG-IVVHLTMYGENIQDVEPE 95 (176)
T ss_pred HHHHHHHHcCCceEEEecC--cHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHHH-h-CC-cEEEEEEecCCccchHHH
Confidence 3789999999997766532 111111111112222 1123666799999999998 3 24 4444444332 23444
Q ss_pred cc----CCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHH
Q 024933 170 IS----YRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAAR 232 (260)
Q Consensus 170 ~~----~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~r 232 (260)
+. -.++..|||| ++|+++++.+.||. .| ..|. .+= -+-.|+||+|-.++.
T Consensus 96 ir~~~~~~~p~LIvvG--g~gvp~evye~aDy------nl---gvg~-qpH-SvrAAlAI~LDRL~~ 149 (176)
T PRK03958 96 IREAHRKGEPLLIVVG--AEKVPREVYELADW------NV---AVGN-QPH-SEVAALAVFLDRLFE 149 (176)
T ss_pred HHHhhccCCcEEEEEc--CCCCCHHHHhhCCE------Ee---ccCC-CCh-HHHHHHHHHHHHhcC
Confidence 42 1578999999 89999999999998 77 3342 333 678899999987763
No 18
>COG4080 SpoU rRNA Methylase family enzyme [General function prediction only]
Probab=97.72 E-value=0.00044 Score=56.91 Aligned_cols=136 Identities=15% Similarity=0.076 Sum_probs=92.3
Q ss_pred cEEEEEeCCCCCCcHHHHHHhhhhcccceEEECCC--CCCCC-hhHHHHhc--CCCcceEEEEEcCCHHHHHHHHhhhcC
Q 024933 78 FLQVVLVSPQIPGNTGCIARTCAASACGLHLVGPL--GFQVD-DTKLKRAG--LDYWPYVVIKVHSTWAEFRDYFRQQEG 152 (260)
Q Consensus 78 ~l~vvLd~i~dp~NlGaIiRta~afGv~~viv~~~--~~~~~-~~k~~rag--~~~~~~v~v~~~~~~~~~l~~lk~~~~ 152 (260)
++++++.|+..+.-+=-+.|++..||++.+++++- ++... -+.+.|-. +| . ++-+.++++++++-|+.
T Consensus 2 ev~vvlHN~~S~~rv~e~ariaygfg~k~lV~tka~g~AAQsGIp~~~kla~k~G-~---~vlvf~dL~DAlevL~P--- 74 (147)
T COG4080 2 EVIVVLHNVSSVQRVLEFARIAYGFGAKRLVLTKAKGSAAQSGIPEVLKLAFKLG-K---PVLVFPDLDDALEVLRP--- 74 (147)
T ss_pred cEEEEEecCCchHHHHHHHHHHcccCccEEEEEecccHhhhhccHHHHHHHHHhC-C---cEEEehhHHHHHHhcCC---
Confidence 57899999999999999999999999997777642 22222 23444322 23 2 23345899999999974
Q ss_pred CcEEEEE--EcCCCcCcccc-cCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHH
Q 024933 153 EKRLLAF--TKRGTSTHSEI-SYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYE 229 (260)
Q Consensus 153 g~~iva~--~~~~~~~l~~~-~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lye 229 (260)
-.++.. ...+.+.+.-- ...+++++||+.=..|+++..++.-+. ..+| ... .+-++ -++||+|||
T Consensus 75 -~v~ll~~~~~~~ek~~dp~e~ie~~vliVf~ga~~gl~k~El~lg~~------~~y~-ve~-~VG~~---g~lAi~Lye 142 (147)
T COG4080 75 -DVTLLVGSASEGEKKLDPNEKIEGRVLIVFSGAEPGLTKRELELGAD------LRYI-VEA-DVGEL---GALAIFLYE 142 (147)
T ss_pred -ceEEEecCcccccccCCccccccceEEEEEecCCCCcChhhcccCCc------EEEE-Eec-cchHH---HHHHHHHHH
Confidence 344444 23344333211 123488999999889999999986666 7777 444 35554 578999999
Q ss_pred HHH
Q 024933 230 AAR 232 (260)
Q Consensus 230 l~r 232 (260)
+.+
T Consensus 143 ll~ 145 (147)
T COG4080 143 LLK 145 (147)
T ss_pred HHc
Confidence 875
No 19
>PF09936 Methyltrn_RNA_4: SAM-dependent RNA methyltransferase; InterPro: IPR019230 This entry contains proteins that have no known function. They are found as separate proteins and as a C-terminal domain to tRNA (guanine-N(1)-)-methyltransferases to which they are structurally related. ; PDB: 3DCM_X.
Probab=97.70 E-value=4.9e-05 Score=65.33 Aligned_cols=129 Identities=24% Similarity=0.319 Sum_probs=66.3
Q ss_pred HHHHHHhhhhcccce-EEECCCCCCC-ChhHHHH---hc--CCC-------cceEEEEEcCCHHHHHHHHhhhcCC-cEE
Q 024933 92 TGCIARTCAASACGL-HLVGPLGFQV-DDTKLKR---AG--LDY-------WPYVVIKVHSTWAEFRDYFRQQEGE-KRL 156 (260)
Q Consensus 92 lGaIiRta~afGv~~-viv~~~~~~~-~~~k~~r---ag--~~~-------~~~v~v~~~~~~~~~l~~lk~~~~g-~~i 156 (260)
+=-|.|+|..+|++. .+|+|-.... --.++.+ .| ..+ +.. ++..++++++++++.+..+. -.+
T Consensus 30 lHDIAR~~rTYgv~~yyiVtPl~~Q~~l~~ril~hW~~G~G~~yNp~R~eAl~~--v~~~~sle~a~~~I~~~~G~~P~~ 107 (185)
T PF09936_consen 30 LHDIARSARTYGVKGYYIVTPLEAQRELAERILGHWQEGYGAEYNPDRKEALSL--VRVVDSLEEAIEDIEEEEGKRPLL 107 (185)
T ss_dssp HHHHHHHHHHTT-SEEEEE---HHHHHHHHHHHHHHHTSGGGGT-SSSHHHHTT--EEEESSHHHHHHHHHHHHSS--EE
T ss_pred HHhhhhhhhccCCcCEEEecchHHHHHHHHHHHHhcccCCCcCcCcCHHHHHhH--hccHhhHHHHHHHHHHHhCCCCEE
Confidence 557999999999984 5555531100 0012221 22 222 223 44469999999999876433 467
Q ss_pred EEEEcCC---CcCcccc-----cCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCC-CCCccccHHHHHHHHH
Q 024933 157 LAFTKRG---TSTHSEI-----SYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVE-TYVRCLNLSVSVGIAV 227 (260)
Q Consensus 157 va~~~~~---~~~l~~~-----~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g-~~v~SLNVsvAaaI~L 227 (260)
++|+++. ..++.++ .-.+|+.|+||. ++||++|+++.||. +==|..| +..+-|-|=.|+||+|
T Consensus 108 v~TsAr~~~~~is~~~lr~~l~~~~~P~LllFGT-GwGL~~ev~~~~D~-------iLePI~g~~~YNHLSVRsAvAIiL 179 (185)
T PF09936_consen 108 VATSARKYPNTISYAELRRMLEEEDRPVLLLFGT-GWGLAPEVMEQCDY-------ILEPIRGAGDYNHLSVRSAVAIIL 179 (185)
T ss_dssp EE--SS--SS-B-HHHHHHHHHH--S-EEEEE---TT---HHHHTT-SE-------EB--TTTTSS-----HHHHHHHHH
T ss_pred EEecCcCCCCCcCHHHHHHHHhccCCeEEEEecC-CCCCCHHHHHhcCe-------eEcccccCCCCccchHHHHHHHHH
Confidence 7777652 2223322 246789999998 99999999999996 3336554 1377788999999998
Q ss_pred HHH
Q 024933 228 YEA 230 (260)
Q Consensus 228 yel 230 (260)
=-+
T Consensus 180 DRL 182 (185)
T PF09936_consen 180 DRL 182 (185)
T ss_dssp HHH
T ss_pred HHH
Confidence 654
No 20
>PF08032 SpoU_sub_bind: RNA 2'-O ribose methyltransferase substrate binding; InterPro: IPR013123 Most cellular RNAs undergo a number of post-transcriptional nucleoside modifications. While the biological role of many of these modifications is unknown, some have been shown to be necessary for cell growth or for resistance to antibiotics [, ]. One of the most common modifications is 2'O-ribose methylation catalysed by the RNA 2'O-ribose methyltransferases, a large enzyme family that transfer a methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the backbone ribose []. This entry represents a substrate-binding domain found in a variety of bacterial and mitochondrial RNA 2'-O ribose methyltransferases. These include the bacterial enzyme RlmB, which specifically methylates the conserved nucleotide guanosine 2251 in 23S RNA, and PET56, which specifically methylates the equivalent guanosine in mitochondrial 21S RNA [, ]. This domain forms a four-stranded mixed beta sheet similar to that found in other RNA binding enzymes []. It shows considerable conformational flexibility which is thought to be important for its ability to bind RNA.; GO: 0008168 methyltransferase activity; PDB: 1GZ0_D 1IPA_A.
Probab=95.87 E-value=0.0017 Score=47.10 Aligned_cols=61 Identities=8% Similarity=-0.012 Sum_probs=35.7
Q ss_pred hhHHHHhhhcCCcceeeecCccccc----cCCCCcCCC--cccCCC--ccccccCCCCCceEEEEEecCC
Q 024933 13 VPLHAHFRSRAPNFTQFKNNFSFSS----PLSSFSSFR--FSPICS--LPERENGGFMPRGVGEAVNGLS 74 (260)
Q Consensus 13 ~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~~~~~~--~~~~~~--~~~~~~~~~~~qGv~a~~~~~~ 74 (260)
+++.++++++.+ +..++++.+... ++......+ .+..++ ..+.++++.+||||+|+++.+.
T Consensus 6 ~~V~eaL~~~~~-i~~l~~~~~~~~~~~~~i~~~~~~~~i~v~~v~~~~l~~ls~~~~hQGv~a~v~~~~ 74 (76)
T PF08032_consen 6 HAVEEALKSGPR-IKKLFVTEEKADKRIKEILKLAKKKGIPVYEVSKKVLDKLSDTENHQGVVAVVKPPQ 74 (76)
T ss_dssp HHHHHHHHCTGG-EEEEEEETT---CCTHHHHHHHHHCT-EEEEE-HHHHHHCTTTSS-TTEEEEEE---
T ss_pred HHHHHHHcCCCC-ccEEEEEcCccchhHHHHHHHHHHcCCeEEEeCHHHHHHHcCCCCCCeEEEEEeCCC
Confidence 789999999988 888888664111 111111111 122222 2355889999999999998753
No 21
>PF09895 DUF2122: RecB-family nuclease (DUF2122); InterPro: IPR018665 This family of archaeal proteins include RecB nuclease-like proteins as well as proteins of no known function.
Probab=95.21 E-value=0.19 Score=39.89 Aligned_cols=80 Identities=14% Similarity=0.151 Sum_probs=58.7
Q ss_pred cCCHHHHHHHHhhhcCCcEEEEEEcCCCc--CcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCC
Q 024933 137 HSTWAEFRDYFRQQEGEKRLLAFTKRGTS--THSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYV 214 (260)
Q Consensus 137 ~~~~~~~l~~lk~~~~g~~iva~~~~~~~--~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v 214 (260)
..++.++++-|+ ...|+.++..+.. ........++++|||+....|+|+..+..-+ .++|.-....+
T Consensus 25 lpdl~DAiEvl~----p~~V~~i~~~~~~~~~~~~~~~~~rvllVf~G~d~gfsk~El~~g~-------~v~~~~v~~~i 93 (106)
T PF09895_consen 25 LPDLKDAIEVLK----PDVVYLISRSGEEEEKLEFLKIEGRVLLVFSGSDPGFSKIELELGE-------AVYIRGVERDI 93 (106)
T ss_pred eCCHHHHHHhcC----CcEEEEEcCcccccccccccCcCCcEEEEEeCCCCCCChhHhcCCc-------eEEeeccCcCc
Confidence 489999999997 4588888876543 2334566788999999999999999999866 57775433123
Q ss_pred ccccHHHHHHHHHHHH
Q 024933 215 RCLNLSVSVGIAVYEA 230 (260)
Q Consensus 215 ~SLNVsvAaaI~Lyel 230 (260)
.| --.+||+||++
T Consensus 94 G~---~g~~ai~Ly~L 106 (106)
T PF09895_consen 94 GP---IGEAAIILYEL 106 (106)
T ss_pred Ch---HHHHHHHHhcC
Confidence 33 45678899874
No 22
>COG4752 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.12 E-value=0.085 Score=44.37 Aligned_cols=157 Identities=20% Similarity=0.203 Sum_probs=92.2
Q ss_pred EEEEecCCCCccEEEEEeCCCCCCcHHHHHHhhhhcccce-EEECCCCCC--CChh--HHHHhcCC--Ccc----eEE-E
Q 024933 67 GEAVNGLSQNKFLQVVLVSPQIPGNTGCIARTCAASACGL-HLVGPLGFQ--VDDT--KLKRAGLD--YWP----YVV-I 134 (260)
Q Consensus 67 ~a~~~~~~~~~~l~vvLd~i~dp~NlGaIiRta~afGv~~-viv~~~~~~--~~~~--k~~rag~~--~~~----~v~-v 134 (260)
+|.+.-|..+++--+++-.+++ ..+-.|+|+|-.+.+++ .+|.|-.+. ...+ +.-+.|.| +-| .++ +
T Consensus 7 iaL~HYP~~~kdg~Ii~TsvTn-~D~HDIaR~artYeikgYyiV~pidAQ~~~~~r~i~yW~~g~G~~yNp~R~e~~~lv 85 (190)
T COG4752 7 IALLHYPAMDKDGKIIVTSVTN-MDLHDIARPARTYEIKGYYIVQPIDAQRIVIQRQINYWLSGEGRKYNPTRYEIVQLV 85 (190)
T ss_pred EEEEeccccCCCCCEEEEeecc-ccHhhhcccccceeeccEEEEeecHHHHHHHHHHHHHHhcccCCcCCcCHHHHHHHH
Confidence 4555555444443455555554 45778999999999974 455543211 0011 11123322 211 111 1
Q ss_pred EEcCCHHHHHHHHhhhcCCcE-EEEEEcCC---CcCcccc-----cCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeE
Q 024933 135 KVHSTWAEFRDYFRQQEGEKR-LLAFTKRG---TSTHSEI-----SYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTI 205 (260)
Q Consensus 135 ~~~~~~~~~l~~lk~~~~g~~-iva~~~~~---~~~l~~~-----~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v 205 (260)
....++++.+++..+.++..+ +++++++. +.++... .-.++..++||. ++||++|+++..|. ++
T Consensus 86 ~l~~~le~ViEdIEk~eG~rPLi~~TsAr~~~N~isy~~lr~~I~e~dkp~LilfGT-GwGlpde~m~~sDY------iL 158 (190)
T COG4752 86 RLAYTLEEVIEDIEKEEGRRPLIVGTSARTYPNTISYSWLRNEIQERDKPWLILFGT-GWGLPDELMNTSDY------IL 158 (190)
T ss_pred hHHHHHHHHHHHHHhhcCCCceEEeccccccCCcccHHHHHHHHhhcCCcEEEEecC-CCCCCHHHHHHhhH------hh
Confidence 223578888888877654444 44454432 2222221 234678899997 99999999999997 33
Q ss_pred EEcC--CCCCCccccHHHHHHHHHHHHHHc
Q 024933 206 RIPM--VETYVRCLNLSVSVGIAVYEAARQ 233 (260)
Q Consensus 206 ~IPm--~g~~v~SLNVsvAaaI~Lyel~rq 233 (260)
=|. .+ ...-|.|-.|+||+|-.++-.
T Consensus 159 -EPIra~s-d~NHLSVRaAvAIIlDRLfge 186 (190)
T COG4752 159 -EPIRAAS-DWNHLSVRAAVAIILDRLFGE 186 (190)
T ss_pred -hhhhccC-CcchhhHHHHHHHHHHHHhcc
Confidence 254 45 478899999999999877643
No 23
>COG1303 Uncharacterized protein conserved in archaea [Function unknown]
Probab=94.96 E-value=0.34 Score=41.08 Aligned_cols=119 Identities=14% Similarity=0.141 Sum_probs=77.8
Q ss_pred HHHhhhhcccceEEECCCCC-CCCh--hHHHHh-cCCCcceEEEEEcCCHHHHHHHHhhhcCCcEEEEEEcCCCc---Cc
Q 024933 95 IARTCAASACGLHLVGPLGF-QVDD--TKLKRA-GLDYWPYVVIKVHSTWAEFRDYFRQQEGEKRLLAFTKRGTS---TH 167 (260)
Q Consensus 95 IiRta~afGv~~viv~~~~~-~~~~--~k~~ra-g~~~~~~v~v~~~~~~~~~l~~lk~~~~g~~iva~~~~~~~---~l 167 (260)
++-||-|||++.+++...+. ...+ .++++. |-. +.+....+|...++.+++ |-.++-++..|.. -.
T Consensus 23 V~LtARAfGA~gil~~~e~De~v~esv~dVv~rwGG~----F~v~~~~nw~~~i~~wk~---gG~vvHLTMYG~~i~dv~ 95 (179)
T COG1303 23 VALTARAFGADGILLDGEEDEKVVESVEDVVERWGGP----FFVKFGVNWRKVIREWKE---GGIVVHLTMYGLNIDDVI 95 (179)
T ss_pred hhhhhHhhCCceEEEcCcccHHHHHHHHHHHHhcCCC----EEEEEcccHHHHHHHhhc---CCEEEEEEecCCcchhhh
Confidence 45589999999999975431 1111 122221 222 124456799999999986 5688888887742 12
Q ss_pred ccccCC-CCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHHc
Q 024933 168 SEISYR-KGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAARQ 233 (260)
Q Consensus 168 ~~~~~~-~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~rq 233 (260)
.++.-. +...+|+|.| -++.++.+.||. .|+|-..+ .|- -.|.||+|--++.-
T Consensus 96 ~ei~~~~k~~lvvVGae--KVp~evYelADy------NV~VgnQP---HSE--VaaLAvFLDRl~~G 149 (179)
T COG1303 96 DEIRESKKDVLVVVGAE--KVPGEVYELADY------NVSVGNQP---HSE--VAALAVFLDRLFEG 149 (179)
T ss_pred HHHHhcCCcEEEEEccc--cCCHHHhhhccc------ceecCCCc---cHH--HHHHHHHHHHHhCC
Confidence 233333 3478999987 589999999999 89886544 222 45778888777653
No 24
>PRK12703 tRNA 2'-O-methylase; Reviewed
Probab=93.39 E-value=0.74 Score=43.59 Aligned_cols=116 Identities=20% Similarity=0.143 Sum_probs=76.5
Q ss_pred HHHhhhhcccceEEECCCCCCCCh--hHHH-HhcCCCcceEEEEEcCCHHHHHHHHhhhcCCcEEEEEEcCCCcC---cc
Q 024933 95 IARTCAASACGLHLVGPLGFQVDD--TKLK-RAGLDYWPYVVIKVHSTWAEFRDYFRQQEGEKRLLAFTKRGTST---HS 168 (260)
Q Consensus 95 IiRta~afGv~~viv~~~~~~~~~--~k~~-rag~~~~~~v~v~~~~~~~~~l~~lk~~~~g~~iva~~~~~~~~---l~ 168 (260)
+.-||-|||++.+++....-..-+ .++. |=|-. +.+....+|...++.. +| .|+-++..|... ..
T Consensus 21 v~l~ara~ga~~~~~~~~d~~~~~~~~~v~~~~gg~----f~~~~~~~~~~~~~~~----~g-~vvhltmyg~~~~~~~~ 91 (339)
T PRK12703 21 VALTARAFGASSILVDERDETLENTIKKVVDNFGGS----FEIKTGIEWKSEFKKF----HG-IRVHLTMYGRPIEDVID 91 (339)
T ss_pred HHHHHHHhcCCeeEecCCcHhHHHHHHHHHHhcCCC----eEEEeccCHHHHHHhc----CC-EEEEEecCCCchHHHHH
Confidence 456888999999988753111111 1111 11222 2244467888887765 24 999999887532 33
Q ss_pred ccc-CCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHHHH
Q 024933 169 EIS-YRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEAAR 232 (260)
Q Consensus 169 ~~~-~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel~r 232 (260)
++. ..++..+|+|.| =+|.++.+.+|. .|+|--.+ .|= ..|.||+|..++.
T Consensus 92 ~i~~~~~~~~~vvg~~--kvp~~~y~~ad~------nv~v~~qp---hse--vaala~fld~~~~ 143 (339)
T PRK12703 92 EIRESGKDVMVLVGSE--KVPIEAYEIADY------NVSVTNQP---ISE--VSALAIFLDRYFD 143 (339)
T ss_pred HHhccCCCEEEEECCC--cCCHHHHhhccc------ceeeCCCC---hHH--HHHHHHHHHHhcc
Confidence 444 456899999987 589999999999 99996544 222 5678888887763
No 25
>PRK02135 hypothetical protein; Provisional
Probab=89.00 E-value=2.3 Score=37.42 Aligned_cols=84 Identities=13% Similarity=0.275 Sum_probs=66.8
Q ss_pred CCHHHHHHHHhhhcCCcEEEEEEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccc
Q 024933 138 STWAEFRDYFRQQEGEKRLLAFTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCL 217 (260)
Q Consensus 138 ~~~~~~l~~lk~~~~g~~iva~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SL 217 (260)
.++++.++.+.+ ++++|-++.+|. ++.+..++...++|+| ...|++++..+..+. .+.+.|+| | -.||
T Consensus 114 ~~fe~ll~~~~e---~~~l~~L~e~G~-~i~~~~~~~~~~FvLg-DH~~~~~ee~~~L~~--~ga~~iSl---G--P~~l 181 (201)
T PRK02135 114 RGFEDLLEELAE---GKTLYYLHEDGE-DIRDVEFPENPVFVLG-DHIGFTEEEENLLKR--LGAEKISL---G--PKML 181 (201)
T ss_pred CCHHHHHHHHhc---CCcEEEEeCCCC-chhhccCCCCCEEEEe-CCCCCCHHHHHHHHH--hCCeEEEe---C--cHHH
Confidence 789999999843 789999998774 6778888888899999 699999988876653 22336666 4 3689
Q ss_pred cHHHHHHHHHHHHHHc
Q 024933 218 NLSVSVGIAVYEAARQ 233 (260)
Q Consensus 218 NVsvAaaI~Lyel~rq 233 (260)
=.+++..++-+|+=+.
T Consensus 182 ~AshcI~~vhn~LD~~ 197 (201)
T PRK02135 182 HADHCITLIHNELDRR 197 (201)
T ss_pred HHHHHHHHHHHHHhhc
Confidence 9999999999998654
No 26
>PF01994 Trm56: tRNA ribose 2'-O-methyltransferase, aTrm56; InterPro: IPR002845 This entry represents tRNA ribose 2'-O-methyltransferase aTrm56, which specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of cytidine at position 56 in tRNAs. The crystal structure of Pyrococcus horikoshii aTrm56 complexed with S-adenosyl-L-methionine has been determined to 2.48 A resolution. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot, and a unique C-terminal beta-hairpin []. A conserved cytidine at position 56 of tRNA contributes to the maintenance of the L-shaped tertiary structure. aTrm56 catalyzes the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Biochemical assays showed that aTrm56 forms a dimer and prefers the L-shaped tRNA to the lambda form as its substrate [, ].; GO: 0008175 tRNA methyltransferase activity, 0002128 tRNA nucleoside ribose methylation, 0005737 cytoplasm; PDB: 2YY8_A 2O3A_B.
Probab=88.31 E-value=1.1 Score=36.17 Aligned_cols=84 Identities=12% Similarity=0.220 Sum_probs=54.8
Q ss_pred EEEcCCHHHHHHHHhhhcCCcEEEEEEcCCCc---Cccccc-CCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcC
Q 024933 134 IKVHSTWAEFRDYFRQQEGEKRLLAFTKRGTS---THSEIS-YRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPM 209 (260)
Q Consensus 134 v~~~~~~~~~l~~lk~~~~g~~iva~~~~~~~---~l~~~~-~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm 209 (260)
+....+|...++..|+. +..|+-+|+.|.. ...++. -.++..+|+|.| =++.++.+.+|. -|+|--
T Consensus 7 ve~~~~w~~~i~~wK~~--~G~VVHLTMYG~~i~dvi~~Ir~~~~~~lvVVGae--KVP~evYe~ADy------NVaVgn 76 (120)
T PF01994_consen 7 VEYGVSWKSYIREWKEK--GGKVVHLTMYGENIDDVIDEIRESCKDLLVVVGAE--KVPGEVYELADY------NVAVGN 76 (120)
T ss_dssp EEEES-HHHHHHC------SSEEEEE-TTSEEHHHCHHHHHHCTSEEEEEE-SS-----CCHHHHSSE------EEESSS
T ss_pred EEECCCHHHHHHHhccc--CCeEEEEEecCCchHHHHHHHhccCCCEEEEECCC--cCCHHHHhhCCc------ceeeCC
Confidence 45568999999999876 7899999998753 233444 567799999987 489999999999 999865
Q ss_pred CCCCCccccHHHHHHHHHHHHHH
Q 024933 210 VETYVRCLNLSVSVGIAVYEAAR 232 (260)
Q Consensus 210 ~g~~v~SLNVsvAaaI~Lyel~r 232 (260)
.+ .|= ..|.||+|..++.
T Consensus 77 QP---HSE--VAALAvFLDrl~~ 94 (120)
T PF01994_consen 77 QP---HSE--VAALAVFLDRLFE 94 (120)
T ss_dssp S------H--HHHHHHHHHHHCT
T ss_pred CC---hHH--HHHHHHHHHHhcC
Confidence 44 232 5678888887753
No 27
>KOG0838 consensus RNA Methylase, SpoU family [RNA processing and modification]
Probab=85.34 E-value=0.2 Score=45.64 Aligned_cols=54 Identities=26% Similarity=0.330 Sum_probs=43.3
Q ss_pred CCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHHHH
Q 024933 173 RKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVYEA 230 (260)
Q Consensus 173 ~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Lyel 230 (260)
..++.++-|++ .++|+.+.+.|-. ....+.|++.+...+||||++|+||.++..
T Consensus 137 ~~~v~lv~~n~-s~lS~~vskss~g---ale~l~I~q~~~~~efl~vsvaaG~~l~~t 190 (271)
T KOG0838|consen 137 ADGVLLVKGNS-SPLSPVVSKSSAG---ALEVLPIRQVDNPLEFLNVSVAAGIRLHGT 190 (271)
T ss_pred CCceEEEeccC-CCCchhHHHhhhc---hhheeeHHHcCCHHHHHHHHHhCceEEEEe
Confidence 56889999999 8999888775432 222899999876689999999999998763
No 28
>PF14419 SPOUT_MTase_2: AF2226-like SPOUT RNA Methylase fused to THUMP
Probab=80.48 E-value=12 Score=31.97 Aligned_cols=128 Identities=16% Similarity=0.165 Sum_probs=73.0
Q ss_pred cHH-HHHHhhhhcccceEEECC-CCCCCChh-HHHHh---cC----------CCc--ceEEEEEcCCHHHHHHHHhhhcC
Q 024933 91 NTG-CIARTCAASACGLHLVGP-LGFQVDDT-KLKRA---GL----------DYW--PYVVIKVHSTWAEFRDYFRQQEG 152 (260)
Q Consensus 91 NlG-aIiRta~afGv~~viv~~-~~~~~~~~-k~~ra---g~----------~~~--~~v~v~~~~~~~~~l~~lk~~~~ 152 (260)
++| .|-|.+-+|.++.+++.+ +..+...- ...|+ |. -.| ..+++.. -++-+++.+ . .
T Consensus 18 ~mGerIGRaaQ~FEV~eLiiap~~~vda~eL~~Fl~gV~~G~eSRy~iQ~ksY~r~v~kvpV~V-~DlYQ~vRd---R-~ 92 (173)
T PF14419_consen 18 KMGERIGRAAQAFEVKELIIAPKEKVDAYELMEFLRGVREGQESRYQIQRKSYGREVRKVPVYV-QDLYQVVRD---R-K 92 (173)
T ss_pred HHHHHHhHHHhhcchheEEEeccCccCHHHHHHHHHHHHHhHHHHHHHHHHhcCCeeeEeeeeH-HHHHHHHHh---c-C
Confidence 344 477999999998666655 33332221 11111 11 111 2344433 245555554 2 3
Q ss_pred CcEEEEEEcCCCcC------c-ccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHH
Q 024933 153 EKRLLAFTKRGTST------H-SEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGI 225 (260)
Q Consensus 153 g~~iva~~~~~~~~------l-~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI 225 (260)
+-.++.+++.|... + ..+...+.+.+++|+ ..|+|.-+...||. +|-+--.-+ +..=-+.-|+.|
T Consensus 93 ~~~lIvtdPkG~~is~vk~~L~~~~r~~~eV~v~iGS-ReGiP~GlfRfAd~------VvDlaP~~t-~aTe~~ipsali 164 (173)
T PF14419_consen 93 GEPLIVTDPKGDPISEVKDKLAEDLRYAKEVVVFIGS-REGIPRGLFRFADY------VVDLAPGVT-FATEHAIPSALI 164 (173)
T ss_pred CCeEEEECCCCCcHHHHHHHHHHHHhhCcEEEEEEEc-ccCCChhHHHHhhh------hhhcCCceE-EeehhhhHHHHH
Confidence 67999999988531 2 233455678899998 89999999999998 665532211 222233344555
Q ss_pred HHHHHH
Q 024933 226 AVYEAA 231 (260)
Q Consensus 226 ~Lyel~ 231 (260)
+|+..+
T Consensus 165 Al~~v~ 170 (173)
T PF14419_consen 165 ALWTVY 170 (173)
T ss_pred HHHHHH
Confidence 565543
No 29
>COG1901 Uncharacterized conserved protein [Function unknown]
Probab=77.87 E-value=21 Score=31.19 Aligned_cols=86 Identities=15% Similarity=0.151 Sum_probs=64.9
Q ss_pred cCCHHHHHHHHhhhcCCcEEEEEEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCcc
Q 024933 137 HSTWAEFRDYFRQQEGEKRLLAFTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRC 216 (260)
Q Consensus 137 ~~~~~~~l~~lk~~~~g~~iva~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~S 216 (260)
..++++.+..+.+ ++.+|-+..+|. .+.++++....++|+|. ..|++++..+.... .+...|++ | --|
T Consensus 111 ~~~~e~ll~~l~~---~~~ly~L~E~G~-DI~~v~~~~np~FIlGD-H~g~t~e~~k~L~r--~~~~~ISl---G--P~~ 178 (197)
T COG1901 111 NGGFEALLAELAE---GRSLYYLHEDGR-DISEVDLIPNPVFILGD-HIGLTEEDEKLLER--HAAKKISL---G--PLS 178 (197)
T ss_pred cCCHHHHHHHHhc---cCcEEEEccCCc-cHhhcccCCCceEEeeC-CCCCCHHHHHHHHH--hhCceeEe---C--chH
Confidence 4789999998864 688999887764 67888888889999997 89999988776553 11224444 2 247
Q ss_pred ccHHHHHHHHHHHHHHcc
Q 024933 217 LNLSVSVGIAVYEAARQL 234 (260)
Q Consensus 217 LNVsvAaaI~Lyel~rq~ 234 (260)
|=.+++..++=+++-||.
T Consensus 179 lha~hcit~~h~~LD~~~ 196 (197)
T COG1901 179 LHADHCITLLHNLLDRQG 196 (197)
T ss_pred HHHHHHHHHHHHHHhhcc
Confidence 888999999988887764
No 30
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.90 E-value=18 Score=32.69 Aligned_cols=140 Identities=14% Similarity=0.124 Sum_probs=81.9
Q ss_pred ccEEEEEeCCCCCCcHHHHHHhhhhcccceEEE--CCCCC-CCChh---------HHHH-h----cCCCcceEEEEEcCC
Q 024933 77 KFLQVVLVSPQIPGNTGCIARTCAASACGLHLV--GPLGF-QVDDT---------KLKR-A----GLDYWPYVVIKVHST 139 (260)
Q Consensus 77 ~~l~vvLd~i~dp~NlGaIiRta~afGv~~viv--~~~~~-~~~~~---------k~~r-a----g~~~~~~v~v~~~~~ 139 (260)
+..+-+.-.+-.+.++=-|+|-|.-+|+..++. +.+|. ..+.. ++.. | |...+|- +....+
T Consensus 77 ~~~i~l~~~i~kg~k~d~iiqkatELGv~~i~p~~ter~~~k~~~~~~~kler~~ki~ieAaEQs~R~~vP~--I~~~~~ 154 (246)
T COG1385 77 PLKITLAQAIPKGDKLELIIQKATELGVSKIIPLITERSVVKLDGKKAAKLERWQKIAIEAAEQSGRNVVPE--IKPPES 154 (246)
T ss_pred CceEEEEEEcCccHHHHHHHHHHHHhCcceEEEEeeeeeEEeccccchhHHHHHHHHHHHHHHhcCCCcCCe--eechhh
Confidence 344566677888889999999999999985543 33332 22222 1111 2 2334554 444578
Q ss_pred HHHHHHHHhhhcCCcEEEEEEcCCCcCcc-----cccCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCC
Q 024933 140 WAEFRDYFRQQEGEKRLLAFTKRGTSTHS-----EISYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYV 214 (260)
Q Consensus 140 ~~~~l~~lk~~~~g~~iva~~~~~~~~l~-----~~~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v 214 (260)
+.++++..... ....+........... +....++.++++|.|+ |+|++.++.... .+...|.+-.
T Consensus 155 ~~~~l~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iiIGPEG-Gfs~~Ei~~l~~----~g~~~v~LGp--- 224 (246)
T COG1385 155 LKELLKEIDDE--DALKLIYEEKAKEGLLALPLLEALPEGKVLLIIGPEG-GFSEDEIELLRE----AGFTPVSLGP--- 224 (246)
T ss_pred HHHHHHhcccc--hhhhheeccccccccccchhhhcccCCcEEEEECCCC-CCCHHHHHHHHH----CCCeEeccCC---
Confidence 88888876632 2223333333322222 2235689999999995 999988887654 1245666643
Q ss_pred ccccHHHHHHHHHH
Q 024933 215 RCLNLSVSVGIAVY 228 (260)
Q Consensus 215 ~SLNVsvAaaI~Ly 228 (260)
+=|=.-+|+-.+|.
T Consensus 225 rILRtETAal~ala 238 (246)
T COG1385 225 RILRTETAALAALA 238 (246)
T ss_pred ceehhhHHHHHHHH
Confidence 33444444444443
No 31
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=72.64 E-value=49 Score=28.98 Aligned_cols=111 Identities=13% Similarity=0.145 Sum_probs=58.6
Q ss_pred EEEEeCCCCCCcHHHHHHhhhhcccceEE--ECCCCC-CCCh----h------HHHH-h----cCCCcceEEEEEcCCHH
Q 024933 80 QVVLVSPQIPGNTGCIARTCAASACGLHL--VGPLGF-QVDD----T------KLKR-A----GLDYWPYVVIKVHSTWA 141 (260)
Q Consensus 80 ~vvLd~i~dp~NlGaIiRta~afGv~~vi--v~~~~~-~~~~----~------k~~r-a----g~~~~~~v~v~~~~~~~ 141 (260)
+.++-.+-.+..+=-+++-|.-+|++.++ .+..+. ..+. . +... | |...+|.+ ....++.
T Consensus 63 i~L~~al~K~~~~d~il~katELGv~~i~p~~s~rsv~k~~~~~~~~k~~R~~~i~~eA~kQs~r~~~P~i--~~~~~l~ 140 (225)
T PF04452_consen 63 ITLAQALPKGDRMDWILQKATELGVSRIIPVISERSVVKSDGKKSDKKLERWQRIAIEAAKQSGRTRLPEI--EPPISLK 140 (225)
T ss_dssp EEEEEE--STTHHHHHHHHHHHTT-SEEEEEE-TTSSS---HHHHHHHHHHHHHHHHHHHHHHT-SS--EE--EEEEEHH
T ss_pred EEEEEEEEcCccHHHHHHHHHhcCCCEEEEEEeeeeeeeccchhhHHHHHHHHHHHHHHHHhcCCCcccee--eccccHH
Confidence 66667777789999999999999998543 345553 2211 1 1111 1 34455544 4456899
Q ss_pred HHHHHHhhhcCCcEEEEEEcCCCcCccccc--CCC----CeEEEEcCCCCCCCHHHHhhCcC
Q 024933 142 EFRDYFRQQEGEKRLLAFTKRGTSTHSEIS--YRK----GDYLIFGSETSGLPPEALLDCTS 197 (260)
Q Consensus 142 ~~l~~lk~~~~g~~iva~~~~~~~~l~~~~--~~~----~~aLV~GnE~~GLs~e~l~~cD~ 197 (260)
+++++.... .. +.+...+......+. ... +.++++|.|+ |.|++.++..-.
T Consensus 141 ~~l~~~~~~---~~-~~~~~~~~~~~~~~~~~~~~~~~~~i~i~IGPEG-Gfs~~E~~~~~~ 197 (225)
T PF04452_consen 141 ELLEDIPDE---DL-LILDEDEEPSLSSLSEILNSEKSFSIAIIIGPEG-GFSEEEIEFLKE 197 (225)
T ss_dssp HHHHHSSEC---SE-EEE-TTTTCBGGGCSHTTSCHHC-EEEEEE--TT----HHHHHHHHH
T ss_pred HHhhccccC---CE-EEEcccccccccchhhhhhcccCCcEEEEECCCC-CCCHHHHHHHHH
Confidence 999887642 22 444444333222221 111 8899999995 999988886654
No 32
>PF04013 Methyltrn_RNA_2: Putative SAM-dependent RNA methyltransferase; InterPro: IPR007158 The proteins in this family are around 200 amino acids long with the exception of O29206 from SWISSPROT that has an additional 100 amino acids at its N terminus. The function of these bacterial protein is unknown, however, they do contain several conserved histidines and aspartates that might form a metal-binding site.; PDB: 2QMM_A 3AIA_A 3AI9_X 2QWV_B.
Probab=71.84 E-value=16 Score=32.07 Aligned_cols=84 Identities=14% Similarity=0.266 Sum_probs=56.7
Q ss_pred CCHHHHHHHHhhhcCCcEEEEEEcCCCcCcccccCCC-CeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCcc
Q 024933 138 STWAEFRDYFRQQEGEKRLLAFTKRGTSTHSEISYRK-GDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRC 216 (260)
Q Consensus 138 ~~~~~~l~~lk~~~~g~~iva~~~~~~~~l~~~~~~~-~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~S 216 (260)
.++++.++.+++ .+++|-+..+| .++.++.++. ..++|+|- ..|++++..+.... .+...|+| | -.|
T Consensus 113 ~~fe~ll~~~~~---~~~l~~L~e~G-~di~~~~~~~~d~~FVLgD-H~g~~~eee~~L~~--~~a~kiSl---G--P~~ 180 (199)
T PF04013_consen 113 GGFEDLLEELAE---EYPLYYLHEDG-EDIRDVEFPGNDPVFVLGD-HIGFTEEEEELLER--LGAEKISL---G--PKS 180 (199)
T ss_dssp --HHHHHHHHHC---TSEEEEESTTS-EEGGGS---S-SEEEEEE--TT-SHHHHHHHHHC--TTSEEEES------SS-
T ss_pred CCHHHHHHHHhc---CCcEEEEcCCC-CcHhhcccCCCCCeEEEeC-CCCCCHHHHHHHHH--ccCceEEe---C--CHH
Confidence 689999999885 38999988776 4788888888 89999996 89999887776654 11235554 3 368
Q ss_pred ccHHHHHHHHHHHHHHc
Q 024933 217 LNLSVSVGIAVYEAARQ 233 (260)
Q Consensus 217 LNVsvAaaI~Lyel~rq 233 (260)
|=.+++..|+-+|+=|.
T Consensus 181 lhAdhcI~ivhn~LD~~ 197 (199)
T PF04013_consen 181 LHADHCITIVHNELDRR 197 (199)
T ss_dssp --HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhc
Confidence 99999999999998654
No 33
>PF04407 DUF531: Protein of unknown function (DUF531); InterPro: IPR007501 This is a family of hypothetical archaeal proteins.
Probab=68.08 E-value=77 Score=27.12 Aligned_cols=47 Identities=21% Similarity=0.228 Sum_probs=38.3
Q ss_pred CCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHHHH
Q 024933 173 RKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIAVY 228 (260)
Q Consensus 173 ~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~Ly 228 (260)
.++..+++|--.+||+.++++.+.+ -+-|- | +--||--..|.|++-.
T Consensus 119 ~~s~~~liGLGR~GLPkei~k~a~y------HLDIT--g-kgiSLETCTAiG~Ipa 165 (173)
T PF04407_consen 119 GKSFLLLIGLGRHGLPKEIFKMAKY------HLDIT--G-KGISLETCTAIGAIPA 165 (173)
T ss_pred CCceEEEEecCCCCCcHHHHHhchh------ceeec--C-CceeeehhhHHhhHHH
Confidence 3578999999999999999999988 66666 4 3568988888887643
No 34
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=64.33 E-value=1e+02 Score=27.29 Aligned_cols=112 Identities=14% Similarity=0.068 Sum_probs=63.9
Q ss_pred EEEEeCCCCCCcHHHHHHhhhhcccceEE--ECCCCCC-CC---hhHH------HH-h----cCCCcceEEEEEcCCHHH
Q 024933 80 QVVLVSPQIPGNTGCIARTCAASACGLHL--VGPLGFQ-VD---DTKL------KR-A----GLDYWPYVVIKVHSTWAE 142 (260)
Q Consensus 80 ~vvLd~i~dp~NlGaIiRta~afGv~~vi--v~~~~~~-~~---~~k~------~r-a----g~~~~~~v~v~~~~~~~~ 142 (260)
+.++-.+-.+.-+=-|++-|.-+|++.++ .+.++.. .+ ..+. .. | +...+|. +....++.+
T Consensus 78 i~l~~al~K~~~~d~il~katELGv~~i~p~~s~rs~~~~~~~~~~k~~rw~~i~~eA~~Q~~r~~lP~--i~~~~~l~~ 155 (240)
T TIGR00046 78 IHLAIVLIKGKKMEFIIRKLTELGVSKIIPFNAERSVVKLDIEAIKKLERWQKIAIEAAEQSGRNIVPE--IKPPKNLKE 155 (240)
T ss_pred EEEEEeecCCccHHHHHHHHHHcCCCEEEEEEeccceeccCchHHHHHHHHHHHHHHHHHhcCCCCCCE--ECCcCCHHH
Confidence 44445556789999999999999998543 3444432 11 1222 11 2 2334454 334578888
Q ss_pred HHHHHhhhcCCcEEEEEEcCCCcCccccc-CCCCeEEEEcCCCCCCCHHHHhhCcC
Q 024933 143 FRDYFRQQEGEKRLLAFTKRGTSTHSEIS-YRKGDYLIFGSETSGLPPEALLDCTS 197 (260)
Q Consensus 143 ~l~~lk~~~~g~~iva~~~~~~~~l~~~~-~~~~~aLV~GnE~~GLs~e~l~~cD~ 197 (260)
+++..... ...++. ...+......+. ..+++++++|.|| |.|++.++.+..
T Consensus 156 ~l~~~~~~--~~~~~~-~~~~~~~~~~l~~~~~~v~~~IGPEG-Gfs~~Ei~~~~~ 207 (240)
T TIGR00046 156 KCAEAYEE--ALKLNF-HPEASPLSANLPIPAGNIVIIIGPEG-GFSEKEIQLLKE 207 (240)
T ss_pred HHhhCcCC--CeEEEE-CCcccchhhhhccCCCcEEEEECCCC-CCCHHHHHHHHH
Confidence 87754321 222333 222221112221 1246899999995 999999887754
No 35
>PF02590 SPOUT_MTase: Predicted SPOUT methyltransferase; InterPro: IPR003742 This family of proteins are predicted to be SPOUT methyltransferases []. ; GO: 0008168 methyltransferase activity, 0006364 rRNA processing, 0005737 cytoplasm; PDB: 1VH0_E 4FAK_A 1TO0_G 1O6D_A 1NS5_B.
Probab=46.53 E-value=23 Score=29.70 Aligned_cols=48 Identities=15% Similarity=0.269 Sum_probs=30.1
Q ss_pred CcEEEEEEcCCCcC--------cccc--cCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEE
Q 024933 153 EKRLLAFTKRGTST--------HSEI--SYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRI 207 (260)
Q Consensus 153 g~~iva~~~~~~~~--------l~~~--~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~I 207 (260)
+..+|+++.+|... +.+. .-..++++++|. ..|+++++++.||. .+++
T Consensus 67 ~~~~i~Ld~~Gk~~sS~~fA~~l~~~~~~g~~~i~F~IGG-~~G~~~~~~~~a~~------~lSL 124 (155)
T PF02590_consen 67 NDYVILLDERGKQLSSEEFAKKLERWMNQGKSDIVFIIGG-ADGLSEEVRKRADE------KLSL 124 (155)
T ss_dssp TSEEEEE-TTSEE--HHHHHHHHHHHHHTTS-EEEEEE-B-TTB--HHHHHH-SE------EEES
T ss_pred CCEEEEEcCCCccCChHHHHHHHHHHHhcCCceEEEEEec-CCCCCHHHHhhcCc------eEEE
Confidence 67899999887532 1111 223478999997 67999999999998 7766
No 36
>PRK00103 rRNA large subunit methyltransferase; Provisional
Probab=44.94 E-value=80 Score=26.54 Aligned_cols=68 Identities=16% Similarity=0.263 Sum_probs=45.4
Q ss_pred CcEEEEEEcCCCcC--------ccccc--CCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEE-cCCCCCCccccHHH
Q 024933 153 EKRLLAFTKRGTST--------HSEIS--YRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRI-PMVETYVRCLNLSV 221 (260)
Q Consensus 153 g~~iva~~~~~~~~--------l~~~~--~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~I-Pm~g~~v~SLNVsv 221 (260)
+..+|+++.+|... +.+.. -..++++++|. ..|+++++++.||. .+++ ||. ++=-.
T Consensus 67 ~~~~i~LDe~Gk~~sS~~fA~~l~~~~~~g~~~i~F~IGG-a~G~~~~v~~~a~~------~lSLS~mT------fpH~l 133 (157)
T PRK00103 67 GARVIALDERGKQLSSEEFAQELERWRDDGRSDVAFVIGG-ADGLSPAVKKRADQ------SLSLSKLT------LPHQL 133 (157)
T ss_pred CCEEEEEcCCCCcCCHHHHHHHHHHHHhcCCccEEEEEcC-ccccCHHHHHhcCc------eEEeccCC------CcHHH
Confidence 45799999888642 11111 12469999997 79999999999998 7776 342 33345
Q ss_pred HHHHHHHHHHHc
Q 024933 222 SVGIAVYEAARQ 233 (260)
Q Consensus 222 AaaI~Lyel~rq 233 (260)
|--|++=.++|.
T Consensus 134 arlvL~EQlYRa 145 (157)
T PRK00103 134 VRVLLAEQLYRA 145 (157)
T ss_pred HHHHHHHHHHHH
Confidence 555655556554
No 37
>COG1576 Uncharacterized conserved protein [Function unknown]
Probab=44.48 E-value=43 Score=28.34 Aligned_cols=45 Identities=11% Similarity=0.214 Sum_probs=32.9
Q ss_pred CCcEEEEEEcCCCcC----c----ccc-cCCCCeEEEEcCCCCCCCHHHHhhCcC
Q 024933 152 GEKRLLAFTKRGTST----H----SEI-SYRKGDYLIFGSETSGLPPEALLDCTS 197 (260)
Q Consensus 152 ~g~~iva~~~~~~~~----l----~~~-~~~~~~aLV~GnE~~GLs~e~l~~cD~ 197 (260)
.|-.+++++.+|... + .+. .....+++++|. ..||++++++.+|.
T Consensus 66 ~~~~vi~Ld~~Gk~~sSe~fA~~l~~~~~~G~~i~f~IGG-~~Gl~~~~~~~a~~ 119 (155)
T COG1576 66 KGSYVVLLDIRGKALSSEEFADFLERLRDDGRDISFLIGG-ADGLSEAVKARADQ 119 (155)
T ss_pred CCCeEEEEecCCCcCChHHHHHHHHHHHhcCCeEEEEEeC-cccCCHHHHHHHhh
Confidence 367999999887532 1 111 112568999998 79999999999997
No 38
>TIGR00246 tRNA_RlmH_YbeA rRNA large subunit m3Psi methyltransferase RlmH. This protein, in the SPOUT methyltransferase family, previously designated YbeA in E. coli, was shown to be responsible for a further modification, a methylation, to a pseudouridine base in ribosomal large subunit RNA.
Probab=43.08 E-value=40 Score=28.26 Aligned_cols=67 Identities=13% Similarity=0.181 Sum_probs=43.8
Q ss_pred cEEEEEEcCCCcC--------cccc-cCCCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEE-cCCCCCCccccHHHHH
Q 024933 154 KRLLAFTKRGTST--------HSEI-SYRKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRI-PMVETYVRCLNLSVSV 223 (260)
Q Consensus 154 ~~iva~~~~~~~~--------l~~~-~~~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~I-Pm~g~~v~SLNVsvAa 223 (260)
..+|+++.+|... +.+. ....++++++|. ..|+++++++.||. .+++ ||. +.=-.|-
T Consensus 66 ~~~i~LDe~Gk~~sS~~fA~~l~~~~~~g~~i~FvIGG-a~G~~~~v~~~a~~------~lSLS~mT------fpH~lar 132 (153)
T TIGR00246 66 AHVVTLDIPGKPWTTPQLADTLEKWKTDGRDVTLLIGG-PEGLSPTCKAAAEQ------SWSLSKLT------LPHPLVR 132 (153)
T ss_pred CeEEEEcCCCCcCCHHHHHHHHHHHhccCCeEEEEEcC-CCcCCHHHHHhcCc------eEEeecCC------CcHHHHH
Confidence 5799999887541 1111 112369999997 79999999999998 7776 342 2334455
Q ss_pred HHHHHHHHHc
Q 024933 224 GIAVYEAARQ 233 (260)
Q Consensus 224 aI~Lyel~rq 233 (260)
-|++=.++|.
T Consensus 133 lvL~EQiYRA 142 (153)
T TIGR00246 133 VIVAESLYRA 142 (153)
T ss_pred HHHHHHHHHH
Confidence 5555455554
No 39
>COG3426 Butyrate kinase [Energy production and conversion]
Probab=39.22 E-value=26 Score=32.88 Aligned_cols=31 Identities=23% Similarity=0.270 Sum_probs=26.6
Q ss_pred CCCCCCcHHHHH--HhhhhcccceEEECCCCCC
Q 024933 85 SPQIPGNTGCIA--RTCAASACGLHLVGPLGFQ 115 (260)
Q Consensus 85 ~i~dp~NlGaIi--Rta~afGv~~viv~~~~~~ 115 (260)
.-+++.|+|+|+ |.|.++|+...||+|-.+|
T Consensus 102 ~G~haSnLGaiiA~~ia~~~gvPayIVDPvvVD 134 (358)
T COG3426 102 QGEHASNLGAIIANRIAKALGVPAYIVDPVVVD 134 (358)
T ss_pred CCcchhhhhHHHHHHHhhhcCCCeeeeCceehh
Confidence 457899999997 8899999999999986554
No 40
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=37.23 E-value=2.9e+02 Score=24.29 Aligned_cols=108 Identities=14% Similarity=0.112 Sum_probs=59.9
Q ss_pred cEEEEEeCCCCCCcHHHHHHhhhhcccceEEE--CCCCCC-CCh-------hH---HH-Hh----cCCCcceEEEEEcCC
Q 024933 78 FLQVVLVSPQIPGNTGCIARTCAASACGLHLV--GPLGFQ-VDD-------TK---LK-RA----GLDYWPYVVIKVHST 139 (260)
Q Consensus 78 ~l~vvLd~i~dp~NlGaIiRta~afGv~~viv--~~~~~~-~~~-------~k---~~-ra----g~~~~~~v~v~~~~~ 139 (260)
.+.++ -.+-.+..+=-+++.|.-+|++.++. +..+.. .+. .+ .. .| +...+|. +..+.+
T Consensus 75 ~l~l~-~al~k~~~~e~il~k~tELGV~~i~p~~sers~~~~~~~~~~~k~~r~~~i~~~A~~Qs~r~~~P~--i~~~~~ 151 (234)
T PRK11713 75 RLTLA-QALPKGDRLELILQKATELGVSAIIPLISERSVVKLDGERADKKLERWQKIAIEAAEQSGRTRIPE--VRPPIS 151 (234)
T ss_pred eEEEE-EeecCCccHHHHHHHHHHhCcCeEEEEEeccceecccchhhHHHHHHHHHHHHHHHHhcCCCCCCE--EcCcCC
Confidence 34444 44557899999999999999985433 343322 111 11 11 22 2334454 344578
Q ss_pred HHHHHHHHhhhcCCcEEEEEEcCCCcCcccccCCCCeEEEEcCCCCCCCHHHHhhCcC
Q 024933 140 WAEFRDYFRQQEGEKRLLAFTKRGTSTHSEISYRKGDYLIFGSETSGLPPEALLDCTS 197 (260)
Q Consensus 140 ~~~~l~~lk~~~~g~~iva~~~~~~~~l~~~~~~~~~aLV~GnE~~GLs~e~l~~cD~ 197 (260)
+.++++.... ..+ .+ .....+.. ...+++++++|.|| |.|++.++....
T Consensus 152 ~~~~l~~~~~----~~~--~~-~~~~~l~~-~~~~~i~viIGPEG-Gfs~~Ei~~l~~ 200 (234)
T PRK11713 152 LKEFLEELLP----ADL--KA-GLKLVLHP-EAGGKVLLLIGPEG-GFSPEEIELLRE 200 (234)
T ss_pred HHHHHhhccc----ccc--ch-hhhhhcCc-CCCCeEEEEECCCC-CCCHHHHHHHHH
Confidence 8888775432 111 00 00001111 11246899999995 999988877654
No 41
>COG1772 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.76 E-value=71 Score=27.04 Aligned_cols=45 Identities=20% Similarity=0.255 Sum_probs=35.9
Q ss_pred CCCeEEEEcCCCCCCCHHHHhhCcCCCCCceeEEEcCCCCCCccccHHHHHHHH
Q 024933 173 RKGDYLIFGSETSGLPPEALLDCTSETFGGGTIRIPMVETYVRCLNLSVSVGIA 226 (260)
Q Consensus 173 ~~~~aLV~GnE~~GLs~e~l~~cD~~~~~~~~v~IPm~g~~v~SLNVsvAaaI~ 226 (260)
.+...+++|--.+||+.|+++.|.+ .+-|--. --||--..|.|++
T Consensus 119 ~ks~~~~iGLGr~GLPke~~~~~~Y------HLDiT~k---gvSLETcTAIGaI 163 (178)
T COG1772 119 GKSFTFLIGLGRHGLPKEMFKSAKY------HLDITDK---GVSLETCTAIGAI 163 (178)
T ss_pred CCceEEEEecCCCCCcHHHHhhcee------eeeeccC---cceeeehhhhcch
Confidence 4567899999999999999999987 5666553 3588888887766
No 42
>PF07047 OPA3: Optic atrophy 3 protein (OPA3); InterPro: IPR010754 OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity []. This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.
Probab=29.41 E-value=38 Score=27.63 Aligned_cols=22 Identities=27% Similarity=0.427 Sum_probs=17.5
Q ss_pred ccccHHHHHHHHHHHHHHcccc
Q 024933 215 RCLNLSVSVGIAVYEAARQLNY 236 (260)
Q Consensus 215 ~SLNVsvAaaI~Lyel~rq~~~ 236 (260)
+.+=-+||+++++||++|+...
T Consensus 81 E~fiF~Va~~li~~E~~Rs~~k 102 (134)
T PF07047_consen 81 EAFIFSVAAGLIIYEYWRSARK 102 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHhh
Confidence 3445579999999999998754
No 43
>PLN03033 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=23.97 E-value=63 Score=30.06 Aligned_cols=49 Identities=22% Similarity=0.306 Sum_probs=32.4
Q ss_pred HHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhh
Q 024933 92 TGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQ 149 (260)
Q Consensus 92 lGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~ 149 (260)
+-.++|.|.|.|++++++. +.+++.+...-|...++. +.+++.++.+++
T Consensus 222 V~~larAAvA~GaDGlfiE---vHpdP~~AlsDg~q~l~~------~~l~~ll~~l~~ 270 (290)
T PLN03033 222 IPCIARTAVAVGVDGIFME---VHDDPLSAPVDGPTQWPL------RHLEELLEELIA 270 (290)
T ss_pred HHHHHHHHHHhCCCEEEEE---ecCCccccCCCcccCcCH------HHHHHHHHHHHH
Confidence 5689999999999999996 234444444445554432 456666666654
No 44
>TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase. In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide.
Probab=22.86 E-value=64 Score=29.55 Aligned_cols=49 Identities=16% Similarity=0.180 Sum_probs=32.0
Q ss_pred HHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhh
Q 024933 92 TGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQ 149 (260)
Q Consensus 92 lGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~ 149 (260)
+-.++|.|.|+|++++++.- .+++.+...-|...++. +.++++++.+++
T Consensus 203 v~~la~AAvA~GaDGl~iEv---HpdP~~AlsDg~q~l~~------~~~~~ll~~l~~ 251 (258)
T TIGR01362 203 VPTLARAAVAVGIDGLFMET---HPDPKNAKSDGPNMLPL------SELEGLLEKLLA 251 (258)
T ss_pred HHHHHHHHHHhCCCEEEEEe---CCCccccCCCccccCCH------HHHHHHHHHHHH
Confidence 66899999999999999862 33444444434444321 566777776654
No 45
>COG4075 Uncharacterized conserved protein, homolog of nitrogen regulatory protein PII [Function unknown]
Probab=22.67 E-value=1.7e+02 Score=23.10 Aligned_cols=63 Identities=13% Similarity=0.029 Sum_probs=37.9
Q ss_pred CCCCCcHHHHHHhhhhcccceEEEC-CCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhhhcCCcEEEEEE
Q 024933 86 PQIPGNTGCIARTCAASACGLHLVG-PLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQQEGEKRLLAFT 160 (260)
Q Consensus 86 i~dp~NlGaIiRta~afGv~~viv~-~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~~~~g~~iva~~ 160 (260)
.-++.|+|-.+...+-.|+.+.++- -++.+|+. |.-+.+ ..|.+.+++.+++....--++++-
T Consensus 10 FVe~eNvGkaiN~mad~GiTGFfl~eYrGvsPd~----------wkgf~~--~EDpE~aik~i~D~s~~AVlI~tV 73 (110)
T COG4075 10 FVEEENVGKAINIMADAGITGFFLHEYRGVSPDK----------WKGFSK--EEDPESAIKAIRDLSDKAVLIGTV 73 (110)
T ss_pred EecHHHHHHHHHHHHhcCcceEEEEEecCcChhH----------hcCccc--ccCHHHHHHHHHHhhhceEEEEEe
Confidence 3478999999999999999865553 34555443 222222 256777776666543233444443
No 46
>PRK12457 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=22.49 E-value=67 Score=29.76 Aligned_cols=49 Identities=14% Similarity=0.126 Sum_probs=32.2
Q ss_pred HHHHHHhhhhcccceEEECCCCCCCChhHHHHhcCCCcceEEEEEcCCHHHHHHHHhh
Q 024933 92 TGCIARTCAASACGLHLVGPLGFQVDDTKLKRAGLDYWPYVVIKVHSTWAEFRDYFRQ 149 (260)
Q Consensus 92 lGaIiRta~afGv~~viv~~~~~~~~~~k~~rag~~~~~~v~v~~~~~~~~~l~~lk~ 149 (260)
+-.++|.|.|+|++++++.- .+++.+...-|...++. +.++++++++++
T Consensus 219 v~~larAAvA~GaDGl~iEv---HpdP~~AlsDg~q~l~~------~~~~~l~~~l~~ 267 (281)
T PRK12457 219 VLDLARAGMAVGLAGLFLEA---HPDPDRARCDGPSALPL------DQLEPFLSQVKA 267 (281)
T ss_pred HHHHHHHHHHhCCCEEEEEe---cCCccccCCCcccccCH------HHHHHHHHHHHH
Confidence 66899999999999999962 33444444445444432 456666666654
No 47
>PRK01889 GTPase RsgA; Reviewed
Probab=20.97 E-value=7e+02 Score=23.44 Aligned_cols=35 Identities=14% Similarity=-0.041 Sum_probs=23.8
Q ss_pred ccEEEEEeCCCCCCcHHHHHHh---hhhcccc-eEEECC
Q 024933 77 KFLQVVLVSPQIPGNTGCIART---CAASACG-LHLVGP 111 (260)
Q Consensus 77 ~~l~vvLd~i~dp~NlGaIiRt---a~afGv~-~viv~~ 111 (260)
-+.++++..+..+.|..-+=|. |...|+. .+++++
T Consensus 113 vD~vliV~s~~p~~~~~~ldr~L~~a~~~~i~piIVLNK 151 (356)
T PRK01889 113 VDTVFIVCSLNHDFNLRRIERYLALAWESGAEPVIVLTK 151 (356)
T ss_pred CCEEEEEEecCCCCChhHHHHHHHHHHHcCCCEEEEEEC
Confidence 3556666677777888777777 6668887 445555
Done!